Starting phenix.real_space_refine on Fri Mar 1 10:11:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvl_17970/03_2024/8pvl_17970_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvl_17970/03_2024/8pvl_17970.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvl_17970/03_2024/8pvl_17970_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvl_17970/03_2024/8pvl_17970_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvl_17970/03_2024/8pvl_17970_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvl_17970/03_2024/8pvl_17970.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvl_17970/03_2024/8pvl_17970.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvl_17970/03_2024/8pvl_17970_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pvl_17970/03_2024/8pvl_17970_updated.pdb" } resolution = 2.19 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= 0.160 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 3362 5.49 5 Mg 3 5.21 5 S 249 5.16 5 C 83185 2.51 5 N 28329 2.21 5 O 37627 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "CF TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CF ASP 46": "OD1" <-> "OD2" Residue "CF TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CF PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CF TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH GLU 385": "OE1" <-> "OE2" Residue "CH GLU 431": "OE1" <-> "OE2" Residue "CI GLU 200": "OE1" <-> "OE2" Residue "CI PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CI ASP 237": "OD1" <-> "OD2" Residue "CI ASP 249": "OD1" <-> "OD2" Residue "CI TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CJ ASP 263": "OD1" <-> "OD2" Residue "CJ GLU 274": "OE1" <-> "OE2" Residue "CK ASP 84": "OD1" <-> "OD2" Residue "CL GLU 30": "OE1" <-> "OE2" Residue "CL ASP 52": "OD1" <-> "OD2" Residue "CL GLU 70": "OE1" <-> "OE2" Residue "CL GLU 72": "OE1" <-> "OE2" Residue "CM TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CM GLU 131": "OE1" <-> "OE2" Residue "CM TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CM ASP 171": "OD1" <-> "OD2" Residue "CN TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CN TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CQ PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CQ GLU 147": "OE1" <-> "OE2" Residue "CQ GLU 163": "OE1" <-> "OE2" Residue "Cb ASP 25": "OD1" <-> "OD2" Residue "Cb GLU 37": "OE1" <-> "OE2" Residue "Cb GLU 62": "OE1" <-> "OE2" Residue "Cd GLU 97": "OE1" <-> "OE2" Residue "Cd GLU 180": "OE1" <-> "OE2" Residue "Cd PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cd GLU 405": "OE1" <-> "OE2" Residue "Cd ASP 458": "OD1" <-> "OD2" Residue "Ce ASP 158": "OD1" <-> "OD2" Residue "Ce ASP 221": "OD1" <-> "OD2" Residue "Ce GLU 243": "OE1" <-> "OE2" Residue "Ce GLU 312": "OE1" <-> "OE2" Residue "Ce GLU 321": "OE1" <-> "OE2" Residue "Ce ASP 380": "OD1" <-> "OD2" Residue "Cf TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cf PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cg ASP 24": "OD1" <-> "OD2" Residue "Cg ASP 43": "OD1" <-> "OD2" Residue "Cg ASP 172": "OD1" <-> "OD2" Residue "Ch PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ch ASP 45": "OD1" <-> "OD2" Residue "Ch TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ch ASP 292": "OD1" <-> "OD2" Residue "Ch GLU 345": "OE1" <-> "OE2" Residue "Ch PHE 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cz GLU 67": "OE1" <-> "OE2" Residue "Cz GLU 92": "OE1" <-> "OE2" Residue "Cz TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LA GLU 80": "OE1" <-> "OE2" Residue "LA GLU 143": "OE1" <-> "OE2" Residue "LB GLU 298": "OE1" <-> "OE2" Residue "LB GLU 356": "OE1" <-> "OE2" Residue "LC GLU 64": "OE1" <-> "OE2" Residue "LC ASP 266": "OD1" <-> "OD2" Residue "LC PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LD PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LD GLU 192": "OE1" <-> "OE2" Residue "LE ASP 77": "OD1" <-> "OD2" Residue "LE ASP 110": "OD1" <-> "OD2" Residue "LE GLU 121": "OE1" <-> "OE2" Residue "LF PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LF GLU 65": "OE1" <-> "OE2" Residue "LG ASP 42": "OD1" <-> "OD2" Residue "LG ASP 161": "OD1" <-> "OD2" Residue "LG ASP 210": "OD1" <-> "OD2" Residue "LG ASP 231": "OD1" <-> "OD2" Residue "LH ASP 74": "OD1" <-> "OD2" Residue "LH GLU 141": "OE1" <-> "OE2" Residue "LH ASP 199": "OD1" <-> "OD2" Residue "LH TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LJ TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LJ ASP 118": "OD1" <-> "OD2" Residue "LJ PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LK GLU 9": "OE1" <-> "OE2" Residue "LK ASP 45": "OD1" <-> "OD2" Residue "LK ASP 52": "OD1" <-> "OD2" Residue "LK ASP 124": "OD1" <-> "OD2" Residue "LK ASP 144": "OD1" <-> "OD2" Residue "LK GLU 159": "OE1" <-> "OE2" Residue "LL ASP 52": "OD1" <-> "OD2" Residue "LL PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LL PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LL GLU 199": "OE1" <-> "OE2" Residue "LM GLU 3": "OE1" <-> "OE2" Residue "LM GLU 15": "OE1" <-> "OE2" Residue "LM ASP 47": "OD1" <-> "OD2" Residue "LM GLU 107": "OE1" <-> "OE2" Residue "LM GLU 130": "OE1" <-> "OE2" Residue "LN TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN ASP 17": "OD1" <-> "OD2" Residue "LN GLU 29": "OE1" <-> "OE2" Residue "LO GLU 102": "OE1" <-> "OE2" Residue "LO GLU 108": "OE1" <-> "OE2" Residue "LO GLU 146": "OE1" <-> "OE2" Residue "LO GLU 182": "OE1" <-> "OE2" Residue "LO GLU 197": "OE1" <-> "OE2" Residue "LP ASP 103": "OD1" <-> "OD2" Residue "LP GLU 152": "OE1" <-> "OE2" Residue "LQ ASP 50": "OD1" <-> "OD2" Residue "LQ GLU 127": "OE1" <-> "OE2" Residue "LQ GLU 142": "OE1" <-> "OE2" Residue "LR GLU 28": "OE1" <-> "OE2" Residue "LR GLU 65": "OE1" <-> "OE2" Residue "LS GLU 96": "OE1" <-> "OE2" Residue "LS GLU 133": "OE1" <-> "OE2" Residue "LT ASP 41": "OD1" <-> "OD2" Residue "LT TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LT GLU 94": "OE1" <-> "OE2" Residue "LT GLU 114": "OE1" <-> "OE2" Residue "LU ASP 31": "OD1" <-> "OD2" Residue "LU PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LU GLU 40": "OE1" <-> "OE2" Residue "LU GLU 45": "OE1" <-> "OE2" Residue "LU ASP 98": "OD1" <-> "OD2" Residue "LV PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LV ASP 91": "OD1" <-> "OD2" Residue "LV PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LV GLU 98": "OE1" <-> "OE2" Residue "LV ASP 99": "OD1" <-> "OD2" Residue "LV GLU 126": "OE1" <-> "OE2" Residue "LX GLU 72": "OE1" <-> "OE2" Residue "LX GLU 90": "OE1" <-> "OE2" Residue "LX GLU 91": "OE1" <-> "OE2" Residue "LY GLU 37": "OE1" <-> "OE2" Residue "LY GLU 54": "OE1" <-> "OE2" Residue "LY GLU 82": "OE1" <-> "OE2" Residue "LZ GLU 46": "OE1" <-> "OE2" Residue "LZ GLU 89": "OE1" <-> "OE2" Residue "LZ ASP 98": "OD1" <-> "OD2" Residue "LZ GLU 102": "OE1" <-> "OE2" Residue "La ASP 76": "OD1" <-> "OD2" Residue "La GLU 120": "OE1" <-> "OE2" Residue "La GLU 140": "OE1" <-> "OE2" Residue "Lc ASP 100": "OD1" <-> "OD2" Residue "Ld PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ld ASP 56": "OD1" <-> "OD2" Residue "Le PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Le ASP 40": "OD1" <-> "OD2" Residue "Le ASP 82": "OD1" <-> "OD2" Residue "Le TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Le GLU 96": "OE1" <-> "OE2" Residue "Le ASP 108": "OD1" <-> "OD2" Residue "Lf ASP 38": "OD1" <-> "OD2" Residue "Lg GLU 97": "OE1" <-> "OE2" Residue "Lh GLU 26": "OE1" <-> "OE2" Residue "Lh ASP 84": "OD1" <-> "OD2" Residue "Li GLU 12": "OE1" <-> "OE2" Residue "Li GLU 68": "OE1" <-> "OE2" Residue "Li GLU 105": "OE1" <-> "OE2" Residue "Lk GLU 4": "OE1" <-> "OE2" Residue "Lk ASP 51": "OD1" <-> "OD2" Residue "Ll TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lq GLU 11": "OE1" <-> "OE2" Residue "Lq GLU 58": "OE1" <-> "OE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 152760 Number of models: 1 Model: "" Number of chains: 67 Chain: "C1" Number of atoms: 65888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3078, 65888 Classifications: {'RNA': 3078} Modifications used: {'rna2p': 4, 'rna2p_pur': 318, 'rna2p_pyr': 219, 'rna3p': 22, 'rna3p_pur': 1357, 'rna3p_pyr': 1150} Link IDs: {'rna2p': 541, 'rna3p': 2536} 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: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Classifications: {'RNA': 3} Modifications used: {'rna2p_pyr': 2, 'rna3p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 1} Chain: "C4" Number of atoms: 2536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2536 Classifications: {'RNA': 119} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 54, 'rna3p_pyr': 53} Link IDs: {'rna2p': 12, 'rna3p': 106} Chain: "CF" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1934 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 232} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "CH" Number of atoms: 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: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 720 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 85} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 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: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1769 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 204} 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: 1977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1977 Classifications: {'peptide': 239} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 224} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Cf" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2282 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 267} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "Cg" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1478 Classifications: {'peptide': 188} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 19, 'TRANS': 168} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Ch" Number of atoms: 3812 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 485, 3809 Classifications: {'peptide': 485} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 466} Conformer: "B" Number of residues, atoms: 485, 3809 Classifications: {'peptide': 485} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 466} bond proxies already assigned to first conformer: 3904 Chain: "Cz" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 869 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "LA" Number of atoms: 1454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1454 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 175} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "LB" Number of atoms: 3104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3104 Classifications: {'peptide': 389} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 373} Chain: "LC" Number of atoms: 2751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2751 Classifications: {'peptide': 363} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 338} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "LD" Number of atoms: 2266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2266 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 6, 'TRANS': 279} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "LE" Number of atoms: 1477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1477 Classifications: {'peptide': 191} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 176} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "LF" Number of atoms: 2023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 2023 Classifications: {'peptide': 248} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 234} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "LG" Number of atoms: 1889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1889 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 223} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "LH" Number of atoms: 1495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1495 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 5, 'TRANS': 184} Chain: "LJ" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1357 Classifications: {'peptide': 169} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 163} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "LK" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1184 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 149} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "LL" Number of atoms: 1587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1587 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 189} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 21 Chain: "LM" Number of atoms: 1126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1126 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "LN" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1704 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 193} Chain: "LO" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1611 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 192} Chain: "LP" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1343 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 164} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "LQ" Number of atoms: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1200 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 7, 'TRANS': 142} Chain: "LR" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1241 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 151} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "LS" Number of atoms: 1426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1426 Classifications: {'peptide': 174} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 163} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "LT" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1027 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 121} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "LU" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 846 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "LV" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 991 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 125} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "LX" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1133 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 136} Chain: "LY" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1056 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 6, 'TRANS': 126} Chain: "LZ" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1112 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 127} Chain: "La" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 872 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain breaks: 1 Chain: "Lc" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 705 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "Ld" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 875 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 105} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'GLU%COO:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "Le" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1017 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "Lf" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 862 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "Lg" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 914 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 109} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Lh" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1003 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "Li" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 827 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 98} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS%COO:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Lj" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 698 Classifications: {'peptide': 88} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 83} Chain: "Lk" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 632 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 4, 'TRANS': 71} Chain: "Ll" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 436 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "Lp" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 698 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 89} Chain: "Lq" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1073 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 6, 'TRANS': 132} Chain: "CH" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "CQ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Cb" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Cd" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' MG': 2, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Lg" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Lj" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Lp" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "CH" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Cd" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 89301 SG CYSCQ 6 146.300 179.700 100.114 1.00 30.73 S ATOM 89329 SG CYSCQ 9 149.885 180.700 100.652 1.00 30.19 S ATOM 89514 SG CYSCQ 32 149.196 177.475 98.843 1.00 29.07 S ATOM 89546 SG CYSCQ 36 148.487 177.911 102.655 1.00 27.66 S ATOM 91158 SG CYSCb 52 127.779 186.540 122.307 1.00 37.31 S ATOM 91181 SG CYSCb 55 131.065 184.511 122.446 1.00 37.54 S ATOM A102V SG CYSLg 45 142.119 159.681 198.302 1.00 29.11 S ATOM A103D SG CYSLg 48 139.777 161.457 195.963 1.00 31.22 S ATOM A10AL SG CYSLg 82 141.692 163.501 198.582 1.00 30.07 S ATOM A10B3 SG CYSLg 85 138.935 161.283 199.692 1.00 31.81 S ATOM A1210 SG CYSLj 19 163.954 112.680 171.231 1.00 21.90 S ATOM A121S SG CYSLj 22 164.714 110.471 168.272 1.00 21.55 S ATOM A124I SG CYSLj 34 161.186 111.688 168.847 1.00 21.08 S ATOM A124Z SG CYSLj 37 162.601 109.124 171.268 1.00 21.42 S ATOM A13IP SG CYSLp 39 123.337 162.244 191.756 1.00 34.31 S ATOM A13JD SG CYSLp 42 125.043 165.582 192.272 1.00 35.14 S ATOM A13MI SG CYSLp 57 126.443 163.273 189.712 1.00 33.60 S ATOM A13N3 SG CYSLp 60 126.832 162.306 193.321 1.00 35.36 S Time building chain proxies: 58.70, per 1000 atoms: 0.38 Number of scatterers: 152760 At special positions: 0 Unit cell: (235.125, 229.9, 288.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 5 29.99 S 249 16.00 P 3362 15.00 Mg 3 11.99 O 37627 8.00 N 28329 7.00 C 83185 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: 57.04 Conformation dependent library (CDL) restraints added in 12.2 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 6 " pdb="ZN ZNCQ1000 " - pdb=" SG CYSCQ 32 " pdb=" ZNCb1000 " pdb="ZN ZNCb1000 " - pdb=" ND1 HISCb 74 " pdb="ZN ZNCb1000 " - pdb=" NE2 HISCb 68 " pdb="ZN ZNCb1000 " - pdb=" SG CYSCb 52 " pdb="ZN ZNCb1000 " - pdb=" SG CYSCb 55 " pdb=" ZNLg1000 " pdb="ZN ZNLg1000 " - pdb=" SG CYSLg 85 " pdb="ZN ZNLg1000 " - pdb=" SG CYSLg 82 " pdb="ZN ZNLg1000 " - pdb=" SG CYSLg 48 " pdb="ZN ZNLg1000 " - pdb=" SG CYSLg 45 " pdb=" ZNLj1000 " pdb="ZN ZNLj1000 " - pdb=" SG CYSLj 34 " pdb="ZN ZNLj1000 " - pdb=" SG CYSLj 37 " pdb="ZN ZNLj1000 " - pdb=" SG CYSLj 19 " pdb="ZN ZNLj1000 " - pdb=" SG CYSLj 22 " pdb=" ZNLp 101 " pdb="ZN ZNLp 101 " - pdb=" SG CYSLp 57 " pdb="ZN ZNLp 101 " - pdb=" SG CYSLp 42 " pdb="ZN ZNLp 101 " - pdb=" SG CYSLp 60 " pdb="ZN ZNLp 101 " - pdb=" SG CYSLp 39 " Number of angles added : 26 20034 Ramachandran restraints generated. 10017 Oldfield, 0 Emsley, 10017 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 19026 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: 363 helices and 99 sheets defined 45.0% alpha, 14.2% beta 1060 base pairs and 1728 stacking pairs defined. Time for finding SS restraints: 82.27 Creating SS restraints... Processing helix chain 'CF' and resid 19 through 37 removed outlier: 3.865A pdb=" N LYSCF 23 " --> pdb=" O GLYCF 19 " (cutoff:3.500A) Proline residue: CF 35 - end of helix Processing helix chain 'CF' and resid 50 through 61 removed outlier: 5.114A pdb=" N LYSCF 54 " --> pdb=" O ASNCF 50 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ASPCF 55 " --> pdb=" O ASNCF 51 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASNCF 61 " --> pdb=" O ARGCF 57 " (cutoff:3.500A) Processing helix chain 'CF' and resid 69 through 78 Processing helix chain 'CF' and resid 88 through 97 removed outlier: 4.307A pdb=" N LEUCF 92 " --> pdb=" O GLYCF 88 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THRCF 93 " --> pdb=" O LEUCF 89 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ARGCF 94 " --> pdb=" O HISCF 90 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N TYRCF 95 " --> pdb=" O ARGCF 91 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEUCF 96 " --> pdb=" O LEUCF 92 " (cutoff:3.500A) removed outlier: 5.562A 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 150 through 155 removed outlier: 5.044A pdb=" N VALCF 155 " --> pdb=" O PROCF 151 " (cutoff:3.500A) Processing helix chain 'CF' and resid 161 through 169 Processing helix chain 'CF' and resid 202 through 213 Processing helix chain 'CF' and resid 237 through 243 removed outlier: 3.720A pdb=" N THRCF 242 " --> pdb=" O GLUCF 238 " (cutoff:3.500A) Processing helix chain 'CH' and resid 12 through 27 Processing helix chain 'CH' and resid 37 through 65 Processing helix chain 'CH' and resid 69 through 74 removed outlier: 3.558A pdb=" N GLNCH 73 " --> pdb=" O VALCH 69 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N HISCH 74 " --> pdb=" O LEUCH 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'CH' and resid 69 through 74' Processing helix chain 'CH' and resid 75 through 85 Processing helix chain 'CH' and resid 86 through 118 removed outlier: 3.949A pdb=" N TYRCH 117 " --> pdb=" O ARGCH 113 " (cutoff:3.500A) Processing helix chain 'CH' and resid 120 through 143 removed outlier: 3.888A pdb=" N LEUCH 142 " --> pdb=" O LEUCH 138 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LYSCH 143 " --> pdb=" O ILECH 139 " (cutoff:3.500A) Processing helix chain 'CH' and resid 144 through 159 Processing helix chain 'CH' and resid 178 through 187 Processing helix chain 'CH' and resid 227 through 232 removed outlier: 3.699A pdb=" N METCH 231 " --> pdb=" O PROCH 227 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ASNCH 232 " --> pdb=" O LEUCH 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'CH' and resid 227 through 232' Processing helix chain 'CH' and resid 233 through 245 removed outlier: 3.953A 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: 4.041A pdb=" N ALACH 278 " --> pdb=" O LYSCH 274 " (cutoff:3.500A) Processing helix chain 'CH' and resid 298 through 311 removed outlier: 4.013A pdb=" N GLNCH 302 " --> pdb=" O ASPCH 298 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THRCH 309 " --> pdb=" O ILECH 305 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N SERCH 311 " --> pdb=" O ASPCH 307 " (cutoff:3.500A) Processing helix chain 'CH' and resid 326 through 351 removed outlier: 4.901A pdb=" N GLYCH 350 " --> pdb=" O LYSCH 346 " (cutoff:3.500A) removed outlier: 4.494A 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: 4.625A pdb=" N LYSCH 388 " --> pdb=" O PROCH 384 " (cutoff:3.500A) removed outlier: 3.916A 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: 4.350A pdb=" N LYSCH 433 " --> pdb=" O ASNCH 429 " (cutoff:3.500A) removed outlier: 5.329A 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 removed outlier: 3.596A pdb=" N TYRCH 449 " --> pdb=" O ASNCH 445 " (cutoff:3.500A) Processing helix chain 'CH' and resid 453 through 472 removed outlier: 3.919A 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: 3.790A pdb=" N VALCH 523 " --> pdb=" O PROCH 519 " (cutoff:3.500A) removed outlier: 5.224A 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: 3.528A pdb=" N ILECH 544 " --> pdb=" O ASPCH 540 " (cutoff:3.500A) Processing helix chain 'CH' and resid 546 through 551 removed outlier: 3.533A pdb=" N ALACH 550 " --> pdb=" O LEUCH 546 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N GLNCH 551 " --> pdb=" O ARGCH 547 " (cutoff:3.500A) No H-bonds generated for 'chain 'CH' and resid 546 through 551' Processing helix chain 'CH' and resid 582 through 597 Processing helix chain 'CH' and resid 609 through 631 removed outlier: 3.995A pdb=" N GLNCH 624 " --> pdb=" O ALACH 620 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ARGCH 625 " --> pdb=" O LYSCH 621 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N LYSCH 626 " --> pdb=" O LEUCH 622 " (cutoff:3.500A) removed outlier: 5.393A 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: 4.043A pdb=" N GLNCI 209 " --> pdb=" O GLYCI 205 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHECI 210 " --> pdb=" O TYRCI 206 " (cutoff:3.500A) Processing helix chain 'CI' and resid 237 through 249 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: 4.009A pdb=" N VALCJ 53 " --> pdb=" O ASPCJ 49 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 65 through 75 removed outlier: 4.083A pdb=" N HISCJ 74 " --> pdb=" O GLNCJ 70 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLUCJ 75 " --> pdb=" O TYRCJ 71 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 76 through 98 removed outlier: 3.532A pdb=" N LYSCJ 80 " --> pdb=" O PROCJ 76 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 99 through 111 removed outlier: 3.835A pdb=" N ASNCJ 109 " --> pdb=" O ARGCJ 105 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALACJ 110 " --> pdb=" O LEUCJ 106 " (cutoff:3.500A) removed outlier: 4.275A 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: 3.676A 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: 4.756A pdb=" N ASPCJ 142 " --> pdb=" O LEUCJ 138 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ASPCJ 143 " --> pdb=" O ARGCJ 139 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASNCJ 153 " --> pdb=" O PHECJ 149 " (cutoff:3.500A) removed outlier: 3.996A 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: 3.618A 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: 4.068A pdb=" N LEUCJ 366 " --> pdb=" O ASPCJ 362 " (cutoff:3.500A) removed outlier: 5.636A 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: 4.388A pdb=" N VALCJ 461 " --> pdb=" O GLNCJ 457 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TRPCJ 462 " --> pdb=" O PROCJ 458 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 472 through 477 removed outlier: 4.377A pdb=" N TYRCJ 476 " --> pdb=" O PROCJ 472 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALACJ 477 " --> pdb=" O PROCJ 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'CJ' and resid 472 through 477' Processing helix chain 'CK' and resid 5 through 14 Processing helix chain 'CK' and resid 19 through 41 removed outlier: 4.848A pdb=" N GLYCK 32 " --> pdb=" O ALACK 28 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N HISCK 33 " --> pdb=" O ALACK 29 " (cutoff:3.500A) Processing helix chain 'CK' and resid 44 through 71 Processing helix chain 'CK' and resid 87 through 92 removed outlier: 5.844A pdb=" N ASPCK 92 " --> pdb=" O SERCK 88 " (cutoff:3.500A) Processing helix chain 'CK' and resid 128 through 133 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 '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: 4.404A 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: 5.142A pdb=" N TRPCM 209 " --> pdb=" O ALACM 205 " (cutoff:3.500A) Processing helix chain 'CM' and resid 215 through 221 removed outlier: 4.803A pdb=" N GLYCM 219 " --> pdb=" O ASNCM 215 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N PHECM 220 " --> pdb=" O PROCM 216 " (cutoff:3.500A) removed outlier: 5.299A 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: 4.626A pdb=" N ALACM 243 " --> pdb=" O GLUCM 239 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEUCM 244 " --> pdb=" O HISCM 240 " (cutoff:3.500A) Processing helix chain 'CN' and resid 12 through 17 removed outlier: 3.737A pdb=" N PHECN 16 " --> pdb=" O GLUCN 12 " (cutoff:3.500A) Processing helix chain 'CN' and resid 32 through 43 removed outlier: 3.599A 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 235 removed outlier: 4.527A pdb=" N ILECN 233 " --> pdb=" O GLYCN 229 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASNCN 234 " --> pdb=" O PROCN 230 " (cutoff:3.500A) Processing helix chain 'CN' and resid 237 through 246 Processing helix chain 'CO' and resid 7 through 21 Processing helix chain 'CO' and resid 22 through 43 Processing helix chain 'CO' and resid 83 through 88 Processing helix chain 'CQ' and resid 33 through 43 Processing helix chain 'CQ' and resid 45 through 50 removed outlier: 5.173A 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: 4.239A pdb=" N GLNCQ 70 " --> pdb=" O ASPCQ 66 " (cutoff:3.500A) removed outlier: 4.618A 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: 5.974A pdb=" N GLYCQ 114 " --> pdb=" O LYSCQ 110 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LYSCQ 115 " --> pdb=" O ARGCQ 111 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ARGCQ 116 " --> pdb=" O METCQ 112 " (cutoff:3.500A) removed outlier: 5.394A 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: 4.630A pdb=" N LYSCQ 171 " --> pdb=" O LEUCQ 167 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 5 through 10 removed outlier: 3.707A pdb=" N METCb 9 " --> pdb=" O ALACb 5 " (cutoff:3.500A) removed outlier: 5.326A 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: 3.834A pdb=" N LYSCb 39 " --> pdb=" O TYRCb 35 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ALACb 40 " --> pdb=" O LYSCb 36 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 61 through 72 removed outlier: 3.610A pdb=" N LYSCb 70 " --> pdb=" O VALCb 66 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLYCb 71 " --> pdb=" O GLYCb 67 " (cutoff:3.500A) removed outlier: 5.497A 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: 3.677A 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: 3.908A pdb=" N LEUCd 41 " --> pdb=" O THRCd 37 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYSCd 42 " --> pdb=" O LEUCd 38 " (cutoff:3.500A) Processing helix chain 'Cd' and resid 73 through 79 removed outlier: 4.664A pdb=" N PHECd 77 " --> pdb=" O ASNCd 73 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THRCd 78 " --> pdb=" O ARGCd 74 " (cutoff:3.500A) removed outlier: 5.922A 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: 3.513A pdb=" N ILECd 117 " --> pdb=" O PROCd 113 " (cutoff:3.500A) Processing helix chain 'Cd' and resid 122 through 140 removed outlier: 3.663A pdb=" N HISCd 130 " --> pdb=" O GLYCd 126 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ALACd 132 " --> pdb=" O LYSCd 128 " (cutoff:3.500A) removed outlier: 5.680A 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: 4.292A pdb=" N ASNCd 215 " --> pdb=" O GLUCd 211 " (cutoff:3.500A) removed outlier: 4.149A 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: 4.253A 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: 3.961A pdb=" N LYSCd 290 " --> pdb=" O ARGCd 286 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ASPCd 291 " --> pdb=" O ILECd 287 " (cutoff:3.500A) Processing helix chain 'Cd' and resid 306 through 322 Processing helix chain 'Cd' and resid 338 through 348 Processing helix chain 'Cd' and resid 389 through 397 Processing helix chain 'Cd' and resid 400 through 405 removed outlier: 4.090A pdb=" N VALCd 404 " --> pdb=" O ARGCd 400 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLUCd 405 " --> pdb=" O VALCd 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'Cd' and resid 400 through 405' Processing helix chain 'Cd' and resid 406 through 419 removed outlier: 4.802A pdb=" N TYRCd 410 " --> pdb=" O HISCd 406 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILECd 411 " --> pdb=" O PROCd 407 " (cutoff:3.500A) Proline residue: Cd 412 - end of helix removed outlier: 5.130A 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: 3.686A pdb=" N GLYCd 471 " --> pdb=" O ASPCd 467 " (cutoff:3.500A) Processing helix chain 'Ce' and resid 186 through 192 removed outlier: 3.565A pdb=" N GLUCe 190 " --> pdb=" O PROCe 186 " (cutoff:3.500A) removed outlier: 5.830A 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 155 through 169 Processing helix chain 'Cf' and resid 264 through 273 Processing helix chain 'Cf' and resid 314 through 319 removed outlier: 5.405A pdb=" N ARGCf 319 " --> pdb=" O LYSCf 315 " (cutoff:3.500A) Processing helix chain 'Cf' and resid 177 through 182 removed outlier: 3.839A pdb=" N LEUCf 181 " --> pdb=" O VALCf 178 " (cutoff:3.500A) removed outlier: 4.906A 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: 3.581A pdb=" N ARGCg 123 " --> pdb=" O ARGCg 119 " (cutoff:3.500A) Processing helix chain 'Cg' and resid 156 through 163 Processing helix chain 'Cg' and resid 168 through 198 removed outlier: 4.272A pdb=" N ASPCg 172 " --> pdb=" O SERCg 168 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N LYSCg 173 " --> pdb=" O VALCg 169 " (cutoff:3.500A) removed outlier: 5.558A 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: 3.659A pdb=" N THRCh 337 " --> pdb=" O HISCh 333 " (cutoff:3.500A) Processing helix chain 'Ch' and resid 349 through 366 Processing helix chain 'Ch' and resid 388 through 393 Processing helix chain 'Cz' and resid 48 through 103 Processing helix chain 'Cz' and resid 104 through 121 Processing helix chain 'LA' and resid 33 through 39 Processing helix chain 'LA' and resid 103 through 108 removed outlier: 3.845A 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: 4.174A pdb=" N VALLA 191 " --> pdb=" O HISLA 187 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYSLA 192 " --> pdb=" O LYSLA 188 " (cutoff:3.500A) Processing helix chain 'LA' and resid 200 through 205 removed outlier: 3.754A pdb=" N METLA 204 " --> pdb=" O ARGLA 200 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ASNLA 205 " --> pdb=" O GLYLA 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'LA' and resid 200 through 205' Processing helix chain 'LB' and resid 13 through 18 removed outlier: 4.813A 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: 4.042A pdb=" N ARGLB 117 " --> pdb=" O GLULB 113 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N PHELB 118 " --> pdb=" O VALLB 114 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N TYRLB 119 " --> pdb=" O LYSLB 115 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N LYSLB 120 " --> pdb=" O ARGLB 116 " (cutoff:3.500A) Processing helix chain 'LB' and resid 130 through 139 removed outlier: 3.860A pdb=" N LYSLB 135 " --> pdb=" O THRLB 131 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYSLB 136 " --> pdb=" O LYSLB 132 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N TYRLB 137 " --> pdb=" O TYRLB 133 " (cutoff:3.500A) removed outlier: 4.261A 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: 4.311A pdb=" N THRLB 170 " --> pdb=" O GLNLB 166 " (cutoff:3.500A) Proline residue: LB 171 - end of helix No H-bonds generated for 'chain 'LB' and resid 166 through 171' Processing helix chain 'LB' and resid 188 through 200 Processing helix chain 'LB' and resid 205 through 210 removed outlier: 4.003A pdb=" N ILELB 209 " --> pdb=" O THRLB 205 " (cutoff:3.500A) Processing helix chain 'LB' and resid 229 through 234 Processing helix chain 'LB' and resid 348 through 353 removed outlier: 3.985A 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: 3.543A pdb=" N LEULB 388 " --> pdb=" O LEULB 384 " (cutoff:3.500A) Processing helix chain 'LC' and resid 24 through 30 removed outlier: 4.548A pdb=" N SERLC 28 " --> pdb=" O PROLC 24 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALALC 29 " --> pdb=" O LYSLC 25 " (cutoff:3.500A) Proline residue: LC 30 - end of helix No H-bonds generated for 'chain 'LC' and resid 24 through 30' Processing helix chain 'LC' and resid 32 through 47 removed outlier: 4.099A pdb=" N LYSLC 45 " --> pdb=" O THRLC 41 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASNLC 46 " --> pdb=" O GLYLC 42 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LYSLC 47 " --> pdb=" O METLC 43 " (cutoff:3.500A) Processing helix chain 'LC' and resid 115 through 133 removed outlier: 3.667A pdb=" N ALALC 131 " --> pdb=" O LEULC 127 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VALLC 132 " --> pdb=" O ALALC 128 " (cutoff:3.500A) removed outlier: 5.554A 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: 3.976A pdb=" N VALLC 158 " --> pdb=" O ASPLC 154 " (cutoff:3.500A) Processing helix chain 'LC' and resid 165 through 177 Processing helix chain 'LC' and resid 178 through 189 removed outlier: 3.902A pdb=" N LYSLC 189 " --> pdb=" O VALLC 185 " (cutoff:3.500A) Processing helix chain 'LC' and resid 195 through 200 Processing helix chain 'LC' and resid 220 through 228 removed outlier: 4.161A pdb=" N LYSLC 224 " --> pdb=" O LYSLC 220 " (cutoff:3.500A) removed outlier: 4.629A 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: 4.877A pdb=" N ASPLC 266 " --> pdb=" O ILELC 262 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ALALC 267 " --> pdb=" O LYSLC 263 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYSLC 272 " --> pdb=" O VALLC 268 " (cutoff:3.500A) Processing helix chain 'LC' and resid 286 through 293 Processing helix chain 'LC' and resid 294 through 300 removed outlier: 4.312A pdb=" N VALLC 299 " --> pdb=" O GLULC 295 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEULC 300 " --> pdb=" O ILELC 296 " (cutoff:3.500A) Processing helix chain 'LC' and resid 318 through 323 removed outlier: 4.548A 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: 4.677A pdb=" N THRLC 335 " --> pdb=" O PROLC 331 " (cutoff:3.500A) Processing helix chain 'LC' and resid 355 through 364 removed outlier: 3.506A pdb=" N LYSLC 359 " --> pdb=" O PROLC 355 " (cutoff:3.500A) Processing helix chain 'LC' and resid 214 through 219 removed outlier: 3.799A 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: 3.675A pdb=" N ARGLD 35 " --> pdb=" O TYRLD 31 " (cutoff:3.500A) Processing helix chain 'LD' and resid 79 through 87 removed outlier: 4.192A pdb=" N LEULD 83 " --> pdb=" O TYRLD 79 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ARGLD 84 " --> pdb=" O SERLD 80 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ALALD 85 " --> pdb=" O HISLD 81 " (cutoff:3.500A) removed outlier: 4.243A 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: 3.635A pdb=" N GLYLD 164 " --> pdb=" O ALALD 160 " (cutoff:3.500A) Processing helix chain 'LD' and resid 194 through 204 Processing helix chain 'LD' and resid 205 through 218 Processing helix chain 'LD' and resid 219 through 227 Processing helix chain 'LD' and resid 228 through 233 Processing helix chain 'LD' and resid 235 through 253 removed outlier: 3.908A pdb=" N LEULD 239 " --> pdb=" O GLULD 235 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N GLULD 240 " --> pdb=" O ALALD 236 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N GLULD 241 " --> pdb=" O ASPLD 237 " (cutoff:3.500A) Processing helix chain 'LD' and resid 266 through 278 removed outlier: 3.786A pdb=" N TYRLD 277 " --> pdb=" O GLULD 273 " (cutoff:3.500A) Processing helix chain 'LD' and resid 283 through 300 Processing helix chain 'LE' and resid 98 through 103 removed outlier: 3.876A pdb=" N VALLE 102 " --> pdb=" O ASNLE 98 " (cutoff:3.500A) removed outlier: 5.909A 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: 4.945A pdb=" N ALALE 168 " --> pdb=" O ALALE 164 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEULE 169 " --> pdb=" O ILELE 165 " (cutoff:3.500A) Processing helix chain 'LE' and resid 178 through 186 removed outlier: 5.347A pdb=" N SERLE 186 " --> pdb=" O TYRLE 182 " (cutoff:3.500A) Processing helix chain 'LF' and resid 8 through 14 removed outlier: 3.543A pdb=" N ILELF 12 " --> pdb=" O THRLF 8 " (cutoff:3.500A) Processing helix chain 'LF' and resid 15 through 34 removed outlier: 5.148A pdb=" N GLULF 31 " --> pdb=" O LYSLF 27 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ARGLF 32 " --> pdb=" O ALALF 28 " (cutoff:3.500A) Processing helix chain 'LF' and resid 35 through 79 removed outlier: 3.702A pdb=" N GLULF 45 " --> pdb=" O GLNLF 41 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLNLF 48 " --> pdb=" O LYSLF 44 " (cutoff:3.500A) Processing helix chain 'LF' and resid 102 through 113 Processing helix chain 'LF' and resid 126 through 137 removed outlier: 4.141A 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: 4.051A 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: 5.220A pdb=" N TRPLF 209 " --> pdb=" O ALALF 205 " (cutoff:3.500A) Processing helix chain 'LF' and resid 240 through 249 removed outlier: 3.807A 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: 5.022A pdb=" N PHELG 81 " --> pdb=" O ALALG 77 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLNLG 82 " --> pdb=" O ILELG 78 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N TYRLG 83 " --> pdb=" O ALALG 79 " (cutoff:3.500A) Processing helix chain 'LG' and resid 86 through 101 removed outlier: 4.363A pdb=" N LYSLG 99 " --> pdb=" O LYSLG 95 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N TYRLG 100 " --> pdb=" O LEULG 96 " (cutoff:3.500A) removed outlier: 3.836A 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: 4.095A pdb=" N VALLG 128 " --> pdb=" O LYSLG 124 " (cutoff:3.500A) Processing helix chain 'LG' and resid 138 through 149 Processing helix chain 'LG' and resid 168 through 177 Processing helix chain 'LG' and resid 185 through 194 Processing helix chain 'LG' and resid 207 through 230 removed outlier: 4.902A pdb=" N ASNLG 212 " --> pdb=" O SERLG 208 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N GLULG 213 " --> pdb=" O GLULG 209 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEULG 226 " --> pdb=" O LYSLG 222 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N GLULG 227 " --> pdb=" O GLULG 223 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N LYSLG 228 " --> pdb=" O GLYLG 224 " (cutoff:3.500A) Processing helix chain 'LG' and resid 231 through 236 removed outlier: 4.135A pdb=" N ARGLG 235 " --> pdb=" O ASPLG 231 " (cutoff:3.500A) removed outlier: 5.769A 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: 3.962A pdb=" N LEULH 105 " --> pdb=" O ASPLH 101 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ARGLH 106 " --> pdb=" O VALLH 102 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THRLH 107 " --> pdb=" O ALALH 103 " (cutoff:3.500A) Processing helix chain 'LH' and resid 189 through 205 removed outlier: 3.740A pdb=" N CYSLH 204 " --> pdb=" O ILELH 200 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LYSLH 205 " --> pdb=" O GLNLH 201 " (cutoff:3.500A) Processing helix chain 'LH' and resid 210 through 215 removed outlier: 4.985A 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 136 through 142 removed outlier: 4.858A pdb=" N ALALJ 140 " --> pdb=" O GLYLJ 136 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYSLJ 141 " --> pdb=" O GLULJ 137 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 150 through 155 removed outlier: 5.622A pdb=" N ILELJ 155 " --> pdb=" O ALALJ 151 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 156 through 168 Processing helix chain 'LJ' and resid 93 through 98 removed outlier: 3.525A pdb=" N PHELJ 97 " --> pdb=" O ARGLJ 94 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N SERLJ 98 " --> pdb=" O ARGLJ 95 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 109 through 114 removed outlier: 4.757A pdb=" N ASPLJ 112 " --> pdb=" O GLULJ 109 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEULJ 113 " --> pdb=" O HISLJ 110 " (cutoff:3.500A) Processing helix chain 'LK' and resid 23 through 33 removed outlier: 4.787A pdb=" N ALALK 27 " --> pdb=" O GLYLK 23 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEULK 28 " --> pdb=" O ALALK 24 " (cutoff:3.500A) Proline residue: LK 30 - end of helix Processing helix chain 'LK' and resid 38 through 51 Processing helix chain 'LK' and resid 76 through 86 removed outlier: 3.972A pdb=" N LYSLK 86 " --> pdb=" O ILELK 82 " (cutoff:3.500A) Processing helix chain 'LK' and resid 105 through 121 removed outlier: 4.995A pdb=" N PHELK 118 " --> pdb=" O ARGLK 114 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N LYSLK 119 " --> pdb=" O THRLK 115 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N PHELK 121 " --> pdb=" O ARGLK 117 " (cutoff:3.500A) Processing helix chain 'LK' and resid 124 through 140 Processing helix chain 'LK' and resid 147 through 158 Processing helix chain 'LL' and resid 17 through 22 removed outlier: 4.367A pdb=" N ARGLL 21 " --> pdb=" O HISLL 17 " (cutoff:3.500A) removed outlier: 3.701A 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: 3.702A pdb=" N GLYLL 94 " --> pdb=" O ALALL 90 " (cutoff:3.500A) Processing helix chain 'LL' and resid 105 through 123 removed outlier: 3.797A pdb=" N LEULL 109 " --> pdb=" O SERLL 105 " (cutoff:3.500A) Processing helix chain 'LL' and resid 139 through 144 removed outlier: 4.329A 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: 3.817A pdb=" N ALALM 62 " --> pdb=" O PROLM 58 " (cutoff:3.500A) removed outlier: 5.261A 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: 5.413A pdb=" N ASNLM 98 " --> pdb=" O TRPLM 94 " (cutoff:3.500A) Processing helix chain 'LM' and resid 99 through 112 removed outlier: 3.876A 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: 4.429A pdb=" N TYRLN 6 " --> pdb=" O GLYLN 2 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYSLN 13 " --> pdb=" O GLULN 9 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N LYSLN 14 " --> pdb=" O LEULN 10 " (cutoff:3.500A) Processing helix chain 'LN' and resid 16 through 34 removed outlier: 4.907A 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: 3.922A 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: 4.562A pdb=" N CYSLN 152 " --> pdb=" O ILELN 148 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASNLN 153 " --> pdb=" O ASNLN 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'LN' and resid 148 through 153' Processing helix chain 'LN' and resid 158 through 163 removed outlier: 3.512A pdb=" N ARGLN 162 " --> pdb=" O HISLN 158 " (cutoff:3.500A) Processing helix chain 'LN' and resid 165 through 173 Processing helix chain 'LN' and resid 186 through 196 Processing helix chain 'LO' and resid 16 through 31 Processing helix chain 'LO' and resid 47 through 61 removed outlier: 3.514A pdb=" N ALALO 51 " --> pdb=" O GLULO 47 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYSLO 61 " --> pdb=" O ALALO 57 " (cutoff:3.500A) Processing helix chain 'LO' and resid 77 through 91 removed outlier: 3.886A pdb=" N METLO 89 " --> pdb=" O ALALO 85 " (cutoff:3.500A) removed outlier: 3.615A 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: 3.719A pdb=" N ARGLO 103 " --> pdb=" O ALALO 99 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEULO 104 " --> pdb=" O ALALO 100 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N LYSLO 105 " --> pdb=" O LEULO 101 " (cutoff:3.500A) Processing helix chain 'LO' and resid 112 through 118 removed outlier: 7.987A pdb=" N LYSLO 116 " --> pdb=" O PROLO 112 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYSLO 117 " --> pdb=" O PROLO 113 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N LYSLO 118 " --> pdb=" O TYRLO 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'LO' and resid 112 through 118' Processing helix chain 'LO' and resid 126 through 131 Processing helix chain 'LO' and resid 139 through 148 Processing helix chain 'LO' and resid 153 through 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: 4.858A 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: 3.869A pdb=" N LYSLQ 74 " --> pdb=" O ALALQ 70 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N METLQ 82 " --> pdb=" O ARGLQ 78 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N SERLQ 83 " --> pdb=" O ARGLQ 79 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 91 through 100 removed outlier: 3.901A 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: 3.694A pdb=" N VALLR 22 " --> pdb=" O GLYLR 18 " (cutoff:3.500A) removed outlier: 5.888A 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: 3.657A pdb=" N ALALR 35 " --> pdb=" O GLULR 31 " (cutoff:3.500A) removed outlier: 5.370A 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: 5.785A 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: 6.644A 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: 3.759A pdb=" N ILELS 121 " --> pdb=" O ARGLS 117 " (cutoff:3.500A) removed outlier: 5.626A 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: 4.446A pdb=" N LEULS 143 " --> pdb=" O TYRLS 139 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALALS 145 " --> pdb=" O LYSLS 141 " (cutoff:3.500A) Processing helix chain 'LT' and resid 92 through 97 removed outlier: 4.011A pdb=" N VALLT 96 " --> pdb=" O ARGLT 92 " (cutoff:3.500A) removed outlier: 5.495A 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: 3.698A pdb=" N ARGLV 72 " --> pdb=" O LYSLV 68 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYSLV 73 " --> pdb=" O PROLV 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'LV' and resid 68 through 73' Processing helix chain 'LV' and resid 121 through 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: 5.332A pdb=" N ILELX 77 " --> pdb=" O HISLX 73 " (cutoff:3.500A) Processing helix chain 'LX' and resid 82 through 92 removed outlier: 4.085A 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: 3.761A pdb=" N VALLY 28 " --> pdb=" O SERLY 24 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N SERLY 31 " --> pdb=" O ARGLY 27 " (cutoff:3.500A) Processing helix chain 'LY' and resid 35 through 43 Processing helix chain 'LY' and resid 99 through 104 removed outlier: 4.119A pdb=" N VALLY 103 " --> pdb=" O HISLY 99 " (cutoff:3.500A) removed outlier: 5.311A 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: 4.140A pdb=" N LYSLZ 66 " --> pdb=" O GLULZ 62 " (cutoff:3.500A) Processing helix chain 'LZ' and resid 75 through 80 removed outlier: 3.711A pdb=" N LEULZ 79 " --> pdb=" O ASNLZ 75 " (cutoff:3.500A) removed outlier: 5.417A 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: 4.233A pdb=" N PHELZ 100 " --> pdb=" O ASNLZ 96 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LYSLZ 101 " --> pdb=" O ALALZ 97 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLULZ 102 " --> pdb=" O ASPLZ 98 " (cutoff:3.500A) Proline residue: LZ 103 - end of helix No H-bonds generated for 'chain 'LZ' and resid 96 through 103' Processing helix chain 'LZ' and resid 104 through 124 removed outlier: 3.608A pdb=" N GLYLZ 124 " --> pdb=" O ARGLZ 120 " (cutoff:3.500A) Processing helix chain 'LZ' and resid 126 through 132 removed outlier: 3.643A 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: 3.969A pdb=" N LYSLa 10 " --> pdb=" O SERLa 6 " (cutoff:3.500A) Processing helix chain 'La' and resid 64 through 69 removed outlier: 4.350A pdb=" N TYRLa 68 " --> pdb=" O LEULa 64 " (cutoff:3.500A) removed outlier: 3.616A 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: 3.611A pdb=" N LEULa 78 " --> pdb=" O ASNLa 74 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N TRPLa 79 " --> pdb=" O ILELa 75 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N SERLa 80 " --> pdb=" O ASPLa 76 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEULa 81 " --> pdb=" O LYSLa 77 " (cutoff:3.500A) removed outlier: 4.230A 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: 3.548A pdb=" N HISLa 107 " --> pdb=" O ASPLa 103 " (cutoff:3.500A) Processing helix chain 'La' and resid 131 through 142 Processing helix chain 'Lc' and resid 12 through 23 Processing helix chain 'Lc' and resid 29 through 40 Processing helix chain 'Lc' and resid 52 through 67 Processing helix chain 'Lc' and resid 76 through 85 Processing helix chain 'Ld' and resid 23 through 29 removed outlier: 4.080A pdb=" N ARGLd 27 " --> pdb=" O HISLd 23 " (cutoff:3.500A) Processing helix chain 'Ld' and resid 32 through 53 removed outlier: 5.270A pdb=" N ALALd 37 " --> pdb=" O PHELd 33 " (cutoff:3.500A) Proline residue: Ld 38 - end of helix Processing helix chain 'Ld' and resid 60 through 69 Processing helix chain 'Le' and resid 22 through 27 removed outlier: 4.918A pdb=" N LYSLe 27 " --> pdb=" O SERLe 23 " (cutoff:3.500A) Processing helix chain 'Le' and resid 41 through 46 Processing helix chain 'Le' and resid 79 through 88 removed outlier: 3.676A pdb=" N LEULe 85 " --> pdb=" O LYSLe 81 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEULe 86 " --> pdb=" O ASPLe 82 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEULe 87 " --> pdb=" O VALLe 83 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N METLe 88 " --> pdb=" O GLULe 84 " (cutoff:3.500A) Processing helix chain 'Le' and resid 102 through 117 Processing helix chain 'Lf' and resid 39 through 47 removed outlier: 4.133A pdb=" N PHELf 45 " --> pdb=" O ALALf 41 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TYRLf 46 " --> pdb=" O ALALf 42 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEULf 47 " --> pdb=" O ALALf 43 " (cutoff:3.500A) Processing helix chain 'Lg' and resid 59 through 67 removed outlier: 3.942A pdb=" N TYRLg 63 " --> pdb=" O ARGLg 59 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ALALg 64 " --> pdb=" O PROLg 60 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N THRLg 65 " --> pdb=" O ARGLg 61 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILELg 66 " --> pdb=" O GLULg 62 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N SERLg 67 " --> pdb=" O TYRLg 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'Lg' and resid 59 through 67' Processing helix chain 'Lg' and resid 82 through 119 Processing helix chain 'Lh' and resid 8 through 16 removed outlier: 3.583A pdb=" N LEULh 12 " --> pdb=" O LYSLh 8 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SERLh 14 " --> pdb=" O GLYLh 10 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYSLh 15 " --> pdb=" O GLNLh 11 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ASNLh 16 " --> pdb=" O LEULh 12 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 17 through 41 removed outlier: 3.642A pdb=" N ILELh 36 " --> pdb=" O SERLh 32 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 44 through 76 removed outlier: 4.180A pdb=" N LYSLh 48 " --> pdb=" O ALALh 44 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 82 through 87 Proline residue: Lh 87 - end of helix Processing helix chain 'Lh' and resid 90 through 96 Processing helix chain 'Lh' and resid 98 through 104 Processing helix chain 'Lh' and resid 106 through 116 Processing helix chain 'Li' and resid 34 through 39 removed outlier: 4.121A pdb=" N ARGLi 38 " --> pdb=" O ARGLi 34 " (cutoff:3.500A) removed outlier: 4.883A 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: 3.805A pdb=" N GLYLj 9 " --> pdb=" O THRLj 5 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LYSLj 10 " --> pdb=" O SERLj 6 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ARGLj 11 " --> pdb=" O SERLj 7 " (cutoff:3.500A) Processing helix chain 'Lj' and resid 50 through 58 removed outlier: 3.705A pdb=" N LYSLj 57 " --> pdb=" O ALALj 53 " (cutoff:3.500A) Processing helix chain 'Lj' and resid 65 through 77 removed outlier: 5.228A pdb=" N THRLj 69 " --> pdb=" O ARGLj 65 " (cutoff:3.500A) removed outlier: 3.826A 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: 4.501A pdb=" N LYSLk 59 " --> pdb=" O ALALk 55 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLNLk 60 " --> pdb=" O GLULk 56 " (cutoff:3.500A) Proline residue: Lk 63 - end of helix Processing helix chain 'Ll' and resid 6 through 21 removed outlier: 5.480A pdb=" N ARGLl 21 " --> pdb=" O GLNLl 17 " (cutoff:3.500A) Processing helix chain 'Ll' and resid 24 through 30 removed outlier: 4.467A pdb=" N ARGLl 28 " --> pdb=" O PROLl 24 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEULl 29 " --> pdb=" O GLNLl 25 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARGLl 30 " --> pdb=" O TRPLl 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ll' and resid 24 through 30' Processing helix chain 'Lp' and resid 19 through 35 removed outlier: 3.915A pdb=" N LYSLp 28 " --> pdb=" O LYSLp 24 " (cutoff:3.500A) removed outlier: 4.213A 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: 5.304A pdb=" N ASPLq 49 " --> pdb=" O GLYLq 45 " (cutoff:3.500A) Processing helix chain 'Lq' and resid 86 through 99 Processing helix chain 'Lq' and resid 104 through 123 removed outlier: 3.948A pdb=" N ARGLq 108 " --> pdb=" O ARGLq 104 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N GLNLq 109 " --> pdb=" O ALALq 105 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ALALq 110 " --> pdb=" O ASPLq 106 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARGLq 123 " --> pdb=" O LEULq 119 " (cutoff:3.500A) Processing helix chain 'Lq' and resid 135 through 140 removed outlier: 5.165A pdb=" N ARGLq 140 " --> pdb=" O GLYLq 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'Lq' and resid 135 through 140' Processing sheet with id= 1, first strand: chain 'CF' and resid 63 through 67 removed outlier: 6.893A pdb=" N VALCF 42 " --> pdb=" O LEUCF 224 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'CF' and resid 135 through 139 removed outlier: 6.757A pdb=" N VALCF 135 " --> pdb=" O ILECF 194 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N GLUCF 190 " --> pdb=" O PROCF 139 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'CF' and resid 172 through 175 Processing sheet with id= 4, first strand: chain 'CF' and resid 232 through 236 removed outlier: 3.585A pdb=" N GLUCF 233 " --> pdb=" O SERCF 228 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'CF' and resid 38 through 42 removed outlier: 8.219A pdb=" N GLNCF 38 " --> pdb=" O SERCF 229 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLYCF 225 " --> pdb=" O VALCF 42 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'CH' and resid 203 through 209 removed outlier: 4.952A pdb=" N ARGCH 167 " --> pdb=" O ARGCH 214 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THRCH 220 " --> pdb=" O VALCH 171 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLYCH 173 " --> pdb=" O THRCH 220 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N METCH 281 " --> pdb=" O ALACH 247 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'CI' and resid 214 through 219 removed outlier: 4.879A pdb=" N ARGCI 230 " --> pdb=" O VALCI 219 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VALCI 188 " --> pdb=" O VALCI 263 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'CJ' and resid 186 through 191 removed outlier: 3.672A pdb=" N GLYCJ 194 " --> pdb=" O SERCJ 191 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'CJ' and resid 394 through 397 Processing sheet with id= 10, first strand: chain 'CK' and resid 148 through 151 Processing sheet with id= 11, first strand: chain 'CK' and resid 190 through 195 removed outlier: 3.631A pdb=" N VALCK 191 " --> pdb=" O HISCK 186 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ASNCK 256 " --> pdb=" O THRCK 246 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N TYRCK 242 " --> pdb=" O LEUCK 260 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N THRCK 219 " --> pdb=" O ILECK 245 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'CM' and resid 139 through 144 removed outlier: 5.475A pdb=" N TRPCM 139 " --> pdb=" O ILECM 95 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYSCM 88 " --> pdb=" O VALCM 125 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASNCM 119 " --> pdb=" O ARGCM 94 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ASNCM 118 " --> pdb=" O LEUCM 213 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'CN' and resid 1 through 4 Processing sheet with id= 14, first strand: chain 'CN' and resid 23 through 27 Processing sheet with id= 15, first strand: chain 'CN' and resid 69 through 73 Processing sheet with id= 16, first strand: chain 'CN' and resid 158 through 161 Processing sheet with id= 17, first strand: chain 'CQ' and resid 3 through 6 removed outlier: 4.541A pdb=" N ARGCQ 11 " --> pdb=" O CYSCQ 6 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'CQ' and resid 18 through 23 removed outlier: 3.736A pdb=" N LYSCQ 27 " --> pdb=" O ARGCQ 23 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'Cb' and resid 50 through 53 removed outlier: 4.532A pdb=" N TYRCb 50 " --> pdb=" O PHECb 59 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'Cd' and resid 293 through 297 removed outlier: 3.850A pdb=" N CYSCd 378 " --> pdb=" O LEUCd 331 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N GLYCd 333 " --> pdb=" O CYSCd 378 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILECd 373 " --> pdb=" O LEUCd 369 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'Cf' and resid 56 through 60 removed outlier: 5.465A pdb=" N ARGCf 34 " --> pdb=" O PHECf 60 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N SERCf 92 " --> pdb=" O GLYCf 35 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N HISCf 98 " --> pdb=" O LEUCf 118 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N LEUCf 111 " --> pdb=" O PROCf 263 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ARGCf 259 " --> pdb=" O GLUCf 115 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'Cf' and resid 140 through 146 removed outlier: 6.818A pdb=" N VALCf 229 " --> pdb=" O HISCf 249 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'Cf' and resid 287 through 290 removed outlier: 4.649A pdb=" N ASPCf 294 " --> pdb=" O ASPCf 290 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'Cg' and resid 21 through 25 Processing sheet with id= 25, first strand: chain 'Cg' and resid 71 through 75 removed outlier: 4.228A pdb=" N THRCg 71 " --> pdb=" O THRCg 82 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'Cg' and resid 124 through 129 removed outlier: 8.763A pdb=" N ASNCg 124 " --> pdb=" O LYSCg 137 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LYSCg 137 " --> pdb=" O ASNCg 124 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'Ch' and resid 52 through 56 Processing sheet with id= 28, first strand: chain 'Ch' and resid 139 through 143 removed outlier: 5.225A pdb=" N ALACh 511 " --> pdb=" O GLYCh 507 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N GLYCh 507 " --> pdb=" O ALACh 511 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N LEUCh 502 " --> pdb=" O ALACh 497 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'Ch' and resid 151 through 155 removed outlier: 6.267A pdb=" N ARGCh 161 " --> pdb=" O SERCh 155 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N SERCh 160 " --> pdb=" O THRCh 176 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N THRCh 170 " --> pdb=" O SERCh 166 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILECh 173 " --> pdb=" O LYSCh 182 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'Ch' and resid 193 through 198 removed outlier: 5.523A pdb=" N TYRCh 203 " --> pdb=" O SERCh 198 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THRCh 212 " --> pdb=" O SERCh 208 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N VALCh 215 " --> pdb=" O VALCh 224 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYSCh 222 " --> pdb=" O ASPCh 217 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'Ch' and resid 236 through 241 removed outlier: 5.845A pdb=" N ARGCh 252 " --> pdb=" O GLNCh 241 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ALACh 251 " --> pdb=" O VALCh 267 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N THRCh 261 " --> pdb=" O SERCh 257 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILECh 264 " --> pdb=" O GLUCh 273 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARGCh 271 " --> pdb=" O LEUCh 266 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'Ch' and resid 284 through 289 removed outlier: 4.292A pdb=" N LEUCh 293 " --> pdb=" O GLYCh 289 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N ASPCh 292 " --> pdb=" O ALACh 308 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SERCh 302 " --> pdb=" O SERCh 298 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VALCh 305 " --> pdb=" O VALCh 314 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'Ch' and resid 326 through 330 removed outlier: 6.611A pdb=" N ARGCh 374 " --> pdb=" O SERCh 330 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N THRCh 383 " --> pdb=" O SERCh 379 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'Ch' and resid 408 through 413 removed outlier: 5.624A pdb=" N LEUCh 418 " --> pdb=" O SERCh 413 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SERCh 427 " --> pdb=" O GLYCh 423 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYSCh 440 " --> pdb=" O LEUCh 430 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'Ch' and resid 451 through 455 removed outlier: 5.824A pdb=" N LEUCh 460 " --> pdb=" O SERCh 455 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ARGCh 459 " --> pdb=" O VALCh 475 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N THRCh 469 " --> pdb=" O SERCh 465 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VALCh 472 " --> pdb=" O ALACh 481 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'Ch' and resid 170 through 173 Processing sheet with id= 37, first strand: chain 'Ch' and resid 261 through 264 removed outlier: 3.815A pdb=" N HISCh 274 " --> pdb=" O ILECh 264 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'Ch' and resid 302 through 305 Processing sheet with id= 39, first strand: chain 'Ch' and resid 469 through 472 Processing sheet with id= 40, first strand: chain 'LA' and resid 47 through 50 removed outlier: 3.702A pdb=" N GLULA 47 " --> pdb=" O ARGLA 60 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARGLA 60 " --> pdb=" O LYSLA 46 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLNLA 86 " --> pdb=" O VALLA 45 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'LA' and resid 111 through 114 removed outlier: 4.418A pdb=" N THRLA 111 " --> pdb=" O VALLA 136 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ARGLA 147 " --> pdb=" O VALLA 137 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'LA' and resid 58 through 64 No H-bonds generated for sheet with id= 42 Processing sheet with id= 43, first strand: chain 'LA' and resid 145 through 150 removed outlier: 4.159A pdb=" N ALALA 154 " --> pdb=" O LEULA 150 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'LB' and resid 41 through 44 removed outlier: 6.428A pdb=" N GLNLB 183 " --> pdb=" O THRLB 44 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N HISLB 178 " --> pdb=" O THRLB 165 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N VALLB 159 " --> pdb=" O ILELB 184 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N GLYLB 186 " --> pdb=" O THRLB 157 " (cutoff:3.500A) removed outlier: 11.198A pdb=" N THRLB 157 " --> pdb=" O GLYLB 186 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VALLB 158 " --> pdb=" O GLYLB 91 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLYLB 91 " --> pdb=" O VALLB 158 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ARGLB 160 " --> pdb=" O LEULB 89 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEULB 89 " --> pdb=" O ARGLB 160 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEULB 162 " --> pdb=" O VALLB 87 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLYLB 91 " --> pdb=" O LEULB 102 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'LB' and resid 53 through 58 removed outlier: 6.790A pdb=" N ILELB 78 " --> pdb=" O ALALB 51 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ARGLB 335 " --> pdb=" O LYSLB 50 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLULB 214 " --> pdb=" O ILELB 283 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'LB' and resid 285 through 289 removed outlier: 3.624A pdb=" N ARGLB 285 " --> pdb=" O METLB 324 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLYLB 289 " --> pdb=" O ASNLB 320 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ASNLB 320 " --> pdb=" O GLYLB 289 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'LB' and resid 76 through 80 Processing sheet with id= 48, first strand: chain 'LB' and resid 87 through 91 removed outlier: 7.979A pdb=" N VALLB 87 " --> pdb=" O ALALB 107 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THRLB 103 " --> pdb=" O GLYLB 91 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'LB' and resid 84 through 87 removed outlier: 3.855A pdb=" N LYSLB 202 " --> pdb=" O VALLB 86 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'LC' and resid 5 through 9 removed outlier: 4.830A pdb=" N ALALC 19 " --> pdb=" O VALLC 9 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'LC' and resid 209 through 212 Processing sheet with id= 52, first strand: chain 'LD' and resid 60 through 66 Processing sheet with id= 53, first strand: chain 'LE' and resid 5 through 9 Processing sheet with id= 54, first strand: chain 'LE' and resid 56 through 61 removed outlier: 4.164A pdb=" N THRLE 56 " --> pdb=" O LEULE 72 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYSLE 68 " --> pdb=" O LEULE 60 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'LF' and resid 139 through 144 removed outlier: 7.629A pdb=" N TRPLF 139 " --> pdb=" O ILELF 95 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LYSLF 88 " --> pdb=" O VALLF 125 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASNLF 119 " --> pdb=" O ARGLF 94 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N ASNLF 118 " --> pdb=" O LEULF 213 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'LF' and resid 158 through 162 removed outlier: 6.454A pdb=" N GLYLF 158 " --> pdb=" O LEULF 169 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'LG' and resid 179 through 184 Processing sheet with id= 58, first strand: chain 'LH' and resid 5 through 12 removed outlier: 5.577A pdb=" N GLYLH 88 " --> pdb=" O VALLH 12 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'LH' and resid 54 through 57 Processing sheet with id= 60, first strand: chain 'LH' and resid 137 through 144 removed outlier: 3.761A pdb=" N CYSLH 148 " --> pdb=" O ASNLH 143 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N TYRLH 149 " --> pdb=" O METLH 167 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'LH' and resid 171 through 176 removed outlier: 5.520A pdb=" N GLULH 182 " --> pdb=" O SERLH 176 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ASPLH 181 " --> pdb=" O TYRLH 129 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'LJ' and resid 46 through 50 removed outlier: 3.514A pdb=" N ALALJ 67 " --> pdb=" O SERLJ 49 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N SERLJ 23 " --> pdb=" O GLYLJ 125 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N GLYLJ 125 " --> pdb=" O SERLJ 23 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'LK' and resid 11 through 16 removed outlier: 4.265A pdb=" N THRLK 59 " --> pdb=" O VALLK 74 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'LL' and resid 56 through 59 Processing sheet with id= 65, first strand: chain 'LM' and resid 18 through 21 removed outlier: 4.616A pdb=" N ARGLM 18 " --> pdb=" O ILELM 30 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEULM 40 " --> pdb=" O VALLM 31 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'LN' and resid 35 through 39 removed outlier: 6.448A pdb=" N VALLN 35 " --> pdb=" O ARGLN 65 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ILELN 61 " --> pdb=" O ALALN 39 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLYLN 58 " --> pdb=" O ASPLN 136 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THRLN 126 " --> pdb=" O ARGLN 68 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILELN 133 " --> pdb=" O LEULN 116 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'LN' and resid 117 through 121 removed outlier: 3.675A pdb=" N ASNLN 117 " --> pdb=" O ILELN 133 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N TYRLN 129 " --> pdb=" O VALLN 121 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'LO' and resid 7 through 11 Processing sheet with id= 69, first strand: chain 'LP' and resid 14 through 20 removed outlier: 6.613A pdb=" N ILELP 149 " --> pdb=" O LYSLP 115 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'LP' and resid 57 through 60 removed outlier: 5.424A pdb=" N ARGLP 80 " --> pdb=" O METLP 60 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'LP' and resid 116 through 122 Processing sheet with id= 72, first strand: chain 'LP' and resid 124 through 131 removed outlier: 4.214A pdb=" N ARGLP 127 " --> pdb=" O TYRLP 139 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARGLP 135 " --> pdb=" O ARGLP 131 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'LQ' and resid 106 through 110 Processing sheet with id= 74, first strand: chain 'LQ' and resid 126 through 129 Processing sheet with id= 75, first strand: chain 'LS' and resid 24 through 30 removed outlier: 6.563A pdb=" N ILELS 10 " --> pdb=" O VALLS 59 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N THRLS 55 " --> pdb=" O LEULS 14 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'LS' and resid 86 through 96 removed outlier: 5.179A pdb=" N ASNLS 74 " --> pdb=" O LEULS 129 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'LS' and resid 6 through 10 removed outlier: 4.737A pdb=" N GLULS 6 " --> pdb=" O ILELS 64 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'LT' and resid 40 through 43 removed outlier: 3.786A pdb=" N LYSLT 60 " --> pdb=" O ILELT 42 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'LT' and resid 72 through 79 Processing sheet with id= 80, first strand: chain 'LU' and resid 60 through 64 removed outlier: 5.397A pdb=" N GLYLU 108 " --> pdb=" O LYSLU 20 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'LV' and resid 22 through 26 removed outlier: 4.313A pdb=" N ALALV 23 " --> pdb=" O ILELV 38 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N METLV 61 " --> pdb=" O ILELV 39 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ASPLV 58 " --> pdb=" O ILELV 80 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASPLV 99 " --> pdb=" O ALALV 84 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALALV 84 " --> pdb=" O ASPLV 99 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'LV' and resid 86 through 89 removed outlier: 4.096A pdb=" N VALLV 93 " --> pdb=" O ARGLV 89 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'LX' and resid 93 through 99 removed outlier: 6.657A pdb=" N ASNLX 93 " --> pdb=" O LEULX 139 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYSLX 133 " --> pdb=" O VALLX 99 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THRLX 132 " --> pdb=" O ARGLX 128 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYSLX 122 " --> pdb=" O ARGLX 138 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'LY' and resid 55 through 58 removed outlier: 4.095A pdb=" N LYSLY 65 " --> pdb=" O ILELY 57 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'LY' and resid 71 through 74 removed outlier: 3.583A pdb=" N SERLY 71 " --> pdb=" O HISLY 80 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'LY' and resid 85 through 88 removed outlier: 5.027A pdb=" N GLNLY 92 " --> pdb=" O LYSLY 88 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'LZ' and resid 8 through 13 removed outlier: 4.394A pdb=" N ARGLZ 8 " --> pdb=" O ILELZ 24 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYSLZ 20 " --> pdb=" O VALLZ 12 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEULZ 41 " --> pdb=" O ILELZ 25 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain 'LZ' and resid 41 through 44 Processing sheet with id= 89, first strand: chain 'La' and resid 99 through 102 Processing sheet with id= 90, first strand: chain 'Lc' and resid 25 through 28 removed outlier: 6.293A pdb=" N LYSLc 25 " --> pdb=" O LEULc 96 " (cutoff:3.500A) Processing sheet with id= 91, first strand: chain 'Ld' and resid 56 through 59 removed outlier: 5.020A pdb=" N ASPLd 56 " --> pdb=" O LEULd 97 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ALALd 17 " --> pdb=" O VALLd 117 " (cutoff:3.500A) Processing sheet with id= 92, first strand: chain 'Le' and resid 72 through 78 Processing sheet with id= 93, first strand: chain 'Lf' and resid 12 through 17 removed outlier: 5.912A pdb=" N LYSLf 12 " --> pdb=" O GLULf 35 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEULf 31 " --> pdb=" O LEULf 16 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ARGLf 84 " --> pdb=" O THRLf 74 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LYSLf 65 " --> pdb=" O ALALf 57 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LYSLf 49 " --> pdb=" O ILELf 73 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ARGLf 50 " --> pdb=" O METLf 103 " (cutoff:3.500A) Processing sheet with id= 94, first strand: chain 'Lf' and resid 10 through 16 removed outlier: 4.071A pdb=" N ALALf 98 " --> pdb=" O HISLf 15 " (cutoff:3.500A) Processing sheet with id= 95, first strand: chain 'Lg' and resid 20 through 25 removed outlier: 4.369A pdb=" N ARGLg 20 " --> pdb=" O ILELg 36 " (cutoff:3.500A) Processing sheet with id= 96, first strand: chain 'Lk' and resid 2 through 5 removed outlier: 4.533A pdb=" N VALLk 48 " --> pdb=" O VALLk 5 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SERLk 22 " --> pdb=" O ARGLk 39 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N LYSLk 27 " --> pdb=" O VALLk 71 " (cutoff:3.500A) Processing sheet with id= 97, first strand: chain 'Lp' and resid 47 through 50 removed outlier: 6.976A pdb=" N ILELp 54 " --> pdb=" O THRLp 50 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N GLYLp 53 " --> pdb=" O GLYLp 66 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYSLp 62 " --> pdb=" O CYSLp 57 " (cutoff:3.500A) Processing sheet with id= 98, first strand: chain 'Lq' and resid 19 through 22 removed outlier: 6.981A pdb=" N PHELq 19 " --> pdb=" O ARGLq 30 " (cutoff:3.500A) Processing sheet with id= 99, first strand: chain 'Lq' and resid 51 through 56 removed outlier: 5.263A pdb=" N ALALq 51 " --> pdb=" O LYSLq 66 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N SERLq 77 " --> pdb=" O LYSLq 67 " (cutoff:3.500A) 3610 hydrogen bonds defined for protein. 10719 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2677 hydrogen bonds 4450 hydrogen bond angles 0 basepair planarities 1060 basepair parallelities 1728 stacking parallelities Total time for adding SS restraints: 192.64 Time building geometry restraints manager: 61.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 16138 1.28 - 1.42: 54760 1.42 - 1.55: 84620 1.55 - 1.68: 6843 1.68 - 1.81: 413 Bond restraints: 162774 Sorted by residual: bond pdb=" C3' A2MC1 858 " pdb=" C2' A2MC1 858 " ideal model delta sigma weight residual 1.544 1.238 0.306 2.00e-02 2.50e+03 2.35e+02 bond pdb=" C2' A2MC1 389 " pdb=" C1' A2MC1 389 " ideal model delta sigma weight residual 1.305 1.611 -0.306 2.00e-02 2.50e+03 2.34e+02 bond pdb=" C3' A2MC12289 " pdb=" C2' A2MC12289 " ideal model delta sigma weight residual 1.544 1.240 0.304 2.00e-02 2.50e+03 2.30e+02 bond pdb=" C3' A2MC11432 " pdb=" C2' A2MC11432 " ideal model delta sigma weight residual 1.544 1.241 0.303 2.00e-02 2.50e+03 2.29e+02 bond pdb=" C3' A2MC1 848 " pdb=" C2' A2MC1 848 " ideal model delta sigma weight residual 1.544 1.242 0.302 2.00e-02 2.50e+03 2.29e+02 ... (remaining 162769 not shown) Histogram of bond angle deviations from ideal: 97.39 - 107.07: 22428 107.07 - 116.76: 113882 116.76 - 126.45: 88800 126.45 - 136.13: 10899 136.13 - 145.82: 14 Bond angle restraints: 236023 Sorted by residual: angle pdb=" C1' OMGC12876 " pdb=" N9 OMGC12876 " pdb=" C8 OMGC12876 " ideal model delta sigma weight residual 142.82 105.39 37.43 3.00e+00 1.11e-01 1.56e+02 angle pdb=" C1' OMGC12876 " pdb=" N9 OMGC12876 " pdb=" C4 OMGC12876 " ideal model delta sigma weight residual 108.29 144.13 -35.84 3.00e+00 1.11e-01 1.43e+02 angle pdb=" C1' OMGC1 787 " pdb=" N9 OMGC1 787 " pdb=" C8 OMGC1 787 " ideal model delta sigma weight residual 142.82 109.62 33.20 3.00e+00 1.11e-01 1.22e+02 angle pdb=" C1' OMGC1 646 " pdb=" N9 OMGC1 646 " pdb=" C8 OMGC1 646 " ideal model delta sigma weight residual 142.82 109.79 33.03 3.00e+00 1.11e-01 1.21e+02 angle pdb=" C1' OMGC1 787 " pdb=" N9 OMGC1 787 " pdb=" C4 OMGC1 787 " ideal model delta sigma weight residual 108.29 140.32 -32.03 3.00e+00 1.11e-01 1.14e+02 ... (remaining 236018 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.33: 93345 35.33 - 70.65: 8869 70.65 - 105.98: 1023 105.98 - 141.30: 31 141.30 - 176.63: 38 Dihedral angle restraints: 103306 sinusoidal: 73899 harmonic: 29407 Sorted by residual: dihedral pdb=" C4' CC13324 " pdb=" C3' CC13324 " pdb=" C2' CC13324 " pdb=" C1' CC13324 " ideal model delta sinusoidal sigma weight residual -35.00 33.92 -68.92 1 8.00e+00 1.56e-02 9.61e+01 dihedral pdb=" C5' CC13324 " pdb=" C4' CC13324 " pdb=" C3' CC13324 " pdb=" O3' CC13324 " ideal model delta sinusoidal sigma weight residual 147.00 80.05 66.95 1 8.00e+00 1.56e-02 9.13e+01 dihedral pdb=" O4' CC1 961 " pdb=" C1' CC1 961 " pdb=" N1 CC1 961 " pdb=" C2 CC1 961 " ideal model delta sinusoidal sigma weight residual 200.00 41.61 158.39 1 1.50e+01 4.44e-03 8.23e+01 ... (remaining 103303 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 27232 0.085 - 0.170: 1517 0.170 - 0.255: 59 0.255 - 0.340: 14 0.340 - 0.425: 3 Chirality restraints: 28825 Sorted by residual: chirality pdb=" CG LEUCM 111 " pdb=" CB LEUCM 111 " pdb=" CD1 LEUCM 111 " pdb=" CD2 LEUCM 111 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.42 2.00e-01 2.50e+01 4.51e+00 chirality pdb=" C3' CC13324 " pdb=" C4' CC13324 " pdb=" O3' CC13324 " pdb=" C2' CC13324 " both_signs ideal model delta sigma weight residual False -2.74 -2.39 -0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" C3' UC11537 " pdb=" C4' UC11537 " pdb=" O3' UC11537 " pdb=" C2' UC11537 " both_signs ideal model delta sigma weight residual False -2.74 -2.39 -0.35 2.00e-01 2.50e+01 3.15e+00 ... (remaining 28822 not shown) Planarity restraints: 17569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMGC1 646 " 0.042 2.00e-02 2.50e+03 1.34e-01 4.03e+02 pdb=" C4' OMGC1 646 " -0.120 2.00e-02 2.50e+03 pdb=" O4' OMGC1 646 " 0.003 2.00e-02 2.50e+03 pdb=" C3' OMGC1 646 " 0.169 2.00e-02 2.50e+03 pdb=" O3' OMGC1 646 " -0.087 2.00e-02 2.50e+03 pdb=" C2' OMGC1 646 " -0.198 2.00e-02 2.50e+03 pdb=" O2' OMGC1 646 " 0.091 2.00e-02 2.50e+03 pdb=" C1' OMGC1 646 " 0.217 2.00e-02 2.50e+03 pdb=" N9 OMGC1 646 " -0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMGC12358 " -0.041 2.00e-02 2.50e+03 1.33e-01 4.00e+02 pdb=" C4' OMGC12358 " 0.117 2.00e-02 2.50e+03 pdb=" O4' OMGC12358 " -0.000 2.00e-02 2.50e+03 pdb=" C3' OMGC12358 " -0.176 2.00e-02 2.50e+03 pdb=" O3' OMGC12358 " 0.089 2.00e-02 2.50e+03 pdb=" C2' OMGC12358 " 0.201 2.00e-02 2.50e+03 pdb=" O2' OMGC12358 " -0.091 2.00e-02 2.50e+03 pdb=" C1' OMGC12358 " -0.210 2.00e-02 2.50e+03 pdb=" N9 OMGC12358 " 0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMCC11812 " -0.048 2.00e-02 2.50e+03 1.33e-01 3.98e+02 pdb=" C4' OMCC11812 " 0.125 2.00e-02 2.50e+03 pdb=" O4' OMCC11812 " 0.000 2.00e-02 2.50e+03 pdb=" C3' OMCC11812 " -0.182 2.00e-02 2.50e+03 pdb=" O3' OMCC11812 " 0.088 2.00e-02 2.50e+03 pdb=" C2' OMCC11812 " 0.205 2.00e-02 2.50e+03 pdb=" O2' OMCC11812 " -0.091 2.00e-02 2.50e+03 pdb=" C1' OMCC11812 " -0.199 2.00e-02 2.50e+03 pdb=" N1 OMCC11812 " 0.101 2.00e-02 2.50e+03 ... (remaining 17566 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 4018 2.65 - 3.22: 122355 3.22 - 3.78: 296386 3.78 - 4.34: 398423 4.34 - 4.90: 552992 Nonbonded interactions: 1374174 Sorted by model distance: nonbonded pdb=" O1B GTPCH 701 " pdb="MG MGCH 702 " model vdw 2.092 2.170 nonbonded pdb="MG MGCd 701 " pdb=" O2G GTPCd 703 " model vdw 2.114 2.170 nonbonded pdb="MG MGCd 701 " pdb=" O1B GTPCd 703 " model vdw 2.117 2.170 nonbonded pdb="MG MGCd 701 " pdb=" O HOHCd 802 " model vdw 2.132 2.170 nonbonded pdb=" OG1 THRCh 61 " pdb=" OD1 ASNCh 64 " model vdw 2.196 2.440 ... (remaining 1374169 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 78 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: 4.660 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: 0.110 Extract box with map and model: 29.280 Check model and map are aligned: 1.650 Set scattering table: 1.050 Process input model: 524.780 Find NCS groups from input model: 4.040 Set up NCS constraints: 0.520 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: 0.040 Load rotamer database and sin/cos tables:12.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 578.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.306 162774 Z= 0.292 Angle : 0.806 37.426 236023 Z= 0.412 Chirality : 0.040 0.425 28825 Planarity : 0.007 0.165 17569 Dihedral : 21.836 176.626 84280 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.09 % Allowed : 14.77 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.21 % 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: 0.66 (0.08), residues: 10017 helix: 1.05 (0.08), residues: 3861 sheet: 0.13 (0.13), residues: 1416 loop : 0.16 (0.08), residues: 4740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRPCg 105 HIS 0.021 0.001 HISLX 66 PHE 0.064 0.002 PHECh 37 TYR 0.044 0.002 TYRLT 65 ARG 0.022 0.001 ARGCL 27 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20034 Ramachandran restraints generated. 10017 Oldfield, 0 Emsley, 10017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20034 Ramachandran restraints generated. 10017 Oldfield, 0 Emsley, 10017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1192 residues out of total 8643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 1100 time to evaluate : 8.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CF 10 TYR cc_start: 0.8848 (t80) cc_final: 0.8623 (t80) REVERT: CF 123 ASP cc_start: 0.8528 (t0) cc_final: 0.8322 (t0) REVERT: CI 230 ARG cc_start: 0.7965 (mtt90) cc_final: 0.7702 (mtt180) REVERT: CQ 25 ASP cc_start: 0.8780 (p0) cc_final: 0.8495 (p0) REVERT: Cf 87 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.8395 (mtm) REVERT: Cz 79 ARG cc_start: 0.7917 (ttm-80) cc_final: 0.7675 (ttp-110) REVERT: Cz 86 ARG cc_start: 0.8008 (ttm170) cc_final: 0.7641 (ttm110) REVERT: LL 150 SER cc_start: 0.8993 (t) cc_final: 0.8743 (t) REVERT: Lc 35 LYS cc_start: 0.8949 (ttmt) cc_final: 0.8449 (mttt) outliers start: 92 outliers final: 70 residues processed: 1175 average time/residue: 2.4295 time to fit residues: 4000.0053 Evaluate side-chains 1115 residues out of total 8643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 1044 time to evaluate : 8.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CF residue 97 THR Chi-restraints excluded: chain CF residue 122 VAL Chi-restraints excluded: chain CF residue 149 VAL Chi-restraints excluded: chain CF residue 178 LYS Chi-restraints excluded: chain CF residue 242 THR Chi-restraints excluded: chain CH residue 79 ASP 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 608 GLN Chi-restraints excluded: chain CH residue 655 ILE Chi-restraints excluded: chain CI residue 198 PHE Chi-restraints excluded: chain CJ residue 101 SER Chi-restraints excluded: chain CJ residue 140 ASP Chi-restraints excluded: chain CJ residue 381 GLN Chi-restraints excluded: chain CJ residue 400 VAL Chi-restraints excluded: chain CJ residue 407 THR Chi-restraints excluded: chain CJ residue 456 VAL Chi-restraints excluded: chain CJ residue 465 ILE Chi-restraints excluded: chain CK residue 37 GLU Chi-restraints excluded: chain CK residue 98 THR Chi-restraints excluded: chain CK residue 190 ASN Chi-restraints excluded: chain CM residue 49 VAL Chi-restraints excluded: chain CM residue 162 VAL Chi-restraints excluded: chain CN residue 51 THR Chi-restraints excluded: chain CN residue 114 THR Chi-restraints excluded: chain Cb residue 28 SER Chi-restraints excluded: chain Cb residue 68 HIS Chi-restraints excluded: chain Cd residue 69 VAL Chi-restraints excluded: chain Cd residue 86 ASP Chi-restraints excluded: chain Cf residue 87 MET Chi-restraints excluded: chain Cf residue 91 SER Chi-restraints excluded: chain Cg residue 15 VAL Chi-restraints excluded: chain Cg residue 19 THR Chi-restraints excluded: chain Cg residue 22 THR Chi-restraints excluded: chain Cg residue 62 LEU Chi-restraints excluded: chain Cg residue 156 SER Chi-restraints excluded: chain Ch residue 285 CYS Chi-restraints excluded: chain LA residue 106 SER Chi-restraints excluded: chain LA residue 161 SER Chi-restraints excluded: chain LA residue 207 VAL Chi-restraints excluded: chain LB residue 352 LEU Chi-restraints excluded: chain LC residue 61 THR Chi-restraints excluded: chain LC residue 354 VAL Chi-restraints excluded: chain LE residue 6 THR Chi-restraints excluded: chain LE residue 155 SER Chi-restraints excluded: chain LF residue 80 SER Chi-restraints excluded: chain LF residue 90 VAL Chi-restraints excluded: chain LH residue 120 THR Chi-restraints excluded: chain LJ residue 45 THR Chi-restraints excluded: chain LK residue 22 VAL Chi-restraints excluded: chain LK residue 104 VAL Chi-restraints excluded: chain LL residue 141 ASP Chi-restraints excluded: chain LM residue 14 VAL Chi-restraints excluded: chain LN residue 60 VAL Chi-restraints excluded: chain LO residue 139 THR Chi-restraints excluded: chain LQ residue 148 THR Chi-restraints excluded: chain LS residue 79 LEU Chi-restraints excluded: chain LU residue 118 VAL Chi-restraints excluded: chain LV residue 114 SER Chi-restraints excluded: chain LX residue 37 THR Chi-restraints excluded: chain LY residue 78 VAL Chi-restraints excluded: chain LZ residue 34 SER Chi-restraints excluded: chain La residue 75 ILE Chi-restraints excluded: chain Lc residue 23 SER Chi-restraints excluded: chain Lc residue 27 VAL Chi-restraints excluded: chain Le residue 83 VAL Chi-restraints excluded: chain Lf residue 51 VAL Chi-restraints excluded: chain Lf residue 72 LYS Chi-restraints excluded: chain Lp residue 21 SER Chi-restraints excluded: chain Lp residue 28 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1325 random chunks: chunk 1118 optimal weight: 8.9990 chunk 1004 optimal weight: 5.9990 chunk 557 optimal weight: 0.8980 chunk 343 optimal weight: 4.9990 chunk 677 optimal weight: 6.9990 chunk 536 optimal weight: 6.9990 chunk 1038 optimal weight: 7.9990 chunk 401 optimal weight: 10.0000 chunk 631 optimal weight: 5.9990 chunk 772 optimal weight: 9.9990 chunk 1203 optimal weight: 4.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CF 29 ASN CH 389 ASN CH 639 HIS CM 163 ASN CM 227 HIS CQ 130 ASN Cb 34 GLN ** Ch 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cz 56 GLN LA 71 GLN LC 38 HIS LE 53 GLN LE 172 ASN LH 179 GLN LH 202 GLN LJ 96 ASN LK 8 ASN LL 159 GLN LM 106 GLN LS 21 ASN LS 147 ASN LU 27 GLN LU 55 ASN LX 66 HIS LX 81 ASN LX 124 ASN LY 56 GLN LY 116 ASN LZ 26 GLN LZ 105 GLN Ld 108 ASN Lk 32 GLN Lk 60 GLN Lp 45 ASN Lq 97 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.0768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 162774 Z= 0.441 Angle : 0.779 19.363 236023 Z= 0.405 Chirality : 0.045 0.303 28825 Planarity : 0.008 0.151 17569 Dihedral : 22.629 178.846 63594 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.28 % Allowed : 13.82 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % 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: 1.12 (0.08), residues: 10017 helix: 1.61 (0.08), residues: 3860 sheet: 0.18 (0.13), residues: 1421 loop : 0.33 (0.09), residues: 4736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRPCd 223 HIS 0.013 0.002 HISLR 125 PHE 0.024 0.003 PHELG 94 TYR 0.022 0.003 TYRCd 256 ARG 0.010 0.001 ARGLN 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20034 Ramachandran restraints generated. 10017 Oldfield, 0 Emsley, 10017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20034 Ramachandran restraints generated. 10017 Oldfield, 0 Emsley, 10017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1253 residues out of total 8643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 1060 time to evaluate : 8.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CF 10 TYR cc_start: 0.8870 (t80) cc_final: 0.8653 (t80) REVERT: CF 123 ASP cc_start: 0.8522 (t0) cc_final: 0.8310 (t0) REVERT: CH 70 LEU cc_start: 0.9550 (OUTLIER) cc_final: 0.9188 (mp) REVERT: CI 230 ARG cc_start: 0.7955 (mtt90) cc_final: 0.7748 (mtt90) REVERT: CL 73 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7508 (ptp-110) REVERT: CM 214 SER cc_start: 0.8984 (p) cc_final: 0.8610 (m) REVERT: CO 26 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8091 (mt-10) REVERT: CQ 25 ASP cc_start: 0.8868 (p0) cc_final: 0.8556 (p0) REVERT: Cd 324 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8541 (mmt-90) REVERT: Cf 252 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.8577 (ttm170) REVERT: Cz 95 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.7016 (ttm170) REVERT: Cz 98 GLN cc_start: 0.7627 (OUTLIER) cc_final: 0.7376 (pm20) REVERT: LA 80 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8374 (tt0) REVERT: LG 251 LYS cc_start: 0.7610 (OUTLIER) cc_final: 0.7353 (ttmt) REVERT: LQ 122 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7975 (mp10) REVERT: LQ 152 ASP cc_start: 0.8774 (p0) cc_final: 0.8574 (p0) REVERT: LT 94 GLU cc_start: 0.8327 (pm20) cc_final: 0.7988 (pm20) REVERT: LY 43 ASN cc_start: 0.9020 (t0) cc_final: 0.8771 (t0) REVERT: Lc 35 LYS cc_start: 0.8993 (ttmt) cc_final: 0.8548 (mttt) REVERT: Lf 86 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8594 (mttp) REVERT: Lh 11 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7702 (pt0) REVERT: Lh 33 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.6979 (mp10) outliers start: 193 outliers final: 96 residues processed: 1177 average time/residue: 2.5974 time to fit residues: 4287.9224 Evaluate side-chains 1157 residues out of total 8643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 1048 time to evaluate : 8.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CF residue 97 THR Chi-restraints excluded: chain CF residue 149 VAL Chi-restraints excluded: chain CF residue 210 LYS Chi-restraints excluded: chain CF residue 242 THR Chi-restraints excluded: chain CH residue 70 LEU Chi-restraints excluded: chain CH residue 79 ASP Chi-restraints excluded: chain CH residue 85 TYR Chi-restraints excluded: chain CH residue 168 THR Chi-restraints excluded: chain CH residue 347 LEU Chi-restraints excluded: chain CH residue 585 GLU Chi-restraints excluded: chain CH residue 655 ILE Chi-restraints excluded: chain CI residue 198 PHE Chi-restraints excluded: chain CI residue 259 THR Chi-restraints excluded: chain CJ residue 140 ASP Chi-restraints excluded: chain CJ residue 221 ASP Chi-restraints excluded: chain CJ residue 381 GLN Chi-restraints excluded: chain CJ residue 400 VAL Chi-restraints excluded: chain CJ residue 407 THR Chi-restraints excluded: chain CJ residue 456 VAL Chi-restraints excluded: chain CJ residue 465 ILE Chi-restraints excluded: chain CK residue 37 GLU Chi-restraints excluded: chain CK residue 98 THR Chi-restraints excluded: chain CL residue 19 ARG Chi-restraints excluded: chain CL residue 58 LEU Chi-restraints excluded: chain CL residue 73 ARG Chi-restraints excluded: chain CM residue 111 LEU Chi-restraints excluded: chain CM residue 162 VAL Chi-restraints excluded: chain CN residue 51 THR Chi-restraints excluded: chain CN residue 75 THR Chi-restraints excluded: chain CN residue 114 THR Chi-restraints excluded: chain CN residue 121 LEU Chi-restraints excluded: chain CO residue 26 GLU Chi-restraints excluded: chain CO residue 106 ILE Chi-restraints excluded: chain CQ residue 64 VAL Chi-restraints excluded: chain Cd residue 119 ASP Chi-restraints excluded: chain Cd residue 324 ARG Chi-restraints excluded: chain Ce residue 210 THR Chi-restraints excluded: chain Ce residue 227 MET Chi-restraints excluded: chain Ce residue 257 SER Chi-restraints excluded: chain Ce residue 363 ASP Chi-restraints excluded: chain Ce residue 365 VAL Chi-restraints excluded: chain Cf residue 36 THR Chi-restraints excluded: chain Cf residue 252 ARG Chi-restraints excluded: chain Cg residue 15 VAL Chi-restraints excluded: chain Cg residue 22 THR Chi-restraints excluded: chain Cg residue 62 LEU Chi-restraints excluded: chain Cg residue 156 SER Chi-restraints excluded: chain Ch residue 142 ILE Chi-restraints excluded: chain Ch residue 285 CYS Chi-restraints excluded: chain Ch residue 426 ASN Chi-restraints excluded: chain Cz residue 67 GLU Chi-restraints excluded: chain Cz residue 95 ARG Chi-restraints excluded: chain Cz residue 98 GLN Chi-restraints excluded: chain LA residue 80 GLU Chi-restraints excluded: chain LA residue 161 SER Chi-restraints excluded: chain LB residue 157 THR Chi-restraints excluded: chain LB residue 352 LEU Chi-restraints excluded: chain LC residue 61 THR Chi-restraints excluded: chain LC residue 354 VAL Chi-restraints excluded: chain LD residue 18 THR Chi-restraints excluded: chain LD residue 51 LEU Chi-restraints excluded: chain LD residue 137 THR Chi-restraints excluded: chain LD residue 261 ASP Chi-restraints excluded: chain LE residue 6 THR Chi-restraints excluded: chain LE residue 124 GLN Chi-restraints excluded: chain LE residue 155 SER Chi-restraints excluded: chain LF residue 65 GLU Chi-restraints excluded: chain LF residue 80 SER Chi-restraints excluded: chain LF residue 90 VAL Chi-restraints excluded: chain LG residue 251 LYS Chi-restraints excluded: chain LH residue 92 LEU Chi-restraints excluded: chain LH residue 120 THR Chi-restraints excluded: chain LJ residue 45 THR Chi-restraints excluded: chain LJ residue 147 SER Chi-restraints excluded: chain LK residue 22 VAL Chi-restraints excluded: chain LK residue 104 VAL Chi-restraints excluded: chain LL residue 141 ASP Chi-restraints excluded: chain LL residue 169 SER Chi-restraints excluded: chain LM residue 14 VAL Chi-restraints excluded: chain LN residue 60 VAL Chi-restraints excluded: chain LN residue 80 THR Chi-restraints excluded: chain LO residue 3 SER Chi-restraints excluded: chain LO residue 139 THR Chi-restraints excluded: chain LP residue 109 THR Chi-restraints excluded: chain LQ residue 122 GLN Chi-restraints excluded: chain LR residue 29 VAL Chi-restraints excluded: chain LR residue 51 ILE Chi-restraints excluded: chain LS residue 79 LEU Chi-restraints excluded: chain LU residue 59 VAL Chi-restraints excluded: chain LU residue 60 ILE Chi-restraints excluded: chain LU residue 118 VAL Chi-restraints excluded: chain LV residue 21 VAL Chi-restraints excluded: chain LX residue 37 THR Chi-restraints excluded: chain LX residue 83 GLU Chi-restraints excluded: chain LY residue 78 VAL Chi-restraints excluded: chain LY residue 90 THR Chi-restraints excluded: chain LY residue 93 THR Chi-restraints excluded: chain LY residue 94 VAL Chi-restraints excluded: chain LZ residue 82 THR Chi-restraints excluded: chain La residue 75 ILE Chi-restraints excluded: chain Ld residue 95 GLU Chi-restraints excluded: chain Le residue 83 VAL Chi-restraints excluded: chain Lf residue 86 LYS Chi-restraints excluded: chain Lh residue 11 GLN Chi-restraints excluded: chain Lh residue 33 GLN Chi-restraints excluded: chain Li residue 106 SER Chi-restraints excluded: chain Lj residue 27 LEU Chi-restraints excluded: chain Ll residue 34 THR Chi-restraints excluded: chain Lp residue 82 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1325 random chunks: chunk 668 optimal weight: 9.9990 chunk 373 optimal weight: 1.9990 chunk 1001 optimal weight: 0.0970 chunk 819 optimal weight: 0.4980 chunk 331 optimal weight: 20.0000 chunk 1205 optimal weight: 8.9990 chunk 1302 optimal weight: 3.9990 chunk 1073 optimal weight: 0.9990 chunk 1195 optimal weight: 0.7980 chunk 410 optimal weight: 4.9990 chunk 967 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CF 29 ASN CH 303 GLN CH 306 ASN CH 389 ASN CM 203 GLN CM 227 HIS Cb 34 GLN Cf 61 HIS Cg 49 GLN ** Ch 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cz 56 GLN LA 71 GLN LE 53 GLN LE 172 ASN LH 179 GLN LH 202 GLN LJ 69 HIS LJ 96 ASN LK 8 ASN LL 159 GLN LQ 153 GLN LS 21 ASN LS 147 ASN LU 55 ASN LX 66 HIS LX 81 ASN LX 124 ASN LY 116 ASN LZ 105 GLN Ld 108 ASN Lf 58 GLN ** Lh 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 67 GLN Li 21 ASN Lk 32 GLN Lp 45 ASN Lq 97 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.0669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 162774 Z= 0.129 Angle : 0.603 18.093 236023 Z= 0.329 Chirality : 0.035 0.286 28825 Planarity : 0.006 0.126 17569 Dihedral : 22.505 178.342 63553 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.85 % Allowed : 14.23 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % 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: 1.55 (0.08), residues: 10017 helix: 2.12 (0.08), residues: 3877 sheet: 0.17 (0.13), residues: 1450 loop : 0.51 (0.09), residues: 4690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRPCg 105 HIS 0.008 0.001 HISLX 66 PHE 0.015 0.001 PHECH 90 TYR 0.014 0.001 TYRLH 129 ARG 0.009 0.000 ARGCL 27 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20034 Ramachandran restraints generated. 10017 Oldfield, 0 Emsley, 10017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20034 Ramachandran restraints generated. 10017 Oldfield, 0 Emsley, 10017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1236 residues out of total 8643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 1079 time to evaluate : 8.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CF 10 TYR cc_start: 0.8844 (t80) cc_final: 0.8620 (t80) REVERT: CF 38 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7939 (mp10) REVERT: CF 123 ASP cc_start: 0.8537 (t0) cc_final: 0.8325 (t0) REVERT: CH 303 GLN cc_start: 0.7983 (tp40) cc_final: 0.7650 (tp40) REVERT: CH 307 ASP cc_start: 0.7767 (m-30) cc_final: 0.7554 (m-30) REVERT: CH 426 ILE cc_start: 0.8961 (OUTLIER) cc_final: 0.8637 (mm) REVERT: CI 217 ARG cc_start: 0.8672 (ptm160) cc_final: 0.8019 (ttt180) REVERT: CI 230 ARG cc_start: 0.7918 (mtt90) cc_final: 0.7703 (mtt180) REVERT: CK 53 GLN cc_start: 0.7867 (tm130) cc_final: 0.7623 (tm130) REVERT: CL 67 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7863 (mt0) REVERT: CL 73 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7458 (ptp-110) REVERT: CO 26 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8209 (mt-10) REVERT: CQ 25 ASP cc_start: 0.8770 (p0) cc_final: 0.8441 (p0) REVERT: CQ 142 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8248 (mtpt) REVERT: Cb 80 GLN cc_start: 0.9288 (mt0) cc_final: 0.9084 (mt0) REVERT: Cd 324 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.8406 (mmt-90) REVERT: Cf 233 ARG cc_start: 0.7680 (mtm-85) cc_final: 0.7475 (ptt90) REVERT: Ch 86 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8257 (mtp180) REVERT: Cz 67 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.7099 (mp0) REVERT: Cz 95 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.6963 (ttm170) REVERT: LC 338 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.8120 (ttmt) REVERT: LE 162 GLN cc_start: 0.8570 (tp40) cc_final: 0.8012 (tp40) REVERT: LJ 132 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8123 (mtp) REVERT: LL 150 SER cc_start: 0.9005 (t) cc_final: 0.8739 (t) REVERT: LQ 122 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.7958 (mp10) REVERT: LR 65 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7300 (mp0) REVERT: Lc 35 LYS cc_start: 0.8946 (ttmt) cc_final: 0.8398 (mttp) REVERT: Lh 11 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7608 (pt0) REVERT: Lh 33 GLN cc_start: 0.7791 (OUTLIER) cc_final: 0.6972 (mp10) outliers start: 157 outliers final: 63 residues processed: 1182 average time/residue: 2.4561 time to fit residues: 4061.3296 Evaluate side-chains 1137 residues out of total 8643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 1058 time to evaluate : 9.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CF residue 34 ILE Chi-restraints excluded: chain CF residue 38 GLN Chi-restraints excluded: chain CF residue 97 THR Chi-restraints excluded: chain CF residue 210 LYS Chi-restraints excluded: chain CH residue 85 TYR Chi-restraints excluded: chain CH residue 168 THR Chi-restraints excluded: chain CH residue 309 THR Chi-restraints excluded: chain CH residue 325 GLU Chi-restraints excluded: chain CH residue 347 LEU Chi-restraints excluded: chain CH residue 374 MET Chi-restraints excluded: chain CH residue 426 ILE Chi-restraints excluded: chain CH residue 469 GLU Chi-restraints excluded: chain CH residue 585 GLU Chi-restraints excluded: chain CH residue 655 ILE Chi-restraints excluded: chain CI residue 198 PHE Chi-restraints excluded: chain CJ residue 140 ASP Chi-restraints excluded: chain CJ residue 221 ASP Chi-restraints excluded: chain CJ residue 407 THR Chi-restraints excluded: chain CK residue 37 GLU Chi-restraints excluded: chain CK residue 73 VAL Chi-restraints excluded: chain CK residue 98 THR Chi-restraints excluded: chain CL residue 67 GLN Chi-restraints excluded: chain CL residue 73 ARG Chi-restraints excluded: chain CM residue 162 VAL Chi-restraints excluded: chain CN residue 75 THR Chi-restraints excluded: chain CN residue 114 THR Chi-restraints excluded: chain CN residue 121 LEU Chi-restraints excluded: chain CO residue 26 GLU Chi-restraints excluded: chain CQ residue 64 VAL Chi-restraints excluded: chain CQ residue 142 LYS Chi-restraints excluded: chain Cd residue 324 ARG Chi-restraints excluded: chain Ce residue 220 THR Chi-restraints excluded: chain Cg residue 15 VAL Chi-restraints excluded: chain Cg residue 62 LEU Chi-restraints excluded: chain Cg residue 156 SER Chi-restraints excluded: chain Ch residue 86 ARG Chi-restraints excluded: chain Ch residue 142 ILE Chi-restraints excluded: chain Ch residue 426 ASN Chi-restraints excluded: chain Cz residue 67 GLU Chi-restraints excluded: chain Cz residue 95 ARG Chi-restraints excluded: chain LB residue 352 LEU Chi-restraints excluded: chain LC residue 61 THR Chi-restraints excluded: chain LC residue 338 LYS Chi-restraints excluded: chain LC residue 354 VAL Chi-restraints excluded: chain LD residue 95 TRP Chi-restraints excluded: chain LD residue 137 THR Chi-restraints excluded: chain LD residue 188 ILE Chi-restraints excluded: chain LD residue 261 ASP Chi-restraints excluded: chain LE residue 155 SER Chi-restraints excluded: chain LF residue 90 VAL Chi-restraints excluded: chain LH residue 87 LYS Chi-restraints excluded: chain LH residue 92 LEU Chi-restraints excluded: chain LH residue 120 THR Chi-restraints excluded: chain LJ residue 45 THR Chi-restraints excluded: chain LJ residue 132 MET Chi-restraints excluded: chain LJ residue 147 SER Chi-restraints excluded: chain LK residue 22 VAL Chi-restraints excluded: chain LK residue 104 VAL Chi-restraints excluded: chain LK residue 164 ASP Chi-restraints excluded: chain LL residue 141 ASP Chi-restraints excluded: chain LL residue 169 SER Chi-restraints excluded: chain LM residue 14 VAL Chi-restraints excluded: chain LN residue 80 THR Chi-restraints excluded: chain LN residue 155 VAL Chi-restraints excluded: chain LO residue 185 LYS Chi-restraints excluded: chain LQ residue 122 GLN Chi-restraints excluded: chain LR residue 65 GLU Chi-restraints excluded: chain LT residue 145 ASP Chi-restraints excluded: chain LX residue 83 GLU Chi-restraints excluded: chain LY residue 78 VAL Chi-restraints excluded: chain LY residue 90 THR Chi-restraints excluded: chain LY residue 93 THR Chi-restraints excluded: chain La residue 75 ILE Chi-restraints excluded: chain Lf residue 51 VAL Chi-restraints excluded: chain Lh residue 11 GLN Chi-restraints excluded: chain Lh residue 33 GLN Chi-restraints excluded: chain Lh residue 73 LEU Chi-restraints excluded: chain Ll residue 34 THR Chi-restraints excluded: chain Lp residue 28 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1325 random chunks: chunk 1190 optimal weight: 4.9990 chunk 906 optimal weight: 8.9990 chunk 625 optimal weight: 4.9990 chunk 133 optimal weight: 7.9990 chunk 575 optimal weight: 0.9980 chunk 809 optimal weight: 6.9990 chunk 1209 optimal weight: 0.9980 chunk 1280 optimal weight: 4.9990 chunk 632 optimal weight: 4.9990 chunk 1146 optimal weight: 10.0000 chunk 345 optimal weight: 3.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CF 29 ASN CH 306 ASN CH 389 ASN CI 229 HIS CM 203 GLN CM 227 HIS Cb 34 GLN Cd 170 GLN ** Ch 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ch 226 GLN Cz 56 GLN LA 71 GLN LA 132 ASN LE 53 GLN LE 172 ASN LH 179 GLN LH 202 GLN LJ 96 ASN LK 8 ASN LL 159 GLN LS 21 ASN LS 147 ASN LU 55 ASN LX 66 HIS LX 81 ASN LX 124 ASN LY 116 ASN LZ 26 GLN Ld 108 ASN Lf 58 GLN ** Lh 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lk 32 GLN Lk 33 GLN Lp 45 ASN Lq 97 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.0747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 162774 Z= 0.323 Angle : 0.693 19.051 236023 Z= 0.367 Chirality : 0.041 0.289 28825 Planarity : 0.007 0.143 17569 Dihedral : 22.508 177.892 63529 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.24 % Allowed : 14.16 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % 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: 10017 helix: 2.09 (0.08), residues: 3868 sheet: 0.20 (0.13), residues: 1429 loop : 0.50 (0.09), residues: 4720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRPCd 223 HIS 0.011 0.001 HISLR 125 PHE 0.027 0.002 PHECh 37 TYR 0.020 0.002 TYRLd 20 ARG 0.009 0.001 ARGCL 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20034 Ramachandran restraints generated. 10017 Oldfield, 0 Emsley, 10017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20034 Ramachandran restraints generated. 10017 Oldfield, 0 Emsley, 10017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1265 residues out of total 8643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 1075 time to evaluate : 8.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CF 10 TYR cc_start: 0.8840 (t80) cc_final: 0.8618 (t80) REVERT: CF 38 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7957 (mp10) REVERT: CH 70 LEU cc_start: 0.9547 (OUTLIER) cc_final: 0.9159 (mp) REVERT: CH 303 GLN cc_start: 0.7972 (tp40) cc_final: 0.7743 (tp40) REVERT: CH 509 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.8054 (ttp80) REVERT: CI 217 ARG cc_start: 0.8730 (ptm160) cc_final: 0.8050 (ttt180) REVERT: CK 53 GLN cc_start: 0.7913 (tm130) cc_final: 0.7713 (tm130) REVERT: CL 67 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7901 (mt0) REVERT: CL 73 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7474 (ptp-110) REVERT: CO 26 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8273 (mt-10) REVERT: CQ 25 ASP cc_start: 0.8826 (p0) cc_final: 0.8540 (p0) REVERT: CQ 136 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.8242 (ptm160) REVERT: CQ 142 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8276 (mtpt) REVERT: Cd 324 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8421 (mmt-90) REVERT: Cf 87 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8527 (mtm) REVERT: Cf 252 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8522 (ttm170) REVERT: Cz 95 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7071 (ttm170) REVERT: LF 63 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7653 (mt-10) REVERT: LJ 18 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.9044 (tp) REVERT: LL 150 SER cc_start: 0.9017 (t) cc_final: 0.8751 (t) REVERT: LQ 122 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7981 (mp10) REVERT: LT 94 GLU cc_start: 0.8251 (pm20) cc_final: 0.7994 (pm20) REVERT: LU 71 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7549 (tm-30) REVERT: LX 22 LYS cc_start: 0.8691 (tppt) cc_final: 0.8468 (tptt) REVERT: Lc 35 LYS cc_start: 0.8985 (ttmt) cc_final: 0.8456 (mttp) REVERT: Lf 86 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8543 (mttp) REVERT: Lh 11 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7712 (pt0) REVERT: Lh 33 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.6979 (mp10) outliers start: 190 outliers final: 92 residues processed: 1190 average time/residue: 2.4740 time to fit residues: 4119.8170 Evaluate side-chains 1165 residues out of total 8643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 1054 time to evaluate : 7.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CF residue 38 GLN Chi-restraints excluded: chain CF residue 210 LYS Chi-restraints excluded: chain CH residue 70 LEU Chi-restraints excluded: chain CH residue 79 ASP Chi-restraints excluded: chain CH residue 85 TYR Chi-restraints excluded: chain CH residue 168 THR Chi-restraints excluded: chain CH residue 301 MET Chi-restraints excluded: chain CH residue 309 THR Chi-restraints excluded: chain CH residue 325 GLU Chi-restraints excluded: chain CH residue 347 LEU Chi-restraints excluded: chain CH residue 374 MET Chi-restraints excluded: chain CH residue 426 ILE Chi-restraints excluded: chain CH residue 469 GLU Chi-restraints excluded: chain CH residue 509 ARG Chi-restraints excluded: chain CH residue 585 GLU Chi-restraints excluded: chain CH residue 655 ILE Chi-restraints excluded: chain CI residue 198 PHE Chi-restraints excluded: chain CI residue 259 THR Chi-restraints excluded: chain CJ residue 140 ASP Chi-restraints excluded: chain CJ residue 221 ASP Chi-restraints excluded: chain CJ residue 407 THR Chi-restraints excluded: chain CJ residue 456 VAL Chi-restraints excluded: chain CJ residue 465 ILE Chi-restraints excluded: chain CK residue 37 GLU Chi-restraints excluded: chain CK residue 73 VAL Chi-restraints excluded: chain CK residue 98 THR Chi-restraints excluded: chain CL residue 19 ARG Chi-restraints excluded: chain CL residue 58 LEU Chi-restraints excluded: chain CL residue 67 GLN Chi-restraints excluded: chain CL residue 73 ARG Chi-restraints excluded: chain CM residue 162 VAL Chi-restraints excluded: chain CN residue 75 THR Chi-restraints excluded: chain CN residue 114 THR Chi-restraints excluded: chain CN residue 121 LEU Chi-restraints excluded: chain CO residue 26 GLU Chi-restraints excluded: chain CQ residue 64 VAL Chi-restraints excluded: chain CQ residue 136 ARG Chi-restraints excluded: chain CQ residue 142 LYS Chi-restraints excluded: chain Cb residue 70 LYS Chi-restraints excluded: chain Cd residue 119 ASP Chi-restraints excluded: chain Cd residue 324 ARG Chi-restraints excluded: chain Ce residue 220 THR Chi-restraints excluded: chain Ce residue 234 ILE Chi-restraints excluded: chain Ce residue 363 ASP Chi-restraints excluded: chain Ce residue 365 VAL Chi-restraints excluded: chain Ce residue 397 LYS Chi-restraints excluded: chain Cf residue 87 MET Chi-restraints excluded: chain Cf residue 252 ARG Chi-restraints excluded: chain Cg residue 15 VAL Chi-restraints excluded: chain Cg residue 62 LEU Chi-restraints excluded: chain Cg residue 102 GLU Chi-restraints excluded: chain Ch residue 142 ILE Chi-restraints excluded: chain Ch residue 285 CYS Chi-restraints excluded: chain Ch residue 426 ASN Chi-restraints excluded: chain Cz residue 67 GLU Chi-restraints excluded: chain Cz residue 95 ARG Chi-restraints excluded: chain LA residue 207 VAL Chi-restraints excluded: chain LB residue 352 LEU Chi-restraints excluded: chain LC residue 61 THR Chi-restraints excluded: chain LC residue 354 VAL Chi-restraints excluded: chain LD residue 95 TRP Chi-restraints excluded: chain LD residue 137 THR Chi-restraints excluded: chain LD residue 261 ASP Chi-restraints excluded: chain LE residue 155 SER Chi-restraints excluded: chain LF residue 63 GLU Chi-restraints excluded: chain LF residue 90 VAL Chi-restraints excluded: chain LH residue 87 LYS Chi-restraints excluded: chain LH residue 92 LEU Chi-restraints excluded: chain LH residue 120 THR Chi-restraints excluded: chain LJ residue 18 LEU Chi-restraints excluded: chain LJ residue 45 THR Chi-restraints excluded: chain LJ residue 147 SER Chi-restraints excluded: chain LK residue 22 VAL Chi-restraints excluded: chain LK residue 104 VAL Chi-restraints excluded: chain LK residue 164 ASP Chi-restraints excluded: chain LL residue 140 LYS Chi-restraints excluded: chain LL residue 141 ASP Chi-restraints excluded: chain LL residue 169 SER Chi-restraints excluded: chain LM residue 14 VAL Chi-restraints excluded: chain LN residue 60 VAL Chi-restraints excluded: chain LN residue 80 THR Chi-restraints excluded: chain LO residue 3 SER Chi-restraints excluded: chain LO residue 139 THR Chi-restraints excluded: chain LO residue 185 LYS Chi-restraints excluded: chain LP residue 109 THR Chi-restraints excluded: chain LQ residue 91 SER Chi-restraints excluded: chain LQ residue 122 GLN Chi-restraints excluded: chain LR residue 51 ILE Chi-restraints excluded: chain LS residue 79 LEU Chi-restraints excluded: chain LT residue 145 ASP Chi-restraints excluded: chain LU residue 59 VAL Chi-restraints excluded: chain LU residue 71 GLU Chi-restraints excluded: chain LU residue 118 VAL Chi-restraints excluded: chain LX residue 83 GLU Chi-restraints excluded: chain LY residue 78 VAL Chi-restraints excluded: chain LY residue 90 THR Chi-restraints excluded: chain LY residue 93 THR Chi-restraints excluded: chain LZ residue 34 SER Chi-restraints excluded: chain LZ residue 82 THR Chi-restraints excluded: chain La residue 75 ILE Chi-restraints excluded: chain Le residue 56 ILE Chi-restraints excluded: chain Le residue 83 VAL Chi-restraints excluded: chain Lf residue 51 VAL Chi-restraints excluded: chain Lf residue 86 LYS Chi-restraints excluded: chain Lh residue 11 GLN Chi-restraints excluded: chain Lh residue 33 GLN Chi-restraints excluded: chain Lh residue 73 LEU Chi-restraints excluded: chain Li residue 106 SER Chi-restraints excluded: chain Ll residue 34 THR Chi-restraints excluded: chain Lp residue 28 LYS Chi-restraints excluded: chain Lq residue 85 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1325 random chunks: chunk 1066 optimal weight: 0.9980 chunk 727 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 953 optimal weight: 7.9990 chunk 528 optimal weight: 10.0000 chunk 1092 optimal weight: 6.9990 chunk 885 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 653 optimal weight: 9.9990 chunk 1149 optimal weight: 2.9990 chunk 323 optimal weight: 7.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CF 29 ASN CH 389 ASN CM 203 GLN CM 227 HIS Cb 34 GLN Cd 170 GLN Cg 133 GLN ** Ch 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ch 226 GLN Cz 56 GLN LA 71 GLN LE 53 GLN LE 172 ASN LH 179 GLN LH 202 GLN LJ 96 ASN LK 8 ASN LL 159 GLN LS 21 ASN LS 147 ASN LU 55 ASN LX 66 HIS LX 81 ASN LX 124 ASN LY 116 ASN LZ 26 GLN LZ 105 GLN Ld 108 ASN ** Lh 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 67 GLN Lk 32 GLN Lk 33 GLN Lp 45 ASN Lq 97 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 162774 Z= 0.354 Angle : 0.722 19.402 236023 Z= 0.381 Chirality : 0.042 0.305 28825 Planarity : 0.007 0.145 17569 Dihedral : 22.555 179.354 63527 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.43 % Allowed : 13.93 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.08), residues: 10017 helix: 1.99 (0.08), residues: 3858 sheet: 0.13 (0.13), residues: 1435 loop : 0.46 (0.09), residues: 4724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRPCd 223 HIS 0.010 0.002 HISLR 125 PHE 0.020 0.002 PHELG 94 TYR 0.020 0.002 TYRLO 55 ARG 0.010 0.001 ARGLp 85 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20034 Ramachandran restraints generated. 10017 Oldfield, 0 Emsley, 10017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20034 Ramachandran restraints generated. 10017 Oldfield, 0 Emsley, 10017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1285 residues out of total 8643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 1079 time to evaluate : 9.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CF 10 TYR cc_start: 0.8853 (t80) cc_final: 0.8608 (t80) REVERT: CF 38 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7974 (mp10) REVERT: CH 70 LEU cc_start: 0.9549 (OUTLIER) cc_final: 0.9195 (mp) REVERT: CH 303 GLN cc_start: 0.7958 (tp40) cc_final: 0.7467 (tp40) REVERT: CH 307 ASP cc_start: 0.7831 (m-30) cc_final: 0.7445 (m-30) REVERT: CH 509 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7752 (ttp80) REVERT: CI 217 ARG cc_start: 0.8775 (ptm160) cc_final: 0.8190 (ttt180) REVERT: CI 237 ASP cc_start: 0.8370 (OUTLIER) cc_final: 0.7839 (t70) REVERT: CK 53 GLN cc_start: 0.7907 (tm130) cc_final: 0.7376 (tm130) REVERT: CK 57 GLN cc_start: 0.7515 (mt0) cc_final: 0.6991 (mt0) REVERT: CL 67 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7926 (mt0) REVERT: CL 73 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7531 (ptp-110) REVERT: CM 214 SER cc_start: 0.8956 (p) cc_final: 0.8594 (m) REVERT: CO 26 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8097 (mt-10) REVERT: CQ 25 ASP cc_start: 0.8860 (p0) cc_final: 0.8545 (p0) REVERT: CQ 93 MET cc_start: 0.9286 (mtp) cc_final: 0.9086 (mtp) REVERT: CQ 136 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.8263 (ptm160) REVERT: CQ 142 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8279 (mtpt) REVERT: Cd 324 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8518 (mmt-90) REVERT: Ce 297 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.7190 (ppt90) REVERT: Cf 87 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.8547 (mtm) REVERT: Cz 95 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7236 (ttm170) REVERT: LD 50 ARG cc_start: 0.9230 (OUTLIER) cc_final: 0.7924 (ptm-80) REVERT: LF 63 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7657 (mt-10) REVERT: LJ 18 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.9017 (tp) REVERT: LQ 122 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.7936 (mp10) REVERT: LT 94 GLU cc_start: 0.8264 (pm20) cc_final: 0.7983 (pm20) REVERT: Lc 35 LYS cc_start: 0.8984 (ttmt) cc_final: 0.8452 (mttp) REVERT: Lf 86 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8567 (mttp) REVERT: Lh 11 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7734 (pt0) REVERT: Lh 33 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.6992 (mp10) outliers start: 206 outliers final: 110 residues processed: 1207 average time/residue: 2.5085 time to fit residues: 4233.2565 Evaluate side-chains 1188 residues out of total 8643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 1058 time to evaluate : 8.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CF residue 38 GLN Chi-restraints excluded: chain CF residue 97 THR Chi-restraints excluded: chain CF residue 149 VAL Chi-restraints excluded: chain CF residue 210 LYS Chi-restraints excluded: chain CH residue 70 LEU Chi-restraints excluded: chain CH residue 79 ASP Chi-restraints excluded: chain CH residue 85 TYR Chi-restraints excluded: chain CH residue 168 THR Chi-restraints excluded: chain CH residue 301 MET Chi-restraints excluded: chain CH residue 309 THR Chi-restraints excluded: chain CH residue 325 GLU Chi-restraints excluded: chain CH residue 347 LEU Chi-restraints excluded: chain CH residue 374 MET Chi-restraints excluded: chain CH residue 426 ILE Chi-restraints excluded: chain CH residue 509 ARG Chi-restraints excluded: chain CH residue 585 GLU Chi-restraints excluded: chain CH residue 610 THR Chi-restraints excluded: chain CH residue 655 ILE Chi-restraints excluded: chain CI residue 198 PHE Chi-restraints excluded: chain CI residue 237 ASP Chi-restraints excluded: chain CI residue 259 THR Chi-restraints excluded: chain CJ residue 140 ASP Chi-restraints excluded: chain CJ residue 221 ASP Chi-restraints excluded: chain CJ residue 407 THR Chi-restraints excluded: chain CJ residue 465 ILE Chi-restraints excluded: chain CK residue 37 GLU Chi-restraints excluded: chain CK residue 73 VAL Chi-restraints excluded: chain CK residue 98 THR Chi-restraints excluded: chain CL residue 19 ARG Chi-restraints excluded: chain CL residue 58 LEU Chi-restraints excluded: chain CL residue 67 GLN Chi-restraints excluded: chain CL residue 73 ARG Chi-restraints excluded: chain CM residue 49 VAL Chi-restraints excluded: chain CM residue 162 VAL Chi-restraints excluded: chain CN residue 75 THR Chi-restraints excluded: chain CN residue 114 THR Chi-restraints excluded: chain CN residue 121 LEU Chi-restraints excluded: chain CN residue 172 GLU Chi-restraints excluded: chain CO residue 26 GLU Chi-restraints excluded: chain CQ residue 16 SER Chi-restraints excluded: chain CQ residue 64 VAL Chi-restraints excluded: chain CQ residue 136 ARG Chi-restraints excluded: chain CQ residue 142 LYS Chi-restraints excluded: chain Cb residue 28 SER Chi-restraints excluded: chain Cb residue 70 LYS Chi-restraints excluded: chain Cd residue 119 ASP Chi-restraints excluded: chain Cd residue 324 ARG Chi-restraints excluded: chain Ce residue 210 THR Chi-restraints excluded: chain Ce residue 227 MET Chi-restraints excluded: chain Ce residue 234 ILE Chi-restraints excluded: chain Ce residue 257 SER Chi-restraints excluded: chain Ce residue 297 ARG Chi-restraints excluded: chain Ce residue 363 ASP Chi-restraints excluded: chain Ce residue 365 VAL Chi-restraints excluded: chain Ce residue 397 LYS Chi-restraints excluded: chain Cf residue 36 THR Chi-restraints excluded: chain Cf residue 87 MET Chi-restraints excluded: chain Cg residue 15 VAL Chi-restraints excluded: chain Cg residue 62 LEU Chi-restraints excluded: chain Ch residue 142 ILE Chi-restraints excluded: chain Ch residue 285 CYS Chi-restraints excluded: chain Ch residue 426 ASN Chi-restraints excluded: chain Cz residue 67 GLU Chi-restraints excluded: chain Cz residue 95 ARG Chi-restraints excluded: chain LA residue 199 THR Chi-restraints excluded: chain LA residue 207 VAL Chi-restraints excluded: chain LB residue 34 LYS Chi-restraints excluded: chain LB residue 352 LEU Chi-restraints excluded: chain LC residue 61 THR Chi-restraints excluded: chain LC residue 104 THR Chi-restraints excluded: chain LC residue 354 VAL Chi-restraints excluded: chain LD residue 50 ARG Chi-restraints excluded: chain LD residue 95 TRP Chi-restraints excluded: chain LD residue 129 TYR Chi-restraints excluded: chain LD residue 137 THR Chi-restraints excluded: chain LD residue 261 ASP Chi-restraints excluded: chain LE residue 155 SER Chi-restraints excluded: chain LF residue 63 GLU Chi-restraints excluded: chain LF residue 65 GLU Chi-restraints excluded: chain LF residue 90 VAL Chi-restraints excluded: chain LH residue 87 LYS Chi-restraints excluded: chain LH residue 92 LEU Chi-restraints excluded: chain LH residue 120 THR Chi-restraints excluded: chain LJ residue 18 LEU Chi-restraints excluded: chain LJ residue 45 THR Chi-restraints excluded: chain LJ residue 147 SER Chi-restraints excluded: chain LK residue 104 VAL Chi-restraints excluded: chain LK residue 164 ASP Chi-restraints excluded: chain LL residue 140 LYS Chi-restraints excluded: chain LL residue 141 ASP Chi-restraints excluded: chain LL residue 169 SER Chi-restraints excluded: chain LM residue 14 VAL Chi-restraints excluded: chain LN residue 60 VAL Chi-restraints excluded: chain LN residue 80 THR Chi-restraints excluded: chain LO residue 3 SER Chi-restraints excluded: chain LO residue 139 THR Chi-restraints excluded: chain LO residue 185 LYS Chi-restraints excluded: chain LO residue 196 SER Chi-restraints excluded: chain LO residue 197 GLU Chi-restraints excluded: chain LP residue 109 THR Chi-restraints excluded: chain LQ residue 91 SER Chi-restraints excluded: chain LQ residue 122 GLN Chi-restraints excluded: chain LR residue 51 ILE Chi-restraints excluded: chain LS residue 79 LEU Chi-restraints excluded: chain LS residue 106 MET Chi-restraints excluded: chain LU residue 18 THR Chi-restraints excluded: chain LU residue 59 VAL Chi-restraints excluded: chain LU residue 118 VAL Chi-restraints excluded: chain LV residue 21 VAL Chi-restraints excluded: chain LX residue 83 GLU Chi-restraints excluded: chain LY residue 78 VAL Chi-restraints excluded: chain LY residue 90 THR Chi-restraints excluded: chain LY residue 93 THR Chi-restraints excluded: chain LY residue 94 VAL Chi-restraints excluded: chain LZ residue 82 THR Chi-restraints excluded: chain La residue 75 ILE Chi-restraints excluded: chain Lc residue 46 LEU Chi-restraints excluded: chain Le residue 56 ILE Chi-restraints excluded: chain Le residue 83 VAL Chi-restraints excluded: chain Lf residue 51 VAL Chi-restraints excluded: chain Lf residue 86 LYS Chi-restraints excluded: chain Lf residue 109 ILE Chi-restraints excluded: chain Lh residue 11 GLN Chi-restraints excluded: chain Lh residue 33 GLN Chi-restraints excluded: chain Lh residue 73 LEU Chi-restraints excluded: chain Ll residue 34 THR Chi-restraints excluded: chain Lp residue 21 SER Chi-restraints excluded: chain Lp residue 28 LYS Chi-restraints excluded: chain Lp residue 50 THR Chi-restraints excluded: chain Lq residue 85 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1325 random chunks: chunk 430 optimal weight: 1.9990 chunk 1153 optimal weight: 3.9990 chunk 253 optimal weight: 7.9990 chunk 751 optimal weight: 5.9990 chunk 316 optimal weight: 7.9990 chunk 1281 optimal weight: 9.9990 chunk 1064 optimal weight: 2.9990 chunk 593 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 424 optimal weight: 10.0000 chunk 673 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CF 29 ASN CH 389 ASN CI 229 HIS CK 143 HIS CM 203 GLN CM 227 HIS Cb 34 GLN Cd 170 GLN Cf 43 GLN Cg 49 GLN Cg 133 GLN Cg 185 GLN ** Ch 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ch 226 GLN Cz 56 GLN LA 71 GLN LE 172 ASN LH 179 GLN LH 202 GLN LJ 96 ASN LK 8 ASN LL 159 GLN LS 21 ASN LS 147 ASN LU 55 ASN LX 66 HIS LX 81 ASN LX 124 ASN LY 116 ASN LZ 26 GLN Ld 108 ASN Lf 58 GLN Lh 16 ASN Lh 67 GLN Lk 32 GLN Lk 33 GLN Lp 45 ASN Lq 97 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 162774 Z= 0.317 Angle : 0.704 19.188 236023 Z= 0.373 Chirality : 0.041 0.302 28825 Planarity : 0.007 0.143 17569 Dihedral : 22.550 179.151 63526 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.33 % Allowed : 14.45 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % 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: 10017 helix: 2.02 (0.08), residues: 3857 sheet: 0.17 (0.13), residues: 1427 loop : 0.46 (0.09), residues: 4733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRPCd 223 HIS 0.010 0.001 HISLX 66 PHE 0.034 0.002 PHECh 37 TYR 0.019 0.002 TYRLO 55 ARG 0.013 0.001 ARGLS 3 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20034 Ramachandran restraints generated. 10017 Oldfield, 0 Emsley, 10017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20034 Ramachandran restraints generated. 10017 Oldfield, 0 Emsley, 10017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1249 residues out of total 8643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 1051 time to evaluate : 8.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CF 10 TYR cc_start: 0.8846 (t80) cc_final: 0.8623 (t80) REVERT: CF 38 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7944 (mp10) REVERT: CH 70 LEU cc_start: 0.9548 (OUTLIER) cc_final: 0.9164 (mp) REVERT: CH 301 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.8126 (mmt) REVERT: CH 303 GLN cc_start: 0.7971 (tp40) cc_final: 0.7395 (tp40) REVERT: CH 307 ASP cc_start: 0.7831 (m-30) cc_final: 0.7381 (m-30) REVERT: CH 509 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7741 (ttp80) REVERT: CI 217 ARG cc_start: 0.8749 (ptm160) cc_final: 0.8159 (ttt180) REVERT: CI 237 ASP cc_start: 0.8356 (OUTLIER) cc_final: 0.7821 (t70) REVERT: CK 53 GLN cc_start: 0.7914 (tm130) cc_final: 0.7645 (tm130) REVERT: CL 67 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7931 (mt0) REVERT: CL 73 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7523 (ptp-110) REVERT: CM 31 GLU cc_start: 0.7095 (pp20) cc_final: 0.6868 (pp20) REVERT: CM 214 SER cc_start: 0.8957 (p) cc_final: 0.8592 (m) REVERT: CO 26 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8259 (mt-10) REVERT: CQ 25 ASP cc_start: 0.8850 (p0) cc_final: 0.8530 (p0) REVERT: CQ 136 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.8257 (ptm160) REVERT: CQ 142 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8271 (mtpt) REVERT: Cd 297 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8094 (tpp) REVERT: Cd 324 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8518 (mmt-90) REVERT: Ce 297 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.7202 (ppt90) REVERT: Cf 87 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8539 (mtm) REVERT: Cz 95 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7174 (ttm170) REVERT: LA 80 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8371 (tt0) REVERT: LE 163 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8386 (mtmt) REVERT: LF 63 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7657 (mt-10) REVERT: LJ 18 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.9020 (tp) REVERT: LL 150 SER cc_start: 0.9024 (t) cc_final: 0.8762 (t) REVERT: LQ 122 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.7947 (mp10) REVERT: LT 94 GLU cc_start: 0.8255 (pm20) cc_final: 0.7961 (pm20) REVERT: LU 71 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7530 (tm-30) REVERT: Lc 35 LYS cc_start: 0.8980 (ttmt) cc_final: 0.8451 (mttp) REVERT: Lf 86 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8550 (mttp) REVERT: Lh 11 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7714 (pt0) REVERT: Lh 16 ASN cc_start: 0.8628 (p0) cc_final: 0.8390 (p0) REVERT: Lh 33 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.6985 (mp10) REVERT: Lq 140 ARG cc_start: 0.5463 (mmp-170) cc_final: 0.5246 (mmp-170) outliers start: 198 outliers final: 120 residues processed: 1173 average time/residue: 2.4708 time to fit residues: 4062.8025 Evaluate side-chains 1193 residues out of total 8643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 1049 time to evaluate : 8.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CF residue 38 GLN Chi-restraints excluded: chain CF residue 97 THR Chi-restraints excluded: chain CF residue 149 VAL Chi-restraints excluded: chain CF residue 210 LYS Chi-restraints excluded: chain CH residue 70 LEU Chi-restraints excluded: chain CH residue 79 ASP Chi-restraints excluded: chain CH residue 85 TYR Chi-restraints excluded: chain CH residue 168 THR Chi-restraints excluded: chain CH residue 301 MET Chi-restraints excluded: chain CH residue 309 THR Chi-restraints excluded: chain CH residue 325 GLU Chi-restraints excluded: chain CH residue 347 LEU Chi-restraints excluded: chain CH residue 374 MET Chi-restraints excluded: chain CH residue 426 ILE Chi-restraints excluded: chain CH residue 509 ARG Chi-restraints excluded: chain CH residue 585 GLU Chi-restraints excluded: chain CH residue 610 THR Chi-restraints excluded: chain CH residue 655 ILE Chi-restraints excluded: chain CI residue 198 PHE Chi-restraints excluded: chain CI residue 237 ASP Chi-restraints excluded: chain CI residue 259 THR Chi-restraints excluded: chain CJ residue 140 ASP Chi-restraints excluded: chain CJ residue 221 ASP Chi-restraints excluded: chain CJ residue 400 VAL Chi-restraints excluded: chain CJ residue 407 THR Chi-restraints excluded: chain CJ residue 456 VAL Chi-restraints excluded: chain CJ residue 465 ILE Chi-restraints excluded: chain CK residue 37 GLU Chi-restraints excluded: chain CK residue 73 VAL Chi-restraints excluded: chain CK residue 98 THR Chi-restraints excluded: chain CL residue 19 ARG Chi-restraints excluded: chain CL residue 58 LEU Chi-restraints excluded: chain CL residue 67 GLN Chi-restraints excluded: chain CL residue 73 ARG Chi-restraints excluded: chain CM residue 49 VAL Chi-restraints excluded: chain CM residue 162 VAL Chi-restraints excluded: chain CM residue 177 GLU Chi-restraints excluded: chain CN residue 51 THR Chi-restraints excluded: chain CN residue 75 THR Chi-restraints excluded: chain CN residue 114 THR Chi-restraints excluded: chain CN residue 121 LEU Chi-restraints excluded: chain CN residue 172 GLU Chi-restraints excluded: chain CO residue 26 GLU Chi-restraints excluded: chain CQ residue 16 SER Chi-restraints excluded: chain CQ residue 64 VAL Chi-restraints excluded: chain CQ residue 136 ARG Chi-restraints excluded: chain CQ residue 142 LYS Chi-restraints excluded: chain Cb residue 28 SER Chi-restraints excluded: chain Cb residue 70 LYS Chi-restraints excluded: chain Cd residue 119 ASP Chi-restraints excluded: chain Cd residue 297 MET Chi-restraints excluded: chain Cd residue 324 ARG Chi-restraints excluded: chain Ce residue 210 THR Chi-restraints excluded: chain Ce residue 220 THR Chi-restraints excluded: chain Ce residue 227 MET Chi-restraints excluded: chain Ce residue 234 ILE Chi-restraints excluded: chain Ce residue 244 LEU Chi-restraints excluded: chain Ce residue 257 SER Chi-restraints excluded: chain Ce residue 297 ARG Chi-restraints excluded: chain Ce residue 363 ASP Chi-restraints excluded: chain Ce residue 365 VAL Chi-restraints excluded: chain Ce residue 397 LYS Chi-restraints excluded: chain Cf residue 36 THR Chi-restraints excluded: chain Cf residue 87 MET Chi-restraints excluded: chain Cg residue 15 VAL Chi-restraints excluded: chain Cg residue 49 GLN Chi-restraints excluded: chain Cg residue 62 LEU Chi-restraints excluded: chain Ch residue 142 ILE Chi-restraints excluded: chain Ch residue 285 CYS Chi-restraints excluded: chain Ch residue 426 ASN Chi-restraints excluded: chain Cz residue 67 GLU Chi-restraints excluded: chain Cz residue 95 ARG Chi-restraints excluded: chain LA residue 80 GLU Chi-restraints excluded: chain LA residue 199 THR Chi-restraints excluded: chain LB residue 34 LYS Chi-restraints excluded: chain LB residue 352 LEU Chi-restraints excluded: chain LC residue 61 THR Chi-restraints excluded: chain LC residue 354 VAL Chi-restraints excluded: chain LD residue 95 TRP Chi-restraints excluded: chain LD residue 129 TYR Chi-restraints excluded: chain LD residue 137 THR Chi-restraints excluded: chain LD residue 261 ASP Chi-restraints excluded: chain LE residue 155 SER Chi-restraints excluded: chain LE residue 163 LYS Chi-restraints excluded: chain LF residue 63 GLU Chi-restraints excluded: chain LF residue 65 GLU Chi-restraints excluded: chain LF residue 80 SER Chi-restraints excluded: chain LF residue 90 VAL Chi-restraints excluded: chain LH residue 87 LYS Chi-restraints excluded: chain LH residue 92 LEU Chi-restraints excluded: chain LH residue 120 THR Chi-restraints excluded: chain LJ residue 18 LEU Chi-restraints excluded: chain LJ residue 45 THR Chi-restraints excluded: chain LJ residue 127 ASP Chi-restraints excluded: chain LJ residue 147 SER Chi-restraints excluded: chain LK residue 104 VAL Chi-restraints excluded: chain LK residue 164 ASP Chi-restraints excluded: chain LL residue 140 LYS Chi-restraints excluded: chain LL residue 141 ASP Chi-restraints excluded: chain LL residue 169 SER Chi-restraints excluded: chain LM residue 3 GLU Chi-restraints excluded: chain LM residue 14 VAL Chi-restraints excluded: chain LN residue 60 VAL Chi-restraints excluded: chain LN residue 80 THR Chi-restraints excluded: chain LO residue 3 SER Chi-restraints excluded: chain LO residue 90 ILE Chi-restraints excluded: chain LO residue 139 THR Chi-restraints excluded: chain LO residue 185 LYS Chi-restraints excluded: chain LO residue 196 SER Chi-restraints excluded: chain LQ residue 91 SER Chi-restraints excluded: chain LQ residue 122 GLN Chi-restraints excluded: chain LR residue 51 ILE Chi-restraints excluded: chain LS residue 79 LEU Chi-restraints excluded: chain LT residue 143 ILE Chi-restraints excluded: chain LT residue 145 ASP Chi-restraints excluded: chain LT residue 154 VAL Chi-restraints excluded: chain LU residue 18 THR Chi-restraints excluded: chain LU residue 59 VAL Chi-restraints excluded: chain LU residue 71 GLU Chi-restraints excluded: chain LV residue 21 VAL Chi-restraints excluded: chain LX residue 83 GLU Chi-restraints excluded: chain LY residue 78 VAL Chi-restraints excluded: chain LY residue 90 THR Chi-restraints excluded: chain LY residue 93 THR Chi-restraints excluded: chain LY residue 94 VAL Chi-restraints excluded: chain LZ residue 34 SER Chi-restraints excluded: chain LZ residue 82 THR Chi-restraints excluded: chain La residue 75 ILE Chi-restraints excluded: chain Lc residue 46 LEU Chi-restraints excluded: chain Ld residue 96 LYS Chi-restraints excluded: chain Le residue 56 ILE Chi-restraints excluded: chain Le residue 83 VAL Chi-restraints excluded: chain Lf residue 51 VAL Chi-restraints excluded: chain Lf residue 86 LYS Chi-restraints excluded: chain Lf residue 109 ILE Chi-restraints excluded: chain Lh residue 11 GLN Chi-restraints excluded: chain Lh residue 33 GLN Chi-restraints excluded: chain Lh residue 73 LEU Chi-restraints excluded: chain Li residue 106 SER Chi-restraints excluded: chain Lj residue 27 LEU Chi-restraints excluded: chain Ll residue 34 THR Chi-restraints excluded: chain Lp residue 21 SER Chi-restraints excluded: chain Lp residue 28 LYS Chi-restraints excluded: chain Lp residue 50 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1325 random chunks: chunk 1236 optimal weight: 0.7980 chunk 144 optimal weight: 5.9990 chunk 730 optimal weight: 0.4980 chunk 936 optimal weight: 0.8980 chunk 725 optimal weight: 0.9980 chunk 1079 optimal weight: 1.9990 chunk 715 optimal weight: 6.9990 chunk 1277 optimal weight: 3.9990 chunk 799 optimal weight: 0.9980 chunk 778 optimal weight: 0.7980 chunk 589 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CF 29 ASN CH 244 HIS CH 389 ASN CI 229 HIS CM 203 GLN CM 227 HIS Cb 34 GLN Cd 170 GLN ** Ch 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ch 153 GLN Ch 226 GLN Cz 56 GLN ** Cz 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LA 71 GLN LE 172 ASN LH 179 GLN LJ 96 ASN LK 8 ASN LL 159 GLN LQ 153 GLN LS 21 ASN LS 147 ASN LU 55 ASN LX 66 HIS LX 81 ASN LX 124 ASN LY 116 ASN LZ 26 GLN Ld 108 ASN Lf 58 GLN Lh 67 GLN Li 21 ASN Lk 32 GLN Lk 33 GLN Lp 45 ASN Lq 97 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.0823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 162774 Z= 0.134 Angle : 0.607 18.136 236023 Z= 0.330 Chirality : 0.035 0.283 28825 Planarity : 0.006 0.127 17569 Dihedral : 22.456 178.289 63526 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.77 % Allowed : 15.05 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % 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: 1.73 (0.08), residues: 10017 helix: 2.31 (0.08), residues: 3877 sheet: 0.20 (0.13), residues: 1444 loop : 0.60 (0.09), residues: 4696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRPCg 105 HIS 0.009 0.001 HISLX 66 PHE 0.018 0.001 PHECH 90 TYR 0.015 0.001 TYRLH 129 ARG 0.010 0.000 ARGLS 3 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20034 Ramachandran restraints generated. 10017 Oldfield, 0 Emsley, 10017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20034 Ramachandran restraints generated. 10017 Oldfield, 0 Emsley, 10017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1226 residues out of total 8643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 1076 time to evaluate : 9.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CF 10 TYR cc_start: 0.8818 (t80) cc_final: 0.8565 (t80) REVERT: CF 38 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7930 (mp10) REVERT: CH 301 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.8094 (mmt) REVERT: CH 303 GLN cc_start: 0.7964 (tp40) cc_final: 0.7324 (tp40) REVERT: CH 307 ASP cc_start: 0.7748 (m-30) cc_final: 0.7233 (m-30) REVERT: CI 217 ARG cc_start: 0.8663 (ptm160) cc_final: 0.8117 (ttt180) REVERT: CI 237 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.7754 (t70) REVERT: CK 53 GLN cc_start: 0.7879 (tm130) cc_final: 0.7584 (tm130) REVERT: CL 67 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7879 (mt0) REVERT: CL 73 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.7515 (ptp-110) REVERT: CO 26 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8232 (mt-10) REVERT: CQ 25 ASP cc_start: 0.8796 (p0) cc_final: 0.8481 (p0) REVERT: CQ 136 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.8232 (ptm160) REVERT: Cb 80 GLN cc_start: 0.9281 (mt0) cc_final: 0.9081 (mt0) REVERT: Cd 324 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.8416 (mmt-90) REVERT: Cf 87 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8328 (mtm) REVERT: Ch 86 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.8193 (mtp180) REVERT: Cz 67 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.7106 (mp0) REVERT: LA 80 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8367 (tt0) REVERT: LC 154 ASP cc_start: 0.8709 (t0) cc_final: 0.8498 (t70) REVERT: LE 162 GLN cc_start: 0.8608 (tp40) cc_final: 0.8157 (tp40) REVERT: LJ 18 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.9048 (tp) REVERT: LL 150 SER cc_start: 0.8993 (t) cc_final: 0.8737 (t) REVERT: LQ 122 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8023 (mp10) REVERT: Lc 35 LYS cc_start: 0.8944 (ttmt) cc_final: 0.8396 (mttp) REVERT: Lh 11 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7641 (pt0) REVERT: Lh 33 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.6935 (mp10) REVERT: Lp 36 ARG cc_start: 0.8337 (mtp85) cc_final: 0.8127 (mtp85) outliers start: 150 outliers final: 88 residues processed: 1174 average time/residue: 2.5158 time to fit residues: 4133.8933 Evaluate side-chains 1158 residues out of total 8643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1054 time to evaluate : 8.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CF residue 34 ILE Chi-restraints excluded: chain CF residue 38 GLN Chi-restraints excluded: chain CF residue 97 THR Chi-restraints excluded: chain CF residue 149 VAL Chi-restraints excluded: chain CF residue 210 LYS Chi-restraints excluded: chain CH residue 79 ASP Chi-restraints excluded: chain CH residue 85 TYR Chi-restraints excluded: chain CH residue 168 THR Chi-restraints excluded: chain CH residue 301 MET Chi-restraints excluded: chain CH residue 325 GLU Chi-restraints excluded: chain CH residue 347 LEU Chi-restraints excluded: chain CH residue 374 MET Chi-restraints excluded: chain CH residue 469 GLU Chi-restraints excluded: chain CH residue 585 GLU Chi-restraints excluded: chain CH residue 655 ILE Chi-restraints excluded: chain CI residue 198 PHE Chi-restraints excluded: chain CI residue 237 ASP Chi-restraints excluded: chain CJ residue 140 ASP Chi-restraints excluded: chain CJ residue 221 ASP Chi-restraints excluded: chain CJ residue 400 VAL Chi-restraints excluded: chain CJ residue 407 THR Chi-restraints excluded: chain CJ residue 456 VAL Chi-restraints excluded: chain CK residue 73 VAL Chi-restraints excluded: chain CK residue 98 THR Chi-restraints excluded: chain CL residue 67 GLN Chi-restraints excluded: chain CL residue 73 ARG Chi-restraints excluded: chain CM residue 49 VAL Chi-restraints excluded: chain CM residue 162 VAL Chi-restraints excluded: chain CN residue 75 THR Chi-restraints excluded: chain CN residue 114 THR Chi-restraints excluded: chain CN residue 121 LEU Chi-restraints excluded: chain CN residue 172 GLU Chi-restraints excluded: chain CO residue 26 GLU Chi-restraints excluded: chain CQ residue 16 SER Chi-restraints excluded: chain CQ residue 42 MET Chi-restraints excluded: chain CQ residue 64 VAL Chi-restraints excluded: chain CQ residue 136 ARG Chi-restraints excluded: chain CQ residue 174 LYS Chi-restraints excluded: chain Cd residue 324 ARG Chi-restraints excluded: chain Ce residue 220 THR Chi-restraints excluded: chain Ce residue 234 ILE Chi-restraints excluded: chain Ce residue 257 SER Chi-restraints excluded: chain Ce residue 363 ASP Chi-restraints excluded: chain Ce residue 397 LYS Chi-restraints excluded: chain Cf residue 87 MET Chi-restraints excluded: chain Cg residue 15 VAL Chi-restraints excluded: chain Cg residue 62 LEU Chi-restraints excluded: chain Cg residue 102 GLU Chi-restraints excluded: chain Ch residue 86 ARG Chi-restraints excluded: chain Ch residue 142 ILE Chi-restraints excluded: chain Ch residue 426 ASN Chi-restraints excluded: chain Cz residue 67 GLU Chi-restraints excluded: chain LA residue 80 GLU Chi-restraints excluded: chain LA residue 199 THR Chi-restraints excluded: chain LA residue 207 VAL Chi-restraints excluded: chain LB residue 352 LEU Chi-restraints excluded: chain LC residue 61 THR Chi-restraints excluded: chain LC residue 354 VAL Chi-restraints excluded: chain LD residue 95 TRP Chi-restraints excluded: chain LD residue 137 THR Chi-restraints excluded: chain LD residue 261 ASP Chi-restraints excluded: chain LE residue 155 SER Chi-restraints excluded: chain LF residue 90 VAL Chi-restraints excluded: chain LH residue 87 LYS Chi-restraints excluded: chain LH residue 92 LEU Chi-restraints excluded: chain LH residue 120 THR Chi-restraints excluded: chain LJ residue 18 LEU Chi-restraints excluded: chain LJ residue 45 THR Chi-restraints excluded: chain LJ residue 147 SER Chi-restraints excluded: chain LK residue 104 VAL Chi-restraints excluded: chain LK residue 164 ASP Chi-restraints excluded: chain LL residue 169 SER Chi-restraints excluded: chain LM residue 3 GLU Chi-restraints excluded: chain LM residue 14 VAL Chi-restraints excluded: chain LN residue 60 VAL Chi-restraints excluded: chain LN residue 80 THR Chi-restraints excluded: chain LO residue 90 ILE Chi-restraints excluded: chain LO residue 185 LYS Chi-restraints excluded: chain LO residue 197 GLU Chi-restraints excluded: chain LQ residue 91 SER Chi-restraints excluded: chain LQ residue 122 GLN Chi-restraints excluded: chain LR residue 51 ILE Chi-restraints excluded: chain LR residue 76 ARG Chi-restraints excluded: chain LS residue 79 LEU Chi-restraints excluded: chain LT residue 145 ASP Chi-restraints excluded: chain LU residue 118 VAL Chi-restraints excluded: chain LX residue 83 GLU Chi-restraints excluded: chain LY residue 78 VAL Chi-restraints excluded: chain LY residue 90 THR Chi-restraints excluded: chain LY residue 93 THR Chi-restraints excluded: chain LY residue 94 VAL Chi-restraints excluded: chain La residue 75 ILE Chi-restraints excluded: chain Lc residue 46 LEU Chi-restraints excluded: chain Le residue 83 VAL Chi-restraints excluded: chain Lf residue 51 VAL Chi-restraints excluded: chain Lg residue 105 VAL Chi-restraints excluded: chain Lh residue 11 GLN Chi-restraints excluded: chain Lh residue 33 GLN Chi-restraints excluded: chain Lh residue 73 LEU Chi-restraints excluded: chain Li residue 106 SER Chi-restraints excluded: chain Ll residue 34 THR Chi-restraints excluded: chain Lp residue 21 SER Chi-restraints excluded: chain Lp residue 28 LYS Chi-restraints excluded: chain Lq residue 85 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1325 random chunks: chunk 790 optimal weight: 7.9990 chunk 509 optimal weight: 7.9990 chunk 762 optimal weight: 9.9990 chunk 384 optimal weight: 1.9990 chunk 250 optimal weight: 10.0000 chunk 247 optimal weight: 10.0000 chunk 811 optimal weight: 4.9990 chunk 870 optimal weight: 2.9990 chunk 631 optimal weight: 1.9990 chunk 119 optimal weight: 7.9990 chunk 1003 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CF 29 ASN CH 389 ASN CI 229 HIS CM 203 GLN CM 227 HIS Cb 34 GLN Cd 170 GLN Cf 43 GLN Cg 121 GLN Cg 133 GLN ** Ch 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ch 226 GLN Cz 56 GLN ** Cz 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LA 71 GLN LE 172 ASN LH 179 GLN LJ 96 ASN LK 8 ASN LL 114 GLN LL 159 GLN LS 21 ASN LS 147 ASN LU 55 ASN LX 66 HIS LX 81 ASN LX 124 ASN LY 116 ASN LZ 26 GLN LZ 105 GLN Ld 108 ASN Lf 58 GLN ** Lh 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 67 GLN Lk 32 GLN Lk 33 GLN Lp 45 ASN Lq 97 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 162774 Z= 0.320 Angle : 0.694 19.023 236023 Z= 0.367 Chirality : 0.041 0.289 28825 Planarity : 0.007 0.143 17569 Dihedral : 22.472 178.729 63521 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.85 % Allowed : 15.27 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % 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: 1.60 (0.08), residues: 10017 helix: 2.16 (0.08), residues: 3867 sheet: 0.20 (0.13), residues: 1434 loop : 0.53 (0.09), residues: 4716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRPCd 223 HIS 0.011 0.001 HISLX 66 PHE 0.030 0.002 PHECh 37 TYR 0.019 0.002 TYRLd 20 ARG 0.013 0.001 ARGLS 3 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20034 Ramachandran restraints generated. 10017 Oldfield, 0 Emsley, 10017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20034 Ramachandran restraints generated. 10017 Oldfield, 0 Emsley, 10017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1207 residues out of total 8643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 1050 time to evaluate : 8.510 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: CF 10 TYR cc_start: 0.8853 (t80) cc_final: 0.8624 (t80) REVERT: CF 38 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7955 (mp10) REVERT: CH 70 LEU cc_start: 0.9540 (OUTLIER) cc_final: 0.9196 (mp) REVERT: CH 301 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.8177 (mmt) REVERT: CH 303 GLN cc_start: 0.7981 (tp40) cc_final: 0.7290 (tp40) REVERT: CH 307 ASP cc_start: 0.7771 (m-30) cc_final: 0.7248 (m-30) REVERT: CI 217 ARG cc_start: 0.8725 (ptm160) cc_final: 0.8167 (ttt180) REVERT: CI 237 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.7757 (t70) REVERT: CK 53 GLN cc_start: 0.7955 (tm130) cc_final: 0.7729 (tm130) REVERT: CL 67 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7910 (mt0) REVERT: CL 73 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.7527 (ptp-110) REVERT: CO 26 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8316 (mt-10) REVERT: CQ 25 ASP cc_start: 0.8844 (p0) cc_final: 0.8532 (p0) REVERT: CQ 93 MET cc_start: 0.9297 (mtp) cc_final: 0.9083 (mtp) REVERT: Cd 324 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.8408 (mmt-90) REVERT: Cf 87 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8544 (mtm) REVERT: LA 80 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8373 (tt0) REVERT: LE 162 GLN cc_start: 0.8560 (tp40) cc_final: 0.8119 (tp40) REVERT: LE 163 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8399 (mtmt) REVERT: LJ 18 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.9048 (tp) REVERT: LL 150 SER cc_start: 0.9007 (t) cc_final: 0.8736 (t) REVERT: LQ 122 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.7933 (mp10) REVERT: LT 94 GLU cc_start: 0.8251 (pm20) cc_final: 0.8023 (pm20) REVERT: LU 71 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7463 (tm-30) REVERT: Lc 35 LYS cc_start: 0.8980 (ttmt) cc_final: 0.8447 (mttp) REVERT: Lh 11 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7701 (pt0) REVERT: Lh 33 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.6999 (mp10) outliers start: 157 outliers final: 101 residues processed: 1154 average time/residue: 2.4887 time to fit residues: 4025.0846 Evaluate side-chains 1165 residues out of total 8643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 1048 time to evaluate : 8.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CF residue 38 GLN Chi-restraints excluded: chain CF residue 97 THR Chi-restraints excluded: chain CF residue 149 VAL Chi-restraints excluded: chain CF residue 210 LYS Chi-restraints excluded: chain CH residue 70 LEU Chi-restraints excluded: chain CH residue 79 ASP Chi-restraints excluded: chain CH residue 85 TYR Chi-restraints excluded: chain CH residue 168 THR Chi-restraints excluded: chain CH residue 301 MET Chi-restraints excluded: chain CH residue 325 GLU Chi-restraints excluded: chain CH residue 347 LEU Chi-restraints excluded: chain CH residue 374 MET Chi-restraints excluded: chain CH residue 426 ILE Chi-restraints excluded: chain CH residue 585 GLU Chi-restraints excluded: chain CH residue 655 ILE Chi-restraints excluded: chain CI residue 198 PHE Chi-restraints excluded: chain CI residue 237 ASP Chi-restraints excluded: chain CI residue 259 THR Chi-restraints excluded: chain CJ residue 140 ASP Chi-restraints excluded: chain CJ residue 221 ASP Chi-restraints excluded: chain CJ residue 407 THR Chi-restraints excluded: chain CJ residue 456 VAL Chi-restraints excluded: chain CK residue 73 VAL Chi-restraints excluded: chain CK residue 98 THR Chi-restraints excluded: chain CL residue 19 ARG Chi-restraints excluded: chain CL residue 67 GLN Chi-restraints excluded: chain CL residue 73 ARG Chi-restraints excluded: chain CL residue 74 ILE Chi-restraints excluded: chain CM residue 49 VAL Chi-restraints excluded: chain CM residue 111 LEU Chi-restraints excluded: chain CM residue 162 VAL Chi-restraints excluded: chain CN residue 75 THR Chi-restraints excluded: chain CN residue 114 THR Chi-restraints excluded: chain CN residue 121 LEU Chi-restraints excluded: chain CN residue 172 GLU Chi-restraints excluded: chain CO residue 26 GLU Chi-restraints excluded: chain CQ residue 16 SER Chi-restraints excluded: chain CQ residue 64 VAL Chi-restraints excluded: chain CQ residue 174 LYS Chi-restraints excluded: chain Cd residue 324 ARG Chi-restraints excluded: chain Ce residue 220 THR Chi-restraints excluded: chain Ce residue 234 ILE Chi-restraints excluded: chain Ce residue 257 SER Chi-restraints excluded: chain Ce residue 363 ASP Chi-restraints excluded: chain Ce residue 365 VAL Chi-restraints excluded: chain Ce residue 397 LYS Chi-restraints excluded: chain Cf residue 36 THR Chi-restraints excluded: chain Cf residue 87 MET Chi-restraints excluded: chain Cg residue 15 VAL Chi-restraints excluded: chain Cg residue 62 LEU Chi-restraints excluded: chain Ch residue 142 ILE Chi-restraints excluded: chain Ch residue 285 CYS Chi-restraints excluded: chain Ch residue 426 ASN Chi-restraints excluded: chain Cz residue 67 GLU Chi-restraints excluded: chain LA residue 80 GLU Chi-restraints excluded: chain LA residue 199 THR Chi-restraints excluded: chain LA residue 207 VAL Chi-restraints excluded: chain LB residue 352 LEU Chi-restraints excluded: chain LC residue 61 THR Chi-restraints excluded: chain LC residue 104 THR Chi-restraints excluded: chain LC residue 354 VAL Chi-restraints excluded: chain LD residue 95 TRP Chi-restraints excluded: chain LD residue 137 THR Chi-restraints excluded: chain LD residue 261 ASP Chi-restraints excluded: chain LE residue 155 SER Chi-restraints excluded: chain LE residue 163 LYS Chi-restraints excluded: chain LF residue 65 GLU Chi-restraints excluded: chain LF residue 90 VAL Chi-restraints excluded: chain LH residue 87 LYS Chi-restraints excluded: chain LH residue 92 LEU Chi-restraints excluded: chain LH residue 120 THR Chi-restraints excluded: chain LJ residue 18 LEU Chi-restraints excluded: chain LJ residue 45 THR Chi-restraints excluded: chain LJ residue 147 SER Chi-restraints excluded: chain LK residue 104 VAL Chi-restraints excluded: chain LK residue 164 ASP Chi-restraints excluded: chain LL residue 141 ASP Chi-restraints excluded: chain LL residue 169 SER Chi-restraints excluded: chain LM residue 3 GLU Chi-restraints excluded: chain LM residue 14 VAL Chi-restraints excluded: chain LN residue 7 LEU Chi-restraints excluded: chain LN residue 60 VAL Chi-restraints excluded: chain LN residue 80 THR Chi-restraints excluded: chain LO residue 3 SER Chi-restraints excluded: chain LO residue 90 ILE Chi-restraints excluded: chain LO residue 185 LYS Chi-restraints excluded: chain LO residue 197 GLU Chi-restraints excluded: chain LQ residue 91 SER Chi-restraints excluded: chain LQ residue 122 GLN Chi-restraints excluded: chain LR residue 51 ILE Chi-restraints excluded: chain LS residue 79 LEU Chi-restraints excluded: chain LT residue 143 ILE Chi-restraints excluded: chain LT residue 145 ASP Chi-restraints excluded: chain LU residue 71 GLU Chi-restraints excluded: chain LU residue 118 VAL Chi-restraints excluded: chain LV residue 21 VAL Chi-restraints excluded: chain LX residue 83 GLU Chi-restraints excluded: chain LY residue 78 VAL Chi-restraints excluded: chain LY residue 90 THR Chi-restraints excluded: chain LY residue 93 THR Chi-restraints excluded: chain LY residue 94 VAL Chi-restraints excluded: chain LZ residue 34 SER Chi-restraints excluded: chain La residue 75 ILE Chi-restraints excluded: chain Lc residue 46 LEU Chi-restraints excluded: chain Ld residue 96 LYS Chi-restraints excluded: chain Le residue 83 VAL Chi-restraints excluded: chain Lf residue 51 VAL Chi-restraints excluded: chain Lf residue 109 ILE Chi-restraints excluded: chain Lh residue 11 GLN Chi-restraints excluded: chain Lh residue 33 GLN Chi-restraints excluded: chain Lh residue 73 LEU Chi-restraints excluded: chain Lh residue 81 LEU Chi-restraints excluded: chain Li residue 106 SER Chi-restraints excluded: chain Ll residue 34 THR Chi-restraints excluded: chain Lp residue 21 SER Chi-restraints excluded: chain Lp residue 28 LYS Chi-restraints excluded: chain Lq residue 85 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1325 random chunks: chunk 1161 optimal weight: 2.9990 chunk 1223 optimal weight: 0.9990 chunk 1116 optimal weight: 4.9990 chunk 1190 optimal weight: 2.9990 chunk 716 optimal weight: 3.9990 chunk 518 optimal weight: 10.0000 chunk 934 optimal weight: 0.8980 chunk 365 optimal weight: 0.6980 chunk 1075 optimal weight: 4.9990 chunk 1125 optimal weight: 10.0000 chunk 1185 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CF 29 ASN CH 389 ASN CI 229 HIS CM 203 GLN CM 227 HIS Cb 34 GLN Cd 170 GLN ** Ch 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ch 226 GLN Cz 56 GLN ** Cz 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LA 71 GLN LA 132 ASN LE 172 ASN LH 179 GLN LJ 96 ASN LK 8 ASN LQ 153 GLN LS 21 ASN LS 147 ASN LU 55 ASN LX 66 HIS LX 81 ASN LX 124 ASN LY 116 ASN LZ 26 GLN LZ 105 GLN Ld 108 ASN Lf 58 GLN ** Lh 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 67 GLN Lk 33 GLN Lp 45 ASN Lq 97 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.0822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 162774 Z= 0.199 Angle : 0.640 18.640 236023 Z= 0.345 Chirality : 0.037 0.286 28825 Planarity : 0.006 0.133 17569 Dihedral : 22.461 178.850 63521 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.61 % Allowed : 15.56 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % 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: 1.66 (0.08), residues: 10017 helix: 2.22 (0.08), residues: 3879 sheet: 0.16 (0.13), residues: 1444 loop : 0.58 (0.09), residues: 4694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRPCg 105 HIS 0.012 0.001 HISLX 66 PHE 0.019 0.001 PHECh 85 TYR 0.018 0.001 TYRLQ 61 ARG 0.013 0.000 ARGLS 3 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20034 Ramachandran restraints generated. 10017 Oldfield, 0 Emsley, 10017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20034 Ramachandran restraints generated. 10017 Oldfield, 0 Emsley, 10017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1198 residues out of total 8643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1062 time to evaluate : 9.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CF 10 TYR cc_start: 0.8838 (t80) cc_final: 0.8576 (t80) REVERT: CF 38 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7946 (mp10) REVERT: CH 70 LEU cc_start: 0.9535 (OUTLIER) cc_final: 0.9166 (mp) REVERT: CH 301 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.8056 (mmt) REVERT: CH 303 GLN cc_start: 0.7979 (tp40) cc_final: 0.7296 (tp40) REVERT: CH 307 ASP cc_start: 0.7743 (m-30) cc_final: 0.7219 (m-30) REVERT: CI 217 ARG cc_start: 0.8708 (ptm160) cc_final: 0.8135 (ttt180) REVERT: CI 237 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.7735 (t70) REVERT: CK 53 GLN cc_start: 0.7906 (tm130) cc_final: 0.7599 (tm130) REVERT: CL 67 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7898 (mt0) REVERT: CL 73 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7508 (ptp-110) REVERT: CO 26 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8302 (mt-10) REVERT: CQ 25 ASP cc_start: 0.8832 (p0) cc_final: 0.8529 (p0) REVERT: Cd 324 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.8430 (mmt-90) REVERT: Ce 397 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8533 (ttmm) REVERT: Cf 87 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8423 (mtm) REVERT: Ch 86 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8175 (mtp180) REVERT: Cz 67 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.7122 (mp0) REVERT: LA 80 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8368 (tt0) REVERT: LE 162 GLN cc_start: 0.8542 (tp40) cc_final: 0.8161 (tp40) REVERT: LJ 18 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.9042 (tp) REVERT: LL 150 SER cc_start: 0.8999 (t) cc_final: 0.8734 (t) REVERT: LN 140 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.8009 (tttt) REVERT: LQ 122 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.7978 (mp10) REVERT: LT 94 GLU cc_start: 0.8288 (pm20) cc_final: 0.7990 (pm20) REVERT: LU 71 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7385 (tm-30) REVERT: LX 22 LYS cc_start: 0.8633 (tppt) cc_final: 0.8410 (tptt) REVERT: Lc 35 LYS cc_start: 0.8976 (ttmt) cc_final: 0.8442 (mttp) REVERT: Lh 11 GLN cc_start: 0.8079 (OUTLIER) cc_final: 0.7670 (pt0) REVERT: Lh 33 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.6958 (mp10) outliers start: 136 outliers final: 91 residues processed: 1149 average time/residue: 2.5320 time to fit residues: 4069.9563 Evaluate side-chains 1163 residues out of total 8643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 1053 time to evaluate : 7.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CF residue 34 ILE Chi-restraints excluded: chain CF residue 38 GLN Chi-restraints excluded: chain CF residue 97 THR Chi-restraints excluded: chain CF residue 149 VAL Chi-restraints excluded: chain CF residue 210 LYS Chi-restraints excluded: chain CH residue 70 LEU Chi-restraints excluded: chain CH residue 79 ASP Chi-restraints excluded: chain CH residue 85 TYR Chi-restraints excluded: chain CH residue 168 THR Chi-restraints excluded: chain CH residue 301 MET Chi-restraints excluded: chain CH residue 325 GLU Chi-restraints excluded: chain CH residue 347 LEU Chi-restraints excluded: chain CH residue 374 MET Chi-restraints excluded: chain CH residue 585 GLU Chi-restraints excluded: chain CH residue 610 THR Chi-restraints excluded: chain CH residue 655 ILE Chi-restraints excluded: chain CI residue 198 PHE Chi-restraints excluded: chain CI residue 237 ASP Chi-restraints excluded: chain CI residue 259 THR Chi-restraints excluded: chain CJ residue 140 ASP Chi-restraints excluded: chain CJ residue 221 ASP Chi-restraints excluded: chain CJ residue 407 THR Chi-restraints excluded: chain CJ residue 456 VAL Chi-restraints excluded: chain CK residue 73 VAL Chi-restraints excluded: chain CK residue 98 THR Chi-restraints excluded: chain CL residue 19 ARG Chi-restraints excluded: chain CL residue 67 GLN Chi-restraints excluded: chain CL residue 73 ARG Chi-restraints excluded: chain CM residue 49 VAL Chi-restraints excluded: chain CM residue 111 LEU Chi-restraints excluded: chain CM residue 162 VAL Chi-restraints excluded: chain CN residue 75 THR Chi-restraints excluded: chain CN residue 114 THR Chi-restraints excluded: chain CN residue 121 LEU Chi-restraints excluded: chain CN residue 172 GLU Chi-restraints excluded: chain CO residue 26 GLU Chi-restraints excluded: chain CQ residue 16 SER Chi-restraints excluded: chain CQ residue 64 VAL Chi-restraints excluded: chain CQ residue 174 LYS Chi-restraints excluded: chain Cb residue 28 SER Chi-restraints excluded: chain Cd residue 324 ARG Chi-restraints excluded: chain Ce residue 220 THR Chi-restraints excluded: chain Ce residue 234 ILE Chi-restraints excluded: chain Ce residue 257 SER Chi-restraints excluded: chain Ce residue 363 ASP Chi-restraints excluded: chain Ce residue 397 LYS Chi-restraints excluded: chain Cf residue 87 MET Chi-restraints excluded: chain Cg residue 15 VAL Chi-restraints excluded: chain Cg residue 62 LEU Chi-restraints excluded: chain Ch residue 86 ARG Chi-restraints excluded: chain Ch residue 142 ILE Chi-restraints excluded: chain Ch residue 285 CYS Chi-restraints excluded: chain Ch residue 426 ASN Chi-restraints excluded: chain Cz residue 67 GLU Chi-restraints excluded: chain LA residue 80 GLU Chi-restraints excluded: chain LA residue 199 THR Chi-restraints excluded: chain LA residue 207 VAL Chi-restraints excluded: chain LB residue 352 LEU Chi-restraints excluded: chain LC residue 61 THR Chi-restraints excluded: chain LC residue 354 VAL Chi-restraints excluded: chain LD residue 95 TRP Chi-restraints excluded: chain LD residue 137 THR Chi-restraints excluded: chain LD residue 261 ASP Chi-restraints excluded: chain LF residue 80 SER Chi-restraints excluded: chain LF residue 90 VAL Chi-restraints excluded: chain LH residue 87 LYS Chi-restraints excluded: chain LH residue 92 LEU Chi-restraints excluded: chain LH residue 120 THR Chi-restraints excluded: chain LJ residue 18 LEU Chi-restraints excluded: chain LJ residue 45 THR Chi-restraints excluded: chain LJ residue 147 SER Chi-restraints excluded: chain LK residue 104 VAL Chi-restraints excluded: chain LK residue 164 ASP Chi-restraints excluded: chain LL residue 169 SER Chi-restraints excluded: chain LM residue 3 GLU Chi-restraints excluded: chain LM residue 14 VAL Chi-restraints excluded: chain LN residue 7 LEU Chi-restraints excluded: chain LN residue 60 VAL Chi-restraints excluded: chain LN residue 80 THR Chi-restraints excluded: chain LN residue 140 LYS Chi-restraints excluded: chain LO residue 3 SER Chi-restraints excluded: chain LO residue 90 ILE Chi-restraints excluded: chain LO residue 185 LYS Chi-restraints excluded: chain LO residue 197 GLU Chi-restraints excluded: chain LQ residue 91 SER Chi-restraints excluded: chain LQ residue 122 GLN Chi-restraints excluded: chain LS residue 79 LEU Chi-restraints excluded: chain LT residue 143 ILE Chi-restraints excluded: chain LT residue 145 ASP Chi-restraints excluded: chain LU residue 59 VAL Chi-restraints excluded: chain LU residue 71 GLU Chi-restraints excluded: chain LU residue 118 VAL Chi-restraints excluded: chain LX residue 83 GLU Chi-restraints excluded: chain LY residue 78 VAL Chi-restraints excluded: chain LY residue 90 THR Chi-restraints excluded: chain LY residue 93 THR Chi-restraints excluded: chain LY residue 94 VAL Chi-restraints excluded: chain LZ residue 34 SER Chi-restraints excluded: chain La residue 75 ILE Chi-restraints excluded: chain Lc residue 46 LEU Chi-restraints excluded: chain Le residue 83 VAL Chi-restraints excluded: chain Lf residue 51 VAL Chi-restraints excluded: chain Lh residue 11 GLN Chi-restraints excluded: chain Lh residue 33 GLN Chi-restraints excluded: chain Lh residue 73 LEU Chi-restraints excluded: chain Lh residue 81 LEU Chi-restraints excluded: chain Ll residue 34 THR Chi-restraints excluded: chain Lp residue 21 SER Chi-restraints excluded: chain Lp residue 28 LYS Chi-restraints excluded: chain Lq residue 85 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1325 random chunks: chunk 781 optimal weight: 5.9990 chunk 1258 optimal weight: 1.9990 chunk 768 optimal weight: 30.0000 chunk 596 optimal weight: 3.9990 chunk 874 optimal weight: 6.9990 chunk 1320 optimal weight: 6.9990 chunk 1214 optimal weight: 0.0980 chunk 1051 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 chunk 811 optimal weight: 0.0980 chunk 644 optimal weight: 1.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CF 29 ASN CH 362 GLN CH 389 ASN CI 229 HIS CM 203 GLN CM 227 HIS Cb 34 GLN Cd 170 GLN Cf 43 GLN ** Ch 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ch 226 GLN Cz 56 GLN ** Cz 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LA 71 GLN LA 132 ASN LE 172 ASN LH 179 GLN LJ 96 ASN LK 8 ASN LS 21 ASN LS 147 ASN LU 55 ASN LX 66 HIS LX 81 ASN LX 124 ASN LY 116 ASN LZ 26 GLN LZ 105 GLN Ld 108 ASN Lf 58 GLN Lh 67 GLN Li 21 ASN Lk 32 GLN Lk 33 GLN Lp 45 ASN Lq 97 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.0827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 162774 Z= 0.194 Angle : 0.636 18.517 236023 Z= 0.343 Chirality : 0.037 0.285 28825 Planarity : 0.006 0.132 17569 Dihedral : 22.453 178.750 63520 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.58 % Allowed : 15.56 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % 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: 1.68 (0.08), residues: 10017 helix: 2.25 (0.08), residues: 3879 sheet: 0.17 (0.13), residues: 1444 loop : 0.59 (0.09), residues: 4694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRPCg 105 HIS 0.010 0.001 HISLX 66 PHE 0.041 0.001 PHECh 37 TYR 0.017 0.001 TYRLO 55 ARG 0.015 0.000 ARGLS 3 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 20034 Ramachandran restraints generated. 10017 Oldfield, 0 Emsley, 10017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 20034 Ramachandran restraints generated. 10017 Oldfield, 0 Emsley, 10017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1192 residues out of total 8643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 1058 time to evaluate : 9.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CF 10 TYR cc_start: 0.8831 (t80) cc_final: 0.8572 (t80) REVERT: CF 38 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7942 (mp10) REVERT: CH 70 LEU cc_start: 0.9533 (OUTLIER) cc_final: 0.9164 (mp) REVERT: CH 301 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8089 (mmt) REVERT: CH 303 GLN cc_start: 0.8000 (tp40) cc_final: 0.7267 (tp40) REVERT: CH 307 ASP cc_start: 0.7739 (m-30) cc_final: 0.7175 (m-30) REVERT: CI 217 ARG cc_start: 0.8702 (ptm160) cc_final: 0.8146 (ttt180) REVERT: CI 237 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.7736 (t70) REVERT: CK 53 GLN cc_start: 0.7889 (tm130) cc_final: 0.7580 (tm130) REVERT: CL 67 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7901 (mt0) REVERT: CL 73 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.7506 (ptp-110) REVERT: CO 26 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8299 (mt-10) REVERT: CQ 25 ASP cc_start: 0.8826 (p0) cc_final: 0.8521 (p0) REVERT: Cd 324 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.8410 (mmt-90) REVERT: Ce 397 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8535 (ttmm) REVERT: Cf 87 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8427 (mtm) REVERT: Ch 86 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8174 (mtp180) REVERT: Cz 67 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.7118 (mp0) REVERT: LA 80 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8368 (tt0) REVERT: LE 162 GLN cc_start: 0.8565 (tp40) cc_final: 0.8275 (tp40) REVERT: LJ 18 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.9039 (tp) REVERT: LL 150 SER cc_start: 0.8997 (t) cc_final: 0.8733 (t) REVERT: LN 140 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.8018 (tttt) REVERT: LQ 122 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7977 (mp10) REVERT: LT 94 GLU cc_start: 0.8250 (pm20) cc_final: 0.7951 (pm20) REVERT: LU 71 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7384 (tm-30) REVERT: LX 22 LYS cc_start: 0.8619 (tppt) cc_final: 0.8409 (tptt) REVERT: Lc 35 LYS cc_start: 0.8975 (ttmt) cc_final: 0.8443 (mttp) REVERT: Lh 11 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7663 (pt0) REVERT: Lh 33 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.6952 (mp10) outliers start: 134 outliers final: 95 residues processed: 1147 average time/residue: 2.5561 time to fit residues: 4097.0399 Evaluate side-chains 1167 residues out of total 8643 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 1053 time to evaluate : 8.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CF residue 34 ILE Chi-restraints excluded: chain CF residue 38 GLN Chi-restraints excluded: chain CF residue 97 THR Chi-restraints excluded: chain CF residue 149 VAL Chi-restraints excluded: chain CF residue 210 LYS Chi-restraints excluded: chain CH residue 70 LEU Chi-restraints excluded: chain CH residue 79 ASP Chi-restraints excluded: chain CH residue 85 TYR Chi-restraints excluded: chain CH residue 168 THR Chi-restraints excluded: chain CH residue 301 MET Chi-restraints excluded: chain CH residue 325 GLU Chi-restraints excluded: chain CH residue 347 LEU Chi-restraints excluded: chain CH residue 374 MET Chi-restraints excluded: chain CH residue 585 GLU Chi-restraints excluded: chain CH residue 610 THR Chi-restraints excluded: chain CH residue 655 ILE Chi-restraints excluded: chain CI residue 198 PHE Chi-restraints excluded: chain CI residue 237 ASP Chi-restraints excluded: chain CI residue 259 THR Chi-restraints excluded: chain CJ residue 140 ASP Chi-restraints excluded: chain CJ residue 221 ASP Chi-restraints excluded: chain CJ residue 407 THR Chi-restraints excluded: chain CJ residue 456 VAL Chi-restraints excluded: chain CK residue 73 VAL Chi-restraints excluded: chain CK residue 98 THR Chi-restraints excluded: chain CL residue 19 ARG Chi-restraints excluded: chain CL residue 67 GLN Chi-restraints excluded: chain CL residue 73 ARG Chi-restraints excluded: chain CL residue 74 ILE Chi-restraints excluded: chain CM residue 49 VAL Chi-restraints excluded: chain CM residue 111 LEU Chi-restraints excluded: chain CM residue 162 VAL Chi-restraints excluded: chain CN residue 75 THR Chi-restraints excluded: chain CN residue 114 THR Chi-restraints excluded: chain CN residue 121 LEU Chi-restraints excluded: chain CN residue 172 GLU Chi-restraints excluded: chain CO residue 26 GLU Chi-restraints excluded: chain CQ residue 16 SER Chi-restraints excluded: chain CQ residue 64 VAL Chi-restraints excluded: chain CQ residue 174 LYS Chi-restraints excluded: chain Cb residue 28 SER Chi-restraints excluded: chain Cd residue 324 ARG Chi-restraints excluded: chain Ce residue 220 THR Chi-restraints excluded: chain Ce residue 257 SER Chi-restraints excluded: chain Ce residue 363 ASP Chi-restraints excluded: chain Ce residue 397 LYS Chi-restraints excluded: chain Cf residue 87 MET Chi-restraints excluded: chain Cg residue 15 VAL Chi-restraints excluded: chain Cg residue 62 LEU Chi-restraints excluded: chain Ch residue 86 ARG Chi-restraints excluded: chain Ch residue 142 ILE Chi-restraints excluded: chain Ch residue 285 CYS Chi-restraints excluded: chain Ch residue 426 ASN Chi-restraints excluded: chain Cz residue 67 GLU Chi-restraints excluded: chain LA residue 80 GLU Chi-restraints excluded: chain LA residue 199 THR Chi-restraints excluded: chain LA residue 207 VAL Chi-restraints excluded: chain LB residue 352 LEU Chi-restraints excluded: chain LC residue 61 THR Chi-restraints excluded: chain LC residue 354 VAL Chi-restraints excluded: chain LD residue 95 TRP Chi-restraints excluded: chain LD residue 137 THR Chi-restraints excluded: chain LD residue 261 ASP Chi-restraints excluded: chain LF residue 80 SER Chi-restraints excluded: chain LF residue 90 VAL Chi-restraints excluded: chain LH residue 87 LYS Chi-restraints excluded: chain LH residue 92 LEU Chi-restraints excluded: chain LH residue 120 THR Chi-restraints excluded: chain LJ residue 18 LEU Chi-restraints excluded: chain LJ residue 45 THR Chi-restraints excluded: chain LJ residue 147 SER Chi-restraints excluded: chain LK residue 104 VAL Chi-restraints excluded: chain LK residue 164 ASP Chi-restraints excluded: chain LL residue 169 SER Chi-restraints excluded: chain LM residue 14 VAL Chi-restraints excluded: chain LN residue 7 LEU Chi-restraints excluded: chain LN residue 60 VAL Chi-restraints excluded: chain LN residue 80 THR Chi-restraints excluded: chain LN residue 140 LYS Chi-restraints excluded: chain LO residue 90 ILE Chi-restraints excluded: chain LO residue 185 LYS Chi-restraints excluded: chain LO residue 197 GLU Chi-restraints excluded: chain LQ residue 91 SER Chi-restraints excluded: chain LQ residue 122 GLN Chi-restraints excluded: chain LR residue 51 ILE Chi-restraints excluded: chain LR residue 76 ARG Chi-restraints excluded: chain LS residue 79 LEU Chi-restraints excluded: chain LT residue 143 ILE Chi-restraints excluded: chain LT residue 145 ASP Chi-restraints excluded: chain LT residue 154 VAL Chi-restraints excluded: chain LU residue 59 VAL Chi-restraints excluded: chain LU residue 71 GLU Chi-restraints excluded: chain LU residue 118 VAL Chi-restraints excluded: chain LX residue 83 GLU Chi-restraints excluded: chain LY residue 78 VAL Chi-restraints excluded: chain LY residue 90 THR Chi-restraints excluded: chain LY residue 93 THR Chi-restraints excluded: chain LY residue 94 VAL Chi-restraints excluded: chain LZ residue 34 SER Chi-restraints excluded: chain La residue 75 ILE Chi-restraints excluded: chain La residue 84 SER Chi-restraints excluded: chain Lc residue 46 LEU Chi-restraints excluded: chain Ld residue 96 LYS Chi-restraints excluded: chain Le residue 83 VAL Chi-restraints excluded: chain Lf residue 51 VAL Chi-restraints excluded: chain Lh residue 11 GLN Chi-restraints excluded: chain Lh residue 33 GLN Chi-restraints excluded: chain Lh residue 73 LEU Chi-restraints excluded: chain Lh residue 81 LEU Chi-restraints excluded: chain Lj residue 27 LEU Chi-restraints excluded: chain Ll residue 34 THR Chi-restraints excluded: chain Lp residue 21 SER Chi-restraints excluded: chain Lp residue 28 LYS Chi-restraints excluded: chain Lq residue 85 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1325 random chunks: chunk 834 optimal weight: 5.9990 chunk 1119 optimal weight: 0.9980 chunk 322 optimal weight: 6.9990 chunk 969 optimal weight: 6.9990 chunk 155 optimal weight: 7.9990 chunk 292 optimal weight: 10.0000 chunk 1052 optimal weight: 2.9990 chunk 440 optimal weight: 5.9990 chunk 1081 optimal weight: 0.9990 chunk 133 optimal weight: 6.9990 chunk 193 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CF 29 ASN CH 389 ASN CI 229 HIS CM 203 GLN CM 227 HIS Cb 34 GLN Cd 170 GLN Cf 43 GLN Cg 133 GLN ** Ch 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ch 226 GLN Cz 56 GLN ** Cz 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LA 71 GLN LE 172 ASN LH 179 GLN LJ 96 ASN LK 8 ASN LS 21 ASN LS 147 ASN LU 55 ASN LX 66 HIS LX 81 ASN LX 124 ASN LY 116 ASN LZ 26 GLN LZ 105 GLN Ld 108 ASN Lf 58 GLN ** Lh 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 67 GLN Lk 32 GLN Lk 33 GLN Lp 45 ASN Lq 97 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.084690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.059675 restraints weight = 232950.268| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 0.95 r_work: 0.2717 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2617 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2617 r_free = 0.2617 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 = 0.2617 r_free = 0.2617 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 162774 Z= 0.338 Angle : 0.711 19.265 236023 Z= 0.375 Chirality : 0.041 0.297 28825 Planarity : 0.007 0.144 17569 Dihedral : 22.482 179.213 63520 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.60 % Allowed : 15.62 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.47 % 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: 1.52 (0.08), residues: 10017 helix: 2.10 (0.08), residues: 3863 sheet: 0.13 (0.13), residues: 1445 loop : 0.50 (0.09), residues: 4709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRPCd 223 HIS 0.014 0.001 HISLT 54 PHE 0.022 0.002 PHECh 85 TYR 0.019 0.002 TYRLd 20 ARG 0.015 0.001 ARGLS 3 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 57713.87 seconds wall clock time: 999 minutes 40.62 seconds (59980.62 seconds total)