Starting phenix.real_space_refine on Tue Feb 20 12:50:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9v_35285/02_2024/8i9v_35285_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9v_35285/02_2024/8i9v_35285.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9v_35285/02_2024/8i9v_35285.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9v_35285/02_2024/8i9v_35285.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9v_35285/02_2024/8i9v_35285_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9v_35285/02_2024/8i9v_35285_updated.pdb" } resolution = 3.1 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= 0.000 sd= 0.010 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: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 2411 5.49 5 S 265 5.16 5 C 77568 2.51 5 N 25498 2.21 5 O 32256 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "CA PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CA TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CA ASP 99": "OD1" <-> "OD2" Residue "CA PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CA PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CA GLU 233": "OE1" <-> "OE2" Residue "CA PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CB GLU 93": "OE1" <-> "OE2" Residue "CB PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CB PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CB GLU 219": "OE1" <-> "OE2" Residue "CB GLU 260": "OE1" <-> "OE2" Residue "CB GLU 268": "OE1" <-> "OE2" Residue "CB PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CB TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CC ASP 142": "OD1" <-> "OD2" Residue "CC ASP 161": "OD1" <-> "OD2" Residue "CC GLU 260": "OE1" <-> "OE2" Residue "CC TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE TYR 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE GLU 482": "OE1" <-> "OE2" Residue "CE PHE 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CF PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CF TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CF TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CF GLU 236": "OE1" <-> "OE2" Residue "CG ASP 22": "OD1" <-> "OD2" Residue "CG TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CG GLU 128": "OE1" <-> "OE2" Residue "CG PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CG ASP 169": "OD1" <-> "OD2" Residue "CH ASP 86": "OD1" <-> "OD2" Residue "CH ASP 88": "OD1" <-> "OD2" Residue "CH PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH ASP 144": "OD1" <-> "OD2" Residue "CH ASP 150": "OD1" <-> "OD2" Residue "CH ASP 190": "OD1" <-> "OD2" Residue "CH TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH ASP 219": "OD1" <-> "OD2" Residue "CH ASP 225": "OD1" <-> "OD2" Residue "CH PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH ASP 290": "OD1" <-> "OD2" Residue "CH ASP 298": "OD1" <-> "OD2" Residue "CH GLU 325": "OE1" <-> "OE2" Residue "CH GLU 408": "OE1" <-> "OE2" Residue "CH TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH ASP 451": "OD1" <-> "OD2" Residue "CH ASP 455": "OD1" <-> "OD2" Residue "CH PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CI PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CI TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CJ TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CJ PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CK GLU 112": "OE1" <-> "OE2" Residue "CK TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CL GLU 35": "OE1" <-> "OE2" Residue "CL ASP 52": "OD1" <-> "OD2" Residue "CM GLU 188": "OE1" <-> "OE2" Residue "CN TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CN GLU 214": "OE1" <-> "OE2" Residue "CN PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CP PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CP ASP 319": "OD1" <-> "OD2" Residue "CP TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CP PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CP PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CP PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CP ASP 451": "OD1" <-> "OD2" Residue "CP ASP 496": "OD1" <-> "OD2" Residue "CP PHE 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CP PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CQ PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CQ PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CR ASP 212": "OD1" <-> "OD2" Residue "CR TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CU PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CU PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CU PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CU GLU 353": "OE1" <-> "OE2" Residue "CU GLU 365": "OE1" <-> "OE2" Residue "CX PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cb GLU 14": "OE1" <-> "OE2" Residue "Cb PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cb ASP 188": "OD1" <-> "OD2" Residue "Cb ASP 212": "OD1" <-> "OD2" Residue "Cb TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cb ASP 244": "OD1" <-> "OD2" Residue "Cb PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cb ASP 327": "OD1" <-> "OD2" Residue "Cb PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cb PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cb TYR 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cb GLU 562": "OE1" <-> "OE2" Residue "Cb TYR 597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cb PHE 709": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cb ASP 711": "OD1" <-> "OD2" Residue "Cb PHE 808": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cb PHE 813": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cb GLU 814": "OE1" <-> "OE2" Residue "LB TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB GLU 181": "OE1" <-> "OE2" Residue "LB GLU 211": "OE1" <-> "OE2" Residue "LB ASP 213": "OD1" <-> "OD2" Residue "LB GLU 214": "OE1" <-> "OE2" Residue "LB ASP 300": "OD1" <-> "OD2" Residue "LB ASP 361": "OD1" <-> "OD2" Residue "LB PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LC GLU 221": "OE1" <-> "OE2" Residue "LE TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LE PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LF PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LG TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LG GLU 121": "OE1" <-> "OE2" Residue "LG PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LG GLU 227": "OE1" <-> "OE2" Residue "LH TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LH TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LK GLU 111": "OE1" <-> "OE2" Residue "LK PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LK ASP 124": "OD1" <-> "OD2" Residue "LK ASP 144": "OD1" <-> "OD2" Residue "LL GLU 79": "OE1" <-> "OE2" Residue "LN PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LO GLU 40": "OE1" <-> "OE2" Residue "LO ASP 115": "OD1" <-> "OD2" Residue "LO TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LO GLU 159": "OE1" <-> "OE2" Residue "LP GLU 31": "OE1" <-> "OE2" Residue "LP PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LS TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LS PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LT TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LT ASP 104": "OD1" <-> "OD2" Residue "LV TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ld PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Le PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Le PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lf TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lf PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lh PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Li PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Li TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lq TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cc PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Cd GLU 42": "OE1" <-> "OE2" Residue "Cd GLU 337": "OE1" <-> "OE2" Residue "Cd GLU 364": "OE1" <-> "OE2" Residue "Cd GLU 369": "OE1" <-> "OE2" Residue "Cd GLU 392": "OE1" <-> "OE2" Time to flip residues: 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 138001 Number of models: 1 Model: "" Number of chains: 60 Chain: "C1" Number of atoms: 46025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2152, 46025 Classifications: {'RNA': 2152} Modifications used: {'rna2p_pur': 216, 'rna2p_pyr': 148, 'rna3p_pur': 963, 'rna3p_pyr': 825} Link IDs: {'rna2p': 363, 'rna3p': 1788} Chain breaks: 17 Chain: "C2" Number of atoms: 3359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3359 Classifications: {'RNA': 158} Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 13, 'rna3p_pur': 63, 'rna3p_pyr': 65} Link IDs: {'rna2p': 29, 'rna3p': 128} Chain: "C3" Number of atoms: 2097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 2097 Classifications: {'RNA': 98} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 8, 'rna3p_pur': 40, 'rna3p_pyr': 39} Link IDs: {'rna2p': 19, 'rna3p': 78} Chain breaks: 1 Chain: "CA" Number of atoms: 2144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2144 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 11, 'TRANS': 248} Chain breaks: 2 Chain: "CB" Number of atoms: 2063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2063 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 20, 'TRANS': 239} Chain breaks: 1 Chain: "CC" Number of atoms: 2388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2388 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 38, 'TRANS': 250} Chain breaks: 2 Chain: "CE" Number of atoms: 3673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3673 Classifications: {'peptide': 463} Link IDs: {'PTRANS': 21, 'TRANS': 441} Chain breaks: 1 Chain: "CF" Number of atoms: 1945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1945 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 11, 'TRANS': 233} Chain: "CG" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1396 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 7, 'TRANS': 169} Chain: "CH" Number of atoms: 3851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3851 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 23, 'TRANS': 452} Chain: "CI" Number of atoms: 1196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1196 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain: "CJ" Number of atoms: 3109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3109 Classifications: {'peptide': 380} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 354} Chain breaks: 2 Chain: "CK" Number of atoms: 1855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1855 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 11, 'TRANS': 220} Chain breaks: 2 Chain: "CL" Number of atoms: 2173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2173 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 255} Link IDs: {'CIS': 1, 'PTRANS': 33, 'TRANS': 355} Chain breaks: 2 Unresolved chain link angles: 27 Unresolved non-hydrogen bonds: 891 Unresolved non-hydrogen angles: 1142 Unresolved non-hydrogen dihedrals: 732 Unresolved non-hydrogen chiralities: 96 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 5, 'TYR:plan': 6, 'ASN:plan1': 9, 'TRP:plan': 3, 'ASP:plan': 17, 'PHE:plan': 8, 'GLU:plan': 8, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 416 Chain: "CM" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1525 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain breaks: 1 Chain: "CN" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1856 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 8, 'TRANS': 237} 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: "CP" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2535 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 19, 'TRANS': 304} Chain: "CQ" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 960 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain: "CR" Number of atoms: 1354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1354 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 8, 'TRANS': 158} Chain breaks: 3 Chain: "CS" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 1750 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 181} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 282} Chain breaks: 1 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 664 Unresolved non-hydrogen angles: 847 Unresolved non-hydrogen dihedrals: 568 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 6, 'TRP:plan': 5, 'ASP:plan': 12, 'PHE:plan': 10, 'GLU:plan': 10, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 323 Chain: "CT" Number of atoms: 2269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 2269 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 401} Link IDs: {'PTRANS': 18, 'TRANS': 439} Chain breaks: 4 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 1454 Unresolved non-hydrogen angles: 1851 Unresolved non-hydrogen dihedrals: 1191 Unresolved non-hydrogen chiralities: 145 Planarities with less than four sites: {'GLN:plan1': 17, 'ASP:plan': 20, 'TYR:plan': 13, 'ASN:plan1': 16, 'TRP:plan': 3, 'HIS:plan': 12, 'PHE:plan': 16, 'GLU:plan': 39, 'ARG:plan': 32} Unresolved non-hydrogen planarities: 766 Chain: "CU" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1415 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 6, 'TRANS': 171} Chain breaks: 1 Chain: "CX" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 701 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 3, 'TRANS': 84} Chain: "CY" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 1608 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 286} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 311} Chain breaks: 7 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1078 Unresolved non-hydrogen angles: 1372 Unresolved non-hydrogen dihedrals: 904 Unresolved non-hydrogen chiralities: 104 Planarities with less than four sites: {'GLN:plan1': 13, 'HIS:plan': 4, 'TYR:plan': 8, 'ASN:plan1': 10, 'TRP:plan': 7, 'ASP:plan': 9, 'PHE:plan': 14, 'GLU:plan': 22, 'ARG:plan': 30} Unresolved non-hydrogen planarities: 570 Chain: "Cz" Number of atoms: 592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 592 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "Cb" Number of atoms: 5058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 5058 Classifications: {'peptide': 642} Link IDs: {'PTRANS': 34, 'TRANS': 607} Chain breaks: 5 Chain: "LB" Number of atoms: 2708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2708 Classifications: {'peptide': 341} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 328} Chain breaks: 1 Chain: "LC" Number of atoms: 2752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2752 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 24, 'TRANS': 337} Chain: "LE" Number of atoms: 1338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1338 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 158} Chain breaks: 1 Chain: "LF" Number of atoms: 1967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1967 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 12, 'TRANS': 227} Chain: "LG" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1583 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 8, 'TRANS': 187} Chain breaks: 1 Chain: "LH" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1496 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 5, 'TRANS': 184} Chain: "LK" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1112 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain breaks: 1 Chain: "LL" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 964 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 8, 'TRANS': 108} Chain: "LM" Number of atoms: 1101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1101 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 7, 'TRANS': 129} Chain: "LN" Number of atoms: 1563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1563 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 177} Chain breaks: 1 Chain: "LO" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1618 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 10, 'TRANS': 193} Chain: "LP" Number of atoms: 1212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1212 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 6, 'TRANS': 147} Chain breaks: 1 Chain: "LQ" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1021 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 7, 'TRANS': 121} Chain: "LS" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1433 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 10, 'TRANS': 163} Chain: "LT" Number of atoms: 1014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1014 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 7, 'TRANS': 118} Chain: "LV" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 995 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 125} Chain: "LX" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 148 Classifications: {'peptide': 22} Link IDs: {'TRANS': 21} Chain: "LY" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1065 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 6, 'TRANS': 127} Chain: "Ld" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 890 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "Le" Number of atoms: 1055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1055 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} 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: "Lh" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 995 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "Li" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 731 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "Lj" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 595 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "Lq" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1600 Classifications: {'peptide': 207} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 197} Chain: "Cc" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1898 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 7, 'TRANS': 228} Chain breaks: 1 Chain: "Cd" Number of atoms: 2763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2763 Classifications: {'peptide': 342} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 319} Chain breaks: 3 Chain: "Ce" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1609 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 8, 'TRANS': 185} Chain: "Cf" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 513 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "CH" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 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: "Lj" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Ce" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 83708 SG CYSCQ 6 137.483 48.298 203.768 1.00 59.61 S ATOM 83736 SG CYSCQ 9 140.747 46.881 202.757 1.00 84.57 S ATOM 83921 SG CYSCQ 32 140.785 49.663 205.004 1.00 91.25 S ATOM 83953 SG CYSCQ 36 140.184 50.034 201.189 1.00 73.76 S ATOM A0MEG SG CYSLj 19 171.379 122.659 136.796 1.00 62.00 S ATOM A0MF8 SG CYSLj 22 172.816 124.188 139.899 1.00 73.38 S ATOM A0MHY SG CYSLj 34 169.072 124.354 139.233 1.00 59.60 S ATOM A0MIF SG CYSLj 37 171.235 126.466 137.124 1.00 49.26 S ATOM A0RW0 SG CYSCe 38 201.541 171.007 196.024 1.00 74.98 S ATOM A0RX4 SG CYSCe 43 203.775 174.458 194.902 1.00 62.89 S Time building chain proxies: 52.33, per 1000 atoms: 0.38 Number of scatterers: 138001 At special positions: 0 Unit cell: (260.205, 263.34, 316.635, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 265 16.00 P 2411 15.00 O 32256 8.00 N 25498 7.00 C 77568 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: 49.64 Conformation dependent library (CDL) restraints added in 12.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNCQ1000 " pdb="ZN ZNCQ1000 " - pdb=" SG CYSCQ 36 " pdb="ZN ZNCQ1000 " - pdb=" SG CYSCQ 9 " pdb="ZN ZNCQ1000 " - pdb=" SG CYSCQ 32 " pdb="ZN ZNCQ1000 " - pdb=" SG CYSCQ 6 " pdb=" ZNCe1000 " pdb="ZN ZNCe1000 " - pdb=" SG CYSCe 43 " pdb="ZN ZNCe1000 " - pdb=" SG CYSCe 38 " pdb=" ZNLj 101 " pdb="ZN ZNLj 101 " - pdb=" SG CYSLj 19 " pdb="ZN ZNLj 101 " - pdb=" SG CYSLj 34 " pdb="ZN ZNLj 101 " - pdb=" SG CYSLj 37 " pdb="ZN ZNLj 101 " - pdb=" SG CYSLj 22 " Number of angles added : 12 22210 Ramachandran restraints generated. 11105 Oldfield, 0 Emsley, 11105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 21256 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: 433 helices and 80 sheets defined 51.7% alpha, 11.5% beta 793 base pairs and 1291 stacking pairs defined. Time for finding SS restraints: 79.20 Creating SS restraints... Processing helix chain 'CA' and resid 45 through 60 removed outlier: 3.710A pdb=" N METCA 58 " --> pdb=" O ASPCA 54 " (cutoff:3.500A) Proline residue: CA 60 - end of helix Processing helix chain 'CA' and resid 73 through 85 removed outlier: 3.797A pdb=" N LEUCA 77 " --> pdb=" O ARGCA 73 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N CYSCA 78 " --> pdb=" O LEUCA 74 " (cutoff:3.500A) Processing helix chain 'CA' and resid 143 through 149 removed outlier: 3.666A pdb=" N GLUCA 149 " --> pdb=" O ALACA 145 " (cutoff:3.500A) Processing helix chain 'CA' and resid 150 through 164 Processing helix chain 'CA' and resid 263 through 295 Processing helix chain 'CA' and resid 310 through 315 Processing helix chain 'CB' and resid 19 through 40 removed outlier: 3.795A pdb=" N THRCB 23 " --> pdb=" O ASPCB 19 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N CYSCB 27 " --> pdb=" O THRCB 23 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYSCB 28 " --> pdb=" O LEUCB 24 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALACB 29 " --> pdb=" O LYSCB 25 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEUCB 30 " --> pdb=" O ALACB 26 " (cutoff:3.500A) Processing helix chain 'CB' and resid 52 through 60 removed outlier: 3.646A pdb=" N GLUCB 59 " --> pdb=" O SERCB 55 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THRCB 60 " --> pdb=" O THRCB 56 " (cutoff:3.500A) Processing helix chain 'CB' and resid 74 through 79 removed outlier: 4.199A pdb=" N GLNCB 79 " --> pdb=" O SERCB 75 " (cutoff:3.500A) Processing helix chain 'CB' and resid 104 through 115 removed outlier: 5.018A pdb=" N TYRCB 108 " --> pdb=" O PROCB 104 " (cutoff:3.500A) Processing helix chain 'CB' and resid 118 through 123 removed outlier: 5.027A pdb=" N ALACB 122 " --> pdb=" O GLUCB 118 " (cutoff:3.500A) Processing helix chain 'CB' and resid 129 through 136 Processing helix chain 'CB' and resid 139 through 151 removed outlier: 3.538A pdb=" N HISCB 150 " --> pdb=" O LEUCB 146 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ASPCB 151 " --> pdb=" O PHECB 147 " (cutoff:3.500A) Processing helix chain 'CB' and resid 156 through 167 removed outlier: 5.198A pdb=" N ASNCB 161 " --> pdb=" O THRCB 157 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ARGCB 162 " --> pdb=" O ARGCB 158 " (cutoff:3.500A) Proline residue: CB 164 - end of helix Processing helix chain 'CB' and resid 216 through 230 removed outlier: 3.882A pdb=" N VALCB 221 " --> pdb=" O ILECB 217 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ALACB 222 " --> pdb=" O PROCB 218 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLUCB 223 " --> pdb=" O GLUCB 219 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILECB 224 " --> pdb=" O ILECB 220 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLYCB 229 " --> pdb=" O ARGCB 225 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALACB 230 " --> pdb=" O LYSCB 226 " (cutoff:3.500A) Processing helix chain 'CB' and resid 251 through 269 removed outlier: 3.533A pdb=" N ASNCB 258 " --> pdb=" O LYSCB 254 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VALCB 267 " --> pdb=" O ILECB 263 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLUCB 268 " --> pdb=" O ARGCB 264 " (cutoff:3.500A) Processing helix chain 'CB' and resid 169 through 174 Processing helix chain 'CC' and resid 202 through 213 Processing helix chain 'CC' and resid 232 through 245 Processing helix chain 'CC' and resid 277 through 283 removed outlier: 4.742A pdb=" N PHECC 281 " --> pdb=" O PROCC 277 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILECC 282 " --> pdb=" O LYSCC 278 " (cutoff:3.500A) Proline residue: CC 283 - end of helix No H-bonds generated for 'chain 'CC' and resid 277 through 283' Processing helix chain 'CC' and resid 284 through 301 Processing helix chain 'CC' and resid 308 through 316 Processing helix chain 'CC' and resid 357 through 362 removed outlier: 3.930A pdb=" N LEUCC 361 " --> pdb=" O PROCC 357 " (cutoff:3.500A) Proline residue: CC 362 - end of helix No H-bonds generated for 'chain 'CC' and resid 357 through 362' Processing helix chain 'CC' and resid 363 through 374 removed outlier: 3.603A pdb=" N ARGCC 367 " --> pdb=" O THRCC 363 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N METCC 373 " --> pdb=" O GLUCC 369 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N ASPCC 374 " --> pdb=" O TRPCC 370 " (cutoff:3.500A) Processing helix chain 'CC' and resid 389 through 394 removed outlier: 3.507A pdb=" N VALCC 393 " --> pdb=" O SERCC 389 " (cutoff:3.500A) Proline residue: CC 394 - end of helix No H-bonds generated for 'chain 'CC' and resid 389 through 394' Processing helix chain 'CC' and resid 398 through 412 Processing helix chain 'CE' and resid 112 through 117 removed outlier: 3.928A pdb=" N LEUCE 116 " --> pdb=" O GLUCE 112 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ASNCE 117 " --> pdb=" O PHECE 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'CE' and resid 112 through 117' Processing helix chain 'CE' and resid 119 through 130 removed outlier: 3.565A pdb=" N GLYCE 130 " --> pdb=" O ILECE 126 " (cutoff:3.500A) Processing helix chain 'CE' and resid 135 through 148 Proline residue: CE 143 - end of helix Processing helix chain 'CE' and resid 160 through 177 removed outlier: 3.559A pdb=" N PHECE 165 " --> pdb=" O LYSCE 161 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEUCE 166 " --> pdb=" O THRCE 162 " (cutoff:3.500A) Proline residue: CE 168 - end of helix Processing helix chain 'CE' and resid 192 through 208 removed outlier: 3.533A pdb=" N ALACE 196 " --> pdb=" O THRCE 192 " (cutoff:3.500A) Processing helix chain 'CE' and resid 222 through 233 removed outlier: 3.584A pdb=" N GLUCE 228 " --> pdb=" O ARGCE 224 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLYCE 233 " --> pdb=" O LYSCE 229 " (cutoff:3.500A) Processing helix chain 'CE' and resid 240 through 250 Processing helix chain 'CE' and resid 265 through 273 removed outlier: 3.541A pdb=" N GLYCE 273 " --> pdb=" O ILECE 269 " (cutoff:3.500A) Processing helix chain 'CE' and resid 274 through 286 Proline residue: CE 286 - end of helix Processing helix chain 'CE' and resid 300 through 311 removed outlier: 3.523A pdb=" N GLUCE 304 " --> pdb=" O THRCE 300 " (cutoff:3.500A) Processing helix chain 'CE' and resid 343 through 356 Processing helix chain 'CE' and resid 366 through 381 Processing helix chain 'CE' and resid 392 through 406 Processing helix chain 'CE' and resid 414 through 422 removed outlier: 4.530A pdb=" N GLYCE 420 " --> pdb=" O VALCE 416 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEUCE 421 " --> pdb=" O ALACE 417 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ASPCE 422 " --> pdb=" O ALACE 418 " (cutoff:3.500A) Processing helix chain 'CE' and resid 437 through 451 removed outlier: 3.630A pdb=" N GLYCE 446 " --> pdb=" O ILECE 442 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARGCE 450 " --> pdb=" O GLYCE 446 " (cutoff:3.500A) Processing helix chain 'CE' and resid 466 through 477 removed outlier: 4.878A pdb=" N LEUCE 470 " --> pdb=" O GLUCE 466 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALACE 471 " --> pdb=" O LEUCE 467 " (cutoff:3.500A) Processing helix chain 'CE' and resid 493 through 504 Processing helix chain 'CE' and resid 505 through 525 removed outlier: 3.813A pdb=" N HISCE 525 " --> pdb=" O ALACE 521 " (cutoff:3.500A) Processing helix chain 'CE' and resid 532 through 537 removed outlier: 4.065A pdb=" N LEUCE 536 " --> pdb=" O ASPCE 532 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ASPCE 537 " --> pdb=" O VALCE 533 " (cutoff:3.500A) No H-bonds generated for 'chain 'CE' and resid 532 through 537' Processing helix chain 'CE' and resid 538 through 546 Processing helix chain 'CF' and resid 19 through 37 removed outlier: 3.602A 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: 4.673A pdb=" N LYSCF 54 " --> pdb=" O ASNCF 50 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ASPCF 55 " --> pdb=" O ASNCF 51 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASNCF 61 " --> pdb=" O ARGCF 57 " (cutoff:3.500A) Processing helix chain 'CF' and resid 69 through 78 Processing helix chain 'CF' and resid 88 through 97 removed outlier: 3.728A pdb=" N LEUCF 92 " --> pdb=" O GLYCF 88 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARGCF 94 " --> pdb=" O HISCF 90 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N THRCF 97 " --> pdb=" O THRCF 93 " (cutoff:3.500A) Processing helix chain 'CF' and resid 108 through 119 removed outlier: 3.724A pdb=" N ILECF 112 " --> pdb=" O ASPCF 108 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLUCF 113 " --> pdb=" O PROCF 109 " (cutoff:3.500A) Processing helix chain 'CF' and resid 158 through 169 removed outlier: 4.246A pdb=" N GLUCF 162 " --> pdb=" O SERCF 158 " (cutoff:3.500A) Proline residue: CF 163 - end of helix Processing helix chain 'CF' and resid 202 through 213 Processing helix chain 'CF' and resid 238 through 243 removed outlier: 4.505A pdb=" N THRCF 242 " --> pdb=" O GLUCF 238 " (cutoff:3.500A) Processing helix chain 'CG' and resid 5 through 20 removed outlier: 3.533A pdb=" N ILECG 11 " --> pdb=" O GLNCG 7 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TYRCG 19 " --> pdb=" O LYSCG 15 " (cutoff:3.500A) Processing helix chain 'CG' and resid 22 through 28 removed outlier: 4.354A pdb=" N LEUCG 26 " --> pdb=" O ASPCG 22 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILECG 27 " --> pdb=" O LEUCG 23 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALACG 28 " --> pdb=" O LYSCG 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'CG' and resid 22 through 28' Processing helix chain 'CG' and resid 49 through 58 removed outlier: 3.613A pdb=" N THRCG 57 " --> pdb=" O ALACG 53 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N CYSCG 58 " --> pdb=" O ASNCG 54 " (cutoff:3.500A) Processing helix chain 'CG' and resid 83 through 94 removed outlier: 4.009A pdb=" N LEUCG 87 " --> pdb=" O HISCG 83 " (cutoff:3.500A) Proline residue: CG 88 - end of helix removed outlier: 3.570A pdb=" N GLNCG 92 " --> pdb=" O PROCG 88 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASNCG 93 " --> pdb=" O ILECG 89 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALACG 94 " --> pdb=" O LEUCG 90 " (cutoff:3.500A) Processing helix chain 'CG' and resid 101 through 111 removed outlier: 3.724A pdb=" N GLNCG 106 " --> pdb=" O ASPCG 102 " (cutoff:3.500A) Proline residue: CG 107 - end of helix Processing helix chain 'CG' and resid 151 through 157 removed outlier: 5.107A pdb=" N ARGCG 155 " --> pdb=" O THRCG 151 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARGCG 156 " --> pdb=" O ALACG 152 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEUCG 157 " --> pdb=" O GLUCG 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'CG' and resid 151 through 157' Processing helix chain 'CG' and resid 170 through 177 removed outlier: 4.590A pdb=" N LEUCG 174 " --> pdb=" O CYSCG 170 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARGCG 175 " --> pdb=" O GLYCG 171 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASPCG 176 " --> pdb=" O GLUCG 172 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N GLUCG 177 " --> pdb=" O TYRCG 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'CG' and resid 170 through 177' Processing helix chain 'CH' and resid 12 through 27 Processing helix chain 'CH' and resid 37 through 66 Processing helix chain 'CH' and resid 74 through 85 removed outlier: 3.706A pdb=" N TYRCH 85 " --> pdb=" O METCH 81 " (cutoff:3.500A) Processing helix chain 'CH' and resid 86 through 118 removed outlier: 3.738A pdb=" N VALCH 92 " --> pdb=" O ASPCH 88 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARGCH 113 " --> pdb=" O ARGCH 109 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYRCH 117 " --> pdb=" O ARGCH 113 " (cutoff:3.500A) Processing helix chain 'CH' and resid 120 through 144 removed outlier: 3.511A pdb=" N LYSCH 143 " --> pdb=" O ILECH 139 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ASPCH 144 " --> pdb=" O LYSCH 140 " (cutoff:3.500A) Processing helix chain 'CH' and resid 145 through 159 removed outlier: 3.604A pdb=" N LEUCH 159 " --> pdb=" O HISCH 155 " (cutoff:3.500A) Processing helix chain 'CH' and resid 178 through 187 Processing helix chain 'CH' and resid 232 through 245 removed outlier: 3.815A pdb=" N SERCH 238 " --> pdb=" O ILECH 234 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALACH 241 " --> pdb=" O GLNCH 237 " (cutoff:3.500A) Processing helix chain 'CH' and resid 262 through 278 Proline residue: CH 275 - end of helix Processing helix chain 'CH' and resid 288 through 293 removed outlier: 3.823A pdb=" N LYSCH 292 " --> pdb=" O LYSCH 288 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYSCH 293 " --> pdb=" O METCH 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'CH' and resid 288 through 293' Processing helix chain 'CH' and resid 298 through 312 removed outlier: 3.866A pdb=" N GLNCH 302 " --> pdb=" O ASPCH 298 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLUCH 304 " --> pdb=" O GLUCH 300 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SERCH 311 " --> pdb=" O ASPCH 307 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N GLYCH 312 " --> pdb=" O LEUCH 308 " (cutoff:3.500A) Processing helix chain 'CH' and resid 326 through 352 removed outlier: 3.659A pdb=" N VALCH 334 " --> pdb=" O VALCH 330 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLYCH 350 " --> pdb=" O LYSCH 346 " (cutoff:3.500A) Processing helix chain 'CH' and resid 358 through 370 removed outlier: 5.548A pdb=" N VALCH 370 " --> pdb=" O ALACH 366 " (cutoff:3.500A) Processing helix chain 'CH' and resid 384 through 390 removed outlier: 4.385A pdb=" N LYSCH 388 " --> pdb=" O PROCH 384 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ASNCH 389 " --> pdb=" O GLUCH 385 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEUCH 390 " --> pdb=" O ALACH 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'CH' and resid 384 through 390' Processing helix chain 'CH' and resid 403 through 412 Processing helix chain 'CH' and resid 420 through 426 removed outlier: 4.627A pdb=" N ASPCH 424 " --> pdb=" O ASPCH 420 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N TRPCH 425 " --> pdb=" O LEUCH 421 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ILECH 426 " --> pdb=" O ARGCH 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'CH' and resid 420 through 426' Processing helix chain 'CH' and resid 445 through 450 removed outlier: 4.137A pdb=" N TYRCH 449 " --> pdb=" O ASNCH 445 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILECH 450 " --> pdb=" O VALCH 446 " (cutoff:3.500A) No H-bonds generated for 'chain 'CH' and resid 445 through 450' Processing helix chain 'CH' and resid 453 through 472 Processing helix chain 'CH' and resid 429 through 435 removed outlier: 5.423A pdb=" N TYRCH 434 " --> pdb=" O GLUCH 431 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASPCH 435 " --> pdb=" O TRPCH 432 " (cutoff:3.500A) Processing helix chain 'CI' and resid 199 through 211 removed outlier: 3.521A pdb=" N PHECI 207 " --> pdb=" O LEUCI 203 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLNCI 209 " --> pdb=" O GLYCI 205 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHECI 210 " --> pdb=" O TYRCI 206 " (cutoff:3.500A) Processing helix chain 'CI' and resid 237 through 249 Processing helix chain 'CI' and resid 284 through 296 removed outlier: 3.906A pdb=" N LEUCI 293 " --> pdb=" O ALACI 289 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLUCI 294 " --> pdb=" O GLYCI 290 " (cutoff:3.500A) Proline residue: CI 296 - end of helix Processing helix chain 'CI' and resid 298 through 322 removed outlier: 3.773A pdb=" N GLNCI 311 " --> pdb=" O ALACI 307 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARGCI 312 " --> pdb=" O LYSCI 308 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALACI 314 " --> pdb=" O GLUCI 310 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALACI 315 " --> pdb=" O GLNCI 311 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLUCI 322 " --> pdb=" O GLUCI 318 " (cutoff:3.500A) Processing helix chain 'CI' and resid 269 through 274 removed outlier: 4.488A pdb=" N PHECI 273 " --> pdb=" O PROCI 270 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYSCI 274 " --> pdb=" O ASPCI 271 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 6 through 11 removed outlier: 4.915A pdb=" N GLYCJ 11 " --> pdb=" O LYSCJ 7 " (cutoff:3.500A) 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 Processing helix chain 'CJ' and resid 65 through 98 removed outlier: 3.763A pdb=" N ILECJ 69 " --> pdb=" O TYRCJ 65 " (cutoff:3.500A) Proline residue: CJ 76 - end of helix removed outlier: 3.526A pdb=" N SERCJ 92 " --> pdb=" O GLUCJ 88 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALACJ 94 " --> pdb=" O LYSCJ 90 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEUCJ 95 " --> pdb=" O ILECJ 91 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 99 through 111 Processing helix chain 'CJ' and resid 112 through 117 removed outlier: 3.618A pdb=" N THRCJ 116 " --> pdb=" O LEUCJ 112 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 123 through 132 Proline residue: CJ 132 - end of helix Processing helix chain 'CJ' and resid 135 through 153 removed outlier: 3.745A pdb=" N ASPCJ 142 " --> pdb=" O LEUCJ 138 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ASPCJ 143 " --> pdb=" O ARGCJ 139 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SERCJ 146 " --> pdb=" O ASPCJ 142 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 161 through 183 Processing helix chain 'CJ' and resid 223 through 250 removed outlier: 3.546A 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 368 removed outlier: 5.322A pdb=" N PHECJ 367 " --> pdb=" O PROCJ 363 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALACJ 368 " --> pdb=" O SERCJ 364 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 379 through 391 removed outlier: 3.569A pdb=" N ILECJ 386 " --> pdb=" O PROCJ 382 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 457 through 468 removed outlier: 3.670A pdb=" N VALCJ 461 " --> pdb=" O GLNCJ 457 " (cutoff:3.500A) Processing helix 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: 4.627A pdb=" N GLYCK 32 " --> pdb=" O ALACK 28 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N HISCK 33 " --> pdb=" O ALACK 29 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SERCK 36 " --> pdb=" O GLYCK 32 " (cutoff:3.500A) Processing helix chain 'CK' and resid 44 through 75 removed outlier: 6.258A pdb=" N LYSCK 48 " --> pdb=" O GLYCK 44 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEUCK 49 " --> pdb=" O LEUCK 45 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYRCK 50 " --> pdb=" O ARGCK 46 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N GLYCK 75 " --> pdb=" O ARGCK 71 " (cutoff:3.500A) Processing helix chain 'CK' and resid 98 through 116 removed outlier: 3.656A pdb=" N LYSCK 113 " --> pdb=" O LYSCK 109 " (cutoff:3.500A) Processing helix chain 'CK' and resid 128 through 139 removed outlier: 3.591A pdb=" N METCK 132 " --> pdb=" O SERCK 128 " (cutoff:3.500A) Processing helix chain 'CK' and resid 165 through 170 removed outlier: 5.047A pdb=" N ARGCK 170 " --> pdb=" O VALCK 166 " (cutoff:3.500A) Processing helix chain 'CK' and resid 206 through 213 removed outlier: 3.672A pdb=" N GLNCK 211 " --> pdb=" O PROCK 207 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEUCK 212 " --> pdb=" O LEUCK 208 " (cutoff:3.500A) Processing helix chain 'CK' and resid 248 through 253 removed outlier: 4.360A pdb=" N GLYCK 253 " --> pdb=" O PROCK 249 " (cutoff:3.500A) Processing helix chain 'CL' and resid 17 through 42 Processing helix chain 'CL' and resid 61 through 80 removed outlier: 3.575A pdb=" N LEUCL 65 " --> pdb=" O TYRCL 61 " (cutoff:3.500A) Processing helix chain 'CL' and resid 190 through 205 removed outlier: 4.910A pdb=" N LYSCL 196 " --> pdb=" O LYSCL 192 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N VALCL 197 " --> pdb=" O ALACL 193 " (cutoff:3.500A) Processing helix chain 'CL' and resid 216 through 233 removed outlier: 5.214A pdb=" N SERCL 222 " --> pdb=" O GLUCL 218 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N HISCL 223 " --> pdb=" O GLYCL 219 " (cutoff:3.500A) removed outlier: 8.911A pdb=" N ASPCL 224 " --> pdb=" O THRCL 220 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VALCL 225 " --> pdb=" O ARGCL 221 " (cutoff:3.500A) Processing helix chain 'CL' and resid 245 through 250 removed outlier: 4.754A pdb=" N VALCL 249 " --> pdb=" O LYSCL 245 " (cutoff:3.500A) Proline residue: CL 250 - end of helix No H-bonds generated for 'chain 'CL' and resid 245 through 250' Processing helix chain 'CL' and resid 251 through 265 removed outlier: 3.682A pdb=" N ARGCL 263 " --> pdb=" O THRCL 259 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N PHECL 264 " --> pdb=" O TYRCL 260 " (cutoff:3.500A) Processing helix chain 'CL' and resid 292 through 308 Processing helix chain 'CL' and resid 324 through 335 Processing helix chain 'CL' and resid 395 through 402 removed outlier: 5.632A pdb=" N LEUCL 399 " --> pdb=" O ALACL 395 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VALCL 400 " --> pdb=" O HISCL 396 " (cutoff:3.500A) Processing helix chain 'CL' and resid 413 through 428 removed outlier: 5.849A pdb=" N VALCL 417 " --> pdb=" O PROCL 413 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THRCL 427 " --> pdb=" O ARGCL 423 " (cutoff:3.500A) Proline residue: CL 428 - end of helix Processing helix chain 'CL' and resid 429 through 439 Processing helix chain 'CL' and resid 450 through 466 removed outlier: 3.576A pdb=" N THRCL 454 " --> pdb=" O GLYCL 450 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N METCL 455 " --> pdb=" O GLYCL 451 " (cutoff:3.500A) Processing helix chain 'CL' and resid 475 through 490 Processing helix chain 'CL' and resid 3 through 8 Proline residue: CL 8 - end of helix No H-bonds generated for 'chain 'CL' and resid 3 through 8' Processing helix chain 'CM' and resid 53 through 78 removed outlier: 3.536A pdb=" N TYRCM 57 " --> pdb=" O ARGCM 53 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYSCM 59 " --> pdb=" O GLUCM 55 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLNCM 78 " --> pdb=" O ILECM 74 " (cutoff:3.500A) Processing helix chain 'CM' and resid 102 through 113 removed outlier: 3.554A pdb=" N ILECM 108 " --> pdb=" O LYSCM 104 " (cutoff:3.500A) Processing helix chain 'CM' and resid 126 through 137 removed outlier: 3.877A pdb=" N GLUCM 131 " --> pdb=" O LYSCM 127 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VALCM 136 " --> pdb=" O METCM 132 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLUCM 137 " --> pdb=" O ILECM 133 " (cutoff:3.500A) Processing helix chain 'CM' and resid 146 through 157 Processing helix chain 'CM' and resid 171 through 179 removed outlier: 3.614A pdb=" N ILECM 175 " --> pdb=" O ASPCM 171 " (cutoff:3.500A) Processing helix chain 'CM' and resid 186 through 197 removed outlier: 3.544A pdb=" N LEUCM 190 " --> pdb=" O CYSCM 186 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VALCM 197 " --> pdb=" O GLUCM 193 " (cutoff:3.500A) Processing helix chain 'CM' and resid 200 through 209 removed outlier: 5.298A pdb=" N TRPCM 209 " --> pdb=" O ALACM 205 " (cutoff:3.500A) Processing helix chain 'CM' and resid 239 through 249 removed outlier: 3.879A pdb=" N ARGCM 246 " --> pdb=" O ASNCM 242 " (cutoff:3.500A) Processing helix chain 'CN' and resid 12 through 17 removed outlier: 3.696A pdb=" N PHECN 16 " --> pdb=" O GLUCN 12 " (cutoff:3.500A) Processing helix chain 'CN' and resid 32 through 43 removed outlier: 3.591A pdb=" N PHECN 38 " --> pdb=" O PHECN 34 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLUCN 41 " --> pdb=" O VALCN 37 " (cutoff:3.500A) Processing helix chain 'CN' and resid 58 through 63 removed outlier: 3.868A pdb=" N LEUCN 62 " --> pdb=" O ILECN 58 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THRCN 63 " --> pdb=" O ILECN 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'CN' and resid 58 through 63' Processing helix chain 'CN' and resid 77 through 88 Processing helix chain 'CN' and resid 103 through 108 Processing helix chain 'CN' and resid 122 through 134 removed outlier: 3.785A pdb=" N ILECN 128 " --> pdb=" O GLUCN 124 " (cutoff:3.500A) 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 removed outlier: 3.667A pdb=" N GLYCN 196 " --> pdb=" O VALCN 192 " (cutoff:3.500A) Processing helix chain 'CN' and resid 211 through 223 Processing helix chain 'CN' and resid 231 through 238 removed outlier: 3.781A pdb=" N THRCN 235 " --> pdb=" O GLYCN 231 " (cutoff:3.500A) Processing helix chain 'CN' and resid 239 through 246 removed outlier: 3.530A pdb=" N GLUCN 243 " --> pdb=" O ASNCN 239 " (cutoff:3.500A) Processing helix chain 'CO' and resid 7 through 20 Processing helix chain 'CO' and resid 21 through 43 removed outlier: 4.497A pdb=" N VALCO 25 " --> pdb=" O ILECO 21 " (cutoff:3.500A) Processing helix chain 'CO' and resid 83 through 88 Processing helix chain 'CP' and resid 262 through 275 Processing helix chain 'CP' and resid 277 through 289 removed outlier: 3.644A pdb=" N LEUCP 287 " --> pdb=" O LYSCP 283 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N PHECP 288 " --> pdb=" O LEUCP 284 " (cutoff:3.500A) Proline residue: CP 289 - end of helix Processing helix chain 'CP' and resid 290 through 302 removed outlier: 3.595A pdb=" N ALACP 299 " --> pdb=" O ALACP 295 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLUCP 301 " --> pdb=" O PHECP 297 " (cutoff:3.500A) Processing helix chain 'CP' and resid 316 through 328 Processing helix chain 'CP' and resid 354 through 360 Processing helix chain 'CP' and resid 366 through 377 removed outlier: 3.783A pdb=" N PHECP 370 " --> pdb=" O ALACP 366 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEUCP 371 " --> pdb=" O ALACP 367 " (cutoff:3.500A) Proline residue: CP 372 - end of helix removed outlier: 4.517A pdb=" N CYSCP 377 " --> pdb=" O VALCP 373 " (cutoff:3.500A) Processing helix chain 'CP' and resid 392 through 403 removed outlier: 3.501A pdb=" N LEUCP 401 " --> pdb=" O HISCP 397 " (cutoff:3.500A) Processing helix chain 'CP' and resid 414 through 429 removed outlier: 3.518A pdb=" N LYSCP 419 " --> pdb=" O LYSCP 415 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLYCP 420 " --> pdb=" O SERCP 416 " (cutoff:3.500A) Processing helix chain 'CP' and resid 439 through 447 removed outlier: 3.738A pdb=" N PHECP 443 " --> pdb=" O ASPCP 439 " (cutoff:3.500A) Proline residue: CP 444 - end of helix Processing helix chain 'CP' and resid 464 through 469 removed outlier: 4.049A pdb=" N ASPCP 468 " --> pdb=" O VALCP 464 " (cutoff:3.500A) Proline residue: CP 469 - end of helix No H-bonds generated for 'chain 'CP' and resid 464 through 469' Processing helix chain 'CP' and resid 476 through 499 removed outlier: 3.567A pdb=" N METCP 481 " --> pdb=" O ALACP 477 " (cutoff:3.500A) Proline residue: CP 484 - end of helix removed outlier: 3.606A pdb=" N GLNCP 489 " --> pdb=" O HISCP 485 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALACP 494 " --> pdb=" O LEUCP 490 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILECP 495 " --> pdb=" O LEUCP 491 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ASNCP 499 " --> pdb=" O ILECP 495 " (cutoff:3.500A) Processing helix chain 'CP' and resid 520 through 532 removed outlier: 6.761A pdb=" N VALCP 524 " --> pdb=" O ASNCP 520 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASNCP 525 " --> pdb=" O GLUCP 521 " (cutoff:3.500A) Proline residue: CP 532 - end of helix Processing helix chain 'CP' and resid 558 through 564 removed outlier: 4.864A pdb=" N LEUCP 562 " --> pdb=" O PROCP 558 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N THRCP 563 " --> pdb=" O SERCP 559 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ARGCP 564 " --> pdb=" O LEUCP 560 " (cutoff:3.500A) No H-bonds generated for 'chain 'CP' and resid 558 through 564' Processing helix chain 'CP' and resid 470 through 475 removed outlier: 4.903A pdb=" N ARGCP 475 " --> pdb=" O SERCP 470 " (cutoff:3.500A) No H-bonds generated for 'chain 'CP' and resid 470 through 475' Processing helix chain 'CQ' and resid 33 through 43 Processing helix chain 'CQ' and resid 45 through 50 removed outlier: 5.890A pdb=" N LYSCQ 50 " --> pdb=" O PROCQ 46 " (cutoff:3.500A) Processing helix chain 'CQ' and resid 52 through 60 removed outlier: 3.757A pdb=" N ARGCQ 56 " --> pdb=" O THRCQ 52 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLYCQ 60 " --> pdb=" O ARGCQ 56 " (cutoff:3.500A) Processing helix chain 'CQ' and resid 82 through 112 removed outlier: 3.539A pdb=" N LEUCQ 90 " --> pdb=" O TRPCQ 86 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLUCQ 94 " --> pdb=" O LEUCQ 90 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N VALCQ 106 " --> pdb=" O ARGCQ 102 " (cutoff:3.500A) Processing helix chain 'CQ' and resid 66 through 72 removed outlier: 3.666A pdb=" N GLNCQ 70 " --> pdb=" O SERCQ 67 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHECQ 71 " --> pdb=" O THRCQ 68 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALACQ 72 " --> pdb=" O LEUCQ 69 " (cutoff:3.500A) Processing helix chain 'CR' and resid 3 through 12 Processing helix chain 'CR' and resid 33 through 39 Processing helix chain 'CR' and resid 44 through 53 Processing helix chain 'CR' and resid 131 through 137 removed outlier: 4.078A pdb=" N GLNCR 135 " --> pdb=" O VALCR 131 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLNCR 136 " --> pdb=" O PROCR 132 " (cutoff:3.500A) Processing helix chain 'CR' and resid 166 through 178 Processing helix chain 'CR' and resid 188 through 202 removed outlier: 3.512A pdb=" N LYSCR 201 " --> pdb=" O ARGCR 197 " (cutoff:3.500A) Processing helix chain 'CR' and resid 205 through 213 removed outlier: 3.801A pdb=" N METCR 209 " --> pdb=" O ASPCR 205 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARGCR 211 " --> pdb=" O ALACR 207 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ARGCR 213 " --> pdb=" O METCR 209 " (cutoff:3.500A) Processing helix chain 'CR' and resid 221 through 233 Processing helix chain 'CS' and resid 14 through 24 Processing helix chain 'CS' and resid 27 through 41 removed outlier: 4.696A pdb=" N PHECS 31 " --> pdb=" O ALACS 27 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYSCS 32 " --> pdb=" O ARGCS 28 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEUCS 33 " --> pdb=" O ALACS 29 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLNCS 35 " --> pdb=" O PHECS 31 " (cutoff:3.500A) Processing helix chain 'CS' and resid 57 through 67 removed outlier: 4.370A pdb=" N METCS 67 " --> pdb=" O CYSCS 63 " (cutoff:3.500A) Processing helix chain 'CS' and resid 96 through 108 removed outlier: 3.525A pdb=" N ARGCS 100 " --> pdb=" O THRCS 96 " (cutoff:3.500A) Processing helix chain 'CS' and resid 126 through 149 removed outlier: 3.937A pdb=" N GLUCS 147 " --> pdb=" O LYSCS 143 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHECS 148 " --> pdb=" O LEUCS 144 " (cutoff:3.500A) Processing helix chain 'CS' and resid 162 through 176 removed outlier: 4.485A pdb=" N ASNCS 166 " --> pdb=" O SERCS 162 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LYSCS 167 " --> pdb=" O LYSCS 163 " (cutoff:3.500A) Processing helix chain 'CS' and resid 208 through 214 Proline residue: CS 214 - end of helix Processing helix chain 'CS' and resid 644 through 653 removed outlier: 5.306A pdb=" N GLYCS 648 " --> pdb=" O LYSCS 644 " (cutoff:3.500A) Proline residue: CS 650 - end of helix Processing helix chain 'CS' and resid 656 through 669 removed outlier: 4.978A pdb=" N GLYCS 669 " --> pdb=" O GLNCS 665 " (cutoff:3.500A) Processing helix chain 'CS' and resid 672 through 682 removed outlier: 5.139A pdb=" N ASNCS 682 " --> pdb=" O ASPCS 678 " (cutoff:3.500A) Processing helix chain 'CS' and resid 693 through 705 removed outlier: 4.745A pdb=" N LYSCS 705 " --> pdb=" O ALACS 701 " (cutoff:3.500A) Processing helix chain 'CS' and resid 711 through 723 Processing helix chain 'CT' and resid 122 through 141 Processing helix chain 'CT' and resid 145 through 158 removed outlier: 3.824A pdb=" N PHECT 149 " --> pdb=" O TYRCT 145 " (cutoff:3.500A) Processing helix chain 'CT' and resid 160 through 179 removed outlier: 3.799A pdb=" N ILECT 179 " --> pdb=" O TYRCT 175 " (cutoff:3.500A) Processing helix chain 'CT' and resid 198 through 228 removed outlier: 3.626A pdb=" N TYRCT 206 " --> pdb=" O ARGCT 202 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEUCT 218 " --> pdb=" O TYRCT 214 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYSCT 219 " --> pdb=" O HISCT 215 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THRCT 220 " --> pdb=" O GLYCT 216 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N SERCT 228 " --> pdb=" O TYRCT 224 " (cutoff:3.500A) Processing helix chain 'CT' and resid 237 through 253 removed outlier: 5.871A pdb=" N ILECT 241 " --> pdb=" O PROCT 237 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALACT 242 " --> pdb=" O ILECT 238 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALACT 252 " --> pdb=" O GLUCT 248 " (cutoff:3.500A) Processing helix chain 'CT' and resid 258 through 273 removed outlier: 3.656A pdb=" N THRCT 272 " --> pdb=" O LYSCT 268 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ARGCT 273 " --> pdb=" O LYSCT 269 " (cutoff:3.500A) Processing helix chain 'CT' and resid 276 through 293 Processing helix chain 'CT' and resid 296 through 314 removed outlier: 3.537A pdb=" N METCT 310 " --> pdb=" O LEUCT 306 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALACT 312 " --> pdb=" O LYSCT 308 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLUCT 314 " --> pdb=" O METCT 310 " (cutoff:3.500A) Processing helix chain 'CT' and resid 319 through 329 removed outlier: 3.567A pdb=" N LEUCT 326 " --> pdb=" O LEUCT 322 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEUCT 328 " --> pdb=" O LEUCT 324 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ARGCT 329 " --> pdb=" O PHECT 325 " (cutoff:3.500A) Processing helix chain 'CT' and resid 389 through 415 removed outlier: 3.580A pdb=" N VALCT 404 " --> pdb=" O ILECT 400 " (cutoff:3.500A) Processing helix chain 'CT' and resid 417 through 431 removed outlier: 3.503A pdb=" N GLYCT 421 " --> pdb=" O PROCT 417 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALACT 422 " --> pdb=" O HISCT 418 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYSCT 429 " --> pdb=" O GLUCT 425 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYRCT 430 " --> pdb=" O GLYCT 426 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALACT 431 " --> pdb=" O LEUCT 427 " (cutoff:3.500A) Processing helix chain 'CT' and resid 435 through 455 removed outlier: 3.842A pdb=" N LEUCT 443 " --> pdb=" O PHECT 439 " (cutoff:3.500A) Processing helix chain 'CT' and resid 477 through 495 removed outlier: 3.592A pdb=" N THRCT 488 " --> pdb=" O LEUCT 484 " (cutoff:3.500A) Processing helix chain 'CT' and resid 496 through 505 removed outlier: 4.700A pdb=" N SERCT 503 " --> pdb=" O HISCT 499 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASPCT 504 " --> pdb=" O ASNCT 500 " (cutoff:3.500A) Processing helix chain 'CT' and resid 509 through 527 removed outlier: 3.979A pdb=" N THRCT 514 " --> pdb=" O SERCT 510 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEUCT 521 " --> pdb=" O TYRCT 517 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N SERCT 522 " --> pdb=" O ARGCT 518 " (cutoff:3.500A) Proline residue: CT 527 - end of helix Processing helix chain 'CT' and resid 562 through 576 Processing helix chain 'CT' and resid 585 through 603 removed outlier: 3.581A pdb=" N GLNCT 602 " --> pdb=" O THRCT 598 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VALCT 603 " --> pdb=" O LEUCT 599 " (cutoff:3.500A) Processing helix chain 'CT' and resid 605 through 623 removed outlier: 3.787A pdb=" N ALACT 610 " --> pdb=" O LYSCT 606 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLNCT 616 " --> pdb=" O LEUCT 612 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ASPCT 617 " --> pdb=" O GLYCT 613 " (cutoff:3.500A) Processing helix chain 'CT' and resid 624 through 632 removed outlier: 3.956A pdb=" N ALACT 628 " --> pdb=" O ARGCT 624 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LEUCT 629 " --> pdb=" O LYSCT 625 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TRPCT 630 " --> pdb=" O VALCT 626 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASNCT 631 " --> pdb=" O ALACT 627 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N THRCT 632 " --> pdb=" O ALACT 628 " (cutoff:3.500A) No H-bonds generated for 'chain 'CT' and resid 624 through 632' Processing helix chain 'CT' and resid 647 through 652 removed outlier: 3.596A pdb=" N SERCT 651 " --> pdb=" O THRCT 647 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ASNCT 652 " --> pdb=" O VALCT 648 " (cutoff:3.500A) No H-bonds generated for 'chain 'CT' and resid 647 through 652' Processing helix chain 'CT' and resid 659 through 669 removed outlier: 3.565A pdb=" N LEUCT 663 " --> pdb=" O TRPCT 659 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYSCT 666 " --> pdb=" O GLUCT 662 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TYRCT 668 " --> pdb=" O LEUCT 664 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N CYSCT 669 " --> pdb=" O ARGCT 665 " (cutoff:3.500A) Processing helix chain 'CT' and resid 670 through 686 removed outlier: 4.507A pdb=" N GLUCT 674 " --> pdb=" O PROCT 670 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLYCT 675 " --> pdb=" O LYSCT 671 " (cutoff:3.500A) Processing helix chain 'CU' and resid 192 through 204 removed outlier: 3.509A pdb=" N ARGCU 202 " --> pdb=" O THRCU 198 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILECU 203 " --> pdb=" O ALACU 199 " (cutoff:3.500A) Processing helix chain 'CU' and resid 213 through 218 removed outlier: 4.306A pdb=" N HISCU 217 " --> pdb=" O PROCU 213 " (cutoff:3.500A) Processing helix chain 'CU' and resid 225 through 231 removed outlier: 6.515A pdb=" N SERCU 229 " --> pdb=" O ARGCU 225 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILECU 230 " --> pdb=" O THRCU 226 " (cutoff:3.500A) Proline residue: CU 231 - end of helix No H-bonds generated for 'chain 'CU' and resid 225 through 231' Processing helix chain 'CU' and resid 235 through 262 Processing helix chain 'CU' and resid 278 through 312 removed outlier: 3.515A pdb=" N LEUCU 289 " --> pdb=" O VALCU 285 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYSCU 296 " --> pdb=" O GLUCU 292 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARGCU 303 " --> pdb=" O ALACU 299 " (cutoff:3.500A) Processing helix chain 'CU' and resid 313 through 344 Processing helix chain 'CU' and resid 358 through 369 removed outlier: 5.985A pdb=" N VALCU 362 " --> pdb=" O PHECU 358 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ASPCU 363 " --> pdb=" O ASPCU 359 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASPCU 369 " --> pdb=" O GLUCU 365 " (cutoff:3.500A) Processing helix chain 'CX' and resid 65 through 70 removed outlier: 4.965A pdb=" N GLYCX 70 " --> pdb=" O GLUCX 66 " (cutoff:3.500A) Processing helix chain 'CX' and resid 98 through 114 removed outlier: 3.741A pdb=" N ALACX 110 " --> pdb=" O ALACX 106 " (cutoff:3.500A) Processing helix chain 'CX' and resid 118 through 150 Processing helix chain 'CY' and resid 371 through 389 Processing helix chain 'CY' and resid 393 through 411 removed outlier: 3.503A pdb=" N THRCY 399 " --> pdb=" O SERCY 395 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VALCY 409 " --> pdb=" O ARGCY 405 " (cutoff:3.500A) Processing helix chain 'CY' and resid 413 through 434 Processing helix chain 'CY' and resid 438 through 456 removed outlier: 3.935A pdb=" N GLUCY 451 " --> pdb=" O ASNCY 447 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEUCY 452 " --> pdb=" O SERCY 448 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEUCY 455 " --> pdb=" O GLUCY 451 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ASPCY 456 " --> pdb=" O LEUCY 452 " (cutoff:3.500A) Processing helix chain 'CY' and resid 457 through 482 removed outlier: 4.045A pdb=" N ARGCY 469 " --> pdb=" O PHECY 465 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N HISCY 474 " --> pdb=" O GLNCY 470 " (cutoff:3.500A) Processing helix chain 'CY' and resid 493 through 511 removed outlier: 3.589A pdb=" N HISCY 509 " --> pdb=" O VALCY 505 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N CYSCY 510 " --> pdb=" O LEUCY 506 " (cutoff:3.500A) Processing helix chain 'CY' and resid 527 through 543 removed outlier: 4.067A pdb=" N LEUCY 531 " --> pdb=" O LEUCY 527 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VALCY 532 " --> pdb=" O ILECY 528 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLNCY 533 " --> pdb=" O TYRCY 529 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ILECY 542 " --> pdb=" O ALACY 538 " (cutoff:3.500A) Proline residue: CY 543 - end of helix Processing helix chain 'CY' and resid 547 through 565 removed outlier: 7.177A pdb=" N ARGCY 551 " --> pdb=" O TYRCY 547 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEUCY 554 " --> pdb=" O LEUCY 550 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SERCY 562 " --> pdb=" O LEUCY 558 " (cutoff:3.500A) Processing helix chain 'CY' and resid 570 through 581 removed outlier: 5.024A pdb=" N ALACY 574 " --> pdb=" O PROCY 570 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VALCY 578 " --> pdb=" O ALACY 574 " (cutoff:3.500A) Processing helix chain 'CY' and resid 582 through 587 Proline residue: CY 587 - end of helix Processing helix chain 'CY' and resid 612 through 635 removed outlier: 5.528A pdb=" N ARGCY 635 " --> pdb=" O VALCY 631 " (cutoff:3.500A) Processing helix chain 'CY' and resid 638 through 659 Proline residue: CY 645 - end of helix Processing helix chain 'CY' and resid 666 through 692 removed outlier: 3.706A pdb=" N ALACY 692 " --> pdb=" O GLUCY 688 " (cutoff:3.500A) Processing helix chain 'CY' and resid 701 through 707 removed outlier: 5.239A pdb=" N ASPCY 705 " --> pdb=" O ARGCY 701 " (cutoff:3.500A) Processing helix chain 'CY' and resid 716 through 748 removed outlier: 3.616A pdb=" N ARGCY 732 " --> pdb=" O LEUCY 728 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYSCY 733 " --> pdb=" O ARGCY 729 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARGCY 734 " --> pdb=" O GLUCY 730 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEUCY 735 " --> pdb=" O GLUCY 731 " (cutoff:3.500A) Processing helix chain 'Cz' and resid 47 through 92 removed outlier: 3.602A pdb=" N LYSCz 53 " --> pdb=" O GLUCz 49 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 18 through 23 removed outlier: 4.948A pdb=" N PHECb 22 " --> pdb=" O ALACb 18 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ALACb 23 " --> pdb=" O GLYCb 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'Cb' and resid 18 through 23' Processing helix chain 'Cb' and resid 91 through 96 removed outlier: 3.677A pdb=" N METCb 95 " --> pdb=" O GLYCb 91 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 98 through 109 removed outlier: 3.564A pdb=" N ARGCb 103 " --> pdb=" O ALACb 99 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 114 through 127 Proline residue: Cb 122 - end of helix removed outlier: 3.707A pdb=" N LEUCb 125 " --> pdb=" O ILECb 121 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 139 through 153 removed outlier: 3.732A pdb=" N VALCb 145 " --> pdb=" O THRCb 141 " (cutoff:3.500A) Proline residue: Cb 147 - end of helix removed outlier: 3.873A pdb=" N LYSCb 153 " --> pdb=" O ILECb 149 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 169 through 185 removed outlier: 3.568A pdb=" N LYSCb 181 " --> pdb=" O LEUCb 177 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYSCb 185 " --> pdb=" O LYSCb 181 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 199 through 210 removed outlier: 4.785A pdb=" N PHECb 204 " --> pdb=" O LEUCb 200 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASNCb 210 " --> pdb=" O LEUCb 206 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 217 through 229 Processing helix chain 'Cb' and resid 242 through 250 removed outlier: 3.739A pdb=" N GLYCb 250 " --> pdb=" O LEUCb 246 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 251 through 263 Proline residue: Cb 263 - end of helix Processing helix chain 'Cb' and resid 276 through 286 removed outlier: 3.567A pdb=" N GLUCb 281 " --> pdb=" O SERCb 277 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHECb 282 " --> pdb=" O SERCb 278 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 316 through 327 Processing helix chain 'Cb' and resid 375 through 390 Processing helix chain 'Cb' and resid 401 through 415 removed outlier: 3.555A pdb=" N LYSCb 406 " --> pdb=" O GLNCb 402 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLNCb 408 " --> pdb=" O ALACb 404 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 423 through 430 removed outlier: 5.875A pdb=" N ALACb 427 " --> pdb=" O THRCb 423 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 446 through 458 removed outlier: 3.819A pdb=" N PHECb 450 " --> pdb=" O GLNCb 446 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VALCb 451 " --> pdb=" O PROCb 447 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARGCb 456 " --> pdb=" O HISCb 452 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N THRCb 457 " --> pdb=" O ARGCb 453 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ALACb 458 " --> pdb=" O VALCb 454 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 474 through 486 Processing helix chain 'Cb' and resid 510 through 528 removed outlier: 3.521A pdb=" N ASNCb 516 " --> pdb=" O VALCb 512 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VALCb 521 " --> pdb=" O ASNCb 517 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 529 through 549 removed outlier: 3.547A pdb=" N LYSCb 547 " --> pdb=" O LYSCb 543 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 553 through 567 removed outlier: 3.691A pdb=" N ARGCb 561 " --> pdb=" O ALACb 557 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLUCb 562 " --> pdb=" O LYSCb 558 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VALCb 563 " --> pdb=" O ARGCb 559 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N LYSCb 567 " --> pdb=" O VALCb 563 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 581 through 592 removed outlier: 3.573A pdb=" N ARGCb 587 " --> pdb=" O GLUCb 583 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N LEUCb 590 " --> pdb=" O VALCb 586 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 615 through 629 removed outlier: 3.540A pdb=" N ARGCb 625 " --> pdb=" O VALCb 621 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLNCb 626 " --> pdb=" O ARGCb 622 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 811 through 821 removed outlier: 3.592A pdb=" N GLNCb 818 " --> pdb=" O GLUCb 814 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HISCb 820 " --> pdb=" O TRPCb 816 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARGCb 821 " --> pdb=" O ARGCb 817 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 833 through 841 removed outlier: 3.649A pdb=" N ARGCb 838 " --> pdb=" O ALACb 834 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 865 through 880 removed outlier: 3.556A pdb=" N LYSCb 871 " --> pdb=" O GLUCb 867 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARGCb 872 " --> pdb=" O VALCb 868 " (cutoff:3.500A) Processing helix chain 'LB' and resid 111 through 120 removed outlier: 3.682A pdb=" N ARGLB 117 " --> pdb=" O GLULB 113 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N PHELB 118 " --> pdb=" O VALLB 114 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYRLB 119 " --> pdb=" O LYSLB 115 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LYSLB 120 " --> pdb=" O ARGLB 116 " (cutoff:3.500A) Processing helix chain 'LB' and resid 130 through 139 removed outlier: 3.561A pdb=" N LYSLB 135 " --> pdb=" O THRLB 131 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYRLB 137 " --> pdb=" O TYRLB 133 " (cutoff:3.500A) Processing helix chain 'LB' and resid 141 through 155 removed outlier: 3.702A pdb=" N ILELB 145 " --> pdb=" O ASNLB 141 " (cutoff:3.500A) Processing helix chain 'LB' and resid 166 through 171 removed outlier: 3.842A 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 removed outlier: 3.590A pdb=" N PHELB 200 " --> pdb=" O GLYLB 196 " (cutoff:3.500A) Processing helix chain 'LB' and resid 205 through 210 Processing helix chain 'LB' and resid 348 through 353 removed outlier: 4.861A pdb=" N LEULB 352 " --> pdb=" O SERLB 348 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLULB 353 " --> pdb=" O ARGLB 349 " (cutoff:3.500A) No H-bonds generated for 'chain 'LB' and resid 348 through 353' Processing helix chain 'LB' and resid 373 through 382 Processing helix chain 'LB' and resid 384 through 391 Processing helix chain 'LC' and resid 24 through 30 removed outlier: 4.312A pdb=" N SERLC 28 " --> pdb=" O PROLC 24 " (cutoff:3.500A) removed outlier: 3.641A 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 48 removed outlier: 3.664A pdb=" N GLYLC 42 " --> pdb=" O HISLC 38 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYSLC 45 " --> pdb=" O THRLC 41 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASNLC 46 " --> pdb=" O GLYLC 42 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LYSLC 47 " --> pdb=" O METLC 43 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ARGLC 48 " --> pdb=" O ALALC 44 " (cutoff:3.500A) Processing helix chain 'LC' and resid 115 through 133 removed outlier: 5.316A pdb=" N ALALC 133 " --> pdb=" O ALALC 129 " (cutoff:3.500A) Processing helix chain 'LC' and resid 134 through 140 removed outlier: 3.505A pdb=" N GLYLC 140 " --> pdb=" O LEULC 136 " (cutoff:3.500A) Processing helix chain 'LC' and resid 154 through 159 removed outlier: 3.793A pdb=" N VALLC 158 " --> pdb=" O ASPLC 154 " (cutoff:3.500A) Processing helix chain 'LC' and resid 165 through 177 Processing helix chain 'LC' and resid 178 through 189 removed outlier: 4.017A pdb=" N LYSLC 189 " --> pdb=" O VALLC 185 " (cutoff:3.500A) Processing helix chain 'LC' and resid 195 through 200 removed outlier: 3.935A pdb=" N ARGLC 199 " --> pdb=" O LYSLC 195 " (cutoff:3.500A) Processing helix chain 'LC' and resid 220 through 227 removed outlier: 4.877A pdb=" N LYSLC 224 " --> pdb=" O LYSLC 220 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLYLC 225 " --> pdb=" O GLULC 221 " (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: 3.766A pdb=" N LYSLC 263 " --> pdb=" O SERLC 259 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASPLC 266 " --> pdb=" O ILELC 262 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALALC 267 " --> pdb=" O LYSLC 263 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYRLC 269 " --> pdb=" O LEULC 265 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYSLC 272 " --> pdb=" O VALLC 268 " (cutoff:3.500A) Processing helix chain 'LC' and resid 286 through 292 Processing helix chain 'LC' and resid 293 through 300 removed outlier: 4.035A pdb=" N VALLC 299 " --> pdb=" O GLULC 295 " (cutoff:3.500A) Processing helix chain 'LC' and resid 318 through 323 removed outlier: 4.473A 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: 4.654A pdb=" N THRLC 335 " --> pdb=" O PROLC 331 " (cutoff:3.500A) Processing helix chain 'LC' and resid 355 through 364 Processing helix chain 'LC' and resid 214 through 219 removed outlier: 3.514A 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 'LE' and resid 98 through 103 removed outlier: 4.053A pdb=" N VALLE 102 " --> pdb=" O ASNLE 98 " (cutoff:3.500A) removed outlier: 5.625A 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 removed outlier: 3.828A pdb=" N GLNLE 124 " --> pdb=" O ASPLE 120 " (cutoff:3.500A) Processing helix chain 'LE' and resid 125 through 130 removed outlier: 3.518A pdb=" N THRLE 129 " --> pdb=" O PROLE 125 " (cutoff:3.500A) Processing helix chain 'LE' and resid 138 through 145 removed outlier: 4.054A pdb=" N GLNLE 145 " --> pdb=" O ALALE 141 " (cutoff:3.500A) Processing helix chain 'LE' and resid 155 through 174 removed outlier: 3.506A pdb=" N ILELE 165 " --> pdb=" O ASPLE 161 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ALALE 168 " --> pdb=" O ALALE 164 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEULE 169 " --> pdb=" O ILELE 165 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALALE 171 " --> pdb=" O LYSLE 167 " (cutoff:3.500A) Processing helix chain 'LE' and resid 178 through 186 removed outlier: 5.342A pdb=" N SERLE 186 " --> pdb=" O TYRLE 182 " (cutoff:3.500A) Processing helix chain 'LF' and resid 15 through 79 removed outlier: 3.620A pdb=" N GLULF 65 " --> pdb=" O TYRLF 61 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALALF 72 " --> pdb=" O LYSLF 68 " (cutoff:3.500A) Processing helix chain 'LF' and resid 102 through 113 removed outlier: 3.811A pdb=" N ARGLF 113 " --> pdb=" O LEULF 109 " (cutoff:3.500A) Processing helix chain 'LF' and resid 126 through 137 removed outlier: 3.599A pdb=" N GLULF 131 " --> pdb=" O LYSLF 127 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N METLF 132 " --> pdb=" O ALALF 128 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILELF 135 " --> pdb=" O GLULF 131 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VALLF 136 " --> pdb=" O METLF 132 " (cutoff:3.500A) Processing helix chain 'LF' and resid 146 through 156 Processing helix chain 'LF' and resid 171 through 179 removed outlier: 4.374A pdb=" N ILELF 175 " --> pdb=" O ASPLF 171 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLULF 176 " --> pdb=" O ASNLF 172 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASNLF 178 " --> pdb=" O ILELF 174 " (cutoff:3.500A) Processing helix chain 'LF' and resid 186 through 196 Processing helix chain 'LF' and resid 200 through 209 removed outlier: 3.742A pdb=" N ASNLF 206 " --> pdb=" O LYSLF 202 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N TRPLF 209 " --> pdb=" O ALALF 205 " (cutoff:3.500A) Processing helix chain 'LF' and resid 239 through 249 removed outlier: 4.788A pdb=" N ALALF 243 " --> pdb=" O GLULF 239 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEULF 244 " --> pdb=" O HISLF 240 " (cutoff:3.500A) Processing helix chain 'LG' and resid 56 through 72 removed outlier: 3.560A pdb=" N LYSLG 66 " --> pdb=" O GLNLG 62 " (cutoff:3.500A) Processing helix chain 'LG' and resid 75 through 84 removed outlier: 3.503A pdb=" N GLNLG 80 " --> pdb=" O PROLG 76 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N PHELG 81 " --> pdb=" O ALALG 77 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLNLG 82 " --> pdb=" O ILELG 78 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N TYRLG 83 " --> pdb=" O ALALG 79 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N THRLG 84 " --> pdb=" O GLNLG 80 " (cutoff:3.500A) Processing helix chain 'LG' and resid 86 through 101 removed outlier: 3.743A pdb=" N LYSLG 99 " --> pdb=" O LYSLG 95 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYRLG 100 " --> pdb=" O LEULG 96 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARGLG 101 " --> pdb=" O LEULG 97 " (cutoff:3.500A) Processing helix chain 'LG' and resid 104 through 121 Processing helix chain 'LG' and resid 138 through 149 Processing helix chain 'LG' and resid 163 through 177 removed outlier: 4.415A pdb=" N PHELG 168 " --> pdb=" O GLULG 164 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LEULG 169 " --> pdb=" O LEULG 165 " (cutoff:3.500A) Proline residue: LG 170 - end of helix Processing helix chain 'LG' and resid 185 through 194 removed outlier: 3.549A pdb=" N LEULG 192 " --> pdb=" O ARGLG 188 " (cutoff:3.500A) Processing helix chain 'LG' and resid 210 through 230 removed outlier: 4.913A pdb=" N GLULG 227 " --> pdb=" O GLULG 223 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N LYSLG 228 " --> pdb=" O GLYLG 224 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLULG 230 " --> pdb=" O LEULG 226 " (cutoff:3.500A) Processing helix chain 'LG' and resid 231 through 236 removed outlier: 3.827A pdb=" N ARGLG 235 " --> pdb=" O ASPLG 231 " (cutoff:3.500A) removed outlier: 5.854A 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 253 Processing helix chain 'LH' and resid 61 through 84 removed outlier: 3.658A pdb=" N LEULH 68 " --> pdb=" O ASPLH 64 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARGLH 69 " --> pdb=" O VALLH 65 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THRLH 70 " --> pdb=" O ALALH 66 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THRLH 73 " --> pdb=" O ARGLH 69 " (cutoff:3.500A) Processing helix chain 'LH' and resid 152 through 168 removed outlier: 4.149A pdb=" N LYSLH 168 " --> pdb=" O GLNLH 164 " (cutoff:3.500A) Processing helix chain 'LH' and resid 173 through 178 removed outlier: 5.005A pdb=" N LEULH 178 " --> pdb=" O ILELH 174 " (cutoff:3.500A) Processing helix chain 'LK' and resid 31 through 36 Processing helix chain 'LK' and resid 38 through 51 removed outlier: 3.702A pdb=" N ALALK 51 " --> pdb=" O ALALK 47 " (cutoff:3.500A) Processing helix chain 'LK' and resid 76 through 86 removed outlier: 4.645A pdb=" N LYSLK 86 " --> pdb=" O ILELK 82 " (cutoff:3.500A) Processing helix chain 'LK' and resid 105 through 118 removed outlier: 3.816A pdb=" N ILELK 109 " --> pdb=" O SERLK 105 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILELK 110 " --> pdb=" O LEULK 106 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLULK 111 " --> pdb=" O ASPLK 107 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N PHELK 118 " --> pdb=" O ARGLK 114 " (cutoff:3.500A) Processing helix chain 'LK' and resid 124 through 140 Processing helix chain 'LK' and resid 147 through 158 removed outlier: 3.599A pdb=" N ILELK 151 " --> pdb=" O SERLK 147 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLULK 156 " --> pdb=" O SERLK 152 " (cutoff:3.500A) Processing helix chain 'LL' and resid 17 through 22 removed outlier: 4.068A pdb=" N ARGLL 21 " --> pdb=" O HISLL 17 " (cutoff:3.500A) removed outlier: 3.614A 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 removed outlier: 3.517A pdb=" N ALALL 47 " --> pdb=" O ALALL 43 " (cutoff:3.500A) 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 Processing helix chain 'LL' and resid 105 through 123 Processing helix chain 'LM' and resid 58 through 63 removed outlier: 5.062A pdb=" N LEULM 63 " --> pdb=" O LEULM 59 " (cutoff:3.500A) Processing helix chain 'LM' and resid 77 through 89 Processing helix chain 'LM' and resid 90 through 98 removed outlier: 5.627A pdb=" N ASNLM 98 " --> pdb=" O TRPLM 94 " (cutoff:3.500A) Processing helix chain 'LM' and resid 99 through 112 removed outlier: 3.689A pdb=" N GLNLM 110 " --> pdb=" O GLNLM 106 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEULM 112 " --> pdb=" O ARGLM 108 " (cutoff:3.500A) Processing helix chain 'LM' and resid 113 through 138 removed outlier: 3.979A pdb=" N GLULM 130 " --> pdb=" O GLNLM 126 " (cutoff:3.500A) Processing helix chain 'LN' and resid 2 through 14 removed outlier: 3.895A pdb=" N TYRLN 6 " --> pdb=" O GLYLN 2 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYSLN 13 " --> pdb=" O GLULN 9 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LYSLN 14 " --> pdb=" O LEULN 10 " (cutoff:3.500A) Processing helix chain 'LN' and resid 16 through 34 removed outlier: 3.609A pdb=" N GLNLN 32 " --> pdb=" O TRPLN 28 " (cutoff:3.500A) removed outlier: 5.018A 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: 3.580A pdb=" N ARGLN 143 " --> pdb=" O HISLN 139 " (cutoff:3.500A) removed outlier: 3.549A 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: 4.255A pdb=" N CYSLN 152 " --> pdb=" O ILELN 148 " (cutoff:3.500A) removed outlier: 4.157A 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: 3.690A pdb=" N ARGLN 162 " --> pdb=" O HISLN 158 " (cutoff:3.500A) Processing helix chain 'LN' and resid 165 through 173 removed outlier: 3.655A pdb=" N GLYLN 173 " --> pdb=" O LYSLN 169 " (cutoff:3.500A) Processing helix chain 'LN' and resid 186 through 196 Processing helix chain 'LO' and resid 16 through 31 removed outlier: 3.572A pdb=" N ILELO 23 " --> pdb=" O ARGLO 19 " (cutoff:3.500A) Processing helix chain 'LO' and resid 47 through 62 removed outlier: 3.519A pdb=" N ALALO 51 " --> pdb=" O GLULO 47 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYSLO 61 " --> pdb=" O ALALO 57 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N METLO 62 " --> pdb=" O TYRLO 58 " (cutoff:3.500A) Processing helix chain 'LO' and resid 77 through 91 removed outlier: 3.734A pdb=" N METLO 89 " --> pdb=" O ALALO 85 " (cutoff:3.500A) removed outlier: 3.608A 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: 3.705A pdb=" N LEULO 104 " --> pdb=" O ALALO 100 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N LYSLO 105 " --> pdb=" O LEULO 101 " (cutoff:3.500A) Processing helix chain 'LO' and resid 111 through 118 removed outlier: 4.243A pdb=" N LYSLO 116 " --> pdb=" O PROLO 112 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LYSLO 117 " --> pdb=" O PROLO 113 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N LYSLO 118 " --> pdb=" O TYRLO 114 " (cutoff:3.500A) Processing helix chain 'LO' and resid 126 through 131 Processing helix chain 'LO' and resid 139 through 148 removed outlier: 3.513A pdb=" N GLULO 146 " --> pdb=" O ARGLO 142 " (cutoff:3.500A) Processing helix chain 'LO' and resid 152 through 188 Processing helix chain 'LO' and resid 192 through 203 removed outlier: 3.800A pdb=" N SERLO 196 " --> pdb=" O ASPLO 192 " (cutoff:3.500A) Processing helix chain 'LP' and resid 10 through 15 removed outlier: 5.251A pdb=" N ALALP 15 " --> pdb=" O PROLP 11 " (cutoff:3.500A) Processing helix chain 'LP' and resid 25 through 37 Processing helix chain 'LP' and resid 40 through 54 Processing helix chain 'LP' and resid 70 through 77 removed outlier: 4.638A pdb=" N LYSLP 74 " --> pdb=" O THRLP 70 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLNLP 75 " --> pdb=" O ALALP 71 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N TRPLP 76 " --> pdb=" O GLNLP 72 " (cutoff:3.500A) Processing helix chain 'LP' and resid 84 through 106 Processing helix chain 'LQ' and resid 51 through 68 Processing helix chain 'LQ' and resid 70 through 83 removed outlier: 4.007A pdb=" N LYSLQ 74 " --> pdb=" O ALALQ 70 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N SERLQ 83 " --> pdb=" O ARGLQ 79 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 91 through 101 removed outlier: 3.544A pdb=" N ASNLQ 98 " --> pdb=" O ARGLQ 94 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASNLQ 101 " --> pdb=" O ARGLQ 97 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 134 through 145 Processing helix chain 'LQ' and resid 150 through 158 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: 3.543A pdb=" N ILELS 121 " --> pdb=" O ARGLS 117 " (cutoff:3.500A) removed outlier: 5.691A 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: 3.643A pdb=" N LEULS 143 " --> pdb=" O TYRLS 139 " (cutoff:3.500A) Processing helix chain 'LT' and resid 54 through 59 removed outlier: 5.664A pdb=" N GLYLT 59 " --> pdb=" O LYSLT 55 " (cutoff:3.500A) Processing helix chain 'LT' and resid 92 through 97 removed outlier: 3.604A pdb=" N VALLT 96 " --> pdb=" O ARGLT 92 " (cutoff:3.500A) removed outlier: 5.543A 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 100 through 123 removed outlier: 4.160A pdb=" N ASPLT 104 " --> pdb=" O ARGLT 100 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHELT 105 " --> pdb=" O SERLT 101 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALALT 113 " --> pdb=" O VALLT 109 " (cutoff:3.500A) Processing helix chain 'LV' and resid 121 through 129 Proline residue: LV 129 - end of helix Processing helix chain 'LV' and resid 130 through 135 Processing helix chain 'LX' and resid 12 through 29 Processing helix chain 'LY' and resid 10 through 21 Processing helix chain 'LY' and resid 22 through 31 removed outlier: 3.789A pdb=" N VALLY 28 " --> pdb=" O SERLY 24 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SERLY 31 " --> pdb=" O ARGLY 27 " (cutoff:3.500A) Processing helix chain 'LY' and resid 35 through 43 Processing helix chain 'LY' and resid 99 through 104 removed outlier: 3.988A pdb=" N VALLY 103 " --> pdb=" O HISLY 99 " (cutoff:3.500A) removed outlier: 5.521A 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 134 Processing helix chain 'Ld' and resid 23 through 29 removed outlier: 4.553A pdb=" N HISLd 29 " --> pdb=" O HISLd 25 " (cutoff:3.500A) Processing helix chain 'Ld' and resid 35 through 53 removed outlier: 3.526A pdb=" N LYSLd 42 " --> pdb=" O PROLd 38 " (cutoff:3.500A) Processing helix chain 'Ld' and resid 60 through 69 Processing helix chain 'Le' and resid 22 through 27 removed outlier: 5.107A 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: 3.736A pdb=" N VALLe 83 " --> pdb=" O ASNLe 79 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEULe 85 " --> pdb=" O LYSLe 81 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEULe 86 " --> pdb=" O ASPLe 82 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEULe 87 " --> pdb=" O VALLe 83 " (cutoff:3.500A) removed outlier: 5.417A 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: 4.119A pdb=" N PHELf 45 " --> pdb=" O ALALf 41 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N TYRLf 46 " --> pdb=" O ALALf 42 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEULf 47 " --> pdb=" O ALALf 43 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 8 through 16 removed outlier: 3.981A pdb=" N LEULh 12 " --> pdb=" O LYSLh 8 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TRPLh 13 " --> pdb=" O ALALh 9 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SERLh 14 " --> pdb=" O GLYLh 10 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYSLh 15 " --> pdb=" O GLNLh 11 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ASNLh 16 " --> pdb=" O LEULh 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'Lh' and resid 8 through 16' Processing helix chain 'Lh' and resid 17 through 42 removed outlier: 3.550A pdb=" N LYSLh 22 " --> pdb=" O GLULh 18 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYSLh 28 " --> pdb=" O LEULh 24 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THRLh 29 " --> pdb=" O GLYLh 25 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILELh 39 " --> pdb=" O ARGLh 35 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N SERLh 40 " --> pdb=" O ILELh 36 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N SERLh 41 " --> pdb=" O GLNLh 37 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SERLh 42 " --> pdb=" O LYSLh 38 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 43 through 76 removed outlier: 3.862A pdb=" N ASNLh 47 " --> pdb=" O GLYLh 43 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 82 through 87 Proline residue: Lh 87 - end of helix Processing helix chain 'Lh' and resid 90 through 96 Processing helix chain 'Lh' and resid 98 through 104 Processing helix chain 'Lh' and resid 106 through 116 removed outlier: 3.744A pdb=" N HISLh 115 " --> pdb=" O LYSLh 111 " (cutoff:3.500A) Processing helix chain 'Li' and resid 43 through 58 removed outlier: 3.545A pdb=" N GLNLi 47 " --> pdb=" O SERLi 43 " (cutoff:3.500A) Processing helix chain 'Li' and resid 60 through 73 Processing helix chain 'Li' and resid 74 through 86 Processing helix chain 'Li' and resid 88 through 110 Processing helix chain 'Lj' and resid 50 through 58 removed outlier: 3.835A pdb=" N LYSLj 54 " --> pdb=" O SERLj 50 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYSLj 57 " --> pdb=" O ALALj 53 " (cutoff:3.500A) Processing helix chain 'Lj' and resid 65 through 77 removed outlier: 5.780A pdb=" N THRLj 69 " --> pdb=" O ARGLj 65 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VALLj 70 " --> pdb=" O TYRLj 66 " (cutoff:3.500A) Proline residue: Lj 71 - end of helix removed outlier: 3.620A pdb=" N ASNLj 76 " --> pdb=" O ARGLj 72 " (cutoff:3.500A) Processing helix chain 'Lq' and resid 5 through 25 removed outlier: 3.692A pdb=" N TYRLq 19 " --> pdb=" O GLULq 15 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ASNLq 21 " --> pdb=" O LEULq 17 " (cutoff:3.500A) Processing helix chain 'Lq' and resid 73 through 81 Processing helix chain 'Lq' and resid 86 through 97 removed outlier: 4.785A pdb=" N LYSLq 97 " --> pdb=" O LEULq 93 " (cutoff:3.500A) Processing helix chain 'Lq' and resid 98 through 108 removed outlier: 4.925A pdb=" N ASPLq 108 " --> pdb=" O ALALq 104 " (cutoff:3.500A) Processing helix chain 'Lq' and resid 113 through 121 Proline residue: Lq 121 - end of helix Processing helix chain 'Lq' and resid 122 through 132 Proline residue: Lq 126 - end of helix removed outlier: 3.529A pdb=" N LYSLq 130 " --> pdb=" O PROLq 126 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ALALq 131 " --> pdb=" O GLYLq 127 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N GLYLq 132 " --> pdb=" O LEULq 128 " (cutoff:3.500A) Processing helix chain 'Lq' and resid 143 through 154 removed outlier: 4.116A pdb=" N LYSLq 147 " --> pdb=" O ASPLq 143 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VALLq 148 " --> pdb=" O LEULq 144 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ASNLq 149 " --> pdb=" O SERLq 145 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N SERLq 153 " --> pdb=" O ASNLq 149 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N THRLq 154 " --> pdb=" O GLULq 150 " (cutoff:3.500A) Processing helix chain 'Lq' and resid 175 through 195 removed outlier: 5.128A pdb=" N LYSLq 195 " --> pdb=" O VALLq 191 " (cutoff:3.500A) Processing helix chain 'Lq' and resid 197 through 202 removed outlier: 4.512A pdb=" N VALLq 201 " --> pdb=" O GLYLq 197 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N GLYLq 202 " --> pdb=" O TRPLq 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'Lq' and resid 197 through 202' Processing helix chain 'Cc' and resid 10 through 17 removed outlier: 3.788A pdb=" N ALACc 15 " --> pdb=" O ILECc 11 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SERCc 16 " --> pdb=" O LYSCc 12 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N SERCc 17 " --> pdb=" O HISCc 13 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 18 through 36 removed outlier: 5.815A pdb=" N ARGCc 36 " --> pdb=" O PHECc 32 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 37 through 42 Processing helix chain 'Cc' and resid 43 through 61 removed outlier: 3.620A pdb=" N CYSCc 61 " --> pdb=" O ALACc 57 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 63 through 81 removed outlier: 4.926A pdb=" N ILECc 78 " --> pdb=" O LEUCc 74 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N TRPCc 79 " --> pdb=" O ALACc 75 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLNCc 80 " --> pdb=" O ASPCc 76 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEUCc 81 " --> pdb=" O LEUCc 77 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 82 through 101 removed outlier: 3.756A pdb=" N VALCc 86 " --> pdb=" O PROCc 82 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ALACc 87 " --> pdb=" O ARGCc 83 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N THRCc 88 " --> pdb=" O GLUCc 84 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 105 through 128 removed outlier: 3.999A pdb=" N GLUCc 110 " --> pdb=" O VALCc 106 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N LYSCc 111 " --> pdb=" O LEUCc 107 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHECc 112 " --> pdb=" O ARGCc 108 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N METCc 127 " --> pdb=" O SERCc 123 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N LYSCc 128 " --> pdb=" O PHECc 124 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 151 through 166 removed outlier: 3.635A pdb=" N GLUCc 157 " --> pdb=" O SERCc 153 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VALCc 158 " --> pdb=" O LYSCc 154 " (cutoff:3.500A) Proline residue: Cc 166 - end of helix Processing helix chain 'Cc' and resid 190 through 209 removed outlier: 3.539A pdb=" N ARGCc 194 " --> pdb=" O PROCc 190 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N VALCc 202 " --> pdb=" O LEUCc 198 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ASPCc 203 " --> pdb=" O ASPCc 199 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 215 through 236 removed outlier: 4.166A pdb=" N ARGCc 219 " --> pdb=" O GLUCc 215 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N METCc 220 " --> pdb=" O GLUCc 216 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N METCc 228 " --> pdb=" O ARGCc 224 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEUCc 232 " --> pdb=" O METCc 228 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 238 through 251 Processing helix chain 'Cd' and resid 13 through 18 Processing helix chain 'Cd' and resid 20 through 54 Proline residue: Cd 54 - end of helix Processing helix chain 'Cd' and resid 55 through 65 removed outlier: 3.572A pdb=" N GLUCd 62 " --> pdb=" O GLNCd 58 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYSCd 63 " --> pdb=" O LYSCd 59 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLNCd 65 " --> pdb=" O LEUCd 61 " (cutoff:3.500A) Processing helix chain 'Cd' and resid 68 through 73 Processing helix chain 'Cd' and resid 88 through 98 Processing helix chain 'Cd' and resid 180 through 188 Proline residue: Cd 188 - end of helix Processing helix chain 'Cd' and resid 211 through 223 removed outlier: 3.710A pdb=" N PHECd 222 " --> pdb=" O ILECd 218 " (cutoff:3.500A) Proline residue: Cd 223 - end of helix Processing helix chain 'Cd' and resid 240 through 252 Processing helix chain 'Cd' and resid 294 through 299 removed outlier: 3.684A pdb=" N ILECd 298 " --> pdb=" O PROCd 294 " (cutoff:3.500A) Proline residue: Cd 299 - end of helix No H-bonds generated for 'chain 'Cd' and resid 294 through 299' Processing helix chain 'Cd' and resid 318 through 333 removed outlier: 3.749A pdb=" N LEUCd 331 " --> pdb=" O SERCd 327 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHECd 332 " --> pdb=" O METCd 328 " (cutoff:3.500A) Proline residue: Cd 333 - end of helix Processing helix chain 'Cd' and resid 409 through 414 removed outlier: 5.452A pdb=" N GLUCd 414 " --> pdb=" O ARGCd 410 " (cutoff:3.500A) Processing helix chain 'Cd' and resid 424 through 430 removed outlier: 5.001A pdb=" N GLUCd 428 " --> pdb=" O LYSCd 424 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYSCd 429 " --> pdb=" O ALACd 425 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N LYSCd 430 " --> pdb=" O LYSCd 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'Cd' and resid 424 through 430' Processing helix chain 'Ce' and resid 2 through 12 Processing helix chain 'Ce' and resid 43 through 48 removed outlier: 4.898A pdb=" N SERCe 48 " --> pdb=" O PROCe 44 " (cutoff:3.500A) Processing helix chain 'Ce' and resid 67 through 72 removed outlier: 4.008A pdb=" N SERCe 71 " --> pdb=" O THRCe 67 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N HISCe 72 " --> pdb=" O ILECe 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ce' and resid 67 through 72' Processing helix chain 'Ce' and resid 86 through 99 Processing helix chain 'Ce' and resid 102 through 134 Processing helix chain 'Ce' and resid 142 through 161 removed outlier: 3.641A pdb=" N ARGCe 154 " --> pdb=" O GLUCe 150 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYSCe 155 " --> pdb=" O ALACe 151 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYSCe 161 " --> pdb=" O LEUCe 157 " (cutoff:3.500A) Processing helix chain 'Ce' and resid 162 through 177 removed outlier: 3.680A pdb=" N GLYCe 177 " --> pdb=" O ARGCe 173 " (cutoff:3.500A) Processing helix chain 'Ce' and resid 187 through 195 removed outlier: 3.720A pdb=" N LYSCe 193 " --> pdb=" O GLNCe 189 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEUCe 195 " --> pdb=" O TRPCe 191 " (cutoff:3.500A) Processing helix chain 'Cf' and resid 486 through 544 Processing sheet with id= 1, first strand: chain 'CA' and resid 61 through 66 removed outlier: 4.684A pdb=" N LEUCA 100 " --> pdb=" O ALACA 117 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THRCA 241 " --> pdb=" O TYRCA 116 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'CA' and resid 111 through 115 removed outlier: 3.629A pdb=" N ILECA 244 " --> pdb=" O LYSCA 114 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'CB' and resid 63 through 68 removed outlier: 5.062A pdb=" N ARGCB 279 " --> pdb=" O GLNCB 295 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLNCB 295 " --> pdb=" O ARGCB 279 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'CB' and resid 80 through 83 Processing sheet with id= 5, first strand: chain 'CB' and resid 125 through 128 Processing sheet with id= 6, first strand: chain 'CC' and resid 137 through 141 Processing sheet with id= 7, first strand: chain 'CE' and resid 213 through 217 removed outlier: 4.096A pdb=" N VALCE 320 " --> pdb=" O ALACE 154 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'CE' and resid 384 through 387 removed outlier: 5.117A pdb=" N SERCE 458 " --> pdb=" O GLUCE 333 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VALCE 338 " --> pdb=" O TYRCE 483 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'CF' and resid 63 through 67 removed outlier: 6.492A pdb=" N CYSCF 40 " --> pdb=" O TYRCF 226 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TYRCF 226 " --> pdb=" O CYSCF 40 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VALCF 42 " --> pdb=" O LEUCF 224 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'CF' and resid 224 through 227 No H-bonds generated for sheet with id= 10 Processing sheet with id= 11, first strand: chain 'CG' and resid 37 through 40 removed outlier: 6.867A pdb=" N VALCG 45 " --> pdb=" O LEUCG 71 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'CG' and resid 96 through 100 removed outlier: 4.769A pdb=" N TYRCG 96 " --> pdb=" O GLYCG 131 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLYCG 143 " --> pdb=" O VALCG 134 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'CH' and resid 203 through 209 removed outlier: 5.278A pdb=" N ARGCH 167 " --> pdb=" O ARGCH 214 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THRCH 220 " --> pdb=" O VALCH 171 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLYCH 173 " --> pdb=" O THRCH 220 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEUCH 170 " --> pdb=" O ALACH 248 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N METCH 281 " --> pdb=" O ALACH 247 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLUCH 315 " --> pdb=" O VALCH 282 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'CI' and resid 214 through 218 removed outlier: 3.782A pdb=" N ARGCI 215 " --> pdb=" O GLUCI 234 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLYCI 187 " --> pdb=" O PHECI 235 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VALCI 188 " --> pdb=" O VALCI 263 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'CJ' and resid 186 through 190 Processing sheet with id= 16, first strand: chain 'CJ' and resid 394 through 397 Processing sheet with id= 17, first strand: chain 'CK' and resid 190 through 194 removed outlier: 3.623A pdb=" N VALCK 191 " --> pdb=" O HISCK 186 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ASNCK 256 " --> pdb=" O THRCK 246 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N TYRCK 242 " --> pdb=" O LEUCK 260 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THRCK 219 " --> pdb=" O ILECK 245 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILECK 220 " --> pdb=" O LYSCK 201 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SERCK 199 " --> pdb=" O GLUCK 222 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'CL' and resid 266 through 270 removed outlier: 6.619A pdb=" N LEUCL 241 " --> pdb=" O PROCL 266 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ILECL 208 " --> pdb=" O ARGCL 238 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLYCL 319 " --> pdb=" O SERCL 373 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'CM' and resid 118 through 124 removed outlier: 4.011A pdb=" N ASNCM 119 " --> pdb=" O ARGCM 94 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLYCM 143 " --> pdb=" O PHECM 91 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N TRPCM 139 " --> pdb=" O ILECM 95 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'CN' and resid 1 through 5 Processing sheet with id= 21, first strand: chain 'CN' and resid 23 through 28 Processing sheet with id= 22, first strand: chain 'CN' and resid 69 through 72 Processing sheet with id= 23, first strand: chain 'CN' and resid 158 through 161 Processing sheet with id= 24, first strand: chain 'CP' and resid 330 through 333 removed outlier: 6.711A pdb=" N THRCP 330 " --> pdb=" O PHECP 345 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VALCP 340 " --> pdb=" O THRCP 310 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N VALCP 306 " --> pdb=" O VALCP 344 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VALCP 307 " --> pdb=" O GLNCP 365 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N HISCP 361 " --> pdb=" O ASNCP 311 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'CP' and resid 433 through 438 removed outlier: 3.873A pdb=" N TYRCP 438 " --> pdb=" O ASPCP 412 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VALCP 407 " --> pdb=" O GLUCP 382 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'CP' and resid 507 through 513 removed outlier: 7.871A pdb=" N ASNCP 533 " --> pdb=" O ILECP 584 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'CP' and resid 565 through 568 removed outlier: 6.904A pdb=" N ASPCP 574 " --> pdb=" O PROCP 568 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'CQ' and resid 3 through 6 removed outlier: 4.810A pdb=" N ARGCQ 11 " --> pdb=" O CYSCQ 6 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'CQ' and resid 18 through 22 Processing sheet with id= 30, first strand: chain 'CS' and resid 87 through 92 removed outlier: 3.581A pdb=" N ASPCS 77 " --> pdb=" O PHECS 90 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'Cb' and resid 190 through 194 removed outlier: 3.532A pdb=" N VALCb 130 " --> pdb=" O THRCb 268 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEUCb 295 " --> pdb=" O METCb 133 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'Cb' and resid 392 through 396 removed outlier: 7.636A pdb=" N ASPCb 503 " --> pdb=" O LEUCb 305 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N SERCb 307 " --> pdb=" O ASPCb 503 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N VALCb 505 " --> pdb=" O SERCb 307 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'LB' and resid 44 through 50 removed outlier: 4.046A pdb=" N GLULB 214 " --> pdb=" O ILELB 283 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'LB' and resid 53 through 59 removed outlier: 5.548A pdb=" N ASNLB 320 " --> pdb=" O GLYLB 289 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLYLB 289 " --> pdb=" O ASNLB 320 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYRLB 322 " --> pdb=" O GLYLB 287 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARGLB 285 " --> pdb=" O METLB 324 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'LB' and resid 84 through 87 removed outlier: 6.467A pdb=" N LEULB 162 " --> pdb=" O VALLB 87 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N GLYLB 91 " --> pdb=" O LEULB 102 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'LB' and resid 160 through 165 removed outlier: 4.259A pdb=" N HISLB 178 " --> pdb=" O THRLB 165 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'LC' and resid 6 through 9 removed outlier: 5.197A pdb=" N ALALC 19 " --> pdb=" O VALLC 9 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'LC' and resid 231 through 235 removed outlier: 5.241A pdb=" N PHELC 254 " --> pdb=" O GLYLC 208 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'LE' and resid 56 through 61 removed outlier: 4.198A pdb=" N THRLE 56 " --> pdb=" O LEULE 72 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYSLE 68 " --> pdb=" O LEULE 60 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLYLE 85 " --> pdb=" O PROLE 93 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'LF' and resid 140 through 144 removed outlier: 6.369A pdb=" N LYSLF 88 " --> pdb=" O VALLF 125 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASNLF 119 " --> pdb=" O ARGLF 94 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ASNLF 118 " --> pdb=" O LEULF 213 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'LG' and resid 178 through 184 Processing sheet with id= 42, first strand: chain 'LH' and resid 5 through 12 removed outlier: 5.476A pdb=" N GLYLH 51 " --> pdb=" O VALLH 12 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'LH' and resid 16 through 20 Processing sheet with id= 44, first strand: chain 'LH' and resid 100 through 106 removed outlier: 4.029A pdb=" N CYSLH 111 " --> pdb=" O ASNLH 106 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N TYRLH 112 " --> pdb=" O METLH 130 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'LH' and resid 134 through 139 removed outlier: 5.242A pdb=" N GLULH 145 " --> pdb=" O SERLH 139 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ASPLH 144 " --> pdb=" O TYRLH 92 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'LK' and resid 11 through 16 removed outlier: 3.777A pdb=" N LYSLK 11 " --> pdb=" O ILELK 64 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N THRLK 59 " --> pdb=" O VALLK 74 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'LL' and resid 55 through 59 Processing sheet with id= 48, first strand: chain 'LM' and resid 18 through 22 removed outlier: 4.785A pdb=" N ARGLM 18 " --> pdb=" O ILELM 30 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N SERLM 26 " --> pdb=" O LEULM 22 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N SERLM 45 " --> pdb=" O LEULM 50 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEULM 50 " --> pdb=" O SERLM 45 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'LM' and resid 39 through 42 Processing sheet with id= 50, first strand: chain 'LN' and resid 35 through 39 removed outlier: 6.773A pdb=" N VALLN 35 " --> pdb=" O ARGLN 65 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILELN 61 " --> pdb=" O ALALN 39 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLYLN 58 " --> pdb=" O ASPLN 136 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILELN 133 " --> pdb=" O LEULN 116 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'LN' and resid 117 through 121 removed outlier: 3.682A pdb=" N ASNLN 117 " --> pdb=" O ILELN 133 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N TYRLN 129 " --> pdb=" O VALLN 121 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'LO' and resid 7 through 11 Processing sheet with id= 53, first strand: chain 'LP' and resid 16 through 20 Processing sheet with id= 54, first strand: chain 'LP' and resid 57 through 60 removed outlier: 5.095A pdb=" N ARGLP 80 " --> pdb=" O METLP 60 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'LP' and resid 116 through 122 Processing sheet with id= 56, first strand: chain 'LQ' and resid 106 through 110 Processing sheet with id= 57, first strand: chain 'LQ' and resid 126 through 129 Processing sheet with id= 58, first strand: chain 'LS' and resid 24 through 30 removed outlier: 6.584A pdb=" N ILELS 10 " --> pdb=" O VALLS 59 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'LS' and resid 86 through 95 removed outlier: 3.545A pdb=" N GLYLS 86 " --> pdb=" O SERLS 83 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ASNLS 74 " --> pdb=" O LEULS 129 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'LS' and resid 6 through 10 removed outlier: 4.526A pdb=" N GLULS 6 " --> pdb=" O ILELS 64 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'LT' and resid 73 through 79 Processing sheet with id= 62, first strand: chain 'LV' and resid 35 through 38 removed outlier: 4.238A pdb=" N ALALV 23 " --> pdb=" O ILELV 38 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ASNLV 100 " --> pdb=" O ILELV 24 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ILELV 104 " --> pdb=" O ALALV 28 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ASPLV 58 " --> pdb=" O ILELV 80 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'LV' and resid 86 through 89 removed outlier: 4.161A pdb=" N VALLV 93 " --> pdb=" O ARGLV 89 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'LV' and resid 81 through 84 removed outlier: 4.050A pdb=" N ALALV 84 " --> pdb=" O ASPLV 99 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ASPLV 99 " --> pdb=" O ALALV 84 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'LY' and resid 64 through 67 removed outlier: 3.863A pdb=" N LYSLY 65 " --> pdb=" O ILELY 57 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLYLY 52 " --> pdb=" O HISLY 109 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N HISLY 109 " --> pdb=" O GLYLY 52 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'LY' and resid 71 through 74 Processing sheet with id= 67, first strand: chain 'LY' and resid 85 through 88 removed outlier: 4.823A pdb=" N GLNLY 92 " --> pdb=" O LYSLY 88 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'Ld' and resid 56 through 59 removed outlier: 4.520A pdb=" N ALALd 17 " --> pdb=" O VALLd 117 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'Le' and resid 72 through 78 No H-bonds generated for sheet with id= 69 Processing sheet with id= 70, first strand: chain 'Lf' and resid 65 through 74 removed outlier: 8.327A pdb=" N LYSLf 65 " --> pdb=" O ALALf 57 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYSLf 49 " --> pdb=" O ILELf 73 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ARGLf 50 " --> pdb=" O METLf 103 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N VALLf 54 " --> pdb=" O SERLf 99 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N SERLf 99 " --> pdb=" O VALLf 54 " (cutoff:3.500A) removed outlier: 13.270A pdb=" N ARGLf 56 " --> pdb=" O GLYLf 97 " (cutoff:3.500A) removed outlier: 15.295A pdb=" N GLYLf 97 " --> pdb=" O ARGLf 56 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALALf 98 " --> pdb=" O HISLf 15 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N LYSLf 12 " --> pdb=" O GLULf 35 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEULf 31 " --> pdb=" O LEULf 16 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'Lj' and resid 15 through 18 removed outlier: 8.528A pdb=" N THRLj 15 " --> pdb=" O HISLj 28 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N HISLj 28 " --> pdb=" O THRLj 15 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N GLYLj 17 " --> pdb=" O SERLj 26 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'Lq' and resid 49 through 53 removed outlier: 6.125A pdb=" N PHELq 49 " --> pdb=" O LEULq 159 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'Lq' and resid 65 through 68 removed outlier: 3.736A pdb=" N CYSLq 66 " --> pdb=" O ALALq 109 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'Lq' and resid 164 through 170 removed outlier: 3.909A pdb=" N VALLq 32 " --> pdb=" O VALLq 169 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'Cc' and resid 172 through 175 Processing sheet with id= 76, first strand: chain 'Cd' and resid 224 through 228 removed outlier: 4.749A pdb=" N THRCd 205 " --> pdb=" O ILECd 228 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N GLUCd 261 " --> pdb=" O GLYCd 206 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N THRCd 254 " --> pdb=" O LEUCd 274 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARGCd 268 " --> pdb=" O GLNCd 260 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N SERCd 267 " --> pdb=" O ILECd 289 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ASNCd 275 " --> pdb=" O PROCd 281 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THRCd 286 " --> pdb=" O ARGCd 402 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N THRCd 398 " --> pdb=" O ARGCd 290 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'Cd' and resid 307 through 314 removed outlier: 6.147A pdb=" N TYRCd 308 " --> pdb=" O GLYCd 340 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N GLNCd 342 " --> pdb=" O TYRCd 308 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ARGCd 341 " --> pdb=" O TYRCd 360 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ARGCd 357 " --> pdb=" O ILECd 393 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'Cd' and resid 283 through 286 Processing sheet with id= 79, first strand: chain 'Ce' and resid 17 through 20 removed outlier: 7.078A pdb=" N PHECe 17 " --> pdb=" O ARGCe 29 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'Ce' and resid 50 through 56 removed outlier: 4.186A pdb=" N THRCe 60 " --> pdb=" O SERCe 56 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ILECe 61 " --> pdb=" O LEUCe 83 " (cutoff:3.500A) 4178 hydrogen bonds defined for protein. 12423 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2004 hydrogen bonds 3330 hydrogen bond angles 0 basepair planarities 793 basepair parallelities 1291 stacking parallelities Total time for adding SS restraints: 117.59 Time building geometry restraints manager: 54.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 24711 1.33 - 1.45: 49628 1.45 - 1.58: 65970 1.58 - 1.71: 4806 1.71 - 1.83: 443 Bond restraints: 145558 Sorted by residual: bond pdb=" C LEUCH 297 " pdb=" N ASPCH 298 " ideal model delta sigma weight residual 1.331 1.401 -0.070 1.48e-02 4.57e+03 2.25e+01 bond pdb=" C VALLj 70 " pdb=" N PROLj 71 " ideal model delta sigma weight residual 1.335 1.388 -0.053 1.28e-02 6.10e+03 1.71e+01 bond pdb=" N CYSCT 669 " pdb=" CA CYSCT 669 " ideal model delta sigma weight residual 1.463 1.491 -0.028 6.90e-03 2.10e+04 1.67e+01 bond pdb=" C VALLC 149 " pdb=" N PROLC 150 " ideal model delta sigma weight residual 1.336 1.383 -0.047 1.20e-02 6.94e+03 1.50e+01 bond pdb=" CA PROCT 577 " pdb=" C PROCT 577 " ideal model delta sigma weight residual 1.517 1.542 -0.025 6.70e-03 2.23e+04 1.35e+01 ... (remaining 145553 not shown) Histogram of bond angle deviations from ideal: 94.36 - 102.62: 3903 102.62 - 110.87: 63896 110.87 - 119.13: 66330 119.13 - 127.38: 68513 127.38 - 135.63: 5667 Bond angle restraints: 208309 Sorted by residual: angle pdb=" CA PROLB 171 " pdb=" N PROLB 171 " pdb=" CD PROLB 171 " ideal model delta sigma weight residual 112.00 98.69 13.31 1.40e+00 5.10e-01 9.03e+01 angle pdb=" CA PROCH 195 " pdb=" N PROCH 195 " pdb=" CD PROCH 195 " ideal model delta sigma weight residual 112.00 100.72 11.28 1.40e+00 5.10e-01 6.49e+01 angle pdb=" CA PROCP 568 " pdb=" N PROCP 568 " pdb=" CD PROCP 568 " ideal model delta sigma weight residual 112.00 101.06 10.94 1.40e+00 5.10e-01 6.11e+01 angle pdb=" C GLNCA 148 " pdb=" N GLUCA 149 " pdb=" CA GLUCA 149 " ideal model delta sigma weight residual 120.39 129.78 -9.39 1.39e+00 5.18e-01 4.56e+01 angle pdb=" CA PROCG 107 " pdb=" N PROCG 107 " pdb=" CD PROCG 107 " ideal model delta sigma weight residual 112.00 102.59 9.41 1.40e+00 5.10e-01 4.52e+01 ... (remaining 208304 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.64: 83649 35.64 - 71.27: 7334 71.27 - 106.91: 797 106.91 - 142.54: 17 142.54 - 178.18: 22 Dihedral angle restraints: 91819 sinusoidal: 59072 harmonic: 32747 Sorted by residual: dihedral pdb=" O4' UC13158 " pdb=" C1' UC13158 " pdb=" N1 UC13158 " pdb=" C2 UC13158 " ideal model delta sinusoidal sigma weight residual 200.00 36.56 163.44 1 1.50e+01 4.44e-03 8.36e+01 dihedral pdb=" O4' UC2 156 " pdb=" C1' UC2 156 " pdb=" N1 UC2 156 " pdb=" C2 UC2 156 " ideal model delta sinusoidal sigma weight residual 200.00 36.64 163.36 1 1.50e+01 4.44e-03 8.35e+01 dihedral pdb=" O4' UC12417 " pdb=" C1' UC12417 " pdb=" N1 UC12417 " pdb=" C2 UC12417 " ideal model delta sinusoidal sigma weight residual -160.00 0.58 -160.58 1 1.50e+01 4.44e-03 8.29e+01 ... (remaining 91816 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.135: 24942 0.135 - 0.270: 364 0.270 - 0.404: 13 0.404 - 0.539: 2 0.539 - 0.674: 1 Chirality restraints: 25322 Sorted by residual: chirality pdb=" CG LEUCK 260 " pdb=" CB LEUCK 260 " pdb=" CD1 LEUCK 260 " pdb=" CD2 LEUCK 260 " both_signs ideal model delta sigma weight residual False -2.59 -1.92 -0.67 2.00e-01 2.50e+01 1.14e+01 chirality pdb=" CB ILELF 12 " pdb=" CA ILELF 12 " pdb=" CG1 ILELF 12 " pdb=" CG2 ILELF 12 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.45 2.00e-01 2.50e+01 5.11e+00 chirality pdb=" CB VALCM 92 " pdb=" CA VALCM 92 " pdb=" CG1 VALCM 92 " pdb=" CG2 VALCM 92 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.44 2.00e-01 2.50e+01 4.81e+00 ... (remaining 25319 not shown) Planarity restraints: 17768 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYRCP 567 " -0.114 5.00e-02 4.00e+02 1.64e-01 4.28e+01 pdb=" N PROCP 568 " 0.283 5.00e-02 4.00e+02 pdb=" CA PROCP 568 " -0.088 5.00e-02 4.00e+02 pdb=" CD PROCP 568 " -0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' GC12866 " -0.026 2.00e-02 2.50e+03 3.34e-02 3.34e+01 pdb=" N9 GC12866 " 0.009 2.00e-02 2.50e+03 pdb=" C8 GC12866 " 0.003 2.00e-02 2.50e+03 pdb=" N7 GC12866 " -0.005 2.00e-02 2.50e+03 pdb=" C5 GC12866 " 0.005 2.00e-02 2.50e+03 pdb=" C6 GC12866 " 0.025 2.00e-02 2.50e+03 pdb=" O6 GC12866 " -0.034 2.00e-02 2.50e+03 pdb=" N1 GC12866 " -0.013 2.00e-02 2.50e+03 pdb=" C2 GC12866 " 0.088 2.00e-02 2.50e+03 pdb=" N2 GC12866 " -0.053 2.00e-02 2.50e+03 pdb=" N3 GC12866 " 0.001 2.00e-02 2.50e+03 pdb=" C4 GC12866 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLNCG 106 " 0.091 5.00e-02 4.00e+02 1.32e-01 2.80e+01 pdb=" N PROCG 107 " -0.229 5.00e-02 4.00e+02 pdb=" CA PROCG 107 " 0.068 5.00e-02 4.00e+02 pdb=" CD PROCG 107 " 0.070 5.00e-02 4.00e+02 ... (remaining 17765 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 4264 2.66 - 3.22: 114426 3.22 - 3.78: 250303 3.78 - 4.34: 326373 4.34 - 4.90: 471707 Nonbonded interactions: 1167073 Sorted by model distance: nonbonded pdb=" O4 UC11055 " pdb=" C4 CC11063 " model vdw 2.101 2.608 nonbonded pdb=" OG1 THRCR 50 " pdb=" O ASNCR 69 " model vdw 2.146 2.440 nonbonded pdb=" O6 GC1 974 " pdb=" O4 UC11038 " model vdw 2.181 2.432 nonbonded pdb=" O2' CC1 83 " pdb=" O2' CC1 687 " model vdw 2.186 2.440 nonbonded pdb=" OG SERCe 33 " pdb=" O SERCe 35 " model vdw 2.198 2.440 ... (remaining 1167068 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 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: 3.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.110 Extract box with map and model: 17.790 Check model and map are aligned: 1.360 Set scattering table: 0.950 Process input model: 429.060 Find NCS groups from input model: 4.030 Set up NCS constraints: 0.430 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 459.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 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 0.138 145558 Z= 0.291 Angle : 0.852 17.795 208309 Z= 0.447 Chirality : 0.047 0.674 25322 Planarity : 0.008 0.164 17768 Dihedral : 22.000 178.178 70563 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.89 % Favored : 95.96 % Rotamer: Outliers : 1.08 % Allowed : 29.18 % Favored : 69.75 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.03 % 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: -2.63 (0.07), residues: 11105 helix: -2.44 (0.05), residues: 4875 sheet: -0.19 (0.14), residues: 1335 loop : -1.25 (0.08), residues: 4895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRPCb 816 HIS 0.015 0.001 HISCP 316 PHE 0.053 0.003 PHECE 485 TYR 0.087 0.002 TYRCC 306 ARG 0.021 0.001 ARGCQ 100 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22210 Ramachandran restraints generated. 11105 Oldfield, 0 Emsley, 11105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22210 Ramachandran restraints generated. 11105 Oldfield, 0 Emsley, 11105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2926 residues out of total 9661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 2834 time to evaluate : 8.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CA 54 ASP cc_start: 0.8756 (m-30) cc_final: 0.8527 (m-30) REVERT: CA 244 ILE cc_start: 0.8950 (tt) cc_final: 0.8498 (tt) REVERT: CA 262 ILE cc_start: 0.8847 (mm) cc_final: 0.8624 (mm) REVERT: CA 266 LYS cc_start: 0.8502 (ttmt) cc_final: 0.8160 (ttpt) REVERT: CB 264 ARG cc_start: 0.8234 (mtp-110) cc_final: 0.7908 (ttp80) REVERT: CB 271 VAL cc_start: 0.9005 (t) cc_final: 0.8747 (t) REVERT: CC 293 LYS cc_start: 0.8881 (ttmm) cc_final: 0.8666 (ttpt) REVERT: CC 304 LEU cc_start: 0.8703 (tp) cc_final: 0.8469 (mt) REVERT: CC 338 MET cc_start: 0.0862 (mmm) cc_final: 0.0403 (tpt) REVERT: CC 361 LEU cc_start: 0.5992 (mt) cc_final: 0.5420 (tp) REVERT: CE 124 LYS cc_start: 0.8564 (ttmt) cc_final: 0.7941 (tttm) REVERT: CE 444 ARG cc_start: 0.8544 (mtm110) cc_final: 0.8288 (ttp80) REVERT: CE 513 GLU cc_start: 0.8235 (mt-10) cc_final: 0.8032 (mm-30) REVERT: CF 25 ARG cc_start: 0.8200 (ttm-80) cc_final: 0.7939 (mtp-110) REVERT: CF 36 LYS cc_start: 0.9125 (ttmt) cc_final: 0.8646 (ttmt) REVERT: CG 43 ASP cc_start: 0.8142 (m-30) cc_final: 0.7857 (m-30) REVERT: CG 63 LYS cc_start: 0.7678 (tppt) cc_final: 0.7426 (tppt) REVERT: CG 116 LYS cc_start: 0.8559 (tptp) cc_final: 0.7731 (ttmt) REVERT: CG 166 ARG cc_start: 0.8688 (tmm-80) cc_final: 0.8202 (ttt-90) REVERT: CH 37 LYS cc_start: 0.8230 (mtmm) cc_final: 0.7920 (mmtt) REVERT: CH 79 ASP cc_start: 0.8487 (m-30) cc_final: 0.8279 (m-30) REVERT: CH 129 ARG cc_start: 0.8656 (mtp-110) cc_final: 0.8262 (mtp85) REVERT: CH 174 PHE cc_start: 0.8987 (OUTLIER) cc_final: 0.8485 (t80) REVERT: CH 224 LEU cc_start: 0.8035 (mm) cc_final: 0.7713 (mt) REVERT: CH 254 ASP cc_start: 0.8530 (t0) cc_final: 0.8136 (t70) REVERT: CH 306 ASN cc_start: 0.8276 (m110) cc_final: 0.7938 (m-40) REVERT: CI 199 TYR cc_start: 0.8302 (m-10) cc_final: 0.7734 (m-10) REVERT: CJ 32 ASP cc_start: 0.6553 (t70) cc_final: 0.6193 (t0) REVERT: CJ 46 GLU cc_start: 0.7312 (mm-30) cc_final: 0.6820 (tp30) REVERT: CJ 97 ARG cc_start: 0.6061 (mmt180) cc_final: 0.5630 (mmm160) REVERT: CJ 99 ASP cc_start: 0.6713 (t0) cc_final: 0.6244 (t70) REVERT: CJ 119 PRO cc_start: 0.5739 (Cg_endo) cc_final: 0.5484 (Cg_exo) REVERT: CJ 384 GLU cc_start: 0.6880 (mm-30) cc_final: 0.6388 (mm-30) REVERT: CJ 466 ASN cc_start: 0.5138 (m110) cc_final: 0.4728 (m-40) REVERT: CK 21 GLU cc_start: 0.7928 (mp0) cc_final: 0.7674 (mp0) REVERT: CK 37 GLU cc_start: 0.7756 (tt0) cc_final: 0.7490 (tt0) REVERT: CK 69 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7542 (tm-30) REVERT: CK 180 LYS cc_start: 0.9207 (mtmm) cc_final: 0.8783 (mttp) REVERT: CL 16 LYS cc_start: 0.6626 (mmmm) cc_final: 0.6404 (mttt) REVERT: CM 113 ARG cc_start: 0.8132 (ptt-90) cc_final: 0.7848 (ptm-80) REVERT: CM 154 ILE cc_start: 0.7617 (OUTLIER) cc_final: 0.7138 (tp) REVERT: CM 213 LEU cc_start: 0.6411 (mp) cc_final: 0.5142 (tt) REVERT: CM 239 GLU cc_start: 0.8572 (mp0) cc_final: 0.8359 (mm-30) REVERT: CP 292 GLU cc_start: 0.7883 (tt0) cc_final: 0.7476 (tm-30) REVERT: CP 369 SER cc_start: 0.8954 (m) cc_final: 0.8569 (p) REVERT: CP 394 LYS cc_start: 0.9058 (mmmm) cc_final: 0.8857 (mmtp) REVERT: CP 468 ASP cc_start: 0.8242 (t70) cc_final: 0.7953 (t0) REVERT: CP 479 ASP cc_start: 0.8404 (m-30) cc_final: 0.8133 (m-30) REVERT: CP 537 VAL cc_start: 0.7907 (m) cc_final: 0.7060 (m) REVERT: CP 577 PHE cc_start: 0.7989 (t80) cc_final: 0.7763 (t80) REVERT: CQ 41 LYS cc_start: 0.8828 (mmpt) cc_final: 0.7940 (mtmt) REVERT: CQ 49 LEU cc_start: 0.8438 (mp) cc_final: 0.8234 (mp) REVERT: CR 4 GLU cc_start: 0.7932 (mp0) cc_final: 0.7630 (mp0) REVERT: CS 700 GLU cc_start: 0.4384 (mm-30) cc_final: 0.3735 (tm-30) REVERT: CU 225 ARG cc_start: 0.7810 (ptp-110) cc_final: 0.7024 (ttm-80) REVERT: CU 241 LEU cc_start: 0.9124 (tp) cc_final: 0.8848 (tp) REVERT: CU 328 ARG cc_start: 0.8621 (mtm180) cc_final: 0.8349 (mtm110) REVERT: CX 101 MET cc_start: 0.6371 (ppp) cc_final: 0.5979 (ptt) REVERT: Cb 166 LEU cc_start: 0.8593 (mm) cc_final: 0.8378 (mm) REVERT: Cb 177 LEU cc_start: 0.8347 (tp) cc_final: 0.8143 (tp) REVERT: Cb 434 VAL cc_start: 0.8421 (t) cc_final: 0.8199 (p) REVERT: Cb 563 VAL cc_start: 0.9309 (m) cc_final: 0.8919 (p) REVERT: Cb 602 THR cc_start: 0.7745 (m) cc_final: 0.7514 (p) REVERT: LB 147 ARG cc_start: 0.8550 (ttp-110) cc_final: 0.8331 (ttp-170) REVERT: LB 211 GLU cc_start: 0.8495 (pt0) cc_final: 0.8290 (pt0) REVERT: LB 217 ASP cc_start: 0.8602 (m-30) cc_final: 0.8378 (m-30) REVERT: LB 271 MET cc_start: 0.8012 (mtp) cc_final: 0.7643 (mmp) REVERT: LB 300 ASP cc_start: 0.8704 (t0) cc_final: 0.8466 (t0) REVERT: LB 337 MET cc_start: 0.9097 (mmt) cc_final: 0.8621 (mmt) REVERT: LB 350 LYS cc_start: 0.8355 (mptt) cc_final: 0.7888 (mmtp) REVERT: LB 354 LYS cc_start: 0.8899 (ptmm) cc_final: 0.8611 (mmtt) REVERT: LC 37 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8417 (tttt) REVERT: LC 187 LYS cc_start: 0.8222 (mtpt) cc_final: 0.7597 (mmmt) REVERT: LC 264 GLN cc_start: 0.8295 (mm-40) cc_final: 0.7973 (mm-40) REVERT: LE 64 ARG cc_start: 0.7268 (ptm160) cc_final: 0.6130 (ptm160) REVERT: LE 118 LYS cc_start: 0.9127 (mmtm) cc_final: 0.8773 (tptp) REVERT: LE 178 MET cc_start: 0.8831 (mtt) cc_final: 0.8363 (mtt) REVERT: LE 191 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7447 (mttp) REVERT: LE 194 LYS cc_start: 0.8878 (mttt) cc_final: 0.8617 (mtmm) REVERT: LF 17 THR cc_start: 0.8754 (m) cc_final: 0.8028 (m) REVERT: LF 88 LYS cc_start: 0.8403 (mtmt) cc_final: 0.8155 (mttp) REVERT: LF 174 ILE cc_start: 0.8520 (pt) cc_final: 0.8260 (pt) REVERT: LF 176 GLU cc_start: 0.8300 (tt0) cc_final: 0.8069 (tt0) REVERT: LF 212 LYS cc_start: 0.8453 (mttt) cc_final: 0.8016 (mtpt) REVERT: LG 52 MET cc_start: 0.2045 (ptm) cc_final: 0.0272 (tmm) REVERT: LG 60 ARG cc_start: 0.7818 (ttp-110) cc_final: 0.7366 (ttp80) REVERT: LG 87 LYS cc_start: 0.8762 (tttt) cc_final: 0.8517 (tttm) REVERT: LH 102 ASN cc_start: 0.8697 (m110) cc_final: 0.8187 (m110) REVERT: LH 182 TYR cc_start: 0.9327 (m-80) cc_final: 0.9100 (m-80) REVERT: LK 135 THR cc_start: 0.8977 (m) cc_final: 0.8701 (m) REVERT: LL 17 HIS cc_start: 0.6357 (t-90) cc_final: 0.6064 (m170) REVERT: LL 23 ARG cc_start: 0.7914 (ttm110) cc_final: 0.7090 (tpt90) REVERT: LL 117 LYS cc_start: 0.8592 (mmmm) cc_final: 0.8224 (mmtt) REVERT: LL 118 ASP cc_start: 0.8448 (m-30) cc_final: 0.8082 (t0) REVERT: LN 9 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8356 (mm-30) REVERT: LN 104 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7886 (mt-10) REVERT: LO 5 GLU cc_start: 0.7433 (mm-30) cc_final: 0.7075 (mm-30) REVERT: LO 102 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7270 (mt-10) REVERT: LO 160 GLU cc_start: 0.8414 (tp30) cc_final: 0.8127 (mm-30) REVERT: LO 161 ARG cc_start: 0.8014 (mtm180) cc_final: 0.7779 (mtm-85) REVERT: LO 192 ASP cc_start: 0.8716 (t0) cc_final: 0.8500 (t0) REVERT: LQ 48 LYS cc_start: 0.7968 (mttt) cc_final: 0.7587 (mttt) REVERT: LQ 69 GLU cc_start: 0.7855 (mp0) cc_final: 0.7569 (pm20) REVERT: LQ 97 ARG cc_start: 0.7289 (mtt90) cc_final: 0.7076 (mtp85) REVERT: LQ 126 MET cc_start: 0.8940 (ptt) cc_final: 0.8711 (ptm) REVERT: LS 91 TYR cc_start: 0.9237 (t80) cc_final: 0.9018 (t80) REVERT: LS 109 ASP cc_start: 0.9192 (t0) cc_final: 0.8982 (t70) REVERT: LT 52 MET cc_start: 0.3205 (ptm) cc_final: 0.2664 (mmt) REVERT: LT 107 ARG cc_start: 0.7438 (ttp80) cc_final: 0.7156 (ttt-90) REVERT: LV 139 MET cc_start: 0.7535 (OUTLIER) cc_final: 0.7051 (mtm) REVERT: Ld 18 ARG cc_start: 0.8179 (ptp-110) cc_final: 0.7798 (ptp-110) REVERT: Le 25 ARG cc_start: 0.6972 (mtp-110) cc_final: 0.6558 (mmm160) REVERT: Le 96 GLU cc_start: 0.8292 (tt0) cc_final: 0.7870 (tt0) REVERT: Lf 24 ASN cc_start: 0.7932 (m-40) cc_final: 0.7664 (m-40) REVERT: Lf 39 ASP cc_start: 0.7760 (m-30) cc_final: 0.7504 (p0) REVERT: Lf 50 ARG cc_start: 0.8425 (mmm160) cc_final: 0.8206 (mmm-85) REVERT: Lh 34 LEU cc_start: 0.8273 (mm) cc_final: 0.7762 (tp) REVERT: Lh 47 ASN cc_start: 0.8055 (m110) cc_final: 0.7315 (t0) REVERT: Lh 96 ARG cc_start: 0.8024 (ttm-80) cc_final: 0.7713 (ttm170) REVERT: Li 107 ARG cc_start: 0.8510 (ptp90) cc_final: 0.8011 (mtt90) REVERT: Lj 51 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7395 (mp0) REVERT: Lj 57 LYS cc_start: 0.8131 (ptpt) cc_final: 0.7338 (ptmm) REVERT: Lq 165 MET cc_start: -0.2382 (ttt) cc_final: -0.3359 (ttt) REVERT: Cc 157 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7978 (mt-10) REVERT: Cd 10 SER cc_start: 0.8504 (m) cc_final: 0.8156 (t) REVERT: Cd 23 LYS cc_start: 0.8087 (tttp) cc_final: 0.7633 (tttt) REVERT: Cd 49 GLU cc_start: 0.8307 (mt-10) cc_final: 0.7922 (mt-10) REVERT: Cd 92 LEU cc_start: 0.8995 (mt) cc_final: 0.8590 (mp) REVERT: Cd 213 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8171 (mmtp) REVERT: Cd 261 GLU cc_start: 0.8129 (pt0) cc_final: 0.7858 (tt0) REVERT: Cd 436 LEU cc_start: 0.7042 (tt) cc_final: 0.6838 (tp) REVERT: Ce 13 GLN cc_start: 0.7584 (mm-40) cc_final: 0.7177 (tm-30) REVERT: Ce 31 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7538 (mt-10) REVERT: Ce 73 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8723 (mtm) REVERT: Ce 103 LYS cc_start: 0.8310 (mtmm) cc_final: 0.8011 (pttp) REVERT: Ce 161 LYS cc_start: 0.8506 (ptpp) cc_final: 0.8275 (mtmm) REVERT: Cf 533 LYS cc_start: 0.8301 (mttt) cc_final: 0.8031 (mttp) REVERT: Cf 537 GLU cc_start: 0.6615 (mt-10) cc_final: 0.6181 (mm-30) outliers start: 92 outliers final: 20 residues processed: 2874 average time/residue: 1.2957 time to fit residues: 6234.5119 Evaluate side-chains 1719 residues out of total 9661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 1692 time to evaluate : 8.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CB residue 89 LEU Chi-restraints excluded: chain CB residue 90 ASN Chi-restraints excluded: chain CB residue 91 THR Chi-restraints excluded: chain CC residue 175 ILE Chi-restraints excluded: chain CH residue 174 PHE Chi-restraints excluded: chain CH residue 323 THR Chi-restraints excluded: chain CM residue 154 ILE Chi-restraints excluded: chain CM residue 197 VAL Chi-restraints excluded: chain CN residue 161 VAL Chi-restraints excluded: chain CP residue 576 PHE Chi-restraints excluded: chain CR residue 212 ASP Chi-restraints excluded: chain CX residue 113 GLN Chi-restraints excluded: chain LC residue 37 LYS Chi-restraints excluded: chain LC residue 223 VAL Chi-restraints excluded: chain LE residue 191 LYS Chi-restraints excluded: chain LH residue 41 ILE Chi-restraints excluded: chain LL residue 58 VAL Chi-restraints excluded: chain LL residue 69 THR Chi-restraints excluded: chain LM residue 14 VAL Chi-restraints excluded: chain LM residue 20 LEU Chi-restraints excluded: chain LS residue 161 THR Chi-restraints excluded: chain LV residue 139 MET Chi-restraints excluded: chain LY residue 78 VAL Chi-restraints excluded: chain LY residue 86 ARG Chi-restraints excluded: chain Ld residue 102 GLN Chi-restraints excluded: chain Cd residue 213 LYS Chi-restraints excluded: chain Ce residue 73 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1346 random chunks: chunk 1136 optimal weight: 9.9990 chunk 1020 optimal weight: 7.9990 chunk 566 optimal weight: 0.7980 chunk 348 optimal weight: 9.9990 chunk 688 optimal weight: 30.0000 chunk 545 optimal weight: 9.9990 chunk 1054 optimal weight: 5.9990 chunk 408 optimal weight: 1.9990 chunk 641 optimal weight: 3.9990 chunk 785 optimal weight: 0.6980 chunk 1222 optimal weight: 6.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CA 167 GLN CA 286 GLN CB 90 ASN CE 299 GLN ** CE 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CF 39 HIS ** CG 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CH 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CH 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CH 333 HIS ** CI 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 153 ASN ** CJ 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CK 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CM 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CN 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CN 140 GLN CO 20 ASN CP 411 ASN ** CQ 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CR 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CR 186 HIS CR 216 ASN Cz 30 GLN Cb 155 HIS ** Cb 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cb 323 HIS LB 109 HIS LB 185 ASN LB 320 ASN LB 368 HIS LC 59 HIS LC 88 GLN LC 250 HIS ** LC 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 292 ASN LE 162 GLN LF 110 GLN LG 140 ASN LG 141 HIS LH 188 ASN LL 66 ASN LM 126 GLN LN 57 GLN LN 138 ASN LN 195 ASN LP 72 GLN LP 158 GLN LS 5 GLN ** LS 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LS 88 HIS LS 142 GLN ** Lh 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 118 GLN Lq 27 ASN Cc 234 GLN Cd 26 GLN Cd 44 HIS Cd 250 ASN ** Ce 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cf 521 GLN Cf 524 GLN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 145558 Z= 0.297 Angle : 0.651 12.720 208309 Z= 0.336 Chirality : 0.041 0.278 25322 Planarity : 0.006 0.119 17768 Dihedral : 21.787 179.824 49869 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.78 % Favored : 96.09 % Rotamer: Outliers : 5.05 % Allowed : 21.94 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.08), residues: 11105 helix: 0.09 (0.07), residues: 4980 sheet: -0.12 (0.14), residues: 1372 loop : -1.08 (0.09), residues: 4753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRPCb 816 HIS 0.011 0.001 HISCH 369 PHE 0.033 0.002 PHECJ 151 TYR 0.029 0.002 TYRLO 151 ARG 0.018 0.001 ARGCJ 217 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22210 Ramachandran restraints generated. 11105 Oldfield, 0 Emsley, 11105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22210 Ramachandran restraints generated. 11105 Oldfield, 0 Emsley, 11105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2090 residues out of total 9661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 431 poor density : 1659 time to evaluate : 8.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CA 71 LYS cc_start: 0.6951 (mmtm) cc_final: 0.6342 (ptpp) REVERT: CA 201 LYS cc_start: 0.7648 (OUTLIER) cc_final: 0.7269 (mttp) REVERT: CA 257 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7821 (mm-30) REVERT: CA 285 GLN cc_start: 0.8041 (mt0) cc_final: 0.7813 (tt0) REVERT: CB 47 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.8270 (tt0) REVERT: CB 276 GLN cc_start: 0.6717 (tm-30) cc_final: 0.5401 (tm-30) REVERT: CC 121 PHE cc_start: 0.7105 (m-80) cc_final: 0.6866 (m-80) REVERT: CC 338 MET cc_start: 0.0572 (mmm) cc_final: 0.0244 (tpt) REVERT: CC 361 LEU cc_start: 0.5950 (mt) cc_final: 0.5233 (tp) REVERT: CC 373 MET cc_start: 0.1849 (ppp) cc_final: 0.0972 (ppp) REVERT: CE 124 LYS cc_start: 0.8387 (ttmt) cc_final: 0.8112 (tttm) REVERT: CE 156 LYS cc_start: 0.7993 (mttt) cc_final: 0.7615 (pttp) REVERT: CE 302 LYS cc_start: 0.8961 (mmmm) cc_final: 0.8630 (mtmt) REVERT: CE 308 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.8224 (ptp-110) REVERT: CE 440 ASP cc_start: 0.8346 (t0) cc_final: 0.7705 (t0) REVERT: CH 37 LYS cc_start: 0.8192 (mtmm) cc_final: 0.7969 (mmtt) REVERT: CH 79 ASP cc_start: 0.8579 (m-30) cc_final: 0.8326 (m-30) REVERT: CH 174 PHE cc_start: 0.8901 (OUTLIER) cc_final: 0.8331 (t80) REVERT: CH 254 ASP cc_start: 0.8527 (t0) cc_final: 0.8148 (t70) REVERT: CH 306 ASN cc_start: 0.8241 (m110) cc_final: 0.7935 (m-40) REVERT: CI 260 CYS cc_start: 0.8846 (m) cc_final: 0.8512 (m) REVERT: CJ 32 ASP cc_start: 0.7016 (t70) cc_final: 0.6358 (t0) REVERT: CJ 97 ARG cc_start: 0.5858 (mmt180) cc_final: 0.5614 (mmm160) REVERT: CK 37 GLU cc_start: 0.7737 (tt0) cc_final: 0.7469 (tt0) REVERT: CK 162 THR cc_start: 0.8216 (p) cc_final: 0.7936 (m) REVERT: CK 180 LYS cc_start: 0.9185 (mtmm) cc_final: 0.8759 (mttp) REVERT: CL 16 LYS cc_start: 0.7051 (mmmm) cc_final: 0.6381 (mttt) REVERT: CL 23 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8356 (ttpp) REVERT: CM 132 MET cc_start: 0.8151 (mmp) cc_final: 0.7913 (mmt) REVERT: CN 26 VAL cc_start: 0.8778 (OUTLIER) cc_final: 0.8565 (m) REVERT: CP 369 SER cc_start: 0.8962 (m) cc_final: 0.8573 (p) REVERT: CP 559 SER cc_start: 0.8329 (OUTLIER) cc_final: 0.8124 (t) REVERT: CQ 100 ARG cc_start: 0.8798 (ttm170) cc_final: 0.8511 (ttt-90) REVERT: CR 135 GLN cc_start: 0.7560 (mt0) cc_final: 0.7329 (mt0) REVERT: CR 196 GLN cc_start: 0.9138 (tp-100) cc_final: 0.8674 (tp40) REVERT: CS 700 GLU cc_start: 0.4336 (mm-30) cc_final: 0.3620 (tm-30) REVERT: CU 241 LEU cc_start: 0.9176 (tp) cc_final: 0.8909 (tp) REVERT: CU 270 ASP cc_start: 0.7260 (t0) cc_final: 0.6982 (t0) REVERT: CU 310 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8033 (ttmm) REVERT: Cb 322 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8310 (mm) REVERT: Cb 395 TYR cc_start: 0.8897 (p90) cc_final: 0.8648 (p90) REVERT: Cb 434 VAL cc_start: 0.8413 (t) cc_final: 0.8180 (p) REVERT: LB 66 LYS cc_start: 0.8941 (ttmm) cc_final: 0.8510 (tttm) REVERT: LB 77 THR cc_start: 0.9196 (t) cc_final: 0.8975 (m) REVERT: LB 123 TYR cc_start: 0.9221 (p90) cc_final: 0.8868 (p90) REVERT: LB 271 MET cc_start: 0.8017 (mtp) cc_final: 0.7615 (mmp) REVERT: LB 350 LYS cc_start: 0.8455 (mptt) cc_final: 0.7768 (mttm) REVERT: LB 354 LYS cc_start: 0.8876 (ptmm) cc_final: 0.8549 (mmtt) REVERT: LB 365 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7223 (pt0) REVERT: LC 37 LYS cc_start: 0.8497 (tttm) cc_final: 0.8159 (tttt) REVERT: LC 64 GLU cc_start: 0.8031 (tp30) cc_final: 0.7704 (pm20) REVERT: LC 187 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7697 (mmmt) REVERT: LC 220 LYS cc_start: 0.8492 (mttt) cc_final: 0.7782 (mtmm) REVERT: LC 233 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8266 (mt-10) REVERT: LC 264 GLN cc_start: 0.8347 (mm-40) cc_final: 0.7967 (mm-40) REVERT: LE 64 ARG cc_start: 0.7512 (ptm160) cc_final: 0.6341 (ptm160) REVERT: LF 37 GLU cc_start: 0.8494 (tp30) cc_final: 0.8158 (tp30) REVERT: LF 88 LYS cc_start: 0.8687 (mtmt) cc_final: 0.8318 (mttp) REVERT: LF 212 LYS cc_start: 0.8451 (mttt) cc_final: 0.8108 (mtmt) REVERT: LG 52 MET cc_start: 0.2349 (ptm) cc_final: 0.0576 (tmm) REVERT: LG 60 ARG cc_start: 0.7794 (ttp-110) cc_final: 0.7566 (ttp80) REVERT: LG 87 LYS cc_start: 0.8503 (tttt) cc_final: 0.8217 (tttm) REVERT: LG 115 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7735 (mt-10) REVERT: LH 182 TYR cc_start: 0.9315 (m-80) cc_final: 0.8950 (m-80) REVERT: LL 17 HIS cc_start: 0.6543 (t-90) cc_final: 0.6174 (m170) REVERT: LL 23 ARG cc_start: 0.7878 (ttm110) cc_final: 0.6954 (tpt90) REVERT: LM 13 ARG cc_start: 0.8360 (mmt-90) cc_final: 0.7972 (mmt180) REVERT: LN 9 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8521 (mm-30) REVERT: LN 104 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7868 (mt-10) REVERT: LN 140 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.7861 (tttt) REVERT: LO 5 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7197 (mm-30) REVERT: LO 89 MET cc_start: 0.8893 (mtt) cc_final: 0.8307 (mtt) REVERT: LO 102 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7149 (mt-10) REVERT: LO 160 GLU cc_start: 0.8271 (tp30) cc_final: 0.7888 (mm-30) REVERT: LO 161 ARG cc_start: 0.7976 (mtm180) cc_final: 0.7759 (mtm-85) REVERT: LO 192 ASP cc_start: 0.8737 (t0) cc_final: 0.8524 (t0) REVERT: LP 12 THR cc_start: 0.8984 (OUTLIER) cc_final: 0.8741 (m) REVERT: LP 18 ARG cc_start: 0.8553 (mtp85) cc_final: 0.8310 (mtp85) REVERT: LP 60 MET cc_start: 0.8517 (mmt) cc_final: 0.8292 (mmt) REVERT: LP 139 TYR cc_start: 0.8010 (m-80) cc_final: 0.7739 (m-80) REVERT: LQ 48 LYS cc_start: 0.8089 (mttt) cc_final: 0.7615 (mmtt) REVERT: LQ 69 GLU cc_start: 0.7835 (mp0) cc_final: 0.7610 (mp0) REVERT: LQ 97 ARG cc_start: 0.7514 (mtt90) cc_final: 0.6493 (mtt90) REVERT: LS 91 TYR cc_start: 0.9403 (t80) cc_final: 0.9165 (t80) REVERT: LT 52 MET cc_start: 0.3553 (ptm) cc_final: 0.2857 (mmt) REVERT: LV 50 ARG cc_start: 0.5692 (ptm160) cc_final: 0.5096 (ptm160) REVERT: LV 139 MET cc_start: 0.7794 (mtm) cc_final: 0.7397 (mtm) REVERT: LY 54 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7843 (mm-30) REVERT: LY 122 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8763 (tttt) REVERT: LY 127 GLN cc_start: 0.8542 (tm-30) cc_final: 0.8170 (tt0) REVERT: Le 25 ARG cc_start: 0.7113 (OUTLIER) cc_final: 0.6593 (mmm160) REVERT: Le 84 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7907 (mp0) REVERT: Le 96 GLU cc_start: 0.8342 (tt0) cc_final: 0.7860 (tt0) REVERT: Le 124 LYS cc_start: 0.8541 (ptpt) cc_final: 0.8312 (pttt) REVERT: Lf 50 ARG cc_start: 0.8445 (mmm160) cc_final: 0.8228 (mmm-85) REVERT: Lh 78 LYS cc_start: 0.8985 (mmtt) cc_final: 0.8761 (mmtt) REVERT: Li 107 ARG cc_start: 0.8339 (ptp90) cc_final: 0.8019 (mtt90) REVERT: Lj 57 LYS cc_start: 0.8424 (ptpt) cc_final: 0.7460 (ptmm) REVERT: Lq 165 MET cc_start: -0.2253 (ttt) cc_final: -0.3325 (mtt) REVERT: Cc 100 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7400 (mm-30) REVERT: Cc 199 ASP cc_start: 0.8514 (m-30) cc_final: 0.8302 (m-30) REVERT: Cc 220 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.8278 (mpp) REVERT: Cd 10 SER cc_start: 0.8599 (m) cc_final: 0.8136 (t) REVERT: Cd 48 LYS cc_start: 0.8498 (mtpt) cc_final: 0.8292 (mtmt) REVERT: Ce 13 GLN cc_start: 0.7724 (mm-40) cc_final: 0.7242 (tm-30) REVERT: Ce 79 GLU cc_start: 0.7814 (tt0) cc_final: 0.7609 (tt0) REVERT: Ce 103 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.8000 (pttp) REVERT: Ce 147 LYS cc_start: 0.8085 (tttt) cc_final: 0.7623 (tttm) REVERT: Ce 161 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8464 (mttp) REVERT: Cf 533 LYS cc_start: 0.8327 (mttt) cc_final: 0.8032 (mttp) outliers start: 431 outliers final: 215 residues processed: 1956 average time/residue: 1.3217 time to fit residues: 4470.9436 Evaluate side-chains 1717 residues out of total 9661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 1482 time to evaluate : 8.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CA residue 72 SER Chi-restraints excluded: chain CA residue 132 CYS Chi-restraints excluded: chain CA residue 149 GLU Chi-restraints excluded: chain CA residue 176 ILE Chi-restraints excluded: chain CA residue 198 GLU Chi-restraints excluded: chain CA residue 201 LYS Chi-restraints excluded: chain CA residue 241 THR Chi-restraints excluded: chain CB residue 47 GLN Chi-restraints excluded: chain CB residue 48 ASN Chi-restraints excluded: chain CB residue 63 TRP Chi-restraints excluded: chain CB residue 70 LYS Chi-restraints excluded: chain CB residue 89 LEU Chi-restraints excluded: chain CB residue 91 THR Chi-restraints excluded: chain CB residue 119 ASP Chi-restraints excluded: chain CB residue 131 SER Chi-restraints excluded: chain CB residue 145 LYS Chi-restraints excluded: chain CB residue 165 LYS Chi-restraints excluded: chain CB residue 232 LEU Chi-restraints excluded: chain CB residue 241 THR Chi-restraints excluded: chain CC residue 175 ILE Chi-restraints excluded: chain CC residue 352 LEU Chi-restraints excluded: chain CE residue 121 LYS Chi-restraints excluded: chain CE residue 175 SER Chi-restraints excluded: chain CE residue 300 THR Chi-restraints excluded: chain CE residue 308 ARG Chi-restraints excluded: chain CE residue 319 ASN Chi-restraints excluded: chain CE residue 382 LEU Chi-restraints excluded: chain CE residue 533 VAL Chi-restraints excluded: chain CF residue 65 ILE Chi-restraints excluded: chain CF residue 79 THR Chi-restraints excluded: chain CF residue 142 VAL Chi-restraints excluded: chain CF residue 155 VAL Chi-restraints excluded: chain CF residue 162 GLU Chi-restraints excluded: chain CF residue 175 ILE Chi-restraints excluded: chain CF residue 202 ASP Chi-restraints excluded: chain CF residue 205 GLN Chi-restraints excluded: chain CG residue 5 THR Chi-restraints excluded: chain CG residue 13 LEU Chi-restraints excluded: chain CG residue 59 VAL Chi-restraints excluded: chain CG residue 65 LEU Chi-restraints excluded: chain CG residue 115 VAL Chi-restraints excluded: chain CG residue 122 TRP Chi-restraints excluded: chain CG residue 130 SER Chi-restraints excluded: chain CH residue 32 ILE Chi-restraints excluded: chain CH residue 69 VAL Chi-restraints excluded: chain CH residue 85 TYR Chi-restraints excluded: chain CH residue 174 PHE Chi-restraints excluded: chain CH residue 233 THR Chi-restraints excluded: chain CH residue 264 LYS Chi-restraints excluded: chain CH residue 330 VAL Chi-restraints excluded: chain CH residue 343 VAL Chi-restraints excluded: chain CH residue 372 THR Chi-restraints excluded: chain CH residue 390 LEU Chi-restraints excluded: chain CH residue 395 LYS Chi-restraints excluded: chain CH residue 406 ASP Chi-restraints excluded: chain CI residue 203 LEU Chi-restraints excluded: chain CI residue 216 LEU Chi-restraints excluded: chain CI residue 218 VAL Chi-restraints excluded: chain CI residue 224 THR Chi-restraints excluded: chain CI residue 303 GLN Chi-restraints excluded: chain CJ residue 68 ASP Chi-restraints excluded: chain CJ residue 263 ASP Chi-restraints excluded: chain CK residue 199 SER Chi-restraints excluded: chain CK residue 254 CYS Chi-restraints excluded: chain CL residue 12 THR Chi-restraints excluded: chain CL residue 18 THR Chi-restraints excluded: chain CL residue 23 LYS Chi-restraints excluded: chain CL residue 27 ARG Chi-restraints excluded: chain CM residue 92 VAL Chi-restraints excluded: chain CM residue 93 ILE Chi-restraints excluded: chain CM residue 95 ILE Chi-restraints excluded: chain CM residue 112 LEU Chi-restraints excluded: chain CM residue 121 VAL Chi-restraints excluded: chain CM residue 140 VAL Chi-restraints excluded: chain CM residue 147 LEU Chi-restraints excluded: chain CM residue 196 THR Chi-restraints excluded: chain CN residue 1 MET Chi-restraints excluded: chain CN residue 18 THR Chi-restraints excluded: chain CN residue 26 VAL Chi-restraints excluded: chain CN residue 49 CYS Chi-restraints excluded: chain CN residue 52 THR Chi-restraints excluded: chain CN residue 98 GLU Chi-restraints excluded: chain CN residue 161 VAL Chi-restraints excluded: chain CN residue 198 VAL Chi-restraints excluded: chain CN residue 242 VAL Chi-restraints excluded: chain CO residue 40 ILE Chi-restraints excluded: chain CP residue 270 ILE Chi-restraints excluded: chain CP residue 334 VAL Chi-restraints excluded: chain CP residue 407 VAL Chi-restraints excluded: chain CP residue 470 SER Chi-restraints excluded: chain CP residue 471 VAL Chi-restraints excluded: chain CP residue 490 LEU Chi-restraints excluded: chain CP residue 559 SER Chi-restraints excluded: chain CQ residue 43 LYS Chi-restraints excluded: chain CR residue 32 ASN Chi-restraints excluded: chain CR residue 33 ASN Chi-restraints excluded: chain CR residue 45 LEU Chi-restraints excluded: chain CR residue 127 GLU Chi-restraints excluded: chain CR residue 131 VAL Chi-restraints excluded: chain CS residue 668 THR Chi-restraints excluded: chain CU residue 196 LEU Chi-restraints excluded: chain CU residue 215 SER Chi-restraints excluded: chain CU residue 228 ASP Chi-restraints excluded: chain CU residue 233 ILE Chi-restraints excluded: chain CU residue 296 LYS Chi-restraints excluded: chain CU residue 310 LYS Chi-restraints excluded: chain CU residue 322 GLU Chi-restraints excluded: chain CU residue 355 ASP Chi-restraints excluded: chain CX residue 141 GLU Chi-restraints excluded: chain Cz residue 30 GLN Chi-restraints excluded: chain Cb residue 141 THR Chi-restraints excluded: chain Cb residue 176 THR Chi-restraints excluded: chain Cb residue 179 VAL Chi-restraints excluded: chain Cb residue 274 THR Chi-restraints excluded: chain Cb residue 275 LEU Chi-restraints excluded: chain Cb residue 304 ASP Chi-restraints excluded: chain Cb residue 322 LEU Chi-restraints excluded: chain Cb residue 388 LEU Chi-restraints excluded: chain Cb residue 393 VAL Chi-restraints excluded: chain Cb residue 490 VAL Chi-restraints excluded: chain LB residue 14 LEU Chi-restraints excluded: chain LB residue 158 VAL Chi-restraints excluded: chain LB residue 199 LEU Chi-restraints excluded: chain LB residue 214 GLU Chi-restraints excluded: chain LB residue 329 VAL Chi-restraints excluded: chain LB residue 359 TRP Chi-restraints excluded: chain LB residue 365 GLU Chi-restraints excluded: chain LC residue 28 SER Chi-restraints excluded: chain LC residue 62 SER Chi-restraints excluded: chain LC residue 68 THR Chi-restraints excluded: chain LC residue 112 VAL Chi-restraints excluded: chain LC residue 146 VAL Chi-restraints excluded: chain LC residue 187 LYS Chi-restraints excluded: chain LC residue 283 SER Chi-restraints excluded: chain LE residue 102 VAL Chi-restraints excluded: chain LE residue 106 SER Chi-restraints excluded: chain LE residue 109 VAL Chi-restraints excluded: chain LF residue 18 LEU Chi-restraints excluded: chain LF residue 74 ILE Chi-restraints excluded: chain LF residue 90 VAL Chi-restraints excluded: chain LF residue 117 ILE Chi-restraints excluded: chain LG residue 68 LEU Chi-restraints excluded: chain LG residue 85 LEU Chi-restraints excluded: chain LG residue 105 LYS Chi-restraints excluded: chain LG residue 191 THR Chi-restraints excluded: chain LG residue 193 VAL Chi-restraints excluded: chain LG residue 210 ASP Chi-restraints excluded: chain LG residue 234 LYS Chi-restraints excluded: chain LH residue 15 ASN Chi-restraints excluded: chain LH residue 19 SER Chi-restraints excluded: chain LH residue 36 LYS Chi-restraints excluded: chain LH residue 41 ILE Chi-restraints excluded: chain LH residue 55 LEU Chi-restraints excluded: chain LH residue 56 GLU Chi-restraints excluded: chain LH residue 82 VAL Chi-restraints excluded: chain LH residue 134 VAL Chi-restraints excluded: chain LL residue 22 VAL Chi-restraints excluded: chain LL residue 46 LEU Chi-restraints excluded: chain LL residue 51 VAL Chi-restraints excluded: chain LL residue 58 VAL Chi-restraints excluded: chain LL residue 63 VAL Chi-restraints excluded: chain LM residue 5 ASN Chi-restraints excluded: chain LM residue 6 VAL Chi-restraints excluded: chain LM residue 9 THR Chi-restraints excluded: chain LM residue 14 VAL Chi-restraints excluded: chain LM residue 19 VAL Chi-restraints excluded: chain LM residue 20 LEU Chi-restraints excluded: chain LM residue 39 VAL Chi-restraints excluded: chain LM residue 57 VAL Chi-restraints excluded: chain LM residue 68 VAL Chi-restraints excluded: chain LN residue 140 LYS Chi-restraints excluded: chain LN residue 167 THR Chi-restraints excluded: chain LN residue 171 SER Chi-restraints excluded: chain LN residue 198 SER Chi-restraints excluded: chain LO residue 117 LYS Chi-restraints excluded: chain LO residue 139 THR Chi-restraints excluded: chain LP residue 12 THR Chi-restraints excluded: chain LP residue 20 SER Chi-restraints excluded: chain LP residue 58 VAL Chi-restraints excluded: chain LQ residue 93 SER Chi-restraints excluded: chain LQ residue 163 ASN Chi-restraints excluded: chain LS residue 36 VAL Chi-restraints excluded: chain LS residue 73 LYS Chi-restraints excluded: chain LS residue 85 SER Chi-restraints excluded: chain LS residue 87 THR Chi-restraints excluded: chain LS residue 135 VAL Chi-restraints excluded: chain LS residue 142 GLN Chi-restraints excluded: chain LS residue 144 VAL Chi-restraints excluded: chain LT residue 118 LYS Chi-restraints excluded: chain LV residue 19 LEU Chi-restraints excluded: chain LV residue 88 LYS Chi-restraints excluded: chain LY residue 3 VAL Chi-restraints excluded: chain LY residue 6 THR Chi-restraints excluded: chain LY residue 7 VAL Chi-restraints excluded: chain LY residue 8 SER Chi-restraints excluded: chain LY residue 66 GLU Chi-restraints excluded: chain LY residue 76 LYS Chi-restraints excluded: chain LY residue 81 VAL Chi-restraints excluded: chain LY residue 85 THR Chi-restraints excluded: chain LY residue 93 THR Chi-restraints excluded: chain LY residue 122 LYS Chi-restraints excluded: chain Ld residue 16 VAL Chi-restraints excluded: chain Ld residue 116 VAL Chi-restraints excluded: chain Le residue 25 ARG Chi-restraints excluded: chain Le residue 60 SER Chi-restraints excluded: chain Le residue 64 THR Chi-restraints excluded: chain Le residue 84 GLU Chi-restraints excluded: chain Le residue 128 THR Chi-restraints excluded: chain Lf residue 58 GLN Chi-restraints excluded: chain Lf residue 108 SER Chi-restraints excluded: chain Lh residue 34 LEU Chi-restraints excluded: chain Lh residue 55 SER Chi-restraints excluded: chain Li residue 27 THR Chi-restraints excluded: chain Li residue 75 ASP Chi-restraints excluded: chain Lj residue 27 LEU Chi-restraints excluded: chain Lj residue 36 SER Chi-restraints excluded: chain Lq residue 162 VAL Chi-restraints excluded: chain Cc residue 100 GLU Chi-restraints excluded: chain Cc residue 220 MET Chi-restraints excluded: chain Cc residue 228 MET Chi-restraints excluded: chain Cc residue 243 THR Chi-restraints excluded: chain Cc residue 245 SER Chi-restraints excluded: chain Cd residue 30 GLN Chi-restraints excluded: chain Cd residue 36 SER Chi-restraints excluded: chain Cd residue 82 SER Chi-restraints excluded: chain Cd residue 267 SER Chi-restraints excluded: chain Cd residue 311 LEU Chi-restraints excluded: chain Cd residue 393 ILE Chi-restraints excluded: chain Ce residue 34 VAL Chi-restraints excluded: chain Ce residue 43 CYS Chi-restraints excluded: chain Ce residue 73 MET Chi-restraints excluded: chain Ce residue 103 LYS Chi-restraints excluded: chain Ce residue 161 LYS Chi-restraints excluded: chain Cf residue 526 LYS Chi-restraints excluded: chain Cf residue 539 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1346 random chunks: chunk 679 optimal weight: 7.9990 chunk 379 optimal weight: 10.0000 chunk 1017 optimal weight: 6.9990 chunk 832 optimal weight: 6.9990 chunk 337 optimal weight: 10.0000 chunk 1224 optimal weight: 7.9990 chunk 1322 optimal weight: 0.8980 chunk 1090 optimal weight: 0.0980 chunk 1214 optimal weight: 5.9990 chunk 417 optimal weight: 3.9990 chunk 982 optimal weight: 3.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** CA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 286 GLN ** CB 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CB 90 ASN CC 191 ASN ** CE 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CF 153 HIS CG 18 ASN ** CG 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CH 73 GLN ** CH 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CH 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CH 333 HIS ** CI 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CJ 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CK 40 GLN CK 105 GLN ** CK 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CM 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CN 9 ASN CN 145 HIS CN 234 ASN ** CP 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CQ 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CR 6 GLN ** CR 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CR 196 GLN ** CS 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CX 113 GLN Cb 155 HIS Cb 175 GLN ** Cb 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cb 517 ASN LB 280 ASN LC 59 HIS LC 88 GLN LF 99 ASN ** LL 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LM 105 GLN LM 106 GLN LN 15 GLN LO 66 ASN LP 28 ASN LP 142 ASN LP 158 GLN LS 5 GLN ** LS 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LS 62 ASN ** LS 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LT 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lh 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 115 HIS Cc 234 GLN Cd 44 HIS Cd 250 ASN Cd 358 HIS ** Ce 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cf 521 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 145558 Z= 0.308 Angle : 0.632 13.089 208309 Z= 0.323 Chirality : 0.041 0.279 25322 Planarity : 0.006 0.111 17768 Dihedral : 21.703 179.874 49830 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.83 % Favored : 96.07 % Rotamer: Outliers : 5.00 % Allowed : 21.82 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.08), residues: 11105 helix: 0.96 (0.07), residues: 5013 sheet: 0.03 (0.14), residues: 1353 loop : -0.98 (0.09), residues: 4739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRPCb 816 HIS 0.013 0.002 HISCb 367 PHE 0.022 0.002 PHECP 577 TYR 0.029 0.002 TYRCM 142 ARG 0.012 0.001 ARGCJ 217 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22210 Ramachandran restraints generated. 11105 Oldfield, 0 Emsley, 11105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22210 Ramachandran restraints generated. 11105 Oldfield, 0 Emsley, 11105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1916 residues out of total 9661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 427 poor density : 1489 time to evaluate : 8.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CA 71 LYS cc_start: 0.7016 (mmtm) cc_final: 0.6255 (ptpp) REVERT: CA 123 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.7551 (mpp) REVERT: CA 201 LYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7403 (mttp) REVERT: CA 285 GLN cc_start: 0.8045 (tt0) cc_final: 0.7806 (tt0) REVERT: CA 310 ASP cc_start: 0.8008 (t0) cc_final: 0.7762 (t0) REVERT: CA 312 ARG cc_start: 0.8384 (mmt-90) cc_final: 0.8015 (mmt90) REVERT: CB 134 LYS cc_start: 0.8940 (mtmm) cc_final: 0.8498 (mtmm) REVERT: CC 304 LEU cc_start: 0.8758 (tp) cc_final: 0.8522 (mt) REVERT: CC 361 LEU cc_start: 0.6033 (mt) cc_final: 0.5314 (tp) REVERT: CC 373 MET cc_start: 0.1341 (ppp) cc_final: 0.0723 (ppp) REVERT: CE 124 LYS cc_start: 0.8527 (ttmt) cc_final: 0.8151 (tttm) REVERT: CE 302 LYS cc_start: 0.8974 (mmmm) cc_final: 0.8583 (mtmt) REVERT: CE 308 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.7752 (ptp-110) REVERT: CH 79 ASP cc_start: 0.8565 (m-30) cc_final: 0.8317 (m-30) REVERT: CH 174 PHE cc_start: 0.8967 (OUTLIER) cc_final: 0.8332 (t80) REVERT: CH 232 ASN cc_start: 0.9105 (OUTLIER) cc_final: 0.8565 (p0) REVERT: CH 254 ASP cc_start: 0.8517 (t0) cc_final: 0.8119 (t70) REVERT: CH 302 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8113 (mp10) REVERT: CH 306 ASN cc_start: 0.8211 (m110) cc_final: 0.7831 (m-40) REVERT: CI 198 PHE cc_start: 0.9112 (OUTLIER) cc_final: 0.8682 (t80) REVERT: CJ 32 ASP cc_start: 0.7126 (t70) cc_final: 0.6410 (t0) REVERT: CJ 97 ARG cc_start: 0.6508 (mmt180) cc_final: 0.5900 (mmm160) REVERT: CK 37 GLU cc_start: 0.7752 (tt0) cc_final: 0.7452 (tt0) REVERT: CK 162 THR cc_start: 0.8307 (p) cc_final: 0.7953 (m) REVERT: CK 170 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.7255 (mtt180) REVERT: CK 180 LYS cc_start: 0.9176 (mtmm) cc_final: 0.8747 (mttm) REVERT: CL 16 LYS cc_start: 0.7060 (mmmm) cc_final: 0.6303 (mttm) REVERT: CL 23 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8287 (ttpp) REVERT: CM 113 ARG cc_start: 0.8125 (ptt-90) cc_final: 0.7731 (ptm-80) REVERT: CN 26 VAL cc_start: 0.8870 (OUTLIER) cc_final: 0.8647 (m) REVERT: CN 140 GLN cc_start: 0.8594 (mm-40) cc_final: 0.8365 (mm-40) REVERT: CN 169 ASP cc_start: 0.8332 (m-30) cc_final: 0.8097 (m-30) REVERT: CN 203 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8429 (pt) REVERT: CP 369 SER cc_start: 0.8952 (m) cc_final: 0.8621 (p) REVERT: CP 559 SER cc_start: 0.8401 (OUTLIER) cc_final: 0.8162 (t) REVERT: CR 73 LEU cc_start: 0.6976 (tp) cc_final: 0.6689 (tp) REVERT: CU 241 LEU cc_start: 0.9153 (tp) cc_final: 0.8901 (tp) REVERT: CU 270 ASP cc_start: 0.7212 (t0) cc_final: 0.6888 (t0) REVERT: Cb 159 PHE cc_start: 0.7692 (t80) cc_final: 0.7360 (t80) REVERT: Cb 242 GLU cc_start: 0.7495 (mp0) cc_final: 0.7262 (mp0) REVERT: Cb 434 VAL cc_start: 0.8440 (t) cc_final: 0.8182 (p) REVERT: Cb 716 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.8019 (mtm) REVERT: LB 66 LYS cc_start: 0.8997 (ttmm) cc_final: 0.8603 (tttm) REVERT: LB 211 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8386 (tt0) REVERT: LB 271 MET cc_start: 0.8010 (mtp) cc_final: 0.7671 (mmp) REVERT: LB 337 MET cc_start: 0.9095 (mmt) cc_final: 0.8589 (mmt) REVERT: LB 350 LYS cc_start: 0.8476 (mptt) cc_final: 0.7806 (mttm) REVERT: LB 354 LYS cc_start: 0.8931 (ptmm) cc_final: 0.8556 (mmtt) REVERT: LC 37 LYS cc_start: 0.8580 (tttm) cc_final: 0.8300 (tttt) REVERT: LC 187 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7853 (mmmt) REVERT: LC 220 LYS cc_start: 0.8491 (mttt) cc_final: 0.7815 (mtmm) REVERT: LC 233 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8468 (mt-10) REVERT: LC 264 GLN cc_start: 0.8334 (mm-40) cc_final: 0.7980 (mm-40) REVERT: LE 64 ARG cc_start: 0.7649 (ptm160) cc_final: 0.6521 (ptm160) REVERT: LF 37 GLU cc_start: 0.8617 (tp30) cc_final: 0.8302 (tp30) REVERT: LF 88 LYS cc_start: 0.8653 (mtmt) cc_final: 0.8322 (mttp) REVERT: LF 212 LYS cc_start: 0.8449 (mttt) cc_final: 0.8108 (mtmt) REVERT: LG 52 MET cc_start: 0.2427 (ptm) cc_final: 0.0970 (tmm) REVERT: LG 87 LYS cc_start: 0.8538 (tttt) cc_final: 0.8213 (tttm) REVERT: LH 43 VAL cc_start: 0.8947 (t) cc_final: 0.8596 (p) REVERT: LH 182 TYR cc_start: 0.9263 (m-80) cc_final: 0.8844 (m-80) REVERT: LL 23 ARG cc_start: 0.7920 (ttm110) cc_final: 0.6908 (tpt170) REVERT: LN 9 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8482 (mm-30) REVERT: LN 104 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7877 (mt-10) REVERT: LN 140 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.7985 (tttt) REVERT: LN 187 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7439 (ptt-90) REVERT: LO 102 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7240 (mt-10) REVERT: LO 160 GLU cc_start: 0.8279 (tp30) cc_final: 0.7901 (mm-30) REVERT: LO 161 ARG cc_start: 0.7904 (mtm180) cc_final: 0.7704 (mtm-85) REVERT: LO 185 LYS cc_start: 0.8781 (mtpp) cc_final: 0.8516 (mtpp) REVERT: LO 202 TYR cc_start: 0.8599 (m-80) cc_final: 0.8266 (m-80) REVERT: LP 60 MET cc_start: 0.8587 (mmt) cc_final: 0.8265 (mmt) REVERT: LP 115 LYS cc_start: 0.8788 (tttm) cc_final: 0.8502 (ttmt) REVERT: LQ 48 LYS cc_start: 0.8015 (mttt) cc_final: 0.7549 (mmtt) REVERT: LV 139 MET cc_start: 0.7946 (mtm) cc_final: 0.7598 (mtm) REVERT: LY 41 LYS cc_start: 0.9305 (OUTLIER) cc_final: 0.8961 (tttm) REVERT: LY 112 LYS cc_start: 0.8530 (ttmt) cc_final: 0.8232 (ttpp) REVERT: LY 122 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8762 (tttt) REVERT: LY 127 GLN cc_start: 0.8592 (tm-30) cc_final: 0.8100 (tt0) REVERT: Le 25 ARG cc_start: 0.6909 (OUTLIER) cc_final: 0.6576 (mmm160) REVERT: Le 84 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7862 (mp0) REVERT: Le 96 GLU cc_start: 0.8393 (tt0) cc_final: 0.7893 (tt0) REVERT: Le 124 LYS cc_start: 0.8604 (ptpt) cc_final: 0.8351 (pttt) REVERT: Lf 24 ASN cc_start: 0.7794 (m110) cc_final: 0.7559 (m-40) REVERT: Lf 84 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.7634 (ptp-170) REVERT: Lh 33 GLN cc_start: 0.8071 (pp30) cc_final: 0.7548 (pp30) REVERT: Lh 78 LYS cc_start: 0.8819 (mmtt) cc_final: 0.8387 (mmtm) REVERT: Li 107 ARG cc_start: 0.8372 (ptp90) cc_final: 0.7930 (mtt90) REVERT: Lj 57 LYS cc_start: 0.8569 (ptpt) cc_final: 0.7582 (ptmm) REVERT: Lq 165 MET cc_start: -0.1729 (ttt) cc_final: -0.2973 (mtt) REVERT: Cc 220 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.8085 (mpp) REVERT: Cd 10 SER cc_start: 0.8582 (m) cc_final: 0.8118 (t) REVERT: Ce 13 GLN cc_start: 0.7886 (mm-40) cc_final: 0.7399 (tm-30) REVERT: Ce 73 MET cc_start: 0.9159 (OUTLIER) cc_final: 0.8919 (mtm) REVERT: Ce 97 ARG cc_start: 0.8981 (mmt-90) cc_final: 0.8570 (mmm160) REVERT: Ce 103 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.7847 (pttp) REVERT: Ce 147 LYS cc_start: 0.8174 (tttt) cc_final: 0.7647 (ttmm) REVERT: Ce 161 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8407 (mttp) REVERT: Cf 533 LYS cc_start: 0.8453 (mttt) cc_final: 0.8059 (mttp) outliers start: 427 outliers final: 254 residues processed: 1770 average time/residue: 1.3781 time to fit residues: 4251.7270 Evaluate side-chains 1675 residues out of total 9661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 280 poor density : 1395 time to evaluate : 8.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CA residue 45 THR Chi-restraints excluded: chain CA residue 70 THR Chi-restraints excluded: chain CA residue 72 SER Chi-restraints excluded: chain CA residue 123 MET Chi-restraints excluded: chain CA residue 149 GLU Chi-restraints excluded: chain CA residue 176 ILE Chi-restraints excluded: chain CA residue 198 GLU Chi-restraints excluded: chain CA residue 201 LYS Chi-restraints excluded: chain CA residue 241 THR Chi-restraints excluded: chain CB residue 63 TRP Chi-restraints excluded: chain CB residue 89 LEU Chi-restraints excluded: chain CB residue 114 ASP Chi-restraints excluded: chain CB residue 131 SER Chi-restraints excluded: chain CB residue 145 LYS Chi-restraints excluded: chain CB residue 165 LYS Chi-restraints excluded: chain CB residue 241 THR Chi-restraints excluded: chain CC residue 167 VAL Chi-restraints excluded: chain CC residue 172 ILE Chi-restraints excluded: chain CC residue 175 ILE Chi-restraints excluded: chain CE residue 121 LYS Chi-restraints excluded: chain CE residue 175 SER Chi-restraints excluded: chain CE residue 190 THR Chi-restraints excluded: chain CE residue 270 LEU Chi-restraints excluded: chain CE residue 296 SER Chi-restraints excluded: chain CE residue 300 THR Chi-restraints excluded: chain CE residue 308 ARG Chi-restraints excluded: chain CE residue 414 THR Chi-restraints excluded: chain CE residue 448 THR Chi-restraints excluded: chain CE residue 478 VAL Chi-restraints excluded: chain CE residue 533 VAL Chi-restraints excluded: chain CF residue 34 ILE Chi-restraints excluded: chain CF residue 48 MET Chi-restraints excluded: chain CF residue 56 VAL Chi-restraints excluded: chain CF residue 79 THR Chi-restraints excluded: chain CF residue 80 THR Chi-restraints excluded: chain CF residue 96 LEU Chi-restraints excluded: chain CF residue 142 VAL Chi-restraints excluded: chain CF residue 175 ILE Chi-restraints excluded: chain CF residue 202 ASP Chi-restraints excluded: chain CF residue 205 GLN Chi-restraints excluded: chain CF residue 221 VAL Chi-restraints excluded: chain CG residue 5 THR Chi-restraints excluded: chain CG residue 6 ASP Chi-restraints excluded: chain CG residue 13 LEU Chi-restraints excluded: chain CG residue 16 LEU Chi-restraints excluded: chain CG residue 40 MET Chi-restraints excluded: chain CG residue 65 LEU Chi-restraints excluded: chain CG residue 109 LEU Chi-restraints excluded: chain CG residue 122 TRP Chi-restraints excluded: chain CG residue 137 MET Chi-restraints excluded: chain CH residue 32 ILE Chi-restraints excluded: chain CH residue 69 VAL Chi-restraints excluded: chain CH residue 85 TYR Chi-restraints excluded: chain CH residue 174 PHE Chi-restraints excluded: chain CH residue 232 ASN Chi-restraints excluded: chain CH residue 233 THR Chi-restraints excluded: chain CH residue 302 GLN Chi-restraints excluded: chain CH residue 343 VAL Chi-restraints excluded: chain CH residue 372 THR Chi-restraints excluded: chain CH residue 390 LEU Chi-restraints excluded: chain CH residue 399 ASN Chi-restraints excluded: chain CI residue 198 PHE Chi-restraints excluded: chain CI residue 202 GLU Chi-restraints excluded: chain CI residue 216 LEU Chi-restraints excluded: chain CI residue 218 VAL Chi-restraints excluded: chain CI residue 224 THR Chi-restraints excluded: chain CI residue 228 ARG Chi-restraints excluded: chain CI residue 303 GLN Chi-restraints excluded: chain CJ residue 158 THR Chi-restraints excluded: chain CJ residue 263 ASP Chi-restraints excluded: chain CJ residue 268 LEU Chi-restraints excluded: chain CJ residue 415 ILE Chi-restraints excluded: chain CK residue 170 ARG Chi-restraints excluded: chain CK residue 199 SER Chi-restraints excluded: chain CK residue 212 LEU Chi-restraints excluded: chain CK residue 254 CYS Chi-restraints excluded: chain CL residue 18 THR Chi-restraints excluded: chain CL residue 23 LYS Chi-restraints excluded: chain CM residue 92 VAL Chi-restraints excluded: chain CM residue 112 LEU Chi-restraints excluded: chain CM residue 119 ASN Chi-restraints excluded: chain CM residue 121 VAL Chi-restraints excluded: chain CM residue 135 ILE Chi-restraints excluded: chain CM residue 140 VAL Chi-restraints excluded: chain CM residue 147 LEU Chi-restraints excluded: chain CM residue 197 VAL Chi-restraints excluded: chain CN residue 1 MET Chi-restraints excluded: chain CN residue 18 THR Chi-restraints excluded: chain CN residue 26 VAL Chi-restraints excluded: chain CN residue 52 THR Chi-restraints excluded: chain CN residue 98 GLU Chi-restraints excluded: chain CN residue 161 VAL Chi-restraints excluded: chain CN residue 203 LEU Chi-restraints excluded: chain CN residue 242 VAL Chi-restraints excluded: chain CO residue 40 ILE Chi-restraints excluded: chain CO residue 85 VAL Chi-restraints excluded: chain CP residue 270 ILE Chi-restraints excluded: chain CP residue 324 LEU Chi-restraints excluded: chain CP residue 334 VAL Chi-restraints excluded: chain CP residue 407 VAL Chi-restraints excluded: chain CP residue 490 LEU Chi-restraints excluded: chain CP residue 500 HIS Chi-restraints excluded: chain CP residue 559 SER Chi-restraints excluded: chain CP residue 571 TYR Chi-restraints excluded: chain CP residue 574 ASP Chi-restraints excluded: chain CQ residue 49 LEU Chi-restraints excluded: chain CQ residue 97 SER Chi-restraints excluded: chain CR residue 27 LEU Chi-restraints excluded: chain CR residue 32 ASN Chi-restraints excluded: chain CR residue 45 LEU Chi-restraints excluded: chain CR residue 47 GLN Chi-restraints excluded: chain CR residue 127 GLU Chi-restraints excluded: chain CR residue 131 VAL Chi-restraints excluded: chain CR residue 145 HIS Chi-restraints excluded: chain CS residue 654 ILE Chi-restraints excluded: chain CS residue 668 THR Chi-restraints excluded: chain CU residue 196 LEU Chi-restraints excluded: chain CU residue 220 VAL Chi-restraints excluded: chain CU residue 228 ASP Chi-restraints excluded: chain CU residue 233 ILE Chi-restraints excluded: chain CU residue 279 ASP Chi-restraints excluded: chain CU residue 322 GLU Chi-restraints excluded: chain CU residue 334 ILE Chi-restraints excluded: chain CX residue 101 MET Chi-restraints excluded: chain CX residue 141 GLU Chi-restraints excluded: chain Cb residue 179 VAL Chi-restraints excluded: chain Cb residue 259 LEU Chi-restraints excluded: chain Cb residue 262 LEU Chi-restraints excluded: chain Cb residue 274 THR Chi-restraints excluded: chain Cb residue 275 LEU Chi-restraints excluded: chain Cb residue 295 LEU Chi-restraints excluded: chain Cb residue 304 ASP Chi-restraints excluded: chain Cb residue 393 VAL Chi-restraints excluded: chain Cb residue 451 VAL Chi-restraints excluded: chain Cb residue 490 VAL Chi-restraints excluded: chain Cb residue 716 MET Chi-restraints excluded: chain Cb residue 842 LEU Chi-restraints excluded: chain LB residue 14 LEU Chi-restraints excluded: chain LB residue 103 THR Chi-restraints excluded: chain LB residue 158 VAL Chi-restraints excluded: chain LB residue 199 LEU Chi-restraints excluded: chain LB residue 211 GLU Chi-restraints excluded: chain LB residue 214 GLU Chi-restraints excluded: chain LB residue 307 THR Chi-restraints excluded: chain LB residue 329 VAL Chi-restraints excluded: chain LB residue 359 TRP Chi-restraints excluded: chain LC residue 8 THR Chi-restraints excluded: chain LC residue 28 SER Chi-restraints excluded: chain LC residue 43 MET Chi-restraints excluded: chain LC residue 62 SER Chi-restraints excluded: chain LC residue 112 VAL Chi-restraints excluded: chain LC residue 146 VAL Chi-restraints excluded: chain LC residue 187 LYS Chi-restraints excluded: chain LC residue 222 LEU Chi-restraints excluded: chain LC residue 238 ASP Chi-restraints excluded: chain LC residue 283 SER Chi-restraints excluded: chain LE residue 83 VAL Chi-restraints excluded: chain LE residue 102 VAL Chi-restraints excluded: chain LE residue 106 SER Chi-restraints excluded: chain LE residue 107 VAL Chi-restraints excluded: chain LE residue 109 VAL Chi-restraints excluded: chain LF residue 18 LEU Chi-restraints excluded: chain LF residue 74 ILE Chi-restraints excluded: chain LF residue 90 VAL Chi-restraints excluded: chain LF residue 117 ILE Chi-restraints excluded: chain LG residue 68 LEU Chi-restraints excluded: chain LG residue 85 LEU Chi-restraints excluded: chain LG residue 167 VAL Chi-restraints excluded: chain LG residue 191 THR Chi-restraints excluded: chain LG residue 193 VAL Chi-restraints excluded: chain LG residue 210 ASP Chi-restraints excluded: chain LG residue 234 LYS Chi-restraints excluded: chain LH residue 15 ASN Chi-restraints excluded: chain LH residue 19 SER Chi-restraints excluded: chain LH residue 25 VAL Chi-restraints excluded: chain LH residue 41 ILE Chi-restraints excluded: chain LH residue 48 VAL Chi-restraints excluded: chain LH residue 55 LEU Chi-restraints excluded: chain LH residue 56 GLU Chi-restraints excluded: chain LH residue 82 VAL Chi-restraints excluded: chain LH residue 134 VAL Chi-restraints excluded: chain LK residue 102 LYS Chi-restraints excluded: chain LL residue 22 VAL Chi-restraints excluded: chain LL residue 46 LEU Chi-restraints excluded: chain LL residue 51 VAL Chi-restraints excluded: chain LL residue 58 VAL Chi-restraints excluded: chain LL residue 69 THR Chi-restraints excluded: chain LM residue 5 ASN Chi-restraints excluded: chain LM residue 6 VAL Chi-restraints excluded: chain LM residue 9 THR Chi-restraints excluded: chain LM residue 19 VAL Chi-restraints excluded: chain LM residue 20 LEU Chi-restraints excluded: chain LM residue 39 VAL Chi-restraints excluded: chain LM residue 57 VAL Chi-restraints excluded: chain LM residue 59 LEU Chi-restraints excluded: chain LM residue 67 ILE Chi-restraints excluded: chain LM residue 68 VAL Chi-restraints excluded: chain LN residue 33 LEU Chi-restraints excluded: chain LN residue 96 ARG Chi-restraints excluded: chain LN residue 101 THR Chi-restraints excluded: chain LN residue 140 LYS Chi-restraints excluded: chain LN residue 167 THR Chi-restraints excluded: chain LN residue 171 SER Chi-restraints excluded: chain LN residue 187 ARG Chi-restraints excluded: chain LN residue 198 SER Chi-restraints excluded: chain LO residue 37 VAL Chi-restraints excluded: chain LO residue 110 VAL Chi-restraints excluded: chain LO residue 139 THR Chi-restraints excluded: chain LP residue 20 SER Chi-restraints excluded: chain LP residue 24 VAL Chi-restraints excluded: chain LP residue 29 THR Chi-restraints excluded: chain LP residue 58 VAL Chi-restraints excluded: chain LQ residue 148 THR Chi-restraints excluded: chain LQ residue 163 ASN Chi-restraints excluded: chain LS residue 35 VAL Chi-restraints excluded: chain LS residue 36 VAL Chi-restraints excluded: chain LS residue 62 ASN Chi-restraints excluded: chain LS residue 73 LYS Chi-restraints excluded: chain LS residue 85 SER Chi-restraints excluded: chain LS residue 87 THR Chi-restraints excluded: chain LS residue 135 VAL Chi-restraints excluded: chain LS residue 144 VAL Chi-restraints excluded: chain LT residue 89 ILE Chi-restraints excluded: chain LT residue 118 LYS Chi-restraints excluded: chain LT residue 142 SER Chi-restraints excluded: chain LT residue 143 ILE Chi-restraints excluded: chain LV residue 19 LEU Chi-restraints excluded: chain LV residue 21 VAL Chi-restraints excluded: chain LV residue 88 LYS Chi-restraints excluded: chain LV residue 120 VAL Chi-restraints excluded: chain LY residue 3 VAL Chi-restraints excluded: chain LY residue 6 THR Chi-restraints excluded: chain LY residue 7 VAL Chi-restraints excluded: chain LY residue 8 SER Chi-restraints excluded: chain LY residue 41 LYS Chi-restraints excluded: chain LY residue 66 GLU Chi-restraints excluded: chain LY residue 76 LYS Chi-restraints excluded: chain LY residue 81 VAL Chi-restraints excluded: chain LY residue 85 THR Chi-restraints excluded: chain LY residue 93 THR Chi-restraints excluded: chain LY residue 122 LYS Chi-restraints excluded: chain Ld residue 54 THR Chi-restraints excluded: chain Ld residue 116 VAL Chi-restraints excluded: chain Le residue 25 ARG Chi-restraints excluded: chain Le residue 60 SER Chi-restraints excluded: chain Le residue 64 THR Chi-restraints excluded: chain Le residue 84 GLU Chi-restraints excluded: chain Le residue 128 THR Chi-restraints excluded: chain Lf residue 37 VAL Chi-restraints excluded: chain Lf residue 58 GLN Chi-restraints excluded: chain Lf residue 84 ARG Chi-restraints excluded: chain Lf residue 108 SER Chi-restraints excluded: chain Lh residue 20 LEU Chi-restraints excluded: chain Lh residue 34 LEU Chi-restraints excluded: chain Lh residue 55 SER Chi-restraints excluded: chain Li residue 27 THR Chi-restraints excluded: chain Li residue 33 GLU Chi-restraints excluded: chain Li residue 75 ASP Chi-restraints excluded: chain Lj residue 27 LEU Chi-restraints excluded: chain Lj residue 36 SER Chi-restraints excluded: chain Cc residue 220 MET Chi-restraints excluded: chain Cc residue 228 MET Chi-restraints excluded: chain Cc residue 243 THR Chi-restraints excluded: chain Cc residue 245 SER Chi-restraints excluded: chain Cd residue 30 GLN Chi-restraints excluded: chain Cd residue 36 SER Chi-restraints excluded: chain Cd residue 82 SER Chi-restraints excluded: chain Cd residue 267 SER Chi-restraints excluded: chain Cd residue 310 GLU Chi-restraints excluded: chain Cd residue 311 LEU Chi-restraints excluded: chain Cd residue 334 SER Chi-restraints excluded: chain Cd residue 393 ILE Chi-restraints excluded: chain Ce residue 43 CYS Chi-restraints excluded: chain Ce residue 48 SER Chi-restraints excluded: chain Ce residue 73 MET Chi-restraints excluded: chain Ce residue 103 LYS Chi-restraints excluded: chain Ce residue 161 LYS Chi-restraints excluded: chain Ce residue 195 LEU Chi-restraints excluded: chain Cf residue 526 LYS Chi-restraints excluded: chain Cf residue 539 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1346 random chunks: chunk 1209 optimal weight: 2.9990 chunk 920 optimal weight: 0.9990 chunk 635 optimal weight: 5.9990 chunk 135 optimal weight: 20.0000 chunk 584 optimal weight: 30.0000 chunk 822 optimal weight: 10.0000 chunk 1228 optimal weight: 0.9990 chunk 1301 optimal weight: 5.9990 chunk 642 optimal weight: 5.9990 chunk 1164 optimal weight: 0.9990 chunk 350 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CA 286 GLN CE 319 ASN ** CE 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CF 121 GLN ** CG 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CG 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CH 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CH 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CI 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CJ 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CK 105 GLN CK 203 ASN ** CM 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CP 300 ASN ** CQ 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CR 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CR 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CS 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cb 155 HIS Cb 175 GLN ** Cb 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cb 367 HIS LB 294 ASN LC 59 HIS LC 284 GLN LF 43 ASN LF 77 GLN LH 5 HIS LL 114 GLN LN 57 GLN ** LQ 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LS 5 GLN LS 8 GLN LS 13 HIS ** LS 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LS 142 GLN LT 58 HIS ** LT 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lh 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cd 58 GLN Ce 185 ASN Cf 521 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 145558 Z= 0.238 Angle : 0.583 11.668 208309 Z= 0.298 Chirality : 0.039 0.272 25322 Planarity : 0.005 0.098 17768 Dihedral : 21.631 179.881 49828 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.87 % Favored : 96.04 % Rotamer: Outliers : 4.57 % Allowed : 22.44 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.08), residues: 11105 helix: 1.41 (0.07), residues: 5022 sheet: 0.04 (0.14), residues: 1349 loop : -0.89 (0.09), residues: 4734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRPCb 816 HIS 0.008 0.001 HISCA 178 PHE 0.023 0.001 PHECB 107 TYR 0.022 0.001 TYRCG 47 ARG 0.007 0.001 ARGCL 73 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22210 Ramachandran restraints generated. 11105 Oldfield, 0 Emsley, 11105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22210 Ramachandran restraints generated. 11105 Oldfield, 0 Emsley, 11105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1840 residues out of total 9661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 390 poor density : 1450 time to evaluate : 8.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CA 69 ASP cc_start: 0.8535 (t0) cc_final: 0.8323 (t0) REVERT: CA 71 LYS cc_start: 0.6956 (mmtm) cc_final: 0.6249 (ptpp) REVERT: CA 201 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.7272 (mttp) REVERT: CA 247 GLU cc_start: 0.8171 (tt0) cc_final: 0.7965 (tt0) REVERT: CA 310 ASP cc_start: 0.8090 (t0) cc_final: 0.7867 (t0) REVERT: CA 312 ARG cc_start: 0.8465 (mmt-90) cc_final: 0.8262 (mmt90) REVERT: CB 134 LYS cc_start: 0.8997 (mtmm) cc_final: 0.8489 (mtmm) REVERT: CC 361 LEU cc_start: 0.6301 (mt) cc_final: 0.5488 (tp) REVERT: CC 373 MET cc_start: 0.1256 (ppp) cc_final: 0.0657 (ppp) REVERT: CE 124 LYS cc_start: 0.8490 (ttmt) cc_final: 0.8162 (tttm) REVERT: CE 302 LYS cc_start: 0.8946 (mmmm) cc_final: 0.8578 (mtmt) REVERT: CE 308 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.7761 (ptp-110) REVERT: CE 513 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8038 (mm-30) REVERT: CF 20 ARG cc_start: 0.8617 (mmm-85) cc_final: 0.8163 (mmm160) REVERT: CG 116 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.7640 (ttmt) REVERT: CH 79 ASP cc_start: 0.8568 (m-30) cc_final: 0.8318 (m-30) REVERT: CH 174 PHE cc_start: 0.9035 (OUTLIER) cc_final: 0.8330 (t80) REVERT: CH 232 ASN cc_start: 0.9005 (OUTLIER) cc_final: 0.8394 (p0) REVERT: CH 254 ASP cc_start: 0.8480 (t0) cc_final: 0.8088 (t70) REVERT: CH 345 GLN cc_start: 0.8620 (mm-40) cc_final: 0.8409 (mm-40) REVERT: CI 202 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8108 (pm20) REVERT: CJ 32 ASP cc_start: 0.7187 (t70) cc_final: 0.6431 (t0) REVERT: CJ 97 ARG cc_start: 0.6512 (mmt180) cc_final: 0.6178 (mmt90) REVERT: CJ 224 PHE cc_start: 0.6027 (m-10) cc_final: 0.5635 (m-80) REVERT: CK 132 MET cc_start: 0.7429 (mmm) cc_final: 0.7123 (mmt) REVERT: CK 162 THR cc_start: 0.8314 (p) cc_final: 0.7942 (m) REVERT: CK 170 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.7213 (mtt180) REVERT: CK 180 LYS cc_start: 0.9157 (mtmm) cc_final: 0.8732 (mttm) REVERT: CL 16 LYS cc_start: 0.7046 (mmmm) cc_final: 0.6293 (mttm) REVERT: CM 113 ARG cc_start: 0.8196 (ptt-90) cc_final: 0.7800 (ptm-80) REVERT: CM 142 TYR cc_start: 0.6925 (p90) cc_final: 0.6619 (p90) REVERT: CN 26 VAL cc_start: 0.8873 (t) cc_final: 0.8624 (m) REVERT: CN 32 GLU cc_start: 0.7708 (mp0) cc_final: 0.7331 (mp0) REVERT: CN 140 GLN cc_start: 0.8621 (mm-40) cc_final: 0.8252 (tm-30) REVERT: CN 169 ASP cc_start: 0.8303 (m-30) cc_final: 0.8082 (m-30) REVERT: CN 203 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8374 (pt) REVERT: CP 369 SER cc_start: 0.8982 (m) cc_final: 0.8711 (p) REVERT: CP 519 GLU cc_start: 0.7501 (tp30) cc_final: 0.7291 (tp30) REVERT: CP 559 SER cc_start: 0.8301 (OUTLIER) cc_final: 0.7984 (t) REVERT: CQ 102 ARG cc_start: 0.8866 (ptm160) cc_final: 0.8642 (ptm160) REVERT: CR 73 LEU cc_start: 0.6953 (tp) cc_final: 0.6650 (tp) REVERT: CS 666 LEU cc_start: 0.2875 (tp) cc_final: 0.2256 (pp) REVERT: CU 200 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.8987 (tp) REVERT: CU 236 ASP cc_start: 0.9158 (m-30) cc_final: 0.8935 (m-30) REVERT: CU 241 LEU cc_start: 0.9135 (tp) cc_final: 0.8878 (tp) REVERT: Cb 159 PHE cc_start: 0.7765 (t80) cc_final: 0.7504 (t80) REVERT: LB 61 ASP cc_start: 0.8172 (OUTLIER) cc_final: 0.7748 (t70) REVERT: LB 66 LYS cc_start: 0.8873 (ttmm) cc_final: 0.8499 (tttm) REVERT: LB 137 TYR cc_start: 0.8087 (OUTLIER) cc_final: 0.6781 (m-80) REVERT: LB 211 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8400 (tt0) REVERT: LB 227 PHE cc_start: 0.8347 (OUTLIER) cc_final: 0.7401 (m-10) REVERT: LB 271 MET cc_start: 0.8021 (mtp) cc_final: 0.7593 (mmp) REVERT: LB 350 LYS cc_start: 0.8423 (mptt) cc_final: 0.7817 (mttm) REVERT: LB 354 LYS cc_start: 0.8906 (ptmm) cc_final: 0.8540 (mmtt) REVERT: LC 37 LYS cc_start: 0.8562 (tttm) cc_final: 0.8266 (tttt) REVERT: LC 187 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7907 (mmmt) REVERT: LC 220 LYS cc_start: 0.8433 (mttt) cc_final: 0.7791 (mtmm) REVERT: LC 224 LYS cc_start: 0.8586 (mmtt) cc_final: 0.7602 (mtmt) REVERT: LC 264 GLN cc_start: 0.8327 (mm-40) cc_final: 0.7979 (mm-40) REVERT: LE 64 ARG cc_start: 0.7583 (ptm160) cc_final: 0.6491 (ptm160) REVERT: LF 37 GLU cc_start: 0.8583 (tp30) cc_final: 0.8272 (tp30) REVERT: LF 88 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8322 (mttp) REVERT: LF 212 LYS cc_start: 0.8369 (mttt) cc_final: 0.8117 (mtmt) REVERT: LG 52 MET cc_start: 0.2968 (ptm) cc_final: 0.1547 (tmm) REVERT: LG 60 ARG cc_start: 0.7886 (ttm170) cc_final: 0.7530 (ttp80) REVERT: LG 87 LYS cc_start: 0.8492 (tttt) cc_final: 0.8198 (tttp) REVERT: LH 43 VAL cc_start: 0.8956 (t) cc_final: 0.8622 (p) REVERT: LH 182 TYR cc_start: 0.9217 (m-80) cc_final: 0.8796 (m-80) REVERT: LL 23 ARG cc_start: 0.7994 (ttm110) cc_final: 0.6958 (tpt170) REVERT: LM 130 GLU cc_start: 0.8704 (mp0) cc_final: 0.8355 (mp0) REVERT: LN 104 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7834 (mt-10) REVERT: LN 187 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7430 (ptt-90) REVERT: LO 102 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7270 (mt-10) REVERT: LO 160 GLU cc_start: 0.8214 (tp30) cc_final: 0.7872 (mm-30) REVERT: LO 202 TYR cc_start: 0.8604 (m-80) cc_final: 0.8273 (m-80) REVERT: LP 60 MET cc_start: 0.8512 (mmt) cc_final: 0.8262 (mmt) REVERT: LP 115 LYS cc_start: 0.8736 (tttm) cc_final: 0.8443 (ttmt) REVERT: LQ 78 ARG cc_start: 0.7774 (ttm110) cc_final: 0.7504 (ttm-80) REVERT: LS 109 ASP cc_start: 0.9137 (t0) cc_final: 0.8873 (t70) REVERT: LT 52 MET cc_start: 0.3553 (ptm) cc_final: 0.3101 (mmt) REVERT: LV 50 ARG cc_start: 0.5445 (OUTLIER) cc_final: 0.5232 (ttt90) REVERT: LV 139 MET cc_start: 0.7886 (mtm) cc_final: 0.7584 (mtm) REVERT: LY 50 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.8727 (ttt-90) REVERT: LY 54 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7915 (mm-30) REVERT: LY 112 LYS cc_start: 0.8487 (ttmt) cc_final: 0.8074 (ttpp) REVERT: LY 122 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8744 (tttt) REVERT: LY 127 GLN cc_start: 0.8594 (tm-30) cc_final: 0.8124 (tt0) REVERT: Le 25 ARG cc_start: 0.6946 (mtp180) cc_final: 0.6689 (mmm160) REVERT: Le 55 SER cc_start: 0.8975 (m) cc_final: 0.8622 (t) REVERT: Le 84 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7831 (mp0) REVERT: Le 96 GLU cc_start: 0.8405 (tt0) cc_final: 0.7858 (tt0) REVERT: Le 124 LYS cc_start: 0.8520 (ptpt) cc_final: 0.8260 (pttt) REVERT: Lf 24 ASN cc_start: 0.7792 (m110) cc_final: 0.7542 (m-40) REVERT: Lh 33 GLN cc_start: 0.7919 (pp30) cc_final: 0.7510 (pp30) REVERT: Lh 78 LYS cc_start: 0.8688 (mmtt) cc_final: 0.8314 (mmtm) REVERT: Lh 120 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8751 (tttt) REVERT: Lj 57 LYS cc_start: 0.8602 (ptpt) cc_final: 0.7596 (ptmm) REVERT: Lq 165 MET cc_start: -0.1523 (ttt) cc_final: -0.2874 (mtt) REVERT: Cc 100 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7557 (mm-30) REVERT: Cc 199 ASP cc_start: 0.8466 (m-30) cc_final: 0.8263 (m-30) REVERT: Cc 220 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7920 (mpp) REVERT: Cc 228 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8442 (ttp) REVERT: Cd 10 SER cc_start: 0.8567 (m) cc_final: 0.8118 (t) REVERT: Cd 94 ARG cc_start: 0.7503 (tmm-80) cc_final: 0.7091 (tmm-80) REVERT: Ce 13 GLN cc_start: 0.7843 (mm-40) cc_final: 0.7405 (tm-30) REVERT: Ce 73 MET cc_start: 0.9185 (OUTLIER) cc_final: 0.8944 (mtm) REVERT: Ce 103 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8170 (mtmm) REVERT: Ce 147 LYS cc_start: 0.8121 (tttt) cc_final: 0.7595 (ttmm) REVERT: Ce 161 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8547 (ptpp) REVERT: Cf 533 LYS cc_start: 0.8397 (mttt) cc_final: 0.8012 (mttp) outliers start: 390 outliers final: 249 residues processed: 1711 average time/residue: 1.2558 time to fit residues: 3692.7327 Evaluate side-chains 1633 residues out of total 9661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 277 poor density : 1356 time to evaluate : 8.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CA residue 70 THR Chi-restraints excluded: chain CA residue 72 SER Chi-restraints excluded: chain CA residue 132 CYS Chi-restraints excluded: chain CA residue 149 GLU Chi-restraints excluded: chain CA residue 176 ILE Chi-restraints excluded: chain CA residue 201 LYS Chi-restraints excluded: chain CA residue 241 THR Chi-restraints excluded: chain CA residue 257 GLU Chi-restraints excluded: chain CB residue 48 ASN Chi-restraints excluded: chain CB residue 63 TRP Chi-restraints excluded: chain CB residue 70 LYS Chi-restraints excluded: chain CB residue 89 LEU Chi-restraints excluded: chain CB residue 114 ASP Chi-restraints excluded: chain CB residue 131 SER Chi-restraints excluded: chain CB residue 145 LYS Chi-restraints excluded: chain CB residue 165 LYS Chi-restraints excluded: chain CB residue 235 LEU Chi-restraints excluded: chain CB residue 278 VAL Chi-restraints excluded: chain CC residue 167 VAL Chi-restraints excluded: chain CC residue 175 ILE Chi-restraints excluded: chain CC residue 326 LEU Chi-restraints excluded: chain CE residue 121 LYS Chi-restraints excluded: chain CE residue 175 SER Chi-restraints excluded: chain CE residue 190 THR Chi-restraints excluded: chain CE residue 270 LEU Chi-restraints excluded: chain CE residue 300 THR Chi-restraints excluded: chain CE residue 308 ARG Chi-restraints excluded: chain CE residue 319 ASN Chi-restraints excluded: chain CE residue 448 THR Chi-restraints excluded: chain CE residue 533 VAL Chi-restraints excluded: chain CF residue 48 MET Chi-restraints excluded: chain CF residue 51 ASN Chi-restraints excluded: chain CF residue 79 THR Chi-restraints excluded: chain CF residue 80 THR Chi-restraints excluded: chain CF residue 142 VAL Chi-restraints excluded: chain CF residue 175 ILE Chi-restraints excluded: chain CF residue 202 ASP Chi-restraints excluded: chain CF residue 221 VAL Chi-restraints excluded: chain CG residue 5 THR Chi-restraints excluded: chain CG residue 6 ASP Chi-restraints excluded: chain CG residue 13 LEU Chi-restraints excluded: chain CG residue 16 LEU Chi-restraints excluded: chain CG residue 40 MET Chi-restraints excluded: chain CG residue 59 VAL Chi-restraints excluded: chain CG residue 65 LEU Chi-restraints excluded: chain CG residue 67 LEU Chi-restraints excluded: chain CG residue 109 LEU Chi-restraints excluded: chain CG residue 116 LYS Chi-restraints excluded: chain CG residue 122 TRP Chi-restraints excluded: chain CG residue 130 SER Chi-restraints excluded: chain CH residue 32 ILE Chi-restraints excluded: chain CH residue 69 VAL Chi-restraints excluded: chain CH residue 85 TYR Chi-restraints excluded: chain CH residue 174 PHE Chi-restraints excluded: chain CH residue 232 ASN Chi-restraints excluded: chain CH residue 233 THR Chi-restraints excluded: chain CH residue 284 ILE Chi-restraints excluded: chain CH residue 316 ILE Chi-restraints excluded: chain CH residue 330 VAL Chi-restraints excluded: chain CH residue 372 THR Chi-restraints excluded: chain CH residue 390 LEU Chi-restraints excluded: chain CH residue 395 LYS Chi-restraints excluded: chain CH residue 399 ASN Chi-restraints excluded: chain CI residue 202 GLU Chi-restraints excluded: chain CI residue 203 LEU Chi-restraints excluded: chain CI residue 214 THR Chi-restraints excluded: chain CI residue 216 LEU Chi-restraints excluded: chain CI residue 218 VAL Chi-restraints excluded: chain CI residue 219 VAL Chi-restraints excluded: chain CI residue 228 ARG Chi-restraints excluded: chain CI residue 303 GLN Chi-restraints excluded: chain CJ residue 158 THR Chi-restraints excluded: chain CJ residue 179 LEU Chi-restraints excluded: chain CJ residue 218 ILE Chi-restraints excluded: chain CJ residue 415 ILE Chi-restraints excluded: chain CK residue 170 ARG Chi-restraints excluded: chain CK residue 199 SER Chi-restraints excluded: chain CK residue 212 LEU Chi-restraints excluded: chain CK residue 254 CYS Chi-restraints excluded: chain CM residue 92 VAL Chi-restraints excluded: chain CM residue 112 LEU Chi-restraints excluded: chain CM residue 121 VAL Chi-restraints excluded: chain CM residue 140 VAL Chi-restraints excluded: chain CM residue 147 LEU Chi-restraints excluded: chain CM residue 197 VAL Chi-restraints excluded: chain CN residue 1 MET Chi-restraints excluded: chain CN residue 18 THR Chi-restraints excluded: chain CN residue 98 GLU Chi-restraints excluded: chain CN residue 161 VAL Chi-restraints excluded: chain CN residue 198 VAL Chi-restraints excluded: chain CN residue 203 LEU Chi-restraints excluded: chain CO residue 40 ILE Chi-restraints excluded: chain CO residue 85 VAL Chi-restraints excluded: chain CP residue 270 ILE Chi-restraints excluded: chain CP residue 324 LEU Chi-restraints excluded: chain CP residue 334 VAL Chi-restraints excluded: chain CP residue 559 SER Chi-restraints excluded: chain CP residue 571 TYR Chi-restraints excluded: chain CP residue 574 ASP Chi-restraints excluded: chain CQ residue 42 MET Chi-restraints excluded: chain CQ residue 49 LEU Chi-restraints excluded: chain CQ residue 67 SER Chi-restraints excluded: chain CQ residue 97 SER Chi-restraints excluded: chain CR residue 5 LEU Chi-restraints excluded: chain CR residue 27 LEU Chi-restraints excluded: chain CR residue 47 GLN Chi-restraints excluded: chain CR residue 131 VAL Chi-restraints excluded: chain CR residue 145 HIS Chi-restraints excluded: chain CS residue 668 THR Chi-restraints excluded: chain CU residue 196 LEU Chi-restraints excluded: chain CU residue 200 LEU Chi-restraints excluded: chain CU residue 220 VAL Chi-restraints excluded: chain CU residue 228 ASP Chi-restraints excluded: chain CU residue 233 ILE Chi-restraints excluded: chain CU residue 256 SER Chi-restraints excluded: chain CU residue 279 ASP Chi-restraints excluded: chain CU residue 322 GLU Chi-restraints excluded: chain CX residue 141 GLU Chi-restraints excluded: chain Cb residue 217 THR Chi-restraints excluded: chain Cb residue 274 THR Chi-restraints excluded: chain Cb residue 275 LEU Chi-restraints excluded: chain Cb residue 295 LEU Chi-restraints excluded: chain Cb residue 304 ASP Chi-restraints excluded: chain Cb residue 393 VAL Chi-restraints excluded: chain Cb residue 490 VAL Chi-restraints excluded: chain Cb residue 589 ASN Chi-restraints excluded: chain Cb residue 842 LEU Chi-restraints excluded: chain LB residue 14 LEU Chi-restraints excluded: chain LB residue 41 VAL Chi-restraints excluded: chain LB residue 61 ASP Chi-restraints excluded: chain LB residue 73 VAL Chi-restraints excluded: chain LB residue 126 LYS Chi-restraints excluded: chain LB residue 137 TYR Chi-restraints excluded: chain LB residue 158 VAL Chi-restraints excluded: chain LB residue 161 VAL Chi-restraints excluded: chain LB residue 211 GLU Chi-restraints excluded: chain LB residue 227 PHE Chi-restraints excluded: chain LB residue 329 VAL Chi-restraints excluded: chain LC residue 8 THR Chi-restraints excluded: chain LC residue 17 THR Chi-restraints excluded: chain LC residue 28 SER Chi-restraints excluded: chain LC residue 43 MET Chi-restraints excluded: chain LC residue 62 SER Chi-restraints excluded: chain LC residue 79 SER Chi-restraints excluded: chain LC residue 100 MET Chi-restraints excluded: chain LC residue 112 VAL Chi-restraints excluded: chain LC residue 146 VAL Chi-restraints excluded: chain LC residue 187 LYS Chi-restraints excluded: chain LC residue 222 LEU Chi-restraints excluded: chain LC residue 238 ASP Chi-restraints excluded: chain LC residue 283 SER Chi-restraints excluded: chain LC residue 338 LYS Chi-restraints excluded: chain LE residue 102 VAL Chi-restraints excluded: chain LE residue 106 SER Chi-restraints excluded: chain LE residue 107 VAL Chi-restraints excluded: chain LE residue 111 LEU Chi-restraints excluded: chain LE residue 165 ILE Chi-restraints excluded: chain LF residue 18 LEU Chi-restraints excluded: chain LF residue 74 ILE Chi-restraints excluded: chain LF residue 88 LYS Chi-restraints excluded: chain LF residue 90 VAL Chi-restraints excluded: chain LF residue 117 ILE Chi-restraints excluded: chain LG residue 68 LEU Chi-restraints excluded: chain LG residue 85 LEU Chi-restraints excluded: chain LG residue 105 LYS Chi-restraints excluded: chain LG residue 191 THR Chi-restraints excluded: chain LG residue 193 VAL Chi-restraints excluded: chain LG residue 210 ASP Chi-restraints excluded: chain LG residue 240 ILE Chi-restraints excluded: chain LH residue 25 VAL Chi-restraints excluded: chain LH residue 26 THR Chi-restraints excluded: chain LH residue 36 LYS Chi-restraints excluded: chain LH residue 41 ILE Chi-restraints excluded: chain LH residue 48 VAL Chi-restraints excluded: chain LH residue 55 LEU Chi-restraints excluded: chain LH residue 56 GLU Chi-restraints excluded: chain LH residue 82 VAL Chi-restraints excluded: chain LH residue 134 VAL Chi-restraints excluded: chain LH residue 157 SER Chi-restraints excluded: chain LK residue 64 ILE Chi-restraints excluded: chain LL residue 22 VAL Chi-restraints excluded: chain LL residue 46 LEU Chi-restraints excluded: chain LL residue 58 VAL Chi-restraints excluded: chain LM residue 5 ASN Chi-restraints excluded: chain LM residue 6 VAL Chi-restraints excluded: chain LM residue 9 THR Chi-restraints excluded: chain LM residue 19 VAL Chi-restraints excluded: chain LM residue 20 LEU Chi-restraints excluded: chain LM residue 39 VAL Chi-restraints excluded: chain LM residue 57 VAL Chi-restraints excluded: chain LM residue 67 ILE Chi-restraints excluded: chain LM residue 68 VAL Chi-restraints excluded: chain LM residue 90 VAL Chi-restraints excluded: chain LN residue 96 ARG Chi-restraints excluded: chain LN residue 125 SER Chi-restraints excluded: chain LN residue 140 LYS Chi-restraints excluded: chain LN residue 167 THR Chi-restraints excluded: chain LN residue 171 SER Chi-restraints excluded: chain LN residue 187 ARG Chi-restraints excluded: chain LN residue 198 SER Chi-restraints excluded: chain LO residue 37 VAL Chi-restraints excluded: chain LO residue 110 VAL Chi-restraints excluded: chain LO residue 139 THR Chi-restraints excluded: chain LP residue 24 VAL Chi-restraints excluded: chain LP residue 58 VAL Chi-restraints excluded: chain LQ residue 148 THR Chi-restraints excluded: chain LS residue 73 LYS Chi-restraints excluded: chain LS residue 85 SER Chi-restraints excluded: chain LS residue 87 THR Chi-restraints excluded: chain LS residue 135 VAL Chi-restraints excluded: chain LS residue 144 VAL Chi-restraints excluded: chain LS residue 149 SER Chi-restraints excluded: chain LS residue 161 THR Chi-restraints excluded: chain LT residue 72 VAL Chi-restraints excluded: chain LT residue 89 ILE Chi-restraints excluded: chain LT residue 118 LYS Chi-restraints excluded: chain LT residue 142 SER Chi-restraints excluded: chain LT residue 143 ILE Chi-restraints excluded: chain LV residue 50 ARG Chi-restraints excluded: chain LV residue 88 LYS Chi-restraints excluded: chain LY residue 3 VAL Chi-restraints excluded: chain LY residue 6 THR Chi-restraints excluded: chain LY residue 7 VAL Chi-restraints excluded: chain LY residue 8 SER Chi-restraints excluded: chain LY residue 50 ARG Chi-restraints excluded: chain LY residue 66 GLU Chi-restraints excluded: chain LY residue 76 LYS Chi-restraints excluded: chain LY residue 81 VAL Chi-restraints excluded: chain LY residue 85 THR Chi-restraints excluded: chain LY residue 87 GLU Chi-restraints excluded: chain LY residue 93 THR Chi-restraints excluded: chain LY residue 96 ILE Chi-restraints excluded: chain LY residue 122 LYS Chi-restraints excluded: chain Ld residue 54 THR Chi-restraints excluded: chain Ld residue 75 VAL Chi-restraints excluded: chain Ld residue 116 VAL Chi-restraints excluded: chain Le residue 64 THR Chi-restraints excluded: chain Le residue 84 GLU Chi-restraints excluded: chain Lf residue 17 SER Chi-restraints excluded: chain Lf residue 37 VAL Chi-restraints excluded: chain Lf residue 58 GLN Chi-restraints excluded: chain Lf residue 108 SER Chi-restraints excluded: chain Lh residue 20 LEU Chi-restraints excluded: chain Lh residue 34 LEU Chi-restraints excluded: chain Lh residue 55 SER Chi-restraints excluded: chain Lh residue 120 LYS Chi-restraints excluded: chain Li residue 27 THR Chi-restraints excluded: chain Li residue 33 GLU Chi-restraints excluded: chain Li residue 75 ASP Chi-restraints excluded: chain Lj residue 27 LEU Chi-restraints excluded: chain Lj residue 36 SER Chi-restraints excluded: chain Lq residue 27 ASN Chi-restraints excluded: chain Lq residue 162 VAL Chi-restraints excluded: chain Lq residue 206 ILE Chi-restraints excluded: chain Cc residue 100 GLU Chi-restraints excluded: chain Cc residue 220 MET Chi-restraints excluded: chain Cc residue 228 MET Chi-restraints excluded: chain Cc residue 243 THR Chi-restraints excluded: chain Cc residue 245 SER Chi-restraints excluded: chain Cd residue 30 GLN Chi-restraints excluded: chain Cd residue 36 SER Chi-restraints excluded: chain Cd residue 82 SER Chi-restraints excluded: chain Cd residue 182 SER Chi-restraints excluded: chain Cd residue 267 SER Chi-restraints excluded: chain Cd residue 310 GLU Chi-restraints excluded: chain Cd residue 311 LEU Chi-restraints excluded: chain Cd residue 334 SER Chi-restraints excluded: chain Cd residue 393 ILE Chi-restraints excluded: chain Ce residue 34 VAL Chi-restraints excluded: chain Ce residue 43 CYS Chi-restraints excluded: chain Ce residue 73 MET Chi-restraints excluded: chain Ce residue 103 LYS Chi-restraints excluded: chain Ce residue 161 LYS Chi-restraints excluded: chain Ce residue 195 LEU Chi-restraints excluded: chain Cf residue 526 LYS Chi-restraints excluded: chain Cf residue 529 GLU Chi-restraints excluded: chain Cf residue 539 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1346 random chunks: chunk 1083 optimal weight: 0.8980 chunk 738 optimal weight: 0.1980 chunk 18 optimal weight: 6.9990 chunk 968 optimal weight: 7.9990 chunk 536 optimal weight: 30.0000 chunk 1110 optimal weight: 5.9990 chunk 899 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 664 optimal weight: 0.6980 chunk 1167 optimal weight: 0.0470 chunk 328 optimal weight: 6.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CA 286 GLN ** CE 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CF 121 GLN CF 205 GLN ** CG 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CG 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CH 96 GLN ** CH 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CI 256 HIS CI 269 HIS ** CJ 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CJ 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CK 105 GLN ** CM 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CQ 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CR 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CR 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CS 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cb 155 HIS Cb 175 GLN ** Cb 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 294 ASN LC 59 HIS LF 77 GLN LG 62 GLN LH 165 GLN ** LL 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 89 GLN LP 116 HIS LQ 86 ASN LQ 163 ASN LS 5 GLN LS 8 GLN ** LS 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LT 131 GLN ** LT 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lh 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lq 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cd 58 GLN Ce 41 GLN Ce 47 ASN Cf 521 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 145558 Z= 0.135 Angle : 0.534 12.112 208309 Z= 0.272 Chirality : 0.036 0.254 25322 Planarity : 0.004 0.095 17768 Dihedral : 21.540 179.544 49828 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.63 % Favored : 96.28 % Rotamer: Outliers : 3.76 % Allowed : 23.23 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.08), residues: 11105 helix: 1.75 (0.07), residues: 5014 sheet: 0.19 (0.14), residues: 1327 loop : -0.76 (0.09), residues: 4764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRPCb 816 HIS 0.008 0.001 HISCb 155 PHE 0.031 0.001 PHECJ 151 TYR 0.061 0.001 TYRCJ 234 ARG 0.009 0.000 ARGCE 279 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22210 Ramachandran restraints generated. 11105 Oldfield, 0 Emsley, 11105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22210 Ramachandran restraints generated. 11105 Oldfield, 0 Emsley, 11105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1797 residues out of total 9661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 321 poor density : 1476 time to evaluate : 8.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CA 123 MET cc_start: 0.8991 (OUTLIER) cc_final: 0.7172 (mpp) REVERT: CA 201 LYS cc_start: 0.7430 (OUTLIER) cc_final: 0.7124 (mttp) REVERT: CA 266 LYS cc_start: 0.7936 (tmmt) cc_final: 0.7676 (tmtt) REVERT: CA 294 ARG cc_start: 0.7688 (tpp80) cc_final: 0.6584 (ttp-170) REVERT: CA 310 ASP cc_start: 0.8084 (t0) cc_final: 0.7806 (t0) REVERT: CA 312 ARG cc_start: 0.8489 (mmt-90) cc_final: 0.8283 (mmt90) REVERT: CB 145 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8460 (ttmm) REVERT: CB 158 ARG cc_start: 0.6105 (OUTLIER) cc_final: 0.5569 (ttt180) REVERT: CC 361 LEU cc_start: 0.6275 (mt) cc_final: 0.5395 (tp) REVERT: CC 373 MET cc_start: 0.1268 (ppp) cc_final: 0.0586 (ppp) REVERT: CE 124 LYS cc_start: 0.8448 (ttmt) cc_final: 0.8179 (tttm) REVERT: CE 302 LYS cc_start: 0.8897 (mmmm) cc_final: 0.8522 (mtmt) REVERT: CE 513 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8010 (mm-30) REVERT: CG 116 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.7750 (ttmt) REVERT: CH 79 ASP cc_start: 0.8531 (m-30) cc_final: 0.8284 (m-30) REVERT: CH 174 PHE cc_start: 0.8993 (OUTLIER) cc_final: 0.8195 (t80) REVERT: CH 220 THR cc_start: 0.9258 (OUTLIER) cc_final: 0.9057 (t) REVERT: CH 232 ASN cc_start: 0.8989 (OUTLIER) cc_final: 0.8408 (p0) REVERT: CH 254 ASP cc_start: 0.8513 (t0) cc_final: 0.8138 (t0) REVERT: CH 341 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7902 (mm-30) REVERT: CH 345 GLN cc_start: 0.8605 (mm-40) cc_final: 0.8383 (mp10) REVERT: CI 198 PHE cc_start: 0.9066 (OUTLIER) cc_final: 0.8406 (t80) REVERT: CI 202 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8165 (pm20) REVERT: CJ 17 MET cc_start: 0.5789 (mpp) cc_final: 0.5502 (mpp) REVERT: CJ 32 ASP cc_start: 0.7198 (t70) cc_final: 0.6499 (t0) REVERT: CJ 97 ARG cc_start: 0.6339 (mmt180) cc_final: 0.6012 (mmm-85) REVERT: CJ 224 PHE cc_start: 0.6014 (m-10) cc_final: 0.5486 (m-80) REVERT: CJ 227 MET cc_start: 0.5339 (OUTLIER) cc_final: 0.4103 (ptm) REVERT: CK 132 MET cc_start: 0.7320 (mmm) cc_final: 0.7003 (mmt) REVERT: CK 180 LYS cc_start: 0.9138 (mtmm) cc_final: 0.8723 (mttm) REVERT: CL 16 LYS cc_start: 0.6895 (mmmm) cc_final: 0.6202 (mttm) REVERT: CM 113 ARG cc_start: 0.8218 (ptt-90) cc_final: 0.7806 (ptm-80) REVERT: CM 132 MET cc_start: 0.8208 (mmm) cc_final: 0.7911 (mmt) REVERT: CN 26 VAL cc_start: 0.8854 (t) cc_final: 0.8601 (m) REVERT: CN 140 GLN cc_start: 0.8605 (mm-40) cc_final: 0.8234 (tm-30) REVERT: CN 203 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8249 (pt) REVERT: CP 369 SER cc_start: 0.8979 (m) cc_final: 0.8730 (p) REVERT: CR 73 LEU cc_start: 0.6841 (tp) cc_final: 0.6545 (tp) REVERT: CS 666 LEU cc_start: 0.2917 (tp) cc_final: 0.2313 (pp) REVERT: CU 236 ASP cc_start: 0.9126 (m-30) cc_final: 0.8884 (m-30) REVERT: CU 241 LEU cc_start: 0.9105 (tp) cc_final: 0.8855 (tp) REVERT: Cb 322 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8446 (mm) REVERT: Cb 395 TYR cc_start: 0.8867 (p90) cc_final: 0.8661 (p90) REVERT: Cb 478 LEU cc_start: 0.9126 (tt) cc_final: 0.8915 (tt) REVERT: LB 66 LYS cc_start: 0.8944 (ttmm) cc_final: 0.8603 (tttm) REVERT: LB 137 TYR cc_start: 0.7931 (OUTLIER) cc_final: 0.6462 (m-80) REVERT: LB 211 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8391 (tt0) REVERT: LB 227 PHE cc_start: 0.8469 (OUTLIER) cc_final: 0.7445 (m-10) REVERT: LB 271 MET cc_start: 0.7957 (mtp) cc_final: 0.7559 (mmp) REVERT: LB 350 LYS cc_start: 0.8424 (mptt) cc_final: 0.7854 (mttm) REVERT: LB 354 LYS cc_start: 0.8892 (ptmm) cc_final: 0.8521 (mmtt) REVERT: LC 37 LYS cc_start: 0.8630 (tttm) cc_final: 0.8298 (tttt) REVERT: LC 187 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.7987 (mmmt) REVERT: LC 220 LYS cc_start: 0.8452 (mttt) cc_final: 0.7770 (mtmm) REVERT: LC 224 LYS cc_start: 0.8475 (mmtt) cc_final: 0.7571 (mtmt) REVERT: LC 264 GLN cc_start: 0.8268 (mm-40) cc_final: 0.7926 (mm-40) REVERT: LC 280 ASN cc_start: 0.8682 (t0) cc_final: 0.8444 (t0) REVERT: LC 282 VAL cc_start: 0.9164 (OUTLIER) cc_final: 0.8917 (m) REVERT: LE 35 GLN cc_start: 0.8193 (pm20) cc_final: 0.7630 (pt0) REVERT: LE 64 ARG cc_start: 0.7511 (ptm160) cc_final: 0.6621 (ptm160) REVERT: LF 37 GLU cc_start: 0.8574 (tp30) cc_final: 0.8231 (tp30) REVERT: LF 88 LYS cc_start: 0.8610 (mtmt) cc_final: 0.8291 (mttp) REVERT: LF 212 LYS cc_start: 0.8271 (mttt) cc_final: 0.8021 (mtmt) REVERT: LG 52 MET cc_start: 0.2941 (ptm) cc_final: 0.1535 (tmm) REVERT: LG 60 ARG cc_start: 0.7855 (ttm170) cc_final: 0.7526 (ttp80) REVERT: LG 68 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7869 (mp) REVERT: LG 87 LYS cc_start: 0.8489 (tttt) cc_final: 0.8182 (tttm) REVERT: LH 43 VAL cc_start: 0.8939 (t) cc_final: 0.8634 (p) REVERT: LK 94 LYS cc_start: 0.7435 (pttm) cc_final: 0.7057 (ptpt) REVERT: LL 23 ARG cc_start: 0.7886 (ttm110) cc_final: 0.6834 (tpt170) REVERT: LM 96 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7778 (mp0) REVERT: LM 130 GLU cc_start: 0.8686 (mp0) cc_final: 0.8406 (mp0) REVERT: LO 160 GLU cc_start: 0.8161 (tp30) cc_final: 0.7914 (mm-30) REVERT: LO 202 TYR cc_start: 0.8513 (m-80) cc_final: 0.8140 (m-80) REVERT: LP 23 ARG cc_start: 0.8408 (mtm-85) cc_final: 0.8176 (mtt90) REVERT: LP 115 LYS cc_start: 0.8686 (tttm) cc_final: 0.8360 (ttmt) REVERT: LQ 69 GLU cc_start: 0.7901 (mp0) cc_final: 0.7664 (pm20) REVERT: LS 109 ASP cc_start: 0.9061 (t0) cc_final: 0.8748 (t70) REVERT: LV 139 MET cc_start: 0.7788 (mtm) cc_final: 0.7451 (mtm) REVERT: LY 50 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.8638 (ttt-90) REVERT: LY 76 LYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8814 (mtpt) REVERT: LY 112 LYS cc_start: 0.8436 (ttmt) cc_final: 0.8044 (ttpp) REVERT: LY 122 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8673 (tttt) REVERT: LY 127 GLN cc_start: 0.8537 (tm-30) cc_final: 0.8082 (tt0) REVERT: Le 25 ARG cc_start: 0.6922 (OUTLIER) cc_final: 0.6665 (mmm160) REVERT: Le 55 SER cc_start: 0.8987 (m) cc_final: 0.8660 (t) REVERT: Le 84 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7772 (mp0) REVERT: Le 96 GLU cc_start: 0.8347 (tt0) cc_final: 0.7795 (tt0) REVERT: Le 124 LYS cc_start: 0.8410 (ptpt) cc_final: 0.8167 (pttt) REVERT: Lf 24 ASN cc_start: 0.7847 (m110) cc_final: 0.7590 (m-40) REVERT: Lf 58 GLN cc_start: 0.7911 (pt0) cc_final: 0.7680 (pm20) REVERT: Lh 33 GLN cc_start: 0.7828 (pp30) cc_final: 0.7445 (pp30) REVERT: Lh 78 LYS cc_start: 0.8499 (mmtt) cc_final: 0.8165 (mmmm) REVERT: Lh 120 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8798 (tttt) REVERT: Lj 57 LYS cc_start: 0.8609 (ptpt) cc_final: 0.7620 (ptmm) REVERT: Lq 165 MET cc_start: -0.1096 (ttt) cc_final: -0.2797 (mtt) REVERT: Cc 193 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8315 (ttp) REVERT: Cc 199 ASP cc_start: 0.8392 (m-30) cc_final: 0.8178 (m-30) REVERT: Cd 10 SER cc_start: 0.8481 (m) cc_final: 0.7990 (t) REVERT: Cd 94 ARG cc_start: 0.7603 (tmm-80) cc_final: 0.7376 (tmm-80) REVERT: Cd 387 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.7287 (mmm160) REVERT: Ce 13 GLN cc_start: 0.7648 (mm-40) cc_final: 0.7375 (tm-30) REVERT: Ce 103 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7820 (pttp) REVERT: Ce 161 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8506 (mttp) REVERT: Ce 172 ASP cc_start: 0.9031 (t0) cc_final: 0.8756 (t0) REVERT: Cf 520 LYS cc_start: 0.8288 (mttt) cc_final: 0.7995 (mtpp) REVERT: Cf 533 LYS cc_start: 0.8353 (mttt) cc_final: 0.7927 (mttt) outliers start: 321 outliers final: 197 residues processed: 1689 average time/residue: 1.2532 time to fit residues: 3639.6741 Evaluate side-chains 1622 residues out of total 9661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 1396 time to evaluate : 8.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CA residue 70 THR Chi-restraints excluded: chain CA residue 123 MET Chi-restraints excluded: chain CA residue 132 CYS Chi-restraints excluded: chain CA residue 149 GLU Chi-restraints excluded: chain CA residue 176 ILE Chi-restraints excluded: chain CA residue 201 LYS Chi-restraints excluded: chain CA residue 232 ILE Chi-restraints excluded: chain CA residue 241 THR Chi-restraints excluded: chain CB residue 48 ASN Chi-restraints excluded: chain CB residue 63 TRP Chi-restraints excluded: chain CB residue 70 LYS Chi-restraints excluded: chain CB residue 89 LEU Chi-restraints excluded: chain CB residue 114 ASP Chi-restraints excluded: chain CB residue 145 LYS Chi-restraints excluded: chain CB residue 158 ARG Chi-restraints excluded: chain CB residue 235 LEU Chi-restraints excluded: chain CB residue 241 THR Chi-restraints excluded: chain CB residue 243 ILE Chi-restraints excluded: chain CB residue 278 VAL Chi-restraints excluded: chain CC residue 167 VAL Chi-restraints excluded: chain CC residue 175 ILE Chi-restraints excluded: chain CC residue 326 LEU Chi-restraints excluded: chain CE residue 121 LYS Chi-restraints excluded: chain CE residue 157 THR Chi-restraints excluded: chain CE residue 175 SER Chi-restraints excluded: chain CE residue 190 THR Chi-restraints excluded: chain CE residue 414 THR Chi-restraints excluded: chain CE residue 448 THR Chi-restraints excluded: chain CE residue 533 VAL Chi-restraints excluded: chain CF residue 44 SER Chi-restraints excluded: chain CF residue 51 ASN Chi-restraints excluded: chain CF residue 65 ILE Chi-restraints excluded: chain CF residue 70 THR Chi-restraints excluded: chain CF residue 80 THR Chi-restraints excluded: chain CF residue 142 VAL Chi-restraints excluded: chain CF residue 175 ILE Chi-restraints excluded: chain CF residue 202 ASP Chi-restraints excluded: chain CF residue 221 VAL Chi-restraints excluded: chain CF residue 222 SER Chi-restraints excluded: chain CG residue 5 THR Chi-restraints excluded: chain CG residue 6 ASP Chi-restraints excluded: chain CG residue 13 LEU Chi-restraints excluded: chain CG residue 40 MET Chi-restraints excluded: chain CG residue 65 LEU Chi-restraints excluded: chain CG residue 67 LEU Chi-restraints excluded: chain CG residue 109 LEU Chi-restraints excluded: chain CG residue 116 LYS Chi-restraints excluded: chain CG residue 122 TRP Chi-restraints excluded: chain CG residue 137 MET Chi-restraints excluded: chain CH residue 32 ILE Chi-restraints excluded: chain CH residue 69 VAL Chi-restraints excluded: chain CH residue 85 TYR Chi-restraints excluded: chain CH residue 174 PHE Chi-restraints excluded: chain CH residue 220 THR Chi-restraints excluded: chain CH residue 232 ASN Chi-restraints excluded: chain CH residue 316 ILE Chi-restraints excluded: chain CH residue 330 VAL Chi-restraints excluded: chain CH residue 390 LEU Chi-restraints excluded: chain CH residue 399 ASN Chi-restraints excluded: chain CI residue 198 PHE Chi-restraints excluded: chain CI residue 202 GLU Chi-restraints excluded: chain CI residue 203 LEU Chi-restraints excluded: chain CI residue 214 THR Chi-restraints excluded: chain CI residue 216 LEU Chi-restraints excluded: chain CI residue 218 VAL Chi-restraints excluded: chain CI residue 303 GLN Chi-restraints excluded: chain CJ residue 192 ILE Chi-restraints excluded: chain CJ residue 218 ILE Chi-restraints excluded: chain CJ residue 227 MET Chi-restraints excluded: chain CJ residue 415 ILE Chi-restraints excluded: chain CK residue 119 VAL Chi-restraints excluded: chain CK residue 212 LEU Chi-restraints excluded: chain CL residue 12 THR Chi-restraints excluded: chain CL residue 18 THR Chi-restraints excluded: chain CM residue 60 GLU Chi-restraints excluded: chain CM residue 92 VAL Chi-restraints excluded: chain CM residue 112 LEU Chi-restraints excluded: chain CM residue 121 VAL Chi-restraints excluded: chain CM residue 125 VAL Chi-restraints excluded: chain CM residue 147 LEU Chi-restraints excluded: chain CM residue 197 VAL Chi-restraints excluded: chain CN residue 1 MET Chi-restraints excluded: chain CN residue 98 GLU Chi-restraints excluded: chain CN residue 173 LEU Chi-restraints excluded: chain CN residue 203 LEU Chi-restraints excluded: chain CN residue 242 VAL Chi-restraints excluded: chain CO residue 40 ILE Chi-restraints excluded: chain CP residue 270 ILE Chi-restraints excluded: chain CP residue 324 LEU Chi-restraints excluded: chain CP residue 334 VAL Chi-restraints excluded: chain CP residue 358 LEU Chi-restraints excluded: chain CP residue 371 LEU Chi-restraints excluded: chain CP residue 407 VAL Chi-restraints excluded: chain CP residue 490 LEU Chi-restraints excluded: chain CP residue 571 TYR Chi-restraints excluded: chain CP residue 574 ASP Chi-restraints excluded: chain CQ residue 16 SER Chi-restraints excluded: chain CQ residue 49 LEU Chi-restraints excluded: chain CR residue 32 ASN Chi-restraints excluded: chain CR residue 33 ASN Chi-restraints excluded: chain CR residue 131 VAL Chi-restraints excluded: chain CR residue 145 HIS Chi-restraints excluded: chain CR residue 212 ASP Chi-restraints excluded: chain CS residue 668 THR Chi-restraints excluded: chain CU residue 196 LEU Chi-restraints excluded: chain CU residue 220 VAL Chi-restraints excluded: chain CU residue 228 ASP Chi-restraints excluded: chain CU residue 233 ILE Chi-restraints excluded: chain CU residue 256 SER Chi-restraints excluded: chain CU residue 322 GLU Chi-restraints excluded: chain CX residue 89 LYS Chi-restraints excluded: chain CX residue 101 MET Chi-restraints excluded: chain CX residue 141 GLU Chi-restraints excluded: chain Cb residue 114 THR Chi-restraints excluded: chain Cb residue 140 LYS Chi-restraints excluded: chain Cb residue 259 LEU Chi-restraints excluded: chain Cb residue 295 LEU Chi-restraints excluded: chain Cb residue 304 ASP Chi-restraints excluded: chain Cb residue 322 LEU Chi-restraints excluded: chain Cb residue 393 VAL Chi-restraints excluded: chain Cb residue 563 VAL Chi-restraints excluded: chain Cb residue 589 ASN Chi-restraints excluded: chain Cb residue 842 LEU Chi-restraints excluded: chain LB residue 41 VAL Chi-restraints excluded: chain LB residue 137 TYR Chi-restraints excluded: chain LB residue 211 GLU Chi-restraints excluded: chain LB residue 227 PHE Chi-restraints excluded: chain LB residue 307 THR Chi-restraints excluded: chain LB residue 385 LYS Chi-restraints excluded: chain LC residue 62 SER Chi-restraints excluded: chain LC residue 112 VAL Chi-restraints excluded: chain LC residue 146 VAL Chi-restraints excluded: chain LC residue 187 LYS Chi-restraints excluded: chain LC residue 222 LEU Chi-restraints excluded: chain LC residue 238 ASP Chi-restraints excluded: chain LC residue 266 ASP Chi-restraints excluded: chain LC residue 282 VAL Chi-restraints excluded: chain LE residue 102 VAL Chi-restraints excluded: chain LE residue 107 VAL Chi-restraints excluded: chain LE residue 111 LEU Chi-restraints excluded: chain LF residue 18 LEU Chi-restraints excluded: chain LF residue 117 ILE Chi-restraints excluded: chain LG residue 68 LEU Chi-restraints excluded: chain LG residue 210 ASP Chi-restraints excluded: chain LG residue 240 ILE Chi-restraints excluded: chain LH residue 25 VAL Chi-restraints excluded: chain LH residue 26 THR Chi-restraints excluded: chain LH residue 41 ILE Chi-restraints excluded: chain LH residue 48 VAL Chi-restraints excluded: chain LH residue 55 LEU Chi-restraints excluded: chain LH residue 56 GLU Chi-restraints excluded: chain LH residue 82 VAL Chi-restraints excluded: chain LH residue 157 SER Chi-restraints excluded: chain LH residue 165 GLN Chi-restraints excluded: chain LK residue 64 ILE Chi-restraints excluded: chain LL residue 22 VAL Chi-restraints excluded: chain LL residue 58 VAL Chi-restraints excluded: chain LL residue 69 THR Chi-restraints excluded: chain LM residue 5 ASN Chi-restraints excluded: chain LM residue 19 VAL Chi-restraints excluded: chain LM residue 20 LEU Chi-restraints excluded: chain LM residue 39 VAL Chi-restraints excluded: chain LM residue 57 VAL Chi-restraints excluded: chain LM residue 68 VAL Chi-restraints excluded: chain LN residue 125 SER Chi-restraints excluded: chain LN residue 140 LYS Chi-restraints excluded: chain LN residue 167 THR Chi-restraints excluded: chain LO residue 37 VAL Chi-restraints excluded: chain LO residue 110 VAL Chi-restraints excluded: chain LP residue 58 VAL Chi-restraints excluded: chain LP residue 92 ILE Chi-restraints excluded: chain LP residue 163 VAL Chi-restraints excluded: chain LS residue 73 LYS Chi-restraints excluded: chain LS residue 85 SER Chi-restraints excluded: chain LS residue 135 VAL Chi-restraints excluded: chain LS residue 144 VAL Chi-restraints excluded: chain LS residue 149 SER Chi-restraints excluded: chain LT residue 72 VAL Chi-restraints excluded: chain LT residue 89 ILE Chi-restraints excluded: chain LT residue 142 SER Chi-restraints excluded: chain LT residue 143 ILE Chi-restraints excluded: chain LV residue 50 ARG Chi-restraints excluded: chain LV residue 72 ARG Chi-restraints excluded: chain LV residue 88 LYS Chi-restraints excluded: chain LV residue 103 VAL Chi-restraints excluded: chain LV residue 120 VAL Chi-restraints excluded: chain LY residue 7 VAL Chi-restraints excluded: chain LY residue 50 ARG Chi-restraints excluded: chain LY residue 76 LYS Chi-restraints excluded: chain LY residue 81 VAL Chi-restraints excluded: chain LY residue 122 LYS Chi-restraints excluded: chain Ld residue 16 VAL Chi-restraints excluded: chain Ld residue 46 LYS Chi-restraints excluded: chain Ld residue 54 THR Chi-restraints excluded: chain Ld residue 75 VAL Chi-restraints excluded: chain Le residue 25 ARG Chi-restraints excluded: chain Le residue 84 GLU Chi-restraints excluded: chain Le residue 130 GLU Chi-restraints excluded: chain Lf residue 17 SER Chi-restraints excluded: chain Lh residue 19 GLU Chi-restraints excluded: chain Lh residue 34 LEU Chi-restraints excluded: chain Lh residue 55 SER Chi-restraints excluded: chain Lh residue 120 LYS Chi-restraints excluded: chain Li residue 27 THR Chi-restraints excluded: chain Lq residue 27 ASN Chi-restraints excluded: chain Lq residue 99 LEU Chi-restraints excluded: chain Lq residue 206 ILE Chi-restraints excluded: chain Cc residue 193 MET Chi-restraints excluded: chain Cd residue 30 GLN Chi-restraints excluded: chain Cd residue 61 LEU Chi-restraints excluded: chain Cd residue 81 ASP Chi-restraints excluded: chain Cd residue 82 SER Chi-restraints excluded: chain Cd residue 182 SER Chi-restraints excluded: chain Cd residue 310 GLU Chi-restraints excluded: chain Cd residue 311 LEU Chi-restraints excluded: chain Cd residue 373 VAL Chi-restraints excluded: chain Cd residue 387 ARG Chi-restraints excluded: chain Cd residue 393 ILE Chi-restraints excluded: chain Ce residue 34 VAL Chi-restraints excluded: chain Ce residue 77 TRP Chi-restraints excluded: chain Ce residue 103 LYS Chi-restraints excluded: chain Ce residue 161 LYS Chi-restraints excluded: chain Ce residue 195 LEU Chi-restraints excluded: chain Cf residue 526 LYS Chi-restraints excluded: chain Cf residue 529 GLU Chi-restraints excluded: chain Cf residue 539 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1346 random chunks: chunk 437 optimal weight: 2.9990 chunk 1171 optimal weight: 5.9990 chunk 257 optimal weight: 3.9990 chunk 763 optimal weight: 20.0000 chunk 321 optimal weight: 9.9990 chunk 1302 optimal weight: 1.9990 chunk 1081 optimal weight: 5.9990 chunk 602 optimal weight: 0.9990 chunk 108 optimal weight: 10.0000 chunk 430 optimal weight: 8.9990 chunk 683 optimal weight: 30.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** CA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 286 GLN CE 319 ASN ** CE 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CE 378 GLN CF 205 GLN ** CG 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CG 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CI 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CJ 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CJ 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CK 105 GLN ** CM 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CQ 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CR 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CR 196 GLN Cb 155 HIS Cb 175 GLN ** Cb 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 185 ASN LC 59 HIS LF 77 GLN LG 62 GLN LL 103 ASN LP 116 HIS LS 5 GLN ** LS 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LS 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LS 142 GLN LS 147 ASN ** LT 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Le 22 GLN ** Lh 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cd 58 GLN Cf 518 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 145558 Z= 0.325 Angle : 0.614 13.597 208309 Z= 0.311 Chirality : 0.041 0.283 25322 Planarity : 0.005 0.097 17768 Dihedral : 21.517 179.225 49824 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.05 % Favored : 95.85 % Rotamer: Outliers : 4.52 % Allowed : 23.00 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.08), residues: 11105 helix: 1.77 (0.07), residues: 5013 sheet: 0.17 (0.14), residues: 1351 loop : -0.76 (0.09), residues: 4741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRPCb 816 HIS 0.009 0.001 HISLB 68 PHE 0.022 0.002 PHECH 473 TYR 0.039 0.002 TYRCJ 234 ARG 0.011 0.001 ARGCL 73 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22210 Ramachandran restraints generated. 11105 Oldfield, 0 Emsley, 11105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22210 Ramachandran restraints generated. 11105 Oldfield, 0 Emsley, 11105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1746 residues out of total 9661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 386 poor density : 1360 time to evaluate : 8.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CA 71 LYS cc_start: 0.6992 (mmtm) cc_final: 0.6245 (ptpp) REVERT: CA 123 MET cc_start: 0.9104 (OUTLIER) cc_final: 0.7425 (mpp) REVERT: CA 294 ARG cc_start: 0.7832 (tpp80) cc_final: 0.6768 (ttp-170) REVERT: CA 310 ASP cc_start: 0.8119 (t0) cc_final: 0.7825 (t0) REVERT: CA 312 ARG cc_start: 0.8537 (mmt-90) cc_final: 0.8285 (mmt90) REVERT: CB 66 LEU cc_start: 0.8414 (tt) cc_final: 0.8028 (tt) REVERT: CC 361 LEU cc_start: 0.6326 (mt) cc_final: 0.5425 (tp) REVERT: CC 373 MET cc_start: 0.1633 (ppp) cc_final: 0.0801 (ppp) REVERT: CE 124 LYS cc_start: 0.8511 (ttmt) cc_final: 0.8202 (tttm) REVERT: CE 302 LYS cc_start: 0.8954 (mmmm) cc_final: 0.8606 (mtmt) REVERT: CE 513 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8044 (mm-30) REVERT: CF 67 PHE cc_start: 0.9144 (t80) cc_final: 0.8797 (t80) REVERT: CG 116 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.7637 (ttpt) REVERT: CH 174 PHE cc_start: 0.9043 (OUTLIER) cc_final: 0.8233 (t80) REVERT: CH 232 ASN cc_start: 0.9070 (OUTLIER) cc_final: 0.8492 (p0) REVERT: CH 254 ASP cc_start: 0.8545 (t0) cc_final: 0.8058 (t0) REVERT: CH 341 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7882 (mm-30) REVERT: CH 345 GLN cc_start: 0.8627 (mm-40) cc_final: 0.8384 (mp10) REVERT: CI 198 PHE cc_start: 0.9100 (OUTLIER) cc_final: 0.8247 (t80) REVERT: CI 202 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8200 (pm20) REVERT: CJ 32 ASP cc_start: 0.7252 (t70) cc_final: 0.6589 (t0) REVERT: CJ 85 LYS cc_start: 0.6579 (ttmt) cc_final: 0.5970 (mtmt) REVERT: CJ 97 ARG cc_start: 0.6447 (mmt180) cc_final: 0.6201 (mmt90) REVERT: CJ 224 PHE cc_start: 0.5899 (m-10) cc_final: 0.5387 (m-80) REVERT: CJ 227 MET cc_start: 0.5179 (OUTLIER) cc_final: 0.4854 (ptm) REVERT: CK 132 MET cc_start: 0.7361 (mmm) cc_final: 0.7039 (mmt) REVERT: CK 180 LYS cc_start: 0.9148 (mtmm) cc_final: 0.8735 (mttm) REVERT: CL 16 LYS cc_start: 0.7080 (mmmm) cc_final: 0.6302 (mttm) REVERT: CM 113 ARG cc_start: 0.8229 (ptt-90) cc_final: 0.7834 (ptm-80) REVERT: CM 132 MET cc_start: 0.8341 (mmm) cc_final: 0.8007 (mmt) REVERT: CN 26 VAL cc_start: 0.8883 (t) cc_final: 0.8632 (m) REVERT: CN 140 GLN cc_start: 0.8670 (mm-40) cc_final: 0.8295 (tm-30) REVERT: CN 203 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8459 (pt) REVERT: CP 559 SER cc_start: 0.8360 (OUTLIER) cc_final: 0.7948 (t) REVERT: CQ 41 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8061 (mtmt) REVERT: CR 73 LEU cc_start: 0.7214 (tp) cc_final: 0.6873 (tp) REVERT: CS 666 LEU cc_start: 0.2781 (tp) cc_final: 0.2206 (pp) REVERT: CS 681 TYR cc_start: 0.0373 (OUTLIER) cc_final: -0.0081 (t80) REVERT: CU 241 LEU cc_start: 0.9143 (tp) cc_final: 0.8872 (tp) REVERT: Cb 164 LEU cc_start: 0.8985 (tp) cc_final: 0.8761 (tp) REVERT: Cb 322 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8444 (mm) REVERT: Cb 835 ASN cc_start: 0.8081 (OUTLIER) cc_final: 0.7845 (p0) REVERT: LB 137 TYR cc_start: 0.8104 (OUTLIER) cc_final: 0.6840 (m-80) REVERT: LB 227 PHE cc_start: 0.8410 (OUTLIER) cc_final: 0.7470 (m-10) REVERT: LB 271 MET cc_start: 0.8018 (mtp) cc_final: 0.7599 (mmp) REVERT: LB 350 LYS cc_start: 0.8448 (mptt) cc_final: 0.7839 (mttm) REVERT: LB 354 LYS cc_start: 0.8936 (ptmm) cc_final: 0.8546 (mmtt) REVERT: LC 187 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7899 (mmmt) REVERT: LC 220 LYS cc_start: 0.8493 (mttt) cc_final: 0.7891 (mtmm) REVERT: LC 264 GLN cc_start: 0.8365 (mm-40) cc_final: 0.8068 (mm-40) REVERT: LC 284 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8156 (tp-100) REVERT: LE 35 GLN cc_start: 0.8183 (pm20) cc_final: 0.7463 (pt0) REVERT: LE 64 ARG cc_start: 0.7670 (ptm160) cc_final: 0.6598 (ptm160) REVERT: LF 37 GLU cc_start: 0.8622 (tp30) cc_final: 0.8304 (tp30) REVERT: LF 88 LYS cc_start: 0.8660 (mtmt) cc_final: 0.8334 (mttp) REVERT: LF 174 ILE cc_start: 0.8675 (pt) cc_final: 0.8347 (pt) REVERT: LF 212 LYS cc_start: 0.8461 (mttt) cc_final: 0.8202 (mtmt) REVERT: LG 52 MET cc_start: 0.3088 (ptm) cc_final: 0.1646 (tmm) REVERT: LG 87 LYS cc_start: 0.8593 (tttt) cc_final: 0.8251 (tttm) REVERT: LH 43 VAL cc_start: 0.8962 (t) cc_final: 0.8637 (p) REVERT: LK 94 LYS cc_start: 0.7342 (pttm) cc_final: 0.6947 (ptpt) REVERT: LL 23 ARG cc_start: 0.7984 (ttm110) cc_final: 0.6944 (tpt170) REVERT: LM 96 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7686 (mp0) REVERT: LM 130 GLU cc_start: 0.8723 (mp0) cc_final: 0.8379 (mp0) REVERT: LO 5 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7296 (mm-30) REVERT: LO 160 GLU cc_start: 0.8245 (tp30) cc_final: 0.7897 (mm-30) REVERT: LO 202 TYR cc_start: 0.8600 (m-80) cc_final: 0.8263 (m-80) REVERT: LP 115 LYS cc_start: 0.8777 (tttm) cc_final: 0.8498 (ttmt) REVERT: LQ 78 ARG cc_start: 0.7799 (ttm110) cc_final: 0.7489 (ttm-80) REVERT: LS 109 ASP cc_start: 0.9188 (t0) cc_final: 0.8923 (t70) REVERT: LT 52 MET cc_start: 0.3684 (ptm) cc_final: 0.3106 (mmt) REVERT: LV 139 MET cc_start: 0.8075 (mtm) cc_final: 0.7704 (mtm) REVERT: LY 50 ARG cc_start: 0.9044 (OUTLIER) cc_final: 0.8610 (ttt-90) REVERT: LY 76 LYS cc_start: 0.9292 (OUTLIER) cc_final: 0.9033 (mtmt) REVERT: LY 112 LYS cc_start: 0.8489 (ttmt) cc_final: 0.8234 (ttpp) REVERT: LY 122 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8748 (tttt) REVERT: LY 127 GLN cc_start: 0.8626 (tm-30) cc_final: 0.8143 (tt0) REVERT: Le 25 ARG cc_start: 0.6983 (OUTLIER) cc_final: 0.6643 (mmm160) REVERT: Le 84 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7767 (mp0) REVERT: Le 96 GLU cc_start: 0.8398 (tt0) cc_final: 0.7857 (tt0) REVERT: Le 124 LYS cc_start: 0.8525 (ptpt) cc_final: 0.8277 (pttt) REVERT: Lh 33 GLN cc_start: 0.7853 (pp30) cc_final: 0.7471 (pp30) REVERT: Lh 78 LYS cc_start: 0.8577 (mmtt) cc_final: 0.8230 (mmmm) REVERT: Lq 165 MET cc_start: -0.0811 (ttt) cc_final: -0.2656 (mtt) REVERT: Cc 100 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7358 (mm-30) REVERT: Cd 10 SER cc_start: 0.8539 (m) cc_final: 0.8120 (t) REVERT: Cd 94 ARG cc_start: 0.7649 (tmm-80) cc_final: 0.7410 (tmm-80) REVERT: Cd 263 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8494 (mt0) REVERT: Cd 387 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.7588 (mmt90) REVERT: Ce 13 GLN cc_start: 0.7814 (mm-40) cc_final: 0.7434 (tm-30) REVERT: Ce 97 ARG cc_start: 0.8977 (mmt-90) cc_final: 0.8569 (mmm160) REVERT: Ce 103 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8206 (mtmm) REVERT: Ce 161 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8529 (ptpp) REVERT: Ce 172 ASP cc_start: 0.9066 (t0) cc_final: 0.8838 (t0) REVERT: Cf 533 LYS cc_start: 0.8384 (mttt) cc_final: 0.7982 (mttp) outliers start: 386 outliers final: 281 residues processed: 1628 average time/residue: 1.2809 time to fit residues: 3612.0717 Evaluate side-chains 1620 residues out of total 9661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 308 poor density : 1312 time to evaluate : 8.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CA residue 45 THR Chi-restraints excluded: chain CA residue 70 THR Chi-restraints excluded: chain CA residue 123 MET Chi-restraints excluded: chain CA residue 132 CYS Chi-restraints excluded: chain CA residue 149 GLU Chi-restraints excluded: chain CA residue 176 ILE Chi-restraints excluded: chain CA residue 201 LYS Chi-restraints excluded: chain CA residue 241 THR Chi-restraints excluded: chain CA residue 257 GLU Chi-restraints excluded: chain CB residue 30 LEU Chi-restraints excluded: chain CB residue 48 ASN Chi-restraints excluded: chain CB residue 63 TRP Chi-restraints excluded: chain CB residue 70 LYS Chi-restraints excluded: chain CB residue 89 LEU Chi-restraints excluded: chain CB residue 114 ASP Chi-restraints excluded: chain CB residue 131 SER Chi-restraints excluded: chain CB residue 145 LYS Chi-restraints excluded: chain CB residue 165 LYS Chi-restraints excluded: chain CB residue 235 LEU Chi-restraints excluded: chain CB residue 241 THR Chi-restraints excluded: chain CB residue 243 ILE Chi-restraints excluded: chain CB residue 278 VAL Chi-restraints excluded: chain CC residue 167 VAL Chi-restraints excluded: chain CC residue 175 ILE Chi-restraints excluded: chain CC residue 258 THR Chi-restraints excluded: chain CC residue 326 LEU Chi-restraints excluded: chain CC residue 408 MET Chi-restraints excluded: chain CE residue 121 LYS Chi-restraints excluded: chain CE residue 157 THR Chi-restraints excluded: chain CE residue 175 SER Chi-restraints excluded: chain CE residue 190 THR Chi-restraints excluded: chain CE residue 319 ASN Chi-restraints excluded: chain CE residue 414 THR Chi-restraints excluded: chain CE residue 448 THR Chi-restraints excluded: chain CE residue 533 VAL Chi-restraints excluded: chain CF residue 44 SER Chi-restraints excluded: chain CF residue 48 MET Chi-restraints excluded: chain CF residue 51 ASN Chi-restraints excluded: chain CF residue 70 THR Chi-restraints excluded: chain CF residue 80 THR Chi-restraints excluded: chain CF residue 142 VAL Chi-restraints excluded: chain CF residue 175 ILE Chi-restraints excluded: chain CF residue 202 ASP Chi-restraints excluded: chain CF residue 221 VAL Chi-restraints excluded: chain CF residue 222 SER Chi-restraints excluded: chain CG residue 5 THR Chi-restraints excluded: chain CG residue 6 ASP Chi-restraints excluded: chain CG residue 13 LEU Chi-restraints excluded: chain CG residue 16 LEU Chi-restraints excluded: chain CG residue 30 LEU Chi-restraints excluded: chain CG residue 40 MET Chi-restraints excluded: chain CG residue 59 VAL Chi-restraints excluded: chain CG residue 65 LEU Chi-restraints excluded: chain CG residue 67 LEU Chi-restraints excluded: chain CG residue 109 LEU Chi-restraints excluded: chain CG residue 116 LYS Chi-restraints excluded: chain CG residue 130 SER Chi-restraints excluded: chain CG residue 137 MET Chi-restraints excluded: chain CH residue 32 ILE Chi-restraints excluded: chain CH residue 69 VAL Chi-restraints excluded: chain CH residue 85 TYR Chi-restraints excluded: chain CH residue 174 PHE Chi-restraints excluded: chain CH residue 232 ASN Chi-restraints excluded: chain CH residue 316 ILE Chi-restraints excluded: chain CH residue 330 VAL Chi-restraints excluded: chain CH residue 381 THR Chi-restraints excluded: chain CH residue 390 LEU Chi-restraints excluded: chain CH residue 399 ASN Chi-restraints excluded: chain CI residue 198 PHE Chi-restraints excluded: chain CI residue 202 GLU Chi-restraints excluded: chain CI residue 214 THR Chi-restraints excluded: chain CI residue 216 LEU Chi-restraints excluded: chain CI residue 218 VAL Chi-restraints excluded: chain CI residue 224 THR Chi-restraints excluded: chain CI residue 283 VAL Chi-restraints excluded: chain CI residue 303 GLN Chi-restraints excluded: chain CJ residue 93 ARG Chi-restraints excluded: chain CJ residue 158 THR Chi-restraints excluded: chain CJ residue 192 ILE Chi-restraints excluded: chain CJ residue 218 ILE Chi-restraints excluded: chain CJ residue 227 MET Chi-restraints excluded: chain CK residue 119 VAL Chi-restraints excluded: chain CK residue 199 SER Chi-restraints excluded: chain CK residue 212 LEU Chi-restraints excluded: chain CL residue 12 THR Chi-restraints excluded: chain CL residue 18 THR Chi-restraints excluded: chain CM residue 92 VAL Chi-restraints excluded: chain CM residue 112 LEU Chi-restraints excluded: chain CM residue 119 ASN Chi-restraints excluded: chain CM residue 121 VAL Chi-restraints excluded: chain CM residue 125 VAL Chi-restraints excluded: chain CM residue 147 LEU Chi-restraints excluded: chain CM residue 197 VAL Chi-restraints excluded: chain CN residue 1 MET Chi-restraints excluded: chain CN residue 18 THR Chi-restraints excluded: chain CN residue 98 GLU Chi-restraints excluded: chain CN residue 173 LEU Chi-restraints excluded: chain CN residue 203 LEU Chi-restraints excluded: chain CN residue 242 VAL Chi-restraints excluded: chain CO residue 40 ILE Chi-restraints excluded: chain CO residue 85 VAL Chi-restraints excluded: chain CP residue 324 LEU Chi-restraints excluded: chain CP residue 334 VAL Chi-restraints excluded: chain CP residue 358 LEU Chi-restraints excluded: chain CP residue 371 LEU Chi-restraints excluded: chain CP residue 407 VAL Chi-restraints excluded: chain CP residue 490 LEU Chi-restraints excluded: chain CP residue 559 SER Chi-restraints excluded: chain CP residue 571 TYR Chi-restraints excluded: chain CP residue 574 ASP Chi-restraints excluded: chain CQ residue 41 LYS Chi-restraints excluded: chain CQ residue 49 LEU Chi-restraints excluded: chain CQ residue 67 SER Chi-restraints excluded: chain CR residue 5 LEU Chi-restraints excluded: chain CR residue 32 ASN Chi-restraints excluded: chain CR residue 47 GLN Chi-restraints excluded: chain CR residue 131 VAL Chi-restraints excluded: chain CR residue 145 HIS Chi-restraints excluded: chain CR residue 204 ASP Chi-restraints excluded: chain CS residue 652 ILE Chi-restraints excluded: chain CS residue 668 THR Chi-restraints excluded: chain CS residue 681 TYR Chi-restraints excluded: chain CU residue 196 LEU Chi-restraints excluded: chain CU residue 220 VAL Chi-restraints excluded: chain CU residue 228 ASP Chi-restraints excluded: chain CU residue 233 ILE Chi-restraints excluded: chain CU residue 322 GLU Chi-restraints excluded: chain CU residue 343 GLU Chi-restraints excluded: chain CU residue 355 ASP Chi-restraints excluded: chain CX residue 74 LEU Chi-restraints excluded: chain CX residue 89 LYS Chi-restraints excluded: chain CX residue 101 MET Chi-restraints excluded: chain CX residue 107 MET Chi-restraints excluded: chain CX residue 141 GLU Chi-restraints excluded: chain Cb residue 114 THR Chi-restraints excluded: chain Cb residue 140 LYS Chi-restraints excluded: chain Cb residue 179 VAL Chi-restraints excluded: chain Cb residue 217 THR Chi-restraints excluded: chain Cb residue 259 LEU Chi-restraints excluded: chain Cb residue 262 LEU Chi-restraints excluded: chain Cb residue 295 LEU Chi-restraints excluded: chain Cb residue 304 ASP Chi-restraints excluded: chain Cb residue 322 LEU Chi-restraints excluded: chain Cb residue 393 VAL Chi-restraints excluded: chain Cb residue 419 ILE Chi-restraints excluded: chain Cb residue 490 VAL Chi-restraints excluded: chain Cb residue 563 VAL Chi-restraints excluded: chain Cb residue 589 ASN Chi-restraints excluded: chain Cb residue 835 ASN Chi-restraints excluded: chain Cb residue 842 LEU Chi-restraints excluded: chain LB residue 41 VAL Chi-restraints excluded: chain LB residue 137 TYR Chi-restraints excluded: chain LB residue 161 VAL Chi-restraints excluded: chain LB residue 211 GLU Chi-restraints excluded: chain LB residue 227 PHE Chi-restraints excluded: chain LB residue 307 THR Chi-restraints excluded: chain LB residue 329 VAL Chi-restraints excluded: chain LB residue 336 ILE Chi-restraints excluded: chain LB residue 385 LYS Chi-restraints excluded: chain LC residue 8 THR Chi-restraints excluded: chain LC residue 17 THR Chi-restraints excluded: chain LC residue 43 MET Chi-restraints excluded: chain LC residue 62 SER Chi-restraints excluded: chain LC residue 79 SER Chi-restraints excluded: chain LC residue 100 MET Chi-restraints excluded: chain LC residue 112 VAL Chi-restraints excluded: chain LC residue 146 VAL Chi-restraints excluded: chain LC residue 187 LYS Chi-restraints excluded: chain LC residue 222 LEU Chi-restraints excluded: chain LC residue 232 VAL Chi-restraints excluded: chain LC residue 238 ASP Chi-restraints excluded: chain LC residue 266 ASP Chi-restraints excluded: chain LC residue 283 SER Chi-restraints excluded: chain LC residue 284 GLN Chi-restraints excluded: chain LE residue 102 VAL Chi-restraints excluded: chain LE residue 107 VAL Chi-restraints excluded: chain LE residue 109 VAL Chi-restraints excluded: chain LE residue 111 LEU Chi-restraints excluded: chain LE residue 138 SER Chi-restraints excluded: chain LF residue 17 THR Chi-restraints excluded: chain LF residue 18 LEU Chi-restraints excluded: chain LF residue 74 ILE Chi-restraints excluded: chain LF residue 90 VAL Chi-restraints excluded: chain LF residue 117 ILE Chi-restraints excluded: chain LF residue 134 LYS Chi-restraints excluded: chain LG residue 68 LEU Chi-restraints excluded: chain LG residue 85 LEU Chi-restraints excluded: chain LG residue 105 LYS Chi-restraints excluded: chain LG residue 167 VAL Chi-restraints excluded: chain LG residue 184 LYS Chi-restraints excluded: chain LG residue 193 VAL Chi-restraints excluded: chain LG residue 210 ASP Chi-restraints excluded: chain LH residue 19 SER Chi-restraints excluded: chain LH residue 25 VAL Chi-restraints excluded: chain LH residue 26 THR Chi-restraints excluded: chain LH residue 41 ILE Chi-restraints excluded: chain LH residue 48 VAL Chi-restraints excluded: chain LH residue 55 LEU Chi-restraints excluded: chain LH residue 56 GLU Chi-restraints excluded: chain LH residue 70 THR Chi-restraints excluded: chain LH residue 82 VAL Chi-restraints excluded: chain LH residue 134 VAL Chi-restraints excluded: chain LH residue 157 SER Chi-restraints excluded: chain LK residue 64 ILE Chi-restraints excluded: chain LL residue 22 VAL Chi-restraints excluded: chain LL residue 46 LEU Chi-restraints excluded: chain LL residue 51 VAL Chi-restraints excluded: chain LL residue 58 VAL Chi-restraints excluded: chain LL residue 69 THR Chi-restraints excluded: chain LM residue 5 ASN Chi-restraints excluded: chain LM residue 6 VAL Chi-restraints excluded: chain LM residue 9 THR Chi-restraints excluded: chain LM residue 19 VAL Chi-restraints excluded: chain LM residue 20 LEU Chi-restraints excluded: chain LM residue 39 VAL Chi-restraints excluded: chain LM residue 57 VAL Chi-restraints excluded: chain LM residue 59 LEU Chi-restraints excluded: chain LM residue 68 VAL Chi-restraints excluded: chain LM residue 90 VAL Chi-restraints excluded: chain LN residue 101 THR Chi-restraints excluded: chain LN residue 125 SER Chi-restraints excluded: chain LN residue 140 LYS Chi-restraints excluded: chain LN residue 167 THR Chi-restraints excluded: chain LN residue 171 SER Chi-restraints excluded: chain LN residue 196 THR Chi-restraints excluded: chain LO residue 37 VAL Chi-restraints excluded: chain LO residue 110 VAL Chi-restraints excluded: chain LO residue 121 VAL Chi-restraints excluded: chain LO residue 139 THR Chi-restraints excluded: chain LP residue 20 SER Chi-restraints excluded: chain LP residue 24 VAL Chi-restraints excluded: chain LP residue 58 VAL Chi-restraints excluded: chain LQ residue 148 THR Chi-restraints excluded: chain LS residue 35 VAL Chi-restraints excluded: chain LS residue 63 VAL Chi-restraints excluded: chain LS residue 85 SER Chi-restraints excluded: chain LS residue 87 THR Chi-restraints excluded: chain LS residue 135 VAL Chi-restraints excluded: chain LS residue 144 VAL Chi-restraints excluded: chain LS residue 149 SER Chi-restraints excluded: chain LS residue 161 THR Chi-restraints excluded: chain LT residue 72 VAL Chi-restraints excluded: chain LT residue 89 ILE Chi-restraints excluded: chain LT residue 142 SER Chi-restraints excluded: chain LT residue 143 ILE Chi-restraints excluded: chain LT residue 154 VAL Chi-restraints excluded: chain LV residue 19 LEU Chi-restraints excluded: chain LV residue 21 VAL Chi-restraints excluded: chain LV residue 72 ARG Chi-restraints excluded: chain LV residue 88 LYS Chi-restraints excluded: chain LV residue 120 VAL Chi-restraints excluded: chain LV residue 133 SER Chi-restraints excluded: chain LY residue 6 THR Chi-restraints excluded: chain LY residue 7 VAL Chi-restraints excluded: chain LY residue 8 SER Chi-restraints excluded: chain LY residue 50 ARG Chi-restraints excluded: chain LY residue 76 LYS Chi-restraints excluded: chain LY residue 81 VAL Chi-restraints excluded: chain LY residue 85 THR Chi-restraints excluded: chain LY residue 87 GLU Chi-restraints excluded: chain LY residue 93 THR Chi-restraints excluded: chain LY residue 122 LYS Chi-restraints excluded: chain Ld residue 16 VAL Chi-restraints excluded: chain Ld residue 54 THR Chi-restraints excluded: chain Ld residue 75 VAL Chi-restraints excluded: chain Ld residue 116 VAL Chi-restraints excluded: chain Le residue 25 ARG Chi-restraints excluded: chain Le residue 64 THR Chi-restraints excluded: chain Le residue 84 GLU Chi-restraints excluded: chain Le residue 118 VAL Chi-restraints excluded: chain Le residue 128 THR Chi-restraints excluded: chain Le residue 130 GLU Chi-restraints excluded: chain Lf residue 17 SER Chi-restraints excluded: chain Lf residue 37 VAL Chi-restraints excluded: chain Lf residue 58 GLN Chi-restraints excluded: chain Lf residue 108 SER Chi-restraints excluded: chain Lh residue 19 GLU Chi-restraints excluded: chain Lh residue 34 LEU Chi-restraints excluded: chain Lh residue 55 SER Chi-restraints excluded: chain Li residue 27 THR Chi-restraints excluded: chain Li residue 33 GLU Chi-restraints excluded: chain Li residue 75 ASP Chi-restraints excluded: chain Lj residue 36 SER Chi-restraints excluded: chain Lq residue 27 ASN Chi-restraints excluded: chain Lq residue 99 LEU Chi-restraints excluded: chain Lq residue 206 ILE Chi-restraints excluded: chain Cc residue 100 GLU Chi-restraints excluded: chain Cc residue 243 THR Chi-restraints excluded: chain Cc residue 245 SER Chi-restraints excluded: chain Cd residue 30 GLN Chi-restraints excluded: chain Cd residue 36 SER Chi-restraints excluded: chain Cd residue 61 LEU Chi-restraints excluded: chain Cd residue 81 ASP Chi-restraints excluded: chain Cd residue 82 SER Chi-restraints excluded: chain Cd residue 182 SER Chi-restraints excluded: chain Cd residue 263 GLN Chi-restraints excluded: chain Cd residue 267 SER Chi-restraints excluded: chain Cd residue 311 LEU Chi-restraints excluded: chain Cd residue 373 VAL Chi-restraints excluded: chain Cd residue 387 ARG Chi-restraints excluded: chain Cd residue 393 ILE Chi-restraints excluded: chain Ce residue 34 VAL Chi-restraints excluded: chain Ce residue 48 SER Chi-restraints excluded: chain Ce residue 103 LYS Chi-restraints excluded: chain Ce residue 161 LYS Chi-restraints excluded: chain Cf residue 526 LYS Chi-restraints excluded: chain Cf residue 529 GLU Chi-restraints excluded: chain Cf residue 539 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1346 random chunks: chunk 1255 optimal weight: 50.0000 chunk 146 optimal weight: 50.0000 chunk 742 optimal weight: 30.0000 chunk 951 optimal weight: 0.6980 chunk 736 optimal weight: 50.0000 chunk 1096 optimal weight: 1.9990 chunk 727 optimal weight: 50.0000 chunk 1297 optimal weight: 2.9990 chunk 811 optimal weight: 30.0000 chunk 790 optimal weight: 20.0000 chunk 598 optimal weight: 0.0270 overall best weight: 5.1446 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** CA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 286 GLN CE 334 GLN CE 425 GLN CF 121 GLN CF 205 GLN ** CG 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CG 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CH 429 ASN ** CI 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CJ 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CJ 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CK 105 GLN ** CM 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CP 432 ASN ** CQ 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CR 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CR 196 GLN Cb 175 GLN ** Cb 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 852 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 59 HIS ** LC 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 77 GLN LG 194 HIS LK 65 GLN LM 106 GLN LO 124 GLN ** LS 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LS 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LT 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lh 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 37 GLN ** Cc 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cd 40 HIS Cd 58 GLN Ce 86 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.106 145558 Z= 0.483 Angle : 0.729 24.314 208309 Z= 0.368 Chirality : 0.047 0.487 25322 Planarity : 0.006 0.091 17768 Dihedral : 21.671 179.192 49824 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.53 % Favored : 95.37 % Rotamer: Outliers : 4.98 % Allowed : 22.93 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.08), residues: 11105 helix: 1.55 (0.07), residues: 5026 sheet: 0.01 (0.14), residues: 1346 loop : -0.87 (0.09), residues: 4733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRPCb 816 HIS 0.016 0.002 HISCI 269 PHE 0.034 0.002 PHELL 14 TYR 0.045 0.002 TYRCJ 234 ARG 0.013 0.001 ARGCc 174 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22210 Ramachandran restraints generated. 11105 Oldfield, 0 Emsley, 11105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22210 Ramachandran restraints generated. 11105 Oldfield, 0 Emsley, 11105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1734 residues out of total 9661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 425 poor density : 1309 time to evaluate : 8.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CA 71 LYS cc_start: 0.7381 (mmtm) cc_final: 0.6393 (ptpp) REVERT: CA 123 MET cc_start: 0.9190 (OUTLIER) cc_final: 0.7609 (mpp) REVERT: CA 310 ASP cc_start: 0.8106 (t0) cc_final: 0.7823 (t0) REVERT: CA 312 ARG cc_start: 0.8723 (mmt-90) cc_final: 0.8449 (mmt90) REVERT: CC 361 LEU cc_start: 0.6405 (mt) cc_final: 0.5484 (tp) REVERT: CC 373 MET cc_start: 0.1694 (ppp) cc_final: 0.1149 (ppp) REVERT: CE 124 LYS cc_start: 0.8510 (ttmt) cc_final: 0.8131 (tttm) REVERT: CE 360 ILE cc_start: 0.9392 (mm) cc_final: 0.9189 (mm) REVERT: CG 116 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.7802 (ttpt) REVERT: CH 174 PHE cc_start: 0.9085 (OUTLIER) cc_final: 0.8296 (t80) REVERT: CH 232 ASN cc_start: 0.9093 (OUTLIER) cc_final: 0.8499 (p0) REVERT: CH 426 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8946 (pt) REVERT: CI 198 PHE cc_start: 0.9207 (OUTLIER) cc_final: 0.8475 (t80) REVERT: CI 202 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8269 (pm20) REVERT: CI 222 LYS cc_start: 0.8871 (tppp) cc_final: 0.8482 (ttmm) REVERT: CJ 17 MET cc_start: 0.5773 (mpp) cc_final: 0.3191 (tpp) REVERT: CJ 32 ASP cc_start: 0.7265 (t70) cc_final: 0.6597 (t0) REVERT: CJ 85 LYS cc_start: 0.6602 (ttmt) cc_final: 0.5825 (ptpp) REVERT: CJ 224 PHE cc_start: 0.5814 (m-10) cc_final: 0.5300 (m-80) REVERT: CJ 227 MET cc_start: 0.5316 (OUTLIER) cc_final: 0.4962 (ptm) REVERT: CK 132 MET cc_start: 0.7409 (mmm) cc_final: 0.7080 (mmt) REVERT: CK 162 THR cc_start: 0.8423 (p) cc_final: 0.8025 (m) REVERT: CK 180 LYS cc_start: 0.9161 (mtmm) cc_final: 0.8766 (mttm) REVERT: CL 16 LYS cc_start: 0.7232 (mmmm) cc_final: 0.6435 (mttm) REVERT: CM 113 ARG cc_start: 0.8256 (ptt-90) cc_final: 0.8011 (ptm-80) REVERT: CM 132 MET cc_start: 0.8329 (mmm) cc_final: 0.7985 (mmt) REVERT: CN 26 VAL cc_start: 0.8950 (t) cc_final: 0.8621 (m) REVERT: CN 140 GLN cc_start: 0.8693 (mm-40) cc_final: 0.8327 (tm-30) REVERT: CN 203 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8632 (pt) REVERT: CP 519 GLU cc_start: 0.7702 (tp30) cc_final: 0.7455 (tp30) REVERT: CP 559 SER cc_start: 0.8455 (OUTLIER) cc_final: 0.7971 (t) REVERT: CQ 1 MET cc_start: 0.7833 (ptm) cc_final: 0.7606 (ptm) REVERT: CQ 41 LYS cc_start: 0.9255 (OUTLIER) cc_final: 0.8142 (mtmt) REVERT: CR 32 ASN cc_start: 0.8436 (OUTLIER) cc_final: 0.8144 (p0) REVERT: CR 73 LEU cc_start: 0.7404 (tp) cc_final: 0.6993 (tp) REVERT: CS 666 LEU cc_start: 0.3082 (tp) cc_final: 0.2497 (pp) REVERT: CS 681 TYR cc_start: 0.0586 (OUTLIER) cc_final: 0.0081 (t80) REVERT: CU 241 LEU cc_start: 0.9212 (tp) cc_final: 0.8947 (tp) REVERT: Cb 3 LYS cc_start: 0.7242 (mmtp) cc_final: 0.6851 (mmmt) REVERT: Cb 245 ARG cc_start: 0.8601 (ttm110) cc_final: 0.7854 (ttm110) REVERT: Cb 322 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8363 (mm) REVERT: Cb 526 HIS cc_start: 0.8976 (t-90) cc_final: 0.8744 (t-90) REVERT: Cb 604 PHE cc_start: 0.7261 (OUTLIER) cc_final: 0.7050 (m-80) REVERT: LB 66 LYS cc_start: 0.8829 (tttp) cc_final: 0.8300 (tttm) REVERT: LB 137 TYR cc_start: 0.8273 (OUTLIER) cc_final: 0.7153 (m-80) REVERT: LB 227 PHE cc_start: 0.8506 (OUTLIER) cc_final: 0.7746 (m-10) REVERT: LB 271 MET cc_start: 0.8082 (mtp) cc_final: 0.7696 (mmp) REVERT: LB 340 ARG cc_start: 0.9157 (OUTLIER) cc_final: 0.6818 (ttm170) REVERT: LB 350 LYS cc_start: 0.8480 (mptt) cc_final: 0.7772 (mttm) REVERT: LB 354 LYS cc_start: 0.8909 (ptmm) cc_final: 0.8427 (mmtt) REVERT: LC 64 GLU cc_start: 0.8137 (tp30) cc_final: 0.7690 (pm20) REVERT: LC 75 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7637 (tp) REVERT: LC 187 LYS cc_start: 0.8361 (mtpt) cc_final: 0.7908 (mmmt) REVERT: LC 220 LYS cc_start: 0.8530 (mttt) cc_final: 0.8019 (mtmm) REVERT: LC 264 GLN cc_start: 0.8363 (mm-40) cc_final: 0.8158 (mm-40) REVERT: LC 284 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8119 (tp-100) REVERT: LE 35 GLN cc_start: 0.8164 (pm20) cc_final: 0.7448 (pt0) REVERT: LE 64 ARG cc_start: 0.7762 (ptm160) cc_final: 0.6802 (ptm160) REVERT: LF 88 LYS cc_start: 0.8663 (mtmt) cc_final: 0.8331 (mttp) REVERT: LF 212 LYS cc_start: 0.8521 (mttt) cc_final: 0.8228 (mtmt) REVERT: LG 52 MET cc_start: 0.3389 (ptm) cc_final: 0.1808 (tmm) REVERT: LG 87 LYS cc_start: 0.8645 (tttt) cc_final: 0.8327 (tttm) REVERT: LL 23 ARG cc_start: 0.8025 (ttm110) cc_final: 0.7080 (tpt90) REVERT: LM 35 ASP cc_start: 0.8309 (m-30) cc_final: 0.8023 (m-30) REVERT: LO 5 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7421 (mm-30) REVERT: LO 202 TYR cc_start: 0.8702 (m-80) cc_final: 0.8313 (m-80) REVERT: LP 23 ARG cc_start: 0.8532 (mtm-85) cc_final: 0.8239 (mtt90) REVERT: LP 115 LYS cc_start: 0.8738 (tttm) cc_final: 0.8430 (ttmt) REVERT: LP 141 SER cc_start: 0.8602 (t) cc_final: 0.8178 (p) REVERT: LT 52 MET cc_start: 0.3793 (ptm) cc_final: 0.3181 (mmt) REVERT: LV 139 MET cc_start: 0.8185 (mtm) cc_final: 0.7870 (mtm) REVERT: LY 50 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.8765 (ttt-90) REVERT: LY 54 GLU cc_start: 0.8332 (mm-30) cc_final: 0.8127 (mm-30) REVERT: LY 112 LYS cc_start: 0.8483 (ttmt) cc_final: 0.8054 (ttpp) REVERT: LY 122 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8775 (tttt) REVERT: LY 127 GLN cc_start: 0.8550 (tm-30) cc_final: 0.8193 (tt0) REVERT: Le 35 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.7810 (ttpt) REVERT: Le 84 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7782 (mp0) REVERT: Le 96 GLU cc_start: 0.8491 (tt0) cc_final: 0.7957 (tt0) REVERT: Le 124 LYS cc_start: 0.8598 (ptpt) cc_final: 0.8285 (pttt) REVERT: Lh 33 GLN cc_start: 0.7949 (pp30) cc_final: 0.7535 (pp30) REVERT: Lh 78 LYS cc_start: 0.8701 (mmtt) cc_final: 0.8272 (mmtm) REVERT: Lj 57 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.7548 (ptmm) REVERT: Lq 165 MET cc_start: -0.0564 (ttt) cc_final: -0.2483 (mtt) REVERT: Cd 10 SER cc_start: 0.8519 (m) cc_final: 0.8099 (t) REVERT: Cd 94 ARG cc_start: 0.7598 (tmm-80) cc_final: 0.7376 (tmm-80) REVERT: Cd 263 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8482 (mt0) REVERT: Cd 387 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8013 (mmt90) REVERT: Ce 103 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8403 (mtmm) REVERT: Ce 161 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8392 (ptpp) REVERT: Ce 172 ASP cc_start: 0.9172 (t0) cc_final: 0.8954 (t0) REVERT: Cf 533 LYS cc_start: 0.8470 (mttt) cc_final: 0.8000 (mttp) outliers start: 425 outliers final: 307 residues processed: 1612 average time/residue: 1.2832 time to fit residues: 3570.1522 Evaluate side-chains 1590 residues out of total 9661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 336 poor density : 1254 time to evaluate : 8.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CA residue 45 THR Chi-restraints excluded: chain CA residue 70 THR Chi-restraints excluded: chain CA residue 72 SER Chi-restraints excluded: chain CA residue 123 MET Chi-restraints excluded: chain CA residue 132 CYS Chi-restraints excluded: chain CA residue 149 GLU Chi-restraints excluded: chain CA residue 176 ILE Chi-restraints excluded: chain CA residue 201 LYS Chi-restraints excluded: chain CA residue 241 THR Chi-restraints excluded: chain CA residue 257 GLU Chi-restraints excluded: chain CB residue 27 CYS Chi-restraints excluded: chain CB residue 30 LEU Chi-restraints excluded: chain CB residue 48 ASN Chi-restraints excluded: chain CB residue 63 TRP Chi-restraints excluded: chain CB residue 70 LYS Chi-restraints excluded: chain CB residue 89 LEU Chi-restraints excluded: chain CB residue 91 THR Chi-restraints excluded: chain CB residue 131 SER Chi-restraints excluded: chain CB residue 145 LYS Chi-restraints excluded: chain CB residue 165 LYS Chi-restraints excluded: chain CB residue 170 THR Chi-restraints excluded: chain CB residue 235 LEU Chi-restraints excluded: chain CB residue 243 ILE Chi-restraints excluded: chain CB residue 278 VAL Chi-restraints excluded: chain CC residue 167 VAL Chi-restraints excluded: chain CC residue 175 ILE Chi-restraints excluded: chain CC residue 258 THR Chi-restraints excluded: chain CC residue 266 GLU Chi-restraints excluded: chain CC residue 326 LEU Chi-restraints excluded: chain CC residue 408 MET Chi-restraints excluded: chain CE residue 157 THR Chi-restraints excluded: chain CE residue 175 SER Chi-restraints excluded: chain CE residue 190 THR Chi-restraints excluded: chain CE residue 270 LEU Chi-restraints excluded: chain CE residue 300 THR Chi-restraints excluded: chain CE residue 361 ILE Chi-restraints excluded: chain CE residue 413 CYS Chi-restraints excluded: chain CE residue 414 THR Chi-restraints excluded: chain CE residue 448 THR Chi-restraints excluded: chain CE residue 459 LEU Chi-restraints excluded: chain CE residue 533 VAL Chi-restraints excluded: chain CF residue 48 MET Chi-restraints excluded: chain CF residue 51 ASN Chi-restraints excluded: chain CF residue 70 THR Chi-restraints excluded: chain CF residue 79 THR Chi-restraints excluded: chain CF residue 80 THR Chi-restraints excluded: chain CF residue 142 VAL Chi-restraints excluded: chain CF residue 175 ILE Chi-restraints excluded: chain CF residue 202 ASP Chi-restraints excluded: chain CF residue 221 VAL Chi-restraints excluded: chain CG residue 5 THR Chi-restraints excluded: chain CG residue 13 LEU Chi-restraints excluded: chain CG residue 16 LEU Chi-restraints excluded: chain CG residue 30 LEU Chi-restraints excluded: chain CG residue 40 MET Chi-restraints excluded: chain CG residue 59 VAL Chi-restraints excluded: chain CG residue 65 LEU Chi-restraints excluded: chain CG residue 67 LEU Chi-restraints excluded: chain CG residue 109 LEU Chi-restraints excluded: chain CG residue 116 LYS Chi-restraints excluded: chain CG residue 130 SER Chi-restraints excluded: chain CH residue 32 ILE Chi-restraints excluded: chain CH residue 69 VAL Chi-restraints excluded: chain CH residue 85 TYR Chi-restraints excluded: chain CH residue 174 PHE Chi-restraints excluded: chain CH residue 200 THR Chi-restraints excluded: chain CH residue 220 THR Chi-restraints excluded: chain CH residue 232 ASN Chi-restraints excluded: chain CH residue 233 THR Chi-restraints excluded: chain CH residue 284 ILE Chi-restraints excluded: chain CH residue 330 VAL Chi-restraints excluded: chain CH residue 372 THR Chi-restraints excluded: chain CH residue 390 LEU Chi-restraints excluded: chain CH residue 399 ASN Chi-restraints excluded: chain CH residue 426 ILE Chi-restraints excluded: chain CI residue 198 PHE Chi-restraints excluded: chain CI residue 202 GLU Chi-restraints excluded: chain CI residue 203 LEU Chi-restraints excluded: chain CI residue 214 THR Chi-restraints excluded: chain CI residue 216 LEU Chi-restraints excluded: chain CI residue 218 VAL Chi-restraints excluded: chain CI residue 219 VAL Chi-restraints excluded: chain CI residue 224 THR Chi-restraints excluded: chain CI residue 240 VAL Chi-restraints excluded: chain CI residue 283 VAL Chi-restraints excluded: chain CJ residue 93 ARG Chi-restraints excluded: chain CJ residue 158 THR Chi-restraints excluded: chain CJ residue 192 ILE Chi-restraints excluded: chain CJ residue 218 ILE Chi-restraints excluded: chain CJ residue 227 MET Chi-restraints excluded: chain CJ residue 237 LEU Chi-restraints excluded: chain CJ residue 238 LEU Chi-restraints excluded: chain CK residue 119 VAL Chi-restraints excluded: chain CK residue 121 ILE Chi-restraints excluded: chain CK residue 199 SER Chi-restraints excluded: chain CK residue 212 LEU Chi-restraints excluded: chain CL residue 12 THR Chi-restraints excluded: chain CL residue 18 THR Chi-restraints excluded: chain CM residue 92 VAL Chi-restraints excluded: chain CM residue 112 LEU Chi-restraints excluded: chain CM residue 119 ASN Chi-restraints excluded: chain CM residue 121 VAL Chi-restraints excluded: chain CM residue 125 VAL Chi-restraints excluded: chain CM residue 147 LEU Chi-restraints excluded: chain CM residue 197 VAL Chi-restraints excluded: chain CN residue 1 MET Chi-restraints excluded: chain CN residue 18 THR Chi-restraints excluded: chain CN residue 59 ILE Chi-restraints excluded: chain CN residue 98 GLU Chi-restraints excluded: chain CN residue 198 VAL Chi-restraints excluded: chain CN residue 203 LEU Chi-restraints excluded: chain CN residue 242 VAL Chi-restraints excluded: chain CO residue 40 ILE Chi-restraints excluded: chain CO residue 85 VAL Chi-restraints excluded: chain CP residue 324 LEU Chi-restraints excluded: chain CP residue 334 VAL Chi-restraints excluded: chain CP residue 358 LEU Chi-restraints excluded: chain CP residue 371 LEU Chi-restraints excluded: chain CP residue 407 VAL Chi-restraints excluded: chain CP residue 471 VAL Chi-restraints excluded: chain CP residue 559 SER Chi-restraints excluded: chain CP residue 571 TYR Chi-restraints excluded: chain CP residue 574 ASP Chi-restraints excluded: chain CQ residue 41 LYS Chi-restraints excluded: chain CQ residue 49 LEU Chi-restraints excluded: chain CQ residue 67 SER Chi-restraints excluded: chain CR residue 5 LEU Chi-restraints excluded: chain CR residue 32 ASN Chi-restraints excluded: chain CR residue 127 GLU Chi-restraints excluded: chain CR residue 131 VAL Chi-restraints excluded: chain CR residue 145 HIS Chi-restraints excluded: chain CR residue 204 ASP Chi-restraints excluded: chain CR residue 206 VAL Chi-restraints excluded: chain CS residue 652 ILE Chi-restraints excluded: chain CS residue 654 ILE Chi-restraints excluded: chain CS residue 681 TYR Chi-restraints excluded: chain CU residue 196 LEU Chi-restraints excluded: chain CU residue 220 VAL Chi-restraints excluded: chain CU residue 228 ASP Chi-restraints excluded: chain CU residue 233 ILE Chi-restraints excluded: chain CU residue 270 ASP Chi-restraints excluded: chain CU residue 322 GLU Chi-restraints excluded: chain CU residue 355 ASP Chi-restraints excluded: chain CX residue 74 LEU Chi-restraints excluded: chain CX residue 89 LYS Chi-restraints excluded: chain CX residue 95 VAL Chi-restraints excluded: chain CX residue 101 MET Chi-restraints excluded: chain CX residue 107 MET Chi-restraints excluded: chain CX residue 141 GLU Chi-restraints excluded: chain Cb residue 114 THR Chi-restraints excluded: chain Cb residue 140 LYS Chi-restraints excluded: chain Cb residue 217 THR Chi-restraints excluded: chain Cb residue 235 ILE Chi-restraints excluded: chain Cb residue 259 LEU Chi-restraints excluded: chain Cb residue 275 LEU Chi-restraints excluded: chain Cb residue 295 LEU Chi-restraints excluded: chain Cb residue 304 ASP Chi-restraints excluded: chain Cb residue 322 LEU Chi-restraints excluded: chain Cb residue 393 VAL Chi-restraints excluded: chain Cb residue 403 THR Chi-restraints excluded: chain Cb residue 490 VAL Chi-restraints excluded: chain Cb residue 563 VAL Chi-restraints excluded: chain Cb residue 589 ASN Chi-restraints excluded: chain Cb residue 604 PHE Chi-restraints excluded: chain Cb residue 842 LEU Chi-restraints excluded: chain LB residue 14 LEU Chi-restraints excluded: chain LB residue 73 VAL Chi-restraints excluded: chain LB residue 137 TYR Chi-restraints excluded: chain LB residue 158 VAL Chi-restraints excluded: chain LB residue 161 VAL Chi-restraints excluded: chain LB residue 211 GLU Chi-restraints excluded: chain LB residue 227 PHE Chi-restraints excluded: chain LB residue 307 THR Chi-restraints excluded: chain LB residue 329 VAL Chi-restraints excluded: chain LB residue 336 ILE Chi-restraints excluded: chain LB residue 340 ARG Chi-restraints excluded: chain LB residue 359 TRP Chi-restraints excluded: chain LB residue 385 LYS Chi-restraints excluded: chain LC residue 8 THR Chi-restraints excluded: chain LC residue 17 THR Chi-restraints excluded: chain LC residue 28 SER Chi-restraints excluded: chain LC residue 43 MET Chi-restraints excluded: chain LC residue 62 SER Chi-restraints excluded: chain LC residue 75 ILE Chi-restraints excluded: chain LC residue 79 SER Chi-restraints excluded: chain LC residue 112 VAL Chi-restraints excluded: chain LC residue 146 VAL Chi-restraints excluded: chain LC residue 222 LEU Chi-restraints excluded: chain LC residue 238 ASP Chi-restraints excluded: chain LC residue 283 SER Chi-restraints excluded: chain LC residue 284 GLN Chi-restraints excluded: chain LC residue 290 LEU Chi-restraints excluded: chain LE residue 71 VAL Chi-restraints excluded: chain LE residue 102 VAL Chi-restraints excluded: chain LE residue 106 SER Chi-restraints excluded: chain LE residue 107 VAL Chi-restraints excluded: chain LE residue 109 VAL Chi-restraints excluded: chain LE residue 111 LEU Chi-restraints excluded: chain LE residue 138 SER Chi-restraints excluded: chain LF residue 17 THR Chi-restraints excluded: chain LF residue 18 LEU Chi-restraints excluded: chain LF residue 74 ILE Chi-restraints excluded: chain LF residue 90 VAL Chi-restraints excluded: chain LF residue 117 ILE Chi-restraints excluded: chain LG residue 85 LEU Chi-restraints excluded: chain LG residue 105 LYS Chi-restraints excluded: chain LG residue 167 VAL Chi-restraints excluded: chain LG residue 184 LYS Chi-restraints excluded: chain LG residue 193 VAL Chi-restraints excluded: chain LG residue 210 ASP Chi-restraints excluded: chain LH residue 19 SER Chi-restraints excluded: chain LH residue 25 VAL Chi-restraints excluded: chain LH residue 26 THR Chi-restraints excluded: chain LH residue 36 LYS Chi-restraints excluded: chain LH residue 41 ILE Chi-restraints excluded: chain LH residue 48 VAL Chi-restraints excluded: chain LH residue 55 LEU Chi-restraints excluded: chain LH residue 56 GLU Chi-restraints excluded: chain LH residue 70 THR Chi-restraints excluded: chain LH residue 82 VAL Chi-restraints excluded: chain LH residue 134 VAL Chi-restraints excluded: chain LH residue 157 SER Chi-restraints excluded: chain LK residue 64 ILE Chi-restraints excluded: chain LL residue 22 VAL Chi-restraints excluded: chain LL residue 46 LEU Chi-restraints excluded: chain LL residue 58 VAL Chi-restraints excluded: chain LL residue 63 VAL Chi-restraints excluded: chain LL residue 69 THR Chi-restraints excluded: chain LM residue 5 ASN Chi-restraints excluded: chain LM residue 6 VAL Chi-restraints excluded: chain LM residue 9 THR Chi-restraints excluded: chain LM residue 19 VAL Chi-restraints excluded: chain LM residue 20 LEU Chi-restraints excluded: chain LM residue 39 VAL Chi-restraints excluded: chain LM residue 57 VAL Chi-restraints excluded: chain LM residue 59 LEU Chi-restraints excluded: chain LM residue 68 VAL Chi-restraints excluded: chain LM residue 90 VAL Chi-restraints excluded: chain LN residue 17 ASP Chi-restraints excluded: chain LN residue 60 VAL Chi-restraints excluded: chain LN residue 97 SER Chi-restraints excluded: chain LN residue 101 THR Chi-restraints excluded: chain LN residue 125 SER Chi-restraints excluded: chain LN residue 140 LYS Chi-restraints excluded: chain LN residue 167 THR Chi-restraints excluded: chain LN residue 171 SER Chi-restraints excluded: chain LN residue 196 THR Chi-restraints excluded: chain LN residue 198 SER Chi-restraints excluded: chain LO residue 37 VAL Chi-restraints excluded: chain LO residue 110 VAL Chi-restraints excluded: chain LO residue 139 THR Chi-restraints excluded: chain LP residue 7 THR Chi-restraints excluded: chain LP residue 20 SER Chi-restraints excluded: chain LP residue 24 VAL Chi-restraints excluded: chain LP residue 58 VAL Chi-restraints excluded: chain LP residue 140 MET Chi-restraints excluded: chain LQ residue 82 MET Chi-restraints excluded: chain LQ residue 148 THR Chi-restraints excluded: chain LS residue 35 VAL Chi-restraints excluded: chain LS residue 66 GLU Chi-restraints excluded: chain LS residue 73 LYS Chi-restraints excluded: chain LS residue 85 SER Chi-restraints excluded: chain LS residue 87 THR Chi-restraints excluded: chain LS residue 142 GLN Chi-restraints excluded: chain LS residue 144 VAL Chi-restraints excluded: chain LS residue 149 SER Chi-restraints excluded: chain LS residue 161 THR Chi-restraints excluded: chain LT residue 72 VAL Chi-restraints excluded: chain LT residue 89 ILE Chi-restraints excluded: chain LT residue 118 LYS Chi-restraints excluded: chain LT residue 143 ILE Chi-restraints excluded: chain LV residue 21 VAL Chi-restraints excluded: chain LV residue 72 ARG Chi-restraints excluded: chain LV residue 88 LYS Chi-restraints excluded: chain LV residue 120 VAL Chi-restraints excluded: chain LV residue 133 SER Chi-restraints excluded: chain LY residue 3 VAL Chi-restraints excluded: chain LY residue 6 THR Chi-restraints excluded: chain LY residue 7 VAL Chi-restraints excluded: chain LY residue 8 SER Chi-restraints excluded: chain LY residue 50 ARG Chi-restraints excluded: chain LY residue 76 LYS Chi-restraints excluded: chain LY residue 78 VAL Chi-restraints excluded: chain LY residue 81 VAL Chi-restraints excluded: chain LY residue 85 THR Chi-restraints excluded: chain LY residue 87 GLU Chi-restraints excluded: chain LY residue 93 THR Chi-restraints excluded: chain LY residue 122 LYS Chi-restraints excluded: chain Ld residue 46 LYS Chi-restraints excluded: chain Ld residue 54 THR Chi-restraints excluded: chain Ld residue 75 VAL Chi-restraints excluded: chain Ld residue 116 VAL Chi-restraints excluded: chain Le residue 35 LYS Chi-restraints excluded: chain Le residue 64 THR Chi-restraints excluded: chain Le residue 84 GLU Chi-restraints excluded: chain Le residue 118 VAL Chi-restraints excluded: chain Le residue 128 THR Chi-restraints excluded: chain Le residue 130 GLU Chi-restraints excluded: chain Lf residue 37 VAL Chi-restraints excluded: chain Lf residue 108 SER Chi-restraints excluded: chain Lh residue 19 GLU Chi-restraints excluded: chain Lh residue 20 LEU Chi-restraints excluded: chain Lh residue 34 LEU Chi-restraints excluded: chain Lh residue 55 SER Chi-restraints excluded: chain Lh residue 113 LEU Chi-restraints excluded: chain Li residue 27 THR Chi-restraints excluded: chain Li residue 33 GLU Chi-restraints excluded: chain Li residue 75 ASP Chi-restraints excluded: chain Lj residue 36 SER Chi-restraints excluded: chain Lj residue 57 LYS Chi-restraints excluded: chain Lq residue 27 ASN Chi-restraints excluded: chain Lq residue 99 LEU Chi-restraints excluded: chain Lq residue 162 VAL Chi-restraints excluded: chain Lq residue 206 ILE Chi-restraints excluded: chain Cc residue 175 ILE Chi-restraints excluded: chain Cc residue 243 THR Chi-restraints excluded: chain Cc residue 245 SER Chi-restraints excluded: chain Cd residue 30 GLN Chi-restraints excluded: chain Cd residue 36 SER Chi-restraints excluded: chain Cd residue 61 LEU Chi-restraints excluded: chain Cd residue 81 ASP Chi-restraints excluded: chain Cd residue 82 SER Chi-restraints excluded: chain Cd residue 182 SER Chi-restraints excluded: chain Cd residue 263 GLN Chi-restraints excluded: chain Cd residue 267 SER Chi-restraints excluded: chain Cd residue 311 LEU Chi-restraints excluded: chain Cd residue 334 SER Chi-restraints excluded: chain Cd residue 387 ARG Chi-restraints excluded: chain Cd residue 393 ILE Chi-restraints excluded: chain Ce residue 34 VAL Chi-restraints excluded: chain Ce residue 43 CYS Chi-restraints excluded: chain Ce residue 48 SER Chi-restraints excluded: chain Ce residue 103 LYS Chi-restraints excluded: chain Ce residue 161 LYS Chi-restraints excluded: chain Cf residue 526 LYS Chi-restraints excluded: chain Cf residue 539 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1346 random chunks: chunk 802 optimal weight: 50.0000 chunk 518 optimal weight: 0.0030 chunk 774 optimal weight: 0.0270 chunk 390 optimal weight: 0.9990 chunk 254 optimal weight: 8.9990 chunk 251 optimal weight: 7.9990 chunk 824 optimal weight: 0.9980 chunk 883 optimal weight: 0.9980 chunk 641 optimal weight: 9.9990 chunk 120 optimal weight: 2.9990 chunk 1019 optimal weight: 1.9990 overall best weight: 0.6050 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** CA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 230 ASN CA 286 GLN CF 205 GLN ** CG 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CG 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CI 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 15 ASN ** CJ 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CJ 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CK 41 ASN ** CQ 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CR 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CR 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CR 196 GLN CS 703 HIS Cb 155 HIS Cb 175 GLN ** Cb 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cb 260 HIS LC 59 HIS LF 77 GLN ** LS 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LS 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LT 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lh 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lq 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cc 152 GLN ** Cc 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cd 58 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 145558 Z= 0.147 Angle : 0.557 12.936 208309 Z= 0.283 Chirality : 0.036 0.279 25322 Planarity : 0.004 0.090 17768 Dihedral : 21.567 179.987 49824 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.57 % Favored : 96.36 % Rotamer: Outliers : 3.02 % Allowed : 25.20 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.08), residues: 11105 helix: 1.89 (0.07), residues: 5010 sheet: 0.06 (0.14), residues: 1355 loop : -0.70 (0.09), residues: 4740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRPCb 816 HIS 0.011 0.001 HISCb 452 PHE 0.043 0.001 PHECS 696 TYR 0.043 0.001 TYRCJ 234 ARG 0.011 0.000 ARGCc 174 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22210 Ramachandran restraints generated. 11105 Oldfield, 0 Emsley, 11105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22210 Ramachandran restraints generated. 11105 Oldfield, 0 Emsley, 11105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1624 residues out of total 9661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 1366 time to evaluate : 8.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CA 79 GLU cc_start: 0.8042 (tp30) cc_final: 0.7709 (tt0) REVERT: CA 123 MET cc_start: 0.9150 (OUTLIER) cc_final: 0.7310 (mpp) REVERT: CA 294 ARG cc_start: 0.7634 (tpp80) cc_final: 0.6824 (ttp-170) REVERT: CA 310 ASP cc_start: 0.8135 (t0) cc_final: 0.7838 (t0) REVERT: CC 361 LEU cc_start: 0.6399 (mt) cc_final: 0.5477 (tp) REVERT: CC 373 MET cc_start: 0.1431 (ppp) cc_final: 0.0851 (ppp) REVERT: CE 124 LYS cc_start: 0.8470 (ttmt) cc_final: 0.8144 (tttm) REVERT: CE 302 LYS cc_start: 0.8876 (mmmm) cc_final: 0.8567 (mtmt) REVERT: CE 513 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8017 (mm-30) REVERT: CG 116 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.7729 (ttpt) REVERT: CH 174 PHE cc_start: 0.8991 (OUTLIER) cc_final: 0.8159 (t80) REVERT: CH 254 ASP cc_start: 0.8415 (t0) cc_final: 0.7942 (t0) REVERT: CH 348 LYS cc_start: 0.8543 (mmmt) cc_final: 0.8341 (ttmm) REVERT: CI 202 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8089 (pm20) REVERT: CJ 17 MET cc_start: 0.5824 (mpp) cc_final: 0.3342 (tpp) REVERT: CJ 32 ASP cc_start: 0.7252 (t70) cc_final: 0.6563 (t0) REVERT: CJ 224 PHE cc_start: 0.5680 (m-10) cc_final: 0.5199 (m-80) REVERT: CJ 227 MET cc_start: 0.5317 (OUTLIER) cc_final: 0.5018 (ptm) REVERT: CK 132 MET cc_start: 0.7375 (mmm) cc_final: 0.7054 (mmt) REVERT: CK 180 LYS cc_start: 0.9115 (mtmm) cc_final: 0.8675 (mttp) REVERT: CL 16 LYS cc_start: 0.7100 (mmmm) cc_final: 0.6333 (mttm) REVERT: CM 113 ARG cc_start: 0.8287 (ptt-90) cc_final: 0.7797 (ptm-80) REVERT: CM 132 MET cc_start: 0.8343 (mmm) cc_final: 0.7989 (mmt) REVERT: CN 26 VAL cc_start: 0.8888 (t) cc_final: 0.8585 (m) REVERT: CN 140 GLN cc_start: 0.8661 (mm-40) cc_final: 0.8281 (tm-30) REVERT: CN 203 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8376 (pt) REVERT: CP 284 LEU cc_start: 0.9575 (mp) cc_final: 0.9369 (mp) REVERT: CQ 41 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.7982 (mtmt) REVERT: CR 32 ASN cc_start: 0.8341 (OUTLIER) cc_final: 0.8036 (p0) REVERT: CR 73 LEU cc_start: 0.7139 (tp) cc_final: 0.6780 (tp) REVERT: CS 681 TYR cc_start: 0.0680 (OUTLIER) cc_final: 0.0054 (t80) REVERT: CS 699 ASP cc_start: 0.3538 (t0) cc_final: 0.3263 (t0) REVERT: CS 700 GLU cc_start: 0.4204 (mm-30) cc_final: 0.3462 (tm-30) REVERT: CU 236 ASP cc_start: 0.9085 (m-30) cc_final: 0.8772 (m-30) REVERT: CU 241 LEU cc_start: 0.9094 (tp) cc_final: 0.8854 (tp) REVERT: CU 358 PHE cc_start: 0.7775 (OUTLIER) cc_final: 0.6930 (m-80) REVERT: CU 365 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8493 (tt0) REVERT: Cb 245 ARG cc_start: 0.8661 (ttm110) cc_final: 0.7986 (ttm110) REVERT: Cb 275 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8012 (tp) REVERT: Cb 526 HIS cc_start: 0.8909 (t-90) cc_final: 0.8641 (t-90) REVERT: LB 66 LYS cc_start: 0.8786 (tttp) cc_final: 0.8213 (tttm) REVERT: LB 137 TYR cc_start: 0.8057 (OUTLIER) cc_final: 0.6686 (m-80) REVERT: LB 227 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.7355 (m-10) REVERT: LB 271 MET cc_start: 0.7954 (mtp) cc_final: 0.7618 (mmp) REVERT: LB 340 ARG cc_start: 0.9248 (OUTLIER) cc_final: 0.7005 (ttm170) REVERT: LB 350 LYS cc_start: 0.8382 (mptt) cc_final: 0.7809 (mttm) REVERT: LB 354 LYS cc_start: 0.8945 (ptmm) cc_final: 0.8470 (mmtt) REVERT: LC 37 LYS cc_start: 0.8661 (tttm) cc_final: 0.8284 (tttt) REVERT: LC 187 LYS cc_start: 0.8342 (mtpt) cc_final: 0.7905 (mmmt) REVERT: LC 220 LYS cc_start: 0.8597 (mttt) cc_final: 0.7882 (mtmm) REVERT: LC 224 LYS cc_start: 0.8499 (mmtt) cc_final: 0.7622 (mtmt) REVERT: LC 264 GLN cc_start: 0.8280 (mm-40) cc_final: 0.7930 (mm-40) REVERT: LE 35 GLN cc_start: 0.8159 (pm20) cc_final: 0.7350 (pt0) REVERT: LE 64 ARG cc_start: 0.7576 (ptm160) cc_final: 0.6745 (ptm160) REVERT: LF 88 LYS cc_start: 0.8623 (mtmt) cc_final: 0.8297 (mttp) REVERT: LF 212 LYS cc_start: 0.8301 (mttt) cc_final: 0.8093 (mtmt) REVERT: LG 52 MET cc_start: 0.3317 (ptm) cc_final: 0.1715 (tmm) REVERT: LG 82 GLN cc_start: 0.8537 (mm-40) cc_final: 0.8199 (mm110) REVERT: LK 94 LYS cc_start: 0.7511 (pttm) cc_final: 0.7268 (ptpt) REVERT: LL 23 ARG cc_start: 0.7890 (ttm110) cc_final: 0.6838 (tpt170) REVERT: LM 130 GLU cc_start: 0.8735 (mp0) cc_final: 0.8410 (mp0) REVERT: LO 5 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7226 (mm-30) REVERT: LO 102 GLU cc_start: 0.7451 (mt-10) cc_final: 0.7105 (mt-10) REVERT: LO 202 TYR cc_start: 0.8518 (m-80) cc_final: 0.8063 (m-80) REVERT: LP 23 ARG cc_start: 0.8498 (mtm-85) cc_final: 0.8237 (mtt90) REVERT: LP 115 LYS cc_start: 0.8691 (tttm) cc_final: 0.8351 (ttmt) REVERT: LQ 69 GLU cc_start: 0.8007 (mp0) cc_final: 0.7558 (mp0) REVERT: LS 109 ASP cc_start: 0.9073 (t0) cc_final: 0.8820 (t70) REVERT: LT 52 MET cc_start: 0.3728 (ptm) cc_final: 0.3186 (mmt) REVERT: LV 68 LYS cc_start: 0.9016 (pttt) cc_final: 0.8791 (mmmt) REVERT: LV 108 LYS cc_start: 0.8415 (ttmt) cc_final: 0.8057 (ttmt) REVERT: LV 139 MET cc_start: 0.7756 (mtm) cc_final: 0.7395 (mtm) REVERT: LY 50 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.8666 (ttt-90) REVERT: LY 112 LYS cc_start: 0.8434 (ttmt) cc_final: 0.8226 (ttpp) REVERT: LY 122 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8715 (tttt) REVERT: LY 127 GLN cc_start: 0.8590 (tm-30) cc_final: 0.8240 (tt0) REVERT: Le 55 SER cc_start: 0.8997 (m) cc_final: 0.8689 (t) REVERT: Le 84 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7777 (mp0) REVERT: Le 96 GLU cc_start: 0.8373 (tt0) cc_final: 0.7837 (tt0) REVERT: Le 124 LYS cc_start: 0.8295 (ptpt) cc_final: 0.8037 (pttt) REVERT: Lh 33 GLN cc_start: 0.7796 (pp30) cc_final: 0.7443 (pp30) REVERT: Lh 78 LYS cc_start: 0.8589 (mmtt) cc_final: 0.8226 (mmtm) REVERT: Lq 165 MET cc_start: -0.0189 (ttt) cc_final: -0.2307 (mtt) REVERT: Cd 10 SER cc_start: 0.8456 (m) cc_final: 0.8056 (t) REVERT: Cd 61 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8811 (mt) REVERT: Cd 94 ARG cc_start: 0.7690 (tmm-80) cc_final: 0.7448 (tmm-80) REVERT: Cd 387 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.7587 (mmt90) REVERT: Ce 13 GLN cc_start: 0.7736 (mm-40) cc_final: 0.7377 (tm-30) REVERT: Ce 147 LYS cc_start: 0.8143 (tttt) cc_final: 0.7552 (tttp) REVERT: Ce 161 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8500 (ptpp) REVERT: Ce 172 ASP cc_start: 0.9092 (t0) cc_final: 0.8875 (t0) REVERT: Cf 528 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7227 (mm-30) REVERT: Cf 533 LYS cc_start: 0.8390 (mttt) cc_final: 0.7965 (mttp) outliers start: 258 outliers final: 187 residues processed: 1551 average time/residue: 1.2165 time to fit residues: 3244.0396 Evaluate side-chains 1513 residues out of total 9661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 1306 time to evaluate : 8.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CA residue 70 THR Chi-restraints excluded: chain CA residue 72 SER Chi-restraints excluded: chain CA residue 123 MET Chi-restraints excluded: chain CA residue 132 CYS Chi-restraints excluded: chain CA residue 149 GLU Chi-restraints excluded: chain CA residue 176 ILE Chi-restraints excluded: chain CA residue 201 LYS Chi-restraints excluded: chain CA residue 241 THR Chi-restraints excluded: chain CA residue 257 GLU Chi-restraints excluded: chain CB residue 27 CYS Chi-restraints excluded: chain CB residue 30 LEU Chi-restraints excluded: chain CB residue 48 ASN Chi-restraints excluded: chain CB residue 63 TRP Chi-restraints excluded: chain CB residue 70 LYS Chi-restraints excluded: chain CB residue 91 THR Chi-restraints excluded: chain CB residue 145 LYS Chi-restraints excluded: chain CB residue 170 THR Chi-restraints excluded: chain CB residue 278 VAL Chi-restraints excluded: chain CC residue 167 VAL Chi-restraints excluded: chain CC residue 175 ILE Chi-restraints excluded: chain CC residue 258 THR Chi-restraints excluded: chain CC residue 266 GLU Chi-restraints excluded: chain CC residue 326 LEU Chi-restraints excluded: chain CC residue 408 MET Chi-restraints excluded: chain CE residue 121 LYS Chi-restraints excluded: chain CE residue 157 THR Chi-restraints excluded: chain CE residue 190 THR Chi-restraints excluded: chain CE residue 300 THR Chi-restraints excluded: chain CE residue 414 THR Chi-restraints excluded: chain CE residue 533 VAL Chi-restraints excluded: chain CF residue 48 MET Chi-restraints excluded: chain CF residue 51 ASN Chi-restraints excluded: chain CF residue 70 THR Chi-restraints excluded: chain CF residue 175 ILE Chi-restraints excluded: chain CF residue 202 ASP Chi-restraints excluded: chain CF residue 221 VAL Chi-restraints excluded: chain CG residue 13 LEU Chi-restraints excluded: chain CG residue 30 LEU Chi-restraints excluded: chain CG residue 40 MET Chi-restraints excluded: chain CG residue 59 VAL Chi-restraints excluded: chain CG residue 65 LEU Chi-restraints excluded: chain CG residue 67 LEU Chi-restraints excluded: chain CG residue 109 LEU Chi-restraints excluded: chain CG residue 116 LYS Chi-restraints excluded: chain CG residue 130 SER Chi-restraints excluded: chain CG residue 137 MET Chi-restraints excluded: chain CH residue 32 ILE Chi-restraints excluded: chain CH residue 69 VAL Chi-restraints excluded: chain CH residue 85 TYR Chi-restraints excluded: chain CH residue 174 PHE Chi-restraints excluded: chain CH residue 233 THR Chi-restraints excluded: chain CH residue 262 SER Chi-restraints excluded: chain CH residue 316 ILE Chi-restraints excluded: chain CH residue 330 VAL Chi-restraints excluded: chain CH residue 390 LEU Chi-restraints excluded: chain CH residue 399 ASN Chi-restraints excluded: chain CI residue 202 GLU Chi-restraints excluded: chain CI residue 203 LEU Chi-restraints excluded: chain CI residue 214 THR Chi-restraints excluded: chain CI residue 216 LEU Chi-restraints excluded: chain CI residue 218 VAL Chi-restraints excluded: chain CI residue 219 VAL Chi-restraints excluded: chain CJ residue 93 ARG Chi-restraints excluded: chain CJ residue 192 ILE Chi-restraints excluded: chain CJ residue 218 ILE Chi-restraints excluded: chain CJ residue 227 MET Chi-restraints excluded: chain CK residue 119 VAL Chi-restraints excluded: chain CL residue 12 THR Chi-restraints excluded: chain CL residue 18 THR Chi-restraints excluded: chain CM residue 60 GLU Chi-restraints excluded: chain CM residue 92 VAL Chi-restraints excluded: chain CM residue 112 LEU Chi-restraints excluded: chain CM residue 121 VAL Chi-restraints excluded: chain CM residue 125 VAL Chi-restraints excluded: chain CM residue 147 LEU Chi-restraints excluded: chain CM residue 197 VAL Chi-restraints excluded: chain CN residue 1 MET Chi-restraints excluded: chain CN residue 87 SER Chi-restraints excluded: chain CN residue 98 GLU Chi-restraints excluded: chain CN residue 203 LEU Chi-restraints excluded: chain CN residue 242 VAL Chi-restraints excluded: chain CO residue 40 ILE Chi-restraints excluded: chain CP residue 270 ILE Chi-restraints excluded: chain CP residue 324 LEU Chi-restraints excluded: chain CP residue 334 VAL Chi-restraints excluded: chain CP residue 358 LEU Chi-restraints excluded: chain CP residue 371 LEU Chi-restraints excluded: chain CP residue 407 VAL Chi-restraints excluded: chain CP residue 571 TYR Chi-restraints excluded: chain CP residue 574 ASP Chi-restraints excluded: chain CQ residue 41 LYS Chi-restraints excluded: chain CQ residue 67 SER Chi-restraints excluded: chain CQ residue 97 SER Chi-restraints excluded: chain CR residue 32 ASN Chi-restraints excluded: chain CR residue 131 VAL Chi-restraints excluded: chain CR residue 145 HIS Chi-restraints excluded: chain CS residue 681 TYR Chi-restraints excluded: chain CU residue 220 VAL Chi-restraints excluded: chain CU residue 228 ASP Chi-restraints excluded: chain CU residue 233 ILE Chi-restraints excluded: chain CU residue 270 ASP Chi-restraints excluded: chain CU residue 322 GLU Chi-restraints excluded: chain CU residue 343 GLU Chi-restraints excluded: chain CU residue 358 PHE Chi-restraints excluded: chain CX residue 74 LEU Chi-restraints excluded: chain CX residue 95 VAL Chi-restraints excluded: chain CX residue 101 MET Chi-restraints excluded: chain CX residue 107 MET Chi-restraints excluded: chain CX residue 141 GLU Chi-restraints excluded: chain Cz residue 23 LEU Chi-restraints excluded: chain Cb residue 114 THR Chi-restraints excluded: chain Cb residue 140 LYS Chi-restraints excluded: chain Cb residue 217 THR Chi-restraints excluded: chain Cb residue 259 LEU Chi-restraints excluded: chain Cb residue 275 LEU Chi-restraints excluded: chain Cb residue 295 LEU Chi-restraints excluded: chain Cb residue 304 ASP Chi-restraints excluded: chain Cb residue 393 VAL Chi-restraints excluded: chain Cb residue 589 ASN Chi-restraints excluded: chain Cb residue 842 LEU Chi-restraints excluded: chain LB residue 14 LEU Chi-restraints excluded: chain LB residue 41 VAL Chi-restraints excluded: chain LB residue 137 TYR Chi-restraints excluded: chain LB residue 161 VAL Chi-restraints excluded: chain LB residue 199 LEU Chi-restraints excluded: chain LB residue 211 GLU Chi-restraints excluded: chain LB residue 227 PHE Chi-restraints excluded: chain LB residue 329 VAL Chi-restraints excluded: chain LB residue 340 ARG Chi-restraints excluded: chain LB residue 385 LYS Chi-restraints excluded: chain LC residue 62 SER Chi-restraints excluded: chain LC residue 79 SER Chi-restraints excluded: chain LC residue 112 VAL Chi-restraints excluded: chain LC residue 146 VAL Chi-restraints excluded: chain LC residue 222 LEU Chi-restraints excluded: chain LC residue 238 ASP Chi-restraints excluded: chain LE residue 102 VAL Chi-restraints excluded: chain LE residue 107 VAL Chi-restraints excluded: chain LE residue 111 LEU Chi-restraints excluded: chain LF residue 18 LEU Chi-restraints excluded: chain LF residue 117 ILE Chi-restraints excluded: chain LG residue 210 ASP Chi-restraints excluded: chain LH residue 25 VAL Chi-restraints excluded: chain LH residue 26 THR Chi-restraints excluded: chain LH residue 41 ILE Chi-restraints excluded: chain LH residue 55 LEU Chi-restraints excluded: chain LH residue 56 GLU Chi-restraints excluded: chain LH residue 82 VAL Chi-restraints excluded: chain LH residue 157 SER Chi-restraints excluded: chain LK residue 105 SER Chi-restraints excluded: chain LL residue 22 VAL Chi-restraints excluded: chain LL residue 51 VAL Chi-restraints excluded: chain LL residue 58 VAL Chi-restraints excluded: chain LL residue 69 THR Chi-restraints excluded: chain LM residue 5 ASN Chi-restraints excluded: chain LM residue 19 VAL Chi-restraints excluded: chain LM residue 20 LEU Chi-restraints excluded: chain LM residue 39 VAL Chi-restraints excluded: chain LM residue 57 VAL Chi-restraints excluded: chain LM residue 68 VAL Chi-restraints excluded: chain LM residue 90 VAL Chi-restraints excluded: chain LN residue 17 ASP Chi-restraints excluded: chain LN residue 125 SER Chi-restraints excluded: chain LN residue 140 LYS Chi-restraints excluded: chain LN residue 167 THR Chi-restraints excluded: chain LN residue 171 SER Chi-restraints excluded: chain LO residue 37 VAL Chi-restraints excluded: chain LO residue 110 VAL Chi-restraints excluded: chain LP residue 24 VAL Chi-restraints excluded: chain LP residue 58 VAL Chi-restraints excluded: chain LS residue 35 VAL Chi-restraints excluded: chain LS residue 142 GLN Chi-restraints excluded: chain LS residue 149 SER Chi-restraints excluded: chain LT residue 72 VAL Chi-restraints excluded: chain LV residue 88 LYS Chi-restraints excluded: chain LV residue 120 VAL Chi-restraints excluded: chain LY residue 7 VAL Chi-restraints excluded: chain LY residue 8 SER Chi-restraints excluded: chain LY residue 50 ARG Chi-restraints excluded: chain LY residue 76 LYS Chi-restraints excluded: chain LY residue 81 VAL Chi-restraints excluded: chain LY residue 122 LYS Chi-restraints excluded: chain Ld residue 54 THR Chi-restraints excluded: chain Ld residue 75 VAL Chi-restraints excluded: chain Ld residue 116 VAL Chi-restraints excluded: chain Le residue 84 GLU Chi-restraints excluded: chain Le residue 130 GLU Chi-restraints excluded: chain Lf residue 108 SER Chi-restraints excluded: chain Lh residue 19 GLU Chi-restraints excluded: chain Lh residue 20 LEU Chi-restraints excluded: chain Lh residue 34 LEU Chi-restraints excluded: chain Lh residue 55 SER Chi-restraints excluded: chain Li residue 27 THR Chi-restraints excluded: chain Lq residue 27 ASN Chi-restraints excluded: chain Lq residue 99 LEU Chi-restraints excluded: chain Lq residue 206 ILE Chi-restraints excluded: chain Cd residue 30 GLN Chi-restraints excluded: chain Cd residue 61 LEU Chi-restraints excluded: chain Cd residue 81 ASP Chi-restraints excluded: chain Cd residue 82 SER Chi-restraints excluded: chain Cd residue 311 LEU Chi-restraints excluded: chain Cd residue 387 ARG Chi-restraints excluded: chain Cd residue 393 ILE Chi-restraints excluded: chain Ce residue 34 VAL Chi-restraints excluded: chain Ce residue 161 LYS Chi-restraints excluded: chain Cf residue 526 LYS Chi-restraints excluded: chain Cf residue 539 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1346 random chunks: chunk 1180 optimal weight: 0.2980 chunk 1242 optimal weight: 4.9990 chunk 1133 optimal weight: 1.9990 chunk 1208 optimal weight: 6.9990 chunk 727 optimal weight: 0.0470 chunk 526 optimal weight: 7.9990 chunk 949 optimal weight: 1.9990 chunk 371 optimal weight: 7.9990 chunk 1092 optimal weight: 0.9990 chunk 1143 optimal weight: 0.6980 chunk 1204 optimal weight: 7.9990 overall best weight: 0.8082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** CA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 286 GLN ** CG 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CG 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CI 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CJ 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CJ 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CP 397 HIS ** CQ 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CR 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CR 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CR 196 GLN Cb 117 GLN Cb 175 GLN ** Cb 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 59 HIS LF 77 GLN LH 165 GLN ** LL 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LM 106 GLN ** LS 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LS 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LT 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lh 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lq 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cd 58 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 145558 Z= 0.152 Angle : 0.541 16.568 208309 Z= 0.274 Chirality : 0.036 0.273 25322 Planarity : 0.004 0.089 17768 Dihedral : 21.435 179.663 49822 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.74 % Favored : 96.19 % Rotamer: Outliers : 2.87 % Allowed : 25.65 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.08), residues: 11105 helix: 2.04 (0.07), residues: 5012 sheet: 0.10 (0.14), residues: 1367 loop : -0.60 (0.09), residues: 4726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRPCb 816 HIS 0.010 0.001 HISCI 269 PHE 0.035 0.001 PHECS 696 TYR 0.048 0.001 TYRCJ 234 ARG 0.014 0.000 ARGCE 279 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22210 Ramachandran restraints generated. 11105 Oldfield, 0 Emsley, 11105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22210 Ramachandran restraints generated. 11105 Oldfield, 0 Emsley, 11105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1591 residues out of total 9661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 1346 time to evaluate : 8.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CA 69 ASP cc_start: 0.8478 (t0) cc_final: 0.8250 (t0) REVERT: CA 71 LYS cc_start: 0.6919 (mmtm) cc_final: 0.6176 (ptpp) REVERT: CA 79 GLU cc_start: 0.8047 (tp30) cc_final: 0.7716 (tt0) REVERT: CA 123 MET cc_start: 0.9112 (OUTLIER) cc_final: 0.7301 (mpp) REVERT: CA 294 ARG cc_start: 0.7567 (tpp80) cc_final: 0.6596 (ttp-170) REVERT: CA 310 ASP cc_start: 0.8169 (t0) cc_final: 0.7871 (t0) REVERT: CB 145 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8451 (ttmm) REVERT: CC 361 LEU cc_start: 0.6406 (mt) cc_final: 0.5467 (tp) REVERT: CC 373 MET cc_start: 0.1408 (ppp) cc_final: 0.0938 (ppp) REVERT: CE 124 LYS cc_start: 0.8473 (ttmt) cc_final: 0.8149 (tttm) REVERT: CE 302 LYS cc_start: 0.8854 (mmmm) cc_final: 0.8555 (mtmt) REVERT: CE 513 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8054 (mm-30) REVERT: CG 116 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.7790 (ttpt) REVERT: CH 174 PHE cc_start: 0.8962 (OUTLIER) cc_final: 0.8120 (t80) REVERT: CH 348 LYS cc_start: 0.8554 (mmmt) cc_final: 0.8321 (ttmm) REVERT: CI 199 TYR cc_start: 0.8342 (m-10) cc_final: 0.8069 (m-10) REVERT: CI 202 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8105 (pm20) REVERT: CI 222 LYS cc_start: 0.8489 (ttmm) cc_final: 0.8270 (mttp) REVERT: CJ 17 MET cc_start: 0.5713 (mpp) cc_final: 0.3437 (tpp) REVERT: CJ 32 ASP cc_start: 0.7240 (t70) cc_final: 0.6609 (t0) REVERT: CJ 224 PHE cc_start: 0.5542 (m-10) cc_final: 0.5133 (m-80) REVERT: CK 132 MET cc_start: 0.7389 (mmm) cc_final: 0.7054 (mmt) REVERT: CK 180 LYS cc_start: 0.9149 (mtmm) cc_final: 0.8688 (mttp) REVERT: CL 16 LYS cc_start: 0.7139 (mmmm) cc_final: 0.6328 (mttm) REVERT: CM 132 MET cc_start: 0.8397 (mmm) cc_final: 0.7998 (mmt) REVERT: CN 26 VAL cc_start: 0.8867 (t) cc_final: 0.8580 (m) REVERT: CN 140 GLN cc_start: 0.8669 (mm-40) cc_final: 0.8305 (tm-30) REVERT: CN 203 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8334 (pt) REVERT: CQ 41 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.7922 (mtmt) REVERT: CR 73 LEU cc_start: 0.7204 (tp) cc_final: 0.6864 (tp) REVERT: CS 681 TYR cc_start: 0.0657 (OUTLIER) cc_final: -0.0131 (t80) REVERT: CS 699 ASP cc_start: 0.3111 (t0) cc_final: 0.2785 (t0) REVERT: CU 236 ASP cc_start: 0.9067 (m-30) cc_final: 0.8794 (m-30) REVERT: CU 241 LEU cc_start: 0.9102 (tp) cc_final: 0.8856 (tp) REVERT: CU 358 PHE cc_start: 0.7893 (OUTLIER) cc_final: 0.7004 (m-80) REVERT: Cb 245 ARG cc_start: 0.8645 (ttm110) cc_final: 0.7970 (ttm110) REVERT: LB 66 LYS cc_start: 0.8772 (tttp) cc_final: 0.8241 (tttm) REVERT: LB 137 TYR cc_start: 0.8071 (OUTLIER) cc_final: 0.6634 (m-80) REVERT: LB 227 PHE cc_start: 0.8374 (OUTLIER) cc_final: 0.7380 (m-10) REVERT: LB 271 MET cc_start: 0.7953 (mtp) cc_final: 0.7689 (mmp) REVERT: LB 337 MET cc_start: 0.8930 (mmt) cc_final: 0.8443 (mmt) REVERT: LB 340 ARG cc_start: 0.9229 (OUTLIER) cc_final: 0.6881 (ttm170) REVERT: LB 350 LYS cc_start: 0.8402 (mptt) cc_final: 0.7841 (mttm) REVERT: LB 354 LYS cc_start: 0.8927 (ptmm) cc_final: 0.8482 (mmtt) REVERT: LC 187 LYS cc_start: 0.8316 (mtpt) cc_final: 0.7909 (mmmt) REVERT: LC 220 LYS cc_start: 0.8572 (mttt) cc_final: 0.7891 (mtmm) REVERT: LC 224 LYS cc_start: 0.8556 (mmtt) cc_final: 0.7745 (mtmt) REVERT: LC 264 GLN cc_start: 0.8287 (mm-40) cc_final: 0.7939 (mm-40) REVERT: LE 35 GLN cc_start: 0.8082 (pm20) cc_final: 0.7338 (pt0) REVERT: LE 64 ARG cc_start: 0.7621 (ptm160) cc_final: 0.6768 (ptm160) REVERT: LF 88 LYS cc_start: 0.8603 (mtmt) cc_final: 0.8271 (mttp) REVERT: LF 212 LYS cc_start: 0.8321 (mttt) cc_final: 0.8069 (mtmt) REVERT: LG 52 MET cc_start: 0.3369 (ptm) cc_final: 0.1785 (tmm) REVERT: LG 82 GLN cc_start: 0.8560 (mm-40) cc_final: 0.8203 (mm110) REVERT: LG 87 LYS cc_start: 0.8526 (tttt) cc_final: 0.8203 (tttm) REVERT: LG 97 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.9008 (mt) REVERT: LK 94 LYS cc_start: 0.7450 (pttm) cc_final: 0.7151 (ptpt) REVERT: LL 23 ARG cc_start: 0.7869 (ttm110) cc_final: 0.6793 (tpt170) REVERT: LM 130 GLU cc_start: 0.8707 (mp0) cc_final: 0.8430 (mp0) REVERT: LN 176 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8312 (ptpt) REVERT: LO 102 GLU cc_start: 0.7450 (mt-10) cc_final: 0.7077 (mm-30) REVERT: LO 197 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8322 (mm-30) REVERT: LO 202 TYR cc_start: 0.8550 (m-80) cc_final: 0.8135 (m-80) REVERT: LP 115 LYS cc_start: 0.8716 (tttm) cc_final: 0.8363 (ttmt) REVERT: LQ 69 GLU cc_start: 0.8004 (mp0) cc_final: 0.7741 (mp0) REVERT: LS 16 THR cc_start: 0.8924 (m) cc_final: 0.8713 (p) REVERT: LS 109 ASP cc_start: 0.9059 (t0) cc_final: 0.8763 (t70) REVERT: LT 52 MET cc_start: 0.3697 (ptm) cc_final: 0.3174 (mmt) REVERT: LV 139 MET cc_start: 0.7794 (mtm) cc_final: 0.7375 (mtm) REVERT: LY 50 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8703 (ttt-90) REVERT: LY 54 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7970 (mm-30) REVERT: LY 76 LYS cc_start: 0.9214 (OUTLIER) cc_final: 0.8806 (mtmt) REVERT: LY 112 LYS cc_start: 0.8387 (ttmt) cc_final: 0.8186 (ttpp) REVERT: LY 122 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8703 (tttt) REVERT: LY 127 GLN cc_start: 0.8618 (tm-30) cc_final: 0.8201 (tt0) REVERT: Le 25 ARG cc_start: 0.7369 (mmm160) cc_final: 0.7107 (mmm160) REVERT: Le 35 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.7546 (ttpt) REVERT: Le 55 SER cc_start: 0.8978 (m) cc_final: 0.8669 (t) REVERT: Le 84 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7731 (mp0) REVERT: Le 96 GLU cc_start: 0.8352 (tt0) cc_final: 0.7784 (tt0) REVERT: Le 124 LYS cc_start: 0.8293 (ptpt) cc_final: 0.8047 (pttt) REVERT: Lh 33 GLN cc_start: 0.7735 (pp30) cc_final: 0.7367 (pp30) REVERT: Lh 78 LYS cc_start: 0.8495 (mmtt) cc_final: 0.8171 (mmmm) REVERT: Lq 165 MET cc_start: -0.0275 (ttt) cc_final: -0.2368 (mtt) REVERT: Cd 10 SER cc_start: 0.8405 (m) cc_final: 0.7989 (t) REVERT: Cd 61 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8765 (mt) REVERT: Cd 94 ARG cc_start: 0.7823 (tmm-80) cc_final: 0.7565 (tmm-80) REVERT: Cd 387 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.7442 (mmt90) REVERT: Ce 13 GLN cc_start: 0.7695 (mm-40) cc_final: 0.7439 (tm-30) REVERT: Ce 103 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7841 (pttp) REVERT: Ce 147 LYS cc_start: 0.8047 (tttt) cc_final: 0.7449 (tttp) REVERT: Ce 161 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8460 (mttp) REVERT: Ce 172 ASP cc_start: 0.9031 (t0) cc_final: 0.8821 (t0) REVERT: Cf 528 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7179 (mm-30) REVERT: Cf 533 LYS cc_start: 0.8382 (mttt) cc_final: 0.7978 (mttp) outliers start: 245 outliers final: 186 residues processed: 1513 average time/residue: 1.2575 time to fit residues: 3273.4245 Evaluate side-chains 1519 residues out of total 9661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 1310 time to evaluate : 8.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CA residue 72 SER Chi-restraints excluded: chain CA residue 123 MET Chi-restraints excluded: chain CA residue 132 CYS Chi-restraints excluded: chain CA residue 149 GLU Chi-restraints excluded: chain CA residue 176 ILE Chi-restraints excluded: chain CA residue 201 LYS Chi-restraints excluded: chain CA residue 241 THR Chi-restraints excluded: chain CB residue 27 CYS Chi-restraints excluded: chain CB residue 30 LEU Chi-restraints excluded: chain CB residue 48 ASN Chi-restraints excluded: chain CB residue 63 TRP Chi-restraints excluded: chain CB residue 91 THR Chi-restraints excluded: chain CB residue 145 LYS Chi-restraints excluded: chain CB residue 278 VAL Chi-restraints excluded: chain CC residue 167 VAL Chi-restraints excluded: chain CC residue 175 ILE Chi-restraints excluded: chain CC residue 257 ASP Chi-restraints excluded: chain CC residue 258 THR Chi-restraints excluded: chain CC residue 266 GLU Chi-restraints excluded: chain CC residue 326 LEU Chi-restraints excluded: chain CC residue 408 MET Chi-restraints excluded: chain CE residue 121 LYS Chi-restraints excluded: chain CE residue 157 THR Chi-restraints excluded: chain CE residue 175 SER Chi-restraints excluded: chain CE residue 190 THR Chi-restraints excluded: chain CE residue 300 THR Chi-restraints excluded: chain CE residue 413 CYS Chi-restraints excluded: chain CE residue 414 THR Chi-restraints excluded: chain CE residue 533 VAL Chi-restraints excluded: chain CF residue 51 ASN Chi-restraints excluded: chain CF residue 70 THR Chi-restraints excluded: chain CF residue 142 VAL Chi-restraints excluded: chain CF residue 175 ILE Chi-restraints excluded: chain CF residue 202 ASP Chi-restraints excluded: chain CF residue 221 VAL Chi-restraints excluded: chain CG residue 6 ASP Chi-restraints excluded: chain CG residue 13 LEU Chi-restraints excluded: chain CG residue 30 LEU Chi-restraints excluded: chain CG residue 40 MET Chi-restraints excluded: chain CG residue 59 VAL Chi-restraints excluded: chain CG residue 65 LEU Chi-restraints excluded: chain CG residue 67 LEU Chi-restraints excluded: chain CG residue 109 LEU Chi-restraints excluded: chain CG residue 116 LYS Chi-restraints excluded: chain CG residue 137 MET Chi-restraints excluded: chain CH residue 32 ILE Chi-restraints excluded: chain CH residue 69 VAL Chi-restraints excluded: chain CH residue 85 TYR Chi-restraints excluded: chain CH residue 174 PHE Chi-restraints excluded: chain CH residue 316 ILE Chi-restraints excluded: chain CH residue 330 VAL Chi-restraints excluded: chain CH residue 390 LEU Chi-restraints excluded: chain CH residue 399 ASN Chi-restraints excluded: chain CI residue 202 GLU Chi-restraints excluded: chain CI residue 214 THR Chi-restraints excluded: chain CI residue 216 LEU Chi-restraints excluded: chain CI residue 218 VAL Chi-restraints excluded: chain CJ residue 93 ARG Chi-restraints excluded: chain CJ residue 192 ILE Chi-restraints excluded: chain CJ residue 218 ILE Chi-restraints excluded: chain CK residue 119 VAL Chi-restraints excluded: chain CL residue 18 THR Chi-restraints excluded: chain CM residue 60 GLU Chi-restraints excluded: chain CM residue 92 VAL Chi-restraints excluded: chain CM residue 112 LEU Chi-restraints excluded: chain CM residue 125 VAL Chi-restraints excluded: chain CM residue 147 LEU Chi-restraints excluded: chain CM residue 197 VAL Chi-restraints excluded: chain CN residue 1 MET Chi-restraints excluded: chain CN residue 98 GLU Chi-restraints excluded: chain CN residue 203 LEU Chi-restraints excluded: chain CN residue 242 VAL Chi-restraints excluded: chain CO residue 40 ILE Chi-restraints excluded: chain CP residue 270 ILE Chi-restraints excluded: chain CP residue 324 LEU Chi-restraints excluded: chain CP residue 334 VAL Chi-restraints excluded: chain CP residue 358 LEU Chi-restraints excluded: chain CP residue 371 LEU Chi-restraints excluded: chain CP residue 407 VAL Chi-restraints excluded: chain CP residue 490 LEU Chi-restraints excluded: chain CP residue 571 TYR Chi-restraints excluded: chain CP residue 574 ASP Chi-restraints excluded: chain CQ residue 41 LYS Chi-restraints excluded: chain CQ residue 67 SER Chi-restraints excluded: chain CR residue 32 ASN Chi-restraints excluded: chain CR residue 131 VAL Chi-restraints excluded: chain CR residue 145 HIS Chi-restraints excluded: chain CS residue 681 TYR Chi-restraints excluded: chain CU residue 203 ILE Chi-restraints excluded: chain CU residue 220 VAL Chi-restraints excluded: chain CU residue 228 ASP Chi-restraints excluded: chain CU residue 233 ILE Chi-restraints excluded: chain CU residue 270 ASP Chi-restraints excluded: chain CU residue 322 GLU Chi-restraints excluded: chain CU residue 343 GLU Chi-restraints excluded: chain CU residue 358 PHE Chi-restraints excluded: chain CX residue 74 LEU Chi-restraints excluded: chain CX residue 95 VAL Chi-restraints excluded: chain CX residue 101 MET Chi-restraints excluded: chain CX residue 107 MET Chi-restraints excluded: chain CX residue 141 GLU Chi-restraints excluded: chain Cb residue 110 PHE Chi-restraints excluded: chain Cb residue 114 THR Chi-restraints excluded: chain Cb residue 140 LYS Chi-restraints excluded: chain Cb residue 175 GLN Chi-restraints excluded: chain Cb residue 217 THR Chi-restraints excluded: chain Cb residue 295 LEU Chi-restraints excluded: chain Cb residue 304 ASP Chi-restraints excluded: chain Cb residue 393 VAL Chi-restraints excluded: chain Cb residue 589 ASN Chi-restraints excluded: chain Cb residue 842 LEU Chi-restraints excluded: chain Cb residue 878 GLU Chi-restraints excluded: chain LB residue 14 LEU Chi-restraints excluded: chain LB residue 41 VAL Chi-restraints excluded: chain LB residue 137 TYR Chi-restraints excluded: chain LB residue 199 LEU Chi-restraints excluded: chain LB residue 211 GLU Chi-restraints excluded: chain LB residue 215 MET Chi-restraints excluded: chain LB residue 227 PHE Chi-restraints excluded: chain LB residue 329 VAL Chi-restraints excluded: chain LB residue 340 ARG Chi-restraints excluded: chain LC residue 62 SER Chi-restraints excluded: chain LC residue 79 SER Chi-restraints excluded: chain LC residue 112 VAL Chi-restraints excluded: chain LC residue 146 VAL Chi-restraints excluded: chain LC residue 222 LEU Chi-restraints excluded: chain LC residue 238 ASP Chi-restraints excluded: chain LC residue 341 LEU Chi-restraints excluded: chain LE residue 102 VAL Chi-restraints excluded: chain LE residue 106 SER Chi-restraints excluded: chain LE residue 107 VAL Chi-restraints excluded: chain LE residue 111 LEU Chi-restraints excluded: chain LF residue 18 LEU Chi-restraints excluded: chain LF residue 74 ILE Chi-restraints excluded: chain LF residue 117 ILE Chi-restraints excluded: chain LG residue 97 LEU Chi-restraints excluded: chain LG residue 193 VAL Chi-restraints excluded: chain LG residue 210 ASP Chi-restraints excluded: chain LH residue 25 VAL Chi-restraints excluded: chain LH residue 26 THR Chi-restraints excluded: chain LH residue 41 ILE Chi-restraints excluded: chain LH residue 55 LEU Chi-restraints excluded: chain LH residue 56 GLU Chi-restraints excluded: chain LH residue 82 VAL Chi-restraints excluded: chain LH residue 157 SER Chi-restraints excluded: chain LK residue 105 SER Chi-restraints excluded: chain LL residue 22 VAL Chi-restraints excluded: chain LL residue 46 LEU Chi-restraints excluded: chain LL residue 58 VAL Chi-restraints excluded: chain LL residue 69 THR Chi-restraints excluded: chain LM residue 5 ASN Chi-restraints excluded: chain LM residue 19 VAL Chi-restraints excluded: chain LM residue 20 LEU Chi-restraints excluded: chain LM residue 39 VAL Chi-restraints excluded: chain LM residue 57 VAL Chi-restraints excluded: chain LM residue 68 VAL Chi-restraints excluded: chain LM residue 90 VAL Chi-restraints excluded: chain LN residue 17 ASP Chi-restraints excluded: chain LN residue 125 SER Chi-restraints excluded: chain LN residue 140 LYS Chi-restraints excluded: chain LN residue 167 THR Chi-restraints excluded: chain LN residue 171 SER Chi-restraints excluded: chain LN residue 176 LYS Chi-restraints excluded: chain LN residue 198 SER Chi-restraints excluded: chain LO residue 37 VAL Chi-restraints excluded: chain LO residue 110 VAL Chi-restraints excluded: chain LP residue 24 VAL Chi-restraints excluded: chain LP residue 58 VAL Chi-restraints excluded: chain LS residue 35 VAL Chi-restraints excluded: chain LS residue 73 LYS Chi-restraints excluded: chain LS residue 149 SER Chi-restraints excluded: chain LT residue 72 VAL Chi-restraints excluded: chain LT residue 85 ILE Chi-restraints excluded: chain LV residue 24 ILE Chi-restraints excluded: chain LV residue 88 LYS Chi-restraints excluded: chain LV residue 120 VAL Chi-restraints excluded: chain LY residue 7 VAL Chi-restraints excluded: chain LY residue 8 SER Chi-restraints excluded: chain LY residue 50 ARG Chi-restraints excluded: chain LY residue 66 GLU Chi-restraints excluded: chain LY residue 76 LYS Chi-restraints excluded: chain LY residue 81 VAL Chi-restraints excluded: chain LY residue 122 LYS Chi-restraints excluded: chain Ld residue 54 THR Chi-restraints excluded: chain Ld residue 75 VAL Chi-restraints excluded: chain Ld residue 116 VAL Chi-restraints excluded: chain Le residue 35 LYS Chi-restraints excluded: chain Le residue 84 GLU Chi-restraints excluded: chain Le residue 130 GLU Chi-restraints excluded: chain Lf residue 17 SER Chi-restraints excluded: chain Lf residue 108 SER Chi-restraints excluded: chain Lh residue 19 GLU Chi-restraints excluded: chain Lh residue 34 LEU Chi-restraints excluded: chain Lh residue 55 SER Chi-restraints excluded: chain Li residue 27 THR Chi-restraints excluded: chain Lq residue 99 LEU Chi-restraints excluded: chain Lq residue 206 ILE Chi-restraints excluded: chain Cd residue 30 GLN Chi-restraints excluded: chain Cd residue 61 LEU Chi-restraints excluded: chain Cd residue 81 ASP Chi-restraints excluded: chain Cd residue 82 SER Chi-restraints excluded: chain Cd residue 311 LEU Chi-restraints excluded: chain Cd residue 387 ARG Chi-restraints excluded: chain Cd residue 393 ILE Chi-restraints excluded: chain Ce residue 34 VAL Chi-restraints excluded: chain Ce residue 103 LYS Chi-restraints excluded: chain Ce residue 161 LYS Chi-restraints excluded: chain Cf residue 526 LYS Chi-restraints excluded: chain Cf residue 539 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1346 random chunks: chunk 793 optimal weight: 40.0000 chunk 1278 optimal weight: 2.9990 chunk 780 optimal weight: 40.0000 chunk 606 optimal weight: 7.9990 chunk 888 optimal weight: 5.9990 chunk 1340 optimal weight: 7.9990 chunk 1234 optimal weight: 0.7980 chunk 1067 optimal weight: 0.5980 chunk 110 optimal weight: 10.0000 chunk 824 optimal weight: 8.9990 chunk 654 optimal weight: 1.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** CA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 286 GLN ** CG 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CG 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CI 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CJ 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CJ 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CK 105 GLN CO 20 ASN CP 397 HIS ** CQ 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CR 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CR 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CR 196 GLN Cb 155 HIS Cb 175 GLN ** Cb 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 59 HIS LF 77 GLN LH 165 GLN ** LL 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LM 106 GLN ** LS 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LS 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LS 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LT 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lh 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Li 72 ASN ** Lq 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cc 212 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.284 145558 Z= 0.271 Angle : 0.581 59.192 208309 Z= 0.298 Chirality : 0.039 0.516 25322 Planarity : 0.005 0.089 17768 Dihedral : 21.430 179.715 49822 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.77 % Favored : 96.15 % Rotamer: Outliers : 2.69 % Allowed : 25.81 % Favored : 71.49 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.08), residues: 11105 helix: 2.04 (0.07), residues: 5011 sheet: 0.10 (0.14), residues: 1371 loop : -0.60 (0.09), residues: 4723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRPCb 816 HIS 0.011 0.001 HISLC 59 PHE 0.065 0.001 PHECJ 151 TYR 0.073 0.002 TYRLT 65 ARG 0.036 0.001 ARGCd 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22210 Ramachandran restraints generated. 11105 Oldfield, 0 Emsley, 11105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22210 Ramachandran restraints generated. 11105 Oldfield, 0 Emsley, 11105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1536 residues out of total 9661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 1306 time to evaluate : 8.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: CA 69 ASP cc_start: 0.8483 (t0) cc_final: 0.8256 (t0) REVERT: CA 71 LYS cc_start: 0.6932 (mmtm) cc_final: 0.6182 (ptpp) REVERT: CA 79 GLU cc_start: 0.8060 (tp30) cc_final: 0.7725 (tt0) REVERT: CA 123 MET cc_start: 0.9119 (OUTLIER) cc_final: 0.7316 (mpp) REVERT: CA 294 ARG cc_start: 0.7592 (tpp80) cc_final: 0.6634 (ttp-170) REVERT: CA 310 ASP cc_start: 0.8151 (t0) cc_final: 0.7875 (t0) REVERT: CB 145 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8455 (ttmm) REVERT: CC 373 MET cc_start: 0.1409 (ppp) cc_final: 0.0938 (ppp) REVERT: CE 124 LYS cc_start: 0.8475 (ttmt) cc_final: 0.8153 (tttm) REVERT: CE 302 LYS cc_start: 0.8858 (mmmm) cc_final: 0.8558 (mtmt) REVERT: CE 513 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8054 (mm-30) REVERT: CG 116 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.7793 (ttpt) REVERT: CH 174 PHE cc_start: 0.8976 (OUTLIER) cc_final: 0.8110 (t80) REVERT: CH 348 LYS cc_start: 0.8556 (mmmt) cc_final: 0.8331 (ttmm) REVERT: CI 198 PHE cc_start: 0.9019 (OUTLIER) cc_final: 0.8103 (t80) REVERT: CI 199 TYR cc_start: 0.8353 (m-10) cc_final: 0.8073 (m-10) REVERT: CI 202 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8120 (pm20) REVERT: CI 222 LYS cc_start: 0.8481 (ttmm) cc_final: 0.8268 (mttp) REVERT: CJ 17 MET cc_start: 0.5710 (mpp) cc_final: 0.3435 (tpp) REVERT: CJ 32 ASP cc_start: 0.7267 (t70) cc_final: 0.6614 (t0) REVERT: CJ 224 PHE cc_start: 0.5613 (m-10) cc_final: 0.5284 (m-80) REVERT: CK 132 MET cc_start: 0.7390 (mmm) cc_final: 0.7051 (mmt) REVERT: CK 180 LYS cc_start: 0.9152 (mtmm) cc_final: 0.8691 (mttp) REVERT: CL 16 LYS cc_start: 0.7152 (mmmm) cc_final: 0.6332 (mttm) REVERT: CM 246 ARG cc_start: 0.7439 (tpt170) cc_final: 0.7191 (tpt90) REVERT: CN 26 VAL cc_start: 0.8876 (t) cc_final: 0.8591 (m) REVERT: CN 140 GLN cc_start: 0.8667 (mm-40) cc_final: 0.8308 (tm-30) REVERT: CN 203 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8344 (pt) REVERT: CQ 41 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.7927 (mtmt) REVERT: CR 73 LEU cc_start: 0.7215 (tp) cc_final: 0.6877 (tp) REVERT: CS 681 TYR cc_start: 0.0664 (OUTLIER) cc_final: -0.0128 (t80) REVERT: CU 241 LEU cc_start: 0.9105 (tp) cc_final: 0.8861 (tp) REVERT: CU 358 PHE cc_start: 0.7905 (OUTLIER) cc_final: 0.7012 (m-80) REVERT: Cb 245 ARG cc_start: 0.8652 (ttm110) cc_final: 0.7971 (ttm110) REVERT: Cb 322 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8432 (mm) REVERT: Cb 814 GLU cc_start: 0.8578 (mp0) cc_final: 0.8238 (mp0) REVERT: LB 66 LYS cc_start: 0.8778 (tttp) cc_final: 0.8248 (tttm) REVERT: LB 137 TYR cc_start: 0.8081 (OUTLIER) cc_final: 0.6649 (m-80) REVERT: LB 227 PHE cc_start: 0.8380 (OUTLIER) cc_final: 0.7390 (m-10) REVERT: LB 271 MET cc_start: 0.7961 (mtp) cc_final: 0.7692 (mmp) REVERT: LB 340 ARG cc_start: 0.9224 (OUTLIER) cc_final: 0.6835 (ttm170) REVERT: LB 350 LYS cc_start: 0.8409 (mptt) cc_final: 0.7844 (mttm) REVERT: LB 354 LYS cc_start: 0.8933 (ptmm) cc_final: 0.8483 (mmtt) REVERT: LC 187 LYS cc_start: 0.8319 (mtpt) cc_final: 0.7913 (mmmt) REVERT: LC 220 LYS cc_start: 0.8575 (mttt) cc_final: 0.7894 (mtmm) REVERT: LC 224 LYS cc_start: 0.8559 (mmtt) cc_final: 0.7749 (mtmt) REVERT: LC 264 GLN cc_start: 0.8301 (mm-40) cc_final: 0.7957 (mm-40) REVERT: LE 35 GLN cc_start: 0.8090 (pm20) cc_final: 0.7348 (pt0) REVERT: LE 64 ARG cc_start: 0.7636 (ptm160) cc_final: 0.6779 (ptm160) REVERT: LF 88 LYS cc_start: 0.8606 (mtmt) cc_final: 0.8276 (mttp) REVERT: LF 212 LYS cc_start: 0.8332 (mttt) cc_final: 0.8081 (mtmt) REVERT: LG 52 MET cc_start: 0.3365 (ptm) cc_final: 0.1786 (tmm) REVERT: LG 82 GLN cc_start: 0.8571 (mm-40) cc_final: 0.8202 (mm110) REVERT: LG 87 LYS cc_start: 0.8535 (tttt) cc_final: 0.8208 (tttm) REVERT: LG 97 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.9007 (mt) REVERT: LK 94 LYS cc_start: 0.7450 (pttm) cc_final: 0.7155 (ptpt) REVERT: LL 23 ARG cc_start: 0.7876 (ttm110) cc_final: 0.6802 (tpt170) REVERT: LM 130 GLU cc_start: 0.8709 (mp0) cc_final: 0.8427 (mp0) REVERT: LN 176 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8327 (ptpt) REVERT: LO 197 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8326 (mm-30) REVERT: LO 202 TYR cc_start: 0.8559 (m-80) cc_final: 0.8143 (m-80) REVERT: LP 69 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7944 (ptm160) REVERT: LP 115 LYS cc_start: 0.8724 (tttm) cc_final: 0.8368 (ttmt) REVERT: LQ 69 GLU cc_start: 0.8010 (mp0) cc_final: 0.7742 (mp0) REVERT: LS 16 THR cc_start: 0.8928 (m) cc_final: 0.8716 (p) REVERT: LS 109 ASP cc_start: 0.9063 (t0) cc_final: 0.8858 (t70) REVERT: LT 52 MET cc_start: 0.3698 (ptm) cc_final: 0.3176 (mmt) REVERT: LV 139 MET cc_start: 0.7757 (mtm) cc_final: 0.7342 (mtm) REVERT: LY 50 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.8699 (ttt-90) REVERT: LY 54 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7964 (mm-30) REVERT: LY 76 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8807 (mtmt) REVERT: LY 122 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8708 (tttt) REVERT: LY 127 GLN cc_start: 0.8621 (tm-30) cc_final: 0.8221 (tt0) REVERT: Le 25 ARG cc_start: 0.7382 (mmm160) cc_final: 0.7121 (mmm160) REVERT: Le 35 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.7556 (ttpt) REVERT: Le 55 SER cc_start: 0.8989 (m) cc_final: 0.8679 (t) REVERT: Le 84 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7733 (mp0) REVERT: Le 96 GLU cc_start: 0.8363 (tt0) cc_final: 0.7797 (tt0) REVERT: Le 124 LYS cc_start: 0.8368 (ptpt) cc_final: 0.8059 (pttt) REVERT: Lh 33 GLN cc_start: 0.7740 (pp30) cc_final: 0.7370 (pp30) REVERT: Lh 78 LYS cc_start: 0.8499 (mmtt) cc_final: 0.8175 (mmmm) REVERT: Lq 165 MET cc_start: -0.0270 (ttt) cc_final: -0.2364 (mtt) REVERT: Cd 10 SER cc_start: 0.8413 (m) cc_final: 0.7997 (t) REVERT: Cd 61 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8772 (mt) REVERT: Cd 94 ARG cc_start: 0.7817 (tmm-80) cc_final: 0.7558 (tmm-80) REVERT: Cd 387 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.7449 (mmt90) REVERT: Ce 13 GLN cc_start: 0.7703 (mm-40) cc_final: 0.7444 (tm-30) REVERT: Ce 147 LYS cc_start: 0.8054 (tttt) cc_final: 0.7458 (tttp) REVERT: Ce 161 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8602 (ptpp) REVERT: Cf 528 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7186 (mm-30) REVERT: Cf 533 LYS cc_start: 0.8389 (mttt) cc_final: 0.7993 (mttp) outliers start: 230 outliers final: 188 residues processed: 1471 average time/residue: 1.2813 time to fit residues: 3236.4875 Evaluate side-chains 1514 residues out of total 9661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 1301 time to evaluate : 8.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CA residue 72 SER Chi-restraints excluded: chain CA residue 123 MET Chi-restraints excluded: chain CA residue 149 GLU Chi-restraints excluded: chain CA residue 176 ILE Chi-restraints excluded: chain CA residue 201 LYS Chi-restraints excluded: chain CA residue 241 THR Chi-restraints excluded: chain CA residue 257 GLU Chi-restraints excluded: chain CB residue 27 CYS Chi-restraints excluded: chain CB residue 30 LEU Chi-restraints excluded: chain CB residue 48 ASN Chi-restraints excluded: chain CB residue 63 TRP Chi-restraints excluded: chain CB residue 91 THR Chi-restraints excluded: chain CB residue 145 LYS Chi-restraints excluded: chain CB residue 165 LYS Chi-restraints excluded: chain CB residue 174 THR Chi-restraints excluded: chain CB residue 278 VAL Chi-restraints excluded: chain CC residue 167 VAL Chi-restraints excluded: chain CC residue 175 ILE Chi-restraints excluded: chain CC residue 257 ASP Chi-restraints excluded: chain CC residue 258 THR Chi-restraints excluded: chain CC residue 266 GLU Chi-restraints excluded: chain CC residue 326 LEU Chi-restraints excluded: chain CC residue 408 MET Chi-restraints excluded: chain CC residue 410 LEU Chi-restraints excluded: chain CE residue 121 LYS Chi-restraints excluded: chain CE residue 175 SER Chi-restraints excluded: chain CE residue 190 THR Chi-restraints excluded: chain CE residue 300 THR Chi-restraints excluded: chain CE residue 413 CYS Chi-restraints excluded: chain CE residue 414 THR Chi-restraints excluded: chain CE residue 533 VAL Chi-restraints excluded: chain CF residue 51 ASN Chi-restraints excluded: chain CF residue 70 THR Chi-restraints excluded: chain CF residue 142 VAL Chi-restraints excluded: chain CF residue 175 ILE Chi-restraints excluded: chain CF residue 202 ASP Chi-restraints excluded: chain CF residue 221 VAL Chi-restraints excluded: chain CG residue 6 ASP Chi-restraints excluded: chain CG residue 13 LEU Chi-restraints excluded: chain CG residue 30 LEU Chi-restraints excluded: chain CG residue 40 MET Chi-restraints excluded: chain CG residue 59 VAL Chi-restraints excluded: chain CG residue 65 LEU Chi-restraints excluded: chain CG residue 67 LEU Chi-restraints excluded: chain CG residue 109 LEU Chi-restraints excluded: chain CG residue 116 LYS Chi-restraints excluded: chain CG residue 137 MET Chi-restraints excluded: chain CH residue 32 ILE Chi-restraints excluded: chain CH residue 69 VAL Chi-restraints excluded: chain CH residue 85 TYR Chi-restraints excluded: chain CH residue 174 PHE Chi-restraints excluded: chain CH residue 233 THR Chi-restraints excluded: chain CH residue 316 ILE Chi-restraints excluded: chain CH residue 330 VAL Chi-restraints excluded: chain CH residue 390 LEU Chi-restraints excluded: chain CH residue 399 ASN Chi-restraints excluded: chain CH residue 468 LEU Chi-restraints excluded: chain CI residue 198 PHE Chi-restraints excluded: chain CI residue 202 GLU Chi-restraints excluded: chain CI residue 214 THR Chi-restraints excluded: chain CI residue 216 LEU Chi-restraints excluded: chain CI residue 218 VAL Chi-restraints excluded: chain CI residue 303 GLN Chi-restraints excluded: chain CJ residue 93 ARG Chi-restraints excluded: chain CJ residue 192 ILE Chi-restraints excluded: chain CJ residue 218 ILE Chi-restraints excluded: chain CK residue 119 VAL Chi-restraints excluded: chain CK residue 212 LEU Chi-restraints excluded: chain CL residue 12 THR Chi-restraints excluded: chain CL residue 18 THR Chi-restraints excluded: chain CM residue 60 GLU Chi-restraints excluded: chain CM residue 92 VAL Chi-restraints excluded: chain CM residue 112 LEU Chi-restraints excluded: chain CM residue 125 VAL Chi-restraints excluded: chain CM residue 147 LEU Chi-restraints excluded: chain CM residue 197 VAL Chi-restraints excluded: chain CN residue 1 MET Chi-restraints excluded: chain CN residue 98 GLU Chi-restraints excluded: chain CN residue 203 LEU Chi-restraints excluded: chain CN residue 242 VAL Chi-restraints excluded: chain CO residue 40 ILE Chi-restraints excluded: chain CP residue 270 ILE Chi-restraints excluded: chain CP residue 324 LEU Chi-restraints excluded: chain CP residue 334 VAL Chi-restraints excluded: chain CP residue 358 LEU Chi-restraints excluded: chain CP residue 407 VAL Chi-restraints excluded: chain CP residue 490 LEU Chi-restraints excluded: chain CP residue 517 VAL Chi-restraints excluded: chain CP residue 571 TYR Chi-restraints excluded: chain CP residue 574 ASP Chi-restraints excluded: chain CQ residue 41 LYS Chi-restraints excluded: chain CR residue 32 ASN Chi-restraints excluded: chain CR residue 131 VAL Chi-restraints excluded: chain CR residue 145 HIS Chi-restraints excluded: chain CS residue 681 TYR Chi-restraints excluded: chain CU residue 203 ILE Chi-restraints excluded: chain CU residue 220 VAL Chi-restraints excluded: chain CU residue 228 ASP Chi-restraints excluded: chain CU residue 233 ILE Chi-restraints excluded: chain CU residue 270 ASP Chi-restraints excluded: chain CU residue 322 GLU Chi-restraints excluded: chain CU residue 358 PHE Chi-restraints excluded: chain CX residue 74 LEU Chi-restraints excluded: chain CX residue 95 VAL Chi-restraints excluded: chain CX residue 101 MET Chi-restraints excluded: chain CX residue 107 MET Chi-restraints excluded: chain CX residue 141 GLU Chi-restraints excluded: chain Cb residue 140 LYS Chi-restraints excluded: chain Cb residue 217 THR Chi-restraints excluded: chain Cb residue 295 LEU Chi-restraints excluded: chain Cb residue 304 ASP Chi-restraints excluded: chain Cb residue 322 LEU Chi-restraints excluded: chain Cb residue 393 VAL Chi-restraints excluded: chain Cb residue 524 VAL Chi-restraints excluded: chain Cb residue 589 ASN Chi-restraints excluded: chain Cb residue 842 LEU Chi-restraints excluded: chain Cb residue 878 GLU Chi-restraints excluded: chain LB residue 41 VAL Chi-restraints excluded: chain LB residue 137 TYR Chi-restraints excluded: chain LB residue 158 VAL Chi-restraints excluded: chain LB residue 199 LEU Chi-restraints excluded: chain LB residue 211 GLU Chi-restraints excluded: chain LB residue 227 PHE Chi-restraints excluded: chain LB residue 307 THR Chi-restraints excluded: chain LB residue 329 VAL Chi-restraints excluded: chain LB residue 340 ARG Chi-restraints excluded: chain LC residue 62 SER Chi-restraints excluded: chain LC residue 79 SER Chi-restraints excluded: chain LC residue 112 VAL Chi-restraints excluded: chain LC residue 146 VAL Chi-restraints excluded: chain LC residue 222 LEU Chi-restraints excluded: chain LC residue 238 ASP Chi-restraints excluded: chain LC residue 341 LEU Chi-restraints excluded: chain LE residue 102 VAL Chi-restraints excluded: chain LE residue 106 SER Chi-restraints excluded: chain LE residue 107 VAL Chi-restraints excluded: chain LE residue 111 LEU Chi-restraints excluded: chain LF residue 18 LEU Chi-restraints excluded: chain LF residue 117 ILE Chi-restraints excluded: chain LG residue 97 LEU Chi-restraints excluded: chain LG residue 193 VAL Chi-restraints excluded: chain LG residue 210 ASP Chi-restraints excluded: chain LH residue 25 VAL Chi-restraints excluded: chain LH residue 26 THR Chi-restraints excluded: chain LH residue 41 ILE Chi-restraints excluded: chain LH residue 55 LEU Chi-restraints excluded: chain LH residue 56 GLU Chi-restraints excluded: chain LH residue 82 VAL Chi-restraints excluded: chain LH residue 157 SER Chi-restraints excluded: chain LK residue 105 SER Chi-restraints excluded: chain LL residue 22 VAL Chi-restraints excluded: chain LL residue 46 LEU Chi-restraints excluded: chain LL residue 58 VAL Chi-restraints excluded: chain LL residue 69 THR Chi-restraints excluded: chain LM residue 5 ASN Chi-restraints excluded: chain LM residue 19 VAL Chi-restraints excluded: chain LM residue 20 LEU Chi-restraints excluded: chain LM residue 39 VAL Chi-restraints excluded: chain LM residue 57 VAL Chi-restraints excluded: chain LM residue 68 VAL Chi-restraints excluded: chain LM residue 90 VAL Chi-restraints excluded: chain LN residue 17 ASP Chi-restraints excluded: chain LN residue 125 SER Chi-restraints excluded: chain LN residue 140 LYS Chi-restraints excluded: chain LN residue 167 THR Chi-restraints excluded: chain LN residue 171 SER Chi-restraints excluded: chain LN residue 176 LYS Chi-restraints excluded: chain LO residue 37 VAL Chi-restraints excluded: chain LO residue 110 VAL Chi-restraints excluded: chain LP residue 24 VAL Chi-restraints excluded: chain LP residue 58 VAL Chi-restraints excluded: chain LP residue 69 ARG Chi-restraints excluded: chain LS residue 35 VAL Chi-restraints excluded: chain LS residue 149 SER Chi-restraints excluded: chain LT residue 72 VAL Chi-restraints excluded: chain LT residue 85 ILE Chi-restraints excluded: chain LV residue 19 LEU Chi-restraints excluded: chain LV residue 21 VAL Chi-restraints excluded: chain LV residue 24 ILE Chi-restraints excluded: chain LV residue 88 LYS Chi-restraints excluded: chain LV residue 120 VAL Chi-restraints excluded: chain LY residue 7 VAL Chi-restraints excluded: chain LY residue 8 SER Chi-restraints excluded: chain LY residue 50 ARG Chi-restraints excluded: chain LY residue 76 LYS Chi-restraints excluded: chain LY residue 81 VAL Chi-restraints excluded: chain LY residue 122 LYS Chi-restraints excluded: chain Ld residue 54 THR Chi-restraints excluded: chain Ld residue 75 VAL Chi-restraints excluded: chain Ld residue 116 VAL Chi-restraints excluded: chain Le residue 35 LYS Chi-restraints excluded: chain Le residue 84 GLU Chi-restraints excluded: chain Le residue 130 GLU Chi-restraints excluded: chain Lf residue 17 SER Chi-restraints excluded: chain Lf residue 108 SER Chi-restraints excluded: chain Lh residue 19 GLU Chi-restraints excluded: chain Lh residue 34 LEU Chi-restraints excluded: chain Lh residue 55 SER Chi-restraints excluded: chain Li residue 27 THR Chi-restraints excluded: chain Lq residue 99 LEU Chi-restraints excluded: chain Lq residue 206 ILE Chi-restraints excluded: chain Cd residue 30 GLN Chi-restraints excluded: chain Cd residue 36 SER Chi-restraints excluded: chain Cd residue 61 LEU Chi-restraints excluded: chain Cd residue 81 ASP Chi-restraints excluded: chain Cd residue 82 SER Chi-restraints excluded: chain Cd residue 311 LEU Chi-restraints excluded: chain Cd residue 387 ARG Chi-restraints excluded: chain Cd residue 393 ILE Chi-restraints excluded: chain Ce residue 34 VAL Chi-restraints excluded: chain Ce residue 161 LYS Chi-restraints excluded: chain Cf residue 526 LYS Chi-restraints excluded: chain Cf residue 539 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1346 random chunks: chunk 848 optimal weight: 0.0970 chunk 1137 optimal weight: 5.9990 chunk 327 optimal weight: 0.0980 chunk 984 optimal weight: 4.9990 chunk 157 optimal weight: 50.0000 chunk 296 optimal weight: 6.9990 chunk 1069 optimal weight: 0.8980 chunk 447 optimal weight: 1.9990 chunk 1098 optimal weight: 3.9990 chunk 135 optimal weight: 20.0000 chunk 196 optimal weight: 8.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** CA 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CA 286 GLN ** CG 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CG 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CI 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CJ 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CJ 485 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CP 397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CQ 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CR 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CR 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 59 HIS LF 77 GLN LH 165 GLN ** LL 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LM 106 GLN ** LS 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LS 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LS 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LT 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lh 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lq 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.177673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.142977 restraints weight = 172693.238| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.01 r_work: 0.3105 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.284 145558 Z= 0.270 Angle : 0.581 59.000 208309 Z= 0.298 Chirality : 0.039 0.515 25322 Planarity : 0.005 0.089 17768 Dihedral : 21.430 179.715 49822 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.77 % Favored : 96.15 % Rotamer: Outliers : 2.53 % Allowed : 25.97 % Favored : 71.50 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.08), residues: 11105 helix: 2.04 (0.07), residues: 5011 sheet: 0.10 (0.14), residues: 1371 loop : -0.60 (0.09), residues: 4723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRPCb 816 HIS 0.011 0.001 HISLC 59 PHE 0.065 0.001 PHECJ 151 TYR 0.073 0.002 TYRLT 65 ARG 0.036 0.001 ARGCd 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 51228.09 seconds wall clock time: 885 minutes 13.99 seconds (53113.99 seconds total)