Starting phenix.real_space_refine on Sun Mar 3 10:43:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9y_35288/03_2024/8i9y_35288_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9y_35288/03_2024/8i9y_35288.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/8i9y_35288/03_2024/8i9y_35288.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9y_35288/03_2024/8i9y_35288.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9y_35288/03_2024/8i9y_35288_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9y_35288/03_2024/8i9y_35288_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= 0.011 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 2 6.06 5 P 2870 5.49 5 S 299 5.16 5 C 87617 2.51 5 N 28816 2.21 5 O 36949 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 GLU 124": "OE1" <-> "OE2" Residue "CA GLU 157": "OE1" <-> "OE2" Residue "CA GLU 233": "OE1" <-> "OE2" Residue "CA PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CA TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CB TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CB PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CC PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CC TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CC ASP 162": "OD1" <-> "OD2" Residue "CC ASP 181": "OD1" <-> "OD2" Residue "CC GLU 276": "OE1" <-> "OE2" Residue "CC TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CC ASP 436": "OD1" <-> "OD2" Residue "CC PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CC ASP 473": "OD1" <-> "OD2" Residue "CC PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CC PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CC PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CC PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CC TYR 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CC PHE 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CD ASP 64": "OD1" <-> "OD2" Residue "CD PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CD PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CD ASP 309": "OD1" <-> "OD2" Residue "CD GLU 399": "OE1" <-> "OE2" Residue "CD GLU 401": "OE1" <-> "OE2" Residue "CD ASP 469": "OD1" <-> "OD2" Residue "CE PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE GLU 277": "OE1" <-> "OE2" Residue "CE TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE PHE 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE TYR 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE ASP 484": "OD1" <-> "OD2" Residue "CE PHE 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE TYR 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE PHE 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CE TYR 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CF PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CF PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CF GLU 238": "OE1" <-> "OE2" Residue "CG TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CG TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CG TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CG PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH ASP 86": "OD1" <-> "OD2" Residue "CH TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH ASP 219": "OD1" <-> "OD2" Residue "CH GLU 230": "OE1" <-> "OE2" Residue "CH TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH GLU 304": "OE1" <-> "OE2" Residue "CH TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH ASP 397": "OD1" <-> "OD2" Residue "CH ASP 420": "OD1" <-> "OD2" Residue "CH ASP 435": "OD1" <-> "OD2" Residue "CH PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH TYR 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CH ASP 535": "OD1" <-> "OD2" Residue "CI PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CI TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CI TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CI PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CI PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CI PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CI GLU 299": "OE1" <-> "OE2" Residue "CI TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CI PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CJ TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CJ PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CJ TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CJ ASP 142": "OD1" <-> "OD2" Residue "CJ TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CJ TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CJ TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CJ PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CJ PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CJ ASP 398": "OD1" <-> "OD2" Residue "CJ ASP 412": "OD1" <-> "OD2" Residue "CJ ASP 421": "OD1" <-> "OD2" Residue "CJ TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CJ TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CJ GLU 468": "OE1" <-> "OE2" Residue "CJ GLU 474": "OE1" <-> "OE2" Residue "CJ PHE 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CJ TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CJ GLU 518": "OE1" <-> "OE2" Residue "CM TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CM TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CM PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CM PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CN TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CN TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CN GLU 80": "OE1" <-> "OE2" Residue "CN PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CO PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CP GLU 255": "OE1" <-> "OE2" Residue "CP TYR 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CP PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CP TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CP PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CP GLU 442": "OE1" <-> "OE2" Residue "CP PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CP ASP 456": "OD1" <-> "OD2" Residue "CP ASP 468": "OD1" <-> "OD2" Residue "CP ASP 476": "OD1" <-> "OD2" Residue "CP PHE 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CP TYR 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CP PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CP TYR 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CP PHE 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CP TYR 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CQ PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CQ PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CQ TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CQ TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CQ GLU 119": "OE1" <-> "OE2" Residue "CR TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CS ASP 466": "OD1" <-> "OD2" Residue "CS GLU 469": "OE1" <-> "OE2" Residue "CS PHE 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CT TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CT PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CT ASP 278": "OD1" <-> "OD2" Residue "CT PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CT TYR 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CT TYR 517": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CT PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CT TYR 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CU PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CU PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CU GLU 240": "OE1" <-> "OE2" Residue "CU PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CU GLU 274": "OE1" <-> "OE2" Residue "CU GLU 353": "OE1" <-> "OE2" Residue "CV TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CV GLU 128": "OE1" <-> "OE2" Residue "CY PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CY PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CY TYR 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CY ASP 500": "OD1" <-> "OD2" Residue "CY ASP 566": "OD1" <-> "OD2" Residue "CY TYR 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CY PHE 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CY TYR 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CY PHE 639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CY PHE 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB ASP 59": "OD1" <-> "OD2" Residue "LB ASP 80": "OD1" <-> "OD2" Residue "LB PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB ASP 213": "OD1" <-> "OD2" Residue "LB GLU 214": "OE1" <-> "OE2" Residue "LB ASP 321": "OD1" <-> "OD2" Residue "LB TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB GLU 353": "OE1" <-> "OE2" Residue "LB PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LC PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LC PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LC PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LC GLU 343": "OE1" <-> "OE2" Residue "LE TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LE TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LF PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LF TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LG ASP 161": "OD1" <-> "OD2" Residue "LG GLU 213": "OE1" <-> "OE2" Residue "LH TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LH TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LH PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LK ASP 153": "OD1" <-> "OD2" Residue "LL PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LM ASP 91": "OD1" <-> "OD2" Residue "LN TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LO PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LO TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LO TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LO TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LO PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LO PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LO GLU 108": "OE1" <-> "OE2" Residue "LO TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LO TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LP PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LP TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LR TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LS TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LU PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LU ASP 50": "OD1" <-> "OD2" Residue "LU ASP 58": "OD1" <-> "OD2" Residue "LU PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LV TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LX PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LX TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LY TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LZ TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LZ PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lc GLU 58": "OE1" <-> "OE2" Residue "Lc GLU 60": "OE1" <-> "OE2" Residue "Lc TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ld TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ld PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ld TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Le ASP 24": "OD1" <-> "OD2" Residue "Le PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Le TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lg GLU 62": "OE1" <-> "OE2" Residue "Lg TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lg PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Li PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Li GLU 105": "OE1" <-> "OE2" Residue "Lk TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lq ASP 18": "OD1" <-> "OD2" Time to flip residues: 0.23s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 156553 Number of models: 1 Model: "" Number of chains: 62 Chain: "C1" Number of atoms: 55815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2609, 55815 Classifications: {'RNA': 2609} Modifications used: {'rna2p_pur': 265, 'rna2p_pyr': 181, 'rna3p_pur': 1165, 'rna3p_pyr': 998} Link IDs: {'rna2p': 445, 'rna3p': 2163} Chain breaks: 14 Chain: "C2" Number of atoms: 5456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 5456 Classifications: {'RNA': 256} Modifications used: {'rna2p_pur': 30, 'rna2p_pyr': 25, 'rna3p_pur': 101, 'rna3p_pyr': 100} Link IDs: {'rna2p': 55, 'rna3p': 200} Chain breaks: 1 Chain: "CA" Number of atoms: 2069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2069 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 11, 'TRANS': 239} Chain breaks: 1 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: 5297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5297 Classifications: {'peptide': 658} Link IDs: {'PTRANS': 65, 'TRANS': 592} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "CD" Number of atoms: 3468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3468 Classifications: {'peptide': 460} Link IDs: {'PTRANS': 25, 'TRANS': 434} Chain breaks: 4 Chain: "CE" Number of atoms: 3669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3669 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 21, 'TRANS': 440} 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: 4388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4388 Classifications: {'peptide': 542} Link IDs: {'PTRANS': 25, 'TRANS': 516} Chain breaks: 1 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: 4040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 4040 Classifications: {'peptide': 494} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 464} Chain breaks: 4 Chain: "CK" Number of atoms: 1835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1835 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 9, 'TRANS': 219} Chain breaks: 2 Chain: "CL" Number of atoms: 2239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 2239 Classifications: {'peptide': 397} Incomplete info: {'truncation_to_alanine': 255} Link IDs: {'CIS': 1, 'PTRANS': 33, 'TRANS': 362} Chain breaks: 1 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: 1820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1820 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 11, 'TRANS': 211} 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: 2798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2798 Classifications: {'peptide': 356} Link IDs: {'PTRANS': 19, 'TRANS': 336} Chain: "CQ" Number of atoms: 1485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1485 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 5, 'TRANS': 173} Chain breaks: 2 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: 2105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2105 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 253} Chain breaks: 7 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "CT" Number of atoms: 3911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3911 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 18, 'TRANS': 469} Chain breaks: 4 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: "CV" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1073 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 6, 'TRANS': 132} Chain: "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: 3399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3399 Classifications: {'peptide': 420} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 405} Chain breaks: 6 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 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: "LB" Number of atoms: 2829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2829 Classifications: {'peptide': 356} Link IDs: {'PTRANS': 12, 'TRANS': 343} 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: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1403 Classifications: {'peptide': 179} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 165} Chain breaks: 1 Chain: "LF" Number of atoms: 2017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 2017 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 13, 'TRANS': 233} Chain: "LG" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1644 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 8, 'TRANS': 195} 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: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1345 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 6, 'TRANS': 162} 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: "LR" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 969 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain breaks: 1 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: "LU" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 850 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 1, 'TRANS': 103} 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: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1062 Classifications: {'peptide': 137} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 128} Chain breaks: 1 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: "LZ" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1112 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 127} Chain: "Lc" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 731 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} 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: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1025 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "Lf" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 862 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "Lg" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 930 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} 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: "Lk" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 620 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 4, 'TRANS': 70} Chain: "Ll" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 322 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 2, 'TRANS': 35} Chain: "Lq" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1600 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 8, 'TRANS': 198} 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A01FW SG CYSCQ 6 142.342 63.273 202.837 1.00 72.85 S ATOM A01GO SG CYSCQ 9 145.710 61.772 201.925 1.00 71.70 S ATOM A01LT SG CYSCQ 32 145.622 64.937 203.785 1.00 75.36 S ATOM A01MP SG CYSCQ 36 144.429 64.703 199.999 1.00 71.47 S ATOM A1582 SG CYSLj 19 172.437 134.646 136.613 1.00 48.35 S ATOM A158U SG CYSLj 22 173.605 136.044 139.890 1.00 46.38 S ATOM A15BK SG CYSLj 34 169.850 135.850 139.193 1.00 48.03 S ATOM A15C1 SG CYSLj 37 171.939 138.277 137.181 1.00 44.98 S Time building chain proxies: 61.52, per 1000 atoms: 0.39 Number of scatterers: 156553 At special positions: 0 Unit cell: (256.025, 275.88, 313.5, 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 2 29.99 S 299 16.00 P 2870 15.00 O 36949 8.00 N 28816 7.00 C 87617 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: 55.99 Conformation dependent library (CDL) restraints added in 13.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNCQ1000 " pdb="ZN ZNCQ1000 " - pdb=" SG CYSCQ 9 " pdb="ZN ZNCQ1000 " - pdb=" SG CYSCQ 6 " pdb="ZN ZNCQ1000 " - pdb=" SG CYSCQ 36 " pdb="ZN ZNCQ1000 " - pdb=" SG CYSCQ 32 " pdb=" ZNLj1001 " pdb="ZN ZNLj1001 " - pdb=" SG CYSLj 34 " pdb="ZN ZNLj1001 " - pdb=" SG CYSLj 37 " pdb="ZN ZNLj1001 " - pdb=" SG CYSLj 22 " pdb="ZN ZNLj1001 " - pdb=" SG CYSLj 19 " Number of angles added : 12 23650 Ramachandran restraints generated. 11825 Oldfield, 0 Emsley, 11825 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 22658 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: 435 helices and 110 sheets defined 48.4% alpha, 13.6% beta 960 base pairs and 1449 stacking pairs defined. Time for finding SS restraints: 91.99 Creating SS restraints... Processing helix chain 'CA' and resid 45 through 60 Proline residue: CA 60 - end of helix Processing helix chain 'CA' and resid 73 through 85 removed outlier: 3.863A pdb=" N CYSCA 78 " --> pdb=" O LEUCA 74 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYRCA 84 " --> pdb=" O LEUCA 80 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASNCA 85 " --> pdb=" O ALACA 81 " (cutoff:3.500A) Processing helix chain 'CA' and resid 143 through 149 Processing helix chain 'CA' and resid 150 through 164 Processing helix chain 'CA' and resid 263 through 295 Processing helix chain 'CB' and resid 19 through 40 Processing helix chain 'CB' and resid 52 through 60 Processing helix chain 'CB' and resid 104 through 114 Processing helix chain 'CB' and resid 117 through 125 removed outlier: 5.184A pdb=" N GLYCB 125 " --> pdb=" O ARGCB 121 " (cutoff:3.500A) Processing helix chain 'CB' and resid 129 through 137 Processing helix chain 'CB' and resid 139 through 150 Processing helix chain 'CB' and resid 159 through 168 Proline residue: CB 164 - end of helix Processing helix chain 'CB' and resid 169 through 175 removed outlier: 4.338A pdb=" N THRCB 174 " --> pdb=" O THRCB 170 " (cutoff:3.500A) Processing helix chain 'CB' and resid 216 through 230 Processing helix chain 'CB' and resid 251 through 269 Processing helix chain 'CB' and resid 274 through 279 removed outlier: 5.861A pdb=" N VALCB 278 " --> pdb=" O LYSCB 274 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ARGCB 279 " --> pdb=" O TRPCB 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'CB' and resid 274 through 279' Processing helix chain 'CC' and resid 177 through 182 removed outlier: 4.173A pdb=" N ASPCC 181 " --> pdb=" O LEUCC 177 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N SERCC 182 " --> pdb=" O SERCC 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'CC' and resid 177 through 182' 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 282 removed outlier: 4.299A pdb=" N PHECC 281 " --> pdb=" O PROCC 277 " (cutoff:3.500A) Processing helix chain 'CC' and resid 284 through 301 Processing helix chain 'CC' and resid 308 through 316 Processing helix chain 'CC' and resid 363 through 373 Processing helix chain 'CC' and resid 389 through 394 removed outlier: 3.885A 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 'CC' and resid 424 through 430 Proline residue: CC 430 - end of helix Processing helix chain 'CC' and resid 434 through 439 removed outlier: 3.834A pdb=" N LEUCC 438 " --> pdb=" O SERCC 434 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LYSCC 439 " --> pdb=" O PROCC 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'CC' and resid 434 through 439' Processing helix chain 'CC' and resid 532 through 545 Processing helix chain 'CC' and resid 573 through 580 Processing helix chain 'CD' and resid 42 through 52 Processing helix chain 'CD' and resid 75 through 84 Processing helix chain 'CD' and resid 124 through 132 Processing helix chain 'CD' and resid 255 through 260 Proline residue: CD 260 - end of helix Processing helix chain 'CD' and resid 443 through 450 Processing helix chain 'CE' and resid 112 through 117 removed outlier: 5.202A pdb=" N LEUCE 116 " --> pdb=" O GLUCE 112 " (cutoff:3.500A) removed outlier: 5.445A 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 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 Proline residue: CE 168 - end of helix Processing helix chain 'CE' and resid 192 through 208 Processing helix chain 'CE' and resid 222 through 233 Processing helix chain 'CE' and resid 240 through 250 Processing helix chain 'CE' and resid 265 through 273 Processing helix chain 'CE' and resid 274 through 285 Processing helix chain 'CE' and resid 300 through 311 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 421 Processing helix chain 'CE' and resid 437 through 451 removed outlier: 3.682A pdb=" N TYRCE 441 " --> pdb=" O ASPCE 437 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VALCE 445 " --> pdb=" O TYRCE 441 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N GLYCE 446 " --> pdb=" O ILECE 442 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARGCE 447 " --> pdb=" O HISCE 443 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ARGCE 450 " --> pdb=" O GLYCE 446 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLYCE 451 " --> pdb=" O ARGCE 447 " (cutoff:3.500A) Processing helix chain 'CE' and resid 466 through 477 removed outlier: 4.259A pdb=" N LEUCE 470 " --> pdb=" O GLUCE 466 " (cutoff:3.500A) Processing helix chain 'CE' and resid 486 through 491 removed outlier: 6.241A pdb=" N LEUCE 491 " --> pdb=" O LYSCE 487 " (cutoff:3.500A) Processing helix chain 'CE' and resid 493 through 504 Processing helix chain 'CE' and resid 505 through 525 Processing helix chain 'CE' and resid 532 through 537 removed outlier: 4.252A pdb=" N LEUCE 536 " --> pdb=" O ASPCE 532 " (cutoff:3.500A) removed outlier: 5.672A 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 Proline residue: CF 35 - end of helix Processing helix chain 'CF' and resid 52 through 61 Processing helix chain 'CF' and resid 69 through 78 Processing helix chain 'CF' and resid 88 through 97 removed outlier: 4.237A pdb=" N ARGCF 94 " --> pdb=" O HISCF 90 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N TYRCF 95 " --> pdb=" O ARGCF 91 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N THRCF 97 " --> pdb=" O THRCF 93 " (cutoff:3.500A) Processing helix chain 'CF' and resid 108 through 120 removed outlier: 5.937A pdb=" N SERCF 120 " --> pdb=" O PHECF 116 " (cutoff:3.500A) Processing helix chain 'CF' and resid 161 through 169 Processing helix chain 'CF' and resid 202 through 213 Processing helix chain 'CF' and resid 237 through 244 removed outlier: 3.556A pdb=" N LYSCF 241 " --> pdb=" O LEUCF 237 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N THRCF 242 " --> pdb=" O GLUCF 238 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARGCF 243 " --> pdb=" O ALACF 239 " (cutoff:3.500A) Proline residue: CF 244 - end of helix No H-bonds generated for 'chain 'CF' and resid 237 through 244' Processing helix chain 'CG' and resid 5 through 20 Processing helix chain 'CG' and resid 22 through 28 removed outlier: 4.701A pdb=" N LEUCG 26 " --> pdb=" O ASPCG 22 " (cutoff:3.500A) Processing helix chain 'CG' and resid 49 through 58 removed outlier: 5.160A pdb=" N CYSCG 58 " --> pdb=" O ASNCG 54 " (cutoff:3.500A) Processing helix chain 'CG' and resid 60 through 65 removed outlier: 5.748A pdb=" N LEUCG 65 " --> pdb=" O ARGCG 61 " (cutoff:3.500A) Processing helix chain 'CG' and resid 83 through 94 Proline residue: CG 88 - end of helix Processing helix chain 'CG' and resid 101 through 111 Proline residue: CG 107 - end of helix Processing helix chain 'CG' and resid 115 through 120 removed outlier: 5.988A pdb=" N GLYCG 120 " --> pdb=" O LYSCG 116 " (cutoff:3.500A) Processing helix chain 'CG' and resid 150 through 157 Processing helix chain 'CG' and resid 170 through 177 removed outlier: 4.346A pdb=" N LEUCG 174 " --> pdb=" O CYSCG 170 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLUCG 177 " --> pdb=" O TYRCG 173 " (cutoff:3.500A) Processing helix chain 'CH' and resid 12 through 27 Processing helix chain 'CH' and resid 37 through 66 Processing helix chain 'CH' and resid 74 through 85 Processing helix chain 'CH' and resid 86 through 118 Processing helix chain 'CH' and resid 120 through 143 Processing helix chain 'CH' and resid 144 through 159 Processing helix chain 'CH' and resid 178 through 187 Processing helix chain 'CH' and resid 232 through 245 removed outlier: 3.876A pdb=" N LEUCH 245 " --> pdb=" O ALACH 241 " (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 298 through 311 removed outlier: 4.320A pdb=" N SERCH 311 " --> pdb=" O ASPCH 307 " (cutoff:3.500A) Processing helix chain 'CH' and resid 326 through 352 removed outlier: 4.988A pdb=" N HISCH 352 " --> pdb=" O LYSCH 348 " (cutoff:3.500A) Processing helix chain 'CH' and resid 358 through 369 Processing helix chain 'CH' and resid 384 through 390 removed outlier: 4.059A pdb=" N LYSCH 388 " --> pdb=" O PROCH 384 " (cutoff:3.500A) Processing helix chain 'CH' and resid 403 through 412 Processing helix chain 'CH' and resid 445 through 450 Processing helix chain 'CH' and resid 453 through 472 removed outlier: 4.486A pdb=" N LYSCH 457 " --> pdb=" O ASPCH 453 " (cutoff:3.500A) Processing helix chain 'CH' and resid 483 through 511 removed outlier: 4.210A pdb=" N SERCH 511 " --> pdb=" O LYSCH 507 " (cutoff:3.500A) Processing helix chain 'CH' and resid 519 through 524 removed outlier: 4.881A pdb=" N LYSCH 524 " --> pdb=" O ARGCH 520 " (cutoff:3.500A) Processing helix chain 'CH' and resid 526 through 538 Processing helix chain 'CI' and resid 199 through 211 removed outlier: 4.006A pdb=" N GLNCI 209 " --> pdb=" O GLYCI 205 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHECI 210 " --> pdb=" O TYRCI 206 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLYCI 211 " --> pdb=" O PHECI 207 " (cutoff:3.500A) Processing helix chain 'CI' and resid 237 through 249 Processing helix chain 'CI' and resid 264 through 269 removed outlier: 6.401A pdb=" N HISCI 269 " --> pdb=" O PROCI 265 " (cutoff:3.500A) Processing helix chain 'CI' and resid 284 through 295 Processing helix chain 'CI' and resid 299 through 322 removed outlier: 4.266A pdb=" N GLUCI 322 " --> pdb=" O GLUCI 318 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 11 through 16 Processing helix chain 'CJ' and resid 18 through 27 Processing helix chain 'CJ' and resid 29 through 41 Processing helix chain 'CJ' and resid 49 through 54 Processing helix chain 'CJ' and resid 65 through 75 Processing helix chain 'CJ' and resid 76 through 98 Processing helix chain 'CJ' and resid 99 through 111 Processing helix chain 'CJ' and resid 112 through 117 Processing helix chain 'CJ' and resid 123 through 132 Proline residue: CJ 132 - end of helix Processing helix chain 'CJ' and resid 133 through 155 removed outlier: 4.713A pdb=" N ASPCJ 142 " --> pdb=" O LEUCJ 138 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ASPCJ 143 " --> pdb=" O ARGCJ 139 " (cutoff:3.500A) Proline residue: CJ 155 - end of helix Processing helix chain 'CJ' and resid 161 through 183 Processing helix chain 'CJ' and resid 225 through 250 Processing helix chain 'CJ' and resid 258 through 265 Processing helix chain 'CJ' and resid 379 through 391 Processing helix chain 'CJ' and resid 457 through 468 removed outlier: 4.162A pdb=" N VALCJ 461 " --> pdb=" O GLNCJ 457 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 472 through 477 Processing helix chain 'CJ' and resid 502 through 507 Processing helix chain 'CJ' and resid 508 through 522 Processing helix chain 'CJ' and resid 582 through 594 Processing helix chain 'CJ' and resid 606 through 639 removed outlier: 5.671A pdb=" N SERCJ 639 " --> pdb=" O LYSCJ 635 " (cutoff:3.500A) Processing helix chain 'CJ' and resid 640 through 673 Processing helix chain 'CK' and resid 5 through 14 Processing helix chain 'CK' and resid 19 through 41 removed outlier: 4.669A pdb=" N GLYCK 32 " --> pdb=" O ALACK 28 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N HISCK 33 " --> pdb=" O ALACK 29 " (cutoff:3.500A) Processing helix chain 'CK' and resid 44 through 75 removed outlier: 6.056A pdb=" N LYSCK 48 " --> pdb=" O GLYCK 44 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N GLYCK 75 " --> pdb=" O ARGCK 71 " (cutoff:3.500A) Processing helix chain 'CK' and resid 98 through 116 Processing helix chain 'CK' and resid 128 through 141 removed outlier: 4.478A pdb=" N LYSCK 141 " --> pdb=" O LYSCK 137 " (cutoff:3.500A) Processing helix chain 'CK' and resid 206 through 213 Processing helix chain 'CK' and resid 248 through 253 removed outlier: 4.400A pdb=" N GLYCK 253 " --> pdb=" O PROCK 249 " (cutoff:3.500A) Processing helix chain 'CL' and resid 17 through 42 removed outlier: 3.533A pdb=" N SERCL 25 " --> pdb=" O ARGCL 21 " (cutoff:3.500A) Processing helix chain 'CL' and resid 61 through 80 Processing helix chain 'CL' and resid 190 through 205 removed outlier: 4.933A pdb=" N LYSCL 196 " --> pdb=" O LYSCL 192 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N VALCL 197 " --> pdb=" O ALACL 193 " (cutoff:3.500A) Processing helix chain 'CL' and resid 216 through 221 Processing helix chain 'CL' and resid 223 through 233 removed outlier: 3.912A pdb=" N GLNCL 227 " --> pdb=" O HISCL 223 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALACL 228 " --> pdb=" O ASPCL 224 " (cutoff:3.500A) Processing helix chain 'CL' and resid 245 through 250 removed outlier: 4.770A 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: 4.456A 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 396 through 402 Processing helix chain 'CL' and resid 413 through 428 removed outlier: 5.292A 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: 4.963A pdb=" N METCL 455 " --> pdb=" O GLYCL 451 " (cutoff:3.500A) Processing helix chain 'CL' and resid 475 through 490 Processing helix chain 'CM' and resid 25 through 47 Processing helix chain 'CM' and resid 53 through 78 Processing helix chain 'CM' and resid 102 through 113 Processing helix chain 'CM' and resid 126 through 137 Processing helix chain 'CM' and resid 146 through 156 Processing helix chain 'CM' and resid 171 through 179 Processing helix chain 'CM' and resid 186 through 197 Processing helix chain 'CM' and resid 200 through 209 removed outlier: 4.957A pdb=" N TRPCM 209 " --> pdb=" O ALACM 205 " (cutoff:3.500A) Processing helix chain 'CM' and resid 239 through 249 removed outlier: 4.142A pdb=" N ALACM 243 " --> pdb=" O GLUCM 239 " (cutoff:3.500A) Processing helix chain 'CN' and resid 12 through 17 removed outlier: 4.151A pdb=" N PHECN 16 " --> pdb=" O GLUCN 12 " (cutoff:3.500A) Processing helix chain 'CN' and resid 32 through 43 Processing helix chain 'CN' and resid 58 through 63 Processing helix chain 'CN' and resid 77 through 89 Proline residue: CN 89 - end of helix Processing helix chain 'CN' and resid 103 through 108 Processing helix chain 'CN' and resid 122 through 134 Processing helix chain 'CN' and resid 147 through 152 Processing helix chain 'CN' and resid 166 through 178 Processing helix chain 'CN' and resid 192 through 197 Processing helix chain 'CN' and resid 211 through 223 Processing helix chain 'CN' and resid 230 through 237 removed outlier: 6.762A pdb=" N ASNCN 234 " --> pdb=" O PROCN 230 " (cutoff:3.500A) Processing helix chain 'CN' and resid 238 through 246 removed outlier: 3.762A pdb=" N TYRCN 246 " --> pdb=" O VALCN 242 " (cutoff:3.500A) Processing helix chain 'CO' and resid 7 through 21 Processing helix chain 'CO' and resid 22 through 43 Processing helix chain 'CO' and resid 83 through 88 Processing helix chain 'CP' and resid 231 through 249 Processing helix chain 'CP' and resid 258 through 274 Processing helix chain 'CP' and resid 277 through 289 Proline residue: CP 289 - end of helix Processing helix chain 'CP' and resid 290 through 303 Proline residue: CP 303 - end of helix 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 Proline residue: CP 372 - end of helix Processing helix chain 'CP' and resid 392 through 403 Processing helix chain 'CP' and resid 414 through 429 removed outlier: 3.776A pdb=" N GLYCP 420 " --> pdb=" O SERCP 416 " (cutoff:3.500A) Processing helix chain 'CP' and resid 442 through 447 Processing helix chain 'CP' and resid 464 through 469 Proline residue: CP 469 - end of helix Processing helix chain 'CP' and resid 476 through 499 Proline residue: CP 484 - end of helix removed outlier: 5.506A pdb=" N ASNCP 499 " --> pdb=" O ILECP 495 " (cutoff:3.500A) Processing helix chain 'CP' and resid 520 through 531 removed outlier: 6.519A pdb=" N VALCP 524 " --> pdb=" O ASNCP 520 " (cutoff:3.500A) Processing helix chain 'CQ' and resid 33 through 43 Processing helix chain 'CQ' and resid 45 through 50 removed outlier: 5.386A pdb=" N LYSCQ 50 " --> pdb=" O PROCQ 46 " (cutoff:3.500A) Processing helix chain 'CQ' and resid 52 through 60 Processing helix chain 'CQ' and resid 66 through 73 removed outlier: 4.294A pdb=" N ALACQ 72 " --> pdb=" O THRCQ 68 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ALACQ 73 " --> pdb=" O LEUCQ 69 " (cutoff:3.500A) Processing helix chain 'CQ' and resid 82 through 131 removed outlier: 5.773A pdb=" N GLYCQ 114 " --> pdb=" O LYSCQ 110 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N LYSCQ 115 " --> pdb=" O ARGCQ 111 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ARGCQ 116 " --> pdb=" O METCQ 112 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ALACQ 117 " --> pdb=" O ALACQ 113 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ARGCQ 118 " --> pdb=" O GLYCQ 114 " (cutoff:3.500A) Processing helix chain 'CQ' and resid 138 through 153 Processing helix chain 'CQ' and resid 155 through 170 removed outlier: 3.828A pdb=" N ALACQ 165 " --> pdb=" O ARGCQ 161 " (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 132 through 137 removed outlier: 4.740A pdb=" N GLNCR 136 " --> pdb=" O PROCR 132 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLNCR 137 " --> pdb=" O GLNCR 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'CR' and resid 132 through 137' Processing helix chain 'CR' and resid 166 through 178 Processing helix chain 'CR' and resid 188 through 202 Processing helix chain 'CR' and resid 205 through 212 Processing helix chain 'CR' and resid 221 through 233 Processing helix chain 'CS' and resid 425 through 434 Processing helix chain 'CS' and resid 465 through 488 removed outlier: 5.049A pdb=" N ASPCS 487 " --> pdb=" O LYSCS 483 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ALACS 488 " --> pdb=" O ALACS 484 " (cutoff:3.500A) Processing helix chain 'CS' and resid 489 through 497 Processing helix chain 'CS' and resid 500 through 505 removed outlier: 4.339A pdb=" N TRPCS 504 " --> pdb=" O ASPCS 500 " (cutoff:3.500A) Processing helix chain 'CS' and resid 563 through 571 removed outlier: 4.219A pdb=" N SERCS 571 " --> pdb=" O ARGCS 567 " (cutoff:3.500A) Processing helix chain 'CS' and resid 572 through 579 Proline residue: CS 579 - end of helix Processing helix chain 'CS' and resid 656 through 669 removed outlier: 4.884A pdb=" N GLYCS 669 " --> pdb=" O GLNCS 665 " (cutoff:3.500A) Processing helix chain 'CS' and resid 672 through 682 removed outlier: 4.938A pdb=" N ASNCS 682 " --> pdb=" O ASPCS 678 " (cutoff:3.500A) Processing helix chain 'CS' and resid 693 through 704 Processing helix chain 'CS' and resid 711 through 723 Processing helix chain 'CS' and resid 729 through 752 Processing helix chain 'CS' and resid 816 through 834 Processing helix chain 'CT' and resid 122 through 141 Processing helix chain 'CT' and resid 147 through 158 removed outlier: 4.260A pdb=" N THRCT 158 " --> pdb=" O ARGCT 154 " (cutoff:3.500A) Processing helix chain 'CT' and resid 160 through 179 Processing helix chain 'CT' and resid 198 through 227 Processing helix chain 'CT' and resid 237 through 253 Processing helix chain 'CT' and resid 258 through 272 removed outlier: 5.099A pdb=" N THRCT 272 " --> pdb=" O LYSCT 268 " (cutoff:3.500A) Processing helix chain 'CT' and resid 276 through 293 Processing helix chain 'CT' and resid 296 through 314 Processing helix chain 'CT' and resid 319 through 328 removed outlier: 4.017A pdb=" N PHECT 325 " --> pdb=" O VALCT 321 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEUCT 326 " --> pdb=" O LEUCT 322 " (cutoff:3.500A) Processing helix chain 'CT' and resid 368 through 415 Processing helix chain 'CT' and resid 416 through 435 removed outlier: 3.626A pdb=" N METCT 420 " --> pdb=" O VALCT 416 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N GLYCT 421 " --> pdb=" O PROCT 417 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ALACT 422 " --> pdb=" O HISCT 418 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N HISCT 432 " --> pdb=" O ALACT 428 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N LEUCT 433 " --> pdb=" O LYSCT 429 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ASNCT 435 " --> pdb=" O ALACT 431 " (cutoff:3.500A) Processing helix chain 'CT' and resid 436 through 455 Processing helix chain 'CT' and resid 477 through 496 removed outlier: 5.750A pdb=" N GLNCT 496 " --> pdb=" O LEUCT 492 " (cutoff:3.500A) Processing helix chain 'CT' and resid 497 through 502 Processing helix chain 'CT' and resid 509 through 526 removed outlier: 4.871A pdb=" N LEUCT 521 " --> pdb=" O TYRCT 517 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N SERCT 522 " --> pdb=" O ARGCT 518 " (cutoff:3.500A) Processing helix chain 'CT' and resid 562 through 576 Processing helix chain 'CT' and resid 585 through 603 Processing helix chain 'CT' and resid 605 through 623 Processing helix chain 'CT' and resid 624 through 632 removed outlier: 4.998A pdb=" N ALACT 628 " --> pdb=" O ARGCT 624 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N LEUCT 629 " --> pdb=" O LYSCT 625 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TRPCT 630 " --> pdb=" O VALCT 626 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N THRCT 632 " --> pdb=" O ALACT 628 " (cutoff:3.500A) Processing helix chain 'CT' and resid 647 through 652 removed outlier: 5.065A pdb=" N ASNCT 652 " --> pdb=" O VALCT 648 " (cutoff:3.500A) Processing helix chain 'CT' and resid 660 through 667 removed outlier: 5.248A pdb=" N LYSCT 666 " --> pdb=" O GLUCT 662 " (cutoff:3.500A) Processing helix chain 'CT' and resid 669 through 686 Processing helix chain 'CU' and resid 192 through 204 Processing helix chain 'CU' and resid 213 through 218 Processing helix chain 'CU' and resid 225 through 231 removed outlier: 3.986A pdb=" N SERCU 229 " --> pdb=" O ARGCU 225 " (cutoff:3.500A) Proline residue: CU 231 - end of helix Processing helix chain 'CU' and resid 235 through 262 Processing helix chain 'CU' and resid 278 through 312 Processing helix chain 'CU' and resid 313 through 344 Processing helix chain 'CU' and resid 357 through 369 Processing helix chain 'CV' and resid 5 through 14 Processing helix chain 'CV' and resid 86 through 99 Processing helix chain 'CV' and resid 104 through 124 removed outlier: 4.782A pdb=" N GLNCV 109 " --> pdb=" O ALACV 105 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ALACV 110 " --> pdb=" O ASPCV 106 " (cutoff:3.500A) Proline residue: CV 124 - end of helix Processing helix chain 'CV' and resid 135 through 140 Processing helix chain 'CX' and resid 65 through 70 removed outlier: 4.902A pdb=" N GLYCX 70 " --> pdb=" O GLUCX 66 " (cutoff:3.500A) Processing helix chain 'CX' and resid 97 through 114 Processing helix chain 'CX' and resid 118 through 150 Processing helix chain 'CY' and resid 7 through 18 Processing helix chain 'CY' and resid 19 through 40 removed outlier: 4.743A pdb=" N LYSCY 31 " --> pdb=" O ASNCY 27 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N ILECY 32 " --> pdb=" O LYSCY 28 " (cutoff:3.500A) Processing helix chain 'CY' and resid 68 through 75 Processing helix chain 'CY' and resid 371 through 389 Processing helix chain 'CY' and resid 393 through 411 Processing helix chain 'CY' and resid 413 through 434 removed outlier: 4.787A pdb=" N THRCY 434 " --> pdb=" O GLYCY 430 " (cutoff:3.500A) Processing helix chain 'CY' and resid 438 through 457 removed outlier: 4.515A pdb=" N GLUCY 451 " --> pdb=" O ASNCY 447 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEUCY 452 " --> pdb=" O SERCY 448 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TRPCY 453 " --> pdb=" O ALACY 449 " (cutoff:3.500A) Processing helix chain 'CY' and resid 458 through 482 Processing helix chain 'CY' and resid 485 through 492 removed outlier: 4.826A pdb=" N ASNCY 492 " --> pdb=" O ARGCY 488 " (cutoff:3.500A) Processing helix chain 'CY' and resid 493 through 510 Processing helix chain 'CY' and resid 522 through 543 Proline residue: CY 526 - end of helix removed outlier: 5.550A pdb=" N TYRCY 529 " --> pdb=" O ARGCY 525 " (cutoff:3.500A) Proline residue: CY 530 - end of helix removed outlier: 5.011A 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: 3.753A pdb=" N ARGCY 551 " --> pdb=" O TYRCY 547 " (cutoff:3.500A) Processing helix chain 'CY' and resid 571 through 581 Processing helix chain 'CY' and resid 611 through 634 removed outlier: 3.547A pdb=" N SERCY 634 " --> pdb=" O PHECY 630 " (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 Processing helix chain 'CY' and resid 701 through 707 Processing helix chain 'CY' and resid 716 through 748 Processing helix chain 'Cz' and resid 47 through 92 Processing helix chain 'LB' and resid 111 through 120 removed outlier: 4.732A pdb=" N LYSLB 120 " --> pdb=" O ARGLB 116 " (cutoff:3.500A) Processing helix chain 'LB' and resid 130 through 140 removed outlier: 4.975A pdb=" N ASNLB 140 " --> pdb=" O LYSLB 136 " (cutoff:3.500A) Processing helix chain 'LB' and resid 141 through 155 Processing helix chain 'LB' and resid 166 through 171 Proline residue: LB 171 - end of helix Processing helix chain 'LB' and resid 188 through 200 Processing helix chain 'LB' and resid 205 through 210 Processing helix chain 'LB' and resid 229 through 234 Processing helix chain 'LB' and resid 348 through 353 removed outlier: 4.165A pdb=" N LEULB 352 " --> pdb=" O SERLB 348 " (cutoff:3.500A) Processing helix chain 'LB' and resid 373 through 382 Processing helix chain 'LB' and resid 384 through 391 Processing helix chain 'LC' and resid 24 through 30 removed outlier: 4.779A pdb=" N SERLC 28 " --> pdb=" O PROLC 24 " (cutoff:3.500A) removed outlier: 4.137A 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: 4.676A pdb=" N LYSLC 47 " --> pdb=" O METLC 43 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ARGLC 48 " --> pdb=" O ALALC 44 " (cutoff:3.500A) Processing helix chain 'LC' and resid 115 through 133 removed outlier: 5.002A pdb=" N ALALC 133 " --> pdb=" O ALALC 129 " (cutoff:3.500A) Processing helix chain 'LC' and resid 134 through 140 Processing helix chain 'LC' and resid 154 through 159 Processing helix chain 'LC' and resid 160 through 165 Processing helix chain 'LC' and resid 166 through 177 Processing helix chain 'LC' and resid 178 through 189 Processing helix chain 'LC' and resid 194 through 200 removed outlier: 4.810A pdb=" N METLC 198 " --> pdb=" O GLYLC 194 " (cutoff:3.500A) Processing helix chain 'LC' and resid 220 through 227 removed outlier: 4.479A pdb=" N LYSLC 224 " --> pdb=" O LYSLC 220 " (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: 3.997A pdb=" N ASPLC 266 " --> pdb=" O ILELC 262 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALALC 267 " --> pdb=" O LYSLC 263 " (cutoff:3.500A) Processing helix chain 'LC' and resid 286 through 293 Processing helix chain 'LC' and resid 294 through 300 Processing helix chain 'LC' and resid 318 through 323 removed outlier: 4.800A 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 332 through 340 Processing helix chain 'LC' and resid 355 through 364 Processing helix chain 'LC' and resid 214 through 219 Processing helix chain 'LE' and resid 98 through 103 removed outlier: 5.123A pdb=" N ILELE 103 " --> pdb=" O ALALE 99 " (cutoff:3.500A) Processing helix chain 'LE' and resid 115 through 124 Processing helix chain 'LE' and resid 127 through 140 removed outlier: 5.448A pdb=" N GLULE 131 " --> pdb=" O TYRLE 127 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALALE 133 " --> pdb=" O THRLE 129 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N LYSLE 134 " --> pdb=" O ALALE 130 " (cutoff:3.500A) Processing helix chain 'LE' and resid 155 through 174 Processing helix chain 'LE' and resid 178 through 186 removed outlier: 5.297A pdb=" N SERLE 186 " --> pdb=" O TYRLE 182 " (cutoff:3.500A) Processing helix chain 'LF' and resid 8 through 14 Processing helix chain 'LF' and resid 15 through 34 removed outlier: 5.448A pdb=" N GLULF 31 " --> pdb=" O LYSLF 27 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ARGLF 32 " --> pdb=" O ALALF 28 " (cutoff:3.500A) Processing helix chain 'LF' and resid 35 through 79 Processing helix chain 'LF' and resid 102 through 113 Processing helix chain 'LF' and resid 126 through 137 Processing helix chain 'LF' and resid 146 through 156 Processing helix chain 'LF' and resid 171 through 179 Processing helix chain 'LF' and resid 186 through 197 removed outlier: 4.191A pdb=" N VALLF 197 " --> pdb=" O GLULF 193 " (cutoff:3.500A) Processing helix chain 'LF' and resid 200 through 209 removed outlier: 5.122A pdb=" N TRPLF 209 " --> pdb=" O ALALF 205 " (cutoff:3.500A) Processing helix chain 'LF' and resid 239 through 249 removed outlier: 4.522A pdb=" N ALALF 243 " --> pdb=" O GLULF 239 " (cutoff:3.500A) Processing helix chain 'LG' and resid 56 through 72 Processing helix chain 'LG' and resid 75 through 84 removed outlier: 4.373A pdb=" N PHELG 81 " --> pdb=" O ALALG 77 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N THRLG 84 " --> pdb=" O GLNLG 80 " (cutoff:3.500A) Processing helix chain 'LG' and resid 86 through 101 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: 4.796A pdb=" N PHELG 168 " --> pdb=" O GLULG 164 " (cutoff:3.500A) removed outlier: 5.912A 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: 4.101A pdb=" N HISLG 194 " --> pdb=" O GLYLG 190 " (cutoff:3.500A) Processing helix chain 'LG' and resid 207 through 233 removed outlier: 4.795A pdb=" N ASNLG 212 " --> pdb=" O SERLG 208 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N GLULG 213 " --> pdb=" O GLULG 209 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LYSLG 228 " --> pdb=" O GLYLG 224 " (cutoff:3.500A) Processing helix chain 'LG' and resid 242 through 257 Processing helix chain 'LH' and resid 61 through 84 Processing helix chain 'LH' and resid 152 through 168 removed outlier: 4.311A pdb=" N LYSLH 168 " --> pdb=" O GLNLH 164 " (cutoff:3.500A) Processing helix chain 'LH' and resid 173 through 178 removed outlier: 4.561A pdb=" N LEULH 178 " --> pdb=" O ILELH 174 " (cutoff:3.500A) Processing helix chain 'LK' and resid 31 through 36 removed outlier: 5.619A pdb=" N LEULK 35 " --> pdb=" O LYSLK 31 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLYLK 36 " --> pdb=" O ILELK 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'LK' and resid 31 through 36' Processing helix chain 'LK' and resid 38 through 51 Processing helix chain 'LK' and resid 76 through 86 Processing helix chain 'LK' and resid 105 through 117 Processing helix chain 'LK' and resid 124 through 140 Processing helix chain 'LK' and resid 147 through 158 Processing helix chain 'LL' and resid 17 through 22 Processing helix chain 'LL' and resid 27 through 47 Processing helix chain 'LL' and resid 76 through 84 Processing helix chain 'LL' and resid 86 through 94 Proline residue: LL 91 - end of helix Processing helix chain 'LL' and resid 105 through 123 Processing helix chain 'LM' and resid 58 through 63 removed outlier: 5.166A 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: 5.526A pdb=" N ASNLM 98 " --> pdb=" O TRPLM 94 " (cutoff:3.500A) Processing helix chain 'LM' and resid 99 through 112 Processing helix chain 'LM' and resid 113 through 136 Processing helix chain 'LN' and resid 2 through 14 removed outlier: 4.509A pdb=" N LYSLN 14 " --> pdb=" O LEULN 10 " (cutoff:3.500A) Processing helix chain 'LN' and resid 16 through 34 removed outlier: 4.431A 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 Proline residue: LN 146 - end of helix Processing helix chain 'LN' and resid 147 through 153 removed outlier: 5.978A pdb=" N ILELN 151 " --> pdb=" O ARGLN 147 " (cutoff:3.500A) Processing helix chain 'LN' and resid 158 through 163 Processing helix chain 'LN' and resid 165 through 173 Processing helix chain 'LN' and resid 186 through 196 Processing helix chain 'LO' and resid 16 through 31 Processing helix chain 'LO' and resid 38 through 43 removed outlier: 5.732A pdb=" N ASNLO 43 " --> pdb=" O CYSLO 39 " (cutoff:3.500A) Processing helix chain 'LO' and resid 47 through 62 removed outlier: 5.136A pdb=" N METLO 62 " --> pdb=" O TYRLO 58 " (cutoff:3.500A) Processing helix chain 'LO' and resid 77 through 91 Proline residue: LO 91 - end of helix Processing helix chain 'LO' and resid 94 through 105 removed outlier: 5.177A pdb=" N LYSLO 105 " --> pdb=" O LEULO 101 " (cutoff:3.500A) Processing helix chain 'LO' and resid 111 through 118 removed outlier: 4.047A pdb=" N LYSLO 116 " --> pdb=" O PROLO 112 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYSLO 117 " --> pdb=" O PROLO 113 " (cutoff:3.500A) removed outlier: 5.499A 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 Processing helix chain 'LO' and resid 152 through 189 Processing helix chain 'LO' and resid 192 through 203 Processing helix chain 'LP' and resid 25 through 37 Processing helix chain 'LP' and resid 40 through 54 Processing helix chain 'LP' and resid 70 through 77 removed outlier: 4.434A pdb=" N LYSLP 74 " --> pdb=" O THRLP 70 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLNLP 75 " --> pdb=" O ALALP 71 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N TRPLP 76 " --> pdb=" O GLNLP 72 " (cutoff:3.500A) Processing helix chain 'LP' and resid 84 through 106 Processing helix chain 'LP' and resid 172 through 185 Processing helix chain 'LQ' and resid 51 through 68 Processing helix chain 'LQ' and resid 70 through 83 removed outlier: 5.375A pdb=" N SERLQ 83 " --> pdb=" O ARGLQ 79 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 91 through 100 Processing helix chain 'LQ' and resid 134 through 145 Processing helix chain 'LQ' and resid 150 through 158 Processing helix chain 'LR' and resid 4 through 16 Processing helix chain 'LR' and resid 18 through 23 removed outlier: 3.513A pdb=" N VALLR 22 " --> pdb=" O GLYLR 18 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N TRPLR 23 " --> pdb=" O GLULR 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'LR' and resid 18 through 23' Processing helix chain 'LR' and resid 28 through 36 removed outlier: 4.979A pdb=" N ASNLR 36 " --> pdb=" O ILELR 32 " (cutoff:3.500A) Processing helix chain 'LR' and resid 37 through 48 Processing helix chain 'LR' and resid 90 through 113 Processing helix chain 'LR' and resid 116 through 130 removed outlier: 4.572A pdb=" N ASNLR 130 " --> pdb=" O LEULR 126 " (cutoff:3.500A) Processing helix chain 'LR' and resid 134 through 147 Processing helix chain 'LS' and resid 33 through 49 Processing helix chain 'LS' and resid 98 through 114 Processing helix chain 'LS' and resid 117 through 122 removed outlier: 5.238A pdb=" N HISLS 122 " --> pdb=" O PHELS 118 " (cutoff:3.500A) Processing helix chain 'LS' and resid 137 through 145 Processing helix chain 'LT' and resid 54 through 59 removed outlier: 5.432A pdb=" N GLYLT 59 " --> pdb=" O LYSLT 55 " (cutoff:3.500A) Processing helix chain 'LT' and resid 92 through 97 removed outlier: 4.070A pdb=" N VALLT 96 " --> pdb=" O ARGLT 92 " (cutoff:3.500A) removed outlier: 5.411A 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 Processing helix chain 'LU' and resid 25 through 32 Processing helix chain 'LU' and resid 35 through 47 Processing helix chain 'LU' and resid 79 through 95 Processing helix chain 'LV' and resid 68 through 74 removed outlier: 3.965A pdb=" N LYSLV 73 " --> pdb=" O PROLV 69 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N LYSLV 74 " --> pdb=" O GLULV 70 " (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 'LX' and resid 71 through 77 removed outlier: 4.990A pdb=" N ILELX 77 " --> pdb=" O HISLX 73 " (cutoff:3.500A) Processing helix chain 'LX' and resid 82 through 92 Processing helix chain 'LX' and resid 104 through 115 Processing helix chain 'LX' and resid 144 through 152 Processing helix chain 'LY' and resid 10 through 21 Processing helix chain 'LY' and resid 22 through 31 Processing helix chain 'LY' and resid 35 through 43 Processing helix chain 'LY' and resid 99 through 104 removed outlier: 4.980A pdb=" N VALLY 104 " --> pdb=" O PROLY 100 " (cutoff:3.500A) Processing helix chain 'LY' and resid 111 through 134 Processing helix chain 'LZ' and resid 57 through 67 removed outlier: 5.606A pdb=" N ILELZ 67 " --> pdb=" O LYSLZ 63 " (cutoff:3.500A) Processing helix chain 'LZ' and resid 75 through 80 removed outlier: 5.397A pdb=" N METLZ 80 " --> pdb=" O TYRLZ 76 " (cutoff:3.500A) Processing helix chain 'LZ' and resid 96 through 103 Proline residue: LZ 103 - end of helix Processing helix chain 'LZ' and resid 104 through 124 Processing helix chain 'LZ' and resid 126 through 131 Processing helix chain 'Lc' and resid 9 through 24 Processing helix chain 'Lc' and resid 29 through 40 Processing helix chain 'Lc' and resid 52 through 67 Processing helix chain 'Lc' and resid 76 through 85 Processing helix chain 'Ld' and resid 23 through 29 Processing helix chain 'Ld' and resid 35 through 53 Processing helix chain 'Ld' and resid 60 through 69 Processing helix chain 'Le' and resid 22 through 27 removed outlier: 4.682A 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: 4.961A pdb=" N METLe 88 " --> pdb=" O GLULe 84 " (cutoff:3.500A) Processing helix chain 'Le' and resid 102 through 117 Processing helix chain 'Lf' and resid 39 through 47 removed outlier: 3.668A pdb=" N TYRLf 46 " --> pdb=" O ALALf 42 " (cutoff:3.500A) Processing helix chain 'Lg' and resid 59 through 67 removed outlier: 4.142A pdb=" N TYRLg 63 " --> pdb=" O ARGLg 59 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ALALg 64 " --> pdb=" O PROLg 60 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N THRLg 65 " --> pdb=" O ARGLg 61 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILELg 66 " --> pdb=" O GLULg 62 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N SERLg 67 " --> pdb=" O TYRLg 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'Lg' and resid 59 through 67' Processing helix chain 'Lg' and resid 68 through 73 removed outlier: 5.356A pdb=" N VALLg 73 " --> pdb=" O PROLg 69 " (cutoff:3.500A) Processing helix chain 'Lg' and resid 82 through 119 Processing helix chain 'Lh' and resid 8 through 16 removed outlier: 5.140A pdb=" N ASNLh 16 " --> pdb=" O LEULh 12 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 17 through 39 Processing helix chain 'Lh' and resid 43 through 76 Processing helix chain 'Lh' and resid 82 through 87 Proline residue: Lh 87 - end of helix Processing helix chain 'Lh' and resid 90 through 96 Processing helix chain 'Lh' and resid 98 through 104 Processing helix chain 'Lh' and resid 106 through 116 Processing helix chain 'Li' and resid 34 through 39 Processing helix chain 'Li' and resid 43 through 58 Processing helix chain 'Li' and resid 60 through 73 Processing helix chain 'Li' and resid 74 through 87 Processing helix chain 'Li' and resid 88 through 110 Processing helix chain 'Lj' and resid 50 through 58 Processing helix chain 'Lj' and resid 65 through 77 removed outlier: 4.876A pdb=" N THRLj 69 " --> pdb=" O ARGLj 65 " (cutoff:3.500A) Proline residue: Lj 71 - end of helix Processing helix chain 'Lk' and resid 7 through 17 Processing helix chain 'Lk' and resid 51 through 62 Processing helix chain 'Ll' and resid 6 through 21 Processing helix chain 'Ll' and resid 24 through 30 Processing helix chain 'Lq' and resid 5 through 25 removed outlier: 3.764A pdb=" N ALALq 14 " --> pdb=" O ARGLq 10 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLULq 15 " --> pdb=" O GLNLq 11 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEULq 16 " --> pdb=" O ASNLq 12 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N TYRLq 19 " --> pdb=" O GLULq 15 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ASNLq 22 " --> pdb=" O ASPLq 18 " (cutoff:3.500A) Processing helix chain 'Lq' and resid 73 through 81 Processing helix chain 'Lq' and resid 86 through 97 removed outlier: 4.877A pdb=" N LYSLq 97 " --> pdb=" O LEULq 93 " (cutoff:3.500A) Processing helix chain 'Lq' and resid 98 through 108 Processing helix chain 'Lq' and resid 113 through 121 Proline residue: Lq 121 - end of helix Processing helix chain 'Lq' and resid 123 through 129 removed outlier: 3.765A pdb=" N GLYLq 127 " --> pdb=" O LEULq 123 " (cutoff:3.500A) Processing helix chain 'Lq' and resid 143 through 153 removed outlier: 4.175A pdb=" N LYSLq 147 " --> pdb=" O ASPLq 143 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ASNLq 149 " --> pdb=" O SERLq 145 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N SERLq 153 " --> pdb=" O ASNLq 149 " (cutoff:3.500A) Processing helix chain 'Lq' and resid 175 through 195 removed outlier: 5.404A pdb=" N LYSLq 195 " --> pdb=" O VALLq 191 " (cutoff:3.500A) Processing helix chain 'Lq' and resid 197 through 202 removed outlier: 5.162A pdb=" N GLYLq 202 " --> pdb=" O GLNLq 199 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'CA' and resid 61 through 66 removed outlier: 6.389A pdb=" N ALACA 94 " --> pdb=" O SERCA 41 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LYSCA 114 " --> pdb=" O ILECA 243 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N GLYCA 235 " --> pdb=" O METCA 123 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N METCA 123 " --> pdb=" O GLYCA 235 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARGCA 237 " --> pdb=" O HISCA 121 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VALCA 239 " --> pdb=" O ASNCA 119 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ASNCA 119 " --> pdb=" O VALCA 239 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'CA' and resid 136 through 142 removed outlier: 7.698A pdb=" N ARGCA 137 " --> pdb=" O ILECA 176 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N HISCA 178 " --> pdb=" O ARGCA 137 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ASPCA 177 " --> pdb=" O ILECA 196 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'CA' and resid 111 through 114 Processing sheet with id= 4, first strand: chain 'CA' and resid 193 through 200 removed outlier: 7.240A pdb=" N ASNCA 193 " --> pdb=" O ILECA 234 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'CB' and resid 80 through 83 Processing sheet with id= 6, first strand: chain 'CB' and resid 96 through 101 Processing sheet with id= 7, first strand: chain 'CB' and resid 240 through 246 removed outlier: 6.376A pdb=" N ILECB 62 " --> pdb=" O VALCB 245 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASNCB 280 " --> pdb=" O THRCB 67 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N PHECB 281 " --> pdb=" O ILECB 293 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'CC' and resid 137 through 141 Processing sheet with id= 9, first strand: chain 'CC' and resid 447 through 450 removed outlier: 5.596A pdb=" N TRPCC 787 " --> pdb=" O HISCC 782 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'CC' and resid 457 through 462 removed outlier: 5.728A pdb=" N ALACC 467 " --> pdb=" O ASPCC 462 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'CC' and resid 501 through 505 removed outlier: 5.587A pdb=" N ILECC 512 " --> pdb=" O ARGCC 505 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'CC' and resid 592 through 597 removed outlier: 5.880A pdb=" N HISCC 602 " --> pdb=" O HISCC 597 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N ASPCC 601 " --> pdb=" O LEUCC 620 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N SERCC 614 " --> pdb=" O SERCC 607 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'CC' and resid 638 through 642 removed outlier: 5.573A pdb=" N LEUCC 647 " --> pdb=" O HISCC 642 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N CYSCC 658 " --> pdb=" O VALCC 667 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'CC' and resid 679 through 683 removed outlier: 5.767A pdb=" N ASNCC 688 " --> pdb=" O HISCC 683 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ASPCC 687 " --> pdb=" O LEUCC 703 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SERCC 693 " --> pdb=" O ARGCC 697 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARGCC 697 " --> pdb=" O SERCC 693 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'CC' and resid 722 through 726 removed outlier: 5.592A pdb=" N LEUCC 732 " --> pdb=" O HISCC 726 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLYCC 747 " --> pdb=" O PROCC 731 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILECC 744 " --> pdb=" O VALCC 762 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'CC' and resid 655 through 658 Processing sheet with id= 17, first strand: chain 'CC' and resid 741 through 744 Processing sheet with id= 18, first strand: chain 'CD' and resid 33 through 38 removed outlier: 6.066A pdb=" N ARGCD 33 " --> pdb=" O PHECD 19 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'CD' and resid 116 through 121 removed outlier: 5.802A pdb=" N LEUCD 155 " --> pdb=" O SERCD 168 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'CD' and resid 182 through 186 removed outlier: 6.234A pdb=" N ARGCD 190 " --> pdb=" O LEUCD 186 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ASPCD 189 " --> pdb=" O TYRCD 205 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VALCD 202 " --> pdb=" O THRCD 218 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N THRCD 212 " --> pdb=" O SERCD 208 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'CD' and resid 229 through 235 removed outlier: 8.393A pdb=" N LYSCD 238 " --> pdb=" O ALACD 254 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'CD' and resid 285 through 288 Processing sheet with id= 23, first strand: chain 'CD' and resid 302 through 306 removed outlier: 6.429A pdb=" N VALCD 312 " --> pdb=" O ASPCD 306 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N THRCD 311 " --> pdb=" O LEUCD 327 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N THRCD 324 " --> pdb=" O VALCD 333 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLNCD 331 " --> pdb=" O ASPCD 326 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'CD' and resid 344 through 350 removed outlier: 3.901A pdb=" N ARGCD 350 " --> pdb=" O SERCD 355 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N SERCD 355 " --> pdb=" O ARGCD 350 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'CD' and resid 392 through 397 removed outlier: 3.628A pdb=" N SERCD 397 " --> pdb=" O SERCD 403 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N SERCD 403 " --> pdb=" O SERCD 397 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'CD' and resid 465 through 469 Processing sheet with id= 27, first strand: chain 'CD' and resid 102 through 105 removed outlier: 6.897A pdb=" N VALCD 484 " --> pdb=" O GLUCD 105 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'CD' and resid 199 through 202 No H-bonds generated for sheet with id= 28 Processing sheet with id= 29, first strand: chain 'CD' and resid 320 through 324 removed outlier: 5.222A pdb=" N HISCD 320 " --> pdb=" O LEUCD 338 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'CE' and resid 213 through 217 Processing sheet with id= 31, first strand: chain 'CE' and resid 384 through 387 removed outlier: 5.104A pdb=" N SERCE 458 " --> pdb=" O GLUCE 333 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLYCE 335 " --> pdb=" O SERCE 458 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N VALCE 338 " --> pdb=" O TYRCE 483 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'CF' and resid 63 through 67 removed outlier: 5.088A pdb=" N THRCF 99 " --> pdb=" O VALCF 45 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VALCF 42 " --> pdb=" O LEUCF 224 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'CF' and resid 135 through 139 removed outlier: 6.963A pdb=" N VALCF 135 " --> pdb=" O ILECF 194 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYRCF 192 " --> pdb=" O VALCF 137 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N THRCF 139 " --> pdb=" O GLUCF 190 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N GLUCF 190 " --> pdb=" O THRCF 139 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'CF' and resid 172 through 175 Processing sheet with id= 35, first strand: chain 'CF' and resid 232 through 236 Processing sheet with id= 36, first strand: chain 'CF' and resid 38 through 42 removed outlier: 8.406A pdb=" N GLNCF 38 " --> pdb=" O SERCF 229 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'CG' and resid 37 through 40 removed outlier: 6.878A pdb=" N VALCG 45 " --> pdb=" O LEUCG 71 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'CG' and resid 96 through 100 Processing sheet with id= 39, first strand: chain 'CH' and resid 202 through 209 removed outlier: 7.059A pdb=" N SERCH 202 " --> pdb=" O PROCH 221 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ARGCH 167 " --> pdb=" O ARGCH 214 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N GLYCH 173 " --> pdb=" O THRCH 220 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'CI' and resid 214 through 219 removed outlier: 5.197A pdb=" N ARGCI 230 " --> pdb=" O VALCI 219 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N VALCI 188 " --> pdb=" O VALCI 263 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'CJ' and resid 194 through 200 Processing sheet with id= 42, first strand: chain 'CJ' and resid 394 through 397 Processing sheet with id= 43, first strand: chain 'CK' and resid 190 through 195 removed outlier: 5.595A pdb=" N TYRCK 242 " --> pdb=" O LEUCK 260 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILECK 220 " --> pdb=" O LYSCK 201 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SERCK 199 " --> pdb=" O GLUCK 222 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'CL' and resid 267 through 270 removed outlier: 6.035A pdb=" N ILECL 208 " --> pdb=" O ARGCL 238 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N GLYCL 319 " --> pdb=" O SERCL 373 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'CM' and resid 118 through 124 Processing sheet with id= 46, first strand: chain 'CN' and resid 1 through 4 Processing sheet with id= 47, first strand: chain 'CN' and resid 23 through 27 Processing sheet with id= 48, first strand: chain 'CN' and resid 69 through 72 Processing sheet with id= 49, first strand: chain 'CN' and resid 114 through 117 Processing sheet with id= 50, first strand: chain 'CN' and resid 158 through 161 Processing sheet with id= 51, first strand: chain 'CP' and resid 330 through 333 removed outlier: 6.912A pdb=" N THRCP 330 " --> pdb=" O PHECP 345 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VALCP 340 " --> pdb=" O THRCP 310 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N HISCP 361 " --> pdb=" O ASNCP 311 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'CP' and resid 407 through 413 removed outlier: 4.418A pdb=" N TYRCP 438 " --> pdb=" O ASPCP 412 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'CP' and resid 452 through 457 removed outlier: 4.713A pdb=" N CYSCP 513 " --> pdb=" O ALACP 457 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N GLYCP 506 " --> pdb=" O LYSCP 583 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LYSCP 580 " --> pdb=" O VALCP 537 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ASNCP 533 " --> pdb=" O ILECP 584 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'CP' and resid 544 through 547 No H-bonds generated for sheet with id= 54 Processing sheet with id= 55, first strand: chain 'CP' and resid 563 through 568 removed outlier: 3.794A pdb=" N ARGCP 564 " --> pdb=" O VALCP 578 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ASPCP 574 " --> pdb=" O PROCP 568 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'CQ' and resid 3 through 6 removed outlier: 5.046A pdb=" N ARGCQ 11 " --> pdb=" O CYSCQ 6 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'CQ' and resid 18 through 22 Processing sheet with id= 58, first strand: chain 'CS' and resid 436 through 440 removed outlier: 6.656A pdb=" N METCS 436 " --> pdb=" O ASPCS 529 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ARGCS 525 " --> pdb=" O THRCS 440 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'CS' and resid 789 through 793 Processing sheet with id= 60, first strand: chain 'CV' and resid 19 through 22 removed outlier: 6.468A pdb=" N PHECV 19 " --> pdb=" O ARGCV 30 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'CV' and resid 51 through 56 removed outlier: 4.981A pdb=" N ALACV 51 " --> pdb=" O LYSCV 66 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N SERCV 77 " --> pdb=" O LYSCV 67 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'LB' and resid 51 through 55 removed outlier: 3.633A pdb=" N GLYLB 52 " --> pdb=" O ILELB 78 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'LB' and resid 98 through 102 removed outlier: 6.858A pdb=" N GLYLB 91 " --> pdb=" O LEULB 102 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N VALLB 87 " --> pdb=" O ALALB 107 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'LB' and resid 178 through 184 removed outlier: 5.087A pdb=" N HISLB 178 " --> pdb=" O THRLB 165 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THRLB 165 " --> pdb=" O HISLB 178 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N VALLB 159 " --> pdb=" O ILELB 184 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'LB' and resid 280 through 283 removed outlier: 3.729A pdb=" N GLULB 214 " --> pdb=" O ILELB 283 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'LB' and resid 87 through 93 removed outlier: 3.637A pdb=" N VALLB 158 " --> pdb=" O TYRLB 92 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'LC' and resid 231 through 236 removed outlier: 5.532A pdb=" N PHELC 254 " --> pdb=" O GLYLC 208 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'LE' and resid 55 through 61 Processing sheet with id= 69, first strand: chain 'LF' and resid 140 through 144 removed outlier: 4.202A pdb=" N ARGLF 94 " --> pdb=" O ASNLF 119 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ASNLF 118 " --> pdb=" O LEULF 213 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'LG' and resid 179 through 184 Processing sheet with id= 71, first strand: chain 'LH' and resid 5 through 12 removed outlier: 6.086A pdb=" N GLYLH 51 " --> pdb=" O VALLH 12 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'LH' and resid 16 through 20 removed outlier: 6.379A pdb=" N ARGLH 23 " --> pdb=" O LEULH 38 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'LH' and resid 100 through 105 removed outlier: 5.066A pdb=" N TYRLH 112 " --> pdb=" O METLH 130 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'LH' and resid 134 through 138 removed outlier: 5.734A pdb=" N ASPLH 144 " --> pdb=" O TYRLH 92 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'LK' and resid 12 through 16 Processing sheet with id= 76, first strand: chain 'LL' and resid 56 through 59 Processing sheet with id= 77, first strand: chain 'LM' and resid 18 through 22 removed outlier: 4.661A pdb=" N ARGLM 18 " --> pdb=" O ILELM 30 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'LM' and resid 39 through 42 Processing sheet with id= 79, first strand: chain 'LN' and resid 35 through 39 removed outlier: 6.425A pdb=" N VALLN 35 " --> pdb=" O ARGLN 65 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLYLN 58 " --> pdb=" O ASPLN 136 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILELN 133 " --> pdb=" O LEULN 116 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'LN' and resid 117 through 121 removed outlier: 6.855A pdb=" N TYRLN 129 " --> pdb=" O VALLN 121 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'LO' and resid 7 through 11 Processing sheet with id= 82, first strand: chain 'LP' and resid 14 through 20 removed outlier: 6.573A pdb=" N ILELP 149 " --> pdb=" O LYSLP 115 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ASNLP 111 " --> pdb=" O ALALP 153 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'LP' and resid 57 through 60 removed outlier: 5.804A pdb=" N ARGLP 80 " --> pdb=" O METLP 60 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'LP' and resid 116 through 122 Processing sheet with id= 85, first strand: chain 'LP' and resid 124 through 130 Processing sheet with id= 86, first strand: chain 'LQ' and resid 146 through 149 removed outlier: 3.765A pdb=" N LEULQ 131 " --> pdb=" O VALLQ 110 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N VALLQ 111 " --> pdb=" O LEULQ 167 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'LS' and resid 24 through 30 removed outlier: 6.595A pdb=" N ILELS 10 " --> pdb=" O VALLS 59 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain 'LS' and resid 86 through 96 removed outlier: 5.238A pdb=" N ASNLS 74 " --> pdb=" O LEULS 129 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'LS' and resid 6 through 10 Processing sheet with id= 90, first strand: chain 'LT' and resid 73 through 77 Processing sheet with id= 91, first strand: chain 'LU' and resid 60 through 64 removed outlier: 5.352A pdb=" N GLYLU 108 " --> pdb=" O LYSLU 20 " (cutoff:3.500A) Processing sheet with id= 92, first strand: chain 'LV' and resid 35 through 38 removed outlier: 6.440A pdb=" N ASNLV 100 " --> pdb=" O ILELV 24 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ILELV 104 " --> pdb=" O ALALV 28 " (cutoff:3.500A) Processing sheet with id= 93, first strand: chain 'LV' and resid 86 through 89 Processing sheet with id= 94, first strand: chain 'LV' and resid 81 through 84 removed outlier: 6.601A pdb=" N ASPLV 99 " --> pdb=" O ALALV 84 " (cutoff:3.500A) Processing sheet with id= 95, first strand: chain 'LX' and resid 93 through 99 removed outlier: 6.707A pdb=" N ASNLX 93 " --> pdb=" O LEULX 139 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THRLX 132 " --> pdb=" O ARGLX 128 " (cutoff:3.500A) Processing sheet with id= 96, first strand: chain 'LY' and resid 55 through 58 Processing sheet with id= 97, first strand: chain 'LY' and resid 85 through 88 removed outlier: 4.843A pdb=" N GLNLY 92 " --> pdb=" O LYSLY 88 " (cutoff:3.500A) Processing sheet with id= 98, first strand: chain 'LZ' and resid 8 through 13 removed outlier: 4.463A pdb=" N ARGLZ 8 " --> pdb=" O ILELZ 24 " (cutoff:3.500A) Processing sheet with id= 99, first strand: chain 'LZ' and resid 41 through 44 Processing sheet with id=100, first strand: chain 'Lc' and resid 25 through 28 removed outlier: 6.123A pdb=" N LYSLc 25 " --> pdb=" O LEULc 96 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALALc 49 " --> pdb=" O TYRLc 73 " (cutoff:3.500A) Processing sheet with id=101, first strand: chain 'Ld' and resid 56 through 59 removed outlier: 5.085A pdb=" N ASPLd 56 " --> pdb=" O LEULd 97 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ALALd 17 " --> pdb=" O VALLd 117 " (cutoff:3.500A) Processing sheet with id=102, first strand: chain 'Le' and resid 72 through 78 Processing sheet with id=103, first strand: chain 'Lf' and resid 12 through 17 removed outlier: 5.909A pdb=" N LYSLf 12 " --> pdb=" O GLULf 35 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEULf 31 " --> pdb=" O LEULf 16 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ARGLf 84 " --> pdb=" O THRLf 74 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LYSLf 65 " --> pdb=" O ALALf 57 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N LYSLf 49 " --> pdb=" O ILELf 73 " (cutoff:3.500A) Processing sheet with id=104, first strand: chain 'Lf' and resid 10 through 16 Processing sheet with id=105, first strand: chain 'Lg' and resid 20 through 25 removed outlier: 4.446A pdb=" N ARGLg 20 " --> pdb=" O ILELg 36 " (cutoff:3.500A) Processing sheet with id=106, first strand: chain 'Lj' and resid 15 through 18 removed outlier: 7.674A pdb=" N THRLj 15 " --> pdb=" O HISLj 28 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N HISLj 28 " --> pdb=" O THRLj 15 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N GLYLj 17 " --> pdb=" O SERLj 26 " (cutoff:3.500A) Processing sheet with id=107, first strand: chain 'Lk' and resid 2 through 6 removed outlier: 6.467A pdb=" N ILELk 34 " --> pdb=" O LEULk 49 " (cutoff:3.500A) Processing sheet with id=108, first strand: chain 'Lq' and resid 30 through 37 removed outlier: 7.798A pdb=" N GLULq 30 " --> pdb=" O ASNLq 171 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASNLq 171 " --> pdb=" O GLULq 30 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VALLq 32 " --> pdb=" O VALLq 169 " (cutoff:3.500A) Processing sheet with id=109, first strand: chain 'Lq' and resid 49 through 54 removed outlier: 6.299A pdb=" N PHELq 49 " --> pdb=" O LEULq 159 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLYLq 51 " --> pdb=" O PHELq 157 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VALLq 53 " --> pdb=" O VALLq 155 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VALLq 155 " --> pdb=" O VALLq 53 " (cutoff:3.500A) Processing sheet with id=110, first strand: chain 'Lq' and resid 65 through 68 4830 hydrogen bonds defined for protein. 14307 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2428 hydrogen bonds 4008 hydrogen bond angles 0 basepair planarities 960 basepair parallelities 1449 stacking parallelities Total time for adding SS restraints: 171.82 Time building geometry restraints manager: 60.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 19916 1.32 - 1.44: 59664 1.44 - 1.57: 79714 1.57 - 1.70: 5718 1.70 - 1.82: 494 Bond restraints: 165506 Sorted by residual: bond pdb=" OG1 TPOCC 163 " pdb=" P TPOCC 163 " ideal model delta sigma weight residual 1.717 1.619 0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" C PROCB 292 " pdb=" O PROCB 292 " ideal model delta sigma weight residual 1.233 1.192 0.041 9.60e-03 1.09e+04 1.81e+01 bond pdb=" N VALLG 166 " pdb=" CA VALLG 166 " ideal model delta sigma weight residual 1.457 1.496 -0.039 9.30e-03 1.16e+04 1.79e+01 bond pdb=" N GLYCE 456 " pdb=" CA GLYCE 456 " ideal model delta sigma weight residual 1.445 1.485 -0.040 1.01e-02 9.80e+03 1.58e+01 bond pdb=" N GLULf 4 " pdb=" CA GLULf 4 " ideal model delta sigma weight residual 1.457 1.507 -0.050 1.29e-02 6.01e+03 1.49e+01 ... (remaining 165501 not shown) Histogram of bond angle deviations from ideal: 95.58 - 103.35: 7063 103.35 - 111.12: 77704 111.12 - 118.90: 68100 118.90 - 126.67: 75609 126.67 - 134.45: 8810 Bond angle restraints: 237286 Sorted by residual: angle pdb=" CA PHECC 733 " pdb=" CB PHECC 733 " pdb=" CG PHECC 733 " ideal model delta sigma weight residual 113.80 122.06 -8.26 1.00e+00 1.00e+00 6.82e+01 angle pdb=" CA PHECA 238 " pdb=" CB PHECA 238 " pdb=" CG PHECA 238 " ideal model delta sigma weight residual 113.80 121.14 -7.34 1.00e+00 1.00e+00 5.38e+01 angle pdb=" N PROCA 236 " pdb=" CA PROCA 236 " pdb=" CB PROCA 236 " ideal model delta sigma weight residual 103.25 95.58 7.67 1.05e+00 9.07e-01 5.34e+01 angle pdb=" CA ALALN 39 " pdb=" C ALALN 39 " pdb=" N SERLN 40 " ideal model delta sigma weight residual 116.28 107.11 9.17 1.26e+00 6.30e-01 5.30e+01 angle pdb=" C PROCP 289 " pdb=" CA PROCP 289 " pdb=" CB PROCP 289 " ideal model delta sigma weight residual 110.92 102.23 8.69 1.22e+00 6.72e-01 5.08e+01 ... (remaining 237281 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 96144 35.99 - 71.98: 7748 71.98 - 107.98: 851 107.98 - 143.97: 23 143.97 - 179.96: 23 Dihedral angle restraints: 104789 sinusoidal: 69859 harmonic: 34930 Sorted by residual: dihedral pdb=" O4' CC1 940 " pdb=" C1' CC1 940 " pdb=" N1 CC1 940 " pdb=" C2 CC1 940 " ideal model delta sinusoidal sigma weight residual 200.00 25.07 174.93 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' UC12417 " pdb=" C1' UC12417 " pdb=" N1 UC12417 " pdb=" C2 UC12417 " ideal model delta sinusoidal sigma weight residual 200.00 26.58 173.42 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" O4' UC13158 " pdb=" C1' UC13158 " pdb=" N1 UC13158 " pdb=" C2 UC13158 " ideal model delta sinusoidal sigma weight residual 200.00 30.84 169.16 1 1.50e+01 4.44e-03 8.46e+01 ... (remaining 104786 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 27712 0.118 - 0.236: 1041 0.236 - 0.354: 46 0.354 - 0.472: 8 0.472 - 0.590: 2 Chirality restraints: 28809 Sorted by residual: chirality pdb=" CB VALLO 191 " pdb=" CA VALLO 191 " pdb=" CG1 VALLO 191 " pdb=" CG2 VALLO 191 " both_signs ideal model delta sigma weight residual False -2.63 -2.04 -0.59 2.00e-01 2.50e+01 8.71e+00 chirality pdb=" CB VALLB 57 " pdb=" CA VALLB 57 " pdb=" CG1 VALLB 57 " pdb=" CG2 VALLB 57 " both_signs ideal model delta sigma weight residual False -2.63 -2.13 -0.50 2.00e-01 2.50e+01 6.14e+00 chirality pdb=" CB VALCN 198 " pdb=" CA VALCN 198 " pdb=" CG1 VALCN 198 " pdb=" CG2 VALCN 198 " both_signs ideal model delta sigma weight residual False -2.63 -2.16 -0.47 2.00e-01 2.50e+01 5.52e+00 ... (remaining 28806 not shown) Planarity restraints: 19593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SERCJ 487 " -0.102 5.00e-02 4.00e+02 1.53e-01 3.75e+01 pdb=" N PROCJ 488 " 0.265 5.00e-02 4.00e+02 pdb=" CA PROCJ 488 " -0.085 5.00e-02 4.00e+02 pdb=" CD PROCJ 488 " -0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRPCY 653 " 0.036 2.00e-02 2.50e+03 3.80e-02 3.60e+01 pdb=" CG TRPCY 653 " -0.096 2.00e-02 2.50e+03 pdb=" CD1 TRPCY 653 " 0.059 2.00e-02 2.50e+03 pdb=" CD2 TRPCY 653 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRPCY 653 " -0.018 2.00e-02 2.50e+03 pdb=" CE2 TRPCY 653 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRPCY 653 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRPCY 653 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRPCY 653 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRPCY 653 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRPCz 48 " 0.024 2.00e-02 2.50e+03 5.03e-02 2.53e+01 pdb=" C TRPCz 48 " -0.087 2.00e-02 2.50e+03 pdb=" O TRPCz 48 " 0.034 2.00e-02 2.50e+03 pdb=" N GLUCz 49 " 0.029 2.00e-02 2.50e+03 ... (remaining 19590 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 921 2.53 - 3.12: 113574 3.12 - 3.72: 278472 3.72 - 4.31: 388805 4.31 - 4.90: 571113 Nonbonded interactions: 1352885 Sorted by model distance: nonbonded pdb=" O4 UC1 670 " pdb=" O6 GC1 684 " model vdw 1.939 3.040 nonbonded pdb=" O2 UC12433 " pdb=" O6 GC12436 " model vdw 1.964 2.432 nonbonded pdb=" OP1 UC11549 " pdb=" OH TYRCC 411 " model vdw 2.047 2.440 nonbonded pdb=" O6 GC1 974 " pdb=" O4 UC11038 " model vdw 2.054 2.432 nonbonded pdb=" OH TYRCG 19 " pdb=" OE1 GLNCG 167 " model vdw 2.055 2.440 ... (remaining 1352880 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'CM' selection = (chain 'LF' and (resid 12 through 219 or resid 235 through 249)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 4.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.100 Extract box with map and model: 20.330 Check model and map are aligned: 1.780 Set scattering table: 1.090 Process input model: 521.680 Find NCS groups from input model: 4.650 Set up NCS constraints: 0.520 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 556.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 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 : 0.004 0.098 165506 Z= 0.270 Angle : 0.783 12.912 237286 Z= 0.477 Chirality : 0.049 0.590 28809 Planarity : 0.007 0.153 19593 Dihedral : 21.130 179.960 82131 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.27 % Favored : 94.47 % Rotamer: Outliers : 1.81 % Allowed : 1.48 % Favored : 96.71 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.01 % Twisted Proline : 0.17 % 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: -0.29 (0.08), residues: 11825 helix: 0.81 (0.07), residues: 5157 sheet: -0.46 (0.12), residues: 1628 loop : -1.12 (0.09), residues: 5040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.096 0.002 TRPCY 653 HIS 0.014 0.001 HISCR 186 PHE 0.045 0.002 PHECC 733 TYR 0.038 0.002 TYRCE 336 ARG 0.014 0.001 ARGCM 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23650 Ramachandran restraints generated. 11825 Oldfield, 0 Emsley, 11825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23650 Ramachandran restraints generated. 11825 Oldfield, 0 Emsley, 11825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3433 residues out of total 10278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 3252 time to evaluate : 9.932 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: CB 46 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7916 (mtmm) REVERT: CB 66 LEU cc_start: 0.8617 (tp) cc_final: 0.8389 (tp) REVERT: CB 148 SER cc_start: 0.9075 (t) cc_final: 0.8713 (p) REVERT: CB 185 MET cc_start: 0.4097 (mmp) cc_final: 0.2894 (ttp) REVERT: CC 299 ARG cc_start: 0.8394 (mtm110) cc_final: 0.8184 (mtm-85) REVERT: CC 307 LYS cc_start: 0.8035 (mtpt) cc_final: 0.7149 (ttmm) REVERT: CC 328 GLN cc_start: 0.7264 (tp40) cc_final: 0.6973 (tp40) REVERT: CC 439 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8454 (tptm) REVERT: CD 111 ASP cc_start: 0.7751 (p0) cc_final: 0.7369 (p0) REVERT: CD 229 ASP cc_start: 0.7282 (m-30) cc_final: 0.7013 (m-30) REVERT: CE 142 ILE cc_start: 0.9022 (mm) cc_final: 0.8812 (mm) REVERT: CE 334 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7157 (tm-30) REVERT: CH 74 HIS cc_start: 0.8532 (t-90) cc_final: 0.8327 (t-90) REVERT: CH 269 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8743 (tp) REVERT: CH 411 ASN cc_start: 0.7154 (m-40) cc_final: 0.6870 (m110) REVERT: CH 509 ARG cc_start: 0.7680 (ttm110) cc_final: 0.7204 (mtm110) REVERT: CH 513 LYS cc_start: 0.6355 (ptpp) cc_final: 0.5964 (pttm) REVERT: CH 532 ASP cc_start: 0.8557 (t70) cc_final: 0.8328 (t0) REVERT: CI 206 TYR cc_start: 0.8881 (t80) cc_final: 0.8414 (t80) REVERT: CI 248 MET cc_start: 0.8916 (mmm) cc_final: 0.8351 (mmm) REVERT: CJ 267 GLU cc_start: 0.7266 (pm20) cc_final: 0.7040 (pm20) REVERT: CK 35 ASN cc_start: 0.8049 (t0) cc_final: 0.7718 (m110) REVERT: CK 57 GLN cc_start: 0.7746 (mt0) cc_final: 0.7527 (mt0) REVERT: CK 150 ILE cc_start: 0.8894 (pt) cc_final: 0.8497 (mt) REVERT: CL 5 ILE cc_start: 0.8466 (mm) cc_final: 0.8224 (mt) REVERT: CM 40 LYS cc_start: 0.6385 (mmtp) cc_final: 0.6138 (tttt) REVERT: CO 38 MET cc_start: 0.7967 (mmm) cc_final: 0.7725 (mmt) REVERT: CP 269 ASP cc_start: 0.6568 (m-30) cc_final: 0.5235 (m-30) REVERT: CP 365 GLN cc_start: 0.8142 (tt0) cc_final: 0.7920 (tt0) REVERT: CP 386 ASP cc_start: 0.8037 (t0) cc_final: 0.7681 (t0) REVERT: CQ 45 ASN cc_start: 0.8615 (t0) cc_final: 0.8412 (t0) REVERT: CQ 63 MET cc_start: 0.8172 (ptp) cc_final: 0.7620 (ptp) REVERT: CR 38 SER cc_start: 0.9093 (m) cc_final: 0.8827 (m) REVERT: CR 57 LYS cc_start: 0.7947 (tttm) cc_final: 0.7041 (mttt) REVERT: CT 366 LYS cc_start: 0.8427 (ttmm) cc_final: 0.8187 (ttmm) REVERT: CT 617 ASP cc_start: 0.6823 (m-30) cc_final: 0.6590 (m-30) REVERT: CU 363 ASP cc_start: 0.7398 (OUTLIER) cc_final: 0.6975 (m-30) REVERT: CV 80 THR cc_start: 0.8997 (t) cc_final: 0.8765 (m) REVERT: CX 112 LYS cc_start: 0.8848 (tppt) cc_final: 0.8395 (mmtt) REVERT: CY 7 ASN cc_start: 0.7438 (m-40) cc_final: 0.7228 (p0) REVERT: CY 491 TYR cc_start: 0.6585 (m-10) cc_final: 0.5930 (m-10) REVERT: CY 584 MET cc_start: 0.7600 (mmm) cc_final: 0.7280 (mmm) REVERT: LB 167 ILE cc_start: 0.7329 (mm) cc_final: 0.7108 (mm) REVERT: LB 197 ARG cc_start: 0.7856 (tmm-80) cc_final: 0.7344 (ttp-170) REVERT: LB 271 MET cc_start: 0.6995 (ttp) cc_final: 0.6552 (ttm) REVERT: LB 337 MET cc_start: 0.7690 (mmt) cc_final: 0.6835 (mmt) REVERT: LC 186 LYS cc_start: 0.8743 (tptp) cc_final: 0.8501 (tptt) REVERT: LC 224 LYS cc_start: 0.8288 (mmtm) cc_final: 0.7965 (mmtp) REVERT: LE 32 ASP cc_start: 0.6700 (p0) cc_final: 0.6431 (p0) REVERT: LF 16 GLU cc_start: 0.8239 (mp0) cc_final: 0.8036 (mp0) REVERT: LF 80 SER cc_start: 0.8946 (m) cc_final: 0.8635 (p) REVERT: LF 88 LYS cc_start: 0.8097 (mtmm) cc_final: 0.7879 (mttp) REVERT: LF 106 ARG cc_start: 0.7475 (ttt180) cc_final: 0.7178 (ttp80) REVERT: LF 115 ARG cc_start: 0.7188 (mpt180) cc_final: 0.6957 (mtt180) REVERT: LF 163 ASN cc_start: 0.8761 (t0) cc_final: 0.8477 (t0) REVERT: LF 248 MET cc_start: 0.8226 (mtt) cc_final: 0.7554 (mtt) REVERT: LH 76 ASN cc_start: 0.8561 (t0) cc_final: 0.8136 (t0) REVERT: LH 91 ARG cc_start: 0.8786 (ptm-80) cc_final: 0.8555 (ptm160) REVERT: LH 164 GLN cc_start: 0.7879 (tt0) cc_final: 0.7554 (tm-30) REVERT: LK 112 ILE cc_start: 0.5830 (mt) cc_final: 0.5540 (mt) REVERT: LN 25 VAL cc_start: 0.8551 (t) cc_final: 0.8232 (m) REVERT: LN 94 TYR cc_start: 0.7691 (t80) cc_final: 0.7320 (t80) REVERT: LN 179 ARG cc_start: 0.8086 (mtp85) cc_final: 0.7805 (mtt180) REVERT: LO 30 SER cc_start: 0.8565 (t) cc_final: 0.8189 (m) REVERT: LP 111 ASN cc_start: 0.7735 (t0) cc_final: 0.7248 (t0) REVERT: LP 140 MET cc_start: 0.6703 (mtm) cc_final: 0.6355 (mtm) REVERT: LR 132 PHE cc_start: 0.8316 (m-80) cc_final: 0.7957 (m-80) REVERT: LR 143 HIS cc_start: 0.8912 (m90) cc_final: 0.8702 (m170) REVERT: LS 43 TYR cc_start: 0.8737 (t80) cc_final: 0.8378 (t80) REVERT: LS 87 THR cc_start: 0.8421 (m) cc_final: 0.8013 (t) REVERT: LS 134 ASP cc_start: 0.8897 (m-30) cc_final: 0.8622 (m-30) REVERT: LT 83 ARG cc_start: 0.3100 (OUTLIER) cc_final: 0.2592 (ttt-90) REVERT: LT 117 LYS cc_start: 0.8859 (tppt) cc_final: 0.8406 (tppt) REVERT: LU 50 ASP cc_start: 0.7253 (OUTLIER) cc_final: 0.6922 (p0) REVERT: LU 98 ASP cc_start: 0.8414 (m-30) cc_final: 0.8141 (m-30) REVERT: LY 9 SER cc_start: 0.8504 (m) cc_final: 0.8258 (p) REVERT: LY 56 GLN cc_start: 0.8605 (tt0) cc_final: 0.8221 (tt0) REVERT: LY 98 ILE cc_start: 0.8664 (mp) cc_final: 0.8398 (mt) REVERT: LZ 121 TYR cc_start: 0.8347 (t80) cc_final: 0.7976 (t80) REVERT: Ld 86 ARG cc_start: 0.8326 (mtt90) cc_final: 0.8016 (mtm-85) REVERT: Le 24 ASP cc_start: 0.8389 (p0) cc_final: 0.8147 (p0) REVERT: Le 37 LYS cc_start: 0.7849 (mmtm) cc_final: 0.7637 (mmmm) REVERT: Lf 59 LYS cc_start: 0.8046 (tttp) cc_final: 0.7754 (mmtm) REVERT: Lf 60 GLU cc_start: 0.7802 (tt0) cc_final: 0.7386 (pt0) REVERT: Lg 15 ASN cc_start: 0.8799 (t0) cc_final: 0.8390 (t0) REVERT: Li 84 LYS cc_start: 0.8240 (tttt) cc_final: 0.8018 (tptt) REVERT: Li 89 PHE cc_start: 0.7073 (m-80) cc_final: 0.6858 (m-10) REVERT: Ll 5 LYS cc_start: 0.7952 (ptpp) cc_final: 0.7751 (pttm) REVERT: Lq 22 ASN cc_start: 0.9217 (m-40) cc_final: 0.8762 (p0) REVERT: Lq 85 MET cc_start: 0.6202 (tmm) cc_final: 0.5957 (tpp) outliers start: 181 outliers final: 34 residues processed: 3347 average time/residue: 1.6253 time to fit residues: 9178.9655 Evaluate side-chains 1900 residues out of total 10278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 1859 time to evaluate : 9.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CB residue 46 LYS Chi-restraints excluded: chain CC residue 161 ASP Chi-restraints excluded: chain CC residue 388 ASP Chi-restraints excluded: chain CC residue 438 LEU Chi-restraints excluded: chain CC residue 439 LYS Chi-restraints excluded: chain CE residue 332 LEU Chi-restraints excluded: chain CE residue 334 GLN Chi-restraints excluded: chain CE residue 473 LEU Chi-restraints excluded: chain CF residue 241 LYS Chi-restraints excluded: chain CH residue 223 ILE Chi-restraints excluded: chain CH residue 239 VAL Chi-restraints excluded: chain CH residue 269 LEU Chi-restraints excluded: chain CL residue 18 THR Chi-restraints excluded: chain CL residue 20 LEU Chi-restraints excluded: chain CP residue 289 PRO Chi-restraints excluded: chain CT residue 174 VAL Chi-restraints excluded: chain CT residue 657 THR Chi-restraints excluded: chain CU residue 363 ASP Chi-restraints excluded: chain CY residue 690 ARG Chi-restraints excluded: chain Cz residue 52 VAL Chi-restraints excluded: chain LB residue 283 ILE Chi-restraints excluded: chain LC residue 22 VAL Chi-restraints excluded: chain LC residue 262 ILE Chi-restraints excluded: chain LC residue 264 GLN Chi-restraints excluded: chain LM residue 112 LEU Chi-restraints excluded: chain LN residue 40 SER Chi-restraints excluded: chain LN residue 41 ARG Chi-restraints excluded: chain LO residue 199 LEU Chi-restraints excluded: chain LT residue 80 VAL Chi-restraints excluded: chain LT residue 83 ARG Chi-restraints excluded: chain LT residue 84 TYR Chi-restraints excluded: chain LU residue 50 ASP Chi-restraints excluded: chain LU residue 59 VAL Chi-restraints excluded: chain LU residue 77 ASP Chi-restraints excluded: chain LZ residue 11 LEU Chi-restraints excluded: chain Lc residue 70 VAL Chi-restraints excluded: chain Ld residue 73 LYS Chi-restraints excluded: chain Lg residue 61 ARG Chi-restraints excluded: chain Lq residue 24 LYS Chi-restraints excluded: chain Lq residue 25 LYS Chi-restraints excluded: chain Lq residue 26 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1459 random chunks: chunk 1232 optimal weight: 5.9990 chunk 1105 optimal weight: 3.9990 chunk 613 optimal weight: 3.9990 chunk 377 optimal weight: 0.7980 chunk 745 optimal weight: 8.9990 chunk 590 optimal weight: 0.7980 chunk 1143 optimal weight: 9.9990 chunk 442 optimal weight: 30.0000 chunk 695 optimal weight: 20.0000 chunk 851 optimal weight: 10.0000 chunk 1324 optimal weight: 3.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CA 121 HIS CA 167 GLN ** CB 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CB 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CB 280 ASN CC 205 GLN CC 206 ASN CC 290 GLN ** CC 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC 528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CC 653 GLN ** CC 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CE 334 GLN CE 405 ASN ** CE 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CE 508 ASN CE 509 GLN CG 113 ASN CH 216 GLN CH 237 GLN CH 258 GLN CI 209 GLN ** CI 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CI 277 ASN CJ 200 ASN CJ 506 GLN CJ 657 ASN CM 43 ASN CM 203 GLN CN 86 ASN CN 106 ASN ** CN 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CP 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CP 397 HIS CP 437 ASN CP 482 GLN CR 202 HIS CR 220 GLN ** CT 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CT 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CV 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CV 97 GLN CY 477 ASN CY 484 ASN CY 580 GLN ** CY 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CY 636 ASN ** CY 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CY 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 93 ASN LC 142 GLN LE 172 ASN LF 78 GLN LF 119 ASN LF 178 ASN LG 246 GLN LH 171 ASN LK 100 HIS LN 57 GLN LN 123 GLN LN 138 ASN LN 195 ASN LO 43 ASN LP 75 GLN ** LP 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LR 34 ASN LR 92 GLN ** LR 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LS 74 ASN LS 89 ASN LS 114 HIS LS 147 ASN ** LU 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LU 75 HIS LV 83 GLN Le 90 ASN Lh 33 GLN Lh 67 GLN Li 100 GLN Lj 29 ASN Lj 76 ASN Lk 3 GLN Lk 33 GLN ** Lq 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lq 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 65 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 165506 Z= 0.278 Angle : 0.643 12.746 237286 Z= 0.331 Chirality : 0.040 0.328 28809 Planarity : 0.006 0.102 19593 Dihedral : 21.947 179.638 58036 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.62 % Favored : 95.26 % Rotamer: Outliers : 2.92 % Allowed : 11.46 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.01 % Twisted Proline : 0.17 % 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: 0.05 (0.08), residues: 11825 helix: 1.17 (0.07), residues: 5165 sheet: -0.32 (0.12), residues: 1597 loop : -1.01 (0.09), residues: 5063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRPCD 158 HIS 0.007 0.001 HISCJ 173 PHE 0.041 0.002 PHECC 733 TYR 0.029 0.002 TYRCP 262 ARG 0.009 0.001 ARGLK 83 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23650 Ramachandran restraints generated. 11825 Oldfield, 0 Emsley, 11825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23650 Ramachandran restraints generated. 11825 Oldfield, 0 Emsley, 11825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2135 residues out of total 10278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 292 poor density : 1843 time to evaluate : 10.293 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: CA 65 ASP cc_start: 0.8507 (t0) cc_final: 0.8108 (t0) REVERT: CA 71 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.6998 (mttp) REVERT: CA 79 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6915 (pm20) REVERT: CA 195 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8142 (pt0) REVERT: CB 148 SER cc_start: 0.9100 (t) cc_final: 0.8751 (p) REVERT: CB 185 MET cc_start: 0.4155 (mmp) cc_final: 0.1964 (ttp) REVERT: CC 299 ARG cc_start: 0.8566 (mtm110) cc_final: 0.8177 (mtm-85) REVERT: CC 328 GLN cc_start: 0.7318 (tp40) cc_final: 0.7073 (tp40) REVERT: CC 439 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8379 (tptm) REVERT: CC 713 MET cc_start: 0.7592 (mtt) cc_final: 0.7200 (mtt) REVERT: CD 111 ASP cc_start: 0.7635 (p0) cc_final: 0.7311 (p0) REVERT: CD 362 THR cc_start: 0.8642 (OUTLIER) cc_final: 0.8383 (t) REVERT: CE 318 ILE cc_start: 0.8869 (mm) cc_final: 0.8663 (mt) REVERT: CF 38 GLN cc_start: 0.7952 (mm-40) cc_final: 0.7576 (mm-40) REVERT: CF 116 PHE cc_start: 0.8984 (m-10) cc_final: 0.8649 (m-10) REVERT: CG 75 THR cc_start: 0.8357 (p) cc_final: 0.8154 (p) REVERT: CH 74 HIS cc_start: 0.8663 (t-90) cc_final: 0.8439 (t-90) REVERT: CH 411 ASN cc_start: 0.7298 (m-40) cc_final: 0.6886 (m110) REVERT: CH 473 PHE cc_start: 0.8399 (t80) cc_final: 0.8121 (t80) REVERT: CH 509 ARG cc_start: 0.7466 (ttm110) cc_final: 0.7204 (mtm110) REVERT: CH 532 ASP cc_start: 0.8494 (t70) cc_final: 0.8172 (t0) REVERT: CI 248 MET cc_start: 0.8666 (mmm) cc_final: 0.8291 (mmm) REVERT: CI 281 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.7902 (mtmt) REVERT: CJ 134 PHE cc_start: 0.7619 (t80) cc_final: 0.7326 (t80) REVERT: CK 11 ARG cc_start: 0.8563 (mmm-85) cc_final: 0.8073 (mtm-85) REVERT: CK 35 ASN cc_start: 0.8208 (t0) cc_final: 0.7774 (m110) REVERT: CL 26 LYS cc_start: 0.7483 (mmmm) cc_final: 0.7119 (mttp) REVERT: CM 40 LYS cc_start: 0.6679 (mmtp) cc_final: 0.6400 (tttt) REVERT: CM 135 ILE cc_start: 0.9018 (mm) cc_final: 0.8774 (mm) REVERT: CN 157 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8246 (mt0) REVERT: CO 38 MET cc_start: 0.7974 (mmm) cc_final: 0.7720 (mmt) REVERT: CP 447 ILE cc_start: 0.7815 (OUTLIER) cc_final: 0.7529 (mp) REVERT: CQ 63 MET cc_start: 0.8156 (ptp) cc_final: 0.7623 (ptp) REVERT: CR 38 SER cc_start: 0.9129 (m) cc_final: 0.8887 (m) REVERT: CR 57 LYS cc_start: 0.8263 (tttm) cc_final: 0.7174 (mttt) REVERT: CS 822 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7837 (mm-30) REVERT: CT 366 LYS cc_start: 0.8614 (ttmm) cc_final: 0.8402 (ttmm) REVERT: CT 652 ASN cc_start: 0.8017 (m110) cc_final: 0.7781 (m-40) REVERT: CU 259 ARG cc_start: 0.8377 (mtt180) cc_final: 0.8172 (mtt180) REVERT: CU 336 GLN cc_start: 0.7644 (mt0) cc_final: 0.7328 (mt0) REVERT: CV 80 THR cc_start: 0.9008 (t) cc_final: 0.8757 (m) REVERT: CY 6 LYS cc_start: 0.8118 (mmmm) cc_final: 0.7900 (tttm) REVERT: CY 473 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8482 (mm) REVERT: CY 602 TYR cc_start: 0.6688 (OUTLIER) cc_final: 0.6435 (t80) REVERT: LB 197 ARG cc_start: 0.7920 (tmm-80) cc_final: 0.7400 (ttp-170) REVERT: LB 271 MET cc_start: 0.7135 (ttp) cc_final: 0.6874 (ttt) REVERT: LB 381 MET cc_start: 0.8311 (mtt) cc_final: 0.7998 (mmm) REVERT: LC 221 GLU cc_start: 0.7709 (mp0) cc_final: 0.7087 (mp0) REVERT: LE 32 ASP cc_start: 0.7002 (p0) cc_final: 0.6624 (p0) REVERT: LF 88 LYS cc_start: 0.8125 (mtmm) cc_final: 0.7887 (mttm) REVERT: LF 106 ARG cc_start: 0.7672 (ttt180) cc_final: 0.7195 (ttp-110) REVERT: LG 250 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7119 (mp0) REVERT: LH 19 SER cc_start: 0.8077 (t) cc_final: 0.7705 (p) REVERT: LH 164 GLN cc_start: 0.7885 (tt0) cc_final: 0.7448 (tm-30) REVERT: LK 112 ILE cc_start: 0.6121 (mt) cc_final: 0.5774 (mt) REVERT: LM 86 GLU cc_start: 0.8419 (mp0) cc_final: 0.8009 (mp0) REVERT: LN 25 VAL cc_start: 0.8547 (t) cc_final: 0.8337 (m) REVERT: LN 67 ARG cc_start: 0.8363 (mtt-85) cc_final: 0.8107 (mtp180) REVERT: LN 179 ARG cc_start: 0.8078 (mtp85) cc_final: 0.7700 (mtt180) REVERT: LO 30 SER cc_start: 0.8742 (t) cc_final: 0.8239 (m) REVERT: LO 80 ARG cc_start: 0.8196 (mmp80) cc_final: 0.7741 (mmm-85) REVERT: LO 178 ARG cc_start: 0.7852 (mtm110) cc_final: 0.7563 (ttm-80) REVERT: LP 78 VAL cc_start: 0.8254 (p) cc_final: 0.7792 (m) REVERT: LQ 147 ARG cc_start: 0.8094 (mtp-110) cc_final: 0.7881 (mtp-110) REVERT: LR 110 ARG cc_start: 0.8946 (ttp80) cc_final: 0.8692 (ttp80) REVERT: LS 91 TYR cc_start: 0.8831 (t80) cc_final: 0.8620 (t80) REVERT: LS 123 ILE cc_start: 0.9327 (mm) cc_final: 0.9002 (mm) REVERT: LS 134 ASP cc_start: 0.8854 (m-30) cc_final: 0.8601 (m-30) REVERT: LT 83 ARG cc_start: 0.3317 (tpp-160) cc_final: 0.2584 (ttt-90) REVERT: LT 84 TYR cc_start: 0.3518 (OUTLIER) cc_final: 0.2431 (m-80) REVERT: LT 102 ARG cc_start: 0.7900 (mtt-85) cc_final: 0.7671 (mmt180) REVERT: LU 50 ASP cc_start: 0.7229 (OUTLIER) cc_final: 0.6974 (p0) REVERT: LY 9 SER cc_start: 0.8619 (m) cc_final: 0.8347 (p) REVERT: LY 98 ILE cc_start: 0.8865 (mp) cc_final: 0.8661 (mt) REVERT: LZ 130 PHE cc_start: 0.9097 (m-10) cc_final: 0.8890 (m-80) REVERT: Lc 78 ILE cc_start: 0.8620 (tp) cc_final: 0.8402 (tp) REVERT: Lc 79 GLU cc_start: 0.8159 (mp0) cc_final: 0.7887 (mp0) REVERT: Ld 98 TYR cc_start: 0.8821 (p90) cc_final: 0.8184 (p90) REVERT: Le 37 LYS cc_start: 0.7903 (mmtm) cc_final: 0.7613 (mmmm) REVERT: Le 84 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7288 (mp0) REVERT: Lf 59 LYS cc_start: 0.8224 (tttp) cc_final: 0.7697 (mmtm) REVERT: Lf 60 GLU cc_start: 0.7898 (tt0) cc_final: 0.7620 (pt0) REVERT: Lg 15 ASN cc_start: 0.8852 (t0) cc_final: 0.8403 (t0) REVERT: Lg 107 LYS cc_start: 0.8707 (ttmm) cc_final: 0.8500 (ttpt) REVERT: Li 55 GLU cc_start: 0.8304 (tt0) cc_final: 0.7961 (tt0) REVERT: Li 84 LYS cc_start: 0.8270 (tttt) cc_final: 0.7856 (tptp) REVERT: Lq 174 MET cc_start: 0.3372 (tmm) cc_final: 0.2620 (ptp) outliers start: 292 outliers final: 176 residues processed: 2010 average time/residue: 1.4099 time to fit residues: 4877.1743 Evaluate side-chains 1786 residues out of total 10278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 1596 time to evaluate : 10.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CA residue 27 ILE Chi-restraints excluded: chain CA residue 40 SER Chi-restraints excluded: chain CA residue 71 LYS Chi-restraints excluded: chain CA residue 79 GLU Chi-restraints excluded: chain CA residue 99 ASP Chi-restraints excluded: chain CA residue 176 ILE Chi-restraints excluded: chain CA residue 195 GLU Chi-restraints excluded: chain CA residue 199 VAL Chi-restraints excluded: chain CB residue 54 GLU Chi-restraints excluded: chain CB residue 68 THR Chi-restraints excluded: chain CB residue 69 LYS Chi-restraints excluded: chain CB residue 89 LEU Chi-restraints excluded: chain CB residue 127 VAL Chi-restraints excluded: chain CB residue 175 THR Chi-restraints excluded: chain CB residue 183 VAL Chi-restraints excluded: chain CB residue 283 VAL Chi-restraints excluded: chain CC residue 191 ASN Chi-restraints excluded: chain CC residue 200 THR Chi-restraints excluded: chain CC residue 388 ASP Chi-restraints excluded: chain CC residue 438 LEU Chi-restraints excluded: chain CC residue 439 LYS Chi-restraints excluded: chain CC residue 459 VAL Chi-restraints excluded: chain CC residue 477 VAL Chi-restraints excluded: chain CC residue 510 THR Chi-restraints excluded: chain CC residue 524 MET Chi-restraints excluded: chain CC residue 537 GLN Chi-restraints excluded: chain CC residue 720 ILE Chi-restraints excluded: chain CC residue 741 SER Chi-restraints excluded: chain CC residue 770 VAL Chi-restraints excluded: chain CD residue 177 THR Chi-restraints excluded: chain CD residue 362 THR Chi-restraints excluded: chain CE residue 116 LEU Chi-restraints excluded: chain CE residue 135 THR Chi-restraints excluded: chain CE residue 190 THR Chi-restraints excluded: chain CE residue 306 LEU Chi-restraints excluded: chain CE residue 402 GLU Chi-restraints excluded: chain CE residue 445 VAL Chi-restraints excluded: chain CE residue 473 LEU Chi-restraints excluded: chain CE residue 478 VAL Chi-restraints excluded: chain CE residue 555 ILE Chi-restraints excluded: chain CF residue 9 VAL Chi-restraints excluded: chain CF residue 97 THR Chi-restraints excluded: chain CF residue 224 LEU Chi-restraints excluded: chain CF residue 241 LYS Chi-restraints excluded: chain CF residue 242 THR Chi-restraints excluded: chain CG residue 69 THR Chi-restraints excluded: chain CG residue 89 ILE Chi-restraints excluded: chain CG residue 130 SER Chi-restraints excluded: chain CH residue 140 LYS Chi-restraints excluded: chain CH residue 238 SER Chi-restraints excluded: chain CH residue 269 LEU Chi-restraints excluded: chain CH residue 276 LEU Chi-restraints excluded: chain CH residue 285 VAL Chi-restraints excluded: chain CH residue 462 GLU Chi-restraints excluded: chain CH residue 544 ILE Chi-restraints excluded: chain CI residue 281 LYS Chi-restraints excluded: chain CJ residue 200 ASN Chi-restraints excluded: chain CJ residue 260 VAL Chi-restraints excluded: chain CK residue 31 GLU Chi-restraints excluded: chain CK residue 260 LEU Chi-restraints excluded: chain CL residue 18 THR Chi-restraints excluded: chain CM residue 19 LEU Chi-restraints excluded: chain CM residue 108 ILE Chi-restraints excluded: chain CM residue 200 ASN Chi-restraints excluded: chain CN residue 4 ARG Chi-restraints excluded: chain CN residue 19 LEU Chi-restraints excluded: chain CN residue 136 GLU Chi-restraints excluded: chain CN residue 137 VAL Chi-restraints excluded: chain CN residue 157 GLN Chi-restraints excluded: chain CN residue 214 GLU Chi-restraints excluded: chain CP residue 331 LEU Chi-restraints excluded: chain CP residue 436 CYS Chi-restraints excluded: chain CP residue 447 ILE Chi-restraints excluded: chain CP residue 459 CYS Chi-restraints excluded: chain CQ residue 20 THR Chi-restraints excluded: chain CQ residue 106 VAL Chi-restraints excluded: chain CR residue 33 ASN Chi-restraints excluded: chain CR residue 138 GLU Chi-restraints excluded: chain CR residue 221 THR Chi-restraints excluded: chain CS residue 507 LEU Chi-restraints excluded: chain CS residue 707 ILE Chi-restraints excluded: chain CS residue 819 MET Chi-restraints excluded: chain CT residue 284 GLU Chi-restraints excluded: chain CT residue 319 GLU Chi-restraints excluded: chain CT residue 573 SER Chi-restraints excluded: chain CT residue 644 LEU Chi-restraints excluded: chain CU residue 190 ILE Chi-restraints excluded: chain CU residue 206 ASP Chi-restraints excluded: chain CU residue 211 THR Chi-restraints excluded: chain CU residue 220 VAL Chi-restraints excluded: chain CU residue 224 LYS Chi-restraints excluded: chain CU residue 229 SER Chi-restraints excluded: chain CU residue 244 MET Chi-restraints excluded: chain CU residue 263 VAL Chi-restraints excluded: chain CU residue 269 THR Chi-restraints excluded: chain CU residue 331 LEU Chi-restraints excluded: chain CU residue 332 ASP Chi-restraints excluded: chain CV residue 68 VAL Chi-restraints excluded: chain CV residue 85 SER Chi-restraints excluded: chain CX residue 84 LYS Chi-restraints excluded: chain CX residue 86 LYS Chi-restraints excluded: chain CX residue 126 LEU Chi-restraints excluded: chain CY residue 473 ILE Chi-restraints excluded: chain CY residue 499 LEU Chi-restraints excluded: chain CY residue 544 THR Chi-restraints excluded: chain CY residue 554 LEU Chi-restraints excluded: chain CY residue 602 TYR Chi-restraints excluded: chain LB residue 84 MET Chi-restraints excluded: chain LB residue 211 GLU Chi-restraints excluded: chain LB residue 278 SER Chi-restraints excluded: chain LB residue 279 VAL Chi-restraints excluded: chain LB residue 283 ILE Chi-restraints excluded: chain LB residue 362 THR Chi-restraints excluded: chain LC residue 22 VAL Chi-restraints excluded: chain LC residue 79 SER Chi-restraints excluded: chain LC residue 158 VAL Chi-restraints excluded: chain LC residue 204 ARG Chi-restraints excluded: chain LC residue 223 VAL Chi-restraints excluded: chain LC residue 264 GLN Chi-restraints excluded: chain LE residue 51 SER Chi-restraints excluded: chain LE residue 52 LEU Chi-restraints excluded: chain LE residue 73 LEU Chi-restraints excluded: chain LE residue 108 LYS Chi-restraints excluded: chain LE residue 135 GLU Chi-restraints excluded: chain LE residue 176 VAL Chi-restraints excluded: chain LG residue 74 VAL Chi-restraints excluded: chain LG residue 167 VAL Chi-restraints excluded: chain LG residue 183 ILE Chi-restraints excluded: chain LG residue 250 GLU Chi-restraints excluded: chain LG residue 251 LYS Chi-restraints excluded: chain LG residue 253 LYS Chi-restraints excluded: chain LH residue 47 VAL Chi-restraints excluded: chain LH residue 53 ILE Chi-restraints excluded: chain LH residue 82 VAL Chi-restraints excluded: chain LH residue 167 CYS Chi-restraints excluded: chain LH residue 174 ILE Chi-restraints excluded: chain LL residue 51 VAL Chi-restraints excluded: chain LL residue 69 THR Chi-restraints excluded: chain LM residue 24 ASN Chi-restraints excluded: chain LM residue 52 THR Chi-restraints excluded: chain LM residue 57 VAL Chi-restraints excluded: chain LM residue 67 ILE Chi-restraints excluded: chain LM residue 78 THR Chi-restraints excluded: chain LM residue 112 LEU Chi-restraints excluded: chain LM residue 138 ILE Chi-restraints excluded: chain LN residue 41 ARG Chi-restraints excluded: chain LO residue 61 LYS Chi-restraints excluded: chain LO residue 115 ASP Chi-restraints excluded: chain LQ residue 48 LYS Chi-restraints excluded: chain LQ residue 108 VAL Chi-restraints excluded: chain LQ residue 113 THR Chi-restraints excluded: chain LR residue 2 VAL Chi-restraints excluded: chain LR residue 41 ILE Chi-restraints excluded: chain LT residue 76 VAL Chi-restraints excluded: chain LT residue 80 VAL Chi-restraints excluded: chain LT residue 84 TYR Chi-restraints excluded: chain LT residue 124 VAL Chi-restraints excluded: chain LU residue 50 ASP Chi-restraints excluded: chain LU residue 59 VAL Chi-restraints excluded: chain LU residue 77 ASP Chi-restraints excluded: chain LV residue 13 LEU Chi-restraints excluded: chain LV residue 120 VAL Chi-restraints excluded: chain LY residue 46 SER Chi-restraints excluded: chain LZ residue 10 CYS Chi-restraints excluded: chain LZ residue 11 LEU Chi-restraints excluded: chain LZ residue 45 ILE Chi-restraints excluded: chain LZ residue 88 LEU Chi-restraints excluded: chain LZ residue 104 SER Chi-restraints excluded: chain LZ residue 123 SER Chi-restraints excluded: chain Lc residue 70 VAL Chi-restraints excluded: chain Lc residue 92 THR Chi-restraints excluded: chain Ld residue 73 LYS Chi-restraints excluded: chain Ld residue 117 VAL Chi-restraints excluded: chain Le residue 8 VAL Chi-restraints excluded: chain Le residue 16 LYS Chi-restraints excluded: chain Le residue 84 GLU Chi-restraints excluded: chain Le residue 92 THR Chi-restraints excluded: chain Lf residue 56 ARG Chi-restraints excluded: chain Lf residue 88 THR Chi-restraints excluded: chain Lf residue 99 SER Chi-restraints excluded: chain Lg residue 47 ASP Chi-restraints excluded: chain Lg residue 102 VAL Chi-restraints excluded: chain Lh residue 34 LEU Chi-restraints excluded: chain Lh residue 113 LEU Chi-restraints excluded: chain Li residue 25 LYS Chi-restraints excluded: chain Lk residue 31 THR Chi-restraints excluded: chain Lk residue 46 THR Chi-restraints excluded: chain Ll residue 27 ILE Chi-restraints excluded: chain Lq residue 100 ILE Chi-restraints excluded: chain Lq residue 206 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1459 random chunks: chunk 736 optimal weight: 1.9990 chunk 411 optimal weight: 20.0000 chunk 1102 optimal weight: 0.7980 chunk 902 optimal weight: 4.9990 chunk 365 optimal weight: 4.9990 chunk 1327 optimal weight: 0.8980 chunk 1433 optimal weight: 2.9990 chunk 1182 optimal weight: 0.5980 chunk 1316 optimal weight: 4.9990 chunk 452 optimal weight: 4.9990 chunk 1064 optimal weight: 0.0040 overall best weight: 0.8594 ------------------------------------------------------------------------------- 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 71 HIS ** CC 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CC 753 GLN CE 222 ASN CE 334 GLN CE 443 HIS ** CE 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CE 509 GLN CH 499 HIS CI 209 GLN ** CI 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CK 57 GLN CL 6 ASN CM 110 GLN ** CN 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CN 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CP 365 GLN CR 134 GLN CR 196 GLN CS 682 ASN ** CT 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CT 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CT 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CT 499 HIS CU 232 GLN ** CV 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CX 73 GLN ** CY 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CY 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 274 HIS LC 118 GLN LF 78 GLN LK 100 HIS LP 75 GLN LP 89 GLN LR 34 ASN LR 92 GLN ** LR 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LS 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LS 89 ASN ** LT 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LU 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LU 75 HIS LU 76 ASN LV 83 GLN Le 90 ASN Ll 11 GLN ** Lq 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 165506 Z= 0.158 Angle : 0.558 12.493 237286 Z= 0.287 Chirality : 0.036 0.260 28809 Planarity : 0.005 0.070 19593 Dihedral : 21.848 179.845 57983 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.19 % Favored : 95.71 % Rotamer: Outliers : 2.83 % Allowed : 13.87 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.01 % Twisted Proline : 0.17 % 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: 0.35 (0.08), residues: 11825 helix: 1.49 (0.07), residues: 5180 sheet: -0.30 (0.12), residues: 1601 loop : -0.91 (0.09), residues: 5044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRPCY 653 HIS 0.005 0.001 HISCE 443 PHE 0.028 0.001 PHECC 733 TYR 0.049 0.001 TYRCY 602 ARG 0.011 0.000 ARGCY 732 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23650 Ramachandran restraints generated. 11825 Oldfield, 0 Emsley, 11825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23650 Ramachandran restraints generated. 11825 Oldfield, 0 Emsley, 11825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2016 residues out of total 10278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 283 poor density : 1733 time to evaluate : 10.086 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: CA 65 ASP cc_start: 0.8490 (t0) cc_final: 0.8211 (t0) REVERT: CB 148 SER cc_start: 0.9035 (t) cc_final: 0.8690 (p) REVERT: CB 185 MET cc_start: 0.4075 (mmp) cc_final: 0.2084 (ttp) REVERT: CC 299 ARG cc_start: 0.8503 (mtm110) cc_final: 0.8127 (mtm-85) REVERT: CC 328 GLN cc_start: 0.7316 (tp40) cc_final: 0.7057 (tp40) REVERT: CC 439 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8353 (tptm) REVERT: CC 713 MET cc_start: 0.7640 (mtt) cc_final: 0.7241 (mtt) REVERT: CD 44 TYR cc_start: 0.6556 (OUTLIER) cc_final: 0.6306 (t80) REVERT: CD 111 ASP cc_start: 0.7672 (p0) cc_final: 0.7273 (p0) REVERT: CD 362 THR cc_start: 0.8660 (OUTLIER) cc_final: 0.8393 (t) REVERT: CE 318 ILE cc_start: 0.8853 (mm) cc_final: 0.8647 (mt) REVERT: CF 8 ARG cc_start: 0.7257 (ptm-80) cc_final: 0.7035 (ptp-170) REVERT: CG 75 THR cc_start: 0.8317 (p) cc_final: 0.8108 (p) REVERT: CH 54 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6844 (mt-10) REVERT: CH 74 HIS cc_start: 0.8603 (t-90) cc_final: 0.8394 (t-90) REVERT: CH 236 MET cc_start: 0.8235 (mmm) cc_final: 0.7802 (tpp) REVERT: CH 289 MET cc_start: 0.7257 (mmm) cc_final: 0.6668 (mmm) REVERT: CH 333 HIS cc_start: 0.8123 (t-170) cc_final: 0.7898 (t-170) REVERT: CH 411 ASN cc_start: 0.7191 (m-40) cc_final: 0.6786 (m110) REVERT: CH 509 ARG cc_start: 0.7458 (ttm110) cc_final: 0.7193 (mtm110) REVERT: CH 532 ASP cc_start: 0.8472 (t70) cc_final: 0.8240 (t0) REVERT: CI 248 MET cc_start: 0.8645 (mmm) cc_final: 0.8263 (mmm) REVERT: CI 281 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.7895 (mtmt) REVERT: CJ 134 PHE cc_start: 0.7433 (t80) cc_final: 0.7202 (t80) REVERT: CJ 504 GLU cc_start: 0.6271 (pp20) cc_final: 0.6038 (pp20) REVERT: CK 11 ARG cc_start: 0.8520 (mmm-85) cc_final: 0.8044 (mtm-85) REVERT: CK 23 ARG cc_start: 0.8069 (mmt90) cc_final: 0.7496 (mpt180) REVERT: CK 35 ASN cc_start: 0.7942 (t0) cc_final: 0.7696 (m110) REVERT: CM 40 LYS cc_start: 0.6683 (mmtp) cc_final: 0.6352 (tttt) REVERT: CM 90 VAL cc_start: 0.8906 (OUTLIER) cc_final: 0.8692 (m) REVERT: CM 106 ARG cc_start: 0.7792 (ttt-90) cc_final: 0.7515 (ttp-110) REVERT: CN 67 ARG cc_start: 0.7933 (ptt180) cc_final: 0.7457 (ttp-110) REVERT: CN 214 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6914 (mt-10) REVERT: CO 38 MET cc_start: 0.7949 (mmm) cc_final: 0.7683 (mmt) REVERT: CP 288 PHE cc_start: 0.7600 (m-10) cc_final: 0.7376 (m-80) REVERT: CP 447 ILE cc_start: 0.7843 (OUTLIER) cc_final: 0.7576 (mp) REVERT: CR 38 SER cc_start: 0.9111 (m) cc_final: 0.8856 (m) REVERT: CR 144 ASN cc_start: 0.6721 (t0) cc_final: 0.6488 (t0) REVERT: CT 366 LYS cc_start: 0.8592 (ttmm) cc_final: 0.8378 (ttmm) REVERT: CU 359 ASP cc_start: 0.7165 (t0) cc_final: 0.6928 (t0) REVERT: CV 80 THR cc_start: 0.9019 (t) cc_final: 0.8765 (m) REVERT: CX 127 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7354 (mt-10) REVERT: CY 6 LYS cc_start: 0.7994 (mmmm) cc_final: 0.7710 (mmmm) REVERT: CY 568 TYR cc_start: 0.7234 (t80) cc_final: 0.6745 (t80) REVERT: CY 700 ASP cc_start: 0.7751 (p0) cc_final: 0.7503 (p0) REVERT: LB 197 ARG cc_start: 0.7781 (tmm-80) cc_final: 0.7398 (ttp-110) REVERT: LB 271 MET cc_start: 0.7125 (ttp) cc_final: 0.6870 (ttt) REVERT: LB 337 MET cc_start: 0.8412 (mmt) cc_final: 0.8143 (mmt) REVERT: LB 381 MET cc_start: 0.8324 (mtt) cc_final: 0.8083 (mmm) REVERT: LE 32 ASP cc_start: 0.7288 (p0) cc_final: 0.6923 (p0) REVERT: LF 88 LYS cc_start: 0.8079 (mtmm) cc_final: 0.7796 (mttm) REVERT: LF 106 ARG cc_start: 0.7539 (ttt180) cc_final: 0.7091 (ttp-110) REVERT: LF 132 MET cc_start: 0.8376 (mtp) cc_final: 0.8131 (mtm) REVERT: LG 65 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8217 (mttm) REVERT: LH 19 SER cc_start: 0.8037 (t) cc_final: 0.7673 (p) REVERT: LH 164 GLN cc_start: 0.7777 (tt0) cc_final: 0.7297 (tm-30) REVERT: LK 112 ILE cc_start: 0.6100 (mt) cc_final: 0.5730 (mt) REVERT: LM 86 GLU cc_start: 0.8363 (mp0) cc_final: 0.7955 (mp0) REVERT: LN 25 VAL cc_start: 0.8460 (t) cc_final: 0.8230 (m) REVERT: LN 41 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.7092 (mtt-85) REVERT: LO 30 SER cc_start: 0.8756 (t) cc_final: 0.8213 (m) REVERT: LO 80 ARG cc_start: 0.8127 (mmp80) cc_final: 0.7606 (mmm-85) REVERT: LO 178 ARG cc_start: 0.7840 (mtm110) cc_final: 0.7630 (ttm-80) REVERT: LQ 118 ASN cc_start: 0.8360 (m-40) cc_final: 0.8048 (t0) REVERT: LQ 147 ARG cc_start: 0.8057 (mtp-110) cc_final: 0.7618 (mtp-110) REVERT: LR 28 GLU cc_start: 0.7360 (mm-30) cc_final: 0.7144 (mm-30) REVERT: LR 99 GLN cc_start: 0.8670 (tp40) cc_final: 0.8398 (tp40) REVERT: LR 110 ARG cc_start: 0.8828 (ttp80) cc_final: 0.8561 (ttp80) REVERT: LS 43 TYR cc_start: 0.8741 (t80) cc_final: 0.8361 (t80) REVERT: LS 90 MET cc_start: 0.8219 (ptm) cc_final: 0.7978 (ptm) REVERT: LS 91 TYR cc_start: 0.8849 (t80) cc_final: 0.8554 (t80) REVERT: LS 93 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8195 (mt-10) REVERT: LS 134 ASP cc_start: 0.8868 (m-30) cc_final: 0.8609 (m-30) REVERT: LT 35 ARG cc_start: 0.6313 (mmp80) cc_final: 0.5797 (ttt180) REVERT: LT 83 ARG cc_start: 0.3363 (tpp-160) cc_final: 0.2568 (ttt-90) REVERT: LU 27 GLN cc_start: 0.7848 (tp40) cc_final: 0.7570 (tp40) REVERT: LU 50 ASP cc_start: 0.7199 (OUTLIER) cc_final: 0.6961 (p0) REVERT: LX 62 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8414 (mtmt) REVERT: LY 9 SER cc_start: 0.8634 (m) cc_final: 0.8360 (p) REVERT: LY 98 ILE cc_start: 0.8715 (mp) cc_final: 0.8495 (mt) REVERT: Lc 78 ILE cc_start: 0.8726 (tp) cc_final: 0.8510 (tp) REVERT: Lc 79 GLU cc_start: 0.8238 (mp0) cc_final: 0.7900 (mp0) REVERT: Ld 98 TYR cc_start: 0.8670 (p90) cc_final: 0.8018 (p90) REVERT: Le 37 LYS cc_start: 0.7907 (mmtm) cc_final: 0.7629 (mmmm) REVERT: Lf 59 LYS cc_start: 0.8226 (tttp) cc_final: 0.7683 (mmtm) REVERT: Lf 60 GLU cc_start: 0.7859 (tt0) cc_final: 0.7589 (pt0) REVERT: Lg 15 ASN cc_start: 0.8797 (t0) cc_final: 0.8343 (t0) REVERT: Lg 107 LYS cc_start: 0.8668 (ttmm) cc_final: 0.8463 (ttpt) REVERT: Li 55 GLU cc_start: 0.8286 (tt0) cc_final: 0.7858 (tt0) REVERT: Li 84 LYS cc_start: 0.8257 (tttt) cc_final: 0.8036 (tptt) outliers start: 283 outliers final: 173 residues processed: 1904 average time/residue: 1.4140 time to fit residues: 4619.9626 Evaluate side-chains 1761 residues out of total 10278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1576 time to evaluate : 9.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CA residue 27 ILE Chi-restraints excluded: chain CA residue 39 LEU Chi-restraints excluded: chain CA residue 40 SER Chi-restraints excluded: chain CA residue 71 LYS Chi-restraints excluded: chain CA residue 99 ASP Chi-restraints excluded: chain CA residue 176 ILE Chi-restraints excluded: chain CA residue 195 GLU Chi-restraints excluded: chain CB residue 68 THR Chi-restraints excluded: chain CB residue 69 LYS Chi-restraints excluded: chain CB residue 70 LYS Chi-restraints excluded: chain CB residue 89 LEU Chi-restraints excluded: chain CB residue 127 VAL Chi-restraints excluded: chain CB residue 183 VAL Chi-restraints excluded: chain CB residue 278 VAL Chi-restraints excluded: chain CC residue 117 ILE Chi-restraints excluded: chain CC residue 191 ASN Chi-restraints excluded: chain CC residue 333 GLN Chi-restraints excluded: chain CC residue 353 SER Chi-restraints excluded: chain CC residue 388 ASP Chi-restraints excluded: chain CC residue 434 SER Chi-restraints excluded: chain CC residue 438 LEU Chi-restraints excluded: chain CC residue 439 LYS Chi-restraints excluded: chain CC residue 459 VAL Chi-restraints excluded: chain CC residue 477 VAL Chi-restraints excluded: chain CC residue 510 THR Chi-restraints excluded: chain CC residue 524 MET Chi-restraints excluded: chain CC residue 537 GLN Chi-restraints excluded: chain CC residue 735 ASP Chi-restraints excluded: chain CC residue 741 SER Chi-restraints excluded: chain CC residue 751 ASN Chi-restraints excluded: chain CC residue 770 VAL Chi-restraints excluded: chain CD residue 44 TYR Chi-restraints excluded: chain CD residue 177 THR Chi-restraints excluded: chain CD residue 362 THR Chi-restraints excluded: chain CD residue 441 ILE Chi-restraints excluded: chain CE residue 116 LEU Chi-restraints excluded: chain CE residue 135 THR Chi-restraints excluded: chain CE residue 188 VAL Chi-restraints excluded: chain CE residue 190 THR Chi-restraints excluded: chain CE residue 390 LYS Chi-restraints excluded: chain CE residue 402 GLU Chi-restraints excluded: chain CE residue 445 VAL Chi-restraints excluded: chain CE residue 473 LEU Chi-restraints excluded: chain CE residue 478 VAL Chi-restraints excluded: chain CF residue 56 VAL Chi-restraints excluded: chain CF residue 97 THR Chi-restraints excluded: chain CF residue 211 LEU Chi-restraints excluded: chain CG residue 69 THR Chi-restraints excluded: chain CH residue 54 GLU Chi-restraints excluded: chain CH residue 140 LYS Chi-restraints excluded: chain CH residue 200 THR Chi-restraints excluded: chain CH residue 269 LEU Chi-restraints excluded: chain CH residue 276 LEU Chi-restraints excluded: chain CH residue 285 VAL Chi-restraints excluded: chain CI residue 281 LYS Chi-restraints excluded: chain CJ residue 260 VAL Chi-restraints excluded: chain CJ residue 372 PHE Chi-restraints excluded: chain CJ residue 638 LEU Chi-restraints excluded: chain CJ residue 663 LEU Chi-restraints excluded: chain CJ residue 672 LYS Chi-restraints excluded: chain CK residue 232 THR Chi-restraints excluded: chain CL residue 18 THR Chi-restraints excluded: chain CM residue 19 LEU Chi-restraints excluded: chain CM residue 90 VAL Chi-restraints excluded: chain CM residue 206 ASN Chi-restraints excluded: chain CN residue 4 ARG Chi-restraints excluded: chain CN residue 136 GLU Chi-restraints excluded: chain CN residue 214 GLU Chi-restraints excluded: chain CP residue 331 LEU Chi-restraints excluded: chain CP residue 340 VAL Chi-restraints excluded: chain CP residue 436 CYS Chi-restraints excluded: chain CP residue 447 ILE Chi-restraints excluded: chain CP residue 459 CYS Chi-restraints excluded: chain CQ residue 20 THR Chi-restraints excluded: chain CQ residue 147 GLU Chi-restraints excluded: chain CR residue 138 GLU Chi-restraints excluded: chain CR residue 184 VAL Chi-restraints excluded: chain CR residue 221 THR Chi-restraints excluded: chain CS residue 485 SER Chi-restraints excluded: chain CS residue 507 LEU Chi-restraints excluded: chain CT residue 166 LEU Chi-restraints excluded: chain CT residue 284 GLU Chi-restraints excluded: chain CT residue 319 GLU Chi-restraints excluded: chain CT residue 573 SER Chi-restraints excluded: chain CT residue 644 LEU Chi-restraints excluded: chain CU residue 203 ILE Chi-restraints excluded: chain CU residue 206 ASP Chi-restraints excluded: chain CU residue 220 VAL Chi-restraints excluded: chain CU residue 229 SER Chi-restraints excluded: chain CU residue 269 THR Chi-restraints excluded: chain CU residue 331 LEU Chi-restraints excluded: chain CU residue 332 ASP Chi-restraints excluded: chain CU residue 356 ASP Chi-restraints excluded: chain CV residue 85 SER Chi-restraints excluded: chain CV residue 86 THR Chi-restraints excluded: chain CX residue 84 LYS Chi-restraints excluded: chain CX residue 86 LYS Chi-restraints excluded: chain CX residue 95 VAL Chi-restraints excluded: chain CX residue 126 LEU Chi-restraints excluded: chain CY residue 394 ASP Chi-restraints excluded: chain CY residue 461 TYR Chi-restraints excluded: chain CY residue 490 VAL Chi-restraints excluded: chain CY residue 495 TYR Chi-restraints excluded: chain CY residue 499 LEU Chi-restraints excluded: chain CY residue 544 THR Chi-restraints excluded: chain CY residue 554 LEU Chi-restraints excluded: chain CY residue 602 TYR Chi-restraints excluded: chain CY residue 714 GLU Chi-restraints excluded: chain CY residue 742 GLU Chi-restraints excluded: chain LB residue 84 MET Chi-restraints excluded: chain LB residue 101 SER Chi-restraints excluded: chain LB residue 211 GLU Chi-restraints excluded: chain LB residue 278 SER Chi-restraints excluded: chain LB residue 279 VAL Chi-restraints excluded: chain LB residue 283 ILE Chi-restraints excluded: chain LB residue 329 VAL Chi-restraints excluded: chain LB residue 362 THR Chi-restraints excluded: chain LC residue 22 VAL Chi-restraints excluded: chain LC residue 79 SER Chi-restraints excluded: chain LC residue 100 MET Chi-restraints excluded: chain LC residue 158 VAL Chi-restraints excluded: chain LC residue 204 ARG Chi-restraints excluded: chain LC residue 256 VAL Chi-restraints excluded: chain LE residue 52 LEU Chi-restraints excluded: chain LE residue 73 LEU Chi-restraints excluded: chain LE residue 108 LYS Chi-restraints excluded: chain LE residue 135 GLU Chi-restraints excluded: chain LE residue 163 LYS Chi-restraints excluded: chain LF residue 18 LEU Chi-restraints excluded: chain LF residue 80 SER Chi-restraints excluded: chain LF residue 189 ASP Chi-restraints excluded: chain LF residue 233 ASP Chi-restraints excluded: chain LG residue 65 LYS Chi-restraints excluded: chain LG residue 167 VAL Chi-restraints excluded: chain LH residue 47 VAL Chi-restraints excluded: chain LH residue 53 ILE Chi-restraints excluded: chain LH residue 82 VAL Chi-restraints excluded: chain LH residue 167 CYS Chi-restraints excluded: chain LK residue 111 GLU Chi-restraints excluded: chain LL residue 51 VAL Chi-restraints excluded: chain LM residue 20 LEU Chi-restraints excluded: chain LM residue 112 LEU Chi-restraints excluded: chain LM residue 121 MET Chi-restraints excluded: chain LM residue 138 ILE Chi-restraints excluded: chain LN residue 41 ARG Chi-restraints excluded: chain LN residue 60 VAL Chi-restraints excluded: chain LN residue 149 ASN Chi-restraints excluded: chain LO residue 147 VAL Chi-restraints excluded: chain LP residue 24 VAL Chi-restraints excluded: chain LQ residue 48 LYS Chi-restraints excluded: chain LQ residue 108 VAL Chi-restraints excluded: chain LQ residue 113 THR Chi-restraints excluded: chain LR residue 41 ILE Chi-restraints excluded: chain LS residue 60 SER Chi-restraints excluded: chain LT residue 52 MET Chi-restraints excluded: chain LT residue 76 VAL Chi-restraints excluded: chain LT residue 80 VAL Chi-restraints excluded: chain LT residue 124 VAL Chi-restraints excluded: chain LU residue 50 ASP Chi-restraints excluded: chain LU residue 59 VAL Chi-restraints excluded: chain LV residue 13 LEU Chi-restraints excluded: chain LV residue 80 ILE Chi-restraints excluded: chain LX residue 62 LYS Chi-restraints excluded: chain LX residue 117 ASP Chi-restraints excluded: chain LY residue 46 SER Chi-restraints excluded: chain LY residue 94 VAL Chi-restraints excluded: chain LZ residue 11 LEU Chi-restraints excluded: chain LZ residue 45 ILE Chi-restraints excluded: chain LZ residue 88 LEU Chi-restraints excluded: chain LZ residue 104 SER Chi-restraints excluded: chain Lc residue 70 VAL Chi-restraints excluded: chain Ld residue 73 LYS Chi-restraints excluded: chain Ld residue 117 VAL Chi-restraints excluded: chain Le residue 8 VAL Chi-restraints excluded: chain Lf residue 99 SER Chi-restraints excluded: chain Lg residue 47 ASP Chi-restraints excluded: chain Lg residue 102 VAL Chi-restraints excluded: chain Lh residue 34 LEU Chi-restraints excluded: chain Lh residue 113 LEU Chi-restraints excluded: chain Lk residue 31 THR Chi-restraints excluded: chain Lk residue 46 THR Chi-restraints excluded: chain Ll residue 23 ILE Chi-restraints excluded: chain Ll residue 27 ILE Chi-restraints excluded: chain Lq residue 26 ARG Chi-restraints excluded: chain Lq residue 206 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1459 random chunks: chunk 1311 optimal weight: 6.9990 chunk 997 optimal weight: 10.0000 chunk 688 optimal weight: 10.0000 chunk 146 optimal weight: 8.9990 chunk 633 optimal weight: 20.0000 chunk 891 optimal weight: 6.9990 chunk 1332 optimal weight: 0.9990 chunk 1410 optimal weight: 3.9990 chunk 695 optimal weight: 20.0000 chunk 1262 optimal weight: 0.8980 chunk 380 optimal weight: 8.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CA 279 HIS CA 286 GLN CB 87 HIS ** CC 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CE 443 HIS CE 463 GLN ** CE 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CF 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CH 389 ASN CI 209 GLN ** CI 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 417 HIS ** CJ 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CK 57 GLN CM 110 GLN ** CN 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CN 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CP 286 ASN ** CT 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CT 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CT 297 ASN ** CT 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CU 232 GLN CU 336 GLN CV 15 ASN CV 17 ASN CY 435 ASN CY 621 GLN ** CY 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CY 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CY 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 320 ASN LF 78 GLN LK 100 HIS LP 89 GLN ** LP 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LR 34 ASN ** LR 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LR 141 HIS LR 143 HIS LS 89 ASN ** LT 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LU 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LV 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Le 90 ASN Lh 37 GLN Lh 115 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.115 165506 Z= 0.386 Angle : 0.666 15.667 237286 Z= 0.337 Chirality : 0.042 0.326 28809 Planarity : 0.006 0.084 19593 Dihedral : 21.782 179.079 57972 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.67 % Favored : 95.22 % Rotamer: Outliers : 3.37 % Allowed : 15.20 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.01 % Twisted Proline : 0.17 % 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: 0.28 (0.08), residues: 11825 helix: 1.44 (0.07), residues: 5162 sheet: -0.29 (0.12), residues: 1617 loop : -0.94 (0.09), residues: 5046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRPCY 713 HIS 0.007 0.001 HISLC 38 PHE 0.026 0.002 PHELC 121 TYR 0.027 0.002 TYRCM 142 ARG 0.023 0.001 ARGCP 244 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23650 Ramachandran restraints generated. 11825 Oldfield, 0 Emsley, 11825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23650 Ramachandran restraints generated. 11825 Oldfield, 0 Emsley, 11825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1957 residues out of total 10278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 337 poor density : 1620 time to evaluate : 10.011 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: CA 71 LYS cc_start: 0.7582 (OUTLIER) cc_final: 0.7051 (mttp) REVERT: CA 272 ARG cc_start: 0.7305 (mtm180) cc_final: 0.6606 (mtt90) REVERT: CB 89 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7938 (tt) REVERT: CB 148 SER cc_start: 0.9053 (t) cc_final: 0.8704 (p) REVERT: CB 185 MET cc_start: 0.4296 (mmp) cc_final: 0.1911 (ttp) REVERT: CC 462 ASP cc_start: 0.7157 (p0) cc_final: 0.6896 (p0) REVERT: CC 540 ARG cc_start: 0.8495 (mtt180) cc_final: 0.8269 (mtt180) REVERT: CC 713 MET cc_start: 0.7835 (mtt) cc_final: 0.7428 (mtt) REVERT: CD 44 TYR cc_start: 0.6752 (OUTLIER) cc_final: 0.6512 (t80) REVERT: CD 111 ASP cc_start: 0.7704 (p0) cc_final: 0.7308 (p0) REVERT: CD 362 THR cc_start: 0.8666 (OUTLIER) cc_final: 0.8405 (t) REVERT: CE 318 ILE cc_start: 0.8843 (mm) cc_final: 0.8629 (mt) REVERT: CE 355 MET cc_start: 0.7925 (mpp) cc_final: 0.7349 (mtt) REVERT: CF 121 GLN cc_start: 0.6519 (tm-30) cc_final: 0.6074 (tm-30) REVERT: CG 106 GLN cc_start: 0.8392 (tp-100) cc_final: 0.8116 (tp40) REVERT: CH 54 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.6868 (mt-10) REVERT: CH 236 MET cc_start: 0.8360 (mmm) cc_final: 0.7843 (tpp) REVERT: CH 289 MET cc_start: 0.7357 (mmm) cc_final: 0.6532 (mmm) REVERT: CH 509 ARG cc_start: 0.7591 (ttm110) cc_final: 0.7379 (mtm110) REVERT: CI 281 LYS cc_start: 0.8598 (mtpt) cc_final: 0.8158 (mtmt) REVERT: CJ 134 PHE cc_start: 0.7856 (t80) cc_final: 0.7580 (t80) REVERT: CK 35 ASN cc_start: 0.8050 (t0) cc_final: 0.7839 (m110) REVERT: CK 57 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7880 (mt0) REVERT: CL 26 LYS cc_start: 0.7505 (mmmm) cc_final: 0.6995 (mttp) REVERT: CM 40 LYS cc_start: 0.6646 (mmtp) cc_final: 0.6272 (tttt) REVERT: CM 90 VAL cc_start: 0.8912 (OUTLIER) cc_final: 0.8711 (m) REVERT: CO 38 MET cc_start: 0.7898 (mmm) cc_final: 0.7668 (mmm) REVERT: CP 288 PHE cc_start: 0.7821 (m-10) cc_final: 0.7564 (m-80) REVERT: CQ 120 VAL cc_start: 0.8659 (OUTLIER) cc_final: 0.8388 (m) REVERT: CR 38 SER cc_start: 0.9133 (m) cc_final: 0.8890 (m) REVERT: CT 366 LYS cc_start: 0.8754 (ttmm) cc_final: 0.8541 (ttmm) REVERT: CY 6 LYS cc_start: 0.7932 (mmmm) cc_final: 0.7622 (mttm) REVERT: CY 602 TYR cc_start: 0.6502 (OUTLIER) cc_final: 0.6042 (t80) REVERT: CY 700 ASP cc_start: 0.7929 (p0) cc_final: 0.7684 (p0) REVERT: Cz 49 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8129 (mp0) REVERT: LB 197 ARG cc_start: 0.7949 (tmm-80) cc_final: 0.7366 (ttp-170) REVERT: LB 271 MET cc_start: 0.7195 (ttp) cc_final: 0.6825 (ttp) REVERT: LB 381 MET cc_start: 0.8333 (mtt) cc_final: 0.8122 (mmm) REVERT: LC 85 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8002 (tpt-90) REVERT: LF 88 LYS cc_start: 0.8260 (mtmm) cc_final: 0.7893 (mttm) REVERT: LF 132 MET cc_start: 0.8632 (mtp) cc_final: 0.8400 (mtm) REVERT: LG 250 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6973 (mp0) REVERT: LH 19 SER cc_start: 0.8101 (t) cc_final: 0.7698 (p) REVERT: LK 112 ILE cc_start: 0.6271 (mt) cc_final: 0.6017 (mt) REVERT: LM 86 GLU cc_start: 0.8375 (mp0) cc_final: 0.7826 (mp0) REVERT: LN 179 ARG cc_start: 0.8215 (mtt180) cc_final: 0.7795 (mtt90) REVERT: LO 30 SER cc_start: 0.8858 (t) cc_final: 0.8290 (m) REVERT: LO 80 ARG cc_start: 0.8255 (mmp80) cc_final: 0.7819 (mmm-85) REVERT: LS 52 LYS cc_start: 0.7452 (mmtm) cc_final: 0.7178 (mmmt) REVERT: LS 90 MET cc_start: 0.8322 (ptm) cc_final: 0.7969 (ptm) REVERT: LS 134 ASP cc_start: 0.8890 (m-30) cc_final: 0.8633 (m-30) REVERT: LT 35 ARG cc_start: 0.6433 (mmp80) cc_final: 0.5964 (ttt180) REVERT: LT 83 ARG cc_start: 0.3639 (tpp-160) cc_final: 0.2682 (ttt-90) REVERT: LU 27 GLN cc_start: 0.7851 (tp40) cc_final: 0.7523 (tp40) REVERT: LU 32 LYS cc_start: 0.8406 (tppt) cc_final: 0.7861 (tptt) REVERT: LU 50 ASP cc_start: 0.7144 (OUTLIER) cc_final: 0.6879 (p0) REVERT: LZ 130 PHE cc_start: 0.9165 (m-10) cc_final: 0.8963 (m-80) REVERT: Lc 30 TYR cc_start: 0.8162 (t80) cc_final: 0.7948 (t80) REVERT: Ld 73 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8704 (mtmt) REVERT: Ld 98 TYR cc_start: 0.8844 (p90) cc_final: 0.8160 (p90) REVERT: Le 37 LYS cc_start: 0.7951 (mmtm) cc_final: 0.7637 (mmmm) REVERT: Le 81 LYS cc_start: 0.7825 (mmtm) cc_final: 0.7439 (mmtt) REVERT: Le 124 LYS cc_start: 0.7443 (mmtt) cc_final: 0.6829 (tmmt) REVERT: Lf 59 LYS cc_start: 0.8354 (tttp) cc_final: 0.7704 (mmtm) REVERT: Lg 15 ASN cc_start: 0.8838 (t0) cc_final: 0.8419 (t0) REVERT: Lh 96 ARG cc_start: 0.8183 (ttm170) cc_final: 0.7803 (ttm170) REVERT: Li 84 LYS cc_start: 0.8312 (tttt) cc_final: 0.7893 (tptp) REVERT: Lj 79 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.7098 (ptt90) REVERT: Lk 7 ASP cc_start: 0.5711 (OUTLIER) cc_final: 0.5411 (p0) REVERT: Lq 174 MET cc_start: 0.3555 (ppp) cc_final: 0.2069 (ptp) outliers start: 337 outliers final: 221 residues processed: 1826 average time/residue: 1.4188 time to fit residues: 4451.6824 Evaluate side-chains 1762 residues out of total 10278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 1525 time to evaluate : 9.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CA residue 27 ILE Chi-restraints excluded: chain CA residue 40 SER Chi-restraints excluded: chain CA residue 71 LYS Chi-restraints excluded: chain CA residue 99 ASP Chi-restraints excluded: chain CA residue 176 ILE Chi-restraints excluded: chain CA residue 195 GLU Chi-restraints excluded: chain CB residue 21 ASP Chi-restraints excluded: chain CB residue 68 THR Chi-restraints excluded: chain CB residue 89 LEU Chi-restraints excluded: chain CB residue 97 VAL Chi-restraints excluded: chain CB residue 127 VAL Chi-restraints excluded: chain CB residue 175 THR Chi-restraints excluded: chain CB residue 183 VAL Chi-restraints excluded: chain CB residue 278 VAL Chi-restraints excluded: chain CB residue 283 VAL Chi-restraints excluded: chain CC residue 181 ASP Chi-restraints excluded: chain CC residue 191 ASN Chi-restraints excluded: chain CC residue 333 GLN Chi-restraints excluded: chain CC residue 379 GLU Chi-restraints excluded: chain CC residue 388 ASP Chi-restraints excluded: chain CC residue 389 SER Chi-restraints excluded: chain CC residue 434 SER Chi-restraints excluded: chain CC residue 459 VAL Chi-restraints excluded: chain CC residue 477 VAL Chi-restraints excluded: chain CC residue 510 THR Chi-restraints excluded: chain CC residue 524 MET Chi-restraints excluded: chain CC residue 537 GLN Chi-restraints excluded: chain CC residue 741 SER Chi-restraints excluded: chain CC residue 751 ASN Chi-restraints excluded: chain CC residue 770 VAL Chi-restraints excluded: chain CC residue 799 LEU Chi-restraints excluded: chain CD residue 44 TYR Chi-restraints excluded: chain CD residue 177 THR Chi-restraints excluded: chain CD residue 362 THR Chi-restraints excluded: chain CD residue 441 ILE Chi-restraints excluded: chain CE residue 135 THR Chi-restraints excluded: chain CE residue 188 VAL Chi-restraints excluded: chain CE residue 189 VAL Chi-restraints excluded: chain CE residue 190 THR Chi-restraints excluded: chain CE residue 306 LEU Chi-restraints excluded: chain CE residue 386 ASP Chi-restraints excluded: chain CE residue 402 GLU Chi-restraints excluded: chain CE residue 445 VAL Chi-restraints excluded: chain CE residue 462 LEU Chi-restraints excluded: chain CE residue 473 LEU Chi-restraints excluded: chain CE residue 478 VAL Chi-restraints excluded: chain CE residue 555 ILE Chi-restraints excluded: chain CF residue 9 VAL Chi-restraints excluded: chain CF residue 53 LEU Chi-restraints excluded: chain CF residue 56 VAL Chi-restraints excluded: chain CF residue 97 THR Chi-restraints excluded: chain CG residue 62 ASP Chi-restraints excluded: chain CG residue 89 ILE Chi-restraints excluded: chain CH residue 54 GLU Chi-restraints excluded: chain CH residue 200 THR Chi-restraints excluded: chain CH residue 223 ILE Chi-restraints excluded: chain CH residue 228 LEU Chi-restraints excluded: chain CH residue 276 LEU Chi-restraints excluded: chain CH residue 277 PHE Chi-restraints excluded: chain CH residue 285 VAL Chi-restraints excluded: chain CH residue 399 ASN Chi-restraints excluded: chain CJ residue 219 VAL Chi-restraints excluded: chain CJ residue 260 VAL Chi-restraints excluded: chain CJ residue 663 LEU Chi-restraints excluded: chain CK residue 57 GLN Chi-restraints excluded: chain CK residue 150 ILE Chi-restraints excluded: chain CK residue 152 THR Chi-restraints excluded: chain CK residue 232 THR Chi-restraints excluded: chain CL residue 18 THR Chi-restraints excluded: chain CM residue 19 LEU Chi-restraints excluded: chain CM residue 90 VAL Chi-restraints excluded: chain CM residue 171 ASP Chi-restraints excluded: chain CM residue 197 VAL Chi-restraints excluded: chain CN residue 4 ARG Chi-restraints excluded: chain CN residue 26 VAL Chi-restraints excluded: chain CN residue 91 ASP Chi-restraints excluded: chain CN residue 136 GLU Chi-restraints excluded: chain CN residue 137 VAL Chi-restraints excluded: chain CN residue 146 VAL Chi-restraints excluded: chain CN residue 190 SER Chi-restraints excluded: chain CN residue 239 ASN Chi-restraints excluded: chain CP residue 329 VAL Chi-restraints excluded: chain CP residue 331 LEU Chi-restraints excluded: chain CP residue 340 VAL Chi-restraints excluded: chain CP residue 428 LEU Chi-restraints excluded: chain CP residue 436 CYS Chi-restraints excluded: chain CP residue 447 ILE Chi-restraints excluded: chain CP residue 519 GLU Chi-restraints excluded: chain CP residue 550 SER Chi-restraints excluded: chain CQ residue 20 THR Chi-restraints excluded: chain CQ residue 120 VAL Chi-restraints excluded: chain CQ residue 147 GLU Chi-restraints excluded: chain CR residue 17 ILE Chi-restraints excluded: chain CR residue 135 GLN Chi-restraints excluded: chain CR residue 184 VAL Chi-restraints excluded: chain CS residue 485 SER Chi-restraints excluded: chain CS residue 507 LEU Chi-restraints excluded: chain CS residue 707 ILE Chi-restraints excluded: chain CS residue 819 MET Chi-restraints excluded: chain CT residue 166 LEU Chi-restraints excluded: chain CT residue 284 GLU Chi-restraints excluded: chain CT residue 319 GLU Chi-restraints excluded: chain CT residue 573 SER Chi-restraints excluded: chain CT residue 644 LEU Chi-restraints excluded: chain CT residue 657 THR Chi-restraints excluded: chain CU residue 190 ILE Chi-restraints excluded: chain CU residue 203 ILE Chi-restraints excluded: chain CU residue 211 THR Chi-restraints excluded: chain CU residue 220 VAL Chi-restraints excluded: chain CU residue 224 LYS Chi-restraints excluded: chain CU residue 229 SER Chi-restraints excluded: chain CU residue 269 THR Chi-restraints excluded: chain CU residue 331 LEU Chi-restraints excluded: chain CU residue 332 ASP Chi-restraints excluded: chain CU residue 355 ASP Chi-restraints excluded: chain CU residue 356 ASP Chi-restraints excluded: chain CV residue 13 SER Chi-restraints excluded: chain CV residue 68 VAL Chi-restraints excluded: chain CV residue 85 SER Chi-restraints excluded: chain CV residue 86 THR Chi-restraints excluded: chain CX residue 84 LYS Chi-restraints excluded: chain CX residue 86 LYS Chi-restraints excluded: chain CX residue 93 VAL Chi-restraints excluded: chain CX residue 95 VAL Chi-restraints excluded: chain CX residue 126 LEU Chi-restraints excluded: chain CY residue 394 ASP Chi-restraints excluded: chain CY residue 417 GLU Chi-restraints excluded: chain CY residue 461 TYR Chi-restraints excluded: chain CY residue 490 VAL Chi-restraints excluded: chain CY residue 495 TYR Chi-restraints excluded: chain CY residue 499 LEU Chi-restraints excluded: chain CY residue 544 THR Chi-restraints excluded: chain CY residue 554 LEU Chi-restraints excluded: chain CY residue 602 TYR Chi-restraints excluded: chain CY residue 742 GLU Chi-restraints excluded: chain Cz residue 49 GLU Chi-restraints excluded: chain LB residue 84 MET Chi-restraints excluded: chain LB residue 101 SER Chi-restraints excluded: chain LB residue 205 THR Chi-restraints excluded: chain LB residue 211 GLU Chi-restraints excluded: chain LB residue 278 SER Chi-restraints excluded: chain LB residue 279 VAL Chi-restraints excluded: chain LB residue 283 ILE Chi-restraints excluded: chain LB residue 329 VAL Chi-restraints excluded: chain LB residue 362 THR Chi-restraints excluded: chain LC residue 79 SER Chi-restraints excluded: chain LC residue 85 ARG Chi-restraints excluded: chain LC residue 100 MET Chi-restraints excluded: chain LC residue 158 VAL Chi-restraints excluded: chain LC residue 204 ARG Chi-restraints excluded: chain LC residue 216 GLU Chi-restraints excluded: chain LC residue 238 ASP Chi-restraints excluded: chain LC residue 256 VAL Chi-restraints excluded: chain LE residue 51 SER Chi-restraints excluded: chain LE residue 52 LEU Chi-restraints excluded: chain LE residue 108 LYS Chi-restraints excluded: chain LE residue 135 GLU Chi-restraints excluded: chain LE residue 163 LYS Chi-restraints excluded: chain LF residue 18 LEU Chi-restraints excluded: chain LF residue 80 SER Chi-restraints excluded: chain LF residue 92 VAL Chi-restraints excluded: chain LF residue 126 THR Chi-restraints excluded: chain LF residue 233 ASP Chi-restraints excluded: chain LG residue 74 VAL Chi-restraints excluded: chain LG residue 85 LEU Chi-restraints excluded: chain LG residue 167 VAL Chi-restraints excluded: chain LG residue 183 ILE Chi-restraints excluded: chain LG residue 232 THR Chi-restraints excluded: chain LG residue 250 GLU Chi-restraints excluded: chain LG residue 253 LYS Chi-restraints excluded: chain LH residue 47 VAL Chi-restraints excluded: chain LH residue 53 ILE Chi-restraints excluded: chain LH residue 82 VAL Chi-restraints excluded: chain LH residue 167 CYS Chi-restraints excluded: chain LH residue 174 ILE Chi-restraints excluded: chain LH residue 179 ASP Chi-restraints excluded: chain LK residue 111 GLU Chi-restraints excluded: chain LL residue 51 VAL Chi-restraints excluded: chain LL residue 69 THR Chi-restraints excluded: chain LM residue 24 ASN Chi-restraints excluded: chain LM residue 67 ILE Chi-restraints excluded: chain LM residue 112 LEU Chi-restraints excluded: chain LM residue 121 MET Chi-restraints excluded: chain LN residue 60 VAL Chi-restraints excluded: chain LO residue 90 ILE Chi-restraints excluded: chain LO residue 110 VAL Chi-restraints excluded: chain LO residue 147 VAL Chi-restraints excluded: chain LQ residue 48 LYS Chi-restraints excluded: chain LQ residue 108 VAL Chi-restraints excluded: chain LQ residue 113 THR Chi-restraints excluded: chain LR residue 2 VAL Chi-restraints excluded: chain LR residue 41 ILE Chi-restraints excluded: chain LR residue 117 LYS Chi-restraints excluded: chain LS residue 60 SER Chi-restraints excluded: chain LS residue 97 THR Chi-restraints excluded: chain LS residue 123 ILE Chi-restraints excluded: chain LT residue 52 MET Chi-restraints excluded: chain LT residue 76 VAL Chi-restraints excluded: chain LT residue 80 VAL Chi-restraints excluded: chain LT residue 96 VAL Chi-restraints excluded: chain LT residue 124 VAL Chi-restraints excluded: chain LT residue 142 SER Chi-restraints excluded: chain LU residue 50 ASP Chi-restraints excluded: chain LU residue 59 VAL Chi-restraints excluded: chain LV residue 13 LEU Chi-restraints excluded: chain LV residue 79 VAL Chi-restraints excluded: chain LV residue 120 VAL Chi-restraints excluded: chain LX residue 62 LYS Chi-restraints excluded: chain LY residue 46 SER Chi-restraints excluded: chain LY residue 96 ILE Chi-restraints excluded: chain LZ residue 10 CYS Chi-restraints excluded: chain LZ residue 11 LEU Chi-restraints excluded: chain LZ residue 45 ILE Chi-restraints excluded: chain LZ residue 88 LEU Chi-restraints excluded: chain LZ residue 104 SER Chi-restraints excluded: chain LZ residue 123 SER Chi-restraints excluded: chain Lc residue 66 SER Chi-restraints excluded: chain Lc residue 70 VAL Chi-restraints excluded: chain Ld residue 73 LYS Chi-restraints excluded: chain Ld residue 117 VAL Chi-restraints excluded: chain Le residue 8 VAL Chi-restraints excluded: chain Le residue 15 THR Chi-restraints excluded: chain Le residue 84 GLU Chi-restraints excluded: chain Lf residue 56 ARG Chi-restraints excluded: chain Lf residue 88 THR Chi-restraints excluded: chain Lf residue 99 SER Chi-restraints excluded: chain Lh residue 34 LEU Chi-restraints excluded: chain Lh residue 113 LEU Chi-restraints excluded: chain Lj residue 79 ARG Chi-restraints excluded: chain Lk residue 7 ASP Chi-restraints excluded: chain Lk residue 25 ILE Chi-restraints excluded: chain Lk residue 31 THR Chi-restraints excluded: chain Lk residue 46 THR Chi-restraints excluded: chain Ll residue 27 ILE Chi-restraints excluded: chain Lq residue 25 LYS Chi-restraints excluded: chain Lq residue 26 ARG Chi-restraints excluded: chain Lq residue 206 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1459 random chunks: chunk 1174 optimal weight: 0.9990 chunk 800 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 1050 optimal weight: 0.9990 chunk 581 optimal weight: 20.0000 chunk 1203 optimal weight: 1.9990 chunk 974 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 720 optimal weight: 0.9990 chunk 1265 optimal weight: 0.8980 chunk 355 optimal weight: 4.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 CC 446 GLN CC 528 HIS ** CC 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CC 753 GLN ** CE 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CF 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CH 389 ASN ** CI 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 650 GLN CK 57 GLN ** CN 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CN 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CR 134 GLN CR 144 ASN CT 141 ASN ** CT 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CT 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CU 232 GLN CU 336 GLN CX 73 GLN ** CY 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CY 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CY 683 ASN LB 274 HIS LF 78 GLN LF 119 ASN LK 100 HIS LN 156 HIS LR 34 ASN ** LR 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LR 143 HIS LS 68 HIS ** LT 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LU 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LV 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Le 90 ASN Lh 115 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.081 165506 Z= 0.158 Angle : 0.560 13.244 237286 Z= 0.286 Chirality : 0.036 0.304 28809 Planarity : 0.005 0.069 19593 Dihedral : 21.750 179.986 57959 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.19 % Favored : 95.71 % Rotamer: Outliers : 2.92 % Allowed : 16.43 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.01 % Twisted Proline : 0.17 % 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: 0.49 (0.08), residues: 11825 helix: 1.65 (0.07), residues: 5183 sheet: -0.26 (0.12), residues: 1607 loop : -0.87 (0.09), residues: 5035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRPCY 713 HIS 0.011 0.001 HISCH 333 PHE 0.026 0.001 PHECH 277 TYR 0.029 0.001 TYRCM 142 ARG 0.013 0.000 ARGCN 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23650 Ramachandran restraints generated. 11825 Oldfield, 0 Emsley, 11825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23650 Ramachandran restraints generated. 11825 Oldfield, 0 Emsley, 11825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1963 residues out of total 10278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 292 poor density : 1671 time to evaluate : 10.190 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: CA 71 LYS cc_start: 0.7564 (OUTLIER) cc_final: 0.7059 (mttp) REVERT: CA 275 LYS cc_start: 0.7920 (mttm) cc_final: 0.7316 (mmmt) REVERT: CB 89 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7997 (tt) REVERT: CB 148 SER cc_start: 0.8991 (t) cc_final: 0.8673 (p) REVERT: CB 185 MET cc_start: 0.3862 (mmp) cc_final: 0.1528 (ttp) REVERT: CC 455 ARG cc_start: 0.7854 (mtm110) cc_final: 0.7569 (ptm-80) REVERT: CC 540 ARG cc_start: 0.8512 (mtt180) cc_final: 0.8056 (mtt180) REVERT: CC 630 ARG cc_start: 0.7956 (mmm-85) cc_final: 0.7710 (mmm160) REVERT: CC 687 ASP cc_start: 0.7411 (m-30) cc_final: 0.6853 (m-30) REVERT: CC 713 MET cc_start: 0.7666 (mtt) cc_final: 0.7295 (mtt) REVERT: CD 44 TYR cc_start: 0.6690 (OUTLIER) cc_final: 0.6462 (t80) REVERT: CD 111 ASP cc_start: 0.7662 (p0) cc_final: 0.7274 (p0) REVERT: CD 362 THR cc_start: 0.8642 (OUTLIER) cc_final: 0.8410 (t) REVERT: CE 318 ILE cc_start: 0.8885 (mm) cc_final: 0.8667 (mt) REVERT: CG 106 GLN cc_start: 0.8359 (tp-100) cc_final: 0.8034 (tp-100) REVERT: CH 54 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.6851 (mt-10) REVERT: CH 236 MET cc_start: 0.8305 (mmm) cc_final: 0.8052 (tpp) REVERT: CH 470 LYS cc_start: 0.8542 (mmtm) cc_final: 0.8306 (mmtm) REVERT: CH 509 ARG cc_start: 0.7525 (ttm110) cc_final: 0.7227 (mtm110) REVERT: CI 281 LYS cc_start: 0.8598 (mtpt) cc_final: 0.8149 (mtmt) REVERT: CK 170 ARG cc_start: 0.7967 (ptt180) cc_final: 0.7658 (ptm160) REVERT: CL 26 LYS cc_start: 0.7512 (mmmm) cc_final: 0.7054 (mttp) REVERT: CM 40 LYS cc_start: 0.6556 (mmtp) cc_final: 0.6222 (tttt) REVERT: CM 90 VAL cc_start: 0.8898 (OUTLIER) cc_final: 0.8693 (m) REVERT: CM 108 ILE cc_start: 0.8308 (mp) cc_final: 0.8074 (mp) REVERT: CO 38 MET cc_start: 0.7923 (mmm) cc_final: 0.7680 (mmm) REVERT: CP 262 TYR cc_start: 0.8675 (m-80) cc_final: 0.8376 (m-10) REVERT: CP 265 GLN cc_start: 0.8220 (tm-30) cc_final: 0.7938 (tm-30) REVERT: CP 288 PHE cc_start: 0.7672 (m-10) cc_final: 0.7371 (m-80) REVERT: CQ 120 VAL cc_start: 0.8629 (OUTLIER) cc_final: 0.8391 (m) REVERT: CR 38 SER cc_start: 0.9099 (m) cc_final: 0.8838 (m) REVERT: CT 366 LYS cc_start: 0.8711 (ttmm) cc_final: 0.8493 (ttmm) REVERT: CX 121 MET cc_start: 0.8194 (mmt) cc_final: 0.7698 (mtt) REVERT: CY 568 TYR cc_start: 0.7373 (t80) cc_final: 0.6839 (t80) REVERT: CY 602 TYR cc_start: 0.6524 (OUTLIER) cc_final: 0.5970 (t80) REVERT: CY 653 TRP cc_start: 0.7724 (t60) cc_final: 0.7475 (t60) REVERT: CY 657 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.7227 (mmm) REVERT: CY 700 ASP cc_start: 0.7888 (p0) cc_final: 0.7687 (p0) REVERT: LB 137 TYR cc_start: 0.7736 (OUTLIER) cc_final: 0.7286 (m-80) REVERT: LB 197 ARG cc_start: 0.7846 (tmm-80) cc_final: 0.7276 (ttp-170) REVERT: LB 271 MET cc_start: 0.7146 (ttp) cc_final: 0.6745 (ttp) REVERT: LE 32 ASP cc_start: 0.7346 (p0) cc_final: 0.7102 (p0) REVERT: LF 23 LYS cc_start: 0.7974 (ptmm) cc_final: 0.6951 (mmmt) REVERT: LF 88 LYS cc_start: 0.8211 (mtmm) cc_final: 0.7778 (mttm) REVERT: LF 106 ARG cc_start: 0.7853 (ttm-80) cc_final: 0.7027 (ttp80) REVERT: LF 119 ASN cc_start: 0.8478 (OUTLIER) cc_final: 0.7944 (t0) REVERT: LG 100 TYR cc_start: 0.8211 (m-80) cc_final: 0.7592 (m-80) REVERT: LG 115 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.5988 (mp0) REVERT: LG 250 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7038 (mp0) REVERT: LH 185 GLU cc_start: 0.7610 (tt0) cc_final: 0.7398 (tt0) REVERT: LK 112 ILE cc_start: 0.6277 (mt) cc_final: 0.5930 (mt) REVERT: LL 20 ARG cc_start: 0.7595 (ptp-170) cc_final: 0.7362 (ptp-170) REVERT: LL 122 ARG cc_start: 0.8707 (mmm-85) cc_final: 0.8385 (mtp85) REVERT: LM 86 GLU cc_start: 0.8341 (mp0) cc_final: 0.7850 (mp0) REVERT: LN 38 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.6928 (ttt180) REVERT: LO 30 SER cc_start: 0.8811 (t) cc_final: 0.8209 (m) REVERT: LO 80 ARG cc_start: 0.8169 (mmp80) cc_final: 0.7730 (mmm-85) REVERT: LQ 48 LYS cc_start: 0.7125 (OUTLIER) cc_final: 0.5828 (tttt) REVERT: LR 99 GLN cc_start: 0.8691 (tp40) cc_final: 0.8476 (tp40) REVERT: LS 1 MET cc_start: 0.6368 (ptm) cc_final: 0.4732 (mtt) REVERT: LS 90 MET cc_start: 0.8041 (ptm) cc_final: 0.7633 (ptm) REVERT: LS 134 ASP cc_start: 0.8886 (m-30) cc_final: 0.8627 (m-30) REVERT: LT 35 ARG cc_start: 0.6212 (mmp80) cc_final: 0.5856 (ttt180) REVERT: LU 32 LYS cc_start: 0.8475 (tppt) cc_final: 0.7859 (tptt) REVERT: LU 50 ASP cc_start: 0.6998 (OUTLIER) cc_final: 0.6715 (p0) REVERT: LX 62 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8433 (mtmt) REVERT: LY 9 SER cc_start: 0.8599 (m) cc_final: 0.8258 (p) REVERT: LY 30 MET cc_start: 0.8726 (mtp) cc_final: 0.8269 (mtp) REVERT: LY 104 VAL cc_start: 0.8589 (t) cc_final: 0.8298 (t) REVERT: Ld 98 TYR cc_start: 0.8700 (p90) cc_final: 0.7974 (p90) REVERT: Le 37 LYS cc_start: 0.7876 (mmtm) cc_final: 0.7542 (mmmm) REVERT: Le 81 LYS cc_start: 0.7693 (mmtm) cc_final: 0.7429 (mmtt) REVERT: Le 87 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8060 (tp) REVERT: Le 124 LYS cc_start: 0.7258 (mmtt) cc_final: 0.6629 (tmmt) REVERT: Lf 59 LYS cc_start: 0.8282 (tttp) cc_final: 0.7689 (mmtm) REVERT: Lg 15 ASN cc_start: 0.8767 (t0) cc_final: 0.8301 (t0) REVERT: Lh 96 ARG cc_start: 0.8156 (ttm170) cc_final: 0.7799 (ttm170) REVERT: Li 84 LYS cc_start: 0.8292 (tttt) cc_final: 0.8060 (tptt) outliers start: 292 outliers final: 178 residues processed: 1849 average time/residue: 1.4148 time to fit residues: 4470.4995 Evaluate side-chains 1739 residues out of total 10278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 1543 time to evaluate : 10.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CA residue 27 ILE Chi-restraints excluded: chain CA residue 39 LEU Chi-restraints excluded: chain CA residue 40 SER Chi-restraints excluded: chain CA residue 71 LYS Chi-restraints excluded: chain CA residue 99 ASP Chi-restraints excluded: chain CA residue 176 ILE Chi-restraints excluded: chain CA residue 195 GLU Chi-restraints excluded: chain CB residue 21 ASP Chi-restraints excluded: chain CB residue 68 THR Chi-restraints excluded: chain CB residue 70 LYS Chi-restraints excluded: chain CB residue 89 LEU Chi-restraints excluded: chain CB residue 97 VAL Chi-restraints excluded: chain CB residue 127 VAL Chi-restraints excluded: chain CB residue 183 VAL Chi-restraints excluded: chain CB residue 278 VAL Chi-restraints excluded: chain CC residue 174 ASN Chi-restraints excluded: chain CC residue 181 ASP Chi-restraints excluded: chain CC residue 191 ASN Chi-restraints excluded: chain CC residue 333 GLN Chi-restraints excluded: chain CC residue 389 SER Chi-restraints excluded: chain CC residue 434 SER Chi-restraints excluded: chain CC residue 477 VAL Chi-restraints excluded: chain CC residue 510 THR Chi-restraints excluded: chain CC residue 524 MET Chi-restraints excluded: chain CC residue 595 SER Chi-restraints excluded: chain CC residue 741 SER Chi-restraints excluded: chain CC residue 751 ASN Chi-restraints excluded: chain CC residue 770 VAL Chi-restraints excluded: chain CD residue 44 TYR Chi-restraints excluded: chain CD residue 177 THR Chi-restraints excluded: chain CD residue 362 THR Chi-restraints excluded: chain CD residue 441 ILE Chi-restraints excluded: chain CE residue 116 LEU Chi-restraints excluded: chain CE residue 135 THR Chi-restraints excluded: chain CE residue 188 VAL Chi-restraints excluded: chain CE residue 190 THR Chi-restraints excluded: chain CE residue 386 ASP Chi-restraints excluded: chain CE residue 390 LYS Chi-restraints excluded: chain CE residue 402 GLU Chi-restraints excluded: chain CE residue 445 VAL Chi-restraints excluded: chain CE residue 473 LEU Chi-restraints excluded: chain CE residue 478 VAL Chi-restraints excluded: chain CE residue 555 ILE Chi-restraints excluded: chain CF residue 97 THR Chi-restraints excluded: chain CF residue 174 MET Chi-restraints excluded: chain CF residue 180 CYS Chi-restraints excluded: chain CG residue 69 THR Chi-restraints excluded: chain CH residue 54 GLU Chi-restraints excluded: chain CH residue 140 LYS Chi-restraints excluded: chain CH residue 234 ILE Chi-restraints excluded: chain CH residue 277 PHE Chi-restraints excluded: chain CH residue 285 VAL Chi-restraints excluded: chain CH residue 399 ASN Chi-restraints excluded: chain CH residue 517 ILE Chi-restraints excluded: chain CJ residue 260 VAL Chi-restraints excluded: chain CK residue 232 THR Chi-restraints excluded: chain CL residue 18 THR Chi-restraints excluded: chain CM residue 90 VAL Chi-restraints excluded: chain CM residue 171 ASP Chi-restraints excluded: chain CN residue 4 ARG Chi-restraints excluded: chain CN residue 136 GLU Chi-restraints excluded: chain CN residue 137 VAL Chi-restraints excluded: chain CN residue 146 VAL Chi-restraints excluded: chain CN residue 161 VAL Chi-restraints excluded: chain CN residue 190 SER Chi-restraints excluded: chain CN residue 239 ASN Chi-restraints excluded: chain CP residue 329 VAL Chi-restraints excluded: chain CP residue 331 LEU Chi-restraints excluded: chain CP residue 340 VAL Chi-restraints excluded: chain CP residue 428 LEU Chi-restraints excluded: chain CP residue 436 CYS Chi-restraints excluded: chain CP residue 537 VAL Chi-restraints excluded: chain CP residue 550 SER Chi-restraints excluded: chain CQ residue 20 THR Chi-restraints excluded: chain CQ residue 120 VAL Chi-restraints excluded: chain CQ residue 147 GLU Chi-restraints excluded: chain CR residue 135 GLN Chi-restraints excluded: chain CR residue 184 VAL Chi-restraints excluded: chain CS residue 507 LEU Chi-restraints excluded: chain CS residue 819 MET Chi-restraints excluded: chain CT residue 284 GLU Chi-restraints excluded: chain CT residue 319 GLU Chi-restraints excluded: chain CT residue 573 SER Chi-restraints excluded: chain CT residue 603 VAL Chi-restraints excluded: chain CT residue 644 LEU Chi-restraints excluded: chain CU residue 190 ILE Chi-restraints excluded: chain CU residue 203 ILE Chi-restraints excluded: chain CU residue 220 VAL Chi-restraints excluded: chain CU residue 224 LYS Chi-restraints excluded: chain CU residue 229 SER Chi-restraints excluded: chain CU residue 269 THR Chi-restraints excluded: chain CU residue 331 LEU Chi-restraints excluded: chain CU residue 356 ASP Chi-restraints excluded: chain CV residue 68 VAL Chi-restraints excluded: chain CV residue 80 THR Chi-restraints excluded: chain CV residue 85 SER Chi-restraints excluded: chain CV residue 86 THR Chi-restraints excluded: chain CX residue 84 LYS Chi-restraints excluded: chain CX residue 86 LYS Chi-restraints excluded: chain CX residue 93 VAL Chi-restraints excluded: chain CX residue 95 VAL Chi-restraints excluded: chain CY residue 394 ASP Chi-restraints excluded: chain CY residue 456 ASP Chi-restraints excluded: chain CY residue 461 TYR Chi-restraints excluded: chain CY residue 490 VAL Chi-restraints excluded: chain CY residue 495 TYR Chi-restraints excluded: chain CY residue 544 THR Chi-restraints excluded: chain CY residue 554 LEU Chi-restraints excluded: chain CY residue 602 TYR Chi-restraints excluded: chain CY residue 657 MET Chi-restraints excluded: chain CY residue 669 LEU Chi-restraints excluded: chain CY residue 742 GLU Chi-restraints excluded: chain LB residue 84 MET Chi-restraints excluded: chain LB residue 101 SER Chi-restraints excluded: chain LB residue 137 TYR Chi-restraints excluded: chain LB residue 205 THR Chi-restraints excluded: chain LB residue 211 GLU Chi-restraints excluded: chain LB residue 279 VAL Chi-restraints excluded: chain LB residue 283 ILE Chi-restraints excluded: chain LB residue 362 THR Chi-restraints excluded: chain LC residue 79 SER Chi-restraints excluded: chain LC residue 100 MET Chi-restraints excluded: chain LC residue 158 VAL Chi-restraints excluded: chain LC residue 204 ARG Chi-restraints excluded: chain LC residue 238 ASP Chi-restraints excluded: chain LC residue 256 VAL Chi-restraints excluded: chain LE residue 51 SER Chi-restraints excluded: chain LE residue 52 LEU Chi-restraints excluded: chain LE residue 108 LYS Chi-restraints excluded: chain LE residue 163 LYS Chi-restraints excluded: chain LE residue 175 LYS Chi-restraints excluded: chain LF residue 18 LEU Chi-restraints excluded: chain LF residue 80 SER Chi-restraints excluded: chain LF residue 92 VAL Chi-restraints excluded: chain LF residue 119 ASN Chi-restraints excluded: chain LF residue 126 THR Chi-restraints excluded: chain LG residue 115 GLU Chi-restraints excluded: chain LG residue 167 VAL Chi-restraints excluded: chain LG residue 232 THR Chi-restraints excluded: chain LG residue 250 GLU Chi-restraints excluded: chain LH residue 47 VAL Chi-restraints excluded: chain LH residue 53 ILE Chi-restraints excluded: chain LH residue 167 CYS Chi-restraints excluded: chain LH residue 174 ILE Chi-restraints excluded: chain LK residue 111 GLU Chi-restraints excluded: chain LL residue 51 VAL Chi-restraints excluded: chain LM residue 9 THR Chi-restraints excluded: chain LM residue 20 LEU Chi-restraints excluded: chain LM residue 112 LEU Chi-restraints excluded: chain LM residue 121 MET Chi-restraints excluded: chain LN residue 11 SER Chi-restraints excluded: chain LN residue 38 ARG Chi-restraints excluded: chain LN residue 60 VAL Chi-restraints excluded: chain LO residue 61 LYS Chi-restraints excluded: chain LO residue 90 ILE Chi-restraints excluded: chain LO residue 147 VAL Chi-restraints excluded: chain LP residue 24 VAL Chi-restraints excluded: chain LQ residue 48 LYS Chi-restraints excluded: chain LQ residue 108 VAL Chi-restraints excluded: chain LQ residue 113 THR Chi-restraints excluded: chain LR residue 2 VAL Chi-restraints excluded: chain LR residue 41 ILE Chi-restraints excluded: chain LS residue 60 SER Chi-restraints excluded: chain LT residue 52 MET Chi-restraints excluded: chain LT residue 76 VAL Chi-restraints excluded: chain LT residue 80 VAL Chi-restraints excluded: chain LT residue 116 LYS Chi-restraints excluded: chain LT residue 124 VAL Chi-restraints excluded: chain LU residue 50 ASP Chi-restraints excluded: chain LU residue 59 VAL Chi-restraints excluded: chain LV residue 13 LEU Chi-restraints excluded: chain LX residue 54 SER Chi-restraints excluded: chain LX residue 62 LYS Chi-restraints excluded: chain LY residue 46 SER Chi-restraints excluded: chain LY residue 94 VAL Chi-restraints excluded: chain LZ residue 11 LEU Chi-restraints excluded: chain LZ residue 45 ILE Chi-restraints excluded: chain LZ residue 88 LEU Chi-restraints excluded: chain LZ residue 104 SER Chi-restraints excluded: chain Ld residue 117 VAL Chi-restraints excluded: chain Le residue 8 VAL Chi-restraints excluded: chain Le residue 87 LEU Chi-restraints excluded: chain Lf residue 56 ARG Chi-restraints excluded: chain Lf residue 99 SER Chi-restraints excluded: chain Lh residue 34 LEU Chi-restraints excluded: chain Lh residue 113 LEU Chi-restraints excluded: chain Li residue 25 LYS Chi-restraints excluded: chain Lj residue 15 THR Chi-restraints excluded: chain Lk residue 31 THR Chi-restraints excluded: chain Lk residue 46 THR Chi-restraints excluded: chain Ll residue 23 ILE Chi-restraints excluded: chain Ll residue 27 ILE Chi-restraints excluded: chain Lq residue 22 ASN Chi-restraints excluded: chain Lq residue 25 LYS Chi-restraints excluded: chain Lq residue 26 ARG Chi-restraints excluded: chain Lq residue 206 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1459 random chunks: chunk 474 optimal weight: 4.9990 chunk 1270 optimal weight: 4.9990 chunk 278 optimal weight: 10.0000 chunk 827 optimal weight: 7.9990 chunk 348 optimal weight: 4.9990 chunk 1411 optimal weight: 1.9990 chunk 1171 optimal weight: 4.9990 chunk 653 optimal weight: 4.9990 chunk 117 optimal weight: 10.0000 chunk 466 optimal weight: 9.9990 chunk 741 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CA 286 GLN ** CC 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CC 753 GLN CE 280 GLN ** CE 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CE 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CF 39 HIS CF 228 ASN CH 389 ASN ** CI 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 70 GLN ** CJ 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 650 GLN CK 35 ASN ** CK 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CN 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CN 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CT 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CT 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CT 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CT 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CU 232 GLN CU 336 GLN CX 73 GLN LG 141 HIS LK 100 HIS LN 195 ASN ** LP 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LR 34 ASN ** LR 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LR 143 HIS LT 139 HIS ** LU 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LV 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Le 90 ASN Lh 115 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 165506 Z= 0.409 Angle : 0.698 13.192 237286 Z= 0.354 Chirality : 0.044 0.308 28809 Planarity : 0.006 0.089 19593 Dihedral : 21.762 178.765 57952 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.85 % Favored : 95.04 % Rotamer: Outliers : 3.58 % Allowed : 17.36 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.01 % Twisted Proline : 0.17 % 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: 0.28 (0.08), residues: 11825 helix: 1.43 (0.07), residues: 5192 sheet: -0.32 (0.12), residues: 1628 loop : -0.95 (0.09), residues: 5005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRPCY 713 HIS 0.013 0.001 HISCH 333 PHE 0.031 0.002 PHECD 63 TYR 0.031 0.002 TYRCM 142 ARG 0.010 0.001 ARGCJ 669 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23650 Ramachandran restraints generated. 11825 Oldfield, 0 Emsley, 11825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23650 Ramachandran restraints generated. 11825 Oldfield, 0 Emsley, 11825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1918 residues out of total 10278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 358 poor density : 1560 time to evaluate : 10.274 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: CA 71 LYS cc_start: 0.7624 (OUTLIER) cc_final: 0.7051 (mttp) REVERT: CA 275 LYS cc_start: 0.8034 (mttm) cc_final: 0.7366 (mmmt) REVERT: CB 21 ASP cc_start: 0.7236 (OUTLIER) cc_final: 0.6975 (p0) REVERT: CB 89 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.7784 (tt) REVERT: CB 148 SER cc_start: 0.9060 (t) cc_final: 0.8713 (p) REVERT: CC 713 MET cc_start: 0.7784 (mtt) cc_final: 0.7401 (mtt) REVERT: CD 44 TYR cc_start: 0.6689 (OUTLIER) cc_final: 0.6452 (t80) REVERT: CD 111 ASP cc_start: 0.7625 (p0) cc_final: 0.7244 (p0) REVERT: CD 362 THR cc_start: 0.8683 (OUTLIER) cc_final: 0.8439 (t) REVERT: CE 318 ILE cc_start: 0.8884 (mm) cc_final: 0.8660 (mt) REVERT: CF 38 GLN cc_start: 0.7562 (mm-40) cc_final: 0.7029 (mm-40) REVERT: CH 54 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.6854 (mt-10) REVERT: CH 236 MET cc_start: 0.8361 (mmm) cc_final: 0.8140 (tpp) REVERT: CH 411 ASN cc_start: 0.7669 (m-40) cc_final: 0.7128 (m110) REVERT: CH 470 LYS cc_start: 0.8612 (mmtm) cc_final: 0.8353 (mmtm) REVERT: CI 281 LYS cc_start: 0.8689 (mtpt) cc_final: 0.8425 (mtpp) REVERT: CI 323 MET cc_start: 0.7013 (mmm) cc_final: 0.6162 (mtp) REVERT: CL 26 LYS cc_start: 0.7455 (mmmm) cc_final: 0.6889 (mttp) REVERT: CL 27 ARG cc_start: 0.7240 (mmm160) cc_final: 0.6716 (mmm-85) REVERT: CL 30 GLU cc_start: 0.7770 (tp30) cc_final: 0.7541 (tp30) REVERT: CM 40 LYS cc_start: 0.6659 (mmtp) cc_final: 0.6291 (tttt) REVERT: CM 108 ILE cc_start: 0.8469 (mp) cc_final: 0.8230 (mp) REVERT: CM 166 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.6331 (ttm-80) REVERT: CO 38 MET cc_start: 0.7928 (mmm) cc_final: 0.7658 (mmm) REVERT: CP 262 TYR cc_start: 0.8685 (m-80) cc_final: 0.8403 (m-10) REVERT: CP 265 GLN cc_start: 0.8256 (tm-30) cc_final: 0.7981 (tm-30) REVERT: CP 288 PHE cc_start: 0.7889 (m-10) cc_final: 0.7555 (m-80) REVERT: CQ 63 MET cc_start: 0.8207 (ptp) cc_final: 0.7729 (ptt) REVERT: CQ 66 ASP cc_start: 0.6976 (OUTLIER) cc_final: 0.6275 (t0) REVERT: CQ 120 VAL cc_start: 0.8701 (OUTLIER) cc_final: 0.8454 (m) REVERT: CR 38 SER cc_start: 0.9206 (m) cc_final: 0.8969 (m) REVERT: CT 366 LYS cc_start: 0.8765 (ttmm) cc_final: 0.8547 (ttmm) REVERT: CT 665 ARG cc_start: 0.7513 (ptm-80) cc_final: 0.7310 (ptm-80) REVERT: CU 332 ASP cc_start: 0.8006 (t70) cc_final: 0.7683 (t0) REVERT: CX 121 MET cc_start: 0.8442 (mmt) cc_final: 0.7735 (mtt) REVERT: CY 6 LYS cc_start: 0.7831 (mmmm) cc_final: 0.7506 (mttm) REVERT: CY 602 TYR cc_start: 0.6505 (OUTLIER) cc_final: 0.5918 (t80) REVERT: CY 653 TRP cc_start: 0.7843 (t60) cc_final: 0.7476 (t60) REVERT: Cz 49 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8147 (mp0) REVERT: LB 36 ASP cc_start: 0.7726 (OUTLIER) cc_final: 0.7203 (p0) REVERT: LB 109 HIS cc_start: 0.7246 (m90) cc_final: 0.6432 (t-90) REVERT: LB 137 TYR cc_start: 0.7915 (OUTLIER) cc_final: 0.7507 (m-80) REVERT: LB 197 ARG cc_start: 0.7980 (tmm-80) cc_final: 0.7398 (ttp-170) REVERT: LC 85 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7986 (tpt-90) REVERT: LC 189 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7649 (tptm) REVERT: LC 221 GLU cc_start: 0.7751 (mp0) cc_final: 0.7281 (mp0) REVERT: LE 32 ASP cc_start: 0.7589 (p0) cc_final: 0.7335 (p0) REVERT: LF 88 LYS cc_start: 0.8199 (mtmm) cc_final: 0.7753 (mttm) REVERT: LF 106 ARG cc_start: 0.7960 (ttm-80) cc_final: 0.7048 (ttp80) REVERT: LG 115 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.6072 (mp0) REVERT: LG 250 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7022 (mp0) REVERT: LK 86 LYS cc_start: 0.7021 (mmtt) cc_final: 0.6748 (tptp) REVERT: LK 112 ILE cc_start: 0.6686 (mt) cc_final: 0.6397 (mt) REVERT: LM 86 GLU cc_start: 0.8389 (mp0) cc_final: 0.7773 (mp0) REVERT: LN 38 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.7297 (ttt180) REVERT: LO 30 SER cc_start: 0.8904 (t) cc_final: 0.8321 (m) REVERT: LO 61 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7326 (mttm) REVERT: LO 80 ARG cc_start: 0.8281 (mmp80) cc_final: 0.7809 (mmm-85) REVERT: LP 18 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7235 (ptm-80) REVERT: LR 39 GLN cc_start: 0.7898 (tt0) cc_final: 0.7484 (tt0) REVERT: LS 90 MET cc_start: 0.8217 (ptm) cc_final: 0.7811 (ptm) REVERT: LS 134 ASP cc_start: 0.8898 (m-30) cc_final: 0.8659 (m-30) REVERT: Ld 98 TYR cc_start: 0.8778 (p90) cc_final: 0.8032 (p90) REVERT: Le 37 LYS cc_start: 0.7982 (mmtm) cc_final: 0.7662 (mmmm) REVERT: Le 81 LYS cc_start: 0.8015 (mmtm) cc_final: 0.7754 (mmtt) REVERT: Le 124 LYS cc_start: 0.7534 (mmtt) cc_final: 0.6948 (tmmt) REVERT: Lf 35 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7062 (tp30) REVERT: Lf 59 LYS cc_start: 0.8424 (tttp) cc_final: 0.7674 (mmtm) REVERT: Lh 96 ARG cc_start: 0.8265 (ttm170) cc_final: 0.7806 (ttm170) REVERT: Li 84 LYS cc_start: 0.8358 (tttt) cc_final: 0.7925 (tptp) REVERT: Lj 30 GLN cc_start: 0.7600 (mt0) cc_final: 0.7366 (tm-30) REVERT: Lj 79 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.7110 (ptt90) REVERT: Lk 7 ASP cc_start: 0.5877 (OUTLIER) cc_final: 0.5253 (p0) REVERT: Ll 19 GLN cc_start: 0.7462 (OUTLIER) cc_final: 0.6890 (mt0) REVERT: Lq 174 MET cc_start: 0.3202 (ppp) cc_final: 0.1630 (ptp) outliers start: 358 outliers final: 241 residues processed: 1799 average time/residue: 1.3870 time to fit residues: 4263.7555 Evaluate side-chains 1764 residues out of total 10278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 1499 time to evaluate : 10.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CA residue 27 ILE Chi-restraints excluded: chain CA residue 39 LEU Chi-restraints excluded: chain CA residue 40 SER Chi-restraints excluded: chain CA residue 71 LYS Chi-restraints excluded: chain CA residue 99 ASP Chi-restraints excluded: chain CA residue 176 ILE Chi-restraints excluded: chain CA residue 195 GLU Chi-restraints excluded: chain CA residue 260 ARG Chi-restraints excluded: chain CB residue 21 ASP Chi-restraints excluded: chain CB residue 68 THR Chi-restraints excluded: chain CB residue 70 LYS Chi-restraints excluded: chain CB residue 89 LEU Chi-restraints excluded: chain CB residue 97 VAL Chi-restraints excluded: chain CB residue 127 VAL Chi-restraints excluded: chain CB residue 183 VAL Chi-restraints excluded: chain CB residue 241 THR Chi-restraints excluded: chain CB residue 278 VAL Chi-restraints excluded: chain CC residue 181 ASP Chi-restraints excluded: chain CC residue 191 ASN Chi-restraints excluded: chain CC residue 333 GLN Chi-restraints excluded: chain CC residue 379 GLU Chi-restraints excluded: chain CC residue 389 SER Chi-restraints excluded: chain CC residue 434 SER Chi-restraints excluded: chain CC residue 459 VAL Chi-restraints excluded: chain CC residue 470 THR Chi-restraints excluded: chain CC residue 477 VAL Chi-restraints excluded: chain CC residue 482 LEU Chi-restraints excluded: chain CC residue 510 THR Chi-restraints excluded: chain CC residue 524 MET Chi-restraints excluded: chain CC residue 531 VAL Chi-restraints excluded: chain CC residue 595 SER Chi-restraints excluded: chain CC residue 720 ILE Chi-restraints excluded: chain CC residue 741 SER Chi-restraints excluded: chain CC residue 751 ASN Chi-restraints excluded: chain CC residue 770 VAL Chi-restraints excluded: chain CC residue 799 LEU Chi-restraints excluded: chain CD residue 44 TYR Chi-restraints excluded: chain CD residue 48 ARG Chi-restraints excluded: chain CD residue 177 THR Chi-restraints excluded: chain CD residue 342 LEU Chi-restraints excluded: chain CD residue 362 THR Chi-restraints excluded: chain CD residue 441 ILE Chi-restraints excluded: chain CE residue 135 THR Chi-restraints excluded: chain CE residue 188 VAL Chi-restraints excluded: chain CE residue 190 THR Chi-restraints excluded: chain CE residue 367 CYS Chi-restraints excluded: chain CE residue 386 ASP Chi-restraints excluded: chain CE residue 390 LYS Chi-restraints excluded: chain CE residue 402 GLU Chi-restraints excluded: chain CE residue 445 VAL Chi-restraints excluded: chain CE residue 462 LEU Chi-restraints excluded: chain CE residue 478 VAL Chi-restraints excluded: chain CE residue 555 ILE Chi-restraints excluded: chain CF residue 9 VAL Chi-restraints excluded: chain CF residue 53 LEU Chi-restraints excluded: chain CF residue 56 VAL Chi-restraints excluded: chain CF residue 97 THR Chi-restraints excluded: chain CF residue 174 MET Chi-restraints excluded: chain CG residue 62 ASP Chi-restraints excluded: chain CH residue 54 GLU Chi-restraints excluded: chain CH residue 200 THR Chi-restraints excluded: chain CH residue 228 LEU Chi-restraints excluded: chain CH residue 277 PHE Chi-restraints excluded: chain CH residue 399 ASN Chi-restraints excluded: chain CJ residue 219 VAL Chi-restraints excluded: chain CJ residue 260 VAL Chi-restraints excluded: chain CJ residue 670 ILE Chi-restraints excluded: chain CK residue 40 GLN Chi-restraints excluded: chain CK residue 63 LYS Chi-restraints excluded: chain CK residue 232 THR Chi-restraints excluded: chain CK residue 252 ASP Chi-restraints excluded: chain CL residue 18 THR Chi-restraints excluded: chain CM residue 19 LEU Chi-restraints excluded: chain CM residue 166 ARG Chi-restraints excluded: chain CM residue 171 ASP Chi-restraints excluded: chain CM residue 197 VAL Chi-restraints excluded: chain CN residue 4 ARG Chi-restraints excluded: chain CN residue 20 THR Chi-restraints excluded: chain CN residue 26 VAL Chi-restraints excluded: chain CN residue 136 GLU Chi-restraints excluded: chain CN residue 137 VAL Chi-restraints excluded: chain CN residue 146 VAL Chi-restraints excluded: chain CN residue 161 VAL Chi-restraints excluded: chain CN residue 190 SER Chi-restraints excluded: chain CN residue 210 THR Chi-restraints excluded: chain CN residue 239 ASN Chi-restraints excluded: chain CP residue 329 VAL Chi-restraints excluded: chain CP residue 331 LEU Chi-restraints excluded: chain CP residue 340 VAL Chi-restraints excluded: chain CP residue 428 LEU Chi-restraints excluded: chain CP residue 447 ILE Chi-restraints excluded: chain CP residue 466 CYS Chi-restraints excluded: chain CP residue 519 GLU Chi-restraints excluded: chain CP residue 537 VAL Chi-restraints excluded: chain CP residue 550 SER Chi-restraints excluded: chain CQ residue 20 THR Chi-restraints excluded: chain CQ residue 66 ASP Chi-restraints excluded: chain CQ residue 79 VAL Chi-restraints excluded: chain CQ residue 120 VAL Chi-restraints excluded: chain CQ residue 147 GLU Chi-restraints excluded: chain CR residue 135 GLN Chi-restraints excluded: chain CR residue 184 VAL Chi-restraints excluded: chain CR residue 234 LEU Chi-restraints excluded: chain CS residue 485 SER Chi-restraints excluded: chain CS residue 507 LEU Chi-restraints excluded: chain CS residue 707 ILE Chi-restraints excluded: chain CS residue 819 MET Chi-restraints excluded: chain CS residue 826 LEU Chi-restraints excluded: chain CT residue 284 GLU Chi-restraints excluded: chain CT residue 319 GLU Chi-restraints excluded: chain CT residue 394 GLU Chi-restraints excluded: chain CT residue 573 SER Chi-restraints excluded: chain CT residue 603 VAL Chi-restraints excluded: chain CT residue 644 LEU Chi-restraints excluded: chain CT residue 657 THR Chi-restraints excluded: chain CU residue 190 ILE Chi-restraints excluded: chain CU residue 203 ILE Chi-restraints excluded: chain CU residue 206 ASP Chi-restraints excluded: chain CU residue 211 THR Chi-restraints excluded: chain CU residue 220 VAL Chi-restraints excluded: chain CU residue 224 LYS Chi-restraints excluded: chain CU residue 229 SER Chi-restraints excluded: chain CU residue 269 THR Chi-restraints excluded: chain CU residue 331 LEU Chi-restraints excluded: chain CU residue 356 ASP Chi-restraints excluded: chain CV residue 13 SER Chi-restraints excluded: chain CV residue 68 VAL Chi-restraints excluded: chain CV residue 80 THR Chi-restraints excluded: chain CV residue 85 SER Chi-restraints excluded: chain CV residue 86 THR Chi-restraints excluded: chain CX residue 84 LYS Chi-restraints excluded: chain CX residue 86 LYS Chi-restraints excluded: chain CX residue 93 VAL Chi-restraints excluded: chain CX residue 95 VAL Chi-restraints excluded: chain CY residue 394 ASP Chi-restraints excluded: chain CY residue 456 ASP Chi-restraints excluded: chain CY residue 461 TYR Chi-restraints excluded: chain CY residue 490 VAL Chi-restraints excluded: chain CY residue 495 TYR Chi-restraints excluded: chain CY residue 544 THR Chi-restraints excluded: chain CY residue 554 LEU Chi-restraints excluded: chain CY residue 602 TYR Chi-restraints excluded: chain CY residue 669 LEU Chi-restraints excluded: chain CY residue 742 GLU Chi-restraints excluded: chain Cz residue 49 GLU Chi-restraints excluded: chain LB residue 36 ASP Chi-restraints excluded: chain LB residue 84 MET Chi-restraints excluded: chain LB residue 101 SER Chi-restraints excluded: chain LB residue 137 TYR Chi-restraints excluded: chain LB residue 167 ILE Chi-restraints excluded: chain LB residue 205 THR Chi-restraints excluded: chain LB residue 211 GLU Chi-restraints excluded: chain LB residue 278 SER Chi-restraints excluded: chain LB residue 279 VAL Chi-restraints excluded: chain LB residue 283 ILE Chi-restraints excluded: chain LB residue 362 THR Chi-restraints excluded: chain LC residue 79 SER Chi-restraints excluded: chain LC residue 85 ARG Chi-restraints excluded: chain LC residue 100 MET Chi-restraints excluded: chain LC residue 149 VAL Chi-restraints excluded: chain LC residue 158 VAL Chi-restraints excluded: chain LC residue 161 ASP Chi-restraints excluded: chain LC residue 189 LYS Chi-restraints excluded: chain LC residue 204 ARG Chi-restraints excluded: chain LC residue 216 GLU Chi-restraints excluded: chain LC residue 238 ASP Chi-restraints excluded: chain LC residue 256 VAL Chi-restraints excluded: chain LC residue 264 GLN Chi-restraints excluded: chain LE residue 51 SER Chi-restraints excluded: chain LE residue 52 LEU Chi-restraints excluded: chain LE residue 108 LYS Chi-restraints excluded: chain LE residue 163 LYS Chi-restraints excluded: chain LE residue 176 VAL Chi-restraints excluded: chain LF residue 18 LEU Chi-restraints excluded: chain LF residue 80 SER Chi-restraints excluded: chain LF residue 126 THR Chi-restraints excluded: chain LF residue 233 ASP Chi-restraints excluded: chain LG residue 74 VAL Chi-restraints excluded: chain LG residue 85 LEU Chi-restraints excluded: chain LG residue 115 GLU Chi-restraints excluded: chain LG residue 167 VAL Chi-restraints excluded: chain LG residue 183 ILE Chi-restraints excluded: chain LG residue 232 THR Chi-restraints excluded: chain LG residue 250 GLU Chi-restraints excluded: chain LH residue 34 LEU Chi-restraints excluded: chain LH residue 53 ILE Chi-restraints excluded: chain LH residue 82 VAL Chi-restraints excluded: chain LH residue 167 CYS Chi-restraints excluded: chain LH residue 174 ILE Chi-restraints excluded: chain LH residue 179 ASP Chi-restraints excluded: chain LK residue 111 GLU Chi-restraints excluded: chain LL residue 51 VAL Chi-restraints excluded: chain LM residue 9 THR Chi-restraints excluded: chain LM residue 14 VAL Chi-restraints excluded: chain LM residue 24 ASN Chi-restraints excluded: chain LM residue 52 THR Chi-restraints excluded: chain LM residue 67 ILE Chi-restraints excluded: chain LM residue 112 LEU Chi-restraints excluded: chain LM residue 121 MET Chi-restraints excluded: chain LM residue 138 ILE Chi-restraints excluded: chain LN residue 11 SER Chi-restraints excluded: chain LN residue 38 ARG Chi-restraints excluded: chain LN residue 60 VAL Chi-restraints excluded: chain LN residue 155 VAL Chi-restraints excluded: chain LO residue 61 LYS Chi-restraints excluded: chain LO residue 90 ILE Chi-restraints excluded: chain LO residue 147 VAL Chi-restraints excluded: chain LO residue 181 SER Chi-restraints excluded: chain LP residue 18 ARG Chi-restraints excluded: chain LP residue 24 VAL Chi-restraints excluded: chain LP residue 113 ILE Chi-restraints excluded: chain LP residue 141 SER Chi-restraints excluded: chain LQ residue 48 LYS Chi-restraints excluded: chain LQ residue 108 VAL Chi-restraints excluded: chain LQ residue 113 THR Chi-restraints excluded: chain LR residue 2 VAL Chi-restraints excluded: chain LR residue 14 VAL Chi-restraints excluded: chain LR residue 41 ILE Chi-restraints excluded: chain LS residue 60 SER Chi-restraints excluded: chain LS residue 97 THR Chi-restraints excluded: chain LS residue 98 SER Chi-restraints excluded: chain LT residue 52 MET Chi-restraints excluded: chain LT residue 76 VAL Chi-restraints excluded: chain LT residue 80 VAL Chi-restraints excluded: chain LT residue 116 LYS Chi-restraints excluded: chain LT residue 124 VAL Chi-restraints excluded: chain LU residue 59 VAL Chi-restraints excluded: chain LV residue 13 LEU Chi-restraints excluded: chain LX residue 54 SER Chi-restraints excluded: chain LX residue 62 LYS Chi-restraints excluded: chain LY residue 46 SER Chi-restraints excluded: chain LY residue 94 VAL Chi-restraints excluded: chain LZ residue 11 LEU Chi-restraints excluded: chain LZ residue 45 ILE Chi-restraints excluded: chain LZ residue 88 LEU Chi-restraints excluded: chain LZ residue 104 SER Chi-restraints excluded: chain Lc residue 17 LEU Chi-restraints excluded: chain Lc residue 66 SER Chi-restraints excluded: chain Ld residue 117 VAL Chi-restraints excluded: chain Le residue 8 VAL Chi-restraints excluded: chain Le residue 15 THR Chi-restraints excluded: chain Lf residue 3 SER Chi-restraints excluded: chain Lf residue 35 GLU Chi-restraints excluded: chain Lf residue 56 ARG Chi-restraints excluded: chain Lf residue 88 THR Chi-restraints excluded: chain Lf residue 99 SER Chi-restraints excluded: chain Lg residue 33 VAL Chi-restraints excluded: chain Lg residue 105 VAL Chi-restraints excluded: chain Lh residue 34 LEU Chi-restraints excluded: chain Lh residue 81 LEU Chi-restraints excluded: chain Lh residue 113 LEU Chi-restraints excluded: chain Li residue 25 LYS Chi-restraints excluded: chain Lj residue 15 THR Chi-restraints excluded: chain Lj residue 79 ARG Chi-restraints excluded: chain Lk residue 7 ASP Chi-restraints excluded: chain Lk residue 25 ILE Chi-restraints excluded: chain Lk residue 31 THR Chi-restraints excluded: chain Lk residue 46 THR Chi-restraints excluded: chain Lk residue 71 VAL Chi-restraints excluded: chain Ll residue 19 GLN Chi-restraints excluded: chain Ll residue 27 ILE Chi-restraints excluded: chain Lq residue 22 ASN Chi-restraints excluded: chain Lq residue 26 ARG Chi-restraints excluded: chain Lq residue 163 LEU Chi-restraints excluded: chain Lq residue 206 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1459 random chunks: chunk 1361 optimal weight: 0.9980 chunk 159 optimal weight: 10.0000 chunk 804 optimal weight: 5.9990 chunk 1030 optimal weight: 0.8980 chunk 798 optimal weight: 3.9990 chunk 1188 optimal weight: 1.9990 chunk 788 optimal weight: 7.9990 chunk 1406 optimal weight: 2.9990 chunk 880 optimal weight: 6.9990 chunk 857 optimal weight: 8.9990 chunk 649 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CA 286 GLN CC 170 ASN ** CC 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CC 753 GLN ** CE 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CE 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CI 209 GLN ** CI 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CJ 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 650 GLN ** CK 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CN 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CN 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CN 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CT 148 HIS ** CT 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CT 251 ASN ** CT 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CU 232 GLN CU 336 GLN LE 53 GLN LK 100 HIS LM 106 GLN LR 34 ASN ** LR 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LR 143 HIS ** LU 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LV 83 GLN Le 90 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 165506 Z= 0.230 Angle : 0.600 13.781 237286 Z= 0.306 Chirality : 0.038 0.313 28809 Planarity : 0.005 0.070 19593 Dihedral : 21.739 179.040 57948 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.32 % Favored : 95.59 % Rotamer: Outliers : 3.17 % Allowed : 18.48 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.01 % Twisted Proline : 0.17 % 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: 0.40 (0.08), residues: 11825 helix: 1.57 (0.07), residues: 5195 sheet: -0.30 (0.12), residues: 1622 loop : -0.91 (0.09), residues: 5008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRPCY 713 HIS 0.012 0.001 HISCH 333 PHE 0.028 0.002 PHECD 63 TYR 0.025 0.001 TYRCM 142 ARG 0.012 0.000 ARGCY 734 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23650 Ramachandran restraints generated. 11825 Oldfield, 0 Emsley, 11825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23650 Ramachandran restraints generated. 11825 Oldfield, 0 Emsley, 11825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1892 residues out of total 10278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 317 poor density : 1575 time to evaluate : 10.121 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 23 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7498 (mtp85) REVERT: CA 71 LYS cc_start: 0.7601 (OUTLIER) cc_final: 0.7057 (mttp) REVERT: CA 275 LYS cc_start: 0.7962 (mttm) cc_final: 0.7306 (mmmt) REVERT: CB 89 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.7852 (tt) REVERT: CB 148 SER cc_start: 0.9013 (t) cc_final: 0.8686 (p) REVERT: CC 434 SER cc_start: 0.8702 (OUTLIER) cc_final: 0.8347 (p) REVERT: CC 540 ARG cc_start: 0.8756 (mtp85) cc_final: 0.8042 (mtt180) REVERT: CC 713 MET cc_start: 0.7688 (mtt) cc_final: 0.7356 (mtt) REVERT: CD 44 TYR cc_start: 0.6822 (OUTLIER) cc_final: 0.6607 (t80) REVERT: CD 111 ASP cc_start: 0.7611 (p0) cc_final: 0.7224 (p0) REVERT: CD 362 THR cc_start: 0.8612 (OUTLIER) cc_final: 0.8370 (t) REVERT: CD 421 VAL cc_start: 0.8097 (t) cc_final: 0.7887 (m) REVERT: CE 447 ARG cc_start: 0.8238 (tpp80) cc_final: 0.7878 (mmt90) REVERT: CF 38 GLN cc_start: 0.7475 (mm-40) cc_final: 0.6921 (mm-40) REVERT: CH 54 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6809 (mt-10) REVERT: CH 411 ASN cc_start: 0.7596 (m-40) cc_final: 0.7086 (m110) REVERT: CH 470 LYS cc_start: 0.8611 (mmtm) cc_final: 0.8359 (mmtm) REVERT: CI 281 LYS cc_start: 0.8696 (mtpt) cc_final: 0.8421 (mtpp) REVERT: CI 323 MET cc_start: 0.6903 (mmm) cc_final: 0.6173 (mtp) REVERT: CJ 17 MET cc_start: 0.8408 (ttp) cc_final: 0.8146 (ttp) REVERT: CJ 134 PHE cc_start: 0.7519 (t80) cc_final: 0.7297 (t80) REVERT: CJ 656 LYS cc_start: 0.8521 (ttmm) cc_final: 0.8291 (mttp) REVERT: CK 170 ARG cc_start: 0.7986 (ptt180) cc_final: 0.7632 (ptm160) REVERT: CL 26 LYS cc_start: 0.7362 (mmmm) cc_final: 0.6842 (mttp) REVERT: CL 27 ARG cc_start: 0.7314 (mmm160) cc_final: 0.6833 (mmm-85) REVERT: CM 40 LYS cc_start: 0.6630 (mmtp) cc_final: 0.6267 (tttt) REVERT: CM 108 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.8150 (mp) REVERT: CM 166 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.6342 (ttm-80) REVERT: CN 1 MET cc_start: 0.4599 (mpp) cc_final: 0.4296 (mpp) REVERT: CO 18 LYS cc_start: 0.7802 (mttm) cc_final: 0.7450 (mptp) REVERT: CO 38 MET cc_start: 0.7953 (mmm) cc_final: 0.7666 (mmm) REVERT: CP 262 TYR cc_start: 0.8706 (m-80) cc_final: 0.8447 (m-10) REVERT: CP 265 GLN cc_start: 0.8205 (tm-30) cc_final: 0.7917 (tm-30) REVERT: CP 288 PHE cc_start: 0.7813 (m-10) cc_final: 0.7476 (m-80) REVERT: CQ 63 MET cc_start: 0.8169 (ptp) cc_final: 0.7699 (ptt) REVERT: CQ 120 VAL cc_start: 0.8689 (OUTLIER) cc_final: 0.8460 (m) REVERT: CR 38 SER cc_start: 0.9153 (m) cc_final: 0.8921 (m) REVERT: CR 178 ARG cc_start: 0.7645 (ttp80) cc_final: 0.7364 (ttp-170) REVERT: CT 245 CYS cc_start: 0.7672 (m) cc_final: 0.7470 (m) REVERT: CT 366 LYS cc_start: 0.8740 (ttmm) cc_final: 0.8505 (ttmm) REVERT: CX 113 GLN cc_start: 0.7499 (tp40) cc_final: 0.7241 (tp40) REVERT: CX 121 MET cc_start: 0.8354 (mmt) cc_final: 0.7796 (mtt) REVERT: CY 6 LYS cc_start: 0.7776 (mmmm) cc_final: 0.7213 (mttt) REVERT: CY 602 TYR cc_start: 0.6493 (t80) cc_final: 0.5922 (t80) REVERT: LB 36 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.7388 (p0) REVERT: LB 109 HIS cc_start: 0.7259 (m90) cc_final: 0.6390 (t70) REVERT: LB 137 TYR cc_start: 0.7741 (OUTLIER) cc_final: 0.7224 (m-80) REVERT: LB 197 ARG cc_start: 0.7953 (tmm-80) cc_final: 0.7373 (ttp-170) REVERT: LC 85 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7953 (tpt-90) REVERT: LC 189 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7460 (tptm) REVERT: LC 301 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.6721 (mtm110) REVERT: LE 32 ASP cc_start: 0.7654 (p0) cc_final: 0.7380 (p0) REVERT: LF 106 ARG cc_start: 0.7938 (ttm-80) cc_final: 0.7111 (ttp80) REVERT: LG 100 TYR cc_start: 0.8336 (m-80) cc_final: 0.7679 (m-80) REVERT: LG 115 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.6074 (mp0) REVERT: LG 250 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6865 (mp0) REVERT: LK 112 ILE cc_start: 0.6833 (mt) cc_final: 0.6570 (mt) REVERT: LL 20 ARG cc_start: 0.7654 (ptp-170) cc_final: 0.7392 (ptp-170) REVERT: LM 86 GLU cc_start: 0.8302 (mp0) cc_final: 0.7702 (mp0) REVERT: LN 38 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.7159 (ttt180) REVERT: LN 196 THR cc_start: 0.8412 (t) cc_final: 0.8049 (m) REVERT: LO 30 SER cc_start: 0.8898 (t) cc_final: 0.8277 (m) REVERT: LO 80 ARG cc_start: 0.8218 (mmp80) cc_final: 0.7752 (mmm-85) REVERT: LS 90 MET cc_start: 0.8033 (ptm) cc_final: 0.7622 (ptm) REVERT: LS 134 ASP cc_start: 0.8887 (m-30) cc_final: 0.8647 (m-30) REVERT: LU 27 GLN cc_start: 0.7991 (tp-100) cc_final: 0.7697 (tp40) REVERT: LU 32 LYS cc_start: 0.8547 (tppt) cc_final: 0.8275 (tmtt) REVERT: LU 41 LYS cc_start: 0.8541 (tptp) cc_final: 0.7740 (tptp) REVERT: LU 45 GLU cc_start: 0.7990 (pt0) cc_final: 0.7289 (pt0) REVERT: LU 50 ASP cc_start: 0.6897 (OUTLIER) cc_final: 0.6460 (p0) REVERT: LY 9 SER cc_start: 0.8592 (m) cc_final: 0.8299 (p) REVERT: Ld 73 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8659 (mtmt) REVERT: Ld 98 TYR cc_start: 0.8759 (p90) cc_final: 0.8047 (p90) REVERT: Le 37 LYS cc_start: 0.7916 (mmtm) cc_final: 0.7604 (mmmm) REVERT: Le 81 LYS cc_start: 0.7797 (mmtm) cc_final: 0.7527 (mmtt) REVERT: Le 87 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8235 (tp) REVERT: Le 124 LYS cc_start: 0.7398 (mmtt) cc_final: 0.6833 (tmmt) REVERT: Lf 59 LYS cc_start: 0.8338 (tttp) cc_final: 0.7653 (mmtm) REVERT: Lh 96 ARG cc_start: 0.8210 (ttm170) cc_final: 0.7765 (ttm170) REVERT: Li 84 LYS cc_start: 0.8341 (tttt) cc_final: 0.7935 (tptp) REVERT: Lk 7 ASP cc_start: 0.5729 (OUTLIER) cc_final: 0.5149 (p0) REVERT: Ll 19 GLN cc_start: 0.7328 (OUTLIER) cc_final: 0.6810 (mt0) REVERT: Lq 174 MET cc_start: 0.3355 (ppp) cc_final: 0.1897 (ptp) outliers start: 317 outliers final: 235 residues processed: 1774 average time/residue: 1.4242 time to fit residues: 4323.4316 Evaluate side-chains 1771 residues out of total 10278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 1513 time to evaluate : 10.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CA residue 23 ARG Chi-restraints excluded: chain CA residue 27 ILE Chi-restraints excluded: chain CA residue 39 LEU Chi-restraints excluded: chain CA residue 40 SER Chi-restraints excluded: chain CA residue 71 LYS Chi-restraints excluded: chain CA residue 99 ASP Chi-restraints excluded: chain CA residue 176 ILE Chi-restraints excluded: chain CA residue 195 GLU Chi-restraints excluded: chain CB residue 21 ASP Chi-restraints excluded: chain CB residue 68 THR Chi-restraints excluded: chain CB residue 70 LYS Chi-restraints excluded: chain CB residue 89 LEU Chi-restraints excluded: chain CB residue 97 VAL Chi-restraints excluded: chain CB residue 127 VAL Chi-restraints excluded: chain CB residue 183 VAL Chi-restraints excluded: chain CB residue 185 MET Chi-restraints excluded: chain CB residue 241 THR Chi-restraints excluded: chain CB residue 278 VAL Chi-restraints excluded: chain CC residue 181 ASP Chi-restraints excluded: chain CC residue 191 ASN Chi-restraints excluded: chain CC residue 389 SER Chi-restraints excluded: chain CC residue 434 SER Chi-restraints excluded: chain CC residue 459 VAL Chi-restraints excluded: chain CC residue 477 VAL Chi-restraints excluded: chain CC residue 480 TRP Chi-restraints excluded: chain CC residue 510 THR Chi-restraints excluded: chain CC residue 524 MET Chi-restraints excluded: chain CC residue 531 VAL Chi-restraints excluded: chain CC residue 586 THR Chi-restraints excluded: chain CC residue 595 SER Chi-restraints excluded: chain CC residue 720 ILE Chi-restraints excluded: chain CC residue 741 SER Chi-restraints excluded: chain CC residue 751 ASN Chi-restraints excluded: chain CC residue 770 VAL Chi-restraints excluded: chain CC residue 799 LEU Chi-restraints excluded: chain CD residue 44 TYR Chi-restraints excluded: chain CD residue 48 ARG Chi-restraints excluded: chain CD residue 177 THR Chi-restraints excluded: chain CD residue 362 THR Chi-restraints excluded: chain CD residue 441 ILE Chi-restraints excluded: chain CE residue 135 THR Chi-restraints excluded: chain CE residue 151 VAL Chi-restraints excluded: chain CE residue 188 VAL Chi-restraints excluded: chain CE residue 190 THR Chi-restraints excluded: chain CE residue 386 ASP Chi-restraints excluded: chain CE residue 402 GLU Chi-restraints excluded: chain CE residue 445 VAL Chi-restraints excluded: chain CE residue 462 LEU Chi-restraints excluded: chain CE residue 473 LEU Chi-restraints excluded: chain CE residue 478 VAL Chi-restraints excluded: chain CE residue 555 ILE Chi-restraints excluded: chain CF residue 97 THR Chi-restraints excluded: chain CF residue 116 PHE Chi-restraints excluded: chain CF residue 174 MET Chi-restraints excluded: chain CF residue 180 CYS Chi-restraints excluded: chain CG residue 153 GLU Chi-restraints excluded: chain CH residue 54 GLU Chi-restraints excluded: chain CH residue 69 VAL Chi-restraints excluded: chain CH residue 137 THR Chi-restraints excluded: chain CH residue 140 LYS Chi-restraints excluded: chain CH residue 200 THR Chi-restraints excluded: chain CH residue 234 ILE Chi-restraints excluded: chain CH residue 277 PHE Chi-restraints excluded: chain CH residue 399 ASN Chi-restraints excluded: chain CI residue 224 THR Chi-restraints excluded: chain CI residue 309 GLU Chi-restraints excluded: chain CJ residue 219 VAL Chi-restraints excluded: chain CJ residue 260 VAL Chi-restraints excluded: chain CJ residue 585 LEU Chi-restraints excluded: chain CJ residue 670 ILE Chi-restraints excluded: chain CK residue 40 GLN Chi-restraints excluded: chain CK residue 57 GLN Chi-restraints excluded: chain CK residue 63 LYS Chi-restraints excluded: chain CK residue 232 THR Chi-restraints excluded: chain CK residue 252 ASP Chi-restraints excluded: chain CL residue 18 THR Chi-restraints excluded: chain CM residue 19 LEU Chi-restraints excluded: chain CM residue 108 ILE Chi-restraints excluded: chain CM residue 166 ARG Chi-restraints excluded: chain CM residue 171 ASP Chi-restraints excluded: chain CM residue 175 ILE Chi-restraints excluded: chain CM residue 197 VAL Chi-restraints excluded: chain CN residue 4 ARG Chi-restraints excluded: chain CN residue 136 GLU Chi-restraints excluded: chain CN residue 137 VAL Chi-restraints excluded: chain CN residue 146 VAL Chi-restraints excluded: chain CN residue 161 VAL Chi-restraints excluded: chain CN residue 190 SER Chi-restraints excluded: chain CN residue 206 THR Chi-restraints excluded: chain CN residue 210 THR Chi-restraints excluded: chain CN residue 239 ASN Chi-restraints excluded: chain CP residue 329 VAL Chi-restraints excluded: chain CP residue 331 LEU Chi-restraints excluded: chain CP residue 340 VAL Chi-restraints excluded: chain CP residue 428 LEU Chi-restraints excluded: chain CP residue 447 ILE Chi-restraints excluded: chain CP residue 466 CYS Chi-restraints excluded: chain CP residue 537 VAL Chi-restraints excluded: chain CP residue 550 SER Chi-restraints excluded: chain CQ residue 20 THR Chi-restraints excluded: chain CQ residue 120 VAL Chi-restraints excluded: chain CR residue 17 ILE Chi-restraints excluded: chain CR residue 135 GLN Chi-restraints excluded: chain CR residue 184 VAL Chi-restraints excluded: chain CR residue 234 LEU Chi-restraints excluded: chain CS residue 485 SER Chi-restraints excluded: chain CS residue 499 VAL Chi-restraints excluded: chain CS residue 507 LEU Chi-restraints excluded: chain CS residue 694 ASP Chi-restraints excluded: chain CS residue 819 MET Chi-restraints excluded: chain CT residue 284 GLU Chi-restraints excluded: chain CT residue 319 GLU Chi-restraints excluded: chain CT residue 394 GLU Chi-restraints excluded: chain CT residue 573 SER Chi-restraints excluded: chain CT residue 603 VAL Chi-restraints excluded: chain CT residue 644 LEU Chi-restraints excluded: chain CT residue 657 THR Chi-restraints excluded: chain CU residue 190 ILE Chi-restraints excluded: chain CU residue 203 ILE Chi-restraints excluded: chain CU residue 206 ASP Chi-restraints excluded: chain CU residue 211 THR Chi-restraints excluded: chain CU residue 220 VAL Chi-restraints excluded: chain CU residue 224 LYS Chi-restraints excluded: chain CU residue 229 SER Chi-restraints excluded: chain CU residue 269 THR Chi-restraints excluded: chain CU residue 331 LEU Chi-restraints excluded: chain CU residue 356 ASP Chi-restraints excluded: chain CV residue 68 VAL Chi-restraints excluded: chain CV residue 80 THR Chi-restraints excluded: chain CV residue 85 SER Chi-restraints excluded: chain CV residue 86 THR Chi-restraints excluded: chain CX residue 84 LYS Chi-restraints excluded: chain CX residue 86 LYS Chi-restraints excluded: chain CX residue 93 VAL Chi-restraints excluded: chain CX residue 95 VAL Chi-restraints excluded: chain CY residue 394 ASP Chi-restraints excluded: chain CY residue 456 ASP Chi-restraints excluded: chain CY residue 461 TYR Chi-restraints excluded: chain CY residue 490 VAL Chi-restraints excluded: chain CY residue 495 TYR Chi-restraints excluded: chain CY residue 544 THR Chi-restraints excluded: chain CY residue 554 LEU Chi-restraints excluded: chain CY residue 669 LEU Chi-restraints excluded: chain CY residue 742 GLU Chi-restraints excluded: chain LB residue 36 ASP Chi-restraints excluded: chain LB residue 84 MET Chi-restraints excluded: chain LB residue 101 SER Chi-restraints excluded: chain LB residue 137 TYR Chi-restraints excluded: chain LB residue 205 THR Chi-restraints excluded: chain LB residue 211 GLU Chi-restraints excluded: chain LB residue 278 SER Chi-restraints excluded: chain LB residue 279 VAL Chi-restraints excluded: chain LB residue 283 ILE Chi-restraints excluded: chain LB residue 362 THR Chi-restraints excluded: chain LC residue 61 THR Chi-restraints excluded: chain LC residue 79 SER Chi-restraints excluded: chain LC residue 85 ARG Chi-restraints excluded: chain LC residue 100 MET Chi-restraints excluded: chain LC residue 149 VAL Chi-restraints excluded: chain LC residue 158 VAL Chi-restraints excluded: chain LC residue 161 ASP Chi-restraints excluded: chain LC residue 189 LYS Chi-restraints excluded: chain LC residue 204 ARG Chi-restraints excluded: chain LC residue 216 GLU Chi-restraints excluded: chain LC residue 238 ASP Chi-restraints excluded: chain LC residue 256 VAL Chi-restraints excluded: chain LC residue 301 ARG Chi-restraints excluded: chain LE residue 51 SER Chi-restraints excluded: chain LE residue 52 LEU Chi-restraints excluded: chain LE residue 108 LYS Chi-restraints excluded: chain LE residue 163 LYS Chi-restraints excluded: chain LF residue 18 LEU Chi-restraints excluded: chain LF residue 80 SER Chi-restraints excluded: chain LF residue 126 THR Chi-restraints excluded: chain LF residue 233 ASP Chi-restraints excluded: chain LG residue 85 LEU Chi-restraints excluded: chain LG residue 115 GLU Chi-restraints excluded: chain LG residue 167 VAL Chi-restraints excluded: chain LG residue 232 THR Chi-restraints excluded: chain LG residue 250 GLU Chi-restraints excluded: chain LH residue 34 LEU Chi-restraints excluded: chain LH residue 53 ILE Chi-restraints excluded: chain LH residue 82 VAL Chi-restraints excluded: chain LH residue 167 CYS Chi-restraints excluded: chain LH residue 174 ILE Chi-restraints excluded: chain LH residue 179 ASP Chi-restraints excluded: chain LK residue 111 GLU Chi-restraints excluded: chain LL residue 51 VAL Chi-restraints excluded: chain LL residue 69 THR Chi-restraints excluded: chain LM residue 9 THR Chi-restraints excluded: chain LM residue 14 VAL Chi-restraints excluded: chain LM residue 52 THR Chi-restraints excluded: chain LM residue 112 LEU Chi-restraints excluded: chain LM residue 121 MET Chi-restraints excluded: chain LM residue 138 ILE Chi-restraints excluded: chain LN residue 11 SER Chi-restraints excluded: chain LN residue 38 ARG Chi-restraints excluded: chain LN residue 60 VAL Chi-restraints excluded: chain LN residue 149 ASN Chi-restraints excluded: chain LO residue 61 LYS Chi-restraints excluded: chain LO residue 90 ILE Chi-restraints excluded: chain LO residue 147 VAL Chi-restraints excluded: chain LO residue 181 SER Chi-restraints excluded: chain LP residue 24 VAL Chi-restraints excluded: chain LP residue 141 SER Chi-restraints excluded: chain LQ residue 48 LYS Chi-restraints excluded: chain LQ residue 49 SER Chi-restraints excluded: chain LQ residue 82 MET Chi-restraints excluded: chain LQ residue 85 ILE Chi-restraints excluded: chain LQ residue 108 VAL Chi-restraints excluded: chain LQ residue 113 THR Chi-restraints excluded: chain LR residue 2 VAL Chi-restraints excluded: chain LR residue 41 ILE Chi-restraints excluded: chain LS residue 60 SER Chi-restraints excluded: chain LS residue 120 SER Chi-restraints excluded: chain LT residue 52 MET Chi-restraints excluded: chain LT residue 63 VAL Chi-restraints excluded: chain LT residue 80 VAL Chi-restraints excluded: chain LT residue 116 LYS Chi-restraints excluded: chain LT residue 124 VAL Chi-restraints excluded: chain LU residue 50 ASP Chi-restraints excluded: chain LU residue 59 VAL Chi-restraints excluded: chain LV residue 13 LEU Chi-restraints excluded: chain LV residue 79 VAL Chi-restraints excluded: chain LV residue 81 VAL Chi-restraints excluded: chain LX residue 54 SER Chi-restraints excluded: chain LX residue 62 LYS Chi-restraints excluded: chain LY residue 40 GLU Chi-restraints excluded: chain LY residue 46 SER Chi-restraints excluded: chain LY residue 94 VAL Chi-restraints excluded: chain LZ residue 11 LEU Chi-restraints excluded: chain LZ residue 45 ILE Chi-restraints excluded: chain LZ residue 88 LEU Chi-restraints excluded: chain LZ residue 104 SER Chi-restraints excluded: chain Ld residue 73 LYS Chi-restraints excluded: chain Ld residue 117 VAL Chi-restraints excluded: chain Le residue 8 VAL Chi-restraints excluded: chain Le residue 15 THR Chi-restraints excluded: chain Le residue 19 MET Chi-restraints excluded: chain Le residue 87 LEU Chi-restraints excluded: chain Lf residue 56 ARG Chi-restraints excluded: chain Lf residue 99 SER Chi-restraints excluded: chain Lg residue 33 VAL Chi-restraints excluded: chain Lh residue 34 LEU Chi-restraints excluded: chain Lh residue 113 LEU Chi-restraints excluded: chain Li residue 25 LYS Chi-restraints excluded: chain Lj residue 15 THR Chi-restraints excluded: chain Lk residue 7 ASP Chi-restraints excluded: chain Lk residue 31 THR Chi-restraints excluded: chain Lk residue 46 THR Chi-restraints excluded: chain Lk residue 71 VAL Chi-restraints excluded: chain Ll residue 19 GLN Chi-restraints excluded: chain Ll residue 23 ILE Chi-restraints excluded: chain Ll residue 27 ILE Chi-restraints excluded: chain Lq residue 22 ASN Chi-restraints excluded: chain Lq residue 26 ARG Chi-restraints excluded: chain Lq residue 163 LEU Chi-restraints excluded: chain Lq residue 206 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1459 random chunks: chunk 869 optimal weight: 9.9990 chunk 561 optimal weight: 4.9990 chunk 839 optimal weight: 7.9990 chunk 423 optimal weight: 30.0000 chunk 276 optimal weight: 20.0000 chunk 272 optimal weight: 10.0000 chunk 894 optimal weight: 0.6980 chunk 958 optimal weight: 5.9990 chunk 695 optimal weight: 50.0000 chunk 131 optimal weight: 4.9990 chunk 1105 optimal weight: 0.9980 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CA 286 GLN ** CC 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CE 391 GLN ** CE 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CF 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CI 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 417 HIS ** CJ 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CK 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CN 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CN 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CN 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CT 215 HIS CT 251 ASN ** CT 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CT 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CU 232 GLN CU 336 GLN LK 100 HIS LM 106 GLN ** LP 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LR 34 ASN ** LR 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LU 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LV 76 HIS LV 83 GLN Le 90 ASN Ll 17 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 165506 Z= 0.336 Angle : 0.659 14.427 237286 Z= 0.335 Chirality : 0.041 0.355 28809 Planarity : 0.006 0.078 19593 Dihedral : 21.728 178.901 57948 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.84 % Favored : 95.07 % Rotamer: Outliers : 3.36 % Allowed : 18.73 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.01 % Twisted Proline : 0.17 % 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: 0.32 (0.08), residues: 11825 helix: 1.50 (0.07), residues: 5191 sheet: -0.31 (0.12), residues: 1617 loop : -0.96 (0.09), residues: 5017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRPLR 95 HIS 0.014 0.001 HISCH 333 PHE 0.028 0.002 PHECH 473 TYR 0.022 0.002 TYRCH 447 ARG 0.013 0.001 ARGCH 337 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23650 Ramachandran restraints generated. 11825 Oldfield, 0 Emsley, 11825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23650 Ramachandran restraints generated. 11825 Oldfield, 0 Emsley, 11825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1874 residues out of total 10278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 336 poor density : 1538 time to evaluate : 10.183 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: CA 23 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7405 (mtp85) REVERT: CA 71 LYS cc_start: 0.7612 (OUTLIER) cc_final: 0.7053 (mttp) REVERT: CB 21 ASP cc_start: 0.7240 (OUTLIER) cc_final: 0.7009 (p0) REVERT: CB 52 ASP cc_start: 0.7530 (p0) cc_final: 0.7229 (p0) REVERT: CB 89 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.7942 (tt) REVERT: CB 126 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7092 (ptt180) REVERT: CB 148 SER cc_start: 0.9029 (t) cc_final: 0.8699 (p) REVERT: CC 540 ARG cc_start: 0.8708 (mtp85) cc_final: 0.8018 (mtt180) REVERT: CC 713 MET cc_start: 0.7733 (mtt) cc_final: 0.7423 (mtt) REVERT: CD 111 ASP cc_start: 0.7489 (p0) cc_final: 0.7090 (p0) REVERT: CD 362 THR cc_start: 0.8601 (OUTLIER) cc_final: 0.8357 (t) REVERT: CD 421 VAL cc_start: 0.8086 (t) cc_final: 0.7872 (m) REVERT: CF 38 GLN cc_start: 0.7481 (mm-40) cc_final: 0.6947 (mm-40) REVERT: CH 54 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.6822 (mt-10) REVERT: CH 470 LYS cc_start: 0.8620 (mmtm) cc_final: 0.8363 (mmtm) REVERT: CI 281 LYS cc_start: 0.8720 (mtpt) cc_final: 0.8445 (mtpp) REVERT: CI 323 MET cc_start: 0.6988 (mmm) cc_final: 0.6209 (mtp) REVERT: CJ 17 MET cc_start: 0.8472 (ttp) cc_final: 0.8144 (ttp) REVERT: CJ 134 PHE cc_start: 0.7692 (t80) cc_final: 0.7466 (t80) REVERT: CJ 267 GLU cc_start: 0.7731 (pm20) cc_final: 0.7422 (pt0) REVERT: CL 26 LYS cc_start: 0.7436 (mmmm) cc_final: 0.6859 (mttp) REVERT: CL 27 ARG cc_start: 0.7366 (mmm160) cc_final: 0.6814 (mmm-85) REVERT: CL 76 ARG cc_start: 0.6837 (tpp-160) cc_final: 0.6584 (tpp-160) REVERT: CM 40 LYS cc_start: 0.6639 (mmtp) cc_final: 0.6289 (tttt) REVERT: CM 108 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8165 (mp) REVERT: CM 166 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.6328 (ttm-80) REVERT: CN 1 MET cc_start: 0.4702 (mpp) cc_final: 0.4321 (mpp) REVERT: CP 262 TYR cc_start: 0.8693 (m-80) cc_final: 0.8433 (m-10) REVERT: CP 265 GLN cc_start: 0.8203 (tm-30) cc_final: 0.7933 (tm-30) REVERT: CP 288 PHE cc_start: 0.7839 (m-10) cc_final: 0.7474 (m-80) REVERT: CQ 63 MET cc_start: 0.8198 (ptp) cc_final: 0.7743 (ptt) REVERT: CQ 66 ASP cc_start: 0.6985 (OUTLIER) cc_final: 0.6350 (t0) REVERT: CQ 120 VAL cc_start: 0.8700 (OUTLIER) cc_final: 0.8473 (m) REVERT: CR 38 SER cc_start: 0.9180 (m) cc_final: 0.8960 (m) REVERT: CR 178 ARG cc_start: 0.7634 (ttp80) cc_final: 0.7326 (ttp-170) REVERT: CT 245 CYS cc_start: 0.7686 (m) cc_final: 0.7471 (m) REVERT: CT 366 LYS cc_start: 0.8759 (ttmm) cc_final: 0.8524 (ttmm) REVERT: CU 336 GLN cc_start: 0.7656 (mt0) cc_final: 0.7378 (mt0) REVERT: CV 23 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.7294 (mt0) REVERT: CV 72 ASN cc_start: 0.7913 (t0) cc_final: 0.7390 (t0) REVERT: CX 113 GLN cc_start: 0.7516 (tp40) cc_final: 0.7264 (tp40) REVERT: CX 121 MET cc_start: 0.8427 (mmt) cc_final: 0.7810 (mtt) REVERT: CY 6 LYS cc_start: 0.7771 (mmmm) cc_final: 0.7204 (mttt) REVERT: CY 602 TYR cc_start: 0.6535 (OUTLIER) cc_final: 0.5898 (t80) REVERT: LB 36 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7483 (p0) REVERT: LB 47 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.7762 (mtt) REVERT: LB 109 HIS cc_start: 0.7241 (m90) cc_final: 0.6459 (t-90) REVERT: LB 137 TYR cc_start: 0.7825 (OUTLIER) cc_final: 0.7282 (m-80) REVERT: LB 197 ARG cc_start: 0.7968 (tmm-80) cc_final: 0.7373 (ttp-170) REVERT: LB 309 MET cc_start: 0.8381 (mmm) cc_final: 0.7796 (mtm) REVERT: LC 85 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7954 (tpt-90) REVERT: LC 189 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7523 (tptm) REVERT: LC 221 GLU cc_start: 0.7817 (mp0) cc_final: 0.7408 (mp0) REVERT: LC 301 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.6774 (mtm110) REVERT: LE 32 ASP cc_start: 0.7690 (p0) cc_final: 0.7114 (p0) REVERT: LG 115 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.6038 (mp0) REVERT: LG 250 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.6994 (mp0) REVERT: LH 19 SER cc_start: 0.8140 (t) cc_final: 0.7837 (p) REVERT: LH 21 LYS cc_start: 0.8047 (tptt) cc_final: 0.7716 (tptp) REVERT: LK 112 ILE cc_start: 0.7135 (mt) cc_final: 0.6886 (mt) REVERT: LK 119 LYS cc_start: 0.8117 (mmtp) cc_final: 0.7327 (mttt) REVERT: LL 20 ARG cc_start: 0.7642 (ptp-170) cc_final: 0.7416 (ptp-170) REVERT: LM 86 GLU cc_start: 0.8370 (mp0) cc_final: 0.7729 (mp0) REVERT: LN 38 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.7234 (ttt180) REVERT: LN 182 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7734 (mmtp) REVERT: LN 196 THR cc_start: 0.8427 (t) cc_final: 0.8062 (m) REVERT: LO 30 SER cc_start: 0.8917 (t) cc_final: 0.8311 (m) REVERT: LO 61 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7305 (mttm) REVERT: LO 80 ARG cc_start: 0.8265 (mmp80) cc_final: 0.7797 (mmm-85) REVERT: LP 18 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7304 (ptm-80) REVERT: LR 39 GLN cc_start: 0.7893 (tt0) cc_final: 0.7441 (tt0) REVERT: LR 95 TRP cc_start: 0.9020 (t-100) cc_final: 0.8777 (t-100) REVERT: LS 24 LEU cc_start: 0.8651 (mp) cc_final: 0.8447 (mp) REVERT: LS 90 MET cc_start: 0.8144 (ptm) cc_final: 0.7737 (ptm) REVERT: LS 134 ASP cc_start: 0.8889 (m-30) cc_final: 0.8656 (m-30) REVERT: LT 35 ARG cc_start: 0.6472 (mmp80) cc_final: 0.5962 (mmm160) REVERT: LU 41 LYS cc_start: 0.8584 (tptp) cc_final: 0.7819 (tptp) REVERT: LU 45 GLU cc_start: 0.8028 (pt0) cc_final: 0.7324 (pt0) REVERT: LU 50 ASP cc_start: 0.6808 (OUTLIER) cc_final: 0.6353 (p0) REVERT: Ld 73 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8677 (mtmt) REVERT: Ld 98 TYR cc_start: 0.8776 (p90) cc_final: 0.8042 (p90) REVERT: Le 81 LYS cc_start: 0.8000 (mmtm) cc_final: 0.7735 (mmtt) REVERT: Le 87 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8366 (tp) REVERT: Le 124 LYS cc_start: 0.7485 (mmtt) cc_final: 0.6894 (tmmt) REVERT: Lf 35 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7114 (tp30) REVERT: Lf 59 LYS cc_start: 0.8413 (tttp) cc_final: 0.7649 (mmtm) REVERT: Li 84 LYS cc_start: 0.8370 (tttt) cc_final: 0.7937 (tptp) REVERT: Lk 7 ASP cc_start: 0.5772 (OUTLIER) cc_final: 0.5076 (p0) REVERT: Ll 19 GLN cc_start: 0.7278 (OUTLIER) cc_final: 0.6784 (mt0) REVERT: Lq 210 MET cc_start: 0.6022 (mmp) cc_final: 0.5468 (mmp) outliers start: 336 outliers final: 248 residues processed: 1754 average time/residue: 1.4277 time to fit residues: 4278.8333 Evaluate side-chains 1751 residues out of total 10278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 279 poor density : 1472 time to evaluate : 10.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CA residue 23 ARG Chi-restraints excluded: chain CA residue 27 ILE Chi-restraints excluded: chain CA residue 39 LEU Chi-restraints excluded: chain CA residue 40 SER Chi-restraints excluded: chain CA residue 71 LYS Chi-restraints excluded: chain CA residue 99 ASP Chi-restraints excluded: chain CA residue 176 ILE Chi-restraints excluded: chain CA residue 195 GLU Chi-restraints excluded: chain CA residue 246 GLN Chi-restraints excluded: chain CA residue 260 ARG Chi-restraints excluded: chain CB residue 21 ASP Chi-restraints excluded: chain CB residue 68 THR Chi-restraints excluded: chain CB residue 70 LYS Chi-restraints excluded: chain CB residue 89 LEU Chi-restraints excluded: chain CB residue 97 VAL Chi-restraints excluded: chain CB residue 126 ARG Chi-restraints excluded: chain CB residue 127 VAL Chi-restraints excluded: chain CB residue 183 VAL Chi-restraints excluded: chain CB residue 185 MET Chi-restraints excluded: chain CB residue 241 THR Chi-restraints excluded: chain CB residue 278 VAL Chi-restraints excluded: chain CC residue 181 ASP Chi-restraints excluded: chain CC residue 191 ASN Chi-restraints excluded: chain CC residue 333 GLN Chi-restraints excluded: chain CC residue 379 GLU Chi-restraints excluded: chain CC residue 389 SER Chi-restraints excluded: chain CC residue 459 VAL Chi-restraints excluded: chain CC residue 477 VAL Chi-restraints excluded: chain CC residue 480 TRP Chi-restraints excluded: chain CC residue 482 LEU Chi-restraints excluded: chain CC residue 510 THR Chi-restraints excluded: chain CC residue 524 MET Chi-restraints excluded: chain CC residue 531 VAL Chi-restraints excluded: chain CC residue 586 THR Chi-restraints excluded: chain CC residue 595 SER Chi-restraints excluded: chain CC residue 741 SER Chi-restraints excluded: chain CC residue 751 ASN Chi-restraints excluded: chain CC residue 770 VAL Chi-restraints excluded: chain CC residue 799 LEU Chi-restraints excluded: chain CD residue 48 ARG Chi-restraints excluded: chain CD residue 177 THR Chi-restraints excluded: chain CD residue 362 THR Chi-restraints excluded: chain CD residue 441 ILE Chi-restraints excluded: chain CE residue 135 THR Chi-restraints excluded: chain CE residue 151 VAL Chi-restraints excluded: chain CE residue 188 VAL Chi-restraints excluded: chain CE residue 190 THR Chi-restraints excluded: chain CE residue 386 ASP Chi-restraints excluded: chain CE residue 402 GLU Chi-restraints excluded: chain CE residue 445 VAL Chi-restraints excluded: chain CE residue 462 LEU Chi-restraints excluded: chain CE residue 478 VAL Chi-restraints excluded: chain CE residue 555 ILE Chi-restraints excluded: chain CF residue 53 LEU Chi-restraints excluded: chain CF residue 56 VAL Chi-restraints excluded: chain CF residue 116 PHE Chi-restraints excluded: chain CF residue 174 MET Chi-restraints excluded: chain CH residue 54 GLU Chi-restraints excluded: chain CH residue 69 VAL Chi-restraints excluded: chain CH residue 137 THR Chi-restraints excluded: chain CH residue 140 LYS Chi-restraints excluded: chain CH residue 200 THR Chi-restraints excluded: chain CH residue 234 ILE Chi-restraints excluded: chain CH residue 277 PHE Chi-restraints excluded: chain CH residue 399 ASN Chi-restraints excluded: chain CI residue 224 THR Chi-restraints excluded: chain CJ residue 219 VAL Chi-restraints excluded: chain CJ residue 260 VAL Chi-restraints excluded: chain CJ residue 374 LEU Chi-restraints excluded: chain CJ residue 585 LEU Chi-restraints excluded: chain CJ residue 670 ILE Chi-restraints excluded: chain CK residue 40 GLN Chi-restraints excluded: chain CK residue 57 GLN Chi-restraints excluded: chain CK residue 63 LYS Chi-restraints excluded: chain CK residue 152 THR Chi-restraints excluded: chain CK residue 232 THR Chi-restraints excluded: chain CK residue 252 ASP Chi-restraints excluded: chain CL residue 18 THR Chi-restraints excluded: chain CM residue 17 THR Chi-restraints excluded: chain CM residue 19 LEU Chi-restraints excluded: chain CM residue 108 ILE Chi-restraints excluded: chain CM residue 166 ARG Chi-restraints excluded: chain CM residue 171 ASP Chi-restraints excluded: chain CM residue 197 VAL Chi-restraints excluded: chain CN residue 4 ARG Chi-restraints excluded: chain CN residue 20 THR Chi-restraints excluded: chain CN residue 26 VAL Chi-restraints excluded: chain CN residue 136 GLU Chi-restraints excluded: chain CN residue 137 VAL Chi-restraints excluded: chain CN residue 146 VAL Chi-restraints excluded: chain CN residue 161 VAL Chi-restraints excluded: chain CN residue 190 SER Chi-restraints excluded: chain CN residue 206 THR Chi-restraints excluded: chain CN residue 210 THR Chi-restraints excluded: chain CN residue 239 ASN Chi-restraints excluded: chain CP residue 234 MET Chi-restraints excluded: chain CP residue 329 VAL Chi-restraints excluded: chain CP residue 331 LEU Chi-restraints excluded: chain CP residue 340 VAL Chi-restraints excluded: chain CP residue 428 LEU Chi-restraints excluded: chain CP residue 433 THR Chi-restraints excluded: chain CP residue 447 ILE Chi-restraints excluded: chain CP residue 466 CYS Chi-restraints excluded: chain CP residue 509 VAL Chi-restraints excluded: chain CP residue 537 VAL Chi-restraints excluded: chain CP residue 550 SER Chi-restraints excluded: chain CQ residue 20 THR Chi-restraints excluded: chain CQ residue 66 ASP Chi-restraints excluded: chain CQ residue 79 VAL Chi-restraints excluded: chain CQ residue 120 VAL Chi-restraints excluded: chain CR residue 17 ILE Chi-restraints excluded: chain CR residue 135 GLN Chi-restraints excluded: chain CR residue 184 VAL Chi-restraints excluded: chain CR residue 234 LEU Chi-restraints excluded: chain CS residue 485 SER Chi-restraints excluded: chain CS residue 499 VAL Chi-restraints excluded: chain CS residue 507 LEU Chi-restraints excluded: chain CS residue 707 ILE Chi-restraints excluded: chain CS residue 819 MET Chi-restraints excluded: chain CT residue 211 VAL Chi-restraints excluded: chain CT residue 284 GLU Chi-restraints excluded: chain CT residue 319 GLU Chi-restraints excluded: chain CT residue 394 GLU Chi-restraints excluded: chain CT residue 573 SER Chi-restraints excluded: chain CT residue 644 LEU Chi-restraints excluded: chain CT residue 657 THR Chi-restraints excluded: chain CU residue 190 ILE Chi-restraints excluded: chain CU residue 203 ILE Chi-restraints excluded: chain CU residue 206 ASP Chi-restraints excluded: chain CU residue 211 THR Chi-restraints excluded: chain CU residue 220 VAL Chi-restraints excluded: chain CU residue 224 LYS Chi-restraints excluded: chain CU residue 229 SER Chi-restraints excluded: chain CU residue 269 THR Chi-restraints excluded: chain CU residue 331 LEU Chi-restraints excluded: chain CU residue 356 ASP Chi-restraints excluded: chain CV residue 13 SER Chi-restraints excluded: chain CV residue 23 GLN Chi-restraints excluded: chain CV residue 68 VAL Chi-restraints excluded: chain CV residue 80 THR Chi-restraints excluded: chain CV residue 85 SER Chi-restraints excluded: chain CV residue 86 THR Chi-restraints excluded: chain CX residue 84 LYS Chi-restraints excluded: chain CX residue 86 LYS Chi-restraints excluded: chain CX residue 93 VAL Chi-restraints excluded: chain CX residue 95 VAL Chi-restraints excluded: chain CY residue 394 ASP Chi-restraints excluded: chain CY residue 456 ASP Chi-restraints excluded: chain CY residue 461 TYR Chi-restraints excluded: chain CY residue 490 VAL Chi-restraints excluded: chain CY residue 495 TYR Chi-restraints excluded: chain CY residue 544 THR Chi-restraints excluded: chain CY residue 554 LEU Chi-restraints excluded: chain CY residue 602 TYR Chi-restraints excluded: chain CY residue 669 LEU Chi-restraints excluded: chain CY residue 742 GLU Chi-restraints excluded: chain LB residue 36 ASP Chi-restraints excluded: chain LB residue 47 MET Chi-restraints excluded: chain LB residue 84 MET Chi-restraints excluded: chain LB residue 101 SER Chi-restraints excluded: chain LB residue 137 TYR Chi-restraints excluded: chain LB residue 205 THR Chi-restraints excluded: chain LB residue 211 GLU Chi-restraints excluded: chain LB residue 278 SER Chi-restraints excluded: chain LB residue 279 VAL Chi-restraints excluded: chain LB residue 283 ILE Chi-restraints excluded: chain LB residue 362 THR Chi-restraints excluded: chain LC residue 61 THR Chi-restraints excluded: chain LC residue 79 SER Chi-restraints excluded: chain LC residue 85 ARG Chi-restraints excluded: chain LC residue 100 MET Chi-restraints excluded: chain LC residue 149 VAL Chi-restraints excluded: chain LC residue 158 VAL Chi-restraints excluded: chain LC residue 161 ASP Chi-restraints excluded: chain LC residue 189 LYS Chi-restraints excluded: chain LC residue 204 ARG Chi-restraints excluded: chain LC residue 216 GLU Chi-restraints excluded: chain LC residue 238 ASP Chi-restraints excluded: chain LC residue 256 VAL Chi-restraints excluded: chain LC residue 264 GLN Chi-restraints excluded: chain LC residue 301 ARG Chi-restraints excluded: chain LE residue 51 SER Chi-restraints excluded: chain LE residue 52 LEU Chi-restraints excluded: chain LE residue 108 LYS Chi-restraints excluded: chain LE residue 163 LYS Chi-restraints excluded: chain LF residue 18 LEU Chi-restraints excluded: chain LF residue 80 SER Chi-restraints excluded: chain LF residue 126 THR Chi-restraints excluded: chain LF residue 233 ASP Chi-restraints excluded: chain LG residue 74 VAL Chi-restraints excluded: chain LG residue 85 LEU Chi-restraints excluded: chain LG residue 97 LEU Chi-restraints excluded: chain LG residue 115 GLU Chi-restraints excluded: chain LG residue 121 GLU Chi-restraints excluded: chain LG residue 167 VAL Chi-restraints excluded: chain LG residue 232 THR Chi-restraints excluded: chain LG residue 250 GLU Chi-restraints excluded: chain LH residue 34 LEU Chi-restraints excluded: chain LH residue 53 ILE Chi-restraints excluded: chain LH residue 82 VAL Chi-restraints excluded: chain LH residue 167 CYS Chi-restraints excluded: chain LH residue 174 ILE Chi-restraints excluded: chain LH residue 179 ASP Chi-restraints excluded: chain LK residue 111 GLU Chi-restraints excluded: chain LL residue 51 VAL Chi-restraints excluded: chain LM residue 9 THR Chi-restraints excluded: chain LM residue 14 VAL Chi-restraints excluded: chain LM residue 52 THR Chi-restraints excluded: chain LM residue 112 LEU Chi-restraints excluded: chain LM residue 121 MET Chi-restraints excluded: chain LM residue 138 ILE Chi-restraints excluded: chain LN residue 11 SER Chi-restraints excluded: chain LN residue 38 ARG Chi-restraints excluded: chain LN residue 60 VAL Chi-restraints excluded: chain LN residue 155 VAL Chi-restraints excluded: chain LN residue 182 LYS Chi-restraints excluded: chain LO residue 61 LYS Chi-restraints excluded: chain LO residue 90 ILE Chi-restraints excluded: chain LO residue 147 VAL Chi-restraints excluded: chain LP residue 18 ARG Chi-restraints excluded: chain LP residue 24 VAL Chi-restraints excluded: chain LQ residue 48 LYS Chi-restraints excluded: chain LQ residue 49 SER Chi-restraints excluded: chain LQ residue 75 VAL Chi-restraints excluded: chain LQ residue 82 MET Chi-restraints excluded: chain LQ residue 108 VAL Chi-restraints excluded: chain LQ residue 113 THR Chi-restraints excluded: chain LR residue 2 VAL Chi-restraints excluded: chain LR residue 41 ILE Chi-restraints excluded: chain LS residue 60 SER Chi-restraints excluded: chain LS residue 98 SER Chi-restraints excluded: chain LT residue 52 MET Chi-restraints excluded: chain LT residue 63 VAL Chi-restraints excluded: chain LT residue 80 VAL Chi-restraints excluded: chain LT residue 116 LYS Chi-restraints excluded: chain LT residue 124 VAL Chi-restraints excluded: chain LU residue 50 ASP Chi-restraints excluded: chain LU residue 59 VAL Chi-restraints excluded: chain LU residue 103 VAL Chi-restraints excluded: chain LV residue 13 LEU Chi-restraints excluded: chain LV residue 79 VAL Chi-restraints excluded: chain LV residue 81 VAL Chi-restraints excluded: chain LX residue 54 SER Chi-restraints excluded: chain LY residue 40 GLU Chi-restraints excluded: chain LY residue 46 SER Chi-restraints excluded: chain LZ residue 11 LEU Chi-restraints excluded: chain LZ residue 45 ILE Chi-restraints excluded: chain LZ residue 88 LEU Chi-restraints excluded: chain LZ residue 104 SER Chi-restraints excluded: chain Lc residue 66 SER Chi-restraints excluded: chain Ld residue 73 LYS Chi-restraints excluded: chain Ld residue 117 VAL Chi-restraints excluded: chain Le residue 8 VAL Chi-restraints excluded: chain Le residue 15 THR Chi-restraints excluded: chain Le residue 19 MET Chi-restraints excluded: chain Le residue 87 LEU Chi-restraints excluded: chain Lf residue 35 GLU Chi-restraints excluded: chain Lf residue 56 ARG Chi-restraints excluded: chain Lf residue 88 THR Chi-restraints excluded: chain Lf residue 99 SER Chi-restraints excluded: chain Lg residue 33 VAL Chi-restraints excluded: chain Lg residue 105 VAL Chi-restraints excluded: chain Lh residue 34 LEU Chi-restraints excluded: chain Lh residue 81 LEU Chi-restraints excluded: chain Lh residue 113 LEU Chi-restraints excluded: chain Li residue 25 LYS Chi-restraints excluded: chain Lj residue 15 THR Chi-restraints excluded: chain Lj residue 79 ARG Chi-restraints excluded: chain Lk residue 7 ASP Chi-restraints excluded: chain Lk residue 31 THR Chi-restraints excluded: chain Lk residue 46 THR Chi-restraints excluded: chain Lk residue 71 VAL Chi-restraints excluded: chain Ll residue 19 GLN Chi-restraints excluded: chain Ll residue 27 ILE Chi-restraints excluded: chain Lq residue 22 ASN Chi-restraints excluded: chain Lq residue 25 LYS Chi-restraints excluded: chain Lq residue 26 ARG Chi-restraints excluded: chain Lq residue 163 LEU Chi-restraints excluded: chain Lq residue 206 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1459 random chunks: chunk 1279 optimal weight: 20.0000 chunk 1347 optimal weight: 5.9990 chunk 1229 optimal weight: 0.8980 chunk 1310 optimal weight: 10.0000 chunk 1346 optimal weight: 20.0000 chunk 788 optimal weight: 7.9990 chunk 570 optimal weight: 7.9990 chunk 1029 optimal weight: 10.0000 chunk 402 optimal weight: 0.8980 chunk 1184 optimal weight: 0.9980 chunk 1239 optimal weight: 1.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CA 286 GLN ** CC 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CC 753 GLN CE 443 HIS ** CE 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CF 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CH 123 GLN ** CI 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CK 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CN 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CN 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CN 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CT 251 ASN ** CT 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CT 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CU 232 GLN LK 100 HIS LM 106 GLN LR 34 ASN ** LR 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LU 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LV 83 GLN Le 90 ASN Ll 17 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 165506 Z= 0.231 Angle : 0.605 15.340 237286 Z= 0.308 Chirality : 0.038 0.392 28809 Planarity : 0.005 0.070 19593 Dihedral : 21.708 179.172 57948 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.36 % Favored : 95.54 % Rotamer: Outliers : 3.07 % Allowed : 19.06 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.01 % Twisted Proline : 0.17 % 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: 0.42 (0.08), residues: 11825 helix: 1.59 (0.07), residues: 5206 sheet: -0.33 (0.12), residues: 1619 loop : -0.90 (0.09), residues: 5000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRPCY 387 HIS 0.014 0.001 HISCH 333 PHE 0.034 0.002 PHECD 63 TYR 0.039 0.001 TYRCD 44 ARG 0.019 0.000 ARGCE 450 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23650 Ramachandran restraints generated. 11825 Oldfield, 0 Emsley, 11825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23650 Ramachandran restraints generated. 11825 Oldfield, 0 Emsley, 11825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1850 residues out of total 10278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 307 poor density : 1543 time to evaluate : 10.198 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: CA 23 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.7421 (mtp85) REVERT: CA 71 LYS cc_start: 0.7597 (OUTLIER) cc_final: 0.7047 (mttp) REVERT: CA 112 THR cc_start: 0.8705 (t) cc_final: 0.8455 (m) REVERT: CB 52 ASP cc_start: 0.7481 (p0) cc_final: 0.7279 (p0) REVERT: CB 89 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.7852 (tt) REVERT: CB 126 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7117 (ptt180) REVERT: CB 148 SER cc_start: 0.9006 (t) cc_final: 0.8691 (p) REVERT: CC 189 ASP cc_start: 0.8315 (p0) cc_final: 0.8072 (p0) REVERT: CC 455 ARG cc_start: 0.8027 (mtm110) cc_final: 0.7622 (ptm-80) REVERT: CC 540 ARG cc_start: 0.8712 (mtp85) cc_final: 0.8040 (mtt180) REVERT: CC 713 MET cc_start: 0.7602 (mtt) cc_final: 0.7344 (mtt) REVERT: CD 111 ASP cc_start: 0.7485 (p0) cc_final: 0.7081 (p0) REVERT: CD 362 THR cc_start: 0.8586 (OUTLIER) cc_final: 0.8335 (t) REVERT: CD 421 VAL cc_start: 0.8079 (t) cc_final: 0.7848 (m) REVERT: CF 38 GLN cc_start: 0.7460 (mm-40) cc_final: 0.6959 (mm-40) REVERT: CH 54 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.6789 (mt-10) REVERT: CH 470 LYS cc_start: 0.8631 (mmtm) cc_final: 0.8399 (mmtm) REVERT: CH 509 ARG cc_start: 0.7645 (ttm110) cc_final: 0.7428 (mtm110) REVERT: CI 281 LYS cc_start: 0.8691 (mtpt) cc_final: 0.8413 (mtpp) REVERT: CJ 17 MET cc_start: 0.8404 (ttp) cc_final: 0.8114 (ttp) REVERT: CJ 656 LYS cc_start: 0.8482 (ttmm) cc_final: 0.8282 (mttp) REVERT: CK 170 ARG cc_start: 0.8009 (ptt180) cc_final: 0.7635 (ptm160) REVERT: CL 26 LYS cc_start: 0.7460 (mmmm) cc_final: 0.6904 (mttp) REVERT: CL 27 ARG cc_start: 0.7361 (mmm160) cc_final: 0.6888 (mmm-85) REVERT: CL 76 ARG cc_start: 0.6821 (tpp-160) cc_final: 0.6596 (tpp-160) REVERT: CM 40 LYS cc_start: 0.6672 (mmtp) cc_final: 0.6313 (tttt) REVERT: CM 106 ARG cc_start: 0.7742 (ttt-90) cc_final: 0.7382 (ttp-110) REVERT: CM 108 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.8127 (mp) REVERT: CM 166 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.6558 (ttm-80) REVERT: CN 1 MET cc_start: 0.4700 (mpp) cc_final: 0.4345 (mpp) REVERT: CP 265 GLN cc_start: 0.8137 (tm-30) cc_final: 0.7866 (tm-30) REVERT: CP 288 PHE cc_start: 0.7784 (m-10) cc_final: 0.7454 (m-80) REVERT: CQ 63 MET cc_start: 0.8170 (ptp) cc_final: 0.7679 (ptt) REVERT: CQ 120 VAL cc_start: 0.8681 (OUTLIER) cc_final: 0.8463 (m) REVERT: CR 38 SER cc_start: 0.9155 (m) cc_final: 0.8921 (m) REVERT: CR 178 ARG cc_start: 0.7624 (ttp80) cc_final: 0.7322 (ttp-170) REVERT: CS 436 MET cc_start: 0.6200 (mmm) cc_final: 0.5925 (mmm) REVERT: CT 245 CYS cc_start: 0.7623 (m) cc_final: 0.7422 (m) REVERT: CT 366 LYS cc_start: 0.8733 (ttmm) cc_final: 0.8505 (ttmm) REVERT: CX 121 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.7852 (mtt) REVERT: CY 6 LYS cc_start: 0.7637 (mmmm) cc_final: 0.7051 (mttt) REVERT: CY 602 TYR cc_start: 0.6513 (OUTLIER) cc_final: 0.5876 (t80) REVERT: Cz 54 LYS cc_start: 0.8402 (mmtt) cc_final: 0.8189 (mmtt) REVERT: LB 36 ASP cc_start: 0.7799 (OUTLIER) cc_final: 0.7452 (p0) REVERT: LB 47 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7523 (mtt) REVERT: LB 137 TYR cc_start: 0.7710 (OUTLIER) cc_final: 0.7327 (m-80) REVERT: LB 197 ARG cc_start: 0.7936 (tmm-80) cc_final: 0.7346 (ttp-170) REVERT: LB 309 MET cc_start: 0.8371 (mmm) cc_final: 0.7773 (mtm) REVERT: LC 85 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7932 (tpt-90) REVERT: LC 189 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7405 (tptm) REVERT: LC 221 GLU cc_start: 0.7781 (mp0) cc_final: 0.7360 (mp0) REVERT: LC 301 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.6800 (mtm110) REVERT: LE 32 ASP cc_start: 0.7643 (p0) cc_final: 0.7249 (p0) REVERT: LF 106 ARG cc_start: 0.7918 (ttm-80) cc_final: 0.7085 (ttp80) REVERT: LG 100 TYR cc_start: 0.8334 (m-80) cc_final: 0.7726 (m-80) REVERT: LG 115 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.6058 (mp0) REVERT: LG 250 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7081 (mp0) REVERT: LH 19 SER cc_start: 0.8417 (t) cc_final: 0.8120 (p) REVERT: LK 112 ILE cc_start: 0.7204 (mt) cc_final: 0.6972 (mt) REVERT: LK 119 LYS cc_start: 0.8203 (mmtp) cc_final: 0.7324 (mttt) REVERT: LL 20 ARG cc_start: 0.7590 (ptp-170) cc_final: 0.7345 (ptp-170) REVERT: LM 86 GLU cc_start: 0.8351 (mp0) cc_final: 0.7719 (mp0) REVERT: LN 38 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.7106 (ttt180) REVERT: LN 182 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7658 (mmtp) REVERT: LN 196 THR cc_start: 0.8411 (t) cc_final: 0.8063 (m) REVERT: LO 30 SER cc_start: 0.8911 (t) cc_final: 0.8273 (m) REVERT: LO 80 ARG cc_start: 0.8233 (mmp80) cc_final: 0.7818 (mmm-85) REVERT: LP 18 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7323 (ptm-80) REVERT: LR 39 GLN cc_start: 0.7854 (tt0) cc_final: 0.7397 (tt0) REVERT: LR 95 TRP cc_start: 0.8988 (t-100) cc_final: 0.8753 (t-100) REVERT: LS 90 MET cc_start: 0.8058 (ptm) cc_final: 0.7660 (ptm) REVERT: LS 134 ASP cc_start: 0.8864 (m-30) cc_final: 0.8632 (m-30) REVERT: LT 35 ARG cc_start: 0.6633 (mmp80) cc_final: 0.6055 (ttt-90) REVERT: LU 41 LYS cc_start: 0.8586 (tptp) cc_final: 0.8264 (tptp) REVERT: LU 50 ASP cc_start: 0.6773 (OUTLIER) cc_final: 0.6314 (p0) REVERT: LX 74 LYS cc_start: 0.8500 (mmmm) cc_final: 0.7798 (mtmm) REVERT: LY 9 SER cc_start: 0.8590 (m) cc_final: 0.8295 (p) REVERT: Ld 73 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8567 (mtmt) REVERT: Ld 98 TYR cc_start: 0.8716 (p90) cc_final: 0.7947 (p90) REVERT: Le 81 LYS cc_start: 0.7947 (mmtm) cc_final: 0.7681 (mmtt) REVERT: Le 124 LYS cc_start: 0.7432 (mmtt) cc_final: 0.6844 (tmmt) REVERT: Lf 35 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7172 (tp30) REVERT: Lf 59 LYS cc_start: 0.8391 (tttp) cc_final: 0.7617 (mmtm) REVERT: Lh 96 ARG cc_start: 0.8262 (ttm-80) cc_final: 0.7924 (ttm170) REVERT: Li 84 LYS cc_start: 0.8359 (tttt) cc_final: 0.7945 (tptp) REVERT: Lk 7 ASP cc_start: 0.5677 (OUTLIER) cc_final: 0.4997 (p0) REVERT: Ll 19 GLN cc_start: 0.7240 (OUTLIER) cc_final: 0.6747 (mt0) REVERT: Lq 174 MET cc_start: 0.2979 (ppp) cc_final: 0.1306 (ttp) outliers start: 307 outliers final: 241 residues processed: 1732 average time/residue: 1.5245 time to fit residues: 4542.9929 Evaluate side-chains 1744 residues out of total 10278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 268 poor density : 1476 time to evaluate : 10.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CA residue 23 ARG Chi-restraints excluded: chain CA residue 27 ILE Chi-restraints excluded: chain CA residue 39 LEU Chi-restraints excluded: chain CA residue 40 SER Chi-restraints excluded: chain CA residue 71 LYS Chi-restraints excluded: chain CA residue 99 ASP Chi-restraints excluded: chain CA residue 176 ILE Chi-restraints excluded: chain CA residue 195 GLU Chi-restraints excluded: chain CA residue 246 GLN Chi-restraints excluded: chain CA residue 260 ARG Chi-restraints excluded: chain CB residue 21 ASP Chi-restraints excluded: chain CB residue 68 THR Chi-restraints excluded: chain CB residue 70 LYS Chi-restraints excluded: chain CB residue 89 LEU Chi-restraints excluded: chain CB residue 97 VAL Chi-restraints excluded: chain CB residue 126 ARG Chi-restraints excluded: chain CB residue 127 VAL Chi-restraints excluded: chain CB residue 183 VAL Chi-restraints excluded: chain CB residue 185 MET Chi-restraints excluded: chain CB residue 241 THR Chi-restraints excluded: chain CB residue 278 VAL Chi-restraints excluded: chain CC residue 181 ASP Chi-restraints excluded: chain CC residue 191 ASN Chi-restraints excluded: chain CC residue 379 GLU Chi-restraints excluded: chain CC residue 389 SER Chi-restraints excluded: chain CC residue 459 VAL Chi-restraints excluded: chain CC residue 477 VAL Chi-restraints excluded: chain CC residue 480 TRP Chi-restraints excluded: chain CC residue 482 LEU Chi-restraints excluded: chain CC residue 510 THR Chi-restraints excluded: chain CC residue 524 MET Chi-restraints excluded: chain CC residue 531 VAL Chi-restraints excluded: chain CC residue 595 SER Chi-restraints excluded: chain CC residue 741 SER Chi-restraints excluded: chain CC residue 751 ASN Chi-restraints excluded: chain CC residue 770 VAL Chi-restraints excluded: chain CC residue 799 LEU Chi-restraints excluded: chain CD residue 48 ARG Chi-restraints excluded: chain CD residue 177 THR Chi-restraints excluded: chain CD residue 362 THR Chi-restraints excluded: chain CD residue 441 ILE Chi-restraints excluded: chain CE residue 134 MET Chi-restraints excluded: chain CE residue 135 THR Chi-restraints excluded: chain CE residue 151 VAL Chi-restraints excluded: chain CE residue 188 VAL Chi-restraints excluded: chain CE residue 190 THR Chi-restraints excluded: chain CE residue 367 CYS Chi-restraints excluded: chain CE residue 386 ASP Chi-restraints excluded: chain CE residue 402 GLU Chi-restraints excluded: chain CE residue 445 VAL Chi-restraints excluded: chain CE residue 462 LEU Chi-restraints excluded: chain CE residue 473 LEU Chi-restraints excluded: chain CE residue 478 VAL Chi-restraints excluded: chain CE residue 555 ILE Chi-restraints excluded: chain CF residue 9 VAL Chi-restraints excluded: chain CF residue 56 VAL Chi-restraints excluded: chain CF residue 116 PHE Chi-restraints excluded: chain CF residue 174 MET Chi-restraints excluded: chain CH residue 54 GLU Chi-restraints excluded: chain CH residue 69 VAL Chi-restraints excluded: chain CH residue 137 THR Chi-restraints excluded: chain CH residue 140 LYS Chi-restraints excluded: chain CH residue 200 THR Chi-restraints excluded: chain CH residue 234 ILE Chi-restraints excluded: chain CH residue 277 PHE Chi-restraints excluded: chain CH residue 399 ASN Chi-restraints excluded: chain CI residue 224 THR Chi-restraints excluded: chain CI residue 309 GLU Chi-restraints excluded: chain CJ residue 219 VAL Chi-restraints excluded: chain CJ residue 260 VAL Chi-restraints excluded: chain CJ residue 374 LEU Chi-restraints excluded: chain CJ residue 585 LEU Chi-restraints excluded: chain CJ residue 670 ILE Chi-restraints excluded: chain CK residue 40 GLN Chi-restraints excluded: chain CK residue 57 GLN Chi-restraints excluded: chain CK residue 63 LYS Chi-restraints excluded: chain CK residue 152 THR Chi-restraints excluded: chain CK residue 232 THR Chi-restraints excluded: chain CK residue 252 ASP Chi-restraints excluded: chain CL residue 18 THR Chi-restraints excluded: chain CM residue 19 LEU Chi-restraints excluded: chain CM residue 108 ILE Chi-restraints excluded: chain CM residue 166 ARG Chi-restraints excluded: chain CM residue 171 ASP Chi-restraints excluded: chain CM residue 197 VAL Chi-restraints excluded: chain CN residue 4 ARG Chi-restraints excluded: chain CN residue 20 THR Chi-restraints excluded: chain CN residue 136 GLU Chi-restraints excluded: chain CN residue 137 VAL Chi-restraints excluded: chain CN residue 146 VAL Chi-restraints excluded: chain CN residue 161 VAL Chi-restraints excluded: chain CN residue 190 SER Chi-restraints excluded: chain CN residue 206 THR Chi-restraints excluded: chain CN residue 210 THR Chi-restraints excluded: chain CN residue 239 ASN Chi-restraints excluded: chain CP residue 234 MET Chi-restraints excluded: chain CP residue 270 ILE Chi-restraints excluded: chain CP residue 329 VAL Chi-restraints excluded: chain CP residue 331 LEU Chi-restraints excluded: chain CP residue 340 VAL Chi-restraints excluded: chain CP residue 428 LEU Chi-restraints excluded: chain CP residue 447 ILE Chi-restraints excluded: chain CP residue 466 CYS Chi-restraints excluded: chain CP residue 509 VAL Chi-restraints excluded: chain CP residue 537 VAL Chi-restraints excluded: chain CP residue 550 SER Chi-restraints excluded: chain CQ residue 20 THR Chi-restraints excluded: chain CQ residue 120 VAL Chi-restraints excluded: chain CR residue 135 GLN Chi-restraints excluded: chain CR residue 184 VAL Chi-restraints excluded: chain CR residue 234 LEU Chi-restraints excluded: chain CS residue 485 SER Chi-restraints excluded: chain CS residue 499 VAL Chi-restraints excluded: chain CS residue 707 ILE Chi-restraints excluded: chain CS residue 819 MET Chi-restraints excluded: chain CT residue 211 VAL Chi-restraints excluded: chain CT residue 284 GLU Chi-restraints excluded: chain CT residue 319 GLU Chi-restraints excluded: chain CT residue 394 GLU Chi-restraints excluded: chain CT residue 573 SER Chi-restraints excluded: chain CT residue 603 VAL Chi-restraints excluded: chain CT residue 657 THR Chi-restraints excluded: chain CT residue 679 MET Chi-restraints excluded: chain CU residue 190 ILE Chi-restraints excluded: chain CU residue 203 ILE Chi-restraints excluded: chain CU residue 206 ASP Chi-restraints excluded: chain CU residue 211 THR Chi-restraints excluded: chain CU residue 220 VAL Chi-restraints excluded: chain CU residue 229 SER Chi-restraints excluded: chain CU residue 269 THR Chi-restraints excluded: chain CU residue 331 LEU Chi-restraints excluded: chain CU residue 356 ASP Chi-restraints excluded: chain CV residue 68 VAL Chi-restraints excluded: chain CV residue 80 THR Chi-restraints excluded: chain CV residue 85 SER Chi-restraints excluded: chain CV residue 86 THR Chi-restraints excluded: chain CX residue 84 LYS Chi-restraints excluded: chain CX residue 86 LYS Chi-restraints excluded: chain CX residue 93 VAL Chi-restraints excluded: chain CX residue 95 VAL Chi-restraints excluded: chain CX residue 121 MET Chi-restraints excluded: chain CY residue 394 ASP Chi-restraints excluded: chain CY residue 461 TYR Chi-restraints excluded: chain CY residue 490 VAL Chi-restraints excluded: chain CY residue 495 TYR Chi-restraints excluded: chain CY residue 544 THR Chi-restraints excluded: chain CY residue 554 LEU Chi-restraints excluded: chain CY residue 602 TYR Chi-restraints excluded: chain CY residue 669 LEU Chi-restraints excluded: chain CY residue 742 GLU Chi-restraints excluded: chain LB residue 36 ASP Chi-restraints excluded: chain LB residue 47 MET Chi-restraints excluded: chain LB residue 84 MET Chi-restraints excluded: chain LB residue 101 SER Chi-restraints excluded: chain LB residue 137 TYR Chi-restraints excluded: chain LB residue 205 THR Chi-restraints excluded: chain LB residue 211 GLU Chi-restraints excluded: chain LB residue 278 SER Chi-restraints excluded: chain LB residue 279 VAL Chi-restraints excluded: chain LB residue 283 ILE Chi-restraints excluded: chain LB residue 362 THR Chi-restraints excluded: chain LC residue 61 THR Chi-restraints excluded: chain LC residue 79 SER Chi-restraints excluded: chain LC residue 85 ARG Chi-restraints excluded: chain LC residue 100 MET Chi-restraints excluded: chain LC residue 149 VAL Chi-restraints excluded: chain LC residue 158 VAL Chi-restraints excluded: chain LC residue 161 ASP Chi-restraints excluded: chain LC residue 189 LYS Chi-restraints excluded: chain LC residue 204 ARG Chi-restraints excluded: chain LC residue 238 ASP Chi-restraints excluded: chain LC residue 256 VAL Chi-restraints excluded: chain LC residue 301 ARG Chi-restraints excluded: chain LE residue 51 SER Chi-restraints excluded: chain LE residue 108 LYS Chi-restraints excluded: chain LE residue 163 LYS Chi-restraints excluded: chain LE residue 172 ASN Chi-restraints excluded: chain LF residue 18 LEU Chi-restraints excluded: chain LF residue 80 SER Chi-restraints excluded: chain LF residue 126 THR Chi-restraints excluded: chain LF residue 136 VAL Chi-restraints excluded: chain LF residue 233 ASP Chi-restraints excluded: chain LG residue 85 LEU Chi-restraints excluded: chain LG residue 115 GLU Chi-restraints excluded: chain LG residue 167 VAL Chi-restraints excluded: chain LG residue 232 THR Chi-restraints excluded: chain LG residue 250 GLU Chi-restraints excluded: chain LH residue 15 ASN Chi-restraints excluded: chain LH residue 34 LEU Chi-restraints excluded: chain LH residue 53 ILE Chi-restraints excluded: chain LH residue 82 VAL Chi-restraints excluded: chain LH residue 167 CYS Chi-restraints excluded: chain LH residue 174 ILE Chi-restraints excluded: chain LH residue 179 ASP Chi-restraints excluded: chain LK residue 111 GLU Chi-restraints excluded: chain LL residue 51 VAL Chi-restraints excluded: chain LM residue 9 THR Chi-restraints excluded: chain LM residue 14 VAL Chi-restraints excluded: chain LM residue 52 THR Chi-restraints excluded: chain LM residue 112 LEU Chi-restraints excluded: chain LM residue 121 MET Chi-restraints excluded: chain LM residue 138 ILE Chi-restraints excluded: chain LN residue 11 SER Chi-restraints excluded: chain LN residue 38 ARG Chi-restraints excluded: chain LN residue 60 VAL Chi-restraints excluded: chain LN residue 155 VAL Chi-restraints excluded: chain LN residue 182 LYS Chi-restraints excluded: chain LO residue 61 LYS Chi-restraints excluded: chain LO residue 90 ILE Chi-restraints excluded: chain LO residue 147 VAL Chi-restraints excluded: chain LP residue 18 ARG Chi-restraints excluded: chain LP residue 24 VAL Chi-restraints excluded: chain LP residue 140 MET Chi-restraints excluded: chain LQ residue 48 LYS Chi-restraints excluded: chain LQ residue 49 SER Chi-restraints excluded: chain LQ residue 82 MET Chi-restraints excluded: chain LQ residue 108 VAL Chi-restraints excluded: chain LQ residue 113 THR Chi-restraints excluded: chain LR residue 2 VAL Chi-restraints excluded: chain LR residue 41 ILE Chi-restraints excluded: chain LS residue 60 SER Chi-restraints excluded: chain LS residue 97 THR Chi-restraints excluded: chain LS residue 98 SER Chi-restraints excluded: chain LT residue 52 MET Chi-restraints excluded: chain LT residue 63 VAL Chi-restraints excluded: chain LT residue 80 VAL Chi-restraints excluded: chain LT residue 116 LYS Chi-restraints excluded: chain LT residue 124 VAL Chi-restraints excluded: chain LU residue 50 ASP Chi-restraints excluded: chain LU residue 59 VAL Chi-restraints excluded: chain LV residue 13 LEU Chi-restraints excluded: chain LV residue 79 VAL Chi-restraints excluded: chain LV residue 81 VAL Chi-restraints excluded: chain LX residue 54 SER Chi-restraints excluded: chain LY residue 40 GLU Chi-restraints excluded: chain LY residue 46 SER Chi-restraints excluded: chain LZ residue 11 LEU Chi-restraints excluded: chain LZ residue 45 ILE Chi-restraints excluded: chain LZ residue 88 LEU Chi-restraints excluded: chain LZ residue 104 SER Chi-restraints excluded: chain Lc residue 27 VAL Chi-restraints excluded: chain Lc residue 66 SER Chi-restraints excluded: chain Ld residue 73 LYS Chi-restraints excluded: chain Ld residue 117 VAL Chi-restraints excluded: chain Le residue 8 VAL Chi-restraints excluded: chain Le residue 15 THR Chi-restraints excluded: chain Le residue 19 MET Chi-restraints excluded: chain Lf residue 35 GLU Chi-restraints excluded: chain Lf residue 56 ARG Chi-restraints excluded: chain Lf residue 99 SER Chi-restraints excluded: chain Lg residue 33 VAL Chi-restraints excluded: chain Lg residue 105 VAL Chi-restraints excluded: chain Lh residue 34 LEU Chi-restraints excluded: chain Lh residue 81 LEU Chi-restraints excluded: chain Lh residue 113 LEU Chi-restraints excluded: chain Li residue 25 LYS Chi-restraints excluded: chain Lj residue 15 THR Chi-restraints excluded: chain Lk residue 7 ASP Chi-restraints excluded: chain Lk residue 31 THR Chi-restraints excluded: chain Lk residue 46 THR Chi-restraints excluded: chain Lk residue 71 VAL Chi-restraints excluded: chain Ll residue 19 GLN Chi-restraints excluded: chain Ll residue 23 ILE Chi-restraints excluded: chain Ll residue 27 ILE Chi-restraints excluded: chain Lq residue 22 ASN Chi-restraints excluded: chain Lq residue 25 LYS Chi-restraints excluded: chain Lq residue 163 LEU Chi-restraints excluded: chain Lq residue 206 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1459 random chunks: chunk 1305 optimal weight: 0.6980 chunk 860 optimal weight: 1.9990 chunk 1385 optimal weight: 0.9980 chunk 845 optimal weight: 1.9990 chunk 657 optimal weight: 6.9990 chunk 963 optimal weight: 10.0000 chunk 1453 optimal weight: 30.0000 chunk 1337 optimal weight: 9.9990 chunk 1157 optimal weight: 4.9990 chunk 120 optimal weight: 7.9990 chunk 894 optimal weight: 0.4980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CA 286 GLN ** CC 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CE 488 ASN ** CF 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CI 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 417 HIS ** CK 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CN 11 ASN ** CN 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CN 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CN 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CT 128 GLN CT 251 ASN ** CT 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CT 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CU 232 GLN ** CU 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 109 HIS LF 119 ASN LK 100 HIS LM 106 GLN LR 34 ASN ** LR 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LU 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LV 83 GLN LY 127 GLN Le 90 ASN Lh 115 HIS Lj 29 ASN Lq 178 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 165506 Z= 0.173 Angle : 0.579 15.954 237286 Z= 0.294 Chirality : 0.036 0.408 28809 Planarity : 0.005 0.069 19593 Dihedral : 21.648 179.917 57948 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.30 % Favored : 95.61 % Rotamer: Outliers : 2.59 % Allowed : 19.55 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.01 % Twisted Proline : 0.17 % 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: 0.56 (0.08), residues: 11825 helix: 1.73 (0.07), residues: 5201 sheet: -0.31 (0.12), residues: 1628 loop : -0.83 (0.09), residues: 4996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRPLR 95 HIS 0.013 0.001 HISCH 333 PHE 0.032 0.001 PHECJ 134 TYR 0.034 0.001 TYRCD 44 ARG 0.015 0.000 ARGCP 417 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23650 Ramachandran restraints generated. 11825 Oldfield, 0 Emsley, 11825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23650 Ramachandran restraints generated. 11825 Oldfield, 0 Emsley, 11825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1836 residues out of total 10278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 1577 time to evaluate : 10.167 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: CA 23 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.7428 (mtp85) REVERT: CA 71 LYS cc_start: 0.7567 (OUTLIER) cc_final: 0.7032 (mttp) REVERT: CA 112 THR cc_start: 0.8691 (t) cc_final: 0.8450 (m) REVERT: CB 52 ASP cc_start: 0.7401 (p0) cc_final: 0.7185 (p0) REVERT: CB 89 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.7771 (tt) REVERT: CB 126 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7605 (ptt180) REVERT: CB 148 SER cc_start: 0.9010 (t) cc_final: 0.8744 (p) REVERT: CC 189 ASP cc_start: 0.8220 (p0) cc_final: 0.7962 (p0) REVERT: CC 455 ARG cc_start: 0.7974 (mtm110) cc_final: 0.6724 (ptm-80) REVERT: CC 540 ARG cc_start: 0.8695 (mtp85) cc_final: 0.8054 (mtt180) REVERT: CC 713 MET cc_start: 0.7594 (mtt) cc_final: 0.7328 (mtt) REVERT: CD 111 ASP cc_start: 0.7507 (p0) cc_final: 0.7122 (p0) REVERT: CD 362 THR cc_start: 0.8523 (OUTLIER) cc_final: 0.8270 (t) REVERT: CE 277 GLU cc_start: 0.8200 (mp0) cc_final: 0.7892 (mp0) REVERT: CF 38 GLN cc_start: 0.7435 (mm-40) cc_final: 0.6924 (mm-40) REVERT: CH 54 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6788 (mt-10) REVERT: CH 253 MET cc_start: 0.6844 (mmm) cc_final: 0.6486 (mmp) REVERT: CH 470 LYS cc_start: 0.8633 (mmtm) cc_final: 0.8383 (mmtm) REVERT: CH 509 ARG cc_start: 0.7542 (ttm110) cc_final: 0.7289 (mtm110) REVERT: CI 281 LYS cc_start: 0.8647 (mtpt) cc_final: 0.8373 (mtpp) REVERT: CJ 17 MET cc_start: 0.8303 (ttp) cc_final: 0.8060 (ttp) REVERT: CK 170 ARG cc_start: 0.8037 (ptt180) cc_final: 0.7671 (ptm160) REVERT: CL 26 LYS cc_start: 0.7445 (mmmm) cc_final: 0.6908 (mttp) REVERT: CL 27 ARG cc_start: 0.7269 (mmm160) cc_final: 0.6830 (mmm-85) REVERT: CL 76 ARG cc_start: 0.6806 (tpp-160) cc_final: 0.6585 (tpp-160) REVERT: CM 40 LYS cc_start: 0.6655 (mmtp) cc_final: 0.6299 (tttt) REVERT: CM 106 ARG cc_start: 0.7758 (ttt-90) cc_final: 0.7385 (ttp-110) REVERT: CM 108 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.8067 (mp) REVERT: CN 1 MET cc_start: 0.4462 (mpp) cc_final: 0.3789 (mpp) REVERT: CP 265 GLN cc_start: 0.8024 (tm-30) cc_final: 0.7629 (tm-30) REVERT: CP 288 PHE cc_start: 0.7662 (m-10) cc_final: 0.7342 (m-80) REVERT: CQ 63 MET cc_start: 0.8114 (ptp) cc_final: 0.7594 (ptp) REVERT: CQ 120 VAL cc_start: 0.8658 (OUTLIER) cc_final: 0.8440 (m) REVERT: CR 38 SER cc_start: 0.9143 (m) cc_final: 0.8908 (m) REVERT: CR 178 ARG cc_start: 0.7648 (ttp80) cc_final: 0.7228 (ttp-170) REVERT: CS 436 MET cc_start: 0.6124 (mmm) cc_final: 0.5798 (mmm) REVERT: CT 366 LYS cc_start: 0.8728 (ttmm) cc_final: 0.8487 (ttmm) REVERT: CX 73 GLN cc_start: 0.8308 (mt0) cc_final: 0.8106 (mt0) REVERT: CX 121 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.8040 (mtt) REVERT: CY 6 LYS cc_start: 0.7593 (mmmm) cc_final: 0.7043 (mttt) REVERT: CY 584 MET cc_start: 0.6970 (mmm) cc_final: 0.6662 (mmm) REVERT: CY 602 TYR cc_start: 0.6430 (OUTLIER) cc_final: 0.5850 (t80) REVERT: Cz 54 LYS cc_start: 0.8391 (mmtt) cc_final: 0.8142 (mmtt) REVERT: Cz 57 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7665 (mt-10) REVERT: LB 36 ASP cc_start: 0.7776 (OUTLIER) cc_final: 0.7413 (p0) REVERT: LB 47 MET cc_start: 0.8164 (OUTLIER) cc_final: 0.7431 (mtt) REVERT: LB 109 HIS cc_start: 0.7176 (m90) cc_final: 0.6324 (t70) REVERT: LB 197 ARG cc_start: 0.7911 (tmm-80) cc_final: 0.7332 (ttp-170) REVERT: LB 309 MET cc_start: 0.8465 (mmm) cc_final: 0.7881 (mtm) REVERT: LC 85 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7859 (tpt-90) REVERT: LC 189 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7224 (tptm) REVERT: LC 221 GLU cc_start: 0.7684 (mp0) cc_final: 0.7257 (mp0) REVERT: LE 32 ASP cc_start: 0.7685 (p0) cc_final: 0.7300 (p0) REVERT: LF 106 ARG cc_start: 0.7861 (ttm-80) cc_final: 0.7057 (ttp80) REVERT: LG 100 TYR cc_start: 0.8185 (m-80) cc_final: 0.7748 (m-80) REVERT: LG 250 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7042 (mp0) REVERT: LH 19 SER cc_start: 0.8510 (t) cc_final: 0.8224 (p) REVERT: LK 112 ILE cc_start: 0.7308 (mt) cc_final: 0.6890 (mt) REVERT: LK 119 LYS cc_start: 0.8241 (mmtp) cc_final: 0.7321 (mttt) REVERT: LK 152 SER cc_start: 0.9189 (t) cc_final: 0.8970 (p) REVERT: LM 86 GLU cc_start: 0.8341 (mp0) cc_final: 0.7729 (mp0) REVERT: LN 5 LYS cc_start: 0.7703 (tttp) cc_final: 0.7013 (tttt) REVERT: LN 38 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.7012 (ttt180) REVERT: LN 182 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7583 (mmtp) REVERT: LN 196 THR cc_start: 0.8382 (t) cc_final: 0.8030 (m) REVERT: LO 30 SER cc_start: 0.8868 (t) cc_final: 0.8216 (m) REVERT: LO 80 ARG cc_start: 0.8221 (mmp80) cc_final: 0.7789 (mmm-85) REVERT: LQ 48 LYS cc_start: 0.7323 (OUTLIER) cc_final: 0.6032 (tttt) REVERT: LR 95 TRP cc_start: 0.8929 (t-100) cc_final: 0.8005 (t-100) REVERT: LR 99 GLN cc_start: 0.8692 (tp40) cc_final: 0.7515 (mp10) REVERT: LS 43 TYR cc_start: 0.8744 (t80) cc_final: 0.8327 (t80) REVERT: LS 52 LYS cc_start: 0.7575 (mmtm) cc_final: 0.7335 (mppt) REVERT: LS 90 MET cc_start: 0.7958 (ptm) cc_final: 0.7570 (ptm) REVERT: LS 134 ASP cc_start: 0.8853 (m-30) cc_final: 0.8617 (m-30) REVERT: LU 32 LYS cc_start: 0.8665 (tppt) cc_final: 0.8453 (tppt) REVERT: LU 41 LYS cc_start: 0.8580 (tptp) cc_final: 0.8331 (tptp) REVERT: LU 50 ASP cc_start: 0.6757 (OUTLIER) cc_final: 0.6299 (p0) REVERT: LX 74 LYS cc_start: 0.8428 (mmmm) cc_final: 0.7752 (mtmm) REVERT: LY 9 SER cc_start: 0.8615 (m) cc_final: 0.8272 (p) REVERT: LY 104 VAL cc_start: 0.8528 (t) cc_final: 0.8255 (t) REVERT: Lc 79 GLU cc_start: 0.8179 (mp0) cc_final: 0.7959 (mp0) REVERT: Ld 73 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8577 (mtmt) REVERT: Ld 98 TYR cc_start: 0.8696 (p90) cc_final: 0.7920 (p90) REVERT: Le 81 LYS cc_start: 0.7848 (mmtm) cc_final: 0.7582 (mmtt) REVERT: Le 124 LYS cc_start: 0.7347 (mmtt) cc_final: 0.6753 (tmmt) REVERT: Lf 59 LYS cc_start: 0.8256 (tttp) cc_final: 0.7534 (mmtm) REVERT: Li 84 LYS cc_start: 0.8340 (tttt) cc_final: 0.7936 (tptp) REVERT: Lk 7 ASP cc_start: 0.5748 (OUTLIER) cc_final: 0.5160 (p0) REVERT: Ll 19 GLN cc_start: 0.7199 (OUTLIER) cc_final: 0.6681 (mt0) REVERT: Lq 174 MET cc_start: 0.2893 (ppp) cc_final: 0.1371 (ptp) outliers start: 259 outliers final: 205 residues processed: 1734 average time/residue: 1.4878 time to fit residues: 4425.7117 Evaluate side-chains 1731 residues out of total 10278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 1504 time to evaluate : 8.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain CA residue 23 ARG Chi-restraints excluded: chain CA residue 27 ILE Chi-restraints excluded: chain CA residue 39 LEU Chi-restraints excluded: chain CA residue 40 SER Chi-restraints excluded: chain CA residue 71 LYS Chi-restraints excluded: chain CA residue 99 ASP Chi-restraints excluded: chain CA residue 176 ILE Chi-restraints excluded: chain CA residue 195 GLU Chi-restraints excluded: chain CA residue 246 GLN Chi-restraints excluded: chain CB residue 70 LYS Chi-restraints excluded: chain CB residue 89 LEU Chi-restraints excluded: chain CB residue 97 VAL Chi-restraints excluded: chain CB residue 126 ARG Chi-restraints excluded: chain CB residue 127 VAL Chi-restraints excluded: chain CB residue 183 VAL Chi-restraints excluded: chain CB residue 185 MET Chi-restraints excluded: chain CB residue 278 VAL Chi-restraints excluded: chain CC residue 181 ASP Chi-restraints excluded: chain CC residue 191 ASN Chi-restraints excluded: chain CC residue 389 SER Chi-restraints excluded: chain CC residue 459 VAL Chi-restraints excluded: chain CC residue 477 VAL Chi-restraints excluded: chain CC residue 480 TRP Chi-restraints excluded: chain CC residue 510 THR Chi-restraints excluded: chain CC residue 531 VAL Chi-restraints excluded: chain CC residue 595 SER Chi-restraints excluded: chain CC residue 638 THR Chi-restraints excluded: chain CC residue 720 ILE Chi-restraints excluded: chain CC residue 751 ASN Chi-restraints excluded: chain CC residue 770 VAL Chi-restraints excluded: chain CC residue 799 LEU Chi-restraints excluded: chain CD residue 48 ARG Chi-restraints excluded: chain CD residue 177 THR Chi-restraints excluded: chain CD residue 362 THR Chi-restraints excluded: chain CD residue 441 ILE Chi-restraints excluded: chain CE residue 135 THR Chi-restraints excluded: chain CE residue 151 VAL Chi-restraints excluded: chain CE residue 188 VAL Chi-restraints excluded: chain CE residue 190 THR Chi-restraints excluded: chain CE residue 367 CYS Chi-restraints excluded: chain CE residue 386 ASP Chi-restraints excluded: chain CE residue 387 LEU Chi-restraints excluded: chain CE residue 402 GLU Chi-restraints excluded: chain CE residue 445 VAL Chi-restraints excluded: chain CE residue 462 LEU Chi-restraints excluded: chain CE residue 478 VAL Chi-restraints excluded: chain CE residue 555 ILE Chi-restraints excluded: chain CF residue 9 VAL Chi-restraints excluded: chain CF residue 116 PHE Chi-restraints excluded: chain CF residue 174 MET Chi-restraints excluded: chain CH residue 54 GLU Chi-restraints excluded: chain CH residue 69 VAL Chi-restraints excluded: chain CH residue 137 THR Chi-restraints excluded: chain CH residue 140 LYS Chi-restraints excluded: chain CH residue 234 ILE Chi-restraints excluded: chain CH residue 277 PHE Chi-restraints excluded: chain CI residue 224 THR Chi-restraints excluded: chain CJ residue 219 VAL Chi-restraints excluded: chain CJ residue 260 VAL Chi-restraints excluded: chain CJ residue 374 LEU Chi-restraints excluded: chain CJ residue 670 ILE Chi-restraints excluded: chain CK residue 40 GLN Chi-restraints excluded: chain CK residue 57 GLN Chi-restraints excluded: chain CK residue 152 THR Chi-restraints excluded: chain CK residue 232 THR Chi-restraints excluded: chain CK residue 252 ASP Chi-restraints excluded: chain CL residue 18 THR Chi-restraints excluded: chain CM residue 108 ILE Chi-restraints excluded: chain CM residue 171 ASP Chi-restraints excluded: chain CM residue 197 VAL Chi-restraints excluded: chain CN residue 20 THR Chi-restraints excluded: chain CN residue 137 VAL Chi-restraints excluded: chain CN residue 161 VAL Chi-restraints excluded: chain CN residue 190 SER Chi-restraints excluded: chain CN residue 239 ASN Chi-restraints excluded: chain CP residue 234 MET Chi-restraints excluded: chain CP residue 270 ILE Chi-restraints excluded: chain CP residue 329 VAL Chi-restraints excluded: chain CP residue 331 LEU Chi-restraints excluded: chain CP residue 447 ILE Chi-restraints excluded: chain CP residue 466 CYS Chi-restraints excluded: chain CP residue 509 VAL Chi-restraints excluded: chain CP residue 537 VAL Chi-restraints excluded: chain CP residue 550 SER Chi-restraints excluded: chain CQ residue 20 THR Chi-restraints excluded: chain CQ residue 120 VAL Chi-restraints excluded: chain CR residue 135 GLN Chi-restraints excluded: chain CR residue 234 LEU Chi-restraints excluded: chain CS residue 485 SER Chi-restraints excluded: chain CS residue 499 VAL Chi-restraints excluded: chain CS residue 819 MET Chi-restraints excluded: chain CT residue 211 VAL Chi-restraints excluded: chain CT residue 284 GLU Chi-restraints excluded: chain CT residue 319 GLU Chi-restraints excluded: chain CT residue 394 GLU Chi-restraints excluded: chain CT residue 573 SER Chi-restraints excluded: chain CT residue 603 VAL Chi-restraints excluded: chain CT residue 644 LEU Chi-restraints excluded: chain CT residue 657 THR Chi-restraints excluded: chain CU residue 190 ILE Chi-restraints excluded: chain CU residue 203 ILE Chi-restraints excluded: chain CU residue 206 ASP Chi-restraints excluded: chain CU residue 211 THR Chi-restraints excluded: chain CU residue 220 VAL Chi-restraints excluded: chain CU residue 229 SER Chi-restraints excluded: chain CU residue 269 THR Chi-restraints excluded: chain CU residue 331 LEU Chi-restraints excluded: chain CU residue 356 ASP Chi-restraints excluded: chain CV residue 68 VAL Chi-restraints excluded: chain CV residue 80 THR Chi-restraints excluded: chain CV residue 85 SER Chi-restraints excluded: chain CV residue 86 THR Chi-restraints excluded: chain CX residue 84 LYS Chi-restraints excluded: chain CX residue 86 LYS Chi-restraints excluded: chain CX residue 93 VAL Chi-restraints excluded: chain CX residue 95 VAL Chi-restraints excluded: chain CX residue 121 MET Chi-restraints excluded: chain CY residue 394 ASP Chi-restraints excluded: chain CY residue 461 TYR Chi-restraints excluded: chain CY residue 490 VAL Chi-restraints excluded: chain CY residue 495 TYR Chi-restraints excluded: chain CY residue 544 THR Chi-restraints excluded: chain CY residue 554 LEU Chi-restraints excluded: chain CY residue 602 TYR Chi-restraints excluded: chain CY residue 669 LEU Chi-restraints excluded: chain LB residue 36 ASP Chi-restraints excluded: chain LB residue 47 MET Chi-restraints excluded: chain LB residue 84 MET Chi-restraints excluded: chain LB residue 205 THR Chi-restraints excluded: chain LB residue 211 GLU Chi-restraints excluded: chain LB residue 278 SER Chi-restraints excluded: chain LB residue 279 VAL Chi-restraints excluded: chain LB residue 283 ILE Chi-restraints excluded: chain LB residue 362 THR Chi-restraints excluded: chain LC residue 79 SER Chi-restraints excluded: chain LC residue 85 ARG Chi-restraints excluded: chain LC residue 100 MET Chi-restraints excluded: chain LC residue 149 VAL Chi-restraints excluded: chain LC residue 158 VAL Chi-restraints excluded: chain LC residue 189 LYS Chi-restraints excluded: chain LC residue 204 ARG Chi-restraints excluded: chain LC residue 238 ASP Chi-restraints excluded: chain LC residue 256 VAL Chi-restraints excluded: chain LE residue 51 SER Chi-restraints excluded: chain LE residue 108 LYS Chi-restraints excluded: chain LE residue 163 LYS Chi-restraints excluded: chain LF residue 80 SER Chi-restraints excluded: chain LG residue 74 VAL Chi-restraints excluded: chain LG residue 85 LEU Chi-restraints excluded: chain LG residue 97 LEU Chi-restraints excluded: chain LG residue 115 GLU Chi-restraints excluded: chain LG residue 121 GLU Chi-restraints excluded: chain LG residue 167 VAL Chi-restraints excluded: chain LG residue 250 GLU Chi-restraints excluded: chain LH residue 34 LEU Chi-restraints excluded: chain LH residue 53 ILE Chi-restraints excluded: chain LH residue 82 VAL Chi-restraints excluded: chain LH residue 167 CYS Chi-restraints excluded: chain LH residue 174 ILE Chi-restraints excluded: chain LL residue 51 VAL Chi-restraints excluded: chain LM residue 9 THR Chi-restraints excluded: chain LM residue 14 VAL Chi-restraints excluded: chain LM residue 112 LEU Chi-restraints excluded: chain LM residue 121 MET Chi-restraints excluded: chain LN residue 38 ARG Chi-restraints excluded: chain LN residue 60 VAL Chi-restraints excluded: chain LN residue 155 VAL Chi-restraints excluded: chain LN residue 182 LYS Chi-restraints excluded: chain LO residue 61 LYS Chi-restraints excluded: chain LO residue 90 ILE Chi-restraints excluded: chain LO residue 147 VAL Chi-restraints excluded: chain LP residue 24 VAL Chi-restraints excluded: chain LP residue 140 MET Chi-restraints excluded: chain LQ residue 48 LYS Chi-restraints excluded: chain LQ residue 49 SER Chi-restraints excluded: chain LQ residue 82 MET Chi-restraints excluded: chain LQ residue 108 VAL Chi-restraints excluded: chain LQ residue 113 THR Chi-restraints excluded: chain LR residue 2 VAL Chi-restraints excluded: chain LR residue 41 ILE Chi-restraints excluded: chain LS residue 60 SER Chi-restraints excluded: chain LS residue 97 THR Chi-restraints excluded: chain LS residue 98 SER Chi-restraints excluded: chain LT residue 52 MET Chi-restraints excluded: chain LT residue 63 VAL Chi-restraints excluded: chain LT residue 80 VAL Chi-restraints excluded: chain LT residue 116 LYS Chi-restraints excluded: chain LT residue 124 VAL Chi-restraints excluded: chain LU residue 50 ASP Chi-restraints excluded: chain LU residue 59 VAL Chi-restraints excluded: chain LV residue 13 LEU Chi-restraints excluded: chain LV residue 79 VAL Chi-restraints excluded: chain LX residue 54 SER Chi-restraints excluded: chain LY residue 40 GLU Chi-restraints excluded: chain LY residue 46 SER Chi-restraints excluded: chain LY residue 127 GLN Chi-restraints excluded: chain LZ residue 11 LEU Chi-restraints excluded: chain LZ residue 45 ILE Chi-restraints excluded: chain LZ residue 88 LEU Chi-restraints excluded: chain LZ residue 104 SER Chi-restraints excluded: chain Lc residue 27 VAL Chi-restraints excluded: chain Ld residue 73 LYS Chi-restraints excluded: chain Ld residue 117 VAL Chi-restraints excluded: chain Le residue 8 VAL Chi-restraints excluded: chain Le residue 15 THR Chi-restraints excluded: chain Le residue 19 MET Chi-restraints excluded: chain Lf residue 56 ARG Chi-restraints excluded: chain Lf residue 99 SER Chi-restraints excluded: chain Lg residue 33 VAL Chi-restraints excluded: chain Lg residue 105 VAL Chi-restraints excluded: chain Lh residue 34 LEU Chi-restraints excluded: chain Lh residue 81 LEU Chi-restraints excluded: chain Lh residue 113 LEU Chi-restraints excluded: chain Li residue 25 LYS Chi-restraints excluded: chain Lj residue 15 THR Chi-restraints excluded: chain Lk residue 7 ASP Chi-restraints excluded: chain Lk residue 31 THR Chi-restraints excluded: chain Lk residue 46 THR Chi-restraints excluded: chain Lk residue 71 VAL Chi-restraints excluded: chain Ll residue 19 GLN Chi-restraints excluded: chain Ll residue 23 ILE Chi-restraints excluded: chain Ll residue 27 ILE Chi-restraints excluded: chain Lq residue 22 ASN Chi-restraints excluded: chain Lq residue 25 LYS Chi-restraints excluded: chain Lq residue 26 ARG Chi-restraints excluded: chain Lq residue 163 LEU Chi-restraints excluded: chain Lq residue 206 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1459 random chunks: chunk 709 optimal weight: 20.0000 chunk 919 optimal weight: 1.9990 chunk 1232 optimal weight: 1.9990 chunk 354 optimal weight: 9.9990 chunk 1067 optimal weight: 1.9990 chunk 170 optimal weight: 8.9990 chunk 321 optimal weight: 7.9990 chunk 1159 optimal weight: 3.9990 chunk 485 optimal weight: 5.9990 chunk 1190 optimal weight: 0.7980 chunk 146 optimal weight: 8.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: CA 286 GLN CC 445 GLN ** CC 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CC 716 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CF 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CH 266 GLN CH 389 ASN ** CI 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CJ 79 GLN ** CK 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CN 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CN 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** CN 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CT 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CT 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CU 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 119 ASN LH 77 ASN LK 100 HIS LM 106 GLN LN 149 ASN LR 34 ASN ** LR 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LU 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LV 83 GLN ** Lc 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ll 17 GLN Lq 178 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.168995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.144328 restraints weight = 202908.189| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 0.92 r_work: 0.3253 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 165506 Z= 0.234 Angle : 0.604 17.038 237286 Z= 0.306 Chirality : 0.038 0.418 28809 Planarity : 0.005 0.074 19593 Dihedral : 21.610 179.832 57948 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.42 % Favored : 95.48 % Rotamer: Outliers : 2.67 % Allowed : 19.76 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.01 % Twisted Proline : 0.17 % 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: 0.54 (0.08), residues: 11825 helix: 1.69 (0.07), residues: 5202 sheet: -0.28 (0.12), residues: 1614 loop : -0.84 (0.09), residues: 5009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRPCY 493 HIS 0.014 0.001 HISCH 333 PHE 0.039 0.002 PHECJ 134 TYR 0.031 0.001 TYRCD 44 ARG 0.014 0.000 ARGLR 144 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 62140.13 seconds wall clock time: 1074 minutes 34.77 seconds (64474.77 seconds total)