Starting phenix.real_space_refine on Sat Mar 23 13:23:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ohd_16880/03_2024/8ohd_16880.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ohd_16880/03_2024/8ohd_16880.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/8ohd_16880/03_2024/8ohd_16880.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ohd_16880/03_2024/8ohd_16880.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ohd_16880/03_2024/8ohd_16880.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ohd_16880/03_2024/8ohd_16880.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= 0.001 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 5 6.06 5 P 3740 5.49 5 Mg 220 5.21 5 S 291 5.16 5 C 77641 2.51 5 N 27381 2.21 5 O 37467 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 29": "OE1" <-> "OE2" Residue "LA ASP 47": "OD1" <-> "OD2" Residue "LA GLU 142": "OE1" <-> "OE2" Residue "LC ASP 288": "OD1" <-> "OD2" Residue "LE ASP 99": "OD1" <-> "OD2" Residue "LE GLU 241": "OE1" <-> "OE2" Residue "LE GLU 244": "OE1" <-> "OE2" Residue "LF ASP 189": "OD1" <-> "OD2" Residue "LF ASP 232": "OD1" <-> "OD2" Residue "LG ASP 162": "OD1" <-> "OD2" Residue "LG PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LG TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LH ASP 11": "OD1" <-> "OD2" Residue "LH GLU 14": "OE1" <-> "OE2" Residue "LH ASP 17": "OD1" <-> "OD2" Residue "LH ASP 58": "OD1" <-> "OD2" Residue "LH GLU 66": "OE1" <-> "OE2" Residue "LH GLU 113": "OE1" <-> "OE2" Residue "LH GLU 183": "OE1" <-> "OE2" Residue "LI GLU 180": "OE1" <-> "OE2" Residue "LI GLU 182": "OE1" <-> "OE2" Residue "LI ASP 207": "OD1" <-> "OD2" Residue "LJ ASP 31": "OD1" <-> "OD2" Residue "LJ ASP 171": "OD1" <-> "OD2" Residue "LL GLU 108": "OE1" <-> "OE2" Residue "LL GLU 142": "OE1" <-> "OE2" Residue "LL TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LL GLU 164": "OE1" <-> "OE2" Residue "LL GLU 172": "OE1" <-> "OE2" Residue "LM ASP 39": "OD1" <-> "OD2" Residue "LM GLU 96": "OE1" <-> "OE2" Residue "LM GLU 126": "OE1" <-> "OE2" Residue "LN ASP 17": "OD1" <-> "OD2" Residue "LN ASP 124": "OD1" <-> "OD2" Residue "LN ASP 147": "OD1" <-> "OD2" Residue "LO ASP 100": "OD1" <-> "OD2" Residue "LO GLU 182": "OE1" <-> "OE2" Residue "LO GLU 194": "OE1" <-> "OE2" Residue "LP ASP 50": "OD1" <-> "OD2" Residue "LP GLU 99": "OE1" <-> "OE2" Residue "LP GLU 103": "OE1" <-> "OE2" Residue "LP ASP 108": "OD1" <-> "OD2" Residue "LP ASP 110": "OD1" <-> "OD2" Residue "LQ GLU 17": "OE1" <-> "OE2" Residue "LQ GLU 147": "OE1" <-> "OE2" Residue "LR GLU 28": "OE1" <-> "OE2" Residue "LR GLU 31": "OE1" <-> "OE2" Residue "LR ASP 47": "OD1" <-> "OD2" Residue "LR GLU 140": "OE1" <-> "OE2" Residue "LR ASP 148": "OD1" <-> "OD2" Residue "LS GLU 69": "OE1" <-> "OE2" Residue "LS ASP 85": "OD1" <-> "OD2" Residue "LS ASP 112": "OD1" <-> "OD2" Residue "LS GLU 131": "OE1" <-> "OE2" Residue "LS ASP 147": "OD1" <-> "OD2" Residue "LT GLU 111": "OE1" <-> "OE2" Residue "LT GLU 118": "OE1" <-> "OE2" Residue "LT GLU 137": "OE1" <-> "OE2" Residue "LT GLU 147": "OE1" <-> "OE2" Residue "LT GLU 157": "OE1" <-> "OE2" Residue "LV ASP 59": "OD1" <-> "OD2" Residue "LV GLU 111": "OE1" <-> "OE2" Residue "LW GLU 37": "OE1" <-> "OE2" Residue "LW PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LX GLU 84": "OE1" <-> "OE2" Residue "LX ASP 118": "OD1" <-> "OD2" Residue "LX ASP 148": "OD1" <-> "OD2" Residue "LY ASP 52": "OD1" <-> "OD2" Residue "LY GLU 54": "OE1" <-> "OE2" Residue "LY GLU 120": "OE1" <-> "OE2" Residue "LZ PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LZ ASP 31": "OD1" <-> "OD2" Residue "LZ ASP 35": "OD1" <-> "OD2" Residue "LZ GLU 113": "OE1" <-> "OE2" Residue "LZ GLU 120": "OE1" <-> "OE2" Residue "La ASP 46": "OD1" <-> "OD2" Residue "La ASP 102": "OD1" <-> "OD2" Residue "Lc TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lc GLU 61": "OE1" <-> "OE2" Residue "Lc ASP 103": "OD1" <-> "OD2" Residue "Ld GLU 19": "OE1" <-> "OE2" Residue "Ld TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ld GLU 48": "OE1" <-> "OE2" Residue "Ld ASP 61": "OD1" <-> "OD2" Residue "Ld GLU 94": "OE1" <-> "OE2" Residue "Ld GLU 96": "OE1" <-> "OE2" Residue "Ld ASP 123": "OD1" <-> "OD2" Residue "Le GLU 84": "OE1" <-> "OE2" Residue "Le GLU 113": "OE1" <-> "OE2" Residue "Lf GLU 40": "OE1" <-> "OE2" Residue "Lh GLU 15": "OE1" <-> "OE2" Residue "Lh GLU 16": "OE1" <-> "OE2" Residue "Lh ASP 22": "OD1" <-> "OD2" Residue "Lh GLU 67": "OE1" <-> "OE2" Residue "Lj GLU 80": "OE1" <-> "OE2" Residue "Lk GLU 51": "OE1" <-> "OE2" Residue "Lk GLU 68": "OE1" <-> "OE2" Residue "Ll TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lo GLU 71": "OE1" <-> "OE2" Residue "Lr GLU 28": "OE1" <-> "OE2" Residue "Lr GLU 52": "OE1" <-> "OE2" Residue "Lz TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 146745 Number of models: 1 Model: "" Number of chains: 62 Chain: "5" Number of atoms: 74502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3474, 74502 Classifications: {'RNA': 3474} Modifications used: {'5*END': 1, 'rna2p_pur': 350, 'rna2p_pyr': 201, 'rna3p_pur': 1565, 'rna3p_pyr': 1358} Link IDs: {'rna2p': 550, 'rna3p': 2923} Chain breaks: 22 Chain: "7" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2561 Classifications: {'RNA': 120} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 55, 'rna3p_pyr': 52} Link IDs: {'rna2p': 12, 'rna3p': 107} Chain: "8" Number of atoms: 3152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 3152 Classifications: {'RNA': 148} Modifications used: {'5*END': 1, 'rna2p_pur': 14, 'rna2p_pyr': 10, 'rna3p_pur': 61, 'rna3p_pyr': 63} Link IDs: {'rna2p': 23, 'rna3p': 124} Chain breaks: 2 Chain: "A" Number of atoms: 5479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 692, 5479 Classifications: {'peptide': 692} Link IDs: {'PTRANS': 14, 'TRANS': 677} Chain breaks: 3 Chain: "B" Number of atoms: 3234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3234 Classifications: {'peptide': 403} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 390} Chain breaks: 2 Chain: "C" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1547 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 1, 'TRANS': 186} Chain: "D" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 588 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 7, 'TRANS': 70} Chain: "K" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1704 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain: "LA" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1898 Classifications: {'peptide': 248} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 233} Chain: "LB" Number of atoms: 3239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3239 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 386} Chain: "LC" Number of atoms: 2927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2927 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 18, 'TRANS': 349} Chain: "LD" Number of atoms: 2382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2382 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 283} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "LE" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1765 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 206} Chain breaks: 2 Chain: "LF" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1870 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "LG" Number of atoms: 1927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1927 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 226} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "LH" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1518 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} Chain: "LI" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1634 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 190} Chain breaks: 1 Chain: "LJ" Number of atoms: 1401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1401 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 5, 'TRANS': 169} Chain: "LL" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1573 Classifications: {'peptide': 194} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 179} Chain: "LM" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1120 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain: "LN" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1701 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 193} Chain: "LO" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1650 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 191} Chain: "LP" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1242 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "LQ" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1513 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain: "LR" Number of atoms: 1294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1294 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 3, 'TRANS': 151} Chain: "LS" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1453 Classifications: {'peptide': 175} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 163} Chain: "LT" Number of atoms: 1298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1298 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 149} Chain: "LU" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 825 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "LV" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 979 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain: "LW" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 519 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 2, 'TRANS': 59} Chain: "LX" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 967 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain: "LY" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1115 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "LZ" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1107 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "La" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1162 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain: "Lb" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 876 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Lc" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 764 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "Ld" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 888 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "Le" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1053 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "Lf" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 876 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "Lg" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 906 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "Lh" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1015 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "Li" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 832 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "Lj" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 705 Classifications: {'peptide': 86} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 82} Chain: "Lk" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "Ll" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 444 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "Lm" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 429 Classifications: {'peptide': 52} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "Lo" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 863 Classifications: {'peptide': 105} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 100} Chain: "Lp" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'TRANS': 90} Chain: "Lr" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1002 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "Lz" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1744 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 208} Chain: "5" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 208 Unusual residues: {' MG': 208} Classifications: {'undetermined': 208} Link IDs: {None: 207} Chain: "7" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "8" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "LI" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LP" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LV" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Le" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Lg" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Lj" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Lm" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Lo" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Lp" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0T2D SG CYSLg 46 85.743 103.035 66.671 1.00104.37 S ATOM A0T2U SG CYSLg 49 83.662 99.877 65.980 1.00 99.77 S ATOM A0TA5 SG CYSLg 83 86.464 100.860 63.642 1.00 86.25 S ATOM A0TAP SG CYSLg 86 83.321 103.044 63.852 1.00 90.56 S ATOM A0V0K SG CYSLj 19 123.579 122.106 106.620 1.00 68.79 S ATOM A0V1C SG CYSLj 22 125.263 122.477 109.986 1.00 83.20 S ATOM A0V3V SG CYSLj 34 121.465 122.263 109.755 1.00 78.65 S ATOM A0V4E SG CYSLj 37 123.249 125.379 108.519 1.00 74.67 S ATOM A0WCW SG CYSLm 96 79.436 73.210 202.361 1.00 71.48 S ATOM A0WDM SG CYSLm 99 81.733 71.215 200.132 1.00 92.41 S ATOM A0WG4 SG CYSLm 110 82.773 71.763 203.781 1.00 75.14 S ATOM A0WHC SG CYSLm 115 82.901 74.592 201.468 1.00 94.08 S ATOM A0WMU SG CYSLo 12 75.310 179.179 166.164 1.00 77.04 S ATOM A0WNI SG CYSLo 15 74.303 182.831 166.460 1.00107.55 S ATOM A0X0J SG CYSLo 72 71.794 180.255 165.093 1.00 89.77 S ATOM A0X1K SG CYSLo 77 74.883 181.258 163.080 1.00104.66 S ATOM A0XGM SG CYSLp 39 69.933 99.853 73.674 1.00103.77 S ATOM A0XH9 SG CYSLp 42 70.678 96.972 71.319 1.00 85.64 S ATOM A0XKN SG CYSLp 57 72.682 97.354 74.483 1.00 82.55 S ATOM A0XL3 SG CYSLp 60 73.199 99.863 71.707 1.00 87.49 S Residues with excluded nonbonded symmetry interactions: 245 residue: pdb=" N SER A 743 " occ=0.00 ... (4 atoms not shown) pdb=" OG SER A 743 " occ=0.00 residue: pdb=" N LYS A 744 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS A 744 " occ=0.00 residue: pdb=" N LYS A 745 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS A 745 " occ=0.00 residue: pdb=" N THR A 746 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 THR A 746 " occ=0.00 residue: pdb=" N GLY A 747 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY A 747 " occ=0.00 residue: pdb=" N LEU A 757 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU A 757 " occ=0.00 residue: pdb=" N ASP A 758 " occ=0.00 ... (6 atoms not shown) pdb=" OD2 ASP A 758 " occ=0.00 residue: pdb=" N LYS A 759 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS A 759 " occ=0.00 residue: pdb=" N GLU A 760 " occ=0.00 ... (7 atoms not shown) pdb=" OE2 GLU A 760 " occ=0.00 residue: pdb=" N GLN A 761 " occ=0.00 ... (7 atoms not shown) pdb=" NE2 GLN A 761 " occ=0.00 residue: pdb=" N GLU A 762 " occ=0.00 ... (7 atoms not shown) pdb=" OE2 GLU A 762 " occ=0.00 residue: pdb=" N ASP A 763 " occ=0.00 ... (6 atoms not shown) pdb=" OD2 ASP A 763 " occ=0.00 ... (remaining 233 not shown) Time building chain proxies: 57.08, per 1000 atoms: 0.39 Number of scatterers: 146745 At special positions: 0 Unit cell: (231.186, 256.631, 281.349, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 5 29.99 S 291 16.00 P 3740 15.00 Mg 220 11.99 O 37467 8.00 N 27381 7.00 C 77641 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 57.81 Conformation dependent library (CDL) restraints added in 9.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNLg 201 " pdb="ZN ZNLg 201 " - pdb=" SG CYSLg 46 " pdb="ZN ZNLg 201 " - pdb=" SG CYSLg 86 " pdb="ZN ZNLg 201 " - pdb=" SG CYSLg 83 " pdb="ZN ZNLg 201 " - pdb=" SG CYSLg 49 " pdb=" ZNLj 102 " pdb="ZN ZNLj 102 " - pdb=" SG CYSLj 19 " pdb="ZN ZNLj 102 " - pdb=" SG CYSLj 34 " pdb="ZN ZNLj 102 " - pdb=" SG CYSLj 22 " pdb="ZN ZNLj 102 " - pdb=" SG CYSLj 37 " pdb=" ZNLm 201 " pdb="ZN ZNLm 201 " - pdb=" SG CYSLm 115 " pdb="ZN ZNLm 201 " - pdb=" SG CYSLm 99 " pdb="ZN ZNLm 201 " - pdb=" SG CYSLm 110 " pdb="ZN ZNLm 201 " - pdb=" SG CYSLm 96 " pdb=" ZNLo 201 " pdb="ZN ZNLo 201 " - pdb=" SG CYSLo 77 " pdb="ZN ZNLo 201 " - pdb=" SG CYSLo 12 " pdb="ZN ZNLo 201 " - pdb=" SG CYSLo 15 " pdb="ZN ZNLo 201 " - pdb=" SG CYSLo 72 " pdb=" ZNLp 101 " pdb="ZN ZNLp 101 " - pdb=" SG CYSLp 57 " pdb="ZN ZNLp 101 " - pdb=" SG CYSLp 42 " pdb="ZN ZNLp 101 " - pdb=" SG CYSLp 39 " pdb="ZN ZNLp 101 " - pdb=" SG CYSLp 60 " Number of angles added : 30 16224 Ramachandran restraints generated. 8112 Oldfield, 0 Emsley, 8112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15394 Finding SS restraints... Secondary structure from input PDB file: 326 helices and 93 sheets defined 46.4% alpha, 14.2% beta 1193 base pairs and 2151 stacking pairs defined. Time for finding SS restraints: 49.88 Creating SS restraints... Processing helix chain 'A' and resid 29 through 42 Processing helix chain 'A' and resid 58 through 74 Processing helix chain 'A' and resid 79 through 87 Processing helix chain 'A' and resid 89 through 104 removed outlier: 3.601A pdb=" N ILE A 93 " --> pdb=" O ASP A 89 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLY A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ASP A 99 " --> pdb=" O ASN A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 135 Processing helix chain 'A' and resid 139 through 147 Processing helix chain 'A' and resid 149 through 161 Processing helix chain 'A' and resid 179 through 197 Processing helix chain 'A' and resid 203 through 211 Processing helix chain 'A' and resid 213 through 227 Processing helix chain 'A' and resid 246 through 265 Processing helix chain 'A' and resid 269 through 276 Processing helix chain 'A' and resid 279 through 288 Processing helix chain 'A' and resid 302 through 320 Processing helix chain 'A' and resid 334 through 347 Processing helix chain 'A' and resid 348 through 350 No H-bonds generated for 'chain 'A' and resid 348 through 350' Processing helix chain 'A' and resid 365 through 375 Processing helix chain 'A' and resid 376 through 389 Processing helix chain 'A' and resid 417 through 427 Processing helix chain 'A' and resid 480 through 489 removed outlier: 4.852A pdb=" N PHE A 485 " --> pdb=" O GLU A 481 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU A 486 " --> pdb=" O ILE A 482 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG A 487 " --> pdb=" O GLU A 483 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LYS A 488 " --> pdb=" O ASP A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 523 removed outlier: 4.604A pdb=" N LYS A 507 " --> pdb=" O GLU A 503 " (cutoff:3.500A) Proline residue: A 508 - end of helix Processing helix chain 'A' and resid 530 through 559 removed outlier: 4.051A pdb=" N LYS A 534 " --> pdb=" O GLY A 530 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG A 535 " --> pdb=" O THR A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 577 removed outlier: 3.688A pdb=" N LEU A 569 " --> pdb=" O THR A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 593 removed outlier: 3.700A pdb=" N ASP A 592 " --> pdb=" O PHE A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 615 removed outlier: 3.557A pdb=" N LYS A 614 " --> pdb=" O LYS A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 632 removed outlier: 4.274A pdb=" N ALA A 622 " --> pdb=" O GLU A 618 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN A 631 " --> pdb=" O HIS A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 649 Processing helix chain 'A' and resid 657 through 679 Processing helix chain 'A' and resid 681 through 699 Processing helix chain 'A' and resid 708 through 717 removed outlier: 3.606A pdb=" N ALA A 714 " --> pdb=" O PRO A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 747 removed outlier: 4.060A pdb=" N GLN A 738 " --> pdb=" O LEU A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 767 removed outlier: 3.661A pdb=" N GLU A 762 " --> pdb=" O ASP A 758 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP A 763 " --> pdb=" O LYS A 759 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 764 " --> pdb=" O GLU A 760 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA A 765 " --> pdb=" O GLN A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 784 removed outlier: 3.753A pdb=" N GLU A 771 " --> pdb=" O THR A 767 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 784 " --> pdb=" O LYS A 780 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 7 Processing helix chain 'B' and resid 14 through 18 removed outlier: 3.928A pdb=" N LEU B 17 " --> pdb=" O SER B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 46 removed outlier: 3.952A pdb=" N LEU B 33 " --> pdb=" O LYS B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 59 removed outlier: 4.186A pdb=" N ALA B 55 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 74 Processing helix chain 'B' and resid 96 through 105 Processing helix chain 'B' and resid 108 through 124 removed outlier: 4.113A pdb=" N VAL B 112 " --> pdb=" O ASN B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 168 Processing helix chain 'B' and resid 174 through 182 removed outlier: 3.784A pdb=" N LEU B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 200 removed outlier: 3.537A pdb=" N GLN B 189 " --> pdb=" O ASP B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 224 through 233 Processing helix chain 'B' and resid 237 through 243 Processing helix chain 'B' and resid 346 through 372 Processing helix chain 'B' and resid 376 through 385 removed outlier: 4.285A pdb=" N LEU B 385 " --> pdb=" O SER B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 392 Processing helix chain 'B' and resid 394 through 414 removed outlier: 3.695A pdb=" N LEU B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 426 Processing helix chain 'B' and resid 426 through 493 removed outlier: 4.170A pdb=" N VAL B 430 " --> pdb=" O SER B 426 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS B 440 " --> pdb=" O PHE B 436 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) Proline residue: B 470 - end of helix removed outlier: 3.719A pdb=" N ASP B 473 " --> pdb=" O GLU B 469 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS B 478 " --> pdb=" O LEU B 474 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS B 492 " --> pdb=" O ALA B 488 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG B 493 " --> pdb=" O ASP B 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 192 Processing helix chain 'C' and resid 193 through 196 Processing helix chain 'C' and resid 208 through 210 No H-bonds generated for 'chain 'C' and resid 208 through 210' Processing helix chain 'C' and resid 211 through 226 removed outlier: 3.541A pdb=" N SER C 226 " --> pdb=" O TYR C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 239 removed outlier: 4.091A pdb=" N VAL C 238 " --> pdb=" O LEU C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 256 Processing helix chain 'C' and resid 272 through 287 Processing helix chain 'C' and resid 291 through 302 removed outlier: 3.656A pdb=" N SER C 300 " --> pdb=" O GLN C 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 41 removed outlier: 3.726A pdb=" N VAL D 32 " --> pdb=" O PRO D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 71 Processing helix chain 'K' and resid 12 through 16 removed outlier: 3.768A pdb=" N PHE K 16 " --> pdb=" O GLU K 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 12 through 16' Processing helix chain 'K' and resid 31 through 43 removed outlier: 3.945A pdb=" N VAL K 37 " --> pdb=" O ASN K 33 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE K 38 " --> pdb=" O PHE K 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 88 Processing helix chain 'K' and resid 103 through 107 Processing helix chain 'K' and resid 122 through 134 Processing helix chain 'K' and resid 141 through 145 removed outlier: 4.207A pdb=" N ASP K 144 " --> pdb=" O THR K 141 " (cutoff:3.500A) Processing helix chain 'K' and resid 147 through 152 Processing helix chain 'K' and resid 166 through 178 Processing helix chain 'K' and resid 192 through 196 Processing helix chain 'K' and resid 211 through 223 Processing helix chain 'LA' and resid 13 through 17 removed outlier: 3.747A pdb=" N ARGLA 17 " --> pdb=" O SERLA 14 " (cutoff:3.500A) Processing helix chain 'LA' and resid 33 through 39 Processing helix chain 'LA' and resid 173 through 177 Processing helix chain 'LA' and resid 181 through 191 removed outlier: 3.605A pdb=" N ALALA 191 " --> pdb=" O HISLA 187 " (cutoff:3.500A) Processing helix chain 'LA' and resid 200 through 204 Processing helix chain 'LA' and resid 205 through 209 removed outlier: 3.512A pdb=" N HISLA 209 " --> pdb=" O PROLA 206 " (cutoff:3.500A) Processing helix chain 'LB' and resid 13 through 17 removed outlier: 3.723A pdb=" N PHELB 16 " --> pdb=" O SERLB 13 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEULB 17 " --> pdb=" O LEULB 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'LB' and resid 13 through 17' Processing helix chain 'LB' and resid 111 through 117 removed outlier: 3.983A pdb=" N ARGLB 117 " --> pdb=" O GLULB 113 " (cutoff:3.500A) Processing helix chain 'LB' and resid 133 through 138 Processing helix chain 'LB' and resid 139 through 157 Processing helix chain 'LB' and resid 167 through 171 Processing helix chain 'LB' and resid 189 through 200 Processing helix chain 'LB' and resid 206 through 210 Processing helix chain 'LB' and resid 230 through 235 Processing helix chain 'LB' and resid 356 through 361 Processing helix chain 'LB' and resid 381 through 390 Processing helix chain 'LB' and resid 392 through 403 Processing helix chain 'LC' and resid 25 through 30 Processing helix chain 'LC' and resid 33 through 45 Processing helix chain 'LC' and resid 46 through 49 removed outlier: 3.525A pdb=" N ARGLC 49 " --> pdb=" O LYSLC 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'LC' and resid 46 through 49' Processing helix chain 'LC' and resid 116 through 132 Processing helix chain 'LC' and resid 133 through 141 Processing helix chain 'LC' and resid 156 through 161 Processing helix chain 'LC' and resid 163 through 174 Processing helix chain 'LC' and resid 176 through 187 removed outlier: 3.712A pdb=" N ILELC 180 " --> pdb=" O ALALC 176 " (cutoff:3.500A) Processing helix chain 'LC' and resid 192 through 197 removed outlier: 3.553A pdb=" N LYSLC 195 " --> pdb=" O GLYLC 192 " (cutoff:3.500A) Processing helix chain 'LC' and resid 216 through 223 removed outlier: 4.454A pdb=" N ASNLC 223 " --> pdb=" O LYSLC 219 " (cutoff:3.500A) Processing helix chain 'LC' and resid 233 through 235 No H-bonds generated for 'chain 'LC' and resid 233 through 235' Processing helix chain 'LC' and resid 236 through 241 Processing helix chain 'LC' and resid 254 through 265 removed outlier: 3.543A pdb=" N LEULC 260 " --> pdb=" O ALALC 256 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ASPLC 261 " --> pdb=" O PHELC 257 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLULC 262 " --> pdb=" O ARGLC 258 " (cutoff:3.500A) Processing helix chain 'LC' and resid 288 through 295 Processing helix chain 'LC' and resid 295 through 302 removed outlier: 3.951A pdb=" N ALALC 301 " --> pdb=" O GLULC 297 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEULC 302 " --> pdb=" O ILELC 298 " (cutoff:3.500A) Processing helix chain 'LC' and resid 321 through 329 Processing helix chain 'LC' and resid 330 through 368 removed outlier: 4.322A pdb=" N THRLC 334 " --> pdb=" O PROLC 330 " (cutoff:3.500A) Processing helix chain 'LD' and resid 9 through 16 Processing helix chain 'LD' and resid 20 through 25 Processing helix chain 'LD' and resid 29 through 38 removed outlier: 4.017A pdb=" N ARGLD 35 " --> pdb=" O TYRLD 31 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILELD 38 " --> pdb=" O LYSLD 34 " (cutoff:3.500A) Processing helix chain 'LD' and resid 40 through 44 Processing helix chain 'LD' and resid 82 through 87 removed outlier: 4.135A pdb=" N TYRLD 86 " --> pdb=" O GLULD 82 " (cutoff:3.500A) Processing helix chain 'LD' and resid 94 through 113 Processing helix chain 'LD' and resid 157 through 170 Processing helix chain 'LD' and resid 191 through 200 Processing helix chain 'LD' and resid 201 through 215 Processing helix chain 'LD' and resid 215 through 223 Processing helix chain 'LD' and resid 223 through 230 Processing helix chain 'LD' and resid 235 through 250 Processing helix chain 'LD' and resid 272 through 294 Processing helix chain 'LE' and resid 58 through 67 Processing helix chain 'LE' and resid 132 through 136 Processing helix chain 'LE' and resid 178 through 183 Processing helix chain 'LE' and resid 190 through 192 No H-bonds generated for 'chain 'LE' and resid 190 through 192' Processing helix chain 'LE' and resid 213 through 218 Processing helix chain 'LE' and resid 243 through 264 removed outlier: 3.707A pdb=" N GLNLE 256 " --> pdb=" O ALALE 252 " (cutoff:3.500A) Proline residue: LE 259 - end of helix removed outlier: 3.893A pdb=" N ILELE 264 " --> pdb=" O LYSLE 260 " (cutoff:3.500A) Processing helix chain 'LE' and resid 266 through 273 Processing helix chain 'LF' and resid 25 through 79 Processing helix chain 'LF' and resid 102 through 112 Processing helix chain 'LF' and resid 126 through 136 Processing helix chain 'LF' and resid 146 through 158 Processing helix chain 'LF' and resid 171 through 180 removed outlier: 4.135A pdb=" N ILELF 175 " --> pdb=" O ASPLF 171 " (cutoff:3.500A) Processing helix chain 'LF' and resid 181 through 183 No H-bonds generated for 'chain 'LF' and resid 181 through 183' Processing helix chain 'LF' and resid 186 through 197 Processing helix chain 'LF' and resid 200 through 208 Processing helix chain 'LF' and resid 239 through 248 removed outlier: 3.577A pdb=" N LEULF 243 " --> pdb=" O GLNLF 239 " (cutoff:3.500A) Processing helix chain 'LG' and resid 51 through 55 removed outlier: 3.585A pdb=" N VALLG 55 " --> pdb=" O THRLG 52 " (cutoff:3.500A) Processing helix chain 'LG' and resid 58 through 74 Processing helix chain 'LG' and resid 77 through 82 Processing helix chain 'LG' and resid 83 through 85 No H-bonds generated for 'chain 'LG' and resid 83 through 85' Processing helix chain 'LG' and resid 88 through 101 removed outlier: 3.725A pdb=" N LYSLG 101 " --> pdb=" O LYSLG 97 " (cutoff:3.500A) Processing helix chain 'LG' and resid 106 through 124 Processing helix chain 'LG' and resid 139 through 149 Processing helix chain 'LG' and resid 164 through 178 removed outlier: 4.731A pdb=" N PHELG 169 " --> pdb=" O GLULG 165 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N LEULG 170 " --> pdb=" O LEULG 166 " (cutoff:3.500A) Proline residue: LG 171 - end of helix Processing helix chain 'LG' and resid 186 through 194 removed outlier: 3.901A pdb=" N LEULG 190 " --> pdb=" O GLYLG 186 " (cutoff:3.500A) Processing helix chain 'LG' and resid 208 through 226 removed outlier: 4.415A pdb=" N GLYLG 213 " --> pdb=" O SERLG 209 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ALALG 214 " --> pdb=" O GLULG 210 " (cutoff:3.500A) Processing helix chain 'LG' and resid 229 through 236 removed outlier: 3.641A pdb=" N ARGLG 235 " --> pdb=" O ASPLG 231 " (cutoff:3.500A) Processing helix chain 'LG' and resid 243 through 265 Processing helix chain 'LH' and resid 63 through 68 Processing helix chain 'LH' and resid 68 through 86 removed outlier: 3.919A pdb=" N THRLH 72 " --> pdb=" O ALALH 68 " (cutoff:3.500A) Processing helix chain 'LH' and resid 116 through 120 Processing helix chain 'LH' and resid 150 through 165 Processing helix chain 'LI' and resid 5 through 10 removed outlier: 3.778A pdb=" N ARGLI 10 " --> pdb=" O ARGLI 7 " (cutoff:3.500A) Processing helix chain 'LI' and resid 42 through 46 removed outlier: 3.642A pdb=" N PHELI 46 " --> pdb=" O VALLI 43 " (cutoff:3.500A) Processing helix chain 'LI' and resid 62 through 81 Processing helix chain 'LI' and resid 144 through 157 removed outlier: 4.053A pdb=" N PHELI 157 " --> pdb=" O ARGLI 153 " (cutoff:3.500A) Processing helix chain 'LI' and resid 177 through 187 removed outlier: 4.328A pdb=" N GLULI 182 " --> pdb=" O ALALI 178 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N ASPLI 183 " --> pdb=" O ASPLI 179 " (cutoff:3.500A) Processing helix chain 'LI' and resid 205 through 214 removed outlier: 3.880A pdb=" N TRPLI 209 " --> pdb=" O PROLI 205 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 10 through 14 Processing helix chain 'LJ' and resid 30 through 45 Processing helix chain 'LJ' and resid 76 through 90 Processing helix chain 'LJ' and resid 97 through 99 No H-bonds generated for 'chain 'LJ' and resid 97 through 99' Processing helix chain 'LJ' and resid 111 through 115 Processing helix chain 'LJ' and resid 138 through 143 removed outlier: 3.505A pdb=" N ILELJ 141 " --> pdb=" O GLYLJ 138 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALALJ 142 " --> pdb=" O PHELJ 139 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 158 through 171 Processing helix chain 'LL' and resid 17 through 20 Processing helix chain 'LL' and resid 27 through 47 Processing helix chain 'LL' and resid 77 through 85 Processing helix chain 'LL' and resid 87 through 95 removed outlier: 3.991A pdb=" N ARGLL 92 " --> pdb=" O LYSLL 88 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N THRLL 93 " --> pdb=" O LYSLL 89 " (cutoff:3.500A) Processing helix chain 'LL' and resid 106 through 123 Processing helix chain 'LL' and resid 139 through 146 removed outlier: 3.784A pdb=" N LEULL 146 " --> pdb=" O GLULL 142 " (cutoff:3.500A) Processing helix chain 'LL' and resid 170 through 176 Processing helix chain 'LL' and resid 177 through 188 Processing helix chain 'LM' and resid 69 through 81 Processing helix chain 'LM' and resid 81 through 89 Processing helix chain 'LM' and resid 89 through 104 Processing helix chain 'LM' and resid 105 through 137 Processing helix chain 'LN' and resid 3 through 13 removed outlier: 3.626A pdb=" N LYSLN 13 " --> pdb=" O GLULN 9 " (cutoff:3.500A) Processing helix chain 'LN' and resid 16 through 33 removed outlier: 3.628A pdb=" N LEULN 33 " --> pdb=" O GLNLN 29 " (cutoff:3.500A) Processing helix chain 'LN' and resid 44 through 52 Processing helix chain 'LN' and resid 75 through 79 Processing helix chain 'LN' and resid 83 through 87 Processing helix chain 'LN' and resid 97 through 110 Processing helix chain 'LN' and resid 139 through 144 Processing helix chain 'LN' and resid 145 through 157 removed outlier: 4.529A pdb=" N TRPLN 150 " --> pdb=" O ASPLN 147 " (cutoff:3.500A) Proline residue: LN 154 - end of helix Processing helix chain 'LN' and resid 165 through 171 removed outlier: 3.902A pdb=" N SERLN 171 " --> pdb=" O ALALN 167 " (cutoff:3.500A) Processing helix chain 'LN' and resid 177 through 184 removed outlier: 4.159A pdb=" N HISLN 181 " --> pdb=" O HISLN 178 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N HISLN 182 " --> pdb=" O LYSLN 179 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THRLN 183 " --> pdb=" O PHELN 180 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILELN 184 " --> pdb=" O HISLN 181 " (cutoff:3.500A) Processing helix chain 'LN' and resid 187 through 197 Processing helix chain 'LO' and resid 15 through 30 Processing helix chain 'LO' and resid 37 through 40 Processing helix chain 'LO' and resid 46 through 60 removed outlier: 3.567A pdb=" N LYSLO 60 " --> pdb=" O ALALO 56 " (cutoff:3.500A) Processing helix chain 'LO' and resid 65 through 69 Processing helix chain 'LO' and resid 75 through 88 Processing helix chain 'LO' and resid 92 through 101 Processing helix chain 'LO' and resid 109 through 114 removed outlier: 4.222A pdb=" N LYSLO 114 " --> pdb=" O PROLO 110 " (cutoff:3.500A) Processing helix chain 'LO' and resid 120 through 123 Processing helix chain 'LO' and resid 124 through 129 Processing helix chain 'LO' and resid 138 through 146 Processing helix chain 'LO' and resid 149 through 185 Processing helix chain 'LO' and resid 189 through 199 Processing helix chain 'LP' and resid 10 through 12 No H-bonds generated for 'chain 'LP' and resid 10 through 12' 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 76 Processing helix chain 'LP' and resid 84 through 105 Processing helix chain 'LP' and resid 108 through 110 No H-bonds generated for 'chain 'LP' and resid 108 through 110' Processing helix chain 'LQ' and resid 22 through 39 Processing helix chain 'LQ' and resid 41 through 53 removed outlier: 4.100A pdb=" N GLNLQ 45 " --> pdb=" O SERLQ 41 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 63 through 71 Processing helix chain 'LQ' and resid 106 through 117 Processing helix chain 'LQ' and resid 122 through 130 Processing helix chain 'LQ' and resid 142 through 146 removed outlier: 3.505A pdb=" N GLYLQ 145 " --> pdb=" O PROLQ 142 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARGLQ 146 " --> pdb=" O ARGLQ 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'LQ' and resid 142 through 146' Processing helix chain 'LQ' and resid 147 through 152 removed outlier: 3.892A pdb=" N HISLQ 151 " --> pdb=" O GLULQ 147 " (cutoff:3.500A) Processing helix chain 'LR' and resid 4 through 16 Processing helix chain 'LR' and resid 18 through 20 No H-bonds generated for 'chain 'LR' and resid 18 through 20' Processing helix chain 'LR' and resid 28 through 34 Processing helix chain 'LR' and resid 37 through 48 Processing helix chain 'LR' and resid 60 through 73 Processing helix chain 'LR' and resid 77 through 81 removed outlier: 3.527A pdb=" N ARGLR 81 " --> pdb=" O ILELR 78 " (cutoff:3.500A) Processing helix chain 'LR' and resid 84 through 89 Processing helix chain 'LR' and resid 90 through 112 Processing helix chain 'LR' and resid 116 through 129 Processing helix chain 'LR' and resid 134 through 156 Processing helix chain 'LS' and resid 36 through 52 Processing helix chain 'LS' and resid 101 through 118 Processing helix chain 'LS' and resid 120 through 122 No H-bonds generated for 'chain 'LS' and resid 120 through 122' Processing helix chain 'LS' and resid 133 through 137 Processing helix chain 'LS' and resid 139 through 144 Processing helix chain 'LT' and resid 27 through 32 Processing helix chain 'LT' and resid 54 through 58 Processing helix chain 'LT' and resid 99 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 55 through 60 Processing helix chain 'LU' and resid 79 through 94 removed outlier: 3.753A pdb=" N LEULU 83 " --> pdb=" O SERLU 79 " (cutoff:3.500A) Processing helix chain 'LV' and resid 69 through 73 Processing helix chain 'LV' and resid 122 through 129 Processing helix chain 'LV' and resid 129 through 136 Processing helix chain 'LW' and resid 33 through 42 Processing helix chain 'LW' and resid 45 through 49 Processing helix chain 'LW' and resid 52 through 60 Processing helix chain 'LX' and resid 72 through 76 Processing helix chain 'LX' and resid 83 through 94 Processing helix chain 'LX' and resid 105 through 118 Processing helix chain 'LX' and resid 145 through 154 Processing helix chain 'LY' and resid 10 through 20 Processing helix chain 'LY' and resid 22 through 30 removed outlier: 3.943A pdb=" N LYSLY 28 " --> pdb=" O HISLY 24 " (cutoff:3.500A) Processing helix chain 'LY' and resid 35 through 43 Processing helix chain 'LY' and resid 100 through 102 No H-bonds generated for 'chain 'LY' and resid 100 through 102' Processing helix chain 'LY' and resid 112 through 134 Processing helix chain 'LZ' and resid 58 through 66 Processing helix chain 'LZ' and resid 97 through 101 removed outlier: 3.909A pdb=" N PHELZ 101 " --> pdb=" O LYSLZ 98 " (cutoff:3.500A) Processing helix chain 'LZ' and resid 103 through 123 Processing helix chain 'LZ' and resid 124 through 126 No H-bonds generated for 'chain 'LZ' and resid 124 through 126' Processing helix chain 'LZ' and resid 127 through 132 removed outlier: 3.661A pdb=" N PHELZ 131 " --> pdb=" O ASNLZ 127 " (cutoff:3.500A) Processing helix chain 'La' and resid 2 through 5 Processing helix chain 'La' and resid 6 through 11 removed outlier: 4.046A pdb=" N LYSLa 10 " --> pdb=" O ARGLa 6 " (cutoff:3.500A) Processing helix chain 'La' and resid 41 through 49 Processing helix chain 'La' and resid 64 through 69 removed outlier: 3.966A pdb=" N SERLa 68 " --> pdb=" O LYSLa 64 " (cutoff:3.500A) Processing helix chain 'La' and resid 77 through 82 Processing helix chain 'La' and resid 83 through 93 Processing helix chain 'La' and resid 103 through 107 Processing helix chain 'La' and resid 130 through 140 Processing helix chain 'Lb' and resid 11 through 20 removed outlier: 4.134A pdb=" N ASNLb 19 " --> pdb=" O LYSLb 15 " (cutoff:3.500A) Processing helix chain 'Lb' and resid 36 through 49 Processing helix chain 'Lb' and resid 50 through 52 No H-bonds generated for 'chain 'Lb' and resid 50 through 52' Processing helix chain 'Lb' and resid 53 through 75 Processing helix chain 'Lb' and resid 91 through 101 Processing helix chain 'Lb' and resid 105 through 118 Processing helix chain 'Lc' and resid 10 through 25 Processing helix chain 'Lc' and resid 30 through 41 Processing helix chain 'Lc' and resid 53 through 68 Processing helix chain 'Lc' and resid 77 through 85 Processing helix chain 'Ld' and resid 29 through 33 Processing helix chain 'Ld' and resid 37 through 39 No H-bonds generated for 'chain 'Ld' and resid 37 through 39' Processing helix chain 'Ld' and resid 40 through 57 Processing helix chain 'Ld' and resid 65 through 73 Processing helix chain 'Le' and resid 43 through 48 Processing helix chain 'Le' and resid 57 through 61 Processing helix chain 'Le' and resid 63 through 67 removed outlier: 3.655A pdb=" N LYSLe 67 " --> pdb=" O LYSLe 64 " (cutoff:3.500A) Processing helix chain 'Le' and resid 81 through 86 Processing helix chain 'Le' and resid 87 through 92 removed outlier: 4.399A pdb=" N METLe 90 " --> pdb=" O VALLe 87 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASNLe 92 " --> pdb=" O LEULe 89 " (cutoff:3.500A) Processing helix chain 'Le' and resid 104 through 118 removed outlier: 3.704A pdb=" N ALALe 110 " --> pdb=" O LYSLe 106 " (cutoff:3.500A) Processing helix chain 'Lf' and resid 35 through 40 removed outlier: 3.898A pdb=" N GLULf 40 " --> pdb=" O ASPLf 37 " (cutoff:3.500A) Processing helix chain 'Lf' and resid 93 through 97 Processing helix chain 'Lg' and resid 15 through 18 Processing helix chain 'Lg' and resid 60 through 67 Processing helix chain 'Lg' and resid 68 through 73 removed outlier: 3.976A pdb=" N HISLg 73 " --> pdb=" O THRLg 70 " (cutoff:3.500A) Processing helix chain 'Lg' and resid 83 through 114 removed outlier: 3.945A pdb=" N GLNLg 114 " --> pdb=" O GLNLg 110 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 5 through 10 Processing helix chain 'Lh' and resid 13 through 37 Processing helix chain 'Lh' and resid 40 through 74 removed outlier: 3.698A pdb=" N ILELh 47 " --> pdb=" O LYSLh 43 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ARGLh 48 " --> pdb=" O LEULh 44 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VALLh 49 " --> pdb=" O SERLh 45 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 88 through 93 Processing helix chain 'Lh' and resid 96 through 102 Processing helix chain 'Lh' and resid 104 through 114 Processing helix chain 'Li' and resid 25 through 30 Processing helix chain 'Li' and resid 34 through 49 Processing helix chain 'Li' and resid 51 through 64 Processing helix chain 'Li' and resid 65 through 78 Processing helix chain 'Li' and resid 79 through 103 Processing helix chain 'Lj' and resid 6 through 11 removed outlier: 3.811A pdb=" N ARGLj 11 " --> pdb=" O PHELj 8 " (cutoff:3.500A) Processing helix chain 'Lj' and resid 50 through 58 removed outlier: 3.656A pdb=" N ASNLj 57 " --> pdb=" O ALALj 53 " (cutoff:3.500A) Processing helix chain 'Lj' and resid 66 through 75 removed outlier: 3.767A pdb=" N ARGLj 75 " --> pdb=" O TYRLj 71 " (cutoff:3.500A) Processing helix chain 'Lk' and resid 7 through 17 Processing helix chain 'Lk' and resid 49 through 59 Processing helix chain 'Ll' and resid 6 through 20 Processing helix chain 'Ll' and resid 24 through 30 Processing helix chain 'Lm' and resid 79 through 91 removed outlier: 3.772A pdb=" N TYRLm 89 " --> pdb=" O LEULm 85 " (cutoff:3.500A) Processing helix chain 'Lo' and resid 35 through 46 Processing helix chain 'Lp' and resid 8 through 15 removed outlier: 3.703A pdb=" N LYSLp 13 " --> pdb=" O ILELp 10 " (cutoff:3.500A) Processing helix chain 'Lp' and resid 19 through 35 removed outlier: 3.862A pdb=" N LYSLp 28 " --> pdb=" O LYSLp 24 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILELp 29 " --> pdb=" O METLp 25 " (cutoff:3.500A) Processing helix chain 'Lp' and resid 73 through 91 Processing helix chain 'Lr' and resid 3 through 11 Processing helix chain 'Lr' and resid 72 through 75 Processing helix chain 'Lr' and resid 85 through 99 Processing helix chain 'Lr' and resid 103 through 105 No H-bonds generated for 'chain 'Lr' and resid 103 through 105' Processing helix chain 'Lr' and resid 106 through 122 Processing helix chain 'Lz' and resid 6 through 21 removed outlier: 3.813A pdb=" N ALALz 13 " --> pdb=" O THRLz 9 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASNLz 21 " --> pdb=" O VALLz 17 " (cutoff:3.500A) Processing helix chain 'Lz' and resid 22 through 25 removed outlier: 3.744A pdb=" N ARGLz 25 " --> pdb=" O GLNLz 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'Lz' and resid 22 through 25' Processing helix chain 'Lz' and resid 70 through 80 Processing helix chain 'Lz' and resid 86 through 93 removed outlier: 3.955A pdb=" N LEULz 93 " --> pdb=" O ALALz 89 " (cutoff:3.500A) Processing helix chain 'Lz' and resid 96 through 107 removed outlier: 3.538A pdb=" N TYRLz 107 " --> pdb=" O LEULz 103 " (cutoff:3.500A) Processing helix chain 'Lz' and resid 114 through 118 removed outlier: 4.361A pdb=" N LYSLz 118 " --> pdb=" O GLULz 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'Lz' and resid 114 through 118' Processing helix chain 'Lz' and resid 119 through 124 Processing helix chain 'Lz' and resid 126 through 132 Processing helix chain 'Lz' and resid 143 through 153 Processing helix chain 'Lz' and resid 175 through 194 removed outlier: 3.819A pdb=" N TYRLz 181 " --> pdb=" O ASPLz 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 49 removed outlier: 3.607A pdb=" N ILE A 57 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 Processing sheet with id=AA3, first strand: chain 'A' and resid 136 through 138 Processing sheet with id=AA4, first strand: chain 'A' and resid 201 through 202 removed outlier: 3.758A pdb=" N THR A 201 " --> pdb=" O PHE A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 266 through 268 Processing sheet with id=AA6, first strand: chain 'A' and resid 322 through 324 Processing sheet with id=AA7, first strand: chain 'B' and resid 9 through 12 removed outlier: 5.630A pdb=" N ILE B 9 " --> pdb=" O ASN B 500 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N MET B 502 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ILE B 11 " --> pdb=" O MET B 502 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 197 through 202 removed outlier: 5.621A pdb=" N VAL C 198 " --> pdb=" O SER D 22 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N SER D 22 " --> pdb=" O VAL C 198 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU C 200 " --> pdb=" O VAL D 20 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 228 through 230 Processing sheet with id=AB1, first strand: chain 'D' and resid 48 through 50 Processing sheet with id=AB2, first strand: chain 'K' and resid 2 through 5 Processing sheet with id=AB3, first strand: chain 'K' and resid 17 through 19 removed outlier: 6.559A pdb=" N CYS K 24 " --> pdb=" O VAL K 49 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ALA K 51 " --> pdb=" O CYS K 24 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N VAL K 26 " --> pdb=" O ALA K 51 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 64 through 65 removed outlier: 3.551A pdb=" N VAL K 64 " --> pdb=" O LEU K 71 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 108 through 110 Processing sheet with id=AB6, first strand: chain 'K' and resid 153 through 154 Processing sheet with id=AB7, first strand: chain 'LA' and resid 71 through 77 removed outlier: 6.826A pdb=" N VALLA 62 " --> pdb=" O VALLA 45 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N VALLA 45 " --> pdb=" O VALLA 62 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N ARGLA 64 " --> pdb=" O GLYLA 43 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N GLYLA 43 " --> pdb=" O ARGLA 64 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'LA' and resid 101 through 103 removed outlier: 5.801A pdb=" N VALLA 136 " --> pdb=" O LYSLA 149 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LYSLA 149 " --> pdb=" O VALLA 136 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'LA' and resid 224 through 225 Processing sheet with id=AC1, first strand: chain 'LB' and resid 42 through 43 removed outlier: 4.953A pdb=" N ILELB 160 " --> pdb=" O VALLB 185 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N HISLB 165 " --> pdb=" O VALLB 86 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N VALLB 86 " --> pdb=" O HISLB 165 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYSLB 103 " --> pdb=" O GLYLB 91 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VALLB 93 " --> pdb=" O THRLB 101 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N THRLB 101 " --> pdb=" O VALLB 93 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N THRLB 95 " --> pdb=" O LEULB 99 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N LEULB 99 " --> pdb=" O THRLB 95 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'LB' and resid 42 through 43 removed outlier: 4.953A pdb=" N ILELB 160 " --> pdb=" O VALLB 185 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N HISLB 165 " --> pdb=" O VALLB 86 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N VALLB 86 " --> pdb=" O HISLB 165 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'LB' and resid 365 through 368 removed outlier: 6.485A pdb=" N VALLB 57 " --> pdb=" O LYSLB 366 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ILELB 368 " --> pdb=" O HISLB 55 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N HISLB 55 " --> pdb=" O ILELB 368 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N VALLB 344 " --> pdb=" O VALLB 222 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N VALLB 222 " --> pdb=" O VALLB 344 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VALLB 219 " --> pdb=" O ILELB 280 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N ILELB 280 " --> pdb=" O VALLB 219 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N GLYLB 221 " --> pdb=" O THRLB 278 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N THRLB 278 " --> pdb=" O GLYLB 221 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ILELB 284 " --> pdb=" O LYSLB 334 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYSLB 334 " --> pdb=" O ILELB 284 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYSLB 286 " --> pdb=" O METLB 332 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLULB 80 " --> pdb=" O LYSLB 50 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N LYSLB 50 " --> pdb=" O GLULB 80 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'LB' and resid 225 through 229 Processing sheet with id=AC5, first strand: chain 'LB' and resid 292 through 293 Processing sheet with id=AC6, first strand: chain 'LC' and resid 17 through 23 removed outlier: 7.205A pdb=" N VALLC 10 " --> pdb=" O SERLC 18 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYSLC 20 " --> pdb=" O ILELC 8 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILELC 8 " --> pdb=" O LYSLC 20 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N VALLC 153 " --> pdb=" O SERLC 9 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEULC 152 " --> pdb=" O TRPLC 252 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N CYSLC 208 " --> pdb=" O ILELC 251 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N THRLC 253 " --> pdb=" O CYSLC 208 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ILELC 210 " --> pdb=" O THRLC 253 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILELC 209 " --> pdb=" O LEULC 230 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'LC' and resid 64 through 65 Processing sheet with id=AC8, first strand: chain 'LC' and resid 188 through 189 Processing sheet with id=AC9, first strand: chain 'LD' and resid 73 through 79 removed outlier: 5.856A pdb=" N ILELD 74 " --> pdb=" O TYRLD 66 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N TYRLD 66 " --> pdb=" O ILELD 74 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N CYSLD 76 " --> pdb=" O ILELD 64 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'LD' and resid 183 through 184 Processing sheet with id=AD2, first strand: chain 'LE' and resid 49 through 51 Processing sheet with id=AD3, first strand: chain 'LE' and resid 91 through 95 Processing sheet with id=AD4, first strand: chain 'LE' and resid 187 through 189 removed outlier: 6.592A pdb=" N THRLE 176 " --> pdb=" O PHELE 164 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N PHELE 164 " --> pdb=" O THRLE 176 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N THRLE 148 " --> pdb=" O PHELE 164 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ILELE 149 " --> pdb=" O THRLE 197 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'LF' and resid 81 through 83 Processing sheet with id=AD6, first strand: chain 'LF' and resid 211 through 212 removed outlier: 4.004A pdb=" N ASNLF 119 " --> pdb=" O ARGLF 94 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILELF 140 " --> pdb=" O GLYLF 234 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ARGLF 236 " --> pdb=" O ILELF 140 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N TRPLF 142 " --> pdb=" O ARGLF 236 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'LF' and resid 159 through 162 Processing sheet with id=AD8, first strand: chain 'LG' and resid 75 through 76 Processing sheet with id=AD9, first strand: chain 'LG' and resid 137 through 138 Processing sheet with id=AE1, first strand: chain 'LH' and resid 3 through 11 removed outlier: 7.208A pdb=" N ILELH 4 " --> pdb=" O TRPLH 61 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARGLH 54 " --> pdb=" O LEULH 48 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'LH' and resid 17 through 21 removed outlier: 3.589A pdb=" N THRLH 24 " --> pdb=" O LYSLH 21 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'LH' and resid 132 through 136 removed outlier: 6.939A pdb=" N ARGLH 89 " --> pdb=" O LYSLH 184 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYSLH 184 " --> pdb=" O ARGLH 89 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LYSLH 91 " --> pdb=" O SERLH 182 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'LH' and resid 103 through 106 Processing sheet with id=AE5, first strand: chain 'LI' and resid 35 through 37 removed outlier: 6.929A pdb=" N VALLI 134 " --> pdb=" O SERLI 54 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N SERLI 54 " --> pdb=" O VALLI 134 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N METLI 136 " --> pdb=" O METLI 52 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N GLYLI 49 " --> pdb=" O SERLI 168 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'LI' and resid 58 through 61 removed outlier: 6.755A pdb=" N ILELI 97 " --> pdb=" O GLNLI 123 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N THRLI 125 " --> pdb=" O HISLI 95 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N HISLI 95 " --> pdb=" O THRLI 125 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'LI' and resid 190 through 192 Processing sheet with id=AE8, first strand: chain 'LJ' and resid 49 through 52 removed outlier: 5.309A pdb=" N ILELJ 17 " --> pdb=" O GLYLJ 135 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLYLJ 135 " --> pdb=" O ILELJ 17 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'LJ' and resid 93 through 95 removed outlier: 6.974A pdb=" N LEULJ 94 " --> pdb=" O LEULJ 175 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'LL' and resid 22 through 24 Processing sheet with id=AF2, first strand: chain 'LL' and resid 58 through 60 Processing sheet with id=AF3, first strand: chain 'LL' and resid 124 through 126 Processing sheet with id=AF4, first strand: chain 'LL' and resid 167 through 168 Processing sheet with id=AF5, first strand: chain 'LM' and resid 7 through 8 Processing sheet with id=AF6, first strand: chain 'LM' and resid 45 through 51 removed outlier: 5.291A pdb=" N ARGLM 46 " --> pdb=" O GLYLM 40 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N GLYLM 40 " --> pdb=" O ARGLM 46 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASPLM 39 " --> pdb=" O ILELM 27 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ILELM 27 " --> pdb=" O ASPLM 39 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ARGLM 11 " --> pdb=" O ILELM 27 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N VALLM 12 " --> pdb=" O THRLM 58 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'LN' and resid 36 through 39 removed outlier: 4.330A pdb=" N ILELN 61 " --> pdb=" O ALALN 39 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N TYRLN 127 " --> pdb=" O GLULN 123 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N GLULN 123 " --> pdb=" O TYRLN 127 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N PHELN 129 " --> pdb=" O VALLN 121 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASNLN 117 " --> pdb=" O ILELN 133 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILELN 135 " --> pdb=" O VALLN 115 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N VALLN 115 " --> pdb=" O ILELN 135 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'LO' and resid 6 through 10 removed outlier: 6.231A pdb=" N LEULO 7 " --> pdb=" O VALLO 34 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VALLO 36 " --> pdb=" O LEULO 7 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEULO 9 " --> pdb=" O VALLO 36 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'LO' and resid 42 through 44 Processing sheet with id=AG1, first strand: chain 'LP' and resid 14 through 22 removed outlier: 4.154A pdb=" N ASNLP 21 " --> pdb=" O CYSLP 144 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N CYSLP 144 " --> pdb=" O ASNLP 21 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THRLP 151 " --> pdb=" O ILELP 114 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ILELP 114 " --> pdb=" O THRLP 151 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'LP' and resid 58 through 59 Processing sheet with id=AG3, first strand: chain 'LP' and resid 128 through 131 removed outlier: 3.716A pdb=" N ARGLP 135 " --> pdb=" O ARGLP 131 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'LQ' and resid 61 through 62 removed outlier: 3.985A pdb=" N LEULQ 103 " --> pdb=" O VALLQ 82 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLYLQ 84 " --> pdb=" O LEULQ 103 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N VALLQ 105 " --> pdb=" O GLYLQ 84 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILELQ 86 " --> pdb=" O VALLQ 105 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'LQ' and resid 61 through 62 Processing sheet with id=AG6, first strand: chain 'LR' and resid 22 through 24 Processing sheet with id=AG7, first strand: chain 'LS' and resid 59 through 66 removed outlier: 5.392A pdb=" N ILELS 61 " --> pdb=" O ARGLS 15 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ARGLS 15 " --> pdb=" O ILELS 61 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'LS' and resid 89 through 99 removed outlier: 3.691A pdb=" N GLYLS 89 " --> pdb=" O SERLS 86 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASNLS 77 " --> pdb=" O ILELS 132 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ARGLS 83 " --> pdb=" O ILELS 126 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ILELS 126 " --> pdb=" O ARGLS 83 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ASPLS 85 " --> pdb=" O ILELS 124 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILELS 124 " --> pdb=" O ASPLS 85 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'LT' and resid 84 through 92 removed outlier: 6.406A pdb=" N VALLT 75 " --> pdb=" O VALLT 64 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N VALLT 64 " --> pdb=" O VALLT 75 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N ASNLT 77 " --> pdb=" O GLYLT 62 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N GLYLT 62 " --> pdb=" O ASNLT 77 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'LU' and resid 61 through 66 removed outlier: 6.677A pdb=" N SERLU 109 " --> pdb=" O ASNLU 105 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASNLU 105 " --> pdb=" O SERLU 109 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'LU' and resid 48 through 49 Processing sheet with id=AH3, first strand: chain 'LV' and resid 20 through 21 Processing sheet with id=AH4, first strand: chain 'LV' and resid 25 through 28 removed outlier: 6.821A pdb=" N METLV 62 " --> pdb=" O ILELV 40 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N VALLV 42 " --> pdb=" O METLV 60 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N METLV 60 " --> pdb=" O VALLV 42 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALALV 102 " --> pdb=" O ILELV 82 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N GLYLV 103 " --> pdb=" O VALLV 25 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ASNLV 27 " --> pdb=" O GLYLV 103 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ILELV 105 " --> pdb=" O ASNLV 27 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'LV' and resid 88 through 89 removed outlier: 6.425A pdb=" N PHELV 95 " --> pdb=" O ARGLW 20 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ALALW 22 " --> pdb=" O PHELV 95 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N TYRLV 97 " --> pdb=" O ALALW 22 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'LV' and resid 120 through 121 Processing sheet with id=AH7, first strand: chain 'LW' and resid 4 through 5 Processing sheet with id=AH8, first strand: chain 'LX' and resid 77 through 80 removed outlier: 3.539A pdb=" N PHELX 79 " --> pdb=" O ILELX 99 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYSLX 134 " --> pdb=" O VALLX 100 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'LY' and resid 31 through 33 Processing sheet with id=AI1, first strand: chain 'LY' and resid 79 through 82 removed outlier: 6.759A pdb=" N GLULY 54 " --> pdb=" O THRLY 107 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'LY' and resid 86 through 88 Processing sheet with id=AI3, first strand: chain 'LZ' and resid 69 through 76 removed outlier: 6.584A pdb=" N LYSLZ 69 " --> pdb=" O ASPLZ 47 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ALALZ 44 " --> pdb=" O ILELZ 25 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ILELZ 25 " --> pdb=" O ALALZ 44 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ILELZ 46 " --> pdb=" O ALALZ 23 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ALALZ 23 " --> pdb=" O ILELZ 46 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LYSLZ 9 " --> pdb=" O ILELZ 25 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N VALLZ 10 " --> pdb=" O THRLZ 83 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'La' and resid 72 through 74 removed outlier: 6.339A pdb=" N VALLa 73 " --> pdb=" O LEULa 112 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'La' and resid 100 through 102 removed outlier: 6.302A pdb=" N VALLa 124 " --> pdb=" O VALLa 145 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'Lc' and resid 26 through 29 removed outlier: 6.452A pdb=" N LYSLc 26 " --> pdb=" O ILELc 97 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VALLc 46 " --> pdb=" O HISLc 72 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'Ld' and resid 62 through 64 Processing sheet with id=AI8, first strand: chain 'Le' and resid 75 through 79 removed outlier: 5.818A pdb=" N ARGLe 75 " --> pdb=" O CYSLe 96 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLULe 98 " --> pdb=" O ARGLe 75 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N PHELe 77 " --> pdb=" O GLULe 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI8 Processing sheet with id=AI9, first strand: chain 'Lf' and resid 7 through 16 removed outlier: 5.748A pdb=" N PHELf 11 " --> pdb=" O LYSLf 29 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LYSLf 29 " --> pdb=" O PHELf 11 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N THRLf 25 " --> pdb=" O LYSLf 15 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N HISLf 24 " --> pdb=" O PHELf 88 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N PHELf 88 " --> pdb=" O HISLf 24 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARGLf 76 " --> pdb=" O ARGLf 85 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LYSLf 87 " --> pdb=" O VALLf 74 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N VALLf 74 " --> pdb=" O LYSLf 87 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N LYSLf 66 " --> pdb=" O ALALf 53 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N VALLf 50 " --> pdb=" O ARGLf 100 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ARGLf 100 " --> pdb=" O VALLf 50 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'Lg' and resid 20 through 24 Processing sheet with id=AJ2, first strand: chain 'Lj' and resid 16 through 17 Processing sheet with id=AJ3, first strand: chain 'Lk' and resid 3 through 5 removed outlier: 6.547A pdb=" N ARGLk 3 " --> pdb=" O THRLk 44 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N VALLk 46 " --> pdb=" O ARGLk 3 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ILELk 5 " --> pdb=" O VALLk 46 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SERLk 22 " --> pdb=" O ARGLk 37 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VALLk 23 " --> pdb=" O LYSLk 67 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'Lm' and resid 102 through 103 Processing sheet with id=AJ5, first strand: chain 'Lo' and resid 3 through 4 Processing sheet with id=AJ6, first strand: chain 'Lo' and resid 7 through 12 removed outlier: 3.577A pdb=" N LYSLo 17 " --> pdb=" O CYSLo 12 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILELo 66 " --> pdb=" O ILELo 85 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'Lp' and resid 47 through 51 removed outlier: 6.903A pdb=" N ILELp 54 " --> pdb=" O ARGLp 50 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'Lr' and resid 17 through 20 Processing sheet with id=AJ9, first strand: chain 'Lr' and resid 49 through 53 Processing sheet with id=AK1, first strand: chain 'Lz' and resid 164 through 171 removed outlier: 6.228A pdb=" N CYSLz 164 " --> pdb=" O LEULz 38 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEULz 38 " --> pdb=" O CYSLz 164 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N ALALz 166 " --> pdb=" O ILELz 36 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ILELz 36 " --> pdb=" O ALALz 166 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ALALz 168 " --> pdb=" O LEULz 34 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEULz 34 " --> pdb=" O ALALz 168 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLYLz 170 " --> pdb=" O VALLz 32 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'Lz' and resid 50 through 54 Processing sheet with id=AK3, first strand: chain 'Lz' and resid 65 through 68 removed outlier: 3.972A pdb=" N SERLz 113 " --> pdb=" O LEULz 68 " (cutoff:3.500A) 3073 hydrogen bonds defined for protein. 8673 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3121 hydrogen bonds 5328 hydrogen bond angles 0 basepair planarities 1193 basepair parallelities 2151 stacking parallelities Total time for adding SS restraints: 340.74 Time building geometry restraints manager: 62.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 36197 1.34 - 1.47: 56446 1.47 - 1.59: 56813 1.59 - 1.72: 7265 1.72 - 1.84: 461 Bond restraints: 157182 Sorted by residual: bond pdb=" N GLYLI 2 " pdb=" CA GLYLI 2 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.34e+00 bond pdb=" N GLYLD 2 " pdb=" CA GLYLD 2 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.32e+00 bond pdb=" N GLYLN 2 " pdb=" CA GLYLN 2 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.21e+00 bond pdb=" N GLYLA 2 " pdb=" CA GLYLA 2 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.20e+00 bond pdb=" N GLYLQ 2 " pdb=" CA GLYLQ 2 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 6.02e+00 ... (remaining 157177 not shown) Histogram of bond angle deviations from ideal: 98.38 - 105.50: 18730 105.50 - 112.63: 89957 112.63 - 119.75: 52499 119.75 - 126.87: 59204 126.87 - 133.99: 9890 Bond angle restraints: 230280 Sorted by residual: angle pdb=" N LYSLS 164 " pdb=" CA LYSLS 164 " pdb=" C LYSLS 164 " ideal model delta sigma weight residual 112.55 107.43 5.12 1.35e+00 5.49e-01 1.44e+01 angle pdb=" C PROLG 129 " pdb=" N THRLG 130 " pdb=" CA THRLG 130 " ideal model delta sigma weight residual 121.54 127.47 -5.93 1.91e+00 2.74e-01 9.65e+00 angle pdb=" CA GLULk 51 " pdb=" CB GLULk 51 " pdb=" CG GLULk 51 " ideal model delta sigma weight residual 114.10 119.87 -5.77 2.00e+00 2.50e-01 8.33e+00 angle pdb=" C SER B 200 " pdb=" N LEU B 201 " pdb=" CA LEU B 201 " ideal model delta sigma weight residual 121.54 126.58 -5.04 1.91e+00 2.74e-01 6.97e+00 angle pdb=" N VALLN 121 " pdb=" CA VALLN 121 " pdb=" C VALLN 121 " ideal model delta sigma weight residual 113.71 111.31 2.40 9.50e-01 1.11e+00 6.40e+00 ... (remaining 230275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 90847 35.97 - 71.94: 9212 71.94 - 107.90: 1208 107.90 - 143.87: 10 143.87 - 179.84: 2 Dihedral angle restraints: 101279 sinusoidal: 77448 harmonic: 23831 Sorted by residual: dihedral pdb=" O4' C 8 1 " pdb=" C1' C 8 1 " pdb=" N1 C 8 1 " pdb=" C2 C 8 1 " ideal model delta sinusoidal sigma weight residual -160.00 -1.77 -158.23 1 1.50e+01 4.44e-03 8.23e+01 dihedral pdb=" O4' U 54512 " pdb=" C1' U 54512 " pdb=" N1 U 54512 " pdb=" C2 U 54512 " ideal model delta sinusoidal sigma weight residual -128.00 51.84 -179.84 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U 54636 " pdb=" C1' U 54636 " pdb=" N1 U 54636 " pdb=" C2 U 54636 " ideal model delta sinusoidal sigma weight residual 200.00 96.38 103.62 1 1.50e+01 4.44e-03 5.27e+01 ... (remaining 101276 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 21849 0.028 - 0.056: 5457 0.056 - 0.085: 560 0.085 - 0.113: 498 0.113 - 0.141: 198 Chirality restraints: 28562 Sorted by residual: chirality pdb=" CA ILELC 76 " pdb=" N ILELC 76 " pdb=" C ILELC 76 " pdb=" CB ILELC 76 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.97e-01 chirality pdb=" CA ILELH 114 " pdb=" N ILELH 114 " pdb=" C ILELH 114 " pdb=" CB ILELH 114 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.88e-01 chirality pdb=" CA ILELE 208 " pdb=" N ILELE 208 " pdb=" C ILELE 208 " pdb=" CB ILELE 208 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.88e-01 ... (remaining 28559 not shown) Planarity restraints: 15225 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLULX 84 " 0.013 2.00e-02 2.50e+03 2.64e-02 6.95e+00 pdb=" CD GLULX 84 " -0.046 2.00e-02 2.50e+03 pdb=" OE1 GLULX 84 " 0.017 2.00e-02 2.50e+03 pdb=" OE2 GLULX 84 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLULZ 113 " -0.010 2.00e-02 2.50e+03 2.11e-02 4.46e+00 pdb=" CD GLULZ 113 " 0.037 2.00e-02 2.50e+03 pdb=" OE1 GLULZ 113 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLULZ 113 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLULf 40 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.17e+00 pdb=" CD GLULf 40 " -0.035 2.00e-02 2.50e+03 pdb=" OE1 GLULf 40 " 0.013 2.00e-02 2.50e+03 pdb=" OE2 GLULf 40 " 0.012 2.00e-02 2.50e+03 ... (remaining 15222 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 692 2.44 - 3.05: 86444 3.05 - 3.67: 253032 3.67 - 4.28: 405053 4.28 - 4.90: 578598 Nonbonded interactions: 1323819 Sorted by model distance: nonbonded pdb=" O2' G 51316 " pdb="MG MG 55124 " model vdw 1.823 2.170 nonbonded pdb=" OE1 GLNLj 30 " pdb="MG MG 55308 " model vdw 1.848 2.170 nonbonded pdb=" OP2 A 5 317 " pdb="MG MG 55150 " model vdw 1.856 2.170 nonbonded pdb=" OP2 A 5 418 " pdb="MG MG 55306 " model vdw 1.864 2.170 nonbonded pdb=" OP2 C 53791 " pdb="MG MG 55303 " model vdw 1.869 2.170 ... (remaining 1323814 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 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: 8.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.150 Extract box with map and model: 36.420 Check model and map are aligned: 1.670 Set scattering table: 1.040 Process input model: 638.120 Find NCS groups from input model: 3.640 Set up NCS constraints: 0.370 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 692.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 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 : 0.001 0.040 157182 Z= 0.095 Angle : 0.310 6.370 230280 Z= 0.167 Chirality : 0.027 0.141 28562 Planarity : 0.002 0.070 15225 Dihedral : 21.901 179.839 85885 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.65 % Favored : 98.32 % Rotamer: Outliers : 0.46 % Allowed : 12.58 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.80 (0.10), residues: 8112 helix: 3.29 (0.09), residues: 3353 sheet: 0.83 (0.17), residues: 1041 loop : 0.93 (0.11), residues: 3718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.000 TRPLR 95 HIS 0.004 0.000 HIS K 162 PHE 0.005 0.000 PHE A 485 TYR 0.006 0.000 TYRLQ 32 ARG 0.012 0.000 ARGLI 82 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16224 Ramachandran restraints generated. 8112 Oldfield, 0 Emsley, 8112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16224 Ramachandran restraints generated. 8112 Oldfield, 0 Emsley, 8112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 994 residues out of total 7104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 961 time to evaluate : 8.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 578 CYS cc_start: 0.8967 (m) cc_final: 0.8599 (m) REVERT: A 652 MET cc_start: 0.3692 (OUTLIER) cc_final: 0.2966 (mmp) REVERT: B 165 CYS cc_start: 0.9005 (m) cc_final: 0.8795 (m) REVERT: LA 33 ASP cc_start: 0.9039 (p0) cc_final: 0.8828 (p0) REVERT: LD 293 ARG cc_start: 0.8261 (mpt180) cc_final: 0.7947 (mpt180) REVERT: LE 245 GLN cc_start: 0.8676 (tp-100) cc_final: 0.7752 (tp40) REVERT: LE 249 ASP cc_start: 0.9019 (m-30) cc_final: 0.8515 (m-30) REVERT: LH 66 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8204 (mp0) REVERT: LH 110 SER cc_start: 0.9144 (t) cc_final: 0.8913 (m) REVERT: LH 137 SER cc_start: 0.9357 (t) cc_final: 0.8938 (p) REVERT: LH 143 GLU cc_start: 0.8579 (tt0) cc_final: 0.8376 (tt0) REVERT: LH 180 TYR cc_start: 0.9295 (m-80) cc_final: 0.9043 (m-80) REVERT: LI 55 ASP cc_start: 0.8675 (t0) cc_final: 0.8326 (t0) REVERT: LI 82 ARG cc_start: 0.8047 (ttp-110) cc_final: 0.7731 (ttp-110) REVERT: LI 83 ASP cc_start: 0.8881 (m-30) cc_final: 0.8282 (m-30) REVERT: LI 150 GLU cc_start: 0.8775 (tp30) cc_final: 0.8530 (tp30) REVERT: LJ 92 TYR cc_start: 0.9102 (m-80) cc_final: 0.8841 (m-10) REVERT: LL 17 ASP cc_start: 0.8658 (t0) cc_final: 0.8425 (t0) REVERT: LM 81 ASP cc_start: 0.8566 (t0) cc_final: 0.8248 (t0) REVERT: LM 108 ASP cc_start: 0.9072 (m-30) cc_final: 0.8786 (m-30) REVERT: LO 113 ASP cc_start: 0.8787 (p0) cc_final: 0.8533 (p0) REVERT: LP 151 THR cc_start: 0.8790 (m) cc_final: 0.8562 (p) REVERT: LS 147 ASP cc_start: 0.8668 (t0) cc_final: 0.8361 (t0) REVERT: LT 111 GLU cc_start: 0.8849 (tp30) cc_final: 0.8522 (tp30) REVERT: LU 39 PHE cc_start: 0.9488 (t80) cc_final: 0.9077 (t80) REVERT: LU 111 GLU cc_start: 0.8744 (tt0) cc_final: 0.8045 (tt0) REVERT: LV 111 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7988 (mp0) REVERT: LW 52 THR cc_start: 0.9556 (m) cc_final: 0.9196 (p) REVERT: LX 145 ASP cc_start: 0.8492 (t0) cc_final: 0.8084 (t0) REVERT: LY 53 ASP cc_start: 0.9100 (m-30) cc_final: 0.8800 (m-30) REVERT: Lb 54 LEU cc_start: 0.9290 (pt) cc_final: 0.9029 (tp) REVERT: Lb 98 TYR cc_start: 0.9376 (t80) cc_final: 0.9134 (t80) REVERT: Ld 61 ASP cc_start: 0.8223 (t0) cc_final: 0.8020 (t0) REVERT: Ld 89 SER cc_start: 0.9216 (m) cc_final: 0.8824 (p) REVERT: Ld 98 SER cc_start: 0.7409 (p) cc_final: 0.7070 (p) REVERT: Le 33 ARG cc_start: 0.7731 (ttp-170) cc_final: 0.7353 (mtm180) REVERT: Lh 16 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7915 (mt-10) REVERT: Lj 57 ASN cc_start: 0.8670 (t0) cc_final: 0.8335 (t0) REVERT: Lk 7 GLU cc_start: 0.7970 (tp30) cc_final: 0.7404 (tm-30) REVERT: Lz 72 GLN cc_start: 0.8818 (pp30) cc_final: 0.8427 (pp30) REVERT: Lz 76 GLU cc_start: 0.7996 (pp20) cc_final: 0.7390 (pp20) REVERT: Lz 81 ASP cc_start: 0.8727 (p0) cc_final: 0.8467 (p0) REVERT: Lz 87 ILE cc_start: 0.9419 (mp) cc_final: 0.9095 (tp) REVERT: Lz 88 GLU cc_start: 0.9309 (pm20) cc_final: 0.9032 (pm20) REVERT: Lz 119 GLN cc_start: 0.8315 (mp10) cc_final: 0.7871 (mp10) REVERT: Lz 184 HIS cc_start: 0.8687 (t-90) cc_final: 0.8286 (t70) outliers start: 33 outliers final: 21 residues processed: 985 average time/residue: 1.3922 time to fit residues: 2496.3546 Evaluate side-chains 877 residues out of total 7104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 855 time to evaluate : 7.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 652 MET Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain K residue 166 SER Chi-restraints excluded: chain K residue 185 THR Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain LD residue 197 LYS Chi-restraints excluded: chain LG residue 159 HIS Chi-restraints excluded: chain LG residue 209 SER Chi-restraints excluded: chain LJ residue 155 HIS Chi-restraints excluded: chain LN residue 124 ASP Chi-restraints excluded: chain LS residue 169 THR Chi-restraints excluded: chain Lc residue 102 SER Chi-restraints excluded: chain Le residue 84 GLU Chi-restraints excluded: chain Lf residue 90 SER Chi-restraints excluded: chain Lh residue 22 ASP Chi-restraints excluded: chain Lj residue 7 SER Chi-restraints excluded: chain Lk residue 12 LEU Chi-restraints excluded: chain Ll residue 47 THR Chi-restraints excluded: chain Lm residue 110 CYS Chi-restraints excluded: chain Lo residue 7 THR Chi-restraints excluded: chain Lp residue 91 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1174 random chunks: chunk 991 optimal weight: 9.9990 chunk 889 optimal weight: 8.9990 chunk 493 optimal weight: 3.9990 chunk 303 optimal weight: 10.0000 chunk 600 optimal weight: 6.9990 chunk 475 optimal weight: 9.9990 chunk 920 optimal weight: 10.0000 chunk 356 optimal weight: 10.0000 chunk 559 optimal weight: 5.9990 chunk 684 optimal weight: 10.0000 chunk 1066 optimal weight: 0.7980 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 248 ASN LG 64 GLN LI 133 GLN ** LJ 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LJ 110 GLN ** LL 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 97 ASN LT 54 HIS LT 139 HIS LU 50 ASN LX 73 HIS Lb 60 ASN Lg 112 GLN Lr 41 ASN Lz 73 HIS Lz 140 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8980 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 157182 Z= 0.304 Angle : 0.498 8.409 230280 Z= 0.258 Chirality : 0.035 0.209 28562 Planarity : 0.004 0.049 15225 Dihedral : 22.309 178.116 68546 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.10 % Favored : 97.87 % Rotamer: Outliers : 1.55 % Allowed : 12.35 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.10), residues: 8112 helix: 2.68 (0.09), residues: 3361 sheet: 0.64 (0.17), residues: 1028 loop : 0.73 (0.11), residues: 3723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRPLT 125 HIS 0.007 0.001 HISLa 40 PHE 0.022 0.001 PHE B 421 TYR 0.019 0.001 TYRLQ 32 ARG 0.008 0.000 ARGLp 84 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16224 Ramachandran restraints generated. 8112 Oldfield, 0 Emsley, 8112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16224 Ramachandran restraints generated. 8112 Oldfield, 0 Emsley, 8112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 942 residues out of total 7104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 832 time to evaluate : 8.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 MET cc_start: 0.8792 (mmm) cc_final: 0.8570 (mmm) REVERT: A 485 PHE cc_start: 0.6637 (p90) cc_final: 0.6386 (p90) REVERT: A 578 CYS cc_start: 0.8927 (m) cc_final: 0.8633 (m) REVERT: A 701 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.7174 (mmt) REVERT: LA 33 ASP cc_start: 0.9019 (p0) cc_final: 0.8802 (p0) REVERT: LD 212 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8525 (ptm) REVERT: LE 245 GLN cc_start: 0.8612 (tp-100) cc_final: 0.8180 (tp40) REVERT: LH 66 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8312 (mp0) REVERT: LH 137 SER cc_start: 0.9390 (t) cc_final: 0.8902 (p) REVERT: LH 143 GLU cc_start: 0.8692 (tt0) cc_final: 0.8489 (tt0) REVERT: LI 55 ASP cc_start: 0.8767 (t0) cc_final: 0.8344 (t0) REVERT: LI 150 GLU cc_start: 0.8845 (tp30) cc_final: 0.8614 (tp30) REVERT: LJ 92 TYR cc_start: 0.9123 (m-80) cc_final: 0.8821 (m-10) REVERT: LL 17 ASP cc_start: 0.8745 (t0) cc_final: 0.8320 (t0) REVERT: LM 81 ASP cc_start: 0.8573 (t0) cc_final: 0.8252 (t0) REVERT: LM 96 GLU cc_start: 0.8469 (tp30) cc_final: 0.8239 (tp30) REVERT: LM 108 ASP cc_start: 0.9066 (m-30) cc_final: 0.8807 (m-30) REVERT: LO 113 ASP cc_start: 0.8877 (p0) cc_final: 0.8667 (p0) REVERT: LO 173 GLN cc_start: 0.8928 (tt0) cc_final: 0.8520 (tp-100) REVERT: LP 151 THR cc_start: 0.8785 (m) cc_final: 0.8478 (p) REVERT: LS 112 ASP cc_start: 0.8983 (t0) cc_final: 0.8420 (t0) REVERT: LS 147 ASP cc_start: 0.8747 (t0) cc_final: 0.8369 (t0) REVERT: LU 39 PHE cc_start: 0.9479 (t80) cc_final: 0.9219 (t80) REVERT: LU 111 GLU cc_start: 0.8753 (tt0) cc_final: 0.8037 (tt0) REVERT: LV 111 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7885 (mp0) REVERT: LX 145 ASP cc_start: 0.8637 (t0) cc_final: 0.8098 (t0) REVERT: LY 53 ASP cc_start: 0.9257 (m-30) cc_final: 0.9002 (m-30) REVERT: LZ 81 MET cc_start: 0.9440 (OUTLIER) cc_final: 0.8560 (tpt) REVERT: Lb 98 TYR cc_start: 0.9400 (t80) cc_final: 0.9096 (t80) REVERT: Lc 57 LYS cc_start: 0.9102 (ttmm) cc_final: 0.8897 (ttmt) REVERT: Lc 98 ASP cc_start: 0.8971 (t0) cc_final: 0.8680 (t0) REVERT: Ld 61 ASP cc_start: 0.8646 (t0) cc_final: 0.8440 (t70) REVERT: Le 86 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.7829 (mp0) REVERT: Lh 16 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7952 (mt-10) REVERT: Li 88 GLU cc_start: 0.8745 (tp30) cc_final: 0.8486 (tp30) REVERT: Lz 76 GLU cc_start: 0.8411 (pp20) cc_final: 0.7974 (pp20) REVERT: Lz 119 GLN cc_start: 0.8424 (mp10) cc_final: 0.7920 (mp10) REVERT: Lz 184 HIS cc_start: 0.8704 (t-90) cc_final: 0.8298 (t70) outliers start: 110 outliers final: 63 residues processed: 882 average time/residue: 1.2063 time to fit residues: 1918.2173 Evaluate side-chains 862 residues out of total 7104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 795 time to evaluate : 8.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 668 HIS Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain K residue 197 MET Chi-restraints excluded: chain LC residue 170 LEU Chi-restraints excluded: chain LD residue 212 MET Chi-restraints excluded: chain LD residue 224 SER Chi-restraints excluded: chain LD residue 239 MET Chi-restraints excluded: chain LE residue 89 LEU Chi-restraints excluded: chain LF residue 25 PHE Chi-restraints excluded: chain LF residue 225 THR Chi-restraints excluded: chain LH residue 46 SER Chi-restraints excluded: chain LH residue 177 ASP Chi-restraints excluded: chain LI residue 35 ASP Chi-restraints excluded: chain LI residue 195 CYS Chi-restraints excluded: chain LJ residue 34 THR Chi-restraints excluded: chain LJ residue 47 THR Chi-restraints excluded: chain LJ residue 129 ASP Chi-restraints excluded: chain LJ residue 155 HIS Chi-restraints excluded: chain LL residue 63 THR Chi-restraints excluded: chain LM residue 43 THR Chi-restraints excluded: chain LO residue 158 GLU Chi-restraints excluded: chain LP residue 5 SER Chi-restraints excluded: chain LQ residue 82 VAL Chi-restraints excluded: chain LR residue 59 SER Chi-restraints excluded: chain LS residue 77 ASN Chi-restraints excluded: chain LS residue 169 THR Chi-restraints excluded: chain LT residue 118 GLU Chi-restraints excluded: chain LU residue 25 CYS Chi-restraints excluded: chain LU residue 47 ILE Chi-restraints excluded: chain LU residue 60 VAL Chi-restraints excluded: chain LU residue 66 SER Chi-restraints excluded: chain LU residue 109 SER Chi-restraints excluded: chain LW residue 9 SER Chi-restraints excluded: chain LW residue 38 SER Chi-restraints excluded: chain LX residue 126 THR Chi-restraints excluded: chain LX residue 148 ASP Chi-restraints excluded: chain LY residue 66 GLN Chi-restraints excluded: chain LZ residue 31 ASP Chi-restraints excluded: chain LZ residue 34 SER Chi-restraints excluded: chain LZ residue 54 THR Chi-restraints excluded: chain LZ residue 81 MET Chi-restraints excluded: chain LZ residue 86 SER Chi-restraints excluded: chain LZ residue 99 ASP Chi-restraints excluded: chain LZ residue 100 VAL Chi-restraints excluded: chain Lc residue 24 SER Chi-restraints excluded: chain Lc residue 102 SER Chi-restraints excluded: chain Ld residue 46 LEU Chi-restraints excluded: chain Ld residue 112 THR Chi-restraints excluded: chain Ld residue 119 THR Chi-restraints excluded: chain Le residue 86 GLU Chi-restraints excluded: chain Lf residue 5 LEU Chi-restraints excluded: chain Lg residue 5 LEU Chi-restraints excluded: chain Li residue 3 LEU Chi-restraints excluded: chain Li residue 12 ASN Chi-restraints excluded: chain Li residue 21 VAL Chi-restraints excluded: chain Lj residue 15 THR Chi-restraints excluded: chain Lk residue 12 LEU Chi-restraints excluded: chain Ll residue 9 ILE Chi-restraints excluded: chain Ll residue 23 ILE Chi-restraints excluded: chain Ll residue 47 THR Chi-restraints excluded: chain Lp residue 25 MET Chi-restraints excluded: chain Lp residue 89 LEU Chi-restraints excluded: chain Lr residue 80 THR Chi-restraints excluded: chain Lz residue 80 VAL Chi-restraints excluded: chain Lz residue 139 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1174 random chunks: chunk 592 optimal weight: 5.9990 chunk 330 optimal weight: 20.0000 chunk 887 optimal weight: 5.9990 chunk 725 optimal weight: 20.0000 chunk 294 optimal weight: 10.0000 chunk 1068 optimal weight: 9.9990 chunk 1153 optimal weight: 40.0000 chunk 951 optimal weight: 3.9990 chunk 1059 optimal weight: 5.9990 chunk 364 optimal weight: 10.0000 chunk 856 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 162 HIS LF 248 ASN LI 177 ASN ** LL 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LP 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LS 91 HIS LU 50 ASN ** Lz 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9021 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 157182 Z= 0.324 Angle : 0.497 9.867 230280 Z= 0.260 Chirality : 0.035 0.225 28562 Planarity : 0.004 0.050 15225 Dihedral : 22.379 177.974 68518 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.28 % Favored : 97.68 % Rotamer: Outliers : 2.07 % Allowed : 12.86 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.09), residues: 8112 helix: 2.35 (0.09), residues: 3360 sheet: 0.51 (0.17), residues: 1025 loop : 0.45 (0.10), residues: 3727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRPLj 49 HIS 0.006 0.001 HISLa 40 PHE 0.022 0.001 PHE B 421 TYR 0.022 0.001 TYRLQ 32 ARG 0.007 0.000 ARGLp 84 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16224 Ramachandran restraints generated. 8112 Oldfield, 0 Emsley, 8112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16224 Ramachandran restraints generated. 8112 Oldfield, 0 Emsley, 8112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 961 residues out of total 7104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 814 time to evaluate : 8.103 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: A 485 PHE cc_start: 0.6747 (p90) cc_final: 0.6531 (p90) REVERT: A 578 CYS cc_start: 0.8925 (m) cc_final: 0.8659 (m) REVERT: A 695 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8077 (tp40) REVERT: B 385 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7756 (tm) REVERT: LA 33 ASP cc_start: 0.9061 (p0) cc_final: 0.8845 (p0) REVERT: LB 4 ARG cc_start: 0.9169 (OUTLIER) cc_final: 0.7777 (ttm170) REVERT: LC 1 MET cc_start: 0.2027 (ppp) cc_final: 0.1212 (tmm) REVERT: LC 209 ILE cc_start: 0.9286 (OUTLIER) cc_final: 0.9082 (mp) REVERT: LD 200 MET cc_start: 0.9550 (OUTLIER) cc_final: 0.9323 (mmt) REVERT: LD 235 MET cc_start: 0.9186 (OUTLIER) cc_final: 0.8791 (ppp) REVERT: LE 245 GLN cc_start: 0.8497 (tp-100) cc_final: 0.7842 (tp40) REVERT: LE 249 ASP cc_start: 0.9019 (m-30) cc_final: 0.8564 (m-30) REVERT: LF 28 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8441 (tt) REVERT: LH 115 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.8151 (ptp90) REVERT: LI 55 ASP cc_start: 0.8793 (t0) cc_final: 0.8391 (t0) REVERT: LI 150 GLU cc_start: 0.8872 (tp30) cc_final: 0.8667 (tp30) REVERT: LL 17 ASP cc_start: 0.8804 (t0) cc_final: 0.8469 (t0) REVERT: LL 173 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8791 (mt-10) REVERT: LM 96 GLU cc_start: 0.8468 (tp30) cc_final: 0.8191 (tp30) REVERT: LO 87 MET cc_start: 0.9181 (OUTLIER) cc_final: 0.8639 (mtt) REVERT: LO 113 ASP cc_start: 0.8923 (p0) cc_final: 0.8646 (p0) REVERT: LP 151 THR cc_start: 0.8932 (m) cc_final: 0.8508 (p) REVERT: LR 31 GLU cc_start: 0.8696 (tp30) cc_final: 0.8476 (tp30) REVERT: LS 112 ASP cc_start: 0.9035 (t0) cc_final: 0.8503 (t0) REVERT: LU 31 ASP cc_start: 0.8572 (m-30) cc_final: 0.8248 (m-30) REVERT: LU 39 PHE cc_start: 0.9516 (t80) cc_final: 0.9153 (t80) REVERT: LU 111 GLU cc_start: 0.8749 (tt0) cc_final: 0.8021 (tt0) REVERT: LX 145 ASP cc_start: 0.8685 (t0) cc_final: 0.8077 (t0) REVERT: LY 88 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8368 (tp30) REVERT: LZ 81 MET cc_start: 0.9440 (OUTLIER) cc_final: 0.8368 (tpt) REVERT: LZ 86 SER cc_start: 0.9517 (OUTLIER) cc_final: 0.9247 (t) REVERT: Lb 68 ARG cc_start: 0.7867 (ttp-110) cc_final: 0.7390 (ttp-110) REVERT: Lb 98 TYR cc_start: 0.9424 (t80) cc_final: 0.9099 (t80) REVERT: Lc 98 ASP cc_start: 0.9019 (t0) cc_final: 0.8729 (t0) REVERT: Ld 61 ASP cc_start: 0.8739 (t0) cc_final: 0.8494 (t70) REVERT: Le 86 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8092 (mp0) REVERT: Lf 40 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8330 (tm-30) REVERT: Lh 16 GLU cc_start: 0.8324 (mt-10) cc_final: 0.8020 (mt-10) REVERT: Li 88 GLU cc_start: 0.8809 (tp30) cc_final: 0.8576 (tp30) REVERT: Lk 58 GLN cc_start: 0.8888 (mm110) cc_final: 0.8179 (mm-40) REVERT: Lo 74 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8458 (tp30) REVERT: Lp 30 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.8781 (mt-10) REVERT: Lr 125 MET cc_start: 0.7264 (tpt) cc_final: 0.6830 (mmp) REVERT: Lz 76 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7847 (pp20) REVERT: Lz 119 GLN cc_start: 0.8594 (mp10) cc_final: 0.8152 (mp10) REVERT: Lz 158 GLN cc_start: 0.8596 (tp40) cc_final: 0.8370 (tm-30) REVERT: Lz 184 HIS cc_start: 0.8698 (t-90) cc_final: 0.8254 (t70) outliers start: 147 outliers final: 73 residues processed: 900 average time/residue: 1.2521 time to fit residues: 2034.6129 Evaluate side-chains 874 residues out of total 7104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 786 time to evaluate : 8.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 695 GLN Chi-restraints excluded: chain A residue 701 MET Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 150 CYS Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain LA residue 159 SER Chi-restraints excluded: chain LB residue 4 ARG Chi-restraints excluded: chain LB residue 60 VAL Chi-restraints excluded: chain LB residue 95 THR Chi-restraints excluded: chain LC residue 170 LEU Chi-restraints excluded: chain LC residue 198 ASN Chi-restraints excluded: chain LC residue 209 ILE Chi-restraints excluded: chain LD residue 200 MET Chi-restraints excluded: chain LD residue 224 SER Chi-restraints excluded: chain LD residue 235 MET Chi-restraints excluded: chain LD residue 239 MET Chi-restraints excluded: chain LE residue 120 ASP Chi-restraints excluded: chain LF residue 25 PHE Chi-restraints excluded: chain LF residue 28 LEU Chi-restraints excluded: chain LF residue 225 THR Chi-restraints excluded: chain LH residue 46 SER Chi-restraints excluded: chain LH residue 115 ARG Chi-restraints excluded: chain LH residue 177 ASP Chi-restraints excluded: chain LI residue 44 ASP Chi-restraints excluded: chain LI residue 189 CYS Chi-restraints excluded: chain LI residue 195 CYS Chi-restraints excluded: chain LJ residue 47 THR Chi-restraints excluded: chain LJ residue 129 ASP Chi-restraints excluded: chain LL residue 36 ARG Chi-restraints excluded: chain LL residue 63 THR Chi-restraints excluded: chain LM residue 43 THR Chi-restraints excluded: chain LM residue 136 LEU Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LO residue 87 MET Chi-restraints excluded: chain LP residue 5 SER Chi-restraints excluded: chain LQ residue 42 THR Chi-restraints excluded: chain LR residue 59 SER Chi-restraints excluded: chain LR residue 112 SER Chi-restraints excluded: chain LS residue 77 ASN Chi-restraints excluded: chain LS residue 169 THR Chi-restraints excluded: chain LU residue 25 CYS Chi-restraints excluded: chain LU residue 56 LEU Chi-restraints excluded: chain LU residue 60 VAL Chi-restraints excluded: chain LU residue 66 SER Chi-restraints excluded: chain LU residue 109 SER Chi-restraints excluded: chain LV residue 22 VAL Chi-restraints excluded: chain LV residue 115 SER Chi-restraints excluded: chain LW residue 9 SER Chi-restraints excluded: chain LW residue 38 SER Chi-restraints excluded: chain LX residue 126 THR Chi-restraints excluded: chain LY residue 12 SER Chi-restraints excluded: chain LY residue 66 GLN Chi-restraints excluded: chain LZ residue 31 ASP Chi-restraints excluded: chain LZ residue 34 SER Chi-restraints excluded: chain LZ residue 81 MET Chi-restraints excluded: chain LZ residue 86 SER Chi-restraints excluded: chain LZ residue 99 ASP Chi-restraints excluded: chain LZ residue 100 VAL Chi-restraints excluded: chain Lb residue 9 THR Chi-restraints excluded: chain Lc residue 24 SER Chi-restraints excluded: chain Lc residue 102 SER Chi-restraints excluded: chain Ld residue 46 LEU Chi-restraints excluded: chain Ld residue 94 GLU Chi-restraints excluded: chain Ld residue 98 SER Chi-restraints excluded: chain Le residue 86 GLU Chi-restraints excluded: chain Lf residue 5 LEU Chi-restraints excluded: chain Li residue 12 ASN Chi-restraints excluded: chain Lk residue 59 SER Chi-restraints excluded: chain Ll residue 9 ILE Chi-restraints excluded: chain Ll residue 23 ILE Chi-restraints excluded: chain Ll residue 37 TYR Chi-restraints excluded: chain Ll residue 47 THR Chi-restraints excluded: chain Lo residue 7 THR Chi-restraints excluded: chain Lo residue 74 GLU Chi-restraints excluded: chain Lp residue 25 MET Chi-restraints excluded: chain Lp residue 30 GLU Chi-restraints excluded: chain Lp residue 73 THR Chi-restraints excluded: chain Lp residue 89 LEU Chi-restraints excluded: chain Lr residue 80 THR Chi-restraints excluded: chain Lz residue 76 GLU Chi-restraints excluded: chain Lz residue 85 MET Chi-restraints excluded: chain Lz residue 139 THR Chi-restraints excluded: chain Lz residue 141 ASN Chi-restraints excluded: chain Lz residue 208 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1174 random chunks: chunk 1055 optimal weight: 9.9990 chunk 802 optimal weight: 9.9990 chunk 554 optimal weight: 3.9990 chunk 118 optimal weight: 10.0000 chunk 509 optimal weight: 30.0000 chunk 717 optimal weight: 9.9990 chunk 1071 optimal weight: 6.9990 chunk 1134 optimal weight: 4.9990 chunk 560 optimal weight: 6.9990 chunk 1015 optimal weight: 9.9990 chunk 305 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 GLN B 418 GLN ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 119 GLN LF 248 ASN ** LL 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LP 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LT 131 GLN LU 94 ASN LZ 132 GLN Ld 93 ASN Lk 58 GLN ** Lz 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lz 182 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9026 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 157182 Z= 0.345 Angle : 0.505 10.136 230280 Z= 0.264 Chirality : 0.035 0.229 28562 Planarity : 0.004 0.052 15225 Dihedral : 22.402 177.324 68514 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.44 % Favored : 97.52 % Rotamer: Outliers : 1.97 % Allowed : 13.31 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.09), residues: 8112 helix: 2.25 (0.09), residues: 3361 sheet: 0.42 (0.16), residues: 1018 loop : 0.34 (0.10), residues: 3733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRPLj 49 HIS 0.009 0.001 HIS A 668 PHE 0.012 0.001 PHE B 229 TYR 0.020 0.001 TYRLQ 32 ARG 0.006 0.000 ARGLp 84 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16224 Ramachandran restraints generated. 8112 Oldfield, 0 Emsley, 8112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16224 Ramachandran restraints generated. 8112 Oldfield, 0 Emsley, 8112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 928 residues out of total 7104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 788 time to evaluate : 8.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 695 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8168 (tp40) REVERT: B 185 ASP cc_start: 0.9560 (OUTLIER) cc_final: 0.9191 (t0) REVERT: B 385 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7784 (tm) REVERT: B 421 PHE cc_start: 0.8769 (m-80) cc_final: 0.8539 (m-80) REVERT: LA 33 ASP cc_start: 0.9043 (p0) cc_final: 0.8837 (p0) REVERT: LB 4 ARG cc_start: 0.9178 (OUTLIER) cc_final: 0.7786 (ttm170) REVERT: LC 287 THR cc_start: 0.9453 (OUTLIER) cc_final: 0.9220 (m) REVERT: LD 200 MET cc_start: 0.9557 (OUTLIER) cc_final: 0.9338 (mmt) REVERT: LD 212 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8624 (ptm) REVERT: LE 119 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8659 (mt-10) REVERT: LE 245 GLN cc_start: 0.8528 (tp-100) cc_final: 0.8233 (tp40) REVERT: LF 238 ASP cc_start: 0.8999 (p0) cc_final: 0.8779 (p0) REVERT: LH 66 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8535 (mt-10) REVERT: LH 115 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.8133 (ptp90) REVERT: LI 55 ASP cc_start: 0.8792 (t0) cc_final: 0.8429 (t0) REVERT: LI 150 GLU cc_start: 0.8869 (tp30) cc_final: 0.8663 (tp30) REVERT: LI 183 ASP cc_start: 0.8491 (t0) cc_final: 0.8257 (t0) REVERT: LL 17 ASP cc_start: 0.8802 (t0) cc_final: 0.8490 (t0) REVERT: LL 173 GLU cc_start: 0.9144 (mt-10) cc_final: 0.8749 (mt-10) REVERT: LM 96 GLU cc_start: 0.8466 (tp30) cc_final: 0.8175 (tp30) REVERT: LN 81 TYR cc_start: 0.9022 (m-80) cc_final: 0.8732 (m-80) REVERT: LN 161 MET cc_start: 0.9212 (ptp) cc_final: 0.9003 (mtt) REVERT: LO 113 ASP cc_start: 0.8838 (p0) cc_final: 0.8577 (p0) REVERT: LP 151 THR cc_start: 0.8940 (m) cc_final: 0.8572 (p) REVERT: LQ 4 ASP cc_start: 0.8781 (t70) cc_final: 0.8536 (t0) REVERT: LR 31 GLU cc_start: 0.8671 (tp30) cc_final: 0.8440 (tp30) REVERT: LS 112 ASP cc_start: 0.9020 (t0) cc_final: 0.8487 (t0) REVERT: LU 31 ASP cc_start: 0.8661 (m-30) cc_final: 0.8354 (m-30) REVERT: LU 39 PHE cc_start: 0.9549 (t80) cc_final: 0.9269 (t80) REVERT: LU 111 GLU cc_start: 0.8761 (tt0) cc_final: 0.8067 (tt0) REVERT: LX 145 ASP cc_start: 0.8695 (t0) cc_final: 0.8331 (t0) REVERT: LY 88 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8383 (tp30) REVERT: LZ 81 MET cc_start: 0.9436 (OUTLIER) cc_final: 0.8330 (tpt) REVERT: LZ 86 SER cc_start: 0.9523 (OUTLIER) cc_final: 0.9280 (t) REVERT: Lb 68 ARG cc_start: 0.7864 (ttp-110) cc_final: 0.7390 (ttp-110) REVERT: Lb 98 TYR cc_start: 0.9432 (t80) cc_final: 0.9136 (t80) REVERT: Lc 98 ASP cc_start: 0.9065 (t0) cc_final: 0.8735 (t0) REVERT: Ld 61 ASP cc_start: 0.8839 (t0) cc_final: 0.8345 (t0) REVERT: Ld 118 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8200 (mm110) REVERT: Le 86 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8066 (mp0) REVERT: Lh 16 GLU cc_start: 0.8355 (mt-10) cc_final: 0.8043 (mt-10) REVERT: Li 88 GLU cc_start: 0.8816 (tp30) cc_final: 0.8597 (tp30) REVERT: Lk 68 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7555 (tp30) REVERT: Lp 30 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8784 (mt-10) REVERT: Lr 125 MET cc_start: 0.7212 (tpt) cc_final: 0.6888 (mmp) REVERT: Lz 76 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7850 (pp20) REVERT: Lz 119 GLN cc_start: 0.8672 (mp10) cc_final: 0.8216 (mp10) REVERT: Lz 158 GLN cc_start: 0.8662 (tp40) cc_final: 0.8409 (tm-30) REVERT: Lz 184 HIS cc_start: 0.8682 (t-90) cc_final: 0.8159 (t70) outliers start: 140 outliers final: 87 residues processed: 866 average time/residue: 1.2019 time to fit residues: 1873.1870 Evaluate side-chains 870 residues out of total 7104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 769 time to evaluate : 7.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 695 GLN Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 456 GLN Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain LA residue 159 SER Chi-restraints excluded: chain LB residue 4 ARG Chi-restraints excluded: chain LB residue 60 VAL Chi-restraints excluded: chain LB residue 95 THR Chi-restraints excluded: chain LB residue 101 THR Chi-restraints excluded: chain LC residue 170 LEU Chi-restraints excluded: chain LC residue 287 THR Chi-restraints excluded: chain LC residue 335 MET Chi-restraints excluded: chain LD residue 200 MET Chi-restraints excluded: chain LD residue 212 MET Chi-restraints excluded: chain LD residue 224 SER Chi-restraints excluded: chain LD residue 239 MET Chi-restraints excluded: chain LE residue 120 ASP Chi-restraints excluded: chain LF residue 25 PHE Chi-restraints excluded: chain LF residue 225 THR Chi-restraints excluded: chain LG residue 209 SER Chi-restraints excluded: chain LH residue 46 SER Chi-restraints excluded: chain LH residue 115 ARG Chi-restraints excluded: chain LH residue 177 ASP Chi-restraints excluded: chain LJ residue 47 THR Chi-restraints excluded: chain LL residue 36 ARG Chi-restraints excluded: chain LL residue 63 THR Chi-restraints excluded: chain LM residue 43 THR Chi-restraints excluded: chain LM residue 67 SER Chi-restraints excluded: chain LN residue 125 SER Chi-restraints excluded: chain LO residue 158 GLU Chi-restraints excluded: chain LP residue 10 ASN Chi-restraints excluded: chain LQ residue 42 THR Chi-restraints excluded: chain LQ residue 82 VAL Chi-restraints excluded: chain LR residue 59 SER Chi-restraints excluded: chain LR residue 112 SER Chi-restraints excluded: chain LS residue 62 VAL Chi-restraints excluded: chain LS residue 77 ASN Chi-restraints excluded: chain LS residue 169 THR Chi-restraints excluded: chain LU residue 25 CYS Chi-restraints excluded: chain LU residue 56 LEU Chi-restraints excluded: chain LU residue 60 VAL Chi-restraints excluded: chain LU residue 66 SER Chi-restraints excluded: chain LU residue 74 SER Chi-restraints excluded: chain LU residue 108 GLU Chi-restraints excluded: chain LU residue 109 SER Chi-restraints excluded: chain LV residue 22 VAL Chi-restraints excluded: chain LV residue 115 SER Chi-restraints excluded: chain LW residue 9 SER Chi-restraints excluded: chain LW residue 38 SER Chi-restraints excluded: chain LX residue 126 THR Chi-restraints excluded: chain LX residue 148 ASP Chi-restraints excluded: chain LY residue 12 SER Chi-restraints excluded: chain LY residue 53 ASP Chi-restraints excluded: chain LY residue 66 GLN Chi-restraints excluded: chain LY residue 111 LEU Chi-restraints excluded: chain LZ residue 31 ASP Chi-restraints excluded: chain LZ residue 34 SER Chi-restraints excluded: chain LZ residue 54 THR Chi-restraints excluded: chain LZ residue 81 MET Chi-restraints excluded: chain LZ residue 86 SER Chi-restraints excluded: chain LZ residue 99 ASP Chi-restraints excluded: chain LZ residue 100 VAL Chi-restraints excluded: chain LZ residue 132 GLN Chi-restraints excluded: chain La residue 105 ARG Chi-restraints excluded: chain Lb residue 9 THR Chi-restraints excluded: chain Lc residue 24 SER Chi-restraints excluded: chain Lc residue 94 LEU Chi-restraints excluded: chain Lc residue 102 SER Chi-restraints excluded: chain Ld residue 46 LEU Chi-restraints excluded: chain Ld residue 94 GLU Chi-restraints excluded: chain Ld residue 98 SER Chi-restraints excluded: chain Ld residue 112 THR Chi-restraints excluded: chain Ld residue 118 GLN Chi-restraints excluded: chain Ld residue 119 THR Chi-restraints excluded: chain Le residue 86 GLU Chi-restraints excluded: chain Lf residue 5 LEU Chi-restraints excluded: chain Lf residue 37 ASP Chi-restraints excluded: chain Li residue 12 ASN Chi-restraints excluded: chain Lj residue 15 THR Chi-restraints excluded: chain Ll residue 9 ILE Chi-restraints excluded: chain Ll residue 23 ILE Chi-restraints excluded: chain Ll residue 47 THR Chi-restraints excluded: chain Lp residue 25 MET Chi-restraints excluded: chain Lp residue 30 GLU Chi-restraints excluded: chain Lp residue 73 THR Chi-restraints excluded: chain Lp residue 74 THR Chi-restraints excluded: chain Lp residue 89 LEU Chi-restraints excluded: chain Lr residue 52 GLU Chi-restraints excluded: chain Lr residue 80 THR Chi-restraints excluded: chain Lz residue 76 GLU Chi-restraints excluded: chain Lz residue 80 VAL Chi-restraints excluded: chain Lz residue 87 ILE Chi-restraints excluded: chain Lz residue 139 THR Chi-restraints excluded: chain Lz residue 208 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1174 random chunks: chunk 945 optimal weight: 7.9990 chunk 644 optimal weight: 0.8980 chunk 16 optimal weight: 20.0000 chunk 844 optimal weight: 6.9990 chunk 468 optimal weight: 5.9990 chunk 968 optimal weight: 9.9990 chunk 784 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 579 optimal weight: 3.9990 chunk 1018 optimal weight: 9.9990 chunk 286 optimal weight: 10.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 GLN ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 248 ASN LG 195 HIS ** LL 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LN 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 97 ASN ** LP 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LU 50 ASN Le 80 HIS Lz 72 GLN Lz 140 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9015 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 157182 Z= 0.268 Angle : 0.480 9.697 230280 Z= 0.251 Chirality : 0.034 0.238 28562 Planarity : 0.004 0.053 15225 Dihedral : 22.434 177.564 68514 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.32 % Favored : 97.65 % Rotamer: Outliers : 2.07 % Allowed : 13.88 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.09), residues: 8112 helix: 2.27 (0.09), residues: 3357 sheet: 0.39 (0.16), residues: 1010 loop : 0.34 (0.10), residues: 3745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRPLN 120 HIS 0.005 0.001 HISLa 40 PHE 0.035 0.001 PHELZ 131 TYR 0.017 0.001 TYRLQ 32 ARG 0.006 0.000 ARGLW 57 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16224 Ramachandran restraints generated. 8112 Oldfield, 0 Emsley, 8112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16224 Ramachandran restraints generated. 8112 Oldfield, 0 Emsley, 8112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 940 residues out of total 7104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 793 time to evaluate : 8.238 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: A 479 GLN cc_start: 0.4031 (OUTLIER) cc_final: 0.3795 (pm20) REVERT: A 652 MET cc_start: 0.6413 (tpp) cc_final: 0.6045 (tpp) REVERT: A 695 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8183 (tp40) REVERT: B 185 ASP cc_start: 0.9556 (OUTLIER) cc_final: 0.9187 (t0) REVERT: B 385 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7752 (tm) REVERT: LB 4 ARG cc_start: 0.9142 (OUTLIER) cc_final: 0.7708 (ttm170) REVERT: LB 200 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.8213 (mtt90) REVERT: LC 1 MET cc_start: 0.1965 (ppp) cc_final: 0.0915 (tmm) REVERT: LC 287 THR cc_start: 0.9465 (OUTLIER) cc_final: 0.9223 (m) REVERT: LE 245 GLN cc_start: 0.8524 (tp-100) cc_final: 0.8222 (tp40) REVERT: LF 28 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8463 (tt) REVERT: LH 66 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8495 (mt-10) REVERT: LH 115 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8078 (ptp90) REVERT: LI 55 ASP cc_start: 0.8767 (t0) cc_final: 0.8399 (t0) REVERT: LL 17 ASP cc_start: 0.8807 (t0) cc_final: 0.8525 (t0) REVERT: LL 173 GLU cc_start: 0.9141 (mt-10) cc_final: 0.8739 (mt-10) REVERT: LM 96 GLU cc_start: 0.8439 (tp30) cc_final: 0.8135 (tp30) REVERT: LN 81 TYR cc_start: 0.9004 (m-80) cc_final: 0.8689 (m-80) REVERT: LN 161 MET cc_start: 0.9205 (OUTLIER) cc_final: 0.8955 (mtt) REVERT: LO 113 ASP cc_start: 0.8834 (p0) cc_final: 0.8568 (p0) REVERT: LO 173 GLN cc_start: 0.8903 (tt0) cc_final: 0.8573 (tp-100) REVERT: LP 151 THR cc_start: 0.8928 (m) cc_final: 0.8588 (p) REVERT: LQ 4 ASP cc_start: 0.8775 (t70) cc_final: 0.8503 (t0) REVERT: LQ 147 GLU cc_start: 0.8745 (tp30) cc_final: 0.8473 (tp30) REVERT: LR 31 GLU cc_start: 0.8692 (tp30) cc_final: 0.8455 (tp30) REVERT: LS 112 ASP cc_start: 0.8986 (t0) cc_final: 0.8400 (t0) REVERT: LU 31 ASP cc_start: 0.8683 (m-30) cc_final: 0.8375 (m-30) REVERT: LU 39 PHE cc_start: 0.9556 (t80) cc_final: 0.9262 (t80) REVERT: LU 40 GLU cc_start: 0.8917 (tt0) cc_final: 0.8347 (tt0) REVERT: LU 44 GLN cc_start: 0.9171 (mt0) cc_final: 0.8904 (mp10) REVERT: LX 145 ASP cc_start: 0.8710 (t0) cc_final: 0.8342 (t0) REVERT: LY 88 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8397 (tp30) REVERT: LZ 81 MET cc_start: 0.9427 (OUTLIER) cc_final: 0.8319 (tpt) REVERT: LZ 86 SER cc_start: 0.9521 (OUTLIER) cc_final: 0.9272 (t) REVERT: LZ 132 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.8136 (mp10) REVERT: Lb 68 ARG cc_start: 0.7881 (ttp-110) cc_final: 0.7400 (ttp-110) REVERT: Lb 98 TYR cc_start: 0.9425 (t80) cc_final: 0.9153 (t80) REVERT: Lc 98 ASP cc_start: 0.9067 (t0) cc_final: 0.8728 (t0) REVERT: Ld 61 ASP cc_start: 0.8798 (t0) cc_final: 0.8299 (t0) REVERT: Ld 118 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8128 (mm110) REVERT: Le 86 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8060 (mp0) REVERT: Lf 40 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8379 (tm-30) REVERT: Lh 16 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8074 (mt-10) REVERT: Li 88 GLU cc_start: 0.8808 (tp30) cc_final: 0.8578 (tp30) REVERT: Lm 79 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7482 (tm-30) REVERT: Lp 30 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8766 (mt-10) REVERT: Lr 125 MET cc_start: 0.7221 (tpt) cc_final: 0.6857 (mmp) REVERT: Lz 76 GLU cc_start: 0.8134 (pp20) cc_final: 0.7806 (pp20) REVERT: Lz 158 GLN cc_start: 0.8688 (tp40) cc_final: 0.8399 (tm-30) outliers start: 147 outliers final: 87 residues processed: 883 average time/residue: 1.2147 time to fit residues: 1935.8013 Evaluate side-chains 883 residues out of total 7104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 780 time to evaluate : 8.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 479 GLN Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 695 GLN Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 456 GLN Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain LA residue 159 SER Chi-restraints excluded: chain LB residue 4 ARG Chi-restraints excluded: chain LB residue 60 VAL Chi-restraints excluded: chain LB residue 101 THR Chi-restraints excluded: chain LB residue 181 MET Chi-restraints excluded: chain LB residue 200 ARG Chi-restraints excluded: chain LC residue 170 LEU Chi-restraints excluded: chain LC residue 287 THR Chi-restraints excluded: chain LC residue 335 MET Chi-restraints excluded: chain LD residue 239 MET Chi-restraints excluded: chain LE residue 120 ASP Chi-restraints excluded: chain LF residue 25 PHE Chi-restraints excluded: chain LF residue 28 LEU Chi-restraints excluded: chain LF residue 225 THR Chi-restraints excluded: chain LG residue 209 SER Chi-restraints excluded: chain LH residue 46 SER Chi-restraints excluded: chain LH residue 115 ARG Chi-restraints excluded: chain LH residue 177 ASP Chi-restraints excluded: chain LI residue 189 CYS Chi-restraints excluded: chain LJ residue 34 THR Chi-restraints excluded: chain LJ residue 47 THR Chi-restraints excluded: chain LL residue 36 ARG Chi-restraints excluded: chain LL residue 63 THR Chi-restraints excluded: chain LL residue 64 VAL Chi-restraints excluded: chain LM residue 43 THR Chi-restraints excluded: chain LM residue 67 SER Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 161 MET Chi-restraints excluded: chain LO residue 158 GLU Chi-restraints excluded: chain LP residue 5 SER Chi-restraints excluded: chain LQ residue 82 VAL Chi-restraints excluded: chain LR residue 59 SER Chi-restraints excluded: chain LR residue 68 LEU Chi-restraints excluded: chain LR residue 112 SER Chi-restraints excluded: chain LS residue 48 VAL Chi-restraints excluded: chain LS residue 77 ASN Chi-restraints excluded: chain LS residue 169 THR Chi-restraints excluded: chain LU residue 25 CYS Chi-restraints excluded: chain LU residue 56 LEU Chi-restraints excluded: chain LU residue 60 VAL Chi-restraints excluded: chain LU residue 66 SER Chi-restraints excluded: chain LU residue 74 SER Chi-restraints excluded: chain LU residue 109 SER Chi-restraints excluded: chain LV residue 22 VAL Chi-restraints excluded: chain LV residue 115 SER Chi-restraints excluded: chain LW residue 9 SER Chi-restraints excluded: chain LW residue 38 SER Chi-restraints excluded: chain LX residue 126 THR Chi-restraints excluded: chain LX residue 148 ASP Chi-restraints excluded: chain LY residue 12 SER Chi-restraints excluded: chain LY residue 53 ASP Chi-restraints excluded: chain LY residue 66 GLN Chi-restraints excluded: chain LY residue 111 LEU Chi-restraints excluded: chain LZ residue 34 SER Chi-restraints excluded: chain LZ residue 54 THR Chi-restraints excluded: chain LZ residue 81 MET Chi-restraints excluded: chain LZ residue 86 SER Chi-restraints excluded: chain LZ residue 99 ASP Chi-restraints excluded: chain LZ residue 100 VAL Chi-restraints excluded: chain LZ residue 132 GLN Chi-restraints excluded: chain La residue 105 ARG Chi-restraints excluded: chain Lb residue 9 THR Chi-restraints excluded: chain Lc residue 11 LEU Chi-restraints excluded: chain Lc residue 24 SER Chi-restraints excluded: chain Lc residue 94 LEU Chi-restraints excluded: chain Ld residue 46 LEU Chi-restraints excluded: chain Ld residue 94 GLU Chi-restraints excluded: chain Ld residue 98 SER Chi-restraints excluded: chain Ld residue 112 THR Chi-restraints excluded: chain Ld residue 118 GLN Chi-restraints excluded: chain Ld residue 119 THR Chi-restraints excluded: chain Le residue 86 GLU Chi-restraints excluded: chain Lf residue 5 LEU Chi-restraints excluded: chain Lf residue 37 ASP Chi-restraints excluded: chain Lf residue 105 LEU Chi-restraints excluded: chain Li residue 12 ASN Chi-restraints excluded: chain Lj residue 15 THR Chi-restraints excluded: chain Ll residue 9 ILE Chi-restraints excluded: chain Ll residue 23 ILE Chi-restraints excluded: chain Ll residue 47 THR Chi-restraints excluded: chain Lo residue 7 THR Chi-restraints excluded: chain Lp residue 30 GLU Chi-restraints excluded: chain Lp residue 73 THR Chi-restraints excluded: chain Lp residue 89 LEU Chi-restraints excluded: chain Lr residue 80 THR Chi-restraints excluded: chain Lz residue 87 ILE Chi-restraints excluded: chain Lz residue 141 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1174 random chunks: chunk 381 optimal weight: 5.9990 chunk 1021 optimal weight: 9.9990 chunk 224 optimal weight: 10.0000 chunk 666 optimal weight: 5.9990 chunk 280 optimal weight: 10.0000 chunk 1135 optimal weight: 3.9990 chunk 942 optimal weight: 9.9990 chunk 525 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 375 optimal weight: 20.0000 chunk 596 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 GLN ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 248 ASN ** LL 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LN 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LP 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LY 18 HIS ** Lz 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lz 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9032 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 157182 Z= 0.339 Angle : 0.507 10.656 230280 Z= 0.265 Chirality : 0.035 0.229 28562 Planarity : 0.004 0.053 15225 Dihedral : 22.419 177.243 68513 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.68 % Favored : 97.29 % Rotamer: Outliers : 2.10 % Allowed : 14.10 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.09), residues: 8112 helix: 2.23 (0.09), residues: 3349 sheet: 0.36 (0.16), residues: 1005 loop : 0.27 (0.10), residues: 3758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRPLj 49 HIS 0.006 0.001 HISLa 40 PHE 0.025 0.001 PHE A 485 TYR 0.024 0.001 TYRLE 115 ARG 0.009 0.000 ARGLp 84 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16224 Ramachandran restraints generated. 8112 Oldfield, 0 Emsley, 8112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16224 Ramachandran restraints generated. 8112 Oldfield, 0 Emsley, 8112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 937 residues out of total 7104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 788 time to evaluate : 8.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 GLN cc_start: 0.4087 (OUTLIER) cc_final: 0.3813 (pm20) REVERT: A 695 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8175 (tp40) REVERT: B 185 ASP cc_start: 0.9555 (OUTLIER) cc_final: 0.9181 (t0) REVERT: B 385 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7772 (tm) REVERT: LA 140 ASN cc_start: 0.9143 (t0) cc_final: 0.8809 (t0) REVERT: LB 4 ARG cc_start: 0.9162 (OUTLIER) cc_final: 0.7778 (ttm170) REVERT: LB 200 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8266 (mtt90) REVERT: LC 1 MET cc_start: 0.2091 (ppp) cc_final: 0.1024 (tmm) REVERT: LC 287 THR cc_start: 0.9477 (OUTLIER) cc_final: 0.9218 (m) REVERT: LE 245 GLN cc_start: 0.8593 (tp-100) cc_final: 0.8286 (tp40) REVERT: LF 28 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8447 (tt) REVERT: LH 66 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8597 (mt-10) REVERT: LH 115 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8212 (ptp90) REVERT: LI 55 ASP cc_start: 0.8763 (t0) cc_final: 0.8385 (t0) REVERT: LL 17 ASP cc_start: 0.8793 (t0) cc_final: 0.8476 (t0) REVERT: LL 173 GLU cc_start: 0.9162 (mt-10) cc_final: 0.8741 (mt-10) REVERT: LM 96 GLU cc_start: 0.8460 (tp30) cc_final: 0.8154 (tp30) REVERT: LN 161 MET cc_start: 0.9236 (OUTLIER) cc_final: 0.8998 (mtt) REVERT: LO 113 ASP cc_start: 0.8850 (p0) cc_final: 0.8588 (p0) REVERT: LP 108 ASP cc_start: 0.8540 (t0) cc_final: 0.8284 (t70) REVERT: LP 151 THR cc_start: 0.8977 (m) cc_final: 0.8594 (p) REVERT: LQ 4 ASP cc_start: 0.8827 (t70) cc_final: 0.8545 (t0) REVERT: LQ 147 GLU cc_start: 0.8797 (tp30) cc_final: 0.8490 (tp30) REVERT: LR 31 GLU cc_start: 0.8716 (tp30) cc_final: 0.8480 (tp30) REVERT: LS 112 ASP cc_start: 0.9024 (t0) cc_final: 0.8404 (t0) REVERT: LU 31 ASP cc_start: 0.8755 (m-30) cc_final: 0.8454 (m-30) REVERT: LU 39 PHE cc_start: 0.9585 (t80) cc_final: 0.9329 (t80) REVERT: LV 111 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8037 (mt-10) REVERT: LX 145 ASP cc_start: 0.8704 (t0) cc_final: 0.8326 (t0) REVERT: LY 88 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8379 (tp30) REVERT: LZ 81 MET cc_start: 0.9435 (OUTLIER) cc_final: 0.8333 (tpt) REVERT: LZ 86 SER cc_start: 0.9509 (OUTLIER) cc_final: 0.9276 (t) REVERT: Lb 68 ARG cc_start: 0.7872 (ttp-110) cc_final: 0.7385 (ttp-110) REVERT: Lb 98 TYR cc_start: 0.9445 (t80) cc_final: 0.9192 (t80) REVERT: Lc 98 ASP cc_start: 0.9077 (t0) cc_final: 0.8711 (t0) REVERT: Ld 61 ASP cc_start: 0.8863 (t0) cc_final: 0.8372 (t0) REVERT: Ld 118 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8131 (mm110) REVERT: Le 86 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8065 (mp0) REVERT: Lf 40 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8417 (tm-30) REVERT: Lh 16 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8045 (mt-10) REVERT: Li 88 GLU cc_start: 0.8811 (tp30) cc_final: 0.8594 (tp30) REVERT: Lk 12 LEU cc_start: 0.9614 (OUTLIER) cc_final: 0.9353 (mm) REVERT: Lk 49 ASP cc_start: 0.8444 (t70) cc_final: 0.7467 (t70) REVERT: Lk 51 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8506 (pm20) REVERT: Lp 30 GLU cc_start: 0.8994 (OUTLIER) cc_final: 0.8789 (mt-10) REVERT: Lr 125 MET cc_start: 0.7212 (tpt) cc_final: 0.6911 (mmp) REVERT: Lz 76 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7739 (pp20) REVERT: Lz 119 GLN cc_start: 0.9191 (mp10) cc_final: 0.8944 (mp10) REVERT: Lz 158 GLN cc_start: 0.8706 (tp40) cc_final: 0.8378 (tm-30) outliers start: 149 outliers final: 102 residues processed: 871 average time/residue: 1.2904 time to fit residues: 2031.9857 Evaluate side-chains 886 residues out of total 7104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 766 time to evaluate : 7.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 432 MET Chi-restraints excluded: chain A residue 479 GLN Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 695 GLN Chi-restraints excluded: chain B residue 46 GLN Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 456 GLN Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain LA residue 159 SER Chi-restraints excluded: chain LB residue 4 ARG Chi-restraints excluded: chain LB residue 60 VAL Chi-restraints excluded: chain LB residue 95 THR Chi-restraints excluded: chain LB residue 101 THR Chi-restraints excluded: chain LB residue 181 MET Chi-restraints excluded: chain LB residue 200 ARG Chi-restraints excluded: chain LC residue 170 LEU Chi-restraints excluded: chain LC residue 287 THR Chi-restraints excluded: chain LD residue 37 VAL Chi-restraints excluded: chain LD residue 239 MET Chi-restraints excluded: chain LE residue 109 LEU Chi-restraints excluded: chain LE residue 120 ASP Chi-restraints excluded: chain LF residue 25 PHE Chi-restraints excluded: chain LF residue 28 LEU Chi-restraints excluded: chain LF residue 178 SER Chi-restraints excluded: chain LF residue 225 THR Chi-restraints excluded: chain LG residue 135 VAL Chi-restraints excluded: chain LG residue 209 SER Chi-restraints excluded: chain LG residue 261 LEU Chi-restraints excluded: chain LH residue 46 SER Chi-restraints excluded: chain LH residue 115 ARG Chi-restraints excluded: chain LH residue 177 ASP Chi-restraints excluded: chain LI residue 44 ASP Chi-restraints excluded: chain LI residue 189 CYS Chi-restraints excluded: chain LJ residue 34 THR Chi-restraints excluded: chain LJ residue 47 THR Chi-restraints excluded: chain LL residue 36 ARG Chi-restraints excluded: chain LL residue 63 THR Chi-restraints excluded: chain LL residue 64 VAL Chi-restraints excluded: chain LM residue 43 THR Chi-restraints excluded: chain LM residue 67 SER Chi-restraints excluded: chain LM residue 125 ASN Chi-restraints excluded: chain LM residue 136 LEU Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 161 MET Chi-restraints excluded: chain LO residue 158 GLU Chi-restraints excluded: chain LP residue 5 SER Chi-restraints excluded: chain LP residue 10 ASN Chi-restraints excluded: chain LQ residue 42 THR Chi-restraints excluded: chain LR residue 59 SER Chi-restraints excluded: chain LR residue 112 SER Chi-restraints excluded: chain LS residue 77 ASN Chi-restraints excluded: chain LS residue 169 THR Chi-restraints excluded: chain LU residue 25 CYS Chi-restraints excluded: chain LU residue 56 LEU Chi-restraints excluded: chain LU residue 60 VAL Chi-restraints excluded: chain LU residue 66 SER Chi-restraints excluded: chain LU residue 108 GLU Chi-restraints excluded: chain LU residue 109 SER Chi-restraints excluded: chain LV residue 22 VAL Chi-restraints excluded: chain LV residue 115 SER Chi-restraints excluded: chain LW residue 9 SER Chi-restraints excluded: chain LW residue 38 SER Chi-restraints excluded: chain LX residue 126 THR Chi-restraints excluded: chain LX residue 148 ASP Chi-restraints excluded: chain LY residue 12 SER Chi-restraints excluded: chain LY residue 53 ASP Chi-restraints excluded: chain LY residue 66 GLN Chi-restraints excluded: chain LY residue 111 LEU Chi-restraints excluded: chain LZ residue 31 ASP Chi-restraints excluded: chain LZ residue 34 SER Chi-restraints excluded: chain LZ residue 54 THR Chi-restraints excluded: chain LZ residue 81 MET Chi-restraints excluded: chain LZ residue 86 SER Chi-restraints excluded: chain LZ residue 99 ASP Chi-restraints excluded: chain LZ residue 100 VAL Chi-restraints excluded: chain LZ residue 132 GLN Chi-restraints excluded: chain Lb residue 9 THR Chi-restraints excluded: chain Lc residue 11 LEU Chi-restraints excluded: chain Lc residue 75 SER Chi-restraints excluded: chain Lc residue 94 LEU Chi-restraints excluded: chain Ld residue 46 LEU Chi-restraints excluded: chain Ld residue 94 GLU Chi-restraints excluded: chain Ld residue 98 SER Chi-restraints excluded: chain Ld residue 118 GLN Chi-restraints excluded: chain Ld residue 119 THR Chi-restraints excluded: chain Le residue 86 GLU Chi-restraints excluded: chain Lf residue 5 LEU Chi-restraints excluded: chain Lf residue 37 ASP Chi-restraints excluded: chain Lf residue 105 LEU Chi-restraints excluded: chain Li residue 12 ASN Chi-restraints excluded: chain Lk residue 12 LEU Chi-restraints excluded: chain Lk residue 51 GLU Chi-restraints excluded: chain Ll residue 9 ILE Chi-restraints excluded: chain Ll residue 23 ILE Chi-restraints excluded: chain Ll residue 47 THR Chi-restraints excluded: chain Lo residue 7 THR Chi-restraints excluded: chain Lo residue 93 LEU Chi-restraints excluded: chain Lp residue 25 MET Chi-restraints excluded: chain Lp residue 30 GLU Chi-restraints excluded: chain Lp residue 73 THR Chi-restraints excluded: chain Lp residue 74 THR Chi-restraints excluded: chain Lp residue 89 LEU Chi-restraints excluded: chain Lr residue 52 GLU Chi-restraints excluded: chain Lr residue 80 THR Chi-restraints excluded: chain Lz residue 76 GLU Chi-restraints excluded: chain Lz residue 80 VAL Chi-restraints excluded: chain Lz residue 87 ILE Chi-restraints excluded: chain Lz residue 139 THR Chi-restraints excluded: chain Lz residue 141 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1174 random chunks: chunk 1095 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 chunk 647 optimal weight: 10.0000 chunk 829 optimal weight: 0.8980 chunk 642 optimal weight: 9.9990 chunk 956 optimal weight: 5.9990 chunk 634 optimal weight: 2.9990 chunk 1131 optimal weight: 10.0000 chunk 708 optimal weight: 10.0000 chunk 689 optimal weight: 3.9990 chunk 522 optimal weight: 30.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 GLN ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LH 189 GLN ** LL 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LN 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LO 42 ASN ** LP 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LU 50 ASN Lz 35 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9015 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 157182 Z= 0.202 Angle : 0.485 11.363 230280 Z= 0.253 Chirality : 0.032 0.232 28562 Planarity : 0.004 0.054 15225 Dihedral : 22.491 177.211 68513 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.40 % Favored : 97.56 % Rotamer: Outliers : 2.07 % Allowed : 14.41 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.09), residues: 8112 helix: 2.23 (0.09), residues: 3348 sheet: 0.39 (0.16), residues: 1007 loop : 0.30 (0.10), residues: 3757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRPLj 49 HIS 0.011 0.001 HIS A 668 PHE 0.015 0.001 PHE A 638 TYR 0.034 0.001 TYRLE 73 ARG 0.007 0.000 ARGLI 82 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16224 Ramachandran restraints generated. 8112 Oldfield, 0 Emsley, 8112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16224 Ramachandran restraints generated. 8112 Oldfield, 0 Emsley, 8112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 946 residues out of total 7104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 799 time to evaluate : 8.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 GLN cc_start: 0.4127 (OUTLIER) cc_final: 0.3852 (pm20) REVERT: A 652 MET cc_start: 0.6490 (tpp) cc_final: 0.6207 (tpp) REVERT: A 695 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.8170 (tp40) REVERT: B 185 ASP cc_start: 0.9553 (OUTLIER) cc_final: 0.9182 (t0) REVERT: B 385 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7766 (tm) REVERT: LA 140 ASN cc_start: 0.9111 (t0) cc_final: 0.8812 (t0) REVERT: LB 4 ARG cc_start: 0.9141 (OUTLIER) cc_final: 0.7756 (ttm170) REVERT: LB 200 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.8178 (mtt90) REVERT: LC 1 MET cc_start: 0.2082 (ppp) cc_final: 0.0984 (tmm) REVERT: LC 287 THR cc_start: 0.9472 (OUTLIER) cc_final: 0.9210 (m) REVERT: LD 212 MET cc_start: 0.8831 (ptp) cc_final: 0.8567 (ptp) REVERT: LE 245 GLN cc_start: 0.8569 (tp-100) cc_final: 0.8269 (tp40) REVERT: LF 28 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8466 (tt) REVERT: LH 66 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8483 (mt-10) REVERT: LH 115 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.8109 (ptp90) REVERT: LI 55 ASP cc_start: 0.8747 (t0) cc_final: 0.8376 (t0) REVERT: LJ 104 ASN cc_start: 0.9589 (OUTLIER) cc_final: 0.9369 (m-40) REVERT: LL 17 ASP cc_start: 0.8789 (t0) cc_final: 0.8486 (t0) REVERT: LL 173 GLU cc_start: 0.9159 (mt-10) cc_final: 0.8735 (mt-10) REVERT: LN 161 MET cc_start: 0.9200 (OUTLIER) cc_final: 0.8957 (mtt) REVERT: LO 87 MET cc_start: 0.9153 (OUTLIER) cc_final: 0.8638 (mtt) REVERT: LO 113 ASP cc_start: 0.8832 (p0) cc_final: 0.8572 (p0) REVERT: LO 173 GLN cc_start: 0.8898 (tt0) cc_final: 0.8599 (tp-100) REVERT: LP 108 ASP cc_start: 0.8501 (t0) cc_final: 0.8238 (t70) REVERT: LP 151 THR cc_start: 0.8934 (m) cc_final: 0.8583 (p) REVERT: LQ 147 GLU cc_start: 0.8782 (tp30) cc_final: 0.8463 (tp30) REVERT: LR 31 GLU cc_start: 0.8698 (tp30) cc_final: 0.8456 (tp30) REVERT: LS 112 ASP cc_start: 0.9002 (t0) cc_final: 0.8458 (t0) REVERT: LU 31 ASP cc_start: 0.8740 (m-30) cc_final: 0.8421 (m-30) REVERT: LU 39 PHE cc_start: 0.9573 (t80) cc_final: 0.9254 (t80) REVERT: LV 111 GLU cc_start: 0.8355 (mt-10) cc_final: 0.8024 (mt-10) REVERT: LX 145 ASP cc_start: 0.8706 (t0) cc_final: 0.8335 (t0) REVERT: LY 88 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8379 (tp30) REVERT: LZ 81 MET cc_start: 0.9429 (OUTLIER) cc_final: 0.8321 (tpt) REVERT: LZ 86 SER cc_start: 0.9502 (OUTLIER) cc_final: 0.9259 (t) REVERT: Lb 42 ASN cc_start: 0.8914 (t0) cc_final: 0.8654 (t0) REVERT: Lb 68 ARG cc_start: 0.7848 (ttp-110) cc_final: 0.7356 (ttp-110) REVERT: Lb 98 TYR cc_start: 0.9431 (t80) cc_final: 0.9185 (t80) REVERT: Lc 98 ASP cc_start: 0.9075 (t0) cc_final: 0.8702 (t0) REVERT: Ld 61 ASP cc_start: 0.8827 (t0) cc_final: 0.8342 (t0) REVERT: Ld 118 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8106 (mm110) REVERT: Le 86 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8053 (mp0) REVERT: Lh 16 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8026 (mt-10) REVERT: Li 88 GLU cc_start: 0.8792 (tp30) cc_final: 0.8574 (tp30) REVERT: Lk 49 ASP cc_start: 0.8360 (t70) cc_final: 0.8043 (t70) REVERT: Lk 54 GLU cc_start: 0.8351 (tp30) cc_final: 0.8119 (tp30) REVERT: Lr 125 MET cc_start: 0.7213 (tpt) cc_final: 0.6912 (mmp) REVERT: Lz 76 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7667 (pp20) REVERT: Lz 119 GLN cc_start: 0.9189 (mp10) cc_final: 0.8939 (mp10) REVERT: Lz 158 GLN cc_start: 0.8687 (tp40) cc_final: 0.8366 (tm-30) outliers start: 147 outliers final: 108 residues processed: 885 average time/residue: 1.2220 time to fit residues: 1952.8555 Evaluate side-chains 909 residues out of total 7104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 784 time to evaluate : 8.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 432 MET Chi-restraints excluded: chain A residue 479 GLN Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 695 GLN Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 456 GLN Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain LA residue 159 SER Chi-restraints excluded: chain LB residue 4 ARG Chi-restraints excluded: chain LB residue 60 VAL Chi-restraints excluded: chain LB residue 101 THR Chi-restraints excluded: chain LB residue 181 MET Chi-restraints excluded: chain LB residue 200 ARG Chi-restraints excluded: chain LC residue 170 LEU Chi-restraints excluded: chain LC residue 198 ASN Chi-restraints excluded: chain LC residue 287 THR Chi-restraints excluded: chain LD residue 37 VAL Chi-restraints excluded: chain LD residue 239 MET Chi-restraints excluded: chain LE residue 109 LEU Chi-restraints excluded: chain LE residue 120 ASP Chi-restraints excluded: chain LF residue 25 PHE Chi-restraints excluded: chain LF residue 28 LEU Chi-restraints excluded: chain LF residue 74 MET Chi-restraints excluded: chain LF residue 178 SER Chi-restraints excluded: chain LF residue 225 THR Chi-restraints excluded: chain LG residue 135 VAL Chi-restraints excluded: chain LG residue 209 SER Chi-restraints excluded: chain LG residue 261 LEU Chi-restraints excluded: chain LH residue 46 SER Chi-restraints excluded: chain LH residue 115 ARG Chi-restraints excluded: chain LH residue 177 ASP Chi-restraints excluded: chain LI residue 189 CYS Chi-restraints excluded: chain LJ residue 34 THR Chi-restraints excluded: chain LJ residue 47 THR Chi-restraints excluded: chain LJ residue 104 ASN Chi-restraints excluded: chain LL residue 36 ARG Chi-restraints excluded: chain LL residue 63 THR Chi-restraints excluded: chain LL residue 64 VAL Chi-restraints excluded: chain LM residue 43 THR Chi-restraints excluded: chain LM residue 125 ASN Chi-restraints excluded: chain LM residue 136 LEU Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 125 SER Chi-restraints excluded: chain LN residue 126 THR Chi-restraints excluded: chain LN residue 161 MET Chi-restraints excluded: chain LO residue 87 MET Chi-restraints excluded: chain LO residue 158 GLU Chi-restraints excluded: chain LP residue 5 SER Chi-restraints excluded: chain LP residue 10 ASN Chi-restraints excluded: chain LP residue 115 GLU Chi-restraints excluded: chain LQ residue 82 VAL Chi-restraints excluded: chain LR residue 59 SER Chi-restraints excluded: chain LR residue 68 LEU Chi-restraints excluded: chain LS residue 48 VAL Chi-restraints excluded: chain LS residue 77 ASN Chi-restraints excluded: chain LS residue 169 THR Chi-restraints excluded: chain LT residue 104 SER Chi-restraints excluded: chain LT residue 118 GLU Chi-restraints excluded: chain LU residue 25 CYS Chi-restraints excluded: chain LU residue 56 LEU Chi-restraints excluded: chain LU residue 60 VAL Chi-restraints excluded: chain LU residue 66 SER Chi-restraints excluded: chain LU residue 74 SER Chi-restraints excluded: chain LU residue 108 GLU Chi-restraints excluded: chain LV residue 22 VAL Chi-restraints excluded: chain LV residue 115 SER Chi-restraints excluded: chain LW residue 9 SER Chi-restraints excluded: chain LW residue 38 SER Chi-restraints excluded: chain LX residue 126 THR Chi-restraints excluded: chain LX residue 148 ASP Chi-restraints excluded: chain LY residue 12 SER Chi-restraints excluded: chain LY residue 53 ASP Chi-restraints excluded: chain LY residue 66 GLN Chi-restraints excluded: chain LY residue 111 LEU Chi-restraints excluded: chain LZ residue 31 ASP Chi-restraints excluded: chain LZ residue 34 SER Chi-restraints excluded: chain LZ residue 54 THR Chi-restraints excluded: chain LZ residue 81 MET Chi-restraints excluded: chain LZ residue 86 SER Chi-restraints excluded: chain LZ residue 99 ASP Chi-restraints excluded: chain LZ residue 100 VAL Chi-restraints excluded: chain LZ residue 132 GLN Chi-restraints excluded: chain La residue 105 ARG Chi-restraints excluded: chain Lb residue 9 THR Chi-restraints excluded: chain Lb residue 76 VAL Chi-restraints excluded: chain Lc residue 11 LEU Chi-restraints excluded: chain Lc residue 94 LEU Chi-restraints excluded: chain Ld residue 46 LEU Chi-restraints excluded: chain Ld residue 94 GLU Chi-restraints excluded: chain Ld residue 118 GLN Chi-restraints excluded: chain Ld residue 119 THR Chi-restraints excluded: chain Le residue 86 GLU Chi-restraints excluded: chain Lf residue 5 LEU Chi-restraints excluded: chain Lf residue 37 ASP Chi-restraints excluded: chain Lf residue 105 LEU Chi-restraints excluded: chain Lh residue 42 SER Chi-restraints excluded: chain Li residue 12 ASN Chi-restraints excluded: chain Lj residue 15 THR Chi-restraints excluded: chain Ll residue 9 ILE Chi-restraints excluded: chain Ll residue 23 ILE Chi-restraints excluded: chain Ll residue 47 THR Chi-restraints excluded: chain Lm residue 127 VAL Chi-restraints excluded: chain Lo residue 7 THR Chi-restraints excluded: chain Lo residue 93 LEU Chi-restraints excluded: chain Lp residue 25 MET Chi-restraints excluded: chain Lp residue 73 THR Chi-restraints excluded: chain Lp residue 89 LEU Chi-restraints excluded: chain Lr residue 52 GLU Chi-restraints excluded: chain Lr residue 80 THR Chi-restraints excluded: chain Lz residue 12 GLU Chi-restraints excluded: chain Lz residue 76 GLU Chi-restraints excluded: chain Lz residue 80 VAL Chi-restraints excluded: chain Lz residue 87 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1174 random chunks: chunk 700 optimal weight: 9.9990 chunk 451 optimal weight: 30.0000 chunk 675 optimal weight: 9.9990 chunk 340 optimal weight: 10.0000 chunk 222 optimal weight: 10.0000 chunk 219 optimal weight: 10.0000 chunk 719 optimal weight: 3.9990 chunk 770 optimal weight: 20.0000 chunk 559 optimal weight: 1.9990 chunk 105 optimal weight: 10.0000 chunk 889 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LL 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LN 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LP 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lz 72 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9037 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 157182 Z= 0.373 Angle : 0.520 10.992 230280 Z= 0.271 Chirality : 0.036 0.234 28562 Planarity : 0.004 0.053 15225 Dihedral : 22.422 177.166 68513 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.61 % Favored : 97.35 % Rotamer: Outliers : 2.10 % Allowed : 14.45 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.09), residues: 8112 helix: 2.16 (0.09), residues: 3356 sheet: 0.33 (0.16), residues: 1001 loop : 0.21 (0.10), residues: 3755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRPLj 49 HIS 0.006 0.001 HISLa 40 PHE 0.016 0.001 PHE B 229 TYR 0.020 0.001 TYRLQ 32 ARG 0.009 0.000 ARGLp 84 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16224 Ramachandran restraints generated. 8112 Oldfield, 0 Emsley, 8112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16224 Ramachandran restraints generated. 8112 Oldfield, 0 Emsley, 8112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 925 residues out of total 7104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 776 time to evaluate : 8.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 GLN cc_start: 0.4222 (OUTLIER) cc_final: 0.3961 (pm20) REVERT: A 652 MET cc_start: 0.6544 (tpp) cc_final: 0.6121 (mmp) REVERT: A 701 MET cc_start: 0.7558 (ttp) cc_final: 0.7323 (ttt) REVERT: B 185 ASP cc_start: 0.9567 (OUTLIER) cc_final: 0.9182 (t0) REVERT: B 385 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7814 (tm) REVERT: LB 4 ARG cc_start: 0.9166 (OUTLIER) cc_final: 0.7789 (ttm170) REVERT: LB 200 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.8249 (mtt90) REVERT: LC 1 MET cc_start: 0.2063 (ppp) cc_final: 0.0977 (tmm) REVERT: LC 287 THR cc_start: 0.9481 (OUTLIER) cc_final: 0.9211 (m) REVERT: LD 212 MET cc_start: 0.8871 (ptp) cc_final: 0.8623 (ptp) REVERT: LE 119 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8553 (mt-10) REVERT: LE 245 GLN cc_start: 0.8626 (tp-100) cc_final: 0.8333 (tp40) REVERT: LF 28 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8474 (tt) REVERT: LH 66 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8578 (mt-10) REVERT: LH 115 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.8263 (ptp90) REVERT: LI 55 ASP cc_start: 0.8753 (t0) cc_final: 0.8376 (t0) REVERT: LL 17 ASP cc_start: 0.8804 (t0) cc_final: 0.8488 (t0) REVERT: LN 161 MET cc_start: 0.9258 (OUTLIER) cc_final: 0.9014 (mtt) REVERT: LO 113 ASP cc_start: 0.8869 (p0) cc_final: 0.8608 (p0) REVERT: LP 151 THR cc_start: 0.8980 (m) cc_final: 0.8586 (p) REVERT: LQ 147 GLU cc_start: 0.8814 (tp30) cc_final: 0.8487 (tp30) REVERT: LR 31 GLU cc_start: 0.8731 (tp30) cc_final: 0.8496 (tp30) REVERT: LS 112 ASP cc_start: 0.9030 (t0) cc_final: 0.8522 (t0) REVERT: LU 31 ASP cc_start: 0.8770 (m-30) cc_final: 0.8457 (m-30) REVERT: LU 39 PHE cc_start: 0.9580 (t80) cc_final: 0.9346 (t80) REVERT: LU 40 GLU cc_start: 0.8956 (tt0) cc_final: 0.8495 (tt0) REVERT: LU 44 GLN cc_start: 0.9196 (mt0) cc_final: 0.8958 (mp10) REVERT: LV 48 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.7195 (ttp80) REVERT: LV 111 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8054 (mt-10) REVERT: LX 145 ASP cc_start: 0.8748 (t0) cc_final: 0.8390 (t0) REVERT: LY 88 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8399 (tp30) REVERT: LZ 81 MET cc_start: 0.9442 (OUTLIER) cc_final: 0.8437 (tpt) REVERT: LZ 86 SER cc_start: 0.9510 (OUTLIER) cc_final: 0.9275 (t) REVERT: LZ 92 ASP cc_start: 0.8813 (t0) cc_final: 0.8436 (t0) REVERT: Lb 98 TYR cc_start: 0.9442 (t80) cc_final: 0.9209 (t80) REVERT: Lc 98 ASP cc_start: 0.9086 (t0) cc_final: 0.8698 (t0) REVERT: Ld 61 ASP cc_start: 0.8878 (t0) cc_final: 0.8637 (t70) REVERT: Ld 118 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.8123 (mm110) REVERT: Le 86 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8080 (mp0) REVERT: Lh 16 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8058 (mt-10) REVERT: Li 88 GLU cc_start: 0.8810 (tp30) cc_final: 0.8605 (tp30) REVERT: Lk 12 LEU cc_start: 0.9594 (OUTLIER) cc_final: 0.9338 (mm) REVERT: Lr 125 MET cc_start: 0.7205 (tpt) cc_final: 0.6947 (mmp) REVERT: Lz 76 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7755 (pp20) REVERT: Lz 119 GLN cc_start: 0.9182 (mp10) cc_final: 0.8922 (mp10) REVERT: Lz 158 GLN cc_start: 0.8716 (tp40) cc_final: 0.8381 (tm-30) outliers start: 149 outliers final: 111 residues processed: 870 average time/residue: 1.2943 time to fit residues: 2042.2492 Evaluate side-chains 889 residues out of total 7104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 762 time to evaluate : 7.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 479 GLN Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 456 GLN Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain LA residue 159 SER Chi-restraints excluded: chain LB residue 4 ARG Chi-restraints excluded: chain LB residue 60 VAL Chi-restraints excluded: chain LB residue 95 THR Chi-restraints excluded: chain LB residue 101 THR Chi-restraints excluded: chain LB residue 181 MET Chi-restraints excluded: chain LB residue 200 ARG Chi-restraints excluded: chain LC residue 170 LEU Chi-restraints excluded: chain LC residue 198 ASN Chi-restraints excluded: chain LC residue 287 THR Chi-restraints excluded: chain LD residue 37 VAL Chi-restraints excluded: chain LD residue 239 MET Chi-restraints excluded: chain LE residue 109 LEU Chi-restraints excluded: chain LE residue 120 ASP Chi-restraints excluded: chain LF residue 25 PHE Chi-restraints excluded: chain LF residue 28 LEU Chi-restraints excluded: chain LF residue 74 MET Chi-restraints excluded: chain LF residue 178 SER Chi-restraints excluded: chain LF residue 225 THR Chi-restraints excluded: chain LG residue 135 VAL Chi-restraints excluded: chain LG residue 209 SER Chi-restraints excluded: chain LG residue 261 LEU Chi-restraints excluded: chain LH residue 46 SER Chi-restraints excluded: chain LH residue 115 ARG Chi-restraints excluded: chain LH residue 177 ASP Chi-restraints excluded: chain LI residue 189 CYS Chi-restraints excluded: chain LJ residue 34 THR Chi-restraints excluded: chain LJ residue 47 THR Chi-restraints excluded: chain LL residue 36 ARG Chi-restraints excluded: chain LL residue 63 THR Chi-restraints excluded: chain LL residue 64 VAL Chi-restraints excluded: chain LM residue 43 THR Chi-restraints excluded: chain LM residue 67 SER Chi-restraints excluded: chain LM residue 125 ASN Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 126 THR Chi-restraints excluded: chain LN residue 161 MET Chi-restraints excluded: chain LO residue 158 GLU Chi-restraints excluded: chain LP residue 5 SER Chi-restraints excluded: chain LP residue 10 ASN Chi-restraints excluded: chain LQ residue 42 THR Chi-restraints excluded: chain LQ residue 82 VAL Chi-restraints excluded: chain LR residue 59 SER Chi-restraints excluded: chain LR residue 68 LEU Chi-restraints excluded: chain LR residue 112 SER Chi-restraints excluded: chain LS residue 19 THR Chi-restraints excluded: chain LS residue 77 ASN Chi-restraints excluded: chain LS residue 169 THR Chi-restraints excluded: chain LT residue 104 SER Chi-restraints excluded: chain LU residue 25 CYS Chi-restraints excluded: chain LU residue 56 LEU Chi-restraints excluded: chain LU residue 60 VAL Chi-restraints excluded: chain LU residue 66 SER Chi-restraints excluded: chain LU residue 74 SER Chi-restraints excluded: chain LU residue 108 GLU Chi-restraints excluded: chain LU residue 109 SER Chi-restraints excluded: chain LV residue 22 VAL Chi-restraints excluded: chain LV residue 48 ARG Chi-restraints excluded: chain LV residue 115 SER Chi-restraints excluded: chain LW residue 9 SER Chi-restraints excluded: chain LW residue 38 SER Chi-restraints excluded: chain LX residue 126 THR Chi-restraints excluded: chain LX residue 148 ASP Chi-restraints excluded: chain LY residue 12 SER Chi-restraints excluded: chain LY residue 53 ASP Chi-restraints excluded: chain LY residue 66 GLN Chi-restraints excluded: chain LY residue 111 LEU Chi-restraints excluded: chain LZ residue 31 ASP Chi-restraints excluded: chain LZ residue 34 SER Chi-restraints excluded: chain LZ residue 54 THR Chi-restraints excluded: chain LZ residue 81 MET Chi-restraints excluded: chain LZ residue 86 SER Chi-restraints excluded: chain LZ residue 99 ASP Chi-restraints excluded: chain LZ residue 100 VAL Chi-restraints excluded: chain La residue 105 ARG Chi-restraints excluded: chain Lb residue 9 THR Chi-restraints excluded: chain Lb residue 76 VAL Chi-restraints excluded: chain Lc residue 11 LEU Chi-restraints excluded: chain Lc residue 24 SER Chi-restraints excluded: chain Lc residue 94 LEU Chi-restraints excluded: chain Ld residue 46 LEU Chi-restraints excluded: chain Ld residue 94 GLU Chi-restraints excluded: chain Ld residue 98 SER Chi-restraints excluded: chain Ld residue 112 THR Chi-restraints excluded: chain Ld residue 118 GLN Chi-restraints excluded: chain Ld residue 119 THR Chi-restraints excluded: chain Le residue 86 GLU Chi-restraints excluded: chain Lf residue 5 LEU Chi-restraints excluded: chain Lf residue 37 ASP Chi-restraints excluded: chain Lf residue 105 LEU Chi-restraints excluded: chain Lh residue 42 SER Chi-restraints excluded: chain Li residue 12 ASN Chi-restraints excluded: chain Lj residue 15 THR Chi-restraints excluded: chain Lk residue 12 LEU Chi-restraints excluded: chain Ll residue 9 ILE Chi-restraints excluded: chain Ll residue 23 ILE Chi-restraints excluded: chain Ll residue 47 THR Chi-restraints excluded: chain Lm residue 78 ILE Chi-restraints excluded: chain Lm residue 127 VAL Chi-restraints excluded: chain Lo residue 7 THR Chi-restraints excluded: chain Lo residue 93 LEU Chi-restraints excluded: chain Lp residue 25 MET Chi-restraints excluded: chain Lp residue 73 THR Chi-restraints excluded: chain Lp residue 89 LEU Chi-restraints excluded: chain Lr residue 80 THR Chi-restraints excluded: chain Lz residue 12 GLU Chi-restraints excluded: chain Lz residue 76 GLU Chi-restraints excluded: chain Lz residue 80 VAL Chi-restraints excluded: chain Lz residue 87 ILE Chi-restraints excluded: chain Lz residue 141 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1174 random chunks: chunk 1029 optimal weight: 0.9980 chunk 1084 optimal weight: 4.9990 chunk 989 optimal weight: 8.9990 chunk 1054 optimal weight: 5.9990 chunk 1083 optimal weight: 0.9980 chunk 634 optimal weight: 2.9990 chunk 459 optimal weight: 6.9990 chunk 828 optimal weight: 2.9990 chunk 323 optimal weight: 30.0000 chunk 952 optimal weight: 10.0000 chunk 997 optimal weight: 9.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 GLN ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LL 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LN 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LP 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LU 50 ASN ** Lz 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9014 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 157182 Z= 0.182 Angle : 0.488 14.741 230280 Z= 0.254 Chirality : 0.032 0.224 28562 Planarity : 0.004 0.054 15225 Dihedral : 22.529 177.158 68513 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.45 % Favored : 97.51 % Rotamer: Outliers : 1.69 % Allowed : 14.89 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.09), residues: 8112 helix: 2.19 (0.09), residues: 3345 sheet: 0.36 (0.17), residues: 985 loop : 0.27 (0.10), residues: 3782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPLj 49 HIS 0.005 0.001 HISLI 147 PHE 0.049 0.001 PHE B 421 TYR 0.019 0.001 TYRLU 90 ARG 0.008 0.000 ARGLI 82 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16224 Ramachandran restraints generated. 8112 Oldfield, 0 Emsley, 8112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16224 Ramachandran restraints generated. 8112 Oldfield, 0 Emsley, 8112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 915 residues out of total 7104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 795 time to evaluate : 8.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 GLN cc_start: 0.4180 (OUTLIER) cc_final: 0.3935 (pm20) REVERT: A 652 MET cc_start: 0.6533 (tpp) cc_final: 0.6149 (mmp) REVERT: A 701 MET cc_start: 0.7363 (ttp) cc_final: 0.7036 (ttt) REVERT: B 185 ASP cc_start: 0.9566 (OUTLIER) cc_final: 0.9182 (t0) REVERT: B 385 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7805 (tm) REVERT: LA 140 ASN cc_start: 0.9166 (t0) cc_final: 0.8779 (t0) REVERT: LB 4 ARG cc_start: 0.9133 (OUTLIER) cc_final: 0.7878 (ttm170) REVERT: LB 200 ARG cc_start: 0.9062 (OUTLIER) cc_final: 0.8196 (mtt90) REVERT: LC 1 MET cc_start: 0.2007 (ppp) cc_final: 0.0898 (tmm) REVERT: LC 287 THR cc_start: 0.9473 (OUTLIER) cc_final: 0.9204 (m) REVERT: LD 3 PHE cc_start: 0.5581 (m-80) cc_final: 0.5355 (m-80) REVERT: LD 212 MET cc_start: 0.8859 (ptp) cc_final: 0.8622 (ptp) REVERT: LE 119 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8542 (mt-10) REVERT: LE 245 GLN cc_start: 0.8587 (tp-100) cc_final: 0.8295 (tp40) REVERT: LF 28 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8455 (tt) REVERT: LH 115 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.8090 (ptp90) REVERT: LI 55 ASP cc_start: 0.8735 (t0) cc_final: 0.8359 (t0) REVERT: LL 17 ASP cc_start: 0.8800 (t0) cc_final: 0.8513 (t0) REVERT: LN 161 MET cc_start: 0.9193 (OUTLIER) cc_final: 0.8946 (mtt) REVERT: LO 113 ASP cc_start: 0.8837 (p0) cc_final: 0.8574 (p0) REVERT: LO 173 GLN cc_start: 0.8904 (tt0) cc_final: 0.8609 (tp-100) REVERT: LP 140 MET cc_start: 0.9170 (mmm) cc_final: 0.8966 (mmt) REVERT: LP 151 THR cc_start: 0.8934 (m) cc_final: 0.8579 (p) REVERT: LQ 93 GLN cc_start: 0.8946 (mp10) cc_final: 0.8733 (mm-40) REVERT: LQ 147 GLU cc_start: 0.8788 (tp30) cc_final: 0.8460 (tp30) REVERT: LR 31 GLU cc_start: 0.8705 (tp30) cc_final: 0.8453 (tp30) REVERT: LS 112 ASP cc_start: 0.8994 (t0) cc_final: 0.8489 (t0) REVERT: LU 31 ASP cc_start: 0.8763 (m-30) cc_final: 0.8453 (m-30) REVERT: LU 39 PHE cc_start: 0.9552 (t80) cc_final: 0.9301 (t80) REVERT: LU 40 GLU cc_start: 0.8934 (tt0) cc_final: 0.8464 (tt0) REVERT: LU 44 GLN cc_start: 0.9187 (mt0) cc_final: 0.8952 (mp10) REVERT: LV 48 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.7282 (ttp80) REVERT: LV 111 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8037 (mt-10) REVERT: LX 145 ASP cc_start: 0.8724 (t0) cc_final: 0.8367 (t0) REVERT: LY 88 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8401 (tp30) REVERT: LZ 86 SER cc_start: 0.9504 (OUTLIER) cc_final: 0.9264 (t) REVERT: Lb 98 TYR cc_start: 0.9433 (t80) cc_final: 0.9206 (t80) REVERT: Lb 119 CYS cc_start: 0.8671 (t) cc_final: 0.8367 (p) REVERT: Lc 98 ASP cc_start: 0.9081 (t0) cc_final: 0.8696 (t0) REVERT: Ld 61 ASP cc_start: 0.8842 (t0) cc_final: 0.8362 (t0) REVERT: Ld 118 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8053 (mm110) REVERT: Le 86 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8056 (mp0) REVERT: Lh 16 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8048 (mt-10) REVERT: Li 88 GLU cc_start: 0.8777 (tp30) cc_final: 0.8568 (tp30) REVERT: Lk 12 LEU cc_start: 0.9588 (OUTLIER) cc_final: 0.9328 (mm) REVERT: Lk 68 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7626 (tp30) REVERT: Lm 79 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7710 (tm-30) REVERT: Lp 30 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8786 (mt-10) REVERT: Lr 125 MET cc_start: 0.7202 (tpt) cc_final: 0.6954 (mmp) REVERT: Lz 76 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7728 (pp20) REVERT: Lz 119 GLN cc_start: 0.9157 (mp10) cc_final: 0.8895 (mp10) REVERT: Lz 158 GLN cc_start: 0.8688 (tp40) cc_final: 0.8367 (tm-30) outliers start: 120 outliers final: 100 residues processed: 865 average time/residue: 1.2429 time to fit residues: 1948.2604 Evaluate side-chains 902 residues out of total 7104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 786 time to evaluate : 8.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 479 GLN Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 456 GLN Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain LA residue 159 SER Chi-restraints excluded: chain LB residue 4 ARG Chi-restraints excluded: chain LB residue 60 VAL Chi-restraints excluded: chain LB residue 101 THR Chi-restraints excluded: chain LB residue 181 MET Chi-restraints excluded: chain LB residue 200 ARG Chi-restraints excluded: chain LC residue 287 THR Chi-restraints excluded: chain LD residue 239 MET Chi-restraints excluded: chain LE residue 99 ASP Chi-restraints excluded: chain LE residue 109 LEU Chi-restraints excluded: chain LE residue 120 ASP Chi-restraints excluded: chain LF residue 25 PHE Chi-restraints excluded: chain LF residue 28 LEU Chi-restraints excluded: chain LF residue 74 MET Chi-restraints excluded: chain LF residue 178 SER Chi-restraints excluded: chain LF residue 225 THR Chi-restraints excluded: chain LG residue 135 VAL Chi-restraints excluded: chain LG residue 209 SER Chi-restraints excluded: chain LH residue 115 ARG Chi-restraints excluded: chain LH residue 177 ASP Chi-restraints excluded: chain LI residue 189 CYS Chi-restraints excluded: chain LJ residue 34 THR Chi-restraints excluded: chain LJ residue 47 THR Chi-restraints excluded: chain LL residue 36 ARG Chi-restraints excluded: chain LL residue 63 THR Chi-restraints excluded: chain LL residue 64 VAL Chi-restraints excluded: chain LM residue 43 THR Chi-restraints excluded: chain LM residue 67 SER Chi-restraints excluded: chain LM residue 125 ASN Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 125 SER Chi-restraints excluded: chain LN residue 126 THR Chi-restraints excluded: chain LN residue 161 MET Chi-restraints excluded: chain LO residue 158 GLU Chi-restraints excluded: chain LP residue 5 SER Chi-restraints excluded: chain LP residue 10 ASN Chi-restraints excluded: chain LQ residue 82 VAL Chi-restraints excluded: chain LR residue 59 SER Chi-restraints excluded: chain LR residue 68 LEU Chi-restraints excluded: chain LS residue 77 ASN Chi-restraints excluded: chain LS residue 169 THR Chi-restraints excluded: chain LT residue 104 SER Chi-restraints excluded: chain LT residue 118 GLU Chi-restraints excluded: chain LU residue 25 CYS Chi-restraints excluded: chain LU residue 56 LEU Chi-restraints excluded: chain LU residue 60 VAL Chi-restraints excluded: chain LU residue 74 SER Chi-restraints excluded: chain LU residue 109 SER Chi-restraints excluded: chain LV residue 22 VAL Chi-restraints excluded: chain LV residue 48 ARG Chi-restraints excluded: chain LV residue 115 SER Chi-restraints excluded: chain LW residue 9 SER Chi-restraints excluded: chain LW residue 38 SER Chi-restraints excluded: chain LX residue 126 THR Chi-restraints excluded: chain LX residue 148 ASP Chi-restraints excluded: chain LY residue 53 ASP Chi-restraints excluded: chain LY residue 66 GLN Chi-restraints excluded: chain LY residue 111 LEU Chi-restraints excluded: chain LZ residue 31 ASP Chi-restraints excluded: chain LZ residue 34 SER Chi-restraints excluded: chain LZ residue 54 THR Chi-restraints excluded: chain LZ residue 86 SER Chi-restraints excluded: chain LZ residue 99 ASP Chi-restraints excluded: chain LZ residue 100 VAL Chi-restraints excluded: chain La residue 105 ARG Chi-restraints excluded: chain Lb residue 9 THR Chi-restraints excluded: chain Lb residue 76 VAL Chi-restraints excluded: chain Lc residue 11 LEU Chi-restraints excluded: chain Lc residue 94 LEU Chi-restraints excluded: chain Ld residue 46 LEU Chi-restraints excluded: chain Ld residue 94 GLU Chi-restraints excluded: chain Ld residue 118 GLN Chi-restraints excluded: chain Ld residue 119 THR Chi-restraints excluded: chain Le residue 86 GLU Chi-restraints excluded: chain Lf residue 5 LEU Chi-restraints excluded: chain Lf residue 37 ASP Chi-restraints excluded: chain Lf residue 105 LEU Chi-restraints excluded: chain Lh residue 42 SER Chi-restraints excluded: chain Li residue 12 ASN Chi-restraints excluded: chain Lj residue 15 THR Chi-restraints excluded: chain Lk residue 12 LEU Chi-restraints excluded: chain Ll residue 9 ILE Chi-restraints excluded: chain Ll residue 23 ILE Chi-restraints excluded: chain Ll residue 47 THR Chi-restraints excluded: chain Lm residue 78 ILE Chi-restraints excluded: chain Lm residue 127 VAL Chi-restraints excluded: chain Lo residue 93 LEU Chi-restraints excluded: chain Lp residue 25 MET Chi-restraints excluded: chain Lp residue 30 GLU Chi-restraints excluded: chain Lp residue 73 THR Chi-restraints excluded: chain Lp residue 89 LEU Chi-restraints excluded: chain Lr residue 31 ASN Chi-restraints excluded: chain Lr residue 80 THR Chi-restraints excluded: chain Lz residue 12 GLU Chi-restraints excluded: chain Lz residue 76 GLU Chi-restraints excluded: chain Lz residue 80 VAL Chi-restraints excluded: chain Lz residue 82 ILE Chi-restraints excluded: chain Lz residue 87 ILE Chi-restraints excluded: chain Lz residue 141 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1174 random chunks: chunk 1050 optimal weight: 3.9990 chunk 692 optimal weight: 6.9990 chunk 1115 optimal weight: 10.0000 chunk 680 optimal weight: 7.9990 chunk 528 optimal weight: 0.6980 chunk 775 optimal weight: 4.9990 chunk 1169 optimal weight: 9.9990 chunk 1076 optimal weight: 0.0020 chunk 931 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 chunk 719 optimal weight: 20.0000 overall best weight: 3.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 GLN ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LL 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LN 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LP 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lz 35 GLN ** Lz 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9008 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 157182 Z= 0.197 Angle : 0.479 9.803 230280 Z= 0.250 Chirality : 0.032 0.228 28562 Planarity : 0.003 0.055 15225 Dihedral : 22.480 177.510 68513 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.40 % Favored : 97.56 % Rotamer: Outliers : 1.58 % Allowed : 15.06 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.09), residues: 8112 helix: 2.23 (0.09), residues: 3346 sheet: 0.38 (0.17), residues: 999 loop : 0.27 (0.10), residues: 3767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRPLN 120 HIS 0.009 0.001 HISLz 140 PHE 0.015 0.001 PHE A 638 TYR 0.015 0.001 TYRLQ 32 ARG 0.008 0.000 ARGLI 82 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16224 Ramachandran restraints generated. 8112 Oldfield, 0 Emsley, 8112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16224 Ramachandran restraints generated. 8112 Oldfield, 0 Emsley, 8112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 902 residues out of total 7104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 790 time to evaluate : 8.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 GLN cc_start: 0.4216 (OUTLIER) cc_final: 0.3974 (pm20) REVERT: A 652 MET cc_start: 0.6703 (tpp) cc_final: 0.6336 (mmp) REVERT: A 701 MET cc_start: 0.7255 (ttp) cc_final: 0.7039 (ttt) REVERT: B 185 ASP cc_start: 0.9565 (OUTLIER) cc_final: 0.9184 (t0) REVERT: B 385 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7763 (tm) REVERT: LA 140 ASN cc_start: 0.9098 (t0) cc_final: 0.8772 (t0) REVERT: LB 4 ARG cc_start: 0.9136 (OUTLIER) cc_final: 0.7757 (ttm170) REVERT: LB 200 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.8204 (mtt90) REVERT: LC 1 MET cc_start: 0.1987 (ppp) cc_final: 0.0919 (tmm) REVERT: LC 287 THR cc_start: 0.9470 (OUTLIER) cc_final: 0.9207 (m) REVERT: LD 3 PHE cc_start: 0.5551 (m-80) cc_final: 0.5320 (m-80) REVERT: LD 212 MET cc_start: 0.8851 (ptp) cc_final: 0.8596 (ptp) REVERT: LE 119 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8531 (mt-10) REVERT: LE 245 GLN cc_start: 0.8579 (tp-100) cc_final: 0.8284 (tp40) REVERT: LF 28 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8460 (tt) REVERT: LH 115 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.8070 (ptp90) REVERT: LI 55 ASP cc_start: 0.8747 (t0) cc_final: 0.8359 (t0) REVERT: LL 17 ASP cc_start: 0.8814 (t0) cc_final: 0.8512 (t0) REVERT: LL 143 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8381 (mm-30) REVERT: LN 161 MET cc_start: 0.9200 (OUTLIER) cc_final: 0.8938 (mtt) REVERT: LO 113 ASP cc_start: 0.8825 (p0) cc_final: 0.8554 (p0) REVERT: LO 173 GLN cc_start: 0.8892 (tt0) cc_final: 0.8590 (tp-100) REVERT: LP 151 THR cc_start: 0.8931 (m) cc_final: 0.8591 (p) REVERT: LQ 147 GLU cc_start: 0.8784 (tp30) cc_final: 0.8454 (tp30) REVERT: LR 31 GLU cc_start: 0.8710 (tp30) cc_final: 0.8456 (tp30) REVERT: LS 112 ASP cc_start: 0.8973 (t0) cc_final: 0.8378 (t0) REVERT: LU 31 ASP cc_start: 0.8769 (m-30) cc_final: 0.8463 (m-30) REVERT: LU 39 PHE cc_start: 0.9542 (t80) cc_final: 0.9308 (t80) REVERT: LU 40 GLU cc_start: 0.8939 (tt0) cc_final: 0.8458 (tt0) REVERT: LU 44 GLN cc_start: 0.9189 (mt0) cc_final: 0.8953 (mp10) REVERT: LV 48 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.7256 (ttp80) REVERT: LV 111 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8034 (mt-10) REVERT: LX 145 ASP cc_start: 0.8742 (t0) cc_final: 0.8377 (t0) REVERT: LZ 81 MET cc_start: 0.9423 (OUTLIER) cc_final: 0.8327 (tpt) REVERT: LZ 86 SER cc_start: 0.9510 (p) cc_final: 0.9269 (t) REVERT: Lb 98 TYR cc_start: 0.9426 (t80) cc_final: 0.9200 (t80) REVERT: Lc 98 ASP cc_start: 0.9092 (t0) cc_final: 0.8711 (t0) REVERT: Ld 61 ASP cc_start: 0.8828 (t0) cc_final: 0.8371 (t0) REVERT: Ld 118 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8093 (mm110) REVERT: Le 86 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8073 (mp0) REVERT: Lh 16 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8051 (mt-10) REVERT: Li 88 GLU cc_start: 0.8779 (tp30) cc_final: 0.8573 (tp30) REVERT: Lk 12 LEU cc_start: 0.9586 (OUTLIER) cc_final: 0.9327 (mm) REVERT: Lk 68 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7629 (tp30) REVERT: Lp 78 THR cc_start: 0.9424 (m) cc_final: 0.9134 (p) REVERT: Lr 125 MET cc_start: 0.7180 (tpt) cc_final: 0.6950 (mmp) REVERT: Lz 76 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7756 (pp20) REVERT: Lz 119 GLN cc_start: 0.9125 (mp10) cc_final: 0.8848 (mp10) REVERT: Lz 158 GLN cc_start: 0.8691 (tp40) cc_final: 0.8368 (tm-30) outliers start: 112 outliers final: 90 residues processed: 856 average time/residue: 1.2414 time to fit residues: 1915.2426 Evaluate side-chains 888 residues out of total 7104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 783 time to evaluate : 8.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 479 GLN Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain B residue 163 HIS Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 456 GLN Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain LA residue 159 SER Chi-restraints excluded: chain LB residue 4 ARG Chi-restraints excluded: chain LB residue 60 VAL Chi-restraints excluded: chain LB residue 101 THR Chi-restraints excluded: chain LB residue 181 MET Chi-restraints excluded: chain LB residue 200 ARG Chi-restraints excluded: chain LC residue 287 THR Chi-restraints excluded: chain LD residue 37 VAL Chi-restraints excluded: chain LD residue 239 MET Chi-restraints excluded: chain LE residue 109 LEU Chi-restraints excluded: chain LE residue 120 ASP Chi-restraints excluded: chain LF residue 25 PHE Chi-restraints excluded: chain LF residue 28 LEU Chi-restraints excluded: chain LF residue 74 MET Chi-restraints excluded: chain LF residue 178 SER Chi-restraints excluded: chain LF residue 225 THR Chi-restraints excluded: chain LG residue 135 VAL Chi-restraints excluded: chain LG residue 209 SER Chi-restraints excluded: chain LH residue 115 ARG Chi-restraints excluded: chain LH residue 177 ASP Chi-restraints excluded: chain LI residue 189 CYS Chi-restraints excluded: chain LJ residue 34 THR Chi-restraints excluded: chain LJ residue 47 THR Chi-restraints excluded: chain LL residue 36 ARG Chi-restraints excluded: chain LL residue 63 THR Chi-restraints excluded: chain LL residue 64 VAL Chi-restraints excluded: chain LM residue 43 THR Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 125 SER Chi-restraints excluded: chain LN residue 126 THR Chi-restraints excluded: chain LN residue 161 MET Chi-restraints excluded: chain LO residue 158 GLU Chi-restraints excluded: chain LP residue 5 SER Chi-restraints excluded: chain LP residue 10 ASN Chi-restraints excluded: chain LQ residue 82 VAL Chi-restraints excluded: chain LR residue 59 SER Chi-restraints excluded: chain LR residue 68 LEU Chi-restraints excluded: chain LS residue 19 THR Chi-restraints excluded: chain LS residue 77 ASN Chi-restraints excluded: chain LS residue 169 THR Chi-restraints excluded: chain LT residue 118 GLU Chi-restraints excluded: chain LU residue 56 LEU Chi-restraints excluded: chain LU residue 60 VAL Chi-restraints excluded: chain LU residue 74 SER Chi-restraints excluded: chain LU residue 109 SER Chi-restraints excluded: chain LV residue 22 VAL Chi-restraints excluded: chain LV residue 48 ARG Chi-restraints excluded: chain LW residue 9 SER Chi-restraints excluded: chain LX residue 126 THR Chi-restraints excluded: chain LX residue 148 ASP Chi-restraints excluded: chain LY residue 53 ASP Chi-restraints excluded: chain LY residue 66 GLN Chi-restraints excluded: chain LY residue 111 LEU Chi-restraints excluded: chain LZ residue 31 ASP Chi-restraints excluded: chain LZ residue 34 SER Chi-restraints excluded: chain LZ residue 54 THR Chi-restraints excluded: chain LZ residue 81 MET Chi-restraints excluded: chain LZ residue 99 ASP Chi-restraints excluded: chain LZ residue 100 VAL Chi-restraints excluded: chain LZ residue 132 GLN Chi-restraints excluded: chain La residue 105 ARG Chi-restraints excluded: chain Lb residue 76 VAL Chi-restraints excluded: chain Lc residue 11 LEU Chi-restraints excluded: chain Lc residue 94 LEU Chi-restraints excluded: chain Ld residue 46 LEU Chi-restraints excluded: chain Ld residue 118 GLN Chi-restraints excluded: chain Ld residue 119 THR Chi-restraints excluded: chain Le residue 86 GLU Chi-restraints excluded: chain Lf residue 5 LEU Chi-restraints excluded: chain Lf residue 37 ASP Chi-restraints excluded: chain Lf residue 105 LEU Chi-restraints excluded: chain Li residue 12 ASN Chi-restraints excluded: chain Lj residue 15 THR Chi-restraints excluded: chain Lk residue 12 LEU Chi-restraints excluded: chain Ll residue 9 ILE Chi-restraints excluded: chain Ll residue 23 ILE Chi-restraints excluded: chain Ll residue 47 THR Chi-restraints excluded: chain Lm residue 78 ILE Chi-restraints excluded: chain Lm residue 127 VAL Chi-restraints excluded: chain Lo residue 93 LEU Chi-restraints excluded: chain Lp residue 73 THR Chi-restraints excluded: chain Lp residue 89 LEU Chi-restraints excluded: chain Lr residue 31 ASN Chi-restraints excluded: chain Lz residue 12 GLU Chi-restraints excluded: chain Lz residue 76 GLU Chi-restraints excluded: chain Lz residue 80 VAL Chi-restraints excluded: chain Lz residue 82 ILE Chi-restraints excluded: chain Lz residue 87 ILE Chi-restraints excluded: chain Lz residue 141 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1174 random chunks: chunk 571 optimal weight: 10.0000 chunk 739 optimal weight: 0.0040 chunk 992 optimal weight: 7.9990 chunk 285 optimal weight: 10.0000 chunk 858 optimal weight: 1.9990 chunk 137 optimal weight: 10.0000 chunk 258 optimal weight: 20.0000 chunk 932 optimal weight: 9.9990 chunk 390 optimal weight: 0.0870 chunk 957 optimal weight: 20.0000 chunk 118 optimal weight: 10.0000 overall best weight: 4.0176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 GLN ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LL 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LN 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LP 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lz 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.057166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.038508 restraints weight = 478243.075| |-----------------------------------------------------------------------------| r_work (start): 0.2541 rms_B_bonded: 1.41 r_work: 0.2425 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2319 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9130 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 157182 Z= 0.223 Angle : 0.474 9.609 230280 Z= 0.248 Chirality : 0.033 0.229 28562 Planarity : 0.003 0.055 15225 Dihedral : 22.460 177.628 68513 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.32 % Favored : 97.65 % Rotamer: Outliers : 1.59 % Allowed : 15.04 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.09), residues: 8112 helix: 2.24 (0.09), residues: 3347 sheet: 0.32 (0.16), residues: 1005 loop : 0.28 (0.10), residues: 3760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPLN 120 HIS 0.005 0.001 HISLa 40 PHE 0.018 0.001 PHE B 229 TYR 0.018 0.001 TYRLU 90 ARG 0.009 0.000 ARGLI 82 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 35806.01 seconds wall clock time: 627 minutes 51.36 seconds (37671.36 seconds total)