Starting phenix.real_space_refine on Tue Mar 26 18:09:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oj0_16902/03_2024/8oj0_16902.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oj0_16902/03_2024/8oj0_16902.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oj0_16902/03_2024/8oj0_16902.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oj0_16902/03_2024/8oj0_16902.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oj0_16902/03_2024/8oj0_16902.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oj0_16902/03_2024/8oj0_16902.pdb" } resolution = 3.3 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 317 5.16 5 C 79898 2.51 5 N 27902 2.21 5 O 38016 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "K ASP 144": "OD1" <-> "OD2" Residue "K PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LA ASP 122": "OD1" <-> "OD2" Residue "LB PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LC ASP 352": "OD1" <-> "OD2" Residue "LG ASP 162": "OD1" <-> "OD2" Residue "LG PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LH GLU 14": "OE1" <-> "OE2" Residue "LH GLU 66": "OE1" <-> "OE2" Residue "LI ASP 28": "OD1" <-> "OD2" Residue "LI ASP 183": "OD1" <-> "OD2" Residue "LL GLU 79": "OE1" <-> "OE2" Residue "LL GLU 108": "OE1" <-> "OE2" Residue "LL GLU 119": "OE1" <-> "OE2" Residue "LM GLU 99": "OE1" <-> "OE2" Residue "LN ASP 147": "OD1" <-> "OD2" Residue "LO ASP 100": "OD1" <-> "OD2" Residue "LO GLU 144": "OE1" <-> "OE2" Residue "LO ASP 190": "OD1" <-> "OD2" Residue "LO GLU 194": "OE1" <-> "OE2" Residue "LP GLU 103": "OE1" <-> "OE2" Residue "LR GLU 28": "OE1" <-> "OE2" Residue "LR GLU 31": "OE1" <-> "OE2" Residue "LR GLU 111": "OE1" <-> "OE2" Residue "LR GLU 140": "OE1" <-> "OE2" Residue "LS GLU 96": "OE1" <-> "OE2" Residue "LS GLU 130": "OE1" <-> "OE2" Residue "LS PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LT GLU 94": "OE1" <-> "OE2" Residue "LT GLU 111": "OE1" <-> "OE2" Residue "LT GLU 149": "OE1" <-> "OE2" Residue "LT GLU 152": "OE1" <-> "OE2" Residue "LV ASP 30": "OD1" <-> "OD2" Residue "LV ASP 92": "OD1" <-> "OD2" Residue "LW GLU 4": "OE1" <-> "OE2" Residue "LX GLU 133": "OE1" <-> "OE2" Residue "LX ASP 148": "OD1" <-> "OD2" Residue "LY GLU 37": "OE1" <-> "OE2" Residue "LZ ASP 31": "OD1" <-> "OD2" Residue "Lc GLU 12": "OE1" <-> "OE2" Residue "Lc TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lc GLU 59": "OE1" <-> "OE2" Residue "Ld GLU 19": "OE1" <-> "OE2" Residue "Lg TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lg TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lg GLU 98": "OE1" <-> "OE2" Residue "Li GLU 59": "OE1" <-> "OE2" Residue "Li GLU 88": "OE1" <-> "OE2" Residue "Lk GLU 6": "OE1" <-> "OE2" Residue "Lk ASP 10": "OD1" <-> "OD2" Residue "Lk GLU 51": "OE1" <-> "OE2" Residue "Lo GLU 71": "OE1" <-> "OE2" Residue "Lo ASP 96": "OD1" <-> "OD2" Residue "Lp GLU 30": "OE1" <-> "OE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 150098 Number of models: 1 Model: "" Number of chains: 66 Chain: "1" Number of atoms: 3322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3322 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 17, 'TRANS': 408} Chain breaks: 2 Chain: "2" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 494 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "3" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Link IDs: {'PTRANS': 2, 'TRANS': 26} 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: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 855 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 1, 'TRANS': 107} 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: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 206 Unusual residues: {' MG': 206} Classifications: {'undetermined': 206} Link IDs: {None: 205} 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: "Lf" 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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 A0VNI SG CYSLg 46 86.018 104.012 66.792 1.00112.19 S ATOM A0VNZ SG CYSLg 49 83.877 100.888 66.049 1.00100.82 S ATOM A0VVA SG CYSLg 83 86.746 101.744 63.761 1.00 93.89 S ATOM A0VVU SG CYSLg 86 83.719 104.047 63.905 1.00101.44 S ATOM A0XLP SG CYSLj 19 123.726 123.155 106.834 1.00 73.55 S ATOM A0XMH SG CYSLj 22 125.401 123.547 110.182 1.00 74.31 S ATOM A0XP0 SG CYSLj 34 121.572 123.457 109.930 1.00 75.64 S ATOM A0XPJ SG CYSLj 37 123.466 126.476 108.639 1.00 72.54 S ATOM A0YY1 SG CYSLm 96 79.193 74.219 202.278 1.00 93.92 S ATOM A0YYR SG CYSLm 99 81.615 72.235 200.284 1.00 99.08 S ATOM A0Z19 SG CYSLm 110 82.521 73.269 203.967 1.00 74.35 S ATOM A0Z2H SG CYSLm 115 82.642 75.729 201.299 1.00103.76 S ATOM A0Z7Z SG CYSLo 12 75.492 180.256 166.377 1.00 85.52 S ATOM A0Z8N SG CYSLo 15 74.191 183.771 166.866 1.00111.85 S ATOM A0ZLO SG CYSLo 72 71.920 181.112 165.193 1.00 71.22 S ATOM A0ZMP SG CYSLo 77 75.142 182.497 163.486 1.00 98.83 S ATOM A101R SG CYSLp 39 70.100 100.998 73.717 1.00109.60 S ATOM A102E SG CYSLp 42 70.887 98.118 71.365 1.00 78.36 S ATOM A105S SG CYSLp 57 72.849 98.536 74.577 1.00 91.13 S ATOM A1068 SG CYSLp 60 73.434 100.973 71.817 1.00104.27 S Residues with excluded nonbonded symmetry interactions: 696 residue: pdb=" N PHE 1 5 " occ=0.00 ... (9 atoms not shown) pdb=" CZ PHE 1 5 " occ=0.00 residue: pdb=" N LEU 1 6 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU 1 6 " occ=0.00 residue: pdb=" N GLU 1 7 " occ=0.00 ... (7 atoms not shown) pdb=" OE2 GLU 1 7 " occ=0.00 residue: pdb=" N VAL 1 8 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 VAL 1 8 " occ=0.00 residue: pdb=" N ILE 1 9 " occ=0.00 ... (6 atoms not shown) pdb=" CD1 ILE 1 9 " occ=0.00 residue: pdb=" N LYS 1 10 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS 1 10 " occ=0.00 residue: pdb=" N PRO 1 11 " occ=0.00 ... (5 atoms not shown) pdb=" CD PRO 1 11 " occ=0.00 residue: pdb=" N PHE 1 12 " occ=0.00 ... (9 atoms not shown) pdb=" CZ PHE 1 12 " occ=0.00 residue: pdb=" N CYS 1 13 " occ=0.00 ... (4 atoms not shown) pdb=" SG CYS 1 13 " occ=0.00 residue: pdb=" N VAL 1 14 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 VAL 1 14 " occ=0.00 residue: pdb=" N ILE 1 15 " occ=0.00 ... (6 atoms not shown) pdb=" CD1 ILE 1 15 " occ=0.00 residue: pdb=" N LEU 1 16 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU 1 16 " occ=0.00 ... (remaining 684 not shown) Time building chain proxies: 58.98, per 1000 atoms: 0.39 Number of scatterers: 150098 At special positions: 0 Unit cell: (234.094, 258.085, 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 317 16.00 P 3740 15.00 Mg 220 11.99 O 38016 8.00 N 27902 7.00 C 79898 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: 62.12 Conformation dependent library (CDL) restraints added in 11.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNLg 201 " pdb="ZN ZNLg 201 " - pdb=" SG CYSLg 86 " pdb="ZN ZNLg 201 " - pdb=" SG CYSLg 46 " pdb="ZN ZNLg 201 " - pdb=" SG CYSLg 49 " pdb="ZN ZNLg 201 " - pdb=" SG CYSLg 83 " 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 37 " pdb="ZN ZNLj 102 " - pdb=" SG CYSLj 22 " pdb=" ZNLm 201 " pdb="ZN ZNLm 201 " - pdb=" SG CYSLm 115 " pdb="ZN ZNLm 201 " - pdb=" SG CYSLm 96 " pdb="ZN ZNLm 201 " - pdb=" SG CYSLm 99 " pdb="ZN ZNLm 201 " - pdb=" SG CYSLm 110 " 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 60 " pdb="ZN ZNLp 101 " - pdb=" SG CYSLp 39 " Number of angles added : 30 17080 Ramachandran restraints generated. 8540 Oldfield, 0 Emsley, 8540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16192 Finding SS restraints... Secondary structure from input PDB file: 347 helices and 92 sheets defined 47.7% alpha, 13.5% beta 1132 base pairs and 1903 stacking pairs defined. Time for finding SS restraints: 50.13 Creating SS restraints... Processing helix chain '1' and resid 5 through 13 Proline residue: 1 11 - end of helix Processing helix chain '1' and resid 28 through 46 removed outlier: 4.303A pdb=" N VAL 1 32 " --> pdb=" O PHE 1 28 " (cutoff:3.500A) Processing helix chain '1' and resid 61 through 69 Processing helix chain '1' and resid 81 through 97 Processing helix chain '1' and resid 105 through 133 removed outlier: 3.629A pdb=" N LYS 1 117 " --> pdb=" O ASN 1 113 " (cutoff:3.500A) Processing helix chain '1' and resid 145 through 149 removed outlier: 3.596A pdb=" N CYS 1 148 " --> pdb=" O ALA 1 145 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU 1 149 " --> pdb=" O GLY 1 146 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 145 through 149' Processing helix chain '1' and resid 150 through 171 removed outlier: 3.748A pdb=" N GLN 1 154 " --> pdb=" O LEU 1 150 " (cutoff:3.500A) Processing helix chain '1' and resid 177 through 196 Processing helix chain '1' and resid 212 through 223 Processing helix chain '1' and resid 225 through 235 Processing helix chain '1' and resid 241 through 260 Processing helix chain '1' and resid 284 through 287 Processing helix chain '1' and resid 288 through 312 removed outlier: 3.855A pdb=" N ILE 1 292 " --> pdb=" O ASN 1 288 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU 1 297 " --> pdb=" O LEU 1 293 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL 1 298 " --> pdb=" O GLN 1 294 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N SER 1 299 " --> pdb=" O SER 1 295 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN 1 300 " --> pdb=" O ALA 1 296 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N MET 1 307 " --> pdb=" O VAL 1 303 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N LEU 1 308 " --> pdb=" O ILE 1 304 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER 1 309 " --> pdb=" O SER 1 305 " (cutoff:3.500A) Processing helix chain '1' and resid 339 through 346 removed outlier: 3.808A pdb=" N HIS 1 343 " --> pdb=" O GLY 1 339 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR 1 344 " --> pdb=" O GLY 1 340 " (cutoff:3.500A) Processing helix chain '1' and resid 357 through 383 removed outlier: 3.503A pdb=" N ALA 1 361 " --> pdb=" O ASP 1 357 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS 1 377 " --> pdb=" O ALA 1 373 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR 1 378 " --> pdb=" O PHE 1 374 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU 1 381 " --> pdb=" O LYS 1 377 " (cutoff:3.500A) Processing helix chain '1' and resid 386 through 398 Processing helix chain '1' and resid 406 through 415 removed outlier: 4.378A pdb=" N VAL 1 410 " --> pdb=" O GLU 1 406 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N HIS 1 411 " --> pdb=" O THR 1 407 " (cutoff:3.500A) Processing helix chain '1' and resid 416 through 439 Processing helix chain '1' and resid 446 through 465 removed outlier: 3.593A pdb=" N VAL 1 451 " --> pdb=" O ILE 1 447 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR 1 452 " --> pdb=" O LEU 1 448 " (cutoff:3.500A) Processing helix chain '2' and resid 8 through 25 removed outlier: 3.630A pdb=" N LYS 2 23 " --> pdb=" O ILE 2 19 " (cutoff:3.500A) Processing helix chain '2' and resid 29 through 68 removed outlier: 4.698A pdb=" N ILE 2 50 " --> pdb=" O ILE 2 46 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N GLY 2 51 " --> pdb=" O MET 2 47 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N PHE 2 52 " --> pdb=" O GLY 2 48 " (cutoff:3.500A) Proline residue: 2 60 - end of helix removed outlier: 4.129A pdb=" N ASN 2 63 " --> pdb=" O ILE 2 59 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE 2 64 " --> pdb=" O PRO 2 60 " (cutoff:3.500A) Processing helix chain '3' and resid 71 through 95 removed outlier: 4.884A pdb=" N LYS 3 92 " --> pdb=" O HIS 3 88 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N TYR 3 93 " --> pdb=" O ILE 3 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 43 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: 3.633A pdb=" N ILE A 93 " --> pdb=" O ASP A 89 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLY A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 4.022A 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 228 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 303 through 320 Processing helix chain 'A' and resid 334 through 347 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: 5.021A pdb=" N PHE A 485 " --> pdb=" O GLU A 481 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU A 486 " --> pdb=" O ILE A 482 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG A 487 " --> pdb=" O GLU A 483 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS A 488 " --> pdb=" O ASP A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 523 removed outlier: 4.586A 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: 4.062A pdb=" N LYS A 534 " --> pdb=" O GLY A 530 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG A 535 " --> pdb=" O THR A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 577 removed outlier: 3.625A pdb=" N LEU A 569 " --> pdb=" O THR A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 594 removed outlier: 3.688A pdb=" N ASP A 592 " --> pdb=" O PHE A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 615 removed outlier: 3.602A pdb=" N LYS A 614 " --> pdb=" O LYS A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 632 removed outlier: 4.215A pdb=" N ALA A 622 " --> pdb=" O GLU A 618 " (cutoff:3.500A) removed outlier: 3.639A 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 705 through 707 No H-bonds generated for 'chain 'A' and resid 705 through 707' Processing helix chain 'A' and resid 708 through 717 removed outlier: 3.643A pdb=" N ILE A 712 " --> pdb=" O CYS A 708 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 747 removed outlier: 4.019A pdb=" N GLN A 738 " --> pdb=" O LEU A 734 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS A 745 " --> pdb=" O SER A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 767 removed outlier: 3.734A pdb=" N GLU A 762 " --> pdb=" O ASP A 758 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASP A 763 " --> pdb=" O LYS A 759 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL A 764 " --> pdb=" O GLU A 760 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A 765 " --> pdb=" O GLN A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 784 removed outlier: 3.699A 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 13 through 18 removed outlier: 4.055A pdb=" N LEU B 17 " --> pdb=" O SER B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 47 removed outlier: 4.215A pdb=" N LEU B 33 " --> pdb=" O LYS B 29 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASP B 47 " --> pdb=" O ALA B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 59 removed outlier: 4.108A pdb=" N ALA B 55 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 3.725A 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 106 Processing helix chain 'B' and resid 108 through 168 removed outlier: 3.948A pdb=" N VAL B 112 " --> pdb=" O ASN B 108 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ILE B 126 " --> pdb=" O VAL B 122 " (cutoff:3.500A) Proline residue: B 127 - end of helix Processing helix chain 'B' and resid 174 through 182 removed outlier: 3.809A pdb=" N LEU B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 200 removed outlier: 3.560A pdb=" N SER B 200 " --> pdb=" O ALA B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 215 removed outlier: 3.640A pdb=" N ASP B 206 " --> pdb=" O GLY B 202 " (cutoff:3.500A) 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: 4.437A 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: 3.641A 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: 4.099A pdb=" N VAL B 430 " --> pdb=" O SER B 426 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS B 440 " --> pdb=" O PHE B 436 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) Proline residue: B 470 - end of helix removed outlier: 3.793A pdb=" N ASP B 473 " --> pdb=" O GLU B 469 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS B 478 " --> pdb=" O LEU B 474 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS B 492 " --> pdb=" O ALA B 488 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG B 493 " --> pdb=" O ASP B 489 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 231 through 239 removed outlier: 4.035A 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 Processing helix chain 'D' and resid 28 through 41 removed outlier: 3.740A 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: 3.671A 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: 4.047A pdb=" N VAL K 37 " --> pdb=" O ASN K 33 " (cutoff:3.500A) removed outlier: 3.883A 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 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: 3.762A 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 removed outlier: 3.624A pdb=" N LYSLA 177 " --> pdb=" O ARGLA 174 " (cutoff:3.500A) Processing helix chain 'LA' and resid 181 through 191 removed outlier: 3.656A pdb=" N ALALA 191 " --> pdb=" O HISLA 187 " (cutoff:3.500A) Processing helix chain 'LA' and resid 205 through 209 removed outlier: 3.502A 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: 3.692A 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: 3.980A pdb=" N ARGLB 117 " --> pdb=" O GLULB 113 " (cutoff:3.500A) Processing helix chain 'LB' and resid 133 through 139 removed outlier: 4.334A pdb=" N TRPLB 137 " --> pdb=" O TYRLB 133 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLNLB 138 " --> pdb=" O CYSLB 134 " (cutoff:3.500A) Processing helix chain 'LB' and resid 139 through 157 Processing helix chain 'LB' and resid 167 through 171 removed outlier: 3.574A pdb=" N LEULB 170 " --> pdb=" O GLNLB 167 " (cutoff:3.500A) 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 46 removed outlier: 3.847A pdb=" N LYSLC 46 " --> pdb=" O THRLC 42 " (cutoff:3.500A) Processing helix chain 'LC' and resid 47 through 49 No H-bonds generated for 'chain 'LC' and resid 47 through 49' Processing helix chain 'LC' and resid 116 through 132 removed outlier: 3.648A pdb=" N ALALC 132 " --> pdb=" O LEULC 128 " (cutoff:3.500A) Processing helix chain 'LC' and resid 133 through 141 Processing helix chain 'LC' and resid 155 through 161 Processing helix chain 'LC' and resid 163 through 175 Processing helix chain 'LC' and resid 176 through 187 removed outlier: 3.667A pdb=" N ILELC 180 " --> pdb=" O ALALC 176 " (cutoff:3.500A) Processing helix chain 'LC' and resid 192 through 197 removed outlier: 3.558A pdb=" N LYSLC 195 " --> pdb=" O GLYLC 192 " (cutoff:3.500A) Processing helix chain 'LC' and resid 216 through 223 removed outlier: 4.507A 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: 4.469A pdb=" N ASPLC 261 " --> pdb=" O PHELC 257 " (cutoff:3.500A) removed outlier: 4.323A 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: 3.969A pdb=" N ALALC 301 " --> pdb=" O GLULC 297 " (cutoff:3.500A) removed outlier: 3.579A 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: 4.270A 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 26 Processing helix chain 'LD' and resid 29 through 38 removed outlier: 3.981A pdb=" N ARGLD 35 " --> pdb=" O TYRLD 31 " (cutoff:3.500A) removed outlier: 3.569A 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: 4.044A 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 201 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 232 through 234 No H-bonds generated for 'chain 'LD' and resid 232 through 234' 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: 3.678A pdb=" N GLNLE 256 " --> pdb=" O ALALE 252 " (cutoff:3.500A) Proline residue: LE 259 - end of helix removed outlier: 3.905A 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 113 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: 4.184A 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: 3.708A pdb=" N LEULF 243 " --> pdb=" O GLNLF 239 " (cutoff:3.500A) Processing helix chain 'LG' and resid 51 through 55 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: 3.743A 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 169 removed outlier: 4.743A pdb=" N PHELG 169 " --> pdb=" O GLULG 165 " (cutoff:3.500A) Processing helix chain 'LG' and resid 169 through 178 Processing helix chain 'LG' and resid 186 through 194 removed outlier: 3.930A pdb=" N LEULG 190 " --> pdb=" O GLYLG 186 " (cutoff:3.500A) Processing helix chain 'LG' and resid 208 through 226 removed outlier: 4.360A pdb=" N GLYLG 213 " --> pdb=" O SERLG 209 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ALALG 214 " --> pdb=" O GLULG 210 " (cutoff:3.500A) Processing helix chain 'LG' and resid 229 through 236 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: 3.946A pdb=" N THRLH 72 " --> pdb=" O ALALH 68 " (cutoff:3.500A) Processing helix chain 'LH' and resid 116 through 120 removed outlier: 3.505A pdb=" N GLYLH 119 " --> pdb=" O ASNLH 116 " (cutoff:3.500A) Processing helix chain 'LH' and resid 150 through 165 Processing helix chain 'LI' and resid 5 through 9 Processing helix chain 'LI' and resid 42 through 46 removed outlier: 3.694A 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: 3.946A pdb=" N PHELI 157 " --> pdb=" O ARGLI 153 " (cutoff:3.500A) Processing helix chain 'LI' and resid 177 through 187 removed outlier: 4.303A pdb=" N GLULI 182 " --> pdb=" O ALALI 178 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ASPLI 183 " --> pdb=" O ASPLI 179 " (cutoff:3.500A) Processing helix chain 'LI' and resid 205 through 214 removed outlier: 3.932A pdb=" N TRPLI 209 " --> pdb=" O PROLI 205 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 10 through 14 removed outlier: 3.561A pdb=" N GLULJ 14 " --> pdb=" O PROLJ 11 " (cutoff:3.500A) 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: 3.750A 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: 4.122A pdb=" N ARGLL 92 " --> pdb=" O LYSLL 88 " (cutoff:3.500A) removed outlier: 4.185A 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 145 Processing helix chain 'LL' and resid 170 through 176 Processing helix chain 'LL' and resid 177 through 188 Processing helix chain 'LM' and resid 41 through 44 removed outlier: 4.107A pdb=" N GLNLM 44 " --> pdb=" O PROLM 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'LM' and resid 41 through 44' 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 12 Processing helix chain 'LN' and resid 16 through 33 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 149 Processing helix chain 'LN' and resid 153 through 157 Processing helix chain 'LN' and resid 158 through 163 Processing helix chain 'LN' and resid 165 through 171 removed outlier: 3.637A 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: 5.546A pdb=" N HISLN 182 " --> pdb=" O LYSLN 179 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THRLN 183 " --> pdb=" O PHELN 180 " (cutoff:3.500A) removed outlier: 3.721A 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: 3.583A 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: 4.321A 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 removed outlier: 3.524A pdb=" N GLULO 162 " --> pdb=" O GLULO 158 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYSLO 163 " --> pdb=" O LYSLO 159 " (cutoff:3.500A) 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 53 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: 4.181A 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: 3.522A pdb=" N GLYLQ 145 " --> pdb=" O PROLQ 142 " (cutoff:3.500A) removed outlier: 4.354A 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: 3.727A 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: 3.510A 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 113 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 26 through 32 removed outlier: 4.390A pdb=" N TYRLT 30 " --> pdb=" O PROLT 26 " (cutoff:3.500A) Processing helix chain 'LT' and resid 54 through 58 Processing helix chain 'LT' and resid 99 through 123 removed outlier: 3.628A pdb=" N ASPLT 103 " --> pdb=" O SERLT 99 " (cutoff:3.500A) 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: 3.643A 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 21 Processing helix chain 'LY' and resid 22 through 30 removed outlier: 3.743A 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: 3.838A 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: 3.571A 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: 4.043A 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: 3.840A pdb=" N SERLa 68 " --> pdb=" O LYSLa 64 " (cutoff:3.500A) Processing helix chain 'La' and resid 75 through 79 removed outlier: 4.278A pdb=" N TRPLa 79 " --> pdb=" O LEULa 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'La' and resid 75 through 79' Processing helix chain 'La' and resid 80 through 82 No H-bonds generated for 'chain 'La' and resid 80 through 82' Processing helix chain 'La' and resid 83 through 93 removed outlier: 3.559A pdb=" N ARGLa 87 " --> pdb=" O SERLa 83 " (cutoff:3.500A) Processing helix chain 'La' and resid 103 through 107 Processing helix chain 'La' and resid 130 through 141 Processing helix chain 'Lb' and resid 11 through 19 removed outlier: 4.157A pdb=" N ASNLb 19 " --> pdb=" O LYSLb 15 " (cutoff:3.500A) Processing helix chain 'Lb' and resid 36 through 50 Processing helix chain 'Lb' and resid 53 through 75 removed outlier: 3.513A pdb=" N GLULb 70 " --> pdb=" O SERLb 66 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYSLb 73 " --> pdb=" O ALALb 69 " (cutoff:3.500A) 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 86 Processing helix chain 'Ld' and resid 29 through 34 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 74 Processing helix chain 'Le' and resid 43 through 48 Processing helix chain 'Le' and resid 57 through 61 Processing helix chain 'Le' and resid 81 through 86 Processing helix chain 'Le' and resid 87 through 92 removed outlier: 4.281A pdb=" N METLe 90 " --> pdb=" O VALLe 87 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASNLe 92 " --> pdb=" O LEULe 89 " (cutoff:3.500A) Processing helix chain 'Le' and resid 104 through 119 removed outlier: 3.680A pdb=" N ALALe 110 " --> pdb=" O LYSLe 106 " (cutoff:3.500A) Processing helix chain 'Lf' and resid 35 through 40 removed outlier: 3.973A 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 62 through 67 Processing helix chain 'Lg' and resid 68 through 72 Processing helix chain 'Lg' and resid 83 through 114 removed outlier: 4.178A 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: 3.764A pdb=" N ILELh 47 " --> pdb=" O LYSLh 43 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ARGLh 48 " --> pdb=" O LEULh 44 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VALLh 49 " --> pdb=" O SERLh 45 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 88 through 94 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 4 through 9 removed outlier: 3.722A pdb=" N GLYLj 9 " --> pdb=" O THRLj 5 " (cutoff:3.500A) Processing helix chain 'Lj' and resid 50 through 58 removed outlier: 3.649A pdb=" N ASNLj 57 " --> pdb=" O ALALj 53 " (cutoff:3.500A) Processing helix chain 'Lj' and resid 64 through 75 removed outlier: 4.030A pdb=" N ILELj 69 " --> pdb=" O ARGLj 65 " (cutoff:3.500A) removed outlier: 3.842A 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 60 Processing helix chain 'Ll' and resid 6 through 20 Processing helix chain 'Ll' and resid 24 through 30 removed outlier: 3.621A pdb=" N ARGLl 28 " --> pdb=" O GLNLl 25 " (cutoff:3.500A) Processing helix chain 'Lm' and resid 79 through 91 removed outlier: 3.741A 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: 3.721A pdb=" N LYSLp 13 " --> pdb=" O ILELp 10 " (cutoff:3.500A) Processing helix chain 'Lp' and resid 19 through 35 removed outlier: 3.907A pdb=" N LYSLp 28 " --> pdb=" O LYSLp 24 " (cutoff:3.500A) removed outlier: 3.910A 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 101 removed outlier: 3.845A pdb=" N ASNLr 100 " --> pdb=" O METLr 96 " (cutoff:3.500A) 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 20 removed outlier: 3.854A pdb=" N ALALz 13 " --> pdb=" O THRLz 9 " (cutoff:3.500A) Processing helix chain 'Lz' and resid 21 through 25 removed outlier: 3.758A pdb=" N ARGLz 25 " --> pdb=" O GLNLz 22 " (cutoff:3.500A) Processing helix chain 'Lz' and resid 70 through 80 Processing helix chain 'Lz' and resid 86 through 92 Processing helix chain 'Lz' and resid 96 through 107 Processing helix chain 'Lz' and resid 114 through 118 removed outlier: 4.262A 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: 3.772A pdb=" N TYRLz 181 " --> pdb=" O ASPLz 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '1' and resid 276 through 281 Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 49 Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 78 Processing sheet with id=AA4, first strand: chain 'A' and resid 136 through 138 Processing sheet with id=AA5, first strand: chain 'A' and resid 201 through 202 removed outlier: 3.734A pdb=" N THR A 201 " --> pdb=" O PHE A 244 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 266 through 268 Processing sheet with id=AA7, first strand: chain 'A' and resid 322 through 324 Processing sheet with id=AA8, first strand: chain 'B' and resid 9 through 10 removed outlier: 5.618A pdb=" N ILE B 9 " --> pdb=" O ASN B 500 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 197 through 202 removed outlier: 6.237A pdb=" N VAL C 198 " --> pdb=" O SER D 22 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N SER D 22 " --> pdb=" O VAL C 198 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLU C 200 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N LEU D 74 " --> pdb=" O SER D 5 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N LYS D 7 " --> pdb=" O LEU D 74 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE D 76 " --> pdb=" O LYS D 7 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N THR D 9 " --> pdb=" O ILE D 76 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 228 through 230 Processing sheet with id=AB2, first strand: chain 'K' and resid 2 through 5 removed outlier: 6.169A pdb=" N VAL K 3 " --> pdb=" O CYS K 206 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 17 through 19 Processing sheet with id=AB4, first strand: chain 'K' and resid 69 through 72 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: 6.716A pdb=" N LEULA 58 " --> pdb=" O ILELA 48 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ILELA 48 " --> pdb=" O LEULA 58 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LYSLA 60 " --> pdb=" O LYSLA 46 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ARGLA 64 " --> pdb=" O LYSLA 42 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N LYSLA 42 " --> pdb=" O ARGLA 64 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'LA' and resid 101 through 103 removed outlier: 5.579A pdb=" N VALLA 136 " --> pdb=" O LYSLA 149 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LYSLA 149 " --> pdb=" O VALLA 136 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'LB' and resid 42 through 43 removed outlier: 4.941A pdb=" N ILELB 160 " --> pdb=" O VALLB 185 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N HISLB 165 " --> pdb=" O VALLB 86 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N VALLB 86 " --> pdb=" O HISLB 165 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYSLB 103 " --> pdb=" O GLYLB 91 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N VALLB 93 " --> pdb=" O THRLB 101 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N THRLB 101 " --> pdb=" O VALLB 93 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N THRLB 95 " --> pdb=" O LEULB 99 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N LEULB 99 " --> pdb=" O THRLB 95 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'LB' and resid 42 through 43 removed outlier: 4.941A pdb=" N ILELB 160 " --> pdb=" O VALLB 185 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N HISLB 165 " --> pdb=" O VALLB 86 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N VALLB 86 " --> pdb=" O HISLB 165 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'LB' and resid 365 through 368 removed outlier: 6.533A pdb=" N VALLB 57 " --> pdb=" O LYSLB 366 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ILELB 368 " --> pdb=" O HISLB 55 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N HISLB 55 " --> pdb=" O ILELB 368 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N VALLB 344 " --> pdb=" O VALLB 222 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N VALLB 222 " --> pdb=" O VALLB 344 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILELB 217 " --> pdb=" O ASNLB 281 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N LYSLB 283 " --> pdb=" O LYSLB 334 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N METLB 332 " --> pdb=" O TYRLB 285 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ILELB 287 " --> pdb=" O PHELB 330 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N PHELB 330 " --> pdb=" O ILELB 287 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLULB 80 " --> pdb=" O LYSLB 50 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N LYSLB 50 " --> pdb=" O GLULB 80 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'LB' and resid 225 through 229 removed outlier: 5.697A pdb=" N LYSLB 272 " --> pdb=" O LYSLB 226 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N TYRLB 228 " --> pdb=" O GLYLB 270 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLYLB 270 " --> pdb=" O TYRLB 228 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'LB' and resid 292 through 293 Processing sheet with id=AC5, first strand: chain 'LC' and resid 7 through 11 removed outlier: 6.573A pdb=" N ILELC 8 " --> pdb=" O LYSLC 20 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LYSLC 20 " --> pdb=" O ILELC 8 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VALLC 10 " --> pdb=" O SERLC 18 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'LC' and resid 64 through 65 Processing sheet with id=AC7, first strand: chain 'LC' and resid 152 through 154 removed outlier: 6.383A pdb=" N LEULC 152 " --> pdb=" O TRPLC 252 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ILELC 209 " --> pdb=" O LEULC 230 " (cutoff:3.500A) 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: 5.852A pdb=" N ILELD 74 " --> pdb=" O TYRLD 66 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N TYRLD 66 " --> pdb=" O ILELD 74 " (cutoff:3.500A) removed outlier: 3.822A 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: 6.605A pdb=" N THRLE 176 " --> pdb=" O PHELE 164 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N PHELE 164 " --> pdb=" O THRLE 176 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N THRLE 148 " --> pdb=" O PHELE 164 " (cutoff:3.500A) removed outlier: 4.461A 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 removed outlier: 3.563A pdb=" N HISLT 139 " --> pdb=" O VALLF 83 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'LF' and resid 211 through 212 removed outlier: 4.003A pdb=" N ASNLF 119 " --> pdb=" O ARGLF 94 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILELF 140 " --> pdb=" O GLYLF 234 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ARGLF 236 " --> pdb=" O ILELF 140 " (cutoff:3.500A) removed outlier: 7.887A 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 137 through 138 removed outlier: 6.305A pdb=" N VALLG 155 " --> pdb=" O CYSLG 182 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ILELG 184 " --> pdb=" O VALLG 155 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ILELG 157 " --> pdb=" O ILELG 184 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'LH' and resid 3 through 11 removed outlier: 7.282A pdb=" N ILELH 4 " --> pdb=" O TRPLH 61 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARGLH 54 " --> pdb=" O LEULH 48 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'LH' and resid 17 through 21 removed outlier: 3.688A pdb=" N THRLH 24 " --> pdb=" O LYSLH 21 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'LH' and resid 132 through 136 removed outlier: 6.842A pdb=" N ARGLH 89 " --> pdb=" O LYSLH 184 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LYSLH 184 " --> pdb=" O ARGLH 89 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LYSLH 91 " --> pdb=" O SERLH 182 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'LH' and resid 103 through 106 Processing sheet with id=AE4, first strand: chain 'LI' and resid 35 through 37 removed outlier: 6.645A pdb=" N METLI 52 " --> pdb=" O ILELI 135 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N SERLI 137 " --> pdb=" O GLYLI 50 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLYLI 50 " --> pdb=" O SERLI 137 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ARGLI 139 " --> pdb=" O LEULI 48 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEULI 48 " --> pdb=" O ARGLI 139 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'LI' and resid 58 through 61 removed outlier: 6.693A pdb=" N ILELI 97 " --> pdb=" O GLNLI 123 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N THRLI 125 " --> pdb=" O HISLI 95 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N HISLI 95 " --> pdb=" O THRLI 125 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'LI' and resid 190 through 192 Processing sheet with id=AE7, first strand: chain 'LJ' and resid 49 through 52 removed outlier: 5.283A pdb=" N ILELJ 17 " --> pdb=" O GLYLJ 135 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLYLJ 135 " --> pdb=" O ILELJ 17 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'LJ' and resid 93 through 95 removed outlier: 6.993A pdb=" N LEULJ 94 " --> pdb=" O LEULJ 175 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'LL' and resid 22 through 24 Processing sheet with id=AF1, first strand: chain 'LL' and resid 58 through 60 Processing sheet with id=AF2, first strand: chain 'LL' and resid 124 through 126 Processing sheet with id=AF3, first strand: chain 'LM' and resid 7 through 8 Processing sheet with id=AF4, first strand: chain 'LM' and resid 45 through 51 removed outlier: 5.114A pdb=" N ARGLM 46 " --> pdb=" O GLYLM 40 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N GLYLM 40 " --> pdb=" O ARGLM 46 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ASPLM 39 " --> pdb=" O ILELM 27 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ILELM 27 " --> pdb=" O ASPLM 39 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ARGLM 11 " --> pdb=" O ILELM 27 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N VALLM 12 " --> pdb=" O THRLM 58 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'LN' and resid 36 through 39 removed outlier: 4.430A pdb=" N ILELN 61 " --> pdb=" O ALALN 39 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N TYRLN 127 " --> pdb=" O GLULN 123 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLULN 123 " --> pdb=" O TYRLN 127 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N PHELN 129 " --> pdb=" O VALLN 121 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASNLN 117 " --> pdb=" O ILELN 133 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILELN 135 " --> pdb=" O VALLN 115 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N VALLN 115 " --> pdb=" O ILELN 135 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'LO' and resid 6 through 10 removed outlier: 6.503A pdb=" N VALLO 33 " --> pdb=" O LYSLO 103 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'LO' and resid 42 through 44 Processing sheet with id=AF8, first strand: chain 'LP' and resid 14 through 22 removed outlier: 3.610A pdb=" N ASNLP 21 " --> pdb=" O CYSLP 144 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N CYSLP 144 " --> pdb=" O ASNLP 21 " (cutoff:3.500A) removed outlier: 6.489A 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=AF9, first strand: chain 'LP' and resid 58 through 59 Processing sheet with id=AG1, first strand: chain 'LP' and resid 126 through 131 removed outlier: 3.664A pdb=" N ARGLP 135 " --> pdb=" O ARGLP 131 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'LQ' and resid 61 through 62 removed outlier: 4.014A pdb=" N LEULQ 103 " --> pdb=" O VALLQ 82 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N GLYLQ 84 " --> pdb=" O LEULQ 103 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N VALLQ 105 " --> pdb=" O GLYLQ 84 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILELQ 86 " --> pdb=" O VALLQ 105 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'LQ' and resid 61 through 62 removed outlier: 6.358A pdb=" N THRLQ 79 " --> pdb=" O VALLQ 137 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LEULQ 139 " --> pdb=" O THRLQ 79 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VALLQ 81 " --> pdb=" O LEULQ 139 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'LQ' and resid 180 through 181 removed outlier: 3.675A pdb=" N TYRLQ 186 " --> pdb=" O ARGLQ 181 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'LR' and resid 22 through 24 Processing sheet with id=AG6, first strand: chain 'LS' and resid 59 through 66 removed outlier: 5.208A pdb=" N ILELS 61 " --> pdb=" O ARGLS 15 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ARGLS 15 " --> pdb=" O ILELS 61 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'LS' and resid 90 through 99 removed outlier: 6.888A pdb=" N ARGLS 83 " --> pdb=" O ILELS 126 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ILELS 126 " --> pdb=" O ARGLS 83 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ASPLS 85 " --> pdb=" O ILELS 124 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILELS 124 " --> pdb=" O ASPLS 85 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'LT' and resid 84 through 92 removed outlier: 6.474A pdb=" N VALLT 75 " --> pdb=" O VALLT 64 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N VALLT 64 " --> pdb=" O VALLT 75 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N ASNLT 77 " --> pdb=" O GLYLT 62 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N GLYLT 62 " --> pdb=" O ASNLT 77 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'LU' and resid 61 through 66 removed outlier: 8.948A pdb=" N TYRLU 110 " --> pdb=" O LYSLU 20 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N THRLU 22 " --> pdb=" O TYRLU 110 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N LEULU 112 " --> pdb=" O THRLU 22 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ASPLU 24 " --> pdb=" O LEULU 112 " (cutoff:3.500A) removed outlier: 9.155A pdb=" N TYRLU 114 " --> pdb=" O ASPLU 24 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'LU' and resid 48 through 49 Processing sheet with id=AH2, first strand: chain 'LV' and resid 20 through 21 Processing sheet with id=AH3, first strand: chain 'LV' and resid 25 through 28 removed outlier: 6.938A pdb=" N ASNLV 36 " --> pdb=" O LYSLV 66 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYSLV 66 " --> pdb=" O ASNLV 36 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N METLV 62 " --> pdb=" O ILELV 40 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N VALLV 42 " --> pdb=" O METLV 60 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N METLV 60 " --> pdb=" O VALLV 42 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALALV 102 " --> pdb=" O ILELV 82 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N GLYLV 103 " --> pdb=" O VALLV 25 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ASNLV 27 " --> pdb=" O GLYLV 103 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ILELV 105 " --> pdb=" O ASNLV 27 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'LV' and resid 88 through 89 removed outlier: 6.326A pdb=" N PHELV 95 " --> pdb=" O ARGLW 20 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ALALW 22 " --> pdb=" O PHELV 95 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TYRLV 97 " --> pdb=" O ALALW 22 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'LV' and resid 120 through 121 Processing sheet with id=AH6, first strand: chain 'LW' and resid 4 through 5 removed outlier: 3.742A pdb=" N GLULW 4 " --> pdb=" O ILELW 13 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'LX' and resid 77 through 80 removed outlier: 3.723A pdb=" N LYSLX 134 " --> pdb=" O VALLX 100 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'LY' and resid 31 through 33 Processing sheet with id=AH9, first strand: chain 'LY' and resid 79 through 82 removed outlier: 6.816A pdb=" N GLULY 54 " --> pdb=" O THRLY 107 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'LY' and resid 86 through 88 Processing sheet with id=AI2, first strand: chain 'LZ' and resid 69 through 76 removed outlier: 6.537A pdb=" N LYSLZ 69 " --> pdb=" O ASPLZ 47 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N HISLZ 40 " --> pdb=" O ASNLZ 28 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ASNLZ 28 " --> pdb=" O HISLZ 40 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEULZ 42 " --> pdb=" O VALLZ 26 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N LYSLZ 22 " --> pdb=" O ILELZ 46 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LYSLZ 9 " --> pdb=" O ILELZ 25 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N TYRLZ 85 " --> pdb=" O VALLZ 10 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N LEULZ 12 " --> pdb=" O THRLZ 83 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N THRLZ 83 " --> pdb=" O LEULZ 12 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'La' and resid 72 through 74 removed outlier: 6.330A pdb=" N VALLa 73 " --> pdb=" O LEULa 112 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'La' and resid 100 through 102 removed outlier: 6.330A pdb=" N VALLa 124 " --> pdb=" O VALLa 145 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'Lc' and resid 26 through 29 removed outlier: 6.370A pdb=" N LYSLc 26 " --> pdb=" O ILELc 97 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'Ld' and resid 62 through 64 Processing sheet with id=AI7, first strand: chain 'Le' and resid 75 through 79 removed outlier: 5.766A pdb=" N ARGLe 75 " --> pdb=" O CYSLe 96 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLULe 98 " --> pdb=" O ARGLe 75 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N PHELe 77 " --> pdb=" O GLULe 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI7 Processing sheet with id=AI8, first strand: chain 'Lf' and resid 7 through 16 removed outlier: 9.898A pdb=" N SERLf 7 " --> pdb=" O ILELf 30 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N ILELf 30 " --> pdb=" O SERLf 7 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ALALf 9 " --> pdb=" O LEULf 28 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N LEULf 28 " --> pdb=" O ALALf 9 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N PHELf 11 " --> pdb=" O ALALf 26 " (cutoff:3.500A) removed outlier: 9.506A pdb=" N ALALf 26 " --> pdb=" O PHELf 11 " (cutoff:3.500A) removed outlier: 11.581A pdb=" N GLYLf 13 " --> pdb=" O HISLf 24 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N HISLf 24 " --> pdb=" O GLYLf 13 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYSLf 15 " --> pdb=" O ARGLf 22 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N HISLf 24 " --> pdb=" O PHELf 88 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N PHELf 88 " --> pdb=" O HISLf 24 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LYSLf 87 " --> pdb=" O VALLf 74 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N VALLf 74 " --> pdb=" O LYSLf 87 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N LYSLf 66 " --> pdb=" O ALALf 53 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N VALLf 50 " --> pdb=" O ARGLf 100 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ARGLf 100 " --> pdb=" O VALLf 50 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'Lg' and resid 20 through 24 Processing sheet with id=AJ1, first strand: chain 'Lj' and resid 16 through 17 Processing sheet with id=AJ2, first strand: chain 'Lk' and resid 3 through 5 removed outlier: 4.317A pdb=" N VALLk 46 " --> pdb=" O ILELk 5 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SERLk 22 " --> pdb=" O ARGLk 37 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VALLk 23 " --> pdb=" O LYSLk 67 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'Lm' and resid 102 through 103 Processing sheet with id=AJ4, first strand: chain 'Lo' and resid 3 through 4 Processing sheet with id=AJ5, first strand: chain 'Lo' and resid 7 through 11 removed outlier: 4.169A pdb=" N ILELo 66 " --> pdb=" O ILELo 85 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'Lp' and resid 47 through 51 removed outlier: 6.890A pdb=" N ILELp 54 " --> pdb=" O ARGLp 50 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'Lr' and resid 17 through 20 Processing sheet with id=AJ8, first strand: chain 'Lr' and resid 49 through 53 Processing sheet with id=AJ9, first strand: chain 'Lz' and resid 164 through 171 removed outlier: 6.300A pdb=" N CYSLz 164 " --> pdb=" O LEULz 38 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LEULz 38 " --> pdb=" O CYSLz 164 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ALALz 166 " --> pdb=" O ILELz 36 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ILELz 36 " --> pdb=" O ALALz 166 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ALALz 168 " --> pdb=" O LEULz 34 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEULz 34 " --> pdb=" O ALALz 168 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'Lz' and resid 50 through 54 Processing sheet with id=AK2, first strand: chain 'Lz' and resid 65 through 68 removed outlier: 4.181A pdb=" N SERLz 113 " --> pdb=" O LEULz 68 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N PHELz 110 " --> pdb=" O SERLz 136 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N LEULz 138 " --> pdb=" O PHELz 110 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ALALz 112 " --> pdb=" O LEULz 138 " (cutoff:3.500A) 3259 hydrogen bonds defined for protein. 9306 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3002 hydrogen bonds 5202 hydrogen bond angles 0 basepair planarities 1132 basepair parallelities 1903 stacking parallelities Total time for adding SS restraints: 288.99 Time building geometry restraints manager: 67.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 18728 1.32 - 1.45: 62854 1.45 - 1.57: 71078 1.57 - 1.69: 7455 1.69 - 1.82: 504 Bond restraints: 160619 Sorted by residual: bond pdb=" N VAL 3 75 " pdb=" CA VAL 3 75 " ideal model delta sigma weight residual 1.461 1.493 -0.031 1.17e-02 7.31e+03 7.23e+00 bond pdb=" N VAL 3 73 " pdb=" CA VAL 3 73 " ideal model delta sigma weight residual 1.463 1.493 -0.030 1.14e-02 7.69e+03 7.10e+00 bond pdb=" C PRO 3 72 " pdb=" O PRO 3 72 " ideal model delta sigma weight residual 1.235 1.201 0.034 1.30e-02 5.92e+03 7.01e+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 6.22e+00 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 6.15e+00 ... (remaining 160614 not shown) Histogram of bond angle deviations from ideal: 98.74 - 105.79: 19825 105.79 - 112.83: 91994 112.83 - 119.88: 55763 119.88 - 126.93: 57871 126.93 - 133.98: 9504 Bond angle restraints: 234957 Sorted by residual: angle pdb=" CA PRO 3 72 " pdb=" N PRO 3 72 " pdb=" CD PRO 3 72 " ideal model delta sigma weight residual 112.00 105.40 6.60 1.40e+00 5.10e-01 2.22e+01 angle pdb=" N SER 3 77 " pdb=" CA SER 3 77 " pdb=" C SER 3 77 " ideal model delta sigma weight residual 111.36 107.08 4.28 1.09e+00 8.42e-01 1.54e+01 angle pdb=" N MET 3 76 " pdb=" CA MET 3 76 " pdb=" C MET 3 76 " ideal model delta sigma weight residual 113.18 108.87 4.31 1.21e+00 6.83e-01 1.27e+01 angle pdb=" N VAL 3 73 " pdb=" CA VAL 3 73 " pdb=" C VAL 3 73 " ideal model delta sigma weight residual 110.23 106.71 3.52 1.04e+00 9.25e-01 1.15e+01 angle pdb=" CB ARGLR 151 " pdb=" CG ARGLR 151 " pdb=" CD ARGLR 151 " ideal model delta sigma weight residual 111.30 119.08 -7.78 2.30e+00 1.89e-01 1.14e+01 ... (remaining 234952 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 92686 35.76 - 71.52: 9351 71.52 - 107.28: 1209 107.28 - 143.04: 13 143.04 - 178.79: 1 Dihedral angle restraints: 103260 sinusoidal: 78183 harmonic: 25077 Sorted by residual: 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 50.79 -178.79 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 98.38 101.62 1 1.50e+01 4.44e-03 5.13e+01 dihedral pdb=" O4' U 8 111 " pdb=" C1' U 8 111 " pdb=" N1 U 8 111 " pdb=" C2 U 8 111 " ideal model delta sinusoidal sigma weight residual 200.00 102.86 97.14 1 1.50e+01 4.44e-03 4.80e+01 ... (remaining 103257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 26911 0.048 - 0.096: 1600 0.096 - 0.144: 610 0.144 - 0.192: 13 0.192 - 0.240: 1 Chirality restraints: 29135 Sorted by residual: chirality pdb=" CA VAL 3 73 " pdb=" N VAL 3 73 " pdb=" C VAL 3 73 " pdb=" CB VAL 3 73 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA VAL 3 75 " pdb=" N VAL 3 75 " pdb=" C VAL 3 75 " pdb=" CB VAL 3 75 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.59e-01 chirality pdb=" C1' U 52580 " pdb=" O4' U 52580 " pdb=" C2' U 52580 " pdb=" N1 U 52580 " both_signs ideal model delta sigma weight residual False 2.47 2.29 0.18 2.00e-01 2.50e+01 8.14e-01 ... (remaining 29132 not shown) Planarity restraints: 15785 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL 3 68 " -0.020 2.00e-02 2.50e+03 4.08e-02 1.66e+01 pdb=" C VAL 3 68 " 0.071 2.00e-02 2.50e+03 pdb=" O VAL 3 68 " -0.027 2.00e-02 2.50e+03 pdb=" N GLY 3 69 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 8 39 " -0.040 2.00e-02 2.50e+03 1.69e-02 8.53e+00 pdb=" N9 G 8 39 " 0.040 2.00e-02 2.50e+03 pdb=" C8 G 8 39 " 0.005 2.00e-02 2.50e+03 pdb=" N7 G 8 39 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G 8 39 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G 8 39 " -0.005 2.00e-02 2.50e+03 pdb=" O6 G 8 39 " -0.010 2.00e-02 2.50e+03 pdb=" N1 G 8 39 " -0.004 2.00e-02 2.50e+03 pdb=" C2 G 8 39 " 0.003 2.00e-02 2.50e+03 pdb=" N2 G 8 39 " 0.002 2.00e-02 2.50e+03 pdb=" N3 G 8 39 " 0.005 2.00e-02 2.50e+03 pdb=" C4 G 8 39 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 52580 " -0.030 2.00e-02 2.50e+03 1.57e-02 5.53e+00 pdb=" N1 U 52580 " 0.034 2.00e-02 2.50e+03 pdb=" C2 U 52580 " 0.003 2.00e-02 2.50e+03 pdb=" O2 U 52580 " 0.003 2.00e-02 2.50e+03 pdb=" N3 U 52580 " -0.002 2.00e-02 2.50e+03 pdb=" C4 U 52580 " -0.004 2.00e-02 2.50e+03 pdb=" O4 U 52580 " -0.009 2.00e-02 2.50e+03 pdb=" C5 U 52580 " 0.001 2.00e-02 2.50e+03 pdb=" C6 U 52580 " 0.006 2.00e-02 2.50e+03 ... (remaining 15782 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 886 2.47 - 3.08: 95659 3.08 - 3.68: 270250 3.68 - 4.29: 401137 4.29 - 4.90: 579105 Nonbonded interactions: 1347037 Sorted by model distance: nonbonded pdb=" OP2 C 53791 " pdb="MG MG 55302 " model vdw 1.860 2.170 nonbonded pdb=" OP2 G 51329 " pdb="MG MG 55251 " model vdw 1.872 2.170 nonbonded pdb=" OP1 U 52530 " pdb="MG MG 55290 " model vdw 1.872 2.170 nonbonded pdb=" O4 U 51636 " pdb="MG MG 55190 " model vdw 1.876 2.170 nonbonded pdb=" O6 G 51626 " pdb="MG MG 55190 " model vdw 1.879 2.170 ... (remaining 1347032 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=0.96 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: 7.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.120 Extract box with map and model: 36.990 Check model and map are aligned: 1.680 Set scattering table: 1.030 Process input model: 598.870 Find NCS groups from input model: 3.480 Set up NCS constraints: 0.380 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:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 652.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 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 : 0.002 0.040 160619 Z= 0.102 Angle : 0.387 9.183 234957 Z= 0.207 Chirality : 0.030 0.240 29135 Planarity : 0.002 0.041 15785 Dihedral : 21.933 178.795 87068 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.18 % Favored : 97.80 % Rotamer: Outliers : 0.08 % Allowed : 13.12 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.76 % 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: 2.39 (0.09), residues: 8540 helix: 2.80 (0.09), residues: 3634 sheet: 0.49 (0.16), residues: 1029 loop : 0.82 (0.10), residues: 3877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 1 379 HIS 0.003 0.000 HIS 1 360 PHE 0.012 0.001 PHE 1 182 TYR 0.008 0.001 TYRLQ 32 ARG 0.002 0.000 ARGLg 29 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17080 Ramachandran restraints generated. 8540 Oldfield, 0 Emsley, 8540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17080 Ramachandran restraints generated. 8540 Oldfield, 0 Emsley, 8540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1161 residues out of total 7475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1155 time to evaluate : 8.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 20 ARG cc_start: -0.2170 (mtm110) cc_final: -0.2634 (mtm180) REVERT: 3 77 SER cc_start: -0.1412 (OUTLIER) cc_final: -0.1837 (t) REVERT: B 185 ASP cc_start: 0.8816 (m-30) cc_final: 0.8511 (p0) REVERT: B 353 PHE cc_start: 0.8743 (t80) cc_final: 0.8253 (t80) REVERT: LA 176 ASP cc_start: 0.8507 (m-30) cc_final: 0.8275 (m-30) REVERT: LB 168 MET cc_start: 0.8695 (mmm) cc_final: 0.8140 (mmm) REVERT: LD 293 ARG cc_start: 0.8476 (mpt180) cc_final: 0.8199 (mpt-90) REVERT: LE 245 GLN cc_start: 0.8138 (tp40) cc_final: 0.7900 (tp40) REVERT: LE 249 ASP cc_start: 0.8356 (m-30) cc_final: 0.7779 (m-30) REVERT: LF 171 ASP cc_start: 0.8548 (t0) cc_final: 0.8212 (t0) REVERT: LG 88 ASP cc_start: 0.8147 (p0) cc_final: 0.7845 (p0) REVERT: LH 4 ILE cc_start: 0.9178 (mt) cc_final: 0.8750 (mt) REVERT: LH 11 ASP cc_start: 0.8620 (m-30) cc_final: 0.8309 (m-30) REVERT: LH 126 VAL cc_start: 0.9435 (t) cc_final: 0.9223 (m) REVERT: LH 137 SER cc_start: 0.9258 (t) cc_final: 0.9028 (p) REVERT: LH 143 GLU cc_start: 0.7882 (tt0) cc_final: 0.7587 (tt0) REVERT: LI 55 ASP cc_start: 0.8704 (t0) cc_final: 0.8126 (t0) REVERT: LJ 140 SER cc_start: 0.8892 (p) cc_final: 0.8661 (t) REVERT: LL 175 ASN cc_start: 0.9071 (m110) cc_final: 0.8836 (m110) REVERT: LM 39 ASP cc_start: 0.7483 (t0) cc_final: 0.6796 (t0) REVERT: LM 96 GLU cc_start: 0.8187 (tp30) cc_final: 0.6728 (tp30) REVERT: LO 162 GLU cc_start: 0.7839 (mp0) cc_final: 0.7470 (mp0) REVERT: LO 194 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8411 (tp30) REVERT: LP 87 SER cc_start: 0.9283 (m) cc_final: 0.8989 (m) REVERT: LP 108 ASP cc_start: 0.7933 (t0) cc_final: 0.7460 (t70) REVERT: LR 28 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8136 (mm-30) REVERT: LR 119 MET cc_start: 0.8927 (ttm) cc_final: 0.8713 (ttm) REVERT: LT 57 TYR cc_start: 0.8731 (m-80) cc_final: 0.8531 (m-80) REVERT: LU 23 LEU cc_start: 0.9112 (mt) cc_final: 0.8875 (tt) REVERT: LU 27 HIS cc_start: 0.8589 (m170) cc_final: 0.7840 (m170) REVERT: LU 46 ARG cc_start: 0.8670 (tpp-160) cc_final: 0.8415 (mmt180) REVERT: LV 108 ASN cc_start: 0.8799 (m-40) cc_final: 0.8592 (m110) REVERT: LV 111 GLU cc_start: 0.7491 (mp0) cc_final: 0.7284 (mp0) REVERT: LW 37 GLU cc_start: 0.8340 (tt0) cc_final: 0.8070 (tt0) REVERT: LW 52 THR cc_start: 0.9159 (m) cc_final: 0.8765 (p) REVERT: LX 95 THR cc_start: 0.8909 (m) cc_final: 0.8673 (t) REVERT: LX 145 ASP cc_start: 0.8117 (t0) cc_final: 0.7445 (t0) REVERT: LY 8 THR cc_start: 0.8447 (t) cc_final: 0.8089 (t) REVERT: LZ 47 ASP cc_start: 0.9238 (t0) cc_final: 0.8839 (t0) REVERT: LZ 78 ASN cc_start: 0.9130 (m110) cc_final: 0.8921 (m-40) REVERT: La 16 SER cc_start: 0.9016 (m) cc_final: 0.8617 (p) REVERT: La 85 GLN cc_start: 0.8649 (tm-30) cc_final: 0.8405 (tt0) REVERT: La 89 ASN cc_start: 0.9055 (m-40) cc_final: 0.8752 (m-40) REVERT: Lc 27 TYR cc_start: 0.8737 (p90) cc_final: 0.8453 (p90) REVERT: Lc 34 THR cc_start: 0.9309 (m) cc_final: 0.8946 (p) REVERT: Lc 106 ARG cc_start: 0.6731 (tpm170) cc_final: 0.6525 (tpp-160) REVERT: Ld 84 ILE cc_start: 0.9002 (tt) cc_final: 0.8749 (tt) REVERT: Lg 98 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8327 (mm-30) REVERT: Li 27 SER cc_start: 0.9383 (p) cc_final: 0.9170 (m) REVERT: Li 42 ASP cc_start: 0.8459 (m-30) cc_final: 0.8191 (m-30) REVERT: Li 88 GLU cc_start: 0.7811 (tp30) cc_final: 0.7284 (tp30) REVERT: Li 92 ASN cc_start: 0.8691 (m-40) cc_final: 0.8408 (m-40) REVERT: Lk 10 ASP cc_start: 0.8234 (m-30) cc_final: 0.7903 (m-30) REVERT: Lm 120 ASN cc_start: 0.8272 (t0) cc_final: 0.7873 (t0) outliers start: 6 outliers final: 3 residues processed: 1159 average time/residue: 1.2331 time to fit residues: 2579.9159 Evaluate side-chains 895 residues out of total 7475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 891 time to evaluate : 8.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 452 THR Chi-restraints excluded: chain 3 residue 77 SER Chi-restraints excluded: chain LG residue 159 HIS Chi-restraints excluded: chain LY residue 120 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1216 random chunks: chunk 1026 optimal weight: 9.9990 chunk 921 optimal weight: 3.9990 chunk 511 optimal weight: 0.6980 chunk 314 optimal weight: 40.0000 chunk 621 optimal weight: 7.9990 chunk 492 optimal weight: 30.0000 chunk 953 optimal weight: 9.9990 chunk 368 optimal weight: 10.0000 chunk 579 optimal weight: 10.0000 chunk 709 optimal weight: 0.3980 chunk 1104 optimal weight: 9.9990 overall best weight: 4.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 549 ASN B 163 HIS B 391 GLN ** K 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LF 63 GLN LF 110 GLN LH 106 GLN LI 133 GLN ** LJ 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LL 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LN 29 GLN LN 87 HIS LP 75 GLN ** LP 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LQ 21 GLN LR 40 GLN LT 54 HIS LU 38 ASN LW 59 HIS LX 93 ASN LY 14 ASN Lb 58 GLN Lb 60 ASN Lo 76 ASN Lz 143 ASN ** Lz 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 160619 Z= 0.237 Angle : 0.528 10.495 234957 Z= 0.270 Chirality : 0.034 0.207 29135 Planarity : 0.004 0.093 15785 Dihedral : 22.221 177.754 68976 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.67 % Favored : 97.32 % Rotamer: Outliers : 2.44 % Allowed : 13.84 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.76 % 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: 1.86 (0.09), residues: 8540 helix: 2.26 (0.09), residues: 3623 sheet: 0.41 (0.16), residues: 1052 loop : 0.60 (0.10), residues: 3865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRPLz 198 HIS 0.012 0.001 HIS B 163 PHE 0.026 0.002 PHELU 39 TYR 0.024 0.002 TYR K 35 ARG 0.009 0.001 ARGLV 131 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17080 Ramachandran restraints generated. 8540 Oldfield, 0 Emsley, 8540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17080 Ramachandran restraints generated. 8540 Oldfield, 0 Emsley, 8540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1102 residues out of total 7475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 920 time to evaluate : 8.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 300 ASN cc_start: 0.1320 (OUTLIER) cc_final: 0.1006 (t0) REVERT: 1 449 LEU cc_start: 0.1439 (pp) cc_final: 0.1224 (pp) REVERT: B 185 ASP cc_start: 0.8917 (OUTLIER) cc_final: 0.8240 (t0) REVERT: B 412 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8089 (tp) REVERT: C 299 ASN cc_start: 0.6481 (OUTLIER) cc_final: 0.6005 (m-40) REVERT: LA 176 ASP cc_start: 0.8660 (m-30) cc_final: 0.8346 (m-30) REVERT: LB 279 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8151 (mm-30) REVERT: LC 61 GLN cc_start: 0.8854 (mt0) cc_final: 0.8555 (mt0) REVERT: LC 325 MET cc_start: 0.9183 (tpp) cc_final: 0.8953 (tpt) REVERT: LD 293 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.8036 (mpt-90) REVERT: LE 112 MET cc_start: 0.8851 (mmt) cc_final: 0.8582 (mmt) REVERT: LE 245 GLN cc_start: 0.8484 (tp40) cc_final: 0.7709 (tp40) REVERT: LE 249 ASP cc_start: 0.8452 (m-30) cc_final: 0.7673 (m-30) REVERT: LF 171 ASP cc_start: 0.8590 (t0) cc_final: 0.8251 (t0) REVERT: LG 88 ASP cc_start: 0.8465 (p0) cc_final: 0.8018 (p0) REVERT: LH 11 ASP cc_start: 0.8755 (m-30) cc_final: 0.8525 (m-30) REVERT: LH 46 SER cc_start: 0.9101 (m) cc_final: 0.8864 (m) REVERT: LH 106 GLN cc_start: 0.7782 (mt0) cc_final: 0.7536 (mt0) REVERT: LH 110 SER cc_start: 0.9179 (t) cc_final: 0.8918 (t) REVERT: LH 115 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.7436 (ptp90) REVERT: LH 137 SER cc_start: 0.9403 (t) cc_final: 0.9111 (p) REVERT: LH 143 GLU cc_start: 0.8288 (tt0) cc_final: 0.7983 (tt0) REVERT: LI 63 GLU cc_start: 0.8807 (mp0) cc_final: 0.8607 (mp0) REVERT: LI 115 MET cc_start: 0.9354 (mmm) cc_final: 0.9086 (mmm) REVERT: LL 142 GLU cc_start: 0.8091 (mp0) cc_final: 0.7852 (pm20) REVERT: LL 145 LYS cc_start: 0.8607 (tptt) cc_final: 0.8341 (tptt) REVERT: LL 171 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8307 (mm-30) REVERT: LL 175 ASN cc_start: 0.9164 (m110) cc_final: 0.8907 (m110) REVERT: LM 44 GLN cc_start: 0.8813 (mp10) cc_final: 0.8610 (mp10) REVERT: LM 75 GLN cc_start: 0.9209 (tt0) cc_final: 0.8989 (tt0) REVERT: LM 96 GLU cc_start: 0.8511 (tp30) cc_final: 0.7924 (tp30) REVERT: LM 99 GLU cc_start: 0.7951 (pp20) cc_final: 0.7633 (pp20) REVERT: LN 6 TYR cc_start: 0.9068 (m-80) cc_final: 0.8670 (m-80) REVERT: LO 168 TYR cc_start: 0.8346 (t80) cc_final: 0.8121 (t80) REVERT: LP 108 ASP cc_start: 0.8210 (t0) cc_final: 0.7764 (t0) REVERT: LR 119 MET cc_start: 0.8961 (ttm) cc_final: 0.8704 (ttm) REVERT: LS 112 ASP cc_start: 0.8861 (t70) cc_final: 0.8505 (t0) REVERT: LU 23 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8767 (tt) REVERT: LU 40 GLU cc_start: 0.8913 (pt0) cc_final: 0.8462 (pp20) REVERT: LU 46 ARG cc_start: 0.8737 (tpp-160) cc_final: 0.8385 (mmt180) REVERT: LU 95 ASN cc_start: 0.8893 (t0) cc_final: 0.8652 (t0) REVERT: LU 98 ASP cc_start: 0.8200 (p0) cc_final: 0.7598 (p0) REVERT: LW 1 MET cc_start: 0.7129 (ttp) cc_final: 0.6705 (mtp) REVERT: LX 145 ASP cc_start: 0.8551 (t0) cc_final: 0.7922 (t0) REVERT: LX 148 ASP cc_start: 0.9078 (m-30) cc_final: 0.8664 (m-30) REVERT: LY 8 THR cc_start: 0.9015 (t) cc_final: 0.8724 (t) REVERT: LY 37 GLU cc_start: 0.8761 (mp0) cc_final: 0.8560 (mp0) REVERT: LY 107 THR cc_start: 0.9588 (m) cc_final: 0.9305 (p) REVERT: La 89 ASN cc_start: 0.9121 (m-40) cc_final: 0.8820 (m-40) REVERT: La 102 ASP cc_start: 0.8686 (t70) cc_final: 0.8387 (t0) REVERT: Lc 34 THR cc_start: 0.9377 (m) cc_final: 0.8937 (p) REVERT: Ld 56 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8157 (tp30) REVERT: Ld 84 ILE cc_start: 0.9176 (tt) cc_final: 0.8969 (tt) REVERT: Lm 120 ASN cc_start: 0.8401 (t0) cc_final: 0.8045 (t0) REVERT: Lz 43 PRO cc_start: 0.8968 (Cg_exo) cc_final: 0.8632 (Cg_endo) REVERT: Lz 110 PHE cc_start: 0.7865 (m-80) cc_final: 0.7544 (m-10) outliers start: 182 outliers final: 84 residues processed: 1038 average time/residue: 1.3269 time to fit residues: 2515.6708 Evaluate side-chains 934 residues out of total 7475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 843 time to evaluate : 8.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 300 ASN Chi-restraints excluded: chain 1 residue 341 LEU Chi-restraints excluded: chain 1 residue 401 MET Chi-restraints excluded: chain 1 residue 428 ILE Chi-restraints excluded: chain 1 residue 451 VAL Chi-restraints excluded: chain 1 residue 452 THR Chi-restraints excluded: chain 2 residue 26 THR Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain C residue 222 TYR Chi-restraints excluded: chain C residue 299 ASN Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain K residue 110 CYS Chi-restraints excluded: chain LA residue 84 THR Chi-restraints excluded: chain LA residue 208 GLU Chi-restraints excluded: chain LB residue 101 THR Chi-restraints excluded: chain LC residue 154 VAL Chi-restraints excluded: chain LD residue 185 SER Chi-restraints excluded: chain LD residue 230 SER Chi-restraints excluded: chain LD residue 293 ARG Chi-restraints excluded: chain LF residue 67 THR Chi-restraints excluded: chain LF residue 74 MET Chi-restraints excluded: chain LG residue 211 ASP Chi-restraints excluded: chain LH residue 6 SER Chi-restraints excluded: chain LH residue 92 MET Chi-restraints excluded: chain LH residue 115 ARG Chi-restraints excluded: chain LI residue 28 ASP Chi-restraints excluded: chain LI residue 195 CYS Chi-restraints excluded: chain LJ residue 47 THR Chi-restraints excluded: chain LJ residue 72 CYS Chi-restraints excluded: chain LJ residue 104 ASN Chi-restraints excluded: chain LL residue 148 THR Chi-restraints excluded: chain LM residue 104 MET Chi-restraints excluded: chain LM residue 105 THR Chi-restraints excluded: chain LN residue 43 THR Chi-restraints excluded: chain LN residue 125 SER Chi-restraints excluded: chain LO residue 132 THR Chi-restraints excluded: chain LO residue 203 VAL Chi-restraints excluded: chain LP residue 14 SER Chi-restraints excluded: chain LP residue 115 GLU Chi-restraints excluded: chain LQ residue 5 ILE Chi-restraints excluded: chain LQ residue 82 VAL Chi-restraints excluded: chain LQ residue 85 THR Chi-restraints excluded: chain LR residue 29 THR Chi-restraints excluded: chain LR residue 55 VAL Chi-restraints excluded: chain LU residue 23 LEU Chi-restraints excluded: chain LU residue 47 ILE Chi-restraints excluded: chain LU residue 76 VAL Chi-restraints excluded: chain LV residue 22 VAL Chi-restraints excluded: chain LW residue 9 SER Chi-restraints excluded: chain LW residue 38 SER Chi-restraints excluded: chain LX residue 151 ASN Chi-restraints excluded: chain LY residue 120 GLU Chi-restraints excluded: chain LZ residue 35 ASP Chi-restraints excluded: chain LZ residue 43 VAL Chi-restraints excluded: chain LZ residue 54 THR Chi-restraints excluded: chain LZ residue 94 THR Chi-restraints excluded: chain LZ residue 99 ASP Chi-restraints excluded: chain Lc residue 24 SER Chi-restraints excluded: chain Lc residue 50 ASN Chi-restraints excluded: chain Lc residue 75 SER Chi-restraints excluded: chain Lc residue 93 THR Chi-restraints excluded: chain Ld residue 46 LEU Chi-restraints excluded: chain Ld residue 106 VAL Chi-restraints excluded: chain Le residue 122 VAL Chi-restraints excluded: chain Lf residue 31 GLU Chi-restraints excluded: chain Lf residue 108 SER Chi-restraints excluded: chain Lg residue 102 ILE Chi-restraints excluded: chain Li residue 21 VAL Chi-restraints excluded: chain Li residue 34 THR Chi-restraints excluded: chain Li residue 59 GLU Chi-restraints excluded: chain Lk residue 30 ASP Chi-restraints excluded: chain Lk residue 46 VAL Chi-restraints excluded: chain Lk residue 59 SER Chi-restraints excluded: chain Lk residue 60 LEU Chi-restraints excluded: chain Ll residue 47 THR Chi-restraints excluded: chain Lm residue 110 CYS Chi-restraints excluded: chain Lo residue 92 GLU Chi-restraints excluded: chain Lo residue 96 ASP Chi-restraints excluded: chain Lp residue 26 VAL Chi-restraints excluded: chain Lp residue 30 GLU Chi-restraints excluded: chain Lp residue 73 THR Chi-restraints excluded: chain Lr residue 13 CYS Chi-restraints excluded: chain Lr residue 75 THR Chi-restraints excluded: chain Lz residue 120 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1216 random chunks: chunk 613 optimal weight: 10.0000 chunk 342 optimal weight: 10.0000 chunk 919 optimal weight: 9.9990 chunk 751 optimal weight: 0.9980 chunk 304 optimal weight: 40.0000 chunk 1106 optimal weight: 10.0000 chunk 1195 optimal weight: 40.0000 chunk 985 optimal weight: 20.0000 chunk 1097 optimal weight: 8.9990 chunk 377 optimal weight: 20.0000 chunk 887 optimal weight: 9.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 627 HIS A 668 HIS A 738 GLN A 742 GLN ** B 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 HIS ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 50 HIS K 68 HIS ** K 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LF 63 GLN LF 110 GLN ** LF 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LJ 104 ASN ** LL 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LO 150 GLN LP 116 HIS ** LP 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LU 27 HIS LV 84 GLN LW 50 ASN LZ 78 ASN ** Lb 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ld 93 ASN Lk 58 GLN Lo 51 GLN Lo 76 ASN ** Lz 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lz 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 160619 Z= 0.360 Angle : 0.545 22.653 234957 Z= 0.281 Chirality : 0.036 0.382 29135 Planarity : 0.004 0.045 15785 Dihedral : 22.287 179.554 68973 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.79 % Favored : 97.18 % Rotamer: Outliers : 2.30 % Allowed : 15.26 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.76 % 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: 1.61 (0.09), residues: 8540 helix: 2.12 (0.09), residues: 3613 sheet: 0.26 (0.16), residues: 1036 loop : 0.41 (0.10), residues: 3891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRPLU 99 HIS 0.007 0.001 HISLz 73 PHE 0.027 0.002 PHELz 189 TYR 0.024 0.002 TYRLS 46 ARG 0.025 0.001 ARGLR 151 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17080 Ramachandran restraints generated. 8540 Oldfield, 0 Emsley, 8540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17080 Ramachandran restraints generated. 8540 Oldfield, 0 Emsley, 8540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 997 residues out of total 7475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 825 time to evaluate : 8.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 68 ILE cc_start: -0.0943 (mt) cc_final: -0.1162 (tp) REVERT: 1 69 LEU cc_start: -0.0471 (OUTLIER) cc_final: -0.0691 (mp) REVERT: 2 33 PHE cc_start: -0.0048 (m-80) cc_final: -0.0318 (m-10) REVERT: B 185 ASP cc_start: 0.8943 (m-30) cc_final: 0.8347 (t0) REVERT: B 401 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.7155 (mpp) REVERT: LB 4 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.7738 (ttm170) REVERT: LC 352 ASP cc_start: 0.8745 (m-30) cc_final: 0.8510 (m-30) REVERT: LD 293 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.8187 (mpt-90) REVERT: LE 245 GLN cc_start: 0.8494 (tp40) cc_final: 0.8240 (tp40) REVERT: LF 171 ASP cc_start: 0.8606 (t0) cc_final: 0.8206 (t0) REVERT: LG 88 ASP cc_start: 0.8377 (p0) cc_final: 0.7838 (p0) REVERT: LG 253 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.9013 (mp) REVERT: LH 106 GLN cc_start: 0.8024 (mt0) cc_final: 0.7527 (mt0) REVERT: LH 110 SER cc_start: 0.9240 (t) cc_final: 0.8937 (t) REVERT: LH 113 GLU cc_start: 0.8429 (mt-10) cc_final: 0.7964 (mt-10) REVERT: LH 115 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8024 (ptp90) REVERT: LH 137 SER cc_start: 0.9393 (t) cc_final: 0.9103 (p) REVERT: LH 143 GLU cc_start: 0.8498 (tt0) cc_final: 0.8234 (tt0) REVERT: LI 63 GLU cc_start: 0.8974 (mp0) cc_final: 0.8726 (mp0) REVERT: LL 142 GLU cc_start: 0.8132 (mp0) cc_final: 0.7900 (pm20) REVERT: LL 145 LYS cc_start: 0.8606 (tptt) cc_final: 0.8346 (tptt) REVERT: LM 96 GLU cc_start: 0.8622 (tp30) cc_final: 0.7919 (tp30) REVERT: LM 99 GLU cc_start: 0.7937 (pp20) cc_final: 0.7592 (pp20) REVERT: LP 108 ASP cc_start: 0.8481 (t0) cc_final: 0.8004 (t0) REVERT: LQ 93 GLN cc_start: 0.8139 (mp10) cc_final: 0.7879 (mp10) REVERT: LS 112 ASP cc_start: 0.9011 (t0) cc_final: 0.8621 (t0) REVERT: LT 27 LEU cc_start: 0.9104 (mp) cc_final: 0.8666 (mp) REVERT: LT 111 GLU cc_start: 0.8463 (tm-30) cc_final: 0.8173 (tm-30) REVERT: LU 23 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8785 (tt) REVERT: LU 41 GLN cc_start: 0.9049 (mm-40) cc_final: 0.8793 (tp-100) REVERT: LU 46 ARG cc_start: 0.8765 (tpp-160) cc_final: 0.8521 (mmt-90) REVERT: LU 64 GLU cc_start: 0.8357 (mp0) cc_final: 0.8116 (mp0) REVERT: LU 91 LEU cc_start: 0.9511 (mm) cc_final: 0.9305 (mp) REVERT: LU 95 ASN cc_start: 0.8955 (t0) cc_final: 0.8636 (t0) REVERT: LU 98 ASP cc_start: 0.7987 (p0) cc_final: 0.7663 (p0) REVERT: LU 114 TYR cc_start: 0.7565 (m-80) cc_final: 0.7290 (m-80) REVERT: LW 1 MET cc_start: 0.7093 (ttp) cc_final: 0.6717 (mtp) REVERT: LX 87 MET cc_start: 0.8933 (mmt) cc_final: 0.8711 (mmp) REVERT: LX 145 ASP cc_start: 0.8414 (t0) cc_final: 0.7140 (t0) REVERT: LX 148 ASP cc_start: 0.8907 (m-30) cc_final: 0.8152 (m-30) REVERT: LY 107 THR cc_start: 0.9614 (m) cc_final: 0.9295 (p) REVERT: La 89 ASN cc_start: 0.9134 (m-40) cc_final: 0.8617 (m110) REVERT: Lc 63 TYR cc_start: 0.9299 (m-80) cc_final: 0.9044 (m-10) REVERT: Ld 56 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8263 (tp30) REVERT: Le 98 GLU cc_start: 0.8217 (tt0) cc_final: 0.7989 (tt0) REVERT: Lk 10 ASP cc_start: 0.8172 (m-30) cc_final: 0.7899 (m-30) REVERT: Lz 43 PRO cc_start: 0.9098 (Cg_exo) cc_final: 0.8859 (Cg_endo) outliers start: 172 outliers final: 101 residues processed: 932 average time/residue: 1.2595 time to fit residues: 2123.5729 Evaluate side-chains 896 residues out of total 7475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 788 time to evaluate : 8.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 54 MET Chi-restraints excluded: chain 1 residue 69 LEU Chi-restraints excluded: chain 1 residue 401 MET Chi-restraints excluded: chain 1 residue 451 VAL Chi-restraints excluded: chain 1 residue 452 THR Chi-restraints excluded: chain 2 residue 26 THR Chi-restraints excluded: chain 2 residue 56 LEU Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain LA residue 243 THR Chi-restraints excluded: chain LB residue 4 ARG Chi-restraints excluded: chain LB residue 101 THR Chi-restraints excluded: chain LB residue 194 LEU Chi-restraints excluded: chain LC residue 154 VAL Chi-restraints excluded: chain LD residue 37 VAL Chi-restraints excluded: chain LD residue 271 MET Chi-restraints excluded: chain LD residue 293 ARG Chi-restraints excluded: chain LF residue 67 THR Chi-restraints excluded: chain LF residue 74 MET Chi-restraints excluded: chain LG residue 211 ASP Chi-restraints excluded: chain LG residue 253 LEU Chi-restraints excluded: chain LG residue 254 GLU Chi-restraints excluded: chain LH residue 6 SER Chi-restraints excluded: chain LH residue 92 MET Chi-restraints excluded: chain LH residue 115 ARG Chi-restraints excluded: chain LH residue 177 ASP Chi-restraints excluded: chain LI residue 45 GLU Chi-restraints excluded: chain LI residue 142 LEU Chi-restraints excluded: chain LI residue 195 CYS Chi-restraints excluded: chain LJ residue 47 THR Chi-restraints excluded: chain LL residue 63 THR Chi-restraints excluded: chain LL residue 148 THR Chi-restraints excluded: chain LM residue 69 HIS Chi-restraints excluded: chain LM residue 105 THR Chi-restraints excluded: chain LN residue 75 VAL Chi-restraints excluded: chain LN residue 87 HIS Chi-restraints excluded: chain LN residue 125 SER Chi-restraints excluded: chain LO residue 6 VAL Chi-restraints excluded: chain LO residue 49 ARG Chi-restraints excluded: chain LO residue 132 THR Chi-restraints excluded: chain LP residue 58 VAL Chi-restraints excluded: chain LQ residue 5 ILE Chi-restraints excluded: chain LQ residue 40 ASN Chi-restraints excluded: chain LQ residue 82 VAL Chi-restraints excluded: chain LR residue 29 THR Chi-restraints excluded: chain LR residue 55 VAL Chi-restraints excluded: chain LS residue 168 THR Chi-restraints excluded: chain LU residue 23 LEU Chi-restraints excluded: chain LU residue 38 ASN Chi-restraints excluded: chain LU residue 47 ILE Chi-restraints excluded: chain LU residue 76 VAL Chi-restraints excluded: chain LV residue 22 VAL Chi-restraints excluded: chain LV residue 128 LEU Chi-restraints excluded: chain LW residue 9 SER Chi-restraints excluded: chain LW residue 38 SER Chi-restraints excluded: chain LX residue 151 ASN Chi-restraints excluded: chain LY residue 10 ASP Chi-restraints excluded: chain LY residue 49 ILE Chi-restraints excluded: chain LY residue 120 GLU Chi-restraints excluded: chain LZ residue 35 ASP Chi-restraints excluded: chain LZ residue 54 THR Chi-restraints excluded: chain LZ residue 94 THR Chi-restraints excluded: chain LZ residue 99 ASP Chi-restraints excluded: chain La residue 86 THR Chi-restraints excluded: chain Lb residue 65 MET Chi-restraints excluded: chain Lc residue 28 VAL Chi-restraints excluded: chain Lc residue 44 LYS Chi-restraints excluded: chain Lc residue 50 ASN Chi-restraints excluded: chain Lc residue 75 SER Chi-restraints excluded: chain Lc residue 93 THR Chi-restraints excluded: chain Ld residue 93 ASN Chi-restraints excluded: chain Ld residue 98 SER Chi-restraints excluded: chain Ld residue 119 THR Chi-restraints excluded: chain Ld residue 122 VAL Chi-restraints excluded: chain Le residue 122 VAL Chi-restraints excluded: chain Lf residue 31 GLU Chi-restraints excluded: chain Lf residue 91 ASN Chi-restraints excluded: chain Lf residue 108 SER Chi-restraints excluded: chain Li residue 11 LEU Chi-restraints excluded: chain Li residue 21 VAL Chi-restraints excluded: chain Li residue 34 THR Chi-restraints excluded: chain Li residue 59 GLU Chi-restraints excluded: chain Lk residue 13 LEU Chi-restraints excluded: chain Lk residue 30 ASP Chi-restraints excluded: chain Lk residue 46 VAL Chi-restraints excluded: chain Lk residue 60 LEU Chi-restraints excluded: chain Ll residue 47 THR Chi-restraints excluded: chain Lm residue 81 SER Chi-restraints excluded: chain Lm residue 110 CYS Chi-restraints excluded: chain Lo residue 96 ASP Chi-restraints excluded: chain Lo residue 104 ILE Chi-restraints excluded: chain Lp residue 8 VAL Chi-restraints excluded: chain Lp residue 26 VAL Chi-restraints excluded: chain Lr residue 13 CYS Chi-restraints excluded: chain Lr residue 32 LEU Chi-restraints excluded: chain Lr residue 80 THR Chi-restraints excluded: chain Lz residue 9 THR Chi-restraints excluded: chain Lz residue 120 ILE Chi-restraints excluded: chain Lz residue 155 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1216 random chunks: chunk 1092 optimal weight: 9.9990 chunk 831 optimal weight: 3.9990 chunk 574 optimal weight: 10.0000 chunk 122 optimal weight: 30.0000 chunk 527 optimal weight: 30.0000 chunk 742 optimal weight: 10.0000 chunk 1110 optimal weight: 9.9990 chunk 1175 optimal weight: 3.9990 chunk 580 optimal weight: 8.9990 chunk 1052 optimal weight: 9.9990 chunk 316 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 GLN ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 GLN K 68 HIS LD 195 HIS ** LF 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LG 195 HIS LH 138 GLN ** LL 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LO 143 HIS ** LP 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LS 50 GLN LS 91 HIS LS 125 GLN ** Lb 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ld 93 ASN Lk 58 GLN Lo 76 ASN Lr 41 ASN ** Lz 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 160619 Z= 0.325 Angle : 0.524 11.138 234957 Z= 0.271 Chirality : 0.035 0.227 29135 Planarity : 0.004 0.054 15785 Dihedral : 22.312 179.348 68973 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.92 % Favored : 97.07 % Rotamer: Outliers : 2.54 % Allowed : 15.86 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.76 % 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: 1.51 (0.09), residues: 8540 helix: 2.08 (0.09), residues: 3604 sheet: 0.22 (0.16), residues: 1010 loop : 0.30 (0.10), residues: 3926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRPLU 99 HIS 0.013 0.001 HIS K 50 PHE 0.032 0.001 PHELz 189 TYR 0.017 0.001 TYR K 35 ARG 0.007 0.000 ARGLp 85 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17080 Ramachandran restraints generated. 8540 Oldfield, 0 Emsley, 8540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17080 Ramachandran restraints generated. 8540 Oldfield, 0 Emsley, 8540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1000 residues out of total 7475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 810 time to evaluate : 8.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 449 LEU cc_start: 0.1465 (pp) cc_final: 0.1244 (pp) REVERT: B 185 ASP cc_start: 0.9002 (m-30) cc_final: 0.8394 (t0) REVERT: B 248 SER cc_start: 0.5741 (OUTLIER) cc_final: 0.5529 (t) REVERT: B 401 MET cc_start: 0.7480 (OUTLIER) cc_final: 0.7235 (mpp) REVERT: C 299 ASN cc_start: 0.6273 (OUTLIER) cc_final: 0.5635 (m-40) REVERT: LA 80 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.7748 (tp30) REVERT: LC 352 ASP cc_start: 0.8739 (m-30) cc_final: 0.8501 (m-30) REVERT: LD 293 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.8126 (mpt-90) REVERT: LE 245 GLN cc_start: 0.8547 (tp40) cc_final: 0.8345 (tp40) REVERT: LF 171 ASP cc_start: 0.8633 (t0) cc_final: 0.8279 (t0) REVERT: LG 88 ASP cc_start: 0.8358 (p0) cc_final: 0.7792 (p0) REVERT: LG 253 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8998 (mp) REVERT: LH 106 GLN cc_start: 0.8159 (mt0) cc_final: 0.7641 (mt0) REVERT: LH 110 SER cc_start: 0.9266 (t) cc_final: 0.8957 (t) REVERT: LH 113 GLU cc_start: 0.8519 (mt-10) cc_final: 0.7909 (mt-10) REVERT: LH 115 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8045 (ptp90) REVERT: LH 137 SER cc_start: 0.9411 (t) cc_final: 0.9158 (p) REVERT: LH 143 GLU cc_start: 0.8569 (tt0) cc_final: 0.8316 (tt0) REVERT: LI 63 GLU cc_start: 0.9026 (mp0) cc_final: 0.8778 (mp0) REVERT: LI 193 ASP cc_start: 0.8652 (p0) cc_final: 0.8452 (p0) REVERT: LL 79 GLU cc_start: 0.8843 (tm-30) cc_final: 0.8485 (tm-30) REVERT: LL 111 GLN cc_start: 0.8652 (mt0) cc_final: 0.8399 (mt0) REVERT: LL 142 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7964 (pm20) REVERT: LL 145 LYS cc_start: 0.8625 (tptt) cc_final: 0.8423 (tptt) REVERT: LM 96 GLU cc_start: 0.8654 (tp30) cc_final: 0.7902 (tp30) REVERT: LM 99 GLU cc_start: 0.7995 (pp20) cc_final: 0.7638 (pp20) REVERT: LO 180 GLN cc_start: 0.9103 (OUTLIER) cc_final: 0.8480 (tp-100) REVERT: LP 108 ASP cc_start: 0.8531 (t0) cc_final: 0.8064 (t0) REVERT: LQ 93 GLN cc_start: 0.8172 (mp10) cc_final: 0.7921 (mp10) REVERT: LR 119 MET cc_start: 0.8876 (ttm) cc_final: 0.8578 (ttp) REVERT: LS 112 ASP cc_start: 0.8903 (t0) cc_final: 0.8562 (t0) REVERT: LU 23 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8768 (tt) REVERT: LU 41 GLN cc_start: 0.9025 (mm-40) cc_final: 0.8685 (tp-100) REVERT: LU 46 ARG cc_start: 0.8795 (tpp-160) cc_final: 0.8481 (mmt-90) REVERT: LU 95 ASN cc_start: 0.8966 (t0) cc_final: 0.8621 (t0) REVERT: LV 135 ASN cc_start: 0.8231 (m-40) cc_final: 0.8014 (t0) REVERT: LW 1 MET cc_start: 0.7134 (ttp) cc_final: 0.6736 (mtp) REVERT: LX 84 GLU cc_start: 0.7894 (pm20) cc_final: 0.7638 (pm20) REVERT: LX 101 ASP cc_start: 0.8811 (t70) cc_final: 0.8589 (t70) REVERT: LX 145 ASP cc_start: 0.8373 (t0) cc_final: 0.7044 (t0) REVERT: LX 148 ASP cc_start: 0.8873 (m-30) cc_final: 0.8103 (m-30) REVERT: LY 107 THR cc_start: 0.9608 (m) cc_final: 0.9350 (p) REVERT: Ld 19 GLU cc_start: 0.8086 (mp0) cc_final: 0.7755 (mt-10) REVERT: Ld 56 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8266 (tp30) REVERT: Lg 98 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8203 (mm-30) REVERT: Lp 30 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8400 (mt-10) REVERT: Lz 43 PRO cc_start: 0.9216 (Cg_exo) cc_final: 0.9013 (Cg_endo) REVERT: Lz 72 GLN cc_start: 0.8550 (pp30) cc_final: 0.8266 (pp30) outliers start: 190 outliers final: 119 residues processed: 933 average time/residue: 1.3039 time to fit residues: 2221.0630 Evaluate side-chains 912 residues out of total 7475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 782 time to evaluate : 8.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 8 VAL Chi-restraints excluded: chain 1 residue 401 MET Chi-restraints excluded: chain 1 residue 451 VAL Chi-restraints excluded: chain 1 residue 452 THR Chi-restraints excluded: chain 2 residue 18 SER Chi-restraints excluded: chain 2 residue 26 THR Chi-restraints excluded: chain 2 residue 56 LEU Chi-restraints excluded: chain 3 residue 83 SER Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain B residue 104 TYR Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 207 MET Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 299 ASN Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain K residue 110 CYS Chi-restraints excluded: chain LA residue 80 GLU Chi-restraints excluded: chain LA residue 84 THR Chi-restraints excluded: chain LA residue 243 THR Chi-restraints excluded: chain LB residue 101 THR Chi-restraints excluded: chain LB residue 181 MET Chi-restraints excluded: chain LB residue 194 LEU Chi-restraints excluded: chain LC residue 154 VAL Chi-restraints excluded: chain LC residue 198 ASN Chi-restraints excluded: chain LD residue 37 VAL Chi-restraints excluded: chain LD residue 271 MET Chi-restraints excluded: chain LD residue 293 ARG Chi-restraints excluded: chain LF residue 67 THR Chi-restraints excluded: chain LF residue 74 MET Chi-restraints excluded: chain LG residue 253 LEU Chi-restraints excluded: chain LG residue 254 GLU Chi-restraints excluded: chain LH residue 6 SER Chi-restraints excluded: chain LH residue 46 SER Chi-restraints excluded: chain LH residue 92 MET Chi-restraints excluded: chain LH residue 115 ARG Chi-restraints excluded: chain LH residue 177 ASP Chi-restraints excluded: chain LI residue 45 GLU Chi-restraints excluded: chain LI residue 102 MET 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 72 CYS Chi-restraints excluded: chain LJ residue 140 SER Chi-restraints excluded: chain LL residue 63 THR Chi-restraints excluded: chain LL residue 142 GLU Chi-restraints excluded: chain LL residue 146 LEU Chi-restraints excluded: chain LL residue 148 THR Chi-restraints excluded: chain LL residue 160 VAL Chi-restraints excluded: chain LM residue 69 HIS Chi-restraints excluded: chain LM residue 104 MET Chi-restraints excluded: chain LM residue 105 THR Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 75 VAL Chi-restraints excluded: chain LN residue 125 SER Chi-restraints excluded: chain LN residue 126 THR Chi-restraints excluded: chain LN residue 197 THR Chi-restraints excluded: chain LO residue 6 VAL Chi-restraints excluded: chain LO residue 180 GLN Chi-restraints excluded: chain LP residue 58 VAL Chi-restraints excluded: chain LQ residue 5 ILE Chi-restraints excluded: chain LQ residue 82 VAL Chi-restraints excluded: chain LQ residue 85 THR Chi-restraints excluded: chain LR residue 55 VAL Chi-restraints excluded: chain LS residue 132 ILE Chi-restraints excluded: chain LS residue 168 THR Chi-restraints excluded: chain LT residue 154 ILE Chi-restraints excluded: chain LU residue 23 LEU Chi-restraints excluded: chain LU residue 38 ASN Chi-restraints excluded: chain LU residue 47 ILE Chi-restraints excluded: chain LU residue 62 THR Chi-restraints excluded: chain LU residue 76 VAL Chi-restraints excluded: chain LU residue 96 LEU Chi-restraints excluded: chain LV residue 22 VAL Chi-restraints excluded: chain LV residue 59 ASP Chi-restraints excluded: chain LV residue 128 LEU Chi-restraints excluded: chain LW residue 9 SER Chi-restraints excluded: chain LX residue 85 SER Chi-restraints excluded: chain LX residue 151 ASN Chi-restraints excluded: chain LY residue 10 ASP Chi-restraints excluded: chain LY residue 49 ILE Chi-restraints excluded: chain LY residue 120 GLU Chi-restraints excluded: chain LZ residue 34 SER Chi-restraints excluded: chain LZ residue 35 ASP Chi-restraints excluded: chain LZ residue 54 THR Chi-restraints excluded: chain LZ residue 94 THR Chi-restraints excluded: chain LZ residue 99 ASP Chi-restraints excluded: chain La residue 130 SER Chi-restraints excluded: chain Lb residue 65 MET Chi-restraints excluded: chain Lc residue 28 VAL Chi-restraints excluded: chain Lc residue 34 THR Chi-restraints excluded: chain Lc residue 44 LYS Chi-restraints excluded: chain Lc residue 50 ASN Chi-restraints excluded: chain Lc residue 78 ASN Chi-restraints excluded: chain Lc residue 93 THR Chi-restraints excluded: chain Ld residue 46 LEU Chi-restraints excluded: chain Ld residue 93 ASN Chi-restraints excluded: chain Le residue 122 VAL Chi-restraints excluded: chain Lf residue 31 GLU Chi-restraints excluded: chain Lf residue 91 ASN Chi-restraints excluded: chain Lf residue 108 SER Chi-restraints excluded: chain Li residue 11 LEU Chi-restraints excluded: chain Li residue 21 VAL Chi-restraints excluded: chain Li residue 34 THR Chi-restraints excluded: chain Li residue 59 GLU Chi-restraints excluded: chain Lk residue 13 LEU Chi-restraints excluded: chain Lk residue 30 ASP Chi-restraints excluded: chain Lk residue 46 VAL Chi-restraints excluded: chain Lk residue 59 SER Chi-restraints excluded: chain Lk residue 60 LEU Chi-restraints excluded: chain Ll residue 47 THR Chi-restraints excluded: chain Lm residue 81 SER Chi-restraints excluded: chain Lm residue 110 CYS Chi-restraints excluded: chain Lo residue 96 ASP Chi-restraints excluded: chain Lp residue 8 VAL Chi-restraints excluded: chain Lp residue 16 THR Chi-restraints excluded: chain Lp residue 26 VAL Chi-restraints excluded: chain Lp residue 30 GLU Chi-restraints excluded: chain Lp residue 32 SER Chi-restraints excluded: chain Lr residue 27 THR Chi-restraints excluded: chain Lz residue 9 THR Chi-restraints excluded: chain Lz residue 17 VAL Chi-restraints excluded: chain Lz residue 120 ILE Chi-restraints excluded: chain Lz residue 155 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1216 random chunks: chunk 978 optimal weight: 10.0000 chunk 667 optimal weight: 8.9990 chunk 17 optimal weight: 50.0000 chunk 875 optimal weight: 10.0000 chunk 484 optimal weight: 9.9990 chunk 1003 optimal weight: 10.0000 chunk 812 optimal weight: 30.0000 chunk 1 optimal weight: 20.0000 chunk 600 optimal weight: 8.9990 chunk 1055 optimal weight: 8.9990 chunk 296 optimal weight: 10.0000 overall best weight: 9.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LB 203 GLN ** LB 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LF 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LL 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 75 GLN ** LP 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LQ 151 HIS LY 65 GLN Lb 50 ASN ** Lb 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ld 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lk 58 GLN Lo 76 ASN Lr 41 ASN ** Lz 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.125 160619 Z= 0.412 Angle : 0.579 19.728 234957 Z= 0.298 Chirality : 0.038 0.240 29135 Planarity : 0.004 0.075 15785 Dihedral : 22.354 179.701 68973 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.43 % Favored : 96.56 % Rotamer: Outliers : 3.16 % Allowed : 15.90 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.76 % 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: 1.26 (0.09), residues: 8540 helix: 1.90 (0.09), residues: 3607 sheet: 0.12 (0.16), residues: 991 loop : 0.11 (0.10), residues: 3942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRPLU 99 HIS 0.006 0.001 HISLa 40 PHE 0.036 0.002 PHELz 189 TYR 0.020 0.002 TYRLQ 32 ARG 0.011 0.001 ARGLR 151 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17080 Ramachandran restraints generated. 8540 Oldfield, 0 Emsley, 8540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17080 Ramachandran restraints generated. 8540 Oldfield, 0 Emsley, 8540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1013 residues out of total 7475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 777 time to evaluate : 8.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 388 MET cc_start: 0.7332 (tmm) cc_final: 0.7047 (ppp) REVERT: A 732 GLN cc_start: 0.8271 (tm-30) cc_final: 0.7906 (mm-40) REVERT: B 185 ASP cc_start: 0.8987 (m-30) cc_final: 0.8373 (t0) REVERT: B 248 SER cc_start: 0.5791 (OUTLIER) cc_final: 0.5576 (t) REVERT: C 299 ASN cc_start: 0.6342 (OUTLIER) cc_final: 0.5601 (m-40) REVERT: LA 80 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.7862 (tp30) REVERT: LA 176 ASP cc_start: 0.8695 (m-30) cc_final: 0.8481 (m-30) REVERT: LC 352 ASP cc_start: 0.8722 (m-30) cc_final: 0.8484 (m-30) REVERT: LD 293 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8129 (mpt-90) REVERT: LG 88 ASP cc_start: 0.8337 (p0) cc_final: 0.7762 (p0) REVERT: LG 253 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8972 (mp) REVERT: LH 110 SER cc_start: 0.9244 (t) cc_final: 0.8931 (t) REVERT: LH 115 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8078 (ptp90) REVERT: LH 137 SER cc_start: 0.9436 (t) cc_final: 0.9187 (p) REVERT: LH 143 GLU cc_start: 0.8643 (tt0) cc_final: 0.8419 (tt0) REVERT: LI 63 GLU cc_start: 0.9043 (mp0) cc_final: 0.8765 (mp0) REVERT: LL 79 GLU cc_start: 0.8848 (tm-30) cc_final: 0.8507 (tm-30) REVERT: LL 142 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7987 (pm20) REVERT: LM 96 GLU cc_start: 0.8723 (tp30) cc_final: 0.7986 (tp30) REVERT: LM 99 GLU cc_start: 0.8089 (pp20) cc_final: 0.7736 (pp20) REVERT: LM 117 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.8946 (ttpt) REVERT: LO 180 GLN cc_start: 0.9128 (OUTLIER) cc_final: 0.8436 (tp-100) REVERT: LP 108 ASP cc_start: 0.8616 (t0) cc_final: 0.8175 (t0) REVERT: LQ 147 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8280 (tp30) REVERT: LS 112 ASP cc_start: 0.8991 (t0) cc_final: 0.8702 (t0) REVERT: LT 45 MET cc_start: 0.8881 (ttp) cc_final: 0.8680 (ttp) REVERT: LU 23 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8756 (tt) REVERT: LU 41 GLN cc_start: 0.9067 (mm-40) cc_final: 0.8818 (tp-100) REVERT: LU 46 ARG cc_start: 0.8822 (tpp-160) cc_final: 0.8562 (mmt-90) REVERT: LU 91 LEU cc_start: 0.9597 (mm) cc_final: 0.9307 (mp) REVERT: LU 95 ASN cc_start: 0.8938 (t0) cc_final: 0.8598 (t0) REVERT: LV 99 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7501 (tt0) REVERT: LV 124 GLU cc_start: 0.8720 (mp0) cc_final: 0.8408 (mp0) REVERT: LX 133 GLU cc_start: 0.8557 (mp0) cc_final: 0.8318 (mp0) REVERT: LX 145 ASP cc_start: 0.8359 (t0) cc_final: 0.7022 (t0) REVERT: LX 148 ASP cc_start: 0.8891 (m-30) cc_final: 0.8146 (m-30) REVERT: LY 52 ASP cc_start: 0.8413 (m-30) cc_final: 0.8193 (t0) REVERT: LY 107 THR cc_start: 0.9634 (m) cc_final: 0.9425 (p) REVERT: Lc 27 TYR cc_start: 0.8946 (p90) cc_final: 0.8642 (p90) REVERT: Lc 106 ARG cc_start: 0.6616 (OUTLIER) cc_final: 0.6056 (tpp-160) REVERT: Ld 19 GLU cc_start: 0.8132 (mp0) cc_final: 0.7814 (mp0) REVERT: Ld 56 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8248 (tp30) REVERT: Ld 118 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8472 (mm-40) REVERT: Lk 7 GLU cc_start: 0.7230 (pm20) cc_final: 0.6916 (pm20) REVERT: Lp 30 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8405 (mt-10) REVERT: Lz 72 GLN cc_start: 0.8603 (pp30) cc_final: 0.8300 (pp30) REVERT: Lz 217 TYR cc_start: 0.8137 (t80) cc_final: 0.7851 (t80) outliers start: 236 outliers final: 159 residues processed: 939 average time/residue: 1.2244 time to fit residues: 2090.1893 Evaluate side-chains 933 residues out of total 7475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 759 time to evaluate : 8.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 8 VAL Chi-restraints excluded: chain 1 residue 54 MET Chi-restraints excluded: chain 1 residue 132 VAL Chi-restraints excluded: chain 1 residue 255 VAL Chi-restraints excluded: chain 1 residue 300 ASN Chi-restraints excluded: chain 1 residue 401 MET Chi-restraints excluded: chain 1 residue 426 LEU Chi-restraints excluded: chain 1 residue 451 VAL Chi-restraints excluded: chain 1 residue 452 THR Chi-restraints excluded: chain 2 residue 18 SER Chi-restraints excluded: chain 2 residue 26 THR Chi-restraints excluded: chain 2 residue 33 PHE Chi-restraints excluded: chain 2 residue 56 LEU Chi-restraints excluded: chain 3 residue 83 SER Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain B residue 104 TYR Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 207 MET Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 299 ASN Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 110 CYS Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain LA residue 80 GLU Chi-restraints excluded: chain LA residue 243 THR Chi-restraints excluded: chain LB residue 101 THR Chi-restraints excluded: chain LB residue 181 MET Chi-restraints excluded: chain LB residue 194 LEU Chi-restraints excluded: chain LC residue 27 VAL Chi-restraints excluded: chain LC residue 154 VAL Chi-restraints excluded: chain LC residue 198 ASN Chi-restraints excluded: chain LD residue 37 VAL Chi-restraints excluded: chain LD residue 271 MET Chi-restraints excluded: chain LD residue 293 ARG Chi-restraints excluded: chain LE residue 241 GLU Chi-restraints excluded: chain LF residue 67 THR Chi-restraints excluded: chain LF residue 74 MET Chi-restraints excluded: chain LG residue 198 THR Chi-restraints excluded: chain LG residue 253 LEU Chi-restraints excluded: chain LG residue 254 GLU Chi-restraints excluded: chain LH residue 6 SER Chi-restraints excluded: chain LH residue 18 ILE Chi-restraints excluded: chain LH residue 24 THR Chi-restraints excluded: chain LH residue 46 SER Chi-restraints excluded: chain LH residue 92 MET Chi-restraints excluded: chain LH residue 115 ARG Chi-restraints excluded: chain LH residue 177 ASP Chi-restraints excluded: chain LI residue 28 ASP Chi-restraints excluded: chain LI residue 45 GLU Chi-restraints excluded: chain LI residue 102 MET Chi-restraints excluded: chain LI residue 142 LEU Chi-restraints excluded: chain LI residue 195 CYS Chi-restraints excluded: chain LJ residue 29 SER Chi-restraints excluded: chain LJ residue 34 THR Chi-restraints excluded: chain LJ residue 47 THR Chi-restraints excluded: chain LJ residue 72 CYS Chi-restraints excluded: chain LJ residue 129 ASP Chi-restraints excluded: chain LJ residue 140 SER Chi-restraints excluded: chain LL residue 63 THR Chi-restraints excluded: chain LL residue 108 GLU Chi-restraints excluded: chain LL residue 142 GLU Chi-restraints excluded: chain LL residue 146 LEU Chi-restraints excluded: chain LL residue 148 THR Chi-restraints excluded: chain LM residue 69 HIS Chi-restraints excluded: chain LM residue 105 THR Chi-restraints excluded: chain LM residue 117 LYS Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 75 VAL Chi-restraints excluded: chain LN residue 87 HIS Chi-restraints excluded: chain LN residue 125 SER Chi-restraints excluded: chain LN residue 126 THR Chi-restraints excluded: chain LN residue 197 THR Chi-restraints excluded: chain LO residue 6 VAL Chi-restraints excluded: chain LO residue 49 ARG Chi-restraints excluded: chain LO residue 132 THR Chi-restraints excluded: chain LO residue 180 GLN Chi-restraints excluded: chain LP residue 58 VAL Chi-restraints excluded: chain LQ residue 5 ILE Chi-restraints excluded: chain LQ residue 82 VAL Chi-restraints excluded: chain LQ residue 85 THR Chi-restraints excluded: chain LQ residue 147 GLU Chi-restraints excluded: chain LR residue 55 VAL Chi-restraints excluded: chain LS residue 132 ILE Chi-restraints excluded: chain LS residue 168 THR Chi-restraints excluded: chain LT residue 109 VAL Chi-restraints excluded: chain LT residue 154 ILE Chi-restraints excluded: chain LU residue 23 LEU Chi-restraints excluded: chain LU residue 33 ILE Chi-restraints excluded: chain LU residue 38 ASN Chi-restraints excluded: chain LU residue 47 ILE Chi-restraints excluded: chain LU residue 76 VAL Chi-restraints excluded: chain LV residue 22 VAL Chi-restraints excluded: chain LV residue 99 GLU Chi-restraints excluded: chain LV residue 128 LEU Chi-restraints excluded: chain LV residue 134 SER Chi-restraints excluded: chain LW residue 9 SER Chi-restraints excluded: chain LW residue 28 VAL Chi-restraints excluded: chain LW residue 38 SER Chi-restraints excluded: chain LX residue 83 THR Chi-restraints excluded: chain LX residue 85 SER Chi-restraints excluded: chain LX residue 119 ILE Chi-restraints excluded: chain LX residue 151 ASN Chi-restraints excluded: chain LY residue 10 ASP Chi-restraints excluded: chain LY residue 49 ILE Chi-restraints excluded: chain LY residue 120 GLU Chi-restraints excluded: chain LZ residue 34 SER Chi-restraints excluded: chain LZ residue 35 ASP Chi-restraints excluded: chain LZ residue 54 THR Chi-restraints excluded: chain LZ residue 94 THR Chi-restraints excluded: chain LZ residue 99 ASP Chi-restraints excluded: chain La residue 86 THR Chi-restraints excluded: chain La residue 130 SER Chi-restraints excluded: chain La residue 140 VAL Chi-restraints excluded: chain Lb residue 50 ASN Chi-restraints excluded: chain Lb residue 54 LEU Chi-restraints excluded: chain Lb residue 65 MET Chi-restraints excluded: chain Lc residue 24 SER Chi-restraints excluded: chain Lc residue 28 VAL Chi-restraints excluded: chain Lc residue 34 THR Chi-restraints excluded: chain Lc residue 44 LYS Chi-restraints excluded: chain Lc residue 50 ASN Chi-restraints excluded: chain Lc residue 78 ASN Chi-restraints excluded: chain Lc residue 93 THR Chi-restraints excluded: chain Lc residue 106 ARG Chi-restraints excluded: chain Ld residue 46 LEU Chi-restraints excluded: chain Ld residue 98 SER Chi-restraints excluded: chain Ld residue 111 VAL Chi-restraints excluded: chain Ld residue 118 GLN Chi-restraints excluded: chain Ld residue 119 THR Chi-restraints excluded: chain Ld residue 122 VAL Chi-restraints excluded: chain Ld residue 123 ASP Chi-restraints excluded: chain Le residue 87 VAL Chi-restraints excluded: chain Lf residue 91 ASN Chi-restraints excluded: chain Lf residue 108 SER Chi-restraints excluded: chain Li residue 11 LEU Chi-restraints excluded: chain Li residue 21 VAL Chi-restraints excluded: chain Li residue 34 THR Chi-restraints excluded: chain Li residue 59 GLU Chi-restraints excluded: chain Lk residue 13 LEU Chi-restraints excluded: chain Lk residue 30 ASP Chi-restraints excluded: chain Lk residue 46 VAL Chi-restraints excluded: chain Lk residue 59 SER Chi-restraints excluded: chain Lk residue 60 LEU Chi-restraints excluded: chain Ll residue 47 THR Chi-restraints excluded: chain Lm residue 81 SER Chi-restraints excluded: chain Lm residue 110 CYS Chi-restraints excluded: chain Lo residue 33 LEU Chi-restraints excluded: chain Lo residue 96 ASP Chi-restraints excluded: chain Lo residue 104 ILE Chi-restraints excluded: chain Lp residue 8 VAL Chi-restraints excluded: chain Lp residue 16 THR Chi-restraints excluded: chain Lp residue 26 VAL Chi-restraints excluded: chain Lp residue 30 GLU Chi-restraints excluded: chain Lp residue 32 SER Chi-restraints excluded: chain Lr residue 27 THR Chi-restraints excluded: chain Lr residue 80 THR Chi-restraints excluded: chain Lz residue 9 THR Chi-restraints excluded: chain Lz residue 120 ILE Chi-restraints excluded: chain Lz residue 155 ILE Chi-restraints excluded: chain Lz residue 210 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1216 random chunks: chunk 395 optimal weight: 10.0000 chunk 1058 optimal weight: 2.9990 chunk 232 optimal weight: 20.0000 chunk 690 optimal weight: 10.0000 chunk 290 optimal weight: 10.0000 chunk 1176 optimal weight: 2.9990 chunk 976 optimal weight: 8.9990 chunk 544 optimal weight: 50.0000 chunk 97 optimal weight: 30.0000 chunk 389 optimal weight: 10.0000 chunk 617 optimal weight: 0.9990 overall best weight: 5.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LF 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LL 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LP 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LY 65 GLN Lb 50 ASN ** Lb 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ld 93 ASN Lh 98 HIS ** Lk 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lo 76 ASN Lr 41 ASN ** Lz 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 160619 Z= 0.240 Angle : 0.499 12.123 234957 Z= 0.259 Chirality : 0.034 0.225 29135 Planarity : 0.004 0.051 15785 Dihedral : 22.402 178.723 68973 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.80 % Favored : 97.19 % Rotamer: Outliers : 2.38 % Allowed : 17.16 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.76 % 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: 1.37 (0.09), residues: 8540 helix: 2.01 (0.09), residues: 3596 sheet: 0.19 (0.17), residues: 962 loop : 0.14 (0.10), residues: 3982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRPLU 99 HIS 0.012 0.001 HISLb 49 PHE 0.030 0.001 PHELU 39 TYR 0.017 0.001 TYRLM 14 ARG 0.011 0.000 ARGLp 85 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17080 Ramachandran restraints generated. 8540 Oldfield, 0 Emsley, 8540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17080 Ramachandran restraints generated. 8540 Oldfield, 0 Emsley, 8540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 988 residues out of total 7475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 810 time to evaluate : 7.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 732 GLN cc_start: 0.8144 (tm-30) cc_final: 0.7771 (mm-40) REVERT: B 185 ASP cc_start: 0.8985 (m-30) cc_final: 0.8367 (t0) REVERT: C 299 ASN cc_start: 0.6242 (t0) cc_final: 0.5600 (m-40) REVERT: LA 80 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.7863 (tp30) REVERT: LC 352 ASP cc_start: 0.8686 (m-30) cc_final: 0.8432 (m-30) REVERT: LD 293 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.8032 (mmt90) REVERT: LE 249 ASP cc_start: 0.8366 (m-30) cc_final: 0.8007 (m-30) REVERT: LG 88 ASP cc_start: 0.8269 (p0) cc_final: 0.7675 (p0) REVERT: LH 110 SER cc_start: 0.9252 (t) cc_final: 0.8929 (t) REVERT: LH 115 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8012 (ptp90) REVERT: LH 137 SER cc_start: 0.9441 (t) cc_final: 0.9193 (p) REVERT: LH 143 GLU cc_start: 0.8622 (tt0) cc_final: 0.8398 (tt0) REVERT: LI 63 GLU cc_start: 0.9084 (mp0) cc_final: 0.8835 (mp0) REVERT: LL 79 GLU cc_start: 0.8739 (tm-30) cc_final: 0.8424 (tm-30) REVERT: LL 111 GLN cc_start: 0.8559 (mt0) cc_final: 0.8208 (mt0) REVERT: LL 142 GLU cc_start: 0.8330 (mp0) cc_final: 0.8093 (pm20) REVERT: LM 96 GLU cc_start: 0.8670 (tp30) cc_final: 0.7894 (tp30) REVERT: LM 99 GLU cc_start: 0.8055 (pp20) cc_final: 0.7691 (pp20) REVERT: LM 117 LYS cc_start: 0.9220 (OUTLIER) cc_final: 0.9004 (ttpt) REVERT: LM 136 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8601 (tt) REVERT: LO 180 GLN cc_start: 0.9116 (OUTLIER) cc_final: 0.8725 (tp-100) REVERT: LP 108 ASP cc_start: 0.8566 (t0) cc_final: 0.8108 (t0) REVERT: LQ 147 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8224 (tp30) REVERT: LS 112 ASP cc_start: 0.8925 (t0) cc_final: 0.8595 (t0) REVERT: LU 23 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8718 (tt) REVERT: LU 46 ARG cc_start: 0.8783 (tpp-160) cc_final: 0.8515 (mmt-90) REVERT: LU 91 LEU cc_start: 0.9563 (mm) cc_final: 0.9247 (mp) REVERT: LU 95 ASN cc_start: 0.8914 (t0) cc_final: 0.8566 (t0) REVERT: LV 124 GLU cc_start: 0.8701 (mp0) cc_final: 0.8427 (mp0) REVERT: LW 1 MET cc_start: 0.7002 (ttp) cc_final: 0.6670 (mtp) REVERT: LX 145 ASP cc_start: 0.8354 (t0) cc_final: 0.6981 (t0) REVERT: LX 148 ASP cc_start: 0.8873 (m-30) cc_final: 0.8113 (m-30) REVERT: LY 52 ASP cc_start: 0.8385 (m-30) cc_final: 0.8164 (t0) REVERT: LY 107 THR cc_start: 0.9607 (m) cc_final: 0.9405 (p) REVERT: Ld 19 GLU cc_start: 0.8134 (mp0) cc_final: 0.7822 (mp0) REVERT: Ld 118 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8309 (mm-40) REVERT: Lk 52 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8777 (mtmm) REVERT: Lp 30 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8392 (mt-10) REVERT: Lz 41 TYR cc_start: 0.8022 (t80) cc_final: 0.6974 (t80) REVERT: Lz 72 GLN cc_start: 0.8553 (pp30) cc_final: 0.8228 (pp30) REVERT: Lz 159 MET cc_start: 0.7679 (ppp) cc_final: 0.7371 (ppp) outliers start: 178 outliers final: 112 residues processed: 922 average time/residue: 1.2508 time to fit residues: 2138.3137 Evaluate side-chains 906 residues out of total 7475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 783 time to evaluate : 8.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 8 VAL Chi-restraints excluded: chain 1 residue 401 MET Chi-restraints excluded: chain 1 residue 452 THR Chi-restraints excluded: chain 2 residue 26 THR Chi-restraints excluded: chain 2 residue 56 LEU Chi-restraints excluded: chain 3 residue 83 SER Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain C residue 207 MET Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 110 CYS Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain LA residue 33 ASP Chi-restraints excluded: chain LA residue 80 GLU Chi-restraints excluded: chain LA residue 243 THR Chi-restraints excluded: chain LB residue 181 MET Chi-restraints excluded: chain LB residue 194 LEU Chi-restraints excluded: chain LC residue 154 VAL Chi-restraints excluded: chain LD residue 37 VAL Chi-restraints excluded: chain LD residue 293 ARG Chi-restraints excluded: chain LE residue 241 GLU Chi-restraints excluded: chain LF residue 67 THR Chi-restraints excluded: chain LF residue 74 MET Chi-restraints excluded: chain LG residue 254 GLU Chi-restraints excluded: chain LH residue 6 SER Chi-restraints excluded: chain LH residue 46 SER Chi-restraints excluded: chain LH residue 92 MET Chi-restraints excluded: chain LH residue 115 ARG Chi-restraints excluded: chain LH residue 177 ASP Chi-restraints excluded: chain LI residue 28 ASP Chi-restraints excluded: chain LI residue 102 MET Chi-restraints excluded: chain LI residue 136 MET 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 72 CYS Chi-restraints excluded: chain LJ residue 140 SER Chi-restraints excluded: chain LL residue 146 LEU Chi-restraints excluded: chain LL residue 148 THR Chi-restraints excluded: chain LM residue 104 MET Chi-restraints excluded: chain LM residue 105 THR Chi-restraints excluded: chain LM residue 117 LYS Chi-restraints excluded: chain LM residue 136 LEU Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 75 VAL Chi-restraints excluded: chain LN residue 87 HIS Chi-restraints excluded: chain LN residue 126 THR Chi-restraints excluded: chain LO residue 6 VAL Chi-restraints excluded: chain LO residue 49 ARG Chi-restraints excluded: chain LO residue 180 GLN Chi-restraints excluded: chain LP residue 58 VAL Chi-restraints excluded: chain LP residue 94 MET Chi-restraints excluded: chain LQ residue 5 ILE Chi-restraints excluded: chain LQ residue 82 VAL Chi-restraints excluded: chain LQ residue 85 THR Chi-restraints excluded: chain LQ residue 100 VAL Chi-restraints excluded: chain LQ residue 147 GLU Chi-restraints excluded: chain LS residue 132 ILE Chi-restraints excluded: chain LS residue 168 THR Chi-restraints excluded: chain LT residue 109 VAL Chi-restraints excluded: chain LT residue 154 ILE Chi-restraints excluded: chain LU residue 23 LEU Chi-restraints excluded: chain LU residue 38 ASN Chi-restraints excluded: chain LU residue 47 ILE Chi-restraints excluded: chain LU residue 96 LEU Chi-restraints excluded: chain LV residue 22 VAL Chi-restraints excluded: chain LV residue 59 ASP Chi-restraints excluded: chain LV residue 128 LEU Chi-restraints excluded: chain LW residue 9 SER Chi-restraints excluded: chain LX residue 85 SER Chi-restraints excluded: chain LY residue 10 ASP Chi-restraints excluded: chain LY residue 49 ILE Chi-restraints excluded: chain LY residue 120 GLU Chi-restraints excluded: chain LZ residue 34 SER Chi-restraints excluded: chain LZ residue 35 ASP Chi-restraints excluded: chain LZ residue 54 THR Chi-restraints excluded: chain LZ residue 94 THR Chi-restraints excluded: chain LZ residue 99 ASP Chi-restraints excluded: chain La residue 86 THR Chi-restraints excluded: chain La residue 130 SER Chi-restraints excluded: chain Lb residue 65 MET Chi-restraints excluded: chain Lc residue 28 VAL Chi-restraints excluded: chain Lc residue 44 LYS Chi-restraints excluded: chain Lc residue 50 ASN Chi-restraints excluded: chain Lc residue 78 ASN Chi-restraints excluded: chain Lc residue 93 THR Chi-restraints excluded: chain Ld residue 24 GLU Chi-restraints excluded: chain Ld residue 46 LEU Chi-restraints excluded: chain Ld residue 59 THR Chi-restraints excluded: chain Ld residue 98 SER Chi-restraints excluded: chain Ld residue 118 GLN Chi-restraints excluded: chain Ld residue 122 VAL Chi-restraints excluded: chain Li residue 11 LEU Chi-restraints excluded: chain Li residue 21 VAL Chi-restraints excluded: chain Li residue 59 GLU Chi-restraints excluded: chain Lk residue 13 LEU Chi-restraints excluded: chain Lk residue 30 ASP Chi-restraints excluded: chain Lk residue 46 VAL Chi-restraints excluded: chain Lk residue 52 LYS Chi-restraints excluded: chain Lk residue 60 LEU Chi-restraints excluded: chain Ll residue 47 THR Chi-restraints excluded: chain Lm residue 81 SER Chi-restraints excluded: chain Lm residue 110 CYS Chi-restraints excluded: chain Lo residue 55 ILE Chi-restraints excluded: chain Lo residue 96 ASP Chi-restraints excluded: chain Lp residue 26 VAL Chi-restraints excluded: chain Lp residue 30 GLU Chi-restraints excluded: chain Lp residue 32 SER Chi-restraints excluded: chain Lr residue 27 THR Chi-restraints excluded: chain Lr residue 80 THR Chi-restraints excluded: chain Lz residue 17 VAL Chi-restraints excluded: chain Lz residue 120 ILE Chi-restraints excluded: chain Lz residue 155 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1216 random chunks: chunk 1134 optimal weight: 9.9990 chunk 132 optimal weight: 20.0000 chunk 670 optimal weight: 8.9990 chunk 859 optimal weight: 5.9990 chunk 665 optimal weight: 7.9990 chunk 990 optimal weight: 10.0000 chunk 656 optimal weight: 5.9990 chunk 1172 optimal weight: 6.9990 chunk 733 optimal weight: 10.0000 chunk 714 optimal weight: 8.9990 chunk 541 optimal weight: 40.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LB 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LL 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LN 29 GLN LP 75 GLN ** LP 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LQ 45 GLN LV 135 ASN LY 65 GLN ** LY 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lb 7 HIS Lb 50 ASN ** Lb 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lk 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lo 76 ASN ** Lz 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 160619 Z= 0.323 Angle : 0.531 10.073 234957 Z= 0.274 Chirality : 0.035 0.286 29135 Planarity : 0.004 0.051 15785 Dihedral : 22.366 179.107 68973 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.23 % Favored : 96.76 % Rotamer: Outliers : 2.52 % Allowed : 17.63 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.76 % 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: 1.30 (0.09), residues: 8540 helix: 1.96 (0.09), residues: 3606 sheet: 0.17 (0.16), residues: 981 loop : 0.09 (0.10), residues: 3953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRPLU 99 HIS 0.005 0.001 HISLa 40 PHE 0.037 0.001 PHELz 189 TYR 0.017 0.001 TYRLQ 32 ARG 0.011 0.000 ARGLp 85 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17080 Ramachandran restraints generated. 8540 Oldfield, 0 Emsley, 8540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17080 Ramachandran restraints generated. 8540 Oldfield, 0 Emsley, 8540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 976 residues out of total 7475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 788 time to evaluate : 8.424 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 692 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7115 (mp) REVERT: A 701 MET cc_start: 0.4392 (mmm) cc_final: 0.3997 (mmm) REVERT: A 732 GLN cc_start: 0.8176 (tm-30) cc_final: 0.7806 (mm-40) REVERT: B 185 ASP cc_start: 0.8991 (m-30) cc_final: 0.8387 (t0) REVERT: C 299 ASN cc_start: 0.6273 (OUTLIER) cc_final: 0.5597 (m-40) REVERT: LA 80 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.7885 (tp30) REVERT: LB 200 ARG cc_start: 0.9038 (OUTLIER) cc_final: 0.8612 (mtt90) REVERT: LC 352 ASP cc_start: 0.8683 (m-30) cc_final: 0.8435 (m-30) REVERT: LD 293 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7992 (mmt90) REVERT: LE 249 ASP cc_start: 0.8359 (m-30) cc_final: 0.8015 (m-30) REVERT: LG 88 ASP cc_start: 0.8256 (p0) cc_final: 0.7650 (p0) REVERT: LH 110 SER cc_start: 0.9238 (t) cc_final: 0.8916 (t) REVERT: LH 115 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8108 (ptp90) REVERT: LH 137 SER cc_start: 0.9457 (t) cc_final: 0.9204 (p) REVERT: LH 143 GLU cc_start: 0.8656 (tt0) cc_final: 0.8446 (tt0) REVERT: LI 63 GLU cc_start: 0.9083 (mp0) cc_final: 0.8828 (mp0) REVERT: LL 79 GLU cc_start: 0.8769 (tm-30) cc_final: 0.8427 (tm-30) REVERT: LL 111 GLN cc_start: 0.8551 (mt0) cc_final: 0.8182 (mt0) REVERT: LL 142 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8086 (pm20) REVERT: LM 96 GLU cc_start: 0.8696 (tp30) cc_final: 0.7928 (tp30) REVERT: LM 99 GLU cc_start: 0.8090 (pp20) cc_final: 0.7730 (pp20) REVERT: LM 117 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.8990 (ttpt) REVERT: LM 136 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8617 (tt) REVERT: LO 180 GLN cc_start: 0.9121 (OUTLIER) cc_final: 0.8728 (tp-100) REVERT: LP 108 ASP cc_start: 0.8587 (t0) cc_final: 0.8150 (t0) REVERT: LQ 147 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8185 (tp30) REVERT: LS 112 ASP cc_start: 0.8926 (t0) cc_final: 0.8623 (t0) REVERT: LU 23 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8690 (tt) REVERT: LU 46 ARG cc_start: 0.8785 (tpp-160) cc_final: 0.8518 (mmt-90) REVERT: LU 95 ASN cc_start: 0.8963 (t0) cc_final: 0.8659 (t0) REVERT: LV 124 GLU cc_start: 0.8706 (mp0) cc_final: 0.8414 (mp0) REVERT: LW 1 MET cc_start: 0.7107 (ttp) cc_final: 0.6814 (mtp) REVERT: LX 133 GLU cc_start: 0.8541 (mp0) cc_final: 0.8314 (mp0) REVERT: LX 145 ASP cc_start: 0.8377 (t0) cc_final: 0.7016 (t0) REVERT: LX 148 ASP cc_start: 0.8897 (m-30) cc_final: 0.8141 (m-30) REVERT: LY 52 ASP cc_start: 0.8407 (m-30) cc_final: 0.8179 (t0) REVERT: LY 107 THR cc_start: 0.9624 (m) cc_final: 0.9410 (p) REVERT: LZ 120 GLU cc_start: 0.8638 (tp30) cc_final: 0.8420 (tp30) REVERT: Lc 106 ARG cc_start: 0.6648 (OUTLIER) cc_final: 0.6098 (tpp-160) REVERT: Ld 19 GLU cc_start: 0.8171 (mp0) cc_final: 0.7874 (mp0) REVERT: Ld 118 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8301 (mm-40) REVERT: Lp 30 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8396 (mt-10) REVERT: Lz 72 GLN cc_start: 0.8587 (pp30) cc_final: 0.8268 (pp30) outliers start: 188 outliers final: 135 residues processed: 907 average time/residue: 1.3263 time to fit residues: 2191.9552 Evaluate side-chains 922 residues out of total 7475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 772 time to evaluate : 8.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 8 VAL Chi-restraints excluded: chain 1 residue 54 MET Chi-restraints excluded: chain 1 residue 132 VAL Chi-restraints excluded: chain 1 residue 401 MET Chi-restraints excluded: chain 1 residue 447 ILE Chi-restraints excluded: chain 1 residue 452 THR Chi-restraints excluded: chain 2 residue 26 THR Chi-restraints excluded: chain 2 residue 56 LEU Chi-restraints excluded: chain 3 residue 83 SER Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain B residue 104 TYR Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain C residue 299 ASN Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 110 CYS Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain LA residue 33 ASP Chi-restraints excluded: chain LA residue 80 GLU Chi-restraints excluded: chain LA residue 243 THR Chi-restraints excluded: chain LB residue 101 THR Chi-restraints excluded: chain LB residue 181 MET Chi-restraints excluded: chain LB residue 194 LEU Chi-restraints excluded: chain LB residue 200 ARG Chi-restraints excluded: chain LC residue 154 VAL Chi-restraints excluded: chain LD residue 37 VAL Chi-restraints excluded: chain LD residue 271 MET Chi-restraints excluded: chain LD residue 293 ARG Chi-restraints excluded: chain LE residue 241 GLU Chi-restraints excluded: chain LF residue 67 THR Chi-restraints excluded: chain LF residue 74 MET Chi-restraints excluded: chain LG residue 198 THR Chi-restraints excluded: chain LG residue 254 GLU Chi-restraints excluded: chain LH residue 6 SER Chi-restraints excluded: chain LH residue 46 SER Chi-restraints excluded: chain LH residue 92 MET Chi-restraints excluded: chain LH residue 115 ARG Chi-restraints excluded: chain LH residue 177 ASP Chi-restraints excluded: chain LI residue 28 ASP Chi-restraints excluded: chain LI residue 136 MET Chi-restraints excluded: chain LI residue 195 CYS Chi-restraints excluded: chain LJ residue 29 SER Chi-restraints excluded: chain LJ residue 34 THR Chi-restraints excluded: chain LJ residue 47 THR Chi-restraints excluded: chain LJ residue 72 CYS Chi-restraints excluded: chain LJ residue 140 SER Chi-restraints excluded: chain LL residue 108 GLU Chi-restraints excluded: chain LL residue 142 GLU Chi-restraints excluded: chain LL residue 146 LEU Chi-restraints excluded: chain LL residue 148 THR Chi-restraints excluded: chain LM residue 104 MET Chi-restraints excluded: chain LM residue 105 THR Chi-restraints excluded: chain LM residue 117 LYS Chi-restraints excluded: chain LM residue 136 LEU Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 75 VAL Chi-restraints excluded: chain LN residue 87 HIS Chi-restraints excluded: chain LN residue 125 SER Chi-restraints excluded: chain LN residue 126 THR Chi-restraints excluded: chain LO residue 6 VAL Chi-restraints excluded: chain LO residue 49 ARG Chi-restraints excluded: chain LO residue 180 GLN Chi-restraints excluded: chain LP residue 58 VAL Chi-restraints excluded: chain LP residue 94 MET Chi-restraints excluded: chain LQ residue 5 ILE Chi-restraints excluded: chain LQ residue 82 VAL Chi-restraints excluded: chain LQ residue 85 THR Chi-restraints excluded: chain LQ residue 100 VAL Chi-restraints excluded: chain LQ residue 147 GLU Chi-restraints excluded: chain LR residue 55 VAL Chi-restraints excluded: chain LS residue 132 ILE Chi-restraints excluded: chain LS residue 168 THR Chi-restraints excluded: chain LT residue 2 THR Chi-restraints excluded: chain LT residue 109 VAL Chi-restraints excluded: chain LT residue 154 ILE Chi-restraints excluded: chain LU residue 23 LEU Chi-restraints excluded: chain LU residue 38 ASN Chi-restraints excluded: chain LU residue 47 ILE Chi-restraints excluded: chain LU residue 62 THR Chi-restraints excluded: chain LU residue 76 VAL Chi-restraints excluded: chain LV residue 22 VAL Chi-restraints excluded: chain LV residue 59 ASP Chi-restraints excluded: chain LV residue 128 LEU Chi-restraints excluded: chain LV residue 134 SER Chi-restraints excluded: chain LV residue 135 ASN Chi-restraints excluded: chain LW residue 9 SER Chi-restraints excluded: chain LW residue 42 SER Chi-restraints excluded: chain LX residue 151 ASN Chi-restraints excluded: chain LY residue 10 ASP Chi-restraints excluded: chain LY residue 49 ILE Chi-restraints excluded: chain LY residue 120 GLU Chi-restraints excluded: chain LZ residue 34 SER Chi-restraints excluded: chain LZ residue 35 ASP Chi-restraints excluded: chain LZ residue 54 THR Chi-restraints excluded: chain LZ residue 94 THR Chi-restraints excluded: chain La residue 86 THR Chi-restraints excluded: chain La residue 130 SER Chi-restraints excluded: chain Lb residue 65 MET Chi-restraints excluded: chain Lc residue 28 VAL Chi-restraints excluded: chain Lc residue 50 ASN Chi-restraints excluded: chain Lc residue 78 ASN Chi-restraints excluded: chain Lc residue 93 THR Chi-restraints excluded: chain Lc residue 106 ARG Chi-restraints excluded: chain Ld residue 24 GLU Chi-restraints excluded: chain Ld residue 46 LEU 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 Ld residue 122 VAL Chi-restraints excluded: chain Ld residue 123 ASP Chi-restraints excluded: chain Le residue 87 VAL Chi-restraints excluded: chain Lf residue 91 ASN Chi-restraints excluded: chain Lh residue 8 ASP Chi-restraints excluded: chain Li residue 11 LEU Chi-restraints excluded: chain Li residue 21 VAL Chi-restraints excluded: chain Li residue 59 GLU Chi-restraints excluded: chain Lk residue 13 LEU Chi-restraints excluded: chain Lk residue 30 ASP Chi-restraints excluded: chain Lk residue 46 VAL Chi-restraints excluded: chain Lk residue 59 SER Chi-restraints excluded: chain Lk residue 60 LEU Chi-restraints excluded: chain Ll residue 47 THR Chi-restraints excluded: chain Lm residue 81 SER Chi-restraints excluded: chain Lm residue 110 CYS Chi-restraints excluded: chain Lo residue 33 LEU Chi-restraints excluded: chain Lo residue 55 ILE Chi-restraints excluded: chain Lo residue 96 ASP Chi-restraints excluded: chain Lo residue 104 ILE Chi-restraints excluded: chain Lp residue 16 THR Chi-restraints excluded: chain Lp residue 26 VAL Chi-restraints excluded: chain Lp residue 30 GLU Chi-restraints excluded: chain Lp residue 32 SER Chi-restraints excluded: chain Lr residue 27 THR Chi-restraints excluded: chain Lr residue 28 GLU Chi-restraints excluded: chain Lr residue 80 THR Chi-restraints excluded: chain Lz residue 17 VAL Chi-restraints excluded: chain Lz residue 120 ILE Chi-restraints excluded: chain Lz residue 155 ILE Chi-restraints excluded: chain Lz residue 183 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1216 random chunks: chunk 725 optimal weight: 10.0000 chunk 468 optimal weight: 7.9990 chunk 699 optimal weight: 10.0000 chunk 353 optimal weight: 10.0000 chunk 230 optimal weight: 10.0000 chunk 227 optimal weight: 30.0000 chunk 745 optimal weight: 10.0000 chunk 798 optimal weight: 9.9990 chunk 579 optimal weight: 8.9990 chunk 109 optimal weight: 20.0000 chunk 921 optimal weight: 8.9990 overall best weight: 9.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN ** B 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LB 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LL 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LP 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LQ 45 GLN LT 144 ASN LX 93 ASN LY 65 GLN ** LY 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lb 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lk 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lo 76 ASN ** Lz 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.118 160619 Z= 0.403 Angle : 0.576 10.491 234957 Z= 0.296 Chirality : 0.037 0.233 29135 Planarity : 0.004 0.053 15785 Dihedral : 22.387 179.140 68973 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.47 % Favored : 96.52 % Rotamer: Outliers : 2.60 % Allowed : 17.86 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.76 % 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: 1.17 (0.09), residues: 8540 helix: 1.87 (0.09), residues: 3602 sheet: 0.14 (0.17), residues: 973 loop : -0.01 (0.10), residues: 3965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRPLU 99 HIS 0.006 0.001 HISLa 40 PHE 0.032 0.001 PHELz 189 TYR 0.021 0.001 TYRLc 31 ARG 0.012 0.000 ARGLp 85 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17080 Ramachandran restraints generated. 8540 Oldfield, 0 Emsley, 8540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17080 Ramachandran restraints generated. 8540 Oldfield, 0 Emsley, 8540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 963 residues out of total 7475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 769 time to evaluate : 8.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 692 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7166 (mp) REVERT: A 701 MET cc_start: 0.4543 (mmm) cc_final: 0.4213 (mmm) REVERT: A 732 GLN cc_start: 0.8166 (tm-30) cc_final: 0.7811 (mm-40) REVERT: B 185 ASP cc_start: 0.9008 (m-30) cc_final: 0.8430 (t0) REVERT: C 299 ASN cc_start: 0.6370 (OUTLIER) cc_final: 0.5631 (m-40) REVERT: LA 80 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.7938 (tp30) REVERT: LC 325 MET cc_start: 0.9396 (tpt) cc_final: 0.9091 (tpt) REVERT: LC 352 ASP cc_start: 0.8699 (m-30) cc_final: 0.8463 (m-30) REVERT: LD 215 ASP cc_start: 0.8380 (OUTLIER) cc_final: 0.7809 (t0) REVERT: LD 293 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.8027 (mmt90) REVERT: LE 249 ASP cc_start: 0.8410 (m-30) cc_final: 0.8178 (m-30) REVERT: LG 88 ASP cc_start: 0.8287 (p0) cc_final: 0.7682 (p0) REVERT: LH 106 GLN cc_start: 0.8389 (mt0) cc_final: 0.8071 (mt0) REVERT: LH 110 SER cc_start: 0.9208 (t) cc_final: 0.8902 (t) REVERT: LH 113 GLU cc_start: 0.8665 (mt-10) cc_final: 0.7859 (mt-10) REVERT: LH 115 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.8118 (ptp90) REVERT: LI 63 GLU cc_start: 0.9070 (mp0) cc_final: 0.8800 (mp0) REVERT: LL 79 GLU cc_start: 0.8787 (tm-30) cc_final: 0.8445 (tm-30) REVERT: LL 111 GLN cc_start: 0.8570 (mt0) cc_final: 0.8198 (mt0) REVERT: LL 142 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8086 (pm20) REVERT: LM 96 GLU cc_start: 0.8741 (tp30) cc_final: 0.7990 (tp30) REVERT: LM 99 GLU cc_start: 0.8119 (pp20) cc_final: 0.7755 (pp20) REVERT: LM 136 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8637 (tt) REVERT: LO 180 GLN cc_start: 0.9140 (OUTLIER) cc_final: 0.8875 (tp40) REVERT: LP 108 ASP cc_start: 0.8626 (t0) cc_final: 0.8194 (t0) REVERT: LQ 147 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8258 (tp30) REVERT: LS 112 ASP cc_start: 0.8978 (t0) cc_final: 0.8673 (t0) REVERT: LU 23 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8604 (tt) REVERT: LU 39 PHE cc_start: 0.9193 (t80) cc_final: 0.8548 (t80) REVERT: LU 46 ARG cc_start: 0.8785 (tpp-160) cc_final: 0.8471 (mmt-90) REVERT: LU 95 ASN cc_start: 0.8957 (t0) cc_final: 0.8632 (t0) REVERT: LV 99 GLU cc_start: 0.8291 (mt-10) cc_final: 0.8086 (tt0) REVERT: LV 124 GLU cc_start: 0.8688 (mp0) cc_final: 0.8384 (mp0) REVERT: LW 1 MET cc_start: 0.7060 (ttp) cc_final: 0.6739 (mtp) REVERT: LX 133 GLU cc_start: 0.8551 (mp0) cc_final: 0.8347 (mp0) REVERT: LX 145 ASP cc_start: 0.8408 (t0) cc_final: 0.7039 (t0) REVERT: LX 148 ASP cc_start: 0.8909 (m-30) cc_final: 0.8177 (m-30) REVERT: LY 52 ASP cc_start: 0.8420 (m-30) cc_final: 0.8161 (t0) REVERT: LY 107 THR cc_start: 0.9636 (m) cc_final: 0.9414 (p) REVERT: Lc 106 ARG cc_start: 0.6583 (OUTLIER) cc_final: 0.6029 (tpp-160) REVERT: Ld 118 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8333 (mm-40) REVERT: Lg 98 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8456 (mm-30) REVERT: Lk 52 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8788 (mtmm) REVERT: Lp 30 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8405 (mt-10) REVERT: Lz 72 GLN cc_start: 0.8608 (pp30) cc_final: 0.8278 (pp30) outliers start: 194 outliers final: 148 residues processed: 895 average time/residue: 1.2492 time to fit residues: 2031.2928 Evaluate side-chains 916 residues out of total 7475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 753 time to evaluate : 8.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 8 VAL Chi-restraints excluded: chain 1 residue 54 MET Chi-restraints excluded: chain 1 residue 132 VAL Chi-restraints excluded: chain 1 residue 400 VAL Chi-restraints excluded: chain 1 residue 401 MET Chi-restraints excluded: chain 1 residue 447 ILE Chi-restraints excluded: chain 1 residue 452 THR Chi-restraints excluded: chain 2 residue 26 THR Chi-restraints excluded: chain 2 residue 56 LEU Chi-restraints excluded: chain 3 residue 83 SER Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain B residue 104 TYR Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain C residue 299 ASN Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 110 CYS Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain LA residue 33 ASP Chi-restraints excluded: chain LA residue 80 GLU Chi-restraints excluded: chain LA residue 243 THR Chi-restraints excluded: chain LB residue 101 THR Chi-restraints excluded: chain LB residue 181 MET Chi-restraints excluded: chain LB residue 194 LEU Chi-restraints excluded: chain LC residue 154 VAL Chi-restraints excluded: chain LC residue 156 ASP Chi-restraints excluded: chain LC residue 198 ASN Chi-restraints excluded: chain LD residue 37 VAL Chi-restraints excluded: chain LD residue 215 ASP Chi-restraints excluded: chain LD residue 271 MET Chi-restraints excluded: chain LD residue 293 ARG Chi-restraints excluded: chain LE residue 241 GLU Chi-restraints excluded: chain LF residue 67 THR Chi-restraints excluded: chain LF residue 74 MET Chi-restraints excluded: chain LG residue 198 THR Chi-restraints excluded: chain LG residue 254 GLU Chi-restraints excluded: chain LH residue 6 SER Chi-restraints excluded: chain LH residue 46 SER Chi-restraints excluded: chain LH residue 92 MET Chi-restraints excluded: chain LH residue 115 ARG Chi-restraints excluded: chain LH residue 177 ASP Chi-restraints excluded: chain LI residue 136 MET Chi-restraints excluded: chain LI residue 195 CYS Chi-restraints excluded: chain LJ residue 29 SER Chi-restraints excluded: chain LJ residue 34 THR Chi-restraints excluded: chain LJ residue 47 THR Chi-restraints excluded: chain LJ residue 72 CYS Chi-restraints excluded: chain LJ residue 140 SER Chi-restraints excluded: chain LL residue 108 GLU Chi-restraints excluded: chain LL residue 142 GLU Chi-restraints excluded: chain LL residue 146 LEU Chi-restraints excluded: chain LL residue 148 THR Chi-restraints excluded: chain LM residue 104 MET Chi-restraints excluded: chain LM residue 105 THR Chi-restraints excluded: chain LM residue 117 LYS Chi-restraints excluded: chain LM residue 136 LEU Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 75 VAL Chi-restraints excluded: chain LN residue 87 HIS Chi-restraints excluded: chain LN residue 125 SER Chi-restraints excluded: chain LN residue 126 THR Chi-restraints excluded: chain LO residue 6 VAL Chi-restraints excluded: chain LO residue 49 ARG Chi-restraints excluded: chain LO residue 132 THR Chi-restraints excluded: chain LO residue 180 GLN Chi-restraints excluded: chain LP residue 58 VAL Chi-restraints excluded: chain LP residue 94 MET Chi-restraints excluded: chain LP residue 115 GLU Chi-restraints excluded: chain LQ residue 5 ILE Chi-restraints excluded: chain LQ residue 82 VAL Chi-restraints excluded: chain LQ residue 85 THR Chi-restraints excluded: chain LQ residue 100 VAL Chi-restraints excluded: chain LQ residue 147 GLU Chi-restraints excluded: chain LR residue 12 SER Chi-restraints excluded: chain LR residue 55 VAL Chi-restraints excluded: chain LS residue 132 ILE Chi-restraints excluded: chain LS residue 168 THR Chi-restraints excluded: chain LT residue 2 THR Chi-restraints excluded: chain LT residue 109 VAL Chi-restraints excluded: chain LU residue 23 LEU Chi-restraints excluded: chain LU residue 38 ASN Chi-restraints excluded: chain LU residue 47 ILE Chi-restraints excluded: chain LU residue 62 THR Chi-restraints excluded: chain LU residue 71 THR Chi-restraints excluded: chain LU residue 76 VAL Chi-restraints excluded: chain LV residue 22 VAL Chi-restraints excluded: chain LV residue 61 VAL Chi-restraints excluded: chain LV residue 128 LEU Chi-restraints excluded: chain LV residue 134 SER Chi-restraints excluded: chain LW residue 9 SER Chi-restraints excluded: chain LW residue 42 SER Chi-restraints excluded: chain LX residue 119 ILE Chi-restraints excluded: chain LX residue 151 ASN Chi-restraints excluded: chain LY residue 10 ASP Chi-restraints excluded: chain LY residue 49 ILE Chi-restraints excluded: chain LY residue 120 GLU Chi-restraints excluded: chain LZ residue 34 SER Chi-restraints excluded: chain LZ residue 35 ASP Chi-restraints excluded: chain LZ residue 54 THR Chi-restraints excluded: chain LZ residue 94 THR Chi-restraints excluded: chain La residue 86 THR Chi-restraints excluded: chain La residue 130 SER Chi-restraints excluded: chain Lb residue 65 MET Chi-restraints excluded: chain Lb residue 75 LEU Chi-restraints excluded: chain Lc residue 28 VAL Chi-restraints excluded: chain Lc residue 34 THR Chi-restraints excluded: chain Lc residue 50 ASN Chi-restraints excluded: chain Lc residue 78 ASN Chi-restraints excluded: chain Lc residue 93 THR Chi-restraints excluded: chain Lc residue 106 ARG Chi-restraints excluded: chain Ld residue 24 GLU Chi-restraints excluded: chain Ld residue 46 LEU Chi-restraints excluded: chain Ld residue 59 THR 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 Ld residue 122 VAL Chi-restraints excluded: chain Ld residue 123 ASP Chi-restraints excluded: chain Le residue 87 VAL Chi-restraints excluded: chain Le residue 126 ASN Chi-restraints excluded: chain Lf residue 91 ASN Chi-restraints excluded: chain Lf residue 108 SER Chi-restraints excluded: chain Lh residue 8 ASP Chi-restraints excluded: chain Lh residue 67 GLU Chi-restraints excluded: chain Li residue 9 VAL Chi-restraints excluded: chain Li residue 11 LEU Chi-restraints excluded: chain Li residue 21 VAL Chi-restraints excluded: chain Li residue 34 THR Chi-restraints excluded: chain Li residue 59 GLU Chi-restraints excluded: chain Lk residue 13 LEU Chi-restraints excluded: chain Lk residue 30 ASP Chi-restraints excluded: chain Lk residue 46 VAL Chi-restraints excluded: chain Lk residue 52 LYS Chi-restraints excluded: chain Lk residue 59 SER Chi-restraints excluded: chain Lk residue 60 LEU Chi-restraints excluded: chain Ll residue 47 THR Chi-restraints excluded: chain Lm residue 81 SER Chi-restraints excluded: chain Lm residue 110 CYS Chi-restraints excluded: chain Lo residue 33 LEU Chi-restraints excluded: chain Lo residue 55 ILE Chi-restraints excluded: chain Lo residue 96 ASP Chi-restraints excluded: chain Lo residue 104 ILE Chi-restraints excluded: chain Lp residue 16 THR Chi-restraints excluded: chain Lp residue 26 VAL Chi-restraints excluded: chain Lp residue 30 GLU Chi-restraints excluded: chain Lp residue 32 SER Chi-restraints excluded: chain Lp residue 70 THR Chi-restraints excluded: chain Lr residue 27 THR Chi-restraints excluded: chain Lr residue 28 GLU Chi-restraints excluded: chain Lr residue 80 THR Chi-restraints excluded: chain Lz residue 17 VAL Chi-restraints excluded: chain Lz residue 120 ILE Chi-restraints excluded: chain Lz residue 155 ILE Chi-restraints excluded: chain Lz residue 183 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1216 random chunks: chunk 1066 optimal weight: 10.0000 chunk 1122 optimal weight: 2.9990 chunk 1024 optimal weight: 0.4980 chunk 1092 optimal weight: 7.9990 chunk 657 optimal weight: 5.9990 chunk 475 optimal weight: 30.0000 chunk 857 optimal weight: 5.9990 chunk 335 optimal weight: 10.0000 chunk 986 optimal weight: 8.9990 chunk 1032 optimal weight: 3.9990 chunk 1088 optimal weight: 0.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN ** B 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LF 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LL 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LM 131 GLN LP 137 ASN LQ 45 GLN LY 65 GLN ** Lb 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lk 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lo 76 ASN ** Lz 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 160619 Z= 0.164 Angle : 0.485 10.922 234957 Z= 0.252 Chirality : 0.032 0.276 29135 Planarity : 0.003 0.054 15785 Dihedral : 22.438 178.209 68973 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.73 % Favored : 97.26 % Rotamer: Outliers : 2.06 % Allowed : 18.39 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.76 % 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: 1.37 (0.09), residues: 8540 helix: 2.07 (0.09), residues: 3594 sheet: 0.13 (0.17), residues: 963 loop : 0.10 (0.10), residues: 3983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRPLU 99 HIS 0.005 0.001 HIS K 50 PHE 0.038 0.001 PHELz 189 TYR 0.029 0.001 TYR K 35 ARG 0.015 0.000 ARGLp 85 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17080 Ramachandran restraints generated. 8540 Oldfield, 0 Emsley, 8540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17080 Ramachandran restraints generated. 8540 Oldfield, 0 Emsley, 8540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 963 residues out of total 7475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 809 time to evaluate : 8.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 732 GLN cc_start: 0.8104 (tm-30) cc_final: 0.7713 (mm-40) REVERT: B 185 ASP cc_start: 0.9028 (m-30) cc_final: 0.8463 (t0) REVERT: B 248 SER cc_start: 0.5586 (OUTLIER) cc_final: 0.5370 (t) REVERT: C 299 ASN cc_start: 0.6191 (OUTLIER) cc_final: 0.5579 (m-40) REVERT: C 301 LEU cc_start: 0.5383 (OUTLIER) cc_final: 0.5074 (tt) REVERT: LA 80 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.7848 (tp30) REVERT: LC 291 ARG cc_start: 0.7890 (ttm110) cc_final: 0.7654 (ttt90) REVERT: LC 352 ASP cc_start: 0.8651 (m-30) cc_final: 0.8399 (m-30) REVERT: LD 215 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.7753 (t0) REVERT: LD 293 ARG cc_start: 0.8392 (OUTLIER) cc_final: 0.7941 (mmt90) REVERT: LE 249 ASP cc_start: 0.8302 (m-30) cc_final: 0.7997 (m-30) REVERT: LG 88 ASP cc_start: 0.8212 (p0) cc_final: 0.7597 (p0) REVERT: LH 110 SER cc_start: 0.9215 (t) cc_final: 0.8904 (t) REVERT: LH 115 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8001 (ptp90) REVERT: LI 63 GLU cc_start: 0.9073 (mp0) cc_final: 0.8840 (mp0) REVERT: LL 79 GLU cc_start: 0.8680 (tm-30) cc_final: 0.8345 (tm-30) REVERT: LL 111 GLN cc_start: 0.8530 (mt0) cc_final: 0.8200 (mt0) REVERT: LL 175 ASN cc_start: 0.9170 (m110) cc_final: 0.8866 (m110) REVERT: LM 96 GLU cc_start: 0.8632 (tp30) cc_final: 0.7840 (tp30) REVERT: LM 99 GLU cc_start: 0.8073 (pp20) cc_final: 0.7687 (pp20) REVERT: LO 180 GLN cc_start: 0.9085 (OUTLIER) cc_final: 0.8755 (tp-100) REVERT: LP 108 ASP cc_start: 0.8537 (t0) cc_final: 0.8056 (t0) REVERT: LQ 147 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8162 (tp30) REVERT: LR 119 MET cc_start: 0.8807 (ttm) cc_final: 0.8527 (ttp) REVERT: LS 112 ASP cc_start: 0.8858 (t0) cc_final: 0.8550 (t0) REVERT: LT 111 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8148 (tm-30) REVERT: LU 23 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8643 (tt) REVERT: LU 39 PHE cc_start: 0.9139 (t80) cc_final: 0.8574 (t80) REVERT: LU 46 ARG cc_start: 0.8734 (tpp-160) cc_final: 0.8484 (mmt-90) REVERT: LU 95 ASN cc_start: 0.8967 (t0) cc_final: 0.8653 (t0) REVERT: LU 115 PHE cc_start: 0.8528 (m-80) cc_final: 0.8167 (m-80) REVERT: LV 99 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7974 (tt0) REVERT: LV 124 GLU cc_start: 0.8713 (mp0) cc_final: 0.8454 (mp0) REVERT: LW 1 MET cc_start: 0.6912 (ttp) cc_final: 0.6597 (mtp) REVERT: LX 145 ASP cc_start: 0.8357 (t0) cc_final: 0.6891 (t0) REVERT: LX 148 ASP cc_start: 0.8886 (m-30) cc_final: 0.8123 (m-30) REVERT: LY 52 ASP cc_start: 0.8403 (m-30) cc_final: 0.8121 (t0) REVERT: LY 107 THR cc_start: 0.9584 (m) cc_final: 0.9364 (p) REVERT: La 93 ASN cc_start: 0.8997 (t0) cc_final: 0.8795 (t0) REVERT: Lc 106 ARG cc_start: 0.6549 (OUTLIER) cc_final: 0.5990 (tpp-160) REVERT: Ld 19 GLU cc_start: 0.8066 (mp0) cc_final: 0.7683 (mt-10) REVERT: Ld 118 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8254 (mm-40) REVERT: Lk 7 GLU cc_start: 0.6906 (pm20) cc_final: 0.4918 (pm20) REVERT: Lp 30 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8413 (mt-10) REVERT: Lr 80 THR cc_start: 0.9517 (OUTLIER) cc_final: 0.9297 (p) REVERT: Lr 102 TYR cc_start: 0.8995 (t80) cc_final: 0.8793 (t80) REVERT: Lz 72 GLN cc_start: 0.8628 (pp30) cc_final: 0.8261 (pp30) outliers start: 154 outliers final: 104 residues processed: 910 average time/residue: 1.2645 time to fit residues: 2077.3586 Evaluate side-chains 899 residues out of total 7475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 781 time to evaluate : 8.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 8 VAL Chi-restraints excluded: chain 1 residue 132 VAL Chi-restraints excluded: chain 1 residue 400 VAL Chi-restraints excluded: chain 1 residue 401 MET Chi-restraints excluded: chain 1 residue 452 THR Chi-restraints excluded: chain 2 residue 56 LEU Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain C residue 299 ASN Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 110 CYS Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain LA residue 33 ASP Chi-restraints excluded: chain LA residue 80 GLU Chi-restraints excluded: chain LA residue 243 THR Chi-restraints excluded: chain LB residue 101 THR Chi-restraints excluded: chain LB residue 181 MET Chi-restraints excluded: chain LC residue 154 VAL Chi-restraints excluded: chain LD residue 37 VAL Chi-restraints excluded: chain LD residue 215 ASP Chi-restraints excluded: chain LD residue 293 ARG Chi-restraints excluded: chain LF residue 74 MET Chi-restraints excluded: chain LG residue 198 THR Chi-restraints excluded: chain LH residue 6 SER Chi-restraints excluded: chain LH residue 115 ARG Chi-restraints excluded: chain LH residue 177 ASP Chi-restraints excluded: chain LI residue 136 MET Chi-restraints excluded: chain LI residue 195 CYS Chi-restraints excluded: chain LJ residue 29 SER Chi-restraints excluded: chain LJ residue 34 THR Chi-restraints excluded: chain LJ residue 47 THR Chi-restraints excluded: chain LJ residue 72 CYS Chi-restraints excluded: chain LJ residue 140 SER Chi-restraints excluded: chain LL residue 108 GLU Chi-restraints excluded: chain LL residue 146 LEU Chi-restraints excluded: chain LL residue 148 THR Chi-restraints excluded: chain LM residue 104 MET Chi-restraints excluded: chain LM residue 105 THR Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 126 THR Chi-restraints excluded: chain LO residue 6 VAL Chi-restraints excluded: chain LO residue 49 ARG Chi-restraints excluded: chain LO residue 180 GLN Chi-restraints excluded: chain LP residue 58 VAL Chi-restraints excluded: chain LP residue 94 MET Chi-restraints excluded: chain LQ residue 5 ILE Chi-restraints excluded: chain LQ residue 82 VAL Chi-restraints excluded: chain LQ residue 85 THR Chi-restraints excluded: chain LQ residue 100 VAL Chi-restraints excluded: chain LQ residue 147 GLU Chi-restraints excluded: chain LS residue 168 THR Chi-restraints excluded: chain LT residue 2 THR Chi-restraints excluded: chain LU residue 23 LEU Chi-restraints excluded: chain LU residue 38 ASN Chi-restraints excluded: chain LU residue 47 ILE Chi-restraints excluded: chain LU residue 62 THR Chi-restraints excluded: chain LU residue 71 THR Chi-restraints excluded: chain LU residue 74 SER Chi-restraints excluded: chain LV residue 128 LEU Chi-restraints excluded: chain LX residue 83 THR Chi-restraints excluded: chain LX residue 85 SER Chi-restraints excluded: chain LY residue 120 GLU Chi-restraints excluded: chain LZ residue 34 SER Chi-restraints excluded: chain LZ residue 35 ASP Chi-restraints excluded: chain LZ residue 54 THR Chi-restraints excluded: chain LZ residue 99 ASP Chi-restraints excluded: chain La residue 86 THR Chi-restraints excluded: chain La residue 130 SER Chi-restraints excluded: chain La residue 140 VAL Chi-restraints excluded: chain Lb residue 65 MET Chi-restraints excluded: chain Lb residue 75 LEU Chi-restraints excluded: chain Lc residue 28 VAL Chi-restraints excluded: chain Lc residue 78 ASN Chi-restraints excluded: chain Lc residue 93 THR Chi-restraints excluded: chain Lc residue 106 ARG Chi-restraints excluded: chain Ld residue 24 GLU Chi-restraints excluded: chain Ld residue 46 LEU Chi-restraints excluded: chain Ld residue 59 THR Chi-restraints excluded: chain Ld residue 98 SER Chi-restraints excluded: chain Ld residue 118 GLN Chi-restraints excluded: chain Ld residue 122 VAL Chi-restraints excluded: chain Ld residue 123 ASP Chi-restraints excluded: chain Le residue 87 VAL Chi-restraints excluded: chain Le residue 122 VAL Chi-restraints excluded: chain Lh residue 8 ASP Chi-restraints excluded: chain Li residue 11 LEU Chi-restraints excluded: chain Li residue 21 VAL Chi-restraints excluded: chain Li residue 59 GLU Chi-restraints excluded: chain Lk residue 13 LEU Chi-restraints excluded: chain Lk residue 46 VAL Chi-restraints excluded: chain Lk residue 59 SER Chi-restraints excluded: chain Lk residue 60 LEU Chi-restraints excluded: chain Ll residue 47 THR Chi-restraints excluded: chain Lm residue 81 SER Chi-restraints excluded: chain Lm residue 110 CYS Chi-restraints excluded: chain Lo residue 55 ILE Chi-restraints excluded: chain Lp residue 16 THR Chi-restraints excluded: chain Lp residue 26 VAL Chi-restraints excluded: chain Lp residue 30 GLU Chi-restraints excluded: chain Lp residue 32 SER Chi-restraints excluded: chain Lr residue 27 THR Chi-restraints excluded: chain Lr residue 80 THR Chi-restraints excluded: chain Lz residue 9 THR Chi-restraints excluded: chain Lz residue 12 GLU Chi-restraints excluded: chain Lz residue 17 VAL Chi-restraints excluded: chain Lz residue 120 ILE Chi-restraints excluded: chain Lz residue 155 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1216 random chunks: chunk 717 optimal weight: 10.0000 chunk 1154 optimal weight: 1.9990 chunk 704 optimal weight: 20.0000 chunk 547 optimal weight: 9.9990 chunk 802 optimal weight: 9.9990 chunk 1211 optimal weight: 40.0000 chunk 1115 optimal weight: 5.9990 chunk 964 optimal weight: 4.9990 chunk 100 optimal weight: 20.0000 chunk 745 optimal weight: 20.0000 chunk 591 optimal weight: 8.9990 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 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LL 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LM 131 GLN LP 75 GLN LQ 45 GLN LX 93 ASN LY 65 GLN ** Lb 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lm 84 GLN Lo 76 ASN Lr 41 ASN ** Lz 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 160619 Z= 0.287 Angle : 0.517 10.272 234957 Z= 0.267 Chirality : 0.034 0.254 29135 Planarity : 0.004 0.058 15785 Dihedral : 22.369 178.990 68973 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.20 % Favored : 96.79 % Rotamer: Outliers : 1.91 % Allowed : 18.74 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.76 % 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: 1.32 (0.09), residues: 8540 helix: 2.02 (0.09), residues: 3598 sheet: 0.15 (0.17), residues: 954 loop : 0.07 (0.10), residues: 3988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRPLU 99 HIS 0.005 0.001 HISLa 40 PHE 0.036 0.001 PHELz 189 TYR 0.020 0.001 TYRLc 27 ARG 0.014 0.000 ARGLp 85 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17080 Ramachandran restraints generated. 8540 Oldfield, 0 Emsley, 8540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17080 Ramachandran restraints generated. 8540 Oldfield, 0 Emsley, 8540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 911 residues out of total 7475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 768 time to evaluate : 8.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 652 MET cc_start: 0.4389 (tpp) cc_final: 0.3986 (tpp) REVERT: A 732 GLN cc_start: 0.8110 (tm-30) cc_final: 0.7743 (mm-40) REVERT: B 185 ASP cc_start: 0.9015 (m-30) cc_final: 0.8435 (t0) REVERT: B 248 SER cc_start: 0.5533 (OUTLIER) cc_final: 0.5288 (t) REVERT: C 299 ASN cc_start: 0.6278 (OUTLIER) cc_final: 0.5589 (m-40) REVERT: C 301 LEU cc_start: 0.5353 (OUTLIER) cc_final: 0.5023 (tt) REVERT: LA 80 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.7884 (tp30) REVERT: LC 352 ASP cc_start: 0.8642 (m-30) cc_final: 0.8391 (m-30) REVERT: LD 215 ASP cc_start: 0.8349 (OUTLIER) cc_final: 0.7768 (t0) REVERT: LD 293 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7955 (mmt90) REVERT: LE 249 ASP cc_start: 0.8346 (m-30) cc_final: 0.8067 (m-30) REVERT: LG 88 ASP cc_start: 0.8217 (p0) cc_final: 0.7608 (p0) REVERT: LH 106 GLN cc_start: 0.8388 (mt0) cc_final: 0.8163 (mt0) REVERT: LH 110 SER cc_start: 0.9189 (t) cc_final: 0.8888 (t) REVERT: LH 115 ARG cc_start: 0.8752 (OUTLIER) cc_final: 0.8103 (ptp90) REVERT: LI 63 GLU cc_start: 0.9083 (mp0) cc_final: 0.8834 (mp0) REVERT: LL 79 GLU cc_start: 0.8731 (tm-30) cc_final: 0.8395 (tm-30) REVERT: LL 111 GLN cc_start: 0.8512 (mt0) cc_final: 0.8180 (mt0) REVERT: LL 175 ASN cc_start: 0.9161 (m110) cc_final: 0.8852 (m110) REVERT: LM 96 GLU cc_start: 0.8665 (tp30) cc_final: 0.7870 (tp30) REVERT: LM 99 GLU cc_start: 0.8086 (pp20) cc_final: 0.7704 (pp20) REVERT: LO 180 GLN cc_start: 0.9107 (OUTLIER) cc_final: 0.8772 (tp-100) REVERT: LP 108 ASP cc_start: 0.8561 (t0) cc_final: 0.8110 (t0) REVERT: LQ 4 ASP cc_start: 0.8714 (t0) cc_final: 0.8401 (t70) REVERT: LQ 147 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8154 (tp30) REVERT: LS 112 ASP cc_start: 0.8919 (t0) cc_final: 0.8593 (t0) REVERT: LT 111 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8134 (tm-30) REVERT: LU 23 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8632 (tt) REVERT: LU 39 PHE cc_start: 0.9150 (t80) cc_final: 0.8524 (t80) REVERT: LU 40 GLU cc_start: 0.8743 (pt0) cc_final: 0.8310 (pt0) REVERT: LU 46 ARG cc_start: 0.8761 (tpp-160) cc_final: 0.8497 (mmt-90) REVERT: LU 65 ARG cc_start: 0.8176 (ttp80) cc_final: 0.7961 (ttp80) REVERT: LU 95 ASN cc_start: 0.8955 (t0) cc_final: 0.8661 (t0) REVERT: LU 115 PHE cc_start: 0.8546 (m-80) cc_final: 0.8189 (m-80) REVERT: LV 99 GLU cc_start: 0.8265 (mt-10) cc_final: 0.8013 (tt0) REVERT: LV 124 GLU cc_start: 0.8694 (mp0) cc_final: 0.8431 (mp0) REVERT: LW 1 MET cc_start: 0.7008 (ttp) cc_final: 0.6577 (mtp) REVERT: LX 145 ASP cc_start: 0.8415 (t0) cc_final: 0.6930 (t0) REVERT: LX 148 ASP cc_start: 0.8910 (m-30) cc_final: 0.8150 (m-30) REVERT: LY 52 ASP cc_start: 0.8384 (m-30) cc_final: 0.8159 (t0) REVERT: LY 107 THR cc_start: 0.9600 (m) cc_final: 0.9364 (p) REVERT: La 93 ASN cc_start: 0.9011 (t0) cc_final: 0.8808 (t0) REVERT: Lc 106 ARG cc_start: 0.6623 (OUTLIER) cc_final: 0.6092 (tpp-160) REVERT: Ld 19 GLU cc_start: 0.8068 (mp0) cc_final: 0.7738 (mt-10) REVERT: Ld 118 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8235 (mm-40) REVERT: Lp 30 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8402 (mt-10) REVERT: Lr 102 TYR cc_start: 0.9011 (t80) cc_final: 0.8810 (t80) REVERT: Lz 72 GLN cc_start: 0.8637 (pp30) cc_final: 0.8206 (pp30) REVERT: Lz 110 PHE cc_start: 0.7782 (m-80) cc_final: 0.7420 (m-80) outliers start: 143 outliers final: 116 residues processed: 862 average time/residue: 1.2775 time to fit residues: 1995.0444 Evaluate side-chains 891 residues out of total 7475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 762 time to evaluate : 8.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 8 VAL Chi-restraints excluded: chain 1 residue 54 MET Chi-restraints excluded: chain 1 residue 132 VAL Chi-restraints excluded: chain 1 residue 400 VAL Chi-restraints excluded: chain 1 residue 401 MET Chi-restraints excluded: chain 1 residue 447 ILE Chi-restraints excluded: chain 1 residue 452 THR Chi-restraints excluded: chain 2 residue 56 LEU Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 595 MET Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain C residue 299 ASN Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain K residue 44 ASP Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 110 CYS Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain LA residue 33 ASP Chi-restraints excluded: chain LA residue 80 GLU Chi-restraints excluded: chain LA residue 243 THR Chi-restraints excluded: chain LB residue 101 THR Chi-restraints excluded: chain LB residue 181 MET Chi-restraints excluded: chain LC residue 154 VAL Chi-restraints excluded: chain LD residue 37 VAL Chi-restraints excluded: chain LD residue 215 ASP Chi-restraints excluded: chain LD residue 293 ARG Chi-restraints excluded: chain LF residue 74 MET Chi-restraints excluded: chain LG residue 198 THR Chi-restraints excluded: chain LH residue 6 SER Chi-restraints excluded: chain LH residue 92 MET Chi-restraints excluded: chain LH residue 115 ARG Chi-restraints excluded: chain LH residue 177 ASP Chi-restraints excluded: chain LI residue 136 MET Chi-restraints excluded: chain LI residue 195 CYS Chi-restraints excluded: chain LJ residue 29 SER Chi-restraints excluded: chain LJ residue 34 THR Chi-restraints excluded: chain LJ residue 47 THR Chi-restraints excluded: chain LJ residue 72 CYS Chi-restraints excluded: chain LJ residue 140 SER Chi-restraints excluded: chain LL residue 108 GLU Chi-restraints excluded: chain LL residue 146 LEU Chi-restraints excluded: chain LL residue 148 THR Chi-restraints excluded: chain LM residue 104 MET Chi-restraints excluded: chain LM residue 105 THR Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 87 HIS Chi-restraints excluded: chain LN residue 126 THR Chi-restraints excluded: chain LO residue 6 VAL Chi-restraints excluded: chain LO residue 49 ARG Chi-restraints excluded: chain LO residue 132 THR Chi-restraints excluded: chain LO residue 180 GLN Chi-restraints excluded: chain LP residue 58 VAL Chi-restraints excluded: chain LP residue 94 MET Chi-restraints excluded: chain LQ residue 5 ILE Chi-restraints excluded: chain LQ residue 82 VAL Chi-restraints excluded: chain LQ residue 85 THR Chi-restraints excluded: chain LQ residue 100 VAL Chi-restraints excluded: chain LQ residue 147 GLU Chi-restraints excluded: chain LR residue 12 SER Chi-restraints excluded: chain LS residue 168 THR Chi-restraints excluded: chain LT residue 2 THR Chi-restraints excluded: chain LU residue 23 LEU Chi-restraints excluded: chain LU residue 38 ASN Chi-restraints excluded: chain LU residue 47 ILE Chi-restraints excluded: chain LU residue 62 THR Chi-restraints excluded: chain LU residue 71 THR Chi-restraints excluded: chain LU residue 74 SER Chi-restraints excluded: chain LV residue 128 LEU Chi-restraints excluded: chain LX residue 85 SER Chi-restraints excluded: chain LX residue 119 ILE Chi-restraints excluded: chain LY residue 10 ASP Chi-restraints excluded: chain LY residue 120 GLU Chi-restraints excluded: chain LZ residue 34 SER Chi-restraints excluded: chain LZ residue 35 ASP Chi-restraints excluded: chain LZ residue 54 THR Chi-restraints excluded: chain La residue 86 THR Chi-restraints excluded: chain La residue 130 SER Chi-restraints excluded: chain La residue 140 VAL Chi-restraints excluded: chain Lb residue 65 MET Chi-restraints excluded: chain Lb residue 75 LEU Chi-restraints excluded: chain Lb residue 93 LEU Chi-restraints excluded: chain Lc residue 28 VAL Chi-restraints excluded: chain Lc residue 78 ASN Chi-restraints excluded: chain Lc residue 93 THR Chi-restraints excluded: chain Lc residue 106 ARG Chi-restraints excluded: chain Ld residue 24 GLU Chi-restraints excluded: chain Ld residue 46 LEU Chi-restraints excluded: chain Ld residue 98 SER Chi-restraints excluded: chain Ld residue 118 GLN Chi-restraints excluded: chain Ld residue 122 VAL Chi-restraints excluded: chain Ld residue 123 ASP Chi-restraints excluded: chain Le residue 87 VAL Chi-restraints excluded: chain Le residue 98 GLU Chi-restraints excluded: chain Le residue 122 VAL Chi-restraints excluded: chain Lf residue 91 ASN Chi-restraints excluded: chain Lh residue 8 ASP Chi-restraints excluded: chain Li residue 11 LEU Chi-restraints excluded: chain Li residue 21 VAL Chi-restraints excluded: chain Li residue 59 GLU Chi-restraints excluded: chain Lk residue 13 LEU Chi-restraints excluded: chain Lk residue 30 ASP Chi-restraints excluded: chain Lk residue 46 VAL Chi-restraints excluded: chain Lk residue 59 SER Chi-restraints excluded: chain Lk residue 60 LEU Chi-restraints excluded: chain Ll residue 47 THR Chi-restraints excluded: chain Lm residue 81 SER Chi-restraints excluded: chain Lm residue 110 CYS Chi-restraints excluded: chain Lo residue 55 ILE Chi-restraints excluded: chain Lp residue 16 THR Chi-restraints excluded: chain Lp residue 26 VAL Chi-restraints excluded: chain Lp residue 30 GLU Chi-restraints excluded: chain Lp residue 32 SER Chi-restraints excluded: chain Lr residue 27 THR Chi-restraints excluded: chain Lr residue 80 THR Chi-restraints excluded: chain Lz residue 9 THR Chi-restraints excluded: chain Lz residue 12 GLU Chi-restraints excluded: chain Lz residue 17 VAL Chi-restraints excluded: chain Lz residue 120 ILE Chi-restraints excluded: chain Lz residue 155 ILE Chi-restraints excluded: chain Lz residue 183 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1216 random chunks: chunk 766 optimal weight: 10.0000 chunk 1027 optimal weight: 8.9990 chunk 295 optimal weight: 10.0000 chunk 889 optimal weight: 7.9990 chunk 142 optimal weight: 30.0000 chunk 268 optimal weight: 30.0000 chunk 966 optimal weight: 10.0000 chunk 404 optimal weight: 10.0000 chunk 992 optimal weight: 2.9990 chunk 122 optimal weight: 30.0000 chunk 177 optimal weight: 10.0000 overall best weight: 7.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LL 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LM 131 GLN LQ 45 GLN LY 65 GLN ** LY 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lb 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lk 58 GLN Lm 84 GLN Lo 76 ASN Lr 41 ASN ** Lz 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.054484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.039234 restraints weight = 624831.701| |-----------------------------------------------------------------------------| r_work (start): 0.2699 rms_B_bonded: 1.73 r_work: 0.2592 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2491 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8984 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 160619 Z= 0.354 Angle : 0.555 11.549 234957 Z= 0.286 Chirality : 0.036 0.256 29135 Planarity : 0.004 0.058 15785 Dihedral : 22.382 179.183 68973 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.41 % Favored : 96.58 % Rotamer: Outliers : 2.01 % Allowed : 18.63 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.76 % 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: 1.22 (0.09), residues: 8540 helix: 1.93 (0.09), residues: 3598 sheet: 0.09 (0.16), residues: 992 loop : 0.02 (0.10), residues: 3950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRPLU 99 HIS 0.005 0.001 HISLa 40 PHE 0.036 0.001 PHELz 189 TYR 0.028 0.001 TYRLH 122 ARG 0.014 0.000 ARGLp 85 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 36495.81 seconds wall clock time: 639 minutes 59.34 seconds (38399.34 seconds total)