Starting phenix.real_space_refine on Thu Mar 21 18:25:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oj8_16908/03_2024/8oj8_16908.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oj8_16908/03_2024/8oj8_16908.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/8oj8_16908/03_2024/8oj8_16908.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oj8_16908/03_2024/8oj8_16908.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oj8_16908/03_2024/8oj8_16908.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oj8_16908/03_2024/8oj8_16908.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 3781 5.49 5 Mg 220 5.21 5 S 296 5.16 5 C 76265 2.51 5 N 26974 2.21 5 O 37084 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 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 481": "OE1" <-> "OE2" Residue "A TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LA ASP 33": "OD1" <-> "OD2" Residue "LA GLU 109": "OE1" <-> "OE2" Residue "LA GLU 142": "OE1" <-> "OE2" Residue "LB PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LB TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LC ASP 214": "OD1" <-> "OD2" Residue "LC ASP 352": "OD1" <-> "OD2" Residue "LE ASP 120": "OD1" <-> "OD2" Residue "LE PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LF PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LH GLU 14": "OE1" <-> "OE2" Residue "LH ASP 17": "OD1" <-> "OD2" Residue "LH ASP 142": "OD1" <-> "OD2" Residue "LL ASP 138": "OD1" <-> "OD2" Residue "LM ASP 39": "OD1" <-> "OD2" Residue "LM GLU 99": "OE1" <-> "OE2" Residue "LN TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN GLU 160": "OE1" <-> "OE2" Residue "LO ASP 100": "OD1" <-> "OD2" Residue "LO GLU 144": "OE1" <-> "OE2" Residue "LO GLU 158": "OE1" <-> "OE2" Residue "LO GLU 162": "OE1" <-> "OE2" Residue "LP GLU 89": "OE1" <-> "OE2" Residue "LP ASP 108": "OD1" <-> "OD2" Residue "LP ASP 110": "OD1" <-> "OD2" Residue "LQ GLU 17": "OE1" <-> "OE2" Residue "LQ TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LS GLU 130": "OE1" <-> "OE2" Residue "LV ASP 100": "OD1" <-> "OD2" Residue "LX GLU 91": "OE1" <-> "OE2" Residue "LX ASP 148": "OD1" <-> "OD2" Residue "LY GLU 37": "OE1" <-> "OE2" Residue "LZ ASP 88": "OD1" <-> "OD2" Residue "LZ ASP 99": "OD1" <-> "OD2" Residue "LZ PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "La GLU 84": "OE1" <-> "OE2" Residue "Lc GLU 59": "OE1" <-> "OE2" Residue "Lc ASP 103": "OD1" <-> "OD2" Residue "Ld GLU 94": "OE1" <-> "OE2" Residue "Ld PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lf GLU 38": "OE1" <-> "OE2" Residue "Lg TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lg TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lh ASP 23": "OD1" <-> "OD2" Residue "Lh GLU 27": "OE1" <-> "OE2" Residue "Lh GLU 67": "OE1" <-> "OE2" Residue "Lh GLU 100": "OE1" <-> "OE2" Residue "Lh GLU 111": "OE1" <-> "OE2" Residue "Li GLU 46": "OE1" <-> "OE2" Residue "Li GLU 59": "OE1" <-> "OE2" Residue "Li ASP 66": "OD1" <-> "OD2" Residue "Li GLU 88": "OE1" <-> "OE2" Residue "Lj TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lj GLU 80": "OE1" <-> "OE2" Residue "Lk GLU 51": "OE1" <-> "OE2" Residue "Lk GLU 68": "OE1" <-> "OE2" Residue "Ll PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lo GLU 71": "OE1" <-> "OE2" Residue "Lp ASP 91": "OD1" <-> "OD2" Residue "Lz PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lz PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lz GLU 150": "OE1" <-> "OE2" Residue "Lz PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 144625 Number of models: 1 Model: "" Number of chains: 64 Chain: "1" Number of atoms: 3322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3322 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 408} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 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: 75376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3515, 75376 Classifications: {'RNA': 3515} Modifications used: {'5*END': 1, 'rna2p_pur': 353, 'rna2p_pyr': 199, 'rna3p_pur': 1581, 'rna3p_pyr': 1382} Link IDs: {'rna2p': 551, 'rna3p': 2963} Chain breaks: 23 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: 3748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3748 Classifications: {'peptide': 474} Link IDs: {'PTRANS': 10, 'TRANS': 463} Chain breaks: 3 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: 1634 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 201, 1626 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 186} Conformer: "B" Number of residues, atoms: 201, 1626 Classifications: {'peptide': 201} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 186} bond proxies already assigned to first conformer: 1648 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: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 204 Unusual residues: {' MG': 204} Classifications: {'undetermined': 204} Link IDs: {None: 203} 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: "LA" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 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 A0RFH SG CYSLg 46 86.126 103.935 66.730 1.00111.68 S ATOM A0RFY SG CYSLg 49 83.999 100.827 66.010 1.00101.16 S ATOM A0RN9 SG CYSLg 83 86.886 101.730 63.702 1.00 95.93 S ATOM A0RNT SG CYSLg 86 83.791 103.960 63.850 1.00103.67 S ATOM A0TDO SG CYSLj 19 123.894 123.109 106.823 1.00 63.88 S ATOM A0TEG SG CYSLj 22 125.550 123.448 110.191 1.00 78.11 S ATOM A0TGZ SG CYSLj 34 121.724 123.329 109.917 1.00 67.19 S ATOM A0THI SG CYSLj 37 123.627 126.389 108.693 1.00 65.94 S ATOM A0UQ0 SG CYSLm 96 79.263 74.143 202.217 1.00 90.45 S ATOM A0UQQ SG CYSLm 99 81.686 72.169 200.256 1.00103.44 S ATOM A0UT8 SG CYSLm 110 82.543 73.221 203.971 1.00 91.78 S ATOM A0UUG SG CYSLm 115 82.721 75.662 201.273 1.00107.37 S ATOM A0UZY SG CYSLo 12 75.511 180.142 166.252 1.00 70.61 S ATOM A0V0M SG CYSLo 15 74.224 183.667 166.704 1.00107.42 S ATOM A0VDN SG CYSLo 72 71.934 180.998 165.098 1.00 78.62 S ATOM A0VEO SG CYSLo 77 75.141 182.325 163.324 1.00 99.62 S ATOM A0VTQ SG CYSLp 39 70.292 100.805 73.704 1.00108.99 S ATOM A0VUD SG CYSLp 42 71.036 97.897 71.370 1.00 92.66 S ATOM A0VXR SG CYSLp 57 73.036 98.307 74.557 1.00 87.86 S ATOM A0VY7 SG CYSLp 60 73.569 100.760 71.763 1.00 93.71 S Residues with excluded nonbonded symmetry interactions: 929 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 917 not shown) Time building chain proxies: 56.45, per 1000 atoms: 0.39 Number of scatterers: 144625 At special positions: 0 Unit cell: (234.094, 229.732, 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 296 16.00 P 3781 15.00 Mg 220 11.99 O 37084 8.00 N 26974 7.00 C 76265 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: 58.97 Conformation dependent library (CDL) restraints added in 9.0 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 83 " pdb="ZN ZNLg 201 " - pdb=" SG CYSLg 49 " pdb=" ZNLj 102 " pdb="ZN ZNLj 102 " - pdb=" SG CYSLj 19 " pdb="ZN ZNLj 102 " - pdb=" SG CYSLj 37 " pdb="ZN ZNLj 102 " - pdb=" SG CYSLj 34 " 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 99 " pdb="ZN ZNLm 201 " - pdb=" SG CYSLm 96 " pdb="ZN ZNLm 201 " - pdb=" SG CYSLm 110 " pdb=" ZNLo 201 " pdb="ZN ZNLo 201 " - pdb=" SG CYSLo 12 " pdb="ZN ZNLo 201 " - pdb=" SG CYSLo 77 " 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 15500 Ramachandran restraints generated. 7750 Oldfield, 0 Emsley, 7750 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14676 Finding SS restraints... Secondary structure from input PDB file: 312 helices and 87 sheets defined 45.6% alpha, 14.1% beta 1137 base pairs and 1925 stacking pairs defined. Time for finding SS restraints: 50.04 Creating SS restraints... Processing helix chain '1' and resid 5 through 13 removed outlier: 3.505A pdb=" N ILE 1 9 " --> pdb=" O PHE 1 5 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS 1 10 " --> pdb=" O LEU 1 6 " (cutoff:3.500A) Proline residue: 1 11 - end of helix No H-bonds generated for 'chain '1' and resid 5 through 13' Processing helix chain '1' and resid 28 through 46 removed outlier: 4.340A pdb=" N VAL 1 32 " --> pdb=" O PHE 1 28 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE 1 42 " --> pdb=" O THR 1 38 " (cutoff:3.500A) Processing helix chain '1' and resid 61 through 69 removed outlier: 3.615A pdb=" N VAL 1 67 " --> pdb=" O TYR 1 63 " (cutoff:3.500A) 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: 3.799A pdb=" N LEU 1 149 " --> pdb=" O GLY 1 146 " (cutoff:3.500A) Processing helix chain '1' and resid 150 through 171 removed outlier: 3.974A pdb=" N GLN 1 154 " --> pdb=" O LEU 1 150 " (cutoff:3.500A) Processing helix chain '1' and resid 177 through 196 removed outlier: 3.600A pdb=" N ILE 1 187 " --> pdb=" O ILE 1 183 " (cutoff:3.500A) 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 296 removed outlier: 3.975A pdb=" N ILE 1 292 " --> pdb=" O ASN 1 288 " (cutoff:3.500A) Processing helix chain '1' and resid 296 through 312 removed outlier: 3.791A pdb=" N ASN 1 300 " --> pdb=" O ALA 1 296 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N MET 1 307 " --> pdb=" O VAL 1 303 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N LEU 1 308 " --> pdb=" O ILE 1 304 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER 1 309 " --> pdb=" O SER 1 305 " (cutoff:3.500A) Processing helix chain '1' and resid 339 through 346 removed outlier: 3.735A pdb=" N HIS 1 343 " --> pdb=" O GLY 1 339 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TYR 1 344 " --> pdb=" O GLY 1 340 " (cutoff:3.500A) Processing helix chain '1' and resid 357 through 383 removed outlier: 3.515A pdb=" N THR 1 378 " --> pdb=" O PHE 1 374 " (cutoff:3.500A) removed outlier: 4.456A 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: 4.345A pdb=" N VAL 1 410 " --> pdb=" O GLU 1 406 " (cutoff:3.500A) removed outlier: 4.498A 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: 3.859A pdb=" N VAL 1 451 " --> pdb=" O ILE 1 447 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N THR 1 452 " --> pdb=" O LEU 1 448 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE 1 453 " --> pdb=" O LEU 1 449 " (cutoff:3.500A) Processing helix chain '2' and resid 8 through 25 removed outlier: 3.521A pdb=" N LYS 2 16 " --> pdb=" O ARG 2 12 " (cutoff:3.500A) Processing helix chain '2' and resid 29 through 68 removed outlier: 5.003A pdb=" N ILE 2 50 " --> pdb=" O ILE 2 46 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY 2 51 " --> pdb=" O MET 2 47 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE 2 52 " --> pdb=" O GLY 2 48 " (cutoff:3.500A) Proline residue: 2 60 - end of helix removed outlier: 4.117A pdb=" N ASN 2 63 " --> pdb=" O ILE 2 59 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE 2 64 " --> pdb=" O PRO 2 60 " (cutoff:3.500A) Processing helix chain '3' and resid 70 through 95 removed outlier: 4.086A pdb=" N LEU 3 74 " --> pdb=" O PRO 3 70 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N LYS 3 92 " --> pdb=" O HIS 3 88 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N TYR 3 93 " --> pdb=" O ILE 3 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 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 removed outlier: 3.893A pdb=" N VAL A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 347 Processing helix chain 'A' and resid 348 through 350 No H-bonds generated for 'chain 'A' and resid 348 through 350' Processing helix chain 'A' and resid 365 through 375 Processing helix chain 'A' and resid 376 through 389 Processing helix chain 'A' and resid 417 through 427 Processing helix chain 'A' and resid 480 through 487 removed outlier: 4.418A pdb=" N PHE A 485 " --> pdb=" O GLU A 481 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU A 486 " --> pdb=" O ILE A 482 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG A 487 " --> pdb=" O GLU A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 523 removed outlier: 4.859A 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: 3.977A pdb=" N LYS A 534 " --> pdb=" O GLY A 530 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG A 535 " --> pdb=" O THR A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 577 removed outlier: 3.572A pdb=" N LEU A 569 " --> pdb=" O THR A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 593 removed outlier: 3.650A pdb=" N ASP A 592 " --> pdb=" O PHE A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 615 removed outlier: 3.621A pdb=" N LYS A 614 " --> pdb=" O LYS A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 632 removed outlier: 4.195A pdb=" N ALA A 622 " --> pdb=" O GLU A 618 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN A 631 " --> pdb=" O HIS A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 649 Processing helix chain 'A' and resid 657 through 679 Processing helix chain 'A' and resid 681 through 699 Processing helix chain 'A' and resid 708 through 717 removed outlier: 3.694A pdb=" N ALA A 714 " --> pdb=" O PRO A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 720 No H-bonds generated for 'chain 'A' and resid 718 through 720' Processing helix chain 'A' and resid 721 through 747 removed outlier: 4.066A pdb=" N GLN A 738 " --> pdb=" O LEU A 734 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS A 745 " --> pdb=" O SER A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 767 removed outlier: 3.840A pdb=" N GLU A 762 " --> pdb=" O ASP A 758 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASP A 763 " --> pdb=" O LYS A 759 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL A 764 " --> pdb=" O GLU A 760 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA A 765 " --> pdb=" O GLN A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 784 removed outlier: 3.751A pdb=" N LEU A 784 " --> pdb=" O LYS A 780 " (cutoff:3.500A) Processing helix chain 'K' and resid 12 through 16 removed outlier: 3.626A 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: 4.029A pdb=" N VAL K 37 " --> pdb=" O ASN K 33 " (cutoff:3.500A) removed outlier: 3.857A 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 197 Processing helix chain 'K' and resid 211 through 223 Processing helix chain 'LA' and resid 13 through 17 removed outlier: 3.977A pdb=" N ARGLA 17 " --> pdb=" O SERLA 14 " (cutoff:3.500A) Processing helix chain 'LA' and resid 33 through 39 Processing helix chain 'LA' and resid 173 through 177 Processing helix chain 'LA' and resid 181 through 191 removed outlier: 3.651A pdb=" N ALALA 191 " --> pdb=" O HISLA 187 " (cutoff:3.500A) Processing helix chain 'LA' and resid 205 through 209 removed outlier: 3.522A pdb=" N HISLA 209 " --> pdb=" O PROLA 206 " (cutoff:3.500A) Processing helix chain 'LB' and resid 13 through 17 removed outlier: 3.794A pdb=" N PHELB 16 " --> pdb=" O SERLB 13 " (cutoff:3.500A) removed outlier: 3.584A 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: 4.265A pdb=" N TRPLB 137 " --> pdb=" O TYRLB 133 " (cutoff:3.500A) removed outlier: 4.118A 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: 3.643A 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: 3.843A 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: 3.654A 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: 3.659A pdb=" N ILELC 180 " --> pdb=" O ALALC 176 " (cutoff:3.500A) Processing helix chain 'LC' and resid 192 through 197 removed outlier: 3.574A pdb=" N LYSLC 195 " --> pdb=" O GLYLC 192 " (cutoff:3.500A) Processing helix chain 'LC' and resid 216 through 223 removed outlier: 4.543A 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: 4.481A pdb=" N ASPLC 261 " --> pdb=" O PHELC 257 " (cutoff:3.500A) removed outlier: 4.346A 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: 3.924A pdb=" N ALALC 301 " --> pdb=" O GLULC 297 " (cutoff:3.500A) removed outlier: 3.523A 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: 4.281A 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: 3.985A pdb=" N ARGLD 35 " --> pdb=" O TYRLD 31 " (cutoff:3.500A) removed outlier: 3.576A 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: 4.056A 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 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: 3.696A pdb=" N GLNLE 256 " --> pdb=" O ALALE 252 " (cutoff:3.500A) Proline residue: LE 259 - end of helix removed outlier: 3.923A 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: 4.175A 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 238 through 248 removed outlier: 4.201A pdb=" N ARGLF 242 " --> pdb=" O ASPLF 238 " (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 102 removed outlier: 3.760A pdb=" N LYSLG 101 " --> pdb=" O LYSLG 97 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYRLG 102 " --> pdb=" O LEULG 98 " (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 163 through 167 Processing helix chain 'LG' and resid 169 through 178 Processing helix chain 'LG' and resid 186 through 194 removed outlier: 3.837A pdb=" N LEULG 190 " --> pdb=" O GLYLG 186 " (cutoff:3.500A) Processing helix chain 'LG' and resid 208 through 226 removed outlier: 4.439A pdb=" N GLYLG 213 " --> pdb=" O SERLG 209 " (cutoff:3.500A) removed outlier: 4.862A 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: 4.019A pdb=" N THRLH 72 " --> pdb=" O ALALH 68 " (cutoff:3.500A) Processing helix chain 'LH' and resid 116 through 120 Processing helix chain 'LH' and resid 150 through 165 Processing helix chain 'LI' and resid 5 through 9 Processing helix chain 'LI' and resid 42 through 46 removed outlier: 3.800A 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: 3.963A pdb=" N PHELI 157 " --> pdb=" O ARGLI 153 " (cutoff:3.500A) Processing helix chain 'LI' and resid 177 through 187 removed outlier: 4.173A pdb=" N GLULI 182 " --> pdb=" O ALALI 178 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ASPLI 183 " --> pdb=" O ASPLI 179 " (cutoff:3.500A) Processing helix chain 'LI' and resid 205 through 214 removed outlier: 3.933A pdb=" N TRPLI 209 " --> pdb=" O PROLI 205 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 10 through 14 removed outlier: 3.589A 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: 3.729A 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 21 removed outlier: 3.504A pdb=" N ARGLL 20 " --> pdb=" O ASPLL 17 " (cutoff:3.500A) Processing helix chain 'LL' and resid 27 through 47 Processing helix chain 'LL' and resid 78 through 85 Processing helix chain 'LL' and resid 87 through 95 removed outlier: 3.891A pdb=" N ARGLL 92 " --> pdb=" O LYSLL 88 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N THRLL 93 " --> pdb=" O LYSLL 89 " (cutoff:3.500A) Processing helix chain 'LL' and resid 106 through 123 Processing helix chain 'LL' and resid 139 through 146 Processing helix chain 'LL' and resid 170 through 176 Processing helix chain 'LL' and resid 177 through 202 removed outlier: 5.130A pdb=" N GLYLL 193 " --> pdb=" O ALALL 189 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ILELL 194 " --> pdb=" O ARGLL 190 " (cutoff:3.500A) Processing helix chain 'LM' and resid 41 through 44 removed outlier: 4.105A 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 removed outlier: 3.591A pdb=" N LYSLM 85 " --> pdb=" O ASPLM 81 " (cutoff:3.500A) 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: 3.653A pdb=" N SERLN 171 " --> pdb=" O ALALN 167 " (cutoff:3.500A) Processing helix chain 'LN' and resid 177 through 184 removed outlier: 4.130A pdb=" N HISLN 181 " --> pdb=" O HISLN 178 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N HISLN 182 " --> pdb=" O LYSLN 179 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THRLN 183 " --> pdb=" O PHELN 180 " (cutoff:3.500A) removed outlier: 3.719A 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: 3.589A 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: 4.351A pdb=" N LYSLO 114 " --> pdb=" O PROLO 110 " (cutoff:3.500A) Processing helix chain 'LO' and resid 120 through 123 Processing helix chain 'LO' and resid 124 through 129 Processing helix chain 'LO' and resid 138 through 146 Processing helix chain 'LO' and resid 149 through 185 Processing helix chain 'LO' and resid 189 through 199 Processing helix chain 'LP' and resid 10 through 12 No H-bonds generated for 'chain 'LP' and resid 10 through 12' Processing helix chain 'LP' and resid 25 through 37 Processing helix chain 'LP' and resid 40 through 53 Processing helix chain 'LP' and resid 70 through 76 Processing helix chain 'LP' and resid 84 through 106 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: 4.073A pdb=" N GLNLQ 45 " --> pdb=" O SERLQ 41 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHELQ 52 " --> pdb=" O LEULQ 48 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N METLQ 53 " --> pdb=" O LYSLQ 49 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 54 through 58 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: 3.553A pdb=" N GLYLQ 145 " --> pdb=" O PROLQ 142 " (cutoff:3.500A) removed outlier: 4.308A 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: 3.797A 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: 3.570A 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: 4.438A 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: 3.664A 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: 3.699A pdb=" N LEULU 83 " --> pdb=" O SERLU 79 " (cutoff:3.500A) Processing helix chain 'LV' and resid 71 through 74 removed outlier: 4.148A pdb=" N LYSLV 74 " --> pdb=" O GLULV 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'LV' and resid 71 through 74' 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 92 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: 3.779A 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: 3.958A 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: 3.606A 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: 4.053A 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: 3.806A pdb=" N SERLa 68 " --> pdb=" O LYSLa 64 " (cutoff:3.500A) Processing helix chain 'La' and resid 77 through 82 Processing helix chain 'La' and resid 83 through 93 removed outlier: 3.574A 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: 4.167A 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: 3.574A pdb=" N GLULb 70 " --> pdb=" O SERLb 66 " (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 40 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: 4.263A pdb=" N METLe 90 " --> pdb=" O VALLe 87 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASNLe 92 " --> pdb=" O LEULe 89 " (cutoff:3.500A) Processing helix chain 'Le' and resid 104 through 119 removed outlier: 3.664A pdb=" N ALALe 110 " --> pdb=" O LYSLe 106 " (cutoff:3.500A) Processing helix chain 'Lf' and resid 35 through 39 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: 4.214A 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: 3.797A pdb=" N ILELh 47 " --> pdb=" O LYSLh 43 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ARGLh 48 " --> pdb=" O LEULh 44 " (cutoff:3.500A) removed outlier: 4.141A 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: 3.714A pdb=" N GLYLj 9 " --> pdb=" O THRLj 5 " (cutoff:3.500A) Processing helix chain 'Lj' and resid 50 through 58 removed outlier: 3.646A pdb=" N ASNLj 57 " --> pdb=" O ALALj 53 " (cutoff:3.500A) Processing helix chain 'Lj' and resid 64 through 75 removed outlier: 4.028A pdb=" N ILELj 69 " --> pdb=" O ARGLj 65 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARGLj 75 " --> pdb=" O TYRLj 71 " (cutoff:3.500A) Processing helix chain 'Lk' and resid 7 through 17 removed outlier: 3.508A pdb=" N PHELk 11 " --> pdb=" O GLULk 7 " (cutoff:3.500A) 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: 3.719A pdb=" N ARGLl 28 " --> pdb=" O GLNLl 25 " (cutoff:3.500A) Processing helix chain 'Lm' and resid 79 through 91 removed outlier: 3.723A 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: 3.736A pdb=" N LYSLp 13 " --> pdb=" O ILELp 10 " (cutoff:3.500A) Processing helix chain 'Lp' and resid 19 through 35 removed outlier: 3.878A pdb=" N LYSLp 28 " --> pdb=" O LYSLp 24 " (cutoff:3.500A) removed outlier: 3.913A 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: 3.805A 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: 3.835A pdb=" N ALALz 13 " --> pdb=" O THRLz 9 " (cutoff:3.500A) Processing helix chain 'Lz' and resid 21 through 25 removed outlier: 3.750A 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 116 through 118 No H-bonds generated for 'chain 'Lz' and resid 116 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 154 Processing helix chain 'Lz' and resid 175 through 194 removed outlier: 3.820A pdb=" N TYRLz 181 " --> pdb=" O ASPLz 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '1' and resid 278 through 281 Processing sheet with id=AA2, first strand: chain 'A' and resid 267 through 268 removed outlier: 3.504A pdb=" N LEU A 294 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 322 through 324 Processing sheet with id=AA4, first strand: chain 'K' and resid 2 through 5 removed outlier: 6.330A pdb=" N VAL K 3 " --> pdb=" O CYS K 206 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 17 through 19 Processing sheet with id=AA6, first strand: chain 'K' and resid 64 through 65 removed outlier: 3.831A pdb=" N VAL K 64 " --> pdb=" O LEU K 71 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 108 through 110 Processing sheet with id=AA8, first strand: chain 'K' and resid 153 through 154 Processing sheet with id=AA9, first strand: chain 'LA' and resid 71 through 77 removed outlier: 6.758A pdb=" N LEULA 58 " --> pdb=" O ILELA 48 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ILELA 48 " --> pdb=" O LEULA 58 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LYSLA 60 " --> pdb=" O LYSLA 46 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ARGLA 64 " --> pdb=" O LYSLA 42 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N LYSLA 42 " --> pdb=" O ARGLA 64 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'LA' and resid 101 through 103 removed outlier: 6.774A pdb=" N ARGLA 147 " --> pdb=" O ILELA 137 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N HISLA 139 " --> pdb=" O LYSLA 145 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LYSLA 145 " --> pdb=" O HISLA 139 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'LB' and resid 42 through 43 removed outlier: 4.974A pdb=" N ILELB 160 " --> pdb=" O VALLB 185 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N HISLB 165 " --> pdb=" O VALLB 86 " (cutoff:3.500A) removed outlier: 5.415A 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: 6.194A pdb=" N VALLB 93 " --> pdb=" O THRLB 101 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N THRLB 101 " --> pdb=" O VALLB 93 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THRLB 95 " --> pdb=" O LEULB 99 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N LEULB 99 " --> pdb=" O THRLB 95 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'LB' and resid 42 through 43 removed outlier: 4.974A pdb=" N ILELB 160 " --> pdb=" O VALLB 185 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N HISLB 165 " --> pdb=" O VALLB 86 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N VALLB 86 " --> pdb=" O HISLB 165 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'LB' and resid 365 through 368 removed outlier: 6.461A pdb=" N VALLB 57 " --> pdb=" O LYSLB 366 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ILELB 368 " --> pdb=" O HISLB 55 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N HISLB 55 " --> pdb=" O ILELB 368 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N VALLB 344 " --> pdb=" O VALLB 222 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N VALLB 222 " --> pdb=" O VALLB 344 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ILELB 217 " --> pdb=" O ASNLB 281 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ILELB 284 " --> pdb=" O LYSLB 334 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LYSLB 334 " --> pdb=" O ILELB 284 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYSLB 286 " --> pdb=" O METLB 332 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLULB 80 " --> pdb=" O LYSLB 50 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LYSLB 50 " --> pdb=" O GLULB 80 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'LB' and resid 225 through 229 Processing sheet with id=AB6, first strand: chain 'LB' and resid 292 through 293 Processing sheet with id=AB7, first strand: chain 'LC' and resid 7 through 11 removed outlier: 6.569A pdb=" N ILELC 8 " --> pdb=" O LYSLC 20 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LYSLC 20 " --> pdb=" O ILELC 8 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VALLC 10 " --> pdb=" O SERLC 18 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'LC' and resid 64 through 65 Processing sheet with id=AB9, 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: 6.250A pdb=" N ILELC 209 " --> pdb=" O LEULC 230 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'LC' and resid 188 through 189 Processing sheet with id=AC2, first strand: chain 'LD' and resid 73 through 79 removed outlier: 5.851A pdb=" N ILELD 74 " --> pdb=" O TYRLD 66 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N TYRLD 66 " --> pdb=" O ILELD 74 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N CYSLD 76 " --> pdb=" O ILELD 64 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'LE' and resid 49 through 51 removed outlier: 3.528A pdb=" N VALLE 51 " --> pdb=" O ILELE 54 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'LE' and resid 91 through 95 Processing sheet with id=AC5, first strand: chain 'LE' and resid 187 through 189 removed outlier: 6.720A pdb=" N LEULE 174 " --> pdb=" O LEULE 165 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N THRLE 148 " --> pdb=" O PHELE 164 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N THRLE 199 " --> pdb=" O ILELE 149 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N ILELE 151 " --> pdb=" O THRLE 197 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N THRLE 197 " --> pdb=" O ILELE 151 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'LF' and resid 81 through 83 removed outlier: 3.599A pdb=" N HISLT 139 " --> pdb=" O VALLF 83 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'LF' and resid 211 through 212 removed outlier: 4.009A pdb=" N ASNLF 119 " --> pdb=" O ARGLF 94 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILELF 140 " --> pdb=" O GLYLF 234 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N ARGLF 236 " --> pdb=" O ILELF 140 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N TRPLF 142 " --> pdb=" O ARGLF 236 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'LF' and resid 159 through 162 Processing sheet with id=AC9, first strand: chain 'LG' and resid 75 through 76 Processing sheet with id=AD1, first strand: chain 'LG' and resid 137 through 138 Processing sheet with id=AD2, first strand: chain 'LH' and resid 3 through 11 removed outlier: 7.241A pdb=" N ILELH 4 " --> pdb=" O TRPLH 61 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARGLH 54 " --> pdb=" O LEULH 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'LH' and resid 17 through 21 removed outlier: 3.700A pdb=" N THRLH 24 " --> pdb=" O LYSLH 21 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'LH' and resid 132 through 136 removed outlier: 6.858A pdb=" N ARGLH 89 " --> pdb=" O LYSLH 184 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LYSLH 184 " --> pdb=" O ARGLH 89 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LYSLH 91 " --> pdb=" O SERLH 182 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'LH' and resid 103 through 106 Processing sheet with id=AD6, first strand: chain 'LI' and resid 35 through 37 removed outlier: 6.708A pdb=" N METLI 52 " --> pdb=" O ILELI 135 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N SERLI 137 " --> pdb=" O GLYLI 50 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLYLI 50 " --> pdb=" O SERLI 137 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ARGLI 139 " --> pdb=" O LEULI 48 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEULI 48 " --> pdb=" O ARGLI 139 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'LI' and resid 58 through 61 removed outlier: 6.702A pdb=" N ILELI 97 " --> pdb=" O GLNLI 123 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N THRLI 125 " --> pdb=" O HISLI 95 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N HISLI 95 " --> pdb=" O THRLI 125 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'LI' and resid 190 through 192 Processing sheet with id=AD9, first strand: chain 'LJ' and resid 49 through 52 removed outlier: 5.270A pdb=" N ILELJ 17 " --> pdb=" O GLYLJ 135 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLYLJ 135 " --> pdb=" O ILELJ 17 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'LJ' and resid 93 through 95 removed outlier: 6.966A pdb=" N LEULJ 94 " --> pdb=" O LEULJ 175 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'LL' and resid 23 through 24 removed outlier: 6.306A pdb=" N ALALL 23 " --> pdb=" O LEULN 200 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'LL' and resid 58 through 60 Processing sheet with id=AE4, first strand: chain 'LL' and resid 76 through 77 removed outlier: 5.657A pdb=" N PHELL 76 " --> pdb=" O ASPLL 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'LL' and resid 124 through 126 Processing sheet with id=AE6, first strand: chain 'LL' and resid 167 through 168 removed outlier: 3.634A pdb=" N ARGLL 167 " --> pdb=" O ALALa 98 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'LM' and resid 7 through 8 Processing sheet with id=AE8, first strand: chain 'LM' and resid 45 through 51 removed outlier: 5.245A pdb=" N ARGLM 46 " --> pdb=" O GLYLM 40 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N GLYLM 40 " --> pdb=" O ARGLM 46 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ASPLM 39 " --> pdb=" O ILELM 27 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ILELM 27 " --> pdb=" O ASPLM 39 " (cutoff:3.500A) removed outlier: 4.523A 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=AE9, first strand: chain 'LN' and resid 36 through 39 removed outlier: 4.396A pdb=" N ILELN 61 " --> pdb=" O ALALN 39 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N TYRLN 127 " --> pdb=" O GLULN 123 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLULN 123 " --> pdb=" O TYRLN 127 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N PHELN 129 " --> pdb=" O VALLN 121 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASNLN 117 " --> pdb=" O ILELN 133 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILELN 135 " --> pdb=" O VALLN 115 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N VALLN 115 " --> pdb=" O ILELN 135 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'LO' and resid 6 through 10 removed outlier: 6.506A pdb=" N VALLO 33 " --> pdb=" O LYSLO 103 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'LO' and resid 42 through 44 Processing sheet with id=AF3, first strand: chain 'LP' and resid 14 through 22 removed outlier: 3.635A pdb=" N ASNLP 21 " --> pdb=" O CYSLP 144 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N CYSLP 144 " --> pdb=" O ASNLP 21 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N HISLP 145 " --> pdb=" O VALLP 119 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VALLP 119 " --> pdb=" O HISLP 145 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLULP 147 " --> pdb=" O ILELP 117 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ILELP 117 " --> pdb=" O GLULP 147 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILELP 149 " --> pdb=" O GLULP 115 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'LP' and resid 58 through 59 Processing sheet with id=AF5, first strand: chain 'LP' and resid 128 through 131 removed outlier: 3.758A pdb=" N ARGLP 135 " --> pdb=" O ARGLP 131 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'LQ' and resid 61 through 62 removed outlier: 4.007A pdb=" N LEULQ 103 " --> pdb=" O VALLQ 82 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N GLYLQ 84 " --> pdb=" O LEULQ 103 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N VALLQ 105 " --> pdb=" O GLYLQ 84 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILELQ 86 " --> pdb=" O VALLQ 105 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'LQ' and resid 61 through 62 removed outlier: 6.405A pdb=" N THRLQ 79 " --> pdb=" O VALLQ 137 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LEULQ 139 " --> pdb=" O THRLQ 79 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N VALLQ 81 " --> pdb=" O LEULQ 139 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'LQ' and resid 180 through 181 removed outlier: 3.644A pdb=" N TYRLQ 186 " --> pdb=" O ARGLQ 181 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'LR' and resid 22 through 24 removed outlier: 3.504A pdb=" N ILELR 51 " --> pdb=" O TRPLR 23 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'LS' and resid 59 through 66 removed outlier: 5.210A pdb=" N ILELS 61 " --> pdb=" O ARGLS 15 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ARGLS 15 " --> pdb=" O ILELS 61 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'LS' and resid 90 through 99 removed outlier: 6.866A pdb=" N ARGLS 83 " --> pdb=" O ILELS 126 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ILELS 126 " --> pdb=" O ARGLS 83 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ASPLS 85 " --> pdb=" O ILELS 124 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILELS 124 " --> pdb=" O ASPLS 85 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'LT' and resid 84 through 92 removed outlier: 6.498A pdb=" N VALLT 75 " --> pdb=" O VALLT 64 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N VALLT 64 " --> pdb=" O VALLT 75 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N ASNLT 77 " --> pdb=" O GLYLT 62 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N GLYLT 62 " --> pdb=" O ASNLT 77 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'LU' and resid 62 through 66 removed outlier: 9.053A pdb=" N TYRLU 110 " --> pdb=" O LYSLU 20 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THRLU 22 " --> pdb=" O TYRLU 110 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N LEULU 112 " --> pdb=" O THRLU 22 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ASPLU 24 " --> pdb=" O LEULU 112 " (cutoff:3.500A) removed outlier: 9.241A pdb=" N TYRLU 114 " --> pdb=" O ASPLU 24 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'LU' and resid 48 through 49 Processing sheet with id=AG6, first strand: chain 'LV' and resid 20 through 21 Processing sheet with id=AG7, first strand: chain 'LV' and resid 25 through 28 removed outlier: 6.760A pdb=" N METLV 62 " --> pdb=" O ILELV 40 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N VALLV 42 " --> pdb=" O METLV 60 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N METLV 60 " --> pdb=" O VALLV 42 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N VALLV 81 " --> pdb=" O VALLV 104 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VALLV 104 " --> pdb=" O VALLV 81 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N GLYLV 103 " --> pdb=" O VALLV 25 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ASNLV 27 " --> pdb=" O GLYLV 103 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ILELV 105 " --> pdb=" O ASNLV 27 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'LV' and resid 88 through 89 removed outlier: 6.223A pdb=" N PHELV 95 " --> pdb=" O ARGLW 20 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ALALW 22 " --> pdb=" O PHELV 95 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TYRLV 97 " --> pdb=" O ALALW 22 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'LV' and resid 120 through 121 Processing sheet with id=AH1, first strand: chain 'LW' and resid 4 through 5 removed outlier: 3.527A pdb=" N GLULW 4 " --> pdb=" O ILELW 13 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'LX' and resid 77 through 80 removed outlier: 3.712A pdb=" N LYSLX 134 " --> pdb=" O VALLX 100 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'LY' and resid 31 through 33 Processing sheet with id=AH4, first strand: chain 'LY' and resid 79 through 82 removed outlier: 6.812A pdb=" N GLULY 54 " --> pdb=" O THRLY 107 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'LY' and resid 86 through 88 Processing sheet with id=AH6, first strand: chain 'LZ' and resid 69 through 76 removed outlier: 6.501A pdb=" N LYSLZ 69 " --> pdb=" O ASPLZ 47 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N HISLZ 40 " --> pdb=" O ASNLZ 28 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ASNLZ 28 " --> pdb=" O HISLZ 40 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEULZ 42 " --> pdb=" O VALLZ 26 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N LYSLZ 22 " --> pdb=" O ILELZ 46 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LYSLZ 9 " --> pdb=" O ILELZ 25 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N TYRLZ 85 " --> pdb=" O VALLZ 10 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N LEULZ 12 " --> pdb=" O THRLZ 83 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N THRLZ 83 " --> pdb=" O LEULZ 12 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'La' and resid 72 through 74 removed outlier: 6.325A pdb=" N VALLa 73 " --> pdb=" O LEULa 112 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'La' and resid 100 through 102 removed outlier: 6.699A pdb=" N ILELa 101 " --> pdb=" O LYSLa 125 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VALLa 124 " --> pdb=" O VALLa 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH8 Processing sheet with id=AH9, first strand: chain 'Lc' and resid 26 through 29 removed outlier: 6.267A pdb=" N LYSLc 26 " --> pdb=" O ILELc 97 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'Ld' and resid 62 through 64 removed outlier: 3.507A pdb=" N LEULd 105 " --> pdb=" O SERLd 89 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'Le' and resid 75 through 79 removed outlier: 5.715A pdb=" N ARGLe 75 " --> pdb=" O CYSLe 96 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLULe 98 " --> pdb=" O ARGLe 75 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N PHELe 77 " --> pdb=" O GLULe 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI2 Processing sheet with id=AI3, first strand: chain 'Lf' and resid 7 through 16 removed outlier: 9.862A pdb=" N SERLf 7 " --> pdb=" O ILELf 30 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ILELf 30 " --> pdb=" O SERLf 7 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ALALf 9 " --> pdb=" O LEULf 28 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N LEULf 28 " --> pdb=" O ALALf 9 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N PHELf 11 " --> pdb=" O ALALf 26 " (cutoff:3.500A) removed outlier: 9.521A pdb=" N ALALf 26 " --> pdb=" O PHELf 11 " (cutoff:3.500A) removed outlier: 11.571A pdb=" N GLYLf 13 " --> pdb=" O HISLf 24 " (cutoff:3.500A) removed outlier: 8.871A pdb=" N HISLf 24 " --> pdb=" O GLYLf 13 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYSLf 15 " --> pdb=" O ARGLf 22 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N HISLf 24 " --> pdb=" O PHELf 88 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N PHELf 88 " --> pdb=" O HISLf 24 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LYSLf 87 " --> pdb=" O VALLf 74 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N VALLf 74 " --> pdb=" O LYSLf 87 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LYSLf 66 " --> pdb=" O ALALf 53 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N VALLf 50 " --> pdb=" O ARGLf 100 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ARGLf 100 " --> pdb=" O VALLf 50 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'Lg' and resid 20 through 24 Processing sheet with id=AI5, first strand: chain 'Lj' and resid 16 through 17 Processing sheet with id=AI6, first strand: chain 'Lk' and resid 3 through 5 removed outlier: 4.332A pdb=" N VALLk 46 " --> pdb=" O ILELk 5 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SERLk 22 " --> pdb=" O ARGLk 37 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VALLk 23 " --> pdb=" O LYSLk 67 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'Lm' and resid 102 through 103 Processing sheet with id=AI8, first strand: chain 'Lo' and resid 3 through 4 Processing sheet with id=AI9, first strand: chain 'Lo' and resid 7 through 11 removed outlier: 4.093A pdb=" N ILELo 66 " --> pdb=" O ILELo 85 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'Lp' and resid 47 through 51 removed outlier: 6.874A pdb=" N ILELp 54 " --> pdb=" O ARGLp 50 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'Lr' and resid 17 through 20 Processing sheet with id=AJ3, first strand: chain 'Lr' and resid 49 through 53 Processing sheet with id=AJ4, first strand: chain 'Lz' and resid 164 through 171 removed outlier: 6.556A pdb=" N CYSLz 164 " --> pdb=" O LEULz 38 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEULz 38 " --> pdb=" O CYSLz 164 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ALALz 166 " --> pdb=" O ILELz 36 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ILELz 36 " --> pdb=" O ALALz 166 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ALALz 168 " --> pdb=" O LEULz 34 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEULz 34 " --> pdb=" O ALALz 168 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'Lz' and resid 50 through 53 Processing sheet with id=AJ6, first strand: chain 'Lz' and resid 65 through 68 removed outlier: 3.946A pdb=" N SERLz 113 " --> pdb=" O LEULz 68 " (cutoff:3.500A) 2834 hydrogen bonds defined for protein. 8018 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3020 hydrogen bonds 5234 hydrogen bond angles 0 basepair planarities 1137 basepair parallelities 1925 stacking parallelities Total time for adding SS restraints: 299.71 Time building geometry restraints manager: 63.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 31492 1.34 - 1.46: 54786 1.46 - 1.58: 60875 1.58 - 1.70: 7535 1.70 - 1.82: 470 Bond restraints: 155158 Sorted by residual: bond pdb=" N VAL A 306 " pdb=" CA VAL A 306 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.43e+00 bond pdb=" N SER A 334 " pdb=" CA SER A 334 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.17e-02 7.31e+03 8.41e+00 bond pdb=" N LEU A 333 " pdb=" CA LEU A 333 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.25e-02 6.40e+03 7.61e+00 bond pdb=" N ASN A 264 " pdb=" CA ASN A 264 " ideal model delta sigma weight residual 1.458 1.491 -0.034 1.28e-02 6.10e+03 6.94e+00 bond pdb=" N TYR A 266 " pdb=" CA TYR A 266 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.32e-02 5.74e+03 6.68e+00 ... (remaining 155153 not shown) Histogram of bond angle deviations from ideal: 98.85 - 105.88: 20671 105.88 - 112.90: 88693 112.90 - 119.93: 54662 119.93 - 126.95: 54330 126.95 - 133.98: 9419 Bond angle restraints: 227775 Sorted by residual: angle pdb=" CA GLYLz 51 " pdb=" C GLYLz 51 " pdb=" O GLYLz 51 " ideal model delta sigma weight residual 121.61 117.22 4.39 1.05e+00 9.07e-01 1.75e+01 angle pdb=" N LEU A 305 " pdb=" CA LEU A 305 " pdb=" C LEU A 305 " ideal model delta sigma weight residual 112.89 108.10 4.79 1.24e+00 6.50e-01 1.49e+01 angle pdb=" N THR A 331 " pdb=" CA THR A 331 " pdb=" C THR A 331 " ideal model delta sigma weight residual 112.54 108.06 4.48 1.22e+00 6.72e-01 1.35e+01 angle pdb=" CA TYR A 266 " pdb=" C TYR A 266 " pdb=" O TYR A 266 " ideal model delta sigma weight residual 121.51 117.47 4.04 1.12e+00 7.97e-01 1.30e+01 angle pdb=" N VALLB 210 " pdb=" CA VALLB 210 " pdb=" C VALLB 210 " ideal model delta sigma weight residual 112.96 109.38 3.58 1.00e+00 1.00e+00 1.28e+01 ... (remaining 227770 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 89286 35.45 - 70.90: 9449 70.90 - 106.35: 1225 106.35 - 141.81: 15 141.81 - 177.26: 1 Dihedral angle restraints: 99976 sinusoidal: 77230 harmonic: 22746 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 232.00 54.74 177.26 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 97.25 102.75 1 1.50e+01 4.44e-03 5.21e+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 200.00 103.81 96.19 1 1.50e+01 4.44e-03 4.73e+01 ... (remaining 99973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 25704 0.044 - 0.087: 1845 0.087 - 0.131: 739 0.131 - 0.174: 26 0.174 - 0.218: 2 Chirality restraints: 28316 Sorted by residual: chirality pdb=" CG LEU 1 118 " pdb=" CB LEU 1 118 " pdb=" CD1 LEU 1 118 " pdb=" CD2 LEU 1 118 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA VAL A 306 " pdb=" N VAL A 306 " pdb=" C VAL A 306 " pdb=" CB VAL A 306 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.00e+00 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 0.17 2.00e-01 2.50e+01 7.43e-01 ... (remaining 28313 not shown) Planarity restraints: 14705 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 8 39 " -0.041 2.00e-02 2.50e+03 1.72e-02 8.91e+00 pdb=" N9 G 8 39 " 0.041 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 " -0.011 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 " 0.006 2.00e-02 2.50e+03 pdb=" C4 G 8 39 " 0.006 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 1.55e-02 5.40e+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 " -0.003 2.00e-02 2.50e+03 pdb=" C4 U 52580 " -0.004 2.00e-02 2.50e+03 pdb=" O4 U 52580 " -0.008 2.00e-02 2.50e+03 pdb=" C5 U 52580 " 0.001 2.00e-02 2.50e+03 pdb=" C6 U 52580 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 52581 " -0.028 2.00e-02 2.50e+03 1.34e-02 4.96e+00 pdb=" N9 A 52581 " 0.034 2.00e-02 2.50e+03 pdb=" C8 A 52581 " 0.000 2.00e-02 2.50e+03 pdb=" N7 A 52581 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A 52581 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A 52581 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A 52581 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A 52581 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A 52581 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A 52581 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A 52581 " 0.000 2.00e-02 2.50e+03 ... (remaining 14702 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 816 2.46 - 3.07: 89922 3.07 - 3.68: 261075 3.68 - 4.29: 390748 4.29 - 4.90: 560233 Nonbonded interactions: 1302794 Sorted by model distance: nonbonded pdb=" OP2 C 53791 " pdb="MG MG 55124 " model vdw 1.849 2.170 nonbonded pdb=" OP2 G 51329 " pdb="MG MG 55272 " model vdw 1.864 2.170 nonbonded pdb=" O4 U 51636 " pdb="MG MG 55232 " model vdw 1.864 2.170 nonbonded pdb=" OP2 A 8 17 " pdb="MG MG 8 201 " model vdw 1.887 2.170 nonbonded pdb=" OP1 A 51534 " pdb="MG MGLj 103 " model vdw 1.889 2.170 ... (remaining 1302789 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=0.95 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: 6.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.140 Extract box with map and model: 34.450 Check model and map are aligned: 1.570 Set scattering table: 1.050 Process input model: 592.930 Find NCS groups from input model: 3.440 Set up NCS constraints: 0.390 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: 0.020 Load rotamer database and sin/cos tables:2.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 642.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 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 0.053 155158 Z= 0.105 Angle : 0.392 8.204 227775 Z= 0.211 Chirality : 0.030 0.218 28316 Planarity : 0.003 0.052 14705 Dihedral : 22.124 177.256 85300 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.35 % Favored : 97.63 % Rotamer: Outliers : 0.09 % Allowed : 13.35 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % 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: 2.20 (0.10), residues: 7750 helix: 2.69 (0.10), residues: 3087 sheet: 0.49 (0.17), residues: 1008 loop : 0.79 (0.11), residues: 3655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPLB 196 HIS 0.010 0.000 HIS A 725 PHE 0.013 0.001 PHE A 666 TYR 0.013 0.001 TYR A 266 ARG 0.005 0.000 ARGLZ 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15500 Ramachandran restraints generated. 7750 Oldfield, 0 Emsley, 7750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15500 Ramachandran restraints generated. 7750 Oldfield, 0 Emsley, 7750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1124 residues out of total 6768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1118 time to evaluate : 7.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 28 PHE cc_start: -0.1917 (m-80) cc_final: -0.2136 (t80) REVERT: 1 345 LEU cc_start: -0.0070 (mt) cc_final: -0.0295 (pt) REVERT: A 336 GLU cc_start: 0.0753 (tt0) cc_final: 0.0426 (tp30) REVERT: A 341 LEU cc_start: -0.1451 (tp) cc_final: -0.1715 (pp) REVERT: A 383 LYS cc_start: 0.0553 (mmmm) cc_final: 0.0350 (mtmm) REVERT: A 443 TYR cc_start: 0.7174 (t80) cc_final: 0.6774 (t80) REVERT: K 94 ILE cc_start: 0.7923 (tp) cc_final: 0.7631 (mt) REVERT: LA 122 ASP cc_start: 0.8773 (t0) cc_final: 0.8472 (t0) REVERT: LB 114 CYS cc_start: 0.9299 (t) cc_final: 0.9033 (t) REVERT: LC 288 ASP cc_start: 0.7990 (t0) cc_final: 0.7516 (t70) REVERT: LD 235 MET cc_start: 0.8878 (ptm) cc_final: 0.8453 (ppp) REVERT: LE 245 GLN cc_start: 0.8331 (tp40) cc_final: 0.8012 (tp40) REVERT: LE 249 ASP cc_start: 0.8157 (m-30) cc_final: 0.7805 (m-30) REVERT: LE 250 GLN cc_start: 0.8651 (tp40) cc_final: 0.8247 (tp-100) REVERT: LF 64 MET cc_start: 0.8379 (mtp) cc_final: 0.8063 (mtm) REVERT: LF 67 THR cc_start: 0.8837 (m) cc_final: 0.8502 (p) REVERT: LF 232 ASP cc_start: 0.8303 (m-30) cc_final: 0.8001 (m-30) REVERT: LG 44 ASP cc_start: 0.8668 (t0) cc_final: 0.8397 (m-30) REVERT: LG 160 ASP cc_start: 0.8303 (p0) cc_final: 0.8103 (p0) REVERT: LH 110 SER cc_start: 0.8738 (t) cc_final: 0.8443 (t) REVERT: LH 140 GLN cc_start: 0.7994 (mm110) cc_final: 0.7550 (mt0) REVERT: LH 150 ASP cc_start: 0.8029 (t0) cc_final: 0.7818 (t0) REVERT: LI 35 ASP cc_start: 0.8085 (m-30) cc_final: 0.7795 (m-30) REVERT: LI 207 ASP cc_start: 0.8933 (t70) cc_final: 0.8674 (m-30) REVERT: LJ 97 ASN cc_start: 0.8072 (p0) cc_final: 0.7721 (p0) REVERT: LL 175 ASN cc_start: 0.9025 (m-40) cc_final: 0.8650 (m110) REVERT: LO 87 MET cc_start: 0.8532 (mtt) cc_final: 0.8317 (mtt) REVERT: LO 108 ILE cc_start: 0.9269 (mt) cc_final: 0.9059 (mt) REVERT: LT 38 ASP cc_start: 0.8342 (m-30) cc_final: 0.8057 (m-30) REVERT: LU 39 PHE cc_start: 0.8241 (t80) cc_final: 0.7911 (t80) REVERT: LU 44 GLN cc_start: 0.8326 (mt0) cc_final: 0.7467 (mt0) REVERT: LV 30 ASP cc_start: 0.7734 (p0) cc_final: 0.7017 (p0) REVERT: LW 52 THR cc_start: 0.8883 (m) cc_final: 0.8446 (p) REVERT: LX 95 THR cc_start: 0.8451 (m) cc_final: 0.7983 (p) REVERT: LY 93 THR cc_start: 0.8656 (m) cc_final: 0.8363 (m) REVERT: LZ 85 TYR cc_start: 0.8668 (m-80) cc_final: 0.8243 (m-80) REVERT: Lb 119 CYS cc_start: 0.8001 (t) cc_final: 0.7606 (p) REVERT: Lc 17 ARG cc_start: 0.8578 (ptp-170) cc_final: 0.8299 (ptp90) REVERT: Lc 22 MET cc_start: 0.7959 (tpp) cc_final: 0.7538 (mmm) REVERT: Lh 107 GLN cc_start: 0.8903 (tp40) cc_final: 0.8695 (tp40) REVERT: Lk 13 LEU cc_start: 0.8581 (mm) cc_final: 0.8225 (mm) REVERT: Lm 88 LYS cc_start: 0.8346 (tttp) cc_final: 0.7992 (tttp) REVERT: Lr 36 ASN cc_start: 0.8769 (t0) cc_final: 0.8525 (t0) outliers start: 6 outliers final: 2 residues processed: 1119 average time/residue: 1.2293 time to fit residues: 2476.5034 Evaluate side-chains 862 residues out of total 6768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 860 time to evaluate : 7.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 307 MET Chi-restraints excluded: chain LC residue 352 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1142 random chunks: chunk 964 optimal weight: 20.0000 chunk 865 optimal weight: 10.0000 chunk 480 optimal weight: 50.0000 chunk 295 optimal weight: 10.0000 chunk 583 optimal weight: 10.0000 chunk 462 optimal weight: 8.9990 chunk 895 optimal weight: 9.9990 chunk 346 optimal weight: 10.0000 chunk 544 optimal weight: 8.9990 chunk 666 optimal weight: 6.9990 chunk 1037 optimal weight: 20.0000 overall best weight: 8.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 10 ASN K 157 GLN ** LB 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 110 GLN LG 195 HIS LH 163 GLN ** LI 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LI 133 GLN LJ 42 GLN LL 113 ASN LL 149 GLN LN 29 GLN LN 87 HIS LO 72 HIS LP 97 ASN LP 137 ASN LS 50 GLN LS 125 GLN LT 54 HIS ** LT 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LT 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LU 38 ASN ** LX 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LX 93 ASN LZ 78 ASN LZ 132 GLN Lb 50 ASN Lb 60 ASN Lg 28 ASN Ll 19 GLN Lz 73 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.150 155158 Z= 0.412 Angle : 0.624 10.287 227775 Z= 0.319 Chirality : 0.039 0.287 28316 Planarity : 0.005 0.088 14705 Dihedral : 22.457 178.422 68791 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.05 % Favored : 96.94 % Rotamer: Outliers : 2.99 % Allowed : 14.22 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % 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: 1.36 (0.10), residues: 7750 helix: 1.89 (0.09), residues: 3082 sheet: 0.38 (0.17), residues: 978 loop : 0.31 (0.10), residues: 3690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRPLT 125 HIS 0.010 0.002 HISLa 40 PHE 0.048 0.002 PHE A 485 TYR 0.031 0.002 TYR K 35 ARG 0.018 0.001 ARGLG 117 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15500 Ramachandran restraints generated. 7750 Oldfield, 0 Emsley, 7750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15500 Ramachandran restraints generated. 7750 Oldfield, 0 Emsley, 7750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1044 residues out of total 6768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 842 time to evaluate : 7.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 1 MET cc_start: 0.4999 (mpp) cc_final: 0.4103 (mmt) REVERT: K 10 ASN cc_start: 0.7264 (OUTLIER) cc_final: 0.7051 (t0) REVERT: K 209 ASP cc_start: 0.5548 (OUTLIER) cc_final: 0.5251 (t0) REVERT: LA 122 ASP cc_start: 0.8892 (t0) cc_final: 0.8645 (t0) REVERT: LB 200 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.8502 (mtt90) REVERT: LB 382 MET cc_start: 0.8515 (ttt) cc_final: 0.8172 (mtm) REVERT: LC 288 ASP cc_start: 0.8652 (t0) cc_final: 0.8418 (t0) REVERT: LD 235 MET cc_start: 0.8919 (ptm) cc_final: 0.8707 (ptt) REVERT: LE 62 MET cc_start: 0.9453 (mmm) cc_final: 0.9222 (tpt) REVERT: LE 245 GLN cc_start: 0.8304 (tp40) cc_final: 0.7941 (tp40) REVERT: LE 249 ASP cc_start: 0.8348 (m-30) cc_final: 0.8073 (m-30) REVERT: LF 232 ASP cc_start: 0.8582 (m-30) cc_final: 0.8198 (m-30) REVERT: LG 160 ASP cc_start: 0.8671 (p0) cc_final: 0.8456 (p0) REVERT: LH 110 SER cc_start: 0.8928 (t) cc_final: 0.8570 (p) REVERT: LH 115 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.8030 (mtp85) REVERT: LH 140 GLN cc_start: 0.8058 (mm110) cc_final: 0.7608 (mt0) REVERT: LI 57 TYR cc_start: 0.9013 (t80) cc_final: 0.8670 (t80) REVERT: LI 63 GLU cc_start: 0.8851 (mp0) cc_final: 0.8244 (mt-10) REVERT: LI 168 SER cc_start: 0.9422 (t) cc_final: 0.9188 (t) REVERT: LJ 51 SER cc_start: 0.9307 (t) cc_final: 0.8855 (p) REVERT: LJ 120 ASP cc_start: 0.8060 (t0) cc_final: 0.7843 (t0) REVERT: LL 175 ASN cc_start: 0.9058 (m-40) cc_final: 0.8640 (m110) REVERT: LM 136 LEU cc_start: 0.9230 (tt) cc_final: 0.8976 (tp) REVERT: LO 87 MET cc_start: 0.9125 (mtt) cc_final: 0.8745 (mtt) REVERT: LR 34 ASN cc_start: 0.8785 (t0) cc_final: 0.8534 (t0) REVERT: LT 27 LEU cc_start: 0.9318 (mm) cc_final: 0.9078 (mm) REVERT: LT 38 ASP cc_start: 0.8550 (m-30) cc_final: 0.8234 (m-30) REVERT: LT 113 ASP cc_start: 0.8869 (m-30) cc_final: 0.8470 (m-30) REVERT: LU 31 ASP cc_start: 0.8623 (t70) cc_final: 0.8387 (t0) REVERT: LU 39 PHE cc_start: 0.9012 (t80) cc_final: 0.8811 (t80) REVERT: LU 40 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7567 (tm-30) REVERT: LU 41 GLN cc_start: 0.8669 (mm-40) cc_final: 0.8403 (tp-100) REVERT: LV 88 TYR cc_start: 0.9295 (p90) cc_final: 0.9045 (p90) REVERT: Lb 119 CYS cc_start: 0.8302 (t) cc_final: 0.7802 (p) REVERT: Lc 75 SER cc_start: 0.9489 (m) cc_final: 0.9264 (p) REVERT: Lf 40 GLU cc_start: 0.8714 (pm20) cc_final: 0.8438 (pm20) REVERT: Lh 107 GLN cc_start: 0.8932 (tp40) cc_final: 0.8691 (tp40) REVERT: Lk 13 LEU cc_start: 0.8845 (mm) cc_final: 0.8533 (mm) REVERT: Lk 19 ASP cc_start: 0.8565 (m-30) cc_final: 0.8147 (p0) REVERT: Lp 88 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8179 (mm-30) REVERT: Lz 159 MET cc_start: 0.6859 (ptm) cc_final: 0.6639 (ptp) outliers start: 202 outliers final: 100 residues processed: 986 average time/residue: 1.1945 time to fit residues: 2114.5125 Evaluate side-chains 872 residues out of total 6768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 768 time to evaluate : 7.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 60 ASP Chi-restraints excluded: chain 1 residue 113 ASN Chi-restraints excluded: chain 1 residue 364 TYR Chi-restraints excluded: chain 1 residue 449 LEU Chi-restraints excluded: chain 3 residue 74 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain K residue 10 ASN Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain K residue 146 VAL Chi-restraints excluded: chain K residue 209 ASP Chi-restraints excluded: chain K residue 217 VAL Chi-restraints excluded: chain LA residue 143 THR Chi-restraints excluded: chain LA residue 159 SER Chi-restraints excluded: chain LB residue 101 THR Chi-restraints excluded: chain LB residue 200 ARG Chi-restraints excluded: chain LB residue 310 SER Chi-restraints excluded: chain LC residue 154 VAL Chi-restraints excluded: chain LC residue 198 ASN Chi-restraints excluded: chain LC residue 352 ASP Chi-restraints excluded: chain LC residue 361 LEU Chi-restraints excluded: chain LF residue 121 THR Chi-restraints excluded: chain LF residue 178 SER Chi-restraints excluded: chain LF residue 228 VAL Chi-restraints excluded: chain LG residue 201 THR Chi-restraints excluded: chain LH residue 84 VAL Chi-restraints excluded: chain LH residue 115 ARG Chi-restraints excluded: chain LH residue 177 ASP Chi-restraints excluded: chain LI residue 44 ASP Chi-restraints excluded: chain LI residue 142 LEU Chi-restraints excluded: chain LI residue 179 ASP Chi-restraints excluded: chain LJ residue 34 THR Chi-restraints excluded: chain LJ residue 47 THR Chi-restraints excluded: chain LJ residue 74 VAL Chi-restraints excluded: chain LJ residue 129 ASP Chi-restraints excluded: chain LL residue 33 ILE Chi-restraints excluded: chain LL residue 63 THR Chi-restraints excluded: chain LL residue 169 ILE Chi-restraints excluded: chain LM residue 108 ASP Chi-restraints excluded: chain LN residue 125 SER Chi-restraints excluded: chain LN residue 197 THR Chi-restraints excluded: chain LO residue 28 LEU Chi-restraints excluded: chain LO residue 49 ARG Chi-restraints excluded: chain LP residue 109 VAL Chi-restraints excluded: chain LQ residue 82 VAL Chi-restraints excluded: chain LQ residue 85 THR Chi-restraints excluded: chain LR residue 30 ASN Chi-restraints excluded: chain LR residue 59 SER Chi-restraints excluded: chain LR residue 122 SER Chi-restraints excluded: chain LS residue 23 HIS Chi-restraints excluded: chain LS residue 24 THR Chi-restraints excluded: chain LT residue 61 THR Chi-restraints excluded: chain LT residue 149 GLU Chi-restraints excluded: chain LU residue 29 VAL Chi-restraints excluded: chain LU residue 33 ILE Chi-restraints excluded: chain LU residue 71 THR Chi-restraints excluded: chain LU residue 115 PHE Chi-restraints excluded: chain LV residue 22 VAL Chi-restraints excluded: chain LX residue 92 ASP Chi-restraints excluded: chain LX residue 140 LEU Chi-restraints excluded: chain LY residue 10 ASP Chi-restraints excluded: chain LY residue 83 GLU Chi-restraints excluded: chain LY residue 94 THR Chi-restraints excluded: chain LZ residue 33 THR Chi-restraints excluded: chain LZ residue 43 VAL Chi-restraints excluded: chain LZ residue 54 THR Chi-restraints excluded: chain LZ residue 66 SER Chi-restraints excluded: chain LZ residue 89 ILE Chi-restraints excluded: chain LZ residue 96 VAL Chi-restraints excluded: chain LZ residue 100 VAL Chi-restraints excluded: chain La residue 3 SER Chi-restraints excluded: chain La residue 86 THR Chi-restraints excluded: chain La residue 95 THR Chi-restraints excluded: chain Lb residue 4 SER 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 93 THR Chi-restraints excluded: chain Lc residue 94 LEU Chi-restraints excluded: chain Ld residue 46 LEU Chi-restraints excluded: chain Ld residue 86 VAL Chi-restraints excluded: chain Ld residue 119 THR Chi-restraints excluded: chain Le residue 13 VAL Chi-restraints excluded: chain Lf residue 81 SER Chi-restraints excluded: chain Lf residue 90 SER Chi-restraints excluded: chain Lf residue 91 ASN Chi-restraints excluded: chain Lg residue 35 THR Chi-restraints excluded: chain Lh residue 8 ASP Chi-restraints excluded: chain Li residue 27 SER Chi-restraints excluded: chain Lj residue 2 THR Chi-restraints excluded: chain Lk residue 59 SER Chi-restraints excluded: chain Ll residue 25 GLN Chi-restraints excluded: chain Ll residue 27 ILE Chi-restraints excluded: chain Ll residue 39 SER Chi-restraints excluded: chain Lm residue 110 CYS Chi-restraints excluded: chain Lp residue 74 THR Chi-restraints excluded: chain Lr residue 13 CYS Chi-restraints excluded: chain Lr residue 37 SER Chi-restraints excluded: chain Lr residue 117 ILE Chi-restraints excluded: chain Lz residue 33 GLU Chi-restraints excluded: chain Lz residue 174 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1142 random chunks: chunk 576 optimal weight: 6.9990 chunk 321 optimal weight: 10.0000 chunk 863 optimal weight: 9.9990 chunk 706 optimal weight: 5.9990 chunk 286 optimal weight: 10.0000 chunk 1038 optimal weight: 9.9990 chunk 1122 optimal weight: 8.9990 chunk 925 optimal weight: 0.6980 chunk 1030 optimal weight: 3.9990 chunk 354 optimal weight: 10.0000 chunk 833 optimal weight: 8.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 10 ASN ** LD 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 63 GLN ** LI 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LL 113 ASN LP 75 GLN LS 146 HIS LT 139 HIS LU 94 ASN LZ 127 ASN Ll 25 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 155158 Z= 0.247 Angle : 0.485 8.512 227775 Z= 0.253 Chirality : 0.033 0.223 28316 Planarity : 0.004 0.046 14705 Dihedral : 22.524 177.359 68788 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.41 % Favored : 97.57 % Rotamer: Outliers : 2.16 % Allowed : 15.58 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % 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: 1.45 (0.10), residues: 7750 helix: 2.04 (0.10), residues: 3090 sheet: 0.39 (0.17), residues: 1002 loop : 0.30 (0.10), residues: 3658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP K 202 HIS 0.005 0.001 HIS A 725 PHE 0.017 0.001 PHE 1 42 TYR 0.020 0.001 TYRLU 110 ARG 0.007 0.000 ARGLB 396 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15500 Ramachandran restraints generated. 7750 Oldfield, 0 Emsley, 7750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15500 Ramachandran restraints generated. 7750 Oldfield, 0 Emsley, 7750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 957 residues out of total 6768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 811 time to evaluate : 7.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 1 MET cc_start: 0.5283 (mpp) cc_final: 0.3934 (mmt) REVERT: K 209 ASP cc_start: 0.5559 (OUTLIER) cc_final: 0.5296 (t0) REVERT: LA 122 ASP cc_start: 0.8878 (t0) cc_final: 0.8610 (t0) REVERT: LB 200 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8502 (mtt90) REVERT: LB 396 ARG cc_start: 0.8569 (ttp-110) cc_final: 0.7843 (ttp80) REVERT: LC 288 ASP cc_start: 0.8613 (t0) cc_final: 0.8197 (t70) REVERT: LC 352 ASP cc_start: 0.8765 (OUTLIER) cc_final: 0.8483 (p0) REVERT: LD 235 MET cc_start: 0.8924 (ptm) cc_final: 0.8716 (ptt) REVERT: LE 62 MET cc_start: 0.9450 (mmm) cc_final: 0.9202 (tpt) REVERT: LE 245 GLN cc_start: 0.8234 (tp40) cc_final: 0.7818 (tp40) REVERT: LE 249 ASP cc_start: 0.8256 (m-30) cc_final: 0.7916 (m-30) REVERT: LF 232 ASP cc_start: 0.8491 (m-30) cc_final: 0.8098 (m-30) REVERT: LG 44 ASP cc_start: 0.8751 (m-30) cc_final: 0.8419 (m-30) REVERT: LG 160 ASP cc_start: 0.8653 (p0) cc_final: 0.8373 (p0) REVERT: LH 78 GLN cc_start: 0.8966 (mm-40) cc_final: 0.8734 (mt0) REVERT: LH 110 SER cc_start: 0.9003 (OUTLIER) cc_final: 0.8582 (p) REVERT: LH 115 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7881 (mtp85) REVERT: LH 140 GLN cc_start: 0.8069 (mm110) cc_final: 0.7530 (mt0) REVERT: LI 35 ASP cc_start: 0.8733 (m-30) cc_final: 0.8399 (m-30) REVERT: LI 57 TYR cc_start: 0.9087 (t80) cc_final: 0.8787 (t80) REVERT: LI 63 GLU cc_start: 0.8866 (mp0) cc_final: 0.8406 (mp0) REVERT: LI 168 SER cc_start: 0.9449 (OUTLIER) cc_final: 0.9231 (t) REVERT: LJ 42 GLN cc_start: 0.8872 (pp30) cc_final: 0.8590 (pp30) REVERT: LL 175 ASN cc_start: 0.9046 (m-40) cc_final: 0.8598 (m110) REVERT: LM 126 GLU cc_start: 0.8990 (tp30) cc_final: 0.8454 (tp30) REVERT: LM 136 LEU cc_start: 0.9222 (tt) cc_final: 0.8977 (tp) REVERT: LO 158 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8293 (tp30) REVERT: LO 162 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8583 (tm-30) REVERT: LP 148 MET cc_start: 0.9066 (ptp) cc_final: 0.8403 (ptp) REVERT: LQ 147 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8403 (tm-30) REVERT: LR 34 ASN cc_start: 0.8748 (t0) cc_final: 0.8504 (t0) REVERT: LT 38 ASP cc_start: 0.8542 (m-30) cc_final: 0.8226 (m-30) REVERT: LT 113 ASP cc_start: 0.8839 (m-30) cc_final: 0.8524 (m-30) REVERT: LU 31 ASP cc_start: 0.8659 (t70) cc_final: 0.8451 (t0) REVERT: LU 40 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7487 (tm-30) REVERT: LU 82 TYR cc_start: 0.8969 (t80) cc_final: 0.8736 (t80) REVERT: LV 99 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7338 (mt-10) REVERT: LV 111 GLU cc_start: 0.8088 (mp0) cc_final: 0.7494 (mp0) REVERT: LZ 18 TYR cc_start: 0.9175 (m-10) cc_final: 0.8873 (m-10) REVERT: LZ 88 ASP cc_start: 0.8168 (p0) cc_final: 0.7792 (p0) REVERT: Lb 119 CYS cc_start: 0.8112 (t) cc_final: 0.7781 (p) REVERT: Lc 75 SER cc_start: 0.9439 (OUTLIER) cc_final: 0.9190 (p) REVERT: Lf 37 ASP cc_start: 0.8821 (p0) cc_final: 0.8242 (p0) REVERT: Lf 40 GLU cc_start: 0.8681 (pm20) cc_final: 0.8387 (pm20) REVERT: Lh 107 GLN cc_start: 0.8867 (tp40) cc_final: 0.8620 (tp40) REVERT: Li 88 GLU cc_start: 0.8094 (pp20) cc_final: 0.7798 (tm-30) REVERT: Lk 13 LEU cc_start: 0.8818 (mm) cc_final: 0.8505 (mm) REVERT: Lk 19 ASP cc_start: 0.8610 (m-30) cc_final: 0.8108 (p0) REVERT: Lp 88 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8142 (mm-30) REVERT: Lz 159 MET cc_start: 0.6883 (ptm) cc_final: 0.6680 (ptp) outliers start: 146 outliers final: 93 residues processed: 909 average time/residue: 1.2035 time to fit residues: 1969.7590 Evaluate side-chains 865 residues out of total 6768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 765 time to evaluate : 7.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 60 ASP Chi-restraints excluded: chain 1 residue 113 ASN Chi-restraints excluded: chain 1 residue 364 TYR Chi-restraints excluded: chain 1 residue 449 LEU Chi-restraints excluded: chain 2 residue 33 PHE Chi-restraints excluded: chain A residue 256 TRP Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 652 MET Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain K residue 62 MET Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain K residue 209 ASP Chi-restraints excluded: chain LA residue 143 THR Chi-restraints excluded: chain LA residue 159 SER Chi-restraints excluded: chain LB residue 13 SER Chi-restraints excluded: chain LB residue 101 THR Chi-restraints excluded: chain LB residue 166 THR Chi-restraints excluded: chain LB residue 200 ARG Chi-restraints excluded: chain LB residue 370 THR Chi-restraints excluded: chain LC residue 154 VAL Chi-restraints excluded: chain LC residue 291 ARG Chi-restraints excluded: chain LC residue 352 ASP Chi-restraints excluded: chain LF residue 228 VAL Chi-restraints excluded: chain LH residue 11 ASP Chi-restraints excluded: chain LH residue 46 SER Chi-restraints excluded: chain LH residue 110 SER Chi-restraints excluded: chain LH residue 115 ARG Chi-restraints excluded: chain LH residue 177 ASP Chi-restraints excluded: chain LI residue 44 ASP Chi-restraints excluded: chain LI residue 142 LEU Chi-restraints excluded: chain LI residue 168 SER Chi-restraints excluded: chain LI residue 179 ASP Chi-restraints excluded: chain LJ residue 47 THR Chi-restraints excluded: chain LJ residue 51 SER Chi-restraints excluded: chain LJ residue 65 ASN Chi-restraints excluded: chain LJ residue 74 VAL Chi-restraints excluded: chain LJ residue 104 ASN Chi-restraints excluded: chain LJ residue 129 ASP Chi-restraints excluded: chain LL residue 33 ILE Chi-restraints excluded: chain LL residue 63 THR Chi-restraints excluded: chain LL residue 169 ILE Chi-restraints excluded: chain LM residue 59 ASP Chi-restraints excluded: chain LM residue 108 ASP Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 104 GLU Chi-restraints excluded: chain LN residue 126 THR Chi-restraints excluded: chain LN residue 197 THR Chi-restraints excluded: chain LP residue 10 ASN Chi-restraints excluded: chain LP residue 12 THR Chi-restraints excluded: chain LP residue 109 VAL Chi-restraints excluded: chain LP residue 141 SER Chi-restraints excluded: chain LR residue 59 SER Chi-restraints excluded: chain LR residue 122 SER Chi-restraints excluded: chain LT residue 80 VAL Chi-restraints excluded: chain LU residue 23 LEU Chi-restraints excluded: chain LU residue 29 VAL Chi-restraints excluded: chain LU residue 33 ILE Chi-restraints excluded: chain LU residue 71 THR Chi-restraints excluded: chain LU residue 115 PHE Chi-restraints excluded: chain LV residue 101 ASN Chi-restraints excluded: chain LX residue 140 LEU Chi-restraints excluded: chain LY residue 83 GLU Chi-restraints excluded: chain LY residue 94 THR Chi-restraints excluded: chain LZ residue 43 VAL Chi-restraints excluded: chain LZ residue 54 THR Chi-restraints excluded: chain La residue 72 THR Chi-restraints excluded: chain La residue 95 THR Chi-restraints excluded: chain La residue 134 GLU Chi-restraints excluded: chain Lc residue 28 VAL Chi-restraints excluded: chain Lc residue 34 THR Chi-restraints excluded: chain Lc residue 75 SER Chi-restraints excluded: chain Lc residue 93 THR Chi-restraints excluded: chain Lc residue 94 LEU Chi-restraints excluded: chain Ld residue 59 THR Chi-restraints excluded: chain Ld residue 89 SER Chi-restraints excluded: chain Le residue 13 VAL Chi-restraints excluded: chain Lf residue 90 SER Chi-restraints excluded: chain Lg residue 25 THR Chi-restraints excluded: chain Lg residue 35 THR Chi-restraints excluded: chain Lh residue 59 THR Chi-restraints excluded: chain Li residue 27 SER Chi-restraints excluded: chain Lj residue 83 THR Chi-restraints excluded: chain Lk residue 59 SER Chi-restraints excluded: chain Ll residue 25 GLN Chi-restraints excluded: chain Ll residue 27 ILE Chi-restraints excluded: chain Ll residue 39 SER Chi-restraints excluded: chain Ll residue 47 THR Chi-restraints excluded: chain Lm residue 110 CYS Chi-restraints excluded: chain Lo residue 33 LEU Chi-restraints excluded: chain Lp residue 16 THR Chi-restraints excluded: chain Lp residue 74 THR Chi-restraints excluded: chain Lr residue 13 CYS Chi-restraints excluded: chain Lr residue 117 ILE Chi-restraints excluded: chain Lz residue 33 GLU Chi-restraints excluded: chain Lz residue 67 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1142 random chunks: chunk 1026 optimal weight: 10.0000 chunk 781 optimal weight: 10.0000 chunk 539 optimal weight: 5.9990 chunk 115 optimal weight: 20.0000 chunk 495 optimal weight: 20.0000 chunk 697 optimal weight: 7.9990 chunk 1042 optimal weight: 0.9990 chunk 1103 optimal weight: 8.9990 chunk 544 optimal weight: 10.0000 chunk 988 optimal weight: 6.9990 chunk 297 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 162 HIS ** LD 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 63 GLN ** LI 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 75 GLN LW 59 HIS ** LX 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LX 93 ASN LY 66 GLN Lg 28 ASN Ll 25 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 155158 Z= 0.295 Angle : 0.501 8.944 227775 Z= 0.260 Chirality : 0.034 0.230 28316 Planarity : 0.004 0.047 14705 Dihedral : 22.480 178.258 68788 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.99 % Favored : 96.99 % Rotamer: Outliers : 2.72 % Allowed : 15.58 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % 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 (0.10), residues: 7750 helix: 2.01 (0.10), residues: 3088 sheet: 0.38 (0.17), residues: 996 loop : 0.20 (0.10), residues: 3666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP K 202 HIS 0.009 0.001 HIS K 50 PHE 0.019 0.001 PHE A 485 TYR 0.017 0.001 TYRLU 85 ARG 0.007 0.000 ARGLl 28 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15500 Ramachandran restraints generated. 7750 Oldfield, 0 Emsley, 7750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15500 Ramachandran restraints generated. 7750 Oldfield, 0 Emsley, 7750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 963 residues out of total 6768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 779 time to evaluate : 7.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 399 MET cc_start: 0.0650 (mmp) cc_final: 0.0314 (mmp) REVERT: 1 401 MET cc_start: 0.3097 (mtm) cc_final: 0.2346 (mtm) REVERT: K 1 MET cc_start: 0.5293 (mpp) cc_final: 0.3965 (mmt) REVERT: K 84 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8468 (mp) REVERT: K 209 ASP cc_start: 0.5656 (OUTLIER) cc_final: 0.5401 (t0) REVERT: LA 122 ASP cc_start: 0.8867 (t0) cc_final: 0.8641 (t0) REVERT: LB 4 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.8101 (ttm170) REVERT: LB 200 ARG cc_start: 0.9009 (OUTLIER) cc_final: 0.8538 (mtt90) REVERT: LB 216 MET cc_start: 0.9037 (mmt) cc_final: 0.8797 (mmt) REVERT: LB 382 MET cc_start: 0.8642 (mtp) cc_final: 0.8175 (mtt) REVERT: LC 288 ASP cc_start: 0.8678 (t0) cc_final: 0.8202 (t70) REVERT: LC 352 ASP cc_start: 0.8748 (OUTLIER) cc_final: 0.8431 (p0) REVERT: LD 235 MET cc_start: 0.8941 (ptm) cc_final: 0.8714 (ptt) REVERT: LE 62 MET cc_start: 0.9429 (mmm) cc_final: 0.9190 (tpt) REVERT: LE 214 ASP cc_start: 0.8521 (m-30) cc_final: 0.8275 (m-30) REVERT: LE 245 GLN cc_start: 0.8257 (tp40) cc_final: 0.7808 (tp40) REVERT: LE 249 ASP cc_start: 0.8286 (m-30) cc_final: 0.7965 (m-30) REVERT: LF 232 ASP cc_start: 0.8521 (m-30) cc_final: 0.8184 (m-30) REVERT: LG 44 ASP cc_start: 0.8753 (m-30) cc_final: 0.8259 (m-30) REVERT: LG 70 LEU cc_start: 0.9567 (OUTLIER) cc_final: 0.9307 (mp) REVERT: LH 78 GLN cc_start: 0.8992 (mm-40) cc_final: 0.8790 (mt0) REVERT: LH 110 SER cc_start: 0.9080 (OUTLIER) cc_final: 0.8562 (p) REVERT: LH 115 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7969 (mtp85) REVERT: LH 140 GLN cc_start: 0.8074 (mm110) cc_final: 0.7469 (mt0) REVERT: LI 35 ASP cc_start: 0.8852 (m-30) cc_final: 0.8486 (m-30) REVERT: LI 57 TYR cc_start: 0.9162 (t80) cc_final: 0.8858 (t80) REVERT: LL 175 ASN cc_start: 0.9024 (m-40) cc_final: 0.8566 (m110) REVERT: LM 81 ASP cc_start: 0.8479 (t0) cc_final: 0.8278 (t0) REVERT: LM 126 GLU cc_start: 0.8999 (tp30) cc_final: 0.8469 (tp30) REVERT: LM 136 LEU cc_start: 0.9237 (tt) cc_final: 0.9000 (tp) REVERT: LO 87 MET cc_start: 0.9189 (mtt) cc_final: 0.8831 (mtt) REVERT: LO 158 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8335 (tp30) REVERT: LO 162 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8509 (tm-30) REVERT: LQ 147 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8280 (tm-30) REVERT: LR 34 ASN cc_start: 0.8784 (t0) cc_final: 0.8541 (t0) REVERT: LT 38 ASP cc_start: 0.8597 (m-30) cc_final: 0.8271 (m-30) REVERT: LT 113 ASP cc_start: 0.8844 (m-30) cc_final: 0.8515 (m-30) REVERT: LU 40 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7685 (tm-30) REVERT: LU 41 GLN cc_start: 0.8612 (tp40) cc_final: 0.8343 (tp40) REVERT: LU 45 GLU cc_start: 0.7864 (pt0) cc_final: 0.7616 (pt0) REVERT: LV 99 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7339 (mt-10) REVERT: LV 111 GLU cc_start: 0.8118 (mp0) cc_final: 0.7544 (mp0) REVERT: LW 30 GLN cc_start: 0.8971 (mp10) cc_final: 0.8739 (mp10) REVERT: LY 88 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7895 (tp30) REVERT: LZ 18 TYR cc_start: 0.9201 (m-10) cc_final: 0.8872 (m-10) REVERT: LZ 88 ASP cc_start: 0.8146 (p0) cc_final: 0.7793 (p0) REVERT: LZ 99 ASP cc_start: 0.8381 (t70) cc_final: 0.7731 (t70) REVERT: Lb 58 GLN cc_start: 0.9089 (pp30) cc_final: 0.8812 (pp30) REVERT: Lb 119 CYS cc_start: 0.8187 (t) cc_final: 0.7813 (p) REVERT: Lc 37 MET cc_start: 0.8842 (mmm) cc_final: 0.8293 (mmm) REVERT: Lc 75 SER cc_start: 0.9423 (m) cc_final: 0.9173 (p) REVERT: Ld 112 THR cc_start: 0.9178 (p) cc_final: 0.8881 (t) REVERT: Lf 37 ASP cc_start: 0.8844 (p0) cc_final: 0.8284 (p0) REVERT: Lf 40 GLU cc_start: 0.8662 (pm20) cc_final: 0.8329 (pm20) REVERT: Lh 107 GLN cc_start: 0.8868 (tp40) cc_final: 0.8591 (tp40) REVERT: Lk 13 LEU cc_start: 0.8855 (mm) cc_final: 0.8543 (mm) REVERT: Lk 19 ASP cc_start: 0.8629 (m-30) cc_final: 0.8195 (p0) REVERT: Lm 79 GLU cc_start: 0.8302 (tp30) cc_final: 0.7977 (tm-30) REVERT: Lp 84 ARG cc_start: 0.8471 (ttp-110) cc_final: 0.8068 (ttp-110) REVERT: Lp 88 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8198 (mm-30) REVERT: Lz 159 MET cc_start: 0.6906 (ptm) cc_final: 0.6702 (ptp) outliers start: 184 outliers final: 120 residues processed: 905 average time/residue: 1.2214 time to fit residues: 1987.4700 Evaluate side-chains 884 residues out of total 6768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 755 time to evaluate : 7.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 60 ASP Chi-restraints excluded: chain 1 residue 113 ASN Chi-restraints excluded: chain 1 residue 128 SER Chi-restraints excluded: chain 1 residue 163 LEU Chi-restraints excluded: chain 1 residue 364 TYR Chi-restraints excluded: chain 1 residue 449 LEU Chi-restraints excluded: chain 2 residue 56 LEU Chi-restraints excluded: chain A residue 256 TRP Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 209 ASP Chi-restraints excluded: chain LA residue 143 THR Chi-restraints excluded: chain LA residue 159 SER Chi-restraints excluded: chain LB residue 4 ARG Chi-restraints excluded: chain LB residue 13 SER Chi-restraints excluded: chain LB residue 101 THR Chi-restraints excluded: chain LB residue 200 ARG Chi-restraints excluded: chain LB residue 231 VAL Chi-restraints excluded: chain LB residue 370 THR Chi-restraints excluded: chain LC residue 154 VAL Chi-restraints excluded: chain LC residue 198 ASN Chi-restraints excluded: chain LC residue 291 ARG Chi-restraints excluded: chain LC residue 335 MET Chi-restraints excluded: chain LC residue 352 ASP Chi-restraints excluded: chain LE residue 120 ASP Chi-restraints excluded: chain LF residue 121 THR Chi-restraints excluded: chain LF residue 228 VAL Chi-restraints excluded: chain LG residue 70 LEU Chi-restraints excluded: chain LG residue 168 VAL Chi-restraints excluded: chain LG residue 201 THR Chi-restraints excluded: chain LH residue 11 ASP Chi-restraints excluded: chain LH residue 46 SER Chi-restraints excluded: chain LH residue 110 SER Chi-restraints excluded: chain LH residue 115 ARG Chi-restraints excluded: chain LH residue 177 ASP Chi-restraints excluded: chain LI residue 44 ASP Chi-restraints excluded: chain LI residue 179 ASP Chi-restraints excluded: chain LI residue 189 CYS Chi-restraints excluded: chain LJ residue 47 THR Chi-restraints excluded: chain LJ residue 51 SER Chi-restraints excluded: chain LJ residue 65 ASN Chi-restraints excluded: chain LJ residue 74 VAL Chi-restraints excluded: chain LJ residue 104 ASN Chi-restraints excluded: chain LJ residue 129 ASP Chi-restraints excluded: chain LJ residue 158 SER Chi-restraints excluded: chain LL residue 33 ILE Chi-restraints excluded: chain LL residue 63 THR Chi-restraints excluded: chain LL residue 169 ILE Chi-restraints excluded: chain LM residue 59 ASP Chi-restraints excluded: chain LM residue 108 ASP Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 104 GLU Chi-restraints excluded: chain LN residue 126 THR Chi-restraints excluded: chain LN residue 197 THR Chi-restraints excluded: chain LO residue 49 ARG Chi-restraints excluded: chain LO residue 152 VAL Chi-restraints excluded: chain LP residue 10 ASN Chi-restraints excluded: chain LP residue 12 THR Chi-restraints excluded: chain LP residue 100 SER Chi-restraints excluded: chain LP residue 109 VAL Chi-restraints excluded: chain LP residue 141 SER Chi-restraints excluded: chain LQ residue 82 VAL Chi-restraints excluded: chain LQ residue 85 THR Chi-restraints excluded: chain LR residue 59 SER Chi-restraints excluded: chain LR residue 122 SER Chi-restraints excluded: chain LS residue 75 VAL Chi-restraints excluded: chain LT residue 80 VAL Chi-restraints excluded: chain LU residue 23 LEU Chi-restraints excluded: chain LU residue 29 VAL Chi-restraints excluded: chain LU residue 33 ILE Chi-restraints excluded: chain LU residue 44 GLN Chi-restraints excluded: chain LU residue 71 THR Chi-restraints excluded: chain LU residue 111 GLU Chi-restraints excluded: chain LU residue 115 PHE Chi-restraints excluded: chain LV residue 22 VAL Chi-restraints excluded: chain LV residue 101 ASN Chi-restraints excluded: chain LX residue 92 ASP Chi-restraints excluded: chain LX residue 140 LEU Chi-restraints excluded: chain LY residue 83 GLU Chi-restraints excluded: chain LY residue 88 GLU Chi-restraints excluded: chain LY residue 94 THR Chi-restraints excluded: chain LZ residue 33 THR Chi-restraints excluded: chain LZ residue 43 VAL Chi-restraints excluded: chain LZ residue 54 THR Chi-restraints excluded: chain LZ residue 96 VAL Chi-restraints excluded: chain LZ residue 100 VAL Chi-restraints excluded: chain La residue 3 SER Chi-restraints excluded: chain La residue 72 THR Chi-restraints excluded: chain La residue 86 THR Chi-restraints excluded: chain La residue 95 THR Chi-restraints excluded: chain La residue 134 GLU Chi-restraints excluded: chain La residue 140 VAL Chi-restraints excluded: chain Lc residue 28 VAL Chi-restraints excluded: chain Lc residue 34 THR Chi-restraints excluded: chain Lc residue 93 THR Chi-restraints excluded: chain Ld residue 46 LEU Chi-restraints excluded: chain Ld residue 59 THR Chi-restraints excluded: chain Ld residue 86 VAL Chi-restraints excluded: chain Ld residue 89 SER Chi-restraints excluded: chain Ld residue 107 THR Chi-restraints excluded: chain Le residue 87 VAL Chi-restraints excluded: chain Lf residue 90 SER Chi-restraints excluded: chain Lg residue 23 SER Chi-restraints excluded: chain Lg residue 25 THR Chi-restraints excluded: chain Lg residue 35 THR Chi-restraints excluded: chain Lh residue 8 ASP Chi-restraints excluded: chain Lh residue 47 ILE Chi-restraints excluded: chain Lh residue 59 THR Chi-restraints excluded: chain Li residue 27 SER Chi-restraints excluded: chain Li residue 66 ASP Chi-restraints excluded: chain Lk residue 59 SER Chi-restraints excluded: chain Ll residue 39 SER Chi-restraints excluded: chain Ll residue 47 THR Chi-restraints excluded: chain Lm residue 110 CYS Chi-restraints excluded: chain Lo residue 7 THR Chi-restraints excluded: chain Lp residue 16 THR Chi-restraints excluded: chain Lp residue 74 THR Chi-restraints excluded: chain Lp residue 79 VAL Chi-restraints excluded: chain Lr residue 13 CYS Chi-restraints excluded: chain Lr residue 117 ILE Chi-restraints excluded: chain Lz residue 33 GLU Chi-restraints excluded: chain Lz residue 46 ASP Chi-restraints excluded: chain Lz residue 67 VAL Chi-restraints excluded: chain Lz residue 164 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1142 random chunks: chunk 919 optimal weight: 10.0000 chunk 626 optimal weight: 10.0000 chunk 16 optimal weight: 50.0000 chunk 821 optimal weight: 10.0000 chunk 455 optimal weight: 9.9990 chunk 941 optimal weight: 6.9990 chunk 763 optimal weight: 9.9990 chunk 1 optimal weight: 50.0000 chunk 563 optimal weight: 9.9990 chunk 990 optimal weight: 10.0000 chunk 278 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: ** LD 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 63 GLN ** LI 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LL 113 ASN ** LN 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LU 94 ASN ** LX 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Lg 28 ASN ** Ll 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lz 184 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.124 155158 Z= 0.432 Angle : 0.578 11.019 227775 Z= 0.298 Chirality : 0.038 0.237 28316 Planarity : 0.004 0.050 14705 Dihedral : 22.522 178.473 68788 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.26 % Favored : 96.72 % Rotamer: Outliers : 3.22 % Allowed : 16.32 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % 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: 1.05 (0.10), residues: 7750 helix: 1.78 (0.10), residues: 3104 sheet: 0.21 (0.17), residues: 996 loop : -0.02 (0.10), residues: 3650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRPLN 120 HIS 0.008 0.001 HISLa 40 PHE 0.020 0.001 PHE A 485 TYR 0.021 0.002 TYRLU 85 ARG 0.010 0.001 ARGLB 396 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15500 Ramachandran restraints generated. 7750 Oldfield, 0 Emsley, 7750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15500 Ramachandran restraints generated. 7750 Oldfield, 0 Emsley, 7750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 968 residues out of total 6768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 750 time to evaluate : 7.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 401 MET cc_start: 0.3437 (mtm) cc_final: 0.3159 (mtm) REVERT: A 292 GLN cc_start: -0.0124 (tm-30) cc_final: -0.0454 (pp30) REVERT: K 209 ASP cc_start: 0.5998 (OUTLIER) cc_final: 0.5739 (t0) REVERT: LA 122 ASP cc_start: 0.8869 (t0) cc_final: 0.8650 (t0) REVERT: LB 4 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8148 (ttm170) REVERT: LB 200 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.8543 (mtt90) REVERT: LB 382 MET cc_start: 0.8684 (mtp) cc_final: 0.8256 (mtm) REVERT: LB 396 ARG cc_start: 0.8575 (ttp-110) cc_final: 0.7876 (ttp80) REVERT: LC 288 ASP cc_start: 0.8832 (t0) cc_final: 0.8384 (t70) REVERT: LD 176 SER cc_start: 0.8955 (p) cc_final: 0.8670 (t) REVERT: LD 235 MET cc_start: 0.8896 (ptm) cc_final: 0.8671 (ptt) REVERT: LE 62 MET cc_start: 0.9410 (mmm) cc_final: 0.9160 (tpt) REVERT: LE 214 ASP cc_start: 0.8580 (m-30) cc_final: 0.8363 (m-30) REVERT: LE 245 GLN cc_start: 0.8276 (tp40) cc_final: 0.7851 (tp40) REVERT: LE 249 ASP cc_start: 0.8341 (m-30) cc_final: 0.8054 (m-30) REVERT: LF 232 ASP cc_start: 0.8568 (m-30) cc_final: 0.8315 (m-30) REVERT: LG 44 ASP cc_start: 0.8804 (m-30) cc_final: 0.8481 (m-30) REVERT: LG 70 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.9349 (mp) REVERT: LH 78 GLN cc_start: 0.9012 (mm-40) cc_final: 0.8788 (mt0) REVERT: LH 110 SER cc_start: 0.9144 (OUTLIER) cc_final: 0.8578 (p) REVERT: LH 115 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8192 (mtp85) REVERT: LI 35 ASP cc_start: 0.8945 (m-30) cc_final: 0.8611 (m-30) REVERT: LI 57 TYR cc_start: 0.9232 (t80) cc_final: 0.8896 (t80) REVERT: LI 63 GLU cc_start: 0.8897 (mp0) cc_final: 0.8478 (mp0) REVERT: LJ 120 ASP cc_start: 0.8152 (t0) cc_final: 0.7845 (t0) REVERT: LL 175 ASN cc_start: 0.9013 (m-40) cc_final: 0.8524 (m110) REVERT: LM 126 GLU cc_start: 0.9010 (tp30) cc_final: 0.8524 (tp30) REVERT: LM 136 LEU cc_start: 0.9268 (tt) cc_final: 0.9021 (tp) REVERT: LO 87 MET cc_start: 0.9243 (mtt) cc_final: 0.8940 (mtt) REVERT: LO 162 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8469 (tm-30) REVERT: LQ 147 GLU cc_start: 0.8709 (tm-30) cc_final: 0.8364 (tm-30) REVERT: LR 34 ASN cc_start: 0.8814 (t0) cc_final: 0.8473 (t0) REVERT: LT 38 ASP cc_start: 0.8662 (m-30) cc_final: 0.8376 (m-30) REVERT: LT 113 ASP cc_start: 0.8858 (m-30) cc_final: 0.8464 (m-30) REVERT: LU 30 GLU cc_start: 0.9005 (pp20) cc_final: 0.8731 (pp20) REVERT: LU 40 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7346 (tm-30) REVERT: LU 41 GLN cc_start: 0.8700 (tp40) cc_final: 0.8488 (tp40) REVERT: LU 44 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7959 (mp10) REVERT: LU 45 GLU cc_start: 0.7847 (pt0) cc_final: 0.7591 (pt0) REVERT: LV 99 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7453 (mt-10) REVERT: LV 111 GLU cc_start: 0.8125 (mp0) cc_final: 0.7516 (mp0) REVERT: LW 25 ASP cc_start: 0.8541 (p0) cc_final: 0.8257 (p0) REVERT: LW 27 LYS cc_start: 0.9119 (mtpp) cc_final: 0.8510 (mtmm) REVERT: LY 88 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7898 (tp30) REVERT: LZ 54 THR cc_start: 0.9165 (OUTLIER) cc_final: 0.8936 (t) REVERT: LZ 88 ASP cc_start: 0.8219 (p0) cc_final: 0.7863 (p0) REVERT: LZ 113 GLU cc_start: 0.9033 (tp30) cc_final: 0.8517 (tm-30) REVERT: La 125 LYS cc_start: 0.9238 (OUTLIER) cc_final: 0.8990 (mmtp) REVERT: Lb 58 GLN cc_start: 0.9046 (pp30) cc_final: 0.8794 (pp30) REVERT: Lb 119 CYS cc_start: 0.8148 (t) cc_final: 0.7911 (p) REVERT: Lc 75 SER cc_start: 0.9490 (OUTLIER) cc_final: 0.9236 (p) REVERT: Ld 112 THR cc_start: 0.9265 (p) cc_final: 0.9012 (t) REVERT: Le 102 ASN cc_start: 0.9028 (p0) cc_final: 0.8821 (p0) REVERT: Lf 40 GLU cc_start: 0.8650 (pm20) cc_final: 0.8381 (pm20) REVERT: Lf 104 MET cc_start: 0.9509 (OUTLIER) cc_final: 0.8656 (mmm) REVERT: Lh 107 GLN cc_start: 0.8872 (tp40) cc_final: 0.8579 (tp40) REVERT: Li 88 GLU cc_start: 0.8297 (pp20) cc_final: 0.8053 (pp20) REVERT: Lk 13 LEU cc_start: 0.8839 (mm) cc_final: 0.8545 (mm) REVERT: Lk 19 ASP cc_start: 0.8662 (m-30) cc_final: 0.8181 (p0) REVERT: Ll 33 ASN cc_start: 0.8676 (t0) cc_final: 0.8430 (t0) REVERT: Lp 84 ARG cc_start: 0.8582 (ttp-110) cc_final: 0.8185 (ttp-110) REVERT: Lp 88 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8130 (mm-30) REVERT: Lr 48 THR cc_start: 0.9443 (m) cc_final: 0.9159 (p) REVERT: Lr 115 SER cc_start: 0.9544 (OUTLIER) cc_final: 0.9304 (p) REVERT: Lz 108 ASP cc_start: 0.2699 (m-30) cc_final: 0.1271 (t0) REVERT: Lz 176 ASP cc_start: 0.3989 (p0) cc_final: 0.3679 (p0) outliers start: 218 outliers final: 154 residues processed: 912 average time/residue: 1.2153 time to fit residues: 1993.7440 Evaluate side-chains 893 residues out of total 6768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 726 time to evaluate : 7.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 26 ILE Chi-restraints excluded: chain 1 residue 60 ASP Chi-restraints excluded: chain 1 residue 113 ASN Chi-restraints excluded: chain 1 residue 128 SER Chi-restraints excluded: chain 1 residue 364 TYR Chi-restraints excluded: chain 1 residue 433 VAL Chi-restraints excluded: chain 1 residue 449 LEU Chi-restraints excluded: chain 2 residue 11 SER Chi-restraints excluded: chain 2 residue 56 LEU Chi-restraints excluded: chain A residue 256 TRP Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 197 MET Chi-restraints excluded: chain K residue 209 ASP Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain LA residue 32 VAL Chi-restraints excluded: chain LA residue 84 THR Chi-restraints excluded: chain LA residue 143 THR Chi-restraints excluded: chain LA residue 159 SER Chi-restraints excluded: chain LB residue 4 ARG Chi-restraints excluded: chain LB residue 13 SER Chi-restraints excluded: chain LB residue 101 THR Chi-restraints excluded: chain LB residue 166 THR Chi-restraints excluded: chain LB residue 200 ARG Chi-restraints excluded: chain LB residue 231 VAL Chi-restraints excluded: chain LB residue 370 THR Chi-restraints excluded: chain LC residue 154 VAL Chi-restraints excluded: chain LC residue 198 ASN Chi-restraints excluded: chain LC residue 291 ARG Chi-restraints excluded: chain LC residue 335 MET Chi-restraints excluded: chain LC residue 361 LEU Chi-restraints excluded: chain LC residue 362 GLN Chi-restraints excluded: chain LD residue 37 VAL Chi-restraints excluded: chain LD residue 75 VAL Chi-restraints excluded: chain LE residue 107 VAL Chi-restraints excluded: chain LE residue 120 ASP Chi-restraints excluded: chain LF residue 121 THR Chi-restraints excluded: chain LF residue 228 VAL Chi-restraints excluded: chain LG residue 70 LEU Chi-restraints excluded: chain LG residue 162 ASP Chi-restraints excluded: chain LG residue 168 VAL Chi-restraints excluded: chain LG residue 198 THR Chi-restraints excluded: chain LG residue 201 THR Chi-restraints excluded: chain LH residue 11 ASP Chi-restraints excluded: chain LH residue 19 THR Chi-restraints excluded: chain LH residue 24 THR Chi-restraints excluded: chain LH residue 46 SER Chi-restraints excluded: chain LH residue 84 VAL Chi-restraints excluded: chain LH residue 110 SER Chi-restraints excluded: chain LH residue 115 ARG Chi-restraints excluded: chain LH residue 135 SER Chi-restraints excluded: chain LH residue 177 ASP Chi-restraints excluded: chain LI residue 44 ASP Chi-restraints excluded: chain LI residue 136 MET Chi-restraints excluded: chain LI residue 168 SER Chi-restraints excluded: chain LI residue 179 ASP Chi-restraints excluded: chain LJ residue 47 THR Chi-restraints excluded: chain LJ residue 51 SER Chi-restraints excluded: chain LJ residue 65 ASN Chi-restraints excluded: chain LJ residue 74 VAL Chi-restraints excluded: chain LJ residue 104 ASN Chi-restraints excluded: chain LJ residue 123 ILE Chi-restraints excluded: chain LJ residue 129 ASP Chi-restraints excluded: chain LJ residue 158 SER Chi-restraints excluded: chain LL residue 33 ILE Chi-restraints excluded: chain LL residue 63 THR Chi-restraints excluded: chain LM residue 59 ASP Chi-restraints excluded: chain LM residue 108 ASP Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 104 GLU Chi-restraints excluded: chain LN residue 126 THR Chi-restraints excluded: chain LN residue 197 THR Chi-restraints excluded: chain LO residue 49 ARG Chi-restraints excluded: chain LO residue 152 VAL Chi-restraints excluded: chain LP residue 10 ASN Chi-restraints excluded: chain LP residue 12 THR Chi-restraints excluded: chain LP residue 109 VAL Chi-restraints excluded: chain LP residue 141 SER 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 111 SER Chi-restraints excluded: chain LR residue 12 SER Chi-restraints excluded: chain LR residue 59 SER Chi-restraints excluded: chain LR residue 122 SER Chi-restraints excluded: chain LS residue 75 VAL Chi-restraints excluded: chain LT residue 27 LEU Chi-restraints excluded: chain LT residue 80 VAL Chi-restraints excluded: chain LU residue 23 LEU Chi-restraints excluded: chain LU residue 25 CYS Chi-restraints excluded: chain LU residue 29 VAL Chi-restraints excluded: chain LU residue 33 ILE Chi-restraints excluded: chain LU residue 34 MET Chi-restraints excluded: chain LU residue 44 GLN Chi-restraints excluded: chain LU residue 62 THR Chi-restraints excluded: chain LU residue 71 THR Chi-restraints excluded: chain LU residue 111 GLU Chi-restraints excluded: chain LU residue 115 PHE Chi-restraints excluded: chain LV residue 22 VAL Chi-restraints excluded: chain LV residue 134 SER Chi-restraints excluded: chain LX residue 92 ASP Chi-restraints excluded: chain LX residue 140 LEU Chi-restraints excluded: chain LY residue 83 GLU Chi-restraints excluded: chain LY residue 88 GLU Chi-restraints excluded: chain LY residue 94 THR Chi-restraints excluded: chain LZ residue 33 THR Chi-restraints excluded: chain LZ residue 43 VAL Chi-restraints excluded: chain LZ residue 54 THR Chi-restraints excluded: chain LZ residue 96 VAL Chi-restraints excluded: chain LZ residue 100 VAL Chi-restraints excluded: chain La residue 3 SER Chi-restraints excluded: chain La residue 56 VAL Chi-restraints excluded: chain La residue 72 THR Chi-restraints excluded: chain La residue 86 THR Chi-restraints excluded: chain La residue 95 THR Chi-restraints excluded: chain La residue 100 ILE Chi-restraints excluded: chain La residue 125 LYS Chi-restraints excluded: chain La residue 134 GLU Chi-restraints excluded: chain La residue 140 VAL Chi-restraints excluded: chain Lc residue 28 VAL Chi-restraints excluded: chain Lc residue 34 THR 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 59 THR Chi-restraints excluded: chain Ld residue 86 VAL Chi-restraints excluded: chain Ld residue 89 SER Chi-restraints excluded: chain Ld residue 119 THR Chi-restraints excluded: chain Le residue 87 VAL Chi-restraints excluded: chain Lf residue 90 SER Chi-restraints excluded: chain Lf residue 91 ASN Chi-restraints excluded: chain Lf residue 104 MET Chi-restraints excluded: chain Lg residue 23 SER Chi-restraints excluded: chain Lg residue 25 THR Chi-restraints excluded: chain Lg residue 35 THR Chi-restraints excluded: chain Lh residue 8 ASP Chi-restraints excluded: chain Li residue 27 SER Chi-restraints excluded: chain Li residue 66 ASP Chi-restraints excluded: chain Li residue 79 THR Chi-restraints excluded: chain Li residue 97 MET Chi-restraints excluded: chain Lk residue 59 SER Chi-restraints excluded: chain Ll residue 27 ILE Chi-restraints excluded: chain Ll residue 39 SER Chi-restraints excluded: chain Ll residue 47 THR Chi-restraints excluded: chain Lm residue 110 CYS Chi-restraints excluded: chain Lo residue 7 THR Chi-restraints excluded: chain Lo residue 33 LEU Chi-restraints excluded: chain Lo residue 67 VAL Chi-restraints excluded: chain Lo residue 103 VAL Chi-restraints excluded: chain Lo residue 104 ILE Chi-restraints excluded: chain Lp residue 16 THR Chi-restraints excluded: chain Lp residue 74 THR Chi-restraints excluded: chain Lp residue 79 VAL Chi-restraints excluded: chain Lr residue 13 CYS Chi-restraints excluded: chain Lr residue 115 SER Chi-restraints excluded: chain Lr residue 117 ILE Chi-restraints excluded: chain Lz residue 33 GLU Chi-restraints excluded: chain Lz residue 46 ASP Chi-restraints excluded: chain Lz residue 67 VAL Chi-restraints excluded: chain Lz residue 164 CYS Chi-restraints excluded: chain Lz residue 174 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1142 random chunks: chunk 371 optimal weight: 10.0000 chunk 994 optimal weight: 6.9990 chunk 218 optimal weight: 10.0000 chunk 648 optimal weight: 7.9990 chunk 272 optimal weight: 30.0000 chunk 1104 optimal weight: 6.9990 chunk 917 optimal weight: 9.9990 chunk 511 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 365 optimal weight: 10.0000 chunk 580 optimal weight: 9.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LD 122 GLN ** LE 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 63 GLN ** LI 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LJ 167 GLN ** LN 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LS 146 HIS LU 38 ASN ** LX 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Lg 28 ASN ** Ll 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 155158 Z= 0.370 Angle : 0.540 10.360 227775 Z= 0.280 Chirality : 0.036 0.242 28316 Planarity : 0.004 0.060 14705 Dihedral : 22.564 177.913 68786 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.15 % Favored : 96.84 % Rotamer: Outliers : 2.93 % Allowed : 17.11 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % 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: 0.99 (0.10), residues: 7750 helix: 1.75 (0.09), residues: 3104 sheet: 0.10 (0.17), residues: 1004 loop : -0.06 (0.10), residues: 3642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRPLN 120 HIS 0.006 0.001 HISLa 40 PHE 0.016 0.001 PHE A 666 TYR 0.018 0.001 TYRLU 85 ARG 0.015 0.000 ARGLk 16 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15500 Ramachandran restraints generated. 7750 Oldfield, 0 Emsley, 7750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15500 Ramachandran restraints generated. 7750 Oldfield, 0 Emsley, 7750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 940 residues out of total 6768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 742 time to evaluate : 7.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 84 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8700 (mp) REVERT: K 209 ASP cc_start: 0.6025 (OUTLIER) cc_final: 0.5754 (t0) REVERT: LA 122 ASP cc_start: 0.8855 (t0) cc_final: 0.8636 (t0) REVERT: LB 4 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.8128 (ttm170) REVERT: LB 200 ARG cc_start: 0.9040 (OUTLIER) cc_final: 0.8533 (mtt90) REVERT: LB 216 MET cc_start: 0.9053 (mmt) cc_final: 0.8832 (mmt) REVERT: LB 382 MET cc_start: 0.8678 (mtp) cc_final: 0.8243 (mtm) REVERT: LC 288 ASP cc_start: 0.8791 (t0) cc_final: 0.8344 (t70) REVERT: LD 176 SER cc_start: 0.8919 (p) cc_final: 0.8622 (t) REVERT: LD 235 MET cc_start: 0.8860 (ptm) cc_final: 0.8633 (ptt) REVERT: LE 62 MET cc_start: 0.9390 (mmm) cc_final: 0.9145 (tpt) REVERT: LE 245 GLN cc_start: 0.8292 (tp40) cc_final: 0.7866 (tp40) REVERT: LE 249 ASP cc_start: 0.8352 (m-30) cc_final: 0.8049 (m-30) REVERT: LF 232 ASP cc_start: 0.8553 (m-30) cc_final: 0.8330 (m-30) REVERT: LG 44 ASP cc_start: 0.8798 (m-30) cc_final: 0.8412 (m-30) REVERT: LG 70 LEU cc_start: 0.9573 (OUTLIER) cc_final: 0.9318 (mp) REVERT: LH 110 SER cc_start: 0.9182 (OUTLIER) cc_final: 0.8601 (p) REVERT: LH 115 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.8097 (mtp85) REVERT: LI 57 TYR cc_start: 0.9265 (t80) cc_final: 0.8948 (t80) REVERT: LI 63 GLU cc_start: 0.8926 (mp0) cc_final: 0.8506 (mp0) REVERT: LJ 120 ASP cc_start: 0.8167 (t0) cc_final: 0.7742 (t0) REVERT: LL 175 ASN cc_start: 0.9048 (m-40) cc_final: 0.8557 (m110) REVERT: LM 126 GLU cc_start: 0.8990 (tp30) cc_final: 0.8504 (tp30) REVERT: LM 136 LEU cc_start: 0.9272 (tt) cc_final: 0.9024 (tp) REVERT: LO 87 MET cc_start: 0.9223 (mtt) cc_final: 0.8898 (mtt) REVERT: LO 162 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8421 (tm-30) REVERT: LQ 147 GLU cc_start: 0.8668 (tm-30) cc_final: 0.8296 (tm-30) REVERT: LR 34 ASN cc_start: 0.8768 (t0) cc_final: 0.8433 (t0) REVERT: LT 38 ASP cc_start: 0.8630 (m-30) cc_final: 0.8335 (m-30) REVERT: LT 113 ASP cc_start: 0.8847 (m-30) cc_final: 0.8482 (m-30) REVERT: LU 30 GLU cc_start: 0.8989 (pp20) cc_final: 0.8652 (pp20) REVERT: LU 40 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7329 (tm-30) REVERT: LU 41 GLN cc_start: 0.8771 (tp40) cc_final: 0.8519 (tp-100) REVERT: LU 44 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7786 (mp10) REVERT: LU 45 GLU cc_start: 0.7867 (pt0) cc_final: 0.7591 (pt0) REVERT: LV 111 GLU cc_start: 0.8232 (mp0) cc_final: 0.7592 (mp0) REVERT: LW 23 ARG cc_start: 0.8928 (mmm-85) cc_final: 0.8621 (mmm-85) REVERT: LW 25 ASP cc_start: 0.8606 (p0) cc_final: 0.8359 (p0) REVERT: LW 27 LYS cc_start: 0.9061 (mtpp) cc_final: 0.8495 (mtmm) REVERT: LY 88 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7895 (tp30) REVERT: LZ 18 TYR cc_start: 0.9228 (m-80) cc_final: 0.8826 (m-10) REVERT: LZ 88 ASP cc_start: 0.8206 (p0) cc_final: 0.7875 (p0) REVERT: LZ 91 LEU cc_start: 0.9271 (mt) cc_final: 0.8749 (mt) REVERT: LZ 113 GLU cc_start: 0.9029 (tp30) cc_final: 0.8583 (tm-30) REVERT: La 125 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.8981 (mmtp) REVERT: Lb 58 GLN cc_start: 0.9079 (pp30) cc_final: 0.8844 (pp30) REVERT: Lb 119 CYS cc_start: 0.8129 (t) cc_final: 0.7884 (p) REVERT: Lc 37 MET cc_start: 0.9077 (mmm) cc_final: 0.8504 (mmm) REVERT: Lc 75 SER cc_start: 0.9486 (m) cc_final: 0.9270 (p) REVERT: Lc 98 ASP cc_start: 0.8616 (t0) cc_final: 0.8313 (t0) REVERT: Ld 112 THR cc_start: 0.9281 (p) cc_final: 0.9053 (t) REVERT: Lf 37 ASP cc_start: 0.8869 (p0) cc_final: 0.8089 (p0) REVERT: Lf 40 GLU cc_start: 0.8638 (pm20) cc_final: 0.8336 (pm20) REVERT: Lf 104 MET cc_start: 0.9475 (OUTLIER) cc_final: 0.8647 (mmm) REVERT: Lh 107 GLN cc_start: 0.8863 (tp40) cc_final: 0.8559 (tp40) REVERT: Li 88 GLU cc_start: 0.8338 (pp20) cc_final: 0.8081 (pp20) REVERT: Lk 13 LEU cc_start: 0.8852 (mm) cc_final: 0.8562 (mm) REVERT: Lk 19 ASP cc_start: 0.8674 (m-30) cc_final: 0.8167 (p0) REVERT: Lk 40 ARG cc_start: 0.8841 (ttt180) cc_final: 0.8640 (ttt180) REVERT: Ll 33 ASN cc_start: 0.8679 (t0) cc_final: 0.8437 (t0) REVERT: Lr 48 THR cc_start: 0.9437 (m) cc_final: 0.9177 (p) REVERT: Lr 115 SER cc_start: 0.9536 (OUTLIER) cc_final: 0.9313 (p) outliers start: 198 outliers final: 150 residues processed: 892 average time/residue: 1.2329 time to fit residues: 1982.7229 Evaluate side-chains 881 residues out of total 6768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 719 time to evaluate : 7.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 26 ILE Chi-restraints excluded: chain 1 residue 60 ASP Chi-restraints excluded: chain 1 residue 113 ASN Chi-restraints excluded: chain 1 residue 128 SER Chi-restraints excluded: chain 1 residue 227 VAL Chi-restraints excluded: chain 1 residue 364 TYR Chi-restraints excluded: chain 1 residue 433 VAL Chi-restraints excluded: chain 1 residue 449 LEU Chi-restraints excluded: chain 2 residue 56 LEU Chi-restraints excluded: chain A residue 256 TRP Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 541 GLN Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain K residue 209 ASP Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain LA residue 32 VAL Chi-restraints excluded: chain LA residue 44 ILE Chi-restraints excluded: chain LA residue 84 THR Chi-restraints excluded: chain LA residue 143 THR Chi-restraints excluded: chain LA residue 159 SER Chi-restraints excluded: chain LB residue 4 ARG Chi-restraints excluded: chain LB residue 13 SER Chi-restraints excluded: chain LB residue 101 THR Chi-restraints excluded: chain LB residue 166 THR Chi-restraints excluded: chain LB residue 200 ARG Chi-restraints excluded: chain LB residue 231 VAL Chi-restraints excluded: chain LB residue 370 THR Chi-restraints excluded: chain LB residue 397 ILE Chi-restraints excluded: chain LC residue 154 VAL Chi-restraints excluded: chain LC residue 198 ASN Chi-restraints excluded: chain LC residue 291 ARG Chi-restraints excluded: chain LC residue 335 MET Chi-restraints excluded: chain LD residue 37 VAL Chi-restraints excluded: chain LD residue 75 VAL Chi-restraints excluded: chain LE residue 120 ASP Chi-restraints excluded: chain LF residue 33 LEU Chi-restraints excluded: chain LF residue 121 THR Chi-restraints excluded: chain LF residue 228 VAL Chi-restraints excluded: chain LG residue 70 LEU Chi-restraints excluded: chain LG residue 168 VAL Chi-restraints excluded: chain LG residue 201 THR Chi-restraints excluded: chain LH residue 11 ASP Chi-restraints excluded: chain LH residue 19 THR Chi-restraints excluded: chain LH residue 24 THR Chi-restraints excluded: chain LH residue 46 SER Chi-restraints excluded: chain LH residue 110 SER Chi-restraints excluded: chain LH residue 115 ARG Chi-restraints excluded: chain LH residue 135 SER Chi-restraints excluded: chain LH residue 177 ASP Chi-restraints excluded: chain LI residue 44 ASP Chi-restraints excluded: chain LI residue 136 MET Chi-restraints excluded: chain LI residue 142 LEU Chi-restraints excluded: chain LI residue 168 SER Chi-restraints excluded: chain LI residue 179 ASP Chi-restraints excluded: chain LJ residue 47 THR Chi-restraints excluded: chain LJ residue 51 SER Chi-restraints excluded: chain LJ residue 74 VAL Chi-restraints excluded: chain LJ residue 104 ASN Chi-restraints excluded: chain LJ residue 123 ILE Chi-restraints excluded: chain LJ residue 129 ASP Chi-restraints excluded: chain LJ residue 158 SER Chi-restraints excluded: chain LL residue 33 ILE Chi-restraints excluded: chain LL residue 63 THR Chi-restraints excluded: chain LL residue 160 VAL Chi-restraints excluded: chain LL residue 169 ILE Chi-restraints excluded: chain LM residue 59 ASP Chi-restraints excluded: chain LM residue 108 ASP Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 104 GLU Chi-restraints excluded: chain LN residue 126 THR Chi-restraints excluded: chain LN residue 197 THR Chi-restraints excluded: chain LO residue 49 ARG Chi-restraints excluded: chain LO residue 119 VAL Chi-restraints excluded: chain LO residue 152 VAL Chi-restraints excluded: chain LP residue 10 ASN Chi-restraints excluded: chain LP residue 12 THR Chi-restraints excluded: chain LP residue 109 VAL Chi-restraints excluded: chain LP residue 141 SER 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 LR residue 12 SER Chi-restraints excluded: chain LR residue 29 THR Chi-restraints excluded: chain LR residue 59 SER Chi-restraints excluded: chain LR residue 122 SER Chi-restraints excluded: chain LS residue 75 VAL Chi-restraints excluded: chain LT residue 80 VAL Chi-restraints excluded: chain LU residue 23 LEU Chi-restraints excluded: chain LU residue 25 CYS Chi-restraints excluded: chain LU residue 29 VAL Chi-restraints excluded: chain LU residue 33 ILE Chi-restraints excluded: chain LU residue 34 MET Chi-restraints excluded: chain LU residue 44 GLN Chi-restraints excluded: chain LU residue 62 THR Chi-restraints excluded: chain LU residue 71 THR Chi-restraints excluded: chain LU residue 111 GLU Chi-restraints excluded: chain LU residue 115 PHE Chi-restraints excluded: chain LV residue 22 VAL Chi-restraints excluded: chain LV residue 134 SER Chi-restraints excluded: chain LX residue 140 LEU Chi-restraints excluded: chain LY residue 83 GLU Chi-restraints excluded: chain LY residue 88 GLU Chi-restraints excluded: chain LY residue 94 THR Chi-restraints excluded: chain LZ residue 33 THR Chi-restraints excluded: chain LZ residue 43 VAL Chi-restraints excluded: chain LZ residue 96 VAL Chi-restraints excluded: chain LZ residue 100 VAL Chi-restraints excluded: chain La residue 3 SER Chi-restraints excluded: chain La residue 56 VAL Chi-restraints excluded: chain La residue 72 THR Chi-restraints excluded: chain La residue 86 THR Chi-restraints excluded: chain La residue 95 THR Chi-restraints excluded: chain La residue 125 LYS Chi-restraints excluded: chain La residue 140 VAL Chi-restraints excluded: chain Lb residue 76 VAL Chi-restraints excluded: chain Lc residue 34 THR Chi-restraints excluded: chain Lc residue 93 THR Chi-restraints excluded: chain Lc residue 94 LEU Chi-restraints excluded: chain Ld residue 46 LEU Chi-restraints excluded: chain Ld residue 54 MET Chi-restraints excluded: chain Ld residue 59 THR Chi-restraints excluded: chain Ld residue 89 SER Chi-restraints excluded: chain Ld residue 119 THR Chi-restraints excluded: chain Le residue 87 VAL Chi-restraints excluded: chain Lf residue 90 SER Chi-restraints excluded: chain Lf residue 104 MET Chi-restraints excluded: chain Lg residue 23 SER Chi-restraints excluded: chain Lg residue 25 THR Chi-restraints excluded: chain Lg residue 35 THR Chi-restraints excluded: chain Lh residue 8 ASP Chi-restraints excluded: chain Li residue 27 SER Chi-restraints excluded: chain Li residue 66 ASP Chi-restraints excluded: chain Li residue 79 THR Chi-restraints excluded: chain Li residue 94 LEU Chi-restraints excluded: chain Li residue 97 MET Chi-restraints excluded: chain Lk residue 59 SER Chi-restraints excluded: chain Ll residue 27 ILE Chi-restraints excluded: chain Ll residue 39 SER Chi-restraints excluded: chain Ll residue 47 THR Chi-restraints excluded: chain Lm residue 110 CYS Chi-restraints excluded: chain Lo residue 7 THR Chi-restraints excluded: chain Lo residue 67 VAL Chi-restraints excluded: chain Lo residue 103 VAL Chi-restraints excluded: chain Lp residue 25 MET Chi-restraints excluded: chain Lp residue 74 THR Chi-restraints excluded: chain Lp residue 89 LEU Chi-restraints excluded: chain Lr residue 13 CYS Chi-restraints excluded: chain Lr residue 37 SER Chi-restraints excluded: chain Lr residue 115 SER Chi-restraints excluded: chain Lr residue 117 ILE Chi-restraints excluded: chain Lz residue 33 GLU Chi-restraints excluded: chain Lz residue 46 ASP Chi-restraints excluded: chain Lz residue 67 VAL Chi-restraints excluded: chain Lz residue 164 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1142 random chunks: chunk 1065 optimal weight: 6.9990 chunk 124 optimal weight: 40.0000 chunk 629 optimal weight: 40.0000 chunk 806 optimal weight: 10.0000 chunk 625 optimal weight: 9.9990 chunk 930 optimal weight: 5.9990 chunk 617 optimal weight: 6.9990 chunk 1100 optimal weight: 9.9990 chunk 688 optimal weight: 9.9990 chunk 671 optimal weight: 0.9980 chunk 508 optimal weight: 9.9990 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LE 250 GLN LF 63 GLN ** LI 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LJ 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LN 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LU 38 ASN ** LX 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LZ 132 GLN Lc 19 GLN Lg 28 ASN Lh 20 GLN ** Lk 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ll 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 155158 Z= 0.291 Angle : 0.509 9.621 227775 Z= 0.264 Chirality : 0.034 0.243 28316 Planarity : 0.004 0.052 14705 Dihedral : 22.580 177.756 68786 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.05 % Favored : 96.94 % Rotamer: Outliers : 2.74 % Allowed : 17.62 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % 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: 1.05 (0.10), residues: 7750 helix: 1.83 (0.10), residues: 3091 sheet: 0.10 (0.17), residues: 1006 loop : -0.04 (0.10), residues: 3653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRPLN 120 HIS 0.006 0.001 HISLa 40 PHE 0.019 0.001 PHE A 666 TYR 0.016 0.001 TYRLU 85 ARG 0.009 0.000 ARGLk 16 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15500 Ramachandran restraints generated. 7750 Oldfield, 0 Emsley, 7750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15500 Ramachandran restraints generated. 7750 Oldfield, 0 Emsley, 7750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 934 residues out of total 6768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 749 time to evaluate : 7.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 401 MET cc_start: 0.3417 (mtm) cc_final: 0.2531 (mtm) REVERT: K 84 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8705 (mp) REVERT: K 209 ASP cc_start: 0.6027 (OUTLIER) cc_final: 0.5763 (t0) REVERT: LA 122 ASP cc_start: 0.8828 (t0) cc_final: 0.8612 (t0) REVERT: LB 4 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8131 (ttm170) REVERT: LB 200 ARG cc_start: 0.9041 (OUTLIER) cc_final: 0.8514 (mtt90) REVERT: LB 216 MET cc_start: 0.9015 (mmt) cc_final: 0.8747 (mmt) REVERT: LB 382 MET cc_start: 0.8654 (mtp) cc_final: 0.8218 (mtm) REVERT: LB 396 ARG cc_start: 0.8499 (ttp-110) cc_final: 0.7731 (ttp80) REVERT: LC 288 ASP cc_start: 0.8760 (t0) cc_final: 0.8339 (t70) REVERT: LD 176 SER cc_start: 0.8884 (p) cc_final: 0.8587 (t) REVERT: LD 235 MET cc_start: 0.8845 (ptm) cc_final: 0.8612 (ptt) REVERT: LE 62 MET cc_start: 0.9384 (mmm) cc_final: 0.9144 (tpt) REVERT: LE 245 GLN cc_start: 0.8251 (tp40) cc_final: 0.7795 (tp40) REVERT: LE 249 ASP cc_start: 0.8329 (m-30) cc_final: 0.7992 (m-30) REVERT: LF 232 ASP cc_start: 0.8560 (m-30) cc_final: 0.8327 (m-30) REVERT: LG 44 ASP cc_start: 0.8765 (m-30) cc_final: 0.8399 (m-30) REVERT: LG 70 LEU cc_start: 0.9561 (OUTLIER) cc_final: 0.9300 (mp) REVERT: LG 160 ASP cc_start: 0.8699 (p0) cc_final: 0.8482 (p0) REVERT: LH 110 SER cc_start: 0.9185 (OUTLIER) cc_final: 0.8609 (p) REVERT: LH 115 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.8032 (mtp85) REVERT: LI 35 ASP cc_start: 0.8806 (m-30) cc_final: 0.8481 (m-30) REVERT: LI 57 TYR cc_start: 0.9250 (t80) cc_final: 0.9007 (t80) REVERT: LJ 120 ASP cc_start: 0.8190 (t0) cc_final: 0.7751 (t0) REVERT: LL 175 ASN cc_start: 0.9040 (m-40) cc_final: 0.8548 (m110) REVERT: LM 126 GLU cc_start: 0.8989 (tp30) cc_final: 0.8494 (tp30) REVERT: LM 136 LEU cc_start: 0.9272 (tt) cc_final: 0.9028 (tp) REVERT: LO 87 MET cc_start: 0.9222 (mtt) cc_final: 0.8900 (mtt) REVERT: LO 162 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8373 (tm-30) REVERT: LQ 147 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8236 (tm-30) REVERT: LR 34 ASN cc_start: 0.8751 (t0) cc_final: 0.8445 (t0) REVERT: LT 38 ASP cc_start: 0.8637 (m-30) cc_final: 0.8346 (m-30) REVERT: LT 113 ASP cc_start: 0.8823 (m-30) cc_final: 0.8506 (m-30) REVERT: LU 30 GLU cc_start: 0.9019 (pp20) cc_final: 0.8659 (pp20) REVERT: LU 40 GLU cc_start: 0.8286 (tm-30) cc_final: 0.7379 (tm-30) REVERT: LU 41 GLN cc_start: 0.8735 (tp40) cc_final: 0.8292 (tp-100) REVERT: LU 44 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7865 (mp10) REVERT: LU 45 GLU cc_start: 0.7772 (pt0) cc_final: 0.7408 (pt0) REVERT: LV 111 GLU cc_start: 0.8191 (mp0) cc_final: 0.7673 (mp0) REVERT: LW 25 ASP cc_start: 0.8625 (p0) cc_final: 0.8376 (p0) REVERT: LW 27 LYS cc_start: 0.9071 (mtpp) cc_final: 0.8522 (mtmm) REVERT: LY 88 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7874 (tp30) REVERT: LZ 88 ASP cc_start: 0.8204 (p0) cc_final: 0.7870 (p0) REVERT: LZ 113 GLU cc_start: 0.9000 (tp30) cc_final: 0.8584 (tm-30) REVERT: La 125 LYS cc_start: 0.9220 (OUTLIER) cc_final: 0.8978 (mmtp) REVERT: Lb 58 GLN cc_start: 0.9063 (pp30) cc_final: 0.8825 (pp30) REVERT: Lb 119 CYS cc_start: 0.8133 (t) cc_final: 0.7897 (p) REVERT: Lc 19 GLN cc_start: 0.9038 (tm130) cc_final: 0.8687 (tm-30) REVERT: Lc 75 SER cc_start: 0.9457 (OUTLIER) cc_final: 0.9234 (p) REVERT: Ld 112 THR cc_start: 0.9273 (p) cc_final: 0.9062 (t) REVERT: Lf 37 ASP cc_start: 0.8849 (p0) cc_final: 0.8102 (p0) REVERT: Lf 40 GLU cc_start: 0.8638 (pm20) cc_final: 0.8289 (pm20) REVERT: Lf 104 MET cc_start: 0.9471 (OUTLIER) cc_final: 0.8637 (mmm) REVERT: Lh 107 GLN cc_start: 0.8844 (tp40) cc_final: 0.8529 (tp40) REVERT: Li 88 GLU cc_start: 0.8363 (pp20) cc_final: 0.8100 (pp20) REVERT: Lk 13 LEU cc_start: 0.8813 (mm) cc_final: 0.8546 (mm) REVERT: Lk 16 ARG cc_start: 0.8554 (ttm-80) cc_final: 0.8130 (mtm-85) REVERT: Lk 19 ASP cc_start: 0.8681 (m-30) cc_final: 0.8183 (p0) REVERT: Lr 48 THR cc_start: 0.9444 (OUTLIER) cc_final: 0.9198 (p) outliers start: 185 outliers final: 142 residues processed: 885 average time/residue: 1.1775 time to fit residues: 1872.9345 Evaluate side-chains 891 residues out of total 6768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 736 time to evaluate : 7.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 8 VAL Chi-restraints excluded: chain 1 residue 26 ILE Chi-restraints excluded: chain 1 residue 60 ASP Chi-restraints excluded: chain 1 residue 113 ASN Chi-restraints excluded: chain 1 residue 227 VAL Chi-restraints excluded: chain 1 residue 364 TYR Chi-restraints excluded: chain 1 residue 449 LEU Chi-restraints excluded: chain 2 residue 11 SER Chi-restraints excluded: chain 2 residue 56 LEU Chi-restraints excluded: chain A residue 256 TRP Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 541 GLN Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 209 ASP Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain LA residue 32 VAL Chi-restraints excluded: chain LA residue 44 ILE Chi-restraints excluded: chain LA residue 84 THR Chi-restraints excluded: chain LA residue 143 THR Chi-restraints excluded: chain LA residue 159 SER Chi-restraints excluded: chain LB residue 4 ARG Chi-restraints excluded: chain LB residue 13 SER Chi-restraints excluded: chain LB residue 101 THR Chi-restraints excluded: chain LB residue 166 THR Chi-restraints excluded: chain LB residue 200 ARG Chi-restraints excluded: chain LB residue 231 VAL Chi-restraints excluded: chain LB residue 370 THR Chi-restraints excluded: chain LC residue 154 VAL Chi-restraints excluded: chain LC residue 198 ASN Chi-restraints excluded: chain LC residue 291 ARG Chi-restraints excluded: chain LC residue 335 MET Chi-restraints excluded: chain LC residue 362 GLN Chi-restraints excluded: chain LD residue 37 VAL Chi-restraints excluded: chain LD residue 75 VAL Chi-restraints excluded: chain LE residue 107 VAL Chi-restraints excluded: chain LE residue 120 ASP Chi-restraints excluded: chain LF residue 33 LEU Chi-restraints excluded: chain LF residue 228 VAL Chi-restraints excluded: chain LG residue 70 LEU Chi-restraints excluded: chain LG residue 135 VAL Chi-restraints excluded: chain LG residue 168 VAL Chi-restraints excluded: chain LG residue 198 THR Chi-restraints excluded: chain LG residue 201 THR Chi-restraints excluded: chain LH residue 19 THR Chi-restraints excluded: chain LH residue 24 THR Chi-restraints excluded: chain LH residue 46 SER Chi-restraints excluded: chain LH residue 110 SER Chi-restraints excluded: chain LH residue 115 ARG Chi-restraints excluded: chain LH residue 135 SER Chi-restraints excluded: chain LH residue 177 ASP Chi-restraints excluded: chain LI residue 44 ASP Chi-restraints excluded: chain LI residue 136 MET Chi-restraints excluded: chain LI residue 168 SER Chi-restraints excluded: chain LI residue 179 ASP Chi-restraints excluded: chain LJ residue 47 THR Chi-restraints excluded: chain LJ residue 51 SER Chi-restraints excluded: chain LJ residue 74 VAL Chi-restraints excluded: chain LJ residue 104 ASN Chi-restraints excluded: chain LJ residue 123 ILE Chi-restraints excluded: chain LJ residue 129 ASP Chi-restraints excluded: chain LJ residue 158 SER Chi-restraints excluded: chain LL residue 33 ILE Chi-restraints excluded: chain LL residue 63 THR Chi-restraints excluded: chain LL residue 160 VAL Chi-restraints excluded: chain LL residue 169 ILE Chi-restraints excluded: chain LM residue 59 ASP Chi-restraints excluded: chain LM residue 108 ASP Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 104 GLU Chi-restraints excluded: chain LN residue 126 THR Chi-restraints excluded: chain LN residue 197 THR Chi-restraints excluded: chain LO residue 49 ARG Chi-restraints excluded: chain LO residue 119 VAL Chi-restraints excluded: chain LO residue 152 VAL Chi-restraints excluded: chain LP residue 10 ASN Chi-restraints excluded: chain LP residue 12 THR Chi-restraints excluded: chain LP residue 109 VAL 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 111 SER Chi-restraints excluded: chain LR residue 29 THR Chi-restraints excluded: chain LR residue 59 SER Chi-restraints excluded: chain LR residue 122 SER Chi-restraints excluded: chain LS residue 75 VAL Chi-restraints excluded: chain LU residue 23 LEU Chi-restraints excluded: chain LU residue 29 VAL Chi-restraints excluded: chain LU residue 33 ILE Chi-restraints excluded: chain LU residue 34 MET Chi-restraints excluded: chain LU residue 44 GLN Chi-restraints excluded: chain LU residue 71 THR Chi-restraints excluded: chain LU residue 111 GLU Chi-restraints excluded: chain LU residue 115 PHE Chi-restraints excluded: chain LV residue 22 VAL Chi-restraints excluded: chain LX residue 140 LEU Chi-restraints excluded: chain LY residue 83 GLU Chi-restraints excluded: chain LY residue 88 GLU Chi-restraints excluded: chain LY residue 94 THR Chi-restraints excluded: chain LZ residue 33 THR Chi-restraints excluded: chain LZ residue 43 VAL Chi-restraints excluded: chain LZ residue 96 VAL Chi-restraints excluded: chain LZ residue 100 VAL Chi-restraints excluded: chain La residue 3 SER Chi-restraints excluded: chain La residue 72 THR Chi-restraints excluded: chain La residue 86 THR Chi-restraints excluded: chain La residue 95 THR Chi-restraints excluded: chain La residue 100 ILE Chi-restraints excluded: chain La residue 125 LYS Chi-restraints excluded: chain La residue 139 SER Chi-restraints excluded: chain Lb residue 76 VAL Chi-restraints excluded: chain Lc residue 34 THR 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 59 THR Chi-restraints excluded: chain Ld residue 86 VAL Chi-restraints excluded: chain Ld residue 89 SER Chi-restraints excluded: chain Ld residue 119 THR Chi-restraints excluded: chain Le residue 87 VAL Chi-restraints excluded: chain Lf residue 90 SER Chi-restraints excluded: chain Lf residue 91 ASN Chi-restraints excluded: chain Lf residue 104 MET Chi-restraints excluded: chain Lg residue 23 SER Chi-restraints excluded: chain Lg residue 25 THR Chi-restraints excluded: chain Lg residue 35 THR Chi-restraints excluded: chain Lg residue 48 VAL Chi-restraints excluded: chain Lh residue 8 ASP Chi-restraints excluded: chain Li residue 27 SER Chi-restraints excluded: chain Li residue 79 THR Chi-restraints excluded: chain Li residue 94 LEU Chi-restraints excluded: chain Lk residue 59 SER Chi-restraints excluded: chain Ll residue 27 ILE Chi-restraints excluded: chain Ll residue 39 SER Chi-restraints excluded: chain Ll residue 47 THR Chi-restraints excluded: chain Lm residue 110 CYS Chi-restraints excluded: chain Lo residue 7 THR Chi-restraints excluded: chain Lo residue 67 VAL Chi-restraints excluded: chain Lo residue 103 VAL Chi-restraints excluded: chain Lp residue 25 MET Chi-restraints excluded: chain Lp residue 74 THR Chi-restraints excluded: chain Lp residue 89 LEU Chi-restraints excluded: chain Lr residue 13 CYS Chi-restraints excluded: chain Lr residue 37 SER Chi-restraints excluded: chain Lr residue 48 THR Chi-restraints excluded: chain Lr residue 117 ILE Chi-restraints excluded: chain Lz residue 33 GLU Chi-restraints excluded: chain Lz residue 46 ASP Chi-restraints excluded: chain Lz residue 67 VAL Chi-restraints excluded: chain Lz residue 164 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1142 random chunks: chunk 680 optimal weight: 7.9990 chunk 439 optimal weight: 7.9990 chunk 657 optimal weight: 6.9990 chunk 331 optimal weight: 10.0000 chunk 216 optimal weight: 10.0000 chunk 213 optimal weight: 10.0000 chunk 699 optimal weight: 0.4980 chunk 749 optimal weight: 10.0000 chunk 544 optimal weight: 0.0170 chunk 102 optimal weight: 40.0000 chunk 865 optimal weight: 8.9990 overall best weight: 4.7024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** LD 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 63 GLN ** LI 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LJ 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LN 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 75 GLN LU 38 ASN LW 59 HIS LZ 132 GLN Lc 40 GLN Lg 28 ASN ** Ll 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 155158 Z= 0.226 Angle : 0.485 10.194 227775 Z= 0.252 Chirality : 0.033 0.245 28316 Planarity : 0.004 0.056 14705 Dihedral : 22.580 177.598 68786 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.96 % Favored : 97.03 % Rotamer: Outliers : 2.50 % Allowed : 18.11 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % 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: 1.15 (0.10), residues: 7750 helix: 1.90 (0.10), residues: 3089 sheet: 0.17 (0.17), residues: 989 loop : 0.03 (0.10), residues: 3672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRPLN 120 HIS 0.005 0.001 HISLa 40 PHE 0.018 0.001 PHE A 666 TYR 0.016 0.001 TYRLE 115 ARG 0.007 0.000 ARGLB 396 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15500 Ramachandran restraints generated. 7750 Oldfield, 0 Emsley, 7750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15500 Ramachandran restraints generated. 7750 Oldfield, 0 Emsley, 7750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 936 residues out of total 6768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 767 time to evaluate : 7.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 84 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8707 (mp) REVERT: K 209 ASP cc_start: 0.5973 (OUTLIER) cc_final: 0.5691 (t0) REVERT: LA 47 ASP cc_start: 0.8616 (t0) cc_final: 0.8411 (t0) REVERT: LA 122 ASP cc_start: 0.8815 (t0) cc_final: 0.8583 (t0) REVERT: LB 4 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8084 (ttm170) REVERT: LB 200 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.8501 (mtt90) REVERT: LB 216 MET cc_start: 0.9026 (mmt) cc_final: 0.8766 (mmt) REVERT: LB 382 MET cc_start: 0.8658 (mtp) cc_final: 0.8221 (mtm) REVERT: LB 396 ARG cc_start: 0.8453 (ttp-110) cc_final: 0.7695 (ttp80) REVERT: LC 288 ASP cc_start: 0.8716 (t0) cc_final: 0.8306 (t70) REVERT: LC 352 ASP cc_start: 0.8805 (OUTLIER) cc_final: 0.8511 (p0) REVERT: LD 176 SER cc_start: 0.8823 (p) cc_final: 0.8515 (t) REVERT: LD 235 MET cc_start: 0.8846 (ptm) cc_final: 0.8617 (ptt) REVERT: LE 62 MET cc_start: 0.9388 (mmm) cc_final: 0.9150 (tpt) REVERT: LE 245 GLN cc_start: 0.8279 (tp40) cc_final: 0.7809 (tp40) REVERT: LE 249 ASP cc_start: 0.8335 (m-30) cc_final: 0.7982 (m-30) REVERT: LF 232 ASP cc_start: 0.8541 (m-30) cc_final: 0.8306 (m-30) REVERT: LG 44 ASP cc_start: 0.8750 (m-30) cc_final: 0.8409 (m-30) REVERT: LG 70 LEU cc_start: 0.9531 (OUTLIER) cc_final: 0.9258 (mp) REVERT: LH 110 SER cc_start: 0.9174 (OUTLIER) cc_final: 0.8592 (p) REVERT: LH 115 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7896 (mtp85) REVERT: LI 57 TYR cc_start: 0.9242 (t80) cc_final: 0.8977 (t80) REVERT: LJ 120 ASP cc_start: 0.8184 (t0) cc_final: 0.7740 (t0) REVERT: LL 175 ASN cc_start: 0.9027 (m-40) cc_final: 0.8537 (m110) REVERT: LM 126 GLU cc_start: 0.8987 (tp30) cc_final: 0.8482 (tp30) REVERT: LM 136 LEU cc_start: 0.9260 (tt) cc_final: 0.9026 (tp) REVERT: LO 87 MET cc_start: 0.9214 (mtt) cc_final: 0.8910 (mtt) REVERT: LO 162 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8339 (tm-30) REVERT: LQ 147 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8137 (tm-30) REVERT: LR 34 ASN cc_start: 0.8770 (t0) cc_final: 0.8468 (t0) REVERT: LT 38 ASP cc_start: 0.8617 (m-30) cc_final: 0.8321 (m-30) REVERT: LT 113 ASP cc_start: 0.8829 (m-30) cc_final: 0.8526 (m-30) REVERT: LU 30 GLU cc_start: 0.8983 (pp20) cc_final: 0.8606 (pp20) REVERT: LU 40 GLU cc_start: 0.8267 (tm-30) cc_final: 0.8060 (tm-30) REVERT: LU 41 GLN cc_start: 0.8780 (tp40) cc_final: 0.8334 (tp-100) REVERT: LU 45 GLU cc_start: 0.7755 (pt0) cc_final: 0.7371 (pt0) REVERT: LV 111 GLU cc_start: 0.8066 (mp0) cc_final: 0.7556 (mp0) REVERT: LW 25 ASP cc_start: 0.8675 (p0) cc_final: 0.8396 (p0) REVERT: LW 27 LYS cc_start: 0.9068 (mtpp) cc_final: 0.8513 (mtmm) REVERT: LZ 88 ASP cc_start: 0.8179 (p0) cc_final: 0.7832 (p0) REVERT: LZ 113 GLU cc_start: 0.8991 (tp30) cc_final: 0.8587 (tm-30) REVERT: La 125 LYS cc_start: 0.9215 (OUTLIER) cc_final: 0.8946 (mmtp) REVERT: Lb 58 GLN cc_start: 0.9052 (pp30) cc_final: 0.8823 (pp30) REVERT: Lb 119 CYS cc_start: 0.8147 (t) cc_final: 0.7887 (p) REVERT: Lc 19 GLN cc_start: 0.9048 (tm130) cc_final: 0.8657 (tm-30) REVERT: Lc 75 SER cc_start: 0.9455 (m) cc_final: 0.9225 (p) REVERT: Ld 112 THR cc_start: 0.9260 (p) cc_final: 0.9059 (t) REVERT: Le 102 ASN cc_start: 0.9023 (p0) cc_final: 0.8789 (p0) REVERT: Lf 37 ASP cc_start: 0.8831 (p0) cc_final: 0.8098 (p0) REVERT: Lf 40 GLU cc_start: 0.8605 (pm20) cc_final: 0.8254 (pm20) REVERT: Lf 104 MET cc_start: 0.9439 (OUTLIER) cc_final: 0.8645 (mmm) REVERT: Lh 107 GLN cc_start: 0.8837 (tp40) cc_final: 0.8529 (tp40) REVERT: Li 88 GLU cc_start: 0.8366 (pp20) cc_final: 0.8108 (pp20) REVERT: Lk 13 LEU cc_start: 0.8849 (mm) cc_final: 0.8496 (mm) REVERT: Lk 19 ASP cc_start: 0.8639 (m-30) cc_final: 0.8198 (p0) REVERT: Lr 48 THR cc_start: 0.9429 (OUTLIER) cc_final: 0.9192 (p) REVERT: Lr 115 SER cc_start: 0.9519 (OUTLIER) cc_final: 0.9297 (p) outliers start: 169 outliers final: 134 residues processed: 888 average time/residue: 1.2416 time to fit residues: 1979.7628 Evaluate side-chains 890 residues out of total 6768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 744 time to evaluate : 7.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 26 ILE Chi-restraints excluded: chain 1 residue 60 ASP Chi-restraints excluded: chain 1 residue 113 ASN Chi-restraints excluded: chain 1 residue 227 VAL Chi-restraints excluded: chain 1 residue 364 TYR Chi-restraints excluded: chain 1 residue 409 MET Chi-restraints excluded: chain 1 residue 449 LEU Chi-restraints excluded: chain 2 residue 11 SER Chi-restraints excluded: chain 2 residue 56 LEU Chi-restraints excluded: chain A residue 256 TRP Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 647 GLU Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 209 ASP Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain LA residue 32 VAL Chi-restraints excluded: chain LA residue 143 THR Chi-restraints excluded: chain LB residue 4 ARG Chi-restraints excluded: chain LB residue 13 SER Chi-restraints excluded: chain LB residue 90 VAL Chi-restraints excluded: chain LB residue 101 THR Chi-restraints excluded: chain LB residue 166 THR Chi-restraints excluded: chain LB residue 200 ARG Chi-restraints excluded: chain LB residue 370 THR Chi-restraints excluded: chain LC residue 154 VAL Chi-restraints excluded: chain LC residue 291 ARG Chi-restraints excluded: chain LC residue 335 MET Chi-restraints excluded: chain LC residue 352 ASP Chi-restraints excluded: chain LC residue 362 GLN Chi-restraints excluded: chain LD residue 37 VAL Chi-restraints excluded: chain LE residue 107 VAL Chi-restraints excluded: chain LE residue 120 ASP Chi-restraints excluded: chain LF residue 33 LEU Chi-restraints excluded: chain LF residue 178 SER Chi-restraints excluded: chain LG residue 70 LEU Chi-restraints excluded: chain LG residue 135 VAL Chi-restraints excluded: chain LG residue 168 VAL Chi-restraints excluded: chain LG residue 198 THR Chi-restraints excluded: chain LG residue 201 THR Chi-restraints excluded: chain LH residue 19 THR Chi-restraints excluded: chain LH residue 46 SER Chi-restraints excluded: chain LH residue 84 VAL Chi-restraints excluded: chain LH residue 110 SER Chi-restraints excluded: chain LH residue 115 ARG Chi-restraints excluded: chain LH residue 135 SER Chi-restraints excluded: chain LI residue 44 ASP Chi-restraints excluded: chain LI residue 136 MET Chi-restraints excluded: chain LI residue 168 SER Chi-restraints excluded: chain LI residue 179 ASP Chi-restraints excluded: chain LI residue 189 CYS Chi-restraints excluded: chain LI residue 207 ASP Chi-restraints excluded: chain LJ residue 47 THR Chi-restraints excluded: chain LJ residue 51 SER Chi-restraints excluded: chain LJ residue 74 VAL Chi-restraints excluded: chain LJ residue 104 ASN Chi-restraints excluded: chain LJ residue 123 ILE Chi-restraints excluded: chain LJ residue 129 ASP Chi-restraints excluded: chain LL residue 33 ILE Chi-restraints excluded: chain LL residue 63 THR Chi-restraints excluded: chain LL residue 160 VAL Chi-restraints excluded: chain LL residue 169 ILE Chi-restraints excluded: chain LM residue 108 ASP Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 104 GLU Chi-restraints excluded: chain LN residue 126 THR Chi-restraints excluded: chain LN residue 197 THR Chi-restraints excluded: chain LO residue 49 ARG Chi-restraints excluded: chain LO residue 119 VAL Chi-restraints excluded: chain LO residue 152 VAL Chi-restraints excluded: chain LP residue 10 ASN Chi-restraints excluded: chain LP residue 12 THR Chi-restraints excluded: chain LP residue 100 SER Chi-restraints excluded: chain LP residue 109 VAL Chi-restraints excluded: chain LQ residue 82 VAL Chi-restraints excluded: chain LQ residue 100 VAL Chi-restraints excluded: chain LQ residue 111 SER Chi-restraints excluded: chain LR residue 12 SER Chi-restraints excluded: chain LR residue 29 THR Chi-restraints excluded: chain LR residue 59 SER Chi-restraints excluded: chain LR residue 122 SER Chi-restraints excluded: chain LS residue 48 VAL Chi-restraints excluded: chain LU residue 23 LEU Chi-restraints excluded: chain LU residue 25 CYS Chi-restraints excluded: chain LU residue 29 VAL Chi-restraints excluded: chain LU residue 33 ILE Chi-restraints excluded: chain LU residue 34 MET Chi-restraints excluded: chain LU residue 62 THR Chi-restraints excluded: chain LU residue 71 THR Chi-restraints excluded: chain LU residue 111 GLU Chi-restraints excluded: chain LU residue 115 PHE Chi-restraints excluded: chain LV residue 22 VAL Chi-restraints excluded: chain LV residue 92 ASP Chi-restraints excluded: chain LV residue 101 ASN Chi-restraints excluded: chain LX residue 140 LEU Chi-restraints excluded: chain LY residue 83 GLU Chi-restraints excluded: chain LY residue 94 THR Chi-restraints excluded: chain LZ residue 33 THR Chi-restraints excluded: chain LZ residue 43 VAL Chi-restraints excluded: chain LZ residue 96 VAL Chi-restraints excluded: chain LZ residue 100 VAL Chi-restraints excluded: chain La residue 3 SER Chi-restraints excluded: chain La residue 72 THR Chi-restraints excluded: chain La residue 86 THR Chi-restraints excluded: chain La residue 95 THR Chi-restraints excluded: chain La residue 125 LYS Chi-restraints excluded: chain La residue 139 SER Chi-restraints excluded: chain La residue 140 VAL Chi-restraints excluded: chain Lb residue 76 VAL Chi-restraints excluded: chain Lc residue 28 VAL Chi-restraints excluded: chain Lc residue 34 THR Chi-restraints excluded: chain Lc residue 93 THR Chi-restraints excluded: chain Ld residue 46 LEU Chi-restraints excluded: chain Ld residue 89 SER Chi-restraints excluded: chain Ld residue 119 THR Chi-restraints excluded: chain Le residue 87 VAL Chi-restraints excluded: chain Lf residue 104 MET Chi-restraints excluded: chain Lg residue 23 SER Chi-restraints excluded: chain Lg residue 25 THR Chi-restraints excluded: chain Lg residue 35 THR Chi-restraints excluded: chain Lg residue 48 VAL Chi-restraints excluded: chain Lh residue 8 ASP Chi-restraints excluded: chain Li residue 27 SER Chi-restraints excluded: chain Li residue 94 LEU Chi-restraints excluded: chain Ll residue 27 ILE Chi-restraints excluded: chain Ll residue 39 SER Chi-restraints excluded: chain Ll residue 47 THR Chi-restraints excluded: chain Lm residue 110 CYS Chi-restraints excluded: chain Lo residue 33 LEU Chi-restraints excluded: chain Lo residue 67 VAL Chi-restraints excluded: chain Lo residue 103 VAL Chi-restraints excluded: chain Lp residue 25 MET Chi-restraints excluded: chain Lp residue 74 THR Chi-restraints excluded: chain Lp residue 89 LEU Chi-restraints excluded: chain Lr residue 13 CYS Chi-restraints excluded: chain Lr residue 37 SER Chi-restraints excluded: chain Lr residue 48 THR Chi-restraints excluded: chain Lr residue 115 SER Chi-restraints excluded: chain Lz residue 33 GLU Chi-restraints excluded: chain Lz residue 46 ASP Chi-restraints excluded: chain Lz residue 67 VAL Chi-restraints excluded: chain Lz residue 164 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1142 random chunks: chunk 1001 optimal weight: 10.0000 chunk 1054 optimal weight: 10.0000 chunk 962 optimal weight: 10.0000 chunk 1025 optimal weight: 0.9980 chunk 617 optimal weight: 7.9990 chunk 446 optimal weight: 0.8980 chunk 805 optimal weight: 8.9990 chunk 314 optimal weight: 20.0000 chunk 926 optimal weight: 3.9990 chunk 970 optimal weight: 10.0000 chunk 1022 optimal weight: 6.9990 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LF 63 GLN ** LI 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LJ 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LN 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LU 38 ASN LZ 132 GLN Lg 28 ASN Ll 25 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 155158 Z= 0.208 Angle : 0.477 10.094 227775 Z= 0.248 Chirality : 0.032 0.246 28316 Planarity : 0.004 0.054 14705 Dihedral : 22.562 177.764 68786 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.83 % Favored : 97.16 % Rotamer: Outliers : 2.51 % Allowed : 18.20 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % 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 (0.10), residues: 7750 helix: 1.90 (0.10), residues: 3096 sheet: 0.18 (0.17), residues: 990 loop : 0.05 (0.10), residues: 3664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRPLB 196 HIS 0.006 0.001 HIS K 50 PHE 0.018 0.001 PHE A 666 TYR 0.025 0.001 TYRLd 103 ARG 0.013 0.000 ARGLk 16 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15500 Ramachandran restraints generated. 7750 Oldfield, 0 Emsley, 7750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15500 Ramachandran restraints generated. 7750 Oldfield, 0 Emsley, 7750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 927 residues out of total 6768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 757 time to evaluate : 7.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 443 TYR cc_start: 0.7309 (t80) cc_final: 0.7105 (t80) REVERT: K 84 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8718 (mp) REVERT: K 209 ASP cc_start: 0.5907 (OUTLIER) cc_final: 0.5616 (t0) REVERT: LA 47 ASP cc_start: 0.8606 (t0) cc_final: 0.8405 (t0) REVERT: LA 122 ASP cc_start: 0.8809 (t0) cc_final: 0.8573 (t0) REVERT: LB 4 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8080 (ttm170) REVERT: LB 200 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8500 (mtt90) REVERT: LB 216 MET cc_start: 0.9019 (mmt) cc_final: 0.8772 (mmt) REVERT: LB 382 MET cc_start: 0.8652 (mtp) cc_final: 0.8213 (mtm) REVERT: LB 396 ARG cc_start: 0.8497 (ttp-110) cc_final: 0.7720 (ttp80) REVERT: LC 288 ASP cc_start: 0.8699 (t0) cc_final: 0.8286 (t70) REVERT: LC 352 ASP cc_start: 0.8765 (OUTLIER) cc_final: 0.8472 (p0) REVERT: LD 176 SER cc_start: 0.8795 (p) cc_final: 0.8493 (t) REVERT: LD 235 MET cc_start: 0.8867 (ptm) cc_final: 0.8652 (ptt) REVERT: LE 62 MET cc_start: 0.9373 (mmm) cc_final: 0.9136 (tpt) REVERT: LE 245 GLN cc_start: 0.8291 (tp40) cc_final: 0.7806 (tp40) REVERT: LE 249 ASP cc_start: 0.8310 (m-30) cc_final: 0.7945 (m-30) REVERT: LF 232 ASP cc_start: 0.8542 (m-30) cc_final: 0.8307 (m-30) REVERT: LG 44 ASP cc_start: 0.8717 (m-30) cc_final: 0.8380 (m-30) REVERT: LG 70 LEU cc_start: 0.9532 (OUTLIER) cc_final: 0.9259 (mp) REVERT: LG 160 ASP cc_start: 0.8648 (p0) cc_final: 0.8425 (p0) REVERT: LH 110 SER cc_start: 0.9171 (OUTLIER) cc_final: 0.8598 (p) REVERT: LI 57 TYR cc_start: 0.9238 (t80) cc_final: 0.8975 (t80) REVERT: LJ 59 SER cc_start: 0.9430 (m) cc_final: 0.9097 (t) REVERT: LJ 120 ASP cc_start: 0.8177 (t0) cc_final: 0.7734 (t0) REVERT: LL 175 ASN cc_start: 0.9026 (m-40) cc_final: 0.8543 (m110) REVERT: LM 126 GLU cc_start: 0.8985 (tp30) cc_final: 0.8470 (tp30) REVERT: LM 136 LEU cc_start: 0.9267 (tt) cc_final: 0.9025 (tp) REVERT: LO 87 MET cc_start: 0.9202 (mtt) cc_final: 0.8902 (mtt) REVERT: LO 162 GLU cc_start: 0.8695 (tm-30) cc_final: 0.8304 (tm-30) REVERT: LQ 147 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8120 (tm-30) REVERT: LR 34 ASN cc_start: 0.8764 (t0) cc_final: 0.8499 (t0) REVERT: LT 38 ASP cc_start: 0.8612 (m-30) cc_final: 0.8300 (m-30) REVERT: LT 113 ASP cc_start: 0.8823 (m-30) cc_final: 0.8512 (m-30) REVERT: LU 30 GLU cc_start: 0.8984 (pp20) cc_final: 0.8607 (pp20) REVERT: LU 40 GLU cc_start: 0.8422 (tm-30) cc_final: 0.7787 (tm-30) REVERT: LU 41 GLN cc_start: 0.8793 (tp40) cc_final: 0.8576 (tp40) REVERT: LV 111 GLU cc_start: 0.8154 (mp0) cc_final: 0.7621 (mp0) REVERT: LW 25 ASP cc_start: 0.8666 (p0) cc_final: 0.8362 (p0) REVERT: LW 27 LYS cc_start: 0.9078 (mtpp) cc_final: 0.8566 (mtmm) REVERT: LY 88 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7874 (tp30) REVERT: LZ 88 ASP cc_start: 0.8155 (p0) cc_final: 0.7822 (p0) REVERT: LZ 113 GLU cc_start: 0.8981 (tp30) cc_final: 0.8582 (tm-30) REVERT: La 125 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8952 (mmtp) REVERT: Lb 58 GLN cc_start: 0.9047 (pp30) cc_final: 0.8826 (pp30) REVERT: Lb 119 CYS cc_start: 0.8151 (t) cc_final: 0.7895 (p) REVERT: Lc 19 GLN cc_start: 0.9035 (tm130) cc_final: 0.8644 (tm-30) REVERT: Lc 61 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8504 (mt-10) REVERT: Lc 75 SER cc_start: 0.9449 (OUTLIER) cc_final: 0.9214 (p) REVERT: Ld 112 THR cc_start: 0.9265 (p) cc_final: 0.9065 (t) REVERT: Le 102 ASN cc_start: 0.9007 (p0) cc_final: 0.8771 (p0) REVERT: Lf 37 ASP cc_start: 0.8828 (p0) cc_final: 0.8086 (p0) REVERT: Lf 40 GLU cc_start: 0.8608 (pm20) cc_final: 0.8257 (pm20) REVERT: Lf 104 MET cc_start: 0.9435 (OUTLIER) cc_final: 0.8644 (mmm) REVERT: Lh 107 GLN cc_start: 0.8844 (tp40) cc_final: 0.8527 (tp40) REVERT: Li 88 GLU cc_start: 0.8375 (pp20) cc_final: 0.8111 (pp20) REVERT: Lk 13 LEU cc_start: 0.8821 (mm) cc_final: 0.8456 (mm) REVERT: Lk 16 ARG cc_start: 0.8482 (ttm-80) cc_final: 0.8068 (mtm-85) REVERT: Lk 19 ASP cc_start: 0.8650 (m-30) cc_final: 0.8203 (p0) REVERT: Lk 40 ARG cc_start: 0.8791 (ttt180) cc_final: 0.8540 (ttt180) REVERT: Lr 48 THR cc_start: 0.9433 (OUTLIER) cc_final: 0.9191 (p) REVERT: Lr 115 SER cc_start: 0.9508 (OUTLIER) cc_final: 0.9288 (p) outliers start: 170 outliers final: 140 residues processed: 880 average time/residue: 1.3063 time to fit residues: 2079.0421 Evaluate side-chains 902 residues out of total 6768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 749 time to evaluate : 7.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 8 VAL Chi-restraints excluded: chain 1 residue 26 ILE Chi-restraints excluded: chain 1 residue 60 ASP Chi-restraints excluded: chain 1 residue 113 ASN Chi-restraints excluded: chain 1 residue 128 SER Chi-restraints excluded: chain 1 residue 227 VAL Chi-restraints excluded: chain 1 residue 364 TYR Chi-restraints excluded: chain 1 residue 409 MET Chi-restraints excluded: chain 1 residue 449 LEU Chi-restraints excluded: chain 2 residue 11 SER Chi-restraints excluded: chain 2 residue 56 LEU Chi-restraints excluded: chain A residue 256 TRP Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 360 ASP Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 541 GLN Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain K residue 209 ASP Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain LA residue 32 VAL Chi-restraints excluded: chain LA residue 143 THR Chi-restraints excluded: chain LB residue 4 ARG Chi-restraints excluded: chain LB residue 13 SER Chi-restraints excluded: chain LB residue 101 THR Chi-restraints excluded: chain LB residue 200 ARG Chi-restraints excluded: chain LB residue 370 THR Chi-restraints excluded: chain LC residue 154 VAL Chi-restraints excluded: chain LC residue 198 ASN Chi-restraints excluded: chain LC residue 291 ARG Chi-restraints excluded: chain LC residue 335 MET Chi-restraints excluded: chain LC residue 352 ASP Chi-restraints excluded: chain LC residue 362 GLN Chi-restraints excluded: chain LD residue 37 VAL Chi-restraints excluded: chain LD residue 75 VAL Chi-restraints excluded: chain LE residue 107 VAL Chi-restraints excluded: chain LE residue 120 ASP Chi-restraints excluded: chain LF residue 33 LEU Chi-restraints excluded: chain LF residue 178 SER Chi-restraints excluded: chain LG residue 70 LEU Chi-restraints excluded: chain LG residue 135 VAL Chi-restraints excluded: chain LG residue 168 VAL Chi-restraints excluded: chain LG residue 198 THR Chi-restraints excluded: chain LG residue 201 THR Chi-restraints excluded: chain LH residue 19 THR Chi-restraints excluded: chain LH residue 46 SER Chi-restraints excluded: chain LH residue 84 VAL Chi-restraints excluded: chain LH residue 110 SER Chi-restraints excluded: chain LH residue 135 SER Chi-restraints excluded: chain LI residue 44 ASP Chi-restraints excluded: chain LI residue 136 MET Chi-restraints excluded: chain LI residue 168 SER Chi-restraints excluded: chain LI residue 179 ASP Chi-restraints excluded: chain LI residue 189 CYS Chi-restraints excluded: chain LI residue 207 ASP Chi-restraints excluded: chain LJ residue 47 THR Chi-restraints excluded: chain LJ residue 51 SER Chi-restraints excluded: chain LJ residue 74 VAL Chi-restraints excluded: chain LJ residue 104 ASN Chi-restraints excluded: chain LJ residue 129 ASP Chi-restraints excluded: chain LL residue 33 ILE Chi-restraints excluded: chain LL residue 63 THR Chi-restraints excluded: chain LL residue 160 VAL Chi-restraints excluded: chain LL residue 169 ILE Chi-restraints excluded: chain LM residue 108 ASP Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 104 GLU Chi-restraints excluded: chain LN residue 126 THR Chi-restraints excluded: chain LN residue 197 THR Chi-restraints excluded: chain LO residue 49 ARG Chi-restraints excluded: chain LO residue 119 VAL Chi-restraints excluded: chain LO residue 152 VAL Chi-restraints excluded: chain LP residue 10 ASN Chi-restraints excluded: chain LP residue 12 THR Chi-restraints excluded: chain LP residue 100 SER Chi-restraints excluded: chain LP residue 109 VAL 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 111 SER Chi-restraints excluded: chain LR residue 12 SER Chi-restraints excluded: chain LR residue 29 THR Chi-restraints excluded: chain LR residue 59 SER Chi-restraints excluded: chain LR residue 111 GLU Chi-restraints excluded: chain LR residue 122 SER Chi-restraints excluded: chain LS residue 48 VAL Chi-restraints excluded: chain LU residue 23 LEU Chi-restraints excluded: chain LU residue 25 CYS Chi-restraints excluded: chain LU residue 29 VAL Chi-restraints excluded: chain LU residue 33 ILE Chi-restraints excluded: chain LU residue 34 MET Chi-restraints excluded: chain LU residue 62 THR Chi-restraints excluded: chain LU residue 71 THR Chi-restraints excluded: chain LV residue 22 VAL Chi-restraints excluded: chain LV residue 92 ASP Chi-restraints excluded: chain LV residue 101 ASN Chi-restraints excluded: chain LX residue 140 LEU Chi-restraints excluded: chain LY residue 83 GLU Chi-restraints excluded: chain LY residue 88 GLU Chi-restraints excluded: chain LY residue 94 THR Chi-restraints excluded: chain LZ residue 33 THR Chi-restraints excluded: chain LZ residue 43 VAL Chi-restraints excluded: chain LZ residue 96 VAL Chi-restraints excluded: chain LZ residue 100 VAL Chi-restraints excluded: chain La residue 3 SER Chi-restraints excluded: chain La residue 72 THR Chi-restraints excluded: chain La residue 86 THR Chi-restraints excluded: chain La residue 95 THR Chi-restraints excluded: chain La residue 100 ILE Chi-restraints excluded: chain La residue 125 LYS Chi-restraints excluded: chain La residue 139 SER Chi-restraints excluded: chain Lb residue 76 VAL Chi-restraints excluded: chain Lc residue 28 VAL Chi-restraints excluded: chain Lc residue 34 THR Chi-restraints excluded: chain Lc residue 75 SER Chi-restraints excluded: chain Lc residue 93 THR Chi-restraints excluded: chain Ld residue 89 SER Chi-restraints excluded: chain Ld residue 119 THR Chi-restraints excluded: chain Le residue 87 VAL Chi-restraints excluded: chain Lf residue 90 SER Chi-restraints excluded: chain Lf residue 104 MET Chi-restraints excluded: chain Lg residue 23 SER Chi-restraints excluded: chain Lg residue 25 THR Chi-restraints excluded: chain Lg residue 35 THR Chi-restraints excluded: chain Lg residue 48 VAL Chi-restraints excluded: chain Lh residue 8 ASP Chi-restraints excluded: chain Li residue 27 SER Chi-restraints excluded: chain Li residue 94 LEU Chi-restraints excluded: chain Ll residue 25 GLN Chi-restraints excluded: chain Ll residue 27 ILE Chi-restraints excluded: chain Ll residue 39 SER Chi-restraints excluded: chain Ll residue 47 THR Chi-restraints excluded: chain Lm residue 110 CYS Chi-restraints excluded: chain Lo residue 33 LEU Chi-restraints excluded: chain Lo residue 67 VAL Chi-restraints excluded: chain Lo residue 103 VAL Chi-restraints excluded: chain Lp residue 25 MET Chi-restraints excluded: chain Lp residue 74 THR Chi-restraints excluded: chain Lp residue 89 LEU Chi-restraints excluded: chain Lr residue 13 CYS Chi-restraints excluded: chain Lr residue 37 SER Chi-restraints excluded: chain Lr residue 48 THR Chi-restraints excluded: chain Lr residue 115 SER Chi-restraints excluded: chain Lz residue 33 GLU Chi-restraints excluded: chain Lz residue 46 ASP Chi-restraints excluded: chain Lz residue 65 VAL Chi-restraints excluded: chain Lz residue 67 VAL Chi-restraints excluded: chain Lz residue 164 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1142 random chunks: chunk 673 optimal weight: 10.0000 chunk 1084 optimal weight: 0.0980 chunk 662 optimal weight: 0.0050 chunk 514 optimal weight: 4.9990 chunk 754 optimal weight: 10.0000 chunk 1137 optimal weight: 0.7980 chunk 1047 optimal weight: 8.9990 chunk 905 optimal weight: 5.9990 chunk 94 optimal weight: 30.0000 chunk 699 optimal weight: 0.9990 chunk 555 optimal weight: 10.0000 overall best weight: 1.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LF 63 GLN ** LI 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LJ 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LL 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LN 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 97 ASN LU 38 ASN LZ 132 GLN Lc 40 GLN Lg 28 ASN Lm 84 GLN Lo 51 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.104 155158 Z= 0.120 Angle : 0.456 15.223 227775 Z= 0.238 Chirality : 0.030 0.348 28316 Planarity : 0.003 0.068 14705 Dihedral : 22.592 177.159 68786 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.61 % Favored : 97.38 % Rotamer: Outliers : 1.42 % Allowed : 19.31 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % 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: 1.27 (0.10), residues: 7750 helix: 1.97 (0.10), residues: 3089 sheet: 0.23 (0.17), residues: 948 loop : 0.12 (0.10), residues: 3713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRPLN 120 HIS 0.005 0.000 HIS K 50 PHE 0.020 0.001 PHELU 39 TYR 0.023 0.001 TYRLd 103 ARG 0.009 0.000 ARGLk 16 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15500 Ramachandran restraints generated. 7750 Oldfield, 0 Emsley, 7750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15500 Ramachandran restraints generated. 7750 Oldfield, 0 Emsley, 7750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 891 residues out of total 6768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 795 time to evaluate : 7.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 84 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8683 (mp) REVERT: K 171 ASP cc_start: 0.7585 (p0) cc_final: 0.7322 (t0) REVERT: K 209 ASP cc_start: 0.5905 (OUTLIER) cc_final: 0.5677 (t0) REVERT: LA 122 ASP cc_start: 0.8806 (t0) cc_final: 0.8541 (t0) REVERT: LB 4 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8018 (ttm170) REVERT: LB 200 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.8574 (mtt90) REVERT: LB 216 MET cc_start: 0.9018 (mmt) cc_final: 0.8725 (mmt) REVERT: LB 382 MET cc_start: 0.8635 (mtp) cc_final: 0.8201 (mtm) REVERT: LB 396 ARG cc_start: 0.8450 (ttp-110) cc_final: 0.7690 (ttp80) REVERT: LC 288 ASP cc_start: 0.8609 (t0) cc_final: 0.8140 (t70) REVERT: LC 352 ASP cc_start: 0.8788 (OUTLIER) cc_final: 0.8508 (p0) REVERT: LD 176 SER cc_start: 0.8653 (p) cc_final: 0.8354 (t) REVERT: LD 235 MET cc_start: 0.8868 (ptm) cc_final: 0.8652 (ptt) REVERT: LE 62 MET cc_start: 0.9364 (mmm) cc_final: 0.9140 (tpt) REVERT: LE 245 GLN cc_start: 0.8258 (tp40) cc_final: 0.7736 (tp40) REVERT: LE 249 ASP cc_start: 0.8285 (m-30) cc_final: 0.7871 (m-30) REVERT: LF 232 ASP cc_start: 0.8500 (m-30) cc_final: 0.8250 (m-30) REVERT: LG 44 ASP cc_start: 0.8649 (m-30) cc_final: 0.8340 (m-30) REVERT: LG 160 ASP cc_start: 0.8572 (p0) cc_final: 0.8370 (p0) REVERT: LH 110 SER cc_start: 0.9118 (OUTLIER) cc_final: 0.8578 (p) REVERT: LI 35 ASP cc_start: 0.8626 (m-30) cc_final: 0.8336 (m-30) REVERT: LI 57 TYR cc_start: 0.9194 (t80) cc_final: 0.8873 (t80) REVERT: LI 207 ASP cc_start: 0.8908 (OUTLIER) cc_final: 0.8627 (t70) REVERT: LJ 59 SER cc_start: 0.9431 (m) cc_final: 0.9123 (t) REVERT: LJ 120 ASP cc_start: 0.8144 (t0) cc_final: 0.7746 (t0) REVERT: LL 175 ASN cc_start: 0.9024 (m-40) cc_final: 0.8558 (m110) REVERT: LM 126 GLU cc_start: 0.8971 (tp30) cc_final: 0.8456 (tp30) REVERT: LM 136 LEU cc_start: 0.9245 (tt) cc_final: 0.9034 (tp) REVERT: LO 87 MET cc_start: 0.9130 (mtt) cc_final: 0.8821 (mtt) REVERT: LO 158 GLU cc_start: 0.8678 (tt0) cc_final: 0.8412 (tp30) REVERT: LO 162 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8296 (tm-30) REVERT: LQ 147 GLU cc_start: 0.8471 (tm-30) cc_final: 0.8002 (tm-30) REVERT: LR 34 ASN cc_start: 0.8747 (t0) cc_final: 0.8490 (t0) REVERT: LT 38 ASP cc_start: 0.8568 (m-30) cc_final: 0.8219 (m-30) REVERT: LT 113 ASP cc_start: 0.8824 (m-30) cc_final: 0.8551 (m-30) REVERT: LU 40 GLU cc_start: 0.8762 (tm-30) cc_final: 0.8216 (tm-30) REVERT: LU 41 GLN cc_start: 0.9019 (tp40) cc_final: 0.8816 (tp40) REVERT: LU 85 TYR cc_start: 0.9271 (t80) cc_final: 0.8931 (t80) REVERT: LV 111 GLU cc_start: 0.7991 (mp0) cc_final: 0.7487 (mp0) REVERT: LW 25 ASP cc_start: 0.8706 (p0) cc_final: 0.8435 (p0) REVERT: LW 27 LYS cc_start: 0.9089 (mtpp) cc_final: 0.8521 (mtmm) REVERT: LZ 88 ASP cc_start: 0.8161 (p0) cc_final: 0.7814 (p0) REVERT: LZ 113 GLU cc_start: 0.8931 (tp30) cc_final: 0.8565 (tm-30) REVERT: Lb 119 CYS cc_start: 0.8122 (t) cc_final: 0.7846 (p) REVERT: Lc 19 GLN cc_start: 0.9016 (tm130) cc_final: 0.8619 (tm-30) REVERT: Lc 61 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8471 (mt-10) REVERT: Lc 75 SER cc_start: 0.9373 (m) cc_final: 0.9124 (p) REVERT: Lf 37 ASP cc_start: 0.8829 (p0) cc_final: 0.8047 (p0) REVERT: Lf 40 GLU cc_start: 0.8569 (pm20) cc_final: 0.8193 (pm20) REVERT: Lh 107 GLN cc_start: 0.8824 (tp40) cc_final: 0.8518 (tp40) REVERT: Li 88 GLU cc_start: 0.8325 (pp20) cc_final: 0.8071 (pp20) REVERT: Lk 13 LEU cc_start: 0.8806 (mm) cc_final: 0.8378 (mt) REVERT: Lk 16 ARG cc_start: 0.8366 (ttm-80) cc_final: 0.7734 (mmt90) REVERT: Lk 19 ASP cc_start: 0.8599 (m-30) cc_final: 0.8200 (p0) REVERT: Lm 79 GLU cc_start: 0.8265 (tp30) cc_final: 0.7525 (tm-30) REVERT: Lr 48 THR cc_start: 0.9400 (OUTLIER) cc_final: 0.9172 (p) outliers start: 96 outliers final: 75 residues processed: 865 average time/residue: 1.2321 time to fit residues: 1910.2830 Evaluate side-chains 844 residues out of total 6768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 761 time to evaluate : 7.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 60 ASP Chi-restraints excluded: chain 1 residue 227 VAL Chi-restraints excluded: chain 1 residue 364 TYR Chi-restraints excluded: chain 1 residue 449 LEU Chi-restraints excluded: chain A residue 256 TRP Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain K residue 192 VAL Chi-restraints excluded: chain K residue 209 ASP Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain LA residue 143 THR Chi-restraints excluded: chain LB residue 4 ARG Chi-restraints excluded: chain LB residue 13 SER Chi-restraints excluded: chain LB residue 166 THR Chi-restraints excluded: chain LB residue 200 ARG Chi-restraints excluded: chain LB residue 231 VAL Chi-restraints excluded: chain LB residue 370 THR Chi-restraints excluded: chain LC residue 154 VAL Chi-restraints excluded: chain LC residue 198 ASN Chi-restraints excluded: chain LC residue 291 ARG Chi-restraints excluded: chain LC residue 352 ASP Chi-restraints excluded: chain LC residue 362 GLN Chi-restraints excluded: chain LD residue 37 VAL Chi-restraints excluded: chain LD residue 75 VAL Chi-restraints excluded: chain LE residue 107 VAL Chi-restraints excluded: chain LF residue 33 LEU Chi-restraints excluded: chain LG residue 198 THR Chi-restraints excluded: chain LH residue 110 SER Chi-restraints excluded: chain LH residue 135 SER Chi-restraints excluded: chain LI residue 44 ASP Chi-restraints excluded: chain LI residue 179 ASP Chi-restraints excluded: chain LI residue 189 CYS Chi-restraints excluded: chain LI residue 207 ASP Chi-restraints excluded: chain LJ residue 47 THR Chi-restraints excluded: chain LJ residue 104 ASN Chi-restraints excluded: chain LJ residue 129 ASP Chi-restraints excluded: chain LL residue 33 ILE Chi-restraints excluded: chain LL residue 63 THR Chi-restraints excluded: chain LL residue 160 VAL Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 104 GLU Chi-restraints excluded: chain LO residue 49 ARG Chi-restraints excluded: chain LO residue 119 VAL Chi-restraints excluded: chain LO residue 152 VAL Chi-restraints excluded: chain LP residue 10 ASN Chi-restraints excluded: chain LQ residue 82 VAL Chi-restraints excluded: chain LQ residue 85 THR Chi-restraints excluded: chain LR residue 12 SER Chi-restraints excluded: chain LR residue 29 THR Chi-restraints excluded: chain LR residue 111 GLU Chi-restraints excluded: chain LU residue 23 LEU Chi-restraints excluded: chain LU residue 25 CYS Chi-restraints excluded: chain LU residue 33 ILE Chi-restraints excluded: chain LU residue 71 THR Chi-restraints excluded: chain LV residue 92 ASP Chi-restraints excluded: chain LV residue 101 ASN Chi-restraints excluded: chain LX residue 140 LEU Chi-restraints excluded: chain LY residue 83 GLU Chi-restraints excluded: chain LY residue 94 THR Chi-restraints excluded: chain LZ residue 43 VAL Chi-restraints excluded: chain LZ residue 100 VAL Chi-restraints excluded: chain Lb residue 76 VAL Chi-restraints excluded: chain Lc residue 28 VAL Chi-restraints excluded: chain Ld residue 119 THR Chi-restraints excluded: chain Le residue 87 VAL Chi-restraints excluded: chain Lf residue 90 SER Chi-restraints excluded: chain Lg residue 23 SER Chi-restraints excluded: chain Lg residue 25 THR Chi-restraints excluded: chain Lg residue 48 VAL Chi-restraints excluded: chain Lg residue 75 SER Chi-restraints excluded: chain Lh residue 8 ASP Chi-restraints excluded: chain Li residue 94 LEU Chi-restraints excluded: chain Lm residue 110 CYS Chi-restraints excluded: chain Lo residue 67 VAL Chi-restraints excluded: chain Lo residue 103 VAL Chi-restraints excluded: chain Lr residue 48 THR Chi-restraints excluded: chain Lz residue 33 GLU Chi-restraints excluded: chain Lz residue 67 VAL Chi-restraints excluded: chain Lz residue 164 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1142 random chunks: chunk 719 optimal weight: 6.9990 chunk 965 optimal weight: 8.9990 chunk 277 optimal weight: 10.0000 chunk 835 optimal weight: 5.9990 chunk 133 optimal weight: 30.0000 chunk 251 optimal weight: 20.0000 chunk 907 optimal weight: 10.0000 chunk 379 optimal weight: 20.0000 chunk 931 optimal weight: 0.0970 chunk 114 optimal weight: 20.0000 chunk 167 optimal weight: 10.0000 overall best weight: 6.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LF 63 GLN ** LI 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LJ 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LN 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 97 ASN LR 40 GLN LU 38 ASN ** LX 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LY 66 GLN LZ 132 GLN Lc 40 GLN Lg 28 ASN ** Lk 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lo 51 GLN Lp 33 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.056091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.040338 restraints weight = 566994.078| |-----------------------------------------------------------------------------| r_work (start): 0.2657 rms_B_bonded: 2.12 r_work: 0.2539 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2442 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2442 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2439 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2439 r_free = 0.2439 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7332 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2439 r_free = 0.2439 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7332 | |-----------------------------------------------------------------------------| r_final: 0.2439 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 155158 Z= 0.305 Angle : 0.509 13.039 227775 Z= 0.263 Chirality : 0.034 0.248 28316 Planarity : 0.004 0.075 14705 Dihedral : 22.480 178.958 68786 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.03 % Favored : 96.95 % Rotamer: Outliers : 1.64 % Allowed : 19.28 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.90 % 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: 1.19 (0.10), residues: 7750 helix: 1.89 (0.10), residues: 3106 sheet: 0.24 (0.17), residues: 982 loop : 0.07 (0.10), residues: 3662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRPLB 196 HIS 0.006 0.001 HISLa 40 PHE 0.037 0.001 PHE 2 44 TYR 0.023 0.001 TYRLd 103 ARG 0.009 0.000 ARGLk 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 34607.31 seconds wall clock time: 606 minutes 43.41 seconds (36403.41 seconds total)