Starting phenix.real_space_refine on Tue Feb 27 17:10:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flb_29273/02_2024/8flb_29273_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flb_29273/02_2024/8flb_29273.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flb_29273/02_2024/8flb_29273_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flb_29273/02_2024/8flb_29273_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flb_29273/02_2024/8flb_29273_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flb_29273/02_2024/8flb_29273.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flb_29273/02_2024/8flb_29273.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flb_29273/02_2024/8flb_29273_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flb_29273/02_2024/8flb_29273_neut_updated.pdb" } resolution = 2.55 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= 0.055 sd= 0.194 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: 8 Type Number sf(0) Gaussians K 1 8.98 5 Zn 6 6.06 5 P 3697 5.49 5 Mg 88 5.21 5 S 290 5.16 5 C 79348 2.51 5 N 28010 2.21 5 O 37594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L9 TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L9 TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LA TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LC GLU 130": "OE1" <-> "OE2" Residue "LE TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LG PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LI ASP 112": "OD1" <-> "OD2" Residue "LK PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SA TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SD PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SF PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SG TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SH PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SH TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SM TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 149034 Number of models: 1 Model: "" Number of chains: 69 Chain: "BA" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 449 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 4, 'TRANS': 86} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 320 Unresolved non-hydrogen dihedrals: 207 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 6, 'ASN:plan1': 5, 'HIS:plan': 4, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 126 Chain: "L1" Number of atoms: 3278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 3278 Classifications: {'RNA': 154} Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 12, 'rna3p': 3, 'rna3p_pur': 61, 'rna3p_pyr': 64} Link IDs: {'rna2p': 25, 'rna3p': 128} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "L3" Number of atoms: 73423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3420, 73423 Classifications: {'RNA': 3420} Modifications used: {'rna2p': 5, 'rna2p_pur': 333, 'rna2p_pyr': 212, 'rna3p': 81, 'rna3p_pur': 1513, 'rna3p_pyr': 1258} Link IDs: {'rna2p': 549, 'rna3p': 2870} Chain breaks: 29 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 33 Chain: "L4" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2561 Classifications: {'RNA': 120} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 54, 'rna3p_pyr': 54} Link IDs: {'rna2p': 12, 'rna3p': 107} Chain: "L5" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1349 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 5, 'TRANS': 162} Chain: "L6" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1701 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 195} Chain: "L7" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1650 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 191} Chain: "L8" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1111 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 4, 'TRANS': 130} Chain: "L9" 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: "LA" 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: "LB" Number of atoms: 1512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1512 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain: "LC" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1461 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 164} Chain: "LD" Number of atoms: 1289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1289 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 3, 'TRANS': 150} Chain: "LE" Number of atoms: 1264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1264 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 9, 'TRANS': 144} Chain breaks: 1 Chain: "LF" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 842 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 2, 'TRANS': 100} Chain: "LG" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1034 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 132} Chain: "LH" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1156 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 134} Chain: "LI" 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: "LJ" 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: "LK" 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: "LL" 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: "LM" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 751 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 4, 'TRANS': 86} Chain breaks: 1 Chain: "LN" Number of atoms: 3239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3239 Classifications: {'peptide': 402} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 386} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "LO" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 738 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "LP" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 879 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "LQ" 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: "LR" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 888 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain: "LS" 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: "LT" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 876 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 104} Chain: "LU" 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: "LV" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 851 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "LW" 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: "LX" 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: "LY" 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: "LZ" 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: "NK" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 581 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain breaks: 1 Chain: "NL" Number of atoms: 2175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2175 Classifications: {'peptide': 263} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 249} Chain breaks: 1 Chain: "NP" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 847 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 7, 'TRANS': 96} Chain breaks: 1 Chain: "NR" Number of atoms: 1299 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 152, 1292 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 4, 'TRANS': 147} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 152, 1292 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 4, 'TRANS': 147} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 1304 Chain: "SA" Number of atoms: 2853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2853 Classifications: {'peptide': 358} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 339} Chain: "SB" Number of atoms: 2243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2243 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 9, 'TRANS': 265} Chain: "SC" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1747 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 202} Chain breaks: 2 Chain: "SD" 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: "SE" Number of atoms: 1869 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 231, 1861 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 217} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 231, 1861 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 217} Chain breaks: 1 bond proxies already assigned to first conformer: 1883 Chain: "SF" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1876 Classifications: {'peptide': 245} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 230} Chain: "SG" 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: "SH" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 773 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain: "SI" Number of atoms: 1952 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 234, 1926 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 223} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 234, 1926 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 223} Chain breaks: 1 bond proxies already assigned to first conformer: 1931 Chain: "SK" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1852 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 7, 'TRANS': 236} Chain: "SM" Number of atoms: 3278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3278 Classifications: {'peptide': 399} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 380} Chain breaks: 2 Chain: "SQ" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 650 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 113} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 449 Unresolved non-hydrogen angles: 565 Unresolved non-hydrogen dihedrals: 390 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 8, 'TRP:plan': 3, 'ASP:plan': 5, 'PHE:plan': 8, 'GLU:plan': 9, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 260 Chain: "SR" Number of atoms: 4932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4932 Classifications: {'peptide': 601} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 577} Chain breaks: 2 Chain: "SV" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1184 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "VB" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 455 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 3, 'TRANS': 54} Chain breaks: 1 Chain: "L1" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "L3" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 74 Unusual residues: {' MG': 74} Classifications: {'undetermined': 74} Link IDs: {None: 73} Chain: "L4" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "LG" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LN" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LQ" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LR" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "LT" 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: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "LW" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "LX" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "NP" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "SF" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "SR" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' K': 1, ' MG': 1, 'GDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "SV" 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 A06IB SG CYSLR 46 86.990 181.206 98.891 1.00 26.64 S ATOM A06IS SG CYSLR 49 85.760 184.309 100.701 1.00 34.19 S ATOM A06Q3 SG CYSLR 83 83.596 183.019 97.962 1.00 21.72 S ATOM A06QN SG CYSLR 86 87.044 184.299 97.018 1.00 24.48 S ATOM A092Z SG CYSLV 12 189.915 113.750 133.826 1.00 11.62 S ATOM A093N SG CYSLV 15 193.043 112.780 132.000 1.00 14.35 S ATOM A09GO SG CYSLV 72 191.888 116.594 132.372 1.00 15.40 S ATOM A09HP SG CYSLV 77 190.092 114.067 130.141 1.00 22.46 S ATOM A09RZ SG CYSLW 19 95.214 126.027 118.392 1.00 13.76 S ATOM A09SR SG CYSLW 22 95.951 123.177 120.823 1.00 13.09 S ATOM A09VA SG CYSLW 34 97.879 126.489 120.991 1.00 11.60 S ATOM A09VT SG CYSLW 37 98.521 124.091 118.165 1.00 14.02 S ATOM A0AG0 SG CYSLX 39 97.674 192.566 107.335 1.00 24.78 S ATOM A0AGN SG CYSLX 42 94.335 194.095 106.955 1.00 24.70 S ATOM A0AK1 SG CYSLX 57 94.708 191.135 109.235 1.00 22.82 S ATOM A0AKH SG CYSLX 60 94.994 190.490 105.552 1.00 25.75 S ATOM A0DYS SG CYSNP 63 76.364 199.573 177.952 1.00 26.73 S ATOM A0DZB SG CYSNP 66 74.364 196.252 178.002 1.00 25.83 S ATOM A10IJ SG CYSSV 6 65.151 180.678 198.200 1.00 20.24 S ATOM A10JC SG CYSSV 9 61.581 179.413 197.892 1.00 19.10 S ATOM A10OG SG CYSSV 32 64.237 176.958 198.763 1.00 17.53 S ATOM A10PA SG CYSSV 36 64.214 178.375 195.292 1.00 17.05 S Time building chain proxies: 57.51, per 1000 atoms: 0.39 Number of scatterers: 149034 At special positions: 0 Unit cell: (258.352, 241.2, 299.088, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 6 29.99 K 1 19.00 S 290 16.00 P 3697 15.00 Mg 88 11.99 O 37594 8.00 N 28010 7.00 C 79348 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 54.58 Conformation dependent library (CDL) restraints added in 9.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNLR 202 " pdb="ZN ZNLR 202 " - pdb=" SG CYSLR 86 " pdb="ZN ZNLR 202 " - pdb=" SG CYSLR 49 " pdb="ZN ZNLR 202 " - pdb=" SG CYSLR 46 " pdb="ZN ZNLR 202 " - pdb=" SG CYSLR 83 " pdb=" ZNLV 200 " pdb="ZN ZNLV 200 " - pdb=" SG CYSLV 77 " pdb="ZN ZNLV 200 " - pdb=" SG CYSLV 12 " pdb="ZN ZNLV 200 " - pdb=" SG CYSLV 15 " pdb="ZN ZNLV 200 " - pdb=" SG CYSLV 72 " pdb=" ZNLW 500 " pdb="ZN ZNLW 500 " - pdb=" SG CYSLW 34 " pdb="ZN ZNLW 500 " - pdb=" SG CYSLW 22 " pdb="ZN ZNLW 500 " - pdb=" SG CYSLW 19 " pdb="ZN ZNLW 500 " - pdb=" SG CYSLW 37 " pdb=" ZNLX 500 " pdb="ZN ZNLX 500 " - pdb=" SG CYSLX 39 " pdb="ZN ZNLX 500 " - pdb=" SG CYSLX 57 " pdb="ZN ZNLX 500 " - pdb=" SG CYSLX 42 " pdb="ZN ZNLX 500 " - pdb=" SG CYSLX 60 " pdb=" ZNNP 500 " pdb="ZN ZNNP 500 " - pdb=" ND1 HISNP 85 " pdb="ZN ZNNP 500 " - pdb=" NE2 HISNP 79 " pdb="ZN ZNNP 500 " - pdb=" SG CYSNP 63 " pdb="ZN ZNNP 500 " - pdb=" SG CYSNP 66 " pdb=" ZNSV 500 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 32 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 9 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 36 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 6 " Number of angles added : 32 17024 Ramachandran restraints generated. 8512 Oldfield, 0 Emsley, 8512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16246 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 314 helices and 76 sheets defined 46.4% alpha, 12.0% beta 1154 base pairs and 1818 stacking pairs defined. Time for finding SS restraints: 81.02 Creating SS restraints... Processing helix chain 'BA' and resid 76 through 86 removed outlier: 3.728A pdb=" N LYSBA 86 " --> pdb=" O ILEBA 82 " (cutoff:3.500A) Processing helix chain 'BA' and resid 105 through 121 removed outlier: 5.051A pdb=" N HISBA 118 " --> pdb=" O ARGBA 114 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ARGBA 119 " --> pdb=" O GLNBA 115 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N LEUBA 121 " --> pdb=" O ARGBA 117 " (cutoff:3.500A) Processing helix chain 'BA' and resid 124 through 140 removed outlier: 3.698A pdb=" N THRBA 128 " --> pdb=" O GLUBA 124 " (cutoff:3.500A) Processing helix chain 'BA' and resid 147 through 158 Processing helix chain 'L5' and resid 30 through 45 Processing helix chain 'L5' and resid 76 through 91 removed outlier: 3.660A pdb=" N GLUL5 80 " --> pdb=" O GLYL5 76 " (cutoff:3.500A) Processing helix chain 'L5' and resid 111 through 116 removed outlier: 4.385A pdb=" N LEUL5 115 " --> pdb=" O GLUL5 111 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLYL5 116 " --> pdb=" O HISL5 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'L5' and resid 111 through 116' Processing helix chain 'L5' and resid 139 through 144 removed outlier: 4.581A pdb=" N ASPL5 143 " --> pdb=" O PHEL5 139 " (cutoff:3.500A) Processing helix chain 'L5' and resid 158 through 170 Processing helix chain 'L6' and resid 17 through 22 removed outlier: 4.282A pdb=" N ARGL6 21 " --> pdb=" O ASPL6 17 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VALL6 22 " --> pdb=" O TRPL6 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'L6' and resid 17 through 22' Processing helix chain 'L6' and resid 27 through 47 Processing helix chain 'L6' and resid 77 through 85 Processing helix chain 'L6' and resid 87 through 95 removed outlier: 4.188A pdb=" N ARGL6 92 " --> pdb=" O LYSL6 88 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N THRL6 93 " --> pdb=" O LYSL6 89 " (cutoff:3.500A) Processing helix chain 'L6' and resid 106 through 124 removed outlier: 3.538A pdb=" N LEUL6 110 " --> pdb=" O SERL6 106 " (cutoff:3.500A) Processing helix chain 'L6' and resid 140 through 147 removed outlier: 4.071A pdb=" N ALAL6 147 " --> pdb=" O GLUL6 143 " (cutoff:3.500A) Processing helix chain 'L6' and resid 170 through 177 removed outlier: 5.891A pdb=" N LYSL6 177 " --> pdb=" O GLUL6 173 " (cutoff:3.500A) Processing helix chain 'L6' and resid 178 through 192 Processing helix chain 'L6' and resid 193 through 211 removed outlier: 3.504A pdb=" N LYSL6 209 " --> pdb=" O GLNL6 205 " (cutoff:3.500A) Processing helix chain 'L7' and resid 15 through 30 removed outlier: 3.559A pdb=" N LYSL7 25 " --> pdb=" O ALAL7 21 " (cutoff:3.500A) Processing helix chain 'L7' and resid 46 through 61 removed outlier: 3.750A pdb=" N LYSL7 60 " --> pdb=" O ALAL7 56 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ARGL7 61 " --> pdb=" O PHEL7 57 " (cutoff:3.500A) Processing helix chain 'L7' and resid 65 through 70 removed outlier: 3.680A pdb=" N GLYL7 69 " --> pdb=" O ASNL7 65 " (cutoff:3.500A) Proline residue: L7 70 - end of helix No H-bonds generated for 'chain 'L7' and resid 65 through 70' Processing helix chain 'L7' and resid 75 through 89 removed outlier: 3.637A pdb=" N METL7 87 " --> pdb=" O THRL7 83 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEUL7 88 " --> pdb=" O VALL7 84 " (cutoff:3.500A) Proline residue: L7 89 - end of helix Processing helix chain 'L7' and resid 92 through 103 removed outlier: 3.667A pdb=" N LEUL7 102 " --> pdb=" O ALAL7 98 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N LYSL7 103 " --> pdb=" O LEUL7 99 " (cutoff:3.500A) Processing helix chain 'L7' and resid 110 through 116 removed outlier: 7.948A pdb=" N LYSL7 114 " --> pdb=" O PROL7 110 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LYSL7 115 " --> pdb=" O PROL7 111 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N LYSL7 116 " --> pdb=" O TYRL7 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'L7' and resid 110 through 116' Processing helix chain 'L7' and resid 124 through 129 Processing helix chain 'L7' and resid 137 through 146 Processing helix chain 'L7' and resid 151 through 190 removed outlier: 3.731A pdb=" N ILEL7 166 " --> pdb=" O GLUL7 162 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N LYSL7 187 " --> pdb=" O LYSL7 183 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LYSL7 188 " --> pdb=" O ASNL7 184 " (cutoff:3.500A) Processing helix chain 'L7' and resid 191 through 200 removed outlier: 3.510A pdb=" N HISL7 199 " --> pdb=" O VALL7 195 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLYL7 200 " --> pdb=" O LEUL7 196 " (cutoff:3.500A) Processing helix chain 'L8' and resid 51 through 56 removed outlier: 3.881A pdb=" N METL8 55 " --> pdb=" O PROL8 51 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N GLNL8 56 " --> pdb=" O PHEL8 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'L8' and resid 51 through 56' Processing helix chain 'L8' and resid 69 through 81 Processing helix chain 'L8' and resid 82 through 90 removed outlier: 5.619A pdb=" N ARGL8 90 " --> pdb=" O TRPL8 86 " (cutoff:3.500A) Processing helix chain 'L8' and resid 91 through 104 removed outlier: 3.903A pdb=" N METL8 104 " --> pdb=" O ARGL8 100 " (cutoff:3.500A) Processing helix chain 'L8' and resid 105 through 136 removed outlier: 3.639A pdb=" N GLUL8 126 " --> pdb=" O ILEL8 122 " (cutoff:3.500A) Processing helix chain 'L9' and resid 2 through 14 removed outlier: 3.897A pdb=" N TYRL9 6 " --> pdb=" O GLYL9 2 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARGL9 12 " --> pdb=" O GLNL9 8 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYSL9 13 " --> pdb=" O GLUL9 9 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LYSL9 14 " --> pdb=" O LEUL9 10 " (cutoff:3.500A) Processing helix chain 'L9' and resid 16 through 34 removed outlier: 3.747A pdb=" N GLNL9 32 " --> pdb=" O TRPL9 28 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEUL9 33 " --> pdb=" O GLNL9 29 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N SERL9 34 " --> pdb=" O TYRL9 30 " (cutoff:3.500A) Processing helix chain 'L9' and resid 44 through 52 Processing helix chain 'L9' and resid 83 through 88 removed outlier: 3.905A pdb=" N HISL9 87 " --> pdb=" O LYSL9 83 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N GLYL9 88 " --> pdb=" O PROL9 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'L9' and resid 83 through 88' Processing helix chain 'L9' and resid 97 through 111 removed outlier: 3.672A pdb=" N GLYL9 111 " --> pdb=" O GLYL9 107 " (cutoff:3.500A) Processing helix chain 'L9' and resid 139 through 146 removed outlier: 3.737A pdb=" N ASNL9 145 " --> pdb=" O ALAL9 141 " (cutoff:3.500A) Proline residue: L9 146 - end of helix Processing helix chain 'L9' and resid 147 through 153 removed outlier: 6.178A pdb=" N ILEL9 151 " --> pdb=" O ASPL9 147 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N THRL9 152 " --> pdb=" O THRL9 148 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYSL9 153 " --> pdb=" O GLNL9 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'L9' and resid 147 through 153' Processing helix chain 'L9' and resid 158 through 163 removed outlier: 3.540A pdb=" N ARGL9 162 " --> pdb=" O HISL9 158 " (cutoff:3.500A) Processing helix chain 'L9' and resid 165 through 173 removed outlier: 3.743A pdb=" N LYSL9 170 " --> pdb=" O SERL9 166 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N SERL9 171 " --> pdb=" O ALAL9 167 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ARGL9 172 " --> pdb=" O GLYL9 168 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLYL9 173 " --> pdb=" O ARGL9 169 " (cutoff:3.500A) Processing helix chain 'L9' and resid 187 through 197 Processing helix chain 'LA' and resid 25 through 37 Processing helix chain 'LA' and resid 40 through 54 removed outlier: 3.541A pdb=" N THRLA 52 " --> pdb=" O LEULA 48 " (cutoff:3.500A) Processing helix chain 'LA' and resid 72 through 77 removed outlier: 4.866A pdb=" N TRPLA 76 " --> pdb=" O GLNLA 72 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLYLA 77 " --> pdb=" O ALALA 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'LA' and resid 72 through 77' Processing helix chain 'LA' and resid 84 through 106 Processing helix chain 'LB' and resid 22 through 39 Processing helix chain 'LB' and resid 41 through 54 removed outlier: 4.147A pdb=" N GLNLB 45 " --> pdb=" O SERLB 41 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHELB 52 " --> pdb=" O LEULB 48 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N METLB 53 " --> pdb=" O LYSLB 49 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N SERLB 54 " --> pdb=" O ARGLB 50 " (cutoff:3.500A) Processing helix chain 'LB' and resid 62 through 72 removed outlier: 4.088A pdb=" N LEULB 72 " --> pdb=" O ARGLB 68 " (cutoff:3.500A) Processing helix chain 'LB' and resid 106 through 117 removed outlier: 3.527A pdb=" N ALALB 116 " --> pdb=" O ARGLB 112 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLYLB 117 " --> pdb=" O ILELB 113 " (cutoff:3.500A) Processing helix chain 'LB' and resid 122 through 130 Processing helix chain 'LB' and resid 146 through 153 removed outlier: 4.553A pdb=" N ARGLB 150 " --> pdb=" O ARGLB 146 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N HISLB 151 " --> pdb=" O GLULB 147 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N GLYLB 153 " --> pdb=" O TYRLB 149 " (cutoff:3.500A) Processing helix chain 'LC' and resid 36 through 52 removed outlier: 3.996A pdb=" N GLNLC 50 " --> pdb=" O TYRLC 46 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEULC 51 " --> pdb=" O PHELC 47 " (cutoff:3.500A) Processing helix chain 'LC' and resid 101 through 117 Processing helix chain 'LC' and resid 120 through 125 removed outlier: 3.896A pdb=" N ILELC 124 " --> pdb=" O ARGLC 120 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N GLNLC 125 " --> pdb=" O ALALC 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'LC' and resid 120 through 125' Processing helix chain 'LC' and resid 139 through 147 removed outlier: 4.558A pdb=" N PHELC 145 " --> pdb=" O ALALC 141 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N HISLC 146 " --> pdb=" O VALLC 142 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ASPLC 147 " --> pdb=" O LYSLC 143 " (cutoff:3.500A) Processing helix chain 'LC' and resid 161 through 166 Proline residue: LC 165 - end of helix No H-bonds generated for 'chain 'LC' and resid 161 through 166' Processing helix chain 'LD' and resid 4 through 16 Processing helix chain 'LD' and resid 18 through 23 removed outlier: 3.744A pdb=" N VALLD 22 " --> pdb=" O GLYLD 18 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N TRPLD 23 " --> pdb=" O LYSLD 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'LD' and resid 18 through 23' Processing helix chain 'LD' and resid 28 through 36 removed outlier: 3.859A pdb=" N ALALD 35 " --> pdb=" O GLULD 31 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N ASNLD 36 " --> pdb=" O ILELD 32 " (cutoff:3.500A) Processing helix chain 'LD' and resid 37 through 48 removed outlier: 3.514A pdb=" N LYSLD 43 " --> pdb=" O GLNLD 39 " (cutoff:3.500A) Processing helix chain 'LD' and resid 60 through 73 Processing helix chain 'LD' and resid 84 through 113 Proline residue: LD 90 - end of helix removed outlier: 6.783A pdb=" N VALLD 93 " --> pdb=" O METLD 89 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THRLD 94 " --> pdb=" O PROLD 90 " (cutoff:3.500A) Processing helix chain 'LD' and resid 116 through 130 removed outlier: 4.434A pdb=" N ASNLD 130 " --> pdb=" O LYSLD 126 " (cutoff:3.500A) Processing helix chain 'LD' and resid 134 through 155 removed outlier: 3.570A pdb=" N LEULD 138 " --> pdb=" O ASNLD 134 " (cutoff:3.500A) Processing helix chain 'LE' and resid 26 through 32 removed outlier: 4.501A pdb=" N TYRLE 30 " --> pdb=" O PROLE 26 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARGLE 32 " --> pdb=" O ALALE 28 " (cutoff:3.500A) Processing helix chain 'LE' and resid 54 through 59 removed outlier: 3.728A pdb=" N HISLE 58 " --> pdb=" O HISLE 54 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N GLYLE 59 " --> pdb=" O LYSLE 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'LE' and resid 54 through 59' Processing helix chain 'LE' and resid 92 through 97 removed outlier: 4.044A pdb=" N ILELE 96 " --> pdb=" O ARGLE 92 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N LYSLE 97 " --> pdb=" O ILELE 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'LE' and resid 92 through 97' Processing helix chain 'LE' and resid 99 through 121 removed outlier: 3.535A pdb=" N ASPLE 103 " --> pdb=" O SERLE 99 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLULE 121 " --> pdb=" O LYSLE 117 " (cutoff:3.500A) Processing helix chain 'LF' and resid 25 through 32 Processing helix chain 'LF' and resid 35 through 47 Processing helix chain 'LF' and resid 55 through 60 removed outlier: 3.528A pdb=" N GLYLF 59 " --> pdb=" O ASNLF 55 " (cutoff:3.500A) Processing helix chain 'LF' and resid 79 through 95 removed outlier: 3.885A pdb=" N LEULF 83 " --> pdb=" O SERLF 79 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYSLF 84 " --> pdb=" O LYSLF 80 " (cutoff:3.500A) Processing helix chain 'LG' and resid 69 through 74 removed outlier: 3.549A pdb=" N ARGLG 73 " --> pdb=" O LYSLG 69 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N LYSLG 74 " --> pdb=" O PROLG 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'LG' and resid 69 through 74' Processing helix chain 'LG' and resid 122 through 130 Proline residue: LG 130 - end of helix Processing helix chain 'LG' and resid 131 through 136 removed outlier: 3.832A pdb=" N ASNLG 135 " --> pdb=" O ARGLG 131 " (cutoff:3.500A) Processing helix chain 'LH' and resid 14 through 30 Processing helix chain 'LH' and resid 72 through 78 removed outlier: 3.553A pdb=" N ILELH 77 " --> pdb=" O HISLH 73 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N LYSLH 78 " --> pdb=" O TYRLH 74 " (cutoff:3.500A) Processing helix chain 'LH' and resid 83 through 92 Processing helix chain 'LH' and resid 105 through 117 Processing helix chain 'LH' and resid 145 through 154 Processing helix chain 'LI' and resid 10 through 21 Processing helix chain 'LI' and resid 22 through 31 removed outlier: 4.032A pdb=" N LYSLI 28 " --> pdb=" O HISLI 24 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N SERLI 31 " --> pdb=" O ARGLI 27 " (cutoff:3.500A) Processing helix chain 'LI' and resid 35 through 43 Processing helix chain 'LI' and resid 100 through 105 removed outlier: 4.034A pdb=" N VALLI 104 " --> pdb=" O HISLI 100 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N VALLI 105 " --> pdb=" O PROLI 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'LI' and resid 100 through 105' Processing helix chain 'LI' and resid 112 through 134 Processing helix chain 'LJ' and resid 58 through 67 removed outlier: 4.049A pdb=" N LYSLJ 67 " --> pdb=" O ALALJ 63 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 76 through 81 removed outlier: 3.696A pdb=" N LEULJ 80 " --> pdb=" O ASNLJ 76 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N METLJ 81 " --> pdb=" O TYRLJ 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'LJ' and resid 76 through 81' Processing helix chain 'LJ' and resid 92 through 97 removed outlier: 4.280A pdb=" N ASNLJ 97 " --> pdb=" O LYSLJ 93 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 98 through 104 removed outlier: 4.681A pdb=" N ARGLJ 102 " --> pdb=" O LYSLJ 98 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ASPLJ 103 " --> pdb=" O ASPLJ 99 " (cutoff:3.500A) Proline residue: LJ 104 - end of helix No H-bonds generated for 'chain 'LJ' and resid 98 through 104' Processing helix chain 'LJ' and resid 105 through 125 removed outlier: 3.714A pdb=" N THRLJ 124 " --> pdb=" O GLULJ 120 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLYLJ 125 " --> pdb=" O ARGLJ 121 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 127 through 133 removed outlier: 3.621A pdb=" N PHELJ 131 " --> pdb=" O ASNLJ 127 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLNLJ 132 " --> pdb=" O LYSLJ 128 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N LYSLJ 133 " --> pdb=" O TRPLJ 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'LJ' and resid 127 through 133' Processing helix chain 'LK' and resid 2 through 7 removed outlier: 4.023A pdb=" N ARGLK 6 " --> pdb=" O PROLK 2 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LYSLK 7 " --> pdb=" O SERLK 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'LK' and resid 2 through 7' Processing helix chain 'LK' and resid 41 through 48 Processing helix chain 'LK' and resid 64 through 69 removed outlier: 4.435A pdb=" N SERLK 68 " --> pdb=" O LYSLK 64 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHELK 69 " --> pdb=" O ARGLK 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'LK' and resid 64 through 69' Processing helix chain 'LK' and resid 74 through 83 removed outlier: 4.569A pdb=" N TRPLK 79 " --> pdb=" O LEULK 75 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N THRLK 80 " --> pdb=" O ASPLK 76 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEULK 81 " --> pdb=" O LYSLK 77 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N VALLK 82 " --> pdb=" O LEULK 78 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N SERLK 83 " --> pdb=" O TRPLK 79 " (cutoff:3.500A) Processing helix chain 'LK' and resid 84 through 93 Processing helix chain 'LK' and resid 102 through 107 removed outlier: 3.683A pdb=" N SERLK 106 " --> pdb=" O ASPLK 102 " (cutoff:3.500A) Processing helix chain 'LK' and resid 130 through 141 removed outlier: 3.670A pdb=" N GLYLK 141 " --> pdb=" O ILELK 137 " (cutoff:3.500A) Processing helix chain 'LL' and resid 2 through 13 removed outlier: 3.571A pdb=" N METLL 8 " --> pdb=" O HISLL 4 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VALLL 9 " --> pdb=" O LEULL 5 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ASNLL 12 " --> pdb=" O METLL 8 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N CYSLL 13 " --> pdb=" O VALLL 9 " (cutoff:3.500A) Processing helix chain 'LL' and resid 85 through 101 removed outlier: 3.676A pdb=" N ASNLL 100 " --> pdb=" O METLL 96 " (cutoff:3.500A) Processing helix chain 'LL' and resid 103 through 123 removed outlier: 4.401A pdb=" N ARGLL 107 " --> pdb=" O ARGLL 103 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N METLL 108 " --> pdb=" O PROLL 104 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ALALL 109 " --> pdb=" O ASPLL 105 " (cutoff:3.500A) Proline residue: LL 123 - end of helix Processing helix chain 'LM' and resid 11 through 20 removed outlier: 4.325A pdb=" N LYSLM 15 " --> pdb=" O ASNLM 11 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ASNLM 19 " --> pdb=" O LYSLM 15 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N GLYLM 20 " --> pdb=" O TRPLM 16 " (cutoff:3.500A) Processing helix chain 'LM' and resid 36 through 54 removed outlier: 4.898A pdb=" N LYSLM 51 " --> pdb=" O LYSLM 47 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LYSLM 52 " --> pdb=" O LYSLM 48 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLYLM 53 " --> pdb=" O HISLM 49 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LEULM 54 " --> pdb=" O ASNLM 50 " (cutoff:3.500A) Processing helix chain 'LM' and resid 55 through 66 Processing helix chain 'LM' and resid 91 through 101 Processing helix chain 'LM' and resid 105 through 118 removed outlier: 3.652A pdb=" N ARGLM 117 " --> pdb=" O ALALM 113 " (cutoff:3.500A) Processing helix chain 'LN' and resid 13 through 18 removed outlier: 4.714A pdb=" N LEULN 17 " --> pdb=" O SERLN 13 " (cutoff:3.500A) Proline residue: LN 18 - end of helix No H-bonds generated for 'chain 'LN' and resid 13 through 18' Processing helix chain 'LN' and resid 111 through 120 removed outlier: 3.984A pdb=" N ARGLN 117 " --> pdb=" O GLULN 113 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N PHELN 118 " --> pdb=" O CYSLN 114 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TYRLN 119 " --> pdb=" O LYSLN 115 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N LYSLN 120 " --> pdb=" O ARGLN 116 " (cutoff:3.500A) Processing helix chain 'LN' and resid 130 through 140 removed outlier: 4.558A pdb=" N LYSLN 135 " --> pdb=" O THRLN 131 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LYSLN 136 " --> pdb=" O LYSLN 132 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N TRPLN 137 " --> pdb=" O TYRLN 133 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLNLN 138 " --> pdb=" O CYSLN 134 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N GLULN 140 " --> pdb=" O LYSLN 136 " (cutoff:3.500A) Processing helix chain 'LN' and resid 141 through 156 Processing helix chain 'LN' and resid 167 through 172 removed outlier: 4.243A pdb=" N LEULN 171 " --> pdb=" O GLNLN 167 " (cutoff:3.500A) Proline residue: LN 172 - end of helix No H-bonds generated for 'chain 'LN' and resid 167 through 172' Processing helix chain 'LN' and resid 189 through 201 Processing helix chain 'LN' and resid 206 through 211 removed outlier: 4.358A pdb=" N VALLN 210 " --> pdb=" O PROLN 206 " (cutoff:3.500A) Processing helix chain 'LN' and resid 230 through 235 Processing helix chain 'LN' and resid 356 through 361 removed outlier: 5.082A pdb=" N LEULN 360 " --> pdb=" O LYSLN 356 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLULN 361 " --> pdb=" O ARGLN 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'LN' and resid 356 through 361' Processing helix chain 'LN' and resid 381 through 390 Processing helix chain 'LN' and resid 392 through 403 Processing helix chain 'LO' and resid 13 through 24 removed outlier: 3.539A pdb=" N LEULO 20 " --> pdb=" O SERLO 16 " (cutoff:3.500A) Processing helix chain 'LO' and resid 30 through 41 Processing helix chain 'LO' and resid 53 through 68 Processing helix chain 'LO' and resid 77 through 86 Processing helix chain 'LP' and resid 28 through 34 removed outlier: 3.753A pdb=" N ARGLP 32 " --> pdb=" O ASNLP 28 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N HISLP 34 " --> pdb=" O HISLP 30 " (cutoff:3.500A) Processing helix chain 'LP' and resid 40 through 57 Processing helix chain 'LP' and resid 65 through 74 Processing helix chain 'LQ' and resid 24 through 29 removed outlier: 3.534A pdb=" N TYRLQ 28 " --> pdb=" O GLNLQ 24 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N VALLQ 29 " --> pdb=" O SERLQ 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'LQ' and resid 24 through 29' Processing helix chain 'LQ' and resid 43 through 48 Processing helix chain 'LQ' and resid 81 through 90 removed outlier: 4.024A pdb=" N VALLQ 87 " --> pdb=" O LYSLQ 83 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N LEULQ 88 " --> pdb=" O GLULQ 84 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LEULQ 89 " --> pdb=" O LEULQ 85 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N METLQ 90 " --> pdb=" O GLULQ 86 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 104 through 119 removed outlier: 3.684A pdb=" N LYSLQ 109 " --> pdb=" O SERLQ 105 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALALQ 110 " --> pdb=" O LYSLQ 106 " (cutoff:3.500A) Processing helix chain 'LR' and resid 60 through 68 removed outlier: 3.679A pdb=" N LEULR 64 " --> pdb=" O ARGLR 60 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N METLR 65 " --> pdb=" O PROLR 61 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ARGLR 66 " --> pdb=" O LYSLR 62 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEULR 67 " --> pdb=" O VALLR 63 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N SERLR 68 " --> pdb=" O LEULR 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'LR' and resid 60 through 68' Processing helix chain 'LR' and resid 83 through 113 Processing helix chain 'LS' and resid 5 through 11 removed outlier: 5.940A pdb=" N GLYLS 11 " --> pdb=" O ARGLS 7 " (cutoff:3.500A) Processing helix chain 'LS' and resid 13 through 38 Processing helix chain 'LS' and resid 40 through 74 removed outlier: 3.600A pdb=" N LYSLS 46 " --> pdb=" O SERLS 42 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILELS 47 " --> pdb=" O LYSLS 43 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ARGLS 48 " --> pdb=" O LEULS 44 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VALLS 49 " --> pdb=" O SERLS 45 " (cutoff:3.500A) Processing helix chain 'LS' and resid 80 through 85 Proline residue: LS 85 - end of helix Processing helix chain 'LS' and resid 88 through 94 Processing helix chain 'LS' and resid 96 through 102 removed outlier: 3.585A pdb=" N LEULS 102 " --> pdb=" O HISLS 98 " (cutoff:3.500A) Processing helix chain 'LS' and resid 104 through 114 Processing helix chain 'LT' and resid 35 through 40 removed outlier: 3.845A pdb=" N THRLT 39 " --> pdb=" O ALALT 35 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLULT 40 " --> pdb=" O ARGLT 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'LT' and resid 35 through 40' Processing helix chain 'LU' and resid 25 through 30 removed outlier: 4.075A pdb=" N ARGLU 29 " --> pdb=" O ARGLU 25 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ARGLU 30 " --> pdb=" O HISLU 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'LU' and resid 25 through 30' Processing helix chain 'LU' and resid 34 through 49 Processing helix chain 'LU' and resid 51 through 64 Processing helix chain 'LU' and resid 65 through 78 Processing helix chain 'LU' and resid 79 through 103 Processing helix chain 'LV' and resid 35 through 46 Processing helix chain 'LW' and resid 4 through 11 removed outlier: 3.924A pdb=" N GLYLW 9 " --> pdb=" O THRLW 5 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LYSLW 10 " --> pdb=" O SERLW 6 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ARGLW 11 " --> pdb=" O SERLW 7 " (cutoff:3.500A) Processing helix chain 'LW' and resid 50 through 58 removed outlier: 3.605A pdb=" N LYSLW 54 " --> pdb=" O SERLW 50 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASNLW 57 " --> pdb=" O ALALW 53 " (cutoff:3.500A) Processing helix chain 'LW' and resid 64 through 77 removed outlier: 4.212A pdb=" N ILELW 69 " --> pdb=" O ARGLW 65 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARGLW 75 " --> pdb=" O TYRLW 71 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N HISLW 76 " --> pdb=" O ARGLW 72 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLYLW 77 " --> pdb=" O ARGLW 73 " (cutoff:3.500A) Processing helix chain 'LX' and resid 19 through 35 removed outlier: 3.945A pdb=" N LYSLX 28 " --> pdb=" O LYSLX 24 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILELX 29 " --> pdb=" O METLX 25 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HISLX 34 " --> pdb=" O GLULX 30 " (cutoff:3.500A) Processing helix chain 'LX' and resid 73 through 92 Processing helix chain 'LY' and resid 7 through 17 Processing helix chain 'LY' and resid 49 through 60 removed outlier: 3.690A pdb=" N GLULY 54 " --> pdb=" O LYSLY 50 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYSLY 55 " --> pdb=" O GLULY 51 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEULY 60 " --> pdb=" O LEULY 56 " (cutoff:3.500A) Processing helix chain 'LZ' and resid 6 through 21 removed outlier: 5.256A pdb=" N ARGLZ 21 " --> pdb=" O GLNLZ 17 " (cutoff:3.500A) Processing helix chain 'LZ' and resid 24 through 31 removed outlier: 4.629A pdb=" N ARGLZ 28 " --> pdb=" O PROLZ 24 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N METLZ 29 " --> pdb=" O GLNLZ 25 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYSLZ 30 " --> pdb=" O TRPLZ 26 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N THRLZ 31 " --> pdb=" O ILELZ 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'LZ' and resid 24 through 31' Processing helix chain 'NK' and resid 12 through 33 removed outlier: 3.535A pdb=" N LYSNK 20 " --> pdb=" O GLUNK 16 " (cutoff:3.500A) Proline residue: NK 23 - end of helix Processing helix chain 'NK' and resid 98 through 112 removed outlier: 3.533A pdb=" N ARGNK 109 " --> pdb=" O LEUNK 105 " (cutoff:3.500A) Processing helix chain 'NL' and resid 185 through 190 Processing helix chain 'NL' and resid 200 through 205 Proline residue: NL 205 - end of helix Processing helix chain 'NL' and resid 210 through 218 Processing helix chain 'NL' and resid 225 through 230 removed outlier: 3.980A pdb=" N HISNL 229 " --> pdb=" O PRONL 225 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N THRNL 230 " --> pdb=" O ALANL 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'NL' and resid 225 through 230' Processing helix chain 'NL' and resid 252 through 280 removed outlier: 3.569A pdb=" N VALNL 264 " --> pdb=" O ALANL 260 " (cutoff:3.500A) Processing helix chain 'NL' and resid 289 through 299 Processing helix chain 'NL' and resid 338 through 371 removed outlier: 4.003A pdb=" N LEUNL 368 " --> pdb=" O ARGNL 364 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N PHENL 369 " --> pdb=" O HISNL 365 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARGNL 370 " --> pdb=" O GLNNL 366 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEUNL 371 " --> pdb=" O GLUNL 367 " (cutoff:3.500A) Processing helix chain 'NL' and resid 372 through 400 Processing helix chain 'NL' and resid 436 through 449 removed outlier: 3.504A pdb=" N GLNNL 446 " --> pdb=" O PHENL 442 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASNNL 449 " --> pdb=" O PHENL 445 " (cutoff:3.500A) Processing helix chain 'NL' and resid 470 through 477 removed outlier: 3.787A pdb=" N ILENL 476 " --> pdb=" O ALANL 472 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N GLNNL 477 " --> pdb=" O PHENL 473 " (cutoff:3.500A) Processing helix chain 'NP' and resid 15 through 20 removed outlier: 4.579A pdb=" N METNP 19 " --> pdb=" O LEUNP 15 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYSNP 20 " --> pdb=" O ALANP 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'NP' and resid 15 through 20' Processing helix chain 'NP' and resid 27 through 36 removed outlier: 3.730A pdb=" N ARGNP 33 " --> pdb=" O ASPNP 29 " (cutoff:3.500A) Processing helix chain 'NP' and resid 72 through 82 removed outlier: 3.866A pdb=" N ARGNP 81 " --> pdb=" O LYSNP 77 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SERNP 82 " --> pdb=" O THRNP 78 " (cutoff:3.500A) Processing helix chain 'NP' and resid 83 through 94 removed outlier: 3.640A pdb=" N LYSNP 90 " --> pdb=" O LYSNP 86 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SERNP 93 " --> pdb=" O LEUNP 89 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N VALNP 94 " --> pdb=" O LYSNP 90 " (cutoff:3.500A) Processing helix chain 'NP' and resid 98 through 107 removed outlier: 3.617A pdb=" N ALANP 106 " --> pdb=" O ALANP 102 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLYNP 107 " --> pdb=" O GLUNP 103 " (cutoff:3.500A) Processing helix chain 'NR' and resid 21 through 62 removed outlier: 3.533A pdb=" N ALANR 25 " --> pdb=" O SERNR 21 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEUNR 62 " --> pdb=" O PHENR 58 " (cutoff:3.500A) Processing helix chain 'NR' and resid 70 through 98 removed outlier: 3.572A pdb=" N ARGNR 84 " --> pdb=" O ARGNR 80 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N PHENR 85 " --> pdb=" O TYRNR 81 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N SERNR 86 " --> pdb=" O LEUNR 82 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N SERNR 87 " --> pdb=" O ASNNR 83 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N GLUNR 88 " --> pdb=" O ARGNR 84 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ILENR 98 " --> pdb=" O LEUNR 94 " (cutoff:3.500A) Processing helix chain 'NR' and resid 106 through 126 Processing helix chain 'NR' and resid 136 through 146 Processing helix chain 'NR' and resid 152 through 157 removed outlier: 3.941A pdb=" N ILENR 156 " --> pdb=" O LYSNR 152 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N LYSNR 157 " --> pdb=" O LEUNR 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'NR' and resid 152 through 157' Processing helix chain 'SA' and resid 25 through 31 removed outlier: 4.487A pdb=" N LYSSA 29 " --> pdb=" O PROSA 25 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALASA 30 " --> pdb=" O ALASA 26 " (cutoff:3.500A) Proline residue: SA 31 - end of helix No H-bonds generated for 'chain 'SA' and resid 25 through 31' Processing helix chain 'SA' and resid 33 through 49 removed outlier: 3.925A pdb=" N LYSSA 46 " --> pdb=" O THRSA 42 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ASNSA 47 " --> pdb=" O ASNSA 43 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ASNSA 48 " --> pdb=" O LEUSA 44 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ARGSA 49 " --> pdb=" O ARGSA 45 " (cutoff:3.500A) Processing helix chain 'SA' and resid 116 through 134 removed outlier: 3.670A pdb=" N ALASA 132 " --> pdb=" O LEUSA 128 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEUSA 133 " --> pdb=" O ALASA 129 " (cutoff:3.500A) Proline residue: SA 134 - end of helix Processing helix chain 'SA' and resid 135 through 141 removed outlier: 3.623A pdb=" N GLYSA 141 " --> pdb=" O VALSA 137 " (cutoff:3.500A) Processing helix chain 'SA' and resid 156 through 161 removed outlier: 4.155A pdb=" N GLYSA 160 " --> pdb=" O ASPSA 156 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N TYRSA 161 " --> pdb=" O LYSSA 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'SA' and resid 156 through 161' Processing helix chain 'SA' and resid 163 through 175 Processing helix chain 'SA' and resid 176 through 187 removed outlier: 3.713A pdb=" N ILESA 180 " --> pdb=" O ALASA 176 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLNSA 187 " --> pdb=" O VALSA 183 " (cutoff:3.500A) Processing helix chain 'SA' and resid 193 through 198 removed outlier: 4.133A pdb=" N ARGSA 197 " --> pdb=" O LYSSA 193 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASNSA 198 " --> pdb=" O GLYSA 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'SA' and resid 193 through 198' Processing helix chain 'SA' and resid 216 through 222 Processing helix chain 'SA' and resid 236 through 242 Proline residue: SA 242 - end of helix Processing helix chain 'SA' and resid 253 through 263 removed outlier: 3.505A pdb=" N LEUSA 260 " --> pdb=" O ALASA 256 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ASPSA 261 " --> pdb=" O PHESA 257 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLUSA 262 " --> pdb=" O ARGSA 258 " (cutoff:3.500A) Processing helix chain 'SA' and resid 288 through 295 Processing helix chain 'SA' and resid 296 through 303 removed outlier: 3.797A pdb=" N ALASA 301 " --> pdb=" O GLUSA 297 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEUSA 302 " --> pdb=" O ILESA 298 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ARGSA 303 " --> pdb=" O GLNSA 299 " (cutoff:3.500A) Processing helix chain 'SA' and resid 317 through 322 removed outlier: 4.952A pdb=" N LEUSA 322 " --> pdb=" O PROSA 318 " (cutoff:3.500A) Processing helix chain 'SA' and resid 323 through 329 Processing helix chain 'SA' and resid 330 through 361 removed outlier: 4.505A pdb=" N THRSA 334 " --> pdb=" O PROSA 330 " (cutoff:3.500A) Processing helix chain 'SB' and resid 9 through 16 Processing helix chain 'SB' and resid 20 through 26 Processing helix chain 'SB' and resid 29 through 37 removed outlier: 3.843A pdb=" N ARGSB 35 " --> pdb=" O TYRSB 31 " (cutoff:3.500A) Processing helix chain 'SB' and resid 79 through 87 removed outlier: 4.184A pdb=" N LEUSB 83 " --> pdb=" O TYRSB 79 " (cutoff:3.500A) Proline residue: SB 84 - end of helix Processing helix chain 'SB' and resid 94 through 114 Processing helix chain 'SB' and resid 115 through 120 removed outlier: 3.726A pdb=" N GLUSB 120 " --> pdb=" O ASPSB 116 " (cutoff:3.500A) Processing helix chain 'SB' and resid 157 through 170 removed outlier: 3.957A pdb=" N GLYSB 161 " --> pdb=" O ASNSB 157 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLYSB 170 " --> pdb=" O ALASB 166 " (cutoff:3.500A) Processing helix chain 'SB' and resid 191 through 201 removed outlier: 3.526A pdb=" N HISSB 195 " --> pdb=" O ASNSB 191 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N METSB 200 " --> pdb=" O ARGSB 196 " (cutoff:3.500A) Processing helix chain 'SB' and resid 202 through 215 Processing helix chain 'SB' and resid 216 through 223 Processing helix chain 'SB' and resid 224 through 230 removed outlier: 4.532A pdb=" N ASNSB 229 " --> pdb=" O GLNSB 225 " (cutoff:3.500A) Processing helix chain 'SB' and resid 232 through 251 removed outlier: 4.797A pdb=" N GLUSB 237 " --> pdb=" O PROSB 233 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N GLUSB 238 " --> pdb=" O ASPSB 234 " (cutoff:3.500A) Proline residue: SB 251 - end of helix Processing helix chain 'SB' and resid 272 through 280 Processing helix chain 'SC' and resid 58 through 67 Processing helix chain 'SC' and resid 190 through 195 removed outlier: 3.666A pdb=" N VALSC 194 " --> pdb=" O HISSC 190 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ILESC 195 " --> pdb=" O GLNSC 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'SC' and resid 190 through 195' Processing helix chain 'SC' and resid 213 through 218 Processing helix chain 'SC' and resid 243 through 262 removed outlier: 3.849A pdb=" N GLNSC 256 " --> pdb=" O ALASC 252 " (cutoff:3.500A) Proline residue: SC 259 - end of helix Processing helix chain 'SC' and resid 266 through 274 removed outlier: 5.332A pdb=" N VALSC 274 " --> pdb=" O TYRSC 270 " (cutoff:3.500A) Processing helix chain 'SC' and resid 282 through 287 removed outlier: 5.439A pdb=" N VALSC 287 " --> pdb=" O PROSC 283 " (cutoff:3.500A) Processing helix chain 'SD' and resid 24 through 79 removed outlier: 3.572A pdb=" N ILESD 69 " --> pdb=" O TYRSD 65 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALASD 72 " --> pdb=" O GLUSD 68 " (cutoff:3.500A) Processing helix chain 'SD' and resid 102 through 113 Processing helix chain 'SD' and resid 126 through 137 removed outlier: 3.640A pdb=" N ILESD 135 " --> pdb=" O ASNSD 131 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VALSD 136 " --> pdb=" O METSD 132 " (cutoff:3.500A) Processing helix chain 'SD' and resid 146 through 156 Processing helix chain 'SD' and resid 171 through 179 removed outlier: 4.136A pdb=" N ILESD 175 " --> pdb=" O ASPSD 171 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SERSD 178 " --> pdb=" O LEUSD 174 " (cutoff:3.500A) Processing helix chain 'SD' and resid 186 through 197 removed outlier: 3.909A pdb=" N VALSD 197 " --> pdb=" O GLUSD 193 " (cutoff:3.500A) Processing helix chain 'SD' and resid 200 through 209 removed outlier: 5.275A pdb=" N TRPSD 209 " --> pdb=" O ASNSD 205 " (cutoff:3.500A) Processing helix chain 'SD' and resid 239 through 248 removed outlier: 3.551A pdb=" N LEUSD 243 " --> pdb=" O GLNSD 239 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARGSD 246 " --> pdb=" O ARGSD 242 " (cutoff:3.500A) Processing helix chain 'SE' and resid 58 through 74 removed outlier: 3.735A pdb=" N LYSSE 72 " --> pdb=" O ALASE 68 " (cutoff:3.500A) Processing helix chain 'SE' and resid 77 through 86 removed outlier: 4.838A pdb=" N PHESE 83 " --> pdb=" O ALASE 79 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N THRSE 84 " --> pdb=" O ILESE 80 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLNSE 85 " --> pdb=" O ASNSE 81 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ALASE 86 " --> pdb=" O GLNSE 82 " (cutoff:3.500A) Processing helix chain 'SE' and resid 88 through 103 removed outlier: 3.573A pdb=" N LYSSE 101 " --> pdb=" O LYSSE 97 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N TYRSE 102 " --> pdb=" O LEUSE 98 " (cutoff:3.500A) Processing helix chain 'SE' and resid 106 through 122 removed outlier: 5.503A pdb=" N ALASE 122 " --> pdb=" O ALASE 118 " (cutoff:3.500A) Processing helix chain 'SE' and resid 139 through 150 Processing helix chain 'SE' and resid 169 through 178 Processing helix chain 'SE' and resid 186 through 195 removed outlier: 3.595A pdb=" N LEUSE 193 " --> pdb=" O ARGSE 189 " (cutoff:3.500A) Processing helix chain 'SE' and resid 208 through 226 removed outlier: 5.008A pdb=" N GLYSE 213 " --> pdb=" O SERSE 209 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ALASE 214 " --> pdb=" O GLUSE 210 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THRSE 224 " --> pdb=" O GLUSE 220 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASNSE 225 " --> pdb=" O ALASE 221 " (cutoff:3.500A) Processing helix chain 'SE' and resid 229 through 236 removed outlier: 3.832A pdb=" N ARGSE 235 " --> pdb=" O ASPSE 231 " (cutoff:3.500A) Processing helix chain 'SE' and resid 243 through 266 removed outlier: 5.105A pdb=" N GLYSE 266 " --> pdb=" O ALASE 262 " (cutoff:3.500A) Processing helix chain 'SF' and resid 5 through 13 removed outlier: 6.466A pdb=" N LYSSF 10 " --> pdb=" O ARGSF 6 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLYSF 11 " --> pdb=" O GLYSF 7 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ALASF 12 " --> pdb=" O GLNSF 8 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLYSF 13 " --> pdb=" O ARGSF 9 " (cutoff:3.500A) Processing helix chain 'SF' and resid 33 through 39 Processing helix chain 'SF' and resid 103 through 108 removed outlier: 3.640A pdb=" N METSF 107 " --> pdb=" O PROSF 103 " (cutoff:3.500A) Proline residue: SF 108 - end of helix No H-bonds generated for 'chain 'SF' and resid 103 through 108' Processing helix chain 'SF' and resid 181 through 193 removed outlier: 3.724A pdb=" N ALASF 191 " --> pdb=" O HISSF 187 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYSSF 192 " --> pdb=" O LYSSF 188 " (cutoff:3.500A) Processing helix chain 'SF' and resid 200 through 205 removed outlier: 3.708A pdb=" N METSF 204 " --> pdb=" O ARGSF 200 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ASNSF 205 " --> pdb=" O GLYSF 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'SF' and resid 200 through 205' Processing helix chain 'SG' and resid 63 through 86 removed outlier: 4.129A pdb=" N THRSG 69 " --> pdb=" O LYSSG 65 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VALSG 70 " --> pdb=" O GLUSG 66 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ARGSG 71 " --> pdb=" O LEUSG 67 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THRSG 72 " --> pdb=" O ALASG 68 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N CYSSG 74 " --> pdb=" O VALSG 70 " (cutoff:3.500A) Processing helix chain 'SG' and resid 150 through 166 removed outlier: 4.296A pdb=" N THRSG 166 " --> pdb=" O GLNSG 162 " (cutoff:3.500A) Processing helix chain 'SG' and resid 171 through 176 removed outlier: 4.443A pdb=" N LEUSG 176 " --> pdb=" O ILESG 172 " (cutoff:3.500A) Processing helix chain 'SH' and resid 57 through 69 removed outlier: 3.724A pdb=" N GLNSH 67 " --> pdb=" O SERSH 63 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N PHESH 68 " --> pdb=" O TYRSH 64 " (cutoff:3.500A) Processing helix chain 'SH' and resid 95 through 107 Processing helix chain 'SI' and resid 23 through 53 Processing helix chain 'SI' and resid 60 through 84 removed outlier: 3.612A pdb=" N PHESI 64 " --> pdb=" O ARGSI 60 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLUSI 82 " --> pdb=" O LEUSI 78 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VALSI 83 " --> pdb=" O ARGSI 79 " (cutoff:3.500A) Processing helix chain 'SI' and resid 109 through 120 Processing helix chain 'SI' and resid 133 through 144 removed outlier: 3.515A pdb=" N VALSI 143 " --> pdb=" O METSI 139 " (cutoff:3.500A) Processing helix chain 'SI' and resid 153 through 164 Processing helix chain 'SI' and resid 178 through 186 removed outlier: 4.054A pdb=" N ILESI 182 " --> pdb=" O ASPSI 178 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HISSI 185 " --> pdb=" O VALSI 181 " (cutoff:3.500A) Processing helix chain 'SI' and resid 193 through 204 Proline residue: SI 204 - end of helix Processing helix chain 'SI' and resid 207 through 216 removed outlier: 3.587A pdb=" N LEUSI 215 " --> pdb=" O ILESI 211 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N CYSSI 216 " --> pdb=" O SERSI 212 " (cutoff:3.500A) Processing helix chain 'SI' and resid 225 through 230 removed outlier: 4.347A pdb=" N ASNSI 229 " --> pdb=" O HISSI 225 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ARGSI 230 " --> pdb=" O ALASI 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'SI' and resid 225 through 230' Processing helix chain 'SI' and resid 231 through 237 Processing helix chain 'SI' and resid 245 through 255 removed outlier: 4.746A pdb=" N GLNSI 249 " --> pdb=" O GLUSI 245 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEUSI 250 " --> pdb=" O ARGSI 246 " (cutoff:3.500A) Processing helix chain 'SK' and resid 12 through 17 removed outlier: 4.126A pdb=" N PHESK 16 " --> pdb=" O GLUSK 12 " (cutoff:3.500A) Processing helix chain 'SK' and resid 32 through 42 removed outlier: 3.702A pdb=" N PHESK 38 " --> pdb=" O PHESK 34 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLUSK 41 " --> pdb=" O VALSK 37 " (cutoff:3.500A) Processing helix chain 'SK' and resid 58 through 63 removed outlier: 3.902A pdb=" N METSK 62 " --> pdb=" O ILESK 58 " (cutoff:3.500A) Processing helix chain 'SK' and resid 77 through 88 Processing helix chain 'SK' and resid 103 through 108 Processing helix chain 'SK' and resid 122 through 133 Processing helix chain 'SK' and resid 147 through 152 Processing helix chain 'SK' and resid 166 through 178 Processing helix chain 'SK' and resid 192 through 197 removed outlier: 3.737A pdb=" N GLYSK 196 " --> pdb=" O VALSK 192 " (cutoff:3.500A) Processing helix chain 'SK' and resid 211 through 223 removed outlier: 4.558A pdb=" N LYSSK 223 " --> pdb=" O GLUSK 219 " (cutoff:3.500A) Processing helix chain 'SK' and resid 231 through 237 removed outlier: 4.050A pdb=" N SERSK 235 " --> pdb=" O THRSK 231 " (cutoff:3.500A) Processing helix chain 'SK' and resid 238 through 244 Processing helix chain 'SM' and resid 12 through 18 removed outlier: 6.153A pdb=" N ILESM 18 " --> pdb=" O ALASM 14 " (cutoff:3.500A) Processing helix chain 'SM' and resid 19 through 28 Processing helix chain 'SM' and resid 30 through 42 Processing helix chain 'SM' and resid 50 through 56 removed outlier: 3.819A pdb=" N VALSM 54 " --> pdb=" O HISSM 50 " (cutoff:3.500A) Processing helix chain 'SM' and resid 66 through 76 removed outlier: 4.030A pdb=" N HISSM 75 " --> pdb=" O ARGSM 71 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLUSM 76 " --> pdb=" O PHESM 72 " (cutoff:3.500A) Processing helix chain 'SM' and resid 77 through 99 removed outlier: 3.798A pdb=" N LYSSM 81 " --> pdb=" O PROSM 77 " (cutoff:3.500A) Processing helix chain 'SM' and resid 100 through 111 Processing helix chain 'SM' and resid 116 through 125 Proline residue: SM 125 - end of helix Processing helix chain 'SM' and resid 126 through 148 removed outlier: 3.756A pdb=" N ASPSM 133 " --> pdb=" O ASPSM 129 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEUSM 134 " --> pdb=" O ALASM 130 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASPSM 135 " --> pdb=" O LEUSM 131 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ASPSM 136 " --> pdb=" O ARGSM 132 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N THRSM 146 " --> pdb=" O PHESM 142 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHESM 147 " --> pdb=" O LEUSM 143 " (cutoff:3.500A) Proline residue: SM 148 - end of helix Processing helix chain 'SM' and resid 154 through 176 Processing helix chain 'SM' and resid 216 through 243 removed outlier: 3.621A pdb=" N THRSM 229 " --> pdb=" O GLUSM 225 " (cutoff:3.500A) Processing helix chain 'SM' and resid 270 through 279 removed outlier: 4.075A pdb=" N LEUSM 279 " --> pdb=" O LYSSM 275 " (cutoff:3.500A) Processing helix chain 'SM' and resid 307 through 326 removed outlier: 3.733A pdb=" N LYSSM 325 " --> pdb=" O GLUSM 321 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEUSM 326 " --> pdb=" O LYSSM 322 " (cutoff:3.500A) Processing helix chain 'SM' and resid 339 through 351 removed outlier: 3.581A pdb=" N PHESM 350 " --> pdb=" O ILESM 346 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLYSM 351 " --> pdb=" O ILESM 347 " (cutoff:3.500A) Processing helix chain 'SM' and resid 394 through 405 removed outlier: 4.525A pdb=" N VALSM 398 " --> pdb=" O GLNSM 394 " (cutoff:3.500A) Processing helix chain 'SM' and resid 409 through 414 removed outlier: 4.572A pdb=" N TYRSM 413 " --> pdb=" O PROSM 409 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 20 through 37 removed outlier: 3.668A pdb=" N GLUSQ 28 " --> pdb=" O GLNSQ 24 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 52 through 61 removed outlier: 3.835A pdb=" N ILESQ 56 " --> pdb=" O LYSSQ 52 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARGSQ 57 " --> pdb=" O LEUSQ 53 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASNSQ 58 " --> pdb=" O LYSSQ 54 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYSSQ 61 " --> pdb=" O ARGSQ 57 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 69 through 78 Processing helix chain 'SQ' and resid 88 through 97 removed outlier: 3.943A pdb=" N VALSQ 92 " --> pdb=" O ASNSQ 88 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARGSQ 95 " --> pdb=" O GLNSQ 91 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEUSQ 96 " --> pdb=" O VALSQ 92 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ARGSQ 97 " --> pdb=" O SERSQ 93 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 108 through 119 removed outlier: 3.707A pdb=" N VALSQ 112 " --> pdb=" O THRSQ 108 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASNSQ 113 " --> pdb=" O LYSSQ 109 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLUSQ 114 " --> pdb=" O GLUSQ 110 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TRPSQ 115 " --> pdb=" O GLUSQ 111 " (cutoff:3.500A) Processing helix chain 'SR' and resid 14 through 29 Processing helix chain 'SR' and resid 39 through 70 removed outlier: 3.579A pdb=" N LYSSR 50 " --> pdb=" O PHESR 46 " (cutoff:3.500A) Proline residue: SR 70 - end of helix Processing helix chain 'SR' and resid 76 through 87 Processing helix chain 'SR' and resid 88 through 120 removed outlier: 3.508A pdb=" N ILESR 101 " --> pdb=" O GLYSR 97 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYSSR 118 " --> pdb=" O VALSR 114 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N TYRSR 119 " --> pdb=" O ARGSR 115 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLYSR 120 " --> pdb=" O LEUSR 116 " (cutoff:3.500A) Processing helix chain 'SR' and resid 122 through 146 removed outlier: 3.628A pdb=" N ARGSR 143 " --> pdb=" O THRSR 139 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLNSR 144 " --> pdb=" O VALSR 140 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYSSR 145 " --> pdb=" O ILESR 141 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N GLNSR 146 " --> pdb=" O LYSSR 142 " (cutoff:3.500A) Processing helix chain 'SR' and resid 147 through 162 removed outlier: 3.770A pdb=" N ARGSR 160 " --> pdb=" O GLNSR 156 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEUSR 161 " --> pdb=" O HISSR 157 " (cutoff:3.500A) Proline residue: SR 162 - end of helix Processing helix chain 'SR' and resid 180 through 189 removed outlier: 3.564A pdb=" N ASNSR 186 " --> pdb=" O SERSR 182 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYSSR 187 " --> pdb=" O SERSR 183 " (cutoff:3.500A) Processing helix chain 'SR' and resid 234 through 247 removed outlier: 3.918A pdb=" N ALASR 240 " --> pdb=" O ILESR 236 " (cutoff:3.500A) Processing helix chain 'SR' and resid 264 through 280 Proline residue: SR 277 - end of helix removed outlier: 3.899A pdb=" N ILESR 280 " --> pdb=" O ARGSR 276 " (cutoff:3.500A) Processing helix chain 'SR' and resid 290 through 295 removed outlier: 3.610A pdb=" N LYSSR 294 " --> pdb=" O LYSSR 290 " (cutoff:3.500A) Processing helix chain 'SR' and resid 300 through 314 removed outlier: 3.754A pdb=" N ILESR 306 " --> pdb=" O ASPSR 302 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHESR 307 " --> pdb=" O ASPSR 303 " (cutoff:3.500A) Processing helix chain 'SR' and resid 327 through 351 removed outlier: 3.663A pdb=" N VALSR 344 " --> pdb=" O LEUSR 340 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLUSR 345 " --> pdb=" O ALASR 341 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THRSR 346 " --> pdb=" O HISSR 342 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASNSR 351 " --> pdb=" O LYSSR 347 " (cutoff:3.500A) Processing helix chain 'SR' and resid 352 through 362 removed outlier: 4.244A pdb=" N VALSR 356 " --> pdb=" O LYSSR 352 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEUSR 357 " --> pdb=" O VALSR 353 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ASNSR 358 " --> pdb=" O ASNSR 354 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ARGSR 359 " --> pdb=" O GLUSR 355 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEUSR 360 " --> pdb=" O VALSR 356 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N LEUSR 362 " --> pdb=" O ASNSR 358 " (cutoff:3.500A) Processing helix chain 'SR' and resid 397 through 406 removed outlier: 4.180A pdb=" N GLYSR 406 " --> pdb=" O GLUSR 402 " (cutoff:3.500A) Processing helix chain 'SR' and resid 412 through 417 removed outlier: 5.143A pdb=" N TYRSR 416 " --> pdb=" O ASPSR 412 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N TRPSR 417 " --> pdb=" O LEUSR 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 412 through 417' Processing helix chain 'SR' and resid 421 through 426 removed outlier: 4.250A pdb=" N LYSSR 425 " --> pdb=" O ASNSR 421 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N HISSR 426 " --> pdb=" O LEUSR 422 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 421 through 426' Processing helix chain 'SR' and resid 437 through 443 removed outlier: 3.956A pdb=" N TYRSR 441 " --> pdb=" O ASNSR 437 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILESR 442 " --> pdb=" O ILESR 438 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASPSR 443 " --> pdb=" O ALASR 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 437 through 443' Processing helix chain 'SR' and resid 445 through 464 removed outlier: 3.612A pdb=" N LYSSR 449 " --> pdb=" O ALASR 445 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLUSR 451 " --> pdb=" O METSR 447 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLUSR 452 " --> pdb=" O LYSSR 448 " (cutoff:3.500A) Processing helix chain 'SR' and resid 474 through 503 removed outlier: 4.780A pdb=" N LEUSR 478 " --> pdb=" O ASPSR 474 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N THRSR 503 " --> pdb=" O LYSSR 499 " (cutoff:3.500A) Processing helix chain 'SR' and resid 509 through 514 removed outlier: 3.655A pdb=" N LYSSR 513 " --> pdb=" O PROSR 509 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N LYSSR 514 " --> pdb=" O ARGSR 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 509 through 514' Processing helix chain 'SR' and resid 516 through 528 removed outlier: 3.650A pdb=" N LEUSR 527 " --> pdb=" O GLUSR 523 " (cutoff:3.500A) Processing helix chain 'SR' and resid 537 through 551 removed outlier: 3.525A pdb=" N ARGSR 544 " --> pdb=" O ALASR 540 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SERSR 548 " --> pdb=" O ARGSR 544 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILESR 549 " --> pdb=" O ARGSR 545 " (cutoff:3.500A) Processing helix chain 'SR' and resid 582 through 604 removed outlier: 3.738A pdb=" N GLNSR 597 " --> pdb=" O METSR 593 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYSSR 598 " --> pdb=" O LYSSR 594 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N LYSSR 599 " --> pdb=" O ASNSR 595 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N METSR 600 " --> pdb=" O ALASR 596 " (cutoff:3.500A) Processing helix chain 'SR' and resid 618 through 623 Processing helix chain 'SV' and resid 33 through 43 removed outlier: 3.554A pdb=" N LYSSV 43 " --> pdb=" O ASNSV 39 " (cutoff:3.500A) Processing helix chain 'SV' and resid 45 through 50 removed outlier: 5.620A pdb=" N ARGSV 50 " --> pdb=" O PROSV 46 " (cutoff:3.500A) Processing helix chain 'SV' and resid 52 through 60 Processing helix chain 'SV' and resid 66 through 71 removed outlier: 4.365A pdb=" N GLUSV 70 " --> pdb=" O ASPSV 66 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N PHESV 71 " --> pdb=" O ASNSV 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'SV' and resid 66 through 71' Processing helix chain 'SV' and resid 82 through 130 removed outlier: 4.057A pdb=" N TRPSV 86 " --> pdb=" O GLNSV 82 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASPSV 91 " --> pdb=" O ASNSV 87 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYSSV 114 " --> pdb=" O ASNSV 110 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ASNSV 115 " --> pdb=" O ARGSV 111 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N LYSSV 116 " --> pdb=" O LEUSV 112 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLUSV 117 " --> pdb=" O LYSSV 113 " (cutoff:3.500A) Processing helix chain 'VB' and resid 41 through 73 removed outlier: 3.529A pdb=" N GLNVB 46 " --> pdb=" O ARGVB 42 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEUVB 49 " --> pdb=" O GLNVB 45 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYSVB 50 " --> pdb=" O GLNVB 46 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'L5' and resid 48 through 51 removed outlier: 3.719A pdb=" N ALAL5 69 " --> pdb=" O SERL5 51 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ILEL5 68 " --> pdb=" O VALL5 26 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYSL5 19 " --> pdb=" O VALL5 133 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASNL5 23 " --> pdb=" O ASPL5 129 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N CYSL5 25 " --> pdb=" O GLYL5 127 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N GLYL5 127 " --> pdb=" O CYSL5 25 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'L5' and resid 92 through 95 Processing sheet with id= 3, first strand: chain 'L6' and resid 57 through 60 Processing sheet with id= 4, first strand: chain 'L7' and resid 6 through 10 Processing sheet with id= 5, first strand: chain 'L8' and resid 11 through 15 removed outlier: 4.487A pdb=" N ARGL8 11 " --> pdb=" O ILEL8 27 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYSL8 23 " --> pdb=" O VALL8 15 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'L8' and resid 28 through 31 removed outlier: 6.698A pdb=" N ARGL8 35 " --> pdb=" O ILEL8 31 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'L9' and resid 35 through 39 removed outlier: 6.139A pdb=" N ALAL9 35 " --> pdb=" O ARGL9 65 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ILEL9 61 " --> pdb=" O ALAL9 39 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLYL9 58 " --> pdb=" O ASPL9 136 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILEL9 133 " --> pdb=" O LEUL9 116 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'L9' and resid 117 through 121 removed outlier: 3.661A pdb=" N ASNL9 117 " --> pdb=" O ILEL9 133 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N PHEL9 129 " --> pdb=" O VALL9 121 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'LA' and resid 13 through 20 removed outlier: 7.467A pdb=" N LYSLA 13 " --> pdb=" O GLULA 152 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILELA 149 " --> pdb=" O GLULA 115 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'LA' and resid 57 through 60 removed outlier: 5.370A pdb=" N GLNLA 80 " --> pdb=" O PHELA 60 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'LA' and resid 116 through 122 Processing sheet with id= 12, first strand: chain 'LA' and resid 124 through 131 removed outlier: 4.067A pdb=" N ARGLA 127 " --> pdb=" O TYRLA 139 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ARGLA 135 " --> pdb=" O ARGLA 131 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'LB' and resid 118 through 121 removed outlier: 3.560A pdb=" N ALALB 102 " --> pdb=" O LEULB 121 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LYSLB 99 " --> pdb=" O LYSLB 78 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'LC' and resid 27 through 33 removed outlier: 6.497A pdb=" N VALLC 13 " --> pdb=" O VALLC 62 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'LC' and resid 91 through 99 removed outlier: 4.256A pdb=" N ASNLC 77 " --> pdb=" O ILELC 132 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'LC' and resid 9 through 13 removed outlier: 4.806A pdb=" N GLULC 9 " --> pdb=" O VALLC 67 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'LE' and resid 39 through 42 removed outlier: 4.049A pdb=" N LYSLE 60 " --> pdb=" O ILELE 42 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'LE' and resid 72 through 79 Processing sheet with id= 19, first strand: chain 'LF' and resid 61 through 65 removed outlier: 5.923A pdb=" N GLULF 108 " --> pdb=" O LYSLF 20 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'LG' and resid 36 through 39 removed outlier: 4.851A pdb=" N ALALG 24 " --> pdb=" O ILELG 39 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ASNLG 101 " --> pdb=" O VALLG 25 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ILELG 105 " --> pdb=" O ALALG 29 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ASPLG 59 " --> pdb=" O VALLG 81 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'LG' and resid 87 through 90 removed outlier: 3.768A pdb=" N VALLG 94 " --> pdb=" O ARGLG 90 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'LG' and resid 82 through 85 removed outlier: 4.303A pdb=" N ARGLG 85 " --> pdb=" O ASPLG 100 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ASPLG 100 " --> pdb=" O ARGLG 85 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'LH' and resid 95 through 100 removed outlier: 3.861A pdb=" N LYSLH 134 " --> pdb=" O VALLH 100 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYSLH 123 " --> pdb=" O ARGLH 139 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'LI' and resid 53 through 56 removed outlier: 4.661A pdb=" N ASPLI 53 " --> pdb=" O VALLI 70 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'LI' and resid 72 through 75 removed outlier: 3.511A pdb=" N GLNLI 72 " --> pdb=" O TYRLI 81 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'LI' and resid 86 through 89 removed outlier: 4.416A pdb=" N THRLI 93 " --> pdb=" O LYSLI 89 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'LJ' and resid 10 through 14 removed outlier: 4.109A pdb=" N ARGLJ 21 " --> pdb=" O VALLJ 13 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'LJ' and resid 27 through 30 removed outlier: 6.136A pdb=" N HISLJ 40 " --> pdb=" O ILELJ 29 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'LK' and resid 98 through 101 Processing sheet with id= 30, first strand: chain 'LL' and resid 48 through 53 removed outlier: 5.302A pdb=" N THRLL 48 " --> pdb=" O LYSLL 65 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N SERLL 76 " --> pdb=" O ARGLL 66 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'LN' and resid 44 through 50 removed outlier: 8.228A pdb=" N THRLN 44 " --> pdb=" O LYSLN 349 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ARGLN 343 " --> pdb=" O LYSLN 50 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'LN' and resid 53 through 59 Processing sheet with id= 33, first strand: chain 'LN' and resid 98 through 102 removed outlier: 6.582A pdb=" N GLYLN 91 " --> pdb=" O PHELN 102 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYSLN 103 " --> pdb=" O GLYLN 91 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'LN' and resid 179 through 185 removed outlier: 4.914A pdb=" N HISLN 179 " --> pdb=" O THRLN 166 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ILELN 160 " --> pdb=" O VALLN 185 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILELN 163 " --> pdb=" O VALLN 87 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLNLN 203 " --> pdb=" O VALLN 86 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'LN' and resid 88 through 93 No H-bonds generated for sheet with id= 35 Processing sheet with id= 36, first strand: chain 'LO' and resid 26 through 29 removed outlier: 6.433A pdb=" N LYSLO 26 " --> pdb=" O ILELO 97 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEULO 45 " --> pdb=" O ILELO 96 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLYLO 70 " --> pdb=" O LYSLO 44 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASNLO 50 " --> pdb=" O TYRLO 74 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'LP' and resid 61 through 64 removed outlier: 4.837A pdb=" N ASPLP 61 " --> pdb=" O LEULP 102 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VALLP 21 " --> pdb=" O ARGLP 90 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N THRLP 22 " --> pdb=" O VALLP 122 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'LQ' and resid 74 through 80 Processing sheet with id= 39, first strand: chain 'LR' and resid 19 through 24 removed outlier: 5.209A pdb=" N LYSLR 19 " --> pdb=" O THRLR 35 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'LT' and resid 9 through 12 removed outlier: 6.958A pdb=" N LEULT 27 " --> pdb=" O ALALT 12 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ARGLT 85 " --> pdb=" O THRLT 75 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ARGLT 46 " --> pdb=" O METLT 104 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'LT' and resid 6 through 12 removed outlier: 4.660A pdb=" N HISLT 99 " --> pdb=" O PHELT 11 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'LV' and resid 7 through 10 removed outlier: 5.346A pdb=" N VALLV 67 " --> pdb=" O TYRLV 26 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'LX' and resid 46 through 50 removed outlier: 8.787A pdb=" N LYSLX 46 " --> pdb=" O GLYLX 58 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLYLX 58 " --> pdb=" O LYSLX 46 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILELX 54 " --> pdb=" O ARGLX 50 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N GLYLX 53 " --> pdb=" O GLYLX 66 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYSLX 62 " --> pdb=" O CYSLX 57 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'LY' and resid 2 through 5 removed outlier: 3.567A pdb=" N ARGLY 3 " --> pdb=" O LEULY 42 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VALLY 46 " --> pdb=" O ILELY 5 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SERLY 22 " --> pdb=" O ARGLY 37 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LYSLY 27 " --> pdb=" O LEULY 69 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'NR' and resid 128 through 132 removed outlier: 3.519A pdb=" N ILENR 161 " --> pdb=" O LEUNR 129 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'SA' and resid 7 through 10 removed outlier: 4.938A pdb=" N LYSSA 20 " --> pdb=" O VALSA 10 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'SA' and resid 226 through 232 removed outlier: 5.501A pdb=" N PHESA 249 " --> pdb=" O GLYSA 206 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'SB' and resid 60 through 66 removed outlier: 3.557A pdb=" N VALSB 53 " --> pdb=" O ASPSB 147 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'SC' and resid 91 through 95 Processing sheet with id= 50, first strand: chain 'SC' and resid 148 through 153 removed outlier: 4.338A pdb=" N THRSC 148 " --> pdb=" O PHESC 164 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYSSC 160 " --> pdb=" O ILESC 152 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'SC' and resid 173 through 176 Processing sheet with id= 52, first strand: chain 'SD' and resid 139 through 144 removed outlier: 7.349A pdb=" N TYRSD 139 " --> pdb=" O ILESD 95 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N LYSSD 88 " --> pdb=" O LEUSD 125 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASNSD 119 " --> pdb=" O ARGSD 94 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N PHESD 118 " --> pdb=" O LEUSD 213 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'SE' and resid 180 through 185 Processing sheet with id= 54, first strand: chain 'SF' and resid 47 through 50 removed outlier: 3.658A pdb=" N ASPSF 47 " --> pdb=" O LYSSF 60 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LYSSF 60 " --> pdb=" O LYSSF 46 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLNSF 86 " --> pdb=" O VALSF 45 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'SF' and resid 110 through 114 removed outlier: 4.315A pdb=" N THRSF 111 " --> pdb=" O VALSF 136 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ARGSF 147 " --> pdb=" O ILESF 137 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SERSF 138 " --> pdb=" O ARGSF 147 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'SF' and resid 58 through 65 No H-bonds generated for sheet with id= 56 Processing sheet with id= 57, first strand: chain 'SF' and resid 146 through 150 removed outlier: 4.276A pdb=" N SERSF 154 " --> pdb=" O LEUSF 150 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'SG' and resid 5 through 12 removed outlier: 4.632A pdb=" N LYSSG 53 " --> pdb=" O ILESG 12 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'SG' and resid 17 through 20 Processing sheet with id= 60, first strand: chain 'SG' and resid 102 through 106 removed outlier: 6.891A pdb=" N SERSG 110 " --> pdb=" O METSG 128 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'SG' and resid 132 through 137 removed outlier: 5.599A pdb=" N GLUSG 143 " --> pdb=" O SERSG 137 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ASPSG 142 " --> pdb=" O SERSG 94 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'SH' and resid 72 through 77 removed outlier: 3.787A pdb=" N ARGSH 73 " --> pdb=" O GLUSH 92 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N TYRSH 88 " --> pdb=" O SERSH 77 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N VALSH 46 " --> pdb=" O METSH 121 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'SI' and resid 147 through 151 removed outlier: 3.651A pdb=" N ARGSI 101 " --> pdb=" O SERSI 126 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N SERSI 126 " --> pdb=" O ARGSI 101 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N PHESI 125 " --> pdb=" O LEUSI 220 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'SK' and resid 1 through 5 Processing sheet with id= 65, first strand: chain 'SK' and resid 23 through 27 Processing sheet with id= 66, first strand: chain 'SK' and resid 69 through 73 Processing sheet with id= 67, first strand: chain 'SK' and resid 114 through 117 Processing sheet with id= 68, first strand: chain 'SK' and resid 158 through 161 Processing sheet with id= 69, first strand: chain 'SM' and resid 179 through 184 removed outlier: 3.625A pdb=" N GLYSM 187 " --> pdb=" O SERSM 184 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'SM' and resid 352 through 356 Processing sheet with id= 71, first strand: chain 'SQ' and resid 63 through 67 removed outlier: 6.866A pdb=" N ILESQ 42 " --> pdb=" O LYSSQ 205 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THRSQ 203 " --> pdb=" O SERSQ 44 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'SQ' and resid 213 through 217 removed outlier: 3.546A pdb=" N ARGSQ 214 " --> pdb=" O ASPSQ 209 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'SQ' and resid 38 through 42 removed outlier: 8.156A pdb=" N LYSSQ 38 " --> pdb=" O SERSQ 210 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'SR' and resid 204 through 211 removed outlier: 7.391A pdb=" N SERSR 204 " --> pdb=" O PROSR 223 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ARGSR 169 " --> pdb=" O ARGSR 216 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N THRSR 222 " --> pdb=" O LEUSR 173 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLYSR 175 " --> pdb=" O THRSR 222 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'SV' and resid 3 through 6 removed outlier: 6.365A pdb=" N GLUSV 4 " --> pdb=" O PROSV 12 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N CYSSV 6 " --> pdb=" O SERSV 10 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'SV' and resid 18 through 22 2873 hydrogen bonds defined for protein. 8553 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3047 hydrogen bonds 5180 hydrogen bond angles 0 basepair planarities 1154 basepair parallelities 1818 stacking parallelities Total time for adding SS restraints: 271.65 Time building geometry restraints manager: 59.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 16122 1.31 - 1.43: 64630 1.43 - 1.56: 70973 1.56 - 1.69: 7379 1.69 - 1.81: 464 Bond restraints: 159568 Sorted by residual: bond pdb=" C2' A2ML32401 " pdb=" C1' A2ML32401 " ideal model delta sigma weight residual 1.305 1.552 -0.247 2.00e-02 2.50e+03 1.53e+02 bond pdb=" C2' A2ML31326 " pdb=" C1' A2ML31326 " ideal model delta sigma weight residual 1.305 1.551 -0.246 2.00e-02 2.50e+03 1.51e+02 bond pdb=" C2' A2ML32815 " pdb=" C1' A2ML32815 " ideal model delta sigma weight residual 1.305 1.551 -0.246 2.00e-02 2.50e+03 1.51e+02 bond pdb=" C2' A2ML31524 " pdb=" C1' A2ML31524 " ideal model delta sigma weight residual 1.305 1.551 -0.246 2.00e-02 2.50e+03 1.51e+02 bond pdb=" C2' A2ML33867 " pdb=" C1' A2ML33867 " ideal model delta sigma weight residual 1.305 1.550 -0.245 2.00e-02 2.50e+03 1.50e+02 ... (remaining 159563 not shown) Histogram of bond angle deviations from ideal: 87.31 - 97.72: 14 97.72 - 108.13: 36098 108.13 - 118.54: 111212 118.54 - 128.95: 82104 128.95 - 139.36: 3712 Bond angle restraints: 233140 Sorted by residual: angle pdb=" C1' A2ML34590 " pdb=" N9 A2ML34590 " pdb=" C8 A2ML34590 " ideal model delta sigma weight residual 88.50 127.79 -39.29 3.00e+00 1.11e-01 1.72e+02 angle pdb=" C1' A2ML32787 " pdb=" N9 A2ML32787 " pdb=" C8 A2ML32787 " ideal model delta sigma weight residual 88.50 127.21 -38.71 3.00e+00 1.11e-01 1.67e+02 angle pdb=" C1' A2ML33724 " pdb=" N9 A2ML33724 " pdb=" C8 A2ML33724 " ideal model delta sigma weight residual 88.50 126.89 -38.39 3.00e+00 1.11e-01 1.64e+02 angle pdb=" C1' A2ML33830 " pdb=" N9 A2ML33830 " pdb=" C8 A2ML33830 " ideal model delta sigma weight residual 88.50 126.85 -38.35 3.00e+00 1.11e-01 1.63e+02 angle pdb=" C1' A2ML3 400 " pdb=" N9 A2ML3 400 " pdb=" C8 A2ML3 400 " ideal model delta sigma weight residual 88.50 126.76 -38.26 3.00e+00 1.11e-01 1.63e+02 ... (remaining 233135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 92856 35.82 - 71.63: 8566 71.63 - 107.45: 1316 107.45 - 143.26: 18 143.26 - 179.08: 13 Dihedral angle restraints: 102769 sinusoidal: 77651 harmonic: 25118 Sorted by residual: dihedral pdb=" C5' GL34305 " pdb=" C4' GL34305 " pdb=" C3' GL34305 " pdb=" O3' GL34305 " ideal model delta sinusoidal sigma weight residual 147.00 73.50 73.50 1 8.00e+00 1.56e-02 1.07e+02 dihedral pdb=" C4' GL31853 " pdb=" C3' GL31853 " pdb=" C2' GL31853 " pdb=" C1' GL31853 " ideal model delta sinusoidal sigma weight residual -35.00 35.07 -70.07 1 8.00e+00 1.56e-02 9.89e+01 dihedral pdb=" C4' GL34305 " pdb=" C3' GL34305 " pdb=" C2' GL34305 " pdb=" C1' GL34305 " ideal model delta sinusoidal sigma weight residual -35.00 35.07 -70.07 1 8.00e+00 1.56e-02 9.89e+01 ... (remaining 102766 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 27381 0.084 - 0.169: 1060 0.169 - 0.253: 44 0.253 - 0.337: 5 0.337 - 0.421: 18 Chirality restraints: 28508 Sorted by residual: chirality pdb=" C2' A2ML32787 " pdb=" C3' A2ML32787 " pdb=" O2' A2ML32787 " pdb=" C1' A2ML32787 " both_signs ideal model delta sigma weight residual False -2.39 -2.81 0.42 2.00e-01 2.50e+01 4.44e+00 chirality pdb=" C3' GL34305 " pdb=" C4' GL34305 " pdb=" O3' GL34305 " pdb=" C2' GL34305 " both_signs ideal model delta sigma weight residual False -2.74 -2.34 -0.41 2.00e-01 2.50e+01 4.18e+00 chirality pdb=" C2' A2ML31871 " pdb=" C3' A2ML31871 " pdb=" O2' A2ML31871 " pdb=" C1' A2ML31871 " both_signs ideal model delta sigma weight residual False -2.39 -2.80 0.40 2.00e-01 2.50e+01 4.08e+00 ... (remaining 28505 not shown) Planarity restraints: 15818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMGL34494 " -0.061 2.00e-02 2.50e+03 6.15e-01 8.52e+03 pdb=" C4' OMGL34494 " -0.457 2.00e-02 2.50e+03 pdb=" O4' OMGL34494 " -0.717 2.00e-02 2.50e+03 pdb=" C3' OMGL34494 " 0.595 2.00e-02 2.50e+03 pdb=" O3' OMGL34494 " 0.637 2.00e-02 2.50e+03 pdb=" C2' OMGL34494 " 0.198 2.00e-02 2.50e+03 pdb=" O2' OMGL34494 " -0.957 2.00e-02 2.50e+03 pdb=" C1' OMGL34494 " -0.200 2.00e-02 2.50e+03 pdb=" N9 OMGL34494 " 0.962 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMGL31625 " -0.940 2.00e-02 2.50e+03 6.08e-01 8.32e+03 pdb=" C4' OMGL31625 " 0.163 2.00e-02 2.50e+03 pdb=" O4' OMGL31625 " 0.928 2.00e-02 2.50e+03 pdb=" C3' OMGL31625 " -0.302 2.00e-02 2.50e+03 pdb=" O3' OMGL31625 " 0.776 2.00e-02 2.50e+03 pdb=" C2' OMGL31625 " -0.590 2.00e-02 2.50e+03 pdb=" O2' OMGL31625 " -0.525 2.00e-02 2.50e+03 pdb=" C1' OMGL31625 " 0.488 2.00e-02 2.50e+03 pdb=" N9 OMGL31625 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMGL34228 " 0.896 2.00e-02 2.50e+03 6.06e-01 8.26e+03 pdb=" C4' OMGL34228 " -0.213 2.00e-02 2.50e+03 pdb=" O4' OMGL34228 " -0.689 2.00e-02 2.50e+03 pdb=" C3' OMGL34228 " 0.190 2.00e-02 2.50e+03 pdb=" O3' OMGL34228 " -0.969 2.00e-02 2.50e+03 pdb=" C2' OMGL34228 " 0.623 2.00e-02 2.50e+03 pdb=" O2' OMGL34228 " 0.650 2.00e-02 2.50e+03 pdb=" C1' OMGL34228 " -0.441 2.00e-02 2.50e+03 pdb=" N9 OMGL34228 " -0.046 2.00e-02 2.50e+03 ... (remaining 15815 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.58: 1048 2.58 - 3.22: 129092 3.22 - 3.86: 333564 3.86 - 4.50: 470322 4.50 - 5.14: 633519 Nonbonded interactions: 1567545 Sorted by model distance: nonbonded pdb=" O2' 1MAL31322 " pdb=" O4' AL31323 " model vdw 1.943 3.040 nonbonded pdb=" O1B GDPSR1001 " pdb="MG MGSR1003 " model vdw 1.947 2.170 nonbonded pdb=" OP2 AL31337 " pdb="MG MGL36009 " model vdw 1.955 2.170 nonbonded pdb=" OP1 CL32393 " pdb="MG MGL36043 " model vdw 1.958 2.170 nonbonded pdb=" OP2 A2ML32363 " pdb="MG MGL36038 " model vdw 1.967 2.170 ... (remaining 1567540 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.100 Extract box with map and model: 26.600 Check model and map are aligned: 1.600 Set scattering table: 1.010 Process input model: 596.000 Find NCS groups from input model: 3.510 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:11.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 647.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 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 : 0.007 0.247 159568 Z= 0.429 Angle : 0.769 39.294 233140 Z= 0.336 Chirality : 0.038 0.421 28508 Planarity : 0.026 0.615 15818 Dihedral : 21.804 179.076 86523 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.46 % Favored : 98.53 % Rotamer: Outliers : 0.01 % Allowed : 0.05 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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: 0.59 (0.09), residues: 8512 helix: 0.86 (0.09), residues: 3309 sheet: 0.56 (0.15), residues: 1098 loop : 0.09 (0.09), residues: 4105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRPSV 86 HIS 0.014 0.001 HISLA 25 PHE 0.021 0.001 PHESR 18 TYR 0.024 0.002 TYRLC 84 ARG 0.009 0.001 ARGSR 169 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17024 Ramachandran restraints generated. 8512 Oldfield, 0 Emsley, 8512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17024 Ramachandran restraints generated. 8512 Oldfield, 0 Emsley, 8512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1632 residues out of total 7502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1631 time to evaluate : 7.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L5 56 THR cc_start: 0.8422 (t) cc_final: 0.8204 (m) REVERT: LD 43 LYS cc_start: 0.8262 (tttm) cc_final: 0.7635 (tttm) REVERT: LI 56 GLN cc_start: 0.8325 (mt0) cc_final: 0.8030 (mt0) REVERT: LM 27 GLN cc_start: 0.7593 (mm-40) cc_final: 0.7366 (mm-40) REVERT: LO 51 ASN cc_start: 0.8746 (p0) cc_final: 0.8517 (p0) REVERT: LQ 95 TYR cc_start: 0.8431 (m-80) cc_final: 0.8158 (m-80) REVERT: LS 112 ARG cc_start: 0.8016 (ttp-110) cc_final: 0.7569 (ttp-110) REVERT: LV 33 LEU cc_start: 0.8031 (tt) cc_final: 0.7822 (tp) REVERT: NK 28 ARG cc_start: 0.7772 (mtm110) cc_final: 0.7392 (mmp-170) REVERT: NR 124 PHE cc_start: 0.8397 (t80) cc_final: 0.8166 (t80) REVERT: SA 35 ASP cc_start: 0.8076 (p0) cc_final: 0.7787 (p0) REVERT: SE 111 LYS cc_start: 0.7771 (ttmt) cc_final: 0.7361 (tttm) REVERT: SG 171 ASP cc_start: 0.7896 (t0) cc_final: 0.7688 (t0) REVERT: SM 140 MET cc_start: 0.8678 (mmm) cc_final: 0.8418 (mmm) REVERT: SM 273 MET cc_start: 0.7460 (mmm) cc_final: 0.7206 (mmt) REVERT: SV 87 ASN cc_start: 0.7139 (m110) cc_final: 0.6661 (m-40) REVERT: SV 91 ASP cc_start: 0.7809 (m-30) cc_final: 0.7501 (m-30) REVERT: VB 51 LYS cc_start: 0.8202 (tttm) cc_final: 0.7988 (tttm) outliers start: 1 outliers final: 3 residues processed: 1632 average time/residue: 2.5875 time to fit residues: 5785.2479 Evaluate side-chains 1101 residues out of total 7502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1098 time to evaluate : 7.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L5 residue 97 ASN Chi-restraints excluded: chain NR residue 156 ILE Chi-restraints excluded: chain SR residue 576 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1211 random chunks: chunk 1022 optimal weight: 6.9990 chunk 917 optimal weight: 0.5980 chunk 509 optimal weight: 0.8980 chunk 313 optimal weight: 0.7980 chunk 619 optimal weight: 0.9990 chunk 490 optimal weight: 7.9990 chunk 949 optimal weight: 1.9990 chunk 367 optimal weight: 5.9990 chunk 577 optimal weight: 2.9990 chunk 706 optimal weight: 5.9990 chunk 1099 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L5 104 ASN L6 67 HIS L6 115 GLN L7 96 GLN L8 69 HIS L8 70 GLN L9 29 GLN LA 40 HIS LA 101 ASN ** LA 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LA 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 108 GLN LC 122 HIS LE 58 HIS LG 27 ASN LH 151 ASN LI 72 GLN LI 86 GLN LJ 78 ASN LL 6 GLN LL 100 ASN LM 11 ASN LM 19 ASN LM 49 HIS ** LN 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LN 322 HIS LO 40 GLN ** LP 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 121 ASN LR 3 GLN LR 14 ASN LS 20 GLN LS 107 GLN LT 55 ASN LU 92 ASN NL 267 GLN NL 341 GLN NP 18 GLN NR 42 ASN NR 83 ASN NR 122 GLN SC 190 HIS SC 256 GLN SE 227 ASN SG 8 GLN SG 39 ASN SG 40 HIS SH 119 HIS SI 66 HIS B SI 225 HIS SK 83 HIS SK 225 ASN SM 102 ASN SM 209 HIS SM 211 HIS SM 245 HIS SR 64 GLN SR 98 GLN SR 100 ASN SR 108 ASN SR 157 HIS SR 209 HIS SR 542 GLN SV 17 HIS SV 24 ASN Total number of N/Q/H flips: 61 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 159568 Z= 0.161 Angle : 0.706 22.828 233140 Z= 0.379 Chirality : 0.034 0.332 28508 Planarity : 0.007 0.130 15818 Dihedral : 23.136 179.758 68345 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.45 % Favored : 98.54 % Rotamer: Outliers : 1.95 % Allowed : 10.46 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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: 1.25 (0.09), residues: 8512 helix: 1.82 (0.09), residues: 3370 sheet: 0.63 (0.15), residues: 1066 loop : 0.12 (0.09), residues: 4076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRPLN 196 HIS 0.008 0.001 HISLA 25 PHE 0.015 0.001 PHESR 18 TYR 0.018 0.001 TYRSB 119 ARG 0.008 0.000 ARGNL 387 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17024 Ramachandran restraints generated. 8512 Oldfield, 0 Emsley, 8512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17024 Ramachandran restraints generated. 8512 Oldfield, 0 Emsley, 8512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1277 residues out of total 7502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 1134 time to evaluate : 7.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L6 184 MET cc_start: 0.7660 (mtp) cc_final: 0.7452 (mtp) REVERT: L7 174 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7886 (tt) REVERT: L9 13 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.7844 (mmpt) REVERT: LE 157 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.6103 (mp0) REVERT: LF 41 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7612 (tt0) REVERT: LL 28 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7271 (pt0) REVERT: LM 27 GLN cc_start: 0.7607 (mm-40) cc_final: 0.7378 (mm-40) REVERT: LM 114 LYS cc_start: 0.6579 (OUTLIER) cc_final: 0.5701 (mtmp) REVERT: LO 44 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7065 (mmtm) REVERT: LP 55 LYS cc_start: 0.8336 (mmmm) cc_final: 0.8073 (tptp) REVERT: LP 92 ARG cc_start: 0.7408 (ttm110) cc_final: 0.7175 (ttp-110) REVERT: LQ 27 ARG cc_start: 0.7350 (OUTLIER) cc_final: 0.6653 (ttp-170) REVERT: LU 60 LEU cc_start: 0.8708 (mt) cc_final: 0.8466 (mp) REVERT: LV 92 GLU cc_start: 0.6619 (OUTLIER) cc_final: 0.6364 (mm-30) REVERT: SA 35 ASP cc_start: 0.7983 (p0) cc_final: 0.7624 (p0) REVERT: SA 308 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8049 (ttmm) REVERT: SB 36 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7983 (tt) REVERT: SE 111 LYS cc_start: 0.7670 (ttmt) cc_final: 0.7412 (tttm) REVERT: SE 250 ILE cc_start: 0.8634 (mm) cc_final: 0.8427 (mt) REVERT: SF 147 ARG cc_start: 0.7815 (ttm-80) cc_final: 0.7568 (mtp-110) REVERT: SG 71 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7119 (ttt180) REVERT: SG 171 ASP cc_start: 0.7915 (t0) cc_final: 0.7713 (t0) REVERT: SM 135 ASP cc_start: 0.7362 (OUTLIER) cc_final: 0.7133 (m-30) REVERT: SR 482 GLN cc_start: 0.7059 (OUTLIER) cc_final: 0.6813 (tm130) REVERT: SR 535 ASP cc_start: 0.5741 (OUTLIER) cc_final: 0.5458 (t70) REVERT: SR 616 MET cc_start: 0.6635 (OUTLIER) cc_final: 0.5449 (mpt) REVERT: SV 87 ASN cc_start: 0.7235 (m110) cc_final: 0.6837 (m-40) REVERT: VB 51 LYS cc_start: 0.7989 (tttm) cc_final: 0.7783 (tttp) outliers start: 143 outliers final: 55 residues processed: 1201 average time/residue: 2.4660 time to fit residues: 4140.7536 Evaluate side-chains 1122 residues out of total 7502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 1051 time to evaluate : 7.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L6 residue 24 THR Chi-restraints excluded: chain L6 residue 140 SER Chi-restraints excluded: chain L7 residue 174 LEU Chi-restraints excluded: chain L7 residue 177 LEU Chi-restraints excluded: chain L8 residue 70 GLN Chi-restraints excluded: chain L9 residue 5 LYS Chi-restraints excluded: chain L9 residue 13 LYS Chi-restraints excluded: chain L9 residue 89 VAL Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LB residue 19 LYS Chi-restraints excluded: chain LB residue 128 LEU Chi-restraints excluded: chain LD residue 119 MET Chi-restraints excluded: chain LE residue 11 THR Chi-restraints excluded: chain LE residue 157 GLU Chi-restraints excluded: chain LF residue 41 GLN Chi-restraints excluded: chain LG residue 92 ASP Chi-restraints excluded: chain LH residue 84 GLU Chi-restraints excluded: chain LI residue 32 SER Chi-restraints excluded: chain LK residue 16 SER Chi-restraints excluded: chain LK residue 83 SER Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LL residue 81 THR Chi-restraints excluded: chain LM residue 31 SER Chi-restraints excluded: chain LM residue 114 LYS Chi-restraints excluded: chain LN residue 295 ASP Chi-restraints excluded: chain LN residue 298 LEU Chi-restraints excluded: chain LO residue 20 LEU Chi-restraints excluded: chain LO residue 44 LYS Chi-restraints excluded: chain LO residue 78 ASN Chi-restraints excluded: chain LP residue 66 THR Chi-restraints excluded: chain LQ residue 27 ARG Chi-restraints excluded: chain LQ residue 53 ILE Chi-restraints excluded: chain LQ residue 129 LEU Chi-restraints excluded: chain LR residue 107 LEU Chi-restraints excluded: chain LS residue 36 VAL Chi-restraints excluded: chain LT residue 90 SER Chi-restraints excluded: chain LU residue 27 SER Chi-restraints excluded: chain LV residue 23 VAL Chi-restraints excluded: chain LV residue 92 GLU Chi-restraints excluded: chain LX residue 26 VAL Chi-restraints excluded: chain LX residue 45 THR Chi-restraints excluded: chain NK residue 27 SER Chi-restraints excluded: chain NP residue 82 SER Chi-restraints excluded: chain NR residue 149 ASP Chi-restraints excluded: chain SA residue 138 MET Chi-restraints excluded: chain SA residue 152 LEU Chi-restraints excluded: chain SA residue 273 LEU Chi-restraints excluded: chain SA residue 297 GLU Chi-restraints excluded: chain SA residue 308 LYS Chi-restraints excluded: chain SB residue 36 LEU Chi-restraints excluded: chain SB residue 217 ASP Chi-restraints excluded: chain SC residue 143 SER Chi-restraints excluded: chain SC residue 212 LEU Chi-restraints excluded: chain SD residue 68 GLU Chi-restraints excluded: chain SD residue 199 LYS Chi-restraints excluded: chain SE residue 209 SER Chi-restraints excluded: chain SG residue 71 ARG Chi-restraints excluded: chain SH residue 50 ARG Chi-restraints excluded: chain SI residue 83 VAL Chi-restraints excluded: chain SI residue 221 SER Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SM residue 135 ASP Chi-restraints excluded: chain SR residue 112 ASP Chi-restraints excluded: chain SR residue 261 CYS Chi-restraints excluded: chain SR residue 306 ILE Chi-restraints excluded: chain SR residue 478 LEU Chi-restraints excluded: chain SR residue 482 GLN Chi-restraints excluded: chain SR residue 535 ASP Chi-restraints excluded: chain SR residue 587 LYS Chi-restraints excluded: chain SR residue 590 LYS Chi-restraints excluded: chain SR residue 616 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1211 random chunks: chunk 611 optimal weight: 7.9990 chunk 341 optimal weight: 10.0000 chunk 915 optimal weight: 2.9990 chunk 748 optimal weight: 6.9990 chunk 303 optimal weight: 4.9990 chunk 1101 optimal weight: 5.9990 chunk 1190 optimal weight: 4.9990 chunk 981 optimal weight: 6.9990 chunk 1092 optimal weight: 0.2980 chunk 375 optimal weight: 5.9990 chunk 883 optimal weight: 7.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L5 112 HIS L6 67 HIS L7 96 GLN L8 70 GLN LA 25 HIS LA 116 HIS LA 118 GLN LB 125 GLN LE 131 GLN LF 119 GLN LG 27 ASN LH 93 ASN LH 151 ASN LI 56 GLN LI 86 GLN LI 127 GLN LJ 78 ASN LJ 132 GLN LL 6 GLN LM 11 ASN LM 19 ASN LN 42 HIS LN 123 HIS LO 40 GLN ** LQ 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LR 3 GLN LR 14 ASN LS 20 GLN LT 55 ASN LU 92 ASN ** NL 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NL 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NP 13 HIS NP 18 GLN NR 42 ASN NR 60 ASN NR 96 ASN NR 122 GLN NR 155 ASN SA 236 ASN SB 229 ASN ** SC 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** SC 256 GLN SD 206 ASN SE 43 GLN SF 50 HIS SG 8 GLN SH 119 HIS SI 185 HIS SK 86 ASN SK 225 ASN SM 102 ASN SM 170 HIS ** SM 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SR 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SR 64 GLN SV 24 ASN SV 39 ASN SV 132 HIS Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 159568 Z= 0.387 Angle : 0.782 19.933 233140 Z= 0.411 Chirality : 0.042 0.334 28508 Planarity : 0.008 0.141 15818 Dihedral : 23.131 179.711 68339 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.93 % Favored : 98.06 % Rotamer: Outliers : 3.06 % Allowed : 11.90 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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 (0.09), residues: 8512 helix: 1.68 (0.09), residues: 3398 sheet: 0.44 (0.15), residues: 1085 loop : -0.10 (0.09), residues: 4029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRPLW 49 HIS 0.016 0.002 HISLA 25 PHE 0.028 0.002 PHESR 18 TYR 0.026 0.002 TYRSB 119 ARG 0.009 0.001 ARGLW 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17024 Ramachandran restraints generated. 8512 Oldfield, 0 Emsley, 8512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17024 Ramachandran restraints generated. 8512 Oldfield, 0 Emsley, 8512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1259 residues out of total 7502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 1035 time to evaluate : 8.044 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: L6 119 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7409 (tm-30) REVERT: L6 184 MET cc_start: 0.7870 (mtp) cc_final: 0.7578 (mtp) REVERT: L7 174 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7908 (tt) REVERT: L9 13 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.7889 (mmpt) REVERT: LE 157 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.6437 (mp0) REVERT: LF 41 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7674 (tt0) REVERT: LL 28 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7398 (pt0) REVERT: LM 27 GLN cc_start: 0.7768 (mm-40) cc_final: 0.7518 (mm-40) REVERT: LM 51 LYS cc_start: 0.7690 (OUTLIER) cc_final: 0.7474 (pttm) REVERT: LM 114 LYS cc_start: 0.6580 (mtmp) cc_final: 0.6163 (tptp) REVERT: LN 145 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7491 (mm-40) REVERT: LO 44 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7065 (mmtm) REVERT: LP 55 LYS cc_start: 0.8292 (mmmm) cc_final: 0.8019 (tptp) REVERT: LQ 57 ASN cc_start: 0.8601 (p0) cc_final: 0.8287 (p0) REVERT: LS 110 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.8030 (mtpt) REVERT: LU 60 LEU cc_start: 0.8568 (mt) cc_final: 0.8357 (mp) REVERT: NL 335 GLU cc_start: 0.6948 (mm-30) cc_final: 0.6746 (mp0) REVERT: SA 143 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7266 (mmm160) REVERT: SA 205 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7284 (mmp80) REVERT: SA 308 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8093 (ttmm) REVERT: SA 325 MET cc_start: 0.8319 (tpp) cc_final: 0.8068 (tpt) REVERT: SB 36 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8057 (tt) REVERT: SD 220 MET cc_start: 0.7733 (ttt) cc_final: 0.7466 (ttt) REVERT: SE 111 LYS cc_start: 0.7823 (ttmt) cc_final: 0.7500 (tttm) REVERT: SG 21 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.8066 (mttt) REVERT: SK 18 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8225 (tptt) REVERT: SK 134 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.8015 (mttp) REVERT: SK 223 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7378 (mttp) REVERT: SK 237 ARG cc_start: 0.7059 (OUTLIER) cc_final: 0.5840 (tmm-80) REVERT: SM 135 ASP cc_start: 0.7394 (OUTLIER) cc_final: 0.7169 (m-30) REVERT: SR 266 ARG cc_start: 0.7416 (tpp80) cc_final: 0.7175 (tpp80) REVERT: SR 535 ASP cc_start: 0.5872 (OUTLIER) cc_final: 0.5539 (t70) REVERT: SR 575 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.6481 (ptp-170) REVERT: SR 616 MET cc_start: 0.6734 (OUTLIER) cc_final: 0.5616 (mpt) REVERT: SV 1 MET cc_start: 0.7930 (OUTLIER) cc_final: 0.7029 (ptt) outliers start: 224 outliers final: 109 residues processed: 1158 average time/residue: 2.4552 time to fit residues: 3974.0415 Evaluate side-chains 1130 residues out of total 7502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 997 time to evaluate : 7.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L5 residue 39 VAL Chi-restraints excluded: chain L5 residue 102 THR Chi-restraints excluded: chain L5 residue 150 CYS Chi-restraints excluded: chain L6 residue 24 THR Chi-restraints excluded: chain L6 residue 52 SER Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 119 GLU Chi-restraints excluded: chain L6 residue 140 SER Chi-restraints excluded: chain L7 residue 174 LEU Chi-restraints excluded: chain L7 residue 177 LEU Chi-restraints excluded: chain L8 residue 38 VAL Chi-restraints excluded: chain L9 residue 5 LYS Chi-restraints excluded: chain L9 residue 13 LYS Chi-restraints excluded: chain L9 residue 89 VAL Chi-restraints excluded: chain L9 residue 170 LYS Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LA residue 141 SER Chi-restraints excluded: chain LB residue 19 LYS Chi-restraints excluded: chain LB residue 42 THR Chi-restraints excluded: chain LC residue 54 MET Chi-restraints excluded: chain LD residue 68 LEU Chi-restraints excluded: chain LD residue 142 ILE Chi-restraints excluded: chain LE residue 32 ARG Chi-restraints excluded: chain LE residue 68 THR Chi-restraints excluded: chain LE residue 81 LYS Chi-restraints excluded: chain LE residue 85 LEU Chi-restraints excluded: chain LE residue 157 GLU Chi-restraints excluded: chain LF residue 41 GLN Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LG residue 69 LYS Chi-restraints excluded: chain LG residue 92 ASP Chi-restraints excluded: chain LG residue 111 GLU Chi-restraints excluded: chain LH residue 115 LYS Chi-restraints excluded: chain LH residue 145 ASP Chi-restraints excluded: chain LH residue 147 LEU Chi-restraints excluded: chain LI residue 32 SER Chi-restraints excluded: chain LI residue 69 LYS Chi-restraints excluded: chain LI residue 128 VAL Chi-restraints excluded: chain LJ residue 100 VAL Chi-restraints excluded: chain LK residue 16 SER Chi-restraints excluded: chain LK residue 83 SER Chi-restraints excluded: chain LK residue 139 SER Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LL residue 81 THR Chi-restraints excluded: chain LL residue 111 ILE Chi-restraints excluded: chain LM residue 31 SER Chi-restraints excluded: chain LM residue 51 LYS Chi-restraints excluded: chain LN residue 144 LYS Chi-restraints excluded: chain LN residue 145 GLN Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 298 LEU Chi-restraints excluded: chain LO residue 20 LEU Chi-restraints excluded: chain LO residue 26 LYS Chi-restraints excluded: chain LO residue 35 LEU Chi-restraints excluded: chain LO residue 44 LYS Chi-restraints excluded: chain LP residue 66 THR Chi-restraints excluded: chain LP residue 101 LYS Chi-restraints excluded: chain LQ residue 53 ILE Chi-restraints excluded: chain LQ residue 123 THR Chi-restraints excluded: chain LQ residue 129 LEU Chi-restraints excluded: chain LR residue 105 LYS Chi-restraints excluded: chain LR residue 107 LEU Chi-restraints excluded: chain LS residue 36 VAL Chi-restraints excluded: chain LS residue 42 SER Chi-restraints excluded: chain LS residue 110 LYS Chi-restraints excluded: chain LT residue 22 ARG Chi-restraints excluded: chain LT residue 90 SER Chi-restraints excluded: chain LU residue 27 SER Chi-restraints excluded: chain LU residue 70 LEU Chi-restraints excluded: chain LV residue 23 VAL Chi-restraints excluded: chain LV residue 24 THR Chi-restraints excluded: chain LX residue 24 LYS Chi-restraints excluded: chain LX residue 26 VAL Chi-restraints excluded: chain LX residue 45 THR Chi-restraints excluded: chain LX residue 72 ASN Chi-restraints excluded: chain LY residue 56 LEU Chi-restraints excluded: chain NL residue 427 SER Chi-restraints excluded: chain NP residue 71 ILE Chi-restraints excluded: chain SA residue 14 LYS Chi-restraints excluded: chain SA residue 143 ARG Chi-restraints excluded: chain SA residue 150 LEU Chi-restraints excluded: chain SA residue 152 LEU Chi-restraints excluded: chain SA residue 205 ARG Chi-restraints excluded: chain SA residue 273 LEU Chi-restraints excluded: chain SA residue 297 GLU Chi-restraints excluded: chain SA residue 308 LYS Chi-restraints excluded: chain SA residue 351 VAL Chi-restraints excluded: chain SB residue 36 LEU Chi-restraints excluded: chain SB residue 125 VAL Chi-restraints excluded: chain SB residue 188 LYS Chi-restraints excluded: chain SB residue 217 ASP Chi-restraints excluded: chain SB residue 272 SER Chi-restraints excluded: chain SC residue 107 VAL Chi-restraints excluded: chain SC residue 134 SER Chi-restraints excluded: chain SC residue 143 SER Chi-restraints excluded: chain SC residue 203 ILE Chi-restraints excluded: chain SC residue 212 LEU Chi-restraints excluded: chain SC residue 255 SER Chi-restraints excluded: chain SD residue 68 GLU Chi-restraints excluded: chain SD residue 199 LYS Chi-restraints excluded: chain SF residue 160 SER Chi-restraints excluded: chain SG residue 21 LYS Chi-restraints excluded: chain SG residue 94 SER Chi-restraints excluded: chain SG residue 95 VAL Chi-restraints excluded: chain SH residue 50 ARG Chi-restraints excluded: chain SI residue 83 VAL Chi-restraints excluded: chain SI residue 212 SER Chi-restraints excluded: chain SI residue 221 SER Chi-restraints excluded: chain SK residue 18 LYS Chi-restraints excluded: chain SK residue 75 ASN Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SK residue 134 LYS Chi-restraints excluded: chain SK residue 223 LYS Chi-restraints excluded: chain SK residue 237 ARG Chi-restraints excluded: chain SM residue 59 THR Chi-restraints excluded: chain SM residue 135 ASP Chi-restraints excluded: chain SM residue 360 LEU Chi-restraints excluded: chain SM residue 361 CYS Chi-restraints excluded: chain SR residue 112 ASP Chi-restraints excluded: chain SR residue 258 SER Chi-restraints excluded: chain SR residue 261 CYS Chi-restraints excluded: chain SR residue 306 ILE Chi-restraints excluded: chain SR residue 313 GLU Chi-restraints excluded: chain SR residue 364 ILE Chi-restraints excluded: chain SR residue 459 LEU Chi-restraints excluded: chain SR residue 478 LEU Chi-restraints excluded: chain SR residue 535 ASP Chi-restraints excluded: chain SR residue 575 ARG Chi-restraints excluded: chain SR residue 576 ASP Chi-restraints excluded: chain SR residue 590 LYS Chi-restraints excluded: chain SR residue 616 MET Chi-restraints excluded: chain SV residue 1 MET Chi-restraints excluded: chain VB residue 35 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1211 random chunks: chunk 1088 optimal weight: 2.9990 chunk 828 optimal weight: 5.9990 chunk 571 optimal weight: 7.9990 chunk 121 optimal weight: 20.0000 chunk 525 optimal weight: 3.9990 chunk 739 optimal weight: 3.9990 chunk 1105 optimal weight: 0.7980 chunk 1170 optimal weight: 6.9990 chunk 577 optimal weight: 0.6980 chunk 1047 optimal weight: 1.9990 chunk 315 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L6 67 HIS L6 104 ASN L7 96 GLN L8 70 GLN LA 118 GLN LF 95 ASN LG 27 ASN LH 73 HIS LH 151 ASN LI 56 GLN LI 86 GLN LI 127 GLN LJ 78 ASN LK 93 ASN LL 6 GLN LM 11 ASN LM 19 ASN LM 58 GLN LN 138 GLN LO 40 GLN ** LQ 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LQ 81 ASN LR 3 GLN LT 55 ASN LU 92 ASN ** NL 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NP 18 GLN NR 42 ASN NR 60 ASN SB 275 GLN SC 211 HIS SC 256 GLN SD 151 ASN SE 43 GLN ** SF 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 8 GLN SK 225 ASN SM 102 ASN SM 243 ASN ** SM 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SR 5 ASN SR 482 GLN SV 24 ASN SV 87 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 159568 Z= 0.229 Angle : 0.701 20.019 233140 Z= 0.379 Chirality : 0.036 0.337 28508 Planarity : 0.007 0.134 15818 Dihedral : 23.080 179.943 68339 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.73 % Allowed : 12.92 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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: 1.13 (0.09), residues: 8512 helix: 1.88 (0.09), residues: 3385 sheet: 0.46 (0.15), residues: 1084 loop : -0.08 (0.09), residues: 4043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRPLN 196 HIS 0.006 0.001 HISLV 21 PHE 0.014 0.001 PHESB 160 TYR 0.022 0.002 TYRSB 119 ARG 0.007 0.000 ARGL7 169 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17024 Ramachandran restraints generated. 8512 Oldfield, 0 Emsley, 8512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17024 Ramachandran restraints generated. 8512 Oldfield, 0 Emsley, 8512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1231 residues out of total 7502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 1031 time to evaluate : 7.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L6 119 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7401 (tm-30) REVERT: L6 184 MET cc_start: 0.7833 (mtp) cc_final: 0.7507 (mtp) REVERT: L7 31 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7398 (ttt180) REVERT: L7 174 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7898 (tt) REVERT: L9 13 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.7873 (mmpt) REVERT: LB 108 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.6680 (ttm170) REVERT: LE 136 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7558 (mtp180) REVERT: LF 41 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7612 (tt0) REVERT: LG 112 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.7942 (mtp) REVERT: LL 28 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7336 (pt0) REVERT: LL 108 MET cc_start: 0.8490 (mmm) cc_final: 0.8272 (mmm) REVERT: LM 27 GLN cc_start: 0.7727 (mm-40) cc_final: 0.7444 (mm-40) REVERT: LM 51 LYS cc_start: 0.7616 (OUTLIER) cc_final: 0.7323 (pttm) REVERT: LM 114 LYS cc_start: 0.6607 (OUTLIER) cc_final: 0.6213 (tptp) REVERT: LN 145 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.7447 (mm-40) REVERT: LO 44 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7046 (mmtm) REVERT: LQ 57 ASN cc_start: 0.8585 (p0) cc_final: 0.8301 (p0) REVERT: NK 28 ARG cc_start: 0.7693 (mtm110) cc_final: 0.7440 (mmp-170) REVERT: SA 205 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7292 (mmp80) REVERT: SA 325 MET cc_start: 0.8289 (tpp) cc_final: 0.7989 (tpt) REVERT: SB 36 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8000 (tt) REVERT: SD 220 MET cc_start: 0.7659 (ttt) cc_final: 0.7270 (ttt) REVERT: SE 111 LYS cc_start: 0.7754 (ttmt) cc_final: 0.7452 (tttm) REVERT: SF 147 ARG cc_start: 0.7842 (ttm-80) cc_final: 0.7593 (mtp85) REVERT: SG 21 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.8073 (mttt) REVERT: SG 86 LEU cc_start: 0.6999 (OUTLIER) cc_final: 0.6302 (mt) REVERT: SK 18 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.8170 (tptt) REVERT: SK 134 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.8011 (mttp) REVERT: SK 223 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7324 (mttp) REVERT: SK 237 ARG cc_start: 0.7046 (OUTLIER) cc_final: 0.5979 (tmm-80) REVERT: SM 135 ASP cc_start: 0.7370 (OUTLIER) cc_final: 0.7141 (m-30) REVERT: SQ 5 LYS cc_start: 0.7292 (pttp) cc_final: 0.7088 (pttp) REVERT: SR 238 MET cc_start: 0.8473 (mmm) cc_final: 0.8223 (mmp) REVERT: SR 301 GLU cc_start: 0.5399 (OUTLIER) cc_final: 0.4834 (mm-30) REVERT: SR 482 GLN cc_start: 0.6990 (OUTLIER) cc_final: 0.6701 (tm130) REVERT: SR 535 ASP cc_start: 0.5866 (OUTLIER) cc_final: 0.5556 (t70) REVERT: SR 575 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.6638 (ptp-170) REVERT: SR 616 MET cc_start: 0.6693 (OUTLIER) cc_final: 0.5553 (mpt) REVERT: SV 1 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.6966 (ptt) outliers start: 200 outliers final: 106 residues processed: 1147 average time/residue: 2.4453 time to fit residues: 3951.4759 Evaluate side-chains 1136 residues out of total 7502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 1002 time to evaluate : 7.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L5 residue 97 ASN Chi-restraints excluded: chain L5 residue 102 THR Chi-restraints excluded: chain L5 residue 150 CYS Chi-restraints excluded: chain L6 residue 24 THR Chi-restraints excluded: chain L6 residue 52 SER Chi-restraints excluded: chain L6 residue 64 VAL Chi-restraints excluded: chain L6 residue 119 GLU Chi-restraints excluded: chain L6 residue 140 SER Chi-restraints excluded: chain L6 residue 143 GLU Chi-restraints excluded: chain L7 residue 31 ARG Chi-restraints excluded: chain L7 residue 174 LEU Chi-restraints excluded: chain L7 residue 177 LEU Chi-restraints excluded: chain L8 residue 38 VAL Chi-restraints excluded: chain L8 residue 70 GLN Chi-restraints excluded: chain L8 residue 113 MET Chi-restraints excluded: chain L9 residue 5 LYS Chi-restraints excluded: chain L9 residue 13 LYS Chi-restraints excluded: chain L9 residue 89 VAL Chi-restraints excluded: chain LA residue 14 SER Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LA residue 141 SER Chi-restraints excluded: chain LB residue 19 LYS Chi-restraints excluded: chain LB residue 42 THR Chi-restraints excluded: chain LB residue 108 ARG Chi-restraints excluded: chain LD residue 68 LEU Chi-restraints excluded: chain LD residue 119 MET Chi-restraints excluded: chain LE residue 11 THR Chi-restraints excluded: chain LE residue 32 ARG Chi-restraints excluded: chain LE residue 68 THR Chi-restraints excluded: chain LE residue 81 LYS Chi-restraints excluded: chain LE residue 136 ARG Chi-restraints excluded: chain LF residue 41 GLN Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LG residue 69 LYS Chi-restraints excluded: chain LG residue 92 ASP Chi-restraints excluded: chain LG residue 112 MET Chi-restraints excluded: chain LH residue 147 LEU Chi-restraints excluded: chain LI residue 32 SER Chi-restraints excluded: chain LI residue 128 VAL Chi-restraints excluded: chain LJ residue 100 VAL Chi-restraints excluded: chain LK residue 16 SER Chi-restraints excluded: chain LK residue 83 SER Chi-restraints excluded: chain LK residue 93 ASN Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LL residue 81 THR Chi-restraints excluded: chain LL residue 105 ASP Chi-restraints excluded: chain LL residue 111 ILE Chi-restraints excluded: chain LM residue 13 SER Chi-restraints excluded: chain LM residue 23 LYS Chi-restraints excluded: chain LM residue 31 SER Chi-restraints excluded: chain LM residue 51 LYS Chi-restraints excluded: chain LM residue 114 LYS Chi-restraints excluded: chain LN residue 144 LYS Chi-restraints excluded: chain LN residue 145 GLN Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 293 ILE Chi-restraints excluded: chain LN residue 298 LEU Chi-restraints excluded: chain LN residue 337 VAL Chi-restraints excluded: chain LO residue 20 LEU Chi-restraints excluded: chain LO residue 26 LYS Chi-restraints excluded: chain LO residue 35 LEU Chi-restraints excluded: chain LO residue 44 LYS Chi-restraints excluded: chain LP residue 66 THR Chi-restraints excluded: chain LP residue 101 LYS Chi-restraints excluded: chain LQ residue 53 ILE Chi-restraints excluded: chain LQ residue 123 THR Chi-restraints excluded: chain LQ residue 129 LEU Chi-restraints excluded: chain LR residue 107 LEU Chi-restraints excluded: chain LT residue 22 ARG Chi-restraints excluded: chain LT residue 90 SER Chi-restraints excluded: chain LU residue 27 SER Chi-restraints excluded: chain LV residue 23 VAL Chi-restraints excluded: chain LV residue 103 VAL Chi-restraints excluded: chain LX residue 26 VAL Chi-restraints excluded: chain LX residue 45 THR Chi-restraints excluded: chain LX residue 72 ASN Chi-restraints excluded: chain LY residue 36 VAL Chi-restraints excluded: chain LY residue 56 LEU Chi-restraints excluded: chain NL residue 427 SER Chi-restraints excluded: chain NP residue 82 SER Chi-restraints excluded: chain NR residue 131 ILE Chi-restraints excluded: chain NR residue 149 ASP Chi-restraints excluded: chain SA residue 14 LYS Chi-restraints excluded: chain SA residue 61 GLN Chi-restraints excluded: chain SA residue 152 LEU Chi-restraints excluded: chain SA residue 205 ARG Chi-restraints excluded: chain SA residue 273 LEU Chi-restraints excluded: chain SA residue 297 GLU Chi-restraints excluded: chain SB residue 36 LEU Chi-restraints excluded: chain SB residue 217 ASP Chi-restraints excluded: chain SB residue 272 SER Chi-restraints excluded: chain SC residue 91 THR Chi-restraints excluded: chain SC residue 134 SER Chi-restraints excluded: chain SC residue 143 SER Chi-restraints excluded: chain SC residue 212 LEU Chi-restraints excluded: chain SD residue 199 LYS Chi-restraints excluded: chain SF residue 169 VAL Chi-restraints excluded: chain SF residue 208 GLU Chi-restraints excluded: chain SG residue 1 MET Chi-restraints excluded: chain SG residue 21 LYS Chi-restraints excluded: chain SG residue 86 LEU Chi-restraints excluded: chain SG residue 94 SER Chi-restraints excluded: chain SH residue 50 ARG Chi-restraints excluded: chain SH residue 76 LEU Chi-restraints excluded: chain SI residue 83 VAL Chi-restraints excluded: chain SI residue 212 SER Chi-restraints excluded: chain SI residue 221 SER Chi-restraints excluded: chain SK residue 18 LYS Chi-restraints excluded: chain SK residue 75 ASN Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SK residue 134 LYS Chi-restraints excluded: chain SK residue 223 LYS Chi-restraints excluded: chain SK residue 237 ARG Chi-restraints excluded: chain SM residue 59 THR Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SM residue 135 ASP Chi-restraints excluded: chain SM residue 229 THR Chi-restraints excluded: chain SM residue 360 LEU Chi-restraints excluded: chain SM residue 406 LEU Chi-restraints excluded: chain SR residue 258 SER Chi-restraints excluded: chain SR residue 261 CYS Chi-restraints excluded: chain SR residue 301 GLU Chi-restraints excluded: chain SR residue 306 ILE Chi-restraints excluded: chain SR residue 313 GLU Chi-restraints excluded: chain SR residue 364 ILE Chi-restraints excluded: chain SR residue 459 LEU Chi-restraints excluded: chain SR residue 478 LEU Chi-restraints excluded: chain SR residue 482 GLN Chi-restraints excluded: chain SR residue 535 ASP Chi-restraints excluded: chain SR residue 575 ARG Chi-restraints excluded: chain SR residue 576 ASP Chi-restraints excluded: chain SR residue 590 LYS Chi-restraints excluded: chain SR residue 616 MET Chi-restraints excluded: chain SV residue 1 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1211 random chunks: chunk 974 optimal weight: 0.9990 chunk 664 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 871 optimal weight: 6.9990 chunk 482 optimal weight: 4.9990 chunk 998 optimal weight: 8.9990 chunk 809 optimal weight: 3.9990 chunk 1 optimal weight: 0.0570 chunk 597 optimal weight: 2.9990 chunk 1050 optimal weight: 5.9990 chunk 295 optimal weight: 10.0000 overall best weight: 2.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L6 67 HIS L7 96 GLN L8 70 GLN ** LA 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LG 27 ASN LH 107 HIS LH 151 ASN LI 56 GLN LI 86 GLN LI 127 GLN LJ 78 ASN LM 11 ASN LM 19 ASN LO 40 GLN ** LQ 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LQ 81 ASN LR 3 GLN LU 92 ASN NL 248 ASN ** NL 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NP 18 GLN NR 42 ASN NR 60 ASN SB 275 GLN SC 256 GLN ** SD 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 43 GLN SE 64 GLN ** SF 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 8 GLN SK 225 ASN SM 102 ASN SM 396 GLN SV 24 ASN SV 87 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 159568 Z= 0.238 Angle : 0.696 19.705 233140 Z= 0.376 Chirality : 0.036 0.334 28508 Planarity : 0.007 0.134 15818 Dihedral : 23.031 179.751 68339 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.02 % Allowed : 13.64 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.09), residues: 8512 helix: 1.95 (0.09), residues: 3388 sheet: 0.47 (0.15), residues: 1070 loop : -0.08 (0.09), residues: 4054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRPLN 196 HIS 0.006 0.001 HISLK 39 PHE 0.015 0.001 PHESB 160 TYR 0.022 0.002 TYRSB 119 ARG 0.006 0.000 ARGL5 32 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17024 Ramachandran restraints generated. 8512 Oldfield, 0 Emsley, 8512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17024 Ramachandran restraints generated. 8512 Oldfield, 0 Emsley, 8512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1237 residues out of total 7502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 1016 time to evaluate : 8.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L6 119 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7196 (tm-30) REVERT: L6 121 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7120 (mmm160) REVERT: L6 184 MET cc_start: 0.7853 (mtp) cc_final: 0.7562 (mtp) REVERT: L7 31 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7384 (ttt-90) REVERT: L7 174 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7905 (tt) REVERT: L9 13 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.7875 (mmpt) REVERT: LB 108 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.6671 (ttm170) REVERT: LD 76 MET cc_start: 0.7461 (OUTLIER) cc_final: 0.7110 (mmt) REVERT: LE 136 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7563 (mtp180) REVERT: LF 41 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7644 (tt0) REVERT: LG 111 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7312 (mp0) REVERT: LK 134 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7316 (tt0) REVERT: LL 28 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7328 (pt0) REVERT: LL 108 MET cc_start: 0.8491 (mmm) cc_final: 0.8249 (mmm) REVERT: LM 27 GLN cc_start: 0.7792 (mm-40) cc_final: 0.7543 (mm-40) REVERT: LM 51 LYS cc_start: 0.7565 (OUTLIER) cc_final: 0.7286 (pttm) REVERT: LM 114 LYS cc_start: 0.6557 (OUTLIER) cc_final: 0.6167 (tptp) REVERT: LN 139 ASP cc_start: 0.6394 (t0) cc_final: 0.6100 (t0) REVERT: LN 145 GLN cc_start: 0.7811 (OUTLIER) cc_final: 0.7485 (mm-40) REVERT: LN 352 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7714 (mt) REVERT: LO 44 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7111 (mmmm) REVERT: LQ 57 ASN cc_start: 0.8577 (p0) cc_final: 0.8279 (p0) REVERT: LU 60 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8224 (mp) REVERT: LV 33 LEU cc_start: 0.8132 (tt) cc_final: 0.7847 (tp) REVERT: NK 28 ARG cc_start: 0.7699 (mtm110) cc_final: 0.7432 (mmp-170) REVERT: NK 34 LYS cc_start: 0.7443 (OUTLIER) cc_final: 0.7191 (ptpp) REVERT: NP 77 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.8180 (mttm) REVERT: SA 205 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7304 (mmp80) REVERT: SA 325 MET cc_start: 0.8312 (tpp) cc_final: 0.7996 (tpt) REVERT: SB 36 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.7961 (tt) REVERT: SB 163 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8112 (tp) REVERT: SB 212 MET cc_start: 0.6850 (mtm) cc_final: 0.6381 (mtt) REVERT: SD 74 MET cc_start: 0.7451 (mtp) cc_final: 0.7098 (mtp) REVERT: SD 220 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.7279 (ttt) REVERT: SE 111 LYS cc_start: 0.7733 (ttmt) cc_final: 0.7470 (tttm) REVERT: SG 21 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8051 (mttt) REVERT: SG 86 LEU cc_start: 0.7029 (OUTLIER) cc_final: 0.6344 (mt) REVERT: SK 18 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.8168 (tptt) REVERT: SK 237 ARG cc_start: 0.7121 (OUTLIER) cc_final: 0.6073 (tmm-80) REVERT: SM 135 ASP cc_start: 0.7331 (OUTLIER) cc_final: 0.7128 (m-30) REVERT: SR 301 GLU cc_start: 0.5371 (OUTLIER) cc_final: 0.4801 (mm-30) REVERT: SR 535 ASP cc_start: 0.5917 (OUTLIER) cc_final: 0.5595 (t70) REVERT: SR 575 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.6667 (ptp-170) REVERT: SR 616 MET cc_start: 0.6714 (OUTLIER) cc_final: 0.5547 (mpt) REVERT: SV 1 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.6986 (ptt) REVERT: SV 87 ASN cc_start: 0.7570 (m110) cc_final: 0.7170 (m-40) outliers start: 221 outliers final: 126 residues processed: 1144 average time/residue: 2.3941 time to fit residues: 3849.0601 Evaluate side-chains 1154 residues out of total 7502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 994 time to evaluate : 7.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L5 residue 39 VAL Chi-restraints excluded: chain L5 residue 102 THR Chi-restraints excluded: chain L5 residue 150 CYS Chi-restraints excluded: chain L6 residue 24 THR Chi-restraints excluded: chain L6 residue 52 SER Chi-restraints excluded: chain L6 residue 64 VAL Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 119 GLU Chi-restraints excluded: chain L6 residue 121 ARG Chi-restraints excluded: chain L6 residue 140 SER Chi-restraints excluded: chain L6 residue 143 GLU Chi-restraints excluded: chain L7 residue 31 ARG Chi-restraints excluded: chain L7 residue 174 LEU Chi-restraints excluded: chain L7 residue 177 LEU Chi-restraints excluded: chain L7 residue 189 ILE Chi-restraints excluded: chain L7 residue 202 LEU Chi-restraints excluded: chain L8 residue 38 VAL Chi-restraints excluded: chain L8 residue 113 MET Chi-restraints excluded: chain L9 residue 5 LYS Chi-restraints excluded: chain L9 residue 13 LYS Chi-restraints excluded: chain L9 residue 89 VAL Chi-restraints excluded: chain LA residue 14 SER Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LA residue 141 SER Chi-restraints excluded: chain LB residue 19 LYS Chi-restraints excluded: chain LB residue 42 THR Chi-restraints excluded: chain LB residue 108 ARG Chi-restraints excluded: chain LB residue 128 LEU Chi-restraints excluded: chain LD residue 68 LEU Chi-restraints excluded: chain LD residue 76 MET Chi-restraints excluded: chain LD residue 119 MET Chi-restraints excluded: chain LE residue 11 THR Chi-restraints excluded: chain LE residue 32 ARG Chi-restraints excluded: chain LE residue 68 THR Chi-restraints excluded: chain LE residue 81 LYS Chi-restraints excluded: chain LE residue 136 ARG Chi-restraints excluded: chain LF residue 41 GLN Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LG residue 69 LYS Chi-restraints excluded: chain LG residue 92 ASP Chi-restraints excluded: chain LG residue 111 GLU Chi-restraints excluded: chain LH residue 115 LYS Chi-restraints excluded: chain LH residue 147 LEU Chi-restraints excluded: chain LI residue 32 SER Chi-restraints excluded: chain LJ residue 100 VAL Chi-restraints excluded: chain LK residue 15 VAL Chi-restraints excluded: chain LK residue 16 SER Chi-restraints excluded: chain LK residue 134 GLU Chi-restraints excluded: chain LK residue 139 SER Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LL residue 81 THR Chi-restraints excluded: chain LL residue 85 ASN Chi-restraints excluded: chain LL residue 105 ASP Chi-restraints excluded: chain LL residue 111 ILE Chi-restraints excluded: chain LM residue 13 SER Chi-restraints excluded: chain LM residue 23 LYS Chi-restraints excluded: chain LM residue 31 SER Chi-restraints excluded: chain LM residue 51 LYS Chi-restraints excluded: chain LM residue 56 LYS Chi-restraints excluded: chain LM residue 114 LYS Chi-restraints excluded: chain LN residue 144 LYS Chi-restraints excluded: chain LN residue 145 GLN Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 293 ILE Chi-restraints excluded: chain LN residue 298 LEU Chi-restraints excluded: chain LN residue 337 VAL Chi-restraints excluded: chain LN residue 352 LEU Chi-restraints excluded: chain LO residue 20 LEU Chi-restraints excluded: chain LO residue 26 LYS Chi-restraints excluded: chain LO residue 35 LEU Chi-restraints excluded: chain LO residue 44 LYS Chi-restraints excluded: chain LP residue 46 LEU Chi-restraints excluded: chain LP residue 66 THR Chi-restraints excluded: chain LP residue 101 LYS Chi-restraints excluded: chain LQ residue 53 ILE Chi-restraints excluded: chain LQ residue 123 THR Chi-restraints excluded: chain LR residue 30 ILE Chi-restraints excluded: chain LR residue 82 MET Chi-restraints excluded: chain LR residue 105 LYS Chi-restraints excluded: chain LS residue 42 SER Chi-restraints excluded: chain LT residue 22 ARG Chi-restraints excluded: chain LT residue 90 SER Chi-restraints excluded: chain LU residue 27 SER Chi-restraints excluded: chain LU residue 60 LEU Chi-restraints excluded: chain LU residue 70 LEU Chi-restraints excluded: chain LV residue 23 VAL Chi-restraints excluded: chain LV residue 103 VAL Chi-restraints excluded: chain LX residue 24 LYS Chi-restraints excluded: chain LX residue 26 VAL Chi-restraints excluded: chain LX residue 45 THR Chi-restraints excluded: chain LX residue 72 ASN Chi-restraints excluded: chain LY residue 36 VAL Chi-restraints excluded: chain LY residue 56 LEU Chi-restraints excluded: chain NK residue 34 LYS Chi-restraints excluded: chain NL residue 427 SER Chi-restraints excluded: chain NL residue 452 GLU Chi-restraints excluded: chain NP residue 77 LYS Chi-restraints excluded: chain NP residue 82 SER Chi-restraints excluded: chain NR residue 49 ASN Chi-restraints excluded: chain NR residue 131 ILE Chi-restraints excluded: chain SA residue 14 LYS Chi-restraints excluded: chain SA residue 61 GLN Chi-restraints excluded: chain SA residue 152 LEU Chi-restraints excluded: chain SA residue 205 ARG Chi-restraints excluded: chain SA residue 273 LEU Chi-restraints excluded: chain SA residue 297 GLU Chi-restraints excluded: chain SB residue 36 LEU Chi-restraints excluded: chain SB residue 125 VAL Chi-restraints excluded: chain SB residue 163 LEU Chi-restraints excluded: chain SB residue 188 LYS Chi-restraints excluded: chain SB residue 217 ASP Chi-restraints excluded: chain SB residue 272 SER Chi-restraints excluded: chain SC residue 91 THR Chi-restraints excluded: chain SC residue 134 SER Chi-restraints excluded: chain SC residue 143 SER Chi-restraints excluded: chain SC residue 212 LEU Chi-restraints excluded: chain SD residue 171 ASP Chi-restraints excluded: chain SD residue 199 LYS Chi-restraints excluded: chain SD residue 220 MET Chi-restraints excluded: chain SF residue 160 SER Chi-restraints excluded: chain SF residue 169 VAL Chi-restraints excluded: chain SF residue 208 GLU Chi-restraints excluded: chain SG residue 1 MET Chi-restraints excluded: chain SG residue 21 LYS Chi-restraints excluded: chain SG residue 85 THR Chi-restraints excluded: chain SG residue 86 LEU Chi-restraints excluded: chain SG residue 94 SER Chi-restraints excluded: chain SG residue 95 VAL Chi-restraints excluded: chain SG residue 187 VAL Chi-restraints excluded: chain SH residue 50 ARG Chi-restraints excluded: chain SH residue 76 LEU Chi-restraints excluded: chain SI residue 83 VAL Chi-restraints excluded: chain SI residue 221 SER Chi-restraints excluded: chain SK residue 18 LYS Chi-restraints excluded: chain SK residue 75 ASN Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SK residue 237 ARG Chi-restraints excluded: chain SM residue 59 THR Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SM residue 135 ASP Chi-restraints excluded: chain SM residue 229 THR Chi-restraints excluded: chain SM residue 317 LEU Chi-restraints excluded: chain SM residue 360 LEU Chi-restraints excluded: chain SM residue 396 GLN Chi-restraints excluded: chain SM residue 406 LEU Chi-restraints excluded: chain SR residue 10 THR Chi-restraints excluded: chain SR residue 258 SER Chi-restraints excluded: chain SR residue 261 CYS Chi-restraints excluded: chain SR residue 301 GLU Chi-restraints excluded: chain SR residue 306 ILE Chi-restraints excluded: chain SR residue 313 GLU Chi-restraints excluded: chain SR residue 459 LEU Chi-restraints excluded: chain SR residue 478 LEU Chi-restraints excluded: chain SR residue 513 LYS Chi-restraints excluded: chain SR residue 535 ASP Chi-restraints excluded: chain SR residue 575 ARG Chi-restraints excluded: chain SR residue 576 ASP Chi-restraints excluded: chain SR residue 590 LYS Chi-restraints excluded: chain SR residue 616 MET Chi-restraints excluded: chain SV residue 1 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1211 random chunks: chunk 393 optimal weight: 3.9990 chunk 1054 optimal weight: 5.9990 chunk 231 optimal weight: 8.9990 chunk 687 optimal weight: 0.8980 chunk 288 optimal weight: 6.9990 chunk 1171 optimal weight: 8.9990 chunk 972 optimal weight: 3.9990 chunk 542 optimal weight: 2.9990 chunk 97 optimal weight: 20.0000 chunk 387 optimal weight: 4.9990 chunk 615 optimal weight: 0.8980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L6 67 HIS L7 96 GLN L8 70 GLN LA 118 GLN LG 27 ASN LI 86 GLN LM 19 ASN LO 40 GLN ** LQ 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LQ 81 ASN LR 3 GLN LU 92 ASN NP 18 GLN NR 42 ASN NR 60 ASN NR 122 GLN SB 275 GLN SC 256 GLN ** SD 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 43 GLN SE 64 GLN SF 97 ASN ** SF 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SK 225 ASN SM 102 ASN SM 253 GLN SM 384 GLN SR 100 ASN SR 482 GLN SV 24 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 159568 Z= 0.267 Angle : 0.707 19.669 233140 Z= 0.380 Chirality : 0.037 0.333 28508 Planarity : 0.007 0.135 15818 Dihedral : 23.017 179.736 68339 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.31 % Allowed : 14.00 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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: 1.13 (0.09), residues: 8512 helix: 1.92 (0.09), residues: 3387 sheet: 0.44 (0.15), residues: 1070 loop : -0.12 (0.09), residues: 4055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRPLN 196 HIS 0.007 0.001 HISLK 39 PHE 0.016 0.002 PHESB 160 TYR 0.023 0.002 TYRSB 119 ARG 0.008 0.000 ARGSR 276 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17024 Ramachandran restraints generated. 8512 Oldfield, 0 Emsley, 8512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17024 Ramachandran restraints generated. 8512 Oldfield, 0 Emsley, 8512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1252 residues out of total 7502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 1010 time to evaluate : 8.102 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: L6 119 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7185 (tm-30) REVERT: L6 121 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.7075 (mmm160) REVERT: L6 184 MET cc_start: 0.7853 (mtp) cc_final: 0.7578 (mtp) REVERT: L7 31 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7400 (ttt-90) REVERT: L8 121 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.6654 (mpt180) REVERT: L9 13 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.7886 (mmpt) REVERT: LB 108 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.6694 (ttm170) REVERT: LE 136 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7571 (mtp180) REVERT: LE 152 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7363 (mt-10) REVERT: LE 157 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.6311 (mp0) REVERT: LF 41 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7673 (tt0) REVERT: LJ 113 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7065 (tp30) REVERT: LK 134 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7322 (tt0) REVERT: LL 28 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7362 (pt0) REVERT: LL 108 MET cc_start: 0.8507 (mmm) cc_final: 0.8266 (mmm) REVERT: LM 51 LYS cc_start: 0.7570 (OUTLIER) cc_final: 0.7275 (pttm) REVERT: LN 139 ASP cc_start: 0.6405 (t0) cc_final: 0.6096 (t0) REVERT: LN 352 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7707 (mt) REVERT: LN 382 MET cc_start: 0.6787 (OUTLIER) cc_final: 0.6474 (mmt) REVERT: LO 44 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7136 (mmmm) REVERT: LS 82 ASP cc_start: 0.8396 (OUTLIER) cc_final: 0.8162 (p0) REVERT: LU 71 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7647 (mttt) REVERT: LV 92 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6585 (mm-30) REVERT: LY 29 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7645 (ttpp) REVERT: NK 28 ARG cc_start: 0.7695 (mtm110) cc_final: 0.7429 (mmp-170) REVERT: NK 34 LYS cc_start: 0.7450 (OUTLIER) cc_final: 0.7179 (ptpp) REVERT: NP 77 LYS cc_start: 0.8383 (mmmm) cc_final: 0.8167 (mttm) REVERT: NR 49 ASN cc_start: 0.7478 (OUTLIER) cc_final: 0.7252 (t0) REVERT: SA 143 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7251 (mmm160) REVERT: SA 205 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7330 (mmp80) REVERT: SA 325 MET cc_start: 0.8340 (tpp) cc_final: 0.8035 (tpt) REVERT: SB 36 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8028 (tt) REVERT: SB 163 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8114 (tp) REVERT: SC 220 LYS cc_start: 0.6994 (OUTLIER) cc_final: 0.6523 (pttm) REVERT: SD 220 MET cc_start: 0.7696 (OUTLIER) cc_final: 0.7351 (ttt) REVERT: SE 111 LYS cc_start: 0.7636 (ttmt) cc_final: 0.7404 (tttm) REVERT: SG 21 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.8052 (mttt) REVERT: SG 86 LEU cc_start: 0.7031 (OUTLIER) cc_final: 0.6327 (mt) REVERT: SK 8 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7310 (mt-10) REVERT: SK 18 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8178 (tptt) REVERT: SK 237 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.6099 (tmm-80) REVERT: SM 135 ASP cc_start: 0.7317 (OUTLIER) cc_final: 0.7113 (m-30) REVERT: SR 482 GLN cc_start: 0.6938 (OUTLIER) cc_final: 0.6729 (tm130) REVERT: SR 535 ASP cc_start: 0.5938 (OUTLIER) cc_final: 0.5622 (t70) REVERT: SR 575 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.6620 (ptp-170) REVERT: SR 616 MET cc_start: 0.6715 (OUTLIER) cc_final: 0.5561 (mpt) REVERT: SV 1 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.6984 (ptt) REVERT: SV 87 ASN cc_start: 0.7597 (m110) cc_final: 0.7154 (m-40) outliers start: 242 outliers final: 139 residues processed: 1152 average time/residue: 2.3922 time to fit residues: 3889.9950 Evaluate side-chains 1156 residues out of total 7502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 977 time to evaluate : 7.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L5 residue 39 VAL Chi-restraints excluded: chain L5 residue 49 VAL Chi-restraints excluded: chain L5 residue 102 THR Chi-restraints excluded: chain L5 residue 150 CYS Chi-restraints excluded: chain L6 residue 24 THR Chi-restraints excluded: chain L6 residue 52 SER Chi-restraints excluded: chain L6 residue 64 VAL Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 119 GLU Chi-restraints excluded: chain L6 residue 121 ARG Chi-restraints excluded: chain L6 residue 140 SER Chi-restraints excluded: chain L7 residue 31 ARG Chi-restraints excluded: chain L7 residue 177 LEU Chi-restraints excluded: chain L7 residue 189 ILE Chi-restraints excluded: chain L8 residue 38 VAL Chi-restraints excluded: chain L8 residue 113 MET Chi-restraints excluded: chain L8 residue 121 ARG Chi-restraints excluded: chain L9 residue 5 LYS Chi-restraints excluded: chain L9 residue 13 LYS Chi-restraints excluded: chain L9 residue 89 VAL Chi-restraints excluded: chain L9 residue 170 LYS Chi-restraints excluded: chain LA residue 14 SER Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LA residue 141 SER Chi-restraints excluded: chain LB residue 19 LYS Chi-restraints excluded: chain LB residue 42 THR Chi-restraints excluded: chain LB residue 108 ARG Chi-restraints excluded: chain LC residue 93 MET Chi-restraints excluded: chain LC residue 164 LYS Chi-restraints excluded: chain LD residue 13 SER Chi-restraints excluded: chain LD residue 68 LEU Chi-restraints excluded: chain LD residue 119 MET Chi-restraints excluded: chain LE residue 11 THR Chi-restraints excluded: chain LE residue 32 ARG Chi-restraints excluded: chain LE residue 68 THR Chi-restraints excluded: chain LE residue 76 VAL Chi-restraints excluded: chain LE residue 81 LYS Chi-restraints excluded: chain LE residue 136 ARG Chi-restraints excluded: chain LE residue 152 GLU Chi-restraints excluded: chain LE residue 157 GLU Chi-restraints excluded: chain LF residue 41 GLN Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LG residue 69 LYS Chi-restraints excluded: chain LG residue 92 ASP Chi-restraints excluded: chain LH residue 115 LYS Chi-restraints excluded: chain LH residue 145 ASP Chi-restraints excluded: chain LI residue 32 SER Chi-restraints excluded: chain LI residue 44 VAL Chi-restraints excluded: chain LI residue 128 VAL Chi-restraints excluded: chain LJ residue 99 ASP Chi-restraints excluded: chain LJ residue 113 GLU Chi-restraints excluded: chain LK residue 15 VAL Chi-restraints excluded: chain LK residue 16 SER Chi-restraints excluded: chain LK residue 83 SER Chi-restraints excluded: chain LK residue 134 GLU Chi-restraints excluded: chain LK residue 139 SER Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LL residue 81 THR Chi-restraints excluded: chain LL residue 105 ASP Chi-restraints excluded: chain LL residue 111 ILE Chi-restraints excluded: chain LM residue 13 SER Chi-restraints excluded: chain LM residue 23 LYS Chi-restraints excluded: chain LM residue 31 SER Chi-restraints excluded: chain LM residue 51 LYS Chi-restraints excluded: chain LM residue 56 LYS Chi-restraints excluded: chain LN residue 144 LYS Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 293 ILE Chi-restraints excluded: chain LN residue 298 LEU Chi-restraints excluded: chain LN residue 337 VAL Chi-restraints excluded: chain LN residue 352 LEU Chi-restraints excluded: chain LN residue 382 MET Chi-restraints excluded: chain LO residue 20 LEU Chi-restraints excluded: chain LO residue 26 LYS Chi-restraints excluded: chain LO residue 35 LEU Chi-restraints excluded: chain LO residue 44 LYS Chi-restraints excluded: chain LP residue 46 LEU Chi-restraints excluded: chain LP residue 66 THR Chi-restraints excluded: chain LP residue 101 LYS Chi-restraints excluded: chain LQ residue 53 ILE Chi-restraints excluded: chain LQ residue 123 THR Chi-restraints excluded: chain LR residue 30 ILE Chi-restraints excluded: chain LR residue 48 VAL Chi-restraints excluded: chain LR residue 82 MET Chi-restraints excluded: chain LR residue 105 LYS Chi-restraints excluded: chain LS residue 42 SER Chi-restraints excluded: chain LS residue 82 ASP Chi-restraints excluded: chain LS residue 116 LEU Chi-restraints excluded: chain LT residue 22 ARG Chi-restraints excluded: chain LT residue 90 SER Chi-restraints excluded: chain LU residue 27 SER Chi-restraints excluded: chain LU residue 58 MET Chi-restraints excluded: chain LU residue 70 LEU Chi-restraints excluded: chain LU residue 71 LYS Chi-restraints excluded: chain LV residue 23 VAL Chi-restraints excluded: chain LV residue 24 THR Chi-restraints excluded: chain LV residue 92 GLU Chi-restraints excluded: chain LV residue 103 VAL Chi-restraints excluded: chain LW residue 80 GLU Chi-restraints excluded: chain LX residue 24 LYS Chi-restraints excluded: chain LX residue 26 VAL Chi-restraints excluded: chain LX residue 45 THR Chi-restraints excluded: chain LX residue 72 ASN Chi-restraints excluded: chain LY residue 29 LYS Chi-restraints excluded: chain LY residue 36 VAL Chi-restraints excluded: chain LY residue 56 LEU Chi-restraints excluded: chain NK residue 34 LYS Chi-restraints excluded: chain NL residue 427 SER Chi-restraints excluded: chain NL residue 452 GLU Chi-restraints excluded: chain NP residue 71 ILE Chi-restraints excluded: chain NP residue 82 SER Chi-restraints excluded: chain NR residue 49 ASN Chi-restraints excluded: chain NR residue 131 ILE Chi-restraints excluded: chain SA residue 14 LYS Chi-restraints excluded: chain SA residue 61 GLN Chi-restraints excluded: chain SA residue 143 ARG Chi-restraints excluded: chain SA residue 152 LEU Chi-restraints excluded: chain SA residue 205 ARG Chi-restraints excluded: chain SA residue 273 LEU Chi-restraints excluded: chain SA residue 297 GLU Chi-restraints excluded: chain SA residue 298 ILE Chi-restraints excluded: chain SB residue 36 LEU Chi-restraints excluded: chain SB residue 125 VAL Chi-restraints excluded: chain SB residue 163 LEU Chi-restraints excluded: chain SB residue 188 LYS Chi-restraints excluded: chain SB residue 217 ASP Chi-restraints excluded: chain SB residue 272 SER Chi-restraints excluded: chain SC residue 91 THR Chi-restraints excluded: chain SC residue 107 VAL Chi-restraints excluded: chain SC residue 134 SER Chi-restraints excluded: chain SC residue 143 SER Chi-restraints excluded: chain SC residue 212 LEU Chi-restraints excluded: chain SC residue 220 LYS Chi-restraints excluded: chain SC residue 255 SER Chi-restraints excluded: chain SD residue 199 LYS Chi-restraints excluded: chain SD residue 220 MET Chi-restraints excluded: chain SF residue 160 SER Chi-restraints excluded: chain SF residue 169 VAL Chi-restraints excluded: chain SF residue 208 GLU Chi-restraints excluded: chain SG residue 1 MET Chi-restraints excluded: chain SG residue 21 LYS Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SG residue 85 THR Chi-restraints excluded: chain SG residue 86 LEU Chi-restraints excluded: chain SG residue 94 SER Chi-restraints excluded: chain SG residue 95 VAL Chi-restraints excluded: chain SG residue 187 VAL Chi-restraints excluded: chain SH residue 50 ARG Chi-restraints excluded: chain SH residue 76 LEU Chi-restraints excluded: chain SI residue 83 VAL Chi-restraints excluded: chain SK residue 8 GLU Chi-restraints excluded: chain SK residue 18 LYS Chi-restraints excluded: chain SK residue 75 ASN Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SK residue 237 ARG Chi-restraints excluded: chain SM residue 59 THR Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SM residue 135 ASP Chi-restraints excluded: chain SM residue 229 THR Chi-restraints excluded: chain SM residue 317 LEU Chi-restraints excluded: chain SM residue 360 LEU Chi-restraints excluded: chain SM residue 406 LEU Chi-restraints excluded: chain SR residue 10 THR Chi-restraints excluded: chain SR residue 174 CYS Chi-restraints excluded: chain SR residue 258 SER Chi-restraints excluded: chain SR residue 261 CYS Chi-restraints excluded: chain SR residue 306 ILE Chi-restraints excluded: chain SR residue 313 GLU Chi-restraints excluded: chain SR residue 459 LEU Chi-restraints excluded: chain SR residue 478 LEU Chi-restraints excluded: chain SR residue 482 GLN Chi-restraints excluded: chain SR residue 513 LYS Chi-restraints excluded: chain SR residue 515 VAL Chi-restraints excluded: chain SR residue 535 ASP Chi-restraints excluded: chain SR residue 575 ARG Chi-restraints excluded: chain SR residue 576 ASP Chi-restraints excluded: chain SR residue 590 LYS Chi-restraints excluded: chain SR residue 616 MET Chi-restraints excluded: chain SV residue 1 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1211 random chunks: chunk 1129 optimal weight: 50.0000 chunk 132 optimal weight: 8.9990 chunk 667 optimal weight: 7.9990 chunk 855 optimal weight: 4.9990 chunk 662 optimal weight: 0.7980 chunk 986 optimal weight: 6.9990 chunk 654 optimal weight: 5.9990 chunk 1167 optimal weight: 10.0000 chunk 730 optimal weight: 0.9990 chunk 711 optimal weight: 3.9990 chunk 538 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L6 67 HIS L8 70 GLN LA 118 GLN LG 27 ASN LI 56 GLN LI 86 GLN LI 127 GLN LM 11 ASN LM 19 ASN LO 40 GLN ** LQ 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LQ 81 ASN LR 3 GLN LU 92 ASN NK 92 GLN ** NL 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NP 18 GLN NR 42 ASN NR 60 ASN NR 122 GLN SB 275 GLN ** SD 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 43 GLN ** SF 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 8 GLN SK 225 ASN SM 102 ASN SM 396 GLN SR 100 ASN SR 482 GLN SV 24 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 159568 Z= 0.266 Angle : 0.706 19.673 233140 Z= 0.380 Chirality : 0.037 0.334 28508 Planarity : 0.007 0.135 15818 Dihedral : 23.002 179.767 68339 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.22 % Allowed : 14.38 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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: 1.11 (0.09), residues: 8512 helix: 1.92 (0.09), residues: 3388 sheet: 0.44 (0.16), residues: 1069 loop : -0.15 (0.09), residues: 4055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRPNR 146 HIS 0.007 0.001 HISLK 39 PHE 0.016 0.002 PHESB 160 TYR 0.021 0.002 TYRSB 119 ARG 0.009 0.000 ARGSR 266 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17024 Ramachandran restraints generated. 8512 Oldfield, 0 Emsley, 8512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17024 Ramachandran restraints generated. 8512 Oldfield, 0 Emsley, 8512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1235 residues out of total 7502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 999 time to evaluate : 8.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L6 119 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7176 (tm-30) REVERT: L6 121 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7013 (mmm160) REVERT: L6 184 MET cc_start: 0.7867 (mtp) cc_final: 0.7597 (mtp) REVERT: L7 31 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7390 (ttt-90) REVERT: L8 121 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.6788 (mpt180) REVERT: L9 13 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.7883 (mmpt) REVERT: LB 108 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.6693 (ttm170) REVERT: LD 76 MET cc_start: 0.7531 (OUTLIER) cc_final: 0.6914 (mmt) REVERT: LE 136 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7565 (mtp180) REVERT: LE 157 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.6248 (mp0) REVERT: LF 41 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7677 (tt0) REVERT: LK 134 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7318 (tt0) REVERT: LL 28 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7361 (pt0) REVERT: LL 108 MET cc_start: 0.8475 (mmm) cc_final: 0.8229 (mmm) REVERT: LM 51 LYS cc_start: 0.7585 (OUTLIER) cc_final: 0.7303 (pttm) REVERT: LN 139 ASP cc_start: 0.6412 (t0) cc_final: 0.6101 (t0) REVERT: LN 382 MET cc_start: 0.6792 (OUTLIER) cc_final: 0.6447 (mmt) REVERT: LO 44 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7126 (mmmm) REVERT: LS 82 ASP cc_start: 0.8406 (OUTLIER) cc_final: 0.8161 (p0) REVERT: LU 71 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7643 (mttt) REVERT: LV 92 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.6601 (mm-30) REVERT: LY 29 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7622 (ttpp) REVERT: NK 28 ARG cc_start: 0.7695 (mtm110) cc_final: 0.7422 (mmp-170) REVERT: NK 34 LYS cc_start: 0.7396 (OUTLIER) cc_final: 0.7118 (ptpp) REVERT: NP 77 LYS cc_start: 0.8389 (mmmm) cc_final: 0.8169 (mttm) REVERT: NR 49 ASN cc_start: 0.7491 (OUTLIER) cc_final: 0.7271 (t0) REVERT: SA 143 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7281 (mmm160) REVERT: SA 205 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7334 (mmp80) REVERT: SA 325 MET cc_start: 0.8349 (tpp) cc_final: 0.8045 (tpt) REVERT: SB 36 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8032 (tt) REVERT: SB 163 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8122 (tp) REVERT: SC 220 LYS cc_start: 0.6930 (OUTLIER) cc_final: 0.6520 (pttm) REVERT: SD 220 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.7365 (ttt) REVERT: SG 21 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.8070 (mttt) REVERT: SG 86 LEU cc_start: 0.7016 (OUTLIER) cc_final: 0.6339 (mt) REVERT: SK 8 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7319 (mt-10) REVERT: SK 18 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8179 (tptt) REVERT: SK 237 ARG cc_start: 0.7165 (OUTLIER) cc_final: 0.6116 (tmm-80) REVERT: SM 135 ASP cc_start: 0.7313 (OUTLIER) cc_final: 0.7109 (m-30) REVERT: SR 535 ASP cc_start: 0.5946 (OUTLIER) cc_final: 0.5638 (t70) REVERT: SR 575 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.6606 (ptp-170) REVERT: SR 616 MET cc_start: 0.6712 (OUTLIER) cc_final: 0.5552 (mpt) REVERT: SV 1 MET cc_start: 0.7898 (OUTLIER) cc_final: 0.6995 (ptt) REVERT: SV 87 ASN cc_start: 0.7599 (m110) cc_final: 0.7147 (m-40) outliers start: 236 outliers final: 141 residues processed: 1137 average time/residue: 2.3979 time to fit residues: 3835.7355 Evaluate side-chains 1154 residues out of total 7502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 976 time to evaluate : 7.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L5 residue 39 VAL Chi-restraints excluded: chain L5 residue 49 VAL Chi-restraints excluded: chain L5 residue 102 THR Chi-restraints excluded: chain L5 residue 150 CYS Chi-restraints excluded: chain L6 residue 24 THR Chi-restraints excluded: chain L6 residue 52 SER Chi-restraints excluded: chain L6 residue 64 VAL Chi-restraints excluded: chain L6 residue 69 LYS Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 119 GLU Chi-restraints excluded: chain L6 residue 121 ARG Chi-restraints excluded: chain L7 residue 31 ARG Chi-restraints excluded: chain L7 residue 93 LYS Chi-restraints excluded: chain L7 residue 177 LEU Chi-restraints excluded: chain L7 residue 189 ILE Chi-restraints excluded: chain L8 residue 38 VAL Chi-restraints excluded: chain L8 residue 70 GLN Chi-restraints excluded: chain L8 residue 113 MET Chi-restraints excluded: chain L8 residue 121 ARG Chi-restraints excluded: chain L9 residue 5 LYS Chi-restraints excluded: chain L9 residue 13 LYS Chi-restraints excluded: chain L9 residue 89 VAL Chi-restraints excluded: chain L9 residue 170 LYS Chi-restraints excluded: chain LA residue 14 SER Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LA residue 141 SER Chi-restraints excluded: chain LB residue 19 LYS Chi-restraints excluded: chain LB residue 42 THR Chi-restraints excluded: chain LB residue 108 ARG Chi-restraints excluded: chain LD residue 13 SER Chi-restraints excluded: chain LD residue 68 LEU Chi-restraints excluded: chain LD residue 76 MET Chi-restraints excluded: chain LD residue 119 MET Chi-restraints excluded: chain LD residue 142 ILE Chi-restraints excluded: chain LE residue 11 THR Chi-restraints excluded: chain LE residue 32 ARG Chi-restraints excluded: chain LE residue 68 THR Chi-restraints excluded: chain LE residue 76 VAL Chi-restraints excluded: chain LE residue 81 LYS Chi-restraints excluded: chain LE residue 136 ARG Chi-restraints excluded: chain LE residue 157 GLU Chi-restraints excluded: chain LF residue 41 GLN Chi-restraints excluded: chain LF residue 52 LYS Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LG residue 92 ASP Chi-restraints excluded: chain LH residue 115 LYS Chi-restraints excluded: chain LI residue 32 SER Chi-restraints excluded: chain LI residue 44 VAL Chi-restraints excluded: chain LI residue 63 LYS Chi-restraints excluded: chain LI residue 128 VAL Chi-restraints excluded: chain LJ residue 99 ASP Chi-restraints excluded: chain LK residue 15 VAL Chi-restraints excluded: chain LK residue 16 SER Chi-restraints excluded: chain LK residue 83 SER Chi-restraints excluded: chain LK residue 134 GLU Chi-restraints excluded: chain LK residue 139 SER Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LL residue 81 THR Chi-restraints excluded: chain LL residue 85 ASN Chi-restraints excluded: chain LL residue 105 ASP Chi-restraints excluded: chain LL residue 111 ILE Chi-restraints excluded: chain LM residue 13 SER Chi-restraints excluded: chain LM residue 23 LYS Chi-restraints excluded: chain LM residue 31 SER Chi-restraints excluded: chain LM residue 51 LYS Chi-restraints excluded: chain LM residue 56 LYS Chi-restraints excluded: chain LN residue 144 LYS Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 293 ILE Chi-restraints excluded: chain LN residue 298 LEU Chi-restraints excluded: chain LN residue 308 ASP Chi-restraints excluded: chain LN residue 337 VAL Chi-restraints excluded: chain LN residue 352 LEU Chi-restraints excluded: chain LN residue 382 MET Chi-restraints excluded: chain LO residue 20 LEU Chi-restraints excluded: chain LO residue 26 LYS Chi-restraints excluded: chain LO residue 35 LEU Chi-restraints excluded: chain LO residue 44 LYS Chi-restraints excluded: chain LP residue 46 LEU Chi-restraints excluded: chain LP residue 66 THR Chi-restraints excluded: chain LP residue 101 LYS Chi-restraints excluded: chain LQ residue 53 ILE Chi-restraints excluded: chain LQ residue 123 THR Chi-restraints excluded: chain LR residue 30 ILE Chi-restraints excluded: chain LR residue 48 VAL Chi-restraints excluded: chain LR residue 82 MET Chi-restraints excluded: chain LS residue 42 SER Chi-restraints excluded: chain LS residue 82 ASP Chi-restraints excluded: chain LT residue 22 ARG Chi-restraints excluded: chain LT residue 90 SER Chi-restraints excluded: chain LU residue 27 SER Chi-restraints excluded: chain LU residue 58 MET Chi-restraints excluded: chain LU residue 70 LEU Chi-restraints excluded: chain LU residue 71 LYS Chi-restraints excluded: chain LV residue 23 VAL Chi-restraints excluded: chain LV residue 24 THR Chi-restraints excluded: chain LV residue 92 GLU Chi-restraints excluded: chain LV residue 103 VAL Chi-restraints excluded: chain LW residue 80 GLU Chi-restraints excluded: chain LX residue 24 LYS Chi-restraints excluded: chain LX residue 26 VAL Chi-restraints excluded: chain LX residue 45 THR Chi-restraints excluded: chain LX residue 72 ASN Chi-restraints excluded: chain LY residue 29 LYS Chi-restraints excluded: chain LY residue 36 VAL Chi-restraints excluded: chain NK residue 34 LYS Chi-restraints excluded: chain NL residue 211 GLU Chi-restraints excluded: chain NL residue 427 SER Chi-restraints excluded: chain NL residue 452 GLU Chi-restraints excluded: chain NP residue 71 ILE Chi-restraints excluded: chain NP residue 82 SER Chi-restraints excluded: chain NR residue 49 ASN Chi-restraints excluded: chain NR residue 131 ILE Chi-restraints excluded: chain SA residue 14 LYS Chi-restraints excluded: chain SA residue 61 GLN Chi-restraints excluded: chain SA residue 143 ARG Chi-restraints excluded: chain SA residue 152 LEU Chi-restraints excluded: chain SA residue 205 ARG Chi-restraints excluded: chain SA residue 273 LEU Chi-restraints excluded: chain SA residue 351 VAL Chi-restraints excluded: chain SB residue 36 LEU Chi-restraints excluded: chain SB residue 125 VAL Chi-restraints excluded: chain SB residue 163 LEU Chi-restraints excluded: chain SB residue 188 LYS Chi-restraints excluded: chain SB residue 217 ASP Chi-restraints excluded: chain SB residue 272 SER Chi-restraints excluded: chain SC residue 107 VAL Chi-restraints excluded: chain SC residue 134 SER Chi-restraints excluded: chain SC residue 143 SER Chi-restraints excluded: chain SC residue 212 LEU Chi-restraints excluded: chain SC residue 220 LYS Chi-restraints excluded: chain SC residue 255 SER Chi-restraints excluded: chain SD residue 171 ASP Chi-restraints excluded: chain SD residue 199 LYS Chi-restraints excluded: chain SD residue 220 MET Chi-restraints excluded: chain SF residue 160 SER Chi-restraints excluded: chain SF residue 169 VAL Chi-restraints excluded: chain SF residue 208 GLU Chi-restraints excluded: chain SG residue 1 MET Chi-restraints excluded: chain SG residue 21 LYS Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SG residue 85 THR Chi-restraints excluded: chain SG residue 86 LEU Chi-restraints excluded: chain SG residue 94 SER Chi-restraints excluded: chain SG residue 95 VAL Chi-restraints excluded: chain SG residue 187 VAL Chi-restraints excluded: chain SH residue 50 ARG Chi-restraints excluded: chain SH residue 76 LEU Chi-restraints excluded: chain SI residue 83 VAL Chi-restraints excluded: chain SI residue 221 SER Chi-restraints excluded: chain SK residue 8 GLU Chi-restraints excluded: chain SK residue 18 LYS Chi-restraints excluded: chain SK residue 75 ASN Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SK residue 237 ARG Chi-restraints excluded: chain SM residue 59 THR Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SM residue 135 ASP Chi-restraints excluded: chain SM residue 229 THR Chi-restraints excluded: chain SM residue 317 LEU Chi-restraints excluded: chain SM residue 360 LEU Chi-restraints excluded: chain SM residue 406 LEU Chi-restraints excluded: chain SR residue 10 THR Chi-restraints excluded: chain SR residue 174 CYS Chi-restraints excluded: chain SR residue 258 SER Chi-restraints excluded: chain SR residue 261 CYS Chi-restraints excluded: chain SR residue 306 ILE Chi-restraints excluded: chain SR residue 313 GLU Chi-restraints excluded: chain SR residue 459 LEU Chi-restraints excluded: chain SR residue 478 LEU Chi-restraints excluded: chain SR residue 513 LYS Chi-restraints excluded: chain SR residue 515 VAL Chi-restraints excluded: chain SR residue 535 ASP Chi-restraints excluded: chain SR residue 575 ARG Chi-restraints excluded: chain SR residue 576 ASP Chi-restraints excluded: chain SR residue 590 LYS Chi-restraints excluded: chain SR residue 616 MET Chi-restraints excluded: chain SV residue 1 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1211 random chunks: chunk 722 optimal weight: 7.9990 chunk 466 optimal weight: 0.9980 chunk 697 optimal weight: 0.9990 chunk 351 optimal weight: 20.0000 chunk 229 optimal weight: 6.9990 chunk 226 optimal weight: 10.0000 chunk 742 optimal weight: 2.9990 chunk 795 optimal weight: 3.9990 chunk 577 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 917 optimal weight: 7.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L6 67 HIS L8 70 GLN LA 97 ASN LA 101 ASN LA 118 GLN LG 27 ASN LI 86 GLN LM 19 ASN LN 213 GLN LO 40 GLN ** LQ 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LQ 81 ASN LR 3 GLN LU 92 ASN NR 42 ASN NR 60 ASN NR 122 GLN SB 275 GLN SC 256 GLN ** SD 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 43 GLN SE 64 GLN ** SF 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 8 GLN SG 162 GLN SI 207 HIS SK 178 GLN SK 225 ASN SM 102 ASN SM 384 GLN SM 396 GLN SR 100 ASN SV 24 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 159568 Z= 0.253 Angle : 0.702 19.680 233140 Z= 0.378 Chirality : 0.037 0.334 28508 Planarity : 0.007 0.134 15818 Dihedral : 22.988 179.678 68339 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.96 % Allowed : 15.04 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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: 1.12 (0.09), residues: 8512 helix: 1.93 (0.09), residues: 3389 sheet: 0.44 (0.16), residues: 1069 loop : -0.14 (0.09), residues: 4054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRPNR 146 HIS 0.006 0.001 HISLV 21 PHE 0.016 0.002 PHESB 160 TYR 0.021 0.002 TYRSB 119 ARG 0.010 0.000 ARGSR 266 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17024 Ramachandran restraints generated. 8512 Oldfield, 0 Emsley, 8512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17024 Ramachandran restraints generated. 8512 Oldfield, 0 Emsley, 8512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1217 residues out of total 7502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 1000 time to evaluate : 7.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L6 119 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7132 (tm-30) REVERT: L6 121 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.7013 (mmm160) REVERT: L6 184 MET cc_start: 0.7862 (mtp) cc_final: 0.7589 (mtp) REVERT: L7 31 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7386 (ttt-90) REVERT: L7 174 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7853 (tt) REVERT: L8 121 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.6740 (mpt180) REVERT: L9 13 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.7877 (mmpt) REVERT: LB 108 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.6692 (ttm170) REVERT: LD 76 MET cc_start: 0.7523 (OUTLIER) cc_final: 0.6815 (mmt) REVERT: LE 136 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7562 (mtp180) REVERT: LE 152 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7352 (mt-10) REVERT: LE 157 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.6181 (mp0) REVERT: LF 41 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7686 (tt0) REVERT: LJ 99 ASP cc_start: 0.7127 (OUTLIER) cc_final: 0.6897 (m-30) REVERT: LJ 113 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7051 (tp30) REVERT: LK 134 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7271 (tt0) REVERT: LL 28 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7357 (pt0) REVERT: LL 108 MET cc_start: 0.8477 (mmm) cc_final: 0.8230 (mmm) REVERT: LM 51 LYS cc_start: 0.7579 (OUTLIER) cc_final: 0.7299 (pttm) REVERT: LN 139 ASP cc_start: 0.6634 (t0) cc_final: 0.6290 (t0) REVERT: LN 382 MET cc_start: 0.6793 (OUTLIER) cc_final: 0.6452 (mmt) REVERT: LO 44 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7121 (mmmm) REVERT: LU 71 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7641 (mttt) REVERT: LV 92 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.6601 (mm-30) REVERT: LY 19 ASP cc_start: 0.7904 (p0) cc_final: 0.7667 (p0) REVERT: LY 29 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7620 (ttpp) REVERT: NK 28 ARG cc_start: 0.7690 (mtm110) cc_final: 0.7419 (mmp-170) REVERT: NK 34 LYS cc_start: 0.7411 (OUTLIER) cc_final: 0.7132 (ptpp) REVERT: NP 77 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.8167 (mttm) REVERT: NR 49 ASN cc_start: 0.7494 (OUTLIER) cc_final: 0.7260 (t0) REVERT: SA 143 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7287 (mmm160) REVERT: SA 205 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7295 (mmp80) REVERT: SA 308 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8012 (ttmm) REVERT: SA 325 MET cc_start: 0.8354 (tpp) cc_final: 0.8046 (tpt) REVERT: SB 36 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8027 (tt) REVERT: SB 163 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8125 (tp) REVERT: SC 41 LYS cc_start: 0.7144 (OUTLIER) cc_final: 0.6143 (mmtm) REVERT: SC 220 LYS cc_start: 0.6935 (OUTLIER) cc_final: 0.6518 (pttm) REVERT: SD 220 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.7339 (ttt) REVERT: SG 21 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8065 (mttt) REVERT: SG 86 LEU cc_start: 0.7024 (OUTLIER) cc_final: 0.6354 (mt) REVERT: SK 8 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7300 (mt-10) REVERT: SK 18 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8180 (tptt) REVERT: SK 90 ASP cc_start: 0.6630 (OUTLIER) cc_final: 0.6302 (m-30) REVERT: SK 237 ARG cc_start: 0.7173 (OUTLIER) cc_final: 0.6108 (tmm-80) REVERT: SM 135 ASP cc_start: 0.7309 (OUTLIER) cc_final: 0.7108 (m-30) REVERT: SR 478 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6507 (tp) REVERT: SR 535 ASP cc_start: 0.5951 (OUTLIER) cc_final: 0.5650 (t70) REVERT: SR 575 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.6611 (ptp-170) REVERT: SR 616 MET cc_start: 0.6704 (OUTLIER) cc_final: 0.5542 (mpt) REVERT: SV 1 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.6976 (ptt) REVERT: SV 87 ASN cc_start: 0.7597 (m110) cc_final: 0.7167 (m-40) outliers start: 217 outliers final: 135 residues processed: 1127 average time/residue: 2.3769 time to fit residues: 3785.0219 Evaluate side-chains 1171 residues out of total 7502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 991 time to evaluate : 7.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L5 residue 39 VAL Chi-restraints excluded: chain L5 residue 49 VAL Chi-restraints excluded: chain L5 residue 102 THR Chi-restraints excluded: chain L5 residue 125 ILE Chi-restraints excluded: chain L5 residue 150 CYS Chi-restraints excluded: chain L6 residue 24 THR Chi-restraints excluded: chain L6 residue 52 SER Chi-restraints excluded: chain L6 residue 64 VAL Chi-restraints excluded: chain L6 residue 69 LYS Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 119 GLU Chi-restraints excluded: chain L6 residue 121 ARG Chi-restraints excluded: chain L7 residue 31 ARG Chi-restraints excluded: chain L7 residue 93 LYS Chi-restraints excluded: chain L7 residue 174 LEU Chi-restraints excluded: chain L7 residue 189 ILE Chi-restraints excluded: chain L8 residue 38 VAL Chi-restraints excluded: chain L8 residue 113 MET Chi-restraints excluded: chain L8 residue 121 ARG Chi-restraints excluded: chain L9 residue 5 LYS Chi-restraints excluded: chain L9 residue 13 LYS Chi-restraints excluded: chain L9 residue 89 VAL Chi-restraints excluded: chain L9 residue 170 LYS Chi-restraints excluded: chain LA residue 14 SER Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LA residue 141 SER Chi-restraints excluded: chain LB residue 19 LYS Chi-restraints excluded: chain LB residue 42 THR Chi-restraints excluded: chain LB residue 108 ARG Chi-restraints excluded: chain LD residue 13 SER Chi-restraints excluded: chain LD residue 68 LEU Chi-restraints excluded: chain LD residue 76 MET Chi-restraints excluded: chain LD residue 119 MET Chi-restraints excluded: chain LE residue 11 THR Chi-restraints excluded: chain LE residue 32 ARG Chi-restraints excluded: chain LE residue 68 THR Chi-restraints excluded: chain LE residue 76 VAL Chi-restraints excluded: chain LE residue 81 LYS Chi-restraints excluded: chain LE residue 136 ARG Chi-restraints excluded: chain LE residue 152 GLU Chi-restraints excluded: chain LE residue 157 GLU Chi-restraints excluded: chain LF residue 41 GLN Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LG residue 92 ASP Chi-restraints excluded: chain LH residue 115 LYS Chi-restraints excluded: chain LH residue 147 LEU Chi-restraints excluded: chain LI residue 32 SER Chi-restraints excluded: chain LI residue 44 VAL Chi-restraints excluded: chain LI residue 63 LYS Chi-restraints excluded: chain LI residue 128 VAL Chi-restraints excluded: chain LJ residue 99 ASP Chi-restraints excluded: chain LJ residue 113 GLU Chi-restraints excluded: chain LK residue 15 VAL Chi-restraints excluded: chain LK residue 16 SER Chi-restraints excluded: chain LK residue 83 SER Chi-restraints excluded: chain LK residue 134 GLU Chi-restraints excluded: chain LK residue 139 SER Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LL residue 81 THR Chi-restraints excluded: chain LL residue 85 ASN Chi-restraints excluded: chain LL residue 105 ASP Chi-restraints excluded: chain LL residue 111 ILE Chi-restraints excluded: chain LM residue 13 SER Chi-restraints excluded: chain LM residue 23 LYS Chi-restraints excluded: chain LM residue 31 SER Chi-restraints excluded: chain LM residue 51 LYS Chi-restraints excluded: chain LM residue 56 LYS Chi-restraints excluded: chain LN residue 144 LYS Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 337 VAL Chi-restraints excluded: chain LN residue 338 VAL Chi-restraints excluded: chain LN residue 352 LEU Chi-restraints excluded: chain LN residue 382 MET Chi-restraints excluded: chain LO residue 20 LEU Chi-restraints excluded: chain LO residue 26 LYS Chi-restraints excluded: chain LO residue 35 LEU Chi-restraints excluded: chain LO residue 44 LYS Chi-restraints excluded: chain LP residue 46 LEU Chi-restraints excluded: chain LP residue 66 THR Chi-restraints excluded: chain LP residue 101 LYS Chi-restraints excluded: chain LQ residue 53 ILE Chi-restraints excluded: chain LQ residue 123 THR Chi-restraints excluded: chain LR residue 30 ILE Chi-restraints excluded: chain LR residue 48 VAL Chi-restraints excluded: chain LR residue 65 MET Chi-restraints excluded: chain LR residue 82 MET Chi-restraints excluded: chain LR residue 105 LYS Chi-restraints excluded: chain LS residue 42 SER Chi-restraints excluded: chain LT residue 22 ARG Chi-restraints excluded: chain LT residue 90 SER Chi-restraints excluded: chain LU residue 27 SER Chi-restraints excluded: chain LU residue 58 MET Chi-restraints excluded: chain LU residue 70 LEU Chi-restraints excluded: chain LU residue 71 LYS Chi-restraints excluded: chain LV residue 23 VAL Chi-restraints excluded: chain LV residue 24 THR Chi-restraints excluded: chain LV residue 92 GLU Chi-restraints excluded: chain LV residue 103 VAL Chi-restraints excluded: chain LW residue 80 GLU Chi-restraints excluded: chain LX residue 24 LYS Chi-restraints excluded: chain LX residue 26 VAL Chi-restraints excluded: chain LX residue 45 THR Chi-restraints excluded: chain LX residue 72 ASN Chi-restraints excluded: chain LY residue 29 LYS Chi-restraints excluded: chain LY residue 36 VAL Chi-restraints excluded: chain LY residue 56 LEU Chi-restraints excluded: chain NK residue 34 LYS Chi-restraints excluded: chain NL residue 211 GLU Chi-restraints excluded: chain NL residue 427 SER Chi-restraints excluded: chain NL residue 452 GLU Chi-restraints excluded: chain NP residue 71 ILE Chi-restraints excluded: chain NP residue 77 LYS Chi-restraints excluded: chain NP residue 82 SER Chi-restraints excluded: chain NR residue 49 ASN Chi-restraints excluded: chain NR residue 131 ILE Chi-restraints excluded: chain SA residue 14 LYS Chi-restraints excluded: chain SA residue 61 GLN Chi-restraints excluded: chain SA residue 143 ARG Chi-restraints excluded: chain SA residue 152 LEU Chi-restraints excluded: chain SA residue 205 ARG Chi-restraints excluded: chain SA residue 273 LEU Chi-restraints excluded: chain SA residue 297 GLU Chi-restraints excluded: chain SA residue 308 LYS Chi-restraints excluded: chain SB residue 36 LEU Chi-restraints excluded: chain SB residue 125 VAL Chi-restraints excluded: chain SB residue 163 LEU Chi-restraints excluded: chain SB residue 188 LYS Chi-restraints excluded: chain SB residue 217 ASP Chi-restraints excluded: chain SB residue 272 SER Chi-restraints excluded: chain SC residue 41 LYS Chi-restraints excluded: chain SC residue 134 SER Chi-restraints excluded: chain SC residue 143 SER Chi-restraints excluded: chain SC residue 212 LEU Chi-restraints excluded: chain SC residue 220 LYS Chi-restraints excluded: chain SC residue 255 SER Chi-restraints excluded: chain SD residue 199 LYS Chi-restraints excluded: chain SD residue 220 MET Chi-restraints excluded: chain SF residue 160 SER Chi-restraints excluded: chain SF residue 169 VAL Chi-restraints excluded: chain SF residue 208 GLU Chi-restraints excluded: chain SG residue 1 MET Chi-restraints excluded: chain SG residue 21 LYS Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SG residue 85 THR Chi-restraints excluded: chain SG residue 86 LEU Chi-restraints excluded: chain SG residue 94 SER Chi-restraints excluded: chain SG residue 95 VAL Chi-restraints excluded: chain SG residue 187 VAL Chi-restraints excluded: chain SH residue 50 ARG Chi-restraints excluded: chain SH residue 76 LEU Chi-restraints excluded: chain SI residue 83 VAL Chi-restraints excluded: chain SI residue 221 SER Chi-restraints excluded: chain SK residue 8 GLU Chi-restraints excluded: chain SK residue 18 LYS Chi-restraints excluded: chain SK residue 75 ASN Chi-restraints excluded: chain SK residue 90 ASP Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SK residue 237 ARG Chi-restraints excluded: chain SM residue 59 THR Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SM residue 135 ASP Chi-restraints excluded: chain SM residue 229 THR Chi-restraints excluded: chain SM residue 317 LEU Chi-restraints excluded: chain SM residue 360 LEU Chi-restraints excluded: chain SM residue 406 LEU Chi-restraints excluded: chain SR residue 10 THR Chi-restraints excluded: chain SR residue 174 CYS Chi-restraints excluded: chain SR residue 258 SER Chi-restraints excluded: chain SR residue 261 CYS Chi-restraints excluded: chain SR residue 306 ILE Chi-restraints excluded: chain SR residue 313 GLU Chi-restraints excluded: chain SR residue 459 LEU Chi-restraints excluded: chain SR residue 478 LEU Chi-restraints excluded: chain SR residue 513 LYS Chi-restraints excluded: chain SR residue 535 ASP Chi-restraints excluded: chain SR residue 575 ARG Chi-restraints excluded: chain SR residue 576 ASP Chi-restraints excluded: chain SR residue 590 LYS Chi-restraints excluded: chain SR residue 616 MET Chi-restraints excluded: chain SV residue 1 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1211 random chunks: chunk 1061 optimal weight: 6.9990 chunk 1118 optimal weight: 0.6980 chunk 1020 optimal weight: 1.9990 chunk 1087 optimal weight: 0.8980 chunk 1117 optimal weight: 2.9990 chunk 654 optimal weight: 5.9990 chunk 473 optimal weight: 6.9990 chunk 854 optimal weight: 7.9990 chunk 333 optimal weight: 6.9990 chunk 982 optimal weight: 8.9990 chunk 1028 optimal weight: 4.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L6 67 HIS LA 118 GLN LG 27 ASN LI 86 GLN LI 127 GLN ** LK 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LM 11 ASN LM 19 ASN ** LN 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LO 40 GLN ** LQ 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LQ 81 ASN LR 3 GLN LU 92 ASN ** NL 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NR 42 ASN NR 56 GLN NR 60 ASN NR 122 GLN SB 275 GLN SC 256 GLN ** SD 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 43 GLN SE 64 GLN ** SF 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 162 GLN SI 42 GLN SI 94 HIS SI 207 HIS SK 178 GLN SK 225 ASN SM 102 ASN SM 396 GLN SR 100 ASN SV 24 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 159568 Z= 0.246 Angle : 0.698 19.663 233140 Z= 0.377 Chirality : 0.036 0.338 28508 Planarity : 0.007 0.134 15818 Dihedral : 22.972 179.646 68339 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.91 % Allowed : 15.35 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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: 1.13 (0.09), residues: 8512 helix: 1.94 (0.09), residues: 3390 sheet: 0.45 (0.16), residues: 1067 loop : -0.15 (0.09), residues: 4055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRPNR 146 HIS 0.006 0.001 HISLV 21 PHE 0.015 0.002 PHESB 160 TYR 0.021 0.002 TYRSB 119 ARG 0.011 0.000 ARGSR 266 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17024 Ramachandran restraints generated. 8512 Oldfield, 0 Emsley, 8512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17024 Ramachandran restraints generated. 8512 Oldfield, 0 Emsley, 8512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1213 residues out of total 7502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 1000 time to evaluate : 7.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L6 119 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7119 (tm-30) REVERT: L6 121 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.7004 (mmm160) REVERT: L6 184 MET cc_start: 0.7860 (mtp) cc_final: 0.7593 (mtp) REVERT: L7 31 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7349 (ttt-90) REVERT: L8 121 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.6720 (mpt180) REVERT: L9 13 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.7863 (mmpt) REVERT: L9 20 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7520 (ttp80) REVERT: LB 108 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.6689 (ttm170) REVERT: LD 76 MET cc_start: 0.7523 (OUTLIER) cc_final: 0.6810 (mmt) REVERT: LE 136 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7559 (mtp180) REVERT: LE 152 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7351 (mt-10) REVERT: LE 157 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.6203 (mp0) REVERT: LF 41 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7700 (tt0) REVERT: LJ 99 ASP cc_start: 0.7115 (OUTLIER) cc_final: 0.6881 (m-30) REVERT: LJ 113 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7042 (tp30) REVERT: LK 134 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7268 (tt0) REVERT: LL 28 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7354 (pt0) REVERT: LL 108 MET cc_start: 0.8461 (mmm) cc_final: 0.8213 (mmm) REVERT: LM 51 LYS cc_start: 0.7580 (OUTLIER) cc_final: 0.7315 (pttm) REVERT: LN 139 ASP cc_start: 0.6671 (t0) cc_final: 0.6331 (t0) REVERT: LN 382 MET cc_start: 0.6845 (OUTLIER) cc_final: 0.6508 (mmt) REVERT: LO 44 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7130 (mmmm) REVERT: LS 82 ASP cc_start: 0.8402 (OUTLIER) cc_final: 0.8176 (p0) REVERT: LU 60 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8210 (mp) REVERT: LU 71 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7638 (mttt) REVERT: LV 78 ARG cc_start: 0.6939 (OUTLIER) cc_final: 0.6583 (mmp-170) REVERT: LV 92 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.6596 (mm-30) REVERT: NK 28 ARG cc_start: 0.7689 (mtm110) cc_final: 0.7413 (mmp-170) REVERT: NK 34 LYS cc_start: 0.7455 (OUTLIER) cc_final: 0.7182 (ptpp) REVERT: NP 77 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.8165 (mttm) REVERT: NR 49 ASN cc_start: 0.7498 (OUTLIER) cc_final: 0.7270 (t0) REVERT: NR 100 ASP cc_start: 0.7400 (m-30) cc_final: 0.7005 (m-30) REVERT: SA 143 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7211 (mmm160) REVERT: SA 205 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7331 (mmp80) REVERT: SA 325 MET cc_start: 0.8357 (tpp) cc_final: 0.8050 (tpt) REVERT: SB 36 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8022 (tt) REVERT: SB 163 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8127 (tp) REVERT: SC 41 LYS cc_start: 0.7085 (OUTLIER) cc_final: 0.6062 (mmtm) REVERT: SC 220 LYS cc_start: 0.6905 (OUTLIER) cc_final: 0.6485 (pttm) REVERT: SD 220 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.7363 (ttt) REVERT: SG 21 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8066 (mttt) REVERT: SG 86 LEU cc_start: 0.7017 (OUTLIER) cc_final: 0.6338 (mt) REVERT: SK 1 MET cc_start: 0.6510 (ttt) cc_final: 0.6215 (ttt) REVERT: SK 8 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7294 (mt-10) REVERT: SK 18 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8178 (tptt) REVERT: SK 90 ASP cc_start: 0.6633 (OUTLIER) cc_final: 0.6308 (m-30) REVERT: SK 237 ARG cc_start: 0.7207 (OUTLIER) cc_final: 0.6140 (tmm-80) REVERT: SR 535 ASP cc_start: 0.5975 (OUTLIER) cc_final: 0.5683 (t70) REVERT: SR 575 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.6636 (ptp-170) REVERT: SR 616 MET cc_start: 0.6699 (OUTLIER) cc_final: 0.5534 (mpt) REVERT: SV 1 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.6955 (ptt) REVERT: SV 87 ASN cc_start: 0.7620 (m110) cc_final: 0.7196 (m-40) REVERT: SV 109 MET cc_start: 0.7754 (mmm) cc_final: 0.7493 (mtt) REVERT: VB 36 ILE cc_start: 0.6193 (OUTLIER) cc_final: 0.5652 (tp) outliers start: 213 outliers final: 133 residues processed: 1123 average time/residue: 2.3948 time to fit residues: 3804.3002 Evaluate side-chains 1161 residues out of total 7502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 983 time to evaluate : 7.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L5 residue 39 VAL Chi-restraints excluded: chain L5 residue 49 VAL Chi-restraints excluded: chain L5 residue 102 THR Chi-restraints excluded: chain L5 residue 150 CYS Chi-restraints excluded: chain L6 residue 24 THR Chi-restraints excluded: chain L6 residue 52 SER Chi-restraints excluded: chain L6 residue 64 VAL Chi-restraints excluded: chain L6 residue 69 LYS Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 119 GLU Chi-restraints excluded: chain L6 residue 121 ARG Chi-restraints excluded: chain L7 residue 31 ARG Chi-restraints excluded: chain L7 residue 189 ILE Chi-restraints excluded: chain L8 residue 38 VAL Chi-restraints excluded: chain L8 residue 113 MET Chi-restraints excluded: chain L8 residue 121 ARG Chi-restraints excluded: chain L9 residue 5 LYS Chi-restraints excluded: chain L9 residue 13 LYS Chi-restraints excluded: chain L9 residue 20 ARG Chi-restraints excluded: chain L9 residue 89 VAL Chi-restraints excluded: chain L9 residue 170 LYS Chi-restraints excluded: chain LA residue 14 SER Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LA residue 141 SER Chi-restraints excluded: chain LB residue 19 LYS Chi-restraints excluded: chain LB residue 42 THR Chi-restraints excluded: chain LB residue 108 ARG Chi-restraints excluded: chain LD residue 13 SER Chi-restraints excluded: chain LD residue 68 LEU Chi-restraints excluded: chain LD residue 76 MET Chi-restraints excluded: chain LD residue 89 MET Chi-restraints excluded: chain LD residue 119 MET Chi-restraints excluded: chain LD residue 142 ILE Chi-restraints excluded: chain LE residue 11 THR Chi-restraints excluded: chain LE residue 68 THR Chi-restraints excluded: chain LE residue 76 VAL Chi-restraints excluded: chain LE residue 81 LYS Chi-restraints excluded: chain LE residue 136 ARG Chi-restraints excluded: chain LE residue 152 GLU Chi-restraints excluded: chain LE residue 157 GLU Chi-restraints excluded: chain LF residue 41 GLN Chi-restraints excluded: chain LF residue 52 LYS Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LG residue 92 ASP Chi-restraints excluded: chain LH residue 115 LYS Chi-restraints excluded: chain LH residue 147 LEU Chi-restraints excluded: chain LI residue 32 SER Chi-restraints excluded: chain LI residue 44 VAL Chi-restraints excluded: chain LI residue 63 LYS Chi-restraints excluded: chain LI residue 128 VAL Chi-restraints excluded: chain LJ residue 99 ASP Chi-restraints excluded: chain LJ residue 113 GLU Chi-restraints excluded: chain LK residue 15 VAL Chi-restraints excluded: chain LK residue 16 SER Chi-restraints excluded: chain LK residue 134 GLU Chi-restraints excluded: chain LK residue 139 SER Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LL residue 81 THR Chi-restraints excluded: chain LL residue 85 ASN Chi-restraints excluded: chain LL residue 105 ASP Chi-restraints excluded: chain LL residue 111 ILE Chi-restraints excluded: chain LM residue 13 SER Chi-restraints excluded: chain LM residue 23 LYS Chi-restraints excluded: chain LM residue 31 SER Chi-restraints excluded: chain LM residue 40 LEU Chi-restraints excluded: chain LM residue 51 LYS Chi-restraints excluded: chain LM residue 56 LYS Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 308 ASP Chi-restraints excluded: chain LN residue 337 VAL Chi-restraints excluded: chain LN residue 338 VAL Chi-restraints excluded: chain LN residue 352 LEU Chi-restraints excluded: chain LN residue 382 MET Chi-restraints excluded: chain LO residue 20 LEU Chi-restraints excluded: chain LO residue 26 LYS Chi-restraints excluded: chain LO residue 35 LEU Chi-restraints excluded: chain LO residue 44 LYS Chi-restraints excluded: chain LP residue 46 LEU Chi-restraints excluded: chain LP residue 66 THR Chi-restraints excluded: chain LP residue 101 LYS Chi-restraints excluded: chain LQ residue 53 ILE Chi-restraints excluded: chain LQ residue 123 THR Chi-restraints excluded: chain LR residue 30 ILE Chi-restraints excluded: chain LR residue 48 VAL Chi-restraints excluded: chain LR residue 65 MET Chi-restraints excluded: chain LR residue 82 MET Chi-restraints excluded: chain LS residue 42 SER Chi-restraints excluded: chain LS residue 82 ASP Chi-restraints excluded: chain LT residue 22 ARG Chi-restraints excluded: chain LT residue 90 SER Chi-restraints excluded: chain LU residue 27 SER Chi-restraints excluded: chain LU residue 58 MET Chi-restraints excluded: chain LU residue 60 LEU Chi-restraints excluded: chain LU residue 70 LEU Chi-restraints excluded: chain LU residue 71 LYS Chi-restraints excluded: chain LV residue 23 VAL Chi-restraints excluded: chain LV residue 24 THR Chi-restraints excluded: chain LV residue 78 ARG Chi-restraints excluded: chain LV residue 92 GLU Chi-restraints excluded: chain LV residue 103 VAL Chi-restraints excluded: chain LX residue 24 LYS Chi-restraints excluded: chain LX residue 26 VAL Chi-restraints excluded: chain LX residue 45 THR Chi-restraints excluded: chain LX residue 72 ASN Chi-restraints excluded: chain LY residue 36 VAL Chi-restraints excluded: chain LY residue 56 LEU Chi-restraints excluded: chain NK residue 34 LYS Chi-restraints excluded: chain NL residue 211 GLU Chi-restraints excluded: chain NL residue 427 SER Chi-restraints excluded: chain NL residue 452 GLU Chi-restraints excluded: chain NP residue 71 ILE Chi-restraints excluded: chain NP residue 77 LYS Chi-restraints excluded: chain NP residue 82 SER Chi-restraints excluded: chain NR residue 49 ASN Chi-restraints excluded: chain SA residue 14 LYS Chi-restraints excluded: chain SA residue 61 GLN Chi-restraints excluded: chain SA residue 143 ARG Chi-restraints excluded: chain SA residue 152 LEU Chi-restraints excluded: chain SA residue 205 ARG Chi-restraints excluded: chain SA residue 269 LYS Chi-restraints excluded: chain SA residue 273 LEU Chi-restraints excluded: chain SA residue 297 GLU Chi-restraints excluded: chain SA residue 351 VAL Chi-restraints excluded: chain SB residue 36 LEU Chi-restraints excluded: chain SB residue 125 VAL Chi-restraints excluded: chain SB residue 163 LEU Chi-restraints excluded: chain SB residue 188 LYS Chi-restraints excluded: chain SB residue 217 ASP Chi-restraints excluded: chain SB residue 272 SER Chi-restraints excluded: chain SC residue 41 LYS Chi-restraints excluded: chain SC residue 134 SER Chi-restraints excluded: chain SC residue 143 SER Chi-restraints excluded: chain SC residue 212 LEU Chi-restraints excluded: chain SC residue 220 LYS Chi-restraints excluded: chain SC residue 243 THR Chi-restraints excluded: chain SC residue 255 SER Chi-restraints excluded: chain SD residue 220 MET Chi-restraints excluded: chain SF residue 160 SER Chi-restraints excluded: chain SF residue 169 VAL Chi-restraints excluded: chain SF residue 208 GLU Chi-restraints excluded: chain SG residue 1 MET Chi-restraints excluded: chain SG residue 21 LYS Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SG residue 85 THR Chi-restraints excluded: chain SG residue 86 LEU Chi-restraints excluded: chain SG residue 94 SER Chi-restraints excluded: chain SG residue 95 VAL Chi-restraints excluded: chain SG residue 187 VAL Chi-restraints excluded: chain SH residue 50 ARG Chi-restraints excluded: chain SI residue 83 VAL Chi-restraints excluded: chain SI residue 221 SER Chi-restraints excluded: chain SK residue 8 GLU Chi-restraints excluded: chain SK residue 18 LYS Chi-restraints excluded: chain SK residue 75 ASN Chi-restraints excluded: chain SK residue 90 ASP Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SK residue 237 ARG Chi-restraints excluded: chain SM residue 59 THR Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SM residue 229 THR Chi-restraints excluded: chain SM residue 317 LEU Chi-restraints excluded: chain SM residue 360 LEU Chi-restraints excluded: chain SM residue 406 LEU Chi-restraints excluded: chain SR residue 10 THR Chi-restraints excluded: chain SR residue 41 HIS Chi-restraints excluded: chain SR residue 174 CYS Chi-restraints excluded: chain SR residue 258 SER Chi-restraints excluded: chain SR residue 261 CYS Chi-restraints excluded: chain SR residue 306 ILE Chi-restraints excluded: chain SR residue 313 GLU Chi-restraints excluded: chain SR residue 459 LEU Chi-restraints excluded: chain SR residue 513 LYS Chi-restraints excluded: chain SR residue 535 ASP Chi-restraints excluded: chain SR residue 575 ARG Chi-restraints excluded: chain SR residue 590 LYS Chi-restraints excluded: chain SR residue 616 MET Chi-restraints excluded: chain SV residue 1 MET Chi-restraints excluded: chain VB residue 36 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1211 random chunks: chunk 1083 optimal weight: 7.9990 chunk 714 optimal weight: 0.7980 chunk 1150 optimal weight: 1.9990 chunk 702 optimal weight: 0.0980 chunk 545 optimal weight: 4.9990 chunk 799 optimal weight: 0.6980 chunk 1206 optimal weight: 5.9990 chunk 1110 optimal weight: 7.9990 chunk 960 optimal weight: 4.9990 chunk 99 optimal weight: 40.0000 chunk 742 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L6 67 HIS LA 101 ASN LA 118 GLN LE 144 ASN LF 95 ASN LG 27 ASN LH 151 ASN LI 86 GLN ** LK 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LM 19 ASN ** LN 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LN 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LO 40 GLN ** LQ 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LQ 81 ASN LR 3 GLN LU 92 ASN NR 42 ASN NR 60 ASN NR 122 GLN ** SB 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SC 256 GLN ** SD 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 43 GLN SE 64 GLN ** SF 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 162 GLN SI 42 GLN SI 207 HIS SK 178 GLN SK 225 ASN SM 102 ASN SM 396 GLN SR 100 ASN SV 24 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 159568 Z= 0.157 Angle : 0.681 19.922 233140 Z= 0.371 Chirality : 0.034 0.342 28508 Planarity : 0.007 0.130 15818 Dihedral : 22.988 179.687 68339 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.35 % Allowed : 16.14 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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: 1.24 (0.09), residues: 8512 helix: 2.05 (0.09), residues: 3381 sheet: 0.46 (0.16), residues: 1069 loop : -0.07 (0.09), residues: 4062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRPSI 69 HIS 0.005 0.001 HISLV 21 PHE 0.014 0.001 PHESB 160 TYR 0.021 0.001 TYRSI 242 ARG 0.021 0.000 ARGSI 73 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17024 Ramachandran restraints generated. 8512 Oldfield, 0 Emsley, 8512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17024 Ramachandran restraints generated. 8512 Oldfield, 0 Emsley, 8512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1172 residues out of total 7502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 1000 time to evaluate : 8.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L6 119 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7107 (tm-30) REVERT: L6 184 MET cc_start: 0.7845 (mtp) cc_final: 0.7630 (mtp) REVERT: L7 31 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7329 (ttt-90) REVERT: L8 121 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.6684 (mpt180) REVERT: LB 108 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.6656 (ttm170) REVERT: LE 136 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7555 (mtp180) REVERT: LF 41 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7688 (tt0) REVERT: LH 152 LYS cc_start: 0.8262 (mptt) cc_final: 0.8030 (mmtm) REVERT: LJ 99 ASP cc_start: 0.7099 (OUTLIER) cc_final: 0.6867 (m-30) REVERT: LJ 113 GLU cc_start: 0.7449 (OUTLIER) cc_final: 0.7004 (tp30) REVERT: LK 68 SER cc_start: 0.8038 (p) cc_final: 0.7811 (m) REVERT: LK 134 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7290 (tt0) REVERT: LL 28 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7323 (pt0) REVERT: LL 108 MET cc_start: 0.8459 (mmm) cc_final: 0.8204 (mmm) REVERT: LN 139 ASP cc_start: 0.6648 (t0) cc_final: 0.6304 (t0) REVERT: LN 382 MET cc_start: 0.6837 (OUTLIER) cc_final: 0.6541 (mmt) REVERT: LO 44 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7105 (mmmm) REVERT: LU 71 LYS cc_start: 0.7846 (OUTLIER) cc_final: 0.7629 (mttt) REVERT: LV 92 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.6578 (mm-30) REVERT: LY 16 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7419 (mtm-85) REVERT: NK 28 ARG cc_start: 0.7673 (mtm110) cc_final: 0.7404 (mmp-170) REVERT: NK 34 LYS cc_start: 0.7434 (OUTLIER) cc_final: 0.7161 (ptpp) REVERT: NP 77 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.8152 (mttm) REVERT: NR 49 ASN cc_start: 0.7494 (OUTLIER) cc_final: 0.7266 (t0) REVERT: SA 143 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7217 (mmm160) REVERT: SA 205 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7291 (mmp80) REVERT: SA 325 MET cc_start: 0.8322 (tpp) cc_final: 0.8011 (tpt) REVERT: SB 36 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.7983 (tt) REVERT: SB 163 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8106 (tp) REVERT: SC 41 LYS cc_start: 0.7076 (OUTLIER) cc_final: 0.6055 (mmtm) REVERT: SC 220 LYS cc_start: 0.6926 (OUTLIER) cc_final: 0.6513 (pttm) REVERT: SD 220 MET cc_start: 0.7700 (OUTLIER) cc_final: 0.7341 (ttt) REVERT: SG 21 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.8057 (mttt) REVERT: SG 86 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6311 (mt) REVERT: SK 1 MET cc_start: 0.6483 (ttt) cc_final: 0.6167 (ttt) REVERT: SK 8 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7282 (mt-10) REVERT: SK 18 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8222 (tptt) REVERT: SK 90 ASP cc_start: 0.6650 (OUTLIER) cc_final: 0.6328 (m-30) REVERT: SK 237 ARG cc_start: 0.7197 (OUTLIER) cc_final: 0.6128 (tmm-80) REVERT: SR 115 ARG cc_start: 0.7653 (ttp-110) cc_final: 0.7442 (ttm110) REVERT: SR 270 GLU cc_start: 0.6187 (OUTLIER) cc_final: 0.5954 (mt-10) REVERT: SR 535 ASP cc_start: 0.5951 (OUTLIER) cc_final: 0.5655 (t70) REVERT: SR 575 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.6647 (ptp-170) REVERT: SR 616 MET cc_start: 0.6678 (OUTLIER) cc_final: 0.5507 (mpt) REVERT: SV 1 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.6976 (ptt) REVERT: SV 87 ASN cc_start: 0.7596 (m110) cc_final: 0.7147 (m-40) outliers start: 172 outliers final: 111 residues processed: 1105 average time/residue: 2.4338 time to fit residues: 3809.0552 Evaluate side-chains 1140 residues out of total 7502 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 993 time to evaluate : 8.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L5 residue 39 VAL Chi-restraints excluded: chain L5 residue 49 VAL Chi-restraints excluded: chain L5 residue 102 THR Chi-restraints excluded: chain L5 residue 150 CYS Chi-restraints excluded: chain L6 residue 24 THR Chi-restraints excluded: chain L6 residue 64 VAL Chi-restraints excluded: chain L6 residue 69 LYS Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 119 GLU Chi-restraints excluded: chain L7 residue 31 ARG Chi-restraints excluded: chain L7 residue 93 LYS Chi-restraints excluded: chain L7 residue 189 ILE Chi-restraints excluded: chain L8 residue 38 VAL Chi-restraints excluded: chain L8 residue 113 MET Chi-restraints excluded: chain L8 residue 121 ARG Chi-restraints excluded: chain L9 residue 5 LYS Chi-restraints excluded: chain L9 residue 89 VAL Chi-restraints excluded: chain LA residue 14 SER Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LB residue 19 LYS Chi-restraints excluded: chain LB residue 108 ARG Chi-restraints excluded: chain LD residue 13 SER Chi-restraints excluded: chain LD residue 68 LEU Chi-restraints excluded: chain LD residue 89 MET Chi-restraints excluded: chain LD residue 119 MET Chi-restraints excluded: chain LD residue 142 ILE Chi-restraints excluded: chain LE residue 11 THR Chi-restraints excluded: chain LE residue 68 THR Chi-restraints excluded: chain LE residue 76 VAL Chi-restraints excluded: chain LE residue 81 LYS Chi-restraints excluded: chain LE residue 136 ARG Chi-restraints excluded: chain LF residue 41 GLN Chi-restraints excluded: chain LG residue 42 VAL Chi-restraints excluded: chain LG residue 92 ASP Chi-restraints excluded: chain LH residue 115 LYS Chi-restraints excluded: chain LH residue 147 LEU Chi-restraints excluded: chain LI residue 32 SER Chi-restraints excluded: chain LI residue 44 VAL Chi-restraints excluded: chain LI residue 63 LYS Chi-restraints excluded: chain LJ residue 99 ASP Chi-restraints excluded: chain LJ residue 113 GLU Chi-restraints excluded: chain LK residue 15 VAL Chi-restraints excluded: chain LK residue 16 SER Chi-restraints excluded: chain LK residue 134 GLU Chi-restraints excluded: chain LK residue 139 SER Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LL residue 81 THR Chi-restraints excluded: chain LL residue 85 ASN Chi-restraints excluded: chain LL residue 105 ASP Chi-restraints excluded: chain LL residue 111 ILE Chi-restraints excluded: chain LM residue 13 SER Chi-restraints excluded: chain LM residue 23 LYS Chi-restraints excluded: chain LM residue 40 LEU Chi-restraints excluded: chain LM residue 56 LYS Chi-restraints excluded: chain LN residue 159 VAL Chi-restraints excluded: chain LN residue 337 VAL Chi-restraints excluded: chain LN residue 352 LEU Chi-restraints excluded: chain LN residue 382 MET Chi-restraints excluded: chain LO residue 20 LEU Chi-restraints excluded: chain LO residue 26 LYS Chi-restraints excluded: chain LO residue 35 LEU Chi-restraints excluded: chain LO residue 44 LYS Chi-restraints excluded: chain LP residue 46 LEU Chi-restraints excluded: chain LP residue 66 THR Chi-restraints excluded: chain LP residue 101 LYS Chi-restraints excluded: chain LQ residue 53 ILE Chi-restraints excluded: chain LR residue 65 MET Chi-restraints excluded: chain LR residue 82 MET Chi-restraints excluded: chain LS residue 42 SER Chi-restraints excluded: chain LT residue 22 ARG Chi-restraints excluded: chain LT residue 90 SER Chi-restraints excluded: chain LU residue 27 SER Chi-restraints excluded: chain LU residue 70 LEU Chi-restraints excluded: chain LU residue 71 LYS Chi-restraints excluded: chain LV residue 23 VAL Chi-restraints excluded: chain LV residue 24 THR Chi-restraints excluded: chain LV residue 92 GLU Chi-restraints excluded: chain LV residue 103 VAL Chi-restraints excluded: chain LX residue 24 LYS Chi-restraints excluded: chain LX residue 26 VAL Chi-restraints excluded: chain LX residue 45 THR Chi-restraints excluded: chain LX residue 72 ASN Chi-restraints excluded: chain LY residue 16 ARG Chi-restraints excluded: chain LY residue 36 VAL Chi-restraints excluded: chain NK residue 34 LYS Chi-restraints excluded: chain NL residue 211 GLU Chi-restraints excluded: chain NL residue 427 SER Chi-restraints excluded: chain NP residue 77 LYS Chi-restraints excluded: chain NP residue 82 SER Chi-restraints excluded: chain NR residue 49 ASN Chi-restraints excluded: chain SA residue 14 LYS Chi-restraints excluded: chain SA residue 143 ARG Chi-restraints excluded: chain SA residue 152 LEU Chi-restraints excluded: chain SA residue 205 ARG Chi-restraints excluded: chain SA residue 273 LEU Chi-restraints excluded: chain SA residue 297 GLU Chi-restraints excluded: chain SB residue 36 LEU Chi-restraints excluded: chain SB residue 125 VAL Chi-restraints excluded: chain SB residue 163 LEU Chi-restraints excluded: chain SB residue 188 LYS Chi-restraints excluded: chain SB residue 217 ASP Chi-restraints excluded: chain SB residue 272 SER Chi-restraints excluded: chain SC residue 41 LYS Chi-restraints excluded: chain SC residue 143 SER Chi-restraints excluded: chain SC residue 212 LEU Chi-restraints excluded: chain SC residue 220 LYS Chi-restraints excluded: chain SC residue 243 THR Chi-restraints excluded: chain SC residue 255 SER Chi-restraints excluded: chain SD residue 220 MET Chi-restraints excluded: chain SF residue 169 VAL Chi-restraints excluded: chain SF residue 208 GLU Chi-restraints excluded: chain SG residue 1 MET Chi-restraints excluded: chain SG residue 21 LYS Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SG residue 85 THR Chi-restraints excluded: chain SG residue 86 LEU Chi-restraints excluded: chain SG residue 94 SER Chi-restraints excluded: chain SG residue 187 VAL Chi-restraints excluded: chain SH residue 50 ARG Chi-restraints excluded: chain SI residue 83 VAL Chi-restraints excluded: chain SI residue 106 ASP Chi-restraints excluded: chain SI residue 221 SER Chi-restraints excluded: chain SK residue 8 GLU Chi-restraints excluded: chain SK residue 18 LYS Chi-restraints excluded: chain SK residue 75 ASN Chi-restraints excluded: chain SK residue 90 ASP Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SK residue 237 ARG Chi-restraints excluded: chain SM residue 59 THR Chi-restraints excluded: chain SM residue 117 ASP Chi-restraints excluded: chain SM residue 229 THR Chi-restraints excluded: chain SM residue 360 LEU Chi-restraints excluded: chain SM residue 406 LEU Chi-restraints excluded: chain SR residue 10 THR Chi-restraints excluded: chain SR residue 174 CYS Chi-restraints excluded: chain SR residue 258 SER Chi-restraints excluded: chain SR residue 261 CYS Chi-restraints excluded: chain SR residue 270 GLU Chi-restraints excluded: chain SR residue 306 ILE Chi-restraints excluded: chain SR residue 313 GLU Chi-restraints excluded: chain SR residue 459 LEU Chi-restraints excluded: chain SR residue 513 LYS Chi-restraints excluded: chain SR residue 535 ASP Chi-restraints excluded: chain SR residue 575 ARG Chi-restraints excluded: chain SR residue 590 LYS Chi-restraints excluded: chain SR residue 616 MET Chi-restraints excluded: chain SV residue 1 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1211 random chunks: chunk 589 optimal weight: 7.9990 chunk 763 optimal weight: 5.9990 chunk 1023 optimal weight: 0.0570 chunk 294 optimal weight: 6.9990 chunk 885 optimal weight: 5.9990 chunk 141 optimal weight: 7.9990 chunk 266 optimal weight: 10.0000 chunk 962 optimal weight: 0.9980 chunk 402 optimal weight: 5.9990 chunk 988 optimal weight: 5.9990 chunk 121 optimal weight: 20.0000 overall best weight: 3.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L5 168 GLN L6 67 HIS LA 118 GLN LE 144 ASN LG 27 ASN LH 151 ASN LI 86 GLN LI 127 GLN LK 85 GLN ** LN 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LO 40 GLN ** LQ 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LQ 81 ASN LR 3 GLN LU 92 ASN NR 42 ASN NR 60 ASN NR 122 GLN SB 275 GLN SC 256 GLN ** SD 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 43 GLN SE 64 GLN ** SF 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SG 162 GLN SI 42 GLN SI 207 HIS SK 178 GLN SK 225 ASN SM 102 ASN SM 253 GLN ** SM 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SR 100 ASN ** SV 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.101161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.071648 restraints weight = 253878.864| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.14 r_work: 0.2818 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2711 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2711 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 159568 Z= 0.383 Angle : 0.763 19.689 233140 Z= 0.403 Chirality : 0.041 0.345 28508 Planarity : 0.008 0.140 15818 Dihedral : 22.998 179.977 68339 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.29 % Favored : 97.70 % Rotamer: Outliers : 2.47 % Allowed : 16.03 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.36 % 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: 0.96 (0.09), residues: 8512 helix: 1.79 (0.09), residues: 3395 sheet: 0.38 (0.15), residues: 1069 loop : -0.23 (0.09), residues: 4048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRPNR 146 HIS 0.009 0.001 HISLK 39 PHE 0.020 0.002 PHESB 160 TYR 0.026 0.002 TYRSB 119 ARG 0.012 0.001 ARGSI 104 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 57246.98 seconds wall clock time: 990 minutes 39.28 seconds (59439.28 seconds total)