Starting phenix.real_space_refine on Mon Feb 19 03:35:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flf_29277/02_2024/8flf_29277_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flf_29277/02_2024/8flf_29277.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flf_29277/02_2024/8flf_29277_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flf_29277/02_2024/8flf_29277_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flf_29277/02_2024/8flf_29277_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flf_29277/02_2024/8flf_29277.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flf_29277/02_2024/8flf_29277.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flf_29277/02_2024/8flf_29277_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8flf_29277/02_2024/8flf_29277_neut_updated.pdb" } resolution = 2.65 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= 0.052 sd= 0.180 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 6 6.06 5 P 3599 5.49 5 Mg 87 5.21 5 S 256 5.16 5 C 70658 2.51 5 N 25365 2.21 5 O 34759 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L7 TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L9 PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L9 TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LD TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LG TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LH PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LO GLU 80": "OE1" <-> "OE2" Residue "LO TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LT TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LU PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SB TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SB TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SB GLU 124": "OE1" <-> "OE2" Residue "SD TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SD PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SF PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SK PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR TYR 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "SR PHE 614": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 134730 Number of models: 1 Model: "" Number of chains: 64 Chain: "BE" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1295 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 153} Chain breaks: 1 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: 71370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3325, 71370 Classifications: {'RNA': 3325} Modifications used: {'rna2p': 6, 'rna2p_pur': 321, 'rna2p_pyr': 203, 'rna3p': 82, 'rna3p_pur': 1470, 'rna3p_pyr': 1225} Link IDs: {'rna2p': 529, 'rna3p': 2795} Chain breaks: 30 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: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1020 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 115} 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: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 723 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 3, 'TRANS': 84} 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: "NP" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 876 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain breaks: 1 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: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2376 Classifications: {'peptide': 292} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 282} Chain: "SC" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1715 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 199} 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: "SK" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1721 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain: "SQ" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 610 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 115} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 456 Unresolved non-hydrogen angles: 573 Unresolved non-hydrogen dihedrals: 396 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': 10, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 264 Chain: "SR" Number of atoms: 2002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 2002 Classifications: {'peptide': 243} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 232} 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: "L1" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "L3" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Unusual residues: {' MG': 71} Classifications: {'undetermined': 71} Link IDs: {None: 70} 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: "LM" 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 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: 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: "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: "SA" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 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: "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 A05G8 SG CYSLR 46 83.218 180.174 81.619 1.00 42.35 S ATOM A05GP SG CYSLR 49 82.859 183.409 83.383 1.00 50.53 S ATOM A05O0 SG CYSLR 83 79.959 182.762 81.155 1.00 42.74 S ATOM A05OK SG CYSLR 86 83.520 183.151 79.663 1.00 43.20 S ATOM A080W SG CYSLV 12 186.533 113.035 117.028 1.00 24.13 S ATOM A081K SG CYSLV 15 189.762 112.020 115.405 1.00 26.29 S ATOM A08EL SG CYSLV 72 188.912 115.776 115.772 1.00 23.60 S ATOM A08FM SG CYSLV 77 186.909 113.420 113.395 1.00 29.45 S ATOM A08PW SG CYSLW 19 91.934 124.945 101.099 1.00 27.57 S ATOM A08QO SG CYSLW 22 92.654 122.238 103.671 1.00 28.42 S ATOM A08T7 SG CYSLW 34 94.590 125.475 103.747 1.00 22.34 S ATOM A08TQ SG CYSLW 37 95.275 123.030 101.001 1.00 24.87 S ATOM A09DX SG CYSLX 39 94.340 191.431 90.048 1.00 37.80 S ATOM A09EK SG CYSLX 42 91.110 193.107 89.576 1.00 39.45 S ATOM A09HY SG CYSLX 57 91.230 189.938 91.706 1.00 38.73 S ATOM A09IE SG CYSLX 60 91.647 189.584 88.013 1.00 40.39 S ATOM A0B8A SG CYSNP 63 73.485 198.641 160.602 1.00 45.20 S ATOM A0B8T SG CYSNP 66 71.393 195.355 160.789 1.00 44.15 S ATOM A0PUO SG CYSSV 6 62.213 179.677 180.969 1.00 35.88 S ATOM A0PVH SG CYSSV 9 58.593 178.523 180.535 1.00 33.10 S ATOM A0Q0L SG CYSSV 32 61.151 176.008 181.664 1.00 33.02 S ATOM A0Q1F SG CYSSV 36 61.306 177.327 178.152 1.00 31.40 S Time building chain proxies: 53.37, per 1000 atoms: 0.40 Number of scatterers: 134730 At special positions: 0 Unit cell: (255.136, 240.128, 283.008, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 S 256 16.00 P 3599 15.00 Mg 87 11.99 O 34759 8.00 N 25365 7.00 C 70658 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 52.93 Conformation dependent library (CDL) restraints added in 8.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNLR 500 " pdb="ZN ZNLR 500 " - pdb=" SG CYSLR 49 " pdb="ZN ZNLR 500 " - pdb=" SG CYSLR 86 " pdb="ZN ZNLR 500 " - pdb=" SG CYSLR 46 " pdb="ZN ZNLR 500 " - pdb=" SG CYSLR 83 " pdb=" ZNLV 200 " pdb="ZN ZNLV 200 " - pdb=" SG CYSLV 12 " pdb="ZN ZNLV 200 " - pdb=" SG CYSLV 77 " pdb="ZN ZNLV 200 " - pdb=" SG CYSLV 15 " pdb="ZN ZNLV 200 " - pdb=" SG CYSLV 72 " pdb=" ZNLW 101 " pdb="ZN ZNLW 101 " - pdb=" SG CYSLW 34 " pdb="ZN ZNLW 101 " - pdb=" SG CYSLW 22 " pdb="ZN ZNLW 101 " - pdb=" SG CYSLW 37 " pdb="ZN ZNLW 101 " - pdb=" SG CYSLW 19 " 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 66 " pdb="ZN ZNNP 500 " - pdb=" SG CYSNP 63 " pdb=" ZNSV 500 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 36 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 9 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 32 " pdb="ZN ZNSV 500 " - pdb=" SG CYSSV 6 " Number of angles added : 32 14038 Ramachandran restraints generated. 7019 Oldfield, 0 Emsley, 7019 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13330 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: 257 helices and 72 sheets defined 43.4% alpha, 13.1% beta 1116 base pairs and 1746 stacking pairs defined. Time for finding SS restraints: 71.43 Creating SS restraints... Processing helix chain 'BE' and resid 42 through 47 removed outlier: 4.181A pdb=" N PHEBE 46 " --> pdb=" O LYSBE 42 " (cutoff:3.500A) Proline residue: BE 47 - end of helix No H-bonds generated for 'chain 'BE' and resid 42 through 47' Processing helix chain 'BE' and resid 61 through 80 Processing helix chain 'BE' and resid 144 through 160 removed outlier: 4.000A pdb=" N LYSBE 158 " --> pdb=" O ARGBE 154 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N PHEBE 159 " --> pdb=" O ALABE 155 " (cutoff:3.500A) Proline residue: BE 160 - end of helix Processing helix chain 'BE' and resid 178 through 188 removed outlier: 3.961A pdb=" N GLUBE 182 " --> pdb=" O ALABE 178 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASPBE 183 " --> pdb=" O ASPBE 179 " (cutoff:3.500A) Processing helix chain 'BE' and resid 205 through 214 removed outlier: 4.119A pdb=" N TRPBE 209 " --> pdb=" O PROBE 205 " (cutoff:3.500A) Processing helix chain 'L5' and resid 30 through 45 Processing helix chain 'L5' and resid 76 through 91 removed outlier: 3.917A pdb=" N GLUL5 80 " --> pdb=" O GLYL5 76 " (cutoff:3.500A) Processing helix chain 'L5' and resid 111 through 116 removed outlier: 4.393A pdb=" N LEUL5 115 " --> pdb=" O GLUL5 111 " (cutoff:3.500A) removed outlier: 4.054A 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 140 through 145 removed outlier: 6.263A pdb=" N LYSL5 145 " --> pdb=" O ILEL5 141 " (cutoff:3.500A) Processing helix chain 'L5' and resid 152 through 157 removed outlier: 5.866A pdb=" N ILEL5 157 " --> pdb=" O ALAL5 153 " (cutoff:3.500A) Processing helix chain 'L5' and resid 158 through 170 Processing helix chain 'L5' and resid 95 through 100 removed outlier: 5.114A pdb=" N SERL5 100 " --> pdb=" O ASNL5 97 " (cutoff:3.500A) Processing helix chain 'L6' and resid 17 through 22 removed outlier: 4.051A pdb=" N ARGL6 21 " --> pdb=" O ASPL6 17 " (cutoff:3.500A) removed outlier: 4.027A 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: 3.974A pdb=" N ARGL6 92 " --> pdb=" O LYSL6 88 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THRL6 93 " --> pdb=" O LYSL6 89 " (cutoff:3.500A) Processing helix chain 'L6' and resid 106 through 124 Processing helix chain 'L6' and resid 140 through 147 removed outlier: 3.504A pdb=" N LEUL6 146 " --> pdb=" O GLUL6 142 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALAL6 147 " --> pdb=" O GLUL6 143 " (cutoff:3.500A) Processing helix chain 'L6' and resid 170 through 176 Processing helix chain 'L6' and resid 177 through 192 Processing helix chain 'L6' and resid 193 through 211 Processing helix chain 'L7' and resid 15 through 30 removed outlier: 3.564A pdb=" N LYSL7 25 " --> pdb=" O ALAL7 21 " (cutoff:3.500A) Processing helix chain 'L7' and resid 46 through 61 removed outlier: 3.809A pdb=" N LYSL7 60 " --> pdb=" O ALAL7 56 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ARGL7 61 " --> pdb=" O PHEL7 57 " (cutoff:3.500A) Processing helix chain 'L7' and resid 65 through 70 removed outlier: 3.767A 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: 3.714A pdb=" N METL7 87 " --> pdb=" O THRL7 83 " (cutoff:3.500A) removed outlier: 3.724A 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: 3.662A pdb=" N ARGL7 101 " --> pdb=" O ALAL7 97 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEUL7 102 " --> pdb=" O ALAL7 98 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LYSL7 103 " --> pdb=" O LEUL7 99 " (cutoff:3.500A) Processing helix chain 'L7' and resid 110 through 116 removed outlier: 7.921A pdb=" N LYSL7 114 " --> pdb=" O PROL7 110 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LYSL7 115 " --> pdb=" O PROL7 111 " (cutoff:3.500A) removed outlier: 5.411A 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 removed outlier: 3.506A pdb=" N GLYL7 146 " --> pdb=" O ALAL7 142 " (cutoff:3.500A) Processing helix chain 'L7' and resid 151 through 190 removed outlier: 5.509A pdb=" N LYSL7 187 " --> pdb=" O LYSL7 183 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LYSL7 188 " --> pdb=" O ASNL7 184 " (cutoff:3.500A) Processing helix chain 'L7' and resid 191 through 200 Processing helix chain 'L8' and resid 51 through 56 removed outlier: 3.981A pdb=" N METL8 55 " --> pdb=" O PROL8 51 " (cutoff:3.500A) removed outlier: 5.363A 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 removed outlier: 3.645A pdb=" N VALL8 73 " --> pdb=" O HISL8 69 " (cutoff:3.500A) Processing helix chain 'L8' and resid 82 through 90 removed outlier: 3.515A pdb=" N THRL8 89 " --> pdb=" O LYSL8 85 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N ARGL8 90 " --> pdb=" O TRPL8 86 " (cutoff:3.500A) Processing helix chain 'L8' and resid 91 through 104 removed outlier: 3.511A pdb=" N ALAL8 102 " --> pdb=" O ARGL8 98 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N METL8 104 " --> pdb=" O ARGL8 100 " (cutoff:3.500A) Processing helix chain 'L8' and resid 105 through 136 removed outlier: 3.514A pdb=" N LEUL8 136 " --> pdb=" O LYSL8 132 " (cutoff:3.500A) Processing helix chain 'L9' and resid 2 through 14 removed outlier: 3.915A pdb=" N TYRL9 6 " --> pdb=" O GLYL9 2 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYSL9 13 " --> pdb=" O GLUL9 9 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LYSL9 14 " --> pdb=" O LEUL9 10 " (cutoff:3.500A) Processing helix chain 'L9' and resid 16 through 34 removed outlier: 3.745A pdb=" N GLNL9 32 " --> pdb=" O TRPL9 28 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEUL9 33 " --> pdb=" O GLNL9 29 " (cutoff:3.500A) removed outlier: 5.138A 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: 3.921A pdb=" N HISL9 87 " --> pdb=" O LYSL9 83 " (cutoff:3.500A) removed outlier: 4.978A 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: 3.761A pdb=" N GLYL9 111 " --> pdb=" O GLYL9 107 " (cutoff:3.500A) Processing helix chain 'L9' and resid 139 through 146 removed outlier: 3.584A 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: 6.224A pdb=" N ILEL9 151 " --> pdb=" O ASPL9 147 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N THRL9 152 " --> pdb=" O THRL9 148 " (cutoff:3.500A) removed outlier: 3.987A 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 Processing helix chain 'L9' and resid 165 through 173 removed outlier: 4.022A pdb=" N SERL9 171 " --> pdb=" O ALAL9 167 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARGL9 172 " --> pdb=" O GLYL9 168 " (cutoff:3.500A) removed outlier: 4.195A 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 Processing helix chain 'LA' and resid 72 through 77 removed outlier: 4.766A pdb=" N TRPLA 76 " --> pdb=" O GLNLA 72 " (cutoff:3.500A) removed outlier: 3.625A 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: 4.111A pdb=" N GLNLB 45 " --> pdb=" O SERLB 41 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHELB 52 " --> pdb=" O LEULB 48 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N METLB 53 " --> pdb=" O LYSLB 49 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N SERLB 54 " --> pdb=" O ARGLB 50 " (cutoff:3.500A) Processing helix chain 'LB' and resid 62 through 72 removed outlier: 3.808A pdb=" N LEULB 72 " --> pdb=" O ARGLB 68 " (cutoff:3.500A) Processing helix chain 'LB' and resid 106 through 117 removed outlier: 3.536A pdb=" N ALALB 116 " --> pdb=" O ARGLB 112 " (cutoff:3.500A) removed outlier: 3.673A 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: 4.509A pdb=" N ARGLB 150 " --> pdb=" O ARGLB 146 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N HISLB 151 " --> pdb=" O GLULB 147 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N GLYLB 153 " --> pdb=" O TYRLB 149 " (cutoff:3.500A) Processing helix chain 'LC' and resid 36 through 52 removed outlier: 3.909A pdb=" N GLNLC 50 " --> pdb=" O TYRLC 46 " (cutoff:3.500A) Processing helix chain 'LC' and resid 101 through 117 Processing helix chain 'LC' and resid 120 through 125 removed outlier: 3.866A pdb=" N ILELC 124 " --> pdb=" O ARGLC 120 " (cutoff:3.500A) removed outlier: 5.544A 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: 4.855A pdb=" N PHELC 145 " --> pdb=" O ALALC 141 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N HISLC 146 " --> pdb=" O VALLC 142 " (cutoff:3.500A) removed outlier: 5.155A 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 removed outlier: 3.543A pdb=" N SERLD 13 " --> pdb=" O ARGLD 9 " (cutoff:3.500A) Processing helix chain 'LD' and resid 18 through 23 removed outlier: 3.653A pdb=" N VALLD 22 " --> pdb=" O GLYLD 18 " (cutoff:3.500A) removed outlier: 5.812A 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: 3.505A pdb=" N ASNLD 34 " --> pdb=" O ASNLD 30 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALALD 35 " --> pdb=" O GLULD 31 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N ASNLD 36 " --> pdb=" O ILELD 32 " (cutoff:3.500A) Processing helix chain 'LD' and resid 37 through 48 removed outlier: 3.501A 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: 6.858A pdb=" N VALLD 93 " --> pdb=" O METLD 89 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THRLD 94 " --> pdb=" O PROLD 90 " (cutoff:3.500A) Processing helix chain 'LD' and resid 116 through 130 removed outlier: 3.520A pdb=" N SERLD 122 " --> pdb=" O HISLD 118 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ASNLD 130 " --> pdb=" O LYSLD 126 " (cutoff:3.500A) Processing helix chain 'LD' and resid 134 through 155 removed outlier: 3.575A pdb=" N LEULD 138 " --> pdb=" O ASNLD 134 " (cutoff:3.500A) Processing helix chain 'LE' and resid 12 through 17 removed outlier: 6.994A pdb=" N SERLE 16 " --> pdb=" O ARGLE 12 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ARGLE 17 " --> pdb=" O TYRLE 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'LE' and resid 12 through 17' Processing helix chain 'LE' and resid 26 through 32 removed outlier: 4.510A pdb=" N TYRLE 30 " --> pdb=" O PROLE 26 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARGLE 32 " --> pdb=" O ALALE 28 " (cutoff:3.500A) Processing helix chain 'LE' and resid 54 through 59 removed outlier: 3.566A pdb=" N HISLE 58 " --> pdb=" O HISLE 54 " (cutoff:3.500A) removed outlier: 5.873A 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: 4.045A pdb=" N ILELE 96 " --> pdb=" O ARGLE 92 " (cutoff:3.500A) removed outlier: 5.374A 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: 3.901A pdb=" N PHELE 105 " --> pdb=" O SERLE 101 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYSLE 107 " --> pdb=" O ASPLE 103 " (cutoff:3.500A) Processing helix chain 'LF' and resid 25 through 32 Processing helix chain 'LF' and resid 35 through 47 removed outlier: 3.592A pdb=" N GLNLF 41 " --> pdb=" O ALALF 37 " (cutoff:3.500A) Processing helix chain 'LF' and resid 55 through 60 removed outlier: 3.560A pdb=" N GLYLF 59 " --> pdb=" O ASNLF 55 " (cutoff:3.500A) Processing helix chain 'LF' and resid 79 through 95 removed outlier: 3.867A pdb=" N LEULF 83 " --> pdb=" O SERLF 79 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYSLF 84 " --> pdb=" O LYSLF 80 " (cutoff:3.500A) Processing helix chain 'LG' and resid 69 through 74 removed outlier: 3.554A pdb=" N ARGLG 73 " --> pdb=" O LYSLG 69 " (cutoff:3.500A) removed outlier: 5.399A 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 removed outlier: 3.831A pdb=" N LEULG 128 " --> pdb=" O GLULG 124 " (cutoff:3.500A) Proline residue: LG 130 - end of helix Processing helix chain 'LG' and resid 131 through 137 removed outlier: 3.905A pdb=" N ASNLG 135 " --> pdb=" O ARGLG 131 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N GLYLG 137 " --> pdb=" O ALALG 133 " (cutoff:3.500A) Processing helix chain 'LH' and resid 72 through 78 removed outlier: 3.602A pdb=" N ILELH 77 " --> pdb=" O HISLH 73 " (cutoff:3.500A) removed outlier: 4.756A 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 removed outlier: 3.589A pdb=" N ALALI 21 " --> pdb=" O ARGLI 17 " (cutoff:3.500A) Processing helix chain 'LI' and resid 22 through 31 removed outlier: 3.821A pdb=" N LYSLI 28 " --> pdb=" O HISLI 24 " (cutoff:3.500A) removed outlier: 4.350A 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: 4.112A pdb=" N VALLI 104 " --> pdb=" O HISLI 100 " (cutoff:3.500A) removed outlier: 5.551A 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: 4.044A pdb=" N LYSLJ 67 " --> pdb=" O ALALJ 63 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 76 through 81 removed outlier: 3.571A pdb=" N LEULJ 80 " --> pdb=" O ASNLJ 76 " (cutoff:3.500A) removed outlier: 5.067A 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: 4.019A pdb=" N ASNLJ 97 " --> pdb=" O LYSLJ 93 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 98 through 104 removed outlier: 4.735A pdb=" N ARGLJ 102 " --> pdb=" O LYSLJ 98 " (cutoff:3.500A) removed outlier: 3.987A 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: 3.730A pdb=" N GLYLJ 125 " --> pdb=" O ARGLJ 121 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 127 through 133 removed outlier: 3.733A pdb=" N PHELJ 131 " --> pdb=" O ASNLJ 127 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N LYSLJ 133 " --> pdb=" O TRPLJ 129 " (cutoff:3.500A) Processing helix chain 'LK' and resid 2 through 7 removed outlier: 3.946A pdb=" N ARGLK 6 " --> pdb=" O PROLK 2 " (cutoff:3.500A) removed outlier: 5.923A 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: 4.468A pdb=" N SERLK 68 " --> pdb=" O LYSLK 64 " (cutoff:3.500A) removed outlier: 3.988A 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: 4.430A pdb=" N TRPLK 79 " --> pdb=" O LEULK 75 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N THRLK 80 " --> pdb=" O ASPLK 76 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEULK 81 " --> pdb=" O LYSLK 77 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N VALLK 82 " --> pdb=" O LEULK 78 " (cutoff:3.500A) removed outlier: 5.285A 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: 3.736A pdb=" N SERLK 106 " --> pdb=" O ASPLK 102 " (cutoff:3.500A) Processing helix chain 'LK' and resid 130 through 141 Processing helix chain 'LL' and resid 2 through 13 removed outlier: 3.559A pdb=" N METLL 8 " --> pdb=" O HISLL 4 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ASNLL 12 " --> pdb=" O METLL 8 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N CYSLL 13 " --> pdb=" O VALLL 9 " (cutoff:3.500A) Processing helix chain 'LL' and resid 85 through 101 removed outlier: 3.719A pdb=" N ASNLL 100 " --> pdb=" O METLL 96 " (cutoff:3.500A) Processing helix chain 'LL' and resid 103 through 123 removed outlier: 4.382A pdb=" N ARGLL 107 " --> pdb=" O ARGLL 103 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N METLL 108 " --> pdb=" O PROLL 104 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ALALL 109 " --> pdb=" O ASPLL 105 " (cutoff:3.500A) Proline residue: LL 123 - end of helix Processing helix chain 'LM' and resid 36 through 55 removed outlier: 3.559A pdb=" N ASNLM 50 " --> pdb=" O ALALM 46 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N LYSLM 51 " --> pdb=" O LYSLM 47 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LYSLM 52 " --> pdb=" O LYSLM 48 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N GLYLM 53 " --> pdb=" O HISLM 49 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEULM 54 " --> pdb=" O ASNLM 50 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N LYSLM 55 " --> pdb=" O LYSLM 51 " (cutoff:3.500A) Processing helix chain 'LM' and resid 56 through 66 Processing helix chain 'LM' and resid 91 through 101 Processing helix chain 'LM' and resid 105 through 116 Processing helix chain 'LN' and resid 13 through 18 removed outlier: 4.479A 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: 4.076A pdb=" N ARGLN 117 " --> pdb=" O GLULN 113 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N PHELN 118 " --> pdb=" O CYSLN 114 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N TYRLN 119 " --> pdb=" O LYSLN 115 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N LYSLN 120 " --> pdb=" O ARGLN 116 " (cutoff:3.500A) Processing helix chain 'LN' and resid 130 through 139 removed outlier: 4.466A pdb=" N LYSLN 135 " --> pdb=" O THRLN 131 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LYSLN 136 " --> pdb=" O LYSLN 132 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N TRPLN 137 " --> pdb=" O TYRLN 133 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLNLN 138 " --> pdb=" O CYSLN 134 " (cutoff:3.500A) Processing helix chain 'LN' and resid 140 through 156 Processing helix chain 'LN' and resid 167 through 172 removed outlier: 4.152A 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 removed outlier: 3.586A pdb=" N ARGLN 200 " --> pdb=" O TRPLN 196 " (cutoff:3.500A) Processing helix chain 'LN' and resid 206 through 211 removed outlier: 3.804A pdb=" N VALLN 210 " --> pdb=" O PROLN 206 " (cutoff:3.500A) Processing helix chain 'LN' and resid 356 through 361 removed outlier: 4.892A pdb=" N LEULN 360 " --> pdb=" O LYSLN 356 " (cutoff:3.500A) removed outlier: 3.877A 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 'LN' and resid 230 through 236 removed outlier: 4.277A pdb=" N TRPLN 235 " --> pdb=" O GLYLN 230 " (cutoff:3.500A) Processing helix chain 'LO' and resid 13 through 25 removed outlier: 3.958A pdb=" N ARGLO 17 " --> pdb=" O SERLO 13 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEULO 20 " --> pdb=" O SERLO 16 " (cutoff:3.500A) Processing helix chain 'LO' and resid 30 through 41 removed outlier: 3.518A pdb=" N LYSLO 36 " --> pdb=" O LYSLO 32 " (cutoff:3.500A) 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: 3.867A pdb=" N ARGLP 32 " --> pdb=" O ASNLP 28 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N HISLP 34 " --> pdb=" O HISLP 30 " (cutoff:3.500A) Processing helix chain 'LP' and resid 40 through 57 removed outlier: 3.533A pdb=" N LYSLP 47 " --> pdb=" O PROLP 43 " (cutoff:3.500A) Processing helix chain 'LP' and resid 65 through 74 Processing helix chain 'LQ' and resid 24 through 29 removed outlier: 3.613A pdb=" N TYRLQ 28 " --> pdb=" O GLNLQ 24 " (cutoff:3.500A) removed outlier: 5.225A 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: 4.018A pdb=" N VALLQ 87 " --> pdb=" O LYSLQ 83 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEULQ 88 " --> pdb=" O GLULQ 84 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEULQ 89 " --> pdb=" O LEULQ 85 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N METLQ 90 " --> pdb=" O GLULQ 86 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 104 through 119 removed outlier: 3.917A pdb=" N ALALQ 110 " --> pdb=" O LYSLQ 106 " (cutoff:3.500A) Processing helix chain 'LR' and resid 60 through 68 removed outlier: 3.883A pdb=" N LEULR 64 " --> pdb=" O ARGLR 60 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N METLR 65 " --> pdb=" O PROLR 61 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ARGLR 66 " --> pdb=" O LYSLR 62 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEULR 67 " --> pdb=" O VALLR 63 " (cutoff:3.500A) removed outlier: 5.613A 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: 5.776A 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: 3.672A pdb=" N ILELS 47 " --> pdb=" O LYSLS 43 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ARGLS 48 " --> pdb=" O LEULS 44 " (cutoff:3.500A) removed outlier: 4.039A 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 removed outlier: 3.596A pdb=" N ARGLS 94 " --> pdb=" O ALALS 90 " (cutoff:3.500A) Processing helix chain 'LS' and resid 96 through 102 removed outlier: 3.507A pdb=" N ASNLS 101 " --> pdb=" O LYSLS 97 " (cutoff:3.500A) removed outlier: 3.503A 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: 3.853A pdb=" N THRLT 39 " --> pdb=" O ALALT 35 " (cutoff:3.500A) removed outlier: 4.596A 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: 4.111A pdb=" N ARGLU 29 " --> pdb=" O ARGLU 25 " (cutoff:3.500A) removed outlier: 4.329A 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 removed outlier: 3.561A pdb=" N GLULU 88 " --> pdb=" O LYSLU 84 " (cutoff:3.500A) Processing helix chain 'LV' and resid 35 through 46 Processing helix chain 'LW' and resid 4 through 11 removed outlier: 3.533A pdb=" N PHELW 8 " --> pdb=" O GLYLW 4 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLYLW 9 " --> pdb=" O THRLW 5 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LYSLW 10 " --> pdb=" O SERLW 6 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ARGLW 11 " --> pdb=" O SERLW 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'LW' and resid 4 through 11' Processing helix chain 'LW' and resid 50 through 58 removed outlier: 3.568A pdb=" N ASNLW 57 " --> pdb=" O ALALW 53 " (cutoff:3.500A) Processing helix chain 'LW' and resid 64 through 77 removed outlier: 4.251A pdb=" N ILELW 69 " --> pdb=" O ARGLW 65 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARGLW 72 " --> pdb=" O LYSLW 68 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARGLW 75 " --> pdb=" O TYRLW 71 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N HISLW 76 " --> pdb=" O ARGLW 72 " (cutoff:3.500A) Processing helix chain 'LX' and resid 20 through 34 removed outlier: 3.915A pdb=" N LYSLX 28 " --> pdb=" O LYSLX 24 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILELX 29 " --> pdb=" O METLX 25 " (cutoff:3.500A) Processing helix chain 'LX' and resid 73 through 92 removed outlier: 3.577A pdb=" N ARGLX 84 " --> pdb=" O LYSLX 80 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARGLX 85 " --> pdb=" O SERLX 81 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLULX 88 " --> pdb=" O ARGLX 84 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEULX 89 " --> pdb=" O ARGLX 85 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYSLX 90 " --> pdb=" O LEULX 86 " (cutoff:3.500A) Processing helix chain 'LY' and resid 7 through 17 removed outlier: 3.542A pdb=" N PHELY 11 " --> pdb=" O GLULY 7 " (cutoff:3.500A) Processing helix chain 'LY' and resid 49 through 60 removed outlier: 3.710A pdb=" N LYSLY 55 " --> pdb=" O GLULY 51 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEULY 60 " --> pdb=" O LEULY 56 " (cutoff:3.500A) Processing helix chain 'LZ' and resid 6 through 21 removed outlier: 5.308A pdb=" N ARGLZ 21 " --> pdb=" O GLNLZ 17 " (cutoff:3.500A) Processing helix chain 'LZ' and resid 24 through 31 removed outlier: 4.698A pdb=" N ARGLZ 28 " --> pdb=" O PROLZ 24 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N METLZ 29 " --> pdb=" O GLNLZ 25 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYSLZ 30 " --> pdb=" O TRPLZ 26 " (cutoff:3.500A) removed outlier: 5.798A 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: 3.547A 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: 3.513A pdb=" N LYSNK 108 " --> pdb=" O ARGNK 104 " (cutoff:3.500A) Processing helix chain 'NP' and resid 15 through 20 removed outlier: 4.584A pdb=" N METNP 19 " --> pdb=" O LEUNP 15 " (cutoff:3.500A) removed outlier: 3.628A 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: 3.759A pdb=" N ARGNP 33 " --> pdb=" O ASPNP 29 " (cutoff:3.500A) Processing helix chain 'NP' and resid 72 through 83 removed outlier: 3.747A pdb=" N ARGNP 81 " --> pdb=" O LYSNP 77 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SERNP 82 " --> pdb=" O THRNP 78 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N LYSNP 83 " --> pdb=" O HISNP 79 " (cutoff:3.500A) Processing helix chain 'NP' and resid 84 through 94 removed outlier: 3.538A pdb=" N LYSNP 90 " --> pdb=" O LYSNP 86 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SERNP 93 " --> pdb=" O LEUNP 89 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N VALNP 94 " --> pdb=" O LYSNP 90 " (cutoff:3.500A) Processing helix chain 'NP' and resid 98 through 107 removed outlier: 3.716A pdb=" N ALANP 106 " --> pdb=" O ALANP 102 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLYNP 107 " --> pdb=" O GLUNP 103 " (cutoff:3.500A) Processing helix chain 'SA' and resid 25 through 31 removed outlier: 4.512A pdb=" N LYSSA 29 " --> pdb=" O PROSA 25 " (cutoff:3.500A) removed outlier: 3.819A 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: 3.923A pdb=" N LYSSA 46 " --> pdb=" O THRSA 42 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASNSA 47 " --> pdb=" O ASNSA 43 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ASNSA 48 " --> pdb=" O LEUSA 44 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ARGSA 49 " --> pdb=" O ARGSA 45 " (cutoff:3.500A) Processing helix chain 'SA' and resid 116 through 134 removed outlier: 3.747A pdb=" N ALASA 132 " --> pdb=" O LEUSA 128 " (cutoff:3.500A) removed outlier: 4.025A 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: 3.833A pdb=" N GLYSA 141 " --> pdb=" O VALSA 137 " (cutoff:3.500A) Processing helix chain 'SA' and resid 156 through 161 removed outlier: 4.300A pdb=" N GLYSA 160 " --> pdb=" O ASPSA 156 " (cutoff:3.500A) removed outlier: 4.123A 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 removed outlier: 3.542A pdb=" N ALASA 167 " --> pdb=" O LYSSA 163 " (cutoff:3.500A) Processing helix chain 'SA' and resid 176 through 187 removed outlier: 3.635A pdb=" N ILESA 180 " --> pdb=" O ALASA 176 " (cutoff:3.500A) Processing helix chain 'SA' and resid 193 through 198 removed outlier: 3.619A pdb=" N ARGSA 197 " --> pdb=" O LYSSA 193 " (cutoff:3.500A) removed outlier: 3.804A 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 264 removed outlier: 4.643A pdb=" N ASPSA 261 " --> pdb=" O PHESA 257 " (cutoff:3.500A) removed outlier: 4.599A 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: 3.935A pdb=" N ALASA 301 " --> pdb=" O GLUSA 297 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ARGSA 303 " --> pdb=" O GLNSA 299 " (cutoff:3.500A) Processing helix chain 'SA' and resid 317 through 322 removed outlier: 4.625A 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: 4.452A 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: 3.941A pdb=" N ARGSB 35 " --> pdb=" O TYRSB 31 " (cutoff:3.500A) Processing helix chain 'SB' and resid 79 through 87 removed outlier: 4.229A 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 Processing helix chain 'SB' and resid 157 through 170 removed outlier: 3.736A pdb=" N GLYSB 161 " --> pdb=" O ASNSB 157 " (cutoff:3.500A) Processing helix chain 'SB' and resid 191 through 201 Processing helix chain 'SB' and resid 202 through 215 removed outlier: 3.737A pdb=" N GLUSB 213 " --> pdb=" O ARGSB 209 " (cutoff:3.500A) Processing helix chain 'SB' and resid 216 through 223 Processing helix chain 'SB' and resid 224 through 230 removed outlier: 4.539A pdb=" N ASNSB 229 " --> pdb=" O GLNSB 225 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SERSB 230 " --> pdb=" O TYRSB 226 " (cutoff:3.500A) Processing helix chain 'SB' and resid 232 through 251 removed outlier: 4.653A pdb=" N GLUSB 237 " --> pdb=" O PROSB 233 " (cutoff:3.500A) removed outlier: 5.023A 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 297 Processing helix chain 'SC' and resid 58 through 67 Processing helix chain 'SC' and resid 190 through 195 removed outlier: 3.935A pdb=" N VALSC 194 " --> pdb=" O HISSC 190 " (cutoff:3.500A) removed outlier: 5.581A 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: 3.908A 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: 5.412A pdb=" N VALSC 274 " --> pdb=" O TYRSC 270 " (cutoff:3.500A) Processing helix chain 'SC' and resid 282 through 287 removed outlier: 5.446A pdb=" N VALSC 287 " --> pdb=" O PROSC 283 " (cutoff:3.500A) Processing helix chain 'SD' and resid 24 through 79 removed outlier: 3.594A pdb=" N GLUSD 68 " --> pdb=" O METSD 64 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILESD 69 " --> pdb=" O TYRSD 65 " (cutoff:3.500A) Processing helix chain 'SD' and resid 102 through 113 Processing helix chain 'SD' and resid 126 through 137 removed outlier: 3.599A pdb=" N ILESD 135 " --> pdb=" O ASNSD 131 " (cutoff:3.500A) removed outlier: 3.633A 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: 4.214A pdb=" N ILESD 175 " --> pdb=" O ASPSD 171 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SERSD 178 " --> pdb=" O LEUSD 174 " (cutoff:3.500A) Processing helix chain 'SD' and resid 186 through 197 removed outlier: 3.881A pdb=" N VALSD 197 " --> pdb=" O GLUSD 193 " (cutoff:3.500A) Processing helix chain 'SD' and resid 200 through 209 removed outlier: 5.224A pdb=" N TRPSD 209 " --> pdb=" O ASNSD 205 " (cutoff:3.500A) Processing helix chain 'SD' and resid 239 through 248 removed outlier: 3.550A pdb=" N LEUSD 243 " --> pdb=" O GLNSD 239 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARGSD 246 " --> pdb=" O ARGSD 242 " (cutoff:3.500A) Processing helix chain 'SE' and resid 58 through 74 removed outlier: 3.794A pdb=" N ALASE 68 " --> pdb=" O GLNSE 64 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYSSE 72 " --> pdb=" O ALASE 68 " (cutoff:3.500A) Processing helix chain 'SE' and resid 77 through 85 removed outlier: 4.677A pdb=" N PHESE 83 " --> pdb=" O ALASE 79 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THRSE 84 " --> pdb=" O ILESE 80 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLNSE 85 " --> pdb=" O ASNSE 81 " (cutoff:3.500A) Processing helix chain 'SE' and resid 88 through 103 removed outlier: 3.610A pdb=" N LEUSE 98 " --> pdb=" O GLNSE 94 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYSSE 101 " --> pdb=" O LYSSE 97 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYRSE 102 " --> pdb=" O LEUSE 98 " (cutoff:3.500A) Processing helix chain 'SE' and resid 106 through 122 removed outlier: 5.623A 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 164 through 178 removed outlier: 5.233A pdb=" N PHESE 169 " --> pdb=" O GLUSE 165 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N LEUSE 170 " --> pdb=" O LEUSE 166 " (cutoff:3.500A) Proline residue: SE 171 - end of helix Processing helix chain 'SE' and resid 186 through 195 removed outlier: 3.512A pdb=" N LEUSE 190 " --> pdb=" O GLYSE 186 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEUSE 193 " --> pdb=" O ARGSE 189 " (cutoff:3.500A) Processing helix chain 'SE' and resid 211 through 226 removed outlier: 3.847A pdb=" N ASNSE 225 " --> pdb=" O ALASE 221 " (cutoff:3.500A) Processing helix chain 'SE' and resid 229 through 236 removed outlier: 3.742A pdb=" N ARGSE 235 " --> pdb=" O ASPSE 231 " (cutoff:3.500A) Processing helix chain 'SE' and resid 243 through 266 removed outlier: 5.111A pdb=" N GLYSE 266 " --> pdb=" O ALASE 262 " (cutoff:3.500A) Processing helix chain 'SF' and resid 5 through 13 removed outlier: 6.540A pdb=" N LYSSF 10 " --> pdb=" O ARGSF 6 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLYSF 11 " --> pdb=" O GLYSF 7 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ALASF 12 " --> pdb=" O GLNSF 8 " (cutoff:3.500A) removed outlier: 4.309A 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 Proline residue: SF 108 - end of helix Processing helix chain 'SF' and resid 181 through 193 removed outlier: 3.859A pdb=" N ALASF 191 " --> pdb=" O HISSF 187 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYSSF 192 " --> pdb=" O LYSSF 188 " (cutoff:3.500A) Processing helix chain 'SF' and resid 200 through 205 removed outlier: 3.811A pdb=" N METSF 204 " --> pdb=" O ARGSF 200 " (cutoff:3.500A) removed outlier: 5.050A 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: 3.639A pdb=" N ALASG 68 " --> pdb=" O ARGSG 64 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N THRSG 69 " --> pdb=" O LYSSG 65 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VALSG 70 " --> pdb=" O GLUSG 66 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ARGSG 71 " --> pdb=" O LEUSG 67 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THRSG 72 " --> pdb=" O ALASG 68 " (cutoff:3.500A) Processing helix chain 'SG' and resid 150 through 166 removed outlier: 3.607A pdb=" N THRSG 165 " --> pdb=" O ILESG 161 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N THRSG 166 " --> pdb=" O GLNSG 162 " (cutoff:3.500A) Processing helix chain 'SG' and resid 171 through 176 removed outlier: 4.242A pdb=" N LEUSG 176 " --> pdb=" O ILESG 172 " (cutoff:3.500A) Processing helix chain 'SK' and resid 12 through 17 removed outlier: 4.214A pdb=" N PHESK 16 " --> pdb=" O GLUSK 12 " (cutoff:3.500A) Processing helix chain 'SK' and resid 32 through 42 removed outlier: 3.507A pdb=" N PHESK 38 " --> pdb=" O PHESK 34 " (cutoff:3.500A) Processing helix chain 'SK' and resid 58 through 63 removed outlier: 3.873A 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: 3.812A pdb=" N GLYSK 196 " --> pdb=" O VALSK 192 " (cutoff:3.500A) Processing helix chain 'SK' and resid 211 through 223 removed outlier: 4.444A pdb=" N LYSSK 223 " --> pdb=" O GLUSK 219 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 20 through 37 Processing helix chain 'SQ' and resid 50 through 61 removed outlier: 3.969A pdb=" N LYSSQ 54 " --> pdb=" O ASNSQ 50 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ASPSQ 55 " --> pdb=" O SERSQ 51 " (cutoff:3.500A) removed outlier: 4.145A 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: 4.149A pdb=" N VALSQ 92 " --> pdb=" O ASNSQ 88 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYSSQ 94 " --> pdb=" O HISSQ 90 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARGSQ 95 " --> pdb=" O GLNSQ 91 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEUSQ 96 " --> pdb=" O VALSQ 92 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ARGSQ 97 " --> pdb=" O SERSQ 93 " (cutoff:3.500A) Processing helix chain 'SQ' and resid 108 through 120 removed outlier: 5.200A pdb=" N THRSQ 120 " --> pdb=" O PHESQ 116 " (cutoff:3.500A) Processing helix chain 'SR' and resid 397 through 406 removed outlier: 4.225A pdb=" N GLYSR 406 " --> pdb=" O GLUSR 402 " (cutoff:3.500A) Processing helix chain 'SR' and resid 412 through 417 removed outlier: 4.934A pdb=" N TYRSR 416 " --> pdb=" O ASPSR 412 " (cutoff:3.500A) removed outlier: 4.570A 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: 4.349A pdb=" N LYSSR 425 " --> pdb=" O ASNSR 421 " (cutoff:3.500A) removed outlier: 5.203A 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 442 removed outlier: 3.893A pdb=" N TYRSR 441 " --> pdb=" O ASNSR 437 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILESR 442 " --> pdb=" O ILESR 438 " (cutoff:3.500A) No H-bonds generated for 'chain 'SR' and resid 437 through 442' Processing helix chain 'SR' and resid 445 through 464 removed outlier: 3.759A pdb=" N LYSSR 449 " --> pdb=" O ALASR 445 " (cutoff:3.500A) Processing helix chain 'SR' and resid 474 through 503 removed outlier: 4.874A pdb=" N LEUSR 478 " --> pdb=" O ASPSR 474 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLNSR 486 " --> pdb=" O GLNSR 482 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N THRSR 503 " --> pdb=" O LYSSR 499 " (cutoff:3.500A) Processing helix chain 'SR' and resid 509 through 514 removed outlier: 4.865A pdb=" N LYSSR 514 " --> pdb=" O ARGSR 510 " (cutoff:3.500A) Processing helix chain 'SR' and resid 516 through 528 removed outlier: 3.875A pdb=" N LEUSR 527 " --> pdb=" O GLUSR 523 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLYSR 528 " --> pdb=" O METSR 524 " (cutoff:3.500A) Processing helix chain 'SR' and resid 537 through 551 removed outlier: 3.778A pdb=" N SERSR 548 " --> pdb=" O ARGSR 544 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILESR 549 " --> pdb=" O ARGSR 545 " (cutoff:3.500A) Processing helix chain 'SR' and resid 574 through 579 removed outlier: 4.373A pdb=" N GLYSR 579 " --> pdb=" O ARGSR 575 " (cutoff:3.500A) Processing helix chain 'SR' and resid 582 through 604 removed outlier: 3.574A pdb=" N GLNSR 597 " --> pdb=" O METSR 593 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYSSR 598 " --> pdb=" O LYSSR 594 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LYSSR 599 " --> pdb=" O ASNSR 595 " (cutoff:3.500A) removed outlier: 5.141A 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: 3.577A pdb=" N LYSSV 43 " --> pdb=" O ASNSV 39 " (cutoff:3.500A) Processing helix chain 'SV' and resid 45 through 50 removed outlier: 5.623A 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: 4.362A pdb=" N GLUSV 70 " --> pdb=" O ASPSV 66 " (cutoff:3.500A) removed outlier: 4.580A 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: 3.911A pdb=" N TRPSV 86 " --> pdb=" O GLNSV 82 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASPSV 91 " --> pdb=" O ASNSV 87 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARGSV 111 " --> pdb=" O PHESV 107 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYSSV 114 " --> pdb=" O ASNSV 110 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ASNSV 115 " --> pdb=" O ARGSV 111 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N LYSSV 116 " --> pdb=" O LEUSV 112 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLUSV 117 " --> pdb=" O LYSSV 113 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYSSV 128 " --> pdb=" O ILESV 124 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'BE' and resid 34 through 37 removed outlier: 5.952A pdb=" N PHEBE 34 " --> pdb=" O VALBE 89 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ILEBE 135 " --> pdb=" O ARGBE 90 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N METBE 136 " --> pdb=" O METBE 52 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N CYSBE 49 " --> pdb=" O SERBE 168 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ARGBE 162 " --> pdb=" O ASPBE 55 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'BE' and resid 189 through 192 removed outlier: 5.461A pdb=" N ARGBE 189 " --> pdb=" O ILEBE 200 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'L5' and resid 48 through 51 removed outlier: 3.604A pdb=" N ALAL5 69 " --> pdb=" O SERL5 51 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ILEL5 68 " --> pdb=" O VALL5 26 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYSL5 19 " --> pdb=" O VALL5 133 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N CYSL5 25 " --> pdb=" O GLYL5 127 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N GLYL5 127 " --> pdb=" O CYSL5 25 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'L6' and resid 57 through 60 Processing sheet with id= 5, first strand: chain 'L7' and resid 6 through 10 Processing sheet with id= 6, first strand: chain 'L8' and resid 11 through 15 removed outlier: 4.569A pdb=" N ARGL8 11 " --> pdb=" O ILEL8 27 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LYSL8 23 " --> pdb=" O VALL8 15 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'L8' and resid 28 through 31 removed outlier: 6.595A pdb=" N ARGL8 35 " --> pdb=" O ILEL8 31 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'L9' and resid 35 through 39 removed outlier: 6.420A pdb=" N ALAL9 35 " --> pdb=" O ARGL9 65 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ILEL9 61 " --> pdb=" O ALAL9 39 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLYL9 58 " --> pdb=" O ASPL9 136 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N PHEL9 129 " --> pdb=" O VALL9 121 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASNL9 117 " --> pdb=" O ILEL9 133 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'LA' and resid 13 through 20 removed outlier: 7.095A pdb=" N LYSLA 13 " --> pdb=" O GLULA 152 " (cutoff:3.500A) removed outlier: 6.685A 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: 5.407A 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: 3.998A pdb=" N ARGLA 127 " --> pdb=" O TYRLA 139 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ARGLA 135 " --> pdb=" O ARGLA 131 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'LB' and resid 78 through 82 Processing sheet with id= 14, first strand: chain 'LB' and resid 98 through 101 Processing sheet with id= 15, first strand: chain 'LC' and resid 27 through 33 removed outlier: 6.444A pdb=" N VALLC 13 " --> pdb=" O VALLC 62 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'LC' and resid 90 through 99 removed outlier: 4.204A pdb=" N ASNLC 77 " --> pdb=" O ILELC 132 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'LC' and resid 9 through 13 removed outlier: 4.639A pdb=" N GLULC 9 " --> pdb=" O VALLC 67 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'LE' and resid 39 through 42 removed outlier: 3.848A pdb=" N LYSLE 60 " --> pdb=" O ILELE 42 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'LE' and resid 72 through 79 Processing sheet with id= 20, first strand: chain 'LF' and resid 61 through 65 removed outlier: 5.887A pdb=" N GLULF 108 " --> pdb=" O LYSLF 20 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'LG' and resid 36 through 39 removed outlier: 5.002A pdb=" N ALALG 24 " --> pdb=" O ILELG 39 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ASNLG 101 " --> pdb=" O VALLG 25 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ASPLG 100 " --> pdb=" O ARGLG 85 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARGLG 85 " --> pdb=" O ASPLG 100 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'LG' and resid 60 through 63 Processing sheet with id= 23, first strand: chain 'LG' and resid 87 through 90 removed outlier: 3.928A pdb=" N VALLG 94 " --> pdb=" O ARGLG 90 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'LH' and resid 95 through 100 removed outlier: 4.021A pdb=" N LYSLH 134 " --> pdb=" O VALLH 100 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYSLH 123 " --> pdb=" O ARGLH 139 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'LI' and resid 53 through 56 removed outlier: 4.643A pdb=" N ASPLI 53 " --> pdb=" O VALLI 70 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'LI' and resid 72 through 75 Processing sheet with id= 27, first strand: chain 'LI' and resid 86 through 89 removed outlier: 4.367A pdb=" N THRLI 93 " --> pdb=" O LYSLI 89 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'LJ' and resid 10 through 14 removed outlier: 4.143A pdb=" N ARGLJ 21 " --> pdb=" O VALLJ 13 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'LJ' and resid 27 through 30 removed outlier: 6.102A pdb=" N HISLJ 40 " --> pdb=" O ILELJ 29 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'LL' and resid 48 through 53 removed outlier: 5.309A pdb=" N THRLL 48 " --> pdb=" O LYSLL 65 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N SERLL 76 " --> pdb=" O ARGLL 66 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'LN' and resid 45 through 50 removed outlier: 4.869A pdb=" N ARGLN 343 " --> pdb=" O LYSLN 50 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VALLN 344 " --> pdb=" O VALLN 222 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N VALLN 222 " --> pdb=" O VALLN 344 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'LN' and resid 53 through 59 removed outlier: 3.639A pdb=" N PHELN 330 " --> pdb=" O GLYLN 288 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYSLN 286 " --> pdb=" O METLN 332 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'LN' and resid 98 through 102 removed outlier: 6.577A pdb=" N GLYLN 91 " --> pdb=" O PHELN 102 " (cutoff:3.500A) removed outlier: 3.604A 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: 4.947A pdb=" N HISLN 179 " --> pdb=" O THRLN 166 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ILELN 160 " --> pdb=" O VALLN 185 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILELN 163 " --> pdb=" O VALLN 87 " (cutoff:3.500A) removed outlier: 3.994A 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 removed outlier: 3.746A pdb=" N VALLN 159 " --> pdb=" O TYRLN 92 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'LN' and resid 215 through 218 removed outlier: 4.220A pdb=" N GLULN 215 " --> pdb=" O ILELN 284 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'LO' and resid 26 through 29 removed outlier: 6.270A pdb=" N LYSLO 26 " --> pdb=" O ILELO 97 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEULO 45 " --> pdb=" O ILELO 96 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLYLO 70 " --> pdb=" O LYSLO 44 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'LP' and resid 61 through 64 removed outlier: 4.742A pdb=" N ASPLP 61 " --> pdb=" O LEULP 102 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VALLP 21 " --> pdb=" O ARGLP 90 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N THRLP 22 " --> pdb=" O VALLP 122 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'LQ' and resid 74 through 80 Processing sheet with id= 40, first strand: chain 'LR' and resid 20 through 24 Processing sheet with id= 41, first strand: chain 'LT' and resid 46 through 49 removed outlier: 5.040A pdb=" N ARGLT 46 " --> pdb=" O METLT 104 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N LYSLT 8 " --> pdb=" O GLULT 31 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEULT 27 " --> pdb=" O ALALT 12 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N METLT 83 " --> pdb=" O HISLT 78 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARGLT 76 " --> pdb=" O ARGLT 85 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'LT' and resid 56 through 60 removed outlier: 5.795A pdb=" N THRLT 57 " --> pdb=" O PROLT 64 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THRLT 59 " --> pdb=" O GLYLT 62 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'LV' and resid 7 through 10 removed outlier: 5.701A pdb=" N VALLV 67 " --> pdb=" O TYRLV 26 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'LX' and resid 47 through 50 removed outlier: 6.954A pdb=" N ILELX 54 " --> pdb=" O ARGLX 50 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLYLX 53 " --> pdb=" O GLYLX 66 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYSLX 62 " --> pdb=" O CYSLX 57 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'LY' and resid 2 through 5 removed outlier: 4.825A pdb=" N VALLY 46 " --> pdb=" O ILELY 5 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SERLY 22 " --> pdb=" O ARGLY 37 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LYSLY 27 " --> pdb=" O LEULY 69 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'SA' and resid 7 through 10 removed outlier: 4.781A 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: 5.467A 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: 3.565A pdb=" N TYRSB 145 " --> pdb=" O TYRSB 49 " (cutoff:3.500A) removed outlier: 3.587A 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 removed outlier: 3.549A pdb=" N ARGSC 105 " --> pdb=" O LYSSC 94 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'SC' and resid 148 through 153 removed outlier: 4.372A pdb=" N THRSC 148 " --> pdb=" O PHESC 164 " (cutoff:3.500A) removed outlier: 4.086A 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: 7.538A pdb=" N TYRSD 139 " --> pdb=" O ILESD 95 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LYSSD 88 " --> pdb=" O LEUSD 125 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ASNSD 119 " --> pdb=" O ARGSD 94 " (cutoff:3.500A) removed outlier: 5.848A 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 removed outlier: 3.663A pdb=" N LEUSE 154 " --> pdb=" O PHESE 204 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'SF' and resid 47 through 50 removed outlier: 3.739A pdb=" N ASPSF 47 " --> pdb=" O LYSSF 60 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LYSSF 60 " --> pdb=" O LYSSF 46 " (cutoff:3.500A) removed outlier: 4.374A 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: 4.082A pdb=" N THRSF 111 " --> pdb=" O VALSF 136 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ARGSF 147 " --> pdb=" O ILESF 137 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYSSF 145 " --> pdb=" O ASNSF 140 " (cutoff:3.500A) removed outlier: 3.698A 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: 4.327A 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: 4.574A 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: 6.626A 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: 5.868A pdb=" N GLUSG 143 " --> pdb=" O SERSG 137 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ASPSG 142 " --> pdb=" O SERSG 94 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LYSSG 91 " --> pdb=" O SERSG 182 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'SG' and resid 87 through 91 removed outlier: 3.535A pdb=" N GLYSG 87 " --> pdb=" O VALSG 187 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'SK' and resid 1 through 5 Processing sheet with id= 64, first strand: chain 'SK' and resid 23 through 27 Processing sheet with id= 65, first strand: chain 'SK' and resid 69 through 73 Processing sheet with id= 66, first strand: chain 'SK' and resid 114 through 117 Processing sheet with id= 67, first strand: chain 'SK' and resid 158 through 161 Processing sheet with id= 68, first strand: chain 'SQ' and resid 63 through 67 removed outlier: 3.502A pdb=" N THRSQ 105 " --> pdb=" O TYRSQ 39 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ILESQ 42 " --> pdb=" O LYSSQ 205 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THRSQ 203 " --> pdb=" O SERSQ 44 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'SQ' and resid 213 through 217 removed outlier: 3.510A pdb=" N ARGSQ 214 " --> pdb=" O ASPSQ 209 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'SQ' and resid 38 through 42 removed outlier: 7.971A pdb=" N LYSSQ 38 " --> pdb=" O SERSQ 210 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYRSQ 206 " --> pdb=" O ILESQ 42 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'SV' and resid 3 through 6 removed outlier: 4.353A pdb=" N GLYSV 11 " --> pdb=" O CYSSV 6 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'SV' and resid 18 through 22 2222 hydrogen bonds defined for protein. 6594 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2953 hydrogen bonds 5050 hydrogen bond angles 0 basepair planarities 1116 basepair parallelities 1746 stacking parallelities Total time for adding SS restraints: 237.48 Time building geometry restraints manager: 57.36 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: 14043 1.31 - 1.44: 60181 1.44 - 1.56: 62963 1.56 - 1.69: 7184 1.69 - 1.81: 413 Bond restraints: 144784 Sorted by residual: bond pdb=" C2' A2ML31326 " pdb=" C1' A2ML31326 " ideal model delta sigma weight residual 1.305 1.555 -0.250 2.00e-02 2.50e+03 1.56e+02 bond pdb=" C2' A2ML32815 " pdb=" C1' A2ML32815 " ideal model delta sigma weight residual 1.305 1.553 -0.248 2.00e-02 2.50e+03 1.53e+02 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' A2ML34523 " pdb=" C1' A2ML34523 " ideal model delta sigma weight residual 1.305 1.552 -0.247 2.00e-02 2.50e+03 1.52e+02 bond pdb=" C2' A2ML31524 " pdb=" C1' A2ML31524 " ideal model delta sigma weight residual 1.305 1.550 -0.245 2.00e-02 2.50e+03 1.51e+02 ... (remaining 144779 not shown) Histogram of bond angle deviations from ideal: 87.12 - 96.76: 14 96.76 - 106.39: 22032 106.39 - 116.02: 98456 116.02 - 125.66: 79403 125.66 - 135.29: 12819 Bond angle restraints: 212724 Sorted by residual: angle pdb=" C1' A2ML34590 " pdb=" N9 A2ML34590 " pdb=" C8 A2ML34590 " ideal model delta sigma weight residual 88.50 127.61 -39.11 3.00e+00 1.11e-01 1.70e+02 angle pdb=" C1' A2ML33867 " pdb=" N9 A2ML33867 " pdb=" C8 A2ML33867 " ideal model delta sigma weight residual 88.50 127.15 -38.65 3.00e+00 1.11e-01 1.66e+02 angle pdb=" C1' A2ML32787 " pdb=" N9 A2ML32787 " pdb=" C8 A2ML32787 " ideal model delta sigma weight residual 88.50 127.08 -38.58 3.00e+00 1.11e-01 1.65e+02 angle pdb=" C1' A2ML31871 " pdb=" N9 A2ML31871 " pdb=" C8 A2ML31871 " ideal model delta sigma weight residual 88.50 126.63 -38.13 3.00e+00 1.11e-01 1.62e+02 angle pdb=" C1' A2ML31524 " pdb=" N9 A2ML31524 " pdb=" C8 A2ML31524 " ideal model delta sigma weight residual 88.50 126.60 -38.10 3.00e+00 1.11e-01 1.61e+02 ... (remaining 212719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 83988 35.90 - 71.80: 8211 71.80 - 107.70: 1265 107.70 - 143.60: 14 143.60 - 179.51: 10 Dihedral angle restraints: 93488 sinusoidal: 72845 harmonic: 20643 Sorted by residual: dihedral pdb=" O4' CL34303 " pdb=" C1' CL34303 " pdb=" N1 CL34303 " pdb=" C2 CL34303 " ideal model delta sinusoidal sigma weight residual 200.00 31.80 168.20 1 1.50e+01 4.44e-03 8.44e+01 dihedral pdb=" O4' UL33641 " pdb=" C1' UL33641 " pdb=" N1 UL33641 " pdb=" C2 UL33641 " ideal model delta sinusoidal sigma weight residual 200.00 40.20 159.80 1 1.50e+01 4.44e-03 8.27e+01 dihedral pdb=" O4' UL34512 " pdb=" C1' UL34512 " pdb=" N1 UL34512 " pdb=" C2 UL34512 " ideal model delta sinusoidal sigma weight residual 232.00 52.49 179.51 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 93485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 25186 0.084 - 0.169: 924 0.169 - 0.253: 44 0.253 - 0.337: 5 0.337 - 0.422: 15 Chirality restraints: 26174 Sorted by residual: chirality pdb=" C2' A2ML32363 " pdb=" C3' A2ML32363 " pdb=" O2' A2ML32363 " pdb=" C1' A2ML32363 " both_signs ideal model delta sigma weight residual False -2.39 -2.81 0.42 2.00e-01 2.50e+01 4.45e+00 chirality pdb=" C2' A2ML3 398 " pdb=" C3' A2ML3 398 " pdb=" O2' A2ML3 398 " pdb=" C1' A2ML3 398 " both_signs ideal model delta sigma weight residual False -2.39 -2.80 0.41 2.00e-01 2.50e+01 4.23e+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 0.41 2.00e-01 2.50e+01 4.17e+00 ... (remaining 26171 not shown) Planarity restraints: 13566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMGL34228 " 0.907 2.00e-02 2.50e+03 6.10e-01 8.36e+03 pdb=" C4' OMGL34228 " -0.212 2.00e-02 2.50e+03 pdb=" O4' OMGL34228 " -0.704 2.00e-02 2.50e+03 pdb=" C3' OMGL34228 " 0.191 2.00e-02 2.50e+03 pdb=" O3' OMGL34228 " -0.966 2.00e-02 2.50e+03 pdb=" C2' OMGL34228 " 0.622 2.00e-02 2.50e+03 pdb=" O2' OMGL34228 " 0.652 2.00e-02 2.50e+03 pdb=" C1' OMGL34228 " -0.447 2.00e-02 2.50e+03 pdb=" N9 OMGL34228 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMGL34494 " -0.050 2.00e-02 2.50e+03 6.09e-01 8.33e+03 pdb=" C4' OMGL34494 " -0.456 2.00e-02 2.50e+03 pdb=" O4' OMGL34494 " -0.729 2.00e-02 2.50e+03 pdb=" C3' OMGL34494 " 0.595 2.00e-02 2.50e+03 pdb=" O3' OMGL34494 " 0.618 2.00e-02 2.50e+03 pdb=" C2' OMGL34494 " 0.210 2.00e-02 2.50e+03 pdb=" O2' OMGL34494 " -0.935 2.00e-02 2.50e+03 pdb=" C1' OMGL34494 " -0.200 2.00e-02 2.50e+03 pdb=" N9 OMGL34494 " 0.948 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMCL33887 " 0.018 2.00e-02 2.50e+03 6.04e-01 8.22e+03 pdb=" C4' OMCL33887 " 0.474 2.00e-02 2.50e+03 pdb=" O4' OMCL33887 " 0.829 2.00e-02 2.50e+03 pdb=" C3' OMCL33887 " -0.576 2.00e-02 2.50e+03 pdb=" O3' OMCL33887 " -0.552 2.00e-02 2.50e+03 pdb=" C2' OMCL33887 " -0.258 2.00e-02 2.50e+03 pdb=" O2' OMCL33887 " 0.843 2.00e-02 2.50e+03 pdb=" C1' OMCL33887 " 0.185 2.00e-02 2.50e+03 pdb=" N1 OMCL33887 " -0.963 2.00e-02 2.50e+03 ... (remaining 13563 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 590 2.52 - 3.11: 91472 3.11 - 3.71: 238958 3.71 - 4.30: 360077 4.30 - 4.90: 504966 Nonbonded interactions: 1196063 Sorted by model distance: nonbonded pdb=" OG1 THRSE 106 " pdb=" OE1 GLUSE 109 " model vdw 1.925 2.440 nonbonded pdb=" OP2 AL31337 " pdb="MG MGL35110 " model vdw 1.929 2.170 nonbonded pdb=" O THRLT 67 " pdb="MG MGLT 201 " model vdw 1.931 2.170 nonbonded pdb=" O1P 6MZL34220 " pdb=" OG1 THRLE 2 " model vdw 1.937 2.440 nonbonded pdb=" O2' CL31480 " pdb=" OP2 GL31482 " model vdw 1.961 2.440 ... (remaining 1196058 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: 5.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 26.350 Check model and map are aligned: 1.540 Set scattering table: 0.970 Process input model: 535.970 Find NCS groups from input model: 3.060 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 585.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 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 0.250 144784 Z= 0.424 Angle : 0.773 39.106 212724 Z= 0.332 Chirality : 0.036 0.422 26174 Planarity : 0.027 0.610 13566 Dihedral : 22.207 179.506 80158 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.78 % 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: 0.65 (0.10), residues: 7019 helix: 0.94 (0.10), residues: 2456 sheet: 0.58 (0.16), residues: 982 loop : 0.15 (0.10), residues: 3581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRPSV 86 HIS 0.009 0.001 HISLN 258 PHE 0.016 0.001 PHEL5 130 TYR 0.027 0.001 TYRSE 60 ARG 0.011 0.001 ARGLX 85 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14038 Ramachandran restraints generated. 7019 Oldfield, 0 Emsley, 7019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14038 Ramachandran restraints generated. 7019 Oldfield, 0 Emsley, 7019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1391 residues out of total 6155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1391 time to evaluate : 7.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BE 136 MET cc_start: 0.7446 (ttm) cc_final: 0.7128 (ttm) REVERT: BE 184 MET cc_start: 0.7492 (mtt) cc_final: 0.7275 (mtp) REVERT: L6 146 LEU cc_start: 0.8576 (mt) cc_final: 0.8373 (pp) REVERT: LB 4 ASP cc_start: 0.7591 (t70) cc_final: 0.7193 (t0) REVERT: LD 37 SER cc_start: 0.8606 (p) cc_final: 0.8330 (m) REVERT: LH 36 LYS cc_start: 0.6668 (ptmt) cc_final: 0.6420 (mptt) REVERT: LJ 5 MET cc_start: 0.6924 (mmm) cc_final: 0.6652 (mmt) REVERT: LK 58 MET cc_start: 0.9253 (ptt) cc_final: 0.8991 (ptt) REVERT: LL 108 MET cc_start: 0.8620 (mmm) cc_final: 0.8406 (mmp) REVERT: LM 36 ASP cc_start: 0.8022 (t70) cc_final: 0.7761 (t70) REVERT: LM 54 LEU cc_start: 0.8186 (tp) cc_final: 0.7820 (tt) REVERT: LM 65 MET cc_start: 0.4573 (mmp) cc_final: 0.4285 (ttp) REVERT: LN 332 MET cc_start: 0.7912 (ttm) cc_final: 0.7557 (ttm) REVERT: LQ 84 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7652 (mt-10) REVERT: LQ 95 TYR cc_start: 0.8724 (m-80) cc_final: 0.8424 (m-80) REVERT: LT 42 TYR cc_start: 0.8539 (m-80) cc_final: 0.8322 (m-80) REVERT: SA 11 TYR cc_start: 0.8126 (m-80) cc_final: 0.7855 (m-80) REVERT: SA 281 MET cc_start: 0.8254 (mmm) cc_final: 0.7985 (mmt) REVERT: SA 284 MET cc_start: 0.8195 (ttt) cc_final: 0.7922 (ttt) REVERT: SB 215 ASP cc_start: 0.6232 (t0) cc_final: 0.5894 (t0) REVERT: SB 272 SER cc_start: 0.8711 (t) cc_final: 0.8481 (m) REVERT: SC 56 ARG cc_start: 0.7746 (ttm-80) cc_final: 0.7409 (tmt170) REVERT: SE 149 ASN cc_start: 0.8220 (m-40) cc_final: 0.7897 (m110) REVERT: SF 73 THR cc_start: 0.8502 (t) cc_final: 0.8273 (m) REVERT: SK 225 ASN cc_start: 0.6564 (p0) cc_final: 0.6263 (OUTLIER) REVERT: SR 514 LYS cc_start: 0.6952 (tppt) cc_final: 0.6723 (ttmm) REVERT: SR 520 LEU cc_start: 0.8526 (tp) cc_final: 0.8233 (tp) outliers start: 0 outliers final: 2 residues processed: 1391 average time/residue: 2.2382 time to fit residues: 4311.8210 Evaluate side-chains 953 residues out of total 6155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 952 time to evaluate : 7.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LL residue 125 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1052 random chunks: chunk 888 optimal weight: 0.4980 chunk 797 optimal weight: 7.9990 chunk 442 optimal weight: 5.9990 chunk 272 optimal weight: 0.7980 chunk 537 optimal weight: 0.5980 chunk 425 optimal weight: 2.9990 chunk 824 optimal weight: 3.9990 chunk 319 optimal weight: 7.9990 chunk 501 optimal weight: 2.9990 chunk 613 optimal weight: 4.9990 chunk 955 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 L6 104 ASN L6 111 GLN L6 149 GLN L6 159 ASN L7 173 GLN L9 15 GLN L9 86 HIS LC 23 HIS LC 37 HIS LC 122 HIS LE 144 ASN LF 50 ASN LG 27 ASN LG 36 ASN LH 107 HIS LH 108 GLN LH 111 GLN LI 86 GLN LK 66 ASN LK 67 GLN LM 49 HIS LM 60 ASN LN 322 HIS LO 72 HIS LQ 117 GLN LS 107 GLN LW 57 ASN LX 72 ASN LZ 20 ASN NP 13 HIS NP 91 GLN NP 99 GLN SA 236 ASN SC 136 HIS SC 190 HIS SC 211 HIS SD 24 ASN SD 63 GLN ** SE 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SE 112 GLN SF 8 GLN SF 86 GLN SF 95 GLN SK 83 HIS ** SR 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SV 17 HIS SV 67 ASN SV 122 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 144784 Z= 0.160 Angle : 0.714 20.149 212724 Z= 0.385 Chirality : 0.033 0.298 26174 Planarity : 0.007 0.134 13566 Dihedral : 23.247 179.343 65086 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.62 % Allowed : 10.33 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.78 % 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: 1.02 (0.10), residues: 7019 helix: 1.53 (0.10), residues: 2548 sheet: 0.61 (0.16), residues: 982 loop : 0.15 (0.10), residues: 3489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRPLW 49 HIS 0.005 0.001 HISLA 25 PHE 0.014 0.001 PHELF 42 TYR 0.027 0.001 TYRBE 75 ARG 0.009 0.000 ARGNK 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14038 Ramachandran restraints generated. 7019 Oldfield, 0 Emsley, 7019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14038 Ramachandran restraints generated. 7019 Oldfield, 0 Emsley, 7019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1154 residues out of total 6155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 996 time to evaluate : 7.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L5 110 GLN cc_start: 0.8210 (mp10) cc_final: 0.7981 (mp10) REVERT: L6 208 GLU cc_start: 0.3007 (OUTLIER) cc_final: 0.2768 (mt-10) REVERT: L8 50 MET cc_start: 0.8327 (ttm) cc_final: 0.7922 (ttm) REVERT: L8 121 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.8109 (mtt90) REVERT: L9 193 ARG cc_start: 0.7200 (OUTLIER) cc_final: 0.6962 (mtp180) REVERT: LB 4 ASP cc_start: 0.7578 (t70) cc_final: 0.7188 (t0) REVERT: LB 14 ARG cc_start: 0.7612 (mtm-85) cc_final: 0.7362 (mtm-85) REVERT: LB 40 ASN cc_start: 0.8351 (p0) cc_final: 0.8084 (p0) REVERT: LG 92 ASP cc_start: 0.7108 (p0) cc_final: 0.6719 (p0) REVERT: LH 36 LYS cc_start: 0.6662 (ptmt) cc_final: 0.6387 (mptt) REVERT: LK 58 MET cc_start: 0.9195 (ptt) cc_final: 0.8925 (ptt) REVERT: LL 28 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7434 (pt0) REVERT: LL 108 MET cc_start: 0.8555 (mmm) cc_final: 0.8245 (tpp) REVERT: LN 199 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6934 (tt0) REVERT: LN 332 MET cc_start: 0.7980 (ttm) cc_final: 0.7610 (ttm) REVERT: LN 399 LYS cc_start: 0.6928 (tptt) cc_final: 0.6661 (tptp) REVERT: LQ 95 TYR cc_start: 0.8730 (m-80) cc_final: 0.8487 (m-80) REVERT: LU 98 ARG cc_start: 0.7084 (ttm110) cc_final: 0.6743 (ttp-170) REVERT: NP 22 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8245 (ptpp) REVERT: SA 281 MET cc_start: 0.8245 (mmm) cc_final: 0.7994 (mmp) REVERT: SA 284 MET cc_start: 0.8255 (ttt) cc_final: 0.7991 (ttt) REVERT: SC 135 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.7862 (mt0) REVERT: SF 73 THR cc_start: 0.8445 (t) cc_final: 0.8238 (m) REVERT: SK 1 MET cc_start: 0.5950 (ttt) cc_final: 0.4147 (mmm) REVERT: SK 134 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.7951 (mttt) REVERT: SK 225 ASN cc_start: 0.6538 (p0) cc_final: 0.6298 (OUTLIER) REVERT: SR 475 GLU cc_start: 0.7207 (tm-30) cc_final: 0.6372 (tp30) REVERT: SR 520 LEU cc_start: 0.8634 (tp) cc_final: 0.8391 (tp) REVERT: SV 128 LYS cc_start: 0.7679 (OUTLIER) cc_final: 0.7378 (mmmt) outliers start: 158 outliers final: 60 residues processed: 1052 average time/residue: 2.1044 time to fit residues: 3163.0277 Evaluate side-chains 958 residues out of total 6155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 890 time to evaluate : 7.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BE residue 168 SER Chi-restraints excluded: chain L5 residue 49 VAL Chi-restraints excluded: chain L6 residue 4 SER Chi-restraints excluded: chain L6 residue 52 SER Chi-restraints excluded: chain L6 residue 107 THR Chi-restraints excluded: chain L6 residue 140 SER Chi-restraints excluded: chain L6 residue 208 GLU Chi-restraints excluded: chain L8 residue 121 ARG Chi-restraints excluded: chain L9 residue 89 VAL Chi-restraints excluded: chain L9 residue 126 THR Chi-restraints excluded: chain L9 residue 193 ARG Chi-restraints excluded: chain LB residue 100 VAL Chi-restraints excluded: chain LB residue 122 THR Chi-restraints excluded: chain LD residue 29 THR Chi-restraints excluded: chain LF residue 66 SER Chi-restraints excluded: chain LF residue 71 THR Chi-restraints excluded: chain LF residue 76 VAL Chi-restraints excluded: chain LG residue 87 SER Chi-restraints excluded: chain LG residue 138 SER Chi-restraints excluded: chain LH residue 40 ILE Chi-restraints excluded: chain LH residue 42 THR Chi-restraints excluded: chain LI residue 118 ILE Chi-restraints excluded: chain LL residue 5 LEU Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LL residue 80 THR Chi-restraints excluded: chain LL residue 81 THR Chi-restraints excluded: chain LL residue 125 MET Chi-restraints excluded: chain LN residue 199 GLU Chi-restraints excluded: chain LP residue 40 LYS Chi-restraints excluded: chain LP residue 57 MET Chi-restraints excluded: chain LP residue 66 THR Chi-restraints excluded: chain LQ residue 17 THR Chi-restraints excluded: chain LQ residue 25 SER Chi-restraints excluded: chain LQ residue 26 ASP Chi-restraints excluded: chain LQ residue 72 SER Chi-restraints excluded: chain LR residue 17 SER Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 57 THR Chi-restraints excluded: chain LT residue 83 MET Chi-restraints excluded: chain LT residue 90 SER Chi-restraints excluded: chain LT residue 108 SER Chi-restraints excluded: chain LV residue 99 ARG Chi-restraints excluded: chain LV residue 103 VAL Chi-restraints excluded: chain LX residue 16 THR Chi-restraints excluded: chain LX residue 45 THR Chi-restraints excluded: chain LX residue 70 THR Chi-restraints excluded: chain LX residue 78 THR Chi-restraints excluded: chain NP residue 22 LYS Chi-restraints excluded: chain NP residue 93 SER Chi-restraints excluded: chain NP residue 101 GLU Chi-restraints excluded: chain SA residue 214 ASP Chi-restraints excluded: chain SA residue 297 GLU Chi-restraints excluded: chain SA residue 335 MET Chi-restraints excluded: chain SB residue 136 ASP Chi-restraints excluded: chain SC residue 49 VAL Chi-restraints excluded: chain SC residue 135 GLN Chi-restraints excluded: chain SD residue 220 MET Chi-restraints excluded: chain SE residue 209 SER Chi-restraints excluded: chain SF residue 135 THR Chi-restraints excluded: chain SG residue 17 ASP Chi-restraints excluded: chain SK residue 134 LYS Chi-restraints excluded: chain SK residue 135 VAL Chi-restraints excluded: chain SK residue 169 ASP Chi-restraints excluded: chain SK residue 188 ARG Chi-restraints excluded: chain SR residue 478 LEU Chi-restraints excluded: chain SR residue 536 ASP Chi-restraints excluded: chain SR residue 583 VAL Chi-restraints excluded: chain SV residue 128 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1052 random chunks: chunk 530 optimal weight: 5.9990 chunk 296 optimal weight: 10.0000 chunk 795 optimal weight: 0.9990 chunk 650 optimal weight: 8.9990 chunk 263 optimal weight: 10.0000 chunk 957 optimal weight: 3.9990 chunk 1033 optimal weight: 10.0000 chunk 852 optimal weight: 3.9990 chunk 949 optimal weight: 10.0000 chunk 326 optimal weight: 8.9990 chunk 767 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BE 73 ASN BE 163 GLN L5 168 GLN L6 19 GLN L6 67 HIS L6 111 GLN L6 149 GLN L7 42 ASN L7 90 HIS L7 96 GLN L7 173 GLN L9 8 GLN L9 15 GLN LA 25 HIS LA 34 GLN LA 116 HIS LC 23 HIS LC 173 ASN LD 58 HIS LE 58 HIS LE 144 ASN LF 38 ASN LF 50 ASN LG 36 ASN LG 77 HIS LH 111 GLN LK 66 ASN LL 12 ASN LN 42 HIS LN 123 HIS LP 30 HIS LW 57 ASN LX 56 HIS LX 72 ASN NK 99 GLN NP 91 GLN SB 81 HIS SB 244 HIS SD 63 GLN SD 239 GLN SE 112 GLN SK 75 ASN ** SK 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** SR 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** SR 504 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 144784 Z= 0.393 Angle : 0.782 19.866 212724 Z= 0.413 Chirality : 0.041 0.322 26174 Planarity : 0.008 0.141 13566 Dihedral : 23.220 178.079 65086 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.43 % Allowed : 12.53 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.78 % 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: 0.74 (0.10), residues: 7019 helix: 1.39 (0.10), residues: 2561 sheet: 0.47 (0.16), residues: 959 loop : -0.10 (0.10), residues: 3499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRPSV 86 HIS 0.014 0.002 HISLA 25 PHE 0.022 0.002 PHESR 376 TYR 0.023 0.002 TYRSB 119 ARG 0.010 0.001 ARGLV 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14038 Ramachandran restraints generated. 7019 Oldfield, 0 Emsley, 7019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14038 Ramachandran restraints generated. 7019 Oldfield, 0 Emsley, 7019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1113 residues out of total 6155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 906 time to evaluate : 7.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L5 16 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.7163 (ptm-80) REVERT: L8 50 MET cc_start: 0.8335 (ttm) cc_final: 0.7997 (ttm) REVERT: L8 118 MET cc_start: 0.8295 (tpt) cc_final: 0.7553 (tpt) REVERT: L8 121 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.8172 (mtt90) REVERT: L8 126 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6907 (tp30) REVERT: L9 193 ARG cc_start: 0.7273 (OUTLIER) cc_final: 0.6885 (mtp180) REVERT: LA 107 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7641 (mt) REVERT: LA 125 MET cc_start: 0.7722 (mpp) cc_final: 0.7257 (mtt) REVERT: LB 4 ASP cc_start: 0.7600 (t70) cc_final: 0.7173 (t0) REVERT: LD 113 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7837 (mtmm) REVERT: LF 99 TRP cc_start: 0.8215 (OUTLIER) cc_final: 0.6660 (m100) REVERT: LH 36 LYS cc_start: 0.6721 (ptmt) cc_final: 0.6332 (mptt) REVERT: LJ 81 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7489 (tpt) REVERT: LK 58 MET cc_start: 0.9158 (ptt) cc_final: 0.8895 (ptt) REVERT: LL 28 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7608 (pt0) REVERT: LL 119 ARG cc_start: 0.7806 (ttm-80) cc_final: 0.7331 (ttm-80) REVERT: LN 199 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6968 (tt0) REVERT: LO 44 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7761 (mmtp) REVERT: LQ 86 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7185 (mp0) REVERT: LT 43 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8609 (mp) REVERT: LY 16 ARG cc_start: 0.8284 (tpp-160) cc_final: 0.8065 (tpp-160) REVERT: NP 22 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8334 (pttp) REVERT: SA 11 TYR cc_start: 0.8118 (m-80) cc_final: 0.7822 (m-80) REVERT: SA 268 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.6906 (mtm180) REVERT: SA 281 MET cc_start: 0.8206 (mmm) cc_final: 0.7994 (mmp) REVERT: SA 284 MET cc_start: 0.8348 (ttt) cc_final: 0.8113 (ttt) REVERT: SC 135 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.7946 (mt0) REVERT: SD 232 ASP cc_start: 0.7541 (OUTLIER) cc_final: 0.7206 (t0) REVERT: SK 134 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8034 (mttt) REVERT: SR 475 GLU cc_start: 0.7035 (tm-30) cc_final: 0.6197 (tp30) REVERT: SR 575 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7107 (ptt180) outliers start: 207 outliers final: 101 residues processed: 999 average time/residue: 2.0705 time to fit residues: 2955.9736 Evaluate side-chains 984 residues out of total 6155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 864 time to evaluate : 7.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BE residue 168 SER Chi-restraints excluded: chain BE residue 195 CYS Chi-restraints excluded: chain L5 residue 16 ARG Chi-restraints excluded: chain L5 residue 49 VAL Chi-restraints excluded: chain L6 residue 52 SER Chi-restraints excluded: chain L6 residue 68 THR Chi-restraints excluded: chain L6 residue 107 THR Chi-restraints excluded: chain L6 residue 121 ARG Chi-restraints excluded: chain L6 residue 140 SER Chi-restraints excluded: chain L6 residue 151 THR Chi-restraints excluded: chain L7 residue 174 LEU Chi-restraints excluded: chain L8 residue 121 ARG Chi-restraints excluded: chain L8 residue 126 GLU Chi-restraints excluded: chain L9 residue 80 THR Chi-restraints excluded: chain L9 residue 89 VAL Chi-restraints excluded: chain L9 residue 126 THR Chi-restraints excluded: chain L9 residue 193 ARG Chi-restraints excluded: chain LA residue 107 LEU Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LA residue 142 SER Chi-restraints excluded: chain LB residue 16 LYS Chi-restraints excluded: chain LB residue 100 VAL Chi-restraints excluded: chain LB residue 122 THR Chi-restraints excluded: chain LC residue 24 THR Chi-restraints excluded: chain LC residue 127 MET Chi-restraints excluded: chain LD residue 29 THR Chi-restraints excluded: chain LD residue 113 LYS Chi-restraints excluded: chain LE residue 106 LEU Chi-restraints excluded: chain LF residue 66 SER Chi-restraints excluded: chain LF residue 71 THR Chi-restraints excluded: chain LF residue 83 LEU Chi-restraints excluded: chain LF residue 99 TRP Chi-restraints excluded: chain LG residue 87 SER Chi-restraints excluded: chain LG residue 134 SER Chi-restraints excluded: chain LG residue 138 SER Chi-restraints excluded: chain LH residue 40 ILE Chi-restraints excluded: chain LH residue 42 THR Chi-restraints excluded: chain LI residue 102 SER Chi-restraints excluded: chain LI residue 118 ILE Chi-restraints excluded: chain LJ residue 81 MET Chi-restraints excluded: chain LK residue 76 ASP Chi-restraints excluded: chain LL residue 5 LEU Chi-restraints excluded: chain LL residue 28 GLU Chi-restraints excluded: chain LL residue 61 VAL Chi-restraints excluded: chain LL residue 63 VAL Chi-restraints excluded: chain LL residue 78 VAL Chi-restraints excluded: chain LL residue 80 THR Chi-restraints excluded: chain LL residue 81 THR Chi-restraints excluded: chain LM residue 13 SER Chi-restraints excluded: chain LM residue 26 SER Chi-restraints excluded: chain LN residue 134 CYS Chi-restraints excluded: chain LN residue 199 GLU Chi-restraints excluded: chain LO residue 44 LYS Chi-restraints excluded: chain LP residue 40 LYS Chi-restraints excluded: chain LP residue 57 MET Chi-restraints excluded: chain LP residue 66 THR Chi-restraints excluded: chain LP residue 86 VAL Chi-restraints excluded: chain LQ residue 17 THR Chi-restraints excluded: chain LQ residue 25 SER Chi-restraints excluded: chain LQ residue 26 ASP Chi-restraints excluded: chain LQ residue 53 ILE Chi-restraints excluded: chain LQ residue 72 SER Chi-restraints excluded: chain LQ residue 86 GLU Chi-restraints excluded: chain LR residue 6 THR Chi-restraints excluded: chain LR residue 17 SER Chi-restraints excluded: chain LR residue 30 ILE Chi-restraints excluded: chain LS residue 71 LYS Chi-restraints excluded: chain LT residue 5 LEU Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 43 LEU Chi-restraints excluded: chain LT residue 57 THR Chi-restraints excluded: chain LT residue 90 SER Chi-restraints excluded: chain LT residue 108 SER Chi-restraints excluded: chain LU residue 91 SER Chi-restraints excluded: chain LV residue 23 VAL Chi-restraints excluded: chain LV residue 99 ARG Chi-restraints excluded: chain LV residue 103 VAL Chi-restraints excluded: chain LX residue 16 THR Chi-restraints excluded: chain LX residue 45 THR Chi-restraints excluded: chain LX residue 70 THR Chi-restraints excluded: chain LX residue 73 THR Chi-restraints excluded: chain LX residue 78 THR Chi-restraints excluded: chain LY residue 44 THR Chi-restraints excluded: chain NP residue 22 LYS Chi-restraints excluded: chain NP residue 93 SER Chi-restraints excluded: chain NP residue 101 GLU Chi-restraints excluded: chain SA residue 201 ARG Chi-restraints excluded: chain SA residue 214 ASP Chi-restraints excluded: chain SA residue 268 ARG Chi-restraints excluded: chain SA residue 297 GLU Chi-restraints excluded: chain SA residue 335 MET Chi-restraints excluded: chain SB residue 89 LYS Chi-restraints excluded: chain SB residue 125 VAL Chi-restraints excluded: chain SB residue 136 ASP Chi-restraints excluded: chain SC residue 49 VAL Chi-restraints excluded: chain SC residue 135 GLN Chi-restraints excluded: chain SC residue 212 LEU Chi-restraints excluded: chain SD residue 220 MET Chi-restraints excluded: chain SD residue 232 ASP Chi-restraints excluded: chain SE residue 209 SER Chi-restraints excluded: chain SE residue 246 SER Chi-restraints excluded: chain SF residue 32 VAL Chi-restraints excluded: chain SF residue 45 VAL Chi-restraints excluded: chain SF residue 135 THR Chi-restraints excluded: chain SF residue 158 ILE Chi-restraints excluded: chain SF residue 169 VAL Chi-restraints excluded: chain SG residue 120 GLU Chi-restraints excluded: chain SG residue 126 VAL Chi-restraints excluded: chain SG residue 172 ILE Chi-restraints excluded: chain SK residue 134 LYS Chi-restraints excluded: chain SK residue 135 VAL Chi-restraints excluded: chain SK residue 169 ASP Chi-restraints excluded: chain SK residue 188 ARG Chi-restraints excluded: chain SK residue 225 ASN Chi-restraints excluded: chain SR residue 446 ILE Chi-restraints excluded: chain SR residue 478 LEU Chi-restraints excluded: chain SR residue 526 SER Chi-restraints excluded: chain SR residue 575 ARG Chi-restraints excluded: chain SR residue 583 VAL Chi-restraints excluded: chain SV residue 24 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1052 random chunks: chunk 945 optimal weight: 4.9990 chunk 719 optimal weight: 5.9990 chunk 496 optimal weight: 0.0670 chunk 105 optimal weight: 10.0000 chunk 456 optimal weight: 0.8980 chunk 642 optimal weight: 5.9990 chunk 960 optimal weight: 3.9990 chunk 1016 optimal weight: 0.9980 chunk 501 optimal weight: 0.8980 chunk 910 optimal weight: 1.9990 chunk 274 optimal weight: 7.9990 overall best weight: 0.9720 ------------------------------------------------------------------------------- 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 L6 111 GLN L9 15 GLN LC 23 HIS LD 58 HIS LF 38 ASN LF 41 GLN LF 50 ASN LG 36 ASN LK 66 ASN LW 57 ASN LX 72 ASN SB 244 HIS SF 95 GLN SK 75 ASN SK 178 GLN SR 437 ASN SR 504 GLN SR 612 HIS SV 67 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.078 144784 Z= 0.142 Angle : 0.677 19.731 212724 Z= 0.372 Chirality : 0.033 0.315 26174 Planarity : 0.007 0.127 13566 Dihedral : 23.158 179.187 65083 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.70 % Allowed : 13.95 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.10), residues: 7019 helix: 1.73 (0.10), residues: 2556 sheet: 0.53 (0.17), residues: 943 loop : 0.06 (0.10), residues: 3520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRPL9 120 HIS 0.005 0.001 HISBE 92 PHE 0.016 0.001 PHEL5 130 TYR 0.027 0.001 TYRBE 75 ARG 0.013 0.000 ARGL6 129 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14038 Ramachandran restraints generated. 7019 Oldfield, 0 Emsley, 7019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14038 Ramachandran restraints generated. 7019 Oldfield, 0 Emsley, 7019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1081 residues out of total 6155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 918 time to evaluate : 7.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BE 183 ASP cc_start: 0.7464 (OUTLIER) cc_final: 0.6969 (p0) REVERT: L5 16 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7012 (ptm-80) REVERT: L8 50 MET cc_start: 0.8424 (ttm) cc_final: 0.8024 (ttm) REVERT: L8 126 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6809 (tm-30) REVERT: L8 130 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8172 (mp) REVERT: LA 107 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7576 (mt) REVERT: LA 125 MET cc_start: 0.7652 (mpp) cc_final: 0.7313 (mtt) REVERT: LB 4 ASP cc_start: 0.7582 (t70) cc_final: 0.7179 (t0) REVERT: LD 113 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7857 (ttmm) REVERT: LF 99 TRP cc_start: 0.8039 (OUTLIER) cc_final: 0.6629 (m100) REVERT: LH 36 LYS cc_start: 0.6638 (ptmt) cc_final: 0.6294 (mptt) REVERT: LK 58 MET cc_start: 0.9151 (ptt) cc_final: 0.8912 (ptt) REVERT: LL 119 ARG cc_start: 0.7788 (ttm-80) cc_final: 0.7292 (ttm-80) REVERT: LN 199 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6965 (tt0) REVERT: LQ 33 ARG cc_start: 0.6931 (OUTLIER) cc_final: 0.6565 (ptt-90) REVERT: LQ 84 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7541 (mt-10) REVERT: LQ 86 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6977 (mp0) REVERT: LX 86 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8646 (mp) REVERT: SA 11 TYR cc_start: 0.8148 (m-80) cc_final: 0.7878 (m-80) REVERT: SA 261 ASP cc_start: 0.8464 (m-30) cc_final: 0.8239 (m-30) REVERT: SA 273 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8179 (mp) REVERT: SA 281 MET cc_start: 0.8194 (mmm) cc_final: 0.7915 (mmt) REVERT: SA 284 MET cc_start: 0.8385 (ttt) cc_final: 0.8142 (ttt) REVERT: SC 135 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.7927 (mt0) REVERT: SF 107 MET cc_start: 0.7434 (mtt) cc_final: 0.6676 (mtt) REVERT: SK 134 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8023 (mttt) REVERT: SK 225 ASN cc_start: 0.6525 (p0) cc_final: 0.6193 (OUTLIER) REVERT: SR 475 GLU cc_start: 0.6616 (tm-30) cc_final: 0.6109 (tp30) REVERT: SV 128 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7617 (mmmt) outliers start: 163 outliers final: 65 residues processed: 995 average time/residue: 2.1180 time to fit residues: 3009.8488 Evaluate side-chains 947 residues out of total 6155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 868 time to evaluate : 7.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BE residue 183 ASP Chi-restraints excluded: chain BE residue 195 CYS Chi-restraints excluded: chain L5 residue 16 ARG Chi-restraints excluded: chain L5 residue 26 VAL Chi-restraints excluded: chain L5 residue 49 VAL Chi-restraints excluded: chain L5 residue 125 ILE Chi-restraints excluded: chain L6 residue 52 SER Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 121 ARG Chi-restraints excluded: chain L6 residue 140 SER Chi-restraints excluded: chain L7 residue 174 LEU Chi-restraints excluded: chain L8 residue 126 GLU Chi-restraints excluded: chain L8 residue 130 LEU Chi-restraints excluded: chain L9 residue 89 VAL Chi-restraints excluded: chain L9 residue 126 THR Chi-restraints excluded: chain LA residue 107 LEU Chi-restraints excluded: chain LA residue 142 SER Chi-restraints excluded: chain LB residue 100 VAL Chi-restraints excluded: chain LB residue 122 THR Chi-restraints excluded: chain LD residue 29 THR Chi-restraints excluded: chain LD residue 113 LYS Chi-restraints excluded: chain LE residue 76 VAL Chi-restraints excluded: chain LF residue 33 ILE Chi-restraints excluded: chain LF residue 76 VAL Chi-restraints excluded: chain LF residue 99 TRP Chi-restraints excluded: chain LG residue 87 SER Chi-restraints excluded: chain LG residue 134 SER Chi-restraints excluded: chain LG residue 138 SER Chi-restraints excluded: chain LH residue 95 THR Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LI residue 118 ILE Chi-restraints excluded: chain LK residue 92 LYS Chi-restraints excluded: chain LL residue 5 LEU Chi-restraints excluded: chain LL residue 78 VAL Chi-restraints excluded: chain LL residue 80 THR Chi-restraints excluded: chain LL residue 81 THR Chi-restraints excluded: chain LL residue 124 VAL Chi-restraints excluded: chain LN residue 199 GLU Chi-restraints excluded: chain LP residue 40 LYS Chi-restraints excluded: chain LP residue 66 THR Chi-restraints excluded: chain LQ residue 17 THR Chi-restraints excluded: chain LQ residue 25 SER Chi-restraints excluded: chain LQ residue 26 ASP Chi-restraints excluded: chain LQ residue 33 ARG Chi-restraints excluded: chain LQ residue 72 SER Chi-restraints excluded: chain LQ residue 86 GLU Chi-restraints excluded: chain LR residue 17 SER Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 90 SER Chi-restraints excluded: chain LT residue 108 SER Chi-restraints excluded: chain LU residue 89 GLU Chi-restraints excluded: chain LV residue 23 VAL Chi-restraints excluded: chain LV residue 103 VAL Chi-restraints excluded: chain LX residue 45 THR Chi-restraints excluded: chain LX residue 48 LYS Chi-restraints excluded: chain LX residue 73 THR Chi-restraints excluded: chain LX residue 86 LEU Chi-restraints excluded: chain SA residue 273 LEU Chi-restraints excluded: chain SA residue 297 GLU Chi-restraints excluded: chain SB residue 125 VAL Chi-restraints excluded: chain SB residue 136 ASP Chi-restraints excluded: chain SC residue 49 VAL Chi-restraints excluded: chain SC residue 135 GLN Chi-restraints excluded: chain SC residue 212 LEU Chi-restraints excluded: chain SD residue 220 MET Chi-restraints excluded: chain SE residue 209 SER Chi-restraints excluded: chain SF residue 135 THR Chi-restraints excluded: chain SF residue 169 VAL Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SG residue 172 ILE Chi-restraints excluded: chain SG residue 187 VAL Chi-restraints excluded: chain SK residue 93 GLN Chi-restraints excluded: chain SK residue 134 LYS Chi-restraints excluded: chain SK residue 182 VAL Chi-restraints excluded: chain SK residue 188 ARG Chi-restraints excluded: chain SR residue 526 SER Chi-restraints excluded: chain SR residue 536 ASP Chi-restraints excluded: chain SR residue 583 VAL Chi-restraints excluded: chain SV residue 128 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1052 random chunks: chunk 846 optimal weight: 0.7980 chunk 577 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 757 optimal weight: 5.9990 chunk 419 optimal weight: 1.9990 chunk 867 optimal weight: 3.9990 chunk 702 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 519 optimal weight: 6.9990 chunk 912 optimal weight: 7.9990 chunk 256 optimal weight: 8.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 L6 104 ASN L6 111 GLN L7 173 GLN LC 23 HIS LE 144 ASN LF 38 ASN LF 41 GLN LF 50 ASN LF 118 ASN LG 36 ASN LK 66 ASN LK 120 GLN LM 101 HIS LS 107 GLN LW 57 ASN LX 72 ASN SA 43 ASN SB 244 HIS SD 239 GLN SF 95 GLN SG 106 GLN SK 75 ASN SR 414 GLN SR 504 GLN SV 67 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 144784 Z= 0.191 Angle : 0.679 19.528 212724 Z= 0.371 Chirality : 0.033 0.313 26174 Planarity : 0.007 0.131 13566 Dihedral : 23.107 179.235 65083 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.70 % Allowed : 15.39 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.78 % 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: 1.06 (0.10), residues: 7019 helix: 1.77 (0.10), residues: 2564 sheet: 0.48 (0.17), residues: 950 loop : 0.05 (0.10), residues: 3505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRPLE 125 HIS 0.008 0.001 HISLM 101 PHE 0.016 0.001 PHESR 376 TYR 0.024 0.001 TYRNP 111 ARG 0.008 0.000 ARGLP 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14038 Ramachandran restraints generated. 7019 Oldfield, 0 Emsley, 7019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14038 Ramachandran restraints generated. 7019 Oldfield, 0 Emsley, 7019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1048 residues out of total 6155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 885 time to evaluate : 7.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BE 183 ASP cc_start: 0.7763 (OUTLIER) cc_final: 0.7288 (p0) REVERT: L5 16 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7064 (ptm-80) REVERT: L7 82 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.7596 (ttt90) REVERT: L8 50 MET cc_start: 0.8327 (ttm) cc_final: 0.8001 (ttm) REVERT: L8 118 MET cc_start: 0.8268 (tpt) cc_final: 0.7712 (tpt) REVERT: LA 107 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7589 (mt) REVERT: LA 125 MET cc_start: 0.7634 (mpp) cc_final: 0.7274 (mtt) REVERT: LA 126 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.7221 (ttp-170) REVERT: LA 152 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7497 (mt-10) REVERT: LB 4 ASP cc_start: 0.7605 (t70) cc_final: 0.7181 (t0) REVERT: LB 147 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6821 (tm-30) REVERT: LD 113 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7942 (ttmm) REVERT: LF 99 TRP cc_start: 0.8074 (OUTLIER) cc_final: 0.6635 (m100) REVERT: LH 36 LYS cc_start: 0.6690 (ptmt) cc_final: 0.6266 (mptt) REVERT: LK 58 MET cc_start: 0.9148 (ptt) cc_final: 0.8925 (ptt) REVERT: LL 119 ARG cc_start: 0.7788 (ttm-80) cc_final: 0.7278 (ttm-80) REVERT: LN 199 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6739 (tt0) REVERT: LQ 86 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.7104 (mp0) REVERT: LX 86 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8647 (mp) REVERT: NP 22 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8266 (ptpp) REVERT: SA 11 TYR cc_start: 0.8163 (m-80) cc_final: 0.7898 (m-80) REVERT: SA 261 ASP cc_start: 0.8501 (m-30) cc_final: 0.8277 (m-30) REVERT: SA 281 MET cc_start: 0.8228 (mmm) cc_final: 0.7938 (mmt) REVERT: SA 284 MET cc_start: 0.8404 (ttt) cc_final: 0.8113 (ttt) REVERT: SC 135 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.7937 (mt0) REVERT: SD 232 ASP cc_start: 0.7415 (OUTLIER) cc_final: 0.7110 (t0) REVERT: SK 225 ASN cc_start: 0.6557 (p0) cc_final: 0.6262 (OUTLIER) REVERT: SR 475 GLU cc_start: 0.6626 (tm-30) cc_final: 0.6043 (tp30) REVERT: SR 575 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7197 (ptt180) REVERT: SV 66 ASP cc_start: 0.8159 (t0) cc_final: 0.7948 (t70) REVERT: SV 128 LYS cc_start: 0.7667 (OUTLIER) cc_final: 0.7456 (mmmt) outliers start: 163 outliers final: 89 residues processed: 971 average time/residue: 2.0983 time to fit residues: 2927.1677 Evaluate side-chains 969 residues out of total 6155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 865 time to evaluate : 7.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BE residue 183 ASP Chi-restraints excluded: chain L5 residue 16 ARG Chi-restraints excluded: chain L5 residue 26 VAL Chi-restraints excluded: chain L5 residue 38 LYS Chi-restraints excluded: chain L5 residue 49 VAL Chi-restraints excluded: chain L5 residue 125 ILE Chi-restraints excluded: chain L5 residue 148 THR Chi-restraints excluded: chain L6 residue 52 SER Chi-restraints excluded: chain L6 residue 68 THR Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 121 ARG Chi-restraints excluded: chain L6 residue 140 SER Chi-restraints excluded: chain L6 residue 151 THR Chi-restraints excluded: chain L7 residue 82 ARG Chi-restraints excluded: chain L7 residue 174 LEU Chi-restraints excluded: chain L9 residue 89 VAL Chi-restraints excluded: chain L9 residue 126 THR Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 107 LEU Chi-restraints excluded: chain LA residue 126 ARG Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LA residue 142 SER Chi-restraints excluded: chain LB residue 100 VAL Chi-restraints excluded: chain LB residue 122 THR Chi-restraints excluded: chain LB residue 147 GLU Chi-restraints excluded: chain LD residue 29 THR Chi-restraints excluded: chain LD residue 113 LYS Chi-restraints excluded: chain LE residue 76 VAL Chi-restraints excluded: chain LE residue 106 LEU Chi-restraints excluded: chain LE residue 157 GLU Chi-restraints excluded: chain LF residue 33 ILE Chi-restraints excluded: chain LF residue 76 VAL Chi-restraints excluded: chain LF residue 99 TRP Chi-restraints excluded: chain LG residue 87 SER Chi-restraints excluded: chain LG residue 134 SER Chi-restraints excluded: chain LH residue 42 THR Chi-restraints excluded: chain LH residue 95 THR Chi-restraints excluded: chain LH residue 131 ASP Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LI residue 102 SER Chi-restraints excluded: chain LI residue 118 ILE Chi-restraints excluded: chain LK residue 76 ASP Chi-restraints excluded: chain LK residue 92 LYS Chi-restraints excluded: chain LL residue 5 LEU Chi-restraints excluded: chain LL residue 63 VAL Chi-restraints excluded: chain LL residue 78 VAL Chi-restraints excluded: chain LL residue 81 THR Chi-restraints excluded: chain LL residue 124 VAL Chi-restraints excluded: chain LM residue 26 SER Chi-restraints excluded: chain LN residue 168 MET Chi-restraints excluded: chain LN residue 199 GLU Chi-restraints excluded: chain LO residue 14 ILE Chi-restraints excluded: chain LP residue 40 LYS Chi-restraints excluded: chain LP residue 66 THR Chi-restraints excluded: chain LQ residue 17 THR Chi-restraints excluded: chain LQ residue 25 SER Chi-restraints excluded: chain LQ residue 26 ASP Chi-restraints excluded: chain LQ residue 53 ILE Chi-restraints excluded: chain LQ residue 72 SER Chi-restraints excluded: chain LQ residue 86 GLU Chi-restraints excluded: chain LQ residue 87 VAL Chi-restraints excluded: chain LR residue 17 SER Chi-restraints excluded: chain LT residue 5 LEU Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 57 THR Chi-restraints excluded: chain LT residue 90 SER Chi-restraints excluded: chain LT residue 108 SER Chi-restraints excluded: chain LV residue 23 VAL Chi-restraints excluded: chain LV residue 103 VAL Chi-restraints excluded: chain LX residue 45 THR Chi-restraints excluded: chain LX residue 48 LYS Chi-restraints excluded: chain LX residue 70 THR Chi-restraints excluded: chain LX residue 73 THR Chi-restraints excluded: chain LX residue 86 LEU Chi-restraints excluded: chain NP residue 22 LYS Chi-restraints excluded: chain NP residue 73 SER Chi-restraints excluded: chain NP residue 89 LEU Chi-restraints excluded: chain NP residue 101 GLU Chi-restraints excluded: chain SA residue 297 GLU Chi-restraints excluded: chain SB residue 88 VAL Chi-restraints excluded: chain SB residue 116 ASP Chi-restraints excluded: chain SB residue 125 VAL Chi-restraints excluded: chain SB residue 136 ASP Chi-restraints excluded: chain SC residue 49 VAL Chi-restraints excluded: chain SC residue 135 GLN Chi-restraints excluded: chain SC residue 212 LEU Chi-restraints excluded: chain SD residue 220 MET Chi-restraints excluded: chain SD residue 232 ASP Chi-restraints excluded: chain SE residue 209 SER Chi-restraints excluded: chain SF residue 135 THR Chi-restraints excluded: chain SF residue 144 LYS Chi-restraints excluded: chain SF residue 169 VAL Chi-restraints excluded: chain SF residue 208 GLU Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SG residue 172 ILE Chi-restraints excluded: chain SG residue 187 VAL Chi-restraints excluded: chain SK residue 182 VAL Chi-restraints excluded: chain SK residue 188 ARG Chi-restraints excluded: chain SR residue 504 GLN Chi-restraints excluded: chain SR residue 526 SER Chi-restraints excluded: chain SR residue 536 ASP Chi-restraints excluded: chain SR residue 575 ARG Chi-restraints excluded: chain SR residue 583 VAL Chi-restraints excluded: chain SV residue 128 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1052 random chunks: chunk 342 optimal weight: 10.0000 chunk 915 optimal weight: 7.9990 chunk 201 optimal weight: 7.9990 chunk 597 optimal weight: 0.9990 chunk 251 optimal weight: 40.0000 chunk 1017 optimal weight: 9.9990 chunk 844 optimal weight: 2.9990 chunk 471 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 336 optimal weight: 5.9990 chunk 534 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BE 73 ASN L5 168 GLN L6 67 HIS L6 111 GLN LC 23 HIS LD 58 HIS LE 144 ASN LF 38 ASN LF 41 GLN LF 50 ASN LG 36 ASN LK 66 ASN LM 7 HIS ** LM 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LQ 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LS 107 GLN LX 72 ASN NP 75 ASN SA 231 ASN SB 244 HIS SD 63 GLN SE 81 ASN SF 95 GLN SG 106 GLN SK 93 GLN SK 162 HIS SR 414 GLN SV 67 ASN SV 104 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 144784 Z= 0.414 Angle : 0.787 19.561 212724 Z= 0.415 Chirality : 0.041 0.325 26174 Planarity : 0.008 0.140 13566 Dihedral : 23.167 178.767 65083 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.51 % Allowed : 15.24 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.78 % 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: 0.68 (0.10), residues: 7019 helix: 1.45 (0.10), residues: 2554 sheet: 0.36 (0.17), residues: 934 loop : -0.20 (0.10), residues: 3531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRPLE 125 HIS 0.009 0.002 HISLA 25 PHE 0.020 0.002 PHEL5 130 TYR 0.024 0.002 TYRNP 111 ARG 0.012 0.001 ARGLP 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14038 Ramachandran restraints generated. 7019 Oldfield, 0 Emsley, 7019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14038 Ramachandran restraints generated. 7019 Oldfield, 0 Emsley, 7019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1098 residues out of total 6155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 886 time to evaluate : 7.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BE 75 TYR cc_start: 0.7672 (t80) cc_final: 0.7264 (t80) REVERT: BE 183 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7499 (p0) REVERT: L5 16 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7132 (ptm-80) REVERT: L6 158 ARG cc_start: 0.6680 (mmm160) cc_final: 0.6476 (ttm-80) REVERT: L7 82 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7604 (ttt90) REVERT: L8 50 MET cc_start: 0.8322 (ttm) cc_final: 0.7978 (ttm) REVERT: L8 118 MET cc_start: 0.8293 (tpt) cc_final: 0.7539 (tpt) REVERT: L8 121 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.8193 (mtt90) REVERT: LA 107 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7665 (mt) REVERT: LA 125 MET cc_start: 0.7704 (mpp) cc_final: 0.7143 (mtt) REVERT: LA 126 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7249 (ttp-170) REVERT: LA 152 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7515 (mt-10) REVERT: LB 4 ASP cc_start: 0.7630 (t70) cc_final: 0.7390 (t70) REVERT: LD 113 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.7856 (mtmm) REVERT: LF 99 TRP cc_start: 0.8219 (OUTLIER) cc_final: 0.6688 (m100) REVERT: LF 108 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.6451 (mm-30) REVERT: LH 36 LYS cc_start: 0.6758 (ptmt) cc_final: 0.6298 (mptt) REVERT: LL 119 ARG cc_start: 0.7786 (ttm-80) cc_final: 0.7229 (ttm-80) REVERT: LN 199 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6787 (tt0) REVERT: LQ 33 ARG cc_start: 0.7043 (OUTLIER) cc_final: 0.6661 (ptt-90) REVERT: LQ 86 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7239 (mp0) REVERT: LS 48 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.6859 (ttp-170) REVERT: SA 281 MET cc_start: 0.8211 (mmm) cc_final: 0.7982 (mmt) REVERT: SA 284 MET cc_start: 0.8416 (ttt) cc_final: 0.8215 (ttt) REVERT: SC 135 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.8002 (mt0) REVERT: SD 232 ASP cc_start: 0.7560 (OUTLIER) cc_final: 0.7240 (t0) REVERT: SF 107 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.6986 (mtt) REVERT: SR 575 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7435 (ptt180) REVERT: SV 66 ASP cc_start: 0.8154 (t0) cc_final: 0.7927 (t0) REVERT: SV 128 LYS cc_start: 0.7705 (OUTLIER) cc_final: 0.7489 (mmmt) REVERT: SV 133 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8354 (mt) outliers start: 212 outliers final: 119 residues processed: 999 average time/residue: 2.1055 time to fit residues: 2998.9043 Evaluate side-chains 1005 residues out of total 6155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 867 time to evaluate : 7.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BE residue 168 SER Chi-restraints excluded: chain BE residue 183 ASP Chi-restraints excluded: chain L5 residue 16 ARG Chi-restraints excluded: chain L5 residue 26 VAL Chi-restraints excluded: chain L5 residue 38 LYS Chi-restraints excluded: chain L5 residue 49 VAL Chi-restraints excluded: chain L5 residue 148 THR Chi-restraints excluded: chain L6 residue 52 SER Chi-restraints excluded: chain L6 residue 68 THR Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 107 THR Chi-restraints excluded: chain L6 residue 121 ARG Chi-restraints excluded: chain L6 residue 140 SER Chi-restraints excluded: chain L6 residue 151 THR Chi-restraints excluded: chain L7 residue 82 ARG Chi-restraints excluded: chain L7 residue 174 LEU Chi-restraints excluded: chain L8 residue 121 ARG Chi-restraints excluded: chain L9 residue 89 VAL Chi-restraints excluded: chain L9 residue 126 THR Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 104 LEU Chi-restraints excluded: chain LA residue 107 LEU Chi-restraints excluded: chain LA residue 126 ARG Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LA residue 142 SER Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 100 VAL Chi-restraints excluded: chain LB residue 122 THR Chi-restraints excluded: chain LC residue 12 VAL Chi-restraints excluded: chain LC residue 85 ASP Chi-restraints excluded: chain LC residue 127 MET Chi-restraints excluded: chain LD residue 29 THR Chi-restraints excluded: chain LD residue 113 LYS Chi-restraints excluded: chain LE residue 76 VAL Chi-restraints excluded: chain LE residue 106 LEU Chi-restraints excluded: chain LF residue 33 ILE Chi-restraints excluded: chain LF residue 71 THR Chi-restraints excluded: chain LF residue 76 VAL Chi-restraints excluded: chain LF residue 83 LEU Chi-restraints excluded: chain LF residue 98 ASP Chi-restraints excluded: chain LF residue 99 TRP Chi-restraints excluded: chain LF residue 108 GLU Chi-restraints excluded: chain LG residue 87 SER Chi-restraints excluded: chain LG residue 134 SER Chi-restraints excluded: chain LG residue 138 SER Chi-restraints excluded: chain LH residue 42 THR Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LI residue 118 ILE Chi-restraints excluded: chain LK residue 76 ASP Chi-restraints excluded: chain LK residue 92 LYS Chi-restraints excluded: chain LL residue 5 LEU Chi-restraints excluded: chain LL residue 27 THR Chi-restraints excluded: chain LL residue 48 THR Chi-restraints excluded: chain LL residue 61 VAL Chi-restraints excluded: chain LL residue 63 VAL Chi-restraints excluded: chain LL residue 78 VAL Chi-restraints excluded: chain LL residue 81 THR Chi-restraints excluded: chain LL residue 124 VAL Chi-restraints excluded: chain LM residue 26 SER Chi-restraints excluded: chain LN residue 168 MET Chi-restraints excluded: chain LN residue 199 GLU Chi-restraints excluded: chain LO residue 14 ILE Chi-restraints excluded: chain LP residue 40 LYS Chi-restraints excluded: chain LP residue 57 MET Chi-restraints excluded: chain LP residue 66 THR Chi-restraints excluded: chain LP residue 80 VAL Chi-restraints excluded: chain LP residue 86 VAL Chi-restraints excluded: chain LQ residue 17 THR Chi-restraints excluded: chain LQ residue 25 SER Chi-restraints excluded: chain LQ residue 26 ASP Chi-restraints excluded: chain LQ residue 33 ARG Chi-restraints excluded: chain LQ residue 48 ARG Chi-restraints excluded: chain LQ residue 53 ILE Chi-restraints excluded: chain LQ residue 72 SER Chi-restraints excluded: chain LQ residue 86 GLU Chi-restraints excluded: chain LQ residue 87 VAL Chi-restraints excluded: chain LR residue 6 THR Chi-restraints excluded: chain LR residue 17 SER Chi-restraints excluded: chain LR residue 30 ILE Chi-restraints excluded: chain LS residue 8 ASP Chi-restraints excluded: chain LS residue 48 ARG Chi-restraints excluded: chain LT residue 5 LEU Chi-restraints excluded: chain LT residue 7 SER Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 57 THR Chi-restraints excluded: chain LT residue 90 SER Chi-restraints excluded: chain LT residue 108 SER Chi-restraints excluded: chain LV residue 23 VAL Chi-restraints excluded: chain LV residue 103 VAL Chi-restraints excluded: chain LX residue 45 THR Chi-restraints excluded: chain LX residue 48 LYS Chi-restraints excluded: chain LX residue 70 THR Chi-restraints excluded: chain LX residue 73 THR Chi-restraints excluded: chain LX residue 78 THR Chi-restraints excluded: chain LY residue 44 THR Chi-restraints excluded: chain NP residue 89 LEU Chi-restraints excluded: chain NP residue 101 GLU Chi-restraints excluded: chain SA residue 214 ASP Chi-restraints excluded: chain SA residue 275 SER Chi-restraints excluded: chain SA residue 297 GLU Chi-restraints excluded: chain SB residue 88 VAL Chi-restraints excluded: chain SB residue 116 ASP Chi-restraints excluded: chain SB residue 125 VAL Chi-restraints excluded: chain SB residue 136 ASP Chi-restraints excluded: chain SC residue 49 VAL Chi-restraints excluded: chain SC residue 135 GLN Chi-restraints excluded: chain SC residue 203 ILE Chi-restraints excluded: chain SC residue 212 LEU Chi-restraints excluded: chain SD residue 220 MET Chi-restraints excluded: chain SD residue 232 ASP Chi-restraints excluded: chain SE residue 246 SER Chi-restraints excluded: chain SF residue 45 VAL Chi-restraints excluded: chain SF residue 73 THR Chi-restraints excluded: chain SF residue 107 MET Chi-restraints excluded: chain SF residue 119 LYS Chi-restraints excluded: chain SF residue 135 THR Chi-restraints excluded: chain SF residue 158 ILE Chi-restraints excluded: chain SF residue 169 VAL Chi-restraints excluded: chain SF residue 208 GLU Chi-restraints excluded: chain SG residue 17 ASP Chi-restraints excluded: chain SG residue 33 THR Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SG residue 120 GLU Chi-restraints excluded: chain SG residue 172 ILE Chi-restraints excluded: chain SG residue 187 VAL Chi-restraints excluded: chain SK residue 75 ASN Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SK residue 169 ASP Chi-restraints excluded: chain SK residue 182 VAL Chi-restraints excluded: chain SK residue 188 ARG Chi-restraints excluded: chain SK residue 225 ASN Chi-restraints excluded: chain SR residue 423 SER Chi-restraints excluded: chain SR residue 478 LEU Chi-restraints excluded: chain SR residue 526 SER Chi-restraints excluded: chain SR residue 575 ARG Chi-restraints excluded: chain SR residue 583 VAL Chi-restraints excluded: chain SV residue 128 LYS Chi-restraints excluded: chain SV residue 133 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1052 random chunks: chunk 981 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 chunk 579 optimal weight: 8.9990 chunk 743 optimal weight: 1.9990 chunk 575 optimal weight: 4.9990 chunk 856 optimal weight: 0.9980 chunk 568 optimal weight: 6.9990 chunk 1013 optimal weight: 50.0000 chunk 634 optimal weight: 0.9990 chunk 618 optimal weight: 6.9990 chunk 468 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BE 73 ASN L5 168 GLN L6 67 HIS L6 111 GLN L6 175 ASN LC 23 HIS LE 144 ASN LF 38 ASN LF 41 GLN LF 50 ASN LG 36 ASN LK 66 ASN LM 11 ASN LQ 101 HIS LS 107 GLN LW 57 ASN LX 72 ASN SB 244 HIS SD 63 GLN SF 95 GLN SG 106 GLN SK 75 ASN SK 82 GLN SK 93 GLN SR 414 GLN SR 504 GLN SV 104 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 144784 Z= 0.265 Angle : 0.719 19.645 212724 Z= 0.388 Chirality : 0.036 0.327 26174 Planarity : 0.007 0.134 13566 Dihedral : 23.152 178.341 65083 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.05 % Allowed : 16.22 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.78 % 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: 0.74 (0.10), residues: 7019 helix: 1.53 (0.10), residues: 2555 sheet: 0.37 (0.17), residues: 937 loop : -0.18 (0.10), residues: 3527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRPLE 125 HIS 0.006 0.001 HISSK 118 PHE 0.024 0.002 PHELF 42 TYR 0.025 0.002 TYRNP 111 ARG 0.012 0.000 ARGLP 92 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14038 Ramachandran restraints generated. 7019 Oldfield, 0 Emsley, 7019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14038 Ramachandran restraints generated. 7019 Oldfield, 0 Emsley, 7019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1067 residues out of total 6155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 883 time to evaluate : 7.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BE 183 ASP cc_start: 0.7795 (OUTLIER) cc_final: 0.7245 (p0) REVERT: L7 82 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7581 (ttt90) REVERT: L8 50 MET cc_start: 0.8320 (ttm) cc_final: 0.8014 (ttm) REVERT: L8 118 MET cc_start: 0.8286 (tpt) cc_final: 0.7475 (tpt) REVERT: LA 107 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7659 (mt) REVERT: LA 125 MET cc_start: 0.7692 (mpp) cc_final: 0.7166 (mtt) REVERT: LA 152 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7522 (mt-10) REVERT: LB 4 ASP cc_start: 0.7608 (t70) cc_final: 0.7356 (t70) REVERT: LB 147 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6824 (tm-30) REVERT: LC 93 MET cc_start: 0.8487 (mtm) cc_final: 0.8236 (mtm) REVERT: LD 113 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7899 (ttmm) REVERT: LD 151 ARG cc_start: 0.6989 (mtm110) cc_final: 0.6741 (ttp80) REVERT: LF 99 TRP cc_start: 0.8144 (OUTLIER) cc_final: 0.6675 (m100) REVERT: LF 117 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8089 (mp) REVERT: LH 36 LYS cc_start: 0.6786 (ptmt) cc_final: 0.6292 (mptt) REVERT: LL 119 ARG cc_start: 0.7798 (ttm-80) cc_final: 0.7248 (ttm-80) REVERT: LN 199 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6750 (tt0) REVERT: LQ 33 ARG cc_start: 0.7008 (OUTLIER) cc_final: 0.6612 (ptt-90) REVERT: LQ 84 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7587 (mt-10) REVERT: LQ 86 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7253 (mp0) REVERT: LR 108 LYS cc_start: 0.7342 (tmmt) cc_final: 0.7072 (tttt) REVERT: LX 84 ARG cc_start: 0.7568 (ttm110) cc_final: 0.7356 (ttp-110) REVERT: SA 281 MET cc_start: 0.8179 (mmm) cc_final: 0.7930 (mmt) REVERT: SA 284 MET cc_start: 0.8423 (ttt) cc_final: 0.8180 (ttt) REVERT: SC 135 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.7984 (mt0) REVERT: SD 232 ASP cc_start: 0.7529 (OUTLIER) cc_final: 0.7213 (t0) REVERT: SF 107 MET cc_start: 0.7526 (mtt) cc_final: 0.7002 (mtt) REVERT: SK 225 ASN cc_start: 0.6486 (p0) cc_final: 0.6167 (OUTLIER) REVERT: SR 575 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7340 (ptt180) REVERT: SV 66 ASP cc_start: 0.8172 (t0) cc_final: 0.7953 (t0) REVERT: SV 128 LYS cc_start: 0.7652 (OUTLIER) cc_final: 0.7435 (mmmt) outliers start: 184 outliers final: 116 residues processed: 977 average time/residue: 2.0831 time to fit residues: 2912.9724 Evaluate side-chains 988 residues out of total 6155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 859 time to evaluate : 6.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BE residue 183 ASP Chi-restraints excluded: chain L5 residue 26 VAL Chi-restraints excluded: chain L5 residue 38 LYS Chi-restraints excluded: chain L5 residue 49 VAL Chi-restraints excluded: chain L5 residue 125 ILE Chi-restraints excluded: chain L5 residue 148 THR Chi-restraints excluded: chain L6 residue 52 SER Chi-restraints excluded: chain L6 residue 68 THR Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 107 THR Chi-restraints excluded: chain L6 residue 121 ARG Chi-restraints excluded: chain L6 residue 140 SER Chi-restraints excluded: chain L6 residue 151 THR Chi-restraints excluded: chain L7 residue 64 THR Chi-restraints excluded: chain L7 residue 82 ARG Chi-restraints excluded: chain L7 residue 174 LEU Chi-restraints excluded: chain L9 residue 89 VAL Chi-restraints excluded: chain L9 residue 126 THR Chi-restraints excluded: chain L9 residue 136 ASP Chi-restraints excluded: chain LA residue 14 SER Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 107 LEU Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LA residue 142 SER Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 100 VAL Chi-restraints excluded: chain LB residue 122 THR Chi-restraints excluded: chain LB residue 147 GLU Chi-restraints excluded: chain LC residue 12 VAL Chi-restraints excluded: chain LD residue 29 THR Chi-restraints excluded: chain LD residue 59 SER Chi-restraints excluded: chain LD residue 113 LYS Chi-restraints excluded: chain LE residue 76 VAL Chi-restraints excluded: chain LE residue 106 LEU Chi-restraints excluded: chain LE residue 157 GLU Chi-restraints excluded: chain LF residue 33 ILE Chi-restraints excluded: chain LF residue 71 THR Chi-restraints excluded: chain LF residue 76 VAL Chi-restraints excluded: chain LF residue 98 ASP Chi-restraints excluded: chain LF residue 99 TRP Chi-restraints excluded: chain LF residue 117 ILE Chi-restraints excluded: chain LG residue 87 SER Chi-restraints excluded: chain LG residue 134 SER Chi-restraints excluded: chain LG residue 138 SER Chi-restraints excluded: chain LH residue 42 THR Chi-restraints excluded: chain LH residue 131 ASP Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LI residue 118 ILE Chi-restraints excluded: chain LK residue 76 ASP Chi-restraints excluded: chain LK residue 92 LYS Chi-restraints excluded: chain LL residue 5 LEU Chi-restraints excluded: chain LL residue 27 THR Chi-restraints excluded: chain LL residue 48 THR Chi-restraints excluded: chain LL residue 61 VAL Chi-restraints excluded: chain LL residue 63 VAL Chi-restraints excluded: chain LL residue 78 VAL Chi-restraints excluded: chain LL residue 81 THR Chi-restraints excluded: chain LL residue 124 VAL Chi-restraints excluded: chain LM residue 26 SER Chi-restraints excluded: chain LN residue 168 MET Chi-restraints excluded: chain LN residue 199 GLU Chi-restraints excluded: chain LN residue 331 VAL Chi-restraints excluded: chain LO residue 14 ILE Chi-restraints excluded: chain LO residue 94 LEU Chi-restraints excluded: chain LP residue 40 LYS Chi-restraints excluded: chain LP residue 66 THR Chi-restraints excluded: chain LP residue 80 VAL Chi-restraints excluded: chain LP residue 86 VAL Chi-restraints excluded: chain LQ residue 17 THR Chi-restraints excluded: chain LQ residue 25 SER Chi-restraints excluded: chain LQ residue 26 ASP Chi-restraints excluded: chain LQ residue 33 ARG Chi-restraints excluded: chain LQ residue 48 ARG Chi-restraints excluded: chain LQ residue 53 ILE Chi-restraints excluded: chain LQ residue 72 SER Chi-restraints excluded: chain LQ residue 86 GLU Chi-restraints excluded: chain LQ residue 87 VAL Chi-restraints excluded: chain LQ residue 101 HIS Chi-restraints excluded: chain LR residue 17 SER Chi-restraints excluded: chain LR residue 30 ILE Chi-restraints excluded: chain LS residue 8 ASP Chi-restraints excluded: chain LT residue 5 LEU Chi-restraints excluded: chain LT residue 7 SER Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 57 THR Chi-restraints excluded: chain LT residue 90 SER Chi-restraints excluded: chain LT residue 108 SER Chi-restraints excluded: chain LV residue 23 VAL Chi-restraints excluded: chain LV residue 103 VAL Chi-restraints excluded: chain LX residue 45 THR Chi-restraints excluded: chain LX residue 70 THR Chi-restraints excluded: chain LX residue 73 THR Chi-restraints excluded: chain LX residue 78 THR Chi-restraints excluded: chain NP residue 89 LEU Chi-restraints excluded: chain NP residue 101 GLU Chi-restraints excluded: chain SA residue 275 SER Chi-restraints excluded: chain SA residue 297 GLU Chi-restraints excluded: chain SA residue 335 MET Chi-restraints excluded: chain SB residue 88 VAL Chi-restraints excluded: chain SB residue 116 ASP Chi-restraints excluded: chain SB residue 125 VAL Chi-restraints excluded: chain SB residue 136 ASP Chi-restraints excluded: chain SC residue 49 VAL Chi-restraints excluded: chain SC residue 135 GLN Chi-restraints excluded: chain SC residue 203 ILE Chi-restraints excluded: chain SC residue 212 LEU Chi-restraints excluded: chain SD residue 220 MET Chi-restraints excluded: chain SD residue 232 ASP Chi-restraints excluded: chain SE residue 246 SER Chi-restraints excluded: chain SF residue 45 VAL Chi-restraints excluded: chain SF residue 73 THR Chi-restraints excluded: chain SF residue 119 LYS Chi-restraints excluded: chain SF residue 135 THR Chi-restraints excluded: chain SF residue 158 ILE Chi-restraints excluded: chain SF residue 169 VAL Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SG residue 120 GLU Chi-restraints excluded: chain SG residue 172 ILE Chi-restraints excluded: chain SG residue 187 VAL Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SK residue 182 VAL Chi-restraints excluded: chain SK residue 188 ARG Chi-restraints excluded: chain SR residue 478 LEU Chi-restraints excluded: chain SR residue 504 GLN Chi-restraints excluded: chain SR residue 515 VAL Chi-restraints excluded: chain SR residue 526 SER Chi-restraints excluded: chain SR residue 575 ARG Chi-restraints excluded: chain SR residue 583 VAL Chi-restraints excluded: chain SV residue 128 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1052 random chunks: chunk 627 optimal weight: 0.7980 chunk 404 optimal weight: 10.0000 chunk 605 optimal weight: 0.0040 chunk 305 optimal weight: 3.9990 chunk 199 optimal weight: 10.0000 chunk 196 optimal weight: 6.9990 chunk 644 optimal weight: 5.9990 chunk 690 optimal weight: 5.9990 chunk 501 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 796 optimal weight: 9.9990 overall best weight: 2.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BE 73 ASN BE 147 HIS L6 67 HIS L6 111 GLN L6 175 ASN LC 23 HIS LE 144 ASN LF 38 ASN LF 41 GLN LF 50 ASN LF 118 ASN LG 36 ASN LK 66 ASN LQ 101 HIS LS 107 GLN LW 57 ASN LX 72 ASN SB 244 HIS SD 63 GLN SF 95 GLN SG 106 GLN SK 75 ASN ** SK 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SK 93 GLN SR 542 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 144784 Z= 0.246 Angle : 0.710 19.592 212724 Z= 0.384 Chirality : 0.036 0.337 26174 Planarity : 0.007 0.133 13566 Dihedral : 23.132 178.226 65083 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.03 % Allowed : 16.72 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.78 % 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: 0.78 (0.10), residues: 7019 helix: 1.57 (0.10), residues: 2555 sheet: 0.36 (0.17), residues: 937 loop : -0.17 (0.10), residues: 3527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRPLE 125 HIS 0.023 0.001 HISLQ 101 PHE 0.020 0.002 PHELF 42 TYR 0.027 0.002 TYRNP 111 ARG 0.013 0.000 ARGLP 92 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14038 Ramachandran restraints generated. 7019 Oldfield, 0 Emsley, 7019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14038 Ramachandran restraints generated. 7019 Oldfield, 0 Emsley, 7019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1056 residues out of total 6155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 873 time to evaluate : 7.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L7 82 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7580 (ttt90) REVERT: L8 50 MET cc_start: 0.8323 (ttm) cc_final: 0.7960 (ttm) REVERT: L8 118 MET cc_start: 0.8279 (tpt) cc_final: 0.7532 (tpt) REVERT: LA 107 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7657 (mt) REVERT: LA 125 MET cc_start: 0.7666 (OUTLIER) cc_final: 0.7141 (mtt) REVERT: LA 126 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7210 (ttp-170) REVERT: LA 152 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7515 (mt-10) REVERT: LB 4 ASP cc_start: 0.7546 (t70) cc_final: 0.7284 (t70) REVERT: LC 93 MET cc_start: 0.8499 (mtm) cc_final: 0.8285 (mtm) REVERT: LD 113 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7867 (ttmm) REVERT: LF 99 TRP cc_start: 0.8087 (OUTLIER) cc_final: 0.6626 (m100) REVERT: LF 108 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6672 (mm-30) REVERT: LF 117 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8059 (mp) REVERT: LH 36 LYS cc_start: 0.6787 (ptmt) cc_final: 0.6206 (mptt) REVERT: LL 119 ARG cc_start: 0.7784 (ttm-80) cc_final: 0.7236 (ttm-80) REVERT: LL 125 MET cc_start: 0.3930 (mpm) cc_final: 0.3458 (mmp) REVERT: LN 199 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6740 (tt0) REVERT: LQ 33 ARG cc_start: 0.7002 (OUTLIER) cc_final: 0.6613 (ptt-90) REVERT: LQ 84 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7587 (mt-10) REVERT: LQ 86 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7296 (mp0) REVERT: LR 108 LYS cc_start: 0.7273 (tmmt) cc_final: 0.7049 (tttt) REVERT: LS 48 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.6695 (ttp-170) REVERT: SA 261 ASP cc_start: 0.8523 (m-30) cc_final: 0.8314 (m-30) REVERT: SA 281 MET cc_start: 0.8176 (mmm) cc_final: 0.7916 (mmt) REVERT: SA 284 MET cc_start: 0.8442 (ttt) cc_final: 0.8183 (ttt) REVERT: SC 135 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.7963 (mt0) REVERT: SD 232 ASP cc_start: 0.7519 (OUTLIER) cc_final: 0.7211 (t0) REVERT: SF 107 MET cc_start: 0.7503 (mtt) cc_final: 0.6977 (mtt) REVERT: SR 575 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7331 (ptt180) REVERT: SV 66 ASP cc_start: 0.8208 (t0) cc_final: 0.7981 (t0) outliers start: 183 outliers final: 120 residues processed: 967 average time/residue: 2.2055 time to fit residues: 3085.1292 Evaluate side-chains 995 residues out of total 6155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 860 time to evaluate : 7.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BE residue 168 SER Chi-restraints excluded: chain L5 residue 26 VAL Chi-restraints excluded: chain L5 residue 38 LYS Chi-restraints excluded: chain L5 residue 49 VAL Chi-restraints excluded: chain L5 residue 101 ASP Chi-restraints excluded: chain L5 residue 125 ILE Chi-restraints excluded: chain L5 residue 148 THR Chi-restraints excluded: chain L6 residue 52 SER Chi-restraints excluded: chain L6 residue 68 THR Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 121 ARG Chi-restraints excluded: chain L6 residue 140 SER Chi-restraints excluded: chain L6 residue 151 THR Chi-restraints excluded: chain L7 residue 64 THR Chi-restraints excluded: chain L7 residue 82 ARG Chi-restraints excluded: chain L7 residue 174 LEU Chi-restraints excluded: chain L9 residue 89 VAL Chi-restraints excluded: chain L9 residue 126 THR Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 107 LEU Chi-restraints excluded: chain LA residue 125 MET Chi-restraints excluded: chain LA residue 126 ARG Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LA residue 142 SER Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 100 VAL Chi-restraints excluded: chain LB residue 122 THR Chi-restraints excluded: chain LC residue 12 VAL Chi-restraints excluded: chain LC residue 127 MET Chi-restraints excluded: chain LD residue 12 SER Chi-restraints excluded: chain LD residue 29 THR Chi-restraints excluded: chain LD residue 59 SER Chi-restraints excluded: chain LD residue 113 LYS Chi-restraints excluded: chain LE residue 76 VAL Chi-restraints excluded: chain LE residue 106 LEU Chi-restraints excluded: chain LE residue 157 GLU Chi-restraints excluded: chain LF residue 33 ILE Chi-restraints excluded: chain LF residue 66 SER Chi-restraints excluded: chain LF residue 71 THR Chi-restraints excluded: chain LF residue 76 VAL Chi-restraints excluded: chain LF residue 98 ASP Chi-restraints excluded: chain LF residue 99 TRP Chi-restraints excluded: chain LF residue 108 GLU Chi-restraints excluded: chain LF residue 117 ILE Chi-restraints excluded: chain LG residue 22 VAL Chi-restraints excluded: chain LG residue 87 SER Chi-restraints excluded: chain LG residue 134 SER Chi-restraints excluded: chain LG residue 138 SER Chi-restraints excluded: chain LH residue 42 THR Chi-restraints excluded: chain LH residue 95 THR Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LI residue 40 GLN Chi-restraints excluded: chain LI residue 118 ILE Chi-restraints excluded: chain LK residue 76 ASP Chi-restraints excluded: chain LL residue 5 LEU Chi-restraints excluded: chain LL residue 27 THR Chi-restraints excluded: chain LL residue 48 THR Chi-restraints excluded: chain LL residue 60 VAL Chi-restraints excluded: chain LL residue 61 VAL Chi-restraints excluded: chain LL residue 63 VAL Chi-restraints excluded: chain LL residue 78 VAL Chi-restraints excluded: chain LL residue 81 THR Chi-restraints excluded: chain LL residue 124 VAL Chi-restraints excluded: chain LM residue 26 SER Chi-restraints excluded: chain LN residue 168 MET Chi-restraints excluded: chain LN residue 199 GLU Chi-restraints excluded: chain LN residue 344 VAL Chi-restraints excluded: chain LO residue 94 LEU Chi-restraints excluded: chain LP residue 40 LYS Chi-restraints excluded: chain LP residue 66 THR Chi-restraints excluded: chain LP residue 80 VAL Chi-restraints excluded: chain LQ residue 17 THR Chi-restraints excluded: chain LQ residue 25 SER Chi-restraints excluded: chain LQ residue 33 ARG Chi-restraints excluded: chain LQ residue 48 ARG Chi-restraints excluded: chain LQ residue 53 ILE Chi-restraints excluded: chain LQ residue 72 SER Chi-restraints excluded: chain LQ residue 86 GLU Chi-restraints excluded: chain LQ residue 87 VAL Chi-restraints excluded: chain LQ residue 101 HIS Chi-restraints excluded: chain LR residue 6 THR Chi-restraints excluded: chain LR residue 17 SER Chi-restraints excluded: chain LR residue 30 ILE Chi-restraints excluded: chain LS residue 48 ARG Chi-restraints excluded: chain LT residue 5 LEU Chi-restraints excluded: chain LT residue 7 SER Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 57 THR Chi-restraints excluded: chain LT residue 90 SER Chi-restraints excluded: chain LT residue 108 SER 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 45 THR Chi-restraints excluded: chain LX residue 70 THR Chi-restraints excluded: chain LX residue 73 THR Chi-restraints excluded: chain NP residue 89 LEU Chi-restraints excluded: chain NP residue 93 SER Chi-restraints excluded: chain NP residue 101 GLU Chi-restraints excluded: chain SA residue 275 SER Chi-restraints excluded: chain SA residue 297 GLU Chi-restraints excluded: chain SA residue 335 MET Chi-restraints excluded: chain SB residue 88 VAL Chi-restraints excluded: chain SB residue 116 ASP Chi-restraints excluded: chain SB residue 125 VAL Chi-restraints excluded: chain SB residue 136 ASP Chi-restraints excluded: chain SC residue 49 VAL Chi-restraints excluded: chain SC residue 135 GLN Chi-restraints excluded: chain SC residue 212 LEU Chi-restraints excluded: chain SD residue 220 MET Chi-restraints excluded: chain SD residue 232 ASP Chi-restraints excluded: chain SE residue 246 SER Chi-restraints excluded: chain SF residue 45 VAL Chi-restraints excluded: chain SF residue 73 THR Chi-restraints excluded: chain SF residue 119 LYS Chi-restraints excluded: chain SF residue 135 THR Chi-restraints excluded: chain SF residue 144 LYS Chi-restraints excluded: chain SF residue 158 ILE Chi-restraints excluded: chain SF residue 169 VAL Chi-restraints excluded: chain SG residue 17 ASP Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SG residue 120 GLU Chi-restraints excluded: chain SG residue 126 VAL Chi-restraints excluded: chain SG residue 172 ILE Chi-restraints excluded: chain SG residue 187 VAL Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SK residue 182 VAL Chi-restraints excluded: chain SK residue 188 ARG Chi-restraints excluded: chain SK residue 225 ASN Chi-restraints excluded: chain SR residue 423 SER Chi-restraints excluded: chain SR residue 478 LEU Chi-restraints excluded: chain SR residue 515 VAL Chi-restraints excluded: chain SR residue 526 SER Chi-restraints excluded: chain SR residue 575 ARG Chi-restraints excluded: chain SR residue 583 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1052 random chunks: chunk 922 optimal weight: 2.9990 chunk 971 optimal weight: 2.9990 chunk 886 optimal weight: 8.9990 chunk 944 optimal weight: 5.9990 chunk 568 optimal weight: 4.9990 chunk 411 optimal weight: 0.1980 chunk 741 optimal weight: 7.9990 chunk 289 optimal weight: 7.9990 chunk 853 optimal weight: 3.9990 chunk 893 optimal weight: 30.0000 chunk 941 optimal weight: 4.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BE 73 ASN L6 67 HIS L6 111 GLN L6 175 ASN LC 23 HIS LE 144 ASN LF 38 ASN LF 41 GLN LF 50 ASN LG 36 ASN LK 66 ASN LQ 102 ASN LS 107 GLN LW 57 ASN LX 72 ASN SB 244 HIS SD 63 GLN SF 95 GLN SG 106 GLN ** SK 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SR 504 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 144784 Z= 0.306 Angle : 0.736 19.684 212724 Z= 0.395 Chirality : 0.038 0.371 26174 Planarity : 0.008 0.135 13566 Dihedral : 23.136 178.535 65083 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.88 % Allowed : 17.10 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.78 % 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: 0.66 (0.10), residues: 7019 helix: 1.47 (0.10), residues: 2560 sheet: 0.32 (0.17), residues: 948 loop : -0.24 (0.10), residues: 3511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRPLE 125 HIS 0.029 0.001 HISLQ 101 PHE 0.021 0.002 PHESR 376 TYR 0.028 0.002 TYRNP 111 ARG 0.013 0.001 ARGLP 92 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14038 Ramachandran restraints generated. 7019 Oldfield, 0 Emsley, 7019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14038 Ramachandran restraints generated. 7019 Oldfield, 0 Emsley, 7019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1038 residues out of total 6155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 864 time to evaluate : 7.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L7 82 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7579 (ttt90) REVERT: L8 50 MET cc_start: 0.8319 (ttm) cc_final: 0.7966 (ttm) REVERT: L8 98 ARG cc_start: 0.7774 (ttp-110) cc_final: 0.7313 (mtm-85) REVERT: L8 118 MET cc_start: 0.8290 (tpt) cc_final: 0.7529 (tpt) REVERT: LA 125 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.7150 (mtt) REVERT: LA 126 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7241 (ttp-170) REVERT: LB 4 ASP cc_start: 0.7557 (t70) cc_final: 0.7288 (t70) REVERT: LD 113 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7871 (ttmm) REVERT: LE 114 GLN cc_start: 0.7244 (OUTLIER) cc_final: 0.6942 (tt0) REVERT: LF 99 TRP cc_start: 0.8117 (OUTLIER) cc_final: 0.6628 (m100) REVERT: LF 108 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6633 (mm-30) REVERT: LF 117 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8208 (mp) REVERT: LH 36 LYS cc_start: 0.6845 (ptmt) cc_final: 0.6252 (mptt) REVERT: LL 119 ARG cc_start: 0.7789 (ttm-80) cc_final: 0.7247 (ttm-80) REVERT: LL 125 MET cc_start: 0.3881 (mpm) cc_final: 0.3379 (mmp) REVERT: LN 199 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6754 (tt0) REVERT: LQ 33 ARG cc_start: 0.7020 (OUTLIER) cc_final: 0.6633 (ptt-90) REVERT: LQ 84 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7549 (mt-10) REVERT: LQ 86 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7323 (mp0) REVERT: LS 48 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.6708 (ttp-170) REVERT: SA 11 TYR cc_start: 0.8197 (m-80) cc_final: 0.7997 (m-80) REVERT: SA 261 ASP cc_start: 0.8529 (m-30) cc_final: 0.8296 (m-30) REVERT: SA 281 MET cc_start: 0.8180 (mmm) cc_final: 0.7934 (mmt) REVERT: SA 284 MET cc_start: 0.8460 (ttt) cc_final: 0.8196 (ttt) REVERT: SC 56 ARG cc_start: 0.7865 (ttm-80) cc_final: 0.7616 (tmt170) REVERT: SC 135 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.7997 (mt0) REVERT: SD 232 ASP cc_start: 0.7537 (OUTLIER) cc_final: 0.7222 (t0) REVERT: SF 107 MET cc_start: 0.7536 (mtt) cc_final: 0.6995 (mtt) REVERT: SR 575 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7346 (ptt180) REVERT: SV 63 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8190 (tt) REVERT: SV 66 ASP cc_start: 0.8214 (t0) cc_final: 0.7977 (t0) REVERT: SV 104 GLN cc_start: 0.8155 (mt0) cc_final: 0.7895 (mt0) REVERT: SV 133 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8335 (mt) outliers start: 174 outliers final: 129 residues processed: 958 average time/residue: 2.0696 time to fit residues: 2844.7164 Evaluate side-chains 996 residues out of total 6155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 850 time to evaluate : 6.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BE residue 168 SER Chi-restraints excluded: chain L5 residue 26 VAL Chi-restraints excluded: chain L5 residue 38 LYS Chi-restraints excluded: chain L5 residue 49 VAL Chi-restraints excluded: chain L5 residue 101 ASP Chi-restraints excluded: chain L5 residue 125 ILE Chi-restraints excluded: chain L5 residue 148 THR Chi-restraints excluded: chain L6 residue 52 SER Chi-restraints excluded: chain L6 residue 68 THR Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 107 THR Chi-restraints excluded: chain L6 residue 121 ARG Chi-restraints excluded: chain L6 residue 140 SER Chi-restraints excluded: chain L6 residue 151 THR Chi-restraints excluded: chain L7 residue 64 THR Chi-restraints excluded: chain L7 residue 82 ARG Chi-restraints excluded: chain L7 residue 174 LEU Chi-restraints excluded: chain L9 residue 18 VAL Chi-restraints excluded: chain L9 residue 89 VAL Chi-restraints excluded: chain L9 residue 126 THR Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 125 MET Chi-restraints excluded: chain LA residue 126 ARG Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LA residue 142 SER Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 100 VAL Chi-restraints excluded: chain LB residue 122 THR Chi-restraints excluded: chain LC residue 12 VAL Chi-restraints excluded: chain LC residue 127 MET Chi-restraints excluded: chain LD residue 29 THR Chi-restraints excluded: chain LD residue 59 SER Chi-restraints excluded: chain LD residue 113 LYS Chi-restraints excluded: chain LE residue 76 VAL Chi-restraints excluded: chain LE residue 106 LEU Chi-restraints excluded: chain LE residue 114 GLN Chi-restraints excluded: chain LE residue 157 GLU Chi-restraints excluded: chain LF residue 33 ILE Chi-restraints excluded: chain LF residue 66 SER Chi-restraints excluded: chain LF residue 71 THR Chi-restraints excluded: chain LF residue 76 VAL Chi-restraints excluded: chain LF residue 98 ASP Chi-restraints excluded: chain LF residue 99 TRP Chi-restraints excluded: chain LF residue 108 GLU Chi-restraints excluded: chain LF residue 117 ILE Chi-restraints excluded: chain LG residue 22 VAL Chi-restraints excluded: chain LG residue 87 SER Chi-restraints excluded: chain LG residue 134 SER Chi-restraints excluded: chain LG residue 138 SER Chi-restraints excluded: chain LH residue 42 THR Chi-restraints excluded: chain LH residue 131 ASP Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LI residue 40 GLN Chi-restraints excluded: chain LI residue 102 SER Chi-restraints excluded: chain LI residue 118 ILE Chi-restraints excluded: chain LK residue 76 ASP Chi-restraints excluded: chain LL residue 5 LEU Chi-restraints excluded: chain LL residue 27 THR Chi-restraints excluded: chain LL residue 48 THR Chi-restraints excluded: chain LL residue 60 VAL Chi-restraints excluded: chain LL residue 61 VAL Chi-restraints excluded: chain LL residue 63 VAL Chi-restraints excluded: chain LL residue 78 VAL Chi-restraints excluded: chain LL residue 81 THR Chi-restraints excluded: chain LL residue 96 MET Chi-restraints excluded: chain LL residue 124 VAL Chi-restraints excluded: chain LM residue 13 SER Chi-restraints excluded: chain LM residue 26 SER Chi-restraints excluded: chain LN residue 168 MET Chi-restraints excluded: chain LN residue 199 GLU Chi-restraints excluded: chain LN residue 331 VAL Chi-restraints excluded: chain LN residue 344 VAL Chi-restraints excluded: chain LO residue 94 LEU Chi-restraints excluded: chain LP residue 40 LYS Chi-restraints excluded: chain LP residue 66 THR Chi-restraints excluded: chain LP residue 80 VAL Chi-restraints excluded: chain LP residue 86 VAL Chi-restraints excluded: chain LQ residue 17 THR Chi-restraints excluded: chain LQ residue 25 SER Chi-restraints excluded: chain LQ residue 33 ARG Chi-restraints excluded: chain LQ residue 48 ARG Chi-restraints excluded: chain LQ residue 53 ILE Chi-restraints excluded: chain LQ residue 72 SER Chi-restraints excluded: chain LQ residue 86 GLU Chi-restraints excluded: chain LQ residue 87 VAL Chi-restraints excluded: chain LR residue 6 THR Chi-restraints excluded: chain LR residue 17 SER Chi-restraints excluded: chain LR residue 30 ILE Chi-restraints excluded: chain LS residue 8 ASP Chi-restraints excluded: chain LS residue 48 ARG Chi-restraints excluded: chain LT residue 5 LEU Chi-restraints excluded: chain LT residue 7 SER Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 57 THR Chi-restraints excluded: chain LT residue 90 SER Chi-restraints excluded: chain LT residue 108 SER Chi-restraints excluded: chain LU residue 70 LEU Chi-restraints excluded: chain LV residue 23 VAL Chi-restraints excluded: chain LX residue 45 THR Chi-restraints excluded: chain LX residue 70 THR Chi-restraints excluded: chain LX residue 73 THR Chi-restraints excluded: chain LX residue 78 THR Chi-restraints excluded: chain NP residue 89 LEU Chi-restraints excluded: chain NP residue 101 GLU Chi-restraints excluded: chain SA residue 214 ASP Chi-restraints excluded: chain SA residue 275 SER Chi-restraints excluded: chain SA residue 297 GLU Chi-restraints excluded: chain SA residue 335 MET Chi-restraints excluded: chain SB residue 88 VAL Chi-restraints excluded: chain SB residue 116 ASP Chi-restraints excluded: chain SB residue 125 VAL Chi-restraints excluded: chain SB residue 136 ASP Chi-restraints excluded: chain SC residue 49 VAL Chi-restraints excluded: chain SC residue 135 GLN Chi-restraints excluded: chain SC residue 203 ILE Chi-restraints excluded: chain SC residue 212 LEU Chi-restraints excluded: chain SD residue 220 MET Chi-restraints excluded: chain SD residue 232 ASP Chi-restraints excluded: chain SE residue 246 SER Chi-restraints excluded: chain SF residue 45 VAL Chi-restraints excluded: chain SF residue 73 THR Chi-restraints excluded: chain SF residue 119 LYS Chi-restraints excluded: chain SF residue 135 THR Chi-restraints excluded: chain SF residue 144 LYS Chi-restraints excluded: chain SF residue 158 ILE Chi-restraints excluded: chain SF residue 169 VAL Chi-restraints excluded: chain SG residue 17 ASP Chi-restraints excluded: chain SG residue 33 THR Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SG residue 120 GLU Chi-restraints excluded: chain SG residue 126 VAL Chi-restraints excluded: chain SG residue 172 ILE Chi-restraints excluded: chain SG residue 187 VAL Chi-restraints excluded: chain SK residue 75 ASN Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SK residue 182 VAL Chi-restraints excluded: chain SK residue 188 ARG Chi-restraints excluded: chain SR residue 423 SER Chi-restraints excluded: chain SR residue 478 LEU Chi-restraints excluded: chain SR residue 504 GLN Chi-restraints excluded: chain SR residue 515 VAL Chi-restraints excluded: chain SR residue 526 SER Chi-restraints excluded: chain SR residue 575 ARG Chi-restraints excluded: chain SR residue 583 VAL Chi-restraints excluded: chain SV residue 63 LEU Chi-restraints excluded: chain SV residue 133 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1052 random chunks: chunk 620 optimal weight: 6.9990 chunk 999 optimal weight: 2.9990 chunk 609 optimal weight: 7.9990 chunk 473 optimal weight: 4.9990 chunk 694 optimal weight: 6.9990 chunk 1048 optimal weight: 6.9990 chunk 964 optimal weight: 0.9990 chunk 834 optimal weight: 6.9990 chunk 86 optimal weight: 20.0000 chunk 644 optimal weight: 0.9980 chunk 511 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L6 67 HIS L6 111 GLN L6 175 ASN LC 23 HIS LE 144 ASN LF 38 ASN LF 41 GLN LF 50 ASN LG 36 ASN LI 86 GLN LK 66 ASN LQ 101 HIS LQ 102 ASN LS 107 GLN LW 57 ASN LX 72 ASN SB 244 HIS SD 63 GLN SF 95 GLN SG 106 GLN ** SK 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SK 225 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 144784 Z= 0.284 Angle : 0.730 19.654 212724 Z= 0.392 Chirality : 0.037 0.392 26174 Planarity : 0.008 0.135 13566 Dihedral : 23.139 178.375 65083 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.81 % Allowed : 17.33 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.78 % 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: 0.66 (0.10), residues: 7019 helix: 1.46 (0.10), residues: 2561 sheet: 0.32 (0.17), residues: 948 loop : -0.23 (0.10), residues: 3510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRPLE 125 HIS 0.006 0.001 HISLK 39 PHE 0.022 0.002 PHESR 376 TYR 0.029 0.002 TYRNP 111 ARG 0.015 0.000 ARGLP 92 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14038 Ramachandran restraints generated. 7019 Oldfield, 0 Emsley, 7019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14038 Ramachandran restraints generated. 7019 Oldfield, 0 Emsley, 7019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1027 residues out of total 6155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 857 time to evaluate : 7.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L7 82 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.7575 (ttt90) REVERT: L8 50 MET cc_start: 0.8320 (ttm) cc_final: 0.7963 (ttm) REVERT: L8 118 MET cc_start: 0.8284 (tpt) cc_final: 0.7525 (tpt) REVERT: LA 125 MET cc_start: 0.7677 (OUTLIER) cc_final: 0.7132 (mtt) REVERT: LA 126 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7198 (ttp-170) REVERT: LB 4 ASP cc_start: 0.7550 (t70) cc_final: 0.7278 (t70) REVERT: LD 113 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7894 (ttmm) REVERT: LD 151 ARG cc_start: 0.6882 (mtm110) cc_final: 0.6637 (ttp80) REVERT: LE 114 GLN cc_start: 0.7204 (OUTLIER) cc_final: 0.6901 (tt0) REVERT: LF 99 TRP cc_start: 0.8094 (OUTLIER) cc_final: 0.6624 (m100) REVERT: LF 108 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6631 (mm-30) REVERT: LF 117 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8188 (mp) REVERT: LH 36 LYS cc_start: 0.6841 (ptmt) cc_final: 0.6249 (mptt) REVERT: LL 119 ARG cc_start: 0.7788 (ttm-80) cc_final: 0.7250 (ttm-80) REVERT: LL 125 MET cc_start: 0.3848 (mpm) cc_final: 0.3349 (mmp) REVERT: LN 199 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6750 (tt0) REVERT: LO 87 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7686 (mtpp) REVERT: LO 97 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8386 (mm) REVERT: LQ 33 ARG cc_start: 0.7019 (OUTLIER) cc_final: 0.6627 (ptt-90) REVERT: LQ 84 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7560 (mt-10) REVERT: LQ 86 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7318 (mp0) REVERT: LR 108 LYS cc_start: 0.7376 (tmmt) cc_final: 0.7020 (tptt) REVERT: LS 48 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.6701 (ttp-170) REVERT: SA 11 TYR cc_start: 0.8188 (m-80) cc_final: 0.7931 (m-80) REVERT: SA 261 ASP cc_start: 0.8519 (m-30) cc_final: 0.8286 (m-30) REVERT: SA 281 MET cc_start: 0.8180 (mmm) cc_final: 0.7935 (mmt) REVERT: SA 284 MET cc_start: 0.8459 (ttt) cc_final: 0.8193 (ttt) REVERT: SC 56 ARG cc_start: 0.7866 (ttm-80) cc_final: 0.7615 (tmt170) REVERT: SD 232 ASP cc_start: 0.7528 (OUTLIER) cc_final: 0.7223 (t0) REVERT: SF 107 MET cc_start: 0.7528 (mtt) cc_final: 0.6770 (mtt) REVERT: SK 225 ASN cc_start: 0.6525 (p0) cc_final: 0.6165 (OUTLIER) REVERT: SR 575 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7331 (ptt180) REVERT: SV 63 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8186 (tt) REVERT: SV 66 ASP cc_start: 0.8216 (t0) cc_final: 0.7978 (t0) REVERT: SV 104 GLN cc_start: 0.8148 (mt0) cc_final: 0.7897 (mt0) REVERT: SV 133 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8350 (mt) outliers start: 170 outliers final: 133 residues processed: 953 average time/residue: 2.0835 time to fit residues: 2857.1840 Evaluate side-chains 1001 residues out of total 6155 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 851 time to evaluate : 7.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BE residue 168 SER Chi-restraints excluded: chain L5 residue 26 VAL Chi-restraints excluded: chain L5 residue 38 LYS Chi-restraints excluded: chain L5 residue 49 VAL Chi-restraints excluded: chain L5 residue 101 ASP Chi-restraints excluded: chain L5 residue 125 ILE Chi-restraints excluded: chain L5 residue 128 LEU Chi-restraints excluded: chain L5 residue 148 THR Chi-restraints excluded: chain L6 residue 52 SER Chi-restraints excluded: chain L6 residue 68 THR Chi-restraints excluded: chain L6 residue 70 VAL Chi-restraints excluded: chain L6 residue 107 THR Chi-restraints excluded: chain L6 residue 121 ARG Chi-restraints excluded: chain L6 residue 140 SER Chi-restraints excluded: chain L6 residue 151 THR Chi-restraints excluded: chain L7 residue 64 THR Chi-restraints excluded: chain L7 residue 82 ARG Chi-restraints excluded: chain L7 residue 129 LEU Chi-restraints excluded: chain L7 residue 174 LEU Chi-restraints excluded: chain L9 residue 18 VAL Chi-restraints excluded: chain L9 residue 89 VAL Chi-restraints excluded: chain L9 residue 126 THR Chi-restraints excluded: chain LA residue 24 VAL Chi-restraints excluded: chain LA residue 125 MET Chi-restraints excluded: chain LA residue 126 ARG Chi-restraints excluded: chain LA residue 129 THR Chi-restraints excluded: chain LA residue 142 SER Chi-restraints excluded: chain LB residue 82 VAL Chi-restraints excluded: chain LB residue 100 VAL Chi-restraints excluded: chain LB residue 122 THR Chi-restraints excluded: chain LC residue 12 VAL Chi-restraints excluded: chain LC residue 127 MET Chi-restraints excluded: chain LD residue 12 SER Chi-restraints excluded: chain LD residue 29 THR Chi-restraints excluded: chain LD residue 59 SER Chi-restraints excluded: chain LD residue 113 LYS Chi-restraints excluded: chain LE residue 76 VAL Chi-restraints excluded: chain LE residue 106 LEU Chi-restraints excluded: chain LE residue 114 GLN Chi-restraints excluded: chain LE residue 157 GLU Chi-restraints excluded: chain LF residue 33 ILE Chi-restraints excluded: chain LF residue 66 SER Chi-restraints excluded: chain LF residue 71 THR Chi-restraints excluded: chain LF residue 76 VAL Chi-restraints excluded: chain LF residue 98 ASP Chi-restraints excluded: chain LF residue 99 TRP Chi-restraints excluded: chain LF residue 108 GLU Chi-restraints excluded: chain LF residue 117 ILE Chi-restraints excluded: chain LG residue 22 VAL Chi-restraints excluded: chain LG residue 87 SER Chi-restraints excluded: chain LG residue 134 SER Chi-restraints excluded: chain LG residue 138 SER Chi-restraints excluded: chain LH residue 42 THR Chi-restraints excluded: chain LH residue 131 ASP Chi-restraints excluded: chain LI residue 8 THR Chi-restraints excluded: chain LI residue 40 GLN Chi-restraints excluded: chain LI residue 102 SER Chi-restraints excluded: chain LI residue 118 ILE Chi-restraints excluded: chain LJ residue 25 ILE Chi-restraints excluded: chain LK residue 76 ASP Chi-restraints excluded: chain LL residue 5 LEU Chi-restraints excluded: chain LL residue 27 THR Chi-restraints excluded: chain LL residue 48 THR Chi-restraints excluded: chain LL residue 60 VAL Chi-restraints excluded: chain LL residue 61 VAL Chi-restraints excluded: chain LL residue 63 VAL Chi-restraints excluded: chain LL residue 78 VAL Chi-restraints excluded: chain LL residue 81 THR Chi-restraints excluded: chain LL residue 96 MET Chi-restraints excluded: chain LL residue 124 VAL Chi-restraints excluded: chain LM residue 13 SER Chi-restraints excluded: chain LM residue 26 SER Chi-restraints excluded: chain LN residue 168 MET Chi-restraints excluded: chain LN residue 199 GLU Chi-restraints excluded: chain LN residue 331 VAL Chi-restraints excluded: chain LN residue 344 VAL Chi-restraints excluded: chain LO residue 87 LYS Chi-restraints excluded: chain LO residue 94 LEU Chi-restraints excluded: chain LO residue 97 ILE Chi-restraints excluded: chain LP residue 40 LYS Chi-restraints excluded: chain LP residue 66 THR Chi-restraints excluded: chain LP residue 80 VAL Chi-restraints excluded: chain LP residue 86 VAL Chi-restraints excluded: chain LQ residue 17 THR Chi-restraints excluded: chain LQ residue 25 SER Chi-restraints excluded: chain LQ residue 33 ARG Chi-restraints excluded: chain LQ residue 48 ARG Chi-restraints excluded: chain LQ residue 53 ILE Chi-restraints excluded: chain LQ residue 72 SER Chi-restraints excluded: chain LQ residue 86 GLU Chi-restraints excluded: chain LQ residue 87 VAL Chi-restraints excluded: chain LR residue 6 THR Chi-restraints excluded: chain LR residue 17 SER Chi-restraints excluded: chain LR residue 30 ILE Chi-restraints excluded: chain LS residue 8 ASP Chi-restraints excluded: chain LS residue 48 ARG Chi-restraints excluded: chain LT residue 5 LEU Chi-restraints excluded: chain LT residue 7 SER Chi-restraints excluded: chain LT residue 37 ASP Chi-restraints excluded: chain LT residue 57 THR Chi-restraints excluded: chain LT residue 90 SER Chi-restraints excluded: chain LT residue 108 SER Chi-restraints excluded: chain LU residue 70 LEU Chi-restraints excluded: chain LV residue 23 VAL Chi-restraints excluded: chain LX residue 45 THR Chi-restraints excluded: chain LX residue 70 THR Chi-restraints excluded: chain LX residue 73 THR Chi-restraints excluded: chain LX residue 78 THR Chi-restraints excluded: chain NP residue 89 LEU Chi-restraints excluded: chain NP residue 101 GLU Chi-restraints excluded: chain SA residue 275 SER Chi-restraints excluded: chain SA residue 297 GLU Chi-restraints excluded: chain SA residue 335 MET Chi-restraints excluded: chain SB residue 88 VAL Chi-restraints excluded: chain SB residue 116 ASP Chi-restraints excluded: chain SB residue 125 VAL Chi-restraints excluded: chain SB residue 136 ASP Chi-restraints excluded: chain SB residue 288 LEU Chi-restraints excluded: chain SC residue 49 VAL Chi-restraints excluded: chain SC residue 203 ILE Chi-restraints excluded: chain SC residue 212 LEU Chi-restraints excluded: chain SD residue 220 MET Chi-restraints excluded: chain SD residue 232 ASP Chi-restraints excluded: chain SE residue 246 SER Chi-restraints excluded: chain SF residue 45 VAL Chi-restraints excluded: chain SF residue 73 THR Chi-restraints excluded: chain SF residue 119 LYS Chi-restraints excluded: chain SF residue 135 THR Chi-restraints excluded: chain SF residue 144 LYS Chi-restraints excluded: chain SF residue 158 ILE Chi-restraints excluded: chain SF residue 169 VAL Chi-restraints excluded: chain SG residue 17 ASP Chi-restraints excluded: chain SG residue 33 THR Chi-restraints excluded: chain SG residue 84 VAL Chi-restraints excluded: chain SG residue 120 GLU Chi-restraints excluded: chain SG residue 126 VAL Chi-restraints excluded: chain SG residue 172 ILE Chi-restraints excluded: chain SG residue 187 VAL Chi-restraints excluded: chain SK residue 75 ASN Chi-restraints excluded: chain SK residue 109 THR Chi-restraints excluded: chain SK residue 182 VAL Chi-restraints excluded: chain SK residue 188 ARG Chi-restraints excluded: chain SR residue 423 SER Chi-restraints excluded: chain SR residue 478 LEU Chi-restraints excluded: chain SR residue 515 VAL Chi-restraints excluded: chain SR residue 526 SER Chi-restraints excluded: chain SR residue 575 ARG Chi-restraints excluded: chain SR residue 583 VAL Chi-restraints excluded: chain SV residue 63 LEU Chi-restraints excluded: chain SV residue 133 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1052 random chunks: chunk 662 optimal weight: 5.9990 chunk 889 optimal weight: 10.0000 chunk 255 optimal weight: 7.9990 chunk 769 optimal weight: 0.8980 chunk 123 optimal weight: 8.9990 chunk 231 optimal weight: 10.0000 chunk 835 optimal weight: 6.9990 chunk 349 optimal weight: 10.0000 chunk 858 optimal weight: 0.9980 chunk 105 optimal weight: 10.0000 chunk 153 optimal weight: 6.9990 overall best weight: 4.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BE 73 ASN ** L6 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L6 111 GLN L6 175 ASN LC 23 HIS LE 144 ASN LF 38 ASN LF 41 GLN LF 50 ASN LG 36 ASN LI 86 GLN LK 66 ASN ** LQ 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LS 107 GLN LX 72 ASN SB 244 HIS SD 63 GLN SD 239 GLN SF 95 GLN SG 106 GLN SR 504 GLN SV 87 ASN SV 119 GLN SV 122 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.101934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.075168 restraints weight = 265070.392| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.30 r_work: 0.2922 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 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 = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2797 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 144784 Z= 0.427 Angle : 0.804 19.971 212724 Z= 0.422 Chirality : 0.042 0.383 26174 Planarity : 0.008 0.140 13566 Dihedral : 23.197 178.855 65083 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.88 % Allowed : 17.41 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.78 % 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: 0.37 (0.10), residues: 7019 helix: 1.22 (0.10), residues: 2567 sheet: 0.22 (0.17), residues: 940 loop : -0.41 (0.10), residues: 3512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRPSA 108 HIS 0.008 0.002 HISLA 133 PHE 0.025 0.002 PHESR 376 TYR 0.031 0.002 TYRNP 111 ARG 0.015 0.001 ARGLP 92 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 45094.64 seconds wall clock time: 782 minutes 20.50 seconds (46940.50 seconds total)