Starting phenix.real_space_refine on Sat Apr 13 05:54:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5s_31465/04_2024/7f5s_31465_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5s_31465/04_2024/7f5s_31465.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5s_31465/04_2024/7f5s_31465_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5s_31465/04_2024/7f5s_31465_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5s_31465/04_2024/7f5s_31465_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5s_31465/04_2024/7f5s_31465.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5s_31465/04_2024/7f5s_31465.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5s_31465/04_2024/7f5s_31465_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f5s_31465/04_2024/7f5s_31465_updated.pdb" } resolution = 2.72 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= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 5 6.06 5 P 3989 5.49 5 Mg 279 5.21 5 S 236 5.16 5 C 71504 2.51 5 N 26006 2.21 5 O 36600 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "LB PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LD TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LE TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LN TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LV TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lf PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 138619 Number of models: 1 Model: "" Number of chains: 69 Chain: "LA" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1898 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 14, 'TRANS': 233} Chain: "LB" Number of atoms: 3238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3238 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 15, 'TRANS': 386} Chain: "L5" Number of atoms: 79671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3715, 79671 Classifications: {'DNA': 4, 'RNA': 3711} Modifications used: {'rna2p': 11, 'rna2p_pur': 355, 'rna2p_pyr': 232, 'rna3p': 109, 'rna3p_pur': 1623, 'rna3p_pyr': 1360} Link IDs: {'rna2p': 597, 'rna3p': 3117} Chain breaks: 11 Unresolved non-hydrogen bonds: 156 Unresolved non-hydrogen angles: 372 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {' U:plan': 1, ' G:plan2': 1, ' C:plan': 3, ' C:plan2': 3, ' G:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "L7" Number of atoms: 2558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2558 Classifications: {'RNA': 120} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 55, 'rna3p_pyr': 53} Link IDs: {'rna2p': 12, 'rna3p': 107} Chain: "L8" Number of atoms: 3315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3315 Classifications: {'RNA': 156} Modifications used: {'5*END': 1, 'rna2p_pur': 14, 'rna2p_pyr': 12, 'rna3p': 1, 'rna3p_pur': 62, 'rna3p_pyr': 67} Link IDs: {'rna2p': 26, 'rna3p': 129} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "LC" Number of atoms: 2928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2928 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 18, 'TRANS': 349} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MLZ:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "LD" Number of atoms: 2382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2382 Classifications: {'peptide': 293} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 283} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "LE" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1791 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 209} Chain breaks: 2 Chain: "LF" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1870 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "LG" Number of atoms: 1922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1922 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 225} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "LH" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1518 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} Chain: "LI" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1656 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 192} Chain breaks: 1 Chain: "LJ" Number of atoms: 1401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1401 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 5, 'TRANS': 169} Chain: "LL" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1682 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 14, 'TRANS': 193} Chain: "LM" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1138 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 5, 'TRANS': 133} Chain: "LN" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1701 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 193} Chain: "LO" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1641 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 190} Chain: "LP" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1242 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "LQ" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1513 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain: "LR" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1566 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain: "LS" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1453 Classifications: {'peptide': 175} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 163} Chain: "LT" Number of atoms: 1298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1298 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 149} Chain: "LU" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 825 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "LV" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 979 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain: "LW" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 639 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "LX" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 976 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 110} Chain: "LY" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1115 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "LZ" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1107 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "La" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1162 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain: "Lb" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 877 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain breaks: 1 Chain: "Lc" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 764 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "Ld" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 888 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "Le" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1053 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "Lf" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 876 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "Lg" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 897 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "Lh" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1015 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "Li" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 832 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "Lj" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 705 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 3, 'TRANS': 82} Chain: "Lk" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "Ll" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 444 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "Lm" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 430 Classifications: {'peptide': 52} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 48} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MLZ:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "Ln" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 230 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Chain: "Lo" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 842 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "Lp" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'TRANS': 90} Chain: "Lr" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1002 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "LA" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "L5" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 260 Unusual residues: {' MG': 260} Classifications: {'undetermined': 260} Link IDs: {None: 259} Chain: "L7" 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: "L8" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "LI" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 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: "LP" 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: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LS" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LV" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Le" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Lf" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Lg" Number of atoms: 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: "Lj" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Lm" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Lo" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Lp" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L5" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "LH" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "La" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "Lb" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Le" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Lf" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Lm" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0NXD SG CYSLg 46 157.844 121.975 69.348 1.00 64.53 S ATOM A0NXU SG CYSLg 49 161.035 121.765 70.082 1.00 67.49 S ATOM A0O55 SG CYSLg 83 161.652 124.275 67.924 1.00 64.18 S ATOM A0O5P SG CYSLg 86 158.928 123.585 66.363 1.00 65.82 S ATOM A0PVB SG CYSLj 19 115.732 142.433 102.933 1.00 45.40 S ATOM A0PW3 SG CYSLj 22 113.290 143.375 105.853 1.00 46.70 S ATOM A0PYM SG CYSLj 34 115.054 140.037 105.730 1.00 43.13 S ATOM A0PZ5 SG CYSLj 37 112.111 141.226 103.394 1.00 44.97 S ATOM A0R7N SG CYSLm 96 136.395 85.062 199.707 1.00 58.91 S ATOM A0R8E SG CYSLm 99 137.922 88.551 199.765 1.00 59.18 S ATOM A0RAW SG CYSLm 110 135.076 87.380 202.511 1.00 59.92 S ATOM A0RC4 SG CYSLm 115 134.237 88.267 199.701 1.00 57.25 S ATOM A0RO0 SG CYSLo 12 58.506 69.842 122.687 1.00 58.23 S ATOM A0ROO SG CYSLo 15 55.705 68.374 121.779 1.00 60.58 S ATOM A0S1P SG CYSLo 72 59.170 66.950 121.040 1.00 62.68 S ATOM A0S2Q SG CYSLo 77 56.700 69.767 118.964 1.00 68.69 S ATOM A0SH7 SG CYSLp 39 162.766 106.648 74.531 1.00 57.40 S ATOM A0SHU SG CYSLp 42 166.004 108.608 73.779 1.00 58.38 S ATOM A0SL8 SG CYSLp 57 163.989 109.610 76.685 1.00 56.21 S ATOM A0SLO SG CYSLp 60 162.529 110.154 73.324 1.00 59.40 S Time building chain proxies: 52.96, per 1000 atoms: 0.38 Number of scatterers: 138619 At special positions: 0 Unit cell: (247.35, 209.52, 274.51, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 5 29.99 S 236 16.00 P 3989 15.00 Mg 279 11.99 O 36600 8.00 N 26006 7.00 C 71504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 58.71 Conformation dependent library (CDL) restraints added in 8.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNLg 202 " pdb="ZN ZNLg 202 " - pdb=" SG CYSLg 83 " pdb="ZN ZNLg 202 " - pdb=" SG CYSLg 46 " pdb="ZN ZNLg 202 " - pdb=" SG CYSLg 49 " pdb="ZN ZNLg 202 " - pdb=" SG CYSLg 86 " pdb=" ZNLj 101 " pdb="ZN ZNLj 101 " - pdb=" SG CYSLj 22 " pdb="ZN ZNLj 101 " - pdb=" SG CYSLj 34 " pdb="ZN ZNLj 101 " - pdb=" SG CYSLj 19 " pdb="ZN ZNLj 101 " - pdb=" SG CYSLj 37 " pdb=" ZNLm 201 " pdb="ZN ZNLm 201 " - pdb=" SG CYSLm 115 " pdb="ZN ZNLm 201 " - pdb=" SG CYSLm 110 " pdb="ZN ZNLm 201 " - pdb=" SG CYSLm 96 " pdb="ZN ZNLm 201 " - pdb=" SG CYSLm 99 " pdb=" ZNLo 201 " pdb="ZN ZNLo 201 " - pdb=" SG CYSLo 12 " pdb="ZN ZNLo 201 " - pdb=" SG CYSLo 72 " pdb="ZN ZNLo 201 " - pdb=" SG CYSLo 15 " pdb="ZN ZNLo 201 " - pdb=" SG CYSLo 77 " pdb=" ZNLp 101 " pdb="ZN ZNLp 101 " - pdb=" SG CYSLp 57 " pdb="ZN ZNLp 101 " - pdb=" SG CYSLp 60 " pdb="ZN ZNLp 101 " - pdb=" SG CYSLp 42 " pdb="ZN ZNLp 101 " - pdb=" SG CYSLp 39 " Number of angles added : 30 12822 Ramachandran restraints generated. 6411 Oldfield, 0 Emsley, 6411 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12140 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: 228 helices and 60 sheets defined 42.7% alpha, 13.4% beta 1145 base pairs and 1938 stacking pairs defined. Time for finding SS restraints: 69.87 Creating SS restraints... Processing helix chain 'LA' and resid 5 through 13 removed outlier: 6.205A pdb=" N LYSLA 10 " --> pdb=" O ARGLA 6 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLYLA 11 " --> pdb=" O GLYLA 7 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ALALA 12 " --> pdb=" O GLNLA 8 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLYLA 13 " --> pdb=" O ARGLA 9 " (cutoff:3.500A) Processing helix chain 'LA' and resid 33 through 39 Processing helix chain 'LA' and resid 103 through 108 removed outlier: 4.207A pdb=" N METLA 107 " --> pdb=" O PROLA 103 " (cutoff:3.500A) Proline residue: LA 108 - end of helix No H-bonds generated for 'chain 'LA' and resid 103 through 108' Processing helix chain 'LA' and resid 181 through 193 removed outlier: 3.563A pdb=" N ALALA 191 " --> pdb=" O HISLA 187 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYSLA 192 " --> pdb=" O LYSLA 188 " (cutoff:3.500A) Processing helix chain 'LA' and resid 200 through 205 removed outlier: 3.703A pdb=" N METLA 204 " --> pdb=" O ARGLA 200 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ASNLA 205 " --> pdb=" O GLYLA 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'LA' and resid 200 through 205' Processing helix chain 'LA' and resid 173 through 178 removed outlier: 3.649A pdb=" N LYSLA 177 " --> pdb=" O ARGLA 174 " (cutoff:3.500A) Proline residue: LA 178 - end of helix Processing helix chain 'LB' and resid 13 through 18 removed outlier: 4.598A pdb=" N LEULB 17 " --> pdb=" O SERLB 13 " (cutoff:3.500A) Proline residue: LB 18 - end of helix No H-bonds generated for 'chain 'LB' and resid 13 through 18' Processing helix chain 'LB' and resid 111 through 120 removed outlier: 4.284A pdb=" N ARGLB 117 " --> pdb=" O GLULB 113 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N PHELB 118 " --> pdb=" O CYSLB 114 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TYRLB 119 " --> pdb=" O LYSLB 115 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N LYSLB 120 " --> pdb=" O ARGLB 116 " (cutoff:3.500A) Processing helix chain 'LB' and resid 130 through 139 removed outlier: 4.117A pdb=" N LYSLB 135 " --> pdb=" O THRLB 131 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LYSLB 136 " --> pdb=" O LYSLB 132 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TRPLB 137 " --> pdb=" O TYRLB 133 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLNLB 138 " --> pdb=" O CYSLB 134 " (cutoff:3.500A) Processing helix chain 'LB' and resid 140 through 157 removed outlier: 3.699A pdb=" N LYSLB 144 " --> pdb=" O GLULB 140 " (cutoff:3.500A) Processing helix chain 'LB' and resid 167 through 172 removed outlier: 4.134A pdb=" N LEULB 171 " --> pdb=" O GLNLB 167 " (cutoff:3.500A) Proline residue: LB 172 - end of helix No H-bonds generated for 'chain 'LB' and resid 167 through 172' Processing helix chain 'LB' and resid 189 through 201 removed outlier: 3.635A pdb=" N ARGLB 200 " --> pdb=" O TRPLB 196 " (cutoff:3.500A) Processing helix chain 'LB' and resid 206 through 211 removed outlier: 3.664A pdb=" N VALLB 210 " --> pdb=" O PROLB 206 " (cutoff:3.500A) Processing helix chain 'LB' and resid 230 through 235 Processing helix chain 'LB' and resid 299 through 304 removed outlier: 5.285A pdb=" N ALALB 303 " --> pdb=" O ILELB 299 " (cutoff:3.500A) Processing helix chain 'LB' and resid 356 through 361 removed outlier: 3.729A pdb=" N GLULB 361 " --> pdb=" O ARGLB 357 " (cutoff:3.500A) Processing helix chain 'LB' and resid 381 through 390 removed outlier: 4.494A pdb=" N GLYLB 390 " --> pdb=" O LYSLB 386 " (cutoff:3.500A) Processing helix chain 'LB' and resid 392 through 402 Processing helix chain 'LC' and resid 25 through 31 removed outlier: 4.387A pdb=" N LYSLC 29 " --> pdb=" O PROLC 25 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALALC 30 " --> pdb=" O ALALC 26 " (cutoff:3.500A) Proline residue: LC 31 - end of helix No H-bonds generated for 'chain 'LC' and resid 25 through 31' Processing helix chain 'LC' and resid 33 through 49 removed outlier: 3.968A pdb=" N LYSLC 46 " --> pdb=" O THRLC 42 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASNLC 47 " --> pdb=" O ASNLC 43 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ASNLC 48 " --> pdb=" O LEULC 44 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ARGLC 49 " --> pdb=" O ARGLC 45 " (cutoff:3.500A) Processing helix chain 'LC' and resid 116 through 134 removed outlier: 3.693A pdb=" N ALALC 132 " --> pdb=" O LEULC 128 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEULC 133 " --> pdb=" O ALALC 129 " (cutoff:3.500A) Proline residue: LC 134 - end of helix Processing helix chain 'LC' and resid 135 through 141 removed outlier: 3.574A pdb=" N GLYLC 141 " --> pdb=" O VALLC 137 " (cutoff:3.500A) Processing helix chain 'LC' and resid 155 through 161 removed outlier: 4.735A pdb=" N GLULC 159 " --> pdb=" O GLULC 155 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLYLC 160 " --> pdb=" O ASPLC 156 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TYRLC 161 " --> pdb=" O LYSLC 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'LC' and resid 155 through 161' Processing helix chain 'LC' and resid 163 through 175 Processing helix chain 'LC' and resid 176 through 187 removed outlier: 3.703A pdb=" N ILELC 180 " --> pdb=" O ALALC 176 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLNLC 187 " --> pdb=" O VALLC 183 " (cutoff:3.500A) Processing helix chain 'LC' and resid 193 through 198 removed outlier: 3.615A pdb=" N ASNLC 198 " --> pdb=" O GLYLC 194 " (cutoff:3.500A) Processing helix chain 'LC' and resid 216 through 222 Processing helix chain 'LC' and resid 236 through 242 Proline residue: LC 242 - end of helix Processing helix chain 'LC' and resid 253 through 263 removed outlier: 3.577A pdb=" N LEULC 260 " --> pdb=" O ALALC 256 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASPLC 261 " --> pdb=" O PHELC 257 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLULC 262 " --> pdb=" O ARGLC 258 " (cutoff:3.500A) Processing helix chain 'LC' and resid 288 through 295 removed outlier: 3.585A pdb=" N SERLC 295 " --> pdb=" O ARGLC 291 " (cutoff:3.500A) Processing helix chain 'LC' and resid 296 through 303 removed outlier: 3.832A pdb=" N ALALC 301 " --> pdb=" O GLULC 297 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ARGLC 303 " --> pdb=" O GLNLC 299 " (cutoff:3.500A) Processing helix chain 'LC' and resid 321 through 329 Processing helix chain 'LC' and resid 330 through 368 removed outlier: 4.435A pdb=" N THRLC 334 " --> pdb=" O PROLC 330 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASPLC 366 " --> pdb=" O GLNLC 362 " (cutoff:3.500A) Processing helix chain 'LC' and resid 58 through 63 removed outlier: 5.627A pdb=" N GLNLC 61 " --> pdb=" O ALALC 58 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N THRLC 62 " --> pdb=" O GLYLC 59 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N SERLC 63 " --> pdb=" O HISLC 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'LC' and resid 58 through 63' Processing helix chain 'LD' and resid 9 through 16 removed outlier: 3.514A pdb=" N PHELD 13 " --> pdb=" O ASNLD 9 " (cutoff:3.500A) Processing helix chain 'LD' and resid 20 through 26 removed outlier: 3.624A pdb=" N GLYLD 26 " --> pdb=" O ARGLD 22 " (cutoff:3.500A) Processing helix chain 'LD' and resid 29 through 37 removed outlier: 3.822A pdb=" N ARGLD 35 " --> pdb=" O TYRLD 31 " (cutoff:3.500A) Processing helix chain 'LD' and resid 79 through 84 removed outlier: 3.879A pdb=" N LEULD 83 " --> pdb=" O TYRLD 79 " (cutoff:3.500A) Proline residue: LD 84 - end of helix No H-bonds generated for 'chain 'LD' and resid 79 through 84' Processing helix chain 'LD' and resid 94 through 114 Processing helix chain 'LD' and resid 115 through 120 removed outlier: 4.308A pdb=" N TYRLD 119 " --> pdb=" O METLD 115 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLULD 120 " --> pdb=" O ASPLD 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'LD' and resid 115 through 120' Processing helix chain 'LD' and resid 157 through 170 removed outlier: 3.577A pdb=" N GLYLD 161 " --> pdb=" O ASNLD 157 " (cutoff:3.500A) Processing helix chain 'LD' and resid 191 through 201 removed outlier: 6.028A pdb=" N HISLD 195 " --> pdb=" O ASNLD 191 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ARGLD 196 " --> pdb=" O ALALD 192 " (cutoff:3.500A) Processing helix chain 'LD' and resid 202 through 215 removed outlier: 3.878A pdb=" N GLULD 213 " --> pdb=" O ARGLD 209 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLULD 214 " --> pdb=" O TYRLD 210 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASPLD 215 " --> pdb=" O LEULD 211 " (cutoff:3.500A) Processing helix chain 'LD' and resid 216 through 224 removed outlier: 3.980A pdb=" N SERLD 224 " --> pdb=" O LYSLD 220 " (cutoff:3.500A) Processing helix chain 'LD' and resid 225 through 230 removed outlier: 4.514A pdb=" N ASNLD 229 " --> pdb=" O GLNLD 225 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SERLD 230 " --> pdb=" O TYRLD 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'LD' and resid 225 through 230' Processing helix chain 'LD' and resid 232 through 250 removed outlier: 4.022A pdb=" N METLD 236 " --> pdb=" O THRLD 232 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N GLULD 237 " --> pdb=" O PROLD 233 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLULD 238 " --> pdb=" O ASPLD 234 " (cutoff:3.500A) Processing helix chain 'LD' and resid 272 through 294 removed outlier: 3.894A pdb=" N ALALD 290 " --> pdb=" O SERLD 286 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARGLD 293 " --> pdb=" O ARGLD 289 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ALALD 294 " --> pdb=" O ALALD 290 " (cutoff:3.500A) Processing helix chain 'LE' and resid 58 through 67 Processing helix chain 'LE' and resid 132 through 137 removed outlier: 6.078A pdb=" N VALLE 137 " --> pdb=" O PHELE 133 " (cutoff:3.500A) Processing helix chain 'LE' and resid 190 through 195 removed outlier: 3.792A pdb=" N VALLE 194 " --> pdb=" O HISLE 190 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILELE 195 " --> pdb=" O GLNLE 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'LE' and resid 190 through 195' Processing helix chain 'LE' and resid 213 through 218 Processing helix chain 'LE' and resid 243 through 262 removed outlier: 4.282A pdb=" N GLNLE 256 " --> pdb=" O ALALE 252 " (cutoff:3.500A) Proline residue: LE 259 - end of helix Processing helix chain 'LE' and resid 266 through 274 removed outlier: 3.520A pdb=" N ARGLE 272 " --> pdb=" O GLNLE 268 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N VALLE 274 " --> pdb=" O TYRLE 270 " (cutoff:3.500A) Processing helix chain 'LE' and resid 282 through 287 removed outlier: 5.629A pdb=" N VALLE 287 " --> pdb=" O PROLE 283 " (cutoff:3.500A) Processing helix chain 'LF' and resid 24 through 79 removed outlier: 4.513A pdb=" N LEULF 28 " --> pdb=" O ASNLF 24 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N LYSLF 29 " --> pdb=" O PHELF 25 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILELF 30 " --> pdb=" O ALALF 26 " (cutoff:3.500A) Processing helix chain 'LF' and resid 102 through 113 Processing helix chain 'LF' and resid 126 through 137 removed outlier: 3.569A pdb=" N METLF 132 " --> pdb=" O ALALF 128 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLULF 137 " --> pdb=" O LEULF 133 " (cutoff:3.500A) Processing helix chain 'LF' and resid 146 through 156 Processing helix chain 'LF' and resid 171 through 179 removed outlier: 4.062A pdb=" N ILELF 175 " --> pdb=" O ASPLF 171 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SERLF 178 " --> pdb=" O LEULF 174 " (cutoff:3.500A) Processing helix chain 'LF' and resid 186 through 197 removed outlier: 4.265A pdb=" N VALLF 197 " --> pdb=" O GLULF 193 " (cutoff:3.500A) Processing helix chain 'LF' and resid 200 through 209 removed outlier: 5.334A pdb=" N TRPLF 209 " --> pdb=" O ASNLF 205 " (cutoff:3.500A) Processing helix chain 'LF' and resid 238 through 248 removed outlier: 4.673A pdb=" N ARGLF 242 " --> pdb=" O ASPLF 238 " (cutoff:3.500A) Processing helix chain 'LG' and resid 58 through 74 removed outlier: 3.946A pdb=" N LYSLG 72 " --> pdb=" O ALALG 68 " (cutoff:3.500A) Processing helix chain 'LG' and resid 77 through 86 removed outlier: 5.094A pdb=" N PHELG 83 " --> pdb=" O ALALG 79 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N THRLG 84 " --> pdb=" O ILELG 80 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLNLG 85 " --> pdb=" O ASNLG 81 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ALALG 86 " --> pdb=" O GLNLG 82 " (cutoff:3.500A) Processing helix chain 'LG' and resid 88 through 103 removed outlier: 4.368A pdb=" N LYSLG 101 " --> pdb=" O LYSLG 97 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N TYRLG 102 " --> pdb=" O LEULG 98 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ARGLG 103 " --> pdb=" O ALALG 99 " (cutoff:3.500A) Processing helix chain 'LG' and resid 106 through 124 removed outlier: 4.254A pdb=" N GLYLG 124 " --> pdb=" O LYSLG 120 " (cutoff:3.500A) Processing helix chain 'LG' and resid 139 through 150 removed outlier: 3.505A pdb=" N ASNLG 149 " --> pdb=" O THRLG 145 " (cutoff:3.500A) Processing helix chain 'LG' and resid 164 through 178 removed outlier: 5.120A pdb=" N VALLG 168 " --> pdb=" O ILELG 164 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N PHELG 169 " --> pdb=" O GLULG 165 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N LEULG 170 " --> pdb=" O LEULG 166 " (cutoff:3.500A) Proline residue: LG 171 - end of helix removed outlier: 3.508A pdb=" N ARGLG 175 " --> pdb=" O PROLG 171 " (cutoff:3.500A) Processing helix chain 'LG' and resid 186 through 195 removed outlier: 3.731A pdb=" N LEULG 190 " --> pdb=" O GLYLG 186 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEULG 193 " --> pdb=" O ARGLG 189 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VALLG 194 " --> pdb=" O LEULG 190 " (cutoff:3.500A) Processing helix chain 'LG' and resid 208 through 226 removed outlier: 5.029A pdb=" N GLYLG 213 " --> pdb=" O SERLG 209 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ALALG 214 " --> pdb=" O GLULG 210 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEULG 218 " --> pdb=" O ALALG 214 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLULG 220 " --> pdb=" O ALALG 216 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASNLG 225 " --> pdb=" O ALALG 221 " (cutoff:3.500A) Processing helix chain 'LG' and resid 229 through 236 removed outlier: 4.148A pdb=" N ILELG 233 " --> pdb=" O ARGLG 229 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARGLG 235 " --> pdb=" O ASPLG 231 " (cutoff:3.500A) Processing helix chain 'LG' and resid 243 through 265 removed outlier: 3.528A pdb=" N LYSLG 259 " --> pdb=" O LYSLG 255 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLULG 260 " --> pdb=" O ALALG 256 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEULG 261 " --> pdb=" O LYSLG 257 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALALG 262 " --> pdb=" O ALALG 258 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N THRLG 263 " --> pdb=" O LYSLG 259 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N LEULG 265 " --> pdb=" O LEULG 261 " (cutoff:3.500A) Processing helix chain 'LH' and resid 63 through 86 removed outlier: 4.092A pdb=" N THRLH 69 " --> pdb=" O LYSLH 65 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VALLH 70 " --> pdb=" O GLULH 66 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ARGLH 71 " --> pdb=" O LEULH 67 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THRLH 72 " --> pdb=" O ALALH 68 " (cutoff:3.500A) Processing helix chain 'LH' and resid 150 through 166 removed outlier: 3.656A pdb=" N ASNLH 156 " --> pdb=" O GLULH 152 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THRLH 166 " --> pdb=" O GLNLH 162 " (cutoff:3.500A) Processing helix chain 'LH' and resid 171 through 176 removed outlier: 3.895A pdb=" N PHELH 175 " --> pdb=" O ASPLH 171 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEULH 176 " --> pdb=" O ILELH 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'LH' and resid 171 through 176' Processing helix chain 'LI' and resid 5 through 10 removed outlier: 4.360A pdb=" N TYRLI 9 " --> pdb=" O PROLI 5 " (cutoff:3.500A) Processing helix chain 'LI' and resid 42 through 47 removed outlier: 6.169A pdb=" N PHELI 46 " --> pdb=" O LYSLI 42 " (cutoff:3.500A) Proline residue: LI 47 - end of helix No H-bonds generated for 'chain 'LI' and resid 42 through 47' Processing helix chain 'LI' and resid 61 through 80 Processing helix chain 'LI' and resid 144 through 160 removed outlier: 3.551A pdb=" N LYSLI 156 " --> pdb=" O LEULI 152 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N PHELI 157 " --> pdb=" O ARGLI 153 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LYSLI 158 " --> pdb=" O ARGLI 154 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N PHELI 159 " --> pdb=" O ALALI 155 " (cutoff:3.500A) Proline residue: LI 160 - end of helix Processing helix chain 'LI' and resid 177 through 188 removed outlier: 4.581A pdb=" N GLULI 182 " --> pdb=" O ALALI 178 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ASPLI 183 " --> pdb=" O ASPLI 179 " (cutoff:3.500A) Processing helix chain 'LI' and resid 205 through 214 removed outlier: 3.969A pdb=" N TRPLI 209 " --> pdb=" O PROLI 205 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 30 through 44 Processing helix chain 'LJ' and resid 76 through 91 removed outlier: 3.835A pdb=" N GLULJ 80 " --> pdb=" O GLYLJ 76 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VALLJ 89 " --> pdb=" O LYSLJ 85 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 111 through 116 removed outlier: 4.266A pdb=" N LEULJ 115 " --> pdb=" O GLULJ 111 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLYLJ 116 " --> pdb=" O HISLJ 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'LJ' and resid 111 through 116' Processing helix chain 'LJ' and resid 139 through 144 removed outlier: 4.580A pdb=" N ASPLJ 143 " --> pdb=" O PHELJ 139 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 158 through 170 removed outlier: 3.544A pdb=" N ARGLJ 164 " --> pdb=" O GLULJ 160 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYRLJ 170 " --> pdb=" O PHELJ 166 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 7 through 12 removed outlier: 5.461A pdb=" N ASNLJ 10 " --> pdb=" O GLULJ 7 " (cutoff:3.500A) Proline residue: LJ 11 - end of helix No H-bonds generated for 'chain 'LJ' and resid 7 through 12' Processing helix chain 'LL' and resid 17 through 22 removed outlier: 4.452A pdb=" N ARGLL 21 " --> pdb=" O ASPLL 17 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VALLL 22 " --> pdb=" O TRPLL 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'LL' and resid 17 through 22' Processing helix chain 'LL' and resid 27 through 47 removed outlier: 4.603A pdb=" N ALALL 47 " --> pdb=" O ALALL 43 " (cutoff:3.500A) Processing helix chain 'LL' and resid 77 through 85 Processing helix chain 'LL' and resid 87 through 95 removed outlier: 4.665A pdb=" N ARGLL 92 " --> pdb=" O LYSLL 88 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N THRLL 93 " --> pdb=" O LYSLL 89 " (cutoff:3.500A) Processing helix chain 'LL' and resid 106 through 124 removed outlier: 3.518A pdb=" N LEULL 110 " --> pdb=" O SERLL 106 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYSLL 123 " --> pdb=" O GLULL 119 " (cutoff:3.500A) Processing helix chain 'LL' and resid 139 through 146 removed outlier: 3.757A pdb=" N LYSLL 145 " --> pdb=" O ALALL 141 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEULL 146 " --> pdb=" O GLULL 142 " (cutoff:3.500A) Processing helix chain 'LL' and resid 170 through 176 removed outlier: 3.648A pdb=" N PHELL 176 " --> pdb=" O GLULL 172 " (cutoff:3.500A) Processing helix chain 'LL' and resid 177 through 192 Processing helix chain 'LL' and resid 193 through 209 removed outlier: 3.699A pdb=" N GLULL 204 " --> pdb=" O LYSLL 200 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLNLL 205 " --> pdb=" O GLULL 201 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYSLL 209 " --> pdb=" O GLNLL 205 " (cutoff:3.500A) Processing helix chain 'LM' and resid 51 through 56 removed outlier: 3.860A pdb=" N METLM 55 " --> pdb=" O PROLM 51 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N GLNLM 56 " --> pdb=" O PHELM 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'LM' and resid 51 through 56' Processing helix chain 'LM' and resid 69 through 81 removed outlier: 4.852A pdb=" N ALALM 80 " --> pdb=" O ALALM 76 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASPLM 81 " --> pdb=" O TRPLM 77 " (cutoff:3.500A) Processing helix chain 'LM' and resid 82 through 90 removed outlier: 4.562A pdb=" N ALALM 87 " --> pdb=" O ASNLM 83 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALALM 88 " --> pdb=" O THRLM 84 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N ARGLM 90 " --> pdb=" O TRPLM 86 " (cutoff:3.500A) Processing helix chain 'LM' and resid 91 through 104 removed outlier: 3.824A pdb=" N METLM 104 " --> pdb=" O ARGLM 100 " (cutoff:3.500A) Processing helix chain 'LM' and resid 106 through 137 removed outlier: 3.624A pdb=" N LYSLM 132 " --> pdb=" O LYSLM 128 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEULM 135 " --> pdb=" O GLNLM 131 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LYSLM 137 " --> pdb=" O ALALM 133 " (cutoff:3.500A) Processing helix chain 'LN' and resid 2 through 14 removed outlier: 4.159A pdb=" N TYRLN 6 " --> pdb=" O GLYLN 2 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYSLN 13 " --> pdb=" O GLULN 9 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N LYSLN 14 " --> pdb=" O LEULN 10 " (cutoff:3.500A) Processing helix chain 'LN' and resid 16 through 34 removed outlier: 3.537A pdb=" N GLNLN 32 " --> pdb=" O TRPLN 28 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEULN 33 " --> pdb=" O GLNLN 29 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N SERLN 34 " --> pdb=" O TYRLN 30 " (cutoff:3.500A) Processing helix chain 'LN' and resid 44 through 52 Processing helix chain 'LN' and resid 83 through 88 removed outlier: 4.171A pdb=" N HISLN 87 " --> pdb=" O LYSLN 83 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N GLYLN 88 " --> pdb=" O PROLN 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'LN' and resid 83 through 88' Processing helix chain 'LN' and resid 97 through 111 removed outlier: 3.716A pdb=" N GLYLN 111 " --> pdb=" O GLYLN 107 " (cutoff:3.500A) Processing helix chain 'LN' and resid 139 through 145 removed outlier: 3.918A pdb=" N ASNLN 145 " --> pdb=" O ALALN 141 " (cutoff:3.500A) Processing helix chain 'LN' and resid 148 through 153 removed outlier: 4.496A pdb=" N THRLN 152 " --> pdb=" O THRLN 148 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LYSLN 153 " --> pdb=" O GLNLN 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'LN' and resid 148 through 153' Processing helix chain 'LN' and resid 158 through 163 removed outlier: 3.505A pdb=" N ARGLN 162 " --> pdb=" O HISLN 158 " (cutoff:3.500A) Processing helix chain 'LN' and resid 165 through 173 removed outlier: 4.146A pdb=" N SERLN 171 " --> pdb=" O ALALN 167 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARGLN 172 " --> pdb=" O GLYLN 168 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLYLN 173 " --> pdb=" O ARGLN 169 " (cutoff:3.500A) Processing helix chain 'LN' and resid 187 through 197 Processing helix chain 'LO' and resid 15 through 30 removed outlier: 3.517A pdb=" N LEULO 29 " --> pdb=" O LYSLO 25 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLYLO 30 " --> pdb=" O GLNLO 26 " (cutoff:3.500A) Processing helix chain 'LO' and resid 46 through 61 removed outlier: 3.726A pdb=" N LYSLO 60 " --> pdb=" O ALALO 56 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ARGLO 61 " --> pdb=" O PHELO 57 " (cutoff:3.500A) Processing helix chain 'LO' and resid 65 through 70 removed outlier: 3.626A pdb=" N GLYLO 69 " --> pdb=" O ASNLO 65 " (cutoff:3.500A) Proline residue: LO 70 - end of helix No H-bonds generated for 'chain 'LO' and resid 65 through 70' Processing helix chain 'LO' and resid 75 through 89 removed outlier: 3.592A pdb=" N METLO 87 " --> pdb=" O THRLO 83 " (cutoff:3.500A) Proline residue: LO 89 - end of helix Processing helix chain 'LO' and resid 92 through 103 removed outlier: 3.519A pdb=" N ARGLO 101 " --> pdb=" O ALALO 97 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEULO 102 " --> pdb=" O ALALO 98 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N LYSLO 103 " --> pdb=" O LEULO 99 " (cutoff:3.500A) Processing helix chain 'LO' and resid 124 through 129 Processing helix chain 'LO' and resid 137 through 146 Processing helix chain 'LO' and resid 151 through 190 removed outlier: 3.871A pdb=" N GLULO 186 " --> pdb=" O GLULO 182 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N LYSLO 187 " --> pdb=" O LYSLO 183 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LYSLO 188 " --> pdb=" O ASNLO 184 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILELO 189 " --> pdb=" O VALLO 185 " (cutoff:3.500A) Processing helix chain 'LO' and resid 191 through 200 removed outlier: 3.540A pdb=" N VALLO 195 " --> pdb=" O LYSLO 191 " (cutoff:3.500A) Processing helix chain 'LP' and resid 10 through 15 removed outlier: 3.776A pdb=" N SERLP 14 " --> pdb=" O ASNLP 10 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N CYSLP 15 " --> pdb=" O PROLP 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'LP' and resid 10 through 15' Processing helix chain 'LP' and resid 25 through 37 Processing helix chain 'LP' and resid 40 through 54 Processing helix chain 'LP' and resid 70 through 77 removed outlier: 4.476A pdb=" N LYSLP 74 " --> pdb=" O CYSLP 70 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N GLNLP 75 " --> pdb=" O ALALP 71 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N TRPLP 76 " --> pdb=" O GLNLP 72 " (cutoff:3.500A) Processing helix chain 'LP' and resid 84 through 106 Processing helix chain 'LQ' and resid 22 through 39 removed outlier: 3.548A pdb=" N PHELQ 34 " --> pdb=" O LYSLQ 30 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 41 through 54 removed outlier: 3.946A pdb=" N GLNLQ 45 " --> pdb=" O SERLQ 41 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHELQ 52 " --> pdb=" O LEULQ 48 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N METLQ 53 " --> pdb=" O LYSLQ 49 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N SERLQ 54 " --> pdb=" O ARGLQ 50 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 62 through 72 removed outlier: 3.891A pdb=" N LEULQ 72 " --> pdb=" O ARGLQ 68 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 106 through 117 removed outlier: 3.684A pdb=" N GLYLQ 117 " --> pdb=" O ILELQ 113 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 122 through 130 Processing helix chain 'LQ' and resid 146 through 153 removed outlier: 4.327A pdb=" N ARGLQ 150 " --> pdb=" O ARGLQ 146 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N HISLQ 151 " --> pdb=" O GLULQ 147 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLYLQ 153 " --> pdb=" O TYRLQ 149 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 171 through 176 removed outlier: 5.087A pdb=" N GLULQ 175 " --> pdb=" O GLYLQ 171 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ARGLQ 176 " --> pdb=" O ARGLQ 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'LQ' and resid 171 through 176' Processing helix chain 'LR' and resid 4 through 16 Processing helix chain 'LR' and resid 18 through 23 removed outlier: 3.707A pdb=" N VALLR 22 " --> pdb=" O GLYLR 18 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N TRPLR 23 " --> pdb=" O LYSLR 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'LR' and resid 18 through 23' Processing helix chain 'LR' and resid 28 through 36 removed outlier: 3.685A pdb=" N ASNLR 34 " --> pdb=" O ASNLR 30 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ALALR 35 " --> pdb=" O GLULR 31 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ASNLR 36 " --> pdb=" O ILELR 32 " (cutoff:3.500A) Processing helix chain 'LR' and resid 37 through 48 Processing helix chain 'LR' and resid 60 through 73 Processing helix chain 'LR' and resid 84 through 113 Proline residue: LR 90 - end of helix removed outlier: 6.456A pdb=" N VALLR 93 " --> pdb=" O METLR 89 " (cutoff:3.500A) Processing helix chain 'LR' and resid 116 through 130 Processing helix chain 'LR' and resid 134 through 188 removed outlier: 3.579A pdb=" N GLULR 160 " --> pdb=" O ALALR 156 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THRLR 166 " --> pdb=" O ARGLR 162 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLULR 175 " --> pdb=" O LYSLR 171 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARGLR 176 " --> pdb=" O ARGLR 172 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N GLNLR 178 " --> pdb=" O GLULR 174 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ALALR 179 " --> pdb=" O GLULR 175 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N LYSLR 180 " --> pdb=" O ARGLR 176 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N LYSLR 181 " --> pdb=" O LEULR 177 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILELR 184 " --> pdb=" O LYSLR 180 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N ILELR 185 " --> pdb=" O LYSLR 181 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N LYSLR 186 " --> pdb=" O GLULR 182 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N THRLR 187 " --> pdb=" O GLULR 183 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEULR 188 " --> pdb=" O ILELR 184 " (cutoff:3.500A) Processing helix chain 'LS' and resid 36 through 52 removed outlier: 3.581A pdb=" N GLNLS 50 " --> pdb=" O TYRLS 46 " (cutoff:3.500A) Processing helix chain 'LS' and resid 101 through 117 Processing helix chain 'LS' and resid 120 through 125 removed outlier: 3.812A pdb=" N ILELS 124 " --> pdb=" O ARGLS 120 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N GLNLS 125 " --> pdb=" O ALALS 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'LS' and resid 120 through 125' Processing helix chain 'LS' and resid 139 through 147 removed outlier: 4.592A pdb=" N PHELS 145 " --> pdb=" O ALALS 141 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N HISLS 146 " --> pdb=" O VALLS 142 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ASPLS 147 " --> pdb=" O LYSLS 143 " (cutoff:3.500A) Processing helix chain 'LS' and resid 161 through 166 Proline residue: LS 165 - end of helix No H-bonds generated for 'chain 'LS' and resid 161 through 166' Processing helix chain 'LT' and resid 11 through 16 removed outlier: 3.555A pdb=" N PHELT 15 " --> pdb=" O THRLT 11 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N SERLT 16 " --> pdb=" O ARGLT 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'LT' and resid 11 through 16' Processing helix chain 'LT' and resid 26 through 32 removed outlier: 4.416A pdb=" N TYRLT 30 " --> pdb=" O PROLT 26 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARGLT 32 " --> pdb=" O ALALT 28 " (cutoff:3.500A) Processing helix chain 'LT' and resid 54 through 59 removed outlier: 3.617A pdb=" N HISLT 58 " --> pdb=" O HISLT 54 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N GLYLT 59 " --> pdb=" O LYSLT 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'LT' and resid 54 through 59' Processing helix chain 'LT' and resid 92 through 97 removed outlier: 4.100A pdb=" N ILELT 96 " --> pdb=" O ARGLT 92 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N LYSLT 97 " --> pdb=" O ILELT 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'LT' and resid 92 through 97' Processing helix chain 'LT' and resid 99 through 123 removed outlier: 4.029A pdb=" N ASPLT 103 " --> pdb=" O SERLT 99 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHELT 105 " --> pdb=" O SERLT 101 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARGLT 108 " --> pdb=" O SERLT 104 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYSLT 120 " --> pdb=" O LYSLT 116 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLULT 121 " --> pdb=" O LYSLT 117 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYSLT 122 " --> pdb=" O GLULT 118 " (cutoff:3.500A) Processing helix chain 'LU' and resid 25 through 32 removed outlier: 3.819A pdb=" N VALLU 29 " --> pdb=" O CYSLU 25 " (cutoff:3.500A) Processing helix chain 'LU' and resid 35 through 46 removed outlier: 3.708A pdb=" N GLULU 45 " --> pdb=" O GLNLU 41 " (cutoff:3.500A) Processing helix chain 'LU' and resid 55 through 60 removed outlier: 3.876A pdb=" N GLYLU 59 " --> pdb=" O ASNLU 55 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VALLU 60 " --> pdb=" O LEULU 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'LU' and resid 55 through 60' Processing helix chain 'LU' and resid 79 through 95 removed outlier: 4.298A pdb=" N LEULU 83 " --> pdb=" O SERLU 79 " (cutoff:3.500A) Processing helix chain 'LV' and resid 69 through 74 removed outlier: 3.564A pdb=" N ARGLV 73 " --> pdb=" O LYSLV 69 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LYSLV 74 " --> pdb=" O PROLV 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'LV' and resid 69 through 74' Processing helix chain 'LV' and resid 122 through 130 removed outlier: 3.596A pdb=" N LEULV 128 " --> pdb=" O GLULV 124 " (cutoff:3.500A) Proline residue: LV 130 - end of helix Processing helix chain 'LV' and resid 131 through 136 removed outlier: 4.366A pdb=" N ASNLV 135 " --> pdb=" O ARGLV 131 " (cutoff:3.500A) Processing helix chain 'LW' and resid 33 through 43 Processing helix chain 'LW' and resid 45 through 50 removed outlier: 3.774A pdb=" N ILELW 49 " --> pdb=" O ASNLW 45 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ASNLW 50 " --> pdb=" O PROLW 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'LW' and resid 45 through 50' Processing helix chain 'LW' and resid 52 through 60 Processing helix chain 'LX' and resid 72 through 78 removed outlier: 4.680A pdb=" N LYSLX 78 " --> pdb=" O TYRLX 74 " (cutoff:3.500A) Processing helix chain 'LX' and resid 83 through 92 Processing helix chain 'LX' and resid 105 through 117 Processing helix chain 'LX' and resid 145 through 154 Processing helix chain 'LY' and resid 10 through 21 removed outlier: 3.627A pdb=" N ALALY 21 " --> pdb=" O ARGLY 17 " (cutoff:3.500A) Processing helix chain 'LY' and resid 22 through 31 removed outlier: 4.065A pdb=" N LYSLY 28 " --> pdb=" O HISLY 24 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SERLY 31 " --> pdb=" O ARGLY 27 " (cutoff:3.500A) Processing helix chain 'LY' and resid 35 through 43 removed outlier: 4.246A pdb=" N ASNLY 43 " --> pdb=" O ARGLY 39 " (cutoff:3.500A) Processing helix chain 'LY' and resid 100 through 105 removed outlier: 3.854A pdb=" N VALLY 104 " --> pdb=" O HISLY 100 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N VALLY 105 " --> pdb=" O PROLY 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'LY' and resid 100 through 105' Processing helix chain 'LY' and resid 112 through 134 removed outlier: 3.733A pdb=" N GLYLY 133 " --> pdb=" O GLYLY 129 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LYSLY 134 " --> pdb=" O LYSLY 130 " (cutoff:3.500A) Processing helix chain 'LZ' and resid 58 through 67 removed outlier: 4.129A pdb=" N LYSLZ 67 " --> pdb=" O ALALZ 63 " (cutoff:3.500A) Processing helix chain 'LZ' and resid 76 through 81 removed outlier: 3.555A pdb=" N LEULZ 80 " --> pdb=" O ASNLZ 76 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N METLZ 81 " --> pdb=" O TYRLZ 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'LZ' and resid 76 through 81' Processing helix chain 'LZ' and resid 92 through 97 removed outlier: 3.856A pdb=" N ASNLZ 97 " --> pdb=" O LYSLZ 93 " (cutoff:3.500A) Processing helix chain 'LZ' and resid 103 through 125 removed outlier: 4.620A pdb=" N THRLZ 124 " --> pdb=" O GLULZ 120 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLYLZ 125 " --> pdb=" O ARGLZ 121 " (cutoff:3.500A) Processing helix chain 'LZ' and resid 127 through 133 removed outlier: 3.557A pdb=" N PHELZ 131 " --> pdb=" O ASNLZ 127 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N LYSLZ 133 " --> pdb=" O TRPLZ 129 " (cutoff:3.500A) Processing helix chain 'La' and resid 2 through 7 removed outlier: 4.262A pdb=" N ARGLa 6 " --> pdb=" O PROLa 2 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N LYSLa 7 " --> pdb=" O SERLa 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'La' and resid 2 through 7' Processing helix chain 'La' and resid 41 through 48 Processing helix chain 'La' and resid 64 through 69 removed outlier: 4.048A pdb=" N SERLa 68 " --> pdb=" O LYSLa 64 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHELa 69 " --> pdb=" O ARGLa 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'La' and resid 64 through 69' Processing helix chain 'La' and resid 74 through 83 removed outlier: 4.532A pdb=" N TRPLa 79 " --> pdb=" O LEULa 75 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N THRLa 80 " --> pdb=" O ASPLa 76 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEULa 81 " --> pdb=" O LYSLa 77 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VALLa 82 " --> pdb=" O LEULa 78 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N SERLa 83 " --> pdb=" O TRPLa 79 " (cutoff:3.500A) Processing helix chain 'La' and resid 84 through 93 Processing helix chain 'La' and resid 102 through 107 removed outlier: 3.648A pdb=" N SERLa 106 " --> pdb=" O ASPLa 102 " (cutoff:3.500A) Processing helix chain 'La' and resid 130 through 141 Processing helix chain 'La' and resid 9 through 14 removed outlier: 4.135A pdb=" N ARGLa 12 " --> pdb=" O ARGLa 9 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLYLa 13 " --> pdb=" O LYSLa 10 " (cutoff:3.500A) Processing helix chain 'Lb' and resid 11 through 20 removed outlier: 3.720A pdb=" N ARGLb 18 " --> pdb=" O ARGLb 14 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ASNLb 19 " --> pdb=" O LYSLb 15 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLYLb 20 " --> pdb=" O TRPLb 16 " (cutoff:3.500A) Processing helix chain 'Lb' and resid 36 through 55 removed outlier: 4.925A pdb=" N LYSLb 51 " --> pdb=" O LYSLb 47 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N LYSLb 52 " --> pdb=" O LYSLb 48 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N GLYLb 53 " --> pdb=" O HISLb 49 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEULb 54 " --> pdb=" O ASNLb 50 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LYSLb 55 " --> pdb=" O LYSLb 51 " (cutoff:3.500A) Processing helix chain 'Lb' and resid 56 through 74 removed outlier: 3.553A pdb=" N ALALb 64 " --> pdb=" O ASNLb 60 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ALALb 71 " --> pdb=" O ALALb 67 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALALb 74 " --> pdb=" O GLULb 70 " (cutoff:3.500A) Processing helix chain 'Lb' and resid 91 through 102 Proline residue: Lb 102 - end of helix Processing helix chain 'Lb' and resid 105 through 118 removed outlier: 3.676A pdb=" N ILELb 112 " --> pdb=" O ALALb 108 " (cutoff:3.500A) Processing helix chain 'Lc' and resid 9 through 25 removed outlier: 3.536A pdb=" N ILELc 14 " --> pdb=" O SERLc 10 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASNLc 15 " --> pdb=" O LEULc 11 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SERLc 16 " --> pdb=" O GLULc 12 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N METLc 22 " --> pdb=" O LEULc 18 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N LYSLc 23 " --> pdb=" O GLNLc 19 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SERLc 24 " --> pdb=" O LEULc 20 " (cutoff:3.500A) Processing helix chain 'Lc' and resid 30 through 41 Processing helix chain 'Lc' and resid 53 through 68 Processing helix chain 'Lc' and resid 77 through 86 Processing helix chain 'Ld' and resid 28 through 34 removed outlier: 3.938A pdb=" N ARGLd 32 " --> pdb=" O ASNLd 28 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N HISLd 34 " --> pdb=" O HISLd 30 " (cutoff:3.500A) Processing helix chain 'Ld' and resid 41 through 57 Processing helix chain 'Ld' and resid 65 through 74 Processing helix chain 'Le' and resid 24 through 29 removed outlier: 3.588A pdb=" N TYRLe 28 " --> pdb=" O GLNLe 24 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N VALLe 29 " --> pdb=" O SERLe 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'Le' and resid 24 through 29' Processing helix chain 'Le' and resid 43 through 48 Processing helix chain 'Le' and resid 81 through 92 removed outlier: 3.639A pdb=" N LEULe 85 " --> pdb=" O ASNLe 81 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLULe 86 " --> pdb=" O VALLe 82 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VALLe 87 " --> pdb=" O LYSLe 83 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N LEULe 88 " --> pdb=" O GLULe 84 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEULe 89 " --> pdb=" O LEULe 85 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N METLe 90 " --> pdb=" O GLULe 86 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N CYSLe 91 " --> pdb=" O VALLe 87 " (cutoff:3.500A) Processing helix chain 'Le' and resid 104 through 119 removed outlier: 4.075A pdb=" N ALALe 110 " --> pdb=" O LYSLe 106 " (cutoff:3.500A) Processing helix chain 'Lf' and resid 35 through 44 removed outlier: 4.484A pdb=" N GLULf 40 " --> pdb=" O ARGLf 36 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N PHELf 41 " --> pdb=" O ASPLf 37 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N TYRLf 42 " --> pdb=" O GLULf 38 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEULf 43 " --> pdb=" O THRLf 39 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N GLYLf 44 " --> pdb=" O GLULf 40 " (cutoff:3.500A) Processing helix chain 'Lg' and resid 60 through 68 removed outlier: 3.624A pdb=" N LEULg 64 " --> pdb=" O ARGLg 60 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N METLg 65 " --> pdb=" O PROLg 61 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ARGLg 66 " --> pdb=" O LYSLg 62 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N SERLg 68 " --> pdb=" O LEULg 64 " (cutoff:3.500A) Processing helix chain 'Lg' and resid 83 through 112 removed outlier: 4.362A pdb=" N GLNLg 112 " --> pdb=" O LYSLg 108 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 5 through 13 removed outlier: 4.647A pdb=" N GLYLh 11 " --> pdb=" O ARGLh 7 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LYSLh 12 " --> pdb=" O ASPLh 8 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N LYSLh 13 " --> pdb=" O LEULh 9 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 14 through 38 removed outlier: 3.557A pdb=" N VALLh 36 " --> pdb=" O ARGLh 32 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLYLh 38 " --> pdb=" O ALALh 34 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 40 through 74 removed outlier: 3.730A pdb=" N LYSLh 46 " --> pdb=" O SERLh 42 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILELh 47 " --> pdb=" O LYSLh 43 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ARGLh 48 " --> pdb=" O LEULh 44 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VALLh 49 " --> pdb=" O SERLh 45 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 80 through 85 Proline residue: Lh 85 - end of helix Processing helix chain 'Lh' and resid 88 through 95 removed outlier: 3.511A pdb=" N ARGLh 94 " --> pdb=" O ALALh 90 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEULh 95 " --> pdb=" O METLh 91 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 96 through 102 Processing helix chain 'Lh' and resid 104 through 115 Proline residue: Lh 115 - end of helix Processing helix chain 'Li' and resid 25 through 30 removed outlier: 4.212A pdb=" N ARGLi 29 " --> pdb=" O ARGLi 25 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ARGLi 30 " --> pdb=" O HISLi 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'Li' and resid 25 through 30' Processing helix chain 'Li' and resid 34 through 49 Processing helix chain 'Li' and resid 51 through 64 removed outlier: 3.600A pdb=" N VALLi 63 " --> pdb=" O GLULi 59 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SERLi 64 " --> pdb=" O LEULi 60 " (cutoff:3.500A) Processing helix chain 'Li' and resid 65 through 78 Processing helix chain 'Li' and resid 79 through 103 removed outlier: 3.504A pdb=" N ASNLi 92 " --> pdb=" O GLULi 88 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LYSLi 103 " --> pdb=" O LYSLi 99 " (cutoff:3.500A) Processing helix chain 'Lj' and resid 4 through 11 removed outlier: 3.749A pdb=" N GLYLj 9 " --> pdb=" O THRLj 5 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LYSLj 10 " --> pdb=" O SERLj 6 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ARGLj 11 " --> pdb=" O SERLj 7 " (cutoff:3.500A) Processing helix chain 'Lj' and resid 50 through 58 removed outlier: 3.770A pdb=" N ASNLj 57 " --> pdb=" O ALALj 53 " (cutoff:3.500A) Processing helix chain 'Lj' and resid 64 through 77 removed outlier: 4.310A pdb=" N ILELj 69 " --> pdb=" O ARGLj 65 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARGLj 72 " --> pdb=" O LYSLj 68 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARGLj 75 " --> pdb=" O TYRLj 71 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N HISLj 76 " --> pdb=" O ARGLj 72 " (cutoff:3.500A) Processing helix chain 'Lk' and resid 7 through 17 Processing helix chain 'Lk' and resid 49 through 60 removed outlier: 3.838A pdb=" N GLULk 54 " --> pdb=" O LYSLk 50 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYSLk 55 " --> pdb=" O GLULk 51 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEULk 60 " --> pdb=" O LEULk 56 " (cutoff:3.500A) Processing helix chain 'Ll' and resid 6 through 21 removed outlier: 3.508A pdb=" N ASNLl 20 " --> pdb=" O LYSLl 16 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ARGLl 21 " --> pdb=" O GLNLl 17 " (cutoff:3.500A) Processing helix chain 'Ll' and resid 24 through 31 removed outlier: 4.124A pdb=" N ARGLl 28 " --> pdb=" O PROLl 24 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N METLl 29 " --> pdb=" O GLNLl 25 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYSLl 30 " --> pdb=" O TRPLl 26 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N THRLl 31 " --> pdb=" O ILELl 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ll' and resid 24 through 31' Processing helix chain 'Lm' and resid 79 through 91 removed outlier: 3.665A pdb=" N TYRLm 89 " --> pdb=" O LEULm 85 " (cutoff:3.500A) Processing helix chain 'Ln' and resid 2 through 24 removed outlier: 3.566A pdb=" N LYSLn 19 " --> pdb=" O ARGLn 15 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SERLn 24 " --> pdb=" O METLn 20 " (cutoff:3.500A) Processing helix chain 'Lo' and resid 35 through 46 Processing helix chain 'Lp' and resid 19 through 35 removed outlier: 3.761A pdb=" N LYSLp 28 " --> pdb=" O LYSLp 24 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILELp 29 " --> pdb=" O METLp 25 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N HISLp 34 " --> pdb=" O GLULp 30 " (cutoff:3.500A) Processing helix chain 'Lp' and resid 73 through 92 removed outlier: 3.894A pdb=" N ASPLp 91 " --> pdb=" O LYSLp 87 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N GLNLp 92 " --> pdb=" O GLULp 88 " (cutoff:3.500A) Processing helix chain 'Lr' and resid 2 through 13 removed outlier: 5.576A pdb=" N ASNLr 12 " --> pdb=" O METLr 8 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N CYSLr 13 " --> pdb=" O VALLr 9 " (cutoff:3.500A) Processing helix chain 'Lr' and resid 85 through 98 Processing helix chain 'Lr' and resid 103 through 123 removed outlier: 4.267A pdb=" N ARGLr 107 " --> pdb=" O ARGLr 103 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N METLr 108 " --> pdb=" O PROLr 104 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ALALr 109 " --> pdb=" O ASPLr 105 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYSLr 122 " --> pdb=" O LEULr 118 " (cutoff:3.500A) Proline residue: Lr 123 - end of helix Processing sheet with id= 1, first strand: chain 'LA' and resid 47 through 50 removed outlier: 3.574A pdb=" N ASPLA 47 " --> pdb=" O LYSLA 60 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LYSLA 60 " --> pdb=" O LYSLA 46 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLNLA 86 " --> pdb=" O VALLA 45 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'LA' and resid 110 through 114 removed outlier: 4.075A pdb=" N THRLA 111 " --> pdb=" O VALLA 136 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ARGLA 147 " --> pdb=" O ILELA 137 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'LA' and resid 58 through 64 Processing sheet with id= 4, first strand: chain 'LA' and resid 145 through 150 removed outlier: 4.012A pdb=" N SERLA 154 " --> pdb=" O LEULA 150 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'LB' and resid 45 through 50 removed outlier: 4.425A pdb=" N ARGLB 343 " --> pdb=" O LYSLB 50 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N VALLB 344 " --> pdb=" O VALLB 222 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N VALLB 222 " --> pdb=" O VALLB 344 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'LB' and resid 53 through 59 removed outlier: 3.658A pdb=" N PHELB 330 " --> pdb=" O GLYLB 288 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'LB' and resid 98 through 102 removed outlier: 6.655A pdb=" N GLYLB 91 " --> pdb=" O PHELB 102 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYSLB 103 " --> pdb=" O GLYLB 91 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'LB' and resid 179 through 185 removed outlier: 4.766A pdb=" N HISLB 179 " --> pdb=" O THRLB 166 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ILELB 160 " --> pdb=" O VALLB 185 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILELB 163 " --> pdb=" O VALLB 87 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLNLB 203 " --> pdb=" O VALLB 86 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'LB' and resid 88 through 93 Processing sheet with id= 10, first strand: chain 'LC' and resid 7 through 10 removed outlier: 4.778A pdb=" N LYSLC 20 " --> pdb=" O VALLC 10 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'LC' and resid 226 through 231 removed outlier: 6.188A pdb=" N TYRLC 211 " --> pdb=" O LEULC 230 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N PHELC 249 " --> pdb=" O GLYLC 206 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'LD' and resid 60 through 66 removed outlier: 3.620A pdb=" N VALLD 53 " --> pdb=" O ASPLD 147 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'LE' and resid 149 through 153 removed outlier: 3.992A pdb=" N LYSLE 160 " --> pdb=" O ILELE 152 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'LE' and resid 173 through 176 Processing sheet with id= 15, first strand: chain 'LF' and resid 139 through 144 removed outlier: 7.453A pdb=" N TYRLF 139 " --> pdb=" O ILELF 95 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N PHELF 118 " --> pdb=" O LEULF 213 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'LG' and resid 180 through 185 Processing sheet with id= 17, first strand: chain 'LH' and resid 5 through 12 removed outlier: 6.092A pdb=" N SERLH 6 " --> pdb=" O LYSLH 59 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N LYSLH 53 " --> pdb=" O ILELH 12 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ARGLH 54 " --> pdb=" O LEULH 48 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLULH 44 " --> pdb=" O ASPLH 58 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'LH' and resid 17 through 20 Processing sheet with id= 19, first strand: chain 'LH' and resid 102 through 106 removed outlier: 6.290A pdb=" N ASNLH 102 " --> pdb=" O ARGLH 115 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEULH 111 " --> pdb=" O GLNLH 106 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N SERLH 110 " --> pdb=" O METLH 128 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'LH' and resid 132 through 137 removed outlier: 5.523A pdb=" N GLULH 143 " --> pdb=" O SERLH 137 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ASPLH 142 " --> pdb=" O SERLH 94 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LYSLH 91 " --> pdb=" O SERLH 182 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'LH' and resid 88 through 91 Processing sheet with id= 22, first strand: chain 'LI' and resid 34 through 37 removed outlier: 6.120A pdb=" N PHELI 34 " --> pdb=" O VALLI 89 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ILELI 135 " --> pdb=" O ARGLI 90 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N METLI 136 " --> pdb=" O METLI 52 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N CYSLI 49 " --> pdb=" O SERLI 168 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'LI' and resid 189 through 192 removed outlier: 5.314A pdb=" N ARGLI 189 " --> pdb=" O ILELI 200 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'LJ' and resid 48 through 52 removed outlier: 4.773A pdb=" N ILELJ 68 " --> pdb=" O VALLJ 26 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N VALLJ 74 " --> pdb=" O LEULJ 20 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N CYSLJ 21 " --> pdb=" O TYRLJ 131 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYRLJ 131 " --> pdb=" O CYSLJ 21 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N CYSLJ 25 " --> pdb=" O GLYLJ 127 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N GLYLJ 127 " --> pdb=" O CYSLJ 25 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'LM' and resid 11 through 16 removed outlier: 4.198A pdb=" N ARGLM 11 " --> pdb=" O ILELM 27 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYSLM 23 " --> pdb=" O VALLM 15 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'LM' and resid 28 through 31 Processing sheet with id= 27, first strand: chain 'LN' and resid 35 through 39 removed outlier: 5.993A pdb=" N ALALN 35 " --> pdb=" O ARGLN 65 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILELN 61 " --> pdb=" O ALALN 39 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLYLN 58 " --> pdb=" O ASPLN 136 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILELN 133 " --> pdb=" O LEULN 116 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'LN' and resid 117 through 121 removed outlier: 3.759A pdb=" N ASNLN 117 " --> pdb=" O ILELN 133 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N PHELN 129 " --> pdb=" O VALLN 121 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'LO' and resid 6 through 10 Processing sheet with id= 30, first strand: chain 'LP' and resid 16 through 20 removed outlier: 5.973A pdb=" N SERLP 111 " --> pdb=" O LYSLP 153 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'LP' and resid 57 through 60 removed outlier: 5.387A pdb=" N GLNLP 80 " --> pdb=" O PHELP 60 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'LP' and resid 116 through 122 Processing sheet with id= 33, first strand: chain 'LP' and resid 124 through 131 No H-bonds generated for sheet with id= 33 Processing sheet with id= 34, first strand: chain 'LQ' and resid 78 through 82 Processing sheet with id= 35, first strand: chain 'LS' and resid 27 through 33 removed outlier: 6.481A pdb=" N VALLS 13 " --> pdb=" O VALLS 62 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'LS' and resid 92 through 99 removed outlier: 4.049A pdb=" N ASNLS 77 " --> pdb=" O ILELS 132 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'LS' and resid 9 through 13 removed outlier: 4.778A pdb=" N GLULS 9 " --> pdb=" O VALLS 67 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'LT' and resid 38 through 42 removed outlier: 4.296A pdb=" N ASPLT 38 " --> pdb=" O VALLT 64 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYSLT 60 " --> pdb=" O ILELT 42 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'LU' and resid 61 through 65 removed outlier: 4.617A pdb=" N PHELU 21 " --> pdb=" O VALLU 72 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N SERLU 74 " --> pdb=" O LEULU 19 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N GLULU 108 " --> pdb=" O LYSLU 20 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYRLU 110 " --> pdb=" O THRLU 22 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N TRPLU 99 " --> pdb=" O PHELU 115 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'LV' and resid 82 through 85 removed outlier: 4.236A pdb=" N ARGLV 85 " --> pdb=" O ASPLV 100 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASPLV 100 " --> pdb=" O ARGLV 85 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ASNLV 101 " --> pdb=" O VALLV 25 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ALALV 24 " --> pdb=" O ILELV 39 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N METLV 62 " --> pdb=" O ILELV 40 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASPLV 59 " --> pdb=" O VALLV 81 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'LV' and resid 87 through 90 removed outlier: 5.196A pdb=" N VALLV 94 " --> pdb=" O ARGLV 90 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'LV' and resid 78 through 81 Processing sheet with id= 43, first strand: chain 'LW' and resid 3 through 6 removed outlier: 5.224A pdb=" N GLULW 4 " --> pdb=" O LYSLW 12 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYSLW 12 " --> pdb=" O GLULW 4 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N CYSLW 6 " --> pdb=" O GLYLW 10 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'LW' and resid 18 through 23 removed outlier: 3.958A pdb=" N LYSLW 27 " --> pdb=" O ARGLW 23 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'LX' and resid 95 through 100 removed outlier: 3.744A pdb=" N LYSLX 134 " --> pdb=" O VALLX 100 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLULX 133 " --> pdb=" O ARGLX 129 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYSLX 123 " --> pdb=" O ARGLX 139 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'LY' and resid 53 through 56 removed outlier: 4.800A pdb=" N ASPLY 53 " --> pdb=" O VALLY 70 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'LY' and resid 71 through 75 Processing sheet with id= 48, first strand: chain 'LY' and resid 85 through 88 removed outlier: 6.366A pdb=" N VALLY 85 " --> pdb=" O VALLY 97 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'LZ' and resid 9 through 14 removed outlier: 4.492A pdb=" N LYSLZ 9 " --> pdb=" O ILELZ 25 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARGLZ 21 " --> pdb=" O VALLZ 13 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEULZ 42 " --> pdb=" O VALLZ 26 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N HISLZ 40 " --> pdb=" O ILELZ 29 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'LZ' and resid 42 through 45 Processing sheet with id= 51, first strand: chain 'Lc' and resid 26 through 29 removed outlier: 6.240A pdb=" N LYSLc 26 " --> pdb=" O ILELc 97 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEULc 45 " --> pdb=" O ILELc 96 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLYLc 70 " --> pdb=" O LYSLc 44 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'Ld' and resid 61 through 64 removed outlier: 5.729A pdb=" N ASPLd 61 " --> pdb=" O LEULd 102 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N THRLd 22 " --> pdb=" O VALLd 122 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'Le' and resid 74 through 80 Processing sheet with id= 54, first strand: chain 'Lf' and resid 46 through 49 removed outlier: 6.455A pdb=" N ARGLf 46 " --> pdb=" O METLf 104 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N HISLf 99 " --> pdb=" O PHELf 11 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N LYSLf 8 " --> pdb=" O GLULf 31 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEULf 27 " --> pdb=" O ALALf 12 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N METLf 83 " --> pdb=" O HISLf 78 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARGLf 76 " --> pdb=" O ARGLf 85 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'Lg' and resid 19 through 24 removed outlier: 5.480A pdb=" N LYSLg 19 " --> pdb=" O THRLg 35 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'Lk' and resid 2 through 5 removed outlier: 4.418A pdb=" N VALLk 46 " --> pdb=" O ILELk 5 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SERLk 22 " --> pdb=" O ARGLk 37 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LYSLk 27 " --> pdb=" O LEULk 69 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'Lm' and resid 93 through 97 removed outlier: 5.725A pdb=" N LYSLm 93 " --> pdb=" O LYSLm 124 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ASNLm 120 " --> pdb=" O ARGLm 97 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'Lo' and resid 6 through 10 removed outlier: 5.363A pdb=" N LYSLo 6 " --> pdb=" O VALLo 23 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THRLo 24 " --> pdb=" O ARGLo 69 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N VALLo 67 " --> pdb=" O TYRLo 26 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'Lp' and resid 53 through 58 removed outlier: 4.718A pdb=" N GLYLp 53 " --> pdb=" O GLYLp 66 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYSLp 62 " --> pdb=" O CYSLp 57 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'Lr' and resid 48 through 53 removed outlier: 5.178A pdb=" N THRLr 48 " --> pdb=" O LYSLr 65 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N SERLr 76 " --> pdb=" O ARGLr 66 " (cutoff:3.500A) 1948 hydrogen bonds defined for protein. 5775 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2998 hydrogen bonds 5070 hydrogen bond angles 0 basepair planarities 1145 basepair parallelities 1938 stacking parallelities Total time for adding SS restraints: 264.33 Time building geometry restraints manager: 63.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 13663 1.30 - 1.43: 63836 1.43 - 1.56: 63562 1.56 - 1.69: 7964 1.69 - 1.81: 378 Bond restraints: 149403 Sorted by residual: bond pdb=" C4 5MUL54083 " pdb=" C5 5MUL54083 " ideal model delta sigma weight residual 1.802 1.464 0.338 2.00e-02 2.50e+03 2.85e+02 bond pdb=" N1 5MUL54083 " pdb=" C6 5MUL54083 " ideal model delta sigma weight residual 1.635 1.325 0.310 2.00e-02 2.50e+03 2.40e+02 bond pdb=" C5 5MUL54083 " pdb=" C6 5MUL54083 " ideal model delta sigma weight residual 1.155 1.374 -0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C2' A2ML51326 " pdb=" C1' A2ML51326 " ideal model delta sigma weight residual 1.305 1.511 -0.206 2.00e-02 2.50e+03 1.06e+02 bond pdb=" O4' A2ML53867 " pdb=" C1' A2ML53867 " ideal model delta sigma weight residual 1.615 1.412 0.203 2.00e-02 2.50e+03 1.03e+02 ... (remaining 149398 not shown) Histogram of bond angle deviations from ideal: 85.84 - 96.10: 13 96.10 - 106.36: 23694 106.36 - 116.63: 106197 116.63 - 126.89: 81259 126.89 - 137.15: 9788 Bond angle restraints: 220951 Sorted by residual: angle pdb=" O2' UL53921 " pdb=" C2' UL53921 " pdb=" C1' UL53921 " ideal model delta sigma weight residual 108.40 85.84 22.56 1.50e+00 4.44e-01 2.26e+02 angle pdb=" N ASNLE 101 " pdb=" CA ASNLE 101 " pdb=" C ASNLE 101 " ideal model delta sigma weight residual 112.72 95.60 17.12 1.14e+00 7.69e-01 2.26e+02 angle pdb=" N METLf 104 " pdb=" CA METLf 104 " pdb=" C METLf 104 " ideal model delta sigma weight residual 113.23 129.70 -16.47 1.24e+00 6.50e-01 1.76e+02 angle pdb=" C1' A2ML52787 " pdb=" N9 A2ML52787 " pdb=" C8 A2ML52787 " ideal model delta sigma weight residual 88.50 126.71 -38.21 3.00e+00 1.11e-01 1.62e+02 angle pdb=" C1' A2ML51326 " pdb=" N9 A2ML51326 " pdb=" C8 A2ML51326 " ideal model delta sigma weight residual 88.50 126.31 -37.81 3.00e+00 1.11e-01 1.59e+02 ... (remaining 220946 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 84719 35.95 - 71.90: 10432 71.90 - 107.85: 1474 107.85 - 143.81: 37 143.81 - 179.76: 31 Dihedral angle restraints: 96693 sinusoidal: 77862 harmonic: 18831 Sorted by residual: dihedral pdb=" N HISLB 258 " pdb=" C HISLB 258 " pdb=" CA HISLB 258 " pdb=" CB HISLB 258 " ideal model delta harmonic sigma weight residual 122.80 161.38 -38.58 0 2.50e+00 1.60e-01 2.38e+02 dihedral pdb=" C HISLB 258 " pdb=" N HISLB 258 " pdb=" CA HISLB 258 " pdb=" CB HISLB 258 " ideal model delta harmonic sigma weight residual -122.60 -160.91 38.31 0 2.50e+00 1.60e-01 2.35e+02 dihedral pdb=" O4' CL51241 " pdb=" C1' CL51241 " pdb=" N1 CL51241 " pdb=" C2 CL51241 " ideal model delta sinusoidal sigma weight residual 200.00 34.01 165.99 1 1.50e+01 4.44e-03 8.41e+01 ... (remaining 96690 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.352: 27240 0.352 - 0.705: 28 0.705 - 1.057: 4 1.057 - 1.409: 0 1.409 - 1.762: 1 Chirality restraints: 27273 Sorted by residual: chirality pdb=" CA HISLB 258 " pdb=" N HISLB 258 " pdb=" C HISLB 258 " pdb=" CB HISLB 258 " both_signs ideal model delta sigma weight residual False 2.51 0.75 1.76 2.00e-01 2.50e+01 7.76e+01 chirality pdb=" CA LEULB 17 " pdb=" N LEULB 17 " pdb=" C LEULB 17 " pdb=" CB LEULB 17 " both_signs ideal model delta sigma weight residual False 2.51 1.55 0.96 2.00e-01 2.50e+01 2.30e+01 chirality pdb=" C3' GL51745 " pdb=" C4' GL51745 " pdb=" O3' GL51745 " pdb=" C2' GL51745 " both_signs ideal model delta sigma weight residual False -2.48 -1.67 -0.80 2.00e-01 2.50e+01 1.61e+01 ... (remaining 27270 not shown) Planarity restraints: 13132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMGL51316 " 0.090 2.00e-02 2.50e+03 6.27e-01 8.83e+03 pdb=" C4' OMGL51316 " 0.442 2.00e-02 2.50e+03 pdb=" O4' OMGL51316 " 0.626 2.00e-02 2.50e+03 pdb=" C3' OMGL51316 " -0.606 2.00e-02 2.50e+03 pdb=" O3' OMGL51316 " -0.700 2.00e-02 2.50e+03 pdb=" C2' OMGL51316 " -0.150 2.00e-02 2.50e+03 pdb=" O2' OMGL51316 " 1.047 2.00e-02 2.50e+03 pdb=" C1' OMGL51316 " 0.209 2.00e-02 2.50e+03 pdb=" N9 OMGL51316 " -0.958 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMGL53899 " 0.076 2.00e-02 2.50e+03 6.11e-01 8.41e+03 pdb=" C4' OMGL53899 " 0.445 2.00e-02 2.50e+03 pdb=" O4' OMGL53899 " 0.623 2.00e-02 2.50e+03 pdb=" C3' OMGL53899 " -0.602 2.00e-02 2.50e+03 pdb=" O3' OMGL53899 " -0.672 2.00e-02 2.50e+03 pdb=" C2' OMGL53899 " -0.167 2.00e-02 2.50e+03 pdb=" O2' OMGL53899 " 1.013 2.00e-02 2.50e+03 pdb=" C1' OMGL53899 " 0.211 2.00e-02 2.50e+03 pdb=" N9 OMGL53899 " -0.927 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMCL53887 " -0.066 2.00e-02 2.50e+03 6.05e-01 8.23e+03 pdb=" C4' OMCL53887 " -0.450 2.00e-02 2.50e+03 pdb=" O4' OMCL53887 " -0.638 2.00e-02 2.50e+03 pdb=" C3' OMCL53887 " 0.593 2.00e-02 2.50e+03 pdb=" O3' OMCL53887 " 0.648 2.00e-02 2.50e+03 pdb=" C2' OMCL53887 " 0.177 2.00e-02 2.50e+03 pdb=" O2' OMCL53887 " -0.978 2.00e-02 2.50e+03 pdb=" C1' OMCL53887 " -0.220 2.00e-02 2.50e+03 pdb=" N1 OMCL53887 " 0.933 2.00e-02 2.50e+03 ... (remaining 13129 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.42: 748 2.42 - 3.04: 79926 3.04 - 3.66: 258730 3.66 - 4.28: 410102 4.28 - 4.90: 562908 Nonbonded interactions: 1312414 Sorted by model distance: nonbonded pdb=" OP1 AL51600 " pdb="MG MGL55210 " model vdw 1.794 2.170 nonbonded pdb="MG MGLI 302 " pdb=" O HOHL55401 " model vdw 1.816 2.170 nonbonded pdb=" OE1 GLNLj 30 " pdb="MG MGL55358 " model vdw 1.818 2.170 nonbonded pdb=" OP2 CL51580 " pdb="MG MGL55178 " model vdw 1.826 2.170 nonbonded pdb=" OP1 A2ML51534 " pdb="MG MGL55358 " model vdw 1.836 2.170 ... (remaining 1312409 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=1.00 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: 10.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.140 Extract box with map and model: 28.490 Check model and map are aligned: 1.460 Set scattering table: 0.950 Process input model: 570.970 Find NCS groups from input model: 2.800 Set up NCS constraints: 0.310 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:13.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 628.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 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 : 0.013 0.338 149403 Z= 0.754 Angle : 1.001 38.212 220951 Z= 0.508 Chirality : 0.052 1.762 27273 Planarity : 0.035 0.627 13132 Dihedral : 24.074 179.757 84553 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.07 % Favored : 93.81 % Rotamer: Outliers : 0.20 % Allowed : 0.72 % Favored : 99.09 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.37 % 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: -1.35 (0.10), residues: 6411 helix: -0.66 (0.11), residues: 2187 sheet: -0.88 (0.17), residues: 910 loop : -0.97 (0.11), residues: 3314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRPLb 16 HIS 0.016 0.001 HISLL 67 PHE 0.028 0.002 PHELJ 60 TYR 0.036 0.002 TYRLB 285 ARG 0.013 0.001 ARGLl 46 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12822 Ramachandran restraints generated. 6411 Oldfield, 0 Emsley, 6411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12822 Ramachandran restraints generated. 6411 Oldfield, 0 Emsley, 6411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 925 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 914 time to evaluate : 6.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: LB 181 MET cc_start: 0.8360 (ttt) cc_final: 0.8140 (ttt) REVERT: LD 86 TYR cc_start: 0.6754 (p90) cc_final: 0.6439 (p90) REVERT: LE 68 MET cc_start: 0.9133 (mmp) cc_final: 0.8893 (mmp) REVERT: LG 211 ASP cc_start: 0.7844 (p0) cc_final: 0.7486 (p0) REVERT: LH 137 SER cc_start: 0.9136 (p) cc_final: 0.8932 (p) REVERT: LJ 114 ASP cc_start: 0.8049 (m-30) cc_final: 0.7800 (m-30) REVERT: LO 180 GLN cc_start: 0.8832 (tp40) cc_final: 0.8561 (tp40) REVERT: LT 157 GLU cc_start: 0.7750 (pp20) cc_final: 0.7484 (pp20) REVERT: LU 22 THR cc_start: 0.8644 (p) cc_final: 0.8431 (p) REVERT: LU 40 GLU cc_start: 0.8477 (tt0) cc_final: 0.7312 (tm-30) REVERT: LU 44 GLN cc_start: 0.8718 (mm110) cc_final: 0.6927 (mp10) REVERT: LW 4 GLU cc_start: 0.7410 (pt0) cc_final: 0.7125 (pt0) REVERT: LX 145 ASP cc_start: 0.8224 (t70) cc_final: 0.7643 (t0) REVERT: LX 148 ASP cc_start: 0.7904 (m-30) cc_final: 0.7674 (m-30) REVERT: Lb 94 ASP cc_start: 0.8403 (m-30) cc_final: 0.8168 (t0) REVERT: Lh 13 LYS cc_start: 0.8596 (ttpt) cc_final: 0.8259 (mtpp) REVERT: Lk 30 ASP cc_start: 0.8333 (p0) cc_final: 0.8011 (p0) REVERT: Lm 81 SER cc_start: 0.9153 (t) cc_final: 0.8669 (p) outliers start: 11 outliers final: 2 residues processed: 922 average time/residue: 2.0566 time to fit residues: 2723.4336 Evaluate side-chains 784 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 782 time to evaluate : 6.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Lc residue 98 ASP Chi-restraints excluded: chain Lf residue 107 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1029 random chunks: chunk 868 optimal weight: 0.9980 chunk 779 optimal weight: 0.8980 chunk 432 optimal weight: 6.9990 chunk 266 optimal weight: 10.0000 chunk 526 optimal weight: 0.9980 chunk 416 optimal weight: 0.9980 chunk 806 optimal weight: 1.9990 chunk 312 optimal weight: 0.8980 chunk 490 optimal weight: 0.9980 chunk 600 optimal weight: 3.9990 chunk 934 optimal weight: 7.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LA 83 HIS LE 245 GLN ** LF 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LG 64 GLN LH 8 GLN LH 78 GLN LH 156 ASN ** LJ 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LM 33 GLN LM 78 GLN LO 150 GLN LP 10 ASN LP 75 GLN LQ 93 GLN LU 50 ASN Lb 19 ASN Lb 60 ASN Ld 18 ASN Le 102 ASN Lg 100 GLN ** Lk 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lk 58 GLN Ln 22 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 149403 Z= 0.173 Angle : 0.848 20.099 220951 Z= 0.458 Chirality : 0.036 0.549 27273 Planarity : 0.009 0.158 13132 Dihedral : 25.329 179.464 70555 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.35 % Favored : 94.60 % Rotamer: Outliers : 1.31 % Allowed : 8.07 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.37 % Cis-general : 0.00 % Twisted Proline : 0.37 % 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: -0.69 (0.10), residues: 6411 helix: 0.35 (0.11), residues: 2203 sheet: -0.79 (0.17), residues: 880 loop : -0.87 (0.11), residues: 3328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRPLb 16 HIS 0.008 0.001 HISLL 67 PHE 0.011 0.001 PHELB 264 TYR 0.027 0.001 TYRLj 39 ARG 0.008 0.000 ARGLV 90 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12822 Ramachandran restraints generated. 6411 Oldfield, 0 Emsley, 6411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12822 Ramachandran restraints generated. 6411 Oldfield, 0 Emsley, 6411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 961 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 888 time to evaluate : 6.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: LB 181 MET cc_start: 0.8484 (ttt) cc_final: 0.8239 (ttt) REVERT: LC 71 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7119 (mtm-85) REVERT: LD 86 TYR cc_start: 0.6479 (p90) cc_final: 0.6117 (p90) REVERT: LE 68 MET cc_start: 0.9064 (mmp) cc_final: 0.8839 (mmp) REVERT: LE 101 ASN cc_start: 0.8087 (t0) cc_final: 0.7559 (m-40) REVERT: LJ 47 THR cc_start: 0.8940 (m) cc_final: 0.8581 (p) REVERT: LO 158 GLU cc_start: 0.7350 (tp30) cc_final: 0.6658 (tp30) REVERT: LO 180 GLN cc_start: 0.8611 (tp40) cc_final: 0.8348 (tp40) REVERT: LR 29 THR cc_start: 0.8946 (p) cc_final: 0.8667 (m) REVERT: LR 109 TYR cc_start: 0.9009 (m-10) cc_final: 0.8674 (m-10) REVERT: LT 157 GLU cc_start: 0.7869 (pp20) cc_final: 0.7105 (pp20) REVERT: LU 41 GLN cc_start: 0.8671 (tp40) cc_final: 0.8102 (tp40) REVERT: LU 44 GLN cc_start: 0.8745 (mm110) cc_final: 0.8429 (mp10) REVERT: LV 111 GLU cc_start: 0.7408 (mp0) cc_final: 0.7170 (mp0) REVERT: LX 145 ASP cc_start: 0.8167 (t70) cc_final: 0.7632 (t0) REVERT: LX 148 ASP cc_start: 0.7908 (m-30) cc_final: 0.7471 (m-30) REVERT: LY 127 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.7838 (mp10) REVERT: LZ 88 ASP cc_start: 0.7464 (p0) cc_final: 0.7229 (p0) REVERT: LZ 97 ASN cc_start: 0.9027 (p0) cc_final: 0.8551 (p0) REVERT: Lb 60 ASN cc_start: 0.8839 (t160) cc_final: 0.8534 (t0) REVERT: Le 98 GLU cc_start: 0.7300 (tt0) cc_final: 0.6933 (tt0) REVERT: Li 46 GLU cc_start: 0.7330 (pt0) cc_final: 0.7093 (pt0) REVERT: Lk 30 ASP cc_start: 0.8303 (p0) cc_final: 0.7996 (p0) REVERT: Lm 81 SER cc_start: 0.9030 (t) cc_final: 0.8591 (p) REVERT: Lo 74 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7621 (tm-30) outliers start: 73 outliers final: 33 residues processed: 911 average time/residue: 1.9883 time to fit residues: 2655.6055 Evaluate side-chains 850 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 815 time to evaluate : 6.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LB residue 258 HIS Chi-restraints excluded: chain LC residue 71 ARG Chi-restraints excluded: chain LD residue 51 MET Chi-restraints excluded: chain LE residue 109 LEU Chi-restraints excluded: chain LF residue 238 ASP Chi-restraints excluded: chain LG residue 89 ARG Chi-restraints excluded: chain LG residue 149 ASN Chi-restraints excluded: chain LI residue 28 ASP Chi-restraints excluded: chain LI residue 44 ASP Chi-restraints excluded: chain LI residue 183 ASP Chi-restraints excluded: chain LJ residue 97 ASN Chi-restraints excluded: chain LL residue 59 VAL Chi-restraints excluded: chain LL residue 151 THR Chi-restraints excluded: chain LO residue 189 ILE Chi-restraints excluded: chain LR residue 12 SER Chi-restraints excluded: chain LS residue 23 HIS Chi-restraints excluded: chain LU residue 62 THR Chi-restraints excluded: chain LU residue 67 LYS Chi-restraints excluded: chain LV residue 115 SER Chi-restraints excluded: chain LW residue 41 LEU Chi-restraints excluded: chain LX residue 92 ASP Chi-restraints excluded: chain LX residue 143 ASP Chi-restraints excluded: chain LY residue 111 LEU Chi-restraints excluded: chain LY residue 127 GLN Chi-restraints excluded: chain Lc residue 24 SER Chi-restraints excluded: chain Ld residue 59 THR Chi-restraints excluded: chain Ld residue 107 THR Chi-restraints excluded: chain Lg residue 48 VAL Chi-restraints excluded: chain Lh residue 8 ASP Chi-restraints excluded: chain Li residue 11 LEU Chi-restraints excluded: chain Lj residue 18 LEU Chi-restraints excluded: chain Lk residue 12 LEU Chi-restraints excluded: chain Lm residue 127 VAL Chi-restraints excluded: chain Lo residue 82 MET Chi-restraints excluded: chain Lr residue 85 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1029 random chunks: chunk 519 optimal weight: 4.9990 chunk 290 optimal weight: 7.9990 chunk 777 optimal weight: 0.0670 chunk 636 optimal weight: 5.9990 chunk 257 optimal weight: 30.0000 chunk 936 optimal weight: 5.9990 chunk 1011 optimal weight: 7.9990 chunk 833 optimal weight: 8.9990 chunk 928 optimal weight: 3.9990 chunk 319 optimal weight: 8.9990 chunk 750 optimal weight: 7.9990 overall best weight: 4.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LA 95 GLN LA 132 ASN LE 245 GLN LF 63 GLN ** LF 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LF 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LG 64 GLN LH 8 GLN LH 106 GLN LM 33 GLN LM 78 GLN LO 96 GLN LP 10 ASN LP 75 GLN LQ 93 GLN LR 34 ASN LU 38 ASN LU 50 ASN LW 30 GLN LW 59 HIS Ld 18 ASN Le 102 ASN Lg 100 GLN ** Lk 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lk 58 GLN Ln 22 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 149403 Z= 0.393 Angle : 0.841 20.169 220951 Z= 0.456 Chirality : 0.040 0.594 27273 Planarity : 0.010 0.151 13132 Dihedral : 25.108 179.993 70550 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.93 % Favored : 94.03 % Rotamer: Outliers : 2.72 % Allowed : 10.62 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.37 % Cis-general : 0.00 % Twisted Proline : 0.37 % 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: -0.55 (0.10), residues: 6411 helix: 0.58 (0.11), residues: 2227 sheet: -0.81 (0.17), residues: 871 loop : -0.85 (0.11), residues: 3313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRPLC 67 HIS 0.009 0.001 HISLL 67 PHE 0.015 0.001 PHELW 40 TYR 0.021 0.002 TYRLD 44 ARG 0.010 0.000 ARGLU 65 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12822 Ramachandran restraints generated. 6411 Oldfield, 0 Emsley, 6411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12822 Ramachandran restraints generated. 6411 Oldfield, 0 Emsley, 6411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 983 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 831 time to evaluate : 6.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: LB 181 MET cc_start: 0.8539 (ttt) cc_final: 0.8307 (ttt) REVERT: LB 258 HIS cc_start: 0.7006 (OUTLIER) cc_final: 0.6391 (t-90) REVERT: LC 67 TRP cc_start: 0.8373 (OUTLIER) cc_final: 0.6902 (t60) REVERT: LD 86 TYR cc_start: 0.6874 (p90) cc_final: 0.6080 (p90) REVERT: LE 101 ASN cc_start: 0.8257 (t0) cc_final: 0.7681 (m-40) REVERT: LE 191 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.8668 (pt0) REVERT: LM 96 GLU cc_start: 0.7718 (tp30) cc_final: 0.7514 (tp30) REVERT: LM 126 GLU cc_start: 0.8435 (tp30) cc_final: 0.7899 (tp30) REVERT: LN 161 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.7572 (mmm) REVERT: LO 158 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7418 (tp30) REVERT: LO 180 GLN cc_start: 0.8730 (tp40) cc_final: 0.8456 (tp40) REVERT: LO 184 ASN cc_start: 0.8732 (m-40) cc_final: 0.8300 (m110) REVERT: LR 29 THR cc_start: 0.8967 (p) cc_final: 0.8655 (m) REVERT: LR 99 MET cc_start: 0.8771 (mmp) cc_final: 0.8525 (mmp) REVERT: LT 79 GLN cc_start: 0.9243 (OUTLIER) cc_final: 0.8671 (tt0) REVERT: LU 23 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8866 (tp) REVERT: LU 40 GLU cc_start: 0.8365 (tt0) cc_final: 0.7896 (tm-30) REVERT: LV 90 ARG cc_start: 0.7644 (ttm-80) cc_final: 0.6870 (ttt90) REVERT: LX 145 ASP cc_start: 0.8177 (t70) cc_final: 0.7671 (t0) REVERT: LX 148 ASP cc_start: 0.7872 (m-30) cc_final: 0.7561 (m-30) REVERT: LY 127 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.7842 (mp10) REVERT: LZ 88 ASP cc_start: 0.7507 (p0) cc_final: 0.7207 (p0) REVERT: LZ 97 ASN cc_start: 0.9111 (p0) cc_final: 0.8605 (p0) REVERT: Lb 60 ASN cc_start: 0.8893 (t160) cc_final: 0.8560 (t0) REVERT: Lc 22 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7815 (mtt) REVERT: Lk 30 ASP cc_start: 0.8283 (p0) cc_final: 0.7949 (p0) REVERT: Lm 81 SER cc_start: 0.9012 (t) cc_final: 0.8675 (p) REVERT: Ln 11 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7150 (mtt-85) REVERT: Lo 74 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7540 (tm-30) REVERT: Lr 111 ILE cc_start: 0.9541 (OUTLIER) cc_final: 0.9255 (mp) outliers start: 152 outliers final: 72 residues processed: 887 average time/residue: 1.9661 time to fit residues: 2551.5598 Evaluate side-chains 882 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 799 time to evaluate : 5.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LA residue 106 THR Chi-restraints excluded: chain LB residue 258 HIS Chi-restraints excluded: chain LC residue 67 TRP Chi-restraints excluded: chain LC residue 71 ARG Chi-restraints excluded: chain LD residue 51 MET Chi-restraints excluded: chain LE residue 100 LYS Chi-restraints excluded: chain LE residue 107 VAL Chi-restraints excluded: chain LE residue 109 LEU Chi-restraints excluded: chain LE residue 191 GLN Chi-restraints excluded: chain LF residue 248 ASN Chi-restraints excluded: chain LG residue 89 ARG Chi-restraints excluded: chain LG residue 165 GLU Chi-restraints excluded: chain LH residue 6 SER Chi-restraints excluded: chain LH residue 11 ASP Chi-restraints excluded: chain LH residue 110 SER Chi-restraints excluded: chain LH residue 183 GLU Chi-restraints excluded: chain LI residue 53 VAL Chi-restraints excluded: chain LI residue 61 SER Chi-restraints excluded: chain LI residue 183 ASP Chi-restraints excluded: chain LI residue 195 CYS Chi-restraints excluded: chain LJ residue 97 ASN Chi-restraints excluded: chain LJ residue 100 SER Chi-restraints excluded: chain LL residue 59 VAL Chi-restraints excluded: chain LL residue 151 THR Chi-restraints excluded: chain LM residue 67 SER Chi-restraints excluded: chain LM residue 113 MET Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 131 GLU Chi-restraints excluded: chain LN residue 161 MET Chi-restraints excluded: chain LO residue 27 VAL Chi-restraints excluded: chain LO residue 158 GLU Chi-restraints excluded: chain LO residue 189 ILE Chi-restraints excluded: chain LP residue 89 GLU Chi-restraints excluded: chain LP residue 115 GLU Chi-restraints excluded: chain LP residue 125 MET Chi-restraints excluded: chain LP residue 147 GLU Chi-restraints excluded: chain LR residue 12 SER Chi-restraints excluded: chain LR residue 30 ASN Chi-restraints excluded: chain LR residue 111 GLU Chi-restraints excluded: chain LS residue 23 HIS Chi-restraints excluded: chain LT residue 79 GLN Chi-restraints excluded: chain LU residue 23 LEU Chi-restraints excluded: chain LU residue 25 CYS Chi-restraints excluded: chain LU residue 62 THR Chi-restraints excluded: chain LU residue 74 SER Chi-restraints excluded: chain LV residue 115 SER Chi-restraints excluded: chain LX residue 92 ASP Chi-restraints excluded: chain LX residue 143 ASP Chi-restraints excluded: chain LY residue 55 VAL Chi-restraints excluded: chain LY residue 111 LEU Chi-restraints excluded: chain LY residue 127 GLN Chi-restraints excluded: chain LZ residue 13 VAL Chi-restraints excluded: chain La residue 134 GLU Chi-restraints excluded: chain La residue 140 VAL Chi-restraints excluded: chain Lc residue 19 GLN Chi-restraints excluded: chain Lc residue 22 MET Chi-restraints excluded: chain Lc residue 57 LYS Chi-restraints excluded: chain Ld residue 59 THR Chi-restraints excluded: chain Ld residue 89 SER Chi-restraints excluded: chain Ld residue 98 SER Chi-restraints excluded: chain Ld residue 107 THR Chi-restraints excluded: chain Lf residue 7 SER Chi-restraints excluded: chain Lf residue 33 VAL Chi-restraints excluded: chain Lf residue 37 ASP Chi-restraints excluded: chain Lg residue 102 ILE Chi-restraints excluded: chain Lh residue 8 ASP Chi-restraints excluded: chain Lh residue 82 ASP Chi-restraints excluded: chain Li residue 11 LEU Chi-restraints excluded: chain Li residue 66 ASP Chi-restraints excluded: chain Li residue 89 GLU Chi-restraints excluded: chain Lj residue 2 THR Chi-restraints excluded: chain Lj residue 7 SER Chi-restraints excluded: chain Lj residue 18 LEU Chi-restraints excluded: chain Ll residue 47 THR Chi-restraints excluded: chain Lm residue 127 VAL Chi-restraints excluded: chain Ln residue 11 ARG Chi-restraints excluded: chain Lo residue 79 SER Chi-restraints excluded: chain Lo residue 82 MET Chi-restraints excluded: chain Lp residue 8 VAL Chi-restraints excluded: chain Lr residue 64 ILE Chi-restraints excluded: chain Lr residue 80 THR Chi-restraints excluded: chain Lr residue 85 ASN Chi-restraints excluded: chain Lr residue 111 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1029 random chunks: chunk 924 optimal weight: 0.9990 chunk 703 optimal weight: 5.9990 chunk 485 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 446 optimal weight: 8.9990 chunk 628 optimal weight: 0.6980 chunk 939 optimal weight: 0.9980 chunk 994 optimal weight: 7.9990 chunk 490 optimal weight: 0.0670 chunk 890 optimal weight: 2.9990 chunk 268 optimal weight: 8.9990 overall best weight: 1.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LA 95 GLN LE 245 GLN LF 63 GLN ** LF 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LG 64 GLN LH 106 GLN LM 33 GLN LM 78 GLN LP 10 ASN LP 75 GLN LQ 93 GLN LS 37 HIS LU 38 ASN LU 50 ASN Lc 33 GLN Ld 18 ASN Le 102 ASN Lh 30 GLN Lh 65 GLN ** Lk 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lk 58 GLN Ln 22 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 149403 Z= 0.164 Angle : 0.786 19.767 220951 Z= 0.436 Chirality : 0.034 0.478 27273 Planarity : 0.009 0.143 13132 Dihedral : 25.030 179.863 70550 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.30 % Favored : 94.65 % Rotamer: Outliers : 2.47 % Allowed : 11.65 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.37 % Cis-general : 0.00 % Twisted Proline : 0.37 % 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: -0.34 (0.10), residues: 6411 helix: 0.86 (0.11), residues: 2227 sheet: -0.76 (0.17), residues: 860 loop : -0.79 (0.11), residues: 3324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRPLT 125 HIS 0.007 0.001 HISLg 73 PHE 0.014 0.001 PHELU 78 TYR 0.019 0.001 TYRLE 63 ARG 0.010 0.000 ARGLm 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12822 Ramachandran restraints generated. 6411 Oldfield, 0 Emsley, 6411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12822 Ramachandran restraints generated. 6411 Oldfield, 0 Emsley, 6411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1004 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 866 time to evaluate : 6.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: LB 258 HIS cc_start: 0.6361 (OUTLIER) cc_final: 0.5999 (t-90) REVERT: LC 67 TRP cc_start: 0.8082 (OUTLIER) cc_final: 0.6628 (t60) REVERT: LF 232 ASP cc_start: 0.7878 (m-30) cc_final: 0.7660 (m-30) REVERT: LH 106 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7770 (mm-40) REVERT: LH 113 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6920 (mt-10) REVERT: LI 203 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7434 (ptt90) REVERT: LJ 47 THR cc_start: 0.8940 (m) cc_final: 0.8579 (p) REVERT: LM 126 GLU cc_start: 0.8410 (tp30) cc_final: 0.7793 (tp30) REVERT: LO 158 GLU cc_start: 0.7471 (tp30) cc_final: 0.7116 (tp30) REVERT: LO 162 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7176 (mm-30) REVERT: LO 180 GLN cc_start: 0.8649 (tp40) cc_final: 0.8404 (tp40) REVERT: LR 29 THR cc_start: 0.8938 (p) cc_final: 0.8694 (m) REVERT: LR 99 MET cc_start: 0.8775 (mmp) cc_final: 0.8446 (mmp) REVERT: LT 79 GLN cc_start: 0.9156 (OUTLIER) cc_final: 0.8295 (tt0) REVERT: LT 111 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7172 (tm-30) REVERT: LT 157 GLU cc_start: 0.7636 (pp20) cc_final: 0.7259 (pp20) REVERT: LV 90 ARG cc_start: 0.7615 (ttm-80) cc_final: 0.7253 (ttt90) REVERT: LX 145 ASP cc_start: 0.8145 (t70) cc_final: 0.7684 (t0) REVERT: LX 148 ASP cc_start: 0.7907 (m-30) cc_final: 0.7565 (m-30) REVERT: LY 127 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.7773 (mp10) REVERT: LZ 88 ASP cc_start: 0.7586 (p0) cc_final: 0.7289 (p0) REVERT: LZ 97 ASN cc_start: 0.9055 (p0) cc_final: 0.8605 (p0) REVERT: LZ 103 ASP cc_start: 0.8646 (t0) cc_final: 0.8442 (t0) REVERT: Le 26 ASP cc_start: 0.7826 (p0) cc_final: 0.7597 (p0) REVERT: Lk 30 ASP cc_start: 0.8238 (p0) cc_final: 0.7908 (p0) REVERT: Lk 40 ARG cc_start: 0.8754 (ttt180) cc_final: 0.8398 (ttt180) REVERT: Lo 74 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7583 (tm-30) REVERT: Lr 111 ILE cc_start: 0.9498 (OUTLIER) cc_final: 0.9215 (mp) outliers start: 138 outliers final: 66 residues processed: 918 average time/residue: 1.9469 time to fit residues: 2633.4981 Evaluate side-chains 901 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 828 time to evaluate : 6.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LA residue 207 VAL Chi-restraints excluded: chain LB residue 258 HIS Chi-restraints excluded: chain LB residue 337 VAL Chi-restraints excluded: chain LC residue 67 TRP Chi-restraints excluded: chain LC residue 71 ARG Chi-restraints excluded: chain LD residue 51 MET Chi-restraints excluded: chain LD residue 118 ILE Chi-restraints excluded: chain LD residue 239 MET Chi-restraints excluded: chain LE residue 100 LYS Chi-restraints excluded: chain LE residue 107 VAL Chi-restraints excluded: chain LE residue 175 VAL Chi-restraints excluded: chain LF residue 238 ASP Chi-restraints excluded: chain LG residue 55 VAL Chi-restraints excluded: chain LG residue 89 ARG Chi-restraints excluded: chain LG residue 106 THR Chi-restraints excluded: chain LG residue 119 GLU Chi-restraints excluded: chain LG residue 149 ASN Chi-restraints excluded: chain LG residue 165 GLU Chi-restraints excluded: chain LH residue 1 MET Chi-restraints excluded: chain LH residue 106 GLN Chi-restraints excluded: chain LH residue 110 SER Chi-restraints excluded: chain LH residue 183 GLU Chi-restraints excluded: chain LI residue 28 ASP Chi-restraints excluded: chain LI residue 43 VAL Chi-restraints excluded: chain LI residue 44 ASP Chi-restraints excluded: chain LI residue 53 VAL Chi-restraints excluded: chain LI residue 61 SER Chi-restraints excluded: chain LI residue 183 ASP Chi-restraints excluded: chain LI residue 203 ARG Chi-restraints excluded: chain LJ residue 100 SER Chi-restraints excluded: chain LJ residue 150 CYS Chi-restraints excluded: chain LL residue 59 VAL Chi-restraints excluded: chain LL residue 151 THR Chi-restraints excluded: chain LM residue 67 SER Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 131 GLU Chi-restraints excluded: chain LO residue 189 ILE Chi-restraints excluded: chain LP residue 2 VAL Chi-restraints excluded: chain LP residue 89 GLU Chi-restraints excluded: chain LP residue 126 ARG Chi-restraints excluded: chain LR residue 111 GLU Chi-restraints excluded: chain LS residue 23 HIS Chi-restraints excluded: chain LT residue 79 GLN Chi-restraints excluded: chain LU residue 25 CYS Chi-restraints excluded: chain LU residue 62 THR Chi-restraints excluded: chain LU residue 74 SER Chi-restraints excluded: chain LW residue 41 LEU Chi-restraints excluded: chain LX residue 143 ASP Chi-restraints excluded: chain LY residue 55 VAL Chi-restraints excluded: chain LY residue 111 LEU Chi-restraints excluded: chain LY residue 127 GLN Chi-restraints excluded: chain LZ residue 13 VAL Chi-restraints excluded: chain LZ residue 100 VAL Chi-restraints excluded: chain LZ residue 120 GLU Chi-restraints excluded: chain La residue 134 GLU Chi-restraints excluded: chain La residue 140 VAL Chi-restraints excluded: chain Ld residue 26 THR Chi-restraints excluded: chain Ld residue 89 SER Chi-restraints excluded: chain Ld residue 107 THR Chi-restraints excluded: chain Lf residue 37 ASP Chi-restraints excluded: chain Lg residue 102 ILE Chi-restraints excluded: chain Lh residue 8 ASP Chi-restraints excluded: chain Li residue 3 LEU Chi-restraints excluded: chain Li residue 11 LEU Chi-restraints excluded: chain Li residue 66 ASP Chi-restraints excluded: chain Lj residue 18 LEU Chi-restraints excluded: chain Ll residue 47 THR Chi-restraints excluded: chain Lm residue 127 VAL Chi-restraints excluded: chain Lo residue 77 CYS Chi-restraints excluded: chain Lo residue 79 SER Chi-restraints excluded: chain Lp residue 74 THR Chi-restraints excluded: chain Lr residue 64 ILE Chi-restraints excluded: chain Lr residue 111 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1029 random chunks: chunk 828 optimal weight: 0.0370 chunk 564 optimal weight: 7.9990 chunk 14 optimal weight: 9.9990 chunk 740 optimal weight: 7.9990 chunk 410 optimal weight: 20.0000 chunk 848 optimal weight: 4.9990 chunk 687 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 507 optimal weight: 10.0000 chunk 892 optimal weight: 5.9990 chunk 250 optimal weight: 8.9990 overall best weight: 5.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LA 95 GLN LA 132 ASN LA 218 HIS LE 245 GLN LF 63 GLN ** LF 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LG 64 GLN ** LH 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LM 78 GLN LO 96 GLN LP 10 ASN LP 75 GLN LQ 93 GLN LR 34 ASN LU 38 ASN LU 50 ASN LV 108 ASN La 66 ASN Lb 60 ASN Ld 18 ASN Le 92 ASN Le 102 ASN Lg 100 GLN Lh 20 GLN ** Lk 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lk 58 GLN Ln 22 GLN Lo 90 HIS Lr 100 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.078 149403 Z= 0.473 Angle : 0.850 19.983 220951 Z= 0.458 Chirality : 0.042 0.572 27273 Planarity : 0.010 0.189 13132 Dihedral : 24.959 179.620 70550 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.13 % Favored : 93.82 % Rotamer: Outliers : 3.11 % Allowed : 12.96 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.37 % Cis-general : 0.00 % Twisted Proline : 0.74 % 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: 6411 helix: 0.85 (0.11), residues: 2230 sheet: -0.78 (0.17), residues: 898 loop : -0.81 (0.11), residues: 3283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRPLC 67 HIS 0.007 0.001 HISLE 128 PHE 0.014 0.002 PHELO 47 TYR 0.025 0.002 TYRLD 44 ARG 0.009 0.001 ARGLn 6 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12822 Ramachandran restraints generated. 6411 Oldfield, 0 Emsley, 6411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12822 Ramachandran restraints generated. 6411 Oldfield, 0 Emsley, 6411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 997 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 823 time to evaluate : 6.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: LB 258 HIS cc_start: 0.7118 (OUTLIER) cc_final: 0.6553 (t-90) REVERT: LC 67 TRP cc_start: 0.8455 (OUTLIER) cc_final: 0.7209 (t60) REVERT: LD 212 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7283 (mpp) REVERT: LM 126 GLU cc_start: 0.8578 (tp30) cc_final: 0.7824 (tp30) REVERT: LO 158 GLU cc_start: 0.7625 (tp30) cc_final: 0.7404 (tp30) REVERT: LO 162 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7381 (mm-30) REVERT: LO 180 GLN cc_start: 0.8767 (tp40) cc_final: 0.8447 (tp40) REVERT: LO 184 ASN cc_start: 0.8761 (m-40) cc_final: 0.8376 (m110) REVERT: LR 29 THR cc_start: 0.9010 (p) cc_final: 0.8711 (m) REVERT: LR 99 MET cc_start: 0.8807 (mmp) cc_final: 0.8536 (mmp) REVERT: LR 140 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7854 (mp0) REVERT: LT 79 GLN cc_start: 0.9253 (OUTLIER) cc_final: 0.8684 (tt0) REVERT: LT 157 GLU cc_start: 0.7864 (pp20) cc_final: 0.7512 (pp20) REVERT: LU 44 GLN cc_start: 0.8643 (mm110) cc_final: 0.8394 (mp10) REVERT: LX 145 ASP cc_start: 0.8196 (t70) cc_final: 0.7685 (t0) REVERT: LX 148 ASP cc_start: 0.7884 (m-30) cc_final: 0.7629 (m-30) REVERT: LY 127 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.7881 (mp10) REVERT: LZ 88 ASP cc_start: 0.7618 (p0) cc_final: 0.7348 (p0) REVERT: LZ 97 ASN cc_start: 0.9091 (p0) cc_final: 0.8638 (p0) REVERT: La 89 ASN cc_start: 0.9277 (m-40) cc_final: 0.9051 (m-40) REVERT: Lb 60 ASN cc_start: 0.8928 (t160) cc_final: 0.8596 (t0) REVERT: Lc 22 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7764 (mtt) REVERT: Ld 59 THR cc_start: 0.9037 (OUTLIER) cc_final: 0.8824 (t) REVERT: Lk 12 LEU cc_start: 0.9477 (OUTLIER) cc_final: 0.9269 (mm) REVERT: Lk 30 ASP cc_start: 0.8296 (p0) cc_final: 0.7949 (p0) REVERT: Lk 40 ARG cc_start: 0.8835 (ttt180) cc_final: 0.8505 (ttt180) REVERT: Lm 126 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.7843 (mttm) REVERT: Ln 11 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7112 (mtt-85) REVERT: Lo 74 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7641 (tm-30) REVERT: Lr 111 ILE cc_start: 0.9529 (OUTLIER) cc_final: 0.9237 (mp) outliers start: 174 outliers final: 98 residues processed: 900 average time/residue: 1.9503 time to fit residues: 2575.6196 Evaluate side-chains 908 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 798 time to evaluate : 6.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LA residue 106 THR Chi-restraints excluded: chain LA residue 114 CYS Chi-restraints excluded: chain LB residue 258 HIS Chi-restraints excluded: chain LC residue 67 TRP Chi-restraints excluded: chain LC residue 71 ARG Chi-restraints excluded: chain LD residue 51 MET Chi-restraints excluded: chain LD residue 118 ILE Chi-restraints excluded: chain LD residue 212 MET Chi-restraints excluded: chain LE residue 107 VAL Chi-restraints excluded: chain LE residue 109 LEU Chi-restraints excluded: chain LE residue 175 VAL Chi-restraints excluded: chain LE residue 199 THR Chi-restraints excluded: chain LF residue 238 ASP Chi-restraints excluded: chain LF residue 248 ASN Chi-restraints excluded: chain LG residue 55 VAL Chi-restraints excluded: chain LG residue 89 ARG Chi-restraints excluded: chain LG residue 106 THR Chi-restraints excluded: chain LG residue 119 GLU Chi-restraints excluded: chain LG residue 165 GLU Chi-restraints excluded: chain LH residue 6 SER Chi-restraints excluded: chain LH residue 11 ASP Chi-restraints excluded: chain LH residue 44 GLU Chi-restraints excluded: chain LH residue 110 SER Chi-restraints excluded: chain LH residue 187 VAL Chi-restraints excluded: chain LI residue 28 ASP Chi-restraints excluded: chain LI residue 53 VAL Chi-restraints excluded: chain LI residue 61 SER Chi-restraints excluded: chain LI residue 183 ASP Chi-restraints excluded: chain LI residue 203 ARG Chi-restraints excluded: chain LJ residue 100 SER Chi-restraints excluded: chain LJ residue 114 ASP Chi-restraints excluded: chain LJ residue 129 ASP Chi-restraints excluded: chain LL residue 59 VAL Chi-restraints excluded: chain LL residue 63 THR Chi-restraints excluded: chain LL residue 64 VAL Chi-restraints excluded: chain LL residue 151 THR Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 131 GLU Chi-restraints excluded: chain LO residue 27 VAL Chi-restraints excluded: chain LO residue 189 ILE Chi-restraints excluded: chain LP residue 2 VAL Chi-restraints excluded: chain LP residue 89 GLU Chi-restraints excluded: chain LP residue 115 GLU Chi-restraints excluded: chain LP residue 147 GLU Chi-restraints excluded: chain LR residue 12 SER Chi-restraints excluded: chain LR residue 13 SER Chi-restraints excluded: chain LR residue 111 GLU Chi-restraints excluded: chain LR residue 140 GLU Chi-restraints excluded: chain LS residue 23 HIS Chi-restraints excluded: chain LS residue 158 VAL Chi-restraints excluded: chain LT residue 79 GLN Chi-restraints excluded: chain LT residue 103 ASP Chi-restraints excluded: chain LU residue 25 CYS Chi-restraints excluded: chain LU residue 62 THR Chi-restraints excluded: chain LU residue 74 SER Chi-restraints excluded: chain LV residue 22 VAL Chi-restraints excluded: chain LV residue 115 SER Chi-restraints excluded: chain LW residue 38 SER Chi-restraints excluded: chain LX residue 85 SER Chi-restraints excluded: chain LX residue 92 ASP Chi-restraints excluded: chain LX residue 143 ASP Chi-restraints excluded: chain LY residue 55 VAL Chi-restraints excluded: chain LY residue 111 LEU Chi-restraints excluded: chain LY residue 127 GLN Chi-restraints excluded: chain LZ residue 13 VAL Chi-restraints excluded: chain LZ residue 100 VAL Chi-restraints excluded: chain La residue 134 GLU Chi-restraints excluded: chain La residue 140 VAL Chi-restraints excluded: chain Lb residue 40 LEU Chi-restraints excluded: chain Lb residue 118 LEU Chi-restraints excluded: chain Lc residue 19 GLN Chi-restraints excluded: chain Lc residue 22 MET Chi-restraints excluded: chain Lc residue 57 LYS Chi-restraints excluded: chain Lc residue 98 ASP Chi-restraints excluded: chain Ld residue 26 THR Chi-restraints excluded: chain Ld residue 59 THR Chi-restraints excluded: chain Ld residue 89 SER Chi-restraints excluded: chain Ld residue 98 SER Chi-restraints excluded: chain Ld residue 107 THR Chi-restraints excluded: chain Le residue 7 LEU Chi-restraints excluded: chain Lf residue 33 VAL Chi-restraints excluded: chain Lf residue 37 ASP Chi-restraints excluded: chain Lg residue 102 ILE Chi-restraints excluded: chain Lh residue 8 ASP Chi-restraints excluded: chain Lh residue 82 ASP Chi-restraints excluded: chain Li residue 3 LEU Chi-restraints excluded: chain Li residue 11 LEU Chi-restraints excluded: chain Li residue 12 ASN Chi-restraints excluded: chain Li residue 70 LEU Chi-restraints excluded: chain Lj residue 2 THR Chi-restraints excluded: chain Lj residue 7 SER Chi-restraints excluded: chain Lj residue 18 LEU Chi-restraints excluded: chain Lk residue 12 LEU Chi-restraints excluded: chain Lk residue 48 THR Chi-restraints excluded: chain Lk residue 60 LEU Chi-restraints excluded: chain Ll residue 25 GLN Chi-restraints excluded: chain Ll residue 47 THR Chi-restraints excluded: chain Lm residue 126 LYS Chi-restraints excluded: chain Lm residue 127 VAL Chi-restraints excluded: chain Ln residue 11 ARG Chi-restraints excluded: chain Lo residue 62 THR Chi-restraints excluded: chain Lo residue 77 CYS Chi-restraints excluded: chain Lo residue 103 VAL Chi-restraints excluded: chain Lp residue 8 VAL Chi-restraints excluded: chain Lp residue 74 THR Chi-restraints excluded: chain Lp residue 88 GLU Chi-restraints excluded: chain Lr residue 64 ILE Chi-restraints excluded: chain Lr residue 80 THR Chi-restraints excluded: chain Lr residue 85 ASN Chi-restraints excluded: chain Lr residue 111 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1029 random chunks: chunk 334 optimal weight: 5.9990 chunk 895 optimal weight: 10.0000 chunk 196 optimal weight: 5.9990 chunk 583 optimal weight: 3.9990 chunk 245 optimal weight: 3.9990 chunk 995 optimal weight: 4.9990 chunk 826 optimal weight: 0.8980 chunk 460 optimal weight: 8.9990 chunk 82 optimal weight: 30.0000 chunk 329 optimal weight: 4.9990 chunk 522 optimal weight: 0.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** LA 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 245 GLN LF 63 GLN ** LF 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LG 64 GLN LM 78 GLN LO 96 GLN LP 10 ASN LP 75 GLN LQ 93 GLN LU 38 ASN LU 94 ASN Ld 18 ASN Le 92 ASN Le 102 ASN Lg 100 GLN Lh 20 GLN ** Lk 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ln 22 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 149403 Z= 0.290 Angle : 0.816 20.046 220951 Z= 0.446 Chirality : 0.037 0.526 27273 Planarity : 0.009 0.159 13132 Dihedral : 25.010 179.837 70550 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.71 % Favored : 94.24 % Rotamer: Outliers : 2.83 % Allowed : 13.95 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.37 % Cis-general : 0.00 % Twisted Proline : 0.74 % 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: -0.30 (0.10), residues: 6411 helix: 0.96 (0.11), residues: 2216 sheet: -0.80 (0.17), residues: 883 loop : -0.78 (0.11), residues: 3312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRPLT 125 HIS 0.006 0.001 HISLa 40 PHE 0.015 0.001 PHELU 78 TYR 0.022 0.001 TYRLD 44 ARG 0.012 0.000 ARGLl 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12822 Ramachandran restraints generated. 6411 Oldfield, 0 Emsley, 6411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12822 Ramachandran restraints generated. 6411 Oldfield, 0 Emsley, 6411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 988 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 830 time to evaluate : 6.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: LB 258 HIS cc_start: 0.6908 (OUTLIER) cc_final: 0.6417 (t-90) REVERT: LC 67 TRP cc_start: 0.8402 (OUTLIER) cc_final: 0.7129 (t60) REVERT: LH 113 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6975 (mt-10) REVERT: LI 143 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8228 (pm20) REVERT: LJ 47 THR cc_start: 0.8963 (m) cc_final: 0.8614 (p) REVERT: LL 21 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.7910 (ptt90) REVERT: LM 126 GLU cc_start: 0.8567 (tp30) cc_final: 0.7826 (tp30) REVERT: LN 19 MET cc_start: 0.9076 (mmm) cc_final: 0.8805 (mmm) REVERT: LO 158 GLU cc_start: 0.7578 (tp30) cc_final: 0.7242 (tp30) REVERT: LO 162 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7200 (mm-30) REVERT: LO 180 GLN cc_start: 0.8725 (tp40) cc_final: 0.8391 (tp40) REVERT: LO 184 ASN cc_start: 0.8740 (m-40) cc_final: 0.8328 (m110) REVERT: LP 103 GLU cc_start: 0.7786 (mt-10) cc_final: 0.6720 (mt-10) REVERT: LQ 124 ASP cc_start: 0.8811 (OUTLIER) cc_final: 0.8517 (p0) REVERT: LR 29 THR cc_start: 0.8989 (p) cc_final: 0.8707 (m) REVERT: LR 99 MET cc_start: 0.8799 (mmp) cc_final: 0.8527 (mmp) REVERT: LR 140 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7826 (mp0) REVERT: LT 79 GLN cc_start: 0.9245 (OUTLIER) cc_final: 0.8588 (tt0) REVERT: LT 157 GLU cc_start: 0.7844 (pp20) cc_final: 0.7421 (pp20) REVERT: LT 159 MET cc_start: 0.6817 (mmm) cc_final: 0.6574 (mmm) REVERT: LU 44 GLN cc_start: 0.8660 (mm110) cc_final: 0.8411 (mp10) REVERT: LX 145 ASP cc_start: 0.8161 (t70) cc_final: 0.7660 (t0) REVERT: LX 148 ASP cc_start: 0.7871 (m-30) cc_final: 0.7616 (m-30) REVERT: LY 127 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.7884 (mp10) REVERT: LZ 88 ASP cc_start: 0.7602 (p0) cc_final: 0.7345 (p0) REVERT: LZ 97 ASN cc_start: 0.9058 (p0) cc_final: 0.8601 (p0) REVERT: La 89 ASN cc_start: 0.9267 (m-40) cc_final: 0.9021 (m-40) REVERT: Lc 17 ARG cc_start: 0.8654 (ptp90) cc_final: 0.8214 (mtm-85) REVERT: Lc 22 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7693 (mtt) REVERT: Ld 59 THR cc_start: 0.9043 (p) cc_final: 0.8834 (t) REVERT: Lk 12 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9247 (mm) REVERT: Lk 30 ASP cc_start: 0.8265 (p0) cc_final: 0.7917 (p0) REVERT: Lk 40 ARG cc_start: 0.8821 (ttt180) cc_final: 0.8501 (ttt180) REVERT: Lm 126 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.7839 (mttm) REVERT: Ln 11 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7095 (mtt-85) REVERT: Lo 74 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7702 (tm-30) REVERT: Lr 111 ILE cc_start: 0.9516 (OUTLIER) cc_final: 0.9225 (mp) outliers start: 158 outliers final: 101 residues processed: 902 average time/residue: 1.9587 time to fit residues: 2590.1470 Evaluate side-chains 924 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 810 time to evaluate : 6.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LA residue 114 CYS Chi-restraints excluded: chain LB residue 258 HIS Chi-restraints excluded: chain LB residue 337 VAL Chi-restraints excluded: chain LC residue 67 TRP Chi-restraints excluded: chain LC residue 71 ARG Chi-restraints excluded: chain LD residue 51 MET Chi-restraints excluded: chain LD residue 118 ILE Chi-restraints excluded: chain LE residue 107 VAL Chi-restraints excluded: chain LE residue 109 LEU Chi-restraints excluded: chain LE residue 175 VAL Chi-restraints excluded: chain LF residue 238 ASP Chi-restraints excluded: chain LF residue 248 ASN Chi-restraints excluded: chain LG residue 55 VAL Chi-restraints excluded: chain LG residue 89 ARG Chi-restraints excluded: chain LG residue 106 THR Chi-restraints excluded: chain LG residue 119 GLU Chi-restraints excluded: chain LG residue 149 ASN Chi-restraints excluded: chain LG residue 165 GLU Chi-restraints excluded: chain LH residue 6 SER Chi-restraints excluded: chain LH residue 11 ASP Chi-restraints excluded: chain LH residue 44 GLU Chi-restraints excluded: chain LH residue 110 SER Chi-restraints excluded: chain LH residue 187 VAL Chi-restraints excluded: chain LI residue 53 VAL Chi-restraints excluded: chain LI residue 61 SER Chi-restraints excluded: chain LI residue 79 SER Chi-restraints excluded: chain LI residue 115 MET Chi-restraints excluded: chain LI residue 143 GLN Chi-restraints excluded: chain LI residue 183 ASP Chi-restraints excluded: chain LI residue 203 ARG Chi-restraints excluded: chain LJ residue 100 SER Chi-restraints excluded: chain LL residue 21 ARG Chi-restraints excluded: chain LL residue 59 VAL Chi-restraints excluded: chain LL residue 90 VAL Chi-restraints excluded: chain LL residue 151 THR Chi-restraints excluded: chain LM residue 67 SER Chi-restraints excluded: chain LM residue 113 MET Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 131 GLU Chi-restraints excluded: chain LN residue 147 ASP Chi-restraints excluded: chain LO residue 27 VAL Chi-restraints excluded: chain LO residue 189 ILE Chi-restraints excluded: chain LP residue 2 VAL Chi-restraints excluded: chain LP residue 89 GLU Chi-restraints excluded: chain LP residue 115 GLU Chi-restraints excluded: chain LP residue 125 MET Chi-restraints excluded: chain LP residue 147 GLU Chi-restraints excluded: chain LQ residue 42 THR Chi-restraints excluded: chain LQ residue 82 VAL Chi-restraints excluded: chain LQ residue 124 ASP Chi-restraints excluded: chain LR residue 12 SER Chi-restraints excluded: chain LR residue 111 GLU Chi-restraints excluded: chain LR residue 140 GLU Chi-restraints excluded: chain LS residue 23 HIS Chi-restraints excluded: chain LS residue 158 VAL Chi-restraints excluded: chain LT residue 3 ASN Chi-restraints excluded: chain LT residue 79 GLN Chi-restraints excluded: chain LT residue 103 ASP Chi-restraints excluded: chain LU residue 25 CYS Chi-restraints excluded: chain LU residue 62 THR Chi-restraints excluded: chain LU residue 63 ILE Chi-restraints excluded: chain LU residue 67 LYS Chi-restraints excluded: chain LV residue 115 SER Chi-restraints excluded: chain LX residue 85 SER Chi-restraints excluded: chain LX residue 92 ASP Chi-restraints excluded: chain LX residue 143 ASP Chi-restraints excluded: chain LY residue 55 VAL Chi-restraints excluded: chain LY residue 111 LEU Chi-restraints excluded: chain LY residue 127 GLN Chi-restraints excluded: chain LZ residue 13 VAL Chi-restraints excluded: chain LZ residue 120 GLU Chi-restraints excluded: chain La residue 134 GLU Chi-restraints excluded: chain La residue 140 VAL Chi-restraints excluded: chain Lb residue 40 LEU Chi-restraints excluded: chain Lc residue 19 GLN Chi-restraints excluded: chain Lc residue 22 MET Chi-restraints excluded: chain Lc residue 24 SER Chi-restraints excluded: chain Lc residue 28 VAL Chi-restraints excluded: chain Lc residue 57 LYS Chi-restraints excluded: chain Ld residue 26 THR Chi-restraints excluded: chain Ld residue 107 THR Chi-restraints excluded: chain Le residue 7 LEU Chi-restraints excluded: chain Le residue 129 LEU Chi-restraints excluded: chain Lf residue 18 LEU Chi-restraints excluded: chain Lf residue 33 VAL Chi-restraints excluded: chain Lf residue 37 ASP Chi-restraints excluded: chain Lf residue 105 LEU Chi-restraints excluded: chain Lg residue 102 ILE Chi-restraints excluded: chain Lh residue 8 ASP Chi-restraints excluded: chain Li residue 3 LEU Chi-restraints excluded: chain Li residue 11 LEU Chi-restraints excluded: chain Li residue 12 ASN Chi-restraints excluded: chain Lj residue 2 THR Chi-restraints excluded: chain Lj residue 18 LEU Chi-restraints excluded: chain Lk residue 12 LEU Chi-restraints excluded: chain Lk residue 14 THR Chi-restraints excluded: chain Lk residue 48 THR Chi-restraints excluded: chain Lk residue 60 LEU Chi-restraints excluded: chain Ll residue 25 GLN Chi-restraints excluded: chain Ll residue 45 ARG Chi-restraints excluded: chain Ll residue 47 THR Chi-restraints excluded: chain Lm residue 126 LYS Chi-restraints excluded: chain Lm residue 127 VAL Chi-restraints excluded: chain Ln residue 11 ARG Chi-restraints excluded: chain Lo residue 62 THR Chi-restraints excluded: chain Lo residue 67 VAL Chi-restraints excluded: chain Lo residue 77 CYS Chi-restraints excluded: chain Lo residue 103 VAL Chi-restraints excluded: chain Lp residue 8 VAL Chi-restraints excluded: chain Lp residue 88 GLU Chi-restraints excluded: chain Lr residue 64 ILE Chi-restraints excluded: chain Lr residue 80 THR Chi-restraints excluded: chain Lr residue 85 ASN Chi-restraints excluded: chain Lr residue 111 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1029 random chunks: chunk 959 optimal weight: 0.7980 chunk 112 optimal weight: 10.0000 chunk 567 optimal weight: 0.4980 chunk 727 optimal weight: 6.9990 chunk 563 optimal weight: 2.9990 chunk 838 optimal weight: 8.9990 chunk 555 optimal weight: 0.0970 chunk 991 optimal weight: 1.9990 chunk 620 optimal weight: 1.9990 chunk 604 optimal weight: 5.9990 chunk 457 optimal weight: 7.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LE 245 GLN ** LF 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LG 64 GLN LH 106 GLN LM 78 GLN LP 10 ASN LP 75 GLN LQ 93 GLN LU 38 ASN LU 50 ASN Ld 18 ASN Le 23 HIS Le 92 ASN Le 102 ASN Lg 100 GLN Lh 20 GLN ** Lk 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ln 22 GLN Lo 90 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 149403 Z= 0.167 Angle : 0.798 19.914 220951 Z= 0.441 Chirality : 0.035 0.487 27273 Planarity : 0.009 0.146 13132 Dihedral : 25.026 179.991 70550 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.66 % Favored : 94.29 % Rotamer: Outliers : 2.51 % Allowed : 14.72 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.37 % Cis-general : 0.00 % Twisted Proline : 0.74 % 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: -0.24 (0.10), residues: 6411 helix: 1.01 (0.11), residues: 2216 sheet: -0.79 (0.17), residues: 898 loop : -0.74 (0.11), residues: 3297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRPLT 125 HIS 0.005 0.001 HISLg 73 PHE 0.018 0.001 PHELU 78 TYR 0.021 0.001 TYRLA 186 ARG 0.009 0.000 ARGLo 99 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12822 Ramachandran restraints generated. 6411 Oldfield, 0 Emsley, 6411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12822 Ramachandran restraints generated. 6411 Oldfield, 0 Emsley, 6411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 995 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 855 time to evaluate : 6.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: LB 258 HIS cc_start: 0.6587 (OUTLIER) cc_final: 0.6166 (t-90) REVERT: LC 67 TRP cc_start: 0.8220 (OUTLIER) cc_final: 0.6942 (t60) REVERT: LD 86 TYR cc_start: 0.8029 (OUTLIER) cc_final: 0.6549 (p90) REVERT: LD 212 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7184 (mpp) REVERT: LH 106 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.7512 (mm-40) REVERT: LJ 47 THR cc_start: 0.8943 (m) cc_final: 0.8619 (p) REVERT: LM 126 GLU cc_start: 0.8502 (tp30) cc_final: 0.7768 (tp30) REVERT: LO 162 GLU cc_start: 0.7587 (mm-30) cc_final: 0.7245 (mm-30) REVERT: LO 180 GLN cc_start: 0.8671 (tp40) cc_final: 0.8365 (tp40) REVERT: LQ 124 ASP cc_start: 0.8796 (OUTLIER) cc_final: 0.8502 (p0) REVERT: LR 29 THR cc_start: 0.8957 (p) cc_final: 0.8715 (m) REVERT: LR 99 MET cc_start: 0.8776 (mmp) cc_final: 0.8448 (mmp) REVERT: LT 79 GLN cc_start: 0.9201 (OUTLIER) cc_final: 0.8401 (tt0) REVERT: LT 157 GLU cc_start: 0.7772 (pp20) cc_final: 0.7512 (pp20) REVERT: LT 159 MET cc_start: 0.6719 (mmm) cc_final: 0.6456 (mmm) REVERT: LU 40 GLU cc_start: 0.8238 (tt0) cc_final: 0.8017 (tm-30) REVERT: LX 145 ASP cc_start: 0.8151 (t70) cc_final: 0.7669 (t0) REVERT: LX 148 ASP cc_start: 0.7850 (m-30) cc_final: 0.7602 (m-30) REVERT: LY 127 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.7830 (mp10) REVERT: LZ 88 ASP cc_start: 0.7602 (p0) cc_final: 0.7325 (p0) REVERT: LZ 97 ASN cc_start: 0.9060 (p0) cc_final: 0.8766 (p0) REVERT: La 89 ASN cc_start: 0.9265 (m-40) cc_final: 0.9008 (m-40) REVERT: Lc 17 ARG cc_start: 0.8677 (ptp90) cc_final: 0.8266 (mtm-85) REVERT: Lc 22 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7623 (mtt) REVERT: Ld 59 THR cc_start: 0.8968 (p) cc_final: 0.8766 (t) REVERT: Lk 12 LEU cc_start: 0.9463 (OUTLIER) cc_final: 0.9230 (mm) REVERT: Lk 30 ASP cc_start: 0.8259 (p0) cc_final: 0.7912 (p0) REVERT: Lk 40 ARG cc_start: 0.8773 (ttt180) cc_final: 0.8444 (ttt180) REVERT: Lm 126 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.7827 (mttm) outliers start: 140 outliers final: 82 residues processed: 921 average time/residue: 1.9889 time to fit residues: 2694.7072 Evaluate side-chains 917 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 824 time to evaluate : 6.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LA residue 114 CYS Chi-restraints excluded: chain LB residue 258 HIS Chi-restraints excluded: chain LB residue 337 VAL Chi-restraints excluded: chain LC residue 67 TRP Chi-restraints excluded: chain LC residue 71 ARG Chi-restraints excluded: chain LC residue 297 GLU Chi-restraints excluded: chain LD residue 51 MET Chi-restraints excluded: chain LD residue 86 TYR Chi-restraints excluded: chain LD residue 118 ILE Chi-restraints excluded: chain LD residue 212 MET Chi-restraints excluded: chain LE residue 107 VAL Chi-restraints excluded: chain LE residue 175 VAL Chi-restraints excluded: chain LE residue 199 THR Chi-restraints excluded: chain LF residue 238 ASP Chi-restraints excluded: chain LF residue 248 ASN Chi-restraints excluded: chain LG residue 55 VAL Chi-restraints excluded: chain LG residue 89 ARG Chi-restraints excluded: chain LG residue 106 THR Chi-restraints excluded: chain LG residue 119 GLU Chi-restraints excluded: chain LG residue 165 GLU Chi-restraints excluded: chain LH residue 6 SER Chi-restraints excluded: chain LH residue 11 ASP Chi-restraints excluded: chain LH residue 44 GLU Chi-restraints excluded: chain LH residue 106 GLN Chi-restraints excluded: chain LH residue 110 SER Chi-restraints excluded: chain LI residue 53 VAL Chi-restraints excluded: chain LI residue 79 SER Chi-restraints excluded: chain LI residue 183 ASP Chi-restraints excluded: chain LI residue 203 ARG Chi-restraints excluded: chain LJ residue 100 SER Chi-restraints excluded: chain LJ residue 129 ASP Chi-restraints excluded: chain LL residue 59 VAL Chi-restraints excluded: chain LL residue 151 THR Chi-restraints excluded: chain LM residue 67 SER Chi-restraints excluded: chain LM residue 113 MET Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 131 GLU Chi-restraints excluded: chain LN residue 147 ASP Chi-restraints excluded: chain LO residue 27 VAL Chi-restraints excluded: chain LO residue 118 MET Chi-restraints excluded: chain LO residue 189 ILE Chi-restraints excluded: chain LP residue 2 VAL Chi-restraints excluded: chain LP residue 89 GLU Chi-restraints excluded: chain LP residue 115 GLU Chi-restraints excluded: chain LQ residue 82 VAL Chi-restraints excluded: chain LQ residue 124 ASP Chi-restraints excluded: chain LR residue 111 GLU Chi-restraints excluded: chain LS residue 23 HIS Chi-restraints excluded: chain LS residue 158 VAL Chi-restraints excluded: chain LT residue 79 GLN Chi-restraints excluded: chain LU residue 23 LEU Chi-restraints excluded: chain LU residue 25 CYS Chi-restraints excluded: chain LU residue 62 THR Chi-restraints excluded: chain LU residue 67 LYS Chi-restraints excluded: chain LW residue 38 SER Chi-restraints excluded: chain LX residue 143 ASP Chi-restraints excluded: chain LY residue 55 VAL Chi-restraints excluded: chain LY residue 111 LEU Chi-restraints excluded: chain LY residue 127 GLN Chi-restraints excluded: chain LZ residue 13 VAL Chi-restraints excluded: chain LZ residue 120 GLU Chi-restraints excluded: chain La residue 134 GLU Chi-restraints excluded: chain La residue 140 VAL Chi-restraints excluded: chain Lb residue 40 LEU Chi-restraints excluded: chain Lc residue 19 GLN Chi-restraints excluded: chain Lc residue 22 MET Chi-restraints excluded: chain Lc residue 28 VAL Chi-restraints excluded: chain Lc residue 57 LYS Chi-restraints excluded: chain Ld residue 26 THR Chi-restraints excluded: chain Ld residue 107 THR Chi-restraints excluded: chain Le residue 7 LEU Chi-restraints excluded: chain Lf residue 18 LEU Chi-restraints excluded: chain Lf residue 37 ASP Chi-restraints excluded: chain Lg residue 102 ILE Chi-restraints excluded: chain Lh residue 8 ASP Chi-restraints excluded: chain Lh residue 22 ASP Chi-restraints excluded: chain Li residue 3 LEU Chi-restraints excluded: chain Li residue 11 LEU Chi-restraints excluded: chain Lj residue 18 LEU Chi-restraints excluded: chain Lk residue 12 LEU Chi-restraints excluded: chain Lk residue 14 THR Chi-restraints excluded: chain Lk residue 48 THR Chi-restraints excluded: chain Lk residue 60 LEU Chi-restraints excluded: chain Ll residue 45 ARG Chi-restraints excluded: chain Ll residue 47 THR Chi-restraints excluded: chain Lm residue 126 LYS Chi-restraints excluded: chain Lm residue 127 VAL Chi-restraints excluded: chain Lo residue 67 VAL Chi-restraints excluded: chain Lo residue 77 CYS Chi-restraints excluded: chain Lo residue 103 VAL Chi-restraints excluded: chain Lr residue 64 ILE Chi-restraints excluded: chain Lr residue 80 THR Chi-restraints excluded: chain Lr residue 85 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1029 random chunks: chunk 613 optimal weight: 1.9990 chunk 396 optimal weight: 10.0000 chunk 592 optimal weight: 0.4980 chunk 298 optimal weight: 10.0000 chunk 194 optimal weight: 40.0000 chunk 192 optimal weight: 7.9990 chunk 630 optimal weight: 3.9990 chunk 675 optimal weight: 1.9990 chunk 490 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 chunk 779 optimal weight: 5.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LA 132 ASN ** LA 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 63 GLN LG 64 GLN LO 96 GLN LP 10 ASN LP 75 GLN LQ 93 GLN LU 38 ASN ** LV 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lb 60 ASN Ld 18 ASN Le 92 ASN Le 102 ASN Lg 100 GLN ** Lh 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Li 92 ASN ** Lk 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ll 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ln 22 GLN Lp 72 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 149403 Z= 0.271 Angle : 0.799 19.942 220951 Z= 0.440 Chirality : 0.036 0.491 27273 Planarity : 0.009 0.143 13132 Dihedral : 24.915 179.989 70550 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.66 % Favored : 94.29 % Rotamer: Outliers : 2.40 % Allowed : 15.59 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.37 % Cis-general : 0.00 % Twisted Proline : 0.74 % 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: -0.19 (0.10), residues: 6411 helix: 1.07 (0.11), residues: 2225 sheet: -0.81 (0.17), residues: 880 loop : -0.72 (0.11), residues: 3306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRPLT 125 HIS 0.005 0.001 HISLa 40 PHE 0.019 0.001 PHELU 39 TYR 0.021 0.001 TYRLE 73 ARG 0.013 0.000 ARGLl 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12822 Ramachandran restraints generated. 6411 Oldfield, 0 Emsley, 6411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12822 Ramachandran restraints generated. 6411 Oldfield, 0 Emsley, 6411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 966 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 832 time to evaluate : 6.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: LB 258 HIS cc_start: 0.6766 (OUTLIER) cc_final: 0.6254 (t-90) REVERT: LC 67 TRP cc_start: 0.8280 (OUTLIER) cc_final: 0.6929 (t60) REVERT: LD 86 TYR cc_start: 0.8086 (OUTLIER) cc_final: 0.6547 (p90) REVERT: LD 212 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7243 (mpp) REVERT: LJ 47 THR cc_start: 0.8943 (m) cc_final: 0.8615 (p) REVERT: LM 126 GLU cc_start: 0.8546 (tp30) cc_final: 0.7830 (tp30) REVERT: LN 161 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8060 (mtp) REVERT: LO 158 GLU cc_start: 0.7538 (tp30) cc_final: 0.7201 (tp30) REVERT: LO 180 GLN cc_start: 0.8721 (tp40) cc_final: 0.8462 (tp40) REVERT: LO 184 ASN cc_start: 0.8771 (m-40) cc_final: 0.8479 (m110) REVERT: LP 103 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7184 (mt-10) REVERT: LQ 124 ASP cc_start: 0.8816 (OUTLIER) cc_final: 0.8534 (p0) REVERT: LR 29 THR cc_start: 0.8968 (p) cc_final: 0.8726 (m) REVERT: LR 99 MET cc_start: 0.8810 (mmp) cc_final: 0.8485 (mmp) REVERT: LT 79 GLN cc_start: 0.9203 (OUTLIER) cc_final: 0.8420 (tt0) REVERT: LT 157 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7505 (pp20) REVERT: LW 44 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8439 (ptp-170) REVERT: LX 145 ASP cc_start: 0.8165 (t70) cc_final: 0.7680 (t0) REVERT: LX 148 ASP cc_start: 0.7869 (m-30) cc_final: 0.7611 (m-30) REVERT: LY 127 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.7884 (mp10) REVERT: LZ 88 ASP cc_start: 0.7578 (p0) cc_final: 0.7314 (p0) REVERT: LZ 97 ASN cc_start: 0.9060 (p0) cc_final: 0.8808 (p0) REVERT: LZ 103 ASP cc_start: 0.8729 (t0) cc_final: 0.8521 (t0) REVERT: La 89 ASN cc_start: 0.9271 (m-40) cc_final: 0.9011 (m-40) REVERT: Lb 60 ASN cc_start: 0.8836 (t160) cc_final: 0.8522 (t0) REVERT: Lc 17 ARG cc_start: 0.8661 (ptp90) cc_final: 0.8231 (mtm-85) REVERT: Lc 22 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7607 (mtt) REVERT: Lc 62 TYR cc_start: 0.8995 (t80) cc_final: 0.8753 (t80) REVERT: Ld 59 THR cc_start: 0.8999 (p) cc_final: 0.8786 (t) REVERT: Le 26 ASP cc_start: 0.7714 (p0) cc_final: 0.7477 (p0) REVERT: Lk 12 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.9214 (mm) REVERT: Lk 30 ASP cc_start: 0.8277 (p0) cc_final: 0.7930 (p0) REVERT: Lk 40 ARG cc_start: 0.8819 (ttt180) cc_final: 0.8488 (ttt180) REVERT: Lm 126 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.7868 (mttm) REVERT: Lr 111 ILE cc_start: 0.9509 (OUTLIER) cc_final: 0.9228 (mp) outliers start: 134 outliers final: 87 residues processed: 890 average time/residue: 1.9719 time to fit residues: 2581.0215 Evaluate side-chains 908 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 807 time to evaluate : 6.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LA residue 114 CYS Chi-restraints excluded: chain LB residue 258 HIS Chi-restraints excluded: chain LB residue 337 VAL Chi-restraints excluded: chain LC residue 67 TRP Chi-restraints excluded: chain LC residue 71 ARG Chi-restraints excluded: chain LC residue 297 GLU Chi-restraints excluded: chain LD residue 51 MET Chi-restraints excluded: chain LD residue 86 TYR Chi-restraints excluded: chain LD residue 118 ILE Chi-restraints excluded: chain LD residue 212 MET Chi-restraints excluded: chain LD residue 239 MET Chi-restraints excluded: chain LE residue 107 VAL Chi-restraints excluded: chain LE residue 175 VAL Chi-restraints excluded: chain LE residue 199 THR Chi-restraints excluded: chain LF residue 238 ASP Chi-restraints excluded: chain LF residue 248 ASN Chi-restraints excluded: chain LG residue 55 VAL Chi-restraints excluded: chain LG residue 89 ARG Chi-restraints excluded: chain LG residue 106 THR Chi-restraints excluded: chain LG residue 119 GLU Chi-restraints excluded: chain LH residue 6 SER Chi-restraints excluded: chain LH residue 11 ASP Chi-restraints excluded: chain LH residue 44 GLU Chi-restraints excluded: chain LH residue 110 SER Chi-restraints excluded: chain LH residue 187 VAL Chi-restraints excluded: chain LI residue 53 VAL Chi-restraints excluded: chain LI residue 183 ASP Chi-restraints excluded: chain LI residue 203 ARG Chi-restraints excluded: chain LJ residue 100 SER Chi-restraints excluded: chain LJ residue 129 ASP Chi-restraints excluded: chain LL residue 59 VAL Chi-restraints excluded: chain LL residue 151 THR Chi-restraints excluded: chain LL residue 155 MET Chi-restraints excluded: chain LM residue 67 SER Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 131 GLU Chi-restraints excluded: chain LN residue 161 MET Chi-restraints excluded: chain LO residue 27 VAL Chi-restraints excluded: chain LO residue 189 ILE Chi-restraints excluded: chain LP residue 2 VAL Chi-restraints excluded: chain LP residue 89 GLU Chi-restraints excluded: chain LP residue 115 GLU Chi-restraints excluded: chain LQ residue 82 VAL Chi-restraints excluded: chain LQ residue 124 ASP Chi-restraints excluded: chain LR residue 111 GLU Chi-restraints excluded: chain LS residue 23 HIS Chi-restraints excluded: chain LS residue 158 VAL Chi-restraints excluded: chain LT residue 79 GLN Chi-restraints excluded: chain LT residue 103 ASP Chi-restraints excluded: chain LT residue 157 GLU Chi-restraints excluded: chain LU residue 25 CYS Chi-restraints excluded: chain LU residue 62 THR Chi-restraints excluded: chain LU residue 67 LYS Chi-restraints excluded: chain LU residue 74 SER Chi-restraints excluded: chain LW residue 38 SER Chi-restraints excluded: chain LW residue 44 ARG Chi-restraints excluded: chain LX residue 92 ASP Chi-restraints excluded: chain LX residue 143 ASP Chi-restraints excluded: chain LX residue 147 LEU Chi-restraints excluded: chain LY residue 55 VAL Chi-restraints excluded: chain LY residue 111 LEU Chi-restraints excluded: chain LY residue 127 GLN Chi-restraints excluded: chain LZ residue 13 VAL Chi-restraints excluded: chain LZ residue 120 GLU Chi-restraints excluded: chain La residue 134 GLU Chi-restraints excluded: chain La residue 140 VAL Chi-restraints excluded: chain Lb residue 36 ASP Chi-restraints excluded: chain Lb residue 40 LEU Chi-restraints excluded: chain Lc residue 19 GLN Chi-restraints excluded: chain Lc residue 22 MET Chi-restraints excluded: chain Lc residue 28 VAL Chi-restraints excluded: chain Lc residue 57 LYS Chi-restraints excluded: chain Ld residue 26 THR Chi-restraints excluded: chain Ld residue 107 THR Chi-restraints excluded: chain Le residue 7 LEU Chi-restraints excluded: chain Lf residue 18 LEU Chi-restraints excluded: chain Lf residue 33 VAL Chi-restraints excluded: chain Lf residue 37 ASP Chi-restraints excluded: chain Lf residue 105 LEU Chi-restraints excluded: chain Lg residue 102 ILE Chi-restraints excluded: chain Lh residue 8 ASP Chi-restraints excluded: chain Lh residue 22 ASP Chi-restraints excluded: chain Li residue 3 LEU Chi-restraints excluded: chain Li residue 11 LEU Chi-restraints excluded: chain Lj residue 18 LEU Chi-restraints excluded: chain Lk residue 12 LEU Chi-restraints excluded: chain Lk residue 14 THR Chi-restraints excluded: chain Lk residue 48 THR Chi-restraints excluded: chain Lk residue 60 LEU Chi-restraints excluded: chain Ll residue 45 ARG Chi-restraints excluded: chain Ll residue 47 THR Chi-restraints excluded: chain Lm residue 126 LYS Chi-restraints excluded: chain Lm residue 127 VAL Chi-restraints excluded: chain Lo residue 67 VAL Chi-restraints excluded: chain Lo residue 77 CYS Chi-restraints excluded: chain Lo residue 103 VAL Chi-restraints excluded: chain Lp residue 88 GLU Chi-restraints excluded: chain Lr residue 64 ILE Chi-restraints excluded: chain Lr residue 80 THR Chi-restraints excluded: chain Lr residue 85 ASN Chi-restraints excluded: chain Lr residue 111 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1029 random chunks: chunk 902 optimal weight: 3.9990 chunk 950 optimal weight: 5.9990 chunk 866 optimal weight: 9.9990 chunk 924 optimal weight: 0.9990 chunk 949 optimal weight: 6.9990 chunk 556 optimal weight: 3.9990 chunk 402 optimal weight: 7.9990 chunk 725 optimal weight: 6.9990 chunk 283 optimal weight: 7.9990 chunk 835 optimal weight: 3.9990 chunk 874 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** LA 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 63 GLN LG 64 GLN LM 78 GLN LP 10 ASN LP 75 GLN LQ 93 GLN LU 38 ASN LU 50 ASN ** LV 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ld 18 ASN Le 102 ASN Lg 100 GLN ** Lh 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Li 92 ASN ** Lk 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ll 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ln 22 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 149403 Z= 0.355 Angle : 0.820 20.154 220951 Z= 0.448 Chirality : 0.038 0.501 27273 Planarity : 0.009 0.143 13132 Dihedral : 24.899 179.461 70550 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.90 % Favored : 94.06 % Rotamer: Outliers : 2.35 % Allowed : 15.93 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.37 % Cis-general : 0.00 % Twisted Proline : 0.74 % 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: -0.23 (0.10), residues: 6411 helix: 1.03 (0.11), residues: 2231 sheet: -0.81 (0.17), residues: 887 loop : -0.74 (0.11), residues: 3293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRPLT 125 HIS 0.006 0.001 HISLa 40 PHE 0.015 0.001 PHELU 78 TYR 0.024 0.002 TYRLD 44 ARG 0.012 0.000 ARGLo 99 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12822 Ramachandran restraints generated. 6411 Oldfield, 0 Emsley, 6411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12822 Ramachandran restraints generated. 6411 Oldfield, 0 Emsley, 6411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 958 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 827 time to evaluate : 6.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: LB 258 HIS cc_start: 0.6937 (OUTLIER) cc_final: 0.6452 (t-90) REVERT: LC 67 TRP cc_start: 0.8411 (OUTLIER) cc_final: 0.7125 (t60) REVERT: LD 86 TYR cc_start: 0.8154 (OUTLIER) cc_final: 0.6621 (p90) REVERT: LD 212 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7281 (mpp) REVERT: LF 220 MET cc_start: 0.8007 (ttp) cc_final: 0.7587 (ttm) REVERT: LH 106 GLN cc_start: 0.7952 (mp10) cc_final: 0.7681 (mt0) REVERT: LJ 47 THR cc_start: 0.8965 (m) cc_final: 0.8644 (p) REVERT: LM 126 GLU cc_start: 0.8599 (tp30) cc_final: 0.8090 (tp30) REVERT: LN 161 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8094 (mtp) REVERT: LO 158 GLU cc_start: 0.7581 (tp30) cc_final: 0.7328 (tp30) REVERT: LO 162 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7281 (mm-30) REVERT: LO 180 GLN cc_start: 0.8743 (tp40) cc_final: 0.8431 (tp40) REVERT: LO 184 ASN cc_start: 0.8791 (m-40) cc_final: 0.8398 (m110) REVERT: LQ 124 ASP cc_start: 0.8829 (OUTLIER) cc_final: 0.8549 (p0) REVERT: LR 29 THR cc_start: 0.8989 (p) cc_final: 0.8727 (m) REVERT: LR 99 MET cc_start: 0.8805 (mmp) cc_final: 0.8524 (mmp) REVERT: LT 79 GLN cc_start: 0.9233 (OUTLIER) cc_final: 0.8613 (tt0) REVERT: LT 157 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7512 (pp20) REVERT: LT 159 MET cc_start: 0.6882 (mmm) cc_final: 0.6585 (mmm) REVERT: LW 44 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.8560 (ptp-170) REVERT: LX 145 ASP cc_start: 0.8177 (t70) cc_final: 0.7690 (t0) REVERT: LX 148 ASP cc_start: 0.7893 (m-30) cc_final: 0.7630 (m-30) REVERT: LY 127 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.7896 (mp10) REVERT: LZ 88 ASP cc_start: 0.7552 (p0) cc_final: 0.7286 (p0) REVERT: LZ 97 ASN cc_start: 0.9073 (p0) cc_final: 0.8807 (p0) REVERT: La 89 ASN cc_start: 0.9263 (m-40) cc_final: 0.9024 (m-40) REVERT: Lb 60 ASN cc_start: 0.8791 (t160) cc_final: 0.8501 (t0) REVERT: Lc 17 ARG cc_start: 0.8670 (ptp90) cc_final: 0.8232 (mtm-85) REVERT: Lc 22 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7691 (mtt) REVERT: Lc 62 TYR cc_start: 0.9009 (t80) cc_final: 0.8774 (t80) REVERT: Le 26 ASP cc_start: 0.7756 (p0) cc_final: 0.7524 (p0) REVERT: Lk 30 ASP cc_start: 0.8283 (p0) cc_final: 0.7927 (p0) REVERT: Lk 40 ARG cc_start: 0.8826 (ttt180) cc_final: 0.8511 (ttt180) REVERT: Lm 126 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.7901 (mttm) REVERT: Ln 11 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7203 (mtt-85) REVERT: Lr 111 ILE cc_start: 0.9518 (OUTLIER) cc_final: 0.9234 (mp) outliers start: 131 outliers final: 86 residues processed: 891 average time/residue: 1.9822 time to fit residues: 2597.6692 Evaluate side-chains 909 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 809 time to evaluate : 6.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LA residue 114 CYS Chi-restraints excluded: chain LB residue 258 HIS Chi-restraints excluded: chain LB residue 337 VAL Chi-restraints excluded: chain LC residue 67 TRP Chi-restraints excluded: chain LC residue 71 ARG Chi-restraints excluded: chain LC residue 297 GLU Chi-restraints excluded: chain LD residue 51 MET Chi-restraints excluded: chain LD residue 86 TYR Chi-restraints excluded: chain LD residue 212 MET Chi-restraints excluded: chain LE residue 107 VAL Chi-restraints excluded: chain LE residue 175 VAL Chi-restraints excluded: chain LE residue 199 THR Chi-restraints excluded: chain LF residue 238 ASP Chi-restraints excluded: chain LF residue 248 ASN Chi-restraints excluded: chain LG residue 55 VAL Chi-restraints excluded: chain LG residue 89 ARG Chi-restraints excluded: chain LG residue 106 THR Chi-restraints excluded: chain LG residue 149 ASN Chi-restraints excluded: chain LH residue 6 SER Chi-restraints excluded: chain LH residue 11 ASP Chi-restraints excluded: chain LH residue 44 GLU Chi-restraints excluded: chain LH residue 110 SER Chi-restraints excluded: chain LH residue 187 VAL Chi-restraints excluded: chain LI residue 35 ASP Chi-restraints excluded: chain LI residue 53 VAL Chi-restraints excluded: chain LI residue 61 SER Chi-restraints excluded: chain LI residue 79 SER Chi-restraints excluded: chain LI residue 183 ASP Chi-restraints excluded: chain LI residue 203 ARG Chi-restraints excluded: chain LJ residue 100 SER Chi-restraints excluded: chain LJ residue 129 ASP Chi-restraints excluded: chain LL residue 59 VAL Chi-restraints excluded: chain LL residue 151 THR Chi-restraints excluded: chain LM residue 67 SER Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 131 GLU Chi-restraints excluded: chain LN residue 161 MET Chi-restraints excluded: chain LO residue 27 VAL Chi-restraints excluded: chain LO residue 189 ILE Chi-restraints excluded: chain LP residue 2 VAL Chi-restraints excluded: chain LP residue 89 GLU Chi-restraints excluded: chain LP residue 115 GLU Chi-restraints excluded: chain LP residue 125 MET Chi-restraints excluded: chain LQ residue 42 THR Chi-restraints excluded: chain LQ residue 82 VAL Chi-restraints excluded: chain LQ residue 124 ASP Chi-restraints excluded: chain LR residue 12 SER Chi-restraints excluded: chain LR residue 111 GLU Chi-restraints excluded: chain LS residue 23 HIS Chi-restraints excluded: chain LS residue 158 VAL Chi-restraints excluded: chain LT residue 79 GLN Chi-restraints excluded: chain LT residue 157 GLU Chi-restraints excluded: chain LU residue 23 LEU Chi-restraints excluded: chain LU residue 25 CYS Chi-restraints excluded: chain LU residue 62 THR Chi-restraints excluded: chain LU residue 74 SER Chi-restraints excluded: chain LV residue 22 VAL Chi-restraints excluded: chain LW residue 38 SER Chi-restraints excluded: chain LW residue 44 ARG Chi-restraints excluded: chain LX residue 92 ASP Chi-restraints excluded: chain LX residue 143 ASP Chi-restraints excluded: chain LY residue 55 VAL Chi-restraints excluded: chain LY residue 111 LEU Chi-restraints excluded: chain LY residue 127 GLN Chi-restraints excluded: chain LZ residue 11 VAL Chi-restraints excluded: chain LZ residue 13 VAL Chi-restraints excluded: chain LZ residue 120 GLU Chi-restraints excluded: chain La residue 134 GLU Chi-restraints excluded: chain La residue 140 VAL Chi-restraints excluded: chain Lb residue 40 LEU Chi-restraints excluded: chain Lc residue 22 MET Chi-restraints excluded: chain Lc residue 28 VAL Chi-restraints excluded: chain Lc residue 57 LYS Chi-restraints excluded: chain Ld residue 26 THR Chi-restraints excluded: chain Ld residue 107 THR Chi-restraints excluded: chain Le residue 7 LEU Chi-restraints excluded: chain Lf residue 18 LEU Chi-restraints excluded: chain Lf residue 33 VAL Chi-restraints excluded: chain Lf residue 37 ASP Chi-restraints excluded: chain Lg residue 102 ILE Chi-restraints excluded: chain Lh residue 8 ASP Chi-restraints excluded: chain Li residue 3 LEU Chi-restraints excluded: chain Li residue 11 LEU Chi-restraints excluded: chain Li residue 12 ASN Chi-restraints excluded: chain Lj residue 2 THR Chi-restraints excluded: chain Lj residue 18 LEU Chi-restraints excluded: chain Lk residue 14 THR Chi-restraints excluded: chain Lk residue 48 THR Chi-restraints excluded: chain Lk residue 60 LEU Chi-restraints excluded: chain Ll residue 47 THR Chi-restraints excluded: chain Lm residue 126 LYS Chi-restraints excluded: chain Lm residue 127 VAL Chi-restraints excluded: chain Ln residue 11 ARG Chi-restraints excluded: chain Lo residue 67 VAL Chi-restraints excluded: chain Lo residue 77 CYS Chi-restraints excluded: chain Lo residue 103 VAL Chi-restraints excluded: chain Lr residue 64 ILE Chi-restraints excluded: chain Lr residue 80 THR Chi-restraints excluded: chain Lr residue 85 ASN Chi-restraints excluded: chain Lr residue 111 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1029 random chunks: chunk 920 optimal weight: 4.9990 chunk 606 optimal weight: 4.9990 chunk 977 optimal weight: 1.9990 chunk 596 optimal weight: 8.9990 chunk 463 optimal weight: 5.9990 chunk 679 optimal weight: 2.9990 chunk 1025 optimal weight: 1.9990 chunk 943 optimal weight: 2.9990 chunk 816 optimal weight: 0.9980 chunk 84 optimal weight: 10.0000 chunk 630 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LA 132 ASN ** LA 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 63 GLN LG 64 GLN LP 10 ASN LP 75 GLN LQ 93 GLN LU 38 ASN ** LV 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ld 18 ASN Le 92 ASN Le 102 ASN Lg 100 GLN Li 92 ASN ** Lk 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lk 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ll 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ln 22 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 149403 Z= 0.240 Angle : 0.807 20.121 220951 Z= 0.443 Chirality : 0.036 0.480 27273 Planarity : 0.009 0.141 13132 Dihedral : 24.933 179.094 70550 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.74 % Favored : 94.21 % Rotamer: Outliers : 2.11 % Allowed : 16.33 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.37 % Cis-general : 0.00 % Twisted Proline : 0.74 % 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: -0.20 (0.10), residues: 6411 helix: 1.07 (0.11), residues: 2224 sheet: -0.80 (0.17), residues: 896 loop : -0.74 (0.11), residues: 3291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRPLT 125 HIS 0.005 0.001 HISLa 40 PHE 0.028 0.001 PHELU 39 TYR 0.020 0.001 TYRLE 73 ARG 0.015 0.000 ARGLl 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12822 Ramachandran restraints generated. 6411 Oldfield, 0 Emsley, 6411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12822 Ramachandran restraints generated. 6411 Oldfield, 0 Emsley, 6411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 945 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 827 time to evaluate : 6.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: LB 258 HIS cc_start: 0.6782 (OUTLIER) cc_final: 0.6342 (t-90) REVERT: LC 67 TRP cc_start: 0.8354 (OUTLIER) cc_final: 0.7064 (t60) REVERT: LD 86 TYR cc_start: 0.8131 (OUTLIER) cc_final: 0.6612 (p90) REVERT: LD 212 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7268 (mpp) REVERT: LH 106 GLN cc_start: 0.8159 (mp10) cc_final: 0.7949 (mt0) REVERT: LJ 47 THR cc_start: 0.8953 (m) cc_final: 0.8695 (p) REVERT: LM 126 GLU cc_start: 0.8553 (tp30) cc_final: 0.8046 (tp30) REVERT: LN 161 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.8093 (mtp) REVERT: LO 158 GLU cc_start: 0.7515 (tp30) cc_final: 0.7218 (tp30) REVERT: LO 162 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7211 (mm-30) REVERT: LO 180 GLN cc_start: 0.8720 (tp40) cc_final: 0.8409 (tp40) REVERT: LO 184 ASN cc_start: 0.8781 (m-40) cc_final: 0.8381 (m110) REVERT: LQ 124 ASP cc_start: 0.8817 (OUTLIER) cc_final: 0.8535 (p0) REVERT: LR 29 THR cc_start: 0.8965 (p) cc_final: 0.8723 (m) REVERT: LR 99 MET cc_start: 0.8813 (mmp) cc_final: 0.8478 (mmp) REVERT: LT 79 GLN cc_start: 0.9213 (OUTLIER) cc_final: 0.8575 (tt0) REVERT: LT 157 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7473 (pp20) REVERT: LT 159 MET cc_start: 0.6861 (mmm) cc_final: 0.6574 (mmm) REVERT: LW 44 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.8460 (ptp-170) REVERT: LX 145 ASP cc_start: 0.8166 (t70) cc_final: 0.7682 (t0) REVERT: LX 148 ASP cc_start: 0.7876 (m-30) cc_final: 0.7617 (m-30) REVERT: LY 127 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.7826 (mp10) REVERT: LZ 88 ASP cc_start: 0.7516 (p0) cc_final: 0.7260 (p0) REVERT: LZ 97 ASN cc_start: 0.9054 (p0) cc_final: 0.8796 (p0) REVERT: La 89 ASN cc_start: 0.9254 (m-40) cc_final: 0.9010 (m-40) REVERT: Lb 60 ASN cc_start: 0.8767 (t160) cc_final: 0.8470 (t0) REVERT: Lc 17 ARG cc_start: 0.8671 (ptp90) cc_final: 0.8248 (mtm-85) REVERT: Lc 22 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7651 (mtt) REVERT: Le 26 ASP cc_start: 0.7713 (p0) cc_final: 0.7474 (p0) REVERT: Lk 30 ASP cc_start: 0.8284 (p0) cc_final: 0.7931 (p0) REVERT: Lk 40 ARG cc_start: 0.8823 (ttt180) cc_final: 0.8486 (ttt180) REVERT: Lm 126 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.7885 (mttm) REVERT: Ln 11 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7192 (mtt-85) REVERT: Lr 111 ILE cc_start: 0.9507 (OUTLIER) cc_final: 0.9227 (mp) outliers start: 118 outliers final: 91 residues processed: 888 average time/residue: 1.9785 time to fit residues: 2593.0746 Evaluate side-chains 916 residues out of total 5589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 811 time to evaluate : 6.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain LA residue 114 CYS Chi-restraints excluded: chain LB residue 258 HIS Chi-restraints excluded: chain LB residue 337 VAL Chi-restraints excluded: chain LC residue 67 TRP Chi-restraints excluded: chain LC residue 71 ARG Chi-restraints excluded: chain LC residue 297 GLU Chi-restraints excluded: chain LD residue 51 MET Chi-restraints excluded: chain LD residue 86 TYR Chi-restraints excluded: chain LD residue 118 ILE Chi-restraints excluded: chain LD residue 212 MET Chi-restraints excluded: chain LD residue 239 MET Chi-restraints excluded: chain LE residue 107 VAL Chi-restraints excluded: chain LE residue 175 VAL Chi-restraints excluded: chain LE residue 199 THR Chi-restraints excluded: chain LF residue 238 ASP Chi-restraints excluded: chain LF residue 248 ASN Chi-restraints excluded: chain LG residue 55 VAL Chi-restraints excluded: chain LG residue 89 ARG Chi-restraints excluded: chain LG residue 106 THR Chi-restraints excluded: chain LH residue 6 SER Chi-restraints excluded: chain LH residue 11 ASP Chi-restraints excluded: chain LH residue 44 GLU Chi-restraints excluded: chain LH residue 110 SER Chi-restraints excluded: chain LH residue 187 VAL Chi-restraints excluded: chain LI residue 53 VAL Chi-restraints excluded: chain LI residue 61 SER Chi-restraints excluded: chain LI residue 79 SER Chi-restraints excluded: chain LI residue 183 ASP Chi-restraints excluded: chain LI residue 203 ARG Chi-restraints excluded: chain LJ residue 100 SER Chi-restraints excluded: chain LJ residue 129 ASP Chi-restraints excluded: chain LL residue 59 VAL Chi-restraints excluded: chain LL residue 151 THR Chi-restraints excluded: chain LL residue 155 MET Chi-restraints excluded: chain LM residue 67 SER Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 131 GLU Chi-restraints excluded: chain LN residue 147 ASP Chi-restraints excluded: chain LN residue 161 MET Chi-restraints excluded: chain LO residue 27 VAL Chi-restraints excluded: chain LO residue 189 ILE Chi-restraints excluded: chain LP residue 2 VAL Chi-restraints excluded: chain LP residue 89 GLU Chi-restraints excluded: chain LP residue 115 GLU Chi-restraints excluded: chain LP residue 125 MET Chi-restraints excluded: chain LQ residue 42 THR Chi-restraints excluded: chain LQ residue 82 VAL Chi-restraints excluded: chain LQ residue 124 ASP Chi-restraints excluded: chain LR residue 12 SER Chi-restraints excluded: chain LR residue 111 GLU Chi-restraints excluded: chain LS residue 23 HIS Chi-restraints excluded: chain LS residue 158 VAL Chi-restraints excluded: chain LT residue 79 GLN Chi-restraints excluded: chain LT residue 157 GLU Chi-restraints excluded: chain LU residue 23 LEU Chi-restraints excluded: chain LU residue 25 CYS Chi-restraints excluded: chain LU residue 62 THR Chi-restraints excluded: chain LU residue 67 LYS Chi-restraints excluded: chain LU residue 74 SER Chi-restraints excluded: chain LV residue 22 VAL Chi-restraints excluded: chain LW residue 38 SER Chi-restraints excluded: chain LW residue 44 ARG Chi-restraints excluded: chain LX residue 92 ASP Chi-restraints excluded: chain LX residue 143 ASP Chi-restraints excluded: chain LX residue 155 ILE Chi-restraints excluded: chain LY residue 55 VAL Chi-restraints excluded: chain LY residue 111 LEU Chi-restraints excluded: chain LY residue 127 GLN Chi-restraints excluded: chain LZ residue 11 VAL Chi-restraints excluded: chain LZ residue 13 VAL Chi-restraints excluded: chain LZ residue 120 GLU Chi-restraints excluded: chain La residue 134 GLU Chi-restraints excluded: chain La residue 140 VAL Chi-restraints excluded: chain Lb residue 40 LEU Chi-restraints excluded: chain Lc residue 22 MET Chi-restraints excluded: chain Lc residue 28 VAL Chi-restraints excluded: chain Lc residue 57 LYS Chi-restraints excluded: chain Ld residue 26 THR Chi-restraints excluded: chain Ld residue 107 THR Chi-restraints excluded: chain Le residue 7 LEU Chi-restraints excluded: chain Le residue 129 LEU Chi-restraints excluded: chain Lf residue 18 LEU Chi-restraints excluded: chain Lf residue 33 VAL Chi-restraints excluded: chain Lf residue 37 ASP Chi-restraints excluded: chain Lg residue 102 ILE Chi-restraints excluded: chain Lh residue 8 ASP Chi-restraints excluded: chain Li residue 3 LEU Chi-restraints excluded: chain Li residue 11 LEU Chi-restraints excluded: chain Li residue 12 ASN Chi-restraints excluded: chain Lj residue 18 LEU Chi-restraints excluded: chain Lk residue 14 THR Chi-restraints excluded: chain Lk residue 48 THR Chi-restraints excluded: chain Lk residue 60 LEU Chi-restraints excluded: chain Ll residue 47 THR Chi-restraints excluded: chain Lm residue 126 LYS Chi-restraints excluded: chain Lm residue 127 VAL Chi-restraints excluded: chain Ln residue 11 ARG Chi-restraints excluded: chain Lo residue 67 VAL Chi-restraints excluded: chain Lo residue 77 CYS Chi-restraints excluded: chain Lo residue 103 VAL Chi-restraints excluded: chain Lp residue 8 VAL Chi-restraints excluded: chain Lr residue 64 ILE Chi-restraints excluded: chain Lr residue 80 THR Chi-restraints excluded: chain Lr residue 85 ASN Chi-restraints excluded: chain Lr residue 111 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1029 random chunks: chunk 500 optimal weight: 0.9990 chunk 648 optimal weight: 9.9990 chunk 869 optimal weight: 4.9990 chunk 250 optimal weight: 8.9990 chunk 752 optimal weight: 4.9990 chunk 120 optimal weight: 20.0000 chunk 226 optimal weight: 8.9990 chunk 817 optimal weight: 5.9990 chunk 342 optimal weight: 50.0000 chunk 839 optimal weight: 4.9990 chunk 103 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: LA 162 ASN LF 63 GLN LG 64 GLN LP 10 ASN LP 75 GLN LQ 93 GLN LU 38 ASN LU 50 ASN ** LV 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ld 18 ASN Le 102 ASN Lg 100 GLN Lh 65 GLN Li 92 ASN ** Lk 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lk 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ll 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ln 22 GLN Lo 25 GLN Lp 72 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.071588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.046225 restraints weight = 356048.217| |-----------------------------------------------------------------------------| r_work (start): 0.2716 rms_B_bonded: 1.25 r_work: 0.2592 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2488 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 149403 Z= 0.404 Angle : 0.837 20.124 220951 Z= 0.454 Chirality : 0.040 0.508 27273 Planarity : 0.009 0.143 13132 Dihedral : 24.892 178.905 70550 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.97 % Favored : 93.98 % Rotamer: Outliers : 2.18 % Allowed : 16.33 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.37 % Cis-general : 0.00 % Twisted Proline : 0.74 % 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: -0.27 (0.10), residues: 6411 helix: 0.99 (0.11), residues: 2226 sheet: -0.80 (0.17), residues: 902 loop : -0.77 (0.11), residues: 3283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRPLT 125 HIS 0.005 0.001 HISLE 128 PHE 0.015 0.001 PHELU 78 TYR 0.021 0.002 TYRLD 44 ARG 0.010 0.000 ARGLn 6 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 40362.28 seconds wall clock time: 705 minutes 50.77 seconds (42350.77 seconds total)