Starting phenix.real_space_refine on Fri Jan 19 02:03:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oiq_16896/01_2024/8oiq_16896_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oiq_16896/01_2024/8oiq_16896.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oiq_16896/01_2024/8oiq_16896_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oiq_16896/01_2024/8oiq_16896_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oiq_16896/01_2024/8oiq_16896_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oiq_16896/01_2024/8oiq_16896.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oiq_16896/01_2024/8oiq_16896.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oiq_16896/01_2024/8oiq_16896_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oiq_16896/01_2024/8oiq_16896_neut_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.130 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: 9 Type Number sf(0) Gaussians K 30 8.98 5 Fe 2 7.16 5 Zn 2 6.06 5 P 1718 5.49 5 Mg 205 5.21 5 S 290 5.16 5 C 64881 2.51 5 N 20583 2.21 5 O 25270 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "BF PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BF TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BL TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BP PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bh TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bl TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bn PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bs PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bt PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Bw TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 112981 Number of models: 1 Model: "" Number of chains: 77 Chain: "B1" Number of atoms: 317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 317 Classifications: {'peptide': 45} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 4, 'TRANS': 40} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "B2" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 213 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "B3" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 222 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "B4" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 213 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "B5" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 213 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "B6" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 205 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Chain: "B7" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 62 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 1, 'rna3p_pyr': 2} Link IDs: {'rna3p': 2} Chain: "B8" Number of atoms: 33427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1571, 33427 Classifications: {'RNA': 1571} Modifications used: {'rna2p': 1, 'rna2p_pur': 177, 'rna2p_pyr': 105, 'rna3p': 4, 'rna3p_pur': 692, 'rna3p_pyr': 592} Link IDs: {'rna2p': 282, 'rna3p': 1288} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 3 Chain: "B9" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1560 Classifications: {'RNA': 73} Modifications used: {'p5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 3, 'rna3p': 1, 'rna3p_pur': 35, 'rna3p_pyr': 30} Link IDs: {'rna2p': 6, 'rna3p': 66} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "BA" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1374 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 10, 'TRANS': 155} Chain: "BB" Number of atoms: 1184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1184 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 12, 'TRANS': 136} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 1, 'ARG:plan': 2, 'AYA:plan-2': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 39 Chain: "BC" Number of atoms: 1678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1678 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 17, 'TRANS': 188} Chain: "BD" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 867 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "BE" Number of atoms: 2036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 2036 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 18, 'TRANS': 225} Chain: "BF" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1548 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 9, 'TRANS': 169} Chain: "BG" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 968 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 11, 'TRANS': 106} Chain: "BH" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 902 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "BI" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 425 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 1, 'TRANS': 50} Chain: "BJ" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 387 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "BK" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 833 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 1, 'TRANS': 93} Chain: "BL" Number of atoms: 1860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1860 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 14, 'TRANS': 225} Chain: "BM" Number of atoms: 2420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2420 Classifications: {'peptide': 307} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 281} Chain: "BN" Number of atoms: 2019 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 250, 2011 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 20, 'TRANS': 229} Conformer: "B" Number of residues, atoms: 250, 2011 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 20, 'TRANS': 229} bond proxies already assigned to first conformer: 2060 Chain: "BO" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1660 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 11, 'TRANS': 190} Chain: "BP" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1705 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 18, 'TRANS': 193} Chain: "BQ" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1339 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 166} Chain: "BR" Number of atoms: 1447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1447 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 15, 'TRANS': 161} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'SAC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "BS" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 896 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 9, 'TRANS': 105} Chain: "BT" Number of atoms: 2312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2312 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 27, 'TRANS': 260} Chain: "BU" Number of atoms: 1803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1803 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 17, 'TRANS': 204} Chain: "BV" Number of atoms: 1240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1240 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 8, 'TRANS': 144} Chain: "BW" Number of atoms: 1168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1168 Classifications: {'peptide': 143} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 136} Chain: "BX" Number of atoms: 1855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1855 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 209} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "BY" Number of atoms: 1159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1159 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "BZ" Number of atoms: 1231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1231 Classifications: {'peptide': 155} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 144} Chain: "Ba" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 772 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 6, 'TRANS': 90} Chain: "Bb" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 745 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Bc" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 716 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 7, 'TRANS': 76} Chain: "Bd" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 571 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 64} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "Be" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 780 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "Bf" Number of atoms: 1198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1198 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 144} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "Bg" Number of atoms: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1131 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 12, 'TRANS': 122} Chain: "Bh" Number of atoms: 1325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1325 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 18, 'TRANS': 143} Chain: "Bi" Number of atoms: 3126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3126 Classifications: {'peptide': 387} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 360} Chain: "Bj" Number of atoms: 1325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1325 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 11, 'TRANS': 152} Chain breaks: 1 Chain: "Bl" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 335 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "Bm" Number of atoms: 3173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3173 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 35, 'TRANS': 357} Chain: "Bn" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2952 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 32, 'TRANS': 321} Chain: "Bo" Number of atoms: 2408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2408 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 15, 'TRANS': 279} Chain: "Bp" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1202 Classifications: {'peptide': 143} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 129} Chain: "Bq" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 972 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 11, 'TRANS': 110} Chain: "Br" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 906 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 12, 'TRANS': 95} Chain: "Bs" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 11, 'TRANS': 138} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'THC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Bt" Number of atoms: 2319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2319 Classifications: {'peptide': 289} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 270} Chain: "Bu" Number of atoms: 2138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2138 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 23, 'TRANS': 236} Chain: "Bv" Number of atoms: 1948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1948 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 227} Chain: "Bw" Number of atoms: 1295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1295 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 158} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "Bx" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1097 Classifications: {'peptide': 133} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 116} Chain: "By" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 893 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 8, 'TRANS': 100} Chain: "Bz" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 837 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "AG" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1502 Classifications: {'RNA': 71} Modifications used: {'p5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 4, 'rna3p_pur': 32, 'rna3p_pyr': 33} Link IDs: {'rna2p': 6, 'rna3p': 64} Chain: "Aa" Number of atoms: 3120 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 381, 3112 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 9, 'TRANS': 371} Conformer: "B" Number of residues, atoms: 381, 3112 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 9, 'TRANS': 371} bond proxies already assigned to first conformer: 3151 Chain: "B8" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 219 Unusual residues: {' K': 26, ' MG': 193} Classifications: {'undetermined': 219} Link IDs: {None: 218} Chain: "B9" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 12 Unusual residues: {' MG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "BH" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "BL" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 1, ' MG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "BM" 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: "BT" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "BU" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "BV" 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: "BW" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "Be" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Bh" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "Bl" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Bq" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Bx" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "AG" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 46350 SG CYSBH 110 206.820 68.400 150.269 1.00 59.93 S ATOM 46372 SG CYSBH 113 208.633 70.524 147.662 1.00 67.27 S ATOM 46453 SG CYSBH 123 205.049 69.607 147.108 1.00 55.90 S ATOM 46475 SG CYSBH 126 207.699 66.898 146.895 1.00 63.54 S ATOM 56889 SG CYSBP 64 116.294 119.446 205.807 1.00 74.19 S ATOM 78959 SG CYSBh 73 116.805 118.233 209.356 1.00 62.37 S ATOM 78938 SG CYSBh 70 116.635 113.782 208.591 1.00 65.06 S ATOM 79256 SG CYSBh 108 115.430 113.882 204.958 1.00 62.04 S ATOM 84527 SG CYSBl 73 99.120 87.298 186.016 1.00 75.98 S ATOM 84552 SG CYSBl 76 102.498 88.808 185.127 1.00 64.53 S ATOM 84676 SG CYSBl 89 102.248 85.085 185.996 1.00 58.40 S Time building chain proxies: 43.73, per 1000 atoms: 0.39 Number of scatterers: 112981 At special positions: 0 Unit cell: (272.64, 232.17, 303.525, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 2 29.99 Fe 2 26.01 K 30 19.00 S 290 16.00 P 1718 15.00 Mg 205 11.99 O 25270 8.00 N 20583 7.00 C 64881 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 36.88 Conformation dependent library (CDL) restraints added in 10.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FESBh 201 " pdb="FE1 FESBh 201 " - pdb=" SG CYSBh 73 " pdb="FE2 FESBh 201 " - pdb=" SG CYSBh 70 " pdb="FE1 FESBh 201 " - pdb=" SG CYSBP 64 " pdb="FE2 FESBh 201 " - pdb=" SG CYSBh 108 " Number of angles added : 6 Zn2+ tetrahedral coordination pdb=" ZNBH 201 " pdb="ZN ZNBH 201 " - pdb=" SG CYSBH 123 " pdb="ZN ZNBH 201 " - pdb=" SG CYSBH 113 " pdb="ZN ZNBH 201 " - pdb=" SG CYSBH 126 " pdb="ZN ZNBH 201 " - pdb=" SG CYSBH 110 " pdb=" ZNBl 201 " pdb="ZN ZNBl 201 " - pdb=" ND1 HISBl 95 " pdb="ZN ZNBl 201 " - pdb=" SG CYSBl 73 " pdb="ZN ZNBl 201 " - pdb=" SG CYSBl 76 " pdb="ZN ZNBl 201 " - pdb=" SG CYSBl 89 " Number of angles added : 9 18510 Ramachandran restraints generated. 9255 Oldfield, 0 Emsley, 9255 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17724 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: 313 helices and 78 sheets defined 42.9% alpha, 13.1% beta 297 base pairs and 895 stacking pairs defined. Time for finding SS restraints: 64.69 Creating SS restraints... Processing helix chain 'B1' and resid 25 through 38 removed outlier: 3.658A pdb=" N GLNB1 29 " --> pdb=" O PROB1 25 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEUB1 38 " --> pdb=" O ASPB1 34 " (cutoff:3.500A) Processing helix chain 'B1' and resid 39 through 54 Processing helix chain 'B2' and resid 64 through 75 removed outlier: 5.434A pdb=" N THRB2 75 " --> pdb=" O ILEB2 71 " (cutoff:3.500A) Processing helix chain 'B2' and resid 76 through 90 Processing helix chain 'B4' and resid 64 through 75 removed outlier: 3.660A pdb=" N LEUB4 74 " --> pdb=" O ASPB4 70 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N THRB4 75 " --> pdb=" O ILEB4 71 " (cutoff:3.500A) Processing helix chain 'B4' and resid 76 through 90 Processing helix chain 'B5' and resid 64 through 75 removed outlier: 3.579A pdb=" N LEUB5 74 " --> pdb=" O ASPB5 70 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N THRB5 75 " --> pdb=" O ILEB5 71 " (cutoff:3.500A) Processing helix chain 'B5' and resid 76 through 90 Processing helix chain 'B3' and resid 64 through 74 removed outlier: 4.128A pdb=" N LEUB3 74 " --> pdb=" O ASPB3 70 " (cutoff:3.500A) Processing helix chain 'B3' and resid 75 through 90 Processing helix chain 'B6' and resid 64 through 75 removed outlier: 3.687A pdb=" N LEUB6 74 " --> pdb=" O ASPB6 70 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N THRB6 75 " --> pdb=" O ILEB6 71 " (cutoff:3.500A) Processing helix chain 'B6' and resid 76 through 89 Processing helix chain 'BA' and resid 47 through 53 removed outlier: 4.946A pdb=" N LYSBA 51 " --> pdb=" O ARGBA 47 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYSBA 52 " --> pdb=" O LYSBA 48 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASNBA 53 " --> pdb=" O TRPBA 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'BA' and resid 47 through 53' Processing helix chain 'BA' and resid 81 through 93 removed outlier: 3.811A pdb=" N TYRBA 87 " --> pdb=" O ASPBA 83 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEUBA 88 " --> pdb=" O LYSBA 84 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILEBA 92 " --> pdb=" O LEUBA 88 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARGBA 93 " --> pdb=" O ALABA 89 " (cutoff:3.500A) Processing helix chain 'BA' and resid 96 through 107 removed outlier: 3.917A pdb=" N PHEBA 106 " --> pdb=" O ALABA 102 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SERBA 107 " --> pdb=" O GLNBA 103 " (cutoff:3.500A) Processing helix chain 'BA' and resid 109 through 129 removed outlier: 4.295A pdb=" N GLNBA 113 " --> pdb=" O LYSBA 109 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILEBA 114 " --> pdb=" O LYSBA 110 " (cutoff:3.500A) Processing helix chain 'BA' and resid 189 through 204 removed outlier: 3.899A pdb=" N ARGBA 204 " --> pdb=" O GLUBA 200 " (cutoff:3.500A) Processing helix chain 'BB' and resid 49 through 59 Processing helix chain 'BB' and resid 114 through 136 Processing helix chain 'BC' and resid 28 through 36 Proline residue: BC 36 - end of helix Processing helix chain 'BC' and resid 50 through 55 removed outlier: 6.153A pdb=" N HISBC 55 " --> pdb=" O ASPBC 51 " (cutoff:3.500A) Processing helix chain 'BC' and resid 116 through 121 removed outlier: 3.822A pdb=" N VALBC 120 " --> pdb=" O LEUBC 116 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LYSBC 121 " --> pdb=" O HISBC 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'BC' and resid 116 through 121' Processing helix chain 'BC' and resid 178 through 184 Processing helix chain 'BC' and resid 193 through 203 Processing helix chain 'BD' and resid 110 through 121 removed outlier: 3.592A pdb=" N LEUBD 120 " --> pdb=" O LEUBD 116 " (cutoff:3.500A) Proline residue: BD 121 - end of helix Processing helix chain 'BE' and resid 7 through 19 removed outlier: 3.780A pdb=" N TRPBE 11 " --> pdb=" O PROBE 7 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N LYSBE 12 " --> pdb=" O VALBE 8 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N GLNBE 13 " --> pdb=" O GLYBE 9 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEUBE 16 " --> pdb=" O LYSBE 12 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TRPBE 17 " --> pdb=" O GLNBE 13 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLUBE 18 " --> pdb=" O LEUBE 14 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N GLYBE 19 " --> pdb=" O ARGBE 15 " (cutoff:3.500A) Processing helix chain 'BE' and resid 25 through 35 removed outlier: 3.531A pdb=" N GLUBE 34 " --> pdb=" O ARGBE 30 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N ALABE 35 " --> pdb=" O SERBE 31 " (cutoff:3.500A) Processing helix chain 'BE' and resid 72 through 79 removed outlier: 4.064A pdb=" N GLNBE 76 " --> pdb=" O PROBE 72 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEUBE 77 " --> pdb=" O PROBE 73 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLYBE 78 " --> pdb=" O GLUBE 74 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LEUBE 79 " --> pdb=" O SERBE 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'BE' and resid 72 through 79' Processing helix chain 'BE' and resid 128 through 139 Processing helix chain 'BE' and resid 140 through 148 Processing helix chain 'BE' and resid 149 through 154 Processing helix chain 'BE' and resid 155 through 172 Processing helix chain 'BE' and resid 180 through 192 removed outlier: 3.624A pdb=" N ARGBE 190 " --> pdb=" O ALABE 186 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N TYRBE 191 " --> pdb=" O ILEBE 187 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYSBE 192 " --> pdb=" O TYRBE 188 " (cutoff:3.500A) Processing helix chain 'BE' and resid 197 through 204 removed outlier: 3.764A pdb=" N GLUBE 202 " --> pdb=" O GLUBE 198 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N TRPBE 203 " --> pdb=" O ALABE 199 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VALBE 204 " --> pdb=" O GLUBE 200 " (cutoff:3.500A) Processing helix chain 'BE' and resid 207 through 220 Processing helix chain 'BE' and resid 225 through 245 removed outlier: 3.622A pdb=" N GLUBE 245 " --> pdb=" O GLNBE 241 " (cutoff:3.500A) Processing helix chain 'BF' and resid 72 through 77 removed outlier: 3.801A pdb=" N TRPBF 76 " --> pdb=" O ASPBF 72 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N GLYBF 77 " --> pdb=" O PROBF 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'BF' and resid 72 through 77' Processing helix chain 'BF' and resid 88 through 96 removed outlier: 3.612A pdb=" N LEUBF 92 " --> pdb=" O THRBF 88 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARGBF 93 " --> pdb=" O CYSBF 89 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASNBF 94 " --> pdb=" O GLNBF 90 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYSBF 95 " --> pdb=" O GLNBF 91 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N SERBF 96 " --> pdb=" O LEUBF 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'BF' and resid 88 through 96' Processing helix chain 'BF' and resid 97 through 125 removed outlier: 3.805A pdb=" N TYRBF 105 " --> pdb=" O HISBF 101 " (cutoff:3.500A) Processing helix chain 'BF' and resid 131 through 160 removed outlier: 4.032A pdb=" N GLUBF 135 " --> pdb=" O PROBF 131 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALABF 154 " --> pdb=" O GLUBF 150 " (cutoff:3.500A) Processing helix chain 'BF' and resid 193 through 200 removed outlier: 3.594A pdb=" N ARGBF 198 " --> pdb=" O LYSBF 194 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYSBF 199 " --> pdb=" O LYSBF 195 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ARGBF 200 " --> pdb=" O TYRBF 196 " (cutoff:3.500A) Processing helix chain 'BF' and resid 204 through 241 removed outlier: 4.026A pdb=" N GLUBF 208 " --> pdb=" O METBF 204 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ARGBF 209 " --> pdb=" O PROBF 205 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N PHEBF 210 " --> pdb=" O TYRBF 206 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYSBF 239 " --> pdb=" O PHEBF 235 " (cutoff:3.500A) Proline residue: BF 241 - end of helix Processing helix chain 'BF' and resid 65 through 70 removed outlier: 3.785A pdb=" N GLUBF 68 " --> pdb=" O GLYBF 65 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHEBF 69 " --> pdb=" O LEUBF 66 " (cutoff:3.500A) Processing helix chain 'BG' and resid 42 through 47 removed outlier: 4.522A pdb=" N PHEBG 46 " --> pdb=" O PROBG 42 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLNBG 47 " --> pdb=" O ASPBG 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'BG' and resid 42 through 47' Processing helix chain 'BG' and resid 49 through 57 removed outlier: 4.014A pdb=" N HISBG 53 " --> pdb=" O SERBG 49 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLUBG 54 " --> pdb=" O PROBG 50 " (cutoff:3.500A) Processing helix chain 'BG' and resid 79 through 90 removed outlier: 3.663A pdb=" N GLYBG 90 " --> pdb=" O ILEBG 86 " (cutoff:3.500A) Processing helix chain 'BG' and resid 103 through 114 removed outlier: 3.793A pdb=" N LYSBG 109 " --> pdb=" O SERBG 105 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VALBG 112 " --> pdb=" O ALABG 108 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VALBG 113 " --> pdb=" O LYSBG 109 " (cutoff:3.500A) Processing helix chain 'BH' and resid 86 through 96 removed outlier: 3.505A pdb=" N CYSBH 92 " --> pdb=" O GLUBH 88 " (cutoff:3.500A) Processing helix chain 'BH' and resid 123 through 146 removed outlier: 3.543A pdb=" N LYSBH 143 " --> pdb=" O ARGBH 139 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLYBH 146 " --> pdb=" O GLYBH 142 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 59 through 67 Processing helix chain 'BJ' and resid 68 through 75 removed outlier: 3.819A pdb=" N THRBJ 75 " --> pdb=" O ARGBJ 71 " (cutoff:3.500A) Processing helix chain 'BJ' and resid 76 through 89 removed outlier: 3.505A pdb=" N GLNBJ 80 " --> pdb=" O PROBJ 76 " (cutoff:3.500A) Processing helix chain 'BK' and resid 107 through 114 removed outlier: 4.013A pdb=" N ILEBK 111 " --> pdb=" O VALBK 107 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARGBK 113 " --> pdb=" O ALABK 109 " (cutoff:3.500A) Processing helix chain 'BK' and resid 132 through 137 removed outlier: 3.791A pdb=" N LYSBK 136 " --> pdb=" O LYSBK 132 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N THRBK 137 " --> pdb=" O LEUBK 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'BK' and resid 132 through 137' Processing helix chain 'BK' and resid 138 through 146 removed outlier: 3.668A pdb=" N GLUBK 146 " --> pdb=" O ARGBK 142 " (cutoff:3.500A) Processing helix chain 'BK' and resid 151 through 163 removed outlier: 3.524A pdb=" N LYSBK 160 " --> pdb=" O LYSBK 156 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THRBK 162 " --> pdb=" O LEUBK 158 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N THRBK 163 " --> pdb=" O ASPBK 159 " (cutoff:3.500A) Processing helix chain 'BK' and resid 177 through 182 removed outlier: 3.618A pdb=" N GLNBK 181 " --> pdb=" O TYRBK 177 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ASPBK 182 " --> pdb=" O GLNBK 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'BK' and resid 177 through 182' Processing helix chain 'BL' and resid 184 through 189 removed outlier: 3.588A pdb=" N LEUBL 188 " --> pdb=" O PROBL 184 " (cutoff:3.500A) Proline residue: BL 189 - end of helix No H-bonds generated for 'chain 'BL' and resid 184 through 189' Processing helix chain 'BL' and resid 252 through 257 removed outlier: 6.129A pdb=" N VALBL 257 " --> pdb=" O HISBL 253 " (cutoff:3.500A) Processing helix chain 'BL' and resid 260 through 268 removed outlier: 4.024A pdb=" N ASNBL 264 " --> pdb=" O LYSBL 260 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARGBL 265 " --> pdb=" O ALABL 261 " (cutoff:3.500A) Processing helix chain 'BM' and resid 54 through 83 Proline residue: BM 59 - end of helix removed outlier: 3.692A pdb=" N LYSBM 76 " --> pdb=" O GLNBM 72 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEUBM 77 " --> pdb=" O LEUBM 73 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N CYSBM 78 " --> pdb=" O ALABM 74 " (cutoff:3.500A) Proline residue: BM 79 - end of helix removed outlier: 4.920A pdb=" N GLUBM 83 " --> pdb=" O PROBM 79 " (cutoff:3.500A) Processing helix chain 'BM' and resid 134 through 139 removed outlier: 3.576A pdb=" N ASNBM 139 " --> pdb=" O LYSBM 135 " (cutoff:3.500A) Processing helix chain 'BM' and resid 158 through 169 removed outlier: 3.636A pdb=" N LEUBM 168 " --> pdb=" O PHEBM 164 " (cutoff:3.500A) Processing helix chain 'BM' and resid 217 through 222 Processing helix chain 'BM' and resid 320 through 325 removed outlier: 3.793A pdb=" N ASPBM 324 " --> pdb=" O PHEBM 320 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLUBM 325 " --> pdb=" O PROBM 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'BM' and resid 320 through 325' Processing helix chain 'BM' and resid 194 through 199 removed outlier: 4.452A pdb=" N ARGBM 199 " --> pdb=" O ALABM 196 " (cutoff:3.500A) Processing helix chain 'BN' and resid 92 through 108 removed outlier: 3.728A pdb=" N LEUBN 96 " --> pdb=" O ARGBN 92 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N HISBN 97 " --> pdb=" O LEUBN 93 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLNBN 98 " --> pdb=" O ASPBN 94 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYSBN 104 " --> pdb=" O ALABN 100 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N LYSBN 107 " --> pdb=" O GLNBN 103 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ARGBN 108 " --> pdb=" O LYSBN 104 " (cutoff:3.500A) Processing helix chain 'BN' and resid 166 through 185 removed outlier: 3.540A pdb=" N ASPBN 185 " --> pdb=" O LYSBN 181 " (cutoff:3.500A) Processing helix chain 'BN' and resid 199 through 211 removed outlier: 4.315A pdb=" N LEUBN 203 " --> pdb=" O ASPBN 199 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILEBN 204 " --> pdb=" O PROBN 200 " (cutoff:3.500A) Processing helix chain 'BN' and resid 227 through 238 removed outlier: 4.300A pdb=" N GLYBN 236 " --> pdb=" O ALABN 232 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEUBN 237 " --> pdb=" O ALABN 233 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N LYSBN 238 " --> pdb=" O THRBN 234 " (cutoff:3.500A) Processing helix chain 'BN' and resid 249 through 257 removed outlier: 4.930A pdb=" N GLNBN 257 " --> pdb=" O METBN 253 " (cutoff:3.500A) Processing helix chain 'BN' and resid 262 through 279 removed outlier: 3.712A pdb=" N TRPBN 275 " --> pdb=" O GLUBN 271 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N HISBN 276 " --> pdb=" O LYSBN 272 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASNBN 277 " --> pdb=" O LEUBN 273 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N SERBN 278 " --> pdb=" O LEUBN 274 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARGBN 279 " --> pdb=" O TRPBN 275 " (cutoff:3.500A) Processing helix chain 'BN' and resid 84 through 89 Processing helix chain 'BO' and resid 74 through 79 removed outlier: 3.899A pdb=" N ARGBO 78 " --> pdb=" O HISBO 74 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VALBO 79 " --> pdb=" O ARGBO 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'BO' and resid 74 through 79' Processing helix chain 'BO' and resid 115 through 122 removed outlier: 3.583A pdb=" N ARGBO 120 " --> pdb=" O LYSBO 116 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASNBO 121 " --> pdb=" O SERBO 117 " (cutoff:3.500A) Processing helix chain 'BO' and resid 133 through 149 removed outlier: 3.567A pdb=" N LYSBO 138 " --> pdb=" O PROBO 134 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEUBO 139 " --> pdb=" O GLUBO 135 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHEBO 140 " --> pdb=" O ASNBO 136 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEUBO 146 " --> pdb=" O GLUBO 142 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARGBO 147 " --> pdb=" O GLUBO 143 " (cutoff:3.500A) Processing helix chain 'BO' and resid 157 through 170 removed outlier: 4.014A pdb=" N ALABO 162 " --> pdb=" O LYSBO 158 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARGBO 169 " --> pdb=" O LYSBO 165 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N CYSBO 170 " --> pdb=" O PHEBO 166 " (cutoff:3.500A) Processing helix chain 'BO' and resid 185 through 196 removed outlier: 3.592A pdb=" N ARGBO 191 " --> pdb=" O GLUBO 187 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HISBO 192 " --> pdb=" O ILEBO 188 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHEBO 193 " --> pdb=" O VALBO 189 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEUBO 194 " --> pdb=" O ALABO 190 " (cutoff:3.500A) Processing helix chain 'BO' and resid 242 through 251 Processing helix chain 'BP' and resid 41 through 52 removed outlier: 4.370A pdb=" N GLUBP 52 " --> pdb=" O METBP 48 " (cutoff:3.500A) Processing helix chain 'BP' and resid 61 through 66 Proline residue: BP 66 - end of helix Processing helix chain 'BP' and resid 76 through 93 removed outlier: 4.093A pdb=" N ASNBP 93 " --> pdb=" O VALBP 89 " (cutoff:3.500A) Processing helix chain 'BP' and resid 105 through 120 removed outlier: 4.017A pdb=" N HISBP 119 " --> pdb=" O GLNBP 115 " (cutoff:3.500A) Processing helix chain 'BP' and resid 127 through 139 Proline residue: BP 133 - end of helix removed outlier: 3.515A pdb=" N GLUBP 137 " --> pdb=" O PROBP 133 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N LYSBP 139 " --> pdb=" O LEUBP 135 " (cutoff:3.500A) Processing helix chain 'BP' and resid 143 through 148 removed outlier: 3.739A pdb=" N VALBP 148 " --> pdb=" O LEUBP 144 " (cutoff:3.500A) Processing helix chain 'BP' and resid 160 through 172 removed outlier: 4.372A pdb=" N METBP 164 " --> pdb=" O LYSBP 160 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARGBP 166 " --> pdb=" O LYSBP 162 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILEBP 167 " --> pdb=" O GLUBP 163 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILEBP 171 " --> pdb=" O ILEBP 167 " (cutoff:3.500A) Proline residue: BP 172 - end of helix Processing helix chain 'BP' and resid 187 through 198 Proline residue: BP 198 - end of helix Processing helix chain 'BP' and resid 199 through 223 removed outlier: 3.520A pdb=" N VALBP 208 " --> pdb=" O GLNBP 204 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLYBP 209 " --> pdb=" O GLYBP 205 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEUBP 214 " --> pdb=" O GLYBP 210 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N THRBP 215 " --> pdb=" O LEUBP 211 " (cutoff:3.500A) Processing helix chain 'BP' and resid 224 through 239 removed outlier: 3.678A pdb=" N LEUBP 229 " --> pdb=" O GLNBP 225 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 33 through 43 Proline residue: BQ 37 - end of helix removed outlier: 3.914A pdb=" N ARGBQ 42 " --> pdb=" O ILEBQ 38 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLYBQ 43 " --> pdb=" O LEUBQ 39 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 45 through 58 removed outlier: 3.923A pdb=" N PHEBQ 49 " --> pdb=" O SERBQ 45 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASNBQ 54 " --> pdb=" O CYSBQ 50 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THRBQ 57 " --> pdb=" O PHEBQ 53 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LYSBQ 58 " --> pdb=" O ASNBQ 54 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 86 through 96 removed outlier: 3.630A pdb=" N PHEBQ 90 " --> pdb=" O THRBQ 86 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 113 through 128 removed outlier: 3.899A pdb=" N VALBQ 117 " --> pdb=" O THRBQ 113 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARGBQ 122 " --> pdb=" O TYRBQ 118 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VALBQ 123 " --> pdb=" O GLUBQ 119 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLNBQ 126 " --> pdb=" O ARGBQ 122 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ASPBQ 127 " --> pdb=" O VALBQ 123 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ASPBQ 128 " --> pdb=" O LYSBQ 124 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 129 through 134 removed outlier: 4.239A pdb=" N GLNBQ 133 " --> pdb=" O ALABQ 129 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 136 through 152 removed outlier: 3.694A pdb=" N VALBQ 140 " --> pdb=" O PROBQ 136 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SERBQ 150 " --> pdb=" O GLYBQ 146 " (cutoff:3.500A) Processing helix chain 'BQ' and resid 160 through 192 Processing helix chain 'BR' and resid 5 through 15 Processing helix chain 'BR' and resid 27 through 41 removed outlier: 3.978A pdb=" N METBR 34 " --> pdb=" O LYSBR 30 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VALBR 37 " --> pdb=" O ALABR 33 " (cutoff:3.500A) Processing helix chain 'BR' and resid 70 through 75 Processing helix chain 'BR' and resid 91 through 99 Processing helix chain 'BR' and resid 101 through 112 Processing helix chain 'BR' and resid 115 through 126 removed outlier: 5.026A pdb=" N ARGBR 119 " --> pdb=" O ASNBR 115 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THRBR 120 " --> pdb=" O LEUBR 116 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLNBR 123 " --> pdb=" O ARGBR 119 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARGBR 124 " --> pdb=" O THRBR 120 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEUBR 125 " --> pdb=" O METBR 121 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N HISBR 126 " --> pdb=" O METBR 122 " (cutoff:3.500A) Processing helix chain 'BR' and resid 134 through 141 removed outlier: 3.762A pdb=" N ASNBR 140 " --> pdb=" O ASPBR 136 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEUBR 141 " --> pdb=" O ILEBR 137 " (cutoff:3.500A) Processing helix chain 'BR' and resid 159 through 167 Proline residue: BR 167 - end of helix Processing helix chain 'BS' and resid 44 through 49 Processing helix chain 'BS' and resid 125 through 131 removed outlier: 4.698A pdb=" N GLNBS 129 " --> pdb=" O SERBS 125 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ARGBS 130 " --> pdb=" O SERBS 126 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N GLUBS 131 " --> pdb=" O LEUBS 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'BS' and resid 125 through 131' Processing helix chain 'BS' and resid 134 through 142 removed outlier: 3.777A pdb=" N ILEBS 140 " --> pdb=" O LYSBS 136 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALABS 141 " --> pdb=" O VALBS 137 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLNBS 142 " --> pdb=" O LEUBS 138 " (cutoff:3.500A) Processing helix chain 'BT' and resid 10 through 20 removed outlier: 4.360A pdb=" N ASPBT 14 " --> pdb=" O PROBT 10 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEUBT 15 " --> pdb=" O ARGBT 11 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARGBT 17 " --> pdb=" O LEUBT 13 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALABT 18 " --> pdb=" O ASPBT 14 " (cutoff:3.500A) Proline residue: BT 20 - end of helix Processing helix chain 'BT' and resid 55 through 60 removed outlier: 3.854A pdb=" N ARGBT 59 " --> pdb=" O GLYBT 55 " (cutoff:3.500A) Processing helix chain 'BT' and resid 73 through 78 removed outlier: 4.121A pdb=" N ILEBT 78 " --> pdb=" O PHEBT 74 " (cutoff:3.500A) Processing helix chain 'BT' and resid 86 through 91 removed outlier: 5.855A pdb=" N HISBT 91 " --> pdb=" O HISBT 87 " (cutoff:3.500A) Processing helix chain 'BT' and resid 97 through 108 Processing helix chain 'BT' and resid 117 through 125 Processing helix chain 'BT' and resid 160 through 171 removed outlier: 3.854A pdb=" N ASNBT 170 " --> pdb=" O ALABT 166 " (cutoff:3.500A) Processing helix chain 'BT' and resid 180 through 190 removed outlier: 3.708A pdb=" N ILEBT 186 " --> pdb=" O ARGBT 182 " (cutoff:3.500A) Proline residue: BT 190 - end of helix Processing helix chain 'BT' and resid 191 through 197 removed outlier: 3.548A pdb=" N ARGBT 196 " --> pdb=" O PROBT 192 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLYBT 197 " --> pdb=" O PHEBT 193 " (cutoff:3.500A) Processing helix chain 'BT' and resid 207 through 216 Proline residue: BT 212 - end of helix Processing helix chain 'BT' and resid 225 through 241 removed outlier: 3.986A pdb=" N PHEBT 229 " --> pdb=" O ASPBT 225 " (cutoff:3.500A) Proline residue: BT 230 - end of helix Processing helix chain 'BT' and resid 252 through 258 removed outlier: 3.651A pdb=" N THRBT 258 " --> pdb=" O LYSBT 254 " (cutoff:3.500A) Processing helix chain 'BT' and resid 287 through 296 Processing helix chain 'BU' and resid 69 through 74 removed outlier: 5.522A pdb=" N GLYBU 74 " --> pdb=" O SERBU 70 " (cutoff:3.500A) Processing helix chain 'BU' and resid 98 through 113 Processing helix chain 'BU' and resid 170 through 184 removed outlier: 4.026A pdb=" N PHEBU 175 " --> pdb=" O GLUBU 171 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEUBU 178 " --> pdb=" O GLYBU 174 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VALBU 179 " --> pdb=" O PHEBU 175 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYSBU 182 " --> pdb=" O LEUBU 178 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEUBU 183 " --> pdb=" O VALBU 179 " (cutoff:3.500A) Proline residue: BU 184 - end of helix Processing helix chain 'BU' and resid 191 through 209 removed outlier: 3.656A pdb=" N GLUBU 203 " --> pdb=" O ARGBU 199 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLUBU 204 " --> pdb=" O LYSBU 200 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLUBU 206 " --> pdb=" O GLNBU 202 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASNBU 209 " --> pdb=" O ARGBU 205 " (cutoff:3.500A) Processing helix chain 'BU' and resid 214 through 222 Processing helix chain 'BU' and resid 226 through 231 removed outlier: 5.216A pdb=" N SERBU 231 " --> pdb=" O ARGBU 227 " (cutoff:3.500A) Processing helix chain 'BU' and resid 232 through 238 removed outlier: 4.735A pdb=" N THRBU 236 " --> pdb=" O PROBU 232 " (cutoff:3.500A) Processing helix chain 'BV' and resid 21 through 40 removed outlier: 3.532A pdb=" N ILEBV 26 " --> pdb=" O PROBV 22 " (cutoff:3.500A) Processing helix chain 'BV' and resid 46 through 66 removed outlier: 3.945A pdb=" N GLYBV 54 " --> pdb=" O ASPBV 50 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYRBV 55 " --> pdb=" O GLUBV 51 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILEBV 60 " --> pdb=" O ALABV 56 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASPBV 61 " --> pdb=" O GLUBV 57 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEUBV 65 " --> pdb=" O ASPBV 61 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLYBV 66 " --> pdb=" O TYRBV 62 " (cutoff:3.500A) Processing helix chain 'BV' and resid 69 through 81 removed outlier: 4.786A pdb=" N THRBV 81 " --> pdb=" O ASPBV 77 " (cutoff:3.500A) Processing helix chain 'BV' and resid 82 through 98 removed outlier: 4.429A pdb=" N ILEBV 86 " --> pdb=" O GLUBV 82 " (cutoff:3.500A) Proline residue: BV 87 - end of helix removed outlier: 3.758A pdb=" N LEUBV 93 " --> pdb=" O LEUBV 89 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ALABV 94 " --> pdb=" O PHEBV 90 " (cutoff:3.500A) Proline residue: BV 95 - end of helix removed outlier: 4.495A pdb=" N GLNBV 98 " --> pdb=" O ALABV 94 " (cutoff:3.500A) Processing helix chain 'BV' and resid 144 through 161 removed outlier: 3.638A pdb=" N LEUBV 153 " --> pdb=" O LEUBV 149 " (cutoff:3.500A) Processing helix chain 'BW' and resid 52 through 60 removed outlier: 4.718A pdb=" N LEUBW 56 " --> pdb=" O ASNBW 52 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLUBW 57 " --> pdb=" O PROBW 53 " (cutoff:3.500A) Processing helix chain 'BW' and resid 109 through 117 removed outlier: 3.507A pdb=" N LYSBW 114 " --> pdb=" O TRPBW 110 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N HISBW 115 " --> pdb=" O ALABW 111 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N TYRBW 117 " --> pdb=" O LYSBW 113 " (cutoff:3.500A) Processing helix chain 'BW' and resid 121 through 140 Processing helix chain 'BW' and resid 149 through 156 removed outlier: 3.781A pdb=" N ALABW 154 " --> pdb=" O PROBW 150 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ASPBW 156 " --> pdb=" O GLUBW 152 " (cutoff:3.500A) Processing helix chain 'BW' and resid 157 through 169 removed outlier: 3.525A pdb=" N HISBW 163 " --> pdb=" O LYSBW 159 " (cutoff:3.500A) Processing helix chain 'BX' and resid 77 through 82 removed outlier: 4.066A pdb=" N ILEBX 81 " --> pdb=" O SERBX 77 " (cutoff:3.500A) Proline residue: BX 82 - end of helix No H-bonds generated for 'chain 'BX' and resid 77 through 82' Processing helix chain 'BX' and resid 88 through 106 removed outlier: 4.040A pdb=" N PHEBX 92 " --> pdb=" O ASNBX 88 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILEBX 105 " --> pdb=" O GLUBX 101 " (cutoff:3.500A) Processing helix chain 'BX' and resid 189 through 194 removed outlier: 3.546A pdb=" N ALABX 193 " --> pdb=" O TYRBX 189 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N LEUBX 194 " --> pdb=" O LEUBX 190 " (cutoff:3.500A) No H-bonds generated for 'chain 'BX' and resid 189 through 194' Processing helix chain 'BX' and resid 195 through 200 removed outlier: 6.171A pdb=" N PHEBX 200 " --> pdb=" O GLUBX 196 " (cutoff:3.500A) Processing helix chain 'BX' and resid 244 through 249 removed outlier: 3.821A pdb=" N CYSBX 248 " --> pdb=" O ARGBX 244 " (cutoff:3.500A) Processing helix chain 'BX' and resid 250 through 262 removed outlier: 3.800A pdb=" N LYSBX 259 " --> pdb=" O ARGBX 255 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N TRPBX 260 " --> pdb=" O GLUBX 256 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N SERBX 261 " --> pdb=" O ALABX 257 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N GLNBX 262 " --> pdb=" O GLNBX 258 " (cutoff:3.500A) Processing helix chain 'BX' and resid 263 through 268 removed outlier: 4.374A pdb=" N PHEBX 267 " --> pdb=" O PROBX 263 " (cutoff:3.500A) Processing helix chain 'BX' and resid 275 through 292 removed outlier: 3.506A pdb=" N ALABX 281 " --> pdb=" O LYSBX 277 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLUBX 285 " --> pdb=" O ALABX 281 " (cutoff:3.500A) Processing helix chain 'BY' and resid 16 through 29 removed outlier: 4.188A pdb=" N VALBY 24 " --> pdb=" O ARGBY 20 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N HISBY 27 " --> pdb=" O GLUBY 23 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALABY 28 " --> pdb=" O VALBY 24 " (cutoff:3.500A) Processing helix chain 'BY' and resid 46 through 79 removed outlier: 3.990A pdb=" N LYSBY 61 " --> pdb=" O ARGBY 57 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARGBY 62 " --> pdb=" O ARGBY 58 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N HISBY 79 " --> pdb=" O ALABY 75 " (cutoff:3.500A) Processing helix chain 'BY' and resid 82 through 94 removed outlier: 3.518A pdb=" N ASNBY 89 " --> pdb=" O ALABY 85 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEUBY 90 " --> pdb=" O PHEBY 86 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N CYSBY 93 " --> pdb=" O ASNBY 89 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLNBY 94 " --> pdb=" O LEUBY 90 " (cutoff:3.500A) Processing helix chain 'BY' and resid 98 through 109 Processing helix chain 'BY' and resid 110 through 134 removed outlier: 4.479A pdb=" N ASPBY 134 " --> pdb=" O ALABY 130 " (cutoff:3.500A) Processing helix chain 'BZ' and resid 72 through 94 removed outlier: 3.743A pdb=" N GLYBZ 94 " --> pdb=" O LEUBZ 90 " (cutoff:3.500A) Processing helix chain 'BZ' and resid 154 through 159 removed outlier: 3.705A pdb=" N VALBZ 158 " --> pdb=" O GLYBZ 154 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ARGBZ 159 " --> pdb=" O LYSBZ 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'BZ' and resid 154 through 159' Processing helix chain 'Ba' and resid 24 through 32 Processing helix chain 'Ba' and resid 41 through 46 removed outlier: 3.849A pdb=" N LEUBa 46 " --> pdb=" O PROBa 42 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 60 through 108 removed outlier: 3.594A pdb=" N GLUBa 71 " --> pdb=" O LYSBa 67 " (cutoff:3.500A) Processing helix chain 'Ba' and resid 114 through 119 removed outlier: 4.964A pdb=" N GLNBa 118 " --> pdb=" O GLYBa 114 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 2 through 9 removed outlier: 3.654A pdb=" N GLYBb 9 " --> pdb=" O LEUBb 5 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 27 through 39 Processing helix chain 'Bb' and resid 40 through 45 removed outlier: 4.515A pdb=" N THRBb 45 " --> pdb=" O LYSBb 41 " (cutoff:3.500A) Processing helix chain 'Bb' and resid 82 through 98 removed outlier: 3.712A pdb=" N GLNBb 95 " --> pdb=" O ALABb 91 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLYBb 98 " --> pdb=" O ILEBb 94 " (cutoff:3.500A) Processing helix chain 'Bc' and resid 64 through 71 Processing helix chain 'Bc' and resid 88 through 93 removed outlier: 3.511A pdb=" N TYRBc 92 " --> pdb=" O PROBc 88 " (cutoff:3.500A) Proline residue: Bc 93 - end of helix No H-bonds generated for 'chain 'Bc' and resid 88 through 93' Processing helix chain 'Bc' and resid 94 through 99 removed outlier: 3.959A pdb=" N GLUBc 98 " --> pdb=" O GLUBc 94 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N METBc 99 " --> pdb=" O TRPBc 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bc' and resid 94 through 99' Processing helix chain 'Bc' and resid 114 through 135 removed outlier: 3.805A pdb=" N TRPBc 118 " --> pdb=" O THRBc 114 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYSBc 134 " --> pdb=" O ASNBc 130 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ASNBc 135 " --> pdb=" O ARGBc 131 " (cutoff:3.500A) Processing helix chain 'Bd' and resid 86 through 103 removed outlier: 3.524A pdb=" N LYSBd 96 " --> pdb=" O ALABd 92 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARGBd 97 " --> pdb=" O ARGBd 93 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLUBd 98 " --> pdb=" O PHEBd 94 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLUBd 103 " --> pdb=" O ALABd 99 " (cutoff:3.500A) Processing helix chain 'Be' and resid 28 through 51 removed outlier: 3.667A pdb=" N TYRBe 47 " --> pdb=" O ALABe 43 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEUBe 49 " --> pdb=" O ASNBe 45 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SERBe 50 " --> pdb=" O GLNBe 46 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ARGBe 51 " --> pdb=" O TYRBe 47 " (cutoff:3.500A) Processing helix chain 'Be' and resid 55 through 60 removed outlier: 3.606A pdb=" N GLUBe 59 " --> pdb=" O THRBe 55 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARGBe 60 " --> pdb=" O ALABe 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'Be' and resid 55 through 60' Processing helix chain 'Be' and resid 63 through 81 removed outlier: 4.432A pdb=" N ARGBe 67 " --> pdb=" O ALABe 63 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ARGBe 81 " --> pdb=" O ALABe 77 " (cutoff:3.500A) Processing helix chain 'Be' and resid 87 through 100 removed outlier: 3.843A pdb=" N GLNBe 91 " --> pdb=" O ARGBe 87 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N HISBe 94 " --> pdb=" O GLUBe 90 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LEUBe 95 " --> pdb=" O GLNBe 91 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEUBe 96 " --> pdb=" O LEUBe 92 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N VALBe 97 " --> pdb=" O GLYBe 93 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N THRBe 98 " --> pdb=" O HISBe 94 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ARGBe 99 " --> pdb=" O LEUBe 95 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LYSBe 100 " --> pdb=" O LEUBe 96 " (cutoff:3.500A) Processing helix chain 'Bf' and resid 44 through 50 Proline residue: Bf 50 - end of helix Processing helix chain 'Bf' and resid 54 through 60 removed outlier: 4.582A pdb=" N ALABf 58 " --> pdb=" O GLYBf 54 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N TRPBf 59 " --> pdb=" O SERBf 55 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARGBf 60 " --> pdb=" O ASPBf 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bf' and resid 54 through 60' Processing helix chain 'Bf' and resid 62 through 67 removed outlier: 4.132A pdb=" N LYSBf 66 " --> pdb=" O PROBf 62 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLNBf 67 " --> pdb=" O ASPBf 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bf' and resid 62 through 67' Processing helix chain 'Bf' and resid 72 through 77 removed outlier: 4.020A pdb=" N LEUBf 76 " --> pdb=" O PROBf 72 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N THRBf 77 " --> pdb=" O VALBf 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bf' and resid 72 through 77' Processing helix chain 'Bf' and resid 111 through 122 removed outlier: 3.532A pdb=" N ALABf 119 " --> pdb=" O ARGBf 115 " (cutoff:3.500A) Processing helix chain 'Bf' and resid 141 through 163 removed outlier: 3.602A pdb=" N GLNBf 162 " --> pdb=" O ALABf 158 " (cutoff:3.500A) Proline residue: Bf 163 - end of helix Processing helix chain 'Bf' and resid 171 through 189 removed outlier: 3.843A pdb=" N ARGBf 176 " --> pdb=" O ALABf 172 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEUBf 187 " --> pdb=" O ASNBf 183 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARGBf 188 " --> pdb=" O ARGBf 184 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYSBf 189 " --> pdb=" O GLUBf 185 " (cutoff:3.500A) Processing helix chain 'Bg' and resid 48 through 53 removed outlier: 4.068A pdb=" N LEUBg 52 " --> pdb=" O PROBg 48 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SERBg 53 " --> pdb=" O ARGBg 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bg' and resid 48 through 53' Processing helix chain 'Bg' and resid 54 through 64 Processing helix chain 'Bg' and resid 71 through 76 removed outlier: 4.649A pdb=" N LEUBg 75 " --> pdb=" O ALABg 71 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N TRPBg 76 " --> pdb=" O ALABg 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bg' and resid 71 through 76' Processing helix chain 'Bg' and resid 78 through 93 Processing helix chain 'Bg' and resid 95 through 159 removed outlier: 3.602A pdb=" N LYSBg 127 " --> pdb=" O GLUBg 123 " (cutoff:3.500A) Proline residue: Bg 129 - end of helix removed outlier: 3.645A pdb=" N GLUBg 133 " --> pdb=" O PROBg 129 " (cutoff:3.500A) Processing helix chain 'Bh' and resid 70 through 76 removed outlier: 3.570A pdb=" N TRPBh 75 " --> pdb=" O PROBh 71 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASNBh 76 " --> pdb=" O ILEBh 72 " (cutoff:3.500A) Processing helix chain 'Bh' and resid 85 through 94 removed outlier: 4.773A pdb=" N GLNBh 91 " --> pdb=" O LEUBh 87 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N PHEBh 92 " --> pdb=" O LEUBh 88 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILEBh 93 " --> pdb=" O LEUBh 89 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ARGBh 94 " --> pdb=" O SERBh 90 " (cutoff:3.500A) Processing helix chain 'Bh' and resid 101 through 106 Processing helix chain 'Bh' and resid 108 through 126 removed outlier: 3.548A pdb=" N LYSBh 114 " --> pdb=" O GLUBh 110 " (cutoff:3.500A) Processing helix chain 'Bh' and resid 135 through 142 removed outlier: 3.534A pdb=" N PHEBh 139 " --> pdb=" O LEUBh 135 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VALBh 140 " --> pdb=" O PROBh 136 " (cutoff:3.500A) Proline residue: Bh 141 - end of helix No H-bonds generated for 'chain 'Bh' and resid 135 through 142' Processing helix chain 'Bh' and resid 178 through 183 removed outlier: 4.140A pdb=" N LYSBh 182 " --> pdb=" O SERBh 178 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASPBh 183 " --> pdb=" O PROBh 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bh' and resid 178 through 183' Processing helix chain 'Bi' and resid 55 through 74 removed outlier: 3.569A pdb=" N HISBi 71 " --> pdb=" O GLNBi 67 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N LYSBi 74 " --> pdb=" O VALBi 70 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 75 through 85 Processing helix chain 'Bi' and resid 101 through 111 removed outlier: 3.965A pdb=" N TRPBi 105 " --> pdb=" O ASNBi 101 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SERBi 108 " --> pdb=" O ASNBi 104 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 132 through 149 Processing helix chain 'Bi' and resid 164 through 187 Proline residue: Bi 169 - end of helix removed outlier: 4.321A pdb=" N VALBi 184 " --> pdb=" O GLYBi 180 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N HISBi 185 " --> pdb=" O LEUBi 181 " (cutoff:3.500A) Proline residue: Bi 187 - end of helix Processing helix chain 'Bi' and resid 188 through 193 removed outlier: 5.484A pdb=" N ALABi 193 " --> pdb=" O LEUBi 189 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 261 through 266 removed outlier: 4.542A pdb=" N LEUBi 265 " --> pdb=" O LYSBi 261 " (cutoff:3.500A) Proline residue: Bi 266 - end of helix No H-bonds generated for 'chain 'Bi' and resid 261 through 266' Processing helix chain 'Bi' and resid 301 through 309 Processing helix chain 'Bi' and resid 312 through 338 removed outlier: 3.582A pdb=" N VALBi 316 " --> pdb=" O ASPBi 312 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHEBi 318 " --> pdb=" O ILEBi 314 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLYBi 338 " --> pdb=" O ALABi 334 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 374 through 379 removed outlier: 3.937A pdb=" N GLNBi 379 " --> pdb=" O ALABi 375 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 408 through 421 removed outlier: 3.584A pdb=" N LEUBi 412 " --> pdb=" O ASNBi 408 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASNBi 421 " --> pdb=" O GLNBi 417 " (cutoff:3.500A) Processing helix chain 'Bj' and resid 62 through 75 Processing helix chain 'Bj' and resid 88 through 93 Proline residue: Bj 93 - end of helix Processing helix chain 'Bj' and resid 98 through 114 Processing helix chain 'Bj' and resid 263 through 283 removed outlier: 4.393A pdb=" N GLNBj 281 " --> pdb=" O GLUBj 277 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ARGBj 282 " --> pdb=" O VALBj 278 " (cutoff:3.500A) Proline residue: Bj 283 - end of helix Processing helix chain 'Bj' and resid 307 through 312 Proline residue: Bj 312 - end of helix Processing helix chain 'Bm' and resid 47 through 52 removed outlier: 4.226A pdb=" N GLUBm 51 " --> pdb=" O ASPBm 47 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILEBm 52 " --> pdb=" O ARGBm 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bm' and resid 47 through 52' Processing helix chain 'Bm' and resid 116 through 125 Processing helix chain 'Bm' and resid 133 through 142 removed outlier: 3.593A pdb=" N ALABm 140 " --> pdb=" O VALBm 136 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASPBm 142 " --> pdb=" O ARGBm 138 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 149 through 163 Processing helix chain 'Bm' and resid 172 through 196 Proline residue: Bm 178 - end of helix removed outlier: 3.648A pdb=" N VALBm 181 " --> pdb=" O CYSBm 177 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLNBm 191 " --> pdb=" O LEUBm 187 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ILEBm 192 " --> pdb=" O CYSBm 188 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LEUBm 193 " --> pdb=" O LYSBm 189 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N LYSBm 194 " --> pdb=" O SERBm 190 " (cutoff:3.500A) Proline residue: Bm 196 - end of helix Processing helix chain 'Bm' and resid 241 through 252 removed outlier: 3.644A pdb=" N LYSBm 249 " --> pdb=" O VALBm 245 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ASNBm 250 " --> pdb=" O GLUBm 246 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N HISBm 251 " --> pdb=" O ALABm 247 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N VALBm 252 " --> pdb=" O THRBm 248 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 299 through 304 removed outlier: 3.650A pdb=" N ARGBm 303 " --> pdb=" O LEUBm 299 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N PHEBm 304 " --> pdb=" O ARGBm 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bm' and resid 299 through 304' Processing helix chain 'Bm' and resid 305 through 329 removed outlier: 3.741A pdb=" N TYRBm 329 " --> pdb=" O ALABm 325 " (cutoff:3.500A) Processing helix chain 'Bm' and resid 407 through 420 removed outlier: 4.269A pdb=" N PHEBm 411 " --> pdb=" O GLNBm 407 " (cutoff:3.500A) Processing helix chain 'Bn' and resid 44 through 49 removed outlier: 3.900A pdb=" N LEUBn 48 " --> pdb=" O ASPBn 44 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N LYSBn 49 " --> pdb=" O LEUBn 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bn' and resid 44 through 49' Processing helix chain 'Bn' and resid 53 through 67 removed outlier: 4.128A pdb=" N TYRBn 57 " --> pdb=" O SERBn 53 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARGBn 59 " --> pdb=" O ASPBn 55 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARGBn 66 " --> pdb=" O GLUBn 62 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LYSBn 67 " --> pdb=" O GLNBn 63 " (cutoff:3.500A) Processing helix chain 'Bn' and resid 73 through 79 removed outlier: 3.660A pdb=" N HISBn 77 " --> pdb=" O THRBn 73 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLYBn 79 " --> pdb=" O ARGBn 75 " (cutoff:3.500A) Processing helix chain 'Bn' and resid 98 through 116 removed outlier: 3.517A pdb=" N GLUBn 112 " --> pdb=" O GLNBn 108 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASNBn 116 " --> pdb=" O GLUBn 112 " (cutoff:3.500A) Processing helix chain 'Bn' and resid 117 through 126 removed outlier: 3.516A pdb=" N LEUBn 125 " --> pdb=" O ARGBn 121 " (cutoff:3.500A) Processing helix chain 'Bn' and resid 131 through 143 removed outlier: 3.515A pdb=" N ARGBn 141 " --> pdb=" O ALABn 137 " (cutoff:3.500A) Processing helix chain 'Bn' and resid 144 through 156 removed outlier: 3.527A pdb=" N ARGBn 150 " --> pdb=" O TYRBn 146 " (cutoff:3.500A) Processing helix chain 'Bn' and resid 157 through 162 Processing helix chain 'Bn' and resid 194 through 199 Processing helix chain 'Bn' and resid 244 through 249 removed outlier: 3.979A pdb=" N GLYBn 248 " --> pdb=" O ARGBn 244 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N GLNBn 249 " --> pdb=" O VALBn 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bn' and resid 244 through 249' Processing helix chain 'Bn' and resid 292 through 297 removed outlier: 3.622A pdb=" N THRBn 297 " --> pdb=" O LEUBn 293 " (cutoff:3.500A) Processing helix chain 'Bn' and resid 299 through 308 removed outlier: 3.713A pdb=" N HISBn 307 " --> pdb=" O PHEBn 303 " (cutoff:3.500A) Processing helix chain 'Bn' and resid 324 through 333 removed outlier: 4.145A pdb=" N THRBn 328 " --> pdb=" O ASPBn 324 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ARGBn 329 " --> pdb=" O ASPBn 325 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VALBn 330 " --> pdb=" O SERBn 326 " (cutoff:3.500A) Processing helix chain 'Bn' and resid 364 through 370 removed outlier: 3.611A pdb=" N ARGBn 368 " --> pdb=" O ARGBn 364 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N TYRBn 369 " --> pdb=" O TYRBn 365 " (cutoff:3.500A) Processing helix chain 'Bo' and resid 33 through 57 removed outlier: 3.925A pdb=" N THRBo 56 " --> pdb=" O GLNBo 52 " (cutoff:3.500A) Proline residue: Bo 57 - end of helix Processing helix chain 'Bo' and resid 84 through 93 removed outlier: 3.822A pdb=" N HISBo 91 " --> pdb=" O SERBo 87 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEUBo 92 " --> pdb=" O CYSBo 88 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SERBo 93 " --> pdb=" O ALABo 89 " (cutoff:3.500A) Processing helix chain 'Bo' and resid 94 through 100 Processing helix chain 'Bo' and resid 132 through 155 removed outlier: 3.999A pdb=" N PHEBo 155 " --> pdb=" O ILEBo 151 " (cutoff:3.500A) Processing helix chain 'Bo' and resid 192 through 210 removed outlier: 5.087A pdb=" N ASPBo 210 " --> pdb=" O LEUBo 206 " (cutoff:3.500A) Processing helix chain 'Bo' and resid 219 through 228 Processing helix chain 'Bo' and resid 230 through 245 removed outlier: 3.711A pdb=" N GLNBo 243 " --> pdb=" O GLUBo 239 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ASNBo 244 " --> pdb=" O LYSBo 240 " (cutoff:3.500A) Proline residue: Bo 245 - end of helix Processing helix chain 'Bo' and resid 305 through 318 removed outlier: 3.663A pdb=" N ARGBo 315 " --> pdb=" O LYSBo 311 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARGBo 317 " --> pdb=" O LEUBo 313 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYSBo 318 " --> pdb=" O GLUBo 314 " (cutoff:3.500A) Processing helix chain 'Bo' and resid 268 through 273 removed outlier: 3.707A pdb=" N ILEBo 271 " --> pdb=" O ARGBo 268 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N PHEBo 273 " --> pdb=" O SERBo 270 " (cutoff:3.500A) Processing helix chain 'Bp' and resid 61 through 79 removed outlier: 3.978A pdb=" N ALABp 78 " --> pdb=" O ARGBp 74 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N SERBp 79 " --> pdb=" O LEUBp 75 " (cutoff:3.500A) Processing helix chain 'Bp' and resid 85 through 90 removed outlier: 3.542A pdb=" N ILEBp 89 " --> pdb=" O ILEBp 85 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N THRBp 90 " --> pdb=" O GLUBp 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bp' and resid 85 through 90' Processing helix chain 'Bp' and resid 91 through 96 removed outlier: 4.206A pdb=" N LEUBp 95 " --> pdb=" O PROBp 91 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ASNBp 96 " --> pdb=" O VALBp 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bp' and resid 91 through 96' Processing helix chain 'Bp' and resid 107 through 154 removed outlier: 3.580A pdb=" N ARGBp 113 " --> pdb=" O GLUBp 109 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARGBp 120 " --> pdb=" O LEUBp 116 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEUBp 152 " --> pdb=" O GLNBp 148 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SERBp 153 " --> pdb=" O GLUBp 149 " (cutoff:3.500A) Processing helix chain 'Bp' and resid 155 through 163 removed outlier: 3.647A pdb=" N GLUBp 160 " --> pdb=" O GLUBp 156 " (cutoff:3.500A) Processing helix chain 'Bq' and resid 22 through 27 removed outlier: 4.114A pdb=" N GLYBq 26 " --> pdb=" O THRBq 22 " (cutoff:3.500A) Proline residue: Bq 27 - end of helix No H-bonds generated for 'chain 'Bq' and resid 22 through 27' Processing helix chain 'Bq' and resid 62 through 67 removed outlier: 4.622A pdb=" N PHEBq 66 " --> pdb=" O GLUBq 62 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N LYSBq 67 " --> pdb=" O LEUBq 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bq' and resid 62 through 67' Processing helix chain 'Bq' and resid 85 through 94 Processing helix chain 'Bq' and resid 95 through 105 Processing helix chain 'Br' and resid 68 through 73 removed outlier: 4.139A pdb=" N THRBr 72 " --> pdb=" O PROBr 68 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N LYSBr 73 " --> pdb=" O TYRBr 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'Br' and resid 68 through 73' Processing helix chain 'Br' and resid 80 through 86 removed outlier: 3.992A pdb=" N GLUBr 85 " --> pdb=" O VALBr 81 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLUBr 86 " --> pdb=" O HISBr 82 " (cutoff:3.500A) Processing helix chain 'Br' and resid 104 through 117 removed outlier: 3.575A pdb=" N GLUBr 110 " --> pdb=" O GLYBr 106 " (cutoff:3.500A) Processing helix chain 'Br' and resid 127 through 134 removed outlier: 3.758A pdb=" N ARGBr 134 " --> pdb=" O HISBr 130 " (cutoff:3.500A) Processing helix chain 'Bs' and resid 2 through 7 removed outlier: 5.187A pdb=" N ALABs 7 " --> pdb=" O ALABs 3 " (cutoff:3.500A) Processing helix chain 'Bs' and resid 16 through 21 removed outlier: 4.765A pdb=" N GLYBs 20 " --> pdb=" O HISBs 16 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ARGBs 21 " --> pdb=" O ASNBs 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bs' and resid 16 through 21' Processing helix chain 'Bs' and resid 40 through 50 Processing helix chain 'Bs' and resid 51 through 59 removed outlier: 3.533A pdb=" N ARGBs 56 " --> pdb=" O THRBs 52 " (cutoff:3.500A) Proline residue: Bs 59 - end of helix Processing helix chain 'Bs' and resid 93 through 108 removed outlier: 6.198A pdb=" N SERBs 108 " --> pdb=" O LEUBs 104 " (cutoff:3.500A) Processing helix chain 'Bs' and resid 131 through 137 removed outlier: 4.719A pdb=" N ASNBs 135 " --> pdb=" O HISBs 131 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N LYSBs 136 " --> pdb=" O PROBs 132 " (cutoff:3.500A) Proline residue: Bs 137 - end of helix No H-bonds generated for 'chain 'Bs' and resid 131 through 137' Processing helix chain 'Bt' and resid 34 through 54 removed outlier: 5.253A pdb=" N ALABt 38 " --> pdb=" O GLYBt 34 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLNBt 42 " --> pdb=" O ALABt 38 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLUBt 44 " --> pdb=" O ARGBt 40 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARGBt 47 " --> pdb=" O LYSBt 43 " (cutoff:3.500A) Proline residue: Bt 54 - end of helix Processing helix chain 'Bt' and resid 59 through 64 removed outlier: 4.027A pdb=" N LYSBt 63 " --> pdb=" O ARGBt 59 " (cutoff:3.500A) Proline residue: Bt 64 - end of helix No H-bonds generated for 'chain 'Bt' and resid 59 through 64' Processing helix chain 'Bt' and resid 67 through 80 removed outlier: 3.552A pdb=" N LEUBt 79 " --> pdb=" O PHEBt 75 " (cutoff:3.500A) Processing helix chain 'Bt' and resid 84 through 94 removed outlier: 3.762A pdb=" N VALBt 93 " --> pdb=" O LYSBt 89 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ASNBt 94 " --> pdb=" O THRBt 90 " (cutoff:3.500A) Processing helix chain 'Bt' and resid 95 through 109 Processing helix chain 'Bt' and resid 114 through 119 removed outlier: 4.183A pdb=" N ASNBt 118 " --> pdb=" O ALABt 114 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEUBt 119 " --> pdb=" O ALABt 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bt' and resid 114 through 119' Processing helix chain 'Bt' and resid 122 through 145 Processing helix chain 'Bt' and resid 149 through 162 Processing helix chain 'Bt' and resid 163 through 174 Processing helix chain 'Bt' and resid 187 through 206 Processing helix chain 'Bt' and resid 207 through 224 removed outlier: 3.686A pdb=" N ILEBt 220 " --> pdb=" O ARGBt 216 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N THRBt 221 " --> pdb=" O ASPBt 217 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N GLNBt 222 " --> pdb=" O PHEBt 218 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N METBt 223 " --> pdb=" O LEUBt 219 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N THRBt 224 " --> pdb=" O ILEBt 220 " (cutoff:3.500A) Processing helix chain 'Bt' and resid 227 through 233 removed outlier: 3.910A pdb=" N METBt 231 " --> pdb=" O GLUBt 227 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N TRPBt 232 " --> pdb=" O LEUBt 228 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N THRBt 233 " --> pdb=" O PHEBt 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bt' and resid 227 through 233' Processing helix chain 'Bt' and resid 236 through 249 Processing helix chain 'Bt' and resid 288 through 306 Processing helix chain 'Bu' and resid 48 through 54 removed outlier: 4.218A pdb=" N SERBu 52 " --> pdb=" O PROBu 48 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LYSBu 54 " --> pdb=" O TYRBu 50 " (cutoff:3.500A) Processing helix chain 'Bu' and resid 65 through 72 removed outlier: 3.758A pdb=" N HISBu 69 " --> pdb=" O LEUBu 65 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEUBu 72 " --> pdb=" O PROBu 68 " (cutoff:3.500A) Processing helix chain 'Bu' and resid 93 through 101 removed outlier: 5.077A pdb=" N SERBu 99 " --> pdb=" O ALABu 95 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEUBu 100 " --> pdb=" O ARGBu 96 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N SERBu 101 " --> pdb=" O ILEBu 97 " (cutoff:3.500A) Processing helix chain 'Bu' and resid 102 through 115 removed outlier: 3.547A pdb=" N ASNBu 115 " --> pdb=" O ARGBu 111 " (cutoff:3.500A) Processing helix chain 'Bu' and resid 116 through 129 Processing helix chain 'Bu' and resid 133 through 155 Proline residue: Bu 138 - end of helix Processing helix chain 'Bu' and resid 156 through 164 removed outlier: 3.706A pdb=" N LEUBu 160 " --> pdb=" O ASPBu 156 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N THRBu 162 " --> pdb=" O ASPBu 158 " (cutoff:3.500A) Processing helix chain 'Bu' and resid 165 through 177 Proline residue: Bu 170 - end of helix removed outlier: 4.961A pdb=" N ASPBu 175 " --> pdb=" O ASPBu 171 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N ILEBu 176 " --> pdb=" O METBu 172 " (cutoff:3.500A) Processing helix chain 'Bv' and resid 64 through 82 Processing helix chain 'Bv' and resid 85 through 103 Processing helix chain 'Bv' and resid 116 through 132 removed outlier: 3.502A pdb=" N LYSBv 127 " --> pdb=" O METBv 123 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LYSBv 132 " --> pdb=" O PHEBv 128 " (cutoff:3.500A) Processing helix chain 'Bv' and resid 138 through 144 removed outlier: 3.712A pdb=" N LYSBv 142 " --> pdb=" O THRBv 138 " (cutoff:3.500A) Processing helix chain 'Bv' and resid 183 through 195 removed outlier: 3.738A pdb=" N ALABv 193 " --> pdb=" O GLUBv 189 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEUBv 195 " --> pdb=" O THRBv 191 " (cutoff:3.500A) Processing helix chain 'Bv' and resid 256 through 265 removed outlier: 4.435A pdb=" N GLYBv 261 " --> pdb=" O LYSBv 257 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ASPBv 262 " --> pdb=" O GLUBv 258 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N TYRBv 263 " --> pdb=" O GLUBv 259 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEUBv 264 " --> pdb=" O LEUBv 260 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LYSBv 265 " --> pdb=" O GLYBv 261 " (cutoff:3.500A) Processing helix chain 'Bv' and resid 266 through 277 removed outlier: 3.526A pdb=" N ALABv 270 " --> pdb=" O PROBv 266 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLNBv 271 " --> pdb=" O LYSBv 267 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VALBv 272 " --> pdb=" O TYRBv 268 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARGBv 274 " --> pdb=" O ALABv 270 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHEBv 275 " --> pdb=" O GLNBv 271 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEUBv 276 " --> pdb=" O VALBv 272 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N LEUBv 277 " --> pdb=" O ARGBv 273 " (cutoff:3.500A) Processing helix chain 'Bw' and resid 59 through 64 removed outlier: 3.630A pdb=" N VALBw 63 " --> pdb=" O TYRBw 59 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N LYSBw 64 " --> pdb=" O LYSBw 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bw' and resid 59 through 64' Processing helix chain 'Bw' and resid 99 through 118 Processing helix chain 'Bw' and resid 164 through 178 removed outlier: 4.390A pdb=" N GLUBw 168 " --> pdb=" O ALABw 164 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILEBw 169 " --> pdb=" O THRBw 165 " (cutoff:3.500A) Processing helix chain 'Bw' and resid 190 through 199 removed outlier: 4.039A pdb=" N GLYBw 196 " --> pdb=" O GLUBw 192 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N ARGBw 197 " --> pdb=" O ASPBw 193 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N PHEBw 198 " --> pdb=" O PHEBw 194 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LYSBw 199 " --> pdb=" O LYSBw 195 " (cutoff:3.500A) Processing helix chain 'Bw' and resid 201 through 212 Processing helix chain 'Bx' and resid 41 through 52 removed outlier: 5.828A pdb=" N TYRBx 45 " --> pdb=" O SERBx 41 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N HISBx 46 " --> pdb=" O VALBx 42 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N PHEBx 47 " --> pdb=" O ASPBx 43 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N VALBx 48 " --> pdb=" O GLUBx 44 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLUBx 49 " --> pdb=" O TYRBx 45 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARGBx 50 " --> pdb=" O HISBx 46 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEUBx 51 " --> pdb=" O PHEBx 47 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEUBx 52 " --> pdb=" O VALBx 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bx' and resid 41 through 52' Processing helix chain 'Bx' and resid 116 through 133 removed outlier: 3.656A pdb=" N LEUBx 120 " --> pdb=" O ASPBx 116 " (cutoff:3.500A) Proline residue: Bx 130 - end of helix Processing helix chain 'Bx' and resid 153 through 165 Processing helix chain 'By' and resid 66 through 79 Processing helix chain 'By' and resid 94 through 110 removed outlier: 3.895A pdb=" N ARGBy 104 " --> pdb=" O SERBy 100 " (cutoff:3.500A) Processing helix chain 'By' and resid 114 through 122 removed outlier: 3.620A pdb=" N LEUBy 118 " --> pdb=" O PROBy 114 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N HISBy 119 " --> pdb=" O ASNBy 115 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N GLNBy 120 " --> pdb=" O SERBy 116 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N CYSBy 122 " --> pdb=" O LEUBy 118 " (cutoff:3.500A) Processing helix chain 'By' and resid 123 through 134 removed outlier: 3.677A pdb=" N VALBy 133 " --> pdb=" O ASPBy 129 " (cutoff:3.500A) Proline residue: By 134 - end of helix Processing helix chain 'By' and resid 139 through 147 removed outlier: 3.667A pdb=" N ALABy 146 " --> pdb=" O ASPBy 142 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SERBy 147 " --> pdb=" O GLUBy 143 " (cutoff:3.500A) Processing helix chain 'Bz' and resid 48 through 54 Processing helix chain 'Bz' and resid 59 through 64 Processing helix chain 'Bz' and resid 69 through 74 removed outlier: 4.576A pdb=" N LEUBz 73 " --> pdb=" O HISBz 69 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ILEBz 74 " --> pdb=" O PROBz 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'Bz' and resid 69 through 74' Processing helix chain 'Bz' and resid 86 through 98 Processing helix chain 'Bz' and resid 103 through 123 Processing helix chain 'Aa' and resid 65 through 72 removed outlier: 3.701A pdb=" N LEUAa 69 " --> pdb=" O ASPAa 65 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N HISAa 72 " --> pdb=" O METAa 68 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 73 through 95 Processing helix chain 'Aa' and resid 99 through 140 removed outlier: 3.614A pdb=" N SERAa 105 " --> pdb=" O GLUAa 101 " (cutoff:3.500A) Proline residue: Aa 115 - end of helix removed outlier: 4.386A pdb=" N LEUAa 140 " --> pdb=" O METAa 136 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 142 through 175 removed outlier: 4.361A pdb=" N LYSAa 146 " --> pdb=" O LYSAa 142 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLNAa 147 " --> pdb=" O GLNAa 143 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEUAa 153 " --> pdb=" O GLNAa 149 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N GLUAa 154 " --> pdb=" O GLUAa 150 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLNAa 157 " --> pdb=" O LEUAa 153 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASNAa 164 " --> pdb=" O ASPAa 160 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N METAa 165 " --> pdb=" O GLNAa 161 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHEAa 171 " --> pdb=" O TYRAa 167 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VALAa 175 " --> pdb=" O PHEAa 171 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 198 through 219 removed outlier: 3.712A pdb=" N ARGAa 205 " --> pdb=" O GLNAa 201 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLUAa 206 " --> pdb=" O GLNAa 202 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYSAa 216 " --> pdb=" O GLNAa 212 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 246 through 252 removed outlier: 3.506A pdb=" N LYSAa 252 " --> pdb=" O TYRAa 248 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 296 through 301 removed outlier: 3.588A pdb=" N LEUAa 300 " --> pdb=" O ASPAa 296 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ARGAa 301 " --> pdb=" O PROAa 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'Aa' and resid 296 through 301' Processing helix chain 'Aa' and resid 312 through 318 removed outlier: 3.552A pdb=" N ASNAa 316 " --> pdb=" O GLYAa 312 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 340 through 377 removed outlier: 4.184A pdb=" N LEUAa 374 " --> pdb=" O SERAa 370 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VALAa 376 " --> pdb=" O ARGAa 372 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLYAa 377 " --> pdb=" O LYSAa 373 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 406 through 413 removed outlier: 3.863A pdb=" N CYSAa 412 " --> pdb=" O LYSAa 408 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLYAa 413 " --> pdb=" O GLUAa 409 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 414 through 445 removed outlier: 3.934A pdb=" N LEUAa 420 " --> pdb=" O GLYAa 416 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARGAa 423 " --> pdb=" O GLNAa 419 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 267 through 272 Processing sheet with id= 1, first strand: chain 'BA' and resid 69 through 76 removed outlier: 4.816A pdb=" N ALABA 69 " --> pdb=" O GLUBA 178 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LYSBA 175 " --> pdb=" O ALABA 141 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'BA' and resid 142 through 148 removed outlier: 3.531A pdb=" N GLUBA 142 " --> pdb=" O LYSBA 175 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N PHEBA 169 " --> pdb=" O GLYBA 148 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'BA' and resid 150 through 157 removed outlier: 3.615A pdb=" N HISBA 157 " --> pdb=" O ARGBA 161 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ARGBA 161 " --> pdb=" O HISBA 157 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'BB' and resid 38 through 44 removed outlier: 6.965A pdb=" N ASPBB 38 " --> pdb=" O LEUBB 99 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYSBB 93 " --> pdb=" O ILEBB 44 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LYSBB 88 " --> pdb=" O ASNBB 77 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ASNBB 77 " --> pdb=" O LYSBB 88 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N GLYBB 75 " --> pdb=" O PROBB 90 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYRBB 92 " --> pdb=" O GLNBB 73 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALABB 67 " --> pdb=" O GLNBB 98 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'BC' and resid 60 through 65 removed outlier: 4.706A pdb=" N ASPBC 60 " --> pdb=" O VALBC 76 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VALBC 76 " --> pdb=" O ASPBC 60 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LYSBC 72 " --> pdb=" O ILEBC 64 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'BC' and resid 92 through 97 removed outlier: 5.726A pdb=" N ASNBC 92 " --> pdb=" O ALABC 113 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'BC' and resid 132 through 135 removed outlier: 7.357A pdb=" N ASPBC 132 " --> pdb=" O THRBC 148 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ARGBC 145 " --> pdb=" O ILEBC 154 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ARGBC 152 " --> pdb=" O SERBC 147 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'BD' and resid 97 through 103 Processing sheet with id= 9, first strand: chain 'BE' and resid 49 through 53 removed outlier: 5.377A pdb=" N LYSBE 49 " --> pdb=" O VALBE 62 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLNBE 58 " --> pdb=" O ASNBE 53 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'BE' and resid 85 through 90 Processing sheet with id= 11, first strand: chain 'BF' and resid 167 through 172 Processing sheet with id= 12, first strand: chain 'BG' and resid 97 through 101 removed outlier: 5.307A pdb=" N LEUBG 66 " --> pdb=" O LEUBG 122 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N LEUBG 116 " --> pdb=" O ILEBG 72 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'BG' and resid 137 through 140 removed outlier: 4.316A pdb=" N GLUBG 144 " --> pdb=" O LYSBG 140 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'BH' and resid 155 through 160 Processing sheet with id= 15, first strand: chain 'BI' and resid 28 through 33 removed outlier: 6.203A pdb=" N PHEBI 28 " --> pdb=" O SERBI 22 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEUBI 17 " --> pdb=" O ILEBI 62 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'BI' and resid 41 through 46 removed outlier: 6.599A pdb=" N LEUBI 41 " --> pdb=" O GLUBI 58 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N HISBI 45 " --> pdb=" O VALBI 54 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'BK' and resid 122 through 125 removed outlier: 5.261A pdb=" N TRPBK 122 " --> pdb=" O CYSBK 150 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYSBK 150 " --> pdb=" O TRPBK 122 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'BL' and resid 122 through 127 removed outlier: 3.561A pdb=" N ASPBL 162 " --> pdb=" O VALBL 127 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLYBL 180 " --> pdb=" O THRBL 163 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N LEUBL 165 " --> pdb=" O GLYBL 180 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'BL' and resid 129 through 132 removed outlier: 3.794A pdb=" N ALABL 129 " --> pdb=" O LEUBL 142 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'BL' and resid 215 through 218 removed outlier: 6.835A pdb=" N ILEBL 226 " --> pdb=" O LEUBL 218 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARGBL 233 " --> pdb=" O LEUBL 229 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'BM' and resid 98 through 101 Processing sheet with id= 22, first strand: chain 'BM' and resid 105 through 111 removed outlier: 3.795A pdb=" N GLYBM 105 " --> pdb=" O LEUBM 121 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLNBM 115 " --> pdb=" O THRBM 111 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ASNBM 281 " --> pdb=" O VALBM 124 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARGBM 275 " --> pdb=" O TYRBM 284 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N GLUBM 330 " --> pdb=" O THRBM 278 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'BM' and resid 175 through 182 removed outlier: 5.747A pdb=" N LYSBM 175 " --> pdb=" O GLYBM 149 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THRBM 146 " --> pdb=" O LEUBM 130 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N HISBM 128 " --> pdb=" O GLYBM 148 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYSBM 150 " --> pdb=" O ASPBM 126 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ASPBM 126 " --> pdb=" O LYSBM 150 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N CYSBM 127 " --> pdb=" O LEUBM 193 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N THRBM 191 " --> pdb=" O VALBM 129 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'BN' and resid 47 through 50 removed outlier: 3.558A pdb=" N ARGBN 49 " --> pdb=" O LEUBN 79 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLYBN 78 " --> pdb=" O ILEBN 66 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'BN' and resid 186 through 189 Processing sheet with id= 26, first strand: chain 'BO' and resid 109 through 113 removed outlier: 3.962A pdb=" N ASPBO 110 " --> pdb=" O LEUBO 98 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'BO' and resid 205 through 208 removed outlier: 5.880A pdb=" N ALABO 205 " --> pdb=" O THRBO 224 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N THRBO 224 " --> pdb=" O ALABO 205 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLUBO 222 " --> pdb=" O LYSBO 207 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASPBO 229 " --> pdb=" O VALBO 225 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'BP' and resid 121 through 125 removed outlier: 6.355A pdb=" N HISBP 150 " --> pdb=" O HISBP 101 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N HISBP 101 " --> pdb=" O HISBP 150 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SERBP 156 " --> pdb=" O METBP 95 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N METBP 95 " --> pdb=" O SERBP 156 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLYBP 178 " --> pdb=" O VALBP 98 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'BQ' and resid 17 through 24 removed outlier: 3.514A pdb=" N LEUBQ 66 " --> pdb=" O VALBQ 24 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLYBQ 83 " --> pdb=" O PROBQ 67 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THRBQ 77 " --> pdb=" O LYSBQ 73 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'BR' and resid 55 through 60 removed outlier: 3.876A pdb=" N GLUBR 143 " --> pdb=" O TRPBR 18 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ASPBR 22 " --> pdb=" O LEUBR 145 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'BR' and resid 77 through 81 removed outlier: 7.435A pdb=" N GLYBR 86 " --> pdb=" O THRBR 81 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'BS' and resid 38 through 41 Processing sheet with id= 33, first strand: chain 'BS' and resid 72 through 76 Processing sheet with id= 34, first strand: chain 'BT' and resid 93 through 96 Processing sheet with id= 35, first strand: chain 'BT' and resid 273 through 277 Processing sheet with id= 36, first strand: chain 'BU' and resid 93 through 97 removed outlier: 6.865A pdb=" N GLYBU 93 " --> pdb=" O ALABU 156 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALABU 156 " --> pdb=" O GLYBU 93 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'BU' and resid 118 through 123 removed outlier: 5.733A pdb=" N ILEBU 160 " --> pdb=" O ARGBU 123 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VALBU 161 " --> pdb=" O ILEBU 89 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'BV' and resid 41 through 45 removed outlier: 3.881A pdb=" N METBV 121 " --> pdb=" O ILEBV 110 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N TYRBV 104 " --> pdb=" O LYSBV 127 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'BW' and resid 80 through 85 removed outlier: 6.530A pdb=" N ILEBW 90 " --> pdb=" O THRBW 107 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VALBW 103 " --> pdb=" O VALBW 94 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'BX' and resid 129 through 136 removed outlier: 4.745A pdb=" N LYSBX 129 " --> pdb=" O ASPBX 123 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILEBX 116 " --> pdb=" O VALBX 177 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLUBX 173 " --> pdb=" O THRBX 120 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'BX' and resid 138 through 142 removed outlier: 7.518A pdb=" N ALABX 147 " --> pdb=" O LEUBX 166 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'BZ' and resid 109 through 113 removed outlier: 7.744A pdb=" N LEUBZ 138 " --> pdb=" O GLYBZ 149 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N PHEBZ 145 " --> pdb=" O ALABZ 142 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'BZ' and resid 115 through 121 removed outlier: 3.629A pdb=" N ASPBZ 116 " --> pdb=" O ILEBZ 199 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VALBZ 196 " --> pdb=" O ILEBZ 165 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N GLUBZ 161 " --> pdb=" O ASNBZ 200 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VALBZ 160 " --> pdb=" O LEUBZ 134 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLUBZ 130 " --> pdb=" O VALBZ 164 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'BZ' and resid 166 through 169 removed outlier: 3.510A pdb=" N GLUBZ 166 " --> pdb=" O VALBZ 196 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'BZ' and resid 172 through 179 removed outlier: 4.558A pdb=" N TYRBZ 184 " --> pdb=" O GLNBZ 179 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'Bb' and resid 49 through 56 removed outlier: 4.146A pdb=" N SERBb 50 " --> pdb=" O LYSBb 14 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VALBb 16 " --> pdb=" O SERBb 50 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLNBb 15 " --> pdb=" O LEUBb 67 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'Bd' and resid 63 through 68 removed outlier: 5.493A pdb=" N SERBd 63 " --> pdb=" O LYSBd 59 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'Bf' and resid 78 through 85 removed outlier: 4.120A pdb=" N GLYBf 85 " --> pdb=" O LYSBf 93 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALABf 98 " --> pdb=" O SERBf 136 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'Bh' and resid 35 through 42 Processing sheet with id= 50, first strand: chain 'Bi' and resid 90 through 93 No H-bonds generated for sheet with id= 50 Processing sheet with id= 51, first strand: chain 'Bi' and resid 112 through 116 removed outlier: 6.801A pdb=" N ASNBi 385 " --> pdb=" O ASNBi 369 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASNBi 369 " --> pdb=" O ASNBi 385 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N CYSBi 387 " --> pdb=" O GLNBi 367 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N GLNBi 367 " --> pdb=" O CYSBi 387 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N GLYBi 389 " --> pdb=" O CYSBi 365 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N CYSBi 365 " --> pdb=" O GLYBi 389 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N GLNBi 391 " --> pdb=" O PHEBi 363 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N PHEBi 363 " --> pdb=" O GLNBi 391 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N LYSBi 359 " --> pdb=" O LEUBi 395 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N TYRBi 360 " --> pdb=" O ASPBi 357 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'Bi' and resid 235 through 238 removed outlier: 6.821A pdb=" N ILEBi 235 " --> pdb=" O HISBi 290 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'Bj' and resid 251 through 260 removed outlier: 5.185A pdb=" N ASNBj 251 " --> pdb=" O LEUBj 127 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VALBj 121 " --> pdb=" O ILEBj 257 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THRBj 259 " --> pdb=" O GLNBj 119 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N GLNBj 119 " --> pdb=" O THRBj 259 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ARGBj 296 " --> pdb=" O TYRBj 122 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ALABj 293 " --> pdb=" O ILEBj 305 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'Bl' and resid 63 through 67 removed outlier: 6.430A pdb=" N HISBl 95 " --> pdb=" O CYSBl 89 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N CYSBl 89 " --> pdb=" O HISBl 95 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N TRPBl 85 " --> pdb=" O GLNBl 99 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'Bm' and resid 126 through 130 removed outlier: 5.467A pdb=" N LEUBm 351 " --> pdb=" O ASPBm 348 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N ARGBm 200 " --> pdb=" O LYSBm 233 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'Bm' and resid 208 through 214 removed outlier: 4.893A pdb=" N LEUBm 219 " --> pdb=" O ALABm 103 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'Bn' and resid 184 through 187 removed outlier: 4.292A pdb=" N VALBn 175 " --> pdb=" O VALBn 187 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'Bn' and resid 190 through 193 removed outlier: 3.602A pdb=" N ASNBn 191 " --> pdb=" O PHEBn 318 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ARGBn 322 " --> pdb=" O VALBn 193 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEUBn 213 " --> pdb=" O GLNBn 275 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'Bn' and resid 272 through 275 removed outlier: 6.776A pdb=" N LEUBn 272 " --> pdb=" O ALABn 314 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'Bo' and resid 61 through 66 removed outlier: 4.134A pdb=" N THRBo 74 " --> pdb=" O HISBo 66 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'Bo' and resid 101 through 104 Processing sheet with id= 62, first strand: chain 'Bo' and resid 160 through 164 removed outlier: 7.109A pdb=" N VALBo 160 " --> pdb=" O ASPBo 183 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ASPBo 179 " --> pdb=" O VALBo 164 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLNBo 294 " --> pdb=" O SERBo 278 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'Bo' and resid 214 through 217 Processing sheet with id= 64, first strand: chain 'Bq' and resid 40 through 43 removed outlier: 5.400A pdb=" N LYSBq 47 " --> pdb=" O GLYBq 43 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'Br' and resid 45 through 52 removed outlier: 5.756A pdb=" N THRBr 57 " --> pdb=" O THRBr 52 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'Bs' and resid 61 through 68 removed outlier: 4.036A pdb=" N LEUBs 33 " --> pdb=" O ASNBs 66 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VALBs 75 " --> pdb=" O GLUBs 86 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N GLUBs 86 " --> pdb=" O VALBs 75 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALABs 77 " --> pdb=" O VALBs 84 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VALBs 84 " --> pdb=" O ALABs 77 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N TYRBs 79 " --> pdb=" O GLYBs 82 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'Bt' and resid 254 through 258 removed outlier: 6.611A pdb=" N PHEBt 271 " --> pdb=" O THRBt 258 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALABt 282 " --> pdb=" O LEUBt 274 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'Bu' and resid 192 through 195 removed outlier: 6.751A pdb=" N THRBu 213 " --> pdb=" O VALBu 195 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'Bu' and resid 199 through 203 removed outlier: 3.523A pdb=" N SERBu 200 " --> pdb=" O TYRBu 209 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYRBu 209 " --> pdb=" O SERBu 200 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'Bv' and resid 174 through 178 removed outlier: 6.257A pdb=" N LEUBv 47 " --> pdb=" O TRPBv 178 " (cutoff:3.500A) removed outlier: 10.934A pdb=" N LEUBv 51 " --> pdb=" O VALBv 161 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N VALBv 161 " --> pdb=" O LEUBv 51 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N LEUBv 53 " --> pdb=" O LEUBv 159 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEUBv 157 " --> pdb=" O ARGBv 55 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ARGBv 155 " --> pdb=" O PROBv 57 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VALBv 255 " --> pdb=" O ILEBv 158 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'Bv' and resid 211 through 216 removed outlier: 3.693A pdb=" N GLYBv 211 " --> pdb=" O PHEBv 233 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'Bv' and resid 44 through 53 No H-bonds generated for sheet with id= 72 Processing sheet with id= 73, first strand: chain 'Bw' and resid 126 through 134 Processing sheet with id= 74, first strand: chain 'Bx' and resid 84 through 87 removed outlier: 5.972A pdb=" N LYSBx 112 " --> pdb=" O ARGBx 87 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'Bx' and resid 95 through 101 removed outlier: 5.452A pdb=" N VALBx 137 " --> pdb=" O LYSBx 150 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'Aa' and resid 220 through 225 removed outlier: 6.520A pdb=" N ALAAa 239 " --> pdb=" O LEUAa 225 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N HISAa 236 " --> pdb=" O ALAAa 191 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N GLYAa 244 " --> pdb=" O ASNAa 183 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ASNAa 183 " --> pdb=" O GLYAa 244 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ASPAa 184 " --> pdb=" O GLNAa 287 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SERAa 281 " --> pdb=" O THRAa 190 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARGAa 386 " --> pdb=" O ILEAa 257 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'Aa' and resid 302 through 306 removed outlier: 3.752A pdb=" N PHEAa 305 " --> pdb=" O ALAAa 321 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEUAa 331 " --> pdb=" O HISAa 326 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'Aa' and resid 226 through 229 removed outlier: 3.874A pdb=" N HISAa 237 " --> pdb=" O THRAa 228 " (cutoff:3.500A) 2845 hydrogen bonds defined for protein. 8424 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 685 hydrogen bonds 1190 hydrogen bond angles 0 basepair planarities 297 basepair parallelities 895 stacking parallelities Total time for adding SS restraints: 66.90 Time building geometry restraints manager: 40.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.41: 48555 1.41 - 1.61: 69881 1.61 - 1.81: 422 1.81 - 2.00: 46 2.00 - 2.20: 4 Bond restraints: 118908 Sorted by residual: bond pdb=" C2 1MAB8 949 " pdb=" N3 1MAB8 949 " ideal model delta sigma weight residual 1.465 1.291 0.174 2.00e-02 2.50e+03 7.60e+01 bond pdb=" C PHEBR 4 " pdb=" N SERBR 5 " ideal model delta sigma weight residual 1.330 1.221 0.109 1.31e-02 5.83e+03 6.89e+01 bond pdb=" C2 OMUB81375 " pdb=" N3 OMUB81375 " ideal model delta sigma weight residual 1.499 1.337 0.162 2.00e-02 2.50e+03 6.53e+01 bond pdb=" N3 OMGB81151 " pdb=" C4 OMGB81151 " ideal model delta sigma weight residual 1.492 1.349 0.143 2.00e-02 2.50e+03 5.08e+01 bond pdb=" N3 OMGB81376 " pdb=" C4 OMGB81376 " ideal model delta sigma weight residual 1.492 1.351 0.141 2.00e-02 2.50e+03 4.97e+01 ... (remaining 118903 not shown) Histogram of bond angle deviations from ideal: 75.36 - 87.43: 2 87.43 - 99.50: 0 99.50 - 111.57: 66285 111.57 - 123.63: 92827 123.63 - 135.70: 9966 Bond angle restraints: 169080 Sorted by residual: angle pdb=" C1' 1MAB8 949 " pdb=" N9 1MAB8 949 " pdb=" C8 1MAB8 949 " ideal model delta sigma weight residual 100.68 126.19 -25.51 3.00e+00 1.11e-01 7.23e+01 angle pdb=" N PROBw 68 " pdb=" CA PROBw 68 " pdb=" CB PROBw 68 " ideal model delta sigma weight residual 103.33 110.37 -7.04 9.30e-01 1.16e+00 5.73e+01 angle pdb=" C1' OMGB81376 " pdb=" N9 OMGB81376 " pdb=" C4 OMGB81376 " ideal model delta sigma weight residual 108.29 125.34 -17.05 3.00e+00 1.11e-01 3.23e+01 angle pdb=" C1' OMGB81151 " pdb=" N9 OMGB81151 " pdb=" C4 OMGB81151 " ideal model delta sigma weight residual 108.29 125.32 -17.03 3.00e+00 1.11e-01 3.22e+01 angle pdb=" C1' OMGB81151 " pdb=" N9 OMGB81151 " pdb=" C8 OMGB81151 " ideal model delta sigma weight residual 142.82 125.93 16.89 3.00e+00 1.11e-01 3.17e+01 ... (remaining 169075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 68809 35.87 - 71.73: 2374 71.73 - 107.60: 456 107.60 - 143.46: 3 143.46 - 179.33: 25 Dihedral angle restraints: 71667 sinusoidal: 44327 harmonic: 27340 Sorted by residual: dihedral pdb=" O4' CB8 825 " pdb=" C1' CB8 825 " pdb=" N1 CB8 825 " pdb=" C2 CB8 825 " ideal model delta sinusoidal sigma weight residual 200.00 26.33 173.67 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" O4' UAG 53 " pdb=" C1' UAG 53 " pdb=" N1 UAG 53 " pdb=" C2 UAG 53 " ideal model delta sinusoidal sigma weight residual 200.00 26.42 173.58 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" O4' UB9 13 " pdb=" C1' UB9 13 " pdb=" N1 UB9 13 " pdb=" C2 UB9 13 " ideal model delta sinusoidal sigma weight residual -160.00 9.68 -169.68 1 1.50e+01 4.44e-03 8.46e+01 ... (remaining 71664 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 17073 0.041 - 0.081: 2011 0.081 - 0.122: 757 0.122 - 0.162: 42 0.162 - 0.203: 3 Chirality restraints: 19886 Sorted by residual: chirality pdb=" CA PROBw 68 " pdb=" N PROBw 68 " pdb=" C PROBw 68 " pdb=" CB PROBw 68 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" C1' UB81527 " pdb=" O4' UB81527 " pdb=" C2' UB81527 " pdb=" N1 UB81527 " both_signs ideal model delta sigma weight residual False 2.47 2.29 0.17 2.00e-01 2.50e+01 7.52e-01 chirality pdb=" CB THRBN 80 " pdb=" CA THRBN 80 " pdb=" OG1 THRBN 80 " pdb=" CG2 THRBN 80 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 6.95e-01 ... (remaining 19883 not shown) Planarity restraints: 15405 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMGB81151 " 0.030 2.00e-02 2.50e+03 5.51e-01 6.82e+03 pdb=" C4' OMGB81151 " 0.431 2.00e-02 2.50e+03 pdb=" O4' OMGB81151 " 0.581 2.00e-02 2.50e+03 pdb=" C3' OMGB81151 " -0.580 2.00e-02 2.50e+03 pdb=" O3' OMGB81151 " -0.542 2.00e-02 2.50e+03 pdb=" C2' OMGB81151 " -0.215 2.00e-02 2.50e+03 pdb=" O2' OMGB81151 " 0.884 2.00e-02 2.50e+03 pdb=" C1' OMGB81151 " 0.240 2.00e-02 2.50e+03 pdb=" N9 OMGB81151 " -0.830 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMGB81376 " 0.023 2.00e-02 2.50e+03 5.37e-01 6.49e+03 pdb=" C4' OMGB81376 " 0.422 2.00e-02 2.50e+03 pdb=" O4' OMGB81376 " 0.561 2.00e-02 2.50e+03 pdb=" C3' OMGB81376 " -0.580 2.00e-02 2.50e+03 pdb=" O3' OMGB81376 " -0.514 2.00e-02 2.50e+03 pdb=" C2' OMGB81376 " -0.224 2.00e-02 2.50e+03 pdb=" O2' OMGB81376 " 0.869 2.00e-02 2.50e+03 pdb=" C1' OMGB81376 " 0.242 2.00e-02 2.50e+03 pdb=" N9 OMGB81376 " -0.799 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 1MAB8 949 " -0.781 2.00e-02 2.50e+03 5.31e-01 6.33e+03 pdb=" C4' 1MAB8 949 " 0.238 2.00e-02 2.50e+03 pdb=" O4' 1MAB8 949 " 0.641 2.00e-02 2.50e+03 pdb=" C3' 1MAB8 949 " -0.251 2.00e-02 2.50e+03 pdb=" O3' 1MAB8 949 " 0.799 2.00e-02 2.50e+03 pdb=" C2' 1MAB8 949 " -0.579 2.00e-02 2.50e+03 pdb=" O2' 1MAB8 949 " -0.475 2.00e-02 2.50e+03 pdb=" C1' 1MAB8 949 " 0.439 2.00e-02 2.50e+03 pdb=" N9 1MAB8 949 " -0.031 2.00e-02 2.50e+03 ... (remaining 15402 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.12: 84 2.12 - 2.87: 37487 2.87 - 3.63: 185973 3.63 - 4.38: 346091 4.38 - 5.14: 547140 Nonbonded interactions: 1116775 Sorted by model distance: nonbonded pdb=" O3' AB9 73 " pdb=" C PHEB9 101 " model vdw 1.362 3.270 nonbonded pdb=" K KB81794 " pdb="MG MGB81815 " model vdw 1.810 1.980 nonbonded pdb=" OP1 AB8 298 " pdb="MG MGB81652 " model vdw 1.926 2.170 nonbonded pdb=" OP1 CB81402 " pdb="MG MGB81644 " model vdw 1.937 2.170 nonbonded pdb=" OP2 AB8 205 " pdb="MG MGB81730 " model vdw 1.951 2.170 ... (remaining 1116770 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B2' and resid 64 through 89) selection = (chain 'B3' and resid 64 through 89) selection = (chain 'B4' and resid 64 through 89) selection = (chain 'B5' and resid 64 through 89) selection = chain 'B6' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 4.480 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: 0.080 Extract box with map and model: 27.320 Check model and map are aligned: 1.170 Set scattering table: 0.730 Process input model: 330.930 Find NCS groups from input model: 3.160 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 370.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 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 : 0.003 0.174 118908 Z= 0.159 Angle : 0.411 25.507 169080 Z= 0.203 Chirality : 0.031 0.203 19886 Planarity : 0.009 0.551 15405 Dihedral : 15.890 179.327 53943 Min Nonbonded Distance : 1.362 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.68 % Favored : 97.30 % Rotamer: Outliers : 0.63 % Allowed : 3.20 % Favored : 96.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.09), residues: 9255 helix: 1.02 (0.09), residues: 3148 sheet: 0.53 (0.15), residues: 1296 loop : -0.16 (0.09), residues: 4811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPBi 66 HIS 0.003 0.001 HISBw 175 PHE 0.012 0.001 PHEBt 271 TYR 0.018 0.001 TYRBm 176 ARG 0.010 0.000 ARGBp 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18510 Ramachandran restraints generated. 9255 Oldfield, 0 Emsley, 9255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18510 Ramachandran restraints generated. 9255 Oldfield, 0 Emsley, 9255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2060 residues out of total 8262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 2008 time to evaluate : 7.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 54 LYS cc_start: 0.8612 (mttt) cc_final: 0.8353 (mttp) REVERT: BB 12 LEU cc_start: 0.8390 (tt) cc_final: 0.7607 (mt) REVERT: BB 62 ASN cc_start: 0.8396 (m110) cc_final: 0.8190 (m-40) REVERT: BC 32 LYS cc_start: 0.6809 (mttt) cc_final: 0.6545 (mmmt) REVERT: BC 69 ASP cc_start: 0.7616 (p0) cc_final: 0.7331 (p0) REVERT: BC 129 LYS cc_start: 0.6088 (mttt) cc_final: 0.5754 (mmtt) REVERT: BC 149 ARG cc_start: 0.6296 (tmm-80) cc_final: 0.6069 (ttp80) REVERT: BE 5 LYS cc_start: 0.8231 (tttp) cc_final: 0.7999 (ttmt) REVERT: BE 71 TYR cc_start: 0.8349 (m-10) cc_final: 0.8006 (m-80) REVERT: BE 117 GLU cc_start: 0.7005 (mt-10) cc_final: 0.6687 (mt-10) REVERT: BE 142 ASP cc_start: 0.7794 (m-30) cc_final: 0.7573 (m-30) REVERT: BE 150 LYS cc_start: 0.7714 (tttm) cc_final: 0.6981 (mtmm) REVERT: BE 152 ASP cc_start: 0.7586 (t0) cc_final: 0.7251 (t0) REVERT: BE 173 ASP cc_start: 0.7416 (m-30) cc_final: 0.7015 (m-30) REVERT: BF 75 ASN cc_start: 0.8501 (t0) cc_final: 0.7932 (t0) REVERT: BF 113 MET cc_start: 0.8665 (tmm) cc_final: 0.8314 (tmm) REVERT: BF 179 ILE cc_start: 0.8239 (tt) cc_final: 0.8027 (pt) REVERT: BF 213 MET cc_start: 0.8655 (mtm) cc_final: 0.8298 (mtp) REVERT: BF 229 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7527 (mt-10) REVERT: BG 35 LYS cc_start: 0.8163 (mttt) cc_final: 0.7743 (mtpp) REVERT: BG 40 ARG cc_start: 0.7845 (ttm170) cc_final: 0.7272 (ttm170) REVERT: BH 153 THR cc_start: 0.9333 (p) cc_final: 0.8811 (t) REVERT: BI 30 PHE cc_start: 0.8322 (p90) cc_final: 0.8097 (p90) REVERT: BI 57 VAL cc_start: 0.8380 (m) cc_final: 0.8171 (t) REVERT: BK 100 ARG cc_start: 0.8424 (mmm-85) cc_final: 0.8028 (mmt-90) REVERT: BK 156 LYS cc_start: 0.8735 (tttt) cc_final: 0.8405 (mptt) REVERT: BL 79 MET cc_start: 0.8555 (ttt) cc_final: 0.8291 (ttt) REVERT: BM 81 LYS cc_start: 0.7552 (mttt) cc_final: 0.6832 (mmtm) REVERT: BM 82 ASP cc_start: 0.7617 (m-30) cc_final: 0.7402 (t0) REVERT: BM 235 LYS cc_start: 0.9249 (mtpt) cc_final: 0.9033 (mtpp) REVERT: BN 201 GLN cc_start: 0.8895 (tp-100) cc_final: 0.7773 (mm-40) REVERT: BO 91 LYS cc_start: 0.7245 (mttm) cc_final: 0.6937 (mttp) REVERT: BO 103 GLU cc_start: 0.8273 (pp20) cc_final: 0.7732 (pp20) REVERT: BO 137 LYS cc_start: 0.7215 (mttt) cc_final: 0.6953 (pttt) REVERT: BP 95 MET cc_start: 0.6664 (ttp) cc_final: 0.6208 (ttp) REVERT: BP 96 ILE cc_start: 0.7864 (mt) cc_final: 0.7437 (tt) REVERT: BP 111 LEU cc_start: 0.7911 (tt) cc_final: 0.7645 (mt) REVERT: BP 114 HIS cc_start: 0.7377 (t70) cc_final: 0.7038 (t-170) REVERT: BP 139 LYS cc_start: 0.6017 (pttt) cc_final: 0.5574 (tmtt) REVERT: BP 167 ILE cc_start: 0.7745 (mt) cc_final: 0.7322 (tp) REVERT: BQ 81 LYS cc_start: 0.6618 (ttpt) cc_final: 0.6390 (ttmt) REVERT: BR 67 PHE cc_start: 0.9128 (OUTLIER) cc_final: 0.8834 (m-80) REVERT: BS 66 VAL cc_start: 0.9405 (p) cc_final: 0.9144 (m) REVERT: BS 113 ASN cc_start: 0.8059 (m-40) cc_final: 0.7651 (m-40) REVERT: BS 142 GLN cc_start: 0.8379 (mm110) cc_final: 0.8094 (mm-40) REVERT: BT 196 ARG cc_start: 0.8348 (mtm-85) cc_final: 0.8073 (mtt180) REVERT: BU 39 PHE cc_start: 0.7561 (m-80) cc_final: 0.7351 (m-80) REVERT: BU 136 MET cc_start: 0.7951 (tpp) cc_final: 0.7688 (tpp) REVERT: BW 84 ILE cc_start: 0.9075 (mt) cc_final: 0.8815 (pt) REVERT: BW 100 GLN cc_start: 0.8019 (mt0) cc_final: 0.7417 (pt0) REVERT: BX 244 ARG cc_start: 0.8618 (mmm-85) cc_final: 0.7887 (mmm160) REVERT: Ba 75 ARG cc_start: 0.8064 (mtt-85) cc_final: 0.7858 (mtt-85) REVERT: Bb 26 ASN cc_start: 0.8498 (p0) cc_final: 0.8057 (p0) REVERT: Bb 47 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.6994 (tp) REVERT: Bc 73 MET cc_start: 0.6795 (mmm) cc_final: 0.5670 (ttm) REVERT: Bc 99 MET cc_start: 0.6954 (mtm) cc_final: 0.6584 (mmt) REVERT: Bc 133 SER cc_start: 0.8823 (m) cc_final: 0.8032 (t) REVERT: Bd 42 THR cc_start: 0.8583 (t) cc_final: 0.8158 (m) REVERT: Bd 48 THR cc_start: 0.8285 (m) cc_final: 0.7925 (p) REVERT: Bd 70 ARG cc_start: 0.7162 (ttm-80) cc_final: 0.6939 (ttp-110) REVERT: Be 12 ILE cc_start: 0.8962 (mt) cc_final: 0.8738 (mm) REVERT: Be 45 ASN cc_start: 0.8897 (m110) cc_final: 0.8627 (m-40) REVERT: Bf 38 GLU cc_start: 0.4722 (mt-10) cc_final: 0.4320 (tp30) REVERT: Bf 99 GLU cc_start: 0.8218 (pt0) cc_final: 0.8000 (pt0) REVERT: Bf 142 GLN cc_start: 0.7165 (pt0) cc_final: 0.6948 (mt0) REVERT: Bf 174 LEU cc_start: 0.7287 (tp) cc_final: 0.6997 (mp) REVERT: Bg 36 GLU cc_start: 0.8194 (pt0) cc_final: 0.7960 (pm20) REVERT: Bg 81 GLN cc_start: 0.7290 (mm-40) cc_final: 0.6878 (tt0) REVERT: Bg 83 ARG cc_start: 0.6403 (mtp-110) cc_final: 0.5950 (mtm110) REVERT: Bh 146 ARG cc_start: 0.6849 (mmt180) cc_final: 0.6635 (ttm110) REVERT: Bi 350 VAL cc_start: 0.9265 (t) cc_final: 0.8933 (p) REVERT: Bi 414 GLN cc_start: 0.8518 (tp-100) cc_final: 0.7980 (tp-100) REVERT: Bj 101 LYS cc_start: 0.5811 (mttt) cc_final: 0.5562 (tppt) REVERT: Bj 107 LYS cc_start: 0.6475 (mttt) cc_final: 0.5982 (pttm) REVERT: Bm 72 ARG cc_start: 0.7739 (ttm110) cc_final: 0.7111 (ptm160) REVERT: Bm 310 ARG cc_start: 0.8495 (mtm-85) cc_final: 0.8254 (mtp180) REVERT: Bn 27 ARG cc_start: 0.7713 (tpt170) cc_final: 0.7346 (ttp-170) REVERT: Bn 141 ARG cc_start: 0.8478 (mtm110) cc_final: 0.8034 (ttm110) REVERT: Bn 160 ASP cc_start: 0.8076 (m-30) cc_final: 0.7713 (m-30) REVERT: Bn 183 ASP cc_start: 0.7105 (m-30) cc_final: 0.6721 (p0) REVERT: Bo 46 ASN cc_start: 0.8819 (m-40) cc_final: 0.8218 (m110) REVERT: Bo 50 ASN cc_start: 0.6299 (m-40) cc_final: 0.6078 (m110) REVERT: Bo 145 MET cc_start: 0.8316 (ttm) cc_final: 0.7979 (ttm) REVERT: Bo 177 CYS cc_start: 0.7699 (p) cc_final: 0.7391 (p) REVERT: Bo 244 ASN cc_start: 0.7375 (m-40) cc_final: 0.7067 (m-40) REVERT: Bo 310 ASN cc_start: 0.7920 (m-40) cc_final: 0.7112 (t0) REVERT: Bp 71 ARG cc_start: 0.7289 (mtt180) cc_final: 0.6742 (tpt-90) REVERT: Bp 97 LYS cc_start: 0.6971 (tppt) cc_final: 0.6595 (tptp) REVERT: Bp 197 LYS cc_start: 0.6335 (mmtt) cc_final: 0.6132 (mtpt) REVERT: Bq 48 PHE cc_start: 0.8820 (t80) cc_final: 0.8246 (t80) REVERT: Br 72 THR cc_start: 0.8543 (p) cc_final: 0.8342 (p) REVERT: Br 73 LYS cc_start: 0.9013 (ptpt) cc_final: 0.8609 (ptmm) REVERT: Bt 45 LEU cc_start: 0.8520 (mt) cc_final: 0.8218 (tt) REVERT: Bt 51 LEU cc_start: 0.8735 (tp) cc_final: 0.8411 (mp) REVERT: Bt 97 TYR cc_start: 0.8430 (t80) cc_final: 0.8187 (t80) REVERT: Bt 150 THR cc_start: 0.8486 (m) cc_final: 0.8248 (p) REVERT: Bt 247 LYS cc_start: 0.6922 (mptt) cc_final: 0.6670 (mtpt) REVERT: Bu 139 GLU cc_start: 0.7869 (mm-30) cc_final: 0.6203 (mp0) REVERT: Bu 174 TRP cc_start: 0.8161 (t-100) cc_final: 0.7847 (t-100) REVERT: Bu 226 ASP cc_start: 0.7158 (t0) cc_final: 0.6563 (t0) REVERT: Bu 237 ASP cc_start: 0.6917 (m-30) cc_final: 0.6660 (t0) REVERT: Bu 238 VAL cc_start: 0.7543 (OUTLIER) cc_final: 0.7309 (m) REVERT: Bu 244 GLU cc_start: 0.7366 (mp0) cc_final: 0.6962 (mp0) REVERT: Bu 249 GLU cc_start: 0.7437 (tt0) cc_final: 0.7216 (tt0) REVERT: Bu 261 MET cc_start: 0.5975 (ttm) cc_final: 0.5205 (ttp) REVERT: Bu 292 GLU cc_start: 0.7428 (mt-10) cc_final: 0.7124 (mm-30) REVERT: Bv 75 GLN cc_start: 0.7446 (mt0) cc_final: 0.7024 (tp40) REVERT: Bv 78 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7831 (mt-10) REVERT: Bv 136 ARG cc_start: 0.5988 (mtp85) cc_final: 0.5267 (ttp80) REVERT: Bv 196 SER cc_start: 0.7682 (t) cc_final: 0.7434 (p) REVERT: Bv 198 ASN cc_start: 0.5365 (p0) cc_final: 0.4749 (p0) REVERT: Bv 233 PHE cc_start: 0.8000 (m-80) cc_final: 0.7664 (m-80) REVERT: Bv 275 PHE cc_start: 0.7472 (p90) cc_final: 0.7258 (p90) REVERT: Bw 135 LEU cc_start: 0.7275 (mt) cc_final: 0.6990 (mt) REVERT: Bw 144 MET cc_start: 0.6465 (mmt) cc_final: 0.6166 (mmm) REVERT: Bx 57 ILE cc_start: 0.8689 (mt) cc_final: 0.8325 (pt) REVERT: Bx 141 ASN cc_start: 0.8442 (t0) cc_final: 0.7900 (t0) REVERT: Bx 144 THR cc_start: 0.9142 (m) cc_final: 0.8642 (m) REVERT: Bz 41 ARG cc_start: 0.7873 (ptm160) cc_final: 0.7596 (ttt-90) REVERT: Bz 83 TRP cc_start: 0.8410 (t60) cc_final: 0.7826 (t60) REVERT: Bz 100 ASN cc_start: 0.7821 (p0) cc_final: 0.7603 (t0) REVERT: Aa 193 ARG cc_start: 0.5097 (mtt180) cc_final: 0.4852 (tpt170) REVERT: Aa 263 ILE cc_start: 0.8798 (mt) cc_final: 0.8574 (tp) REVERT: Aa 287 GLN cc_start: 0.7606 (tp40) cc_final: 0.7374 (mm110) REVERT: Aa 324 LEU cc_start: 0.7538 (mt) cc_final: 0.7311 (mt) REVERT: Aa 373 LYS cc_start: 0.6984 (mtmt) cc_final: 0.6212 (tptm) REVERT: Aa 404 VAL cc_start: 0.6401 (t) cc_final: 0.5668 (p) REVERT: Aa 423 ARG cc_start: 0.5885 (mtt90) cc_final: 0.5574 (ttm110) outliers start: 52 outliers final: 21 residues processed: 2047 average time/residue: 1.1382 time to fit residues: 3908.7077 Evaluate side-chains 1257 residues out of total 8262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1233 time to evaluate : 6.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BI residue 50 VAL Chi-restraints excluded: chain BL residue 216 VAL Chi-restraints excluded: chain BN residue 106 PHE Chi-restraints excluded: chain BO residue 238 VAL Chi-restraints excluded: chain BP residue 171 ILE Chi-restraints excluded: chain BQ residue 58 LYS Chi-restraints excluded: chain BR residue 67 PHE Chi-restraints excluded: chain BS residue 89 HIS Chi-restraints excluded: chain BU residue 59 VAL Chi-restraints excluded: chain BW residue 101 VAL Chi-restraints excluded: chain BX residue 265 LEU Chi-restraints excluded: chain Bb residue 46 ASN Chi-restraints excluded: chain Bb residue 47 LEU Chi-restraints excluded: chain Bb residue 75 ILE Chi-restraints excluded: chain Be residue 101 TRP Chi-restraints excluded: chain Bi residue 399 ILE Chi-restraints excluded: chain Bm residue 270 VAL Chi-restraints excluded: chain Bm residue 398 VAL Chi-restraints excluded: chain Bo residue 260 VAL Chi-restraints excluded: chain Bp residue 195 ILE Chi-restraints excluded: chain Br residue 41 ASP Chi-restraints excluded: chain Bs residue 75 VAL Chi-restraints excluded: chain Bs residue 84 VAL Chi-restraints excluded: chain Bu residue 238 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1081 random chunks: chunk 912 optimal weight: 0.9990 chunk 819 optimal weight: 0.0970 chunk 454 optimal weight: 8.9990 chunk 279 optimal weight: 9.9990 chunk 552 optimal weight: 8.9990 chunk 437 optimal weight: 10.0000 chunk 847 optimal weight: 5.9990 chunk 327 optimal weight: 4.9990 chunk 515 optimal weight: 10.0000 chunk 630 optimal weight: 10.0000 chunk 981 optimal weight: 6.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 60 GLN BA 73 HIS BA 113 GLN BA 171 HIS BA 199 GLN BA 203 ASN BE 89 HIS BE 177 HIS BF 91 GLN BF 112 ASN BH 118 GLN BH 144 GLN BJ 57 GLN BK 118 HIS BL 183 HIS ** BL 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BM 117 HIS BM 154 HIS BM 277 ASN BN 97 HIS ** BN 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BN 241 ASN BN 276 HIS BN 277 ASN ** BO 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BO 178 ASN ** BO 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BP 73 GLN BP 119 HIS BP 150 HIS BP 224 HIS BQ 84 GLN BQ 103 HIS BQ 133 GLN BR 48 HIS BR 89 GLN BS 33 GLN BT 94 GLN BT 123 ASN BU 138 GLN BV 98 GLN BV 155 GLN ** BW 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BW 88 HIS ** BX 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BX 253 GLN BY 94 GLN BY 148 HIS BZ 88 ASN ** BZ 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BZ 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BZ 175 ASN Bb 84 GLN Bc 82 GLN Bc 124 HIS Bd 60 GLN Be 45 ASN Bf 40 GLN Bf 103 HIS ** Bf 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 106 GLN Bg 130 GLN Bh 112 HIS Bh 148 ASN ** Bh 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bi 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bi 201 HIS Bi 228 ASN Bi 379 GLN Bi 414 GLN Bj 266 GLN Bm 84 HIS Bm 149 ASN Bm 186 GLN Bm 266 GLN Bm 280 GLN ** Bm 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bm 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bm 358 GLN Bo 81 ASN Bo 230 ASN Bo 305 HIS Bp 186 GLN Bs 24 GLN Bs 58 ASN Bs 129 GLN Bt 42 GLN Bt 69 HIS Bu 69 HIS Bu 196 GLN ** Bu 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bv 87 HIS ** Bv 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bw 81 ASN Bw 136 GLN Bx 155 GLN By 86 ASN By 88 GLN By 96 HIS Bz 69 HIS Aa 107 ASN Aa 124 GLN ** Aa 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 250 HIS Aa 258 HIS Aa 341 GLN Aa 368 GLN Aa 381 GLN Total number of N/Q/H flips: 92 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 118908 Z= 0.366 Angle : 0.639 17.403 169080 Z= 0.326 Chirality : 0.040 0.206 19886 Planarity : 0.005 0.142 15405 Dihedral : 18.187 179.888 34239 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.38 % Favored : 96.58 % Rotamer: Outliers : 2.88 % Allowed : 9.48 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.09), residues: 9255 helix: 1.23 (0.09), residues: 3249 sheet: 0.35 (0.15), residues: 1243 loop : -0.41 (0.09), residues: 4763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRPBp 121 HIS 0.007 0.001 HISBw 175 PHE 0.027 0.002 PHEBQ 78 TYR 0.028 0.002 TYRBm 176 ARG 0.008 0.001 ARGBt 36 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18510 Ramachandran restraints generated. 9255 Oldfield, 0 Emsley, 9255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18510 Ramachandran restraints generated. 9255 Oldfield, 0 Emsley, 9255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1508 residues out of total 8262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 1271 time to evaluate : 7.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 54 LYS cc_start: 0.8678 (mttt) cc_final: 0.8386 (mttp) REVERT: BB 12 LEU cc_start: 0.8353 (tt) cc_final: 0.7578 (mt) REVERT: BB 58 GLU cc_start: 0.8004 (tp30) cc_final: 0.7787 (tp30) REVERT: BC 32 LYS cc_start: 0.6806 (mttt) cc_final: 0.6511 (mmmt) REVERT: BC 111 SER cc_start: 0.7856 (m) cc_final: 0.7617 (p) REVERT: BC 127 ASP cc_start: 0.4997 (t70) cc_final: 0.4656 (t70) REVERT: BC 129 LYS cc_start: 0.5851 (mttt) cc_final: 0.5565 (mmtt) REVERT: BC 149 ARG cc_start: 0.6429 (tmm-80) cc_final: 0.6213 (ttp80) REVERT: BE 5 LYS cc_start: 0.8311 (tttp) cc_final: 0.8006 (ttmt) REVERT: BE 71 TYR cc_start: 0.8442 (m-10) cc_final: 0.8105 (m-80) REVERT: BE 109 LEU cc_start: 0.8888 (mt) cc_final: 0.8650 (mp) REVERT: BE 150 LYS cc_start: 0.7487 (tttm) cc_final: 0.6833 (mtmm) REVERT: BF 75 ASN cc_start: 0.8669 (t0) cc_final: 0.8018 (t0) REVERT: BF 113 MET cc_start: 0.8776 (tmm) cc_final: 0.8336 (tmm) REVERT: BF 155 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8289 (tt) REVERT: BF 213 MET cc_start: 0.8650 (mtm) cc_final: 0.8243 (mtp) REVERT: BF 229 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7272 (mt-10) REVERT: BG 35 LYS cc_start: 0.8222 (mttt) cc_final: 0.7801 (mtpp) REVERT: BG 40 ARG cc_start: 0.7856 (ttm170) cc_final: 0.7290 (ttm170) REVERT: BG 44 LYS cc_start: 0.8969 (tptp) cc_final: 0.8741 (tppt) REVERT: BG 56 TYR cc_start: 0.8695 (m-10) cc_final: 0.8332 (m-80) REVERT: BG 88 MET cc_start: 0.8445 (ptp) cc_final: 0.7935 (ptp) REVERT: BG 134 MET cc_start: 0.8587 (mmp) cc_final: 0.8379 (tpp) REVERT: BH 153 THR cc_start: 0.9455 (p) cc_final: 0.8888 (t) REVERT: BH 176 GLU cc_start: 0.8036 (mp0) cc_final: 0.7695 (mm-30) REVERT: BI 57 VAL cc_start: 0.8345 (m) cc_final: 0.7983 (t) REVERT: BK 100 ARG cc_start: 0.8443 (mmm-85) cc_final: 0.8056 (mmt-90) REVERT: BK 156 LYS cc_start: 0.8575 (tttt) cc_final: 0.8288 (mptt) REVERT: BL 168 ASP cc_start: 0.8801 (p0) cc_final: 0.8489 (p0) REVERT: BL 235 MET cc_start: 0.8468 (ttp) cc_final: 0.8254 (ttp) REVERT: BM 81 LYS cc_start: 0.7418 (mttt) cc_final: 0.6870 (mmtm) REVERT: BM 82 ASP cc_start: 0.7508 (m-30) cc_final: 0.7033 (t0) REVERT: BM 113 ASP cc_start: 0.8457 (p0) cc_final: 0.8125 (p0) REVERT: BN 50 LYS cc_start: 0.7494 (mmmt) cc_final: 0.6357 (mmtt) REVERT: BO 103 GLU cc_start: 0.8247 (pp20) cc_final: 0.7845 (pp20) REVERT: BO 137 LYS cc_start: 0.7264 (mttt) cc_final: 0.6906 (pttt) REVERT: BP 83 ARG cc_start: 0.7403 (mmm160) cc_final: 0.6841 (mtm180) REVERT: BP 95 MET cc_start: 0.6910 (ttp) cc_final: 0.6517 (ttp) REVERT: BQ 52 GLU cc_start: 0.5744 (pt0) cc_final: 0.5396 (mt-10) REVERT: BR 67 PHE cc_start: 0.9194 (OUTLIER) cc_final: 0.8753 (m-10) REVERT: BS 43 ASN cc_start: 0.8440 (p0) cc_final: 0.8200 (p0) REVERT: BT 142 GLU cc_start: 0.8030 (pm20) cc_final: 0.7829 (pm20) REVERT: BT 155 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7204 (tt0) REVERT: BT 204 MET cc_start: 0.7721 (mmm) cc_final: 0.7499 (mmt) REVERT: BU 136 MET cc_start: 0.7957 (tpp) cc_final: 0.7745 (tpp) REVERT: BW 100 GLN cc_start: 0.7937 (mt0) cc_final: 0.7490 (pt0) REVERT: BX 244 ARG cc_start: 0.8659 (mmm-85) cc_final: 0.8244 (mtp85) REVERT: Bc 73 MET cc_start: 0.6868 (mmm) cc_final: 0.5559 (ttm) REVERT: Bc 99 MET cc_start: 0.7028 (mtm) cc_final: 0.6634 (mmt) REVERT: Bc 133 SER cc_start: 0.8779 (m) cc_final: 0.8266 (t) REVERT: Bd 42 THR cc_start: 0.8774 (t) cc_final: 0.8562 (p) REVERT: Bd 48 THR cc_start: 0.8289 (m) cc_final: 0.7950 (p) REVERT: Bd 66 HIS cc_start: 0.8699 (OUTLIER) cc_final: 0.8062 (t-170) REVERT: Bd 70 ARG cc_start: 0.7147 (ttm-80) cc_final: 0.6698 (ttp-110) REVERT: Bd 73 ARG cc_start: 0.7030 (ptm160) cc_final: 0.6522 (ttp-170) REVERT: Be 12 ILE cc_start: 0.9039 (mt) cc_final: 0.8803 (mm) REVERT: Bf 38 GLU cc_start: 0.4817 (mt-10) cc_final: 0.4166 (tp30) REVERT: Bf 175 ARG cc_start: 0.6907 (mtm-85) cc_final: 0.6614 (mtm-85) REVERT: Bg 36 GLU cc_start: 0.8198 (pt0) cc_final: 0.7887 (pm20) REVERT: Bg 81 GLN cc_start: 0.7091 (mm-40) cc_final: 0.6845 (tt0) REVERT: Bg 83 ARG cc_start: 0.6621 (mtp-110) cc_final: 0.6086 (mtm110) REVERT: Bh 134 LYS cc_start: 0.6344 (ptmm) cc_final: 0.5988 (ptmm) REVERT: Bj 101 LYS cc_start: 0.6024 (mttt) cc_final: 0.5683 (tppt) REVERT: Bj 107 LYS cc_start: 0.6798 (mttt) cc_final: 0.6204 (pttm) REVERT: Bm 72 ARG cc_start: 0.7825 (ttm110) cc_final: 0.7164 (ptm160) REVERT: Bn 27 ARG cc_start: 0.7827 (tpt170) cc_final: 0.7268 (ttm170) REVERT: Bn 160 ASP cc_start: 0.8087 (m-30) cc_final: 0.7859 (m-30) REVERT: Bn 185 MET cc_start: 0.8755 (tpp) cc_final: 0.8489 (tpp) REVERT: Bo 46 ASN cc_start: 0.8825 (m-40) cc_final: 0.8188 (m110) REVERT: Bo 50 ASN cc_start: 0.6204 (m-40) cc_final: 0.5942 (m110) REVERT: Bo 244 ASN cc_start: 0.7248 (m-40) cc_final: 0.6813 (t0) REVERT: Bo 310 ASN cc_start: 0.7929 (m-40) cc_final: 0.6997 (t0) REVERT: Bp 69 LYS cc_start: 0.7610 (ptpp) cc_final: 0.7403 (pttt) REVERT: Bp 71 ARG cc_start: 0.7267 (mtt180) cc_final: 0.6576 (tpt-90) REVERT: Bp 97 LYS cc_start: 0.7029 (tppt) cc_final: 0.6639 (tptp) REVERT: Bq 50 GLN cc_start: 0.8888 (tt0) cc_final: 0.8597 (tt0) REVERT: Br 73 LYS cc_start: 0.8991 (ptpt) cc_final: 0.8635 (ptmm) REVERT: Br 141 ASP cc_start: 0.7357 (t0) cc_final: 0.7114 (t0) REVERT: Bt 45 LEU cc_start: 0.8408 (mt) cc_final: 0.8045 (tt) REVERT: Bt 97 TYR cc_start: 0.8396 (t80) cc_final: 0.8155 (t80) REVERT: Bt 183 GLU cc_start: 0.7479 (mt-10) cc_final: 0.6973 (tt0) REVERT: Bu 110 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7035 (mt-10) REVERT: Bu 147 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7164 (mm-30) REVERT: Bu 174 TRP cc_start: 0.8219 (t-100) cc_final: 0.7587 (t-100) REVERT: Bu 236 GLU cc_start: 0.7350 (pm20) cc_final: 0.7013 (pm20) REVERT: Bu 244 GLU cc_start: 0.7595 (mp0) cc_final: 0.7015 (mp0) REVERT: Bu 261 MET cc_start: 0.6293 (ttm) cc_final: 0.5808 (ttp) REVERT: Bu 292 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7167 (mm-30) REVERT: Bv 58 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7524 (mt) REVERT: Bv 75 GLN cc_start: 0.7641 (mt0) cc_final: 0.7276 (tp40) REVERT: Bv 78 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8139 (mt-10) REVERT: Bv 120 LEU cc_start: 0.8164 (mt) cc_final: 0.7921 (tp) REVERT: Bv 263 TYR cc_start: 0.7025 (m-80) cc_final: 0.6679 (m-10) REVERT: Bw 88 TYR cc_start: 0.7291 (m-80) cc_final: 0.7069 (m-10) REVERT: Bw 144 MET cc_start: 0.6498 (mmt) cc_final: 0.6194 (mmm) REVERT: Bx 142 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8557 (mt-10) REVERT: Bz 41 ARG cc_start: 0.7846 (ptm160) cc_final: 0.7590 (ttt-90) REVERT: Bz 83 TRP cc_start: 0.8572 (t60) cc_final: 0.7903 (t60) REVERT: Bz 106 ASP cc_start: 0.8393 (m-30) cc_final: 0.8167 (m-30) REVERT: Aa 165 MET cc_start: -0.1010 (ptt) cc_final: -0.1265 (mmt) REVERT: Aa 373 LYS cc_start: 0.7191 (mtmt) cc_final: 0.6469 (tptm) REVERT: Aa 409 GLU cc_start: 0.5493 (tp30) cc_final: 0.5023 (mm-30) REVERT: Aa 423 ARG cc_start: 0.5876 (mtt90) cc_final: 0.5182 (tpp80) outliers start: 237 outliers final: 159 residues processed: 1419 average time/residue: 0.9912 time to fit residues: 2413.0867 Evaluate side-chains 1292 residues out of total 8262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 1128 time to evaluate : 7.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 170 CYS Chi-restraints excluded: chain BA residue 198 ILE Chi-restraints excluded: chain BB residue 70 THR Chi-restraints excluded: chain BB residue 91 ASP Chi-restraints excluded: chain BC residue 60 ASP Chi-restraints excluded: chain BC residue 147 SER Chi-restraints excluded: chain BC residue 166 VAL Chi-restraints excluded: chain BC residue 181 ASP Chi-restraints excluded: chain BD residue 109 SER Chi-restraints excluded: chain BE residue 128 THR Chi-restraints excluded: chain BF residue 88 THR Chi-restraints excluded: chain BF residue 155 LEU Chi-restraints excluded: chain BF residue 160 THR Chi-restraints excluded: chain BF residue 174 ILE Chi-restraints excluded: chain BG residue 74 SER Chi-restraints excluded: chain BG residue 105 SER Chi-restraints excluded: chain BI residue 49 VAL Chi-restraints excluded: chain BI residue 50 VAL Chi-restraints excluded: chain BJ residue 92 SER Chi-restraints excluded: chain BL residue 68 SER Chi-restraints excluded: chain BL residue 73 THR Chi-restraints excluded: chain BL residue 125 GLU Chi-restraints excluded: chain BL residue 175 VAL Chi-restraints excluded: chain BL residue 231 SER Chi-restraints excluded: chain BL residue 237 VAL Chi-restraints excluded: chain BL residue 257 VAL Chi-restraints excluded: chain BM residue 136 GLU Chi-restraints excluded: chain BM residue 153 SER Chi-restraints excluded: chain BM residue 279 LYS Chi-restraints excluded: chain BM residue 296 LEU Chi-restraints excluded: chain BM residue 309 ASP Chi-restraints excluded: chain BN residue 94 ASP Chi-restraints excluded: chain BN residue 106 PHE Chi-restraints excluded: chain BN residue 129 VAL Chi-restraints excluded: chain BN residue 151 VAL Chi-restraints excluded: chain BO residue 53 THR Chi-restraints excluded: chain BO residue 114 VAL Chi-restraints excluded: chain BO residue 130 VAL Chi-restraints excluded: chain BO residue 238 VAL Chi-restraints excluded: chain BP residue 30 SER Chi-restraints excluded: chain BP residue 99 CYS Chi-restraints excluded: chain BP residue 150 HIS Chi-restraints excluded: chain BP residue 187 SER Chi-restraints excluded: chain BQ residue 58 LYS Chi-restraints excluded: chain BQ residue 123 VAL Chi-restraints excluded: chain BQ residue 143 SER Chi-restraints excluded: chain BR residue 3 SER Chi-restraints excluded: chain BR residue 31 LEU Chi-restraints excluded: chain BR residue 67 PHE Chi-restraints excluded: chain BR residue 140 ASN Chi-restraints excluded: chain BS residue 48 THR Chi-restraints excluded: chain BS residue 71 ASP Chi-restraints excluded: chain BS residue 89 HIS Chi-restraints excluded: chain BS residue 117 THR Chi-restraints excluded: chain BS residue 126 SER Chi-restraints excluded: chain BT residue 33 SER Chi-restraints excluded: chain BT residue 116 ILE Chi-restraints excluded: chain BT residue 155 GLU Chi-restraints excluded: chain BU residue 59 VAL Chi-restraints excluded: chain BU residue 121 LEU Chi-restraints excluded: chain BU residue 224 LEU Chi-restraints excluded: chain BV residue 86 ILE Chi-restraints excluded: chain BW residue 101 VAL Chi-restraints excluded: chain BW residue 149 THR Chi-restraints excluded: chain BW residue 157 SER Chi-restraints excluded: chain BX residue 154 THR Chi-restraints excluded: chain BX residue 177 VAL Chi-restraints excluded: chain BX residue 265 LEU Chi-restraints excluded: chain BX residue 286 ILE Chi-restraints excluded: chain BX residue 289 SER Chi-restraints excluded: chain BY residue 12 SER Chi-restraints excluded: chain BY residue 59 LEU Chi-restraints excluded: chain BY residue 63 SER Chi-restraints excluded: chain BY residue 76 SER Chi-restraints excluded: chain BZ residue 58 THR Chi-restraints excluded: chain BZ residue 69 VAL Chi-restraints excluded: chain BZ residue 113 THR Chi-restraints excluded: chain BZ residue 158 VAL Chi-restraints excluded: chain Ba residue 107 LYS Chi-restraints excluded: chain Bb residue 8 LEU Chi-restraints excluded: chain Bb residue 45 THR Chi-restraints excluded: chain Bb residue 75 ILE Chi-restraints excluded: chain Bd residue 66 HIS Chi-restraints excluded: chain Be residue 101 TRP Chi-restraints excluded: chain Bf residue 40 GLN Chi-restraints excluded: chain Bf residue 110 ILE Chi-restraints excluded: chain Bf residue 133 ILE Chi-restraints excluded: chain Bf residue 185 GLU Chi-restraints excluded: chain Bg residue 41 ASP Chi-restraints excluded: chain Bh residue 38 VAL Chi-restraints excluded: chain Bh residue 67 THR Chi-restraints excluded: chain Bh residue 140 VAL Chi-restraints excluded: chain Bh residue 188 SER Chi-restraints excluded: chain Bh residue 192 LEU Chi-restraints excluded: chain Bi residue 76 VAL Chi-restraints excluded: chain Bi residue 184 VAL Chi-restraints excluded: chain Bi residue 260 CYS Chi-restraints excluded: chain Bi residue 399 ILE Chi-restraints excluded: chain Bi residue 410 ASP Chi-restraints excluded: chain Bj residue 262 MET Chi-restraints excluded: chain Bl residue 100 MET Chi-restraints excluded: chain Bm residue 38 THR Chi-restraints excluded: chain Bm residue 137 LEU Chi-restraints excluded: chain Bm residue 151 ASP Chi-restraints excluded: chain Bm residue 166 SER Chi-restraints excluded: chain Bm residue 175 THR Chi-restraints excluded: chain Bm residue 185 ILE Chi-restraints excluded: chain Bm residue 203 CYS Chi-restraints excluded: chain Bm residue 248 THR Chi-restraints excluded: chain Bm residue 252 VAL Chi-restraints excluded: chain Bm residue 256 PHE Chi-restraints excluded: chain Bm residue 259 ILE Chi-restraints excluded: chain Bm residue 270 VAL Chi-restraints excluded: chain Bm residue 344 SER Chi-restraints excluded: chain Bm residue 379 ASP Chi-restraints excluded: chain Bm residue 398 VAL Chi-restraints excluded: chain Bn residue 151 LEU Chi-restraints excluded: chain Bn residue 205 THR Chi-restraints excluded: chain Bn residue 222 ASP Chi-restraints excluded: chain Bn residue 226 LEU Chi-restraints excluded: chain Bn residue 302 ASP Chi-restraints excluded: chain Bo residue 126 THR Chi-restraints excluded: chain Bo residue 214 GLU Chi-restraints excluded: chain Bo residue 215 THR Chi-restraints excluded: chain Bo residue 260 VAL Chi-restraints excluded: chain Bp residue 87 ASP Chi-restraints excluded: chain Bp residue 132 GLU Chi-restraints excluded: chain Bp residue 167 SER Chi-restraints excluded: chain Bq residue 39 THR Chi-restraints excluded: chain Br residue 38 SER Chi-restraints excluded: chain Br residue 41 ASP Chi-restraints excluded: chain Br residue 93 LYS Chi-restraints excluded: chain Bs residue 30 SER Chi-restraints excluded: chain Bs residue 34 SER Chi-restraints excluded: chain Bs residue 75 VAL Chi-restraints excluded: chain Bs residue 84 VAL Chi-restraints excluded: chain Bs residue 91 CYS Chi-restraints excluded: chain Bs residue 126 ILE Chi-restraints excluded: chain Bs residue 139 THR Chi-restraints excluded: chain Bt residue 84 SER Chi-restraints excluded: chain Bt residue 85 LEU Chi-restraints excluded: chain Bt residue 93 VAL Chi-restraints excluded: chain Bt residue 148 LEU Chi-restraints excluded: chain Bt residue 224 THR Chi-restraints excluded: chain Bt residue 265 THR Chi-restraints excluded: chain Bu residue 76 ILE Chi-restraints excluded: chain Bu residue 155 SER Chi-restraints excluded: chain Bu residue 165 THR Chi-restraints excluded: chain Bu residue 266 ILE Chi-restraints excluded: chain Bv residue 58 LEU Chi-restraints excluded: chain Bv residue 77 ILE Chi-restraints excluded: chain Bv residue 121 GLU Chi-restraints excluded: chain Bv residue 179 GLN Chi-restraints excluded: chain Bw residue 53 THR Chi-restraints excluded: chain Bw residue 90 VAL Chi-restraints excluded: chain Bw residue 102 LEU Chi-restraints excluded: chain Bw residue 149 VAL Chi-restraints excluded: chain Bw residue 204 LEU Chi-restraints excluded: chain Bz residue 43 VAL Chi-restraints excluded: chain Bz residue 104 ILE Chi-restraints excluded: chain Aa residue 199 ILE Chi-restraints excluded: chain Aa residue 207 ILE Chi-restraints excluded: chain Aa residue 269 SER Chi-restraints excluded: chain Aa residue 284 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1081 random chunks: chunk 545 optimal weight: 0.7980 chunk 304 optimal weight: 4.9990 chunk 817 optimal weight: 6.9990 chunk 668 optimal weight: 8.9990 chunk 270 optimal weight: 0.9980 chunk 983 optimal weight: 20.0000 chunk 1062 optimal weight: 9.9990 chunk 875 optimal weight: 1.9990 chunk 975 optimal weight: 0.0470 chunk 335 optimal weight: 9.9990 chunk 788 optimal weight: 4.9990 overall best weight: 1.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 60 GLN BA 99 GLN BD 41 ASN BE 56 ASN BL 236 GLN BM 277 ASN BN 97 HIS ** BN 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BN 201 GLN ** BO 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BP 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BQ 103 HIS BS 113 ASN BT 99 ASN ** BU 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BU 138 GLN ** BV 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BV 147 ASN BV 155 GLN ** BW 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BX 209 GLN BZ 80 HIS ** BZ 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BZ 122 ASN Be 45 ASN ** Bf 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bi 148 HIS ** Bi 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bm 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bm 343 GLN ** Bn 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bo 230 ASN Bo 294 GLN Bp 143 GLN Br 44 ASN ** Bv 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bx 141 ASN Aa 164 ASN ** Aa 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 202 GLN Aa 250 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 118908 Z= 0.196 Angle : 0.549 14.987 169080 Z= 0.283 Chirality : 0.037 0.230 19886 Planarity : 0.004 0.122 15405 Dihedral : 18.222 179.808 34229 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.82 % Favored : 97.16 % Rotamer: Outliers : 2.79 % Allowed : 11.20 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.09), residues: 9255 helix: 1.47 (0.09), residues: 3209 sheet: 0.32 (0.15), residues: 1238 loop : -0.38 (0.09), residues: 4808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRPBp 121 HIS 0.012 0.001 HISBP 150 PHE 0.025 0.001 PHEBy 99 TYR 0.023 0.001 TYRBm 176 ARG 0.013 0.000 ARGBv 146 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18510 Ramachandran restraints generated. 9255 Oldfield, 0 Emsley, 9255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18510 Ramachandran restraints generated. 9255 Oldfield, 0 Emsley, 9255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1426 residues out of total 8262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 1197 time to evaluate : 7.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 54 LYS cc_start: 0.8654 (mttt) cc_final: 0.8312 (mttp) REVERT: BB 12 LEU cc_start: 0.8298 (tt) cc_final: 0.7543 (mt) REVERT: BB 58 GLU cc_start: 0.8140 (tp30) cc_final: 0.7919 (tp30) REVERT: BC 32 LYS cc_start: 0.6791 (mttt) cc_final: 0.6521 (mmmt) REVERT: BC 111 SER cc_start: 0.8073 (m) cc_final: 0.7868 (p) REVERT: BC 149 ARG cc_start: 0.6224 (tmm-80) cc_final: 0.5983 (ttp80) REVERT: BC 202 MET cc_start: 0.7165 (ptp) cc_final: 0.6778 (ptp) REVERT: BE 5 LYS cc_start: 0.8319 (tttp) cc_final: 0.7979 (ttmt) REVERT: BE 71 TYR cc_start: 0.8413 (m-10) cc_final: 0.8113 (m-80) REVERT: BE 136 ASP cc_start: 0.8311 (m-30) cc_final: 0.7753 (t0) REVERT: BE 150 LYS cc_start: 0.7503 (tttm) cc_final: 0.6907 (mtmm) REVERT: BF 75 ASN cc_start: 0.8631 (t0) cc_final: 0.7962 (t0) REVERT: BF 113 MET cc_start: 0.8745 (tmm) cc_final: 0.8275 (tmm) REVERT: BF 213 MET cc_start: 0.8615 (mtm) cc_final: 0.8289 (mtp) REVERT: BG 35 LYS cc_start: 0.8158 (mttt) cc_final: 0.7733 (mtpp) REVERT: BG 40 ARG cc_start: 0.7835 (ttm170) cc_final: 0.7236 (ttm170) REVERT: BG 88 MET cc_start: 0.8336 (ptp) cc_final: 0.7839 (ptp) REVERT: BH 136 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8463 (mm-30) REVERT: BH 153 THR cc_start: 0.9475 (p) cc_final: 0.8894 (t) REVERT: BH 175 ILE cc_start: 0.8716 (mm) cc_final: 0.8336 (mt) REVERT: BH 176 GLU cc_start: 0.7953 (mp0) cc_final: 0.7664 (mm-30) REVERT: BI 21 MET cc_start: 0.6107 (mmm) cc_final: 0.5798 (mtp) REVERT: BI 57 VAL cc_start: 0.8267 (m) cc_final: 0.7826 (t) REVERT: BK 100 ARG cc_start: 0.8386 (mmm-85) cc_final: 0.7994 (mmt-90) REVERT: BL 235 MET cc_start: 0.8482 (ttp) cc_final: 0.8213 (ttp) REVERT: BM 81 LYS cc_start: 0.7463 (mttt) cc_final: 0.6730 (mmtm) REVERT: BM 275 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7135 (ttp-170) REVERT: BN 50 LYS cc_start: 0.7427 (mmmt) cc_final: 0.6425 (mmtt) REVERT: BN 119 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7718 (mt-10) REVERT: BN 205 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8152 (mp0) REVERT: BO 137 LYS cc_start: 0.7232 (mttt) cc_final: 0.7006 (pttt) REVERT: BP 75 GLU cc_start: 0.6722 (mm-30) cc_final: 0.6325 (mt-10) REVERT: BP 82 LEU cc_start: 0.8327 (mm) cc_final: 0.8124 (mm) REVERT: BP 95 MET cc_start: 0.6804 (ttp) cc_final: 0.5855 (ttp) REVERT: BP 107 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7375 (pm20) REVERT: BQ 19 MET cc_start: 0.5213 (mmm) cc_final: 0.4424 (mmm) REVERT: BQ 51 LYS cc_start: 0.5413 (mttp) cc_final: 0.5025 (pptt) REVERT: BQ 52 GLU cc_start: 0.6140 (pt0) cc_final: 0.5575 (pt0) REVERT: BQ 103 HIS cc_start: 0.8025 (m170) cc_final: 0.7806 (m-70) REVERT: BR 67 PHE cc_start: 0.9139 (OUTLIER) cc_final: 0.8821 (m-80) REVERT: BS 66 VAL cc_start: 0.9477 (p) cc_final: 0.9252 (m) REVERT: BT 235 GLU cc_start: 0.6764 (mm-30) cc_final: 0.6461 (mm-30) REVERT: BT 242 TYR cc_start: 0.7020 (p90) cc_final: 0.5982 (p90) REVERT: BU 224 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8312 (mp) REVERT: BV 114 ASN cc_start: 0.8647 (t0) cc_final: 0.8195 (t0) REVERT: BW 98 ASN cc_start: 0.8477 (p0) cc_final: 0.7748 (p0) REVERT: BW 100 GLN cc_start: 0.8054 (mt0) cc_final: 0.7763 (pt0) REVERT: BX 244 ARG cc_start: 0.8648 (mmm-85) cc_final: 0.8071 (mmm160) REVERT: BY 148 HIS cc_start: 0.7494 (t-90) cc_final: 0.7289 (t-170) REVERT: Bc 73 MET cc_start: 0.6961 (mmm) cc_final: 0.5605 (ttm) REVERT: Bc 99 MET cc_start: 0.7024 (mtm) cc_final: 0.6641 (mmt) REVERT: Bc 131 ARG cc_start: 0.7979 (ptp90) cc_final: 0.7750 (ptp90) REVERT: Bc 133 SER cc_start: 0.8723 (m) cc_final: 0.8168 (t) REVERT: Bd 48 THR cc_start: 0.8132 (m) cc_final: 0.7797 (p) REVERT: Bd 49 TYR cc_start: 0.7901 (p90) cc_final: 0.7647 (p90) REVERT: Bd 66 HIS cc_start: 0.8534 (OUTLIER) cc_final: 0.8029 (t-170) REVERT: Bd 70 ARG cc_start: 0.7185 (ttm-80) cc_final: 0.6741 (ttp-110) REVERT: Bd 90 ARG cc_start: 0.7743 (mtt180) cc_final: 0.6873 (tmm160) REVERT: Be 12 ILE cc_start: 0.8991 (mt) cc_final: 0.8750 (mm) REVERT: Bf 38 GLU cc_start: 0.4966 (mt-10) cc_final: 0.4050 (tp30) REVERT: Bf 99 GLU cc_start: 0.8630 (pt0) cc_final: 0.8213 (tt0) REVERT: Bg 36 GLU cc_start: 0.8195 (pt0) cc_final: 0.7874 (pm20) REVERT: Bg 81 GLN cc_start: 0.7078 (mm-40) cc_final: 0.6841 (tt0) REVERT: Bh 37 GLU cc_start: 0.7238 (mm-30) cc_final: 0.6969 (mm-30) REVERT: Bh 134 LYS cc_start: 0.6426 (ptmm) cc_final: 0.6199 (ptmm) REVERT: Bj 101 LYS cc_start: 0.5963 (mttt) cc_final: 0.5621 (tppt) REVERT: Bj 107 LYS cc_start: 0.6963 (mttt) cc_final: 0.6377 (pttm) REVERT: Bj 262 MET cc_start: 0.4193 (OUTLIER) cc_final: 0.3643 (ptp) REVERT: Bm 72 ARG cc_start: 0.7914 (ttm110) cc_final: 0.7162 (ptm160) REVERT: Bn 27 ARG cc_start: 0.7828 (tpt170) cc_final: 0.7401 (ttp-170) REVERT: Bn 160 ASP cc_start: 0.8051 (m-30) cc_final: 0.7811 (m-30) REVERT: Bo 46 ASN cc_start: 0.8858 (m-40) cc_final: 0.8504 (m110) REVERT: Bo 140 TRP cc_start: 0.8530 (OUTLIER) cc_final: 0.6146 (m-90) REVERT: Bo 176 PHE cc_start: 0.8264 (p90) cc_final: 0.7871 (p90) REVERT: Bo 244 ASN cc_start: 0.7119 (m-40) cc_final: 0.6702 (t0) REVERT: Bo 310 ASN cc_start: 0.7865 (m-40) cc_final: 0.7322 (t0) REVERT: Bp 71 ARG cc_start: 0.7089 (mtt180) cc_final: 0.6353 (tpt-90) REVERT: Bp 97 LYS cc_start: 0.7014 (tppt) cc_final: 0.6610 (tptp) REVERT: Bp 124 TYR cc_start: 0.8121 (t80) cc_final: 0.7804 (t80) REVERT: Bq 48 PHE cc_start: 0.8925 (t80) cc_final: 0.8579 (t80) REVERT: Bq 50 GLN cc_start: 0.8926 (tt0) cc_final: 0.8525 (tt0) REVERT: Br 56 ARG cc_start: 0.8529 (mmt90) cc_final: 0.8065 (tpp80) REVERT: Br 73 LYS cc_start: 0.8985 (ptpt) cc_final: 0.8635 (ptmm) REVERT: Bt 45 LEU cc_start: 0.8367 (mt) cc_final: 0.8084 (tt) REVERT: Bt 97 TYR cc_start: 0.8301 (t80) cc_final: 0.8057 (t80) REVERT: Bu 110 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7062 (mt-10) REVERT: Bu 174 TRP cc_start: 0.8218 (t-100) cc_final: 0.7596 (t-100) REVERT: Bu 226 ASP cc_start: 0.7137 (t0) cc_final: 0.6452 (t0) REVERT: Bu 244 GLU cc_start: 0.7522 (mp0) cc_final: 0.6933 (mp0) REVERT: Bu 261 MET cc_start: 0.6265 (ttm) cc_final: 0.5757 (ttp) REVERT: Bu 292 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7170 (mm-30) REVERT: Bv 58 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7444 (mm) REVERT: Bv 75 GLN cc_start: 0.7672 (mt0) cc_final: 0.7259 (tp40) REVERT: Bv 78 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8177 (mt-10) REVERT: Bv 165 LEU cc_start: 0.5898 (OUTLIER) cc_final: 0.5025 (mp) REVERT: Bv 200 MET cc_start: 0.5411 (mtm) cc_final: 0.5158 (mtm) REVERT: Bv 278 ASP cc_start: 0.6848 (OUTLIER) cc_final: 0.5494 (t0) REVERT: Bw 86 TYR cc_start: 0.6665 (m-80) cc_final: 0.6015 (m-80) REVERT: Bw 127 MET cc_start: 0.8874 (mmm) cc_final: 0.8629 (mmm) REVERT: Bw 144 MET cc_start: 0.6199 (mmt) cc_final: 0.5966 (mmm) REVERT: Bw 186 VAL cc_start: 0.8684 (m) cc_final: 0.8358 (p) REVERT: By 61 TYR cc_start: 0.7665 (t80) cc_final: 0.7439 (t80) REVERT: Bz 41 ARG cc_start: 0.7823 (ptm160) cc_final: 0.7545 (ttt-90) REVERT: Bz 83 TRP cc_start: 0.8459 (t60) cc_final: 0.7777 (t60) REVERT: Aa 236 HIS cc_start: 0.5979 (t-90) cc_final: 0.5680 (t70) REVERT: Aa 409 GLU cc_start: 0.5646 (tp30) cc_final: 0.5346 (mm-30) REVERT: Aa 423 ARG cc_start: 0.5942 (mtt90) cc_final: 0.5340 (tpp80) outliers start: 229 outliers final: 152 residues processed: 1335 average time/residue: 0.9723 time to fit residues: 2229.6301 Evaluate side-chains 1264 residues out of total 8262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 1101 time to evaluate : 7.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 170 CYS Chi-restraints excluded: chain BA residue 198 ILE Chi-restraints excluded: chain BB residue 113 GLU Chi-restraints excluded: chain BC residue 60 ASP Chi-restraints excluded: chain BC residue 147 SER Chi-restraints excluded: chain BC residue 166 VAL Chi-restraints excluded: chain BC residue 181 ASP Chi-restraints excluded: chain BD residue 117 VAL Chi-restraints excluded: chain BE residue 22 SER Chi-restraints excluded: chain BE residue 128 THR Chi-restraints excluded: chain BF residue 79 GLU Chi-restraints excluded: chain BF residue 88 THR Chi-restraints excluded: chain BF residue 160 THR Chi-restraints excluded: chain BF residue 215 ILE Chi-restraints excluded: chain BG residue 146 VAL Chi-restraints excluded: chain BH residue 157 VAL Chi-restraints excluded: chain BI residue 49 VAL Chi-restraints excluded: chain BI residue 50 VAL Chi-restraints excluded: chain BJ residue 92 SER Chi-restraints excluded: chain BL residue 68 SER Chi-restraints excluded: chain BL residue 91 ILE Chi-restraints excluded: chain BL residue 175 VAL Chi-restraints excluded: chain BM residue 63 GLN Chi-restraints excluded: chain BM residue 136 GLU Chi-restraints excluded: chain BM residue 153 SER Chi-restraints excluded: chain BM residue 275 ARG Chi-restraints excluded: chain BM residue 279 LYS Chi-restraints excluded: chain BM residue 296 LEU Chi-restraints excluded: chain BM residue 313 ASN Chi-restraints excluded: chain BN residue 94 ASP Chi-restraints excluded: chain BN residue 106 PHE Chi-restraints excluded: chain BN residue 129 VAL Chi-restraints excluded: chain BN residue 151 VAL Chi-restraints excluded: chain BN residue 205 GLU Chi-restraints excluded: chain BN residue 262 THR Chi-restraints excluded: chain BO residue 53 THR Chi-restraints excluded: chain BO residue 93 ASN Chi-restraints excluded: chain BO residue 184 LEU Chi-restraints excluded: chain BO residue 238 VAL Chi-restraints excluded: chain BP residue 30 SER Chi-restraints excluded: chain BP residue 99 CYS Chi-restraints excluded: chain BP residue 107 GLU Chi-restraints excluded: chain BP residue 144 LEU Chi-restraints excluded: chain BP residue 150 HIS Chi-restraints excluded: chain BP residue 164 MET Chi-restraints excluded: chain BQ residue 58 LYS Chi-restraints excluded: chain BQ residue 128 ASP Chi-restraints excluded: chain BQ residue 143 SER Chi-restraints excluded: chain BR residue 67 PHE Chi-restraints excluded: chain BS residue 48 THR Chi-restraints excluded: chain BS residue 71 ASP Chi-restraints excluded: chain BS residue 89 HIS Chi-restraints excluded: chain BS residue 115 VAL Chi-restraints excluded: chain BS residue 126 SER Chi-restraints excluded: chain BT residue 33 SER Chi-restraints excluded: chain BU residue 59 VAL Chi-restraints excluded: chain BU residue 113 MET Chi-restraints excluded: chain BU residue 121 LEU Chi-restraints excluded: chain BU residue 224 LEU Chi-restraints excluded: chain BW residue 74 SER Chi-restraints excluded: chain BW residue 101 VAL Chi-restraints excluded: chain BW residue 104 SER Chi-restraints excluded: chain BW residue 157 SER Chi-restraints excluded: chain BX residue 154 THR Chi-restraints excluded: chain BX residue 177 VAL Chi-restraints excluded: chain BX residue 265 LEU Chi-restraints excluded: chain BX residue 286 ILE Chi-restraints excluded: chain BX residue 289 SER Chi-restraints excluded: chain BY residue 12 SER Chi-restraints excluded: chain BY residue 59 LEU Chi-restraints excluded: chain BY residue 63 SER Chi-restraints excluded: chain BY residue 76 SER Chi-restraints excluded: chain BY residue 87 ILE Chi-restraints excluded: chain BZ residue 58 THR Chi-restraints excluded: chain BZ residue 69 VAL Chi-restraints excluded: chain BZ residue 84 VAL Chi-restraints excluded: chain BZ residue 113 THR Chi-restraints excluded: chain BZ residue 122 ASN Chi-restraints excluded: chain BZ residue 158 VAL Chi-restraints excluded: chain Bb residue 8 LEU Chi-restraints excluded: chain Bb residue 30 THR Chi-restraints excluded: chain Bb residue 34 LEU Chi-restraints excluded: chain Bb residue 45 THR Chi-restraints excluded: chain Bb residue 75 ILE Chi-restraints excluded: chain Bd residue 66 HIS Chi-restraints excluded: chain Be residue 50 SER Chi-restraints excluded: chain Be residue 101 TRP Chi-restraints excluded: chain Bf residue 110 ILE Chi-restraints excluded: chain Bg residue 41 ASP Chi-restraints excluded: chain Bh residue 56 THR Chi-restraints excluded: chain Bh residue 86 VAL Chi-restraints excluded: chain Bh residue 140 VAL Chi-restraints excluded: chain Bh residue 188 SER Chi-restraints excluded: chain Bh residue 192 LEU Chi-restraints excluded: chain Bi residue 76 VAL Chi-restraints excluded: chain Bi residue 260 CYS Chi-restraints excluded: chain Bi residue 274 ASN Chi-restraints excluded: chain Bi residue 350 VAL Chi-restraints excluded: chain Bi residue 399 ILE Chi-restraints excluded: chain Bi residue 403 ASN Chi-restraints excluded: chain Bi residue 410 ASP Chi-restraints excluded: chain Bj residue 262 MET Chi-restraints excluded: chain Bl residue 100 MET Chi-restraints excluded: chain Bm residue 38 THR Chi-restraints excluded: chain Bm residue 64 MET Chi-restraints excluded: chain Bm residue 101 ASP Chi-restraints excluded: chain Bm residue 117 VAL Chi-restraints excluded: chain Bm residue 137 LEU Chi-restraints excluded: chain Bm residue 151 ASP Chi-restraints excluded: chain Bm residue 166 SER Chi-restraints excluded: chain Bm residue 248 THR Chi-restraints excluded: chain Bm residue 256 PHE Chi-restraints excluded: chain Bm residue 270 VAL Chi-restraints excluded: chain Bm residue 344 SER Chi-restraints excluded: chain Bm residue 379 ASP Chi-restraints excluded: chain Bm residue 398 VAL Chi-restraints excluded: chain Bn residue 32 LEU Chi-restraints excluded: chain Bn residue 151 LEU Chi-restraints excluded: chain Bn residue 205 THR Chi-restraints excluded: chain Bn residue 222 ASP Chi-restraints excluded: chain Bo residue 126 THR Chi-restraints excluded: chain Bo residue 140 TRP Chi-restraints excluded: chain Bo residue 215 THR Chi-restraints excluded: chain Bo residue 260 VAL Chi-restraints excluded: chain Bo residue 290 VAL Chi-restraints excluded: chain Bp residue 87 ASP Chi-restraints excluded: chain Bp residue 94 PHE Chi-restraints excluded: chain Bp residue 167 SER Chi-restraints excluded: chain Bq residue 39 THR Chi-restraints excluded: chain Br residue 38 SER Chi-restraints excluded: chain Br residue 41 ASP Chi-restraints excluded: chain Br residue 93 LYS Chi-restraints excluded: chain Br residue 115 MET Chi-restraints excluded: chain Bs residue 75 VAL Chi-restraints excluded: chain Bs residue 84 VAL Chi-restraints excluded: chain Bs residue 93 SER Chi-restraints excluded: chain Bs residue 126 ILE Chi-restraints excluded: chain Bs residue 139 THR Chi-restraints excluded: chain Bt residue 85 LEU Chi-restraints excluded: chain Bt residue 93 VAL Chi-restraints excluded: chain Bt residue 148 LEU Chi-restraints excluded: chain Bt residue 176 GLU Chi-restraints excluded: chain Bt residue 224 THR Chi-restraints excluded: chain Bt residue 265 THR Chi-restraints excluded: chain Bu residue 76 ILE Chi-restraints excluded: chain Bu residue 218 THR Chi-restraints excluded: chain Bu residue 266 ILE Chi-restraints excluded: chain Bv residue 58 LEU Chi-restraints excluded: chain Bv residue 157 LEU Chi-restraints excluded: chain Bv residue 165 LEU Chi-restraints excluded: chain Bv residue 179 GLN Chi-restraints excluded: chain Bv residue 278 ASP Chi-restraints excluded: chain Bw residue 90 VAL Chi-restraints excluded: chain Bw residue 102 LEU Chi-restraints excluded: chain Bw residue 149 VAL Chi-restraints excluded: chain Bw residue 182 VAL Chi-restraints excluded: chain Bw residue 204 LEU Chi-restraints excluded: chain Bz residue 43 VAL Chi-restraints excluded: chain Bz residue 100 ASN Chi-restraints excluded: chain Bz residue 115 SER Chi-restraints excluded: chain Aa residue 284 VAL Chi-restraints excluded: chain Aa residue 314 HIS Chi-restraints excluded: chain Aa residue 391 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1081 random chunks: chunk 971 optimal weight: 7.9990 chunk 739 optimal weight: 6.9990 chunk 510 optimal weight: 0.0270 chunk 108 optimal weight: 7.9990 chunk 469 optimal weight: 4.9990 chunk 660 optimal weight: 0.0980 chunk 986 optimal weight: 0.0270 chunk 1044 optimal weight: 8.9990 chunk 515 optimal weight: 8.9990 chunk 935 optimal weight: 5.9990 chunk 281 optimal weight: 9.9990 overall best weight: 2.2300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 60 GLN BB 82 HIS BF 112 ASN BM 115 GLN BN 58 HIS BN 97 HIS ** BN 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BP 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BP 150 HIS ** BS 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BT 99 ASN BU 138 GLN BV 155 GLN ** BW 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BZ 109 GLN BZ 122 ASN ** Bf 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bf 162 GLN Bg 79 GLN Bh 196 HIS ** Bi 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bj 272 GLN Bm 109 GLN ** Bm 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bn 234 HIS Bo 230 ASN ** Bp 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bv 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bx 92 HIS Bz 33 HIS Aa 107 ASN ** Aa 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 118908 Z= 0.232 Angle : 0.555 14.668 169080 Z= 0.285 Chirality : 0.037 0.227 19886 Planarity : 0.004 0.123 15405 Dihedral : 18.233 179.323 34229 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.43 % Favored : 96.54 % Rotamer: Outliers : 3.26 % Allowed : 11.84 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.09), residues: 9255 helix: 1.53 (0.09), residues: 3208 sheet: 0.25 (0.15), residues: 1245 loop : -0.41 (0.09), residues: 4802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRPAa 70 HIS 0.008 0.001 HISBB 82 PHE 0.022 0.001 PHEBp 171 TYR 0.027 0.001 TYRBm 176 ARG 0.009 0.000 ARGBN 60 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18510 Ramachandran restraints generated. 9255 Oldfield, 0 Emsley, 9255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18510 Ramachandran restraints generated. 9255 Oldfield, 0 Emsley, 9255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1411 residues out of total 8262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 268 poor density : 1143 time to evaluate : 7.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 54 LYS cc_start: 0.8666 (mttt) cc_final: 0.8339 (mttp) REVERT: BA 105 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7060 (tt0) REVERT: BB 12 LEU cc_start: 0.8313 (tt) cc_final: 0.7526 (mt) REVERT: BC 111 SER cc_start: 0.7898 (m) cc_final: 0.7690 (p) REVERT: BC 127 ASP cc_start: 0.5313 (t70) cc_final: 0.4505 (t70) REVERT: BC 129 LYS cc_start: 0.5088 (mptt) cc_final: 0.4861 (mmtt) REVERT: BE 5 LYS cc_start: 0.8369 (tttp) cc_final: 0.8121 (ttmt) REVERT: BE 71 TYR cc_start: 0.8436 (m-10) cc_final: 0.8101 (m-80) REVERT: BE 150 LYS cc_start: 0.7470 (tttm) cc_final: 0.6838 (mtmm) REVERT: BF 75 ASN cc_start: 0.8674 (t0) cc_final: 0.7939 (t0) REVERT: BF 113 MET cc_start: 0.8762 (tmm) cc_final: 0.8024 (tmm) REVERT: BF 194 LYS cc_start: 0.7553 (tttt) cc_final: 0.7210 (ptpt) REVERT: BF 213 MET cc_start: 0.8632 (mtm) cc_final: 0.8277 (mtp) REVERT: BG 35 LYS cc_start: 0.8149 (mttt) cc_final: 0.7763 (mtpp) REVERT: BG 40 ARG cc_start: 0.7849 (ttm170) cc_final: 0.7264 (ttm170) REVERT: BG 88 MET cc_start: 0.8311 (ptp) cc_final: 0.7803 (ptp) REVERT: BH 136 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8433 (mm-30) REVERT: BH 153 THR cc_start: 0.9481 (p) cc_final: 0.8874 (t) REVERT: BH 175 ILE cc_start: 0.8723 (mm) cc_final: 0.8368 (mt) REVERT: BH 176 GLU cc_start: 0.7945 (mp0) cc_final: 0.7661 (mm-30) REVERT: BI 21 MET cc_start: 0.6020 (mmm) cc_final: 0.5721 (mtp) REVERT: BK 100 ARG cc_start: 0.8317 (mmm-85) cc_final: 0.8117 (mmm160) REVERT: BL 168 ASP cc_start: 0.8650 (p0) cc_final: 0.8335 (p0) REVERT: BL 235 MET cc_start: 0.8505 (ttp) cc_final: 0.8241 (ttp) REVERT: BM 81 LYS cc_start: 0.7581 (mttt) cc_final: 0.6796 (mmtm) REVERT: BN 50 LYS cc_start: 0.7389 (mmmt) cc_final: 0.6439 (mmtt) REVERT: BN 205 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8184 (mp0) REVERT: BO 137 LYS cc_start: 0.7400 (mttt) cc_final: 0.7083 (pttt) REVERT: BP 75 GLU cc_start: 0.6759 (mm-30) cc_final: 0.6386 (mt-10) REVERT: BP 82 LEU cc_start: 0.8274 (mm) cc_final: 0.7804 (mt) REVERT: BP 95 MET cc_start: 0.6710 (ttp) cc_final: 0.5581 (tmm) REVERT: BP 107 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7276 (pm20) REVERT: BP 115 GLN cc_start: 0.7172 (mm110) cc_final: 0.6862 (mm110) REVERT: BQ 19 MET cc_start: 0.5295 (mmm) cc_final: 0.4855 (mmm) REVERT: BQ 52 GLU cc_start: 0.6233 (pt0) cc_final: 0.5696 (mt-10) REVERT: BR 67 PHE cc_start: 0.9166 (OUTLIER) cc_final: 0.8828 (m-80) REVERT: BS 43 ASN cc_start: 0.8258 (p0) cc_final: 0.8018 (p0) REVERT: BS 142 GLN cc_start: 0.8194 (tp40) cc_final: 0.7984 (tp40) REVERT: BT 61 THR cc_start: 0.8757 (m) cc_final: 0.8541 (m) REVERT: BT 235 GLU cc_start: 0.6906 (mm-30) cc_final: 0.6570 (mm-30) REVERT: BT 236 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7910 (tp) REVERT: BV 114 ASN cc_start: 0.8635 (t0) cc_final: 0.8167 (t0) REVERT: BW 98 ASN cc_start: 0.8510 (p0) cc_final: 0.7785 (p0) REVERT: BW 100 GLN cc_start: 0.7987 (mt0) cc_final: 0.7696 (pt0) REVERT: BX 99 MET cc_start: 0.8804 (mtp) cc_final: 0.8564 (mtm) REVERT: BX 244 ARG cc_start: 0.8657 (mmm-85) cc_final: 0.7988 (mmm160) REVERT: BY 148 HIS cc_start: 0.7421 (t-90) cc_final: 0.7148 (t-170) REVERT: Bc 73 MET cc_start: 0.7006 (mmm) cc_final: 0.5702 (ttm) REVERT: Bc 131 ARG cc_start: 0.7978 (ptp90) cc_final: 0.7637 (ptp90) REVERT: Bc 133 SER cc_start: 0.8788 (m) cc_final: 0.8270 (t) REVERT: Bd 48 THR cc_start: 0.8216 (m) cc_final: 0.7920 (p) REVERT: Bd 66 HIS cc_start: 0.8540 (OUTLIER) cc_final: 0.7940 (t-170) REVERT: Bd 70 ARG cc_start: 0.7226 (ttm-80) cc_final: 0.6640 (ttp-110) REVERT: Bd 90 ARG cc_start: 0.7731 (mtt180) cc_final: 0.6840 (tmm160) REVERT: Be 12 ILE cc_start: 0.8993 (mt) cc_final: 0.8750 (mm) REVERT: Bf 38 GLU cc_start: 0.4914 (mt-10) cc_final: 0.4027 (tp30) REVERT: Bf 99 GLU cc_start: 0.8604 (pt0) cc_final: 0.8202 (tt0) REVERT: Bg 81 GLN cc_start: 0.7104 (mm-40) cc_final: 0.6856 (tt0) REVERT: Bh 37 GLU cc_start: 0.7352 (mm-30) cc_final: 0.7070 (mm-30) REVERT: Bh 73 CYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7747 (p) REVERT: Bi 172 ASP cc_start: 0.7612 (m-30) cc_final: 0.7254 (m-30) REVERT: Bj 101 LYS cc_start: 0.5973 (mttt) cc_final: 0.5631 (tppt) REVERT: Bj 107 LYS cc_start: 0.6982 (mttt) cc_final: 0.6421 (pttm) REVERT: Bm 72 ARG cc_start: 0.7929 (ttm110) cc_final: 0.7179 (ptm160) REVERT: Bm 262 THR cc_start: 0.9165 (m) cc_final: 0.8940 (m) REVERT: Bn 27 ARG cc_start: 0.7855 (tpt170) cc_final: 0.7399 (ttp-170) REVERT: Bn 160 ASP cc_start: 0.7992 (m-30) cc_final: 0.7694 (m-30) REVERT: Bo 46 ASN cc_start: 0.8891 (m-40) cc_final: 0.8552 (m110) REVERT: Bo 140 TRP cc_start: 0.8503 (OUTLIER) cc_final: 0.6231 (m-90) REVERT: Bo 176 PHE cc_start: 0.8233 (p90) cc_final: 0.7778 (p90) REVERT: Bo 244 ASN cc_start: 0.7111 (m-40) cc_final: 0.6705 (t0) REVERT: Bo 310 ASN cc_start: 0.7938 (m-40) cc_final: 0.7372 (t0) REVERT: Bp 71 ARG cc_start: 0.7125 (mtt180) cc_final: 0.6375 (tpt-90) REVERT: Bp 97 LYS cc_start: 0.7111 (tppt) cc_final: 0.6696 (tptp) REVERT: Bq 48 PHE cc_start: 0.8971 (t80) cc_final: 0.8609 (t80) REVERT: Br 51 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8790 (tp) REVERT: Br 56 ARG cc_start: 0.8540 (mmt90) cc_final: 0.8203 (tpp80) REVERT: Br 73 LYS cc_start: 0.9009 (ptpt) cc_final: 0.8552 (ptmm) REVERT: Bt 45 LEU cc_start: 0.8392 (mt) cc_final: 0.8122 (tt) REVERT: Bt 59 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7406 (mtm180) REVERT: Bt 183 GLU cc_start: 0.7288 (mt-10) cc_final: 0.6817 (tt0) REVERT: Bu 174 TRP cc_start: 0.8163 (t-100) cc_final: 0.7613 (t-100) REVERT: Bu 226 ASP cc_start: 0.7079 (t0) cc_final: 0.6386 (t0) REVERT: Bu 238 VAL cc_start: 0.7490 (OUTLIER) cc_final: 0.7283 (m) REVERT: Bu 244 GLU cc_start: 0.7483 (mp0) cc_final: 0.6879 (mp0) REVERT: Bu 261 MET cc_start: 0.6233 (ttm) cc_final: 0.5717 (ttp) REVERT: Bu 292 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7183 (mm-30) REVERT: Bv 53 LEU cc_start: 0.6274 (tp) cc_final: 0.6024 (tp) REVERT: Bv 58 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7464 (mm) REVERT: Bv 75 GLN cc_start: 0.7693 (mt0) cc_final: 0.7313 (tp40) REVERT: Bv 78 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8077 (mt-10) REVERT: Bv 200 MET cc_start: 0.5422 (mtm) cc_final: 0.5170 (mtm) REVERT: Bv 238 LEU cc_start: 0.6485 (mt) cc_final: 0.5531 (pp) REVERT: Bv 278 ASP cc_start: 0.6790 (OUTLIER) cc_final: 0.5445 (t0) REVERT: Bw 144 MET cc_start: 0.6205 (mmt) cc_final: 0.5958 (mmm) REVERT: Bx 141 ASN cc_start: 0.8097 (OUTLIER) cc_final: 0.7503 (t0) REVERT: By 121 MET cc_start: 0.7086 (mmp) cc_final: 0.6784 (mmt) REVERT: By 159 TYR cc_start: 0.6723 (OUTLIER) cc_final: 0.5925 (m-80) REVERT: Bz 41 ARG cc_start: 0.7840 (ptm160) cc_final: 0.7552 (ttt-90) REVERT: Bz 83 TRP cc_start: 0.8454 (t60) cc_final: 0.7790 (t60) REVERT: Aa 214 TYR cc_start: 0.8134 (t80) cc_final: 0.7701 (t80) REVERT: Aa 236 HIS cc_start: 0.5672 (t-90) cc_final: 0.5364 (t70) REVERT: Aa 409 GLU cc_start: 0.5261 (tp30) cc_final: 0.5050 (mm-30) outliers start: 268 outliers final: 190 residues processed: 1311 average time/residue: 0.9610 time to fit residues: 2176.4612 Evaluate side-chains 1284 residues out of total 8262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 1079 time to evaluate : 7.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 105 GLU Chi-restraints excluded: chain BA residue 170 CYS Chi-restraints excluded: chain BA residue 198 ILE Chi-restraints excluded: chain BB residue 91 ASP Chi-restraints excluded: chain BB residue 113 GLU Chi-restraints excluded: chain BC residue 60 ASP Chi-restraints excluded: chain BC residue 147 SER Chi-restraints excluded: chain BC residue 166 VAL Chi-restraints excluded: chain BC residue 181 ASP Chi-restraints excluded: chain BC residue 183 LEU Chi-restraints excluded: chain BD residue 67 LEU Chi-restraints excluded: chain BD residue 83 LEU Chi-restraints excluded: chain BD residue 109 SER Chi-restraints excluded: chain BD residue 141 THR Chi-restraints excluded: chain BE residue 22 SER Chi-restraints excluded: chain BE residue 128 THR Chi-restraints excluded: chain BF residue 79 GLU Chi-restraints excluded: chain BF residue 88 THR Chi-restraints excluded: chain BF residue 160 THR Chi-restraints excluded: chain BF residue 174 ILE Chi-restraints excluded: chain BG residue 146 VAL Chi-restraints excluded: chain BH residue 157 VAL Chi-restraints excluded: chain BI residue 49 VAL Chi-restraints excluded: chain BI residue 50 VAL Chi-restraints excluded: chain BI residue 59 GLN Chi-restraints excluded: chain BJ residue 92 SER Chi-restraints excluded: chain BK residue 111 ILE Chi-restraints excluded: chain BL residue 68 SER Chi-restraints excluded: chain BL residue 73 THR Chi-restraints excluded: chain BL residue 91 ILE Chi-restraints excluded: chain BL residue 173 MET Chi-restraints excluded: chain BL residue 175 VAL Chi-restraints excluded: chain BL residue 231 SER Chi-restraints excluded: chain BL residue 237 VAL Chi-restraints excluded: chain BL residue 257 VAL Chi-restraints excluded: chain BM residue 153 SER Chi-restraints excluded: chain BM residue 275 ARG Chi-restraints excluded: chain BM residue 279 LYS Chi-restraints excluded: chain BM residue 295 CYS Chi-restraints excluded: chain BM residue 296 LEU Chi-restraints excluded: chain BN residue 94 ASP Chi-restraints excluded: chain BN residue 106 PHE Chi-restraints excluded: chain BN residue 129 VAL Chi-restraints excluded: chain BN residue 151 VAL Chi-restraints excluded: chain BN residue 205 GLU Chi-restraints excluded: chain BN residue 262 THR Chi-restraints excluded: chain BO residue 114 VAL Chi-restraints excluded: chain BO residue 141 GLU Chi-restraints excluded: chain BO residue 238 VAL Chi-restraints excluded: chain BP residue 30 SER Chi-restraints excluded: chain BP residue 99 CYS Chi-restraints excluded: chain BP residue 107 GLU Chi-restraints excluded: chain BP residue 150 HIS Chi-restraints excluded: chain BP residue 164 MET Chi-restraints excluded: chain BQ residue 58 LYS Chi-restraints excluded: chain BQ residue 128 ASP Chi-restraints excluded: chain BQ residue 143 SER Chi-restraints excluded: chain BQ residue 183 LEU Chi-restraints excluded: chain BR residue 31 LEU Chi-restraints excluded: chain BR residue 67 PHE Chi-restraints excluded: chain BS residue 48 THR Chi-restraints excluded: chain BS residue 71 ASP Chi-restraints excluded: chain BS residue 89 HIS Chi-restraints excluded: chain BS residue 126 SER Chi-restraints excluded: chain BT residue 33 SER Chi-restraints excluded: chain BT residue 146 ASP Chi-restraints excluded: chain BT residue 236 LEU Chi-restraints excluded: chain BT residue 243 VAL Chi-restraints excluded: chain BU residue 39 PHE Chi-restraints excluded: chain BU residue 59 VAL Chi-restraints excluded: chain BU residue 113 MET Chi-restraints excluded: chain BU residue 121 LEU Chi-restraints excluded: chain BV residue 9 ILE Chi-restraints excluded: chain BV residue 86 ILE Chi-restraints excluded: chain BV residue 124 ILE Chi-restraints excluded: chain BW residue 101 VAL Chi-restraints excluded: chain BW residue 157 SER Chi-restraints excluded: chain BW residue 166 THR Chi-restraints excluded: chain BX residue 154 THR Chi-restraints excluded: chain BX residue 171 ILE Chi-restraints excluded: chain BX residue 177 VAL Chi-restraints excluded: chain BX residue 265 LEU Chi-restraints excluded: chain BX residue 289 SER Chi-restraints excluded: chain BY residue 12 SER Chi-restraints excluded: chain BY residue 59 LEU Chi-restraints excluded: chain BY residue 63 SER Chi-restraints excluded: chain BY residue 76 SER Chi-restraints excluded: chain BY residue 87 ILE Chi-restraints excluded: chain BZ residue 58 THR Chi-restraints excluded: chain BZ residue 69 VAL Chi-restraints excluded: chain BZ residue 84 VAL Chi-restraints excluded: chain BZ residue 113 THR Chi-restraints excluded: chain BZ residue 158 VAL Chi-restraints excluded: chain Ba residue 71 GLU Chi-restraints excluded: chain Bb residue 8 LEU Chi-restraints excluded: chain Bb residue 30 THR Chi-restraints excluded: chain Bb residue 39 SER Chi-restraints excluded: chain Bb residue 45 THR Chi-restraints excluded: chain Bb residue 75 ILE Chi-restraints excluded: chain Bd residue 58 VAL Chi-restraints excluded: chain Bd residue 66 HIS Chi-restraints excluded: chain Be residue 41 THR Chi-restraints excluded: chain Be residue 97 VAL Chi-restraints excluded: chain Be residue 101 TRP Chi-restraints excluded: chain Bf residue 40 GLN Chi-restraints excluded: chain Bf residue 110 ILE Chi-restraints excluded: chain Bg residue 41 ASP Chi-restraints excluded: chain Bh residue 38 VAL Chi-restraints excluded: chain Bh residue 56 THR Chi-restraints excluded: chain Bh residue 73 CYS Chi-restraints excluded: chain Bh residue 86 VAL Chi-restraints excluded: chain Bh residue 140 VAL Chi-restraints excluded: chain Bh residue 188 SER Chi-restraints excluded: chain Bh residue 192 LEU Chi-restraints excluded: chain Bi residue 76 VAL Chi-restraints excluded: chain Bi residue 132 ASP Chi-restraints excluded: chain Bi residue 184 VAL Chi-restraints excluded: chain Bi residue 260 CYS Chi-restraints excluded: chain Bi residue 274 ASN Chi-restraints excluded: chain Bi residue 350 VAL Chi-restraints excluded: chain Bi residue 369 ASN Chi-restraints excluded: chain Bi residue 399 ILE Chi-restraints excluded: chain Bi residue 403 ASN Chi-restraints excluded: chain Bi residue 410 ASP Chi-restraints excluded: chain Bi residue 418 PHE Chi-restraints excluded: chain Bm residue 38 THR Chi-restraints excluded: chain Bm residue 64 MET Chi-restraints excluded: chain Bm residue 101 ASP Chi-restraints excluded: chain Bm residue 117 VAL Chi-restraints excluded: chain Bm residue 151 ASP Chi-restraints excluded: chain Bm residue 166 SER Chi-restraints excluded: chain Bm residue 203 CYS Chi-restraints excluded: chain Bm residue 248 THR Chi-restraints excluded: chain Bm residue 256 PHE Chi-restraints excluded: chain Bm residue 270 VAL Chi-restraints excluded: chain Bm residue 344 SER Chi-restraints excluded: chain Bm residue 379 ASP Chi-restraints excluded: chain Bm residue 398 VAL Chi-restraints excluded: chain Bn residue 32 LEU Chi-restraints excluded: chain Bn residue 151 LEU Chi-restraints excluded: chain Bn residue 205 THR Chi-restraints excluded: chain Bn residue 226 LEU Chi-restraints excluded: chain Bn residue 276 ASP Chi-restraints excluded: chain Bn residue 279 ILE Chi-restraints excluded: chain Bn residue 302 ASP Chi-restraints excluded: chain Bo residue 126 THR Chi-restraints excluded: chain Bo residue 140 TRP Chi-restraints excluded: chain Bo residue 214 GLU Chi-restraints excluded: chain Bo residue 215 THR Chi-restraints excluded: chain Bo residue 260 VAL Chi-restraints excluded: chain Bo residue 290 VAL Chi-restraints excluded: chain Bp residue 94 PHE Chi-restraints excluded: chain Bp residue 167 SER Chi-restraints excluded: chain Bq residue 39 THR Chi-restraints excluded: chain Br residue 38 SER Chi-restraints excluded: chain Br residue 41 ASP Chi-restraints excluded: chain Br residue 51 LEU Chi-restraints excluded: chain Br residue 59 VAL Chi-restraints excluded: chain Br residue 65 VAL Chi-restraints excluded: chain Br residue 93 LYS Chi-restraints excluded: chain Br residue 115 MET Chi-restraints excluded: chain Bs residue 34 SER Chi-restraints excluded: chain Bs residue 75 VAL Chi-restraints excluded: chain Bs residue 84 VAL Chi-restraints excluded: chain Bs residue 91 CYS Chi-restraints excluded: chain Bs residue 93 SER Chi-restraints excluded: chain Bs residue 113 ILE Chi-restraints excluded: chain Bs residue 126 ILE Chi-restraints excluded: chain Bs residue 139 THR Chi-restraints excluded: chain Bt residue 59 ARG Chi-restraints excluded: chain Bt residue 85 LEU Chi-restraints excluded: chain Bt residue 93 VAL Chi-restraints excluded: chain Bt residue 148 LEU Chi-restraints excluded: chain Bt residue 224 THR Chi-restraints excluded: chain Bt residue 231 MET Chi-restraints excluded: chain Bt residue 265 THR Chi-restraints excluded: chain Bu residue 76 ILE Chi-restraints excluded: chain Bu residue 143 ASP Chi-restraints excluded: chain Bu residue 165 THR Chi-restraints excluded: chain Bu residue 218 THR Chi-restraints excluded: chain Bu residue 238 VAL Chi-restraints excluded: chain Bu residue 266 ILE Chi-restraints excluded: chain Bv residue 58 LEU Chi-restraints excluded: chain Bv residue 131 PHE Chi-restraints excluded: chain Bv residue 176 SER Chi-restraints excluded: chain Bv residue 179 GLN Chi-restraints excluded: chain Bv residue 278 ASP Chi-restraints excluded: chain Bw residue 90 VAL Chi-restraints excluded: chain Bw residue 108 GLN Chi-restraints excluded: chain Bw residue 132 MET Chi-restraints excluded: chain Bw residue 149 VAL Chi-restraints excluded: chain Bw residue 182 VAL Chi-restraints excluded: chain Bx residue 107 MET Chi-restraints excluded: chain Bx residue 141 ASN Chi-restraints excluded: chain Bx residue 146 THR Chi-restraints excluded: chain By residue 128 LEU Chi-restraints excluded: chain By residue 159 TYR Chi-restraints excluded: chain Bz residue 43 VAL Chi-restraints excluded: chain Bz residue 100 ASN Chi-restraints excluded: chain Bz residue 115 SER Chi-restraints excluded: chain Aa residue 126 THR Chi-restraints excluded: chain Aa residue 284 VAL Chi-restraints excluded: chain Aa residue 314 HIS Chi-restraints excluded: chain Aa residue 391 THR Chi-restraints excluded: chain Aa residue 404 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1081 random chunks: chunk 870 optimal weight: 9.9990 chunk 593 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 778 optimal weight: 4.9990 chunk 431 optimal weight: 0.7980 chunk 891 optimal weight: 5.9990 chunk 722 optimal weight: 0.0870 chunk 1 optimal weight: 3.9990 chunk 533 optimal weight: 0.8980 chunk 937 optimal weight: 1.9990 chunk 263 optimal weight: 1.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 60 GLN BF 112 ASN BH 96 ASN BM 115 GLN ** BO 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BP 150 HIS ** BS 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BT 53 HIS BT 99 ASN ** BU 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BU 138 GLN ** BV 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BV 155 GLN ** BW 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bd 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bf 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bf 162 GLN Bh 196 HIS ** Bi 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bm 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bq 88 GLN Br 44 ASN Bs 27 GLN ** Bv 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bw 92 ASN ** Bw 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aa 258 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 118908 Z= 0.151 Angle : 0.519 14.779 169080 Z= 0.266 Chirality : 0.035 0.203 19886 Planarity : 0.004 0.121 15405 Dihedral : 18.210 178.873 34229 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.79 % Favored : 97.19 % Rotamer: Outliers : 2.95 % Allowed : 13.07 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.09), residues: 9255 helix: 1.67 (0.09), residues: 3230 sheet: 0.31 (0.15), residues: 1233 loop : -0.37 (0.09), residues: 4792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRPBi 66 HIS 0.029 0.001 HISBP 150 PHE 0.018 0.001 PHEBQ 78 TYR 0.021 0.001 TYRBm 176 ARG 0.009 0.000 ARGBW 97 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18510 Ramachandran restraints generated. 9255 Oldfield, 0 Emsley, 9255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18510 Ramachandran restraints generated. 9255 Oldfield, 0 Emsley, 9255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1392 residues out of total 8262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 1150 time to evaluate : 7.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 54 LYS cc_start: 0.8643 (mttt) cc_final: 0.8316 (mttp) REVERT: BA 105 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7090 (tt0) REVERT: BB 12 LEU cc_start: 0.8270 (tt) cc_final: 0.7506 (mt) REVERT: BC 111 SER cc_start: 0.7960 (m) cc_final: 0.7747 (p) REVERT: BC 127 ASP cc_start: 0.5235 (t70) cc_final: 0.4508 (t70) REVERT: BC 129 LYS cc_start: 0.5057 (mptt) cc_final: 0.4797 (mmtt) REVERT: BD 118 THR cc_start: 0.9091 (m) cc_final: 0.8791 (p) REVERT: BE 5 LYS cc_start: 0.8320 (tttp) cc_final: 0.7904 (ttmt) REVERT: BE 71 TYR cc_start: 0.8504 (m-10) cc_final: 0.8159 (m-80) REVERT: BE 150 LYS cc_start: 0.7447 (tttm) cc_final: 0.6810 (mtmm) REVERT: BF 75 ASN cc_start: 0.8654 (t0) cc_final: 0.7928 (t0) REVERT: BF 113 MET cc_start: 0.8756 (tmm) cc_final: 0.8067 (tmm) REVERT: BF 213 MET cc_start: 0.8545 (mtm) cc_final: 0.8297 (mtp) REVERT: BG 35 LYS cc_start: 0.8128 (mttt) cc_final: 0.7692 (mtpp) REVERT: BG 40 ARG cc_start: 0.7827 (ttm170) cc_final: 0.7224 (ttm170) REVERT: BG 88 MET cc_start: 0.8251 (ptp) cc_final: 0.7770 (ptp) REVERT: BG 133 ASP cc_start: 0.8213 (p0) cc_final: 0.8003 (p0) REVERT: BH 153 THR cc_start: 0.9470 (p) cc_final: 0.8844 (t) REVERT: BH 175 ILE cc_start: 0.8762 (mm) cc_final: 0.8419 (mt) REVERT: BH 176 GLU cc_start: 0.7999 (mp0) cc_final: 0.7665 (mm-30) REVERT: BI 21 MET cc_start: 0.5938 (mmm) cc_final: 0.5502 (mtp) REVERT: BL 168 ASP cc_start: 0.8576 (p0) cc_final: 0.8252 (p0) REVERT: BL 235 MET cc_start: 0.8531 (ttp) cc_final: 0.8279 (ttp) REVERT: BM 81 LYS cc_start: 0.7559 (mttt) cc_final: 0.6775 (mmtm) REVERT: BN 50 LYS cc_start: 0.7404 (mmmt) cc_final: 0.6438 (mmtt) REVERT: BN 205 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8125 (mp0) REVERT: BO 137 LYS cc_start: 0.7330 (mttt) cc_final: 0.7006 (pttt) REVERT: BO 143 GLU cc_start: 0.7414 (tp30) cc_final: 0.7201 (mm-30) REVERT: BP 75 GLU cc_start: 0.6785 (mm-30) cc_final: 0.6332 (mt-10) REVERT: BP 82 LEU cc_start: 0.8286 (mm) cc_final: 0.7818 (mt) REVERT: BP 95 MET cc_start: 0.6569 (ttp) cc_final: 0.5532 (tmm) REVERT: BP 107 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7460 (pm20) REVERT: BP 126 PHE cc_start: 0.8119 (m-80) cc_final: 0.7843 (m-10) REVERT: BQ 19 MET cc_start: 0.5312 (mmm) cc_final: 0.4698 (mmm) REVERT: BR 67 PHE cc_start: 0.9127 (OUTLIER) cc_final: 0.8876 (m-80) REVERT: BR 131 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7443 (mt-10) REVERT: BS 43 ASN cc_start: 0.8220 (p0) cc_final: 0.7944 (p0) REVERT: BS 66 VAL cc_start: 0.9487 (p) cc_final: 0.9281 (m) REVERT: BT 61 THR cc_start: 0.8639 (m) cc_final: 0.8407 (m) REVERT: BT 236 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7954 (tp) REVERT: BV 114 ASN cc_start: 0.8691 (t0) cc_final: 0.8263 (t0) REVERT: BW 98 ASN cc_start: 0.8501 (p0) cc_final: 0.7764 (p0) REVERT: BW 100 GLN cc_start: 0.7957 (mt0) cc_final: 0.7615 (pt0) REVERT: BX 244 ARG cc_start: 0.8613 (mmm-85) cc_final: 0.7997 (mmm160) REVERT: BX 284 ASP cc_start: 0.8165 (t70) cc_final: 0.7847 (m-30) REVERT: BY 22 GLN cc_start: 0.8200 (mm110) cc_final: 0.7771 (tp40) REVERT: BY 148 HIS cc_start: 0.7409 (t-90) cc_final: 0.7087 (t-170) REVERT: Bc 73 MET cc_start: 0.7027 (mmm) cc_final: 0.5699 (ttm) REVERT: Bc 99 MET cc_start: 0.6216 (mtm) cc_final: 0.5558 (mmt) REVERT: Bc 131 ARG cc_start: 0.7967 (ptp90) cc_final: 0.7756 (ptp90) REVERT: Bc 133 SER cc_start: 0.8823 (m) cc_final: 0.8278 (t) REVERT: Bd 48 THR cc_start: 0.8093 (m) cc_final: 0.7749 (p) REVERT: Bd 66 HIS cc_start: 0.8469 (OUTLIER) cc_final: 0.7937 (t-170) REVERT: Bd 70 ARG cc_start: 0.7353 (ttm-80) cc_final: 0.6555 (ttp-110) REVERT: Bd 73 ARG cc_start: 0.7006 (ptm160) cc_final: 0.6418 (ptt-90) REVERT: Bd 75 MET cc_start: 0.8000 (ptt) cc_final: 0.7510 (ptt) REVERT: Bd 90 ARG cc_start: 0.7722 (mtt180) cc_final: 0.6821 (tmm160) REVERT: Be 12 ILE cc_start: 0.8957 (mt) cc_final: 0.8709 (mm) REVERT: Bf 38 GLU cc_start: 0.5508 (mt-10) cc_final: 0.4482 (tp30) REVERT: Bf 99 GLU cc_start: 0.8589 (pt0) cc_final: 0.8142 (tt0) REVERT: Bg 78 SER cc_start: 0.6903 (m) cc_final: 0.6703 (p) REVERT: Bh 37 GLU cc_start: 0.7388 (mm-30) cc_final: 0.7125 (mm-30) REVERT: Bh 73 CYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7768 (p) REVERT: Bi 164 GLU cc_start: 0.7408 (tp30) cc_final: 0.7041 (tp30) REVERT: Bj 101 LYS cc_start: 0.6005 (mttt) cc_final: 0.5625 (tppt) REVERT: Bj 107 LYS cc_start: 0.7206 (mttt) cc_final: 0.6741 (pttm) REVERT: Bm 72 ARG cc_start: 0.7878 (ttm110) cc_final: 0.7150 (ptm160) REVERT: Bm 262 THR cc_start: 0.9113 (m) cc_final: 0.8899 (m) REVERT: Bn 27 ARG cc_start: 0.7831 (tpt170) cc_final: 0.7358 (ttp-170) REVERT: Bn 160 ASP cc_start: 0.8045 (m-30) cc_final: 0.7798 (m-30) REVERT: Bn 311 MET cc_start: 0.8634 (mtm) cc_final: 0.8372 (mtm) REVERT: Bo 46 ASN cc_start: 0.8877 (m-40) cc_final: 0.8532 (m110) REVERT: Bo 78 MET cc_start: 0.8970 (mmm) cc_final: 0.8616 (mmp) REVERT: Bo 140 TRP cc_start: 0.8472 (OUTLIER) cc_final: 0.6058 (m-90) REVERT: Bo 176 PHE cc_start: 0.8120 (p90) cc_final: 0.7843 (p90) REVERT: Bo 178 TYR cc_start: 0.9008 (t80) cc_final: 0.8432 (t80) REVERT: Bo 243 GLN cc_start: 0.7666 (tp40) cc_final: 0.7364 (tp-100) REVERT: Bo 244 ASN cc_start: 0.7119 (m-40) cc_final: 0.6621 (t0) REVERT: Bo 310 ASN cc_start: 0.7881 (m-40) cc_final: 0.7415 (t0) REVERT: Bp 71 ARG cc_start: 0.7102 (mtt180) cc_final: 0.6344 (tpt-90) REVERT: Bq 48 PHE cc_start: 0.8859 (t80) cc_final: 0.8623 (t80) REVERT: Bq 82 THR cc_start: 0.7831 (p) cc_final: 0.7584 (p) REVERT: Br 56 ARG cc_start: 0.8501 (mmt90) cc_final: 0.8201 (tpp80) REVERT: Br 73 LYS cc_start: 0.9001 (ptpt) cc_final: 0.8523 (ptmm) REVERT: Br 114 LYS cc_start: 0.8590 (ttpt) cc_final: 0.8153 (tttm) REVERT: Bt 45 LEU cc_start: 0.8278 (mt) cc_final: 0.8076 (tt) REVERT: Bt 59 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7447 (mtm180) REVERT: Bu 110 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7152 (mt-10) REVERT: Bu 226 ASP cc_start: 0.6905 (t0) cc_final: 0.6339 (t0) REVERT: Bu 244 GLU cc_start: 0.7609 (mp0) cc_final: 0.6954 (mp0) REVERT: Bu 261 MET cc_start: 0.6217 (ttm) cc_final: 0.5665 (ttp) REVERT: Bu 292 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7178 (mm-30) REVERT: Bv 58 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7385 (mm) REVERT: Bv 75 GLN cc_start: 0.7668 (mt0) cc_final: 0.7256 (tp40) REVERT: Bv 78 GLU cc_start: 0.8347 (mt-10) cc_final: 0.7905 (mt-10) REVERT: Bv 87 HIS cc_start: 0.7815 (t-90) cc_final: 0.7572 (t70) REVERT: Bv 195 LEU cc_start: 0.7341 (mt) cc_final: 0.7064 (mp) REVERT: Bv 238 LEU cc_start: 0.6333 (mt) cc_final: 0.5327 (pp) REVERT: Bw 85 ASP cc_start: 0.7317 (t70) cc_final: 0.6867 (t0) REVERT: Bw 86 TYR cc_start: 0.6765 (m-80) cc_final: 0.6226 (m-10) REVERT: Bw 144 MET cc_start: 0.6111 (mmt) cc_final: 0.5863 (mmm) REVERT: Bw 186 VAL cc_start: 0.8796 (m) cc_final: 0.8456 (p) REVERT: Bx 141 ASN cc_start: 0.8013 (OUTLIER) cc_final: 0.7448 (t0) REVERT: By 121 MET cc_start: 0.6854 (mmp) cc_final: 0.6626 (mmt) REVERT: By 159 TYR cc_start: 0.6709 (OUTLIER) cc_final: 0.5940 (m-80) REVERT: Bz 41 ARG cc_start: 0.7794 (ptm160) cc_final: 0.7479 (ttt-90) REVERT: Bz 83 TRP cc_start: 0.8424 (t60) cc_final: 0.7747 (t60) REVERT: Aa 236 HIS cc_start: 0.5652 (t-90) cc_final: 0.5451 (t70) REVERT: Aa 373 LYS cc_start: 0.7197 (mtmt) cc_final: 0.6180 (tptm) REVERT: Aa 409 GLU cc_start: 0.5290 (tp30) cc_final: 0.5011 (mm-30) outliers start: 242 outliers final: 179 residues processed: 1305 average time/residue: 0.9548 time to fit residues: 2148.1151 Evaluate side-chains 1269 residues out of total 8262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 1078 time to evaluate : 7.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 105 GLU Chi-restraints excluded: chain BA residue 164 ILE Chi-restraints excluded: chain BA residue 170 CYS Chi-restraints excluded: chain BA residue 198 ILE Chi-restraints excluded: chain BB residue 113 GLU Chi-restraints excluded: chain BC residue 60 ASP Chi-restraints excluded: chain BC residue 147 SER Chi-restraints excluded: chain BC residue 166 VAL Chi-restraints excluded: chain BC residue 181 ASP Chi-restraints excluded: chain BC residue 183 LEU Chi-restraints excluded: chain BD residue 67 LEU Chi-restraints excluded: chain BD residue 83 LEU Chi-restraints excluded: chain BE residue 22 SER Chi-restraints excluded: chain BE residue 128 THR Chi-restraints excluded: chain BF residue 79 GLU Chi-restraints excluded: chain BF residue 88 THR Chi-restraints excluded: chain BH residue 157 VAL Chi-restraints excluded: chain BI residue 49 VAL Chi-restraints excluded: chain BI residue 50 VAL Chi-restraints excluded: chain BI residue 59 GLN Chi-restraints excluded: chain BJ residue 92 SER Chi-restraints excluded: chain BL residue 68 SER Chi-restraints excluded: chain BL residue 91 ILE Chi-restraints excluded: chain BL residue 173 MET Chi-restraints excluded: chain BL residue 175 VAL Chi-restraints excluded: chain BL residue 231 SER Chi-restraints excluded: chain BL residue 237 VAL Chi-restraints excluded: chain BM residue 63 GLN Chi-restraints excluded: chain BM residue 153 SER Chi-restraints excluded: chain BM residue 275 ARG Chi-restraints excluded: chain BM residue 279 LYS Chi-restraints excluded: chain BM residue 296 LEU Chi-restraints excluded: chain BM residue 313 ASN Chi-restraints excluded: chain BN residue 94 ASP Chi-restraints excluded: chain BN residue 106 PHE Chi-restraints excluded: chain BN residue 129 VAL Chi-restraints excluded: chain BN residue 133 SER Chi-restraints excluded: chain BN residue 151 VAL Chi-restraints excluded: chain BN residue 205 GLU Chi-restraints excluded: chain BN residue 262 THR Chi-restraints excluded: chain BN residue 281 THR Chi-restraints excluded: chain BO residue 93 ASN Chi-restraints excluded: chain BO residue 114 VAL Chi-restraints excluded: chain BO residue 128 LEU Chi-restraints excluded: chain BO residue 184 LEU Chi-restraints excluded: chain BO residue 238 VAL Chi-restraints excluded: chain BP residue 30 SER Chi-restraints excluded: chain BP residue 99 CYS Chi-restraints excluded: chain BP residue 107 GLU Chi-restraints excluded: chain BP residue 112 LEU Chi-restraints excluded: chain BP residue 150 HIS Chi-restraints excluded: chain BP residue 164 MET Chi-restraints excluded: chain BQ residue 44 VAL Chi-restraints excluded: chain BQ residue 72 VAL Chi-restraints excluded: chain BQ residue 143 SER Chi-restraints excluded: chain BQ residue 153 ILE Chi-restraints excluded: chain BQ residue 183 LEU Chi-restraints excluded: chain BR residue 67 PHE Chi-restraints excluded: chain BS residue 48 THR Chi-restraints excluded: chain BS residue 71 ASP Chi-restraints excluded: chain BS residue 89 HIS Chi-restraints excluded: chain BS residue 115 VAL Chi-restraints excluded: chain BS residue 126 SER Chi-restraints excluded: chain BT residue 33 SER Chi-restraints excluded: chain BT residue 236 LEU Chi-restraints excluded: chain BU residue 39 PHE Chi-restraints excluded: chain BU residue 59 VAL Chi-restraints excluded: chain BU residue 113 MET Chi-restraints excluded: chain BU residue 121 LEU Chi-restraints excluded: chain BU residue 161 VAL Chi-restraints excluded: chain BV residue 9 ILE Chi-restraints excluded: chain BV residue 124 ILE Chi-restraints excluded: chain BV residue 141 SER Chi-restraints excluded: chain BW residue 101 VAL Chi-restraints excluded: chain BX residue 154 THR Chi-restraints excluded: chain BX residue 177 VAL Chi-restraints excluded: chain BX residue 207 ILE Chi-restraints excluded: chain BX residue 265 LEU Chi-restraints excluded: chain BX residue 289 SER Chi-restraints excluded: chain BY residue 12 SER Chi-restraints excluded: chain BY residue 59 LEU Chi-restraints excluded: chain BY residue 63 SER Chi-restraints excluded: chain BY residue 76 SER Chi-restraints excluded: chain BZ residue 58 THR Chi-restraints excluded: chain BZ residue 69 VAL Chi-restraints excluded: chain BZ residue 84 VAL Chi-restraints excluded: chain BZ residue 112 VAL Chi-restraints excluded: chain BZ residue 113 THR Chi-restraints excluded: chain BZ residue 158 VAL Chi-restraints excluded: chain Bb residue 8 LEU Chi-restraints excluded: chain Bb residue 30 THR Chi-restraints excluded: chain Bb residue 39 SER Chi-restraints excluded: chain Bb residue 45 THR Chi-restraints excluded: chain Bb residue 75 ILE Chi-restraints excluded: chain Bd residue 40 LEU Chi-restraints excluded: chain Bd residue 58 VAL Chi-restraints excluded: chain Bd residue 66 HIS Chi-restraints excluded: chain Be residue 50 SER Chi-restraints excluded: chain Be residue 101 TRP Chi-restraints excluded: chain Bf residue 110 ILE Chi-restraints excluded: chain Bf residue 185 GLU Chi-restraints excluded: chain Bg residue 41 ASP Chi-restraints excluded: chain Bh residue 67 THR Chi-restraints excluded: chain Bh residue 73 CYS Chi-restraints excluded: chain Bh residue 86 VAL Chi-restraints excluded: chain Bh residue 140 VAL Chi-restraints excluded: chain Bh residue 188 SER Chi-restraints excluded: chain Bi residue 76 VAL Chi-restraints excluded: chain Bi residue 132 ASP Chi-restraints excluded: chain Bi residue 260 CYS Chi-restraints excluded: chain Bi residue 274 ASN Chi-restraints excluded: chain Bi residue 345 VAL Chi-restraints excluded: chain Bi residue 350 VAL Chi-restraints excluded: chain Bi residue 399 ILE Chi-restraints excluded: chain Bi residue 403 ASN Chi-restraints excluded: chain Bi residue 410 ASP Chi-restraints excluded: chain Bj residue 305 ILE Chi-restraints excluded: chain Bm residue 64 MET Chi-restraints excluded: chain Bm residue 101 ASP Chi-restraints excluded: chain Bm residue 151 ASP Chi-restraints excluded: chain Bm residue 166 SER Chi-restraints excluded: chain Bm residue 248 THR Chi-restraints excluded: chain Bm residue 256 PHE Chi-restraints excluded: chain Bm residue 270 VAL Chi-restraints excluded: chain Bm residue 379 ASP Chi-restraints excluded: chain Bm residue 398 VAL Chi-restraints excluded: chain Bn residue 32 LEU Chi-restraints excluded: chain Bn residue 151 LEU Chi-restraints excluded: chain Bn residue 226 LEU Chi-restraints excluded: chain Bn residue 231 GLU Chi-restraints excluded: chain Bn residue 245 VAL Chi-restraints excluded: chain Bn residue 276 ASP Chi-restraints excluded: chain Bn residue 279 ILE Chi-restraints excluded: chain Bn residue 302 ASP Chi-restraints excluded: chain Bo residue 58 ARG Chi-restraints excluded: chain Bo residue 126 THR Chi-restraints excluded: chain Bo residue 140 TRP Chi-restraints excluded: chain Bo residue 214 GLU Chi-restraints excluded: chain Bo residue 215 THR Chi-restraints excluded: chain Bo residue 260 VAL Chi-restraints excluded: chain Bo residue 290 VAL Chi-restraints excluded: chain Bp residue 87 ASP Chi-restraints excluded: chain Bp residue 94 PHE Chi-restraints excluded: chain Bp residue 167 SER Chi-restraints excluded: chain Br residue 38 SER Chi-restraints excluded: chain Br residue 41 ASP Chi-restraints excluded: chain Br residue 93 LYS Chi-restraints excluded: chain Br residue 110 GLU Chi-restraints excluded: chain Br residue 115 MET Chi-restraints excluded: chain Bs residue 34 SER Chi-restraints excluded: chain Bs residue 45 GLU Chi-restraints excluded: chain Bs residue 75 VAL Chi-restraints excluded: chain Bs residue 84 VAL Chi-restraints excluded: chain Bs residue 93 SER Chi-restraints excluded: chain Bs residue 113 ILE Chi-restraints excluded: chain Bs residue 139 THR Chi-restraints excluded: chain Bt residue 59 ARG Chi-restraints excluded: chain Bt residue 85 LEU Chi-restraints excluded: chain Bt residue 93 VAL Chi-restraints excluded: chain Bt residue 148 LEU Chi-restraints excluded: chain Bt residue 176 GLU Chi-restraints excluded: chain Bt residue 231 MET Chi-restraints excluded: chain Bt residue 265 THR Chi-restraints excluded: chain Bu residue 76 ILE Chi-restraints excluded: chain Bu residue 150 LEU Chi-restraints excluded: chain Bu residue 165 THR Chi-restraints excluded: chain Bu residue 218 THR Chi-restraints excluded: chain Bu residue 266 ILE Chi-restraints excluded: chain Bu residue 281 MET Chi-restraints excluded: chain Bv residue 58 LEU Chi-restraints excluded: chain Bv residue 157 LEU Chi-restraints excluded: chain Bv residue 176 SER Chi-restraints excluded: chain Bv residue 179 GLN Chi-restraints excluded: chain Bv residue 255 VAL Chi-restraints excluded: chain Bw residue 90 VAL Chi-restraints excluded: chain Bw residue 96 ILE Chi-restraints excluded: chain Bw residue 132 MET Chi-restraints excluded: chain Bw residue 149 VAL Chi-restraints excluded: chain Bw residue 182 VAL Chi-restraints excluded: chain Bx residue 126 ASP Chi-restraints excluded: chain Bx residue 141 ASN Chi-restraints excluded: chain By residue 128 LEU Chi-restraints excluded: chain By residue 159 TYR Chi-restraints excluded: chain Bz residue 43 VAL Chi-restraints excluded: chain Bz residue 115 SER Chi-restraints excluded: chain Aa residue 126 THR Chi-restraints excluded: chain Aa residue 247 VAL Chi-restraints excluded: chain Aa residue 269 SER Chi-restraints excluded: chain Aa residue 284 VAL Chi-restraints excluded: chain Aa residue 314 HIS Chi-restraints excluded: chain Aa residue 391 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1081 random chunks: chunk 351 optimal weight: 0.8980 chunk 940 optimal weight: 6.9990 chunk 206 optimal weight: 20.0000 chunk 613 optimal weight: 1.9990 chunk 257 optimal weight: 0.0970 chunk 1045 optimal weight: 20.0000 chunk 868 optimal weight: 9.9990 chunk 484 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 345 optimal weight: 5.9990 chunk 549 optimal weight: 0.9980 overall best weight: 1.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 60 GLN BF 112 ASN ** BM 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BN 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BP 119 HIS BP 150 HIS BQ 103 HIS ** BS 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BT 99 ASN BU 138 GLN BU 210 GLN BV 39 HIS ** BV 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BV 155 GLN ** BW 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bd 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bf 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bf 162 GLN Bh 196 HIS ** Bi 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bm 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bp 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bq 88 GLN ** Bv 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bv 207 ASN ** Bw 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 118908 Z= 0.210 Angle : 0.540 14.603 169080 Z= 0.277 Chirality : 0.036 0.215 19886 Planarity : 0.004 0.123 15405 Dihedral : 18.207 178.860 34225 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.32 % Favored : 96.66 % Rotamer: Outliers : 3.24 % Allowed : 13.22 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.09), residues: 9255 helix: 1.68 (0.09), residues: 3213 sheet: 0.28 (0.15), residues: 1229 loop : -0.40 (0.09), residues: 4813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPBi 66 HIS 0.014 0.001 HISBP 150 PHE 0.021 0.001 PHEBF 235 TYR 0.025 0.001 TYRBT 222 ARG 0.009 0.000 ARGBW 97 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18510 Ramachandran restraints generated. 9255 Oldfield, 0 Emsley, 9255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18510 Ramachandran restraints generated. 9255 Oldfield, 0 Emsley, 9255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1360 residues out of total 8262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 1094 time to evaluate : 7.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 54 LYS cc_start: 0.8665 (mttt) cc_final: 0.8346 (mttp) REVERT: BA 105 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7126 (tt0) REVERT: BB 12 LEU cc_start: 0.8263 (tt) cc_final: 0.7524 (mt) REVERT: BB 58 GLU cc_start: 0.8111 (tp30) cc_final: 0.7708 (tp30) REVERT: BC 111 SER cc_start: 0.8059 (m) cc_final: 0.7818 (p) REVERT: BC 127 ASP cc_start: 0.5617 (t70) cc_final: 0.4838 (t70) REVERT: BC 129 LYS cc_start: 0.5042 (mptt) cc_final: 0.4773 (mmtt) REVERT: BE 71 TYR cc_start: 0.8492 (m-10) cc_final: 0.8159 (m-80) REVERT: BE 150 LYS cc_start: 0.7435 (tttm) cc_final: 0.6842 (ptpp) REVERT: BF 75 ASN cc_start: 0.8698 (t0) cc_final: 0.8147 (t0) REVERT: BF 113 MET cc_start: 0.8768 (tmm) cc_final: 0.8071 (tmm) REVERT: BF 164 LYS cc_start: 0.6230 (mttm) cc_final: 0.5766 (mttm) REVERT: BF 213 MET cc_start: 0.8539 (mtm) cc_final: 0.8209 (mtp) REVERT: BG 35 LYS cc_start: 0.8178 (mttt) cc_final: 0.7732 (mtpp) REVERT: BG 40 ARG cc_start: 0.7796 (ttm170) cc_final: 0.7307 (mmt90) REVERT: BG 88 MET cc_start: 0.8258 (ptp) cc_final: 0.7748 (ptp) REVERT: BH 153 THR cc_start: 0.9473 (p) cc_final: 0.8845 (t) REVERT: BH 176 GLU cc_start: 0.8005 (mp0) cc_final: 0.7671 (mm-30) REVERT: BI 21 MET cc_start: 0.5944 (mmm) cc_final: 0.5493 (mtp) REVERT: BL 168 ASP cc_start: 0.8562 (p0) cc_final: 0.8300 (p0) REVERT: BL 235 MET cc_start: 0.8574 (ttp) cc_final: 0.8318 (ttp) REVERT: BM 81 LYS cc_start: 0.7556 (mttt) cc_final: 0.6910 (mmtm) REVERT: BN 50 LYS cc_start: 0.7431 (mmmt) cc_final: 0.6445 (mmtt) REVERT: BN 205 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8139 (mp0) REVERT: BO 131 TYR cc_start: 0.7821 (m-80) cc_final: 0.7195 (m-80) REVERT: BO 137 LYS cc_start: 0.7331 (mttt) cc_final: 0.6929 (pttt) REVERT: BO 143 GLU cc_start: 0.7475 (tp30) cc_final: 0.7114 (mm-30) REVERT: BP 75 GLU cc_start: 0.6889 (mm-30) cc_final: 0.6440 (mt-10) REVERT: BP 82 LEU cc_start: 0.8302 (mm) cc_final: 0.7843 (mt) REVERT: BP 95 MET cc_start: 0.6552 (ttp) cc_final: 0.5975 (tmm) REVERT: BP 126 PHE cc_start: 0.8148 (m-80) cc_final: 0.7867 (m-10) REVERT: BQ 19 MET cc_start: 0.5261 (mmm) cc_final: 0.4635 (mmm) REVERT: BR 67 PHE cc_start: 0.9163 (OUTLIER) cc_final: 0.8890 (m-80) REVERT: BS 66 VAL cc_start: 0.9516 (p) cc_final: 0.9309 (m) REVERT: BT 61 THR cc_start: 0.8783 (m) cc_final: 0.8557 (m) REVERT: BT 236 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7790 (tp) REVERT: BV 114 ASN cc_start: 0.8650 (t0) cc_final: 0.8227 (t0) REVERT: BW 98 ASN cc_start: 0.8540 (p0) cc_final: 0.8124 (p0) REVERT: BW 100 GLN cc_start: 0.7964 (mt0) cc_final: 0.7565 (pt0) REVERT: BX 99 MET cc_start: 0.8338 (mtm) cc_final: 0.8118 (mtp) REVERT: BX 244 ARG cc_start: 0.8678 (mmm-85) cc_final: 0.8036 (mmm160) REVERT: BY 22 GLN cc_start: 0.8245 (mm110) cc_final: 0.7789 (tp40) REVERT: BY 148 HIS cc_start: 0.7438 (t-90) cc_final: 0.7127 (t-170) REVERT: Ba 67 LYS cc_start: 0.8521 (mtpm) cc_final: 0.8277 (mtmt) REVERT: Bb 37 VAL cc_start: 0.8302 (t) cc_final: 0.8094 (p) REVERT: Bc 73 MET cc_start: 0.7098 (mmm) cc_final: 0.5836 (ttm) REVERT: Bc 99 MET cc_start: 0.5777 (mtm) cc_final: 0.5030 (mmt) REVERT: Bc 133 SER cc_start: 0.8839 (m) cc_final: 0.8340 (t) REVERT: Bd 48 THR cc_start: 0.8238 (m) cc_final: 0.8021 (p) REVERT: Bd 49 TYR cc_start: 0.8057 (p90) cc_final: 0.7755 (p90) REVERT: Bd 55 VAL cc_start: 0.8108 (t) cc_final: 0.7883 (m) REVERT: Bd 66 HIS cc_start: 0.8463 (OUTLIER) cc_final: 0.7955 (t-170) REVERT: Bd 70 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.6607 (ttp-110) REVERT: Bd 73 ARG cc_start: 0.7043 (ptm160) cc_final: 0.6533 (ptt-90) REVERT: Bd 75 MET cc_start: 0.7841 (ptt) cc_final: 0.7327 (ptt) REVERT: Bd 90 ARG cc_start: 0.7766 (mtt180) cc_final: 0.6824 (tmm160) REVERT: Be 12 ILE cc_start: 0.8982 (mt) cc_final: 0.8728 (mm) REVERT: Bf 38 GLU cc_start: 0.5512 (mt-10) cc_final: 0.4442 (tp30) REVERT: Bf 131 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7506 (mt-10) REVERT: Bg 78 SER cc_start: 0.6830 (m) cc_final: 0.6618 (p) REVERT: Bh 37 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7151 (mm-30) REVERT: Bh 73 CYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7700 (p) REVERT: Bi 164 GLU cc_start: 0.7445 (tp30) cc_final: 0.7137 (tp30) REVERT: Bi 172 ASP cc_start: 0.7676 (m-30) cc_final: 0.7391 (m-30) REVERT: Bj 101 LYS cc_start: 0.6092 (mttt) cc_final: 0.5683 (tppt) REVERT: Bj 107 LYS cc_start: 0.6958 (mttt) cc_final: 0.6536 (pttm) REVERT: Bm 72 ARG cc_start: 0.7916 (ttm110) cc_final: 0.7183 (ptm160) REVERT: Bn 27 ARG cc_start: 0.7851 (tpt170) cc_final: 0.7268 (ttm170) REVERT: Bn 48 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8176 (mm) REVERT: Bn 160 ASP cc_start: 0.7987 (m-30) cc_final: 0.7708 (m-30) REVERT: Bo 46 ASN cc_start: 0.8871 (m-40) cc_final: 0.8524 (m110) REVERT: Bo 140 TRP cc_start: 0.8483 (OUTLIER) cc_final: 0.6298 (m-90) REVERT: Bo 176 PHE cc_start: 0.8172 (p90) cc_final: 0.7853 (p90) REVERT: Bo 178 TYR cc_start: 0.9103 (t80) cc_final: 0.8356 (t80) REVERT: Bo 243 GLN cc_start: 0.7688 (tp40) cc_final: 0.7366 (tp-100) REVERT: Bo 244 ASN cc_start: 0.7096 (m-40) cc_final: 0.6623 (t0) REVERT: Bo 310 ASN cc_start: 0.7930 (m-40) cc_final: 0.7463 (t0) REVERT: Bp 71 ARG cc_start: 0.7073 (mtt180) cc_final: 0.6320 (tpt-90) REVERT: Bp 97 LYS cc_start: 0.7057 (tppt) cc_final: 0.6632 (tptp) REVERT: Bq 48 PHE cc_start: 0.8965 (t80) cc_final: 0.8717 (t80) REVERT: Br 56 ARG cc_start: 0.8552 (mmt90) cc_final: 0.8181 (tpp80) REVERT: Br 73 LYS cc_start: 0.9009 (ptpt) cc_final: 0.8536 (ptmm) REVERT: Br 114 LYS cc_start: 0.8599 (ttpt) cc_final: 0.8163 (tttm) REVERT: Bt 45 LEU cc_start: 0.8332 (mt) cc_final: 0.8117 (tt) REVERT: Bt 59 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7469 (mtm180) REVERT: Bt 183 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6771 (tt0) REVERT: Bt 240 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8180 (tt) REVERT: Bu 226 ASP cc_start: 0.6950 (t0) cc_final: 0.6368 (t0) REVERT: Bu 244 GLU cc_start: 0.7625 (mp0) cc_final: 0.6991 (mp0) REVERT: Bu 261 MET cc_start: 0.6309 (ttm) cc_final: 0.5789 (ttp) REVERT: Bu 292 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7236 (mm-30) REVERT: Bv 58 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.7291 (mm) REVERT: Bv 78 GLU cc_start: 0.8334 (mt-10) cc_final: 0.8003 (mm-30) REVERT: Bv 238 LEU cc_start: 0.6395 (mt) cc_final: 0.5587 (pp) REVERT: Bv 278 ASP cc_start: 0.6774 (OUTLIER) cc_final: 0.5460 (t0) REVERT: Bw 85 ASP cc_start: 0.7244 (t70) cc_final: 0.6866 (t0) REVERT: Bw 86 TYR cc_start: 0.6801 (m-80) cc_final: 0.6436 (m-10) REVERT: Bw 144 MET cc_start: 0.6117 (mmt) cc_final: 0.5870 (mmm) REVERT: Bw 186 VAL cc_start: 0.8780 (m) cc_final: 0.8447 (p) REVERT: Bx 141 ASN cc_start: 0.8082 (OUTLIER) cc_final: 0.7475 (t0) REVERT: By 159 TYR cc_start: 0.6844 (OUTLIER) cc_final: 0.6218 (m-80) REVERT: Bz 41 ARG cc_start: 0.7749 (ptm160) cc_final: 0.7453 (ttt-90) REVERT: Bz 83 TRP cc_start: 0.8442 (t60) cc_final: 0.7765 (t60) REVERT: Aa 373 LYS cc_start: 0.7235 (mtmt) cc_final: 0.6117 (tptm) REVERT: Aa 409 GLU cc_start: 0.5438 (tp30) cc_final: 0.5144 (mm-30) REVERT: Aa 442 LYS cc_start: 0.2350 (mmtt) cc_final: 0.1990 (ttmt) outliers start: 266 outliers final: 207 residues processed: 1265 average time/residue: 0.9628 time to fit residues: 2118.4112 Evaluate side-chains 1276 residues out of total 8262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 1054 time to evaluate : 7.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 105 GLU Chi-restraints excluded: chain BA residue 164 ILE Chi-restraints excluded: chain BA residue 170 CYS Chi-restraints excluded: chain BA residue 198 ILE Chi-restraints excluded: chain BB residue 70 THR Chi-restraints excluded: chain BB residue 91 ASP Chi-restraints excluded: chain BB residue 113 GLU Chi-restraints excluded: chain BC residue 60 ASP Chi-restraints excluded: chain BC residue 78 GLN Chi-restraints excluded: chain BC residue 147 SER Chi-restraints excluded: chain BC residue 166 VAL Chi-restraints excluded: chain BC residue 181 ASP Chi-restraints excluded: chain BC residue 183 LEU Chi-restraints excluded: chain BD residue 67 LEU Chi-restraints excluded: chain BD residue 83 LEU Chi-restraints excluded: chain BD residue 141 THR Chi-restraints excluded: chain BE residue 22 SER Chi-restraints excluded: chain BE residue 128 THR Chi-restraints excluded: chain BF residue 79 GLU Chi-restraints excluded: chain BF residue 88 THR Chi-restraints excluded: chain BF residue 160 THR Chi-restraints excluded: chain BF residue 174 ILE Chi-restraints excluded: chain BG residue 74 SER Chi-restraints excluded: chain BG residue 137 THR Chi-restraints excluded: chain BI residue 49 VAL Chi-restraints excluded: chain BI residue 50 VAL Chi-restraints excluded: chain BI residue 59 GLN Chi-restraints excluded: chain BJ residue 92 SER Chi-restraints excluded: chain BL residue 68 SER Chi-restraints excluded: chain BL residue 91 ILE Chi-restraints excluded: chain BL residue 173 MET Chi-restraints excluded: chain BL residue 175 VAL Chi-restraints excluded: chain BL residue 231 SER Chi-restraints excluded: chain BL residue 237 VAL Chi-restraints excluded: chain BM residue 63 GLN Chi-restraints excluded: chain BM residue 97 VAL Chi-restraints excluded: chain BM residue 153 SER Chi-restraints excluded: chain BM residue 275 ARG Chi-restraints excluded: chain BM residue 279 LYS Chi-restraints excluded: chain BM residue 295 CYS Chi-restraints excluded: chain BM residue 296 LEU Chi-restraints excluded: chain BM residue 313 ASN Chi-restraints excluded: chain BN residue 94 ASP Chi-restraints excluded: chain BN residue 106 PHE Chi-restraints excluded: chain BN residue 129 VAL Chi-restraints excluded: chain BN residue 151 VAL Chi-restraints excluded: chain BN residue 205 GLU Chi-restraints excluded: chain BN residue 225 ASP Chi-restraints excluded: chain BN residue 262 THR Chi-restraints excluded: chain BN residue 280 TYR Chi-restraints excluded: chain BN residue 281 THR Chi-restraints excluded: chain BO residue 114 VAL Chi-restraints excluded: chain BO residue 184 LEU Chi-restraints excluded: chain BO residue 238 VAL Chi-restraints excluded: chain BP residue 30 SER Chi-restraints excluded: chain BP residue 99 CYS Chi-restraints excluded: chain BP residue 107 GLU Chi-restraints excluded: chain BP residue 116 LEU Chi-restraints excluded: chain BP residue 164 MET Chi-restraints excluded: chain BQ residue 44 VAL Chi-restraints excluded: chain BQ residue 128 ASP Chi-restraints excluded: chain BQ residue 135 VAL Chi-restraints excluded: chain BQ residue 143 SER Chi-restraints excluded: chain BQ residue 153 ILE Chi-restraints excluded: chain BQ residue 183 LEU Chi-restraints excluded: chain BR residue 67 PHE Chi-restraints excluded: chain BS residue 48 THR Chi-restraints excluded: chain BS residue 89 HIS Chi-restraints excluded: chain BS residue 115 VAL Chi-restraints excluded: chain BS residue 126 SER Chi-restraints excluded: chain BT residue 33 SER Chi-restraints excluded: chain BT residue 146 ASP Chi-restraints excluded: chain BT residue 236 LEU Chi-restraints excluded: chain BU residue 39 PHE Chi-restraints excluded: chain BU residue 59 VAL Chi-restraints excluded: chain BU residue 113 MET Chi-restraints excluded: chain BU residue 121 LEU Chi-restraints excluded: chain BU residue 161 VAL Chi-restraints excluded: chain BV residue 9 ILE Chi-restraints excluded: chain BV residue 124 ILE Chi-restraints excluded: chain BV residue 141 SER Chi-restraints excluded: chain BV residue 156 ASP Chi-restraints excluded: chain BW residue 101 VAL Chi-restraints excluded: chain BW residue 157 SER Chi-restraints excluded: chain BX residue 130 THR Chi-restraints excluded: chain BX residue 154 THR Chi-restraints excluded: chain BX residue 171 ILE Chi-restraints excluded: chain BX residue 177 VAL Chi-restraints excluded: chain BX residue 207 ILE Chi-restraints excluded: chain BX residue 265 LEU Chi-restraints excluded: chain BX residue 289 SER Chi-restraints excluded: chain BY residue 12 SER Chi-restraints excluded: chain BY residue 59 LEU Chi-restraints excluded: chain BY residue 63 SER Chi-restraints excluded: chain BY residue 76 SER Chi-restraints excluded: chain BY residue 87 ILE Chi-restraints excluded: chain BZ residue 58 THR Chi-restraints excluded: chain BZ residue 69 VAL Chi-restraints excluded: chain BZ residue 84 VAL Chi-restraints excluded: chain BZ residue 112 VAL Chi-restraints excluded: chain BZ residue 113 THR Chi-restraints excluded: chain BZ residue 158 VAL Chi-restraints excluded: chain Bb residue 8 LEU Chi-restraints excluded: chain Bb residue 30 THR Chi-restraints excluded: chain Bb residue 45 THR Chi-restraints excluded: chain Bb residue 75 ILE Chi-restraints excluded: chain Bd residue 40 LEU Chi-restraints excluded: chain Bd residue 58 VAL Chi-restraints excluded: chain Bd residue 66 HIS Chi-restraints excluded: chain Bd residue 70 ARG Chi-restraints excluded: chain Be residue 41 THR Chi-restraints excluded: chain Be residue 50 SER Chi-restraints excluded: chain Be residue 59 GLU Chi-restraints excluded: chain Be residue 97 VAL Chi-restraints excluded: chain Be residue 101 TRP Chi-restraints excluded: chain Bf residue 40 GLN Chi-restraints excluded: chain Bf residue 110 ILE Chi-restraints excluded: chain Bg residue 41 ASP Chi-restraints excluded: chain Bh residue 67 THR Chi-restraints excluded: chain Bh residue 73 CYS Chi-restraints excluded: chain Bh residue 86 VAL Chi-restraints excluded: chain Bh residue 140 VAL Chi-restraints excluded: chain Bh residue 188 SER Chi-restraints excluded: chain Bh residue 192 LEU Chi-restraints excluded: chain Bi residue 76 VAL Chi-restraints excluded: chain Bi residue 132 ASP Chi-restraints excluded: chain Bi residue 159 VAL Chi-restraints excluded: chain Bi residue 182 LEU Chi-restraints excluded: chain Bi residue 260 CYS Chi-restraints excluded: chain Bi residue 274 ASN Chi-restraints excluded: chain Bi residue 345 VAL Chi-restraints excluded: chain Bi residue 350 VAL Chi-restraints excluded: chain Bi residue 356 THR Chi-restraints excluded: chain Bi residue 369 ASN Chi-restraints excluded: chain Bi residue 399 ILE Chi-restraints excluded: chain Bi residue 403 ASN Chi-restraints excluded: chain Bi residue 410 ASP Chi-restraints excluded: chain Bi residue 418 PHE Chi-restraints excluded: chain Bj residue 305 ILE Chi-restraints excluded: chain Bm residue 64 MET Chi-restraints excluded: chain Bm residue 101 ASP Chi-restraints excluded: chain Bm residue 117 VAL Chi-restraints excluded: chain Bm residue 151 ASP Chi-restraints excluded: chain Bm residue 166 SER Chi-restraints excluded: chain Bm residue 203 CYS Chi-restraints excluded: chain Bm residue 248 THR Chi-restraints excluded: chain Bm residue 256 PHE Chi-restraints excluded: chain Bm residue 270 VAL Chi-restraints excluded: chain Bm residue 379 ASP Chi-restraints excluded: chain Bm residue 398 VAL Chi-restraints excluded: chain Bn residue 32 LEU Chi-restraints excluded: chain Bn residue 48 LEU Chi-restraints excluded: chain Bn residue 151 LEU Chi-restraints excluded: chain Bn residue 205 THR Chi-restraints excluded: chain Bn residue 226 LEU Chi-restraints excluded: chain Bn residue 227 GLU Chi-restraints excluded: chain Bn residue 231 GLU Chi-restraints excluded: chain Bn residue 245 VAL Chi-restraints excluded: chain Bn residue 276 ASP Chi-restraints excluded: chain Bn residue 302 ASP Chi-restraints excluded: chain Bn residue 321 CYS Chi-restraints excluded: chain Bo residue 58 ARG Chi-restraints excluded: chain Bo residue 126 THR Chi-restraints excluded: chain Bo residue 140 TRP Chi-restraints excluded: chain Bo residue 214 GLU Chi-restraints excluded: chain Bo residue 215 THR Chi-restraints excluded: chain Bo residue 260 VAL Chi-restraints excluded: chain Bo residue 290 VAL Chi-restraints excluded: chain Bp residue 87 ASP Chi-restraints excluded: chain Bp residue 94 PHE Chi-restraints excluded: chain Bp residue 167 SER Chi-restraints excluded: chain Bq residue 39 THR Chi-restraints excluded: chain Br residue 38 SER Chi-restraints excluded: chain Br residue 41 ASP Chi-restraints excluded: chain Br residue 93 LYS Chi-restraints excluded: chain Br residue 110 GLU Chi-restraints excluded: chain Br residue 115 MET Chi-restraints excluded: chain Bs residue 34 SER Chi-restraints excluded: chain Bs residue 75 VAL Chi-restraints excluded: chain Bs residue 84 VAL Chi-restraints excluded: chain Bs residue 91 CYS Chi-restraints excluded: chain Bs residue 93 SER Chi-restraints excluded: chain Bs residue 139 THR Chi-restraints excluded: chain Bt residue 59 ARG Chi-restraints excluded: chain Bt residue 85 LEU Chi-restraints excluded: chain Bt residue 93 VAL Chi-restraints excluded: chain Bt residue 148 LEU Chi-restraints excluded: chain Bt residue 176 GLU Chi-restraints excluded: chain Bt residue 231 MET Chi-restraints excluded: chain Bt residue 240 LEU Chi-restraints excluded: chain Bt residue 265 THR Chi-restraints excluded: chain Bu residue 76 ILE Chi-restraints excluded: chain Bu residue 150 LEU Chi-restraints excluded: chain Bu residue 165 THR Chi-restraints excluded: chain Bu residue 218 THR Chi-restraints excluded: chain Bu residue 266 ILE Chi-restraints excluded: chain Bv residue 58 LEU Chi-restraints excluded: chain Bv residue 131 PHE Chi-restraints excluded: chain Bv residue 207 ASN Chi-restraints excluded: chain Bv residue 278 ASP Chi-restraints excluded: chain Bv residue 279 LEU Chi-restraints excluded: chain Bw residue 90 VAL Chi-restraints excluded: chain Bw residue 132 MET Chi-restraints excluded: chain Bw residue 149 VAL Chi-restraints excluded: chain Bw residue 182 VAL Chi-restraints excluded: chain Bw residue 185 SER Chi-restraints excluded: chain Bx residue 107 MET Chi-restraints excluded: chain Bx residue 141 ASN Chi-restraints excluded: chain By residue 118 LEU Chi-restraints excluded: chain By residue 128 LEU Chi-restraints excluded: chain By residue 159 TYR Chi-restraints excluded: chain Bz residue 43 VAL Chi-restraints excluded: chain Bz residue 75 LYS Chi-restraints excluded: chain Bz residue 100 ASN Chi-restraints excluded: chain Bz residue 115 SER Chi-restraints excluded: chain Aa residue 126 THR Chi-restraints excluded: chain Aa residue 247 VAL Chi-restraints excluded: chain Aa residue 269 SER Chi-restraints excluded: chain Aa residue 284 VAL Chi-restraints excluded: chain Aa residue 314 HIS Chi-restraints excluded: chain Aa residue 391 THR Chi-restraints excluded: chain Aa residue 404 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1081 random chunks: chunk 1008 optimal weight: 3.9990 chunk 117 optimal weight: 7.9990 chunk 595 optimal weight: 3.9990 chunk 763 optimal weight: 0.0000 chunk 591 optimal weight: 0.8980 chunk 880 optimal weight: 20.0000 chunk 584 optimal weight: 8.9990 chunk 1041 optimal weight: 30.0000 chunk 652 optimal weight: 0.9980 chunk 635 optimal weight: 9.9990 chunk 481 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 60 GLN BF 112 ASN BM 139 ASN ** BO 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BP 119 HIS BQ 103 HIS BS 43 ASN BT 99 ASN BU 138 GLN ** BV 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BV 155 GLN ** BW 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bd 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bf 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bh 196 HIS ** Bi 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bj 116 ASN ** Bp 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bq 88 GLN Br 44 ASN ** Bv 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bv 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bv 207 ASN ** Bw 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 118908 Z= 0.191 Angle : 0.532 14.612 169080 Z= 0.272 Chirality : 0.036 0.216 19886 Planarity : 0.004 0.122 15405 Dihedral : 18.219 179.580 34225 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.11 % Favored : 96.87 % Rotamer: Outliers : 3.19 % Allowed : 13.62 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.09), residues: 9255 helix: 1.73 (0.09), residues: 3220 sheet: 0.26 (0.15), residues: 1264 loop : -0.38 (0.09), residues: 4771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRPBu 174 HIS 0.007 0.001 HISBw 175 PHE 0.020 0.001 PHEBt 184 TYR 0.024 0.001 TYRBt 97 ARG 0.009 0.000 ARGBW 97 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18510 Ramachandran restraints generated. 9255 Oldfield, 0 Emsley, 9255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18510 Ramachandran restraints generated. 9255 Oldfield, 0 Emsley, 9255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1364 residues out of total 8262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 1102 time to evaluate : 7.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 54 LYS cc_start: 0.8659 (mttt) cc_final: 0.8349 (mttp) REVERT: BA 105 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7119 (tt0) REVERT: BB 12 LEU cc_start: 0.8257 (tt) cc_final: 0.7512 (mt) REVERT: BB 58 GLU cc_start: 0.8152 (tp30) cc_final: 0.7769 (tp30) REVERT: BC 111 SER cc_start: 0.8072 (m) cc_final: 0.7829 (p) REVERT: BC 127 ASP cc_start: 0.5550 (t70) cc_final: 0.4729 (t70) REVERT: BC 129 LYS cc_start: 0.5000 (mptt) cc_final: 0.4734 (mmtt) REVERT: BD 118 THR cc_start: 0.9062 (m) cc_final: 0.8752 (p) REVERT: BE 71 TYR cc_start: 0.8470 (m-10) cc_final: 0.8140 (m-80) REVERT: BE 150 LYS cc_start: 0.7456 (tttm) cc_final: 0.6885 (ptpp) REVERT: BE 159 MET cc_start: 0.7056 (mmm) cc_final: 0.6809 (mmm) REVERT: BF 75 ASN cc_start: 0.8678 (t0) cc_final: 0.8134 (t0) REVERT: BF 113 MET cc_start: 0.8774 (tmm) cc_final: 0.8111 (tmm) REVERT: BF 164 LYS cc_start: 0.6230 (mttm) cc_final: 0.5940 (mttm) REVERT: BF 213 MET cc_start: 0.8548 (mtm) cc_final: 0.8306 (mtp) REVERT: BG 35 LYS cc_start: 0.8153 (mttt) cc_final: 0.7717 (mtpp) REVERT: BG 40 ARG cc_start: 0.7839 (ttm170) cc_final: 0.7292 (mmt90) REVERT: BG 88 MET cc_start: 0.8244 (ptp) cc_final: 0.7757 (ptp) REVERT: BH 153 THR cc_start: 0.9482 (p) cc_final: 0.8883 (t) REVERT: BH 175 ILE cc_start: 0.8778 (mm) cc_final: 0.8442 (mt) REVERT: BH 176 GLU cc_start: 0.8019 (mp0) cc_final: 0.7682 (mm-30) REVERT: BI 21 MET cc_start: 0.6014 (mmm) cc_final: 0.5589 (mtp) REVERT: BL 168 ASP cc_start: 0.8592 (p0) cc_final: 0.8316 (p0) REVERT: BL 235 MET cc_start: 0.8550 (ttp) cc_final: 0.8311 (ttp) REVERT: BM 81 LYS cc_start: 0.7538 (mttt) cc_final: 0.6921 (mmtm) REVERT: BM 279 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8333 (ttpp) REVERT: BN 50 LYS cc_start: 0.7421 (mmmt) cc_final: 0.6451 (mmtt) REVERT: BN 205 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8142 (mp0) REVERT: BO 131 TYR cc_start: 0.7831 (m-80) cc_final: 0.7107 (m-80) REVERT: BO 137 LYS cc_start: 0.7279 (mttt) cc_final: 0.6911 (pttt) REVERT: BO 143 GLU cc_start: 0.7423 (tp30) cc_final: 0.7063 (mm-30) REVERT: BP 82 LEU cc_start: 0.8294 (mm) cc_final: 0.7839 (mt) REVERT: BP 95 MET cc_start: 0.6536 (ttp) cc_final: 0.5947 (tmm) REVERT: BP 115 GLN cc_start: 0.6886 (mm110) cc_final: 0.6651 (mm110) REVERT: BP 126 PHE cc_start: 0.8121 (m-80) cc_final: 0.7847 (m-10) REVERT: BQ 19 MET cc_start: 0.5272 (mmm) cc_final: 0.5011 (mmm) REVERT: BR 67 PHE cc_start: 0.9158 (OUTLIER) cc_final: 0.8837 (m-80) REVERT: BS 66 VAL cc_start: 0.9527 (OUTLIER) cc_final: 0.9310 (m) REVERT: BT 61 THR cc_start: 0.8781 (m) cc_final: 0.8551 (m) REVERT: BT 236 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7800 (tp) REVERT: BV 114 ASN cc_start: 0.8669 (t0) cc_final: 0.8283 (t0) REVERT: BW 98 ASN cc_start: 0.8557 (p0) cc_final: 0.8124 (p0) REVERT: BW 100 GLN cc_start: 0.8027 (mt0) cc_final: 0.7608 (pt0) REVERT: BX 99 MET cc_start: 0.8326 (mtm) cc_final: 0.8106 (mtp) REVERT: BX 244 ARG cc_start: 0.8634 (mmm-85) cc_final: 0.8017 (mmm160) REVERT: BX 284 ASP cc_start: 0.8233 (t70) cc_final: 0.7972 (m-30) REVERT: BY 22 GLN cc_start: 0.8233 (mm110) cc_final: 0.7783 (tp40) REVERT: BY 148 HIS cc_start: 0.7433 (t-90) cc_final: 0.7085 (t-170) REVERT: Bb 37 VAL cc_start: 0.8388 (t) cc_final: 0.8174 (p) REVERT: Bc 73 MET cc_start: 0.7018 (mmm) cc_final: 0.5765 (ttm) REVERT: Bc 133 SER cc_start: 0.8848 (m) cc_final: 0.8385 (t) REVERT: Bd 48 THR cc_start: 0.8261 (m) cc_final: 0.7967 (p) REVERT: Bd 66 HIS cc_start: 0.8457 (OUTLIER) cc_final: 0.7964 (t-170) REVERT: Bd 70 ARG cc_start: 0.7261 (OUTLIER) cc_final: 0.6473 (ttp-110) REVERT: Bd 73 ARG cc_start: 0.7084 (ptm160) cc_final: 0.6610 (ptt-90) REVERT: Bd 75 MET cc_start: 0.7797 (ptt) cc_final: 0.7172 (ptt) REVERT: Bd 90 ARG cc_start: 0.7813 (mtt180) cc_final: 0.6833 (tmm160) REVERT: Be 12 ILE cc_start: 0.8982 (mt) cc_final: 0.8722 (mm) REVERT: Bf 38 GLU cc_start: 0.5519 (mt-10) cc_final: 0.4461 (tp30) REVERT: Bf 131 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7722 (mt-10) REVERT: Bg 78 SER cc_start: 0.6708 (m) cc_final: 0.6501 (p) REVERT: Bh 37 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7183 (mm-30) REVERT: Bh 73 CYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7706 (p) REVERT: Bi 172 ASP cc_start: 0.7648 (m-30) cc_final: 0.7345 (m-30) REVERT: Bj 101 LYS cc_start: 0.6104 (mttt) cc_final: 0.5675 (tppt) REVERT: Bj 107 LYS cc_start: 0.6691 (mttt) cc_final: 0.6353 (pttm) REVERT: Bm 72 ARG cc_start: 0.7894 (ttm110) cc_final: 0.7168 (ptm160) REVERT: Bn 27 ARG cc_start: 0.7850 (tpt170) cc_final: 0.7259 (ttm170) REVERT: Bn 48 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8165 (mm) REVERT: Bn 160 ASP cc_start: 0.7873 (m-30) cc_final: 0.7618 (m-30) REVERT: Bo 46 ASN cc_start: 0.8883 (m-40) cc_final: 0.8542 (m110) REVERT: Bo 140 TRP cc_start: 0.8504 (OUTLIER) cc_final: 0.6365 (m-90) REVERT: Bo 176 PHE cc_start: 0.8156 (p90) cc_final: 0.7801 (p90) REVERT: Bo 178 TYR cc_start: 0.9144 (t80) cc_final: 0.8493 (t80) REVERT: Bo 243 GLN cc_start: 0.7719 (tp40) cc_final: 0.7390 (tp-100) REVERT: Bo 244 ASN cc_start: 0.6970 (m-40) cc_final: 0.6648 (t0) REVERT: Bo 310 ASN cc_start: 0.7946 (m-40) cc_final: 0.7486 (t0) REVERT: Bp 71 ARG cc_start: 0.7092 (mtt180) cc_final: 0.6351 (tpt-90) REVERT: Bp 97 LYS cc_start: 0.7056 (tppt) cc_final: 0.6624 (tptp) REVERT: Bq 48 PHE cc_start: 0.8926 (t80) cc_final: 0.8704 (t80) REVERT: Br 56 ARG cc_start: 0.8536 (mmt90) cc_final: 0.8189 (tpp80) REVERT: Br 73 LYS cc_start: 0.9004 (ptpt) cc_final: 0.8530 (ptmm) REVERT: Br 114 LYS cc_start: 0.8599 (ttpt) cc_final: 0.8168 (tttm) REVERT: Bt 45 LEU cc_start: 0.8317 (mt) cc_final: 0.8116 (tt) REVERT: Bt 59 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7411 (mtm180) REVERT: Bt 183 GLU cc_start: 0.7215 (mt-10) cc_final: 0.6730 (tt0) REVERT: Bt 240 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8196 (tt) REVERT: Bu 110 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7179 (mt-10) REVERT: Bu 226 ASP cc_start: 0.6987 (t0) cc_final: 0.6387 (t0) REVERT: Bu 244 GLU cc_start: 0.7632 (mp0) cc_final: 0.6978 (mp0) REVERT: Bu 261 MET cc_start: 0.6332 (ttm) cc_final: 0.5819 (ttp) REVERT: Bu 292 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7233 (mm-30) REVERT: Bv 58 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7292 (mm) REVERT: Bv 179 GLN cc_start: 0.6129 (OUTLIER) cc_final: 0.5870 (tm-30) REVERT: Bv 238 LEU cc_start: 0.6406 (mt) cc_final: 0.5482 (pp) REVERT: Bw 85 ASP cc_start: 0.7204 (t70) cc_final: 0.6817 (t0) REVERT: Bw 86 TYR cc_start: 0.6826 (m-80) cc_final: 0.6460 (m-10) REVERT: Bw 144 MET cc_start: 0.6109 (mmt) cc_final: 0.5865 (mmm) REVERT: Bw 186 VAL cc_start: 0.8773 (m) cc_final: 0.8445 (p) REVERT: Bx 141 ASN cc_start: 0.8090 (OUTLIER) cc_final: 0.7461 (t0) REVERT: By 121 MET cc_start: 0.6839 (mmp) cc_final: 0.6528 (mmt) REVERT: By 159 TYR cc_start: 0.6803 (OUTLIER) cc_final: 0.6253 (m-80) REVERT: Bz 41 ARG cc_start: 0.7760 (ptm160) cc_final: 0.7454 (ttt-90) REVERT: Bz 83 TRP cc_start: 0.8447 (t60) cc_final: 0.7851 (t60) REVERT: Aa 409 GLU cc_start: 0.5609 (tp30) cc_final: 0.5375 (mm-30) REVERT: Aa 442 LYS cc_start: 0.2365 (mmtt) cc_final: 0.2061 (ptmt) outliers start: 262 outliers final: 209 residues processed: 1264 average time/residue: 0.9527 time to fit residues: 2086.9591 Evaluate side-chains 1279 residues out of total 8262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 1053 time to evaluate : 7.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 105 GLU Chi-restraints excluded: chain BA residue 164 ILE Chi-restraints excluded: chain BA residue 170 CYS Chi-restraints excluded: chain BA residue 198 ILE Chi-restraints excluded: chain BB residue 70 THR Chi-restraints excluded: chain BB residue 113 GLU Chi-restraints excluded: chain BC residue 60 ASP Chi-restraints excluded: chain BC residue 78 GLN Chi-restraints excluded: chain BC residue 147 SER Chi-restraints excluded: chain BC residue 166 VAL Chi-restraints excluded: chain BC residue 181 ASP Chi-restraints excluded: chain BC residue 183 LEU Chi-restraints excluded: chain BC residue 204 ILE Chi-restraints excluded: chain BD residue 67 LEU Chi-restraints excluded: chain BD residue 83 LEU Chi-restraints excluded: chain BD residue 141 THR Chi-restraints excluded: chain BE residue 22 SER Chi-restraints excluded: chain BE residue 128 THR Chi-restraints excluded: chain BF residue 88 THR Chi-restraints excluded: chain BF residue 174 ILE Chi-restraints excluded: chain BG residue 74 SER Chi-restraints excluded: chain BG residue 137 THR Chi-restraints excluded: chain BI residue 49 VAL Chi-restraints excluded: chain BI residue 50 VAL Chi-restraints excluded: chain BI residue 59 GLN Chi-restraints excluded: chain BJ residue 92 SER Chi-restraints excluded: chain BL residue 68 SER Chi-restraints excluded: chain BL residue 73 THR Chi-restraints excluded: chain BL residue 91 ILE Chi-restraints excluded: chain BL residue 173 MET Chi-restraints excluded: chain BL residue 175 VAL Chi-restraints excluded: chain BL residue 237 VAL Chi-restraints excluded: chain BM residue 63 GLN Chi-restraints excluded: chain BM residue 97 VAL Chi-restraints excluded: chain BM residue 153 SER Chi-restraints excluded: chain BM residue 275 ARG Chi-restraints excluded: chain BM residue 279 LYS Chi-restraints excluded: chain BM residue 296 LEU Chi-restraints excluded: chain BM residue 313 ASN Chi-restraints excluded: chain BN residue 94 ASP Chi-restraints excluded: chain BN residue 106 PHE Chi-restraints excluded: chain BN residue 129 VAL Chi-restraints excluded: chain BN residue 151 VAL Chi-restraints excluded: chain BN residue 205 GLU Chi-restraints excluded: chain BN residue 225 ASP Chi-restraints excluded: chain BN residue 262 THR Chi-restraints excluded: chain BN residue 280 TYR Chi-restraints excluded: chain BN residue 281 THR Chi-restraints excluded: chain BO residue 93 ASN Chi-restraints excluded: chain BO residue 114 VAL Chi-restraints excluded: chain BO residue 184 LEU Chi-restraints excluded: chain BO residue 238 VAL Chi-restraints excluded: chain BP residue 30 SER Chi-restraints excluded: chain BP residue 99 CYS Chi-restraints excluded: chain BP residue 107 GLU Chi-restraints excluded: chain BP residue 116 LEU Chi-restraints excluded: chain BP residue 164 MET Chi-restraints excluded: chain BQ residue 44 VAL Chi-restraints excluded: chain BQ residue 128 ASP Chi-restraints excluded: chain BQ residue 135 VAL Chi-restraints excluded: chain BQ residue 143 SER Chi-restraints excluded: chain BQ residue 153 ILE Chi-restraints excluded: chain BQ residue 183 LEU Chi-restraints excluded: chain BR residue 67 PHE Chi-restraints excluded: chain BS residue 48 THR Chi-restraints excluded: chain BS residue 66 VAL Chi-restraints excluded: chain BS residue 71 ASP Chi-restraints excluded: chain BS residue 89 HIS Chi-restraints excluded: chain BS residue 126 SER Chi-restraints excluded: chain BT residue 33 SER Chi-restraints excluded: chain BT residue 146 ASP Chi-restraints excluded: chain BT residue 236 LEU Chi-restraints excluded: chain BT residue 243 VAL Chi-restraints excluded: chain BU residue 39 PHE Chi-restraints excluded: chain BU residue 58 LEU Chi-restraints excluded: chain BU residue 59 VAL Chi-restraints excluded: chain BU residue 113 MET Chi-restraints excluded: chain BU residue 121 LEU Chi-restraints excluded: chain BU residue 161 VAL Chi-restraints excluded: chain BV residue 9 ILE Chi-restraints excluded: chain BV residue 124 ILE Chi-restraints excluded: chain BV residue 141 SER Chi-restraints excluded: chain BV residue 156 ASP Chi-restraints excluded: chain BW residue 101 VAL Chi-restraints excluded: chain BW residue 157 SER Chi-restraints excluded: chain BW residue 166 THR Chi-restraints excluded: chain BX residue 130 THR Chi-restraints excluded: chain BX residue 154 THR Chi-restraints excluded: chain BX residue 177 VAL Chi-restraints excluded: chain BX residue 207 ILE Chi-restraints excluded: chain BX residue 265 LEU Chi-restraints excluded: chain BX residue 289 SER Chi-restraints excluded: chain BY residue 12 SER Chi-restraints excluded: chain BY residue 59 LEU Chi-restraints excluded: chain BY residue 63 SER Chi-restraints excluded: chain BY residue 76 SER Chi-restraints excluded: chain BY residue 87 ILE Chi-restraints excluded: chain BZ residue 58 THR Chi-restraints excluded: chain BZ residue 69 VAL Chi-restraints excluded: chain BZ residue 84 VAL Chi-restraints excluded: chain BZ residue 113 THR Chi-restraints excluded: chain BZ residue 158 VAL Chi-restraints excluded: chain Ba residue 71 GLU Chi-restraints excluded: chain Ba residue 77 VAL Chi-restraints excluded: chain Bb residue 8 LEU Chi-restraints excluded: chain Bb residue 30 THR Chi-restraints excluded: chain Bb residue 45 THR Chi-restraints excluded: chain Bb residue 75 ILE Chi-restraints excluded: chain Bd residue 40 LEU Chi-restraints excluded: chain Bd residue 58 VAL Chi-restraints excluded: chain Bd residue 66 HIS Chi-restraints excluded: chain Bd residue 70 ARG Chi-restraints excluded: chain Be residue 27 VAL Chi-restraints excluded: chain Be residue 41 THR Chi-restraints excluded: chain Be residue 59 GLU Chi-restraints excluded: chain Be residue 97 VAL Chi-restraints excluded: chain Be residue 101 TRP Chi-restraints excluded: chain Bf residue 110 ILE Chi-restraints excluded: chain Bf residue 185 GLU Chi-restraints excluded: chain Bg residue 41 ASP Chi-restraints excluded: chain Bh residue 38 VAL Chi-restraints excluded: chain Bh residue 67 THR Chi-restraints excluded: chain Bh residue 73 CYS Chi-restraints excluded: chain Bh residue 86 VAL Chi-restraints excluded: chain Bh residue 140 VAL Chi-restraints excluded: chain Bh residue 188 SER Chi-restraints excluded: chain Bh residue 192 LEU Chi-restraints excluded: chain Bi residue 76 VAL Chi-restraints excluded: chain Bi residue 132 ASP Chi-restraints excluded: chain Bi residue 159 VAL Chi-restraints excluded: chain Bi residue 260 CYS Chi-restraints excluded: chain Bi residue 274 ASN Chi-restraints excluded: chain Bi residue 345 VAL Chi-restraints excluded: chain Bi residue 350 VAL Chi-restraints excluded: chain Bi residue 356 THR Chi-restraints excluded: chain Bi residue 369 ASN Chi-restraints excluded: chain Bi residue 399 ILE Chi-restraints excluded: chain Bi residue 403 ASN Chi-restraints excluded: chain Bi residue 410 ASP Chi-restraints excluded: chain Bi residue 418 PHE Chi-restraints excluded: chain Bj residue 305 ILE Chi-restraints excluded: chain Bm residue 38 THR Chi-restraints excluded: chain Bm residue 64 MET Chi-restraints excluded: chain Bm residue 101 ASP Chi-restraints excluded: chain Bm residue 117 VAL Chi-restraints excluded: chain Bm residue 151 ASP Chi-restraints excluded: chain Bm residue 166 SER Chi-restraints excluded: chain Bm residue 203 CYS Chi-restraints excluded: chain Bm residue 248 THR Chi-restraints excluded: chain Bm residue 256 PHE Chi-restraints excluded: chain Bm residue 270 VAL Chi-restraints excluded: chain Bm residue 379 ASP Chi-restraints excluded: chain Bm residue 398 VAL Chi-restraints excluded: chain Bn residue 32 LEU Chi-restraints excluded: chain Bn residue 48 LEU Chi-restraints excluded: chain Bn residue 151 LEU Chi-restraints excluded: chain Bn residue 205 THR Chi-restraints excluded: chain Bn residue 227 GLU Chi-restraints excluded: chain Bn residue 231 GLU Chi-restraints excluded: chain Bn residue 245 VAL Chi-restraints excluded: chain Bn residue 276 ASP Chi-restraints excluded: chain Bn residue 279 ILE Chi-restraints excluded: chain Bn residue 302 ASP Chi-restraints excluded: chain Bn residue 321 CYS Chi-restraints excluded: chain Bo residue 126 THR Chi-restraints excluded: chain Bo residue 140 TRP Chi-restraints excluded: chain Bo residue 214 GLU Chi-restraints excluded: chain Bo residue 215 THR Chi-restraints excluded: chain Bo residue 260 VAL Chi-restraints excluded: chain Bo residue 290 VAL Chi-restraints excluded: chain Bp residue 87 ASP Chi-restraints excluded: chain Bp residue 94 PHE Chi-restraints excluded: chain Bp residue 167 SER Chi-restraints excluded: chain Bq residue 39 THR Chi-restraints excluded: chain Br residue 38 SER Chi-restraints excluded: chain Br residue 41 ASP Chi-restraints excluded: chain Br residue 59 VAL Chi-restraints excluded: chain Br residue 60 CYS Chi-restraints excluded: chain Br residue 93 LYS Chi-restraints excluded: chain Br residue 110 GLU Chi-restraints excluded: chain Br residue 115 MET Chi-restraints excluded: chain Bs residue 34 SER Chi-restraints excluded: chain Bs residue 45 GLU Chi-restraints excluded: chain Bs residue 75 VAL Chi-restraints excluded: chain Bs residue 84 VAL Chi-restraints excluded: chain Bs residue 93 SER Chi-restraints excluded: chain Bs residue 139 THR Chi-restraints excluded: chain Bt residue 59 ARG Chi-restraints excluded: chain Bt residue 85 LEU Chi-restraints excluded: chain Bt residue 93 VAL Chi-restraints excluded: chain Bt residue 148 LEU Chi-restraints excluded: chain Bt residue 176 GLU Chi-restraints excluded: chain Bt residue 231 MET Chi-restraints excluded: chain Bt residue 240 LEU Chi-restraints excluded: chain Bt residue 265 THR Chi-restraints excluded: chain Bu residue 76 ILE Chi-restraints excluded: chain Bu residue 150 LEU Chi-restraints excluded: chain Bu residue 165 THR Chi-restraints excluded: chain Bu residue 218 THR Chi-restraints excluded: chain Bu residue 266 ILE Chi-restraints excluded: chain Bu residue 281 MET Chi-restraints excluded: chain Bv residue 58 LEU Chi-restraints excluded: chain Bv residue 131 PHE Chi-restraints excluded: chain Bv residue 179 GLN Chi-restraints excluded: chain Bv residue 207 ASN Chi-restraints excluded: chain Bv residue 279 LEU Chi-restraints excluded: chain Bw residue 84 THR Chi-restraints excluded: chain Bw residue 90 VAL Chi-restraints excluded: chain Bw residue 132 MET Chi-restraints excluded: chain Bw residue 149 VAL Chi-restraints excluded: chain Bw residue 182 VAL Chi-restraints excluded: chain Bx residue 141 ASN Chi-restraints excluded: chain Bx residue 146 THR Chi-restraints excluded: chain By residue 128 LEU Chi-restraints excluded: chain By residue 159 TYR Chi-restraints excluded: chain Bz residue 43 VAL Chi-restraints excluded: chain Bz residue 75 LYS Chi-restraints excluded: chain Bz residue 100 ASN Chi-restraints excluded: chain Bz residue 115 SER Chi-restraints excluded: chain Aa residue 126 THR Chi-restraints excluded: chain Aa residue 247 VAL Chi-restraints excluded: chain Aa residue 269 SER Chi-restraints excluded: chain Aa residue 284 VAL Chi-restraints excluded: chain Aa residue 314 HIS Chi-restraints excluded: chain Aa residue 391 THR Chi-restraints excluded: chain Aa residue 404 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1081 random chunks: chunk 644 optimal weight: 10.0000 chunk 416 optimal weight: 1.9990 chunk 622 optimal weight: 2.9990 chunk 313 optimal weight: 0.7980 chunk 204 optimal weight: 3.9990 chunk 201 optimal weight: 7.9990 chunk 662 optimal weight: 3.9990 chunk 709 optimal weight: 10.0000 chunk 515 optimal weight: 8.9990 chunk 97 optimal weight: 7.9990 chunk 818 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 60 GLN ** BF 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 97 ASN BF 112 ASN ** BN 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BP 119 HIS BQ 103 HIS BS 142 GLN BT 99 ASN BU 138 GLN BU 210 GLN BV 155 GLN ** BW 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BW 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bd 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bf 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bh 196 HIS ** Bi 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bq 88 GLN Bs 27 GLN Bt 177 GLN ** Bv 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bv 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bv 207 ASN ** Bw 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 118908 Z= 0.271 Angle : 0.575 14.417 169080 Z= 0.294 Chirality : 0.038 0.231 19886 Planarity : 0.004 0.124 15405 Dihedral : 18.261 179.781 34225 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.75 % Favored : 96.23 % Rotamer: Outliers : 3.37 % Allowed : 13.61 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.09), residues: 9255 helix: 1.60 (0.09), residues: 3245 sheet: 0.18 (0.15), residues: 1257 loop : -0.47 (0.09), residues: 4753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRPBu 174 HIS 0.008 0.001 HISAa 110 PHE 0.020 0.001 PHEBy 99 TYR 0.034 0.002 TYRBt 97 ARG 0.009 0.000 ARGBW 97 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18510 Ramachandran restraints generated. 9255 Oldfield, 0 Emsley, 9255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18510 Ramachandran restraints generated. 9255 Oldfield, 0 Emsley, 9255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1354 residues out of total 8262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 277 poor density : 1077 time to evaluate : 7.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 54 LYS cc_start: 0.8682 (mttt) cc_final: 0.8373 (mttp) REVERT: BA 105 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7138 (tt0) REVERT: BB 12 LEU cc_start: 0.8256 (tt) cc_final: 0.7554 (mt) REVERT: BB 58 GLU cc_start: 0.8183 (tp30) cc_final: 0.7815 (tp30) REVERT: BC 111 SER cc_start: 0.8099 (m) cc_final: 0.7861 (p) REVERT: BC 127 ASP cc_start: 0.5474 (t70) cc_final: 0.4669 (t70) REVERT: BC 129 LYS cc_start: 0.4944 (mptt) cc_final: 0.4678 (mmtt) REVERT: BE 71 TYR cc_start: 0.8508 (m-80) cc_final: 0.8183 (m-80) REVERT: BE 150 LYS cc_start: 0.7451 (tttm) cc_final: 0.6911 (ptpp) REVERT: BE 159 MET cc_start: 0.7098 (mmm) cc_final: 0.6887 (mmm) REVERT: BF 75 ASN cc_start: 0.8690 (t0) cc_final: 0.8118 (t0) REVERT: BF 113 MET cc_start: 0.8784 (tmm) cc_final: 0.8115 (tmm) REVERT: BF 164 LYS cc_start: 0.6223 (mttm) cc_final: 0.5898 (mttm) REVERT: BF 213 MET cc_start: 0.8574 (mtm) cc_final: 0.8287 (mtp) REVERT: BG 35 LYS cc_start: 0.8212 (mttt) cc_final: 0.7755 (mtpp) REVERT: BG 40 ARG cc_start: 0.7798 (ttm170) cc_final: 0.7288 (mmt90) REVERT: BG 88 MET cc_start: 0.8240 (ptp) cc_final: 0.7729 (ptp) REVERT: BH 153 THR cc_start: 0.9486 (p) cc_final: 0.8921 (t) REVERT: BH 176 GLU cc_start: 0.8023 (mp0) cc_final: 0.7679 (mm-30) REVERT: BI 21 MET cc_start: 0.6085 (mmm) cc_final: 0.5640 (mtp) REVERT: BL 168 ASP cc_start: 0.8666 (p0) cc_final: 0.8307 (p0) REVERT: BL 235 MET cc_start: 0.8525 (ttp) cc_final: 0.8280 (ttp) REVERT: BM 81 LYS cc_start: 0.7545 (mttt) cc_final: 0.6991 (mmtm) REVERT: BM 234 THR cc_start: 0.8655 (OUTLIER) cc_final: 0.8445 (t) REVERT: BM 279 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8357 (ttpp) REVERT: BN 50 LYS cc_start: 0.7457 (mmmt) cc_final: 0.6417 (mmtt) REVERT: BN 209 TYR cc_start: 0.8515 (t80) cc_final: 0.7910 (t80) REVERT: BO 131 TYR cc_start: 0.7823 (m-80) cc_final: 0.7059 (m-80) REVERT: BO 137 LYS cc_start: 0.7322 (mttt) cc_final: 0.6926 (pttt) REVERT: BO 143 GLU cc_start: 0.7431 (tp30) cc_final: 0.7057 (mm-30) REVERT: BP 95 MET cc_start: 0.6543 (ttp) cc_final: 0.5857 (tmm) REVERT: BP 126 PHE cc_start: 0.8108 (m-80) cc_final: 0.7822 (m-80) REVERT: BQ 19 MET cc_start: 0.5514 (mmm) cc_final: 0.5148 (mmm) REVERT: BR 67 PHE cc_start: 0.9178 (OUTLIER) cc_final: 0.8739 (m-10) REVERT: BS 66 VAL cc_start: 0.9543 (OUTLIER) cc_final: 0.9327 (m) REVERT: BT 61 THR cc_start: 0.8878 (m) cc_final: 0.8647 (m) REVERT: BU 34 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.8021 (mp) REVERT: BV 114 ASN cc_start: 0.8666 (t0) cc_final: 0.8286 (t0) REVERT: BW 98 ASN cc_start: 0.8641 (p0) cc_final: 0.8169 (p0) REVERT: BW 100 GLN cc_start: 0.7980 (mt0) cc_final: 0.7499 (pt0) REVERT: BX 244 ARG cc_start: 0.8689 (mmm-85) cc_final: 0.8161 (mmm160) REVERT: BX 268 ASP cc_start: 0.8997 (t0) cc_final: 0.8673 (m-30) REVERT: BX 284 ASP cc_start: 0.8255 (t70) cc_final: 0.7955 (m-30) REVERT: BY 22 GLN cc_start: 0.8272 (mm110) cc_final: 0.8070 (tp40) REVERT: BY 148 HIS cc_start: 0.7471 (t-90) cc_final: 0.7138 (t-170) REVERT: Bb 37 VAL cc_start: 0.8378 (t) cc_final: 0.8168 (p) REVERT: Bc 73 MET cc_start: 0.7108 (mmm) cc_final: 0.5889 (ttm) REVERT: Bc 131 ARG cc_start: 0.8349 (ptp90) cc_final: 0.7669 (ptp90) REVERT: Bc 133 SER cc_start: 0.8905 (m) cc_final: 0.8480 (t) REVERT: Bd 48 THR cc_start: 0.8309 (m) cc_final: 0.8024 (p) REVERT: Bd 55 VAL cc_start: 0.8136 (p) cc_final: 0.7854 (m) REVERT: Bd 66 HIS cc_start: 0.8565 (OUTLIER) cc_final: 0.8103 (t-170) REVERT: Bd 70 ARG cc_start: 0.7410 (OUTLIER) cc_final: 0.6592 (ttp-110) REVERT: Bd 73 ARG cc_start: 0.7165 (ptm160) cc_final: 0.6484 (ptt-90) REVERT: Bd 75 MET cc_start: 0.7805 (ptt) cc_final: 0.7225 (ptt) REVERT: Bd 90 ARG cc_start: 0.7870 (mtt180) cc_final: 0.6837 (tmm160) REVERT: Be 12 ILE cc_start: 0.9006 (mt) cc_final: 0.8744 (mm) REVERT: Bf 38 GLU cc_start: 0.5447 (mt-10) cc_final: 0.4447 (tp30) REVERT: Bg 78 SER cc_start: 0.6691 (m) cc_final: 0.6421 (p) REVERT: Bh 73 CYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7601 (p) REVERT: Bj 101 LYS cc_start: 0.6118 (mttt) cc_final: 0.5738 (tppt) REVERT: Bj 107 LYS cc_start: 0.6566 (mttt) cc_final: 0.6238 (pttm) REVERT: Bl 79 VAL cc_start: 0.8595 (OUTLIER) cc_final: 0.8359 (m) REVERT: Bl 99 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7932 (tt0) REVERT: Bm 72 ARG cc_start: 0.7822 (ttm110) cc_final: 0.7131 (ptm160) REVERT: Bm 262 THR cc_start: 0.9201 (OUTLIER) cc_final: 0.8956 (m) REVERT: Bn 27 ARG cc_start: 0.7877 (tpt170) cc_final: 0.7260 (ttm170) REVERT: Bn 48 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8186 (mm) REVERT: Bn 160 ASP cc_start: 0.7982 (m-30) cc_final: 0.7718 (m-30) REVERT: Bo 46 ASN cc_start: 0.8858 (m-40) cc_final: 0.8522 (m110) REVERT: Bo 140 TRP cc_start: 0.8590 (OUTLIER) cc_final: 0.6573 (m-90) REVERT: Bo 176 PHE cc_start: 0.8240 (p90) cc_final: 0.7886 (p90) REVERT: Bo 178 TYR cc_start: 0.9250 (t80) cc_final: 0.8459 (t80) REVERT: Bo 243 GLN cc_start: 0.7777 (tp40) cc_final: 0.7443 (tp-100) REVERT: Bo 244 ASN cc_start: 0.6950 (m-40) cc_final: 0.6701 (t0) REVERT: Bo 310 ASN cc_start: 0.7995 (m-40) cc_final: 0.7473 (t0) REVERT: Bp 71 ARG cc_start: 0.7097 (mtt180) cc_final: 0.6319 (tpt170) REVERT: Bp 97 LYS cc_start: 0.6992 (tppt) cc_final: 0.6574 (tptp) REVERT: Bq 48 PHE cc_start: 0.9023 (t80) cc_final: 0.8716 (t80) REVERT: Br 56 ARG cc_start: 0.8569 (mmt90) cc_final: 0.8187 (tpp80) REVERT: Br 73 LYS cc_start: 0.9012 (ptpt) cc_final: 0.8546 (ptmm) REVERT: Br 114 LYS cc_start: 0.8616 (ttpt) cc_final: 0.8168 (tttm) REVERT: Bt 45 LEU cc_start: 0.8327 (mt) cc_final: 0.8125 (tt) REVERT: Bt 59 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7450 (mtm180) REVERT: Bt 183 GLU cc_start: 0.7261 (mt-10) cc_final: 0.6858 (tt0) REVERT: Bt 240 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8202 (tt) REVERT: Bu 110 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7125 (mt-10) REVERT: Bu 209 TYR cc_start: 0.7628 (m-80) cc_final: 0.7005 (m-80) REVERT: Bu 226 ASP cc_start: 0.6964 (t0) cc_final: 0.6337 (t0) REVERT: Bu 244 GLU cc_start: 0.7660 (mp0) cc_final: 0.7017 (mp0) REVERT: Bu 261 MET cc_start: 0.6237 (ttm) cc_final: 0.5734 (ttp) REVERT: Bu 292 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7162 (mm-30) REVERT: Bv 179 GLN cc_start: 0.5874 (OUTLIER) cc_final: 0.5663 (tm-30) REVERT: Bv 238 LEU cc_start: 0.6618 (mt) cc_final: 0.5813 (pp) REVERT: Bv 278 ASP cc_start: 0.6832 (OUTLIER) cc_final: 0.5534 (t0) REVERT: Bw 85 ASP cc_start: 0.7266 (t70) cc_final: 0.6753 (t0) REVERT: Bw 86 TYR cc_start: 0.6856 (m-80) cc_final: 0.6527 (m-10) REVERT: Bw 144 MET cc_start: 0.6194 (mmt) cc_final: 0.5926 (mmm) REVERT: Bw 186 VAL cc_start: 0.8784 (m) cc_final: 0.8420 (p) REVERT: Bx 141 ASN cc_start: 0.8114 (OUTLIER) cc_final: 0.7466 (t0) REVERT: By 159 TYR cc_start: 0.6891 (OUTLIER) cc_final: 0.6301 (m-80) REVERT: Bz 41 ARG cc_start: 0.7803 (ptm160) cc_final: 0.7461 (ttt-90) REVERT: Bz 83 TRP cc_start: 0.8496 (t60) cc_final: 0.7888 (t60) REVERT: Aa 206 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8276 (mp0) REVERT: Aa 373 LYS cc_start: 0.7205 (mtmt) cc_final: 0.6249 (tptm) REVERT: Aa 442 LYS cc_start: 0.2402 (mmtt) cc_final: 0.2125 (ptmt) outliers start: 277 outliers final: 220 residues processed: 1252 average time/residue: 0.9494 time to fit residues: 2062.3981 Evaluate side-chains 1276 residues out of total 8262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 1035 time to evaluate : 7.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 105 GLU Chi-restraints excluded: chain BA residue 164 ILE Chi-restraints excluded: chain BA residue 170 CYS Chi-restraints excluded: chain BA residue 198 ILE Chi-restraints excluded: chain BB residue 70 THR Chi-restraints excluded: chain BB residue 91 ASP Chi-restraints excluded: chain BB residue 113 GLU Chi-restraints excluded: chain BC residue 44 VAL Chi-restraints excluded: chain BC residue 60 ASP Chi-restraints excluded: chain BC residue 78 GLN Chi-restraints excluded: chain BC residue 147 SER Chi-restraints excluded: chain BC residue 166 VAL Chi-restraints excluded: chain BC residue 181 ASP Chi-restraints excluded: chain BC residue 183 LEU Chi-restraints excluded: chain BC residue 204 ILE Chi-restraints excluded: chain BD residue 67 LEU Chi-restraints excluded: chain BD residue 83 LEU Chi-restraints excluded: chain BD residue 109 SER Chi-restraints excluded: chain BD residue 141 THR Chi-restraints excluded: chain BE residue 22 SER Chi-restraints excluded: chain BE residue 46 HIS Chi-restraints excluded: chain BE residue 128 THR Chi-restraints excluded: chain BE residue 166 LEU Chi-restraints excluded: chain BF residue 88 THR Chi-restraints excluded: chain BF residue 160 THR Chi-restraints excluded: chain BF residue 174 ILE Chi-restraints excluded: chain BG residue 74 SER Chi-restraints excluded: chain BG residue 137 THR Chi-restraints excluded: chain BI residue 49 VAL Chi-restraints excluded: chain BI residue 50 VAL Chi-restraints excluded: chain BI residue 59 GLN Chi-restraints excluded: chain BJ residue 92 SER Chi-restraints excluded: chain BL residue 68 SER Chi-restraints excluded: chain BL residue 73 THR Chi-restraints excluded: chain BL residue 91 ILE Chi-restraints excluded: chain BL residue 175 VAL Chi-restraints excluded: chain BL residue 237 VAL Chi-restraints excluded: chain BM residue 63 GLN Chi-restraints excluded: chain BM residue 97 VAL Chi-restraints excluded: chain BM residue 153 SER Chi-restraints excluded: chain BM residue 234 THR Chi-restraints excluded: chain BM residue 275 ARG Chi-restraints excluded: chain BM residue 279 LYS Chi-restraints excluded: chain BM residue 295 CYS Chi-restraints excluded: chain BM residue 296 LEU Chi-restraints excluded: chain BM residue 313 ASN Chi-restraints excluded: chain BN residue 94 ASP Chi-restraints excluded: chain BN residue 106 PHE Chi-restraints excluded: chain BN residue 129 VAL Chi-restraints excluded: chain BN residue 151 VAL Chi-restraints excluded: chain BN residue 225 ASP Chi-restraints excluded: chain BN residue 262 THR Chi-restraints excluded: chain BN residue 281 THR Chi-restraints excluded: chain BO residue 92 ASP Chi-restraints excluded: chain BO residue 114 VAL Chi-restraints excluded: chain BO residue 184 LEU Chi-restraints excluded: chain BP residue 30 SER Chi-restraints excluded: chain BP residue 99 CYS Chi-restraints excluded: chain BP residue 107 GLU Chi-restraints excluded: chain BP residue 116 LEU Chi-restraints excluded: chain BP residue 164 MET Chi-restraints excluded: chain BP residue 187 SER Chi-restraints excluded: chain BQ residue 44 VAL Chi-restraints excluded: chain BQ residue 128 ASP Chi-restraints excluded: chain BQ residue 135 VAL Chi-restraints excluded: chain BQ residue 143 SER Chi-restraints excluded: chain BQ residue 153 ILE Chi-restraints excluded: chain BQ residue 183 LEU Chi-restraints excluded: chain BR residue 67 PHE Chi-restraints excluded: chain BS residue 48 THR Chi-restraints excluded: chain BS residue 66 VAL Chi-restraints excluded: chain BS residue 71 ASP Chi-restraints excluded: chain BS residue 89 HIS Chi-restraints excluded: chain BS residue 115 VAL Chi-restraints excluded: chain BS residue 126 SER Chi-restraints excluded: chain BS residue 142 GLN Chi-restraints excluded: chain BT residue 33 SER Chi-restraints excluded: chain BT residue 243 VAL Chi-restraints excluded: chain BU residue 34 LEU Chi-restraints excluded: chain BU residue 39 PHE Chi-restraints excluded: chain BU residue 58 LEU Chi-restraints excluded: chain BU residue 59 VAL Chi-restraints excluded: chain BU residue 113 MET Chi-restraints excluded: chain BU residue 121 LEU Chi-restraints excluded: chain BU residue 161 VAL Chi-restraints excluded: chain BV residue 9 ILE Chi-restraints excluded: chain BV residue 124 ILE Chi-restraints excluded: chain BV residue 141 SER Chi-restraints excluded: chain BV residue 156 ASP Chi-restraints excluded: chain BW residue 101 VAL Chi-restraints excluded: chain BW residue 157 SER Chi-restraints excluded: chain BW residue 166 THR Chi-restraints excluded: chain BX residue 154 THR Chi-restraints excluded: chain BX residue 171 ILE Chi-restraints excluded: chain BX residue 177 VAL Chi-restraints excluded: chain BX residue 207 ILE Chi-restraints excluded: chain BX residue 265 LEU Chi-restraints excluded: chain BX residue 289 SER Chi-restraints excluded: chain BY residue 12 SER Chi-restraints excluded: chain BY residue 59 LEU Chi-restraints excluded: chain BY residue 63 SER Chi-restraints excluded: chain BY residue 76 SER Chi-restraints excluded: chain BY residue 87 ILE Chi-restraints excluded: chain BZ residue 58 THR Chi-restraints excluded: chain BZ residue 69 VAL Chi-restraints excluded: chain BZ residue 84 VAL Chi-restraints excluded: chain BZ residue 113 THR Chi-restraints excluded: chain BZ residue 158 VAL Chi-restraints excluded: chain Ba residue 71 GLU Chi-restraints excluded: chain Ba residue 77 VAL Chi-restraints excluded: chain Bb residue 8 LEU Chi-restraints excluded: chain Bb residue 30 THR Chi-restraints excluded: chain Bb residue 45 THR Chi-restraints excluded: chain Bb residue 75 ILE Chi-restraints excluded: chain Bd residue 40 LEU Chi-restraints excluded: chain Bd residue 58 VAL Chi-restraints excluded: chain Bd residue 66 HIS Chi-restraints excluded: chain Bd residue 70 ARG Chi-restraints excluded: chain Be residue 27 VAL Chi-restraints excluded: chain Be residue 41 THR Chi-restraints excluded: chain Be residue 59 GLU Chi-restraints excluded: chain Be residue 97 VAL Chi-restraints excluded: chain Be residue 101 TRP Chi-restraints excluded: chain Bf residue 40 GLN Chi-restraints excluded: chain Bf residue 110 ILE Chi-restraints excluded: chain Bg residue 41 ASP Chi-restraints excluded: chain Bh residue 38 VAL Chi-restraints excluded: chain Bh residue 67 THR Chi-restraints excluded: chain Bh residue 73 CYS Chi-restraints excluded: chain Bh residue 86 VAL Chi-restraints excluded: chain Bh residue 99 MET Chi-restraints excluded: chain Bh residue 140 VAL Chi-restraints excluded: chain Bh residue 188 SER Chi-restraints excluded: chain Bh residue 192 LEU Chi-restraints excluded: chain Bi residue 76 VAL Chi-restraints excluded: chain Bi residue 132 ASP Chi-restraints excluded: chain Bi residue 159 VAL Chi-restraints excluded: chain Bi residue 182 LEU Chi-restraints excluded: chain Bi residue 260 CYS Chi-restraints excluded: chain Bi residue 274 ASN Chi-restraints excluded: chain Bi residue 345 VAL Chi-restraints excluded: chain Bi residue 350 VAL Chi-restraints excluded: chain Bi residue 356 THR Chi-restraints excluded: chain Bi residue 369 ASN Chi-restraints excluded: chain Bi residue 399 ILE Chi-restraints excluded: chain Bi residue 403 ASN Chi-restraints excluded: chain Bi residue 410 ASP Chi-restraints excluded: chain Bi residue 418 PHE Chi-restraints excluded: chain Bj residue 305 ILE Chi-restraints excluded: chain Bl residue 79 VAL Chi-restraints excluded: chain Bl residue 99 GLN Chi-restraints excluded: chain Bm residue 38 THR Chi-restraints excluded: chain Bm residue 64 MET Chi-restraints excluded: chain Bm residue 101 ASP Chi-restraints excluded: chain Bm residue 151 ASP Chi-restraints excluded: chain Bm residue 166 SER Chi-restraints excluded: chain Bm residue 203 CYS Chi-restraints excluded: chain Bm residue 207 ASN Chi-restraints excluded: chain Bm residue 248 THR Chi-restraints excluded: chain Bm residue 256 PHE Chi-restraints excluded: chain Bm residue 262 THR Chi-restraints excluded: chain Bm residue 270 VAL Chi-restraints excluded: chain Bm residue 379 ASP Chi-restraints excluded: chain Bm residue 398 VAL Chi-restraints excluded: chain Bn residue 32 LEU Chi-restraints excluded: chain Bn residue 48 LEU Chi-restraints excluded: chain Bn residue 73 THR Chi-restraints excluded: chain Bn residue 151 LEU Chi-restraints excluded: chain Bn residue 205 THR Chi-restraints excluded: chain Bn residue 227 GLU Chi-restraints excluded: chain Bn residue 245 VAL Chi-restraints excluded: chain Bn residue 276 ASP Chi-restraints excluded: chain Bn residue 279 ILE Chi-restraints excluded: chain Bn residue 302 ASP Chi-restraints excluded: chain Bn residue 321 CYS Chi-restraints excluded: chain Bo residue 58 ARG Chi-restraints excluded: chain Bo residue 102 LEU Chi-restraints excluded: chain Bo residue 126 THR Chi-restraints excluded: chain Bo residue 140 TRP Chi-restraints excluded: chain Bo residue 214 GLU Chi-restraints excluded: chain Bo residue 215 THR Chi-restraints excluded: chain Bo residue 290 VAL Chi-restraints excluded: chain Bp residue 87 ASP Chi-restraints excluded: chain Bp residue 94 PHE Chi-restraints excluded: chain Bp residue 167 SER Chi-restraints excluded: chain Bq residue 39 THR Chi-restraints excluded: chain Br residue 38 SER Chi-restraints excluded: chain Br residue 59 VAL Chi-restraints excluded: chain Br residue 60 CYS Chi-restraints excluded: chain Br residue 65 VAL Chi-restraints excluded: chain Br residue 110 GLU Chi-restraints excluded: chain Br residue 115 MET Chi-restraints excluded: chain Bs residue 34 SER Chi-restraints excluded: chain Bs residue 45 GLU Chi-restraints excluded: chain Bs residue 75 VAL Chi-restraints excluded: chain Bs residue 84 VAL Chi-restraints excluded: chain Bs residue 91 CYS Chi-restraints excluded: chain Bs residue 93 SER Chi-restraints excluded: chain Bs residue 113 ILE Chi-restraints excluded: chain Bs residue 139 THR Chi-restraints excluded: chain Bt residue 59 ARG Chi-restraints excluded: chain Bt residue 85 LEU Chi-restraints excluded: chain Bt residue 93 VAL Chi-restraints excluded: chain Bt residue 148 LEU Chi-restraints excluded: chain Bt residue 176 GLU Chi-restraints excluded: chain Bt residue 231 MET Chi-restraints excluded: chain Bt residue 240 LEU Chi-restraints excluded: chain Bt residue 265 THR Chi-restraints excluded: chain Bu residue 76 ILE Chi-restraints excluded: chain Bu residue 150 LEU Chi-restraints excluded: chain Bu residue 165 THR Chi-restraints excluded: chain Bu residue 218 THR Chi-restraints excluded: chain Bu residue 266 ILE Chi-restraints excluded: chain Bu residue 281 MET Chi-restraints excluded: chain Bv residue 58 LEU Chi-restraints excluded: chain Bv residue 131 PHE Chi-restraints excluded: chain Bv residue 179 GLN Chi-restraints excluded: chain Bv residue 207 ASN Chi-restraints excluded: chain Bv residue 278 ASP Chi-restraints excluded: chain Bv residue 279 LEU Chi-restraints excluded: chain Bw residue 84 THR Chi-restraints excluded: chain Bw residue 90 VAL Chi-restraints excluded: chain Bw residue 182 VAL Chi-restraints excluded: chain Bx residue 141 ASN Chi-restraints excluded: chain Bx residue 144 THR Chi-restraints excluded: chain Bx residue 146 THR Chi-restraints excluded: chain By residue 128 LEU Chi-restraints excluded: chain By residue 159 TYR Chi-restraints excluded: chain Bz residue 43 VAL Chi-restraints excluded: chain Bz residue 75 LYS Chi-restraints excluded: chain Bz residue 100 ASN Chi-restraints excluded: chain Bz residue 102 MET Chi-restraints excluded: chain Bz residue 115 SER Chi-restraints excluded: chain Aa residue 126 THR Chi-restraints excluded: chain Aa residue 206 GLU Chi-restraints excluded: chain Aa residue 247 VAL Chi-restraints excluded: chain Aa residue 269 SER Chi-restraints excluded: chain Aa residue 284 VAL Chi-restraints excluded: chain Aa residue 314 HIS Chi-restraints excluded: chain Aa residue 391 THR Chi-restraints excluded: chain Aa residue 404 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1081 random chunks: chunk 947 optimal weight: 9.9990 chunk 998 optimal weight: 9.9990 chunk 910 optimal weight: 0.5980 chunk 970 optimal weight: 8.9990 chunk 997 optimal weight: 9.9990 chunk 584 optimal weight: 6.9990 chunk 422 optimal weight: 7.9990 chunk 762 optimal weight: 9.9990 chunk 297 optimal weight: 10.0000 chunk 877 optimal weight: 8.9990 chunk 918 optimal weight: 3.9990 overall best weight: 5.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 60 GLN BA 99 GLN BD 86 ASN ** BF 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BF 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 112 ASN BH 96 ASN BH 120 HIS ** BN 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BN 251 HIS ** BO 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BP 93 ASN BQ 103 HIS BR 126 HIS BS 142 GLN ** BT 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BT 99 ASN BU 138 GLN BV 155 GLN ** BX 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bd 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Be 30 GLN ** Bf 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bg 100 GLN Bi 161 GLN ** Bi 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bn 77 HIS Bn 266 HIS Bo 91 HIS ** Bp 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bq 88 GLN Bu 119 GLN ** Bv 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bv 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bw 189 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.112 118908 Z= 0.525 Angle : 0.763 14.142 169080 Z= 0.386 Chirality : 0.045 0.294 19886 Planarity : 0.006 0.129 15405 Dihedral : 18.544 179.900 34221 Min Nonbonded Distance : 1.695 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.16 % Favored : 94.81 % Rotamer: Outliers : 3.30 % Allowed : 14.26 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.09), residues: 9255 helix: 1.05 (0.09), residues: 3225 sheet: -0.30 (0.14), residues: 1265 loop : -0.83 (0.09), residues: 4765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRPBL 151 HIS 0.010 0.002 HISBz 69 PHE 0.029 0.002 PHEBm 414 TYR 0.032 0.003 TYRBr 43 ARG 0.009 0.001 ARGBW 97 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18510 Ramachandran restraints generated. 9255 Oldfield, 0 Emsley, 9255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18510 Ramachandran restraints generated. 9255 Oldfield, 0 Emsley, 9255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1346 residues out of total 8262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 271 poor density : 1075 time to evaluate : 6.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 54 LYS cc_start: 0.8680 (mttt) cc_final: 0.8407 (mttp) REVERT: BA 105 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7306 (tt0) REVERT: BA 150 TYR cc_start: 0.9175 (m-80) cc_final: 0.8968 (m-80) REVERT: BB 12 LEU cc_start: 0.8411 (tt) cc_final: 0.7701 (mt) REVERT: BB 58 GLU cc_start: 0.8229 (tp30) cc_final: 0.7943 (tp30) REVERT: BC 127 ASP cc_start: 0.5188 (t70) cc_final: 0.4556 (t70) REVERT: BC 129 LYS cc_start: 0.4973 (mptt) cc_final: 0.4719 (mmtt) REVERT: BD 86 ASN cc_start: 0.9269 (OUTLIER) cc_final: 0.9048 (p0) REVERT: BE 71 TYR cc_start: 0.8571 (m-80) cc_final: 0.8238 (m-80) REVERT: BE 150 LYS cc_start: 0.7370 (tttm) cc_final: 0.6794 (ptpp) REVERT: BF 75 ASN cc_start: 0.8808 (t0) cc_final: 0.8195 (t0) REVERT: BF 113 MET cc_start: 0.8836 (tmm) cc_final: 0.8055 (tmm) REVERT: BF 164 LYS cc_start: 0.6188 (mttm) cc_final: 0.5980 (mttm) REVERT: BF 213 MET cc_start: 0.8666 (mtm) cc_final: 0.8338 (mtp) REVERT: BG 35 LYS cc_start: 0.8331 (mttt) cc_final: 0.7834 (mtpp) REVERT: BG 40 ARG cc_start: 0.7787 (ttm170) cc_final: 0.7379 (mmt90) REVERT: BG 88 MET cc_start: 0.8385 (ptp) cc_final: 0.7882 (ptp) REVERT: BH 176 GLU cc_start: 0.8013 (mp0) cc_final: 0.7552 (mm-30) REVERT: BI 21 MET cc_start: 0.6120 (mmm) cc_final: 0.5803 (mtp) REVERT: BL 235 MET cc_start: 0.8515 (ttp) cc_final: 0.8237 (ttp) REVERT: BM 81 LYS cc_start: 0.7733 (mttt) cc_final: 0.7151 (mmtm) REVERT: BM 275 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7360 (ttp80) REVERT: BM 279 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8462 (ttpp) REVERT: BN 50 LYS cc_start: 0.7494 (mmmt) cc_final: 0.6471 (mmtt) REVERT: BO 131 TYR cc_start: 0.7892 (m-80) cc_final: 0.7305 (m-80) REVERT: BO 137 LYS cc_start: 0.7414 (mttt) cc_final: 0.6917 (pttt) REVERT: BO 143 GLU cc_start: 0.7424 (tp30) cc_final: 0.7044 (mm-30) REVERT: BP 95 MET cc_start: 0.6676 (ttp) cc_final: 0.5491 (ttp) REVERT: BQ 19 MET cc_start: 0.5617 (mmm) cc_final: 0.5258 (mmm) REVERT: BQ 113 THR cc_start: 0.7504 (t) cc_final: 0.7301 (t) REVERT: BR 67 PHE cc_start: 0.9207 (OUTLIER) cc_final: 0.8638 (m-10) REVERT: BR 83 TYR cc_start: 0.8947 (m-80) cc_final: 0.8734 (m-80) REVERT: BR 132 ASP cc_start: 0.7491 (t0) cc_final: 0.7290 (t0) REVERT: BU 34 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8041 (mp) REVERT: BV 70 GLU cc_start: 0.8483 (mm-30) cc_final: 0.7982 (tp30) REVERT: BW 98 ASN cc_start: 0.8698 (p0) cc_final: 0.8193 (p0) REVERT: BW 100 GLN cc_start: 0.8126 (mt0) cc_final: 0.7543 (pt0) REVERT: BX 99 MET cc_start: 0.8862 (mtp) cc_final: 0.8645 (mtm) REVERT: BX 113 VAL cc_start: 0.9132 (t) cc_final: 0.8851 (p) REVERT: BX 244 ARG cc_start: 0.8751 (mmm-85) cc_final: 0.8143 (mmm160) REVERT: BX 268 ASP cc_start: 0.9036 (t0) cc_final: 0.8648 (m-30) REVERT: BY 22 GLN cc_start: 0.8407 (mm110) cc_final: 0.8186 (tp40) REVERT: BY 148 HIS cc_start: 0.7526 (t-90) cc_final: 0.7227 (t-170) REVERT: BZ 122 ASN cc_start: 0.8599 (p0) cc_final: 0.8350 (p0) REVERT: BZ 125 ASP cc_start: 0.6875 (p0) cc_final: 0.6665 (p0) REVERT: BZ 155 LYS cc_start: 0.8529 (mttt) cc_final: 0.8249 (mmmt) REVERT: Bc 73 MET cc_start: 0.7210 (mmm) cc_final: 0.5874 (ttm) REVERT: Bc 131 ARG cc_start: 0.8316 (ptp90) cc_final: 0.7678 (ptp90) REVERT: Bc 133 SER cc_start: 0.8966 (m) cc_final: 0.8677 (t) REVERT: Bd 48 THR cc_start: 0.8328 (m) cc_final: 0.8100 (p) REVERT: Bd 66 HIS cc_start: 0.8854 (OUTLIER) cc_final: 0.8171 (t-170) REVERT: Bd 70 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.7127 (ttm170) REVERT: Bd 73 ARG cc_start: 0.7155 (ptm160) cc_final: 0.6304 (ttp80) REVERT: Bd 75 MET cc_start: 0.7744 (ptt) cc_final: 0.7252 (ptt) REVERT: Be 12 ILE cc_start: 0.9070 (mt) cc_final: 0.8832 (mm) REVERT: Bf 155 ASP cc_start: 0.7102 (m-30) cc_final: 0.6505 (m-30) REVERT: Bg 78 SER cc_start: 0.6729 (m) cc_final: 0.6425 (p) REVERT: Bh 73 CYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7510 (p) REVERT: Bi 152 ARG cc_start: 0.8482 (ptp-170) cc_final: 0.8182 (mtm180) REVERT: Bi 288 TYR cc_start: 0.8005 (m-10) cc_final: 0.7706 (m-80) REVERT: Bj 101 LYS cc_start: 0.6158 (mttt) cc_final: 0.5736 (tppt) REVERT: Bj 107 LYS cc_start: 0.6635 (mttt) cc_final: 0.6302 (pttm) REVERT: Bl 99 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.8038 (tt0) REVERT: Bm 72 ARG cc_start: 0.7808 (ttm110) cc_final: 0.7075 (ptm160) REVERT: Bm 262 THR cc_start: 0.9356 (OUTLIER) cc_final: 0.9107 (m) REVERT: Bn 27 ARG cc_start: 0.7898 (tpt170) cc_final: 0.7350 (ttm170) REVERT: Bn 48 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8154 (mm) REVERT: Bn 160 ASP cc_start: 0.7887 (m-30) cc_final: 0.7539 (m-30) REVERT: Bo 46 ASN cc_start: 0.8805 (m-40) cc_final: 0.8518 (m110) REVERT: Bo 140 TRP cc_start: 0.8752 (OUTLIER) cc_final: 0.6859 (m-90) REVERT: Bo 176 PHE cc_start: 0.8537 (p90) cc_final: 0.8135 (p90) REVERT: Bo 178 TYR cc_start: 0.9385 (t80) cc_final: 0.8675 (t80) REVERT: Bo 310 ASN cc_start: 0.8086 (m-40) cc_final: 0.7444 (t0) REVERT: Bp 71 ARG cc_start: 0.7059 (mtt180) cc_final: 0.6295 (tpt170) REVERT: Bp 97 LYS cc_start: 0.7106 (tppt) cc_final: 0.6694 (tptp) REVERT: Bq 50 GLN cc_start: 0.9134 (tt0) cc_final: 0.8888 (tt0) REVERT: Br 56 ARG cc_start: 0.8649 (mmt90) cc_final: 0.8150 (tpp80) REVERT: Br 114 LYS cc_start: 0.8639 (ttpt) cc_final: 0.8156 (tttm) REVERT: Bt 45 LEU cc_start: 0.8463 (mt) cc_final: 0.8054 (tt) REVERT: Bt 59 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7408 (mtm180) REVERT: Bt 183 GLU cc_start: 0.7266 (mt-10) cc_final: 0.6918 (tt0) REVERT: Bt 240 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8213 (tt) REVERT: Bu 226 ASP cc_start: 0.7360 (t0) cc_final: 0.6791 (t0) REVERT: Bu 244 GLU cc_start: 0.7586 (mp0) cc_final: 0.6962 (mp0) REVERT: Bu 261 MET cc_start: 0.6273 (ttm) cc_final: 0.5806 (ttp) REVERT: Bu 292 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7258 (mm-30) REVERT: Bv 58 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7088 (mm) REVERT: Bv 78 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8243 (mt-10) REVERT: Bv 238 LEU cc_start: 0.6711 (mt) cc_final: 0.6048 (pp) REVERT: Bv 278 ASP cc_start: 0.6720 (OUTLIER) cc_final: 0.5384 (t0) REVERT: Bw 85 ASP cc_start: 0.7073 (t70) cc_final: 0.6798 (t0) REVERT: Bw 138 GLN cc_start: 0.5357 (tm-30) cc_final: 0.5127 (tm-30) REVERT: Bw 144 MET cc_start: 0.6139 (mmt) cc_final: 0.5863 (mmm) REVERT: Bx 94 ILE cc_start: 0.9050 (mm) cc_final: 0.8810 (mt) REVERT: By 121 MET cc_start: 0.7102 (mmp) cc_final: 0.6688 (mmt) REVERT: By 159 TYR cc_start: 0.6947 (OUTLIER) cc_final: 0.6421 (m-80) REVERT: Bz 83 TRP cc_start: 0.8617 (t60) cc_final: 0.8029 (t60) REVERT: Aa 206 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8335 (mp0) REVERT: Aa 280 MET cc_start: 0.6531 (ppp) cc_final: 0.6126 (ptm) REVERT: Aa 384 ARG cc_start: 0.6673 (ptt-90) cc_final: 0.5925 (ptt180) REVERT: Aa 442 LYS cc_start: 0.2268 (mmtt) cc_final: 0.1996 (ttmt) outliers start: 271 outliers final: 201 residues processed: 1255 average time/residue: 1.0413 time to fit residues: 2275.8333 Evaluate side-chains 1261 residues out of total 8262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 1041 time to evaluate : 7.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 105 GLU Chi-restraints excluded: chain BA residue 164 ILE Chi-restraints excluded: chain BA residue 170 CYS Chi-restraints excluded: chain BA residue 198 ILE Chi-restraints excluded: chain BB residue 70 THR Chi-restraints excluded: chain BB residue 91 ASP Chi-restraints excluded: chain BC residue 60 ASP Chi-restraints excluded: chain BC residue 78 GLN Chi-restraints excluded: chain BC residue 166 VAL Chi-restraints excluded: chain BC residue 181 ASP Chi-restraints excluded: chain BC residue 183 LEU Chi-restraints excluded: chain BD residue 67 LEU Chi-restraints excluded: chain BD residue 83 LEU Chi-restraints excluded: chain BD residue 86 ASN Chi-restraints excluded: chain BD residue 109 SER Chi-restraints excluded: chain BD residue 141 THR Chi-restraints excluded: chain BE residue 22 SER Chi-restraints excluded: chain BE residue 128 THR Chi-restraints excluded: chain BE residue 166 LEU Chi-restraints excluded: chain BF residue 88 THR Chi-restraints excluded: chain BF residue 160 THR Chi-restraints excluded: chain BF residue 174 ILE Chi-restraints excluded: chain BG residue 74 SER Chi-restraints excluded: chain BG residue 137 THR Chi-restraints excluded: chain BI residue 49 VAL Chi-restraints excluded: chain BI residue 50 VAL Chi-restraints excluded: chain BI residue 59 GLN Chi-restraints excluded: chain BJ residue 92 SER Chi-restraints excluded: chain BL residue 68 SER Chi-restraints excluded: chain BL residue 73 THR Chi-restraints excluded: chain BL residue 91 ILE Chi-restraints excluded: chain BL residue 175 VAL Chi-restraints excluded: chain BL residue 237 VAL Chi-restraints excluded: chain BM residue 63 GLN Chi-restraints excluded: chain BM residue 97 VAL Chi-restraints excluded: chain BM residue 153 SER Chi-restraints excluded: chain BM residue 275 ARG Chi-restraints excluded: chain BM residue 279 LYS Chi-restraints excluded: chain BM residue 295 CYS Chi-restraints excluded: chain BM residue 296 LEU Chi-restraints excluded: chain BM residue 313 ASN Chi-restraints excluded: chain BN residue 94 ASP Chi-restraints excluded: chain BN residue 106 PHE Chi-restraints excluded: chain BN residue 133 SER Chi-restraints excluded: chain BN residue 151 VAL Chi-restraints excluded: chain BN residue 225 ASP Chi-restraints excluded: chain BN residue 281 THR Chi-restraints excluded: chain BO residue 92 ASP Chi-restraints excluded: chain BO residue 114 VAL Chi-restraints excluded: chain BO residue 184 LEU Chi-restraints excluded: chain BP residue 30 SER Chi-restraints excluded: chain BP residue 99 CYS Chi-restraints excluded: chain BP residue 107 GLU Chi-restraints excluded: chain BP residue 116 LEU Chi-restraints excluded: chain BP residue 150 HIS Chi-restraints excluded: chain BP residue 164 MET Chi-restraints excluded: chain BP residue 187 SER Chi-restraints excluded: chain BQ residue 44 VAL Chi-restraints excluded: chain BQ residue 135 VAL Chi-restraints excluded: chain BQ residue 143 SER Chi-restraints excluded: chain BQ residue 153 ILE Chi-restraints excluded: chain BQ residue 183 LEU Chi-restraints excluded: chain BR residue 67 PHE Chi-restraints excluded: chain BS residue 89 HIS Chi-restraints excluded: chain BS residue 115 VAL Chi-restraints excluded: chain BS residue 126 SER Chi-restraints excluded: chain BT residue 33 SER Chi-restraints excluded: chain BT residue 99 ASN Chi-restraints excluded: chain BT residue 236 LEU Chi-restraints excluded: chain BT residue 243 VAL Chi-restraints excluded: chain BU residue 34 LEU Chi-restraints excluded: chain BU residue 59 VAL Chi-restraints excluded: chain BU residue 121 LEU Chi-restraints excluded: chain BU residue 161 VAL Chi-restraints excluded: chain BV residue 86 ILE Chi-restraints excluded: chain BV residue 124 ILE Chi-restraints excluded: chain BV residue 156 ASP Chi-restraints excluded: chain BW residue 101 VAL Chi-restraints excluded: chain BW residue 157 SER Chi-restraints excluded: chain BW residue 166 THR Chi-restraints excluded: chain BX residue 154 THR Chi-restraints excluded: chain BX residue 171 ILE Chi-restraints excluded: chain BX residue 177 VAL Chi-restraints excluded: chain BX residue 207 ILE Chi-restraints excluded: chain BX residue 265 LEU Chi-restraints excluded: chain BX residue 289 SER Chi-restraints excluded: chain BY residue 12 SER Chi-restraints excluded: chain BY residue 63 SER Chi-restraints excluded: chain BY residue 76 SER Chi-restraints excluded: chain BY residue 87 ILE Chi-restraints excluded: chain BZ residue 58 THR Chi-restraints excluded: chain BZ residue 69 VAL Chi-restraints excluded: chain BZ residue 113 THR Chi-restraints excluded: chain BZ residue 158 VAL Chi-restraints excluded: chain Ba residue 71 GLU Chi-restraints excluded: chain Ba residue 77 VAL Chi-restraints excluded: chain Bb residue 8 LEU Chi-restraints excluded: chain Bb residue 30 THR Chi-restraints excluded: chain Bb residue 45 THR Chi-restraints excluded: chain Bb residue 75 ILE Chi-restraints excluded: chain Bc residue 89 ASP Chi-restraints excluded: chain Bd residue 40 LEU Chi-restraints excluded: chain Bd residue 58 VAL Chi-restraints excluded: chain Bd residue 66 HIS Chi-restraints excluded: chain Bd residue 70 ARG Chi-restraints excluded: chain Be residue 27 VAL Chi-restraints excluded: chain Be residue 41 THR Chi-restraints excluded: chain Be residue 55 THR Chi-restraints excluded: chain Be residue 59 GLU Chi-restraints excluded: chain Be residue 97 VAL Chi-restraints excluded: chain Be residue 101 TRP Chi-restraints excluded: chain Bf residue 40 GLN Chi-restraints excluded: chain Bf residue 110 ILE Chi-restraints excluded: chain Bg residue 41 ASP Chi-restraints excluded: chain Bh residue 38 VAL Chi-restraints excluded: chain Bh residue 67 THR Chi-restraints excluded: chain Bh residue 73 CYS Chi-restraints excluded: chain Bh residue 85 ASP Chi-restraints excluded: chain Bh residue 86 VAL Chi-restraints excluded: chain Bh residue 99 MET Chi-restraints excluded: chain Bh residue 140 VAL Chi-restraints excluded: chain Bh residue 188 SER Chi-restraints excluded: chain Bh residue 192 LEU Chi-restraints excluded: chain Bi residue 76 VAL Chi-restraints excluded: chain Bi residue 159 VAL Chi-restraints excluded: chain Bi residue 182 LEU Chi-restraints excluded: chain Bi residue 260 CYS Chi-restraints excluded: chain Bi residue 274 ASN Chi-restraints excluded: chain Bi residue 345 VAL Chi-restraints excluded: chain Bi residue 350 VAL Chi-restraints excluded: chain Bi residue 356 THR Chi-restraints excluded: chain Bi residue 369 ASN Chi-restraints excluded: chain Bi residue 399 ILE Chi-restraints excluded: chain Bi residue 403 ASN Chi-restraints excluded: chain Bi residue 410 ASP Chi-restraints excluded: chain Bi residue 416 VAL Chi-restraints excluded: chain Bi residue 418 PHE Chi-restraints excluded: chain Bj residue 305 ILE Chi-restraints excluded: chain Bl residue 99 GLN Chi-restraints excluded: chain Bm residue 64 MET Chi-restraints excluded: chain Bm residue 101 ASP Chi-restraints excluded: chain Bm residue 166 SER Chi-restraints excluded: chain Bm residue 203 CYS Chi-restraints excluded: chain Bm residue 207 ASN Chi-restraints excluded: chain Bm residue 248 THR Chi-restraints excluded: chain Bm residue 256 PHE Chi-restraints excluded: chain Bm residue 262 THR Chi-restraints excluded: chain Bm residue 270 VAL Chi-restraints excluded: chain Bm residue 379 ASP Chi-restraints excluded: chain Bm residue 398 VAL Chi-restraints excluded: chain Bn residue 32 LEU Chi-restraints excluded: chain Bn residue 48 LEU Chi-restraints excluded: chain Bn residue 73 THR Chi-restraints excluded: chain Bn residue 151 LEU Chi-restraints excluded: chain Bn residue 205 THR Chi-restraints excluded: chain Bn residue 227 GLU Chi-restraints excluded: chain Bn residue 245 VAL Chi-restraints excluded: chain Bn residue 276 ASP Chi-restraints excluded: chain Bn residue 302 ASP Chi-restraints excluded: chain Bn residue 321 CYS Chi-restraints excluded: chain Bo residue 58 ARG Chi-restraints excluded: chain Bo residue 126 THR Chi-restraints excluded: chain Bo residue 140 TRP Chi-restraints excluded: chain Bo residue 197 HIS Chi-restraints excluded: chain Bo residue 214 GLU Chi-restraints excluded: chain Bo residue 215 THR Chi-restraints excluded: chain Bo residue 290 VAL Chi-restraints excluded: chain Bp residue 94 PHE Chi-restraints excluded: chain Bp residue 167 SER Chi-restraints excluded: chain Bq residue 39 THR Chi-restraints excluded: chain Br residue 38 SER Chi-restraints excluded: chain Br residue 59 VAL Chi-restraints excluded: chain Br residue 60 CYS Chi-restraints excluded: chain Br residue 65 VAL Chi-restraints excluded: chain Br residue 110 GLU Chi-restraints excluded: chain Br residue 115 MET Chi-restraints excluded: chain Bs residue 34 SER Chi-restraints excluded: chain Bs residue 75 VAL Chi-restraints excluded: chain Bs residue 84 VAL Chi-restraints excluded: chain Bs residue 91 CYS Chi-restraints excluded: chain Bs residue 113 ILE Chi-restraints excluded: chain Bs residue 126 ILE Chi-restraints excluded: chain Bs residue 139 THR Chi-restraints excluded: chain Bt residue 59 ARG Chi-restraints excluded: chain Bt residue 85 LEU Chi-restraints excluded: chain Bt residue 93 VAL Chi-restraints excluded: chain Bt residue 148 LEU Chi-restraints excluded: chain Bt residue 224 THR Chi-restraints excluded: chain Bt residue 231 MET Chi-restraints excluded: chain Bt residue 240 LEU Chi-restraints excluded: chain Bt residue 265 THR Chi-restraints excluded: chain Bu residue 76 ILE Chi-restraints excluded: chain Bu residue 150 LEU Chi-restraints excluded: chain Bu residue 165 THR Chi-restraints excluded: chain Bu residue 218 THR Chi-restraints excluded: chain Bu residue 266 ILE Chi-restraints excluded: chain Bu residue 281 MET Chi-restraints excluded: chain Bv residue 58 LEU Chi-restraints excluded: chain Bv residue 131 PHE Chi-restraints excluded: chain Bv residue 156 ASN Chi-restraints excluded: chain Bv residue 194 THR Chi-restraints excluded: chain Bv residue 207 ASN Chi-restraints excluded: chain Bv residue 278 ASP Chi-restraints excluded: chain Bv residue 279 LEU Chi-restraints excluded: chain Bw residue 84 THR Chi-restraints excluded: chain Bw residue 90 VAL Chi-restraints excluded: chain Bw residue 182 VAL Chi-restraints excluded: chain Bx residue 144 THR Chi-restraints excluded: chain Bx residue 146 THR Chi-restraints excluded: chain By residue 118 LEU Chi-restraints excluded: chain By residue 159 TYR Chi-restraints excluded: chain Bz residue 43 VAL Chi-restraints excluded: chain Bz residue 100 ASN Chi-restraints excluded: chain Bz residue 115 SER Chi-restraints excluded: chain Aa residue 126 THR Chi-restraints excluded: chain Aa residue 206 GLU Chi-restraints excluded: chain Aa residue 247 VAL Chi-restraints excluded: chain Aa residue 269 SER Chi-restraints excluded: chain Aa residue 284 VAL Chi-restraints excluded: chain Aa residue 391 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1081 random chunks: chunk 967 optimal weight: 7.9990 chunk 637 optimal weight: 0.8980 chunk 1026 optimal weight: 4.9990 chunk 626 optimal weight: 4.9990 chunk 487 optimal weight: 2.9990 chunk 713 optimal weight: 0.9990 chunk 1076 optimal weight: 0.9980 chunk 991 optimal weight: 4.9990 chunk 857 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 662 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BE 56 ASN ** BF 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BF 112 ASN ** BM 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BO 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BP 119 HIS BQ 103 HIS BT 99 ASN ** BU 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BU 138 GLN ** BV 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BV 155 GLN ** BW 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bd 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bf 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bi 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bi 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bi 337 GLN ** Bp 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bq 88 GLN ** Bv 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bv 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Bv 207 ASN ** Bw 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 118908 Z= 0.200 Angle : 0.579 14.606 169080 Z= 0.297 Chirality : 0.037 0.248 19886 Planarity : 0.004 0.122 15405 Dihedral : 18.448 179.890 34221 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.19 % Favored : 96.79 % Rotamer: Outliers : 2.13 % Allowed : 15.68 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.09), residues: 9255 helix: 1.39 (0.09), residues: 3236 sheet: -0.08 (0.15), residues: 1268 loop : -0.64 (0.09), residues: 4751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRPBi 66 HIS 0.007 0.001 HISAa 110 PHE 0.025 0.001 PHEBy 99 TYR 0.025 0.001 TYRBt 97 ARG 0.019 0.000 ARGBT 100 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18510 Ramachandran restraints generated. 9255 Oldfield, 0 Emsley, 9255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18510 Ramachandran restraints generated. 9255 Oldfield, 0 Emsley, 9255 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1238 residues out of total 8262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 1063 time to evaluate : 7.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 54 LYS cc_start: 0.8679 (mttt) cc_final: 0.8374 (mttp) REVERT: BA 105 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7186 (tt0) REVERT: BB 58 GLU cc_start: 0.8165 (tp30) cc_final: 0.7866 (tp30) REVERT: BC 127 ASP cc_start: 0.5202 (t70) cc_final: 0.4323 (t70) REVERT: BC 129 LYS cc_start: 0.4805 (mptt) cc_final: 0.4513 (mmtt) REVERT: BD 118 THR cc_start: 0.9111 (m) cc_final: 0.8772 (p) REVERT: BE 71 TYR cc_start: 0.8573 (m-80) cc_final: 0.8256 (m-80) REVERT: BE 150 LYS cc_start: 0.7303 (tttm) cc_final: 0.6872 (mttp) REVERT: BF 75 ASN cc_start: 0.8701 (t0) cc_final: 0.8161 (t0) REVERT: BF 113 MET cc_start: 0.8788 (tmm) cc_final: 0.8291 (tmm) REVERT: BF 164 LYS cc_start: 0.6131 (mttm) cc_final: 0.5625 (mttm) REVERT: BF 213 MET cc_start: 0.8604 (mtm) cc_final: 0.8259 (mtp) REVERT: BG 35 LYS cc_start: 0.8119 (mttt) cc_final: 0.7684 (mtpp) REVERT: BG 40 ARG cc_start: 0.7821 (ttm170) cc_final: 0.7248 (mmt90) REVERT: BG 88 MET cc_start: 0.8314 (ptp) cc_final: 0.7849 (ptp) REVERT: BH 176 GLU cc_start: 0.8035 (mp0) cc_final: 0.7687 (mm-30) REVERT: BI 21 MET cc_start: 0.6142 (mmm) cc_final: 0.5625 (mtp) REVERT: BL 235 MET cc_start: 0.8447 (ttp) cc_final: 0.8195 (ttp) REVERT: BM 81 LYS cc_start: 0.7688 (mttt) cc_final: 0.7139 (mmtm) REVERT: BM 219 MET cc_start: 0.9102 (ttm) cc_final: 0.8669 (tpp) REVERT: BM 279 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8343 (ttpp) REVERT: BN 50 LYS cc_start: 0.7457 (mmmt) cc_final: 0.6450 (mmtt) REVERT: BN 209 TYR cc_start: 0.8332 (t80) cc_final: 0.7762 (t80) REVERT: BO 126 GLN cc_start: 0.7394 (mm-40) cc_final: 0.7122 (mt0) REVERT: BO 131 TYR cc_start: 0.7876 (m-80) cc_final: 0.7131 (m-80) REVERT: BO 137 LYS cc_start: 0.7270 (mttt) cc_final: 0.6842 (pttt) REVERT: BO 143 GLU cc_start: 0.7306 (tp30) cc_final: 0.6708 (mm-30) REVERT: BO 147 ARG cc_start: 0.6420 (mtt180) cc_final: 0.6132 (mtt180) REVERT: BP 95 MET cc_start: 0.6647 (ttp) cc_final: 0.5680 (ttp) REVERT: BP 126 PHE cc_start: 0.8126 (m-80) cc_final: 0.7906 (m-10) REVERT: BQ 19 MET cc_start: 0.5485 (mmm) cc_final: 0.5064 (mmm) REVERT: BQ 103 HIS cc_start: 0.8145 (m170) cc_final: 0.7943 (m-70) REVERT: BR 67 PHE cc_start: 0.9143 (OUTLIER) cc_final: 0.8734 (m-10) REVERT: BW 98 ASN cc_start: 0.8691 (p0) cc_final: 0.8188 (p0) REVERT: BW 100 GLN cc_start: 0.8202 (mt0) cc_final: 0.7627 (pt0) REVERT: BX 244 ARG cc_start: 0.8659 (mmm-85) cc_final: 0.8135 (mmm160) REVERT: BX 268 ASP cc_start: 0.8901 (t0) cc_final: 0.8680 (m-30) REVERT: BY 148 HIS cc_start: 0.7473 (t-90) cc_final: 0.7130 (t-170) REVERT: BZ 155 LYS cc_start: 0.8456 (mttt) cc_final: 0.8210 (mmmt) REVERT: Bb 14 LYS cc_start: 0.7519 (mttt) cc_final: 0.7271 (mttt) REVERT: Bc 73 MET cc_start: 0.7163 (mmm) cc_final: 0.5857 (ttm) REVERT: Bc 131 ARG cc_start: 0.8279 (ptp90) cc_final: 0.7392 (ptp90) REVERT: Bc 133 SER cc_start: 0.8874 (m) cc_final: 0.8496 (t) REVERT: Bd 48 THR cc_start: 0.8423 (m) cc_final: 0.8166 (p) REVERT: Bd 55 VAL cc_start: 0.8016 (p) cc_final: 0.7689 (m) REVERT: Bd 66 HIS cc_start: 0.8831 (OUTLIER) cc_final: 0.8196 (t-170) REVERT: Bd 70 ARG cc_start: 0.7493 (OUTLIER) cc_final: 0.6611 (ttp-110) REVERT: Bd 73 ARG cc_start: 0.7131 (ptm160) cc_final: 0.6443 (ptt-90) REVERT: Bd 75 MET cc_start: 0.7828 (ptt) cc_final: 0.7261 (ptt) REVERT: Bd 90 ARG cc_start: 0.7984 (mtt180) cc_final: 0.6808 (tmm-80) REVERT: Be 12 ILE cc_start: 0.8993 (mt) cc_final: 0.8729 (mm) REVERT: Bg 78 SER cc_start: 0.6681 (m) cc_final: 0.6361 (p) REVERT: Bh 37 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7184 (mm-30) REVERT: Bh 73 CYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7548 (p) REVERT: Bi 152 ARG cc_start: 0.8459 (ptp-170) cc_final: 0.8144 (mtm180) REVERT: Bi 164 GLU cc_start: 0.7556 (tp30) cc_final: 0.7308 (tp30) REVERT: Bj 101 LYS cc_start: 0.6082 (mttt) cc_final: 0.5672 (tppt) REVERT: Bj 107 LYS cc_start: 0.6589 (mttt) cc_final: 0.6284 (pttm) REVERT: Bl 79 VAL cc_start: 0.8589 (OUTLIER) cc_final: 0.8332 (m) REVERT: Bm 72 ARG cc_start: 0.7660 (ttm110) cc_final: 0.6903 (ptm160) REVERT: Bm 262 THR cc_start: 0.9266 (m) cc_final: 0.8986 (m) REVERT: Bn 27 ARG cc_start: 0.7823 (tpt170) cc_final: 0.7216 (ttm170) REVERT: Bn 48 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8183 (mm) REVERT: Bn 160 ASP cc_start: 0.7778 (m-30) cc_final: 0.7439 (m-30) REVERT: Bo 46 ASN cc_start: 0.8838 (m-40) cc_final: 0.8539 (m110) REVERT: Bo 140 TRP cc_start: 0.8602 (OUTLIER) cc_final: 0.6610 (m-90) REVERT: Bo 176 PHE cc_start: 0.8235 (p90) cc_final: 0.7858 (p90) REVERT: Bo 178 TYR cc_start: 0.9356 (t80) cc_final: 0.9045 (t80) REVERT: Bo 310 ASN cc_start: 0.7983 (m-40) cc_final: 0.7478 (t0) REVERT: Bp 71 ARG cc_start: 0.6989 (mtt180) cc_final: 0.6222 (tpt-90) REVERT: Bp 97 LYS cc_start: 0.7037 (tppt) cc_final: 0.6611 (tptp) REVERT: Bq 48 PHE cc_start: 0.8988 (t80) cc_final: 0.8730 (t80) REVERT: Bq 50 GLN cc_start: 0.9118 (tt0) cc_final: 0.8902 (tt0) REVERT: Br 56 ARG cc_start: 0.8640 (mmt90) cc_final: 0.8431 (tpp80) REVERT: Br 73 LYS cc_start: 0.9013 (ptpt) cc_final: 0.8568 (ptmm) REVERT: Br 111 GLN cc_start: 0.7991 (tp40) cc_final: 0.7665 (tt0) REVERT: Br 114 LYS cc_start: 0.8599 (ttpt) cc_final: 0.8148 (tttm) REVERT: Bt 45 LEU cc_start: 0.8383 (mt) cc_final: 0.8159 (tt) REVERT: Bt 183 GLU cc_start: 0.7317 (mt-10) cc_final: 0.6901 (tt0) REVERT: Bt 240 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8211 (tt) REVERT: Bu 226 ASP cc_start: 0.7065 (t0) cc_final: 0.6448 (t0) REVERT: Bu 244 GLU cc_start: 0.7637 (mp0) cc_final: 0.7121 (mp0) REVERT: Bu 261 MET cc_start: 0.6189 (ttm) cc_final: 0.5717 (ttp) REVERT: Bu 292 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7295 (mm-30) REVERT: Bv 58 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7196 (mm) REVERT: Bv 78 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8006 (mt-10) REVERT: Bv 195 LEU cc_start: 0.7966 (mp) cc_final: 0.7660 (mt) REVERT: Bv 238 LEU cc_start: 0.6612 (mt) cc_final: 0.6052 (pp) REVERT: Bv 278 ASP cc_start: 0.6870 (OUTLIER) cc_final: 0.5536 (t0) REVERT: Bw 85 ASP cc_start: 0.7171 (t70) cc_final: 0.6880 (t0) REVERT: Bw 133 GLU cc_start: 0.7671 (tp30) cc_final: 0.7052 (tp30) REVERT: Bw 144 MET cc_start: 0.6047 (mmt) cc_final: 0.5803 (mmm) REVERT: Bw 186 VAL cc_start: 0.8881 (m) cc_final: 0.8593 (p) REVERT: Bx 141 ASN cc_start: 0.8184 (OUTLIER) cc_final: 0.7448 (t0) REVERT: By 159 TYR cc_start: 0.6831 (OUTLIER) cc_final: 0.6394 (m-80) REVERT: Bz 51 ARG cc_start: 0.8920 (mtt90) cc_final: 0.8432 (mtt90) REVERT: Bz 83 TRP cc_start: 0.8480 (t60) cc_final: 0.7957 (t60) REVERT: Aa 206 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8223 (mp0) REVERT: Aa 280 MET cc_start: 0.6493 (ppp) cc_final: 0.6083 (ptm) REVERT: Aa 373 LYS cc_start: 0.7058 (mtmt) cc_final: 0.6350 (tptm) REVERT: Aa 442 LYS cc_start: 0.2084 (mmtt) cc_final: 0.1874 (ttmt) outliers start: 175 outliers final: 142 residues processed: 1184 average time/residue: 0.9601 time to fit residues: 1969.9296 Evaluate side-chains 1184 residues out of total 8262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 1027 time to evaluate : 7.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 105 GLU Chi-restraints excluded: chain BA residue 164 ILE Chi-restraints excluded: chain BA residue 170 CYS Chi-restraints excluded: chain BA residue 198 ILE Chi-restraints excluded: chain BB residue 91 ASP Chi-restraints excluded: chain BC residue 60 ASP Chi-restraints excluded: chain BC residue 166 VAL Chi-restraints excluded: chain BC residue 183 LEU Chi-restraints excluded: chain BD residue 67 LEU Chi-restraints excluded: chain BD residue 83 LEU Chi-restraints excluded: chain BE residue 22 SER Chi-restraints excluded: chain BE residue 128 THR Chi-restraints excluded: chain BE residue 166 LEU Chi-restraints excluded: chain BF residue 88 THR Chi-restraints excluded: chain BF residue 160 THR Chi-restraints excluded: chain BI residue 49 VAL Chi-restraints excluded: chain BI residue 50 VAL Chi-restraints excluded: chain BI residue 59 GLN Chi-restraints excluded: chain BJ residue 92 SER Chi-restraints excluded: chain BL residue 91 ILE Chi-restraints excluded: chain BL residue 175 VAL Chi-restraints excluded: chain BL residue 237 VAL Chi-restraints excluded: chain BM residue 63 GLN Chi-restraints excluded: chain BM residue 153 SER Chi-restraints excluded: chain BM residue 275 ARG Chi-restraints excluded: chain BM residue 279 LYS Chi-restraints excluded: chain BM residue 295 CYS Chi-restraints excluded: chain BM residue 296 LEU Chi-restraints excluded: chain BN residue 106 PHE Chi-restraints excluded: chain BN residue 133 SER Chi-restraints excluded: chain BN residue 151 VAL Chi-restraints excluded: chain BN residue 225 ASP Chi-restraints excluded: chain BN residue 281 THR Chi-restraints excluded: chain BO residue 92 ASP Chi-restraints excluded: chain BO residue 114 VAL Chi-restraints excluded: chain BP residue 30 SER Chi-restraints excluded: chain BP residue 99 CYS Chi-restraints excluded: chain BP residue 107 GLU Chi-restraints excluded: chain BP residue 116 LEU Chi-restraints excluded: chain BP residue 150 HIS Chi-restraints excluded: chain BP residue 164 MET Chi-restraints excluded: chain BQ residue 128 ASP Chi-restraints excluded: chain BQ residue 135 VAL Chi-restraints excluded: chain BQ residue 143 SER Chi-restraints excluded: chain BQ residue 183 LEU Chi-restraints excluded: chain BR residue 67 PHE Chi-restraints excluded: chain BS residue 89 HIS Chi-restraints excluded: chain BT residue 33 SER Chi-restraints excluded: chain BT residue 243 VAL Chi-restraints excluded: chain BU residue 59 VAL Chi-restraints excluded: chain BU residue 121 LEU Chi-restraints excluded: chain BU residue 161 VAL Chi-restraints excluded: chain BV residue 124 ILE Chi-restraints excluded: chain BV residue 156 ASP Chi-restraints excluded: chain BW residue 101 VAL Chi-restraints excluded: chain BW residue 157 SER Chi-restraints excluded: chain BX residue 154 THR Chi-restraints excluded: chain BX residue 171 ILE Chi-restraints excluded: chain BX residue 177 VAL Chi-restraints excluded: chain BX residue 192 ASP Chi-restraints excluded: chain BX residue 265 LEU Chi-restraints excluded: chain BX residue 289 SER Chi-restraints excluded: chain BY residue 12 SER Chi-restraints excluded: chain BY residue 63 SER Chi-restraints excluded: chain BY residue 76 SER Chi-restraints excluded: chain BY residue 87 ILE Chi-restraints excluded: chain BZ residue 58 THR Chi-restraints excluded: chain BZ residue 69 VAL Chi-restraints excluded: chain BZ residue 84 VAL Chi-restraints excluded: chain BZ residue 113 THR Chi-restraints excluded: chain BZ residue 158 VAL Chi-restraints excluded: chain Bb residue 8 LEU Chi-restraints excluded: chain Bb residue 30 THR Chi-restraints excluded: chain Bb residue 45 THR Chi-restraints excluded: chain Bb residue 75 ILE Chi-restraints excluded: chain Bd residue 66 HIS Chi-restraints excluded: chain Bd residue 70 ARG Chi-restraints excluded: chain Be residue 27 VAL Chi-restraints excluded: chain Be residue 59 GLU Chi-restraints excluded: chain Be residue 97 VAL Chi-restraints excluded: chain Be residue 101 TRP Chi-restraints excluded: chain Bf residue 40 GLN Chi-restraints excluded: chain Bf residue 110 ILE Chi-restraints excluded: chain Bg residue 41 ASP Chi-restraints excluded: chain Bh residue 38 VAL Chi-restraints excluded: chain Bh residue 73 CYS Chi-restraints excluded: chain Bh residue 99 MET Chi-restraints excluded: chain Bh residue 140 VAL Chi-restraints excluded: chain Bh residue 188 SER Chi-restraints excluded: chain Bh residue 192 LEU Chi-restraints excluded: chain Bi residue 76 VAL Chi-restraints excluded: chain Bi residue 132 ASP Chi-restraints excluded: chain Bi residue 159 VAL Chi-restraints excluded: chain Bi residue 260 CYS Chi-restraints excluded: chain Bi residue 350 VAL Chi-restraints excluded: chain Bi residue 356 THR Chi-restraints excluded: chain Bi residue 369 ASN Chi-restraints excluded: chain Bi residue 399 ILE Chi-restraints excluded: chain Bi residue 410 ASP Chi-restraints excluded: chain Bi residue 416 VAL Chi-restraints excluded: chain Bi residue 418 PHE Chi-restraints excluded: chain Bl residue 79 VAL Chi-restraints excluded: chain Bm residue 101 ASP Chi-restraints excluded: chain Bm residue 166 SER Chi-restraints excluded: chain Bm residue 207 ASN Chi-restraints excluded: chain Bm residue 248 THR Chi-restraints excluded: chain Bm residue 256 PHE Chi-restraints excluded: chain Bm residue 270 VAL Chi-restraints excluded: chain Bm residue 379 ASP Chi-restraints excluded: chain Bm residue 398 VAL Chi-restraints excluded: chain Bn residue 32 LEU Chi-restraints excluded: chain Bn residue 48 LEU Chi-restraints excluded: chain Bn residue 73 THR Chi-restraints excluded: chain Bn residue 151 LEU Chi-restraints excluded: chain Bn residue 227 GLU Chi-restraints excluded: chain Bn residue 276 ASP Chi-restraints excluded: chain Bn residue 279 ILE Chi-restraints excluded: chain Bn residue 302 ASP Chi-restraints excluded: chain Bn residue 321 CYS Chi-restraints excluded: chain Bo residue 126 THR Chi-restraints excluded: chain Bo residue 140 TRP Chi-restraints excluded: chain Bo residue 215 THR Chi-restraints excluded: chain Bo residue 290 VAL Chi-restraints excluded: chain Bp residue 87 ASP Chi-restraints excluded: chain Bp residue 94 PHE Chi-restraints excluded: chain Br residue 38 SER Chi-restraints excluded: chain Br residue 59 VAL Chi-restraints excluded: chain Br residue 60 CYS Chi-restraints excluded: chain Br residue 110 GLU Chi-restraints excluded: chain Br residue 115 MET Chi-restraints excluded: chain Bs residue 34 SER Chi-restraints excluded: chain Bs residue 75 VAL Chi-restraints excluded: chain Bs residue 84 VAL Chi-restraints excluded: chain Bs residue 139 THR Chi-restraints excluded: chain Bt residue 93 VAL Chi-restraints excluded: chain Bt residue 148 LEU Chi-restraints excluded: chain Bt residue 231 MET Chi-restraints excluded: chain Bt residue 240 LEU Chi-restraints excluded: chain Bu residue 150 LEU Chi-restraints excluded: chain Bu residue 218 THR Chi-restraints excluded: chain Bu residue 266 ILE Chi-restraints excluded: chain Bu residue 281 MET Chi-restraints excluded: chain Bv residue 58 LEU Chi-restraints excluded: chain Bv residue 131 PHE Chi-restraints excluded: chain Bv residue 278 ASP Chi-restraints excluded: chain Bv residue 279 LEU Chi-restraints excluded: chain Bx residue 141 ASN Chi-restraints excluded: chain Bx residue 146 THR Chi-restraints excluded: chain By residue 118 LEU Chi-restraints excluded: chain By residue 159 TYR Chi-restraints excluded: chain Bz residue 43 VAL Chi-restraints excluded: chain Bz residue 100 ASN Chi-restraints excluded: chain Aa residue 126 THR Chi-restraints excluded: chain Aa residue 206 GLU Chi-restraints excluded: chain Aa residue 284 VAL Chi-restraints excluded: chain Aa residue 314 HIS Chi-restraints excluded: chain Aa residue 391 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1081 random chunks: chunk 525 optimal weight: 7.9990 chunk 681 optimal weight: 0.9990 chunk 913 optimal weight: 1.9990 chunk 262 optimal weight: 0.4980 chunk 790 optimal weight: 0.9980 chunk 126 optimal weight: 30.0000 chunk 238 optimal weight: 9.9990 chunk 858 optimal weight: 5.9990 chunk 359 optimal weight: 0.8980 chunk 882 optimal weight: 2.9990 chunk 108 optimal weight: 8.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 99 GLN BA 103 GLN ** BE 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BE 70 HIS ** BF 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BH 96 ASN BM 139 ASN ** BO 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BP 119 HIS ** BU 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BU 138 GLN ** BV 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BV 155 GLN ** BW 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BZ 109 GLN Bd 37 ASN ** Bf 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Bi 161 GLN ** Bi 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bp 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bq 88 GLN Bt 222 GLN ** Bv 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bv 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bw 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.151945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.112581 restraints weight = 193467.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.112894 restraints weight = 102136.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.114682 restraints weight = 63174.546| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3413 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3413 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 118908 Z= 0.155 Angle : 0.539 14.632 169080 Z= 0.276 Chirality : 0.035 0.220 19886 Planarity : 0.004 0.122 15405 Dihedral : 18.295 179.793 34221 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.42 % Favored : 96.56 % Rotamer: Outliers : 1.91 % Allowed : 16.09 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.09), residues: 9255 helix: 1.69 (0.09), residues: 3236 sheet: 0.10 (0.15), residues: 1279 loop : -0.50 (0.09), residues: 4740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRPBi 66 HIS 0.007 0.001 HISBw 175 PHE 0.016 0.001 PHEBt 184 TYR 0.038 0.001 TYRBt 97 ARG 0.009 0.000 ARGBW 97 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31654.11 seconds wall clock time: 551 minutes 22.92 seconds (33082.92 seconds total)