Starting phenix.real_space_refine on Sun Feb 18 14:08:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gaz_4369/02_2024/6gaz_4369_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gaz_4369/02_2024/6gaz_4369.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gaz_4369/02_2024/6gaz_4369.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gaz_4369/02_2024/6gaz_4369.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gaz_4369/02_2024/6gaz_4369_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gaz_4369/02_2024/6gaz_4369_neut_updated.pdb" } resolution = 3.1 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= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Zn 3 6.06 5 P 1052 5.49 5 Mg 111 5.21 5 S 235 5.16 5 Na 1 4.78 5 C 42203 2.51 5 N 13241 2.21 5 O 16326 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "BC PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC GLU 429": "OE1" <-> "OE2" Residue "BC TYR 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC TYR 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC PHE 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC TYR 600": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BC PHE 727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AB TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AB PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AB PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AB TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AB PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AB PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AC TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AC GLU 88": "OE1" <-> "OE2" Residue "AC ASP 89": "OD1" <-> "OD2" Residue "AC PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AE PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AE GLU 224": "OE1" <-> "OE2" Residue "AE PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AE PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AE TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AE GLU 398": "OE1" <-> "OE2" Residue "AE GLU 400": "OE1" <-> "OE2" Residue "AF TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AF PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AG PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AG GLU 87": "OE1" <-> "OE2" Residue "AG PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AG TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AG PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AG PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AG GLU 231": "OE1" <-> "OE2" Residue "AI PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AI PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AI PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AI PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AI TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AI TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AI TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AI PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AJ PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AJ TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AK TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AK TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AN TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AN ASP 37": "OD1" <-> "OD2" Residue "AP ASP 71": "OD1" <-> "OD2" Residue "AQ PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AQ PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AR TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AR ASP 127": "OD1" <-> "OD2" Residue "AU PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AU TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Aa PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Aa TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Aa PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Aa TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Aa PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Aa PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Aa GLU 258": "OE1" <-> "OE2" Residue "Aa PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Aa TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ab TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ab PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ab PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ab PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ac TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ac PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ac PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ac PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ac TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ad TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ae GLU 102": "OE1" <-> "OE2" Residue "Ae PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ae ARG 122": "NH1" <-> "NH2" Residue "Ae TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ae TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ae TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ae PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ae ASP 180": "OD1" <-> "OD2" Residue "Ae PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ae TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ae TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ae ARG 242": "NH1" <-> "NH2" Residue "Ae TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ae GLU 362": "OE1" <-> "OE2" Residue "Ae TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ae TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Af PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ag PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ag ASP 277": "OD1" <-> "OD2" Residue "Ag PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ag TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ah PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ah PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ah PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ah PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ai TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ai TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Aj TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Aj TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Aj TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ak PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ak TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ak ASP 186": "OD1" <-> "OD2" Residue "Ak TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ak GLU 247": "OE1" <-> "OE2" Residue "Am ARG 17": "NH1" <-> "NH2" Residue "Am GLU 42": "OE1" <-> "OE2" Residue "Am PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "An PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "An TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ao TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ao TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ao PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ao PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ao PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ao TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ao PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ao GLU 362": "OE1" <-> "OE2" Residue "Ao TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ao PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ao PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ao TYR 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ao PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ao PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ao TYR 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ao PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ao PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ao PHE 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ap TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ap TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ap TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ap TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ap TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Ap TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 73172 Number of models: 1 Model: "" Number of chains: 48 Chain: "BC" Number of atoms: 4364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4364 Classifications: {'peptide': 571} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 21, 'TRANS': 549} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "BT" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 109 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 11} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "AA" Number of atoms: 20411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 960, 20411 Classifications: {'RNA': 960} Modifications used: {'rna2p_pur': 82, 'rna2p_pyr': 65, 'rna3p_pur': 440, 'rna3p_pyr': 373} Link IDs: {'rna2p': 147, 'rna3p': 812} Chain: "AB" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1762 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 12, 'TRANS': 207} Chain: "AC" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1075 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 7, 'TRANS': 124} Chain: "AE" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2732 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 13, 'TRANS': 329} Chain: "AF" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 981 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain: "AG" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1721 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 12, 'TRANS': 195} Chain: "AI" Number of atoms: 2650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2650 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 14, 'TRANS': 313} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "AJ" Number of atoms: 1155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1155 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 8, 'TRANS': 131} Chain: "AK" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1007 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 9, 'TRANS': 127} Chain: "AL" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 10, 'TRANS': 98} Chain: "AN" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 858 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "AO" Number of atoms: 1448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1448 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain: "AP" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 932 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "AQ" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 875 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "AR" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 784 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 8, 'TRANS': 88} Chain: "AU" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 734 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain: "AV" Number of atoms: 1498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1498 Classifications: {'RNA': 71} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 2, 'rna3p_pur': 29, 'rna3p_pyr': 35} Link IDs: {'rna2p': 6, 'rna3p': 64} Chain: "AX" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 354 Classifications: {'RNA': 17} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 7, 'rna3p_pyr': 7} Link IDs: {'rna2p': 3, 'rna3p': 13} Chain: "AZ" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 90 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain: "Aa" Number of atoms: 2378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2378 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 13, 'TRANS': 278} Chain: "Ab" Number of atoms: 1101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1101 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 7, 'TRANS': 127} Chain: "Ac" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1367 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 11, 'TRANS': 157} Chain: "Ad" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1467 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 7, 'TRANS': 169} Chain: "Ae" Number of atoms: 3109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3109 Classifications: {'peptide': 388} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 12, 'TRANS': 375} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "Af" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 778 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 3, 'TRANS': 95} Chain: "Ag" Number of atoms: 2875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2875 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 17, 'TRANS': 335} Chain: "Ah" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1015 Classifications: {'peptide': 120} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 114} Chain: "Ai" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 824 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "Aj" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1788 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 16, 'TRANS': 196} Chain: "Ak" Number of atoms: 2222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2222 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 17, 'TRANS': 257} Chain: "Am" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 930 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 9, 'TRANS': 106} Chain: "An" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 639 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "Ao" Number of atoms: 4527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 572, 4527 Classifications: {'peptide': 572} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 27, 'TRANS': 544} Chain breaks: 3 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'UNK:plan-1': 34} Unresolved non-hydrogen planarities: 34 Chain: "Ap" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1564 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 21, 'TRANS': 168} Chain: "BC" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Unusual residues: {' MG': 2, ' NA': 1, 'GSP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "AA" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 119 Unusual residues: {' MG': 105, 'SPM': 1} Classifications: {'undetermined': 106} Link IDs: {None: 105} Chain: "AB" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "AR" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "AV" 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 Chain: "AX" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Ac" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Ag" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "An" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Ap" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "BC" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "Ag" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 31288 SG CYSAF 105 144.746 116.477 34.685 1.00 60.27 S ATOM 43081 SG CYSAR 66 143.105 119.747 33.716 1.00 46.44 S ATOM 43103 SG CYSAR 69 141.755 116.461 32.714 1.00 51.69 S ATOM 43360 SG CYSAR 101 141.665 117.670 36.276 1.00 56.49 S ATOM 41239 SG CYSAP 26 142.641 68.045 127.823 1.00 87.25 S ATOM 51000 SG CYSAc 139 141.465 67.292 124.361 1.00 56.38 S ATOM 51014 SG CYSAc 141 140.242 65.246 127.130 1.00 48.45 S ATOM 51072 SG CYSAc 149 139.140 68.870 127.021 1.00 40.25 S ATOM 71799 SG CYSAp 94 113.666 84.579 124.842 1.00 49.97 S ATOM 71876 SG CYSAp 105 114.263 84.131 121.220 1.00 46.26 S ATOM 71897 SG CYSAp 108 112.700 81.430 123.207 1.00128.68 S ATOM 72182 SG CYSAp 143 116.370 82.229 123.581 1.00 38.09 S Time building chain proxies: 29.54, per 1000 atoms: 0.40 Number of scatterers: 73172 At special positions: 0 Unit cell: (248.81, 252.98, 204.33, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 3 29.99 S 235 16.00 P 1052 15.00 Mg 111 11.99 Na 1 11.00 O 16326 8.00 N 13241 7.00 C 42203 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYSAm 45 " - pdb=" SG CYSAm 76 " distance=2.05 Simple disulfide: pdb=" SG CYSAm 55 " - pdb=" SG CYSAm 66 " distance=2.04 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: 26.06 Conformation dependent library (CDL) restraints added in 7.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNAR 500 " pdb="ZN ZNAR 500 " - pdb=" SG CYSAR 101 " pdb="ZN ZNAR 500 " - pdb=" SG CYSAF 105 " pdb="ZN ZNAR 500 " - pdb=" SG CYSAR 66 " pdb="ZN ZNAR 500 " - pdb=" SG CYSAR 69 " pdb=" ZNAc 500 " pdb="ZN ZNAc 500 " - pdb=" SG CYSAP 26 " pdb="ZN ZNAc 500 " - pdb=" SG CYSAc 141 " pdb="ZN ZNAc 500 " - pdb=" SG CYSAc 139 " pdb="ZN ZNAc 500 " - pdb=" SG CYSAc 149 " pdb=" ZNAp 500 " pdb="ZN ZNAp 500 " - pdb=" SG CYSAp 105 " pdb="ZN ZNAp 500 " - pdb=" SG CYSAp 108 " pdb="ZN ZNAp 500 " - pdb=" SG CYSAp 94 " pdb="ZN ZNAp 500 " - pdb=" SG CYSAp 143 " Number of angles added : 18 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11928 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 244 helices and 39 sheets defined 44.3% alpha, 9.8% beta 298 base pairs and 568 stacking pairs defined. Time for finding SS restraints: 27.42 Creating SS restraints... Processing helix chain 'BC' and resid 193 through 201 Processing helix chain 'BC' and resid 210 through 212 No H-bonds generated for 'chain 'BC' and resid 210 through 212' Processing helix chain 'BC' and resid 239 through 250 removed outlier: 3.714A pdb=" N SERBC 242 " --> pdb=" O ALABC 239 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ALABC 243 " --> pdb=" O ALABC 240 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARGBC 245 " --> pdb=" O SERBC 242 " (cutoff:3.500A) Processing helix chain 'BC' and resid 267 through 278 Processing helix chain 'BC' and resid 297 through 306 Processing helix chain 'BC' and resid 312 through 314 No H-bonds generated for 'chain 'BC' and resid 312 through 314' Processing helix chain 'BC' and resid 331 through 345 Processing helix chain 'BC' and resid 437 through 479 Processing helix chain 'BC' and resid 486 through 494 removed outlier: 4.251A pdb=" N PHEBC 494 " --> pdb=" O SERBC 490 " (cutoff:3.500A) Processing helix chain 'BC' and resid 525 through 536 Processing helix chain 'BC' and resid 558 through 567 Processing helix chain 'BC' and resid 580 through 588 Processing helix chain 'BC' and resid 599 through 613 Processing helix chain 'AB' and resid 56 through 67 Proline residue: AB 65 - end of helix Processing helix chain 'AB' and resid 74 through 77 Processing helix chain 'AB' and resid 80 through 86 removed outlier: 3.519A pdb=" N ALAAB 86 " --> pdb=" O SERAB 82 " (cutoff:3.500A) Processing helix chain 'AB' and resid 94 through 96 No H-bonds generated for 'chain 'AB' and resid 94 through 96' Processing helix chain 'AB' and resid 99 through 104 removed outlier: 3.518A pdb=" N GLUAB 102 " --> pdb=" O ARGAB 99 " (cutoff:3.500A) Proline residue: AB 103 - end of helix No H-bonds generated for 'chain 'AB' and resid 99 through 104' Processing helix chain 'AB' and resid 117 through 136 removed outlier: 3.679A pdb=" N LEUAB 126 " --> pdb=" O ALAAB 122 " (cutoff:3.500A) Processing helix chain 'AB' and resid 151 through 161 Processing helix chain 'AB' and resid 178 through 181 No H-bonds generated for 'chain 'AB' and resid 178 through 181' Processing helix chain 'AB' and resid 206 through 213 Processing helix chain 'AB' and resid 242 through 272 Processing helix chain 'AC' and resid 59 through 61 No H-bonds generated for 'chain 'AC' and resid 59 through 61' Processing helix chain 'AC' and resid 73 through 75 No H-bonds generated for 'chain 'AC' and resid 73 through 75' Processing helix chain 'AC' and resid 82 through 99 Processing helix chain 'AC' and resid 129 through 147 Processing helix chain 'AE' and resid 95 through 103 Processing helix chain 'AE' and resid 162 through 183 Processing helix chain 'AE' and resid 264 through 277 removed outlier: 4.297A pdb=" N HISAE 277 " --> pdb=" O ASNAE 273 " (cutoff:3.500A) Processing helix chain 'AE' and resid 285 through 287 No H-bonds generated for 'chain 'AE' and resid 285 through 287' Processing helix chain 'AE' and resid 318 through 327 Processing helix chain 'AE' and resid 342 through 355 Processing helix chain 'AE' and resid 359 through 366 Processing helix chain 'AE' and resid 408 through 414 Processing helix chain 'AF' and resid 15 through 31 Processing helix chain 'AF' and resid 72 through 84 removed outlier: 3.702A pdb=" N VALAF 75 " --> pdb=" O ALAAF 72 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLUAF 76 " --> pdb=" O THRAF 73 " (cutoff:3.500A) Processing helix chain 'AG' and resid 48 through 52 Processing helix chain 'AG' and resid 58 through 69 Processing helix chain 'AG' and resid 89 through 98 Processing helix chain 'AG' and resid 104 through 127 Processing helix chain 'AG' and resid 131 through 136 Processing helix chain 'AG' and resid 141 through 152 Processing helix chain 'AG' and resid 176 through 193 Processing helix chain 'AG' and resid 201 through 213 Processing helix chain 'AG' and resid 218 through 232 Processing helix chain 'AG' and resid 234 through 238 Processing helix chain 'AI' and resid 71 through 91 Processing helix chain 'AI' and resid 101 through 111 Processing helix chain 'AI' and resid 119 through 121 No H-bonds generated for 'chain 'AI' and resid 119 through 121' Processing helix chain 'AI' and resid 128 through 131 No H-bonds generated for 'chain 'AI' and resid 128 through 131' Processing helix chain 'AI' and resid 151 through 153 No H-bonds generated for 'chain 'AI' and resid 151 through 153' Processing helix chain 'AI' and resid 156 through 181 Processing helix chain 'AI' and resid 194 through 196 No H-bonds generated for 'chain 'AI' and resid 194 through 196' Processing helix chain 'AI' and resid 203 through 209 Processing helix chain 'AI' and resid 216 through 230 Processing helix chain 'AI' and resid 236 through 244 removed outlier: 3.671A pdb=" N ARGAI 244 " --> pdb=" O ASPAI 240 " (cutoff:3.500A) Processing helix chain 'AI' and resid 301 through 304 No H-bonds generated for 'chain 'AI' and resid 301 through 304' Processing helix chain 'AI' and resid 308 through 321 Proline residue: AI 317 - end of helix Processing helix chain 'AI' and resid 338 through 352 Processing helix chain 'AI' and resid 359 through 367 removed outlier: 3.584A pdb=" N GLUAI 363 " --> pdb=" O GLUAI 359 " (cutoff:3.500A) Processing helix chain 'AJ' and resid 85 through 101 Processing helix chain 'AJ' and resid 150 through 162 Processing helix chain 'AK' and resid 123 through 125 No H-bonds generated for 'chain 'AK' and resid 123 through 125' Processing helix chain 'AK' and resid 127 through 144 removed outlier: 3.680A pdb=" N LYSAK 144 " --> pdb=" O LYSAK 140 " (cutoff:3.500A) Processing helix chain 'AK' and resid 160 through 169 Processing helix chain 'AL' and resid 33 through 39 Processing helix chain 'AN' and resid 32 through 58 removed outlier: 3.514A pdb=" N ALAAN 48 " --> pdb=" O ALAAN 44 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ASPAN 49 " --> pdb=" O TYRAN 45 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N GLUAN 50 " --> pdb=" O GLUAN 46 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEUAN 57 " --> pdb=" O ARGAN 53 " (cutoff:3.500A) Processing helix chain 'AN' and resid 65 through 77 removed outlier: 3.736A pdb=" N VALAN 70 " --> pdb=" O ASPAN 66 " (cutoff:3.500A) Processing helix chain 'AN' and resid 80 through 82 No H-bonds generated for 'chain 'AN' and resid 80 through 82' Processing helix chain 'AN' and resid 84 through 86 No H-bonds generated for 'chain 'AN' and resid 84 through 86' Processing helix chain 'AN' and resid 108 through 117 removed outlier: 3.840A pdb=" N HISAN 117 " --> pdb=" O HISAN 113 " (cutoff:3.500A) Processing helix chain 'AO' and resid 75 through 77 No H-bonds generated for 'chain 'AO' and resid 75 through 77' Processing helix chain 'AO' and resid 83 through 85 No H-bonds generated for 'chain 'AO' and resid 83 through 85' Processing helix chain 'AO' and resid 88 through 93 Processing helix chain 'AO' and resid 101 through 116 Processing helix chain 'AO' and resid 126 through 146 Processing helix chain 'AO' and resid 151 through 172 Processing helix chain 'AO' and resid 176 through 185 Processing helix chain 'AO' and resid 202 through 238 Processing helix chain 'AP' and resid 70 through 79 Processing helix chain 'AP' and resid 85 through 94 Processing helix chain 'AP' and resid 101 through 125 Processing helix chain 'AR' and resid 78 through 83 Processing helix chain 'AR' and resid 95 through 98 No H-bonds generated for 'chain 'AR' and resid 95 through 98' Processing helix chain 'AR' and resid 102 through 118 Processing helix chain 'AR' and resid 128 through 132 removed outlier: 4.269A pdb=" N LYSAR 132 " --> pdb=" O ALAAR 129 " (cutoff:3.500A) Processing helix chain 'AU' and resid 19 through 32 Processing helix chain 'AU' and resid 35 through 41 Processing helix chain 'AU' and resid 48 through 79 removed outlier: 5.248A pdb=" N ARGAU 77 " --> pdb=" O ASNAU 73 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N LYSAU 78 " --> pdb=" O PHEAU 74 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASNAU 79 " --> pdb=" O LEUAU 75 " (cutoff:3.500A) Processing helix chain 'AZ' and resid 699 through 706 Processing helix chain 'Aa' and resid 95 through 105 Processing helix chain 'Aa' and resid 109 through 112 No H-bonds generated for 'chain 'Aa' and resid 109 through 112' Processing helix chain 'Aa' and resid 130 through 148 Processing helix chain 'Aa' and resid 168 through 170 No H-bonds generated for 'chain 'Aa' and resid 168 through 170' Processing helix chain 'Aa' and resid 208 through 218 Processing helix chain 'Aa' and resid 230 through 232 No H-bonds generated for 'chain 'Aa' and resid 230 through 232' Processing helix chain 'Aa' and resid 234 through 242 Processing helix chain 'Aa' and resid 246 through 256 Processing helix chain 'Aa' and resid 262 through 278 Processing helix chain 'Aa' and resid 281 through 284 Processing helix chain 'Aa' and resid 290 through 299 Processing helix chain 'Aa' and resid 304 through 312 Processing helix chain 'Aa' and resid 316 through 330 Processing helix chain 'Aa' and resid 334 through 341 Processing helix chain 'Aa' and resid 346 through 356 Processing helix chain 'Aa' and resid 361 through 378 Processing helix chain 'Ab' and resid 12 through 21 Processing helix chain 'Ab' and resid 30 through 37 Processing helix chain 'Ab' and resid 66 through 78 removed outlier: 4.180A pdb=" N LYSAb 73 " --> pdb=" O ARGAb 69 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 95 through 107 Processing helix chain 'Ab' and resid 114 through 128 removed outlier: 3.791A pdb=" N GLUAb 128 " --> pdb=" O ALAAb 124 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 8 through 11 Processing helix chain 'Ac' and resid 13 through 18 Processing helix chain 'Ac' and resid 40 through 58 removed outlier: 4.131A pdb=" N GLYAc 43 " --> pdb=" O LEUAc 40 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ASNAc 51 " --> pdb=" O VALAc 48 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ILEAc 52 " --> pdb=" O PHEAc 49 " (cutoff:3.500A) Proline residue: Ac 53 - end of helix removed outlier: 3.647A pdb=" N GLNAc 56 " --> pdb=" O PROAc 53 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 95 through 105 Processing helix chain 'Ac' and resid 110 through 121 Processing helix chain 'Ac' and resid 161 through 169 Processing helix chain 'Ad' and resid 50 through 86 Processing helix chain 'Ad' and resid 89 through 166 removed outlier: 4.047A pdb=" N LYSAd 165 " --> pdb=" O GLNAd 161 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N THRAd 166 " --> pdb=" O GLUAd 162 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 172 through 182 removed outlier: 3.605A pdb=" N ASPAd 182 " --> pdb=" O GLUAd 178 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 200 through 202 No H-bonds generated for 'chain 'Ad' and resid 200 through 202' Processing helix chain 'Ae' and resid 69 through 74 Processing helix chain 'Ae' and resid 76 through 83 Processing helix chain 'Ae' and resid 90 through 102 Processing helix chain 'Ae' and resid 109 through 117 Processing helix chain 'Ae' and resid 122 through 136 Processing helix chain 'Ae' and resid 146 through 158 Processing helix chain 'Ae' and resid 164 through 171 Processing helix chain 'Ae' and resid 182 through 193 Processing helix chain 'Ae' and resid 197 through 209 Processing helix chain 'Ae' and resid 216 through 231 removed outlier: 3.906A pdb=" N LEUAe 223 " --> pdb=" O LEUAe 220 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 238 through 249 Processing helix chain 'Ae' and resid 258 through 277 Processing helix chain 'Ae' and resid 280 through 284 removed outlier: 3.688A pdb=" N TYRAe 284 " --> pdb=" O LEUAe 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ae' and resid 280 through 284' Processing helix chain 'Ae' and resid 296 through 304 Processing helix chain 'Ae' and resid 316 through 333 removed outlier: 3.783A pdb=" N ALAAe 332 " --> pdb=" O LYSAe 328 " (cutoff:3.500A) Proline residue: Ae 333 - end of helix Processing helix chain 'Ae' and resid 335 through 338 No H-bonds generated for 'chain 'Ae' and resid 335 through 338' Processing helix chain 'Ae' and resid 346 through 351 Processing helix chain 'Ae' and resid 364 through 366 No H-bonds generated for 'chain 'Ae' and resid 364 through 366' Processing helix chain 'Ae' and resid 368 through 385 removed outlier: 3.529A pdb=" N GLUAe 373 " --> pdb=" O PROAe 369 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SERAe 380 " --> pdb=" O GLUAe 376 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLNAe 383 " --> pdb=" O ARGAe 379 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALAAe 384 " --> pdb=" O SERAe 380 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 393 through 450 Proline residue: Ae 406 - end of helix removed outlier: 4.179A pdb=" N ALAAe 414 " --> pdb=" O ALAAe 410 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VALAe 415 " --> pdb=" O GLUAe 411 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLNAe 418 " --> pdb=" O ALAAe 414 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HISAe 424 " --> pdb=" O LEUAe 420 " (cutoff:3.500A) Processing helix chain 'Af' and resid 81 through 87 removed outlier: 3.533A pdb=" N HISAf 87 " --> pdb=" O SERAf 83 " (cutoff:3.500A) Processing helix chain 'Af' and resid 89 through 92 No H-bonds generated for 'chain 'Af' and resid 89 through 92' Processing helix chain 'Af' and resid 132 through 134 No H-bonds generated for 'chain 'Af' and resid 132 through 134' Processing helix chain 'Ag' and resid 60 through 62 No H-bonds generated for 'chain 'Ag' and resid 60 through 62' Processing helix chain 'Ag' and resid 71 through 77 Processing helix chain 'Ag' and resid 84 through 93 Processing helix chain 'Ag' and resid 102 through 112 Processing helix chain 'Ag' and resid 133 through 146 removed outlier: 3.808A pdb=" N ILEAg 140 " --> pdb=" O SERAg 136 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 158 through 161 No H-bonds generated for 'chain 'Ag' and resid 158 through 161' Processing helix chain 'Ag' and resid 180 through 193 removed outlier: 3.908A pdb=" N THRAg 192 " --> pdb=" O LYSAg 188 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 196 through 200 removed outlier: 3.749A pdb=" N GLNAg 200 " --> pdb=" O HISAg 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ag' and resid 196 through 200' Processing helix chain 'Ag' and resid 221 through 230 Processing helix chain 'Ag' and resid 235 through 248 Processing helix chain 'Ag' and resid 264 through 268 Processing helix chain 'Ag' and resid 287 through 296 removed outlier: 3.757A pdb=" N LYSAg 294 " --> pdb=" O HISAg 290 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N METAg 295 " --> pdb=" O ASNAg 291 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VALAg 296 " --> pdb=" O LEUAg 292 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 324 through 334 removed outlier: 6.527A pdb=" N LYSAg 330 " --> pdb=" O GLUAg 326 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N GLUAg 331 " --> pdb=" O LEUAg 327 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 349 through 361 Processing helix chain 'Ag' and resid 368 through 371 removed outlier: 4.028A pdb=" N HISAg 371 " --> pdb=" O GLUAg 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ag' and resid 368 through 371' Processing helix chain 'Ag' and resid 373 through 383 Processing helix chain 'Ag' and resid 387 through 395 Processing helix chain 'Ah' and resid 269 through 282 removed outlier: 3.568A pdb=" N VALAh 281 " --> pdb=" O GLNAh 277 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 289 through 299 Processing helix chain 'Ah' and resid 320 through 324 removed outlier: 4.296A pdb=" N ILEAh 324 " --> pdb=" O HISAh 321 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 327 through 330 Processing helix chain 'Ah' and resid 338 through 352 Processing helix chain 'Ah' and resid 358 through 374 Processing helix chain 'Ah' and resid 377 through 381 Processing helix chain 'Ai' and resid 6 through 19 Processing helix chain 'Ai' and resid 31 through 38 Processing helix chain 'Ai' and resid 42 through 44 No H-bonds generated for 'chain 'Ai' and resid 42 through 44' Processing helix chain 'Ai' and resid 46 through 49 No H-bonds generated for 'chain 'Ai' and resid 46 through 49' Processing helix chain 'Ai' and resid 55 through 67 Processing helix chain 'Ai' and resid 74 through 89 Processing helix chain 'Aj' and resid 11 through 25 Processing helix chain 'Aj' and resid 30 through 33 No H-bonds generated for 'chain 'Aj' and resid 30 through 33' Processing helix chain 'Aj' and resid 52 through 60 removed outlier: 5.143A pdb=" N ALAAj 56 " --> pdb=" O ARGAj 53 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASPAj 57 " --> pdb=" O ALAAj 54 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N HISAj 60 " --> pdb=" O ASPAj 57 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 64 through 68 Processing helix chain 'Aj' and resid 83 through 88 Processing helix chain 'Aj' and resid 146 through 150 Processing helix chain 'Aj' and resid 168 through 180 Processing helix chain 'Aj' and resid 193 through 196 Processing helix chain 'Ak' and resid 68 through 70 No H-bonds generated for 'chain 'Ak' and resid 68 through 70' Processing helix chain 'Ak' and resid 105 through 109 Processing helix chain 'Ak' and resid 114 through 116 No H-bonds generated for 'chain 'Ak' and resid 114 through 116' Processing helix chain 'Ak' and resid 118 through 128 Processing helix chain 'Ak' and resid 137 through 140 Processing helix chain 'Ak' and resid 142 through 148 Processing helix chain 'Ak' and resid 168 through 171 removed outlier: 3.506A pdb=" N ARGAk 171 " --> pdb=" O PROAk 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ak' and resid 168 through 171' Processing helix chain 'Ak' and resid 179 through 181 No H-bonds generated for 'chain 'Ak' and resid 179 through 181' Processing helix chain 'Ak' and resid 186 through 199 removed outlier: 6.722A pdb=" N ASPAk 198 " --> pdb=" O LYSAk 194 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ARGAk 199 " --> pdb=" O LEUAk 195 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 217 through 235 Processing helix chain 'Ak' and resid 240 through 243 Processing helix chain 'Ak' and resid 247 through 249 No H-bonds generated for 'chain 'Ak' and resid 247 through 249' Processing helix chain 'Ak' and resid 259 through 274 Processing helix chain 'Ak' and resid 282 through 286 Processing helix chain 'Ak' and resid 289 through 304 Processing helix chain 'Ak' and resid 308 through 322 Processing helix chain 'Am' and resid 46 through 59 Processing helix chain 'Am' and resid 68 through 93 removed outlier: 3.735A pdb=" N SERAm 88 " --> pdb=" O ARGAm 84 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILEAm 89 " --> pdb=" O LYSAm 85 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLNAm 90 " --> pdb=" O METAm 86 " (cutoff:3.500A) Processing helix chain 'Am' and resid 101 through 110 Processing helix chain 'An' and resid 130 through 149 Processing helix chain 'An' and resid 151 through 179 Processing helix chain 'Ao' and resid 69 through 75 Processing helix chain 'Ao' and resid 100 through 123 Processing helix chain 'Ao' and resid 125 through 128 Processing helix chain 'Ao' and resid 138 through 140 No H-bonds generated for 'chain 'Ao' and resid 138 through 140' Processing helix chain 'Ao' and resid 153 through 162 removed outlier: 4.546A pdb=" N GLNAo 158 " --> pdb=" O GLUAo 154 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 202 through 212 Processing helix chain 'Ao' and resid 222 through 232 Processing helix chain 'Ao' and resid 241 through 252 Processing helix chain 'Ao' and resid 258 through 271 removed outlier: 4.603A pdb=" N CYSAo 263 " --> pdb=" O ALAAo 259 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VALAo 270 " --> pdb=" O ILEAo 266 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYSAo 271 " --> pdb=" O ARGAo 267 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 276 through 287 Processing helix chain 'Ao' and resid 294 through 306 Processing helix chain 'Ao' and resid 313 through 328 removed outlier: 3.616A pdb=" N ASNAo 318 " --> pdb=" O GLUAo 314 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 335 through 346 Processing helix chain 'Ao' and resid 353 through 366 removed outlier: 3.916A pdb=" N LYSAo 364 " --> pdb=" O LEUAo 360 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILEAo 366 " --> pdb=" O GLUAo 362 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 372 through 384 Processing helix chain 'Ao' and resid 391 through 405 removed outlier: 4.274A pdb=" N GLYAo 405 " --> pdb=" O ASNAo 401 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 415 through 428 removed outlier: 4.335A pdb=" N ALAAo 422 " --> pdb=" O PHEAo 419 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N METAo 423 " --> pdb=" O GLNAo 420 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARGAo 424 " --> pdb=" O SERAo 421 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VALAo 425 " --> pdb=" O ALAAo 422 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 433 through 442 Processing helix chain 'Ao' and resid 448 through 450 No H-bonds generated for 'chain 'Ao' and resid 448 through 450' Processing helix chain 'Ao' and resid 454 through 471 removed outlier: 3.879A pdb=" N TYRAo 460 " --> pdb=" O ARGAo 456 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYRAo 461 " --> pdb=" O ARGAo 457 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHEAo 470 " --> pdb=" O ASNAo 466 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 474 through 484 removed outlier: 3.867A pdb=" N LYSAo 479 " --> pdb=" O ASPAo 475 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYSAo 482 " --> pdb=" O LEUAo 478 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASPAo 483 " --> pdb=" O LYSAo 479 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 493 through 505 removed outlier: 3.536A pdb=" N ASPAo 498 " --> pdb=" O GLNAo 494 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEUAo 499 " --> pdb=" O THRAo 495 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEUAo 500 " --> pdb=" O METAo 496 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASPAo 504 " --> pdb=" O LEUAo 500 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VALAo 505 " --> pdb=" O GLNAo 501 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 512 through 522 removed outlier: 3.596A pdb=" N GLUAo 521 " --> pdb=" O LYSAo 517 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 527 through 538 removed outlier: 4.315A pdb=" N GLUAo 532 " --> pdb=" O ASNAo 528 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N GLUAo 533 " --> pdb=" O GLUAo 529 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N METAo 536 " --> pdb=" O GLUAo 532 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEUAo 537 " --> pdb=" O GLUAo 533 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N METAo 538 " --> pdb=" O ILEAo 534 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 548 through 562 removed outlier: 3.606A pdb=" N ILEAo 558 " --> pdb=" O CYSAo 554 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 576 through 589 Processing helix chain 'Ao' and resid 592 through 603 removed outlier: 3.564A pdb=" N LYSAo 597 " --> pdb=" O GLNAo 593 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 611 through 623 Processing helix chain 'Ao' and resid 627 through 639 Processing helix chain 'Ao' and resid 645 through 658 Processing helix chain 'Ao' and resid 662 through 673 Processing helix chain 'Ap' and resid 55 through 60 Processing helix chain 'Ap' and resid 62 through 68 Processing helix chain 'Ap' and resid 106 through 109 No H-bonds generated for 'chain 'Ap' and resid 106 through 109' Processing helix chain 'Ap' and resid 120 through 126 removed outlier: 4.247A pdb=" N GLNAp 125 " --> pdb=" O LYSAp 121 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N PHEAp 126 " --> pdb=" O LEUAp 122 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 137 through 140 No H-bonds generated for 'chain 'Ap' and resid 137 through 140' Processing helix chain 'Ap' and resid 144 through 159 Processing helix chain 'Ap' and resid 191 through 195 removed outlier: 3.913A pdb=" N SERAp 195 " --> pdb=" O PROAp 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'Ap' and resid 191 through 195' Processing helix chain 'Ap' and resid 201 through 203 No H-bonds generated for 'chain 'Ap' and resid 201 through 203' Processing helix chain 'Ap' and resid 210 through 219 Processing sheet with id= A, first strand: chain 'BC' and resid 319 through 323 removed outlier: 4.235A pdb=" N GLNBC 319 " --> pdb=" O ILEBC 283 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLYBC 218 " --> pdb=" O ASPBC 234 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'BC' and resid 392 through 395 removed outlier: 4.307A pdb=" N VALBC 386 " --> pdb=" O VALBC 434 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N THRBC 358 " --> pdb=" O ILEBC 376 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ILEBC 376 " --> pdb=" O THRBC 358 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'BC' and resid 361 through 365 Processing sheet with id= D, first strand: chain 'BC' and resid 592 through 596 removed outlier: 4.706A pdb=" N LYSBC 592 " --> pdb=" O GLYBC 569 " (cutoff:3.500A) removed outlier: 8.651A pdb=" N VALBC 570 " --> pdb=" O VALBC 515 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N SERBC 517 " --> pdb=" O VALBC 570 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N TYRBC 572 " --> pdb=" O SERBC 517 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILEBC 519 " --> pdb=" O TYRBC 572 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N PHEBC 574 " --> pdb=" O ILEBC 519 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LYSBC 521 " --> pdb=" O PHEBC 574 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLUBC 545 " --> pdb=" O LEUBC 516 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VALBC 518 " --> pdb=" O GLUBC 545 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLUBC 547 " --> pdb=" O VALBC 518 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ILEBC 520 " --> pdb=" O GLUBC 547 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VALBC 549 " --> pdb=" O ILEBC 520 " (cutoff:3.500A) removed outlier: 12.808A pdb=" N GLYBC 522 " --> pdb=" O VALBC 549 " (cutoff:3.500A) removed outlier: 10.022A pdb=" N PHEBC 551 " --> pdb=" O GLYBC 522 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'BC' and resid 631 through 635 removed outlier: 4.876A pdb=" N LEUBC 696 " --> pdb=" O PROBC 642 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'BC' and resid 646 through 651 removed outlier: 6.827A pdb=" N GLUBC 625 " --> pdb=" O GLNBC 649 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N GLYBC 651 " --> pdb=" O VALBC 623 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N VALBC 623 " --> pdb=" O GLYBC 651 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N CYSBC 711 " --> pdb=" O VALBC 623 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLUBC 625 " --> pdb=" O ILEBC 709 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILEBC 709 " --> pdb=" O GLUBC 625 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TRPBC 669 " --> pdb=" O LEUBC 661 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ARGBC 663 " --> pdb=" O VALBC 667 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N VALBC 667 " --> pdb=" O ARGBC 663 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'AB' and resid 164 through 166 removed outlier: 6.782A pdb=" N LEUAB 191 " --> pdb=" O LEUAB 142 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N VALAB 144 " --> pdb=" O LEUAB 191 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILEAB 193 " --> pdb=" O VALAB 144 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N PHEAB 194 " --> pdb=" O PROAB 217 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VALAB 219 " --> pdb=" O PHEAB 194 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N TYRAB 233 " --> pdb=" O GLYAB 220 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N VALAB 222 " --> pdb=" O TYRAB 233 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VALAB 235 " --> pdb=" O VALAB 222 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'AB' and resid 105 through 109 removed outlier: 6.844A pdb=" N ILEAB 114 " --> pdb=" O PHEAB 106 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SERAB 108 " --> pdb=" O GLNAB 112 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N GLNAB 112 " --> pdb=" O SERAB 108 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'AC' and resid 109 through 113 Processing sheet with id= J, first strand: chain 'AE' and resid 254 through 261 removed outlier: 6.338A pdb=" N ALAAE 246 " --> pdb=" O ILEAE 222 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ILEAE 222 " --> pdb=" O ALAAE 246 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N GLYAE 248 " --> pdb=" O THRAE 220 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N THRAE 220 " --> pdb=" O GLYAE 248 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'AE' and resid 294 through 298 Processing sheet with id= L, first strand: chain 'AE' and resid 370 through 372 removed outlier: 6.456A pdb=" N GLUAE 372 " --> pdb=" O VALAE 383 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N VALAE 383 " --> pdb=" O GLUAE 372 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'AF' and resid 43 through 46 removed outlier: 3.835A pdb=" N GLYAF 43 " --> pdb=" O TYRAF 63 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'AF' and resid 51 through 53 Processing sheet with id= O, first strand: chain 'AF' and resid 35 through 41 removed outlier: 6.722A pdb=" N ASPAF 67 " --> pdb=" O ARGAF 37 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LEUAF 39 " --> pdb=" O LEUAF 65 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEUAF 65 " --> pdb=" O LEUAF 39 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'AG' and resid 156 through 163 Processing sheet with id= Q, first strand: chain 'AI' and resid 198 through 200 Processing sheet with id= R, first strand: chain 'AI' and resid 270 through 277 removed outlier: 6.606A pdb=" N ARGAI 293 " --> pdb=" O METAI 329 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N CYSAI 331 " --> pdb=" O ARGAI 293 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ASPAI 295 " --> pdb=" O CYSAI 331 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N VALAI 333 " --> pdb=" O ASPAI 295 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'AJ' and resid 106 through 109 removed outlier: 4.695A pdb=" N LEUAJ 72 " --> pdb=" O LEUAJ 177 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N THRAJ 175 " --> pdb=" O LYSAJ 74 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEUAJ 76 " --> pdb=" O THRAJ 173 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THRAJ 173 " --> pdb=" O LEUAJ 76 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VALAJ 78 " --> pdb=" O GLUAJ 171 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLUAJ 171 " --> pdb=" O VALAJ 78 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N VALAJ 80 " --> pdb=" O ALAAJ 169 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ALAAJ 169 " --> pdb=" O VALAJ 80 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'AJ' and resid 114 through 121 Processing sheet with id= U, first strand: chain 'AK' and resid 108 through 113 removed outlier: 6.698A pdb=" N VALAK 101 " --> pdb=" O LEUAK 109 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N HISAK 111 " --> pdb=" O ILEAK 99 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILEAK 99 " --> pdb=" O HISAK 111 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N SERAK 113 " --> pdb=" O THRAK 97 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N THRAK 97 " --> pdb=" O SERAK 113 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'AL' and resid 107 through 111 removed outlier: 6.561A pdb=" N ARGAL 82 " --> pdb=" O LEUAL 63 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N THRAL 65 " --> pdb=" O CYSAL 80 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N CYSAL 80 " --> pdb=" O THRAL 65 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILEAL 67 " --> pdb=" O ARGAL 78 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ARGAL 78 " --> pdb=" O ILEAL 67 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'AP' and resid 17 through 26 Processing sheet with id= X, first strand: chain 'AP' and resid 52 through 55 removed outlier: 3.605A pdb=" N LEUAP 65 " --> pdb=" O ASPAP 55 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'AQ' and resid 79 through 81 removed outlier: 15.295A pdb=" N TRPAQ 12 " --> pdb=" O LEUAQ 33 " (cutoff:3.500A) removed outlier: 11.814A pdb=" N LEUAQ 33 " --> pdb=" O TRPAQ 12 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VALAQ 14 " --> pdb=" O THRAQ 31 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N THRAQ 31 " --> pdb=" O VALAQ 14 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LYSAQ 27 " --> pdb=" O ILEAQ 18 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'AQ' and resid 63 through 65 removed outlier: 6.738A pdb=" N LEUAQ 65 " --> pdb=" O ILEAQ 84 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ILEAQ 84 " --> pdb=" O LEUAQ 65 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'Aa' and resid 178 through 181 removed outlier: 6.535A pdb=" N LYSAa 205 " --> pdb=" O VALAa 163 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VALAa 163 " --> pdb=" O LYSAa 205 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'Ac' and resid 63 through 68 removed outlier: 6.704A pdb=" N TYRAc 79 " --> pdb=" O LYSAc 28 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N METAc 30 " --> pdb=" O ARGAc 77 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ARGAc 77 " --> pdb=" O METAc 30 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VALAc 32 " --> pdb=" O PHEAc 75 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N PHEAc 75 " --> pdb=" O VALAc 32 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'Ad' and resid 190 through 192 removed outlier: 3.661A pdb=" N LEUAd 196 " --> pdb=" O THRAd 192 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'Af' and resid 123 through 126 removed outlier: 3.535A pdb=" N HISAf 107 " --> pdb=" O TYRAf 114 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ASPAf 116 " --> pdb=" O ILEAf 105 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ILEAf 105 " --> pdb=" O ASPAf 116 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLYAf 172 " --> pdb=" O ARGAf 142 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ARGAf 144 " --> pdb=" O LEUAf 170 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N LEUAf 170 " --> pdb=" O ARGAf 144 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'Ag' and resid 66 through 69 removed outlier: 4.321A pdb=" N ALAAg 96 " --> pdb=" O ILEAg 69 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'Ag' and resid 340 through 344 removed outlier: 4.052A pdb=" N VALAg 121 " --> pdb=" O GLYAg 303 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEUAg 257 " --> pdb=" O ALAAg 304 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VALAg 306 " --> pdb=" O LEUAg 257 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VALAg 259 " --> pdb=" O VALAg 306 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N THRAg 308 " --> pdb=" O VALAg 259 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VALAg 261 " --> pdb=" O THRAg 308 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LEUAg 150 " --> pdb=" O LEUAg 258 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ALAAg 260 " --> pdb=" O LEUAg 150 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEUAg 152 " --> pdb=" O ALAAg 260 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ASPAg 262 " --> pdb=" O LEUAg 152 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILEAg 154 " --> pdb=" O ASPAg 262 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'Ag' and resid 168 through 170 Processing sheet with id= AH, first strand: chain 'Ag' and resid 206 through 208 Processing sheet with id= AI, first strand: chain 'Aj' and resid 80 through 82 Processing sheet with id= AJ, first strand: chain 'Aj' and resid 94 through 97 Processing sheet with id= AK, first strand: chain 'Aj' and resid 100 through 103 removed outlier: 4.712A pdb=" N HISAj 111 " --> pdb=" O ASPAj 103 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'Aj' and resid 163 through 165 Processing sheet with id= AM, first strand: chain 'Ak' and resid 151 through 155 2080 hydrogen bonds defined for protein. 5931 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 727 hydrogen bonds 1284 hydrogen bond angles 0 basepair planarities 298 basepair parallelities 568 stacking parallelities Total time for adding SS restraints: 36.93 Time building geometry restraints manager: 28.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 22128 1.35 - 1.51: 30416 1.51 - 1.67: 23874 1.67 - 1.82: 356 1.82 - 1.98: 19 Bond restraints: 76793 Sorted by residual: bond pdb=" CA ILEAc 52 " pdb=" CB ILEAc 52 " ideal model delta sigma weight residual 1.537 1.566 -0.029 5.00e-03 4.00e+04 3.39e+01 bond pdb=" CA PHEAJ 127 " pdb=" C PHEAJ 127 " ideal model delta sigma weight residual 1.526 1.469 0.057 1.08e-02 8.57e+03 2.78e+01 bond pdb=" CB CYSAc 139 " pdb=" SG CYSAc 139 " ideal model delta sigma weight residual 1.808 1.980 -0.172 3.30e-02 9.18e+02 2.71e+01 bond pdb=" C LEUAb 30 " pdb=" O LEUAb 30 " ideal model delta sigma weight residual 1.236 1.294 -0.057 1.15e-02 7.56e+03 2.47e+01 bond pdb=" CA GLUAB 138 " pdb=" C GLUAB 138 " ideal model delta sigma weight residual 1.532 1.489 0.043 9.60e-03 1.09e+04 2.03e+01 ... (remaining 76788 not shown) Histogram of bond angle deviations from ideal: 97.30 - 105.40: 6237 105.40 - 113.49: 44680 113.49 - 121.58: 39335 121.58 - 129.68: 17319 129.68 - 137.77: 1194 Bond angle restraints: 108765 Sorted by residual: angle pdb=" C PROAK 66 " pdb=" N PROAK 67 " pdb=" CA PROAK 67 " ideal model delta sigma weight residual 119.84 134.02 -14.18 1.25e+00 6.40e-01 1.29e+02 angle pdb=" C ASPAQ 36 " pdb=" N PROAQ 37 " pdb=" CA PROAQ 37 " ideal model delta sigma weight residual 118.85 129.37 -10.52 1.09e+00 8.42e-01 9.32e+01 angle pdb=" C VALAe 215 " pdb=" N PROAe 216 " pdb=" CA PROAe 216 " ideal model delta sigma weight residual 119.84 107.91 11.93 1.25e+00 6.40e-01 9.11e+01 angle pdb=" C ASNAB 227 " pdb=" N PROAB 228 " pdb=" CA PROAB 228 " ideal model delta sigma weight residual 119.87 128.72 -8.85 1.04e+00 9.25e-01 7.24e+01 angle pdb=" C ARGAd 199 " pdb=" N PROAd 200 " pdb=" CA PROAd 200 " ideal model delta sigma weight residual 119.56 127.92 -8.36 1.01e+00 9.80e-01 6.85e+01 ... (remaining 108760 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.39: 43771 35.39 - 70.78: 3285 70.78 - 106.17: 362 106.17 - 141.56: 12 141.56 - 176.95: 10 Dihedral angle restraints: 47440 sinusoidal: 29034 harmonic: 18406 Sorted by residual: dihedral pdb=" CA GLYAe 313 " pdb=" C GLYAe 313 " pdb=" N GLNAe 314 " pdb=" CA GLNAe 314 " ideal model delta harmonic sigma weight residual 180.00 60.83 119.17 0 5.00e+00 4.00e-02 5.68e+02 dihedral pdb=" O4' CAA 745 " pdb=" C1' CAA 745 " pdb=" N1 CAA 745 " pdb=" C2 CAA 745 " ideal model delta sinusoidal sigma weight residual -160.00 7.14 -167.14 1 1.50e+01 4.44e-03 8.43e+01 dihedral pdb=" O4' CAA 744 " pdb=" C1' CAA 744 " pdb=" N1 CAA 744 " pdb=" C2 CAA 744 " ideal model delta sinusoidal sigma weight residual 200.00 39.17 160.83 1 1.50e+01 4.44e-03 8.30e+01 ... (remaining 47437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 10712 0.064 - 0.129: 1833 0.129 - 0.193: 246 0.193 - 0.258: 25 0.258 - 0.322: 2 Chirality restraints: 12818 Sorted by residual: chirality pdb=" C1' AAA 476 " pdb=" O4' AAA 476 " pdb=" C2' AAA 476 " pdb=" N9 AAA 476 " both_signs ideal model delta sigma weight residual False 2.44 2.12 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CA VALAb 135 " pdb=" N VALAb 135 " pdb=" C VALAb 135 " pdb=" CB VALAb 135 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" C1' GAA 383 " pdb=" O4' GAA 383 " pdb=" C2' GAA 383 " pdb=" N9 GAA 383 " both_signs ideal model delta sigma weight residual False 2.46 2.20 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 12815 not shown) Planarity restraints: 10078 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' CAA 4 " -0.043 2.00e-02 2.50e+03 2.13e-02 1.02e+01 pdb=" N1 CAA 4 " 0.042 2.00e-02 2.50e+03 pdb=" C2 CAA 4 " 0.009 2.00e-02 2.50e+03 pdb=" O2 CAA 4 " 0.005 2.00e-02 2.50e+03 pdb=" N3 CAA 4 " -0.004 2.00e-02 2.50e+03 pdb=" C4 CAA 4 " -0.009 2.00e-02 2.50e+03 pdb=" N4 CAA 4 " -0.010 2.00e-02 2.50e+03 pdb=" C5 CAA 4 " -0.001 2.00e-02 2.50e+03 pdb=" C6 CAA 4 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYSAp 105 " 0.052 5.00e-02 4.00e+02 7.92e-02 1.00e+01 pdb=" N PROAp 106 " -0.137 5.00e-02 4.00e+02 pdb=" CA PROAp 106 " 0.042 5.00e-02 4.00e+02 pdb=" CD PROAp 106 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYSAJ 186 " -0.049 5.00e-02 4.00e+02 7.43e-02 8.84e+00 pdb=" N PROAJ 187 " 0.129 5.00e-02 4.00e+02 pdb=" CA PROAJ 187 " -0.038 5.00e-02 4.00e+02 pdb=" CD PROAJ 187 " -0.042 5.00e-02 4.00e+02 ... (remaining 10075 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 320 2.50 - 3.10: 49599 3.10 - 3.70: 120542 3.70 - 4.30: 182637 4.30 - 4.90: 268019 Nonbonded interactions: 621117 Sorted by model distance: nonbonded pdb=" O6 GAA 762 " pdb="MG MGAA3048 " model vdw 1.895 2.170 nonbonded pdb=" OP2 GAA 147 " pdb="MG MGAA3027 " model vdw 1.916 2.170 nonbonded pdb=" OP2 AAA 925 " pdb="MG MGAA3011 " model vdw 1.926 2.170 nonbonded pdb=" OE1 GLUAd 58 " pdb=" NH1 ARGAd 61 " model vdw 1.961 2.520 nonbonded pdb=" OP2 AAA 235 " pdb="MG MGAA3002 " model vdw 1.964 2.170 ... (remaining 621112 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 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: 0.050 Extract box with map and model: 7.710 Check model and map are aligned: 0.850 Set scattering table: 0.520 Process input model: 188.880 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.190 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: 0.010 Load rotamer database and sin/cos tables:3.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 204.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 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 : 0.008 0.172 76793 Z= 0.509 Angle : 1.210 14.178 108765 Z= 0.774 Chirality : 0.049 0.322 12818 Planarity : 0.006 0.079 10078 Dihedral : 20.675 176.952 35506 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.60 % Favored : 96.26 % Rotamer: Outliers : 9.58 % Allowed : 11.09 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -3.26 (0.08), residues: 6199 helix: -2.83 (0.07), residues: 2781 sheet: -1.00 (0.17), residues: 644 loop : -1.53 (0.10), residues: 2774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRPBC 446 HIS 0.016 0.002 HISBC 621 PHE 0.032 0.003 PHEAU 74 TYR 0.028 0.003 TYRAe 224 ARG 0.007 0.001 ARGAb 48 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2097 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 517 poor density : 1580 time to evaluate : 5.327 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BC 197 LEU cc_start: 0.8712 (mt) cc_final: 0.8492 (tp) REVERT: BC 215 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.7319 (mt0) REVERT: BC 232 PHE cc_start: 0.7792 (m-80) cc_final: 0.7489 (m-80) REVERT: BC 300 VAL cc_start: 0.7448 (t) cc_final: 0.6944 (t) REVERT: BC 373 THR cc_start: 0.8829 (OUTLIER) cc_final: 0.8551 (p) REVERT: BC 520 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8786 (mt) REVERT: BC 575 ASN cc_start: 0.8171 (OUTLIER) cc_final: 0.7849 (m110) REVERT: BC 580 ASN cc_start: 0.8155 (m-40) cc_final: 0.7650 (m-40) REVERT: BC 687 LYS cc_start: 0.7520 (mptt) cc_final: 0.7218 (tppt) REVERT: AB 61 ILE cc_start: 0.9153 (tt) cc_final: 0.8873 (mt) REVERT: AB 101 MET cc_start: 0.8716 (mmt) cc_final: 0.8477 (mmm) REVERT: AB 171 LYS cc_start: 0.9150 (mtmt) cc_final: 0.8926 (mtpt) REVERT: AB 267 GLU cc_start: 0.8670 (mm-30) cc_final: 0.7848 (tp30) REVERT: AC 44 VAL cc_start: 0.9025 (OUTLIER) cc_final: 0.8724 (p) REVERT: AC 89 ASP cc_start: 0.8557 (OUTLIER) cc_final: 0.8278 (m-30) REVERT: AC 93 ARG cc_start: 0.8778 (mmt180) cc_final: 0.8534 (mmt180) REVERT: AC 104 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8621 (mt) REVERT: AC 107 GLN cc_start: 0.8624 (mt0) cc_final: 0.8289 (mp10) REVERT: AC 139 SER cc_start: 0.8712 (m) cc_final: 0.8501 (p) REVERT: AC 140 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8602 (mt-10) REVERT: AC 144 SER cc_start: 0.9303 (m) cc_final: 0.8654 (m) REVERT: AC 152 HIS cc_start: 0.8375 (m-70) cc_final: 0.7860 (m-70) REVERT: AE 157 ILE cc_start: 0.8477 (mp) cc_final: 0.8112 (mt) REVERT: AE 178 GLU cc_start: 0.8123 (tt0) cc_final: 0.7549 (tp30) REVERT: AE 191 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.8171 (ptt-90) REVERT: AE 227 ASN cc_start: 0.8896 (m-40) cc_final: 0.8632 (m-40) REVERT: AE 240 SER cc_start: 0.8832 (OUTLIER) cc_final: 0.8554 (p) REVERT: AE 242 ARG cc_start: 0.9264 (OUTLIER) cc_final: 0.8810 (ptt90) REVERT: AE 290 ILE cc_start: 0.9398 (OUTLIER) cc_final: 0.8959 (pt) REVERT: AE 321 MET cc_start: 0.9200 (mtp) cc_final: 0.8908 (mtp) REVERT: AE 339 SER cc_start: 0.9114 (t) cc_final: 0.8895 (m) REVERT: AE 342 MET cc_start: 0.9164 (tpp) cc_final: 0.8633 (tpp) REVERT: AE 344 ASN cc_start: 0.9008 (m-40) cc_final: 0.8771 (m-40) REVERT: AE 355 ARG cc_start: 0.9155 (OUTLIER) cc_final: 0.8870 (mmt-90) REVERT: AE 403 ASP cc_start: 0.8196 (t0) cc_final: 0.7968 (t0) REVERT: AE 427 ARG cc_start: 0.9135 (OUTLIER) cc_final: 0.8841 (mmt180) REVERT: AF 5 GLU cc_start: 0.8527 (tp30) cc_final: 0.8248 (tp30) REVERT: AF 73 THR cc_start: 0.8971 (m) cc_final: 0.8712 (p) REVERT: AF 78 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.8173 (mpp) REVERT: AF 104 GLU cc_start: 0.8346 (mp0) cc_final: 0.8013 (mm-30) REVERT: AG 50 TYR cc_start: 0.8203 (t80) cc_final: 0.7815 (t80) REVERT: AG 72 GLN cc_start: 0.7755 (mt0) cc_final: 0.7535 (mt0) REVERT: AG 73 LEU cc_start: 0.8817 (mt) cc_final: 0.8357 (mp) REVERT: AI 73 PHE cc_start: 0.8020 (t80) cc_final: 0.7623 (t80) REVERT: AI 213 LYS cc_start: 0.8432 (mttt) cc_final: 0.8123 (mmtm) REVERT: AI 217 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8118 (mp10) REVERT: AI 256 GLN cc_start: 0.6866 (OUTLIER) cc_final: 0.6078 (mm-40) REVERT: AI 314 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9063 (mp) REVERT: AI 390 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.7221 (ttt180) REVERT: AJ 64 THR cc_start: 0.7598 (OUTLIER) cc_final: 0.7368 (p) REVERT: AJ 140 TYR cc_start: 0.8555 (m-80) cc_final: 0.8302 (m-80) REVERT: AJ 145 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8145 (mt) REVERT: AJ 163 ASN cc_start: 0.8295 (m-40) cc_final: 0.7850 (m110) REVERT: AK 183 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8690 (tp) REVERT: AK 195 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7712 (mtm-85) REVERT: AL 131 ASP cc_start: 0.8574 (m-30) cc_final: 0.8332 (m-30) REVERT: AN 61 THR cc_start: 0.8973 (m) cc_final: 0.8626 (p) REVERT: AN 98 ARG cc_start: 0.8686 (ptt180) cc_final: 0.8471 (ptt180) REVERT: AO 72 MET cc_start: 0.9076 (OUTLIER) cc_final: 0.8792 (tpp) REVERT: AO 73 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8976 (tp) REVERT: AO 100 ASN cc_start: 0.8832 (t0) cc_final: 0.8586 (t0) REVERT: AO 124 SER cc_start: 0.8714 (p) cc_final: 0.8494 (p) REVERT: AO 133 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9230 (tp) REVERT: AO 158 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.8965 (mt) REVERT: AO 167 MET cc_start: 0.9070 (mtp) cc_final: 0.8718 (mtt) REVERT: AO 182 ILE cc_start: 0.9036 (mm) cc_final: 0.8806 (mt) REVERT: AO 217 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8396 (tp30) REVERT: AP 90 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9106 (mt) REVERT: AP 102 MET cc_start: 0.8874 (OUTLIER) cc_final: 0.8618 (mmm) REVERT: AP 120 LEU cc_start: 0.8766 (tp) cc_final: 0.8527 (mp) REVERT: AQ 22 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8078 (mtm) REVERT: AR 83 GLN cc_start: 0.9198 (OUTLIER) cc_final: 0.8317 (tt0) REVERT: AR 117 ILE cc_start: 0.9355 (OUTLIER) cc_final: 0.9148 (tp) REVERT: AU 10 ARG cc_start: 0.9264 (OUTLIER) cc_final: 0.8855 (mtm180) REVERT: AU 52 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8081 (ttm110) REVERT: AU 82 ASP cc_start: 0.9126 (OUTLIER) cc_final: 0.8838 (p0) REVERT: Aa 129 THR cc_start: 0.8940 (OUTLIER) cc_final: 0.8708 (p) REVERT: Aa 150 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8217 (mtp) REVERT: Aa 214 MET cc_start: 0.9129 (tpp) cc_final: 0.8706 (mmm) REVERT: Aa 321 SER cc_start: 0.8912 (m) cc_final: 0.8410 (p) REVERT: Aa 359 GLN cc_start: 0.8576 (tp40) cc_final: 0.8315 (tm-30) REVERT: Ab 86 ASP cc_start: 0.8769 (t0) cc_final: 0.8434 (t70) REVERT: Ab 115 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7821 (tm-30) REVERT: Ab 116 LYS cc_start: 0.8336 (mttt) cc_final: 0.8037 (mtmm) REVERT: Ab 119 VAL cc_start: 0.8665 (t) cc_final: 0.8353 (m) REVERT: Ac 3 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8498 (mmm) REVERT: Ac 4 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8465 (mttm) REVERT: Ac 33 ASN cc_start: 0.8956 (OUTLIER) cc_final: 0.8674 (t0) REVERT: Ac 70 MET cc_start: 0.9127 (mtp) cc_final: 0.8891 (mtt) REVERT: Ac 89 ASP cc_start: 0.8908 (t0) cc_final: 0.8685 (t0) REVERT: Ac 115 LYS cc_start: 0.8761 (mttt) cc_final: 0.8250 (mmtm) REVERT: Ac 119 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7960 (mt-10) REVERT: Ad 32 ASP cc_start: 0.8430 (m-30) cc_final: 0.8011 (m-30) REVERT: Ad 41 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7656 (tmt-80) REVERT: Ad 51 THR cc_start: 0.8745 (m) cc_final: 0.8131 (p) REVERT: Ad 145 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8509 (tp30) REVERT: Ad 183 SER cc_start: 0.9020 (t) cc_final: 0.8742 (p) REVERT: Ad 196 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8820 (mp) REVERT: Ae 142 TRP cc_start: 0.7843 (t60) cc_final: 0.7299 (t60) REVERT: Ae 152 TRP cc_start: 0.7754 (t60) cc_final: 0.7503 (t60) REVERT: Ae 159 TYR cc_start: 0.6977 (OUTLIER) cc_final: 0.5875 (t80) REVERT: Ae 184 PHE cc_start: 0.7275 (m-10) cc_final: 0.7035 (m-10) REVERT: Ae 201 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7520 (tp) REVERT: Ae 208 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.7705 (tmm) REVERT: Ae 257 ASN cc_start: 0.6881 (OUTLIER) cc_final: 0.6598 (p0) REVERT: Ae 311 GLU cc_start: 0.6637 (mt-10) cc_final: 0.5616 (pt0) REVERT: Af 109 VAL cc_start: 0.8789 (OUTLIER) cc_final: 0.8518 (t) REVERT: Ag 50 THR cc_start: 0.5831 (OUTLIER) cc_final: 0.5621 (m) REVERT: Ag 99 MET cc_start: 0.8517 (ttp) cc_final: 0.7891 (ttp) REVERT: Ag 172 TYR cc_start: 0.6657 (OUTLIER) cc_final: 0.5178 (t80) REVERT: Ag 204 GLN cc_start: 0.7566 (pt0) cc_final: 0.7277 (pt0) REVERT: Ag 252 LEU cc_start: 0.7044 (OUTLIER) cc_final: 0.6457 (mt) REVERT: Ag 295 MET cc_start: 0.8727 (tpp) cc_final: 0.7995 (tpp) REVERT: Ag 353 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8150 (tp30) REVERT: Ag 372 THR cc_start: 0.7753 (OUTLIER) cc_final: 0.7497 (p) REVERT: Ag 393 LEU cc_start: 0.8761 (mt) cc_final: 0.8342 (tp) REVERT: Ag 397 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7330 (mt) REVERT: Ah 286 PHE cc_start: 0.8263 (m-80) cc_final: 0.7997 (m-80) REVERT: Ah 294 ILE cc_start: 0.9093 (mt) cc_final: 0.8801 (mp) REVERT: Ah 359 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8852 (tttp) REVERT: Ah 373 ASN cc_start: 0.7971 (t0) cc_final: 0.7199 (t0) REVERT: Ai 6 GLU cc_start: 0.8680 (tt0) cc_final: 0.8453 (tp30) REVERT: Ai 11 MET cc_start: 0.8919 (OUTLIER) cc_final: 0.8687 (mmt) REVERT: Ai 29 LYS cc_start: 0.9077 (tttt) cc_final: 0.8575 (mtpt) REVERT: Ai 38 SER cc_start: 0.9332 (t) cc_final: 0.9006 (p) REVERT: Ai 52 TYR cc_start: 0.8889 (m-80) cc_final: 0.8436 (m-80) REVERT: Ai 73 ASP cc_start: 0.8384 (t0) cc_final: 0.8057 (t0) REVERT: Ai 77 ASP cc_start: 0.9352 (m-30) cc_final: 0.9078 (m-30) REVERT: Ai 80 ASP cc_start: 0.7935 (m-30) cc_final: 0.7725 (m-30) REVERT: Ai 87 LYS cc_start: 0.8697 (mtpp) cc_final: 0.8481 (mtmt) REVERT: Aj 41 MET cc_start: 0.8599 (tpp) cc_final: 0.8387 (mmt) REVERT: Aj 94 TYR cc_start: 0.8320 (p90) cc_final: 0.8032 (p90) REVERT: Aj 99 ARG cc_start: 0.6762 (OUTLIER) cc_final: 0.6395 (ttp80) REVERT: Aj 130 GLU cc_start: 0.8358 (tt0) cc_final: 0.8096 (tt0) REVERT: Aj 150 PHE cc_start: 0.7295 (m-80) cc_final: 0.6884 (t80) REVERT: Aj 203 TYR cc_start: 0.8663 (t80) cc_final: 0.8186 (t80) REVERT: Ak 53 LYS cc_start: 0.5967 (OUTLIER) cc_final: 0.5623 (ptmt) REVERT: Ak 59 THR cc_start: 0.8420 (m) cc_final: 0.8040 (p) REVERT: Ak 72 TYR cc_start: 0.8227 (m-10) cc_final: 0.7977 (m-10) REVERT: Ak 93 VAL cc_start: 0.8942 (OUTLIER) cc_final: 0.8724 (m) REVERT: Ak 95 ARG cc_start: 0.8448 (mmt90) cc_final: 0.7886 (mtt90) REVERT: Ak 241 TRP cc_start: 0.8784 (p-90) cc_final: 0.8173 (p-90) REVERT: Am 17 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8201 (ptm160) REVERT: An 145 LYS cc_start: 0.9331 (OUTLIER) cc_final: 0.9012 (mtpp) REVERT: An 154 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8527 (mtp85) REVERT: An 158 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.8230 (ptm160) REVERT: An 163 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.8737 (mtm110) REVERT: Ao 71 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.9038 (mt) REVERT: Ao 144 TYR cc_start: 0.7397 (m-80) cc_final: 0.6976 (m-80) REVERT: Ao 254 MET cc_start: 0.5612 (ptp) cc_final: 0.4562 (tpt) REVERT: Ao 262 TYR cc_start: 0.2255 (OUTLIER) cc_final: 0.1818 (p90) REVERT: Ao 410 PRO cc_start: 0.5263 (Cg_endo) cc_final: 0.4335 (Cg_exo) REVERT: Ao 416 ASP cc_start: 0.6778 (OUTLIER) cc_final: 0.6410 (t70) REVERT: Ao 439 HIS cc_start: 0.5121 (t70) cc_final: 0.4898 (t70) REVERT: Ao 471 MET cc_start: 0.7104 (tpp) cc_final: 0.6493 (tpp) REVERT: Ao 485 ILE cc_start: 0.6727 (mm) cc_final: 0.6422 (mm) REVERT: Ao 492 HIS cc_start: 0.5111 (t70) cc_final: 0.4703 (t70) REVERT: Ao 528 ASN cc_start: 0.6632 (m-40) cc_final: 0.5761 (p0) REVERT: Ao 557 ASP cc_start: 0.7941 (m-30) cc_final: 0.7631 (p0) REVERT: Ao 558 ILE cc_start: 0.5704 (mt) cc_final: 0.5456 (mt) REVERT: Ao 612 GLU cc_start: 0.4921 (mt-10) cc_final: 0.4475 (mp0) REVERT: Ao 645 CYS cc_start: -0.0160 (OUTLIER) cc_final: -0.0674 (t) REVERT: Ao 652 VAL cc_start: 0.1526 (OUTLIER) cc_final: 0.0849 (m) REVERT: Ao 661 GLU cc_start: 0.3550 (OUTLIER) cc_final: 0.2832 (mm-30) REVERT: Ap 68 TYR cc_start: 0.9047 (m-80) cc_final: 0.8407 (m-80) REVERT: Ap 110 ASP cc_start: 0.8358 (t0) cc_final: 0.8089 (t0) REVERT: Ap 120 VAL cc_start: 0.9375 (t) cc_final: 0.9017 (m) REVERT: Ap 139 TYR cc_start: 0.9265 (t80) cc_final: 0.9056 (t80) REVERT: Ap 169 GLN cc_start: 0.8840 (mt0) cc_final: 0.8637 (mt0) REVERT: Ap 193 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8522 (mt) REVERT: Ap 235 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7513 (ptp) outliers start: 517 outliers final: 145 residues processed: 1926 average time/residue: 0.7865 time to fit residues: 2431.1915 Evaluate side-chains 1150 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 936 time to evaluate : 5.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BC residue 215 GLN Chi-restraints excluded: chain BC residue 283 ILE Chi-restraints excluded: chain BC residue 373 THR Chi-restraints excluded: chain BC residue 424 LEU Chi-restraints excluded: chain BC residue 472 GLU Chi-restraints excluded: chain BC residue 520 ILE Chi-restraints excluded: chain BC residue 575 ASN Chi-restraints excluded: chain BC residue 727 PHE Chi-restraints excluded: chain BT residue 61 VAL Chi-restraints excluded: chain AB residue 57 LEU Chi-restraints excluded: chain AB residue 141 ILE Chi-restraints excluded: chain AB residue 186 VAL Chi-restraints excluded: chain AB residue 197 THR Chi-restraints excluded: chain AB residue 224 THR Chi-restraints excluded: chain AB residue 235 VAL Chi-restraints excluded: chain AB residue 241 SER Chi-restraints excluded: chain AC residue 41 ARG Chi-restraints excluded: chain AC residue 44 VAL Chi-restraints excluded: chain AC residue 89 ASP Chi-restraints excluded: chain AC residue 103 CYS Chi-restraints excluded: chain AC residue 104 LEU Chi-restraints excluded: chain AC residue 115 ASN Chi-restraints excluded: chain AC residue 153 LEU Chi-restraints excluded: chain AC residue 167 ILE Chi-restraints excluded: chain AE residue 137 HIS Chi-restraints excluded: chain AE residue 191 ARG Chi-restraints excluded: chain AE residue 194 SER Chi-restraints excluded: chain AE residue 203 LEU Chi-restraints excluded: chain AE residue 215 TYR Chi-restraints excluded: chain AE residue 216 ASP Chi-restraints excluded: chain AE residue 239 ARG Chi-restraints excluded: chain AE residue 240 SER Chi-restraints excluded: chain AE residue 241 VAL Chi-restraints excluded: chain AE residue 242 ARG Chi-restraints excluded: chain AE residue 289 THR Chi-restraints excluded: chain AE residue 290 ILE Chi-restraints excluded: chain AE residue 320 ILE Chi-restraints excluded: chain AE residue 336 VAL Chi-restraints excluded: chain AE residue 337 SER Chi-restraints excluded: chain AE residue 346 THR Chi-restraints excluded: chain AE residue 355 ARG Chi-restraints excluded: chain AE residue 370 VAL Chi-restraints excluded: chain AE residue 427 ARG Chi-restraints excluded: chain AF residue 13 MET Chi-restraints excluded: chain AF residue 78 MET Chi-restraints excluded: chain AG residue 109 SER Chi-restraints excluded: chain AG residue 118 VAL Chi-restraints excluded: chain AG residue 200 LEU Chi-restraints excluded: chain AG residue 219 VAL Chi-restraints excluded: chain AI residue 98 THR Chi-restraints excluded: chain AI residue 100 THR Chi-restraints excluded: chain AI residue 153 THR Chi-restraints excluded: chain AI residue 172 VAL Chi-restraints excluded: chain AI residue 206 LEU Chi-restraints excluded: chain AI residue 217 GLN Chi-restraints excluded: chain AI residue 229 LEU Chi-restraints excluded: chain AI residue 256 GLN Chi-restraints excluded: chain AI residue 314 LEU Chi-restraints excluded: chain AI residue 338 ARG Chi-restraints excluded: chain AI residue 390 ARG Chi-restraints excluded: chain AJ residue 64 THR Chi-restraints excluded: chain AJ residue 80 VAL Chi-restraints excluded: chain AJ residue 133 GLN Chi-restraints excluded: chain AJ residue 145 LEU Chi-restraints excluded: chain AJ residue 166 GLU Chi-restraints excluded: chain AJ residue 168 VAL Chi-restraints excluded: chain AJ residue 184 ILE Chi-restraints excluded: chain AK residue 68 ILE Chi-restraints excluded: chain AK residue 85 ILE Chi-restraints excluded: chain AK residue 97 THR Chi-restraints excluded: chain AK residue 121 ASN Chi-restraints excluded: chain AK residue 147 THR Chi-restraints excluded: chain AK residue 164 ILE Chi-restraints excluded: chain AK residue 177 ILE Chi-restraints excluded: chain AK residue 183 ILE Chi-restraints excluded: chain AK residue 188 CYS Chi-restraints excluded: chain AK residue 195 ARG Chi-restraints excluded: chain AL residue 32 THR Chi-restraints excluded: chain AL residue 55 ARG Chi-restraints excluded: chain AL residue 67 ILE Chi-restraints excluded: chain AL residue 93 CYS Chi-restraints excluded: chain AL residue 95 ILE Chi-restraints excluded: chain AL residue 102 LEU Chi-restraints excluded: chain AL residue 107 VAL Chi-restraints excluded: chain AN residue 30 VAL Chi-restraints excluded: chain AN residue 80 ARG Chi-restraints excluded: chain AN residue 93 MET Chi-restraints excluded: chain AN residue 125 ARG Chi-restraints excluded: chain AO residue 72 MET Chi-restraints excluded: chain AO residue 73 LEU Chi-restraints excluded: chain AO residue 74 LEU Chi-restraints excluded: chain AO residue 83 ILE Chi-restraints excluded: chain AO residue 105 LEU Chi-restraints excluded: chain AO residue 122 ASP Chi-restraints excluded: chain AO residue 130 ILE Chi-restraints excluded: chain AO residue 133 LEU Chi-restraints excluded: chain AO residue 158 LEU Chi-restraints excluded: chain AP residue 90 LEU Chi-restraints excluded: chain AP residue 94 SER Chi-restraints excluded: chain AP residue 102 MET Chi-restraints excluded: chain AQ residue 6 SER Chi-restraints excluded: chain AQ residue 22 MET Chi-restraints excluded: chain AQ residue 40 LEU Chi-restraints excluded: chain AQ residue 64 VAL Chi-restraints excluded: chain AQ residue 81 LEU Chi-restraints excluded: chain AR residue 83 GLN Chi-restraints excluded: chain AR residue 86 SER Chi-restraints excluded: chain AR residue 117 ILE Chi-restraints excluded: chain AR residue 131 LEU Chi-restraints excluded: chain AU residue 10 ARG Chi-restraints excluded: chain AU residue 13 MET Chi-restraints excluded: chain AU residue 14 VAL Chi-restraints excluded: chain AU residue 35 LEU Chi-restraints excluded: chain AU residue 50 ARG Chi-restraints excluded: chain AU residue 52 ARG Chi-restraints excluded: chain AU residue 77 ARG Chi-restraints excluded: chain AU residue 82 ASP Chi-restraints excluded: chain Aa residue 129 THR Chi-restraints excluded: chain Aa residue 150 MET Chi-restraints excluded: chain Aa residue 167 ASP Chi-restraints excluded: chain Aa residue 183 ILE Chi-restraints excluded: chain Aa residue 197 ARG Chi-restraints excluded: chain Aa residue 202 THR Chi-restraints excluded: chain Aa residue 204 ARG Chi-restraints excluded: chain Aa residue 239 THR Chi-restraints excluded: chain Aa residue 276 ASP Chi-restraints excluded: chain Aa residue 325 LEU Chi-restraints excluded: chain Aa residue 347 LEU Chi-restraints excluded: chain Ab residue 6 LEU Chi-restraints excluded: chain Ab residue 14 SER Chi-restraints excluded: chain Ab residue 30 LEU Chi-restraints excluded: chain Ab residue 67 GLU Chi-restraints excluded: chain Ac residue 3 MET Chi-restraints excluded: chain Ac residue 4 LYS Chi-restraints excluded: chain Ac residue 9 ILE Chi-restraints excluded: chain Ac residue 31 THR Chi-restraints excluded: chain Ac residue 33 ASN Chi-restraints excluded: chain Ac residue 106 LEU Chi-restraints excluded: chain Ad residue 41 ARG Chi-restraints excluded: chain Ad residue 56 LEU Chi-restraints excluded: chain Ad residue 196 LEU Chi-restraints excluded: chain Ae residue 136 ARG Chi-restraints excluded: chain Ae residue 159 TYR Chi-restraints excluded: chain Ae residue 201 LEU Chi-restraints excluded: chain Ae residue 208 MET Chi-restraints excluded: chain Ae residue 220 LEU Chi-restraints excluded: chain Ae residue 253 LEU Chi-restraints excluded: chain Ae residue 257 ASN Chi-restraints excluded: chain Ae residue 388 VAL Chi-restraints excluded: chain Af residue 85 LEU Chi-restraints excluded: chain Af residue 88 SER Chi-restraints excluded: chain Af residue 90 LEU Chi-restraints excluded: chain Af residue 108 ILE Chi-restraints excluded: chain Af residue 109 VAL Chi-restraints excluded: chain Af residue 148 LEU Chi-restraints excluded: chain Af residue 162 THR Chi-restraints excluded: chain Ag residue 50 THR Chi-restraints excluded: chain Ag residue 172 TYR Chi-restraints excluded: chain Ag residue 252 LEU Chi-restraints excluded: chain Ag residue 264 VAL Chi-restraints excluded: chain Ag residue 265 ASN Chi-restraints excluded: chain Ag residue 337 ASP Chi-restraints excluded: chain Ag residue 372 THR Chi-restraints excluded: chain Ag residue 397 LEU Chi-restraints excluded: chain Ah residue 302 LEU Chi-restraints excluded: chain Ah residue 308 ASN Chi-restraints excluded: chain Ah residue 328 LYS Chi-restraints excluded: chain Ah residue 359 LYS Chi-restraints excluded: chain Ai residue 11 MET Chi-restraints excluded: chain Ai residue 50 ASP Chi-restraints excluded: chain Aj residue 65 LEU Chi-restraints excluded: chain Aj residue 99 ARG Chi-restraints excluded: chain Aj residue 118 LEU Chi-restraints excluded: chain Aj residue 170 LEU Chi-restraints excluded: chain Ak residue 53 LYS Chi-restraints excluded: chain Ak residue 79 LYS Chi-restraints excluded: chain Ak residue 93 VAL Chi-restraints excluded: chain Ak residue 108 LEU Chi-restraints excluded: chain Ak residue 117 THR Chi-restraints excluded: chain Ak residue 165 ILE Chi-restraints excluded: chain Ak residue 166 ARG Chi-restraints excluded: chain Ak residue 175 LEU Chi-restraints excluded: chain Ak residue 309 ASN Chi-restraints excluded: chain Am residue 6 LEU Chi-restraints excluded: chain Am residue 17 ARG Chi-restraints excluded: chain Am residue 29 LEU Chi-restraints excluded: chain Am residue 33 VAL Chi-restraints excluded: chain Am residue 72 ASP Chi-restraints excluded: chain Am residue 113 ASN Chi-restraints excluded: chain An residue 145 LYS Chi-restraints excluded: chain An residue 154 ARG Chi-restraints excluded: chain An residue 158 ARG Chi-restraints excluded: chain An residue 163 ARG Chi-restraints excluded: chain Ao residue 71 LEU Chi-restraints excluded: chain Ao residue 243 THR Chi-restraints excluded: chain Ao residue 262 TYR Chi-restraints excluded: chain Ao residue 296 THR Chi-restraints excluded: chain Ao residue 372 LEU Chi-restraints excluded: chain Ao residue 416 ASP Chi-restraints excluded: chain Ao residue 488 VAL Chi-restraints excluded: chain Ao residue 608 ILE Chi-restraints excluded: chain Ao residue 645 CYS Chi-restraints excluded: chain Ao residue 652 VAL Chi-restraints excluded: chain Ao residue 661 GLU Chi-restraints excluded: chain Ap residue 53 ASP Chi-restraints excluded: chain Ap residue 103 ASN Chi-restraints excluded: chain Ap residue 107 ILE Chi-restraints excluded: chain Ap residue 108 CYS Chi-restraints excluded: chain Ap residue 155 GLN Chi-restraints excluded: chain Ap residue 167 ILE Chi-restraints excluded: chain Ap residue 177 PHE Chi-restraints excluded: chain Ap residue 186 SER Chi-restraints excluded: chain Ap residue 193 LEU Chi-restraints excluded: chain Ap residue 235 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 719 random chunks: chunk 607 optimal weight: 7.9990 chunk 544 optimal weight: 20.0000 chunk 302 optimal weight: 2.9990 chunk 186 optimal weight: 5.9990 chunk 367 optimal weight: 5.9990 chunk 291 optimal weight: 1.9990 chunk 563 optimal weight: 0.8980 chunk 218 optimal weight: 4.9990 chunk 342 optimal weight: 5.9990 chunk 419 optimal weight: 6.9990 chunk 652 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BC 215 GLN BC 238 HIS BC 330 ASN BC 514 ASN BC 533 ASN AB 125 GLN AB 133 HIS AB 215 ASN ** AB 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 57 HIS AC 115 ASN AE 127 ASN AE 130 GLN AE 145 ASN AE 174 GLN AE 175 GLN AE 292 HIS AE 317 HIS AE 356 GLN AE 360 GLN AE 415 GLN AF 41 ASN AG 196 HIS AG 227 HIS AG 233 ASN AI 82 ASN AI 87 HIS AI 90 ASN AI 127 HIS AI 139 GLN ** AI 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AI 256 GLN AI 319 HIS ** AI 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AI 367 GLN AJ 109 HIS AJ 179 GLN ** AK 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 35 GLN AL 37 HIS ** AL 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 77 ASN ** AL 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AN 119 GLN AO 100 ASN AO 147 HIS AO 153 HIS AO 197 HIS AO 201 HIS AP 28 ASN AP 100 HIS AQ 76 HIS AQ 79 HIS AU 3 ASN AU 79 ASN Aa 245 GLN Aa 246 HIS Aa 251 ASN Aa 299 ASN ** Aa 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 63 GLN Ac 69 ASN Ac 125 HIS Ac 146 GLN Ad 102 HIS Ad 109 ASN Ad 117 HIS Ae 140 ASN ** Ae 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 257 ASN ** Ae 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 107 HIS Ag 196 HIS Ag 234 ASN ** Ag 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 301 GLN Ag 386 ASN Ah 309 ASN Ah 321 HIS Ah 364 HIS ** Ai 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 60 HIS Aj 108 ASN Aj 111 HIS Ak 124 HIS Ak 263 ASN Ak 303 ASN ** Am 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ao 129 GLN Ao 258 ASN Ao 385 HIS Ao 492 HIS Ao 605 HIS ** Ap 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 147 HIS Ap 169 GLN Ap 181 HIS Total number of N/Q/H flips: 84 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 76793 Z= 0.289 Angle : 0.682 10.566 108765 Z= 0.353 Chirality : 0.041 0.242 12818 Planarity : 0.006 0.094 10078 Dihedral : 21.033 179.152 23033 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 6.27 % Allowed : 16.18 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.91 (0.10), residues: 6199 helix: -0.20 (0.09), residues: 2782 sheet: -0.63 (0.18), residues: 648 loop : -0.89 (0.11), residues: 2769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRPAk 236 HIS 0.009 0.001 HISAE 288 PHE 0.020 0.002 PHEAo 617 TYR 0.026 0.002 TYRAG 64 ARG 0.010 0.001 ARGAm 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1343 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 338 poor density : 1005 time to evaluate : 5.378 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: 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: BC 197 LEU cc_start: 0.8874 (mt) cc_final: 0.8666 (tp) REVERT: BC 215 GLN cc_start: 0.7675 (OUTLIER) cc_final: 0.7423 (mt0) REVERT: BC 266 MET cc_start: 0.5958 (mtp) cc_final: 0.5700 (mtp) REVERT: BC 285 LEU cc_start: 0.7141 (tp) cc_final: 0.6734 (mt) REVERT: BC 308 ASP cc_start: 0.7638 (m-30) cc_final: 0.7347 (t0) REVERT: BC 405 LYS cc_start: 0.9032 (tppt) cc_final: 0.8499 (ptmm) REVERT: BC 424 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8104 (tp) REVERT: BC 464 GLU cc_start: 0.8248 (mt-10) cc_final: 0.8029 (mt-10) REVERT: BC 476 LYS cc_start: 0.8559 (ttmt) cc_final: 0.7999 (tmtt) REVERT: BC 520 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8768 (mp) REVERT: BC 672 SER cc_start: 0.6772 (t) cc_final: 0.6378 (p) REVERT: BC 690 MET cc_start: 0.5542 (mmm) cc_final: 0.5128 (mmm) REVERT: AB 61 ILE cc_start: 0.9080 (tt) cc_final: 0.8821 (mt) REVERT: AB 101 MET cc_start: 0.8688 (mmt) cc_final: 0.8484 (mmm) REVERT: AB 146 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7910 (tpt-90) REVERT: AB 171 LYS cc_start: 0.9166 (mtmt) cc_final: 0.8825 (mtpt) REVERT: AB 267 GLU cc_start: 0.8536 (mm-30) cc_final: 0.7774 (tp30) REVERT: AC 41 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.6522 (mtm-85) REVERT: AC 104 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8339 (tp) REVERT: AC 140 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8412 (mt-10) REVERT: AC 144 SER cc_start: 0.9361 (m) cc_final: 0.8737 (m) REVERT: AC 152 HIS cc_start: 0.8206 (m-70) cc_final: 0.7649 (m-70) REVERT: AE 137 HIS cc_start: 0.8497 (OUTLIER) cc_final: 0.8182 (m90) REVERT: AE 178 GLU cc_start: 0.8049 (tt0) cc_final: 0.7470 (tp30) REVERT: AE 179 TRP cc_start: 0.7610 (m-10) cc_final: 0.6691 (m-10) REVERT: AE 227 ASN cc_start: 0.8973 (m-40) cc_final: 0.8656 (m-40) REVERT: AE 239 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.8139 (tmm160) REVERT: AE 241 VAL cc_start: 0.9177 (OUTLIER) cc_final: 0.8912 (t) REVERT: AE 242 ARG cc_start: 0.9084 (OUTLIER) cc_final: 0.8760 (ttt180) REVERT: AE 305 MET cc_start: 0.8762 (mtm) cc_final: 0.8291 (mtm) REVERT: AE 321 MET cc_start: 0.9125 (mtp) cc_final: 0.8717 (mtp) REVERT: AE 342 MET cc_start: 0.8870 (tpp) cc_final: 0.8523 (tpp) REVERT: AE 344 ASN cc_start: 0.8859 (m-40) cc_final: 0.8624 (m-40) REVERT: AG 72 GLN cc_start: 0.7247 (mt0) cc_final: 0.6895 (mt0) REVERT: AI 73 PHE cc_start: 0.8011 (t80) cc_final: 0.7773 (t80) REVERT: AI 91 MET cc_start: 0.7817 (ptp) cc_final: 0.7331 (ptp) REVERT: AI 95 ASP cc_start: 0.8643 (t0) cc_final: 0.8302 (t70) REVERT: AI 155 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8452 (pttt) REVERT: AI 213 LYS cc_start: 0.8281 (mttt) cc_final: 0.8048 (mmtt) REVERT: AI 217 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.8310 (mp10) REVERT: AI 268 MET cc_start: 0.8861 (mmt) cc_final: 0.7940 (ppp) REVERT: AI 338 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8500 (ptm-80) REVERT: AI 366 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8581 (ttp-170) REVERT: AJ 64 THR cc_start: 0.7333 (OUTLIER) cc_final: 0.7071 (p) REVERT: AJ 145 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8140 (mt) REVERT: AJ 160 ILE cc_start: 0.8868 (mm) cc_final: 0.8527 (tt) REVERT: AK 191 ARG cc_start: 0.8621 (ptm160) cc_final: 0.8362 (ptm-80) REVERT: AL 55 ARG cc_start: 0.9315 (OUTLIER) cc_final: 0.8930 (mtt-85) REVERT: AL 63 LEU cc_start: 0.9020 (mt) cc_final: 0.8544 (mt) REVERT: AL 131 ASP cc_start: 0.8369 (m-30) cc_final: 0.8094 (m-30) REVERT: AN 43 MET cc_start: 0.8789 (ttm) cc_final: 0.8331 (ttp) REVERT: AN 72 ASP cc_start: 0.8058 (t0) cc_final: 0.7761 (t0) REVERT: AO 72 MET cc_start: 0.9111 (OUTLIER) cc_final: 0.8804 (tpp) REVERT: AO 144 MET cc_start: 0.8797 (tpp) cc_final: 0.8330 (mmt) REVERT: AO 158 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8907 (mt) REVERT: AO 167 MET cc_start: 0.8964 (mtp) cc_final: 0.8631 (mtt) REVERT: AO 182 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8576 (mt) REVERT: AO 198 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8522 (mtt180) REVERT: AP 120 LEU cc_start: 0.8717 (tp) cc_final: 0.8479 (mt) REVERT: AR 83 GLN cc_start: 0.9119 (OUTLIER) cc_final: 0.8911 (tt0) REVERT: AU 10 ARG cc_start: 0.9227 (OUTLIER) cc_final: 0.8853 (mtm180) REVERT: AU 23 TYR cc_start: 0.9027 (t80) cc_final: 0.8669 (t80) REVERT: Aa 129 THR cc_start: 0.8854 (OUTLIER) cc_final: 0.8602 (p) REVERT: Aa 150 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8239 (mtt) REVERT: Aa 183 ILE cc_start: 0.9244 (OUTLIER) cc_final: 0.8720 (pt) REVERT: Aa 185 TYR cc_start: 0.7950 (t80) cc_final: 0.7712 (t80) REVERT: Aa 197 ARG cc_start: 0.9167 (OUTLIER) cc_final: 0.7588 (mmt90) REVERT: Aa 204 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7881 (ptt-90) REVERT: Aa 222 GLU cc_start: 0.8569 (pm20) cc_final: 0.8314 (mp0) REVERT: Aa 347 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8425 (mt) REVERT: Ab 116 LYS cc_start: 0.8160 (mttt) cc_final: 0.7454 (mtmm) REVERT: Ac 4 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8206 (mttm) REVERT: Ac 33 ASN cc_start: 0.8701 (OUTLIER) cc_final: 0.8293 (m-40) REVERT: Ad 94 LYS cc_start: 0.8826 (mmmt) cc_final: 0.8584 (mptt) REVERT: Ad 144 ARG cc_start: 0.8976 (mtp180) cc_final: 0.8717 (mtp-110) REVERT: Ad 161 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.8444 (tm-30) REVERT: Ae 152 TRP cc_start: 0.7834 (t60) cc_final: 0.7328 (t60) REVERT: Ae 159 TYR cc_start: 0.6867 (OUTLIER) cc_final: 0.5488 (t80) REVERT: Ae 184 PHE cc_start: 0.7184 (m-10) cc_final: 0.6916 (m-10) REVERT: Ae 221 LEU cc_start: 0.8705 (mt) cc_final: 0.8470 (mp) REVERT: Ae 228 HIS cc_start: 0.7256 (t70) cc_final: 0.6818 (t-170) REVERT: Ae 253 LEU cc_start: 0.6252 (OUTLIER) cc_final: 0.5566 (mt) REVERT: Ae 257 ASN cc_start: 0.6994 (OUTLIER) cc_final: 0.6726 (p0) REVERT: Ae 285 CYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8243 (p) REVERT: Af 111 ASP cc_start: 0.7699 (t0) cc_final: 0.7305 (t0) REVERT: Af 134 LYS cc_start: 0.9149 (mttm) cc_final: 0.8823 (mttp) REVERT: Af 149 GLU cc_start: 0.8138 (tt0) cc_final: 0.7690 (tt0) REVERT: Ag 50 THR cc_start: 0.4994 (OUTLIER) cc_final: 0.4649 (m) REVERT: Ag 88 MET cc_start: 0.8484 (mmp) cc_final: 0.8247 (mmm) REVERT: Ag 172 TYR cc_start: 0.6394 (OUTLIER) cc_final: 0.4594 (t80) REVERT: Ag 252 LEU cc_start: 0.6813 (OUTLIER) cc_final: 0.6282 (mt) REVERT: Ag 295 MET cc_start: 0.8474 (tpp) cc_final: 0.7954 (tpp) REVERT: Ah 294 ILE cc_start: 0.9037 (mt) cc_final: 0.8777 (mp) REVERT: Ah 328 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7643 (ptpp) REVERT: Ah 359 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8712 (tttp) REVERT: Ah 373 ASN cc_start: 0.7745 (t0) cc_final: 0.7224 (t0) REVERT: Ai 52 TYR cc_start: 0.8854 (m-80) cc_final: 0.8490 (m-80) REVERT: Ai 73 ASP cc_start: 0.8026 (t0) cc_final: 0.7790 (t70) REVERT: Ai 77 ASP cc_start: 0.9166 (m-30) cc_final: 0.8910 (m-30) REVERT: Ai 80 ASP cc_start: 0.7715 (m-30) cc_final: 0.7456 (m-30) REVERT: Ai 81 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8451 (tm-30) REVERT: Aj 94 TYR cc_start: 0.8351 (p90) cc_final: 0.8039 (p90) REVERT: Aj 150 PHE cc_start: 0.7100 (m-80) cc_final: 0.6736 (t80) REVERT: Ak 53 LYS cc_start: 0.6150 (OUTLIER) cc_final: 0.5748 (ptmt) REVERT: Ak 59 THR cc_start: 0.8577 (m) cc_final: 0.8204 (p) REVERT: Ak 95 ARG cc_start: 0.8471 (mmt90) cc_final: 0.7862 (mtt90) REVERT: Ak 241 TRP cc_start: 0.8771 (p-90) cc_final: 0.8345 (p-90) REVERT: Ak 271 ILE cc_start: 0.6942 (mm) cc_final: 0.6613 (tp) REVERT: Ak 310 THR cc_start: 0.8369 (OUTLIER) cc_final: 0.8161 (m) REVERT: Am 17 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8088 (ptm160) REVERT: Am 53 MET cc_start: 0.8378 (mmt) cc_final: 0.7816 (mmt) REVERT: Ao 249 ARG cc_start: 0.5870 (mtt180) cc_final: 0.5495 (ptp-170) REVERT: Ao 262 TYR cc_start: 0.2063 (OUTLIER) cc_final: 0.1079 (p90) REVERT: Ao 285 LEU cc_start: 0.6037 (OUTLIER) cc_final: 0.5630 (tp) REVERT: Ao 411 ARG cc_start: 0.5899 (ptt-90) cc_final: 0.4673 (mtm110) REVERT: Ao 416 ASP cc_start: 0.6383 (OUTLIER) cc_final: 0.5984 (t0) REVERT: Ao 439 HIS cc_start: 0.5296 (t70) cc_final: 0.5082 (t70) REVERT: Ao 471 MET cc_start: 0.6714 (tpp) cc_final: 0.6084 (tpp) REVERT: Ao 485 ILE cc_start: 0.6877 (mm) cc_final: 0.6580 (mm) REVERT: Ao 528 ASN cc_start: 0.6463 (m-40) cc_final: 0.5595 (p0) REVERT: Ao 557 ASP cc_start: 0.8110 (m-30) cc_final: 0.7717 (p0) REVERT: Ao 612 GLU cc_start: 0.5108 (mt-10) cc_final: 0.4719 (mp0) REVERT: Ao 632 GLU cc_start: 0.5507 (OUTLIER) cc_final: 0.4633 (tt0) REVERT: Ao 663 ARG cc_start: 0.4484 (tmt170) cc_final: 0.4153 (tpt90) REVERT: Ap 68 TYR cc_start: 0.8978 (m-80) cc_final: 0.8472 (m-80) REVERT: Ap 103 ASN cc_start: 0.9034 (OUTLIER) cc_final: 0.7980 (p0) REVERT: Ap 120 VAL cc_start: 0.9380 (t) cc_final: 0.9179 (m) REVERT: Ap 193 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8385 (mt) REVERT: Ap 235 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7730 (ptp) REVERT: Ap 238 VAL cc_start: 0.6549 (t) cc_final: 0.6289 (m) outliers start: 338 outliers final: 160 residues processed: 1264 average time/residue: 0.7948 time to fit residues: 1667.0056 Evaluate side-chains 1065 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 854 time to evaluate : 5.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BC residue 215 GLN Chi-restraints excluded: chain BC residue 283 ILE Chi-restraints excluded: chain BC residue 332 MET Chi-restraints excluded: chain BC residue 424 LEU Chi-restraints excluded: chain BC residue 468 LYS Chi-restraints excluded: chain BC residue 472 GLU Chi-restraints excluded: chain BC residue 520 ILE Chi-restraints excluded: chain BC residue 524 VAL Chi-restraints excluded: chain BC residue 545 GLU Chi-restraints excluded: chain BC residue 675 SER Chi-restraints excluded: chain BC residue 720 LYS Chi-restraints excluded: chain BT residue 61 VAL Chi-restraints excluded: chain AB residue 63 SER Chi-restraints excluded: chain AB residue 141 ILE Chi-restraints excluded: chain AB residue 145 SER Chi-restraints excluded: chain AB residue 146 ARG Chi-restraints excluded: chain AB residue 186 VAL Chi-restraints excluded: chain AB residue 206 VAL Chi-restraints excluded: chain AB residue 218 THR Chi-restraints excluded: chain AB residue 224 THR Chi-restraints excluded: chain AB residue 235 VAL Chi-restraints excluded: chain AB residue 241 SER Chi-restraints excluded: chain AC residue 41 ARG Chi-restraints excluded: chain AC residue 44 VAL Chi-restraints excluded: chain AC residue 66 LYS Chi-restraints excluded: chain AC residue 73 THR Chi-restraints excluded: chain AC residue 103 CYS Chi-restraints excluded: chain AC residue 104 LEU Chi-restraints excluded: chain AC residue 115 ASN Chi-restraints excluded: chain AE residue 105 GLU Chi-restraints excluded: chain AE residue 137 HIS Chi-restraints excluded: chain AE residue 154 VAL Chi-restraints excluded: chain AE residue 203 LEU Chi-restraints excluded: chain AE residue 215 TYR Chi-restraints excluded: chain AE residue 216 ASP Chi-restraints excluded: chain AE residue 239 ARG Chi-restraints excluded: chain AE residue 241 VAL Chi-restraints excluded: chain AE residue 242 ARG Chi-restraints excluded: chain AE residue 289 THR Chi-restraints excluded: chain AE residue 336 VAL Chi-restraints excluded: chain AE residue 337 SER Chi-restraints excluded: chain AE residue 346 THR Chi-restraints excluded: chain AE residue 370 VAL Chi-restraints excluded: chain AF residue 52 SER Chi-restraints excluded: chain AF residue 59 SER Chi-restraints excluded: chain AF residue 65 LEU Chi-restraints excluded: chain AF residue 83 SER Chi-restraints excluded: chain AG residue 46 ILE Chi-restraints excluded: chain AG residue 80 THR Chi-restraints excluded: chain AG residue 200 LEU Chi-restraints excluded: chain AG residue 219 VAL Chi-restraints excluded: chain AI residue 98 THR Chi-restraints excluded: chain AI residue 100 THR Chi-restraints excluded: chain AI residue 108 ILE Chi-restraints excluded: chain AI residue 153 THR Chi-restraints excluded: chain AI residue 155 LYS Chi-restraints excluded: chain AI residue 206 LEU Chi-restraints excluded: chain AI residue 217 GLN Chi-restraints excluded: chain AI residue 237 THR Chi-restraints excluded: chain AI residue 256 GLN Chi-restraints excluded: chain AI residue 259 GLU Chi-restraints excluded: chain AI residue 322 ASP Chi-restraints excluded: chain AI residue 334 SER Chi-restraints excluded: chain AI residue 338 ARG Chi-restraints excluded: chain AI residue 366 ARG Chi-restraints excluded: chain AJ residue 64 THR Chi-restraints excluded: chain AJ residue 80 VAL Chi-restraints excluded: chain AJ residue 133 GLN Chi-restraints excluded: chain AJ residue 145 LEU Chi-restraints excluded: chain AJ residue 166 GLU Chi-restraints excluded: chain AJ residue 168 VAL Chi-restraints excluded: chain AK residue 68 ILE Chi-restraints excluded: chain AK residue 85 ILE Chi-restraints excluded: chain AK residue 87 ILE Chi-restraints excluded: chain AK residue 121 ASN Chi-restraints excluded: chain AK residue 142 THR Chi-restraints excluded: chain AK residue 147 THR Chi-restraints excluded: chain AK residue 177 ILE Chi-restraints excluded: chain AL residue 32 THR Chi-restraints excluded: chain AL residue 55 ARG Chi-restraints excluded: chain AL residue 67 ILE Chi-restraints excluded: chain AL residue 87 THR Chi-restraints excluded: chain AL residue 117 ASP Chi-restraints excluded: chain AL residue 125 VAL Chi-restraints excluded: chain AN residue 30 VAL Chi-restraints excluded: chain AN residue 93 MET Chi-restraints excluded: chain AN residue 127 MET Chi-restraints excluded: chain AO residue 72 MET Chi-restraints excluded: chain AO residue 74 LEU Chi-restraints excluded: chain AO residue 105 LEU Chi-restraints excluded: chain AO residue 107 ILE Chi-restraints excluded: chain AO residue 158 LEU Chi-restraints excluded: chain AO residue 182 ILE Chi-restraints excluded: chain AO residue 198 ARG Chi-restraints excluded: chain AP residue 97 TYR Chi-restraints excluded: chain AQ residue 6 SER Chi-restraints excluded: chain AQ residue 7 SER Chi-restraints excluded: chain AQ residue 40 LEU Chi-restraints excluded: chain AQ residue 64 VAL Chi-restraints excluded: chain AQ residue 74 THR Chi-restraints excluded: chain AR residue 83 GLN Chi-restraints excluded: chain AR residue 89 THR Chi-restraints excluded: chain AR residue 117 ILE Chi-restraints excluded: chain AR residue 131 LEU Chi-restraints excluded: chain AU residue 10 ARG Chi-restraints excluded: chain AU residue 13 MET Chi-restraints excluded: chain AU residue 14 VAL Chi-restraints excluded: chain AU residue 19 VAL Chi-restraints excluded: chain AU residue 35 LEU Chi-restraints excluded: chain AU residue 77 ARG Chi-restraints excluded: chain Aa residue 117 LEU Chi-restraints excluded: chain Aa residue 129 THR Chi-restraints excluded: chain Aa residue 150 MET Chi-restraints excluded: chain Aa residue 169 ILE Chi-restraints excluded: chain Aa residue 183 ILE Chi-restraints excluded: chain Aa residue 197 ARG Chi-restraints excluded: chain Aa residue 202 THR Chi-restraints excluded: chain Aa residue 204 ARG Chi-restraints excluded: chain Aa residue 239 THR Chi-restraints excluded: chain Aa residue 325 LEU Chi-restraints excluded: chain Aa residue 347 LEU Chi-restraints excluded: chain Ab residue 67 GLU Chi-restraints excluded: chain Ab residue 91 ASN Chi-restraints excluded: chain Ab residue 101 GLU Chi-restraints excluded: chain Ac residue 4 LYS Chi-restraints excluded: chain Ac residue 9 ILE Chi-restraints excluded: chain Ac residue 31 THR Chi-restraints excluded: chain Ac residue 33 ASN Chi-restraints excluded: chain Ac residue 59 ASN Chi-restraints excluded: chain Ac residue 96 LYS Chi-restraints excluded: chain Ac residue 106 LEU Chi-restraints excluded: chain Ac residue 168 LYS Chi-restraints excluded: chain Ad residue 56 LEU Chi-restraints excluded: chain Ad residue 161 GLN Chi-restraints excluded: chain Ad residue 166 THR Chi-restraints excluded: chain Ae residue 76 ASP Chi-restraints excluded: chain Ae residue 95 SER Chi-restraints excluded: chain Ae residue 107 VAL Chi-restraints excluded: chain Ae residue 146 ASP Chi-restraints excluded: chain Ae residue 159 TYR Chi-restraints excluded: chain Ae residue 183 THR Chi-restraints excluded: chain Ae residue 189 ASP Chi-restraints excluded: chain Ae residue 220 LEU Chi-restraints excluded: chain Ae residue 253 LEU Chi-restraints excluded: chain Ae residue 257 ASN Chi-restraints excluded: chain Ae residue 259 VAL Chi-restraints excluded: chain Ae residue 285 CYS Chi-restraints excluded: chain Ae residue 323 LEU Chi-restraints excluded: chain Ae residue 326 VAL Chi-restraints excluded: chain Ae residue 388 VAL Chi-restraints excluded: chain Af residue 85 LEU Chi-restraints excluded: chain Af residue 108 ILE Chi-restraints excluded: chain Af residue 130 VAL Chi-restraints excluded: chain Af residue 155 LEU Chi-restraints excluded: chain Ag residue 50 THR Chi-restraints excluded: chain Ag residue 71 LEU Chi-restraints excluded: chain Ag residue 172 TYR Chi-restraints excluded: chain Ag residue 194 ASN Chi-restraints excluded: chain Ag residue 196 HIS Chi-restraints excluded: chain Ag residue 252 LEU Chi-restraints excluded: chain Ag residue 255 PHE Chi-restraints excluded: chain Ag residue 264 VAL Chi-restraints excluded: chain Ag residue 265 ASN Chi-restraints excluded: chain Ag residue 337 ASP Chi-restraints excluded: chain Ah residue 308 ASN Chi-restraints excluded: chain Ah residue 328 LYS Chi-restraints excluded: chain Ah residue 345 LEU Chi-restraints excluded: chain Ah residue 359 LYS Chi-restraints excluded: chain Ai residue 15 SER Chi-restraints excluded: chain Ai residue 26 THR Chi-restraints excluded: chain Ai residue 50 ASP Chi-restraints excluded: chain Aj residue 18 VAL Chi-restraints excluded: chain Aj residue 65 LEU Chi-restraints excluded: chain Aj residue 84 SER Chi-restraints excluded: chain Ak residue 53 LYS Chi-restraints excluded: chain Ak residue 79 LYS Chi-restraints excluded: chain Ak residue 93 VAL Chi-restraints excluded: chain Ak residue 117 THR Chi-restraints excluded: chain Ak residue 154 ASP Chi-restraints excluded: chain Ak residue 165 ILE Chi-restraints excluded: chain Ak residue 166 ARG Chi-restraints excluded: chain Ak residue 298 VAL Chi-restraints excluded: chain Ak residue 309 ASN Chi-restraints excluded: chain Ak residue 310 THR Chi-restraints excluded: chain Am residue 17 ARG Chi-restraints excluded: chain Am residue 29 LEU Chi-restraints excluded: chain Am residue 33 VAL Chi-restraints excluded: chain Am residue 44 THR Chi-restraints excluded: chain Am residue 113 ASN Chi-restraints excluded: chain An residue 199 GLN Chi-restraints excluded: chain Ao residue 96 ILE Chi-restraints excluded: chain Ao residue 243 THR Chi-restraints excluded: chain Ao residue 260 HIS Chi-restraints excluded: chain Ao residue 262 TYR Chi-restraints excluded: chain Ao residue 279 LEU Chi-restraints excluded: chain Ao residue 285 LEU Chi-restraints excluded: chain Ao residue 338 PHE Chi-restraints excluded: chain Ao residue 416 ASP Chi-restraints excluded: chain Ao residue 454 ASP Chi-restraints excluded: chain Ao residue 488 VAL Chi-restraints excluded: chain Ao residue 510 ASP Chi-restraints excluded: chain Ao residue 632 GLU Chi-restraints excluded: chain Ao residue 652 VAL Chi-restraints excluded: chain Ap residue 53 ASP Chi-restraints excluded: chain Ap residue 103 ASN Chi-restraints excluded: chain Ap residue 108 CYS Chi-restraints excluded: chain Ap residue 167 ILE Chi-restraints excluded: chain Ap residue 177 PHE Chi-restraints excluded: chain Ap residue 193 LEU Chi-restraints excluded: chain Ap residue 214 SER Chi-restraints excluded: chain Ap residue 235 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 719 random chunks: chunk 362 optimal weight: 5.9990 chunk 202 optimal weight: 1.9990 chunk 543 optimal weight: 10.0000 chunk 444 optimal weight: 3.9990 chunk 180 optimal weight: 9.9990 chunk 654 optimal weight: 20.0000 chunk 706 optimal weight: 5.9990 chunk 582 optimal weight: 2.9990 chunk 648 optimal weight: 10.0000 chunk 222 optimal weight: 0.0980 chunk 524 optimal weight: 8.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BC 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AB 119 GLN AB 177 ASN AB 265 GLN AE 127 ASN AE 130 GLN ** AE 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AI 175 HIS ** AI 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 133 GLN AJ 179 GLN AJ 183 HIS AK 100 GLN ** AL 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AL 100 HIS AL 105 HIS AN 119 GLN AO 119 ASN AU 15 GLN AU 79 ASN ** Aa 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 109 ASN ** Ae 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 185 ASN Ae 243 ASN ** Ae 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 189 ASN Ag 196 HIS Ag 234 ASN Ag 389 GLN Ah 331 GLN Ai 56 ASN ** Ai 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 112 ASN ** Ak 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Am 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 58 GLN Ao 245 ASN Ao 548 GLN Ap 81 HIS ** Ap 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 76793 Z= 0.304 Angle : 0.640 12.211 108765 Z= 0.328 Chirality : 0.040 0.244 12818 Planarity : 0.005 0.108 10078 Dihedral : 20.702 179.298 22835 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 5.69 % Allowed : 17.35 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.10 (0.10), residues: 6199 helix: 0.68 (0.10), residues: 2786 sheet: -0.44 (0.19), residues: 655 loop : -0.65 (0.11), residues: 2758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRPAk 236 HIS 0.008 0.001 HISAg 196 PHE 0.024 0.002 PHEAo 617 TYR 0.025 0.002 TYRAG 64 ARG 0.011 0.001 ARGAI 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1203 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 307 poor density : 896 time to evaluate : 5.438 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: 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: BC 197 LEU cc_start: 0.8832 (mt) cc_final: 0.8596 (tp) REVERT: BC 232 PHE cc_start: 0.7870 (m-80) cc_final: 0.7611 (m-80) REVERT: BC 266 MET cc_start: 0.5890 (mtp) cc_final: 0.5629 (mtp) REVERT: BC 308 ASP cc_start: 0.7769 (m-30) cc_final: 0.7435 (t0) REVERT: BC 361 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7484 (mt-10) REVERT: BC 405 LYS cc_start: 0.9028 (tppt) cc_final: 0.8481 (ptmm) REVERT: BC 464 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7940 (mt-10) REVERT: BC 520 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8725 (mp) REVERT: BC 672 SER cc_start: 0.6638 (t) cc_final: 0.6396 (p) REVERT: BC 690 MET cc_start: 0.5395 (OUTLIER) cc_final: 0.5094 (mmm) REVERT: AB 61 ILE cc_start: 0.9082 (tt) cc_final: 0.8802 (mt) REVERT: AB 146 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.8097 (tpt-90) REVERT: AB 171 LYS cc_start: 0.9149 (mtmt) cc_final: 0.8901 (mtpt) REVERT: AB 213 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8655 (mttm) REVERT: AC 41 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.6409 (mtm-85) REVERT: AC 81 HIS cc_start: 0.8529 (m-70) cc_final: 0.8316 (m90) REVERT: AC 122 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.9044 (mp) REVERT: AC 140 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8360 (mt-10) REVERT: AC 144 SER cc_start: 0.9428 (m) cc_final: 0.8850 (m) REVERT: AC 152 HIS cc_start: 0.8208 (m-70) cc_final: 0.7636 (m-70) REVERT: AE 137 HIS cc_start: 0.8526 (OUTLIER) cc_final: 0.8227 (m90) REVERT: AE 157 ILE cc_start: 0.8377 (mp) cc_final: 0.8010 (mt) REVERT: AE 178 GLU cc_start: 0.8074 (tt0) cc_final: 0.7466 (tp30) REVERT: AE 227 ASN cc_start: 0.8973 (m-40) cc_final: 0.8568 (m-40) REVERT: AE 241 VAL cc_start: 0.9119 (OUTLIER) cc_final: 0.8872 (t) REVERT: AE 242 ARG cc_start: 0.9143 (OUTLIER) cc_final: 0.8934 (ptt-90) REVERT: AE 305 MET cc_start: 0.8774 (mtm) cc_final: 0.8232 (mtm) REVERT: AE 321 MET cc_start: 0.9087 (mtp) cc_final: 0.8713 (mtp) REVERT: AE 344 ASN cc_start: 0.8863 (m-40) cc_final: 0.8650 (m-40) REVERT: AG 68 PHE cc_start: 0.6965 (p90) cc_final: 0.6758 (p90) REVERT: AI 155 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8480 (pttt) REVERT: AI 213 LYS cc_start: 0.8299 (mttt) cc_final: 0.8013 (mttm) REVERT: AI 293 ARG cc_start: 0.6796 (ptp-170) cc_final: 0.6524 (ptp-170) REVERT: AI 338 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8529 (ptm-80) REVERT: AJ 64 THR cc_start: 0.7409 (OUTLIER) cc_final: 0.7124 (p) REVERT: AJ 145 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8171 (mt) REVERT: AJ 179 GLN cc_start: 0.8061 (pt0) cc_final: 0.7797 (pt0) REVERT: AK 121 ASN cc_start: 0.8685 (OUTLIER) cc_final: 0.8458 (m-40) REVERT: AL 55 ARG cc_start: 0.9296 (OUTLIER) cc_final: 0.9067 (mtt-85) REVERT: AN 72 ASP cc_start: 0.8029 (t0) cc_final: 0.7796 (t0) REVERT: AO 72 MET cc_start: 0.9114 (OUTLIER) cc_final: 0.8861 (tpp) REVERT: AO 144 MET cc_start: 0.8743 (tpp) cc_final: 0.8428 (mmt) REVERT: AO 167 MET cc_start: 0.8891 (mtp) cc_final: 0.8515 (mtt) REVERT: AO 182 ILE cc_start: 0.8906 (OUTLIER) cc_final: 0.8590 (mt) REVERT: AO 198 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.8452 (mtt180) REVERT: AO 217 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8301 (tp30) REVERT: AP 120 LEU cc_start: 0.8716 (tp) cc_final: 0.8465 (mt) REVERT: AR 70 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8453 (mm-30) REVERT: AR 83 GLN cc_start: 0.9126 (OUTLIER) cc_final: 0.8922 (tt0) REVERT: AU 10 ARG cc_start: 0.9238 (OUTLIER) cc_final: 0.8737 (mtm180) REVERT: AU 23 TYR cc_start: 0.9023 (t80) cc_final: 0.8756 (t80) REVERT: AU 77 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7838 (mtp-110) REVERT: Aa 129 THR cc_start: 0.8752 (OUTLIER) cc_final: 0.8496 (p) REVERT: Aa 150 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8236 (mtp) REVERT: Aa 183 ILE cc_start: 0.9239 (OUTLIER) cc_final: 0.8865 (pt) REVERT: Aa 197 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.7441 (mmt90) REVERT: Aa 204 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7923 (ptt-90) REVERT: Aa 222 GLU cc_start: 0.8674 (pm20) cc_final: 0.8385 (mp0) REVERT: Aa 334 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7909 (pm20) REVERT: Ab 102 LYS cc_start: 0.8925 (mptt) cc_final: 0.8446 (mptt) REVERT: Ab 116 LYS cc_start: 0.8001 (mttt) cc_final: 0.7775 (mtmm) REVERT: Ac 33 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.8351 (m-40) REVERT: Ac 117 GLU cc_start: 0.8230 (pp20) cc_final: 0.7992 (pp20) REVERT: Ad 94 LYS cc_start: 0.8805 (mmmt) cc_final: 0.8547 (mptt) REVERT: Ad 161 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8391 (tm-30) REVERT: Ae 152 TRP cc_start: 0.7880 (t60) cc_final: 0.7420 (t60) REVERT: Ae 159 TYR cc_start: 0.7115 (OUTLIER) cc_final: 0.5755 (t80) REVERT: Ae 211 GLU cc_start: 0.6928 (mt-10) cc_final: 0.6165 (pp20) REVERT: Ae 221 LEU cc_start: 0.8660 (mt) cc_final: 0.8450 (mp) REVERT: Ae 228 HIS cc_start: 0.7191 (t70) cc_final: 0.6707 (t-170) REVERT: Ae 253 LEU cc_start: 0.5948 (OUTLIER) cc_final: 0.5453 (mt) REVERT: Ae 257 ASN cc_start: 0.7159 (OUTLIER) cc_final: 0.6813 (p0) REVERT: Ae 285 CYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8298 (p) REVERT: Ae 311 GLU cc_start: 0.6686 (mt-10) cc_final: 0.5875 (pt0) REVERT: Af 111 ASP cc_start: 0.7853 (t0) cc_final: 0.7306 (t0) REVERT: Af 149 GLU cc_start: 0.8457 (tt0) cc_final: 0.8146 (tt0) REVERT: Ag 50 THR cc_start: 0.4687 (OUTLIER) cc_final: 0.4425 (m) REVERT: Ag 88 MET cc_start: 0.8474 (mmp) cc_final: 0.8229 (mmm) REVERT: Ag 150 LEU cc_start: 0.6982 (OUTLIER) cc_final: 0.6743 (tm) REVERT: Ag 172 TYR cc_start: 0.6371 (OUTLIER) cc_final: 0.4665 (t80) REVERT: Ag 188 LYS cc_start: 0.8133 (mtmt) cc_final: 0.7863 (pttt) REVERT: Ag 234 ASN cc_start: 0.7363 (OUTLIER) cc_final: 0.6917 (p0) REVERT: Ag 252 LEU cc_start: 0.6780 (OUTLIER) cc_final: 0.6275 (mt) REVERT: Ag 295 MET cc_start: 0.8543 (tpp) cc_final: 0.8055 (tpp) REVERT: Ah 285 PRO cc_start: 0.8109 (Cg_exo) cc_final: 0.7682 (Cg_endo) REVERT: Ah 294 ILE cc_start: 0.9132 (mt) cc_final: 0.8772 (mp) REVERT: Ah 328 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7672 (ptpp) REVERT: Ah 373 ASN cc_start: 0.7738 (t0) cc_final: 0.7322 (t0) REVERT: Ai 52 TYR cc_start: 0.8971 (m-80) cc_final: 0.8541 (m-80) REVERT: Ai 73 ASP cc_start: 0.8249 (t0) cc_final: 0.7796 (t70) REVERT: Ai 77 ASP cc_start: 0.9163 (m-30) cc_final: 0.8849 (m-30) REVERT: Ai 80 ASP cc_start: 0.7811 (m-30) cc_final: 0.7519 (m-30) REVERT: Ai 81 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8349 (tm-30) REVERT: Ak 53 LYS cc_start: 0.6119 (OUTLIER) cc_final: 0.5724 (ptmt) REVERT: Ak 59 THR cc_start: 0.8443 (m) cc_final: 0.8126 (p) REVERT: Ak 79 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.7956 (mmtt) REVERT: Ak 95 ARG cc_start: 0.8619 (mmt90) cc_final: 0.7952 (mtt90) REVERT: Ak 241 TRP cc_start: 0.8721 (p-90) cc_final: 0.8294 (p-90) REVERT: Am 17 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8127 (ptm160) REVERT: Am 53 MET cc_start: 0.8360 (mmt) cc_final: 0.7936 (mmt) REVERT: Am 81 GLU cc_start: 0.8277 (tp30) cc_final: 0.7512 (tm-30) REVERT: Am 85 LYS cc_start: 0.7955 (mmtt) cc_final: 0.7526 (mmpt) REVERT: Ao 262 TYR cc_start: 0.2561 (OUTLIER) cc_final: 0.1644 (p90) REVERT: Ao 265 MET cc_start: 0.5521 (mmt) cc_final: 0.5315 (mmm) REVERT: Ao 285 LEU cc_start: 0.6085 (OUTLIER) cc_final: 0.5538 (tp) REVERT: Ao 383 TYR cc_start: 0.5138 (t80) cc_final: 0.4685 (t80) REVERT: Ao 411 ARG cc_start: 0.5900 (ptt-90) cc_final: 0.4599 (mtm110) REVERT: Ao 439 HIS cc_start: 0.5471 (t70) cc_final: 0.5128 (t70) REVERT: Ao 441 LEU cc_start: 0.8153 (tt) cc_final: 0.7890 (tp) REVERT: Ao 485 ILE cc_start: 0.6998 (mm) cc_final: 0.6682 (mm) REVERT: Ao 612 GLU cc_start: 0.4212 (mt-10) cc_final: 0.3665 (mp0) REVERT: Ao 632 GLU cc_start: 0.5422 (OUTLIER) cc_final: 0.4671 (pt0) REVERT: Ao 663 ARG cc_start: 0.4442 (tmt170) cc_final: 0.3814 (tpt90) REVERT: Ao 666 LEU cc_start: 0.6840 (tt) cc_final: 0.6541 (mt) REVERT: Ap 169 GLN cc_start: 0.8859 (mt0) cc_final: 0.8601 (mt0) REVERT: Ap 235 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.7787 (ptp) outliers start: 307 outliers final: 185 residues processed: 1132 average time/residue: 0.7933 time to fit residues: 1501.6943 Evaluate side-chains 1076 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 845 time to evaluate : 5.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BC residue 230 ILE Chi-restraints excluded: chain BC residue 255 VAL Chi-restraints excluded: chain BC residue 283 ILE Chi-restraints excluded: chain BC residue 332 MET Chi-restraints excluded: chain BC residue 468 LYS Chi-restraints excluded: chain BC residue 486 TRP Chi-restraints excluded: chain BC residue 520 ILE Chi-restraints excluded: chain BC residue 560 ASP Chi-restraints excluded: chain BC residue 565 GLU Chi-restraints excluded: chain BC residue 606 LEU Chi-restraints excluded: chain BC residue 662 THR Chi-restraints excluded: chain BC residue 686 VAL Chi-restraints excluded: chain BC residue 690 MET Chi-restraints excluded: chain BT residue 61 VAL Chi-restraints excluded: chain AB residue 63 SER Chi-restraints excluded: chain AB residue 145 SER Chi-restraints excluded: chain AB residue 146 ARG Chi-restraints excluded: chain AB residue 186 VAL Chi-restraints excluded: chain AB residue 206 VAL Chi-restraints excluded: chain AB residue 213 LYS Chi-restraints excluded: chain AB residue 218 THR Chi-restraints excluded: chain AB residue 224 THR Chi-restraints excluded: chain AB residue 235 VAL Chi-restraints excluded: chain AC residue 41 ARG Chi-restraints excluded: chain AC residue 44 VAL Chi-restraints excluded: chain AC residue 73 THR Chi-restraints excluded: chain AC residue 103 CYS Chi-restraints excluded: chain AC residue 115 ASN Chi-restraints excluded: chain AC residue 122 LEU Chi-restraints excluded: chain AC residue 157 THR Chi-restraints excluded: chain AC residue 162 VAL Chi-restraints excluded: chain AE residue 105 GLU Chi-restraints excluded: chain AE residue 137 HIS Chi-restraints excluded: chain AE residue 154 VAL Chi-restraints excluded: chain AE residue 171 ASP Chi-restraints excluded: chain AE residue 215 TYR Chi-restraints excluded: chain AE residue 216 ASP Chi-restraints excluded: chain AE residue 238 LYS Chi-restraints excluded: chain AE residue 239 ARG Chi-restraints excluded: chain AE residue 241 VAL Chi-restraints excluded: chain AE residue 242 ARG Chi-restraints excluded: chain AE residue 258 ILE Chi-restraints excluded: chain AE residue 336 VAL Chi-restraints excluded: chain AE residue 370 VAL Chi-restraints excluded: chain AF residue 52 SER Chi-restraints excluded: chain AF residue 56 GLN Chi-restraints excluded: chain AF residue 59 SER Chi-restraints excluded: chain AF residue 65 LEU Chi-restraints excluded: chain AG residue 46 ILE Chi-restraints excluded: chain AG residue 80 THR Chi-restraints excluded: chain AG residue 109 SER Chi-restraints excluded: chain AG residue 200 LEU Chi-restraints excluded: chain AG residue 219 VAL Chi-restraints excluded: chain AI residue 98 THR Chi-restraints excluded: chain AI residue 100 THR Chi-restraints excluded: chain AI residue 108 ILE Chi-restraints excluded: chain AI residue 153 THR Chi-restraints excluded: chain AI residue 155 LYS Chi-restraints excluded: chain AI residue 172 VAL Chi-restraints excluded: chain AI residue 206 LEU Chi-restraints excluded: chain AI residue 237 THR Chi-restraints excluded: chain AI residue 254 LYS Chi-restraints excluded: chain AI residue 256 GLN Chi-restraints excluded: chain AI residue 259 GLU Chi-restraints excluded: chain AI residue 299 VAL Chi-restraints excluded: chain AI residue 322 ASP Chi-restraints excluded: chain AI residue 334 SER Chi-restraints excluded: chain AI residue 338 ARG Chi-restraints excluded: chain AI residue 393 THR Chi-restraints excluded: chain AJ residue 64 THR Chi-restraints excluded: chain AJ residue 80 VAL Chi-restraints excluded: chain AJ residue 145 LEU Chi-restraints excluded: chain AJ residue 166 GLU Chi-restraints excluded: chain AJ residue 168 VAL Chi-restraints excluded: chain AJ residue 175 THR Chi-restraints excluded: chain AK residue 68 ILE Chi-restraints excluded: chain AK residue 85 ILE Chi-restraints excluded: chain AK residue 87 ILE Chi-restraints excluded: chain AK residue 121 ASN Chi-restraints excluded: chain AK residue 142 THR Chi-restraints excluded: chain AK residue 147 THR Chi-restraints excluded: chain AK residue 183 ILE Chi-restraints excluded: chain AL residue 32 THR Chi-restraints excluded: chain AL residue 55 ARG Chi-restraints excluded: chain AL residue 67 ILE Chi-restraints excluded: chain AL residue 77 ASN Chi-restraints excluded: chain AL residue 87 THR Chi-restraints excluded: chain AL residue 101 SER Chi-restraints excluded: chain AL residue 117 ASP Chi-restraints excluded: chain AL residue 125 VAL Chi-restraints excluded: chain AN residue 30 VAL Chi-restraints excluded: chain AN residue 67 LEU Chi-restraints excluded: chain AN residue 93 MET Chi-restraints excluded: chain AN residue 120 LEU Chi-restraints excluded: chain AN residue 127 MET Chi-restraints excluded: chain AO residue 72 MET Chi-restraints excluded: chain AO residue 74 LEU Chi-restraints excluded: chain AO residue 107 ILE Chi-restraints excluded: chain AO residue 126 LEU Chi-restraints excluded: chain AO residue 182 ILE Chi-restraints excluded: chain AO residue 198 ARG Chi-restraints excluded: chain AO residue 218 VAL Chi-restraints excluded: chain AP residue 97 TYR Chi-restraints excluded: chain AQ residue 6 SER Chi-restraints excluded: chain AQ residue 7 SER Chi-restraints excluded: chain AQ residue 20 THR Chi-restraints excluded: chain AQ residue 40 LEU Chi-restraints excluded: chain AQ residue 64 VAL Chi-restraints excluded: chain AQ residue 74 THR Chi-restraints excluded: chain AR residue 83 GLN Chi-restraints excluded: chain AR residue 89 THR Chi-restraints excluded: chain AR residue 117 ILE Chi-restraints excluded: chain AR residue 131 LEU Chi-restraints excluded: chain AU residue 10 ARG Chi-restraints excluded: chain AU residue 14 VAL Chi-restraints excluded: chain AU residue 19 VAL Chi-restraints excluded: chain AU residue 35 LEU Chi-restraints excluded: chain AU residue 38 ASP Chi-restraints excluded: chain AU residue 77 ARG Chi-restraints excluded: chain Aa residue 117 LEU Chi-restraints excluded: chain Aa residue 129 THR Chi-restraints excluded: chain Aa residue 150 MET Chi-restraints excluded: chain Aa residue 169 ILE Chi-restraints excluded: chain Aa residue 183 ILE Chi-restraints excluded: chain Aa residue 197 ARG Chi-restraints excluded: chain Aa residue 202 THR Chi-restraints excluded: chain Aa residue 204 ARG Chi-restraints excluded: chain Aa residue 325 LEU Chi-restraints excluded: chain Aa residue 334 GLN Chi-restraints excluded: chain Ab residue 6 LEU Chi-restraints excluded: chain Ab residue 14 SER Chi-restraints excluded: chain Ab residue 67 GLU Chi-restraints excluded: chain Ab residue 91 ASN Chi-restraints excluded: chain Ab residue 101 GLU Chi-restraints excluded: chain Ac residue 9 ILE Chi-restraints excluded: chain Ac residue 31 THR Chi-restraints excluded: chain Ac residue 33 ASN Chi-restraints excluded: chain Ac residue 59 ASN Chi-restraints excluded: chain Ac residue 96 LYS Chi-restraints excluded: chain Ac residue 106 LEU Chi-restraints excluded: chain Ac residue 168 LYS Chi-restraints excluded: chain Ad residue 44 THR Chi-restraints excluded: chain Ad residue 56 LEU Chi-restraints excluded: chain Ad residue 161 GLN Chi-restraints excluded: chain Ad residue 166 THR Chi-restraints excluded: chain Ae residue 95 SER Chi-restraints excluded: chain Ae residue 107 VAL Chi-restraints excluded: chain Ae residue 146 ASP Chi-restraints excluded: chain Ae residue 150 HIS Chi-restraints excluded: chain Ae residue 159 TYR Chi-restraints excluded: chain Ae residue 185 ASN Chi-restraints excluded: chain Ae residue 189 ASP Chi-restraints excluded: chain Ae residue 192 ILE Chi-restraints excluded: chain Ae residue 220 LEU Chi-restraints excluded: chain Ae residue 253 LEU Chi-restraints excluded: chain Ae residue 257 ASN Chi-restraints excluded: chain Ae residue 259 VAL Chi-restraints excluded: chain Ae residue 285 CYS Chi-restraints excluded: chain Ae residue 312 ASP Chi-restraints excluded: chain Ae residue 315 LEU Chi-restraints excluded: chain Ae residue 323 LEU Chi-restraints excluded: chain Ae residue 326 VAL Chi-restraints excluded: chain Ae residue 388 VAL Chi-restraints excluded: chain Af residue 85 LEU Chi-restraints excluded: chain Af residue 130 VAL Chi-restraints excluded: chain Af residue 155 LEU Chi-restraints excluded: chain Ag residue 50 THR Chi-restraints excluded: chain Ag residue 54 ASP Chi-restraints excluded: chain Ag residue 71 LEU Chi-restraints excluded: chain Ag residue 150 LEU Chi-restraints excluded: chain Ag residue 172 TYR Chi-restraints excluded: chain Ag residue 194 ASN Chi-restraints excluded: chain Ag residue 234 ASN Chi-restraints excluded: chain Ag residue 252 LEU Chi-restraints excluded: chain Ag residue 255 PHE Chi-restraints excluded: chain Ag residue 262 ASP Chi-restraints excluded: chain Ag residue 264 VAL Chi-restraints excluded: chain Ag residue 265 ASN Chi-restraints excluded: chain Ag residue 296 VAL Chi-restraints excluded: chain Ag residue 309 VAL Chi-restraints excluded: chain Ah residue 308 ASN Chi-restraints excluded: chain Ah residue 328 LYS Chi-restraints excluded: chain Ah residue 345 LEU Chi-restraints excluded: chain Ah residue 387 ASN Chi-restraints excluded: chain Ai residue 15 SER Chi-restraints excluded: chain Ai residue 26 THR Chi-restraints excluded: chain Ai residue 38 SER Chi-restraints excluded: chain Ai residue 50 ASP Chi-restraints excluded: chain Aj residue 6 VAL Chi-restraints excluded: chain Aj residue 18 VAL Chi-restraints excluded: chain Aj residue 65 LEU Chi-restraints excluded: chain Aj residue 84 SER Chi-restraints excluded: chain Aj residue 184 THR Chi-restraints excluded: chain Ak residue 53 LYS Chi-restraints excluded: chain Ak residue 64 VAL Chi-restraints excluded: chain Ak residue 79 LYS Chi-restraints excluded: chain Ak residue 93 VAL Chi-restraints excluded: chain Ak residue 117 THR Chi-restraints excluded: chain Ak residue 130 ASP Chi-restraints excluded: chain Ak residue 154 ASP Chi-restraints excluded: chain Ak residue 165 ILE Chi-restraints excluded: chain Ak residue 166 ARG Chi-restraints excluded: chain Ak residue 298 VAL Chi-restraints excluded: chain Ak residue 309 ASN Chi-restraints excluded: chain Am residue 17 ARG Chi-restraints excluded: chain Am residue 44 THR Chi-restraints excluded: chain Am residue 113 ASN Chi-restraints excluded: chain An residue 194 ILE Chi-restraints excluded: chain Ao residue 96 ILE Chi-restraints excluded: chain Ao residue 243 THR Chi-restraints excluded: chain Ao residue 260 HIS Chi-restraints excluded: chain Ao residue 262 TYR Chi-restraints excluded: chain Ao residue 263 CYS Chi-restraints excluded: chain Ao residue 279 LEU Chi-restraints excluded: chain Ao residue 285 LEU Chi-restraints excluded: chain Ao residue 338 PHE Chi-restraints excluded: chain Ao residue 416 ASP Chi-restraints excluded: chain Ao residue 454 ASP Chi-restraints excluded: chain Ao residue 510 ASP Chi-restraints excluded: chain Ao residue 521 GLU Chi-restraints excluded: chain Ao residue 632 GLU Chi-restraints excluded: chain Ao residue 645 CYS Chi-restraints excluded: chain Ao residue 652 VAL Chi-restraints excluded: chain Ao residue 659 THR Chi-restraints excluded: chain Ap residue 103 ASN Chi-restraints excluded: chain Ap residue 108 CYS Chi-restraints excluded: chain Ap residue 154 ILE Chi-restraints excluded: chain Ap residue 167 ILE Chi-restraints excluded: chain Ap residue 177 PHE Chi-restraints excluded: chain Ap residue 193 LEU Chi-restraints excluded: chain Ap residue 235 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 719 random chunks: chunk 646 optimal weight: 9.9990 chunk 491 optimal weight: 5.9990 chunk 339 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 chunk 312 optimal weight: 2.9990 chunk 439 optimal weight: 4.9990 chunk 656 optimal weight: 20.0000 chunk 694 optimal weight: 10.0000 chunk 342 optimal weight: 8.9990 chunk 622 optimal weight: 6.9990 chunk 187 optimal weight: 0.8980 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BC 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BC 457 GLN AB 265 GLN ** AC 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 127 ASN AE 130 GLN ** AE 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AF 100 GLN ** AI 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AJ 51 HIS AN 119 GLN AU 79 ASN ** Aa 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ac 35 ASN ** Ae 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 185 ASN ** Ae 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 194 ASN Ag 196 HIS Ag 227 GLN ** Ag 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 301 GLN Ag 311 GLN Ai 55 HIS ** Ai 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 88 GLN Ak 112 ASN Ak 263 ASN Am 15 ASN ** Am 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 58 GLN ** Ap 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 76793 Z= 0.412 Angle : 0.685 10.488 108765 Z= 0.348 Chirality : 0.043 0.244 12818 Planarity : 0.006 0.106 10078 Dihedral : 20.593 179.308 22781 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.81 % Favored : 96.18 % Rotamer: Outliers : 6.27 % Allowed : 17.63 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.31 % 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: -0.00 (0.10), residues: 6199 helix: 0.84 (0.10), residues: 2813 sheet: -0.34 (0.20), residues: 636 loop : -0.73 (0.11), residues: 2750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRPAk 236 HIS 0.010 0.001 HISAg 196 PHE 0.035 0.002 PHEAe 191 TYR 0.023 0.002 TYRAo 262 ARG 0.021 0.001 ARGAi 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1184 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 338 poor density : 846 time to evaluate : 5.347 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: symmetry clash revert: symmetry clash REVERT: BC 197 LEU cc_start: 0.8900 (mt) cc_final: 0.8697 (tp) REVERT: BC 266 MET cc_start: 0.6232 (mtp) cc_final: 0.5857 (mtp) REVERT: BC 285 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7119 (mt) REVERT: BC 308 ASP cc_start: 0.7787 (m-30) cc_final: 0.7436 (t70) REVERT: BC 464 GLU cc_start: 0.8373 (mt-10) cc_final: 0.8034 (mt-10) REVERT: BC 488 LYS cc_start: 0.7238 (mttt) cc_final: 0.6852 (tptt) REVERT: BC 520 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8755 (mp) REVERT: AB 61 ILE cc_start: 0.9062 (tt) cc_final: 0.8639 (mt) REVERT: AB 146 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.8108 (tpt-90) REVERT: AB 171 LYS cc_start: 0.9105 (mtmt) cc_final: 0.8847 (mtpt) REVERT: AB 213 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8663 (mttm) REVERT: AC 41 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.6801 (mtm-85) REVERT: AC 43 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8341 (mmt180) REVERT: AC 80 ASP cc_start: 0.8322 (t70) cc_final: 0.8107 (t70) REVERT: AC 122 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9036 (mp) REVERT: AC 144 SER cc_start: 0.9478 (m) cc_final: 0.8908 (m) REVERT: AE 137 HIS cc_start: 0.8607 (OUTLIER) cc_final: 0.8246 (m90) REVERT: AE 157 ILE cc_start: 0.8417 (mp) cc_final: 0.8045 (mt) REVERT: AE 178 GLU cc_start: 0.8097 (tt0) cc_final: 0.7361 (tp30) REVERT: AE 241 VAL cc_start: 0.9100 (OUTLIER) cc_final: 0.8883 (t) REVERT: AE 242 ARG cc_start: 0.9203 (OUTLIER) cc_final: 0.8964 (ptt-90) REVERT: AE 305 MET cc_start: 0.8731 (mtm) cc_final: 0.8438 (mtm) REVERT: AE 321 MET cc_start: 0.9087 (mtp) cc_final: 0.8685 (mtp) REVERT: AG 72 GLN cc_start: 0.7498 (mt0) cc_final: 0.7050 (mt0) REVERT: AI 73 PHE cc_start: 0.7892 (t80) cc_final: 0.7673 (t80) REVERT: AI 155 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8544 (pttt) REVERT: AI 213 LYS cc_start: 0.8343 (mttt) cc_final: 0.8097 (mttm) REVERT: AI 338 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8211 (ptm-80) REVERT: AJ 64 THR cc_start: 0.7464 (OUTLIER) cc_final: 0.7214 (p) REVERT: AJ 106 ILE cc_start: 0.9243 (pt) cc_final: 0.8947 (pt) REVERT: AJ 145 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8222 (mt) REVERT: AL 55 ARG cc_start: 0.9320 (OUTLIER) cc_final: 0.9074 (mtt-85) REVERT: AL 103 GLN cc_start: 0.8343 (mp10) cc_final: 0.8056 (mt0) REVERT: AL 104 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7374 (mm-30) REVERT: AL 118 LEU cc_start: 0.9334 (mt) cc_final: 0.9052 (mt) REVERT: AO 72 MET cc_start: 0.9179 (OUTLIER) cc_final: 0.8832 (tpp) REVERT: AO 167 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8479 (mtt) REVERT: AO 173 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7627 (mp0) REVERT: AO 182 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8584 (mt) REVERT: AO 198 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8568 (mtt180) REVERT: AO 217 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8302 (tp30) REVERT: AP 120 LEU cc_start: 0.8749 (tp) cc_final: 0.8435 (mt) REVERT: AU 10 ARG cc_start: 0.9278 (OUTLIER) cc_final: 0.8998 (mtm180) REVERT: AU 77 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8040 (mtp-110) REVERT: Aa 129 THR cc_start: 0.8733 (OUTLIER) cc_final: 0.8526 (p) REVERT: Aa 150 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8349 (mtt) REVERT: Aa 183 ILE cc_start: 0.9237 (OUTLIER) cc_final: 0.8874 (pt) REVERT: Aa 204 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7932 (ptt180) REVERT: Aa 265 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8772 (mm) REVERT: Aa 334 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7930 (pm20) REVERT: Ab 102 LYS cc_start: 0.8987 (mptt) cc_final: 0.8550 (mptt) REVERT: Ac 117 GLU cc_start: 0.8305 (pp20) cc_final: 0.7938 (pp20) REVERT: Ad 161 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8437 (tm-30) REVERT: Ae 152 TRP cc_start: 0.7905 (t60) cc_final: 0.7554 (t60) REVERT: Ae 159 TYR cc_start: 0.7084 (OUTLIER) cc_final: 0.5639 (t80) REVERT: Ae 209 MET cc_start: 0.7927 (mmm) cc_final: 0.7713 (mmm) REVERT: Ae 211 GLU cc_start: 0.6781 (mt-10) cc_final: 0.6037 (pp20) REVERT: Ae 228 HIS cc_start: 0.7293 (t70) cc_final: 0.6836 (t-170) REVERT: Ae 257 ASN cc_start: 0.7098 (OUTLIER) cc_final: 0.6570 (p0) REVERT: Ae 285 CYS cc_start: 0.8639 (t) cc_final: 0.8298 (p) REVERT: Af 111 ASP cc_start: 0.8037 (t0) cc_final: 0.7427 (t0) REVERT: Ag 88 MET cc_start: 0.8510 (mmp) cc_final: 0.8250 (mmm) REVERT: Ag 150 LEU cc_start: 0.7090 (OUTLIER) cc_final: 0.6412 (tm) REVERT: Ag 172 TYR cc_start: 0.6244 (OUTLIER) cc_final: 0.4710 (t80) REVERT: Ag 182 GLU cc_start: 0.7479 (mp0) cc_final: 0.7126 (mp0) REVERT: Ag 188 LYS cc_start: 0.8282 (mtmt) cc_final: 0.7876 (pttt) REVERT: Ag 252 LEU cc_start: 0.6793 (OUTLIER) cc_final: 0.6321 (mt) REVERT: Ag 295 MET cc_start: 0.8537 (tpp) cc_final: 0.8157 (tpp) REVERT: Ah 328 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7930 (ptpp) REVERT: Ah 329 TYR cc_start: 0.8090 (m-80) cc_final: 0.7847 (m-80) REVERT: Ah 373 ASN cc_start: 0.8062 (t0) cc_final: 0.7545 (t0) REVERT: Ai 18 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8316 (mp) REVERT: Ai 52 TYR cc_start: 0.9035 (m-80) cc_final: 0.8584 (m-80) REVERT: Ai 73 ASP cc_start: 0.8043 (t0) cc_final: 0.7464 (t70) REVERT: Ai 77 ASP cc_start: 0.9141 (m-30) cc_final: 0.8849 (m-30) REVERT: Ai 80 ASP cc_start: 0.8015 (m-30) cc_final: 0.7704 (m-30) REVERT: Ai 81 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8351 (tm-30) REVERT: Aj 150 PHE cc_start: 0.7351 (OUTLIER) cc_final: 0.6392 (t80) REVERT: Ak 53 LYS cc_start: 0.6015 (OUTLIER) cc_final: 0.5625 (ptmt) REVERT: Ak 59 THR cc_start: 0.8422 (m) cc_final: 0.8211 (p) REVERT: Ak 79 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8304 (mtmt) REVERT: Ak 95 ARG cc_start: 0.8802 (mmt90) cc_final: 0.8016 (mtt90) REVERT: Ak 166 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.8151 (mpt180) REVERT: Ak 241 TRP cc_start: 0.8707 (p-90) cc_final: 0.8282 (p-90) REVERT: Ak 289 LYS cc_start: 0.8180 (ptmm) cc_final: 0.7911 (pptt) REVERT: Am 17 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.8189 (ptm160) REVERT: Am 53 MET cc_start: 0.8351 (mmt) cc_final: 0.7872 (mmt) REVERT: Am 81 GLU cc_start: 0.8227 (tp30) cc_final: 0.7653 (tm-30) REVERT: Am 85 LYS cc_start: 0.7924 (mmtt) cc_final: 0.7680 (mmpt) REVERT: An 151 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7776 (ttt-90) REVERT: Ao 91 ASP cc_start: 0.8368 (t0) cc_final: 0.8070 (t0) REVERT: Ao 134 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6530 (mm-30) REVERT: Ao 262 TYR cc_start: 0.2364 (OUTLIER) cc_final: 0.1707 (p90) REVERT: Ao 265 MET cc_start: 0.5507 (mmt) cc_final: 0.5289 (mmm) REVERT: Ao 289 ARG cc_start: 0.5292 (mmm160) cc_final: 0.4549 (mmt90) REVERT: Ao 326 MET cc_start: 0.4142 (tpt) cc_final: 0.3402 (mmm) REVERT: Ao 383 TYR cc_start: 0.5039 (t80) cc_final: 0.4541 (t80) REVERT: Ao 411 ARG cc_start: 0.5693 (ptt-90) cc_final: 0.4539 (mtm110) REVERT: Ao 439 HIS cc_start: 0.5167 (t70) cc_final: 0.4808 (t70) REVERT: Ao 485 ILE cc_start: 0.7135 (mm) cc_final: 0.6890 (mm) REVERT: Ao 608 ILE cc_start: 0.5607 (mm) cc_final: 0.5367 (tp) REVERT: Ao 612 GLU cc_start: 0.4678 (mt-10) cc_final: 0.3856 (mp0) REVERT: Ao 632 GLU cc_start: 0.5512 (OUTLIER) cc_final: 0.4798 (pt0) REVERT: Ao 666 LEU cc_start: 0.6750 (tt) cc_final: 0.6487 (mt) REVERT: Ap 54 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.7031 (pt0) REVERT: Ap 169 GLN cc_start: 0.8904 (mt0) cc_final: 0.8478 (mt0) REVERT: Ap 223 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.6462 (mmt90) REVERT: Ap 235 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.7905 (ptp) outliers start: 338 outliers final: 220 residues processed: 1109 average time/residue: 0.7321 time to fit residues: 1344.3727 Evaluate side-chains 1068 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 801 time to evaluate : 5.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BC residue 189 VAL Chi-restraints excluded: chain BC residue 208 VAL Chi-restraints excluded: chain BC residue 230 ILE Chi-restraints excluded: chain BC residue 255 VAL Chi-restraints excluded: chain BC residue 283 ILE Chi-restraints excluded: chain BC residue 285 LEU Chi-restraints excluded: chain BC residue 332 MET Chi-restraints excluded: chain BC residue 399 MET Chi-restraints excluded: chain BC residue 468 LYS Chi-restraints excluded: chain BC residue 486 TRP Chi-restraints excluded: chain BC residue 520 ILE Chi-restraints excluded: chain BC residue 545 GLU Chi-restraints excluded: chain BC residue 560 ASP Chi-restraints excluded: chain BC residue 606 LEU Chi-restraints excluded: chain BC residue 662 THR Chi-restraints excluded: chain BC residue 686 VAL Chi-restraints excluded: chain BC residue 720 LYS Chi-restraints excluded: chain BC residue 722 SER Chi-restraints excluded: chain BT residue 61 VAL Chi-restraints excluded: chain AB residue 63 SER Chi-restraints excluded: chain AB residue 131 THR Chi-restraints excluded: chain AB residue 145 SER Chi-restraints excluded: chain AB residue 146 ARG Chi-restraints excluded: chain AB residue 186 VAL Chi-restraints excluded: chain AB residue 206 VAL Chi-restraints excluded: chain AB residue 213 LYS Chi-restraints excluded: chain AB residue 218 THR Chi-restraints excluded: chain AB residue 235 VAL Chi-restraints excluded: chain AC residue 41 ARG Chi-restraints excluded: chain AC residue 43 ARG Chi-restraints excluded: chain AC residue 73 THR Chi-restraints excluded: chain AC residue 92 LEU Chi-restraints excluded: chain AC residue 103 CYS Chi-restraints excluded: chain AC residue 115 ASN Chi-restraints excluded: chain AC residue 117 LEU Chi-restraints excluded: chain AC residue 122 LEU Chi-restraints excluded: chain AC residue 157 THR Chi-restraints excluded: chain AC residue 162 VAL Chi-restraints excluded: chain AE residue 93 LEU Chi-restraints excluded: chain AE residue 105 GLU Chi-restraints excluded: chain AE residue 137 HIS Chi-restraints excluded: chain AE residue 154 VAL Chi-restraints excluded: chain AE residue 171 ASP Chi-restraints excluded: chain AE residue 180 ASP Chi-restraints excluded: chain AE residue 194 SER Chi-restraints excluded: chain AE residue 216 ASP Chi-restraints excluded: chain AE residue 238 LYS Chi-restraints excluded: chain AE residue 239 ARG Chi-restraints excluded: chain AE residue 241 VAL Chi-restraints excluded: chain AE residue 242 ARG Chi-restraints excluded: chain AE residue 258 ILE Chi-restraints excluded: chain AE residue 336 VAL Chi-restraints excluded: chain AE residue 370 VAL Chi-restraints excluded: chain AE residue 384 VAL Chi-restraints excluded: chain AF residue 52 SER Chi-restraints excluded: chain AF residue 59 SER Chi-restraints excluded: chain AF residue 65 LEU Chi-restraints excluded: chain AF residue 103 LYS Chi-restraints excluded: chain AG residue 46 ILE Chi-restraints excluded: chain AG residue 64 TYR Chi-restraints excluded: chain AG residue 80 THR Chi-restraints excluded: chain AG residue 103 ASN Chi-restraints excluded: chain AG residue 109 SER Chi-restraints excluded: chain AG residue 162 LEU Chi-restraints excluded: chain AG residue 219 VAL Chi-restraints excluded: chain AI residue 95 ASP Chi-restraints excluded: chain AI residue 98 THR Chi-restraints excluded: chain AI residue 100 THR Chi-restraints excluded: chain AI residue 108 ILE Chi-restraints excluded: chain AI residue 153 THR Chi-restraints excluded: chain AI residue 155 LYS Chi-restraints excluded: chain AI residue 172 VAL Chi-restraints excluded: chain AI residue 206 LEU Chi-restraints excluded: chain AI residue 237 THR Chi-restraints excluded: chain AI residue 259 GLU Chi-restraints excluded: chain AI residue 279 THR Chi-restraints excluded: chain AI residue 299 VAL Chi-restraints excluded: chain AI residue 322 ASP Chi-restraints excluded: chain AI residue 334 SER Chi-restraints excluded: chain AI residue 338 ARG Chi-restraints excluded: chain AI residue 393 THR Chi-restraints excluded: chain AJ residue 64 THR Chi-restraints excluded: chain AJ residue 80 VAL Chi-restraints excluded: chain AJ residue 143 LEU Chi-restraints excluded: chain AJ residue 145 LEU Chi-restraints excluded: chain AJ residue 166 GLU Chi-restraints excluded: chain AJ residue 168 VAL Chi-restraints excluded: chain AK residue 68 ILE Chi-restraints excluded: chain AK residue 74 SER Chi-restraints excluded: chain AK residue 85 ILE Chi-restraints excluded: chain AK residue 87 ILE Chi-restraints excluded: chain AK residue 121 ASN Chi-restraints excluded: chain AK residue 142 THR Chi-restraints excluded: chain AK residue 147 THR Chi-restraints excluded: chain AK residue 183 ILE Chi-restraints excluded: chain AL residue 32 THR Chi-restraints excluded: chain AL residue 52 THR Chi-restraints excluded: chain AL residue 55 ARG Chi-restraints excluded: chain AL residue 77 ASN Chi-restraints excluded: chain AL residue 87 THR Chi-restraints excluded: chain AL residue 102 LEU Chi-restraints excluded: chain AL residue 117 ASP Chi-restraints excluded: chain AL residue 125 VAL Chi-restraints excluded: chain AN residue 30 VAL Chi-restraints excluded: chain AN residue 66 ASP Chi-restraints excluded: chain AN residue 67 LEU Chi-restraints excluded: chain AN residue 85 VAL Chi-restraints excluded: chain AN residue 93 MET Chi-restraints excluded: chain AN residue 120 LEU Chi-restraints excluded: chain AN residue 127 MET Chi-restraints excluded: chain AO residue 72 MET Chi-restraints excluded: chain AO residue 74 LEU Chi-restraints excluded: chain AO residue 105 LEU Chi-restraints excluded: chain AO residue 107 ILE Chi-restraints excluded: chain AO residue 124 SER Chi-restraints excluded: chain AO residue 167 MET Chi-restraints excluded: chain AO residue 182 ILE Chi-restraints excluded: chain AO residue 198 ARG Chi-restraints excluded: chain AO residue 218 VAL Chi-restraints excluded: chain AP residue 71 ASP Chi-restraints excluded: chain AP residue 97 TYR Chi-restraints excluded: chain AQ residue 6 SER Chi-restraints excluded: chain AQ residue 7 SER Chi-restraints excluded: chain AQ residue 20 THR Chi-restraints excluded: chain AQ residue 30 VAL Chi-restraints excluded: chain AQ residue 40 LEU Chi-restraints excluded: chain AQ residue 64 VAL Chi-restraints excluded: chain AQ residue 74 THR Chi-restraints excluded: chain AR residue 69 CYS Chi-restraints excluded: chain AR residue 89 THR Chi-restraints excluded: chain AR residue 117 ILE Chi-restraints excluded: chain AR residue 131 LEU Chi-restraints excluded: chain AU residue 10 ARG Chi-restraints excluded: chain AU residue 14 VAL Chi-restraints excluded: chain AU residue 19 VAL Chi-restraints excluded: chain AU residue 35 LEU Chi-restraints excluded: chain AU residue 38 ASP Chi-restraints excluded: chain AU residue 77 ARG Chi-restraints excluded: chain Aa residue 117 LEU Chi-restraints excluded: chain Aa residue 129 THR Chi-restraints excluded: chain Aa residue 150 MET Chi-restraints excluded: chain Aa residue 169 ILE Chi-restraints excluded: chain Aa residue 183 ILE Chi-restraints excluded: chain Aa residue 197 ARG Chi-restraints excluded: chain Aa residue 202 THR Chi-restraints excluded: chain Aa residue 204 ARG Chi-restraints excluded: chain Aa residue 265 ILE Chi-restraints excluded: chain Aa residue 304 ASP Chi-restraints excluded: chain Aa residue 325 LEU Chi-restraints excluded: chain Aa residue 334 GLN Chi-restraints excluded: chain Aa residue 348 HIS Chi-restraints excluded: chain Aa residue 375 PHE Chi-restraints excluded: chain Ab residue 6 LEU Chi-restraints excluded: chain Ab residue 14 SER Chi-restraints excluded: chain Ab residue 30 LEU Chi-restraints excluded: chain Ab residue 67 GLU Chi-restraints excluded: chain Ab residue 91 ASN Chi-restraints excluded: chain Ac residue 9 ILE Chi-restraints excluded: chain Ac residue 31 THR Chi-restraints excluded: chain Ac residue 59 ASN Chi-restraints excluded: chain Ac residue 70 MET Chi-restraints excluded: chain Ac residue 106 LEU Chi-restraints excluded: chain Ac residue 168 LYS Chi-restraints excluded: chain Ad residue 44 THR Chi-restraints excluded: chain Ad residue 56 LEU Chi-restraints excluded: chain Ad residue 161 GLN Chi-restraints excluded: chain Ad residue 166 THR Chi-restraints excluded: chain Ad residue 183 SER Chi-restraints excluded: chain Ae residue 76 ASP Chi-restraints excluded: chain Ae residue 95 SER Chi-restraints excluded: chain Ae residue 107 VAL Chi-restraints excluded: chain Ae residue 146 ASP Chi-restraints excluded: chain Ae residue 149 ILE Chi-restraints excluded: chain Ae residue 159 TYR Chi-restraints excluded: chain Ae residue 169 LEU Chi-restraints excluded: chain Ae residue 220 LEU Chi-restraints excluded: chain Ae residue 257 ASN Chi-restraints excluded: chain Ae residue 259 VAL Chi-restraints excluded: chain Ae residue 312 ASP Chi-restraints excluded: chain Ae residue 315 LEU Chi-restraints excluded: chain Ae residue 326 VAL Chi-restraints excluded: chain Ae residue 388 VAL Chi-restraints excluded: chain Af residue 85 LEU Chi-restraints excluded: chain Af residue 130 VAL Chi-restraints excluded: chain Af residue 151 THR Chi-restraints excluded: chain Af residue 155 LEU Chi-restraints excluded: chain Ag residue 54 ASP Chi-restraints excluded: chain Ag residue 71 LEU Chi-restraints excluded: chain Ag residue 135 LEU Chi-restraints excluded: chain Ag residue 150 LEU Chi-restraints excluded: chain Ag residue 167 LEU Chi-restraints excluded: chain Ag residue 172 TYR Chi-restraints excluded: chain Ag residue 194 ASN Chi-restraints excluded: chain Ag residue 252 LEU Chi-restraints excluded: chain Ag residue 255 PHE Chi-restraints excluded: chain Ag residue 262 ASP Chi-restraints excluded: chain Ag residue 264 VAL Chi-restraints excluded: chain Ag residue 265 ASN Chi-restraints excluded: chain Ag residue 296 VAL Chi-restraints excluded: chain Ag residue 305 ILE Chi-restraints excluded: chain Ag residue 309 VAL Chi-restraints excluded: chain Ah residue 308 ASN Chi-restraints excluded: chain Ah residue 310 GLU Chi-restraints excluded: chain Ah residue 328 LYS Chi-restraints excluded: chain Ah residue 345 LEU Chi-restraints excluded: chain Ah residue 387 ASN Chi-restraints excluded: chain Ai residue 12 SER Chi-restraints excluded: chain Ai residue 15 SER Chi-restraints excluded: chain Ai residue 18 LEU Chi-restraints excluded: chain Ai residue 26 THR Chi-restraints excluded: chain Ai residue 50 ASP Chi-restraints excluded: chain Aj residue 6 VAL Chi-restraints excluded: chain Aj residue 18 VAL Chi-restraints excluded: chain Aj residue 65 LEU Chi-restraints excluded: chain Aj residue 82 ARG Chi-restraints excluded: chain Aj residue 84 SER Chi-restraints excluded: chain Aj residue 98 THR Chi-restraints excluded: chain Aj residue 108 ASN Chi-restraints excluded: chain Aj residue 150 PHE Chi-restraints excluded: chain Aj residue 162 LEU Chi-restraints excluded: chain Aj residue 184 THR Chi-restraints excluded: chain Aj residue 202 ASP Chi-restraints excluded: chain Ak residue 53 LYS Chi-restraints excluded: chain Ak residue 64 VAL Chi-restraints excluded: chain Ak residue 79 LYS Chi-restraints excluded: chain Ak residue 93 VAL Chi-restraints excluded: chain Ak residue 112 ASN Chi-restraints excluded: chain Ak residue 117 THR Chi-restraints excluded: chain Ak residue 130 ASP Chi-restraints excluded: chain Ak residue 154 ASP Chi-restraints excluded: chain Ak residue 159 VAL Chi-restraints excluded: chain Ak residue 165 ILE Chi-restraints excluded: chain Ak residue 166 ARG Chi-restraints excluded: chain Ak residue 298 VAL Chi-restraints excluded: chain Ak residue 309 ASN Chi-restraints excluded: chain Am residue 17 ARG Chi-restraints excluded: chain Am residue 44 THR Chi-restraints excluded: chain Am residue 113 ASN Chi-restraints excluded: chain An residue 151 ARG Chi-restraints excluded: chain An residue 173 LEU Chi-restraints excluded: chain An residue 194 ILE Chi-restraints excluded: chain Ao residue 77 THR Chi-restraints excluded: chain Ao residue 96 ILE Chi-restraints excluded: chain Ao residue 134 GLU Chi-restraints excluded: chain Ao residue 243 THR Chi-restraints excluded: chain Ao residue 260 HIS Chi-restraints excluded: chain Ao residue 262 TYR Chi-restraints excluded: chain Ao residue 263 CYS Chi-restraints excluded: chain Ao residue 269 MET Chi-restraints excluded: chain Ao residue 279 LEU Chi-restraints excluded: chain Ao residue 304 THR Chi-restraints excluded: chain Ao residue 416 ASP Chi-restraints excluded: chain Ao residue 454 ASP Chi-restraints excluded: chain Ao residue 510 ASP Chi-restraints excluded: chain Ao residue 521 GLU Chi-restraints excluded: chain Ao residue 632 GLU Chi-restraints excluded: chain Ao residue 645 CYS Chi-restraints excluded: chain Ao residue 652 VAL Chi-restraints excluded: chain Ao residue 659 THR Chi-restraints excluded: chain Ap residue 54 GLU Chi-restraints excluded: chain Ap residue 103 ASN Chi-restraints excluded: chain Ap residue 154 ILE Chi-restraints excluded: chain Ap residue 167 ILE Chi-restraints excluded: chain Ap residue 177 PHE Chi-restraints excluded: chain Ap residue 193 LEU Chi-restraints excluded: chain Ap residue 223 ARG Chi-restraints excluded: chain Ap residue 235 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 719 random chunks: chunk 578 optimal weight: 8.9990 chunk 394 optimal weight: 20.0000 chunk 10 optimal weight: 8.9990 chunk 517 optimal weight: 1.9990 chunk 286 optimal weight: 0.0370 chunk 593 optimal weight: 0.0070 chunk 480 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 354 optimal weight: 0.9980 chunk 623 optimal weight: 10.0000 chunk 175 optimal weight: 5.9990 overall best weight: 1.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BC 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BC 268 GLN AB 265 GLN ** AC 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 137 HIS ** AE 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AI 77 GLN ** AI 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AK 98 GLN ** AN 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AN 119 GLN AU 79 ASN Aa 268 HIS ** Aa 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 243 ASN ** Ae 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 189 ASN ** Ah 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 88 GLN ** Am 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 58 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 76793 Z= 0.211 Angle : 0.582 9.607 108765 Z= 0.297 Chirality : 0.037 0.228 12818 Planarity : 0.005 0.094 10078 Dihedral : 20.471 179.840 22761 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.36 % Favored : 96.60 % Rotamer: Outliers : 4.86 % Allowed : 19.41 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.31 % 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: 0.42 (0.11), residues: 6199 helix: 1.26 (0.10), residues: 2806 sheet: -0.19 (0.20), residues: 638 loop : -0.58 (0.12), residues: 2755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRPAk 236 HIS 0.007 0.001 HISAE 288 PHE 0.039 0.001 PHEAe 191 TYR 0.026 0.001 TYRAc 163 ARG 0.007 0.000 ARGAg 231 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1135 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 873 time to evaluate : 5.472 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: symmetry clash revert: symmetry clash REVERT: BC 197 LEU cc_start: 0.8875 (mt) cc_final: 0.8628 (tp) REVERT: BC 244 MET cc_start: 0.7763 (mtp) cc_final: 0.7539 (mtm) REVERT: BC 285 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7301 (mt) REVERT: BC 308 ASP cc_start: 0.7777 (m-30) cc_final: 0.7455 (t70) REVERT: BC 464 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7925 (mt-10) REVERT: BC 488 LYS cc_start: 0.7244 (mttt) cc_final: 0.6860 (tptt) REVERT: BC 520 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8795 (mp) REVERT: BC 690 MET cc_start: 0.5199 (mmm) cc_final: 0.4729 (mmm) REVERT: BC 712 TYR cc_start: 0.5253 (p90) cc_final: 0.4760 (p90) REVERT: AB 146 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7891 (tpt-90) REVERT: AC 41 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.6884 (mtm-85) REVERT: AC 43 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8155 (mmt180) REVERT: AC 122 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.9016 (mp) REVERT: AC 144 SER cc_start: 0.9468 (m) cc_final: 0.9095 (m) REVERT: AE 157 ILE cc_start: 0.8407 (mp) cc_final: 0.8031 (mt) REVERT: AE 178 GLU cc_start: 0.8164 (tt0) cc_final: 0.7432 (tp30) REVERT: AE 179 TRP cc_start: 0.7663 (m-10) cc_final: 0.6808 (m-10) REVERT: AE 242 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.8824 (ptt-90) REVERT: AE 305 MET cc_start: 0.8638 (mtm) cc_final: 0.8273 (mtm) REVERT: AE 321 MET cc_start: 0.9048 (mtp) cc_final: 0.8671 (mtp) REVERT: AI 91 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.7263 (mtm) REVERT: AI 213 LYS cc_start: 0.8313 (mttt) cc_final: 0.8090 (mttm) REVERT: AI 338 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.7476 (ptm-80) REVERT: AJ 64 THR cc_start: 0.7431 (OUTLIER) cc_final: 0.7216 (p) REVERT: AJ 106 ILE cc_start: 0.9232 (pt) cc_final: 0.8946 (pt) REVERT: AJ 145 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8199 (mt) REVERT: AL 55 ARG cc_start: 0.9231 (OUTLIER) cc_final: 0.8927 (mtt-85) REVERT: AL 103 GLN cc_start: 0.8351 (mp10) cc_final: 0.8088 (mt0) REVERT: AL 118 LEU cc_start: 0.9315 (mt) cc_final: 0.9059 (mt) REVERT: AO 72 MET cc_start: 0.9067 (OUTLIER) cc_final: 0.8756 (tpp) REVERT: AO 167 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8509 (mtt) REVERT: AO 198 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8355 (mtt180) REVERT: AO 217 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8280 (tp30) REVERT: AP 120 LEU cc_start: 0.8721 (tp) cc_final: 0.8436 (mt) REVERT: AQ 45 LYS cc_start: 0.8659 (ttmt) cc_final: 0.8198 (tttm) REVERT: AQ 107 GLU cc_start: 0.8500 (tp30) cc_final: 0.8256 (tp30) REVERT: AU 10 ARG cc_start: 0.9235 (OUTLIER) cc_final: 0.8983 (mtm180) REVERT: AU 23 TYR cc_start: 0.8976 (t80) cc_final: 0.8774 (t80) REVERT: AU 77 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7717 (mtt-85) REVERT: Aa 129 THR cc_start: 0.8678 (OUTLIER) cc_final: 0.8448 (p) REVERT: Aa 150 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8404 (mtt) REVERT: Aa 183 ILE cc_start: 0.9147 (OUTLIER) cc_final: 0.8801 (pt) REVERT: Aa 197 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.7658 (mmt90) REVERT: Aa 334 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7888 (pm20) REVERT: Ab 102 LYS cc_start: 0.8984 (mptt) cc_final: 0.8554 (mptt) REVERT: Ac 106 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8705 (pp) REVERT: Ac 117 GLU cc_start: 0.8311 (pp20) cc_final: 0.7999 (pp20) REVERT: Ad 161 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.8444 (tm-30) REVERT: Ae 152 TRP cc_start: 0.7956 (t60) cc_final: 0.7586 (t60) REVERT: Ae 159 TYR cc_start: 0.7153 (OUTLIER) cc_final: 0.5776 (t80) REVERT: Ae 201 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7676 (tp) REVERT: Ae 209 MET cc_start: 0.7955 (mmm) cc_final: 0.7655 (mmm) REVERT: Ae 211 GLU cc_start: 0.6658 (mt-10) cc_final: 0.5933 (pp20) REVERT: Ae 221 LEU cc_start: 0.8965 (mt) cc_final: 0.8627 (mp) REVERT: Ae 285 CYS cc_start: 0.8567 (t) cc_final: 0.8272 (p) REVERT: Ae 375 PHE cc_start: 0.6816 (t80) cc_final: 0.6557 (t80) REVERT: Af 111 ASP cc_start: 0.8063 (t0) cc_final: 0.7451 (t0) REVERT: Af 149 GLU cc_start: 0.8503 (tt0) cc_final: 0.8303 (tt0) REVERT: Ag 150 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6233 (tm) REVERT: Ag 172 TYR cc_start: 0.6146 (OUTLIER) cc_final: 0.4342 (t80) REVERT: Ag 182 GLU cc_start: 0.7449 (mp0) cc_final: 0.7064 (mp0) REVERT: Ag 188 LYS cc_start: 0.8235 (mtmt) cc_final: 0.7900 (pttt) REVERT: Ag 295 MET cc_start: 0.8562 (tpp) cc_final: 0.8118 (tpp) REVERT: Ah 285 PRO cc_start: 0.8150 (Cg_exo) cc_final: 0.7736 (Cg_endo) REVERT: Ah 294 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8652 (mp) REVERT: Ah 329 TYR cc_start: 0.8007 (m-80) cc_final: 0.7781 (m-80) REVERT: Ah 332 ASP cc_start: 0.8602 (p0) cc_final: 0.7927 (p0) REVERT: Ah 373 ASN cc_start: 0.8076 (t0) cc_final: 0.7492 (t0) REVERT: Ai 18 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8278 (mp) REVERT: Ai 52 TYR cc_start: 0.8978 (m-80) cc_final: 0.8593 (m-80) REVERT: Ai 73 ASP cc_start: 0.7983 (t0) cc_final: 0.7202 (t70) REVERT: Ai 77 ASP cc_start: 0.9095 (m-30) cc_final: 0.8706 (m-30) REVERT: Ai 81 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8350 (tm-30) REVERT: Aj 150 PHE cc_start: 0.7256 (OUTLIER) cc_final: 0.6368 (t80) REVERT: Ak 79 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8181 (mtmt) REVERT: Ak 95 ARG cc_start: 0.8785 (mmt90) cc_final: 0.7901 (mtm-85) REVERT: Ak 241 TRP cc_start: 0.8743 (p-90) cc_final: 0.8368 (p-90) REVERT: Ak 289 LYS cc_start: 0.8185 (ptmm) cc_final: 0.7948 (pptt) REVERT: Am 17 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8130 (ptm160) REVERT: Am 53 MET cc_start: 0.8269 (mmt) cc_final: 0.7924 (mmt) REVERT: Am 81 GLU cc_start: 0.8142 (tp30) cc_final: 0.7676 (tm-30) REVERT: Am 85 LYS cc_start: 0.7909 (mmtt) cc_final: 0.7699 (mmpt) REVERT: An 165 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.7979 (ttmm) REVERT: Ao 91 ASP cc_start: 0.8237 (t0) cc_final: 0.7906 (t0) REVERT: Ao 134 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6199 (mm-30) REVERT: Ao 265 MET cc_start: 0.5453 (mmt) cc_final: 0.5223 (mmm) REVERT: Ao 326 MET cc_start: 0.4332 (tpt) cc_final: 0.3788 (mmm) REVERT: Ao 383 TYR cc_start: 0.5039 (t80) cc_final: 0.4544 (t80) REVERT: Ao 411 ARG cc_start: 0.5676 (ptt-90) cc_final: 0.4498 (mtm110) REVERT: Ao 418 PHE cc_start: 0.6027 (t80) cc_final: 0.5592 (t80) REVERT: Ao 439 HIS cc_start: 0.5179 (t70) cc_final: 0.4968 (t-170) REVERT: Ao 441 LEU cc_start: 0.7850 (tp) cc_final: 0.7534 (mt) REVERT: Ao 485 ILE cc_start: 0.6963 (mm) cc_final: 0.6634 (mm) REVERT: Ao 608 ILE cc_start: 0.5559 (mm) cc_final: 0.5340 (tp) REVERT: Ao 612 GLU cc_start: 0.4763 (mt-10) cc_final: 0.3933 (mp0) REVERT: Ao 632 GLU cc_start: 0.5561 (OUTLIER) cc_final: 0.4841 (pt0) REVERT: Ao 666 LEU cc_start: 0.6839 (tt) cc_final: 0.6573 (mt) REVERT: Ap 54 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7200 (pt0) REVERT: Ap 103 ASN cc_start: 0.8917 (OUTLIER) cc_final: 0.8029 (p0) REVERT: Ap 169 GLN cc_start: 0.8874 (mt0) cc_final: 0.8652 (mt0) REVERT: Ap 210 GLU cc_start: 0.8064 (tp30) cc_final: 0.7761 (tp30) REVERT: Ap 223 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.6483 (mmt90) REVERT: Ap 235 MET cc_start: 0.8516 (ptm) cc_final: 0.7900 (ptp) outliers start: 262 outliers final: 170 residues processed: 1066 average time/residue: 0.7306 time to fit residues: 1285.3150 Evaluate side-chains 1025 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 816 time to evaluate : 5.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BC residue 230 ILE Chi-restraints excluded: chain BC residue 255 VAL Chi-restraints excluded: chain BC residue 283 ILE Chi-restraints excluded: chain BC residue 285 LEU Chi-restraints excluded: chain BC residue 332 MET Chi-restraints excluded: chain BC residue 362 SER Chi-restraints excluded: chain BC residue 468 LYS Chi-restraints excluded: chain BC residue 486 TRP Chi-restraints excluded: chain BC residue 520 ILE Chi-restraints excluded: chain BC residue 535 ILE Chi-restraints excluded: chain BC residue 560 ASP Chi-restraints excluded: chain BC residue 606 LEU Chi-restraints excluded: chain BC residue 662 THR Chi-restraints excluded: chain BC residue 686 VAL Chi-restraints excluded: chain BT residue 61 VAL Chi-restraints excluded: chain AB residue 63 SER Chi-restraints excluded: chain AB residue 145 SER Chi-restraints excluded: chain AB residue 146 ARG Chi-restraints excluded: chain AB residue 186 VAL Chi-restraints excluded: chain AB residue 206 VAL Chi-restraints excluded: chain AB residue 218 THR Chi-restraints excluded: chain AB residue 235 VAL Chi-restraints excluded: chain AC residue 41 ARG Chi-restraints excluded: chain AC residue 43 ARG Chi-restraints excluded: chain AC residue 71 LEU Chi-restraints excluded: chain AC residue 73 THR Chi-restraints excluded: chain AC residue 92 LEU Chi-restraints excluded: chain AC residue 103 CYS Chi-restraints excluded: chain AC residue 115 ASN Chi-restraints excluded: chain AC residue 117 LEU Chi-restraints excluded: chain AC residue 122 LEU Chi-restraints excluded: chain AC residue 157 THR Chi-restraints excluded: chain AE residue 105 GLU Chi-restraints excluded: chain AE residue 154 VAL Chi-restraints excluded: chain AE residue 171 ASP Chi-restraints excluded: chain AE residue 216 ASP Chi-restraints excluded: chain AE residue 238 LYS Chi-restraints excluded: chain AE residue 239 ARG Chi-restraints excluded: chain AE residue 242 ARG Chi-restraints excluded: chain AE residue 258 ILE Chi-restraints excluded: chain AE residue 336 VAL Chi-restraints excluded: chain AE residue 370 VAL Chi-restraints excluded: chain AF residue 52 SER Chi-restraints excluded: chain AF residue 56 GLN Chi-restraints excluded: chain AF residue 65 LEU Chi-restraints excluded: chain AF residue 103 LYS Chi-restraints excluded: chain AG residue 46 ILE Chi-restraints excluded: chain AG residue 64 TYR Chi-restraints excluded: chain AG residue 219 VAL Chi-restraints excluded: chain AI residue 91 MET Chi-restraints excluded: chain AI residue 98 THR Chi-restraints excluded: chain AI residue 100 THR Chi-restraints excluded: chain AI residue 108 ILE Chi-restraints excluded: chain AI residue 153 THR Chi-restraints excluded: chain AI residue 155 LYS Chi-restraints excluded: chain AI residue 172 VAL Chi-restraints excluded: chain AI residue 206 LEU Chi-restraints excluded: chain AI residue 229 LEU Chi-restraints excluded: chain AI residue 237 THR Chi-restraints excluded: chain AI residue 334 SER Chi-restraints excluded: chain AI residue 338 ARG Chi-restraints excluded: chain AJ residue 64 THR Chi-restraints excluded: chain AJ residue 80 VAL Chi-restraints excluded: chain AJ residue 143 LEU Chi-restraints excluded: chain AJ residue 145 LEU Chi-restraints excluded: chain AJ residue 166 GLU Chi-restraints excluded: chain AJ residue 168 VAL Chi-restraints excluded: chain AK residue 68 ILE Chi-restraints excluded: chain AK residue 74 SER Chi-restraints excluded: chain AK residue 85 ILE Chi-restraints excluded: chain AK residue 142 THR Chi-restraints excluded: chain AK residue 147 THR Chi-restraints excluded: chain AK residue 183 ILE Chi-restraints excluded: chain AL residue 32 THR Chi-restraints excluded: chain AL residue 52 THR Chi-restraints excluded: chain AL residue 55 ARG Chi-restraints excluded: chain AL residue 67 ILE Chi-restraints excluded: chain AL residue 77 ASN Chi-restraints excluded: chain AL residue 87 THR Chi-restraints excluded: chain AL residue 102 LEU Chi-restraints excluded: chain AL residue 117 ASP Chi-restraints excluded: chain AL residue 125 VAL Chi-restraints excluded: chain AN residue 66 ASP Chi-restraints excluded: chain AN residue 93 MET Chi-restraints excluded: chain AN residue 120 LEU Chi-restraints excluded: chain AO residue 72 MET Chi-restraints excluded: chain AO residue 105 LEU Chi-restraints excluded: chain AO residue 167 MET Chi-restraints excluded: chain AO residue 198 ARG Chi-restraints excluded: chain AO residue 218 VAL Chi-restraints excluded: chain AP residue 71 ASP Chi-restraints excluded: chain AP residue 97 TYR Chi-restraints excluded: chain AP residue 117 GLU Chi-restraints excluded: chain AQ residue 6 SER Chi-restraints excluded: chain AQ residue 7 SER Chi-restraints excluded: chain AQ residue 22 MET Chi-restraints excluded: chain AQ residue 30 VAL Chi-restraints excluded: chain AQ residue 40 LEU Chi-restraints excluded: chain AQ residue 64 VAL Chi-restraints excluded: chain AQ residue 74 THR Chi-restraints excluded: chain AR residue 69 CYS Chi-restraints excluded: chain AR residue 89 THR Chi-restraints excluded: chain AR residue 117 ILE Chi-restraints excluded: chain AR residue 131 LEU Chi-restraints excluded: chain AU residue 10 ARG Chi-restraints excluded: chain AU residue 14 VAL Chi-restraints excluded: chain AU residue 35 LEU Chi-restraints excluded: chain AU residue 38 ASP Chi-restraints excluded: chain AU residue 77 ARG Chi-restraints excluded: chain Aa residue 117 LEU Chi-restraints excluded: chain Aa residue 129 THR Chi-restraints excluded: chain Aa residue 150 MET Chi-restraints excluded: chain Aa residue 169 ILE Chi-restraints excluded: chain Aa residue 183 ILE Chi-restraints excluded: chain Aa residue 197 ARG Chi-restraints excluded: chain Aa residue 202 THR Chi-restraints excluded: chain Aa residue 304 ASP Chi-restraints excluded: chain Aa residue 325 LEU Chi-restraints excluded: chain Aa residue 334 GLN Chi-restraints excluded: chain Aa residue 348 HIS Chi-restraints excluded: chain Ab residue 6 LEU Chi-restraints excluded: chain Ab residue 30 LEU Chi-restraints excluded: chain Ab residue 67 GLU Chi-restraints excluded: chain Ab residue 91 ASN Chi-restraints excluded: chain Ac residue 9 ILE Chi-restraints excluded: chain Ac residue 59 ASN Chi-restraints excluded: chain Ac residue 70 MET Chi-restraints excluded: chain Ac residue 95 ASN Chi-restraints excluded: chain Ac residue 106 LEU Chi-restraints excluded: chain Ad residue 56 LEU Chi-restraints excluded: chain Ad residue 161 GLN Chi-restraints excluded: chain Ad residue 183 SER Chi-restraints excluded: chain Ae residue 76 ASP Chi-restraints excluded: chain Ae residue 95 SER Chi-restraints excluded: chain Ae residue 107 VAL Chi-restraints excluded: chain Ae residue 146 ASP Chi-restraints excluded: chain Ae residue 149 ILE Chi-restraints excluded: chain Ae residue 159 TYR Chi-restraints excluded: chain Ae residue 201 LEU Chi-restraints excluded: chain Ae residue 229 CYS Chi-restraints excluded: chain Ae residue 312 ASP Chi-restraints excluded: chain Ae residue 323 LEU Chi-restraints excluded: chain Ae residue 326 VAL Chi-restraints excluded: chain Ae residue 388 VAL Chi-restraints excluded: chain Ae residue 424 HIS Chi-restraints excluded: chain Af residue 85 LEU Chi-restraints excluded: chain Af residue 130 VAL Chi-restraints excluded: chain Af residue 155 LEU Chi-restraints excluded: chain Ag residue 54 ASP Chi-restraints excluded: chain Ag residue 71 LEU Chi-restraints excluded: chain Ag residue 150 LEU Chi-restraints excluded: chain Ag residue 167 LEU Chi-restraints excluded: chain Ag residue 172 TYR Chi-restraints excluded: chain Ag residue 194 ASN Chi-restraints excluded: chain Ag residue 255 PHE Chi-restraints excluded: chain Ag residue 264 VAL Chi-restraints excluded: chain Ag residue 265 ASN Chi-restraints excluded: chain Ag residue 296 VAL Chi-restraints excluded: chain Ag residue 309 VAL Chi-restraints excluded: chain Ah residue 294 ILE Chi-restraints excluded: chain Ah residue 310 GLU Chi-restraints excluded: chain Ah residue 387 ASN Chi-restraints excluded: chain Ai residue 12 SER Chi-restraints excluded: chain Ai residue 15 SER Chi-restraints excluded: chain Ai residue 18 LEU Chi-restraints excluded: chain Ai residue 26 THR Chi-restraints excluded: chain Ai residue 50 ASP Chi-restraints excluded: chain Aj residue 6 VAL Chi-restraints excluded: chain Aj residue 82 ARG Chi-restraints excluded: chain Aj residue 84 SER Chi-restraints excluded: chain Aj residue 108 ASN Chi-restraints excluded: chain Aj residue 150 PHE Chi-restraints excluded: chain Aj residue 184 THR Chi-restraints excluded: chain Aj residue 202 ASP Chi-restraints excluded: chain Ak residue 64 VAL Chi-restraints excluded: chain Ak residue 79 LYS Chi-restraints excluded: chain Ak residue 93 VAL Chi-restraints excluded: chain Ak residue 117 THR Chi-restraints excluded: chain Ak residue 130 ASP Chi-restraints excluded: chain Ak residue 154 ASP Chi-restraints excluded: chain Ak residue 159 VAL Chi-restraints excluded: chain Ak residue 165 ILE Chi-restraints excluded: chain Ak residue 309 ASN Chi-restraints excluded: chain Am residue 17 ARG Chi-restraints excluded: chain Am residue 44 THR Chi-restraints excluded: chain Am residue 113 ASN Chi-restraints excluded: chain An residue 165 LYS Chi-restraints excluded: chain An residue 194 ILE Chi-restraints excluded: chain Ao residue 96 ILE Chi-restraints excluded: chain Ao residue 134 GLU Chi-restraints excluded: chain Ao residue 243 THR Chi-restraints excluded: chain Ao residue 260 HIS Chi-restraints excluded: chain Ao residue 263 CYS Chi-restraints excluded: chain Ao residue 269 MET Chi-restraints excluded: chain Ao residue 338 PHE Chi-restraints excluded: chain Ao residue 409 SER Chi-restraints excluded: chain Ao residue 454 ASP Chi-restraints excluded: chain Ao residue 510 ASP Chi-restraints excluded: chain Ao residue 521 GLU Chi-restraints excluded: chain Ao residue 632 GLU Chi-restraints excluded: chain Ao residue 645 CYS Chi-restraints excluded: chain Ao residue 652 VAL Chi-restraints excluded: chain Ao residue 659 THR Chi-restraints excluded: chain Ap residue 54 GLU Chi-restraints excluded: chain Ap residue 103 ASN Chi-restraints excluded: chain Ap residue 154 ILE Chi-restraints excluded: chain Ap residue 193 LEU Chi-restraints excluded: chain Ap residue 197 ASP Chi-restraints excluded: chain Ap residue 223 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 719 random chunks: chunk 233 optimal weight: 7.9990 chunk 625 optimal weight: 0.9990 chunk 137 optimal weight: 8.9990 chunk 408 optimal weight: 6.9990 chunk 171 optimal weight: 0.8980 chunk 695 optimal weight: 20.0000 chunk 577 optimal weight: 8.9990 chunk 322 optimal weight: 6.9990 chunk 57 optimal weight: 0.4980 chunk 230 optimal weight: 0.9990 chunk 365 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BC 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AB 265 GLN ** AC 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 137 HIS ** AE 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 175 GLN AG 166 HIS ** AI 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AK 121 ASN ** AN 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AN 117 HIS AN 119 GLN AU 79 ASN ** Aa 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 172 ASN ** Ae 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 181 ASN ** Ae 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 194 ASN ** Ag 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 313 GLN ** Am 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 58 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 76793 Z= 0.186 Angle : 0.559 11.015 108765 Z= 0.283 Chirality : 0.036 0.224 12818 Planarity : 0.004 0.085 10078 Dihedral : 20.298 178.832 22715 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.63 % Favored : 96.32 % Rotamer: Outliers : 4.43 % Allowed : 19.84 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.31 % 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: 0.69 (0.11), residues: 6199 helix: 1.52 (0.10), residues: 2803 sheet: -0.02 (0.20), residues: 631 loop : -0.48 (0.12), residues: 2765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRPAk 236 HIS 0.006 0.001 HISAE 288 PHE 0.017 0.001 PHEAo 617 TYR 0.025 0.001 TYRAc 163 ARG 0.014 0.000 ARGAo 456 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1108 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 869 time to evaluate : 5.323 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: symmetry clash REVERT: BC 197 LEU cc_start: 0.8796 (mt) cc_final: 0.8561 (tp) REVERT: BC 244 MET cc_start: 0.7711 (mtp) cc_final: 0.7313 (mtm) REVERT: BC 285 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.7014 (mt) REVERT: BC 308 ASP cc_start: 0.7738 (m-30) cc_final: 0.7423 (t70) REVERT: BC 464 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7878 (mt-10) REVERT: BC 488 LYS cc_start: 0.7283 (mttt) cc_final: 0.6917 (tptt) REVERT: BC 589 LYS cc_start: 0.8697 (mttm) cc_final: 0.8300 (mttp) REVERT: BC 712 TYR cc_start: 0.5328 (p90) cc_final: 0.4787 (p90) REVERT: AC 43 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8104 (mmt180) REVERT: AC 144 SER cc_start: 0.9463 (m) cc_final: 0.9095 (m) REVERT: AE 157 ILE cc_start: 0.8381 (mp) cc_final: 0.8008 (mt) REVERT: AE 178 GLU cc_start: 0.8114 (tt0) cc_final: 0.7353 (tp30) REVERT: AE 179 TRP cc_start: 0.7663 (m-10) cc_final: 0.6832 (m-10) REVERT: AE 225 VAL cc_start: 0.9316 (p) cc_final: 0.9057 (t) REVERT: AE 242 ARG cc_start: 0.9029 (OUTLIER) cc_final: 0.8779 (ptt-90) REVERT: AE 321 MET cc_start: 0.9027 (mtp) cc_final: 0.8644 (mtp) REVERT: AG 72 GLN cc_start: 0.7624 (mt0) cc_final: 0.7378 (mt0) REVERT: AI 91 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.7248 (mtm) REVERT: AI 213 LYS cc_start: 0.8251 (mttt) cc_final: 0.7968 (mttm) REVERT: AI 268 MET cc_start: 0.8602 (mmt) cc_final: 0.7720 (ppp) REVERT: AJ 64 THR cc_start: 0.7410 (OUTLIER) cc_final: 0.7151 (p) REVERT: AJ 106 ILE cc_start: 0.9199 (pt) cc_final: 0.8917 (pt) REVERT: AJ 145 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8208 (mt) REVERT: AL 55 ARG cc_start: 0.9163 (OUTLIER) cc_final: 0.8867 (mtt-85) REVERT: AL 118 LEU cc_start: 0.9302 (mt) cc_final: 0.9043 (mt) REVERT: AO 72 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8780 (tpp) REVERT: AO 107 ILE cc_start: 0.9114 (mm) cc_final: 0.8904 (mt) REVERT: AO 167 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8346 (mtt) REVERT: AO 217 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8284 (tp30) REVERT: AP 120 LEU cc_start: 0.8703 (tp) cc_final: 0.8425 (mt) REVERT: AQ 45 LYS cc_start: 0.8622 (ttmt) cc_final: 0.8220 (tttm) REVERT: AQ 107 GLU cc_start: 0.8648 (tp30) cc_final: 0.8369 (tp30) REVERT: AU 77 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7723 (mtt-85) REVERT: Aa 129 THR cc_start: 0.8564 (OUTLIER) cc_final: 0.8359 (p) REVERT: Aa 183 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8799 (pt) REVERT: Aa 197 ARG cc_start: 0.9094 (OUTLIER) cc_final: 0.7614 (mmt90) REVERT: Aa 334 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7838 (pm20) REVERT: Ab 7 GLU cc_start: 0.8863 (pm20) cc_final: 0.8636 (pm20) REVERT: Ab 102 LYS cc_start: 0.8965 (mptt) cc_final: 0.8530 (mptt) REVERT: Ac 106 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8757 (pp) REVERT: Ac 117 GLU cc_start: 0.8321 (pp20) cc_final: 0.7988 (pp20) REVERT: Ad 161 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8452 (tm-30) REVERT: Ae 146 ASP cc_start: 0.7590 (OUTLIER) cc_final: 0.7386 (t0) REVERT: Ae 152 TRP cc_start: 0.7949 (t60) cc_final: 0.7528 (t60) REVERT: Ae 159 TYR cc_start: 0.7105 (OUTLIER) cc_final: 0.5723 (t80) REVERT: Ae 201 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7404 (tp) REVERT: Ae 209 MET cc_start: 0.7806 (mmm) cc_final: 0.7532 (mmm) REVERT: Ae 211 GLU cc_start: 0.6194 (mt-10) cc_final: 0.5930 (tm-30) REVERT: Ae 291 TRP cc_start: 0.7627 (OUTLIER) cc_final: 0.7205 (p90) REVERT: Af 111 ASP cc_start: 0.7961 (t0) cc_final: 0.7476 (t0) REVERT: Ag 150 LEU cc_start: 0.6978 (OUTLIER) cc_final: 0.6246 (tm) REVERT: Ag 172 TYR cc_start: 0.5954 (OUTLIER) cc_final: 0.4365 (t80) REVERT: Ag 182 GLU cc_start: 0.7387 (mp0) cc_final: 0.7046 (mp0) REVERT: Ag 295 MET cc_start: 0.8505 (tpp) cc_final: 0.8054 (tpp) REVERT: Ah 285 PRO cc_start: 0.8163 (Cg_exo) cc_final: 0.7794 (Cg_endo) REVERT: Ah 294 ILE cc_start: 0.8896 (OUTLIER) cc_final: 0.8618 (mp) REVERT: Ah 373 ASN cc_start: 0.8029 (t0) cc_final: 0.7393 (t0) REVERT: Ai 18 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8338 (mp) REVERT: Ai 52 TYR cc_start: 0.8889 (m-80) cc_final: 0.8480 (m-80) REVERT: Ai 73 ASP cc_start: 0.7934 (t0) cc_final: 0.7423 (t70) REVERT: Ai 77 ASP cc_start: 0.9067 (m-30) cc_final: 0.8819 (m-30) REVERT: Ai 81 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8354 (tm-30) REVERT: Aj 150 PHE cc_start: 0.7237 (OUTLIER) cc_final: 0.6360 (t80) REVERT: Ak 241 TRP cc_start: 0.8729 (p-90) cc_final: 0.8410 (p-90) REVERT: Ak 289 LYS cc_start: 0.8169 (ptmm) cc_final: 0.7933 (pptt) REVERT: Am 53 MET cc_start: 0.8222 (mmt) cc_final: 0.7944 (mmt) REVERT: Am 81 GLU cc_start: 0.8122 (tp30) cc_final: 0.7692 (tm-30) REVERT: An 165 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8008 (ttmm) REVERT: Ao 262 TYR cc_start: 0.2353 (OUTLIER) cc_final: 0.1796 (p90) REVERT: Ao 326 MET cc_start: 0.4043 (OUTLIER) cc_final: 0.3441 (mmm) REVERT: Ao 411 ARG cc_start: 0.5775 (ptt-90) cc_final: 0.4566 (mtm110) REVERT: Ao 439 HIS cc_start: 0.5108 (t70) cc_final: 0.4874 (t-170) REVERT: Ao 441 LEU cc_start: 0.7861 (tp) cc_final: 0.7567 (mt) REVERT: Ao 485 ILE cc_start: 0.7061 (mm) cc_final: 0.6751 (mm) REVERT: Ao 540 ARG cc_start: 0.4779 (mmt90) cc_final: 0.4260 (ttm170) REVERT: Ao 608 ILE cc_start: 0.5534 (mm) cc_final: 0.5181 (pt) REVERT: Ao 612 GLU cc_start: 0.4386 (mt-10) cc_final: 0.3569 (mp0) REVERT: Ao 632 GLU cc_start: 0.5710 (OUTLIER) cc_final: 0.4996 (pt0) REVERT: Ap 103 ASN cc_start: 0.8853 (OUTLIER) cc_final: 0.7986 (p0) REVERT: Ap 210 GLU cc_start: 0.8081 (tp30) cc_final: 0.7786 (tp30) REVERT: Ap 235 MET cc_start: 0.8483 (ptm) cc_final: 0.8091 (ptp) outliers start: 239 outliers final: 162 residues processed: 1042 average time/residue: 0.7353 time to fit residues: 1270.3914 Evaluate side-chains 1011 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 819 time to evaluate : 5.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BC residue 208 VAL Chi-restraints excluded: chain BC residue 255 VAL Chi-restraints excluded: chain BC residue 283 ILE Chi-restraints excluded: chain BC residue 285 LEU Chi-restraints excluded: chain BC residue 332 MET Chi-restraints excluded: chain BC residue 362 SER Chi-restraints excluded: chain BC residue 399 MET Chi-restraints excluded: chain BC residue 468 LYS Chi-restraints excluded: chain BC residue 486 TRP Chi-restraints excluded: chain BC residue 560 ASP Chi-restraints excluded: chain BC residue 606 LEU Chi-restraints excluded: chain BC residue 662 THR Chi-restraints excluded: chain BC residue 686 VAL Chi-restraints excluded: chain BC residue 722 SER Chi-restraints excluded: chain BT residue 61 VAL Chi-restraints excluded: chain AB residue 63 SER Chi-restraints excluded: chain AB residue 131 THR Chi-restraints excluded: chain AB residue 145 SER Chi-restraints excluded: chain AB residue 186 VAL Chi-restraints excluded: chain AB residue 206 VAL Chi-restraints excluded: chain AB residue 218 THR Chi-restraints excluded: chain AB residue 235 VAL Chi-restraints excluded: chain AC residue 43 ARG Chi-restraints excluded: chain AC residue 73 THR Chi-restraints excluded: chain AC residue 92 LEU Chi-restraints excluded: chain AC residue 115 ASN Chi-restraints excluded: chain AC residue 117 LEU Chi-restraints excluded: chain AC residue 157 THR Chi-restraints excluded: chain AE residue 105 GLU Chi-restraints excluded: chain AE residue 106 SER Chi-restraints excluded: chain AE residue 154 VAL Chi-restraints excluded: chain AE residue 216 ASP Chi-restraints excluded: chain AE residue 238 LYS Chi-restraints excluded: chain AE residue 239 ARG Chi-restraints excluded: chain AE residue 242 ARG Chi-restraints excluded: chain AE residue 258 ILE Chi-restraints excluded: chain AE residue 336 VAL Chi-restraints excluded: chain AE residue 370 VAL Chi-restraints excluded: chain AF residue 52 SER Chi-restraints excluded: chain AF residue 56 GLN Chi-restraints excluded: chain AF residue 65 LEU Chi-restraints excluded: chain AG residue 46 ILE Chi-restraints excluded: chain AG residue 64 TYR Chi-restraints excluded: chain AG residue 103 ASN Chi-restraints excluded: chain AG residue 219 VAL Chi-restraints excluded: chain AI residue 91 MET Chi-restraints excluded: chain AI residue 98 THR Chi-restraints excluded: chain AI residue 100 THR Chi-restraints excluded: chain AI residue 108 ILE Chi-restraints excluded: chain AI residue 153 THR Chi-restraints excluded: chain AI residue 155 LYS Chi-restraints excluded: chain AI residue 172 VAL Chi-restraints excluded: chain AI residue 206 LEU Chi-restraints excluded: chain AI residue 229 LEU Chi-restraints excluded: chain AI residue 237 THR Chi-restraints excluded: chain AI residue 259 GLU Chi-restraints excluded: chain AI residue 334 SER Chi-restraints excluded: chain AJ residue 64 THR Chi-restraints excluded: chain AJ residue 80 VAL Chi-restraints excluded: chain AJ residue 143 LEU Chi-restraints excluded: chain AJ residue 145 LEU Chi-restraints excluded: chain AJ residue 166 GLU Chi-restraints excluded: chain AJ residue 168 VAL Chi-restraints excluded: chain AK residue 68 ILE Chi-restraints excluded: chain AK residue 74 SER Chi-restraints excluded: chain AK residue 142 THR Chi-restraints excluded: chain AK residue 147 THR Chi-restraints excluded: chain AK residue 183 ILE Chi-restraints excluded: chain AL residue 32 THR Chi-restraints excluded: chain AL residue 52 THR Chi-restraints excluded: chain AL residue 55 ARG Chi-restraints excluded: chain AL residue 67 ILE Chi-restraints excluded: chain AL residue 77 ASN Chi-restraints excluded: chain AL residue 87 THR Chi-restraints excluded: chain AL residue 102 LEU Chi-restraints excluded: chain AL residue 117 ASP Chi-restraints excluded: chain AL residue 125 VAL Chi-restraints excluded: chain AN residue 66 ASP Chi-restraints excluded: chain AN residue 67 LEU Chi-restraints excluded: chain AN residue 120 LEU Chi-restraints excluded: chain AO residue 72 MET Chi-restraints excluded: chain AO residue 105 LEU Chi-restraints excluded: chain AO residue 167 MET Chi-restraints excluded: chain AO residue 218 VAL Chi-restraints excluded: chain AP residue 97 TYR Chi-restraints excluded: chain AP residue 117 GLU Chi-restraints excluded: chain AQ residue 7 SER Chi-restraints excluded: chain AQ residue 40 LEU Chi-restraints excluded: chain AQ residue 64 VAL Chi-restraints excluded: chain AQ residue 74 THR Chi-restraints excluded: chain AR residue 89 THR Chi-restraints excluded: chain AR residue 117 ILE Chi-restraints excluded: chain AR residue 131 LEU Chi-restraints excluded: chain AU residue 14 VAL Chi-restraints excluded: chain AU residue 19 VAL Chi-restraints excluded: chain AU residue 35 LEU Chi-restraints excluded: chain AU residue 38 ASP Chi-restraints excluded: chain AU residue 77 ARG Chi-restraints excluded: chain Aa residue 117 LEU Chi-restraints excluded: chain Aa residue 129 THR Chi-restraints excluded: chain Aa residue 169 ILE Chi-restraints excluded: chain Aa residue 183 ILE Chi-restraints excluded: chain Aa residue 197 ARG Chi-restraints excluded: chain Aa residue 202 THR Chi-restraints excluded: chain Aa residue 304 ASP Chi-restraints excluded: chain Aa residue 325 LEU Chi-restraints excluded: chain Aa residue 334 GLN Chi-restraints excluded: chain Ab residue 6 LEU Chi-restraints excluded: chain Ab residue 30 LEU Chi-restraints excluded: chain Ab residue 67 GLU Chi-restraints excluded: chain Ab residue 91 ASN Chi-restraints excluded: chain Ac residue 59 ASN Chi-restraints excluded: chain Ac residue 70 MET Chi-restraints excluded: chain Ac residue 95 ASN Chi-restraints excluded: chain Ac residue 96 LYS Chi-restraints excluded: chain Ac residue 106 LEU Chi-restraints excluded: chain Ad residue 44 THR Chi-restraints excluded: chain Ad residue 56 LEU Chi-restraints excluded: chain Ad residue 89 VAL Chi-restraints excluded: chain Ad residue 161 GLN Chi-restraints excluded: chain Ad residue 183 SER Chi-restraints excluded: chain Ad residue 192 THR Chi-restraints excluded: chain Ae residue 76 ASP Chi-restraints excluded: chain Ae residue 107 VAL Chi-restraints excluded: chain Ae residue 146 ASP Chi-restraints excluded: chain Ae residue 159 TYR Chi-restraints excluded: chain Ae residue 201 LEU Chi-restraints excluded: chain Ae residue 291 TRP Chi-restraints excluded: chain Ae residue 312 ASP Chi-restraints excluded: chain Ae residue 315 LEU Chi-restraints excluded: chain Ae residue 323 LEU Chi-restraints excluded: chain Ae residue 326 VAL Chi-restraints excluded: chain Ae residue 388 VAL Chi-restraints excluded: chain Ae residue 424 HIS Chi-restraints excluded: chain Af residue 85 LEU Chi-restraints excluded: chain Af residue 130 VAL Chi-restraints excluded: chain Af residue 155 LEU Chi-restraints excluded: chain Ag residue 54 ASP Chi-restraints excluded: chain Ag residue 71 LEU Chi-restraints excluded: chain Ag residue 150 LEU Chi-restraints excluded: chain Ag residue 172 TYR Chi-restraints excluded: chain Ag residue 194 ASN Chi-restraints excluded: chain Ag residue 255 PHE Chi-restraints excluded: chain Ag residue 264 VAL Chi-restraints excluded: chain Ag residue 265 ASN Chi-restraints excluded: chain Ag residue 296 VAL Chi-restraints excluded: chain Ag residue 309 VAL Chi-restraints excluded: chain Ah residue 294 ILE Chi-restraints excluded: chain Ah residue 307 ILE Chi-restraints excluded: chain Ah residue 310 GLU Chi-restraints excluded: chain Ah residue 387 ASN Chi-restraints excluded: chain Ai residue 12 SER Chi-restraints excluded: chain Ai residue 15 SER Chi-restraints excluded: chain Ai residue 18 LEU Chi-restraints excluded: chain Aj residue 6 VAL Chi-restraints excluded: chain Aj residue 84 SER Chi-restraints excluded: chain Aj residue 108 ASN Chi-restraints excluded: chain Aj residue 150 PHE Chi-restraints excluded: chain Aj residue 202 ASP Chi-restraints excluded: chain Ak residue 64 VAL Chi-restraints excluded: chain Ak residue 117 THR Chi-restraints excluded: chain Ak residue 130 ASP Chi-restraints excluded: chain Ak residue 159 VAL Chi-restraints excluded: chain Ak residue 165 ILE Chi-restraints excluded: chain Ak residue 298 VAL Chi-restraints excluded: chain Ak residue 309 ASN Chi-restraints excluded: chain Am residue 44 THR Chi-restraints excluded: chain Am residue 113 ASN Chi-restraints excluded: chain An residue 165 LYS Chi-restraints excluded: chain An residue 194 ILE Chi-restraints excluded: chain Ao residue 77 THR Chi-restraints excluded: chain Ao residue 96 ILE Chi-restraints excluded: chain Ao residue 260 HIS Chi-restraints excluded: chain Ao residue 262 TYR Chi-restraints excluded: chain Ao residue 263 CYS Chi-restraints excluded: chain Ao residue 269 MET Chi-restraints excluded: chain Ao residue 279 LEU Chi-restraints excluded: chain Ao residue 326 MET Chi-restraints excluded: chain Ao residue 338 PHE Chi-restraints excluded: chain Ao residue 447 ASN Chi-restraints excluded: chain Ao residue 454 ASP Chi-restraints excluded: chain Ao residue 510 ASP Chi-restraints excluded: chain Ao residue 521 GLU Chi-restraints excluded: chain Ao residue 615 ASN Chi-restraints excluded: chain Ao residue 632 GLU Chi-restraints excluded: chain Ao residue 652 VAL Chi-restraints excluded: chain Ao residue 659 THR Chi-restraints excluded: chain Ap residue 53 ASP Chi-restraints excluded: chain Ap residue 103 ASN Chi-restraints excluded: chain Ap residue 108 CYS Chi-restraints excluded: chain Ap residue 154 ILE Chi-restraints excluded: chain Ap residue 193 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 719 random chunks: chunk 670 optimal weight: 20.0000 chunk 78 optimal weight: 7.9990 chunk 396 optimal weight: 20.0000 chunk 508 optimal weight: 8.9990 chunk 393 optimal weight: 8.9990 chunk 585 optimal weight: 5.9990 chunk 388 optimal weight: 4.9990 chunk 692 optimal weight: 5.9990 chunk 433 optimal weight: 7.9990 chunk 422 optimal weight: 10.0000 chunk 319 optimal weight: 2.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BC 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BC 457 GLN AB 152 HIS AB 265 GLN ** AC 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AE 175 GLN AE 288 HIS ** AG 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AI 221 GLN ** AI 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AN 119 GLN AQ 9 HIS ** AU 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 126 GLN Ad 172 ASN Ae 243 ASN ** Ae 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 357 GLN ** Ae 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 418 GLN Af 104 GLN ** Ag 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 194 ASN ** Ag 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 45 HIS Aj 88 GLN Ak 112 ASN ** Am 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 58 GLN Am 113 ASN ** Ao 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.117 76793 Z= 0.508 Angle : 0.730 10.586 108765 Z= 0.369 Chirality : 0.045 0.252 12818 Planarity : 0.006 0.093 10078 Dihedral : 20.404 178.695 22677 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.19 % Favored : 95.74 % Rotamer: Outliers : 5.25 % Allowed : 19.71 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.31 % 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: 0.21 (0.10), residues: 6199 helix: 1.10 (0.10), residues: 2796 sheet: -0.41 (0.20), residues: 649 loop : -0.67 (0.12), residues: 2754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRPAe 238 HIS 0.015 0.002 HISAE 317 PHE 0.023 0.003 PHEAo 617 TYR 0.032 0.003 TYRAc 163 ARG 0.013 0.001 ARGAN 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1090 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 283 poor density : 807 time to evaluate : 5.350 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: BC 197 LEU cc_start: 0.8891 (mt) cc_final: 0.8660 (tp) REVERT: BC 285 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7424 (mt) REVERT: BC 308 ASP cc_start: 0.7812 (m-30) cc_final: 0.7477 (t70) REVERT: BC 464 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7910 (mt-10) REVERT: BC 488 LYS cc_start: 0.7303 (mttt) cc_final: 0.6942 (tptt) REVERT: AB 146 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8127 (tpt-90) REVERT: AC 41 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.6209 (mtm-85) REVERT: AC 43 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8364 (mmt180) REVERT: AC 122 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.9018 (mp) REVERT: AC 144 SER cc_start: 0.9489 (m) cc_final: 0.8934 (m) REVERT: AE 157 ILE cc_start: 0.8458 (mp) cc_final: 0.8084 (mt) REVERT: AE 178 GLU cc_start: 0.8117 (tt0) cc_final: 0.7493 (tp30) REVERT: AE 321 MET cc_start: 0.9085 (mtp) cc_final: 0.8707 (mtp) REVERT: AI 86 ARG cc_start: 0.8735 (mmm-85) cc_final: 0.8503 (mtp-110) REVERT: AI 91 MET cc_start: 0.7786 (OUTLIER) cc_final: 0.7303 (mtm) REVERT: AI 155 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8567 (pttt) REVERT: AI 268 MET cc_start: 0.8653 (mmt) cc_final: 0.7803 (ppp) REVERT: AJ 64 THR cc_start: 0.7525 (OUTLIER) cc_final: 0.7194 (p) REVERT: AJ 145 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8148 (mt) REVERT: AL 55 ARG cc_start: 0.9324 (OUTLIER) cc_final: 0.9094 (mtt-85) REVERT: AL 118 LEU cc_start: 0.9300 (mt) cc_final: 0.9071 (mt) REVERT: AO 72 MET cc_start: 0.9197 (OUTLIER) cc_final: 0.8847 (tpp) REVERT: AO 167 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.8465 (mtt) REVERT: AO 198 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.8543 (mtt180) REVERT: AO 217 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8303 (tp30) REVERT: AP 120 LEU cc_start: 0.8776 (tp) cc_final: 0.8431 (mt) REVERT: AQ 45 LYS cc_start: 0.8726 (ttmt) cc_final: 0.8311 (tttm) REVERT: AQ 107 GLU cc_start: 0.8617 (tp30) cc_final: 0.8253 (tp30) REVERT: AR 83 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.8768 (tt0) REVERT: AU 10 ARG cc_start: 0.9264 (OUTLIER) cc_final: 0.8905 (mtm180) REVERT: AU 23 TYR cc_start: 0.9054 (t80) cc_final: 0.8520 (t80) REVERT: AU 77 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8056 (mtp-110) REVERT: Aa 183 ILE cc_start: 0.9201 (OUTLIER) cc_final: 0.8923 (pt) REVERT: Aa 334 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7909 (pm20) REVERT: Ac 106 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8768 (pp) REVERT: Ac 162 LYS cc_start: 0.9211 (OUTLIER) cc_final: 0.8785 (ttpt) REVERT: Ad 98 ASP cc_start: 0.8447 (m-30) cc_final: 0.8107 (m-30) REVERT: Ad 161 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8499 (tm-30) REVERT: Ae 152 TRP cc_start: 0.7962 (t60) cc_final: 0.7325 (t60) REVERT: Ae 159 TYR cc_start: 0.7182 (OUTLIER) cc_final: 0.5595 (t80) REVERT: Ae 209 MET cc_start: 0.7930 (mmm) cc_final: 0.7650 (mmm) REVERT: Ae 211 GLU cc_start: 0.6476 (mt-10) cc_final: 0.6050 (tm-30) REVERT: Ae 357 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.7282 (tm-30) REVERT: Ae 389 GLU cc_start: 0.6699 (OUTLIER) cc_final: 0.6496 (mt-10) REVERT: Af 111 ASP cc_start: 0.8119 (t0) cc_final: 0.7667 (t0) REVERT: Af 155 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8451 (tt) REVERT: Ag 150 LEU cc_start: 0.6881 (OUTLIER) cc_final: 0.6215 (tm) REVERT: Ag 172 TYR cc_start: 0.6561 (OUTLIER) cc_final: 0.4698 (t80) REVERT: Ag 182 GLU cc_start: 0.7457 (mp0) cc_final: 0.7243 (mp0) REVERT: Ag 252 LEU cc_start: 0.6780 (OUTLIER) cc_final: 0.6371 (mt) REVERT: Ah 285 PRO cc_start: 0.8206 (Cg_exo) cc_final: 0.7818 (Cg_endo) REVERT: Ah 294 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8764 (mp) REVERT: Ah 373 ASN cc_start: 0.8121 (t0) cc_final: 0.7468 (t0) REVERT: Ai 52 TYR cc_start: 0.9011 (m-80) cc_final: 0.8638 (m-80) REVERT: Ai 73 ASP cc_start: 0.8017 (t0) cc_final: 0.7356 (t70) REVERT: Ai 77 ASP cc_start: 0.9138 (m-30) cc_final: 0.8759 (m-30) REVERT: Ai 80 ASP cc_start: 0.8022 (m-30) cc_final: 0.7702 (m-30) REVERT: Ai 81 GLU cc_start: 0.8707 (tm-30) cc_final: 0.8433 (tm-30) REVERT: Aj 150 PHE cc_start: 0.7554 (OUTLIER) cc_final: 0.6397 (t80) REVERT: Ak 95 ARG cc_start: 0.8868 (mmt90) cc_final: 0.8097 (mtm-85) REVERT: Ak 236 TRP cc_start: 0.7242 (m-10) cc_final: 0.7025 (m-10) REVERT: Ak 241 TRP cc_start: 0.8713 (p-90) cc_final: 0.8242 (p-90) REVERT: Ak 294 TYR cc_start: 0.7231 (t80) cc_final: 0.6994 (t80) REVERT: Am 53 MET cc_start: 0.8310 (mmt) cc_final: 0.7797 (mmt) REVERT: Am 60 GLU cc_start: 0.8519 (tm-30) cc_final: 0.8313 (tm-30) REVERT: Am 81 GLU cc_start: 0.8056 (tp30) cc_final: 0.7826 (tm-30) REVERT: An 151 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7642 (ttt-90) REVERT: An 165 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8044 (ttmm) REVERT: Ao 91 ASP cc_start: 0.8594 (t0) cc_final: 0.8360 (t0) REVERT: Ao 262 TYR cc_start: 0.2154 (OUTLIER) cc_final: 0.1153 (p90) REVERT: Ao 285 LEU cc_start: 0.5588 (OUTLIER) cc_final: 0.5148 (tp) REVERT: Ao 326 MET cc_start: 0.4129 (OUTLIER) cc_final: 0.3441 (tpp) REVERT: Ao 411 ARG cc_start: 0.5317 (ptt-90) cc_final: 0.4597 (mtm110) REVERT: Ao 433 GLU cc_start: 0.5689 (mm-30) cc_final: 0.5293 (tp30) REVERT: Ao 439 HIS cc_start: 0.4874 (t70) cc_final: 0.4601 (t70) REVERT: Ao 441 LEU cc_start: 0.7630 (tp) cc_final: 0.7393 (mt) REVERT: Ao 447 ASN cc_start: 0.6313 (OUTLIER) cc_final: 0.5250 (p0) REVERT: Ao 485 ILE cc_start: 0.7106 (mm) cc_final: 0.6769 (mm) REVERT: Ao 588 ARG cc_start: 0.0868 (OUTLIER) cc_final: 0.0439 (mtt90) REVERT: Ao 608 ILE cc_start: 0.5648 (mm) cc_final: 0.5274 (pt) REVERT: Ao 661 GLU cc_start: 0.3707 (OUTLIER) cc_final: 0.3274 (mm-30) REVERT: Ap 54 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7324 (pt0) REVERT: Ap 103 ASN cc_start: 0.9150 (OUTLIER) cc_final: 0.8240 (p0) REVERT: Ap 169 GLN cc_start: 0.9020 (mt0) cc_final: 0.8660 (mt0) REVERT: Ap 235 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8335 (ptp) outliers start: 283 outliers final: 201 residues processed: 1014 average time/residue: 0.7436 time to fit residues: 1248.2118 Evaluate side-chains 1011 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 769 time to evaluate : 5.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BC residue 202 LYS Chi-restraints excluded: chain BC residue 208 VAL Chi-restraints excluded: chain BC residue 230 ILE Chi-restraints excluded: chain BC residue 255 VAL Chi-restraints excluded: chain BC residue 283 ILE Chi-restraints excluded: chain BC residue 285 LEU Chi-restraints excluded: chain BC residue 332 MET Chi-restraints excluded: chain BC residue 362 SER Chi-restraints excluded: chain BC residue 399 MET Chi-restraints excluded: chain BC residue 468 LYS Chi-restraints excluded: chain BC residue 486 TRP Chi-restraints excluded: chain BC residue 560 ASP Chi-restraints excluded: chain BC residue 599 ILE Chi-restraints excluded: chain BC residue 606 LEU Chi-restraints excluded: chain BC residue 662 THR Chi-restraints excluded: chain BC residue 686 VAL Chi-restraints excluded: chain BC residue 690 MET Chi-restraints excluded: chain BC residue 720 LYS Chi-restraints excluded: chain BC residue 722 SER Chi-restraints excluded: chain BT residue 61 VAL Chi-restraints excluded: chain AB residue 63 SER Chi-restraints excluded: chain AB residue 131 THR Chi-restraints excluded: chain AB residue 145 SER Chi-restraints excluded: chain AB residue 146 ARG Chi-restraints excluded: chain AB residue 186 VAL Chi-restraints excluded: chain AB residue 206 VAL Chi-restraints excluded: chain AB residue 218 THR Chi-restraints excluded: chain AB residue 235 VAL Chi-restraints excluded: chain AB residue 270 TYR Chi-restraints excluded: chain AC residue 41 ARG Chi-restraints excluded: chain AC residue 43 ARG Chi-restraints excluded: chain AC residue 44 VAL Chi-restraints excluded: chain AC residue 73 THR Chi-restraints excluded: chain AC residue 92 LEU Chi-restraints excluded: chain AC residue 115 ASN Chi-restraints excluded: chain AC residue 117 LEU Chi-restraints excluded: chain AC residue 122 LEU Chi-restraints excluded: chain AC residue 157 THR Chi-restraints excluded: chain AE residue 105 GLU Chi-restraints excluded: chain AE residue 106 SER Chi-restraints excluded: chain AE residue 154 VAL Chi-restraints excluded: chain AE residue 171 ASP Chi-restraints excluded: chain AE residue 202 SER Chi-restraints excluded: chain AE residue 216 ASP Chi-restraints excluded: chain AE residue 238 LYS Chi-restraints excluded: chain AE residue 239 ARG Chi-restraints excluded: chain AE residue 244 LEU Chi-restraints excluded: chain AE residue 258 ILE Chi-restraints excluded: chain AE residue 336 VAL Chi-restraints excluded: chain AE residue 337 SER Chi-restraints excluded: chain AE residue 407 ASP Chi-restraints excluded: chain AF residue 59 SER Chi-restraints excluded: chain AF residue 103 LYS Chi-restraints excluded: chain AG residue 46 ILE Chi-restraints excluded: chain AG residue 64 TYR Chi-restraints excluded: chain AG residue 80 THR Chi-restraints excluded: chain AG residue 103 ASN Chi-restraints excluded: chain AG residue 109 SER Chi-restraints excluded: chain AG residue 118 VAL Chi-restraints excluded: chain AG residue 167 PHE Chi-restraints excluded: chain AG residue 206 SER Chi-restraints excluded: chain AG residue 219 VAL Chi-restraints excluded: chain AI residue 91 MET Chi-restraints excluded: chain AI residue 98 THR Chi-restraints excluded: chain AI residue 100 THR Chi-restraints excluded: chain AI residue 108 ILE Chi-restraints excluded: chain AI residue 153 THR Chi-restraints excluded: chain AI residue 155 LYS Chi-restraints excluded: chain AI residue 172 VAL Chi-restraints excluded: chain AI residue 206 LEU Chi-restraints excluded: chain AI residue 229 LEU Chi-restraints excluded: chain AI residue 237 THR Chi-restraints excluded: chain AI residue 259 GLU Chi-restraints excluded: chain AI residue 299 VAL Chi-restraints excluded: chain AI residue 322 ASP Chi-restraints excluded: chain AI residue 329 MET Chi-restraints excluded: chain AI residue 334 SER Chi-restraints excluded: chain AI residue 338 ARG Chi-restraints excluded: chain AI residue 393 THR Chi-restraints excluded: chain AJ residue 64 THR Chi-restraints excluded: chain AJ residue 80 VAL Chi-restraints excluded: chain AJ residue 143 LEU Chi-restraints excluded: chain AJ residue 145 LEU Chi-restraints excluded: chain AJ residue 166 GLU Chi-restraints excluded: chain AJ residue 168 VAL Chi-restraints excluded: chain AK residue 68 ILE Chi-restraints excluded: chain AK residue 74 SER Chi-restraints excluded: chain AK residue 142 THR Chi-restraints excluded: chain AK residue 147 THR Chi-restraints excluded: chain AK residue 183 ILE Chi-restraints excluded: chain AL residue 32 THR Chi-restraints excluded: chain AL residue 52 THR Chi-restraints excluded: chain AL residue 55 ARG Chi-restraints excluded: chain AL residue 67 ILE Chi-restraints excluded: chain AL residue 77 ASN Chi-restraints excluded: chain AL residue 87 THR Chi-restraints excluded: chain AL residue 102 LEU Chi-restraints excluded: chain AL residue 117 ASP Chi-restraints excluded: chain AN residue 30 VAL Chi-restraints excluded: chain AN residue 66 ASP Chi-restraints excluded: chain AN residue 67 LEU Chi-restraints excluded: chain AN residue 85 VAL Chi-restraints excluded: chain AN residue 87 ILE Chi-restraints excluded: chain AN residue 120 LEU Chi-restraints excluded: chain AN residue 127 MET Chi-restraints excluded: chain AO residue 72 MET Chi-restraints excluded: chain AO residue 105 LEU Chi-restraints excluded: chain AO residue 107 ILE Chi-restraints excluded: chain AO residue 124 SER Chi-restraints excluded: chain AO residue 167 MET Chi-restraints excluded: chain AO residue 198 ARG Chi-restraints excluded: chain AO residue 218 VAL Chi-restraints excluded: chain AP residue 71 ASP Chi-restraints excluded: chain AP residue 97 TYR Chi-restraints excluded: chain AP residue 117 GLU Chi-restraints excluded: chain AQ residue 7 SER Chi-restraints excluded: chain AQ residue 30 VAL Chi-restraints excluded: chain AQ residue 40 LEU Chi-restraints excluded: chain AQ residue 64 VAL Chi-restraints excluded: chain AQ residue 74 THR Chi-restraints excluded: chain AQ residue 80 GLU Chi-restraints excluded: chain AR residue 69 CYS Chi-restraints excluded: chain AR residue 83 GLN Chi-restraints excluded: chain AR residue 89 THR Chi-restraints excluded: chain AR residue 117 ILE Chi-restraints excluded: chain AR residue 131 LEU Chi-restraints excluded: chain AU residue 10 ARG Chi-restraints excluded: chain AU residue 14 VAL Chi-restraints excluded: chain AU residue 19 VAL Chi-restraints excluded: chain AU residue 35 LEU Chi-restraints excluded: chain AU residue 38 ASP Chi-restraints excluded: chain AU residue 77 ARG Chi-restraints excluded: chain Aa residue 129 THR Chi-restraints excluded: chain Aa residue 169 ILE Chi-restraints excluded: chain Aa residue 183 ILE Chi-restraints excluded: chain Aa residue 197 ARG Chi-restraints excluded: chain Aa residue 202 THR Chi-restraints excluded: chain Aa residue 304 ASP Chi-restraints excluded: chain Aa residue 325 LEU Chi-restraints excluded: chain Aa residue 334 GLN Chi-restraints excluded: chain Ab residue 6 LEU Chi-restraints excluded: chain Ab residue 30 LEU Chi-restraints excluded: chain Ab residue 91 ASN Chi-restraints excluded: chain Ac residue 59 ASN Chi-restraints excluded: chain Ac residue 70 MET Chi-restraints excluded: chain Ac residue 95 ASN Chi-restraints excluded: chain Ac residue 106 LEU Chi-restraints excluded: chain Ac residue 162 LYS Chi-restraints excluded: chain Ad residue 44 THR Chi-restraints excluded: chain Ad residue 56 LEU Chi-restraints excluded: chain Ad residue 89 VAL Chi-restraints excluded: chain Ad residue 161 GLN Chi-restraints excluded: chain Ad residue 166 THR Chi-restraints excluded: chain Ad residue 183 SER Chi-restraints excluded: chain Ad residue 192 THR Chi-restraints excluded: chain Ae residue 76 ASP Chi-restraints excluded: chain Ae residue 107 VAL Chi-restraints excluded: chain Ae residue 159 TYR Chi-restraints excluded: chain Ae residue 169 LEU Chi-restraints excluded: chain Ae residue 192 ILE Chi-restraints excluded: chain Ae residue 197 TYR Chi-restraints excluded: chain Ae residue 229 CYS Chi-restraints excluded: chain Ae residue 253 LEU Chi-restraints excluded: chain Ae residue 312 ASP Chi-restraints excluded: chain Ae residue 323 LEU Chi-restraints excluded: chain Ae residue 326 VAL Chi-restraints excluded: chain Ae residue 331 THR Chi-restraints excluded: chain Ae residue 357 GLN Chi-restraints excluded: chain Ae residue 388 VAL Chi-restraints excluded: chain Ae residue 389 GLU Chi-restraints excluded: chain Ae residue 424 HIS Chi-restraints excluded: chain Af residue 85 LEU Chi-restraints excluded: chain Af residue 130 VAL Chi-restraints excluded: chain Af residue 155 LEU Chi-restraints excluded: chain Af residue 159 THR Chi-restraints excluded: chain Af residue 167 ASP Chi-restraints excluded: chain Ag residue 54 ASP Chi-restraints excluded: chain Ag residue 71 LEU Chi-restraints excluded: chain Ag residue 135 LEU Chi-restraints excluded: chain Ag residue 150 LEU Chi-restraints excluded: chain Ag residue 172 TYR Chi-restraints excluded: chain Ag residue 252 LEU Chi-restraints excluded: chain Ag residue 262 ASP Chi-restraints excluded: chain Ag residue 264 VAL Chi-restraints excluded: chain Ag residue 265 ASN Chi-restraints excluded: chain Ag residue 296 VAL Chi-restraints excluded: chain Ah residue 294 ILE Chi-restraints excluded: chain Ah residue 307 ILE Chi-restraints excluded: chain Ah residue 310 GLU Chi-restraints excluded: chain Ah residue 387 ASN Chi-restraints excluded: chain Ai residue 12 SER Chi-restraints excluded: chain Ai residue 15 SER Chi-restraints excluded: chain Aj residue 6 VAL Chi-restraints excluded: chain Aj residue 18 VAL Chi-restraints excluded: chain Aj residue 26 GLU Chi-restraints excluded: chain Aj residue 84 SER Chi-restraints excluded: chain Aj residue 98 THR Chi-restraints excluded: chain Aj residue 108 ASN Chi-restraints excluded: chain Aj residue 117 ILE Chi-restraints excluded: chain Aj residue 150 PHE Chi-restraints excluded: chain Aj residue 162 LEU Chi-restraints excluded: chain Aj residue 202 ASP Chi-restraints excluded: chain Ak residue 64 VAL Chi-restraints excluded: chain Ak residue 117 THR Chi-restraints excluded: chain Ak residue 130 ASP Chi-restraints excluded: chain Ak residue 154 ASP Chi-restraints excluded: chain Ak residue 159 VAL Chi-restraints excluded: chain Ak residue 165 ILE Chi-restraints excluded: chain Ak residue 187 HIS Chi-restraints excluded: chain Ak residue 212 ASP Chi-restraints excluded: chain Ak residue 298 VAL Chi-restraints excluded: chain Ak residue 309 ASN Chi-restraints excluded: chain Am residue 44 THR Chi-restraints excluded: chain Am residue 68 LYS Chi-restraints excluded: chain An residue 151 ARG Chi-restraints excluded: chain An residue 165 LYS Chi-restraints excluded: chain An residue 194 ILE Chi-restraints excluded: chain Ao residue 77 THR Chi-restraints excluded: chain Ao residue 96 ILE Chi-restraints excluded: chain Ao residue 260 HIS Chi-restraints excluded: chain Ao residue 262 TYR Chi-restraints excluded: chain Ao residue 263 CYS Chi-restraints excluded: chain Ao residue 279 LEU Chi-restraints excluded: chain Ao residue 285 LEU Chi-restraints excluded: chain Ao residue 304 THR Chi-restraints excluded: chain Ao residue 326 MET Chi-restraints excluded: chain Ao residue 409 SER Chi-restraints excluded: chain Ao residue 447 ASN Chi-restraints excluded: chain Ao residue 454 ASP Chi-restraints excluded: chain Ao residue 510 ASP Chi-restraints excluded: chain Ao residue 521 GLU Chi-restraints excluded: chain Ao residue 588 ARG Chi-restraints excluded: chain Ao residue 615 ASN Chi-restraints excluded: chain Ao residue 632 GLU Chi-restraints excluded: chain Ao residue 659 THR Chi-restraints excluded: chain Ao residue 661 GLU Chi-restraints excluded: chain Ap residue 54 GLU Chi-restraints excluded: chain Ap residue 103 ASN Chi-restraints excluded: chain Ap residue 154 ILE Chi-restraints excluded: chain Ap residue 187 THR Chi-restraints excluded: chain Ap residue 193 LEU Chi-restraints excluded: chain Ap residue 235 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 719 random chunks: chunk 428 optimal weight: 1.9990 chunk 276 optimal weight: 10.0000 chunk 413 optimal weight: 0.9990 chunk 208 optimal weight: 1.9990 chunk 136 optimal weight: 6.9990 chunk 134 optimal weight: 8.9990 chunk 440 optimal weight: 0.9990 chunk 472 optimal weight: 7.9990 chunk 342 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 544 optimal weight: 0.8980 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BC 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BC 457 GLN AB 152 HIS AB 265 GLN ** AE 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AN 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ac 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 243 ASN ** Ae 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 104 GLN ** Ag 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 88 GLN Ak 112 ASN Am 24 ASN Am 58 GLN ** Ao 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 76793 Z= 0.188 Angle : 0.578 10.471 108765 Z= 0.292 Chirality : 0.037 0.225 12818 Planarity : 0.004 0.084 10078 Dihedral : 20.294 179.184 22666 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.58 % Favored : 96.35 % Rotamer: Outliers : 3.82 % Allowed : 21.56 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.31 % 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: 0.62 (0.11), residues: 6199 helix: 1.48 (0.10), residues: 2798 sheet: -0.20 (0.20), residues: 649 loop : -0.50 (0.12), residues: 2752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRPAe 238 HIS 0.004 0.001 HISAJ 125 PHE 0.024 0.001 PHEAo 617 TYR 0.036 0.001 TYRAc 163 ARG 0.008 0.000 ARGAO 216 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1041 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 835 time to evaluate : 5.454 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: BC 197 LEU cc_start: 0.8782 (mt) cc_final: 0.8579 (tp) REVERT: BC 285 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.7018 (mt) REVERT: BC 308 ASP cc_start: 0.7791 (m-30) cc_final: 0.7447 (t0) REVERT: BC 464 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7823 (mt-10) REVERT: BC 465 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8609 (pt0) REVERT: BC 488 LYS cc_start: 0.7349 (mttt) cc_final: 0.6977 (tptt) REVERT: BC 589 LYS cc_start: 0.8720 (mttm) cc_final: 0.8359 (mttp) REVERT: AC 43 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.8133 (mmt180) REVERT: AC 144 SER cc_start: 0.9464 (m) cc_final: 0.8936 (m) REVERT: AE 157 ILE cc_start: 0.8462 (mp) cc_final: 0.8078 (mt) REVERT: AE 178 GLU cc_start: 0.8409 (tt0) cc_final: 0.7431 (tp30) REVERT: AE 179 TRP cc_start: 0.7441 (m-10) cc_final: 0.6927 (m-10) REVERT: AE 225 VAL cc_start: 0.9328 (p) cc_final: 0.9059 (t) REVERT: AE 321 MET cc_start: 0.9015 (mtp) cc_final: 0.8647 (mtp) REVERT: AF 76 GLU cc_start: 0.8268 (pm20) cc_final: 0.7959 (pm20) REVERT: AI 268 MET cc_start: 0.8533 (mmt) cc_final: 0.7565 (ppp) REVERT: AI 272 ARG cc_start: 0.8127 (tpp80) cc_final: 0.7838 (tpp-160) REVERT: AJ 64 THR cc_start: 0.7463 (OUTLIER) cc_final: 0.7243 (p) REVERT: AL 55 ARG cc_start: 0.9197 (OUTLIER) cc_final: 0.8864 (mtt-85) REVERT: AL 118 LEU cc_start: 0.9261 (mt) cc_final: 0.9038 (mt) REVERT: AN 66 ASP cc_start: 0.8752 (OUTLIER) cc_final: 0.8192 (t0) REVERT: AO 72 MET cc_start: 0.9087 (OUTLIER) cc_final: 0.8775 (tpp) REVERT: AO 167 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8391 (mtt) REVERT: AO 198 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.8204 (mtt180) REVERT: AO 217 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8291 (tp30) REVERT: AO 226 ARG cc_start: 0.5401 (ttp80) cc_final: 0.5159 (ptm-80) REVERT: AP 120 LEU cc_start: 0.8727 (tp) cc_final: 0.8420 (mt) REVERT: AQ 5 ARG cc_start: 0.6708 (mmm-85) cc_final: 0.6500 (mmm-85) REVERT: AQ 45 LYS cc_start: 0.8673 (ttmt) cc_final: 0.8273 (tttm) REVERT: AU 10 ARG cc_start: 0.9200 (OUTLIER) cc_final: 0.8790 (mtm180) REVERT: AU 23 TYR cc_start: 0.8894 (t80) cc_final: 0.8590 (t80) REVERT: AU 77 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7935 (mtp-110) REVERT: Aa 183 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8822 (pt) REVERT: Aa 197 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.7678 (mmt90) REVERT: Aa 222 GLU cc_start: 0.8471 (mp0) cc_final: 0.8178 (mp0) REVERT: Aa 334 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7829 (pm20) REVERT: Ac 106 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8691 (pp) REVERT: Ad 161 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8466 (tm-30) REVERT: Ae 97 MET cc_start: 0.5416 (mtm) cc_final: 0.5192 (mtm) REVERT: Ae 152 TRP cc_start: 0.8019 (t60) cc_final: 0.7502 (t60) REVERT: Ae 159 TYR cc_start: 0.7185 (OUTLIER) cc_final: 0.5752 (t80) REVERT: Ae 209 MET cc_start: 0.7930 (mmm) cc_final: 0.7665 (mmm) REVERT: Ae 211 GLU cc_start: 0.6506 (mt-10) cc_final: 0.5943 (tm-30) REVERT: Ae 287 MET cc_start: 0.6424 (mtt) cc_final: 0.6131 (mtm) REVERT: Ae 325 ARG cc_start: 0.6965 (OUTLIER) cc_final: 0.6681 (mmm160) REVERT: Af 111 ASP cc_start: 0.7936 (t0) cc_final: 0.7489 (t0) REVERT: Af 155 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8325 (tt) REVERT: Ag 150 LEU cc_start: 0.6897 (OUTLIER) cc_final: 0.6163 (tm) REVERT: Ag 172 TYR cc_start: 0.6372 (OUTLIER) cc_final: 0.4515 (t80) REVERT: Ag 188 LYS cc_start: 0.8405 (mtmt) cc_final: 0.8165 (pttt) REVERT: Ag 252 LEU cc_start: 0.6725 (OUTLIER) cc_final: 0.6349 (mt) REVERT: Ag 336 LEU cc_start: 0.7511 (tt) cc_final: 0.6716 (tp) REVERT: Ah 285 PRO cc_start: 0.8142 (Cg_exo) cc_final: 0.7787 (Cg_endo) REVERT: Ah 294 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8590 (mp) REVERT: Ah 373 ASN cc_start: 0.7996 (t0) cc_final: 0.7383 (t0) REVERT: Ai 6 GLU cc_start: 0.8547 (tp30) cc_final: 0.8330 (tp30) REVERT: Ai 29 LYS cc_start: 0.9061 (tttt) cc_final: 0.8768 (mtmt) REVERT: Ai 52 TYR cc_start: 0.8918 (m-80) cc_final: 0.8576 (m-80) REVERT: Ai 73 ASP cc_start: 0.7901 (t0) cc_final: 0.7276 (t70) REVERT: Ai 77 ASP cc_start: 0.9075 (m-30) cc_final: 0.8739 (m-30) REVERT: Ai 81 GLU cc_start: 0.8663 (tm-30) cc_final: 0.8371 (tm-30) REVERT: Ai 87 LYS cc_start: 0.8857 (mtpp) cc_final: 0.8599 (mtmt) REVERT: Aj 150 PHE cc_start: 0.7398 (OUTLIER) cc_final: 0.6364 (t80) REVERT: Ak 95 ARG cc_start: 0.8895 (mmt90) cc_final: 0.8178 (mtt90) REVERT: Ak 143 GLU cc_start: 0.7928 (mp0) cc_final: 0.7708 (mp0) REVERT: Ak 241 TRP cc_start: 0.8714 (p-90) cc_final: 0.8360 (p-90) REVERT: Ak 255 TRP cc_start: 0.7790 (t60) cc_final: 0.7554 (t60) REVERT: Ak 289 LYS cc_start: 0.8148 (ptmm) cc_final: 0.7902 (pptt) REVERT: Ak 309 ASN cc_start: 0.8382 (OUTLIER) cc_final: 0.8125 (p0) REVERT: Am 53 MET cc_start: 0.8253 (mmt) cc_final: 0.7973 (mmt) REVERT: Am 81 GLU cc_start: 0.8140 (tp30) cc_final: 0.7879 (tm-30) REVERT: An 165 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.7991 (ttmm) REVERT: Ao 91 ASP cc_start: 0.8552 (t0) cc_final: 0.8351 (t0) REVERT: Ao 285 LEU cc_start: 0.5620 (OUTLIER) cc_final: 0.5260 (tp) REVERT: Ao 326 MET cc_start: 0.4451 (OUTLIER) cc_final: 0.3577 (mmt) REVERT: Ao 411 ARG cc_start: 0.5270 (ptt-90) cc_final: 0.4572 (mtm110) REVERT: Ao 439 HIS cc_start: 0.4853 (t70) cc_final: 0.4612 (t70) REVERT: Ao 441 LEU cc_start: 0.7565 (tp) cc_final: 0.7338 (mt) REVERT: Ao 447 ASN cc_start: 0.6015 (OUTLIER) cc_final: 0.5027 (p0) REVERT: Ao 471 MET cc_start: 0.6409 (tpp) cc_final: 0.5919 (tpp) REVERT: Ao 485 ILE cc_start: 0.7007 (mm) cc_final: 0.6673 (mm) REVERT: Ao 540 ARG cc_start: 0.4112 (mmt90) cc_final: 0.2935 (mtm-85) REVERT: Ao 608 ILE cc_start: 0.5716 (mm) cc_final: 0.5366 (pt) REVERT: Ao 612 GLU cc_start: 0.3705 (pm20) cc_final: 0.2170 (mp0) REVERT: Ao 632 GLU cc_start: 0.5228 (OUTLIER) cc_final: 0.4552 (pt0) REVERT: Ap 54 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7184 (pt0) REVERT: Ap 103 ASN cc_start: 0.8890 (OUTLIER) cc_final: 0.8256 (p0) REVERT: Ap 169 GLN cc_start: 0.8879 (mt0) cc_final: 0.8577 (mt0) REVERT: Ap 235 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8394 (ptp) outliers start: 206 outliers final: 145 residues processed: 984 average time/residue: 0.7411 time to fit residues: 1200.6507 Evaluate side-chains 981 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 804 time to evaluate : 5.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BC residue 208 VAL Chi-restraints excluded: chain BC residue 230 ILE Chi-restraints excluded: chain BC residue 255 VAL Chi-restraints excluded: chain BC residue 283 ILE Chi-restraints excluded: chain BC residue 285 LEU Chi-restraints excluded: chain BC residue 332 MET Chi-restraints excluded: chain BC residue 362 SER Chi-restraints excluded: chain BC residue 399 MET Chi-restraints excluded: chain BC residue 468 LYS Chi-restraints excluded: chain BC residue 486 TRP Chi-restraints excluded: chain BC residue 560 ASP Chi-restraints excluded: chain BC residue 606 LEU Chi-restraints excluded: chain BC residue 662 THR Chi-restraints excluded: chain BC residue 686 VAL Chi-restraints excluded: chain BC residue 690 MET Chi-restraints excluded: chain BT residue 61 VAL Chi-restraints excluded: chain AB residue 145 SER Chi-restraints excluded: chain AB residue 186 VAL Chi-restraints excluded: chain AB residue 206 VAL Chi-restraints excluded: chain AB residue 218 THR Chi-restraints excluded: chain AB residue 235 VAL Chi-restraints excluded: chain AC residue 43 ARG Chi-restraints excluded: chain AC residue 44 VAL Chi-restraints excluded: chain AC residue 71 LEU Chi-restraints excluded: chain AC residue 73 THR Chi-restraints excluded: chain AC residue 92 LEU Chi-restraints excluded: chain AC residue 115 ASN Chi-restraints excluded: chain AC residue 117 LEU Chi-restraints excluded: chain AC residue 157 THR Chi-restraints excluded: chain AE residue 105 GLU Chi-restraints excluded: chain AE residue 106 SER Chi-restraints excluded: chain AE residue 154 VAL Chi-restraints excluded: chain AE residue 171 ASP Chi-restraints excluded: chain AE residue 216 ASP Chi-restraints excluded: chain AE residue 239 ARG Chi-restraints excluded: chain AE residue 258 ILE Chi-restraints excluded: chain AE residue 336 VAL Chi-restraints excluded: chain AE residue 407 ASP Chi-restraints excluded: chain AF residue 56 GLN Chi-restraints excluded: chain AF residue 103 LYS Chi-restraints excluded: chain AG residue 46 ILE Chi-restraints excluded: chain AG residue 64 TYR Chi-restraints excluded: chain AG residue 109 SER Chi-restraints excluded: chain AG residue 219 VAL Chi-restraints excluded: chain AI residue 98 THR Chi-restraints excluded: chain AI residue 100 THR Chi-restraints excluded: chain AI residue 108 ILE Chi-restraints excluded: chain AI residue 153 THR Chi-restraints excluded: chain AI residue 155 LYS Chi-restraints excluded: chain AI residue 172 VAL Chi-restraints excluded: chain AI residue 206 LEU Chi-restraints excluded: chain AI residue 229 LEU Chi-restraints excluded: chain AI residue 237 THR Chi-restraints excluded: chain AI residue 259 GLU Chi-restraints excluded: chain AI residue 299 VAL Chi-restraints excluded: chain AI residue 329 MET Chi-restraints excluded: chain AI residue 393 THR Chi-restraints excluded: chain AJ residue 64 THR Chi-restraints excluded: chain AJ residue 80 VAL Chi-restraints excluded: chain AJ residue 143 LEU Chi-restraints excluded: chain AJ residue 145 LEU Chi-restraints excluded: chain AJ residue 166 GLU Chi-restraints excluded: chain AJ residue 168 VAL Chi-restraints excluded: chain AK residue 68 ILE Chi-restraints excluded: chain AK residue 142 THR Chi-restraints excluded: chain AK residue 147 THR Chi-restraints excluded: chain AK residue 183 ILE Chi-restraints excluded: chain AL residue 32 THR Chi-restraints excluded: chain AL residue 52 THR Chi-restraints excluded: chain AL residue 55 ARG Chi-restraints excluded: chain AL residue 67 ILE Chi-restraints excluded: chain AL residue 77 ASN Chi-restraints excluded: chain AL residue 117 ASP Chi-restraints excluded: chain AN residue 30 VAL Chi-restraints excluded: chain AN residue 66 ASP Chi-restraints excluded: chain AO residue 72 MET Chi-restraints excluded: chain AO residue 105 LEU Chi-restraints excluded: chain AO residue 167 MET Chi-restraints excluded: chain AO residue 198 ARG Chi-restraints excluded: chain AO residue 218 VAL Chi-restraints excluded: chain AP residue 97 TYR Chi-restraints excluded: chain AP residue 117 GLU Chi-restraints excluded: chain AQ residue 7 SER Chi-restraints excluded: chain AQ residue 30 VAL Chi-restraints excluded: chain AQ residue 40 LEU Chi-restraints excluded: chain AQ residue 64 VAL Chi-restraints excluded: chain AQ residue 74 THR Chi-restraints excluded: chain AR residue 69 CYS Chi-restraints excluded: chain AR residue 89 THR Chi-restraints excluded: chain AR residue 117 ILE Chi-restraints excluded: chain AR residue 131 LEU Chi-restraints excluded: chain AU residue 10 ARG Chi-restraints excluded: chain AU residue 35 LEU Chi-restraints excluded: chain AU residue 38 ASP Chi-restraints excluded: chain AU residue 77 ARG Chi-restraints excluded: chain Aa residue 117 LEU Chi-restraints excluded: chain Aa residue 129 THR Chi-restraints excluded: chain Aa residue 169 ILE Chi-restraints excluded: chain Aa residue 183 ILE Chi-restraints excluded: chain Aa residue 197 ARG Chi-restraints excluded: chain Aa residue 202 THR Chi-restraints excluded: chain Aa residue 325 LEU Chi-restraints excluded: chain Aa residue 334 GLN Chi-restraints excluded: chain Aa residue 348 HIS Chi-restraints excluded: chain Ab residue 6 LEU Chi-restraints excluded: chain Ab residue 30 LEU Chi-restraints excluded: chain Ab residue 91 ASN Chi-restraints excluded: chain Ac residue 59 ASN Chi-restraints excluded: chain Ac residue 95 ASN Chi-restraints excluded: chain Ac residue 106 LEU Chi-restraints excluded: chain Ad residue 89 VAL Chi-restraints excluded: chain Ad residue 161 GLN Chi-restraints excluded: chain Ad residue 166 THR Chi-restraints excluded: chain Ad residue 183 SER Chi-restraints excluded: chain Ad residue 192 THR Chi-restraints excluded: chain Ae residue 76 ASP Chi-restraints excluded: chain Ae residue 107 VAL Chi-restraints excluded: chain Ae residue 159 TYR Chi-restraints excluded: chain Ae residue 197 TYR Chi-restraints excluded: chain Ae residue 249 LEU Chi-restraints excluded: chain Ae residue 323 LEU Chi-restraints excluded: chain Ae residue 325 ARG Chi-restraints excluded: chain Ae residue 388 VAL Chi-restraints excluded: chain Ae residue 424 HIS Chi-restraints excluded: chain Af residue 85 LEU Chi-restraints excluded: chain Af residue 130 VAL Chi-restraints excluded: chain Af residue 155 LEU Chi-restraints excluded: chain Ag residue 54 ASP Chi-restraints excluded: chain Ag residue 71 LEU Chi-restraints excluded: chain Ag residue 150 LEU Chi-restraints excluded: chain Ag residue 172 TYR Chi-restraints excluded: chain Ag residue 252 LEU Chi-restraints excluded: chain Ag residue 262 ASP Chi-restraints excluded: chain Ag residue 264 VAL Chi-restraints excluded: chain Ag residue 265 ASN Chi-restraints excluded: chain Ah residue 294 ILE Chi-restraints excluded: chain Ah residue 307 ILE Chi-restraints excluded: chain Ah residue 310 GLU Chi-restraints excluded: chain Ah residue 387 ASN Chi-restraints excluded: chain Ai residue 15 SER Chi-restraints excluded: chain Aj residue 18 VAL Chi-restraints excluded: chain Aj residue 82 ARG Chi-restraints excluded: chain Aj residue 84 SER Chi-restraints excluded: chain Aj residue 108 ASN Chi-restraints excluded: chain Aj residue 150 PHE Chi-restraints excluded: chain Aj residue 202 ASP Chi-restraints excluded: chain Ak residue 64 VAL Chi-restraints excluded: chain Ak residue 112 ASN Chi-restraints excluded: chain Ak residue 117 THR Chi-restraints excluded: chain Ak residue 130 ASP Chi-restraints excluded: chain Ak residue 159 VAL Chi-restraints excluded: chain Ak residue 165 ILE Chi-restraints excluded: chain Ak residue 187 HIS Chi-restraints excluded: chain Ak residue 309 ASN Chi-restraints excluded: chain Am residue 44 THR Chi-restraints excluded: chain An residue 165 LYS Chi-restraints excluded: chain An residue 194 ILE Chi-restraints excluded: chain Ao residue 77 THR Chi-restraints excluded: chain Ao residue 96 ILE Chi-restraints excluded: chain Ao residue 260 HIS Chi-restraints excluded: chain Ao residue 263 CYS Chi-restraints excluded: chain Ao residue 285 LEU Chi-restraints excluded: chain Ao residue 304 THR Chi-restraints excluded: chain Ao residue 326 MET Chi-restraints excluded: chain Ao residue 409 SER Chi-restraints excluded: chain Ao residue 447 ASN Chi-restraints excluded: chain Ao residue 454 ASP Chi-restraints excluded: chain Ao residue 510 ASP Chi-restraints excluded: chain Ao residue 521 GLU Chi-restraints excluded: chain Ao residue 615 ASN Chi-restraints excluded: chain Ao residue 632 GLU Chi-restraints excluded: chain Ap residue 53 ASP Chi-restraints excluded: chain Ap residue 54 GLU Chi-restraints excluded: chain Ap residue 103 ASN Chi-restraints excluded: chain Ap residue 187 THR Chi-restraints excluded: chain Ap residue 193 LEU Chi-restraints excluded: chain Ap residue 235 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 719 random chunks: chunk 630 optimal weight: 9.9990 chunk 663 optimal weight: 30.0000 chunk 605 optimal weight: 0.9990 chunk 645 optimal weight: 10.0000 chunk 388 optimal weight: 3.9990 chunk 281 optimal weight: 0.7980 chunk 507 optimal weight: 9.9990 chunk 198 optimal weight: 0.1980 chunk 583 optimal weight: 8.9990 chunk 610 optimal weight: 10.0000 chunk 643 optimal weight: 9.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BC 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AB 152 HIS AB 265 GLN ** AC 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AE 369 HIS ** AI 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AN 119 GLN AQ 9 HIS AR 77 ASN ** Aa 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ae 228 HIS ** Ae 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 104 GLN ** Ag 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 189 ASN ** Ag 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ah 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 88 GLN Ak 112 ASN Am 58 GLN ** Ao 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 76793 Z= 0.297 Angle : 0.615 11.915 108765 Z= 0.311 Chirality : 0.039 0.232 12818 Planarity : 0.005 0.086 10078 Dihedral : 20.230 179.724 22663 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.10 % Favored : 95.84 % Rotamer: Outliers : 4.00 % Allowed : 21.32 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.31 % 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 (0.11), residues: 6199 helix: 1.47 (0.10), residues: 2792 sheet: -0.28 (0.20), residues: 671 loop : -0.48 (0.12), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRPAk 236 HIS 0.008 0.001 HISAE 317 PHE 0.017 0.002 PHEBC 232 TYR 0.033 0.002 TYRAc 163 ARG 0.008 0.001 ARGAO 216 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1024 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 808 time to evaluate : 5.486 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: BC 244 MET cc_start: 0.7907 (ttm) cc_final: 0.7656 (ttm) REVERT: BC 308 ASP cc_start: 0.7814 (m-30) cc_final: 0.7452 (t0) REVERT: BC 464 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7826 (mt-10) REVERT: BC 465 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8618 (pt0) REVERT: BC 488 LYS cc_start: 0.7281 (mttt) cc_final: 0.6934 (tptt) REVERT: BC 609 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8575 (mm-30) REVERT: AB 146 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7947 (tpt-90) REVERT: AC 43 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8280 (mmt180) REVERT: AC 144 SER cc_start: 0.9492 (m) cc_final: 0.8964 (m) REVERT: AE 157 ILE cc_start: 0.8483 (mp) cc_final: 0.8093 (mt) REVERT: AE 178 GLU cc_start: 0.8381 (tt0) cc_final: 0.7433 (tp30) REVERT: AE 179 TRP cc_start: 0.7452 (m-10) cc_final: 0.6989 (m-10) REVERT: AE 321 MET cc_start: 0.9053 (mtp) cc_final: 0.8688 (mtp) REVERT: AF 76 GLU cc_start: 0.8284 (pm20) cc_final: 0.8001 (pm20) REVERT: AI 268 MET cc_start: 0.8473 (mmt) cc_final: 0.7557 (ppp) REVERT: AI 272 ARG cc_start: 0.8141 (tpp80) cc_final: 0.7852 (tpp-160) REVERT: AI 315 MET cc_start: 0.8870 (ttp) cc_final: 0.8544 (ttt) REVERT: AJ 64 THR cc_start: 0.7494 (OUTLIER) cc_final: 0.7257 (p) REVERT: AL 55 ARG cc_start: 0.9241 (OUTLIER) cc_final: 0.8980 (mtt-85) REVERT: AL 118 LEU cc_start: 0.9278 (mt) cc_final: 0.9054 (mt) REVERT: AO 72 MET cc_start: 0.9097 (OUTLIER) cc_final: 0.8766 (tpp) REVERT: AO 167 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8427 (mtt) REVERT: AO 198 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8384 (mtt180) REVERT: AO 217 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8304 (tp30) REVERT: AO 226 ARG cc_start: 0.5367 (ttp80) cc_final: 0.5117 (ptm-80) REVERT: AP 120 LEU cc_start: 0.8746 (tp) cc_final: 0.8421 (mt) REVERT: AQ 45 LYS cc_start: 0.8703 (ttmt) cc_final: 0.8297 (tttm) REVERT: AR 138 ASN cc_start: 0.8551 (m-40) cc_final: 0.8286 (m110) REVERT: AU 10 ARG cc_start: 0.9206 (OUTLIER) cc_final: 0.8964 (mtm180) REVERT: AU 23 TYR cc_start: 0.8953 (t80) cc_final: 0.8492 (t80) REVERT: AU 77 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7958 (mtp-110) REVERT: Aa 183 ILE cc_start: 0.9116 (OUTLIER) cc_final: 0.8858 (pt) REVERT: Aa 197 ARG cc_start: 0.9134 (OUTLIER) cc_final: 0.7615 (mmt90) REVERT: Aa 334 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7808 (pm20) REVERT: Ab 102 LYS cc_start: 0.8906 (mmtm) cc_final: 0.8194 (mptt) REVERT: Ac 106 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8768 (pp) REVERT: Ad 98 ASP cc_start: 0.8421 (m-30) cc_final: 0.8104 (m-30) REVERT: Ad 161 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8490 (tm-30) REVERT: Ae 152 TRP cc_start: 0.8013 (t60) cc_final: 0.7438 (t60) REVERT: Ae 159 TYR cc_start: 0.7231 (OUTLIER) cc_final: 0.5807 (t80) REVERT: Ae 209 MET cc_start: 0.7901 (mmm) cc_final: 0.7630 (mmm) REVERT: Ae 211 GLU cc_start: 0.6417 (mt-10) cc_final: 0.6142 (tm-30) REVERT: Ae 287 MET cc_start: 0.6693 (mtt) cc_final: 0.6334 (mtm) REVERT: Ae 325 ARG cc_start: 0.7043 (OUTLIER) cc_final: 0.6763 (mmm160) REVERT: Af 111 ASP cc_start: 0.8045 (t0) cc_final: 0.7600 (t0) REVERT: Ag 150 LEU cc_start: 0.6991 (OUTLIER) cc_final: 0.6274 (tm) REVERT: Ag 172 TYR cc_start: 0.6308 (OUTLIER) cc_final: 0.4590 (t80) REVERT: Ag 204 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7017 (mp10) REVERT: Ag 252 LEU cc_start: 0.6748 (OUTLIER) cc_final: 0.6355 (mt) REVERT: Ag 336 LEU cc_start: 0.7542 (tt) cc_final: 0.6810 (tp) REVERT: Ah 285 PRO cc_start: 0.8141 (Cg_exo) cc_final: 0.7796 (Cg_endo) REVERT: Ah 294 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8663 (mp) REVERT: Ah 373 ASN cc_start: 0.8031 (t0) cc_final: 0.7418 (t0) REVERT: Ai 6 GLU cc_start: 0.8602 (tp30) cc_final: 0.8351 (tp30) REVERT: Ai 52 TYR cc_start: 0.8929 (m-80) cc_final: 0.8585 (m-80) REVERT: Ai 73 ASP cc_start: 0.7934 (t0) cc_final: 0.7368 (t70) REVERT: Ai 77 ASP cc_start: 0.9113 (m-30) cc_final: 0.8826 (m-30) REVERT: Ai 80 ASP cc_start: 0.7809 (m-30) cc_final: 0.7483 (m-30) REVERT: Ai 81 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8400 (tm-30) REVERT: Aj 150 PHE cc_start: 0.7458 (OUTLIER) cc_final: 0.6390 (t80) REVERT: Ak 95 ARG cc_start: 0.8763 (mmt90) cc_final: 0.7998 (mtt90) REVERT: Ak 241 TRP cc_start: 0.8670 (p-90) cc_final: 0.8264 (p-90) REVERT: Ak 289 LYS cc_start: 0.8132 (ptmm) cc_final: 0.7857 (pptt) REVERT: Am 53 MET cc_start: 0.8217 (mmt) cc_final: 0.7802 (mmt) REVERT: Am 81 GLU cc_start: 0.8037 (tp30) cc_final: 0.7822 (tm-30) REVERT: An 165 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8069 (ttmm) REVERT: Ao 91 ASP cc_start: 0.8596 (t0) cc_final: 0.8388 (t0) REVERT: Ao 285 LEU cc_start: 0.5628 (OUTLIER) cc_final: 0.5360 (tp) REVERT: Ao 326 MET cc_start: 0.4615 (OUTLIER) cc_final: 0.4032 (tpp) REVERT: Ao 411 ARG cc_start: 0.5322 (ptt-90) cc_final: 0.4645 (mtm110) REVERT: Ao 439 HIS cc_start: 0.4870 (t70) cc_final: 0.4656 (t70) REVERT: Ao 447 ASN cc_start: 0.6139 (OUTLIER) cc_final: 0.5169 (p0) REVERT: Ao 485 ILE cc_start: 0.7040 (mm) cc_final: 0.6695 (mm) REVERT: Ao 540 ARG cc_start: 0.4471 (mmt90) cc_final: 0.3776 (ttm170) REVERT: Ao 608 ILE cc_start: 0.5725 (mm) cc_final: 0.5384 (pt) REVERT: Ao 632 GLU cc_start: 0.5242 (OUTLIER) cc_final: 0.4554 (pt0) REVERT: Ap 54 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7283 (pt0) REVERT: Ap 103 ASN cc_start: 0.8912 (OUTLIER) cc_final: 0.8221 (p0) REVERT: Ap 169 GLN cc_start: 0.8941 (mt0) cc_final: 0.8615 (mt0) REVERT: Ap 235 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.8404 (ptp) outliers start: 216 outliers final: 168 residues processed: 962 average time/residue: 0.7367 time to fit residues: 1176.6314 Evaluate side-chains 974 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 776 time to evaluate : 5.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BC residue 208 VAL Chi-restraints excluded: chain BC residue 230 ILE Chi-restraints excluded: chain BC residue 255 VAL Chi-restraints excluded: chain BC residue 283 ILE Chi-restraints excluded: chain BC residue 332 MET Chi-restraints excluded: chain BC residue 362 SER Chi-restraints excluded: chain BC residue 399 MET Chi-restraints excluded: chain BC residue 468 LYS Chi-restraints excluded: chain BC residue 486 TRP Chi-restraints excluded: chain BC residue 535 ILE Chi-restraints excluded: chain BC residue 560 ASP Chi-restraints excluded: chain BC residue 606 LEU Chi-restraints excluded: chain BC residue 662 THR Chi-restraints excluded: chain BC residue 686 VAL Chi-restraints excluded: chain BC residue 690 MET Chi-restraints excluded: chain BC residue 720 LYS Chi-restraints excluded: chain BC residue 722 SER Chi-restraints excluded: chain BT residue 61 VAL Chi-restraints excluded: chain AB residue 63 SER Chi-restraints excluded: chain AB residue 145 SER Chi-restraints excluded: chain AB residue 146 ARG Chi-restraints excluded: chain AB residue 186 VAL Chi-restraints excluded: chain AB residue 206 VAL Chi-restraints excluded: chain AB residue 218 THR Chi-restraints excluded: chain AB residue 235 VAL Chi-restraints excluded: chain AC residue 43 ARG Chi-restraints excluded: chain AC residue 44 VAL Chi-restraints excluded: chain AC residue 73 THR Chi-restraints excluded: chain AC residue 92 LEU Chi-restraints excluded: chain AC residue 115 ASN Chi-restraints excluded: chain AC residue 117 LEU Chi-restraints excluded: chain AC residue 157 THR Chi-restraints excluded: chain AE residue 105 GLU Chi-restraints excluded: chain AE residue 106 SER Chi-restraints excluded: chain AE residue 154 VAL Chi-restraints excluded: chain AE residue 171 ASP Chi-restraints excluded: chain AE residue 194 SER Chi-restraints excluded: chain AE residue 216 ASP Chi-restraints excluded: chain AE residue 239 ARG Chi-restraints excluded: chain AE residue 258 ILE Chi-restraints excluded: chain AE residue 336 VAL Chi-restraints excluded: chain AE residue 407 ASP Chi-restraints excluded: chain AF residue 103 LYS Chi-restraints excluded: chain AG residue 46 ILE Chi-restraints excluded: chain AG residue 64 TYR Chi-restraints excluded: chain AG residue 103 ASN Chi-restraints excluded: chain AG residue 109 SER Chi-restraints excluded: chain AG residue 219 VAL Chi-restraints excluded: chain AI residue 91 MET Chi-restraints excluded: chain AI residue 98 THR Chi-restraints excluded: chain AI residue 100 THR Chi-restraints excluded: chain AI residue 108 ILE Chi-restraints excluded: chain AI residue 153 THR Chi-restraints excluded: chain AI residue 155 LYS Chi-restraints excluded: chain AI residue 172 VAL Chi-restraints excluded: chain AI residue 206 LEU Chi-restraints excluded: chain AI residue 229 LEU Chi-restraints excluded: chain AI residue 237 THR Chi-restraints excluded: chain AI residue 259 GLU Chi-restraints excluded: chain AI residue 299 VAL Chi-restraints excluded: chain AI residue 329 MET Chi-restraints excluded: chain AI residue 393 THR Chi-restraints excluded: chain AJ residue 64 THR Chi-restraints excluded: chain AJ residue 80 VAL Chi-restraints excluded: chain AJ residue 143 LEU Chi-restraints excluded: chain AJ residue 145 LEU Chi-restraints excluded: chain AJ residue 166 GLU Chi-restraints excluded: chain AJ residue 168 VAL Chi-restraints excluded: chain AK residue 68 ILE Chi-restraints excluded: chain AK residue 142 THR Chi-restraints excluded: chain AK residue 147 THR Chi-restraints excluded: chain AK residue 183 ILE Chi-restraints excluded: chain AK residue 191 ARG Chi-restraints excluded: chain AL residue 32 THR Chi-restraints excluded: chain AL residue 52 THR Chi-restraints excluded: chain AL residue 55 ARG Chi-restraints excluded: chain AL residue 67 ILE Chi-restraints excluded: chain AL residue 77 ASN Chi-restraints excluded: chain AL residue 101 SER Chi-restraints excluded: chain AL residue 102 LEU Chi-restraints excluded: chain AL residue 117 ASP Chi-restraints excluded: chain AN residue 30 VAL Chi-restraints excluded: chain AN residue 66 ASP Chi-restraints excluded: chain AN residue 85 VAL Chi-restraints excluded: chain AN residue 87 ILE Chi-restraints excluded: chain AN residue 120 LEU Chi-restraints excluded: chain AN residue 127 MET Chi-restraints excluded: chain AO residue 72 MET Chi-restraints excluded: chain AO residue 105 LEU Chi-restraints excluded: chain AO residue 124 SER Chi-restraints excluded: chain AO residue 167 MET Chi-restraints excluded: chain AO residue 198 ARG Chi-restraints excluded: chain AO residue 218 VAL Chi-restraints excluded: chain AP residue 71 ASP Chi-restraints excluded: chain AP residue 97 TYR Chi-restraints excluded: chain AP residue 117 GLU Chi-restraints excluded: chain AQ residue 7 SER Chi-restraints excluded: chain AQ residue 30 VAL Chi-restraints excluded: chain AQ residue 40 LEU Chi-restraints excluded: chain AQ residue 64 VAL Chi-restraints excluded: chain AQ residue 74 THR Chi-restraints excluded: chain AQ residue 80 GLU Chi-restraints excluded: chain AR residue 69 CYS Chi-restraints excluded: chain AR residue 77 ASN Chi-restraints excluded: chain AR residue 89 THR Chi-restraints excluded: chain AR residue 117 ILE Chi-restraints excluded: chain AR residue 131 LEU Chi-restraints excluded: chain AU residue 10 ARG Chi-restraints excluded: chain AU residue 14 VAL Chi-restraints excluded: chain AU residue 19 VAL Chi-restraints excluded: chain AU residue 35 LEU Chi-restraints excluded: chain AU residue 38 ASP Chi-restraints excluded: chain AU residue 77 ARG Chi-restraints excluded: chain Aa residue 129 THR Chi-restraints excluded: chain Aa residue 169 ILE Chi-restraints excluded: chain Aa residue 183 ILE Chi-restraints excluded: chain Aa residue 197 ARG Chi-restraints excluded: chain Aa residue 202 THR Chi-restraints excluded: chain Aa residue 325 LEU Chi-restraints excluded: chain Aa residue 334 GLN Chi-restraints excluded: chain Aa residue 348 HIS Chi-restraints excluded: chain Ab residue 6 LEU Chi-restraints excluded: chain Ab residue 30 LEU Chi-restraints excluded: chain Ab residue 91 ASN Chi-restraints excluded: chain Ac residue 59 ASN Chi-restraints excluded: chain Ac residue 70 MET Chi-restraints excluded: chain Ac residue 95 ASN Chi-restraints excluded: chain Ac residue 106 LEU Chi-restraints excluded: chain Ad residue 89 VAL Chi-restraints excluded: chain Ad residue 161 GLN Chi-restraints excluded: chain Ad residue 166 THR Chi-restraints excluded: chain Ad residue 183 SER Chi-restraints excluded: chain Ad residue 192 THR Chi-restraints excluded: chain Ae residue 76 ASP Chi-restraints excluded: chain Ae residue 107 VAL Chi-restraints excluded: chain Ae residue 159 TYR Chi-restraints excluded: chain Ae residue 249 LEU Chi-restraints excluded: chain Ae residue 323 LEU Chi-restraints excluded: chain Ae residue 325 ARG Chi-restraints excluded: chain Ae residue 388 VAL Chi-restraints excluded: chain Ae residue 424 HIS Chi-restraints excluded: chain Af residue 85 LEU Chi-restraints excluded: chain Af residue 130 VAL Chi-restraints excluded: chain Af residue 155 LEU Chi-restraints excluded: chain Ag residue 54 ASP Chi-restraints excluded: chain Ag residue 71 LEU Chi-restraints excluded: chain Ag residue 150 LEU Chi-restraints excluded: chain Ag residue 172 TYR Chi-restraints excluded: chain Ag residue 194 ASN Chi-restraints excluded: chain Ag residue 204 GLN Chi-restraints excluded: chain Ag residue 252 LEU Chi-restraints excluded: chain Ag residue 262 ASP Chi-restraints excluded: chain Ag residue 264 VAL Chi-restraints excluded: chain Ag residue 265 ASN Chi-restraints excluded: chain Ah residue 294 ILE Chi-restraints excluded: chain Ah residue 307 ILE Chi-restraints excluded: chain Ah residue 310 GLU Chi-restraints excluded: chain Ah residue 387 ASN Chi-restraints excluded: chain Ai residue 15 SER Chi-restraints excluded: chain Aj residue 6 VAL Chi-restraints excluded: chain Aj residue 18 VAL Chi-restraints excluded: chain Aj residue 82 ARG Chi-restraints excluded: chain Aj residue 84 SER Chi-restraints excluded: chain Aj residue 108 ASN Chi-restraints excluded: chain Aj residue 150 PHE Chi-restraints excluded: chain Aj residue 202 ASP Chi-restraints excluded: chain Ak residue 64 VAL Chi-restraints excluded: chain Ak residue 112 ASN Chi-restraints excluded: chain Ak residue 117 THR Chi-restraints excluded: chain Ak residue 130 ASP Chi-restraints excluded: chain Ak residue 154 ASP Chi-restraints excluded: chain Ak residue 159 VAL Chi-restraints excluded: chain Ak residue 165 ILE Chi-restraints excluded: chain Ak residue 187 HIS Chi-restraints excluded: chain Am residue 44 THR Chi-restraints excluded: chain Am residue 68 LYS Chi-restraints excluded: chain An residue 165 LYS Chi-restraints excluded: chain An residue 194 ILE Chi-restraints excluded: chain Ao residue 77 THR Chi-restraints excluded: chain Ao residue 96 ILE Chi-restraints excluded: chain Ao residue 260 HIS Chi-restraints excluded: chain Ao residue 263 CYS Chi-restraints excluded: chain Ao residue 285 LEU Chi-restraints excluded: chain Ao residue 304 THR Chi-restraints excluded: chain Ao residue 326 MET Chi-restraints excluded: chain Ao residue 409 SER Chi-restraints excluded: chain Ao residue 447 ASN Chi-restraints excluded: chain Ao residue 454 ASP Chi-restraints excluded: chain Ao residue 510 ASP Chi-restraints excluded: chain Ao residue 521 GLU Chi-restraints excluded: chain Ao residue 615 ASN Chi-restraints excluded: chain Ao residue 632 GLU Chi-restraints excluded: chain Ap residue 53 ASP Chi-restraints excluded: chain Ap residue 54 GLU Chi-restraints excluded: chain Ap residue 103 ASN Chi-restraints excluded: chain Ap residue 108 CYS Chi-restraints excluded: chain Ap residue 193 LEU Chi-restraints excluded: chain Ap residue 235 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 719 random chunks: chunk 424 optimal weight: 2.9990 chunk 682 optimal weight: 50.0000 chunk 416 optimal weight: 3.9990 chunk 323 optimal weight: 1.9990 chunk 474 optimal weight: 5.9990 chunk 716 optimal weight: 5.9990 chunk 659 optimal weight: 30.0000 chunk 570 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 440 optimal weight: 2.9990 chunk 349 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BC 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AB 152 HIS AB 265 GLN ** AE 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AI 163 HIS ** AI 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AQ 9 HIS AR 77 ASN ** Aa 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 104 GLN ** Ag 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Ag 179 GLN ** Ag 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ah 331 GLN ** Ai 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 88 GLN Ak 112 ASN ** Am 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 58 GLN ** Ao 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 76793 Z= 0.283 Angle : 0.612 12.450 108765 Z= 0.310 Chirality : 0.039 0.269 12818 Planarity : 0.005 0.085 10078 Dihedral : 20.224 179.887 22661 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.10 % Favored : 95.84 % Rotamer: Outliers : 3.78 % Allowed : 21.45 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.31 % 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: 0.62 (0.11), residues: 6199 helix: 1.47 (0.10), residues: 2794 sheet: -0.28 (0.20), residues: 671 loop : -0.47 (0.12), residues: 2734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRPAk 255 HIS 0.007 0.001 HISAE 317 PHE 0.016 0.002 PHEAa 297 TYR 0.035 0.002 TYRAc 163 ARG 0.012 0.001 ARGAN 98 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12398 Ramachandran restraints generated. 6199 Oldfield, 0 Emsley, 6199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 994 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 790 time to evaluate : 5.507 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: BC 302 LYS cc_start: 0.7835 (tppt) cc_final: 0.7556 (mmmt) REVERT: BC 308 ASP cc_start: 0.7819 (m-30) cc_final: 0.7444 (t0) REVERT: BC 464 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7815 (mt-10) REVERT: BC 465 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8614 (pt0) REVERT: BC 488 LYS cc_start: 0.7270 (mttt) cc_final: 0.6929 (tptt) REVERT: AC 41 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.6795 (mtm-85) REVERT: AC 43 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8215 (mmt180) REVERT: AC 144 SER cc_start: 0.9487 (m) cc_final: 0.8962 (m) REVERT: AE 157 ILE cc_start: 0.8489 (mp) cc_final: 0.8097 (mt) REVERT: AE 178 GLU cc_start: 0.8361 (tt0) cc_final: 0.7547 (tp30) REVERT: AE 242 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8786 (ptt-90) REVERT: AE 321 MET cc_start: 0.9052 (mtp) cc_final: 0.8686 (mtp) REVERT: AF 76 GLU cc_start: 0.8266 (pm20) cc_final: 0.7995 (pm20) REVERT: AI 268 MET cc_start: 0.8494 (mmt) cc_final: 0.7554 (ppp) REVERT: AI 315 MET cc_start: 0.8878 (ttp) cc_final: 0.8576 (ttt) REVERT: AJ 64 THR cc_start: 0.7501 (OUTLIER) cc_final: 0.7261 (p) REVERT: AL 55 ARG cc_start: 0.9229 (OUTLIER) cc_final: 0.8972 (mtt-85) REVERT: AL 118 LEU cc_start: 0.9281 (mt) cc_final: 0.9060 (mt) REVERT: AO 72 MET cc_start: 0.9102 (OUTLIER) cc_final: 0.8764 (tpp) REVERT: AO 167 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8407 (mtt) REVERT: AO 198 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8363 (mtt180) REVERT: AO 217 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8311 (tp30) REVERT: AP 120 LEU cc_start: 0.8741 (tp) cc_final: 0.8416 (mt) REVERT: AQ 45 LYS cc_start: 0.8711 (ttmt) cc_final: 0.8300 (tttm) REVERT: AR 138 ASN cc_start: 0.8550 (m-40) cc_final: 0.8289 (m110) REVERT: AU 10 ARG cc_start: 0.9229 (OUTLIER) cc_final: 0.8991 (mtm180) REVERT: AU 23 TYR cc_start: 0.8932 (t80) cc_final: 0.8476 (t80) REVERT: AU 77 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7950 (mtp-110) REVERT: Aa 183 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8853 (pt) REVERT: Aa 197 ARG cc_start: 0.9127 (OUTLIER) cc_final: 0.7649 (mmt90) REVERT: Aa 334 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7917 (pm20) REVERT: Ab 102 LYS cc_start: 0.8868 (mmtm) cc_final: 0.8158 (mptt) REVERT: Ac 106 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8736 (pp) REVERT: Ad 94 LYS cc_start: 0.8405 (mptt) cc_final: 0.8062 (mptt) REVERT: Ad 98 ASP cc_start: 0.8448 (m-30) cc_final: 0.8136 (m-30) REVERT: Ad 161 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8493 (tm-30) REVERT: Ae 152 TRP cc_start: 0.8016 (t60) cc_final: 0.7446 (t60) REVERT: Ae 159 TYR cc_start: 0.7011 (OUTLIER) cc_final: 0.5539 (t80) REVERT: Ae 209 MET cc_start: 0.7986 (mmm) cc_final: 0.7702 (mmm) REVERT: Ae 211 GLU cc_start: 0.6406 (mt-10) cc_final: 0.6073 (tm-30) REVERT: Ae 228 HIS cc_start: 0.7498 (t-90) cc_final: 0.7152 (m-70) REVERT: Ae 287 MET cc_start: 0.6598 (mtt) cc_final: 0.6198 (mtm) REVERT: Ae 325 ARG cc_start: 0.7035 (OUTLIER) cc_final: 0.6757 (mmm160) REVERT: Af 111 ASP cc_start: 0.8063 (t0) cc_final: 0.7594 (t0) REVERT: Ag 150 LEU cc_start: 0.7009 (OUTLIER) cc_final: 0.6297 (tm) REVERT: Ag 172 TYR cc_start: 0.5730 (OUTLIER) cc_final: 0.4856 (t80) REVERT: Ag 188 LYS cc_start: 0.8418 (mtmt) cc_final: 0.8141 (pttt) REVERT: Ag 204 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7047 (mp10) REVERT: Ag 252 LEU cc_start: 0.6745 (OUTLIER) cc_final: 0.6360 (mt) REVERT: Ag 336 LEU cc_start: 0.7548 (tt) cc_final: 0.6798 (tp) REVERT: Ah 285 PRO cc_start: 0.8119 (Cg_exo) cc_final: 0.7779 (Cg_endo) REVERT: Ah 294 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8652 (mp) REVERT: Ah 373 ASN cc_start: 0.8012 (t0) cc_final: 0.7387 (t0) REVERT: Ai 6 GLU cc_start: 0.8596 (tp30) cc_final: 0.8329 (tp30) REVERT: Ai 52 TYR cc_start: 0.8927 (m-80) cc_final: 0.8596 (m-80) REVERT: Ai 73 ASP cc_start: 0.7944 (t0) cc_final: 0.7383 (t70) REVERT: Ai 77 ASP cc_start: 0.9111 (m-30) cc_final: 0.8819 (m-30) REVERT: Ai 80 ASP cc_start: 0.7807 (m-30) cc_final: 0.7482 (m-30) REVERT: Ai 81 GLU cc_start: 0.8683 (tm-30) cc_final: 0.8403 (tm-30) REVERT: Aj 150 PHE cc_start: 0.7455 (OUTLIER) cc_final: 0.6390 (t80) REVERT: Ak 95 ARG cc_start: 0.8754 (mmt90) cc_final: 0.7988 (mtt90) REVERT: Ak 241 TRP cc_start: 0.8679 (p-90) cc_final: 0.8301 (p-90) REVERT: Ak 289 LYS cc_start: 0.8129 (ptmm) cc_final: 0.7855 (pptt) REVERT: Am 53 MET cc_start: 0.8209 (mmt) cc_final: 0.7802 (mmt) REVERT: Am 81 GLU cc_start: 0.8069 (tp30) cc_final: 0.7864 (tm-30) REVERT: An 165 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8052 (ttmm) REVERT: Ao 91 ASP cc_start: 0.8604 (t0) cc_final: 0.8397 (t0) REVERT: Ao 326 MET cc_start: 0.4369 (OUTLIER) cc_final: 0.2786 (tmm) REVERT: Ao 411 ARG cc_start: 0.5329 (ptt-90) cc_final: 0.4660 (mtm110) REVERT: Ao 439 HIS cc_start: 0.4858 (t70) cc_final: 0.4652 (t70) REVERT: Ao 441 LEU cc_start: 0.7894 (mt) cc_final: 0.7310 (mt) REVERT: Ao 447 ASN cc_start: 0.6065 (OUTLIER) cc_final: 0.5137 (p0) REVERT: Ao 485 ILE cc_start: 0.7040 (mm) cc_final: 0.6693 (mm) REVERT: Ao 524 HIS cc_start: 0.4792 (t70) cc_final: 0.4486 (t70) REVERT: Ao 540 ARG cc_start: 0.4713 (mmt90) cc_final: 0.4031 (ttm170) REVERT: Ao 557 ASP cc_start: 0.7614 (m-30) cc_final: 0.6954 (p0) REVERT: Ao 580 ASN cc_start: 0.4957 (m-40) cc_final: 0.4543 (t0) REVERT: Ao 598 MET cc_start: 0.4405 (ptp) cc_final: 0.4112 (ptm) REVERT: Ao 608 ILE cc_start: 0.5723 (mm) cc_final: 0.5395 (pt) REVERT: Ao 612 GLU cc_start: 0.3970 (pm20) cc_final: 0.2260 (mp0) REVERT: Ao 632 GLU cc_start: 0.5248 (OUTLIER) cc_final: 0.4560 (pt0) REVERT: Ao 661 GLU cc_start: 0.3839 (OUTLIER) cc_final: 0.3321 (mm-30) REVERT: Ap 54 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7279 (pt0) REVERT: Ap 103 ASN cc_start: 0.8954 (OUTLIER) cc_final: 0.8321 (p0) REVERT: Ap 169 GLN cc_start: 0.8926 (mt0) cc_final: 0.8605 (mt0) REVERT: Ap 235 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.8298 (ptm) outliers start: 204 outliers final: 165 residues processed: 938 average time/residue: 0.7411 time to fit residues: 1152.3015 Evaluate side-chains 983 residues out of total 5442 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 787 time to evaluate : 5.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BC residue 208 VAL Chi-restraints excluded: chain BC residue 230 ILE Chi-restraints excluded: chain BC residue 255 VAL Chi-restraints excluded: chain BC residue 283 ILE Chi-restraints excluded: chain BC residue 332 MET Chi-restraints excluded: chain BC residue 362 SER Chi-restraints excluded: chain BC residue 399 MET Chi-restraints excluded: chain BC residue 468 LYS Chi-restraints excluded: chain BC residue 486 TRP Chi-restraints excluded: chain BC residue 535 ILE Chi-restraints excluded: chain BC residue 560 ASP Chi-restraints excluded: chain BC residue 606 LEU Chi-restraints excluded: chain BC residue 662 THR Chi-restraints excluded: chain BC residue 686 VAL Chi-restraints excluded: chain BC residue 690 MET Chi-restraints excluded: chain BC residue 722 SER Chi-restraints excluded: chain BT residue 61 VAL Chi-restraints excluded: chain AB residue 63 SER Chi-restraints excluded: chain AB residue 145 SER Chi-restraints excluded: chain AB residue 186 VAL Chi-restraints excluded: chain AB residue 206 VAL Chi-restraints excluded: chain AB residue 218 THR Chi-restraints excluded: chain AB residue 235 VAL Chi-restraints excluded: chain AC residue 41 ARG Chi-restraints excluded: chain AC residue 43 ARG Chi-restraints excluded: chain AC residue 44 VAL Chi-restraints excluded: chain AC residue 73 THR Chi-restraints excluded: chain AC residue 92 LEU Chi-restraints excluded: chain AC residue 115 ASN Chi-restraints excluded: chain AC residue 117 LEU Chi-restraints excluded: chain AC residue 157 THR Chi-restraints excluded: chain AE residue 105 GLU Chi-restraints excluded: chain AE residue 106 SER Chi-restraints excluded: chain AE residue 154 VAL Chi-restraints excluded: chain AE residue 171 ASP Chi-restraints excluded: chain AE residue 194 SER Chi-restraints excluded: chain AE residue 216 ASP Chi-restraints excluded: chain AE residue 239 ARG Chi-restraints excluded: chain AE residue 242 ARG Chi-restraints excluded: chain AE residue 258 ILE Chi-restraints excluded: chain AE residue 336 VAL Chi-restraints excluded: chain AE residue 407 ASP Chi-restraints excluded: chain AF residue 103 LYS Chi-restraints excluded: chain AG residue 46 ILE Chi-restraints excluded: chain AG residue 64 TYR Chi-restraints excluded: chain AG residue 103 ASN Chi-restraints excluded: chain AG residue 109 SER Chi-restraints excluded: chain AG residue 219 VAL Chi-restraints excluded: chain AI residue 91 MET Chi-restraints excluded: chain AI residue 98 THR Chi-restraints excluded: chain AI residue 100 THR Chi-restraints excluded: chain AI residue 108 ILE Chi-restraints excluded: chain AI residue 153 THR Chi-restraints excluded: chain AI residue 155 LYS Chi-restraints excluded: chain AI residue 172 VAL Chi-restraints excluded: chain AI residue 206 LEU Chi-restraints excluded: chain AI residue 229 LEU Chi-restraints excluded: chain AI residue 237 THR Chi-restraints excluded: chain AI residue 259 GLU Chi-restraints excluded: chain AI residue 299 VAL Chi-restraints excluded: chain AI residue 329 MET Chi-restraints excluded: chain AI residue 393 THR Chi-restraints excluded: chain AJ residue 64 THR Chi-restraints excluded: chain AJ residue 80 VAL Chi-restraints excluded: chain AJ residue 143 LEU Chi-restraints excluded: chain AJ residue 145 LEU Chi-restraints excluded: chain AJ residue 166 GLU Chi-restraints excluded: chain AJ residue 168 VAL Chi-restraints excluded: chain AK residue 68 ILE Chi-restraints excluded: chain AK residue 142 THR Chi-restraints excluded: chain AK residue 147 THR Chi-restraints excluded: chain AK residue 183 ILE Chi-restraints excluded: chain AL residue 32 THR Chi-restraints excluded: chain AL residue 52 THR Chi-restraints excluded: chain AL residue 55 ARG Chi-restraints excluded: chain AL residue 67 ILE Chi-restraints excluded: chain AL residue 77 ASN Chi-restraints excluded: chain AL residue 101 SER Chi-restraints excluded: chain AL residue 117 ASP Chi-restraints excluded: chain AL residue 125 VAL Chi-restraints excluded: chain AN residue 30 VAL Chi-restraints excluded: chain AN residue 66 ASP Chi-restraints excluded: chain AN residue 85 VAL Chi-restraints excluded: chain AN residue 87 ILE Chi-restraints excluded: chain AN residue 120 LEU Chi-restraints excluded: chain AO residue 72 MET Chi-restraints excluded: chain AO residue 105 LEU Chi-restraints excluded: chain AO residue 107 ILE Chi-restraints excluded: chain AO residue 124 SER Chi-restraints excluded: chain AO residue 167 MET Chi-restraints excluded: chain AO residue 198 ARG Chi-restraints excluded: chain AO residue 218 VAL Chi-restraints excluded: chain AP residue 97 TYR Chi-restraints excluded: chain AP residue 117 GLU Chi-restraints excluded: chain AQ residue 7 SER Chi-restraints excluded: chain AQ residue 30 VAL Chi-restraints excluded: chain AQ residue 40 LEU Chi-restraints excluded: chain AQ residue 64 VAL Chi-restraints excluded: chain AQ residue 74 THR Chi-restraints excluded: chain AQ residue 80 GLU Chi-restraints excluded: chain AR residue 69 CYS Chi-restraints excluded: chain AR residue 77 ASN Chi-restraints excluded: chain AR residue 89 THR Chi-restraints excluded: chain AR residue 117 ILE Chi-restraints excluded: chain AR residue 131 LEU Chi-restraints excluded: chain AU residue 10 ARG Chi-restraints excluded: chain AU residue 14 VAL Chi-restraints excluded: chain AU residue 35 LEU Chi-restraints excluded: chain AU residue 38 ASP Chi-restraints excluded: chain AU residue 77 ARG Chi-restraints excluded: chain Aa residue 129 THR Chi-restraints excluded: chain Aa residue 169 ILE Chi-restraints excluded: chain Aa residue 183 ILE Chi-restraints excluded: chain Aa residue 197 ARG Chi-restraints excluded: chain Aa residue 202 THR Chi-restraints excluded: chain Aa residue 325 LEU Chi-restraints excluded: chain Aa residue 334 GLN Chi-restraints excluded: chain Ab residue 6 LEU Chi-restraints excluded: chain Ab residue 30 LEU Chi-restraints excluded: chain Ab residue 91 ASN Chi-restraints excluded: chain Ac residue 59 ASN Chi-restraints excluded: chain Ac residue 70 MET Chi-restraints excluded: chain Ac residue 95 ASN Chi-restraints excluded: chain Ac residue 106 LEU Chi-restraints excluded: chain Ad residue 44 THR Chi-restraints excluded: chain Ad residue 89 VAL Chi-restraints excluded: chain Ad residue 161 GLN Chi-restraints excluded: chain Ad residue 166 THR Chi-restraints excluded: chain Ad residue 183 SER Chi-restraints excluded: chain Ad residue 192 THR Chi-restraints excluded: chain Ae residue 76 ASP Chi-restraints excluded: chain Ae residue 107 VAL Chi-restraints excluded: chain Ae residue 159 TYR Chi-restraints excluded: chain Ae residue 249 LEU Chi-restraints excluded: chain Ae residue 323 LEU Chi-restraints excluded: chain Ae residue 325 ARG Chi-restraints excluded: chain Ae residue 388 VAL Chi-restraints excluded: chain Ae residue 424 HIS Chi-restraints excluded: chain Af residue 85 LEU Chi-restraints excluded: chain Af residue 130 VAL Chi-restraints excluded: chain Ag residue 54 ASP Chi-restraints excluded: chain Ag residue 71 LEU Chi-restraints excluded: chain Ag residue 150 LEU Chi-restraints excluded: chain Ag residue 172 TYR Chi-restraints excluded: chain Ag residue 194 ASN Chi-restraints excluded: chain Ag residue 204 GLN Chi-restraints excluded: chain Ag residue 252 LEU Chi-restraints excluded: chain Ag residue 262 ASP Chi-restraints excluded: chain Ag residue 264 VAL Chi-restraints excluded: chain Ag residue 265 ASN Chi-restraints excluded: chain Ag residue 305 ILE Chi-restraints excluded: chain Ah residue 294 ILE Chi-restraints excluded: chain Ah residue 307 ILE Chi-restraints excluded: chain Ah residue 310 GLU Chi-restraints excluded: chain Ah residue 331 GLN Chi-restraints excluded: chain Ah residue 387 ASN Chi-restraints excluded: chain Ai residue 15 SER Chi-restraints excluded: chain Aj residue 6 VAL Chi-restraints excluded: chain Aj residue 18 VAL Chi-restraints excluded: chain Aj residue 82 ARG Chi-restraints excluded: chain Aj residue 84 SER Chi-restraints excluded: chain Aj residue 108 ASN Chi-restraints excluded: chain Aj residue 150 PHE Chi-restraints excluded: chain Aj residue 202 ASP Chi-restraints excluded: chain Ak residue 64 VAL Chi-restraints excluded: chain Ak residue 112 ASN Chi-restraints excluded: chain Ak residue 117 THR Chi-restraints excluded: chain Ak residue 130 ASP Chi-restraints excluded: chain Ak residue 154 ASP Chi-restraints excluded: chain Ak residue 159 VAL Chi-restraints excluded: chain Ak residue 165 ILE Chi-restraints excluded: chain Ak residue 187 HIS Chi-restraints excluded: chain Am residue 44 THR Chi-restraints excluded: chain Am residue 68 LYS Chi-restraints excluded: chain An residue 165 LYS Chi-restraints excluded: chain An residue 194 ILE Chi-restraints excluded: chain Ao residue 77 THR Chi-restraints excluded: chain Ao residue 96 ILE Chi-restraints excluded: chain Ao residue 260 HIS Chi-restraints excluded: chain Ao residue 263 CYS Chi-restraints excluded: chain Ao residue 304 THR Chi-restraints excluded: chain Ao residue 326 MET Chi-restraints excluded: chain Ao residue 409 SER Chi-restraints excluded: chain Ao residue 447 ASN Chi-restraints excluded: chain Ao residue 454 ASP Chi-restraints excluded: chain Ao residue 510 ASP Chi-restraints excluded: chain Ao residue 521 GLU Chi-restraints excluded: chain Ao residue 615 ASN Chi-restraints excluded: chain Ao residue 632 GLU Chi-restraints excluded: chain Ao residue 661 GLU Chi-restraints excluded: chain Ap residue 53 ASP Chi-restraints excluded: chain Ap residue 54 GLU Chi-restraints excluded: chain Ap residue 103 ASN Chi-restraints excluded: chain Ap residue 108 CYS Chi-restraints excluded: chain Ap residue 193 LEU Chi-restraints excluded: chain Ap residue 235 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 719 random chunks: chunk 453 optimal weight: 8.9990 chunk 607 optimal weight: 8.9990 chunk 174 optimal weight: 4.9990 chunk 525 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 158 optimal weight: 4.9990 chunk 571 optimal weight: 0.6980 chunk 239 optimal weight: 0.9980 chunk 586 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 chunk 105 optimal weight: 6.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BC 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BC 377 GLN AB 152 HIS AB 265 GLN ** AC 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AE 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AI 163 HIS ** AI 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AI 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aa 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ad 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ae 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Af 104 GLN ** Ag 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ag 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Aj 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ak 112 ASN ** Am 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 58 GLN ** Ao 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.119291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.085647 restraints weight = 147335.711| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.96 r_work: 0.2943 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 76793 Z= 0.338 Angle : 0.637 14.512 108765 Z= 0.322 Chirality : 0.040 0.282 12818 Planarity : 0.005 0.085 10078 Dihedral : 20.228 179.400 22661 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.32 % Favored : 95.61 % Rotamer: Outliers : 4.06 % Allowed : 21.28 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.31 % 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: 0.53 (0.11), residues: 6199 helix: 1.39 (0.10), residues: 2797 sheet: -0.34 (0.20), residues: 672 loop : -0.50 (0.12), residues: 2730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRPAk 255 HIS 0.009 0.001 HISAE 317 PHE 0.023 0.002 PHEAo 617 TYR 0.040 0.002 TYRAc 163 ARG 0.009 0.001 ARGAN 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22029.51 seconds wall clock time: 385 minutes 4.71 seconds (23104.71 seconds total)