Starting phenix.real_space_refine on Fri Mar 1 04:47:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u9g_8522/03_2024/5u9g_8522.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u9g_8522/03_2024/5u9g_8522.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u9g_8522/03_2024/5u9g_8522.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u9g_8522/03_2024/5u9g_8522.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u9g_8522/03_2024/5u9g_8522.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u9g_8522/03_2024/5u9g_8522.pdb" } resolution = 3.2 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= -1.160 sd= 1.507 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 4723 5.49 5 Mg 348 5.21 5 S 168 5.16 5 C 77027 2.51 5 N 28367 2.21 5 O 42015 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Y ARG 26": "NH1" <-> "NH2" Residue "05 ARG 13": "NH1" <-> "NH2" Residue "05 ARG 33": "NH1" <-> "NH2" Residue "05 ARG 59": "NH1" <-> "NH2" Residue "05 ARG 77": "NH1" <-> "NH2" Residue "05 ARG 83": "NH1" <-> "NH2" Residue "05 ARG 169": "NH1" <-> "NH2" Residue "05 ARG 184": "NH1" <-> "NH2" Residue "06 ARG 21": "NH1" <-> "NH2" Residue "06 ARG 44": "NH1" <-> "NH2" Residue "06 ARG 49": "NH1" <-> "NH2" Residue "06 ARG 61": "NH1" <-> "NH2" Residue "06 ARG 88": "NH1" <-> "NH2" Residue "06 ARG 102": "NH1" <-> "NH2" Residue "06 ARG 162": "NH1" <-> "NH2" Residue "06 ARG 170": "NH1" <-> "NH2" Residue "07 ARG 70": "NH1" <-> "NH2" Residue "07 ARG 79": "NH1" <-> "NH2" Residue "07 ARG 91": "NH1" <-> "NH2" Residue "07 ARG 101": "NH1" <-> "NH2" Residue "07 ARG 109": "NH1" <-> "NH2" Residue "07 ARG 111": "NH1" <-> "NH2" Residue "07 ARG 114": "NH1" <-> "NH2" Residue "07 ARG 132": "NH1" <-> "NH2" Residue "08 ARG 2": "NH1" <-> "NH2" Residue "08 ARG 152": "NH1" <-> "NH2" Residue "08 ARG 162": "NH1" <-> "NH2" Residue "08 ARG 169": "NH1" <-> "NH2" Residue "10 TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "12 ARG 13": "NH1" <-> "NH2" Residue "12 ARG 37": "NH1" <-> "NH2" Residue "12 ARG 96": "NH1" <-> "NH2" Residue "12 ARG 120": "NH1" <-> "NH2" Residue "14 ARG 21": "NH1" <-> "NH2" Residue "14 ARG 33": "NH1" <-> "NH2" Residue "14 ARG 41": "NH1" <-> "NH2" Residue "14 ARG 47": "NH1" <-> "NH2" Residue "14 ARG 60": "NH1" <-> "NH2" Residue "14 ARG 78": "NH1" <-> "NH2" Residue "14 ARG 126": "NH1" <-> "NH2" Residue "15 ARG 10": "NH1" <-> "NH2" Residue "15 ARG 18": "NH1" <-> "NH2" Residue "15 ARG 40": "NH1" <-> "NH2" Residue "15 ARG 44": "NH1" <-> "NH2" Residue "15 ARG 50": "NH1" <-> "NH2" Residue "15 ARG 55": "NH1" <-> "NH2" Residue "15 ARG 59": "NH1" <-> "NH2" Residue "15 ARG 114": "NH1" <-> "NH2" Residue "16 ARG 8": "NH1" <-> "NH2" Residue "16 ARG 12": "NH1" <-> "NH2" Residue "16 ARG 17": "NH1" <-> "NH2" Residue "16 ARG 22": "NH1" <-> "NH2" Residue "16 ARG 46": "NH1" <-> "NH2" Residue "16 ARG 63": "NH1" <-> "NH2" Residue "16 ARG 64": "NH1" <-> "NH2" Residue "16 ARG 69": "NH1" <-> "NH2" Residue "16 ARG 71": "NH1" <-> "NH2" Residue "16 ARG 96": "NH1" <-> "NH2" Residue "16 ARG 118": "NH1" <-> "NH2" Residue "17 ARG 10": "NH1" <-> "NH2" Residue "17 ARG 16": "NH1" <-> "NH2" Residue "17 ARG 25": "NH1" <-> "NH2" Residue "17 ARG 81": "NH1" <-> "NH2" Residue "17 ARG 94": "NH1" <-> "NH2" Residue "17 ARG 102": "NH1" <-> "NH2" Residue "17 ARG 111": "NH1" <-> "NH2" Residue "18 ARG 20": "NH1" <-> "NH2" Residue "18 ARG 38": "NH1" <-> "NH2" Residue "18 ARG 61": "NH1" <-> "NH2" Residue "18 ARG 88": "NH1" <-> "NH2" Residue "18 ARG 100": "NH1" <-> "NH2" Residue "18 ARG 108": "NH1" <-> "NH2" Residue "19 ARG 2": "NH1" <-> "NH2" Residue "19 ARG 5": "NH1" <-> "NH2" Residue "19 ARG 12": "NH1" <-> "NH2" Residue "19 ARG 32": "NH1" <-> "NH2" Residue "19 ARG 47": "NH1" <-> "NH2" Residue "19 ARG 69": "NH1" <-> "NH2" Residue "20 ARG 21": "NH1" <-> "NH2" Residue "20 ARG 68": "NH1" <-> "NH2" Residue "20 ARG 78": "NH1" <-> "NH2" Residue "20 ARG 79": "NH1" <-> "NH2" Residue "20 ARG 84": "NH1" <-> "NH2" Residue "21 ARG 84": "NH1" <-> "NH2" Residue "21 ARG 88": "NH1" <-> "NH2" Residue "21 ARG 95": "NH1" <-> "NH2" Residue "21 ARG 110": "NH1" <-> "NH2" Residue "22 ARG 73": "NH1" <-> "NH2" Residue "23 ARG 5": "NH1" <-> "NH2" Residue "23 ARG 6": "NH1" <-> "NH2" Residue "23 ARG 81": "NH1" <-> "NH2" Residue "23 ARG 85": "NH1" <-> "NH2" Residue "23 ARG 93": "NH1" <-> "NH2" Residue "27 ARG 29": "NH1" <-> "NH2" Residue "27 ARG 47": "NH1" <-> "NH2" Residue "27 ARG 52": "NH1" <-> "NH2" Residue "28 ARG 10": "NH1" <-> "NH2" Residue "28 ARG 29": "NH1" <-> "NH2" Residue "28 ARG 44": "NH1" <-> "NH2" Residue "29 ARG 49": "NH1" <-> "NH2" Residue "29 ARG 56": "NH1" <-> "NH2" Residue "30 ARG 9": "NH1" <-> "NH2" Residue "30 ARG 15": "NH1" <-> "NH2" Residue "30 ARG 39": "NH1" <-> "NH2" Residue "30 ARG 51": "NH1" <-> "NH2" Residue "31 ARG 43": "NH1" <-> "NH2" Residue "32 ARG 3": "NH1" <-> "NH2" Residue "32 ARG 12": "NH1" <-> "NH2" Residue "32 ARG 14": "NH1" <-> "NH2" Residue "32 ARG 19": "NH1" <-> "NH2" Residue "32 ARG 21": "NH1" <-> "NH2" Residue "32 ARG 33": "NH1" <-> "NH2" Residue "32 ARG 41": "NH1" <-> "NH2" Residue "33 ARG 12": "NH1" <-> "NH2" Residue "33 ARG 29": "NH1" <-> "NH2" Residue "33 ARG 39": "NH1" <-> "NH2" Residue "33 ARG 41": "NH1" <-> "NH2" Residue "34 ARG 12": "NH1" <-> "NH2" Residue "34 ARG 24": "NH1" <-> "NH2" Residue "Z ARG 117": "NH1" <-> "NH2" Residue "B ARG 107": "NH1" <-> "NH2" Residue "B ARG 224": "NH1" <-> "NH2" Residue "C ARG 106": "NH1" <-> "NH2" Residue "C ARG 130": "NH1" <-> "NH2" Residue "E ARG 156": "NH1" <-> "NH2" Residue "I ARG 123": "NH1" <-> "NH2" Residue "L ARG 55": "NH1" <-> "NH2" Residue "P ARG 28": "NH1" <-> "NH2" Residue "R ARG 11": "NH1" <-> "NH2" Residue "U ARG 66": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 152649 Number of models: 1 Model: "" Number of chains: 70 Chain: "A" Number of atoms: 33012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33012 Classifications: {'RNA': 1539} Modifications used: {'5*END': 1, 'rna2p_pur': 92, 'rna2p_pyr': 57, 'rna3p_pur': 782, 'rna3p_pyr': 608} Link IDs: {'rna2p': 149, 'rna3p': 1389} Chain: "01" Number of atoms: 62318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62318 Classifications: {'RNA': 2903} Modifications used: {'5*END': 1, 'rna2p_pur': 220, 'rna2p_pyr': 98, 'rna3p_pur': 1454, 'rna3p_pyr': 1131} Link IDs: {'rna2p': 318, 'rna3p': 2584} Chain: "02" Number of atoms: 2546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2546 Classifications: {'RNA': 119} Modifications used: {'5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 3, 'rna3p_pur': 60, 'rna3p_pyr': 52} Link IDs: {'rna2p': 7, 'rna3p': 111} Chain: "Y" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 249 Classifications: {'peptide': 32} Incomplete info: {'backbone_only': 3} Link IDs: {'PTRANS': 1, 'TRANS': 30} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "X" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1622 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 7, 'rna3p_pur': 35, 'rna3p_pyr': 31} Link IDs: {'rna2p': 11, 'rna3p': 65} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {' C%rna3p_pyr:plan2': 1, ' C%rna3p_pyr:plan': 1, ' A%rna3p_pur:plan2': 1, ' A%rna3p_pur:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "03" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1353 Classifications: {'peptide': 220} Incomplete info: {'backbone_only': 80} Link IDs: {'PTRANS': 7, 'TRANS': 212} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 291 Unresolved non-hydrogen angles: 426 Unresolved non-hydrogen dihedrals: 165 Unresolved non-hydrogen chiralities: 103 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 5, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 110 Chain: "04" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "05" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "06" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "07" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "08" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "09" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "10" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 988 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "11" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1032 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "12" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "13" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "14" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "15" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "16" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "17" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "18" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "19" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "20" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "21" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "22" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "23" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "24" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "25" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "26" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "27" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "28" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "29" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "30" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "31" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 409 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "32" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "33" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "34" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "V" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 306 Classifications: {'RNA': 14} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 11, 'rna3p_pyr': 2} Link IDs: {'rna3p': 13} Chain: "W" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1640 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 34, 'rna3p_pyr': 34} Link IDs: {'rna2p': 9, 'rna3p': 67} Chain: "Z" Number of atoms: 2814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2814 Classifications: {'peptide': 361} Incomplete info: {'backbone_only': 13} Link IDs: {'PTRANS': 7, 'TRANS': 353} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1704 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "C" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1156 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "F" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 817 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "G" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "I" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "K" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 869 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "L" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "M" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 95} Chain: "O" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "R" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 535 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "S" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "T" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "U" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 544 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "A" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 97 Unusual residues: {' MG': 97} Classifications: {'undetermined': 97} Link IDs: {None: 96} Chain: "01" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 239 Unusual residues: {' MG': 239} Classifications: {'undetermined': 239} Link IDs: {None: 238} Chain: "02" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "X" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "14" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "25" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "30" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "34" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0LZV SG CYS34 11 147.649 179.358 91.145 1.00122.75 S ATOM A0M0K SG CYS34 14 151.711 179.748 90.680 1.00101.67 S ATOM A0M3F SG CYS34 27 151.472 181.566 93.176 1.00154.83 S Time building chain proxies: 59.11, per 1000 atoms: 0.39 Number of scatterers: 152649 At special positions: 0 Unit cell: (270.945, 255.15, 241.785, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 168 16.00 P 4723 15.00 Mg 348 11.99 O 42015 8.00 N 28367 7.00 C 77027 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 60.92 Conformation dependent library (CDL) restraints added in 7.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN34 101 " pdb="ZN ZN34 101 " - pdb=" SG CYS34 27 " pdb="ZN ZN34 101 " - pdb=" SG CYS34 14 " pdb="ZN ZN34 101 " - pdb=" SG CYS34 11 " 12906 Ramachandran restraints generated. 6453 Oldfield, 0 Emsley, 6453 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11868 Finding SS restraints... Secondary structure from input PDB file: 207 helices and 79 sheets defined 35.0% alpha, 16.7% beta 1460 base pairs and 2754 stacking pairs defined. Time for finding SS restraints: 53.20 Creating SS restraints... Processing helix chain '03' and resid 7 through 14 removed outlier: 3.504A pdb=" N ILE03 11 " --> pdb=" O ARG03 7 " (cutoff:3.500A) Processing helix chain '03' and resid 22 through 34 removed outlier: 3.593A pdb=" N LYS03 31 " --> pdb=" O ILE03 27 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU03 32 " --> pdb=" O ALA03 28 " (cutoff:3.500A) Processing helix chain '03' and resid 81 through 89 removed outlier: 3.858A pdb=" N GLU03 85 " --> pdb=" O GLY03 81 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA03 87 " --> pdb=" O ASN03 83 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS03 88 " --> pdb=" O ALA03 84 " (cutoff:3.500A) Processing helix chain '03' and resid 100 through 108 Processing helix chain '03' and resid 120 through 125 removed outlier: 3.697A pdb=" N GLY03 125 " --> pdb=" O MET03 121 " (cutoff:3.500A) Processing helix chain '03' and resid 127 through 132 removed outlier: 4.188A pdb=" N LEU03 131 " --> pdb=" O LEU03 127 " (cutoff:3.500A) Processing helix chain '03' and resid 150 through 159 removed outlier: 3.758A pdb=" N LYS03 154 " --> pdb=" O ALA03 150 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA03 156 " --> pdb=" O ALA03 152 " (cutoff:3.500A) Processing helix chain '03' and resid 181 through 199 Processing helix chain '04' and resid 29 through 33 removed outlier: 3.583A pdb=" N LEU04 32 " --> pdb=" O PHE04 29 " (cutoff:3.500A) Processing helix chain '04' and resid 132 through 134 No H-bonds generated for 'chain '04' and resid 132 through 134' Processing helix chain '04' and resid 196 through 202 removed outlier: 3.971A pdb=" N MET04 200 " --> pdb=" O ALA04 197 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG04 202 " --> pdb=" O HIS04 199 " (cutoff:3.500A) Processing helix chain '04' and resid 206 through 212 removed outlier: 3.891A pdb=" N ALA04 210 " --> pdb=" O LYS04 206 " (cutoff:3.500A) Processing helix chain '04' and resid 220 through 224 Processing helix chain '04' and resid 261 through 264 removed outlier: 4.171A pdb=" N LYS04 264 " --> pdb=" O ARG04 261 " (cutoff:3.500A) No H-bonds generated for 'chain '04' and resid 261 through 264' Processing helix chain '05' and resid 61 through 72 removed outlier: 3.513A pdb=" N HIS05 67 " --> pdb=" O PRO05 63 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA05 71 " --> pdb=" O HIS05 67 " (cutoff:3.500A) Processing helix chain '05' and resid 98 through 103 removed outlier: 4.383A pdb=" N ASP05 103 " --> pdb=" O LEU05 100 " (cutoff:3.500A) Processing helix chain '05' and resid 120 through 125 Processing helix chain '06' and resid 15 through 20 removed outlier: 3.619A pdb=" N PHE06 19 " --> pdb=" O SER06 15 " (cutoff:3.500A) Processing helix chain '06' and resid 24 through 40 removed outlier: 3.530A pdb=" N ALA06 36 " --> pdb=" O VAL06 32 " (cutoff:3.500A) Processing helix chain '06' and resid 97 through 115 removed outlier: 3.555A pdb=" N SER06 110 " --> pdb=" O LYS06 106 " (cutoff:3.500A) Processing helix chain '06' and resid 130 through 141 removed outlier: 3.684A pdb=" N LEU06 134 " --> pdb=" O LYS06 130 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS06 137 " --> pdb=" O LEU06 133 " (cutoff:3.500A) Processing helix chain '06' and resid 154 through 159 Processing helix chain '06' and resid 160 through 162 No H-bonds generated for 'chain '06' and resid 160 through 162' Processing helix chain '06' and resid 176 through 181 removed outlier: 3.810A pdb=" N LEU06 180 " --> pdb=" O ASP06 176 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE06 181 " --> pdb=" O PRO06 177 " (cutoff:3.500A) No H-bonds generated for 'chain '06' and resid 176 through 181' Processing helix chain '06' and resid 190 through 200 removed outlier: 3.802A pdb=" N LYS06 194 " --> pdb=" O ALA06 190 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN06 195 " --> pdb=" O ASP06 191 " (cutoff:3.500A) Processing helix chain '07' and resid 2 through 17 removed outlier: 4.641A pdb=" N VAL07 12 " --> pdb=" O LYS07 8 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR07 17 " --> pdb=" O LYS07 13 " (cutoff:3.500A) Processing helix chain '07' and resid 45 through 52 removed outlier: 3.727A pdb=" N LEU07 49 " --> pdb=" O ASP07 45 " (cutoff:3.500A) Processing helix chain '07' and resid 52 through 61 removed outlier: 3.501A pdb=" N LEU07 56 " --> pdb=" O ALA07 52 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE07 59 " --> pdb=" O ASP07 55 " (cutoff:3.500A) Processing helix chain '07' and resid 93 through 105 removed outlier: 3.660A pdb=" N PHE07 99 " --> pdb=" O MET07 95 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE07 103 " --> pdb=" O PHE07 99 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE07 105 " --> pdb=" O ARG07 101 " (cutoff:3.500A) Processing helix chain '07' and resid 105 through 110 removed outlier: 3.597A pdb=" N ARG07 109 " --> pdb=" O ILE07 105 " (cutoff:3.500A) Processing helix chain '07' and resid 161 through 171 removed outlier: 3.541A pdb=" N GLY07 165 " --> pdb=" O SER07 161 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA07 171 " --> pdb=" O ALA07 167 " (cutoff:3.500A) Processing helix chain '08' and resid 59 through 80 removed outlier: 3.575A pdb=" N GLY08 65 " --> pdb=" O TRP08 61 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR08 66 " --> pdb=" O ALA08 62 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA08 69 " --> pdb=" O GLY08 65 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU08 70 " --> pdb=" O THR08 66 " (cutoff:3.500A) Processing helix chain '08' and resid 136 through 149 removed outlier: 3.875A pdb=" N ILE08 140 " --> pdb=" O ASP08 136 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY08 141 " --> pdb=" O LYS08 137 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA08 149 " --> pdb=" O ALA08 145 " (cutoff:3.500A) Processing helix chain '09' and resid 22 through 30 Processing helix chain '09' and resid 40 through 49 removed outlier: 4.407A pdb=" N ALA09 49 " --> pdb=" O GLU09 45 " (cutoff:3.500A) Processing helix chain '09' and resid 54 through 73 removed outlier: 3.669A pdb=" N ALA09 63 " --> pdb=" O ALA09 59 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA09 64 " --> pdb=" O GLU09 60 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS09 71 " --> pdb=" O ALA09 67 " (cutoff:3.500A) Processing helix chain '09' and resid 96 through 106 Processing helix chain '10' and resid 3 through 18 removed outlier: 4.103A pdb=" N GLN10 9 " --> pdb=" O LEU10 5 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA10 10 " --> pdb=" O GLN10 6 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE10 11 " --> pdb=" O ASP10 7 " (cutoff:3.500A) Processing helix chain '10' and resid 33 through 47 removed outlier: 3.581A pdb=" N GLU10 40 " --> pdb=" O ASP10 36 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA10 44 " --> pdb=" O GLU10 40 " (cutoff:3.500A) Processing helix chain '10' and resid 71 through 77 Processing helix chain '10' and resid 96 through 104 removed outlier: 3.756A pdb=" N ALA10 100 " --> pdb=" O PHE10 96 " (cutoff:3.500A) Processing helix chain '11' and resid 24 through 29 removed outlier: 3.639A pdb=" N GLY11 28 " --> pdb=" O GLY11 24 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN11 29 " --> pdb=" O PRO11 25 " (cutoff:3.500A) No H-bonds generated for 'chain '11' and resid 24 through 29' Processing helix chain '11' and resid 33 through 43 removed outlier: 3.853A pdb=" N PHE11 41 " --> pdb=" O PHE11 37 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASN11 42 " --> pdb=" O CYS11 38 " (cutoff:3.500A) Processing helix chain '11' and resid 74 through 84 removed outlier: 3.670A pdb=" N LYS11 80 " --> pdb=" O ALA11 76 " (cutoff:3.500A) Processing helix chain '11' and resid 101 through 116 removed outlier: 3.526A pdb=" N GLU11 107 " --> pdb=" O ALA11 103 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE11 108 " --> pdb=" O GLN11 104 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP11 115 " --> pdb=" O THR11 111 " (cutoff:3.500A) Processing helix chain '11' and resid 120 through 135 Processing helix chain '12' and resid 24 through 38 removed outlier: 4.165A pdb=" N GLU12 31 " --> pdb=" O ARG12 27 " (cutoff:3.500A) Processing helix chain '12' and resid 58 through 62 removed outlier: 3.519A pdb=" N VAL12 62 " --> pdb=" O ALA12 59 " (cutoff:3.500A) Processing helix chain '12' and resid 67 through 72 Processing helix chain '12' and resid 88 through 94 Processing helix chain '12' and resid 96 through 107 removed outlier: 3.926A pdb=" N VAL12 100 " --> pdb=" O ARG12 96 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE12 101 " --> pdb=" O PRO12 97 " (cutoff:3.500A) Processing helix chain '12' and resid 112 through 120 removed outlier: 3.548A pdb=" N ARG12 120 " --> pdb=" O ARG12 116 " (cutoff:3.500A) Processing helix chain '12' and resid 132 through 136 removed outlier: 3.721A pdb=" N GLN12 135 " --> pdb=" O HIS12 132 " (cutoff:3.500A) Processing helix chain '13' and resid 104 through 108 Processing helix chain '13' and resid 112 through 119 removed outlier: 3.633A pdb=" N LEU13 118 " --> pdb=" O LYS13 114 " (cutoff:3.500A) Processing helix chain '14' and resid 56 through 61 removed outlier: 3.560A pdb=" N LEU14 61 " --> pdb=" O LEU14 57 " (cutoff:3.500A) Processing helix chain '14' and resid 68 through 72 removed outlier: 3.514A pdb=" N ALA14 72 " --> pdb=" O ARG14 69 " (cutoff:3.500A) Processing helix chain '14' and resid 78 through 82 Processing helix chain '14' and resid 93 through 98 Processing helix chain '14' and resid 128 through 139 removed outlier: 3.704A pdb=" N ALA14 134 " --> pdb=" O GLY14 130 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU14 136 " --> pdb=" O ARG14 132 " (cutoff:3.500A) Processing helix chain '15' and resid 43 through 55 removed outlier: 3.542A pdb=" N ARG15 55 " --> pdb=" O ARG15 51 " (cutoff:3.500A) Processing helix chain '15' and resid 109 through 122 removed outlier: 3.545A pdb=" N LYS15 118 " --> pdb=" O ARG15 114 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA15 122 " --> pdb=" O LYS15 118 " (cutoff:3.500A) Processing helix chain '16' and resid 13 through 32 removed outlier: 3.689A pdb=" N ALA16 19 " --> pdb=" O SER16 15 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU16 28 " --> pdb=" O MET16 24 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG16 30 " --> pdb=" O GLY16 26 " (cutoff:3.500A) Processing helix chain '16' and resid 38 through 55 removed outlier: 4.206A pdb=" N GLU16 43 " --> pdb=" O PRO16 39 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ARG16 46 " --> pdb=" O LYS16 42 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL16 47 " --> pdb=" O GLU16 43 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU16 49 " --> pdb=" O ARG16 45 " (cutoff:3.500A) Proline residue: 16 50 - end of helix Processing helix chain '16' and resid 61 through 69 Processing helix chain '16' and resid 72 through 79 Processing helix chain '16' and resid 82 through 87 removed outlier: 3.870A pdb=" N PHE16 87 " --> pdb=" O LEU16 83 " (cutoff:3.500A) Processing helix chain '17' and resid 3 through 22 removed outlier: 3.507A pdb=" N ARG17 10 " --> pdb=" O ALA17 6 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ARG17 13 " --> pdb=" O ARG17 9 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N ALA17 14 " --> pdb=" O ARG17 10 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU17 18 " --> pdb=" O ALA17 14 " (cutoff:3.500A) Processing helix chain '17' and resid 55 through 60 Processing helix chain '17' and resid 67 through 85 removed outlier: 3.675A pdb=" N ALA17 73 " --> pdb=" O ASP17 69 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL17 78 " --> pdb=" O VAL17 74 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG17 81 " --> pdb=" O ALA17 77 " (cutoff:3.500A) Processing helix chain '17' and resid 101 through 113 removed outlier: 3.585A pdb=" N ALA17 109 " --> pdb=" O ALA17 105 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA17 110 " --> pdb=" O LEU17 106 " (cutoff:3.500A) Processing helix chain '18' and resid 2 through 10 Processing helix chain '18' and resid 52 through 55 Processing helix chain '18' and resid 96 through 101 removed outlier: 3.633A pdb=" N LEU18 99 " --> pdb=" O LEU18 96 " (cutoff:3.500A) Processing helix chain '18' and resid 103 through 108 removed outlier: 3.781A pdb=" N ARG18 108 " --> pdb=" O LYS18 105 " (cutoff:3.500A) Processing helix chain '19' and resid 6 through 18 removed outlier: 3.504A pdb=" N ARG19 12 " --> pdb=" O ILE19 8 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE19 16 " --> pdb=" O ARG19 12 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS19 18 " --> pdb=" O LYS19 14 " (cutoff:3.500A) Processing helix chain '19' and resid 24 through 28 removed outlier: 3.630A pdb=" N SER19 28 " --> pdb=" O GLY19 25 " (cutoff:3.500A) Processing helix chain '19' and resid 30 through 72 removed outlier: 4.495A pdb=" N GLN19 36 " --> pdb=" O ARG19 32 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ARG19 50 " --> pdb=" O TYR19 46 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LYS19 53 " --> pdb=" O ARG19 49 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG19 54 " --> pdb=" O ARG19 50 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG19 57 " --> pdb=" O LYS19 53 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN19 70 " --> pdb=" O ALA19 66 " (cutoff:3.500A) Processing helix chain '19' and resid 74 through 85 Processing helix chain '19' and resid 90 through 100 Processing helix chain '19' and resid 101 through 117 removed outlier: 3.522A pdb=" N PHE19 105 " --> pdb=" O ASP19 101 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA19 115 " --> pdb=" O LYS19 111 " (cutoff:3.500A) Processing helix chain '21' and resid 13 through 22 removed outlier: 3.582A pdb=" N VAL21 20 " --> pdb=" O LYS21 16 " (cutoff:3.500A) Processing helix chain '21' and resid 28 through 38 removed outlier: 3.857A pdb=" N TYR21 38 " --> pdb=" O ASP21 34 " (cutoff:3.500A) Processing helix chain '21' and resid 41 through 61 removed outlier: 3.602A pdb=" N VAL21 45 " --> pdb=" O LYS21 41 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU21 46 " --> pdb=" O LYS21 42 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS21 49 " --> pdb=" O VAL21 45 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL21 50 " --> pdb=" O LEU21 46 " (cutoff:3.500A) Processing helix chain '21' and resid 89 through 91 No H-bonds generated for 'chain '21' and resid 89 through 91' Processing helix chain '22' and resid 2 through 8 Processing helix chain '22' and resid 17 through 26 removed outlier: 3.609A pdb=" N GLU22 25 " --> pdb=" O SER22 21 " (cutoff:3.500A) Processing helix chain '22' and resid 39 through 51 removed outlier: 3.726A pdb=" N LYS22 49 " --> pdb=" O ALA22 45 " (cutoff:3.500A) Processing helix chain '24' and resid 13 through 22 removed outlier: 3.589A pdb=" N SER24 17 " --> pdb=" O GLY24 13 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG24 19 " --> pdb=" O GLY24 15 " (cutoff:3.500A) Processing helix chain '24' and resid 44 through 49 Processing helix chain '24' and resid 53 through 58 removed outlier: 3.510A pdb=" N SER24 58 " --> pdb=" O GLU24 55 " (cutoff:3.500A) Processing helix chain '26' and resid 52 through 61 Processing helix chain '26' and resid 62 through 73 Processing helix chain '27' and resid 4 through 8 removed outlier: 3.575A pdb=" N ARG27 7 " --> pdb=" O LYS27 4 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU27 8 " --> pdb=" O GLU27 5 " (cutoff:3.500A) No H-bonds generated for 'chain '27' and resid 4 through 8' Processing helix chain '27' and resid 11 through 23 Processing helix chain '27' and resid 26 through 31 Processing helix chain '27' and resid 40 through 60 removed outlier: 3.739A pdb=" N LYS27 44 " --> pdb=" O SER27 40 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG27 47 " --> pdb=" O LEU27 43 " (cutoff:3.500A) Processing helix chain '28' and resid 16 through 27 removed outlier: 3.703A pdb=" N THR28 22 " --> pdb=" O LYS28 18 " (cutoff:3.500A) Processing helix chain '28' and resid 42 through 50 removed outlier: 3.626A pdb=" N VAL28 50 " --> pdb=" O MET28 46 " (cutoff:3.500A) Processing helix chain '29' and resid 42 through 47 Processing helix chain '29' and resid 56 through 64 removed outlier: 3.520A pdb=" N LYS29 62 " --> pdb=" O ASP29 58 " (cutoff:3.500A) Processing helix chain '30' and resid 8 through 16 Processing helix chain '30' and resid 17 through 19 No H-bonds generated for 'chain '30' and resid 17 through 19' Processing helix chain '32' and resid 8 through 16 Processing helix chain '32' and resid 17 through 24 removed outlier: 4.425A pdb=" N THR32 24 " --> pdb=" O ALA32 20 " (cutoff:3.500A) Processing helix chain '32' and resid 24 through 37 Processing helix chain '33' and resid 8 through 12 Processing helix chain '33' and resid 36 through 42 Processing helix chain '33' and resid 50 through 52 No H-bonds generated for 'chain '33' and resid 50 through 52' Processing helix chain '33' and resid 53 through 61 removed outlier: 3.613A pdb=" N ALA33 59 " --> pdb=" O GLY33 55 " (cutoff:3.500A) Processing helix chain '34' and resid 30 through 33 Processing helix chain 'Z' and resid 5 through 26 removed outlier: 3.550A pdb=" N LEU Z 25 " --> pdb=" O LEU Z 21 " (cutoff:3.500A) Processing helix chain 'Z' and resid 26 through 43 removed outlier: 3.534A pdb=" N LYS Z 31 " --> pdb=" O TYR Z 27 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU Z 35 " --> pdb=" O LYS Z 31 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU Z 42 " --> pdb=" O ASN Z 38 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN Z 43 " --> pdb=" O ALA Z 39 " (cutoff:3.500A) Processing helix chain 'Z' and resid 49 through 89 removed outlier: 3.568A pdb=" N LEU Z 63 " --> pdb=" O GLU Z 59 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL Z 66 " --> pdb=" O SER Z 62 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP Z 68 " --> pdb=" O GLU Z 64 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N THR Z 69 " --> pdb=" O ALA Z 65 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU Z 85 " --> pdb=" O SER Z 81 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA Z 87 " --> pdb=" O LEU Z 83 " (cutoff:3.500A) Processing helix chain 'Z' and resid 92 through 119 removed outlier: 3.650A pdb=" N VAL Z 100 " --> pdb=" O PHE Z 96 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA Z 101 " --> pdb=" O ASN Z 97 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU Z 106 " --> pdb=" O GLU Z 102 " (cutoff:3.500A) Processing helix chain 'Z' and resid 138 through 160 removed outlier: 3.556A pdb=" N GLN Z 142 " --> pdb=" O GLY Z 138 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU Z 157 " --> pdb=" O LEU Z 153 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER Z 158 " --> pdb=" O ARG Z 154 " (cutoff:3.500A) Processing helix chain 'Z' and resid 192 through 196 removed outlier: 3.501A pdb=" N THR Z 196 " --> pdb=" O ARG Z 193 " (cutoff:3.500A) Processing helix chain 'Z' and resid 253 through 257 removed outlier: 3.583A pdb=" N THR Z 257 " --> pdb=" O VAL Z 254 " (cutoff:3.500A) Processing helix chain 'Z' and resid 279 through 307 removed outlier: 3.518A pdb=" N LYS Z 289 " --> pdb=" O ASP Z 285 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU Z 298 " --> pdb=" O LYS Z 294 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS Z 303 " --> pdb=" O GLU Z 299 " (cutoff:3.500A) Processing helix chain 'Z' and resid 344 through 349 removed outlier: 3.511A pdb=" N VAL Z 348 " --> pdb=" O ASN Z 344 " (cutoff:3.500A) Processing helix chain 'Z' and resid 353 through 363 removed outlier: 3.522A pdb=" N ALA Z 359 " --> pdb=" O GLN Z 355 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA Z 363 " --> pdb=" O ALA Z 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 62 removed outlier: 3.895A pdb=" N VAL B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Proline residue: B 47 - end of helix removed outlier: 3.749A pdb=" N GLU B 51 " --> pdb=" O PRO B 47 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA B 52 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA B 60 " --> pdb=" O LEU B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 84 Processing helix chain 'B' and resid 102 through 123 removed outlier: 3.803A pdb=" N GLN B 108 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER B 109 " --> pdb=" O THR B 105 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR B 118 " --> pdb=" O LYS B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 148 removed outlier: 3.642A pdb=" N MET B 135 " --> pdb=" O LYS B 131 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER B 146 " --> pdb=" O LYS B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 176 removed outlier: 3.564A pdb=" N ALA B 175 " --> pdb=" O ALA B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 222 removed outlier: 3.570A pdb=" N THR B 219 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 11 removed outlier: 3.878A pdb=" N LEU C 11 " --> pdb=" O GLY C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 38 removed outlier: 4.531A pdb=" N ALA C 29 " --> pdb=" O THR C 25 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ASP C 30 " --> pdb=" O LYS C 26 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE C 36 " --> pdb=" O LEU C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 44 Processing helix chain 'C' and resid 71 through 76 Processing helix chain 'C' and resid 80 through 95 removed outlier: 3.661A pdb=" N GLU C 84 " --> pdb=" O GLY C 80 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 124 removed outlier: 3.584A pdb=" N SER C 118 " --> pdb=" O LEU C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 removed outlier: 3.838A pdb=" N ALA C 136 " --> pdb=" O ALA C 132 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL C 137 " --> pdb=" O MET C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 159 removed outlier: 4.009A pdb=" N ALA C 159 " --> pdb=" O LEU C 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 156 through 159' Processing helix chain 'D' and resid 8 through 15 removed outlier: 3.742A pdb=" N GLU D 14 " --> pdb=" O LEU D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 43 removed outlier: 4.370A pdb=" N ALA D 42 " --> pdb=" O GLN D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 65 removed outlier: 3.845A pdb=" N GLN D 53 " --> pdb=" O ASP D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 81 removed outlier: 3.639A pdb=" N ASN D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU D 77 " --> pdb=" O ASN D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 95 removed outlier: 3.551A pdb=" N LEU D 89 " --> pdb=" O THR D 85 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU D 90 " --> pdb=" O GLY D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 105 Processing helix chain 'D' and resid 109 through 119 Processing helix chain 'D' and resid 146 through 149 Processing helix chain 'D' and resid 153 through 161 Processing helix chain 'D' and resid 162 through 164 No H-bonds generated for 'chain 'D' and resid 162 through 164' Processing helix chain 'D' and resid 186 through 190 removed outlier: 3.599A pdb=" N LEU D 190 " --> pdb=" O ARG D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 204 removed outlier: 3.680A pdb=" N VAL D 200 " --> pdb=" O GLU D 196 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU D 201 " --> pdb=" O HIS D 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 67 removed outlier: 3.531A pdb=" N ILE E 59 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS E 65 " --> pdb=" O LYS E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 117 removed outlier: 3.659A pdb=" N LEU E 114 " --> pdb=" O MET E 110 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL E 116 " --> pdb=" O ALA E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 145 removed outlier: 3.513A pdb=" N GLU E 144 " --> pdb=" O ILE E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 156 removed outlier: 3.625A pdb=" N LYS E 155 " --> pdb=" O MET E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 165 removed outlier: 3.653A pdb=" N LEU E 164 " --> pdb=" O VAL E 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 31 removed outlier: 3.686A pdb=" N ALA F 28 " --> pdb=" O ARG F 24 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE F 29 " --> pdb=" O TYR F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 80 removed outlier: 3.503A pdb=" N GLU F 73 " --> pdb=" O GLU F 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 28 removed outlier: 3.630A pdb=" N ALA G 23 " --> pdb=" O SER G 19 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN G 27 " --> pdb=" O ALA G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 54 removed outlier: 3.505A pdb=" N ILE G 41 " --> pdb=" O THR G 37 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR G 48 " --> pdb=" O SER G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 64 removed outlier: 3.669A pdb=" N PHE G 61 " --> pdb=" O GLU G 57 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 108 removed outlier: 4.118A pdb=" N ASN G 96 " --> pdb=" O PRO G 92 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA G 97 " --> pdb=" O VAL G 93 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG G 101 " --> pdb=" O ALA G 97 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TRP G 102 " --> pdb=" O LEU G 98 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL G 104 " --> pdb=" O MET G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 128 removed outlier: 3.534A pdb=" N SER G 124 " --> pdb=" O ALA G 120 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU G 128 " --> pdb=" O SER G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 146 removed outlier: 4.460A pdb=" N VAL G 134 " --> pdb=" O LYS G 130 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG G 137 " --> pdb=" O ALA G 133 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU G 145 " --> pdb=" O HIS G 141 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA G 146 " --> pdb=" O ARG G 142 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 19 removed outlier: 3.537A pdb=" N ARG H 12 " --> pdb=" O ASP H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 42 Processing helix chain 'H' and resid 93 through 98 Processing helix chain 'H' and resid 111 through 119 Processing helix chain 'I' and resid 10 through 14 removed outlier: 4.078A pdb=" N SER I 13 " --> pdb=" O ARG I 10 " (cutoff:3.500A) Processing helix chain 'I' and resid 34 through 38 Processing helix chain 'I' and resid 48 through 53 removed outlier: 3.675A pdb=" N LEU I 53 " --> pdb=" O GLN I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 86 removed outlier: 3.751A pdb=" N GLN I 74 " --> pdb=" O GLY I 70 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR I 83 " --> pdb=" O ARG I 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 99 removed outlier: 3.795A pdb=" N GLU I 96 " --> pdb=" O SER I 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 32 removed outlier: 4.933A pdb=" N GLN J 20 " --> pdb=" O ARG J 16 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA J 21 " --> pdb=" O LEU J 17 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU J 24 " --> pdb=" O GLN J 20 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL J 26 " --> pdb=" O THR J 22 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR J 32 " --> pdb=" O THR J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 87 removed outlier: 3.598A pdb=" N LEU J 87 " --> pdb=" O THR J 83 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 57 Processing helix chain 'K' and resid 58 through 71 Processing helix chain 'K' and resid 95 through 102 Processing helix chain 'L' and resid 2 through 9 removed outlier: 3.892A pdb=" N ARG L 8 " --> pdb=" O ASN L 4 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 118 removed outlier: 4.658A pdb=" N VAL L 118 " --> pdb=" O LYS L 115 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 20 Processing helix chain 'M' and resid 25 through 36 removed outlier: 3.610A pdb=" N LYS M 30 " --> pdb=" O LYS M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 47 Processing helix chain 'M' and resid 48 through 59 removed outlier: 3.560A pdb=" N ASP M 57 " --> pdb=" O ASP M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 62 No H-bonds generated for 'chain 'M' and resid 60 through 62' Processing helix chain 'M' and resid 64 through 81 removed outlier: 3.669A pdb=" N ARG M 69 " --> pdb=" O GLU M 65 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG M 70 " --> pdb=" O GLY M 66 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 92 removed outlier: 3.500A pdb=" N ARG M 92 " --> pdb=" O LEU M 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 105 through 110 Processing helix chain 'N' and resid 4 through 19 removed outlier: 4.181A pdb=" N VAL N 10 " --> pdb=" O LYS N 6 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG N 12 " --> pdb=" O ARG N 8 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP N 17 " --> pdb=" O VAL N 13 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR N 19 " --> pdb=" O LEU N 15 " (cutoff:3.500A) Processing helix chain 'N' and resid 24 through 29 Processing helix chain 'N' and resid 30 through 32 No H-bonds generated for 'chain 'N' and resid 30 through 32' Processing helix chain 'N' and resid 39 through 50 removed outlier: 3.730A pdb=" N LEU N 45 " --> pdb=" O TRP N 41 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLN N 48 " --> pdb=" O VAL N 44 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 90 Processing helix chain 'O' and resid 3 through 15 removed outlier: 3.542A pdb=" N LYS O 9 " --> pdb=" O GLU O 5 " (cutoff:3.500A) Processing helix chain 'O' and resid 23 through 44 removed outlier: 3.565A pdb=" N ALA O 29 " --> pdb=" O GLU O 25 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLY O 40 " --> pdb=" O ASN O 36 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N HIS O 41 " --> pdb=" O HIS O 37 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU O 44 " --> pdb=" O GLY O 40 " (cutoff:3.500A) Processing helix chain 'O' and resid 51 through 73 removed outlier: 3.552A pdb=" N LEU O 55 " --> pdb=" O SER O 51 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG O 71 " --> pdb=" O ASP O 67 " (cutoff:3.500A) Processing helix chain 'O' and resid 73 through 85 Processing helix chain 'P' and resid 53 through 64 removed outlier: 3.521A pdb=" N GLY P 62 " --> pdb=" O ALA P 58 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 79 removed outlier: 3.516A pdb=" N LEU P 74 " --> pdb=" O ARG P 70 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 29 removed outlier: 3.840A pdb=" N LEU R 28 " --> pdb=" O ASP R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 47 through 64 removed outlier: 3.550A pdb=" N GLN R 51 " --> pdb=" O ARG R 47 " (cutoff:3.500A) Processing helix chain 'S' and resid 11 through 24 removed outlier: 3.681A pdb=" N LYS S 17 " --> pdb=" O HIS S 13 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA S 21 " --> pdb=" O LYS S 17 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER S 24 " --> pdb=" O LYS S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 69 through 74 removed outlier: 3.820A pdb=" N ALA S 74 " --> pdb=" O GLY S 71 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 6 No H-bonds generated for 'chain 'T' and resid 4 through 6' Processing helix chain 'T' and resid 7 through 41 removed outlier: 3.663A pdb=" N ILE T 11 " --> pdb=" O LYS T 7 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU T 14 " --> pdb=" O ALA T 10 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG T 23 " --> pdb=" O HIS T 19 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL T 34 " --> pdb=" O PHE T 30 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR T 35 " --> pdb=" O ILE T 31 " (cutoff:3.500A) Processing helix chain 'T' and resid 42 through 58 removed outlier: 3.570A pdb=" N ASN T 51 " --> pdb=" O GLN T 47 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN T 54 " --> pdb=" O PHE T 50 " (cutoff:3.500A) Proline residue: T 55 - end of helix Processing helix chain 'T' and resid 58 through 63 Processing helix chain 'T' and resid 67 through 85 removed outlier: 3.672A pdb=" N ASN T 77 " --> pdb=" O ARG T 73 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU T 78 " --> pdb=" O HIS T 74 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN T 81 " --> pdb=" O ASN T 77 " (cutoff:3.500A) Processing helix chain 'U' and resid 16 through 21 Processing helix chain 'U' and resid 27 through 32 Processing helix chain 'U' and resid 38 through 59 removed outlier: 3.516A pdb=" N ARG U 54 " --> pdb=" O SER U 50 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS U 55 " --> pdb=" O ALA U 51 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Y' and resid 28 through 29 removed outlier: 6.811A pdb=" N LYS Z 177 " --> pdb=" O ALA Z 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Z' and resid 162 through 170 removed outlier: 6.494A pdb=" N THR Z 180 " --> pdb=" O ILE Z 166 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N GLU Z 168 " --> pdb=" O SER Z 178 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N SER Z 178 " --> pdb=" O GLU Z 168 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLU Z 170 " --> pdb=" O ILE Z 176 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ILE Z 176 " --> pdb=" O GLU Z 170 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LYS Z 177 " --> pdb=" O ALA Z 134 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL Z 198 " --> pdb=" O GLN Z 322 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG Z 324 " --> pdb=" O VAL Z 198 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '03' and resid 170 through 176 removed outlier: 7.244A pdb=" N VAL03 42 " --> pdb=" O ILE03 175 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '03' and resid 60 through 63 removed outlier: 3.687A pdb=" N VAL03 161 " --> pdb=" O THR03 63 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '03' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain '04' and resid 2 through 4 Processing sheet with id=AA7, first strand: chain '04' and resid 100 through 104 removed outlier: 7.023A pdb=" N ILE04 90 " --> pdb=" O LEU04 80 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N LEU04 80 " --> pdb=" O ILE04 90 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU04 92 " --> pdb=" O GLU04 78 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '04' and resid 128 through 130 removed outlier: 6.578A pdb=" N THR04 172 " --> pdb=" O VAL04 164 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ARG04 166 " --> pdb=" O TYR04 170 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N TYR04 170 " --> pdb=" O ARG04 166 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LYS04 182 " --> pdb=" O ILE04 266 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ILE04 266 " --> pdb=" O LYS04 182 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '05' and resid 169 through 176 removed outlier: 5.247A pdb=" N THR05 171 " --> pdb=" O GLY05 111 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N GLY05 111 " --> pdb=" O THR05 171 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N GLN05 173 " --> pdb=" O VAL05 109 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL05 109 " --> pdb=" O GLN05 173 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N THR05 112 " --> pdb=" O ASP05 200 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ASP05 200 " --> pdb=" O THR05 112 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N LYS05 8 " --> pdb=" O GLU05 28 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N GLU05 28 " --> pdb=" O LYS05 8 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLY05 10 " --> pdb=" O VAL05 26 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '05' and resid 79 through 83 removed outlier: 6.722A pdb=" N THR05 51 " --> pdb=" O VAL05 34 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N VAL05 34 " --> pdb=" O THR05 51 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '05' and resid 115 through 119 removed outlier: 5.529A pdb=" N MET05 165 " --> pdb=" O LYS05 116 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N PHE05 118 " --> pdb=" O GLY05 163 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N GLY05 163 " --> pdb=" O PHE05 118 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '06' and resid 2 through 3 Processing sheet with id=AB4, first strand: chain '06' and resid 118 through 121 removed outlier: 6.087A pdb=" N ILE06 119 " --> pdb=" O MET06 188 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N ILE06 149 " --> pdb=" O THR06 189 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE06 148 " --> pdb=" O ARG06 170 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain '07' and resid 67 through 68 removed outlier: 3.698A pdb=" N GLY07 85 " --> pdb=" O THR07 67 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '08' and resid 15 through 19 removed outlier: 3.737A pdb=" N GLY08 30 " --> pdb=" O GLY08 27 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '08' and resid 120 through 126 removed outlier: 6.891A pdb=" N GLU08 129 " --> pdb=" O PRO08 125 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL08 89 " --> pdb=" O GLY08 160 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '08' and resid 94 through 98 removed outlier: 3.517A pdb=" N ARG08 94 " --> pdb=" O SER08 105 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '09' and resid 18 through 20 Processing sheet with id=AC1, first strand: chain '09' and resid 78 through 81 removed outlier: 7.237A pdb=" N VAL09 78 " --> pdb=" O ASN09 145 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N VAL09 147 " --> pdb=" O VAL09 78 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE09 80 " --> pdb=" O VAL09 147 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL09 144 " --> pdb=" O HIS09 128 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS09 128 " --> pdb=" O VAL09 144 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER09 131 " --> pdb=" O ARG09 116 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG09 116 " --> pdb=" O SER09 131 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '11' and resid 56 through 60 Processing sheet with id=AC3, first strand: chain '12' and resid 122 through 124 removed outlier: 6.284A pdb=" N TYR12 16 " --> pdb=" O ILE12 55 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LEU12 57 " --> pdb=" O TYR12 16 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL12 18 " --> pdb=" O LEU12 57 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '12' and resid 76 through 77 Processing sheet with id=AC5, first strand: chain '13' and resid 6 through 7 removed outlier: 3.680A pdb=" N THR13 6 " --> pdb=" O CYS13 21 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA13 16 " --> pdb=" O ALA13 46 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA13 46 " --> pdb=" O ALA13 16 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ARG13 18 " --> pdb=" O LYS13 44 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LYS13 40 " --> pdb=" O ILE13 22 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N VAL13 24 " --> pdb=" O ILE13 38 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ILE13 38 " --> pdb=" O VAL13 24 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N VAL13 62 " --> pdb=" O VAL13 85 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N VAL13 85 " --> pdb=" O VAL13 62 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG13 64 " --> pdb=" O ALA13 83 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '13' and resid 69 through 70 removed outlier: 4.292A pdb=" N VAL13 76 " --> pdb=" O VAL18 72 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ARG18 61 " --> pdb=" O VAL18 46 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N VAL18 46 " --> pdb=" O ARG18 61 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N ILE18 63 " --> pdb=" O GLY18 44 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N GLY18 44 " --> pdb=" O ILE18 63 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N TRP18 30 " --> pdb=" O VAL18 80 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL18 80 " --> pdb=" O TRP18 30 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '13' and resid 69 through 70 removed outlier: 4.292A pdb=" N VAL13 76 " --> pdb=" O VAL18 72 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ARG18 61 " --> pdb=" O VAL18 46 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N VAL18 46 " --> pdb=" O ARG18 61 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N ILE18 63 " --> pdb=" O GLY18 44 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N GLY18 44 " --> pdb=" O ILE18 63 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR18 24 " --> pdb=" O LYS18 86 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain '14' and resid 74 through 77 removed outlier: 6.703A pdb=" N ALA14 108 " --> pdb=" O ARG14 126 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain '14' and resid 89 through 90 Processing sheet with id=AD1, first strand: chain '15' and resid 62 through 65 removed outlier: 3.547A pdb=" N LYS15 62 " --> pdb=" O ASP15 106 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL15 101 " --> pdb=" O ALA15 35 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ALA15 35 " --> pdb=" O VAL15 101 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR15 103 " --> pdb=" O LEU15 33 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain '15' and resid 39 through 42 removed outlier: 6.034A pdb=" N VAL15 89 " --> pdb=" O GLU15 75 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLU15 75 " --> pdb=" O VAL15 89 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain '16' and resid 33 through 37 removed outlier: 4.541A pdb=" N MET16 110 " --> pdb=" O CYS16 100 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain '17' and resid 47 through 50 removed outlier: 6.713A pdb=" N VAL17 39 " --> pdb=" O LEU17 48 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ALA17 50 " --> pdb=" O ALA17 37 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ALA17 37 " --> pdb=" O ALA17 50 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N HIS17 34 " --> pdb=" O THR17 31 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain '18' and resid 89 through 90 removed outlier: 4.333A pdb=" N LYS18 110 " --> pdb=" O ALA18 90 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain '20' and resid 11 through 15 removed outlier: 6.750A pdb=" N TYR20 2 " --> pdb=" O ILE20 41 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ILE20 41 " --> pdb=" O TYR20 2 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL20 4 " --> pdb=" O LEU20 39 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain '20' and resid 21 through 23 removed outlier: 6.996A pdb=" N PHE20 93 " --> pdb=" O HIS20 66 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N HIS20 66 " --> pdb=" O PHE20 93 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ASP20 95 " --> pdb=" O VAL20 64 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LYS20 60 " --> pdb=" O THR20 99 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain '20' and resid 74 through 78 removed outlier: 4.079A pdb=" N TYR20 83 " --> pdb=" O ARG20 78 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain '21' and resid 4 through 5 removed outlier: 6.426A pdb=" N ASP21 94 " --> pdb=" O ILE21 85 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ILE21 85 " --> pdb=" O ASP21 94 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE21 96 " --> pdb=" O LYS21 83 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LYS21 83 " --> pdb=" O ILE21 96 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LYS21 98 " --> pdb=" O SER21 81 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N SER21 81 " --> pdb=" O LYS21 98 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N THR21 100 " --> pdb=" O GLY21 79 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N SER21 108 " --> pdb=" O VAL21 71 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL21 71 " --> pdb=" O SER21 108 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain '22' and resid 11 through 14 removed outlier: 4.358A pdb=" N ALA22 13 " --> pdb=" O LYS22 33 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS22 81 " --> pdb=" O VAL22 34 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N TRP22 80 " --> pdb=" O VAL22 62 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N VAL22 62 " --> pdb=" O TRP22 80 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LYS22 82 " --> pdb=" O THR22 60 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N THR22 60 " --> pdb=" O LYS22 82 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N TYR22 84 " --> pdb=" O VAL22 58 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL22 58 " --> pdb=" O TYR22 84 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR22 86 " --> pdb=" O GLU22 56 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain '23' and resid 64 through 65 removed outlier: 6.702A pdb=" N LYS23 32 " --> pdb=" O VAL23 27 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N VAL23 27 " --> pdb=" O LYS23 32 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ILE23 34 " --> pdb=" O LYS23 25 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain '23' and resid 40 through 44 Processing sheet with id=AE4, first strand: chain '23' and resid 85 through 87 Processing sheet with id=AE5, first strand: chain '24' and resid 3 through 8 removed outlier: 7.661A pdb=" N ASN24 5 " --> pdb=" O ASP24 43 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ASP24 43 " --> pdb=" O ASN24 5 " (cutoff:3.500A) removed outlier: 9.027A pdb=" N LYS24 25 " --> pdb=" O GLN24 87 " (cutoff:3.500A) removed outlier: 10.029A pdb=" N ILE24 89 " --> pdb=" O LYS24 25 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N PHE24 91 " --> pdb=" O PRO24 27 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ILE24 29 " --> pdb=" O PHE24 91 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ARG24 93 " --> pdb=" O ILE24 29 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N TYR24 31 " --> pdb=" O ARG24 93 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N VAL24 92 " --> pdb=" O ALA24 74 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ALA24 74 " --> pdb=" O VAL24 92 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain '25' and resid 18 through 19 removed outlier: 6.658A pdb=" N ILE25 32 " --> pdb=" O ALA25 57 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA25 57 " --> pdb=" O ILE25 32 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL25 34 " --> pdb=" O LEU25 55 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain '25' and resid 26 through 27 removed outlier: 6.956A pdb=" N HIS25 42 " --> pdb=" O ILE25 76 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N ILE25 78 " --> pdb=" O HIS25 42 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain '26' and resid 12 through 15 Processing sheet with id=AE9, first strand: chain '26' and resid 32 through 39 Processing sheet with id=AF1, first strand: chain '28' and resid 34 through 38 Processing sheet with id=AF2, first strand: chain '29' and resid 12 through 15 Processing sheet with id=AF3, first strand: chain '30' and resid 28 through 29 Processing sheet with id=AF4, first strand: chain '30' and resid 47 through 48 Processing sheet with id=AF5, first strand: chain '31' and resid 19 through 25 Processing sheet with id=AF6, first strand: chain '31' and resid 38 through 39 Processing sheet with id=AF7, first strand: chain '33' and resid 14 through 15 Processing sheet with id=AF8, first strand: chain '34' and resid 2 through 4 removed outlier: 7.229A pdb=" N LYS34 2 " --> pdb=" O ARG34 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain '34' and resid 17 through 19 Processing sheet with id=AG1, first strand: chain 'Z' and resid 239 through 240 removed outlier: 4.074A pdb=" N ARG Z 240 " --> pdb=" O THR Z 264 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR Z 264 " --> pdb=" O ARG Z 240 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Z' and resid 239 through 240 removed outlier: 4.074A pdb=" N ARG Z 240 " --> pdb=" O THR Z 264 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR Z 264 " --> pdb=" O ARG Z 240 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 16 through 17 removed outlier: 3.744A pdb=" N HIS B 17 " --> pdb=" O HIS B 38 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N HIS B 38 " --> pdb=" O HIS B 17 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'B' and resid 89 through 91 removed outlier: 3.573A pdb=" N PHE B 89 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU B 67 " --> pdb=" O PHE B 161 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 19 through 20 removed outlier: 6.640A pdb=" N HIS C 68 " --> pdb=" O SER C 52 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE C 54 " --> pdb=" O THR C 66 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR C 66 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ILE C 56 " --> pdb=" O ARG C 64 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ARG C 64 " --> pdb=" O ILE C 56 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 163 through 170 removed outlier: 3.622A pdb=" N GLY C 154 " --> pdb=" O ARG C 163 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY C 147 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY C 193 " --> pdb=" O THR C 190 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL C 199 " --> pdb=" O ASN C 184 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN C 184 " --> pdb=" O VAL C 199 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'D' and resid 127 through 128 Processing sheet with id=AG8, first strand: chain 'E' and resid 13 through 17 removed outlier: 5.282A pdb=" N LEU E 14 " --> pdb=" O VAL E 37 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL E 37 " --> pdb=" O LEU E 14 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA E 16 " --> pdb=" O LEU E 35 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 44 through 45 Processing sheet with id=AH1, first strand: chain 'E' and resid 84 through 87 removed outlier: 4.213A pdb=" N VAL E 93 " --> pdb=" O GLY E 86 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N GLY E 103 " --> pdb=" O VAL E 122 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ALA E 124 " --> pdb=" O GLY E 103 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE E 105 " --> pdb=" O ALA E 124 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 2 through 3 Processing sheet with id=AH3, first strand: chain 'F' and resid 41 through 43 removed outlier: 5.068A pdb=" N ASP F 41 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU F 61 " --> pdb=" O ASP F 41 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY F 43 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL F 7 " --> pdb=" O SER F 87 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER F 87 " --> pdb=" O VAL F 7 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N MET F 9 " --> pdb=" O ILE F 85 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 72 through 75 Processing sheet with id=AH5, first strand: chain 'H' and resid 23 through 27 Processing sheet with id=AH6, first strand: chain 'H' and resid 73 through 76 Processing sheet with id=AH7, first strand: chain 'H' and resid 73 through 76 removed outlier: 6.642A pdb=" N VAL H 102 " --> pdb=" O ILE H 125 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N TYR H 127 " --> pdb=" O ILE H 100 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ILE H 100 " --> pdb=" O TYR H 127 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'I' and resid 5 through 7 removed outlier: 3.527A pdb=" N PHE I 19 " --> pdb=" O TYR I 63 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'J' and resid 45 through 52 removed outlier: 3.525A pdb=" N GLU J 47 " --> pdb=" O ILE J 67 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL J 51 " --> pdb=" O ASP J 63 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'K' and resid 40 through 45 removed outlier: 6.073A pdb=" N ALA K 40 " --> pdb=" O ASP K 35 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ASP K 35 " --> pdb=" O ALA K 40 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY K 42 " --> pdb=" O ILE K 33 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLY K 18 " --> pdb=" O GLU K 82 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N MET K 84 " --> pdb=" O GLY K 18 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ALA K 20 " --> pdb=" O MET K 84 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N LYS K 86 " --> pdb=" O ALA K 20 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ILE K 22 " --> pdb=" O LYS K 86 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU K 81 " --> pdb=" O ILE K 106 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ASN K 108 " --> pdb=" O LEU K 81 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'L' and resid 28 through 30 removed outlier: 4.317A pdb=" N TYR L 94 " --> pdb=" O THR L 63 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N LYS L 50 " --> pdb=" O ILE L 66 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ARG L 35 " --> pdb=" O ARG L 53 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'P' and resid 8 through 11 removed outlier: 6.932A pdb=" N TYR P 17 " --> pdb=" O PHE P 38 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N PHE P 38 " --> pdb=" O TYR P 17 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL P 19 " --> pdb=" O VAL P 36 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG P 51 " --> pdb=" O PHE P 38 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'P' and resid 8 through 11 removed outlier: 6.988A pdb=" N VAL P 2 " --> pdb=" O THR P 66 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'Q' and resid 7 through 13 removed outlier: 7.328A pdb=" N VAL Q 21 " --> pdb=" O VAL Q 12 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TRP Q 72 " --> pdb=" O HIS Q 44 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY Q 9 " --> pdb=" O VAL Q 58 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'Q' and resid 28 through 29 Processing sheet with id=AI7, first strand: chain 'S' and resid 31 through 32 1837 hydrogen bonds defined for protein. 5130 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3668 hydrogen bonds 5906 hydrogen bond angles 0 basepair planarities 1460 basepair parallelities 2754 stacking parallelities Total time for adding SS restraints: 275.57 Time building geometry restraints manager: 66.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 22691 1.33 - 1.45: 66084 1.45 - 1.57: 66623 1.57 - 1.69: 9449 1.69 - 1.81: 300 Bond restraints: 165147 Sorted by residual: bond pdb=" CA PRO10 68 " pdb=" C PRO10 68 " ideal model delta sigma weight residual 1.524 1.576 -0.052 1.06e-02 8.90e+03 2.41e+01 bond pdb=" CA PRO11 73 " pdb=" C PRO11 73 " ideal model delta sigma weight residual 1.514 1.540 -0.026 5.50e-03 3.31e+04 2.19e+01 bond pdb=" N LYS B 27 " pdb=" CA LYS B 27 " ideal model delta sigma weight residual 1.462 1.429 0.032 8.50e-03 1.38e+04 1.45e+01 bond pdb=" N SER N 54 " pdb=" CA SER N 54 " ideal model delta sigma weight residual 1.457 1.506 -0.049 1.29e-02 6.01e+03 1.44e+01 bond pdb=" CA PRO U 10 " pdb=" C PRO U 10 " ideal model delta sigma weight residual 1.520 1.572 -0.053 1.42e-02 4.96e+03 1.39e+01 ... (remaining 165142 not shown) Histogram of bond angle deviations from ideal: 94.08 - 104.15: 17122 104.15 - 114.22: 114380 114.22 - 124.30: 94022 124.30 - 134.37: 20803 134.37 - 144.45: 1 Bond angle restraints: 246328 Sorted by residual: angle pdb=" N VAL K 73 " pdb=" CA VAL K 73 " pdb=" C VAL K 73 " ideal model delta sigma weight residual 113.20 104.12 9.08 9.60e-01 1.09e+00 8.95e+01 angle pdb=" N ASP20 55 " pdb=" CA ASP20 55 " pdb=" C ASP20 55 " ideal model delta sigma weight residual 111.02 122.15 -11.13 1.22e+00 6.72e-01 8.33e+01 angle pdb=" N PHE U 11 " pdb=" CA PHE U 11 " pdb=" C PHE U 11 " ideal model delta sigma weight residual 112.72 123.32 -10.60 1.28e+00 6.10e-01 6.86e+01 angle pdb=" N GLU F 98 " pdb=" CA GLU F 98 " pdb=" C GLU F 98 " ideal model delta sigma weight residual 109.63 121.69 -12.06 1.49e+00 4.50e-01 6.56e+01 angle pdb=" N GLY06 81 " pdb=" CA GLY06 81 " pdb=" C GLY06 81 " ideal model delta sigma weight residual 113.18 94.08 19.10 2.37e+00 1.78e-01 6.50e+01 ... (remaining 246323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 94645 35.87 - 71.75: 9769 71.75 - 107.62: 1137 107.62 - 143.50: 13 143.50 - 179.37: 26 Dihedral angle restraints: 105590 sinusoidal: 87087 harmonic: 18503 Sorted by residual: dihedral pdb=" C4' C X 34 " pdb=" C3' C X 34 " pdb=" C2' C X 34 " pdb=" C1' C X 34 " ideal model delta sinusoidal sigma weight residual 36.00 -36.47 72.47 1 8.00e+00 1.56e-02 1.05e+02 dihedral pdb=" O4' U012457 " pdb=" C1' U012457 " pdb=" N1 U012457 " pdb=" C2 U012457 " ideal model delta sinusoidal sigma weight residual -160.00 17.16 -177.16 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U011917 " pdb=" C1' U011917 " pdb=" N1 U011917 " pdb=" C2 U011917 " ideal model delta sinusoidal sigma weight residual 200.00 30.63 169.37 1 1.50e+01 4.44e-03 8.46e+01 ... (remaining 105587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 24786 0.100 - 0.199: 5887 0.199 - 0.299: 579 0.299 - 0.399: 61 0.399 - 0.498: 14 Chirality restraints: 31327 Sorted by residual: chirality pdb=" CA PRO14 119 " pdb=" N PRO14 119 " pdb=" C PRO14 119 " pdb=" CB PRO14 119 " both_signs ideal model delta sigma weight residual False 2.72 2.22 0.50 2.00e-01 2.50e+01 6.21e+00 chirality pdb=" CA PRO32 7 " pdb=" N PRO32 7 " pdb=" C PRO32 7 " pdb=" CB PRO32 7 " both_signs ideal model delta sigma weight residual False 2.72 2.24 0.48 2.00e-01 2.50e+01 5.78e+00 chirality pdb=" CA PRO C 72 " pdb=" N PRO C 72 " pdb=" C PRO C 72 " pdb=" CB PRO C 72 " both_signs ideal model delta sigma weight residual False 2.72 2.26 0.46 2.00e-01 2.50e+01 5.37e+00 ... (remaining 31324 not shown) Planarity restraints: 13708 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U012504 " 0.099 2.00e-02 2.50e+03 5.86e-02 7.74e+01 pdb=" N1 U012504 " 0.002 2.00e-02 2.50e+03 pdb=" C2 U012504 " -0.018 2.00e-02 2.50e+03 pdb=" O2 U012504 " -0.035 2.00e-02 2.50e+03 pdb=" N3 U012504 " -0.027 2.00e-02 2.50e+03 pdb=" C4 U012504 " -0.027 2.00e-02 2.50e+03 pdb=" O4 U012504 " 0.112 2.00e-02 2.50e+03 pdb=" C5 U012504 " -0.062 2.00e-02 2.50e+03 pdb=" C6 U012504 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U012109 " 0.084 2.00e-02 2.50e+03 4.45e-02 4.46e+01 pdb=" N1 U012109 " -0.005 2.00e-02 2.50e+03 pdb=" C2 U012109 " -0.016 2.00e-02 2.50e+03 pdb=" O2 U012109 " -0.033 2.00e-02 2.50e+03 pdb=" N3 U012109 " -0.011 2.00e-02 2.50e+03 pdb=" C4 U012109 " -0.011 2.00e-02 2.50e+03 pdb=" O4 U012109 " 0.076 2.00e-02 2.50e+03 pdb=" C5 U012109 " -0.042 2.00e-02 2.50e+03 pdb=" C6 U012109 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 305 " -0.091 2.00e-02 2.50e+03 3.85e-02 4.45e+01 pdb=" N9 G A 305 " 0.007 2.00e-02 2.50e+03 pdb=" C8 G A 305 " 0.045 2.00e-02 2.50e+03 pdb=" N7 G A 305 " 0.039 2.00e-02 2.50e+03 pdb=" C5 G A 305 " 0.016 2.00e-02 2.50e+03 pdb=" C6 G A 305 " -0.018 2.00e-02 2.50e+03 pdb=" O6 G A 305 " -0.061 2.00e-02 2.50e+03 pdb=" N1 G A 305 " -0.011 2.00e-02 2.50e+03 pdb=" C2 G A 305 " 0.010 2.00e-02 2.50e+03 pdb=" N2 G A 305 " 0.022 2.00e-02 2.50e+03 pdb=" N3 G A 305 " 0.020 2.00e-02 2.50e+03 pdb=" C4 G A 305 " 0.022 2.00e-02 2.50e+03 ... (remaining 13705 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 5434 2.67 - 3.23: 129972 3.23 - 3.78: 282176 3.78 - 4.34: 390558 4.34 - 4.90: 540937 Nonbonded interactions: 1349077 Sorted by model distance: nonbonded pdb=" OG SER C 19 " pdb=" O GLU N 91 " model vdw 2.111 2.440 nonbonded pdb=" N GLY20 50 " pdb=" N VAL20 51 " model vdw 2.318 2.560 nonbonded pdb=" O PRO Z 267 " pdb=" OG1 THR Z 268 " model vdw 2.329 2.440 nonbonded pdb=" O ALA11 14 " pdb=" OG1 THR11 45 " model vdw 2.332 2.440 nonbonded pdb=" OG1 THR E 79 " pdb=" O PRO E 97 " model vdw 2.332 2.440 ... (remaining 1349072 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'W' and (resid 1 through 33 or (resid 34 through 35 and (name P or name O \ P1 or name OP2 or name O5' or name C5' or name C4' or name O4' or name C3' or na \ me O3' or name C2' or name O2' or name C1')) or resid 36 through 76 or resid 101 \ through 102)) selection = chain 'X' } 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: 1.890 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: 0.180 Extract box with map and model: 13.430 Check model and map are aligned: 1.830 Set scattering table: 1.150 Process input model: 579.030 Find NCS groups from input model: 3.160 Set up NCS constraints: 0.400 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 603.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 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 : 0.006 0.072 165147 Z= 0.354 Angle : 0.918 19.104 246328 Z= 0.601 Chirality : 0.083 0.498 31327 Planarity : 0.008 0.085 13708 Dihedral : 21.992 179.371 93722 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.96 % Allowed : 10.57 % Favored : 88.47 % Rotamer: Outliers : 0.93 % Allowed : 5.42 % Favored : 93.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -5.08 (0.08), residues: 6453 helix: -3.92 (0.06), residues: 2051 sheet: -2.76 (0.13), residues: 1189 loop : -3.21 (0.09), residues: 3213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.007 TRP04 212 HIS 0.001 0.000 HIS J 70 PHE 0.029 0.004 PHE U 36 TYR 0.038 0.005 TYR04 170 ARG 0.009 0.000 ARG D 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12906 Ramachandran restraints generated. 6453 Oldfield, 0 Emsley, 6453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12906 Ramachandran restraints generated. 6453 Oldfield, 0 Emsley, 6453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2147 residues out of total 5356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 2098 time to evaluate : 7.131 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 03 173 THR cc_start: 0.6784 (p) cc_final: 0.6271 (t) REVERT: 04 29 PHE cc_start: 0.7700 (t80) cc_final: 0.7298 (t80) REVERT: 08 57 TYR cc_start: 0.7849 (m-80) cc_final: 0.7605 (m-80) REVERT: 08 74 MET cc_start: 0.8619 (mtp) cc_final: 0.8337 (mtm) REVERT: 08 76 ILE cc_start: 0.9142 (mm) cc_final: 0.8909 (mm) REVERT: 09 27 ARG cc_start: 0.7308 (ptt180) cc_final: 0.7047 (ptt180) REVERT: 09 43 ASN cc_start: 0.9451 (m-40) cc_final: 0.9070 (m-40) REVERT: 09 58 LEU cc_start: 0.9238 (mt) cc_final: 0.8886 (mt) REVERT: 09 130 VAL cc_start: 0.8344 (t) cc_final: 0.8094 (t) REVERT: 10 5 LEU cc_start: 0.9485 (tt) cc_final: 0.9266 (tt) REVERT: 10 39 THR cc_start: 0.9030 (m) cc_final: 0.8484 (p) REVERT: 11 36 GLU cc_start: 0.8792 (tp30) cc_final: 0.8548 (tm-30) REVERT: 11 61 TYR cc_start: 0.8929 (m-80) cc_final: 0.8492 (m-80) REVERT: 11 67 THR cc_start: 0.9160 (m) cc_final: 0.8747 (m) REVERT: 11 116 MET cc_start: 0.7443 (mtt) cc_final: 0.4624 (ttm) REVERT: 11 124 MET cc_start: 0.9358 (mmm) cc_final: 0.8978 (mmp) REVERT: 11 129 GLU cc_start: 0.9527 (tt0) cc_final: 0.9308 (pt0) REVERT: 11 137 LEU cc_start: 0.9240 (tp) cc_final: 0.8981 (tp) REVERT: 20 11 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7766 (mt0) REVERT: 22 1 MET cc_start: 0.5407 (ptp) cc_final: 0.4721 (ptt) REVERT: 26 55 MET cc_start: 0.7990 (mtp) cc_final: 0.7552 (mtt) REVERT: 27 2 LYS cc_start: 0.8659 (pttm) cc_final: 0.8314 (pttm) REVERT: 27 10 SER cc_start: 0.9078 (t) cc_final: 0.8262 (p) REVERT: 27 58 ASN cc_start: 0.8763 (t0) cc_final: 0.8508 (t0) REVERT: 29 9 TYR cc_start: 0.7066 (t80) cc_final: 0.5916 (t80) REVERT: 29 60 PHE cc_start: 0.8534 (t80) cc_final: 0.7461 (t80) REVERT: 33 16 THR cc_start: 0.8190 (p) cc_final: 0.7891 (t) REVERT: Z 153 LEU cc_start: 0.8912 (tp) cc_final: 0.8526 (tp) REVERT: Z 221 PHE cc_start: 0.8841 (t80) cc_final: 0.8598 (t80) REVERT: Z 223 TYR cc_start: 0.8904 (p90) cc_final: 0.7556 (p90) REVERT: Z 244 TYR cc_start: 0.8947 (p90) cc_final: 0.8584 (p90) REVERT: Z 296 TYR cc_start: 0.9522 (t80) cc_final: 0.9312 (t80) REVERT: Z 350 ASP cc_start: 0.7717 (t70) cc_final: 0.7483 (t0) REVERT: E 139 THR cc_start: 0.8877 (p) cc_final: 0.8660 (p) REVERT: F 8 PHE cc_start: 0.8509 (p90) cc_final: 0.8278 (p90) REVERT: F 21 MET cc_start: 0.8947 (mmm) cc_final: 0.8735 (mmm) REVERT: F 74 LEU cc_start: 0.9587 (tp) cc_final: 0.9347 (tp) REVERT: F 78 PHE cc_start: 0.8904 (m-80) cc_final: 0.8529 (m-80) REVERT: F 92 THR cc_start: 0.5752 (p) cc_final: 0.5349 (p) REVERT: I 46 VAL cc_start: 0.8390 (m) cc_final: 0.7955 (m) REVERT: I 55 ASP cc_start: 0.8133 (t70) cc_final: 0.7471 (t0) REVERT: I 67 LYS cc_start: 0.8671 (ptmm) cc_final: 0.8153 (tptp) REVERT: I 99 LYS cc_start: 0.9303 (tttt) cc_final: 0.9057 (mtpt) REVERT: J 91 ASP cc_start: 0.6996 (OUTLIER) cc_final: 0.6714 (p0) REVERT: J 100 ILE cc_start: 0.8773 (pt) cc_final: 0.8383 (mp) REVERT: J 101 SER cc_start: 0.8829 (m) cc_final: 0.8595 (p) REVERT: K 35 ASP cc_start: 0.8596 (t70) cc_final: 0.8026 (t70) REVERT: L 61 GLU cc_start: 0.7208 (tt0) cc_final: 0.6749 (tt0) REVERT: L 76 HIS cc_start: 0.8089 (m90) cc_final: 0.7661 (m-70) REVERT: S 66 VAL cc_start: 0.8315 (m) cc_final: 0.7667 (m) REVERT: T 85 LEU cc_start: 0.8802 (mt) cc_final: 0.8597 (tp) REVERT: U 65 ARG cc_start: 0.8343 (mmt-90) cc_final: 0.8109 (mmp80) outliers start: 49 outliers final: 7 residues processed: 2120 average time/residue: 1.4578 time to fit residues: 5245.4667 Evaluate side-chains 1313 residues out of total 5356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1304 time to evaluate : 7.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 202 ARG Chi-restraints excluded: chain 10 residue 8 LYS Chi-restraints excluded: chain 11 residue 2 LYS Chi-restraints excluded: chain 20 residue 11 GLN Chi-restraints excluded: chain 22 residue 9 LYS Chi-restraints excluded: chain 24 residue 83 LYS Chi-restraints excluded: chain 34 residue 14 CYS Chi-restraints excluded: chain 34 residue 27 CYS Chi-restraints excluded: chain J residue 91 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1102 random chunks: chunk 930 optimal weight: 4.9990 chunk 835 optimal weight: 40.0000 chunk 463 optimal weight: 50.0000 chunk 285 optimal weight: 20.0000 chunk 563 optimal weight: 10.0000 chunk 446 optimal weight: 30.0000 chunk 863 optimal weight: 2.9990 chunk 334 optimal weight: 20.0000 chunk 525 optimal weight: 10.0000 chunk 642 optimal weight: 7.9990 chunk 1000 optimal weight: 7.9990 overall best weight: 6.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 03 67 HIS ** 03 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 04 45 ASN 04 59 GLN 04 85 ASN 04 89 ASN ** 04 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 04 133 ASN 04 142 ASN 04 152 GLN 04 196 ASN 04 199 HIS 04 259 ASN 05 32 ASN 05 36 GLN ** 05 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 05 140 HIS 05 173 GLN ** 06 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 06 163 ASN 07 51 ASN 07 126 ASN 08 37 ASN ** 08 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 09 135 HIS ** 11 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 12 128 ASN 12 132 HIS ** 12 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 82 ASN ** 13 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 93 GLN 14 54 GLN 16 11 ASN 16 13 ASN 16 62 ASN 16 73 ASN ** 17 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 18 51 ASN 19 80 ASN 20 11 GLN 20 18 GLN ** 20 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 21 57 ASN 22 59 ASN 23 68 ASN ** 25 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 25 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 26 16 ASN 26 33 HIS ** 27 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 27 36 GLN 27 58 ASN 29 6 HIS 29 41 HIS 30 40 HIS 32 6 GLN 32 13 ASN ** 34 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 8 ASN Z 9 ASN Z 48 ASN Z 133 GLN Z 199 HIS ** Z 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 275 GLN Z 286 GLN Z 346 GLN B 23 ASN B 38 HIS B 176 ASN B 177 ASN C 40 GLN C 138 GLN C 139 ASN C 175 HIS D 40 HIS D 73 ASN D 88 ASN ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 GLN E 81 GLN ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 131 ASN E 145 ASN F 37 HIS F 52 ASN ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 81 ASN G 27 ASN G 96 ASN G 121 ASN G 141 HIS H 20 ASN H 66 GLN I 31 GLN ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 35 GLN J 58 ASN K 100 ASN L 45 ASN L 72 ASN ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 13 HIS ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 ASN N 65 GLN O 27 GLN ** O 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 26 ASN ** P 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 30 ASN R 53 GLN R 73 HIS S 68 HIS ** T 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 51 ASN ** T 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 83 ASN Total number of N/Q/H flips: 94 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 165147 Z= 0.268 Angle : 0.710 13.113 246328 Z= 0.368 Chirality : 0.040 0.473 31327 Planarity : 0.006 0.089 13708 Dihedral : 22.718 179.882 81084 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.55 % Favored : 91.20 % Rotamer: Outliers : 3.85 % Allowed : 16.28 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -3.45 (0.09), residues: 6453 helix: -1.57 (0.10), residues: 2157 sheet: -2.30 (0.14), residues: 1163 loop : -2.80 (0.10), residues: 3133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP N 41 HIS 0.016 0.002 HIS M 11 PHE 0.026 0.002 PHE17 92 TYR 0.024 0.002 TYR F 4 ARG 0.020 0.001 ARG U 44 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12906 Ramachandran restraints generated. 6453 Oldfield, 0 Emsley, 6453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12906 Ramachandran restraints generated. 6453 Oldfield, 0 Emsley, 6453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1703 residues out of total 5356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 1500 time to evaluate : 7.100 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: 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: 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: symmetry clash revert: symmetry clash REVERT: 03 189 LEU cc_start: 0.9055 (tt) cc_final: 0.8808 (mt) REVERT: 06 1 MET cc_start: 0.7884 (pmm) cc_final: 0.7570 (pmm) REVERT: 08 172 GLU cc_start: 0.7565 (tp30) cc_final: 0.7311 (tp30) REVERT: 09 4 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8102 (mm) REVERT: 09 130 VAL cc_start: 0.8494 (t) cc_final: 0.8262 (t) REVERT: 09 132 PHE cc_start: 0.8421 (m-80) cc_final: 0.8103 (m-80) REVERT: 10 39 THR cc_start: 0.9250 (m) cc_final: 0.8789 (p) REVERT: 11 18 ASN cc_start: 0.8711 (t0) cc_final: 0.8304 (p0) REVERT: 11 35 MET cc_start: 0.9154 (tpp) cc_final: 0.8847 (tpt) REVERT: 11 61 TYR cc_start: 0.8947 (m-80) cc_final: 0.8496 (m-80) REVERT: 11 116 MET cc_start: 0.7075 (mtt) cc_final: 0.4846 (ttm) REVERT: 11 124 MET cc_start: 0.9358 (mmm) cc_final: 0.8985 (mmp) REVERT: 11 135 MET cc_start: 0.5321 (mmp) cc_final: 0.4546 (mmm) REVERT: 11 137 LEU cc_start: 0.9188 (tp) cc_final: 0.8927 (tp) REVERT: 12 60 ASP cc_start: 0.8394 (p0) cc_final: 0.7846 (p0) REVERT: 13 82 ASN cc_start: 0.7021 (m-40) cc_final: 0.6816 (m-40) REVERT: 13 89 ASN cc_start: 0.7528 (m-40) cc_final: 0.7244 (m-40) REVERT: 13 93 GLN cc_start: 0.9019 (mm-40) cc_final: 0.8791 (mm110) REVERT: 18 8 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7343 (tm-30) REVERT: 18 26 GLU cc_start: 0.8223 (tp30) cc_final: 0.7634 (tp30) REVERT: 20 55 ASP cc_start: 0.8369 (p0) cc_final: 0.8073 (p0) REVERT: 22 93 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7612 (mt) REVERT: 25 11 ASP cc_start: 0.7665 (t0) cc_final: 0.7098 (t0) REVERT: 27 2 LYS cc_start: 0.8798 (pttm) cc_final: 0.8576 (ptpp) REVERT: 27 58 ASN cc_start: 0.8729 (t0) cc_final: 0.8496 (t0) REVERT: 28 24 LEU cc_start: 0.8723 (tp) cc_final: 0.8498 (tt) REVERT: 29 56 ARG cc_start: 0.6689 (tpt90) cc_final: 0.5823 (tpt90) REVERT: 29 60 PHE cc_start: 0.8421 (t80) cc_final: 0.7792 (t80) REVERT: 31 26 LYS cc_start: 0.9522 (tptp) cc_final: 0.9302 (tptp) REVERT: 31 28 THR cc_start: 0.9058 (m) cc_final: 0.8242 (p) REVERT: 34 4 ARG cc_start: 0.8182 (mtp85) cc_final: 0.7324 (mtp85) REVERT: Z 24 TYR cc_start: 0.8622 (m-80) cc_final: 0.7825 (m-80) REVERT: Z 123 TYR cc_start: 0.8111 (m-80) cc_final: 0.7598 (m-80) REVERT: Z 221 PHE cc_start: 0.8914 (t80) cc_final: 0.8709 (t80) REVERT: Z 244 TYR cc_start: 0.9074 (p90) cc_final: 0.8625 (p90) REVERT: Z 262 ARG cc_start: 0.8514 (tmt90) cc_final: 0.8306 (ttp80) REVERT: Z 265 HIS cc_start: 0.8728 (t70) cc_final: 0.8436 (t70) REVERT: Z 296 TYR cc_start: 0.9450 (t80) cc_final: 0.9191 (t80) REVERT: C 33 ASP cc_start: 0.8477 (t0) cc_final: 0.8118 (t0) REVERT: C 133 MET cc_start: 0.7596 (tmm) cc_final: 0.7386 (tmm) REVERT: F 21 MET cc_start: 0.8977 (mmm) cc_final: 0.8564 (mmm) REVERT: F 68 GLN cc_start: 0.8853 (pp30) cc_final: 0.8484 (pp30) REVERT: F 78 PHE cc_start: 0.8938 (m-80) cc_final: 0.8691 (m-80) REVERT: I 55 ASP cc_start: 0.8535 (t70) cc_final: 0.7846 (t0) REVERT: I 63 TYR cc_start: 0.7906 (t80) cc_final: 0.7681 (t80) REVERT: J 42 LEU cc_start: 0.8567 (mp) cc_final: 0.8331 (mp) REVERT: J 82 LYS cc_start: 0.9097 (pttp) cc_final: 0.8612 (pttm) REVERT: K 63 GLN cc_start: 0.8358 (tm-30) cc_final: 0.7540 (tm-30) REVERT: K 112 VAL cc_start: 0.8423 (m) cc_final: 0.8128 (m) REVERT: L 76 HIS cc_start: 0.8090 (m90) cc_final: 0.7592 (m90) REVERT: M 47 LEU cc_start: 0.8639 (mt) cc_final: 0.8242 (tp) REVERT: N 5 MET cc_start: 0.8626 (tpt) cc_final: 0.8180 (mmm) REVERT: R 71 ASP cc_start: 0.7851 (m-30) cc_final: 0.7541 (m-30) REVERT: T 85 LEU cc_start: 0.8881 (mt) cc_final: 0.8669 (tp) REVERT: U 3 ILE cc_start: 0.7544 (mp) cc_final: 0.7334 (mt) REVERT: U 4 LYS cc_start: 0.8285 (tptp) cc_final: 0.8037 (tptp) REVERT: U 8 ASN cc_start: 0.8989 (p0) cc_final: 0.8526 (p0) REVERT: U 48 LYS cc_start: 0.8850 (mmtt) cc_final: 0.8528 (ttmt) outliers start: 203 outliers final: 119 residues processed: 1592 average time/residue: 1.3211 time to fit residues: 3635.3458 Evaluate side-chains 1380 residues out of total 5356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 1259 time to evaluate : 6.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 03 residue 193 LEU Chi-restraints excluded: chain 04 residue 34 GLU Chi-restraints excluded: chain 04 residue 39 SER Chi-restraints excluded: chain 05 residue 18 ASP Chi-restraints excluded: chain 05 residue 60 VAL Chi-restraints excluded: chain 05 residue 97 SER Chi-restraints excluded: chain 05 residue 199 SER Chi-restraints excluded: chain 06 residue 51 GLU Chi-restraints excluded: chain 06 residue 84 THR Chi-restraints excluded: chain 07 residue 30 VAL Chi-restraints excluded: chain 07 residue 154 THR Chi-restraints excluded: chain 08 residue 10 VAL Chi-restraints excluded: chain 08 residue 15 ASP Chi-restraints excluded: chain 08 residue 19 ASN Chi-restraints excluded: chain 08 residue 165 ASP Chi-restraints excluded: chain 09 residue 4 ILE Chi-restraints excluded: chain 09 residue 17 ASP Chi-restraints excluded: chain 10 residue 67 THR Chi-restraints excluded: chain 11 residue 2 LYS Chi-restraints excluded: chain 11 residue 10 LEU Chi-restraints excluded: chain 11 residue 65 SER Chi-restraints excluded: chain 13 residue 21 CYS Chi-restraints excluded: chain 13 residue 100 PHE Chi-restraints excluded: chain 13 residue 104 THR Chi-restraints excluded: chain 14 residue 42 SER Chi-restraints excluded: chain 14 residue 57 LEU Chi-restraints excluded: chain 14 residue 76 GLU Chi-restraints excluded: chain 14 residue 100 ILE Chi-restraints excluded: chain 15 residue 24 THR Chi-restraints excluded: chain 15 residue 28 PHE Chi-restraints excluded: chain 15 residue 42 THR Chi-restraints excluded: chain 15 residue 124 LEU Chi-restraints excluded: chain 15 residue 126 ILE Chi-restraints excluded: chain 16 residue 13 ASN Chi-restraints excluded: chain 16 residue 57 THR Chi-restraints excluded: chain 17 residue 76 LYS Chi-restraints excluded: chain 17 residue 83 LEU Chi-restraints excluded: chain 18 residue 45 VAL Chi-restraints excluded: chain 18 residue 84 SER Chi-restraints excluded: chain 19 residue 17 LEU Chi-restraints excluded: chain 21 residue 66 ILE Chi-restraints excluded: chain 22 residue 93 LEU Chi-restraints excluded: chain 23 residue 27 VAL Chi-restraints excluded: chain 23 residue 82 VAL Chi-restraints excluded: chain 24 residue 38 LEU Chi-restraints excluded: chain 24 residue 83 LYS Chi-restraints excluded: chain 24 residue 90 ASP Chi-restraints excluded: chain 25 residue 10 ARG Chi-restraints excluded: chain 26 residue 39 VAL Chi-restraints excluded: chain 26 residue 70 LEU Chi-restraints excluded: chain 27 residue 15 ASN Chi-restraints excluded: chain 27 residue 27 ASN Chi-restraints excluded: chain 28 residue 23 LEU Chi-restraints excluded: chain 28 residue 31 ILE Chi-restraints excluded: chain 30 residue 22 THR Chi-restraints excluded: chain 30 residue 45 ASP Chi-restraints excluded: chain 31 residue 13 SER Chi-restraints excluded: chain 31 residue 16 THR Chi-restraints excluded: chain 31 residue 23 THR Chi-restraints excluded: chain 31 residue 47 ILE Chi-restraints excluded: chain 32 residue 15 SER Chi-restraints excluded: chain 32 residue 30 VAL Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 33 residue 31 ILE Chi-restraints excluded: chain 33 residue 61 LEU Chi-restraints excluded: chain 34 residue 13 ASN Chi-restraints excluded: chain 34 residue 14 CYS Chi-restraints excluded: chain Z residue 130 LEU Chi-restraints excluded: chain Z residue 234 ILE Chi-restraints excluded: chain Z residue 246 THR Chi-restraints excluded: chain Z residue 298 LEU Chi-restraints excluded: chain Z residue 328 LEU Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 31 CYS Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain J residue 27 GLU Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 49 PHE Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain K residue 14 GLN Chi-restraints excluded: chain K residue 37 GLN Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 116 TYR Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 79 SER Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain O residue 1 SER Chi-restraints excluded: chain O residue 17 ASP Chi-restraints excluded: chain O residue 19 ASN Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain Q residue 13 SER Chi-restraints excluded: chain R residue 35 SER Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain U residue 36 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1102 random chunks: chunk 556 optimal weight: 30.0000 chunk 310 optimal weight: 20.0000 chunk 832 optimal weight: 30.0000 chunk 681 optimal weight: 20.0000 chunk 276 optimal weight: 20.0000 chunk 1002 optimal weight: 6.9990 chunk 1083 optimal weight: 20.0000 chunk 892 optimal weight: 0.8980 chunk 994 optimal weight: 9.9990 chunk 341 optimal weight: 20.0000 chunk 804 optimal weight: 20.0000 overall best weight: 11.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 03 20 GLN ** 03 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 04 59 GLN ** 04 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 04 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 04 259 ASN ** 05 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 06 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 06 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 07 22 ASN 08 47 ASN 09 43 ASN 09 66 ASN 09 135 HIS 10 9 GLN 11 5 GLN 11 11 GLN ** 11 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 42 ASN 12 58 ASN 12 80 HIS 12 128 ASN ** 12 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 20 6 GLN ** 20 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 21 31 GLN 22 92 ASN 24 75 GLN 25 36 GLN ** 25 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 26 15 ASN 26 16 ASN ** 27 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 28 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 29 20 ASN 29 61 ASN 32 13 ASN 32 29 GLN ** Z 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 304 ASN C 2 GLN ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 GLN D 119 HIS ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 GLN G 141 HIS I 49 GLN I 80 HIS J 56 HIS J 58 ASN J 70 HIS ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 27 GLN ** O 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 12 GLN T 47 GLN ** T 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 63 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 165147 Z= 0.383 Angle : 0.711 12.376 246328 Z= 0.370 Chirality : 0.039 0.347 31327 Planarity : 0.006 0.107 13708 Dihedral : 23.166 176.578 81066 Min Nonbonded Distance : 1.681 Molprobity Statistics. All-atom Clashscore : 20.90 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.90 % Favored : 89.87 % Rotamer: Outliers : 5.78 % Allowed : 17.66 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.83 (0.10), residues: 6453 helix: -0.81 (0.10), residues: 2175 sheet: -2.14 (0.15), residues: 1114 loop : -2.57 (0.10), residues: 3164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP N 41 HIS 0.014 0.002 HIS Q 30 PHE 0.028 0.003 PHE28 52 TYR 0.033 0.003 TYR Z 187 ARG 0.036 0.001 ARG29 59 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12906 Ramachandran restraints generated. 6453 Oldfield, 0 Emsley, 6453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12906 Ramachandran restraints generated. 6453 Oldfield, 0 Emsley, 6453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1597 residues out of total 5356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 305 poor density : 1292 time to evaluate : 7.272 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: 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: 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: 03 8 MET cc_start: 0.7771 (pmm) cc_final: 0.7100 (mpp) REVERT: 03 20 GLN cc_start: 0.8812 (mt0) cc_final: 0.8399 (tt0) REVERT: 03 189 LEU cc_start: 0.9121 (tt) cc_final: 0.8856 (mt) REVERT: 06 100 MET cc_start: 0.8389 (mtp) cc_final: 0.8187 (mmt) REVERT: 07 82 TYR cc_start: 0.7575 (t80) cc_final: 0.7374 (t80) REVERT: 07 151 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8993 (pp) REVERT: 08 38 ASP cc_start: 0.8662 (p0) cc_final: 0.8210 (p0) REVERT: 08 57 TYR cc_start: 0.7491 (m-80) cc_final: 0.7063 (m-80) REVERT: 08 74 MET cc_start: 0.8980 (mtp) cc_final: 0.8495 (mtm) REVERT: 08 172 GLU cc_start: 0.7605 (tp30) cc_final: 0.7068 (tp30) REVERT: 09 2 GLN cc_start: 0.8393 (mm-40) cc_final: 0.8166 (mm-40) REVERT: 09 40 THR cc_start: 0.8906 (m) cc_final: 0.8697 (p) REVERT: 09 46 PHE cc_start: 0.8925 (t80) cc_final: 0.8692 (t80) REVERT: 09 53 GLU cc_start: 0.8014 (mp0) cc_final: 0.7549 (mp0) REVERT: 10 1 MET cc_start: 0.7714 (ttp) cc_final: 0.6884 (tpt) REVERT: 10 46 ARG cc_start: 0.8772 (tpp-160) cc_final: 0.8384 (tpp-160) REVERT: 11 61 TYR cc_start: 0.8987 (m-80) cc_final: 0.8567 (m-80) REVERT: 11 116 MET cc_start: 0.6959 (mtt) cc_final: 0.4778 (ttm) REVERT: 11 124 MET cc_start: 0.9344 (mmm) cc_final: 0.8948 (ttm) REVERT: 11 135 MET cc_start: 0.5634 (mmp) cc_final: 0.4970 (mmm) REVERT: 11 137 LEU cc_start: 0.9100 (tp) cc_final: 0.8886 (tp) REVERT: 12 60 ASP cc_start: 0.8480 (p0) cc_final: 0.7940 (p0) REVERT: 13 82 ASN cc_start: 0.7180 (m-40) cc_final: 0.6975 (m110) REVERT: 17 80 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8152 (mt-10) REVERT: 18 8 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7415 (tm-30) REVERT: 22 1 MET cc_start: 0.5716 (ptp) cc_final: 0.2436 (ttm) REVERT: 25 52 ASP cc_start: 0.8513 (p0) cc_final: 0.8307 (p0) REVERT: 27 58 ASN cc_start: 0.8994 (t0) cc_final: 0.8774 (t0) REVERT: 29 9 TYR cc_start: 0.7115 (t80) cc_final: 0.6073 (t80) REVERT: 29 56 ARG cc_start: 0.5887 (OUTLIER) cc_final: 0.5175 (tpt90) REVERT: 29 59 ARG cc_start: 0.8934 (ttp80) cc_final: 0.8709 (tmm160) REVERT: 29 60 PHE cc_start: 0.8229 (t80) cc_final: 0.7599 (t80) REVERT: 29 62 LYS cc_start: 0.9334 (mmmm) cc_final: 0.9096 (mmmm) REVERT: 31 24 LYS cc_start: 0.8974 (tptp) cc_final: 0.8629 (tptp) REVERT: 31 28 THR cc_start: 0.8374 (m) cc_final: 0.8011 (p) REVERT: Z 265 HIS cc_start: 0.8868 (t70) cc_final: 0.8440 (t70) REVERT: Z 288 MET cc_start: 0.9268 (mtt) cc_final: 0.9017 (ptp) REVERT: Z 296 TYR cc_start: 0.9490 (t80) cc_final: 0.9276 (t80) REVERT: C 133 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7123 (ttp) REVERT: F 56 LYS cc_start: 0.8476 (mtpp) cc_final: 0.7983 (ttmm) REVERT: F 68 GLN cc_start: 0.8727 (pp30) cc_final: 0.8512 (pp30) REVERT: H 37 ASN cc_start: 0.8698 (t0) cc_final: 0.8453 (t0) REVERT: I 55 ASP cc_start: 0.8556 (t70) cc_final: 0.7747 (t0) REVERT: J 63 ASP cc_start: 0.7689 (p0) cc_final: 0.6129 (p0) REVERT: J 65 TYR cc_start: 0.7623 (m-10) cc_final: 0.7359 (m-10) REVERT: K 63 GLN cc_start: 0.8276 (tm-30) cc_final: 0.7620 (tm-30) REVERT: K 67 GLU cc_start: 0.8226 (mm-30) cc_final: 0.8017 (mm-30) REVERT: K 69 CYS cc_start: 0.8351 (t) cc_final: 0.7897 (t) REVERT: Q 10 ARG cc_start: 0.8634 (tmm-80) cc_final: 0.8208 (tmm-80) REVERT: Q 39 ARG cc_start: 0.8648 (mmm-85) cc_final: 0.8410 (mmm-85) REVERT: Q 52 CYS cc_start: 0.8139 (p) cc_final: 0.7720 (p) REVERT: Q 61 ARG cc_start: 0.7419 (tmm-80) cc_final: 0.7012 (tmm-80) REVERT: R 71 ASP cc_start: 0.7938 (m-30) cc_final: 0.7613 (m-30) REVERT: S 46 LEU cc_start: 0.8710 (mm) cc_final: 0.8489 (tt) REVERT: T 85 LEU cc_start: 0.8979 (mt) cc_final: 0.8751 (tp) REVERT: U 4 LYS cc_start: 0.8520 (tptp) cc_final: 0.8163 (tptp) REVERT: U 42 THR cc_start: 0.8214 (OUTLIER) cc_final: 0.7909 (m) outliers start: 305 outliers final: 188 residues processed: 1440 average time/residue: 1.3237 time to fit residues: 3316.9535 Evaluate side-chains 1331 residues out of total 5356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 1139 time to evaluate : 7.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 34 LYS Chi-restraints excluded: chain 03 residue 39 VAL Chi-restraints excluded: chain 03 residue 193 LEU Chi-restraints excluded: chain 04 residue 34 GLU Chi-restraints excluded: chain 04 residue 39 SER Chi-restraints excluded: chain 04 residue 44 ASN Chi-restraints excluded: chain 04 residue 103 ILE Chi-restraints excluded: chain 04 residue 138 SER Chi-restraints excluded: chain 05 residue 40 LEU Chi-restraints excluded: chain 05 residue 60 VAL Chi-restraints excluded: chain 05 residue 97 SER Chi-restraints excluded: chain 05 residue 137 SER Chi-restraints excluded: chain 05 residue 199 SER Chi-restraints excluded: chain 05 residue 201 LEU Chi-restraints excluded: chain 06 residue 51 GLU Chi-restraints excluded: chain 06 residue 77 ILE Chi-restraints excluded: chain 06 residue 108 ILE Chi-restraints excluded: chain 06 residue 181 ILE Chi-restraints excluded: chain 07 residue 30 VAL Chi-restraints excluded: chain 07 residue 151 LEU Chi-restraints excluded: chain 07 residue 154 THR Chi-restraints excluded: chain 08 residue 10 VAL Chi-restraints excluded: chain 08 residue 15 ASP Chi-restraints excluded: chain 08 residue 19 ASN Chi-restraints excluded: chain 08 residue 49 LEU Chi-restraints excluded: chain 08 residue 130 ILE Chi-restraints excluded: chain 08 residue 165 ASP Chi-restraints excluded: chain 09 residue 17 ASP Chi-restraints excluded: chain 10 residue 35 VAL Chi-restraints excluded: chain 10 residue 38 MET Chi-restraints excluded: chain 10 residue 55 VAL Chi-restraints excluded: chain 10 residue 67 THR Chi-restraints excluded: chain 10 residue 74 ASP Chi-restraints excluded: chain 11 residue 2 LYS Chi-restraints excluded: chain 11 residue 10 LEU Chi-restraints excluded: chain 13 residue 21 CYS Chi-restraints excluded: chain 13 residue 87 LEU Chi-restraints excluded: chain 13 residue 97 THR Chi-restraints excluded: chain 13 residue 100 PHE Chi-restraints excluded: chain 13 residue 104 THR Chi-restraints excluded: chain 14 residue 42 SER Chi-restraints excluded: chain 14 residue 46 VAL Chi-restraints excluded: chain 14 residue 57 LEU Chi-restraints excluded: chain 14 residue 76 GLU Chi-restraints excluded: chain 14 residue 100 ILE Chi-restraints excluded: chain 15 residue 24 THR Chi-restraints excluded: chain 15 residue 28 PHE Chi-restraints excluded: chain 15 residue 42 THR Chi-restraints excluded: chain 15 residue 45 GLN Chi-restraints excluded: chain 15 residue 78 LEU Chi-restraints excluded: chain 15 residue 126 ILE Chi-restraints excluded: chain 15 residue 128 THR Chi-restraints excluded: chain 16 residue 24 MET Chi-restraints excluded: chain 16 residue 36 THR Chi-restraints excluded: chain 16 residue 52 ILE Chi-restraints excluded: chain 16 residue 57 THR Chi-restraints excluded: chain 17 residue 46 GLU Chi-restraints excluded: chain 17 residue 58 ILE Chi-restraints excluded: chain 17 residue 69 ASP Chi-restraints excluded: chain 17 residue 76 LYS Chi-restraints excluded: chain 17 residue 83 LEU Chi-restraints excluded: chain 18 residue 45 VAL Chi-restraints excluded: chain 18 residue 82 SER Chi-restraints excluded: chain 19 residue 7 VAL Chi-restraints excluded: chain 19 residue 17 LEU Chi-restraints excluded: chain 20 residue 58 VAL Chi-restraints excluded: chain 20 residue 99 THR Chi-restraints excluded: chain 21 residue 24 ILE Chi-restraints excluded: chain 21 residue 40 ASN Chi-restraints excluded: chain 21 residue 66 ILE Chi-restraints excluded: chain 22 residue 18 GLU Chi-restraints excluded: chain 22 residue 58 VAL Chi-restraints excluded: chain 22 residue 74 ILE Chi-restraints excluded: chain 23 residue 17 ASP Chi-restraints excluded: chain 23 residue 27 VAL Chi-restraints excluded: chain 24 residue 38 LEU Chi-restraints excluded: chain 24 residue 83 LYS Chi-restraints excluded: chain 24 residue 90 ASP Chi-restraints excluded: chain 25 residue 19 VAL Chi-restraints excluded: chain 26 residue 39 VAL Chi-restraints excluded: chain 26 residue 63 ILE Chi-restraints excluded: chain 26 residue 70 LEU Chi-restraints excluded: chain 27 residue 15 ASN Chi-restraints excluded: chain 27 residue 27 ASN Chi-restraints excluded: chain 28 residue 51 SER Chi-restraints excluded: chain 29 residue 56 ARG Chi-restraints excluded: chain 29 residue 57 VAL Chi-restraints excluded: chain 30 residue 22 THR Chi-restraints excluded: chain 30 residue 45 ASP Chi-restraints excluded: chain 31 residue 11 VAL Chi-restraints excluded: chain 31 residue 13 SER Chi-restraints excluded: chain 31 residue 16 THR Chi-restraints excluded: chain 32 residue 15 SER Chi-restraints excluded: chain 32 residue 24 THR Chi-restraints excluded: chain 32 residue 25 LYS Chi-restraints excluded: chain 32 residue 30 VAL Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 32 residue 45 SER Chi-restraints excluded: chain 33 residue 31 ILE Chi-restraints excluded: chain 33 residue 53 ASP Chi-restraints excluded: chain 34 residue 13 ASN Chi-restraints excluded: chain Z residue 130 LEU Chi-restraints excluded: chain Z residue 162 LYS Chi-restraints excluded: chain Z residue 234 ILE Chi-restraints excluded: chain Z residue 246 THR Chi-restraints excluded: chain Z residue 298 LEU Chi-restraints excluded: chain Z residue 328 LEU Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 169 HIS Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 31 CYS Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain G residue 51 GLN Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 96 ASN Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain I residue 24 ASN Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain I residue 96 GLU Chi-restraints excluded: chain J residue 49 PHE Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain K residue 14 GLN Chi-restraints excluded: chain K residue 35 ASP Chi-restraints excluded: chain K residue 51 PHE Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain N residue 5 MET Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 49 THR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 79 SER Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain O residue 1 SER Chi-restraints excluded: chain O residue 17 ASP Chi-restraints excluded: chain O residue 19 ASN Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 68 SER Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain R residue 32 ILE Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 35 SER Chi-restraints excluded: chain S residue 10 ILE Chi-restraints excluded: chain S residue 65 MET Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 36 PHE Chi-restraints excluded: chain U residue 42 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1102 random chunks: chunk 990 optimal weight: 6.9990 chunk 753 optimal weight: 9.9990 chunk 520 optimal weight: 20.0000 chunk 110 optimal weight: 20.0000 chunk 478 optimal weight: 20.0000 chunk 673 optimal weight: 0.9990 chunk 1006 optimal weight: 4.9990 chunk 1065 optimal weight: 20.0000 chunk 525 optimal weight: 9.9990 chunk 953 optimal weight: 30.0000 chunk 287 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 32 ASN ** 03 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 04 59 GLN ** 04 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 04 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 04 162 GLN 04 259 ASN 05 130 GLN ** 05 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 05 167 ASN ** 06 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 06 156 ASN 09 66 ASN ** 11 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 42 ASN 12 58 ASN ** 12 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 3 GLN ** 15 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 15 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 17 61 GLN ** 17 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 19 36 GLN 19 43 GLN ** 20 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 20 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 24 75 GLN ** 25 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 27 38 GLN ** 28 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 29 20 ASN 32 13 ASN ** Z 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 276 ASN ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 GLN C 138 GLN ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 141 HIS ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 12 GLN T 54 GLN ** T 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 165147 Z= 0.232 Angle : 0.611 13.838 246328 Z= 0.315 Chirality : 0.035 0.374 31327 Planarity : 0.005 0.091 13708 Dihedral : 23.301 178.417 81065 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.52 % Favored : 91.29 % Rotamer: Outliers : 4.23 % Allowed : 20.52 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.31 (0.10), residues: 6453 helix: -0.25 (0.11), residues: 2181 sheet: -1.79 (0.15), residues: 1129 loop : -2.40 (0.10), residues: 3143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP N 41 HIS 0.013 0.001 HIS20 82 PHE 0.039 0.002 PHE F 78 TYR 0.023 0.002 TYR U 37 ARG 0.012 0.001 ARG E 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12906 Ramachandran restraints generated. 6453 Oldfield, 0 Emsley, 6453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12906 Ramachandran restraints generated. 6453 Oldfield, 0 Emsley, 6453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1491 residues out of total 5356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 1268 time to evaluate : 7.298 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: 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: 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: 03 20 GLN cc_start: 0.8733 (mt0) cc_final: 0.8382 (tt0) REVERT: 03 189 LEU cc_start: 0.9114 (tt) cc_final: 0.8904 (mt) REVERT: 04 97 ASP cc_start: 0.7892 (p0) cc_final: 0.7620 (p0) REVERT: 08 38 ASP cc_start: 0.8887 (p0) cc_final: 0.8661 (p0) REVERT: 08 172 GLU cc_start: 0.7690 (tp30) cc_final: 0.7045 (tp30) REVERT: 09 2 GLN cc_start: 0.8291 (mm-40) cc_final: 0.8081 (mm-40) REVERT: 09 4 ILE cc_start: 0.8415 (mm) cc_final: 0.8210 (mm) REVERT: 10 1 MET cc_start: 0.7782 (ttp) cc_final: 0.7530 (tpp) REVERT: 10 9 GLN cc_start: 0.8728 (mm-40) cc_final: 0.8476 (mm-40) REVERT: 11 18 ASN cc_start: 0.8748 (t0) cc_final: 0.8499 (p0) REVERT: 11 61 TYR cc_start: 0.9063 (m-80) cc_final: 0.8625 (m-80) REVERT: 11 116 MET cc_start: 0.6958 (mtt) cc_final: 0.4626 (ttm) REVERT: 11 124 MET cc_start: 0.9346 (mmm) cc_final: 0.8925 (mmp) REVERT: 11 135 MET cc_start: 0.5374 (mmp) cc_final: 0.4842 (mmm) REVERT: 11 137 LEU cc_start: 0.9130 (tp) cc_final: 0.8929 (tp) REVERT: 13 82 ASN cc_start: 0.6965 (m-40) cc_final: 0.6741 (m110) REVERT: 22 1 MET cc_start: 0.5673 (ptp) cc_final: 0.5299 (ptp) REVERT: 22 18 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7519 (mp0) REVERT: 25 11 ASP cc_start: 0.8091 (t0) cc_final: 0.7722 (t0) REVERT: 25 52 ASP cc_start: 0.8498 (p0) cc_final: 0.8230 (p0) REVERT: 26 55 MET cc_start: 0.8479 (mmm) cc_final: 0.8230 (tpp) REVERT: 27 58 ASN cc_start: 0.9020 (t0) cc_final: 0.8760 (t0) REVERT: 27 60 LYS cc_start: 0.8538 (mmtm) cc_final: 0.8256 (mmtm) REVERT: 29 9 TYR cc_start: 0.6720 (t80) cc_final: 0.6238 (t80) REVERT: 29 22 MET cc_start: 0.9032 (ppp) cc_final: 0.8577 (pmm) REVERT: 29 60 PHE cc_start: 0.8276 (t80) cc_final: 0.8033 (t80) REVERT: 31 34 GLU cc_start: 0.7582 (tp30) cc_final: 0.6659 (tp30) REVERT: Z 262 ARG cc_start: 0.8886 (tmt90) cc_final: 0.8662 (ttp80) REVERT: Z 265 HIS cc_start: 0.8699 (t70) cc_final: 0.8409 (t70) REVERT: Z 288 MET cc_start: 0.9293 (mtt) cc_final: 0.9030 (ptp) REVERT: Z 296 TYR cc_start: 0.9384 (t80) cc_final: 0.9095 (t80) REVERT: C 133 MET cc_start: 0.8480 (tmm) cc_final: 0.6626 (tmm) REVERT: F 45 ARG cc_start: 0.8682 (ttm110) cc_final: 0.8306 (ttm110) REVERT: F 56 LYS cc_start: 0.8454 (mtpp) cc_final: 0.7916 (ttmm) REVERT: F 68 GLN cc_start: 0.8727 (pp30) cc_final: 0.8281 (pp30) REVERT: F 90 MET cc_start: 0.8461 (mmm) cc_final: 0.8136 (mmm) REVERT: G 30 MET cc_start: 0.8016 (tmm) cc_final: 0.7385 (tmm) REVERT: I 55 ASP cc_start: 0.8533 (t70) cc_final: 0.7735 (t0) REVERT: J 91 ASP cc_start: 0.6511 (OUTLIER) cc_final: 0.6210 (p0) REVERT: K 63 GLN cc_start: 0.8186 (tm-30) cc_final: 0.7526 (tm-30) REVERT: K 67 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7529 (mm-30) REVERT: K 69 CYS cc_start: 0.8364 (t) cc_final: 0.7999 (t) REVERT: L 75 GLU cc_start: 0.8463 (pm20) cc_final: 0.8178 (pm20) REVERT: S 60 PHE cc_start: 0.8586 (t80) cc_final: 0.8337 (t80) REVERT: T 23 ARG cc_start: 0.8575 (mmm-85) cc_final: 0.8357 (mmt90) outliers start: 223 outliers final: 154 residues processed: 1391 average time/residue: 1.3391 time to fit residues: 3243.9850 Evaluate side-chains 1305 residues out of total 5356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1149 time to evaluate : 7.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain 03 residue 193 LEU Chi-restraints excluded: chain 04 residue 34 GLU Chi-restraints excluded: chain 04 residue 103 ILE Chi-restraints excluded: chain 04 residue 138 SER Chi-restraints excluded: chain 04 residue 159 THR Chi-restraints excluded: chain 04 residue 202 ARG Chi-restraints excluded: chain 05 residue 18 ASP Chi-restraints excluded: chain 05 residue 60 VAL Chi-restraints excluded: chain 05 residue 96 ILE Chi-restraints excluded: chain 05 residue 97 SER Chi-restraints excluded: chain 05 residue 177 VAL Chi-restraints excluded: chain 05 residue 199 SER Chi-restraints excluded: chain 06 residue 84 THR Chi-restraints excluded: chain 06 residue 108 ILE Chi-restraints excluded: chain 06 residue 175 ILE Chi-restraints excluded: chain 06 residue 181 ILE Chi-restraints excluded: chain 07 residue 22 ASN Chi-restraints excluded: chain 07 residue 30 VAL Chi-restraints excluded: chain 07 residue 154 THR Chi-restraints excluded: chain 08 residue 10 VAL Chi-restraints excluded: chain 08 residue 15 ASP Chi-restraints excluded: chain 08 residue 19 ASN Chi-restraints excluded: chain 08 residue 91 VAL Chi-restraints excluded: chain 08 residue 130 ILE Chi-restraints excluded: chain 08 residue 154 GLU Chi-restraints excluded: chain 08 residue 165 ASP Chi-restraints excluded: chain 10 residue 67 THR Chi-restraints excluded: chain 10 residue 74 ASP Chi-restraints excluded: chain 10 residue 129 LEU Chi-restraints excluded: chain 11 residue 2 LYS Chi-restraints excluded: chain 11 residue 10 LEU Chi-restraints excluded: chain 11 residue 86 LYS Chi-restraints excluded: chain 12 residue 81 ILE Chi-restraints excluded: chain 13 residue 32 TYR Chi-restraints excluded: chain 13 residue 100 PHE Chi-restraints excluded: chain 13 residue 104 THR Chi-restraints excluded: chain 14 residue 42 SER Chi-restraints excluded: chain 14 residue 57 LEU Chi-restraints excluded: chain 14 residue 76 GLU Chi-restraints excluded: chain 15 residue 24 THR Chi-restraints excluded: chain 15 residue 28 PHE Chi-restraints excluded: chain 15 residue 42 THR Chi-restraints excluded: chain 15 residue 78 LEU Chi-restraints excluded: chain 15 residue 126 ILE Chi-restraints excluded: chain 15 residue 128 THR Chi-restraints excluded: chain 16 residue 24 MET Chi-restraints excluded: chain 16 residue 57 THR Chi-restraints excluded: chain 17 residue 83 LEU Chi-restraints excluded: chain 17 residue 93 ASP Chi-restraints excluded: chain 18 residue 45 VAL Chi-restraints excluded: chain 18 residue 82 SER Chi-restraints excluded: chain 18 residue 85 VAL Chi-restraints excluded: chain 19 residue 7 VAL Chi-restraints excluded: chain 20 residue 6 GLN Chi-restraints excluded: chain 20 residue 38 VAL Chi-restraints excluded: chain 21 residue 24 ILE Chi-restraints excluded: chain 21 residue 81 SER Chi-restraints excluded: chain 22 residue 18 GLU Chi-restraints excluded: chain 22 residue 58 VAL Chi-restraints excluded: chain 23 residue 92 VAL Chi-restraints excluded: chain 24 residue 38 LEU Chi-restraints excluded: chain 24 residue 83 LYS Chi-restraints excluded: chain 24 residue 90 ASP Chi-restraints excluded: chain 25 residue 19 VAL Chi-restraints excluded: chain 26 residue 39 VAL Chi-restraints excluded: chain 27 residue 27 ASN Chi-restraints excluded: chain 28 residue 51 SER Chi-restraints excluded: chain 29 residue 20 ASN Chi-restraints excluded: chain 30 residue 22 THR Chi-restraints excluded: chain 30 residue 45 ASP Chi-restraints excluded: chain 31 residue 11 VAL Chi-restraints excluded: chain 31 residue 13 SER Chi-restraints excluded: chain 31 residue 16 THR Chi-restraints excluded: chain 31 residue 23 THR Chi-restraints excluded: chain 32 residue 30 VAL Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 33 residue 53 ASP Chi-restraints excluded: chain 34 residue 13 ASN Chi-restraints excluded: chain Z residue 130 LEU Chi-restraints excluded: chain Z residue 227 ASP Chi-restraints excluded: chain Z residue 234 ILE Chi-restraints excluded: chain Z residue 246 THR Chi-restraints excluded: chain Z residue 298 LEU Chi-restraints excluded: chain Z residue 328 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 169 HIS Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 31 CYS Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 96 ASN Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 96 GLU Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain K residue 14 GLN Chi-restraints excluded: chain K residue 26 PHE Chi-restraints excluded: chain K residue 35 ASP Chi-restraints excluded: chain K residue 51 PHE Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 108 ASP Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 44 ILE Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 49 THR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 81 ILE Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain O residue 1 SER Chi-restraints excluded: chain O residue 17 ASP Chi-restraints excluded: chain O residue 19 ASN Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 68 SER Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain S residue 10 ILE Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain U residue 36 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1102 random chunks: chunk 887 optimal weight: 8.9990 chunk 604 optimal weight: 20.0000 chunk 15 optimal weight: 20.0000 chunk 793 optimal weight: 9.9990 chunk 439 optimal weight: 20.0000 chunk 908 optimal weight: 10.0000 chunk 736 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 543 optimal weight: 5.9990 chunk 956 optimal weight: 2.9990 chunk 268 optimal weight: 20.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 03 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 04 24 HIS 04 59 GLN ** 04 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 04 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 04 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 04 225 ASN ** 05 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 06 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 09 43 ASN 09 66 ASN ** 11 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 15 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 15 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 22 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 22 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 24 75 GLN ** 25 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 26 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 28 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 32 13 ASN ** 34 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 290 GLN ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 GLN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 141 HIS ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN ** K 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 12 GLN T 47 GLN ** T 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 74 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 165147 Z= 0.266 Angle : 0.621 13.130 246328 Z= 0.320 Chirality : 0.035 0.280 31327 Planarity : 0.005 0.086 13708 Dihedral : 23.349 177.705 81065 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.58 % Favored : 90.25 % Rotamer: Outliers : 4.64 % Allowed : 21.62 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.10 (0.10), residues: 6453 helix: -0.04 (0.11), residues: 2184 sheet: -1.75 (0.15), residues: 1102 loop : -2.27 (0.10), residues: 3167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP06 60 HIS 0.011 0.001 HIS20 82 PHE 0.030 0.002 PHE G 61 TYR 0.039 0.002 TYR C 167 ARG 0.011 0.001 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12906 Ramachandran restraints generated. 6453 Oldfield, 0 Emsley, 6453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12906 Ramachandran restraints generated. 6453 Oldfield, 0 Emsley, 6453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1448 residues out of total 5356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 1203 time to evaluate : 7.245 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: 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: symmetry clash REVERT: 03 8 MET cc_start: 0.8234 (pmm) cc_final: 0.7996 (ppp) REVERT: 03 189 LEU cc_start: 0.9171 (tt) cc_final: 0.8946 (mt) REVERT: 06 5 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7964 (tt) REVERT: 08 38 ASP cc_start: 0.8831 (p0) cc_final: 0.8519 (p0) REVERT: 09 53 GLU cc_start: 0.7891 (mp0) cc_final: 0.7415 (mp0) REVERT: 09 112 LYS cc_start: 0.8726 (mmmm) cc_final: 0.8459 (mmtp) REVERT: 10 9 GLN cc_start: 0.8662 (mm-40) cc_final: 0.8312 (mm-40) REVERT: 10 42 ARG cc_start: 0.8446 (tpm170) cc_final: 0.8185 (tpm170) REVERT: 11 18 ASN cc_start: 0.8741 (t0) cc_final: 0.8397 (p0) REVERT: 11 61 TYR cc_start: 0.9124 (m-80) cc_final: 0.8671 (m-80) REVERT: 11 116 MET cc_start: 0.7337 (mtt) cc_final: 0.4896 (ttm) REVERT: 11 124 MET cc_start: 0.9344 (mmm) cc_final: 0.8911 (mmp) REVERT: 11 135 MET cc_start: 0.5419 (mmp) cc_final: 0.4849 (mmm) REVERT: 11 137 LEU cc_start: 0.9120 (tp) cc_final: 0.8910 (tp) REVERT: 12 60 ASP cc_start: 0.8534 (p0) cc_final: 0.7960 (p0) REVERT: 13 51 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7808 (pttp) REVERT: 15 59 ARG cc_start: 0.7859 (mmp80) cc_final: 0.7453 (tpp80) REVERT: 22 1 MET cc_start: 0.5681 (ptp) cc_final: 0.5255 (ptp) REVERT: 22 18 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7597 (mp0) REVERT: 24 75 GLN cc_start: 0.9174 (OUTLIER) cc_final: 0.8655 (tp40) REVERT: 25 11 ASP cc_start: 0.8347 (t0) cc_final: 0.8036 (t0) REVERT: 25 52 ASP cc_start: 0.8539 (p0) cc_final: 0.8271 (p0) REVERT: 28 18 LYS cc_start: 0.8068 (tptt) cc_final: 0.7774 (tptp) REVERT: 29 9 TYR cc_start: 0.7044 (t80) cc_final: 0.6527 (t80) REVERT: 29 22 MET cc_start: 0.9010 (ppp) cc_final: 0.8494 (pmm) REVERT: 29 25 ARG cc_start: 0.7161 (mtm180) cc_final: 0.6917 (mtm-85) REVERT: 29 62 LYS cc_start: 0.9303 (mmmm) cc_final: 0.9054 (mmmm) REVERT: 31 49 LYS cc_start: 0.8800 (mmtm) cc_final: 0.8573 (mmtm) REVERT: Z 151 MET cc_start: 0.8636 (tmm) cc_final: 0.7931 (tmm) REVERT: Z 262 ARG cc_start: 0.8955 (tmt90) cc_final: 0.8691 (ttp80) REVERT: Z 265 HIS cc_start: 0.8759 (t70) cc_final: 0.8471 (t70) REVERT: Z 288 MET cc_start: 0.9300 (mtt) cc_final: 0.9045 (ptp) REVERT: Z 296 TYR cc_start: 0.9387 (t80) cc_final: 0.9102 (t80) REVERT: F 45 ARG cc_start: 0.8658 (ttm110) cc_final: 0.8283 (ttm110) REVERT: F 78 PHE cc_start: 0.8945 (m-80) cc_final: 0.8590 (m-80) REVERT: F 90 MET cc_start: 0.8493 (mmm) cc_final: 0.8196 (mmm) REVERT: G 30 MET cc_start: 0.8266 (tmm) cc_final: 0.7514 (tmm) REVERT: I 30 ASN cc_start: 0.8619 (p0) cc_final: 0.8223 (p0) REVERT: I 55 ASP cc_start: 0.8500 (t70) cc_final: 0.7657 (t0) REVERT: J 63 ASP cc_start: 0.7870 (p0) cc_final: 0.7149 (p0) REVERT: K 63 GLN cc_start: 0.8255 (tm-30) cc_final: 0.7991 (tm-30) REVERT: K 69 CYS cc_start: 0.8371 (t) cc_final: 0.8013 (t) REVERT: T 23 ARG cc_start: 0.8618 (mmm-85) cc_final: 0.8400 (mmt90) REVERT: U 48 LYS cc_start: 0.8784 (mmtt) cc_final: 0.8398 (tttt) outliers start: 245 outliers final: 187 residues processed: 1339 average time/residue: 1.3206 time to fit residues: 3091.8894 Evaluate side-chains 1306 residues out of total 5356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 1115 time to evaluate : 7.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 03 residue 39 VAL Chi-restraints excluded: chain 03 residue 193 LEU Chi-restraints excluded: chain 04 residue 34 GLU Chi-restraints excluded: chain 04 residue 103 ILE Chi-restraints excluded: chain 04 residue 138 SER Chi-restraints excluded: chain 04 residue 202 ARG Chi-restraints excluded: chain 05 residue 1 MET Chi-restraints excluded: chain 05 residue 18 ASP Chi-restraints excluded: chain 05 residue 60 VAL Chi-restraints excluded: chain 05 residue 97 SER Chi-restraints excluded: chain 05 residue 137 SER Chi-restraints excluded: chain 05 residue 177 VAL Chi-restraints excluded: chain 05 residue 185 ASN Chi-restraints excluded: chain 05 residue 199 SER Chi-restraints excluded: chain 05 residue 201 LEU Chi-restraints excluded: chain 06 residue 5 LEU Chi-restraints excluded: chain 06 residue 84 THR Chi-restraints excluded: chain 06 residue 108 ILE Chi-restraints excluded: chain 06 residue 175 ILE Chi-restraints excluded: chain 07 residue 22 ASN Chi-restraints excluded: chain 07 residue 30 VAL Chi-restraints excluded: chain 07 residue 154 THR Chi-restraints excluded: chain 08 residue 10 VAL Chi-restraints excluded: chain 08 residue 15 ASP Chi-restraints excluded: chain 08 residue 19 ASN Chi-restraints excluded: chain 08 residue 130 ILE Chi-restraints excluded: chain 08 residue 154 GLU Chi-restraints excluded: chain 08 residue 165 ASP Chi-restraints excluded: chain 10 residue 27 VAL Chi-restraints excluded: chain 10 residue 35 VAL Chi-restraints excluded: chain 10 residue 60 LEU Chi-restraints excluded: chain 10 residue 67 THR Chi-restraints excluded: chain 10 residue 129 LEU Chi-restraints excluded: chain 11 residue 2 LYS Chi-restraints excluded: chain 11 residue 4 VAL Chi-restraints excluded: chain 11 residue 10 LEU Chi-restraints excluded: chain 11 residue 68 PHE Chi-restraints excluded: chain 11 residue 86 LYS Chi-restraints excluded: chain 12 residue 81 ILE Chi-restraints excluded: chain 12 residue 101 ILE Chi-restraints excluded: chain 13 residue 32 TYR Chi-restraints excluded: chain 13 residue 45 GLU Chi-restraints excluded: chain 13 residue 51 LYS Chi-restraints excluded: chain 13 residue 97 THR Chi-restraints excluded: chain 13 residue 100 PHE Chi-restraints excluded: chain 13 residue 104 THR Chi-restraints excluded: chain 14 residue 42 SER Chi-restraints excluded: chain 14 residue 57 LEU Chi-restraints excluded: chain 14 residue 67 THR Chi-restraints excluded: chain 14 residue 76 GLU Chi-restraints excluded: chain 14 residue 111 ILE Chi-restraints excluded: chain 15 residue 24 THR Chi-restraints excluded: chain 15 residue 28 PHE Chi-restraints excluded: chain 15 residue 42 THR Chi-restraints excluded: chain 15 residue 78 LEU Chi-restraints excluded: chain 15 residue 126 ILE Chi-restraints excluded: chain 15 residue 128 THR Chi-restraints excluded: chain 15 residue 136 MET Chi-restraints excluded: chain 16 residue 15 SER Chi-restraints excluded: chain 16 residue 24 MET Chi-restraints excluded: chain 16 residue 36 THR Chi-restraints excluded: chain 16 residue 52 ILE Chi-restraints excluded: chain 16 residue 57 THR Chi-restraints excluded: chain 17 residue 43 ASN Chi-restraints excluded: chain 17 residue 69 ASP Chi-restraints excluded: chain 17 residue 83 LEU Chi-restraints excluded: chain 17 residue 93 ASP Chi-restraints excluded: chain 18 residue 45 VAL Chi-restraints excluded: chain 18 residue 82 SER Chi-restraints excluded: chain 19 residue 7 VAL Chi-restraints excluded: chain 20 residue 38 VAL Chi-restraints excluded: chain 20 residue 58 VAL Chi-restraints excluded: chain 20 residue 99 THR Chi-restraints excluded: chain 22 residue 18 GLU Chi-restraints excluded: chain 22 residue 58 VAL Chi-restraints excluded: chain 23 residue 17 ASP Chi-restraints excluded: chain 23 residue 27 VAL Chi-restraints excluded: chain 24 residue 38 LEU Chi-restraints excluded: chain 24 residue 59 GLU Chi-restraints excluded: chain 24 residue 75 GLN Chi-restraints excluded: chain 24 residue 83 LYS Chi-restraints excluded: chain 24 residue 90 ASP Chi-restraints excluded: chain 25 residue 19 VAL Chi-restraints excluded: chain 26 residue 39 VAL Chi-restraints excluded: chain 27 residue 27 ASN Chi-restraints excluded: chain 28 residue 51 SER Chi-restraints excluded: chain 29 residue 57 VAL Chi-restraints excluded: chain 30 residue 22 THR Chi-restraints excluded: chain 30 residue 45 ASP Chi-restraints excluded: chain 31 residue 11 VAL Chi-restraints excluded: chain 31 residue 13 SER Chi-restraints excluded: chain 31 residue 16 THR Chi-restraints excluded: chain 31 residue 23 THR Chi-restraints excluded: chain 32 residue 15 SER Chi-restraints excluded: chain 32 residue 30 VAL Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 33 residue 53 ASP Chi-restraints excluded: chain 34 residue 3 VAL Chi-restraints excluded: chain 34 residue 10 LEU Chi-restraints excluded: chain 34 residue 13 ASN Chi-restraints excluded: chain Z residue 130 LEU Chi-restraints excluded: chain Z residue 162 LYS Chi-restraints excluded: chain Z residue 227 ASP Chi-restraints excluded: chain Z residue 234 ILE Chi-restraints excluded: chain Z residue 246 THR Chi-restraints excluded: chain Z residue 298 LEU Chi-restraints excluded: chain Z residue 328 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 169 HIS Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 31 CYS Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain E residue 12 GLU Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 96 ASN Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain H residue 9 MET Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 96 GLU Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain K residue 14 GLN Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 35 ASP Chi-restraints excluded: chain K residue 51 PHE Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain K residue 118 ASN Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 108 ASP Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 44 ILE Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 49 THR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 81 ILE Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain O residue 1 SER Chi-restraints excluded: chain O residue 17 ASP Chi-restraints excluded: chain O residue 19 ASN Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 68 SER Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain R residue 32 ILE Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 36 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1102 random chunks: chunk 358 optimal weight: 20.0000 chunk 959 optimal weight: 40.0000 chunk 210 optimal weight: 20.0000 chunk 625 optimal weight: 4.9990 chunk 262 optimal weight: 30.0000 chunk 1066 optimal weight: 7.9990 chunk 885 optimal weight: 30.0000 chunk 493 optimal weight: 30.0000 chunk 88 optimal weight: 20.0000 chunk 352 optimal weight: 20.0000 chunk 559 optimal weight: 20.0000 overall best weight: 14.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 32 ASN 03 20 GLN 03 165 ASN 04 59 GLN ** 04 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 04 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 04 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 06 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 06 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 07 4 HIS 11 11 GLN ** 11 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 3 GLN 13 5 GLN 18 76 HIS 19 58 GLN 20 18 GLN ** 22 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 22 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 22 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 23 52 ASN ** 23 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 28 8 GLN ** 28 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 31 18 HIS 32 6 GLN 32 13 ASN 32 29 GLN ** 34 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 ASN ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 ASN E 147 ASN ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 141 HIS ** G 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 47 GLN ** T 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.5184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.135 165147 Z= 0.474 Angle : 0.764 16.005 246328 Z= 0.392 Chirality : 0.041 0.315 31327 Planarity : 0.006 0.094 13708 Dihedral : 23.642 177.326 81065 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 27.44 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.16 % Favored : 88.59 % Rotamer: Outliers : 6.05 % Allowed : 21.62 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.28 (0.10), residues: 6453 helix: -0.34 (0.11), residues: 2183 sheet: -1.75 (0.15), residues: 1064 loop : -2.29 (0.10), residues: 3206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP N 41 HIS 0.015 0.002 HIS20 82 PHE 0.033 0.003 PHE28 52 TYR 0.039 0.003 TYR J 65 ARG 0.012 0.001 ARG31 27 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12906 Ramachandran restraints generated. 6453 Oldfield, 0 Emsley, 6453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12906 Ramachandran restraints generated. 6453 Oldfield, 0 Emsley, 6453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1449 residues out of total 5356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 319 poor density : 1130 time to evaluate : 7.339 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: 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: 03 7 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7844 (tmm-80) REVERT: 03 20 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8619 (tt0) REVERT: 03 189 LEU cc_start: 0.9245 (tt) cc_final: 0.9035 (mt) REVERT: 03 198 LYS cc_start: 0.8788 (pttt) cc_final: 0.8530 (pttm) REVERT: 08 74 MET cc_start: 0.8991 (mtp) cc_final: 0.8524 (mtm) REVERT: 09 89 LYS cc_start: 0.8612 (tptt) cc_final: 0.7893 (tmtt) REVERT: 09 132 PHE cc_start: 0.8654 (m-80) cc_final: 0.8397 (m-80) REVERT: 10 8 LYS cc_start: 0.9214 (tppt) cc_final: 0.8599 (mmmt) REVERT: 10 9 GLN cc_start: 0.8881 (mm-40) cc_final: 0.8611 (mm-40) REVERT: 11 61 TYR cc_start: 0.9019 (m-80) cc_final: 0.8601 (m-80) REVERT: 11 116 MET cc_start: 0.7634 (mtt) cc_final: 0.5195 (ttm) REVERT: 11 124 MET cc_start: 0.9461 (mmm) cc_final: 0.8888 (mmp) REVERT: 12 60 ASP cc_start: 0.8718 (p0) cc_final: 0.8206 (p0) REVERT: 22 1 MET cc_start: 0.6107 (ptp) cc_final: 0.5863 (ptp) REVERT: 25 52 ASP cc_start: 0.8625 (p0) cc_final: 0.8393 (p0) REVERT: 27 1 MET cc_start: 0.8974 (tmm) cc_final: 0.8398 (tmm) REVERT: 29 9 TYR cc_start: 0.7245 (t80) cc_final: 0.6472 (t80) REVERT: 29 62 LYS cc_start: 0.9320 (mmmm) cc_final: 0.9074 (mmmm) REVERT: Z 265 HIS cc_start: 0.8842 (t70) cc_final: 0.8538 (t70) REVERT: E 146 MET cc_start: 0.8735 (tmm) cc_final: 0.8448 (tmm) REVERT: F 45 ARG cc_start: 0.8539 (ttm110) cc_final: 0.8194 (ttm110) REVERT: F 78 PHE cc_start: 0.9004 (m-80) cc_final: 0.8511 (m-80) REVERT: G 30 MET cc_start: 0.8442 (tmm) cc_final: 0.7710 (tmm) REVERT: H 53 ASP cc_start: 0.7201 (p0) cc_final: 0.6977 (p0) REVERT: I 55 ASP cc_start: 0.8703 (t70) cc_final: 0.7947 (t0) REVERT: I 99 LYS cc_start: 0.9224 (mtpp) cc_final: 0.8975 (mtmm) REVERT: J 91 ASP cc_start: 0.6647 (OUTLIER) cc_final: 0.6275 (p0) REVERT: K 26 PHE cc_start: 0.8115 (OUTLIER) cc_final: 0.7897 (t80) REVERT: K 63 GLN cc_start: 0.8364 (tm-30) cc_final: 0.7145 (tm-30) REVERT: K 69 CYS cc_start: 0.8590 (t) cc_final: 0.8237 (t) REVERT: N 47 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8490 (tt) REVERT: S 16 LYS cc_start: 0.8939 (mtmm) cc_final: 0.8680 (pttm) REVERT: U 4 LYS cc_start: 0.8580 (tptp) cc_final: 0.8277 (tptp) REVERT: U 38 GLU cc_start: 0.7435 (pp20) cc_final: 0.7231 (pp20) outliers start: 319 outliers final: 255 residues processed: 1300 average time/residue: 1.3103 time to fit residues: 2973.3208 Evaluate side-chains 1308 residues out of total 5356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 1048 time to evaluate : 7.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain 03 residue 7 ARG Chi-restraints excluded: chain 03 residue 20 GLN Chi-restraints excluded: chain 03 residue 39 VAL Chi-restraints excluded: chain 03 residue 193 LEU Chi-restraints excluded: chain 04 residue 34 GLU Chi-restraints excluded: chain 04 residue 37 SER Chi-restraints excluded: chain 04 residue 39 SER Chi-restraints excluded: chain 04 residue 103 ILE Chi-restraints excluded: chain 04 residue 113 ASP Chi-restraints excluded: chain 04 residue 138 SER Chi-restraints excluded: chain 04 residue 159 THR Chi-restraints excluded: chain 04 residue 202 ARG Chi-restraints excluded: chain 05 residue 1 MET Chi-restraints excluded: chain 05 residue 18 ASP Chi-restraints excluded: chain 05 residue 60 VAL Chi-restraints excluded: chain 05 residue 91 THR Chi-restraints excluded: chain 05 residue 96 ILE Chi-restraints excluded: chain 05 residue 97 SER Chi-restraints excluded: chain 05 residue 170 VAL Chi-restraints excluded: chain 05 residue 177 VAL Chi-restraints excluded: chain 05 residue 185 ASN Chi-restraints excluded: chain 05 residue 199 SER Chi-restraints excluded: chain 05 residue 201 LEU Chi-restraints excluded: chain 06 residue 13 THR Chi-restraints excluded: chain 06 residue 60 TRP Chi-restraints excluded: chain 06 residue 73 ILE Chi-restraints excluded: chain 06 residue 77 ILE Chi-restraints excluded: chain 06 residue 84 THR Chi-restraints excluded: chain 06 residue 108 ILE Chi-restraints excluded: chain 06 residue 175 ILE Chi-restraints excluded: chain 07 residue 22 ASN Chi-restraints excluded: chain 07 residue 30 VAL Chi-restraints excluded: chain 07 residue 154 THR Chi-restraints excluded: chain 08 residue 10 VAL Chi-restraints excluded: chain 08 residue 15 ASP Chi-restraints excluded: chain 08 residue 19 ASN Chi-restraints excluded: chain 08 residue 91 VAL Chi-restraints excluded: chain 08 residue 130 ILE Chi-restraints excluded: chain 08 residue 154 GLU Chi-restraints excluded: chain 08 residue 165 ASP Chi-restraints excluded: chain 09 residue 14 SER Chi-restraints excluded: chain 10 residue 38 MET Chi-restraints excluded: chain 10 residue 67 THR Chi-restraints excluded: chain 10 residue 129 LEU Chi-restraints excluded: chain 11 residue 2 LYS Chi-restraints excluded: chain 11 residue 10 LEU Chi-restraints excluded: chain 11 residue 67 THR Chi-restraints excluded: chain 11 residue 68 PHE Chi-restraints excluded: chain 11 residue 86 LYS Chi-restraints excluded: chain 12 residue 81 ILE Chi-restraints excluded: chain 12 residue 101 ILE Chi-restraints excluded: chain 13 residue 32 TYR Chi-restraints excluded: chain 13 residue 45 GLU Chi-restraints excluded: chain 13 residue 97 THR Chi-restraints excluded: chain 13 residue 100 PHE Chi-restraints excluded: chain 13 residue 104 THR Chi-restraints excluded: chain 14 residue 42 SER Chi-restraints excluded: chain 14 residue 46 VAL Chi-restraints excluded: chain 14 residue 57 LEU Chi-restraints excluded: chain 14 residue 67 THR Chi-restraints excluded: chain 14 residue 76 GLU Chi-restraints excluded: chain 14 residue 91 ASP Chi-restraints excluded: chain 14 residue 103 ILE Chi-restraints excluded: chain 14 residue 116 VAL Chi-restraints excluded: chain 15 residue 24 THR Chi-restraints excluded: chain 15 residue 28 PHE Chi-restraints excluded: chain 15 residue 42 THR Chi-restraints excluded: chain 15 residue 78 LEU Chi-restraints excluded: chain 15 residue 88 ASN Chi-restraints excluded: chain 15 residue 126 ILE Chi-restraints excluded: chain 15 residue 128 THR Chi-restraints excluded: chain 15 residue 136 MET Chi-restraints excluded: chain 16 residue 15 SER Chi-restraints excluded: chain 16 residue 24 MET Chi-restraints excluded: chain 16 residue 36 THR Chi-restraints excluded: chain 16 residue 52 ILE Chi-restraints excluded: chain 16 residue 57 THR Chi-restraints excluded: chain 17 residue 43 ASN Chi-restraints excluded: chain 17 residue 58 ILE Chi-restraints excluded: chain 17 residue 69 ASP Chi-restraints excluded: chain 17 residue 78 VAL Chi-restraints excluded: chain 17 residue 83 LEU Chi-restraints excluded: chain 17 residue 93 ASP Chi-restraints excluded: chain 18 residue 43 GLU Chi-restraints excluded: chain 18 residue 45 VAL Chi-restraints excluded: chain 18 residue 82 SER Chi-restraints excluded: chain 18 residue 85 VAL Chi-restraints excluded: chain 19 residue 7 VAL Chi-restraints excluded: chain 20 residue 38 VAL Chi-restraints excluded: chain 20 residue 58 VAL Chi-restraints excluded: chain 20 residue 99 THR Chi-restraints excluded: chain 21 residue 24 ILE Chi-restraints excluded: chain 21 residue 52 GLU Chi-restraints excluded: chain 21 residue 81 SER Chi-restraints excluded: chain 22 residue 11 LEU Chi-restraints excluded: chain 22 residue 18 GLU Chi-restraints excluded: chain 22 residue 58 VAL Chi-restraints excluded: chain 22 residue 74 ILE Chi-restraints excluded: chain 23 residue 17 ASP Chi-restraints excluded: chain 23 residue 27 VAL Chi-restraints excluded: chain 24 residue 38 LEU Chi-restraints excluded: chain 24 residue 59 GLU Chi-restraints excluded: chain 24 residue 83 LYS Chi-restraints excluded: chain 24 residue 90 ASP Chi-restraints excluded: chain 25 residue 19 VAL Chi-restraints excluded: chain 25 residue 67 VAL Chi-restraints excluded: chain 26 residue 6 VAL Chi-restraints excluded: chain 26 residue 15 ASN Chi-restraints excluded: chain 26 residue 39 VAL Chi-restraints excluded: chain 26 residue 63 ILE Chi-restraints excluded: chain 27 residue 15 ASN Chi-restraints excluded: chain 27 residue 27 ASN Chi-restraints excluded: chain 27 residue 43 LEU Chi-restraints excluded: chain 28 residue 31 ILE Chi-restraints excluded: chain 28 residue 51 SER Chi-restraints excluded: chain 29 residue 22 MET Chi-restraints excluded: chain 30 residue 22 THR Chi-restraints excluded: chain 30 residue 45 ASP Chi-restraints excluded: chain 31 residue 11 VAL Chi-restraints excluded: chain 31 residue 13 SER Chi-restraints excluded: chain 31 residue 16 THR Chi-restraints excluded: chain 31 residue 23 THR Chi-restraints excluded: chain 31 residue 33 LEU Chi-restraints excluded: chain 32 residue 15 SER Chi-restraints excluded: chain 32 residue 24 THR Chi-restraints excluded: chain 32 residue 30 VAL Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 32 residue 45 SER Chi-restraints excluded: chain 33 residue 53 ASP Chi-restraints excluded: chain 33 residue 57 VAL Chi-restraints excluded: chain 34 residue 3 VAL Chi-restraints excluded: chain 34 residue 10 LEU Chi-restraints excluded: chain 34 residue 13 ASN Chi-restraints excluded: chain 34 residue 16 ILE Chi-restraints excluded: chain 34 residue 26 ILE Chi-restraints excluded: chain Z residue 162 LYS Chi-restraints excluded: chain Z residue 227 ASP Chi-restraints excluded: chain Z residue 246 THR Chi-restraints excluded: chain Z residue 298 LEU Chi-restraints excluded: chain Z residue 328 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 169 HIS Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 31 CYS Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 96 ASN Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain H residue 9 MET Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain I residue 24 ASN Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 96 GLU Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain K residue 14 GLN Chi-restraints excluded: chain K residue 26 PHE Chi-restraints excluded: chain K residue 34 THR Chi-restraints excluded: chain K residue 35 ASP Chi-restraints excluded: chain K residue 51 PHE Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain L residue 17 LYS Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 39 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 116 TYR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 44 ILE Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain N residue 32 ASP Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 49 THR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 81 ILE Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain O residue 1 SER Chi-restraints excluded: chain O residue 17 ASP Chi-restraints excluded: chain O residue 19 ASN Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 57 ILE Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 68 SER Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain R residue 32 ILE Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain S residue 10 ILE Chi-restraints excluded: chain S residue 30 LEU Chi-restraints excluded: chain S residue 65 MET Chi-restraints excluded: chain T residue 20 ASN Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 12 ASP Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 36 PHE Chi-restraints excluded: chain U residue 37 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1102 random chunks: chunk 1027 optimal weight: 5.9990 chunk 120 optimal weight: 20.0000 chunk 607 optimal weight: 7.9990 chunk 778 optimal weight: 4.9990 chunk 603 optimal weight: 50.0000 chunk 897 optimal weight: 5.9990 chunk 595 optimal weight: 6.9990 chunk 1062 optimal weight: 9.9990 chunk 664 optimal weight: 7.9990 chunk 647 optimal weight: 0.8980 chunk 490 optimal weight: 6.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 32 ASN ** 04 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 04 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 04 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 04 259 ASN ** 05 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 06 9 GLN ** 06 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 3 GLN 13 5 GLN ** 18 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 22 92 ASN ** 26 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 28 8 GLN 29 33 ASN 32 13 ASN ** 32 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 34 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 75 GLN ** Z 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 ASN C 138 GLN ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 HIS ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 141 HIS G 147 ASN ** I 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 ASN ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 54 GLN ** T 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.5091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 165147 Z= 0.202 Angle : 0.623 14.840 246328 Z= 0.318 Chirality : 0.034 0.276 31327 Planarity : 0.004 0.083 13708 Dihedral : 23.665 177.432 81065 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 19.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.41 % Favored : 90.44 % Rotamer: Outliers : 4.24 % Allowed : 25.15 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.10), residues: 6453 helix: 0.03 (0.11), residues: 2178 sheet: -1.61 (0.16), residues: 1060 loop : -2.10 (0.11), residues: 3215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP N 41 HIS 0.010 0.001 HIS Q 30 PHE 0.029 0.002 PHE G 61 TYR 0.043 0.002 TYR B 212 ARG 0.013 0.001 ARG29 56 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12906 Ramachandran restraints generated. 6453 Oldfield, 0 Emsley, 6453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12906 Ramachandran restraints generated. 6453 Oldfield, 0 Emsley, 6453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1395 residues out of total 5356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 1171 time to evaluate : 7.304 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: 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: 03 8 MET cc_start: 0.8275 (pmm) cc_final: 0.7936 (ppp) REVERT: 03 20 GLN cc_start: 0.9000 (mt0) cc_final: 0.8661 (tt0) REVERT: 03 198 LYS cc_start: 0.8799 (pttt) cc_final: 0.8587 (pttm) REVERT: 08 57 TYR cc_start: 0.7525 (m-80) cc_final: 0.6598 (m-10) REVERT: 08 172 GLU cc_start: 0.8434 (tp30) cc_final: 0.7948 (tp30) REVERT: 09 18 GLN cc_start: 0.8082 (tp-100) cc_final: 0.7866 (mm-40) REVERT: 09 53 GLU cc_start: 0.8279 (mp0) cc_final: 0.7992 (mp0) REVERT: 09 89 LYS cc_start: 0.8557 (tptt) cc_final: 0.7728 (tmmt) REVERT: 09 112 LYS cc_start: 0.9092 (mmmm) cc_final: 0.8865 (mmtt) REVERT: 10 1 MET cc_start: 0.8162 (tpp) cc_final: 0.7661 (tpp) REVERT: 10 8 LYS cc_start: 0.9143 (tppt) cc_final: 0.8703 (mmmt) REVERT: 11 18 ASN cc_start: 0.8818 (t0) cc_final: 0.8495 (p0) REVERT: 11 61 TYR cc_start: 0.9065 (m-80) cc_final: 0.8571 (m-80) REVERT: 11 116 MET cc_start: 0.7712 (mtt) cc_final: 0.5311 (ttm) REVERT: 11 124 MET cc_start: 0.9401 (mmm) cc_final: 0.8902 (mmp) REVERT: 12 60 ASP cc_start: 0.8653 (p0) cc_final: 0.8127 (p0) REVERT: 13 82 ASN cc_start: 0.7094 (m-40) cc_final: 0.6768 (m110) REVERT: 13 113 MET cc_start: 0.8325 (mmp) cc_final: 0.8116 (mpp) REVERT: 22 1 MET cc_start: 0.6111 (ptp) cc_final: 0.5182 (ptt) REVERT: 22 18 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7816 (mp0) REVERT: 24 48 MET cc_start: 0.8531 (tpt) cc_final: 0.8294 (tpt) REVERT: 25 11 ASP cc_start: 0.8172 (t0) cc_final: 0.7903 (t0) REVERT: 25 52 ASP cc_start: 0.8499 (p0) cc_final: 0.8272 (p0) REVERT: 29 9 TYR cc_start: 0.7139 (t80) cc_final: 0.5819 (t80) REVERT: 29 62 LYS cc_start: 0.9317 (mmmm) cc_final: 0.9037 (mmmm) REVERT: Z 192 LEU cc_start: 0.9385 (mp) cc_final: 0.9135 (mp) REVERT: Z 262 ARG cc_start: 0.8928 (tmt90) cc_final: 0.8488 (tpt-90) REVERT: Z 265 HIS cc_start: 0.8677 (t70) cc_final: 0.8414 (t70) REVERT: B 189 ASN cc_start: 0.8947 (OUTLIER) cc_final: 0.8624 (m-40) REVERT: E 146 MET cc_start: 0.8590 (tmm) cc_final: 0.8372 (tmm) REVERT: F 78 PHE cc_start: 0.8915 (m-80) cc_final: 0.8509 (m-80) REVERT: G 30 MET cc_start: 0.8266 (tmm) cc_final: 0.7548 (tmm) REVERT: H 53 ASP cc_start: 0.7287 (p0) cc_final: 0.6997 (p0) REVERT: I 55 ASP cc_start: 0.8590 (t70) cc_final: 0.7835 (t0) REVERT: I 56 MET cc_start: 0.8872 (mmm) cc_final: 0.8589 (mmm) REVERT: I 99 LYS cc_start: 0.9184 (mtpp) cc_final: 0.8889 (mtmm) REVERT: K 26 PHE cc_start: 0.8029 (OUTLIER) cc_final: 0.7809 (t80) REVERT: K 63 GLN cc_start: 0.8261 (tm-30) cc_final: 0.7820 (tm-30) REVERT: K 67 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7689 (mm-30) REVERT: K 69 CYS cc_start: 0.8417 (t) cc_final: 0.8079 (t) REVERT: M 33 LEU cc_start: 0.8971 (pp) cc_final: 0.8758 (pp) REVERT: N 46 LYS cc_start: 0.9101 (mmmm) cc_final: 0.8893 (mmmm) REVERT: O 35 ILE cc_start: 0.8983 (mm) cc_final: 0.8745 (mm) outliers start: 224 outliers final: 171 residues processed: 1307 average time/residue: 1.3227 time to fit residues: 3026.5247 Evaluate side-chains 1277 residues out of total 5356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 1103 time to evaluate : 7.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 21 HIS Chi-restraints excluded: chain 03 residue 39 VAL Chi-restraints excluded: chain 03 residue 46 VAL Chi-restraints excluded: chain 03 residue 193 LEU Chi-restraints excluded: chain 04 residue 34 GLU Chi-restraints excluded: chain 04 residue 44 ASN Chi-restraints excluded: chain 04 residue 103 ILE Chi-restraints excluded: chain 04 residue 159 THR Chi-restraints excluded: chain 04 residue 172 THR Chi-restraints excluded: chain 04 residue 202 ARG Chi-restraints excluded: chain 05 residue 1 MET Chi-restraints excluded: chain 05 residue 18 ASP Chi-restraints excluded: chain 05 residue 60 VAL Chi-restraints excluded: chain 05 residue 91 THR Chi-restraints excluded: chain 05 residue 96 ILE Chi-restraints excluded: chain 05 residue 97 SER Chi-restraints excluded: chain 05 residue 137 SER Chi-restraints excluded: chain 05 residue 177 VAL Chi-restraints excluded: chain 05 residue 199 SER Chi-restraints excluded: chain 05 residue 201 LEU Chi-restraints excluded: chain 05 residue 207 VAL Chi-restraints excluded: chain 06 residue 84 THR Chi-restraints excluded: chain 06 residue 175 ILE Chi-restraints excluded: chain 07 residue 22 ASN Chi-restraints excluded: chain 07 residue 154 THR Chi-restraints excluded: chain 08 residue 10 VAL Chi-restraints excluded: chain 08 residue 15 ASP Chi-restraints excluded: chain 08 residue 19 ASN Chi-restraints excluded: chain 08 residue 130 ILE Chi-restraints excluded: chain 08 residue 154 GLU Chi-restraints excluded: chain 08 residue 165 ASP Chi-restraints excluded: chain 09 residue 17 ASP Chi-restraints excluded: chain 10 residue 27 VAL Chi-restraints excluded: chain 10 residue 35 VAL Chi-restraints excluded: chain 10 residue 60 LEU Chi-restraints excluded: chain 10 residue 67 THR Chi-restraints excluded: chain 10 residue 129 LEU Chi-restraints excluded: chain 11 residue 2 LYS Chi-restraints excluded: chain 11 residue 10 LEU Chi-restraints excluded: chain 11 residue 68 PHE Chi-restraints excluded: chain 11 residue 86 LYS Chi-restraints excluded: chain 13 residue 32 TYR Chi-restraints excluded: chain 13 residue 100 PHE Chi-restraints excluded: chain 13 residue 104 THR Chi-restraints excluded: chain 13 residue 117 SER Chi-restraints excluded: chain 14 residue 57 LEU Chi-restraints excluded: chain 14 residue 76 GLU Chi-restraints excluded: chain 14 residue 103 ILE Chi-restraints excluded: chain 14 residue 116 VAL Chi-restraints excluded: chain 15 residue 24 THR Chi-restraints excluded: chain 15 residue 28 PHE Chi-restraints excluded: chain 15 residue 42 THR Chi-restraints excluded: chain 15 residue 78 LEU Chi-restraints excluded: chain 15 residue 88 ASN Chi-restraints excluded: chain 15 residue 124 LEU Chi-restraints excluded: chain 15 residue 128 THR Chi-restraints excluded: chain 15 residue 136 MET Chi-restraints excluded: chain 16 residue 15 SER Chi-restraints excluded: chain 16 residue 24 MET Chi-restraints excluded: chain 16 residue 57 THR Chi-restraints excluded: chain 17 residue 83 LEU Chi-restraints excluded: chain 17 residue 93 ASP Chi-restraints excluded: chain 18 residue 45 VAL Chi-restraints excluded: chain 18 residue 85 VAL Chi-restraints excluded: chain 19 residue 7 VAL Chi-restraints excluded: chain 20 residue 58 VAL Chi-restraints excluded: chain 22 residue 18 GLU Chi-restraints excluded: chain 22 residue 58 VAL Chi-restraints excluded: chain 23 residue 27 VAL Chi-restraints excluded: chain 24 residue 38 LEU Chi-restraints excluded: chain 24 residue 59 GLU Chi-restraints excluded: chain 24 residue 83 LYS Chi-restraints excluded: chain 24 residue 90 ASP Chi-restraints excluded: chain 25 residue 19 VAL Chi-restraints excluded: chain 25 residue 67 VAL Chi-restraints excluded: chain 26 residue 39 VAL Chi-restraints excluded: chain 28 residue 23 LEU Chi-restraints excluded: chain 28 residue 31 ILE Chi-restraints excluded: chain 28 residue 51 SER Chi-restraints excluded: chain 29 residue 22 MET Chi-restraints excluded: chain 30 residue 22 THR Chi-restraints excluded: chain 30 residue 45 ASP Chi-restraints excluded: chain 31 residue 11 VAL Chi-restraints excluded: chain 31 residue 13 SER Chi-restraints excluded: chain 31 residue 16 THR Chi-restraints excluded: chain 31 residue 23 THR Chi-restraints excluded: chain 32 residue 30 VAL Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 33 residue 53 ASP Chi-restraints excluded: chain Z residue 162 LYS Chi-restraints excluded: chain Z residue 227 ASP Chi-restraints excluded: chain Z residue 234 ILE Chi-restraints excluded: chain Z residue 246 THR Chi-restraints excluded: chain Z residue 298 LEU Chi-restraints excluded: chain Z residue 328 LEU Chi-restraints excluded: chain B residue 21 TYR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 169 HIS Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 31 CYS Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain E residue 12 GLU Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 96 ASN Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain I residue 24 ASN Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 96 GLU Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain K residue 14 GLN Chi-restraints excluded: chain K residue 26 PHE Chi-restraints excluded: chain K residue 35 ASP Chi-restraints excluded: chain K residue 51 PHE Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain L residue 17 LYS Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain N residue 32 ASP Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 49 THR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain O residue 17 ASP Chi-restraints excluded: chain O residue 19 ASN Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 68 SER Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 69 THR Chi-restraints excluded: chain Q residue 74 LEU Chi-restraints excluded: chain R residue 32 ILE Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain S residue 10 ILE Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 23 GLU Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 36 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1102 random chunks: chunk 657 optimal weight: 6.9990 chunk 424 optimal weight: 20.0000 chunk 634 optimal weight: 10.0000 chunk 319 optimal weight: 20.0000 chunk 208 optimal weight: 20.0000 chunk 205 optimal weight: 20.0000 chunk 675 optimal weight: 4.9990 chunk 723 optimal weight: 9.9990 chunk 525 optimal weight: 7.9990 chunk 98 optimal weight: 20.0000 chunk 834 optimal weight: 20.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 03 20 GLN ** 04 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 04 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 04 259 ASN ** 05 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 06 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 3 GLN ** 22 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 26 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 32 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 ASN ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 141 HIS ** I 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 12 GLN T 47 GLN ** T 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.5229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 165147 Z= 0.280 Angle : 0.653 14.780 246328 Z= 0.333 Chirality : 0.036 0.285 31327 Planarity : 0.005 0.096 13708 Dihedral : 23.632 177.153 81065 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 21.82 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.98 % Favored : 89.85 % Rotamer: Outliers : 4.24 % Allowed : 25.45 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.10), residues: 6453 helix: 0.04 (0.11), residues: 2187 sheet: -1.56 (0.16), residues: 1034 loop : -2.08 (0.11), residues: 3232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP06 60 HIS 0.010 0.001 HIS Q 30 PHE 0.030 0.002 PHE28 52 TYR 0.041 0.002 TYR B 212 ARG 0.012 0.001 ARG10 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12906 Ramachandran restraints generated. 6453 Oldfield, 0 Emsley, 6453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12906 Ramachandran restraints generated. 6453 Oldfield, 0 Emsley, 6453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1346 residues out of total 5356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 1122 time to evaluate : 7.239 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: 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: 03 8 MET cc_start: 0.8320 (pmm) cc_final: 0.8047 (ppp) REVERT: 03 20 GLN cc_start: 0.8993 (mt0) cc_final: 0.8667 (tt0) REVERT: 09 2 GLN cc_start: 0.8446 (mm-40) cc_final: 0.8237 (mm-40) REVERT: 09 18 GLN cc_start: 0.8115 (tp-100) cc_final: 0.7823 (mm-40) REVERT: 09 53 GLU cc_start: 0.8309 (mp0) cc_final: 0.8108 (mp0) REVERT: 09 89 LYS cc_start: 0.8569 (tptt) cc_final: 0.7749 (tmmt) REVERT: 10 8 LYS cc_start: 0.9153 (tppt) cc_final: 0.8728 (mmmt) REVERT: 10 42 ARG cc_start: 0.8619 (tpm170) cc_final: 0.8387 (tpm170) REVERT: 11 3 LYS cc_start: 0.8023 (tptt) cc_final: 0.7823 (tptt) REVERT: 11 18 ASN cc_start: 0.8830 (t0) cc_final: 0.8495 (p0) REVERT: 11 61 TYR cc_start: 0.9011 (m-80) cc_final: 0.8480 (m-80) REVERT: 11 116 MET cc_start: 0.7685 (mtt) cc_final: 0.5263 (ttm) REVERT: 11 124 MET cc_start: 0.9447 (mmm) cc_final: 0.8936 (mmp) REVERT: 12 60 ASP cc_start: 0.8706 (p0) cc_final: 0.8187 (p0) REVERT: 13 82 ASN cc_start: 0.7082 (m-40) cc_final: 0.6744 (m110) REVERT: 22 1 MET cc_start: 0.6044 (ptp) cc_final: 0.5570 (ptp) REVERT: 22 6 ARG cc_start: 0.8725 (mmm160) cc_final: 0.8521 (mmm160) REVERT: 22 42 GLU cc_start: 0.8616 (pp20) cc_final: 0.8378 (pp20) REVERT: 24 48 MET cc_start: 0.8529 (tpt) cc_final: 0.8238 (tpt) REVERT: 25 11 ASP cc_start: 0.8236 (t0) cc_final: 0.7997 (t0) REVERT: 25 52 ASP cc_start: 0.8561 (p0) cc_final: 0.8330 (p0) REVERT: 29 9 TYR cc_start: 0.7115 (t80) cc_final: 0.5874 (t80) REVERT: 29 62 LYS cc_start: 0.9329 (mmmm) cc_final: 0.9029 (mmmm) REVERT: Z 73 MET cc_start: 0.7954 (mmm) cc_final: 0.7745 (mmm) REVERT: Z 265 HIS cc_start: 0.8648 (t70) cc_final: 0.8414 (t70) REVERT: B 189 ASN cc_start: 0.9062 (OUTLIER) cc_final: 0.8600 (m-40) REVERT: E 85 LYS cc_start: 0.8059 (mmmt) cc_final: 0.7809 (mmmm) REVERT: E 146 MET cc_start: 0.8665 (tmm) cc_final: 0.8408 (tmm) REVERT: F 78 PHE cc_start: 0.8966 (m-80) cc_final: 0.8592 (m-80) REVERT: G 30 MET cc_start: 0.8324 (tmm) cc_final: 0.7603 (tmm) REVERT: H 53 ASP cc_start: 0.7427 (p0) cc_final: 0.7140 (p0) REVERT: I 55 ASP cc_start: 0.8573 (t70) cc_final: 0.7821 (t0) REVERT: I 56 MET cc_start: 0.8903 (mmm) cc_final: 0.8672 (mmm) REVERT: I 99 LYS cc_start: 0.9211 (mtpp) cc_final: 0.8915 (mtmm) REVERT: J 90 LEU cc_start: 0.7568 (pp) cc_final: 0.6978 (pt) REVERT: K 26 PHE cc_start: 0.8079 (OUTLIER) cc_final: 0.7857 (t80) REVERT: K 63 GLN cc_start: 0.8168 (tm-30) cc_final: 0.7935 (tm-30) REVERT: K 67 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7839 (mm-30) REVERT: K 69 CYS cc_start: 0.8459 (t) cc_final: 0.8147 (t) REVERT: L 61 GLU cc_start: 0.7954 (tp30) cc_final: 0.7742 (tp30) REVERT: N 5 MET cc_start: 0.8845 (mmm) cc_final: 0.8641 (mmm) REVERT: T 23 ARG cc_start: 0.8569 (mmm-85) cc_final: 0.8279 (mmt90) outliers start: 224 outliers final: 200 residues processed: 1254 average time/residue: 1.3114 time to fit residues: 2876.8503 Evaluate side-chains 1291 residues out of total 5356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 1089 time to evaluate : 7.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 03 residue 39 VAL Chi-restraints excluded: chain 03 residue 46 VAL Chi-restraints excluded: chain 03 residue 193 LEU Chi-restraints excluded: chain 04 residue 34 GLU Chi-restraints excluded: chain 04 residue 37 SER Chi-restraints excluded: chain 04 residue 39 SER Chi-restraints excluded: chain 04 residue 44 ASN Chi-restraints excluded: chain 04 residue 103 ILE Chi-restraints excluded: chain 04 residue 159 THR Chi-restraints excluded: chain 04 residue 172 THR Chi-restraints excluded: chain 04 residue 202 ARG Chi-restraints excluded: chain 05 residue 1 MET Chi-restraints excluded: chain 05 residue 18 ASP Chi-restraints excluded: chain 05 residue 60 VAL Chi-restraints excluded: chain 05 residue 91 THR Chi-restraints excluded: chain 05 residue 96 ILE Chi-restraints excluded: chain 05 residue 97 SER Chi-restraints excluded: chain 05 residue 177 VAL Chi-restraints excluded: chain 05 residue 199 SER Chi-restraints excluded: chain 05 residue 201 LEU Chi-restraints excluded: chain 05 residue 207 VAL Chi-restraints excluded: chain 06 residue 84 THR Chi-restraints excluded: chain 06 residue 108 ILE Chi-restraints excluded: chain 06 residue 175 ILE Chi-restraints excluded: chain 07 residue 22 ASN Chi-restraints excluded: chain 07 residue 154 THR Chi-restraints excluded: chain 08 residue 10 VAL Chi-restraints excluded: chain 08 residue 15 ASP Chi-restraints excluded: chain 08 residue 19 ASN Chi-restraints excluded: chain 08 residue 91 VAL Chi-restraints excluded: chain 08 residue 130 ILE Chi-restraints excluded: chain 08 residue 154 GLU Chi-restraints excluded: chain 08 residue 165 ASP Chi-restraints excluded: chain 09 residue 17 ASP Chi-restraints excluded: chain 10 residue 27 VAL Chi-restraints excluded: chain 10 residue 35 VAL Chi-restraints excluded: chain 10 residue 60 LEU Chi-restraints excluded: chain 10 residue 67 THR Chi-restraints excluded: chain 10 residue 129 LEU Chi-restraints excluded: chain 11 residue 2 LYS Chi-restraints excluded: chain 11 residue 10 LEU Chi-restraints excluded: chain 11 residue 68 PHE Chi-restraints excluded: chain 11 residue 86 LYS Chi-restraints excluded: chain 12 residue 101 ILE Chi-restraints excluded: chain 13 residue 32 TYR Chi-restraints excluded: chain 13 residue 97 THR Chi-restraints excluded: chain 13 residue 100 PHE Chi-restraints excluded: chain 13 residue 104 THR Chi-restraints excluded: chain 14 residue 42 SER Chi-restraints excluded: chain 14 residue 57 LEU Chi-restraints excluded: chain 14 residue 103 ILE Chi-restraints excluded: chain 14 residue 116 VAL Chi-restraints excluded: chain 15 residue 24 THR Chi-restraints excluded: chain 15 residue 28 PHE Chi-restraints excluded: chain 15 residue 42 THR Chi-restraints excluded: chain 15 residue 78 LEU Chi-restraints excluded: chain 15 residue 88 ASN Chi-restraints excluded: chain 15 residue 124 LEU Chi-restraints excluded: chain 15 residue 128 THR Chi-restraints excluded: chain 15 residue 136 MET Chi-restraints excluded: chain 16 residue 15 SER Chi-restraints excluded: chain 16 residue 24 MET Chi-restraints excluded: chain 16 residue 36 THR Chi-restraints excluded: chain 16 residue 57 THR Chi-restraints excluded: chain 17 residue 47 VAL Chi-restraints excluded: chain 17 residue 69 ASP Chi-restraints excluded: chain 17 residue 83 LEU Chi-restraints excluded: chain 17 residue 93 ASP Chi-restraints excluded: chain 18 residue 43 GLU Chi-restraints excluded: chain 18 residue 45 VAL Chi-restraints excluded: chain 18 residue 82 SER Chi-restraints excluded: chain 18 residue 85 VAL Chi-restraints excluded: chain 19 residue 7 VAL Chi-restraints excluded: chain 20 residue 38 VAL Chi-restraints excluded: chain 20 residue 58 VAL Chi-restraints excluded: chain 20 residue 99 THR Chi-restraints excluded: chain 21 residue 24 ILE Chi-restraints excluded: chain 21 residue 36 LEU Chi-restraints excluded: chain 21 residue 81 SER Chi-restraints excluded: chain 22 residue 58 VAL Chi-restraints excluded: chain 23 residue 27 VAL Chi-restraints excluded: chain 24 residue 38 LEU Chi-restraints excluded: chain 24 residue 47 VAL Chi-restraints excluded: chain 24 residue 59 GLU Chi-restraints excluded: chain 24 residue 83 LYS Chi-restraints excluded: chain 24 residue 90 ASP Chi-restraints excluded: chain 25 residue 19 VAL Chi-restraints excluded: chain 25 residue 67 VAL Chi-restraints excluded: chain 26 residue 15 ASN Chi-restraints excluded: chain 26 residue 39 VAL Chi-restraints excluded: chain 26 residue 63 ILE Chi-restraints excluded: chain 28 residue 23 LEU Chi-restraints excluded: chain 28 residue 31 ILE Chi-restraints excluded: chain 28 residue 51 SER Chi-restraints excluded: chain 29 residue 22 MET Chi-restraints excluded: chain 30 residue 22 THR Chi-restraints excluded: chain 30 residue 45 ASP Chi-restraints excluded: chain 31 residue 11 VAL Chi-restraints excluded: chain 31 residue 13 SER Chi-restraints excluded: chain 31 residue 16 THR Chi-restraints excluded: chain 31 residue 23 THR Chi-restraints excluded: chain 31 residue 47 ILE Chi-restraints excluded: chain 32 residue 30 VAL Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 33 residue 53 ASP Chi-restraints excluded: chain Z residue 162 LYS Chi-restraints excluded: chain Z residue 227 ASP Chi-restraints excluded: chain Z residue 234 ILE Chi-restraints excluded: chain Z residue 246 THR Chi-restraints excluded: chain Z residue 298 LEU Chi-restraints excluded: chain Z residue 328 LEU Chi-restraints excluded: chain B residue 21 TYR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 169 HIS Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 31 CYS Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 96 ASN Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain I residue 24 ASN Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 96 GLU Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain K residue 14 GLN Chi-restraints excluded: chain K residue 26 PHE Chi-restraints excluded: chain K residue 35 ASP Chi-restraints excluded: chain K residue 51 PHE Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain L residue 17 LYS Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain N residue 32 ASP Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 49 THR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 79 SER Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain O residue 17 ASP Chi-restraints excluded: chain O residue 19 ASN Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 68 SER Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain Q residue 69 THR Chi-restraints excluded: chain Q residue 74 LEU Chi-restraints excluded: chain Q residue 76 ARG Chi-restraints excluded: chain R residue 32 ILE Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain S residue 10 ILE Chi-restraints excluded: chain S residue 23 GLU Chi-restraints excluded: chain T residue 22 SER Chi-restraints excluded: chain T residue 47 GLN Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 36 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1102 random chunks: chunk 966 optimal weight: 7.9990 chunk 1017 optimal weight: 10.0000 chunk 928 optimal weight: 8.9990 chunk 989 optimal weight: 20.0000 chunk 595 optimal weight: 20.0000 chunk 431 optimal weight: 20.0000 chunk 777 optimal weight: 10.0000 chunk 303 optimal weight: 30.0000 chunk 894 optimal weight: 0.0970 chunk 936 optimal weight: 5.9990 chunk 986 optimal weight: 10.0000 overall best weight: 6.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 04 59 GLN ** 04 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 04 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 04 259 ASN 05 134 HIS ** 06 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 18 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 18 76 HIS ** 22 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 28 33 HIS 32 29 GLN ** Z 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 GLN ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 141 HIS ** J 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.5300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 165147 Z= 0.237 Angle : 0.636 14.950 246328 Z= 0.323 Chirality : 0.035 0.286 31327 Planarity : 0.005 0.092 13708 Dihedral : 23.645 178.301 81065 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.24 % Favored : 90.58 % Rotamer: Outliers : 3.98 % Allowed : 26.45 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.10), residues: 6453 helix: 0.10 (0.11), residues: 2181 sheet: -1.50 (0.16), residues: 1049 loop : -2.03 (0.11), residues: 3223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP N 41 HIS 0.009 0.001 HIS18 76 PHE 0.040 0.002 PHE T 50 TYR 0.040 0.002 TYR B 212 ARG 0.017 0.001 ARG08 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12906 Ramachandran restraints generated. 6453 Oldfield, 0 Emsley, 6453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12906 Ramachandran restraints generated. 6453 Oldfield, 0 Emsley, 6453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1355 residues out of total 5356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 1145 time to evaluate : 7.317 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: 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: 03 8 MET cc_start: 0.8270 (pmm) cc_final: 0.8051 (ppp) REVERT: 03 50 ILE cc_start: 0.6722 (OUTLIER) cc_final: 0.5209 (mm) REVERT: 03 214 ILE cc_start: 0.9036 (pt) cc_final: 0.8731 (mm) REVERT: 09 18 GLN cc_start: 0.8074 (tp-100) cc_final: 0.7794 (mm-40) REVERT: 09 89 LYS cc_start: 0.8559 (tptt) cc_final: 0.7728 (tmmt) REVERT: 10 8 LYS cc_start: 0.9153 (tppt) cc_final: 0.8699 (mmmt) REVERT: 11 18 ASN cc_start: 0.8819 (t0) cc_final: 0.8425 (p0) REVERT: 11 116 MET cc_start: 0.7511 (mtt) cc_final: 0.5074 (ttm) REVERT: 11 124 MET cc_start: 0.9452 (mmm) cc_final: 0.8928 (mmp) REVERT: 12 60 ASP cc_start: 0.8745 (p0) cc_final: 0.8237 (p0) REVERT: 13 82 ASN cc_start: 0.6976 (m-40) cc_final: 0.6642 (m110) REVERT: 22 1 MET cc_start: 0.5978 (ptp) cc_final: 0.4970 (ptt) REVERT: 22 42 GLU cc_start: 0.8550 (pp20) cc_final: 0.8325 (pp20) REVERT: 24 48 MET cc_start: 0.8581 (tpt) cc_final: 0.8259 (tpt) REVERT: 25 11 ASP cc_start: 0.8115 (t0) cc_final: 0.7869 (t0) REVERT: 25 52 ASP cc_start: 0.8498 (p0) cc_final: 0.8262 (p0) REVERT: 29 9 TYR cc_start: 0.7122 (OUTLIER) cc_final: 0.6230 (t80) REVERT: 29 59 ARG cc_start: 0.8828 (tmm160) cc_final: 0.8473 (tmm160) REVERT: 29 62 LYS cc_start: 0.9359 (mmmm) cc_final: 0.9095 (mmmm) REVERT: 31 36 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.8008 (ttpt) REVERT: Z 73 MET cc_start: 0.7950 (mmm) cc_final: 0.7714 (mmm) REVERT: Z 262 ARG cc_start: 0.9001 (tmt90) cc_final: 0.8395 (tpt-90) REVERT: C 133 MET cc_start: 0.8011 (ppp) cc_final: 0.7745 (ppp) REVERT: E 85 LYS cc_start: 0.8085 (mmmt) cc_final: 0.7870 (mmmm) REVERT: F 78 PHE cc_start: 0.8914 (m-80) cc_final: 0.8526 (m-80) REVERT: G 30 MET cc_start: 0.8276 (tmm) cc_final: 0.7561 (tmm) REVERT: H 53 ASP cc_start: 0.7397 (p0) cc_final: 0.7114 (p0) REVERT: I 55 ASP cc_start: 0.8631 (t70) cc_final: 0.7898 (t0) REVERT: I 56 MET cc_start: 0.8898 (mmm) cc_final: 0.8634 (mmm) REVERT: I 99 LYS cc_start: 0.9171 (mtpp) cc_final: 0.8895 (mtmm) REVERT: J 90 LEU cc_start: 0.7697 (pp) cc_final: 0.7104 (pt) REVERT: K 63 GLN cc_start: 0.8170 (tm-30) cc_final: 0.7893 (tm-30) REVERT: K 67 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7750 (mm-30) REVERT: K 69 CYS cc_start: 0.8440 (t) cc_final: 0.8121 (t) REVERT: T 23 ARG cc_start: 0.8609 (mmm-85) cc_final: 0.8356 (mmt90) REVERT: U 30 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8397 (pm20) outliers start: 210 outliers final: 186 residues processed: 1263 average time/residue: 1.3248 time to fit residues: 2926.2089 Evaluate side-chains 1298 residues out of total 5356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 1109 time to evaluate : 7.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 03 residue 39 VAL Chi-restraints excluded: chain 03 residue 46 VAL Chi-restraints excluded: chain 03 residue 50 ILE Chi-restraints excluded: chain 03 residue 193 LEU Chi-restraints excluded: chain 04 residue 34 GLU Chi-restraints excluded: chain 04 residue 39 SER Chi-restraints excluded: chain 04 residue 44 ASN Chi-restraints excluded: chain 04 residue 103 ILE Chi-restraints excluded: chain 04 residue 159 THR Chi-restraints excluded: chain 04 residue 172 THR Chi-restraints excluded: chain 04 residue 202 ARG Chi-restraints excluded: chain 05 residue 18 ASP Chi-restraints excluded: chain 05 residue 60 VAL Chi-restraints excluded: chain 05 residue 91 THR Chi-restraints excluded: chain 05 residue 96 ILE Chi-restraints excluded: chain 05 residue 97 SER Chi-restraints excluded: chain 05 residue 170 VAL Chi-restraints excluded: chain 05 residue 177 VAL Chi-restraints excluded: chain 05 residue 199 SER Chi-restraints excluded: chain 05 residue 201 LEU Chi-restraints excluded: chain 05 residue 207 VAL Chi-restraints excluded: chain 06 residue 84 THR Chi-restraints excluded: chain 06 residue 108 ILE Chi-restraints excluded: chain 06 residue 175 ILE Chi-restraints excluded: chain 07 residue 22 ASN Chi-restraints excluded: chain 07 residue 154 THR Chi-restraints excluded: chain 08 residue 10 VAL Chi-restraints excluded: chain 08 residue 15 ASP Chi-restraints excluded: chain 08 residue 19 ASN Chi-restraints excluded: chain 08 residue 91 VAL Chi-restraints excluded: chain 08 residue 130 ILE Chi-restraints excluded: chain 08 residue 154 GLU Chi-restraints excluded: chain 08 residue 165 ASP Chi-restraints excluded: chain 09 residue 17 ASP Chi-restraints excluded: chain 10 residue 27 VAL Chi-restraints excluded: chain 10 residue 35 VAL Chi-restraints excluded: chain 10 residue 38 MET Chi-restraints excluded: chain 10 residue 60 LEU Chi-restraints excluded: chain 10 residue 67 THR Chi-restraints excluded: chain 10 residue 129 LEU Chi-restraints excluded: chain 11 residue 2 LYS Chi-restraints excluded: chain 11 residue 10 LEU Chi-restraints excluded: chain 11 residue 68 PHE Chi-restraints excluded: chain 11 residue 86 LYS Chi-restraints excluded: chain 12 residue 101 ILE Chi-restraints excluded: chain 13 residue 32 TYR Chi-restraints excluded: chain 13 residue 100 PHE Chi-restraints excluded: chain 13 residue 104 THR Chi-restraints excluded: chain 14 residue 42 SER Chi-restraints excluded: chain 14 residue 57 LEU Chi-restraints excluded: chain 14 residue 116 VAL Chi-restraints excluded: chain 15 residue 24 THR Chi-restraints excluded: chain 15 residue 28 PHE Chi-restraints excluded: chain 15 residue 42 THR Chi-restraints excluded: chain 15 residue 78 LEU Chi-restraints excluded: chain 15 residue 88 ASN Chi-restraints excluded: chain 15 residue 124 LEU Chi-restraints excluded: chain 15 residue 128 THR Chi-restraints excluded: chain 16 residue 15 SER Chi-restraints excluded: chain 16 residue 24 MET Chi-restraints excluded: chain 16 residue 36 THR Chi-restraints excluded: chain 16 residue 57 THR Chi-restraints excluded: chain 17 residue 28 VAL Chi-restraints excluded: chain 17 residue 83 LEU Chi-restraints excluded: chain 17 residue 93 ASP Chi-restraints excluded: chain 18 residue 45 VAL Chi-restraints excluded: chain 18 residue 85 VAL Chi-restraints excluded: chain 19 residue 7 VAL Chi-restraints excluded: chain 20 residue 38 VAL Chi-restraints excluded: chain 20 residue 58 VAL Chi-restraints excluded: chain 21 residue 24 ILE Chi-restraints excluded: chain 22 residue 58 VAL Chi-restraints excluded: chain 23 residue 17 ASP Chi-restraints excluded: chain 23 residue 27 VAL Chi-restraints excluded: chain 24 residue 38 LEU Chi-restraints excluded: chain 24 residue 47 VAL Chi-restraints excluded: chain 24 residue 59 GLU Chi-restraints excluded: chain 24 residue 83 LYS Chi-restraints excluded: chain 24 residue 90 ASP Chi-restraints excluded: chain 25 residue 19 VAL Chi-restraints excluded: chain 25 residue 67 VAL Chi-restraints excluded: chain 26 residue 15 ASN Chi-restraints excluded: chain 26 residue 39 VAL Chi-restraints excluded: chain 26 residue 63 ILE Chi-restraints excluded: chain 28 residue 23 LEU Chi-restraints excluded: chain 28 residue 31 ILE Chi-restraints excluded: chain 28 residue 51 SER Chi-restraints excluded: chain 29 residue 9 TYR Chi-restraints excluded: chain 29 residue 22 MET Chi-restraints excluded: chain 30 residue 22 THR Chi-restraints excluded: chain 31 residue 11 VAL Chi-restraints excluded: chain 31 residue 13 SER Chi-restraints excluded: chain 31 residue 16 THR Chi-restraints excluded: chain 31 residue 23 THR Chi-restraints excluded: chain 31 residue 36 LYS Chi-restraints excluded: chain 32 residue 29 GLN Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 33 residue 53 ASP Chi-restraints excluded: chain Z residue 162 LYS Chi-restraints excluded: chain Z residue 227 ASP Chi-restraints excluded: chain Z residue 234 ILE Chi-restraints excluded: chain Z residue 298 LEU Chi-restraints excluded: chain Z residue 328 LEU Chi-restraints excluded: chain B residue 21 TYR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 169 HIS Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 31 CYS Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 96 ASN Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 96 GLU Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain K residue 14 GLN Chi-restraints excluded: chain K residue 35 ASP Chi-restraints excluded: chain K residue 51 PHE Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain L residue 17 LYS Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain N residue 32 ASP Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 49 THR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain O residue 17 ASP Chi-restraints excluded: chain O residue 19 ASN Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 68 SER Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 58 VAL Chi-restraints excluded: chain Q residue 69 THR Chi-restraints excluded: chain Q residue 74 LEU Chi-restraints excluded: chain Q residue 76 ARG Chi-restraints excluded: chain R residue 32 ILE Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain S residue 10 ILE Chi-restraints excluded: chain S residue 23 GLU Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 36 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1102 random chunks: chunk 649 optimal weight: 5.9990 chunk 1046 optimal weight: 7.9990 chunk 638 optimal weight: 1.9990 chunk 496 optimal weight: 0.4980 chunk 727 optimal weight: 10.0000 chunk 1097 optimal weight: 3.9990 chunk 1010 optimal weight: 0.0570 chunk 874 optimal weight: 0.0870 chunk 90 optimal weight: 20.0000 chunk 675 optimal weight: 7.9990 chunk 536 optimal weight: 5.9990 overall best weight: 1.3280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 03 165 ASN ** 04 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 04 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 04 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 04 259 ASN 05 167 ASN ** 07 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 07 62 GLN 08 72 ASN 11 42 ASN ** 12 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 13 ASN 16 3 HIS ** 18 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 18 11 GLN ** 27 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 32 29 GLN ** Z 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 HIS ** F 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 141 HIS I 125 GLN ** J 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 47 GLN T 67 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.5284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 165147 Z= 0.147 Angle : 0.629 23.894 246328 Z= 0.314 Chirality : 0.032 0.283 31327 Planarity : 0.005 0.094 13708 Dihedral : 23.552 179.727 81065 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.60 % Favored : 91.26 % Rotamer: Outliers : 2.79 % Allowed : 27.61 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.10), residues: 6453 helix: 0.15 (0.11), residues: 2185 sheet: -1.32 (0.16), residues: 1053 loop : -1.99 (0.11), residues: 3215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP N 41 HIS 0.009 0.001 HIS S 13 PHE 0.028 0.002 PHE29 60 TYR 0.043 0.002 TYR B 212 ARG 0.017 0.001 ARG D 46 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12906 Ramachandran restraints generated. 6453 Oldfield, 0 Emsley, 6453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12906 Ramachandran restraints generated. 6453 Oldfield, 0 Emsley, 6453 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1373 residues out of total 5356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 1226 time to evaluate : 7.259 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: 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: 03 164 ARG cc_start: 0.8839 (ttp-170) cc_final: 0.8311 (ptt90) REVERT: 03 214 ILE cc_start: 0.8969 (pt) cc_final: 0.8636 (mm) REVERT: 04 224 MET cc_start: 0.7452 (mtp) cc_final: 0.7155 (mtt) REVERT: 09 89 LYS cc_start: 0.8516 (tptt) cc_final: 0.7644 (tmmt) REVERT: 10 1 MET cc_start: 0.7988 (tpp) cc_final: 0.6747 (tpp) REVERT: 10 8 LYS cc_start: 0.9035 (tppt) cc_final: 0.8688 (mmmt) REVERT: 10 9 GLN cc_start: 0.8719 (mm-40) cc_final: 0.8424 (mm110) REVERT: 11 18 ASN cc_start: 0.8766 (t0) cc_final: 0.8445 (p0) REVERT: 11 61 TYR cc_start: 0.8979 (m-80) cc_final: 0.8447 (m-80) REVERT: 11 116 MET cc_start: 0.7490 (mtt) cc_final: 0.4866 (ttt) REVERT: 11 124 MET cc_start: 0.9464 (mmm) cc_final: 0.8941 (mmp) REVERT: 12 60 ASP cc_start: 0.8628 (p0) cc_final: 0.8068 (p0) REVERT: 13 82 ASN cc_start: 0.6906 (m-40) cc_final: 0.6634 (m110) REVERT: 13 89 ASN cc_start: 0.7926 (m-40) cc_final: 0.7636 (m-40) REVERT: 18 8 GLU cc_start: 0.7645 (tm-30) cc_final: 0.7375 (tm-30) REVERT: 22 1 MET cc_start: 0.5713 (ptp) cc_final: 0.4650 (ptt) REVERT: 24 48 MET cc_start: 0.8449 (tpt) cc_final: 0.8093 (tpt) REVERT: 25 11 ASP cc_start: 0.8239 (t0) cc_final: 0.7977 (t0) REVERT: 25 52 ASP cc_start: 0.8474 (p0) cc_final: 0.8255 (p0) REVERT: 29 9 TYR cc_start: 0.6891 (OUTLIER) cc_final: 0.6047 (t80) REVERT: 29 22 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8400 (pmm) REVERT: 29 56 ARG cc_start: 0.5634 (tpt90) cc_final: 0.5127 (tpt90) REVERT: 29 62 LYS cc_start: 0.9364 (mmmm) cc_final: 0.9113 (mmmm) REVERT: 31 24 LYS cc_start: 0.9221 (tppt) cc_final: 0.8419 (tptp) REVERT: 34 37 GLN cc_start: 0.8760 (mm-40) cc_final: 0.8487 (tm-30) REVERT: Z 73 MET cc_start: 0.7920 (mmm) cc_final: 0.7700 (mmm) REVERT: Z 151 MET cc_start: 0.8462 (tmm) cc_final: 0.7970 (tmm) REVERT: Z 262 ARG cc_start: 0.8988 (tmt90) cc_final: 0.8368 (tpt-90) REVERT: C 133 MET cc_start: 0.8002 (ppp) cc_final: 0.7754 (ppp) REVERT: E 146 MET cc_start: 0.8479 (tmm) cc_final: 0.8169 (tmm) REVERT: F 78 PHE cc_start: 0.8931 (m-80) cc_final: 0.8602 (m-80) REVERT: G 30 MET cc_start: 0.8081 (tmm) cc_final: 0.7346 (tmm) REVERT: G 125 ASP cc_start: 0.9097 (p0) cc_final: 0.8808 (p0) REVERT: H 74 ILE cc_start: 0.8980 (tp) cc_final: 0.8707 (tp) REVERT: I 55 ASP cc_start: 0.8565 (t70) cc_final: 0.7765 (t0) REVERT: I 96 GLU cc_start: 0.9092 (OUTLIER) cc_final: 0.8606 (pp20) REVERT: J 63 ASP cc_start: 0.7945 (p0) cc_final: 0.7423 (p0) REVERT: J 90 LEU cc_start: 0.7689 (pp) cc_final: 0.7304 (pt) REVERT: K 63 GLN cc_start: 0.8069 (tm-30) cc_final: 0.7709 (tm-30) REVERT: K 67 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7372 (mm-30) REVERT: K 69 CYS cc_start: 0.8356 (t) cc_final: 0.8031 (t) REVERT: N 38 GLU cc_start: 0.8687 (tp30) cc_final: 0.8305 (tp30) REVERT: Q 15 LYS cc_start: 0.7881 (ptmm) cc_final: 0.7565 (ptmm) REVERT: R 13 THR cc_start: 0.7624 (p) cc_final: 0.7202 (p) REVERT: T 23 ARG cc_start: 0.8535 (mmm-85) cc_final: 0.8267 (mmt90) REVERT: U 30 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8278 (pm20) REVERT: U 39 LYS cc_start: 0.8472 (mmmt) cc_final: 0.8092 (mmmt) outliers start: 147 outliers final: 122 residues processed: 1310 average time/residue: 1.3205 time to fit residues: 3011.8451 Evaluate side-chains 1265 residues out of total 5356 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 1140 time to evaluate : 6.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 03 residue 39 VAL Chi-restraints excluded: chain 03 residue 193 LEU Chi-restraints excluded: chain 04 residue 34 GLU Chi-restraints excluded: chain 04 residue 44 ASN Chi-restraints excluded: chain 04 residue 103 ILE Chi-restraints excluded: chain 04 residue 159 THR Chi-restraints excluded: chain 04 residue 172 THR Chi-restraints excluded: chain 04 residue 202 ARG Chi-restraints excluded: chain 05 residue 18 ASP Chi-restraints excluded: chain 05 residue 91 THR Chi-restraints excluded: chain 05 residue 97 SER Chi-restraints excluded: chain 05 residue 137 SER Chi-restraints excluded: chain 05 residue 177 VAL Chi-restraints excluded: chain 05 residue 201 LEU Chi-restraints excluded: chain 05 residue 207 VAL Chi-restraints excluded: chain 06 residue 84 THR Chi-restraints excluded: chain 06 residue 175 ILE Chi-restraints excluded: chain 07 residue 22 ASN Chi-restraints excluded: chain 08 residue 10 VAL Chi-restraints excluded: chain 08 residue 15 ASP Chi-restraints excluded: chain 08 residue 19 ASN Chi-restraints excluded: chain 08 residue 91 VAL Chi-restraints excluded: chain 08 residue 154 GLU Chi-restraints excluded: chain 08 residue 165 ASP Chi-restraints excluded: chain 09 residue 17 ASP Chi-restraints excluded: chain 10 residue 35 VAL Chi-restraints excluded: chain 10 residue 38 MET Chi-restraints excluded: chain 10 residue 60 LEU Chi-restraints excluded: chain 10 residue 67 THR Chi-restraints excluded: chain 10 residue 129 LEU Chi-restraints excluded: chain 11 residue 2 LYS Chi-restraints excluded: chain 11 residue 10 LEU Chi-restraints excluded: chain 11 residue 68 PHE Chi-restraints excluded: chain 12 residue 101 ILE Chi-restraints excluded: chain 13 residue 32 TYR Chi-restraints excluded: chain 13 residue 100 PHE Chi-restraints excluded: chain 13 residue 104 THR Chi-restraints excluded: chain 14 residue 42 SER Chi-restraints excluded: chain 14 residue 67 THR Chi-restraints excluded: chain 14 residue 116 VAL Chi-restraints excluded: chain 15 residue 28 PHE Chi-restraints excluded: chain 15 residue 42 THR Chi-restraints excluded: chain 15 residue 88 ASN Chi-restraints excluded: chain 15 residue 124 LEU Chi-restraints excluded: chain 15 residue 128 THR Chi-restraints excluded: chain 16 residue 18 GLN Chi-restraints excluded: chain 16 residue 24 MET Chi-restraints excluded: chain 16 residue 57 THR Chi-restraints excluded: chain 17 residue 93 ASP Chi-restraints excluded: chain 18 residue 85 VAL Chi-restraints excluded: chain 19 residue 7 VAL Chi-restraints excluded: chain 20 residue 38 VAL Chi-restraints excluded: chain 20 residue 58 VAL Chi-restraints excluded: chain 23 residue 27 VAL Chi-restraints excluded: chain 24 residue 47 VAL Chi-restraints excluded: chain 24 residue 59 GLU Chi-restraints excluded: chain 24 residue 83 LYS Chi-restraints excluded: chain 24 residue 90 ASP Chi-restraints excluded: chain 25 residue 19 VAL Chi-restraints excluded: chain 25 residue 67 VAL Chi-restraints excluded: chain 26 residue 15 ASN Chi-restraints excluded: chain 26 residue 39 VAL Chi-restraints excluded: chain 28 residue 23 LEU Chi-restraints excluded: chain 29 residue 9 TYR Chi-restraints excluded: chain 29 residue 22 MET Chi-restraints excluded: chain 30 residue 22 THR Chi-restraints excluded: chain 31 residue 11 VAL Chi-restraints excluded: chain 31 residue 13 SER Chi-restraints excluded: chain 31 residue 23 THR Chi-restraints excluded: chain 31 residue 47 ILE Chi-restraints excluded: chain 33 residue 53 ASP Chi-restraints excluded: chain Z residue 234 ILE Chi-restraints excluded: chain Z residue 298 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 169 HIS Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 96 GLU Chi-restraints excluded: chain J residue 32 THR Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain K residue 35 ASP Chi-restraints excluded: chain K residue 51 PHE Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain K residue 111 ASP Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain N residue 32 ASP Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 49 THR Chi-restraints excluded: chain N residue 79 SER Chi-restraints excluded: chain O residue 19 ASN Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 68 SER Chi-restraints excluded: chain Q residue 69 THR Chi-restraints excluded: chain Q residue 74 LEU Chi-restraints excluded: chain Q residue 76 ARG Chi-restraints excluded: chain S residue 10 ILE Chi-restraints excluded: chain S residue 23 GLU Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain U residue 36 PHE Chi-restraints excluded: chain U residue 67 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1102 random chunks: chunk 694 optimal weight: 5.9990 chunk 931 optimal weight: 7.9990 chunk 267 optimal weight: 20.0000 chunk 806 optimal weight: 8.9990 chunk 129 optimal weight: 30.0000 chunk 242 optimal weight: 40.0000 chunk 875 optimal weight: 8.9990 chunk 366 optimal weight: 50.0000 chunk 899 optimal weight: 8.9990 chunk 110 optimal weight: 20.0000 chunk 161 optimal weight: 20.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 03 165 ASN ** 04 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 04 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 05 167 ASN ** 06 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 72 ASN ** 08 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 13 ASN ** 17 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 18 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 18 76 HIS 19 43 GLN 22 28 ASN ** 22 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 54 GLN ** Z 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 141 HIS ** I 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 14 GLN ** K 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 12 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.037203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.028766 restraints weight = 1215359.966| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 2.71 r_work: 0.2617 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9043 moved from start: 0.5439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 165147 Z= 0.283 Angle : 0.656 14.755 246328 Z= 0.333 Chirality : 0.035 0.289 31327 Planarity : 0.005 0.094 13708 Dihedral : 23.537 179.170 81065 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 21.51 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.36 % Favored : 90.45 % Rotamer: Outliers : 3.05 % Allowed : 28.08 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.10), residues: 6453 helix: 0.18 (0.11), residues: 2187 sheet: -1.27 (0.16), residues: 1046 loop : -1.98 (0.11), residues: 3220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP N 41 HIS 0.012 0.001 HIS20 82 PHE 0.033 0.002 PHE G 61 TYR 0.038 0.002 TYR B 212 ARG 0.015 0.001 ARG E 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 46863.80 seconds wall clock time: 816 minutes 54.99 seconds (49014.99 seconds total)