Starting phenix.real_space_refine on Fri Mar 1 05:29:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u9f_8521/03_2024/5u9f_8521.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u9f_8521/03_2024/5u9f_8521.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/5u9f_8521/03_2024/5u9f_8521.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u9f_8521/03_2024/5u9f_8521.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u9f_8521/03_2024/5u9f_8521.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u9f_8521/03_2024/5u9f_8521.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= -1.164 sd= 1.530 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 360 5.21 5 S 169 5.16 5 C 77125 2.51 5 N 28396 2.21 5 O 42045 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Y ARG 3": "NH1" <-> "NH2" 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 "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 "34 GLU 30": "OE1" <-> "OE2" Residue "Z ARG 213": "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 "G TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 152819 Number of models: 1 Model: "" Number of chains: 72 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': 94, 'rna2p_pyr': 54, 'rna3p_pur': 780, 'rna3p_pyr': 611} Link IDs: {'rna2p': 148, 'rna3p': 1390} 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': 218, 'rna2p_pyr': 101, 'rna3p_pur': 1456, 'rna3p_pyr': 1128} Link IDs: {'rna2p': 319, 'rna3p': 2583} 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': 3, 'rna2p_pyr': 2, 'rna3p_pur': 61, 'rna3p_pyr': 53} Link IDs: {'rna2p': 5, 'rna3p': 113} Chain: "Y" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 377 Classifications: {'peptide': 47} Incomplete info: {'backbone_only': 2} Link IDs: {'PTRANS': 1, 'TRANS': 45} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 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': 9, 'rna3p_pur': 35, 'rna3p_pyr': 29} Link IDs: {'rna2p': 13, 'rna3p': 63} 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': 5, 'rna3p_pur': 34, 'rna3p_pyr': 33} Link IDs: {'rna2p': 10, 'rna3p': 66} Chain: "Z" Number of atoms: 2844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2844 Classifications: {'peptide': 361} Incomplete info: {'backbone_only': 4} Link IDs: {'PTRANS': 7, 'TRANS': 353} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 3} Unresolved non-hydrogen planarities: 12 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: {'PTRANS': 4, '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: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 118 Unusual residues: {' MG': 118} Classifications: {'undetermined': 118} Link IDs: {None: 117} Chain: "01" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 221 Unusual residues: {' MG': 221} Classifications: {'undetermined': 221} Link IDs: {None: 220} Chain: "02" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' MG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "X" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "17" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "19" 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: "31" 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" 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 A0M3F SG CYS34 11 148.361 180.996 89.201 1.00106.41 S ATOM A0M44 SG CYS34 14 151.000 179.082 90.640 1.00119.79 S ATOM A0M6Z SG CYS34 27 149.307 183.094 92.092 1.00171.53 S Time building chain proxies: 56.11, per 1000 atoms: 0.37 Number of scatterers: 152819 At special positions: 0 Unit cell: (270.945, 260.01, 240.57, 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 169 16.00 P 4723 15.00 Mg 360 11.99 O 42045 8.00 N 28396 7.00 C 77125 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: 56.41 Conformation dependent library (CDL) restraints added in 7.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN34 102 " pdb="ZN ZN34 102 " - pdb=" SG CYS34 14 " pdb="ZN ZN34 102 " - pdb=" SG CYS34 11 " pdb="ZN ZN34 102 " - pdb=" SG CYS34 27 " pdb="ZN ZN34 102 " - pdb=" ND1 HIS34 33 " Number of angles added : 3 12936 Ramachandran restraints generated. 6468 Oldfield, 0 Emsley, 6468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11916 Finding SS restraints... Secondary structure from input PDB file: 205 helices and 84 sheets defined 34.1% alpha, 16.6% beta 1443 base pairs and 2770 stacking pairs defined. Time for finding SS restraints: 50.29 Creating SS restraints... Processing helix chain 'Y' and resid 15 through 21 removed outlier: 3.872A pdb=" N HIS Y 21 " --> pdb=" O GLU Y 17 " (cutoff:3.500A) Processing helix chain 'Y' and resid 22 through 26 removed outlier: 3.697A pdb=" N ARG Y 26 " --> pdb=" O PRO Y 23 " (cutoff:3.500A) Processing helix chain '03' and resid 7 through 13 removed outlier: 4.037A pdb=" N ILE03 11 " --> pdb=" O ARG03 7 " (cutoff:3.500A) Processing helix chain '03' and resid 22 through 32 removed outlier: 3.910A pdb=" N LEU03 29 " --> pdb=" O GLU03 25 " (cutoff:3.500A) Processing helix chain '03' and resid 82 through 89 removed outlier: 3.682A pdb=" N ALA03 89 " --> pdb=" O GLU03 85 " (cutoff:3.500A) Processing helix chain '03' and resid 100 through 106 removed outlier: 4.079A pdb=" N ILE03 104 " --> pdb=" O LEU03 100 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS03 106 " --> pdb=" O ASP03 102 " (cutoff:3.500A) Processing helix chain '03' and resid 120 through 125 Processing helix chain '03' and resid 131 through 135 Processing helix chain '03' and resid 148 through 157 removed outlier: 4.141A pdb=" N ASN03 155 " --> pdb=" O GLU03 151 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA03 156 " --> pdb=" O ALA03 152 " (cutoff:3.500A) Processing helix chain '03' and resid 181 through 192 removed outlier: 3.612A pdb=" N LYS03 186 " --> pdb=" O ALA03 182 " (cutoff:3.500A) Processing helix chain '03' and resid 192 through 199 Processing helix chain '04' and resid 29 through 31 No H-bonds generated for 'chain '04' and resid 29 through 31' Processing helix chain '04' and resid 196 through 202 removed outlier: 3.689A pdb=" N MET04 200 " --> pdb=" O ALA04 197 " (cutoff:3.500A) Processing helix chain '04' and resid 207 through 212 Processing helix chain '05' and resid 61 through 72 removed outlier: 4.478A pdb=" N ALA05 71 " --> pdb=" O HIS05 67 " (cutoff:3.500A) Processing helix chain '05' and resid 97 through 103 removed outlier: 3.897A pdb=" N LEU05 100 " --> pdb=" O SER05 97 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP05 103 " --> pdb=" O LEU05 100 " (cutoff:3.500A) Processing helix chain '05' and resid 120 through 126 Processing helix chain '06' and resid 15 through 20 Processing helix chain '06' and resid 24 through 40 removed outlier: 3.624A pdb=" N VAL06 28 " --> pdb=" O ASN06 24 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA06 36 " --> pdb=" O VAL06 32 " (cutoff:3.500A) Processing helix chain '06' and resid 97 through 115 removed outlier: 3.542A pdb=" N SER06 107 " --> pdb=" O GLY06 103 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL06 113 " --> pdb=" O LEU06 109 " (cutoff:3.500A) Processing helix chain '06' and resid 130 through 141 removed outlier: 3.525A pdb=" N LEU06 134 " --> pdb=" O LYS06 130 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N MET06 141 " --> pdb=" O LYS06 137 " (cutoff:3.500A) Processing helix chain '06' and resid 154 through 161 removed outlier: 3.564A pdb=" N ALA06 160 " --> pdb=" O ASN06 156 " (cutoff:3.500A) Processing helix chain '06' and resid 178 through 183 removed outlier: 3.631A pdb=" N PHE06 183 " --> pdb=" O SER06 179 " (cutoff:3.500A) Processing helix chain '06' and resid 190 through 200 removed outlier: 3.545A pdb=" N LYS06 194 " --> pdb=" O ALA06 190 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU06 198 " --> pdb=" O LYS06 194 " (cutoff:3.500A) Processing helix chain '07' and resid 3 through 9 Processing helix chain '07' and resid 9 through 17 removed outlier: 3.644A pdb=" N THR07 17 " --> pdb=" O LYS07 13 " (cutoff:3.500A) Processing helix chain '07' and resid 40 through 44 removed outlier: 3.981A pdb=" N ILE07 43 " --> pdb=" O GLY07 40 " (cutoff:3.500A) Processing helix chain '07' and resid 46 through 60 removed outlier: 3.977A pdb=" N ALA07 57 " --> pdb=" O ALA07 53 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA07 58 " --> pdb=" O ALA07 54 " (cutoff:3.500A) Processing helix chain '07' and resid 92 through 104 removed outlier: 3.586A pdb=" N ARG07 101 " --> pdb=" O GLU07 97 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE07 103 " --> pdb=" O PHE07 99 " (cutoff:3.500A) Processing helix chain '07' and resid 161 through 171 removed outlier: 3.522A pdb=" N ALA07 167 " --> pdb=" O GLU07 163 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA07 171 " --> pdb=" O ALA07 167 " (cutoff:3.500A) Processing helix chain '08' and resid 59 through 64 Processing helix chain '08' and resid 64 through 80 removed outlier: 3.612A pdb=" N LEU08 70 " --> pdb=" O THR08 66 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY08 77 " --> pdb=" O SER08 73 " (cutoff:3.500A) Processing helix chain '08' and resid 136 through 149 removed outlier: 3.510A pdb=" N ILE08 140 " --> pdb=" O ASP08 136 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY08 141 " --> pdb=" O LYS08 137 " (cutoff:3.500A) Processing helix chain '09' and resid 22 through 29 removed outlier: 3.552A pdb=" N PHE09 29 " --> pdb=" O TYR09 25 " (cutoff:3.500A) Processing helix chain '09' and resid 29 through 34 removed outlier: 3.861A pdb=" N GLN09 33 " --> pdb=" O PHE09 29 " (cutoff:3.500A) Processing helix chain '09' and resid 44 through 49 Processing helix chain '09' and resid 54 through 71 removed outlier: 3.617A pdb=" N LEU09 58 " --> pdb=" O LEU09 54 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU09 60 " --> pdb=" O ALA09 56 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN09 66 " --> pdb=" O LEU09 62 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA09 67 " --> pdb=" O ALA09 63 " (cutoff:3.500A) Processing helix chain '09' and resid 98 through 103 Processing helix chain '09' and resid 104 through 107 removed outlier: 3.738A pdb=" N GLY09 107 " --> pdb=" O THR09 104 " (cutoff:3.500A) No H-bonds generated for 'chain '09' and resid 104 through 107' Processing helix chain '10' and resid 3 through 20 removed outlier: 3.608A pdb=" N GLU10 14 " --> pdb=" O ALA10 10 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU10 17 " --> pdb=" O ALA10 13 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL10 18 " --> pdb=" O GLU10 14 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA10 19 " --> pdb=" O VAL10 15 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LYS10 20 " --> pdb=" O SER10 16 " (cutoff:3.500A) Processing helix chain '10' and resid 35 through 38 Processing helix chain '10' and resid 39 through 45 removed outlier: 3.637A pdb=" N ALA10 44 " --> pdb=" O GLU10 40 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLY10 45 " --> pdb=" O LEU10 41 " (cutoff:3.500A) Processing helix chain '10' and resid 71 through 78 Processing helix chain '10' and resid 94 through 105 removed outlier: 3.980A pdb=" N GLU10 98 " --> pdb=" O ARG10 94 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE10 99 " --> pdb=" O LEU10 95 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN10 103 " --> pdb=" O PHE10 99 " (cutoff:3.500A) Processing helix chain '11' and resid 23 through 28 removed outlier: 3.824A pdb=" N LEU11 27 " --> pdb=" O VAL11 23 " (cutoff:3.500A) Processing helix chain '11' and resid 33 through 46 removed outlier: 3.714A pdb=" N ASP11 46 " --> pdb=" O ASN11 42 " (cutoff:3.500A) Processing helix chain '11' and resid 74 through 83 removed outlier: 3.705A pdb=" N LYS11 80 " --> pdb=" O ALA11 76 " (cutoff:3.500A) Processing helix chain '11' and resid 101 through 115 Processing helix chain '11' and resid 120 through 135 removed outlier: 3.622A pdb=" N ARG11 126 " --> pdb=" O GLU11 122 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER11 127 " --> pdb=" O ALA11 123 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE11 128 " --> pdb=" O MET11 124 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU11 129 " --> pdb=" O THR11 125 " (cutoff:3.500A) Processing helix chain '12' and resid 24 through 38 removed outlier: 4.260A pdb=" N GLU12 31 " --> pdb=" O ARG12 27 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG12 37 " --> pdb=" O ALA12 33 " (cutoff:3.500A) Processing helix chain '12' and resid 67 through 71 removed outlier: 3.742A pdb=" N THR12 70 " --> pdb=" O ASN12 67 " (cutoff:3.500A) Processing helix chain '12' and resid 89 through 96 removed outlier: 3.556A pdb=" N ALA12 94 " --> pdb=" O GLU12 90 " (cutoff:3.500A) Processing helix chain '12' and resid 97 through 107 removed outlier: 4.066A pdb=" N ILE12 101 " --> pdb=" O PRO12 97 " (cutoff:3.500A) Processing helix chain '12' and resid 112 through 118 Processing helix chain '12' and resid 132 through 136 Processing helix chain '13' and resid 104 through 108 Processing helix chain '13' and resid 112 through 119 Processing helix chain '14' and resid 2 through 6 removed outlier: 3.838A pdb=" N LEU14 6 " --> pdb=" O LEU14 3 " (cutoff:3.500A) Processing helix chain '14' and resid 56 through 60 Processing helix chain '14' and resid 70 through 74 removed outlier: 3.610A pdb=" N THR14 74 " --> pdb=" O ALA14 71 " (cutoff:3.500A) Processing helix chain '14' and resid 78 through 83 removed outlier: 3.588A pdb=" N LEU14 82 " --> pdb=" O LEU14 79 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA14 83 " --> pdb=" O SER14 80 " (cutoff:3.500A) Processing helix chain '14' and resid 91 through 96 removed outlier: 3.670A pdb=" N LYS14 96 " --> pdb=" O LEU14 92 " (cutoff:3.500A) Processing helix chain '14' and resid 128 through 137 Processing helix chain '15' and resid 43 through 55 removed outlier: 3.563A pdb=" N ALA15 52 " --> pdb=" O ALA15 48 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET15 53 " --> pdb=" O ALA15 49 " (cutoff:3.500A) Processing helix chain '15' and resid 109 through 122 removed outlier: 3.584A pdb=" N GLU15 115 " --> pdb=" O GLU15 111 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS15 118 " --> pdb=" O ARG15 114 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA15 122 " --> pdb=" O LYS15 118 " (cutoff:3.500A) Processing helix chain '16' and resid 13 through 31 removed outlier: 3.862A pdb=" N ALA16 19 " --> pdb=" O SER16 15 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG16 22 " --> pdb=" O GLN16 18 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA16 25 " --> pdb=" O PHE16 21 " (cutoff:3.500A) Processing helix chain '16' and resid 38 through 55 removed outlier: 4.044A pdb=" N GLU16 43 " --> pdb=" O PRO16 39 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG16 46 " --> pdb=" O LYS16 42 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL16 47 " --> pdb=" O GLU16 43 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU16 49 " --> pdb=" O ARG16 45 " (cutoff:3.500A) Proline residue: 16 50 - end of helix Processing helix chain '16' and resid 59 through 69 removed outlier: 3.671A pdb=" N ARG16 69 " --> pdb=" O LEU16 65 " (cutoff:3.500A) Processing helix chain '16' and resid 72 through 79 Processing helix chain '16' and resid 82 through 87 Processing helix chain '17' and resid 4 through 22 removed outlier: 4.239A pdb=" N ARG17 9 " --> pdb=" O SER17 5 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG17 10 " --> pdb=" O ALA17 6 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ARG17 13 " --> pdb=" O ARG17 9 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ALA17 14 " --> pdb=" O ARG17 10 " (cutoff:3.500A) removed outlier: 3.530A 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: 3.794A pdb=" N ALA17 79 " --> pdb=" O GLY17 75 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU17 83 " --> pdb=" O ALA17 79 " (cutoff:3.500A) Processing helix chain '17' and resid 101 through 114 removed outlier: 3.529A pdb=" N GLU17 112 " --> pdb=" O ASP17 108 " (cutoff:3.500A) Processing helix chain '18' and resid 2 through 10 removed outlier: 3.548A pdb=" N LEU18 7 " --> pdb=" O ILE18 3 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU18 10 " --> pdb=" O GLN18 6 " (cutoff:3.500A) Processing helix chain '18' and resid 52 through 55 Processing helix chain '18' and resid 96 through 101 removed outlier: 3.802A pdb=" N LEU18 99 " --> pdb=" O LEU18 96 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU18 101 " --> pdb=" O TYR18 98 " (cutoff:3.500A) Processing helix chain '19' and resid 6 through 18 removed outlier: 3.526A pdb=" N ALA19 11 " --> pdb=" O VAL19 7 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG19 12 " --> pdb=" O ILE19 8 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS19 15 " --> pdb=" O ALA19 11 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE19 16 " --> pdb=" O ARG19 12 " (cutoff:3.500A) Processing helix chain '19' and resid 24 through 29 removed outlier: 3.690A pdb=" N SER19 28 " --> pdb=" O GLY19 25 " (cutoff:3.500A) Processing helix chain '19' and resid 30 through 72 removed outlier: 3.633A pdb=" N GLN19 36 " --> pdb=" O ARG19 32 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE19 39 " --> pdb=" O PHE19 35 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ARG19 50 " --> pdb=" O TYR19 46 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG19 52 " --> pdb=" O ASP19 48 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LYS19 53 " --> pdb=" O ARG19 49 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG19 54 " --> pdb=" O ARG19 50 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ARG19 57 " --> pdb=" O LYS19 53 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU19 59 " --> pdb=" O GLN19 55 " (cutoff:3.500A) Processing helix chain '19' and resid 74 through 85 removed outlier: 3.548A pdb=" N PHE19 78 " --> pdb=" O SER19 74 " (cutoff:3.500A) Processing helix chain '19' and resid 90 through 101 removed outlier: 3.565A pdb=" N ALA19 95 " --> pdb=" O ARG19 91 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASP19 96 " --> pdb=" O LYS19 92 " (cutoff:3.500A) Processing helix chain '19' and resid 101 through 117 Processing helix chain '21' and resid 15 through 22 removed outlier: 3.856A pdb=" N VAL21 20 " --> pdb=" O LYS21 16 " (cutoff:3.500A) Processing helix chain '21' and resid 28 through 39 removed outlier: 3.556A pdb=" N ILE21 35 " --> pdb=" O GLN21 31 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR21 37 " --> pdb=" O LEU21 33 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR21 38 " --> pdb=" O ASP21 34 " (cutoff:3.500A) Processing helix chain '21' and resid 41 through 59 removed outlier: 3.679A 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 3 through 10 removed outlier: 3.847A pdb=" N LEU22 8 " --> pdb=" O GLU22 4 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N LYS22 9 " --> pdb=" O GLU22 5 " (cutoff:3.500A) Processing helix chain '22' and resid 17 through 28 removed outlier: 3.640A pdb=" N ASN22 28 " --> pdb=" O MET22 24 " (cutoff:3.500A) Processing helix chain '22' and resid 39 through 51 removed outlier: 3.661A pdb=" N LYS22 44 " --> pdb=" O LYS22 40 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA22 45 " --> pdb=" O ALA22 41 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS22 49 " --> pdb=" O ALA22 45 " (cutoff:3.500A) Processing helix chain '24' and resid 13 through 22 removed outlier: 3.752A pdb=" N SER24 17 " --> pdb=" O GLY24 13 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU24 20 " --> pdb=" O ALA24 16 " (cutoff:3.500A) Processing helix chain '24' and resid 44 through 51 Processing helix chain '24' and resid 52 through 53 No H-bonds generated for 'chain '24' and resid 52 through 53' Processing helix chain '24' and resid 54 through 58 removed outlier: 3.671A pdb=" N TYR24 57 " --> pdb=" O ALA24 54 " (cutoff:3.500A) Processing helix chain '26' and resid 51 through 62 removed outlier: 3.511A pdb=" N MET26 55 " --> pdb=" O SER26 51 " (cutoff:3.500A) Processing helix chain '26' and resid 62 through 74 removed outlier: 3.743A pdb=" N ALA26 72 " --> pdb=" O ALA26 68 " (cutoff:3.500A) Processing helix chain '27' and resid 3 through 7 removed outlier: 3.988A pdb=" N LEU27 6 " --> pdb=" O ALA27 3 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ARG27 7 " --> pdb=" O LYS27 4 " (cutoff:3.500A) No H-bonds generated for 'chain '27' and resid 3 through 7' Processing helix chain '27' and resid 9 through 23 removed outlier: 3.505A pdb=" N ARG27 23 " --> pdb=" O LEU27 19 " (cutoff:3.500A) Processing helix chain '27' and resid 23 through 34 removed outlier: 3.605A pdb=" N LEU27 28 " --> pdb=" O GLU27 24 " (cutoff:3.500A) Processing helix chain '27' and resid 40 through 61 removed outlier: 3.902A pdb=" N LYS27 44 " --> pdb=" O SER27 40 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS27 54 " --> pdb=" O VAL27 50 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR27 55 " --> pdb=" O ALA27 51 " (cutoff:3.500A) Processing helix chain '28' and resid 16 through 27 Processing helix chain '28' and resid 40 through 50 Processing helix chain '29' and resid 56 through 62 Processing helix chain '30' and resid 8 through 16 Processing helix chain '32' and resid 9 through 14 Processing helix chain '32' and resid 18 through 23 Processing helix chain '32' and resid 24 through 38 removed outlier: 3.535A pdb=" N ARG32 35 " --> pdb=" O LEU32 31 " (cutoff:3.500A) Processing helix chain '33' and resid 6 through 11 Processing helix chain '33' and resid 36 through 42 removed outlier: 3.527A pdb=" N HIS33 42 " --> pdb=" O LYS33 38 " (cutoff:3.500A) 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 59 removed outlier: 3.728A pdb=" N VAL33 57 " --> pdb=" O ASP33 53 " (cutoff:3.500A) Processing helix chain 'Z' and resid 5 through 26 removed outlier: 4.175A pdb=" N VAL Z 20 " --> pdb=" O GLU Z 16 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU Z 21 " --> pdb=" O ARG Z 17 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU Z 25 " --> pdb=" O LEU Z 21 " (cutoff:3.500A) Processing helix chain 'Z' and resid 28 through 42 removed outlier: 3.994A pdb=" N LEU Z 34 " --> pdb=" O LYS Z 30 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU Z 35 " --> pdb=" O LYS Z 31 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU Z 36 " --> pdb=" O GLU Z 32 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA Z 39 " --> pdb=" O GLU Z 35 " (cutoff:3.500A) Processing helix chain 'Z' and resid 43 through 47 removed outlier: 3.888A pdb=" N VAL Z 46 " --> pdb=" O GLN Z 43 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TRP Z 47 " --> pdb=" O PRO Z 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 43 through 47' Processing helix chain 'Z' and resid 49 through 58 removed outlier: 4.031A pdb=" N LYS Z 58 " --> pdb=" O GLN Z 54 " (cutoff:3.500A) Processing helix chain 'Z' and resid 58 through 63 Processing helix chain 'Z' and resid 63 through 91 removed outlier: 4.361A pdb=" N THR Z 69 " --> pdb=" O ALA Z 65 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN Z 72 " --> pdb=" O ASP Z 68 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLN Z 75 " --> pdb=" O ASP Z 71 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU Z 77 " --> pdb=" O MET Z 73 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLU Z 78 " --> pdb=" O LYS Z 74 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER Z 81 " --> pdb=" O LEU Z 77 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU Z 84 " --> pdb=" O VAL Z 80 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU Z 89 " --> pdb=" O GLU Z 85 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA Z 90 " --> pdb=" O LEU Z 86 " (cutoff:3.500A) Processing helix chain 'Z' and resid 92 through 118 removed outlier: 3.912A pdb=" N VAL Z 100 " --> pdb=" O PHE Z 96 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA Z 101 " --> pdb=" O ASN Z 97 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU Z 102 " --> pdb=" O GLU Z 98 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP Z 104 " --> pdb=" O VAL Z 100 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU Z 106 " --> pdb=" O GLU Z 102 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU Z 107 " --> pdb=" O LEU Z 103 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS Z 109 " --> pdb=" O ALA Z 105 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG Z 116 " --> pdb=" O GLN Z 112 " (cutoff:3.500A) Processing helix chain 'Z' and resid 138 through 160 removed outlier: 3.808A pdb=" N GLN Z 142 " --> pdb=" O GLY Z 138 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER Z 146 " --> pdb=" O GLN Z 142 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR Z 152 " --> pdb=" O LEU Z 148 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP Z 155 " --> pdb=" O MET Z 151 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU Z 157 " --> pdb=" O LEU Z 153 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY Z 160 " --> pdb=" O ALA Z 156 " (cutoff:3.500A) Processing helix chain 'Z' and resid 187 through 192 removed outlier: 3.692A pdb=" N TRP Z 191 " --> pdb=" O TYR Z 187 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU Z 192 " --> pdb=" O ALA Z 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 187 through 192' Processing helix chain 'Z' and resid 193 through 196 removed outlier: 3.952A pdb=" N THR Z 196 " --> pdb=" O ARG Z 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 193 through 196' Processing helix chain 'Z' and resid 250 through 255 removed outlier: 4.162A pdb=" N VAL Z 254 " --> pdb=" O GLY Z 250 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASN Z 255 " --> pdb=" O GLY Z 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 250 through 255' Processing helix chain 'Z' and resid 279 through 312 removed outlier: 3.853A pdb=" N ASP Z 285 " --> pdb=" O HIS Z 281 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN Z 286 " --> pdb=" O LYS Z 282 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR Z 296 " --> pdb=" O LYS Z 292 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU Z 298 " --> pdb=" O LYS Z 294 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN Z 301 " --> pdb=" O GLU Z 297 " (cutoff:3.500A) Processing helix chain 'Z' and resid 344 through 349 removed outlier: 3.627A pdb=" N LEU Z 349 " --> pdb=" O THR Z 345 " (cutoff:3.500A) Processing helix chain 'Z' and resid 354 through 359 removed outlier: 3.603A pdb=" N ALA Z 359 " --> pdb=" O GLN Z 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 27 removed outlier: 3.546A pdb=" N LYS B 27 " --> pdb=" O PRO B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 61 Proline residue: B 47 - end of helix removed outlier: 3.598A pdb=" N ALA B 52 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU B 55 " --> pdb=" O GLU B 51 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 83 removed outlier: 3.528A pdb=" N VAL B 79 " --> pdb=" O ALA B 75 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS B 80 " --> pdb=" O SER B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 119 removed outlier: 4.535A pdb=" N GLN B 108 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG B 112 " --> pdb=" O GLN B 108 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B 113 " --> pdb=" O SER B 109 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR B 118 " --> pdb=" O LYS B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 147 removed outlier: 3.664A pdb=" N ARG B 136 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG B 138 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER B 146 " --> pdb=" O LYS B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 153 removed outlier: 3.520A pdb=" N LYS B 151 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP B 152 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 178 removed outlier: 3.841A pdb=" N GLU B 174 " --> pdb=" O ILE B 170 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 221 removed outlier: 3.511A pdb=" N THR B 219 " --> pdb=" O ALA B 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 11 removed outlier: 4.015A pdb=" N LEU C 11 " --> pdb=" O GLY C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 46 removed outlier: 3.527A pdb=" N PHE C 36 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS C 37 " --> pdb=" O ASP C 33 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU C 42 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 49 No H-bonds generated for 'chain 'C' and resid 47 through 49' Processing helix chain 'C' and resid 71 through 77 removed outlier: 3.617A pdb=" N VAL C 75 " --> pdb=" O ARG C 71 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY C 77 " --> pdb=" O GLY C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 95 removed outlier: 3.508A pdb=" N VAL C 89 " --> pdb=" O LYS C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 124 removed outlier: 3.896A pdb=" N ILE C 119 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU C 124 " --> pdb=" O THR C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 142 removed outlier: 3.924A pdb=" N LYS C 134 " --> pdb=" O ARG C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 159 removed outlier: 4.060A 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 7 through 15 removed outlier: 3.830A pdb=" N SER D 11 " --> pdb=" O LYS D 7 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU D 14 " --> pdb=" O LEU D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 65 removed outlier: 3.567A pdb=" N ARG D 55 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS D 57 " --> pdb=" O GLN D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 81 removed outlier: 3.929A pdb=" N ASN D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR D 74 " --> pdb=" O GLN D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 96 Processing helix chain 'D' and resid 96 through 104 removed outlier: 3.766A pdb=" N TYR D 102 " --> pdb=" O ASP D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 119 Processing helix chain 'D' and resid 155 through 161 removed outlier: 3.758A pdb=" N LEU D 160 " --> pdb=" O ALA D 156 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA D 161 " --> pdb=" O ALA D 157 " (cutoff:3.500A) 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 196 through 205 removed outlier: 3.848A pdb=" N LYS D 205 " --> pdb=" O GLU D 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 68 removed outlier: 3.514A pdb=" N ILE E 59 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN E 60 " --> pdb=" O PRO E 56 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS E 65 " --> pdb=" O LYS E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 145 Processing helix chain 'E' and resid 148 through 156 Processing helix chain 'E' and resid 159 through 165 removed outlier: 3.552A pdb=" N LEU E 164 " --> pdb=" O VAL E 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 17 removed outlier: 3.801A pdb=" N GLU F 16 " --> pdb=" O ASP F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 31 removed outlier: 3.517A pdb=" N TYR F 25 " --> pdb=" O MET F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 80 removed outlier: 3.694A pdb=" N THR F 76 " --> pdb=" O ASP F 72 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR F 77 " --> pdb=" O GLU F 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 30 removed outlier: 3.830A pdb=" N ALA G 23 " --> pdb=" O SER G 19 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU G 29 " --> pdb=" O PHE G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 53 removed outlier: 3.893A pdb=" N ALA G 50 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN G 51 " --> pdb=" O GLU G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 62 Processing helix chain 'G' and resid 91 through 109 removed outlier: 3.772A pdb=" N ASN G 96 " --> pdb=" O PRO G 92 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA G 97 " --> pdb=" O VAL G 93 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG G 101 " --> pdb=" O ALA G 97 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TRP G 102 " --> pdb=" O LEU G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 127 removed outlier: 3.653A pdb=" N SER G 124 " --> pdb=" O ALA G 120 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA G 127 " --> pdb=" O LEU G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 146 removed outlier: 3.573A pdb=" N MET G 143 " --> pdb=" O ASP G 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 19 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 34 through 38 Processing helix chain 'I' and resid 44 through 49 removed outlier: 4.653A pdb=" N ARG I 48 " --> pdb=" O ARG I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 53 Processing helix chain 'I' and resid 70 through 86 removed outlier: 4.061A pdb=" N THR I 83 " --> pdb=" O ARG I 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 89 through 98 removed outlier: 4.236A pdb=" N GLU I 96 " --> pdb=" O SER I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 101 No H-bonds generated for 'chain 'I' and resid 99 through 101' Processing helix chain 'J' and resid 14 through 32 removed outlier: 3.924A pdb=" N ASP J 19 " --> pdb=" O HIS J 15 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N GLN J 20 " --> pdb=" O ARG J 16 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU J 24 " --> pdb=" O GLN J 20 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE J 25 " --> pdb=" O ALA J 21 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL J 26 " --> pdb=" O THR J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 85 Processing helix chain 'K' and resid 53 through 57 removed outlier: 3.831A pdb=" N LYS K 56 " --> pdb=" O GLY K 53 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER K 57 " --> pdb=" O SER K 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 53 through 57' Processing helix chain 'K' and resid 58 through 71 removed outlier: 3.661A pdb=" N GLU K 67 " --> pdb=" O GLN K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 93 removed outlier: 4.512A pdb=" N GLU K 93 " --> pdb=" O PRO K 90 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 102 removed outlier: 3.680A pdb=" N LEU K 99 " --> pdb=" O THR K 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 7 Processing helix chain 'L' and resid 114 through 118 removed outlier: 4.581A pdb=" N VAL L 118 " --> pdb=" O LYS L 115 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 19 Processing helix chain 'M' and resid 25 through 36 removed outlier: 3.616A pdb=" N ALA M 34 " --> pdb=" O LYS M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 60 removed outlier: 4.951A pdb=" N THR M 54 " --> pdb=" O GLY M 50 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG M 56 " --> pdb=" O ILE M 52 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU M 58 " --> pdb=" O THR M 54 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL M 59 " --> pdb=" O LEU M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 81 removed outlier: 3.670A pdb=" N ARG M 69 " --> pdb=" O GLU M 65 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU M 79 " --> pdb=" O SER M 75 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 89 Processing helix chain 'N' and resid 2 through 15 removed outlier: 3.728A pdb=" N LYS N 6 " --> pdb=" O LYS N 2 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU N 9 " --> pdb=" O MET N 5 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL N 10 " --> pdb=" O LYS N 6 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS N 11 " --> pdb=" O ALA N 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 50 removed outlier: 3.651A pdb=" N TRP N 41 " --> pdb=" O ASP N 37 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLN N 48 " --> pdb=" O VAL N 44 " (cutoff:3.500A) Processing helix chain 'N' and resid 54 through 59 removed outlier: 3.929A pdb=" N ARG N 58 " --> pdb=" O SER N 54 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN N 59 " --> pdb=" O SER N 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 54 through 59' Processing helix chain 'O' and resid 3 through 15 Processing helix chain 'O' and resid 23 through 38 removed outlier: 3.689A pdb=" N ALA O 29 " --> pdb=" O GLU O 25 " (cutoff:3.500A) Processing helix chain 'O' and resid 38 through 43 Processing helix chain 'O' and resid 48 through 73 removed outlier: 3.888A pdb=" N GLY O 54 " --> pdb=" O HIS O 50 " (cutoff:3.500A) Processing helix chain 'O' and resid 73 through 84 removed outlier: 3.539A pdb=" N ILE O 81 " --> pdb=" O TYR O 77 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU O 82 " --> pdb=" O THR O 78 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 64 removed outlier: 3.680A pdb=" N HIS P 59 " --> pdb=" O ASP P 55 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN P 63 " --> pdb=" O HIS P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 78 Processing helix chain 'R' and resid 24 through 29 removed outlier: 4.155A pdb=" N LEU R 28 " --> pdb=" O ASP R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 45 Processing helix chain 'R' and resid 47 through 64 removed outlier: 3.621A pdb=" N LYS R 59 " --> pdb=" O ALA R 55 " (cutoff:3.500A) Processing helix chain 'S' and resid 11 through 25 removed outlier: 3.761A pdb=" N LEU S 15 " --> pdb=" O ASP S 11 " (cutoff:3.500A) Processing helix chain 'S' and resid 69 through 73 removed outlier: 3.582A pdb=" N GLU S 72 " --> pdb=" O LYS S 69 " (cutoff:3.500A) Processing helix chain 'T' and resid 7 through 41 removed outlier: 3.877A pdb=" N ILE T 11 " --> pdb=" O LYS T 7 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA T 16 " --> pdb=" O GLN T 12 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER T 22 " --> pdb=" O LYS T 18 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG T 23 " --> pdb=" O HIS T 19 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE T 30 " --> pdb=" O MET T 26 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL T 34 " --> pdb=" O PHE T 30 " (cutoff:3.500A) Processing helix chain 'T' and resid 42 through 63 removed outlier: 3.693A pdb=" N ALA T 46 " --> pdb=" O ASP T 42 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN T 47 " --> pdb=" O LYS T 43 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU T 52 " --> pdb=" O LYS T 48 " (cutoff:3.500A) removed outlier: 3.750A 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 67 through 86 removed outlier: 3.501A pdb=" N ALA T 71 " --> pdb=" O HIS T 67 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN T 77 " --> pdb=" O ARG T 73 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS T 84 " --> pdb=" O ALA T 80 " (cutoff:3.500A) Processing helix chain 'U' and resid 38 through 60 removed outlier: 3.639A pdb=" N VAL U 52 " --> pdb=" O LYS U 48 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS U 53 " --> pdb=" O ALA U 49 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS U 58 " --> pdb=" O ARG U 54 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Y' and resid 3 through 4 removed outlier: 7.090A pdb=" N ARG Y 3 " --> pdb=" O THR L 38 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ARG L 35 " --> pdb=" O ARG L 53 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Y' and resid 28 through 29 removed outlier: 3.752A pdb=" N TYR Z 223 " --> pdb=" O TYR Z 129 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N THR Z 180 " --> pdb=" O ILE Z 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Y' and resid 28 through 29 removed outlier: 7.787A pdb=" N VAL Z 198 " --> pdb=" O ARG Z 324 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N TYR Z 326 " --> pdb=" O VAL Z 198 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ARG Z 200 " --> pdb=" O TYR Z 326 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL Z 340 " --> pdb=" O ASP Z 335 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '03' and resid 170 through 176 removed outlier: 3.756A pdb=" N ILE03 175 " --> pdb=" O VAL03 42 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N VAL03 42 " --> pdb=" O ILE03 175 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS03 211 " --> pdb=" O ASN03 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '03' and resid 60 through 63 removed outlier: 3.676A pdb=" N THR03 63 " --> pdb=" O VAL03 161 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL03 161 " --> pdb=" O THR03 63 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '03' and resid 76 through 79 removed outlier: 5.816A pdb=" N VAL03 77 " --> pdb=" O GLY03 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain '04' and resid 2 through 4 Processing sheet with id=AA8, first strand: chain '04' and resid 33 through 34 Processing sheet with id=AA9, first strand: chain '04' and resid 99 through 104 removed outlier: 4.226A pdb=" N GLU04 99 " --> pdb=" O TYR04 95 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE04 90 " --> pdb=" O LEU04 80 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N LEU04 80 " --> pdb=" O ILE04 90 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU04 92 " --> pdb=" O GLU04 78 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ILE04 73 " --> pdb=" O SER04 117 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N SER04 117 " --> pdb=" O ILE04 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '04' and resid 128 through 130 removed outlier: 3.712A pdb=" N LEU04 129 " --> pdb=" O ALA04 189 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA04 189 " --> pdb=" O LEU04 129 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN04 162 " --> pdb=" O ARG04 174 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N THR04 172 " --> pdb=" O VAL04 164 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ARG04 166 " --> pdb=" O TYR04 170 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TYR04 170 " --> pdb=" O ARG04 166 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '05' and resid 4 through 15 removed outlier: 4.179A pdb=" N VAL05 26 " --> pdb=" O VAL05 9 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N MET05 11 " --> pdb=" O VAL05 24 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL05 24 " --> pdb=" O MET05 11 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ARG05 13 " --> pdb=" O ILE05 22 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE05 22 " --> pdb=" O ARG05 13 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU05 188 " --> pdb=" O VAL05 178 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ASP05 176 " --> pdb=" O LYS05 190 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N THR05 171 " --> pdb=" O GLY05 111 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N GLY05 111 " --> pdb=" O THR05 171 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N GLN05 173 " --> pdb=" O VAL05 109 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL05 109 " --> pdb=" O GLN05 173 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THR05 112 " --> pdb=" O ASP05 200 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ASP05 200 " --> pdb=" O THR05 112 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '05' and resid 82 through 83 removed outlier: 6.457A pdb=" N ALA05 47 " --> pdb=" O VAL05 37 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N VAL05 37 " --> pdb=" O ALA05 47 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLN05 49 " --> pdb=" O THR05 35 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '05' and resid 118 through 119 Processing sheet with id=AB5, first strand: chain '06' and resid 2 through 3 Processing sheet with id=AB6, first strand: chain '06' and resid 118 through 121 removed outlier: 3.592A pdb=" N ILE06 119 " --> pdb=" O VAL06 186 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '06' and resid 146 through 150 removed outlier: 6.900A pdb=" N VAL06 146 " --> pdb=" O ASP06 168 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ARG06 170 " --> pdb=" O VAL06 146 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE06 148 " --> pdb=" O ARG06 170 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain '07' and resid 89 through 90 removed outlier: 7.131A pdb=" N THR07 156 " --> pdb=" O GLU07 31 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE07 33 " --> pdb=" O THR07 154 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N THR07 154 " --> pdb=" O ILE07 33 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '07' and resid 37 through 38 Processing sheet with id=AC1, first strand: chain '08' and resid 8 through 9 removed outlier: 3.589A pdb=" N VAL08 8 " --> pdb=" O LEU08 49 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '08' and resid 15 through 19 Processing sheet with id=AC3, first strand: chain '08' and resid 129 through 134 Processing sheet with id=AC4, first strand: chain '08' and resid 94 through 98 Processing sheet with id=AC5, first strand: chain '09' and resid 18 through 19 removed outlier: 3.746A pdb=" N VAL09 3 " --> pdb=" O VAL09 19 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '09' and resid 77 through 82 removed outlier: 3.701A pdb=" N SER09 131 " --> pdb=" O ARG09 116 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG09 116 " --> pdb=" O SER09 131 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '11' and resid 7 through 10 removed outlier: 3.543A pdb=" N SER11 65 " --> pdb=" O TYR11 61 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain '12' and resid 122 through 124 removed outlier: 7.518A pdb=" N ILE12 54 " --> pdb=" O LYS12 123 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N TYR12 16 " --> pdb=" O ILE12 55 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LEU12 57 " --> pdb=" O TYR12 16 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL12 18 " --> pdb=" O LEU12 57 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain '12' and resid 73 through 77 Processing sheet with id=AD1, first strand: chain '13' and resid 6 through 10 removed outlier: 3.842A pdb=" N THR13 6 " --> pdb=" O CYS13 21 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL13 10 " --> pdb=" O ARG13 17 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ARG13 17 " --> pdb=" O VAL13 10 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLU13 45 " --> pdb=" O ARG13 17 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL13 19 " --> pdb=" O ILE13 43 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE13 43 " --> pdb=" O VAL13 19 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N CYS13 21 " --> pdb=" O ILE13 41 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE13 41 " --> pdb=" O CYS13 21 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LYS13 23 " --> pdb=" O ILE13 39 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ILE13 39 " --> pdb=" O LYS13 23 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ALA13 83 " --> pdb=" O VAL13 63 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N CYS13 84 " --> pdb=" O MET13 7 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASN13 9 " --> pdb=" O CYS13 84 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU13 86 " --> pdb=" O ASN13 9 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain '13' and resid 70 through 71 removed outlier: 3.790A pdb=" N SER13 75 " --> pdb=" O ARG13 71 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain '14' and resid 89 through 90 Processing sheet with id=AD4, first strand: chain '15' and resid 62 through 65 removed outlier: 3.683A pdb=" N LYS15 100 " --> pdb=" O ALA15 35 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU15 33 " --> pdb=" O LEU15 102 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLU15 104 " --> pdb=" O PHE15 31 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N PHE15 31 " --> pdb=" O GLU15 104 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain '15' and resid 39 through 42 removed outlier: 3.977A pdb=" N ASN15 88 " --> pdb=" O GLU15 75 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE15 73 " --> pdb=" O GLU15 90 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N TRP15 92 " --> pdb=" O LYS15 71 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LYS15 71 " --> pdb=" O TRP15 92 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain '16' and resid 33 through 37 Processing sheet with id=AD7, first strand: chain '16' and resid 33 through 37 removed outlier: 3.747A pdb=" N GLY16 101 " --> pdb=" O MET16 110 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N TYR16 112 " --> pdb=" O LYS16 99 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N LYS16 99 " --> pdb=" O TYR16 112 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain '17' and resid 47 through 52 removed outlier: 3.597A pdb=" N ALA17 51 " --> pdb=" O ALA17 37 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N HIS17 34 " --> pdb=" O THR17 31 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG17 25 " --> pdb=" O ILE17 40 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain '18' and resid 36 through 39 removed outlier: 6.328A pdb=" N THR18 59 " --> pdb=" O ILE18 47 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILE18 49 " --> pdb=" O ALA18 57 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ALA18 57 " --> pdb=" O ILE18 49 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain '18' and resid 36 through 39 removed outlier: 7.076A pdb=" N THR18 24 " --> pdb=" O VAL18 85 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N VAL18 85 " --> pdb=" O THR18 24 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLU18 26 " --> pdb=" O ILE18 83 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE18 83 " --> pdb=" O GLU18 26 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N LYS18 28 " --> pdb=" O ASP18 81 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain '20' and resid 11 through 14 removed outlier: 6.382A pdb=" N VAL20 4 " --> pdb=" O LEU20 39 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain '20' and resid 18 through 22 removed outlier: 6.684A pdb=" N ASP20 95 " --> pdb=" O VAL20 64 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain '20' and resid 72 through 78 removed outlier: 4.267A pdb=" N TYR20 83 " --> pdb=" O ARG20 78 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain '21' and resid 7 through 10 removed outlier: 4.897A pdb=" N ARG21 8 " --> pdb=" O ILE21 103 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE21 103 " --> pdb=" O ARG21 8 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N HIS21 102 " --> pdb=" O GLU21 78 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N GLU21 78 " --> pdb=" O HIS21 102 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N THR21 104 " --> pdb=" O VAL21 76 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N VAL21 76 " --> pdb=" O THR21 104 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL21 106 " --> pdb=" O ILE21 74 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ILE21 74 " --> pdb=" O VAL21 106 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N SER21 108 " --> pdb=" O THR21 72 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N THR21 72 " --> pdb=" O SER21 108 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain '22' and resid 11 through 14 removed outlier: 6.460A pdb=" N LYS22 33 " --> pdb=" O ARG22 12 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL22 31 " --> pdb=" O PRO22 14 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LYS22 81 " --> pdb=" O VAL22 34 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain '22' and resid 67 through 70 removed outlier: 4.020A pdb=" N ARG22 73 " --> pdb=" O HIS22 70 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain '23' and resid 64 through 65 removed outlier: 7.100A pdb=" N LYS23 32 " --> pdb=" O VAL23 27 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N VAL23 27 " --> pdb=" O LYS23 32 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE23 34 " --> pdb=" O LYS23 25 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain '23' and resid 40 through 44 Processing sheet with id=AF1, first strand: chain '23' and resid 82 through 87 removed outlier: 3.781A pdb=" N LYS23 90 " --> pdb=" O GLU23 87 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain '24' and resid 3 through 6 removed outlier: 3.553A pdb=" N ILE24 4 " --> pdb=" O THR24 62 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ASP24 90 " --> pdb=" O GLN24 75 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N VAL24 77 " --> pdb=" O HIS24 88 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N HIS24 88 " --> pdb=" O VAL24 77 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ARG24 79 " --> pdb=" O LEU24 86 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU24 86 " --> pdb=" O ARG24 79 " (cutoff:3.500A) removed outlier: 9.379A pdb=" N LYS24 25 " --> pdb=" O GLN24 87 " (cutoff:3.500A) removed outlier: 10.471A pdb=" N ILE24 89 " --> pdb=" O LYS24 25 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N PHE24 91 " --> pdb=" O PRO24 27 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE24 29 " --> pdb=" O PHE24 91 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ARG24 93 " --> pdb=" O ILE24 29 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N TYR24 31 " --> pdb=" O ARG24 93 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE24 40 " --> pdb=" O ALA24 28 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain '25' and resid 18 through 19 removed outlier: 6.636A pdb=" N ILE25 32 " --> pdb=" O ALA25 57 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA25 57 " --> pdb=" O ILE25 32 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL25 34 " --> pdb=" O LEU25 55 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain '25' and resid 26 through 27 Processing sheet with id=AF5, first strand: chain '26' and resid 12 through 15 removed outlier: 3.522A pdb=" N VAL26 12 " --> pdb=" O PHE26 28 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain '26' and resid 33 through 39 Processing sheet with id=AF7, first strand: chain '28' and resid 34 through 38 removed outlier: 4.219A pdb=" N LYS28 5 " --> pdb=" O GLU28 57 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain '29' and resid 10 through 16 removed outlier: 4.447A pdb=" N CYS29 16 " --> pdb=" O ASN29 20 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ASN29 20 " --> pdb=" O CYS29 16 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain '31' and resid 21 through 24 removed outlier: 3.546A pdb=" N LYS31 37 " --> pdb=" O VAL31 46 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain '33' and resid 14 through 15 Processing sheet with id=AG2, first strand: chain '34' and resid 2 through 4 removed outlier: 6.652A pdb=" N LYS34 2 " --> pdb=" O ARG34 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain '34' and resid 15 through 19 removed outlier: 3.678A pdb=" N ARG34 19 " --> pdb=" O VAL34 22 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'Z' and resid 240 through 244 removed outlier: 3.561A pdb=" N VAL Z 261 " --> pdb=" O CYS Z 274 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'B' and resid 16 through 17 removed outlier: 3.776A pdb=" N HIS B 38 " --> pdb=" O HIS B 17 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'B' and resid 89 through 91 removed outlier: 6.258A pdb=" N PHE B 68 " --> pdb=" O VAL B 91 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'B' and resid 183 through 184 removed outlier: 3.534A pdb=" N ALA B 184 " --> pdb=" O PHE B 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'C' and resid 19 through 20 removed outlier: 6.080A pdb=" N VAL C 65 " --> pdb=" O ASN C 101 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N ALA C 103 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ILE C 67 " --> pdb=" O ALA C 103 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 163 through 170 removed outlier: 3.678A pdb=" N GLY C 147 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ASP C 180 " --> pdb=" O LYS C 203 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 163 through 170 removed outlier: 3.678A pdb=" N GLY C 147 " --> pdb=" O PHE C 202 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'D' and resid 127 through 129 removed outlier: 4.794A pdb=" N ILE D 122 " --> pdb=" O VAL D 129 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'E' and resid 13 through 14 Processing sheet with id=AH4, first strand: chain 'E' and resid 18 through 20 Processing sheet with id=AH5, first strand: chain 'E' and resid 84 through 87 removed outlier: 3.550A pdb=" N VAL E 93 " --> pdb=" O GLY E 86 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'F' and resid 2 through 3 Processing sheet with id=AH7, first strand: chain 'F' and resid 41 through 46 removed outlier: 4.638A pdb=" N ASP F 41 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU F 61 " --> pdb=" O ASP F 41 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY F 43 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N MET F 9 " --> pdb=" O ARG F 86 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ARG F 86 " --> pdb=" O MET F 9 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 72 through 75 Processing sheet with id=AH9, first strand: chain 'H' and resid 23 through 27 Processing sheet with id=AI1, first strand: chain 'H' and resid 74 through 76 Processing sheet with id=AI2, first strand: chain 'H' and resid 85 through 86 Processing sheet with id=AI3, first strand: chain 'I' and resid 5 through 7 removed outlier: 5.991A pdb=" N VAL I 28 " --> pdb=" O ILE I 64 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'J' and resid 40 through 42 removed outlier: 4.471A pdb=" N LEU J 71 " --> pdb=" O LEU J 42 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'J' and resid 47 through 52 Processing sheet with id=AI6, first strand: chain 'K' and resid 40 through 44 removed outlier: 6.637A pdb=" N ALA K 40 " --> pdb=" O ASP K 35 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ASP K 35 " --> pdb=" O ALA K 40 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLY K 42 " --> pdb=" O ILE K 33 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE K 33 " --> pdb=" O GLY K 42 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N GLY K 18 " --> pdb=" O GLU K 82 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N MET K 84 " --> pdb=" O GLY K 18 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ALA K 20 " --> pdb=" O MET K 84 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N LYS K 86 " --> pdb=" O ALA K 20 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ILE K 22 " --> pdb=" O LYS K 86 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N LEU K 81 " --> pdb=" O THR K 107 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE K 109 " --> pdb=" O LEU K 81 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL K 83 " --> pdb=" O ILE K 109 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE K 109 " --> pdb=" O VAL U 5 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'L' and resid 28 through 31 Processing sheet with id=AI8, first strand: chain 'P' and resid 2 through 6 Processing sheet with id=AI9, first strand: chain 'P' and resid 9 through 11 Processing sheet with id=AJ1, first strand: chain 'P' and resid 38 through 39 removed outlier: 3.723A pdb=" N ARG P 51 " --> pdb=" O PHE P 38 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'Q' and resid 7 through 13 removed outlier: 15.477A pdb=" N LEU Q 7 " --> pdb=" O PHE Q 27 " (cutoff:3.500A) removed outlier: 13.790A pdb=" N PHE Q 27 " --> pdb=" O LEU Q 7 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N GLY Q 9 " --> pdb=" O GLU Q 25 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N GLU Q 25 " --> pdb=" O GLY Q 9 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N VAL Q 11 " --> pdb=" O ALA Q 23 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ALA Q 23 " --> pdb=" O VAL Q 11 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N LYS Q 70 " --> pdb=" O LYS Q 42 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N HIS Q 44 " --> pdb=" O LYS Q 70 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TRP Q 72 " --> pdb=" O HIS Q 44 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N SER Q 71 " --> pdb=" O CYS Q 63 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLU Q 59 " --> pdb=" O VAL Q 75 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N VAL Q 77 " --> pdb=" O VAL Q 57 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N VAL Q 57 " --> pdb=" O VAL Q 77 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'S' and resid 31 through 32 removed outlier: 7.297A pdb=" N THR S 32 " --> pdb=" O HIS S 51 " (cutoff:3.500A) 1752 hydrogen bonds defined for protein. 4851 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3613 hydrogen bonds 5854 hydrogen bond angles 0 basepair planarities 1443 basepair parallelities 2770 stacking parallelities Total time for adding SS restraints: 276.02 Time building geometry restraints manager: 61.61 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: 24882 1.33 - 1.45: 65283 1.45 - 1.57: 65394 1.57 - 1.69: 9446 1.69 - 1.81: 302 Bond restraints: 165307 Sorted by residual: bond pdb=" CA ALA N 87 " pdb=" C ALA N 87 " ideal model delta sigma weight residual 1.523 1.458 0.065 1.34e-02 5.57e+03 2.38e+01 bond pdb=" N PRO10 119 " pdb=" CA PRO10 119 " ideal model delta sigma weight residual 1.469 1.409 0.060 1.28e-02 6.10e+03 2.20e+01 bond pdb=" CA PRO04 246 " pdb=" C PRO04 246 " ideal model delta sigma weight residual 1.520 1.558 -0.038 9.50e-03 1.11e+04 1.56e+01 bond pdb=" CA GLN15 60 " pdb=" C GLN15 60 " ideal model delta sigma weight residual 1.529 1.480 0.049 1.41e-02 5.03e+03 1.22e+01 bond pdb=" CA PRO05 152 " pdb=" C PRO05 152 " ideal model delta sigma weight residual 1.520 1.567 -0.047 1.42e-02 4.96e+03 1.11e+01 ... (remaining 165302 not shown) Histogram of bond angle deviations from ideal: 80.67 - 95.25: 2 95.25 - 109.84: 78758 109.84 - 124.42: 147209 124.42 - 139.00: 20574 139.00 - 153.59: 1 Bond angle restraints: 246544 Sorted by residual: angle pdb=" C ILE10 118 " pdb=" N PRO10 119 " pdb=" CA PRO10 119 " ideal model delta sigma weight residual 119.84 153.59 -33.75 1.25e+00 6.40e-01 7.29e+02 angle pdb=" N LYS K 125 " pdb=" CA LYS K 125 " pdb=" C LYS K 125 " ideal model delta sigma weight residual 110.70 129.21 -18.51 1.55e+00 4.16e-01 1.43e+02 angle pdb=" C ILE10 118 " pdb=" N PRO10 119 " pdb=" CD PRO10 119 " ideal model delta sigma weight residual 125.00 80.67 44.33 4.10e+00 5.95e-02 1.17e+02 angle pdb=" N VAL10 54 " pdb=" CA VAL10 54 " pdb=" C VAL10 54 " ideal model delta sigma weight residual 110.62 122.20 -11.58 1.14e+00 7.69e-01 1.03e+02 angle pdb=" N GLN15 60 " pdb=" CA GLN15 60 " pdb=" C GLN15 60 " ideal model delta sigma weight residual 110.33 122.97 -12.64 1.29e+00 6.01e-01 9.60e+01 ... (remaining 246539 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 94749 35.99 - 71.98: 9804 71.98 - 107.97: 1121 107.97 - 143.96: 10 143.96 - 179.95: 24 Dihedral angle restraints: 105708 sinusoidal: 87141 harmonic: 18567 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 -36.00 72.00 1 8.00e+00 1.56e-02 1.04e+02 dihedral pdb=" O4' U012457 " pdb=" C1' U012457 " pdb=" N1 U012457 " pdb=" C2 U012457 " ideal model delta sinusoidal sigma weight residual 200.00 28.76 171.24 1 1.50e+01 4.44e-03 8.48e+01 dihedral pdb=" O4' U012580 " pdb=" C1' U012580 " pdb=" N1 U012580 " pdb=" C2 U012580 " ideal model delta sinusoidal sigma weight residual 200.00 29.05 170.95 1 1.50e+01 4.44e-03 8.48e+01 ... (remaining 105705 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 29403 0.147 - 0.293: 1837 0.293 - 0.440: 101 0.440 - 0.586: 9 0.586 - 0.733: 4 Chirality restraints: 31354 Sorted by residual: chirality pdb=" CA SER N 55 " pdb=" N SER N 55 " pdb=" C SER N 55 " pdb=" CB SER N 55 " both_signs ideal model delta sigma weight residual False 2.51 1.78 0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" CA ALA N 87 " pdb=" N ALA N 87 " pdb=" C ALA N 87 " pdb=" CB ALA N 87 " both_signs ideal model delta sigma weight residual False 2.48 1.79 0.69 2.00e-01 2.50e+01 1.20e+01 chirality pdb=" CA PRO F 12 " pdb=" N PRO F 12 " pdb=" C PRO F 12 " pdb=" CB PRO F 12 " both_signs ideal model delta sigma weight residual False 2.72 2.07 0.65 2.00e-01 2.50e+01 1.06e+01 ... (remaining 31351 not shown) Planarity restraints: 13734 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U011060 " -0.093 2.00e-02 2.50e+03 5.25e-02 6.20e+01 pdb=" N1 U011060 " 0.003 2.00e-02 2.50e+03 pdb=" C2 U011060 " 0.020 2.00e-02 2.50e+03 pdb=" O2 U011060 " 0.033 2.00e-02 2.50e+03 pdb=" N3 U011060 " 0.021 2.00e-02 2.50e+03 pdb=" C4 U011060 " 0.022 2.00e-02 2.50e+03 pdb=" O4 U011060 " -0.097 2.00e-02 2.50e+03 pdb=" C5 U011060 " 0.051 2.00e-02 2.50e+03 pdb=" C6 U011060 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U011818 " 0.082 2.00e-02 2.50e+03 4.56e-02 4.68e+01 pdb=" N1 U011818 " -0.004 2.00e-02 2.50e+03 pdb=" C2 U011818 " -0.016 2.00e-02 2.50e+03 pdb=" O2 U011818 " -0.029 2.00e-02 2.50e+03 pdb=" N3 U011818 " -0.017 2.00e-02 2.50e+03 pdb=" C4 U011818 " -0.018 2.00e-02 2.50e+03 pdb=" O4 U011818 " 0.083 2.00e-02 2.50e+03 pdb=" C5 U011818 " -0.044 2.00e-02 2.50e+03 pdb=" C6 U011818 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A011328 " 0.090 2.00e-02 2.50e+03 3.93e-02 4.25e+01 pdb=" N9 A011328 " -0.006 2.00e-02 2.50e+03 pdb=" C8 A011328 " -0.036 2.00e-02 2.50e+03 pdb=" N7 A011328 " -0.031 2.00e-02 2.50e+03 pdb=" C5 A011328 " -0.018 2.00e-02 2.50e+03 pdb=" C6 A011328 " 0.014 2.00e-02 2.50e+03 pdb=" N6 A011328 " 0.061 2.00e-02 2.50e+03 pdb=" N1 A011328 " 0.006 2.00e-02 2.50e+03 pdb=" C2 A011328 " -0.019 2.00e-02 2.50e+03 pdb=" N3 A011328 " -0.032 2.00e-02 2.50e+03 pdb=" C4 A011328 " -0.029 2.00e-02 2.50e+03 ... (remaining 13731 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 37428 2.82 - 3.34: 130406 3.34 - 3.86: 306989 3.86 - 4.38: 369075 4.38 - 4.90: 505877 Nonbonded interactions: 1349775 Sorted by model distance: nonbonded pdb=" O LYS14 29 " pdb=" OG1 THR14 30 " model vdw 2.301 2.440 nonbonded pdb=" OD2 ASP B 187 " pdb=" OD2 ASP B 203 " model vdw 2.316 3.040 nonbonded pdb=" O2' U011130 " pdb=" OP1 G011131 " model vdw 2.321 2.440 nonbonded pdb=" O ARG14 2 " pdb=" OG1 THR14 5 " model vdw 2.323 2.440 nonbonded pdb=" OP1 C01 671 " pdb=" N GLY14 43 " model vdw 2.331 2.520 ... (remaining 1349770 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 103)) selection = (chain 'X' and (resid 1 through 76 or resid 101 through 103)) } 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: 1.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 12.600 Check model and map are aligned: 1.640 Set scattering table: 1.000 Process input model: 562.880 Find NCS groups from input model: 3.160 Set up NCS constraints: 0.390 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 586.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 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 0.115 165307 Z= 0.357 Angle : 0.946 44.330 246544 Z= 0.620 Chirality : 0.085 0.733 31354 Planarity : 0.008 0.121 13734 Dihedral : 22.017 179.952 93792 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 1.04 % Allowed : 10.76 % Favored : 88.20 % Rotamer: Outliers : 1.02 % Allowed : 4.59 % Favored : 94.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.04 (0.08), residues: 6468 helix: -3.88 (0.06), residues: 2054 sheet: -2.64 (0.14), residues: 1155 loop : -3.24 (0.09), residues: 3259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.006 TRP04 212 HIS 0.002 0.000 HIS B 17 PHE 0.040 0.003 PHE U 36 TYR 0.072 0.005 TYR11 61 ARG 0.006 0.000 ARG Z 256 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12936 Ramachandran restraints generated. 6468 Oldfield, 0 Emsley, 6468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12936 Ramachandran restraints generated. 6468 Oldfield, 0 Emsley, 6468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2213 residues out of total 5369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 2159 time to evaluate : 6.606 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: Y 17 GLU cc_start: 0.7597 (tm-30) cc_final: 0.7382 (tm-30) REVERT: 03 21 TYR cc_start: 0.7511 (m-80) cc_final: 0.6889 (m-10) REVERT: 03 190 GLU cc_start: 0.9282 (tt0) cc_final: 0.8975 (mm-30) REVERT: 03 218 MET cc_start: 0.1407 (mtp) cc_final: 0.0227 (mtt) REVERT: 05 100 LEU cc_start: 0.8782 (mp) cc_final: 0.8514 (mp) REVERT: 07 17 THR cc_start: 0.8230 (p) cc_final: 0.7972 (p) REVERT: 07 34 THR cc_start: 0.7138 (p) cc_final: 0.6783 (p) REVERT: 08 57 TYR cc_start: 0.7660 (m-80) cc_final: 0.6905 (m-80) REVERT: 09 47 PHE cc_start: 0.8180 (t80) cc_final: 0.7831 (t80) REVERT: 09 122 LEU cc_start: 0.8822 (mt) cc_final: 0.8525 (mm) REVERT: 09 135 HIS cc_start: 0.8602 (t-170) cc_final: 0.8339 (t70) REVERT: 10 11 ILE cc_start: 0.8817 (mm) cc_final: 0.8530 (mm) REVERT: 15 119 LEU cc_start: 0.8301 (mt) cc_final: 0.7863 (mt) REVERT: 16 15 SER cc_start: 0.8274 (p) cc_final: 0.8031 (p) REVERT: 16 28 LEU cc_start: 0.7845 (tp) cc_final: 0.7557 (tt) REVERT: 16 106 ASP cc_start: 0.5738 (p0) cc_final: 0.5396 (p0) REVERT: 28 3 THR cc_start: 0.8391 (p) cc_final: 0.8141 (p) REVERT: 29 32 LEU cc_start: 0.8192 (tp) cc_final: 0.7950 (tp) REVERT: 29 56 ARG cc_start: 0.4943 (tpt90) cc_final: 0.4676 (tpt170) REVERT: 30 19 ASP cc_start: 0.7680 (OUTLIER) cc_final: 0.7287 (m-30) REVERT: 34 31 PRO cc_start: 0.8429 (Cg_endo) cc_final: 0.8102 (Cg_exo) REVERT: Z 153 LEU cc_start: 0.8376 (tt) cc_final: 0.8114 (tt) REVERT: Z 298 LEU cc_start: 0.9700 (tp) cc_final: 0.9449 (tp) REVERT: C 129 PHE cc_start: 0.8584 (p90) cc_final: 0.8162 (p90) REVERT: D 139 ASN cc_start: 0.8581 (t0) cc_final: 0.8332 (t0) REVERT: E 68 ARG cc_start: 0.7627 (mtm180) cc_final: 0.6879 (mtm180) REVERT: F 13 ASP cc_start: 0.8619 (p0) cc_final: 0.8346 (p0) REVERT: F 72 ASP cc_start: 0.9168 (m-30) cc_final: 0.8840 (m-30) REVERT: G 115 MET cc_start: 0.9062 (tpp) cc_final: 0.8812 (ttp) REVERT: H 20 ASN cc_start: 0.8097 (t0) cc_final: 0.7880 (t0) REVERT: I 35 GLU cc_start: 0.7909 (tp30) cc_final: 0.7622 (tp30) REVERT: I 42 THR cc_start: 0.8325 (p) cc_final: 0.6713 (p) REVERT: J 81 GLU cc_start: 0.8416 (mp0) cc_final: 0.8188 (tm-30) REVERT: J 88 MET cc_start: 0.8584 (mmm) cc_final: 0.8330 (mmm) REVERT: L 34 THR cc_start: 0.8428 (p) cc_final: 0.8221 (t) REVERT: M 41 ASP cc_start: 0.7156 (m-30) cc_final: 0.5226 (m-30) REVERT: U 20 ARG cc_start: 0.8090 (ttp80) cc_final: 0.7464 (ttt180) outliers start: 54 outliers final: 6 residues processed: 2195 average time/residue: 1.4388 time to fit residues: 5302.4909 Evaluate side-chains 1287 residues out of total 5369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1280 time to evaluate : 6.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 12 residue 81 ILE Chi-restraints excluded: chain 19 residue 71 ASN Chi-restraints excluded: chain 23 residue 27 VAL Chi-restraints excluded: chain 30 residue 19 ASP Chi-restraints excluded: chain E residue 156 ARG Chi-restraints excluded: chain N residue 22 LYS Chi-restraints excluded: chain P residue 46 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1103 random chunks: chunk 931 optimal weight: 8.9990 chunk 836 optimal weight: 30.0000 chunk 463 optimal weight: 50.0000 chunk 285 optimal weight: 20.0000 chunk 563 optimal weight: 6.9990 chunk 446 optimal weight: 30.0000 chunk 864 optimal weight: 20.0000 chunk 334 optimal weight: 20.0000 chunk 525 optimal weight: 20.0000 chunk 643 optimal weight: 20.0000 chunk 1001 optimal weight: 20.0000 overall best weight: 15.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 03 47 ASN 03 168 ASN ** 03 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 04 20 ASN 04 44 ASN 04 69 ASN 04 89 ASN ** 04 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 04 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 04 133 ASN 04 142 ASN 04 238 ASN 05 42 ASN 05 130 GLN 05 140 HIS 05 150 GLN 05 173 GLN 06 136 GLN 06 156 ASN ** 07 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 37 ASN 08 63 GLN 08 138 GLN 09 11 ASN ** 09 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 09 135 HIS 11 42 ASN 11 93 ASN 13 3 GLN 13 13 ASN 13 82 ASN 13 89 ASN ** 14 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 14 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 14 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 16 11 ASN 16 13 ASN 17 98 GLN 18 74 GLN ** 18 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 19 51 GLN 19 55 GLN 19 71 ASN ** 20 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 20 18 GLN ** 20 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 20 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 20 89 HIS 21 9 HIS 21 40 ASN 22 59 ASN 23 98 ASN ** 24 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 24 78 GLN ** 24 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 25 72 ASN 26 22 ASN ** 26 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 27 39 GLN 27 58 ASN 28 8 GLN 29 41 HIS 30 40 HIS 31 25 ASN 32 13 ASN 32 29 GLN Z 5 ASN Z 8 ASN Z 38 ASN Z 48 ASN Z 54 GLN Z 97 ASN Z 255 ASN ** Z 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 290 GLN B 23 ASN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 ASN B 167 HIS C 24 ASN C 139 ASN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 ASN D 119 HIS ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 GLN E 69 ASN E 81 GLN E 134 ASN E 145 ASN ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 51 GLN ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 ASN I 4 GLN I 24 ASN I 36 GLN ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 ASN ** K 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 ASN ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 7 ASN O 27 GLN O 36 ASN P 9 HIS ** Q 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 18 GLN R 51 GLN S 42 ASN Total number of N/Q/H flips: 85 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.153 165307 Z= 0.519 Angle : 0.852 21.251 246544 Z= 0.440 Chirality : 0.048 0.541 31354 Planarity : 0.007 0.183 13734 Dihedral : 23.057 179.737 81093 Min Nonbonded Distance : 1.655 Molprobity Statistics. All-atom Clashscore : 22.63 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.83 % Favored : 89.86 % Rotamer: Outliers : 4.96 % Allowed : 17.06 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.29 % 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: -3.68 (0.09), residues: 6468 helix: -1.91 (0.10), residues: 2157 sheet: -2.46 (0.14), residues: 1106 loop : -2.82 (0.10), residues: 3205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP Q 72 HIS 0.019 0.002 HIS21 102 PHE 0.070 0.003 PHE U 36 TYR 0.039 0.003 TYR13 32 ARG 0.033 0.002 ARG Y 3 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12936 Ramachandran restraints generated. 6468 Oldfield, 0 Emsley, 6468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12936 Ramachandran restraints generated. 6468 Oldfield, 0 Emsley, 6468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1597 residues out of total 5369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 263 poor density : 1334 time to evaluate : 6.644 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: Y 8 LYS cc_start: 0.7748 (mttp) cc_final: 0.7547 (mttp) REVERT: Y 31 LYS cc_start: 0.8567 (tmtt) cc_final: 0.8335 (tptp) REVERT: 03 20 GLN cc_start: 0.8176 (mm-40) cc_final: 0.7856 (tp-100) REVERT: 03 40 GLU cc_start: 0.5935 (mm-30) cc_final: 0.5497 (tp30) REVERT: 04 184 GLU cc_start: 0.8205 (tp30) cc_final: 0.7658 (tp30) REVERT: 04 186 ASP cc_start: 0.7762 (m-30) cc_final: 0.7217 (m-30) REVERT: 08 34 ARG cc_start: 0.8217 (mmm160) cc_final: 0.7893 (mmm160) REVERT: 08 169 ARG cc_start: 0.7566 (ptp90) cc_final: 0.7357 (ptp90) REVERT: 09 60 GLU cc_start: 0.9213 (mm-30) cc_final: 0.8995 (mp0) REVERT: 09 114 GLU cc_start: 0.5889 (pp20) cc_final: 0.5683 (pp20) REVERT: 09 122 LEU cc_start: 0.8875 (mt) cc_final: 0.8631 (mm) REVERT: 09 135 HIS cc_start: 0.8769 (t70) cc_final: 0.7832 (t70) REVERT: 09 137 GLU cc_start: 0.7411 (tt0) cc_final: 0.7014 (pt0) REVERT: 10 36 ASP cc_start: 0.9279 (m-30) cc_final: 0.9063 (p0) REVERT: 11 124 MET cc_start: 0.8057 (mtt) cc_final: 0.7707 (mtp) REVERT: 11 135 MET cc_start: 0.7551 (mmt) cc_final: 0.7131 (mmp) REVERT: 12 71 ASP cc_start: 0.8071 (m-30) cc_final: 0.7609 (m-30) REVERT: 13 108 ARG cc_start: 0.8455 (mtm180) cc_final: 0.7977 (mtm180) REVERT: 16 106 ASP cc_start: 0.6233 (p0) cc_final: 0.5959 (p0) REVERT: 18 74 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7858 (mm110) REVERT: 22 5 GLU cc_start: 0.8782 (mp0) cc_final: 0.8528 (mp0) REVERT: 23 40 LEU cc_start: 0.8649 (tp) cc_final: 0.7897 (tp) REVERT: 23 97 SER cc_start: 0.8588 (m) cc_final: 0.8202 (p) REVERT: 27 58 ASN cc_start: 0.8644 (OUTLIER) cc_final: 0.8251 (t0) REVERT: 29 3 LYS cc_start: 0.8542 (mmtt) cc_final: 0.7760 (mmtp) REVERT: 29 32 LEU cc_start: 0.8134 (tp) cc_final: 0.7899 (tp) REVERT: 30 47 TYR cc_start: 0.7828 (m-10) cc_final: 0.7616 (m-10) REVERT: 33 18 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8254 (tptt) REVERT: Z 244 TYR cc_start: 0.8055 (p90) cc_final: 0.7601 (p90) REVERT: B 153 MET cc_start: 0.8496 (mtp) cc_final: 0.8011 (tpp) REVERT: C 36 PHE cc_start: 0.8151 (t80) cc_final: 0.7820 (t80) REVERT: D 139 ASN cc_start: 0.8895 (t0) cc_final: 0.8574 (t0) REVERT: G 115 MET cc_start: 0.8951 (tpp) cc_final: 0.8630 (ttp) REVERT: H 20 ASN cc_start: 0.8341 (t0) cc_final: 0.8129 (t0) REVERT: H 72 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7888 (mp0) REVERT: I 35 GLU cc_start: 0.8083 (tp30) cc_final: 0.7774 (tp30) REVERT: I 61 ASP cc_start: 0.7577 (t70) cc_final: 0.7339 (t70) REVERT: J 87 LEU cc_start: 0.8948 (pp) cc_final: 0.8680 (pp) REVERT: L 4 ASN cc_start: 0.7763 (OUTLIER) cc_final: 0.7437 (t0) REVERT: M 62 PHE cc_start: 0.7843 (t80) cc_final: 0.7586 (t80) REVERT: M 80 MET cc_start: 0.8581 (mtp) cc_final: 0.8273 (mmm) REVERT: O 9 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8126 (ptmm) REVERT: O 88 ARG cc_start: 0.6948 (OUTLIER) cc_final: 0.6327 (mmm-85) REVERT: Q 20 ILE cc_start: 0.8769 (tt) cc_final: 0.8400 (tt) REVERT: T 23 ARG cc_start: 0.7908 (mmm-85) cc_final: 0.7654 (mmt90) REVERT: U 57 LYS cc_start: 0.8552 (pptt) cc_final: 0.8138 (ptpp) REVERT: U 58 LYS cc_start: 0.9256 (mtpp) cc_final: 0.9034 (mmtt) outliers start: 263 outliers final: 147 residues processed: 1476 average time/residue: 1.4364 time to fit residues: 3690.1843 Evaluate side-chains 1261 residues out of total 5369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 1108 time to evaluate : 6.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 03 residue 47 ASN Chi-restraints excluded: chain 03 residue 196 LEU Chi-restraints excluded: chain 04 residue 50 THR Chi-restraints excluded: chain 04 residue 138 SER Chi-restraints excluded: chain 04 residue 159 THR Chi-restraints excluded: chain 04 residue 162 GLN Chi-restraints excluded: chain 04 residue 198 GLU Chi-restraints excluded: chain 04 residue 263 ASP Chi-restraints excluded: chain 05 residue 39 ASP Chi-restraints excluded: chain 05 residue 60 VAL Chi-restraints excluded: chain 05 residue 89 GLU Chi-restraints excluded: chain 06 residue 46 GLN Chi-restraints excluded: chain 06 residue 73 ILE Chi-restraints excluded: chain 06 residue 111 GLU Chi-restraints excluded: chain 06 residue 149 ILE Chi-restraints excluded: chain 06 residue 178 VAL Chi-restraints excluded: chain 06 residue 187 VAL Chi-restraints excluded: chain 07 residue 18 GLU Chi-restraints excluded: chain 07 residue 30 VAL Chi-restraints excluded: chain 08 residue 55 ASP Chi-restraints excluded: chain 08 residue 91 VAL Chi-restraints excluded: chain 09 residue 17 ASP Chi-restraints excluded: chain 10 residue 65 GLU Chi-restraints excluded: chain 12 residue 84 ILE Chi-restraints excluded: chain 13 residue 35 VAL Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 56 ASP Chi-restraints excluded: chain 13 residue 84 CYS Chi-restraints excluded: chain 14 residue 12 SER Chi-restraints excluded: chain 14 residue 19 LEU Chi-restraints excluded: chain 14 residue 46 VAL Chi-restraints excluded: chain 15 residue 128 THR Chi-restraints excluded: chain 16 residue 36 THR Chi-restraints excluded: chain 16 residue 57 THR Chi-restraints excluded: chain 16 residue 76 VAL Chi-restraints excluded: chain 16 residue 97 ILE Chi-restraints excluded: chain 16 residue 117 ASP Chi-restraints excluded: chain 17 residue 28 VAL Chi-restraints excluded: chain 17 residue 69 ASP Chi-restraints excluded: chain 17 residue 87 ILE Chi-restraints excluded: chain 18 residue 3 ILE Chi-restraints excluded: chain 18 residue 31 VAL Chi-restraints excluded: chain 18 residue 64 SER Chi-restraints excluded: chain 18 residue 65 ASN Chi-restraints excluded: chain 18 residue 74 GLN Chi-restraints excluded: chain 19 residue 16 ILE Chi-restraints excluded: chain 20 residue 26 ASP Chi-restraints excluded: chain 21 residue 46 LEU Chi-restraints excluded: chain 21 residue 72 THR Chi-restraints excluded: chain 23 residue 27 VAL Chi-restraints excluded: chain 23 residue 39 ASN Chi-restraints excluded: chain 23 residue 98 ASN Chi-restraints excluded: chain 24 residue 5 ASN Chi-restraints excluded: chain 24 residue 24 ASN Chi-restraints excluded: chain 25 residue 26 SER Chi-restraints excluded: chain 26 residue 3 VAL Chi-restraints excluded: chain 26 residue 7 THR Chi-restraints excluded: chain 26 residue 34 SER Chi-restraints excluded: chain 26 residue 39 VAL Chi-restraints excluded: chain 26 residue 41 SER Chi-restraints excluded: chain 26 residue 58 ILE Chi-restraints excluded: chain 26 residue 65 THR Chi-restraints excluded: chain 27 residue 11 VAL Chi-restraints excluded: chain 27 residue 44 LYS Chi-restraints excluded: chain 27 residue 58 ASN Chi-restraints excluded: chain 28 residue 5 LYS Chi-restraints excluded: chain 28 residue 7 THR Chi-restraints excluded: chain 28 residue 51 SER Chi-restraints excluded: chain 30 residue 45 ASP Chi-restraints excluded: chain 31 residue 16 THR Chi-restraints excluded: chain 32 residue 30 VAL Chi-restraints excluded: chain 33 residue 18 LYS Chi-restraints excluded: chain 33 residue 50 SER Chi-restraints excluded: chain 33 residue 57 VAL Chi-restraints excluded: chain 34 residue 3 VAL Chi-restraints excluded: chain 34 residue 15 LYS Chi-restraints excluded: chain Z residue 71 ASP Chi-restraints excluded: chain Z residue 125 SER Chi-restraints excluded: chain Z residue 143 ASP Chi-restraints excluded: chain Z residue 321 SER Chi-restraints excluded: chain B residue 17 HIS Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 120 HIS Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 156 ARG Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain G residue 84 TYR Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 20 ILE Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 92 SER Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 73 LEU Chi-restraints excluded: chain K residue 14 GLN Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain L residue 4 ASN Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 102 ASP Chi-restraints excluded: chain M residue 48 SER Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain N residue 17 ASP Chi-restraints excluded: chain N residue 38 GLU Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain O residue 9 LYS Chi-restraints excluded: chain O residue 12 SER Chi-restraints excluded: chain O residue 17 ASP Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 69 LEU Chi-restraints excluded: chain O residue 88 ARG Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 26 ASN Chi-restraints excluded: chain P residue 44 SER Chi-restraints excluded: chain P residue 46 LYS Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain R residue 24 ASP Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain S residue 14 LEU Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 43 MET Chi-restraints excluded: chain S residue 72 GLU Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain T residue 20 ASN Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain T residue 82 ILE Chi-restraints excluded: chain U residue 18 PHE Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 36 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1103 random chunks: chunk 556 optimal weight: 0.0970 chunk 310 optimal weight: 20.0000 chunk 833 optimal weight: 20.0000 chunk 682 optimal weight: 20.0000 chunk 276 optimal weight: 10.0000 chunk 1003 optimal weight: 7.9990 chunk 1084 optimal weight: 30.0000 chunk 893 optimal weight: 6.9990 chunk 995 optimal weight: 8.9990 chunk 342 optimal weight: 10.0000 chunk 805 optimal weight: 9.9990 overall best weight: 6.8186 ------------------------------------------------------------------------------- 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 47 ASN 03 172 HIS ** 03 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 04 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 04 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 04 225 ASN 04 238 ASN ** 07 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 07 80 GLN 09 11 ASN 09 20 ASN 09 28 ASN 09 43 ASN ** 12 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 90 ASN ** 14 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 14 99 ASN ** 14 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 15 60 GLN ** 18 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 19 51 GLN ** 20 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 20 43 ASN 20 82 HIS 23 44 HIS 23 98 ASN ** 24 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 26 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 ASN D 39 GLN D 53 GLN ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 ASN L 4 ASN ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 95 HIS O 61 GLN S 51 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 165307 Z= 0.247 Angle : 0.642 11.650 246544 Z= 0.332 Chirality : 0.035 0.350 31354 Planarity : 0.005 0.092 13734 Dihedral : 23.251 179.484 81083 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 17.65 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.60 % Favored : 90.20 % Rotamer: Outliers : 4.66 % Allowed : 18.27 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.21 % 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: -2.97 (0.10), residues: 6468 helix: -1.13 (0.10), residues: 2156 sheet: -2.12 (0.15), residues: 1098 loop : -2.52 (0.10), residues: 3214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP06 78 HIS 0.012 0.001 HIS24 80 PHE 0.061 0.002 PHE U 36 TYR 0.026 0.002 TYR B 212 ARG 0.009 0.001 ARG S 54 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12936 Ramachandran restraints generated. 6468 Oldfield, 0 Emsley, 6468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12936 Ramachandran restraints generated. 6468 Oldfield, 0 Emsley, 6468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1527 residues out of total 5369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 1280 time to evaluate : 6.628 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: Y 44 LYS cc_start: 0.7574 (mtpp) cc_final: 0.7322 (mmmt) REVERT: 03 40 GLU cc_start: 0.5902 (mm-30) cc_final: 0.5569 (tp30) REVERT: 03 187 GLU cc_start: 0.9267 (tp30) cc_final: 0.8881 (mt-10) REVERT: 03 190 GLU cc_start: 0.9478 (tt0) cc_final: 0.9163 (mm-30) REVERT: 04 95 TYR cc_start: 0.7741 (m-80) cc_final: 0.7405 (m-80) REVERT: 07 144 LYS cc_start: 0.6649 (OUTLIER) cc_final: 0.6380 (pttm) REVERT: 08 34 ARG cc_start: 0.8115 (mmm160) cc_final: 0.7775 (mmm160) REVERT: 08 165 ASP cc_start: 0.8642 (p0) cc_final: 0.8269 (p0) REVERT: 09 46 PHE cc_start: 0.9437 (t80) cc_final: 0.9222 (t80) REVERT: 09 73 ASN cc_start: 0.7812 (t0) cc_final: 0.7588 (t0) REVERT: 09 122 LEU cc_start: 0.8860 (mt) cc_final: 0.8523 (mm) REVERT: 09 135 HIS cc_start: 0.8754 (t70) cc_final: 0.8403 (t70) REVERT: 10 52 MET cc_start: 0.2297 (mmm) cc_final: 0.2030 (mmm) REVERT: 11 124 MET cc_start: 0.8066 (mtt) cc_final: 0.7777 (mtp) REVERT: 11 135 MET cc_start: 0.7412 (mmt) cc_final: 0.6048 (mmt) REVERT: 12 71 ASP cc_start: 0.7838 (m-30) cc_final: 0.7438 (m-30) REVERT: 13 105 ARG cc_start: 0.7932 (tpp-160) cc_final: 0.6802 (tpp80) REVERT: 13 109 SER cc_start: 0.7604 (m) cc_final: 0.7295 (p) REVERT: 15 134 THR cc_start: 0.8777 (p) cc_final: 0.8540 (t) REVERT: 16 97 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.8141 (mp) REVERT: 16 106 ASP cc_start: 0.6286 (p0) cc_final: 0.5944 (p0) REVERT: 22 1 MET cc_start: 0.3582 (tpt) cc_final: 0.2803 (tpt) REVERT: 22 2 ILE cc_start: 0.7260 (pt) cc_final: 0.6902 (pt) REVERT: 22 25 GLU cc_start: 0.8473 (pp20) cc_final: 0.8001 (pp20) REVERT: 23 59 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7963 (tp30) REVERT: 23 97 SER cc_start: 0.8538 (m) cc_final: 0.8215 (p) REVERT: 27 11 VAL cc_start: 0.9299 (t) cc_final: 0.8778 (p) REVERT: 27 58 ASN cc_start: 0.8766 (OUTLIER) cc_final: 0.8478 (t0) REVERT: 29 62 LYS cc_start: 0.9160 (mmmt) cc_final: 0.8682 (tppt) REVERT: 30 47 TYR cc_start: 0.7603 (m-10) cc_final: 0.7402 (m-10) REVERT: 34 7 VAL cc_start: 0.8741 (m) cc_final: 0.8537 (m) REVERT: Z 282 LYS cc_start: 0.9316 (mmmm) cc_final: 0.8949 (mtpt) REVERT: B 17 HIS cc_start: 0.4658 (OUTLIER) cc_final: 0.4200 (m90) REVERT: B 153 MET cc_start: 0.8288 (mtp) cc_final: 0.8031 (tpp) REVERT: D 139 ASN cc_start: 0.8915 (t0) cc_final: 0.8606 (t0) REVERT: E 68 ARG cc_start: 0.7772 (mtm180) cc_final: 0.7199 (mtm180) REVERT: G 115 MET cc_start: 0.8851 (tpp) cc_final: 0.8540 (ttp) REVERT: G 143 MET cc_start: 0.9536 (ppp) cc_final: 0.9208 (ppp) REVERT: H 20 ASN cc_start: 0.8183 (t0) cc_final: 0.7923 (t0) REVERT: I 35 GLU cc_start: 0.8137 (tp30) cc_final: 0.7819 (tp30) REVERT: K 14 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8573 (tp40) REVERT: M 62 PHE cc_start: 0.7745 (t80) cc_final: 0.7497 (t80) REVERT: M 80 MET cc_start: 0.8469 (mtp) cc_final: 0.7968 (mmm) REVERT: N 46 LYS cc_start: 0.9067 (mmtm) cc_final: 0.8781 (mmtm) REVERT: T 23 ARG cc_start: 0.7710 (mmm-85) cc_final: 0.7494 (mmt90) REVERT: T 53 MET cc_start: 0.8677 (ppp) cc_final: 0.8356 (ppp) REVERT: U 58 LYS cc_start: 0.9259 (mtpp) cc_final: 0.8909 (mttm) outliers start: 247 outliers final: 143 residues processed: 1408 average time/residue: 1.2933 time to fit residues: 3160.6624 Evaluate side-chains 1276 residues out of total 5369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 1127 time to evaluate : 6.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 17 GLU Chi-restraints excluded: chain Y residue 29 VAL Chi-restraints excluded: chain 03 residue 16 ASP Chi-restraints excluded: chain 03 residue 47 ASN Chi-restraints excluded: chain 03 residue 224 VAL Chi-restraints excluded: chain 04 residue 107 LYS Chi-restraints excluded: chain 04 residue 138 SER Chi-restraints excluded: chain 04 residue 162 GLN Chi-restraints excluded: chain 04 residue 263 ASP Chi-restraints excluded: chain 05 residue 89 GLU Chi-restraints excluded: chain 05 residue 176 ASP Chi-restraints excluded: chain 06 residue 57 LYS Chi-restraints excluded: chain 06 residue 70 SER Chi-restraints excluded: chain 06 residue 149 ILE Chi-restraints excluded: chain 06 residue 178 VAL Chi-restraints excluded: chain 06 residue 187 VAL Chi-restraints excluded: chain 07 residue 34 THR Chi-restraints excluded: chain 07 residue 102 LEU Chi-restraints excluded: chain 07 residue 144 LYS Chi-restraints excluded: chain 08 residue 19 ASN Chi-restraints excluded: chain 08 residue 55 ASP Chi-restraints excluded: chain 09 residue 8 LYS Chi-restraints excluded: chain 09 residue 9 VAL Chi-restraints excluded: chain 09 residue 17 ASP Chi-restraints excluded: chain 09 residue 147 VAL Chi-restraints excluded: chain 10 residue 58 THR Chi-restraints excluded: chain 10 residue 65 GLU Chi-restraints excluded: chain 11 residue 97 VAL Chi-restraints excluded: chain 11 residue 104 GLN Chi-restraints excluded: chain 12 residue 32 LEU Chi-restraints excluded: chain 12 residue 93 ILE Chi-restraints excluded: chain 13 residue 32 TYR Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 42 THR Chi-restraints excluded: chain 13 residue 56 ASP Chi-restraints excluded: chain 13 residue 90 ASN Chi-restraints excluded: chain 13 residue 121 GLU Chi-restraints excluded: chain 14 residue 19 LEU Chi-restraints excluded: chain 14 residue 103 ILE Chi-restraints excluded: chain 14 residue 111 ILE Chi-restraints excluded: chain 15 residue 42 THR Chi-restraints excluded: chain 15 residue 70 ASP Chi-restraints excluded: chain 15 residue 128 THR Chi-restraints excluded: chain 16 residue 13 ASN Chi-restraints excluded: chain 16 residue 36 THR Chi-restraints excluded: chain 16 residue 76 VAL Chi-restraints excluded: chain 16 residue 97 ILE Chi-restraints excluded: chain 16 residue 117 ASP Chi-restraints excluded: chain 17 residue 28 VAL Chi-restraints excluded: chain 17 residue 69 ASP Chi-restraints excluded: chain 17 residue 80 GLU Chi-restraints excluded: chain 18 residue 3 ILE Chi-restraints excluded: chain 18 residue 65 ASN Chi-restraints excluded: chain 19 residue 8 ILE Chi-restraints excluded: chain 19 residue 16 ILE Chi-restraints excluded: chain 19 residue 82 LEU Chi-restraints excluded: chain 20 residue 26 ASP Chi-restraints excluded: chain 20 residue 99 THR Chi-restraints excluded: chain 21 residue 46 LEU Chi-restraints excluded: chain 21 residue 81 SER Chi-restraints excluded: chain 23 residue 27 VAL Chi-restraints excluded: chain 23 residue 39 ASN Chi-restraints excluded: chain 23 residue 48 VAL Chi-restraints excluded: chain 23 residue 59 GLU Chi-restraints excluded: chain 23 residue 98 ASN Chi-restraints excluded: chain 24 residue 5 ASN Chi-restraints excluded: chain 24 residue 24 ASN Chi-restraints excluded: chain 24 residue 65 VAL Chi-restraints excluded: chain 24 residue 66 ASP Chi-restraints excluded: chain 25 residue 11 ASP Chi-restraints excluded: chain 26 residue 3 VAL Chi-restraints excluded: chain 26 residue 7 THR Chi-restraints excluded: chain 26 residue 39 VAL Chi-restraints excluded: chain 26 residue 58 ILE Chi-restraints excluded: chain 27 residue 44 LYS Chi-restraints excluded: chain 27 residue 58 ASN Chi-restraints excluded: chain 28 residue 7 THR Chi-restraints excluded: chain 28 residue 56 VAL 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 32 residue 24 THR Chi-restraints excluded: chain 32 residue 30 VAL Chi-restraints excluded: chain 34 residue 3 VAL Chi-restraints excluded: chain 34 residue 28 SER Chi-restraints excluded: chain Z residue 71 ASP Chi-restraints excluded: chain Z residue 143 ASP Chi-restraints excluded: chain Z residue 149 GLU Chi-restraints excluded: chain Z residue 321 SER Chi-restraints excluded: chain Z residue 345 THR Chi-restraints excluded: chain B residue 17 HIS Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 120 HIS Chi-restraints excluded: chain E residue 156 ARG Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain K residue 14 GLN Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain K residue 96 ILE Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 17 LYS Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 102 ASP Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain O residue 17 ASP Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 26 ASN Chi-restraints excluded: chain P residue 44 SER Chi-restraints excluded: chain P residue 46 LYS Chi-restraints excluded: chain Q residue 28 VAL Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain R residue 24 ASP Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain T residue 20 ASN Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain U residue 13 VAL Chi-restraints excluded: chain U residue 18 PHE Chi-restraints excluded: chain U residue 36 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1103 random chunks: chunk 991 optimal weight: 5.9990 chunk 754 optimal weight: 8.9990 chunk 520 optimal weight: 10.0000 chunk 111 optimal weight: 30.0000 chunk 478 optimal weight: 8.9990 chunk 673 optimal weight: 6.9990 chunk 1007 optimal weight: 9.9990 chunk 1066 optimal weight: 20.0000 chunk 526 optimal weight: 5.9990 chunk 954 optimal weight: 8.9990 chunk 287 optimal weight: 20.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 03 47 ASN ** 04 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 04 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 04 238 ASN 05 185 ASN ** 06 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 07 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 09 11 ASN 09 43 ASN ** 12 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 89 ASN ** 14 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 14 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 15 60 GLN 18 74 GLN 19 43 GLN 19 58 GLN ** 20 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 24 49 ASN ** 24 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 26 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 27 58 ASN 32 29 GLN ** Z 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 GLN D 53 GLN ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 ASN O 61 GLN ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 165307 Z= 0.265 Angle : 0.636 11.026 246544 Z= 0.328 Chirality : 0.035 0.269 31354 Planarity : 0.005 0.092 13734 Dihedral : 23.353 177.862 81083 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.60 % Favored : 90.23 % Rotamer: Outliers : 4.93 % Allowed : 20.01 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.17 % 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: -2.56 (0.10), residues: 6468 helix: -0.71 (0.11), residues: 2167 sheet: -1.89 (0.15), residues: 1073 loop : -2.33 (0.10), residues: 3228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP06 78 HIS 0.008 0.001 HIS24 80 PHE 0.047 0.002 PHE U 36 TYR 0.053 0.002 TYR I 89 ARG 0.007 0.001 ARG13 31 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12936 Ramachandran restraints generated. 6468 Oldfield, 0 Emsley, 6468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12936 Ramachandran restraints generated. 6468 Oldfield, 0 Emsley, 6468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1487 residues out of total 5369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 1226 time to evaluate : 6.744 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: Y 12 LYS cc_start: 0.8370 (mmtm) cc_final: 0.8047 (mmtm) REVERT: 03 187 GLU cc_start: 0.9272 (tp30) cc_final: 0.8879 (mt-10) REVERT: 03 190 GLU cc_start: 0.9493 (tt0) cc_final: 0.9188 (mm-30) REVERT: 07 129 MET cc_start: 0.9193 (pmm) cc_final: 0.8981 (pmm) REVERT: 07 144 LYS cc_start: 0.6809 (OUTLIER) cc_final: 0.6551 (pttm) REVERT: 08 34 ARG cc_start: 0.8068 (mmm160) cc_final: 0.7844 (mmm160) REVERT: 08 57 TYR cc_start: 0.7688 (m-80) cc_final: 0.7468 (m-80) REVERT: 08 129 GLU cc_start: 0.8011 (tp30) cc_final: 0.7785 (tp30) REVERT: 09 46 PHE cc_start: 0.9411 (t80) cc_final: 0.9169 (t80) REVERT: 09 73 ASN cc_start: 0.7880 (t0) cc_final: 0.7633 (t0) REVERT: 09 122 LEU cc_start: 0.8852 (mt) cc_final: 0.8529 (mm) REVERT: 09 135 HIS cc_start: 0.8729 (t70) cc_final: 0.8429 (t70) REVERT: 10 99 PHE cc_start: 0.8001 (m-80) cc_final: 0.7508 (m-80) REVERT: 11 135 MET cc_start: 0.7460 (mmt) cc_final: 0.7230 (mmp) REVERT: 12 71 ASP cc_start: 0.7971 (m-30) cc_final: 0.7600 (m-30) REVERT: 13 108 ARG cc_start: 0.8208 (mtm180) cc_final: 0.7872 (mtt180) REVERT: 15 134 THR cc_start: 0.8711 (p) cc_final: 0.8502 (t) REVERT: 16 106 ASP cc_start: 0.6483 (p0) cc_final: 0.6126 (p0) REVERT: 17 89 ASP cc_start: 0.8250 (p0) cc_final: 0.7880 (p0) REVERT: 17 90 VAL cc_start: 0.8145 (m) cc_final: 0.7836 (t) REVERT: 20 15 SER cc_start: 0.6564 (p) cc_final: 0.5925 (p) REVERT: 20 85 LYS cc_start: 0.8680 (mmmm) cc_final: 0.8476 (mtpt) REVERT: 22 1 MET cc_start: 0.3522 (OUTLIER) cc_final: 0.2274 (tpt) REVERT: 22 2 ILE cc_start: 0.7510 (pt) cc_final: 0.7189 (pt) REVERT: 22 25 GLU cc_start: 0.8092 (pp20) cc_final: 0.7745 (pp20) REVERT: 22 89 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8201 (mp0) REVERT: 23 40 LEU cc_start: 0.8843 (mm) cc_final: 0.8442 (tp) REVERT: 23 97 SER cc_start: 0.8607 (m) cc_final: 0.8234 (p) REVERT: 29 62 LYS cc_start: 0.9133 (mmmt) cc_final: 0.8751 (tppt) REVERT: 31 34 GLU cc_start: 0.5722 (mm-30) cc_final: 0.4862 (mm-30) REVERT: 34 7 VAL cc_start: 0.8563 (m) cc_final: 0.8307 (m) REVERT: Z 282 LYS cc_start: 0.9259 (mmmm) cc_final: 0.8971 (mtmt) REVERT: B 153 MET cc_start: 0.8376 (mtp) cc_final: 0.8152 (tpp) REVERT: D 139 ASN cc_start: 0.8987 (t0) cc_final: 0.8695 (t0) REVERT: E 146 MET cc_start: 0.8656 (tpp) cc_final: 0.8362 (tpt) REVERT: H 2 MET cc_start: 0.8778 (ppp) cc_final: 0.8549 (ppp) REVERT: H 20 ASN cc_start: 0.8299 (t0) cc_final: 0.8057 (t0) REVERT: H 41 GLU cc_start: 0.8262 (pp20) cc_final: 0.7107 (pp20) REVERT: K 14 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.8652 (tp40) REVERT: L 4 ASN cc_start: 0.7812 (OUTLIER) cc_final: 0.7361 (t0) REVERT: M 80 MET cc_start: 0.8475 (mtp) cc_final: 0.7995 (mmm) REVERT: S 19 GLU cc_start: 0.8879 (tm-30) cc_final: 0.8439 (pp20) REVERT: S 20 LYS cc_start: 0.9108 (mmmm) cc_final: 0.8623 (mmmm) REVERT: S 61 VAL cc_start: 0.9068 (t) cc_final: 0.8673 (m) outliers start: 261 outliers final: 173 residues processed: 1369 average time/residue: 1.3089 time to fit residues: 3119.5423 Evaluate side-chains 1278 residues out of total 5369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 1101 time to evaluate : 6.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 7 THR Chi-restraints excluded: chain 03 residue 16 ASP Chi-restraints excluded: chain 03 residue 47 ASN Chi-restraints excluded: chain 03 residue 224 VAL Chi-restraints excluded: chain 04 residue 129 LEU Chi-restraints excluded: chain 04 residue 138 SER Chi-restraints excluded: chain 04 residue 140 VAL Chi-restraints excluded: chain 04 residue 162 GLN Chi-restraints excluded: chain 05 residue 60 VAL Chi-restraints excluded: chain 05 residue 176 ASP Chi-restraints excluded: chain 05 residue 177 VAL Chi-restraints excluded: chain 06 residue 57 LYS Chi-restraints excluded: chain 06 residue 149 ILE Chi-restraints excluded: chain 06 residue 178 VAL Chi-restraints excluded: chain 07 residue 30 VAL Chi-restraints excluded: chain 07 residue 34 THR Chi-restraints excluded: chain 07 residue 144 LYS Chi-restraints excluded: chain 08 residue 19 ASN Chi-restraints excluded: chain 08 residue 91 VAL Chi-restraints excluded: chain 08 residue 113 ASP Chi-restraints excluded: chain 09 residue 8 LYS Chi-restraints excluded: chain 09 residue 9 VAL Chi-restraints excluded: chain 09 residue 17 ASP Chi-restraints excluded: chain 09 residue 77 THR Chi-restraints excluded: chain 09 residue 137 GLU Chi-restraints excluded: chain 10 residue 58 THR Chi-restraints excluded: chain 10 residue 65 GLU Chi-restraints excluded: chain 10 residue 77 VAL Chi-restraints excluded: chain 11 residue 61 TYR Chi-restraints excluded: chain 11 residue 93 ASN Chi-restraints excluded: chain 11 residue 97 VAL Chi-restraints excluded: chain 12 residue 32 LEU Chi-restraints excluded: chain 12 residue 70 THR Chi-restraints excluded: chain 12 residue 81 ILE Chi-restraints excluded: chain 13 residue 32 TYR Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 56 ASP Chi-restraints excluded: chain 13 residue 121 GLU Chi-restraints excluded: chain 14 residue 19 LEU Chi-restraints excluded: chain 14 residue 103 ILE Chi-restraints excluded: chain 14 residue 111 ILE Chi-restraints excluded: chain 14 residue 116 VAL Chi-restraints excluded: chain 14 residue 136 GLU Chi-restraints excluded: chain 15 residue 42 THR Chi-restraints excluded: chain 15 residue 63 ILE Chi-restraints excluded: chain 15 residue 70 ASP Chi-restraints excluded: chain 15 residue 108 VAL Chi-restraints excluded: chain 15 residue 119 LEU Chi-restraints excluded: chain 15 residue 128 THR Chi-restraints excluded: chain 16 residue 13 ASN Chi-restraints excluded: chain 16 residue 36 THR Chi-restraints excluded: chain 16 residue 76 VAL Chi-restraints excluded: chain 16 residue 116 VAL Chi-restraints excluded: chain 16 residue 117 ASP Chi-restraints excluded: chain 17 residue 28 VAL Chi-restraints excluded: chain 17 residue 69 ASP Chi-restraints excluded: chain 17 residue 87 ILE Chi-restraints excluded: chain 18 residue 3 ILE Chi-restraints excluded: chain 18 residue 54 LEU Chi-restraints excluded: chain 18 residue 65 ASN Chi-restraints excluded: chain 18 residue 75 THR Chi-restraints excluded: chain 19 residue 8 ILE Chi-restraints excluded: chain 20 residue 26 ASP Chi-restraints excluded: chain 20 residue 102 SER Chi-restraints excluded: chain 21 residue 46 LEU Chi-restraints excluded: chain 21 residue 72 THR Chi-restraints excluded: chain 21 residue 81 SER Chi-restraints excluded: chain 21 residue 97 LEU Chi-restraints excluded: chain 21 residue 109 ASP Chi-restraints excluded: chain 22 residue 1 MET Chi-restraints excluded: chain 23 residue 17 ASP Chi-restraints excluded: chain 23 residue 27 VAL Chi-restraints excluded: chain 23 residue 39 ASN Chi-restraints excluded: chain 23 residue 48 VAL Chi-restraints excluded: chain 23 residue 59 GLU Chi-restraints excluded: chain 23 residue 98 ASN Chi-restraints excluded: chain 24 residue 5 ASN Chi-restraints excluded: chain 24 residue 66 ASP Chi-restraints excluded: chain 25 residue 26 SER Chi-restraints excluded: chain 26 residue 3 VAL Chi-restraints excluded: chain 26 residue 7 THR Chi-restraints excluded: chain 26 residue 39 VAL Chi-restraints excluded: chain 26 residue 58 ILE Chi-restraints excluded: chain 27 residue 44 LYS Chi-restraints excluded: chain 28 residue 7 THR Chi-restraints excluded: chain 28 residue 31 ILE Chi-restraints excluded: chain 28 residue 56 VAL 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 32 residue 24 THR Chi-restraints excluded: chain 32 residue 30 VAL Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 34 residue 3 VAL Chi-restraints excluded: chain 34 residue 25 VAL Chi-restraints excluded: chain Z residue 71 ASP Chi-restraints excluded: chain Z residue 143 ASP Chi-restraints excluded: chain Z residue 149 GLU Chi-restraints excluded: chain Z residue 246 THR Chi-restraints excluded: chain Z residue 273 GLN Chi-restraints excluded: chain Z residue 285 ASP Chi-restraints excluded: chain Z residue 321 SER Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 120 HIS Chi-restraints excluded: chain E residue 156 ARG Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain F residue 11 HIS Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain K residue 14 GLN Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain L residue 4 ASN Chi-restraints excluded: chain L residue 17 LYS Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 102 ASP Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain O residue 17 ASP Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 26 ASN Chi-restraints excluded: chain P residue 44 SER Chi-restraints excluded: chain P residue 46 LYS Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain Q residue 68 LYS Chi-restraints excluded: chain R residue 24 ASP Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain T residue 20 ASN Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain U residue 18 PHE Chi-restraints excluded: chain U residue 30 GLU Chi-restraints excluded: chain U residue 36 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1103 random chunks: chunk 887 optimal weight: 20.0000 chunk 605 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 793 optimal weight: 7.9990 chunk 439 optimal weight: 20.0000 chunk 909 optimal weight: 7.9990 chunk 736 optimal weight: 8.9990 chunk 1 optimal weight: 20.0000 chunk 544 optimal weight: 9.9990 chunk 956 optimal weight: 20.0000 chunk 269 optimal weight: 20.0000 overall best weight: 8.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 03 47 ASN ** 04 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 04 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 04 238 ASN 06 90 GLN ** 07 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 09 11 ASN 09 43 ASN 11 18 ASN ** 12 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 12 67 ASN 13 3 GLN ** 13 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 14 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 14 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 15 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 15 60 GLN 19 43 GLN ** 20 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 22 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 23 98 ASN ** 24 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 26 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 28 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN D 58 GLN ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 ASN ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 ASN O 61 GLN ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 60 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 165307 Z= 0.302 Angle : 0.649 12.782 246544 Z= 0.333 Chirality : 0.036 0.278 31354 Planarity : 0.005 0.091 13734 Dihedral : 23.488 177.254 81083 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 21.47 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.11 % Favored : 89.70 % Rotamer: Outliers : 5.12 % Allowed : 21.61 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: -2.33 (0.10), residues: 6468 helix: -0.52 (0.11), residues: 2151 sheet: -1.75 (0.15), residues: 1043 loop : -2.21 (0.10), residues: 3274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP06 78 HIS 0.012 0.001 HIS F 11 PHE 0.060 0.002 PHE U 36 TYR 0.032 0.002 TYR19 24 ARG 0.010 0.001 ARG13 31 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12936 Ramachandran restraints generated. 6468 Oldfield, 0 Emsley, 6468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12936 Ramachandran restraints generated. 6468 Oldfield, 0 Emsley, 6468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1452 residues out of total 5369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 271 poor density : 1181 time to evaluate : 6.660 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: Y 12 LYS cc_start: 0.8305 (mmtm) cc_final: 0.8011 (mmtm) REVERT: 03 16 ASP cc_start: 0.6904 (OUTLIER) cc_final: 0.6402 (m-30) REVERT: 03 20 GLN cc_start: 0.8113 (mm-40) cc_final: 0.7799 (tp-100) REVERT: 03 187 GLU cc_start: 0.9356 (tp30) cc_final: 0.8799 (mm-30) REVERT: 03 190 GLU cc_start: 0.9431 (tt0) cc_final: 0.9143 (mm-30) REVERT: 04 22 GLU cc_start: 0.7810 (pm20) cc_final: 0.7579 (pm20) REVERT: 07 119 LYS cc_start: 0.7515 (OUTLIER) cc_final: 0.7288 (ptpp) REVERT: 07 129 MET cc_start: 0.9169 (pmm) cc_final: 0.8874 (pmm) REVERT: 07 144 LYS cc_start: 0.6837 (OUTLIER) cc_final: 0.6586 (pttm) REVERT: 08 25 ILE cc_start: 0.9180 (mm) cc_final: 0.8903 (tt) REVERT: 08 57 TYR cc_start: 0.7751 (m-80) cc_final: 0.7515 (m-80) REVERT: 09 43 ASN cc_start: 0.8382 (t160) cc_final: 0.8062 (t0) REVERT: 09 60 GLU cc_start: 0.9282 (mm-30) cc_final: 0.9055 (mp0) REVERT: 09 122 LEU cc_start: 0.8858 (mt) cc_final: 0.8535 (mm) REVERT: 09 135 HIS cc_start: 0.8763 (t70) cc_final: 0.7891 (t70) REVERT: 09 137 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7180 (pt0) REVERT: 10 52 MET cc_start: 0.2515 (mmm) cc_final: 0.2315 (mmm) REVERT: 10 99 PHE cc_start: 0.8078 (m-80) cc_final: 0.7535 (m-80) REVERT: 11 135 MET cc_start: 0.7240 (mmt) cc_final: 0.6421 (mmt) REVERT: 12 71 ASP cc_start: 0.7924 (m-30) cc_final: 0.7721 (m-30) REVERT: 15 134 THR cc_start: 0.8777 (p) cc_final: 0.8480 (t) REVERT: 16 106 ASP cc_start: 0.6529 (p0) cc_final: 0.6093 (p0) REVERT: 17 89 ASP cc_start: 0.8113 (p0) cc_final: 0.7656 (p0) REVERT: 17 90 VAL cc_start: 0.8089 (m) cc_final: 0.7793 (t) REVERT: 22 1 MET cc_start: 0.3662 (tpt) cc_final: 0.2493 (tpt) REVERT: 22 25 GLU cc_start: 0.8207 (pp20) cc_final: 0.7941 (pp20) REVERT: 29 3 LYS cc_start: 0.8071 (mmtt) cc_final: 0.7679 (mmtt) REVERT: 29 62 LYS cc_start: 0.9139 (mmmt) cc_final: 0.8803 (tppt) REVERT: 31 44 GLN cc_start: 0.8046 (tm-30) cc_final: 0.7744 (pp30) REVERT: Z 129 TYR cc_start: 0.7730 (m-10) cc_final: 0.7454 (m-10) REVERT: Z 151 MET cc_start: 0.6625 (mmm) cc_final: 0.6115 (mmm) REVERT: Z 168 GLU cc_start: 0.8554 (tp30) cc_final: 0.8085 (tp30) REVERT: Z 170 GLU cc_start: 0.8325 (mp0) cc_final: 0.8007 (mp0) REVERT: D 139 ASN cc_start: 0.9062 (t0) cc_final: 0.8753 (t0) REVERT: G 52 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7662 (mtm-85) REVERT: G 65 LEU cc_start: 0.9325 (tp) cc_final: 0.8922 (tt) REVERT: G 115 MET cc_start: 0.8423 (ttt) cc_final: 0.8178 (ttp) REVERT: G 123 LEU cc_start: 0.9256 (mp) cc_final: 0.8994 (mp) REVERT: H 20 ASN cc_start: 0.8346 (t0) cc_final: 0.8108 (t0) REVERT: K 37 GLN cc_start: 0.9206 (mp10) cc_final: 0.8925 (pm20) REVERT: M 80 MET cc_start: 0.8415 (mtp) cc_final: 0.7943 (mmm) REVERT: O 10 ILE cc_start: 0.9213 (mm) cc_final: 0.8903 (mm) REVERT: T 53 MET cc_start: 0.8769 (ppp) cc_final: 0.8331 (ppp) REVERT: T 57 VAL cc_start: 0.9335 (OUTLIER) cc_final: 0.9041 (t) REVERT: U 58 LYS cc_start: 0.9167 (mtpp) cc_final: 0.8683 (mttm) outliers start: 271 outliers final: 198 residues processed: 1325 average time/residue: 1.3016 time to fit residues: 3010.9491 Evaluate side-chains 1283 residues out of total 5369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 1079 time to evaluate : 6.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 03 residue 16 ASP Chi-restraints excluded: chain 03 residue 47 ASN Chi-restraints excluded: chain 03 residue 175 ILE Chi-restraints excluded: chain 03 residue 224 VAL Chi-restraints excluded: chain 04 residue 63 ILE Chi-restraints excluded: chain 04 residue 138 SER Chi-restraints excluded: chain 04 residue 140 VAL Chi-restraints excluded: chain 04 residue 159 THR Chi-restraints excluded: chain 04 residue 162 GLN Chi-restraints excluded: chain 04 residue 186 ASP Chi-restraints excluded: chain 04 residue 258 SER Chi-restraints excluded: chain 05 residue 177 VAL Chi-restraints excluded: chain 06 residue 25 GLU Chi-restraints excluded: chain 06 residue 57 LYS Chi-restraints excluded: chain 06 residue 73 ILE Chi-restraints excluded: chain 06 residue 178 VAL Chi-restraints excluded: chain 06 residue 180 LEU Chi-restraints excluded: chain 06 residue 187 VAL Chi-restraints excluded: chain 06 residue 194 LYS Chi-restraints excluded: chain 07 residue 34 THR Chi-restraints excluded: chain 07 residue 119 LYS Chi-restraints excluded: chain 07 residue 144 LYS Chi-restraints excluded: chain 08 residue 19 ASN Chi-restraints excluded: chain 08 residue 113 ASP Chi-restraints excluded: chain 09 residue 8 LYS Chi-restraints excluded: chain 09 residue 9 VAL Chi-restraints excluded: chain 09 residue 17 ASP Chi-restraints excluded: chain 09 residue 77 THR Chi-restraints excluded: chain 09 residue 137 GLU Chi-restraints excluded: chain 10 residue 33 VAL Chi-restraints excluded: chain 10 residue 58 THR Chi-restraints excluded: chain 10 residue 65 GLU Chi-restraints excluded: chain 10 residue 77 VAL Chi-restraints excluded: chain 11 residue 61 TYR Chi-restraints excluded: chain 11 residue 68 PHE Chi-restraints excluded: chain 11 residue 93 ASN Chi-restraints excluded: chain 11 residue 129 GLU Chi-restraints excluded: chain 12 residue 32 LEU Chi-restraints excluded: chain 12 residue 70 THR Chi-restraints excluded: chain 12 residue 84 ILE Chi-restraints excluded: chain 13 residue 32 TYR Chi-restraints excluded: chain 13 residue 35 VAL Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 56 ASP Chi-restraints excluded: chain 13 residue 75 SER Chi-restraints excluded: chain 13 residue 117 SER Chi-restraints excluded: chain 13 residue 121 GLU Chi-restraints excluded: chain 14 residue 19 LEU Chi-restraints excluded: chain 14 residue 46 VAL Chi-restraints excluded: chain 14 residue 57 LEU Chi-restraints excluded: chain 14 residue 81 ASP Chi-restraints excluded: chain 14 residue 103 ILE Chi-restraints excluded: chain 14 residue 111 ILE Chi-restraints excluded: chain 14 residue 116 VAL Chi-restraints excluded: chain 14 residue 136 GLU Chi-restraints excluded: chain 15 residue 42 THR Chi-restraints excluded: chain 15 residue 63 ILE Chi-restraints excluded: chain 15 residue 108 VAL Chi-restraints excluded: chain 15 residue 119 LEU Chi-restraints excluded: chain 15 residue 128 THR Chi-restraints excluded: chain 16 residue 13 ASN Chi-restraints excluded: chain 16 residue 36 THR Chi-restraints excluded: chain 16 residue 76 VAL Chi-restraints excluded: chain 16 residue 97 ILE Chi-restraints excluded: chain 16 residue 116 VAL Chi-restraints excluded: chain 16 residue 117 ASP Chi-restraints excluded: chain 17 residue 27 VAL Chi-restraints excluded: chain 17 residue 28 VAL Chi-restraints excluded: chain 17 residue 69 ASP Chi-restraints excluded: chain 17 residue 78 VAL Chi-restraints excluded: chain 18 residue 3 ILE Chi-restraints excluded: chain 18 residue 4 ILE Chi-restraints excluded: chain 18 residue 8 GLU Chi-restraints excluded: chain 18 residue 54 LEU Chi-restraints excluded: chain 18 residue 65 ASN Chi-restraints excluded: chain 19 residue 8 ILE Chi-restraints excluded: chain 19 residue 82 LEU Chi-restraints excluded: chain 20 residue 26 ASP Chi-restraints excluded: chain 20 residue 99 THR Chi-restraints excluded: chain 20 residue 102 SER Chi-restraints excluded: chain 21 residue 46 LEU Chi-restraints excluded: chain 21 residue 72 THR Chi-restraints excluded: chain 23 residue 7 ASP Chi-restraints excluded: chain 23 residue 17 ASP Chi-restraints excluded: chain 23 residue 27 VAL Chi-restraints excluded: chain 23 residue 39 ASN Chi-restraints excluded: chain 23 residue 48 VAL Chi-restraints excluded: chain 24 residue 4 ILE Chi-restraints excluded: chain 24 residue 5 ASN Chi-restraints excluded: chain 24 residue 65 VAL Chi-restraints excluded: chain 24 residue 66 ASP Chi-restraints excluded: chain 26 residue 3 VAL Chi-restraints excluded: chain 26 residue 7 THR Chi-restraints excluded: chain 26 residue 39 VAL Chi-restraints excluded: chain 26 residue 58 ILE Chi-restraints excluded: chain 26 residue 70 LEU Chi-restraints excluded: chain 27 residue 13 GLU Chi-restraints excluded: chain 27 residue 44 LYS Chi-restraints excluded: chain 28 residue 56 VAL 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 47 ILE Chi-restraints excluded: chain 32 residue 24 THR Chi-restraints excluded: chain 32 residue 30 VAL Chi-restraints excluded: chain 34 residue 3 VAL Chi-restraints excluded: chain 34 residue 10 LEU Chi-restraints excluded: chain 34 residue 28 SER Chi-restraints excluded: chain Z residue 71 ASP Chi-restraints excluded: chain Z residue 143 ASP Chi-restraints excluded: chain Z residue 149 GLU Chi-restraints excluded: chain Z residue 242 ASP Chi-restraints excluded: chain Z residue 246 THR Chi-restraints excluded: chain Z residue 273 GLN Chi-restraints excluded: chain Z residue 285 ASP Chi-restraints excluded: chain Z residue 321 SER Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 111 ASP Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 120 HIS Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 156 ARG Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain F residue 11 HIS Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 52 ARG Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 92 SER Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain L residue 17 LYS Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 102 ASP Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 88 MET Chi-restraints excluded: chain O residue 17 ASP Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 26 ASN Chi-restraints excluded: chain P residue 44 SER Chi-restraints excluded: chain P residue 46 LYS Chi-restraints excluded: chain Q residue 11 VAL Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain Q residue 68 LYS Chi-restraints excluded: chain R residue 24 ASP Chi-restraints excluded: chain S residue 14 LEU Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 19 GLU Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain T residue 20 ASN Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain U residue 13 VAL Chi-restraints excluded: chain U residue 18 PHE Chi-restraints excluded: chain U residue 23 GLU Chi-restraints excluded: chain U residue 30 GLU Chi-restraints excluded: chain U residue 36 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1103 random chunks: chunk 358 optimal weight: 20.0000 chunk 960 optimal weight: 7.9990 chunk 210 optimal weight: 20.0000 chunk 625 optimal weight: 3.9990 chunk 263 optimal weight: 30.0000 chunk 1067 optimal weight: 0.0370 chunk 885 optimal weight: 0.0020 chunk 494 optimal weight: 30.0000 chunk 88 optimal weight: 20.0000 chunk 353 optimal weight: 20.0000 chunk 560 optimal weight: 20.0000 overall best weight: 6.4074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 03 47 ASN ** 04 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 04 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 07 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 09 11 ASN 09 20 ASN ** 12 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 12 67 ASN ** 13 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 14 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 14 104 GLN 19 43 GLN ** 20 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 21 15 GLN ** 21 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 22 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 22 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 26 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 28 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 ASN ** H 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 ASN O 61 GLN ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.4854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 165307 Z= 0.230 Angle : 0.620 15.359 246544 Z= 0.316 Chirality : 0.034 0.272 31354 Planarity : 0.005 0.093 13734 Dihedral : 23.539 177.428 81083 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 19.83 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.62 % Favored : 90.23 % Rotamer: Outliers : 4.76 % Allowed : 22.67 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: -2.21 (0.10), residues: 6468 helix: -0.41 (0.11), residues: 2144 sheet: -1.70 (0.15), residues: 1081 loop : -2.12 (0.10), residues: 3243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP06 78 HIS 0.009 0.001 HIS F 11 PHE 0.055 0.002 PHE U 36 TYR 0.044 0.002 TYR I 89 ARG 0.013 0.001 ARG Q 10 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12936 Ramachandran restraints generated. 6468 Oldfield, 0 Emsley, 6468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12936 Ramachandran restraints generated. 6468 Oldfield, 0 Emsley, 6468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1418 residues out of total 5369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 1166 time to evaluate : 6.744 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: Y 12 LYS cc_start: 0.8279 (mmtm) cc_final: 0.8077 (mmtm) REVERT: 03 16 ASP cc_start: 0.6664 (OUTLIER) cc_final: 0.6336 (p0) REVERT: 03 20 GLN cc_start: 0.8006 (mm-40) cc_final: 0.7664 (tp-100) REVERT: 03 25 GLU cc_start: 0.6429 (tm-30) cc_final: 0.5771 (pm20) REVERT: 03 187 GLU cc_start: 0.9365 (tp30) cc_final: 0.8796 (mm-30) REVERT: 03 190 GLU cc_start: 0.9413 (tt0) cc_final: 0.9141 (mm-30) REVERT: 07 129 MET cc_start: 0.9173 (pmm) cc_final: 0.8934 (pmm) REVERT: 07 144 LYS cc_start: 0.6786 (pttp) cc_final: 0.6553 (pttm) REVERT: 08 31 GLU cc_start: 0.8184 (tp30) cc_final: 0.7501 (tp30) REVERT: 09 43 ASN cc_start: 0.8342 (t160) cc_final: 0.8038 (t0) REVERT: 09 60 GLU cc_start: 0.9315 (mm-30) cc_final: 0.9098 (mp0) REVERT: 09 122 LEU cc_start: 0.8859 (mt) cc_final: 0.8518 (mm) REVERT: 09 135 HIS cc_start: 0.8752 (t70) cc_final: 0.7857 (t70) REVERT: 09 137 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7308 (pt0) REVERT: 11 135 MET cc_start: 0.6907 (mmt) cc_final: 0.6265 (mmt) REVERT: 14 106 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7874 (mp0) REVERT: 16 34 ILE cc_start: 0.6741 (pt) cc_final: 0.6382 (pt) REVERT: 16 106 ASP cc_start: 0.6528 (p0) cc_final: 0.6145 (p0) REVERT: 22 1 MET cc_start: 0.3628 (tpt) cc_final: 0.3399 (tpt) REVERT: 23 40 LEU cc_start: 0.8721 (mm) cc_final: 0.8450 (tp) REVERT: 26 69 GLU cc_start: 0.8977 (pm20) cc_final: 0.8659 (pm20) REVERT: 29 3 LYS cc_start: 0.8416 (mmtt) cc_final: 0.8118 (mmtt) REVERT: 31 32 LYS cc_start: 0.8590 (mmmt) cc_final: 0.8231 (mmmt) REVERT: 31 44 GLN cc_start: 0.8093 (tm-30) cc_final: 0.7793 (pp30) REVERT: 34 7 VAL cc_start: 0.8469 (m) cc_final: 0.8139 (m) REVERT: Z 73 MET cc_start: 0.8298 (mmt) cc_final: 0.7869 (mmm) REVERT: Z 168 GLU cc_start: 0.8521 (tp30) cc_final: 0.8013 (tp30) REVERT: Z 170 GLU cc_start: 0.8323 (mp0) cc_final: 0.8027 (mp0) REVERT: B 153 MET cc_start: 0.8221 (tpp) cc_final: 0.7932 (tpp) REVERT: C 133 MET cc_start: 0.8036 (ppp) cc_final: 0.7373 (ppp) REVERT: D 139 ASN cc_start: 0.9094 (t0) cc_final: 0.8804 (t0) REVERT: G 52 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7679 (mtm-85) REVERT: G 65 LEU cc_start: 0.9342 (tp) cc_final: 0.8916 (tt) REVERT: H 20 ASN cc_start: 0.8289 (t0) cc_final: 0.8039 (t0) REVERT: J 10 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8477 (mt) REVERT: M 77 LYS cc_start: 0.9295 (tttm) cc_final: 0.9031 (tppt) REVERT: M 80 MET cc_start: 0.8182 (mtp) cc_final: 0.7655 (mmm) REVERT: U 58 LYS cc_start: 0.9128 (mtpp) cc_final: 0.8679 (mttm) outliers start: 252 outliers final: 195 residues processed: 1304 average time/residue: 1.3012 time to fit residues: 2969.4885 Evaluate side-chains 1265 residues out of total 5369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 1066 time to evaluate : 6.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 03 residue 16 ASP Chi-restraints excluded: chain 03 residue 175 ILE Chi-restraints excluded: chain 04 residue 99 GLU Chi-restraints excluded: chain 04 residue 138 SER Chi-restraints excluded: chain 04 residue 140 VAL Chi-restraints excluded: chain 04 residue 159 THR Chi-restraints excluded: chain 04 residue 162 GLN Chi-restraints excluded: chain 04 residue 258 SER Chi-restraints excluded: chain 05 residue 60 VAL Chi-restraints excluded: chain 05 residue 176 ASP Chi-restraints excluded: chain 05 residue 177 VAL Chi-restraints excluded: chain 06 residue 48 THR Chi-restraints excluded: chain 06 residue 57 LYS Chi-restraints excluded: chain 06 residue 178 VAL Chi-restraints excluded: chain 06 residue 180 LEU Chi-restraints excluded: chain 06 residue 187 VAL Chi-restraints excluded: chain 07 residue 30 VAL Chi-restraints excluded: chain 07 residue 34 THR Chi-restraints excluded: chain 07 residue 86 CYS Chi-restraints excluded: chain 08 residue 19 ASN Chi-restraints excluded: chain 08 residue 113 ASP Chi-restraints excluded: chain 09 residue 8 LYS Chi-restraints excluded: chain 09 residue 9 VAL Chi-restraints excluded: chain 09 residue 17 ASP Chi-restraints excluded: chain 09 residue 77 THR Chi-restraints excluded: chain 09 residue 137 GLU Chi-restraints excluded: chain 09 residue 147 VAL Chi-restraints excluded: chain 10 residue 33 VAL Chi-restraints excluded: chain 10 residue 54 VAL Chi-restraints excluded: chain 10 residue 58 THR Chi-restraints excluded: chain 10 residue 65 GLU Chi-restraints excluded: chain 10 residue 77 VAL Chi-restraints excluded: chain 11 residue 61 TYR Chi-restraints excluded: chain 11 residue 68 PHE Chi-restraints excluded: chain 11 residue 93 ASN Chi-restraints excluded: chain 12 residue 32 LEU Chi-restraints excluded: chain 12 residue 70 THR Chi-restraints excluded: chain 12 residue 81 ILE Chi-restraints excluded: chain 12 residue 84 ILE Chi-restraints excluded: chain 13 residue 4 GLU Chi-restraints excluded: chain 13 residue 32 TYR Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 56 ASP Chi-restraints excluded: chain 13 residue 90 ASN Chi-restraints excluded: chain 13 residue 117 SER Chi-restraints excluded: chain 13 residue 121 GLU Chi-restraints excluded: chain 14 residue 19 LEU Chi-restraints excluded: chain 14 residue 103 ILE Chi-restraints excluded: chain 14 residue 111 ILE Chi-restraints excluded: chain 14 residue 116 VAL Chi-restraints excluded: chain 15 residue 42 THR Chi-restraints excluded: chain 15 residue 63 ILE Chi-restraints excluded: chain 15 residue 70 ASP Chi-restraints excluded: chain 15 residue 119 LEU Chi-restraints excluded: chain 15 residue 128 THR Chi-restraints excluded: chain 16 residue 13 ASN Chi-restraints excluded: chain 16 residue 36 THR Chi-restraints excluded: chain 16 residue 76 VAL Chi-restraints excluded: chain 16 residue 116 VAL Chi-restraints excluded: chain 16 residue 117 ASP Chi-restraints excluded: chain 17 residue 28 VAL Chi-restraints excluded: chain 17 residue 69 ASP Chi-restraints excluded: chain 17 residue 87 ILE Chi-restraints excluded: chain 18 residue 3 ILE Chi-restraints excluded: chain 18 residue 54 LEU Chi-restraints excluded: chain 18 residue 65 ASN Chi-restraints excluded: chain 18 residue 109 ILE Chi-restraints excluded: chain 19 residue 8 ILE Chi-restraints excluded: chain 19 residue 82 LEU Chi-restraints excluded: chain 20 residue 22 LEU Chi-restraints excluded: chain 20 residue 102 SER Chi-restraints excluded: chain 21 residue 15 GLN Chi-restraints excluded: chain 21 residue 46 LEU Chi-restraints excluded: chain 21 residue 72 THR Chi-restraints excluded: chain 21 residue 109 ASP Chi-restraints excluded: chain 23 residue 7 ASP Chi-restraints excluded: chain 23 residue 27 VAL Chi-restraints excluded: chain 23 residue 39 ASN Chi-restraints excluded: chain 23 residue 48 VAL Chi-restraints excluded: chain 23 residue 64 ILE Chi-restraints excluded: chain 24 residue 4 ILE Chi-restraints excluded: chain 24 residue 5 ASN Chi-restraints excluded: chain 24 residue 65 VAL Chi-restraints excluded: chain 24 residue 66 ASP Chi-restraints excluded: chain 25 residue 26 SER Chi-restraints excluded: chain 26 residue 3 VAL Chi-restraints excluded: chain 26 residue 7 THR Chi-restraints excluded: chain 26 residue 39 VAL Chi-restraints excluded: chain 26 residue 58 ILE Chi-restraints excluded: chain 27 residue 44 LYS Chi-restraints excluded: chain 28 residue 31 ILE Chi-restraints excluded: chain 28 residue 56 VAL Chi-restraints excluded: chain 30 residue 45 ASP Chi-restraints excluded: chain 30 residue 53 VAL Chi-restraints excluded: chain 31 residue 16 THR Chi-restraints excluded: chain 32 residue 24 THR Chi-restraints excluded: chain 32 residue 30 VAL Chi-restraints excluded: chain 33 residue 48 MET Chi-restraints excluded: chain 34 residue 3 VAL Chi-restraints excluded: chain Z residue 71 ASP Chi-restraints excluded: chain Z residue 143 ASP Chi-restraints excluded: chain Z residue 149 GLU Chi-restraints excluded: chain Z residue 242 ASP Chi-restraints excluded: chain Z residue 246 THR Chi-restraints excluded: chain Z residue 285 ASP Chi-restraints excluded: chain Z residue 321 SER Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 120 HIS Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 156 ARG Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 14 GLN Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 52 ARG Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 92 SER Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 17 LYS Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 81 ILE Chi-restraints excluded: chain L residue 102 ASP Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain O residue 2 LEU Chi-restraints excluded: chain O residue 17 ASP Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 26 ASN Chi-restraints excluded: chain P residue 44 SER Chi-restraints excluded: chain P residue 46 LYS Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain Q residue 68 LYS Chi-restraints excluded: chain R residue 17 VAL Chi-restraints excluded: chain R residue 24 ASP Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 53 GLN Chi-restraints excluded: chain S residue 3 SER Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 19 GLU Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain T residue 20 ASN Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain U residue 13 VAL Chi-restraints excluded: chain U residue 18 PHE Chi-restraints excluded: chain U residue 23 GLU Chi-restraints excluded: chain U residue 30 GLU Chi-restraints excluded: chain U residue 36 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1103 random chunks: chunk 1028 optimal weight: 6.9990 chunk 120 optimal weight: 20.0000 chunk 608 optimal weight: 50.0000 chunk 779 optimal weight: 10.0000 chunk 603 optimal weight: 30.0000 chunk 898 optimal weight: 6.9990 chunk 595 optimal weight: 10.0000 chunk 1063 optimal weight: 2.9990 chunk 665 optimal weight: 4.9990 chunk 648 optimal weight: 8.9990 chunk 490 optimal weight: 30.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 04 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 04 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 06 97 ASN ** 07 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 09 11 ASN 09 20 ASN ** 12 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 13 3 GLN 13 90 ASN ** 14 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 16 62 ASN ** 18 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 18 76 HIS 19 43 GLN ** 20 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 21 15 GLN ** 21 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 22 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 22 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 22 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 26 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 28 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 304 ASN ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN ** H 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 ASN J 35 GLN ** K 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 7 ASN O 61 GLN ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.5020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 165307 Z= 0.227 Angle : 0.619 12.004 246544 Z= 0.315 Chirality : 0.034 0.274 31354 Planarity : 0.005 0.091 13734 Dihedral : 23.554 177.399 81083 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 20.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.83 % Favored : 90.06 % Rotamer: Outliers : 4.85 % Allowed : 23.73 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.11 % 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: -2.11 (0.10), residues: 6468 helix: -0.36 (0.11), residues: 2136 sheet: -1.62 (0.15), residues: 1082 loop : -2.04 (0.10), residues: 3250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP08 61 HIS 0.010 0.001 HIS F 11 PHE 0.052 0.002 PHE U 36 TYR 0.038 0.002 TYR I 89 ARG 0.028 0.001 ARG30 16 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12936 Ramachandran restraints generated. 6468 Oldfield, 0 Emsley, 6468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12936 Ramachandran restraints generated. 6468 Oldfield, 0 Emsley, 6468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1395 residues out of total 5369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 1138 time to evaluate : 6.700 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: 03 16 ASP cc_start: 0.6975 (OUTLIER) cc_final: 0.6619 (p0) REVERT: 03 20 GLN cc_start: 0.8000 (mm-40) cc_final: 0.7755 (tp-100) REVERT: 03 25 GLU cc_start: 0.6619 (tm-30) cc_final: 0.5875 (pm20) REVERT: 03 40 GLU cc_start: 0.5858 (tp30) cc_final: 0.5636 (tp30) REVERT: 03 187 GLU cc_start: 0.9372 (tp30) cc_final: 0.8824 (mm-30) REVERT: 03 190 GLU cc_start: 0.9388 (tt0) cc_final: 0.9125 (mm-30) REVERT: 07 129 MET cc_start: 0.9169 (pmm) cc_final: 0.8942 (pmm) REVERT: 07 144 LYS cc_start: 0.6795 (OUTLIER) cc_final: 0.6586 (pttm) REVERT: 08 31 GLU cc_start: 0.8285 (tp30) cc_final: 0.7173 (tp30) REVERT: 09 43 ASN cc_start: 0.8275 (t160) cc_final: 0.8015 (t0) REVERT: 09 60 GLU cc_start: 0.9309 (mm-30) cc_final: 0.9089 (mp0) REVERT: 09 122 LEU cc_start: 0.8844 (mt) cc_final: 0.8492 (mm) REVERT: 09 129 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7704 (mm-30) REVERT: 09 135 HIS cc_start: 0.8695 (t70) cc_final: 0.7798 (t70) REVERT: 09 137 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7506 (pt0) REVERT: 11 135 MET cc_start: 0.6977 (mmt) cc_final: 0.6582 (mmt) REVERT: 14 39 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7160 (ptpp) REVERT: 16 34 ILE cc_start: 0.6837 (pt) cc_final: 0.6465 (pt) REVERT: 16 106 ASP cc_start: 0.6630 (p0) cc_final: 0.6255 (p0) REVERT: 19 110 GLU cc_start: 0.8007 (pp20) cc_final: 0.7791 (pp20) REVERT: 22 1 MET cc_start: 0.3775 (OUTLIER) cc_final: 0.2527 (tpt) REVERT: 22 25 GLU cc_start: 0.8188 (pp20) cc_final: 0.7988 (pp20) REVERT: 23 40 LEU cc_start: 0.8665 (mm) cc_final: 0.8434 (tp) REVERT: 26 69 GLU cc_start: 0.8928 (pm20) cc_final: 0.8599 (pm20) REVERT: 29 9 TYR cc_start: 0.7512 (t80) cc_final: 0.7021 (t80) REVERT: 29 56 ARG cc_start: 0.4317 (tpt170) cc_final: 0.3845 (tpt170) REVERT: 31 44 GLN cc_start: 0.8135 (tm-30) cc_final: 0.7855 (pp30) REVERT: 34 4 ARG cc_start: 0.8458 (mtm-85) cc_final: 0.8257 (mtm110) REVERT: Z 129 TYR cc_start: 0.7754 (m-10) cc_final: 0.7551 (m-10) REVERT: Z 288 MET cc_start: 0.8956 (mmm) cc_final: 0.8578 (mmm) REVERT: B 153 MET cc_start: 0.8257 (tpp) cc_final: 0.7950 (tpp) REVERT: D 139 ASN cc_start: 0.9128 (t0) cc_final: 0.8874 (t0) REVERT: G 52 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7827 (mtm180) REVERT: G 65 LEU cc_start: 0.9344 (tp) cc_final: 0.8924 (tt) REVERT: H 20 ASN cc_start: 0.8307 (t0) cc_final: 0.8079 (t0) REVERT: I 45 MET cc_start: 0.7861 (pmm) cc_final: 0.7571 (pmm) REVERT: J 10 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8413 (mt) REVERT: M 80 MET cc_start: 0.8303 (mtp) cc_final: 0.7276 (mmm) REVERT: M 81 ASP cc_start: 0.8709 (p0) cc_final: 0.8473 (p0) REVERT: U 4 LYS cc_start: 0.7327 (tppt) cc_final: 0.6975 (tppt) REVERT: U 58 LYS cc_start: 0.9107 (mtpp) cc_final: 0.8704 (mttm) outliers start: 257 outliers final: 202 residues processed: 1275 average time/residue: 1.3937 time to fit residues: 3137.7416 Evaluate side-chains 1274 residues out of total 5369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 1065 time to evaluate : 6.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 03 residue 16 ASP Chi-restraints excluded: chain 03 residue 175 ILE Chi-restraints excluded: chain 04 residue 99 GLU Chi-restraints excluded: chain 04 residue 138 SER Chi-restraints excluded: chain 04 residue 140 VAL Chi-restraints excluded: chain 04 residue 159 THR Chi-restraints excluded: chain 04 residue 162 GLN Chi-restraints excluded: chain 04 residue 258 SER Chi-restraints excluded: chain 05 residue 60 VAL Chi-restraints excluded: chain 05 residue 176 ASP Chi-restraints excluded: chain 05 residue 177 VAL Chi-restraints excluded: chain 06 residue 25 GLU Chi-restraints excluded: chain 06 residue 48 THR Chi-restraints excluded: chain 06 residue 57 LYS Chi-restraints excluded: chain 06 residue 70 SER Chi-restraints excluded: chain 06 residue 178 VAL Chi-restraints excluded: chain 06 residue 180 LEU Chi-restraints excluded: chain 06 residue 187 VAL Chi-restraints excluded: chain 07 residue 30 VAL Chi-restraints excluded: chain 07 residue 34 THR Chi-restraints excluded: chain 07 residue 86 CYS Chi-restraints excluded: chain 07 residue 144 LYS Chi-restraints excluded: chain 08 residue 19 ASN Chi-restraints excluded: chain 08 residue 91 VAL Chi-restraints excluded: chain 08 residue 113 ASP Chi-restraints excluded: chain 09 residue 8 LYS Chi-restraints excluded: chain 09 residue 9 VAL Chi-restraints excluded: chain 09 residue 17 ASP Chi-restraints excluded: chain 09 residue 20 ASN Chi-restraints excluded: chain 09 residue 77 THR Chi-restraints excluded: chain 09 residue 137 GLU Chi-restraints excluded: chain 10 residue 65 GLU Chi-restraints excluded: chain 10 residue 77 VAL Chi-restraints excluded: chain 10 residue 123 ILE Chi-restraints excluded: chain 11 residue 61 TYR Chi-restraints excluded: chain 11 residue 68 PHE Chi-restraints excluded: chain 11 residue 72 THR Chi-restraints excluded: chain 11 residue 93 ASN Chi-restraints excluded: chain 12 residue 32 LEU Chi-restraints excluded: chain 12 residue 81 ILE Chi-restraints excluded: chain 12 residue 84 ILE Chi-restraints excluded: chain 13 residue 4 GLU Chi-restraints excluded: chain 13 residue 35 VAL Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 56 ASP Chi-restraints excluded: chain 13 residue 117 SER Chi-restraints excluded: chain 13 residue 121 GLU Chi-restraints excluded: chain 14 residue 19 LEU Chi-restraints excluded: chain 14 residue 39 LYS Chi-restraints excluded: chain 14 residue 57 LEU Chi-restraints excluded: chain 14 residue 103 ILE Chi-restraints excluded: chain 14 residue 111 ILE Chi-restraints excluded: chain 14 residue 116 VAL Chi-restraints excluded: chain 15 residue 42 THR Chi-restraints excluded: chain 15 residue 70 ASP Chi-restraints excluded: chain 15 residue 112 LEU Chi-restraints excluded: chain 15 residue 128 THR Chi-restraints excluded: chain 16 residue 13 ASN Chi-restraints excluded: chain 16 residue 15 SER Chi-restraints excluded: chain 16 residue 36 THR Chi-restraints excluded: chain 16 residue 57 THR Chi-restraints excluded: chain 16 residue 76 VAL Chi-restraints excluded: chain 16 residue 116 VAL Chi-restraints excluded: chain 16 residue 117 ASP Chi-restraints excluded: chain 17 residue 28 VAL Chi-restraints excluded: chain 17 residue 69 ASP Chi-restraints excluded: chain 17 residue 87 ILE Chi-restraints excluded: chain 18 residue 3 ILE Chi-restraints excluded: chain 18 residue 54 LEU Chi-restraints excluded: chain 18 residue 65 ASN Chi-restraints excluded: chain 18 residue 109 ILE Chi-restraints excluded: chain 19 residue 8 ILE Chi-restraints excluded: chain 19 residue 30 VAL Chi-restraints excluded: chain 19 residue 82 LEU Chi-restraints excluded: chain 20 residue 22 LEU Chi-restraints excluded: chain 20 residue 26 ASP Chi-restraints excluded: chain 20 residue 102 SER Chi-restraints excluded: chain 21 residue 46 LEU Chi-restraints excluded: chain 21 residue 72 THR Chi-restraints excluded: chain 21 residue 97 LEU Chi-restraints excluded: chain 21 residue 109 ASP Chi-restraints excluded: chain 22 residue 1 MET Chi-restraints excluded: chain 23 residue 7 ASP Chi-restraints excluded: chain 23 residue 27 VAL Chi-restraints excluded: chain 23 residue 39 ASN Chi-restraints excluded: chain 23 residue 48 VAL Chi-restraints excluded: chain 23 residue 59 GLU Chi-restraints excluded: chain 23 residue 98 ASN Chi-restraints excluded: chain 24 residue 4 ILE Chi-restraints excluded: chain 24 residue 5 ASN Chi-restraints excluded: chain 24 residue 66 ASP Chi-restraints excluded: chain 25 residue 26 SER Chi-restraints excluded: chain 26 residue 3 VAL Chi-restraints excluded: chain 26 residue 7 THR Chi-restraints excluded: chain 26 residue 24 THR Chi-restraints excluded: chain 26 residue 39 VAL Chi-restraints excluded: chain 26 residue 41 SER Chi-restraints excluded: chain 26 residue 58 ILE Chi-restraints excluded: chain 27 residue 44 LYS Chi-restraints excluded: chain 28 residue 7 THR Chi-restraints excluded: chain 28 residue 8 GLN Chi-restraints excluded: chain 28 residue 56 VAL Chi-restraints excluded: chain 30 residue 22 THR Chi-restraints excluded: chain 30 residue 35 GLU Chi-restraints excluded: chain 30 residue 45 ASP Chi-restraints excluded: chain 30 residue 53 VAL Chi-restraints excluded: chain 31 residue 16 THR Chi-restraints excluded: chain 32 residue 24 THR Chi-restraints excluded: chain 32 residue 30 VAL Chi-restraints excluded: chain 33 residue 48 MET Chi-restraints excluded: chain 33 residue 54 LEU Chi-restraints excluded: chain 34 residue 3 VAL Chi-restraints excluded: chain 34 residue 28 SER Chi-restraints excluded: chain Z residue 71 ASP Chi-restraints excluded: chain Z residue 143 ASP Chi-restraints excluded: chain Z residue 149 GLU Chi-restraints excluded: chain Z residue 242 ASP Chi-restraints excluded: chain Z residue 246 THR Chi-restraints excluded: chain Z residue 273 GLN Chi-restraints excluded: chain Z residue 285 ASP Chi-restraints excluded: chain Z residue 321 SER Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 156 ARG Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 52 ARG Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain H residue 1 SER Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 118 ASN Chi-restraints excluded: chain L residue 17 LYS Chi-restraints excluded: chain L residue 26 CYS Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 81 ILE Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 102 ASP Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain O residue 2 LEU Chi-restraints excluded: chain O residue 17 ASP Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 26 ASN Chi-restraints excluded: chain P residue 44 SER Chi-restraints excluded: chain P residue 46 LYS Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain Q residue 68 LYS Chi-restraints excluded: chain R residue 17 VAL Chi-restraints excluded: chain R residue 24 ASP Chi-restraints excluded: chain S residue 3 SER Chi-restraints excluded: chain S residue 14 LEU Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain U residue 13 VAL Chi-restraints excluded: chain U residue 18 PHE Chi-restraints excluded: chain U residue 23 GLU Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 30 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1103 random chunks: chunk 657 optimal weight: 2.9990 chunk 424 optimal weight: 20.0000 chunk 634 optimal weight: 5.9990 chunk 320 optimal weight: 20.0000 chunk 208 optimal weight: 20.0000 chunk 205 optimal weight: 20.0000 chunk 675 optimal weight: 9.9990 chunk 724 optimal weight: 8.9990 chunk 525 optimal weight: 30.0000 chunk 99 optimal weight: 30.0000 chunk 835 optimal weight: 20.0000 overall best weight: 9.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 10 GLN ** Y 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 03 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 04 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 04 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 07 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 09 11 ASN ** 09 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 10 9 GLN ** 12 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 14 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 18 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 18 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 18 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 19 43 GLN ** 20 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 22 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 22 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 22 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 23 39 ASN ** 24 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 26 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 28 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 313 ASN ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 HIS ** F 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 61 GLN ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.5285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 165307 Z= 0.320 Angle : 0.671 12.440 246544 Z= 0.342 Chirality : 0.036 0.340 31354 Planarity : 0.005 0.091 13734 Dihedral : 23.644 177.042 81083 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 23.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.22 % Favored : 89.66 % Rotamer: Outliers : 4.87 % Allowed : 24.69 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: -2.20 (0.10), residues: 6468 helix: -0.53 (0.11), residues: 2138 sheet: -1.68 (0.15), residues: 1092 loop : -2.01 (0.11), residues: 3238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP06 78 HIS 0.010 0.002 HIS E 82 PHE 0.056 0.002 PHE U 36 TYR 0.026 0.002 TYR Z 27 ARG 0.010 0.001 ARG F 44 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12936 Ramachandran restraints generated. 6468 Oldfield, 0 Emsley, 6468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12936 Ramachandran restraints generated. 6468 Oldfield, 0 Emsley, 6468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1330 residues out of total 5369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 1072 time to evaluate : 6.647 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: 03 16 ASP cc_start: 0.6987 (OUTLIER) cc_final: 0.6626 (p0) REVERT: 03 20 GLN cc_start: 0.7946 (mm-40) cc_final: 0.7686 (tp-100) REVERT: 03 187 GLU cc_start: 0.9353 (tp30) cc_final: 0.8802 (mm-30) REVERT: 03 190 GLU cc_start: 0.9357 (tt0) cc_final: 0.9125 (mm-30) REVERT: 07 144 LYS cc_start: 0.6791 (OUTLIER) cc_final: 0.6372 (pttm) REVERT: 09 43 ASN cc_start: 0.8322 (OUTLIER) cc_final: 0.8036 (t0) REVERT: 09 60 GLU cc_start: 0.9303 (mm-30) cc_final: 0.9073 (mp0) REVERT: 09 122 LEU cc_start: 0.8903 (mt) cc_final: 0.8584 (mm) REVERT: 09 135 HIS cc_start: 0.8729 (t70) cc_final: 0.8517 (t70) REVERT: 11 135 MET cc_start: 0.6816 (mmt) cc_final: 0.5445 (mmt) REVERT: 14 23 ILE cc_start: 0.8371 (tp) cc_final: 0.8160 (tp) REVERT: 14 39 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7201 (ptpp) REVERT: 16 34 ILE cc_start: 0.6833 (pt) cc_final: 0.6475 (pt) REVERT: 16 106 ASP cc_start: 0.6641 (p0) cc_final: 0.6222 (p0) REVERT: 22 1 MET cc_start: 0.3835 (tpt) cc_final: 0.3498 (tpt) REVERT: 23 40 LEU cc_start: 0.8671 (mm) cc_final: 0.8410 (tp) REVERT: 23 97 SER cc_start: 0.8190 (m) cc_final: 0.7812 (p) REVERT: 26 69 GLU cc_start: 0.8966 (pm20) cc_final: 0.8669 (pm20) REVERT: 31 44 GLN cc_start: 0.8215 (tm-30) cc_final: 0.7924 (pp30) REVERT: 34 4 ARG cc_start: 0.8551 (mtm-85) cc_final: 0.8309 (mtm110) REVERT: Z 71 ASP cc_start: 0.9106 (OUTLIER) cc_final: 0.8766 (m-30) REVERT: Z 73 MET cc_start: 0.8308 (mmt) cc_final: 0.7763 (mmm) REVERT: Z 278 ARG cc_start: 0.7479 (ptp90) cc_final: 0.7015 (ptp90) REVERT: Z 288 MET cc_start: 0.9028 (mmm) cc_final: 0.8656 (mmm) REVERT: B 153 MET cc_start: 0.8344 (tpp) cc_final: 0.8084 (tpp) REVERT: D 139 ASN cc_start: 0.9114 (t0) cc_final: 0.8908 (t0) REVERT: F 68 GLN cc_start: 0.9029 (pm20) cc_final: 0.8826 (pm20) REVERT: G 65 LEU cc_start: 0.9340 (tp) cc_final: 0.8956 (tt) REVERT: H 20 ASN cc_start: 0.8230 (t0) cc_final: 0.7970 (t0) REVERT: I 45 MET cc_start: 0.7845 (pmm) cc_final: 0.7412 (pmm) REVERT: M 80 MET cc_start: 0.8092 (mtp) cc_final: 0.7603 (mmm) REVERT: M 81 ASP cc_start: 0.8680 (p0) cc_final: 0.8465 (p0) REVERT: S 19 GLU cc_start: 0.8938 (pp20) cc_final: 0.8651 (pp20) REVERT: S 20 LYS cc_start: 0.9285 (mmmm) cc_final: 0.8801 (mmmm) REVERT: U 58 LYS cc_start: 0.9145 (mtpp) cc_final: 0.8737 (mttm) outliers start: 258 outliers final: 206 residues processed: 1220 average time/residue: 1.3213 time to fit residues: 2821.8928 Evaluate side-chains 1239 residues out of total 5369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 1028 time to evaluate : 6.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 03 residue 16 ASP Chi-restraints excluded: chain 03 residue 175 ILE Chi-restraints excluded: chain 04 residue 25 LYS Chi-restraints excluded: chain 04 residue 99 GLU Chi-restraints excluded: chain 04 residue 138 SER Chi-restraints excluded: chain 04 residue 140 VAL Chi-restraints excluded: chain 04 residue 159 THR Chi-restraints excluded: chain 04 residue 162 GLN Chi-restraints excluded: chain 04 residue 258 SER Chi-restraints excluded: chain 05 residue 60 VAL Chi-restraints excluded: chain 05 residue 176 ASP Chi-restraints excluded: chain 05 residue 177 VAL Chi-restraints excluded: chain 06 residue 48 THR Chi-restraints excluded: chain 06 residue 57 LYS Chi-restraints excluded: chain 06 residue 70 SER Chi-restraints excluded: chain 06 residue 73 ILE Chi-restraints excluded: chain 06 residue 178 VAL Chi-restraints excluded: chain 06 residue 180 LEU Chi-restraints excluded: chain 06 residue 187 VAL Chi-restraints excluded: chain 07 residue 30 VAL Chi-restraints excluded: chain 07 residue 34 THR Chi-restraints excluded: chain 07 residue 86 CYS Chi-restraints excluded: chain 07 residue 144 LYS Chi-restraints excluded: chain 08 residue 19 ASN Chi-restraints excluded: chain 08 residue 91 VAL Chi-restraints excluded: chain 08 residue 113 ASP Chi-restraints excluded: chain 09 residue 9 VAL Chi-restraints excluded: chain 09 residue 17 ASP Chi-restraints excluded: chain 09 residue 22 LYS Chi-restraints excluded: chain 09 residue 43 ASN Chi-restraints excluded: chain 09 residue 77 THR Chi-restraints excluded: chain 09 residue 147 VAL Chi-restraints excluded: chain 10 residue 54 VAL Chi-restraints excluded: chain 10 residue 58 THR Chi-restraints excluded: chain 10 residue 77 VAL Chi-restraints excluded: chain 11 residue 61 TYR Chi-restraints excluded: chain 11 residue 68 PHE Chi-restraints excluded: chain 11 residue 72 THR Chi-restraints excluded: chain 11 residue 93 ASN Chi-restraints excluded: chain 12 residue 32 LEU Chi-restraints excluded: chain 12 residue 81 ILE Chi-restraints excluded: chain 12 residue 84 ILE Chi-restraints excluded: chain 13 residue 35 VAL Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 56 ASP Chi-restraints excluded: chain 13 residue 117 SER Chi-restraints excluded: chain 13 residue 121 GLU Chi-restraints excluded: chain 14 residue 39 LYS Chi-restraints excluded: chain 14 residue 57 LEU Chi-restraints excluded: chain 14 residue 103 ILE Chi-restraints excluded: chain 14 residue 111 ILE Chi-restraints excluded: chain 14 residue 116 VAL Chi-restraints excluded: chain 15 residue 42 THR Chi-restraints excluded: chain 15 residue 70 ASP Chi-restraints excluded: chain 15 residue 108 VAL Chi-restraints excluded: chain 15 residue 128 THR Chi-restraints excluded: chain 16 residue 13 ASN Chi-restraints excluded: chain 16 residue 15 SER Chi-restraints excluded: chain 16 residue 36 THR Chi-restraints excluded: chain 16 residue 57 THR Chi-restraints excluded: chain 16 residue 76 VAL Chi-restraints excluded: chain 16 residue 116 VAL Chi-restraints excluded: chain 16 residue 117 ASP Chi-restraints excluded: chain 17 residue 27 VAL Chi-restraints excluded: chain 17 residue 28 VAL Chi-restraints excluded: chain 17 residue 48 LEU Chi-restraints excluded: chain 17 residue 69 ASP Chi-restraints excluded: chain 18 residue 3 ILE Chi-restraints excluded: chain 18 residue 54 LEU Chi-restraints excluded: chain 18 residue 65 ASN Chi-restraints excluded: chain 18 residue 109 ILE Chi-restraints excluded: chain 19 residue 8 ILE Chi-restraints excluded: chain 19 residue 30 VAL Chi-restraints excluded: chain 19 residue 82 LEU Chi-restraints excluded: chain 20 residue 22 LEU Chi-restraints excluded: chain 20 residue 26 ASP Chi-restraints excluded: chain 20 residue 49 ILE Chi-restraints excluded: chain 20 residue 99 THR Chi-restraints excluded: chain 20 residue 102 SER Chi-restraints excluded: chain 21 residue 46 LEU Chi-restraints excluded: chain 21 residue 72 THR Chi-restraints excluded: chain 23 residue 27 VAL Chi-restraints excluded: chain 23 residue 39 ASN Chi-restraints excluded: chain 23 residue 48 VAL Chi-restraints excluded: chain 23 residue 59 GLU Chi-restraints excluded: chain 23 residue 98 ASN Chi-restraints excluded: chain 24 residue 4 ILE Chi-restraints excluded: chain 24 residue 5 ASN Chi-restraints excluded: chain 24 residue 64 VAL Chi-restraints excluded: chain 24 residue 66 ASP Chi-restraints excluded: chain 25 residue 26 SER Chi-restraints excluded: chain 25 residue 54 THR Chi-restraints excluded: chain 26 residue 3 VAL Chi-restraints excluded: chain 26 residue 7 THR Chi-restraints excluded: chain 26 residue 24 THR Chi-restraints excluded: chain 26 residue 58 ILE Chi-restraints excluded: chain 26 residue 70 LEU Chi-restraints excluded: chain 27 residue 7 ARG Chi-restraints excluded: chain 27 residue 44 LYS Chi-restraints excluded: chain 28 residue 56 VAL Chi-restraints excluded: chain 30 residue 53 VAL Chi-restraints excluded: chain 31 residue 16 THR Chi-restraints excluded: chain 32 residue 24 THR Chi-restraints excluded: chain 32 residue 30 VAL Chi-restraints excluded: chain 33 residue 48 MET Chi-restraints excluded: chain 33 residue 54 LEU Chi-restraints excluded: chain 34 residue 3 VAL Chi-restraints excluded: chain 34 residue 28 SER Chi-restraints excluded: chain Z residue 71 ASP Chi-restraints excluded: chain Z residue 143 ASP Chi-restraints excluded: chain Z residue 149 GLU Chi-restraints excluded: chain Z residue 242 ASP Chi-restraints excluded: chain Z residue 246 THR Chi-restraints excluded: chain Z residue 273 GLN Chi-restraints excluded: chain Z residue 285 ASP Chi-restraints excluded: chain Z residue 321 SER Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 156 ARG Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 11 HIS Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain H residue 1 SER Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain K residue 86 LYS Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 118 ASN Chi-restraints excluded: chain L residue 17 LYS Chi-restraints excluded: chain L residue 26 CYS Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 81 ILE Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 102 ASP Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain O residue 2 LEU Chi-restraints excluded: chain O residue 9 LYS Chi-restraints excluded: chain O residue 17 ASP Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 26 ASN Chi-restraints excluded: chain P residue 44 SER Chi-restraints excluded: chain P residue 46 LYS Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain Q residue 68 LYS Chi-restraints excluded: chain R residue 17 VAL Chi-restraints excluded: chain R residue 24 ASP Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 32 ILE Chi-restraints excluded: chain S residue 3 SER Chi-restraints excluded: chain S residue 14 LEU Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain U residue 13 VAL Chi-restraints excluded: chain U residue 18 PHE Chi-restraints excluded: chain U residue 23 GLU Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 30 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1103 random chunks: chunk 967 optimal weight: 9.9990 chunk 1018 optimal weight: 0.0770 chunk 929 optimal weight: 20.0000 chunk 990 optimal weight: 9.9990 chunk 596 optimal weight: 6.9990 chunk 431 optimal weight: 20.0000 chunk 777 optimal weight: 0.8980 chunk 304 optimal weight: 20.0000 chunk 895 optimal weight: 20.0000 chunk 936 optimal weight: 20.0000 chunk 987 optimal weight: 20.0000 overall best weight: 5.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 03 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 04 114 GLN ** 04 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 07 62 GLN 08 29 ASN 09 11 ASN ** 12 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 14 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 18 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 18 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 19 43 GLN ** 20 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 21 15 GLN ** 21 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 21 61 ASN 22 15 HIS ** 22 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 22 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 26 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 27 58 ASN ** 28 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 HIS ** C 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 61 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.5323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 165307 Z= 0.215 Angle : 0.635 14.346 246544 Z= 0.321 Chirality : 0.034 0.356 31354 Planarity : 0.005 0.089 13734 Dihedral : 23.672 177.719 81083 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 20.35 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.74 % Favored : 90.15 % Rotamer: Outliers : 4.06 % Allowed : 25.76 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: -2.11 (0.10), residues: 6468 helix: -0.43 (0.11), residues: 2145 sheet: -1.58 (0.15), residues: 1089 loop : -2.01 (0.11), residues: 3234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP Q 72 HIS 0.011 0.001 HIS E 82 PHE 0.051 0.002 PHE U 36 TYR 0.043 0.002 TYR03 208 ARG 0.015 0.001 ARG E 68 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12936 Ramachandran restraints generated. 6468 Oldfield, 0 Emsley, 6468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12936 Ramachandran restraints generated. 6468 Oldfield, 0 Emsley, 6468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1307 residues out of total 5369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 1092 time to evaluate : 6.761 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: 03 16 ASP cc_start: 0.6924 (OUTLIER) cc_final: 0.6602 (p0) REVERT: 03 20 GLN cc_start: 0.7896 (mm-40) cc_final: 0.7624 (tp-100) REVERT: 03 47 ASN cc_start: 0.7647 (OUTLIER) cc_final: 0.7230 (t0) REVERT: 03 187 GLU cc_start: 0.9341 (tp30) cc_final: 0.8794 (mm-30) REVERT: 03 190 GLU cc_start: 0.9356 (tt0) cc_final: 0.9127 (mm-30) REVERT: 07 144 LYS cc_start: 0.6714 (OUTLIER) cc_final: 0.6311 (pttm) REVERT: 09 60 GLU cc_start: 0.9305 (mm-30) cc_final: 0.9065 (mp0) REVERT: 09 122 LEU cc_start: 0.8899 (mt) cc_final: 0.8558 (mm) REVERT: 09 135 HIS cc_start: 0.8704 (t70) cc_final: 0.8472 (t70) REVERT: 10 52 MET cc_start: 0.2652 (mmm) cc_final: 0.2404 (mmm) REVERT: 11 135 MET cc_start: 0.6700 (mmt) cc_final: 0.5256 (mmt) REVERT: 14 39 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7169 (ptpp) REVERT: 15 75 GLU cc_start: 0.7772 (pm20) cc_final: 0.7197 (pm20) REVERT: 16 24 MET cc_start: 0.6643 (ptp) cc_final: 0.6352 (ptp) REVERT: 16 34 ILE cc_start: 0.6879 (pt) cc_final: 0.6656 (pt) REVERT: 16 106 ASP cc_start: 0.6590 (p0) cc_final: 0.6194 (p0) REVERT: 17 89 ASP cc_start: 0.8219 (p0) cc_final: 0.7841 (p0) REVERT: 22 1 MET cc_start: 0.3352 (tpt) cc_final: 0.2987 (tpt) REVERT: 22 25 GLU cc_start: 0.8387 (pp20) cc_final: 0.8119 (pp20) REVERT: 22 89 GLU cc_start: 0.8446 (mp0) cc_final: 0.8239 (mp0) REVERT: 23 40 LEU cc_start: 0.8663 (mm) cc_final: 0.8387 (tp) REVERT: 23 97 SER cc_start: 0.8161 (m) cc_final: 0.7780 (p) REVERT: 26 69 GLU cc_start: 0.8924 (pm20) cc_final: 0.8593 (pm20) REVERT: 29 8 LYS cc_start: 0.8584 (tppt) cc_final: 0.8148 (tptp) REVERT: 31 44 GLN cc_start: 0.8234 (tm-30) cc_final: 0.7948 (pp30) REVERT: Z 73 MET cc_start: 0.8340 (mmt) cc_final: 0.7824 (mmm) REVERT: Z 129 TYR cc_start: 0.7934 (m-10) cc_final: 0.7697 (m-10) REVERT: Z 312 ASP cc_start: 0.8317 (m-30) cc_final: 0.8108 (m-30) REVERT: B 153 MET cc_start: 0.8307 (tpp) cc_final: 0.8083 (tpp) REVERT: D 139 ASN cc_start: 0.9102 (t0) cc_final: 0.8897 (t0) REVERT: F 68 GLN cc_start: 0.9022 (pm20) cc_final: 0.8754 (pm20) REVERT: H 20 ASN cc_start: 0.8223 (t0) cc_final: 0.7967 (t0) REVERT: M 80 MET cc_start: 0.8049 (mtp) cc_final: 0.7528 (mmm) REVERT: S 20 LYS cc_start: 0.9314 (mmmm) cc_final: 0.8935 (mmmm) REVERT: S 46 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7682 (mm) REVERT: U 4 LYS cc_start: 0.7513 (tppt) cc_final: 0.6962 (tppt) REVERT: U 58 LYS cc_start: 0.9109 (mtpp) cc_final: 0.8713 (mttm) outliers start: 215 outliers final: 184 residues processed: 1208 average time/residue: 1.2901 time to fit residues: 2723.2978 Evaluate side-chains 1233 residues out of total 5369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 1044 time to evaluate : 5.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 03 residue 16 ASP Chi-restraints excluded: chain 03 residue 47 ASN Chi-restraints excluded: chain 03 residue 175 ILE Chi-restraints excluded: chain 04 residue 25 LYS Chi-restraints excluded: chain 04 residue 99 GLU Chi-restraints excluded: chain 04 residue 138 SER Chi-restraints excluded: chain 04 residue 140 VAL Chi-restraints excluded: chain 04 residue 159 THR Chi-restraints excluded: chain 04 residue 162 GLN Chi-restraints excluded: chain 05 residue 60 VAL Chi-restraints excluded: chain 05 residue 176 ASP Chi-restraints excluded: chain 06 residue 48 THR Chi-restraints excluded: chain 06 residue 57 LYS Chi-restraints excluded: chain 06 residue 70 SER Chi-restraints excluded: chain 06 residue 178 VAL Chi-restraints excluded: chain 06 residue 180 LEU Chi-restraints excluded: chain 06 residue 187 VAL Chi-restraints excluded: chain 07 residue 30 VAL Chi-restraints excluded: chain 07 residue 34 THR Chi-restraints excluded: chain 07 residue 86 CYS Chi-restraints excluded: chain 07 residue 144 LYS Chi-restraints excluded: chain 08 residue 19 ASN Chi-restraints excluded: chain 08 residue 91 VAL Chi-restraints excluded: chain 08 residue 113 ASP Chi-restraints excluded: chain 09 residue 9 VAL Chi-restraints excluded: chain 09 residue 22 LYS Chi-restraints excluded: chain 09 residue 77 THR Chi-restraints excluded: chain 10 residue 54 VAL Chi-restraints excluded: chain 10 residue 58 THR Chi-restraints excluded: chain 10 residue 77 VAL Chi-restraints excluded: chain 11 residue 61 TYR Chi-restraints excluded: chain 11 residue 68 PHE Chi-restraints excluded: chain 11 residue 93 ASN Chi-restraints excluded: chain 12 residue 32 LEU Chi-restraints excluded: chain 12 residue 81 ILE Chi-restraints excluded: chain 12 residue 84 ILE Chi-restraints excluded: chain 13 residue 4 GLU Chi-restraints excluded: chain 13 residue 32 TYR Chi-restraints excluded: chain 13 residue 35 VAL Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 56 ASP Chi-restraints excluded: chain 13 residue 117 SER Chi-restraints excluded: chain 13 residue 121 GLU Chi-restraints excluded: chain 14 residue 39 LYS Chi-restraints excluded: chain 14 residue 57 LEU Chi-restraints excluded: chain 14 residue 103 ILE Chi-restraints excluded: chain 14 residue 136 GLU Chi-restraints excluded: chain 15 residue 42 THR Chi-restraints excluded: chain 15 residue 70 ASP Chi-restraints excluded: chain 15 residue 112 LEU Chi-restraints excluded: chain 15 residue 128 THR Chi-restraints excluded: chain 15 residue 133 LYS Chi-restraints excluded: chain 16 residue 13 ASN Chi-restraints excluded: chain 16 residue 15 SER Chi-restraints excluded: chain 16 residue 36 THR Chi-restraints excluded: chain 16 residue 76 VAL Chi-restraints excluded: chain 16 residue 116 VAL Chi-restraints excluded: chain 16 residue 117 ASP Chi-restraints excluded: chain 17 residue 27 VAL Chi-restraints excluded: chain 17 residue 28 VAL Chi-restraints excluded: chain 17 residue 69 ASP Chi-restraints excluded: chain 18 residue 54 LEU Chi-restraints excluded: chain 18 residue 65 ASN Chi-restraints excluded: chain 18 residue 109 ILE Chi-restraints excluded: chain 19 residue 8 ILE Chi-restraints excluded: chain 19 residue 30 VAL Chi-restraints excluded: chain 20 residue 22 LEU Chi-restraints excluded: chain 20 residue 49 ILE Chi-restraints excluded: chain 20 residue 99 THR Chi-restraints excluded: chain 21 residue 46 LEU Chi-restraints excluded: chain 21 residue 72 THR Chi-restraints excluded: chain 23 residue 7 ASP Chi-restraints excluded: chain 23 residue 27 VAL Chi-restraints excluded: chain 23 residue 48 VAL Chi-restraints excluded: chain 23 residue 59 GLU Chi-restraints excluded: chain 23 residue 98 ASN Chi-restraints excluded: chain 24 residue 4 ILE Chi-restraints excluded: chain 24 residue 5 ASN Chi-restraints excluded: chain 24 residue 64 VAL Chi-restraints excluded: chain 24 residue 66 ASP Chi-restraints excluded: chain 25 residue 26 SER Chi-restraints excluded: chain 26 residue 3 VAL Chi-restraints excluded: chain 26 residue 7 THR Chi-restraints excluded: chain 26 residue 24 THR Chi-restraints excluded: chain 26 residue 39 VAL Chi-restraints excluded: chain 26 residue 58 ILE Chi-restraints excluded: chain 27 residue 7 ARG Chi-restraints excluded: chain 27 residue 44 LYS Chi-restraints excluded: chain 28 residue 56 VAL Chi-restraints excluded: chain 30 residue 22 THR Chi-restraints excluded: chain 30 residue 53 VAL Chi-restraints excluded: chain 31 residue 16 THR Chi-restraints excluded: chain 32 residue 24 THR Chi-restraints excluded: chain 33 residue 48 MET Chi-restraints excluded: chain 33 residue 54 LEU Chi-restraints excluded: chain 34 residue 3 VAL Chi-restraints excluded: chain 34 residue 28 SER Chi-restraints excluded: chain Z residue 71 ASP Chi-restraints excluded: chain Z residue 123 TYR Chi-restraints excluded: chain Z residue 143 ASP Chi-restraints excluded: chain Z residue 149 GLU Chi-restraints excluded: chain Z residue 246 THR Chi-restraints excluded: chain Z residue 273 GLN Chi-restraints excluded: chain Z residue 285 ASP Chi-restraints excluded: chain Z residue 321 SER Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 156 ARG Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain K residue 86 LYS Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 118 ASN Chi-restraints excluded: chain L residue 17 LYS Chi-restraints excluded: chain L residue 26 CYS Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 81 ILE Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 102 ASP Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain O residue 2 LEU Chi-restraints excluded: chain O residue 9 LYS Chi-restraints excluded: chain O residue 17 ASP Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 26 ASN Chi-restraints excluded: chain P residue 44 SER Chi-restraints excluded: chain P residue 46 LYS Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain Q residue 68 LYS Chi-restraints excluded: chain R residue 17 VAL Chi-restraints excluded: chain R residue 24 ASP Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain S residue 3 SER Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain U residue 13 VAL Chi-restraints excluded: chain U residue 18 PHE Chi-restraints excluded: chain U residue 23 GLU Chi-restraints excluded: chain U residue 30 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1103 random chunks: chunk 650 optimal weight: 10.0000 chunk 1047 optimal weight: 6.9990 chunk 639 optimal weight: 6.9990 chunk 496 optimal weight: 3.9990 chunk 728 optimal weight: 8.9990 chunk 1098 optimal weight: 20.0000 chunk 1011 optimal weight: 10.0000 chunk 875 optimal weight: 7.9990 chunk 90 optimal weight: 20.0000 chunk 675 optimal weight: 8.9990 chunk 536 optimal weight: 3.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 03 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 04 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 09 11 ASN 09 33 GLN ** 12 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 14 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 18 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 18 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 19 43 GLN ** 20 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 22 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 22 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 26 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 28 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 HIS ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 61 GLN S 42 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.5405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 165307 Z= 0.228 Angle : 0.647 15.854 246544 Z= 0.326 Chirality : 0.034 0.422 31354 Planarity : 0.005 0.090 13734 Dihedral : 23.662 177.613 81083 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 20.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.88 % Favored : 90.00 % Rotamer: Outliers : 3.94 % Allowed : 26.22 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.16 % 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: -2.11 (0.10), residues: 6468 helix: -0.46 (0.11), residues: 2136 sheet: -1.57 (0.15), residues: 1095 loop : -1.98 (0.11), residues: 3237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP15 64 HIS 0.019 0.001 HIS24 44 PHE 0.050 0.002 PHE U 36 TYR 0.041 0.002 TYR I 89 ARG 0.015 0.001 ARG34 4 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12936 Ramachandran restraints generated. 6468 Oldfield, 0 Emsley, 6468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12936 Ramachandran restraints generated. 6468 Oldfield, 0 Emsley, 6468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1277 residues out of total 5369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 1068 time to evaluate : 6.638 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 16 ASP cc_start: 0.6941 (OUTLIER) cc_final: 0.6539 (p0) REVERT: 03 20 GLN cc_start: 0.7911 (mm-40) cc_final: 0.7603 (tp-100) REVERT: 03 187 GLU cc_start: 0.9345 (tp30) cc_final: 0.8797 (mm-30) REVERT: 03 190 GLU cc_start: 0.9350 (tt0) cc_final: 0.9122 (mm-30) REVERT: 07 144 LYS cc_start: 0.6631 (OUTLIER) cc_final: 0.6217 (pttm) REVERT: 09 25 TYR cc_start: 0.8138 (t80) cc_final: 0.7881 (t80) REVERT: 09 60 GLU cc_start: 0.9286 (mm-30) cc_final: 0.9064 (mp0) REVERT: 09 122 LEU cc_start: 0.8904 (mt) cc_final: 0.8558 (mm) REVERT: 09 135 HIS cc_start: 0.8654 (t70) cc_final: 0.8432 (t70) REVERT: 10 31 ARG cc_start: 0.7695 (mmp80) cc_final: 0.7312 (mmp80) REVERT: 10 52 MET cc_start: 0.2464 (mmm) cc_final: 0.2257 (mmm) REVERT: 11 107 GLU cc_start: 0.9254 (tm-30) cc_final: 0.8949 (pp20) REVERT: 11 135 MET cc_start: 0.6878 (mmt) cc_final: 0.5461 (mmt) REVERT: 12 84 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8225 (tt) REVERT: 14 39 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7172 (ptpp) REVERT: 15 90 GLU cc_start: 0.7726 (mp0) cc_final: 0.7514 (mp0) REVERT: 16 24 MET cc_start: 0.6735 (ptp) cc_final: 0.6469 (ptp) REVERT: 16 34 ILE cc_start: 0.6728 (pt) cc_final: 0.6315 (pt) REVERT: 16 106 ASP cc_start: 0.6591 (p0) cc_final: 0.6225 (p0) REVERT: 21 3 THR cc_start: 0.8774 (OUTLIER) cc_final: 0.8422 (p) REVERT: 22 1 MET cc_start: 0.3200 (tpt) cc_final: 0.2976 (tpt) REVERT: 22 25 GLU cc_start: 0.8378 (pp20) cc_final: 0.8131 (pp20) REVERT: 23 40 LEU cc_start: 0.8729 (mm) cc_final: 0.8444 (tp) REVERT: 23 97 SER cc_start: 0.8163 (m) cc_final: 0.7784 (p) REVERT: 26 69 GLU cc_start: 0.8961 (pm20) cc_final: 0.8606 (pm20) REVERT: 29 8 LYS cc_start: 0.8624 (tppt) cc_final: 0.8152 (tptp) REVERT: 29 11 GLU cc_start: 0.8084 (mp0) cc_final: 0.7796 (mp0) REVERT: 31 44 GLN cc_start: 0.8266 (tm-30) cc_final: 0.7969 (pp30) REVERT: 34 7 VAL cc_start: 0.8410 (m) cc_final: 0.8133 (m) REVERT: Z 73 MET cc_start: 0.8342 (mmt) cc_final: 0.7822 (mmm) REVERT: Z 288 MET cc_start: 0.8891 (mmm) cc_final: 0.8552 (mmm) REVERT: Z 312 ASP cc_start: 0.8318 (m-30) cc_final: 0.8109 (m-30) REVERT: B 153 MET cc_start: 0.8332 (tpp) cc_final: 0.8101 (tpp) REVERT: E 127 TYR cc_start: 0.7894 (m-80) cc_final: 0.7541 (m-10) REVERT: H 20 ASN cc_start: 0.8173 (t0) cc_final: 0.7915 (t0) REVERT: M 80 MET cc_start: 0.8155 (mtp) cc_final: 0.7621 (mmm) REVERT: S 46 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7646 (mm) REVERT: U 4 LYS cc_start: 0.7383 (tppt) cc_final: 0.6908 (tppt) REVERT: U 58 LYS cc_start: 0.9107 (mtpp) cc_final: 0.8713 (mttm) outliers start: 209 outliers final: 183 residues processed: 1181 average time/residue: 1.2983 time to fit residues: 2687.1254 Evaluate side-chains 1233 residues out of total 5369 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 1044 time to evaluate : 6.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 03 residue 16 ASP Chi-restraints excluded: chain 03 residue 175 ILE Chi-restraints excluded: chain 04 residue 25 LYS Chi-restraints excluded: chain 04 residue 99 GLU Chi-restraints excluded: chain 04 residue 138 SER Chi-restraints excluded: chain 04 residue 140 VAL Chi-restraints excluded: chain 04 residue 159 THR Chi-restraints excluded: chain 04 residue 162 GLN Chi-restraints excluded: chain 04 residue 258 SER Chi-restraints excluded: chain 05 residue 60 VAL Chi-restraints excluded: chain 05 residue 176 ASP Chi-restraints excluded: chain 06 residue 25 GLU Chi-restraints excluded: chain 06 residue 48 THR Chi-restraints excluded: chain 06 residue 57 LYS Chi-restraints excluded: chain 06 residue 70 SER Chi-restraints excluded: chain 06 residue 178 VAL Chi-restraints excluded: chain 06 residue 180 LEU Chi-restraints excluded: chain 06 residue 187 VAL Chi-restraints excluded: chain 07 residue 30 VAL Chi-restraints excluded: chain 07 residue 34 THR Chi-restraints excluded: chain 07 residue 86 CYS Chi-restraints excluded: chain 07 residue 144 LYS Chi-restraints excluded: chain 08 residue 19 ASN Chi-restraints excluded: chain 08 residue 91 VAL Chi-restraints excluded: chain 08 residue 113 ASP Chi-restraints excluded: chain 09 residue 9 VAL Chi-restraints excluded: chain 09 residue 77 THR Chi-restraints excluded: chain 10 residue 54 VAL Chi-restraints excluded: chain 10 residue 58 THR Chi-restraints excluded: chain 10 residue 77 VAL Chi-restraints excluded: chain 11 residue 61 TYR Chi-restraints excluded: chain 11 residue 68 PHE Chi-restraints excluded: chain 11 residue 93 ASN Chi-restraints excluded: chain 12 residue 32 LEU Chi-restraints excluded: chain 12 residue 75 TYR Chi-restraints excluded: chain 12 residue 81 ILE Chi-restraints excluded: chain 12 residue 84 ILE Chi-restraints excluded: chain 13 residue 35 VAL Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 56 ASP Chi-restraints excluded: chain 13 residue 117 SER Chi-restraints excluded: chain 13 residue 121 GLU Chi-restraints excluded: chain 14 residue 39 LYS Chi-restraints excluded: chain 14 residue 57 LEU Chi-restraints excluded: chain 14 residue 103 ILE Chi-restraints excluded: chain 14 residue 136 GLU Chi-restraints excluded: chain 15 residue 42 THR Chi-restraints excluded: chain 15 residue 70 ASP Chi-restraints excluded: chain 15 residue 112 LEU Chi-restraints excluded: chain 15 residue 128 THR Chi-restraints excluded: chain 15 residue 133 LYS Chi-restraints excluded: chain 16 residue 13 ASN Chi-restraints excluded: chain 16 residue 15 SER Chi-restraints excluded: chain 16 residue 36 THR Chi-restraints excluded: chain 16 residue 76 VAL Chi-restraints excluded: chain 16 residue 116 VAL Chi-restraints excluded: chain 16 residue 117 ASP Chi-restraints excluded: chain 17 residue 27 VAL Chi-restraints excluded: chain 17 residue 28 VAL Chi-restraints excluded: chain 17 residue 40 ILE Chi-restraints excluded: chain 17 residue 48 LEU Chi-restraints excluded: chain 17 residue 69 ASP Chi-restraints excluded: chain 18 residue 54 LEU Chi-restraints excluded: chain 18 residue 65 ASN Chi-restraints excluded: chain 18 residue 109 ILE Chi-restraints excluded: chain 19 residue 8 ILE Chi-restraints excluded: chain 19 residue 30 VAL Chi-restraints excluded: chain 20 residue 22 LEU Chi-restraints excluded: chain 20 residue 26 ASP Chi-restraints excluded: chain 20 residue 49 ILE Chi-restraints excluded: chain 21 residue 3 THR Chi-restraints excluded: chain 21 residue 46 LEU Chi-restraints excluded: chain 21 residue 72 THR Chi-restraints excluded: chain 21 residue 97 LEU Chi-restraints excluded: chain 23 residue 7 ASP Chi-restraints excluded: chain 23 residue 27 VAL Chi-restraints excluded: chain 23 residue 48 VAL Chi-restraints excluded: chain 23 residue 59 GLU Chi-restraints excluded: chain 23 residue 98 ASN Chi-restraints excluded: chain 24 residue 4 ILE Chi-restraints excluded: chain 24 residue 5 ASN Chi-restraints excluded: chain 24 residue 64 VAL Chi-restraints excluded: chain 24 residue 66 ASP Chi-restraints excluded: chain 25 residue 26 SER Chi-restraints excluded: chain 26 residue 3 VAL Chi-restraints excluded: chain 26 residue 7 THR Chi-restraints excluded: chain 26 residue 24 THR Chi-restraints excluded: chain 26 residue 39 VAL Chi-restraints excluded: chain 26 residue 58 ILE Chi-restraints excluded: chain 26 residue 70 LEU Chi-restraints excluded: chain 27 residue 44 LYS Chi-restraints excluded: chain 28 residue 56 VAL Chi-restraints excluded: chain 30 residue 53 VAL Chi-restraints excluded: chain 31 residue 16 THR Chi-restraints excluded: chain 32 residue 24 THR Chi-restraints excluded: chain 33 residue 48 MET Chi-restraints excluded: chain 33 residue 54 LEU Chi-restraints excluded: chain 34 residue 3 VAL Chi-restraints excluded: chain Z residue 71 ASP Chi-restraints excluded: chain Z residue 123 TYR Chi-restraints excluded: chain Z residue 143 ASP Chi-restraints excluded: chain Z residue 149 GLU Chi-restraints excluded: chain Z residue 246 THR Chi-restraints excluded: chain Z residue 273 GLN Chi-restraints excluded: chain Z residue 285 ASP Chi-restraints excluded: chain Z residue 321 SER Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 156 ARG Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain I residue 24 ASN Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 49 SER Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain K residue 74 LYS Chi-restraints excluded: chain K residue 86 LYS Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 17 LYS Chi-restraints excluded: chain L residue 26 CYS Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 46 SER Chi-restraints excluded: chain L residue 81 ILE Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 102 ASP Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain O residue 2 LEU Chi-restraints excluded: chain O residue 17 ASP Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 13 LYS Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 26 ASN Chi-restraints excluded: chain P residue 44 SER Chi-restraints excluded: chain P residue 46 LYS Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain Q residue 68 LYS Chi-restraints excluded: chain R residue 17 VAL Chi-restraints excluded: chain R residue 24 ASP Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain S residue 3 SER Chi-restraints excluded: chain S residue 14 LEU Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain U residue 13 VAL Chi-restraints excluded: chain U residue 18 PHE Chi-restraints excluded: chain U residue 23 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1103 random chunks: chunk 695 optimal weight: 6.9990 chunk 932 optimal weight: 20.0000 chunk 268 optimal weight: 20.0000 chunk 806 optimal weight: 10.0000 chunk 129 optimal weight: 30.0000 chunk 243 optimal weight: 30.0000 chunk 876 optimal weight: 30.0000 chunk 366 optimal weight: 50.0000 chunk 899 optimal weight: 0.0870 chunk 110 optimal weight: 20.0000 chunk 161 optimal weight: 20.0000 overall best weight: 11.4172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 03 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 04 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 72 ASN 09 11 ASN 09 33 GLN ** 12 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 14 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 18 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 19 13 HIS 19 43 GLN ** 20 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 22 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 22 92 ASN ** 24 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 26 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 28 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 GLN K 27 ASN O 61 GLN ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.038176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.030078 restraints weight = 1228726.159| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 2.84 r_work: 0.2687 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.5666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.118 165307 Z= 0.371 Angle : 0.720 14.590 246544 Z= 0.364 Chirality : 0.038 0.340 31354 Planarity : 0.005 0.090 13734 Dihedral : 23.794 177.027 81083 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 25.76 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.04 % Favored : 88.84 % Rotamer: Outliers : 4.11 % Allowed : 26.14 % Favored : 69.74 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.14 % 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: -2.21 (0.10), residues: 6468 helix: -0.61 (0.11), residues: 2144 sheet: -1.60 (0.15), residues: 1074 loop : -2.00 (0.11), residues: 3250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP06 78 HIS 0.016 0.002 HIS B 17 PHE 0.048 0.002 PHE U 36 TYR 0.030 0.003 TYR12 75 ARG 0.016 0.001 ARG34 4 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 46461.68 seconds wall clock time: 811 minutes 9.88 seconds (48669.88 seconds total)