Starting phenix.real_space_refine on Tue Mar 26 02:23:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5l3p_4001/03_2024/5l3p_4001_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5l3p_4001/03_2024/5l3p_4001.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5l3p_4001/03_2024/5l3p_4001_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5l3p_4001/03_2024/5l3p_4001_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5l3p_4001/03_2024/5l3p_4001_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5l3p_4001/03_2024/5l3p_4001.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5l3p_4001/03_2024/5l3p_4001.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5l3p_4001/03_2024/5l3p_4001_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5l3p_4001/03_2024/5l3p_4001_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4705 5.49 5 S 156 5.16 5 C 75261 2.51 5 N 27981 2.21 5 O 41503 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 13": "NH1" <-> "NH2" Residue "E ARG 33": "NH1" <-> "NH2" Residue "E TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 59": "NH1" <-> "NH2" Residue "E ARG 77": "NH1" <-> "NH2" Residue "E ARG 83": "NH1" <-> "NH2" Residue "E ARG 169": "NH1" <-> "NH2" Residue "E ARG 184": "NH1" <-> "NH2" Residue "F ARG 21": "NH1" <-> "NH2" Residue "F ARG 44": "NH1" <-> "NH2" Residue "F ARG 49": "NH1" <-> "NH2" Residue "F ARG 61": "NH1" <-> "NH2" Residue "F ARG 88": "NH1" <-> "NH2" Residue "F ARG 102": "NH1" <-> "NH2" Residue "F ARG 162": "NH1" <-> "NH2" Residue "F ARG 170": "NH1" <-> "NH2" Residue "G ARG 70": "NH1" <-> "NH2" Residue "G ARG 79": "NH1" <-> "NH2" Residue "G ARG 91": "NH1" <-> "NH2" Residue "G ARG 101": "NH1" <-> "NH2" Residue "G ARG 109": "NH1" <-> "NH2" Residue "G ARG 111": "NH1" <-> "NH2" Residue "G ARG 114": "NH1" <-> "NH2" Residue "G ARG 132": "NH1" <-> "NH2" Residue "H ARG 2": "NH1" <-> "NH2" Residue "H ARG 152": "NH1" <-> "NH2" Residue "H ARG 162": "NH1" <-> "NH2" Residue "H ARG 169": "NH1" <-> "NH2" Residue "N ARG 13": "NH1" <-> "NH2" Residue "N ARG 37": "NH1" <-> "NH2" Residue "N TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N ARG 120": "NH1" <-> "NH2" Residue "O TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 21": "NH1" <-> "NH2" Residue "P ARG 33": "NH1" <-> "NH2" Residue "P ARG 41": "NH1" <-> "NH2" Residue "P ARG 47": "NH1" <-> "NH2" Residue "P ARG 60": "NH1" <-> "NH2" Residue "P PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 78": "NH1" <-> "NH2" Residue "P ARG 126": "NH1" <-> "NH2" Residue "Q ARG 10": "NH1" <-> "NH2" Residue "Q ARG 18": "NH1" <-> "NH2" Residue "Q ARG 40": "NH1" <-> "NH2" Residue "Q ARG 44": "NH1" <-> "NH2" Residue "Q ARG 50": "NH1" <-> "NH2" Residue "Q ARG 59": "NH1" <-> "NH2" Residue "Q TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 114": "NH1" <-> "NH2" Residue "R ARG 8": "NH1" <-> "NH2" Residue "R ARG 12": "NH1" <-> "NH2" Residue "R ARG 17": "NH1" <-> "NH2" Residue "R ARG 22": "NH1" <-> "NH2" Residue "R ARG 46": "NH1" <-> "NH2" Residue "R ARG 63": "NH1" <-> "NH2" Residue "R ARG 64": "NH1" <-> "NH2" Residue "R ARG 69": "NH1" <-> "NH2" Residue "R ARG 71": "NH1" <-> "NH2" Residue "R ARG 96": "NH1" <-> "NH2" Residue "R ARG 118": "NH1" <-> "NH2" Residue "S ARG 10": "NH1" <-> "NH2" Residue "S ARG 16": "NH1" <-> "NH2" Residue "S ARG 25": "NH1" <-> "NH2" Residue "S ARG 81": "NH1" <-> "NH2" Residue "S ARG 94": "NH1" <-> "NH2" Residue "S ARG 102": "NH1" <-> "NH2" Residue "S ARG 111": "NH1" <-> "NH2" Residue "S PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 20": "NH1" <-> "NH2" Residue "T ARG 38": "NH1" <-> "NH2" Residue "T PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 61": "NH1" <-> "NH2" Residue "T ARG 88": "NH1" <-> "NH2" Residue "T ARG 100": "NH1" <-> "NH2" Residue "T ARG 108": "NH1" <-> "NH2" Residue "U ARG 2": "NH1" <-> "NH2" Residue "U ARG 5": "NH1" <-> "NH2" Residue "U ARG 12": "NH1" <-> "NH2" Residue "U ARG 32": "NH1" <-> "NH2" Residue "U ARG 47": "NH1" <-> "NH2" Residue "U ARG 69": "NH1" <-> "NH2" Residue "V TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 21": "NH1" <-> "NH2" Residue "V ARG 68": "NH1" <-> "NH2" Residue "V ARG 78": "NH1" <-> "NH2" Residue "V ARG 79": "NH1" <-> "NH2" Residue "V ARG 84": "NH1" <-> "NH2" Residue "W ARG 84": "NH1" <-> "NH2" Residue "W ARG 88": "NH1" <-> "NH2" Residue "W ARG 95": "NH1" <-> "NH2" Residue "W ARG 110": "NH1" <-> "NH2" Residue "X ARG 73": "NH1" <-> "NH2" Residue "Y ARG 5": "NH1" <-> "NH2" Residue "Y ARG 6": "NH1" <-> "NH2" Residue "Y ARG 81": "NH1" <-> "NH2" Residue "Y ARG 85": "NH1" <-> "NH2" Residue "Y ARG 93": "NH1" <-> "NH2" Residue "Y PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 29": "NH1" <-> "NH2" Residue "2 ARG 47": "NH1" <-> "NH2" Residue "2 ARG 52": "NH1" <-> "NH2" Residue "3 ARG 10": "NH1" <-> "NH2" Residue "3 ARG 29": "NH1" <-> "NH2" Residue "3 ARG 44": "NH1" <-> "NH2" Residue "4 PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 49": "NH1" <-> "NH2" Residue "4 ARG 56": "NH1" <-> "NH2" Residue "5 ARG 9": "NH1" <-> "NH2" Residue "5 ARG 15": "NH1" <-> "NH2" Residue "5 ARG 39": "NH1" <-> "NH2" Residue "5 ARG 51": "NH1" <-> "NH2" Residue "6 ARG 43": "NH1" <-> "NH2" Residue "7 ARG 3": "NH1" <-> "NH2" Residue "7 ARG 12": "NH1" <-> "NH2" Residue "7 ARG 14": "NH1" <-> "NH2" Residue "7 ARG 19": "NH1" <-> "NH2" Residue "7 ARG 21": "NH1" <-> "NH2" Residue "7 ARG 33": "NH1" <-> "NH2" Residue "7 ARG 41": "NH1" <-> "NH2" Residue "8 ARG 12": "NH1" <-> "NH2" Residue "8 ARG 29": "NH1" <-> "NH2" Residue "8 ARG 39": "NH1" <-> "NH2" Residue "8 ARG 41": "NH1" <-> "NH2" Residue "9 ARG 12": "NH1" <-> "NH2" Residue "9 ARG 24": "NH1" <-> "NH2" Residue "b PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 107": "NH1" <-> "NH2" Residue "b PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 224": "NH1" <-> "NH2" Residue "c ARG 106": "NH1" <-> "NH2" Residue "c PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 130": "NH1" <-> "NH2" Residue "e PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 156": "NH1" <-> "NH2" Residue "f TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 123": "NH1" <-> "NH2" Residue "l TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 55": "NH1" <-> "NH2" Residue "p ARG 28": "NH1" <-> "NH2" Residue "r TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.25s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 149606 Number of models: 1 Model: "" Number of chains: 58 Chain: "A" Number of atoms: 62057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2890, 62057 Classifications: {'RNA': 2890} Modifications used: {'p5*END': 1, 'rna2p': 7, 'rna2p_pur': 203, 'rna2p_pyr': 88, 'rna3p': 17, 'rna3p_pur': 1457, 'rna3p_pyr': 1117} Link IDs: {'rna2p': 298, 'rna3p': 2591} Chain breaks: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 3 Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2572 Classifications: {'RNA': 120} Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 62, 'rna3p_pyr': 53} Link IDs: {'rna2p': 5, 'rna3p': 114} Chain: "D" 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: "E" 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: "F" 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: "G" 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: "H" 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: "I" 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: "N" 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: "O" 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: "P" 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: "Q" 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: "R" 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: "S" 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: "T" 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: "U" 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: "V" 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: "W" 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: "X" 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: "Y" 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: "Z" 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: "0" 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: "1" 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: "2" 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: "3" 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: "4" 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: "5" 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: "6" 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: "7" 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: "8" 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: "9" 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: "a" Number of atoms: 33029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33029 Classifications: {'RNA': 1539} Modifications used: {'p5*END': 1, 'rna2p': 3, 'rna2p_pur': 87, 'rna2p_pyr': 42, 'rna3p': 8, 'rna3p_pur': 781, 'rna3p_pyr': 618} Link IDs: {'rna2p': 132, 'rna3p': 1406} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 8 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: {'PCIS': 1, 'PTRANS': 6, '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: 1141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1141 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 151} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 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: "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: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 504 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 62} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 25 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: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 495 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 62} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "v" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 3, 'rna3p_pyr': 2} Link IDs: {'rna3p': 5} Chain: "x" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1644 Classifications: {'RNA': 77} Modifications used: {'p5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 2, 'rna3p': 4, 'rna3p_pur': 34, 'rna3p_pyr': 32} Link IDs: {'rna2p': 6, 'rna3p': 70} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 Chain: "J" 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: "K" 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: "n" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 799 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 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: "z" Number of atoms: 2255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 2255 Classifications: {'peptide': 545} Incomplete info: {'backbone_only': 442, 'truncation_to_alanine': 75} Link IDs: {'PTRANS': 15, 'TRANS': 529} Chain breaks: 11 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 2104 Unresolved non-hydrogen angles: 3053 Unresolved non-hydrogen dihedrals: 1319 Unresolved non-hydrogen chiralities: 588 Planarities with less than four sites: {'GLN:plan1': 19, 'ARG:plan': 37, 'TYR:plan': 17, 'ASN:plan1': 13, 'TRP:plan': 6, 'ASP:plan': 34, 'PHE:plan': 12, 'GLU:plan': 31, 'HIS:plan': 16, 'UNK:plan-1': 75} Unresolved non-hydrogen planarities: 1024 Chain: "y" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1581 Classifications: {'RNA': 73} Modifications used: {'p5*END': 1, 'rna2p': 2, 'rna2p_pur': 5, 'rna2p_pyr': 2, 'rna3p': 5, 'rna3p_pur': 32, 'rna3p_pyr': 27} Link IDs: {'rna2p': 9, 'rna3p': 63} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 5 Time building chain proxies: 56.20, per 1000 atoms: 0.38 Number of scatterers: 149606 At special positions: 0 Unit cell: (267.315, 276.9, 246.015, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 156 16.00 P 4705 15.00 O 41503 8.00 N 27981 7.00 C 75261 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 4 18 " - pdb=" SG CYS 4 40 " distance=2.03 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: 63.23 Conformation dependent library (CDL) restraints added in 7.6 seconds 12610 Ramachandran restraints generated. 6305 Oldfield, 0 Emsley, 6305 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11082 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 206 helices and 63 sheets defined 40.5% alpha, 14.5% beta 1200 base pairs and 2704 stacking pairs defined. Time for finding SS restraints: 75.31 Creating SS restraints... Processing helix chain 'D' and resid 11 through 16 removed outlier: 4.921A pdb=" N VAL D 15 " --> pdb=" O GLY D 11 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N VAL D 16 " --> pdb=" O ARG D 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 11 through 16' Processing helix chain 'D' and resid 29 through 34 removed outlier: 4.022A pdb=" N LEU D 33 " --> pdb=" O PHE D 29 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N GLU D 34 " --> pdb=" O ALA D 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 29 through 34' Processing helix chain 'D' and resid 130 through 135 removed outlier: 4.468A pdb=" N ILE D 134 " --> pdb=" O PRO D 130 " (cutoff:3.500A) Proline residue: D 135 - end of helix No H-bonds generated for 'chain 'D' and resid 130 through 135' Processing helix chain 'D' and resid 208 through 214 removed outlier: 3.929A pdb=" N TRP D 212 " --> pdb=" O GLY D 208 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG D 213 " --> pdb=" O ALA D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 225 removed outlier: 3.530A pdb=" N MET D 224 " --> pdb=" O ARG D 220 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ASN D 225 " --> pdb=" O GLY D 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 220 through 225' Processing helix chain 'D' and resid 259 through 267 removed outlier: 5.870A pdb=" N ASP D 263 " --> pdb=" O ASN D 259 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LYS D 264 " --> pdb=" O LYS D 260 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N PHE D 265 " --> pdb=" O ARG D 261 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE D 266 " --> pdb=" O THR D 262 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N VAL D 267 " --> pdb=" O ASP D 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 259 through 267' Processing helix chain 'E' and resid 61 through 72 removed outlier: 3.743A pdb=" N ALA E 69 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS E 70 " --> pdb=" O GLY E 66 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ALA E 71 " --> pdb=" O HIS E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 105 removed outlier: 3.950A pdb=" N ALA E 102 " --> pdb=" O VAL E 98 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ASP E 103 " --> pdb=" O GLU E 99 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL E 104 " --> pdb=" O LEU E 100 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N LYS E 105 " --> pdb=" O PHE E 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 98 through 105' Processing helix chain 'E' and resid 120 through 125 Processing helix chain 'F' and resid 15 through 20 Processing helix chain 'F' and resid 24 through 40 removed outlier: 3.814A pdb=" N ARG F 40 " --> pdb=" O ALA F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 53 removed outlier: 5.870A pdb=" N THR F 53 " --> pdb=" O ARG F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 116 removed outlier: 3.516A pdb=" N ARG F 114 " --> pdb=" O SER F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 142 removed outlier: 4.544A pdb=" N LEU F 134 " --> pdb=" O LYS F 130 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS F 139 " --> pdb=" O ALA F 135 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET F 141 " --> pdb=" O LYS F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 163 removed outlier: 4.112A pdb=" N ALA F 160 " --> pdb=" O ASN F 156 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ASN F 163 " --> pdb=" O LEU F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 184 removed outlier: 3.716A pdb=" N LEU F 180 " --> pdb=" O ASP F 176 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ASP F 184 " --> pdb=" O LEU F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 201 removed outlier: 3.755A pdb=" N LYS F 194 " --> pdb=" O ALA F 190 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN F 195 " --> pdb=" O ASP F 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 1 through 19 removed outlier: 4.186A pdb=" N ASP G 5 " --> pdb=" O ALA G 1 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TYR G 6 " --> pdb=" O LYS G 2 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS G 8 " --> pdb=" O HIS G 4 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASP G 9 " --> pdb=" O ASP G 5 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU G 10 " --> pdb=" O TYR G 6 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL G 11 " --> pdb=" O TYR G 7 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N VAL G 12 " --> pdb=" O LYS G 8 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS G 14 " --> pdb=" O GLU G 10 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR G 17 " --> pdb=" O LYS G 13 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU G 18 " --> pdb=" O LYS G 14 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE G 19 " --> pdb=" O LEU G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 46 removed outlier: 3.578A pdb=" N ASP G 45 " --> pdb=" O GLU G 41 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS G 46 " --> pdb=" O ALA G 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 41 through 46' Processing helix chain 'G' and resid 47 through 60 removed outlier: 3.534A pdb=" N ALA G 58 " --> pdb=" O ALA G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 110 removed outlier: 4.113A pdb=" N TRP G 96 " --> pdb=" O GLY G 92 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU G 97 " --> pdb=" O GLU G 93 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR G 104 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE G 105 " --> pdb=" O ARG G 101 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL G 107 " --> pdb=" O ILE G 103 " (cutoff:3.500A) Proline residue: G 108 - end of helix Processing helix chain 'G' and resid 141 through 146 removed outlier: 6.301A pdb=" N VAL G 145 " --> pdb=" O ASP G 141 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ASP G 146 " --> pdb=" O TYR G 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 141 through 146' Processing helix chain 'G' and resid 161 through 173 removed outlier: 4.653A pdb=" N ALA G 167 " --> pdb=" O GLU G 163 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LEU G 168 " --> pdb=" O GLU G 164 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU G 169 " --> pdb=" O GLY G 165 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE G 172 " --> pdb=" O LEU G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 138 removed outlier: 3.718A pdb=" N ILE G 136 " --> pdb=" O GLU G 133 " (cutoff:3.500A) Proline residue: G 138 - end of helix Processing helix chain 'H' and resid 1 through 6 removed outlier: 3.539A pdb=" N LYS H 5 " --> pdb=" O SER H 1 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ALA H 6 " --> pdb=" O ARG H 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 1 through 6' Processing helix chain 'H' and resid 59 through 80 removed outlier: 3.595A pdb=" N GLN H 63 " --> pdb=" O ASP H 59 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA H 69 " --> pdb=" O GLY H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 152 removed outlier: 3.508A pdb=" N TYR H 150 " --> pdb=" O ASP H 146 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ARG H 151 " --> pdb=" O LEU H 147 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG H 152 " --> pdb=" O ARG H 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 29 removed outlier: 3.560A pdb=" N PHE I 29 " --> pdb=" O TYR I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 50 removed outlier: 4.618A pdb=" N ILE I 44 " --> pdb=" O THR I 40 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU I 45 " --> pdb=" O LYS I 41 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA I 49 " --> pdb=" O GLU I 45 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG I 50 " --> pdb=" O PHE I 46 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 73 removed outlier: 6.303A pdb=" N LYS I 57 " --> pdb=" O GLU I 53 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ASN I 73 " --> pdb=" O ALA I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 107 removed outlier: 3.531A pdb=" N ILE I 99 " --> pdb=" O GLY I 95 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA I 106 " --> pdb=" O ALA I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 116 removed outlier: 4.025A pdb=" N VAL I 115 " --> pdb=" O ALA I 111 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ARG I 116 " --> pdb=" O LYS I 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 111 through 116' Processing helix chain 'N' and resid 24 through 38 removed outlier: 3.648A pdb=" N GLU N 31 " --> pdb=" O ARG N 27 " (cutoff:3.500A) Processing helix chain 'N' and resid 67 through 72 Processing helix chain 'N' and resid 88 through 96 removed outlier: 3.559A pdb=" N MET N 92 " --> pdb=" O THR N 88 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE N 93 " --> pdb=" O PHE N 89 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA N 94 " --> pdb=" O GLU N 90 " (cutoff:3.500A) Processing helix chain 'N' and resid 97 through 110 removed outlier: 4.137A pdb=" N ILE N 101 " --> pdb=" O PRO N 97 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA N 104 " --> pdb=" O VAL N 100 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N MET N 108 " --> pdb=" O ALA N 104 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU N 109 " --> pdb=" O VAL N 105 " (cutoff:3.500A) Proline residue: N 110 - end of helix Processing helix chain 'N' and resid 112 through 122 removed outlier: 4.299A pdb=" N LYS N 121 " --> pdb=" O ALA N 117 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU N 122 " --> pdb=" O MET N 118 " (cutoff:3.500A) Processing helix chain 'N' and resid 130 through 135 removed outlier: 4.049A pdb=" N ALA N 133 " --> pdb=" O HIS N 130 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA N 134 " --> pdb=" O ASN N 131 " (cutoff:3.500A) Processing helix chain 'O' and resid 109 through 120 removed outlier: 5.666A pdb=" N MET O 113 " --> pdb=" O SER O 109 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N LYS O 114 " --> pdb=" O GLU O 110 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ILE O 115 " --> pdb=" O LYS O 111 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU O 118 " --> pdb=" O LYS O 114 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA O 119 " --> pdb=" O ILE O 115 " (cutoff:3.500A) Proline residue: O 120 - end of helix Processing helix chain 'P' and resid 56 through 62 Proline residue: P 62 - end of helix Processing helix chain 'P' and resid 68 through 75 removed outlier: 3.566A pdb=" N ALA P 72 " --> pdb=" O SER P 68 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ILE P 73 " --> pdb=" O ARG P 69 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR P 74 " --> pdb=" O LYS P 70 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ALA P 75 " --> pdb=" O ALA P 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 68 through 75' Processing helix chain 'P' and resid 78 through 83 removed outlier: 3.551A pdb=" N LEU P 82 " --> pdb=" O ARG P 78 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ALA P 83 " --> pdb=" O LEU P 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 78 through 83' Processing helix chain 'P' and resid 91 through 99 removed outlier: 4.485A pdb=" N LEU P 95 " --> pdb=" O ASP P 91 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LYS P 96 " --> pdb=" O LEU P 92 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ALA P 97 " --> pdb=" O ASN P 93 " (cutoff:3.500A) Processing helix chain 'P' and resid 128 through 139 removed outlier: 5.522A pdb=" N ARG P 132 " --> pdb=" O THR P 128 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA P 133 " --> pdb=" O LYS P 129 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 58 removed outlier: 3.715A pdb=" N ILE Q 46 " --> pdb=" O THR Q 42 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU Q 47 " --> pdb=" O ALA Q 43 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG Q 55 " --> pdb=" O ARG Q 51 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA Q 56 " --> pdb=" O ALA Q 52 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL Q 57 " --> pdb=" O MET Q 53 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS Q 58 " --> pdb=" O THR Q 54 " (cutoff:3.500A) Processing helix chain 'Q' and resid 109 through 125 removed outlier: 3.638A pdb=" N GLU Q 115 " --> pdb=" O GLU Q 111 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS Q 123 " --> pdb=" O LEU Q 119 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU Q 124 " --> pdb=" O ALA Q 120 " (cutoff:3.500A) Proline residue: Q 125 - end of helix Processing helix chain 'R' and resid 13 through 32 removed outlier: 3.988A pdb=" N GLY R 26 " --> pdb=" O ARG R 22 " (cutoff:3.500A) Processing helix chain 'R' and resid 38 through 56 removed outlier: 4.268A pdb=" N ARG R 46 " --> pdb=" O LYS R 42 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL R 47 " --> pdb=" O GLU R 43 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU R 49 " --> pdb=" O ARG R 45 " (cutoff:3.500A) Proline residue: R 50 - end of helix Processing helix chain 'R' and resid 59 through 71 removed outlier: 5.335A pdb=" N ARG R 63 " --> pdb=" O SER R 59 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG R 64 " --> pdb=" O VAL R 60 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG R 69 " --> pdb=" O LEU R 65 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N THR R 70 " --> pdb=" O ALA R 66 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ARG R 71 " --> pdb=" O PHE R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 72 through 87 removed outlier: 3.599A pdb=" N LYS R 78 " --> pdb=" O GLU R 74 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N PHE R 80 " --> pdb=" O VAL R 76 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASN R 81 " --> pdb=" O ALA R 77 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LEU R 83 " --> pdb=" O LEU R 79 " (cutoff:3.500A) Proline residue: R 85 - end of helix Processing helix chain 'S' and resid 2 through 22 removed outlier: 3.881A pdb=" N ARG S 7 " --> pdb=" O LYS S 3 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE S 8 " --> pdb=" O LYS S 4 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ARG S 13 " --> pdb=" O ARG S 9 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ALA S 14 " --> pdb=" O ARG S 10 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN S 19 " --> pdb=" O ARG S 15 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU S 20 " --> pdb=" O ARG S 16 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU S 21 " --> pdb=" O LYS S 17 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY S 22 " --> pdb=" O LEU S 18 " (cutoff:3.500A) Processing helix chain 'S' and resid 55 through 63 removed outlier: 5.074A pdb=" N GLN S 61 " --> pdb=" O ALA S 57 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N LYS S 63 " --> pdb=" O ALA S 59 " (cutoff:3.500A) Processing helix chain 'S' and resid 67 through 86 removed outlier: 3.594A pdb=" N ALA S 79 " --> pdb=" O GLY S 75 " (cutoff:3.500A) Processing helix chain 'S' and resid 101 through 114 removed outlier: 3.560A pdb=" N ALA S 105 " --> pdb=" O GLY S 101 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY S 114 " --> pdb=" O ALA S 110 " (cutoff:3.500A) Processing helix chain 'T' and resid 1 through 12 removed outlier: 3.515A pdb=" N LEU T 7 " --> pdb=" O ILE T 3 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLN T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 96 through 103 removed outlier: 4.019A pdb=" N ARG T 100 " --> pdb=" O LEU T 96 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLU T 101 " --> pdb=" O TYR T 97 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ARG T 102 " --> pdb=" O TYR T 98 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N THR T 103 " --> pdb=" O LEU T 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 96 through 103' Processing helix chain 'U' and resid 5 through 21 removed outlier: 4.039A pdb=" N ARG U 10 " --> pdb=" O GLY U 6 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA U 11 " --> pdb=" O VAL U 7 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG U 12 " --> pdb=" O ILE U 8 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS U 15 " --> pdb=" O ALA U 11 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLN U 19 " --> pdb=" O LYS U 15 " (cutoff:3.500A) Processing helix chain 'U' and resid 25 through 30 removed outlier: 4.298A pdb=" N ARG U 29 " --> pdb=" O GLY U 25 " (cutoff:3.500A) Processing helix chain 'U' and resid 38 through 71 removed outlier: 3.707A pdb=" N ARG U 49 " --> pdb=" O ALA U 45 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG U 50 " --> pdb=" O TYR U 46 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LYS U 53 " --> pdb=" O ARG U 49 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ARG U 54 " --> pdb=" O ARG U 50 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG U 57 " --> pdb=" O LYS U 53 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU U 59 " --> pdb=" O GLN U 55 " (cutoff:3.500A) Processing helix chain 'U' and resid 74 through 86 Processing helix chain 'U' and resid 90 through 101 removed outlier: 3.736A pdb=" N ASP U 96 " --> pdb=" O LYS U 92 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA U 98 " --> pdb=" O LEU U 94 " (cutoff:3.500A) Processing helix chain 'U' and resid 102 through 117 Processing helix chain 'W' and resid 13 through 25 removed outlier: 3.533A pdb=" N LEU W 19 " --> pdb=" O GLN W 15 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL W 20 " --> pdb=" O LYS W 16 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU W 23 " --> pdb=" O LEU W 19 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE W 24 " --> pdb=" O VAL W 20 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG W 25 " --> pdb=" O ALA W 21 " (cutoff:3.500A) Processing helix chain 'W' and resid 28 through 39 removed outlier: 4.015A pdb=" N TYR W 38 " --> pdb=" O ASP W 34 " (cutoff:3.500A) Processing helix chain 'W' and resid 41 through 61 removed outlier: 3.870A pdb=" N VAL W 50 " --> pdb=" O LEU W 46 " (cutoff:3.500A) Processing helix chain 'X' and resid 1 through 11 removed outlier: 4.364A pdb=" N GLU X 5 " --> pdb=" O MET X 1 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU X 7 " --> pdb=" O ARG X 3 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU X 8 " --> pdb=" O GLU X 4 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS X 9 " --> pdb=" O GLU X 5 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU X 11 " --> pdb=" O LEU X 7 " (cutoff:3.500A) Processing helix chain 'X' and resid 17 through 26 Processing helix chain 'X' and resid 39 through 50 removed outlier: 3.717A pdb=" N LYS X 49 " --> pdb=" O ALA X 45 " (cutoff:3.500A) Processing helix chain 'Y' and resid 65 through 70 removed outlier: 3.925A pdb=" N VAL Y 69 " --> pdb=" O GLN Y 65 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ALA Y 70 " --> pdb=" O VAL Y 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 65 through 70' Processing helix chain 'Z' and resid 13 through 24 removed outlier: 3.538A pdb=" N ARG Z 19 " --> pdb=" O GLY Z 15 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA Z 22 " --> pdb=" O ARG Z 18 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA Z 23 " --> pdb=" O ARG Z 19 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ASN Z 24 " --> pdb=" O LEU Z 20 " (cutoff:3.500A) Processing helix chain 'Z' and resid 43 through 53 removed outlier: 4.140A pdb=" N VAL Z 47 " --> pdb=" O ASP Z 43 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN Z 49 " --> pdb=" O ASP Z 45 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ALA Z 52 " --> pdb=" O MET Z 48 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LYS Z 53 " --> pdb=" O ASN Z 49 " (cutoff:3.500A) Processing helix chain 'Z' and resid 54 through 59 Processing helix chain '1' and resid 51 through 62 removed outlier: 3.614A pdb=" N VAL 1 57 " --> pdb=" O LYS 1 53 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N GLY 1 62 " --> pdb=" O ILE 1 58 " (cutoff:3.500A) Processing helix chain '1' and resid 63 through 74 Processing helix chain '2' and resid 1 through 8 removed outlier: 3.785A pdb=" N LEU 2 6 " --> pdb=" O LYS 2 2 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ARG 2 7 " --> pdb=" O ALA 2 3 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N GLU 2 8 " --> pdb=" O LYS 2 4 " (cutoff:3.500A) Processing helix chain '2' and resid 9 through 23 Processing helix chain '2' and resid 25 through 35 removed outlier: 4.442A pdb=" N ARG 2 29 " --> pdb=" O GLN 2 25 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA 2 33 " --> pdb=" O ARG 2 29 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER 2 34 " --> pdb=" O MET 2 30 " (cutoff:3.500A) Processing helix chain '2' and resid 39 through 62 removed outlier: 4.463A pdb=" N LEU 2 43 " --> pdb=" O GLN 2 39 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS 2 44 " --> pdb=" O SER 2 40 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL 2 46 " --> pdb=" O LEU 2 42 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG 2 47 " --> pdb=" O LEU 2 43 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS 2 54 " --> pdb=" O VAL 2 50 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR 2 55 " --> pdb=" O ALA 2 51 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS 2 60 " --> pdb=" O LEU 2 56 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N GLY 2 62 " --> pdb=" O ASN 2 58 " (cutoff:3.500A) Processing helix chain '3' and resid 16 through 27 Processing helix chain '3' and resid 40 through 51 Processing helix chain '4' and resid 42 through 54 removed outlier: 3.859A pdb=" N GLN 4 48 " --> pdb=" O PHE 4 44 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA 4 52 " --> pdb=" O GLN 4 48 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N GLY 4 54 " --> pdb=" O ASP 4 50 " (cutoff:3.500A) Processing helix chain '4' and resid 55 through 65 removed outlier: 5.639A pdb=" N ARG 4 59 " --> pdb=" O GLY 4 55 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE 4 60 " --> pdb=" O ARG 4 56 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG 4 63 " --> pdb=" O ARG 4 59 " (cutoff:3.500A) Processing helix chain '5' and resid 8 through 20 removed outlier: 3.694A pdb=" N SER 5 17 " --> pdb=" O GLY 5 13 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N HIS 5 18 " --> pdb=" O MET 5 14 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ASP 5 19 " --> pdb=" O ARG 5 15 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA 5 20 " --> pdb=" O ARG 5 16 " (cutoff:3.500A) Processing helix chain '6' and resid 25 through 30 Proline residue: 6 30 - end of helix Processing helix chain '7' and resid 8 through 16 Processing helix chain '7' and resid 17 through 25 removed outlier: 4.567A pdb=" N THR 7 24 " --> pdb=" O ALA 7 20 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N LYS 7 25 " --> pdb=" O ARG 7 21 " (cutoff:3.500A) Processing helix chain '7' and resid 26 through 38 Processing helix chain '8' and resid 6 through 13 removed outlier: 3.702A pdb=" N ALA 8 10 " --> pdb=" O VAL 8 6 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS 8 11 " --> pdb=" O ARG 8 7 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG 8 12 " --> pdb=" O GLY 8 8 " (cutoff:3.500A) Processing helix chain '8' and resid 31 through 36 removed outlier: 5.042A pdb=" N LYS 8 35 " --> pdb=" O ILE 8 31 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N ALA 8 36 " --> pdb=" O LEU 8 32 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 31 through 36' Processing helix chain '8' and resid 37 through 44 removed outlier: 3.973A pdb=" N HIS 8 42 " --> pdb=" O LYS 8 38 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU 8 43 " --> pdb=" O ARG 8 39 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG 8 44 " --> pdb=" O LYS 8 40 " (cutoff:3.500A) Processing helix chain '8' and resid 50 through 62 removed outlier: 4.447A pdb=" N GLY 8 55 " --> pdb=" O LYS 8 51 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N LEU 8 56 " --> pdb=" O GLY 8 52 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL 8 57 " --> pdb=" O ASP 8 53 " (cutoff:3.500A) Proline residue: 8 62 - end of helix Processing helix chain '8' and resid 25 through 30 removed outlier: 4.362A pdb=" N LEU 8 28 " --> pdb=" O HIS 8 25 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ARG 8 29 " --> pdb=" O ALA 8 26 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N HIS 8 30 " --> pdb=" O ASN 8 27 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 25 through 30' Processing helix chain 'b' and resid 43 through 63 Proline residue: b 47 - end of helix removed outlier: 3.850A pdb=" N SER b 61 " --> pdb=" O ASN b 57 " (cutoff:3.500A) Processing helix chain 'b' and resid 73 through 87 removed outlier: 4.042A pdb=" N GLU b 77 " --> pdb=" O ARG b 73 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA b 78 " --> pdb=" O ALA b 74 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL b 79 " --> pdb=" O ALA b 75 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER b 85 " --> pdb=" O ASP b 81 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N CYS b 86 " --> pdb=" O ALA b 82 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP b 87 " --> pdb=" O ALA b 83 " (cutoff:3.500A) Processing helix chain 'b' and resid 102 through 123 removed outlier: 3.568A pdb=" N VAL b 106 " --> pdb=" O ASN b 102 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLN b 108 " --> pdb=" O LYS b 104 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER b 109 " --> pdb=" O THR b 105 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN b 119 " --> pdb=" O ASP b 115 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER b 120 " --> pdb=" O LEU b 116 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN b 121 " --> pdb=" O GLU b 117 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP b 122 " --> pdb=" O THR b 118 " (cutoff:3.500A) Processing helix chain 'b' and resid 129 through 147 removed outlier: 3.895A pdb=" N SER b 146 " --> pdb=" O LYS b 142 " (cutoff:3.500A) Processing helix chain 'b' and resid 164 through 169 removed outlier: 3.806A pdb=" N GLU b 168 " --> pdb=" O ASP b 164 " (cutoff:3.500A) Processing helix chain 'b' and resid 170 through 179 removed outlier: 3.712A pdb=" N ALA b 175 " --> pdb=" O ALA b 171 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN b 177 " --> pdb=" O LYS b 173 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LEU b 178 " --> pdb=" O GLU b 174 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N GLY b 179 " --> pdb=" O ALA b 175 " (cutoff:3.500A) Processing helix chain 'b' and resid 205 through 225 removed outlier: 3.689A pdb=" N VAL b 209 " --> pdb=" O ALA b 205 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR b 210 " --> pdb=" O ILE b 206 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU b 211 " --> pdb=" O ARG b 207 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA b 218 " --> pdb=" O GLY b 214 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY b 223 " --> pdb=" O THR b 219 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG b 224 " --> pdb=" O VAL b 220 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N SER b 225 " --> pdb=" O ARG b 221 " (cutoff:3.500A) Processing helix chain 'c' and resid 5 through 12 removed outlier: 3.576A pdb=" N ILE c 9 " --> pdb=" O HIS c 5 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG c 10 " --> pdb=" O PRO c 6 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU c 11 " --> pdb=" O ASN c 7 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N GLY c 12 " --> pdb=" O GLY c 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 5 through 12' Processing helix chain 'c' and resid 26 through 47 removed outlier: 4.711A pdb=" N ASP c 30 " --> pdb=" O LYS c 26 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASP c 33 " --> pdb=" O ALA c 29 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER c 34 " --> pdb=" O ASP c 30 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL c 38 " --> pdb=" O SER c 34 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ARG c 39 " --> pdb=" O ASP c 35 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLN c 40 " --> pdb=" O PHE c 36 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N TYR c 41 " --> pdb=" O LYS c 37 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU c 42 " --> pdb=" O VAL c 38 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 77 removed outlier: 3.705A pdb=" N VAL c 75 " --> pdb=" O ARG c 71 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 94 removed outlier: 4.091A pdb=" N GLU c 84 " --> pdb=" O GLY c 80 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS c 85 " --> pdb=" O GLU c 81 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS c 88 " --> pdb=" O GLU c 84 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA c 91 " --> pdb=" O ARG c 87 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP c 92 " --> pdb=" O LYS c 88 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ILE c 93 " --> pdb=" O VAL c 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 111 through 126 removed outlier: 3.566A pdb=" N VAL c 115 " --> pdb=" O ASP c 111 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN c 122 " --> pdb=" O SER c 118 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU c 123 " --> pdb=" O ILE c 119 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLU c 124 " --> pdb=" O THR c 120 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ARG c 125 " --> pdb=" O SER c 121 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG c 126 " --> pdb=" O GLN c 122 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 144 removed outlier: 3.723A pdb=" N ARG c 135 " --> pdb=" O ARG c 131 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA c 136 " --> pdb=" O ALA c 132 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL c 137 " --> pdb=" O MET c 133 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA c 140 " --> pdb=" O ALA c 136 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU c 143 " --> pdb=" O ASN c 139 " (cutoff:3.500A) Processing helix chain 'd' and resid 6 through 15 removed outlier: 3.675A pdb=" N SER d 11 " --> pdb=" O LYS d 7 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ARG d 12 " --> pdb=" O LEU d 8 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG d 13 " --> pdb=" O LYS d 9 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU d 14 " --> pdb=" O LEU d 10 " (cutoff:3.500A) Processing helix chain 'd' and resid 48 through 65 removed outlier: 4.244A pdb=" N GLN d 53 " --> pdb=" O ASP d 49 " (cutoff:3.500A) Processing helix chain 'd' and resid 67 through 82 removed outlier: 3.689A pdb=" N ASN d 73 " --> pdb=" O ARG d 69 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR d 74 " --> pdb=" O GLN d 70 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG d 80 " --> pdb=" O LYS d 76 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU d 81 " --> pdb=" O GLU d 77 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N LYS d 82 " --> pdb=" O ALA d 78 " (cutoff:3.500A) Processing helix chain 'd' and resid 84 through 96 removed outlier: 3.501A pdb=" N ASN d 88 " --> pdb=" O ASN d 84 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU d 90 " --> pdb=" O GLY d 86 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 105 removed outlier: 3.691A pdb=" N GLY d 105 " --> pdb=" O VAL d 101 " (cutoff:3.500A) Processing helix chain 'd' and resid 109 through 120 removed outlier: 3.508A pdb=" N VAL d 117 " --> pdb=" O ALA d 113 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LYS d 120 " --> pdb=" O LEU d 116 " (cutoff:3.500A) Processing helix chain 'd' and resid 151 through 165 removed outlier: 5.481A pdb=" N LYS d 155 " --> pdb=" O GLN d 151 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA d 156 " --> pdb=" O SER d 152 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA d 157 " --> pdb=" O ARG d 153 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU d 158 " --> pdb=" O VAL d 154 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLU d 159 " --> pdb=" O LYS d 155 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU d 160 " --> pdb=" O ALA d 156 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA d 161 " --> pdb=" O ALA d 157 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU d 162 " --> pdb=" O LEU d 158 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLN d 163 " --> pdb=" O GLU d 159 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N GLU d 165 " --> pdb=" O ALA d 161 " (cutoff:3.500A) Processing helix chain 'd' and resid 186 through 191 removed outlier: 5.312A pdb=" N SER d 191 " --> pdb=" O ARG d 187 " (cutoff:3.500A) Processing helix chain 'd' and resid 195 through 205 removed outlier: 4.058A pdb=" N ILE d 199 " --> pdb=" O ASN d 195 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL d 200 " --> pdb=" O GLU d 196 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU d 201 " --> pdb=" O HIS d 197 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU d 202 " --> pdb=" O LEU d 198 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR d 203 " --> pdb=" O ILE d 199 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS d 205 " --> pdb=" O GLU d 201 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 70 removed outlier: 3.597A pdb=" N MET e 63 " --> pdb=" O ILE e 59 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU e 64 " --> pdb=" O GLN e 60 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS e 65 " --> pdb=" O LYS e 61 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG e 67 " --> pdb=" O MET e 63 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG e 68 " --> pdb=" O GLU e 64 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 118 removed outlier: 5.962A pdb=" N ALA e 112 " --> pdb=" O GLY e 108 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL e 113 " --> pdb=" O ALA e 109 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU e 114 " --> pdb=" O MET e 110 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA e 117 " --> pdb=" O VAL e 113 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY e 118 " --> pdb=" O LEU e 114 " (cutoff:3.500A) Processing helix chain 'e' and resid 131 through 147 removed outlier: 3.814A pdb=" N VAL e 136 " --> pdb=" O PRO e 132 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ARG e 137 " --> pdb=" O ILE e 133 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ASN e 147 " --> pdb=" O LEU e 143 " (cutoff:3.500A) Processing helix chain 'e' and resid 148 through 156 removed outlier: 4.095A pdb=" N ALA e 154 " --> pdb=" O GLU e 150 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS e 155 " --> pdb=" O MET e 151 " (cutoff:3.500A) Processing helix chain 'e' and resid 159 through 165 removed outlier: 3.568A pdb=" N ILE e 163 " --> pdb=" O SER e 159 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU e 164 " --> pdb=" O VAL e 160 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY e 165 " --> pdb=" O GLU e 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 159 through 165' Processing helix chain 'f' and resid 11 through 19 removed outlier: 4.434A pdb=" N GLU f 16 " --> pdb=" O PRO f 12 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N GLN f 17 " --> pdb=" O ASP f 13 " (cutoff:3.500A) Proline residue: f 19 - end of helix Processing helix chain 'f' and resid 20 through 33 removed outlier: 3.672A pdb=" N ARG f 24 " --> pdb=" O GLY f 20 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE f 29 " --> pdb=" O TYR f 25 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 81 removed outlier: 3.834A pdb=" N GLU f 73 " --> pdb=" O GLU f 69 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR f 77 " --> pdb=" O GLU f 73 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE f 78 " --> pdb=" O LEU f 74 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG f 79 " --> pdb=" O GLU f 75 " (cutoff:3.500A) Processing helix chain 'g' and resid 19 through 30 removed outlier: 4.415A pdb=" N PHE g 25 " --> pdb=" O LEU g 21 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL g 26 " --> pdb=" O LEU g 22 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASN g 27 " --> pdb=" O ALA g 23 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE g 28 " --> pdb=" O LYS g 24 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEU g 29 " --> pdb=" O PHE g 25 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET g 30 " --> pdb=" O VAL g 26 " (cutoff:3.500A) Processing helix chain 'g' and resid 34 through 54 removed outlier: 4.173A pdb=" N LEU g 46 " --> pdb=" O VAL g 42 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU g 47 " --> pdb=" O TYR g 43 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR g 48 " --> pdb=" O SER g 44 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 69 removed outlier: 3.510A pdb=" N GLU g 62 " --> pdb=" O LEU g 58 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ALA g 64 " --> pdb=" O ALA g 60 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU g 66 " --> pdb=" O GLU g 62 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASN g 67 " --> pdb=" O VAL g 63 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL g 68 " --> pdb=" O ALA g 64 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 111 removed outlier: 3.963A pdb=" N ASN g 96 " --> pdb=" O PRO g 92 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA g 97 " --> pdb=" O VAL g 93 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA g 99 " --> pdb=" O ARG g 95 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG g 101 " --> pdb=" O ALA g 97 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS g 109 " --> pdb=" O GLU g 105 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG g 110 " --> pdb=" O ALA g 106 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N GLY g 111 " --> pdb=" O ALA g 107 " (cutoff:3.500A) Processing helix chain 'g' and resid 114 through 129 removed outlier: 4.279A pdb=" N GLU g 128 " --> pdb=" O SER g 124 " (cutoff:3.500A) Processing helix chain 'g' and resid 131 through 145 removed outlier: 3.657A pdb=" N LYS g 135 " --> pdb=" O GLY g 131 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS g 136 " --> pdb=" O THR g 132 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG g 137 " --> pdb=" O ALA g 133 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU g 145 " --> pdb=" O HIS g 141 " (cutoff:3.500A) Processing helix chain 'h' and resid 4 through 20 removed outlier: 3.600A pdb=" N ILE h 13 " --> pdb=" O MET h 9 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY h 16 " --> pdb=" O ARG h 12 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA h 18 " --> pdb=" O ARG h 14 " (cutoff:3.500A) Processing helix chain 'h' and resid 29 through 43 removed outlier: 3.563A pdb=" N ILE h 35 " --> pdb=" O LEU h 31 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL h 38 " --> pdb=" O ALA h 34 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU h 42 " --> pdb=" O VAL h 38 " (cutoff:3.500A) Processing helix chain 'h' and resid 111 through 119 removed outlier: 3.574A pdb=" N ARG h 116 " --> pdb=" O ASP h 112 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN h 117 " --> pdb=" O ARG h 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 33 through 38 Processing helix chain 'i' and resid 45 through 55 Proline residue: i 50 - end of helix removed outlier: 4.867A pdb=" N LEU i 53 " --> pdb=" O GLN i 49 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N VAL i 54 " --> pdb=" O PRO i 50 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASP i 55 " --> pdb=" O LEU i 51 " (cutoff:3.500A) Processing helix chain 'i' and resid 70 through 86 removed outlier: 3.783A pdb=" N GLN i 74 " --> pdb=" O GLY i 70 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR i 83 " --> pdb=" O ARG i 79 " (cutoff:3.500A) Processing helix chain 'i' and resid 91 through 98 removed outlier: 4.918A pdb=" N GLU i 96 " --> pdb=" O SER i 92 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 30 removed outlier: 3.666A pdb=" N ILE j 18 " --> pdb=" O ASP j 14 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASP j 19 " --> pdb=" O HIS j 15 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN j 20 " --> pdb=" O ARG j 16 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA j 21 " --> pdb=" O LEU j 17 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE j 25 " --> pdb=" O ALA j 21 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA j 29 " --> pdb=" O ILE j 25 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 90 removed outlier: 3.832A pdb=" N ASP j 85 " --> pdb=" O GLU j 81 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ALA j 86 " --> pdb=" O LYS j 82 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N MET j 88 " --> pdb=" O VAL j 84 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ARG j 89 " --> pdb=" O ASP j 85 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU j 90 " --> pdb=" O ALA j 86 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 50 removed outlier: 4.539A pdb=" N GLY k 50 " --> pdb=" O ALA k 46 " (cutoff:3.500A) Processing helix chain 'k' and resid 53 through 58 removed outlier: 4.193A pdb=" N SER k 57 " --> pdb=" O GLY k 53 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N THR k 58 " --> pdb=" O SER k 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 53 through 58' Processing helix chain 'k' and resid 59 through 72 removed outlier: 3.561A pdb=" N ALA k 66 " --> pdb=" O ALA k 62 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU k 67 " --> pdb=" O GLN k 63 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ALA k 72 " --> pdb=" O ARG k 68 " (cutoff:3.500A) Processing helix chain 'k' and resid 92 through 103 removed outlier: 3.757A pdb=" N ILE k 96 " --> pdb=" O ARG k 92 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ARG k 97 " --> pdb=" O GLU k 93 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA k 98 " --> pdb=" O SER k 94 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU k 99 " --> pdb=" O THR k 95 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN k 100 " --> pdb=" O ILE k 96 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY k 103 " --> pdb=" O LEU k 99 " (cutoff:3.500A) Processing helix chain 'l' and resid 2 through 10 removed outlier: 3.902A pdb=" N LEU l 6 " --> pdb=" O THR l 2 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL l 7 " --> pdb=" O VAL l 3 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG l 8 " --> pdb=" O ASN l 4 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS l 9 " --> pdb=" O GLN l 5 " (cutoff:3.500A) Proline residue: l 10 - end of helix No H-bonds generated for 'chain 'l' and resid 2 through 10' Processing helix chain 'l' and resid 112 through 117 removed outlier: 5.233A pdb=" N TYR l 116 " --> pdb=" O ALA l 112 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY l 117 " --> pdb=" O ARG l 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 112 through 117' Processing helix chain 'm' and resid 13 through 22 removed outlier: 3.606A pdb=" N LEU m 18 " --> pdb=" O ALA m 14 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR m 19 " --> pdb=" O VAL m 15 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER m 20 " --> pdb=" O ILE m 16 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE m 21 " --> pdb=" O ALA m 17 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N TYR m 22 " --> pdb=" O LEU m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 25 through 37 Processing helix chain 'm' and resid 43 through 48 removed outlier: 5.130A pdb=" N SER m 48 " --> pdb=" O ILE m 44 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 63 removed outlier: 4.434A pdb=" N ASP m 53 " --> pdb=" O GLU m 49 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N THR m 54 " --> pdb=" O GLY m 50 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU m 55 " --> pdb=" O GLN m 51 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP m 57 " --> pdb=" O ASP m 53 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU m 58 " --> pdb=" O THR m 54 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS m 61 " --> pdb=" O ASP m 57 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE m 62 " --> pdb=" O GLU m 58 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N VAL m 63 " --> pdb=" O VAL m 59 " (cutoff:3.500A) Processing helix chain 'm' and resid 65 through 83 removed outlier: 3.520A pdb=" N ARG m 69 " --> pdb=" O GLU m 65 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU m 71 " --> pdb=" O ASP m 67 " (cutoff:3.500A) Processing helix chain 'm' and resid 84 through 93 removed outlier: 4.319A pdb=" N HIS m 90 " --> pdb=" O ARG m 86 " (cutoff:3.500A) Processing helix chain 'm' and resid 105 through 110 Processing helix chain 'o' and resid 3 through 15 removed outlier: 3.649A pdb=" N ALA o 8 " --> pdb=" O THR o 4 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS o 9 " --> pdb=" O GLU o 5 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE o 10 " --> pdb=" O ALA o 6 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU o 13 " --> pdb=" O LYS o 9 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE o 14 " --> pdb=" O ILE o 10 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY o 15 " --> pdb=" O VAL o 11 " (cutoff:3.500A) Processing helix chain 'o' and resid 23 through 42 removed outlier: 3.845A pdb=" N ALA o 29 " --> pdb=" O GLU o 25 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU o 31 " --> pdb=" O GLN o 27 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLY o 40 " --> pdb=" O ASN o 36 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N HIS o 41 " --> pdb=" O HIS o 37 " (cutoff:3.500A) Processing helix chain 'o' and resid 48 through 73 removed outlier: 3.630A pdb=" N ARG o 52 " --> pdb=" O ASP o 48 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY o 54 " --> pdb=" O HIS o 50 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET o 58 " --> pdb=" O GLY o 54 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG o 71 " --> pdb=" O ASP o 67 " (cutoff:3.500A) Processing helix chain 'o' and resid 74 through 85 removed outlier: 3.823A pdb=" N GLN o 79 " --> pdb=" O ALA o 75 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU o 80 " --> pdb=" O ARG o 76 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG o 83 " --> pdb=" O GLN o 79 " (cutoff:3.500A) Processing helix chain 'p' and resid 53 through 64 removed outlier: 3.683A pdb=" N ILE p 57 " --> pdb=" O ASP p 53 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N HIS p 59 " --> pdb=" O ASP p 55 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY p 62 " --> pdb=" O ALA p 58 " (cutoff:3.500A) Processing helix chain 'p' and resid 68 through 79 removed outlier: 3.647A pdb=" N LEU p 74 " --> pdb=" O ARG p 70 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN p 79 " --> pdb=" O ILE p 75 " (cutoff:3.500A) Processing helix chain 'r' and resid 11 through 16 removed outlier: 6.089A pdb=" N GLU r 15 " --> pdb=" O ARG r 11 " (cutoff:3.500A) Processing helix chain 'r' and resid 24 through 33 removed outlier: 4.167A pdb=" N ASN r 30 " --> pdb=" O ALA r 26 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N TYR r 31 " --> pdb=" O THR r 27 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE r 32 " --> pdb=" O LEU r 28 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N THR r 33 " --> pdb=" O LYS r 29 " (cutoff:3.500A) Processing helix chain 'r' and resid 40 through 45 removed outlier: 3.625A pdb=" N THR r 44 " --> pdb=" O PRO r 40 " (cutoff:3.500A) Processing helix chain 'r' and resid 47 through 65 removed outlier: 4.031A pdb=" N GLN r 53 " --> pdb=" O LYS r 49 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA r 61 " --> pdb=" O ALA r 57 " (cutoff:3.500A) Processing helix chain 't' and resid 6 through 41 removed outlier: 4.746A pdb=" N ALA t 10 " --> pdb=" O ALA t 6 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE t 11 " --> pdb=" O LYS t 7 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS t 18 " --> pdb=" O GLU t 14 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N HIS t 19 " --> pdb=" O LYS t 15 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG t 23 " --> pdb=" O HIS t 19 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE t 30 " --> pdb=" O MET t 26 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL t 34 " --> pdb=" O PHE t 30 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR t 35 " --> pdb=" O ILE t 31 " (cutoff:3.500A) Processing helix chain 't' and resid 42 through 64 Proline residue: t 55 - end of helix removed outlier: 3.634A pdb=" N ARG t 59 " --> pdb=" O PRO t 55 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA t 61 " --> pdb=" O VAL t 57 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA t 62 " --> pdb=" O ASP t 58 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS t 63 " --> pdb=" O ARG t 59 " (cutoff:3.500A) Processing helix chain 't' and resid 67 through 86 removed outlier: 6.583A pdb=" N ALA t 71 " --> pdb=" O HIS t 67 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ALA t 72 " --> pdb=" O LYS t 68 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS t 74 " --> pdb=" O LYS t 70 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU t 78 " --> pdb=" O HIS t 74 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR t 79 " --> pdb=" O LYS t 75 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS t 84 " --> pdb=" O ALA t 80 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU t 85 " --> pdb=" O GLN t 81 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA t 86 " --> pdb=" O ILE t 82 " (cutoff:3.500A) Processing helix chain 'u' and resid 16 through 23 removed outlier: 4.417A pdb=" N ARG u 20 " --> pdb=" O ARG u 16 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER u 21 " --> pdb=" O ARG u 17 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N CYS u 22 " --> pdb=" O PHE u 18 " (cutoff:3.500A) Processing helix chain 'u' and resid 26 through 32 removed outlier: 6.650A pdb=" N GLU u 30 " --> pdb=" O GLY u 26 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL u 31 " --> pdb=" O VAL u 27 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ARG u 32 " --> pdb=" O LEU u 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 26 through 32' Processing helix chain 'u' and resid 37 through 61 removed outlier: 4.138A pdb=" N THR u 41 " --> pdb=" O TYR u 37 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR u 42 " --> pdb=" O GLU u 38 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS u 45 " --> pdb=" O THR u 41 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA u 51 " --> pdb=" O ALA u 47 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG u 54 " --> pdb=" O SER u 50 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS u 58 " --> pdb=" O ARG u 54 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU u 59 " --> pdb=" O HIS u 55 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA u 60 " --> pdb=" O ALA u 56 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 21 removed outlier: 3.819A pdb=" N GLN J 9 " --> pdb=" O LEU J 5 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE J 11 " --> pdb=" O ASP J 7 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU J 14 " --> pdb=" O ALA J 10 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU J 17 " --> pdb=" O ALA J 13 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS J 20 " --> pdb=" O SER J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 33 through 48 removed outlier: 3.761A pdb=" N THR J 39 " --> pdb=" O VAL J 35 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU J 40 " --> pdb=" O ASP J 36 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU J 41 " --> pdb=" O LYS J 37 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ARG J 42 " --> pdb=" O MET J 38 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA J 44 " --> pdb=" O GLU J 40 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY J 45 " --> pdb=" O LEU J 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 71 removed outlier: 4.047A pdb=" N GLY J 66 " --> pdb=" O ARG J 62 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR J 67 " --> pdb=" O ALA J 63 " (cutoff:3.500A) Proline residue: J 68 - end of helix removed outlier: 3.727A pdb=" N CYS J 71 " --> pdb=" O THR J 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 62 through 71' Processing helix chain 'J' and resid 72 through 79 removed outlier: 4.660A pdb=" N PHE J 76 " --> pdb=" O LEU J 72 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL J 77 " --> pdb=" O LYS J 73 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY J 78 " --> pdb=" O ASP J 74 " (cutoff:3.500A) Proline residue: J 79 - end of helix No H-bonds generated for 'chain 'J' and resid 72 through 79' Processing helix chain 'J' and resid 94 through 106 removed outlier: 3.890A pdb=" N GLU J 98 " --> pdb=" O ARG J 94 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE J 99 " --> pdb=" O LEU J 95 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ALA J 100 " --> pdb=" O PHE J 96 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN J 103 " --> pdb=" O PHE J 99 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA J 104 " --> pdb=" O ALA J 100 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE J 106 " --> pdb=" O ALA J 102 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 114 removed outlier: 6.485A pdb=" N ALA J 112 " --> pdb=" O LYS J 109 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU J 114 " --> pdb=" O ALA J 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 29 removed outlier: 4.074A pdb=" N GLY K 28 " --> pdb=" O GLY K 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 33 through 49 removed outlier: 4.318A pdb=" N PHE K 37 " --> pdb=" O ASN K 33 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N CYS K 38 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA K 40 " --> pdb=" O GLU K 36 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N PHE K 41 " --> pdb=" O PHE K 37 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ALA K 43 " --> pdb=" O LYS K 39 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LYS K 44 " --> pdb=" O ALA K 40 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N THR K 45 " --> pdb=" O PHE K 41 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N SER K 47 " --> pdb=" O ALA K 43 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE K 48 " --> pdb=" O LYS K 44 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLU K 49 " --> pdb=" O THR K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 74 through 83 removed outlier: 4.675A pdb=" N LYS K 80 " --> pdb=" O ALA K 76 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LYS K 81 " --> pdb=" O VAL K 77 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA K 82 " --> pdb=" O LEU K 78 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ALA K 83 " --> pdb=" O LEU K 79 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 113 removed outlier: 4.164A pdb=" N GLU K 107 " --> pdb=" O ALA K 103 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLN K 110 " --> pdb=" O GLN K 106 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N THR K 111 " --> pdb=" O GLU K 107 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS K 112 " --> pdb=" O ILE K 108 " (cutoff:3.500A) Processing helix chain 'K' and resid 120 through 136 removed outlier: 3.822A pdb=" N ARG K 126 " --> pdb=" O GLU K 122 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER K 127 " --> pdb=" O ALA K 123 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR K 131 " --> pdb=" O SER K 127 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA K 132 " --> pdb=" O ILE K 128 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG K 133 " --> pdb=" O GLU K 129 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER K 134 " --> pdb=" O GLY K 130 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N MET K 135 " --> pdb=" O THR K 131 " (cutoff:3.500A) Processing helix chain 'n' and resid 2 through 20 removed outlier: 3.842A pdb=" N ARG n 12 " --> pdb=" O ARG n 8 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP n 17 " --> pdb=" O VAL n 13 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS n 18 " --> pdb=" O ALA n 14 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR n 19 " --> pdb=" O LEU n 15 " (cutoff:3.500A) Processing helix chain 'n' and resid 24 through 29 Processing helix chain 'n' and resid 38 through 51 removed outlier: 3.855A pdb=" N TRP n 42 " --> pdb=" O ASP n 38 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN n 43 " --> pdb=" O GLU n 39 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA n 44 " --> pdb=" O ASP n 40 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLN n 49 " --> pdb=" O VAL n 45 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N THR n 50 " --> pdb=" O LEU n 46 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU n 51 " --> pdb=" O LYS n 47 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 61 removed outlier: 3.555A pdb=" N GLN n 60 " --> pdb=" O SER n 56 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ARG n 61 " --> pdb=" O PRO n 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 56 through 61' Processing helix chain 'n' and resid 80 through 91 removed outlier: 3.687A pdb=" N ARG n 85 " --> pdb=" O ARG n 81 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG n 90 " --> pdb=" O GLU n 86 " (cutoff:3.500A) Processing helix chain 's' and resid 11 through 25 removed outlier: 3.524A pdb=" N LEU s 15 " --> pdb=" O ASP s 11 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS s 16 " --> pdb=" O LEU s 12 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS s 17 " --> pdb=" O HIS s 13 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU s 23 " --> pdb=" O GLU s 19 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER s 24 " --> pdb=" O LYS s 20 " (cutoff:3.500A) Processing helix chain 's' and resid 69 through 75 removed outlier: 4.497A pdb=" N PHE s 73 " --> pdb=" O LYS s 69 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA s 74 " --> pdb=" O LEU s 70 " (cutoff:3.500A) Proline residue: s 75 - end of helix No H-bonds generated for 'chain 's' and resid 69 through 75' Processing helix chain 'z' and resid 17 through 29 removed outlier: 3.533A pdb=" N ALA z 22 " --> pdb=" O GLU z 18 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY z 25 " --> pdb=" O ILE z 21 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR z 27 " --> pdb=" O SER z 23 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N SER z 28 " --> pdb=" O LEU z 24 " (cutoff:3.500A) Processing helix chain 'z' and resid 30 through 49 removed outlier: 3.630A pdb=" N ALA z 36 " --> pdb=" O CYS z 32 " (cutoff:3.500A) Processing helix chain 'z' and resid 58 through 74 removed outlier: 4.142A pdb=" N MET z 62 " --> pdb=" O ARG z 58 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL z 63 " --> pdb=" O GLY z 59 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE z 73 " --> pdb=" O LEU z 69 " (cutoff:3.500A) Processing helix chain 'z' and resid 76 through 92 removed outlier: 3.767A pdb=" N PHE z 82 " --> pdb=" O ALA z 78 " (cutoff:3.500A) Proline residue: z 83 - end of helix removed outlier: 4.944A pdb=" N ALA z 87 " --> pdb=" O PRO z 83 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ASN z 88 " --> pdb=" O LEU z 84 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL z 89 " --> pdb=" O ALA z 85 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N VAL z 90 " --> pdb=" O ASP z 86 " (cutoff:3.500A) Processing helix chain 'z' and resid 95 through 103 removed outlier: 3.834A pdb=" N SER z 102 " --> pdb=" O SER z 98 " (cutoff:3.500A) Processing helix chain 'z' and resid 104 through 118 removed outlier: 3.832A pdb=" N GLN z 118 " --> pdb=" O ALA z 114 " (cutoff:3.500A) Processing helix chain 'z' and resid 135 through 141 removed outlier: 4.339A pdb=" N LEU z 139 " --> pdb=" O VAL z 135 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ALA z 141 " --> pdb=" O ARG z 137 " (cutoff:3.500A) Processing helix chain 'z' and resid 143 through 161 removed outlier: 4.190A pdb=" N ARG z 147 " --> pdb=" O VAL z 143 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU z 160 " --> pdb=" O ARG z 156 " (cutoff:3.500A) Processing helix chain 'z' and resid 168 through 188 removed outlier: 4.827A pdb=" N ILE z 181 " --> pdb=" O GLU z 177 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N TYR z 182 " --> pdb=" O CYS z 178 " (cutoff:3.500A) Proline residue: z 184 - end of helix Processing helix chain 'z' and resid 189 through 205 removed outlier: 4.146A pdb=" N LYS z 195 " --> pdb=" O ILE z 191 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE z 203 " --> pdb=" O GLU z 199 " (cutoff:3.500A) Processing helix chain 'z' and resid 206 through 220 removed outlier: 3.771A pdb=" N LEU z 217 " --> pdb=" O ARG z 213 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU z 218 " --> pdb=" O ILE z 214 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N HIS z 219 " --> pdb=" O ALA z 215 " (cutoff:3.500A) Processing helix chain 'z' and resid 221 through 242 removed outlier: 3.739A pdb=" N LYS z 241 " --> pdb=" O ARG z 237 " (cutoff:3.500A) Processing helix chain 'z' and resid 253 through 265 removed outlier: 3.604A pdb=" N SER z 258 " --> pdb=" O LYS z 254 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET z 263 " --> pdb=" O ILE z 259 " (cutoff:3.500A) Processing helix chain 'z' and resid 270 through 276 removed outlier: 4.307A pdb=" N PHE z 274 " --> pdb=" O PHE z 270 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N VAL z 276 " --> pdb=" O GLU z 272 " (cutoff:3.500A) Processing helix chain 'z' and resid 283 through 299 removed outlier: 3.618A pdb=" N HIS z 297 " --> pdb=" O LEU z 293 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR z 298 " --> pdb=" O GLY z 294 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N HIS z 299 " --> pdb=" O ILE z 295 " (cutoff:3.500A) Processing helix chain 'z' and resid 307 through 312 Processing helix chain 'z' and resid 337 through 346 removed outlier: 3.638A pdb=" N MET z 343 " --> pdb=" O ARG z 339 " (cutoff:3.500A) Processing helix chain 'z' and resid 372 through 380 removed outlier: 3.695A pdb=" N TRP z 376 " --> pdb=" O ASP z 372 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG z 378 " --> pdb=" O ILE z 374 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU z 380 " --> pdb=" O TRP z 376 " (cutoff:3.500A) Processing helix chain 'z' and resid 423 through 432 removed outlier: 3.533A pdb=" N ALA z 428 " --> pdb=" O PRO z 424 " (cutoff:3.500A) Processing helix chain 'z' and resid 433 through 439 removed outlier: 3.604A pdb=" N HIS z 437 " --> pdb=" O SER z 433 " (cutoff:3.500A) Processing helix chain 'z' and resid 678 through 691 removed outlier: 5.825A pdb=" N LYS z 691 " --> pdb=" O LEU z 687 " (cutoff:3.500A) Processing helix chain 'z' and resid 716 through 731 removed outlier: 3.581A pdb=" N LEU z 722 " --> pdb=" O ASN z 718 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASN z 730 " --> pdb=" O LEU z 726 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N GLN z 731 " --> pdb=" O GLY z 727 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'D' and resid 74 through 77 removed outlier: 4.824A pdb=" N ASP D 113 " --> pdb=" O VAL D 77 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'D' and resid 79 through 82 removed outlier: 3.826A pdb=" N ARG D 79 " --> pdb=" O LEU D 92 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ASN D 89 " --> pdb=" O ALA D 105 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG D 101 " --> pdb=" O VAL D 93 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'D' and resid 170 through 175 removed outlier: 3.835A pdb=" N LEU D 175 " --> pdb=" O GLU D 179 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLU D 179 " --> pdb=" O LEU D 175 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.651A pdb=" N LEU E 4 " --> pdb=" O VAL E 203 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ASP E 200 " --> pdb=" O THR E 112 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N THR E 112 " --> pdb=" O ASP E 200 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL E 109 " --> pdb=" O VAL E 172 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL E 172 " --> pdb=" O VAL E 109 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N SER E 113 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLU E 168 " --> pdb=" O SER E 113 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'E' and resid 11 through 16 removed outlier: 4.066A pdb=" N VAL E 20 " --> pdb=" O THR E 16 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU E 186 " --> pdb=" O ASP E 181 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG E 179 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'E' and resid 37 through 40 removed outlier: 6.512A pdb=" N LYS E 38 " --> pdb=" O ARG E 46 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ARG E 46 " --> pdb=" O LYS E 38 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU E 40 " --> pdb=" O GLY E 44 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'F' and resid 117 through 120 removed outlier: 3.741A pdb=" N VAL F 187 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE F 149 " --> pdb=" O VAL F 187 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL F 146 " --> pdb=" O LYS F 166 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP F 168 " --> pdb=" O VAL F 146 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'G' and resid 64 through 68 removed outlier: 3.796A pdb=" N LEU G 90 " --> pdb=" O ILE G 33 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE G 33 " --> pdb=" O LEU G 90 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS G 32 " --> pdb=" O THR G 156 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN G 36 " --> pdb=" O ASP G 152 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N THR G 157 " --> pdb=" O GLY G 125 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N GLY G 125 " --> pdb=" O THR G 157 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'H' and resid 22 through 26 removed outlier: 3.554A pdb=" N ARG H 34 " --> pdb=" O ILE H 23 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU H 32 " --> pdb=" O ILE H 25 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'H' and resid 93 through 97 removed outlier: 3.677A pdb=" N ALA H 96 " --> pdb=" O ASN H 103 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'H' and resid 120 through 124 removed outlier: 5.848A pdb=" N THR H 128 " --> pdb=" O LEU H 88 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS H 84 " --> pdb=" O LEU H 132 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY H 134 " --> pdb=" O PHE H 82 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE H 82 " --> pdb=" O GLY H 134 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'I' and resid 2 through 6 removed outlier: 5.859A pdb=" N GLN I 2 " --> pdb=" O ALA I 39 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ALA I 39 " --> pdb=" O GLN I 2 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LYS I 35 " --> pdb=" O LEU I 6 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'I' and resid 76 through 80 removed outlier: 7.229A pdb=" N GLU I 76 " --> pdb=" O LYS I 141 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL I 78 " --> pdb=" O ILE I 143 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE I 80 " --> pdb=" O ASN I 145 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE I 132 " --> pdb=" O ALA I 140 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL I 142 " --> pdb=" O VAL I 130 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'N' and resid 52 through 57 removed outlier: 4.278A pdb=" N LEU N 57 " --> pdb=" O VAL N 18 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN N 138 " --> pdb=" O TRP N 15 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ASP N 19 " --> pdb=" O LEU N 140 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'O' and resid 6 through 9 removed outlier: 3.829A pdb=" N THR O 6 " --> pdb=" O CYS O 21 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'O' and resid 38 through 41 removed outlier: 4.284A pdb=" N LYS O 59 " --> pdb=" O LEU O 87 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'Q' and resid 62 through 66 removed outlier: 3.597A pdb=" N ARG Q 66 " --> pdb=" O LEU Q 102 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N LEU Q 102 " --> pdb=" O ARG Q 66 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N TYR Q 103 " --> pdb=" O LEU Q 33 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N SER Q 30 " --> pdb=" O LYS Q 133 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY Q 32 " --> pdb=" O VAL Q 131 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL Q 131 " --> pdb=" O GLY Q 32 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LYS Q 127 " --> pdb=" O VAL Q 36 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'R' and resid 33 through 37 removed outlier: 5.345A pdb=" N MET R 110 " --> pdb=" O CYS R 100 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU R 114 " --> pdb=" O ARG R 96 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'S' and resid 35 through 41 removed outlier: 3.998A pdb=" N ARG S 25 " --> pdb=" O ILE S 40 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL S 28 " --> pdb=" O ASP S 93 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'T' and resid 37 through 44 removed outlier: 5.938A pdb=" N THR T 24 " --> pdb=" O LYS T 86 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS T 86 " --> pdb=" O THR T 24 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS T 28 " --> pdb=" O SER T 82 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER T 82 " --> pdb=" O LYS T 28 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'T' and resid 56 through 63 removed outlier: 7.889A pdb=" N SER T 56 " --> pdb=" O THR T 75 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG T 71 " --> pdb=" O VAL T 60 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS T 62 " --> pdb=" O VAL T 69 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'V' and resid 2 through 6 Processing sheet with id= 23, first strand: chain 'V' and resid 19 through 23 removed outlier: 6.897A pdb=" N ASP V 95 " --> pdb=" O VAL V 64 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL V 64 " --> pdb=" O ASP V 95 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LYS V 60 " --> pdb=" O THR V 99 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'V' and resid 69 through 78 removed outlier: 5.374A pdb=" N GLU V 70 " --> pdb=" O GLN V 91 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N GLN V 91 " --> pdb=" O GLU V 70 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL V 72 " --> pdb=" O HIS V 89 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR V 83 " --> pdb=" O ARG V 78 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'W' and resid 4 through 8 removed outlier: 3.812A pdb=" N ALA W 5 " --> pdb=" O VAL W 105 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL W 105 " --> pdb=" O ALA W 5 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N THR W 100 " --> pdb=" O GLY W 79 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR W 104 " --> pdb=" O PHE W 75 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL W 106 " --> pdb=" O LYS W 73 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS W 73 " --> pdb=" O VAL W 106 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'X' and resid 29 through 33 removed outlier: 3.600A pdb=" N LEU X 32 " --> pdb=" O ALA X 83 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN X 59 " --> pdb=" O TYR X 84 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL X 57 " --> pdb=" O THR X 86 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N LYS X 66 " --> pdb=" O ARG X 77 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'Y' and resid 82 through 86 Processing sheet with id= 28, first strand: chain 'Z' and resid 6 through 9 removed outlier: 3.782A pdb=" N ARG Z 9 " --> pdb=" O ALA Z 39 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ALA Z 39 " --> pdb=" O ARG Z 9 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU Z 42 " --> pdb=" O PHE Z 26 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ILE Z 89 " --> pdb=" O PRO Z 27 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE Z 29 " --> pdb=" O ILE Z 89 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR Z 31 " --> pdb=" O PHE Z 91 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N LYS Z 71 " --> pdb=" O ALA Z 94 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'Z' and resid 2 through 5 removed outlier: 4.180A pdb=" N ILE Z 4 " --> pdb=" O THR Z 62 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain '0' and resid 47 through 50 removed outlier: 4.305A pdb=" N THR 0 54 " --> pdb=" O GLY 0 50 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain '0' and resid 63 through 67 Processing sheet with id= 32, first strand: chain '1' and resid 11 through 18 removed outlier: 3.898A pdb=" N VAL 1 12 " --> pdb=" O PHE 1 28 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N THR 1 24 " --> pdb=" O ASN 1 16 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N SER 1 18 " --> pdb=" O ASN 1 22 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ASN 1 22 " --> pdb=" O SER 1 18 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain '1' and resid 33 through 40 Processing sheet with id= 34, first strand: chain '3' and resid 32 through 38 removed outlier: 4.062A pdb=" N HIS 3 33 " --> pdb=" O GLN 3 8 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN 3 8 " --> pdb=" O HIS 3 33 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG 3 37 " --> pdb=" O ILE 3 4 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS 3 5 " --> pdb=" O GLU 3 57 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU 3 57 " --> pdb=" O LYS 3 5 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR 3 7 " --> pdb=" O LYS 3 55 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N MET 3 53 " --> pdb=" O THR 3 9 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain '4' and resid 11 through 15 removed outlier: 3.989A pdb=" N MET 4 22 " --> pdb=" O ALA 4 14 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain '5' and resid 27 through 30 removed outlier: 6.108A pdb=" N SER 5 28 " --> pdb=" O LYS 5 36 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LYS 5 36 " --> pdb=" O SER 5 28 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP 5 30 " --> pdb=" O GLY 5 34 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain '6' and resid 19 through 24 removed outlier: 3.517A pdb=" N GLU 6 6 " --> pdb=" O LYS 6 24 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain '9' and resid 14 through 19 Processing sheet with id= 39, first strand: chain 'b' and resid 88 through 92 removed outlier: 3.655A pdb=" N VAL b 91 " --> pdb=" O PHE b 68 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU b 67 " --> pdb=" O ALA b 159 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE b 161 " --> pdb=" O LEU b 67 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL b 69 " --> pdb=" O PHE b 161 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'c' and resid 18 through 21 removed outlier: 5.660A pdb=" N ASN c 18 " --> pdb=" O ILE c 54 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR c 20 " --> pdb=" O ILE c 56 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG c 58 " --> pdb=" O THR c 20 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG c 53 " --> pdb=" O HIS c 68 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU c 57 " --> pdb=" O ARG c 64 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN c 99 " --> pdb=" O ILE c 63 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL c 105 " --> pdb=" O THR c 69 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'c' and resid 164 through 170 removed outlier: 3.572A pdb=" N GLU c 165 " --> pdb=" O VAL c 152 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VAL c 152 " --> pdb=" O GLU c 165 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY c 147 " --> pdb=" O PHE c 202 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N SER c 186 " --> pdb=" O VAL c 197 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL c 199 " --> pdb=" O ASN c 184 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN c 184 " --> pdb=" O VAL c 199 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ASP c 180 " --> pdb=" O LYS c 203 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'd' and resid 140 through 143 removed outlier: 3.690A pdb=" N VAL d 142 " --> pdb=" O GLY d 179 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N GLU d 178 " --> pdb=" O ASP d 173 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU d 171 " --> pdb=" O THR d 180 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'e' and resid 10 through 15 removed outlier: 3.960A pdb=" N GLN e 11 " --> pdb=" O GLY e 39 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLY e 39 " --> pdb=" O GLN e 11 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LYS e 13 " --> pdb=" O VAL e 37 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL e 37 " --> pdb=" O LYS e 13 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N LEU e 35 " --> pdb=" O ILE e 15 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'e' and resid 82 through 87 removed outlier: 7.641A pdb=" N HIS e 82 " --> pdb=" O PRO e 97 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL e 84 " --> pdb=" O MET e 95 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N MET e 95 " --> pdb=" O VAL e 84 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N VAL e 93 " --> pdb=" O GLY e 86 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'e' and resid 33 through 39 removed outlier: 4.763A pdb=" N ALA e 34 " --> pdb=" O GLY e 50 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLY e 50 " --> pdb=" O ALA e 34 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL e 38 " --> pdb=" O GLY e 46 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY e 46 " --> pdb=" O VAL e 38 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'f' and resid 3 through 10 removed outlier: 6.050A pdb=" N ILE f 6 " --> pdb=" O MET f 62 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE f 8 " --> pdb=" O VAL f 60 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'g' and resid 72 through 76 Processing sheet with id= 48, first strand: chain 'h' and resid 22 through 27 removed outlier: 6.561A pdb=" N ALA h 22 " --> pdb=" O LEU h 62 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU h 62 " --> pdb=" O ALA h 22 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU h 60 " --> pdb=" O VAL h 24 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'h' and resid 73 through 76 removed outlier: 4.338A pdb=" N SER h 73 " --> pdb=" O ALA h 129 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN h 75 " --> pdb=" O TYR h 127 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR h 127 " --> pdb=" O GLN h 75 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'h' and resid 102 through 105 removed outlier: 7.297A pdb=" N VAL h 102 " --> pdb=" O ILE h 125 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'i' and resid 4 through 10 removed outlier: 4.383A pdb=" N GLY i 9 " --> pdb=" O ALA i 16 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS i 67 " --> pdb=" O ALA i 15 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LYS i 26 " --> pdb=" O LEU i 60 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU i 62 " --> pdb=" O LYS i 26 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'j' and resid 44 through 52 removed outlier: 3.859A pdb=" N GLU j 47 " --> pdb=" O ILE j 67 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA j 12 " --> pdb=" O HIS j 70 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU j 10 " --> pdb=" O ARG j 72 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL j 74 " --> pdb=" O ILE j 8 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE j 8 " --> pdb=" O VAL j 74 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE j 76 " --> pdb=" O ILE j 6 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG j 9 " --> pdb=" O GLN j 99 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'k' and resid 29 through 34 removed outlier: 3.548A pdb=" N ILE k 30 " --> pdb=" O HIS k 23 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'l' and resid 28 through 31 removed outlier: 5.039A pdb=" N LEU l 80 " --> pdb=" O VAL l 97 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'l' and resid 34 through 41 removed outlier: 4.649A pdb=" N ARG l 35 " --> pdb=" O ARG l 53 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ALA l 47 " --> pdb=" O PRO l 41 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LYS l 50 " --> pdb=" O ILE l 66 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N CYS l 52 " --> pdb=" O SER l 64 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL l 62 " --> pdb=" O VAL l 54 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'p' and resid 4 through 10 removed outlier: 5.536A pdb=" N GLN p 18 " --> pdb=" O ALA p 7 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'q' and resid 6 through 10 removed outlier: 3.755A pdb=" N ILE q 60 " --> pdb=" O LEU q 7 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY q 9 " --> pdb=" O VAL q 58 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N GLU q 59 " --> pdb=" O VAL q 75 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'q' and resid 18 through 27 No H-bonds generated for sheet with id= 58 Processing sheet with id= 59, first strand: chain 'K' and resid 54 through 58 No H-bonds generated for sheet with id= 59 Processing sheet with id= 60, first strand: chain 's' and resid 46 through 51 removed outlier: 5.011A pdb=" N LEU s 46 " --> pdb=" O VAL s 61 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE s 48 " --> pdb=" O VAL s 59 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'z' and resid 245 through 249 removed outlier: 3.819A pdb=" N LYS z 246 " --> pdb=" O ARG z 280 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG z 280 " --> pdb=" O LYS z 246 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR z 324 " --> pdb=" O GLY z 331 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'z' and resid 405 through 410 removed outlier: 3.567A pdb=" N VAL z 416 " --> pdb=" O VAL z 408 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ASP z 414 " --> pdb=" O THR z 410 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'z' and resid 696 through 701 removed outlier: 3.567A pdb=" N GLY z 696 " --> pdb=" O ASP z 711 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP z 711 " --> pdb=" O GLY z 696 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N THR z 709 " --> pdb=" O ALA z 698 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL z 671 " --> pdb=" O ALA z 708 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL z 669 " --> pdb=" O ILE z 710 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASP z 737 " --> pdb=" O ARG z 670 " (cutoff:3.500A) 1540 hydrogen bonds defined for protein. 4566 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2924 hydrogen bonds 4500 hydrogen bond angles 0 basepair planarities 1200 basepair parallelities 2704 stacking parallelities Total time for adding SS restraints: 229.87 Time building geometry restraints manager: 68.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 28360 1.33 - 1.45: 62546 1.45 - 1.57: 61730 1.57 - 1.69: 9405 1.69 - 1.81: 278 Bond restraints: 162319 Sorted by residual: bond pdb=" C4 5MU x 54 " pdb=" C5 5MU x 54 " ideal model delta sigma weight residual 1.802 1.457 0.345 2.00e-02 2.50e+03 2.97e+02 bond pdb=" C4 5MU A1939 " pdb=" C5 5MU A1939 " ideal model delta sigma weight residual 1.802 1.459 0.343 2.00e-02 2.50e+03 2.93e+02 bond pdb=" C4 5MU y 54 " pdb=" C5 5MU y 54 " ideal model delta sigma weight residual 1.802 1.460 0.342 2.00e-02 2.50e+03 2.93e+02 bond pdb=" N1 5MU A1939 " pdb=" C6 5MU A1939 " ideal model delta sigma weight residual 1.635 1.327 0.308 2.00e-02 2.50e+03 2.38e+02 bond pdb=" N1 5MU y 54 " pdb=" C6 5MU y 54 " ideal model delta sigma weight residual 1.635 1.327 0.308 2.00e-02 2.50e+03 2.37e+02 ... (remaining 162314 not shown) Histogram of bond angle deviations from ideal: 99.17 - 106.85: 28482 106.85 - 114.53: 103641 114.53 - 122.21: 76328 122.21 - 129.89: 30882 129.89 - 137.57: 2929 Bond angle restraints: 242262 Sorted by residual: angle pdb=" C GLY K 24 " pdb=" N PRO K 25 " pdb=" CA PRO K 25 " ideal model delta sigma weight residual 119.28 126.57 -7.29 1.10e+00 8.26e-01 4.40e+01 angle pdb=" C1' 2MA A2503 " pdb=" N9 2MA A2503 " pdb=" C8 2MA A2503 " ideal model delta sigma weight residual 106.32 125.64 -19.32 3.00e+00 1.11e-01 4.15e+01 angle pdb=" C1' 2MG A1835 " pdb=" N9 2MG A1835 " pdb=" C8 2MG A1835 " ideal model delta sigma weight residual 110.07 128.87 -18.80 3.00e+00 1.11e-01 3.93e+01 angle pdb=" C1' OMG A2251 " pdb=" N9 OMG A2251 " pdb=" C4 OMG A2251 " ideal model delta sigma weight residual 108.29 126.62 -18.33 3.00e+00 1.11e-01 3.73e+01 angle pdb=" C LEU l 101 " pdb=" CA LEU l 101 " pdb=" CB LEU l 101 " ideal model delta sigma weight residual 116.54 109.60 6.94 1.15e+00 7.56e-01 3.65e+01 ... (remaining 242257 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 91297 35.73 - 71.45: 10422 71.45 - 107.18: 1290 107.18 - 142.91: 41 142.91 - 178.63: 50 Dihedral angle restraints: 103100 sinusoidal: 85474 harmonic: 17626 Sorted by residual: dihedral pdb=" C5* PSU A2604 " pdb=" C4* PSU A2604 " pdb=" C3* PSU A2604 " pdb=" O3* PSU A2604 " ideal model delta sinusoidal sigma weight residual 82.00 -38.93 120.93 1 8.00e+00 1.56e-02 2.27e+02 dihedral pdb=" C5* PSU A2604 " pdb=" C4* PSU A2604 " pdb=" O4* PSU A2604 " pdb=" C1* PSU A2604 " ideal model delta sinusoidal sigma weight residual 145.00 -96.65 -118.35 1 8.00e+00 1.56e-02 2.21e+02 dihedral pdb=" C5* PSU A2504 " pdb=" C4* PSU A2504 " pdb=" C3* PSU A2504 " pdb=" O3* PSU A2504 " ideal model delta sinusoidal sigma weight residual 82.00 -32.21 114.21 1 8.00e+00 1.56e-02 2.12e+02 ... (remaining 103097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.101: 30508 1.101 - 2.203: 0 2.203 - 3.304: 0 3.304 - 4.406: 0 4.406 - 5.507: 39 Chirality restraints: 30547 Sorted by residual: chirality pdb=" C2' 4SU x 8 " pdb=" C3' 4SU x 8 " pdb=" O2' 4SU x 8 " pdb=" C1' 4SU x 8 " both_signs ideal model delta sigma weight residual False -2.75 2.75 -5.51 2.00e-01 2.50e+01 7.58e+02 chirality pdb=" C2' MA6 a1518 " pdb=" C3' MA6 a1518 " pdb=" O2' MA6 a1518 " pdb=" C1' MA6 a1518 " both_signs ideal model delta sigma weight residual False -2.75 2.75 -5.50 2.00e-01 2.50e+01 7.57e+02 chirality pdb=" C2* PSU A2604 " pdb=" C3* PSU A2604 " pdb=" O2* PSU A2604 " pdb=" C1* PSU A2604 " both_signs ideal model delta sigma weight residual False -2.75 2.74 -5.50 2.00e-01 2.50e+01 7.56e+02 ... (remaining 30544 not shown) Planarity restraints: 13408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a1207 " -1.126 2.00e-02 2.50e+03 6.45e-01 9.36e+03 pdb=" C4' 2MG a1207 " 0.282 2.00e-02 2.50e+03 pdb=" O4' 2MG a1207 " 0.312 2.00e-02 2.50e+03 pdb=" C3' 2MG a1207 " 0.798 2.00e-02 2.50e+03 pdb=" O3' 2MG a1207 " 0.205 2.00e-02 2.50e+03 pdb=" C2' 2MG a1207 " 0.306 2.00e-02 2.50e+03 pdb=" O2' 2MG a1207 " -1.057 2.00e-02 2.50e+03 pdb=" C1' 2MG a1207 " 0.570 2.00e-02 2.50e+03 pdb=" N9 2MG a1207 " -0.291 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A2445 " 0.960 2.00e-02 2.50e+03 5.97e-01 8.02e+03 pdb=" C4' 2MG A2445 " -0.330 2.00e-02 2.50e+03 pdb=" O4' 2MG A2445 " -0.164 2.00e-02 2.50e+03 pdb=" C3' 2MG A2445 " -0.800 2.00e-02 2.50e+03 pdb=" O3' 2MG A2445 " -0.116 2.00e-02 2.50e+03 pdb=" C2' 2MG A2445 " -0.332 2.00e-02 2.50e+03 pdb=" O2' 2MG A2445 " 1.007 2.00e-02 2.50e+03 pdb=" C1' 2MG A2445 " -0.530 2.00e-02 2.50e+03 pdb=" N9 2MG A2445 " 0.305 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a 966 " 0.948 2.00e-02 2.50e+03 5.95e-01 7.96e+03 pdb=" C4' 2MG a 966 " -0.332 2.00e-02 2.50e+03 pdb=" O4' 2MG a 966 " -0.153 2.00e-02 2.50e+03 pdb=" C3' 2MG a 966 " -0.794 2.00e-02 2.50e+03 pdb=" O3' 2MG a 966 " -0.124 2.00e-02 2.50e+03 pdb=" C2' 2MG a 966 " -0.323 2.00e-02 2.50e+03 pdb=" O2' 2MG a 966 " 1.020 2.00e-02 2.50e+03 pdb=" C1' 2MG a 966 " -0.530 2.00e-02 2.50e+03 pdb=" N9 2MG a 966 " 0.287 2.00e-02 2.50e+03 ... (remaining 13405 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 7024 2.67 - 3.23: 130043 3.23 - 3.79: 288073 3.79 - 4.34: 397713 4.34 - 4.90: 514012 Nonbonded interactions: 1336865 Sorted by model distance: nonbonded pdb=" O2' 5MU x 54 " pdb=" O4* PSU x 55 " model vdw 2.115 3.040 nonbonded pdb=" O2' A A1912 " pdb=" O2' G a1494 " model vdw 2.159 2.440 nonbonded pdb=" O2' MA6 a1519 " pdb=" O5' C a1520 " model vdw 2.161 2.440 nonbonded pdb=" OG1 THR F 48 " pdb=" OE1 GLU F 51 " model vdw 2.161 2.440 nonbonded pdb=" OP2 C A 672 " pdb=" OG SER P 42 " model vdw 2.165 2.440 ... (remaining 1336860 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.120 Extract box with map and model: 15.920 Check model and map are aligned: 1.590 Set scattering table: 1.000 Process input model: 528.090 Find NCS groups from input model: 3.400 Set up NCS constraints: 0.420 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: 0.030 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 555.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1090 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 0.345 162319 Z= 0.372 Angle : 0.599 19.322 242262 Z= 0.391 Chirality : 0.186 5.507 30547 Planarity : 0.019 0.645 13408 Dihedral : 22.197 178.634 92015 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 2.41 % Allowed : 8.18 % Favored : 89.41 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.10), residues: 6305 helix: -3.34 (0.06), residues: 1881 sheet: -3.59 (0.13), residues: 872 loop : 0.81 (0.12), residues: 3552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP D 212 HIS 0.006 0.001 HIS m 11 PHE 0.020 0.001 PHE D 239 TYR 0.019 0.001 TYR 4 9 ARG 0.006 0.000 ARG l 35 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12610 Ramachandran restraints generated. 6305 Oldfield, 0 Emsley, 6305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12610 Ramachandran restraints generated. 6305 Oldfield, 0 Emsley, 6305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 5255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 609 time to evaluate : 6.129 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: D 166 ARG cc_start: 0.0372 (ttt180) cc_final: 0.0044 (ptm160) REVERT: E 161 MET cc_start: 0.0833 (mtp) cc_final: 0.0389 (mtp) REVERT: F 141 MET cc_start: -0.5784 (mtp) cc_final: -0.6053 (mtm) REVERT: G 169 LEU cc_start: 0.6975 (mt) cc_final: 0.6768 (mp) REVERT: Z 50 MET cc_start: 0.5357 (mmm) cc_final: 0.5030 (mmm) REVERT: e 95 MET cc_start: -0.3805 (ptm) cc_final: -0.4548 (ppp) REVERT: e 110 MET cc_start: 0.0599 (ttp) cc_final: -0.0065 (mpp) REVERT: h 9 MET cc_start: -0.0098 (ttt) cc_final: -0.0660 (ttt) REVERT: m 80 MET cc_start: -0.4292 (mtm) cc_final: -0.4608 (tmm) REVERT: K 116 MET cc_start: -0.2561 (mmp) cc_final: -0.2913 (mmt) REVERT: K 135 MET cc_start: 0.0515 (mmt) cc_final: 0.0255 (mmt) REVERT: s 65 MET cc_start: 0.5834 (mtm) cc_final: 0.5455 (ttm) outliers start: 0 outliers final: 0 residues processed: 609 average time/residue: 1.5032 time to fit residues: 1509.1978 Evaluate side-chains 327 residues out of total 5255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 327 time to evaluate : 5.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1094 random chunks: chunk 923 optimal weight: 8.9990 chunk 829 optimal weight: 7.9990 chunk 460 optimal weight: 9.9990 chunk 283 optimal weight: 20.0000 chunk 559 optimal weight: 0.9990 chunk 442 optimal weight: 0.7980 chunk 857 optimal weight: 8.9990 chunk 331 optimal weight: 9.9990 chunk 521 optimal weight: 7.9990 chunk 638 optimal weight: 30.0000 chunk 993 optimal weight: 0.9980 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 225 ASN F 165 HIS H 138 GLN N 40 HIS ** N 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 3 GLN Q 13 HIS R 9 GLN S 38 GLN T 2 ASN T 11 GLN U 19 GLN ** U 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 7 HIS ** W 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 73 ASN 0 8 ASN 0 42 HIS 2 25 GLN 2 41 HIS 2 45 GLN 2 58 ASN 3 19 HIS 6 18 HIS ** 6 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 23 HIS b 18 GLN d 119 HIS d 125 ASN e 69 ASN f 55 HIS f 58 HIS ** g 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 141 HIS ** g 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 3 GLN ** i 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 70 HIS k 100 ASN m 51 GLN o 27 GLN ** o 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 9 HIS p 26 ASN p 63 GLN p 79 ASN q 30 HIS r 73 HIS ** t 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 60 GLN t 74 HIS J 4 ASN J 88 HIS ** K 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 34 ASN n 60 GLN s 55 GLN s 68 HIS Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1380 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 162319 Z= 0.185 Angle : 0.728 15.674 242262 Z= 0.384 Chirality : 0.034 0.634 30547 Planarity : 0.007 0.124 13408 Dihedral : 23.057 179.728 80415 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.82 % Allowed : 6.23 % Favored : 92.94 % Rotamer: Outliers : 1.14 % Allowed : 5.93 % Favored : 92.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % 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: -1.53 (0.10), residues: 6305 helix: -1.23 (0.10), residues: 1976 sheet: -3.30 (0.13), residues: 913 loop : -0.00 (0.11), residues: 3416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP V 92 HIS 0.015 0.001 HIS f 11 PHE 0.030 0.002 PHE s 73 TYR 0.026 0.002 TYR f 59 ARG 0.008 0.001 ARG d 145 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12610 Ramachandran restraints generated. 6305 Oldfield, 0 Emsley, 6305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12610 Ramachandran restraints generated. 6305 Oldfield, 0 Emsley, 6305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 5255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 375 time to evaluate : 6.056 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: D 166 ARG cc_start: 0.0704 (ttt180) cc_final: 0.0203 (ptm160) REVERT: E 161 MET cc_start: 0.0928 (mtp) cc_final: 0.0414 (mtp) REVERT: F 141 MET cc_start: -0.5800 (mtp) cc_final: -0.6120 (mtm) REVERT: I 1 MET cc_start: -0.0728 (mmm) cc_final: -0.1016 (mmm) REVERT: I 22 LYS cc_start: 0.1922 (mttp) cc_final: 0.1630 (tptt) REVERT: Z 50 MET cc_start: 0.5438 (mmm) cc_final: 0.5114 (mmm) REVERT: e 95 MET cc_start: -0.3665 (ptm) cc_final: -0.5682 (mtt) REVERT: e 110 MET cc_start: 0.1484 (ttp) cc_final: 0.0984 (ptp) REVERT: f 9 MET cc_start: -0.4327 (OUTLIER) cc_final: -0.4643 (ttt) REVERT: g 4 ARG cc_start: 0.3339 (mpp-170) cc_final: 0.3135 (mpp-170) REVERT: g 84 TYR cc_start: 0.4153 (p90) cc_final: 0.3335 (m-80) REVERT: m 77 LYS cc_start: 0.4323 (mmtt) cc_final: 0.3954 (mmtt) REVERT: m 80 MET cc_start: -0.4014 (mtm) cc_final: -0.5044 (tmm) REVERT: J 1 MET cc_start: 0.0822 (OUTLIER) cc_final: 0.0340 (ppp) REVERT: K 16 MET cc_start: 0.7545 (mmt) cc_final: 0.7249 (mpp) REVERT: K 18 ASN cc_start: 0.8376 (OUTLIER) cc_final: 0.8107 (m-40) REVERT: K 116 MET cc_start: -0.2778 (mmp) cc_final: -0.3270 (mmt) outliers start: 55 outliers final: 32 residues processed: 405 average time/residue: 1.4248 time to fit residues: 977.7279 Evaluate side-chains 340 residues out of total 5255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 305 time to evaluate : 5.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain E residue 190 LYS Chi-restraints excluded: chain F residue 191 ASP Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 163 TYR Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 88 THR Chi-restraints excluded: chain O residue 9 ASN Chi-restraints excluded: chain O residue 82 ASN Chi-restraints excluded: chain V residue 22 LEU Chi-restraints excluded: chain X residue 30 ILE Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 44 HIS Chi-restraints excluded: chain Z residue 79 ARG Chi-restraints excluded: chain Z residue 83 LYS Chi-restraints excluded: chain 0 residue 16 ARG Chi-restraints excluded: chain 0 residue 49 CYS Chi-restraints excluded: chain 9 residue 9 LYS Chi-restraints excluded: chain b residue 38 HIS Chi-restraints excluded: chain b residue 40 ILE Chi-restraints excluded: chain c residue 42 LEU Chi-restraints excluded: chain d residue 27 ILE Chi-restraints excluded: chain e residue 96 GLN Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain g residue 44 SER Chi-restraints excluded: chain j residue 69 THR Chi-restraints excluded: chain k residue 60 PHE Chi-restraints excluded: chain k residue 100 ASN Chi-restraints excluded: chain t residue 53 MET Chi-restraints excluded: chain u residue 8 ASN Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain K residue 18 ASN Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain s residue 46 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1094 random chunks: chunk 552 optimal weight: 4.9990 chunk 308 optimal weight: 4.9990 chunk 826 optimal weight: 0.9990 chunk 676 optimal weight: 20.0000 chunk 274 optimal weight: 30.0000 chunk 995 optimal weight: 20.0000 chunk 1075 optimal weight: 30.0000 chunk 886 optimal weight: 0.4980 chunk 986 optimal weight: 20.0000 chunk 339 optimal weight: 5.9990 chunk 798 optimal weight: 8.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN F 94 GLN G 80 GLN ** N 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 3 GLN P 35 HIS ** P 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 9 GLN ** V 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 70 HIS ** Y 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 41 HIS ** 6 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 175 HIS ** g 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 20 ASN ** h 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 109 GLN k 21 HIS k 100 ASN m 13 HIS q 46 HIS t 2 ASN ** K 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1647 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 162319 Z= 0.186 Angle : 0.681 21.813 242262 Z= 0.368 Chirality : 0.033 0.469 30547 Planarity : 0.007 0.135 13408 Dihedral : 23.099 179.596 80415 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.76 % Allowed : 6.88 % Favored : 92.36 % Rotamer: Outliers : 1.97 % Allowed : 6.99 % Favored : 91.04 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.47 % 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: -1.24 (0.10), residues: 6305 helix: -0.28 (0.11), residues: 1982 sheet: -2.90 (0.15), residues: 866 loop : -0.45 (0.11), residues: 3457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP n 101 HIS 0.018 0.002 HIS k 117 PHE 0.045 0.002 PHE F 23 TYR 0.037 0.002 TYR N 74 ARG 0.019 0.001 ARG Q 66 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12610 Ramachandran restraints generated. 6305 Oldfield, 0 Emsley, 6305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12610 Ramachandran restraints generated. 6305 Oldfield, 0 Emsley, 6305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 5255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 339 time to evaluate : 6.030 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: D 166 ARG cc_start: 0.0868 (ttt180) cc_final: 0.0232 (ptt180) REVERT: F 199 MET cc_start: 0.0587 (OUTLIER) cc_final: 0.0085 (mtp) REVERT: I 1 MET cc_start: -0.0548 (mmm) cc_final: -0.1054 (mmm) REVERT: I 22 LYS cc_start: 0.2373 (mttp) cc_final: 0.2117 (tptt) REVERT: d 104 MET cc_start: -0.3855 (mmt) cc_final: -0.4321 (mpp) REVERT: e 95 MET cc_start: -0.3440 (ptm) cc_final: -0.5278 (mtp) REVERT: e 110 MET cc_start: 0.1456 (ttp) cc_final: 0.1060 (mpp) REVERT: g 84 TYR cc_start: 0.4384 (p90) cc_final: 0.3942 (m-80) REVERT: h 9 MET cc_start: -0.0524 (ttt) cc_final: -0.0894 (ttt) REVERT: m 77 LYS cc_start: 0.4240 (mmtt) cc_final: 0.3967 (mmtt) REVERT: m 80 MET cc_start: -0.4051 (mtm) cc_final: -0.5109 (tmm) REVERT: J 1 MET cc_start: 0.1426 (ppp) cc_final: 0.1092 (ppp) REVERT: K 18 ASN cc_start: 0.8299 (OUTLIER) cc_final: 0.7975 (m110) REVERT: K 116 MET cc_start: -0.3271 (mmp) cc_final: -0.3524 (mmt) REVERT: K 124 MET cc_start: 0.2011 (mmp) cc_final: 0.1656 (mmp) REVERT: n 34 ASN cc_start: 0.4211 (m-40) cc_final: 0.3991 (m110) REVERT: s 43 MET cc_start: 0.0099 (ttm) cc_final: -0.0251 (mtt) REVERT: s 64 GLU cc_start: 0.7224 (pm20) cc_final: 0.6965 (pm20) outliers start: 95 outliers final: 46 residues processed: 398 average time/residue: 1.3802 time to fit residues: 944.9365 Evaluate side-chains 342 residues out of total 5255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 294 time to evaluate : 8.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 160 TYR Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain E residue 11 MET Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain F residue 199 MET Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 163 TYR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 88 THR Chi-restraints excluded: chain O residue 9 ASN Chi-restraints excluded: chain O residue 58 LEU Chi-restraints excluded: chain O residue 63 VAL Chi-restraints excluded: chain O residue 82 ASN Chi-restraints excluded: chain S residue 29 HIS Chi-restraints excluded: chain S residue 49 VAL Chi-restraints excluded: chain S residue 97 PHE Chi-restraints excluded: chain T residue 75 THR Chi-restraints excluded: chain W residue 74 ILE Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 44 HIS Chi-restraints excluded: chain Z residue 79 ARG Chi-restraints excluded: chain Z residue 83 LYS Chi-restraints excluded: chain 0 residue 49 CYS Chi-restraints excluded: chain 5 residue 9 ARG Chi-restraints excluded: chain b residue 38 HIS Chi-restraints excluded: chain b residue 68 PHE Chi-restraints excluded: chain b residue 96 LEU Chi-restraints excluded: chain b residue 135 MET Chi-restraints excluded: chain c residue 42 LEU Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain g residue 43 TYR Chi-restraints excluded: chain g residue 143 MET Chi-restraints excluded: chain i residue 5 TYR Chi-restraints excluded: chain i residue 45 MET Chi-restraints excluded: chain j residue 69 THR Chi-restraints excluded: chain j residue 71 LEU Chi-restraints excluded: chain k residue 60 PHE Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain o residue 58 MET Chi-restraints excluded: chain p residue 1 MET Chi-restraints excluded: chain q residue 7 LEU Chi-restraints excluded: chain t residue 53 MET Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 18 ASN Chi-restraints excluded: chain K residue 54 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1094 random chunks: chunk 983 optimal weight: 20.0000 chunk 748 optimal weight: 20.0000 chunk 516 optimal weight: 3.9990 chunk 110 optimal weight: 20.0000 chunk 474 optimal weight: 5.9990 chunk 668 optimal weight: 20.0000 chunk 998 optimal weight: 50.0000 chunk 1057 optimal weight: 10.0000 chunk 521 optimal weight: 9.9990 chunk 946 optimal weight: 30.0000 chunk 284 optimal weight: 20.0000 overall best weight: 9.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 ASN D 225 ASN E 173 GLN ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 43 ASN ** N 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 29 HIS P 104 GLN ** Q 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 107 ASN ** T 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 19 GLN U 55 GLN U 58 GLN ** V 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 89 HIS ** W 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 73 ASN ** Z 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 87 GLN ** 1 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 20 ASN ** 2 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 4 GLN ** 6 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 44 GLN ** 6 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 42 HIS 9 35 GLN b 41 ASN c 68 HIS c 189 HIS ** d 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 36 GLN ** i 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 64 GLN ** j 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 27 ASN k 28 ASN ** k 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 71 HIS ** s 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2680 moved from start: 0.8437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.341 162319 Z= 0.482 Angle : 1.358 29.022 242262 Z= 0.671 Chirality : 0.059 0.754 30547 Planarity : 0.012 0.360 13408 Dihedral : 24.565 179.468 80415 Min Nonbonded Distance : 1.643 Molprobity Statistics. All-atom Clashscore : 54.09 Ramachandran Plot: Outliers : 0.90 % Allowed : 8.33 % Favored : 90.77 % Rotamer: Outliers : 3.59 % Allowed : 8.75 % Favored : 87.66 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.10), residues: 6305 helix: -1.38 (0.11), residues: 1974 sheet: -2.79 (0.16), residues: 800 loop : -1.62 (0.10), residues: 3531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.005 TRP H 61 HIS 0.035 0.004 HIS T 76 PHE 0.152 0.006 PHE 2 26 TYR 0.070 0.005 TYR n 19 ARG 0.086 0.002 ARG i 79 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12610 Ramachandran restraints generated. 6305 Oldfield, 0 Emsley, 6305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12610 Ramachandran restraints generated. 6305 Oldfield, 0 Emsley, 6305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 5255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 380 time to evaluate : 6.224 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: D 160 TYR cc_start: 0.5912 (OUTLIER) cc_final: 0.4034 (p90) REVERT: F 69 ARG cc_start: -0.1147 (OUTLIER) cc_final: -0.1381 (ptp90) REVERT: F 199 MET cc_start: 0.2151 (OUTLIER) cc_final: 0.1697 (mtp) REVERT: G 95 MET cc_start: -0.3410 (mtp) cc_final: -0.4300 (mmm) REVERT: G 166 ARG cc_start: 0.8485 (mmm160) cc_final: 0.8076 (tpt90) REVERT: I 1 MET cc_start: -0.1088 (mmm) cc_final: -0.1774 (mmm) REVERT: X 1 MET cc_start: 0.3845 (tmm) cc_final: 0.2894 (tmm) REVERT: Z 48 MET cc_start: -0.1687 (OUTLIER) cc_final: -0.1962 (ptm) REVERT: e 95 MET cc_start: -0.3307 (ptm) cc_final: -0.5783 (mtp) REVERT: e 110 MET cc_start: 0.2251 (ttp) cc_final: 0.2047 (ptp) REVERT: e 121 ASN cc_start: 0.4419 (OUTLIER) cc_final: 0.4152 (p0) REVERT: g 84 TYR cc_start: 0.4367 (p90) cc_final: 0.3019 (m-80) REVERT: h 2 MET cc_start: 0.1785 (ppp) cc_final: 0.1031 (ptm) REVERT: h 9 MET cc_start: 0.0395 (ttt) cc_final: -0.0317 (ttt) REVERT: j 10 LEU cc_start: 0.6125 (OUTLIER) cc_final: 0.5670 (pt) REVERT: j 69 THR cc_start: 0.5725 (OUTLIER) cc_final: 0.5510 (m) REVERT: m 77 LYS cc_start: 0.4693 (mmtt) cc_final: 0.4332 (mmtt) REVERT: m 78 ARG cc_start: 0.7177 (ttp80) cc_final: 0.6774 (ptm160) REVERT: m 80 MET cc_start: -0.3535 (mtm) cc_final: -0.4669 (tmm) REVERT: t 26 MET cc_start: -0.3974 (ttt) cc_final: -0.4264 (ttt) REVERT: J 52 MET cc_start: 0.2265 (mtp) cc_final: 0.1750 (mtp) REVERT: K 10 LEU cc_start: 0.4095 (OUTLIER) cc_final: 0.3861 (pp) REVERT: K 18 ASN cc_start: 0.8267 (OUTLIER) cc_final: 0.7996 (m-40) outliers start: 173 outliers final: 84 residues processed: 499 average time/residue: 1.3661 time to fit residues: 1180.6109 Evaluate side-chains 412 residues out of total 5255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 319 time to evaluate : 6.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 69 ASN Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 160 TYR Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain F residue 32 VAL Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 199 MET Chi-restraints excluded: chain G residue 6 TYR Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 146 ASP Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 163 TYR Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain O residue 9 ASN Chi-restraints excluded: chain O residue 38 ILE Chi-restraints excluded: chain O residue 58 LEU Chi-restraints excluded: chain O residue 82 ASN Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain S residue 29 HIS Chi-restraints excluded: chain S residue 48 LEU Chi-restraints excluded: chain U residue 8 ILE Chi-restraints excluded: chain U residue 50 ARG Chi-restraints excluded: chain V residue 12 HIS Chi-restraints excluded: chain V residue 22 LEU Chi-restraints excluded: chain V residue 41 ILE Chi-restraints excluded: chain W residue 62 ASP Chi-restraints excluded: chain W residue 74 ILE Chi-restraints excluded: chain W residue 76 VAL Chi-restraints excluded: chain X residue 30 ILE Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 27 VAL Chi-restraints excluded: chain Y residue 71 ILE Chi-restraints excluded: chain Z residue 48 MET Chi-restraints excluded: chain Z residue 79 ARG Chi-restraints excluded: chain Z residue 83 LYS Chi-restraints excluded: chain 0 residue 49 CYS Chi-restraints excluded: chain 2 residue 30 MET Chi-restraints excluded: chain 5 residue 9 ARG Chi-restraints excluded: chain 8 residue 4 LYS Chi-restraints excluded: chain b residue 38 HIS Chi-restraints excluded: chain b residue 68 PHE Chi-restraints excluded: chain b residue 96 LEU Chi-restraints excluded: chain c residue 42 LEU Chi-restraints excluded: chain d residue 27 ILE Chi-restraints excluded: chain d residue 170 LEU Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 152 VAL Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 37 HIS Chi-restraints excluded: chain g residue 6 ILE Chi-restraints excluded: chain g residue 43 TYR Chi-restraints excluded: chain g residue 96 ASN Chi-restraints excluded: chain g residue 143 MET Chi-restraints excluded: chain h residue 62 LEU Chi-restraints excluded: chain h residue 64 TYR Chi-restraints excluded: chain i residue 5 TYR Chi-restraints excluded: chain i residue 20 ILE Chi-restraints excluded: chain i residue 45 MET Chi-restraints excluded: chain j residue 9 ARG Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 69 THR Chi-restraints excluded: chain k residue 84 MET Chi-restraints excluded: chain m residue 21 ILE Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 51 GLN Chi-restraints excluded: chain m residue 76 ILE Chi-restraints excluded: chain m residue 82 LEU Chi-restraints excluded: chain q residue 7 LEU Chi-restraints excluded: chain r residue 66 LEU Chi-restraints excluded: chain t residue 53 MET Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 18 ASN Chi-restraints excluded: chain K residue 85 ILE Chi-restraints excluded: chain n residue 15 LEU Chi-restraints excluded: chain n residue 73 PHE Chi-restraints excluded: chain n residue 96 LEU Chi-restraints excluded: chain n residue 101 TRP Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 65 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1094 random chunks: chunk 880 optimal weight: 5.9990 chunk 600 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 chunk 787 optimal weight: 6.9990 chunk 436 optimal weight: 5.9990 chunk 902 optimal weight: 20.0000 chunk 730 optimal weight: 30.0000 chunk 1 optimal weight: 20.0000 chunk 539 optimal weight: 5.9990 chunk 949 optimal weight: 8.9990 chunk 266 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 HIS ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 13 ASN T 11 GLN U 36 GLN U 58 GLN ** W 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 22 ASN 2 25 GLN ** 4 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 18 HIS ** 6 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 14 HIS c 68 HIS ** d 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 17 GLN ** h 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 109 GLN j 64 GLN ** k 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 9 HIS p 79 ASN t 54 GLN t 81 GLN ** K 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2559 moved from start: 0.9011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 162319 Z= 0.253 Angle : 0.870 15.029 242262 Z= 0.461 Chirality : 0.043 0.600 30547 Planarity : 0.008 0.160 13408 Dihedral : 24.450 178.817 80415 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 32.18 Ramachandran Plot: Outliers : 0.70 % Allowed : 7.57 % Favored : 91.74 % Rotamer: Outliers : 2.92 % Allowed : 12.13 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.10), residues: 6305 helix: -0.83 (0.11), residues: 1976 sheet: -2.74 (0.16), residues: 827 loop : -1.62 (0.10), residues: 3502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP c 166 HIS 0.016 0.002 HIS 8 25 PHE 0.041 0.003 PHE 2 26 TYR 0.036 0.003 TYR n 19 ARG 0.023 0.001 ARG i 79 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12610 Ramachandran restraints generated. 6305 Oldfield, 0 Emsley, 6305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12610 Ramachandran restraints generated. 6305 Oldfield, 0 Emsley, 6305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 5255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 354 time to evaluate : 6.125 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: D 145 MET cc_start: 0.3464 (mmm) cc_final: 0.1928 (mtt) REVERT: D 160 TYR cc_start: 0.5749 (OUTLIER) cc_final: 0.4067 (p90) REVERT: F 199 MET cc_start: 0.2848 (ttp) cc_final: 0.2479 (mtp) REVERT: G 3 LEU cc_start: 0.5639 (OUTLIER) cc_final: 0.5365 (tt) REVERT: G 129 MET cc_start: 0.5886 (ptp) cc_final: 0.5482 (ptp) REVERT: H 74 MET cc_start: 0.2855 (OUTLIER) cc_final: 0.2592 (ppp) REVERT: I 1 MET cc_start: -0.1838 (mmm) cc_final: -0.2489 (mmm) REVERT: Q 53 MET cc_start: -0.0592 (ttp) cc_final: -0.0902 (ttm) REVERT: X 1 MET cc_start: 0.4283 (tmm) cc_final: 0.3307 (tmm) REVERT: X 37 ASP cc_start: 0.1942 (OUTLIER) cc_final: 0.0836 (m-30) REVERT: Z 50 MET cc_start: 0.5201 (mmm) cc_final: 0.4911 (mmm) REVERT: 2 26 PHE cc_start: 0.3465 (OUTLIER) cc_final: 0.3205 (p90) REVERT: e 95 MET cc_start: -0.4000 (ptm) cc_final: -0.5709 (mtp) REVERT: e 121 ASN cc_start: 0.4073 (OUTLIER) cc_final: 0.3859 (p0) REVERT: g 84 TYR cc_start: 0.4669 (p90) cc_final: 0.2932 (m-80) REVERT: h 2 MET cc_start: 0.1590 (ppp) cc_final: 0.1162 (ptm) REVERT: h 9 MET cc_start: 0.0975 (ttt) cc_final: 0.0546 (ttt) REVERT: k 117 HIS cc_start: -0.1021 (OUTLIER) cc_final: -0.1325 (t70) REVERT: m 80 MET cc_start: -0.3322 (mtm) cc_final: -0.4810 (tmm) REVERT: K 18 ASN cc_start: 0.8284 (OUTLIER) cc_final: 0.8008 (m-40) outliers start: 141 outliers final: 80 residues processed: 452 average time/residue: 1.3280 time to fit residues: 1036.1758 Evaluate side-chains 409 residues out of total 5255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 321 time to evaluate : 5.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 160 TYR Chi-restraints excluded: chain D residue 200 MET Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain G residue 3 LEU Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 74 MET Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 163 TYR Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 52 ASP Chi-restraints excluded: chain N residue 81 ILE Chi-restraints excluded: chain O residue 9 ASN Chi-restraints excluded: chain O residue 13 ASN Chi-restraints excluded: chain O residue 82 ASN Chi-restraints excluded: chain P residue 27 LEU Chi-restraints excluded: chain P residue 111 ILE Chi-restraints excluded: chain Q residue 80 VAL Chi-restraints excluded: chain Q residue 96 ILE Chi-restraints excluded: chain Q residue 106 ASP Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 33 ILE Chi-restraints excluded: chain S residue 29 HIS Chi-restraints excluded: chain U residue 8 ILE Chi-restraints excluded: chain U residue 108 LEU Chi-restraints excluded: chain W residue 62 ASP Chi-restraints excluded: chain W residue 74 ILE Chi-restraints excluded: chain X residue 30 ILE Chi-restraints excluded: chain X residue 32 LEU Chi-restraints excluded: chain X residue 37 ASP Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 44 HIS Chi-restraints excluded: chain Y residue 81 ARG Chi-restraints excluded: chain Z residue 79 ARG Chi-restraints excluded: chain Z residue 83 LYS Chi-restraints excluded: chain 0 residue 49 CYS Chi-restraints excluded: chain 1 residue 67 LEU Chi-restraints excluded: chain 2 residue 26 PHE Chi-restraints excluded: chain 3 residue 40 THR Chi-restraints excluded: chain 4 residue 22 MET Chi-restraints excluded: chain 5 residue 9 ARG Chi-restraints excluded: chain 9 residue 10 LEU Chi-restraints excluded: chain b residue 38 HIS Chi-restraints excluded: chain b residue 68 PHE Chi-restraints excluded: chain b residue 69 VAL Chi-restraints excluded: chain b residue 96 LEU Chi-restraints excluded: chain b residue 162 VAL Chi-restraints excluded: chain c residue 20 THR Chi-restraints excluded: chain c residue 42 LEU Chi-restraints excluded: chain c residue 105 VAL Chi-restraints excluded: chain c residue 115 VAL Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 37 HIS Chi-restraints excluded: chain f residue 88 MET Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain g residue 143 MET Chi-restraints excluded: chain h residue 64 TYR Chi-restraints excluded: chain i residue 5 TYR Chi-restraints excluded: chain i residue 45 MET Chi-restraints excluded: chain i residue 59 LYS Chi-restraints excluded: chain i residue 110 VAL Chi-restraints excluded: chain j residue 9 ARG Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 117 HIS Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain m residue 42 VAL Chi-restraints excluded: chain m residue 53 ASP Chi-restraints excluded: chain o residue 58 MET Chi-restraints excluded: chain o residue 86 LEU Chi-restraints excluded: chain q residue 7 LEU Chi-restraints excluded: chain t residue 53 MET Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain K residue 18 ASN Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 85 ILE Chi-restraints excluded: chain n residue 101 TRP Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 65 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1094 random chunks: chunk 355 optimal weight: 0.0770 chunk 952 optimal weight: 40.0000 chunk 209 optimal weight: 30.0000 chunk 620 optimal weight: 30.0000 chunk 261 optimal weight: 30.0000 chunk 1058 optimal weight: 40.0000 chunk 878 optimal weight: 0.7980 chunk 490 optimal weight: 20.0000 chunk 88 optimal weight: 20.0000 chunk 350 optimal weight: 0.9990 chunk 555 optimal weight: 0.4980 overall best weight: 4.4744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 GLN E 49 GLN E 67 HIS ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 136 GLN ** P 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 9 HIS ** W 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 16 ASN 4 65 ASN ** 6 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 177 ASN c 101 ASN ** d 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 63 ASN ** g 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 27 ASN ** k 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2594 moved from start: 0.9788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 162319 Z= 0.216 Angle : 0.803 14.654 242262 Z= 0.427 Chirality : 0.039 0.633 30547 Planarity : 0.007 0.123 13408 Dihedral : 24.355 179.560 80415 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 30.62 Ramachandran Plot: Outliers : 0.65 % Allowed : 7.84 % Favored : 91.51 % Rotamer: Outliers : 3.05 % Allowed : 12.61 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % 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: -2.11 (0.10), residues: 6305 helix: -0.52 (0.11), residues: 1999 sheet: -2.65 (0.16), residues: 838 loop : -1.59 (0.10), residues: 3468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP c 21 HIS 0.013 0.002 HIS 2 41 PHE 0.045 0.002 PHE h 44 TYR 0.045 0.003 TYR e 127 ARG 0.053 0.001 ARG k 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12610 Ramachandran restraints generated. 6305 Oldfield, 0 Emsley, 6305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12610 Ramachandran restraints generated. 6305 Oldfield, 0 Emsley, 6305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 5255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 338 time to evaluate : 6.184 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: D 145 MET cc_start: 0.3721 (mmm) cc_final: 0.2267 (mtt) REVERT: D 160 TYR cc_start: 0.5660 (OUTLIER) cc_final: 0.4172 (p90) REVERT: F 199 MET cc_start: 0.3144 (ttp) cc_final: 0.2782 (mtp) REVERT: I 1 MET cc_start: -0.1433 (mmm) cc_final: -0.1961 (mmm) REVERT: S 60 GLU cc_start: 0.8053 (pm20) cc_final: 0.7800 (pm20) REVERT: X 1 MET cc_start: 0.4129 (tmm) cc_final: 0.3350 (tmm) REVERT: X 37 ASP cc_start: 0.1385 (OUTLIER) cc_final: 0.0323 (m-30) REVERT: Z 48 MET cc_start: -0.0935 (OUTLIER) cc_final: -0.1420 (ptm) REVERT: 1 16 ASN cc_start: 0.5318 (OUTLIER) cc_final: 0.4837 (m-40) REVERT: 2 26 PHE cc_start: 0.3628 (OUTLIER) cc_final: 0.3301 (p90) REVERT: 9 35 GLN cc_start: -0.2743 (OUTLIER) cc_final: -0.5108 (mt0) REVERT: e 75 LEU cc_start: 0.3464 (OUTLIER) cc_final: 0.3009 (mt) REVERT: e 95 MET cc_start: -0.4217 (ptm) cc_final: -0.5699 (mtp) REVERT: g 84 TYR cc_start: 0.4317 (p90) cc_final: 0.3091 (m-80) REVERT: h 2 MET cc_start: 0.1065 (ppp) cc_final: 0.0706 (ptm) REVERT: h 9 MET cc_start: 0.0134 (ttt) cc_final: -0.0181 (ttt) REVERT: h 44 PHE cc_start: 0.4531 (OUTLIER) cc_final: 0.4292 (m-80) REVERT: k 117 HIS cc_start: -0.0603 (OUTLIER) cc_final: -0.0864 (t70) REVERT: m 80 MET cc_start: -0.3695 (mtm) cc_final: -0.4023 (mtt) REVERT: r 71 ASP cc_start: -0.1161 (OUTLIER) cc_final: -0.2479 (t0) REVERT: t 26 MET cc_start: -0.4191 (ttt) cc_final: -0.4514 (ttt) REVERT: J 1 MET cc_start: 0.3758 (OUTLIER) cc_final: 0.1925 (mmp) REVERT: J 52 MET cc_start: 0.0914 (mtp) cc_final: 0.0643 (mtt) outliers start: 147 outliers final: 81 residues processed: 435 average time/residue: 1.3051 time to fit residues: 980.8726 Evaluate side-chains 399 residues out of total 5255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 307 time to evaluate : 5.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 160 TYR Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain E residue 67 HIS Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 163 TYR Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain N residue 52 ASP Chi-restraints excluded: chain N residue 81 ILE Chi-restraints excluded: chain N residue 120 ARG Chi-restraints excluded: chain O residue 9 ASN Chi-restraints excluded: chain O residue 12 ASP Chi-restraints excluded: chain O residue 82 ASN Chi-restraints excluded: chain P residue 77 ILE Chi-restraints excluded: chain P residue 111 ILE Chi-restraints excluded: chain Q residue 96 ILE Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 95 THR Chi-restraints excluded: chain S residue 29 HIS Chi-restraints excluded: chain S residue 49 VAL Chi-restraints excluded: chain U residue 8 ILE Chi-restraints excluded: chain U residue 59 LEU Chi-restraints excluded: chain V residue 41 ILE Chi-restraints excluded: chain W residue 62 ASP Chi-restraints excluded: chain W residue 74 ILE Chi-restraints excluded: chain X residue 32 LEU Chi-restraints excluded: chain X residue 37 ASP Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 27 VAL Chi-restraints excluded: chain Z residue 48 MET Chi-restraints excluded: chain Z residue 79 ARG Chi-restraints excluded: chain 0 residue 49 CYS Chi-restraints excluded: chain 1 residue 2 ARG Chi-restraints excluded: chain 1 residue 16 ASN Chi-restraints excluded: chain 2 residue 26 PHE Chi-restraints excluded: chain 5 residue 9 ARG Chi-restraints excluded: chain 8 residue 48 MET Chi-restraints excluded: chain 9 residue 10 LEU Chi-restraints excluded: chain 9 residue 35 GLN Chi-restraints excluded: chain b residue 38 HIS Chi-restraints excluded: chain b residue 40 ILE Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 68 PHE Chi-restraints excluded: chain b residue 96 LEU Chi-restraints excluded: chain b residue 162 VAL Chi-restraints excluded: chain c residue 20 THR Chi-restraints excluded: chain c residue 42 LEU Chi-restraints excluded: chain c residue 51 VAL Chi-restraints excluded: chain c residue 105 VAL Chi-restraints excluded: chain c residue 115 VAL Chi-restraints excluded: chain d residue 170 LEU Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 37 HIS Chi-restraints excluded: chain f residue 88 MET Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain g residue 21 LEU Chi-restraints excluded: chain g residue 143 MET Chi-restraints excluded: chain h residue 44 PHE Chi-restraints excluded: chain i residue 5 TYR Chi-restraints excluded: chain i residue 20 ILE Chi-restraints excluded: chain i residue 45 MET Chi-restraints excluded: chain j residue 9 ARG Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 84 MET Chi-restraints excluded: chain k residue 92 ARG Chi-restraints excluded: chain k residue 117 HIS Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain m residue 42 VAL Chi-restraints excluded: chain m residue 53 ASP Chi-restraints excluded: chain m residue 73 SER Chi-restraints excluded: chain m residue 102 LYS Chi-restraints excluded: chain o residue 20 ASP Chi-restraints excluded: chain o residue 58 MET Chi-restraints excluded: chain q residue 7 LEU Chi-restraints excluded: chain r residue 33 THR Chi-restraints excluded: chain r residue 71 ASP Chi-restraints excluded: chain t residue 53 MET Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 85 ILE Chi-restraints excluded: chain K residue 125 THR Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 57 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1094 random chunks: chunk 1020 optimal weight: 8.9990 chunk 119 optimal weight: 20.0000 chunk 603 optimal weight: 7.9990 chunk 772 optimal weight: 10.0000 chunk 598 optimal weight: 0.4980 chunk 891 optimal weight: 7.9990 chunk 591 optimal weight: 0.4980 chunk 1054 optimal weight: 6.9990 chunk 659 optimal weight: 20.0000 chunk 642 optimal weight: 20.0000 chunk 486 optimal weight: 0.5980 overall best weight: 3.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 HIS ** H 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 54 GLN T 11 GLN ** U 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 49 ASN ** 1 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 58 ASN ** 6 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 101 ASN d 39 GLN ** d 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 11 HIS ** g 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 20 ASN t 69 ASN ** K 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2558 moved from start: 1.0278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.166 162319 Z= 0.174 Angle : 0.741 20.105 242262 Z= 0.397 Chirality : 0.036 0.547 30547 Planarity : 0.007 0.122 13408 Dihedral : 24.305 178.911 80415 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 26.91 Ramachandran Plot: Outliers : 0.63 % Allowed : 7.30 % Favored : 92.07 % Rotamer: Outliers : 2.67 % Allowed : 13.66 % Favored : 83.66 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.47 % 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: -1.85 (0.10), residues: 6305 helix: -0.21 (0.12), residues: 2013 sheet: -2.40 (0.16), residues: 899 loop : -1.49 (0.10), residues: 3393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP n 101 HIS 0.054 0.002 HIS E 67 PHE 0.033 0.002 PHE 7 18 TYR 0.035 0.002 TYR g 43 ARG 0.021 0.001 ARG o 62 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12610 Ramachandran restraints generated. 6305 Oldfield, 0 Emsley, 6305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12610 Ramachandran restraints generated. 6305 Oldfield, 0 Emsley, 6305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 5255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 342 time to evaluate : 5.944 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: D 160 TYR cc_start: 0.5589 (OUTLIER) cc_final: 0.4316 (p90) REVERT: G 139 GLU cc_start: 0.5795 (mp0) cc_final: 0.5501 (mp0) REVERT: I 1 MET cc_start: -0.1373 (mmm) cc_final: -0.2059 (mmm) REVERT: N 108 MET cc_start: -0.4296 (tpt) cc_final: -0.4868 (tpt) REVERT: O 45 GLU cc_start: 0.4139 (mm-30) cc_final: 0.3637 (mp0) REVERT: S 60 GLU cc_start: 0.8112 (pm20) cc_final: 0.7883 (pm20) REVERT: X 1 MET cc_start: 0.4233 (tmm) cc_final: 0.3497 (tmm) REVERT: X 37 ASP cc_start: 0.0645 (OUTLIER) cc_final: -0.0590 (m-30) REVERT: e 95 MET cc_start: -0.4138 (ptm) cc_final: -0.5381 (mtp) REVERT: g 84 TYR cc_start: 0.4299 (p90) cc_final: 0.3086 (m-80) REVERT: h 2 MET cc_start: 0.1011 (ppp) cc_final: 0.0604 (ptm) REVERT: h 9 MET cc_start: 0.0106 (ttt) cc_final: -0.0217 (ttt) REVERT: k 117 HIS cc_start: -0.0313 (OUTLIER) cc_final: -0.0578 (t70) REVERT: r 71 ASP cc_start: -0.0935 (OUTLIER) cc_final: -0.1704 (t0) REVERT: t 26 MET cc_start: -0.3736 (ttt) cc_final: -0.4095 (ttt) REVERT: J 52 MET cc_start: 0.1034 (mtp) cc_final: 0.0735 (mtt) REVERT: K 18 ASN cc_start: 0.8212 (t0) cc_final: 0.7849 (m-40) outliers start: 129 outliers final: 77 residues processed: 427 average time/residue: 1.3793 time to fit residues: 1037.6633 Evaluate side-chains 395 residues out of total 5255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 314 time to evaluate : 6.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 160 TYR Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 163 TYR Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 56 VAL Chi-restraints excluded: chain O residue 9 ASN Chi-restraints excluded: chain O residue 82 ASN Chi-restraints excluded: chain P residue 77 ILE Chi-restraints excluded: chain P residue 111 ILE Chi-restraints excluded: chain Q residue 96 ILE Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 95 THR Chi-restraints excluded: chain S residue 29 HIS Chi-restraints excluded: chain S residue 69 ASP Chi-restraints excluded: chain U residue 8 ILE Chi-restraints excluded: chain V residue 12 HIS Chi-restraints excluded: chain V residue 20 VAL Chi-restraints excluded: chain W residue 62 ASP Chi-restraints excluded: chain W residue 74 ILE Chi-restraints excluded: chain X residue 32 LEU Chi-restraints excluded: chain X residue 37 ASP Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 64 ILE Chi-restraints excluded: chain Z residue 79 ARG Chi-restraints excluded: chain 1 residue 2 ARG Chi-restraints excluded: chain 1 residue 55 MET Chi-restraints excluded: chain 5 residue 9 ARG Chi-restraints excluded: chain 9 residue 10 LEU Chi-restraints excluded: chain b residue 38 HIS Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 68 PHE Chi-restraints excluded: chain b residue 96 LEU Chi-restraints excluded: chain b residue 162 VAL Chi-restraints excluded: chain c residue 20 THR Chi-restraints excluded: chain c residue 42 LEU Chi-restraints excluded: chain c residue 105 VAL Chi-restraints excluded: chain c residue 115 VAL Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 37 HIS Chi-restraints excluded: chain f residue 88 MET Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain g residue 26 VAL Chi-restraints excluded: chain g residue 130 LYS Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain g residue 143 MET Chi-restraints excluded: chain i residue 5 TYR Chi-restraints excluded: chain i residue 45 MET Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain k residue 45 THR Chi-restraints excluded: chain k residue 84 MET Chi-restraints excluded: chain k residue 92 ARG Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain k residue 117 HIS Chi-restraints excluded: chain m residue 42 VAL Chi-restraints excluded: chain m residue 53 ASP Chi-restraints excluded: chain m residue 73 SER Chi-restraints excluded: chain o residue 86 LEU Chi-restraints excluded: chain p residue 1 MET Chi-restraints excluded: chain q residue 7 LEU Chi-restraints excluded: chain q residue 69 THR Chi-restraints excluded: chain r residue 71 ASP Chi-restraints excluded: chain t residue 53 MET Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain J residue 23 LEU Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 16 MET Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 85 ILE Chi-restraints excluded: chain s residue 43 MET Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 51 HIS Chi-restraints excluded: chain s residue 57 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1094 random chunks: chunk 652 optimal weight: 30.0000 chunk 421 optimal weight: 20.0000 chunk 629 optimal weight: 20.0000 chunk 317 optimal weight: 6.9990 chunk 207 optimal weight: 20.0000 chunk 204 optimal weight: 20.0000 chunk 670 optimal weight: 20.0000 chunk 718 optimal weight: 10.0000 chunk 521 optimal weight: 5.9990 chunk 98 optimal weight: 20.0000 chunk 828 optimal weight: 10.0000 overall best weight: 10.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN E 164 GLN ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 138 GLN ** H 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 73 ASN ** U 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 16 ASN ** 4 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 111 GLN ** t 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 5 GLN ** K 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3284 moved from start: 1.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.189 162319 Z= 0.436 Angle : 1.295 24.326 242262 Z= 0.644 Chirality : 0.058 0.688 30547 Planarity : 0.011 0.322 13408 Dihedral : 25.447 179.954 80415 Min Nonbonded Distance : 1.710 Molprobity Statistics. All-atom Clashscore : 59.04 Ramachandran Plot: Outliers : 0.75 % Allowed : 11.10 % Favored : 88.15 % Rotamer: Outliers : 3.26 % Allowed : 14.45 % Favored : 82.29 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.10), residues: 6305 helix: -1.27 (0.11), residues: 1965 sheet: -2.64 (0.16), residues: 818 loop : -2.21 (0.10), residues: 3522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.005 TRP b 22 HIS 0.103 0.005 HIS b 38 PHE 0.081 0.005 PHE R 87 TYR 0.051 0.005 TYR e 127 ARG 0.086 0.002 ARG 2 48 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12610 Ramachandran restraints generated. 6305 Oldfield, 0 Emsley, 6305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12610 Ramachandran restraints generated. 6305 Oldfield, 0 Emsley, 6305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 5255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 367 time to evaluate : 6.078 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: D 160 TYR cc_start: 0.6323 (OUTLIER) cc_final: 0.4317 (p90) REVERT: D 215 VAL cc_start: 0.3281 (OUTLIER) cc_final: 0.2652 (t) REVERT: N 108 MET cc_start: -0.3429 (tpt) cc_final: -0.3820 (tpt) REVERT: N 118 MET cc_start: -0.3650 (ppp) cc_final: -0.3971 (ppp) REVERT: T 108 ARG cc_start: 0.4060 (ptt-90) cc_final: 0.3127 (mmp-170) REVERT: X 1 MET cc_start: 0.6135 (tmm) cc_final: 0.5280 (tmm) REVERT: X 37 ASP cc_start: 0.1676 (OUTLIER) cc_final: 0.0706 (m-30) REVERT: 2 56 LEU cc_start: 0.7908 (mt) cc_final: 0.6999 (mt) REVERT: 9 35 GLN cc_start: -0.1082 (OUTLIER) cc_final: -0.4867 (mm-40) REVERT: b 96 LEU cc_start: 0.5502 (mp) cc_final: 0.5276 (mt) REVERT: e 95 MET cc_start: -0.4726 (ptm) cc_final: -0.5518 (mtp) REVERT: e 156 ARG cc_start: 0.4491 (OUTLIER) cc_final: 0.3758 (ptm-80) REVERT: h 2 MET cc_start: 0.2186 (ppp) cc_final: 0.1910 (ptm) REVERT: h 9 MET cc_start: 0.0647 (ttt) cc_final: 0.0355 (ttt) REVERT: m 10 ASP cc_start: 0.7976 (t70) cc_final: 0.7692 (t0) REVERT: m 80 MET cc_start: -0.2812 (mtt) cc_final: -0.3983 (mmt) REVERT: t 26 MET cc_start: -0.4060 (ttt) cc_final: -0.4345 (ttt) REVERT: K 9 LYS cc_start: 0.7146 (mmtm) cc_final: 0.6739 (tmtt) REVERT: K 59 THR cc_start: 0.9024 (t) cc_final: 0.8684 (m) outliers start: 157 outliers final: 102 residues processed: 478 average time/residue: 1.3262 time to fit residues: 1099.4059 Evaluate side-chains 430 residues out of total 5255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 323 time to evaluate : 6.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 160 TYR Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain D residue 200 MET Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 202 ILE Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain G residue 6 TYR Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 163 TYR Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain N residue 52 ASP Chi-restraints excluded: chain N residue 81 ILE Chi-restraints excluded: chain O residue 9 ASN Chi-restraints excluded: chain O residue 20 MET Chi-restraints excluded: chain O residue 39 ILE Chi-restraints excluded: chain O residue 40 LYS Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 82 ASN Chi-restraints excluded: chain P residue 111 ILE Chi-restraints excluded: chain P residue 144 GLU Chi-restraints excluded: chain Q residue 46 ILE Chi-restraints excluded: chain Q residue 65 ILE Chi-restraints excluded: chain Q residue 96 ILE Chi-restraints excluded: chain S residue 29 HIS Chi-restraints excluded: chain S residue 69 ASP Chi-restraints excluded: chain U residue 8 ILE Chi-restraints excluded: chain V residue 12 HIS Chi-restraints excluded: chain V residue 20 VAL Chi-restraints excluded: chain V residue 41 ILE Chi-restraints excluded: chain W residue 62 ASP Chi-restraints excluded: chain W residue 74 ILE Chi-restraints excluded: chain X residue 37 ASP Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 27 VAL Chi-restraints excluded: chain Y residue 64 ILE Chi-restraints excluded: chain Z residue 47 VAL Chi-restraints excluded: chain Z residue 65 VAL Chi-restraints excluded: chain Z residue 79 ARG Chi-restraints excluded: chain 1 residue 2 ARG Chi-restraints excluded: chain 5 residue 9 ARG Chi-restraints excluded: chain 9 residue 10 LEU Chi-restraints excluded: chain 9 residue 35 GLN Chi-restraints excluded: chain b residue 38 HIS Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 68 PHE Chi-restraints excluded: chain b residue 162 VAL Chi-restraints excluded: chain c residue 42 LEU Chi-restraints excluded: chain c residue 61 LYS Chi-restraints excluded: chain c residue 63 ILE Chi-restraints excluded: chain c residue 128 MET Chi-restraints excluded: chain d residue 170 LEU Chi-restraints excluded: chain e residue 105 ILE Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain e residue 156 ARG Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 37 HIS Chi-restraints excluded: chain f residue 88 MET Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain g residue 21 LEU Chi-restraints excluded: chain g residue 43 TYR Chi-restraints excluded: chain g residue 46 LEU Chi-restraints excluded: chain g residue 96 ASN Chi-restraints excluded: chain g residue 130 LYS Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain i residue 27 ILE Chi-restraints excluded: chain i residue 45 MET Chi-restraints excluded: chain i residue 110 VAL Chi-restraints excluded: chain k residue 92 ARG Chi-restraints excluded: chain k residue 100 ASN Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain k residue 117 HIS Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 111 GLN Chi-restraints excluded: chain m residue 53 ASP Chi-restraints excluded: chain m residue 73 SER Chi-restraints excluded: chain m residue 76 ILE Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 58 MET Chi-restraints excluded: chain o residue 61 GLN Chi-restraints excluded: chain o residue 86 LEU Chi-restraints excluded: chain p residue 1 MET Chi-restraints excluded: chain q residue 7 LEU Chi-restraints excluded: chain q residue 69 THR Chi-restraints excluded: chain t residue 53 MET Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain J residue 86 MET Chi-restraints excluded: chain K residue 16 MET Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 85 ILE Chi-restraints excluded: chain n residue 19 TYR Chi-restraints excluded: chain n residue 79 LEU Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 51 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1094 random chunks: chunk 959 optimal weight: 0.5980 chunk 1010 optimal weight: 1.9990 chunk 921 optimal weight: 1.9990 chunk 982 optimal weight: 20.0000 chunk 1009 optimal weight: 0.0070 chunk 591 optimal weight: 20.0000 chunk 428 optimal weight: 8.9990 chunk 771 optimal weight: 8.9990 chunk 301 optimal weight: 0.6980 chunk 887 optimal weight: 0.7980 chunk 929 optimal weight: 8.9990 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN D 152 GLN E 67 HIS E 149 ASN ** H 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 65 GLN ** Y 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 15 ASN c 101 ASN ** d 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 81 GLN ** e 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 51 GLN h 75 GLN ** i 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 58 ASN l 4 ASN ** m 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 27 GLN q 30 HIS t 2 ASN K 5 GLN ** K 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 68 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2729 moved from start: 1.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.159 162319 Z= 0.188 Angle : 0.819 16.087 242262 Z= 0.431 Chirality : 0.040 0.386 30547 Planarity : 0.007 0.121 13408 Dihedral : 24.868 179.405 80415 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 26.20 Ramachandran Plot: Outliers : 0.67 % Allowed : 7.63 % Favored : 91.70 % Rotamer: Outliers : 1.76 % Allowed : 16.30 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.25 (0.10), residues: 6305 helix: -0.48 (0.12), residues: 1983 sheet: -2.33 (0.16), residues: 878 loop : -1.88 (0.10), residues: 3444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP s 33 HIS 0.021 0.002 HIS 6 18 PHE 0.033 0.002 PHE 7 18 TYR 0.034 0.002 TYR g 43 ARG 0.022 0.001 ARG l 113 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12610 Ramachandran restraints generated. 6305 Oldfield, 0 Emsley, 6305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12610 Ramachandran restraints generated. 6305 Oldfield, 0 Emsley, 6305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 5255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 357 time to evaluate : 6.122 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: D 160 TYR cc_start: 0.5309 (OUTLIER) cc_final: 0.3904 (p90) REVERT: G 9 ASP cc_start: 0.7609 (p0) cc_final: 0.7372 (p0) REVERT: H 74 MET cc_start: 0.1989 (ppp) cc_final: 0.1599 (ptp) REVERT: N 108 MET cc_start: -0.4327 (tpt) cc_final: -0.4842 (tpt) REVERT: N 118 MET cc_start: -0.4037 (ppp) cc_final: -0.4402 (ppp) REVERT: S 60 GLU cc_start: 0.7953 (pm20) cc_final: 0.7698 (pm20) REVERT: W 92 ARG cc_start: 0.1822 (ptp90) cc_final: 0.0470 (ttt-90) REVERT: X 1 MET cc_start: 0.5677 (tmm) cc_final: 0.4782 (tmm) REVERT: 0 32 ILE cc_start: 0.2975 (mt) cc_final: 0.2736 (mm) REVERT: 9 35 GLN cc_start: -0.1683 (OUTLIER) cc_final: -0.4957 (mm-40) REVERT: b 48 MET cc_start: 0.2231 (OUTLIER) cc_final: 0.1845 (ptt) REVERT: d 56 GLU cc_start: 0.7856 (tp30) cc_final: 0.7622 (tp30) REVERT: e 95 MET cc_start: -0.5096 (ptm) cc_final: -0.5568 (mtp) REVERT: f 21 MET cc_start: 0.3809 (pmm) cc_final: 0.3443 (pmm) REVERT: g 61 PHE cc_start: 0.3941 (OUTLIER) cc_final: 0.3667 (m-80) REVERT: g 84 TYR cc_start: 0.4599 (p90) cc_final: 0.3026 (m-80) REVERT: h 2 MET cc_start: 0.0986 (ppp) cc_final: 0.0632 (ptm) REVERT: m 77 LYS cc_start: 0.4909 (mmtt) cc_final: 0.4498 (mmtt) REVERT: m 80 MET cc_start: -0.3982 (mtt) cc_final: -0.5699 (tmm) REVERT: t 26 MET cc_start: -0.4067 (ttt) cc_final: -0.4419 (ttt) REVERT: J 1 MET cc_start: 0.3909 (OUTLIER) cc_final: 0.2304 (mmm) REVERT: J 52 MET cc_start: 0.1944 (mtp) cc_final: 0.1716 (mtt) REVERT: K 59 THR cc_start: 0.8957 (t) cc_final: 0.8550 (m) REVERT: K 100 ILE cc_start: 0.7776 (tp) cc_final: 0.7221 (mp) REVERT: s 65 MET cc_start: 0.3610 (mtp) cc_final: 0.2746 (mtp) outliers start: 85 outliers final: 56 residues processed: 412 average time/residue: 1.3192 time to fit residues: 945.8252 Evaluate side-chains 383 residues out of total 5255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 322 time to evaluate : 5.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 160 TYR Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 173 THR Chi-restraints excluded: chain G residue 4 HIS Chi-restraints excluded: chain G residue 136 ILE Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 163 TYR Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain O residue 9 ASN Chi-restraints excluded: chain O residue 39 ILE Chi-restraints excluded: chain O residue 40 LYS Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 82 ASN Chi-restraints excluded: chain P residue 111 ILE Chi-restraints excluded: chain Q residue 96 ILE Chi-restraints excluded: chain S residue 29 HIS Chi-restraints excluded: chain U residue 8 ILE Chi-restraints excluded: chain W residue 62 ASP Chi-restraints excluded: chain W residue 74 ILE Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Z residue 79 ARG Chi-restraints excluded: chain 5 residue 9 ARG Chi-restraints excluded: chain 5 residue 45 ASP Chi-restraints excluded: chain 9 residue 35 GLN Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 48 MET Chi-restraints excluded: chain b residue 68 PHE Chi-restraints excluded: chain c residue 42 LEU Chi-restraints excluded: chain c residue 105 VAL Chi-restraints excluded: chain d residue 170 LEU Chi-restraints excluded: chain f residue 18 VAL Chi-restraints excluded: chain f residue 37 HIS Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain g residue 26 VAL Chi-restraints excluded: chain g residue 46 LEU Chi-restraints excluded: chain g residue 61 PHE Chi-restraints excluded: chain g residue 96 ASN Chi-restraints excluded: chain g residue 130 LYS Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain i residue 45 MET Chi-restraints excluded: chain i residue 56 MET Chi-restraints excluded: chain k residue 92 ARG Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain o residue 86 LEU Chi-restraints excluded: chain p residue 1 MET Chi-restraints excluded: chain t residue 53 MET Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain K residue 85 ILE Chi-restraints excluded: chain n residue 79 LEU Chi-restraints excluded: chain s residue 43 MET Chi-restraints excluded: chain s residue 51 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1094 random chunks: chunk 979 optimal weight: 10.0000 chunk 645 optimal weight: 20.0000 chunk 1039 optimal weight: 0.1980 chunk 634 optimal weight: 20.0000 chunk 492 optimal weight: 30.0000 chunk 722 optimal weight: 20.0000 chunk 1089 optimal weight: 40.0000 chunk 1003 optimal weight: 5.9990 chunk 867 optimal weight: 5.9990 chunk 90 optimal weight: 20.0000 chunk 670 optimal weight: 10.0000 overall best weight: 6.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 142 GLN ** I 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 73 ASN ** U 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 45 GLN ** Y 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 101 ASN ** d 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 75 GLN i 4 GLN ** j 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 2 ASN K 5 GLN ** K 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 68 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3130 moved from start: 1.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.173 162319 Z= 0.276 Angle : 0.941 21.128 242262 Z= 0.482 Chirality : 0.044 0.455 30547 Planarity : 0.008 0.124 13408 Dihedral : 25.027 179.769 80415 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 41.41 Ramachandran Plot: Outliers : 0.57 % Allowed : 10.39 % Favored : 89.04 % Rotamer: Outliers : 1.62 % Allowed : 16.77 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.47 % 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: -2.39 (0.10), residues: 6305 helix: -0.64 (0.12), residues: 1983 sheet: -2.33 (0.17), residues: 844 loop : -1.98 (0.10), residues: 3478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP b 95 HIS 0.019 0.002 HIS 2 41 PHE 0.040 0.003 PHE 7 18 TYR 0.032 0.003 TYR O 32 ARG 0.034 0.001 ARG R 30 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12610 Ramachandran restraints generated. 6305 Oldfield, 0 Emsley, 6305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12610 Ramachandran restraints generated. 6305 Oldfield, 0 Emsley, 6305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 5255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 336 time to evaluate : 6.141 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: D 160 TYR cc_start: 0.5996 (OUTLIER) cc_final: 0.4644 (p90) REVERT: F 95 LYS cc_start: 0.3483 (mtpt) cc_final: 0.2844 (mtpt) REVERT: F 109 LEU cc_start: 0.4802 (pp) cc_final: 0.4435 (tp) REVERT: F 141 MET cc_start: -0.5862 (ptt) cc_final: -0.6141 (ptt) REVERT: H 74 MET cc_start: 0.1910 (ppp) cc_final: 0.1446 (ptp) REVERT: N 108 MET cc_start: -0.3655 (tpt) cc_final: -0.4004 (tpt) REVERT: N 118 MET cc_start: -0.3897 (ppp) cc_final: -0.4160 (ppp) REVERT: R 110 MET cc_start: 0.2481 (tpt) cc_final: 0.2225 (tpt) REVERT: X 1 MET cc_start: 0.6173 (tmm) cc_final: 0.5105 (tmm) REVERT: X 37 ASP cc_start: -0.0212 (OUTLIER) cc_final: -0.1045 (m-30) REVERT: 0 32 ILE cc_start: 0.2792 (mt) cc_final: 0.2483 (mm) REVERT: 2 43 LEU cc_start: 0.6756 (mt) cc_final: 0.6521 (mp) REVERT: 9 35 GLN cc_start: -0.1680 (OUTLIER) cc_final: -0.5137 (mm-40) REVERT: e 95 MET cc_start: -0.5057 (ptm) cc_final: -0.5654 (mtp) REVERT: f 21 MET cc_start: 0.4146 (pmm) cc_final: 0.3877 (pmm) REVERT: h 2 MET cc_start: 0.1776 (ppp) cc_final: 0.1411 (ptm) REVERT: m 80 MET cc_start: -0.3458 (mtt) cc_final: -0.5431 (tmm) REVERT: t 26 MET cc_start: -0.4187 (ttt) cc_final: -0.4454 (ttt) REVERT: K 9 LYS cc_start: 0.7294 (mmtm) cc_final: 0.6881 (tmtt) REVERT: K 59 THR cc_start: 0.8992 (t) cc_final: 0.8631 (m) REVERT: K 100 ILE cc_start: 0.7701 (tp) cc_final: 0.7146 (mp) outliers start: 78 outliers final: 66 residues processed: 389 average time/residue: 1.3439 time to fit residues: 911.7877 Evaluate side-chains 383 residues out of total 5255 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 314 time to evaluate : 6.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 160 TYR Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain F residue 69 ARG Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 163 TYR Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain N residue 52 ASP Chi-restraints excluded: chain O residue 9 ASN Chi-restraints excluded: chain O residue 39 ILE Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 82 ASN Chi-restraints excluded: chain P residue 111 ILE Chi-restraints excluded: chain P residue 144 GLU Chi-restraints excluded: chain Q residue 65 ILE Chi-restraints excluded: chain Q residue 96 ILE Chi-restraints excluded: chain R residue 73 ASN Chi-restraints excluded: chain S residue 29 HIS Chi-restraints excluded: chain S residue 49 VAL Chi-restraints excluded: chain U residue 8 ILE Chi-restraints excluded: chain V residue 12 HIS Chi-restraints excluded: chain W residue 62 ASP Chi-restraints excluded: chain W residue 74 ILE Chi-restraints excluded: chain X residue 37 ASP Chi-restraints excluded: chain Y residue 11 ILE Chi-restraints excluded: chain Y residue 64 ILE Chi-restraints excluded: chain Z residue 79 ARG Chi-restraints excluded: chain 5 residue 9 ARG Chi-restraints excluded: chain 9 residue 35 GLN Chi-restraints excluded: chain b residue 22 TRP Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 68 PHE Chi-restraints excluded: chain b residue 96 LEU Chi-restraints excluded: chain c residue 42 LEU Chi-restraints excluded: chain c residue 63 ILE Chi-restraints excluded: chain d residue 170 LEU Chi-restraints excluded: chain e residue 105 ILE Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain f residue 37 HIS Chi-restraints excluded: chain f residue 97 THR Chi-restraints excluded: chain g residue 26 VAL Chi-restraints excluded: chain g residue 93 VAL Chi-restraints excluded: chain g residue 96 ASN Chi-restraints excluded: chain g residue 130 LYS Chi-restraints excluded: chain g residue 134 VAL Chi-restraints excluded: chain i residue 45 MET Chi-restraints excluded: chain i residue 56 MET Chi-restraints excluded: chain k residue 92 ARG Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain l residue 63 THR Chi-restraints excluded: chain m residue 20 SER Chi-restraints excluded: chain o residue 61 GLN Chi-restraints excluded: chain o residue 86 LEU Chi-restraints excluded: chain p residue 1 MET Chi-restraints excluded: chain t residue 53 MET Chi-restraints excluded: chain t residue 57 VAL Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 85 ILE Chi-restraints excluded: chain n residue 19 TYR Chi-restraints excluded: chain n residue 79 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1094 random chunks: chunk 532 optimal weight: 0.0980 chunk 689 optimal weight: 30.0000 chunk 924 optimal weight: 20.0000 chunk 265 optimal weight: 20.0000 chunk 800 optimal weight: 40.0000 chunk 128 optimal weight: 20.0000 chunk 241 optimal weight: 20.0000 chunk 869 optimal weight: 20.0000 chunk 363 optimal weight: 0.5980 chunk 892 optimal weight: 6.9990 chunk 110 optimal weight: 20.0000 overall best weight: 9.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 75 GLN ** j 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 2 ASN ** K 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4730 r_free = 0.4730 target = 0.138233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.125267 restraints weight = 833019.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.128045 restraints weight = 494602.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.129836 restraints weight = 321964.407| |-----------------------------------------------------------------------------| r_work (final): 0.4638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4144 moved from start: 1.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.313 162319 Z= 0.324 Angle : 0.955 59.199 242262 Z= 0.494 Chirality : 0.044 0.782 30547 Planarity : 0.008 0.149 13408 Dihedral : 25.029 179.754 80415 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 42.82 Ramachandran Plot: Outliers : 0.57 % Allowed : 10.42 % Favored : 89.01 % Rotamer: Outliers : 1.80 % Allowed : 16.92 % Favored : 81.28 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.47 % 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: -2.39 (0.10), residues: 6305 helix: -0.64 (0.12), residues: 1982 sheet: -2.33 (0.17), residues: 844 loop : -1.99 (0.10), residues: 3479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP s 33 HIS 0.016 0.002 HIS 2 41 PHE 0.072 0.003 PHE i 102 TYR 0.028 0.003 TYR g 43 ARG 0.064 0.001 ARG g 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21854.12 seconds wall clock time: 394 minutes 53.32 seconds (23693.32 seconds total)