Starting phenix.real_space_refine on Sat Mar 23 20:27:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h4n_0137/03_2024/6h4n_0137_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h4n_0137/03_2024/6h4n_0137.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h4n_0137/03_2024/6h4n_0137.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h4n_0137/03_2024/6h4n_0137.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h4n_0137/03_2024/6h4n_0137_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h4n_0137/03_2024/6h4n_0137_neut.pdb" } resolution = 3.0 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= 0.002 sd= 0.018 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 4636 5.49 5 S 154 5.16 5 C 74269 2.51 5 N 27457 2.21 5 O 40766 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b ARG 107": "NH1" <-> "NH2" Residue "b ARG 224": "NH1" <-> "NH2" Residue "c ARG 106": "NH1" <-> "NH2" Residue "c ARG 130": "NH1" <-> "NH2" Residue "e ARG 156": "NH1" <-> "NH2" Residue "f TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 123": "NH1" <-> "NH2" Residue "l ARG 55": "NH1" <-> "NH2" Residue "p ARG 28": "NH1" <-> "NH2" Residue "p PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "F ARG 70": "NH1" <-> "NH2" Residue "F ARG 79": "NH1" <-> "NH2" Residue "F ARG 91": "NH1" <-> "NH2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F ARG 111": "NH1" <-> "NH2" Residue "F ARG 114": "NH1" <-> "NH2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "G ARG 2": "NH1" <-> "NH2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G ARG 162": "NH1" <-> "NH2" Residue "G ARG 169": "NH1" <-> "NH2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M ARG 40": "NH1" <-> "NH2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M ARG 59": "NH1" <-> "NH2" Residue "M TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 114": "NH1" <-> "NH2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "N ARG 17": "NH1" <-> "NH2" Residue "N ARG 22": "NH1" <-> "NH2" Residue "N ARG 46": "NH1" <-> "NH2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N ARG 71": "NH1" <-> "NH2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "O ARG 10": "NH1" <-> "NH2" Residue "O ARG 16": "NH1" <-> "NH2" Residue "O ARG 25": "NH1" <-> "NH2" Residue "O ARG 81": "NH1" <-> "NH2" Residue "O ARG 94": "NH1" <-> "NH2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "O PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P ARG 61": "NH1" <-> "NH2" Residue "P ARG 88": "NH1" <-> "NH2" Residue "P TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 100": "NH1" <-> "NH2" Residue "P ARG 108": "NH1" <-> "NH2" Residue "Q ARG 2": "NH1" <-> "NH2" Residue "Q ARG 5": "NH1" <-> "NH2" Residue "Q ARG 12": "NH1" <-> "NH2" Residue "Q ARG 32": "NH1" <-> "NH2" Residue "Q ARG 47": "NH1" <-> "NH2" Residue "Q ARG 69": "NH1" <-> "NH2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 95": "NH1" <-> "NH2" Residue "S ARG 110": "NH1" <-> "NH2" Residue "T ARG 73": "NH1" <-> "NH2" Residue "U ARG 5": "NH1" <-> "NH2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U ARG 81": "NH1" <-> "NH2" Residue "U ARG 85": "NH1" <-> "NH2" Residue "U ARG 93": "NH1" <-> "NH2" Residue "V TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 10": "NH1" <-> "NH2" Residue "Z ARG 29": "NH1" <-> "NH2" Residue "Z ARG 44": "NH1" <-> "NH2" Residue "0 ARG 9": "NH1" <-> "NH2" Residue "0 ARG 15": "NH1" <-> "NH2" Residue "0 ARG 39": "NH1" <-> "NH2" Residue "0 ARG 51": "NH1" <-> "NH2" Residue "1 ARG 43": "NH1" <-> "NH2" Residue "1 TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 3": "NH1" <-> "NH2" Residue "2 ARG 12": "NH1" <-> "NH2" Residue "2 ARG 14": "NH1" <-> "NH2" Residue "2 ARG 19": "NH1" <-> "NH2" Residue "2 ARG 21": "NH1" <-> "NH2" Residue "2 ARG 33": "NH1" <-> "NH2" Residue "2 ARG 41": "NH1" <-> "NH2" Residue "3 ARG 12": "NH1" <-> "NH2" Residue "3 ARG 29": "NH1" <-> "NH2" Residue "3 ARG 39": "NH1" <-> "NH2" Residue "3 ARG 41": "NH1" <-> "NH2" Residue "4 ARG 12": "NH1" <-> "NH2" Residue "4 ARG 24": "NH1" <-> "NH2" Residue "6 ARG 49": "NH1" <-> "NH2" Residue "6 ARG 56": "NH1" <-> "NH2" Residue "y ASP 73": "OD1" <-> "OD2" Residue "y GLU 76": "OE1" <-> "OE2" Residue "y ARG 273": "NH1" <-> "NH2" Residue "y ARG 283": "NH1" <-> "NH2" Residue "y TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y ARG 340": "NH1" <-> "NH2" Residue "x ARG 17": "NH1" <-> "NH2" Residue "x TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 147282 Number of models: 1 Model: "" Number of chains: 57 Chain: "a" Number of atoms: 32916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1534, 32916 Classifications: {'RNA': 1534} Modifications used: {'p5*END': 1, 'rna2p_pur': 110, 'rna2p_pyr': 68, 'rna3p_pur': 764, 'rna3p_pyr': 592} Link IDs: {'rna2p': 178, 'rna3p': 1355} 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: 1266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1266 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 5, 'TRANS': 155} Chain: "h" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "i" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "j" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "k" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 869 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "l" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "m" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "n" Number of atoms: 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: "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: "s" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "t" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "u" Number of atoms: 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: "A" Number of atoms: 62261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2900, 62261 Classifications: {'RNA': 2900} Modifications used: {'p5*END': 1, 'rna2p_pur': 248, 'rna2p_pyr': 121, 'rna3p_pur': 1426, 'rna3p_pyr': 1105} Link IDs: {'rna2p': 369, 'rna3p': 2530} Chain breaks: 1 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': 8, 'rna2p_pyr': 5, 'rna3p_pur': 57, 'rna3p_pyr': 50} Link IDs: {'rna2p': 13, 'rna3p': 106} Chain: "C" 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: "D" 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: "E" 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: "F" 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: "G" 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: "H" 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: "J" 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: "K" 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: "L" 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: "M" 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: "N" 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: "O" 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: "P" 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: "Q" 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: "R" 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: "S" 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: "T" 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: "U" 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: "V" 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: "W" 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: "X" 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: "Y" 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: "Z" 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: "0" 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: "1" 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: "2" 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: "3" 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: "4" 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: "6" 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: "w" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1642 Classifications: {'RNA': 77} Modifications used: {'p5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 6, 'rna3p_pur': 30, 'rna3p_pyr': 32} Link IDs: {'rna2p': 14, 'rna3p': 62} Chain breaks: 1 Chain: "v" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 453 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "y" Number of atoms: 2180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2180 Classifications: {'peptide': 351} Incomplete info: {'truncation_to_alanine': 159} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 340} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 575 Unresolved non-hydrogen angles: 733 Unresolved non-hydrogen dihedrals: 468 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 7, 'TRP:plan': 3, 'ASP:plan': 12, 'PHE:plan': 6, 'GLU:plan': 21, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 318 Chain: "x" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 754 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 94} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 4, 'rna3p_pyr': 1} Link IDs: {'rna2p': 3, 'rna3p': 1} Time building chain proxies: 56.71, per 1000 atoms: 0.39 Number of scatterers: 147282 At special positions: 0 Unit cell: (267.748, 277.504, 231.976, 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 154 16.00 P 4636 15.00 O 40766 8.00 N 27457 7.00 C 74269 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 6 18 " - pdb=" SG CYS 6 40 " distance=2.02 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: 59.42 Conformation dependent library (CDL) restraints added in 7.2 seconds 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11368 Finding SS restraints... Secondary structure from input PDB file: 179 helices and 77 sheets defined 33.4% alpha, 16.9% beta 1555 base pairs and 2549 stacking pairs defined. Time for finding SS restraints: 54.26 Creating SS restraints... Processing helix chain 'b' and resid 23 through 27 removed outlier: 3.583A pdb=" N LYS b 27 " --> pdb=" O PRO b 24 " (cutoff:3.500A) Processing helix chain 'b' and resid 41 through 61 removed outlier: 3.874A pdb=" N VAL b 46 " --> pdb=" O LEU b 42 " (cutoff:3.500A) Proline residue: b 47 - end of helix removed outlier: 3.739A pdb=" N GLU b 55 " --> pdb=" O GLU b 51 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS b 58 " --> pdb=" O ALA b 54 " (cutoff:3.500A) Processing helix chain 'b' and resid 75 through 85 removed outlier: 3.760A pdb=" N VAL b 79 " --> pdb=" O ALA b 75 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS b 80 " --> pdb=" O SER b 76 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER b 85 " --> pdb=" O ASP b 81 " (cutoff:3.500A) Processing helix chain 'b' and resid 102 through 122 removed outlier: 4.675A pdb=" N GLN b 108 " --> pdb=" O LYS b 104 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N SER b 109 " --> pdb=" O THR b 105 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN b 119 " --> pdb=" O ASP b 115 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ASP b 122 " --> pdb=" O THR b 118 " (cutoff:3.500A) Processing helix chain 'b' and resid 129 through 148 removed outlier: 3.779A pdb=" N ARG b 138 " --> pdb=" O LEU b 134 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASN b 145 " --> pdb=" O GLU b 141 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER b 146 " --> pdb=" O LYS b 142 " (cutoff:3.500A) Processing helix chain 'b' and resid 168 through 178 removed outlier: 3.971A pdb=" N LEU b 178 " --> pdb=" O GLU b 174 " (cutoff:3.500A) Processing helix chain 'b' and resid 205 through 224 removed outlier: 4.200A pdb=" N LEU b 213 " --> pdb=" O VAL b 209 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 46 removed outlier: 4.011A pdb=" N ASP c 35 " --> pdb=" O ASN c 31 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG c 39 " --> pdb=" O ASP c 35 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 77 removed outlier: 3.707A pdb=" N VAL c 75 " --> pdb=" O ARG c 71 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 94 removed outlier: 3.995A pdb=" N GLU c 84 " --> pdb=" O GLY c 80 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL c 89 " --> pdb=" O LYS c 85 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE c 93 " --> pdb=" O VAL c 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 111 through 125 Processing helix chain 'c' and resid 128 through 142 removed outlier: 3.881A pdb=" N VAL c 137 " --> pdb=" O MET c 133 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 15 Processing helix chain 'd' and resid 48 through 65 removed outlier: 3.751A pdb=" N GLN d 53 " --> pdb=" O ASP d 49 " (cutoff:3.500A) Processing helix chain 'd' and resid 67 through 81 Processing helix chain 'd' and resid 84 through 94 Processing helix chain 'd' and resid 96 through 105 Processing helix chain 'd' and resid 109 through 119 Processing helix chain 'd' and resid 152 through 161 Processing helix chain 'd' and resid 162 through 164 No H-bonds generated for 'chain 'd' and resid 162 through 164' Processing helix chain 'd' and resid 186 through 190 Processing helix chain 'd' and resid 195 through 205 removed outlier: 4.047A pdb=" N ILE d 199 " --> pdb=" O ASN d 195 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 68 removed outlier: 3.986A pdb=" N ARG e 68 " --> pdb=" O GLU e 64 " (cutoff:3.500A) Processing helix chain 'e' and resid 110 through 118 Processing helix chain 'e' and resid 131 through 146 Processing helix chain 'e' and resid 148 through 156 Processing helix chain 'e' and resid 159 through 164 Processing helix chain 'f' and resid 12 through 16 removed outlier: 5.454A pdb=" N GLU f 16 " --> pdb=" O ASP f 13 " (cutoff:3.500A) Processing helix chain 'f' and resid 17 through 31 Processing helix chain 'f' and resid 67 through 80 Processing helix chain 'g' and resid 20 through 30 removed outlier: 3.570A pdb=" N LEU g 29 " --> pdb=" O PHE g 25 " (cutoff:3.500A) Processing helix chain 'g' and resid 31 through 33 No H-bonds generated for 'chain 'g' and resid 31 through 33' Processing helix chain 'g' and resid 34 through 52 removed outlier: 3.999A pdb=" N ALA g 38 " --> pdb=" O LYS g 34 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR g 48 " --> pdb=" O SER g 44 " (cutoff:3.500A) Processing helix chain 'g' and resid 56 through 66 Processing helix chain 'g' and resid 91 through 109 removed outlier: 4.456A pdb=" N ASN g 96 " --> pdb=" O PRO g 92 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA g 97 " --> pdb=" O VAL g 93 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TRP g 102 " --> pdb=" O LEU g 98 " (cutoff:3.500A) Processing helix chain 'g' and resid 114 through 128 Processing helix chain 'g' and resid 132 through 147 Processing helix chain 'h' and resid 4 through 20 removed outlier: 3.628A pdb=" N ARG h 12 " --> pdb=" O ASP h 8 " (cutoff:3.500A) Processing helix chain 'h' and resid 29 through 43 Processing helix chain 'h' and resid 112 through 119 removed outlier: 3.594A pdb=" N GLN h 117 " --> pdb=" O ARG h 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 44 through 49 removed outlier: 4.148A pdb=" N ARG i 48 " --> pdb=" O ARG i 44 " (cutoff:3.500A) Processing helix chain 'i' and resid 49 through 54 removed outlier: 3.938A pdb=" N LEU i 53 " --> pdb=" O GLN i 49 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL i 54 " --> pdb=" O PRO i 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 49 through 54' Processing helix chain 'i' and resid 70 through 86 removed outlier: 3.667A pdb=" N THR i 83 " --> pdb=" O ARG i 79 " (cutoff:3.500A) Processing helix chain 'i' and resid 90 through 95 Processing helix chain 'j' and resid 14 through 32 removed outlier: 4.614A pdb=" N GLN j 20 " --> pdb=" O ARG j 16 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA j 23 " --> pdb=" O ASP j 19 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU j 27 " --> pdb=" O ALA j 23 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N THR j 28 " --> pdb=" O GLU j 24 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 88 removed outlier: 3.771A pdb=" N MET j 88 " --> pdb=" O VAL j 84 " (cutoff:3.500A) Processing helix chain 'k' and resid 52 through 57 Processing helix chain 'k' and resid 58 through 71 removed outlier: 3.667A pdb=" N ALA k 62 " --> pdb=" O THR k 58 " (cutoff:3.500A) Processing helix chain 'k' and resid 73 through 77 Processing helix chain 'k' and resid 93 through 101 removed outlier: 3.537A pdb=" N LEU k 99 " --> pdb=" O THR k 95 " (cutoff:3.500A) Processing helix chain 'l' and resid 2 through 9 Processing helix chain 'l' and resid 114 through 118 removed outlier: 4.490A pdb=" N VAL l 118 " --> pdb=" O LYS l 115 " (cutoff:3.500A) Processing helix chain 'm' and resid 13 through 18 Processing helix chain 'm' and resid 19 through 21 No H-bonds generated for 'chain 'm' and resid 19 through 21' Processing helix chain 'm' and resid 27 through 37 removed outlier: 3.557A pdb=" N LEU m 33 " --> pdb=" O SER m 29 " (cutoff:3.500A) Processing helix chain 'm' and resid 48 through 60 removed outlier: 4.539A pdb=" N THR m 54 " --> pdb=" O GLY m 50 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP m 57 " --> pdb=" O ASP m 53 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU m 58 " --> pdb=" O THR m 54 " (cutoff:3.500A) Processing helix chain 'm' and resid 64 through 83 Processing helix chain 'm' and resid 84 through 91 Processing helix chain 'm' and resid 105 through 110 Processing helix chain 'n' and resid 2 through 19 Processing helix chain 'n' and resid 24 through 29 Processing helix chain 'n' and resid 38 through 48 removed outlier: 3.656A pdb=" N TRP n 42 " --> pdb=" O ASP n 38 " (cutoff:3.500A) Processing helix chain 'n' and resid 52 through 60 removed outlier: 3.687A pdb=" N SER n 56 " --> pdb=" O ARG n 53 " (cutoff:3.500A) Proline residue: n 57 - end of helix removed outlier: 3.751A pdb=" N GLN n 60 " --> pdb=" O PRO n 57 " (cutoff:3.500A) Processing helix chain 'n' and resid 82 through 91 Processing helix chain 'o' and resid 3 through 15 Processing helix chain 'o' and resid 23 through 42 removed outlier: 4.473A pdb=" N GLY o 40 " --> pdb=" O ASN o 36 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N HIS o 41 " --> pdb=" O HIS o 37 " (cutoff:3.500A) Processing helix chain 'o' and resid 48 through 73 removed outlier: 4.076A pdb=" N GLY o 54 " --> pdb=" O HIS o 50 " (cutoff:3.500A) Processing helix chain 'o' and resid 73 through 85 Processing helix chain 'p' and resid 53 through 64 Processing helix chain 'p' and resid 68 through 78 removed outlier: 3.555A pdb=" N LYS p 76 " --> pdb=" O ALA p 72 " (cutoff:3.500A) Processing helix chain 'r' and resid 11 through 16 Processing helix chain 'r' and resid 24 through 29 Processing helix chain 'r' and resid 40 through 45 Processing helix chain 'r' and resid 47 through 64 Processing helix chain 's' and resid 11 through 24 removed outlier: 4.425A pdb=" N LYS s 17 " --> pdb=" O HIS s 13 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLU s 23 " --> pdb=" O GLU s 19 " (cutoff:3.500A) Processing helix chain 's' and resid 40 through 44 removed outlier: 3.569A pdb=" N ILE s 44 " --> pdb=" O PRO s 41 " (cutoff:3.500A) Processing helix chain 's' and resid 62 through 66 removed outlier: 3.904A pdb=" N VAL s 66 " --> pdb=" O ASP s 63 " (cutoff:3.500A) Processing helix chain 's' and resid 69 through 74 removed outlier: 3.561A pdb=" N PHE s 73 " --> pdb=" O LEU s 70 " (cutoff:3.500A) Processing helix chain 't' and resid 7 through 28 removed outlier: 3.640A pdb=" N ILE t 11 " --> pdb=" O LYS t 7 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU t 14 " --> pdb=" O ALA t 10 " (cutoff:3.500A) Processing helix chain 't' and resid 29 through 41 removed outlier: 3.721A pdb=" N VAL t 34 " --> pdb=" O PHE t 30 " (cutoff:3.500A) Processing helix chain 't' and resid 42 through 63 Proline residue: t 55 - end of helix Processing helix chain 't' and resid 68 through 86 removed outlier: 3.712A pdb=" N LYS t 84 " --> pdb=" O ALA t 80 " (cutoff:3.500A) Processing helix chain 'u' and resid 13 through 32 Processing helix chain 'u' and resid 40 through 61 Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 196 through 202 removed outlier: 4.124A pdb=" N MET C 200 " --> pdb=" O ALA C 197 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG C 202 " --> pdb=" O HIS C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 214 removed outlier: 4.007A pdb=" N ALA C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 264 No H-bonds generated for 'chain 'C' and resid 262 through 264' Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'D' and resid 61 through 72 Processing helix chain 'D' and resid 97 through 102 Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 40 removed outlier: 3.879A pdb=" N ARG E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 115 Processing helix chain 'E' and resid 130 through 141 removed outlier: 3.899A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 162 removed outlier: 3.751A pdb=" N ALA E 160 " --> pdb=" O ASN E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 Processing helix chain 'E' and resid 190 through 201 Processing helix chain 'F' and resid 2 through 10 Processing helix chain 'F' and resid 10 through 20 Processing helix chain 'F' and resid 23 through 27 Processing helix chain 'F' and resid 47 through 60 removed outlier: 3.933A pdb=" N ASN F 51 " --> pdb=" O LYS F 47 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA F 57 " --> pdb=" O ALA F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 106 Processing helix chain 'F' and resid 161 through 172 removed outlier: 3.675A pdb=" N GLY F 165 " --> pdb=" O SER F 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 80 Processing helix chain 'G' and resid 136 through 151 removed outlier: 4.068A pdb=" N ARG G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 29 Processing helix chain 'H' and resid 42 through 48 Processing helix chain 'H' and resid 53 through 59 removed outlier: 3.861A pdb=" N LYS H 57 " --> pdb=" O GLU H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 71 removed outlier: 4.475A pdb=" N ALA H 64 " --> pdb=" O GLU H 60 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA H 69 " --> pdb=" O ALA H 65 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 106 Processing helix chain 'J' and resid 24 through 38 removed outlier: 4.043A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 62 removed outlier: 3.644A pdb=" N LYS J 61 " --> pdb=" O ASN J 58 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL J 62 " --> pdb=" O ALA J 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 58 through 62' Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 89 through 96 Processing helix chain 'J' and resid 98 through 107 Processing helix chain 'J' and resid 112 through 119 Processing helix chain 'J' and resid 132 through 136 Processing helix chain 'K' and resid 104 through 108 Processing helix chain 'K' and resid 112 through 118 Processing helix chain 'L' and resid 37 through 41 Processing helix chain 'L' and resid 56 through 61 removed outlier: 3.602A pdb=" N LEU L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 138 Processing helix chain 'M' and resid 43 through 57 removed outlier: 3.548A pdb=" N ALA M 52 " --> pdb=" O ALA M 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 122 Processing helix chain 'N' and resid 13 through 32 removed outlier: 3.591A pdb=" N GLY N 26 " --> pdb=" O ARG N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 55 removed outlier: 4.385A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU N 49 " --> pdb=" O ARG N 45 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 59 through 69 Processing helix chain 'N' and resid 74 through 82 removed outlier: 4.825A pdb=" N PHE N 80 " --> pdb=" O VAL N 76 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 22 removed outlier: 4.800A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 60 Processing helix chain 'O' and resid 67 through 86 removed outlier: 3.937A pdb=" N LEU O 83 " --> pdb=" O ALA O 79 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 113 Processing helix chain 'P' and resid 2 through 10 removed outlier: 3.532A pdb=" N GLN P 6 " --> pdb=" O ASN P 2 " (cutoff:3.500A) Processing helix chain 'P' and resid 96 through 102 removed outlier: 3.643A pdb=" N ARG P 100 " --> pdb=" O TYR P 97 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG P 102 " --> pdb=" O LEU P 99 " (cutoff:3.500A) Processing helix chain 'P' and resid 103 through 107 removed outlier: 3.647A pdb=" N ALA P 106 " --> pdb=" O THR P 103 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 20 removed outlier: 3.838A pdb=" N ALA Q 9 " --> pdb=" O ARG Q 5 " (cutoff:3.500A) Processing helix chain 'Q' and resid 24 through 28 Processing helix chain 'Q' and resid 30 through 71 removed outlier: 4.372A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 85 Processing helix chain 'Q' and resid 90 through 101 Processing helix chain 'Q' and resid 101 through 117 Processing helix chain 'S' and resid 13 through 22 removed outlier: 4.302A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 37 Processing helix chain 'S' and resid 42 through 62 removed outlier: 3.872A pdb=" N VAL S 50 " --> pdb=" O LEU S 46 " (cutoff:3.500A) Processing helix chain 'S' and resid 88 through 92 removed outlier: 3.680A pdb=" N GLY S 91 " --> pdb=" O ARG S 88 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 8 removed outlier: 3.554A pdb=" N LEU T 8 " --> pdb=" O GLU T 4 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 27 Processing helix chain 'T' and resid 39 through 52 Processing helix chain 'V' and resid 14 through 23 Processing helix chain 'V' and resid 44 through 51 Processing helix chain 'V' and resid 52 through 57 removed outlier: 6.101A pdb=" N GLU V 55 " --> pdb=" O ALA V 52 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR V 57 " --> pdb=" O ALA V 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 61 Processing helix chain 'X' and resid 62 through 71 Processing helix chain 'Y' and resid 9 through 23 Processing helix chain 'Y' and resid 24 through 35 Processing helix chain 'Y' and resid 41 through 61 removed outlier: 3.537A pdb=" N GLN Y 45 " --> pdb=" O HIS Y 41 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 40 through 50 Processing helix chain '0' and resid 8 through 16 Processing helix chain '2' and resid 8 through 17 Processing helix chain '2' and resid 17 through 23 Processing helix chain '2' and resid 24 through 38 removed outlier: 3.517A pdb=" N ARG 2 28 " --> pdb=" O THR 2 24 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN 2 29 " --> pdb=" O LYS 2 25 " (cutoff:3.500A) Processing helix chain '3' and resid 6 through 13 Processing helix chain '3' and resid 36 through 42 Processing helix chain '3' and resid 54 through 61 Processing helix chain '4' and resid 30 through 33 Processing helix chain '6' and resid 56 through 61 Processing helix chain 'v' and resid 11 through 22 Processing helix chain 'v' and resid 33 through 53 removed outlier: 4.763A pdb=" N GLN v 39 " --> pdb=" O ASN v 35 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA v 49 " --> pdb=" O ARG v 45 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP v 50 " --> pdb=" O GLU v 46 " (cutoff:3.500A) Processing helix chain 'y' and resid 4 through 16 Processing helix chain 'y' and resid 84 through 104 removed outlier: 3.964A pdb=" N LYS y 88 " --> pdb=" O LEU y 84 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA y 89 " --> pdb=" O SER y 85 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS y 90 " --> pdb=" O ARG y 86 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG y 91 " --> pdb=" O GLU y 87 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS y 92 " --> pdb=" O LYS y 88 " (cutoff:3.500A) Processing helix chain 'y' and resid 317 through 322 removed outlier: 3.877A pdb=" N VAL y 321 " --> pdb=" O HIS y 317 " (cutoff:3.500A) Processing helix chain 'y' and resid 350 through 361 removed outlier: 3.563A pdb=" N TRP y 354 " --> pdb=" O LYS y 350 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS y 361 " --> pdb=" O PHE y 357 " (cutoff:3.500A) Processing helix chain 'y' and resid 405 through 410 removed outlier: 3.897A pdb=" N TYR y 409 " --> pdb=" O ALA y 405 " (cutoff:3.500A) Processing helix chain 'y' and resid 425 through 428 removed outlier: 4.164A pdb=" N ARG y 428 " --> pdb=" O GLU y 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 425 through 428' Processing helix chain 'x' and resid 13 through 32 removed outlier: 3.703A pdb=" N ASP x 32 " --> pdb=" O GLU x 28 " (cutoff:3.500A) Processing helix chain 'x' and resid 70 through 92 Processing sheet with id=AA1, first strand: chain 'b' and resid 89 through 91 removed outlier: 6.133A pdb=" N ILE b 66 " --> pdb=" O PHE b 89 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N VAL b 91 " --> pdb=" O ILE b 66 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N PHE b 68 " --> pdb=" O VAL b 91 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LEU b 160 " --> pdb=" O PHE b 183 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE b 185 " --> pdb=" O LEU b 160 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL b 162 " --> pdb=" O ILE b 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'c' and resid 51 through 57 removed outlier: 6.624A pdb=" N HIS c 68 " --> pdb=" O SER c 52 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE c 54 " --> pdb=" O THR c 66 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N THR c 66 " --> pdb=" O ILE c 54 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE c 56 " --> pdb=" O ARG c 64 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ARG c 64 " --> pdb=" O ILE c 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'c' and resid 163 through 166 Processing sheet with id=AA4, first strand: chain 'c' and resid 163 through 166 removed outlier: 4.862A pdb=" N VAL c 194 " --> pdb=" O THR c 190 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR c 190 " --> pdb=" O VAL c 194 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLY c 196 " --> pdb=" O ALA c 188 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ALA c 188 " --> pdb=" O GLY c 196 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N LYS c 198 " --> pdb=" O SER c 186 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N SER c 186 " --> pdb=" O LYS c 198 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N TRP c 200 " --> pdb=" O ASN c 184 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ASN c 184 " --> pdb=" O TRP c 200 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N PHE c 202 " --> pdb=" O ASP c 182 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASP c 182 " --> pdb=" O PHE c 202 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY c 204 " --> pdb=" O ASP c 180 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'd' and resid 127 through 128 removed outlier: 3.705A pdb=" N ASP d 140 " --> pdb=" O PHE d 181 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'e' and resid 13 through 14 Processing sheet with id=AA7, first strand: chain 'e' and resid 18 through 21 Processing sheet with id=AA8, first strand: chain 'e' and resid 93 through 96 removed outlier: 5.915A pdb=" N GLY e 103 " --> pdb=" O VAL e 122 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ALA e 124 " --> pdb=" O GLY e 103 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE e 105 " --> pdb=" O ALA e 124 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ALA e 126 " --> pdb=" O ILE e 105 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'f' and resid 41 through 45 removed outlier: 4.652A pdb=" N ASP f 41 " --> pdb=" O LEU f 61 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU f 61 " --> pdb=" O ASP f 41 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY f 43 " --> pdb=" O TYR f 59 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET f 9 " --> pdb=" O ILE f 85 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'g' and resid 72 through 76 Processing sheet with id=AB2, first strand: chain 'h' and resid 23 through 27 removed outlier: 5.053A pdb=" N ASP h 47 " --> pdb=" O THR h 61 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'h' and resid 74 through 76 removed outlier: 5.346A pdb=" N ILE h 124 " --> pdb=" O SER h 104 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N SER h 104 " --> pdb=" O ILE h 124 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'i' and resid 5 through 7 removed outlier: 6.182A pdb=" N VAL i 28 " --> pdb=" O ILE i 64 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'j' and resid 40 through 45 removed outlier: 4.604A pdb=" N LEU j 71 " --> pdb=" O LEU j 42 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N THR j 44 " --> pdb=" O THR j 69 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N THR j 69 " --> pdb=" O THR j 44 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'j' and resid 48 through 52 Processing sheet with id=AB7, first strand: chain 'k' and resid 40 through 45 removed outlier: 7.091A pdb=" N ALA k 40 " --> pdb=" O ASP k 35 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ASP k 35 " --> pdb=" O ALA k 40 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LEU k 81 " --> pdb=" O ASN k 108 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N THR k 110 " --> pdb=" O LEU k 81 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL k 83 " --> pdb=" O THR k 110 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'l' and resid 29 through 31 removed outlier: 4.236A pdb=" N TYR l 94 " --> pdb=" O THR l 63 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'p' and resid 50 through 52 removed outlier: 5.791A pdb=" N ARG p 35 " --> pdb=" O VAL p 21 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL p 21 " --> pdb=" O ARG p 35 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL p 2 " --> pdb=" O THR p 66 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'q' and resid 6 through 7 removed outlier: 5.625A pdb=" N ILE q 60 " --> pdb=" O ARG q 76 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ARG q 76 " --> pdb=" O ILE q 60 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N GLU q 62 " --> pdb=" O LEU q 74 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N LEU q 74 " --> pdb=" O GLU q 62 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ARG q 64 " --> pdb=" O TRP q 72 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N TRP q 72 " --> pdb=" O ARG q 64 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LYS q 70 " --> pdb=" O LEU q 66 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N HIS q 44 " --> pdb=" O LYS q 70 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TRP q 72 " --> pdb=" O HIS q 44 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL q 21 " --> pdb=" O VAL q 12 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'q' and resid 25 through 29 Processing sheet with id=AC3, first strand: chain 's' and resid 30 through 32 removed outlier: 6.241A pdb=" N LEU s 30 " --> pdb=" O ALA s 49 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N HIS s 51 " --> pdb=" O LEU s 30 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N THR s 32 " --> pdb=" O HIS s 51 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=AC5, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AC6, first strand: chain 'C' and resid 100 through 104 removed outlier: 6.776A pdb=" N ILE C 90 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LEU C 80 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU C 92 " --> pdb=" O GLU C 78 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 128 through 130 removed outlier: 3.528A pdb=" N ALA C 189 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N THR C 172 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ARG C 166 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N TYR C 170 " --> pdb=" O ARG C 166 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N MET C 180 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 4 through 15 removed outlier: 5.756A pdb=" N LYS D 8 " --> pdb=" O GLU D 28 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLU D 28 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N GLY D 10 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL D 26 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LYS D 190 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL D 177 " --> pdb=" O LYS D 190 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N VAL D 107 " --> pdb=" O SER D 174 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 77 through 83 removed outlier: 5.312A pdb=" N GLY D 78 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N THR D 52 " --> pdb=" O GLY D 78 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ALA D 47 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N VAL D 37 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 117 through 119 Processing sheet with id=AD2, first strand: chain 'E' and resid 2 through 4 removed outlier: 3.647A pdb=" N LEU E 12 " --> pdb=" O LEU E 3 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 118 through 121 removed outlier: 6.521A pdb=" N ILE E 119 " --> pdb=" O MET E 188 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL E 146 " --> pdb=" O ASP E 168 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ARG E 170 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE E 148 " --> pdb=" O ARG E 170 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 65 through 68 Processing sheet with id=AD5, first strand: chain 'G' and resid 8 through 9 Processing sheet with id=AD6, first strand: chain 'G' and resid 22 through 26 Processing sheet with id=AD7, first strand: chain 'G' and resid 121 through 123 Processing sheet with id=AD8, first strand: chain 'G' and resid 94 through 98 removed outlier: 3.556A pdb=" N VAL G 101 " --> pdb=" O LYS G 98 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 18 through 20 Processing sheet with id=AE1, first strand: chain 'H' and resid 77 through 80 removed outlier: 3.584A pdb=" N VAL H 142 " --> pdb=" O VAL H 130 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 122 through 124 removed outlier: 6.398A pdb=" N TRP J 15 " --> pdb=" O GLN J 138 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 73 through 77 Processing sheet with id=AE4, first strand: chain 'K' and resid 6 through 10 removed outlier: 3.899A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL K 10 " --> pdb=" O ARG K 17 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N ARG K 17 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLU K 45 " --> pdb=" O ARG K 17 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL K 19 " --> pdb=" O ILE K 43 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE K 43 " --> pdb=" O VAL K 19 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N CYS K 21 " --> pdb=" O ILE K 41 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE K 41 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LYS K 23 " --> pdb=" O ILE K 39 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ILE K 39 " --> pdb=" O LYS K 23 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N CYS K 84 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ASN K 9 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N LEU K 86 " --> pdb=" O ASN K 9 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 69 through 70 removed outlier: 3.542A pdb=" N VAL K 69 " --> pdb=" O ILE K 77 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL K 76 " --> pdb=" O VAL P 72 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA P 57 " --> pdb=" O ILE P 49 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ILE P 49 " --> pdb=" O ALA P 57 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR P 59 " --> pdb=" O ILE P 47 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ILE P 63 " --> pdb=" O GLU P 43 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N GLU P 43 " --> pdb=" O ILE P 63 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N GLU P 26 " --> pdb=" O VAL P 85 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N VAL P 85 " --> pdb=" O GLU P 26 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LYS P 28 " --> pdb=" O ILE P 83 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ILE P 83 " --> pdb=" O LYS P 28 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N TRP P 30 " --> pdb=" O ASP P 81 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ASP P 81 " --> pdb=" O TRP P 30 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 89 through 90 removed outlier: 5.771A pdb=" N VAL L 90 " --> pdb=" O ARG L 123 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU L 143 " --> pdb=" O VAL L 122 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 109 through 110 Processing sheet with id=AE8, first strand: chain 'M' and resid 62 through 65 removed outlier: 3.505A pdb=" N LYS M 100 " --> pdb=" O ALA M 35 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU M 33 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLU M 104 " --> pdb=" O PHE M 31 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N PHE M 31 " --> pdb=" O GLU M 104 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 39 through 42 removed outlier: 3.721A pdb=" N ASN M 88 " --> pdb=" O GLU M 75 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE M 73 " --> pdb=" O GLU M 90 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'N' and resid 33 through 37 removed outlier: 4.642A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'O' and resid 47 through 49 removed outlier: 6.396A pdb=" N VAL O 39 " --> pdb=" O LEU O 48 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL O 28 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'R' and resid 11 through 14 removed outlier: 6.192A pdb=" N VAL R 4 " --> pdb=" O LEU R 39 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'R' and resid 19 through 22 removed outlier: 7.381A pdb=" N VAL R 96 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N VAL R 64 " --> pdb=" O VAL R 96 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ILE R 98 " --> pdb=" O GLU R 62 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU R 62 " --> pdb=" O ILE R 98 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'R' and resid 72 through 78 removed outlier: 4.131A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'S' and resid 4 through 10 removed outlier: 5.419A pdb=" N ILE S 4 " --> pdb=" O VAL S 107 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL S 107 " --> pdb=" O ILE S 4 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LYS S 6 " --> pdb=" O VAL S 105 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N VAL S 105 " --> pdb=" O LYS S 6 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ARG S 8 " --> pdb=" O ILE S 103 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE S 103 " --> pdb=" O ARG S 8 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N SER S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N VAL S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'S' and resid 82 through 85 Processing sheet with id=AF8, first strand: chain 'T' and resid 11 through 14 removed outlier: 4.180A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL T 57 " --> pdb=" O THR T 86 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'T' and resid 67 through 70 removed outlier: 3.769A pdb=" N ARG T 73 " --> pdb=" O HIS T 70 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'U' and resid 64 through 65 removed outlier: 6.443A pdb=" N LYS U 32 " --> pdb=" O VAL U 27 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N VAL U 27 " --> pdb=" O LYS U 32 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE U 34 " --> pdb=" O LYS U 25 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'U' and resid 42 through 44 Processing sheet with id=AG3, first strand: chain 'U' and resid 82 through 86 Processing sheet with id=AG4, first strand: chain 'V' and resid 2 through 8 removed outlier: 7.813A pdb=" N ASN V 5 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ASP V 43 " --> pdb=" O ASN V 5 " (cutoff:3.500A) removed outlier: 9.064A pdb=" N LYS V 25 " --> pdb=" O GLN V 87 " (cutoff:3.500A) removed outlier: 9.669A pdb=" N ILE V 89 " --> pdb=" O LYS V 25 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N PHE V 91 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ILE V 29 " --> pdb=" O PHE V 91 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ARG V 93 " --> pdb=" O ILE V 29 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N TYR V 31 " --> pdb=" O ARG V 93 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLN V 78 " --> pdb=" O GLN V 87 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE V 89 " --> pdb=" O ASP V 76 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ASP V 76 " --> pdb=" O ILE V 89 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHE V 91 " --> pdb=" O ALA V 74 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ALA V 74 " --> pdb=" O PHE V 91 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ARG V 93 " --> pdb=" O VAL V 72 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL V 72 " --> pdb=" O ARG V 93 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'W' and resid 18 through 19 removed outlier: 6.667A pdb=" N LEU W 55 " --> pdb=" O ILE W 33 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'W' and resid 26 through 27 removed outlier: 3.526A pdb=" N LYS W 62 " --> pdb=" O GLU W 79 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N HIS W 42 " --> pdb=" O ILE W 76 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N ILE W 78 " --> pdb=" O HIS W 42 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'X' and resid 12 through 15 Processing sheet with id=AG8, first strand: chain 'X' and resid 32 through 39 Processing sheet with id=AG9, first strand: chain 'Z' and resid 34 through 38 Processing sheet with id=AH1, first strand: chain '0' and resid 28 through 29 Processing sheet with id=AH2, first strand: chain '1' and resid 19 through 23 removed outlier: 3.596A pdb=" N GLN 1 44 " --> pdb=" O ASP 1 39 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain '3' and resid 14 through 15 Processing sheet with id=AH4, first strand: chain '4' and resid 2 through 3 removed outlier: 6.979A pdb=" N LYS 4 2 " --> pdb=" O ARG 4 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH4 Processing sheet with id=AH5, first strand: chain '4' and resid 14 through 19 Processing sheet with id=AH6, first strand: chain '6' and resid 22 through 26 removed outlier: 3.518A pdb=" N LEU 6 32 " --> pdb=" O THR 6 13 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'y' and resid 26 through 27 removed outlier: 3.914A pdb=" N GLY y 26 " --> pdb=" O VAL y 68 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL y 68 " --> pdb=" O GLY y 26 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain 'y' and resid 30 through 32 removed outlier: 3.727A pdb=" N ALA y 30 " --> pdb=" O LEU y 37 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'y' and resid 121 through 124 Processing sheet with id=AI1, first strand: chain 'y' and resid 156 through 159 Processing sheet with id=AI2, first strand: chain 'y' and resid 282 through 283 Processing sheet with id=AI3, first strand: chain 'y' and resid 370 through 371 Processing sheet with id=AI4, first strand: chain 'y' and resid 423 through 424 removed outlier: 3.722A pdb=" N ILE y 429 " --> pdb=" O ALA y 424 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'x' and resid 2 through 8 removed outlier: 3.703A pdb=" N GLN x 2 " --> pdb=" O ASN x 35 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN x 36 " --> pdb=" O HIS x 55 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N HIS x 48 " --> pdb=" O GLY x 67 " (cutoff:3.500A) 1833 hydrogen bonds defined for protein. 5151 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3924 hydrogen bonds 6224 hydrogen bond angles 0 basepair planarities 1555 basepair parallelities 2549 stacking parallelities Total time for adding SS restraints: 258.71 Time building geometry restraints manager: 64.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.70 - 0.93: 1 0.93 - 1.15: 0 1.15 - 1.37: 50530 1.37 - 1.59: 104371 1.59 - 1.82: 4948 Bond restraints: 159850 Sorted by residual: bond pdb=" C GLN x 2 " pdb=" N LEU x 3 " ideal model delta sigma weight residual 1.328 0.704 0.624 1.42e-02 4.96e+03 1.93e+03 bond pdb=" N SER y 169 " pdb=" CA SER y 169 " ideal model delta sigma weight residual 1.457 1.608 -0.151 1.29e-02 6.01e+03 1.37e+02 bond pdb=" N LYS y 88 " pdb=" CA LYS y 88 " ideal model delta sigma weight residual 1.457 1.547 -0.090 1.29e-02 6.01e+03 4.85e+01 bond pdb=" C VAL y 168 " pdb=" N SER y 169 " ideal model delta sigma weight residual 1.332 1.422 -0.090 1.40e-02 5.10e+03 4.14e+01 bond pdb=" CA LYS y 88 " pdb=" C LYS y 88 " ideal model delta sigma weight residual 1.523 1.602 -0.079 1.34e-02 5.57e+03 3.46e+01 ... (remaining 159845 not shown) Histogram of bond angle deviations from ideal: 84.94 - 98.70: 12 98.70 - 112.47: 112440 112.47 - 126.24: 111277 126.24 - 140.00: 15092 140.00 - 153.77: 3 Bond angle restraints: 238824 Sorted by residual: angle pdb=" O LEU x 3 " pdb=" C LEU x 3 " pdb=" N ASN x 4 " ideal model delta sigma weight residual 123.03 84.94 38.09 1.13e+00 7.83e-01 1.14e+03 angle pdb=" CA LEU x 3 " pdb=" C LEU x 3 " pdb=" N ASN x 4 " ideal model delta sigma weight residual 115.23 153.77 -38.54 1.30e+00 5.92e-01 8.79e+02 angle pdb=" C LYS y 88 " pdb=" N ALA y 89 " pdb=" CA ALA y 89 " ideal model delta sigma weight residual 120.38 143.60 -23.22 1.37e+00 5.33e-01 2.87e+02 angle pdb=" C LEU x 3 " pdb=" N ASN x 4 " pdb=" CA ASN x 4 " ideal model delta sigma weight residual 121.33 144.38 -23.05 1.40e+00 5.10e-01 2.71e+02 angle pdb=" N VAL y 332 " pdb=" CA VAL y 332 " pdb=" C VAL y 332 " ideal model delta sigma weight residual 110.62 124.63 -14.01 1.02e+00 9.61e-01 1.89e+02 ... (remaining 238819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 90684 35.96 - 71.92: 10358 71.92 - 107.88: 1184 107.88 - 143.84: 15 143.84 - 179.80: 34 Dihedral angle restraints: 102275 sinusoidal: 84655 harmonic: 17620 Sorted by residual: dihedral pdb=" CA HIS b 17 " pdb=" C HIS b 17 " pdb=" N GLN b 18 " pdb=" CA GLN b 18 " ideal model delta harmonic sigma weight residual -180.00 -114.10 -65.90 0 5.00e+00 4.00e-02 1.74e+02 dihedral pdb=" CA HIS g 152 " pdb=" C HIS g 152 " pdb=" N TYR g 153 " pdb=" CA TYR g 153 " ideal model delta harmonic sigma weight residual -180.00 -122.34 -57.66 0 5.00e+00 4.00e-02 1.33e+02 dihedral pdb=" CA ALA l 22 " pdb=" C ALA l 22 " pdb=" N LEU l 23 " pdb=" CA LEU l 23 " ideal model delta harmonic sigma weight residual -180.00 -128.46 -51.54 0 5.00e+00 4.00e-02 1.06e+02 ... (remaining 102272 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.160: 30199 0.160 - 0.319: 271 0.319 - 0.479: 22 0.479 - 0.639: 4 0.639 - 0.799: 2 Chirality restraints: 30498 Sorted by residual: chirality pdb=" C3' U I1537 " pdb=" C4' U I1537 " pdb=" O3' U I1537 " pdb=" C2' U I1537 " both_signs ideal model delta sigma weight residual False -2.74 -1.95 -0.80 2.00e-01 2.50e+01 1.59e+01 chirality pdb=" CA HIS y 305 " pdb=" N HIS y 305 " pdb=" C HIS y 305 " pdb=" CB HIS y 305 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" CA SER y 169 " pdb=" N SER y 169 " pdb=" C SER y 169 " pdb=" CB SER y 169 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.23e+00 ... (remaining 30495 not shown) Planarity restraints: 13064 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U I1537 " 0.057 2.00e-02 2.50e+03 3.15e-02 2.23e+01 pdb=" N1 U I1537 " -0.049 2.00e-02 2.50e+03 pdb=" C2 U I1537 " -0.033 2.00e-02 2.50e+03 pdb=" O2 U I1537 " 0.002 2.00e-02 2.50e+03 pdb=" N3 U I1537 " 0.007 2.00e-02 2.50e+03 pdb=" C4 U I1537 " 0.040 2.00e-02 2.50e+03 pdb=" O4 U I1537 " -0.001 2.00e-02 2.50e+03 pdb=" C5 U I1537 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U I1537 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U A2137 " -0.051 2.00e-02 2.50e+03 2.59e-02 1.51e+01 pdb=" N1 U A2137 " 0.053 2.00e-02 2.50e+03 pdb=" C2 U A2137 " 0.004 2.00e-02 2.50e+03 pdb=" O2 U A2137 " 0.006 2.00e-02 2.50e+03 pdb=" N3 U A2137 " 0.003 2.00e-02 2.50e+03 pdb=" C4 U A2137 " -0.012 2.00e-02 2.50e+03 pdb=" O4 U A2137 " -0.015 2.00e-02 2.50e+03 pdb=" C5 U A2137 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U A2137 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE m 8 " 0.063 5.00e-02 4.00e+02 9.58e-02 1.47e+01 pdb=" N PRO m 9 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO m 9 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO m 9 " 0.053 5.00e-02 4.00e+02 ... (remaining 13061 not shown) Histogram of nonbonded interaction distances: 0.42 - 1.31: 5 1.31 - 2.21: 50 2.21 - 3.11: 95205 3.11 - 4.00: 478352 4.00 - 4.90: 775672 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1349284 Sorted by model distance: nonbonded pdb=" CD2 HIS b 17 " pdb=" CE LYS y 43 " model vdw 0.418 3.660 nonbonded pdb=" O ALA y 358 " pdb=" CB ASN y 362 " model vdw 0.920 3.440 nonbonded pdb=" N ARG y 163 " pdb=" CG GLU y 298 " model vdw 1.135 3.520 nonbonded pdb=" NH1 ARG b 34 " pdb=" NH2 ARG y 19 " model vdw 1.210 3.200 nonbonded pdb=" OP1 C a1533 " pdb=" NZ LYS v 26 " model vdw 1.305 2.520 ... (remaining 1349279 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.190 Extract box with map and model: 15.050 Check model and map are aligned: 1.620 Set scattering table: 0.880 Process input model: 536.070 Find NCS groups from input model: 2.880 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 571.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 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 : 0.007 0.624 159850 Z= 0.446 Angle : 0.960 38.537 238824 Z= 0.502 Chirality : 0.050 0.799 30498 Planarity : 0.007 0.096 13064 Dihedral : 22.672 179.802 90904 Min Nonbonded Distance : 0.418 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.54 % Allowed : 10.10 % Favored : 89.36 % Rotamer: Outliers : 0.74 % Allowed : 5.18 % Favored : 94.08 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.02 % Twisted Proline : 1.55 % Twisted General : 0.50 % 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: -4.18 (0.09), residues: 6082 helix: -3.02 (0.08), residues: 1855 sheet: -2.05 (0.14), residues: 1132 loop : -2.90 (0.09), residues: 3095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.004 TRP C 212 HIS 0.022 0.003 HIS k 117 PHE 0.040 0.004 PHE u 11 TYR 0.039 0.003 TYR H 25 ARG 0.016 0.001 ARG Y 29 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2509 residues out of total 5071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 2473 time to evaluate : 6.286 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: b 55 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7631 (mp0) REVERT: b 132 GLU cc_start: 0.8424 (tp30) cc_final: 0.7701 (tp30) REVERT: b 164 ASP cc_start: 0.7512 (t0) cc_final: 0.6498 (t0) REVERT: b 168 GLU cc_start: 0.8160 (mp0) cc_final: 0.7697 (mp0) REVERT: b 174 GLU cc_start: 0.8355 (tp30) cc_final: 0.8022 (mm-30) REVERT: b 187 ASP cc_start: 0.6542 (t0) cc_final: 0.6089 (t0) REVERT: b 191 ASP cc_start: 0.7964 (t0) cc_final: 0.6938 (t0) REVERT: b 203 ASP cc_start: 0.7894 (p0) cc_final: 0.7380 (p0) REVERT: c 27 GLU cc_start: 0.7768 (pm20) cc_final: 0.7514 (pm20) REVERT: c 31 ASN cc_start: 0.8758 (OUTLIER) cc_final: 0.8244 (t0) REVERT: c 37 LYS cc_start: 0.8645 (mtmm) cc_final: 0.8147 (mtmt) REVERT: c 57 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7136 (mt-10) REVERT: c 85 LYS cc_start: 0.9030 (tppt) cc_final: 0.8807 (mmtm) REVERT: c 139 ASN cc_start: 0.9341 (m-40) cc_final: 0.8873 (m110) REVERT: c 141 MET cc_start: 0.8671 (mmm) cc_final: 0.8436 (mmm) REVERT: c 186 SER cc_start: 0.8708 (t) cc_final: 0.8424 (t) REVERT: c 198 LYS cc_start: 0.9299 (ptpt) cc_final: 0.8988 (ptpt) REVERT: d 58 GLN cc_start: 0.8700 (mm-40) cc_final: 0.8497 (mm110) REVERT: d 188 SER cc_start: 0.9388 (p) cc_final: 0.9150 (t) REVERT: e 13 LYS cc_start: 0.8832 (ttmm) cc_final: 0.8492 (tppt) REVERT: e 51 LYS cc_start: 0.8853 (ptmt) cc_final: 0.8612 (ttpt) REVERT: e 69 ASN cc_start: 0.8742 (t160) cc_final: 0.8252 (t0) REVERT: e 77 ASN cc_start: 0.8894 (m-40) cc_final: 0.8514 (p0) REVERT: e 127 TYR cc_start: 0.8491 (m-80) cc_final: 0.8241 (m-80) REVERT: e 129 SER cc_start: 0.9316 (t) cc_final: 0.9095 (t) REVERT: e 131 ASN cc_start: 0.8873 (t0) cc_final: 0.8606 (t0) REVERT: e 133 ILE cc_start: 0.8941 (mp) cc_final: 0.8641 (tp) REVERT: e 155 LYS cc_start: 0.9242 (pttt) cc_final: 0.9015 (pttp) REVERT: f 1 MET cc_start: 0.7116 (mtm) cc_final: 0.6895 (mtm) REVERT: f 11 HIS cc_start: 0.8646 (t70) cc_final: 0.8367 (t-90) REVERT: f 30 THR cc_start: 0.8968 (m) cc_final: 0.8612 (p) REVERT: g 14 ASP cc_start: 0.7890 (t70) cc_final: 0.7686 (t0) REVERT: g 53 SER cc_start: 0.8450 (t) cc_final: 0.8232 (p) REVERT: g 79 VAL cc_start: 0.8831 (m) cc_final: 0.8592 (p) REVERT: g 100 MET cc_start: 0.8574 (mtm) cc_final: 0.8212 (mtp) REVERT: g 121 ASN cc_start: 0.8836 (m-40) cc_final: 0.8524 (m-40) REVERT: g 130 LYS cc_start: 0.8523 (tttt) cc_final: 0.8304 (tptm) REVERT: g 135 LYS cc_start: 0.8861 (ttpt) cc_final: 0.8661 (tttm) REVERT: h 4 ASP cc_start: 0.8126 (t0) cc_final: 0.7715 (t0) REVERT: h 8 ASP cc_start: 0.7687 (m-30) cc_final: 0.7469 (m-30) REVERT: h 35 ILE cc_start: 0.9187 (mt) cc_final: 0.8960 (mp) REVERT: h 61 THR cc_start: 0.9345 (m) cc_final: 0.9005 (p) REVERT: i 24 ASN cc_start: 0.8118 (t160) cc_final: 0.7756 (t0) REVERT: i 60 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8709 (pp) REVERT: i 106 ASP cc_start: 0.8413 (t70) cc_final: 0.8064 (t70) REVERT: j 15 HIS cc_start: 0.8960 (p-80) cc_final: 0.8678 (p90) REVERT: j 45 ARG cc_start: 0.7346 (mmt180) cc_final: 0.6973 (ttt180) REVERT: k 63 GLN cc_start: 0.8887 (tt0) cc_final: 0.8519 (tt0) REVERT: l 82 ARG cc_start: 0.9222 (ptt90) cc_final: 0.8813 (ptm-80) REVERT: n 97 LYS cc_start: 0.8797 (pttt) cc_final: 0.8550 (ptpp) REVERT: o 17 ASP cc_start: 0.8882 (p0) cc_final: 0.8529 (p0) REVERT: o 64 LYS cc_start: 0.9322 (mtmt) cc_final: 0.9088 (mtmm) REVERT: p 56 ARG cc_start: 0.8648 (mmm160) cc_final: 0.8406 (mmm-85) REVERT: q 19 SER cc_start: 0.9130 (p) cc_final: 0.8821 (p) REVERT: q 66 LEU cc_start: 0.9080 (mt) cc_final: 0.8828 (mt) REVERT: r 30 ASN cc_start: 0.8631 (m-40) cc_final: 0.8431 (m-40) REVERT: r 47 ARG cc_start: 0.7553 (mmt-90) cc_final: 0.7032 (mtt-85) REVERT: s 17 LYS cc_start: 0.8968 (tttm) cc_final: 0.8767 (ttmm) REVERT: s 30 LEU cc_start: 0.8573 (mp) cc_final: 0.8361 (mp) REVERT: s 65 MET cc_start: 0.8546 (mtt) cc_final: 0.8324 (mtp) REVERT: t 25 SER cc_start: 0.9079 (t) cc_final: 0.8668 (m) REVERT: t 59 ARG cc_start: 0.8959 (ttm110) cc_final: 0.8726 (ttp80) REVERT: u 19 LYS cc_start: 0.6616 (pttm) cc_final: 0.6373 (tppt) REVERT: C 20 ASN cc_start: 0.8719 (t0) cc_final: 0.8414 (t0) REVERT: C 65 ASP cc_start: 0.8511 (t0) cc_final: 0.8213 (t0) REVERT: D 7 LYS cc_start: 0.8571 (ttmt) cc_final: 0.8332 (ttpp) REVERT: D 97 SER cc_start: 0.9115 (t) cc_final: 0.8701 (p) REVERT: D 100 LEU cc_start: 0.8986 (tp) cc_final: 0.8590 (tt) REVERT: D 168 GLU cc_start: 0.7127 (tm-30) cc_final: 0.6837 (tm-30) REVERT: D 181 ASP cc_start: 0.8421 (t70) cc_final: 0.8138 (t0) REVERT: E 1 MET cc_start: 0.6473 (tpp) cc_final: 0.5571 (tpt) REVERT: E 17 THR cc_start: 0.8093 (p) cc_final: 0.7600 (t) REVERT: E 106 LYS cc_start: 0.8990 (mttt) cc_final: 0.8729 (mtpt) REVERT: E 136 GLN cc_start: 0.8931 (tp-100) cc_final: 0.8646 (tp40) REVERT: E 168 ASP cc_start: 0.8061 (t0) cc_final: 0.7802 (t0) REVERT: E 176 ASP cc_start: 0.7684 (p0) cc_final: 0.7444 (p0) REVERT: E 200 LEU cc_start: 0.8888 (mp) cc_final: 0.8612 (mt) REVERT: F 41 GLU cc_start: 0.7553 (mt-10) cc_final: 0.6931 (mt-10) REVERT: F 51 ASN cc_start: 0.9097 (m-40) cc_final: 0.8595 (m110) REVERT: F 146 ASP cc_start: 0.7934 (p0) cc_final: 0.7508 (p0) REVERT: G 57 TYR cc_start: 0.8498 (m-80) cc_final: 0.8108 (m-80) REVERT: G 100 ASN cc_start: 0.8667 (p0) cc_final: 0.7959 (p0) REVERT: G 115 GLN cc_start: 0.8702 (tp-100) cc_final: 0.8307 (tp40) REVERT: G 142 GLN cc_start: 0.8921 (tp40) cc_final: 0.8554 (tp40) REVERT: G 148 ARG cc_start: 0.8733 (ttt-90) cc_final: 0.8311 (ttt-90) REVERT: G 156 TYR cc_start: 0.8895 (m-80) cc_final: 0.8518 (m-80) REVERT: G 166 GLU cc_start: 0.8103 (tt0) cc_final: 0.7494 (tt0) REVERT: H 54 LEU cc_start: 0.8865 (tp) cc_final: 0.8643 (pp) REVERT: J 2 LYS cc_start: 0.8309 (mtpp) cc_final: 0.7849 (mtpt) REVERT: J 5 THR cc_start: 0.9228 (m) cc_final: 0.8896 (t) REVERT: J 16 TYR cc_start: 0.9022 (m-10) cc_final: 0.8818 (m-80) REVERT: J 19 ASP cc_start: 0.8183 (t70) cc_final: 0.7927 (t0) REVERT: J 21 THR cc_start: 0.8935 (m) cc_final: 0.8685 (p) REVERT: J 41 LYS cc_start: 0.9217 (mmtp) cc_final: 0.8941 (mmtm) REVERT: J 58 ASN cc_start: 0.9144 (m110) cc_final: 0.8673 (m-40) REVERT: K 17 ARG cc_start: 0.8083 (tpp80) cc_final: 0.7818 (tpp80) REVERT: K 51 LYS cc_start: 0.9122 (mtmm) cc_final: 0.8910 (mttm) REVERT: K 106 GLU cc_start: 0.7200 (mp0) cc_final: 0.6999 (mp0) REVERT: K 108 ARG cc_start: 0.8282 (ttm-80) cc_final: 0.7828 (mtp85) REVERT: K 114 LYS cc_start: 0.8643 (tptt) cc_final: 0.8310 (tptp) REVERT: L 5 THR cc_start: 0.9307 (m) cc_final: 0.8993 (p) REVERT: L 51 GLU cc_start: 0.7688 (tt0) cc_final: 0.7369 (tt0) REVERT: L 101 ILE cc_start: 0.9045 (pt) cc_final: 0.8833 (pt) REVERT: M 42 THR cc_start: 0.9207 (p) cc_final: 0.8898 (t) REVERT: M 50 ARG cc_start: 0.8415 (tmm160) cc_final: 0.7834 (ttp-110) REVERT: M 66 ARG cc_start: 0.8600 (mmm-85) cc_final: 0.8276 (mmm-85) REVERT: N 43 GLU cc_start: 0.8482 (tp30) cc_final: 0.7958 (tp30) REVERT: N 72 ASP cc_start: 0.7922 (t0) cc_final: 0.7585 (t0) REVERT: N 82 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7542 (mt-10) REVERT: N 107 ASN cc_start: 0.8951 (t0) cc_final: 0.8529 (t0) REVERT: O 81 ARG cc_start: 0.8564 (mtt180) cc_final: 0.8358 (mtp85) REVERT: P 12 MET cc_start: 0.8520 (mtp) cc_final: 0.8317 (mtm) REVERT: P 37 LYS cc_start: 0.9129 (tmtp) cc_final: 0.8790 (tptp) REVERT: Q 29 ARG cc_start: 0.8891 (mtt90) cc_final: 0.8374 (mtt90) REVERT: Q 48 ASP cc_start: 0.7874 (m-30) cc_final: 0.7579 (m-30) REVERT: Q 70 GLN cc_start: 0.8617 (tp40) cc_final: 0.7824 (tp40) REVERT: R 58 VAL cc_start: 0.9027 (t) cc_final: 0.8715 (t) REVERT: S 4 ILE cc_start: 0.9392 (pt) cc_final: 0.9152 (mp) REVERT: S 12 SER cc_start: 0.9043 (t) cc_final: 0.8811 (m) REVERT: S 37 THR cc_start: 0.9068 (m) cc_final: 0.8791 (m) REVERT: T 28 ASN cc_start: 0.8726 (t0) cc_final: 0.8316 (t0) REVERT: U 5 ARG cc_start: 0.8498 (ptp-170) cc_final: 0.8206 (ptp-170) REVERT: U 11 ILE cc_start: 0.9208 (tt) cc_final: 0.8991 (tp) REVERT: V 55 GLU cc_start: 0.8401 (mp0) cc_final: 0.8046 (mm-30) REVERT: V 58 SER cc_start: 0.8779 (p) cc_final: 0.7134 (p) REVERT: V 64 VAL cc_start: 0.8998 (t) cc_final: 0.8702 (p) REVERT: V 90 ASP cc_start: 0.8325 (m-30) cc_final: 0.7789 (m-30) REVERT: W 66 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7435 (mt-10) REVERT: X 15 ASN cc_start: 0.9232 (m-40) cc_final: 0.9003 (m110) REVERT: Y 26 PHE cc_start: 0.8740 (t80) cc_final: 0.8344 (t80) REVERT: Y 27 ASN cc_start: 0.8244 (m-40) cc_final: 0.6754 (m-40) REVERT: Z 5 LYS cc_start: 0.9053 (mtpp) cc_final: 0.8822 (mmtp) REVERT: Z 7 THR cc_start: 0.9019 (m) cc_final: 0.8787 (m) REVERT: Z 36 GLU cc_start: 0.7949 (tp30) cc_final: 0.7575 (tp30) REVERT: 0 11 LYS cc_start: 0.8682 (tptm) cc_final: 0.8323 (tppt) REVERT: 0 30 ASP cc_start: 0.8664 (t70) cc_final: 0.8384 (t0) REVERT: 1 34 GLU cc_start: 0.7428 (mm-30) cc_final: 0.7171 (mm-30) REVERT: 3 51 LYS cc_start: 0.8982 (tmmt) cc_final: 0.8733 (tmmm) REVERT: 4 13 ASN cc_start: 0.8988 (m110) cc_final: 0.8653 (m110) REVERT: 4 36 ARG cc_start: 0.8261 (ttp80) cc_final: 0.7766 (ttp80) REVERT: 4 37 GLN cc_start: 0.7498 (tp-100) cc_final: 0.7179 (tp-100) REVERT: 6 1 MET cc_start: 0.7678 (ttm) cc_final: 0.7431 (ttm) REVERT: 6 56 ARG cc_start: 0.7067 (mmm-85) cc_final: 0.6621 (mtp180) REVERT: 6 57 VAL cc_start: 0.8899 (t) cc_final: 0.8595 (t) REVERT: y 312 THR cc_start: 0.5388 (p) cc_final: 0.4465 (m) REVERT: y 335 ILE cc_start: 0.7653 (mt) cc_final: 0.7045 (mm) outliers start: 36 outliers final: 11 residues processed: 2489 average time/residue: 2.1890 time to fit residues: 7774.6377 Evaluate side-chains 1908 residues out of total 5071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 1895 time to evaluate : 6.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 211 LEU Chi-restraints excluded: chain c residue 31 ASN Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 6 residue 28 VAL Chi-restraints excluded: chain y residue 294 VAL Chi-restraints excluded: chain y residue 305 HIS Chi-restraints excluded: chain x residue 27 LEU Chi-restraints excluded: chain x residue 28 GLU Chi-restraints excluded: chain x residue 29 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 892 optimal weight: 0.8980 chunk 801 optimal weight: 2.9990 chunk 444 optimal weight: 10.0000 chunk 273 optimal weight: 7.9990 chunk 540 optimal weight: 10.0000 chunk 428 optimal weight: 7.9990 chunk 828 optimal weight: 0.9990 chunk 320 optimal weight: 0.7980 chunk 503 optimal weight: 10.0000 chunk 616 optimal weight: 8.9990 chunk 959 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 23 ASN b 41 ASN ** b 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 31 ASN c 101 ASN c 138 GLN c 139 ASN c 189 HIS d 53 GLN d 70 GLN d 99 ASN e 69 ASN e 76 ASN e 88 HIS f 3 HIS ** g 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 4 GLN i 24 ASN i 30 ASN i 109 GLN i 125 GLN j 70 HIS k 28 ASN l 4 ASN l 28 GLN m 51 GLN n 3 GLN n 60 GLN o 45 HIS o 79 GLN p 18 GLN p 79 ASN ** q 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 30 HIS r 51 GLN s 55 GLN s 68 HIS t 12 GLN t 20 ASN t 51 ASN ** t 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN C 238 ASN C 259 ASN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN D 130 GLN D 136 ASN D 150 GLN D 164 GLN E 41 GLN F 134 GLN G 103 ASN H 11 ASN H 73 ASN H 133 GLN H 135 HIS H 145 ASN J 40 HIS K 5 GLN K 29 HIS L 4 ASN L 35 HIS M 22 GLN N 9 GLN N 81 ASN O 38 GLN P 40 GLN Q 19 GLN Q 36 GLN Q 43 GLN Q 55 GLN Q 71 ASN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 HIS S 61 ASN U 65 GLN ** U 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 73 ASN W 8 ASN Y 45 GLN Y 58 ASN Z 8 GLN ** Z 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 29 GLN 4 35 GLN v 14 GLN v 18 GLN x 8 ASN x 36 GLN x 55 HIS x 95 HIS Total number of N/Q/H flips: 84 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 159850 Z= 0.168 Angle : 0.598 14.197 238824 Z= 0.312 Chirality : 0.035 0.338 30498 Planarity : 0.005 0.066 13064 Dihedral : 23.442 179.426 79194 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.35 % Favored : 91.38 % Rotamer: Outliers : 5.94 % Allowed : 22.77 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.02 % Twisted Proline : 1.03 % Twisted General : 0.22 % 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: -2.79 (0.10), residues: 6082 helix: -1.06 (0.11), residues: 1888 sheet: -1.58 (0.14), residues: 1125 loop : -2.50 (0.10), residues: 3069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 212 HIS 0.013 0.001 HIS t 67 PHE 0.021 0.002 PHE 6 60 TYR 0.025 0.002 TYR O 36 ARG 0.011 0.001 ARG j 16 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2343 residues out of total 5071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 290 poor density : 2053 time to evaluate : 6.361 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: b 29 PHE cc_start: 0.8233 (OUTLIER) cc_final: 0.7589 (m-80) REVERT: b 51 GLU cc_start: 0.7989 (tp30) cc_final: 0.6683 (tp30) REVERT: b 168 GLU cc_start: 0.8206 (mp0) cc_final: 0.7752 (mp0) REVERT: b 174 GLU cc_start: 0.8240 (tp30) cc_final: 0.8015 (mm-30) REVERT: b 183 PHE cc_start: 0.8108 (OUTLIER) cc_final: 0.7229 (p90) REVERT: b 191 ASP cc_start: 0.7863 (t0) cc_final: 0.7512 (t0) REVERT: c 27 GLU cc_start: 0.7929 (pm20) cc_final: 0.7673 (pm20) REVERT: c 31 ASN cc_start: 0.8703 (t0) cc_final: 0.8441 (t0) REVERT: c 35 ASP cc_start: 0.8817 (m-30) cc_final: 0.8389 (m-30) REVERT: c 129 PHE cc_start: 0.9064 (p90) cc_final: 0.8679 (p90) REVERT: c 139 ASN cc_start: 0.9305 (m110) cc_final: 0.9027 (m110) REVERT: c 141 MET cc_start: 0.8640 (mmm) cc_final: 0.8408 (mmp) REVERT: d 19 PHE cc_start: 0.9063 (m-10) cc_final: 0.8841 (m-10) REVERT: d 58 GLN cc_start: 0.8657 (mm-40) cc_final: 0.8437 (mm110) REVERT: d 137 SER cc_start: 0.8990 (t) cc_final: 0.8633 (p) REVERT: d 177 MET cc_start: 0.8303 (mtm) cc_final: 0.7650 (mpp) REVERT: d 188 SER cc_start: 0.9337 (p) cc_final: 0.9025 (t) REVERT: e 13 LYS cc_start: 0.8754 (ttmm) cc_final: 0.8537 (ttmm) REVERT: e 51 LYS cc_start: 0.8774 (ptmt) cc_final: 0.8562 (ttpt) REVERT: e 59 ILE cc_start: 0.8980 (pt) cc_final: 0.8592 (mt) REVERT: e 61 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8780 (mttp) REVERT: e 64 GLU cc_start: 0.8055 (tp30) cc_final: 0.7756 (tp30) REVERT: e 67 ARG cc_start: 0.8904 (mtm-85) cc_final: 0.8250 (mtm-85) REVERT: e 69 ASN cc_start: 0.8697 (t0) cc_final: 0.8231 (t0) REVERT: e 77 ASN cc_start: 0.8898 (m-40) cc_final: 0.8556 (p0) REVERT: e 127 TYR cc_start: 0.8395 (m-80) cc_final: 0.8187 (m-80) REVERT: e 131 ASN cc_start: 0.8708 (t0) cc_final: 0.8420 (t0) REVERT: f 30 THR cc_start: 0.9312 (m) cc_final: 0.8929 (p) REVERT: f 38 ARG cc_start: 0.7941 (mtm-85) cc_final: 0.7419 (mtm-85) REVERT: f 65 GLU cc_start: 0.7495 (tm-30) cc_final: 0.7220 (tm-30) REVERT: f 88 MET cc_start: 0.7634 (tmm) cc_final: 0.7298 (tmm) REVERT: g 17 PHE cc_start: 0.8755 (m-80) cc_final: 0.8449 (m-80) REVERT: g 55 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8279 (ptpt) REVERT: g 59 GLU cc_start: 0.8240 (pt0) cc_final: 0.7922 (pp20) REVERT: g 100 MET cc_start: 0.8608 (mtm) cc_final: 0.8219 (mtp) REVERT: h 57 GLU cc_start: 0.7246 (mp0) cc_final: 0.7037 (mp0) REVERT: h 59 GLU cc_start: 0.7416 (pt0) cc_final: 0.7191 (pt0) REVERT: h 61 THR cc_start: 0.9395 (m) cc_final: 0.8943 (p) REVERT: i 21 LYS cc_start: 0.8965 (mtpp) cc_final: 0.8753 (mtpt) REVERT: i 60 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8628 (pp) REVERT: i 90 ASP cc_start: 0.7911 (t70) cc_final: 0.7644 (t70) REVERT: j 45 ARG cc_start: 0.7433 (mmt180) cc_final: 0.7069 (ttm170) REVERT: k 36 ARG cc_start: 0.8170 (mmm-85) cc_final: 0.7918 (mmm-85) REVERT: k 63 GLN cc_start: 0.8835 (tt0) cc_final: 0.8606 (tt0) REVERT: l 61 GLU cc_start: 0.7399 (tt0) cc_final: 0.7177 (tt0) REVERT: l 75 GLU cc_start: 0.7833 (mp0) cc_final: 0.7418 (tm-30) REVERT: l 93 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.7785 (mtp180) REVERT: n 15 LEU cc_start: 0.9060 (mp) cc_final: 0.8859 (mp) REVERT: n 60 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.8431 (mp-120) REVERT: n 62 ASN cc_start: 0.8657 (t0) cc_final: 0.8275 (t0) REVERT: n 97 LYS cc_start: 0.8515 (pttt) cc_final: 0.8264 (ptpp) REVERT: o 17 ASP cc_start: 0.9051 (p0) cc_final: 0.8767 (p0) REVERT: o 71 ARG cc_start: 0.8566 (ttp80) cc_final: 0.8309 (ttm170) REVERT: o 79 GLN cc_start: 0.8400 (tp40) cc_final: 0.8193 (tp-100) REVERT: p 17 TYR cc_start: 0.8909 (m-80) cc_final: 0.8653 (m-10) REVERT: q 19 SER cc_start: 0.9105 (p) cc_final: 0.8810 (p) REVERT: q 47 ASP cc_start: 0.8260 (p0) cc_final: 0.7940 (p0) REVERT: r 47 ARG cc_start: 0.7369 (mmt-90) cc_final: 0.7062 (mtt-85) REVERT: s 54 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7653 (ptt90) REVERT: t 23 ARG cc_start: 0.8640 (mmp80) cc_final: 0.8418 (mmp-170) REVERT: t 25 SER cc_start: 0.9056 (t) cc_final: 0.8765 (m) REVERT: u 19 LYS cc_start: 0.6704 (pttm) cc_final: 0.6326 (tppt) REVERT: C 4 LYS cc_start: 0.8798 (mmtp) cc_final: 0.8569 (mtpp) REVERT: C 20 ASN cc_start: 0.8411 (t0) cc_final: 0.7908 (t0) REVERT: C 65 ASP cc_start: 0.8354 (t0) cc_final: 0.7964 (t0) REVERT: C 99 GLU cc_start: 0.8189 (tt0) cc_final: 0.7844 (tt0) REVERT: C 110 LYS cc_start: 0.8046 (mmmt) cc_final: 0.7756 (mtmm) REVERT: C 116 GLN cc_start: 0.8724 (pt0) cc_final: 0.8389 (pt0) REVERT: D 7 LYS cc_start: 0.8460 (ttmt) cc_final: 0.8230 (ttpp) REVERT: D 28 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7756 (pp20) REVERT: D 39 ASP cc_start: 0.8043 (p0) cc_final: 0.7783 (p0) REVERT: D 97 SER cc_start: 0.9188 (t) cc_final: 0.8770 (p) REVERT: D 99 GLU cc_start: 0.7766 (pp20) cc_final: 0.7551 (pp20) REVERT: D 181 ASP cc_start: 0.8362 (t70) cc_final: 0.8150 (t0) REVERT: E 17 THR cc_start: 0.8460 (p) cc_final: 0.8131 (t) REVERT: E 106 LYS cc_start: 0.9000 (mttt) cc_final: 0.8791 (mtpt) REVERT: E 136 GLN cc_start: 0.8922 (tp-100) cc_final: 0.8669 (tp40) REVERT: E 168 ASP cc_start: 0.8040 (t0) cc_final: 0.7668 (t0) REVERT: E 181 ILE cc_start: 0.9425 (mm) cc_final: 0.9189 (mm) REVERT: E 194 LYS cc_start: 0.9076 (mmmt) cc_final: 0.8836 (mmmm) REVERT: F 25 MET cc_start: 0.9062 (mmm) cc_final: 0.8466 (mtm) REVERT: F 51 ASN cc_start: 0.8961 (m-40) cc_final: 0.8681 (m110) REVERT: F 80 GLN cc_start: 0.8436 (tp40) cc_final: 0.8161 (tp40) REVERT: F 82 TYR cc_start: 0.7760 (t80) cc_final: 0.7090 (t80) REVERT: F 114 ARG cc_start: 0.8232 (tpp-160) cc_final: 0.7939 (tpp80) REVERT: F 146 ASP cc_start: 0.7799 (p0) cc_final: 0.7490 (p0) REVERT: G 100 ASN cc_start: 0.8858 (p0) cc_final: 0.8133 (p0) REVERT: G 115 GLN cc_start: 0.8661 (tp-100) cc_final: 0.8221 (tp40) REVERT: G 148 ARG cc_start: 0.8696 (ttt-90) cc_final: 0.8296 (ttt-90) REVERT: G 156 TYR cc_start: 0.8773 (m-80) cc_final: 0.8428 (m-80) REVERT: G 166 GLU cc_start: 0.8182 (tt0) cc_final: 0.7492 (tt0) REVERT: J 16 TYR cc_start: 0.9141 (m-10) cc_final: 0.8909 (m-80) REVERT: J 58 ASN cc_start: 0.9138 (m110) cc_final: 0.8764 (m-40) REVERT: K 108 ARG cc_start: 0.8255 (ttm-80) cc_final: 0.7926 (tpp80) REVERT: L 5 THR cc_start: 0.9309 (m) cc_final: 0.9082 (p) REVERT: L 27 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.8994 (pp) REVERT: L 136 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7921 (mm-30) REVERT: M 12 MET cc_start: 0.7734 (ttm) cc_final: 0.7452 (tpt) REVERT: M 96 ILE cc_start: 0.9283 (mm) cc_final: 0.9031 (mp) REVERT: M 114 ARG cc_start: 0.8711 (tpp80) cc_final: 0.8510 (mtt-85) REVERT: N 75 ILE cc_start: 0.9268 (mm) cc_final: 0.9006 (mp) REVERT: N 82 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7664 (mt-10) REVERT: N 107 ASN cc_start: 0.8955 (t0) cc_final: 0.8565 (t0) REVERT: O 21 LEU cc_start: 0.9263 (mt) cc_final: 0.9041 (mp) REVERT: O 87 ILE cc_start: 0.8702 (mp) cc_final: 0.8350 (pp) REVERT: O 108 ASP cc_start: 0.8536 (m-30) cc_final: 0.8287 (m-30) REVERT: P 5 LYS cc_start: 0.8740 (ttpp) cc_final: 0.8458 (ttmt) REVERT: P 9 GLN cc_start: 0.8555 (mt0) cc_final: 0.7819 (tp-100) REVERT: P 12 MET cc_start: 0.8369 (mtp) cc_final: 0.8101 (mtm) REVERT: P 37 LYS cc_start: 0.9126 (tmtp) cc_final: 0.8684 (ptmm) REVERT: P 84 SER cc_start: 0.8306 (t) cc_final: 0.8046 (p) REVERT: P 86 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.8746 (mmpt) REVERT: Q 14 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8648 (ttmm) REVERT: Q 29 ARG cc_start: 0.8882 (mtt90) cc_final: 0.8181 (mtt90) REVERT: Q 48 ASP cc_start: 0.7896 (m-30) cc_final: 0.7664 (m-30) REVERT: Q 70 GLN cc_start: 0.8702 (tp40) cc_final: 0.8036 (tp40) REVERT: Q 109 VAL cc_start: 0.9388 (t) cc_final: 0.9127 (t) REVERT: R 13 ARG cc_start: 0.8670 (ttp80) cc_final: 0.8441 (ttp80) REVERT: R 99 THR cc_start: 0.8559 (p) cc_final: 0.8181 (m) REVERT: S 12 SER cc_start: 0.8864 (t) cc_final: 0.8447 (m) REVERT: S 55 ILE cc_start: 0.9334 (OUTLIER) cc_final: 0.9132 (mp) REVERT: S 92 ARG cc_start: 0.7843 (mtm110) cc_final: 0.7610 (ptm160) REVERT: T 12 ARG cc_start: 0.8800 (mmp-170) cc_final: 0.8580 (mmp80) REVERT: T 28 ASN cc_start: 0.8681 (t0) cc_final: 0.8145 (t0) REVERT: T 33 LYS cc_start: 0.8502 (mtpm) cc_final: 0.8227 (mtmm) REVERT: U 5 ARG cc_start: 0.8523 (ptp-170) cc_final: 0.8188 (ptp-170) REVERT: W 35 ARG cc_start: 0.8455 (mtm110) cc_final: 0.8230 (mtt-85) REVERT: W 64 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8521 (ttpp) REVERT: W 66 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7335 (mt-10) REVERT: X 1 SER cc_start: 0.9096 (p) cc_final: 0.8781 (t) REVERT: Y 13 GLU cc_start: 0.8296 (pt0) cc_final: 0.7984 (pt0) REVERT: Y 27 ASN cc_start: 0.8062 (m-40) cc_final: 0.7788 (t0) REVERT: Y 36 GLN cc_start: 0.8067 (mp10) cc_final: 0.7837 (mp10) REVERT: Y 39 GLN cc_start: 0.8111 (mm-40) cc_final: 0.7771 (mm-40) REVERT: Z 5 LYS cc_start: 0.9055 (mtpp) cc_final: 0.8813 (mmtp) REVERT: Z 36 GLU cc_start: 0.7755 (tp30) cc_final: 0.7360 (tp30) REVERT: 0 11 LYS cc_start: 0.8662 (tptm) cc_final: 0.8362 (tppt) REVERT: 0 29 VAL cc_start: 0.9518 (t) cc_final: 0.9280 (m) REVERT: 0 30 ASP cc_start: 0.8472 (t70) cc_final: 0.8228 (t0) REVERT: 0 36 LYS cc_start: 0.8798 (mmtp) cc_final: 0.8419 (mmmm) REVERT: 1 9 LYS cc_start: 0.8673 (ttmt) cc_final: 0.8339 (ttmm) REVERT: 1 32 LYS cc_start: 0.8444 (mmtp) cc_final: 0.8085 (mmtp) REVERT: 1 50 GLU cc_start: 0.7568 (tt0) cc_final: 0.7329 (tt0) REVERT: 3 51 LYS cc_start: 0.8985 (tmmt) cc_final: 0.8771 (tmmm) REVERT: 4 13 ASN cc_start: 0.8789 (m110) cc_final: 0.8524 (m110) REVERT: 4 20 ASP cc_start: 0.7915 (m-30) cc_final: 0.7688 (m-30) REVERT: 4 22 VAL cc_start: 0.8918 (OUTLIER) cc_final: 0.8662 (m) REVERT: 4 30 GLU cc_start: 0.7235 (mp0) cc_final: 0.6967 (mp0) REVERT: 6 56 ARG cc_start: 0.6867 (mmm-85) cc_final: 0.5803 (mmm-85) REVERT: 6 59 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.7141 (ttp-170) REVERT: v 14 GLN cc_start: 0.7156 (OUTLIER) cc_final: 0.6890 (tm-30) outliers start: 290 outliers final: 99 residues processed: 2150 average time/residue: 2.0843 time to fit residues: 6500.3812 Evaluate side-chains 1954 residues out of total 5071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 1839 time to evaluate : 5.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 29 PHE Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 128 LEU Chi-restraints excluded: chain b residue 183 PHE Chi-restraints excluded: chain b residue 216 VAL Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 63 ILE Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain e residue 10 LEU Chi-restraints excluded: chain e residue 61 LYS Chi-restraints excluded: chain e residue 63 MET Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain g residue 55 LYS Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 125 ILE Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain j residue 22 THR Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain k residue 57 SER Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 93 ARG Chi-restraints excluded: chain m residue 20 SER Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 67 ASP Chi-restraints excluded: chain m residue 73 SER Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain m residue 103 THR Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 60 GLN Chi-restraints excluded: chain n residue 86 GLU Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain r residue 41 SER Chi-restraints excluded: chain s residue 54 ARG Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain t residue 22 SER Chi-restraints excluded: chain u residue 13 VAL Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 61 LYS Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 45 SER Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain P residue 36 LYS Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 14 LYS Chi-restraints excluded: chain Q residue 103 VAL Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 55 ILE Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 64 LYS Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Z residue 24 LEU Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 45 ASP Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 33 THR Chi-restraints excluded: chain 3 residue 57 VAL Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain 6 residue 21 VAL Chi-restraints excluded: chain 6 residue 28 VAL Chi-restraints excluded: chain 6 residue 59 ARG Chi-restraints excluded: chain v residue 14 GLN Chi-restraints excluded: chain y residue 13 LEU Chi-restraints excluded: chain y residue 294 VAL Chi-restraints excluded: chain y residue 296 ILE Chi-restraints excluded: chain x residue 28 GLU Chi-restraints excluded: chain x residue 29 GLN Chi-restraints excluded: chain x residue 33 ARG Chi-restraints excluded: chain x residue 77 LEU Chi-restraints excluded: chain x residue 84 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 533 optimal weight: 20.0000 chunk 297 optimal weight: 1.9990 chunk 798 optimal weight: 30.0000 chunk 653 optimal weight: 10.0000 chunk 264 optimal weight: 7.9990 chunk 961 optimal weight: 5.9990 chunk 1038 optimal weight: 9.9990 chunk 856 optimal weight: 2.9990 chunk 953 optimal weight: 5.9990 chunk 327 optimal weight: 9.9990 chunk 771 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 57 ASN ** b 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 7 ASN c 138 GLN c 139 ASN d 70 GLN e 42 ASN ** e 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 GLN ** g 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 85 GLN ** g 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 152 HIS i 4 GLN i 30 ASN i 109 GLN i 125 GLN l 111 GLN n 43 ASN o 36 ASN o 39 GLN p 63 GLN ** q 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 19 HIS t 20 ASN t 47 GLN C 52 HIS D 32 ASN D 49 GLN D 130 GLN D 136 ASN ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 GLN G 103 ASN H 2 GLN K 29 HIS L 4 ASN L 38 GLN L 99 ASN N 9 GLN N 23 ASN O 38 GLN P 2 ASN P 11 GLN ** P 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN Q 51 GLN Q 71 ASN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 61 ASN U 65 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 ASN Y 58 ASN ** Z 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 26 ASN 2 29 GLN 4 35 GLN 4 37 GLN x 36 GLN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 159850 Z= 0.349 Angle : 0.637 14.770 238824 Z= 0.330 Chirality : 0.038 0.398 30498 Planarity : 0.005 0.071 13064 Dihedral : 23.299 179.439 79182 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.47 % Favored : 90.35 % Rotamer: Outliers : 8.48 % Allowed : 25.13 % Favored : 66.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.02 % Twisted Proline : 1.03 % Twisted General : 0.24 % 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: -2.15 (0.10), residues: 6082 helix: -0.18 (0.12), residues: 1896 sheet: -1.36 (0.15), residues: 1140 loop : -2.31 (0.10), residues: 3046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP y 311 HIS 0.010 0.001 HIS f 11 PHE 0.024 0.002 PHE V 26 TYR 0.027 0.002 TYR O 36 ARG 0.009 0.001 ARG b 224 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2326 residues out of total 5071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 414 poor density : 1912 time to evaluate : 6.151 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: b 29 PHE cc_start: 0.8488 (OUTLIER) cc_final: 0.8018 (m-80) REVERT: b 51 GLU cc_start: 0.7877 (tp30) cc_final: 0.7014 (tp30) REVERT: b 55 GLU cc_start: 0.7979 (mp0) cc_final: 0.7357 (mp0) REVERT: b 139 GLU cc_start: 0.8122 (tm-30) cc_final: 0.7903 (tm-30) REVERT: b 168 GLU cc_start: 0.8450 (mp0) cc_final: 0.7798 (mp0) REVERT: b 174 GLU cc_start: 0.8336 (tp30) cc_final: 0.8088 (mm-30) REVERT: b 183 PHE cc_start: 0.8298 (OUTLIER) cc_final: 0.7274 (p90) REVERT: b 191 ASP cc_start: 0.7847 (t0) cc_final: 0.7424 (t0) REVERT: c 24 ASN cc_start: 0.8602 (m-40) cc_final: 0.8268 (m-40) REVERT: c 31 ASN cc_start: 0.8677 (t0) cc_final: 0.8154 (t0) REVERT: c 35 ASP cc_start: 0.8840 (m-30) cc_final: 0.8448 (m-30) REVERT: c 44 LYS cc_start: 0.9072 (tmmt) cc_final: 0.8711 (tppp) REVERT: c 129 PHE cc_start: 0.9012 (p90) cc_final: 0.8682 (p90) REVERT: c 161 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8907 (pp) REVERT: d 58 GLN cc_start: 0.8838 (mm-40) cc_final: 0.8437 (mm-40) REVERT: d 137 SER cc_start: 0.8962 (OUTLIER) cc_final: 0.8578 (p) REVERT: d 177 MET cc_start: 0.8317 (mtm) cc_final: 0.7811 (mpp) REVERT: d 178 GLU cc_start: 0.7389 (pm20) cc_final: 0.7147 (pm20) REVERT: e 13 LYS cc_start: 0.8674 (ttmm) cc_final: 0.8251 (tppt) REVERT: e 19 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.8305 (ttm-80) REVERT: e 54 GLU cc_start: 0.6557 (tt0) cc_final: 0.6255 (mt-10) REVERT: e 64 GLU cc_start: 0.8170 (tp30) cc_final: 0.7870 (tp30) REVERT: e 69 ASN cc_start: 0.8770 (t0) cc_final: 0.8300 (t0) REVERT: e 77 ASN cc_start: 0.8919 (m-40) cc_final: 0.8500 (p0) REVERT: e 95 MET cc_start: 0.8554 (mtm) cc_final: 0.8304 (mtp) REVERT: f 10 VAL cc_start: 0.9447 (OUTLIER) cc_final: 0.9164 (p) REVERT: f 17 GLN cc_start: 0.7748 (mp10) cc_final: 0.7501 (mp10) REVERT: f 30 THR cc_start: 0.9507 (m) cc_final: 0.9120 (p) REVERT: f 65 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7870 (tm-30) REVERT: f 88 MET cc_start: 0.7846 (tmm) cc_final: 0.7628 (tmm) REVERT: g 100 MET cc_start: 0.8711 (mtm) cc_final: 0.8390 (mtp) REVERT: g 129 ASN cc_start: 0.8329 (m-40) cc_final: 0.7987 (m-40) REVERT: h 42 GLU cc_start: 0.7991 (tp30) cc_final: 0.7789 (tp30) REVERT: h 51 GLU cc_start: 0.6863 (pt0) cc_final: 0.6651 (pt0) REVERT: h 64 TYR cc_start: 0.8467 (m-80) cc_final: 0.8119 (m-80) REVERT: i 21 LYS cc_start: 0.9060 (mtpp) cc_final: 0.8853 (mtpt) REVERT: i 30 ASN cc_start: 0.8859 (m-40) cc_final: 0.8515 (m110) REVERT: i 60 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8626 (pp) REVERT: i 90 ASP cc_start: 0.8054 (t70) cc_final: 0.7749 (t70) REVERT: j 9 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.7480 (ttp80) REVERT: j 14 ASP cc_start: 0.7899 (t0) cc_final: 0.7647 (t0) REVERT: j 64 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8228 (mt0) REVERT: k 36 ARG cc_start: 0.8349 (mmm-85) cc_final: 0.8058 (mmm-85) REVERT: k 69 CYS cc_start: 0.8607 (t) cc_final: 0.8404 (t) REVERT: k 97 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.8041 (mpp80) REVERT: l 8 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8209 (mtp85) REVERT: l 75 GLU cc_start: 0.7908 (mp0) cc_final: 0.7537 (tm-30) REVERT: l 85 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.8080 (ppp80) REVERT: l 113 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7577 (ptm-80) REVERT: m 43 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7930 (mtpp) REVERT: m 62 PHE cc_start: 0.6571 (t80) cc_final: 0.6287 (t80) REVERT: m 88 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.9210 (mt) REVERT: n 3 GLN cc_start: 0.8419 (mm-40) cc_final: 0.8214 (mm-40) REVERT: n 5 MET cc_start: 0.8362 (mtp) cc_final: 0.7992 (mmm) REVERT: n 62 ASN cc_start: 0.8749 (t0) cc_final: 0.8183 (t0) REVERT: o 9 LYS cc_start: 0.9145 (tmtm) cc_final: 0.8943 (tptp) REVERT: o 17 ASP cc_start: 0.9036 (p0) cc_final: 0.8753 (p0) REVERT: o 70 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8926 (ttpp) REVERT: o 71 ARG cc_start: 0.8603 (ttp80) cc_final: 0.8334 (ttm170) REVERT: o 79 GLN cc_start: 0.8496 (tp40) cc_final: 0.8282 (tp-100) REVERT: o 82 GLU cc_start: 0.8323 (tp30) cc_final: 0.8061 (tp30) REVERT: o 86 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8418 (pp) REVERT: p 53 ASP cc_start: 0.8009 (t0) cc_final: 0.7781 (t0) REVERT: q 47 ASP cc_start: 0.8326 (p0) cc_final: 0.8045 (p0) REVERT: r 42 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8275 (ptp90) REVERT: r 47 ARG cc_start: 0.7587 (mmt-90) cc_final: 0.7188 (mtt-85) REVERT: s 20 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8714 (tptm) REVERT: s 54 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7170 (ptt90) REVERT: s 55 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.6453 (mp10) REVERT: t 25 SER cc_start: 0.9157 (t) cc_final: 0.8830 (m) REVERT: u 19 LYS cc_start: 0.6721 (pttm) cc_final: 0.6452 (tppt) REVERT: u 28 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.9069 (tm) REVERT: C 20 ASN cc_start: 0.8356 (t0) cc_final: 0.7709 (t0) REVERT: C 65 ASP cc_start: 0.8528 (t0) cc_final: 0.8200 (t0) REVERT: C 110 LYS cc_start: 0.8109 (mmmt) cc_final: 0.7889 (mtmm) REVERT: C 116 GLN cc_start: 0.8877 (pt0) cc_final: 0.8492 (pt0) REVERT: C 180 MET cc_start: 0.8433 (mpp) cc_final: 0.8168 (mpp) REVERT: D 7 LYS cc_start: 0.8504 (ttmt) cc_final: 0.8215 (ttpp) REVERT: D 97 SER cc_start: 0.9141 (t) cc_final: 0.8800 (p) REVERT: D 99 GLU cc_start: 0.7784 (pp20) cc_final: 0.7583 (pp20) REVERT: D 181 ASP cc_start: 0.8408 (t70) cc_final: 0.8180 (t0) REVERT: E 17 THR cc_start: 0.8514 (p) cc_final: 0.8191 (t) REVERT: E 136 GLN cc_start: 0.9002 (tp-100) cc_final: 0.7792 (tp40) REVERT: E 168 ASP cc_start: 0.8020 (t0) cc_final: 0.7690 (t0) REVERT: E 181 ILE cc_start: 0.9390 (mm) cc_final: 0.9170 (mm) REVERT: F 6 TYR cc_start: 0.8919 (t80) cc_final: 0.8552 (t80) REVERT: F 10 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8314 (mt-10) REVERT: F 51 ASN cc_start: 0.8988 (m-40) cc_final: 0.8422 (m110) REVERT: F 82 TYR cc_start: 0.7888 (t80) cc_final: 0.7365 (t80) REVERT: G 17 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8110 (mtmm) REVERT: G 26 LYS cc_start: 0.8991 (ttmt) cc_final: 0.8730 (mtpp) REVERT: G 100 ASN cc_start: 0.8883 (p0) cc_final: 0.8158 (p0) REVERT: G 115 GLN cc_start: 0.8668 (tp-100) cc_final: 0.8424 (tp40) REVERT: G 137 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8453 (tppp) REVERT: G 148 ARG cc_start: 0.8845 (ttt-90) cc_final: 0.8586 (ttt-90) REVERT: G 156 TYR cc_start: 0.8834 (m-80) cc_final: 0.8461 (m-80) REVERT: G 166 GLU cc_start: 0.8153 (tt0) cc_final: 0.7742 (tt0) REVERT: J 2 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8126 (mmtp) REVERT: J 16 TYR cc_start: 0.9262 (m-80) cc_final: 0.9058 (m-80) REVERT: J 58 ASN cc_start: 0.9283 (m110) cc_final: 0.9071 (m-40) REVERT: J 95 ARG cc_start: 0.8033 (ttp-110) cc_final: 0.7754 (ttp-110) REVERT: K 82 ASN cc_start: 0.9247 (OUTLIER) cc_final: 0.8898 (m-40) REVERT: K 108 ARG cc_start: 0.8287 (ttm-80) cc_final: 0.8051 (tpp80) REVERT: L 5 THR cc_start: 0.9319 (m) cc_final: 0.9092 (p) REVERT: L 27 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8983 (pp) REVERT: L 104 GLN cc_start: 0.8899 (mm-40) cc_final: 0.8579 (mm110) REVERT: M 12 MET cc_start: 0.7865 (ttm) cc_final: 0.7559 (tpt) REVERT: M 22 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7846 (mm-40) REVERT: M 58 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8570 (mtmm) REVERT: M 96 ILE cc_start: 0.9346 (mm) cc_final: 0.9111 (mp) REVERT: N 32 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8286 (mt-10) REVERT: N 43 GLU cc_start: 0.8606 (tp30) cc_final: 0.8344 (tp30) REVERT: N 72 ASP cc_start: 0.8047 (t0) cc_final: 0.7540 (t0) REVERT: N 75 ILE cc_start: 0.9394 (mm) cc_final: 0.8987 (mp) REVERT: N 82 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7792 (mt-10) REVERT: N 107 ASN cc_start: 0.9074 (t0) cc_final: 0.8635 (t0) REVERT: O 19 GLN cc_start: 0.9346 (tm-30) cc_final: 0.8945 (tm-30) REVERT: O 21 LEU cc_start: 0.9298 (mt) cc_final: 0.9073 (mp) REVERT: O 87 ILE cc_start: 0.8738 (mp) cc_final: 0.8218 (pp) REVERT: P 9 GLN cc_start: 0.8521 (mt0) cc_final: 0.8175 (tm-30) REVERT: P 12 MET cc_start: 0.8478 (mtp) cc_final: 0.8218 (mtm) REVERT: P 51 ASN cc_start: 0.8325 (m-40) cc_final: 0.8123 (m-40) REVERT: P 86 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8433 (mmpt) REVERT: P 110 LYS cc_start: 0.8836 (mppt) cc_final: 0.8635 (mtpt) REVERT: Q 70 GLN cc_start: 0.8738 (tp40) cc_final: 0.8026 (tp40) REVERT: Q 109 VAL cc_start: 0.9489 (t) cc_final: 0.9207 (t) REVERT: Q 110 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7893 (tm-30) REVERT: R 68 ARG cc_start: 0.8691 (mtp180) cc_final: 0.8444 (mtp180) REVERT: S 12 SER cc_start: 0.8827 (t) cc_final: 0.8547 (m) REVERT: S 62 ASP cc_start: 0.8547 (OUTLIER) cc_final: 0.7664 (p0) REVERT: S 70 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8267 (ttpt) REVERT: T 28 ASN cc_start: 0.8726 (t0) cc_final: 0.8133 (t0) REVERT: U 5 ARG cc_start: 0.8661 (ptp-170) cc_final: 0.8361 (ptp-170) REVERT: U 98 ASN cc_start: 0.7503 (p0) cc_final: 0.6605 (p0) REVERT: W 64 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8652 (ttpp) REVERT: Y 12 GLU cc_start: 0.7422 (tm-30) cc_final: 0.6793 (tm-30) REVERT: Y 13 GLU cc_start: 0.8263 (pt0) cc_final: 0.8041 (pt0) REVERT: Y 27 ASN cc_start: 0.7975 (m-40) cc_final: 0.7689 (t0) REVERT: Y 39 GLN cc_start: 0.8230 (mm-40) cc_final: 0.7911 (mm-40) REVERT: Z 5 LYS cc_start: 0.9104 (mtpp) cc_final: 0.8804 (mmtp) REVERT: Z 36 GLU cc_start: 0.7639 (tp30) cc_final: 0.7241 (tp30) REVERT: 0 11 LYS cc_start: 0.8743 (tptm) cc_final: 0.8414 (tppt) REVERT: 0 30 ASP cc_start: 0.8666 (t70) cc_final: 0.8451 (t0) REVERT: 0 36 LYS cc_start: 0.8918 (mmtp) cc_final: 0.8552 (mmmm) REVERT: 0 51 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7704 (ttt-90) REVERT: 4 20 ASP cc_start: 0.7902 (m-30) cc_final: 0.7696 (m-30) REVERT: 4 30 GLU cc_start: 0.7443 (mp0) cc_final: 0.7187 (mp0) REVERT: v 14 GLN cc_start: 0.7224 (pp30) cc_final: 0.7006 (tm-30) REVERT: x 38 TYR cc_start: 0.8412 (OUTLIER) cc_final: 0.7583 (m-10) REVERT: x 86 THR cc_start: 0.8936 (OUTLIER) cc_final: 0.8292 (m) outliers start: 414 outliers final: 205 residues processed: 2059 average time/residue: 2.0594 time to fit residues: 6213.9141 Evaluate side-chains 2071 residues out of total 5071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 1830 time to evaluate : 6.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 15 PHE Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 29 PHE Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 128 LEU Chi-restraints excluded: chain b residue 152 ASP Chi-restraints excluded: chain b residue 158 ASP Chi-restraints excluded: chain b residue 182 VAL Chi-restraints excluded: chain b residue 183 PHE Chi-restraints excluded: chain b residue 216 VAL Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 118 SER Chi-restraints excluded: chain c residue 121 SER Chi-restraints excluded: chain c residue 161 ILE Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 67 LEU Chi-restraints excluded: chain d residue 133 SER Chi-restraints excluded: chain d residue 137 SER Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 143 SER Chi-restraints excluded: chain e residue 10 LEU Chi-restraints excluded: chain e residue 19 ARG Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 65 LYS Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain g residue 14 ASP Chi-restraints excluded: chain g residue 47 GLU Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 132 THR Chi-restraints excluded: chain h residue 10 LEU Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 125 ILE Chi-restraints excluded: chain i residue 13 SER Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain i residue 72 SER Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain j residue 9 ARG Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 64 GLN Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 57 SER Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 97 ARG Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain l residue 8 ARG Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 85 ARG Chi-restraints excluded: chain l residue 93 ARG Chi-restraints excluded: chain l residue 113 ARG Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 20 SER Chi-restraints excluded: chain m residue 27 THR Chi-restraints excluded: chain m residue 43 LYS Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 73 SER Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain m residue 103 THR Chi-restraints excluded: chain m residue 107 THR Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 32 ASP Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 70 LYS Chi-restraints excluded: chain o residue 86 LEU Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain q residue 52 CYS Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain r residue 42 ARG Chi-restraints excluded: chain r residue 43 ILE Chi-restraints excluded: chain r residue 70 THR Chi-restraints excluded: chain s residue 3 SER Chi-restraints excluded: chain s residue 18 VAL Chi-restraints excluded: chain s residue 20 LYS Chi-restraints excluded: chain s residue 54 ARG Chi-restraints excluded: chain s residue 55 GLN Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 5 SER Chi-restraints excluded: chain t residue 11 ILE Chi-restraints excluded: chain t residue 22 SER Chi-restraints excluded: chain t residue 85 LEU Chi-restraints excluded: chain u residue 13 VAL Chi-restraints excluded: chain u residue 16 ARG Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 41 THR Chi-restraints excluded: chain u residue 50 SER Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 150 GLN Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 126 ASN Chi-restraints excluded: chain F residue 135 ILE Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 17 LYS Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 137 LYS Chi-restraints excluded: chain G residue 170 THR Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain J residue 2 LYS Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 51 LYS Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 91 SER Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 4 ASN Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain M residue 22 GLN Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 58 LYS Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 45 SER Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 36 LYS Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 103 VAL Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 43 ASN Chi-restraints excluded: chain R residue 46 GLU Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 70 LYS Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 58 SER Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 64 LYS Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain X residue 1 SER Chi-restraints excluded: chain X residue 17 ARG Chi-restraints excluded: chain X residue 41 SER Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 51 ARG Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 2 residue 8 SER Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 57 VAL Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain 6 residue 10 GLU Chi-restraints excluded: chain 6 residue 28 VAL Chi-restraints excluded: chain 6 residue 36 VAL Chi-restraints excluded: chain 6 residue 43 PHE Chi-restraints excluded: chain 6 residue 59 ARG Chi-restraints excluded: chain 6 residue 61 ASN Chi-restraints excluded: chain y residue 13 LEU Chi-restraints excluded: chain y residue 24 VAL Chi-restraints excluded: chain y residue 35 VAL Chi-restraints excluded: chain y residue 82 THR Chi-restraints excluded: chain y residue 278 THR Chi-restraints excluded: chain y residue 281 THR Chi-restraints excluded: chain y residue 294 VAL Chi-restraints excluded: chain y residue 296 ILE Chi-restraints excluded: chain y residue 346 LEU Chi-restraints excluded: chain x residue 27 LEU Chi-restraints excluded: chain x residue 28 GLU Chi-restraints excluded: chain x residue 29 GLN Chi-restraints excluded: chain x residue 38 TYR Chi-restraints excluded: chain x residue 44 GLU Chi-restraints excluded: chain x residue 54 LEU Chi-restraints excluded: chain x residue 77 LEU Chi-restraints excluded: chain x residue 84 GLN Chi-restraints excluded: chain x residue 86 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 950 optimal weight: 3.9990 chunk 722 optimal weight: 2.9990 chunk 499 optimal weight: 10.0000 chunk 106 optimal weight: 8.9990 chunk 458 optimal weight: 8.9990 chunk 645 optimal weight: 8.9990 chunk 965 optimal weight: 0.8980 chunk 1021 optimal weight: 40.0000 chunk 504 optimal weight: 10.0000 chunk 914 optimal weight: 7.9990 chunk 275 optimal weight: 5.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 138 GLN e 42 ASN ** e 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 96 GLN ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 GLN f 94 HIS ** g 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 85 GLN ** g 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 141 HIS g 152 HIS i 4 GLN i 109 GLN i 125 GLN l 5 GLN l 111 GLN p 63 GLN ** q 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 46 HIS s 13 HIS ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN D 136 ASN E 136 GLN E 195 GLN F 134 GLN G 44 HIS ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 ASN K 29 HIS ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 ASN L 38 GLN N 9 GLN N 23 ASN O 38 GLN P 2 ASN ** P 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN ** Q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN T 48 GLN T 70 HIS U 65 GLN Y 58 ASN Z 19 HIS 2 29 GLN 3 27 ASN 4 35 GLN v 32 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 159850 Z= 0.317 Angle : 0.615 11.768 238824 Z= 0.319 Chirality : 0.037 0.390 30498 Planarity : 0.005 0.094 13064 Dihedral : 23.268 179.795 79182 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.39 % Favored : 90.41 % Rotamer: Outliers : 8.62 % Allowed : 27.77 % Favored : 63.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.02 % Twisted Proline : 1.03 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.10), residues: 6082 helix: 0.22 (0.12), residues: 1882 sheet: -1.21 (0.15), residues: 1139 loop : -2.18 (0.10), residues: 3061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP y 311 HIS 0.010 0.001 HIS t 67 PHE 0.019 0.002 PHE H 91 TYR 0.026 0.002 TYR O 36 ARG 0.013 0.001 ARG j 16 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2313 residues out of total 5071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 421 poor density : 1892 time to evaluate : 6.315 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: b 29 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.8057 (m-80) REVERT: b 51 GLU cc_start: 0.7882 (tp30) cc_final: 0.6950 (tp30) REVERT: b 55 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7390 (mp0) REVERT: b 168 GLU cc_start: 0.8440 (mp0) cc_final: 0.7825 (mp0) REVERT: b 174 GLU cc_start: 0.8111 (tp30) cc_final: 0.7880 (mm-30) REVERT: b 183 PHE cc_start: 0.8328 (OUTLIER) cc_final: 0.7319 (p90) REVERT: b 191 ASP cc_start: 0.7843 (t0) cc_final: 0.7433 (t0) REVERT: c 31 ASN cc_start: 0.8725 (t0) cc_final: 0.8291 (t0) REVERT: c 35 ASP cc_start: 0.8887 (m-30) cc_final: 0.8491 (m-30) REVERT: c 129 PHE cc_start: 0.9062 (p90) cc_final: 0.8701 (p90) REVERT: c 131 ARG cc_start: 0.8473 (tpp80) cc_final: 0.8269 (ttm110) REVERT: c 161 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8885 (pp) REVERT: c 167 TYR cc_start: 0.7973 (m-10) cc_final: 0.7727 (m-10) REVERT: c 168 ARG cc_start: 0.8340 (tmm-80) cc_final: 0.8122 (ttp80) REVERT: d 44 LYS cc_start: 0.8893 (tppp) cc_final: 0.8673 (tptm) REVERT: d 58 GLN cc_start: 0.8823 (mm-40) cc_final: 0.8406 (mm-40) REVERT: d 68 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7673 (tp30) REVERT: d 130 ASN cc_start: 0.8093 (t160) cc_final: 0.7877 (t0) REVERT: d 137 SER cc_start: 0.8964 (OUTLIER) cc_final: 0.8546 (p) REVERT: d 151 GLN cc_start: 0.8650 (pp30) cc_final: 0.8005 (pp30) REVERT: d 177 MET cc_start: 0.8369 (mtm) cc_final: 0.7831 (mpp) REVERT: d 178 GLU cc_start: 0.7435 (pm20) cc_final: 0.7188 (pm20) REVERT: e 11 GLN cc_start: 0.8677 (tt0) cc_final: 0.8360 (tp40) REVERT: e 13 LYS cc_start: 0.8664 (ttmm) cc_final: 0.8462 (ttmm) REVERT: e 19 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.8267 (ttm-80) REVERT: e 64 GLU cc_start: 0.8191 (tp30) cc_final: 0.7858 (tp30) REVERT: e 69 ASN cc_start: 0.8798 (t0) cc_final: 0.8294 (t0) REVERT: e 77 ASN cc_start: 0.8847 (m-40) cc_final: 0.8293 (p0) REVERT: f 5 GLU cc_start: 0.7196 (mp0) cc_final: 0.6977 (mp0) REVERT: f 10 VAL cc_start: 0.9494 (OUTLIER) cc_final: 0.9172 (p) REVERT: f 13 ASP cc_start: 0.8508 (OUTLIER) cc_final: 0.8213 (p0) REVERT: f 88 MET cc_start: 0.7880 (tmm) cc_final: 0.7646 (tmm) REVERT: g 79 VAL cc_start: 0.8842 (OUTLIER) cc_final: 0.8621 (p) REVERT: g 100 MET cc_start: 0.8724 (mtm) cc_final: 0.8414 (mtp) REVERT: g 129 ASN cc_start: 0.8303 (m-40) cc_final: 0.8007 (m-40) REVERT: h 57 GLU cc_start: 0.7485 (mp0) cc_final: 0.7231 (mp0) REVERT: h 64 TYR cc_start: 0.8539 (m-80) cc_final: 0.8257 (m-80) REVERT: i 60 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8688 (pp) REVERT: i 90 ASP cc_start: 0.8005 (t70) cc_final: 0.7655 (t70) REVERT: j 45 ARG cc_start: 0.7656 (mmt180) cc_final: 0.6984 (ttm170) REVERT: j 64 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8183 (mt0) REVERT: k 69 CYS cc_start: 0.8611 (t) cc_final: 0.8392 (t) REVERT: l 2 THR cc_start: 0.8805 (m) cc_final: 0.8311 (p) REVERT: l 8 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.8301 (mtp85) REVERT: l 75 GLU cc_start: 0.7914 (mp0) cc_final: 0.7544 (tm-30) REVERT: l 85 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.8074 (ppp80) REVERT: l 113 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7471 (ptm-80) REVERT: m 88 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9187 (mt) REVERT: n 3 GLN cc_start: 0.8392 (mm-40) cc_final: 0.8172 (mm-40) REVERT: n 5 MET cc_start: 0.8385 (mtp) cc_final: 0.8006 (mmm) REVERT: n 60 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.8328 (mp10) REVERT: n 62 ASN cc_start: 0.8750 (t0) cc_final: 0.8176 (t0) REVERT: o 9 LYS cc_start: 0.9140 (tmtm) cc_final: 0.8873 (tptp) REVERT: o 17 ASP cc_start: 0.9057 (p0) cc_final: 0.8746 (p0) REVERT: o 70 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8917 (ttpp) REVERT: o 71 ARG cc_start: 0.8627 (ttp80) cc_final: 0.8379 (ttm170) REVERT: o 82 GLU cc_start: 0.8325 (tp30) cc_final: 0.8027 (tp30) REVERT: o 86 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8429 (pp) REVERT: p 53 ASP cc_start: 0.7988 (t0) cc_final: 0.7684 (t0) REVERT: q 10 ARG cc_start: 0.8035 (mtp-110) cc_final: 0.7674 (ttm110) REVERT: q 17 GLU cc_start: 0.8070 (tp30) cc_final: 0.7866 (tp30) REVERT: q 47 ASP cc_start: 0.8401 (p0) cc_final: 0.8061 (p0) REVERT: r 47 ARG cc_start: 0.7588 (mmt-90) cc_final: 0.7206 (mtt-85) REVERT: s 17 LYS cc_start: 0.8981 (ttmm) cc_final: 0.8733 (mtpp) REVERT: s 20 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8681 (tptm) REVERT: s 54 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7296 (ptt90) REVERT: s 55 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.6472 (mp10) REVERT: t 14 GLU cc_start: 0.8515 (tp30) cc_final: 0.8265 (mm-30) REVERT: t 25 SER cc_start: 0.9132 (t) cc_final: 0.8846 (m) REVERT: u 19 LYS cc_start: 0.6728 (pttm) cc_final: 0.6486 (tppt) REVERT: C 65 ASP cc_start: 0.8520 (t0) cc_final: 0.8139 (t0) REVERT: C 110 LYS cc_start: 0.8211 (mmmt) cc_final: 0.7953 (mtmm) REVERT: C 116 GLN cc_start: 0.8846 (pt0) cc_final: 0.8447 (pt0) REVERT: C 124 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8295 (ttpp) REVERT: C 180 MET cc_start: 0.8447 (mpp) cc_final: 0.8154 (mpp) REVERT: D 7 LYS cc_start: 0.8521 (ttmt) cc_final: 0.8215 (ttpp) REVERT: D 39 ASP cc_start: 0.8083 (p0) cc_final: 0.7874 (p0) REVERT: D 97 SER cc_start: 0.9184 (t) cc_final: 0.8839 (p) REVERT: D 99 GLU cc_start: 0.7837 (pp20) cc_final: 0.7630 (pp20) REVERT: D 181 ASP cc_start: 0.8381 (t70) cc_final: 0.8171 (t0) REVERT: E 25 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7005 (tm-30) REVERT: E 136 GLN cc_start: 0.8694 (tp40) cc_final: 0.8052 (tp40) REVERT: E 140 ASP cc_start: 0.7832 (m-30) cc_final: 0.7422 (m-30) REVERT: E 168 ASP cc_start: 0.8020 (t0) cc_final: 0.7706 (t0) REVERT: E 181 ILE cc_start: 0.9362 (mm) cc_final: 0.9117 (mm) REVERT: F 51 ASN cc_start: 0.8902 (m-40) cc_final: 0.8552 (m110) REVERT: F 71 LYS cc_start: 0.8033 (mmmm) cc_final: 0.7394 (mtpp) REVERT: F 141 ASP cc_start: 0.6898 (p0) cc_final: 0.6659 (p0) REVERT: F 146 ASP cc_start: 0.7929 (p0) cc_final: 0.7565 (p0) REVERT: G 17 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8091 (mtmm) REVERT: G 26 LYS cc_start: 0.8988 (ttmt) cc_final: 0.8715 (mtpp) REVERT: G 100 ASN cc_start: 0.8936 (p0) cc_final: 0.8183 (p0) REVERT: G 115 GLN cc_start: 0.8652 (tp-100) cc_final: 0.8381 (tp40) REVERT: G 137 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8490 (tppp) REVERT: G 148 ARG cc_start: 0.8849 (ttt-90) cc_final: 0.8620 (ttt-90) REVERT: G 156 TYR cc_start: 0.8844 (m-80) cc_final: 0.8466 (m-80) REVERT: G 166 GLU cc_start: 0.8149 (tt0) cc_final: 0.7697 (tt0) REVERT: J 2 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8025 (mmtp) REVERT: J 14 ASP cc_start: 0.7884 (m-30) cc_final: 0.7520 (m-30) REVERT: J 16 TYR cc_start: 0.9262 (m-80) cc_final: 0.8912 (m-80) REVERT: J 52 ASP cc_start: 0.8568 (m-30) cc_final: 0.8275 (m-30) REVERT: K 82 ASN cc_start: 0.9251 (OUTLIER) cc_final: 0.8974 (m-40) REVERT: K 108 ARG cc_start: 0.8219 (ttm-80) cc_final: 0.8011 (tpp80) REVERT: L 104 GLN cc_start: 0.8890 (mm-40) cc_final: 0.8647 (mm110) REVERT: M 12 MET cc_start: 0.7898 (OUTLIER) cc_final: 0.7552 (tpt) REVERT: M 22 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7845 (mm-40) REVERT: M 40 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.8096 (mtm180) REVERT: M 54 THR cc_start: 0.8976 (m) cc_final: 0.8743 (p) REVERT: M 58 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8443 (mtmm) REVERT: M 96 ILE cc_start: 0.9367 (mm) cc_final: 0.9140 (mp) REVERT: N 43 GLU cc_start: 0.8612 (tp30) cc_final: 0.8400 (tp30) REVERT: N 72 ASP cc_start: 0.8125 (t0) cc_final: 0.7683 (t0) REVERT: N 75 ILE cc_start: 0.9340 (mm) cc_final: 0.8930 (mp) REVERT: N 82 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7788 (mt-10) REVERT: N 107 ASN cc_start: 0.9062 (t0) cc_final: 0.8640 (t0) REVERT: N 114 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7711 (pp20) REVERT: O 19 GLN cc_start: 0.9323 (tm-30) cc_final: 0.8842 (tm-30) REVERT: O 55 GLU cc_start: 0.8422 (pt0) cc_final: 0.8157 (pp20) REVERT: O 87 ILE cc_start: 0.8877 (mp) cc_final: 0.8316 (pp) REVERT: P 9 GLN cc_start: 0.8624 (mt0) cc_final: 0.8232 (tm-30) REVERT: P 51 ASN cc_start: 0.8298 (m-40) cc_final: 0.8082 (m110) REVERT: P 86 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8468 (mmpt) REVERT: Q 70 GLN cc_start: 0.8760 (tp40) cc_final: 0.8035 (tp40) REVERT: Q 109 VAL cc_start: 0.9455 (t) cc_final: 0.9178 (t) REVERT: Q 110 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7858 (tm-30) REVERT: R 21 ARG cc_start: 0.8949 (ttm170) cc_final: 0.8262 (ttm-80) REVERT: S 12 SER cc_start: 0.8812 (t) cc_final: 0.8601 (m) REVERT: S 70 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8240 (ttpt) REVERT: T 28 ASN cc_start: 0.8706 (t0) cc_final: 0.8143 (t0) REVERT: U 5 ARG cc_start: 0.8653 (ptp-170) cc_final: 0.8128 (ptp-170) REVERT: U 98 ASN cc_start: 0.7185 (p0) cc_final: 0.6870 (p0) REVERT: V 90 ASP cc_start: 0.8390 (m-30) cc_final: 0.8035 (m-30) REVERT: X 15 ASN cc_start: 0.9267 (m-40) cc_final: 0.9061 (m-40) REVERT: Y 5 GLU cc_start: 0.8239 (mp0) cc_final: 0.8005 (OUTLIER) REVERT: Y 36 GLN cc_start: 0.7885 (mp10) cc_final: 0.7495 (mp10) REVERT: Y 39 GLN cc_start: 0.8094 (mm-40) cc_final: 0.7819 (mm-40) REVERT: Z 5 LYS cc_start: 0.9112 (mtpp) cc_final: 0.8805 (mmtp) REVERT: Z 8 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8126 (tt0) REVERT: Z 36 GLU cc_start: 0.7610 (tp30) cc_final: 0.7251 (tp30) REVERT: 0 11 LYS cc_start: 0.8713 (tptm) cc_final: 0.8377 (tppt) REVERT: 0 30 ASP cc_start: 0.8611 (t70) cc_final: 0.8395 (t0) REVERT: 0 36 LYS cc_start: 0.8947 (mmtp) cc_final: 0.8643 (mmmm) REVERT: 4 20 ASP cc_start: 0.7920 (m-30) cc_final: 0.7717 (m-30) REVERT: 6 56 ARG cc_start: 0.7198 (mmm-85) cc_final: 0.6869 (mtp180) REVERT: x 38 TYR cc_start: 0.8394 (OUTLIER) cc_final: 0.7590 (m-10) outliers start: 421 outliers final: 234 residues processed: 2058 average time/residue: 2.0175 time to fit residues: 6055.8085 Evaluate side-chains 2111 residues out of total 5071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 270 poor density : 1841 time to evaluate : 6.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 15 PHE Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 29 PHE Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 55 GLU Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 128 LEU Chi-restraints excluded: chain b residue 158 ASP Chi-restraints excluded: chain b residue 182 VAL Chi-restraints excluded: chain b residue 183 PHE Chi-restraints excluded: chain b residue 216 VAL Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 93 ILE Chi-restraints excluded: chain c residue 118 SER Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 121 SER Chi-restraints excluded: chain c residue 161 ILE Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 63 ILE Chi-restraints excluded: chain d residue 67 LEU Chi-restraints excluded: chain d residue 68 GLU Chi-restraints excluded: chain d residue 133 SER Chi-restraints excluded: chain d residue 137 SER Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 142 VAL Chi-restraints excluded: chain d residue 143 SER Chi-restraints excluded: chain d residue 182 LYS Chi-restraints excluded: chain e residue 10 LEU Chi-restraints excluded: chain e residue 19 ARG Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 65 LYS Chi-restraints excluded: chain e residue 79 THR Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 13 ASP Chi-restraints excluded: chain f residue 51 ILE Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain g residue 14 ASP Chi-restraints excluded: chain g residue 37 THR Chi-restraints excluded: chain g residue 55 LYS Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 114 SER Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 110 MET Chi-restraints excluded: chain h residue 125 ILE Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain j residue 22 THR Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 64 GLN Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain k residue 25 SER Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 57 SER Chi-restraints excluded: chain k residue 80 ASN Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain l residue 8 ARG Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 46 SER Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 85 ARG Chi-restraints excluded: chain l residue 93 ARG Chi-restraints excluded: chain l residue 113 ARG Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 19 THR Chi-restraints excluded: chain m residue 20 SER Chi-restraints excluded: chain m residue 27 THR Chi-restraints excluded: chain m residue 44 ILE Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 67 ASP Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain m residue 103 THR Chi-restraints excluded: chain m residue 107 THR Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 32 ASP Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 60 GLN Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain n residue 86 GLU Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 70 LYS Chi-restraints excluded: chain o residue 86 LEU Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 46 LYS Chi-restraints excluded: chain p residue 79 ASN Chi-restraints excluded: chain q residue 14 ASP Chi-restraints excluded: chain q residue 19 SER Chi-restraints excluded: chain q residue 43 LEU Chi-restraints excluded: chain r residue 43 ILE Chi-restraints excluded: chain r residue 70 THR Chi-restraints excluded: chain s residue 12 LEU Chi-restraints excluded: chain s residue 18 VAL Chi-restraints excluded: chain s residue 20 LYS Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain s residue 54 ARG Chi-restraints excluded: chain s residue 55 GLN Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 11 ILE Chi-restraints excluded: chain t residue 85 LEU Chi-restraints excluded: chain u residue 13 VAL Chi-restraints excluded: chain u residue 16 ARG Chi-restraints excluded: chain u residue 31 VAL Chi-restraints excluded: chain u residue 41 THR Chi-restraints excluded: chain u residue 50 SER Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 126 ASN Chi-restraints excluded: chain F residue 134 GLN Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 17 LYS Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 137 LYS Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain J residue 2 LYS Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 91 SER Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 22 GLN Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 40 ARG Chi-restraints excluded: chain M residue 58 LYS Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 12 THR Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 36 LYS Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 103 VAL Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 46 GLU Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 70 LYS Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 58 SER Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain V residue 73 LYS Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain X residue 41 SER Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Z residue 8 GLN Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 48 ASN Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 45 ASP Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 8 SER Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 57 VAL Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain 4 residue 37 GLN Chi-restraints excluded: chain 6 residue 28 VAL Chi-restraints excluded: chain 6 residue 34 LEU Chi-restraints excluded: chain 6 residue 36 VAL Chi-restraints excluded: chain 6 residue 43 PHE Chi-restraints excluded: chain y residue 13 LEU Chi-restraints excluded: chain y residue 24 VAL Chi-restraints excluded: chain y residue 35 VAL Chi-restraints excluded: chain y residue 36 VAL Chi-restraints excluded: chain y residue 82 THR Chi-restraints excluded: chain y residue 272 LYS Chi-restraints excluded: chain y residue 281 THR Chi-restraints excluded: chain y residue 294 VAL Chi-restraints excluded: chain y residue 296 ILE Chi-restraints excluded: chain y residue 342 ILE Chi-restraints excluded: chain y residue 344 LEU Chi-restraints excluded: chain y residue 346 LEU Chi-restraints excluded: chain x residue 28 GLU Chi-restraints excluded: chain x residue 33 ARG Chi-restraints excluded: chain x residue 38 TYR Chi-restraints excluded: chain x residue 44 GLU Chi-restraints excluded: chain x residue 54 LEU Chi-restraints excluded: chain x residue 77 LEU Chi-restraints excluded: chain x residue 84 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 850 optimal weight: 5.9990 chunk 579 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 760 optimal weight: 10.0000 chunk 421 optimal weight: 10.0000 chunk 871 optimal weight: 10.0000 chunk 706 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 521 optimal weight: 10.0000 chunk 917 optimal weight: 8.9990 chunk 257 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 138 GLN e 42 ASN ** e 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 96 GLN ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 GLN g 67 ASN g 85 GLN g 129 ASN g 141 HIS h 17 GLN i 4 GLN i 30 ASN i 109 GLN i 125 GLN k 118 ASN l 111 GLN p 29 ASN p 63 GLN ** q 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 19 HIS ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN D 136 ASN E 62 GLN E 195 GLN F 51 ASN F 134 GLN G 29 ASN G 63 GLN G 103 ASN H 2 GLN J 80 HIS K 29 HIS ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 9 GLN N 18 GLN N 23 ASN O 38 GLN P 2 ASN ** P 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN ** Q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN S 61 ASN T 15 HIS T 48 GLN U 65 GLN ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 58 ASN 2 29 GLN 4 35 GLN v 32 GLN ** v 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 159850 Z= 0.447 Angle : 0.680 13.711 238824 Z= 0.350 Chirality : 0.041 0.417 30498 Planarity : 0.005 0.101 13064 Dihedral : 23.252 179.287 79179 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.05 % Favored : 89.79 % Rotamer: Outliers : 9.58 % Allowed : 28.26 % Favored : 62.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.02 % Twisted Proline : 1.03 % Twisted General : 0.20 % 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: -1.79 (0.10), residues: 6082 helix: 0.31 (0.12), residues: 1886 sheet: -1.22 (0.15), residues: 1152 loop : -2.19 (0.10), residues: 3044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP y 311 HIS 0.013 0.002 HIS t 67 PHE 0.024 0.002 PHE H 91 TYR 0.027 0.002 TYR 1 48 ARG 0.010 0.001 ARG b 138 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2345 residues out of total 5071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 468 poor density : 1877 time to evaluate : 5.875 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: b 20 ARG cc_start: 0.7198 (OUTLIER) cc_final: 0.5920 (ptt180) REVERT: b 29 PHE cc_start: 0.8626 (OUTLIER) cc_final: 0.8187 (m-80) REVERT: b 43 GLU cc_start: 0.6656 (OUTLIER) cc_final: 0.6059 (tp30) REVERT: b 51 GLU cc_start: 0.7909 (tp30) cc_final: 0.6849 (tp30) REVERT: b 55 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7316 (mp0) REVERT: b 62 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.8091 (mpp80) REVERT: b 139 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7971 (tp30) REVERT: b 168 GLU cc_start: 0.8414 (mp0) cc_final: 0.7985 (mp0) REVERT: b 174 GLU cc_start: 0.8149 (tp30) cc_final: 0.7645 (mt-10) REVERT: b 183 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.7566 (p90) REVERT: b 191 ASP cc_start: 0.7971 (t0) cc_final: 0.7733 (t0) REVERT: c 31 ASN cc_start: 0.8752 (m-40) cc_final: 0.8253 (t0) REVERT: c 35 ASP cc_start: 0.8913 (m-30) cc_final: 0.8615 (m-30) REVERT: c 44 LYS cc_start: 0.9013 (tmmt) cc_final: 0.8684 (tppp) REVERT: c 129 PHE cc_start: 0.9098 (p90) cc_final: 0.8786 (p90) REVERT: c 161 ILE cc_start: 0.9175 (OUTLIER) cc_final: 0.8896 (pp) REVERT: d 44 LYS cc_start: 0.8912 (tppp) cc_final: 0.8697 (tmtt) REVERT: d 58 GLN cc_start: 0.8875 (mm-40) cc_final: 0.8469 (mm-40) REVERT: d 68 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7656 (tp30) REVERT: d 137 SER cc_start: 0.8933 (OUTLIER) cc_final: 0.8530 (p) REVERT: d 151 GLN cc_start: 0.8738 (OUTLIER) cc_final: 0.8142 (pp30) REVERT: e 11 GLN cc_start: 0.8638 (tt0) cc_final: 0.8341 (tp40) REVERT: e 13 LYS cc_start: 0.8757 (ttmm) cc_final: 0.8511 (ttmm) REVERT: e 19 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.8269 (ttm-80) REVERT: e 51 LYS cc_start: 0.8983 (ttpt) cc_final: 0.8692 (ttpt) REVERT: e 61 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8820 (mttp) REVERT: e 64 GLU cc_start: 0.8306 (tp30) cc_final: 0.7982 (tp30) REVERT: e 69 ASN cc_start: 0.8818 (t0) cc_final: 0.8276 (t0) REVERT: e 92 ARG cc_start: 0.8438 (mpp80) cc_final: 0.8197 (mpp80) REVERT: f 10 VAL cc_start: 0.9533 (OUTLIER) cc_final: 0.9302 (m) REVERT: f 13 ASP cc_start: 0.8633 (OUTLIER) cc_final: 0.8387 (p0) REVERT: f 17 GLN cc_start: 0.7967 (mp10) cc_final: 0.7720 (mp10) REVERT: f 30 THR cc_start: 0.9652 (m) cc_final: 0.9274 (p) REVERT: g 78 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7613 (ppp80) REVERT: g 79 VAL cc_start: 0.8863 (OUTLIER) cc_final: 0.8661 (p) REVERT: g 100 MET cc_start: 0.8748 (mtm) cc_final: 0.8468 (mtp) REVERT: g 129 ASN cc_start: 0.8386 (m110) cc_final: 0.8157 (m-40) REVERT: h 57 GLU cc_start: 0.7563 (mp0) cc_final: 0.7326 (mp0) REVERT: i 60 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8721 (pp) REVERT: i 90 ASP cc_start: 0.8165 (t70) cc_final: 0.7792 (t70) REVERT: j 14 ASP cc_start: 0.7958 (t0) cc_final: 0.7710 (t0) REVERT: j 45 ARG cc_start: 0.7726 (mmt180) cc_final: 0.6969 (ttm170) REVERT: j 64 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8207 (mt0) REVERT: l 2 THR cc_start: 0.8676 (m) cc_final: 0.8239 (p) REVERT: l 8 ARG cc_start: 0.8908 (OUTLIER) cc_final: 0.8320 (mtp85) REVERT: l 85 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8119 (ppp80) REVERT: l 93 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.7915 (mtp180) REVERT: m 88 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9184 (mt) REVERT: n 5 MET cc_start: 0.8429 (mtp) cc_final: 0.8027 (mmm) REVERT: n 62 ASN cc_start: 0.8800 (t0) cc_final: 0.8236 (t0) REVERT: o 9 LYS cc_start: 0.9119 (tmtm) cc_final: 0.8871 (tptp) REVERT: o 17 ASP cc_start: 0.9100 (p0) cc_final: 0.8779 (p0) REVERT: o 70 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8922 (ttpp) REVERT: o 86 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8465 (pp) REVERT: p 53 ASP cc_start: 0.8117 (t0) cc_final: 0.7864 (t0) REVERT: q 47 ASP cc_start: 0.8428 (p0) cc_final: 0.8180 (p0) REVERT: r 23 LYS cc_start: 0.9092 (mtmm) cc_final: 0.8882 (mtmm) REVERT: r 47 ARG cc_start: 0.7651 (mmt-90) cc_final: 0.7269 (mtt-85) REVERT: s 20 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8664 (tptm) REVERT: s 54 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7798 (ptt90) REVERT: s 55 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.6739 (mp10) REVERT: t 25 SER cc_start: 0.9137 (t) cc_final: 0.8883 (m) REVERT: u 19 LYS cc_start: 0.6902 (pttm) cc_final: 0.6613 (tppt) REVERT: C 20 ASN cc_start: 0.8275 (t0) cc_final: 0.8003 (t0) REVERT: C 65 ASP cc_start: 0.8599 (t0) cc_final: 0.8262 (t0) REVERT: C 110 LYS cc_start: 0.8242 (mmmt) cc_final: 0.7945 (mtmm) REVERT: C 116 GLN cc_start: 0.8900 (pt0) cc_final: 0.8444 (pt0) REVERT: C 176 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.8244 (tpt-90) REVERT: D 7 LYS cc_start: 0.8584 (ttmt) cc_final: 0.8319 (ttpp) REVERT: D 28 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8054 (tm-30) REVERT: D 39 ASP cc_start: 0.8157 (p0) cc_final: 0.7941 (p0) REVERT: D 97 SER cc_start: 0.9202 (t) cc_final: 0.8863 (p) REVERT: D 99 GLU cc_start: 0.7945 (pp20) cc_final: 0.7741 (pp20) REVERT: D 181 ASP cc_start: 0.8367 (t70) cc_final: 0.8155 (t0) REVERT: E 136 GLN cc_start: 0.8639 (tp40) cc_final: 0.7911 (tp40) REVERT: E 140 ASP cc_start: 0.8077 (m-30) cc_final: 0.7591 (m-30) REVERT: E 156 ASN cc_start: 0.9165 (m-40) cc_final: 0.8743 (t0) REVERT: E 168 ASP cc_start: 0.7976 (t0) cc_final: 0.7691 (t0) REVERT: E 181 ILE cc_start: 0.9379 (mm) cc_final: 0.9141 (mm) REVERT: F 51 ASN cc_start: 0.8857 (m110) cc_final: 0.8555 (m110) REVERT: F 117 SER cc_start: 0.8521 (t) cc_final: 0.8228 (p) REVERT: F 128 SER cc_start: 0.9048 (t) cc_final: 0.8777 (t) REVERT: F 134 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7890 (mt0) REVERT: F 164 GLU cc_start: 0.8893 (mp0) cc_final: 0.8662 (mp0) REVERT: G 17 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8121 (mtmm) REVERT: G 26 LYS cc_start: 0.8989 (ttmt) cc_final: 0.8743 (mtpp) REVERT: G 43 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8303 (mmmt) REVERT: G 100 ASN cc_start: 0.8965 (p0) cc_final: 0.8271 (p0) REVERT: G 148 ARG cc_start: 0.8897 (ttt-90) cc_final: 0.8684 (ttt-90) REVERT: G 156 TYR cc_start: 0.8886 (m-80) cc_final: 0.8488 (m-80) REVERT: J 2 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8116 (mmtp) REVERT: J 14 ASP cc_start: 0.7932 (m-30) cc_final: 0.7590 (m-30) REVERT: J 16 TYR cc_start: 0.9280 (m-80) cc_final: 0.8966 (m-80) REVERT: J 52 ASP cc_start: 0.8590 (m-30) cc_final: 0.8302 (m-30) REVERT: J 96 ARG cc_start: 0.7864 (ttt-90) cc_final: 0.7608 (ttp80) REVERT: K 82 ASN cc_start: 0.9337 (OUTLIER) cc_final: 0.9004 (m-40) REVERT: K 108 ARG cc_start: 0.8277 (ttm-80) cc_final: 0.8024 (tpp80) REVERT: L 5 THR cc_start: 0.9308 (m) cc_final: 0.9060 (p) REVERT: L 27 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8919 (pp) REVERT: L 58 TYR cc_start: 0.8634 (p90) cc_final: 0.8201 (p90) REVERT: L 104 GLN cc_start: 0.8884 (mm-40) cc_final: 0.8655 (mm110) REVERT: L 106 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7333 (tm-30) REVERT: M 40 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8171 (mtm180) REVERT: M 54 THR cc_start: 0.8938 (m) cc_final: 0.8617 (p) REVERT: N 72 ASP cc_start: 0.8236 (t0) cc_final: 0.7733 (t0) REVERT: N 75 ILE cc_start: 0.9322 (OUTLIER) cc_final: 0.8961 (mp) REVERT: N 82 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7650 (mt-10) REVERT: N 107 ASN cc_start: 0.9132 (t0) cc_final: 0.8707 (t0) REVERT: N 114 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7828 (pp20) REVERT: O 19 GLN cc_start: 0.9316 (tm-30) cc_final: 0.8896 (tm-30) REVERT: O 87 ILE cc_start: 0.8868 (mp) cc_final: 0.8427 (pp) REVERT: O 104 GLN cc_start: 0.9079 (tt0) cc_final: 0.8805 (tt0) REVERT: P 9 GLN cc_start: 0.8640 (mt0) cc_final: 0.8241 (tm-30) REVERT: P 51 ASN cc_start: 0.8453 (m-40) cc_final: 0.8245 (m110) REVERT: P 86 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8476 (mmpt) REVERT: Q 70 GLN cc_start: 0.8804 (tp40) cc_final: 0.8126 (tp40) REVERT: Q 109 VAL cc_start: 0.9470 (t) cc_final: 0.9206 (t) REVERT: Q 110 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7908 (tm-30) REVERT: R 13 ARG cc_start: 0.8768 (ttp80) cc_final: 0.8516 (ttp80) REVERT: R 21 ARG cc_start: 0.8987 (ttm170) cc_final: 0.8484 (ttm-80) REVERT: R 31 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7852 (mt-10) REVERT: R 40 MET cc_start: 0.8568 (ttm) cc_final: 0.8334 (ttm) REVERT: R 84 ARG cc_start: 0.9195 (OUTLIER) cc_final: 0.8399 (ptt-90) REVERT: S 12 SER cc_start: 0.8813 (t) cc_final: 0.8581 (m) REVERT: S 70 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8343 (ttpt) REVERT: S 82 MET cc_start: 0.8337 (ptp) cc_final: 0.7995 (ptm) REVERT: T 28 ASN cc_start: 0.8769 (t0) cc_final: 0.8153 (t0) REVERT: U 5 ARG cc_start: 0.8601 (ptp-170) cc_final: 0.8056 (ptp-170) REVERT: U 9 GLU cc_start: 0.7744 (tp30) cc_final: 0.7403 (tp30) REVERT: U 21 ARG cc_start: 0.8537 (mtp-110) cc_final: 0.8327 (mtp-110) REVERT: U 98 ASN cc_start: 0.7599 (p0) cc_final: 0.7258 (p0) REVERT: V 9 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8788 (mmm-85) REVERT: V 79 ARG cc_start: 0.9270 (OUTLIER) cc_final: 0.8442 (mmm-85) REVERT: V 90 ASP cc_start: 0.8491 (m-30) cc_final: 0.8220 (m-30) REVERT: X 10 ARG cc_start: 0.8641 (mtp85) cc_final: 0.8345 (mtp85) REVERT: Y 30 MET cc_start: 0.7183 (pp-130) cc_final: 0.6885 (pp-130) REVERT: Y 39 GLN cc_start: 0.8171 (mm-40) cc_final: 0.7848 (mm-40) REVERT: Z 5 LYS cc_start: 0.9128 (mtpp) cc_final: 0.8704 (mmmm) REVERT: Z 8 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8151 (tt0) REVERT: Z 36 GLU cc_start: 0.7699 (tp30) cc_final: 0.7187 (tp30) REVERT: 0 11 LYS cc_start: 0.8741 (tptm) cc_final: 0.8391 (tppt) REVERT: 4 22 VAL cc_start: 0.8930 (OUTLIER) cc_final: 0.8679 (m) REVERT: y 57 GLN cc_start: 0.5602 (OUTLIER) cc_final: 0.5335 (pm20) REVERT: y 280 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7607 (mt) REVERT: x 38 TYR cc_start: 0.8443 (OUTLIER) cc_final: 0.7744 (m-10) outliers start: 468 outliers final: 275 residues processed: 2058 average time/residue: 2.0281 time to fit residues: 6091.0678 Evaluate side-chains 2131 residues out of total 5071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 323 poor density : 1808 time to evaluate : 6.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 15 PHE Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain b residue 20 ARG Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 29 PHE Chi-restraints excluded: chain b residue 43 GLU Chi-restraints excluded: chain b residue 55 GLU Chi-restraints excluded: chain b residue 62 ARG Chi-restraints excluded: chain b residue 109 SER Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 128 LEU Chi-restraints excluded: chain b residue 152 ASP Chi-restraints excluded: chain b residue 158 ASP Chi-restraints excluded: chain b residue 166 ASP Chi-restraints excluded: chain b residue 182 VAL Chi-restraints excluded: chain b residue 183 PHE Chi-restraints excluded: chain b residue 198 VAL Chi-restraints excluded: chain b residue 207 ARG Chi-restraints excluded: chain b residue 216 VAL Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 93 ILE Chi-restraints excluded: chain c residue 118 SER Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 121 SER Chi-restraints excluded: chain c residue 143 LEU Chi-restraints excluded: chain c residue 161 ILE Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 67 LEU Chi-restraints excluded: chain d residue 68 GLU Chi-restraints excluded: chain d residue 133 SER Chi-restraints excluded: chain d residue 137 SER Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 142 VAL Chi-restraints excluded: chain d residue 143 SER Chi-restraints excluded: chain d residue 151 GLN Chi-restraints excluded: chain e residue 10 LEU Chi-restraints excluded: chain e residue 19 ARG Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 61 LYS Chi-restraints excluded: chain e residue 65 LYS Chi-restraints excluded: chain e residue 79 THR Chi-restraints excluded: chain e residue 104 ILE Chi-restraints excluded: chain e residue 115 GLU Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain e residue 131 ASN Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 13 ASP Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain g residue 14 ASP Chi-restraints excluded: chain g residue 29 LEU Chi-restraints excluded: chain g residue 37 THR Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 74 VAL Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 78 ARG Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 114 SER Chi-restraints excluded: chain g residue 132 THR Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 88 LYS Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 124 ILE Chi-restraints excluded: chain h residue 125 ILE Chi-restraints excluded: chain i residue 13 SER Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 22 THR Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 53 ILE Chi-restraints excluded: chain j residue 64 GLN Chi-restraints excluded: chain k residue 25 SER Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 57 SER Chi-restraints excluded: chain k residue 80 ASN Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain k residue 126 ARG Chi-restraints excluded: chain l residue 8 ARG Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 46 SER Chi-restraints excluded: chain l residue 56 LEU Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 85 ARG Chi-restraints excluded: chain l residue 93 ARG Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 19 THR Chi-restraints excluded: chain m residue 20 SER Chi-restraints excluded: chain m residue 27 THR Chi-restraints excluded: chain m residue 44 ILE Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 73 SER Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain m residue 103 THR Chi-restraints excluded: chain m residue 107 THR Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 32 ASP Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 67 THR Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain n residue 86 GLU Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 60 SER Chi-restraints excluded: chain o residue 70 LYS Chi-restraints excluded: chain o residue 86 LEU Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 79 ASN Chi-restraints excluded: chain q residue 14 ASP Chi-restraints excluded: chain q residue 19 SER Chi-restraints excluded: chain q residue 43 LEU Chi-restraints excluded: chain q residue 52 CYS Chi-restraints excluded: chain r residue 43 ILE Chi-restraints excluded: chain r residue 70 THR Chi-restraints excluded: chain s residue 12 LEU Chi-restraints excluded: chain s residue 18 VAL Chi-restraints excluded: chain s residue 20 LYS Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain s residue 54 ARG Chi-restraints excluded: chain s residue 55 GLN Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 5 SER Chi-restraints excluded: chain t residue 11 ILE Chi-restraints excluded: chain t residue 85 LEU Chi-restraints excluded: chain u residue 13 VAL Chi-restraints excluded: chain u residue 16 ARG Chi-restraints excluded: chain u residue 31 VAL Chi-restraints excluded: chain u residue 41 THR Chi-restraints excluded: chain u residue 50 SER Chi-restraints excluded: chain u residue 52 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 176 ARG Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 184 ASP Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 126 ASN Chi-restraints excluded: chain F residue 134 GLN Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 17 LYS Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 170 THR Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain J residue 2 LYS Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 51 LYS Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 91 SER Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 40 ARG Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 3 LYS Chi-restraints excluded: chain O residue 12 THR Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 60 GLU Chi-restraints excluded: chain O residue 91 SER Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 36 LYS Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 103 VAL Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 43 ASN Chi-restraints excluded: chain R residue 84 ARG Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 70 LYS Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain V residue 9 ARG Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain V residue 58 SER Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain V residue 73 LYS Chi-restraints excluded: chain V residue 79 ARG Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain W residue 74 LYS Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain W residue 79 GLU Chi-restraints excluded: chain X residue 1 SER Chi-restraints excluded: chain X residue 41 SER Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Z residue 8 GLN Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 48 ASN Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 1 residue 4 ILE Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 8 SER Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 57 VAL Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain 4 residue 37 GLN Chi-restraints excluded: chain 6 residue 28 VAL Chi-restraints excluded: chain 6 residue 33 ASN Chi-restraints excluded: chain 6 residue 34 LEU Chi-restraints excluded: chain 6 residue 36 VAL Chi-restraints excluded: chain 6 residue 43 PHE Chi-restraints excluded: chain 6 residue 57 VAL Chi-restraints excluded: chain 6 residue 59 ARG Chi-restraints excluded: chain 6 residue 61 ASN Chi-restraints excluded: chain v residue 9 LEU Chi-restraints excluded: chain v residue 53 VAL Chi-restraints excluded: chain y residue 13 LEU Chi-restraints excluded: chain y residue 24 VAL Chi-restraints excluded: chain y residue 35 VAL Chi-restraints excluded: chain y residue 36 VAL Chi-restraints excluded: chain y residue 57 GLN Chi-restraints excluded: chain y residue 82 THR Chi-restraints excluded: chain y residue 272 LYS Chi-restraints excluded: chain y residue 278 THR Chi-restraints excluded: chain y residue 280 LEU Chi-restraints excluded: chain y residue 281 THR Chi-restraints excluded: chain y residue 294 VAL Chi-restraints excluded: chain y residue 296 ILE Chi-restraints excluded: chain y residue 312 THR Chi-restraints excluded: chain y residue 342 ILE Chi-restraints excluded: chain y residue 344 LEU Chi-restraints excluded: chain y residue 346 LEU Chi-restraints excluded: chain x residue 27 LEU Chi-restraints excluded: chain x residue 29 GLN Chi-restraints excluded: chain x residue 33 ARG Chi-restraints excluded: chain x residue 38 TYR Chi-restraints excluded: chain x residue 44 GLU Chi-restraints excluded: chain x residue 54 LEU Chi-restraints excluded: chain x residue 77 LEU Chi-restraints excluded: chain x residue 84 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 343 optimal weight: 0.6980 chunk 920 optimal weight: 3.9990 chunk 201 optimal weight: 0.9990 chunk 599 optimal weight: 40.0000 chunk 252 optimal weight: 7.9990 chunk 1022 optimal weight: 20.0000 chunk 848 optimal weight: 6.9990 chunk 473 optimal weight: 8.9990 chunk 85 optimal weight: 9.9990 chunk 338 optimal weight: 0.8980 chunk 536 optimal weight: 20.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 41 ASN b 167 HIS c 138 GLN c 139 ASN e 42 ASN e 60 GLN ** e 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 96 GLN ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 GLN g 85 GLN g 141 HIS h 17 GLN i 4 GLN i 30 ASN i 109 GLN i 125 GLN l 111 GLN n 3 GLN n 43 ASN n 60 GLN n 66 GLN o 39 GLN p 63 GLN ** q 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 47 GLN C 238 ASN D 130 GLN D 136 ASN E 195 GLN F 134 GLN G 44 HIS ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 ASN J 80 HIS K 29 HIS L 4 ASN M 22 GLN N 9 GLN N 23 ASN O 38 GLN P 2 ASN Q 19 GLN ** Q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 61 ASN T 48 GLN U 65 GLN ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 32 GLN ** v 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 159850 Z= 0.218 Angle : 0.593 15.071 238824 Z= 0.308 Chirality : 0.035 0.372 30498 Planarity : 0.005 0.087 13064 Dihedral : 23.257 179.966 79176 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.26 % Favored : 90.60 % Rotamer: Outliers : 7.45 % Allowed : 31.13 % Favored : 61.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.02 % Twisted Proline : 1.03 % 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: -1.55 (0.11), residues: 6082 helix: 0.55 (0.12), residues: 1885 sheet: -1.08 (0.15), residues: 1105 loop : -2.08 (0.10), residues: 3092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP y 311 HIS 0.010 0.001 HIS b 17 PHE 0.023 0.002 PHE u 36 TYR 0.022 0.002 TYR O 36 ARG 0.012 0.001 ARG u 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2258 residues out of total 5071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 364 poor density : 1894 time to evaluate : 6.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 8 MET cc_start: 0.6402 (pmm) cc_final: 0.5701 (ppp) REVERT: b 29 PHE cc_start: 0.8521 (OUTLIER) cc_final: 0.8061 (m-80) REVERT: b 51 GLU cc_start: 0.7924 (tp30) cc_final: 0.7670 (tp30) REVERT: b 62 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.8146 (mpp80) REVERT: b 168 GLU cc_start: 0.8385 (mp0) cc_final: 0.7837 (mp0) REVERT: b 174 GLU cc_start: 0.8047 (tp30) cc_final: 0.7564 (mt-10) REVERT: b 183 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.7318 (p90) REVERT: b 191 ASP cc_start: 0.7837 (t0) cc_final: 0.7450 (t0) REVERT: c 31 ASN cc_start: 0.8685 (m-40) cc_final: 0.8241 (t0) REVERT: c 35 ASP cc_start: 0.8878 (m-30) cc_final: 0.8573 (m-30) REVERT: c 44 LYS cc_start: 0.9004 (tmmt) cc_final: 0.8686 (tppp) REVERT: c 84 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8582 (mm-30) REVERT: c 129 PHE cc_start: 0.9053 (p90) cc_final: 0.8731 (p90) REVERT: c 161 ILE cc_start: 0.9280 (OUTLIER) cc_final: 0.9003 (pp) REVERT: c 187 GLU cc_start: 0.6875 (mm-30) cc_final: 0.6546 (mm-30) REVERT: d 58 GLN cc_start: 0.8783 (mm-40) cc_final: 0.8357 (mm-40) REVERT: d 68 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7565 (tp30) REVERT: d 137 SER cc_start: 0.8973 (OUTLIER) cc_final: 0.8553 (p) REVERT: d 151 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.7950 (pp30) REVERT: e 11 GLN cc_start: 0.8568 (tt0) cc_final: 0.8324 (tp40) REVERT: e 13 LYS cc_start: 0.8725 (ttmm) cc_final: 0.8443 (ttmm) REVERT: e 19 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8266 (ttm-80) REVERT: e 64 GLU cc_start: 0.8262 (tp30) cc_final: 0.7857 (tp30) REVERT: e 69 ASN cc_start: 0.8756 (t0) cc_final: 0.8263 (t0) REVERT: e 77 ASN cc_start: 0.8790 (m-40) cc_final: 0.8238 (p0) REVERT: f 10 VAL cc_start: 0.9543 (OUTLIER) cc_final: 0.9330 (m) REVERT: f 13 ASP cc_start: 0.8628 (OUTLIER) cc_final: 0.8379 (p0) REVERT: f 30 THR cc_start: 0.9649 (m) cc_final: 0.9248 (p) REVERT: g 78 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7731 (ppp80) REVERT: g 79 VAL cc_start: 0.8813 (OUTLIER) cc_final: 0.8596 (p) REVERT: g 100 MET cc_start: 0.8709 (mtm) cc_final: 0.8374 (mtp) REVERT: g 114 SER cc_start: 0.9049 (OUTLIER) cc_final: 0.8830 (p) REVERT: h 57 GLU cc_start: 0.7618 (mp0) cc_final: 0.7348 (mp0) REVERT: i 60 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8768 (pp) REVERT: i 90 ASP cc_start: 0.8059 (t70) cc_final: 0.7734 (t70) REVERT: j 14 ASP cc_start: 0.7888 (t0) cc_final: 0.7645 (t0) REVERT: j 45 ARG cc_start: 0.7734 (mmt180) cc_final: 0.6974 (ttm170) REVERT: k 12 ARG cc_start: 0.4220 (OUTLIER) cc_final: 0.3642 (mpp-170) REVERT: k 68 ARG cc_start: 0.8350 (mtp-110) cc_final: 0.8095 (mtp-110) REVERT: l 8 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8376 (mtp85) REVERT: l 85 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8115 (ppp80) REVERT: l 93 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.7831 (mtp180) REVERT: m 88 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9126 (mt) REVERT: n 5 MET cc_start: 0.8342 (mtp) cc_final: 0.7908 (mmm) REVERT: n 43 ASN cc_start: 0.9068 (m-40) cc_final: 0.8841 (m110) REVERT: n 60 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.8307 (mp-120) REVERT: n 62 ASN cc_start: 0.8757 (t0) cc_final: 0.8137 (t0) REVERT: o 9 LYS cc_start: 0.9112 (tmtm) cc_final: 0.8843 (tptp) REVERT: o 17 ASP cc_start: 0.9106 (p0) cc_final: 0.8806 (p0) REVERT: o 70 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8911 (ttpp) REVERT: o 71 ARG cc_start: 0.8564 (ttp80) cc_final: 0.8314 (ttm170) REVERT: o 82 GLU cc_start: 0.8414 (tp30) cc_final: 0.8099 (tp30) REVERT: p 53 ASP cc_start: 0.8012 (t0) cc_final: 0.7762 (t0) REVERT: q 10 ARG cc_start: 0.8006 (mtp-110) cc_final: 0.7644 (ttm110) REVERT: q 47 ASP cc_start: 0.8396 (p0) cc_final: 0.8075 (p0) REVERT: q 64 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8464 (ptm-80) REVERT: q 68 LYS cc_start: 0.9037 (ttpp) cc_final: 0.8776 (ttmt) REVERT: q 80 LYS cc_start: 0.8509 (ttmt) cc_final: 0.8262 (tptt) REVERT: r 47 ARG cc_start: 0.7563 (mmt-90) cc_final: 0.7184 (mtt-85) REVERT: s 17 LYS cc_start: 0.9049 (ttmm) cc_final: 0.8840 (mtpm) REVERT: s 54 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7609 (ptt90) REVERT: s 55 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.6652 (mp10) REVERT: t 14 GLU cc_start: 0.8499 (tp30) cc_final: 0.8250 (mm-30) REVERT: t 25 SER cc_start: 0.9077 (t) cc_final: 0.8819 (m) REVERT: t 56 ILE cc_start: 0.9445 (mp) cc_final: 0.9226 (mp) REVERT: u 19 LYS cc_start: 0.6827 (pttm) cc_final: 0.6585 (tppt) REVERT: C 20 ASN cc_start: 0.8286 (t0) cc_final: 0.8011 (t0) REVERT: C 65 ASP cc_start: 0.8505 (t0) cc_final: 0.8121 (t0) REVERT: C 110 LYS cc_start: 0.8274 (mmmt) cc_final: 0.8024 (mtmm) REVERT: C 116 GLN cc_start: 0.8840 (pt0) cc_final: 0.8399 (pt0) REVERT: D 7 LYS cc_start: 0.8508 (ttmt) cc_final: 0.8228 (ttpp) REVERT: D 97 SER cc_start: 0.9179 (t) cc_final: 0.8842 (p) REVERT: D 99 GLU cc_start: 0.7899 (pp20) cc_final: 0.7686 (pp20) REVERT: D 130 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8417 (mt0) REVERT: E 136 GLN cc_start: 0.8580 (tp40) cc_final: 0.7756 (tp40) REVERT: E 140 ASP cc_start: 0.7972 (m-30) cc_final: 0.7449 (m-30) REVERT: E 168 ASP cc_start: 0.7963 (t0) cc_final: 0.7687 (t0) REVERT: E 181 ILE cc_start: 0.9335 (mm) cc_final: 0.9077 (mm) REVERT: F 51 ASN cc_start: 0.8787 (m110) cc_final: 0.8304 (m-40) REVERT: F 117 SER cc_start: 0.8417 (t) cc_final: 0.8153 (p) REVERT: G 17 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8096 (mtmm) REVERT: G 26 LYS cc_start: 0.8949 (ttmt) cc_final: 0.8691 (mtpp) REVERT: G 43 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8287 (mmmt) REVERT: G 100 ASN cc_start: 0.8769 (p0) cc_final: 0.8259 (p0) REVERT: G 148 ARG cc_start: 0.8819 (ttt-90) cc_final: 0.8590 (ttt-90) REVERT: G 156 TYR cc_start: 0.8838 (m-80) cc_final: 0.8508 (m-80) REVERT: J 2 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8066 (mmtp) REVERT: J 14 ASP cc_start: 0.7863 (m-30) cc_final: 0.7543 (m-30) REVERT: J 16 TYR cc_start: 0.9250 (m-80) cc_final: 0.8967 (m-80) REVERT: J 52 ASP cc_start: 0.8538 (m-30) cc_final: 0.8250 (m-30) REVERT: J 96 ARG cc_start: 0.7824 (ttt-90) cc_final: 0.7514 (ttp80) REVERT: J 99 ARG cc_start: 0.8379 (mtp85) cc_final: 0.8174 (mtp85) REVERT: K 108 ARG cc_start: 0.8145 (ttm-80) cc_final: 0.7889 (tpp80) REVERT: L 5 THR cc_start: 0.9318 (m) cc_final: 0.9085 (p) REVERT: L 27 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8934 (pp) REVERT: L 106 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7321 (tm-30) REVERT: M 40 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8117 (mtm180) REVERT: N 72 ASP cc_start: 0.8220 (t0) cc_final: 0.7778 (t0) REVERT: N 75 ILE cc_start: 0.9317 (mm) cc_final: 0.8913 (mp) REVERT: N 82 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7738 (mt-10) REVERT: N 107 ASN cc_start: 0.9055 (t0) cc_final: 0.8687 (t0) REVERT: N 114 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7814 (pp20) REVERT: O 17 LYS cc_start: 0.9359 (tppt) cc_final: 0.9100 (tppt) REVERT: O 19 GLN cc_start: 0.9275 (tm-30) cc_final: 0.8854 (tm-30) REVERT: O 87 ILE cc_start: 0.8961 (mp) cc_final: 0.8651 (pp) REVERT: O 104 GLN cc_start: 0.9012 (tt0) cc_final: 0.8799 (tt0) REVERT: P 9 GLN cc_start: 0.8591 (mt0) cc_final: 0.8174 (tm-30) REVERT: P 86 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8520 (mmpt) REVERT: Q 10 ARG cc_start: 0.8089 (ttm-80) cc_final: 0.7883 (ttm-80) REVERT: Q 48 ASP cc_start: 0.7854 (m-30) cc_final: 0.7548 (m-30) REVERT: Q 70 GLN cc_start: 0.8775 (tp40) cc_final: 0.8197 (tp40) REVERT: Q 96 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.8273 (t0) REVERT: Q 109 VAL cc_start: 0.9439 (t) cc_final: 0.9174 (t) REVERT: Q 110 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7851 (tm-30) REVERT: R 13 ARG cc_start: 0.8757 (ttp80) cc_final: 0.8534 (ttp80) REVERT: R 21 ARG cc_start: 0.8962 (ttm170) cc_final: 0.8425 (ttm-80) REVERT: R 31 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7886 (mt-10) REVERT: R 46 GLU cc_start: 0.7324 (tm-30) cc_final: 0.7047 (tm-30) REVERT: S 1 MET cc_start: 0.7003 (tpp) cc_final: 0.6792 (tpp) REVERT: S 70 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8310 (ttpt) REVERT: T 12 ARG cc_start: 0.8689 (mmp80) cc_final: 0.8468 (mmp80) REVERT: T 28 ASN cc_start: 0.8740 (t0) cc_final: 0.8129 (t0) REVERT: U 5 ARG cc_start: 0.8630 (ptp-170) cc_final: 0.8277 (ptp-170) REVERT: U 98 ASN cc_start: 0.7576 (p0) cc_final: 0.7200 (p0) REVERT: V 9 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.8709 (mmm-85) REVERT: V 42 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8660 (pp) REVERT: V 90 ASP cc_start: 0.8416 (m-30) cc_final: 0.8137 (m-30) REVERT: Y 30 MET cc_start: 0.7116 (pp-130) cc_final: 0.6865 (pp-130) REVERT: Y 36 GLN cc_start: 0.7856 (mp10) cc_final: 0.7566 (mp10) REVERT: Y 39 GLN cc_start: 0.8171 (mm-40) cc_final: 0.7913 (mm-40) REVERT: Y 60 LYS cc_start: 0.8700 (ttpt) cc_final: 0.8460 (pttt) REVERT: Z 5 LYS cc_start: 0.9105 (mtpp) cc_final: 0.8740 (mmmm) REVERT: Z 8 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.7862 (tt0) REVERT: Z 31 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8821 (mt) REVERT: 0 11 LYS cc_start: 0.8728 (tptm) cc_final: 0.8388 (tppt) REVERT: 0 36 LYS cc_start: 0.8957 (mmtp) cc_final: 0.8600 (mmmm) REVERT: 1 9 LYS cc_start: 0.8734 (ttmt) cc_final: 0.7991 (ttmm) REVERT: 4 9 LYS cc_start: 0.8755 (mtmp) cc_final: 0.8496 (mtpp) REVERT: 4 22 VAL cc_start: 0.8907 (OUTLIER) cc_final: 0.8610 (m) REVERT: 6 56 ARG cc_start: 0.7614 (mmm160) cc_final: 0.6878 (mmm-85) REVERT: 6 59 ARG cc_start: 0.7889 (ttp-170) cc_final: 0.7418 (ttp-170) REVERT: y 57 GLN cc_start: 0.5525 (OUTLIER) cc_final: 0.5313 (pm20) outliers start: 364 outliers final: 218 residues processed: 2037 average time/residue: 2.0370 time to fit residues: 6097.3221 Evaluate side-chains 2097 residues out of total 5071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 1839 time to evaluate : 6.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 15 PHE Chi-restraints excluded: chain b residue 17 HIS Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 29 PHE Chi-restraints excluded: chain b residue 62 ARG Chi-restraints excluded: chain b residue 109 SER Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 128 LEU Chi-restraints excluded: chain b residue 158 ASP Chi-restraints excluded: chain b residue 182 VAL Chi-restraints excluded: chain b residue 183 PHE Chi-restraints excluded: chain b residue 198 VAL Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 161 ILE Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 63 ILE Chi-restraints excluded: chain d residue 67 LEU Chi-restraints excluded: chain d residue 68 GLU Chi-restraints excluded: chain d residue 133 SER Chi-restraints excluded: chain d residue 137 SER Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 142 VAL Chi-restraints excluded: chain d residue 151 GLN Chi-restraints excluded: chain e residue 10 LEU Chi-restraints excluded: chain e residue 19 ARG Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 104 ILE Chi-restraints excluded: chain e residue 113 VAL Chi-restraints excluded: chain e residue 115 GLU Chi-restraints excluded: chain e residue 133 ILE Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 13 ASP Chi-restraints excluded: chain f residue 51 ILE Chi-restraints excluded: chain g residue 14 ASP Chi-restraints excluded: chain g residue 29 LEU Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 37 THR Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 78 ARG Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 114 SER Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 88 LYS Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 104 SER Chi-restraints excluded: chain h residue 125 ILE Chi-restraints excluded: chain i residue 31 GLN Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain i residue 86 LEU Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 11 LYS Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 50 THR Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain k residue 12 ARG Chi-restraints excluded: chain k residue 19 VAL Chi-restraints excluded: chain k residue 25 SER Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 57 SER Chi-restraints excluded: chain k residue 80 ASN Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain k residue 126 ARG Chi-restraints excluded: chain l residue 8 ARG Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 46 SER Chi-restraints excluded: chain l residue 85 ARG Chi-restraints excluded: chain l residue 93 ARG Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 27 THR Chi-restraints excluded: chain m residue 55 LEU Chi-restraints excluded: chain m residue 57 ASP Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 67 ASP Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain m residue 107 THR Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 60 GLN Chi-restraints excluded: chain n residue 67 THR Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain n residue 86 GLU Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 70 LYS Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 79 ASN Chi-restraints excluded: chain q residue 14 ASP Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain q residue 64 ARG Chi-restraints excluded: chain r residue 70 THR Chi-restraints excluded: chain s residue 12 LEU Chi-restraints excluded: chain s residue 18 VAL Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain s residue 54 ARG Chi-restraints excluded: chain s residue 55 GLN Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 5 SER Chi-restraints excluded: chain t residue 22 SER Chi-restraints excluded: chain t residue 85 LEU Chi-restraints excluded: chain u residue 13 VAL Chi-restraints excluded: chain u residue 16 ARG Chi-restraints excluded: chain u residue 31 VAL Chi-restraints excluded: chain u residue 50 SER Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 126 ASN Chi-restraints excluded: chain F residue 134 GLN Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 17 LYS Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain J residue 2 LYS Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 91 SER Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 115 GLU Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 40 ARG Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 3 LYS Chi-restraints excluded: chain O residue 12 THR Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 60 GLU Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 36 LYS Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 96 ASP Chi-restraints excluded: chain Q residue 103 VAL Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 43 ASN Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 70 LYS Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain V residue 9 ARG Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain V residue 58 SER Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain X residue 1 SER Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Z residue 8 GLN Chi-restraints excluded: chain Z residue 26 LEU Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 48 ASN Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 45 ASP Chi-restraints excluded: chain 1 residue 4 ILE Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 8 SER Chi-restraints excluded: chain 2 residue 22 MET Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 57 VAL Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain 4 residue 37 GLN Chi-restraints excluded: chain 6 residue 28 VAL Chi-restraints excluded: chain 6 residue 34 LEU Chi-restraints excluded: chain 6 residue 43 PHE Chi-restraints excluded: chain v residue 9 LEU Chi-restraints excluded: chain v residue 53 VAL Chi-restraints excluded: chain y residue 13 LEU Chi-restraints excluded: chain y residue 24 VAL Chi-restraints excluded: chain y residue 35 VAL Chi-restraints excluded: chain y residue 36 VAL Chi-restraints excluded: chain y residue 57 GLN Chi-restraints excluded: chain y residue 272 LYS Chi-restraints excluded: chain y residue 281 THR Chi-restraints excluded: chain y residue 294 VAL Chi-restraints excluded: chain y residue 342 ILE Chi-restraints excluded: chain y residue 343 SER Chi-restraints excluded: chain y residue 344 LEU Chi-restraints excluded: chain y residue 346 LEU Chi-restraints excluded: chain x residue 27 LEU Chi-restraints excluded: chain x residue 29 GLN Chi-restraints excluded: chain x residue 44 GLU Chi-restraints excluded: chain x residue 84 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 986 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 582 optimal weight: 8.9990 chunk 746 optimal weight: 0.3980 chunk 578 optimal weight: 10.0000 chunk 860 optimal weight: 10.0000 chunk 571 optimal weight: 10.0000 chunk 1018 optimal weight: 7.9990 chunk 637 optimal weight: 7.9990 chunk 621 optimal weight: 10.0000 chunk 470 optimal weight: 10.0000 overall best weight: 7.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 7 ASN c 138 GLN c 139 ASN d 70 GLN ** e 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 96 GLN ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 GLN g 85 GLN g 141 HIS h 17 GLN i 4 GLN i 30 ASN i 109 GLN i 125 GLN j 64 GLN l 111 GLN n 3 GLN n 60 GLN n 66 GLN p 63 GLN ** q 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 51 HIS s 56 HIS t 19 HIS ** t 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN D 130 GLN D 136 ASN E 195 GLN ** F 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 GLN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 ASN J 80 HIS K 29 HIS N 9 GLN N 18 GLN N 23 ASN O 38 GLN P 2 ASN ** P 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 51 ASN Q 19 GLN ** Q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 61 ASN T 48 GLN U 65 GLN ** X 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 32 GLN ** v 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.095 159850 Z= 0.490 Angle : 0.703 19.271 238824 Z= 0.360 Chirality : 0.042 0.421 30498 Planarity : 0.006 0.098 13064 Dihedral : 23.211 179.889 79176 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.28 % Favored : 89.56 % Rotamer: Outliers : 8.52 % Allowed : 31.46 % Favored : 60.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.02 % Twisted Proline : 1.03 % Twisted General : 0.19 % 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: -1.63 (0.10), residues: 6082 helix: 0.46 (0.12), residues: 1895 sheet: -1.10 (0.15), residues: 1122 loop : -2.13 (0.10), residues: 3065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP y 311 HIS 0.013 0.002 HIS t 67 PHE 0.025 0.002 PHE H 91 TYR 0.031 0.003 TYR 1 48 ARG 0.013 0.001 ARG j 31 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2238 residues out of total 5071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 416 poor density : 1822 time to evaluate : 6.470 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: b 20 ARG cc_start: 0.7254 (OUTLIER) cc_final: 0.5917 (ptt180) REVERT: b 29 PHE cc_start: 0.8706 (OUTLIER) cc_final: 0.8185 (m-80) REVERT: b 51 GLU cc_start: 0.7926 (tp30) cc_final: 0.6887 (tp30) REVERT: b 55 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7308 (mp0) REVERT: b 57 ASN cc_start: 0.9182 (t0) cc_final: 0.8832 (t0) REVERT: b 168 GLU cc_start: 0.8410 (mp0) cc_final: 0.7920 (mp0) REVERT: b 174 GLU cc_start: 0.8085 (tp30) cc_final: 0.7690 (mt-10) REVERT: b 183 PHE cc_start: 0.8468 (OUTLIER) cc_final: 0.7639 (p90) REVERT: b 191 ASP cc_start: 0.8044 (t0) cc_final: 0.7800 (t0) REVERT: c 31 ASN cc_start: 0.8773 (m-40) cc_final: 0.8283 (t0) REVERT: c 35 ASP cc_start: 0.8929 (m-30) cc_final: 0.8662 (m-30) REVERT: c 44 LYS cc_start: 0.9029 (tmmt) cc_final: 0.8720 (tppp) REVERT: c 129 PHE cc_start: 0.9099 (p90) cc_final: 0.8798 (p90) REVERT: c 161 ILE cc_start: 0.9315 (OUTLIER) cc_final: 0.9022 (pp) REVERT: c 187 GLU cc_start: 0.6934 (mm-30) cc_final: 0.6717 (mm-30) REVERT: d 58 GLN cc_start: 0.8883 (mm-40) cc_final: 0.8475 (mm-40) REVERT: d 68 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7622 (tp30) REVERT: d 137 SER cc_start: 0.8917 (OUTLIER) cc_final: 0.8513 (p) REVERT: d 151 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8152 (pp30) REVERT: d 177 MET cc_start: 0.8625 (mpp) cc_final: 0.8362 (mtm) REVERT: e 11 GLN cc_start: 0.8512 (tt0) cc_final: 0.8243 (tp40) REVERT: e 13 LYS cc_start: 0.8762 (ttmm) cc_final: 0.8502 (ttmm) REVERT: e 19 ARG cc_start: 0.8981 (OUTLIER) cc_final: 0.8302 (ttm-80) REVERT: e 64 GLU cc_start: 0.8364 (tp30) cc_final: 0.8006 (tp30) REVERT: e 69 ASN cc_start: 0.8857 (t0) cc_final: 0.8311 (t0) REVERT: e 77 ASN cc_start: 0.8778 (m-40) cc_final: 0.8259 (p0) REVERT: e 92 ARG cc_start: 0.8485 (mpp80) cc_final: 0.8150 (mpp80) REVERT: f 10 VAL cc_start: 0.9535 (OUTLIER) cc_final: 0.9327 (m) REVERT: f 13 ASP cc_start: 0.8744 (OUTLIER) cc_final: 0.8532 (p0) REVERT: f 30 THR cc_start: 0.9585 (m) cc_final: 0.9205 (p) REVERT: g 30 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.7992 (ttm) REVERT: g 78 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7601 (ppp80) REVERT: g 100 MET cc_start: 0.8756 (mtm) cc_final: 0.8466 (mtp) REVERT: h 57 GLU cc_start: 0.7745 (mp0) cc_final: 0.7523 (mp0) REVERT: i 60 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8807 (pp) REVERT: i 90 ASP cc_start: 0.8279 (t70) cc_final: 0.7965 (t70) REVERT: j 30 LYS cc_start: 0.9311 (mtpp) cc_final: 0.9050 (tmmt) REVERT: j 45 ARG cc_start: 0.7796 (mmt180) cc_final: 0.7023 (ttm170) REVERT: k 12 ARG cc_start: 0.4832 (OUTLIER) cc_final: 0.4213 (mpp-170) REVERT: k 69 CYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8471 (t) REVERT: l 8 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8326 (mtp85) REVERT: l 85 ARG cc_start: 0.8691 (OUTLIER) cc_final: 0.8133 (ppp80) REVERT: l 93 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.7969 (mtp180) REVERT: m 88 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9187 (mt) REVERT: n 5 MET cc_start: 0.8429 (mtp) cc_final: 0.8016 (mmm) REVERT: n 62 ASN cc_start: 0.8817 (t0) cc_final: 0.8211 (t0) REVERT: o 17 ASP cc_start: 0.9110 (p0) cc_final: 0.8802 (p0) REVERT: o 70 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8924 (ttpp) REVERT: o 82 GLU cc_start: 0.8481 (tp30) cc_final: 0.8109 (tp30) REVERT: p 53 ASP cc_start: 0.8137 (t0) cc_final: 0.7903 (t0) REVERT: q 47 ASP cc_start: 0.8448 (p0) cc_final: 0.8204 (p0) REVERT: q 64 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.8465 (ptm-80) REVERT: r 47 ARG cc_start: 0.7620 (mmt-90) cc_final: 0.7255 (mtt-85) REVERT: s 5 LYS cc_start: 0.4999 (pttt) cc_final: 0.4741 (pttt) REVERT: s 17 LYS cc_start: 0.9087 (ttmm) cc_final: 0.8870 (mtpm) REVERT: s 24 SER cc_start: 0.9132 (t) cc_final: 0.8913 (t) REVERT: s 54 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7872 (ptt90) REVERT: s 55 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.6944 (mp10) REVERT: t 25 SER cc_start: 0.9160 (t) cc_final: 0.8918 (m) REVERT: u 19 LYS cc_start: 0.6941 (pttm) cc_final: 0.6645 (tppt) REVERT: C 20 ASN cc_start: 0.8266 (t0) cc_final: 0.7996 (t0) REVERT: C 65 ASP cc_start: 0.8628 (t0) cc_final: 0.8301 (t0) REVERT: C 110 LYS cc_start: 0.8265 (mmmt) cc_final: 0.7967 (mtmm) REVERT: C 116 GLN cc_start: 0.8912 (pt0) cc_final: 0.8468 (pt0) REVERT: C 176 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.8239 (tpt-90) REVERT: D 7 LYS cc_start: 0.8581 (ttmt) cc_final: 0.8278 (ttpp) REVERT: D 97 SER cc_start: 0.9209 (t) cc_final: 0.8870 (p) REVERT: D 99 GLU cc_start: 0.7992 (pp20) cc_final: 0.7790 (pp20) REVERT: D 130 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.8444 (mt0) REVERT: E 136 GLN cc_start: 0.8645 (tp40) cc_final: 0.7911 (tp40) REVERT: E 140 ASP cc_start: 0.8125 (m-30) cc_final: 0.7674 (m-30) REVERT: E 168 ASP cc_start: 0.7959 (t0) cc_final: 0.7684 (t0) REVERT: E 181 ILE cc_start: 0.9352 (mm) cc_final: 0.9121 (mm) REVERT: F 51 ASN cc_start: 0.8637 (m110) cc_final: 0.8430 (m110) REVERT: F 82 TYR cc_start: 0.7933 (t80) cc_final: 0.7549 (t80) REVERT: F 117 SER cc_start: 0.8456 (t) cc_final: 0.8196 (p) REVERT: F 128 SER cc_start: 0.9090 (t) cc_final: 0.8815 (t) REVERT: G 17 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8174 (mtmm) REVERT: G 26 LYS cc_start: 0.8970 (ttmt) cc_final: 0.8762 (mtpp) REVERT: G 43 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8236 (mmmt) REVERT: G 100 ASN cc_start: 0.8866 (p0) cc_final: 0.8383 (p0) REVERT: G 137 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8100 (tppp) REVERT: G 148 ARG cc_start: 0.8888 (ttt-90) cc_final: 0.8624 (ttt-90) REVERT: G 156 TYR cc_start: 0.8897 (m-80) cc_final: 0.8547 (m-80) REVERT: J 2 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8152 (mmtp) REVERT: J 14 ASP cc_start: 0.7943 (m-30) cc_final: 0.7620 (m-30) REVERT: J 16 TYR cc_start: 0.9290 (m-80) cc_final: 0.9013 (m-80) REVERT: J 52 ASP cc_start: 0.8591 (m-30) cc_final: 0.8303 (m-30) REVERT: J 102 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7885 (mt-10) REVERT: K 108 ARG cc_start: 0.8299 (ttm-80) cc_final: 0.7973 (mtp-110) REVERT: L 5 THR cc_start: 0.9332 (m) cc_final: 0.9088 (p) REVERT: L 27 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8923 (pp) REVERT: L 58 TYR cc_start: 0.8626 (p90) cc_final: 0.8205 (p90) REVERT: L 106 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7344 (tm-30) REVERT: M 40 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8212 (mtm180) REVERT: N 72 ASP cc_start: 0.8335 (t0) cc_final: 0.7834 (t0) REVERT: N 75 ILE cc_start: 0.9315 (OUTLIER) cc_final: 0.8944 (mp) REVERT: N 82 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7715 (mt-10) REVERT: N 107 ASN cc_start: 0.9149 (t0) cc_final: 0.8688 (t0) REVERT: O 19 GLN cc_start: 0.9302 (tm-30) cc_final: 0.8902 (tm-30) REVERT: O 87 ILE cc_start: 0.8995 (mp) cc_final: 0.8770 (pp) REVERT: O 104 GLN cc_start: 0.9039 (tt0) cc_final: 0.8800 (tt0) REVERT: P 9 GLN cc_start: 0.8618 (mt0) cc_final: 0.8240 (tm-30) REVERT: P 86 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8435 (mmpt) REVERT: Q 10 ARG cc_start: 0.8110 (ttm-80) cc_final: 0.7878 (ttm-80) REVERT: Q 70 GLN cc_start: 0.8787 (tp40) cc_final: 0.8119 (tp40) REVERT: Q 96 ASP cc_start: 0.8578 (OUTLIER) cc_final: 0.8287 (t0) REVERT: Q 109 VAL cc_start: 0.9477 (t) cc_final: 0.9215 (t) REVERT: Q 110 GLU cc_start: 0.8326 (mm-30) cc_final: 0.7925 (tm-30) REVERT: R 21 ARG cc_start: 0.9002 (ttm170) cc_final: 0.8483 (ttm-80) REVERT: S 1 MET cc_start: 0.7045 (tpp) cc_final: 0.6829 (tpp) REVERT: S 3 THR cc_start: 0.9383 (m) cc_final: 0.8808 (p) REVERT: S 70 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8368 (ttpt) REVERT: S 82 MET cc_start: 0.8314 (ptp) cc_final: 0.7959 (ptm) REVERT: T 1 MET cc_start: 0.3190 (ptp) cc_final: 0.2611 (ptm) REVERT: T 28 ASN cc_start: 0.8785 (t0) cc_final: 0.8157 (t0) REVERT: U 5 ARG cc_start: 0.8611 (ptp-170) cc_final: 0.8110 (ptp-170) REVERT: U 98 ASN cc_start: 0.7703 (p0) cc_final: 0.7348 (p0) REVERT: V 9 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.8805 (mmm-85) REVERT: V 42 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8636 (pp) REVERT: V 79 ARG cc_start: 0.9241 (OUTLIER) cc_final: 0.8225 (mmm-85) REVERT: V 90 ASP cc_start: 0.8496 (m-30) cc_final: 0.8227 (m-30) REVERT: W 25 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7799 (tp30) REVERT: X 10 ARG cc_start: 0.8652 (mtp85) cc_final: 0.8376 (mtp85) REVERT: Y 5 GLU cc_start: 0.7827 (mp0) cc_final: 0.7597 (mp0) REVERT: Y 28 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9239 (mp) REVERT: Y 30 MET cc_start: 0.7168 (pp-130) cc_final: 0.6939 (pp-130) REVERT: Y 36 GLN cc_start: 0.7928 (mp10) cc_final: 0.7666 (mp10) REVERT: Y 39 GLN cc_start: 0.8193 (mm-40) cc_final: 0.7928 (mm-40) REVERT: Z 5 LYS cc_start: 0.9112 (mtpp) cc_final: 0.8732 (mmmm) REVERT: Z 8 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8162 (tt0) REVERT: 0 11 LYS cc_start: 0.8783 (tptm) cc_final: 0.8439 (tppt) REVERT: 4 9 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8537 (mtmt) REVERT: 4 18 LYS cc_start: 0.8870 (ttpt) cc_final: 0.8661 (tppt) REVERT: 4 22 VAL cc_start: 0.8883 (OUTLIER) cc_final: 0.8655 (m) REVERT: v 54 MET cc_start: 0.6657 (ppp) cc_final: 0.6432 (ptt) REVERT: y 39 ASP cc_start: 0.7616 (t0) cc_final: 0.7405 (t0) REVERT: y 57 GLN cc_start: 0.5635 (OUTLIER) cc_final: 0.5358 (pm20) outliers start: 416 outliers final: 267 residues processed: 1990 average time/residue: 2.0880 time to fit residues: 6072.1008 Evaluate side-chains 2096 residues out of total 5071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 313 poor density : 1783 time to evaluate : 6.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 15 PHE Chi-restraints excluded: chain b residue 17 HIS Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain b residue 20 ARG Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 29 PHE Chi-restraints excluded: chain b residue 55 GLU Chi-restraints excluded: chain b residue 62 ARG Chi-restraints excluded: chain b residue 109 SER Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 128 LEU Chi-restraints excluded: chain b residue 152 ASP Chi-restraints excluded: chain b residue 158 ASP Chi-restraints excluded: chain b residue 178 LEU Chi-restraints excluded: chain b residue 182 VAL Chi-restraints excluded: chain b residue 183 PHE Chi-restraints excluded: chain b residue 193 ASP Chi-restraints excluded: chain b residue 198 VAL Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 118 SER Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 121 SER Chi-restraints excluded: chain c residue 143 LEU Chi-restraints excluded: chain c residue 161 ILE Chi-restraints excluded: chain c residue 182 ASP Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 67 LEU Chi-restraints excluded: chain d residue 68 GLU Chi-restraints excluded: chain d residue 133 SER Chi-restraints excluded: chain d residue 137 SER Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 142 VAL Chi-restraints excluded: chain d residue 151 GLN Chi-restraints excluded: chain d residue 188 SER Chi-restraints excluded: chain e residue 10 LEU Chi-restraints excluded: chain e residue 19 ARG Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 65 LYS Chi-restraints excluded: chain e residue 79 THR Chi-restraints excluded: chain e residue 104 ILE Chi-restraints excluded: chain e residue 113 VAL Chi-restraints excluded: chain e residue 115 GLU Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain e residue 146 MET Chi-restraints excluded: chain e residue 160 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 13 ASP Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain g residue 14 ASP Chi-restraints excluded: chain g residue 30 MET Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 37 THR Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 78 ARG Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 28 SER Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 88 LYS Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 104 SER Chi-restraints excluded: chain h residue 124 ILE Chi-restraints excluded: chain i residue 13 SER Chi-restraints excluded: chain i residue 31 GLN Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain i residue 67 LYS Chi-restraints excluded: chain i residue 86 LEU Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain k residue 12 ARG Chi-restraints excluded: chain k residue 19 VAL Chi-restraints excluded: chain k residue 25 SER Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 57 SER Chi-restraints excluded: chain k residue 69 CYS Chi-restraints excluded: chain k residue 80 ASN Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain k residue 126 ARG Chi-restraints excluded: chain l residue 2 THR Chi-restraints excluded: chain l residue 8 ARG Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 46 SER Chi-restraints excluded: chain l residue 56 LEU Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 85 ARG Chi-restraints excluded: chain l residue 93 ARG Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 19 THR Chi-restraints excluded: chain m residue 20 SER Chi-restraints excluded: chain m residue 27 THR Chi-restraints excluded: chain m residue 44 ILE Chi-restraints excluded: chain m residue 57 ASP Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 73 SER Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain m residue 103 THR Chi-restraints excluded: chain m residue 107 THR Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 32 ASP Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 67 THR Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain n residue 86 GLU Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 60 SER Chi-restraints excluded: chain o residue 70 LYS Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 79 ASN Chi-restraints excluded: chain q residue 14 ASP Chi-restraints excluded: chain q residue 19 SER Chi-restraints excluded: chain q residue 43 LEU Chi-restraints excluded: chain q residue 64 ARG Chi-restraints excluded: chain r residue 24 ASP Chi-restraints excluded: chain r residue 70 THR Chi-restraints excluded: chain s residue 12 LEU Chi-restraints excluded: chain s residue 18 VAL Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain s residue 54 ARG Chi-restraints excluded: chain s residue 55 GLN Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 5 SER Chi-restraints excluded: chain t residue 11 ILE Chi-restraints excluded: chain t residue 26 MET Chi-restraints excluded: chain t residue 85 LEU Chi-restraints excluded: chain u residue 13 VAL Chi-restraints excluded: chain u residue 16 ARG Chi-restraints excluded: chain u residue 31 VAL Chi-restraints excluded: chain u residue 41 THR Chi-restraints excluded: chain u residue 50 SER Chi-restraints excluded: chain u residue 52 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 176 ARG Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 126 ASN Chi-restraints excluded: chain F residue 134 GLN Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 17 LYS Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 137 LYS Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain J residue 2 LYS Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 91 SER Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 92 LEU Chi-restraints excluded: chain L residue 115 GLU Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 40 ARG Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain O residue 3 LYS Chi-restraints excluded: chain O residue 12 THR Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 60 GLU Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 36 LYS Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain P residue 111 GLU Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 96 ASP Chi-restraints excluded: chain Q residue 103 VAL Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 43 ASN Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 46 LEU Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 70 LYS Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain U residue 21 ARG Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain V residue 9 ARG Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain V residue 58 SER Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain V residue 73 LYS Chi-restraints excluded: chain V residue 79 ARG Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 25 GLU Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain X residue 1 SER Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 28 LEU Chi-restraints excluded: chain Z residue 8 GLN Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 48 ASN Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 8 SER Chi-restraints excluded: chain 2 residue 22 MET Chi-restraints excluded: chain 3 residue 57 VAL Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 4 residue 9 LYS Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain 6 residue 28 VAL Chi-restraints excluded: chain 6 residue 34 LEU Chi-restraints excluded: chain 6 residue 35 ASP Chi-restraints excluded: chain 6 residue 43 PHE Chi-restraints excluded: chain 6 residue 61 ASN Chi-restraints excluded: chain v residue 9 LEU Chi-restraints excluded: chain v residue 53 VAL Chi-restraints excluded: chain y residue 13 LEU Chi-restraints excluded: chain y residue 14 LYS Chi-restraints excluded: chain y residue 24 VAL Chi-restraints excluded: chain y residue 35 VAL Chi-restraints excluded: chain y residue 36 VAL Chi-restraints excluded: chain y residue 57 GLN Chi-restraints excluded: chain y residue 82 THR Chi-restraints excluded: chain y residue 272 LYS Chi-restraints excluded: chain y residue 278 THR Chi-restraints excluded: chain y residue 281 THR Chi-restraints excluded: chain y residue 294 VAL Chi-restraints excluded: chain y residue 312 THR Chi-restraints excluded: chain y residue 342 ILE Chi-restraints excluded: chain y residue 344 LEU Chi-restraints excluded: chain y residue 346 LEU Chi-restraints excluded: chain x residue 21 THR Chi-restraints excluded: chain x residue 29 GLN Chi-restraints excluded: chain x residue 44 GLU Chi-restraints excluded: chain x residue 54 LEU Chi-restraints excluded: chain x residue 84 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 630 optimal weight: 10.0000 chunk 406 optimal weight: 8.9990 chunk 608 optimal weight: 7.9990 chunk 306 optimal weight: 0.9990 chunk 200 optimal weight: 5.9990 chunk 197 optimal weight: 9.9990 chunk 647 optimal weight: 7.9990 chunk 694 optimal weight: 3.9990 chunk 503 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 chunk 800 optimal weight: 0.0060 overall best weight: 3.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 7 ASN c 138 GLN c 139 ASN e 42 ASN e 60 GLN ** e 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 96 GLN f 3 HIS f 68 GLN g 85 GLN g 141 HIS h 17 GLN i 4 GLN i 30 ASN i 109 GLN i 125 GLN l 111 GLN n 3 GLN n 43 ASN n 60 GLN p 63 GLN ** q 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 19 HIS t 47 GLN ** t 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN F 134 GLN G 44 HIS ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 ASN J 80 HIS K 29 HIS N 9 GLN N 18 GLN N 23 ASN O 38 GLN P 2 ASN ** P 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN ** Q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 9 HIS S 61 ASN T 48 GLN T 92 ASN U 65 GLN ** Y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 33 ASN v 32 GLN ** v 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 62 HIS Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 159850 Z= 0.284 Angle : 0.625 20.986 238824 Z= 0.322 Chirality : 0.037 0.390 30498 Planarity : 0.005 0.092 13064 Dihedral : 23.227 179.482 79176 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.52 % Favored : 90.33 % Rotamer: Outliers : 7.41 % Allowed : 33.42 % Favored : 59.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.02 % Twisted Proline : 1.03 % 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: -1.50 (0.11), residues: 6082 helix: 0.59 (0.12), residues: 1897 sheet: -1.04 (0.15), residues: 1108 loop : -2.06 (0.11), residues: 3077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP y 311 HIS 0.010 0.001 HIS t 67 PHE 0.021 0.002 PHE g 17 TYR 0.023 0.002 TYR 1 48 ARG 0.015 0.001 ARG j 31 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2206 residues out of total 5071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 362 poor density : 1844 time to evaluate : 6.445 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: b 8 MET cc_start: 0.6456 (pmm) cc_final: 0.5692 (ppp) REVERT: b 20 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.5614 (ptt180) REVERT: b 29 PHE cc_start: 0.8581 (OUTLIER) cc_final: 0.8112 (m-80) REVERT: b 51 GLU cc_start: 0.7913 (tp30) cc_final: 0.7658 (tp30) REVERT: b 62 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.8162 (mpp80) REVERT: b 158 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.8018 (m-30) REVERT: b 168 GLU cc_start: 0.8294 (mp0) cc_final: 0.8003 (mp0) REVERT: b 174 GLU cc_start: 0.8011 (tp30) cc_final: 0.7626 (mt-10) REVERT: b 183 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.7422 (p90) REVERT: b 191 ASP cc_start: 0.7932 (t0) cc_final: 0.7571 (t0) REVERT: c 31 ASN cc_start: 0.8723 (m-40) cc_final: 0.8273 (t0) REVERT: c 35 ASP cc_start: 0.8914 (m-30) cc_final: 0.8680 (m-30) REVERT: c 44 LYS cc_start: 0.9005 (tmmt) cc_final: 0.8736 (tppp) REVERT: c 129 PHE cc_start: 0.9044 (p90) cc_final: 0.8737 (p90) REVERT: c 161 ILE cc_start: 0.9300 (OUTLIER) cc_final: 0.9014 (pp) REVERT: d 58 GLN cc_start: 0.8808 (mm-40) cc_final: 0.8432 (mm-40) REVERT: d 68 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7559 (tp30) REVERT: d 77 GLU cc_start: 0.8454 (tp30) cc_final: 0.8144 (tp30) REVERT: d 137 SER cc_start: 0.8919 (OUTLIER) cc_final: 0.8513 (p) REVERT: d 151 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8086 (pp30) REVERT: e 11 GLN cc_start: 0.8466 (tt0) cc_final: 0.8208 (tp40) REVERT: e 13 LYS cc_start: 0.8785 (ttmm) cc_final: 0.8544 (tppt) REVERT: e 19 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.8281 (ttm-80) REVERT: e 64 GLU cc_start: 0.8331 (tp30) cc_final: 0.7953 (tp30) REVERT: e 69 ASN cc_start: 0.8779 (t0) cc_final: 0.8244 (t0) REVERT: e 77 ASN cc_start: 0.8792 (m-40) cc_final: 0.8292 (p0) REVERT: f 13 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.8463 (p0) REVERT: f 30 THR cc_start: 0.9614 (m) cc_final: 0.9216 (p) REVERT: f 39 LEU cc_start: 0.8951 (mt) cc_final: 0.8714 (tm) REVERT: g 78 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7773 (ppp80) REVERT: g 100 MET cc_start: 0.8702 (mtm) cc_final: 0.8328 (mtp) REVERT: h 57 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7507 (mp0) REVERT: i 60 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8789 (pp) REVERT: i 90 ASP cc_start: 0.8194 (t70) cc_final: 0.7868 (t70) REVERT: j 30 LYS cc_start: 0.9308 (mtpp) cc_final: 0.9057 (tmmt) REVERT: j 45 ARG cc_start: 0.7756 (mmt180) cc_final: 0.6999 (ttm170) REVERT: k 12 ARG cc_start: 0.4358 (OUTLIER) cc_final: 0.3816 (mpp-170) REVERT: k 68 ARG cc_start: 0.8391 (mtp-110) cc_final: 0.8065 (mtp-110) REVERT: l 8 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8398 (mtp85) REVERT: l 85 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.8103 (ppp80) REVERT: l 93 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.7835 (mtp180) REVERT: m 3 ILE cc_start: 0.8747 (pt) cc_final: 0.8405 (mp) REVERT: m 88 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9172 (mt) REVERT: n 60 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8331 (mp-120) REVERT: n 62 ASN cc_start: 0.8702 (t0) cc_final: 0.8030 (t0) REVERT: o 9 LYS cc_start: 0.9098 (tmtt) cc_final: 0.8860 (tptp) REVERT: o 17 ASP cc_start: 0.9097 (p0) cc_final: 0.8826 (p0) REVERT: o 70 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8907 (ttpp) REVERT: o 82 GLU cc_start: 0.8408 (tp30) cc_final: 0.8066 (tp30) REVERT: p 53 ASP cc_start: 0.8058 (t0) cc_final: 0.7815 (t0) REVERT: q 10 ARG cc_start: 0.7977 (mtp-110) cc_final: 0.7616 (ttm110) REVERT: q 47 ASP cc_start: 0.8425 (p0) cc_final: 0.8096 (p0) REVERT: q 64 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.8427 (ptm-80) REVERT: q 68 LYS cc_start: 0.9028 (ttpp) cc_final: 0.8803 (ttmt) REVERT: q 80 LYS cc_start: 0.8556 (ttmt) cc_final: 0.8266 (tptt) REVERT: r 47 ARG cc_start: 0.7606 (mmt-90) cc_final: 0.7230 (mtt-85) REVERT: s 17 LYS cc_start: 0.9066 (ttmm) cc_final: 0.8847 (mtpm) REVERT: s 24 SER cc_start: 0.9085 (t) cc_final: 0.8854 (t) REVERT: s 54 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.7721 (ptt90) REVERT: s 55 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.6818 (mp10) REVERT: t 14 GLU cc_start: 0.8537 (tp30) cc_final: 0.8306 (mm-30) REVERT: t 25 SER cc_start: 0.9045 (t) cc_final: 0.8830 (m) REVERT: t 47 GLN cc_start: 0.9131 (tp40) cc_final: 0.8442 (tp40) REVERT: t 51 ASN cc_start: 0.8683 (m110) cc_final: 0.8018 (m110) REVERT: u 19 LYS cc_start: 0.6922 (pttm) cc_final: 0.6694 (tppt) REVERT: C 20 ASN cc_start: 0.8257 (t0) cc_final: 0.7996 (t0) REVERT: C 59 GLN cc_start: 0.8991 (pt0) cc_final: 0.8605 (mt0) REVERT: C 65 ASP cc_start: 0.8518 (t0) cc_final: 0.8162 (t0) REVERT: C 110 LYS cc_start: 0.8288 (mmmt) cc_final: 0.8012 (mtmm) REVERT: C 116 GLN cc_start: 0.8872 (pt0) cc_final: 0.8427 (pt0) REVERT: D 7 LYS cc_start: 0.8545 (ttmt) cc_final: 0.8246 (ttpp) REVERT: D 130 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8618 (mt0) REVERT: E 166 LYS cc_start: 0.8155 (mmtt) cc_final: 0.7775 (mmpt) REVERT: E 168 ASP cc_start: 0.7930 (t0) cc_final: 0.7673 (t0) REVERT: E 181 ILE cc_start: 0.9330 (mm) cc_final: 0.9089 (mm) REVERT: F 82 TYR cc_start: 0.7864 (t80) cc_final: 0.7609 (t80) REVERT: F 141 ASP cc_start: 0.6909 (p0) cc_final: 0.6627 (p0) REVERT: G 17 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8155 (mtmm) REVERT: G 26 LYS cc_start: 0.8917 (ttmt) cc_final: 0.8707 (mtpp) REVERT: G 41 GLU cc_start: 0.8233 (tt0) cc_final: 0.7964 (pt0) REVERT: G 43 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8328 (mmmm) REVERT: G 100 ASN cc_start: 0.8853 (p0) cc_final: 0.8390 (p0) REVERT: G 137 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8201 (tppp) REVERT: G 148 ARG cc_start: 0.8853 (ttt-90) cc_final: 0.8619 (ttt-90) REVERT: G 156 TYR cc_start: 0.8871 (m-80) cc_final: 0.8487 (m-80) REVERT: J 2 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8114 (mmtp) REVERT: J 14 ASP cc_start: 0.7906 (m-30) cc_final: 0.7575 (m-30) REVERT: J 16 TYR cc_start: 0.9253 (m-80) cc_final: 0.8990 (m-80) REVERT: J 28 LEU cc_start: 0.9494 (tp) cc_final: 0.9275 (tm) REVERT: J 52 ASP cc_start: 0.8584 (m-30) cc_final: 0.8302 (m-30) REVERT: J 102 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7846 (mt-10) REVERT: K 108 ARG cc_start: 0.8036 (ttm-80) cc_final: 0.7811 (mtp-110) REVERT: L 5 THR cc_start: 0.9284 (m) cc_final: 0.9054 (p) REVERT: L 27 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8926 (pp) REVERT: L 106 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7297 (tm-30) REVERT: M 40 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8144 (mtm180) REVERT: N 72 ASP cc_start: 0.8313 (t0) cc_final: 0.7859 (t0) REVERT: N 75 ILE cc_start: 0.9303 (OUTLIER) cc_final: 0.8922 (mp) REVERT: N 82 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7740 (mt-10) REVERT: N 107 ASN cc_start: 0.9097 (t0) cc_final: 0.8672 (t0) REVERT: N 114 GLU cc_start: 0.8010 (pp20) cc_final: 0.7676 (pp20) REVERT: O 19 GLN cc_start: 0.9282 (tm-30) cc_final: 0.8899 (tm-30) REVERT: O 61 GLN cc_start: 0.9317 (tp40) cc_final: 0.8782 (mp10) REVERT: O 104 GLN cc_start: 0.8978 (tt0) cc_final: 0.8443 (tt0) REVERT: O 108 ASP cc_start: 0.8405 (m-30) cc_final: 0.8050 (m-30) REVERT: P 9 GLN cc_start: 0.8608 (mt0) cc_final: 0.8217 (tm-30) REVERT: P 62 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8606 (ttmt) REVERT: P 86 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8450 (mmpt) REVERT: Q 70 GLN cc_start: 0.8767 (tp40) cc_final: 0.8183 (tp40) REVERT: Q 109 VAL cc_start: 0.9439 (t) cc_final: 0.9172 (t) REVERT: Q 110 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7882 (tm-30) REVERT: R 21 ARG cc_start: 0.8948 (ttm170) cc_final: 0.8411 (ttm-80) REVERT: R 40 MET cc_start: 0.8222 (ttm) cc_final: 0.8019 (tpt) REVERT: S 3 THR cc_start: 0.9341 (m) cc_final: 0.8799 (p) REVERT: S 70 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8326 (ttpt) REVERT: T 28 ASN cc_start: 0.8773 (t0) cc_final: 0.8148 (t0) REVERT: U 5 ARG cc_start: 0.8449 (ptp-170) cc_final: 0.8110 (ptp-170) REVERT: U 98 ASN cc_start: 0.7642 (p0) cc_final: 0.6615 (p0) REVERT: V 9 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.8804 (mmm-85) REVERT: V 42 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8655 (pp) REVERT: V 79 ARG cc_start: 0.9203 (OUTLIER) cc_final: 0.8181 (mmm-85) REVERT: V 90 ASP cc_start: 0.8459 (m-30) cc_final: 0.8198 (m-30) REVERT: X 10 ARG cc_start: 0.8642 (mtp85) cc_final: 0.8322 (mtp85) REVERT: Y 4 LYS cc_start: 0.8910 (mmtm) cc_final: 0.8133 (mmtm) REVERT: Y 7 ARG cc_start: 0.7752 (ptt-90) cc_final: 0.7501 (ptt-90) REVERT: Y 36 GLN cc_start: 0.7952 (mp10) cc_final: 0.7752 (mp10) REVERT: Y 39 GLN cc_start: 0.8230 (mm-40) cc_final: 0.7948 (mm-40) REVERT: Y 60 LYS cc_start: 0.8737 (ttpt) cc_final: 0.8530 (pttt) REVERT: Z 5 LYS cc_start: 0.9094 (mtpp) cc_final: 0.8748 (mmmm) REVERT: Z 8 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.7861 (tt0) REVERT: Z 31 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8820 (mt) REVERT: 0 11 LYS cc_start: 0.8743 (tptm) cc_final: 0.8408 (tppt) REVERT: 0 14 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.8384 (mtm) REVERT: 0 36 LYS cc_start: 0.9085 (mmtp) cc_final: 0.8680 (mmmm) REVERT: 4 9 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8491 (mtmt) REVERT: 4 22 VAL cc_start: 0.8897 (OUTLIER) cc_final: 0.8685 (m) REVERT: 6 20 ASN cc_start: 0.8018 (m-40) cc_final: 0.7803 (m-40) REVERT: y 57 GLN cc_start: 0.5574 (OUTLIER) cc_final: 0.5305 (pm20) outliers start: 362 outliers final: 235 residues processed: 2002 average time/residue: 2.0314 time to fit residues: 5958.3312 Evaluate side-chains 2092 residues out of total 5071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 280 poor density : 1812 time to evaluate : 6.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 15 PHE Chi-restraints excluded: chain b residue 17 HIS Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain b residue 20 ARG Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 29 PHE Chi-restraints excluded: chain b residue 55 GLU Chi-restraints excluded: chain b residue 62 ARG Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 128 LEU Chi-restraints excluded: chain b residue 152 ASP Chi-restraints excluded: chain b residue 158 ASP Chi-restraints excluded: chain b residue 166 ASP Chi-restraints excluded: chain b residue 182 VAL Chi-restraints excluded: chain b residue 183 PHE Chi-restraints excluded: chain b residue 193 ASP Chi-restraints excluded: chain b residue 198 VAL Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 121 SER Chi-restraints excluded: chain c residue 161 ILE Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 63 ILE Chi-restraints excluded: chain d residue 67 LEU Chi-restraints excluded: chain d residue 68 GLU Chi-restraints excluded: chain d residue 133 SER Chi-restraints excluded: chain d residue 137 SER Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 142 VAL Chi-restraints excluded: chain d residue 151 GLN Chi-restraints excluded: chain d residue 188 SER Chi-restraints excluded: chain e residue 10 LEU Chi-restraints excluded: chain e residue 19 ARG Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 79 THR Chi-restraints excluded: chain e residue 104 ILE Chi-restraints excluded: chain e residue 113 VAL Chi-restraints excluded: chain e residue 115 GLU Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain e residue 146 MET Chi-restraints excluded: chain e residue 160 VAL Chi-restraints excluded: chain f residue 13 ASP Chi-restraints excluded: chain f residue 51 ILE Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain g residue 29 LEU Chi-restraints excluded: chain g residue 37 THR Chi-restraints excluded: chain g residue 39 GLU Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 78 ARG Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain g residue 130 LYS Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 37 ASN Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 57 GLU Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 88 LYS Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 104 SER Chi-restraints excluded: chain h residue 125 ILE Chi-restraints excluded: chain i residue 13 SER Chi-restraints excluded: chain i residue 31 GLN Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain i residue 86 LEU Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 11 LYS Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain k residue 12 ARG Chi-restraints excluded: chain k residue 25 SER Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 57 SER Chi-restraints excluded: chain k residue 80 ASN Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain k residue 126 ARG Chi-restraints excluded: chain l residue 2 THR Chi-restraints excluded: chain l residue 8 ARG Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 46 SER Chi-restraints excluded: chain l residue 56 LEU Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 85 ARG Chi-restraints excluded: chain l residue 93 ARG Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 20 SER Chi-restraints excluded: chain m residue 27 THR Chi-restraints excluded: chain m residue 44 ILE Chi-restraints excluded: chain m residue 55 LEU Chi-restraints excluded: chain m residue 57 ASP Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 67 ASP Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain m residue 107 THR Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 60 GLN Chi-restraints excluded: chain n residue 67 THR Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain n residue 86 GLU Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 60 SER Chi-restraints excluded: chain o residue 70 LYS Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 79 ASN Chi-restraints excluded: chain q residue 14 ASP Chi-restraints excluded: chain q residue 19 SER Chi-restraints excluded: chain q residue 43 LEU Chi-restraints excluded: chain q residue 64 ARG Chi-restraints excluded: chain r residue 70 THR Chi-restraints excluded: chain s residue 12 LEU Chi-restraints excluded: chain s residue 18 VAL Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain s residue 54 ARG Chi-restraints excluded: chain s residue 55 GLN Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 5 SER Chi-restraints excluded: chain t residue 85 LEU Chi-restraints excluded: chain u residue 13 VAL Chi-restraints excluded: chain u residue 16 ARG Chi-restraints excluded: chain u residue 31 VAL Chi-restraints excluded: chain u residue 41 THR Chi-restraints excluded: chain u residue 50 SER Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 126 ASN Chi-restraints excluded: chain F residue 134 GLN Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 17 LYS Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 137 LYS Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain J residue 2 LYS Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 91 SER Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 115 GLU Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 40 ARG Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain O residue 12 THR Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 60 GLU Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 36 LYS Chi-restraints excluded: chain P residue 62 LYS Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 103 VAL Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 43 ASN Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 70 LYS Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain U residue 21 ARG Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain V residue 9 ARG Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain V residue 58 SER Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain V residue 79 ARG Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain X residue 1 SER Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Z residue 8 GLN Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 48 ASN Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 14 MET Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 45 ASP Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 8 SER Chi-restraints excluded: chain 2 residue 22 MET Chi-restraints excluded: chain 3 residue 57 VAL Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 4 residue 9 LYS Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain 6 residue 28 VAL Chi-restraints excluded: chain 6 residue 33 ASN Chi-restraints excluded: chain 6 residue 35 ASP Chi-restraints excluded: chain 6 residue 43 PHE Chi-restraints excluded: chain 6 residue 59 ARG Chi-restraints excluded: chain v residue 9 LEU Chi-restraints excluded: chain v residue 53 VAL Chi-restraints excluded: chain y residue 13 LEU Chi-restraints excluded: chain y residue 14 LYS Chi-restraints excluded: chain y residue 24 VAL Chi-restraints excluded: chain y residue 35 VAL Chi-restraints excluded: chain y residue 36 VAL Chi-restraints excluded: chain y residue 57 GLN Chi-restraints excluded: chain y residue 272 LYS Chi-restraints excluded: chain y residue 281 THR Chi-restraints excluded: chain y residue 294 VAL Chi-restraints excluded: chain y residue 342 ILE Chi-restraints excluded: chain y residue 344 LEU Chi-restraints excluded: chain y residue 346 LEU Chi-restraints excluded: chain x residue 21 THR Chi-restraints excluded: chain x residue 29 GLN Chi-restraints excluded: chain x residue 44 GLU Chi-restraints excluded: chain x residue 84 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 926 optimal weight: 7.9990 chunk 976 optimal weight: 1.9990 chunk 890 optimal weight: 0.9980 chunk 949 optimal weight: 0.0980 chunk 975 optimal weight: 6.9990 chunk 571 optimal weight: 10.0000 chunk 413 optimal weight: 10.0000 chunk 745 optimal weight: 0.9980 chunk 291 optimal weight: 10.0000 chunk 857 optimal weight: 3.9990 chunk 897 optimal weight: 6.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 145 ASN c 7 ASN c 138 GLN c 139 ASN e 42 ASN ** e 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 96 GLN ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 GLN g 85 GLN g 141 HIS h 17 GLN h 75 GLN i 4 GLN i 30 ASN i 109 GLN i 125 GLN l 111 GLN n 3 GLN n 43 ASN o 39 GLN ** q 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN D 130 GLN ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN F 51 ASN F 134 GLN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 ASN J 80 HIS K 29 HIS N 9 GLN N 23 ASN O 38 GLN P 2 ASN Q 19 GLN ** Q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN Q 71 ASN ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 61 ASN T 48 GLN U 65 GLN V 49 ASN ** Y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 19 HIS v 32 GLN ** v 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 159850 Z= 0.171 Angle : 0.590 21.052 238824 Z= 0.304 Chirality : 0.034 0.432 30498 Planarity : 0.005 0.086 13064 Dihedral : 23.208 179.395 79176 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.32 % Favored : 90.55 % Rotamer: Outliers : 5.67 % Allowed : 35.70 % Favored : 58.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.02 % Twisted Proline : 1.03 % Twisted General : 0.12 % 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: -1.34 (0.11), residues: 6082 helix: 0.72 (0.12), residues: 1897 sheet: -0.90 (0.16), residues: 1094 loop : -1.97 (0.11), residues: 3091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP y 311 HIS 0.010 0.001 HIS f 11 PHE 0.021 0.001 PHE g 17 TYR 0.032 0.002 TYR 6 9 ARG 0.018 0.001 ARG j 31 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2168 residues out of total 5071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 277 poor density : 1891 time to evaluate : 6.372 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: b 8 MET cc_start: 0.6322 (pmm) cc_final: 0.5324 (ppp) REVERT: b 29 PHE cc_start: 0.8460 (OUTLIER) cc_final: 0.7912 (m-80) REVERT: b 51 GLU cc_start: 0.7890 (tp30) cc_final: 0.7636 (tp30) REVERT: b 144 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7651 (pp20) REVERT: b 168 GLU cc_start: 0.8347 (mp0) cc_final: 0.8046 (mp0) REVERT: b 183 PHE cc_start: 0.8191 (OUTLIER) cc_final: 0.7263 (p90) REVERT: b 191 ASP cc_start: 0.7912 (t0) cc_final: 0.7509 (t0) REVERT: c 31 ASN cc_start: 0.8652 (m-40) cc_final: 0.8198 (t0) REVERT: c 35 ASP cc_start: 0.8866 (m-30) cc_final: 0.8603 (m-30) REVERT: c 44 LYS cc_start: 0.9018 (tmmt) cc_final: 0.8754 (tppp) REVERT: c 129 PHE cc_start: 0.8986 (p90) cc_final: 0.8709 (p90) REVERT: c 161 ILE cc_start: 0.9195 (OUTLIER) cc_final: 0.8920 (pp) REVERT: d 137 SER cc_start: 0.8967 (OUTLIER) cc_final: 0.8550 (p) REVERT: d 151 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8142 (pp30) REVERT: e 11 GLN cc_start: 0.8419 (tt0) cc_final: 0.8167 (tp40) REVERT: e 13 LYS cc_start: 0.8768 (ttmm) cc_final: 0.8517 (tppt) REVERT: e 19 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8236 (ttm-80) REVERT: e 64 GLU cc_start: 0.8312 (tp30) cc_final: 0.7889 (tp30) REVERT: e 69 ASN cc_start: 0.8721 (t0) cc_final: 0.8222 (t0) REVERT: f 13 ASP cc_start: 0.8691 (OUTLIER) cc_final: 0.8488 (p0) REVERT: f 30 THR cc_start: 0.9607 (m) cc_final: 0.9163 (p) REVERT: f 35 LYS cc_start: 0.8456 (mppt) cc_final: 0.8165 (mptm) REVERT: g 20 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7767 (mm-30) REVERT: g 30 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7827 (ttp) REVERT: g 100 MET cc_start: 0.8643 (mtm) cc_final: 0.8263 (mtp) REVERT: h 57 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7364 (mp0) REVERT: i 60 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8797 (pp) REVERT: i 90 ASP cc_start: 0.8060 (t70) cc_final: 0.7658 (t70) REVERT: i 99 LYS cc_start: 0.9227 (ttmt) cc_final: 0.9009 (ttpp) REVERT: j 30 LYS cc_start: 0.9282 (mtpp) cc_final: 0.9056 (tmmt) REVERT: j 45 ARG cc_start: 0.7780 (mmt180) cc_final: 0.7008 (ttm170) REVERT: k 12 ARG cc_start: 0.4284 (OUTLIER) cc_final: 0.3730 (mpp-170) REVERT: k 68 ARG cc_start: 0.8320 (mtp-110) cc_final: 0.8033 (mtp-110) REVERT: l 8 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.8524 (mtp85) REVERT: l 75 GLU cc_start: 0.7893 (mp0) cc_final: 0.7489 (tm-30) REVERT: l 85 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8099 (ppp80) REVERT: l 93 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8129 (mtp180) REVERT: m 3 ILE cc_start: 0.8723 (pt) cc_final: 0.8425 (mp) REVERT: m 88 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9130 (mt) REVERT: n 43 ASN cc_start: 0.9195 (m-40) cc_final: 0.8864 (m110) REVERT: n 62 ASN cc_start: 0.8545 (t0) cc_final: 0.7988 (t0) REVERT: o 9 LYS cc_start: 0.9097 (tmtt) cc_final: 0.8831 (tptp) REVERT: o 17 ASP cc_start: 0.9116 (p0) cc_final: 0.8861 (p0) REVERT: o 70 LYS cc_start: 0.9143 (OUTLIER) cc_final: 0.8897 (ttpp) REVERT: o 71 ARG cc_start: 0.8521 (ttp80) cc_final: 0.8187 (ttm170) REVERT: o 73 ASP cc_start: 0.7582 (t0) cc_final: 0.7322 (t0) REVERT: o 76 ARG cc_start: 0.8941 (mtp-110) cc_final: 0.8533 (mtm-85) REVERT: o 82 GLU cc_start: 0.8386 (tp30) cc_final: 0.8073 (tp30) REVERT: p 17 TYR cc_start: 0.9073 (m-80) cc_final: 0.8805 (m-80) REVERT: q 10 ARG cc_start: 0.7835 (mtp-110) cc_final: 0.7531 (ttm110) REVERT: q 47 ASP cc_start: 0.8406 (p0) cc_final: 0.8125 (p0) REVERT: q 64 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8430 (ptm-80) REVERT: q 68 LYS cc_start: 0.9001 (ttpp) cc_final: 0.8784 (ttmt) REVERT: r 47 ARG cc_start: 0.7521 (mmt-90) cc_final: 0.7261 (mtt-85) REVERT: t 12 GLN cc_start: 0.8637 (tt0) cc_final: 0.8397 (tp40) REVERT: u 19 LYS cc_start: 0.6887 (pttm) cc_final: 0.6559 (tppt) REVERT: C 20 ASN cc_start: 0.8248 (t0) cc_final: 0.7965 (t0) REVERT: C 65 ASP cc_start: 0.8475 (t0) cc_final: 0.8084 (t0) REVERT: C 110 LYS cc_start: 0.8288 (mmmt) cc_final: 0.8079 (mtmm) REVERT: C 116 GLN cc_start: 0.8818 (pt0) cc_final: 0.8428 (pt0) REVERT: D 7 LYS cc_start: 0.8487 (ttmt) cc_final: 0.8166 (ttpp) REVERT: D 97 SER cc_start: 0.9127 (t) cc_final: 0.8606 (p) REVERT: D 99 GLU cc_start: 0.7965 (pp20) cc_final: 0.7651 (pp20) REVERT: E 166 LYS cc_start: 0.8086 (mmtt) cc_final: 0.7652 (mmpt) REVERT: E 168 ASP cc_start: 0.7898 (t0) cc_final: 0.7665 (t0) REVERT: F 4 HIS cc_start: 0.8816 (t-170) cc_final: 0.8544 (t-90) REVERT: F 82 TYR cc_start: 0.7757 (t80) cc_final: 0.7550 (t80) REVERT: G 26 LYS cc_start: 0.8873 (ttmt) cc_final: 0.8617 (mtpp) REVERT: G 100 ASN cc_start: 0.8816 (p0) cc_final: 0.8378 (p0) REVERT: G 148 ARG cc_start: 0.8800 (ttt-90) cc_final: 0.8561 (ttt-90) REVERT: G 156 TYR cc_start: 0.8834 (m-80) cc_final: 0.8513 (m-80) REVERT: J 16 TYR cc_start: 0.9236 (m-80) cc_final: 0.8998 (m-80) REVERT: J 28 LEU cc_start: 0.9460 (tp) cc_final: 0.9241 (tm) REVERT: J 52 ASP cc_start: 0.8536 (m-30) cc_final: 0.8287 (m-30) REVERT: J 102 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7741 (mt-10) REVERT: L 5 THR cc_start: 0.9267 (m) cc_final: 0.9059 (p) REVERT: L 104 GLN cc_start: 0.8816 (mm-40) cc_final: 0.8535 (mm110) REVERT: L 106 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7288 (tm-30) REVERT: M 40 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.8069 (mtm180) REVERT: N 72 ASP cc_start: 0.8251 (t0) cc_final: 0.7803 (t0) REVERT: N 75 ILE cc_start: 0.9326 (mm) cc_final: 0.8942 (mp) REVERT: N 82 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7728 (mt-10) REVERT: N 107 ASN cc_start: 0.9048 (t0) cc_final: 0.8674 (t0) REVERT: N 114 GLU cc_start: 0.7956 (pp20) cc_final: 0.7507 (pp20) REVERT: O 19 GLN cc_start: 0.9223 (tm-30) cc_final: 0.8873 (tm-30) REVERT: O 61 GLN cc_start: 0.9322 (tp40) cc_final: 0.8815 (mp10) REVERT: O 104 GLN cc_start: 0.8922 (tt0) cc_final: 0.8569 (tt0) REVERT: O 108 ASP cc_start: 0.8414 (m-30) cc_final: 0.8037 (m-30) REVERT: P 9 GLN cc_start: 0.8644 (mt0) cc_final: 0.8262 (tm-30) REVERT: P 62 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8658 (ttmt) REVERT: Q 44 TYR cc_start: 0.8811 (m-80) cc_final: 0.8564 (m-80) REVERT: Q 70 GLN cc_start: 0.8748 (tp40) cc_final: 0.8111 (tp-100) REVERT: Q 109 VAL cc_start: 0.9424 (t) cc_final: 0.9198 (t) REVERT: Q 110 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7918 (tm-30) REVERT: R 2 TYR cc_start: 0.8778 (p90) cc_final: 0.8455 (p90) REVERT: R 21 ARG cc_start: 0.8975 (ttm170) cc_final: 0.8452 (ttm-80) REVERT: R 40 MET cc_start: 0.7978 (ttm) cc_final: 0.7352 (tpt) REVERT: R 45 GLU cc_start: 0.8029 (pp20) cc_final: 0.7819 (pp20) REVERT: R 46 GLU cc_start: 0.7387 (tm-30) cc_final: 0.5816 (tm-30) REVERT: R 68 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8429 (mtp180) REVERT: S 3 THR cc_start: 0.9299 (m) cc_final: 0.8814 (p) REVERT: T 26 LYS cc_start: 0.8963 (mmmm) cc_final: 0.8742 (mmmt) REVERT: T 28 ASN cc_start: 0.8722 (t0) cc_final: 0.8125 (t0) REVERT: T 76 ARG cc_start: 0.7422 (ttt-90) cc_final: 0.7180 (ttt-90) REVERT: U 5 ARG cc_start: 0.8429 (ptp-170) cc_final: 0.8159 (ptp-170) REVERT: U 98 ASN cc_start: 0.8075 (p0) cc_final: 0.7315 (p0) REVERT: U 100 GLU cc_start: 0.8026 (mp0) cc_final: 0.7576 (mp0) REVERT: V 9 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.8760 (mmm-85) REVERT: V 42 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8528 (pp) REVERT: V 65 VAL cc_start: 0.8738 (m) cc_final: 0.8470 (m) REVERT: V 68 LYS cc_start: 0.8576 (mtpp) cc_final: 0.8293 (tmtt) REVERT: V 90 ASP cc_start: 0.8377 (m-30) cc_final: 0.8122 (m-30) REVERT: X 10 ARG cc_start: 0.8621 (mtp85) cc_final: 0.8358 (mtp85) REVERT: Y 1 MET cc_start: 0.8001 (mmm) cc_final: 0.7748 (tpt) REVERT: Y 4 LYS cc_start: 0.8867 (mmtm) cc_final: 0.8025 (mmtm) REVERT: Y 5 GLU cc_start: 0.7749 (mp0) cc_final: 0.7437 (mp0) REVERT: Y 7 ARG cc_start: 0.7743 (ptt-90) cc_final: 0.7508 (ptt-90) REVERT: Y 39 GLN cc_start: 0.8214 (mm-40) cc_final: 0.7956 (mm-40) REVERT: Y 60 LYS cc_start: 0.8730 (ttpt) cc_final: 0.8525 (pttt) REVERT: Z 5 LYS cc_start: 0.9077 (mtpp) cc_final: 0.8728 (mmmm) REVERT: Z 8 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7754 (tt0) REVERT: 0 11 LYS cc_start: 0.8705 (tptm) cc_final: 0.8381 (tppt) REVERT: 0 14 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8376 (mtm) REVERT: 0 36 LYS cc_start: 0.8944 (mmtp) cc_final: 0.8547 (mmmm) REVERT: 2 41 ARG cc_start: 0.7840 (ttm-80) cc_final: 0.7371 (mpp80) REVERT: 4 4 ARG cc_start: 0.8078 (mmt90) cc_final: 0.7604 (mtp180) REVERT: 4 9 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8417 (mtpp) REVERT: 4 22 VAL cc_start: 0.8878 (t) cc_final: 0.8631 (m) REVERT: 6 37 CYS cc_start: 0.8432 (p) cc_final: 0.8172 (p) REVERT: y 34 ASP cc_start: 0.7452 (t0) cc_final: 0.7164 (t0) REVERT: y 57 GLN cc_start: 0.5543 (OUTLIER) cc_final: 0.5307 (pm20) outliers start: 277 outliers final: 188 residues processed: 1999 average time/residue: 2.0159 time to fit residues: 5922.3203 Evaluate side-chains 2044 residues out of total 5071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 1829 time to evaluate : 6.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 15 PHE Chi-restraints excluded: chain b residue 17 HIS Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 29 PHE Chi-restraints excluded: chain b residue 55 GLU Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 128 LEU Chi-restraints excluded: chain b residue 182 VAL Chi-restraints excluded: chain b residue 183 PHE Chi-restraints excluded: chain b residue 193 ASP Chi-restraints excluded: chain b residue 198 VAL Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 40 GLN Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 161 ILE Chi-restraints excluded: chain c residue 164 THR Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 63 ILE Chi-restraints excluded: chain d residue 67 LEU Chi-restraints excluded: chain d residue 133 SER Chi-restraints excluded: chain d residue 137 SER Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 142 VAL Chi-restraints excluded: chain d residue 151 GLN Chi-restraints excluded: chain d residue 202 LEU Chi-restraints excluded: chain e residue 10 LEU Chi-restraints excluded: chain e residue 19 ARG Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 104 ILE Chi-restraints excluded: chain e residue 115 GLU Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain e residue 146 MET Chi-restraints excluded: chain f residue 13 ASP Chi-restraints excluded: chain g residue 29 LEU Chi-restraints excluded: chain g residue 30 MET Chi-restraints excluded: chain g residue 39 GLU Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 57 GLU Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 104 SER Chi-restraints excluded: chain i residue 45 MET Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain i residue 86 LEU Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 11 LYS Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain k residue 12 ARG Chi-restraints excluded: chain k residue 25 SER Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 80 ASN Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain k residue 126 ARG Chi-restraints excluded: chain l residue 8 ARG Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 46 SER Chi-restraints excluded: chain l residue 56 LEU Chi-restraints excluded: chain l residue 85 ARG Chi-restraints excluded: chain l residue 93 ARG Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 27 THR Chi-restraints excluded: chain m residue 55 LEU Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 67 ASP Chi-restraints excluded: chain m residue 73 SER Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain m residue 107 THR Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain n residue 86 GLU Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain o residue 60 SER Chi-restraints excluded: chain o residue 70 LYS Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 55 ASP Chi-restraints excluded: chain p residue 79 ASN Chi-restraints excluded: chain q residue 19 SER Chi-restraints excluded: chain q residue 60 ILE Chi-restraints excluded: chain q residue 64 ARG Chi-restraints excluded: chain r residue 24 ASP Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 85 LEU Chi-restraints excluded: chain u residue 13 VAL Chi-restraints excluded: chain u residue 16 ARG Chi-restraints excluded: chain u residue 50 SER Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 50 ASP Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 160 LYS Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 115 GLU Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 40 ARG Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain O residue 12 THR Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 60 GLU Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 36 LYS Chi-restraints excluded: chain P residue 62 LYS Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 43 ASN Chi-restraints excluded: chain R residue 68 ARG Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain V residue 9 ARG Chi-restraints excluded: chain V residue 25 LYS Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain X residue 1 SER Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Z residue 8 GLN Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 48 ASN Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 14 MET Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 2 residue 8 SER Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 57 VAL Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 4 residue 9 LYS Chi-restraints excluded: chain 6 residue 28 VAL Chi-restraints excluded: chain 6 residue 35 ASP Chi-restraints excluded: chain 6 residue 36 VAL Chi-restraints excluded: chain 6 residue 59 ARG Chi-restraints excluded: chain v residue 9 LEU Chi-restraints excluded: chain v residue 53 VAL Chi-restraints excluded: chain y residue 13 LEU Chi-restraints excluded: chain y residue 24 VAL Chi-restraints excluded: chain y residue 36 VAL Chi-restraints excluded: chain y residue 57 GLN Chi-restraints excluded: chain y residue 272 LYS Chi-restraints excluded: chain y residue 281 THR Chi-restraints excluded: chain y residue 294 VAL Chi-restraints excluded: chain y residue 342 ILE Chi-restraints excluded: chain y residue 344 LEU Chi-restraints excluded: chain y residue 346 LEU Chi-restraints excluded: chain x residue 21 THR Chi-restraints excluded: chain x residue 29 GLN Chi-restraints excluded: chain x residue 44 GLU Chi-restraints excluded: chain x residue 84 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 946 optimal weight: 7.9990 chunk 623 optimal weight: 10.0000 chunk 1003 optimal weight: 30.0000 chunk 612 optimal weight: 10.0000 chunk 476 optimal weight: 10.0000 chunk 697 optimal weight: 9.9990 chunk 1053 optimal weight: 6.9990 chunk 969 optimal weight: 7.9990 chunk 838 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 647 optimal weight: 10.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 145 ASN ** b 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 7 ASN c 138 GLN c 139 ASN e 42 ASN e 60 GLN e 72 ASN ** e 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 96 GLN f 68 GLN g 85 GLN g 141 HIS h 75 GLN i 30 ASN i 109 GLN l 111 GLN n 3 GLN p 26 ASN p 63 GLN t 20 ASN t 47 GLN C 238 ASN D 130 GLN D 136 ASN F 51 ASN ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 ASN J 80 HIS ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 9 GLN N 18 GLN N 23 ASN O 38 GLN P 2 ASN ** P 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN ** Q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 71 ASN ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN T 48 GLN U 65 GLN ** Y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 8 GLN 2 13 ASN v 32 GLN v 36 GLN x 88 HIS Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.086 159850 Z= 0.589 Angle : 0.769 21.008 238824 Z= 0.391 Chirality : 0.045 0.435 30498 Planarity : 0.006 0.099 13064 Dihedral : 23.199 179.159 79176 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.77 % Favored : 89.07 % Rotamer: Outliers : 5.82 % Allowed : 36.33 % Favored : 57.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.02 % Twisted Proline : 1.03 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.10), residues: 6082 helix: 0.45 (0.12), residues: 1890 sheet: -1.08 (0.15), residues: 1120 loop : -2.07 (0.11), residues: 3072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 212 HIS 0.010 0.002 HIS t 67 PHE 0.029 0.002 PHE H 91 TYR 0.033 0.003 TYR R 83 ARG 0.016 0.001 ARG u 32 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12164 Ramachandran restraints generated. 6082 Oldfield, 0 Emsley, 6082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2101 residues out of total 5071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 284 poor density : 1817 time to evaluate : 6.443 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: b 17 HIS cc_start: 0.6110 (OUTLIER) cc_final: 0.5356 (t70) REVERT: b 20 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.5769 (ptt180) REVERT: b 29 PHE cc_start: 0.8756 (OUTLIER) cc_final: 0.8226 (m-80) REVERT: b 51 GLU cc_start: 0.7929 (tp30) cc_final: 0.6911 (tp30) REVERT: b 55 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7309 (mp0) REVERT: b 144 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7783 (pp20) REVERT: b 168 GLU cc_start: 0.8321 (mp0) cc_final: 0.7974 (mp0) REVERT: b 183 PHE cc_start: 0.8484 (OUTLIER) cc_final: 0.7567 (p90) REVERT: b 191 ASP cc_start: 0.8044 (t0) cc_final: 0.7659 (t70) REVERT: b 193 ASP cc_start: 0.7155 (m-30) cc_final: 0.6487 (m-30) REVERT: c 35 ASP cc_start: 0.8964 (m-30) cc_final: 0.8754 (m-30) REVERT: c 129 PHE cc_start: 0.9054 (p90) cc_final: 0.8806 (p90) REVERT: c 161 ILE cc_start: 0.9328 (OUTLIER) cc_final: 0.9036 (pp) REVERT: d 58 GLN cc_start: 0.8907 (mm-40) cc_final: 0.8483 (mm-40) REVERT: d 137 SER cc_start: 0.8878 (OUTLIER) cc_final: 0.8459 (p) REVERT: d 151 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8072 (pp30) REVERT: e 11 GLN cc_start: 0.8387 (tt0) cc_final: 0.8148 (tp40) REVERT: e 13 LYS cc_start: 0.8894 (ttmm) cc_final: 0.8638 (ttmm) REVERT: e 19 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.8276 (ttm-80) REVERT: e 64 GLU cc_start: 0.8377 (tp30) cc_final: 0.8017 (tp30) REVERT: e 69 ASN cc_start: 0.8903 (t0) cc_final: 0.8308 (t0) REVERT: e 77 ASN cc_start: 0.8777 (m-40) cc_final: 0.8258 (p0) REVERT: e 122 VAL cc_start: 0.9616 (OUTLIER) cc_final: 0.9330 (p) REVERT: f 39 LEU cc_start: 0.9233 (mt) cc_final: 0.8958 (tm) REVERT: g 30 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.8056 (ttm) REVERT: g 100 MET cc_start: 0.8760 (mtm) cc_final: 0.8475 (mtp) REVERT: i 90 ASP cc_start: 0.8403 (t70) cc_final: 0.8090 (t70) REVERT: i 99 LYS cc_start: 0.9285 (ttmt) cc_final: 0.9069 (ttpp) REVERT: j 30 LYS cc_start: 0.9272 (mtpp) cc_final: 0.9009 (tmmt) REVERT: j 45 ARG cc_start: 0.7830 (mmt180) cc_final: 0.7053 (ttm170) REVERT: k 12 ARG cc_start: 0.5186 (OUTLIER) cc_final: 0.4574 (mpp-170) REVERT: k 67 GLU cc_start: 0.7866 (pt0) cc_final: 0.7579 (pt0) REVERT: k 68 ARG cc_start: 0.8421 (mtp-110) cc_final: 0.8059 (mtp-110) REVERT: l 8 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.8320 (mtp85) REVERT: l 85 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8164 (ppp80) REVERT: l 93 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.7958 (mtp180) REVERT: m 3 ILE cc_start: 0.8737 (pt) cc_final: 0.8504 (mp) REVERT: m 88 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9194 (mt) REVERT: n 62 ASN cc_start: 0.8792 (t0) cc_final: 0.8183 (t0) REVERT: o 9 LYS cc_start: 0.9106 (tmtt) cc_final: 0.8824 (tptp) REVERT: o 17 ASP cc_start: 0.9116 (p0) cc_final: 0.8837 (p0) REVERT: o 70 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8920 (ttpp) REVERT: p 17 TYR cc_start: 0.9141 (m-80) cc_final: 0.8864 (m-80) REVERT: q 10 ARG cc_start: 0.7955 (mtp-110) cc_final: 0.7562 (ttm110) REVERT: q 47 ASP cc_start: 0.8431 (p0) cc_final: 0.8201 (p0) REVERT: q 64 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.8488 (ptm-80) REVERT: r 47 ARG cc_start: 0.7609 (mmt-90) cc_final: 0.7240 (mtt-85) REVERT: s 55 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7071 (mt0) REVERT: t 51 ASN cc_start: 0.8714 (m110) cc_final: 0.8144 (m110) REVERT: u 19 LYS cc_start: 0.6943 (pttm) cc_final: 0.6690 (tppt) REVERT: C 20 ASN cc_start: 0.8253 (t0) cc_final: 0.8039 (t0) REVERT: C 65 ASP cc_start: 0.8613 (t0) cc_final: 0.8280 (t0) REVERT: C 110 LYS cc_start: 0.8387 (mmmt) cc_final: 0.8076 (mtmm) REVERT: C 116 GLN cc_start: 0.8962 (pt0) cc_final: 0.8509 (pt0) REVERT: C 176 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.8270 (tpt-90) REVERT: D 7 LYS cc_start: 0.8603 (ttmt) cc_final: 0.8302 (ttpp) REVERT: D 97 SER cc_start: 0.9179 (t) cc_final: 0.8855 (p) REVERT: E 168 ASP cc_start: 0.7794 (t0) cc_final: 0.7549 (t0) REVERT: E 181 ILE cc_start: 0.9349 (mm) cc_final: 0.9116 (mm) REVERT: F 128 SER cc_start: 0.9080 (t) cc_final: 0.8768 (t) REVERT: G 26 LYS cc_start: 0.8946 (ttmt) cc_final: 0.8709 (mtpp) REVERT: G 100 ASN cc_start: 0.8873 (p0) cc_final: 0.8378 (p0) REVERT: G 148 ARG cc_start: 0.8914 (ttt-90) cc_final: 0.8652 (ttt-90) REVERT: G 156 TYR cc_start: 0.8936 (m-80) cc_final: 0.8565 (m-80) REVERT: J 14 ASP cc_start: 0.7970 (m-30) cc_final: 0.7662 (m-30) REVERT: J 52 ASP cc_start: 0.8606 (m-30) cc_final: 0.8328 (m-30) REVERT: J 102 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7919 (mt-10) REVERT: L 5 THR cc_start: 0.9321 (m) cc_final: 0.9076 (p) REVERT: L 58 TYR cc_start: 0.8655 (p90) cc_final: 0.8228 (p90) REVERT: L 104 GLN cc_start: 0.8958 (mm-40) cc_final: 0.8687 (mm110) REVERT: M 40 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.8239 (mtm180) REVERT: N 72 ASP cc_start: 0.8360 (t0) cc_final: 0.7781 (t0) REVERT: N 75 ILE cc_start: 0.9333 (mm) cc_final: 0.8971 (mp) REVERT: N 82 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7690 (mt-10) REVERT: N 107 ASN cc_start: 0.9157 (t0) cc_final: 0.8692 (t0) REVERT: O 19 GLN cc_start: 0.9294 (tm-30) cc_final: 0.8991 (tm-30) REVERT: O 61 GLN cc_start: 0.9441 (tp40) cc_final: 0.9105 (mm110) REVERT: O 104 GLN cc_start: 0.9078 (tt0) cc_final: 0.8797 (tt0) REVERT: P 9 GLN cc_start: 0.8611 (mt0) cc_final: 0.8259 (tm-30) REVERT: P 62 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8585 (ttmt) REVERT: Q 48 ASP cc_start: 0.7782 (m-30) cc_final: 0.7446 (m-30) REVERT: Q 70 GLN cc_start: 0.8741 (tp40) cc_final: 0.8070 (tp-100) REVERT: Q 88 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8144 (mm-30) REVERT: Q 109 VAL cc_start: 0.9562 (t) cc_final: 0.9311 (t) REVERT: Q 110 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7943 (tm-30) REVERT: R 21 ARG cc_start: 0.9034 (ttm170) cc_final: 0.8464 (ttm-80) REVERT: R 68 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8460 (mtp180) REVERT: S 1 MET cc_start: 0.6697 (tpp) cc_final: 0.6475 (tpp) REVERT: S 3 THR cc_start: 0.9405 (m) cc_final: 0.8852 (p) REVERT: S 4 ILE cc_start: 0.9487 (pt) cc_final: 0.9246 (mp) REVERT: S 82 MET cc_start: 0.8327 (ptp) cc_final: 0.8091 (ptm) REVERT: T 1 MET cc_start: 0.2963 (ptp) cc_final: 0.2676 (ptm) REVERT: T 28 ASN cc_start: 0.8809 (t0) cc_final: 0.8168 (t0) REVERT: U 5 ARG cc_start: 0.8529 (ptp-170) cc_final: 0.8105 (ptp-170) REVERT: U 9 GLU cc_start: 0.7746 (tp30) cc_final: 0.7483 (tp30) REVERT: U 21 ARG cc_start: 0.8321 (mtp-110) cc_final: 0.8090 (mtp-110) REVERT: U 98 ASN cc_start: 0.8049 (p0) cc_final: 0.7267 (p0) REVERT: U 100 GLU cc_start: 0.8070 (mp0) cc_final: 0.7632 (mp0) REVERT: V 9 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.8856 (mmm-85) REVERT: V 42 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8596 (pp) REVERT: V 79 ARG cc_start: 0.9228 (OUTLIER) cc_final: 0.8200 (mmm-85) REVERT: V 83 LYS cc_start: 0.8639 (mttp) cc_final: 0.8187 (mttm) REVERT: V 90 ASP cc_start: 0.8540 (m-30) cc_final: 0.8291 (m-30) REVERT: Y 1 MET cc_start: 0.8165 (mmm) cc_final: 0.7926 (tpt) REVERT: Y 4 LYS cc_start: 0.8979 (mmtm) cc_final: 0.8274 (mmtm) REVERT: Y 39 GLN cc_start: 0.8228 (mm-40) cc_final: 0.7969 (mm-40) REVERT: Y 60 LYS cc_start: 0.8762 (ttpt) cc_final: 0.8460 (pttt) REVERT: Z 5 LYS cc_start: 0.9118 (mtpp) cc_final: 0.8593 (mmmm) REVERT: Z 36 GLU cc_start: 0.7656 (tp30) cc_final: 0.7043 (tp30) REVERT: 0 11 LYS cc_start: 0.8733 (tptm) cc_final: 0.8396 (tppt) REVERT: 0 14 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.8450 (mtm) REVERT: 4 1 MET cc_start: 0.8632 (ptm) cc_final: 0.8315 (ppp) REVERT: v 54 MET cc_start: 0.6534 (ppp) cc_final: 0.6207 (ptt) REVERT: y 57 GLN cc_start: 0.5577 (OUTLIER) cc_final: 0.5280 (pm20) REVERT: y 314 LYS cc_start: 0.6526 (pptt) cc_final: 0.6296 (pmtt) outliers start: 284 outliers final: 196 residues processed: 1943 average time/residue: 2.0478 time to fit residues: 5841.5596 Evaluate side-chains 2002 residues out of total 5071 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 1777 time to evaluate : 6.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 15 PHE Chi-restraints excluded: chain b residue 17 HIS Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain b residue 20 ARG Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 29 PHE Chi-restraints excluded: chain b residue 55 GLU Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 128 LEU Chi-restraints excluded: chain b residue 152 ASP Chi-restraints excluded: chain b residue 182 VAL Chi-restraints excluded: chain b residue 183 PHE Chi-restraints excluded: chain b residue 198 VAL Chi-restraints excluded: chain b residue 216 VAL Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 40 GLN Chi-restraints excluded: chain c residue 50 SER Chi-restraints excluded: chain c residue 118 SER Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 121 SER Chi-restraints excluded: chain c residue 161 ILE Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 52 VAL Chi-restraints excluded: chain d residue 67 LEU Chi-restraints excluded: chain d residue 133 SER Chi-restraints excluded: chain d residue 137 SER Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 142 VAL Chi-restraints excluded: chain d residue 151 GLN Chi-restraints excluded: chain e residue 10 LEU Chi-restraints excluded: chain e residue 19 ARG Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 104 ILE Chi-restraints excluded: chain e residue 115 GLU Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain e residue 146 MET Chi-restraints excluded: chain e residue 160 VAL Chi-restraints excluded: chain g residue 30 MET Chi-restraints excluded: chain g residue 37 THR Chi-restraints excluded: chain g residue 39 GLU Chi-restraints excluded: chain g residue 72 VAL Chi-restraints excluded: chain g residue 76 SER Chi-restraints excluded: chain g residue 79 VAL Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 50 VAL Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 88 LYS Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 104 SER Chi-restraints excluded: chain h residue 125 ILE Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 60 LEU Chi-restraints excluded: chain i residue 86 LEU Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain k residue 12 ARG Chi-restraints excluded: chain k residue 25 SER Chi-restraints excluded: chain k residue 32 THR Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 80 ASN Chi-restraints excluded: chain k residue 85 VAL Chi-restraints excluded: chain k residue 110 THR Chi-restraints excluded: chain l residue 8 ARG Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 46 SER Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 85 ARG Chi-restraints excluded: chain l residue 88 ASP Chi-restraints excluded: chain l residue 93 ARG Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 27 THR Chi-restraints excluded: chain m residue 44 ILE Chi-restraints excluded: chain m residue 57 ASP Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 73 SER Chi-restraints excluded: chain m residue 88 LEU Chi-restraints excluded: chain m residue 103 THR Chi-restraints excluded: chain m residue 107 THR Chi-restraints excluded: chain n residue 13 VAL Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 67 THR Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain n residue 86 GLU Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain o residue 60 SER Chi-restraints excluded: chain o residue 70 LYS Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 79 ASN Chi-restraints excluded: chain q residue 19 SER Chi-restraints excluded: chain q residue 64 ARG Chi-restraints excluded: chain r residue 70 THR Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain s residue 55 GLN Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 26 MET Chi-restraints excluded: chain t residue 85 LEU Chi-restraints excluded: chain u residue 13 VAL Chi-restraints excluded: chain u residue 50 SER Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 176 ARG Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain K residue 8 LEU Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 115 GLU Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 40 ARG Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain O residue 12 THR Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 36 LYS Chi-restraints excluded: chain P residue 62 LYS Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 86 LYS Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 43 ASN Chi-restraints excluded: chain R residue 68 ARG Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain V residue 9 ARG Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain V residue 79 ARG Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain X residue 1 SER Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 48 ASN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 14 MET Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 8 SER Chi-restraints excluded: chain 3 residue 57 VAL Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 6 residue 28 VAL Chi-restraints excluded: chain 6 residue 35 ASP Chi-restraints excluded: chain 6 residue 61 ASN Chi-restraints excluded: chain v residue 9 LEU Chi-restraints excluded: chain v residue 53 VAL Chi-restraints excluded: chain y residue 13 LEU Chi-restraints excluded: chain y residue 24 VAL Chi-restraints excluded: chain y residue 36 VAL Chi-restraints excluded: chain y residue 38 VAL Chi-restraints excluded: chain y residue 57 GLN Chi-restraints excluded: chain y residue 272 LYS Chi-restraints excluded: chain y residue 281 THR Chi-restraints excluded: chain y residue 284 VAL Chi-restraints excluded: chain y residue 294 VAL Chi-restraints excluded: chain y residue 303 LEU Chi-restraints excluded: chain y residue 342 ILE Chi-restraints excluded: chain y residue 344 LEU Chi-restraints excluded: chain y residue 346 LEU Chi-restraints excluded: chain x residue 21 THR Chi-restraints excluded: chain x residue 29 GLN Chi-restraints excluded: chain x residue 44 GLU Chi-restraints excluded: chain x residue 84 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1057 random chunks: chunk 514 optimal weight: 6.9990 chunk 666 optimal weight: 6.9990 chunk 893 optimal weight: 1.9990 chunk 256 optimal weight: 0.9980 chunk 773 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 chunk 233 optimal weight: 5.9990 chunk 839 optimal weight: 9.9990 chunk 351 optimal weight: 3.9990 chunk 862 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 167 HIS ** b 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 7 ASN c 138 GLN c 139 ASN e 42 ASN ** e 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 GLN g 141 HIS h 75 GLN i 4 GLN i 30 ASN i 109 GLN l 111 GLN n 3 GLN o 39 GLN p 63 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN E 195 GLN ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 103 ASN ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 66 ASN J 80 HIS K 29 HIS L 93 ASN N 9 GLN N 13 ASN N 18 GLN N 23 ASN P 2 ASN Q 19 GLN ** Q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 71 ASN ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 61 ASN T 48 GLN U 65 GLN V 49 ASN ** Y 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 32 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.092640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.068068 restraints weight = 305770.231| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 1.28 r_work: 0.2717 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2604 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2604 r_free = 0.2604 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2604 r_free = 0.2604 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2604 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 159850 Z= 0.221 Angle : 0.624 21.157 238824 Z= 0.321 Chirality : 0.036 0.405 30498 Planarity : 0.005 0.087 13064 Dihedral : 23.214 179.983 79176 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.13 % Favored : 90.71 % Rotamer: Outliers : 4.79 % Allowed : 38.03 % Favored : 57.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.52 % Cis-general : 0.02 % Twisted Proline : 1.03 % Twisted General : 0.12 % 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: -1.42 (0.11), residues: 6082 helix: 0.60 (0.12), residues: 1905 sheet: -0.97 (0.16), residues: 1090 loop : -1.97 (0.11), residues: 3087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP b 95 HIS 0.008 0.001 HIS t 67 PHE 0.024 0.001 PHE R 53 TYR 0.028 0.002 TYR d 75 ARG 0.018 0.001 ARG j 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 76009.86 seconds wall clock time: 1305 minutes 23.12 seconds (78323.12 seconds total)