Starting phenix.real_space_refine on Sat Mar 23 11:30:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5np6_3618/03_2024/5np6_3618_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5np6_3618/03_2024/5np6_3618.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5np6_3618/03_2024/5np6_3618_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5np6_3618/03_2024/5np6_3618_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5np6_3618/03_2024/5np6_3618_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5np6_3618/03_2024/5np6_3618.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5np6_3618/03_2024/5np6_3618.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5np6_3618/03_2024/5np6_3618_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5np6_3618/03_2024/5np6_3618_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 4667 5.49 5 S 159 5.16 5 C 73945 2.51 5 N 27351 2.21 5 O 40761 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 107": "NH1" <-> "NH2" Residue "E PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 224": "NH1" <-> "NH2" Residue "F ARG 106": "NH1" <-> "NH2" Residue "F ARG 130": "NH1" <-> "NH2" Residue "H PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 156": "NH1" <-> "NH2" Residue "I TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 123": "NH1" <-> "NH2" Residue "O TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 55": "NH1" <-> "NH2" Residue "S ARG 28": "NH1" <-> "NH2" Residue "U TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 13": "NH1" <-> "NH2" Residue "b ARG 33": "NH1" <-> "NH2" Residue "b TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 59": "NH1" <-> "NH2" Residue "b ARG 77": "NH1" <-> "NH2" Residue "b ARG 83": "NH1" <-> "NH2" Residue "b ARG 169": "NH1" <-> "NH2" Residue "b ARG 184": "NH1" <-> "NH2" Residue "c ARG 21": "NH1" <-> "NH2" Residue "c ARG 44": "NH1" <-> "NH2" Residue "c ARG 49": "NH1" <-> "NH2" Residue "c ARG 88": "NH1" <-> "NH2" Residue "c ARG 102": "NH1" <-> "NH2" Residue "c ARG 162": "NH1" <-> "NH2" Residue "c ARG 170": "NH1" <-> "NH2" Residue "d ARG 70": "NH1" <-> "NH2" Residue "d ARG 79": "NH1" <-> "NH2" Residue "d ARG 91": "NH1" <-> "NH2" Residue "d ARG 101": "NH1" <-> "NH2" Residue "d ARG 109": "NH1" <-> "NH2" Residue "d ARG 111": "NH1" <-> "NH2" Residue "d ARG 114": "NH1" <-> "NH2" Residue "d ARG 132": "NH1" <-> "NH2" Residue "e ARG 2": "NH1" <-> "NH2" Residue "e ARG 152": "NH1" <-> "NH2" Residue "e ARG 162": "NH1" <-> "NH2" Residue "e ARG 169": "NH1" <-> "NH2" Residue "g TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 13": "NH1" <-> "NH2" Residue "h ARG 37": "NH1" <-> "NH2" Residue "h ARG 96": "NH1" <-> "NH2" Residue "h ARG 120": "NH1" <-> "NH2" Residue "j ARG 21": "NH1" <-> "NH2" Residue "j ARG 33": "NH1" <-> "NH2" Residue "j ARG 41": "NH1" <-> "NH2" Residue "j ARG 47": "NH1" <-> "NH2" Residue "j ARG 60": "NH1" <-> "NH2" Residue "j PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 78": "NH1" <-> "NH2" Residue "j ARG 126": "NH1" <-> "NH2" Residue "k ARG 10": "NH1" <-> "NH2" Residue "k ARG 18": "NH1" <-> "NH2" Residue "k ARG 40": "NH1" <-> "NH2" Residue "k ARG 44": "NH1" <-> "NH2" Residue "k ARG 50": "NH1" <-> "NH2" Residue "k ARG 55": "NH1" <-> "NH2" Residue "k ARG 59": "NH1" <-> "NH2" Residue "k TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 114": "NH1" <-> "NH2" Residue "l ARG 8": "NH1" <-> "NH2" Residue "l ARG 12": "NH1" <-> "NH2" Residue "l ARG 17": "NH1" <-> "NH2" Residue "l ARG 22": "NH1" <-> "NH2" Residue "l ARG 46": "NH1" <-> "NH2" Residue "l ARG 63": "NH1" <-> "NH2" Residue "l ARG 64": "NH1" <-> "NH2" Residue "l ARG 69": "NH1" <-> "NH2" Residue "l ARG 71": "NH1" <-> "NH2" Residue "l ARG 96": "NH1" <-> "NH2" Residue "l ARG 118": "NH1" <-> "NH2" Residue "m ARG 10": "NH1" <-> "NH2" Residue "m ARG 16": "NH1" <-> "NH2" Residue "m ARG 25": "NH1" <-> "NH2" Residue "m ARG 81": "NH1" <-> "NH2" Residue "m ARG 94": "NH1" <-> "NH2" Residue "m ARG 102": "NH1" <-> "NH2" Residue "m ARG 111": "NH1" <-> "NH2" Residue "n PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 20": "NH1" <-> "NH2" Residue "n ARG 38": "NH1" <-> "NH2" Residue "n ARG 61": "NH1" <-> "NH2" Residue "n ARG 88": "NH1" <-> "NH2" Residue "n ARG 100": "NH1" <-> "NH2" Residue "n ARG 108": "NH1" <-> "NH2" Residue "o ARG 2": "NH1" <-> "NH2" Residue "o ARG 5": "NH1" <-> "NH2" Residue "o ARG 12": "NH1" <-> "NH2" Residue "o ARG 32": "NH1" <-> "NH2" Residue "o ARG 47": "NH1" <-> "NH2" Residue "o ARG 69": "NH1" <-> "NH2" Residue "p ARG 21": "NH1" <-> "NH2" Residue "p ARG 68": "NH1" <-> "NH2" Residue "p ARG 78": "NH1" <-> "NH2" Residue "p ARG 79": "NH1" <-> "NH2" Residue "p ARG 84": "NH1" <-> "NH2" Residue "q ARG 84": "NH1" <-> "NH2" Residue "q ARG 88": "NH1" <-> "NH2" Residue "q ARG 95": "NH1" <-> "NH2" Residue "q ARG 110": "NH1" <-> "NH2" Residue "r ARG 73": "NH1" <-> "NH2" Residue "s ARG 5": "NH1" <-> "NH2" Residue "s ARG 6": "NH1" <-> "NH2" Residue "s ARG 81": "NH1" <-> "NH2" Residue "s ARG 85": "NH1" <-> "NH2" Residue "s ARG 93": "NH1" <-> "NH2" Residue "t TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ARG 29": "NH1" <-> "NH2" Residue "w ARG 47": "NH1" <-> "NH2" Residue "w ARG 52": "NH1" <-> "NH2" Residue "x ARG 10": "NH1" <-> "NH2" Residue "x ARG 29": "NH1" <-> "NH2" Residue "x ARG 44": "NH1" <-> "NH2" Residue "y ARG 9": "NH1" <-> "NH2" Residue "y ARG 15": "NH1" <-> "NH2" Residue "y ARG 39": "NH1" <-> "NH2" Residue "y ARG 51": "NH1" <-> "NH2" Residue "z ARG 43": "NH1" <-> "NH2" Residue "z TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 3": "NH1" <-> "NH2" Residue "0 ARG 12": "NH1" <-> "NH2" Residue "0 ARG 14": "NH1" <-> "NH2" Residue "0 ARG 19": "NH1" <-> "NH2" Residue "0 ARG 21": "NH1" <-> "NH2" Residue "0 ARG 33": "NH1" <-> "NH2" Residue "0 ARG 41": "NH1" <-> "NH2" Residue "1 ARG 12": "NH1" <-> "NH2" Residue "1 ARG 29": "NH1" <-> "NH2" Residue "1 ARG 39": "NH1" <-> "NH2" Residue "1 ARG 41": "NH1" <-> "NH2" Residue "2 ARG 12": "NH1" <-> "NH2" Residue "2 ARG 24": "NH1" <-> "NH2" Residue "3 PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 49": "NH1" <-> "NH2" Residue "4 ARG 56": "NH1" <-> "NH2" 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: 146883 Number of models: 1 Model: "" Number of chains: 57 Chain: "A" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 621 Classifications: {'RNA': 29} Modifications used: {'p5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 3, 'rna3p_pur': 11, 'rna3p_pyr': 10} Link IDs: {'rna2p': 7, 'rna3p': 21} Chain: "B" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1623 Classifications: {'RNA': 76} Modifications used: {'p5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 31, 'rna3p_pyr': 33} Link IDs: {'rna2p': 11, 'rna3p': 64} Chain: "C" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 362 Classifications: {'peptide': 46} Link IDs: {'TRANS': 45} Chain: "D" Number of atoms: 33028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33028 Classifications: {'RNA': 1539} Modifications used: {'rna2p': 1, 'rna2p_pur': 100, 'rna2p_pyr': 57, 'rna3p': 10, 'rna3p_pur': 768, 'rna3p_pyr': 603} Link IDs: {'rna2p': 158, 'rna3p': 1380} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 8 Chain: "E" 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: "F" 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: "G" 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: "H" 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: "I" 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: "J" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "K" 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: "L" 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: "M" 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: "N" 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: "O" 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: "P" 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: "Q" 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: "R" 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: "S" 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: "T" 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: "U" 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: "V" 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: "W" 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: "X" 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: "Y" Number of atoms: 62338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62338 Classifications: {'RNA': 2903} Modifications used: {'p5*END': 1, 'rna2p': 7, 'rna2p_pur': 214, 'rna2p_pyr': 102, 'rna3p': 17, 'rna3p_pur': 1453, 'rna3p_pyr': 1110} Link IDs: {'rna2p': 323, 'rna3p': 2579} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 11 Chain: "Z" 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': 4, 'rna2p_pyr': 2, 'rna3p_pur': 61, 'rna3p_pyr': 53} Link IDs: {'rna2p': 6, 'rna3p': 113} Chain: "a" 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: "b" 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: "c" 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: "d" 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: "e" 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: "f" 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: "g" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1032 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "h" 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: "i" 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: "j" 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: "k" 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: "l" 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: "m" 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: "n" 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: "o" 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: "p" 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: "q" 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: "r" 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: "s" 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: "t" 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: "u" 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: "v" 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: "w" 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: "x" 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: "y" 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: "z" 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: "0" 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: "1" 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: "2" 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: "3" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 988 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "4" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Time building chain proxies: 55.34, per 1000 atoms: 0.38 Number of scatterers: 146883 At special positions: 0 Unit cell: (280.9, 270.3, 243.8, 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 159 16.00 P 4667 15.00 O 40761 8.00 N 27351 7.00 C 73945 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 4 18 " - pdb=" SG CYS 4 40 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 68.43 Conformation dependent library (CDL) restraints added in 6.7 seconds 11782 Ramachandran restraints generated. 5891 Oldfield, 0 Emsley, 5891 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11022 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 189 helices and 71 sheets defined 39.1% alpha, 16.5% beta 1459 base pairs and 2159 stacking pairs defined. Time for finding SS restraints: 72.96 Creating SS restraints... Processing helix chain 'C' and resid 8 through 25 removed outlier: 3.511A pdb=" N ASP C 12 " --> pdb=" O SER C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 36 Processing helix chain 'C' and resid 37 through 43 removed outlier: 3.504A pdb=" N ASP C 41 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP C 43 " --> pdb=" O MET C 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 28 removed outlier: 4.216A pdb=" N LYS E 27 " --> pdb=" O ASN E 23 " (cutoff:3.500A) Proline residue: E 28 - end of helix No H-bonds generated for 'chain 'E' and resid 23 through 28' Processing helix chain 'E' and resid 41 through 63 removed outlier: 3.750A pdb=" N THR E 45 " --> pdb=" O ASN E 41 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL E 46 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Proline residue: E 47 - end of helix Processing helix chain 'E' and resid 73 through 87 removed outlier: 4.093A pdb=" N GLU E 77 " --> pdb=" O ARG E 73 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ALA E 78 " --> pdb=" O ALA E 74 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS E 86 " --> pdb=" O ALA E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 122 removed outlier: 3.938A pdb=" N VAL E 106 " --> pdb=" O ASN E 102 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN E 108 " --> pdb=" O LYS E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 147 Processing helix chain 'E' and resid 168 through 179 removed outlier: 3.874A pdb=" N ILE E 172 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU E 178 " --> pdb=" O GLU E 174 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLY E 179 " --> pdb=" O ALA E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 225 removed outlier: 3.683A pdb=" N VAL E 209 " --> pdb=" O ALA E 205 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N SER E 225 " --> pdb=" O ARG E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 154 removed outlier: 3.803A pdb=" N LYS E 151 " --> pdb=" O GLY E 148 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ASP E 152 " --> pdb=" O GLY E 149 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLY E 154 " --> pdb=" O LYS E 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 11 removed outlier: 3.813A pdb=" N ILE F 9 " --> pdb=" O HIS F 5 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG F 10 " --> pdb=" O PRO F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 47 Processing helix chain 'F' and resid 71 through 77 removed outlier: 3.747A pdb=" N VAL F 75 " --> pdb=" O ARG F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 95 removed outlier: 3.631A pdb=" N GLY F 95 " --> pdb=" O ALA F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 112 removed outlier: 4.270A pdb=" N ASP F 111 " --> pdb=" O LYS F 107 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ALA F 112 " --> pdb=" O PRO F 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 107 through 112' Processing helix chain 'F' and resid 113 through 126 Processing helix chain 'F' and resid 128 through 144 removed outlier: 3.919A pdb=" N ALA F 132 " --> pdb=" O MET F 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 15 removed outlier: 3.850A pdb=" N LEU G 10 " --> pdb=" O PRO G 6 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER G 11 " --> pdb=" O LYS G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 65 Processing helix chain 'G' and resid 67 through 82 removed outlier: 3.880A pdb=" N ARG G 80 " --> pdb=" O LYS G 76 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N LYS G 82 " --> pdb=" O ALA G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 96 Processing helix chain 'G' and resid 97 through 105 Processing helix chain 'G' and resid 109 through 120 removed outlier: 3.705A pdb=" N LYS G 120 " --> pdb=" O LEU G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 165 removed outlier: 4.365A pdb=" N LYS G 155 " --> pdb=" O GLN G 151 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLN G 163 " --> pdb=" O GLU G 159 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ARG G 164 " --> pdb=" O LEU G 160 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N GLU G 165 " --> pdb=" O ALA G 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 191 removed outlier: 4.374A pdb=" N LEU G 190 " --> pdb=" O GLU G 186 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N SER G 191 " --> pdb=" O ARG G 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 186 through 191' Processing helix chain 'G' and resid 195 through 205 removed outlier: 4.263A pdb=" N ILE G 199 " --> pdb=" O ASN G 195 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 70 removed outlier: 4.142A pdb=" N GLU H 64 " --> pdb=" O GLN H 60 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS H 65 " --> pdb=" O LYS H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 118 removed outlier: 6.349A pdb=" N ALA H 112 " --> pdb=" O GLY H 108 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA H 117 " --> pdb=" O VAL H 113 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY H 118 " --> pdb=" O LEU H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 146 Processing helix chain 'H' and resid 148 through 156 removed outlier: 3.604A pdb=" N VAL H 152 " --> pdb=" O SER H 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 165 Processing helix chain 'I' and resid 11 through 33 removed outlier: 4.651A pdb=" N GLN I 17 " --> pdb=" O ASP I 13 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL I 18 " --> pdb=" O GLN I 14 " (cutoff:3.500A) Proline residue: I 19 - end of helix Processing helix chain 'I' and resid 67 through 81 removed outlier: 3.724A pdb=" N ILE I 71 " --> pdb=" O PRO I 67 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 30 removed outlier: 4.100A pdb=" N ALA J 23 " --> pdb=" O SER J 19 " (cutoff:3.500A) Processing helix chain 'J' and resid 34 through 54 removed outlier: 4.205A pdb=" N ALA J 38 " --> pdb=" O LYS J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 69 removed outlier: 6.694A pdb=" N ALA J 60 " --> pdb=" O SER J 56 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE J 61 " --> pdb=" O GLU J 57 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN J 67 " --> pdb=" O VAL J 63 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL J 68 " --> pdb=" O ALA J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 91 through 111 removed outlier: 3.826A pdb=" N LYS J 109 " --> pdb=" O GLU J 105 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ARG J 110 " --> pdb=" O ALA J 106 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N GLY J 111 " --> pdb=" O ALA J 107 " (cutoff:3.500A) Processing helix chain 'J' and resid 114 through 129 removed outlier: 3.548A pdb=" N ARG J 118 " --> pdb=" O SER J 114 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 148 removed outlier: 3.516A pdb=" N GLU J 145 " --> pdb=" O HIS J 141 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA J 146 " --> pdb=" O ARG J 142 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASN J 147 " --> pdb=" O MET J 143 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N LYS J 148 " --> pdb=" O ALA J 144 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 20 removed outlier: 3.730A pdb=" N ASP K 8 " --> pdb=" O ASP K 4 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 43 Processing helix chain 'K' and resid 111 through 119 Processing helix chain 'L' and resid 33 through 38 removed outlier: 4.107A pdb=" N PHE L 38 " --> pdb=" O LEU L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 55 removed outlier: 4.486A pdb=" N ARG L 48 " --> pdb=" O ARG L 44 " (cutoff:3.500A) Proline residue: L 50 - end of helix removed outlier: 4.063A pdb=" N LEU L 53 " --> pdb=" O GLN L 49 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N VAL L 54 " --> pdb=" O PRO L 50 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASP L 55 " --> pdb=" O LEU L 51 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 61 removed outlier: 5.112A pdb=" N LEU L 60 " --> pdb=" O MET L 56 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ASP L 61 " --> pdb=" O VAL L 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 56 through 61' Processing helix chain 'L' and resid 70 through 86 Processing helix chain 'L' and resid 90 through 101 removed outlier: 5.286A pdb=" N GLU L 96 " --> pdb=" O SER L 92 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA L 100 " --> pdb=" O GLU L 96 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY L 101 " --> pdb=" O LEU L 97 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 33 removed outlier: 3.519A pdb=" N ILE M 18 " --> pdb=" O ASP M 14 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLN M 20 " --> pdb=" O ARG M 16 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N THR M 32 " --> pdb=" O THR M 28 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 91 removed outlier: 5.475A pdb=" N ARG M 89 " --> pdb=" O ASP M 85 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU M 90 " --> pdb=" O ALA M 86 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ASP M 91 " --> pdb=" O LEU M 87 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 50 removed outlier: 3.656A pdb=" N SER N 49 " --> pdb=" O THR N 45 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLY N 50 " --> pdb=" O ALA N 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 45 through 50' Processing helix chain 'N' and resid 53 through 58 removed outlier: 4.157A pdb=" N SER N 57 " --> pdb=" O GLY N 53 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N THR N 58 " --> pdb=" O SER N 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 53 through 58' Processing helix chain 'N' and resid 59 through 74 removed outlier: 3.892A pdb=" N ASP N 71 " --> pdb=" O GLU N 67 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ALA N 72 " --> pdb=" O ARG N 68 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N VAL N 73 " --> pdb=" O CYS N 69 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LYS N 74 " --> pdb=" O ALA N 70 " (cutoff:3.500A) Processing helix chain 'N' and resid 92 through 103 removed outlier: 4.164A pdb=" N ILE N 96 " --> pdb=" O ARG N 92 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ALA N 98 " --> pdb=" O SER N 94 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU N 99 " --> pdb=" O THR N 95 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLY N 103 " --> pdb=" O LEU N 99 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 10 removed outlier: 3.621A pdb=" N LEU O 6 " --> pdb=" O THR O 2 " (cutoff:3.500A) Proline residue: O 10 - end of helix Processing helix chain 'O' and resid 112 through 117 removed outlier: 4.534A pdb=" N TYR O 116 " --> pdb=" O ALA O 112 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLY O 117 " --> pdb=" O ARG O 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 112 through 117' Processing helix chain 'P' and resid 13 through 21 removed outlier: 3.575A pdb=" N SER P 20 " --> pdb=" O ILE P 16 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE P 21 " --> pdb=" O ALA P 17 " (cutoff:3.500A) Processing helix chain 'P' and resid 25 through 37 removed outlier: 3.603A pdb=" N SER P 29 " --> pdb=" O GLY P 25 " (cutoff:3.500A) Processing helix chain 'P' and resid 43 through 48 removed outlier: 4.991A pdb=" N SER P 48 " --> pdb=" O ILE P 44 " (cutoff:3.500A) Processing helix chain 'P' and resid 49 through 63 removed outlier: 4.183A pdb=" N THR P 54 " --> pdb=" O GLY P 50 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LYS P 61 " --> pdb=" O ASP P 57 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N PHE P 62 " --> pdb=" O GLU P 58 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N VAL P 63 " --> pdb=" O VAL P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 65 through 83 removed outlier: 3.778A pdb=" N GLY P 83 " --> pdb=" O LEU P 79 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 93 Processing helix chain 'P' and resid 105 through 110 removed outlier: 3.654A pdb=" N LYS P 109 " --> pdb=" O ALA P 105 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 20 removed outlier: 3.750A pdb=" N LYS Q 6 " --> pdb=" O LYS Q 2 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 29 removed outlier: 4.911A pdb=" N LEU Q 26 " --> pdb=" O LYS Q 22 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LYS Q 27 " --> pdb=" O ARG Q 23 " (cutoff:3.500A) Processing helix chain 'Q' and resid 38 through 52 removed outlier: 4.177A pdb=" N TRP Q 42 " --> pdb=" O ASP Q 38 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLN Q 49 " --> pdb=" O VAL Q 45 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N THR Q 50 " --> pdb=" O LEU Q 46 " (cutoff:3.500A) Proline residue: Q 52 - end of helix Processing helix chain 'Q' and resid 80 through 91 Processing helix chain 'R' and resid 3 through 15 Processing helix chain 'R' and resid 23 through 42 removed outlier: 5.151A pdb=" N GLY R 40 " --> pdb=" O ASN R 36 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N HIS R 41 " --> pdb=" O HIS R 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 73 removed outlier: 3.906A pdb=" N ARG R 52 " --> pdb=" O ASP R 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 74 through 85 Processing helix chain 'S' and resid 53 through 64 removed outlier: 3.995A pdb=" N ILE S 57 " --> pdb=" O ASP S 53 " (cutoff:3.500A) Processing helix chain 'S' and resid 68 through 79 Processing helix chain 'U' and resid 11 through 17 removed outlier: 6.391A pdb=" N GLU U 15 " --> pdb=" O ARG U 11 " (cutoff:3.500A) Processing helix chain 'U' and resid 24 through 33 removed outlier: 3.812A pdb=" N LEU U 28 " --> pdb=" O ASP U 24 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE U 32 " --> pdb=" O LEU U 28 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N THR U 33 " --> pdb=" O LYS U 29 " (cutoff:3.500A) Processing helix chain 'U' and resid 40 through 45 removed outlier: 4.116A pdb=" N THR U 44 " --> pdb=" O PRO U 40 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY U 45 " --> pdb=" O SER U 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 40 through 45' Processing helix chain 'U' and resid 47 through 65 removed outlier: 3.511A pdb=" N GLN U 51 " --> pdb=" O ARG U 47 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU U 64 " --> pdb=" O ARG U 60 " (cutoff:3.500A) Processing helix chain 'V' and resid 11 through 25 Processing helix chain 'V' and resid 69 through 75 removed outlier: 4.787A pdb=" N PHE V 73 " --> pdb=" O LYS V 69 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA V 74 " --> pdb=" O LEU V 70 " (cutoff:3.500A) Proline residue: V 75 - end of helix No H-bonds generated for 'chain 'V' and resid 69 through 75' Processing helix chain 'W' and resid 6 through 41 removed outlier: 4.732A pdb=" N ALA W 10 " --> pdb=" O ALA W 6 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE W 11 " --> pdb=" O LYS W 7 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG W 23 " --> pdb=" O HIS W 19 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA W 37 " --> pdb=" O LYS W 33 " (cutoff:3.500A) Processing helix chain 'W' and resid 43 through 64 Proline residue: W 55 - end of helix removed outlier: 3.979A pdb=" N GLY W 64 " --> pdb=" O GLN W 60 " (cutoff:3.500A) Processing helix chain 'W' and resid 67 through 86 removed outlier: 6.392A pdb=" N ALA W 71 " --> pdb=" O HIS W 67 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA W 72 " --> pdb=" O LYS W 68 " (cutoff:3.500A) Processing helix chain 'X' and resid 17 through 22 Processing helix chain 'X' and resid 24 through 32 removed outlier: 4.480A pdb=" N LEU X 28 " --> pdb=" O LYS X 24 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU X 30 " --> pdb=" O GLY X 26 " (cutoff:3.500A) Processing helix chain 'X' and resid 38 through 61 removed outlier: 3.908A pdb=" N THR X 42 " --> pdb=" O GLU X 38 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ARG X 61 " --> pdb=" O LYS X 57 " (cutoff:3.500A) Processing helix chain 'a' and resid 9 through 15 removed outlier: 3.593A pdb=" N ARG a 13 " --> pdb=" O SER a 9 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N HIS a 14 " --> pdb=" O PRO a 10 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N VAL a 15 " --> pdb=" O GLY a 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 9 through 15' Processing helix chain 'a' and resid 29 through 34 removed outlier: 4.231A pdb=" N LEU a 33 " --> pdb=" O PHE a 29 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLU a 34 " --> pdb=" O ALA a 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 29 through 34' Processing helix chain 'a' and resid 130 through 135 removed outlier: 4.089A pdb=" N ILE a 134 " --> pdb=" O PRO a 130 " (cutoff:3.500A) Proline residue: a 135 - end of helix No H-bonds generated for 'chain 'a' and resid 130 through 135' Processing helix chain 'a' and resid 196 through 202 removed outlier: 4.914A pdb=" N MET a 200 " --> pdb=" O ASN a 196 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LEU a 201 " --> pdb=" O ALA a 197 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG a 202 " --> pdb=" O GLU a 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 196 through 202' Processing helix chain 'a' and resid 206 through 214 removed outlier: 4.256A pdb=" N ALA a 210 " --> pdb=" O LYS a 206 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG a 211 " --> pdb=" O ALA a 207 " (cutoff:3.500A) Processing helix chain 'a' and resid 220 through 225 removed outlier: 4.053A pdb=" N MET a 224 " --> pdb=" O ARG a 220 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ASN a 225 " --> pdb=" O GLY a 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 220 through 225' Processing helix chain 'a' and resid 259 through 267 removed outlier: 6.526A pdb=" N ASP a 263 " --> pdb=" O ASN a 259 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N LYS a 264 " --> pdb=" O LYS a 260 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N PHE a 265 " --> pdb=" O ARG a 261 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N VAL a 267 " --> pdb=" O ASP a 263 " (cutoff:3.500A) Processing helix chain 'b' and resid 56 through 61 removed outlier: 5.853A pdb=" N THR b 61 " --> pdb=" O ALA b 57 " (cutoff:3.500A) Processing helix chain 'b' and resid 62 through 72 removed outlier: 4.749A pdb=" N ALA b 71 " --> pdb=" O HIS b 67 " (cutoff:3.500A) Processing helix chain 'b' and resid 98 through 103 removed outlier: 4.019A pdb=" N ALA b 102 " --> pdb=" O VAL b 98 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ASP b 103 " --> pdb=" O GLU b 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 98 through 103' Processing helix chain 'b' and resid 120 through 125 Processing helix chain 'c' and resid 15 through 20 Processing helix chain 'c' and resid 24 through 41 removed outlier: 3.929A pdb=" N VAL c 28 " --> pdb=" O ASN c 24 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL c 33 " --> pdb=" O HIS c 29 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA c 34 " --> pdb=" O GLN c 30 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA c 39 " --> pdb=" O TYR c 35 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N GLN c 41 " --> pdb=" O ALA c 37 " (cutoff:3.500A) Processing helix chain 'c' and resid 97 through 116 removed outlier: 4.058A pdb=" N LYS c 106 " --> pdb=" O ARG c 102 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER c 107 " --> pdb=" O GLY c 103 " (cutoff:3.500A) Processing helix chain 'c' and resid 130 through 142 removed outlier: 3.689A pdb=" N ASP c 140 " --> pdb=" O GLN c 136 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET c 141 " --> pdb=" O LYS c 137 " (cutoff:3.500A) Processing helix chain 'c' and resid 154 through 164 removed outlier: 3.584A pdb=" N PHE c 158 " --> pdb=" O ASP c 154 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU c 159 " --> pdb=" O GLU c 155 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ALA c 160 " --> pdb=" O ASN c 156 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN c 163 " --> pdb=" O LEU c 159 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LEU c 164 " --> pdb=" O ALA c 160 " (cutoff:3.500A) Processing helix chain 'c' and resid 176 through 184 removed outlier: 3.779A pdb=" N LEU c 180 " --> pdb=" O ASP c 176 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE c 183 " --> pdb=" O SER c 179 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ASP c 184 " --> pdb=" O LEU c 180 " (cutoff:3.500A) Processing helix chain 'c' and resid 189 through 201 removed outlier: 3.630A pdb=" N VAL c 196 " --> pdb=" O ALA c 192 " (cutoff:3.500A) Processing helix chain 'd' and resid 1 through 20 removed outlier: 3.647A pdb=" N TYR d 6 " --> pdb=" O LYS d 2 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS d 8 " --> pdb=" O HIS d 4 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP d 9 " --> pdb=" O ASP d 5 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N VAL d 12 " --> pdb=" O LYS d 8 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS d 13 " --> pdb=" O ASP d 9 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLU d 18 " --> pdb=" O LYS d 14 " (cutoff:3.500A) Processing helix chain 'd' and resid 41 through 46 Processing helix chain 'd' and resid 47 through 60 removed outlier: 3.684A pdb=" N ALA d 52 " --> pdb=" O LEU d 48 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP d 55 " --> pdb=" O ASN d 51 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU d 56 " --> pdb=" O ALA d 52 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA d 57 " --> pdb=" O ALA d 53 " (cutoff:3.500A) Processing helix chain 'd' and resid 92 through 110 removed outlier: 3.866A pdb=" N TRP d 96 " --> pdb=" O GLY d 92 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU d 97 " --> pdb=" O GLU d 93 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ILE d 105 " --> pdb=" O ARG d 101 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL d 107 " --> pdb=" O ILE d 103 " (cutoff:3.500A) Proline residue: d 108 - end of helix Processing helix chain 'd' and resid 161 through 173 removed outlier: 3.713A pdb=" N ARG d 166 " --> pdb=" O ASP d 162 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP d 173 " --> pdb=" O LEU d 169 " (cutoff:3.500A) Processing helix chain 'd' and resid 133 through 138 removed outlier: 4.038A pdb=" N ILE d 136 " --> pdb=" O GLU d 133 " (cutoff:3.500A) Proline residue: d 138 - end of helix Processing helix chain 'e' and resid 1 through 7 removed outlier: 4.053A pdb=" N ALA e 6 " --> pdb=" O ARG e 2 " (cutoff:3.500A) Proline residue: e 7 - end of helix Processing helix chain 'e' and resid 59 through 80 removed outlier: 3.713A pdb=" N THR e 66 " --> pdb=" O ALA e 62 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA e 67 " --> pdb=" O GLN e 63 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASN e 72 " --> pdb=" O ARG e 68 " (cutoff:3.500A) Processing helix chain 'e' and resid 136 through 152 removed outlier: 3.612A pdb=" N ILE e 140 " --> pdb=" O ASP e 136 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY e 141 " --> pdb=" O LYS e 137 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN e 142 " --> pdb=" O GLN e 138 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ARG e 151 " --> pdb=" O LEU e 147 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG e 152 " --> pdb=" O ARG e 148 " (cutoff:3.500A) Processing helix chain 'f' and resid 22 through 27 Processing helix chain 'f' and resid 29 through 34 removed outlier: 3.691A pdb=" N GLN f 33 " --> pdb=" O PHE f 29 " (cutoff:3.500A) Processing helix chain 'f' and resid 40 through 50 removed outlier: 4.236A pdb=" N ILE f 44 " --> pdb=" O THR f 40 " (cutoff:3.500A) Processing helix chain 'f' and resid 54 through 74 removed outlier: 3.535A pdb=" N LEU f 58 " --> pdb=" O LEU f 54 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA f 59 " --> pdb=" O GLU f 55 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU f 60 " --> pdb=" O ALA f 56 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL f 61 " --> pdb=" O LYS f 57 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N LEU f 62 " --> pdb=" O LEU f 58 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ALA f 63 " --> pdb=" O ALA f 59 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA f 64 " --> pdb=" O GLU f 60 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA f 67 " --> pdb=" O ALA f 63 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU f 70 " --> pdb=" O ASN f 66 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASN f 73 " --> pdb=" O ALA f 69 " (cutoff:3.500A) Processing helix chain 'f' and resid 95 through 107 removed outlier: 3.808A pdb=" N ALA f 106 " --> pdb=" O ALA f 102 " (cutoff:3.500A) Processing helix chain 'g' and resid 19 through 31 removed outlier: 3.704A pdb=" N VAL g 23 " --> pdb=" O PRO g 19 " (cutoff:3.500A) Proline residue: g 25 - end of helix removed outlier: 4.590A pdb=" N GLY g 28 " --> pdb=" O GLY g 24 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN g 30 " --> pdb=" O ALA g 26 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLY g 31 " --> pdb=" O LEU g 27 " (cutoff:3.500A) Processing helix chain 'g' and resid 36 through 49 removed outlier: 4.347A pdb=" N ALA g 40 " --> pdb=" O GLU g 36 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE g 41 " --> pdb=" O PHE g 37 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASN g 42 " --> pdb=" O CYS g 38 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA g 43 " --> pdb=" O LYS g 39 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS g 44 " --> pdb=" O ALA g 40 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER g 47 " --> pdb=" O ALA g 43 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILE g 48 " --> pdb=" O LYS g 44 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU g 49 " --> pdb=" O THR g 45 " (cutoff:3.500A) Processing helix chain 'g' and resid 74 through 79 Processing helix chain 'g' and resid 101 through 112 removed outlier: 3.877A pdb=" N LEU g 105 " --> pdb=" O SER g 101 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N GLU g 107 " --> pdb=" O ALA g 103 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE g 108 " --> pdb=" O GLN g 104 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN g 110 " --> pdb=" O GLN g 106 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N THR g 111 " --> pdb=" O GLU g 107 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS g 112 " --> pdb=" O ILE g 108 " (cutoff:3.500A) Processing helix chain 'g' and resid 120 through 136 removed outlier: 3.801A pdb=" N THR g 125 " --> pdb=" O ILE g 121 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ARG g 126 " --> pdb=" O GLU g 122 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER g 127 " --> pdb=" O ALA g 123 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE g 128 " --> pdb=" O MET g 124 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N THR g 131 " --> pdb=" O SER g 127 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N MET g 135 " --> pdb=" O THR g 131 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLY g 136 " --> pdb=" O ALA g 132 " (cutoff:3.500A) Processing helix chain 'h' and resid 24 through 38 removed outlier: 4.361A pdb=" N GLU h 31 " --> pdb=" O ARG h 27 " (cutoff:3.500A) Processing helix chain 'h' and resid 67 through 72 Processing helix chain 'h' and resid 88 through 96 Processing helix chain 'h' and resid 97 through 110 removed outlier: 4.251A pdb=" N ILE h 101 " --> pdb=" O PRO h 97 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LYS h 106 " --> pdb=" O GLU h 102 " (cutoff:3.500A) Proline residue: h 110 - end of helix Processing helix chain 'h' and resid 112 through 123 removed outlier: 3.515A pdb=" N LYS h 121 " --> pdb=" O ALA h 117 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU h 122 " --> pdb=" O MET h 118 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N LYS h 123 " --> pdb=" O PHE h 119 " (cutoff:3.500A) Processing helix chain 'i' and resid 104 through 109 removed outlier: 4.187A pdb=" N ARG i 108 " --> pdb=" O THR i 104 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N SER i 109 " --> pdb=" O ARG i 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 104 through 109' Processing helix chain 'i' and resid 112 through 119 removed outlier: 3.644A pdb=" N ILE i 116 " --> pdb=" O PHE i 112 " (cutoff:3.500A) Processing helix chain 'j' and resid 56 through 62 Proline residue: j 62 - end of helix Processing helix chain 'j' and resid 70 through 75 removed outlier: 4.127A pdb=" N THR j 74 " --> pdb=" O LYS j 70 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N ALA j 75 " --> pdb=" O ALA j 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 70 through 75' Processing helix chain 'j' and resid 78 through 85 removed outlier: 3.872A pdb=" N LEU j 82 " --> pdb=" O ARG j 78 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA j 83 " --> pdb=" O LEU j 79 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LYS j 84 " --> pdb=" O SER j 80 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL j 85 " --> pdb=" O ASP j 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 78 through 85' Processing helix chain 'j' and resid 91 through 99 removed outlier: 4.021A pdb=" N LEU j 95 " --> pdb=" O ASP j 91 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ALA j 97 " --> pdb=" O ASN j 93 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA j 98 " --> pdb=" O THR j 94 " (cutoff:3.500A) Processing helix chain 'j' and resid 128 through 139 removed outlier: 5.884A pdb=" N ARG j 132 " --> pdb=" O THR j 128 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA j 138 " --> pdb=" O ALA j 134 " (cutoff:3.500A) Processing helix chain 'k' and resid 42 through 58 removed outlier: 3.724A pdb=" N ALA k 52 " --> pdb=" O ALA k 48 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL k 57 " --> pdb=" O MET k 53 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS k 58 " --> pdb=" O THR k 54 " (cutoff:3.500A) Processing helix chain 'k' and resid 109 through 125 removed outlier: 3.925A pdb=" N GLU k 115 " --> pdb=" O GLU k 111 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA k 116 " --> pdb=" O LEU k 112 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA k 122 " --> pdb=" O LYS k 118 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS k 123 " --> pdb=" O LEU k 119 " (cutoff:3.500A) Proline residue: k 125 - end of helix Processing helix chain 'l' and resid 13 through 32 removed outlier: 4.107A pdb=" N PHE l 21 " --> pdb=" O ARG l 17 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG l 22 " --> pdb=" O GLN l 18 " (cutoff:3.500A) Processing helix chain 'l' and resid 38 through 57 removed outlier: 4.628A pdb=" N ARG l 46 " --> pdb=" O LYS l 42 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N VAL l 47 " --> pdb=" O GLU l 43 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU l 49 " --> pdb=" O ARG l 45 " (cutoff:3.500A) Proline residue: l 50 - end of helix removed outlier: 4.880A pdb=" N THR l 57 " --> pdb=" O THR l 53 " (cutoff:3.500A) Processing helix chain 'l' and resid 59 through 71 removed outlier: 3.506A pdb=" N ARG l 63 " --> pdb=" O SER l 59 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THR l 70 " --> pdb=" O ALA l 66 " (cutoff:3.500A) Processing helix chain 'l' and resid 72 through 82 removed outlier: 3.796A pdb=" N VAL l 76 " --> pdb=" O ASP l 72 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE l 80 " --> pdb=" O VAL l 76 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASN l 81 " --> pdb=" O ALA l 77 " (cutoff:3.500A) Processing helix chain 'l' and resid 83 through 88 removed outlier: 3.697A pdb=" N ALA l 88 " --> pdb=" O GLY l 84 " (cutoff:3.500A) Processing helix chain 'm' and resid 3 through 22 removed outlier: 3.726A pdb=" N ARG m 7 " --> pdb=" O LYS m 3 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE m 8 " --> pdb=" O LYS m 4 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG m 13 " --> pdb=" O ARG m 9 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ALA m 14 " --> pdb=" O ARG m 10 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG m 15 " --> pdb=" O ALA m 11 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU m 21 " --> pdb=" O LYS m 17 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY m 22 " --> pdb=" O LEU m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 55 through 63 removed outlier: 4.160A pdb=" N GLU m 60 " --> pdb=" O LYS m 56 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N GLN m 61 " --> pdb=" O ALA m 57 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU m 62 " --> pdb=" O ILE m 58 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N LYS m 63 " --> pdb=" O ALA m 59 " (cutoff:3.500A) Processing helix chain 'm' and resid 67 through 86 removed outlier: 3.664A pdb=" N LYS m 76 " --> pdb=" O ALA m 72 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU m 83 " --> pdb=" O ALA m 79 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY m 86 " --> pdb=" O ALA m 82 " (cutoff:3.500A) Processing helix chain 'm' and resid 101 through 114 removed outlier: 3.577A pdb=" N ALA m 109 " --> pdb=" O ALA m 105 " (cutoff:3.500A) Processing helix chain 'n' and resid 1 through 13 removed outlier: 4.071A pdb=" N GLN n 9 " --> pdb=" O LYS n 5 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N GLU n 10 " --> pdb=" O GLN n 6 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLN n 11 " --> pdb=" O LEU n 7 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N LYS n 13 " --> pdb=" O GLN n 9 " (cutoff:3.500A) Processing helix chain 'n' and resid 96 through 103 removed outlier: 4.488A pdb=" N ARG n 100 " --> pdb=" O LEU n 96 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N GLU n 101 " --> pdb=" O TYR n 97 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ARG n 102 " --> pdb=" O TYR n 98 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N THR n 103 " --> pdb=" O LEU n 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 96 through 103' Processing helix chain 'o' and resid 5 through 21 removed outlier: 6.135A pdb=" N ALA o 9 " --> pdb=" O ARG o 5 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ARG o 10 " --> pdb=" O GLY o 6 " (cutoff:3.500A) Processing helix chain 'o' and resid 25 through 30 removed outlier: 3.782A pdb=" N ARG o 29 " --> pdb=" O GLY o 25 " (cutoff:3.500A) Processing helix chain 'o' and resid 38 through 60 removed outlier: 3.832A pdb=" N GLN o 43 " --> pdb=" O ILE o 39 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ARG o 50 " --> pdb=" O TYR o 46 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN o 51 " --> pdb=" O ARG o 47 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS o 53 " --> pdb=" O ARG o 49 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ARG o 54 " --> pdb=" O ARG o 50 " (cutoff:3.500A) Processing helix chain 'o' and resid 62 through 72 removed outlier: 3.521A pdb=" N ALA o 66 " --> pdb=" O ALA o 62 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA o 67 " --> pdb=" O ARG o 63 " (cutoff:3.500A) Processing helix chain 'o' and resid 74 through 86 Processing helix chain 'o' and resid 90 through 101 removed outlier: 3.548A pdb=" N PHE o 100 " --> pdb=" O ASP o 96 " (cutoff:3.500A) Processing helix chain 'o' and resid 102 through 117 removed outlier: 3.803A pdb=" N GLU o 110 " --> pdb=" O THR o 106 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LYS o 111 " --> pdb=" O ALA o 107 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA o 112 " --> pdb=" O LEU o 108 " (cutoff:3.500A) Processing helix chain 'q' and resid 13 through 25 removed outlier: 4.001A pdb=" N VAL q 20 " --> pdb=" O LYS q 16 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP q 22 " --> pdb=" O ARG q 18 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU q 23 " --> pdb=" O LEU q 19 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE q 24 " --> pdb=" O VAL q 20 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG q 25 " --> pdb=" O ALA q 21 " (cutoff:3.500A) Processing helix chain 'q' and resid 28 through 39 removed outlier: 3.628A pdb=" N ALA q 32 " --> pdb=" O LYS q 28 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU q 33 " --> pdb=" O VAL q 29 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR q 38 " --> pdb=" O ASP q 34 " (cutoff:3.500A) Processing helix chain 'q' and resid 41 through 61 removed outlier: 4.289A pdb=" N VAL q 45 " --> pdb=" O LYS q 41 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU q 46 " --> pdb=" O LYS q 42 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL q 50 " --> pdb=" O LEU q 46 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE q 55 " --> pdb=" O LEU q 51 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N HIS q 60 " --> pdb=" O ALA q 56 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASN q 61 " --> pdb=" O ASN q 57 " (cutoff:3.500A) Processing helix chain 'r' and resid 1 through 11 removed outlier: 3.530A pdb=" N LEU r 8 " --> pdb=" O GLU r 4 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU r 11 " --> pdb=" O LEU r 7 " (cutoff:3.500A) Processing helix chain 'r' and resid 17 through 26 Processing helix chain 'r' and resid 39 through 51 removed outlier: 3.702A pdb=" N ALA r 46 " --> pdb=" O GLU r 42 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE r 51 " --> pdb=" O VAL r 47 " (cutoff:3.500A) Processing helix chain 's' and resid 65 through 70 removed outlier: 4.386A pdb=" N VAL s 69 " --> pdb=" O GLN s 65 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ALA s 70 " --> pdb=" O VAL s 66 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 65 through 70' Processing helix chain 't' and resid 13 through 24 removed outlier: 4.351A pdb=" N ALA t 23 " --> pdb=" O ARG t 19 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASN t 24 " --> pdb=" O LEU t 20 " (cutoff:3.500A) Processing helix chain 't' and resid 43 through 53 removed outlier: 4.082A pdb=" N VAL t 47 " --> pdb=" O ASP t 43 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN t 49 " --> pdb=" O ASP t 45 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA t 52 " --> pdb=" O MET t 48 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N LYS t 53 " --> pdb=" O ASN t 49 " (cutoff:3.500A) Processing helix chain 't' and resid 54 through 59 Processing helix chain 'v' and resid 51 through 61 removed outlier: 3.723A pdb=" N MET v 55 " --> pdb=" O SER v 51 " (cutoff:3.500A) Processing helix chain 'v' and resid 62 through 74 removed outlier: 3.841A pdb=" N GLU v 69 " --> pdb=" O THR v 65 " (cutoff:3.500A) Processing helix chain 'w' and resid 1 through 6 Processing helix chain 'w' and resid 9 through 35 removed outlier: 3.742A pdb=" N LEU w 21 " --> pdb=" O GLU w 17 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG w 23 " --> pdb=" O LEU w 19 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLU w 24 " --> pdb=" O ASN w 20 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLN w 25 " --> pdb=" O LEU w 21 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N PHE w 26 " --> pdb=" O LEU w 22 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ASN w 27 " --> pdb=" O ARG w 23 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA w 33 " --> pdb=" O ARG w 29 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY w 35 " --> pdb=" O GLN w 31 " (cutoff:3.500A) Processing helix chain 'w' and resid 39 through 61 removed outlier: 5.109A pdb=" N LEU w 43 " --> pdb=" O GLN w 39 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS w 44 " --> pdb=" O SER w 40 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN w 45 " --> pdb=" O HIS w 41 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL w 46 " --> pdb=" O LEU w 42 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA w 51 " --> pdb=" O ARG w 47 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG w 52 " --> pdb=" O ARG w 48 " (cutoff:3.500A) Processing helix chain 'x' and resid 16 through 27 Processing helix chain 'x' and resid 40 through 51 removed outlier: 3.840A pdb=" N MET x 46 " --> pdb=" O ALA x 42 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA x 49 " --> pdb=" O GLY x 45 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL x 50 " --> pdb=" O MET x 46 " (cutoff:3.500A) Processing helix chain 'y' and resid 8 through 18 removed outlier: 3.878A pdb=" N ARG y 12 " --> pdb=" O THR y 8 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER y 17 " --> pdb=" O GLY y 13 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N HIS y 18 " --> pdb=" O MET y 14 " (cutoff:3.500A) Processing helix chain '0' and resid 8 through 16 removed outlier: 4.043A pdb=" N HIS 0 16 " --> pdb=" O ARG 0 12 " (cutoff:3.500A) Processing helix chain '0' and resid 17 through 24 removed outlier: 4.166A pdb=" N THR 0 24 " --> pdb=" O ALA 0 20 " (cutoff:3.500A) Processing helix chain '0' and resid 25 through 38 removed outlier: 3.588A pdb=" N LEU 0 31 " --> pdb=" O GLY 0 27 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA 0 32 " --> pdb=" O ARG 0 28 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG 0 33 " --> pdb=" O GLN 0 29 " (cutoff:3.500A) Processing helix chain '1' and resid 6 through 13 removed outlier: 3.764A pdb=" N ALA 1 10 " --> pdb=" O VAL 1 6 " (cutoff:3.500A) Processing helix chain '1' and resid 31 through 36 removed outlier: 4.609A pdb=" N LYS 1 35 " --> pdb=" O ILE 1 31 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ALA 1 36 " --> pdb=" O LEU 1 32 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 31 through 36' Processing helix chain '1' and resid 37 through 45 Proline residue: 1 45 - end of helix Processing helix chain '1' and resid 50 through 62 removed outlier: 4.007A pdb=" N GLY 1 55 " --> pdb=" O LYS 1 51 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N LEU 1 56 " --> pdb=" O GLY 1 52 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL 1 57 " --> pdb=" O ASP 1 53 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA 1 59 " --> pdb=" O GLY 1 55 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N CYS 1 60 " --> pdb=" O LEU 1 56 " (cutoff:3.500A) Proline residue: 1 62 - end of helix Processing helix chain '1' and resid 25 through 30 removed outlier: 4.676A pdb=" N LEU 1 28 " --> pdb=" O HIS 1 25 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ARG 1 29 " --> pdb=" O ALA 1 26 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N HIS 1 30 " --> pdb=" O ASN 1 27 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 25 through 30' Processing helix chain '2' and resid 30 through 35 removed outlier: 4.231A pdb=" N LYS 2 34 " --> pdb=" O GLU 2 30 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N GLN 2 35 " --> pdb=" O PRO 2 31 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 30 through 35' Processing helix chain '3' and resid 3 through 20 removed outlier: 4.246A pdb=" N ALA 3 10 " --> pdb=" O GLN 3 6 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ILE 3 11 " --> pdb=" O ASP 3 7 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER 3 16 " --> pdb=" O VAL 3 12 " (cutoff:3.500A) Processing helix chain '3' and resid 33 through 47 removed outlier: 3.748A pdb=" N LYS 3 37 " --> pdb=" O VAL 3 33 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU 3 40 " --> pdb=" O ASP 3 36 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ARG 3 42 " --> pdb=" O MET 3 38 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA 3 44 " --> pdb=" O GLU 3 40 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLY 3 45 " --> pdb=" O LEU 3 41 " (cutoff:3.500A) Processing helix chain '3' and resid 62 through 68 removed outlier: 3.699A pdb=" N GLY 3 66 " --> pdb=" O ARG 3 62 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N THR 3 67 " --> pdb=" O ALA 3 63 " (cutoff:3.500A) Proline residue: 3 68 - end of helix No H-bonds generated for 'chain '3' and resid 62 through 68' Processing helix chain '3' and resid 74 through 79 removed outlier: 3.595A pdb=" N GLY 3 78 " --> pdb=" O ASP 3 74 " (cutoff:3.500A) Proline residue: 3 79 - end of helix No H-bonds generated for 'chain '3' and resid 74 through 79' Processing helix chain '3' and resid 95 through 103 removed outlier: 3.715A pdb=" N PHE 3 99 " --> pdb=" O LEU 3 95 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA 3 100 " --> pdb=" O PHE 3 96 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS 3 101 " --> pdb=" O LYS 3 97 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA 3 102 " --> pdb=" O GLU 3 98 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ASN 3 103 " --> pdb=" O PHE 3 99 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 95 through 103' Processing helix chain '3' and resid 109 through 114 removed outlier: 6.109A pdb=" N ALA 3 112 " --> pdb=" O LYS 3 109 " (cutoff:3.500A) Processing helix chain '4' and resid 43 through 51 removed outlier: 4.568A pdb=" N LYS 4 47 " --> pdb=" O PHE 4 43 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP 4 50 " --> pdb=" O GLY 4 46 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N VAL 4 51 " --> pdb=" O LYS 4 47 " (cutoff:3.500A) Processing helix chain '4' and resid 55 through 65 removed outlier: 5.504A pdb=" N ARG 4 59 " --> pdb=" O GLY 4 55 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG 4 63 " --> pdb=" O ARG 4 59 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE 4 64 " --> pdb=" O PHE 4 60 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'E' and resid 30 through 33 removed outlier: 4.470A pdb=" N VAL E 37 " --> pdb=" O ALA E 33 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'E' and resid 88 through 91 removed outlier: 3.959A pdb=" N ILE E 163 " --> pdb=" O VAL E 69 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE E 183 " --> pdb=" O LEU E 160 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL E 162 " --> pdb=" O PHE E 183 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE E 185 " --> pdb=" O VAL E 162 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'F' and resid 18 through 21 removed outlier: 5.578A pdb=" N ASN F 18 " --> pdb=" O ILE F 54 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG F 58 " --> pdb=" O THR F 20 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'F' and resid 163 through 168 removed outlier: 3.589A pdb=" N GLY F 147 " --> pdb=" O PHE F 202 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ASP F 180 " --> pdb=" O LYS F 203 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'G' and resid 140 through 143 removed outlier: 4.086A pdb=" N GLY G 179 " --> pdb=" O VAL G 142 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'H' and resid 15 through 23 removed outlier: 4.067A pdb=" N ALA H 16 " --> pdb=" O LEU H 35 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS H 22 " --> pdb=" O ILE H 29 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE H 29 " --> pdb=" O LYS H 22 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLY H 50 " --> pdb=" O ALA H 34 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'H' and resid 82 through 87 removed outlier: 7.549A pdb=" N HIS H 82 " --> pdb=" O PRO H 97 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N VAL H 93 " --> pdb=" O GLY H 86 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG H 92 " --> pdb=" O TYR H 127 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N TYR H 127 " --> pdb=" O ARG H 92 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'I' and resid 39 through 42 removed outlier: 3.717A pdb=" N GLU I 40 " --> pdb=" O LEU I 61 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TRP I 42 " --> pdb=" O TYR I 59 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N TYR I 59 " --> pdb=" O TRP I 42 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ILE I 6 " --> pdb=" O MET I 62 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N HIS I 3 " --> pdb=" O THR I 92 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR I 92 " --> pdb=" O HIS I 3 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU I 5 " --> pdb=" O MET I 90 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET I 90 " --> pdb=" O GLU I 5 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'I' and resid 43 through 47 removed outlier: 5.898A pdb=" N LEU I 47 " --> pdb=" O HIS I 55 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N HIS I 55 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'J' and resid 72 through 78 Processing sheet with id= 11, first strand: chain 'K' and resid 22 through 28 removed outlier: 6.022A pdb=" N ALA K 22 " --> pdb=" O LEU K 62 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU K 57 " --> pdb=" O GLU K 51 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU K 51 " --> pdb=" O GLU K 57 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N THR K 61 " --> pdb=" O ASP K 47 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ASP K 47 " --> pdb=" O THR K 61 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'K' and resid 122 through 125 Processing sheet with id= 13, first strand: chain 'L' and resid 4 through 10 removed outlier: 4.400A pdb=" N GLY L 9 " --> pdb=" O ALA L 16 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA L 15 " --> pdb=" O LYS L 67 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS L 67 " --> pdb=" O ALA L 15 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'M' and resid 44 through 52 removed outlier: 3.521A pdb=" N VAL M 74 " --> pdb=" O ILE M 8 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ILE M 8 " --> pdb=" O VAL M 74 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'N' and resid 41 through 44 removed outlier: 3.857A pdb=" N GLY N 42 " --> pdb=" O ILE N 33 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ASN N 108 " --> pdb=" O LEU N 81 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N GLY N 87 " --> pdb=" O VAL N 112 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'O' and resid 28 through 31 removed outlier: 3.708A pdb=" N LYS O 29 " --> pdb=" O ILE O 81 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N LEU O 80 " --> pdb=" O VAL O 97 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'O' and resid 35 through 40 removed outlier: 4.711A pdb=" N ARG O 35 " --> pdb=" O ARG O 53 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N LYS O 50 " --> pdb=" O ILE O 66 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE O 66 " --> pdb=" O LYS O 50 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'S' and resid 4 through 10 removed outlier: 6.010A pdb=" N GLN S 18 " --> pdb=" O ALA S 7 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL S 19 " --> pdb=" O GLY S 37 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N GLY S 37 " --> pdb=" O VAL S 19 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N GLY S 49 " --> pdb=" O ASN S 40 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'T' and resid 6 through 10 removed outlier: 6.853A pdb=" N GLU T 59 " --> pdb=" O VAL T 75 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL T 75 " --> pdb=" O GLU T 59 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'T' and resid 19 through 29 No H-bonds generated for sheet with id= 20 Processing sheet with id= 21, first strand: chain 'V' and resid 29 through 33 removed outlier: 4.882A pdb=" N LEU V 30 " --> pdb=" O THR V 47 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N HIS V 51 " --> pdb=" O THR V 32 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N LEU V 46 " --> pdb=" O VAL V 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE V 48 " --> pdb=" O VAL V 59 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL V 59 " --> pdb=" O ILE V 48 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'a' and resid 1 through 4 Processing sheet with id= 23, first strand: chain 'a' and resid 74 through 77 removed outlier: 5.249A pdb=" N ASP a 113 " --> pdb=" O VAL a 77 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'a' and resid 79 through 82 removed outlier: 3.948A pdb=" N ARG a 79 " --> pdb=" O LEU a 92 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE a 90 " --> pdb=" O GLU a 81 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'a' and resid 137 through 140 removed outlier: 4.371A pdb=" N SER a 138 " --> pdb=" O ILE a 163 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN a 162 " --> pdb=" O ARG a 174 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N THR a 172 " --> pdb=" O VAL a 164 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU a 179 " --> pdb=" O LEU a 175 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'b' and resid 3 through 8 removed outlier: 4.484A pdb=" N SER b 199 " --> pdb=" O LYS b 8 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ASP b 200 " --> pdb=" O THR b 112 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N THR b 112 " --> pdb=" O ASP b 200 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY b 111 " --> pdb=" O VAL b 170 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLU b 168 " --> pdb=" O SER b 113 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'b' and resid 11 through 16 removed outlier: 3.792A pdb=" N THR b 12 " --> pdb=" O VAL b 24 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL b 20 " --> pdb=" O THR b 16 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG b 179 " --> pdb=" O LEU b 188 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'b' and resid 36 through 40 removed outlier: 3.510A pdb=" N GLN b 36 " --> pdb=" O GLN b 49 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU b 40 " --> pdb=" O TYR b 45 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N TYR b 45 " --> pdb=" O LEU b 40 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE b 48 " --> pdb=" O PHE b 82 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TRP b 80 " --> pdb=" O VAL b 50 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'b' and resid 105 through 108 removed outlier: 6.108A pdb=" N LYS b 105 " --> pdb=" O VAL b 177 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'c' and resid 1 through 5 removed outlier: 3.877A pdb=" N SER c 10 " --> pdb=" O LEU c 5 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'c' and resid 117 through 120 removed outlier: 3.599A pdb=" N VAL c 186 " --> pdb=" O ARG c 117 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS c 185 " --> pdb=" O ASP c 145 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL c 187 " --> pdb=" O LEU c 147 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE c 149 " --> pdb=" O VAL c 187 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP c 168 " --> pdb=" O VAL c 146 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'd' and resid 32 through 38 removed outlier: 3.574A pdb=" N CYS d 86 " --> pdb=" O MET d 37 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY d 85 " --> pdb=" O THR d 67 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'd' and resid 71 through 74 removed outlier: 5.337A pdb=" N SER d 72 " --> pdb=" O ARG d 79 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ARG d 79 " --> pdb=" O SER d 72 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA d 74 " --> pdb=" O LYS d 77 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'd' and resid 126 through 132 removed outlier: 4.256A pdb=" N LEU d 151 " --> pdb=" O VAL d 131 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'e' and resid 15 through 18 Processing sheet with id= 36, first strand: chain 'e' and resid 39 through 44 removed outlier: 7.586A pdb=" N ALA e 39 " --> pdb=" O ARG e 54 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG e 54 " --> pdb=" O ALA e 39 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'e' and resid 81 through 88 removed outlier: 5.968A pdb=" N THR e 128 " --> pdb=" O LEU e 88 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'e' and resid 93 through 97 removed outlier: 3.521A pdb=" N LEU e 104 " --> pdb=" O VAL e 112 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL e 112 " --> pdb=" O LEU e 104 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'f' and resid 2 through 6 removed outlier: 6.406A pdb=" N GLN f 2 " --> pdb=" O ALA f 39 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ALA f 39 " --> pdb=" O GLN f 2 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N LYS f 35 " --> pdb=" O LEU f 6 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'f' and resid 76 through 81 removed outlier: 4.939A pdb=" N GLU f 76 " --> pdb=" O LYS f 141 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE f 132 " --> pdb=" O ALA f 140 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'h' and resid 14 through 19 Processing sheet with id= 42, first strand: chain 'h' and resid 74 through 77 Processing sheet with id= 43, first strand: chain 'i' and resid 6 through 9 removed outlier: 3.758A pdb=" N THR i 6 " --> pdb=" O CYS i 21 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'i' and resid 39 through 43 removed outlier: 4.864A pdb=" N ASP i 56 " --> pdb=" O ILE i 43 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'i' and resid 63 through 66 No H-bonds generated for sheet with id= 45 Processing sheet with id= 46, first strand: chain 'i' and resid 68 through 71 removed outlier: 3.531A pdb=" N VAL i 69 " --> pdb=" O ILE i 77 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N SER i 75 " --> pdb=" O ARG i 71 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'k' and resid 63 through 66 removed outlier: 6.563A pdb=" N LEU k 102 " --> pdb=" O ARG k 66 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR k 103 " --> pdb=" O LEU k 33 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET k 105 " --> pdb=" O PHE k 31 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N SER k 30 " --> pdb=" O LYS k 133 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY k 32 " --> pdb=" O VAL k 131 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LYS k 127 " --> pdb=" O VAL k 36 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'l' and resid 33 through 36 removed outlier: 3.530A pdb=" N THR l 36 " --> pdb=" O ALA l 111 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET l 110 " --> pdb=" O CYS l 100 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'm' and resid 49 through 52 removed outlier: 4.283A pdb=" N VAL m 49 " --> pdb=" O VAL m 39 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER m 91 " --> pdb=" O THR m 24 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL m 28 " --> pdb=" O ASP m 93 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'n' and resid 37 through 44 removed outlier: 3.616A pdb=" N ARG n 38 " --> pdb=" O VAL n 31 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL n 31 " --> pdb=" O ARG n 38 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN n 40 " --> pdb=" O VAL n 29 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR n 24 " --> pdb=" O LYS n 86 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU n 26 " --> pdb=" O SER n 84 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS n 28 " --> pdb=" O SER n 82 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER n 82 " --> pdb=" O LYS n 28 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'n' and resid 48 through 52 removed outlier: 4.415A pdb=" N ALA n 48 " --> pdb=" O THR n 59 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ARG n 52 " --> pdb=" O HIS n 55 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N HIS n 55 " --> pdb=" O ARG n 52 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE n 58 " --> pdb=" O PHE n 73 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'p' and resid 11 through 15 removed outlier: 3.666A pdb=" N TYR p 2 " --> pdb=" O ALA p 42 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N MET p 40 " --> pdb=" O VAL p 4 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'p' and resid 18 through 21 removed outlier: 4.908A pdb=" N GLN p 18 " --> pdb=" O ILE p 98 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE p 98 " --> pdb=" O GLN p 18 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ASP p 95 " --> pdb=" O VAL p 64 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N LYS p 60 " --> pdb=" O THR p 99 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA p 61 " --> pdb=" O VAL p 33 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N VAL p 63 " --> pdb=" O GLU p 31 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLU p 31 " --> pdb=" O VAL p 63 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'p' and resid 57 through 60 No H-bonds generated for sheet with id= 54 Processing sheet with id= 55, first strand: chain 'p' and resid 66 through 72 removed outlier: 3.542A pdb=" N GLY p 67 " --> pdb=" O PHE p 93 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLN p 91 " --> pdb=" O GLY p 69 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LYS p 71 " --> pdb=" O HIS p 89 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N HIS p 89 " --> pdb=" O LYS p 71 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'q' and resid 74 through 88 No H-bonds generated for sheet with id= 56 Processing sheet with id= 57, first strand: chain 'r' and resid 12 through 15 removed outlier: 4.120A pdb=" N ALA r 13 " --> pdb=" O LYS r 33 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N HIS r 15 " --> pdb=" O VAL r 31 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N VAL r 31 " --> pdb=" O HIS r 15 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LYS r 81 " --> pdb=" O VAL r 34 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG r 77 " --> pdb=" O LYS r 66 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LYS r 66 " --> pdb=" O ARG r 77 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ASP r 79 " --> pdb=" O LYS r 64 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LYS r 64 " --> pdb=" O ASP r 79 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LYS r 81 " --> pdb=" O VAL r 62 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N VAL r 62 " --> pdb=" O LYS r 81 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ALA r 83 " --> pdb=" O THR r 60 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THR r 60 " --> pdb=" O ALA r 83 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N VAL r 85 " --> pdb=" O VAL r 58 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL r 58 " --> pdb=" O VAL r 85 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 's' and resid 39 through 44 removed outlier: 5.389A pdb=" N ASN s 39 " --> pdb=" O ALA s 62 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 's' and resid 82 through 86 Processing sheet with id= 60, first strand: chain 't' and resid 2 through 5 removed outlier: 3.797A pdb=" N VAL t 72 " --> pdb=" O LEU t 61 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 't' and resid 37 through 42 removed outlier: 3.791A pdb=" N ILE t 89 " --> pdb=" O PRO t 27 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'u' and resid 47 through 50 removed outlier: 3.994A pdb=" N PHE u 56 " --> pdb=" O GLY u 48 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N THR u 54 " --> pdb=" O GLY u 50 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'u' and resid 61 through 66 removed outlier: 3.588A pdb=" N SER u 77 " --> pdb=" O LYS u 64 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'v' and resid 11 through 18 removed outlier: 3.572A pdb=" N VAL v 12 " --> pdb=" O PHE v 28 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY v 14 " --> pdb=" O ARG v 26 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ASN v 22 " --> pdb=" O SER v 18 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'v' and resid 34 through 40 Processing sheet with id= 66, first strand: chain 'x' and resid 34 through 38 removed outlier: 3.678A pdb=" N LYS x 5 " --> pdb=" O GLU x 57 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N MET x 53 " --> pdb=" O THR x 9 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'z' and resid 19 through 23 removed outlier: 7.779A pdb=" N ILE z 47 " --> pdb=" O SER z 13 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU z 35 " --> pdb=" O TYR z 48 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain '1' and resid 21 through 24 removed outlier: 6.169A pdb=" N PHE 1 21 " --> pdb=" O VAL 1 49 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain '2' and resid 14 through 18 Processing sheet with id= 70, first strand: chain '3' and resid 23 through 28 Processing sheet with id= 71, first strand: chain '4' and resid 21 through 25 removed outlier: 3.933A pdb=" N SER 4 15 " --> pdb=" O LEU 4 32 " (cutoff:3.500A) 1617 hydrogen bonds defined for protein. 4785 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3691 hydrogen bonds 5920 hydrogen bond angles 0 basepair planarities 1459 basepair parallelities 2159 stacking parallelities Total time for adding SS restraints: 228.47 Time building geometry restraints manager: 73.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 12062 1.30 - 1.43: 71302 1.43 - 1.56: 66544 1.56 - 1.69: 9330 1.69 - 1.82: 286 Bond restraints: 159524 Sorted by residual: bond pdb=" C5 5MU Y1939 " pdb=" C6 5MU Y1939 " ideal model delta sigma weight residual 1.155 1.436 -0.281 2.00e-02 2.50e+03 1.97e+02 bond pdb=" C4 5MU Y1939 " pdb=" C5 5MU Y1939 " ideal model delta sigma weight residual 1.802 1.609 0.193 2.00e-02 2.50e+03 9.29e+01 bond pdb=" O3' 2MA Y2503 " pdb=" P PSU Y2504 " ideal model delta sigma weight residual 1.607 1.738 -0.131 1.50e-02 4.44e+03 7.64e+01 bond pdb=" C ALA c 128 " pdb=" N PRO c 129 " ideal model delta sigma weight residual 1.334 1.533 -0.199 2.34e-02 1.83e+03 7.21e+01 bond pdb=" C2 4OC D1402 " pdb=" N3 4OC D1402 " ideal model delta sigma weight residual 1.507 1.350 0.157 2.00e-02 2.50e+03 6.14e+01 ... (remaining 159519 not shown) Histogram of bond angle deviations from ideal: 92.32 - 101.63: 3157 101.63 - 110.94: 86736 110.94 - 120.25: 90328 120.25 - 129.56: 55297 129.56 - 138.87: 2982 Bond angle restraints: 238500 Sorted by residual: angle pdb=" N ASP C 43 " pdb=" CA ASP C 43 " pdb=" C ASP C 43 " ideal model delta sigma weight residual 111.28 123.30 -12.02 1.09e+00 8.42e-01 1.22e+02 angle pdb=" C1' 2MG D 966 " pdb=" N9 2MG D 966 " pdb=" C8 2MG D 966 " ideal model delta sigma weight residual 110.07 134.20 -24.13 3.00e+00 1.11e-01 6.47e+01 angle pdb=" O3' 2MA Y2503 " pdb=" P PSU Y2504 " pdb=" O5* PSU Y2504 " ideal model delta sigma weight residual 104.00 92.32 11.68 1.50e+00 4.44e-01 6.07e+01 angle pdb=" C1' 2MG Y2445 " pdb=" N9 2MG Y2445 " pdb=" C8 2MG Y2445 " ideal model delta sigma weight residual 110.07 132.84 -22.77 3.00e+00 1.11e-01 5.76e+01 angle pdb=" C1' 2MG D1516 " pdb=" N9 2MG D1516 " pdb=" C8 2MG D1516 " ideal model delta sigma weight residual 110.07 132.32 -22.25 3.00e+00 1.11e-01 5.50e+01 ... (remaining 238495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 89906 35.95 - 71.90: 10715 71.90 - 107.85: 1372 107.85 - 143.80: 72 143.80 - 179.75: 42 Dihedral angle restraints: 102107 sinusoidal: 85027 harmonic: 17080 Sorted by residual: dihedral pdb=" C5' G A 15 " pdb=" C4' G A 15 " pdb=" C3' G A 15 " pdb=" O3' G A 15 " ideal model delta sinusoidal sigma weight residual 82.00 -76.94 158.94 1 8.00e+00 1.56e-02 2.90e+02 dihedral pdb=" C4' A D 298 " pdb=" C3' A D 298 " pdb=" C2' A D 298 " pdb=" C1' A D 298 " ideal model delta sinusoidal sigma weight residual -35.00 33.98 -68.98 1 8.00e+00 1.56e-02 9.62e+01 dihedral pdb=" O4' G A 15 " pdb=" C4' G A 15 " pdb=" C3' G A 15 " pdb=" C2' G A 15 " ideal model delta sinusoidal sigma weight residual -35.00 31.30 -66.30 1 8.00e+00 1.56e-02 8.97e+01 ... (remaining 102104 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.028: 30374 1.028 - 2.056: 0 2.056 - 3.084: 0 3.084 - 4.112: 0 4.112 - 5.140: 3 Chirality restraints: 30377 Sorted by residual: chirality pdb=" C4' G A 15 " pdb=" C5' G A 15 " pdb=" O4' G A 15 " pdb=" C3' G A 15 " both_signs ideal model delta sigma weight residual False -2.50 2.64 -5.14 2.00e-01 2.50e+01 6.60e+02 chirality pdb=" C2' G A 15 " pdb=" C3' G A 15 " pdb=" O2' G A 15 " pdb=" C1' G A 15 " both_signs ideal model delta sigma weight residual False -2.75 2.34 -5.09 2.00e-01 2.50e+01 6.49e+02 chirality pdb=" C3' G A 15 " pdb=" C4' G A 15 " pdb=" O3' G A 15 " pdb=" C2' G A 15 " both_signs ideal model delta sigma weight residual False -2.48 2.01 -4.49 2.00e-01 2.50e+01 5.03e+02 ... (remaining 30374 not shown) Planarity restraints: 12889 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG D1516 " -0.054 2.00e-02 2.50e+03 6.23e-01 8.74e+03 pdb=" C4' 2MG D1516 " -0.479 2.00e-02 2.50e+03 pdb=" O4' 2MG D1516 " -0.828 2.00e-02 2.50e+03 pdb=" C3' 2MG D1516 " 0.587 2.00e-02 2.50e+03 pdb=" O3' 2MG D1516 " 0.594 2.00e-02 2.50e+03 pdb=" C2' 2MG D1516 " 0.238 2.00e-02 2.50e+03 pdb=" O2' 2MG D1516 " -0.888 2.00e-02 2.50e+03 pdb=" C1' 2MG D1516 " -0.172 2.00e-02 2.50e+03 pdb=" N9 2MG D1516 " 1.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC D1407 " -0.074 2.00e-02 2.50e+03 6.19e-01 8.62e+03 pdb=" C4' 5MC D1407 " -0.441 2.00e-02 2.50e+03 pdb=" O4' 5MC D1407 " -0.631 2.00e-02 2.50e+03 pdb=" C3' 5MC D1407 " 0.602 2.00e-02 2.50e+03 pdb=" O3' 5MC D1407 " 0.686 2.00e-02 2.50e+03 pdb=" C2' 5MC D1407 " 0.148 2.00e-02 2.50e+03 pdb=" O2' 5MC D1407 " -1.021 2.00e-02 2.50e+03 pdb=" C1' 5MC D1407 " -0.221 2.00e-02 2.50e+03 pdb=" N1 5MC D1407 " 0.951 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 7MG Y2069 " -0.068 2.00e-02 2.50e+03 6.15e-01 8.52e+03 pdb=" C4' 7MG Y2069 " -0.452 2.00e-02 2.50e+03 pdb=" O4' 7MG Y2069 " -0.673 2.00e-02 2.50e+03 pdb=" C3' 7MG Y2069 " 0.597 2.00e-02 2.50e+03 pdb=" O3' 7MG Y2069 " 0.655 2.00e-02 2.50e+03 pdb=" C2' 7MG Y2069 " 0.176 2.00e-02 2.50e+03 pdb=" O2' 7MG Y2069 " -0.984 2.00e-02 2.50e+03 pdb=" C1' 7MG Y2069 " -0.209 2.00e-02 2.50e+03 pdb=" N9 7MG Y2069 " 0.958 2.00e-02 2.50e+03 ... (remaining 12886 not shown) Histogram of nonbonded interaction distances: 0.61 - 1.47: 3 1.47 - 2.33: 689 2.33 - 3.18: 136774 3.18 - 4.04: 465843 4.04 - 4.90: 717242 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1320551 Sorted by model distance: nonbonded pdb=" O3' A B 76 " pdb=" O GLY C 46 " model vdw 0.612 3.040 nonbonded pdb=" N7 G A 27 " pdb=" NH1 ARG G 46 " model vdw 1.370 2.600 nonbonded pdb=" O2' A B 76 " pdb=" CA GLY C 46 " model vdw 1.432 3.440 nonbonded pdb=" O2' U A 25 " pdb=" O5' A A 26 " model vdw 1.508 2.440 nonbonded pdb=" O3' A B 76 " pdb=" C GLY C 46 " model vdw 1.543 3.270 ... (remaining 1320546 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.140 Extract box with map and model: 13.960 Check model and map are aligned: 1.590 Set scattering table: 1.000 Process input model: 528.290 Find NCS groups from input model: 3.110 Set up NCS constraints: 0.440 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: 0.040 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 553.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 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 : 0.004 0.281 159524 Z= 0.226 Angle : 0.665 24.125 238500 Z= 0.349 Chirality : 0.060 5.140 30377 Planarity : 0.020 0.623 12889 Dihedral : 23.406 179.746 91082 Min Nonbonded Distance : 0.612 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.58 % Allowed : 14.90 % Favored : 84.52 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -4.69 (0.08), residues: 5891 helix: -4.14 (0.07), residues: 1744 sheet: -2.52 (0.13), residues: 945 loop : -2.70 (0.09), residues: 3202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP a 212 HIS 0.009 0.001 HIS E 17 PHE 0.020 0.002 PHE S 16 TYR 0.025 0.002 TYR o 44 ARG 0.011 0.001 ARG X 34 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11782 Ramachandran restraints generated. 5891 Oldfield, 0 Emsley, 5891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11782 Ramachandran restraints generated. 5891 Oldfield, 0 Emsley, 5891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2111 residues out of total 4893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 2111 time to evaluate : 6.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 108 GLN cc_start: 0.9254 (mt0) cc_final: 0.9019 (mt0) REVERT: E 190 SER cc_start: 0.9381 (m) cc_final: 0.9110 (p) REVERT: F 19 SER cc_start: 0.9054 (m) cc_final: 0.8695 (p) REVERT: F 120 THR cc_start: 0.8870 (m) cc_final: 0.8412 (p) REVERT: F 124 GLU cc_start: 0.8400 (mp0) cc_final: 0.7862 (mp0) REVERT: G 197 HIS cc_start: 0.7888 (t-90) cc_final: 0.7366 (t70) REVERT: H 11 GLN cc_start: 0.9007 (tt0) cc_final: 0.8805 (pt0) REVERT: H 81 GLN cc_start: 0.9441 (mm110) cc_final: 0.9122 (mm110) REVERT: H 104 ILE cc_start: 0.8743 (tp) cc_final: 0.8303 (pt) REVERT: I 40 GLU cc_start: 0.8087 (tt0) cc_final: 0.7746 (tt0) REVERT: I 72 ASP cc_start: 0.9345 (m-30) cc_final: 0.9115 (m-30) REVERT: K 26 MET cc_start: 0.9290 (ptp) cc_final: 0.8678 (ptm) REVERT: K 49 LYS cc_start: 0.8894 (mttp) cc_final: 0.8501 (ttpp) REVERT: K 110 MET cc_start: 0.9081 (ptp) cc_final: 0.8864 (ptp) REVERT: K 112 ASP cc_start: 0.9009 (p0) cc_final: 0.8686 (p0) REVERT: L 5 TYR cc_start: 0.8718 (m-80) cc_final: 0.8174 (m-10) REVERT: L 49 GLN cc_start: 0.9181 (pt0) cc_final: 0.8450 (pt0) REVERT: L 93 LEU cc_start: 0.8981 (mt) cc_final: 0.8574 (mt) REVERT: M 28 THR cc_start: 0.9376 (m) cc_final: 0.9132 (m) REVERT: M 36 VAL cc_start: 0.8800 (p) cc_final: 0.8550 (m) REVERT: M 82 LYS cc_start: 0.9255 (mmtm) cc_final: 0.9019 (pttm) REVERT: O 2 THR cc_start: 0.7598 (m) cc_final: 0.6476 (m) REVERT: P 80 MET cc_start: 0.9206 (mtm) cc_final: 0.8970 (mtp) REVERT: Q 13 VAL cc_start: 0.9255 (t) cc_final: 0.8961 (t) REVERT: Q 32 ASP cc_start: 0.6962 (t70) cc_final: 0.6380 (t70) REVERT: Q 33 VAL cc_start: 0.9131 (m) cc_final: 0.8884 (m) REVERT: R 34 GLN cc_start: 0.8847 (tp-100) cc_final: 0.8612 (tp-100) REVERT: T 47 ASP cc_start: 0.8113 (p0) cc_final: 0.7021 (p0) REVERT: V 15 LEU cc_start: 0.9338 (tp) cc_final: 0.9111 (tp) REVERT: X 18 PHE cc_start: 0.7780 (t80) cc_final: 0.7223 (t80) REVERT: X 27 VAL cc_start: 0.7789 (m) cc_final: 0.7584 (p) REVERT: X 44 ARG cc_start: 0.8841 (tpp-160) cc_final: 0.8548 (tpp-160) REVERT: a 20 ASN cc_start: 0.8462 (t0) cc_final: 0.7940 (t0) REVERT: b 28 GLU cc_start: 0.8582 (pt0) cc_final: 0.8355 (pm20) REVERT: b 81 GLU cc_start: 0.8940 (tt0) cc_final: 0.8729 (mm-30) REVERT: b 88 GLU cc_start: 0.7300 (pm20) cc_final: 0.6969 (pm20) REVERT: c 2 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8379 (mm-30) REVERT: c 195 GLN cc_start: 0.9241 (mt0) cc_final: 0.8974 (mp10) REVERT: e 87 GLN cc_start: 0.8976 (mt0) cc_final: 0.8709 (mt0) REVERT: e 138 GLN cc_start: 0.8315 (tp40) cc_final: 0.8067 (tp40) REVERT: e 163 TYR cc_start: 0.8886 (m-80) cc_final: 0.8641 (m-80) REVERT: f 137 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8537 (pt0) REVERT: g 12 VAL cc_start: 0.5580 (m) cc_final: 0.4667 (t) REVERT: g 50 LYS cc_start: 0.7460 (mtmm) cc_final: 0.7200 (ttpt) REVERT: g 69 VAL cc_start: 0.6448 (t) cc_final: 0.5639 (p) REVERT: h 49 ASP cc_start: 0.8236 (t0) cc_final: 0.7893 (t0) REVERT: h 96 ARG cc_start: 0.8945 (mmm160) cc_final: 0.8623 (mmm-85) REVERT: h 99 ARG cc_start: 0.9403 (mmm160) cc_final: 0.9017 (mmm-85) REVERT: i 82 ASN cc_start: 0.8957 (m-40) cc_final: 0.8756 (m-40) REVERT: i 104 THR cc_start: 0.9066 (m) cc_final: 0.8586 (t) REVERT: i 106 GLU cc_start: 0.9474 (mp0) cc_final: 0.9031 (mp0) REVERT: j 104 GLN cc_start: 0.9298 (mm110) cc_final: 0.8969 (mm-40) REVERT: k 47 GLU cc_start: 0.8920 (tm-30) cc_final: 0.7929 (tm-30) REVERT: k 68 PHE cc_start: 0.8352 (t80) cc_final: 0.8128 (t80) REVERT: m 76 LYS cc_start: 0.9503 (tttt) cc_final: 0.8836 (tptt) REVERT: m 85 LYS cc_start: 0.9426 (mmtm) cc_final: 0.9221 (mmmt) REVERT: m 104 GLN cc_start: 0.8984 (tt0) cc_final: 0.8784 (tt0) REVERT: m 108 ASP cc_start: 0.9078 (m-30) cc_final: 0.8743 (m-30) REVERT: n 39 LEU cc_start: 0.8933 (tp) cc_final: 0.8607 (tt) REVERT: n 65 ASN cc_start: 0.8413 (p0) cc_final: 0.8049 (p0) REVERT: p 99 THR cc_start: 0.8865 (p) cc_final: 0.8599 (p) REVERT: q 52 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8680 (tm-30) REVERT: r 50 LEU cc_start: 0.8097 (mp) cc_final: 0.7372 (mp) REVERT: s 7 ASP cc_start: 0.8769 (m-30) cc_final: 0.8331 (t0) REVERT: t 12 GLN cc_start: 0.8807 (pt0) cc_final: 0.8582 (pp30) REVERT: t 24 ASN cc_start: 0.9222 (m-40) cc_final: 0.8845 (t0) REVERT: t 41 GLU cc_start: 0.7660 (tm-30) cc_final: 0.6466 (tm-30) REVERT: t 45 ASP cc_start: 0.9394 (m-30) cc_final: 0.9161 (m-30) REVERT: t 60 VAL cc_start: 0.9229 (t) cc_final: 0.8641 (p) REVERT: u 53 HIS cc_start: 0.8815 (m170) cc_final: 0.8466 (m90) REVERT: v 16 ASN cc_start: 0.8658 (t0) cc_final: 0.8414 (t0) REVERT: v 67 LEU cc_start: 0.9208 (mp) cc_final: 0.9001 (mp) REVERT: w 39 GLN cc_start: 0.8955 (mt0) cc_final: 0.8709 (mm-40) REVERT: x 5 LYS cc_start: 0.9383 (mtpp) cc_final: 0.8795 (mtpp) REVERT: 0 26 ASN cc_start: 0.8741 (m110) cc_final: 0.8433 (m-40) REVERT: 4 38 SER cc_start: 0.8970 (p) cc_final: 0.8612 (m) outliers start: 0 outliers final: 0 residues processed: 2111 average time/residue: 1.3786 time to fit residues: 4868.8115 Evaluate side-chains 1346 residues out of total 4893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1346 time to evaluate : 6.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 878 optimal weight: 9.9990 chunk 788 optimal weight: 5.9990 chunk 437 optimal weight: 20.0000 chunk 269 optimal weight: 9.9990 chunk 531 optimal weight: 10.0000 chunk 421 optimal weight: 20.0000 chunk 815 optimal weight: 4.9990 chunk 315 optimal weight: 30.0000 chunk 495 optimal weight: 20.0000 chunk 606 optimal weight: 60.0000 chunk 944 optimal weight: 20.0000 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 ASN F 7 ASN G 130 ASN ** G 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 52 ASN K 3 GLN ** L 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 21 HIS ** N 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 63 GLN O 19 ASN O 76 HIS P 99 GLN ** Q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 34 GLN T 46 HIS W 12 GLN W 54 GLN b 134 HIS c 30 GLN c 90 GLN c 92 HIS c 94 GLN c 136 GLN ** e 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 114 HIS e 142 GLN f 128 HIS j 54 GLN k 3 GLN ** l 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 55 HIS ** s 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 49 ASN ** t 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 78 GLN u 36 GLN w 58 ASN y 18 HIS z 18 HIS Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 159524 Z= 0.307 Angle : 0.766 15.662 238500 Z= 0.404 Chirality : 0.038 0.423 30377 Planarity : 0.007 0.133 12889 Dihedral : 24.169 179.566 79389 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.05 % Favored : 91.58 % Rotamer: Outliers : 3.39 % Allowed : 14.98 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.10), residues: 5891 helix: -1.98 (0.10), residues: 1846 sheet: -1.87 (0.15), residues: 940 loop : -2.05 (0.10), residues: 3105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP e 61 HIS 0.009 0.002 HIS E 17 PHE 0.021 0.002 PHE X 18 TYR 0.030 0.002 TYR R 77 ARG 0.015 0.001 ARG g 64 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11782 Ramachandran restraints generated. 5891 Oldfield, 0 Emsley, 5891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11782 Ramachandran restraints generated. 5891 Oldfield, 0 Emsley, 5891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1717 residues out of total 4893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 1552 time to evaluate : 6.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 99 MET cc_start: 0.8619 (ptp) cc_final: 0.8415 (ptp) REVERT: E 121 GLN cc_start: 0.8892 (tm-30) cc_final: 0.8673 (pp30) REVERT: E 122 ASP cc_start: 0.8275 (p0) cc_final: 0.8050 (p0) REVERT: E 135 MET cc_start: 0.9120 (mtm) cc_final: 0.8891 (mtm) REVERT: E 190 SER cc_start: 0.9345 (m) cc_final: 0.9102 (p) REVERT: E 191 ASP cc_start: 0.9303 (OUTLIER) cc_final: 0.9046 (t0) REVERT: F 141 MET cc_start: 0.9378 (mmt) cc_final: 0.8234 (mmp) REVERT: G 203 TYR cc_start: 0.8885 (m-80) cc_final: 0.8434 (m-80) REVERT: H 53 ARG cc_start: 0.8642 (tpp-160) cc_final: 0.8434 (mtt-85) REVERT: I 5 GLU cc_start: 0.8046 (tt0) cc_final: 0.7798 (tt0) REVERT: I 61 LEU cc_start: 0.8721 (tp) cc_final: 0.8438 (tt) REVERT: I 88 MET cc_start: 0.8688 (ppp) cc_final: 0.8380 (tmm) REVERT: K 53 ASP cc_start: 0.8349 (p0) cc_final: 0.8013 (p0) REVERT: K 59 GLU cc_start: 0.8610 (pm20) cc_final: 0.8324 (pm20) REVERT: L 24 ASN cc_start: 0.8267 (p0) cc_final: 0.7985 (p0) REVERT: L 26 LYS cc_start: 0.8905 (ptpp) cc_final: 0.8512 (ptpp) REVERT: L 28 VAL cc_start: 0.8938 (t) cc_final: 0.8616 (p) REVERT: L 31 GLN cc_start: 0.9125 (mp10) cc_final: 0.8883 (mp10) REVERT: L 33 SER cc_start: 0.8959 (OUTLIER) cc_final: 0.8747 (p) REVERT: L 49 GLN cc_start: 0.9030 (pt0) cc_final: 0.8764 (pt0) REVERT: L 52 GLU cc_start: 0.8759 (mp0) cc_final: 0.8559 (mp0) REVERT: P 43 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8242 (tppp) REVERT: P 62 PHE cc_start: 0.7609 (t80) cc_final: 0.6716 (m-80) REVERT: P 77 LYS cc_start: 0.9451 (ttmm) cc_final: 0.8824 (tppp) REVERT: T 47 ASP cc_start: 0.8106 (p0) cc_final: 0.7660 (p0) REVERT: U 56 ARG cc_start: 0.9104 (mtt90) cc_final: 0.8863 (mtt90) REVERT: U 60 ARG cc_start: 0.8570 (mtm180) cc_final: 0.7906 (ttm170) REVERT: W 23 ARG cc_start: 0.8907 (mmm-85) cc_final: 0.8620 (mmm-85) REVERT: W 59 ARG cc_start: 0.9161 (ttm110) cc_final: 0.8682 (ttm-80) REVERT: X 34 ARG cc_start: 0.8170 (mmt180) cc_final: 0.7608 (mmt180) REVERT: X 44 ARG cc_start: 0.8832 (tpp-160) cc_final: 0.8541 (tpp-160) REVERT: c 195 GLN cc_start: 0.9306 (mt0) cc_final: 0.8840 (mt0) REVERT: d 26 GLN cc_start: 0.7999 (mt0) cc_final: 0.7733 (mp10) REVERT: e 87 GLN cc_start: 0.9080 (mt0) cc_final: 0.8800 (mt0) REVERT: e 142 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8520 (tp40) REVERT: g 58 ILE cc_start: 0.4325 (mt) cc_final: 0.4070 (mt) REVERT: g 85 ILE cc_start: 0.0429 (OUTLIER) cc_final: -0.0014 (pt) REVERT: g 124 MET cc_start: 0.2505 (mtm) cc_final: 0.2101 (mpp) REVERT: h 71 ASP cc_start: 0.8920 (m-30) cc_final: 0.8691 (m-30) REVERT: i 51 LYS cc_start: 0.8423 (mttt) cc_final: 0.8025 (mtmm) REVERT: i 59 LYS cc_start: 0.9288 (mttt) cc_final: 0.8915 (mttp) REVERT: i 104 THR cc_start: 0.9162 (m) cc_final: 0.8764 (t) REVERT: i 106 GLU cc_start: 0.9419 (mp0) cc_final: 0.9127 (mp0) REVERT: m 76 LYS cc_start: 0.9345 (tttt) cc_final: 0.8884 (tptt) REVERT: m 104 GLN cc_start: 0.8869 (tt0) cc_final: 0.8499 (tt0) REVERT: r 1 MET cc_start: 0.8044 (ptm) cc_final: 0.7488 (tmm) REVERT: t 24 ASN cc_start: 0.9338 (m-40) cc_final: 0.9034 (t0) REVERT: t 69 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7633 (tm-30) REVERT: v 43 LYS cc_start: 0.9340 (mmtm) cc_final: 0.9073 (mmtt) REVERT: w 1 MET cc_start: 0.8971 (ttt) cc_final: 0.7744 (tpp) REVERT: w 39 GLN cc_start: 0.9227 (mt0) cc_final: 0.8748 (mm-40) REVERT: y 51 ARG cc_start: 0.9021 (mtp85) cc_final: 0.8804 (ttp80) REVERT: z 7 LYS cc_start: 0.9253 (pttt) cc_final: 0.8979 (pttp) REVERT: 4 12 ILE cc_start: 0.9102 (pt) cc_final: 0.8568 (pt) REVERT: 4 24 ILE cc_start: 0.9350 (pt) cc_final: 0.9105 (mp) REVERT: 4 38 SER cc_start: 0.8733 (p) cc_final: 0.8359 (m) outliers start: 165 outliers final: 103 residues processed: 1616 average time/residue: 1.2971 time to fit residues: 3626.5621 Evaluate side-chains 1404 residues out of total 4893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 1296 time to evaluate : 6.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain I residue 52 ASN Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 55 HIS Chi-restraints excluded: chain J residue 148 LYS Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain L residue 33 SER Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 108 ASN Chi-restraints excluded: chain O residue 18 SER Chi-restraints excluded: chain O residue 26 CYS Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain P residue 19 THR Chi-restraints excluded: chain P residue 43 LYS Chi-restraints excluded: chain P residue 48 SER Chi-restraints excluded: chain P residue 67 ASP Chi-restraints excluded: chain Q residue 58 SER Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 55 ASP Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain T residue 56 ASP Chi-restraints excluded: chain T residue 60 ILE Chi-restraints excluded: chain U residue 20 ILE Chi-restraints excluded: chain U residue 24 ASP Chi-restraints excluded: chain U residue 32 ILE Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain V residue 3 SER Chi-restraints excluded: chain W residue 11 ILE Chi-restraints excluded: chain X residue 30 GLU Chi-restraints excluded: chain a residue 66 PHE Chi-restraints excluded: chain b residue 2 ILE Chi-restraints excluded: chain b residue 103 ASP Chi-restraints excluded: chain b residue 126 ASN Chi-restraints excluded: chain b residue 137 SER Chi-restraints excluded: chain b residue 174 SER Chi-restraints excluded: chain b residue 199 SER Chi-restraints excluded: chain c residue 77 ILE Chi-restraints excluded: chain c residue 155 GLU Chi-restraints excluded: chain d residue 22 ASN Chi-restraints excluded: chain d residue 39 VAL Chi-restraints excluded: chain d residue 51 ASN Chi-restraints excluded: chain d residue 89 THR Chi-restraints excluded: chain e residue 59 ASP Chi-restraints excluded: chain e residue 142 GLN Chi-restraints excluded: chain f residue 130 VAL Chi-restraints excluded: chain g residue 10 LEU Chi-restraints excluded: chain g residue 85 ILE Chi-restraints excluded: chain h residue 114 LEU Chi-restraints excluded: chain i residue 32 TYR Chi-restraints excluded: chain i residue 88 ASN Chi-restraints excluded: chain i residue 90 ASN Chi-restraints excluded: chain j residue 46 VAL Chi-restraints excluded: chain j residue 74 THR Chi-restraints excluded: chain j residue 90 VAL Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain k residue 3 GLN Chi-restraints excluded: chain k residue 46 ILE Chi-restraints excluded: chain k residue 74 THR Chi-restraints excluded: chain k residue 126 ILE Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 57 THR Chi-restraints excluded: chain l residue 97 ILE Chi-restraints excluded: chain l residue 117 ASP Chi-restraints excluded: chain m residue 115 LEU Chi-restraints excluded: chain o residue 17 LEU Chi-restraints excluded: chain o residue 28 SER Chi-restraints excluded: chain o residue 86 SER Chi-restraints excluded: chain p residue 10 LYS Chi-restraints excluded: chain p residue 19 THR Chi-restraints excluded: chain q residue 12 SER Chi-restraints excluded: chain q residue 13 SER Chi-restraints excluded: chain q residue 74 ILE Chi-restraints excluded: chain q residue 96 ILE Chi-restraints excluded: chain q residue 101 SER Chi-restraints excluded: chain r residue 78 SER Chi-restraints excluded: chain s residue 26 ASN Chi-restraints excluded: chain t residue 5 ASN Chi-restraints excluded: chain t residue 89 ILE Chi-restraints excluded: chain u residue 49 CYS Chi-restraints excluded: chain u residue 63 VAL Chi-restraints excluded: chain v residue 13 THR Chi-restraints excluded: chain v residue 64 ASP Chi-restraints excluded: chain x residue 9 THR Chi-restraints excluded: chain x residue 24 LEU Chi-restraints excluded: chain x residue 34 THR Chi-restraints excluded: chain z residue 4 ILE Chi-restraints excluded: chain z residue 21 THR Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain z residue 28 THR Chi-restraints excluded: chain 0 residue 4 THR Chi-restraints excluded: chain 0 residue 24 THR Chi-restraints excluded: chain 2 residue 3 VAL Chi-restraints excluded: chain 4 residue 22 MET Chi-restraints excluded: chain 4 residue 62 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 524 optimal weight: 20.0000 chunk 293 optimal weight: 6.9990 chunk 786 optimal weight: 8.9990 chunk 643 optimal weight: 20.0000 chunk 260 optimal weight: 5.9990 chunk 946 optimal weight: 0.9980 chunk 1022 optimal weight: 40.0000 chunk 842 optimal weight: 8.9990 chunk 938 optimal weight: 8.9990 chunk 322 optimal weight: 3.9990 chunk 759 optimal weight: 30.0000 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 57 ASN ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 7 ASN ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 GLN ** G 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 27 ASN K 3 GLN L 30 ASN L 49 GLN M 58 ASN ** N 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 63 GLN O 72 ASN P 99 GLN ** Q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 19 ASN ** X 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 152 GLN b 32 ASN b 134 HIS c 41 GLN c 115 GLN c 136 GLN e 142 GLN i 5 GLN j 104 GLN k 3 GLN ** l 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 43 GLN o 51 GLN ** o 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 6 GLN ** q 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 65 GLN v 15 ASN ** w 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 45 HIS 0 26 ASN 1 25 HIS 4 65 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 159524 Z= 0.222 Angle : 0.689 13.947 238500 Z= 0.370 Chirality : 0.036 0.426 30377 Planarity : 0.007 0.126 12889 Dihedral : 24.008 179.851 79389 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.30 % Favored : 91.31 % Rotamer: Outliers : 3.99 % Allowed : 17.62 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.10), residues: 5891 helix: -0.44 (0.12), residues: 1845 sheet: -1.41 (0.16), residues: 986 loop : -1.78 (0.11), residues: 3060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 42 HIS 0.018 0.001 HIS G 197 PHE 0.018 0.002 PHE 0 18 TYR 0.036 0.002 TYR l 112 ARG 0.007 0.001 ARG V 54 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11782 Ramachandran restraints generated. 5891 Oldfield, 0 Emsley, 5891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11782 Ramachandran restraints generated. 5891 Oldfield, 0 Emsley, 5891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1669 residues out of total 4893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 1475 time to evaluate : 6.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 21 TYR cc_start: 0.8632 (OUTLIER) cc_final: 0.8308 (p90) REVERT: E 93 HIS cc_start: 0.8842 (m90) cc_final: 0.8234 (m170) REVERT: E 99 MET cc_start: 0.8695 (ptp) cc_final: 0.8418 (ptp) REVERT: E 122 ASP cc_start: 0.8098 (p0) cc_final: 0.7871 (p0) REVERT: E 190 SER cc_start: 0.9426 (m) cc_final: 0.9203 (p) REVERT: F 99 GLN cc_start: 0.8280 (tt0) cc_final: 0.7988 (tm-30) REVERT: G 102 TYR cc_start: 0.8481 (t80) cc_final: 0.8260 (t80) REVERT: H 11 GLN cc_start: 0.9113 (pt0) cc_final: 0.8825 (pp30) REVERT: H 53 ARG cc_start: 0.8677 (tpp-160) cc_final: 0.8392 (mtt-85) REVERT: H 69 ASN cc_start: 0.9148 (t0) cc_final: 0.8798 (t0) REVERT: I 79 ARG cc_start: 0.9330 (mmt180) cc_final: 0.8909 (mmt180) REVERT: K 26 MET cc_start: 0.8984 (ptm) cc_final: 0.8768 (ptm) REVERT: K 42 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8506 (mm-30) REVERT: K 53 ASP cc_start: 0.8343 (p0) cc_final: 0.7824 (p0) REVERT: L 24 ASN cc_start: 0.8187 (p0) cc_final: 0.7855 (p0) REVERT: L 26 LYS cc_start: 0.8960 (ptpp) cc_final: 0.8522 (ptpp) REVERT: L 28 VAL cc_start: 0.9003 (t) cc_final: 0.8720 (p) REVERT: L 38 PHE cc_start: 0.8780 (p90) cc_final: 0.8561 (p90) REVERT: L 52 GLU cc_start: 0.8919 (mp0) cc_final: 0.8628 (mp0) REVERT: M 82 LYS cc_start: 0.9137 (mmmm) cc_final: 0.8780 (mmmm) REVERT: N 79 LYS cc_start: 0.8415 (pttm) cc_final: 0.8203 (pttm) REVERT: P 62 PHE cc_start: 0.7649 (t80) cc_final: 0.6910 (m-80) REVERT: P 77 LYS cc_start: 0.9453 (ttmm) cc_final: 0.9108 (tppp) REVERT: T 16 MET cc_start: 0.8770 (ptm) cc_final: 0.8519 (ptm) REVERT: T 47 ASP cc_start: 0.8248 (p0) cc_final: 0.7685 (p0) REVERT: V 19 GLU cc_start: 0.8681 (pp20) cc_final: 0.8443 (pp20) REVERT: V 28 LYS cc_start: 0.8812 (mmmt) cc_final: 0.8188 (mmmt) REVERT: W 23 ARG cc_start: 0.8794 (mmm-85) cc_final: 0.8503 (mmm-85) REVERT: X 34 ARG cc_start: 0.8106 (mmt180) cc_final: 0.7802 (mmt180) REVERT: X 44 ARG cc_start: 0.8803 (tpp-160) cc_final: 0.8472 (tpp-160) REVERT: c 136 GLN cc_start: 0.8953 (tp40) cc_final: 0.8716 (tp-100) REVERT: c 195 GLN cc_start: 0.9303 (mt0) cc_final: 0.9056 (mt0) REVERT: d 26 GLN cc_start: 0.8059 (mt0) cc_final: 0.7807 (mt0) REVERT: e 57 TYR cc_start: 0.8743 (m-10) cc_final: 0.8442 (m-10) REVERT: e 87 GLN cc_start: 0.9084 (mt0) cc_final: 0.8781 (mt0) REVERT: e 154 GLU cc_start: 0.9157 (tm-30) cc_final: 0.8777 (tm-30) REVERT: f 8 LYS cc_start: 0.8869 (mmmt) cc_final: 0.8437 (tppt) REVERT: f 114 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8204 (tm-30) REVERT: h 49 ASP cc_start: 0.8333 (t0) cc_final: 0.8071 (t0) REVERT: h 71 ASP cc_start: 0.8884 (m-30) cc_final: 0.8604 (m-30) REVERT: h 96 ARG cc_start: 0.8881 (mtm180) cc_final: 0.8582 (mtm180) REVERT: i 5 GLN cc_start: 0.8827 (mm-40) cc_final: 0.8510 (mm-40) REVERT: j 135 ILE cc_start: 0.9477 (mt) cc_final: 0.9252 (tp) REVERT: l 107 ASN cc_start: 0.8809 (t0) cc_final: 0.8400 (t0) REVERT: m 76 LYS cc_start: 0.9401 (tttt) cc_final: 0.9161 (tptt) REVERT: m 87 ILE cc_start: 0.9094 (mm) cc_final: 0.8851 (mm) REVERT: n 111 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8365 (tm-30) REVERT: p 6 GLN cc_start: 0.8644 (mt0) cc_final: 0.8436 (mt0) REVERT: t 24 ASN cc_start: 0.9358 (m-40) cc_final: 0.9027 (t0) REVERT: t 45 ASP cc_start: 0.9494 (OUTLIER) cc_final: 0.9236 (m-30) REVERT: t 48 MET cc_start: 0.9163 (mmm) cc_final: 0.8778 (mmm) REVERT: t 50 MET cc_start: 0.9463 (OUTLIER) cc_final: 0.9171 (mpp) REVERT: v 43 LYS cc_start: 0.9310 (mmtm) cc_final: 0.9074 (mmtt) REVERT: w 36 GLN cc_start: 0.8541 (mp10) cc_final: 0.8148 (mp10) REVERT: w 39 GLN cc_start: 0.9160 (mt0) cc_final: 0.8747 (mm-40) REVERT: 1 6 VAL cc_start: 0.9512 (t) cc_final: 0.9302 (m) REVERT: 3 40 GLU cc_start: 0.5533 (OUTLIER) cc_final: 0.5207 (mm-30) REVERT: 3 50 VAL cc_start: 0.4064 (OUTLIER) cc_final: 0.3810 (t) REVERT: 4 11 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8202 (tm-30) REVERT: 4 23 LYS cc_start: 0.9023 (ptpp) cc_final: 0.8435 (mtpp) REVERT: 4 24 ILE cc_start: 0.9388 (pt) cc_final: 0.9042 (mp) REVERT: 4 38 SER cc_start: 0.8576 (p) cc_final: 0.8202 (m) outliers start: 194 outliers final: 110 residues processed: 1548 average time/residue: 1.2701 time to fit residues: 3416.6215 Evaluate side-chains 1419 residues out of total 4893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 1303 time to evaluate : 6.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 21 TYR Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 60 GLN Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain I residue 16 GLU Chi-restraints excluded: chain I residue 52 ASN Chi-restraints excluded: chain I residue 55 HIS Chi-restraints excluded: chain I residue 98 GLU Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 89 ASP Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 106 SER Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain M residue 14 ASP Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 29 THR Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain O residue 18 SER Chi-restraints excluded: chain O residue 26 CYS Chi-restraints excluded: chain O residue 85 ARG Chi-restraints excluded: chain O residue 108 ASP Chi-restraints excluded: chain Q residue 58 SER Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain T residue 6 THR Chi-restraints excluded: chain T residue 56 ASP Chi-restraints excluded: chain T residue 60 ILE Chi-restraints excluded: chain V residue 3 SER Chi-restraints excluded: chain V residue 10 ILE Chi-restraints excluded: chain W residue 11 ILE Chi-restraints excluded: chain W residue 56 ILE Chi-restraints excluded: chain W residue 82 ILE Chi-restraints excluded: chain X residue 28 LEU Chi-restraints excluded: chain X residue 30 GLU Chi-restraints excluded: chain a residue 66 PHE Chi-restraints excluded: chain b residue 2 ILE Chi-restraints excluded: chain b residue 103 ASP Chi-restraints excluded: chain b residue 126 ASN Chi-restraints excluded: chain b residue 174 SER Chi-restraints excluded: chain b residue 199 SER Chi-restraints excluded: chain c residue 19 PHE Chi-restraints excluded: chain c residue 25 GLU Chi-restraints excluded: chain c residue 77 ILE Chi-restraints excluded: chain c residue 155 GLU Chi-restraints excluded: chain c residue 175 ILE Chi-restraints excluded: chain d residue 22 ASN Chi-restraints excluded: chain d residue 51 ASN Chi-restraints excluded: chain e residue 36 LEU Chi-restraints excluded: chain e residue 46 ASP Chi-restraints excluded: chain e residue 136 ASP Chi-restraints excluded: chain f residue 47 PHE Chi-restraints excluded: chain f residue 114 GLU Chi-restraints excluded: chain f residue 130 VAL Chi-restraints excluded: chain g residue 10 LEU Chi-restraints excluded: chain g residue 77 VAL Chi-restraints excluded: chain h residue 114 LEU Chi-restraints excluded: chain i residue 32 TYR Chi-restraints excluded: chain i residue 86 LEU Chi-restraints excluded: chain i residue 90 ASN Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain k residue 3 GLN Chi-restraints excluded: chain k residue 126 ILE Chi-restraints excluded: chain k residue 136 MET Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 51 LEU Chi-restraints excluded: chain l residue 57 THR Chi-restraints excluded: chain l residue 117 ASP Chi-restraints excluded: chain m residue 35 ILE Chi-restraints excluded: chain m residue 115 LEU Chi-restraints excluded: chain n residue 64 SER Chi-restraints excluded: chain o residue 7 VAL Chi-restraints excluded: chain o residue 8 ILE Chi-restraints excluded: chain o residue 39 ILE Chi-restraints excluded: chain o residue 79 ILE Chi-restraints excluded: chain o residue 86 SER Chi-restraints excluded: chain o residue 99 VAL Chi-restraints excluded: chain q residue 13 SER Chi-restraints excluded: chain q residue 74 ILE Chi-restraints excluded: chain q residue 96 ILE Chi-restraints excluded: chain r residue 78 SER Chi-restraints excluded: chain t residue 5 ASN Chi-restraints excluded: chain t residue 45 ASP Chi-restraints excluded: chain t residue 50 MET Chi-restraints excluded: chain u residue 52 ASP Chi-restraints excluded: chain u residue 63 VAL Chi-restraints excluded: chain v residue 64 ASP Chi-restraints excluded: chain x residue 4 ILE Chi-restraints excluded: chain y residue 54 ILE Chi-restraints excluded: chain z residue 4 ILE Chi-restraints excluded: chain z residue 21 THR Chi-restraints excluded: chain 0 residue 15 SER Chi-restraints excluded: chain 0 residue 44 VAL Chi-restraints excluded: chain 3 residue 40 GLU Chi-restraints excluded: chain 3 residue 50 VAL Chi-restraints excluded: chain 4 residue 22 MET Chi-restraints excluded: chain 4 residue 31 ASP Chi-restraints excluded: chain 4 residue 58 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 934 optimal weight: 50.0000 chunk 711 optimal weight: 10.0000 chunk 491 optimal weight: 10.0000 chunk 104 optimal weight: 20.0000 chunk 451 optimal weight: 20.0000 chunk 635 optimal weight: 20.0000 chunk 949 optimal weight: 2.9990 chunk 1005 optimal weight: 20.0000 chunk 496 optimal weight: 20.0000 chunk 899 optimal weight: 8.9990 chunk 270 optimal weight: 5.9990 overall best weight: 7.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 57 ASN ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 HIS F 7 ASN ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 52 ASN N 27 ASN ** N 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 63 GLN P 99 GLN ** Q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 39 GLN U 53 GLN ** W 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 152 GLN a 259 ASN b 134 HIS b 167 ASN c 115 GLN e 142 GLN ** f 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 29 HIS j 104 GLN ** k 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 23 ASN m 29 HIS o 36 GLN ** o 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 68 ASN v 15 ASN ** w 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 58 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 159524 Z= 0.284 Angle : 0.702 14.204 238500 Z= 0.376 Chirality : 0.037 0.387 30377 Planarity : 0.006 0.126 12889 Dihedral : 23.929 179.883 79389 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.76 % Favored : 90.87 % Rotamer: Outliers : 4.73 % Allowed : 18.77 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.11), residues: 5891 helix: -0.05 (0.12), residues: 1855 sheet: -1.27 (0.16), residues: 1042 loop : -1.66 (0.11), residues: 2994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP c 60 HIS 0.011 0.001 HIS o 13 PHE 0.020 0.002 PHE X 18 TYR 0.038 0.002 TYR o 31 ARG 0.012 0.001 ARG X 34 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11782 Ramachandran restraints generated. 5891 Oldfield, 0 Emsley, 5891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11782 Ramachandran restraints generated. 5891 Oldfield, 0 Emsley, 5891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1632 residues out of total 4893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 1402 time to evaluate : 5.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 31 MET cc_start: 0.6135 (ppp) cc_final: 0.5721 (pmm) REVERT: E 21 TYR cc_start: 0.8728 (OUTLIER) cc_final: 0.8305 (p90) REVERT: E 93 HIS cc_start: 0.8869 (m90) cc_final: 0.8208 (m170) REVERT: E 99 MET cc_start: 0.8986 (ptp) cc_final: 0.8667 (ptp) REVERT: E 190 SER cc_start: 0.9326 (m) cc_final: 0.9049 (p) REVERT: G 102 TYR cc_start: 0.8727 (t80) cc_final: 0.8378 (t80) REVERT: H 60 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8076 (tp-100) REVERT: H 61 LYS cc_start: 0.8860 (mtmt) cc_final: 0.8604 (ptmt) REVERT: H 64 GLU cc_start: 0.8737 (mp0) cc_final: 0.8108 (mp0) REVERT: H 69 ASN cc_start: 0.9168 (t0) cc_final: 0.8787 (t0) REVERT: I 79 ARG cc_start: 0.9343 (mmt180) cc_final: 0.8893 (mmt180) REVERT: K 26 MET cc_start: 0.9132 (ptm) cc_final: 0.8853 (ptm) REVERT: K 42 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8438 (mm-30) REVERT: K 53 ASP cc_start: 0.8402 (p0) cc_final: 0.7898 (p0) REVERT: L 24 ASN cc_start: 0.7971 (p0) cc_final: 0.7096 (p0) REVERT: L 26 LYS cc_start: 0.8972 (ptpp) cc_final: 0.8507 (ptpp) REVERT: L 31 GLN cc_start: 0.9197 (mp10) cc_final: 0.8912 (mp10) REVERT: L 46 VAL cc_start: 0.9359 (m) cc_final: 0.9114 (t) REVERT: L 49 GLN cc_start: 0.9272 (pt0) cc_final: 0.8851 (pt0) REVERT: L 52 GLU cc_start: 0.9003 (mp0) cc_final: 0.8617 (mp0) REVERT: M 47 GLU cc_start: 0.8449 (mp0) cc_final: 0.8218 (mm-30) REVERT: N 64 VAL cc_start: 0.9408 (m) cc_final: 0.8353 (t) REVERT: N 79 LYS cc_start: 0.8577 (pttm) cc_final: 0.8333 (pttm) REVERT: N 93 GLU cc_start: 0.8792 (pm20) cc_final: 0.8530 (pp20) REVERT: P 62 PHE cc_start: 0.7528 (t80) cc_final: 0.6951 (m-80) REVERT: P 77 LYS cc_start: 0.9441 (ttmm) cc_final: 0.9179 (tppp) REVERT: S 76 LYS cc_start: 0.9357 (OUTLIER) cc_final: 0.9133 (mmmt) REVERT: T 5 ARG cc_start: 0.8937 (tpp80) cc_final: 0.8727 (mmm-85) REVERT: T 16 MET cc_start: 0.8809 (ptm) cc_final: 0.8443 (ptm) REVERT: T 47 ASP cc_start: 0.8174 (p0) cc_final: 0.7596 (p0) REVERT: U 56 ARG cc_start: 0.9058 (mtt90) cc_final: 0.8839 (mtt90) REVERT: V 23 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8677 (mm-30) REVERT: W 59 ARG cc_start: 0.9238 (ttm-80) cc_final: 0.8847 (ttm-80) REVERT: X 44 ARG cc_start: 0.8921 (tpp-160) cc_final: 0.8504 (tpp-160) REVERT: c 136 GLN cc_start: 0.8872 (tp40) cc_final: 0.8665 (tp-100) REVERT: c 195 GLN cc_start: 0.9492 (mt0) cc_final: 0.9194 (mt0) REVERT: d 89 THR cc_start: 0.9256 (OUTLIER) cc_final: 0.8930 (p) REVERT: e 57 TYR cc_start: 0.8748 (m-10) cc_final: 0.8527 (m-10) REVERT: e 87 GLN cc_start: 0.9085 (mt0) cc_final: 0.8803 (mt0) REVERT: f 1 MET cc_start: 0.9331 (mmm) cc_final: 0.9076 (mmt) REVERT: f 8 LYS cc_start: 0.8937 (mmmt) cc_final: 0.8568 (tppt) REVERT: f 114 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8225 (tm-30) REVERT: g 58 ILE cc_start: 0.4471 (mt) cc_final: 0.4265 (mt) REVERT: g 85 ILE cc_start: 0.0400 (OUTLIER) cc_final: -0.0061 (pt) REVERT: h 49 ASP cc_start: 0.8454 (t0) cc_final: 0.8196 (t0) REVERT: h 96 ARG cc_start: 0.8883 (mtm180) cc_final: 0.8558 (mtm180) REVERT: h 108 MET cc_start: 0.8488 (mmm) cc_final: 0.8089 (mmm) REVERT: i 5 GLN cc_start: 0.8943 (mm-40) cc_final: 0.8680 (mm-40) REVERT: i 104 THR cc_start: 0.9168 (t) cc_final: 0.8321 (t) REVERT: i 106 GLU cc_start: 0.9294 (mp0) cc_final: 0.9022 (mp0) REVERT: k 47 GLU cc_start: 0.9026 (tm-30) cc_final: 0.8615 (tm-30) REVERT: k 90 GLU cc_start: 0.8590 (mp0) cc_final: 0.8281 (mp0) REVERT: l 74 GLU cc_start: 0.9345 (tt0) cc_final: 0.9111 (tm-30) REVERT: l 107 ASN cc_start: 0.8962 (t0) cc_final: 0.8760 (t0) REVERT: m 76 LYS cc_start: 0.9520 (tttt) cc_final: 0.9107 (tptt) REVERT: n 111 GLU cc_start: 0.8848 (tm-30) cc_final: 0.8134 (tm-30) REVERT: o 86 SER cc_start: 0.9021 (OUTLIER) cc_final: 0.8616 (p) REVERT: q 52 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8445 (tm-30) REVERT: q 69 LEU cc_start: 0.9122 (tp) cc_final: 0.8888 (tp) REVERT: r 2 ILE cc_start: 0.7847 (OUTLIER) cc_final: 0.7170 (pt) REVERT: r 4 GLU cc_start: 0.8725 (mp0) cc_final: 0.8389 (mp0) REVERT: t 24 ASN cc_start: 0.9378 (m-40) cc_final: 0.9009 (t0) REVERT: t 45 ASP cc_start: 0.9541 (OUTLIER) cc_final: 0.9210 (m-30) REVERT: t 48 MET cc_start: 0.9184 (mmm) cc_final: 0.8922 (mmm) REVERT: t 50 MET cc_start: 0.9519 (OUTLIER) cc_final: 0.9195 (mtm) REVERT: u 68 LYS cc_start: 0.9481 (pttp) cc_final: 0.9158 (ptpt) REVERT: u 79 GLU cc_start: 0.8690 (pm20) cc_final: 0.8103 (pm20) REVERT: v 43 LYS cc_start: 0.9318 (mmtm) cc_final: 0.9060 (mmtt) REVERT: w 39 GLN cc_start: 0.9205 (mt0) cc_final: 0.8755 (mm-40) REVERT: y 43 THR cc_start: 0.8937 (p) cc_final: 0.8378 (p) REVERT: z 7 LYS cc_start: 0.9220 (pttt) cc_final: 0.8950 (pttp) REVERT: 1 6 VAL cc_start: 0.9581 (t) cc_final: 0.9334 (m) REVERT: 3 8 LYS cc_start: 0.7356 (ttpp) cc_final: 0.7130 (tppt) REVERT: 4 12 ILE cc_start: 0.9076 (pt) cc_final: 0.8843 (pt) REVERT: 4 23 LYS cc_start: 0.9027 (ptpp) cc_final: 0.8625 (mttm) REVERT: 4 32 LEU cc_start: 0.9131 (tp) cc_final: 0.8854 (tt) REVERT: 4 38 SER cc_start: 0.8578 (p) cc_final: 0.8250 (m) outliers start: 230 outliers final: 159 residues processed: 1502 average time/residue: 1.2304 time to fit residues: 3218.3249 Evaluate side-chains 1447 residues out of total 4893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 1278 time to evaluate : 5.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 21 TYR Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 60 GLN Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 121 ASN Chi-restraints excluded: chain H residue 133 ILE Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain I residue 16 GLU Chi-restraints excluded: chain I residue 52 ASN Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 55 HIS Chi-restraints excluded: chain I residue 93 LYS Chi-restraints excluded: chain J residue 91 ARG Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 67 LYS Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 34 THR Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain O residue 18 SER Chi-restraints excluded: chain O residue 26 CYS Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 85 ARG Chi-restraints excluded: chain O residue 108 ASP Chi-restraints excluded: chain P residue 6 ILE Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain Q residue 58 SER Chi-restraints excluded: chain R residue 13 GLU Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 76 LYS Chi-restraints excluded: chain T residue 6 THR Chi-restraints excluded: chain T residue 56 ASP Chi-restraints excluded: chain T residue 60 ILE Chi-restraints excluded: chain U residue 24 ASP Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 32 ILE Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain V residue 3 SER Chi-restraints excluded: chain W residue 11 ILE Chi-restraints excluded: chain W residue 27 MET Chi-restraints excluded: chain W residue 56 ILE Chi-restraints excluded: chain W residue 82 ILE Chi-restraints excluded: chain X residue 12 ASP Chi-restraints excluded: chain X residue 28 LEU Chi-restraints excluded: chain X residue 30 GLU Chi-restraints excluded: chain a residue 66 PHE Chi-restraints excluded: chain b residue 2 ILE Chi-restraints excluded: chain b residue 126 ASN Chi-restraints excluded: chain b residue 174 SER Chi-restraints excluded: chain b residue 199 SER Chi-restraints excluded: chain c residue 19 PHE Chi-restraints excluded: chain c residue 77 ILE Chi-restraints excluded: chain c residue 175 ILE Chi-restraints excluded: chain d residue 39 VAL Chi-restraints excluded: chain d residue 51 ASN Chi-restraints excluded: chain d residue 89 THR Chi-restraints excluded: chain d residue 148 VAL Chi-restraints excluded: chain d residue 158 THR Chi-restraints excluded: chain e residue 36 LEU Chi-restraints excluded: chain e residue 59 ASP Chi-restraints excluded: chain f residue 47 PHE Chi-restraints excluded: chain f residue 50 ARG Chi-restraints excluded: chain f residue 114 GLU Chi-restraints excluded: chain f residue 130 VAL Chi-restraints excluded: chain g residue 10 LEU Chi-restraints excluded: chain g residue 27 LEU Chi-restraints excluded: chain g residue 77 VAL Chi-restraints excluded: chain g residue 85 ILE Chi-restraints excluded: chain h residue 60 ASP Chi-restraints excluded: chain h residue 114 LEU Chi-restraints excluded: chain i residue 3 GLN Chi-restraints excluded: chain i residue 32 TYR Chi-restraints excluded: chain i residue 90 ASN Chi-restraints excluded: chain j residue 6 LEU Chi-restraints excluded: chain j residue 42 SER Chi-restraints excluded: chain j residue 67 THR Chi-restraints excluded: chain j residue 74 THR Chi-restraints excluded: chain j residue 77 ILE Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain k residue 3 GLN Chi-restraints excluded: chain k residue 126 ILE Chi-restraints excluded: chain k residue 136 MET Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 36 THR Chi-restraints excluded: chain l residue 48 VAL Chi-restraints excluded: chain l residue 57 THR Chi-restraints excluded: chain l residue 117 ASP Chi-restraints excluded: chain m residue 28 VAL Chi-restraints excluded: chain m residue 47 VAL Chi-restraints excluded: chain m residue 62 LEU Chi-restraints excluded: chain m residue 115 LEU Chi-restraints excluded: chain n residue 49 ILE Chi-restraints excluded: chain n residue 64 SER Chi-restraints excluded: chain n residue 82 SER Chi-restraints excluded: chain o residue 3 VAL Chi-restraints excluded: chain o residue 7 VAL Chi-restraints excluded: chain o residue 17 LEU Chi-restraints excluded: chain o residue 39 ILE Chi-restraints excluded: chain o residue 79 ILE Chi-restraints excluded: chain o residue 86 SER Chi-restraints excluded: chain p residue 19 THR Chi-restraints excluded: chain p residue 38 VAL Chi-restraints excluded: chain q residue 4 ILE Chi-restraints excluded: chain q residue 13 SER Chi-restraints excluded: chain q residue 23 LEU Chi-restraints excluded: chain q residue 67 ASP Chi-restraints excluded: chain q residue 74 ILE Chi-restraints excluded: chain q residue 78 GLU Chi-restraints excluded: chain q residue 95 ARG Chi-restraints excluded: chain q residue 96 ILE Chi-restraints excluded: chain q residue 100 THR Chi-restraints excluded: chain q residue 101 SER Chi-restraints excluded: chain q residue 103 ILE Chi-restraints excluded: chain r residue 2 ILE Chi-restraints excluded: chain r residue 78 SER Chi-restraints excluded: chain s residue 40 LEU Chi-restraints excluded: chain s residue 48 VAL Chi-restraints excluded: chain t residue 5 ASN Chi-restraints excluded: chain t residue 45 ASP Chi-restraints excluded: chain t residue 50 MET Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 52 ASP Chi-restraints excluded: chain u residue 63 VAL Chi-restraints excluded: chain v residue 57 VAL Chi-restraints excluded: chain v residue 64 ASP Chi-restraints excluded: chain x residue 8 GLN Chi-restraints excluded: chain x residue 9 THR Chi-restraints excluded: chain x residue 28 LEU Chi-restraints excluded: chain x residue 47 ILE Chi-restraints excluded: chain x residue 56 VAL Chi-restraints excluded: chain y residue 5 ASN Chi-restraints excluded: chain z residue 4 ILE Chi-restraints excluded: chain z residue 21 THR Chi-restraints excluded: chain z residue 22 THR Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain 0 residue 4 THR Chi-restraints excluded: chain 0 residue 42 LEU Chi-restraints excluded: chain 0 residue 44 VAL Chi-restraints excluded: chain 3 residue 54 VAL Chi-restraints excluded: chain 4 residue 22 MET Chi-restraints excluded: chain 4 residue 34 LEU Chi-restraints excluded: chain 4 residue 58 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 837 optimal weight: 20.0000 chunk 570 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 748 optimal weight: 9.9990 chunk 414 optimal weight: 10.0000 chunk 857 optimal weight: 30.0000 chunk 694 optimal weight: 20.0000 chunk 1 optimal weight: 50.0000 chunk 513 optimal weight: 20.0000 chunk 902 optimal weight: 6.9990 chunk 253 optimal weight: 10.0000 overall best weight: 9.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 7 ASN ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN ** G 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 63 ASN M 58 ASN ** N 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 63 GLN P 99 GLN ** Q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 36 ASN U 53 GLN V 51 HIS ** X 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 133 ASN a 152 GLN a 242 HIS ** b 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 167 ASN c 115 GLN ** e 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 142 GLN i 29 HIS j 104 GLN k 3 GLN l 9 GLN ** l 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 36 GLN o 51 GLN ** o 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 6 GLN ** p 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 15 ASN ** w 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 159524 Z= 0.332 Angle : 0.725 13.936 238500 Z= 0.388 Chirality : 0.038 0.384 30377 Planarity : 0.007 0.127 12889 Dihedral : 23.916 179.990 79389 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.41 % Allowed : 9.06 % Favored : 90.53 % Rotamer: Outliers : 5.86 % Allowed : 19.63 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.11), residues: 5891 helix: 0.00 (0.12), residues: 1868 sheet: -1.15 (0.16), residues: 1054 loop : -1.65 (0.11), residues: 2969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 42 HIS 0.011 0.002 HIS O 76 PHE 0.026 0.002 PHE L 38 TYR 0.031 0.002 TYR n 98 ARG 0.018 0.001 ARG 3 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11782 Ramachandran restraints generated. 5891 Oldfield, 0 Emsley, 5891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11782 Ramachandran restraints generated. 5891 Oldfield, 0 Emsley, 5891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1664 residues out of total 4893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 1379 time to evaluate : 6.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 21 TYR cc_start: 0.8862 (OUTLIER) cc_final: 0.8234 (p90) REVERT: E 93 HIS cc_start: 0.8817 (m90) cc_final: 0.8306 (m-70) REVERT: E 190 SER cc_start: 0.9359 (m) cc_final: 0.9156 (p) REVERT: G 102 TYR cc_start: 0.8884 (t80) cc_final: 0.8491 (t80) REVERT: G 203 TYR cc_start: 0.8862 (m-80) cc_final: 0.8562 (m-80) REVERT: H 11 GLN cc_start: 0.9100 (pp30) cc_final: 0.8829 (pp30) REVERT: H 15 ILE cc_start: 0.9394 (OUTLIER) cc_final: 0.9102 (mp) REVERT: H 60 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8117 (tp-100) REVERT: H 61 LYS cc_start: 0.8913 (mtmt) cc_final: 0.8568 (mtmt) REVERT: H 64 GLU cc_start: 0.8773 (mp0) cc_final: 0.8165 (mp0) REVERT: H 69 ASN cc_start: 0.9185 (t0) cc_final: 0.8810 (t0) REVERT: I 2 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.7365 (mmm-85) REVERT: J 124 SER cc_start: 0.8315 (OUTLIER) cc_final: 0.7644 (p) REVERT: J 125 ASP cc_start: 0.8800 (t0) cc_final: 0.8279 (t0) REVERT: K 26 MET cc_start: 0.9145 (ptm) cc_final: 0.8877 (ptm) REVERT: K 53 ASP cc_start: 0.8458 (p0) cc_final: 0.7874 (p0) REVERT: K 59 GLU cc_start: 0.8939 (pm20) cc_final: 0.8683 (pm20) REVERT: K 110 MET cc_start: 0.9296 (ptp) cc_final: 0.9046 (pmm) REVERT: L 46 VAL cc_start: 0.9394 (m) cc_final: 0.9145 (t) REVERT: L 49 GLN cc_start: 0.9317 (pt0) cc_final: 0.9060 (pt0) REVERT: L 52 GLU cc_start: 0.9082 (mp0) cc_final: 0.8860 (mp0) REVERT: L 58 GLU cc_start: 0.9120 (mp0) cc_final: 0.8693 (tp30) REVERT: M 97 ASP cc_start: 0.8706 (t0) cc_final: 0.8504 (t0) REVERT: N 79 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8431 (pttm) REVERT: N 93 GLU cc_start: 0.8937 (pm20) cc_final: 0.8600 (pp20) REVERT: P 77 LYS cc_start: 0.9446 (ttmm) cc_final: 0.8939 (tppp) REVERT: P 80 MET cc_start: 0.9052 (mtp) cc_final: 0.8677 (ttm) REVERT: Q 19 TYR cc_start: 0.8414 (m-10) cc_final: 0.7717 (m-10) REVERT: T 16 MET cc_start: 0.8940 (ptm) cc_final: 0.8440 (ptm) REVERT: T 17 GLU cc_start: 0.8540 (tm-30) cc_final: 0.8336 (tm-30) REVERT: V 28 LYS cc_start: 0.8803 (mmmt) cc_final: 0.8120 (mmmt) REVERT: W 59 ARG cc_start: 0.9237 (ttm-80) cc_final: 0.8852 (ttm-80) REVERT: X 48 LYS cc_start: 0.8651 (mmmt) cc_final: 0.8433 (mmmt) REVERT: c 195 GLN cc_start: 0.9489 (mt0) cc_final: 0.9181 (mt0) REVERT: d 26 GLN cc_start: 0.7938 (mt0) cc_final: 0.7718 (mp10) REVERT: d 89 THR cc_start: 0.9300 (OUTLIER) cc_final: 0.8961 (p) REVERT: d 99 PHE cc_start: 0.9355 (t80) cc_final: 0.9080 (t80) REVERT: e 87 GLN cc_start: 0.9076 (mt0) cc_final: 0.8773 (mt0) REVERT: e 163 TYR cc_start: 0.8964 (m-80) cc_final: 0.8758 (m-80) REVERT: f 8 LYS cc_start: 0.8879 (mmmt) cc_final: 0.8535 (tppt) REVERT: f 114 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8248 (tm-30) REVERT: g 85 ILE cc_start: 0.0322 (OUTLIER) cc_final: -0.0148 (pt) REVERT: h 49 ASP cc_start: 0.8486 (t0) cc_final: 0.8111 (t0) REVERT: h 108 MET cc_start: 0.8743 (mmm) cc_final: 0.8461 (mmm) REVERT: i 5 GLN cc_start: 0.8968 (mm-40) cc_final: 0.8742 (mm-40) REVERT: i 104 THR cc_start: 0.9166 (t) cc_final: 0.8335 (t) REVERT: i 106 GLU cc_start: 0.9203 (mp0) cc_final: 0.8969 (mp0) REVERT: j 135 ILE cc_start: 0.9603 (mt) cc_final: 0.9299 (tp) REVERT: m 56 LYS cc_start: 0.8630 (tptt) cc_final: 0.8368 (tptt) REVERT: m 76 LYS cc_start: 0.9438 (tttt) cc_final: 0.9100 (tptt) REVERT: n 111 GLU cc_start: 0.8885 (tm-30) cc_final: 0.8572 (tm-30) REVERT: p 34 GLU cc_start: 0.8384 (mm-30) cc_final: 0.8116 (mm-30) REVERT: q 52 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8456 (tm-30) REVERT: r 4 GLU cc_start: 0.8817 (mp0) cc_final: 0.8557 (mp0) REVERT: t 24 ASN cc_start: 0.9322 (m-40) cc_final: 0.8878 (t0) REVERT: t 45 ASP cc_start: 0.9550 (OUTLIER) cc_final: 0.9136 (m-30) REVERT: t 48 MET cc_start: 0.9207 (mmm) cc_final: 0.8870 (mmm) REVERT: t 50 MET cc_start: 0.9546 (OUTLIER) cc_final: 0.9126 (mtm) REVERT: u 64 LYS cc_start: 0.9101 (tppp) cc_final: 0.8848 (ttmm) REVERT: u 79 GLU cc_start: 0.8660 (pm20) cc_final: 0.8229 (pm20) REVERT: v 43 LYS cc_start: 0.9333 (mmtm) cc_final: 0.9054 (mmtt) REVERT: w 13 GLU cc_start: 0.8911 (pp20) cc_final: 0.8632 (pp20) REVERT: w 36 GLN cc_start: 0.8516 (mp10) cc_final: 0.8256 (mp10) REVERT: w 39 GLN cc_start: 0.9276 (mt0) cc_final: 0.8786 (mm-40) REVERT: 1 6 VAL cc_start: 0.9568 (t) cc_final: 0.9337 (m) REVERT: 3 8 LYS cc_start: 0.7513 (ttpp) cc_final: 0.7272 (tppt) REVERT: 3 50 VAL cc_start: 0.4251 (OUTLIER) cc_final: 0.4006 (t) REVERT: 4 23 LYS cc_start: 0.9117 (ptpp) cc_final: 0.8752 (mttm) REVERT: 4 24 ILE cc_start: 0.9385 (pt) cc_final: 0.9052 (mp) REVERT: 4 32 LEU cc_start: 0.9177 (tp) cc_final: 0.8872 (tt) outliers start: 285 outliers final: 191 residues processed: 1513 average time/residue: 1.2559 time to fit residues: 3324.1153 Evaluate side-chains 1505 residues out of total 4893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 1302 time to evaluate : 5.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 21 TYR Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 189 ASP Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 60 GLN Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 121 ASN Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain I residue 2 ARG Chi-restraints excluded: chain I residue 16 GLU Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 93 LYS Chi-restraints excluded: chain I residue 98 GLU Chi-restraints excluded: chain J residue 91 ARG Chi-restraints excluded: chain J residue 124 SER Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 62 LEU Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 89 ASP Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 67 LYS Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain M residue 14 ASP Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 45 ARG Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 34 THR Chi-restraints excluded: chain N residue 79 LYS Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain O residue 18 SER Chi-restraints excluded: chain O residue 26 CYS Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 89 LEU Chi-restraints excluded: chain O residue 108 ASP Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 67 ASP Chi-restraints excluded: chain Q residue 58 SER Chi-restraints excluded: chain R residue 13 GLU Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain S residue 55 ASP Chi-restraints excluded: chain T residue 6 THR Chi-restraints excluded: chain T residue 56 ASP Chi-restraints excluded: chain T residue 60 ILE Chi-restraints excluded: chain U residue 24 ASP Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 29 LYS Chi-restraints excluded: chain U residue 32 ILE Chi-restraints excluded: chain U residue 67 LEU Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain V residue 3 SER Chi-restraints excluded: chain V residue 66 VAL Chi-restraints excluded: chain W residue 11 ILE Chi-restraints excluded: chain W residue 38 ILE Chi-restraints excluded: chain W residue 56 ILE Chi-restraints excluded: chain W residue 82 ILE Chi-restraints excluded: chain X residue 20 ARG Chi-restraints excluded: chain X residue 28 LEU Chi-restraints excluded: chain X residue 30 GLU Chi-restraints excluded: chain a residue 44 ASN Chi-restraints excluded: chain a residue 66 PHE Chi-restraints excluded: chain b residue 2 ILE Chi-restraints excluded: chain b residue 86 GLU Chi-restraints excluded: chain b residue 126 ASN Chi-restraints excluded: chain b residue 174 SER Chi-restraints excluded: chain b residue 199 SER Chi-restraints excluded: chain c residue 19 PHE Chi-restraints excluded: chain c residue 77 ILE Chi-restraints excluded: chain c residue 141 MET Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain c residue 175 ILE Chi-restraints excluded: chain d residue 39 VAL Chi-restraints excluded: chain d residue 51 ASN Chi-restraints excluded: chain d residue 89 THR Chi-restraints excluded: chain d residue 133 GLU Chi-restraints excluded: chain d residue 148 VAL Chi-restraints excluded: chain d residue 158 THR Chi-restraints excluded: chain e residue 36 LEU Chi-restraints excluded: chain f residue 50 ARG Chi-restraints excluded: chain f residue 114 GLU Chi-restraints excluded: chain f residue 130 VAL Chi-restraints excluded: chain g residue 27 LEU Chi-restraints excluded: chain g residue 77 VAL Chi-restraints excluded: chain g residue 85 ILE Chi-restraints excluded: chain h residue 60 ASP Chi-restraints excluded: chain h residue 114 LEU Chi-restraints excluded: chain i residue 3 GLN Chi-restraints excluded: chain i residue 32 TYR Chi-restraints excluded: chain i residue 90 ASN Chi-restraints excluded: chain j residue 6 LEU Chi-restraints excluded: chain j residue 42 SER Chi-restraints excluded: chain j residue 67 THR Chi-restraints excluded: chain j residue 74 THR Chi-restraints excluded: chain j residue 77 ILE Chi-restraints excluded: chain k residue 12 MET Chi-restraints excluded: chain k residue 46 ILE Chi-restraints excluded: chain k residue 126 ILE Chi-restraints excluded: chain k residue 132 THR Chi-restraints excluded: chain k residue 136 MET Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 48 VAL Chi-restraints excluded: chain l residue 51 LEU Chi-restraints excluded: chain l residue 57 THR Chi-restraints excluded: chain l residue 117 ASP Chi-restraints excluded: chain m residue 28 VAL Chi-restraints excluded: chain m residue 47 VAL Chi-restraints excluded: chain m residue 53 THR Chi-restraints excluded: chain m residue 62 LEU Chi-restraints excluded: chain m residue 67 ASN Chi-restraints excluded: chain m residue 115 LEU Chi-restraints excluded: chain n residue 64 SER Chi-restraints excluded: chain n residue 75 THR Chi-restraints excluded: chain n residue 83 ILE Chi-restraints excluded: chain o residue 3 VAL Chi-restraints excluded: chain o residue 8 ILE Chi-restraints excluded: chain o residue 17 LEU Chi-restraints excluded: chain o residue 28 SER Chi-restraints excluded: chain o residue 39 ILE Chi-restraints excluded: chain o residue 79 ILE Chi-restraints excluded: chain o residue 86 SER Chi-restraints excluded: chain p residue 38 VAL Chi-restraints excluded: chain q residue 4 ILE Chi-restraints excluded: chain q residue 13 SER Chi-restraints excluded: chain q residue 23 LEU Chi-restraints excluded: chain q residue 67 ASP Chi-restraints excluded: chain q residue 74 ILE Chi-restraints excluded: chain q residue 78 GLU Chi-restraints excluded: chain q residue 95 ARG Chi-restraints excluded: chain q residue 96 ILE Chi-restraints excluded: chain q residue 101 SER Chi-restraints excluded: chain r residue 47 VAL Chi-restraints excluded: chain r residue 78 SER Chi-restraints excluded: chain s residue 40 LEU Chi-restraints excluded: chain s residue 48 VAL Chi-restraints excluded: chain t residue 45 ASP Chi-restraints excluded: chain t residue 50 MET Chi-restraints excluded: chain u residue 17 LEU Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 32 ILE Chi-restraints excluded: chain u residue 52 ASP Chi-restraints excluded: chain u residue 63 VAL Chi-restraints excluded: chain v residue 13 THR Chi-restraints excluded: chain v residue 57 VAL Chi-restraints excluded: chain v residue 63 ILE Chi-restraints excluded: chain v residue 64 ASP Chi-restraints excluded: chain x residue 3 THR Chi-restraints excluded: chain x residue 4 ILE Chi-restraints excluded: chain x residue 9 THR Chi-restraints excluded: chain x residue 34 THR Chi-restraints excluded: chain x residue 47 ILE Chi-restraints excluded: chain x residue 56 VAL Chi-restraints excluded: chain y residue 5 ASN Chi-restraints excluded: chain y residue 27 LEU Chi-restraints excluded: chain y residue 32 THR Chi-restraints excluded: chain z residue 4 ILE Chi-restraints excluded: chain z residue 12 SER Chi-restraints excluded: chain z residue 21 THR Chi-restraints excluded: chain z residue 22 THR Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain z residue 28 THR Chi-restraints excluded: chain 0 residue 4 THR Chi-restraints excluded: chain 0 residue 24 THR Chi-restraints excluded: chain 0 residue 42 LEU Chi-restraints excluded: chain 0 residue 44 VAL Chi-restraints excluded: chain 2 residue 17 VAL Chi-restraints excluded: chain 3 residue 50 VAL Chi-restraints excluded: chain 3 residue 54 VAL Chi-restraints excluded: chain 3 residue 108 VAL Chi-restraints excluded: chain 4 residue 4 ASP Chi-restraints excluded: chain 4 residue 22 MET Chi-restraints excluded: chain 4 residue 31 ASP Chi-restraints excluded: chain 4 residue 34 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 338 optimal weight: 9.9990 chunk 905 optimal weight: 7.9990 chunk 198 optimal weight: 10.0000 chunk 590 optimal weight: 10.0000 chunk 248 optimal weight: 20.0000 chunk 1006 optimal weight: 7.9990 chunk 835 optimal weight: 6.9990 chunk 465 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 332 optimal weight: 30.0000 chunk 528 optimal weight: 20.0000 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 58 ASN ** N 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 63 GLN P 99 GLN ** Q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 19 HIS ** X 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 152 GLN ** b 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 115 GLN c 136 GLN ** e 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 142 GLN h 80 HIS i 29 HIS j 104 GLN ** l 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 19 GLN n 11 GLN ** o 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 12 GLN ** t 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 15 ASN ** w 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 159524 Z= 0.307 Angle : 0.710 13.931 238500 Z= 0.381 Chirality : 0.037 0.383 30377 Planarity : 0.006 0.126 12889 Dihedral : 23.906 179.944 79389 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.27 % Favored : 90.29 % Rotamer: Outliers : 5.49 % Allowed : 21.46 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.11), residues: 5891 helix: 0.03 (0.12), residues: 1876 sheet: -1.11 (0.16), residues: 1060 loop : -1.60 (0.11), residues: 2955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 212 HIS 0.015 0.001 HIS 4 6 PHE 0.025 0.002 PHE L 38 TYR 0.036 0.002 TYR f 25 ARG 0.013 0.001 ARG X 34 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11782 Ramachandran restraints generated. 5891 Oldfield, 0 Emsley, 5891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11782 Ramachandran restraints generated. 5891 Oldfield, 0 Emsley, 5891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1640 residues out of total 4893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 1373 time to evaluate : 6.255 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: C 45 ASP cc_start: 0.6758 (OUTLIER) cc_final: 0.6522 (p0) REVERT: E 21 TYR cc_start: 0.8844 (OUTLIER) cc_final: 0.8164 (p90) REVERT: E 93 HIS cc_start: 0.8873 (m90) cc_final: 0.8245 (m170) REVERT: E 119 GLN cc_start: 0.9260 (mt0) cc_final: 0.8983 (pp30) REVERT: G 102 TYR cc_start: 0.8911 (t80) cc_final: 0.8609 (t80) REVERT: G 139 ASN cc_start: 0.9257 (t0) cc_final: 0.8977 (p0) REVERT: H 11 GLN cc_start: 0.9014 (pp30) cc_final: 0.8690 (pp30) REVERT: H 15 ILE cc_start: 0.9410 (OUTLIER) cc_final: 0.9131 (mp) REVERT: H 60 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8106 (tp-100) REVERT: H 61 LYS cc_start: 0.8908 (mtmt) cc_final: 0.8625 (mtmt) REVERT: H 64 GLU cc_start: 0.8805 (mp0) cc_final: 0.8226 (mp0) REVERT: H 69 ASN cc_start: 0.9188 (t0) cc_final: 0.8751 (t0) REVERT: I 2 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.7071 (mmm-85) REVERT: I 90 MET cc_start: 0.8977 (mmm) cc_final: 0.8736 (mmm) REVERT: J 143 MET cc_start: 0.9355 (mmm) cc_final: 0.9137 (mmp) REVERT: K 42 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8363 (mm-30) REVERT: K 53 ASP cc_start: 0.8495 (p0) cc_final: 0.7829 (p0) REVERT: K 59 GLU cc_start: 0.8902 (pm20) cc_final: 0.8651 (pm20) REVERT: L 26 LYS cc_start: 0.9227 (ptpp) cc_final: 0.9013 (ptpp) REVERT: L 31 GLN cc_start: 0.9286 (mp10) cc_final: 0.9031 (mp10) REVERT: L 46 VAL cc_start: 0.9410 (m) cc_final: 0.9149 (t) REVERT: L 49 GLN cc_start: 0.9322 (pt0) cc_final: 0.9038 (pt0) REVERT: L 52 GLU cc_start: 0.9110 (mp0) cc_final: 0.8872 (mp0) REVERT: L 56 MET cc_start: 0.9284 (tpp) cc_final: 0.8472 (tpp) REVERT: L 58 GLU cc_start: 0.9126 (mp0) cc_final: 0.8821 (tp30) REVERT: L 87 MET cc_start: 0.8358 (pmm) cc_final: 0.8097 (pmm) REVERT: M 32 THR cc_start: 0.8552 (OUTLIER) cc_final: 0.7619 (p) REVERT: N 79 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8426 (pttm) REVERT: N 93 GLU cc_start: 0.8923 (pm20) cc_final: 0.8538 (pp20) REVERT: P 62 PHE cc_start: 0.7568 (t80) cc_final: 0.6973 (m-80) REVERT: P 77 LYS cc_start: 0.9431 (ttmm) cc_final: 0.8940 (tppp) REVERT: Q 86 GLU cc_start: 0.9000 (pp20) cc_final: 0.8746 (pp20) REVERT: T 16 MET cc_start: 0.8955 (ptm) cc_final: 0.8406 (ptm) REVERT: T 17 GLU cc_start: 0.8473 (tm-30) cc_final: 0.8227 (tm-30) REVERT: U 56 ARG cc_start: 0.9138 (mtt90) cc_final: 0.8879 (mtt90) REVERT: V 19 GLU cc_start: 0.9081 (pp20) cc_final: 0.8742 (pp20) REVERT: V 28 LYS cc_start: 0.8713 (mmmt) cc_final: 0.8058 (mmmt) REVERT: W 26 MET cc_start: 0.8954 (ppp) cc_final: 0.8743 (ppp) REVERT: W 59 ARG cc_start: 0.9270 (ttm-80) cc_final: 0.8879 (ttm-80) REVERT: X 20 ARG cc_start: 0.7086 (OUTLIER) cc_final: 0.6485 (mtt90) REVERT: c 195 GLN cc_start: 0.9517 (mt0) cc_final: 0.9201 (mt0) REVERT: d 25 MET cc_start: 0.9427 (mmt) cc_final: 0.9112 (mmm) REVERT: d 26 GLN cc_start: 0.7939 (mt0) cc_final: 0.7711 (mp10) REVERT: d 89 THR cc_start: 0.9284 (OUTLIER) cc_final: 0.8950 (p) REVERT: d 99 PHE cc_start: 0.9349 (t80) cc_final: 0.9086 (t80) REVERT: f 8 LYS cc_start: 0.8841 (mmmt) cc_final: 0.8301 (tptp) REVERT: f 114 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8254 (tm-30) REVERT: g 85 ILE cc_start: 0.0323 (OUTLIER) cc_final: -0.0130 (pt) REVERT: h 49 ASP cc_start: 0.8583 (t0) cc_final: 0.8196 (t0) REVERT: h 57 LEU cc_start: 0.9486 (pp) cc_final: 0.9261 (pp) REVERT: h 96 ARG cc_start: 0.8948 (mtm180) cc_final: 0.8599 (mtm180) REVERT: h 108 MET cc_start: 0.8712 (mmm) cc_final: 0.8476 (mmm) REVERT: h 131 ASN cc_start: 0.8530 (p0) cc_final: 0.8311 (p0) REVERT: i 104 THR cc_start: 0.9172 (t) cc_final: 0.8320 (t) REVERT: i 106 GLU cc_start: 0.9150 (mp0) cc_final: 0.8924 (mp0) REVERT: j 135 ILE cc_start: 0.9631 (mt) cc_final: 0.9313 (tp) REVERT: m 76 LYS cc_start: 0.9486 (tttt) cc_final: 0.9186 (tptt) REVERT: n 7 LEU cc_start: 0.9008 (tt) cc_final: 0.8695 (tp) REVERT: n 111 GLU cc_start: 0.8949 (tm-30) cc_final: 0.8331 (tm-30) REVERT: o 86 SER cc_start: 0.9218 (OUTLIER) cc_final: 0.8775 (p) REVERT: q 52 GLU cc_start: 0.8760 (tm-30) cc_final: 0.8455 (tm-30) REVERT: r 1 MET cc_start: 0.8175 (ppp) cc_final: 0.7727 (ppp) REVERT: r 4 GLU cc_start: 0.8933 (mp0) cc_final: 0.8626 (mp0) REVERT: r 79 ASP cc_start: 0.8822 (m-30) cc_final: 0.8600 (m-30) REVERT: t 24 ASN cc_start: 0.9329 (m-40) cc_final: 0.8895 (t0) REVERT: t 45 ASP cc_start: 0.9541 (OUTLIER) cc_final: 0.9121 (m-30) REVERT: t 48 MET cc_start: 0.9242 (mmm) cc_final: 0.8878 (mmm) REVERT: t 50 MET cc_start: 0.9496 (OUTLIER) cc_final: 0.9153 (mtm) REVERT: u 64 LYS cc_start: 0.9140 (tppp) cc_final: 0.8863 (ttmm) REVERT: w 13 GLU cc_start: 0.8918 (pp20) cc_final: 0.8658 (pp20) REVERT: w 36 GLN cc_start: 0.8426 (mp10) cc_final: 0.8056 (mp10) REVERT: w 39 GLN cc_start: 0.9263 (mt0) cc_final: 0.8785 (mm-40) REVERT: 1 6 VAL cc_start: 0.9545 (t) cc_final: 0.9318 (m) REVERT: 3 1 MET cc_start: 0.7628 (ptt) cc_final: 0.7307 (mpp) REVERT: 4 23 LYS cc_start: 0.9057 (ptpp) cc_final: 0.8747 (mttm) REVERT: 4 32 LEU cc_start: 0.9149 (tp) cc_final: 0.8847 (tt) outliers start: 267 outliers final: 197 residues processed: 1490 average time/residue: 1.3363 time to fit residues: 3506.1816 Evaluate side-chains 1518 residues out of total 4893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 1307 time to evaluate : 6.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 21 TYR Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 60 GLN Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 133 ILE Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 141 ASP Chi-restraints excluded: chain I residue 2 ARG Chi-restraints excluded: chain I residue 16 GLU Chi-restraints excluded: chain I residue 33 GLU Chi-restraints excluded: chain I residue 52 ASN Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 55 HIS Chi-restraints excluded: chain I residue 93 LYS Chi-restraints excluded: chain I residue 98 GLU Chi-restraints excluded: chain J residue 91 ARG Chi-restraints excluded: chain J residue 124 SER Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 89 ASP Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 67 LYS Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain M residue 17 LEU Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain N residue 31 VAL Chi-restraints excluded: chain N residue 34 THR Chi-restraints excluded: chain N residue 79 LYS Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 120 CYS Chi-restraints excluded: chain O residue 18 SER Chi-restraints excluded: chain O residue 26 CYS Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 89 LEU Chi-restraints excluded: chain O residue 108 ASP Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 48 SER Chi-restraints excluded: chain Q residue 58 SER Chi-restraints excluded: chain R residue 13 GLU Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain S residue 55 ASP Chi-restraints excluded: chain T residue 56 ASP Chi-restraints excluded: chain T residue 60 ILE Chi-restraints excluded: chain U residue 24 ASP Chi-restraints excluded: chain U residue 29 LYS Chi-restraints excluded: chain U residue 32 ILE Chi-restraints excluded: chain U residue 67 LEU Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain V residue 3 SER Chi-restraints excluded: chain V residue 10 ILE Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain W residue 11 ILE Chi-restraints excluded: chain W residue 38 ILE Chi-restraints excluded: chain W residue 56 ILE Chi-restraints excluded: chain W residue 82 ILE Chi-restraints excluded: chain X residue 20 ARG Chi-restraints excluded: chain X residue 28 LEU Chi-restraints excluded: chain X residue 30 GLU Chi-restraints excluded: chain a residue 44 ASN Chi-restraints excluded: chain a residue 66 PHE Chi-restraints excluded: chain b residue 2 ILE Chi-restraints excluded: chain b residue 81 GLU Chi-restraints excluded: chain b residue 86 GLU Chi-restraints excluded: chain b residue 126 ASN Chi-restraints excluded: chain b residue 199 SER Chi-restraints excluded: chain c residue 19 PHE Chi-restraints excluded: chain c residue 77 ILE Chi-restraints excluded: chain c residue 141 MET Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain c residue 175 ILE Chi-restraints excluded: chain d residue 39 VAL Chi-restraints excluded: chain d residue 51 ASN Chi-restraints excluded: chain d residue 89 THR Chi-restraints excluded: chain d residue 133 GLU Chi-restraints excluded: chain d residue 148 VAL Chi-restraints excluded: chain d residue 158 THR Chi-restraints excluded: chain e residue 36 LEU Chi-restraints excluded: chain f residue 50 ARG Chi-restraints excluded: chain f residue 114 GLU Chi-restraints excluded: chain f residue 130 VAL Chi-restraints excluded: chain g residue 85 ILE Chi-restraints excluded: chain h residue 60 ASP Chi-restraints excluded: chain h residue 80 HIS Chi-restraints excluded: chain h residue 114 LEU Chi-restraints excluded: chain i residue 3 GLN Chi-restraints excluded: chain i residue 32 TYR Chi-restraints excluded: chain i residue 37 ASP Chi-restraints excluded: chain i residue 90 ASN Chi-restraints excluded: chain j residue 6 LEU Chi-restraints excluded: chain j residue 42 SER Chi-restraints excluded: chain j residue 67 THR Chi-restraints excluded: chain j residue 74 THR Chi-restraints excluded: chain j residue 77 ILE Chi-restraints excluded: chain k residue 12 MET Chi-restraints excluded: chain k residue 46 ILE Chi-restraints excluded: chain k residue 124 LEU Chi-restraints excluded: chain k residue 126 ILE Chi-restraints excluded: chain k residue 132 THR Chi-restraints excluded: chain k residue 136 MET Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 24 MET Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 48 VAL Chi-restraints excluded: chain l residue 51 LEU Chi-restraints excluded: chain l residue 57 THR Chi-restraints excluded: chain l residue 117 ASP Chi-restraints excluded: chain m residue 19 GLN Chi-restraints excluded: chain m residue 28 VAL Chi-restraints excluded: chain m residue 47 VAL Chi-restraints excluded: chain m residue 49 VAL Chi-restraints excluded: chain m residue 53 THR Chi-restraints excluded: chain m residue 67 ASN Chi-restraints excluded: chain n residue 49 ILE Chi-restraints excluded: chain n residue 64 SER Chi-restraints excluded: chain n residue 65 ASN Chi-restraints excluded: chain n residue 82 SER Chi-restraints excluded: chain n residue 83 ILE Chi-restraints excluded: chain o residue 8 ILE Chi-restraints excluded: chain o residue 17 LEU Chi-restraints excluded: chain o residue 28 SER Chi-restraints excluded: chain o residue 39 ILE Chi-restraints excluded: chain o residue 79 ILE Chi-restraints excluded: chain o residue 86 SER Chi-restraints excluded: chain p residue 7 SER Chi-restraints excluded: chain p residue 38 VAL Chi-restraints excluded: chain q residue 4 ILE Chi-restraints excluded: chain q residue 23 LEU Chi-restraints excluded: chain q residue 36 LEU Chi-restraints excluded: chain q residue 67 ASP Chi-restraints excluded: chain q residue 74 ILE Chi-restraints excluded: chain q residue 95 ARG Chi-restraints excluded: chain q residue 96 ILE Chi-restraints excluded: chain q residue 101 SER Chi-restraints excluded: chain r residue 11 LEU Chi-restraints excluded: chain r residue 39 THR Chi-restraints excluded: chain r residue 78 SER Chi-restraints excluded: chain s residue 40 LEU Chi-restraints excluded: chain s residue 48 VAL Chi-restraints excluded: chain t residue 5 ASN Chi-restraints excluded: chain t residue 45 ASP Chi-restraints excluded: chain t residue 50 MET Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 32 ILE Chi-restraints excluded: chain u residue 49 CYS Chi-restraints excluded: chain u residue 52 ASP Chi-restraints excluded: chain u residue 63 VAL Chi-restraints excluded: chain v residue 13 THR Chi-restraints excluded: chain v residue 64 ASP Chi-restraints excluded: chain x residue 4 ILE Chi-restraints excluded: chain x residue 8 GLN Chi-restraints excluded: chain x residue 9 THR Chi-restraints excluded: chain x residue 23 LEU Chi-restraints excluded: chain x residue 34 THR Chi-restraints excluded: chain y residue 5 ASN Chi-restraints excluded: chain y residue 27 LEU Chi-restraints excluded: chain z residue 4 ILE Chi-restraints excluded: chain z residue 12 SER Chi-restraints excluded: chain z residue 21 THR Chi-restraints excluded: chain z residue 22 THR Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain z residue 28 THR Chi-restraints excluded: chain 0 residue 4 THR Chi-restraints excluded: chain 0 residue 42 LEU Chi-restraints excluded: chain 0 residue 44 VAL Chi-restraints excluded: chain 1 residue 60 CYS Chi-restraints excluded: chain 2 residue 17 VAL Chi-restraints excluded: chain 3 residue 50 VAL Chi-restraints excluded: chain 3 residue 54 VAL Chi-restraints excluded: chain 3 residue 108 VAL Chi-restraints excluded: chain 4 residue 4 ASP Chi-restraints excluded: chain 4 residue 22 MET Chi-restraints excluded: chain 4 residue 31 ASP Chi-restraints excluded: chain 4 residue 34 LEU Chi-restraints excluded: chain 4 residue 58 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 970 optimal weight: 9.9990 chunk 113 optimal weight: 40.0000 chunk 573 optimal weight: 10.0000 chunk 734 optimal weight: 6.9990 chunk 569 optimal weight: 20.0000 chunk 847 optimal weight: 9.9990 chunk 561 optimal weight: 10.0000 chunk 1002 optimal weight: 10.0000 chunk 627 optimal weight: 20.0000 chunk 611 optimal weight: 60.0000 chunk 462 optimal weight: 10.0000 overall best weight: 9.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN ** G 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 121 ASN ** L 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 58 ASN ** N 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 115 GLN c 136 GLN ** e 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 142 GLN h 40 HIS h 58 ASN h 80 HIS h 128 ASN i 29 HIS ** l 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 15 ASN ** w 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 159524 Z= 0.333 Angle : 0.726 13.962 238500 Z= 0.388 Chirality : 0.038 0.380 30377 Planarity : 0.007 0.127 12889 Dihedral : 23.908 179.833 79389 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.56 % Favored : 90.02 % Rotamer: Outliers : 5.36 % Allowed : 22.59 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.11), residues: 5891 helix: -0.02 (0.12), residues: 1880 sheet: -1.11 (0.16), residues: 1085 loop : -1.64 (0.11), residues: 2926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 95 HIS 0.017 0.001 HIS F 5 PHE 0.020 0.002 PHE a 66 TYR 0.033 0.002 TYR E 212 ARG 0.012 0.001 ARG T 10 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11782 Ramachandran restraints generated. 5891 Oldfield, 0 Emsley, 5891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11782 Ramachandran restraints generated. 5891 Oldfield, 0 Emsley, 5891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1621 residues out of total 4893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 1360 time to evaluate : 6.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 21 TYR cc_start: 0.8893 (OUTLIER) cc_final: 0.8146 (p90) REVERT: E 93 HIS cc_start: 0.8888 (m90) cc_final: 0.8278 (m-70) REVERT: E 119 GLN cc_start: 0.9331 (mt0) cc_final: 0.9064 (pp30) REVERT: F 141 MET cc_start: 0.9289 (mmm) cc_final: 0.8917 (mmm) REVERT: F 169 GLU cc_start: 0.9149 (tm-30) cc_final: 0.8877 (tm-30) REVERT: G 102 TYR cc_start: 0.8950 (t80) cc_final: 0.8632 (t80) REVERT: G 139 ASN cc_start: 0.9228 (t0) cc_final: 0.8991 (p0) REVERT: G 203 TYR cc_start: 0.8977 (m-80) cc_final: 0.8611 (m-80) REVERT: H 11 GLN cc_start: 0.9013 (pp30) cc_final: 0.8655 (pp30) REVERT: H 60 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8110 (tp-100) REVERT: H 61 LYS cc_start: 0.8939 (mtmt) cc_final: 0.8645 (mtmt) REVERT: H 64 GLU cc_start: 0.8822 (mp0) cc_final: 0.8198 (mp0) REVERT: H 69 ASN cc_start: 0.9194 (t0) cc_final: 0.8734 (t0) REVERT: H 121 ASN cc_start: 0.7229 (OUTLIER) cc_final: 0.6793 (m110) REVERT: I 2 ARG cc_start: 0.7257 (OUTLIER) cc_final: 0.6956 (mmm-85) REVERT: I 90 MET cc_start: 0.9011 (mmm) cc_final: 0.8792 (mmm) REVERT: K 26 MET cc_start: 0.8831 (ptm) cc_final: 0.8593 (ptm) REVERT: K 53 ASP cc_start: 0.8495 (p0) cc_final: 0.7805 (p0) REVERT: K 57 GLU cc_start: 0.8425 (tp30) cc_final: 0.7827 (tp30) REVERT: K 59 GLU cc_start: 0.8911 (pm20) cc_final: 0.8628 (pm20) REVERT: L 21 LYS cc_start: 0.9040 (ptmm) cc_final: 0.8724 (ptmm) REVERT: L 26 LYS cc_start: 0.9225 (ptpp) cc_final: 0.9015 (ptpp) REVERT: L 52 GLU cc_start: 0.9167 (mp0) cc_final: 0.8931 (mp0) REVERT: L 56 MET cc_start: 0.9172 (tpp) cc_final: 0.8386 (tpp) REVERT: L 87 MET cc_start: 0.8397 (pmm) cc_final: 0.8075 (pmm) REVERT: M 19 ASP cc_start: 0.9341 (m-30) cc_final: 0.9084 (p0) REVERT: N 79 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8434 (pttm) REVERT: N 93 GLU cc_start: 0.8932 (pm20) cc_final: 0.8498 (pp20) REVERT: P 65 GLU cc_start: 0.8915 (mp0) cc_final: 0.8699 (mp0) REVERT: P 77 LYS cc_start: 0.9425 (ttmm) cc_final: 0.8952 (tppp) REVERT: P 80 MET cc_start: 0.8997 (mtp) cc_final: 0.8779 (ttm) REVERT: T 16 MET cc_start: 0.9045 (ptm) cc_final: 0.8459 (ptm) REVERT: T 17 GLU cc_start: 0.8492 (tm-30) cc_final: 0.8223 (tm-30) REVERT: U 56 ARG cc_start: 0.9134 (mtt90) cc_final: 0.8893 (mtt90) REVERT: V 19 GLU cc_start: 0.9115 (pp20) cc_final: 0.8843 (pp20) REVERT: V 28 LYS cc_start: 0.8755 (mmmt) cc_final: 0.8248 (mmmt) REVERT: W 26 MET cc_start: 0.9000 (ppp) cc_final: 0.8759 (ppp) REVERT: W 58 ASP cc_start: 0.9084 (p0) cc_final: 0.8879 (p0) REVERT: X 17 ARG cc_start: 0.6997 (mmp80) cc_final: 0.6748 (mmp80) REVERT: X 20 ARG cc_start: 0.7145 (OUTLIER) cc_final: 0.6565 (mtt90) REVERT: c 195 GLN cc_start: 0.9533 (mt0) cc_final: 0.9192 (mt0) REVERT: d 25 MET cc_start: 0.9494 (mmt) cc_final: 0.9214 (mmm) REVERT: d 89 THR cc_start: 0.9277 (OUTLIER) cc_final: 0.8936 (p) REVERT: d 99 PHE cc_start: 0.9378 (t80) cc_final: 0.9140 (t80) REVERT: e 94 ARG cc_start: 0.8979 (mmm-85) cc_final: 0.8761 (mmm-85) REVERT: f 8 LYS cc_start: 0.8818 (mmmt) cc_final: 0.8292 (tptp) REVERT: f 114 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8268 (tm-30) REVERT: g 85 ILE cc_start: 0.0311 (OUTLIER) cc_final: -0.0030 (pt) REVERT: h 49 ASP cc_start: 0.8628 (t0) cc_final: 0.8279 (t0) REVERT: h 131 ASN cc_start: 0.8597 (p0) cc_final: 0.8370 (p0) REVERT: i 104 THR cc_start: 0.9147 (t) cc_final: 0.8265 (t) REVERT: j 135 ILE cc_start: 0.9645 (mt) cc_final: 0.9331 (tp) REVERT: m 76 LYS cc_start: 0.9576 (tttt) cc_final: 0.9218 (tptt) REVERT: m 78 VAL cc_start: 0.9723 (t) cc_final: 0.9504 (p) REVERT: n 111 GLU cc_start: 0.8980 (tm-30) cc_final: 0.8130 (tm-30) REVERT: q 52 GLU cc_start: 0.8777 (tm-30) cc_final: 0.8460 (tm-30) REVERT: r 1 MET cc_start: 0.8160 (ppp) cc_final: 0.7671 (ppp) REVERT: r 2 ILE cc_start: 0.7347 (pt) cc_final: 0.7033 (pt) REVERT: r 4 GLU cc_start: 0.8949 (mp0) cc_final: 0.8655 (mp0) REVERT: t 24 ASN cc_start: 0.9312 (m-40) cc_final: 0.8892 (t0) REVERT: t 45 ASP cc_start: 0.9556 (OUTLIER) cc_final: 0.9065 (m-30) REVERT: t 48 MET cc_start: 0.9251 (mmm) cc_final: 0.8844 (mmm) REVERT: t 50 MET cc_start: 0.9502 (OUTLIER) cc_final: 0.9114 (mtm) REVERT: v 76 LYS cc_start: 0.9337 (mmtt) cc_final: 0.9075 (mmtt) REVERT: w 13 GLU cc_start: 0.8952 (pp20) cc_final: 0.8552 (pp20) REVERT: w 39 GLN cc_start: 0.9248 (mt0) cc_final: 0.8771 (mm-40) REVERT: x 5 LYS cc_start: 0.8882 (mmmm) cc_final: 0.8682 (mmmm) REVERT: 0 1 MET cc_start: 0.6173 (ptt) cc_final: 0.5711 (ptt) REVERT: 1 6 VAL cc_start: 0.9557 (t) cc_final: 0.9336 (m) REVERT: 3 52 MET cc_start: -0.1716 (ptt) cc_final: -0.1976 (ptt) REVERT: 4 23 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8759 (mmtp) REVERT: 4 32 LEU cc_start: 0.9170 (tp) cc_final: 0.8883 (tt) outliers start: 261 outliers final: 213 residues processed: 1462 average time/residue: 1.2589 time to fit residues: 3225.2123 Evaluate side-chains 1525 residues out of total 4893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 1300 time to evaluate : 5.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 21 TYR Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 60 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 166 LYS Chi-restraints excluded: chain G residue 189 ASP Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 60 GLN Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 121 ASN Chi-restraints excluded: chain H residue 133 ILE Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 141 ASP Chi-restraints excluded: chain I residue 2 ARG Chi-restraints excluded: chain I residue 16 GLU Chi-restraints excluded: chain I residue 33 GLU Chi-restraints excluded: chain I residue 52 ASN Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 55 HIS Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 93 LYS Chi-restraints excluded: chain I residue 98 GLU Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 84 TYR Chi-restraints excluded: chain J residue 91 ARG Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain K residue 125 ILE Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 67 LYS Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain N residue 31 VAL Chi-restraints excluded: chain N residue 34 THR Chi-restraints excluded: chain N residue 79 LYS Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 120 CYS Chi-restraints excluded: chain O residue 18 SER Chi-restraints excluded: chain O residue 26 CYS Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 89 LEU Chi-restraints excluded: chain O residue 108 ASP Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 48 SER Chi-restraints excluded: chain P residue 67 ASP Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 58 SER Chi-restraints excluded: chain R residue 13 GLU Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 19 VAL Chi-restraints excluded: chain S residue 55 ASP Chi-restraints excluded: chain T residue 56 ASP Chi-restraints excluded: chain T residue 60 ILE Chi-restraints excluded: chain U residue 24 ASP Chi-restraints excluded: chain U residue 29 LYS Chi-restraints excluded: chain U residue 32 ILE Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain U residue 67 LEU Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain V residue 3 SER Chi-restraints excluded: chain V residue 10 ILE Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain W residue 11 ILE Chi-restraints excluded: chain W residue 56 ILE Chi-restraints excluded: chain W residue 82 ILE Chi-restraints excluded: chain X residue 5 VAL Chi-restraints excluded: chain X residue 20 ARG Chi-restraints excluded: chain X residue 27 VAL Chi-restraints excluded: chain X residue 28 LEU Chi-restraints excluded: chain X residue 30 GLU Chi-restraints excluded: chain a residue 5 CYS Chi-restraints excluded: chain a residue 44 ASN Chi-restraints excluded: chain a residue 66 PHE Chi-restraints excluded: chain b residue 2 ILE Chi-restraints excluded: chain b residue 81 GLU Chi-restraints excluded: chain b residue 86 GLU Chi-restraints excluded: chain b residue 126 ASN Chi-restraints excluded: chain b residue 199 SER Chi-restraints excluded: chain c residue 19 PHE Chi-restraints excluded: chain c residue 25 GLU Chi-restraints excluded: chain c residue 77 ILE Chi-restraints excluded: chain c residue 141 MET Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain c residue 175 ILE Chi-restraints excluded: chain d residue 39 VAL Chi-restraints excluded: chain d residue 51 ASN Chi-restraints excluded: chain d residue 89 THR Chi-restraints excluded: chain d residue 133 GLU Chi-restraints excluded: chain d residue 148 VAL Chi-restraints excluded: chain d residue 158 THR Chi-restraints excluded: chain e residue 36 LEU Chi-restraints excluded: chain f residue 50 ARG Chi-restraints excluded: chain f residue 114 GLU Chi-restraints excluded: chain f residue 130 VAL Chi-restraints excluded: chain g residue 85 ILE Chi-restraints excluded: chain h residue 60 ASP Chi-restraints excluded: chain h residue 114 LEU Chi-restraints excluded: chain i residue 3 GLN Chi-restraints excluded: chain i residue 32 TYR Chi-restraints excluded: chain i residue 37 ASP Chi-restraints excluded: chain i residue 90 ASN Chi-restraints excluded: chain j residue 6 LEU Chi-restraints excluded: chain j residue 42 SER Chi-restraints excluded: chain j residue 74 THR Chi-restraints excluded: chain j residue 77 ILE Chi-restraints excluded: chain j residue 100 ILE Chi-restraints excluded: chain k residue 12 MET Chi-restraints excluded: chain k residue 46 ILE Chi-restraints excluded: chain k residue 124 LEU Chi-restraints excluded: chain k residue 132 THR Chi-restraints excluded: chain k residue 136 MET Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 36 THR Chi-restraints excluded: chain l residue 48 VAL Chi-restraints excluded: chain l residue 51 LEU Chi-restraints excluded: chain l residue 57 THR Chi-restraints excluded: chain l residue 117 ASP Chi-restraints excluded: chain m residue 28 VAL Chi-restraints excluded: chain m residue 47 VAL Chi-restraints excluded: chain m residue 53 THR Chi-restraints excluded: chain m residue 67 ASN Chi-restraints excluded: chain m residue 69 ASP Chi-restraints excluded: chain n residue 49 ILE Chi-restraints excluded: chain n residue 64 SER Chi-restraints excluded: chain n residue 65 ASN Chi-restraints excluded: chain n residue 82 SER Chi-restraints excluded: chain n residue 83 ILE Chi-restraints excluded: chain o residue 8 ILE Chi-restraints excluded: chain o residue 17 LEU Chi-restraints excluded: chain o residue 28 SER Chi-restraints excluded: chain o residue 39 ILE Chi-restraints excluded: chain o residue 43 GLN Chi-restraints excluded: chain o residue 79 ILE Chi-restraints excluded: chain o residue 86 SER Chi-restraints excluded: chain p residue 7 SER Chi-restraints excluded: chain p residue 38 VAL Chi-restraints excluded: chain q residue 4 ILE Chi-restraints excluded: chain q residue 19 LEU Chi-restraints excluded: chain q residue 23 LEU Chi-restraints excluded: chain q residue 36 LEU Chi-restraints excluded: chain q residue 67 ASP Chi-restraints excluded: chain q residue 69 LEU Chi-restraints excluded: chain q residue 74 ILE Chi-restraints excluded: chain q residue 95 ARG Chi-restraints excluded: chain q residue 96 ILE Chi-restraints excluded: chain q residue 101 SER Chi-restraints excluded: chain r residue 39 THR Chi-restraints excluded: chain r residue 78 SER Chi-restraints excluded: chain s residue 40 LEU Chi-restraints excluded: chain s residue 48 VAL Chi-restraints excluded: chain t residue 45 ASP Chi-restraints excluded: chain t residue 50 MET Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 32 ILE Chi-restraints excluded: chain u residue 49 CYS Chi-restraints excluded: chain u residue 52 ASP Chi-restraints excluded: chain u residue 63 VAL Chi-restraints excluded: chain v residue 13 THR Chi-restraints excluded: chain v residue 63 ILE Chi-restraints excluded: chain v residue 64 ASP Chi-restraints excluded: chain x residue 4 ILE Chi-restraints excluded: chain x residue 8 GLN Chi-restraints excluded: chain x residue 9 THR Chi-restraints excluded: chain x residue 23 LEU Chi-restraints excluded: chain x residue 28 LEU Chi-restraints excluded: chain x residue 34 THR Chi-restraints excluded: chain y residue 5 ASN Chi-restraints excluded: chain y residue 27 LEU Chi-restraints excluded: chain z residue 4 ILE Chi-restraints excluded: chain z residue 12 SER Chi-restraints excluded: chain z residue 21 THR Chi-restraints excluded: chain z residue 22 THR Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain z residue 28 THR Chi-restraints excluded: chain 0 residue 4 THR Chi-restraints excluded: chain 0 residue 42 LEU Chi-restraints excluded: chain 0 residue 44 VAL Chi-restraints excluded: chain 1 residue 5 THR Chi-restraints excluded: chain 2 residue 17 VAL Chi-restraints excluded: chain 3 residue 50 VAL Chi-restraints excluded: chain 3 residue 54 VAL Chi-restraints excluded: chain 3 residue 108 VAL Chi-restraints excluded: chain 4 residue 4 ASP Chi-restraints excluded: chain 4 residue 22 MET Chi-restraints excluded: chain 4 residue 23 LYS Chi-restraints excluded: chain 4 residue 31 ASP Chi-restraints excluded: chain 4 residue 34 LEU Chi-restraints excluded: chain 4 residue 58 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 620 optimal weight: 9.9990 chunk 400 optimal weight: 20.0000 chunk 598 optimal weight: 10.0000 chunk 301 optimal weight: 5.9990 chunk 196 optimal weight: 6.9990 chunk 194 optimal weight: 0.2980 chunk 637 optimal weight: 20.0000 chunk 682 optimal weight: 20.0000 chunk 495 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 787 optimal weight: 30.0000 overall best weight: 6.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 ASN H 121 ASN ** L 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 152 GLN ** b 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 115 GLN c 136 GLN ** e 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 142 GLN i 29 HIS ** l 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 19 GLN ** o 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 82 HIS ** p 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 28 ASN v 15 ASN ** w 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 159524 Z= 0.251 Angle : 0.694 14.187 238500 Z= 0.374 Chirality : 0.036 0.401 30377 Planarity : 0.006 0.124 12889 Dihedral : 23.894 179.956 79389 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.41 % Allowed : 9.27 % Favored : 90.32 % Rotamer: Outliers : 5.14 % Allowed : 24.09 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.11), residues: 5891 helix: 0.09 (0.12), residues: 1879 sheet: -1.01 (0.16), residues: 1076 loop : -1.59 (0.11), residues: 2936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 95 HIS 0.017 0.001 HIS h 80 PHE 0.025 0.001 PHE K 65 TYR 0.037 0.002 TYR E 212 ARG 0.014 0.001 ARG X 6 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11782 Ramachandran restraints generated. 5891 Oldfield, 0 Emsley, 5891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11782 Ramachandran restraints generated. 5891 Oldfield, 0 Emsley, 5891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1630 residues out of total 4893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 1380 time to evaluate : 8.436 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: E 21 TYR cc_start: 0.8873 (OUTLIER) cc_final: 0.8322 (p90) REVERT: E 119 GLN cc_start: 0.9296 (mt0) cc_final: 0.9093 (pp30) REVERT: E 162 VAL cc_start: 0.9595 (t) cc_final: 0.9354 (t) REVERT: F 141 MET cc_start: 0.9279 (mmm) cc_final: 0.8852 (mmm) REVERT: F 169 GLU cc_start: 0.9127 (tm-30) cc_final: 0.8833 (tm-30) REVERT: G 102 TYR cc_start: 0.8900 (t80) cc_final: 0.8610 (t80) REVERT: G 139 ASN cc_start: 0.9240 (t0) cc_final: 0.9015 (p0) REVERT: H 11 GLN cc_start: 0.8951 (pp30) cc_final: 0.8627 (pp30) REVERT: H 15 ILE cc_start: 0.9399 (OUTLIER) cc_final: 0.9138 (mp) REVERT: H 60 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8128 (tp-100) REVERT: H 64 GLU cc_start: 0.8815 (mp0) cc_final: 0.8296 (mp0) REVERT: H 69 ASN cc_start: 0.9202 (t0) cc_final: 0.8782 (t0) REVERT: H 151 MET cc_start: 0.9558 (mmp) cc_final: 0.9086 (mpp) REVERT: I 90 MET cc_start: 0.8943 (mmm) cc_final: 0.8728 (mmm) REVERT: J 84 TYR cc_start: 0.7590 (OUTLIER) cc_final: 0.7288 (p90) REVERT: K 26 MET cc_start: 0.8887 (ptm) cc_final: 0.8620 (ptm) REVERT: K 53 ASP cc_start: 0.8448 (p0) cc_final: 0.7760 (p0) REVERT: K 57 GLU cc_start: 0.8468 (tp30) cc_final: 0.8222 (tp30) REVERT: K 59 GLU cc_start: 0.8850 (pm20) cc_final: 0.8570 (pm20) REVERT: L 21 LYS cc_start: 0.9068 (ptmm) cc_final: 0.8737 (ptmm) REVERT: L 31 GLN cc_start: 0.9337 (mp10) cc_final: 0.9130 (mp10) REVERT: L 49 GLN cc_start: 0.9340 (pt0) cc_final: 0.9070 (pt0) REVERT: L 52 GLU cc_start: 0.9110 (mp0) cc_final: 0.8886 (mp0) REVERT: L 56 MET cc_start: 0.9365 (tpp) cc_final: 0.9139 (tpt) REVERT: L 71 ILE cc_start: 0.9516 (OUTLIER) cc_final: 0.9135 (tp) REVERT: N 79 LYS cc_start: 0.8677 (pttm) cc_final: 0.8374 (pttm) REVERT: N 93 GLU cc_start: 0.8908 (pm20) cc_final: 0.8467 (pp20) REVERT: P 62 PHE cc_start: 0.7651 (t80) cc_final: 0.7005 (m-80) REVERT: P 77 LYS cc_start: 0.9411 (ttmm) cc_final: 0.8928 (tppp) REVERT: P 80 MET cc_start: 0.8959 (mtp) cc_final: 0.8675 (ttm) REVERT: T 16 MET cc_start: 0.9070 (ptm) cc_final: 0.8536 (ptm) REVERT: T 17 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8285 (tm-30) REVERT: T 78 VAL cc_start: 0.8159 (OUTLIER) cc_final: 0.7880 (m) REVERT: U 56 ARG cc_start: 0.9110 (mtt90) cc_final: 0.8853 (mtt90) REVERT: V 19 GLU cc_start: 0.9099 (pp20) cc_final: 0.8828 (pp20) REVERT: V 28 LYS cc_start: 0.8800 (mmmt) cc_final: 0.8390 (mmmt) REVERT: W 58 ASP cc_start: 0.9058 (p0) cc_final: 0.8851 (p0) REVERT: W 59 ARG cc_start: 0.9252 (ttm-80) cc_final: 0.8964 (ttm-80) REVERT: X 20 ARG cc_start: 0.7170 (OUTLIER) cc_final: 0.6789 (mtt90) REVERT: X 50 SER cc_start: 0.9395 (t) cc_final: 0.9074 (p) REVERT: a 97 ASP cc_start: 0.8997 (p0) cc_final: 0.8005 (p0) REVERT: c 195 GLN cc_start: 0.9505 (mt0) cc_final: 0.9178 (mt0) REVERT: d 25 MET cc_start: 0.9424 (mmt) cc_final: 0.9201 (mmm) REVERT: d 99 PHE cc_start: 0.9332 (t80) cc_final: 0.9089 (t80) REVERT: d 126 ASN cc_start: 0.8613 (m-40) cc_final: 0.8385 (m110) REVERT: f 8 LYS cc_start: 0.8779 (mmmt) cc_final: 0.8387 (tptp) REVERT: f 114 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8301 (tm-30) REVERT: g 85 ILE cc_start: 0.0029 (OUTLIER) cc_final: -0.0438 (pt) REVERT: h 49 ASP cc_start: 0.8645 (t0) cc_final: 0.8308 (t0) REVERT: h 131 ASN cc_start: 0.8588 (p0) cc_final: 0.8326 (p0) REVERT: i 73 ASP cc_start: 0.9259 (p0) cc_final: 0.8467 (p0) REVERT: j 77 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8793 (tp) REVERT: j 135 ILE cc_start: 0.9625 (mt) cc_final: 0.9345 (tp) REVERT: m 76 LYS cc_start: 0.9573 (tttt) cc_final: 0.9214 (tptt) REVERT: n 111 GLU cc_start: 0.8977 (tm-30) cc_final: 0.8087 (tm-30) REVERT: q 1 MET cc_start: 0.8592 (tpp) cc_final: 0.8101 (tpt) REVERT: q 52 GLU cc_start: 0.8781 (tm-30) cc_final: 0.8487 (tm-30) REVERT: r 2 ILE cc_start: 0.7441 (pt) cc_final: 0.7200 (pt) REVERT: r 79 ASP cc_start: 0.8772 (m-30) cc_final: 0.8537 (m-30) REVERT: t 24 ASN cc_start: 0.9325 (m-40) cc_final: 0.8898 (t0) REVERT: t 45 ASP cc_start: 0.9544 (OUTLIER) cc_final: 0.9062 (m-30) REVERT: t 48 MET cc_start: 0.9262 (mmm) cc_final: 0.8837 (mmm) REVERT: t 50 MET cc_start: 0.9435 (mpp) cc_final: 0.9183 (mtm) REVERT: u 51 ARG cc_start: 0.8582 (ptm160) cc_final: 0.7611 (ptm160) REVERT: v 40 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8141 (mm-30) REVERT: v 75 GLU cc_start: 0.7860 (tt0) cc_final: 0.7579 (tm-30) REVERT: w 13 GLU cc_start: 0.8815 (pp20) cc_final: 0.8447 (pp20) REVERT: w 39 GLN cc_start: 0.9211 (mt0) cc_final: 0.8662 (mm-40) REVERT: z 36 LYS cc_start: 0.9493 (ttpp) cc_final: 0.9244 (ttpp) REVERT: 0 1 MET cc_start: 0.6186 (ptt) cc_final: 0.5821 (ptt) REVERT: 1 6 VAL cc_start: 0.9534 (t) cc_final: 0.9331 (m) REVERT: 3 1 MET cc_start: 0.7745 (ptt) cc_final: 0.6923 (mpp) REVERT: 3 52 MET cc_start: -0.1536 (ptt) cc_final: -0.1841 (ptt) REVERT: 4 32 LEU cc_start: 0.9168 (tp) cc_final: 0.8894 (tt) outliers start: 250 outliers final: 191 residues processed: 1479 average time/residue: 1.2379 time to fit residues: 3209.4245 Evaluate side-chains 1526 residues out of total 4893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 1324 time to evaluate : 6.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 21 TYR Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 35 ASP Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 166 LYS Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 60 GLN Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 141 ASP Chi-restraints excluded: chain I residue 16 GLU Chi-restraints excluded: chain I residue 33 GLU Chi-restraints excluded: chain I residue 52 ASN Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 98 GLU Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 84 TYR Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 89 ASP Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain L residue 20 ILE Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain M residue 87 LEU Chi-restraints excluded: chain N residue 31 VAL Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 34 THR Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 120 CYS Chi-restraints excluded: chain O residue 18 SER Chi-restraints excluded: chain O residue 26 CYS Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 89 LEU Chi-restraints excluded: chain O residue 108 ASP Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 48 SER Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 58 SER Chi-restraints excluded: chain Q residue 80 SER Chi-restraints excluded: chain R residue 13 GLU Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain T residue 56 ASP Chi-restraints excluded: chain T residue 60 ILE Chi-restraints excluded: chain T residue 78 VAL Chi-restraints excluded: chain U residue 67 LEU Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain V residue 3 SER Chi-restraints excluded: chain W residue 11 ILE Chi-restraints excluded: chain W residue 56 ILE Chi-restraints excluded: chain W residue 82 ILE Chi-restraints excluded: chain X residue 5 VAL Chi-restraints excluded: chain X residue 12 ASP Chi-restraints excluded: chain X residue 20 ARG Chi-restraints excluded: chain X residue 27 VAL Chi-restraints excluded: chain X residue 28 LEU Chi-restraints excluded: chain X residue 30 GLU Chi-restraints excluded: chain X residue 34 ARG Chi-restraints excluded: chain a residue 44 ASN Chi-restraints excluded: chain a residue 66 PHE Chi-restraints excluded: chain b residue 81 GLU Chi-restraints excluded: chain b residue 86 GLU Chi-restraints excluded: chain b residue 126 ASN Chi-restraints excluded: chain b residue 199 SER Chi-restraints excluded: chain c residue 19 PHE Chi-restraints excluded: chain c residue 25 GLU Chi-restraints excluded: chain c residue 77 ILE Chi-restraints excluded: chain c residue 141 MET Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain c residue 175 ILE Chi-restraints excluded: chain d residue 39 VAL Chi-restraints excluded: chain d residue 51 ASN Chi-restraints excluded: chain d residue 133 GLU Chi-restraints excluded: chain d residue 148 VAL Chi-restraints excluded: chain d residue 158 THR Chi-restraints excluded: chain e residue 36 LEU Chi-restraints excluded: chain f residue 50 ARG Chi-restraints excluded: chain f residue 114 GLU Chi-restraints excluded: chain f residue 130 VAL Chi-restraints excluded: chain g residue 85 ILE Chi-restraints excluded: chain h residue 60 ASP Chi-restraints excluded: chain h residue 80 HIS Chi-restraints excluded: chain h residue 114 LEU Chi-restraints excluded: chain i residue 3 GLN Chi-restraints excluded: chain i residue 32 TYR Chi-restraints excluded: chain i residue 90 ASN Chi-restraints excluded: chain j residue 6 LEU Chi-restraints excluded: chain j residue 74 THR Chi-restraints excluded: chain j residue 77 ILE Chi-restraints excluded: chain j residue 100 ILE Chi-restraints excluded: chain k residue 12 MET Chi-restraints excluded: chain k residue 46 ILE Chi-restraints excluded: chain k residue 124 LEU Chi-restraints excluded: chain k residue 132 THR Chi-restraints excluded: chain k residue 136 MET Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 36 THR Chi-restraints excluded: chain l residue 48 VAL Chi-restraints excluded: chain l residue 51 LEU Chi-restraints excluded: chain l residue 57 THR Chi-restraints excluded: chain l residue 117 ASP Chi-restraints excluded: chain m residue 19 GLN Chi-restraints excluded: chain m residue 28 VAL Chi-restraints excluded: chain m residue 47 VAL Chi-restraints excluded: chain m residue 53 THR Chi-restraints excluded: chain m residue 67 ASN Chi-restraints excluded: chain m residue 69 ASP Chi-restraints excluded: chain m residue 115 LEU Chi-restraints excluded: chain n residue 49 ILE Chi-restraints excluded: chain n residue 64 SER Chi-restraints excluded: chain n residue 65 ASN Chi-restraints excluded: chain n residue 82 SER Chi-restraints excluded: chain n residue 83 ILE Chi-restraints excluded: chain o residue 8 ILE Chi-restraints excluded: chain o residue 17 LEU Chi-restraints excluded: chain o residue 28 SER Chi-restraints excluded: chain o residue 39 ILE Chi-restraints excluded: chain o residue 43 GLN Chi-restraints excluded: chain o residue 79 ILE Chi-restraints excluded: chain o residue 86 SER Chi-restraints excluded: chain o residue 93 ILE Chi-restraints excluded: chain p residue 7 SER Chi-restraints excluded: chain p residue 38 VAL Chi-restraints excluded: chain p residue 98 ILE Chi-restraints excluded: chain q residue 4 ILE Chi-restraints excluded: chain q residue 23 LEU Chi-restraints excluded: chain q residue 36 LEU Chi-restraints excluded: chain q residue 59 GLU Chi-restraints excluded: chain q residue 67 ASP Chi-restraints excluded: chain q residue 74 ILE Chi-restraints excluded: chain q residue 95 ARG Chi-restraints excluded: chain q residue 96 ILE Chi-restraints excluded: chain q residue 101 SER Chi-restraints excluded: chain r residue 39 THR Chi-restraints excluded: chain r residue 78 SER Chi-restraints excluded: chain s residue 40 LEU Chi-restraints excluded: chain s residue 48 VAL Chi-restraints excluded: chain t residue 5 ASN Chi-restraints excluded: chain t residue 45 ASP Chi-restraints excluded: chain t residue 65 VAL Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 32 ILE Chi-restraints excluded: chain u residue 52 ASP Chi-restraints excluded: chain u residue 63 VAL Chi-restraints excluded: chain v residue 63 ILE Chi-restraints excluded: chain v residue 64 ASP Chi-restraints excluded: chain x residue 4 ILE Chi-restraints excluded: chain x residue 9 THR Chi-restraints excluded: chain x residue 23 LEU Chi-restraints excluded: chain x residue 28 LEU Chi-restraints excluded: chain x residue 31 ILE Chi-restraints excluded: chain x residue 34 THR Chi-restraints excluded: chain x residue 56 VAL Chi-restraints excluded: chain y residue 5 ASN Chi-restraints excluded: chain y residue 27 LEU Chi-restraints excluded: chain z residue 12 SER Chi-restraints excluded: chain z residue 21 THR Chi-restraints excluded: chain z residue 22 THR Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain 0 residue 4 THR Chi-restraints excluded: chain 0 residue 42 LEU Chi-restraints excluded: chain 1 residue 5 THR Chi-restraints excluded: chain 2 residue 17 VAL Chi-restraints excluded: chain 3 residue 50 VAL Chi-restraints excluded: chain 3 residue 54 VAL Chi-restraints excluded: chain 3 residue 108 VAL Chi-restraints excluded: chain 4 residue 4 ASP Chi-restraints excluded: chain 4 residue 22 MET Chi-restraints excluded: chain 4 residue 31 ASP Chi-restraints excluded: chain 4 residue 34 LEU Chi-restraints excluded: chain 4 residue 58 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 911 optimal weight: 7.9990 chunk 960 optimal weight: 6.9990 chunk 876 optimal weight: 20.0000 chunk 934 optimal weight: 20.0000 chunk 562 optimal weight: 10.0000 chunk 406 optimal weight: 20.0000 chunk 733 optimal weight: 10.0000 chunk 286 optimal weight: 20.0000 chunk 844 optimal weight: 10.0000 chunk 883 optimal weight: 7.9990 chunk 930 optimal weight: 9.9990 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 115 GLN ** e 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 142 GLN ** h 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 29 HIS ** l 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 19 GLN o 36 GLN ** o 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 15 ASN ** w 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 58 ASN ** 4 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 159524 Z= 0.312 Angle : 0.721 14.273 238500 Z= 0.386 Chirality : 0.038 0.374 30377 Planarity : 0.007 0.126 12889 Dihedral : 23.888 179.459 79389 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.78 % Favored : 89.83 % Rotamer: Outliers : 5.12 % Allowed : 24.73 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.11), residues: 5891 helix: 0.03 (0.12), residues: 1886 sheet: -0.92 (0.16), residues: 1051 loop : -1.63 (0.11), residues: 2954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 95 HIS 0.013 0.001 HIS G 197 PHE 0.054 0.002 PHE K 65 TYR 0.046 0.002 TYR o 31 ARG 0.035 0.001 ARG X 44 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11782 Ramachandran restraints generated. 5891 Oldfield, 0 Emsley, 5891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11782 Ramachandran restraints generated. 5891 Oldfield, 0 Emsley, 5891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1589 residues out of total 4893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 1340 time to evaluate : 6.334 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: E 21 TYR cc_start: 0.8863 (OUTLIER) cc_final: 0.8377 (p90) REVERT: E 93 HIS cc_start: 0.8883 (m90) cc_final: 0.8291 (m-70) REVERT: E 119 GLN cc_start: 0.9375 (mt0) cc_final: 0.9157 (pp30) REVERT: F 141 MET cc_start: 0.9290 (mmm) cc_final: 0.8841 (mmm) REVERT: F 169 GLU cc_start: 0.9122 (tm-30) cc_final: 0.8800 (tm-30) REVERT: G 102 TYR cc_start: 0.8961 (t80) cc_final: 0.8669 (t80) REVERT: H 11 GLN cc_start: 0.8959 (pp30) cc_final: 0.8609 (pp30) REVERT: H 15 ILE cc_start: 0.9418 (OUTLIER) cc_final: 0.9187 (mp) REVERT: H 60 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8117 (tp-100) REVERT: H 61 LYS cc_start: 0.8847 (mtmt) cc_final: 0.8505 (ptpt) REVERT: H 64 GLU cc_start: 0.8820 (mp0) cc_final: 0.8184 (mp0) REVERT: H 69 ASN cc_start: 0.9196 (t0) cc_final: 0.8776 (t0) REVERT: I 2 ARG cc_start: 0.7100 (OUTLIER) cc_final: 0.6862 (mmm-85) REVERT: I 40 GLU cc_start: 0.7850 (tt0) cc_final: 0.7517 (tt0) REVERT: I 69 GLU cc_start: 0.9116 (pm20) cc_final: 0.8912 (pm20) REVERT: I 90 MET cc_start: 0.9024 (mmm) cc_final: 0.8809 (mmm) REVERT: K 26 MET cc_start: 0.8950 (ptm) cc_final: 0.8696 (ptm) REVERT: K 53 ASP cc_start: 0.8480 (p0) cc_final: 0.7775 (p0) REVERT: K 57 GLU cc_start: 0.8476 (tp30) cc_final: 0.8233 (tp30) REVERT: K 59 GLU cc_start: 0.8860 (pm20) cc_final: 0.8586 (pm20) REVERT: K 117 GLN cc_start: 0.9463 (mp10) cc_final: 0.9203 (mm-40) REVERT: L 21 LYS cc_start: 0.9084 (ptmm) cc_final: 0.8741 (ptmm) REVERT: L 31 GLN cc_start: 0.9374 (mp10) cc_final: 0.9165 (mp10) REVERT: L 52 GLU cc_start: 0.9164 (mp0) cc_final: 0.8945 (mp0) REVERT: L 56 MET cc_start: 0.9354 (tpp) cc_final: 0.9136 (tpt) REVERT: L 71 ILE cc_start: 0.9494 (OUTLIER) cc_final: 0.9155 (tp) REVERT: M 30 LYS cc_start: 0.9618 (ttmm) cc_final: 0.9141 (mmtt) REVERT: N 79 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8388 (pttm) REVERT: N 93 GLU cc_start: 0.8941 (pm20) cc_final: 0.8516 (pp20) REVERT: P 62 PHE cc_start: 0.7693 (t80) cc_final: 0.7001 (m-80) REVERT: P 77 LYS cc_start: 0.9421 (ttmm) cc_final: 0.8940 (tppp) REVERT: P 80 MET cc_start: 0.8980 (mtp) cc_final: 0.8686 (ttm) REVERT: T 16 MET cc_start: 0.9096 (ptm) cc_final: 0.8524 (ptm) REVERT: T 17 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8292 (tm-30) REVERT: T 78 VAL cc_start: 0.8161 (OUTLIER) cc_final: 0.7870 (m) REVERT: U 56 ARG cc_start: 0.9110 (mtt90) cc_final: 0.8842 (mtt90) REVERT: V 19 GLU cc_start: 0.9130 (pp20) cc_final: 0.8856 (pp20) REVERT: V 28 LYS cc_start: 0.8833 (mmmt) cc_final: 0.8456 (mmmt) REVERT: W 58 ASP cc_start: 0.9027 (p0) cc_final: 0.8813 (p0) REVERT: W 59 ARG cc_start: 0.9257 (ttm-80) cc_final: 0.9014 (ttm-80) REVERT: X 20 ARG cc_start: 0.7061 (OUTLIER) cc_final: 0.6494 (mtt90) REVERT: X 44 ARG cc_start: 0.9092 (ppt90) cc_final: 0.8846 (ppt90) REVERT: X 50 SER cc_start: 0.9411 (t) cc_final: 0.9104 (p) REVERT: a 271 SER cc_start: 0.9212 (t) cc_final: 0.8932 (p) REVERT: c 195 GLN cc_start: 0.9517 (mt0) cc_final: 0.9212 (mt0) REVERT: d 99 PHE cc_start: 0.9347 (t80) cc_final: 0.9084 (t80) REVERT: e 74 MET cc_start: 0.8739 (ptp) cc_final: 0.8346 (ptm) REVERT: f 8 LYS cc_start: 0.8794 (mmmt) cc_final: 0.8382 (tptp) REVERT: f 114 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8354 (tm-30) REVERT: g 85 ILE cc_start: 0.0082 (OUTLIER) cc_final: -0.0402 (pt) REVERT: h 49 ASP cc_start: 0.8690 (t0) cc_final: 0.8351 (t0) REVERT: h 131 ASN cc_start: 0.8640 (p0) cc_final: 0.8385 (p0) REVERT: j 42 SER cc_start: 0.8900 (m) cc_final: 0.8358 (t) REVERT: j 77 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8821 (tp) REVERT: j 81 ASP cc_start: 0.9391 (p0) cc_final: 0.9159 (p0) REVERT: j 135 ILE cc_start: 0.9614 (mt) cc_final: 0.9347 (tp) REVERT: m 76 LYS cc_start: 0.9573 (tttt) cc_final: 0.9233 (tptt) REVERT: n 111 GLU cc_start: 0.8986 (tm-30) cc_final: 0.8155 (tm-30) REVERT: q 52 GLU cc_start: 0.8807 (tm-30) cc_final: 0.8506 (tm-30) REVERT: t 24 ASN cc_start: 0.9338 (m-40) cc_final: 0.8889 (t0) REVERT: t 45 ASP cc_start: 0.9552 (OUTLIER) cc_final: 0.8984 (m-30) REVERT: t 48 MET cc_start: 0.9288 (mmm) cc_final: 0.8863 (mmm) REVERT: t 50 MET cc_start: 0.9451 (OUTLIER) cc_final: 0.9120 (mtm) REVERT: v 25 LYS cc_start: 0.9097 (mtpp) cc_final: 0.8891 (tttp) REVERT: v 40 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8135 (mm-30) REVERT: w 13 GLU cc_start: 0.8794 (pp20) cc_final: 0.8450 (pp20) REVERT: w 39 GLN cc_start: 0.9179 (mt0) cc_final: 0.8579 (mm-40) REVERT: z 36 LYS cc_start: 0.9512 (ttpp) cc_final: 0.9256 (ttpp) REVERT: 0 1 MET cc_start: 0.6234 (ptt) cc_final: 0.5959 (ptt) REVERT: 1 6 VAL cc_start: 0.9553 (t) cc_final: 0.9347 (m) REVERT: 4 32 LEU cc_start: 0.9213 (tp) cc_final: 0.8977 (tt) outliers start: 249 outliers final: 215 residues processed: 1433 average time/residue: 1.2714 time to fit residues: 3193.6156 Evaluate side-chains 1542 residues out of total 4893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 1314 time to evaluate : 6.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 21 TYR Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 35 ASP Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 117 ASP Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 166 LYS Chi-restraints excluded: chain G residue 189 ASP Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 60 GLN Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 133 ILE Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 141 ASP Chi-restraints excluded: chain I residue 2 ARG Chi-restraints excluded: chain I residue 16 GLU Chi-restraints excluded: chain I residue 33 GLU Chi-restraints excluded: chain I residue 52 ASN Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 98 GLU Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 84 TYR Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 89 ASP Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain M residue 87 LEU Chi-restraints excluded: chain N residue 31 VAL Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 34 THR Chi-restraints excluded: chain N residue 79 LYS Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 120 CYS Chi-restraints excluded: chain O residue 18 SER Chi-restraints excluded: chain O residue 26 CYS Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 89 LEU Chi-restraints excluded: chain O residue 108 ASP Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 48 SER Chi-restraints excluded: chain P residue 58 GLU Chi-restraints excluded: chain P residue 67 ASP Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 58 SER Chi-restraints excluded: chain Q residue 80 SER Chi-restraints excluded: chain R residue 13 GLU Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain T residue 56 ASP Chi-restraints excluded: chain T residue 60 ILE Chi-restraints excluded: chain T residue 78 VAL Chi-restraints excluded: chain U residue 24 ASP Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain U residue 67 LEU Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain V residue 3 SER Chi-restraints excluded: chain W residue 11 ILE Chi-restraints excluded: chain W residue 56 ILE Chi-restraints excluded: chain W residue 82 ILE Chi-restraints excluded: chain X residue 5 VAL Chi-restraints excluded: chain X residue 12 ASP Chi-restraints excluded: chain X residue 20 ARG Chi-restraints excluded: chain X residue 27 VAL Chi-restraints excluded: chain X residue 28 LEU Chi-restraints excluded: chain X residue 30 GLU Chi-restraints excluded: chain X residue 34 ARG Chi-restraints excluded: chain a residue 5 CYS Chi-restraints excluded: chain a residue 44 ASN Chi-restraints excluded: chain a residue 66 PHE Chi-restraints excluded: chain b residue 2 ILE Chi-restraints excluded: chain b residue 81 GLU Chi-restraints excluded: chain b residue 86 GLU Chi-restraints excluded: chain b residue 126 ASN Chi-restraints excluded: chain b residue 199 SER Chi-restraints excluded: chain c residue 19 PHE Chi-restraints excluded: chain c residue 25 GLU Chi-restraints excluded: chain c residue 77 ILE Chi-restraints excluded: chain c residue 141 MET Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain c residue 175 ILE Chi-restraints excluded: chain d residue 39 VAL Chi-restraints excluded: chain d residue 51 ASN Chi-restraints excluded: chain d residue 133 GLU Chi-restraints excluded: chain d residue 148 VAL Chi-restraints excluded: chain d residue 158 THR Chi-restraints excluded: chain e residue 36 LEU Chi-restraints excluded: chain f residue 5 LEU Chi-restraints excluded: chain f residue 50 ARG Chi-restraints excluded: chain f residue 114 GLU Chi-restraints excluded: chain f residue 130 VAL Chi-restraints excluded: chain g residue 85 ILE Chi-restraints excluded: chain h residue 60 ASP Chi-restraints excluded: chain h residue 114 LEU Chi-restraints excluded: chain i residue 3 GLN Chi-restraints excluded: chain i residue 32 TYR Chi-restraints excluded: chain i residue 90 ASN Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain j residue 6 LEU Chi-restraints excluded: chain j residue 74 THR Chi-restraints excluded: chain j residue 77 ILE Chi-restraints excluded: chain j residue 100 ILE Chi-restraints excluded: chain k residue 12 MET Chi-restraints excluded: chain k residue 46 ILE Chi-restraints excluded: chain k residue 124 LEU Chi-restraints excluded: chain k residue 132 THR Chi-restraints excluded: chain k residue 136 MET Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 24 MET Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 36 THR Chi-restraints excluded: chain l residue 48 VAL Chi-restraints excluded: chain l residue 51 LEU Chi-restraints excluded: chain l residue 57 THR Chi-restraints excluded: chain l residue 117 ASP Chi-restraints excluded: chain m residue 19 GLN Chi-restraints excluded: chain m residue 28 VAL Chi-restraints excluded: chain m residue 47 VAL Chi-restraints excluded: chain m residue 53 THR Chi-restraints excluded: chain m residue 67 ASN Chi-restraints excluded: chain m residue 69 ASP Chi-restraints excluded: chain m residue 115 LEU Chi-restraints excluded: chain n residue 49 ILE Chi-restraints excluded: chain n residue 64 SER Chi-restraints excluded: chain n residue 65 ASN Chi-restraints excluded: chain n residue 82 SER Chi-restraints excluded: chain n residue 83 ILE Chi-restraints excluded: chain o residue 3 VAL Chi-restraints excluded: chain o residue 8 ILE Chi-restraints excluded: chain o residue 17 LEU Chi-restraints excluded: chain o residue 28 SER Chi-restraints excluded: chain o residue 36 GLN Chi-restraints excluded: chain o residue 39 ILE Chi-restraints excluded: chain o residue 43 GLN Chi-restraints excluded: chain o residue 79 ILE Chi-restraints excluded: chain o residue 86 SER Chi-restraints excluded: chain o residue 89 ILE Chi-restraints excluded: chain o residue 93 ILE Chi-restraints excluded: chain p residue 7 SER Chi-restraints excluded: chain p residue 38 VAL Chi-restraints excluded: chain q residue 4 ILE Chi-restraints excluded: chain q residue 19 LEU Chi-restraints excluded: chain q residue 23 LEU Chi-restraints excluded: chain q residue 36 LEU Chi-restraints excluded: chain q residue 66 ILE Chi-restraints excluded: chain q residue 67 ASP Chi-restraints excluded: chain q residue 69 LEU Chi-restraints excluded: chain q residue 74 ILE Chi-restraints excluded: chain q residue 95 ARG Chi-restraints excluded: chain q residue 96 ILE Chi-restraints excluded: chain q residue 101 SER Chi-restraints excluded: chain r residue 8 LEU Chi-restraints excluded: chain r residue 39 THR Chi-restraints excluded: chain r residue 78 SER Chi-restraints excluded: chain t residue 5 ASN Chi-restraints excluded: chain t residue 41 GLU Chi-restraints excluded: chain t residue 45 ASP Chi-restraints excluded: chain t residue 50 MET Chi-restraints excluded: chain t residue 65 VAL Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 40 LYS Chi-restraints excluded: chain u residue 49 CYS Chi-restraints excluded: chain u residue 52 ASP Chi-restraints excluded: chain u residue 63 VAL Chi-restraints excluded: chain v residue 13 THR Chi-restraints excluded: chain v residue 64 ASP Chi-restraints excluded: chain w residue 17 GLU Chi-restraints excluded: chain x residue 4 ILE Chi-restraints excluded: chain x residue 8 GLN Chi-restraints excluded: chain x residue 9 THR Chi-restraints excluded: chain x residue 23 LEU Chi-restraints excluded: chain x residue 28 LEU Chi-restraints excluded: chain x residue 31 ILE Chi-restraints excluded: chain x residue 34 THR Chi-restraints excluded: chain x residue 56 VAL Chi-restraints excluded: chain y residue 5 ASN Chi-restraints excluded: chain y residue 27 LEU Chi-restraints excluded: chain z residue 12 SER Chi-restraints excluded: chain z residue 21 THR Chi-restraints excluded: chain z residue 22 THR Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain z residue 33 LEU Chi-restraints excluded: chain 0 residue 4 THR Chi-restraints excluded: chain 0 residue 42 LEU Chi-restraints excluded: chain 0 residue 44 VAL Chi-restraints excluded: chain 1 residue 5 THR Chi-restraints excluded: chain 2 residue 17 VAL Chi-restraints excluded: chain 3 residue 50 VAL Chi-restraints excluded: chain 3 residue 54 VAL Chi-restraints excluded: chain 3 residue 108 VAL Chi-restraints excluded: chain 4 residue 4 ASP Chi-restraints excluded: chain 4 residue 34 LEU Chi-restraints excluded: chain 4 residue 58 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 613 optimal weight: 50.0000 chunk 987 optimal weight: 20.0000 chunk 602 optimal weight: 10.0000 chunk 468 optimal weight: 10.0000 chunk 686 optimal weight: 20.0000 chunk 1036 optimal weight: 30.0000 chunk 953 optimal weight: 8.9990 chunk 825 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 637 optimal weight: 20.0000 chunk 505 optimal weight: 40.0000 overall best weight: 9.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 66 GLN ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 115 GLN c 136 GLN d 126 ASN ** e 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 142 GLN ** h 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 29 HIS ** l 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 12 GLN v 15 ASN ** w 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 58 ASN ** 4 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 65 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 159524 Z= 0.341 Angle : 0.742 14.391 238500 Z= 0.396 Chirality : 0.039 0.377 30377 Planarity : 0.007 0.127 12889 Dihedral : 23.908 179.678 79389 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.85 % Favored : 89.73 % Rotamer: Outliers : 4.93 % Allowed : 25.14 % Favored : 69.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.11), residues: 5891 helix: 0.01 (0.12), residues: 1883 sheet: -0.94 (0.16), residues: 1067 loop : -1.67 (0.11), residues: 2941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 42 HIS 0.014 0.002 HIS h 80 PHE 0.048 0.002 PHE f 46 TYR 0.036 0.002 TYR E 212 ARG 0.016 0.001 ARG X 44 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11782 Ramachandran restraints generated. 5891 Oldfield, 0 Emsley, 5891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11782 Ramachandran restraints generated. 5891 Oldfield, 0 Emsley, 5891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1568 residues out of total 4893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 1328 time to evaluate : 6.256 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: E 21 TYR cc_start: 0.8880 (OUTLIER) cc_final: 0.8475 (p90) REVERT: E 93 HIS cc_start: 0.8856 (m90) cc_final: 0.8254 (m-70) REVERT: E 119 GLN cc_start: 0.9389 (mt0) cc_final: 0.9158 (pt0) REVERT: F 141 MET cc_start: 0.9276 (mmm) cc_final: 0.8921 (mmm) REVERT: F 167 TYR cc_start: 0.9174 (m-80) cc_final: 0.8925 (m-80) REVERT: F 169 GLU cc_start: 0.9172 (tm-30) cc_final: 0.8883 (tm-30) REVERT: G 102 TYR cc_start: 0.8972 (t80) cc_final: 0.8657 (t80) REVERT: G 203 TYR cc_start: 0.8948 (m-80) cc_final: 0.8723 (m-80) REVERT: H 11 GLN cc_start: 0.8964 (pp30) cc_final: 0.8630 (pp30) REVERT: H 60 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8123 (tp-100) REVERT: H 64 GLU cc_start: 0.8829 (mp0) cc_final: 0.8186 (mp0) REVERT: H 69 ASN cc_start: 0.9185 (t0) cc_final: 0.8722 (t0) REVERT: I 2 ARG cc_start: 0.7219 (OUTLIER) cc_final: 0.6953 (mmm-85) REVERT: I 40 GLU cc_start: 0.7918 (tt0) cc_final: 0.7670 (mt-10) REVERT: I 69 GLU cc_start: 0.9116 (pm20) cc_final: 0.8913 (pm20) REVERT: I 90 MET cc_start: 0.9064 (mmm) cc_final: 0.8844 (mmm) REVERT: K 26 MET cc_start: 0.8983 (ptm) cc_final: 0.8700 (ptm) REVERT: K 53 ASP cc_start: 0.8512 (p0) cc_final: 0.7823 (p0) REVERT: K 57 GLU cc_start: 0.8468 (tp30) cc_final: 0.8177 (tp30) REVERT: K 59 GLU cc_start: 0.8863 (pm20) cc_final: 0.8562 (pm20) REVERT: K 117 GLN cc_start: 0.9474 (mp10) cc_final: 0.9238 (mm-40) REVERT: L 26 LYS cc_start: 0.8921 (ptpp) cc_final: 0.8511 (ptpp) REVERT: L 31 GLN cc_start: 0.9401 (mp10) cc_final: 0.9200 (mp10) REVERT: L 56 MET cc_start: 0.9338 (tpp) cc_final: 0.9093 (tpt) REVERT: L 58 GLU cc_start: 0.8935 (mp0) cc_final: 0.8387 (tp30) REVERT: L 71 ILE cc_start: 0.9460 (OUTLIER) cc_final: 0.9145 (tp) REVERT: N 79 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8409 (pttm) REVERT: N 93 GLU cc_start: 0.8962 (pm20) cc_final: 0.8529 (pp20) REVERT: P 49 GLU cc_start: 0.9028 (pm20) cc_final: 0.8553 (tm-30) REVERT: P 62 PHE cc_start: 0.7576 (t80) cc_final: 0.6940 (m-80) REVERT: P 77 LYS cc_start: 0.9429 (ttmm) cc_final: 0.8955 (tppp) REVERT: P 80 MET cc_start: 0.8989 (mtp) cc_final: 0.8687 (ttm) REVERT: T 16 MET cc_start: 0.9118 (ptm) cc_final: 0.8558 (ptm) REVERT: T 17 GLU cc_start: 0.8563 (tm-30) cc_final: 0.8320 (tm-30) REVERT: T 78 VAL cc_start: 0.8142 (OUTLIER) cc_final: 0.7896 (m) REVERT: U 56 ARG cc_start: 0.9141 (mtt90) cc_final: 0.8935 (mtt90) REVERT: V 19 GLU cc_start: 0.9165 (pp20) cc_final: 0.8869 (pp20) REVERT: V 28 LYS cc_start: 0.8837 (mmmt) cc_final: 0.8457 (mmmt) REVERT: W 58 ASP cc_start: 0.9022 (p0) cc_final: 0.8806 (p0) REVERT: W 59 ARG cc_start: 0.9258 (ttm-80) cc_final: 0.9036 (ttm-80) REVERT: X 19 LYS cc_start: 0.8993 (mmmt) cc_final: 0.8646 (mmmt) REVERT: X 20 ARG cc_start: 0.6984 (OUTLIER) cc_final: 0.6452 (mpt90) REVERT: X 44 ARG cc_start: 0.9017 (ppt90) cc_final: 0.8792 (ppt90) REVERT: X 50 SER cc_start: 0.9413 (t) cc_final: 0.9097 (p) REVERT: a 271 SER cc_start: 0.9218 (t) cc_final: 0.8933 (p) REVERT: c 195 GLN cc_start: 0.9522 (mt0) cc_final: 0.9223 (mt0) REVERT: d 99 PHE cc_start: 0.9382 (t80) cc_final: 0.9176 (t80) REVERT: e 74 MET cc_start: 0.8767 (ptp) cc_final: 0.8395 (ptm) REVERT: e 94 ARG cc_start: 0.8987 (mmm-85) cc_final: 0.8775 (mmm-85) REVERT: f 8 LYS cc_start: 0.8791 (mmmt) cc_final: 0.8375 (tptp) REVERT: f 50 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7385 (mtm180) REVERT: f 114 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8329 (tm-30) REVERT: g 85 ILE cc_start: 0.0535 (OUTLIER) cc_final: 0.0185 (pt) REVERT: g 125 THR cc_start: 0.6385 (m) cc_final: 0.6096 (p) REVERT: h 49 ASP cc_start: 0.8715 (t0) cc_final: 0.8392 (t0) REVERT: h 131 ASN cc_start: 0.8682 (p0) cc_final: 0.8417 (p0) REVERT: j 42 SER cc_start: 0.8915 (m) cc_final: 0.8388 (t) REVERT: j 81 ASP cc_start: 0.9410 (p0) cc_final: 0.9180 (p0) REVERT: j 135 ILE cc_start: 0.9616 (mt) cc_final: 0.9350 (tp) REVERT: m 76 LYS cc_start: 0.9569 (tttt) cc_final: 0.9223 (tptt) REVERT: n 111 GLU cc_start: 0.8999 (tm-30) cc_final: 0.8211 (tm-30) REVERT: p 6 GLN cc_start: 0.8384 (mt0) cc_final: 0.8112 (tm-30) REVERT: q 52 GLU cc_start: 0.8838 (tm-30) cc_final: 0.8543 (tm-30) REVERT: s 53 GLN cc_start: 0.8156 (mp10) cc_final: 0.7935 (mp10) REVERT: s 61 GLU cc_start: 0.9344 (mp0) cc_final: 0.8948 (mm-30) REVERT: t 48 MET cc_start: 0.9310 (mmm) cc_final: 0.8974 (mmm) REVERT: t 50 MET cc_start: 0.9458 (OUTLIER) cc_final: 0.9132 (mtm) REVERT: v 40 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8072 (mm-30) REVERT: v 43 LYS cc_start: 0.9395 (tppt) cc_final: 0.9002 (tppt) REVERT: w 13 GLU cc_start: 0.8848 (pp20) cc_final: 0.8512 (pp20) REVERT: w 39 GLN cc_start: 0.9164 (mt0) cc_final: 0.8486 (mm-40) REVERT: w 48 ARG cc_start: 0.8752 (mmt90) cc_final: 0.8511 (mmt90) REVERT: z 36 LYS cc_start: 0.9521 (ttpp) cc_final: 0.9208 (ttpp) REVERT: 3 52 MET cc_start: -0.1771 (ptt) cc_final: -0.3733 (tpt) REVERT: 4 23 LYS cc_start: 0.9170 (mmmm) cc_final: 0.8958 (mmmm) REVERT: 4 32 LEU cc_start: 0.9209 (tp) cc_final: 0.8939 (tt) outliers start: 240 outliers final: 209 residues processed: 1421 average time/residue: 1.2560 time to fit residues: 3125.1008 Evaluate side-chains 1522 residues out of total 4893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 1302 time to evaluate : 6.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 21 TYR Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 166 ASP Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 105 VAL Chi-restraints excluded: chain F residue 153 SER Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain G residue 109 THR Chi-restraints excluded: chain G residue 166 LYS Chi-restraints excluded: chain G residue 189 ASP Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 60 GLN Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 133 ILE Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 141 ASP Chi-restraints excluded: chain I residue 2 ARG Chi-restraints excluded: chain I residue 16 GLU Chi-restraints excluded: chain I residue 33 GLU Chi-restraints excluded: chain I residue 52 ASN Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 98 GLU Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 84 TYR Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 89 ASP Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 112 ASP Chi-restraints excluded: chain K residue 124 ILE Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 71 ILE Chi-restraints excluded: chain M residue 18 ILE Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 60 ASP Chi-restraints excluded: chain M residue 87 LEU Chi-restraints excluded: chain N residue 31 VAL Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 34 THR Chi-restraints excluded: chain N residue 79 LYS Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain N residue 120 CYS Chi-restraints excluded: chain O residue 18 SER Chi-restraints excluded: chain O residue 26 CYS Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 89 LEU Chi-restraints excluded: chain O residue 108 ASP Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 48 SER Chi-restraints excluded: chain P residue 58 GLU Chi-restraints excluded: chain P residue 67 ASP Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 58 SER Chi-restraints excluded: chain Q residue 80 SER Chi-restraints excluded: chain R residue 13 GLU Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain T residue 56 ASP Chi-restraints excluded: chain T residue 60 ILE Chi-restraints excluded: chain T residue 78 VAL Chi-restraints excluded: chain U residue 27 THR Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain U residue 67 LEU Chi-restraints excluded: chain U residue 70 THR Chi-restraints excluded: chain V residue 3 SER Chi-restraints excluded: chain W residue 11 ILE Chi-restraints excluded: chain W residue 56 ILE Chi-restraints excluded: chain W residue 82 ILE Chi-restraints excluded: chain X residue 5 VAL Chi-restraints excluded: chain X residue 12 ASP Chi-restraints excluded: chain X residue 20 ARG Chi-restraints excluded: chain X residue 27 VAL Chi-restraints excluded: chain X residue 28 LEU Chi-restraints excluded: chain X residue 30 GLU Chi-restraints excluded: chain X residue 34 ARG Chi-restraints excluded: chain a residue 5 CYS Chi-restraints excluded: chain a residue 44 ASN Chi-restraints excluded: chain a residue 66 PHE Chi-restraints excluded: chain a residue 263 ASP Chi-restraints excluded: chain b residue 2 ILE Chi-restraints excluded: chain b residue 81 GLU Chi-restraints excluded: chain b residue 86 GLU Chi-restraints excluded: chain b residue 126 ASN Chi-restraints excluded: chain b residue 199 SER Chi-restraints excluded: chain c residue 19 PHE Chi-restraints excluded: chain c residue 25 GLU Chi-restraints excluded: chain c residue 77 ILE Chi-restraints excluded: chain c residue 141 MET Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain c residue 175 ILE Chi-restraints excluded: chain d residue 39 VAL Chi-restraints excluded: chain d residue 51 ASN Chi-restraints excluded: chain d residue 133 GLU Chi-restraints excluded: chain d residue 148 VAL Chi-restraints excluded: chain e residue 36 LEU Chi-restraints excluded: chain f residue 5 LEU Chi-restraints excluded: chain f residue 50 ARG Chi-restraints excluded: chain f residue 114 GLU Chi-restraints excluded: chain f residue 130 VAL Chi-restraints excluded: chain g residue 85 ILE Chi-restraints excluded: chain h residue 60 ASP Chi-restraints excluded: chain h residue 114 LEU Chi-restraints excluded: chain i residue 3 GLN Chi-restraints excluded: chain i residue 32 TYR Chi-restraints excluded: chain i residue 90 ASN Chi-restraints excluded: chain i residue 104 THR Chi-restraints excluded: chain j residue 6 LEU Chi-restraints excluded: chain j residue 74 THR Chi-restraints excluded: chain j residue 100 ILE Chi-restraints excluded: chain k residue 12 MET Chi-restraints excluded: chain k residue 46 ILE Chi-restraints excluded: chain k residue 124 LEU Chi-restraints excluded: chain k residue 132 THR Chi-restraints excluded: chain k residue 136 MET Chi-restraints excluded: chain l residue 1 MET Chi-restraints excluded: chain l residue 24 MET Chi-restraints excluded: chain l residue 29 VAL Chi-restraints excluded: chain l residue 36 THR Chi-restraints excluded: chain l residue 48 VAL Chi-restraints excluded: chain l residue 51 LEU Chi-restraints excluded: chain l residue 57 THR Chi-restraints excluded: chain l residue 117 ASP Chi-restraints excluded: chain m residue 28 VAL Chi-restraints excluded: chain m residue 47 VAL Chi-restraints excluded: chain m residue 53 THR Chi-restraints excluded: chain m residue 67 ASN Chi-restraints excluded: chain m residue 69 ASP Chi-restraints excluded: chain m residue 115 LEU Chi-restraints excluded: chain n residue 49 ILE Chi-restraints excluded: chain n residue 64 SER Chi-restraints excluded: chain n residue 65 ASN Chi-restraints excluded: chain n residue 82 SER Chi-restraints excluded: chain n residue 83 ILE Chi-restraints excluded: chain o residue 3 VAL Chi-restraints excluded: chain o residue 8 ILE Chi-restraints excluded: chain o residue 17 LEU Chi-restraints excluded: chain o residue 28 SER Chi-restraints excluded: chain o residue 36 GLN Chi-restraints excluded: chain o residue 39 ILE Chi-restraints excluded: chain o residue 43 GLN Chi-restraints excluded: chain o residue 79 ILE Chi-restraints excluded: chain o residue 86 SER Chi-restraints excluded: chain o residue 93 ILE Chi-restraints excluded: chain p residue 7 SER Chi-restraints excluded: chain p residue 38 VAL Chi-restraints excluded: chain q residue 4 ILE Chi-restraints excluded: chain q residue 19 LEU Chi-restraints excluded: chain q residue 23 LEU Chi-restraints excluded: chain q residue 66 ILE Chi-restraints excluded: chain q residue 67 ASP Chi-restraints excluded: chain q residue 69 LEU Chi-restraints excluded: chain q residue 74 ILE Chi-restraints excluded: chain q residue 95 ARG Chi-restraints excluded: chain q residue 96 ILE Chi-restraints excluded: chain q residue 101 SER Chi-restraints excluded: chain r residue 39 THR Chi-restraints excluded: chain r residue 78 SER Chi-restraints excluded: chain t residue 5 ASN Chi-restraints excluded: chain t residue 41 GLU Chi-restraints excluded: chain t residue 50 MET Chi-restraints excluded: chain t residue 65 VAL Chi-restraints excluded: chain u residue 28 LEU Chi-restraints excluded: chain u residue 32 ILE Chi-restraints excluded: chain u residue 40 LYS Chi-restraints excluded: chain u residue 49 CYS Chi-restraints excluded: chain u residue 52 ASP Chi-restraints excluded: chain u residue 63 VAL Chi-restraints excluded: chain v residue 13 THR Chi-restraints excluded: chain w residue 17 GLU Chi-restraints excluded: chain x residue 4 ILE Chi-restraints excluded: chain x residue 8 GLN Chi-restraints excluded: chain x residue 9 THR Chi-restraints excluded: chain x residue 23 LEU Chi-restraints excluded: chain x residue 28 LEU Chi-restraints excluded: chain x residue 31 ILE Chi-restraints excluded: chain x residue 34 THR Chi-restraints excluded: chain x residue 56 VAL Chi-restraints excluded: chain y residue 5 ASN Chi-restraints excluded: chain y residue 27 LEU Chi-restraints excluded: chain z residue 12 SER Chi-restraints excluded: chain z residue 21 THR Chi-restraints excluded: chain z residue 22 THR Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain 0 residue 4 THR Chi-restraints excluded: chain 0 residue 42 LEU Chi-restraints excluded: chain 0 residue 44 VAL Chi-restraints excluded: chain 1 residue 5 THR Chi-restraints excluded: chain 2 residue 17 VAL Chi-restraints excluded: chain 3 residue 50 VAL Chi-restraints excluded: chain 3 residue 54 VAL Chi-restraints excluded: chain 3 residue 108 VAL Chi-restraints excluded: chain 4 residue 4 ASP Chi-restraints excluded: chain 4 residue 34 LEU Chi-restraints excluded: chain 4 residue 58 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 655 optimal weight: 20.0000 chunk 878 optimal weight: 6.9990 chunk 252 optimal weight: 10.0000 chunk 760 optimal weight: 0.0670 chunk 121 optimal weight: 20.0000 chunk 229 optimal weight: 7.9990 chunk 826 optimal weight: 8.9990 chunk 345 optimal weight: 10.0000 chunk 848 optimal weight: 20.0000 chunk 104 optimal weight: 10.0000 chunk 152 optimal weight: 10.0000 overall best weight: 6.8128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 28 ASN ** Q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 19 ASN ** W 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 115 GLN d 126 ASN ** e 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 72 ASN e 142 GLN i 29 HIS ** l 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 19 GLN ** o 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.046071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.033983 restraints weight = 783799.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.035194 restraints weight = 232537.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.035936 restraints weight = 119554.246| |-----------------------------------------------------------------------------| r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 159524 Z= 0.256 Angle : 0.705 14.015 238500 Z= 0.379 Chirality : 0.037 0.371 30377 Planarity : 0.006 0.124 12889 Dihedral : 23.895 179.632 79389 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.57 % Favored : 90.00 % Rotamer: Outliers : 4.67 % Allowed : 25.76 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.11), residues: 5891 helix: 0.10 (0.12), residues: 1879 sheet: -0.88 (0.16), residues: 1081 loop : -1.63 (0.12), residues: 2931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 212 HIS 0.013 0.001 HIS G 197 PHE 0.025 0.002 PHE e 51 TYR 0.038 0.002 TYR E 212 ARG 0.015 0.001 ARG X 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 43873.24 seconds wall clock time: 764 minutes 26.14 seconds (45866.14 seconds total)