Starting phenix.real_space_refine on Sun Feb 25 17:50:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mgp_3508/02_2024/5mgp_3508.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mgp_3508/02_2024/5mgp_3508.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mgp_3508/02_2024/5mgp_3508.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mgp_3508/02_2024/5mgp_3508.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mgp_3508/02_2024/5mgp_3508.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mgp_3508/02_2024/5mgp_3508.pdb" } resolution = 3.1 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 ------------------------------------------------------------------------------- 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= 0.022 sd= 0.140 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 4642 5.49 5 S 155 5.16 5 C 74160 2.51 5 N 27412 2.21 5 O 40786 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "F ARG 70": "NH1" <-> "NH2" Residue "F ARG 79": "NH1" <-> "NH2" Residue "F ARG 91": "NH1" <-> "NH2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F ARG 111": "NH1" <-> "NH2" Residue "F ARG 114": "NH1" <-> "NH2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "G ARG 2": "NH1" <-> "NH2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G ARG 162": "NH1" <-> "NH2" Residue "G ARG 169": "NH1" <-> "NH2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "K TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M ARG 40": "NH1" <-> "NH2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M ARG 59": "NH1" <-> "NH2" Residue "M ARG 114": "NH1" <-> "NH2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "N ARG 17": "NH1" <-> "NH2" Residue "N ARG 22": "NH1" <-> "NH2" Residue "N ARG 46": "NH1" <-> "NH2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N ARG 71": "NH1" <-> "NH2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "O ARG 10": "NH1" <-> "NH2" Residue "O ARG 16": "NH1" <-> "NH2" Residue "O ARG 25": "NH1" <-> "NH2" Residue "O ARG 81": "NH1" <-> "NH2" Residue "O ARG 94": "NH1" <-> "NH2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P ARG 61": "NH1" <-> "NH2" Residue "P ARG 88": "NH1" <-> "NH2" Residue "P TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 100": "NH1" <-> "NH2" Residue "P ARG 108": "NH1" <-> "NH2" Residue "Q ARG 2": "NH1" <-> "NH2" Residue "Q ARG 5": "NH1" <-> "NH2" Residue "Q ARG 12": "NH1" <-> "NH2" Residue "Q ARG 32": "NH1" <-> "NH2" Residue "Q ARG 47": "NH1" <-> "NH2" Residue "Q ARG 69": "NH1" <-> "NH2" Residue "R TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "R PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 95": "NH1" <-> "NH2" Residue "S ARG 110": "NH1" <-> "NH2" Residue "T ARG 73": "NH1" <-> "NH2" Residue "U ARG 5": "NH1" <-> "NH2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U ARG 81": "NH1" <-> "NH2" Residue "U ARG 85": "NH1" <-> "NH2" Residue "U ARG 93": "NH1" <-> "NH2" Residue "V TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 10": "NH1" <-> "NH2" Residue "Z ARG 29": "NH1" <-> "NH2" Residue "Z ARG 44": "NH1" <-> "NH2" Residue "0 ARG 9": "NH1" <-> "NH2" Residue "0 ARG 15": "NH1" <-> "NH2" Residue "0 ARG 39": "NH1" <-> "NH2" Residue "0 ARG 51": "NH1" <-> "NH2" Residue "1 ARG 43": "NH1" <-> "NH2" Residue "1 TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 3": "NH1" <-> "NH2" Residue "2 ARG 12": "NH1" <-> "NH2" Residue "2 ARG 14": "NH1" <-> "NH2" Residue "2 ARG 19": "NH1" <-> "NH2" Residue "2 ARG 21": "NH1" <-> "NH2" Residue "2 ARG 33": "NH1" <-> "NH2" Residue "2 ARG 41": "NH1" <-> "NH2" Residue "3 ARG 12": "NH1" <-> "NH2" Residue "3 ARG 29": "NH1" <-> "NH2" Residue "3 ARG 39": "NH1" <-> "NH2" Residue "3 ARG 41": "NH1" <-> "NH2" Residue "4 ARG 12": "NH1" <-> "NH2" Residue "4 ARG 24": "NH1" <-> "NH2" Residue "6 ARG 49": "NH1" <-> "NH2" Residue "6 ARG 56": "NH1" <-> "NH2" Residue "b PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 107": "NH1" <-> "NH2" Residue "b PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 224": "NH1" <-> "NH2" Residue "c ARG 106": "NH1" <-> "NH2" Residue "c ARG 130": "NH1" <-> "NH2" Residue "e ARG 156": "NH1" <-> "NH2" Residue "f PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 123": "NH1" <-> "NH2" Residue "l TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 55": "NH1" <-> "NH2" Residue "p ARG 28": "NH1" <-> "NH2" Residue "p PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z TYR 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 147155 Number of models: 1 Model: "" Number of chains: 56 Chain: "A" Number of atoms: 62261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2900, 62261 Classifications: {'RNA': 2900} Modifications used: {'p5*END': 1, 'rna2p_pur': 222, 'rna2p_pyr': 103, 'rna3p_pur': 1452, 'rna3p_pyr': 1123} Link IDs: {'rna2p': 325, 'rna3p': 2574} Chain breaks: 1 Chain: "B" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2572 Classifications: {'RNA': 120} Modifications used: {'p5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 3, 'rna3p_pur': 61, 'rna3p_pyr': 52} Link IDs: {'rna2p': 7, 'rna3p': 112} Chain: "C" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "D" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "F" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "G" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "H" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "K" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "M" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "N" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "T" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "U" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "W" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "X" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "Z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "0" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "1" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 409 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "2" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "3" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "4" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "6" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "a" Number of atoms: 33016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33016 Classifications: {'RNA': 1539} Modifications used: {'p5*END': 1, 'rna2p_pur': 97, 'rna2p_pyr': 56, 'rna3p_pur': 777, 'rna3p_pyr': 609} Link IDs: {'rna2p': 153, 'rna3p': 1385} Chain: "b" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1704 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "c" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "d" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "e" Number of atoms: 1141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1141 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 151} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "f" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 817 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "g" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "h" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "i" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "j" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "k" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 869 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "l" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "m" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "n" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 799 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "o" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "p" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "r" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 504 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 62} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "s" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "t" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "u" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 495 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 62} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "v" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 1, 'rna3p_pyr': 4} Link IDs: {'rna3p': 5} Chain: "w" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 369 Classifications: {'peptide': 45} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 42} Chain: "x" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1646 Classifications: {'RNA': 77} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 33, 'rna3p_pyr': 31} Link IDs: {'rna2p': 13, 'rna3p': 63} Chain: "z" Number of atoms: 2846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2846 Classifications: {'peptide': 359} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 351} Time building chain proxies: 57.80, per 1000 atoms: 0.39 Number of scatterers: 147155 At special positions: 0 Unit cell: (266.664, 279.672, 229.808, 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 155 16.00 P 4642 15.00 O 40786 8.00 N 27412 7.00 C 74160 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 6 18 " - pdb=" SG CYS 6 40 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 61.80 Conformation dependent library (CDL) restraints added in 7.6 seconds 11958 Ramachandran restraints generated. 5979 Oldfield, 0 Emsley, 5979 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11178 Finding SS restraints... Secondary structure from input PDB file: 184 helices and 75 sheets defined 33.5% alpha, 17.4% beta 1376 base pairs and 2750 stacking pairs defined. Time for finding SS restraints: 56.13 Creating SS restraints... Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 198 through 202 removed outlier: 3.505A pdb=" N ARG C 202 " --> pdb=" O HIS C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 212 removed outlier: 3.651A pdb=" N ARG C 211 " --> pdb=" O ALA C 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 72 removed outlier: 3.517A pdb=" N PHE D 68 " --> pdb=" O GLU D 64 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS D 70 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 103 removed outlier: 3.596A pdb=" N LEU D 100 " --> pdb=" O SER D 97 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA D 102 " --> pdb=" O GLU D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'E' and resid 24 through 38 removed outlier: 3.817A pdb=" N ALA E 34 " --> pdb=" O GLN E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 115 removed outlier: 3.537A pdb=" N SER E 110 " --> pdb=" O LYS E 106 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU E 111 " --> pdb=" O SER E 107 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 141 removed outlier: 3.671A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET E 141 " --> pdb=" O LYS E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 159 removed outlier: 3.605A pdb=" N LEU E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 removed outlier: 3.558A pdb=" N ILE E 181 " --> pdb=" O PRO E 177 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 201 removed outlier: 3.596A pdb=" N LYS E 194 " --> pdb=" O ALA E 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 10 removed outlier: 3.503A pdb=" N TYR F 7 " --> pdb=" O LEU F 3 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP F 9 " --> pdb=" O ASP F 5 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 19 removed outlier: 4.182A pdb=" N THR F 17 " --> pdb=" O LYS F 13 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU F 18 " --> pdb=" O LYS F 14 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE F 19 " --> pdb=" O LEU F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 27 Processing helix chain 'F' and resid 40 through 45 removed outlier: 3.782A pdb=" N ALA F 44 " --> pdb=" O GLU F 41 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASP F 45 " --> pdb=" O ALA F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 60 removed outlier: 3.953A pdb=" N ASP F 50 " --> pdb=" O LYS F 46 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP F 55 " --> pdb=" O ASN F 51 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA F 57 " --> pdb=" O ALA F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 106 removed outlier: 3.858A pdb=" N TRP F 96 " --> pdb=" O GLY F 92 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU F 100 " --> pdb=" O TRP F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 171 removed outlier: 4.084A pdb=" N ALA F 167 " --> pdb=" O GLU F 163 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU F 168 " --> pdb=" O GLU F 164 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU F 169 " --> pdb=" O GLY F 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 80 removed outlier: 3.710A pdb=" N ALA G 69 " --> pdb=" O GLY G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 149 Processing helix chain 'H' and resid 22 through 29 Processing helix chain 'H' and resid 42 through 51 removed outlier: 3.940A pdb=" N ALA H 49 " --> pdb=" O GLU H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 66 Processing helix chain 'H' and resid 67 through 70 removed outlier: 3.821A pdb=" N GLU H 70 " --> pdb=" O ALA H 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 67 through 70' Processing helix chain 'H' and resid 96 through 104 removed outlier: 3.782A pdb=" N ALA H 102 " --> pdb=" O ASP H 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 4.239A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG J 37 " --> pdb=" O ALA J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 98 through 107 removed outlier: 3.594A pdb=" N LYS J 106 " --> pdb=" O GLU J 102 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 118 Processing helix chain 'J' and resid 132 through 136 removed outlier: 3.552A pdb=" N GLN J 135 " --> pdb=" O HIS J 132 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN J 136 " --> pdb=" O ALA J 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 132 through 136' Processing helix chain 'K' and resid 104 through 108 Processing helix chain 'K' and resid 112 through 119 Processing helix chain 'L' and resid 56 through 61 removed outlier: 3.677A pdb=" N LEU L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 73 removed outlier: 3.563A pdb=" N ALA L 72 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE L 73 " --> pdb=" O LYS L 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 69 through 73' Processing helix chain 'L' and resid 79 through 85 removed outlier: 3.967A pdb=" N ALA L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS L 84 " --> pdb=" O ASP L 81 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL L 85 " --> pdb=" O LEU L 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 136 removed outlier: 3.652A pdb=" N GLU L 136 " --> pdb=" O ARG L 132 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 56 removed outlier: 3.558A pdb=" N ALA M 52 " --> pdb=" O ALA M 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 121 removed outlier: 3.573A pdb=" N LYS M 118 " --> pdb=" O ARG M 114 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 124 No H-bonds generated for 'chain 'M' and resid 122 through 124' Processing helix chain 'N' and resid 13 through 32 removed outlier: 3.730A pdb=" N GLY N 26 " --> pdb=" O ARG N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 55 removed outlier: 3.552A pdb=" N GLU N 43 " --> pdb=" O PRO N 39 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 59 through 69 Processing helix chain 'N' and resid 74 through 79 Processing helix chain 'O' and resid 4 through 22 removed outlier: 4.539A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 60 removed outlier: 3.934A pdb=" N GLU O 60 " --> pdb=" O LYS O 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 removed outlier: 3.640A pdb=" N ALA O 73 " --> pdb=" O ASP O 69 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA O 79 " --> pdb=" O GLY O 75 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU O 83 " --> pdb=" O ALA O 79 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU O 84 " --> pdb=" O GLU O 80 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS O 85 " --> pdb=" O ARG O 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 112 Processing helix chain 'P' and resid 2 through 10 removed outlier: 3.537A pdb=" N GLU P 10 " --> pdb=" O GLN P 6 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 55 removed outlier: 3.735A pdb=" N HIS P 55 " --> pdb=" O ARG P 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 52 through 55' Processing helix chain 'P' and resid 96 through 101 removed outlier: 3.514A pdb=" N LEU P 99 " --> pdb=" O LEU P 96 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG P 100 " --> pdb=" O TYR P 97 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU P 101 " --> pdb=" O TYR P 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 96 through 101' Processing helix chain 'Q' and resid 6 through 20 removed outlier: 3.568A pdb=" N ARG Q 10 " --> pdb=" O GLY Q 6 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA Q 11 " --> pdb=" O VAL Q 7 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ARG Q 12 " --> pdb=" O ILE Q 8 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN Q 19 " --> pdb=" O LYS Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 removed outlier: 3.845A pdb=" N ARG Q 29 " --> pdb=" O GLY Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 30 through 71 removed outlier: 4.268A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS Q 40 " --> pdb=" O GLN Q 36 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE Q 56 " --> pdb=" O ARG Q 52 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG Q 57 " --> pdb=" O LYS Q 53 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 85 removed outlier: 3.527A pdb=" N ASN Q 80 " --> pdb=" O SER Q 76 " (cutoff:3.500A) Processing helix chain 'Q' and resid 90 through 101 Processing helix chain 'Q' and resid 101 through 117 removed outlier: 3.595A pdb=" N GLU Q 110 " --> pdb=" O THR Q 106 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA Q 112 " --> pdb=" O LEU Q 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 22 removed outlier: 4.111A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 38 Processing helix chain 'S' and resid 41 through 62 removed outlier: 3.533A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS S 49 " --> pdb=" O VAL S 45 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL S 50 " --> pdb=" O LEU S 46 " (cutoff:3.500A) Processing helix chain 'S' and resid 89 through 91 No H-bonds generated for 'chain 'S' and resid 89 through 91' Processing helix chain 'T' and resid 2 through 8 removed outlier: 3.547A pdb=" N LEU T 8 " --> pdb=" O GLU T 4 " (cutoff:3.500A) Processing helix chain 'T' and resid 19 through 26 removed outlier: 3.922A pdb=" N GLU T 25 " --> pdb=" O SER T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 51 Processing helix chain 'V' and resid 13 through 22 removed outlier: 3.532A pdb=" N LEU V 20 " --> pdb=" O ALA V 16 " (cutoff:3.500A) Processing helix chain 'V' and resid 44 through 51 removed outlier: 3.976A pdb=" N ASN V 49 " --> pdb=" O ASP V 45 " (cutoff:3.500A) Processing helix chain 'V' and resid 53 through 57 removed outlier: 3.857A pdb=" N TYR V 57 " --> pdb=" O ALA V 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 53 through 61 Processing helix chain 'X' and resid 62 through 74 Processing helix chain 'Y' and resid 11 through 20 removed outlier: 3.619A pdb=" N ASN Y 15 " --> pdb=" O VAL Y 11 " (cutoff:3.500A) Processing helix chain 'Y' and resid 25 through 34 removed outlier: 3.504A pdb=" N SER Y 34 " --> pdb=" O MET Y 30 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 61 removed outlier: 3.959A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG Y 47 " --> pdb=" O LEU Y 43 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 removed outlier: 3.533A pdb=" N ALA Z 21 " --> pdb=" O PRO Z 17 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU Z 24 " --> pdb=" O LYS Z 20 " (cutoff:3.500A) Processing helix chain 'Z' and resid 42 through 50 removed outlier: 3.508A pdb=" N VAL Z 50 " --> pdb=" O MET Z 46 " (cutoff:3.500A) Processing helix chain '0' and resid 8 through 16 removed outlier: 3.703A pdb=" N ARG 0 15 " --> pdb=" O LYS 0 11 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG 0 16 " --> pdb=" O ARG 0 12 " (cutoff:3.500A) Processing helix chain '2' and resid 8 through 17 Processing helix chain '2' and resid 17 through 22 Processing helix chain '2' and resid 24 through 38 removed outlier: 3.578A pdb=" N ARG 2 28 " --> pdb=" O THR 2 24 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN 2 29 " --> pdb=" O LYS 2 25 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY 2 38 " --> pdb=" O ARG 2 34 " (cutoff:3.500A) Processing helix chain '3' and resid 6 through 11 removed outlier: 3.787A pdb=" N LYS 3 11 " --> pdb=" O ARG 3 7 " (cutoff:3.500A) Processing helix chain '3' and resid 36 through 43 removed outlier: 3.595A pdb=" N HIS 3 42 " --> pdb=" O LYS 3 38 " (cutoff:3.500A) Processing helix chain '3' and resid 51 through 53 No H-bonds generated for 'chain '3' and resid 51 through 53' Processing helix chain '3' and resid 54 through 61 Processing helix chain '4' and resid 30 through 34 Processing helix chain '6' and resid 56 through 65 removed outlier: 4.090A pdb=" N LYS 6 62 " --> pdb=" O ASP 6 58 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ARG 6 63 " --> pdb=" O ARG 6 59 " (cutoff:3.500A) Processing helix chain 'b' and resid 23 through 28 removed outlier: 3.749A pdb=" N LYS b 27 " --> pdb=" O PRO b 24 " (cutoff:3.500A) Proline residue: b 28 - end of helix Processing helix chain 'b' and resid 41 through 62 removed outlier: 3.782A pdb=" N VAL b 46 " --> pdb=" O LEU b 42 " (cutoff:3.500A) Proline residue: b 47 - end of helix removed outlier: 3.570A pdb=" N LYS b 58 " --> pdb=" O ALA b 54 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE b 59 " --> pdb=" O GLU b 55 " (cutoff:3.500A) Processing helix chain 'b' and resid 74 through 87 removed outlier: 3.765A pdb=" N ALA b 78 " --> pdb=" O ALA b 74 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS b 80 " --> pdb=" O SER b 76 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP b 81 " --> pdb=" O GLU b 77 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU b 84 " --> pdb=" O LYS b 80 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER b 85 " --> pdb=" O ASP b 81 " (cutoff:3.500A) Processing helix chain 'b' and resid 102 through 117 removed outlier: 3.621A pdb=" N VAL b 106 " --> pdb=" O ASN b 102 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLN b 108 " --> pdb=" O LYS b 104 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER b 109 " --> pdb=" O THR b 105 " (cutoff:3.500A) Processing helix chain 'b' and resid 117 through 122 removed outlier: 3.962A pdb=" N GLN b 121 " --> pdb=" O GLU b 117 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP b 122 " --> pdb=" O THR b 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 117 through 122' Processing helix chain 'b' and resid 129 through 147 removed outlier: 4.131A pdb=" N SER b 146 " --> pdb=" O LYS b 142 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU b 147 " --> pdb=" O LEU b 143 " (cutoff:3.500A) Processing helix chain 'b' and resid 168 through 178 removed outlier: 3.566A pdb=" N ILE b 172 " --> pdb=" O GLU b 168 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU b 178 " --> pdb=" O GLU b 174 " (cutoff:3.500A) Processing helix chain 'b' and resid 208 through 224 removed outlier: 3.579A pdb=" N LEU b 213 " --> pdb=" O VAL b 209 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA b 218 " --> pdb=" O GLY b 214 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR b 219 " --> pdb=" O ALA b 215 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG b 221 " --> pdb=" O ALA b 217 " (cutoff:3.500A) Processing helix chain 'c' and resid 7 through 11 removed outlier: 3.793A pdb=" N LEU c 11 " --> pdb=" O GLY c 8 " (cutoff:3.500A) Processing helix chain 'c' and resid 29 through 46 removed outlier: 3.760A pdb=" N ASP c 35 " --> pdb=" O ASN c 31 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU c 42 " --> pdb=" O VAL c 38 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 77 removed outlier: 4.007A pdb=" N VAL c 75 " --> pdb=" O ARG c 71 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY c 77 " --> pdb=" O GLY c 73 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 91 removed outlier: 4.204A pdb=" N VAL c 89 " --> pdb=" O LYS c 85 " (cutoff:3.500A) Processing helix chain 'c' and resid 111 through 125 removed outlier: 3.726A pdb=" N GLN c 122 " --> pdb=" O SER c 118 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG c 125 " --> pdb=" O SER c 121 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 142 removed outlier: 3.595A pdb=" N ALA c 140 " --> pdb=" O ALA c 136 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 15 removed outlier: 3.808A pdb=" N ARG d 12 " --> pdb=" O LEU d 8 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU d 14 " --> pdb=" O LEU d 10 " (cutoff:3.500A) Processing helix chain 'd' and resid 50 through 65 removed outlier: 3.779A pdb=" N GLU d 56 " --> pdb=" O VAL d 52 " (cutoff:3.500A) Processing helix chain 'd' and resid 67 through 81 removed outlier: 3.797A pdb=" N ARG d 80 " --> pdb=" O LYS d 76 " (cutoff:3.500A) Processing helix chain 'd' and resid 84 through 95 removed outlier: 3.625A pdb=" N LEU d 90 " --> pdb=" O GLY d 86 " (cutoff:3.500A) Processing helix chain 'd' and resid 96 through 105 Processing helix chain 'd' and resid 109 through 119 Processing helix chain 'd' and resid 153 through 161 Processing helix chain 'd' and resid 162 through 164 No H-bonds generated for 'chain 'd' and resid 162 through 164' Processing helix chain 'd' and resid 196 through 203 removed outlier: 3.538A pdb=" N VAL d 200 " --> pdb=" O GLU d 196 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU d 201 " --> pdb=" O HIS d 197 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR d 203 " --> pdb=" O ILE d 199 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 68 removed outlier: 3.511A pdb=" N GLN e 60 " --> pdb=" O PRO e 56 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS e 61 " --> pdb=" O ALA e 57 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU e 64 " --> pdb=" O GLN e 60 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS e 65 " --> pdb=" O LYS e 61 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG e 68 " --> pdb=" O GLU e 64 " (cutoff:3.500A) Processing helix chain 'e' and resid 110 through 118 removed outlier: 3.520A pdb=" N LEU e 114 " --> pdb=" O MET e 110 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL e 116 " --> pdb=" O ALA e 112 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY e 118 " --> pdb=" O LEU e 114 " (cutoff:3.500A) Processing helix chain 'e' and resid 131 through 145 removed outlier: 3.688A pdb=" N ARG e 137 " --> pdb=" O ILE e 133 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE e 140 " --> pdb=" O VAL e 136 " (cutoff:3.500A) Processing helix chain 'e' and resid 151 through 155 removed outlier: 3.576A pdb=" N LYS e 155 " --> pdb=" O VAL e 152 " (cutoff:3.500A) Processing helix chain 'e' and resid 159 through 164 removed outlier: 3.594A pdb=" N LEU e 164 " --> pdb=" O VAL e 160 " (cutoff:3.500A) Processing helix chain 'f' and resid 12 through 16 removed outlier: 4.711A pdb=" N GLU f 16 " --> pdb=" O ASP f 13 " (cutoff:3.500A) Processing helix chain 'f' and resid 17 through 31 removed outlier: 3.987A pdb=" N ALA f 28 " --> pdb=" O ARG f 24 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 81 removed outlier: 3.655A pdb=" N THR f 77 " --> pdb=" O GLU f 73 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG f 79 " --> pdb=" O GLU f 75 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE f 80 " --> pdb=" O THR f 76 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 30 removed outlier: 3.695A pdb=" N ASN g 27 " --> pdb=" O ALA g 23 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 54 removed outlier: 3.559A pdb=" N SER g 40 " --> pdb=" O SER g 36 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE g 41 " --> pdb=" O THR g 37 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER g 44 " --> pdb=" O SER g 40 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR g 48 " --> pdb=" O SER g 44 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG g 52 " --> pdb=" O THR g 48 " (cutoff:3.500A) Processing helix chain 'g' and resid 58 through 67 removed outlier: 3.663A pdb=" N VAL g 63 " --> pdb=" O GLU g 59 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN g 67 " --> pdb=" O VAL g 63 " (cutoff:3.500A) Processing helix chain 'g' and resid 91 through 109 removed outlier: 4.164A pdb=" N ASN g 96 " --> pdb=" O PRO g 92 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA g 97 " --> pdb=" O VAL g 93 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA g 99 " --> pdb=" O ARG g 95 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL g 104 " --> pdb=" O MET g 100 " (cutoff:3.500A) Processing helix chain 'g' and resid 114 through 128 removed outlier: 3.691A pdb=" N GLU g 128 " --> pdb=" O SER g 124 " (cutoff:3.500A) Processing helix chain 'g' and resid 131 through 144 removed outlier: 3.557A pdb=" N ASP g 139 " --> pdb=" O LYS g 135 " (cutoff:3.500A) Processing helix chain 'h' and resid 4 through 19 removed outlier: 3.641A pdb=" N ASP h 8 " --> pdb=" O ASP h 4 " (cutoff:3.500A) Processing helix chain 'h' and resid 29 through 42 removed outlier: 3.510A pdb=" N ALA h 34 " --> pdb=" O LYS h 30 " (cutoff:3.500A) Processing helix chain 'h' and resid 93 through 98 removed outlier: 4.303A pdb=" N ALA h 96 " --> pdb=" O LYS h 93 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU h 98 " --> pdb=" O MET h 95 " (cutoff:3.500A) Processing helix chain 'h' and resid 111 through 119 removed outlier: 3.526A pdb=" N GLN h 117 " --> pdb=" O ARG h 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 34 through 38 removed outlier: 3.803A pdb=" N PHE i 38 " --> pdb=" O LEU i 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 34 through 38' Processing helix chain 'i' and resid 48 through 54 removed outlier: 3.538A pdb=" N LEU i 53 " --> pdb=" O GLN i 49 " (cutoff:3.500A) Processing helix chain 'i' and resid 70 through 86 removed outlier: 3.540A pdb=" N THR i 83 " --> pdb=" O ARG i 79 " (cutoff:3.500A) Processing helix chain 'i' and resid 89 through 94 Processing helix chain 'i' and resid 95 through 100 Processing helix chain 'j' and resid 14 through 33 removed outlier: 4.920A pdb=" N GLN j 20 " --> pdb=" O ARG j 16 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE j 25 " --> pdb=" O ALA j 21 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG j 31 " --> pdb=" O GLU j 27 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N THR j 32 " --> pdb=" O THR j 28 " (cutoff:3.500A) Processing helix chain 'k' and resid 47 through 50 removed outlier: 3.736A pdb=" N GLY k 50 " --> pdb=" O GLY k 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 47 through 50' Processing helix chain 'k' and resid 54 through 57 removed outlier: 3.560A pdb=" N SER k 57 " --> pdb=" O SER k 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 54 through 57' Processing helix chain 'k' and resid 58 through 71 removed outlier: 3.608A pdb=" N ALA k 62 " --> pdb=" O THR k 58 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP k 71 " --> pdb=" O GLU k 67 " (cutoff:3.500A) Processing helix chain 'k' and resid 95 through 101 Processing helix chain 'l' and resid 4 through 9 removed outlier: 3.824A pdb=" N ARG l 8 " --> pdb=" O ASN l 4 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS l 9 " --> pdb=" O GLN l 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 4 through 9' Processing helix chain 'm' and resid 13 through 19 removed outlier: 3.618A pdb=" N THR m 19 " --> pdb=" O VAL m 15 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 37 Processing helix chain 'm' and resid 48 through 57 removed outlier: 4.169A pdb=" N ASP m 53 " --> pdb=" O GLU m 49 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N THR m 54 " --> pdb=" O GLY m 50 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU m 55 " --> pdb=" O GLN m 51 " (cutoff:3.500A) Processing helix chain 'm' and resid 68 through 83 removed outlier: 3.886A pdb=" N MET m 74 " --> pdb=" O ARG m 70 " (cutoff:3.500A) Processing helix chain 'm' and resid 84 through 93 Processing helix chain 'm' and resid 105 through 110 Processing helix chain 'n' and resid 2 through 19 removed outlier: 3.588A pdb=" N LYS n 6 " --> pdb=" O LYS n 2 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL n 10 " --> pdb=" O LYS n 6 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG n 12 " --> pdb=" O ARG n 8 " (cutoff:3.500A) Processing helix chain 'n' and resid 24 through 29 removed outlier: 3.710A pdb=" N ALA n 28 " --> pdb=" O ALA n 24 " (cutoff:3.500A) Processing helix chain 'n' and resid 38 through 43 removed outlier: 3.773A pdb=" N TRP n 42 " --> pdb=" O ASP n 38 " (cutoff:3.500A) Processing helix chain 'n' and resid 43 through 51 removed outlier: 4.251A pdb=" N GLN n 49 " --> pdb=" O VAL n 45 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR n 50 " --> pdb=" O LEU n 46 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU n 51 " --> pdb=" O LYS n 47 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 60 Processing helix chain 'n' and resid 82 through 91 Processing helix chain 'o' and resid 3 through 15 removed outlier: 3.577A pdb=" N LYS o 9 " --> pdb=" O GLU o 5 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE o 10 " --> pdb=" O ALA o 6 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU o 13 " --> pdb=" O LYS o 9 " (cutoff:3.500A) Processing helix chain 'o' and resid 23 through 42 removed outlier: 4.613A pdb=" N GLY o 40 " --> pdb=" O ASN o 36 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N HIS o 41 " --> pdb=" O HIS o 37 " (cutoff:3.500A) Processing helix chain 'o' and resid 48 through 73 removed outlier: 3.509A pdb=" N ARG o 53 " --> pdb=" O HIS o 49 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY o 54 " --> pdb=" O HIS o 50 " (cutoff:3.500A) Processing helix chain 'o' and resid 73 through 85 removed outlier: 3.564A pdb=" N GLN o 79 " --> pdb=" O ALA o 75 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU o 80 " --> pdb=" O ARG o 76 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU o 82 " --> pdb=" O THR o 78 " (cutoff:3.500A) Processing helix chain 'p' and resid 53 through 64 Processing helix chain 'p' and resid 68 through 76 Processing helix chain 'r' and resid 11 through 16 removed outlier: 3.859A pdb=" N GLY r 16 " --> pdb=" O PHE r 12 " (cutoff:3.500A) Processing helix chain 'r' and resid 24 through 29 Processing helix chain 'r' and resid 30 through 32 No H-bonds generated for 'chain 'r' and resid 30 through 32' Processing helix chain 'r' and resid 40 through 45 Processing helix chain 'r' and resid 47 through 64 Processing helix chain 's' and resid 11 through 24 removed outlier: 3.865A pdb=" N LYS s 17 " --> pdb=" O HIS s 13 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LYS s 20 " --> pdb=" O LYS s 16 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU s 23 " --> pdb=" O GLU s 19 " (cutoff:3.500A) Processing helix chain 's' and resid 40 through 44 Processing helix chain 's' and resid 70 through 74 Processing helix chain 't' and resid 4 through 6 No H-bonds generated for 'chain 't' and resid 4 through 6' Processing helix chain 't' and resid 7 through 41 removed outlier: 3.601A pdb=" N ILE t 11 " --> pdb=" O LYS t 7 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU t 14 " --> pdb=" O ALA t 10 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS t 19 " --> pdb=" O LYS t 15 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE t 30 " --> pdb=" O MET t 26 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL t 34 " --> pdb=" O PHE t 30 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA t 37 " --> pdb=" O LYS t 33 " (cutoff:3.500A) Processing helix chain 't' and resid 42 through 63 removed outlier: 3.636A pdb=" N ALA t 46 " --> pdb=" O ASP t 42 " (cutoff:3.500A) Proline residue: t 55 - end of helix Processing helix chain 't' and resid 69 through 83 removed outlier: 3.877A pdb=" N LEU t 78 " --> pdb=" O HIS t 74 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR t 79 " --> pdb=" O LYS t 75 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE t 82 " --> pdb=" O LEU t 78 " (cutoff:3.500A) Processing helix chain 'u' and resid 25 through 30 removed outlier: 3.605A pdb=" N GLU u 30 " --> pdb=" O GLY u 26 " (cutoff:3.500A) Processing helix chain 'u' and resid 38 through 60 removed outlier: 4.272A pdb=" N ARG u 44 " --> pdb=" O PRO u 40 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS u 53 " --> pdb=" O ALA u 49 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS u 57 " --> pdb=" O LYS u 53 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS u 58 " --> pdb=" O ARG u 54 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU u 59 " --> pdb=" O HIS u 55 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA u 60 " --> pdb=" O ALA u 56 " (cutoff:3.500A) Processing helix chain 'w' and resid 22 through 26 removed outlier: 3.852A pdb=" N ARG w 26 " --> pdb=" O PRO w 23 " (cutoff:3.500A) Processing helix chain 'z' and resid 7 through 24 removed outlier: 3.594A pdb=" N ILE z 11 " --> pdb=" O VAL z 7 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR z 15 " --> pdb=" O ILE z 11 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU z 16 " --> pdb=" O GLN z 12 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG z 17 " --> pdb=" O ASP z 13 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER z 18 " --> pdb=" O LEU z 14 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP z 19 " --> pdb=" O THR z 15 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL z 20 " --> pdb=" O GLU z 16 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LEU z 21 " --> pdb=" O ARG z 17 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG z 22 " --> pdb=" O SER z 18 " (cutoff:3.500A) Processing helix chain 'z' and resid 26 through 42 removed outlier: 4.092A pdb=" N LYS z 31 " --> pdb=" O TYR z 27 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU z 32 " --> pdb=" O ASP z 28 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA z 39 " --> pdb=" O GLU z 35 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU z 40 " --> pdb=" O GLU z 36 " (cutoff:3.500A) Processing helix chain 'z' and resid 43 through 48 removed outlier: 4.155A pdb=" N VAL z 46 " --> pdb=" O GLN z 43 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TRP z 47 " --> pdb=" O PRO z 44 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN z 48 " --> pdb=" O ASP z 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 43 through 48' Processing helix chain 'z' and resid 49 through 87 removed outlier: 4.034A pdb=" N ALA z 55 " --> pdb=" O GLU z 51 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER z 62 " --> pdb=" O LYS z 58 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL z 67 " --> pdb=" O LEU z 63 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU z 70 " --> pdb=" O VAL z 66 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN z 75 " --> pdb=" O ASP z 71 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU z 78 " --> pdb=" O LYS z 74 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL z 80 " --> pdb=" O GLY z 76 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER z 81 " --> pdb=" O LEU z 77 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU z 84 " --> pdb=" O VAL z 80 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU z 86 " --> pdb=" O GLY z 82 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA z 87 " --> pdb=" O LEU z 83 " (cutoff:3.500A) Processing helix chain 'z' and resid 92 through 118 removed outlier: 3.749A pdb=" N PHE z 96 " --> pdb=" O ASP z 92 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL z 100 " --> pdb=" O PHE z 96 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA z 101 " --> pdb=" O ASN z 97 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU z 102 " --> pdb=" O GLU z 98 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA z 105 " --> pdb=" O ALA z 101 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ARG z 117 " --> pdb=" O LEU z 113 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N MET z 118 " --> pdb=" O GLU z 114 " (cutoff:3.500A) Processing helix chain 'z' and resid 138 through 156 removed outlier: 3.558A pdb=" N GLN z 142 " --> pdb=" O GLY z 138 " (cutoff:3.500A) Processing helix chain 'z' and resid 187 through 193 removed outlier: 3.586A pdb=" N TRP z 191 " --> pdb=" O TYR z 187 " (cutoff:3.500A) Processing helix chain 'z' and resid 194 through 196 No H-bonds generated for 'chain 'z' and resid 194 through 196' Processing helix chain 'z' and resid 235 through 237 No H-bonds generated for 'chain 'z' and resid 235 through 237' Processing helix chain 'z' and resid 252 through 256 removed outlier: 4.017A pdb=" N ARG z 256 " --> pdb=" O HIS z 253 " (cutoff:3.500A) Processing helix chain 'z' and resid 279 through 310 removed outlier: 3.519A pdb=" N GLU z 306 " --> pdb=" O LYS z 302 " (cutoff:3.500A) Processing helix chain 'z' and resid 310 through 316 removed outlier: 3.639A pdb=" N LYS z 314 " --> pdb=" O MET z 310 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER z 315 " --> pdb=" O GLU z 311 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP z 316 " --> pdb=" O ASP z 312 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 310 through 316' Processing helix chain 'z' and resid 344 through 349 removed outlier: 3.623A pdb=" N VAL z 348 " --> pdb=" O ASN z 344 " (cutoff:3.500A) Processing helix chain 'z' and resid 353 through 362 removed outlier: 3.776A pdb=" N ALA z 359 " --> pdb=" O GLN z 355 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS z 362 " --> pdb=" O GLU z 358 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=AA2, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AA3, first strand: chain 'C' and resid 100 through 104 removed outlier: 6.228A pdb=" N LEU C 94 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N VAL C 77 " --> pdb=" O LEU C 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 128 through 130 removed outlier: 5.705A pdb=" N ILE C 163 " --> pdb=" O ARG C 174 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ARG C 174 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR C 170 " --> pdb=" O ASP C 167 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 4 through 16 removed outlier: 3.767A pdb=" N VAL D 26 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N MET D 11 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL D 24 " --> pdb=" O MET D 11 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ARG D 13 " --> pdb=" O ILE D 22 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE D 22 " --> pdb=" O ARG D 13 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N PHE D 15 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL D 20 " --> pdb=" O PHE D 15 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU D 186 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N VAL D 180 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU D 188 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ASP D 176 " --> pdb=" O LYS D 190 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N THR D 171 " --> pdb=" O GLY D 111 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N GLY D 111 " --> pdb=" O THR D 171 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N GLN D 173 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL D 109 " --> pdb=" O GLN D 173 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 33 through 38 removed outlier: 5.530A pdb=" N VAL D 34 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N THR D 51 " --> pdb=" O VAL D 34 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 117 through 119 removed outlier: 3.714A pdb=" N GLY D 117 " --> pdb=" O MET D 165 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 2 through 5 Processing sheet with id=AA9, first strand: chain 'E' and resid 118 through 121 Processing sheet with id=AB1, first strand: chain 'F' and resid 65 through 68 removed outlier: 3.654A pdb=" N GLY F 85 " --> pdb=" O THR F 67 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 8 through 9 Processing sheet with id=AB3, first strand: chain 'G' and resid 15 through 19 Processing sheet with id=AB4, first strand: chain 'G' and resid 121 through 123 Processing sheet with id=AB5, first strand: chain 'G' and resid 97 through 98 Processing sheet with id=AB6, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AB7, first strand: chain 'H' and resid 127 through 133 Processing sheet with id=AB8, first strand: chain 'J' and resid 122 through 124 removed outlier: 6.443A pdb=" N ILE J 54 " --> pdb=" O LYS J 123 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N TYR J 16 " --> pdb=" O ILE J 55 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LEU J 57 " --> pdb=" O TYR J 16 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL J 18 " --> pdb=" O LEU J 57 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 74 through 77 Processing sheet with id=AC1, first strand: chain 'K' and resid 7 through 10 removed outlier: 6.775A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N VAL K 24 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ILE K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N CYS K 84 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ASN K 9 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N LEU K 86 " --> pdb=" O ASN K 9 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 69 through 70 removed outlier: 3.932A pdb=" N VAL K 76 " --> pdb=" O VAL P 72 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA P 48 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ARG P 61 " --> pdb=" O VAL P 46 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL P 46 " --> pdb=" O ARG P 61 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ILE P 63 " --> pdb=" O GLY P 44 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N GLY P 44 " --> pdb=" O ILE P 63 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LYS P 36 " --> pdb=" O GLU P 33 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR P 24 " --> pdb=" O LYS P 86 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N TRP P 30 " --> pdb=" O VAL P 80 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL P 80 " --> pdb=" O TRP P 30 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 89 through 90 removed outlier: 5.739A pdb=" N VAL L 90 " --> pdb=" O ARG L 123 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL L 122 " --> pdb=" O GLU L 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'M' and resid 62 through 65 removed outlier: 3.628A pdb=" N LYS M 100 " --> pdb=" O ALA M 35 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU M 33 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLU M 104 " --> pdb=" O PHE M 31 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N PHE M 31 " --> pdb=" O GLU M 104 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 39 through 42 removed outlier: 5.801A pdb=" N VAL M 89 " --> pdb=" O GLU M 75 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N GLU M 75 " --> pdb=" O VAL M 89 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 33 through 37 removed outlier: 4.647A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'O' and resid 47 through 50 removed outlier: 3.505A pdb=" N VAL O 28 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'R' and resid 11 through 14 removed outlier: 3.510A pdb=" N PHE R 5 " --> pdb=" O HIS R 12 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'R' and resid 19 through 23 removed outlier: 6.657A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ILE R 101 " --> pdb=" O VAL R 58 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL R 58 " --> pdb=" O ILE R 101 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'R' and resid 74 through 78 removed outlier: 4.114A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'S' and resid 4 through 10 removed outlier: 5.074A pdb=" N ILE S 4 " --> pdb=" O VAL S 107 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL S 107 " --> pdb=" O ILE S 4 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LYS S 6 " --> pdb=" O VAL S 105 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL S 105 " --> pdb=" O LYS S 6 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ARG S 8 " --> pdb=" O ILE S 103 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE S 103 " --> pdb=" O ARG S 8 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N SER S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N VAL S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'S' and resid 82 through 87 Processing sheet with id=AD4, first strand: chain 'T' and resid 11 through 14 removed outlier: 6.738A pdb=" N LYS T 33 " --> pdb=" O ARG T 12 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N VAL T 31 " --> pdb=" O PRO T 14 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL T 57 " --> pdb=" O THR T 86 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'T' and resid 69 through 70 removed outlier: 3.662A pdb=" N ARG T 73 " --> pdb=" O HIS T 70 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'U' and resid 64 through 65 removed outlier: 6.346A pdb=" N LYS U 32 " --> pdb=" O VAL U 27 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N VAL U 27 " --> pdb=" O LYS U 32 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE U 34 " --> pdb=" O LYS U 25 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'U' and resid 40 through 44 Processing sheet with id=AD8, first strand: chain 'U' and resid 82 through 85 Processing sheet with id=AD9, first strand: chain 'V' and resid 78 through 79 removed outlier: 3.600A pdb=" N HIS V 88 " --> pdb=" O GLN V 78 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ASN V 5 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ASP V 43 " --> pdb=" O ASN V 5 " (cutoff:3.500A) removed outlier: 8.776A pdb=" N LYS V 25 " --> pdb=" O GLN V 87 " (cutoff:3.500A) removed outlier: 9.824A pdb=" N ILE V 89 " --> pdb=" O LYS V 25 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N PHE V 91 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE V 29 " --> pdb=" O PHE V 91 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ARG V 93 " --> pdb=" O ILE V 29 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N TYR V 31 " --> pdb=" O ARG V 93 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'W' and resid 18 through 19 removed outlier: 6.929A pdb=" N LEU W 55 " --> pdb=" O ILE W 33 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'W' and resid 26 through 27 Processing sheet with id=AE3, first strand: chain 'X' and resid 12 through 17 removed outlier: 3.631A pdb=" N THR X 24 " --> pdb=" O ASN X 16 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'X' and resid 32 through 39 removed outlier: 3.719A pdb=" N VAL X 50 " --> pdb=" O HIS X 33 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Z' and resid 34 through 38 Processing sheet with id=AE6, first strand: chain '0' and resid 28 through 29 Processing sheet with id=AE7, first strand: chain '0' and resid 47 through 48 Processing sheet with id=AE8, first strand: chain '1' and resid 19 through 24 removed outlier: 3.736A pdb=" N GLN 1 44 " --> pdb=" O ASP 1 39 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain '3' and resid 14 through 15 Processing sheet with id=AF1, first strand: chain '4' and resid 14 through 19 Processing sheet with id=AF2, first strand: chain '6' and resid 20 through 26 removed outlier: 4.108A pdb=" N ASN 6 20 " --> pdb=" O CYS 6 16 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU 6 32 " --> pdb=" O THR 6 13 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'b' and resid 30 through 32 Processing sheet with id=AF4, first strand: chain 'b' and resid 89 through 91 removed outlier: 5.885A pdb=" N ILE b 66 " --> pdb=" O PHE b 89 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N VAL b 91 " --> pdb=" O ILE b 66 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N PHE b 68 " --> pdb=" O VAL b 91 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU b 67 " --> pdb=" O PHE b 161 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'b' and resid 184 through 186 Processing sheet with id=AF6, first strand: chain 'c' and resid 19 through 20 removed outlier: 7.100A pdb=" N HIS c 68 " --> pdb=" O SER c 52 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILE c 54 " --> pdb=" O THR c 66 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N THR c 66 " --> pdb=" O ILE c 54 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ILE c 56 " --> pdb=" O ARG c 64 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ARG c 64 " --> pdb=" O ILE c 56 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR c 69 " --> pdb=" O ALA c 103 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'c' and resid 163 through 170 removed outlier: 3.625A pdb=" N GLY c 154 " --> pdb=" O ARG c 163 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY c 147 " --> pdb=" O PHE c 202 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN c 184 " --> pdb=" O VAL c 199 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ASP c 180 " --> pdb=" O LYS c 203 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'd' and resid 127 through 128 Processing sheet with id=AF9, first strand: chain 'e' and resid 13 through 14 Processing sheet with id=AG1, first strand: chain 'e' and resid 18 through 21 Processing sheet with id=AG2, first strand: chain 'e' and resid 84 through 85 Processing sheet with id=AG3, first strand: chain 'f' and resid 2 through 3 Processing sheet with id=AG4, first strand: chain 'f' and resid 41 through 44 removed outlier: 4.619A pdb=" N ASP f 41 " --> pdb=" O LEU f 61 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU f 61 " --> pdb=" O ASP f 41 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL f 7 " --> pdb=" O SER f 87 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N SER f 87 " --> pdb=" O VAL f 7 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET f 9 " --> pdb=" O ILE f 85 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'g' and resid 72 through 79 removed outlier: 3.841A pdb=" N ARG g 77 " --> pdb=" O TYR g 84 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N TYR g 84 " --> pdb=" O ARG g 77 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER g 82 " --> pdb=" O VAL g 79 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'h' and resid 23 through 27 removed outlier: 4.113A pdb=" N THR h 61 " --> pdb=" O ASP h 47 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASP h 47 " --> pdb=" O THR h 61 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'h' and resid 74 through 76 removed outlier: 3.702A pdb=" N GLN h 75 " --> pdb=" O TYR h 127 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL h 102 " --> pdb=" O ILE h 125 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N TYR h 127 " --> pdb=" O ILE h 100 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE h 100 " --> pdb=" O TYR h 127 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'i' and resid 5 through 7 removed outlier: 3.834A pdb=" N THR i 65 " --> pdb=" O ARG i 17 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N VAL i 28 " --> pdb=" O ILE i 64 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N VAL i 66 " --> pdb=" O VAL i 28 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'j' and resid 45 through 52 removed outlier: 3.661A pdb=" N THR j 69 " --> pdb=" O ARG j 45 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'j' and resid 45 through 52 removed outlier: 3.661A pdb=" N THR j 69 " --> pdb=" O ARG j 45 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'k' and resid 40 through 45 removed outlier: 6.580A pdb=" N ILE k 33 " --> pdb=" O LEU k 41 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N TRP k 43 " --> pdb=" O VAL k 31 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL k 31 " --> pdb=" O TRP k 43 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N THR k 45 " --> pdb=" O THR k 29 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR k 29 " --> pdb=" O THR k 45 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL k 83 " --> pdb=" O THR k 107 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ILE k 109 " --> pdb=" O VAL k 83 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL k 85 " --> pdb=" O ILE k 109 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ASP k 111 " --> pdb=" O VAL k 85 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'l' and resid 28 through 31 Processing sheet with id=AH4, first strand: chain 'l' and resid 36 through 39 Processing sheet with id=AH5, first strand: chain 'p' and resid 32 through 35 removed outlier: 6.949A pdb=" N VAL p 21 " --> pdb=" O ILE p 33 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'p' and resid 9 through 11 removed outlier: 3.665A pdb=" N ARG p 14 " --> pdb=" O ALA p 11 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'p' and resid 37 through 39 removed outlier: 3.639A pdb=" N ARG p 51 " --> pdb=" O PHE p 38 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'q' and resid 6 through 13 removed outlier: 16.593A pdb=" N THR q 6 " --> pdb=" O PHE q 27 " (cutoff:3.500A) removed outlier: 12.898A pdb=" N PHE q 27 " --> pdb=" O THR q 6 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N GLN q 8 " --> pdb=" O GLU q 25 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLU q 25 " --> pdb=" O GLN q 8 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL q 21 " --> pdb=" O VAL q 12 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N TRP q 72 " --> pdb=" O HIS q 44 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLU q 59 " --> pdb=" O VAL q 75 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 's' and resid 31 through 32 Processing sheet with id=AI1, first strand: chain 'w' and resid 28 through 29 Processing sheet with id=AI2, first strand: chain 'z' and resid 162 through 170 removed outlier: 6.822A pdb=" N THR z 163 " --> pdb=" O ILE z 183 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE z 183 " --> pdb=" O THR z 163 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ILE z 165 " --> pdb=" O ILE z 181 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE z 181 " --> pdb=" O ILE z 165 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU z 167 " --> pdb=" O VAL z 179 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N VAL z 179 " --> pdb=" O GLU z 167 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N SER z 169 " --> pdb=" O LYS z 177 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG z 203 " --> pdb=" O HIS z 214 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N TYR z 326 " --> pdb=" O VAL z 198 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ARG z 200 " --> pdb=" O TYR z 326 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'z' and resid 239 through 242 1644 hydrogen bonds defined for protein. 4605 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3406 hydrogen bonds 5400 hydrogen bond angles 0 basepair planarities 1376 basepair parallelities 2750 stacking parallelities Total time for adding SS restraints: 291.62 Time building geometry restraints manager: 67.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 18069 1.32 - 1.45: 68313 1.45 - 1.57: 63811 1.57 - 1.69: 9278 1.69 - 1.82: 277 Bond restraints: 159748 Sorted by residual: bond pdb=" C PHE X 28 " pdb=" N LEU X 29 " ideal model delta sigma weight residual 1.331 1.228 0.103 2.07e-02 2.33e+03 2.45e+01 bond pdb=" C VAL c 96 " pdb=" N PRO c 97 " ideal model delta sigma weight residual 1.331 1.380 -0.049 1.31e-02 5.83e+03 1.41e+01 bond pdb=" C THR O 31 " pdb=" N PRO O 32 " ideal model delta sigma weight residual 1.335 1.376 -0.042 1.28e-02 6.10e+03 1.06e+01 bond pdb=" C ALA O 41 " pdb=" N PRO O 42 " ideal model delta sigma weight residual 1.335 1.371 -0.037 1.19e-02 7.06e+03 9.44e+00 bond pdb=" CA ARG i 17 " pdb=" CB ARG i 17 " ideal model delta sigma weight residual 1.524 1.566 -0.041 1.46e-02 4.69e+03 8.03e+00 ... (remaining 159743 not shown) Histogram of bond angle deviations from ideal: 95.12 - 103.38: 11158 103.38 - 111.63: 91818 111.63 - 119.89: 69761 119.89 - 128.14: 58201 128.14 - 136.40: 7732 Bond angle restraints: 238670 Sorted by residual: angle pdb=" C THR b 45 " pdb=" N VAL b 46 " pdb=" CA VAL b 46 " ideal model delta sigma weight residual 120.24 124.67 -4.43 6.30e-01 2.52e+00 4.95e+01 angle pdb=" C HIS w 21 " pdb=" N ASP w 22 " pdb=" CA ASP w 22 " ideal model delta sigma weight residual 120.51 130.41 -9.90 1.45e+00 4.76e-01 4.67e+01 angle pdb=" O3' G A1930 " pdb=" C3' G A1930 " pdb=" C2' G A1930 " ideal model delta sigma weight residual 109.50 119.66 -10.16 1.50e+00 4.44e-01 4.59e+01 angle pdb=" C GLU u 35 " pdb=" N PHE u 36 " pdb=" CA PHE u 36 " ideal model delta sigma weight residual 121.54 133.66 -12.12 1.91e+00 2.74e-01 4.02e+01 angle pdb=" C PHE z 119 " pdb=" N SER z 120 " pdb=" CA SER z 120 " ideal model delta sigma weight residual 121.70 132.74 -11.04 1.80e+00 3.09e-01 3.76e+01 ... (remaining 238665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 90593 35.94 - 71.89: 10404 71.89 - 107.83: 1244 107.83 - 143.77: 16 143.77 - 179.72: 44 Dihedral angle restraints: 102301 sinusoidal: 84971 harmonic: 17330 Sorted by residual: dihedral pdb=" CA ASN f 52 " pdb=" C ASN f 52 " pdb=" N LYS f 53 " pdb=" CA LYS f 53 " ideal model delta harmonic sigma weight residual -180.00 -106.61 -73.39 0 5.00e+00 4.00e-02 2.15e+02 dihedral pdb=" CA HIS b 17 " pdb=" C HIS b 17 " pdb=" N GLN b 18 " pdb=" CA GLN b 18 " ideal model delta harmonic sigma weight residual -180.00 -113.43 -66.57 0 5.00e+00 4.00e-02 1.77e+02 dihedral pdb=" CA ILE m 3 " pdb=" C ILE m 3 " pdb=" N ALA m 4 " pdb=" CA ALA m 4 " ideal model delta harmonic sigma weight residual -180.00 -123.61 -56.39 0 5.00e+00 4.00e-02 1.27e+02 ... (remaining 102298 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 29768 0.121 - 0.242: 604 0.242 - 0.363: 51 0.363 - 0.484: 11 0.484 - 0.605: 1 Chirality restraints: 30435 Sorted by residual: chirality pdb=" C3' G A1930 " pdb=" C4' G A1930 " pdb=" O3' G A1930 " pdb=" C2' G A1930 " both_signs ideal model delta sigma weight residual False -2.74 -2.14 -0.61 2.00e-01 2.50e+01 9.16e+00 chirality pdb=" C3' G A 858 " pdb=" C4' G A 858 " pdb=" O3' G A 858 " pdb=" C2' G A 858 " both_signs ideal model delta sigma weight residual False -2.74 -2.26 -0.48 2.00e-01 2.50e+01 5.85e+00 chirality pdb=" C3' G a 86 " pdb=" C4' G a 86 " pdb=" O3' G a 86 " pdb=" C2' G a 86 " both_signs ideal model delta sigma weight residual False -2.74 -2.34 -0.40 2.00e-01 2.50e+01 4.01e+00 ... (remaining 30432 not shown) Planarity restraints: 13013 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA m 4 " -0.032 2.00e-02 2.50e+03 6.49e-02 4.21e+01 pdb=" C ALA m 4 " 0.112 2.00e-02 2.50e+03 pdb=" O ALA m 4 " -0.042 2.00e-02 2.50e+03 pdb=" N GLY m 5 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS w 44 " -0.021 2.00e-02 2.50e+03 4.31e-02 1.86e+01 pdb=" C LYS w 44 " 0.075 2.00e-02 2.50e+03 pdb=" O LYS w 44 " -0.028 2.00e-02 2.50e+03 pdb=" N HIS w 45 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS l 76 " -0.019 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C HIS l 76 " 0.065 2.00e-02 2.50e+03 pdb=" O HIS l 76 " -0.024 2.00e-02 2.50e+03 pdb=" N SER l 77 " -0.022 2.00e-02 2.50e+03 ... (remaining 13010 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 11782 2.70 - 3.25: 120681 3.25 - 3.80: 295391 3.80 - 4.35: 396558 4.35 - 4.90: 523318 Nonbonded interactions: 1347730 Sorted by model distance: nonbonded pdb=" N ALA w 15 " pdb=" OE1 GLU z 311 " model vdw 2.151 2.520 nonbonded pdb=" O2 C A 948 " pdb=" O2' A A 984 " model vdw 2.228 2.440 nonbonded pdb=" O GLY w 35 " pdb=" N GLY w 37 " model vdw 2.232 2.520 nonbonded pdb=" O ASP w 13 " pdb=" OE1 GLU z 311 " model vdw 2.233 3.040 nonbonded pdb=" O2' G A1136 " pdb=" O2' G A2038 " model vdw 2.234 2.440 ... (remaining 1347725 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.180 Extract box with map and model: 10.190 Check model and map are aligned: 1.640 Set scattering table: 1.050 Process input model: 578.650 Find NCS groups from input model: 3.130 Set up NCS constraints: 0.470 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:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 598.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.103 159748 Z= 0.414 Angle : 0.907 17.696 238670 Z= 0.479 Chirality : 0.047 0.605 30435 Planarity : 0.006 0.068 13013 Dihedral : 22.761 179.715 91120 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.03 % Favored : 90.65 % Rotamer: Outliers : 0.59 % Allowed : 3.01 % Favored : 96.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -4.84 (0.08), residues: 5979 helix: -4.33 (0.06), residues: 1796 sheet: -2.47 (0.14), residues: 1137 loop : -2.75 (0.09), residues: 3046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.004 TRP C 212 HIS 0.025 0.003 HIS k 117 PHE 0.056 0.004 PHE u 36 TYR 0.039 0.003 TYR H 25 ARG 0.021 0.001 ARG Q 27 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11958 Ramachandran restraints generated. 5979 Oldfield, 0 Emsley, 5979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11958 Ramachandran restraints generated. 5979 Oldfield, 0 Emsley, 5979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1912 residues out of total 4985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 1883 time to evaluate : 6.499 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: D 165 MET cc_start: 0.8586 (ttt) cc_final: 0.8360 (ttt) REVERT: E 130 LYS cc_start: 0.8338 (mttm) cc_final: 0.8111 (mttt) REVERT: E 139 LYS cc_start: 0.8771 (tttt) cc_final: 0.8178 (ttpp) REVERT: E 189 THR cc_start: 0.8754 (m) cc_final: 0.8494 (p) REVERT: F 21 TYR cc_start: 0.7879 (m-80) cc_final: 0.7528 (m-80) REVERT: F 140 ILE cc_start: 0.6751 (OUTLIER) cc_final: 0.6456 (mp) REVERT: F 144 LYS cc_start: 0.7799 (mptt) cc_final: 0.6943 (ttpt) REVERT: G 24 THR cc_start: 0.7877 (m) cc_final: 0.7628 (t) REVERT: J 31 GLU cc_start: 0.7715 (tp30) cc_final: 0.7513 (tp30) REVERT: J 57 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8281 (pp) REVERT: J 58 ASN cc_start: 0.9037 (m110) cc_final: 0.7897 (m-40) REVERT: L 96 LYS cc_start: 0.8817 (ttmp) cc_final: 0.8597 (mttm) REVERT: L 99 ASN cc_start: 0.8752 (t0) cc_final: 0.8536 (t0) REVERT: M 6 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.7231 (ppp-140) REVERT: M 96 ILE cc_start: 0.9292 (mm) cc_final: 0.9087 (mm) REVERT: P 26 GLU cc_start: 0.7406 (tm-30) cc_final: 0.7188 (tm-30) REVERT: P 29 VAL cc_start: 0.8997 (t) cc_final: 0.8779 (p) REVERT: P 70 GLU cc_start: 0.7718 (tt0) cc_final: 0.7060 (tt0) REVERT: Q 12 ARG cc_start: 0.8167 (mtp85) cc_final: 0.7839 (mtp85) REVERT: Q 92 LYS cc_start: 0.7993 (tttt) cc_final: 0.7782 (ttpt) REVERT: R 1 MET cc_start: 0.5282 (tpp) cc_final: 0.5027 (tpt) REVERT: R 11 GLN cc_start: 0.8050 (mp10) cc_final: 0.7646 (mt0) REVERT: R 90 ARG cc_start: 0.9079 (mtp85) cc_final: 0.8878 (mtm180) REVERT: S 29 VAL cc_start: 0.8399 (t) cc_final: 0.8198 (m) REVERT: U 5 ARG cc_start: 0.8625 (ptp-170) cc_final: 0.8345 (ptp-170) REVERT: U 85 ARG cc_start: 0.7374 (ptp-170) cc_final: 0.7118 (ptp90) REVERT: V 93 ARG cc_start: 0.7750 (ttm110) cc_final: 0.7338 (ttm110) REVERT: Y 18 LEU cc_start: 0.8515 (tp) cc_final: 0.8218 (tp) REVERT: Y 44 LYS cc_start: 0.8636 (tttp) cc_final: 0.8396 (ttpt) REVERT: 0 14 MET cc_start: 0.8683 (mtm) cc_final: 0.8438 (mtt) REVERT: 1 36 LYS cc_start: 0.8564 (tttt) cc_final: 0.8285 (ttmt) REVERT: 4 15 LYS cc_start: 0.8463 (ttmm) cc_final: 0.8238 (mmtp) REVERT: b 67 LEU cc_start: 0.7581 (mt) cc_final: 0.7327 (mt) REVERT: b 99 MET cc_start: 0.7002 (ptp) cc_final: 0.6802 (ptp) REVERT: b 139 GLU cc_start: 0.7582 (tm-30) cc_final: 0.7270 (tm-30) REVERT: c 44 LYS cc_start: 0.8453 (tppp) cc_final: 0.8199 (mptt) REVERT: c 101 ASN cc_start: 0.8450 (m-40) cc_final: 0.8162 (m-40) REVERT: c 113 LYS cc_start: 0.8309 (tptt) cc_final: 0.7946 (tptt) REVERT: c 168 ARG cc_start: 0.6947 (ptt90) cc_final: 0.6299 (ptt180) REVERT: d 72 ARG cc_start: 0.7797 (ttp80) cc_final: 0.7595 (ttp80) REVERT: d 77 GLU cc_start: 0.7744 (tp30) cc_final: 0.7482 (tp30) REVERT: d 104 MET cc_start: 0.7132 (mmt) cc_final: 0.6854 (mmm) REVERT: d 140 ASP cc_start: 0.7797 (m-30) cc_final: 0.7575 (m-30) REVERT: e 151 MET cc_start: 0.7412 (mmp) cc_final: 0.6899 (mmm) REVERT: e 156 ARG cc_start: 0.6551 (OUTLIER) cc_final: 0.4641 (ppp-140) REVERT: g 55 LYS cc_start: 0.7290 (mmmm) cc_final: 0.6973 (mtpt) REVERT: g 77 ARG cc_start: 0.4507 (mmm160) cc_final: 0.3579 (ptt180) REVERT: g 135 LYS cc_start: 0.8514 (tptt) cc_final: 0.8199 (ttmm) REVERT: h 32 LYS cc_start: 0.8236 (mmtp) cc_final: 0.7951 (mmmm) REVERT: h 40 LYS cc_start: 0.8639 (tptp) cc_final: 0.8283 (tptt) REVERT: h 100 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8389 (pt) REVERT: h 120 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7880 (pp) REVERT: h 124 ILE cc_start: 0.8504 (pt) cc_final: 0.8278 (pt) REVERT: l 30 ARG cc_start: 0.9048 (ttp-170) cc_final: 0.8836 (ttp-170) REVERT: n 19 TYR cc_start: 0.8073 (m-80) cc_final: 0.7605 (m-80) REVERT: o 23 SER cc_start: 0.8960 (t) cc_final: 0.8611 (p) REVERT: o 36 ASN cc_start: 0.8292 (m-40) cc_final: 0.8060 (m110) REVERT: o 64 LYS cc_start: 0.8850 (mtmt) cc_final: 0.8570 (mttt) REVERT: p 63 GLN cc_start: 0.8385 (mm110) cc_final: 0.7937 (mm-40) REVERT: q 36 PHE cc_start: 0.8913 (m-80) cc_final: 0.8682 (m-80) REVERT: r 50 TYR cc_start: 0.8952 (m-80) cc_final: 0.8648 (m-80) REVERT: t 78 LEU cc_start: 0.9095 (tp) cc_final: 0.8795 (tp) REVERT: z 131 ASP cc_start: 0.6786 (t70) cc_final: 0.6525 (t0) REVERT: z 140 GLU cc_start: 0.7990 (tp30) cc_final: 0.7629 (tp30) REVERT: z 177 LYS cc_start: 0.8365 (mtpp) cc_final: 0.8149 (mtpp) REVERT: z 270 ILE cc_start: 0.7142 (OUTLIER) cc_final: 0.6572 (tp) REVERT: z 279 SER cc_start: 0.8462 (p) cc_final: 0.8155 (t) REVERT: z 307 LYS cc_start: 0.7450 (mttt) cc_final: 0.7200 (ttpt) outliers start: 29 outliers final: 6 residues processed: 1902 average time/residue: 1.4747 time to fit residues: 4603.5782 Evaluate side-chains 1445 residues out of total 4985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 1432 time to evaluate : 6.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain e residue 156 ARG Chi-restraints excluded: chain h residue 100 ILE Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain o residue 86 LEU Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain z residue 270 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1046 random chunks: chunk 883 optimal weight: 7.9990 chunk 792 optimal weight: 7.9990 chunk 439 optimal weight: 7.9990 chunk 270 optimal weight: 10.0000 chunk 534 optimal weight: 10.0000 chunk 423 optimal weight: 0.9990 chunk 819 optimal weight: 2.9990 chunk 317 optimal weight: 7.9990 chunk 498 optimal weight: 6.9990 chunk 610 optimal weight: 3.9990 chunk 949 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 ASN C 238 ASN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN D 126 ASN D 150 GLN D 164 GLN D 173 GLN E 195 GLN F 134 GLN H 66 ASN J 40 HIS J 58 ASN J 67 ASN ** J 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN P 2 ASN P 11 GLN Q 43 GLN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 43 ASN R 91 GLN S 7 HIS T 15 HIS U 68 ASN V 78 GLN W 8 ASN Z 8 GLN Z 33 HIS 0 4 GLN 3 42 HIS 4 37 GLN b 18 GLN b 119 GLN b 169 HIS c 7 ASN c 184 ASN c 189 HIS ** d 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 55 HIS f 68 GLN g 121 ASN h 3 GLN h 66 GLN i 3 ASN i 4 GLN i 74 GLN ** i 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 23 HIS k 118 ASN l 19 ASN ** m 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 43 ASN n 60 GLN p 18 GLN p 63 GLN p 79 ASN ** q 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 30 HIS r 51 GLN s 51 HIS ** t 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 47 GLN t 51 ASN t 60 GLN ** w 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 21 HIS z 8 ASN z 54 GLN z 275 GLN z 283 ASN Total number of N/Q/H flips: 62 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 159748 Z= 0.228 Angle : 0.633 13.040 238670 Z= 0.330 Chirality : 0.038 0.357 30435 Planarity : 0.005 0.062 13013 Dihedral : 23.602 179.524 79222 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.96 % Favored : 91.84 % Rotamer: Outliers : 3.55 % Allowed : 10.99 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -3.51 (0.09), residues: 5979 helix: -2.41 (0.09), residues: 1902 sheet: -1.97 (0.14), residues: 1092 loop : -2.37 (0.10), residues: 2985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 212 HIS 0.011 0.001 HIS f 11 PHE 0.029 0.002 PHE u 36 TYR 0.031 0.002 TYR z 187 ARG 0.015 0.001 ARG t 23 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11958 Ramachandran restraints generated. 5979 Oldfield, 0 Emsley, 5979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11958 Ramachandran restraints generated. 5979 Oldfield, 0 Emsley, 5979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1656 residues out of total 4985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 1480 time to evaluate : 6.572 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: C 29 PHE cc_start: 0.8731 (t80) cc_final: 0.8408 (t80) REVERT: D 28 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.7123 (pt0) REVERT: D 137 SER cc_start: 0.8695 (m) cc_final: 0.8359 (t) REVERT: D 165 MET cc_start: 0.8487 (ttt) cc_final: 0.8218 (ttt) REVERT: D 167 ASN cc_start: 0.8693 (t0) cc_final: 0.8440 (t0) REVERT: D 187 LEU cc_start: 0.9028 (tp) cc_final: 0.8812 (tp) REVERT: E 111 GLU cc_start: 0.7639 (tp30) cc_final: 0.7140 (tp30) REVERT: E 130 LYS cc_start: 0.8271 (mttm) cc_final: 0.7951 (mttt) REVERT: E 136 GLN cc_start: 0.8385 (tp40) cc_final: 0.7986 (tp40) REVERT: E 139 LYS cc_start: 0.8887 (tttt) cc_final: 0.8213 (ttpp) REVERT: F 3 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8134 (pp) REVERT: F 16 MET cc_start: 0.8168 (mmt) cc_final: 0.7936 (mmm) REVERT: F 124 ARG cc_start: 0.7374 (tpp-160) cc_final: 0.7139 (mmt180) REVERT: F 133 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7618 (mm-30) REVERT: F 144 LYS cc_start: 0.7687 (mptt) cc_final: 0.6888 (ttpt) REVERT: F 158 THR cc_start: 0.8695 (p) cc_final: 0.8459 (p) REVERT: F 174 PHE cc_start: 0.6952 (OUTLIER) cc_final: 0.6324 (m-80) REVERT: F 176 PHE cc_start: 0.8508 (OUTLIER) cc_final: 0.8256 (m-10) REVERT: G 24 THR cc_start: 0.7854 (m) cc_final: 0.7536 (t) REVERT: J 57 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8275 (pp) REVERT: J 58 ASN cc_start: 0.9091 (m-40) cc_final: 0.8275 (m-40) REVERT: J 92 MET cc_start: 0.7869 (ttt) cc_final: 0.7571 (ttt) REVERT: J 131 ASN cc_start: 0.7798 (p0) cc_final: 0.7573 (p0) REVERT: K 59 LYS cc_start: 0.9043 (mttm) cc_final: 0.8613 (mttm) REVERT: L 99 ASN cc_start: 0.8768 (t0) cc_final: 0.8495 (t0) REVERT: L 112 LEU cc_start: 0.8775 (tp) cc_final: 0.8476 (tt) REVERT: N 12 ARG cc_start: 0.8681 (mtt90) cc_final: 0.8396 (mtt-85) REVERT: P 19 PHE cc_start: 0.8871 (p90) cc_final: 0.8667 (p90) REVERT: P 28 LYS cc_start: 0.8647 (mtpt) cc_final: 0.8426 (mmmm) REVERT: P 70 GLU cc_start: 0.7703 (tt0) cc_final: 0.7039 (tt0) REVERT: P 88 ARG cc_start: 0.7961 (mtm-85) cc_final: 0.7647 (mtt-85) REVERT: Q 12 ARG cc_start: 0.7913 (mtp85) cc_final: 0.7633 (mtp85) REVERT: Q 92 LYS cc_start: 0.7910 (tttt) cc_final: 0.7690 (ttpt) REVERT: R 1 MET cc_start: 0.5105 (tpp) cc_final: 0.4864 (tpt) REVERT: T 6 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7654 (ttm-80) REVERT: T 48 GLN cc_start: 0.7924 (mm-40) cc_final: 0.7702 (mm-40) REVERT: U 5 ARG cc_start: 0.8574 (ptp-170) cc_final: 0.8284 (ptp-170) REVERT: V 93 ARG cc_start: 0.7656 (ttm110) cc_final: 0.7282 (mtp180) REVERT: Z 37 ARG cc_start: 0.8909 (mmt-90) cc_final: 0.8706 (mmt-90) REVERT: Z 48 ASN cc_start: 0.8242 (t0) cc_final: 0.8035 (t0) REVERT: 0 11 LYS cc_start: 0.8415 (tppt) cc_final: 0.8102 (mmtt) REVERT: 0 14 MET cc_start: 0.8638 (mtm) cc_final: 0.8271 (mtt) REVERT: 1 36 LYS cc_start: 0.8451 (tttt) cc_final: 0.8210 (ttmt) REVERT: 4 15 LYS cc_start: 0.8412 (ttmm) cc_final: 0.8047 (mmtp) REVERT: b 42 LEU cc_start: 0.5833 (OUTLIER) cc_final: 0.5535 (mm) REVERT: b 104 LYS cc_start: 0.8183 (ptmm) cc_final: 0.7862 (tttm) REVERT: b 139 GLU cc_start: 0.7457 (tm-30) cc_final: 0.7127 (tm-30) REVERT: b 169 HIS cc_start: 0.8683 (p90) cc_final: 0.8404 (p90) REVERT: c 128 MET cc_start: 0.8152 (mmm) cc_final: 0.7722 (tpp) REVERT: d 32 LYS cc_start: 0.6903 (tptp) cc_final: 0.6633 (ttpp) REVERT: d 39 GLN cc_start: 0.7821 (tt0) cc_final: 0.7566 (tt0) REVERT: d 143 SER cc_start: 0.8969 (OUTLIER) cc_final: 0.8634 (p) REVERT: e 151 MET cc_start: 0.7381 (mmp) cc_final: 0.6940 (mmm) REVERT: g 62 GLU cc_start: 0.8693 (tp30) cc_final: 0.8472 (tp30) REVERT: g 77 ARG cc_start: 0.4750 (mmm160) cc_final: 0.3841 (ptt180) REVERT: g 135 LYS cc_start: 0.8480 (tptt) cc_final: 0.8088 (ttmm) REVERT: h 32 LYS cc_start: 0.8229 (mmtp) cc_final: 0.8000 (mmmm) REVERT: h 40 LYS cc_start: 0.8649 (tptp) cc_final: 0.8310 (tptt) REVERT: h 90 GLU cc_start: 0.6881 (tt0) cc_final: 0.6679 (tt0) REVERT: h 100 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8516 (pt) REVERT: h 120 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7875 (pp) REVERT: j 48 ARG cc_start: 0.7923 (mtt-85) cc_final: 0.7705 (mtt-85) REVERT: k 55 ARG cc_start: 0.7830 (mtm-85) cc_final: 0.7614 (mtm-85) REVERT: m 3 ILE cc_start: 0.8033 (pt) cc_final: 0.7711 (pt) REVERT: m 32 ILE cc_start: 0.9034 (mt) cc_final: 0.8758 (mt) REVERT: n 19 TYR cc_start: 0.7903 (m-80) cc_final: 0.7502 (m-80) REVERT: o 36 ASN cc_start: 0.8280 (m-40) cc_final: 0.8028 (m110) REVERT: o 64 LYS cc_start: 0.9048 (mtmt) cc_final: 0.8781 (mttt) REVERT: s 54 ARG cc_start: 0.8126 (ptt-90) cc_final: 0.7889 (ptt-90) REVERT: t 78 LEU cc_start: 0.8957 (tp) cc_final: 0.8752 (tp) REVERT: z 40 GLU cc_start: 0.5750 (tt0) cc_final: 0.4681 (pt0) REVERT: z 131 ASP cc_start: 0.6679 (t70) cc_final: 0.6441 (t0) REVERT: z 270 ILE cc_start: 0.7199 (OUTLIER) cc_final: 0.6809 (tp) REVERT: z 279 SER cc_start: 0.8476 (p) cc_final: 0.8212 (t) REVERT: z 301 GLN cc_start: 0.7464 (mp10) cc_final: 0.7004 (mt0) REVERT: z 350 ASP cc_start: 0.5276 (t70) cc_final: 0.4958 (t70) outliers start: 176 outliers final: 115 residues processed: 1556 average time/residue: 1.4129 time to fit residues: 3708.1079 Evaluate side-chains 1496 residues out of total 4985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 1370 time to evaluate : 6.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 63 LYS Chi-restraints excluded: chain F residue 132 ARG Chi-restraints excluded: chain F residue 134 GLN Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 174 PHE Chi-restraints excluded: chain F residue 176 PHE Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 157 LYS Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 111 GLU Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain T residue 6 ARG Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain U residue 60 LYS Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain X residue 1 SER Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain Y residue 8 GLU Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 3 residue 37 THR Chi-restraints excluded: chain b residue 23 ASN Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 58 LYS Chi-restraints excluded: chain b residue 130 LYS Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 177 ASN Chi-restraints excluded: chain b residue 185 ILE Chi-restraints excluded: chain b residue 196 ASP Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 88 LYS Chi-restraints excluded: chain c residue 96 VAL Chi-restraints excluded: chain c residue 146 LYS Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 184 ASN Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 143 SER Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 197 HIS Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 95 MET Chi-restraints excluded: chain e residue 119 VAL Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain e residue 133 ILE Chi-restraints excluded: chain e residue 152 VAL Chi-restraints excluded: chain e residue 155 LYS Chi-restraints excluded: chain e residue 156 ARG Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 63 ASN Chi-restraints excluded: chain g residue 20 GLU Chi-restraints excluded: chain g residue 37 THR Chi-restraints excluded: chain g residue 93 VAL Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 57 GLU Chi-restraints excluded: chain h residue 100 ILE Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain i residue 65 THR Chi-restraints excluded: chain i residue 110 VAL Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain m residue 101 THR Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain o residue 25 GLU Chi-restraints excluded: chain o residue 51 SER Chi-restraints excluded: chain o residue 86 LEU Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain s residue 48 ILE Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain t residue 85 LEU Chi-restraints excluded: chain u residue 13 VAL Chi-restraints excluded: chain w residue 33 LYS Chi-restraints excluded: chain z residue 110 LEU Chi-restraints excluded: chain z residue 118 MET Chi-restraints excluded: chain z residue 170 GLU Chi-restraints excluded: chain z residue 173 VAL Chi-restraints excluded: chain z residue 270 ILE Chi-restraints excluded: chain z residue 298 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1046 random chunks: chunk 527 optimal weight: 0.4980 chunk 294 optimal weight: 20.0000 chunk 790 optimal weight: 5.9990 chunk 646 optimal weight: 20.0000 chunk 262 optimal weight: 10.0000 chunk 951 optimal weight: 20.0000 chunk 1027 optimal weight: 0.4980 chunk 847 optimal weight: 5.9990 chunk 943 optimal weight: 10.0000 chunk 324 optimal weight: 5.9990 chunk 763 optimal weight: 20.0000 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN E 195 GLN J 67 ASN J 128 ASN J 136 GLN N 107 ASN P 6 GLN Q 43 GLN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 18 GLN R 87 GLN S 60 HIS S 61 ASN V 78 GLN 0 4 GLN c 18 ASN c 99 GLN d 39 GLN ** m 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 47 GLN t 54 GLN ** w 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 38 ASN z 54 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 159748 Z= 0.191 Angle : 0.571 11.210 238670 Z= 0.298 Chirality : 0.035 0.290 30435 Planarity : 0.004 0.055 13013 Dihedral : 23.402 179.126 79219 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.01 % Favored : 91.84 % Rotamer: Outliers : 4.10 % Allowed : 13.38 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.10), residues: 5979 helix: -1.16 (0.11), residues: 1889 sheet: -1.62 (0.15), residues: 1104 loop : -2.08 (0.10), residues: 2986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 212 HIS 0.013 0.001 HIS f 11 PHE 0.050 0.002 PHE u 36 TYR 0.020 0.002 TYR F 21 ARG 0.014 0.001 ARG b 224 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11958 Ramachandran restraints generated. 5979 Oldfield, 0 Emsley, 5979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11958 Ramachandran restraints generated. 5979 Oldfield, 0 Emsley, 5979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1609 residues out of total 4985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 1406 time to evaluate : 6.611 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: D 13 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.7926 (ptt180) REVERT: D 28 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6814 (pt0) REVERT: D 46 ARG cc_start: 0.8593 (ptm-80) cc_final: 0.8273 (ptm-80) REVERT: D 165 MET cc_start: 0.8555 (ttt) cc_final: 0.8285 (ttt) REVERT: E 4 VAL cc_start: 0.8422 (OUTLIER) cc_final: 0.8105 (t) REVERT: E 111 GLU cc_start: 0.7557 (tp30) cc_final: 0.6929 (tp30) REVERT: E 115 GLN cc_start: 0.7584 (mt0) cc_final: 0.6008 (mt0) REVERT: E 130 LYS cc_start: 0.8271 (mttm) cc_final: 0.8025 (mttt) REVERT: E 136 GLN cc_start: 0.8331 (tp40) cc_final: 0.8052 (tp40) REVERT: E 139 LYS cc_start: 0.8846 (tttt) cc_final: 0.8205 (ttpp) REVERT: F 16 MET cc_start: 0.8212 (mmt) cc_final: 0.7979 (mmm) REVERT: F 133 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7420 (mm-30) REVERT: F 144 LYS cc_start: 0.7631 (mptt) cc_final: 0.6823 (ttpt) REVERT: F 158 THR cc_start: 0.8734 (p) cc_final: 0.8507 (p) REVERT: F 174 PHE cc_start: 0.6510 (OUTLIER) cc_final: 0.6085 (m-80) REVERT: J 57 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8254 (pp) REVERT: J 95 ARG cc_start: 0.7973 (tpp-160) cc_final: 0.7488 (mmm160) REVERT: J 131 ASN cc_start: 0.7900 (p0) cc_final: 0.7685 (p0) REVERT: J 140 LEU cc_start: 0.8630 (tt) cc_final: 0.8246 (mt) REVERT: L 99 ASN cc_start: 0.8760 (t0) cc_final: 0.8452 (t0) REVERT: L 129 LYS cc_start: 0.8451 (ttmt) cc_final: 0.8059 (ttpt) REVERT: L 141 LYS cc_start: 0.8561 (pttp) cc_final: 0.8331 (pttm) REVERT: M 18 ARG cc_start: 0.8263 (mtm-85) cc_final: 0.7766 (mtp180) REVERT: M 63 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8519 (mm) REVERT: M 136 MET cc_start: 0.5634 (tmm) cc_final: 0.5424 (tmm) REVERT: N 12 ARG cc_start: 0.8672 (mtt90) cc_final: 0.8377 (mtt-85) REVERT: N 24 MET cc_start: 0.8101 (ttt) cc_final: 0.7867 (ttm) REVERT: N 73 ASN cc_start: 0.8542 (t0) cc_final: 0.8321 (t0) REVERT: P 6 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.7732 (tt0) REVERT: P 88 ARG cc_start: 0.7918 (mtm-85) cc_final: 0.7669 (mtt-85) REVERT: Q 12 ARG cc_start: 0.7891 (mtp85) cc_final: 0.7606 (mtp85) REVERT: Q 92 LYS cc_start: 0.8016 (tttt) cc_final: 0.7519 (ttpt) REVERT: R 1 MET cc_start: 0.5017 (tpp) cc_final: 0.4771 (tpt) REVERT: T 6 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7608 (ttm-80) REVERT: U 5 ARG cc_start: 0.8606 (ptp-170) cc_final: 0.8317 (ptp-170) REVERT: V 93 ARG cc_start: 0.7544 (ttm110) cc_final: 0.7285 (mtp180) REVERT: W 35 ARG cc_start: 0.7993 (mtp85) cc_final: 0.7647 (mtp180) REVERT: 0 11 LYS cc_start: 0.8413 (tppt) cc_final: 0.8087 (mmtt) REVERT: 1 36 LYS cc_start: 0.8452 (tttt) cc_final: 0.8224 (ttmt) REVERT: 3 14 LYS cc_start: 0.8710 (mmtt) cc_final: 0.8407 (mmmt) REVERT: 4 15 LYS cc_start: 0.8428 (ttmm) cc_final: 0.8009 (mmtp) REVERT: b 42 LEU cc_start: 0.5823 (OUTLIER) cc_final: 0.5597 (mm) REVERT: c 146 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8149 (tttt) REVERT: d 32 LYS cc_start: 0.7145 (tptp) cc_final: 0.6925 (tttp) REVERT: d 39 GLN cc_start: 0.7740 (tt0) cc_final: 0.7538 (tt0) REVERT: e 114 LEU cc_start: 0.8951 (mt) cc_final: 0.8733 (mt) REVERT: e 151 MET cc_start: 0.7407 (mmp) cc_final: 0.6979 (mmm) REVERT: e 156 ARG cc_start: 0.6324 (OUTLIER) cc_final: 0.4259 (ppp-140) REVERT: f 79 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7434 (ttm-80) REVERT: g 62 GLU cc_start: 0.8637 (tp30) cc_final: 0.8357 (tp30) REVERT: g 77 ARG cc_start: 0.4600 (mmm160) cc_final: 0.4161 (ptt180) REVERT: g 136 LYS cc_start: 0.8699 (tptt) cc_final: 0.8067 (tttp) REVERT: h 32 LYS cc_start: 0.8282 (mmtp) cc_final: 0.7992 (mmmm) REVERT: h 90 GLU cc_start: 0.6886 (tt0) cc_final: 0.6657 (tt0) REVERT: h 100 ILE cc_start: 0.8839 (pp) cc_final: 0.8427 (pt) REVERT: h 120 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8073 (pp) REVERT: j 10 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.7959 (pp) REVERT: j 48 ARG cc_start: 0.7906 (mtt-85) cc_final: 0.7656 (mtt-85) REVERT: k 105 ARG cc_start: 0.7223 (mtp-110) cc_final: 0.6756 (ttm170) REVERT: m 32 ILE cc_start: 0.9003 (mt) cc_final: 0.8734 (mt) REVERT: n 25 GLU cc_start: 0.7545 (pm20) cc_final: 0.7338 (pm20) REVERT: o 64 LYS cc_start: 0.9044 (mtmt) cc_final: 0.8802 (mttt) REVERT: o 69 LEU cc_start: 0.8876 (tp) cc_final: 0.8674 (tp) REVERT: q 26 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.7289 (ptt90) REVERT: q 80 LYS cc_start: 0.8137 (tmmt) cc_final: 0.7803 (ttpp) REVERT: w 22 ASP cc_start: 0.8445 (t0) cc_final: 0.8192 (t0) REVERT: z 40 GLU cc_start: 0.5600 (OUTLIER) cc_final: 0.4666 (pt0) REVERT: z 54 GLN cc_start: 0.6488 (tt0) cc_final: 0.5924 (tp-100) REVERT: z 131 ASP cc_start: 0.6688 (t70) cc_final: 0.6438 (t0) REVERT: z 270 ILE cc_start: 0.7211 (OUTLIER) cc_final: 0.5932 (tp) REVERT: z 279 SER cc_start: 0.8407 (p) cc_final: 0.8195 (t) REVERT: z 300 MET cc_start: 0.6973 (mmm) cc_final: 0.6237 (mtp) REVERT: z 301 GLN cc_start: 0.7427 (OUTLIER) cc_final: 0.7010 (mt0) outliers start: 203 outliers final: 127 residues processed: 1496 average time/residue: 1.3493 time to fit residues: 3392.8955 Evaluate side-chains 1476 residues out of total 4985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 1331 time to evaluate : 6.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 50 ASP Chi-restraints excluded: chain F residue 63 LYS Chi-restraints excluded: chain F residue 134 GLN Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 174 PHE Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 157 LYS Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain P residue 6 GLN Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 111 GLU Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain T residue 6 ARG Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain V residue 46 LYS Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain X residue 1 SER Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain Y residue 8 GLU Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 23 LEU Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 21 LEU Chi-restraints excluded: chain 0 residue 33 SER Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 3 residue 37 THR Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain b residue 40 ILE Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 56 LEU Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 185 ILE Chi-restraints excluded: chain b residue 196 ASP Chi-restraints excluded: chain c residue 43 THR Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 96 VAL Chi-restraints excluded: chain c residue 146 LYS Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 164 THR Chi-restraints excluded: chain c residue 165 GLU Chi-restraints excluded: chain c residue 184 ASN Chi-restraints excluded: chain c residue 206 ILE Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 128 VAL Chi-restraints excluded: chain d residue 147 LYS Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain d residue 197 HIS Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain e residue 133 ILE Chi-restraints excluded: chain e residue 155 LYS Chi-restraints excluded: chain e residue 156 ARG Chi-restraints excluded: chain f residue 63 ASN Chi-restraints excluded: chain f residue 79 ARG Chi-restraints excluded: chain g residue 20 GLU Chi-restraints excluded: chain g residue 36 SER Chi-restraints excluded: chain g residue 93 VAL Chi-restraints excluded: chain g residue 105 GLU Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 46 GLU Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 104 SER Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain i residue 17 ARG Chi-restraints excluded: chain i residue 110 VAL Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 80 ASN Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 101 THR Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain o residue 86 LEU Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 52 LEU Chi-restraints excluded: chain q residue 26 ARG Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain s residue 48 ILE Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain t residue 85 LEU Chi-restraints excluded: chain w residue 33 LYS Chi-restraints excluded: chain z residue 40 GLU Chi-restraints excluded: chain z residue 118 MET Chi-restraints excluded: chain z residue 170 GLU Chi-restraints excluded: chain z residue 173 VAL Chi-restraints excluded: chain z residue 181 ILE Chi-restraints excluded: chain z residue 226 VAL Chi-restraints excluded: chain z residue 270 ILE Chi-restraints excluded: chain z residue 298 LEU Chi-restraints excluded: chain z residue 301 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1046 random chunks: chunk 940 optimal weight: 9.9990 chunk 715 optimal weight: 20.0000 chunk 493 optimal weight: 9.9990 chunk 105 optimal weight: 40.0000 chunk 454 optimal weight: 50.0000 chunk 638 optimal weight: 40.0000 chunk 955 optimal weight: 10.0000 chunk 1011 optimal weight: 5.9990 chunk 498 optimal weight: 8.9990 chunk 905 optimal weight: 0.0470 chunk 272 optimal weight: 10.0000 overall best weight: 7.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 238 ASN D 167 ASN E 115 GLN E 195 GLN F 134 GLN G 142 GLN J 67 ASN J 136 GLN ** N 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 6 GLN Q 43 GLN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 87 GLN S 9 HIS S 60 HIS T 48 GLN U 39 ASN U 73 ASN V 78 GLN W 72 ASN 4 37 GLN 6 61 ASN b 14 HIS b 23 ASN c 7 ASN c 68 HIS c 122 GLN c 184 ASN ** h 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 36 GLN ** i 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 36 ASN s 13 HIS ** t 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 47 GLN w 5 GLN w 27 GLN ** w 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 159748 Z= 0.302 Angle : 0.627 14.419 238670 Z= 0.325 Chirality : 0.039 0.327 30435 Planarity : 0.005 0.059 13013 Dihedral : 23.388 179.375 79217 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.90 % Favored : 90.90 % Rotamer: Outliers : 5.20 % Allowed : 14.91 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.10), residues: 5979 helix: -0.83 (0.11), residues: 1904 sheet: -1.49 (0.15), residues: 1108 loop : -1.97 (0.11), residues: 2967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 212 HIS 0.011 0.002 HIS f 11 PHE 0.041 0.002 PHE u 36 TYR 0.022 0.002 TYR F 6 ARG 0.011 0.001 ARG z 278 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11958 Ramachandran restraints generated. 5979 Oldfield, 0 Emsley, 5979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11958 Ramachandran restraints generated. 5979 Oldfield, 0 Emsley, 5979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1640 residues out of total 4985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 1382 time to evaluate : 6.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 81 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7494 (mt-10) REVERT: C 184 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7798 (mm-30) REVERT: D 13 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.7921 (ptt180) REVERT: D 28 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6749 (pt0) REVERT: D 165 MET cc_start: 0.8576 (ttt) cc_final: 0.8260 (ttt) REVERT: E 4 VAL cc_start: 0.8425 (OUTLIER) cc_final: 0.8109 (t) REVERT: E 107 SER cc_start: 0.8872 (t) cc_final: 0.8563 (p) REVERT: E 130 LYS cc_start: 0.8326 (mttm) cc_final: 0.8104 (mttt) REVERT: E 136 GLN cc_start: 0.8393 (tp40) cc_final: 0.8135 (tp40) REVERT: E 139 LYS cc_start: 0.8841 (tttt) cc_final: 0.8209 (ttpp) REVERT: F 70 ARG cc_start: 0.7944 (ttp-110) cc_final: 0.7017 (ttp-170) REVERT: F 90 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7991 (pp) REVERT: F 133 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7403 (mp0) REVERT: F 144 LYS cc_start: 0.7706 (mptt) cc_final: 0.6946 (ttpt) REVERT: F 158 THR cc_start: 0.8754 (p) cc_final: 0.8552 (p) REVERT: G 114 HIS cc_start: 0.8572 (t70) cc_final: 0.8285 (t70) REVERT: J 57 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8257 (pp) REVERT: J 95 ARG cc_start: 0.7963 (tpp-160) cc_final: 0.7488 (mmm160) REVERT: J 131 ASN cc_start: 0.7894 (p0) cc_final: 0.7638 (p0) REVERT: J 140 LEU cc_start: 0.8671 (tt) cc_final: 0.8278 (mt) REVERT: K 59 LYS cc_start: 0.9023 (mttm) cc_final: 0.8783 (mttm) REVERT: L 99 ASN cc_start: 0.8772 (t0) cc_final: 0.8491 (t0) REVERT: M 106 ASP cc_start: 0.7737 (t70) cc_final: 0.7443 (t70) REVERT: M 136 MET cc_start: 0.5675 (tmm) cc_final: 0.5415 (tmm) REVERT: N 24 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.8068 (ttm) REVERT: N 73 ASN cc_start: 0.8553 (t0) cc_final: 0.8266 (t0) REVERT: O 46 GLU cc_start: 0.7880 (pm20) cc_final: 0.7672 (pm20) REVERT: P 6 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8127 (pt0) REVERT: P 88 ARG cc_start: 0.7949 (mtm-85) cc_final: 0.7670 (mtt-85) REVERT: P 98 TYR cc_start: 0.9145 (p90) cc_final: 0.8897 (p90) REVERT: Q 12 ARG cc_start: 0.7895 (mtp85) cc_final: 0.7610 (mtp85) REVERT: Q 92 LYS cc_start: 0.8038 (tttt) cc_final: 0.7556 (ttpt) REVERT: Q 101 ASP cc_start: 0.6586 (t70) cc_final: 0.6379 (t70) REVERT: R 1 MET cc_start: 0.5119 (tpp) cc_final: 0.4770 (tpt) REVERT: T 6 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7492 (ttm-80) REVERT: U 5 ARG cc_start: 0.8635 (ptp-170) cc_final: 0.8368 (ptp-170) REVERT: U 68 ASN cc_start: 0.8288 (m-40) cc_final: 0.7650 (m110) REVERT: U 85 ARG cc_start: 0.7781 (ptp90) cc_final: 0.7276 (ptp90) REVERT: W 35 ARG cc_start: 0.8016 (mtp85) cc_final: 0.7534 (mtp180) REVERT: W 71 LYS cc_start: 0.8724 (mttm) cc_final: 0.8504 (mtmt) REVERT: W 73 ARG cc_start: 0.7898 (ptp-170) cc_final: 0.7545 (mtm180) REVERT: Z 37 ARG cc_start: 0.8701 (mmt-90) cc_final: 0.8347 (mmt-90) REVERT: 0 11 LYS cc_start: 0.8494 (tppt) cc_final: 0.8104 (mmtt) REVERT: 0 51 ARG cc_start: 0.7339 (ttm110) cc_final: 0.7133 (ttm110) REVERT: 1 36 LYS cc_start: 0.8556 (tttt) cc_final: 0.8315 (ttmt) REVERT: 1 49 LYS cc_start: 0.8557 (mptt) cc_final: 0.8254 (mmtp) REVERT: 3 14 LYS cc_start: 0.8705 (mmtt) cc_final: 0.8337 (mmtt) REVERT: 4 15 LYS cc_start: 0.8440 (ttmm) cc_final: 0.7974 (mmtp) REVERT: 6 63 ARG cc_start: 0.7378 (mtt-85) cc_final: 0.6929 (mtm-85) REVERT: b 42 LEU cc_start: 0.6122 (OUTLIER) cc_final: 0.5730 (mm) REVERT: c 128 MET cc_start: 0.8064 (mmm) cc_final: 0.7315 (tpp) REVERT: d 32 LYS cc_start: 0.7192 (tptp) cc_final: 0.6875 (tttm) REVERT: d 143 SER cc_start: 0.9014 (OUTLIER) cc_final: 0.8668 (p) REVERT: e 151 MET cc_start: 0.7410 (mmp) cc_final: 0.7021 (mtp) REVERT: f 79 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.7335 (ttm-80) REVERT: f 90 MET cc_start: 0.8159 (mmm) cc_final: 0.7679 (mmm) REVERT: g 62 GLU cc_start: 0.8616 (tp30) cc_final: 0.8322 (tp30) REVERT: g 77 ARG cc_start: 0.4652 (mmm160) cc_final: 0.4050 (ptt180) REVERT: h 32 LYS cc_start: 0.8392 (mmtp) cc_final: 0.8014 (mmmm) REVERT: h 100 ILE cc_start: 0.9045 (pp) cc_final: 0.8798 (pt) REVERT: h 120 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8024 (pp) REVERT: j 10 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.7953 (pp) REVERT: j 48 ARG cc_start: 0.8063 (mpt-90) cc_final: 0.7655 (mtt-85) REVERT: k 99 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6845 (mp) REVERT: l 5 GLN cc_start: 0.8993 (mt0) cc_final: 0.8682 (mt0) REVERT: l 55 ARG cc_start: 0.7748 (tpp-160) cc_final: 0.7539 (tpp-160) REVERT: l 61 GLU cc_start: 0.6894 (tp30) cc_final: 0.6454 (tp30) REVERT: m 32 ILE cc_start: 0.9080 (mt) cc_final: 0.8822 (mt) REVERT: n 25 GLU cc_start: 0.7591 (pm20) cc_final: 0.7299 (pm20) REVERT: o 36 ASN cc_start: 0.8188 (m-40) cc_final: 0.7961 (m110) REVERT: o 39 GLN cc_start: 0.8513 (mm-40) cc_final: 0.8215 (mt0) REVERT: s 10 ILE cc_start: 0.7989 (OUTLIER) cc_final: 0.7701 (pp) REVERT: t 32 LYS cc_start: 0.8389 (mmtp) cc_final: 0.8049 (mmtt) REVERT: z 40 GLU cc_start: 0.5666 (OUTLIER) cc_final: 0.4614 (pt0) REVERT: z 54 GLN cc_start: 0.6296 (tt0) cc_final: 0.6004 (tp-100) REVERT: z 64 GLU cc_start: 0.6346 (mt-10) cc_final: 0.6136 (mt-10) REVERT: z 131 ASP cc_start: 0.6596 (t70) cc_final: 0.6385 (t0) REVERT: z 168 GLU cc_start: 0.6993 (tm-30) cc_final: 0.5984 (tt0) REVERT: z 270 ILE cc_start: 0.6874 (OUTLIER) cc_final: 0.6276 (pp) outliers start: 258 outliers final: 203 residues processed: 1498 average time/residue: 1.3602 time to fit residues: 3449.8084 Evaluate side-chains 1562 residues out of total 4985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 1341 time to evaluate : 6.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 50 ASP Chi-restraints excluded: chain F residue 63 LYS Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 134 GLN Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain F residue 174 PHE Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 157 LYS Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain K residue 20 MET Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 24 MET Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 45 SER Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain P residue 6 GLN Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 111 GLU Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain T residue 6 ARG Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 60 LYS Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain V residue 46 LYS Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain X residue 1 SER Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain Y residue 8 GLU Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 21 LEU Chi-restraints excluded: chain 0 residue 33 SER Chi-restraints excluded: chain 1 residue 45 HIS Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 3 residue 37 THR Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain b residue 23 ASN Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 56 LEU Chi-restraints excluded: chain b residue 89 PHE Chi-restraints excluded: chain b residue 99 MET Chi-restraints excluded: chain b residue 163 ILE Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 177 ASN Chi-restraints excluded: chain b residue 185 ILE Chi-restraints excluded: chain b residue 196 ASP Chi-restraints excluded: chain c residue 54 ILE Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 88 LYS Chi-restraints excluded: chain c residue 96 VAL Chi-restraints excluded: chain c residue 146 LYS Chi-restraints excluded: chain c residue 152 VAL Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 164 THR Chi-restraints excluded: chain c residue 184 ASN Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain c residue 206 ILE Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 128 VAL Chi-restraints excluded: chain d residue 143 SER Chi-restraints excluded: chain d residue 147 LYS Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain d residue 197 HIS Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain e residue 87 VAL Chi-restraints excluded: chain e residue 95 MET Chi-restraints excluded: chain e residue 113 VAL Chi-restraints excluded: chain e residue 119 VAL Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain e residue 133 ILE Chi-restraints excluded: chain e residue 152 VAL Chi-restraints excluded: chain e residue 155 LYS Chi-restraints excluded: chain e residue 156 ARG Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 52 ASN Chi-restraints excluded: chain f residue 63 ASN Chi-restraints excluded: chain f residue 79 ARG Chi-restraints excluded: chain g residue 20 GLU Chi-restraints excluded: chain g residue 28 ILE Chi-restraints excluded: chain g residue 36 SER Chi-restraints excluded: chain g residue 37 THR Chi-restraints excluded: chain g residue 93 VAL Chi-restraints excluded: chain g residue 138 GLU Chi-restraints excluded: chain h residue 9 MET Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 46 GLU Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 104 SER Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain i residue 17 ARG Chi-restraints excluded: chain i residue 66 VAL Chi-restraints excluded: chain i residue 110 VAL Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 59 LYS Chi-restraints excluded: chain k residue 15 VAL Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 71 ASP Chi-restraints excluded: chain k residue 80 ASN Chi-restraints excluded: chain k residue 99 LEU Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 101 THR Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain o residue 25 GLU Chi-restraints excluded: chain o residue 86 LEU Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 52 LEU Chi-restraints excluded: chain p residue 61 VAL Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain s residue 18 VAL Chi-restraints excluded: chain s residue 48 ILE Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain t residue 26 MET Chi-restraints excluded: chain t residue 34 VAL Chi-restraints excluded: chain t residue 85 LEU Chi-restraints excluded: chain u residue 13 VAL Chi-restraints excluded: chain w residue 33 LYS Chi-restraints excluded: chain z residue 16 GLU Chi-restraints excluded: chain z residue 40 GLU Chi-restraints excluded: chain z residue 110 LEU Chi-restraints excluded: chain z residue 113 LEU Chi-restraints excluded: chain z residue 118 MET Chi-restraints excluded: chain z residue 153 LEU Chi-restraints excluded: chain z residue 173 VAL Chi-restraints excluded: chain z residue 181 ILE Chi-restraints excluded: chain z residue 226 VAL Chi-restraints excluded: chain z residue 270 ILE Chi-restraints excluded: chain z residue 298 LEU Chi-restraints excluded: chain z residue 301 GLN Chi-restraints excluded: chain z residue 340 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1046 random chunks: chunk 842 optimal weight: 3.9990 chunk 573 optimal weight: 7.9990 chunk 14 optimal weight: 30.0000 chunk 752 optimal weight: 10.0000 chunk 417 optimal weight: 7.9990 chunk 862 optimal weight: 7.9990 chunk 698 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 516 optimal weight: 10.0000 chunk 907 optimal weight: 8.9990 chunk 255 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 150 GLN D 173 GLN E 41 GLN E 115 GLN E 195 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 2 GLN J 136 GLN ** N 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 GLN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 87 GLN S 60 HIS V 78 GLN 4 37 GLN b 23 ASN c 7 ASN c 122 GLN c 138 GLN ** c 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 159748 Z= 0.316 Angle : 0.639 14.321 238670 Z= 0.330 Chirality : 0.039 0.338 30435 Planarity : 0.005 0.058 13013 Dihedral : 23.375 179.831 79217 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.85 % Favored : 90.90 % Rotamer: Outliers : 6.07 % Allowed : 15.82 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.10), residues: 5979 helix: -0.66 (0.12), residues: 1904 sheet: -1.40 (0.15), residues: 1119 loop : -1.92 (0.11), residues: 2956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP b 22 HIS 0.012 0.002 HIS f 11 PHE 0.044 0.002 PHE u 36 TYR 0.030 0.002 TYR b 21 ARG 0.009 0.001 ARG L 69 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11958 Ramachandran restraints generated. 5979 Oldfield, 0 Emsley, 5979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11958 Ramachandran restraints generated. 5979 Oldfield, 0 Emsley, 5979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1668 residues out of total 4985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 301 poor density : 1367 time to evaluate : 6.539 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: C 81 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7492 (mt-10) REVERT: C 184 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7849 (mm-30) REVERT: D 13 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.7907 (ptt180) REVERT: D 99 GLU cc_start: 0.6842 (tm-30) cc_final: 0.6640 (tm-30) REVERT: D 165 MET cc_start: 0.8605 (ttt) cc_final: 0.8316 (ttt) REVERT: E 4 VAL cc_start: 0.8493 (OUTLIER) cc_final: 0.8164 (t) REVERT: E 107 SER cc_start: 0.8897 (t) cc_final: 0.8580 (p) REVERT: E 136 GLN cc_start: 0.8394 (tp40) cc_final: 0.8144 (tp40) REVERT: E 139 LYS cc_start: 0.8865 (tttt) cc_final: 0.8240 (ttpp) REVERT: F 133 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7450 (mp0) REVERT: F 144 LYS cc_start: 0.7790 (mptt) cc_final: 0.6966 (ttpt) REVERT: F 164 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7549 (mm-30) REVERT: G 114 HIS cc_start: 0.8570 (t70) cc_final: 0.8309 (t70) REVERT: J 57 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8294 (pp) REVERT: J 58 ASN cc_start: 0.8914 (m-40) cc_final: 0.8339 (m-40) REVERT: J 95 ARG cc_start: 0.7934 (tpp-160) cc_final: 0.7446 (mmm160) REVERT: J 131 ASN cc_start: 0.7929 (p0) cc_final: 0.7675 (p0) REVERT: J 136 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.8336 (mt0) REVERT: J 140 LEU cc_start: 0.8641 (tt) cc_final: 0.8273 (mt) REVERT: K 105 ARG cc_start: 0.8097 (ttm-80) cc_final: 0.7785 (mtp-110) REVERT: L 99 ASN cc_start: 0.8761 (t0) cc_final: 0.8556 (t0) REVERT: M 63 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8591 (mm) REVERT: M 106 ASP cc_start: 0.7772 (t70) cc_final: 0.7483 (t70) REVERT: N 24 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.8102 (ttm) REVERT: N 65 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8268 (mp) REVERT: N 73 ASN cc_start: 0.8607 (t0) cc_final: 0.8248 (t0) REVERT: O 46 GLU cc_start: 0.7874 (pm20) cc_final: 0.7674 (pm20) REVERT: P 6 GLN cc_start: 0.8300 (tt0) cc_final: 0.7849 (tp40) REVERT: P 24 THR cc_start: 0.8556 (m) cc_final: 0.8319 (m) REVERT: P 88 ARG cc_start: 0.7949 (mtm-85) cc_final: 0.7692 (mtt-85) REVERT: P 98 TYR cc_start: 0.9209 (p90) cc_final: 0.8998 (p90) REVERT: Q 12 ARG cc_start: 0.7882 (mtp85) cc_final: 0.7624 (mtp85) REVERT: Q 92 LYS cc_start: 0.8050 (tttt) cc_final: 0.7575 (ttpt) REVERT: Q 101 ASP cc_start: 0.6793 (t70) cc_final: 0.6499 (t70) REVERT: R 1 MET cc_start: 0.5221 (tpp) cc_final: 0.4963 (tpt) REVERT: T 6 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7429 (ttm-80) REVERT: T 48 GLN cc_start: 0.7963 (mm110) cc_final: 0.7676 (mt0) REVERT: U 5 ARG cc_start: 0.8603 (ptp-170) cc_final: 0.8310 (ptp-170) REVERT: U 68 ASN cc_start: 0.8330 (m-40) cc_final: 0.7727 (m110) REVERT: V 62 THR cc_start: 0.8750 (m) cc_final: 0.8523 (t) REVERT: W 35 ARG cc_start: 0.8059 (mtp85) cc_final: 0.7559 (mtp180) REVERT: W 71 LYS cc_start: 0.8744 (mttm) cc_final: 0.8519 (mtmt) REVERT: Y 31 GLN cc_start: 0.8550 (tt0) cc_final: 0.8289 (mt0) REVERT: Z 37 ARG cc_start: 0.8751 (mmt-90) cc_final: 0.8451 (mmt-90) REVERT: 0 11 LYS cc_start: 0.8497 (tppt) cc_final: 0.8099 (mmtt) REVERT: 1 36 LYS cc_start: 0.8576 (tttt) cc_final: 0.8321 (ttmt) REVERT: 1 49 LYS cc_start: 0.8564 (mptt) cc_final: 0.8340 (mmtp) REVERT: 3 14 LYS cc_start: 0.8702 (mmtt) cc_final: 0.8339 (mmtt) REVERT: 3 54 LEU cc_start: 0.8769 (tp) cc_final: 0.8536 (tt) REVERT: 4 15 LYS cc_start: 0.8435 (ttmm) cc_final: 0.7952 (mmtp) REVERT: 6 63 ARG cc_start: 0.7373 (mtt-85) cc_final: 0.6931 (mtm-85) REVERT: b 42 LEU cc_start: 0.6127 (OUTLIER) cc_final: 0.5723 (mm) REVERT: c 128 MET cc_start: 0.8105 (mmm) cc_final: 0.7413 (tpp) REVERT: d 32 LYS cc_start: 0.7273 (OUTLIER) cc_final: 0.6791 (tttp) REVERT: d 39 GLN cc_start: 0.7854 (tt0) cc_final: 0.7590 (tt0) REVERT: e 151 MET cc_start: 0.7413 (mmp) cc_final: 0.7042 (mtp) REVERT: f 79 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7430 (ttm-80) REVERT: g 62 GLU cc_start: 0.8609 (tp30) cc_final: 0.8311 (tp30) REVERT: g 77 ARG cc_start: 0.4361 (mmm160) cc_final: 0.4009 (ptt180) REVERT: h 32 LYS cc_start: 0.8438 (mmtp) cc_final: 0.8045 (mmmm) REVERT: h 60 LEU cc_start: 0.9115 (mp) cc_final: 0.8859 (mt) REVERT: h 100 ILE cc_start: 0.9116 (pp) cc_final: 0.8882 (pt) REVERT: h 120 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8187 (pp) REVERT: j 10 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.7831 (pp) REVERT: j 48 ARG cc_start: 0.8066 (mpt-90) cc_final: 0.7647 (mtt-85) REVERT: k 84 MET cc_start: 0.8047 (mmt) cc_final: 0.7790 (mmt) REVERT: k 99 LEU cc_start: 0.7053 (OUTLIER) cc_final: 0.6716 (mp) REVERT: m 32 ILE cc_start: 0.9070 (mt) cc_final: 0.8850 (mt) REVERT: m 70 ARG cc_start: 0.7801 (mtp85) cc_final: 0.7594 (mtm110) REVERT: o 36 ASN cc_start: 0.8143 (m-40) cc_final: 0.7912 (m110) REVERT: o 39 GLN cc_start: 0.8533 (mm-40) cc_final: 0.8275 (mt0) REVERT: q 26 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7499 (ptt90) REVERT: s 10 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7767 (pp) REVERT: z 40 GLU cc_start: 0.5364 (OUTLIER) cc_final: 0.4297 (pt0) REVERT: z 64 GLU cc_start: 0.6505 (mt-10) cc_final: 0.6231 (mt-10) REVERT: z 131 ASP cc_start: 0.6551 (t70) cc_final: 0.6335 (t0) REVERT: z 270 ILE cc_start: 0.6890 (OUTLIER) cc_final: 0.6369 (pp) REVERT: z 299 GLU cc_start: 0.6811 (mt-10) cc_final: 0.6483 (mt-10) outliers start: 301 outliers final: 228 residues processed: 1514 average time/residue: 1.3596 time to fit residues: 3483.8983 Evaluate side-chains 1591 residues out of total 4985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 1343 time to evaluate : 6.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 50 ASP Chi-restraints excluded: chain F residue 63 LYS Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain F residue 174 PHE Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 157 LYS Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 136 GLN Chi-restraints excluded: chain K residue 20 MET Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 24 MET Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 45 SER Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain P residue 10 GLU Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 111 GLU Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain T residue 6 ARG Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 60 LYS Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain V residue 46 LYS Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 70 ILE Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain X residue 1 SER Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain Y residue 8 GLU Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 23 LEU Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 21 LEU Chi-restraints excluded: chain 0 residue 33 SER Chi-restraints excluded: chain 1 residue 45 HIS Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 3 residue 37 THR Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain b residue 17 HIS Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain b residue 23 ASN Chi-restraints excluded: chain b residue 40 ILE Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 58 LYS Chi-restraints excluded: chain b residue 89 PHE Chi-restraints excluded: chain b residue 99 MET Chi-restraints excluded: chain b residue 138 ARG Chi-restraints excluded: chain b residue 163 ILE Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 178 LEU Chi-restraints excluded: chain b residue 185 ILE Chi-restraints excluded: chain b residue 196 ASP Chi-restraints excluded: chain c residue 43 THR Chi-restraints excluded: chain c residue 54 ILE Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 88 LYS Chi-restraints excluded: chain c residue 96 VAL Chi-restraints excluded: chain c residue 146 LYS Chi-restraints excluded: chain c residue 152 VAL Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 164 THR Chi-restraints excluded: chain c residue 165 GLU Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain c residue 206 ILE Chi-restraints excluded: chain d residue 32 LYS Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 128 VAL Chi-restraints excluded: chain d residue 147 LYS Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain d residue 197 HIS Chi-restraints excluded: chain e residue 10 LEU Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 87 VAL Chi-restraints excluded: chain e residue 95 MET Chi-restraints excluded: chain e residue 113 VAL Chi-restraints excluded: chain e residue 119 VAL Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain e residue 152 VAL Chi-restraints excluded: chain e residue 156 ARG Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 52 ASN Chi-restraints excluded: chain f residue 63 ASN Chi-restraints excluded: chain f residue 79 ARG Chi-restraints excluded: chain f residue 88 MET Chi-restraints excluded: chain g residue 20 GLU Chi-restraints excluded: chain g residue 28 ILE Chi-restraints excluded: chain g residue 36 SER Chi-restraints excluded: chain g residue 37 THR Chi-restraints excluded: chain g residue 93 VAL Chi-restraints excluded: chain g residue 138 GLU Chi-restraints excluded: chain h residue 9 MET Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 46 GLU Chi-restraints excluded: chain h residue 57 GLU Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 104 SER Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain i residue 17 ARG Chi-restraints excluded: chain i residue 66 VAL Chi-restraints excluded: chain i residue 110 VAL Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 59 LYS Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain k residue 15 VAL Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 71 ASP Chi-restraints excluded: chain k residue 80 ASN Chi-restraints excluded: chain k residue 99 LEU Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 101 THR Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain o residue 25 GLU Chi-restraints excluded: chain o residue 60 SER Chi-restraints excluded: chain o residue 61 GLN Chi-restraints excluded: chain o residue 86 LEU Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 52 LEU Chi-restraints excluded: chain p residue 61 VAL Chi-restraints excluded: chain q residue 12 VAL Chi-restraints excluded: chain q residue 26 ARG Chi-restraints excluded: chain q residue 28 VAL Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain s residue 18 VAL Chi-restraints excluded: chain s residue 48 ILE Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain t residue 26 MET Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain t residue 85 LEU Chi-restraints excluded: chain u residue 13 VAL Chi-restraints excluded: chain w residue 33 LYS Chi-restraints excluded: chain z residue 16 GLU Chi-restraints excluded: chain z residue 40 GLU Chi-restraints excluded: chain z residue 110 LEU Chi-restraints excluded: chain z residue 113 LEU Chi-restraints excluded: chain z residue 117 ARG Chi-restraints excluded: chain z residue 118 MET Chi-restraints excluded: chain z residue 153 LEU Chi-restraints excluded: chain z residue 173 VAL Chi-restraints excluded: chain z residue 181 ILE Chi-restraints excluded: chain z residue 226 VAL Chi-restraints excluded: chain z residue 270 ILE Chi-restraints excluded: chain z residue 298 LEU Chi-restraints excluded: chain z residue 301 GLN Chi-restraints excluded: chain z residue 340 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1046 random chunks: chunk 340 optimal weight: 5.9990 chunk 910 optimal weight: 5.9990 chunk 199 optimal weight: 10.0000 chunk 593 optimal weight: 10.0000 chunk 249 optimal weight: 10.0000 chunk 1012 optimal weight: 40.0000 chunk 840 optimal weight: 10.0000 chunk 468 optimal weight: 3.9990 chunk 84 optimal weight: 20.0000 chunk 334 optimal weight: 9.9990 chunk 531 optimal weight: 0.9980 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 32 ASN E 115 GLN E 195 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 GLN ** N 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 6 GLN Q 43 GLN Q 71 ASN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 60 HIS V 78 GLN 4 37 GLN b 23 ASN c 7 ASN c 18 ASN c 138 GLN ** d 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 36 GLN ** i 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 159748 Z= 0.246 Angle : 0.605 15.199 238670 Z= 0.314 Chirality : 0.037 0.324 30435 Planarity : 0.005 0.108 13013 Dihedral : 23.375 179.418 79217 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.63 % Favored : 91.15 % Rotamer: Outliers : 5.85 % Allowed : 16.72 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.10), residues: 5979 helix: -0.47 (0.12), residues: 1896 sheet: -1.36 (0.15), residues: 1118 loop : -1.84 (0.11), residues: 2965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP d 169 HIS 0.010 0.001 HIS f 11 PHE 0.042 0.002 PHE u 36 TYR 0.020 0.002 TYR z 326 ARG 0.015 0.001 ARG u 17 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11958 Ramachandran restraints generated. 5979 Oldfield, 0 Emsley, 5979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11958 Ramachandran restraints generated. 5979 Oldfield, 0 Emsley, 5979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1633 residues out of total 4985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 290 poor density : 1343 time to evaluate : 6.658 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: C 81 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7476 (mt-10) REVERT: C 184 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7863 (mm-30) REVERT: D 13 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.7867 (ptt180) REVERT: D 46 ARG cc_start: 0.8636 (ptm-80) cc_final: 0.8128 (ptm-80) REVERT: D 165 MET cc_start: 0.8623 (ttt) cc_final: 0.8343 (ttt) REVERT: E 4 VAL cc_start: 0.8548 (OUTLIER) cc_final: 0.8233 (t) REVERT: E 107 SER cc_start: 0.8870 (t) cc_final: 0.8574 (p) REVERT: E 136 GLN cc_start: 0.8371 (tp40) cc_final: 0.8123 (tp40) REVERT: E 139 LYS cc_start: 0.8864 (tttt) cc_final: 0.8239 (ttpp) REVERT: F 80 GLN cc_start: 0.8366 (tp40) cc_final: 0.8038 (tp40) REVERT: F 133 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7437 (mp0) REVERT: F 144 LYS cc_start: 0.7779 (mptt) cc_final: 0.7350 (mmtt) REVERT: G 114 HIS cc_start: 0.8516 (t70) cc_final: 0.8217 (t70) REVERT: J 57 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8256 (pp) REVERT: J 95 ARG cc_start: 0.7923 (tpp-160) cc_final: 0.7438 (mmm160) REVERT: J 102 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7829 (mt-10) REVERT: J 136 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8012 (mt0) REVERT: J 140 LEU cc_start: 0.8628 (tt) cc_final: 0.8244 (mt) REVERT: L 99 ASN cc_start: 0.8747 (t0) cc_final: 0.8525 (t0) REVERT: M 63 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8564 (mm) REVERT: M 106 ASP cc_start: 0.7710 (t70) cc_final: 0.7437 (t70) REVERT: N 12 ARG cc_start: 0.8720 (mtt90) cc_final: 0.8514 (mtt-85) REVERT: N 24 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.8029 (ttm) REVERT: N 65 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8220 (mp) REVERT: N 73 ASN cc_start: 0.8600 (t0) cc_final: 0.8268 (t0) REVERT: P 88 ARG cc_start: 0.8006 (mtm-85) cc_final: 0.7704 (mtt-85) REVERT: Q 12 ARG cc_start: 0.7842 (mtp85) cc_final: 0.7590 (mtp85) REVERT: Q 92 LYS cc_start: 0.8002 (tttt) cc_final: 0.7666 (ttpt) REVERT: Q 101 ASP cc_start: 0.6938 (t70) cc_final: 0.6665 (t70) REVERT: R 1 MET cc_start: 0.5287 (tpp) cc_final: 0.5061 (tpt) REVERT: T 6 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7412 (ttm-80) REVERT: T 48 GLN cc_start: 0.7950 (mm110) cc_final: 0.7703 (mt0) REVERT: U 5 ARG cc_start: 0.8599 (ptp-170) cc_final: 0.8349 (ptp-170) REVERT: U 68 ASN cc_start: 0.8206 (m-40) cc_final: 0.7583 (m110) REVERT: V 62 THR cc_start: 0.8745 (m) cc_final: 0.8522 (t) REVERT: W 35 ARG cc_start: 0.8060 (mtp85) cc_final: 0.7575 (mtp180) REVERT: W 71 LYS cc_start: 0.8793 (mttm) cc_final: 0.8475 (mtmt) REVERT: Y 31 GLN cc_start: 0.8554 (tt0) cc_final: 0.8298 (mt0) REVERT: 0 11 LYS cc_start: 0.8479 (tppt) cc_final: 0.8108 (mmtt) REVERT: 1 36 LYS cc_start: 0.8531 (tttt) cc_final: 0.8282 (ttmt) REVERT: 1 49 LYS cc_start: 0.8564 (mptt) cc_final: 0.8337 (mmtp) REVERT: 3 14 LYS cc_start: 0.8675 (mmtt) cc_final: 0.8329 (mmtt) REVERT: 4 15 LYS cc_start: 0.8426 (ttmm) cc_final: 0.7961 (mmtp) REVERT: 6 63 ARG cc_start: 0.7348 (mtt-85) cc_final: 0.6903 (mtm-85) REVERT: b 56 LEU cc_start: 0.7546 (mm) cc_final: 0.7327 (mm) REVERT: c 44 LYS cc_start: 0.8536 (tttp) cc_final: 0.8049 (mptt) REVERT: c 128 MET cc_start: 0.8075 (mmm) cc_final: 0.7408 (tpp) REVERT: c 146 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8250 (tttt) REVERT: d 32 LYS cc_start: 0.7242 (OUTLIER) cc_final: 0.6778 (tttp) REVERT: d 39 GLN cc_start: 0.7804 (tt0) cc_final: 0.7538 (tt0) REVERT: d 104 MET cc_start: 0.8335 (mtt) cc_final: 0.8117 (mtt) REVERT: d 143 SER cc_start: 0.9109 (p) cc_final: 0.8803 (p) REVERT: e 151 MET cc_start: 0.7409 (mmp) cc_final: 0.7042 (mtp) REVERT: f 79 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7415 (ttm-80) REVERT: h 32 LYS cc_start: 0.8429 (mmtp) cc_final: 0.8013 (mmmm) REVERT: h 40 LYS cc_start: 0.8703 (tptp) cc_final: 0.8322 (tppt) REVERT: h 60 LEU cc_start: 0.9120 (mp) cc_final: 0.8875 (mt) REVERT: h 100 ILE cc_start: 0.9162 (pp) cc_final: 0.8926 (pt) REVERT: h 120 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8197 (pp) REVERT: i 56 MET cc_start: 0.7422 (ppp) cc_final: 0.6983 (ppp) REVERT: i 114 LYS cc_start: 0.9072 (mptt) cc_final: 0.8773 (mptt) REVERT: j 10 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.7814 (pp) REVERT: j 48 ARG cc_start: 0.8047 (mpt-90) cc_final: 0.7611 (mtt-85) REVERT: k 84 MET cc_start: 0.8025 (mmt) cc_final: 0.7793 (mmt) REVERT: k 99 LEU cc_start: 0.7018 (OUTLIER) cc_final: 0.6698 (mp) REVERT: k 105 ARG cc_start: 0.7252 (mtp-110) cc_final: 0.6646 (mtp85) REVERT: m 32 ILE cc_start: 0.9063 (mt) cc_final: 0.8813 (mt) REVERT: n 25 GLU cc_start: 0.7518 (pm20) cc_final: 0.7276 (pm20) REVERT: o 36 ASN cc_start: 0.8146 (m-40) cc_final: 0.7925 (m110) REVERT: o 39 GLN cc_start: 0.8474 (mt0) cc_final: 0.8210 (mt0) REVERT: q 26 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7554 (ptt90) REVERT: s 10 ILE cc_start: 0.8045 (OUTLIER) cc_final: 0.7768 (pp) REVERT: z 40 GLU cc_start: 0.5483 (OUTLIER) cc_final: 0.4371 (pt0) REVERT: z 64 GLU cc_start: 0.6508 (mt-10) cc_final: 0.6221 (mt-10) REVERT: z 131 ASP cc_start: 0.6561 (t70) cc_final: 0.6358 (t0) REVERT: z 270 ILE cc_start: 0.6879 (OUTLIER) cc_final: 0.6364 (pp) REVERT: z 299 GLU cc_start: 0.6773 (mt-10) cc_final: 0.6431 (mt-10) outliers start: 290 outliers final: 236 residues processed: 1485 average time/residue: 1.3510 time to fit residues: 3399.0841 Evaluate side-chains 1580 residues out of total 4985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 1323 time to evaluate : 6.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 50 ASP Chi-restraints excluded: chain F residue 63 LYS Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain F residue 174 PHE Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 157 LYS Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 136 GLN Chi-restraints excluded: chain K residue 20 MET Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 24 MET Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 45 SER Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain P residue 10 GLU Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 111 GLU Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain T residue 6 ARG Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 59 ASN Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 60 LYS Chi-restraints excluded: chain V residue 46 LYS Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 70 ILE Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain X residue 1 SER Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain Y residue 5 GLU Chi-restraints excluded: chain Y residue 8 GLU Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 23 LEU Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 10 SER Chi-restraints excluded: chain 0 residue 21 LEU Chi-restraints excluded: chain 0 residue 33 SER Chi-restraints excluded: chain 1 residue 45 HIS Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 37 THR Chi-restraints excluded: chain 3 residue 51 LYS Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain b residue 17 HIS Chi-restraints excluded: chain b residue 40 ILE Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 58 LYS Chi-restraints excluded: chain b residue 66 ILE Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 89 PHE Chi-restraints excluded: chain b residue 99 MET Chi-restraints excluded: chain b residue 138 ARG Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 177 ASN Chi-restraints excluded: chain b residue 178 LEU Chi-restraints excluded: chain b residue 185 ILE Chi-restraints excluded: chain b residue 196 ASP Chi-restraints excluded: chain c residue 43 THR Chi-restraints excluded: chain c residue 54 ILE Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 88 LYS Chi-restraints excluded: chain c residue 96 VAL Chi-restraints excluded: chain c residue 134 LYS Chi-restraints excluded: chain c residue 146 LYS Chi-restraints excluded: chain c residue 152 VAL Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 164 THR Chi-restraints excluded: chain c residue 165 GLU Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain c residue 206 ILE Chi-restraints excluded: chain d residue 22 SER Chi-restraints excluded: chain d residue 32 LYS Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 128 VAL Chi-restraints excluded: chain d residue 147 LYS Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 170 LEU Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain d residue 197 HIS Chi-restraints excluded: chain e residue 10 LEU Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain e residue 87 VAL Chi-restraints excluded: chain e residue 95 MET Chi-restraints excluded: chain e residue 113 VAL Chi-restraints excluded: chain e residue 119 VAL Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain e residue 152 VAL Chi-restraints excluded: chain e residue 155 LYS Chi-restraints excluded: chain e residue 156 ARG Chi-restraints excluded: chain f residue 52 ASN Chi-restraints excluded: chain f residue 63 ASN Chi-restraints excluded: chain f residue 79 ARG Chi-restraints excluded: chain f residue 88 MET Chi-restraints excluded: chain g residue 20 GLU Chi-restraints excluded: chain g residue 36 SER Chi-restraints excluded: chain g residue 37 THR Chi-restraints excluded: chain g residue 93 VAL Chi-restraints excluded: chain g residue 98 LEU Chi-restraints excluded: chain g residue 138 GLU Chi-restraints excluded: chain g residue 145 GLU Chi-restraints excluded: chain h residue 9 MET Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 46 GLU Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 61 THR Chi-restraints excluded: chain h residue 70 VAL Chi-restraints excluded: chain h residue 89 ASP Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 104 SER Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 113 ARG Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain i residue 17 ARG Chi-restraints excluded: chain i residue 110 VAL Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 59 LYS Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain k residue 15 VAL Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 71 ASP Chi-restraints excluded: chain k residue 80 ASN Chi-restraints excluded: chain k residue 99 LEU Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 101 THR Chi-restraints excluded: chain n residue 11 LYS Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain o residue 25 GLU Chi-restraints excluded: chain o residue 60 SER Chi-restraints excluded: chain o residue 61 GLN Chi-restraints excluded: chain o residue 86 LEU Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 52 LEU Chi-restraints excluded: chain q residue 12 VAL Chi-restraints excluded: chain q residue 26 ARG Chi-restraints excluded: chain q residue 28 VAL Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain s residue 18 VAL Chi-restraints excluded: chain s residue 48 ILE Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain t residue 26 MET Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain t residue 85 LEU Chi-restraints excluded: chain u residue 13 VAL Chi-restraints excluded: chain w residue 33 LYS Chi-restraints excluded: chain z residue 16 GLU Chi-restraints excluded: chain z residue 40 GLU Chi-restraints excluded: chain z residue 110 LEU Chi-restraints excluded: chain z residue 113 LEU Chi-restraints excluded: chain z residue 117 ARG Chi-restraints excluded: chain z residue 118 MET Chi-restraints excluded: chain z residue 153 LEU Chi-restraints excluded: chain z residue 173 VAL Chi-restraints excluded: chain z residue 181 ILE Chi-restraints excluded: chain z residue 226 VAL Chi-restraints excluded: chain z residue 270 ILE Chi-restraints excluded: chain z residue 298 LEU Chi-restraints excluded: chain z residue 301 GLN Chi-restraints excluded: chain z residue 329 ASP Chi-restraints excluded: chain z residue 340 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1046 random chunks: chunk 975 optimal weight: 10.0000 chunk 114 optimal weight: 20.0000 chunk 576 optimal weight: 6.9990 chunk 739 optimal weight: 20.0000 chunk 572 optimal weight: 20.0000 chunk 851 optimal weight: 20.0000 chunk 565 optimal weight: 9.9990 chunk 1008 optimal weight: 20.0000 chunk 630 optimal weight: 20.0000 chunk 614 optimal weight: 30.0000 chunk 465 optimal weight: 9.9990 overall best weight: 11.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 GLN E 195 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 66 ASN H 135 HIS J 136 GLN N 62 ASN N 107 ASN Q 43 GLN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 87 GLN S 60 HIS V 78 GLN 4 37 GLN c 7 ASN c 18 ASN ** d 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 36 GLN ** i 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 15 HIS ** l 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 322 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.076 159748 Z= 0.472 Angle : 0.750 15.443 238670 Z= 0.382 Chirality : 0.045 0.373 30435 Planarity : 0.006 0.084 13013 Dihedral : 23.449 179.071 79217 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.27 % Allowed : 9.58 % Favored : 90.15 % Rotamer: Outliers : 6.27 % Allowed : 17.43 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.10), residues: 5979 helix: -0.70 (0.11), residues: 1899 sheet: -1.49 (0.15), residues: 1128 loop : -1.89 (0.11), residues: 2952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 212 HIS 0.012 0.002 HIS f 11 PHE 0.054 0.003 PHE u 36 TYR 0.028 0.002 TYR b 21 ARG 0.012 0.001 ARG z 154 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11958 Ramachandran restraints generated. 5979 Oldfield, 0 Emsley, 5979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11958 Ramachandran restraints generated. 5979 Oldfield, 0 Emsley, 5979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1662 residues out of total 4985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 311 poor density : 1351 time to evaluate : 6.633 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: C 81 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7506 (mt-10) REVERT: C 184 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7995 (mm-30) REVERT: D 13 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8577 (ptt180) REVERT: D 90 PHE cc_start: 0.8592 (m-80) cc_final: 0.8391 (m-80) REVERT: D 165 MET cc_start: 0.8715 (ttt) cc_final: 0.8426 (ttt) REVERT: E 136 GLN cc_start: 0.8405 (tp40) cc_final: 0.8129 (tp40) REVERT: E 139 LYS cc_start: 0.8861 (tttt) cc_final: 0.8219 (ttpp) REVERT: F 56 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8357 (tt) REVERT: F 80 GLN cc_start: 0.8337 (tp40) cc_final: 0.8039 (tp40) REVERT: F 133 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7402 (mp0) REVERT: F 144 LYS cc_start: 0.7772 (mptt) cc_final: 0.7300 (mmtt) REVERT: G 114 HIS cc_start: 0.8611 (t70) cc_final: 0.8335 (t70) REVERT: J 57 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8348 (pp) REVERT: J 102 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7990 (mt-10) REVERT: J 140 LEU cc_start: 0.8670 (tt) cc_final: 0.8312 (mt) REVERT: K 105 ARG cc_start: 0.8205 (ttm-80) cc_final: 0.7876 (mtp-110) REVERT: M 63 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8584 (mm) REVERT: M 106 ASP cc_start: 0.7720 (t70) cc_final: 0.7422 (t70) REVERT: M 119 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8929 (mp) REVERT: N 24 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.8140 (ttm) REVERT: N 65 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8348 (mp) REVERT: N 73 ASN cc_start: 0.8625 (t0) cc_final: 0.8206 (t0) REVERT: P 88 ARG cc_start: 0.8032 (mtm-85) cc_final: 0.7705 (mtt-85) REVERT: Q 12 ARG cc_start: 0.7918 (mtp85) cc_final: 0.7680 (mtp85) REVERT: Q 92 LYS cc_start: 0.8059 (tttt) cc_final: 0.7821 (ttpt) REVERT: Q 101 ASP cc_start: 0.7165 (t70) cc_final: 0.6875 (t70) REVERT: R 1 MET cc_start: 0.5395 (tpp) cc_final: 0.5169 (tpt) REVERT: T 6 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7430 (ttm-80) REVERT: T 48 GLN cc_start: 0.8002 (mm110) cc_final: 0.7679 (mt0) REVERT: U 68 ASN cc_start: 0.8539 (m-40) cc_final: 0.8041 (m-40) REVERT: U 85 ARG cc_start: 0.7871 (ptp90) cc_final: 0.7305 (ptp90) REVERT: V 62 THR cc_start: 0.8772 (m) cc_final: 0.8554 (t) REVERT: V 90 ASP cc_start: 0.8299 (m-30) cc_final: 0.8027 (m-30) REVERT: W 35 ARG cc_start: 0.8109 (mtp85) cc_final: 0.7563 (mtp180) REVERT: Y 31 GLN cc_start: 0.8638 (tt0) cc_final: 0.8352 (mt0) REVERT: Z 48 ASN cc_start: 0.8443 (t0) cc_final: 0.8198 (t0) REVERT: 0 11 LYS cc_start: 0.8517 (tppt) cc_final: 0.8127 (mmtt) REVERT: 1 32 LYS cc_start: 0.8414 (mmtt) cc_final: 0.8204 (mmtt) REVERT: 1 36 LYS cc_start: 0.8586 (tttt) cc_final: 0.8337 (ttmt) REVERT: 3 14 LYS cc_start: 0.8676 (mmtt) cc_final: 0.8257 (mmtt) REVERT: 3 54 LEU cc_start: 0.8709 (tp) cc_final: 0.8457 (tt) REVERT: 6 63 ARG cc_start: 0.7432 (mtt-85) cc_final: 0.6957 (mtm-85) REVERT: c 44 LYS cc_start: 0.8600 (tttp) cc_final: 0.8088 (mptt) REVERT: c 64 ARG cc_start: 0.8672 (ttp-110) cc_final: 0.8463 (ttp-110) REVERT: c 128 MET cc_start: 0.8154 (mmm) cc_final: 0.7528 (tpp) REVERT: d 32 LYS cc_start: 0.7344 (OUTLIER) cc_final: 0.6693 (tttp) REVERT: d 104 MET cc_start: 0.8330 (mtt) cc_final: 0.8105 (mtt) REVERT: d 143 SER cc_start: 0.9046 (p) cc_final: 0.8745 (p) REVERT: e 151 MET cc_start: 0.7572 (mmp) cc_final: 0.7177 (mmm) REVERT: f 79 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.7402 (ttm-80) REVERT: g 3 ARG cc_start: 0.8064 (ptm160) cc_final: 0.7777 (ptp90) REVERT: g 82 SER cc_start: 0.7352 (p) cc_final: 0.7115 (p) REVERT: h 40 LYS cc_start: 0.8749 (tptp) cc_final: 0.8396 (tppt) REVERT: h 100 ILE cc_start: 0.9251 (pp) cc_final: 0.9020 (pt) REVERT: h 120 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8328 (pp) REVERT: i 56 MET cc_start: 0.7461 (ppp) cc_final: 0.7041 (ppp) REVERT: j 10 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8015 (pp) REVERT: j 48 ARG cc_start: 0.8148 (mpt-90) cc_final: 0.7693 (mtt-85) REVERT: k 76 TYR cc_start: 0.8473 (m-80) cc_final: 0.8272 (m-80) REVERT: k 99 LEU cc_start: 0.7135 (OUTLIER) cc_final: 0.6759 (mp) REVERT: m 32 ILE cc_start: 0.9028 (mt) cc_final: 0.8780 (mt) REVERT: n 19 TYR cc_start: 0.7922 (m-80) cc_final: 0.7294 (m-80) REVERT: o 39 GLN cc_start: 0.8521 (mt0) cc_final: 0.8305 (mt0) REVERT: p 63 GLN cc_start: 0.8621 (mm-40) cc_final: 0.8103 (mm-40) REVERT: q 26 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7513 (ptt90) REVERT: s 10 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7789 (pp) REVERT: u 38 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7303 (tp30) REVERT: z 64 GLU cc_start: 0.6477 (mt-10) cc_final: 0.6155 (mt-10) REVERT: z 164 GLU cc_start: 0.7585 (tm-30) cc_final: 0.7316 (tm-30) REVERT: z 299 GLU cc_start: 0.6784 (mt-10) cc_final: 0.6421 (mt-10) outliers start: 311 outliers final: 244 residues processed: 1506 average time/residue: 1.4890 time to fit residues: 3840.3803 Evaluate side-chains 1582 residues out of total 4985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 263 poor density : 1319 time to evaluate : 6.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 50 ASP Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 63 LYS Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 131 VAL Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 174 PHE Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 92 MET Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain K residue 20 MET Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 24 MET Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 45 SER Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain P residue 10 GLU Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 111 GLU Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain T residue 6 ARG Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 59 ASN Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 60 LYS Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 70 ILE Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain X residue 1 SER Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain Y residue 5 GLU Chi-restraints excluded: chain Y residue 8 GLU Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 23 LEU Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 21 LEU Chi-restraints excluded: chain 0 residue 27 LEU Chi-restraints excluded: chain 0 residue 33 SER Chi-restraints excluded: chain 1 residue 45 HIS Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 3 residue 37 THR Chi-restraints excluded: chain 3 residue 51 LYS Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain b residue 17 HIS Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain b residue 40 ILE Chi-restraints excluded: chain b residue 58 LYS Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 99 MET Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 178 LEU Chi-restraints excluded: chain b residue 185 ILE Chi-restraints excluded: chain b residue 196 ASP Chi-restraints excluded: chain c residue 43 THR Chi-restraints excluded: chain c residue 54 ILE Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 88 LYS Chi-restraints excluded: chain c residue 96 VAL Chi-restraints excluded: chain c residue 118 SER Chi-restraints excluded: chain c residue 146 LYS Chi-restraints excluded: chain c residue 152 VAL Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 164 THR Chi-restraints excluded: chain c residue 165 GLU Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain c residue 206 ILE Chi-restraints excluded: chain d residue 22 SER Chi-restraints excluded: chain d residue 32 LYS Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 128 VAL Chi-restraints excluded: chain d residue 147 LYS Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 170 LEU Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain d residue 197 HIS Chi-restraints excluded: chain e residue 10 LEU Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 87 VAL Chi-restraints excluded: chain e residue 89 THR Chi-restraints excluded: chain e residue 95 MET Chi-restraints excluded: chain e residue 113 VAL Chi-restraints excluded: chain e residue 119 VAL Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain e residue 152 VAL Chi-restraints excluded: chain e residue 156 ARG Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 15 SER Chi-restraints excluded: chain f residue 52 ASN Chi-restraints excluded: chain f residue 63 ASN Chi-restraints excluded: chain f residue 79 ARG Chi-restraints excluded: chain f residue 88 MET Chi-restraints excluded: chain g residue 20 GLU Chi-restraints excluded: chain g residue 28 ILE Chi-restraints excluded: chain g residue 36 SER Chi-restraints excluded: chain g residue 37 THR Chi-restraints excluded: chain g residue 59 GLU Chi-restraints excluded: chain g residue 93 VAL Chi-restraints excluded: chain g residue 98 LEU Chi-restraints excluded: chain h residue 9 MET Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 45 ILE Chi-restraints excluded: chain h residue 46 GLU Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 70 VAL Chi-restraints excluded: chain h residue 89 ASP Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 104 SER Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain i residue 17 ARG Chi-restraints excluded: chain i residue 66 VAL Chi-restraints excluded: chain i residue 110 VAL Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 59 LYS Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain k residue 15 VAL Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 71 ASP Chi-restraints excluded: chain k residue 80 ASN Chi-restraints excluded: chain k residue 99 LEU Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 93 ARG Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 101 THR Chi-restraints excluded: chain n residue 45 VAL Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain o residue 25 GLU Chi-restraints excluded: chain o residue 60 SER Chi-restraints excluded: chain o residue 61 GLN Chi-restraints excluded: chain o residue 86 LEU Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 52 LEU Chi-restraints excluded: chain q residue 12 VAL Chi-restraints excluded: chain q residue 26 ARG Chi-restraints excluded: chain q residue 28 VAL Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain s residue 18 VAL Chi-restraints excluded: chain s residue 48 ILE Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain t residue 26 MET Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain t residue 34 VAL Chi-restraints excluded: chain t residue 85 LEU Chi-restraints excluded: chain u residue 13 VAL Chi-restraints excluded: chain u residue 38 GLU Chi-restraints excluded: chain w residue 16 ILE Chi-restraints excluded: chain w residue 33 LYS Chi-restraints excluded: chain z residue 16 GLU Chi-restraints excluded: chain z residue 86 LEU Chi-restraints excluded: chain z residue 110 LEU Chi-restraints excluded: chain z residue 117 ARG Chi-restraints excluded: chain z residue 118 MET Chi-restraints excluded: chain z residue 173 VAL Chi-restraints excluded: chain z residue 181 ILE Chi-restraints excluded: chain z residue 226 VAL Chi-restraints excluded: chain z residue 270 ILE Chi-restraints excluded: chain z residue 298 LEU Chi-restraints excluded: chain z residue 301 GLN Chi-restraints excluded: chain z residue 329 ASP Chi-restraints excluded: chain z residue 340 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1046 random chunks: chunk 623 optimal weight: 10.0000 chunk 402 optimal weight: 7.9990 chunk 602 optimal weight: 6.9990 chunk 303 optimal weight: 1.9990 chunk 198 optimal weight: 10.0000 chunk 195 optimal weight: 10.0000 chunk 640 optimal weight: 20.0000 chunk 686 optimal weight: 10.0000 chunk 498 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 792 optimal weight: 0.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 GLN E 195 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 GLN ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 GLN R 6 GLN R 18 GLN S 60 HIS V 78 GLN 4 37 GLN c 18 ASN c 138 GLN ** d 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 36 ASN ** t 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 159748 Z= 0.225 Angle : 0.593 14.955 238670 Z= 0.307 Chirality : 0.037 0.310 30435 Planarity : 0.004 0.054 13013 Dihedral : 23.357 179.871 79217 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.04 % Favored : 91.77 % Rotamer: Outliers : 5.29 % Allowed : 19.00 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.11), residues: 5979 helix: -0.32 (0.12), residues: 1894 sheet: -1.30 (0.15), residues: 1131 loop : -1.79 (0.11), residues: 2954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP d 169 HIS 0.010 0.001 HIS f 11 PHE 0.049 0.002 PHE u 36 TYR 0.022 0.002 TYR b 21 ARG 0.010 0.001 ARG u 33 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11958 Ramachandran restraints generated. 5979 Oldfield, 0 Emsley, 5979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11958 Ramachandran restraints generated. 5979 Oldfield, 0 Emsley, 5979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1608 residues out of total 4985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 1346 time to evaluate : 6.654 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: C 81 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7496 (mt-10) REVERT: C 184 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7974 (mm-30) REVERT: C 235 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7833 (mm-30) REVERT: D 13 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.7856 (ptt180) REVERT: D 165 MET cc_start: 0.8615 (ttt) cc_final: 0.8374 (ttt) REVERT: E 4 VAL cc_start: 0.8523 (OUTLIER) cc_final: 0.8221 (t) REVERT: E 30 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8047 (tt0) REVERT: E 136 GLN cc_start: 0.8357 (tp40) cc_final: 0.8127 (tp40) REVERT: E 139 LYS cc_start: 0.8868 (tttt) cc_final: 0.8248 (ttpp) REVERT: F 80 GLN cc_start: 0.8344 (tp40) cc_final: 0.8002 (tp40) REVERT: F 133 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7357 (mp0) REVERT: F 144 LYS cc_start: 0.7554 (mptt) cc_final: 0.7220 (mmtt) REVERT: G 114 HIS cc_start: 0.8396 (t70) cc_final: 0.8141 (t70) REVERT: J 57 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8280 (pp) REVERT: J 58 ASN cc_start: 0.8977 (m-40) cc_final: 0.8590 (m-40) REVERT: J 102 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7847 (mt-10) REVERT: J 140 LEU cc_start: 0.8636 (tt) cc_final: 0.8277 (mt) REVERT: K 105 ARG cc_start: 0.8040 (ttm-80) cc_final: 0.7767 (mtp-110) REVERT: L 100 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8448 (mp) REVERT: M 106 ASP cc_start: 0.7626 (t70) cc_final: 0.7379 (t70) REVERT: N 24 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.8004 (ttm) REVERT: N 73 ASN cc_start: 0.8603 (t0) cc_final: 0.8259 (t0) REVERT: P 88 ARG cc_start: 0.7979 (mtm-85) cc_final: 0.7721 (mtt-85) REVERT: Q 12 ARG cc_start: 0.7779 (mtp85) cc_final: 0.7541 (mtp85) REVERT: Q 92 LYS cc_start: 0.8034 (tttt) cc_final: 0.7600 (ttpt) REVERT: Q 101 ASP cc_start: 0.7100 (t70) cc_final: 0.6681 (t70) REVERT: T 6 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7620 (ttm-80) REVERT: U 68 ASN cc_start: 0.8288 (m-40) cc_final: 0.7727 (m-40) REVERT: U 85 ARG cc_start: 0.7908 (ptp90) cc_final: 0.7337 (ptp90) REVERT: V 62 THR cc_start: 0.8696 (m) cc_final: 0.8471 (t) REVERT: V 93 ARG cc_start: 0.7890 (ttp-170) cc_final: 0.7642 (mtt180) REVERT: W 35 ARG cc_start: 0.8085 (mtp85) cc_final: 0.7568 (mtp180) REVERT: Y 31 GLN cc_start: 0.8585 (tt0) cc_final: 0.8325 (mt0) REVERT: 0 11 LYS cc_start: 0.8482 (tppt) cc_final: 0.8107 (mmtt) REVERT: 1 36 LYS cc_start: 0.8550 (tttt) cc_final: 0.8266 (ttmt) REVERT: 3 14 LYS cc_start: 0.8727 (mmtt) cc_final: 0.8360 (mmtt) REVERT: 3 54 LEU cc_start: 0.8733 (tp) cc_final: 0.8471 (tt) REVERT: b 42 LEU cc_start: 0.6041 (OUTLIER) cc_final: 0.5536 (mm) REVERT: b 191 ASP cc_start: 0.7273 (t0) cc_final: 0.6748 (t0) REVERT: c 44 LYS cc_start: 0.8537 (tttp) cc_final: 0.8156 (mmtm) REVERT: c 128 MET cc_start: 0.8099 (mmm) cc_final: 0.7437 (tpp) REVERT: c 130 ARG cc_start: 0.7804 (mtp85) cc_final: 0.7478 (mtp85) REVERT: c 146 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8196 (tttt) REVERT: d 32 LYS cc_start: 0.7254 (OUTLIER) cc_final: 0.6775 (tttm) REVERT: d 39 GLN cc_start: 0.7706 (tt0) cc_final: 0.7457 (tt0) REVERT: d 143 SER cc_start: 0.9013 (p) cc_final: 0.8726 (p) REVERT: e 151 MET cc_start: 0.7500 (mmp) cc_final: 0.7031 (mtp) REVERT: g 3 ARG cc_start: 0.8162 (ptm160) cc_final: 0.7825 (ptp90) REVERT: h 29 SER cc_start: 0.8636 (OUTLIER) cc_final: 0.8353 (m) REVERT: h 100 ILE cc_start: 0.9224 (pp) cc_final: 0.8945 (pt) REVERT: h 120 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8421 (pp) REVERT: i 45 MET cc_start: 0.8040 (pmm) cc_final: 0.7746 (ppp) REVERT: i 114 LYS cc_start: 0.9059 (mptt) cc_final: 0.8753 (mptt) REVERT: j 10 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8119 (pp) REVERT: j 48 ARG cc_start: 0.8087 (mpt-90) cc_final: 0.7659 (mtt-85) REVERT: k 99 LEU cc_start: 0.6998 (OUTLIER) cc_final: 0.6656 (mp) REVERT: k 105 ARG cc_start: 0.7242 (mtp-110) cc_final: 0.6774 (ttm170) REVERT: m 32 ILE cc_start: 0.8990 (mt) cc_final: 0.8742 (mt) REVERT: n 19 TYR cc_start: 0.7721 (m-80) cc_final: 0.7009 (m-80) REVERT: n 25 GLU cc_start: 0.7561 (pm20) cc_final: 0.7290 (pm20) REVERT: q 17 GLU cc_start: 0.7674 (tp30) cc_final: 0.7433 (tp30) REVERT: q 39 ARG cc_start: 0.8260 (mmp-170) cc_final: 0.7989 (mmp-170) REVERT: r 34 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7375 (mm-30) REVERT: s 10 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7821 (pp) REVERT: u 38 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6300 (tp30) REVERT: z 33 ARG cc_start: 0.6364 (tpt90) cc_final: 0.5544 (mmm160) REVERT: z 64 GLU cc_start: 0.6516 (mt-10) cc_final: 0.6190 (mt-10) REVERT: z 270 ILE cc_start: 0.7074 (OUTLIER) cc_final: 0.6389 (pp) REVERT: z 299 GLU cc_start: 0.6723 (mt-10) cc_final: 0.6382 (mt-10) outliers start: 262 outliers final: 203 residues processed: 1471 average time/residue: 1.4314 time to fit residues: 3588.1289 Evaluate side-chains 1528 residues out of total 4985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 1306 time to evaluate : 5.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain E residue 30 GLN Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 50 ASP Chi-restraints excluded: chain F residue 63 LYS Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain F residue 174 PHE Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain K residue 20 MET Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 24 MET Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain P residue 10 GLU Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain P residue 111 GLU Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain T residue 6 ARG Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 60 LYS Chi-restraints excluded: chain V residue 46 LYS Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 70 ILE Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain X residue 1 SER Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 67 LEU Chi-restraints excluded: chain Y residue 5 GLU Chi-restraints excluded: chain Y residue 8 GLU Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain Y residue 43 LEU Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 23 LEU Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 33 SER Chi-restraints excluded: chain 1 residue 45 HIS Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 37 THR Chi-restraints excluded: chain 3 residue 51 LYS Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 6 residue 22 MET Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain b residue 17 HIS Chi-restraints excluded: chain b residue 40 ILE Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 89 PHE Chi-restraints excluded: chain b residue 99 MET Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 177 ASN Chi-restraints excluded: chain b residue 178 LEU Chi-restraints excluded: chain b residue 185 ILE Chi-restraints excluded: chain c residue 43 THR Chi-restraints excluded: chain c residue 50 SER Chi-restraints excluded: chain c residue 54 ILE Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 88 LYS Chi-restraints excluded: chain c residue 96 VAL Chi-restraints excluded: chain c residue 134 LYS Chi-restraints excluded: chain c residue 146 LYS Chi-restraints excluded: chain c residue 152 VAL Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 164 THR Chi-restraints excluded: chain c residue 165 GLU Chi-restraints excluded: chain d residue 22 SER Chi-restraints excluded: chain d residue 32 LYS Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 147 LYS Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 170 LEU Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain d residue 197 HIS Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 87 VAL Chi-restraints excluded: chain e residue 95 MET Chi-restraints excluded: chain e residue 113 VAL Chi-restraints excluded: chain e residue 119 VAL Chi-restraints excluded: chain e residue 129 SER Chi-restraints excluded: chain e residue 152 VAL Chi-restraints excluded: chain e residue 155 LYS Chi-restraints excluded: chain e residue 156 ARG Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 52 ASN Chi-restraints excluded: chain f residue 63 ASN Chi-restraints excluded: chain f residue 88 MET Chi-restraints excluded: chain g residue 20 GLU Chi-restraints excluded: chain g residue 36 SER Chi-restraints excluded: chain g residue 59 GLU Chi-restraints excluded: chain g residue 93 VAL Chi-restraints excluded: chain g residue 138 GLU Chi-restraints excluded: chain h residue 9 MET Chi-restraints excluded: chain h residue 29 SER Chi-restraints excluded: chain h residue 45 ILE Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 70 VAL Chi-restraints excluded: chain h residue 89 ASP Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 104 SER Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain i residue 17 ARG Chi-restraints excluded: chain i residue 110 VAL Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 59 LYS Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 71 ASP Chi-restraints excluded: chain k residue 80 ASN Chi-restraints excluded: chain k residue 99 LEU Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 6 ILE Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 101 THR Chi-restraints excluded: chain n residue 45 VAL Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain o residue 25 GLU Chi-restraints excluded: chain o residue 61 GLN Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 52 LEU Chi-restraints excluded: chain q residue 12 VAL Chi-restraints excluded: chain q residue 28 VAL Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain s residue 18 VAL Chi-restraints excluded: chain s residue 44 ILE Chi-restraints excluded: chain s residue 48 ILE Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain t residue 26 MET Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain t residue 85 LEU Chi-restraints excluded: chain u residue 13 VAL Chi-restraints excluded: chain u residue 38 GLU Chi-restraints excluded: chain z residue 110 LEU Chi-restraints excluded: chain z residue 117 ARG Chi-restraints excluded: chain z residue 118 MET Chi-restraints excluded: chain z residue 173 VAL Chi-restraints excluded: chain z residue 226 VAL Chi-restraints excluded: chain z residue 270 ILE Chi-restraints excluded: chain z residue 278 ARG Chi-restraints excluded: chain z residue 298 LEU Chi-restraints excluded: chain z residue 301 GLN Chi-restraints excluded: chain z residue 323 ILE Chi-restraints excluded: chain z residue 329 ASP Chi-restraints excluded: chain z residue 340 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1046 random chunks: chunk 917 optimal weight: 8.9990 chunk 965 optimal weight: 0.8980 chunk 881 optimal weight: 8.9990 chunk 939 optimal weight: 9.9990 chunk 565 optimal weight: 0.8980 chunk 409 optimal weight: 0.7980 chunk 737 optimal weight: 10.0000 chunk 288 optimal weight: 20.0000 chunk 848 optimal weight: 8.9990 chunk 888 optimal weight: 20.0000 chunk 936 optimal weight: 5.9990 overall best weight: 3.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 238 ASN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 GLN ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 GLN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 87 GLN S 60 HIS V 78 GLN c 18 ASN d 39 GLN f 3 HIS ** h 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 74 GLN ** i 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 60 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 159748 Z= 0.181 Angle : 0.562 14.519 238670 Z= 0.291 Chirality : 0.034 0.297 30435 Planarity : 0.004 0.051 13013 Dihedral : 23.293 179.679 79215 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.36 % Favored : 91.45 % Rotamer: Outliers : 4.80 % Allowed : 19.75 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.11), residues: 5979 helix: -0.08 (0.12), residues: 1904 sheet: -1.17 (0.15), residues: 1109 loop : -1.70 (0.11), residues: 2966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 61 HIS 0.010 0.001 HIS f 11 PHE 0.043 0.002 PHE u 36 TYR 0.022 0.002 TYR b 21 ARG 0.010 0.000 ARG u 33 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11958 Ramachandran restraints generated. 5979 Oldfield, 0 Emsley, 5979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11958 Ramachandran restraints generated. 5979 Oldfield, 0 Emsley, 5979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1554 residues out of total 4985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 1316 time to evaluate : 6.649 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: C 81 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7438 (mt-10) REVERT: C 113 ASP cc_start: 0.7232 (m-30) cc_final: 0.7007 (m-30) REVERT: C 184 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7977 (mm-30) REVERT: C 235 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7805 (mm-30) REVERT: D 13 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.7812 (ptt180) REVERT: D 165 MET cc_start: 0.8593 (ttt) cc_final: 0.8350 (ttt) REVERT: E 4 VAL cc_start: 0.8514 (OUTLIER) cc_final: 0.8207 (t) REVERT: E 19 PHE cc_start: 0.8468 (OUTLIER) cc_final: 0.8100 (t80) REVERT: E 30 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8080 (tt0) REVERT: E 139 LYS cc_start: 0.8855 (tttt) cc_final: 0.8271 (ttpp) REVERT: F 80 GLN cc_start: 0.8312 (tp40) cc_final: 0.7975 (tp40) REVERT: F 100 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7449 (tm-30) REVERT: F 133 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7424 (mp0) REVERT: F 144 LYS cc_start: 0.7542 (mptt) cc_final: 0.7210 (mmtt) REVERT: G 114 HIS cc_start: 0.8366 (t70) cc_final: 0.8123 (t70) REVERT: J 57 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8231 (pp) REVERT: J 102 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7765 (mt-10) REVERT: K 105 ARG cc_start: 0.7987 (ttm-80) cc_final: 0.7746 (mtp-110) REVERT: L 100 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8428 (mp) REVERT: M 63 ILE cc_start: 0.8677 (mm) cc_final: 0.8365 (mm) REVERT: M 106 ASP cc_start: 0.7582 (t70) cc_final: 0.7321 (t70) REVERT: N 24 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.8068 (ttm) REVERT: N 65 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8137 (mp) REVERT: N 73 ASN cc_start: 0.8588 (t0) cc_final: 0.8282 (t0) REVERT: P 88 ARG cc_start: 0.7968 (mtm-85) cc_final: 0.7731 (mtt-85) REVERT: Q 12 ARG cc_start: 0.7771 (mtp85) cc_final: 0.7539 (mtp85) REVERT: Q 92 LYS cc_start: 0.8065 (tttt) cc_final: 0.7617 (ttpt) REVERT: Q 101 ASP cc_start: 0.7014 (t70) cc_final: 0.6563 (t70) REVERT: T 6 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7738 (ttm-80) REVERT: T 59 ASN cc_start: 0.8432 (m-40) cc_final: 0.8227 (m-40) REVERT: U 68 ASN cc_start: 0.8292 (m-40) cc_final: 0.7719 (m110) REVERT: U 85 ARG cc_start: 0.7895 (ptp90) cc_final: 0.7327 (ptp90) REVERT: V 62 THR cc_start: 0.8703 (m) cc_final: 0.8484 (t) REVERT: V 93 ARG cc_start: 0.7883 (ttp-170) cc_final: 0.7635 (mtt180) REVERT: W 35 ARG cc_start: 0.8085 (mtp85) cc_final: 0.7578 (mtp180) REVERT: X 43 LYS cc_start: 0.8417 (mtmt) cc_final: 0.7681 (tptm) REVERT: Y 31 GLN cc_start: 0.8563 (tt0) cc_final: 0.8318 (mt0) REVERT: Z 24 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8368 (tp) REVERT: 0 11 LYS cc_start: 0.8430 (tppt) cc_final: 0.8089 (mmtt) REVERT: 1 23 THR cc_start: 0.8738 (p) cc_final: 0.8497 (p) REVERT: 1 36 LYS cc_start: 0.8549 (tttt) cc_final: 0.8264 (ttmt) REVERT: 3 14 LYS cc_start: 0.8722 (mmtt) cc_final: 0.8355 (mmtt) REVERT: 4 15 LYS cc_start: 0.8425 (ttmt) cc_final: 0.7911 (mmtp) REVERT: b 138 ARG cc_start: 0.6842 (ptt90) cc_final: 0.6139 (ptt90) REVERT: c 44 LYS cc_start: 0.8496 (tttp) cc_final: 0.8133 (mmtm) REVERT: c 128 MET cc_start: 0.8085 (mmm) cc_final: 0.7504 (tpp) REVERT: c 146 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8197 (tttt) REVERT: d 32 LYS cc_start: 0.7251 (OUTLIER) cc_final: 0.6776 (tttp) REVERT: d 147 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7764 (tptt) REVERT: e 151 MET cc_start: 0.7489 (mmp) cc_final: 0.7028 (mmm) REVERT: g 138 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7470 (pp20) REVERT: h 29 SER cc_start: 0.8640 (p) cc_final: 0.8374 (m) REVERT: h 100 ILE cc_start: 0.9178 (pp) cc_final: 0.8940 (pt) REVERT: h 120 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8406 (pp) REVERT: i 45 MET cc_start: 0.8023 (pmm) cc_final: 0.7702 (ppp) REVERT: i 56 MET cc_start: 0.7405 (ppp) cc_final: 0.7014 (ppp) REVERT: i 114 LYS cc_start: 0.9029 (mptt) cc_final: 0.8758 (mptt) REVERT: j 10 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8102 (pp) REVERT: j 48 ARG cc_start: 0.8060 (mpt-90) cc_final: 0.7683 (mtt-85) REVERT: k 99 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6627 (mp) REVERT: k 105 ARG cc_start: 0.7184 (mtp-110) cc_final: 0.6748 (ttm170) REVERT: l 53 ARG cc_start: 0.7517 (ttm-80) cc_final: 0.7194 (ttt90) REVERT: m 32 ILE cc_start: 0.8918 (mt) cc_final: 0.8671 (mt) REVERT: s 10 ILE cc_start: 0.8038 (OUTLIER) cc_final: 0.7779 (pp) REVERT: t 32 LYS cc_start: 0.8359 (mmtp) cc_final: 0.8080 (mmtt) REVERT: u 38 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6375 (tp30) REVERT: z 33 ARG cc_start: 0.6196 (tpt90) cc_final: 0.5404 (mmm160) REVERT: z 64 GLU cc_start: 0.6600 (mt-10) cc_final: 0.6261 (mt-10) REVERT: z 270 ILE cc_start: 0.6922 (OUTLIER) cc_final: 0.6377 (pp) REVERT: z 299 GLU cc_start: 0.6657 (mt-10) cc_final: 0.6333 (mt-10) outliers start: 238 outliers final: 188 residues processed: 1429 average time/residue: 1.3638 time to fit residues: 3297.2544 Evaluate side-chains 1503 residues out of total 4985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 1292 time to evaluate : 6.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain E residue 30 GLN Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 50 ASP Chi-restraints excluded: chain F residue 63 LYS Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain F residue 174 PHE Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain K residue 20 MET Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 24 MET Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain P residue 10 GLU Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain P residue 111 GLU Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain T residue 6 ARG Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 60 LYS Chi-restraints excluded: chain U residue 98 ASN Chi-restraints excluded: chain V residue 46 LYS Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 70 ILE Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain X residue 1 SER Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 67 LEU Chi-restraints excluded: chain Y residue 8 GLU Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 23 LEU Chi-restraints excluded: chain Z residue 24 LEU Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 1 residue 45 HIS Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 3 residue 37 THR Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain b residue 17 HIS Chi-restraints excluded: chain b residue 66 ILE Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 89 PHE Chi-restraints excluded: chain b residue 99 MET Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 177 ASN Chi-restraints excluded: chain b residue 178 LEU Chi-restraints excluded: chain b residue 185 ILE Chi-restraints excluded: chain c residue 54 ILE Chi-restraints excluded: chain c residue 88 LYS Chi-restraints excluded: chain c residue 96 VAL Chi-restraints excluded: chain c residue 146 LYS Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 164 THR Chi-restraints excluded: chain c residue 165 GLU Chi-restraints excluded: chain d residue 22 SER Chi-restraints excluded: chain d residue 32 LYS Chi-restraints excluded: chain d residue 49 ASP Chi-restraints excluded: chain d residue 128 VAL Chi-restraints excluded: chain d residue 147 LYS Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 170 LEU Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain d residue 197 HIS Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 87 VAL Chi-restraints excluded: chain e residue 113 VAL Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain e residue 155 LYS Chi-restraints excluded: chain e residue 156 ARG Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 52 ASN Chi-restraints excluded: chain f residue 63 ASN Chi-restraints excluded: chain f residue 88 MET Chi-restraints excluded: chain g residue 20 GLU Chi-restraints excluded: chain g residue 36 SER Chi-restraints excluded: chain g residue 59 GLU Chi-restraints excluded: chain g residue 93 VAL Chi-restraints excluded: chain g residue 138 GLU Chi-restraints excluded: chain h residue 45 ILE Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 70 VAL Chi-restraints excluded: chain h residue 89 ASP Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 104 SER Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain i residue 17 ARG Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 59 LYS Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain k residue 15 VAL Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 71 ASP Chi-restraints excluded: chain k residue 80 ASN Chi-restraints excluded: chain k residue 99 LEU Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 85 ARG Chi-restraints excluded: chain l residue 93 ARG Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 101 THR Chi-restraints excluded: chain n residue 45 VAL Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain o residue 25 GLU Chi-restraints excluded: chain o residue 61 GLN Chi-restraints excluded: chain o residue 86 LEU Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 52 LEU Chi-restraints excluded: chain q residue 12 VAL Chi-restraints excluded: chain q residue 28 VAL Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain q residue 60 ILE Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain s residue 18 VAL Chi-restraints excluded: chain s residue 44 ILE Chi-restraints excluded: chain s residue 48 ILE Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain t residue 26 MET Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain t residue 85 LEU Chi-restraints excluded: chain u residue 13 VAL Chi-restraints excluded: chain u residue 38 GLU Chi-restraints excluded: chain u residue 44 ARG Chi-restraints excluded: chain w residue 40 MET Chi-restraints excluded: chain z residue 110 LEU Chi-restraints excluded: chain z residue 117 ARG Chi-restraints excluded: chain z residue 118 MET Chi-restraints excluded: chain z residue 173 VAL Chi-restraints excluded: chain z residue 226 VAL Chi-restraints excluded: chain z residue 259 SER Chi-restraints excluded: chain z residue 270 ILE Chi-restraints excluded: chain z residue 298 LEU Chi-restraints excluded: chain z residue 323 ILE Chi-restraints excluded: chain z residue 329 ASP Chi-restraints excluded: chain z residue 340 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1046 random chunks: chunk 616 optimal weight: 6.9990 chunk 993 optimal weight: 10.0000 chunk 606 optimal weight: 20.0000 chunk 471 optimal weight: 10.0000 chunk 690 optimal weight: 10.0000 chunk 1042 optimal weight: 10.0000 chunk 959 optimal weight: 9.9990 chunk 829 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 640 optimal weight: 20.0000 chunk 508 optimal weight: 8.9990 overall best weight: 8.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 GLN E 195 GLN J 136 GLN ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 GLN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 87 GLN S 60 HIS V 78 GLN 4 37 GLN b 14 HIS ** h 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 159748 Z= 0.373 Angle : 0.671 14.607 238670 Z= 0.344 Chirality : 0.041 0.410 30435 Planarity : 0.005 0.095 13013 Dihedral : 23.325 179.339 79215 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.13 % Favored : 90.65 % Rotamer: Outliers : 5.04 % Allowed : 19.75 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.11), residues: 5979 helix: -0.30 (0.12), residues: 1899 sheet: -1.28 (0.15), residues: 1139 loop : -1.74 (0.11), residues: 2941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP d 169 HIS 0.011 0.002 HIS f 11 PHE 0.048 0.002 PHE u 36 TYR 0.025 0.002 TYR b 21 ARG 0.014 0.001 ARG i 123 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11958 Ramachandran restraints generated. 5979 Oldfield, 0 Emsley, 5979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11958 Ramachandran restraints generated. 5979 Oldfield, 0 Emsley, 5979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1555 residues out of total 4985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 1305 time to evaluate : 6.543 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: C 81 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7509 (mt-10) REVERT: C 184 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7988 (mm-30) REVERT: D 13 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.7903 (ptt180) REVERT: D 165 MET cc_start: 0.8717 (ttt) cc_final: 0.8444 (ttt) REVERT: E 4 VAL cc_start: 0.8552 (OUTLIER) cc_final: 0.8240 (t) REVERT: E 30 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8133 (tt0) REVERT: E 139 LYS cc_start: 0.8885 (tttt) cc_final: 0.8285 (ttpp) REVERT: F 80 GLN cc_start: 0.8386 (tp40) cc_final: 0.8049 (tp40) REVERT: F 133 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7390 (mp0) REVERT: F 144 LYS cc_start: 0.7593 (mptt) cc_final: 0.7249 (mmtt) REVERT: G 61 TRP cc_start: 0.8311 (m100) cc_final: 0.8061 (m100) REVERT: G 114 HIS cc_start: 0.8500 (t70) cc_final: 0.8216 (t70) REVERT: J 57 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8264 (pp) REVERT: J 102 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7881 (mt-10) REVERT: M 106 ASP cc_start: 0.7623 (t70) cc_final: 0.7379 (t70) REVERT: N 24 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.8160 (ttm) REVERT: N 65 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8206 (mp) REVERT: N 73 ASN cc_start: 0.8600 (t0) cc_final: 0.8249 (t0) REVERT: P 88 ARG cc_start: 0.7999 (mtm-85) cc_final: 0.7715 (mtt-85) REVERT: Q 12 ARG cc_start: 0.7871 (mtp85) cc_final: 0.7633 (mtp85) REVERT: Q 92 LYS cc_start: 0.8100 (tttt) cc_final: 0.7758 (ttpt) REVERT: Q 101 ASP cc_start: 0.7043 (t70) cc_final: 0.6569 (t70) REVERT: R 46 GLU cc_start: 0.6593 (pm20) cc_final: 0.6392 (pm20) REVERT: T 6 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7447 (ttm-80) REVERT: U 68 ASN cc_start: 0.8435 (m-40) cc_final: 0.7943 (m-40) REVERT: U 85 ARG cc_start: 0.7877 (ptp90) cc_final: 0.7236 (ptp90) REVERT: V 62 THR cc_start: 0.8774 (m) cc_final: 0.8546 (t) REVERT: X 43 LYS cc_start: 0.8423 (mtmt) cc_final: 0.7715 (tppt) REVERT: Y 31 GLN cc_start: 0.8611 (tt0) cc_final: 0.8333 (mt0) REVERT: Z 24 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8318 (tp) REVERT: Z 48 ASN cc_start: 0.8387 (t0) cc_final: 0.8146 (t0) REVERT: 0 11 LYS cc_start: 0.8505 (tppt) cc_final: 0.8106 (mmtt) REVERT: 1 36 LYS cc_start: 0.8600 (tttt) cc_final: 0.8321 (ttmt) REVERT: 3 14 LYS cc_start: 0.8742 (mmtt) cc_final: 0.8360 (mmtt) REVERT: 6 63 ARG cc_start: 0.7424 (mtt-85) cc_final: 0.6980 (mtm-85) REVERT: b 138 ARG cc_start: 0.6873 (ptt90) cc_final: 0.6103 (ptt90) REVERT: c 44 LYS cc_start: 0.8530 (tttp) cc_final: 0.8147 (mmtm) REVERT: c 130 ARG cc_start: 0.7837 (mtp85) cc_final: 0.7429 (mtp85) REVERT: d 32 LYS cc_start: 0.7295 (OUTLIER) cc_final: 0.6759 (tttm) REVERT: d 143 SER cc_start: 0.9053 (p) cc_final: 0.8748 (p) REVERT: d 195 ASN cc_start: 0.8043 (m-40) cc_final: 0.7626 (m110) REVERT: e 151 MET cc_start: 0.7513 (mmp) cc_final: 0.7135 (mmm) REVERT: f 79 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7557 (ttm-80) REVERT: g 3 ARG cc_start: 0.8123 (ptm160) cc_final: 0.7877 (ptp90) REVERT: h 29 SER cc_start: 0.8766 (p) cc_final: 0.8400 (m) REVERT: h 100 ILE cc_start: 0.9274 (pp) cc_final: 0.8995 (pt) REVERT: h 120 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8414 (pp) REVERT: j 10 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8062 (pp) REVERT: j 48 ARG cc_start: 0.8124 (mpt-90) cc_final: 0.7706 (mtt-85) REVERT: k 99 LEU cc_start: 0.7053 (OUTLIER) cc_final: 0.6706 (mp) REVERT: k 105 ARG cc_start: 0.7317 (mtp-110) cc_final: 0.6888 (ttm-80) REVERT: l 53 ARG cc_start: 0.7553 (ttm-80) cc_final: 0.7246 (ttt90) REVERT: m 32 ILE cc_start: 0.9044 (mt) cc_final: 0.8825 (mt) REVERT: s 10 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7836 (pp) REVERT: u 38 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6423 (tp30) REVERT: z 33 ARG cc_start: 0.6353 (tpt90) cc_final: 0.5508 (mmm160) REVERT: z 64 GLU cc_start: 0.6592 (mt-10) cc_final: 0.6346 (mm-30) REVERT: z 270 ILE cc_start: 0.7073 (OUTLIER) cc_final: 0.6362 (pp) REVERT: z 299 GLU cc_start: 0.6766 (mt-10) cc_final: 0.6409 (mt-10) outliers start: 250 outliers final: 211 residues processed: 1429 average time/residue: 1.4386 time to fit residues: 3518.2227 Evaluate side-chains 1523 residues out of total 4985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 1293 time to evaluate : 6.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain E residue 30 GLN Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 50 ASP Chi-restraints excluded: chain F residue 63 LYS Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 133 GLU Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain F residue 174 PHE Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 104 LEU Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 92 MET Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain K residue 20 MET Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 24 MET Chi-restraints excluded: chain N residue 38 LEU Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain O residue 20 GLU Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain P residue 10 GLU Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain P residue 111 GLU Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain T residue 6 ARG Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 60 LYS Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 70 ILE Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain X residue 1 SER Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 67 LEU Chi-restraints excluded: chain Y residue 5 GLU Chi-restraints excluded: chain Y residue 8 GLU Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 23 LEU Chi-restraints excluded: chain Z residue 24 LEU Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 1 residue 16 THR Chi-restraints excluded: chain 1 residue 45 HIS Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 3 residue 37 THR Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain 6 residue 27 THR Chi-restraints excluded: chain 6 residue 34 LEU Chi-restraints excluded: chain b residue 17 HIS Chi-restraints excluded: chain b residue 89 PHE Chi-restraints excluded: chain b residue 99 MET Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 177 ASN Chi-restraints excluded: chain b residue 178 LEU Chi-restraints excluded: chain b residue 185 ILE Chi-restraints excluded: chain c residue 54 ILE Chi-restraints excluded: chain c residue 88 LYS Chi-restraints excluded: chain c residue 96 VAL Chi-restraints excluded: chain c residue 146 LYS Chi-restraints excluded: chain c residue 152 VAL Chi-restraints excluded: chain c residue 153 SER Chi-restraints excluded: chain c residue 164 THR Chi-restraints excluded: chain c residue 165 GLU Chi-restraints excluded: chain d residue 22 SER Chi-restraints excluded: chain d residue 32 LYS Chi-restraints excluded: chain d residue 49 ASP Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 128 VAL Chi-restraints excluded: chain d residue 147 LYS Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 170 LEU Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain d residue 197 HIS Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 87 VAL Chi-restraints excluded: chain e residue 93 VAL Chi-restraints excluded: chain e residue 105 ILE Chi-restraints excluded: chain e residue 113 VAL Chi-restraints excluded: chain e residue 136 VAL Chi-restraints excluded: chain e residue 156 ARG Chi-restraints excluded: chain f residue 1 MET Chi-restraints excluded: chain f residue 52 ASN Chi-restraints excluded: chain f residue 63 ASN Chi-restraints excluded: chain f residue 79 ARG Chi-restraints excluded: chain f residue 88 MET Chi-restraints excluded: chain g residue 20 GLU Chi-restraints excluded: chain g residue 36 SER Chi-restraints excluded: chain g residue 59 GLU Chi-restraints excluded: chain g residue 93 VAL Chi-restraints excluded: chain h residue 30 LYS Chi-restraints excluded: chain h residue 45 ILE Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 70 VAL Chi-restraints excluded: chain h residue 89 ASP Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 104 SER Chi-restraints excluded: chain h residue 106 SER Chi-restraints excluded: chain h residue 120 LEU Chi-restraints excluded: chain i residue 17 ARG Chi-restraints excluded: chain i residue 66 VAL Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 59 LYS Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain k residue 15 VAL Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 49 SER Chi-restraints excluded: chain k residue 71 ASP Chi-restraints excluded: chain k residue 80 ASN Chi-restraints excluded: chain k residue 99 LEU Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 85 ARG Chi-restraints excluded: chain l residue 93 ARG Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 101 THR Chi-restraints excluded: chain n residue 11 LYS Chi-restraints excluded: chain n residue 45 VAL Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain o residue 25 GLU Chi-restraints excluded: chain o residue 60 SER Chi-restraints excluded: chain o residue 61 GLN Chi-restraints excluded: chain p residue 1 MET Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 52 LEU Chi-restraints excluded: chain q residue 12 VAL Chi-restraints excluded: chain q residue 28 VAL Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain q residue 60 ILE Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain s residue 18 VAL Chi-restraints excluded: chain s residue 44 ILE Chi-restraints excluded: chain s residue 48 ILE Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain t residue 26 MET Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain t residue 85 LEU Chi-restraints excluded: chain u residue 13 VAL Chi-restraints excluded: chain u residue 38 GLU Chi-restraints excluded: chain w residue 16 ILE Chi-restraints excluded: chain w residue 40 MET Chi-restraints excluded: chain z residue 16 GLU Chi-restraints excluded: chain z residue 110 LEU Chi-restraints excluded: chain z residue 117 ARG Chi-restraints excluded: chain z residue 118 MET Chi-restraints excluded: chain z residue 173 VAL Chi-restraints excluded: chain z residue 226 VAL Chi-restraints excluded: chain z residue 259 SER Chi-restraints excluded: chain z residue 270 ILE Chi-restraints excluded: chain z residue 298 LEU Chi-restraints excluded: chain z residue 323 ILE Chi-restraints excluded: chain z residue 329 ASP Chi-restraints excluded: chain z residue 340 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1046 random chunks: chunk 659 optimal weight: 20.0000 chunk 883 optimal weight: 3.9990 chunk 254 optimal weight: 10.0000 chunk 765 optimal weight: 20.0000 chunk 122 optimal weight: 10.0000 chunk 230 optimal weight: 20.0000 chunk 831 optimal weight: 10.0000 chunk 347 optimal weight: 5.9990 chunk 853 optimal weight: 4.9990 chunk 105 optimal weight: 30.0000 chunk 153 optimal weight: 40.0000 overall best weight: 6.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN J 136 GLN ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 GLN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 60 HIS V 78 GLN 4 37 GLN ** h 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.131553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.101862 restraints weight = 222941.275| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 0.97 r_work: 0.2986 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 159748 Z= 0.307 Angle : 0.641 16.607 238670 Z= 0.331 Chirality : 0.039 0.431 30435 Planarity : 0.005 0.077 13013 Dihedral : 23.329 179.118 79215 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.05 % Favored : 90.73 % Rotamer: Outliers : 4.94 % Allowed : 20.31 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.11), residues: 5979 helix: -0.30 (0.12), residues: 1896 sheet: -1.28 (0.15), residues: 1133 loop : -1.74 (0.11), residues: 2950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP d 169 HIS 0.010 0.001 HIS f 11 PHE 0.049 0.002 PHE u 36 TYR 0.026 0.002 TYR b 21 ARG 0.013 0.001 ARG i 123 =============================================================================== Job complete usr+sys time: 48428.32 seconds wall clock time: 842 minutes 16.68 seconds (50536.68 seconds total)