Starting phenix.real_space_refine on Mon Feb 26 09:18:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o2r_3730/02_2024/5o2r_3730.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o2r_3730/02_2024/5o2r_3730.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o2r_3730/02_2024/5o2r_3730.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o2r_3730/02_2024/5o2r_3730.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o2r_3730/02_2024/5o2r_3730.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5o2r_3730/02_2024/5o2r_3730.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 sd= 0.084 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 4643 5.49 5 S 163 5.16 5 C 74701 2.51 5 N 27580 2.21 5 O 40898 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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 TYR 74": "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 "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 PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P ARG 61": "NH1" <-> "NH2" Residue "P ARG 88": "NH1" <-> "NH2" Residue "P TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 100": "NH1" <-> "NH2" Residue "P ARG 108": "NH1" <-> "NH2" Residue "Q ARG 2": "NH1" <-> "NH2" Residue "Q ARG 5": "NH1" <-> "NH2" Residue "Q ARG 12": "NH1" <-> "NH2" Residue "Q ARG 32": "NH1" <-> "NH2" Residue "Q ARG 47": "NH1" <-> "NH2" Residue "Q ARG 69": "NH1" <-> "NH2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "R PHE 93": "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 "T TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 5": "NH1" <-> "NH2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U ARG 81": "NH1" <-> "NH2" Residue "U PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 85": "NH1" <-> "NH2" Residue "U ARG 93": "NH1" <-> "NH2" Residue "V PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 75": "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 "Z PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "5 PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 49": "NH1" <-> "NH2" Residue "6 ARG 56": "NH1" <-> "NH2" Residue "b TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 68": "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 PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 106": "NH1" <-> "NH2" Residue "c ARG 130": "NH1" <-> "NH2" Residue "e ARG 156": "NH1" <-> "NH2" Residue "f TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 123": "NH1" <-> "NH2" Residue "l ARG 55": "NH1" <-> "NH2" Residue "p ARG 28": "NH1" <-> "NH2" Residue "p PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ARG 133": "NH1" <-> "NH2" Residue "v ARG 137": "NH1" <-> "NH2" Residue "v ARG 306": "NH1" <-> "NH2" Residue "v ARG 316": "NH1" <-> "NH2" Residue "v ARG 321": "NH1" <-> "NH2" Residue "z ARG 12": "NH1" <-> "NH2" 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: 147985 Number of models: 1 Model: "" Number of chains: 58 Chain: "A" Number of atoms: 62262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2900, 62262 Classifications: {'RNA': 2900} Modifications used: {'p5*END': 1, 'rna2p_pur': 220, 'rna2p_pyr': 99, 'rna3p_pur': 1454, 'rna3p_pyr': 1127} Link IDs: {'rna2p': 319, 'rna3p': 2580} 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': 3, 'rna2p_pyr': 4, 'rna3p_pur': 62, 'rna3p_pyr': 51} 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: "I" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1032 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "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: "5" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 988 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "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: "7" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 149 Classifications: {'RNA': 7} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 2, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 5} 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': 96, 'rna2p_pyr': 53, 'rna3p_pur': 778, 'rna3p_pyr': 612} Link IDs: {'rna2p': 149, 'rna3p': 1389} 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: 1880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1880 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 8, 'TRANS': 233} Chain: "x" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1647 Classifications: {'RNA': 77} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 5, 'rna3p_pur': 32, 'rna3p_pyr': 31} Link IDs: {'rna2p': 14, 'rna3p': 62} Chain: "z" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 120 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 5, 'TRANS': 8} Time building chain proxies: 57.09, per 1000 atoms: 0.39 Number of scatterers: 147985 At special positions: 0 Unit cell: (267.748, 277.504, 244.984, 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 163 16.00 P 4643 15.00 O 40898 8.00 N 27580 7.00 C 74701 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 6 18 " - pdb=" SG CYS 6 40 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 61.02 Conformation dependent library (CDL) restraints added in 8.4 seconds 12198 Ramachandran restraints generated. 6099 Oldfield, 0 Emsley, 6099 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11400 Finding SS restraints... Secondary structure from input PDB file: 182 helices and 77 sheets defined 31.4% alpha, 15.7% beta 1418 base pairs and 2449 stacking pairs defined. Time for finding SS restraints: 51.77 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 196 through 202 removed outlier: 4.006A pdb=" N MET C 200 " --> pdb=" O ALA C 197 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG C 202 " --> pdb=" O HIS C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 212 Processing helix chain 'D' and resid 61 through 70 Processing helix chain 'D' and resid 120 through 126 Processing helix chain 'E' and resid 24 through 37 removed outlier: 3.578A pdb=" N VAL E 28 " --> pdb=" O ASN E 24 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN E 30 " --> pdb=" O ALA E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 115 Processing helix chain 'E' and resid 130 through 141 removed outlier: 3.849A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N MET E 141 " --> pdb=" O LYS E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 160 removed outlier: 3.601A pdb=" N PHE E 158 " --> pdb=" O ASP E 154 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA E 160 " --> pdb=" O ASN E 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 154 through 160' Processing helix chain 'E' and resid 178 through 183 Processing helix chain 'E' and resid 189 through 201 removed outlier: 3.664A pdb=" N GLU E 198 " --> pdb=" O LYS E 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 17 removed outlier: 4.641A pdb=" N ASP F 9 " --> pdb=" O ASP F 5 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N VAL F 12 " --> pdb=" O LYS F 8 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS F 13 " --> pdb=" O ASP F 9 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 60 removed outlier: 4.403A pdb=" N ASN F 51 " --> pdb=" O LYS F 47 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU F 56 " --> pdb=" O ALA F 52 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA F 58 " --> pdb=" O ALA F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 106 removed outlier: 4.021A pdb=" N TRP F 96 " --> pdb=" O GLY F 92 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE F 105 " --> pdb=" O ARG F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 171 removed outlier: 3.872A pdb=" N ALA F 167 " --> pdb=" O GLU F 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 79 removed outlier: 3.663A pdb=" N GLN G 63 " --> pdb=" O ASP G 59 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA G 69 " --> pdb=" O GLY G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 150 removed outlier: 3.720A pdb=" N ILE G 140 " --> pdb=" O ASP G 136 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG G 148 " --> pdb=" O ALA G 144 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR G 150 " --> pdb=" O ASP G 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 29 removed outlier: 3.857A pdb=" N PHE H 29 " --> pdb=" O TYR H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 48 removed outlier: 3.644A pdb=" N PHE H 46 " --> pdb=" O LYS H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 71 removed outlier: 3.883A pdb=" N LEU H 58 " --> pdb=" O LEU H 54 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N LEU H 62 " --> pdb=" O LEU H 58 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA H 63 " --> pdb=" O ALA H 59 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN H 66 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA H 67 " --> pdb=" O ALA H 63 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 106 removed outlier: 3.603A pdb=" N ALA H 105 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 38 removed outlier: 3.621A pdb=" N GLU I 36 " --> pdb=" O ASN I 33 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE I 37 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N CYS I 38 " --> pdb=" O MET I 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 33 through 38' Processing helix chain 'I' and resid 41 through 46 removed outlier: 3.610A pdb=" N THR I 45 " --> pdb=" O PHE I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 105 Processing helix chain 'I' and resid 110 through 114 removed outlier: 4.018A pdb=" N ALA I 113 " --> pdb=" O GLN I 110 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA I 114 " --> pdb=" O THR I 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 110 through 114' Processing helix chain 'J' and resid 24 through 38 removed outlier: 3.947A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 88 through 96 removed outlier: 3.584A pdb=" N ALA J 94 " --> pdb=" O GLU J 90 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG J 96 " --> pdb=" O MET J 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 107 removed outlier: 4.299A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 120 removed outlier: 3.833A pdb=" N GLY J 115 " --> pdb=" O LYS J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 132 through 136 removed outlier: 3.588A pdb=" N GLN J 136 " --> pdb=" O ALA J 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 104 through 108 removed outlier: 3.571A pdb=" N ARG K 108 " --> pdb=" O ARG K 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 114 through 119 Processing helix chain 'L' and resid 37 through 41 Processing helix chain 'L' and resid 56 through 61 removed outlier: 3.603A pdb=" N LEU L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 72 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.504A pdb=" N LEU L 82 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 79 through 83' Processing helix chain 'L' and resid 129 through 139 removed outlier: 3.636A pdb=" N ALA L 133 " --> pdb=" O LYS L 129 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 58 removed outlier: 3.974A pdb=" N ALA M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 121 removed outlier: 3.658A pdb=" N LEU M 119 " --> pdb=" O GLU M 115 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 32 removed outlier: 3.769A pdb=" N ALA N 19 " --> pdb=" O SER N 15 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY N 26 " --> pdb=" O ARG N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 54 removed outlier: 4.881A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.659A 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 removed outlier: 3.779A pdb=" N ARG N 63 " --> pdb=" O SER N 59 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 79 Processing helix chain 'N' and resid 83 through 87 Processing helix chain 'O' and resid 4 through 11 Processing helix chain 'O' and resid 11 through 22 Processing helix chain 'O' and resid 55 through 60 Processing helix chain 'O' and resid 67 through 86 removed outlier: 3.624A pdb=" N ALA O 72 " --> pdb=" O LYS O 68 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU O 80 " --> pdb=" O LYS O 76 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 111 Processing helix chain 'P' and resid 2 through 9 Processing helix chain 'P' and resid 52 through 55 removed outlier: 3.963A 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: 3.556A pdb=" N LEU P 99 " --> pdb=" O LEU P 96 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG P 100 " --> pdb=" O TYR P 97 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 20 removed outlier: 3.612A pdb=" N ALA Q 9 " --> pdb=" O ARG Q 5 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA Q 11 " --> pdb=" O VAL Q 7 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN Q 19 " --> pdb=" O LYS Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 24 through 28 removed outlier: 3.577A pdb=" N ARG Q 27 " --> pdb=" O TYR Q 24 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER Q 28 " --> pdb=" O GLY Q 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 24 through 28' Processing helix chain 'Q' and resid 30 through 71 removed outlier: 4.338A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS Q 40 " --> pdb=" O GLN Q 36 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA Q 45 " --> pdb=" O ALA Q 41 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG Q 49 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU Q 59 " --> pdb=" O GLN Q 55 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 85 removed outlier: 3.504A pdb=" N ALA Q 85 " --> pdb=" O GLY Q 81 " (cutoff:3.500A) Processing helix chain 'Q' and resid 90 through 101 removed outlier: 3.636A pdb=" N LEU Q 94 " --> pdb=" O ASP Q 90 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA Q 98 " --> pdb=" O LEU Q 94 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL Q 99 " --> pdb=" O ALA Q 95 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 117 removed outlier: 3.724A pdb=" N PHE Q 105 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA Q 115 " --> pdb=" O LYS Q 111 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.837A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 39 removed outlier: 4.161A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 62 removed outlier: 4.063A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS S 49 " --> pdb=" O VAL S 45 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL S 50 " --> pdb=" O LEU S 46 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP S 62 " --> pdb=" O ALA S 58 " (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 10 removed outlier: 3.973A pdb=" N LEU T 7 " --> pdb=" O ARG T 3 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N LEU T 8 " --> pdb=" O GLU T 4 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL T 10 " --> pdb=" O ARG T 6 " (cutoff:3.500A) Processing helix chain 'T' and resid 20 through 25 Processing helix chain 'T' and resid 39 through 51 removed outlier: 3.891A pdb=" N ALA T 46 " --> pdb=" O GLU T 42 " (cutoff:3.500A) Processing helix chain 'V' and resid 13 through 21 Processing helix chain 'V' and resid 44 through 51 removed outlier: 3.990A pdb=" N ASN V 49 " --> pdb=" O ASP V 45 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 61 removed outlier: 3.818A pdb=" N ILE X 58 " --> pdb=" O GLY X 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 62 through 74 Processing helix chain 'Y' and resid 3 through 7 removed outlier: 4.063A pdb=" N ARG Y 7 " --> pdb=" O LYS Y 4 " (cutoff:3.500A) Processing helix chain 'Y' and resid 11 through 22 Processing helix chain 'Y' and resid 25 through 34 Processing helix chain 'Y' and resid 40 through 61 removed outlier: 3.815A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA Y 51 " --> pdb=" O ARG Y 47 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 40 through 50 removed outlier: 3.560A pdb=" N ALA Z 49 " --> pdb=" O GLY Z 45 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL Z 50 " --> pdb=" O MET Z 46 " (cutoff:3.500A) Processing helix chain '0' and resid 9 through 16 Processing helix chain '0' and resid 17 through 19 No H-bonds generated for 'chain '0' and resid 17 through 19' 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 37 removed outlier: 4.126A pdb=" N ARG 2 35 " --> pdb=" O LEU 2 31 " (cutoff:3.500A) Processing helix chain '3' and resid 6 through 11 removed outlier: 3.532A pdb=" N LYS 3 11 " --> pdb=" O ARG 3 7 " (cutoff:3.500A) Processing helix chain '3' and resid 36 through 42 Processing helix chain '3' and resid 54 through 61 Processing helix chain '4' and resid 30 through 34 Processing helix chain '5' and resid 3 through 8 removed outlier: 3.634A pdb=" N ASP 5 7 " --> pdb=" O LEU 5 3 " (cutoff:3.500A) Processing helix chain '5' and resid 9 through 17 removed outlier: 3.721A pdb=" N ALA 5 13 " --> pdb=" O GLN 5 9 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU 5 17 " --> pdb=" O ALA 5 13 " (cutoff:3.500A) Processing helix chain '5' and resid 33 through 48 removed outlier: 4.188A pdb=" N LYS 5 37 " --> pdb=" O VAL 5 33 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET 5 38 " --> pdb=" O THR 5 34 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU 5 40 " --> pdb=" O ASP 5 36 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG 5 42 " --> pdb=" O MET 5 38 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA 5 44 " --> pdb=" O GLU 5 40 " (cutoff:3.500A) Processing helix chain '5' and resid 71 through 78 removed outlier: 3.780A pdb=" N PHE 5 76 " --> pdb=" O LYS 5 73 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY 5 78 " --> pdb=" O ALA 5 75 " (cutoff:3.500A) Processing helix chain '5' and resid 100 through 105 removed outlier: 3.685A pdb=" N ALA 5 104 " --> pdb=" O ALA 5 100 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS 5 105 " --> pdb=" O LYS 5 101 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 100 through 105' Processing helix chain '5' and resid 110 through 114 removed outlier: 3.536A pdb=" N GLU 5 114 " --> pdb=" O ALA 5 111 " (cutoff:3.500A) Processing helix chain '6' and resid 45 through 50 removed outlier: 4.103A pdb=" N ASP 6 50 " --> pdb=" O GLY 6 46 " (cutoff:3.500A) Processing helix chain '6' and resid 56 through 65 removed outlier: 3.828A pdb=" N ARG 6 63 " --> pdb=" O ARG 6 59 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE 6 64 " --> pdb=" O PHE 6 60 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN 6 65 " --> pdb=" O ASN 6 61 " (cutoff:3.500A) Processing helix chain 'b' and resid 23 through 27 removed outlier: 3.703A pdb=" N LYS b 27 " --> pdb=" O PRO b 24 " (cutoff:3.500A) Processing helix chain 'b' and resid 45 through 61 removed outlier: 3.733A pdb=" N GLU b 51 " --> pdb=" O PRO b 47 " (cutoff:3.500A) Processing helix chain 'b' and resid 77 through 86 Processing helix chain 'b' and resid 102 through 115 removed outlier: 3.553A pdb=" N VAL b 106 " --> pdb=" O ASN b 102 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N GLN b 108 " --> pdb=" O LYS b 104 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER b 109 " --> pdb=" O THR b 105 " (cutoff:3.500A) Processing helix chain 'b' and resid 116 through 122 removed outlier: 3.504A pdb=" N SER b 120 " --> pdb=" O LEU b 116 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLN b 121 " --> pdb=" O GLU b 117 " (cutoff:3.500A) Processing helix chain 'b' and resid 129 through 148 removed outlier: 4.060A pdb=" N ASN b 145 " --> pdb=" O GLU b 141 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N SER b 146 " --> pdb=" O LYS b 142 " (cutoff:3.500A) Processing helix chain 'b' and resid 168 through 178 Processing helix chain 'b' and resid 207 through 221 removed outlier: 4.044A pdb=" N THR b 219 " --> pdb=" O ALA b 215 " (cutoff:3.500A) Processing helix chain 'b' and resid 222 through 225 Processing helix chain 'c' and resid 5 through 10 removed outlier: 3.581A pdb=" N ARG c 10 " --> pdb=" O PRO c 6 " (cutoff:3.500A) Processing helix chain 'c' and resid 28 through 41 removed outlier: 4.103A pdb=" N SER c 34 " --> pdb=" O ASP c 30 " (cutoff:3.500A) Processing helix chain 'c' and resid 41 through 46 Processing helix chain 'c' and resid 71 through 77 removed outlier: 4.229A pdb=" N VAL c 75 " --> pdb=" O ARG c 71 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE c 76 " --> pdb=" O PRO c 72 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 86 removed outlier: 4.313A pdb=" N GLU c 84 " --> pdb=" O GLY c 80 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYS c 85 " --> pdb=" O GLU c 81 " (cutoff:3.500A) Processing helix chain 'c' and resid 111 through 125 Processing helix chain 'c' and resid 128 through 144 removed outlier: 3.871A pdb=" N ALA c 136 " --> pdb=" O ALA c 132 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL c 137 " --> pdb=" O MET c 133 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN c 138 " --> pdb=" O LYS c 134 " (cutoff:3.500A) Processing helix chain 'c' and resid 156 through 159 removed outlier: 3.992A pdb=" N ALA c 159 " --> pdb=" O LEU c 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 156 through 159' Processing helix chain 'd' and resid 8 through 14 Processing helix chain 'd' and resid 48 through 65 removed outlier: 3.873A pdb=" N GLN d 53 " --> pdb=" O ASP d 49 " (cutoff:3.500A) Processing helix chain 'd' and resid 67 through 81 removed outlier: 3.705A pdb=" N LEU d 81 " --> pdb=" O GLU d 77 " (cutoff:3.500A) Processing helix chain 'd' and resid 84 through 95 removed outlier: 3.683A pdb=" N ASN d 88 " --> pdb=" O ASN d 84 " (cutoff:3.500A) Processing helix chain 'd' and resid 96 through 105 Processing helix chain 'd' and resid 109 through 119 removed outlier: 3.619A pdb=" N ALA d 113 " --> pdb=" O THR d 109 " (cutoff:3.500A) Processing helix chain 'd' and resid 155 through 157 No H-bonds generated for 'chain 'd' and resid 155 through 157' Processing helix chain 'd' and resid 158 through 164 removed outlier: 4.067A pdb=" N GLU d 162 " --> pdb=" O LEU d 158 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN d 163 " --> pdb=" O GLU d 159 " (cutoff:3.500A) Processing helix chain 'd' and resid 195 through 203 removed outlier: 3.843A pdb=" N ILE d 199 " --> pdb=" O ASN d 195 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL d 200 " --> pdb=" O GLU d 196 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU d 201 " --> pdb=" O HIS d 197 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR d 203 " --> pdb=" O ILE d 199 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 69 removed outlier: 4.377A pdb=" N GLU e 64 " --> pdb=" O GLN e 60 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS e 65 " --> pdb=" O LYS e 61 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG e 68 " --> pdb=" O GLU e 64 " (cutoff:3.500A) Processing helix chain 'e' and resid 110 through 116 removed outlier: 3.669A pdb=" N VAL e 116 " --> pdb=" O ALA e 112 " (cutoff:3.500A) Processing helix chain 'e' and resid 131 through 146 removed outlier: 3.976A pdb=" N ILE e 140 " --> pdb=" O VAL e 136 " (cutoff:3.500A) Processing helix chain 'e' and resid 148 through 154 Processing helix chain 'e' and resid 159 through 165 removed outlier: 3.724A pdb=" N ILE e 163 " --> pdb=" O SER e 159 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU e 164 " --> pdb=" O VAL e 160 " (cutoff:3.500A) Processing helix chain 'f' and resid 12 through 15 Processing helix chain 'f' and resid 17 through 31 Processing helix chain 'f' and resid 67 through 80 removed outlier: 3.805A pdb=" N GLU f 73 " --> pdb=" O GLU f 69 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 30 Processing helix chain 'g' and resid 35 through 54 removed outlier: 4.099A pdb=" N ILE g 41 " --> pdb=" O THR g 37 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N THR g 48 " --> pdb=" O SER g 44 " (cutoff:3.500A) Processing helix chain 'g' and resid 56 through 67 removed outlier: 3.695A pdb=" N ALA g 64 " --> pdb=" O ALA g 60 " (cutoff:3.500A) Processing helix chain 'g' and resid 91 through 106 removed outlier: 3.668A pdb=" N ASN g 96 " --> pdb=" O PRO g 92 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL g 104 " --> pdb=" O MET g 100 " (cutoff:3.500A) Processing helix chain 'g' and resid 114 through 128 removed outlier: 3.720A pdb=" N GLU g 128 " --> pdb=" O SER g 124 " (cutoff:3.500A) Processing helix chain 'g' and resid 131 through 142 removed outlier: 3.611A pdb=" N LYS g 136 " --> pdb=" O THR g 132 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG g 137 " --> pdb=" O ALA g 133 " (cutoff:3.500A) Processing helix chain 'h' and resid 4 through 19 removed outlier: 3.676A pdb=" N ASP h 8 " --> pdb=" O ASP h 4 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 42 Processing helix chain 'h' and resid 112 through 119 removed outlier: 3.545A pdb=" N GLN h 117 " --> pdb=" O ARG h 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 48 through 52 Processing helix chain 'i' and resid 70 through 86 Processing helix chain 'j' and resid 14 through 31 removed outlier: 5.370A pdb=" N GLN j 20 " --> pdb=" O ARG j 16 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA j 21 " --> pdb=" O LEU j 17 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ARG j 31 " --> pdb=" O GLU j 27 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 87 Processing helix chain 'k' and resid 53 through 57 Processing helix chain 'k' and resid 58 through 71 removed outlier: 4.306A pdb=" N ASP k 71 " --> pdb=" O GLU k 67 " (cutoff:3.500A) Processing helix chain 'k' and resid 95 through 102 Processing helix chain 'l' and resid 2 through 9 Processing helix chain 'l' and resid 22 through 26 Processing helix chain 'm' and resid 13 through 18 Processing helix chain 'm' and resid 19 through 21 No H-bonds generated for 'chain 'm' and resid 19 through 21' Processing helix chain 'm' and resid 25 through 36 removed outlier: 3.606A pdb=" N SER m 29 " --> pdb=" O GLY m 25 " (cutoff:3.500A) Processing helix chain 'm' and resid 48 through 53 Processing helix chain 'm' and resid 66 through 83 removed outlier: 4.320A pdb=" N ARG m 70 " --> pdb=" O GLY m 66 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY m 83 " --> pdb=" O LEU m 79 " (cutoff:3.500A) Processing helix chain 'm' and resid 84 through 91 Processing helix chain 'n' and resid 2 through 19 removed outlier: 3.598A pdb=" N LYS n 6 " --> pdb=" O LYS n 2 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR n 19 " --> pdb=" O LEU n 15 " (cutoff:3.500A) Processing helix chain 'n' and resid 24 through 29 Processing helix chain 'n' and resid 39 through 48 removed outlier: 3.587A pdb=" N VAL n 45 " --> pdb=" O ARG n 41 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 60 removed outlier: 3.501A pdb=" N GLN n 60 " --> pdb=" O PRO n 57 " (cutoff:3.500A) Processing helix chain 'n' and resid 82 through 89 Processing helix chain 'o' and resid 3 through 15 removed outlier: 3.585A pdb=" N ALA o 8 " --> pdb=" O THR o 4 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE o 10 " --> pdb=" O ALA o 6 " (cutoff:3.500A) Processing helix chain 'o' and resid 23 through 39 removed outlier: 3.744A pdb=" N ALA o 29 " --> pdb=" O GLU o 25 " (cutoff:3.500A) Processing helix chain 'o' and resid 48 through 73 removed outlier: 3.840A pdb=" N GLY o 54 " --> pdb=" O HIS o 50 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG o 62 " --> pdb=" O MET o 58 " (cutoff:3.500A) Processing helix chain 'o' and resid 74 through 85 removed outlier: 3.981A pdb=" N GLU o 82 " --> pdb=" O THR o 78 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY o 85 " --> pdb=" O ILE o 81 " (cutoff:3.500A) Processing helix chain 'p' and resid 53 through 63 Processing helix chain 'p' and resid 68 through 76 removed outlier: 3.576A pdb=" N ILE p 75 " --> pdb=" O VAL p 71 " (cutoff:3.500A) Processing helix chain 'r' and resid 24 through 29 removed outlier: 3.577A pdb=" N LEU r 28 " --> pdb=" O ASP r 24 " (cutoff:3.500A) Processing helix chain 'r' and resid 47 through 64 removed outlier: 3.516A pdb=" N GLN r 51 " --> pdb=" O ARG r 47 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN r 53 " --> pdb=" O LYS r 49 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS r 59 " --> pdb=" O ALA r 55 " (cutoff:3.500A) Processing helix chain 's' and resid 11 through 24 removed outlier: 3.935A pdb=" N LYS s 17 " --> pdb=" O HIS s 13 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU s 23 " --> pdb=" O GLU s 19 " (cutoff:3.500A) Processing helix chain 's' and resid 40 through 44 removed outlier: 3.747A pdb=" N ILE s 44 " --> pdb=" O PRO s 41 " (cutoff:3.500A) Processing helix chain 's' and resid 69 through 74 removed outlier: 3.647A pdb=" N GLU s 72 " --> pdb=" O LYS s 69 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA s 74 " --> pdb=" O GLY s 71 " (cutoff:3.500A) Processing helix chain 't' and resid 7 through 39 removed outlier: 3.714A pdb=" N GLU t 14 " --> pdb=" O ALA t 10 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS t 19 " --> pdb=" O LYS t 15 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET t 27 " --> pdb=" O ARG t 23 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ARG t 28 " --> pdb=" O ARG t 24 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE t 30 " --> pdb=" O MET t 26 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS t 32 " --> pdb=" O ARG t 28 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA t 37 " --> pdb=" O LYS t 33 " (cutoff:3.500A) Processing helix chain 't' and resid 44 through 52 removed outlier: 4.453A pdb=" N PHE t 50 " --> pdb=" O ALA t 46 " (cutoff:3.500A) Processing helix chain 't' and resid 54 through 63 removed outlier: 4.686A pdb=" N GLN t 60 " --> pdb=" O ILE t 56 " (cutoff:3.500A) Processing helix chain 't' and resid 69 through 86 removed outlier: 4.096A pdb=" N LYS t 84 " --> pdb=" O ALA t 80 " (cutoff:3.500A) Processing helix chain 'u' and resid 18 through 23 Processing helix chain 'u' and resid 25 through 32 Processing helix chain 'u' and resid 38 through 57 removed outlier: 4.028A pdb=" N LYS u 45 " --> pdb=" O THR u 41 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LYS u 53 " --> pdb=" O ALA u 49 " (cutoff:3.500A) Processing helix chain 'v' and resid 122 through 140 removed outlier: 3.879A pdb=" N ASP v 130 " --> pdb=" O LEU v 126 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N MET v 134 " --> pdb=" O ASP v 130 " (cutoff:3.500A) Processing helix chain 'v' and resid 170 through 176 removed outlier: 3.548A pdb=" N ARG v 174 " --> pdb=" O GLY v 170 " (cutoff:3.500A) Processing helix chain 'v' and resid 177 through 179 No H-bonds generated for 'chain 'v' and resid 177 through 179' Processing helix chain 'v' and resid 234 through 240 removed outlier: 3.789A pdb=" N ASN v 238 " --> pdb=" O GLY v 234 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR v 239 " --> pdb=" O GLN v 235 " (cutoff:3.500A) Processing helix chain 'v' and resid 263 through 268 Processing helix chain 'v' and resid 268 through 298 removed outlier: 4.018A pdb=" N LEU v 274 " --> pdb=" O ALA v 270 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS v 285 " --> pdb=" O ALA v 281 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA v 291 " --> pdb=" O GLN v 287 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR v 293 " --> pdb=" O ALA v 289 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASN v 296 " --> pdb=" O SER v 292 " (cutoff:3.500A) Processing helix chain 'v' and resid 320 through 324 removed outlier: 3.643A pdb=" N ASN v 323 " --> pdb=" O HIS v 320 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU v 324 " --> pdb=" O ARG v 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 320 through 324' Processing helix chain 'v' and resid 337 through 347 Proline residue: v 343 - end of helix Processing sheet with id=AA1, first strand: chain 'C' and resid 3 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: 6.780A pdb=" N ILE C 90 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LEU C 80 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU C 92 " --> pdb=" O GLU C 78 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 128 through 130 removed outlier: 3.568A pdb=" N GLN C 162 " --> pdb=" O ARG C 174 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 169 through 171 removed outlier: 3.547A pdb=" N GLY D 111 " --> pdb=" O VAL D 170 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS D 204 " --> pdb=" O ASP D 108 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL D 26 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N MET D 11 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL D 24 " --> pdb=" O MET D 11 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ARG D 13 " --> pdb=" O ILE D 22 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE D 22 " --> pdb=" O ARG D 13 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU D 186 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N VAL D 180 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LEU D 188 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ASP D 176 " --> pdb=" O LYS D 190 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 33 through 34 removed outlier: 5.013A pdb=" N THR D 52 " --> pdb=" O GLY D 78 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N GLY D 78 " --> pdb=" O THR D 52 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 117 through 119 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 120 removed outlier: 3.860A pdb=" N ASP E 168 " --> pdb=" O VAL E 146 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 65 through 68 removed outlier: 3.596A pdb=" N GLY F 85 " --> pdb=" O THR F 67 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR F 154 " --> pdb=" O THR F 34 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 17 through 19 Processing sheet with id=AB2, first strand: chain 'G' and resid 40 through 41 Processing sheet with id=AB3, first strand: chain 'G' and resid 120 through 126 removed outlier: 7.042A pdb=" N GLU G 129 " --> pdb=" O PRO G 125 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 94 through 98 removed outlier: 3.584A pdb=" N SER G 105 " --> pdb=" O ARG G 94 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS G 98 " --> pdb=" O VAL G 101 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL G 101 " --> pdb=" O LYS G 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AB6, first strand: chain 'H' and resid 77 through 82 removed outlier: 6.621A pdb=" N VAL H 78 " --> pdb=" O ASN H 145 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL H 147 " --> pdb=" O VAL H 78 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ILE H 80 " --> pdb=" O VAL H 147 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 131 through 133 removed outlier: 3.647A pdb=" N ALA H 140 " --> pdb=" O PHE H 132 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 59 through 60 removed outlier: 4.570A pdb=" N THR I 59 " --> pdb=" O THR I 67 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N THR I 67 " --> pdb=" O THR I 59 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'J' and resid 122 through 124 removed outlier: 6.746A pdb=" N ILE J 54 " --> pdb=" O LYS J 123 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN J 138 " --> pdb=" O TRP J 15 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 76 through 77 Processing sheet with id=AC2, first strand: chain 'K' and resid 2 through 3 Processing sheet with id=AC3, first strand: chain 'K' and resid 7 through 10 removed outlier: 3.513A pdb=" N VAL K 10 " --> pdb=" O ARG K 17 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ARG K 17 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA K 16 " --> pdb=" O ALA K 46 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ALA K 46 " --> pdb=" O ALA K 16 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ARG K 18 " --> pdb=" O LYS K 44 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL K 24 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N ILE K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N VAL K 62 " --> pdb=" O VAL K 85 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VAL K 85 " --> pdb=" O VAL K 62 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N CYS K 84 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASN K 9 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N LEU K 86 " --> pdb=" O ASN K 9 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 76 through 79 removed outlier: 3.752A pdb=" N VAL K 76 " --> pdb=" O VAL P 72 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ALA P 57 " --> pdb=" O ILE P 49 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ILE P 49 " --> pdb=" O ALA P 57 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N THR P 59 " --> pdb=" O ILE P 47 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ILE P 63 " --> pdb=" O GLU P 43 " (cutoff:3.500A) removed outlier: 9.274A pdb=" N GLU P 43 " --> pdb=" O ILE P 63 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N THR P 24 " --> pdb=" O VAL P 85 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N VAL P 85 " --> pdb=" O THR P 24 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLU P 26 " --> pdb=" O ILE P 83 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE P 83 " --> pdb=" O GLU P 26 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LYS P 28 " --> pdb=" O ASP P 81 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 74 through 77 removed outlier: 3.738A pdb=" N LYS L 109 " --> pdb=" O ALA L 75 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ALA L 108 " --> pdb=" O ARG L 126 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 89 through 90 removed outlier: 6.137A pdb=" N VAL L 90 " --> pdb=" O ARG L 123 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL L 122 " --> pdb=" O GLU L 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'M' and resid 62 through 65 removed outlier: 3.858A pdb=" N LYS M 100 " --> pdb=" O ALA M 35 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU M 33 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLU M 104 " --> pdb=" O PHE M 31 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N PHE M 31 " --> pdb=" O GLU M 104 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 39 through 41 Processing sheet with id=AC9, first strand: chain 'M' and resid 72 through 75 removed outlier: 6.574A pdb=" N GLU M 75 " --> pdb=" O VAL M 89 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N VAL M 89 " --> pdb=" O GLU M 75 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 33 through 37 Processing sheet with id=AD2, first strand: chain 'O' and resid 47 through 52 removed outlier: 6.763A pdb=" N VAL O 39 " --> pdb=" O LEU O 48 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ALA O 50 " --> pdb=" O ALA O 37 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ALA O 37 " --> pdb=" O ALA O 50 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL O 28 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'R' and resid 11 through 14 removed outlier: 6.792A pdb=" N GLN R 6 " --> pdb=" O VAL R 38 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VAL R 38 " --> pdb=" O GLN R 6 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'R' and resid 19 through 22 removed outlier: 6.328A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'R' and resid 72 through 78 removed outlier: 4.151A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'S' and resid 4 through 10 removed outlier: 5.367A pdb=" N ILE S 4 " --> pdb=" O VAL S 107 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL S 107 " --> pdb=" O ILE S 4 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N LYS S 6 " --> pdb=" O VAL S 105 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL S 105 " --> pdb=" O LYS S 6 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ARG S 8 " --> pdb=" O ILE S 103 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE S 103 " --> pdb=" O ARG S 8 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N HIS S 102 " --> pdb=" O VAL S 76 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N VAL S 76 " --> pdb=" O HIS S 102 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N THR S 104 " --> pdb=" O ILE S 74 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE S 74 " --> pdb=" O THR S 104 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL S 106 " --> pdb=" O THR S 72 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS S 27 " --> pdb=" O VAL S 71 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'S' and resid 82 through 87 Processing sheet with id=AD8, first strand: chain 'T' and resid 11 through 14 removed outlier: 3.679A pdb=" N ALA T 13 " --> pdb=" O LYS T 33 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'T' and resid 67 through 70 Processing sheet with id=AE1, first strand: chain 'U' and resid 64 through 65 removed outlier: 6.255A pdb=" N LYS U 32 " --> pdb=" O VAL U 27 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL U 27 " --> pdb=" O LYS U 32 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE U 34 " --> pdb=" O LYS U 25 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'U' and resid 40 through 44 Processing sheet with id=AE3, first strand: chain 'U' and resid 82 through 87 removed outlier: 3.905A pdb=" N LYS U 90 " --> pdb=" O GLU U 87 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'V' and resid 3 through 5 removed outlier: 6.560A pdb=" N ILE V 4 " --> pdb=" O VAL V 64 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ASP V 90 " --> pdb=" O GLN V 75 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL V 77 " --> pdb=" O HIS V 88 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N HIS V 88 " --> pdb=" O VAL V 77 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ARG V 79 " --> pdb=" O LEU V 86 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU V 86 " --> pdb=" O ARG V 79 " (cutoff:3.500A) removed outlier: 9.093A pdb=" N LYS V 25 " --> pdb=" O GLN V 87 " (cutoff:3.500A) removed outlier: 9.910A pdb=" N ILE V 89 " --> pdb=" O LYS V 25 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N PHE V 91 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE V 29 " --> pdb=" O PHE V 91 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ARG V 93 " --> pdb=" O ILE V 29 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N TYR V 31 " --> pdb=" O ARG V 93 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'W' and resid 18 through 19 removed outlier: 6.815A pdb=" N LEU W 55 " --> pdb=" O ILE W 33 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'W' and resid 26 through 27 removed outlier: 3.617A pdb=" N LYS W 68 " --> pdb=" O ARG W 73 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG W 73 " --> pdb=" O LYS W 68 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'X' and resid 12 through 15 Processing sheet with id=AE8, first strand: chain 'X' and resid 33 through 39 Processing sheet with id=AE9, first strand: chain 'Z' and resid 34 through 37 Processing sheet with id=AF1, first strand: chain '0' and resid 28 through 29 Processing sheet with id=AF2, first strand: chain '0' and resid 47 through 48 Processing sheet with id=AF3, first strand: chain '1' and resid 6 through 11 Processing sheet with id=AF4, first strand: chain '1' and resid 36 through 39 removed outlier: 3.556A pdb=" N GLN 1 44 " --> pdb=" O ASP 1 39 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain '3' and resid 14 through 15 Processing sheet with id=AF6, first strand: chain '4' and resid 14 through 19 Processing sheet with id=AF7, first strand: chain '5' and resid 54 through 55 Processing sheet with id=AF8, first strand: chain '6' and resid 10 through 12 Processing sheet with id=AF9, first strand: chain 'b' and resid 32 through 33 removed outlier: 3.610A pdb=" N VAL b 37 " --> pdb=" O ALA b 33 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'b' and resid 66 through 68 Processing sheet with id=AG2, first strand: chain 'b' and resid 185 through 186 Processing sheet with id=AG3, first strand: chain 'c' and resid 19 through 20 removed outlier: 4.190A pdb=" N ARG c 53 " --> pdb=" O HIS c 68 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL c 65 " --> pdb=" O ASN c 101 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ALA c 103 " --> pdb=" O VAL c 65 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE c 67 " --> pdb=" O ALA c 103 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'c' and resid 165 through 170 removed outlier: 3.706A pdb=" N GLY c 147 " --> pdb=" O PHE c 202 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL c 199 " --> pdb=" O ASN c 184 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN c 184 " --> pdb=" O VAL c 199 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ASP c 180 " --> pdb=" O LYS c 203 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'd' and resid 123 through 124 Processing sheet with id=AG6, first strand: chain 'e' and resid 12 through 21 removed outlier: 6.573A pdb=" N LEU e 35 " --> pdb=" O ILE e 15 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N VAL e 17 " --> pdb=" O THR e 33 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N THR e 33 " --> pdb=" O VAL e 17 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ARG e 19 " --> pdb=" O SER e 31 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N SER e 31 " --> pdb=" O ARG e 19 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'e' and resid 12 through 21 removed outlier: 6.573A pdb=" N LEU e 35 " --> pdb=" O ILE e 15 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N VAL e 17 " --> pdb=" O THR e 33 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N THR e 33 " --> pdb=" O VAL e 17 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ARG e 19 " --> pdb=" O SER e 31 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N SER e 31 " --> pdb=" O ARG e 19 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'e' and resid 84 through 88 removed outlier: 3.630A pdb=" N SER e 91 " --> pdb=" O HIS e 88 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG e 92 " --> pdb=" O TYR e 127 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'f' and resid 2 through 3 Processing sheet with id=AH1, first strand: chain 'f' and resid 58 through 61 removed outlier: 3.535A pdb=" N VAL f 7 " --> pdb=" O MET f 88 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N MET f 9 " --> pdb=" O ARG f 86 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ARG f 86 " --> pdb=" O MET f 9 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'g' and resid 72 through 76 Processing sheet with id=AH3, first strand: chain 'h' and resid 23 through 27 removed outlier: 4.106A pdb=" N THR h 61 " --> pdb=" O ASP h 47 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ASP h 47 " --> pdb=" O THR h 61 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'h' and resid 73 through 76 removed outlier: 6.757A pdb=" N VAL h 102 " --> pdb=" O ILE h 125 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N TYR h 127 " --> pdb=" O ILE h 100 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ILE h 100 " --> pdb=" O TYR h 127 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'i' and resid 5 through 7 removed outlier: 6.417A pdb=" N VAL i 28 " --> pdb=" O ILE i 64 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N VAL i 66 " --> pdb=" O VAL i 28 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'j' and resid 45 through 52 Processing sheet with id=AH7, first strand: chain 'j' and resid 45 through 52 removed outlier: 3.563A pdb=" N GLU j 66 " --> pdb=" O LYS n 97 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS n 97 " --> pdb=" O GLU j 66 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'k' and resid 40 through 45 removed outlier: 6.979A pdb=" N ALA k 40 " --> pdb=" O ASP k 35 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ASP k 35 " --> pdb=" O ALA k 40 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY k 42 " --> pdb=" O ILE k 33 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY k 18 " --> pdb=" O ASN k 80 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL k 83 " --> pdb=" O THR k 107 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ILE k 109 " --> pdb=" O VAL k 83 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N VAL k 85 " --> pdb=" O ILE k 109 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ASP k 111 " --> pdb=" O VAL k 85 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'l' and resid 28 through 31 removed outlier: 10.060A pdb=" N TYR l 94 " --> pdb=" O GLU l 61 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N THR l 63 " --> pdb=" O TYR l 94 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N THR l 96 " --> pdb=" O THR l 63 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N TYR l 65 " --> pdb=" O THR l 96 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ARG l 35 " --> pdb=" O ARG l 53 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'p' and resid 34 through 35 removed outlier: 3.506A pdb=" N GLU p 34 " --> pdb=" O VAL p 21 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL p 2 " --> pdb=" O THR p 66 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'q' and resid 6 through 7 removed outlier: 7.039A pdb=" N GLU q 59 " --> pdb=" O VAL q 75 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TRP q 72 " --> pdb=" O HIS q 44 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL q 21 " --> pdb=" O VAL q 12 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 's' and resid 31 through 32 removed outlier: 3.673A pdb=" N HIS s 51 " --> pdb=" O THR s 32 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'v' and resid 145 through 153 removed outlier: 5.186A pdb=" N VAL v 146 " --> pdb=" O SER v 167 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N SER v 167 " --> pdb=" O VAL v 146 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ILE v 148 " --> pdb=" O LYS v 165 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LYS v 165 " --> pdb=" O ILE v 148 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU v 161 " --> pdb=" O SER v 152 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LYS v 160 " --> pdb=" O ALA v 117 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'v' and resid 222 through 226 removed outlier: 3.674A pdb=" N ILE v 253 " --> pdb=" O HIS v 248 " (cutoff:3.500A) 1574 hydrogen bonds defined for protein. 4398 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3587 hydrogen bonds 5790 hydrogen bond angles 0 basepair planarities 1418 basepair parallelities 2449 stacking parallelities Total time for adding SS restraints: 241.28 Time building geometry restraints manager: 66.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 15431 1.31 - 1.44: 70651 1.44 - 1.57: 65041 1.57 - 1.71: 9187 1.71 - 1.84: 291 Bond restraints: 160601 Sorted by residual: bond pdb=" CA PHE E 85 " pdb=" CB PHE E 85 " ideal model delta sigma weight residual 1.528 1.380 0.149 2.61e-02 1.47e+03 3.25e+01 bond pdb=" CA PRO z 13 " pdb=" C PRO z 13 " ideal model delta sigma weight residual 1.514 1.543 -0.029 5.50e-03 3.31e+04 2.73e+01 bond pdb=" CA TYR L 58 " pdb=" C TYR L 58 " ideal model delta sigma weight residual 1.523 1.445 0.079 1.80e-02 3.09e+03 1.90e+01 bond pdb=" CA LYS 4 18 " pdb=" CB LYS 4 18 " ideal model delta sigma weight residual 1.527 1.451 0.076 1.75e-02 3.27e+03 1.90e+01 bond pdb=" CA THR j 50 " pdb=" CB THR j 50 " ideal model delta sigma weight residual 1.526 1.458 0.068 1.70e-02 3.46e+03 1.61e+01 ... (remaining 160596 not shown) Histogram of bond angle deviations from ideal: 85.91 - 96.78: 5 96.78 - 107.65: 41655 107.65 - 118.52: 114562 118.52 - 129.38: 79836 129.38 - 140.25: 3786 Bond angle restraints: 239844 Sorted by residual: angle pdb=" N GLU c 81 " pdb=" CA GLU c 81 " pdb=" C GLU c 81 " ideal model delta sigma weight residual 111.36 131.11 -19.75 1.09e+00 8.42e-01 3.28e+02 angle pdb=" N ARG H 97 " pdb=" CA ARG H 97 " pdb=" C ARG H 97 " ideal model delta sigma weight residual 111.28 124.96 -13.68 1.09e+00 8.42e-01 1.58e+02 angle pdb=" N ARG u 34 " pdb=" CA ARG u 34 " pdb=" C ARG u 34 " ideal model delta sigma weight residual 110.91 124.24 -13.33 1.17e+00 7.31e-01 1.30e+02 angle pdb=" N LYS G 174 " pdb=" CA LYS G 174 " pdb=" C LYS G 174 " ideal model delta sigma weight residual 111.07 122.09 -11.02 1.07e+00 8.73e-01 1.06e+02 angle pdb=" N LYS l 43 " pdb=" CA LYS l 43 " pdb=" C LYS l 43 " ideal model delta sigma weight residual 113.16 126.79 -13.63 1.42e+00 4.96e-01 9.21e+01 ... (remaining 239839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.15: 90739 35.15 - 70.30: 10753 70.30 - 105.45: 1278 105.45 - 140.61: 16 140.61 - 175.76: 35 Dihedral angle restraints: 102821 sinusoidal: 85149 harmonic: 17672 Sorted by residual: dihedral pdb=" C5' G a1300 " pdb=" C4' G a1300 " pdb=" C3' G a1300 " pdb=" O3' G a1300 " ideal model delta sinusoidal sigma weight residual 147.00 72.28 74.72 1 8.00e+00 1.56e-02 1.10e+02 dihedral pdb=" C THR 5 80 " pdb=" N THR 5 80 " pdb=" CA THR 5 80 " pdb=" CB THR 5 80 " ideal model delta harmonic sigma weight residual -122.00 -145.23 23.23 0 2.50e+00 1.60e-01 8.63e+01 dihedral pdb=" O4' U A1911 " pdb=" C1' U A1911 " pdb=" N1 U A1911 " pdb=" C2 U A1911 " ideal model delta sinusoidal sigma weight residual 200.00 30.79 169.21 1 1.50e+01 4.44e-03 8.46e+01 ... (remaining 102818 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.180: 30151 0.180 - 0.360: 409 0.360 - 0.540: 26 0.540 - 0.721: 6 0.721 - 0.901: 1 Chirality restraints: 30593 Sorted by residual: chirality pdb=" CA THR 5 80 " pdb=" N THR 5 80 " pdb=" C THR 5 80 " pdb=" CB THR 5 80 " both_signs ideal model delta sigma weight residual False 2.53 1.63 0.90 2.00e-01 2.50e+01 2.03e+01 chirality pdb=" CA GLU c 81 " pdb=" N GLU c 81 " pdb=" C GLU c 81 " pdb=" CB GLU c 81 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.22e+01 chirality pdb=" CA VAL f 96 " pdb=" N VAL f 96 " pdb=" C VAL f 96 " pdb=" CB VAL f 96 " both_signs ideal model delta sigma weight residual False 2.44 1.82 0.62 2.00e-01 2.50e+01 9.72e+00 ... (remaining 30590 not shown) Planarity restraints: 13157 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL c 96 " -0.144 5.00e-02 4.00e+02 2.24e-01 8.03e+01 pdb=" N PRO c 97 " 0.386 5.00e-02 4.00e+02 pdb=" CA PRO c 97 " -0.152 5.00e-02 4.00e+02 pdb=" CD PRO c 97 " -0.090 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU j 42 " -0.143 5.00e-02 4.00e+02 2.23e-01 7.97e+01 pdb=" N PRO j 43 " 0.384 5.00e-02 4.00e+02 pdb=" CA PRO j 43 " -0.153 5.00e-02 4.00e+02 pdb=" CD PRO j 43 " -0.088 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG v 303 " 0.638 9.50e-02 1.11e+02 2.86e-01 5.01e+01 pdb=" NE ARG v 303 " -0.036 2.00e-02 2.50e+03 pdb=" CZ ARG v 303 " -0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG v 303 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG v 303 " 0.023 2.00e-02 2.50e+03 ... (remaining 13154 not shown) Histogram of nonbonded interaction distances: 0.78 - 1.60: 6 1.60 - 2.43: 567 2.43 - 3.25: 136310 3.25 - 4.08: 476856 4.08 - 4.90: 732625 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1346364 Sorted by model distance: nonbonded pdb=" OP2 U A 714 " pdb=" NH2 ARG o 88 " model vdw 0.776 2.520 nonbonded pdb=" O2' G A2255 " pdb=" OP2 G x 3 " model vdw 1.401 2.440 nonbonded pdb=" CB HIS f 37 " pdb=" CG1 VAL f 96 " model vdw 1.427 3.860 nonbonded pdb=" OP1 U A1915 " pdb=" NH2 ARG v 116 " model vdw 1.507 2.520 nonbonded pdb=" C5 C A1914 " pdb=" NH2 ARG v 295 " model vdw 1.514 3.420 ... (remaining 1346359 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: 0.010 Normalize map: mean=0, sd=1: 2.790 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: 0.170 Extract box with map and model: 15.380 Check model and map are aligned: 1.580 Set scattering table: 1.020 Process input model: 520.230 Find NCS groups from input model: 3.040 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 547.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 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 : 0.011 0.163 160601 Z= 0.668 Angle : 1.263 39.085 239844 Z= 0.638 Chirality : 0.065 0.901 30593 Planarity : 0.009 0.286 13157 Dihedral : 23.009 175.757 91418 Min Nonbonded Distance : 0.776 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.52 % Allowed : 11.58 % Favored : 87.90 % Rotamer: Outliers : 1.03 % Allowed : 4.13 % Favored : 94.83 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.11 (0.08), residues: 6099 helix: -3.88 (0.07), residues: 1791 sheet: -3.01 (0.13), residues: 1089 loop : -3.25 (0.09), residues: 3219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.005 TRP C 212 HIS 0.025 0.004 HIS k 117 PHE 0.046 0.005 PHE u 36 TYR 0.054 0.004 TYR l 116 ARG 0.026 0.002 ARG z 17 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12198 Ramachandran restraints generated. 6099 Oldfield, 0 Emsley, 6099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12198 Ramachandran restraints generated. 6099 Oldfield, 0 Emsley, 6099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1935 residues out of total 5060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 1883 time to evaluate : 6.228 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: C 4 LYS cc_start: 0.8376 (tttt) cc_final: 0.8124 (mtpp) REVERT: C 180 MET cc_start: 0.7306 (mmm) cc_final: 0.7025 (mmm) REVERT: C 188 ARG cc_start: 0.8492 (mtt-85) cc_final: 0.8266 (mtp85) REVERT: D 7 LYS cc_start: 0.8298 (ttmt) cc_final: 0.8070 (ttmt) REVERT: D 33 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7144 (ptt90) REVERT: D 167 ASN cc_start: 0.8586 (t0) cc_final: 0.8191 (t0) REVERT: E 57 LYS cc_start: 0.9185 (tmtp) cc_final: 0.8912 (tttp) REVERT: E 145 ASP cc_start: 0.7126 (t70) cc_final: 0.6899 (t70) REVERT: E 171 ASP cc_start: 0.7573 (t70) cc_final: 0.7083 (p0) REVERT: G 162 ARG cc_start: 0.7407 (ptp-170) cc_final: 0.6790 (mtm180) REVERT: I 99 LYS cc_start: 0.6507 (ptmt) cc_final: 0.5729 (mttp) REVERT: J 96 ARG cc_start: 0.7338 (mmm160) cc_final: 0.6822 (mmm160) REVERT: J 99 ARG cc_start: 0.8017 (mmm160) cc_final: 0.6850 (mmt90) REVERT: K 17 ARG cc_start: 0.6543 (tpp80) cc_final: 0.6321 (tpp80) REVERT: L 104 GLN cc_start: 0.8365 (mm110) cc_final: 0.8049 (mm110) REVERT: L 105 ILE cc_start: 0.8734 (mm) cc_final: 0.8435 (mt) REVERT: M 6 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.7140 (ptm-80) REVERT: M 16 ARG cc_start: 0.8610 (mmt-90) cc_final: 0.8406 (mpt180) REVERT: N 42 LYS cc_start: 0.9103 (mttm) cc_final: 0.8677 (mtmt) REVERT: O 18 LEU cc_start: 0.8287 (tp) cc_final: 0.8029 (tp) REVERT: O 91 SER cc_start: 0.8153 (m) cc_final: 0.7770 (p) REVERT: P 6 GLN cc_start: 0.8070 (tt0) cc_final: 0.7341 (tt0) REVERT: P 99 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7726 (tt) REVERT: Q 12 ARG cc_start: 0.8261 (mtp85) cc_final: 0.7895 (ttm110) REVERT: Q 70 GLN cc_start: 0.7045 (mm110) cc_final: 0.6839 (mm110) REVERT: Q 92 LYS cc_start: 0.8135 (tttm) cc_final: 0.7926 (tptm) REVERT: R 7 SER cc_start: 0.8405 (t) cc_final: 0.8183 (p) REVERT: R 84 ARG cc_start: 0.7729 (ptt-90) cc_final: 0.7513 (ptt-90) REVERT: T 15 HIS cc_start: 0.7837 (t-90) cc_final: 0.7434 (t-170) REVERT: T 30 ILE cc_start: 0.8382 (tt) cc_final: 0.8147 (pt) REVERT: U 58 VAL cc_start: 0.8488 (t) cc_final: 0.8212 (m) REVERT: V 45 ASP cc_start: 0.7699 (m-30) cc_final: 0.7462 (m-30) REVERT: V 93 ARG cc_start: 0.7980 (ttm110) cc_final: 0.7736 (ttm170) REVERT: W 64 LYS cc_start: 0.8262 (tptm) cc_final: 0.7818 (ttpt) REVERT: X 51 SER cc_start: 0.8986 (p) cc_final: 0.8686 (p) REVERT: Y 38 GLN cc_start: 0.7059 (tp40) cc_final: 0.6568 (mp10) REVERT: 0 31 LYS cc_start: 0.8335 (tttt) cc_final: 0.7975 (ttmm) REVERT: 1 29 LYS cc_start: 0.8082 (mmtt) cc_final: 0.6862 (ptmm) REVERT: 2 1 MET cc_start: 0.6009 (ptm) cc_final: 0.4855 (ptm) REVERT: 3 14 LYS cc_start: 0.8313 (tttt) cc_final: 0.8108 (mmtp) REVERT: 5 1 MET cc_start: 0.1450 (tpt) cc_final: 0.0474 (tpt) REVERT: 5 86 MET cc_start: 0.2775 (mmm) cc_final: 0.1642 (pmm) REVERT: 6 58 ASP cc_start: 0.6865 (p0) cc_final: 0.6374 (t0) REVERT: b 137 THR cc_start: 0.7251 (m) cc_final: 0.6492 (p) REVERT: b 224 ARG cc_start: 0.5721 (mtm110) cc_final: 0.5375 (mmp-170) REVERT: c 17 TRP cc_start: 0.7946 (m-90) cc_final: 0.7729 (m-90) REVERT: c 64 ARG cc_start: 0.6875 (tmt90) cc_final: 0.6618 (ttp80) REVERT: c 125 ARG cc_start: 0.6731 (ttp-110) cc_final: 0.6164 (ttm110) REVERT: c 131 ARG cc_start: 0.7314 (mmm160) cc_final: 0.6957 (mmm160) REVERT: d 76 LYS cc_start: 0.7436 (ttmt) cc_final: 0.7096 (mtpt) REVERT: d 131 ILE cc_start: 0.8663 (mp) cc_final: 0.8404 (mm) REVERT: d 183 ARG cc_start: 0.5337 (pmt-80) cc_final: 0.5117 (ptt-90) REVERT: e 60 GLN cc_start: 0.8182 (pt0) cc_final: 0.7239 (pt0) REVERT: e 65 LYS cc_start: 0.8175 (mttm) cc_final: 0.7922 (mmmt) REVERT: e 68 ARG cc_start: 0.7834 (ptp90) cc_final: 0.7536 (ptp-110) REVERT: f 29 ILE cc_start: 0.7893 (mt) cc_final: 0.7601 (mt) REVERT: f 53 LYS cc_start: 0.5689 (OUTLIER) cc_final: 0.5063 (mmtm) REVERT: f 67 PRO cc_start: 0.8083 (Cg_endo) cc_final: 0.7636 (Cg_exo) REVERT: g 25 PHE cc_start: 0.8735 (t80) cc_final: 0.8229 (t80) REVERT: g 46 LEU cc_start: 0.7446 (mp) cc_final: 0.7107 (mt) REVERT: g 115 MET cc_start: 0.6917 (tpp) cc_final: 0.6507 (tpp) REVERT: h 42 GLU cc_start: 0.7403 (tp30) cc_final: 0.7129 (tp30) REVERT: i 104 THR cc_start: 0.8123 (m) cc_final: 0.7813 (p) REVERT: j 72 ARG cc_start: 0.7179 (mmt-90) cc_final: 0.6856 (mpt180) REVERT: j 88 MET cc_start: 0.5100 (tpt) cc_final: 0.4416 (mtm) REVERT: k 115 ILE cc_start: 0.8679 (mt) cc_final: 0.8419 (pt) REVERT: m 52 ILE cc_start: 0.8007 (mt) cc_final: 0.7630 (mt) REVERT: m 56 ARG cc_start: 0.5924 (mtt90) cc_final: 0.5677 (mtt90) REVERT: n 5 MET cc_start: 0.7431 (mmm) cc_final: 0.7215 (mmm) REVERT: n 34 ASN cc_start: 0.4692 (p0) cc_final: 0.4372 (p0) REVERT: n 43 ASN cc_start: 0.7875 (m-40) cc_final: 0.7487 (m110) REVERT: n 93 ILE cc_start: 0.8894 (OUTLIER) cc_final: 0.8666 (mt) REVERT: o 34 GLN cc_start: 0.8274 (tp-100) cc_final: 0.7984 (tp-100) REVERT: o 36 ASN cc_start: 0.8579 (m-40) cc_final: 0.8150 (m-40) REVERT: q 42 LYS cc_start: 0.7841 (mtpt) cc_final: 0.7487 (mtmt) REVERT: r 44 THR cc_start: 0.8336 (p) cc_final: 0.7993 (t) REVERT: t 33 LYS cc_start: 0.8431 (tppp) cc_final: 0.8140 (ttpp) REVERT: t 58 ASP cc_start: 0.7520 (m-30) cc_final: 0.7264 (m-30) REVERT: t 79 THR cc_start: 0.8656 (m) cc_final: 0.8359 (m) REVERT: v 138 TYR cc_start: 0.8153 (t80) cc_final: 0.7842 (t80) REVERT: v 321 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.7142 (mmp80) outliers start: 52 outliers final: 13 residues processed: 1916 average time/residue: 1.4470 time to fit residues: 4594.9578 Evaluate side-chains 1475 residues out of total 5060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 1456 time to evaluate : 6.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain K residue 69 VAL 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 P residue 99 LEU Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain f residue 53 LYS Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 6 ILE Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain n residue 93 ILE Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain v residue 321 ARG Chi-restraints excluded: chain v residue 340 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1059 random chunks: chunk 894 optimal weight: 3.9990 chunk 802 optimal weight: 7.9990 chunk 445 optimal weight: 4.9990 chunk 274 optimal weight: 10.0000 chunk 541 optimal weight: 3.9990 chunk 428 optimal weight: 10.0000 chunk 830 optimal weight: 3.9990 chunk 321 optimal weight: 0.9990 chunk 504 optimal weight: 0.9980 chunk 617 optimal weight: 1.9990 chunk 961 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 36 ASN C 114 GLN C 133 ASN ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 HIS D 49 GLN D 130 GLN D 164 GLN E 30 GLN E 156 ASN F 20 ASN F 80 GLN F 134 GLN G 47 ASN G 110 HIS G 138 GLN H 20 ASN ** H 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 GLN K 13 ASN M 13 HIS O 38 GLN Q 55 GLN R 18 GLN R 43 ASN R 89 HIS R 91 GLN ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 GLN T 15 HIS ** U 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 8 ASN X 16 ASN X 22 ASN X 33 HIS Y 25 GLN Y 58 ASN Z 8 GLN Z 19 HIS 0 41 HIS 2 6 GLN 3 27 ASN 3 42 HIS ** b 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 18 GLN b 23 ASN b 35 ASN b 108 GLN b 167 HIS ** b 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 101 ASN ** c 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 70 GLN d 73 ASN ** d 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 82 HIS g 147 ASN h 66 GLN i 4 GLN i 125 GLN j 56 HIS j 64 GLN l 45 ASN ** l 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 111 GLN m 7 ASN m 104 ASN o 37 HIS o 39 GLN p 59 HIS p 63 GLN ** q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 68 HIS t 60 GLN v 110 ASN v 185 GLN v 235 GLN ** v 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 160601 Z= 0.201 Angle : 0.673 13.955 239844 Z= 0.352 Chirality : 0.039 0.415 30593 Planarity : 0.006 0.155 13157 Dihedral : 23.858 179.728 79363 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.10 % Favored : 90.62 % Rotamer: Outliers : 3.95 % Allowed : 13.79 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.02 (0.09), residues: 6099 helix: -2.47 (0.10), residues: 1873 sheet: -2.64 (0.13), residues: 1088 loop : -2.81 (0.10), residues: 3138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP X 38 HIS 0.020 0.001 HIS f 37 PHE 0.058 0.002 PHE u 36 TYR 0.034 0.002 TYR b 21 ARG 0.013 0.001 ARG u 34 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12198 Ramachandran restraints generated. 6099 Oldfield, 0 Emsley, 6099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12198 Ramachandran restraints generated. 6099 Oldfield, 0 Emsley, 6099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1735 residues out of total 5060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 1536 time to evaluate : 6.351 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: C 131 MET cc_start: 0.7178 (mtm) cc_final: 0.6802 (mtm) REVERT: C 182 LYS cc_start: 0.8233 (mttt) cc_final: 0.8028 (mtpt) REVERT: D 7 LYS cc_start: 0.8246 (ttmt) cc_final: 0.7808 (tttm) REVERT: D 148 GLN cc_start: 0.9061 (mp10) cc_final: 0.8856 (mp10) REVERT: D 167 ASN cc_start: 0.8458 (t0) cc_final: 0.8087 (t0) REVERT: E 30 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7871 (tt0) REVERT: E 102 ARG cc_start: 0.7363 (mtm180) cc_final: 0.7111 (mtt180) REVERT: E 171 ASP cc_start: 0.7407 (t70) cc_final: 0.7139 (p0) REVERT: F 87 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8436 (pttm) REVERT: G 162 ARG cc_start: 0.7397 (ptp-170) cc_final: 0.6937 (mtm180) REVERT: I 99 LYS cc_start: 0.6021 (ptmt) cc_final: 0.5339 (mttp) REVERT: J 96 ARG cc_start: 0.7328 (mmm160) cc_final: 0.6850 (mmm160) REVERT: J 99 ARG cc_start: 0.7727 (mmm160) cc_final: 0.7172 (mpt180) REVERT: L 104 GLN cc_start: 0.8178 (mm110) cc_final: 0.7850 (mm110) REVERT: L 105 ILE cc_start: 0.8687 (mm) cc_final: 0.8438 (mt) REVERT: M 18 ARG cc_start: 0.7764 (ttm110) cc_final: 0.7222 (mtp85) REVERT: N 42 LYS cc_start: 0.9122 (mttm) cc_final: 0.8725 (mtmt) REVERT: N 102 PHE cc_start: 0.7929 (m-80) cc_final: 0.7577 (m-80) REVERT: P 9 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.7442 (mp10) REVERT: P 99 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7562 (tt) REVERT: Q 10 ARG cc_start: 0.8481 (mmm160) cc_final: 0.8176 (mmm160) REVERT: Q 12 ARG cc_start: 0.8188 (mtp85) cc_final: 0.7848 (ttm110) REVERT: Q 77 LYS cc_start: 0.8200 (mttt) cc_final: 0.7935 (mptt) REVERT: Q 94 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8513 (mt) REVERT: R 15 SER cc_start: 0.7295 (OUTLIER) cc_final: 0.6948 (p) REVERT: S 18 ARG cc_start: 0.8229 (ttm170) cc_final: 0.7890 (mtt90) REVERT: S 70 LYS cc_start: 0.7886 (mtpp) cc_final: 0.7588 (mtmm) REVERT: S 88 ARG cc_start: 0.7612 (mmm-85) cc_final: 0.7304 (mmm-85) REVERT: T 15 HIS cc_start: 0.7596 (t70) cc_final: 0.7343 (t-90) REVERT: T 30 ILE cc_start: 0.8228 (tt) cc_final: 0.7981 (pt) REVERT: U 60 LYS cc_start: 0.8229 (ttmt) cc_final: 0.7989 (ptmm) REVERT: U 86 PHE cc_start: 0.7574 (m-80) cc_final: 0.7292 (m-80) REVERT: W 40 LYS cc_start: 0.8135 (tptt) cc_final: 0.7924 (tppt) REVERT: W 64 LYS cc_start: 0.8207 (tptm) cc_final: 0.7754 (ttpp) REVERT: W 76 ILE cc_start: 0.8316 (mt) cc_final: 0.7703 (tt) REVERT: X 51 SER cc_start: 0.8746 (p) cc_final: 0.8484 (p) REVERT: Y 38 GLN cc_start: 0.7139 (tp40) cc_final: 0.6447 (pm20) REVERT: 0 31 LYS cc_start: 0.8374 (tttt) cc_final: 0.8008 (ttmm) REVERT: 1 29 LYS cc_start: 0.8116 (mmtt) cc_final: 0.6828 (ptmm) REVERT: 2 1 MET cc_start: 0.5895 (ptm) cc_final: 0.4734 (ptm) REVERT: 5 1 MET cc_start: 0.1155 (tpt) cc_final: 0.0179 (tpt) REVERT: 5 86 MET cc_start: 0.2452 (mmm) cc_final: 0.1613 (pmm) REVERT: 6 3 LYS cc_start: 0.7523 (ttpp) cc_final: 0.7304 (ttpp) REVERT: 6 58 ASP cc_start: 0.6955 (p0) cc_final: 0.6632 (t0) REVERT: 6 60 PHE cc_start: 0.7095 (t80) cc_final: 0.6660 (t80) REVERT: b 21 TYR cc_start: 0.7397 (p90) cc_final: 0.7160 (p90) REVERT: b 23 ASN cc_start: 0.7407 (t0) cc_final: 0.7194 (t0) REVERT: b 224 ARG cc_start: 0.5776 (mtm110) cc_final: 0.5205 (mmp-170) REVERT: c 97 PRO cc_start: 0.6885 (OUTLIER) cc_final: 0.6605 (Cg_endo) REVERT: c 131 ARG cc_start: 0.7515 (mmm160) cc_final: 0.7128 (mmm160) REVERT: d 11 SER cc_start: 0.8192 (m) cc_final: 0.7712 (p) REVERT: d 76 LYS cc_start: 0.7631 (ttmt) cc_final: 0.7111 (mtpt) REVERT: e 28 ARG cc_start: 0.8341 (ptp-170) cc_final: 0.8124 (ptp-110) REVERT: e 68 ARG cc_start: 0.7767 (ptp90) cc_final: 0.7471 (ptp-110) REVERT: e 155 LYS cc_start: 0.7753 (mtmt) cc_final: 0.7217 (mtpt) REVERT: f 5 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7545 (mt-10) REVERT: f 29 ILE cc_start: 0.7907 (mt) cc_final: 0.7683 (mt) REVERT: f 38 ARG cc_start: 0.7620 (mmm-85) cc_final: 0.7281 (mtp180) REVERT: g 25 PHE cc_start: 0.8651 (t80) cc_final: 0.8317 (t80) REVERT: g 115 MET cc_start: 0.6829 (tpp) cc_final: 0.6432 (tpp) REVERT: j 88 MET cc_start: 0.5230 (tpt) cc_final: 0.4285 (mtm) REVERT: k 56 LYS cc_start: 0.8417 (ttpp) cc_final: 0.8136 (ttpp) REVERT: k 97 ARG cc_start: 0.7365 (mtm-85) cc_final: 0.7048 (mmt90) REVERT: k 115 ILE cc_start: 0.8715 (mt) cc_final: 0.8397 (pt) REVERT: l 69 GLU cc_start: 0.6427 (mt-10) cc_final: 0.6179 (mt-10) REVERT: n 43 ASN cc_start: 0.7725 (m-40) cc_final: 0.7331 (m110) REVERT: o 36 ASN cc_start: 0.8395 (m-40) cc_final: 0.8044 (m-40) REVERT: o 72 LYS cc_start: 0.8266 (tttp) cc_final: 0.7902 (tttm) REVERT: t 33 LYS cc_start: 0.8352 (tppp) cc_final: 0.8071 (ttpp) REVERT: v 110 ASN cc_start: 0.6539 (OUTLIER) cc_final: 0.6263 (m110) outliers start: 199 outliers final: 126 residues processed: 1628 average time/residue: 1.3884 time to fit residues: 3789.3665 Evaluate side-chains 1548 residues out of total 5060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 1414 time to evaluate : 6.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 49 GLN Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 105 LYS Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 30 GLN Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 86 CYS Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 98 GLU Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 136 MET Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 93 ASP Chi-restraints excluded: chain P residue 9 GLN Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 54 GLU Chi-restraints excluded: chain U residue 92 VAL Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 29 VAL Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 6 residue 24 ILE Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 59 ILE Chi-restraints excluded: chain b residue 71 THR Chi-restraints excluded: chain b residue 139 GLU Chi-restraints excluded: chain b residue 163 ILE Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 190 SER Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 97 PRO Chi-restraints excluded: chain c residue 164 THR Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 137 SER Chi-restraints excluded: chain d residue 142 VAL Chi-restraints excluded: chain d residue 170 LEU Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain e residue 23 THR Chi-restraints excluded: chain e residue 105 ILE Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 133 ILE Chi-restraints excluded: chain e residue 152 VAL Chi-restraints excluded: chain f residue 53 LYS Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 6 ILE Chi-restraints excluded: chain g residue 48 THR Chi-restraints excluded: chain h residue 38 VAL Chi-restraints excluded: chain h residue 45 ILE Chi-restraints excluded: chain h residue 59 GLU Chi-restraints excluded: chain h residue 63 LYS Chi-restraints excluded: chain h residue 84 ILE Chi-restraints excluded: chain i residue 72 SER Chi-restraints excluded: chain i residue 90 ASP Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 54 SER Chi-restraints excluded: chain l residue 76 HIS Chi-restraints excluded: chain l residue 78 VAL Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 15 VAL Chi-restraints excluded: chain m residue 16 ILE Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 75 SER Chi-restraints excluded: chain m residue 82 LEU Chi-restraints excluded: chain n residue 45 VAL Chi-restraints excluded: chain o residue 3 SER Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 78 VAL Chi-restraints excluded: chain q residue 28 VAL Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain s residue 14 LEU Chi-restraints excluded: chain s residue 24 SER Chi-restraints excluded: chain s residue 30 LEU Chi-restraints excluded: chain s residue 38 THR Chi-restraints excluded: chain s residue 50 VAL Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain v residue 110 ASN Chi-restraints excluded: chain v residue 209 LEU Chi-restraints excluded: chain v residue 224 ILE Chi-restraints excluded: chain v residue 226 THR Chi-restraints excluded: chain v residue 340 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1059 random chunks: chunk 534 optimal weight: 1.9990 chunk 298 optimal weight: 10.0000 chunk 800 optimal weight: 4.9990 chunk 654 optimal weight: 20.0000 chunk 265 optimal weight: 10.0000 chunk 963 optimal weight: 9.9990 chunk 1040 optimal weight: 10.0000 chunk 858 optimal weight: 0.5980 chunk 955 optimal weight: 0.0870 chunk 328 optimal weight: 0.0270 chunk 772 optimal weight: 10.0000 overall best weight: 1.5420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN F 134 GLN H 66 ASN ** I 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 GLN P 6 GLN Q 36 GLN Q 55 GLN R 18 GLN ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 GLN ** U 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 15 ASN X 16 ASN X 22 ASN b 17 HIS b 202 ASN ** c 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 73 ASN d 119 HIS ** d 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 60 GLN ** e 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 14 GLN ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 56 HIS k 14 GLN k 63 GLN ** l 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 7 ASN m 104 ASN t 60 GLN v 110 ASN ** v 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 160601 Z= 0.164 Angle : 0.593 11.941 239844 Z= 0.311 Chirality : 0.036 0.362 30593 Planarity : 0.005 0.145 13157 Dihedral : 23.610 179.460 79349 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.49 % Favored : 90.33 % Rotamer: Outliers : 4.95 % Allowed : 16.22 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.10), residues: 6099 helix: -1.59 (0.11), residues: 1900 sheet: -2.34 (0.14), residues: 1106 loop : -2.57 (0.10), residues: 3093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP s 33 HIS 0.009 0.001 HIS f 11 PHE 0.052 0.002 PHE u 36 TYR 0.025 0.002 TYR b 21 ARG 0.008 0.001 ARG M 50 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12198 Ramachandran restraints generated. 6099 Oldfield, 0 Emsley, 6099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12198 Ramachandran restraints generated. 6099 Oldfield, 0 Emsley, 6099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1732 residues out of total 5060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 1483 time to evaluate : 6.410 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: C 131 MET cc_start: 0.7259 (mtm) cc_final: 0.6963 (mtm) REVERT: D 7 LYS cc_start: 0.8285 (ttmt) cc_final: 0.7744 (tttm) REVERT: D 167 ASN cc_start: 0.8434 (t0) cc_final: 0.8043 (t0) REVERT: D 184 ARG cc_start: 0.6669 (mmm-85) cc_final: 0.5989 (mmm-85) REVERT: G 162 ARG cc_start: 0.7333 (ptp-170) cc_final: 0.6901 (mtm180) REVERT: I 99 LYS cc_start: 0.5610 (ptmt) cc_final: 0.5264 (mttp) REVERT: J 96 ARG cc_start: 0.7351 (mmm160) cc_final: 0.6868 (mmm160) REVERT: K 20 MET cc_start: 0.8119 (ttt) cc_final: 0.7749 (ttm) REVERT: L 2 ARG cc_start: 0.7121 (mtp180) cc_final: 0.6764 (mtm-85) REVERT: L 104 GLN cc_start: 0.8093 (mm110) cc_final: 0.7738 (mm110) REVERT: M 18 ARG cc_start: 0.7669 (ttm110) cc_final: 0.7262 (mtp85) REVERT: N 102 PHE cc_start: 0.7995 (m-80) cc_final: 0.7759 (m-80) REVERT: O 80 GLU cc_start: 0.8088 (mp0) cc_final: 0.7881 (mp0) REVERT: P 9 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.7498 (mp10) REVERT: Q 12 ARG cc_start: 0.8112 (mtp85) cc_final: 0.7829 (ttm110) REVERT: R 15 SER cc_start: 0.7026 (m) cc_final: 0.6787 (p) REVERT: R 18 GLN cc_start: 0.5581 (pt0) cc_final: 0.5296 (pt0) REVERT: S 1 MET cc_start: 0.6272 (tmm) cc_final: 0.6066 (tmm) REVERT: S 70 LYS cc_start: 0.7841 (mtpp) cc_final: 0.7633 (mtmm) REVERT: T 30 ILE cc_start: 0.8320 (tt) cc_final: 0.8100 (pt) REVERT: T 91 GLN cc_start: 0.5106 (OUTLIER) cc_final: 0.4310 (tt0) REVERT: U 58 VAL cc_start: 0.8636 (t) cc_final: 0.8381 (m) REVERT: U 60 LYS cc_start: 0.8123 (ttmt) cc_final: 0.7911 (ttpt) REVERT: U 86 PHE cc_start: 0.7387 (m-80) cc_final: 0.7141 (m-80) REVERT: W 40 LYS cc_start: 0.8088 (tptt) cc_final: 0.7843 (tppt) REVERT: W 64 LYS cc_start: 0.8220 (tptm) cc_final: 0.7844 (ttpt) REVERT: X 51 SER cc_start: 0.8859 (p) cc_final: 0.8590 (p) REVERT: 0 31 LYS cc_start: 0.8325 (tttt) cc_final: 0.8065 (ttmm) REVERT: 1 29 LYS cc_start: 0.8113 (mmtt) cc_final: 0.6804 (ptmm) REVERT: 2 1 MET cc_start: 0.5783 (ptm) cc_final: 0.4644 (ptm) REVERT: 2 22 MET cc_start: 0.8013 (tpt) cc_final: 0.7792 (mmm) REVERT: 3 14 LYS cc_start: 0.8295 (mmtp) cc_final: 0.7974 (mptt) REVERT: 5 1 MET cc_start: 0.1187 (tpt) cc_final: 0.0168 (tpt) REVERT: 5 74 ASP cc_start: 0.2273 (OUTLIER) cc_final: 0.1984 (m-30) REVERT: 5 86 MET cc_start: 0.2466 (mmm) cc_final: 0.1559 (pmm) REVERT: b 224 ARG cc_start: 0.5815 (mtm110) cc_final: 0.4892 (mmt180) REVERT: c 54 ILE cc_start: 0.8000 (pt) cc_final: 0.7756 (mt) REVERT: c 84 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7192 (tm-30) REVERT: c 97 PRO cc_start: 0.6634 (OUTLIER) cc_final: 0.6362 (Cg_endo) REVERT: c 135 ARG cc_start: 0.7199 (mtt180) cc_final: 0.6774 (mtt-85) REVERT: c 184 ASN cc_start: 0.7959 (t0) cc_final: 0.7557 (t0) REVERT: d 76 LYS cc_start: 0.7596 (ttmt) cc_final: 0.7085 (mtpt) REVERT: e 68 ARG cc_start: 0.7711 (ptp90) cc_final: 0.7119 (ttp-110) REVERT: e 127 TYR cc_start: 0.8550 (m-80) cc_final: 0.8131 (m-80) REVERT: e 151 MET cc_start: 0.7565 (mtt) cc_final: 0.7343 (mtm) REVERT: e 155 LYS cc_start: 0.7729 (mtmt) cc_final: 0.7165 (pttp) REVERT: f 53 LYS cc_start: 0.6543 (OUTLIER) cc_final: 0.5779 (ttmt) REVERT: f 55 HIS cc_start: 0.6736 (OUTLIER) cc_final: 0.6188 (m-70) REVERT: g 25 PHE cc_start: 0.8671 (t80) cc_final: 0.8393 (t80) REVERT: g 115 MET cc_start: 0.6840 (tpp) cc_final: 0.6501 (tpp) REVERT: h 26 MET cc_start: 0.7108 (OUTLIER) cc_final: 0.6533 (ptp) REVERT: i 31 GLN cc_start: 0.7929 (mp10) cc_final: 0.7647 (mp10) REVERT: j 88 MET cc_start: 0.5462 (tpt) cc_final: 0.5123 (mmm) REVERT: k 56 LYS cc_start: 0.8670 (ttpp) cc_final: 0.8303 (tttp) REVERT: k 82 GLU cc_start: 0.7245 (mm-30) cc_final: 0.7043 (mm-30) REVERT: k 115 ILE cc_start: 0.8720 (mt) cc_final: 0.8391 (pt) REVERT: l 69 GLU cc_start: 0.6236 (mt-10) cc_final: 0.6033 (mt-10) REVERT: n 43 ASN cc_start: 0.7608 (m-40) cc_final: 0.7257 (m110) REVERT: n 97 LYS cc_start: 0.8464 (pttt) cc_final: 0.8084 (pttm) REVERT: o 36 ASN cc_start: 0.8444 (m-40) cc_final: 0.8220 (m-40) REVERT: o 72 LYS cc_start: 0.8192 (tttp) cc_final: 0.7856 (tttm) REVERT: t 28 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.7100 (mtm110) REVERT: t 33 LYS cc_start: 0.8197 (tppp) cc_final: 0.7931 (ttpp) REVERT: t 52 GLU cc_start: 0.6360 (OUTLIER) cc_final: 0.6118 (tt0) REVERT: v 288 GLN cc_start: 0.8154 (tp40) cc_final: 0.7783 (tt0) outliers start: 249 outliers final: 162 residues processed: 1605 average time/residue: 1.3766 time to fit residues: 3726.9397 Evaluate side-chains 1536 residues out of total 5060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 1364 time to evaluate : 5.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 86 CYS Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 98 GLU Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 136 MET Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain P residue 9 GLN Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 36 LYS Chi-restraints excluded: chain P residue 38 ARG Chi-restraints excluded: chain P residue 65 ASN Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 103 VAL Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 91 GLN Chi-restraints excluded: chain U residue 92 VAL Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 60 ASP Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain X residue 16 ASN Chi-restraints excluded: chain Y residue 39 GLN Chi-restraints excluded: chain 0 residue 6 LYS Chi-restraints excluded: chain 0 residue 10 SER Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 29 VAL Chi-restraints excluded: chain 1 residue 11 VAL Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 5 residue 54 VAL Chi-restraints excluded: chain 5 residue 74 ASP Chi-restraints excluded: chain 6 residue 12 ILE Chi-restraints excluded: chain 6 residue 24 ILE Chi-restraints excluded: chain b residue 71 THR Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 139 GLU Chi-restraints excluded: chain b residue 162 VAL Chi-restraints excluded: chain b residue 163 ILE Chi-restraints excluded: chain b residue 182 VAL Chi-restraints excluded: chain b residue 206 ILE Chi-restraints excluded: chain c residue 84 GLU Chi-restraints excluded: chain c residue 97 PRO Chi-restraints excluded: chain c residue 164 THR Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 20 LEU Chi-restraints excluded: chain d residue 116 LEU Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 137 SER Chi-restraints excluded: chain d residue 170 LEU Chi-restraints excluded: chain d residue 172 VAL Chi-restraints excluded: chain d residue 177 MET Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain e residue 10 LEU Chi-restraints excluded: chain e residue 105 ILE Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 133 ILE Chi-restraints excluded: chain e residue 152 VAL Chi-restraints excluded: chain f residue 26 THR Chi-restraints excluded: chain f residue 53 LYS Chi-restraints excluded: chain f residue 55 HIS Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 6 ILE Chi-restraints excluded: chain g residue 48 THR Chi-restraints excluded: chain h residue 26 MET Chi-restraints excluded: chain h residue 38 VAL Chi-restraints excluded: chain h residue 54 THR Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 124 ILE Chi-restraints excluded: chain i residue 38 PHE Chi-restraints excluded: chain i residue 90 ASP Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 91 ASP Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 31 VAL Chi-restraints excluded: chain k residue 54 SER Chi-restraints excluded: chain k residue 81 LEU Chi-restraints excluded: chain l residue 2 THR Chi-restraints excluded: chain l residue 76 HIS Chi-restraints excluded: chain l residue 78 VAL Chi-restraints excluded: chain l residue 103 CYS Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 59 VAL Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain n residue 45 VAL Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain p residue 78 VAL Chi-restraints excluded: chain q residue 28 VAL Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain q residue 75 VAL Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain s residue 14 LEU Chi-restraints excluded: chain s residue 24 SER Chi-restraints excluded: chain s residue 30 LEU Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain t residue 28 ARG Chi-restraints excluded: chain t residue 52 GLU Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain v residue 126 LEU Chi-restraints excluded: chain v residue 136 SER Chi-restraints excluded: chain v residue 187 VAL Chi-restraints excluded: chain v residue 209 LEU Chi-restraints excluded: chain v residue 224 ILE Chi-restraints excluded: chain v residue 226 THR Chi-restraints excluded: chain v residue 229 SER Chi-restraints excluded: chain v residue 340 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1059 random chunks: chunk 951 optimal weight: 3.9990 chunk 724 optimal weight: 10.0000 chunk 499 optimal weight: 6.9990 chunk 106 optimal weight: 20.0000 chunk 459 optimal weight: 10.0000 chunk 646 optimal weight: 10.0000 chunk 966 optimal weight: 8.9990 chunk 1023 optimal weight: 0.0770 chunk 505 optimal weight: 9.9990 chunk 916 optimal weight: 8.9990 chunk 275 optimal weight: 10.0000 overall best weight: 5.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 30 GLN F 134 GLN ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN Q 71 ASN R 12 HIS ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 48 GLN ** U 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 22 ASN Y 31 GLN 2 6 GLN 4 35 GLN ** 5 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 96 GLN ** f 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 111 GLN ** m 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 104 ASN n 49 GLN ** o 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 36 ASN o 37 HIS ** v 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 160601 Z= 0.421 Angle : 0.782 12.574 239844 Z= 0.397 Chirality : 0.045 0.386 30593 Planarity : 0.006 0.095 13157 Dihedral : 23.657 177.207 79345 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.38 % Favored : 88.39 % Rotamer: Outliers : 7.27 % Allowed : 17.37 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.10), residues: 6099 helix: -1.49 (0.11), residues: 1879 sheet: -2.30 (0.14), residues: 1085 loop : -2.60 (0.10), residues: 3135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.003 TRP s 33 HIS 0.024 0.002 HIS X 33 PHE 0.045 0.003 PHE u 36 TYR 0.023 0.002 TYR F 6 ARG 0.009 0.001 ARG m 28 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12198 Ramachandran restraints generated. 6099 Oldfield, 0 Emsley, 6099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12198 Ramachandran restraints generated. 6099 Oldfield, 0 Emsley, 6099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1773 residues out of total 5060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 366 poor density : 1407 time to evaluate : 6.390 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: C 96 LYS cc_start: 0.7749 (tptt) cc_final: 0.7538 (ttpp) REVERT: C 113 ASP cc_start: 0.7565 (m-30) cc_final: 0.7211 (m-30) REVERT: C 131 MET cc_start: 0.7271 (mtm) cc_final: 0.7010 (mtm) REVERT: D 148 GLN cc_start: 0.8990 (mp10) cc_final: 0.8787 (mp10) REVERT: D 167 ASN cc_start: 0.8587 (t0) cc_final: 0.8201 (t0) REVERT: E 200 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.7017 (mp) REVERT: F 71 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.7969 (pttm) REVERT: G 162 ARG cc_start: 0.7384 (ptp-170) cc_final: 0.6745 (mtm180) REVERT: I 99 LYS cc_start: 0.6028 (ptmt) cc_final: 0.5430 (mttp) REVERT: J 56 VAL cc_start: 0.8812 (OUTLIER) cc_final: 0.8605 (p) REVERT: J 80 HIS cc_start: 0.7996 (OUTLIER) cc_final: 0.6712 (t-90) REVERT: J 96 ARG cc_start: 0.7524 (mmm160) cc_final: 0.7004 (mmm160) REVERT: J 99 ARG cc_start: 0.7756 (mmm160) cc_final: 0.7039 (mpt180) REVERT: K 85 VAL cc_start: 0.9136 (OUTLIER) cc_final: 0.8902 (p) REVERT: L 2 ARG cc_start: 0.7047 (mtp180) cc_final: 0.6772 (mtm-85) REVERT: M 18 ARG cc_start: 0.7654 (ttm110) cc_final: 0.7369 (mtm-85) REVERT: P 9 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.7519 (mp10) REVERT: P 38 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7617 (mtm110) REVERT: Q 12 ARG cc_start: 0.8131 (mtp85) cc_final: 0.7806 (ttm110) REVERT: Q 77 LYS cc_start: 0.8345 (mttt) cc_final: 0.8028 (mptt) REVERT: Q 94 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8771 (mt) REVERT: R 15 SER cc_start: 0.7238 (OUTLIER) cc_final: 0.6889 (p) REVERT: R 18 GLN cc_start: 0.5968 (pt0) cc_final: 0.5756 (pt0) REVERT: S 1 MET cc_start: 0.6482 (tmm) cc_final: 0.5946 (tmm) REVERT: S 70 LYS cc_start: 0.7809 (mtpp) cc_final: 0.7578 (mtmm) REVERT: T 30 ILE cc_start: 0.8418 (tt) cc_final: 0.8176 (pt) REVERT: T 50 LEU cc_start: 0.8739 (mp) cc_final: 0.8505 (mp) REVERT: U 60 LYS cc_start: 0.8196 (ttmt) cc_final: 0.7930 (ttpt) REVERT: U 86 PHE cc_start: 0.7436 (m-80) cc_final: 0.7179 (m-80) REVERT: W 64 LYS cc_start: 0.8251 (tptm) cc_final: 0.7862 (ttpt) REVERT: X 51 SER cc_start: 0.9074 (p) cc_final: 0.8718 (p) REVERT: Y 38 GLN cc_start: 0.7245 (tp40) cc_final: 0.6843 (mp10) REVERT: 0 31 LYS cc_start: 0.8410 (tttt) cc_final: 0.8085 (ttmm) REVERT: 1 24 LYS cc_start: 0.7183 (OUTLIER) cc_final: 0.6695 (tttp) REVERT: 2 1 MET cc_start: 0.6035 (ptm) cc_final: 0.4720 (ptm) REVERT: 5 1 MET cc_start: 0.1875 (tpt) cc_final: 0.0540 (tpt) REVERT: 5 74 ASP cc_start: 0.2439 (OUTLIER) cc_final: 0.1995 (m-30) REVERT: 5 86 MET cc_start: 0.2281 (mmm) cc_final: 0.1452 (pmm) REVERT: 6 60 PHE cc_start: 0.6942 (t80) cc_final: 0.6535 (t80) REVERT: b 108 GLN cc_start: 0.7045 (OUTLIER) cc_final: 0.6812 (pt0) REVERT: b 224 ARG cc_start: 0.5916 (mtm110) cc_final: 0.5000 (mmt180) REVERT: c 57 GLU cc_start: 0.7055 (pm20) cc_final: 0.6773 (pm20) REVERT: d 76 LYS cc_start: 0.7659 (ttmt) cc_final: 0.7178 (mtpt) REVERT: d 115 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.7188 (tt0) REVERT: f 55 HIS cc_start: 0.6643 (OUTLIER) cc_final: 0.6354 (m-70) REVERT: g 25 PHE cc_start: 0.8761 (t80) cc_final: 0.8517 (t80) REVERT: g 115 MET cc_start: 0.6997 (tpp) cc_final: 0.6524 (tpp) REVERT: g 117 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7538 (tp) REVERT: i 31 GLN cc_start: 0.8007 (mp10) cc_final: 0.7633 (mp10) REVERT: i 118 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7953 (ttp80) REVERT: k 36 ARG cc_start: 0.7145 (mmm-85) cc_final: 0.6786 (mtt-85) REVERT: k 115 ILE cc_start: 0.8757 (mt) cc_final: 0.8459 (pt) REVERT: l 69 GLU cc_start: 0.6489 (mt-10) cc_final: 0.6241 (mt-10) REVERT: m 28 ARG cc_start: 0.7306 (tpt170) cc_final: 0.6696 (tpt170) REVERT: n 43 ASN cc_start: 0.7534 (m-40) cc_final: 0.7040 (m110) REVERT: o 36 ASN cc_start: 0.8483 (m110) cc_final: 0.8240 (m-40) REVERT: o 72 LYS cc_start: 0.8387 (tttp) cc_final: 0.7945 (tttm) REVERT: p 5 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.6794 (ptt-90) REVERT: p 18 GLN cc_start: 0.7300 (OUTLIER) cc_final: 0.7041 (tp40) REVERT: p 56 ARG cc_start: 0.7700 (mmm-85) cc_final: 0.7273 (mmm160) REVERT: t 28 ARG cc_start: 0.7445 (OUTLIER) cc_final: 0.7080 (mtm110) REVERT: t 33 LYS cc_start: 0.8380 (tppp) cc_final: 0.8165 (ttpp) REVERT: v 138 TYR cc_start: 0.7987 (t80) cc_final: 0.7740 (t80) REVERT: v 288 GLN cc_start: 0.8170 (tp40) cc_final: 0.7839 (tt0) outliers start: 366 outliers final: 270 residues processed: 1589 average time/residue: 1.4565 time to fit residues: 3943.1178 Evaluate side-chains 1657 residues out of total 5060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 289 poor density : 1368 time to evaluate : 6.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 238 ASN Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 145 ASP Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 50 ASP Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 71 LYS Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 86 CYS Chi-restraints excluded: chain F residue 139 GLU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain M residue 136 MET Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain P residue 9 GLN Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 36 LYS Chi-restraints excluded: chain P residue 38 ARG Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 65 ASN Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 113 LEU Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 73 ILE Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 103 VAL Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain U residue 92 VAL Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain V residue 48 MET Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 89 ILE Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain X residue 16 ASN Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain Y residue 27 ASN Chi-restraints excluded: chain Y residue 39 GLN Chi-restraints excluded: chain Y residue 53 VAL Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 6 LYS Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 29 VAL Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 1 residue 11 VAL Chi-restraints excluded: chain 1 residue 24 LYS Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 1 residue 43 ARG Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 49 VAL Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain 5 residue 54 VAL Chi-restraints excluded: chain 5 residue 55 VAL Chi-restraints excluded: chain 5 residue 74 ASP Chi-restraints excluded: chain 6 residue 24 ILE Chi-restraints excluded: chain b residue 29 PHE Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 71 THR Chi-restraints excluded: chain b residue 108 GLN Chi-restraints excluded: chain b residue 110 ILE Chi-restraints excluded: chain b residue 139 GLU Chi-restraints excluded: chain b residue 163 ILE Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 182 VAL Chi-restraints excluded: chain b residue 190 SER Chi-restraints excluded: chain b residue 206 ILE Chi-restraints excluded: chain b residue 220 VAL Chi-restraints excluded: chain c residue 54 ILE Chi-restraints excluded: chain c residue 63 ILE Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 113 LYS Chi-restraints excluded: chain c residue 164 THR Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 185 THR Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 20 LEU Chi-restraints excluded: chain d residue 27 ILE Chi-restraints excluded: chain d residue 115 GLN Chi-restraints excluded: chain d residue 116 LEU Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 133 SER Chi-restraints excluded: chain d residue 137 SER Chi-restraints excluded: chain d residue 170 LEU Chi-restraints excluded: chain d residue 172 VAL Chi-restraints excluded: chain d residue 177 MET Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain e residue 10 LEU Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain e residue 87 VAL Chi-restraints excluded: chain e residue 105 ILE Chi-restraints excluded: chain e residue 115 GLU Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 152 VAL Chi-restraints excluded: chain f residue 26 THR Chi-restraints excluded: chain f residue 30 THR Chi-restraints excluded: chain f residue 53 LYS Chi-restraints excluded: chain f residue 55 HIS Chi-restraints excluded: chain f residue 63 ASN Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 6 ILE Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 42 VAL Chi-restraints excluded: chain g residue 48 THR Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain h residue 26 MET Chi-restraints excluded: chain h residue 38 VAL Chi-restraints excluded: chain h residue 45 ILE Chi-restraints excluded: chain h residue 54 THR Chi-restraints excluded: chain h residue 63 LYS Chi-restraints excluded: chain h residue 84 ILE Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 124 ILE Chi-restraints excluded: chain i residue 38 PHE Chi-restraints excluded: chain i residue 55 ASP Chi-restraints excluded: chain i residue 62 LEU Chi-restraints excluded: chain i residue 65 THR Chi-restraints excluded: chain i residue 84 ARG Chi-restraints excluded: chain i residue 90 ASP Chi-restraints excluded: chain i residue 110 VAL Chi-restraints excluded: chain i residue 118 ARG Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 71 LEU Chi-restraints excluded: chain k residue 31 VAL Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 54 SER Chi-restraints excluded: chain k residue 71 ASP Chi-restraints excluded: chain k residue 81 LEU Chi-restraints excluded: chain k residue 111 ASP Chi-restraints excluded: chain l residue 2 THR Chi-restraints excluded: chain l residue 3 VAL Chi-restraints excluded: chain l residue 76 HIS Chi-restraints excluded: chain l residue 78 VAL Chi-restraints excluded: chain l residue 101 LEU Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 71 GLU Chi-restraints excluded: chain m residue 75 SER Chi-restraints excluded: chain n residue 45 VAL Chi-restraints excluded: chain o residue 3 SER Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain p residue 3 THR Chi-restraints excluded: chain p residue 5 ARG Chi-restraints excluded: chain p residue 18 GLN Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain p residue 78 VAL Chi-restraints excluded: chain q residue 19 SER Chi-restraints excluded: chain q residue 28 VAL Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 47 ASP Chi-restraints excluded: chain q residue 75 VAL Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 14 LEU Chi-restraints excluded: chain s residue 24 SER Chi-restraints excluded: chain s residue 30 LEU Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 11 ILE Chi-restraints excluded: chain t residue 28 ARG Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 43 GLU Chi-restraints excluded: chain u residue 52 VAL Chi-restraints excluded: chain v residue 126 LEU Chi-restraints excluded: chain v residue 136 SER Chi-restraints excluded: chain v residue 162 ILE Chi-restraints excluded: chain v residue 224 ILE Chi-restraints excluded: chain v residue 226 THR Chi-restraints excluded: chain v residue 229 SER Chi-restraints excluded: chain v residue 333 MET Chi-restraints excluded: chain v residue 338 ASP Chi-restraints excluded: chain v residue 340 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1059 random chunks: chunk 852 optimal weight: 0.8980 chunk 581 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 762 optimal weight: 10.0000 chunk 422 optimal weight: 20.0000 chunk 873 optimal weight: 3.9990 chunk 707 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 522 optimal weight: 0.7980 chunk 918 optimal weight: 2.9990 chunk 258 optimal weight: 5.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 GLN ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 44 HIS ** U 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 31 GLN ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 101 ASN ** c 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 14 GLN h 3 GLN ** k 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 7 ASN ** m 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 104 ASN ** o 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 235 GLN ** v 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 160601 Z= 0.210 Angle : 0.622 12.208 239844 Z= 0.324 Chirality : 0.038 0.373 30593 Planarity : 0.005 0.076 13157 Dihedral : 23.592 178.248 79345 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.54 % Favored : 90.28 % Rotamer: Outliers : 6.20 % Allowed : 19.12 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.10), residues: 6099 helix: -1.08 (0.12), residues: 1891 sheet: -2.12 (0.14), residues: 1091 loop : -2.45 (0.10), residues: 3117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP s 33 HIS 0.009 0.001 HIS f 11 PHE 0.033 0.002 PHE u 36 TYR 0.021 0.002 TYR C 160 ARG 0.011 0.001 ARG u 6 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12198 Ramachandran restraints generated. 6099 Oldfield, 0 Emsley, 6099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12198 Ramachandran restraints generated. 6099 Oldfield, 0 Emsley, 6099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1729 residues out of total 5060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 312 poor density : 1417 time to evaluate : 6.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 131 MET cc_start: 0.7228 (mtm) cc_final: 0.6989 (mtm) REVERT: C 269 ARG cc_start: 0.6765 (mmm160) cc_final: 0.6343 (mmm160) REVERT: D 7 LYS cc_start: 0.8201 (ttmt) cc_final: 0.7717 (mtpp) REVERT: D 148 GLN cc_start: 0.8982 (mp10) cc_final: 0.8770 (mp10) REVERT: D 167 ASN cc_start: 0.8530 (t0) cc_final: 0.8169 (t0) REVERT: E 200 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7207 (mp) REVERT: G 162 ARG cc_start: 0.7356 (ptp-170) cc_final: 0.6916 (mtm180) REVERT: I 99 LYS cc_start: 0.5675 (ptmt) cc_final: 0.5466 (mttp) REVERT: J 80 HIS cc_start: 0.7924 (OUTLIER) cc_final: 0.6524 (t-90) REVERT: J 96 ARG cc_start: 0.7381 (mmm160) cc_final: 0.6823 (mmm160) REVERT: K 20 MET cc_start: 0.7904 (ttt) cc_final: 0.7644 (ttm) REVERT: K 85 VAL cc_start: 0.9056 (OUTLIER) cc_final: 0.8801 (p) REVERT: M 18 ARG cc_start: 0.7559 (ttm110) cc_final: 0.6919 (mtp85) REVERT: N 102 PHE cc_start: 0.7940 (m-80) cc_final: 0.7705 (m-80) REVERT: O 80 GLU cc_start: 0.8178 (mp0) cc_final: 0.7911 (mm-30) REVERT: P 9 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.7450 (mp10) REVERT: P 28 LYS cc_start: 0.8788 (mttt) cc_final: 0.8352 (mtpp) REVERT: Q 12 ARG cc_start: 0.8141 (mtp85) cc_final: 0.7845 (ttm110) REVERT: Q 77 LYS cc_start: 0.8287 (mttt) cc_final: 0.8069 (mptt) REVERT: Q 94 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8697 (mt) REVERT: R 15 SER cc_start: 0.7027 (OUTLIER) cc_final: 0.6783 (p) REVERT: S 1 MET cc_start: 0.6383 (tmm) cc_final: 0.5392 (tmm) REVERT: T 30 ILE cc_start: 0.8343 (tt) cc_final: 0.8071 (pt) REVERT: T 50 LEU cc_start: 0.8714 (mp) cc_final: 0.8505 (mp) REVERT: U 60 LYS cc_start: 0.8137 (ttmt) cc_final: 0.7858 (ttpt) REVERT: U 86 PHE cc_start: 0.7431 (m-80) cc_final: 0.7164 (m-80) REVERT: W 21 ARG cc_start: 0.8289 (mmt90) cc_final: 0.7932 (mmt-90) REVERT: W 64 LYS cc_start: 0.8218 (tptm) cc_final: 0.7825 (ttpt) REVERT: X 51 SER cc_start: 0.8792 (p) cc_final: 0.8510 (p) REVERT: Y 38 GLN cc_start: 0.7105 (tp40) cc_final: 0.6334 (pm20) REVERT: 0 31 LYS cc_start: 0.8311 (tttt) cc_final: 0.8088 (ttmm) REVERT: 1 29 LYS cc_start: 0.8382 (mptt) cc_final: 0.6595 (ptmm) REVERT: 2 1 MET cc_start: 0.5936 (ptm) cc_final: 0.4675 (ptm) REVERT: 2 22 MET cc_start: 0.8087 (tpt) cc_final: 0.7804 (mmm) REVERT: 5 1 MET cc_start: 0.1588 (tpt) cc_final: 0.0353 (tpt) REVERT: 5 74 ASP cc_start: 0.2359 (OUTLIER) cc_final: 0.2096 (m-30) REVERT: 5 86 MET cc_start: 0.2045 (mmm) cc_final: 0.1337 (pmm) REVERT: 6 60 PHE cc_start: 0.6883 (t80) cc_final: 0.6551 (t80) REVERT: b 96 LEU cc_start: 0.7425 (mt) cc_final: 0.7151 (mt) REVERT: b 144 GLU cc_start: 0.6992 (tp30) cc_final: 0.6677 (tp30) REVERT: b 224 ARG cc_start: 0.5788 (mtm110) cc_final: 0.4853 (mmp80) REVERT: c 163 ARG cc_start: 0.6500 (OUTLIER) cc_final: 0.5127 (ptp-170) REVERT: d 76 LYS cc_start: 0.7621 (ttmt) cc_final: 0.7038 (mtpt) REVERT: e 68 ARG cc_start: 0.7758 (ptp90) cc_final: 0.6989 (ttp-110) REVERT: e 127 TYR cc_start: 0.8582 (m-80) cc_final: 0.8273 (m-80) REVERT: e 155 LYS cc_start: 0.8007 (pttp) cc_final: 0.7720 (pttp) REVERT: f 55 HIS cc_start: 0.6533 (OUTLIER) cc_final: 0.6225 (m-70) REVERT: g 25 PHE cc_start: 0.8594 (t80) cc_final: 0.8324 (t80) REVERT: g 117 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7531 (tp) REVERT: h 26 MET cc_start: 0.7050 (OUTLIER) cc_final: 0.6455 (ptp) REVERT: i 31 GLN cc_start: 0.7904 (mp10) cc_final: 0.7547 (mp10) REVERT: i 118 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7784 (ttp80) REVERT: k 36 ARG cc_start: 0.7245 (mmm-85) cc_final: 0.6982 (mtt-85) REVERT: k 56 LYS cc_start: 0.8677 (ttpp) cc_final: 0.8399 (ttpp) REVERT: k 115 ILE cc_start: 0.8716 (mt) cc_final: 0.8406 (pt) REVERT: k 124 LYS cc_start: 0.7153 (OUTLIER) cc_final: 0.6783 (pptt) REVERT: l 69 GLU cc_start: 0.6460 (mt-10) cc_final: 0.6178 (mt-10) REVERT: n 18 LYS cc_start: 0.8108 (tptt) cc_final: 0.7898 (tptt) REVERT: n 43 ASN cc_start: 0.7463 (m-40) cc_final: 0.7013 (m110) REVERT: o 36 ASN cc_start: 0.8363 (m110) cc_final: 0.8101 (m-40) REVERT: o 72 LYS cc_start: 0.8256 (tttp) cc_final: 0.7997 (tttm) REVERT: p 5 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.6687 (ptt-90) REVERT: p 18 GLN cc_start: 0.7163 (OUTLIER) cc_final: 0.6817 (tp-100) REVERT: p 56 ARG cc_start: 0.7609 (mmm-85) cc_final: 0.7245 (mmm160) REVERT: t 28 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.7283 (mtm110) REVERT: t 33 LYS cc_start: 0.8346 (tppp) cc_final: 0.8123 (ttpp) REVERT: v 288 GLN cc_start: 0.8198 (tp40) cc_final: 0.7943 (tt0) outliers start: 312 outliers final: 239 residues processed: 1571 average time/residue: 1.3536 time to fit residues: 3598.5266 Evaluate side-chains 1623 residues out of total 5060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 1368 time to evaluate : 5.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 238 ASN Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 145 ASP Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 50 ASP Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 86 CYS Chi-restraints excluded: chain F residue 134 GLN Chi-restraints excluded: chain F residue 139 GLU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 56 VAL Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 90 GLU Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 136 MET Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain P residue 9 GLN Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 36 LYS Chi-restraints excluded: chain P residue 65 ASN Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 113 LEU Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 103 VAL Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 31 GLN Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 92 ARG Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 91 GLN Chi-restraints excluded: chain U residue 92 VAL Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 53 LYS Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 89 ILE Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 60 ASP Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain W residue 73 ARG Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 39 GLN Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain Y residue 43 LEU Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 6 LYS Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 29 VAL Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 1 residue 11 VAL Chi-restraints excluded: chain 1 residue 43 ARG Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 5 residue 3 LEU Chi-restraints excluded: chain 5 residue 54 VAL Chi-restraints excluded: chain 5 residue 74 ASP Chi-restraints excluded: chain 6 residue 13 THR Chi-restraints excluded: chain 6 residue 24 ILE Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain b residue 13 VAL Chi-restraints excluded: chain b residue 29 PHE Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 71 THR Chi-restraints excluded: chain b residue 127 LYS Chi-restraints excluded: chain b residue 139 GLU Chi-restraints excluded: chain b residue 163 ILE Chi-restraints excluded: chain b residue 166 ASP Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 182 VAL Chi-restraints excluded: chain b residue 190 SER Chi-restraints excluded: chain b residue 206 ILE Chi-restraints excluded: chain b residue 220 VAL Chi-restraints excluded: chain b residue 222 GLU Chi-restraints excluded: chain c residue 54 ILE Chi-restraints excluded: chain c residue 63 ILE Chi-restraints excluded: chain c residue 163 ARG Chi-restraints excluded: chain c residue 164 THR Chi-restraints excluded: chain c residue 185 THR Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 20 LEU Chi-restraints excluded: chain d residue 116 LEU Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 137 SER Chi-restraints excluded: chain d residue 170 LEU Chi-restraints excluded: chain d residue 172 VAL Chi-restraints excluded: chain d residue 173 ASP Chi-restraints excluded: chain d residue 177 MET Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain e residue 10 LEU Chi-restraints excluded: chain e residue 55 VAL Chi-restraints excluded: chain e residue 105 ILE Chi-restraints excluded: chain e residue 115 GLU Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 133 ILE Chi-restraints excluded: chain e residue 152 VAL Chi-restraints excluded: chain f residue 26 THR Chi-restraints excluded: chain f residue 53 LYS Chi-restraints excluded: chain f residue 55 HIS Chi-restraints excluded: chain f residue 63 ASN Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 6 ILE Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 42 VAL Chi-restraints excluded: chain g residue 46 LEU Chi-restraints excluded: chain g residue 48 THR Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain h residue 3 GLN Chi-restraints excluded: chain h residue 26 MET Chi-restraints excluded: chain h residue 38 VAL Chi-restraints excluded: chain h residue 45 ILE Chi-restraints excluded: chain h residue 54 THR Chi-restraints excluded: chain h residue 84 ILE Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 124 ILE Chi-restraints excluded: chain i residue 38 PHE Chi-restraints excluded: chain i residue 55 ASP Chi-restraints excluded: chain i residue 84 ARG Chi-restraints excluded: chain i residue 90 ASP Chi-restraints excluded: chain i residue 118 ARG Chi-restraints excluded: chain i residue 126 PHE Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 22 THR Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain j residue 91 ASP Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 54 SER Chi-restraints excluded: chain k residue 71 ASP Chi-restraints excluded: chain k residue 81 LEU Chi-restraints excluded: chain k residue 93 GLU Chi-restraints excluded: chain k residue 111 ASP Chi-restraints excluded: chain k residue 124 LYS Chi-restraints excluded: chain l residue 42 LYS Chi-restraints excluded: chain l residue 76 HIS Chi-restraints excluded: chain l residue 78 VAL Chi-restraints excluded: chain l residue 101 LEU Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 59 VAL Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 71 GLU Chi-restraints excluded: chain m residue 75 SER Chi-restraints excluded: chain n residue 45 VAL Chi-restraints excluded: chain o residue 3 SER Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain p residue 3 THR Chi-restraints excluded: chain p residue 5 ARG Chi-restraints excluded: chain p residue 18 GLN Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain p residue 78 VAL Chi-restraints excluded: chain q residue 19 SER Chi-restraints excluded: chain q residue 28 VAL Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain q residue 37 ILE Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 47 ASP Chi-restraints excluded: chain q residue 75 VAL Chi-restraints excluded: chain s residue 14 LEU Chi-restraints excluded: chain s residue 24 SER Chi-restraints excluded: chain s residue 30 LEU Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 28 ARG Chi-restraints excluded: chain u residue 43 GLU Chi-restraints excluded: chain v residue 126 LEU Chi-restraints excluded: chain v residue 162 ILE Chi-restraints excluded: chain v residue 224 ILE Chi-restraints excluded: chain v residue 226 THR Chi-restraints excluded: chain v residue 229 SER Chi-restraints excluded: chain v residue 333 MET Chi-restraints excluded: chain v residue 340 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1059 random chunks: chunk 344 optimal weight: 0.7980 chunk 921 optimal weight: 4.9990 chunk 202 optimal weight: 7.9990 chunk 600 optimal weight: 0.3980 chunk 252 optimal weight: 10.0000 chunk 1024 optimal weight: 0.8980 chunk 850 optimal weight: 9.9990 chunk 474 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 338 optimal weight: 10.0000 chunk 537 optimal weight: 5.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 ASN ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 18 GLN ** U 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 15 ASN X 16 ASN Y 31 GLN ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 6 GLN ** 5 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 131 ASN f 14 GLN ** k 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 99 GLN m 104 ASN ** o 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 258 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 160601 Z= 0.215 Angle : 0.610 12.220 239844 Z= 0.317 Chirality : 0.037 0.378 30593 Planarity : 0.005 0.081 13157 Dihedral : 23.515 179.567 79343 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.05 % Favored : 89.79 % Rotamer: Outliers : 6.86 % Allowed : 19.57 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.10), residues: 6099 helix: -0.79 (0.12), residues: 1888 sheet: -2.00 (0.15), residues: 1083 loop : -2.33 (0.10), residues: 3128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP s 33 HIS 0.009 0.001 HIS f 11 PHE 0.024 0.002 PHE u 36 TYR 0.026 0.002 TYR F 6 ARG 0.012 0.001 ARG u 6 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12198 Ramachandran restraints generated. 6099 Oldfield, 0 Emsley, 6099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12198 Ramachandran restraints generated. 6099 Oldfield, 0 Emsley, 6099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1720 residues out of total 5060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 345 poor density : 1375 time to evaluate : 6.401 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: C 131 MET cc_start: 0.7147 (mtm) cc_final: 0.6897 (mtm) REVERT: C 269 ARG cc_start: 0.6862 (mmm160) cc_final: 0.6634 (mmm160) REVERT: D 7 LYS cc_start: 0.8203 (ttmt) cc_final: 0.7782 (mtpp) REVERT: D 148 GLN cc_start: 0.9044 (mp10) cc_final: 0.8757 (mp10) REVERT: D 167 ASN cc_start: 0.8521 (t0) cc_final: 0.8158 (t0) REVERT: E 200 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7326 (mp) REVERT: F 62 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7934 (pt0) REVERT: F 71 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7895 (pttm) REVERT: F 76 PHE cc_start: 0.7997 (m-10) cc_final: 0.7793 (m-10) REVERT: F 174 PHE cc_start: 0.7248 (OUTLIER) cc_final: 0.6596 (m-80) REVERT: G 162 ARG cc_start: 0.7368 (ptp-170) cc_final: 0.7014 (mtm180) REVERT: J 80 HIS cc_start: 0.7872 (OUTLIER) cc_final: 0.6445 (t-90) REVERT: J 96 ARG cc_start: 0.7268 (mmm160) cc_final: 0.6755 (mmm160) REVERT: K 20 MET cc_start: 0.7893 (ttt) cc_final: 0.7612 (ttm) REVERT: K 31 ARG cc_start: 0.8144 (mmt90) cc_final: 0.7925 (mmt90) REVERT: K 66 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8172 (ttpt) REVERT: K 85 VAL cc_start: 0.9032 (OUTLIER) cc_final: 0.8813 (p) REVERT: L 38 GLN cc_start: 0.8928 (tt0) cc_final: 0.8665 (tt0) REVERT: N 102 PHE cc_start: 0.7973 (m-80) cc_final: 0.7727 (m-80) REVERT: O 80 GLU cc_start: 0.8193 (mp0) cc_final: 0.7906 (mm-30) REVERT: P 9 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7451 (mp10) REVERT: Q 12 ARG cc_start: 0.8104 (mtp85) cc_final: 0.7831 (ttm110) REVERT: Q 77 LYS cc_start: 0.8341 (mttt) cc_final: 0.8104 (mptt) REVERT: T 30 ILE cc_start: 0.8279 (tt) cc_final: 0.8009 (pt) REVERT: T 50 LEU cc_start: 0.8635 (mp) cc_final: 0.8427 (mp) REVERT: U 60 LYS cc_start: 0.8088 (ttmt) cc_final: 0.7796 (ttpt) REVERT: U 86 PHE cc_start: 0.7445 (m-80) cc_final: 0.7128 (m-80) REVERT: W 21 ARG cc_start: 0.8229 (mmt90) cc_final: 0.7902 (mmt-90) REVERT: W 64 LYS cc_start: 0.8245 (tptm) cc_final: 0.7884 (ttpt) REVERT: X 51 SER cc_start: 0.8887 (p) cc_final: 0.8605 (p) REVERT: Y 38 GLN cc_start: 0.7156 (tp40) cc_final: 0.6347 (pm20) REVERT: 0 31 LYS cc_start: 0.8290 (tttt) cc_final: 0.8083 (ttmm) REVERT: 1 29 LYS cc_start: 0.8405 (mptt) cc_final: 0.6720 (ptmm) REVERT: 2 1 MET cc_start: 0.5868 (ptm) cc_final: 0.4525 (ptm) REVERT: 2 22 MET cc_start: 0.8066 (tpt) cc_final: 0.7761 (mmm) REVERT: 5 1 MET cc_start: 0.1688 (tpt) cc_final: 0.0351 (tpt) REVERT: 5 74 ASP cc_start: 0.2357 (OUTLIER) cc_final: 0.2091 (m-30) REVERT: 5 86 MET cc_start: 0.2005 (mmm) cc_final: 0.1338 (pmm) REVERT: 6 60 PHE cc_start: 0.7025 (t80) cc_final: 0.6691 (t80) REVERT: b 108 GLN cc_start: 0.6945 (OUTLIER) cc_final: 0.6655 (pt0) REVERT: b 224 ARG cc_start: 0.5825 (mtm110) cc_final: 0.4751 (mmt180) REVERT: c 54 ILE cc_start: 0.8070 (OUTLIER) cc_final: 0.7852 (mt) REVERT: c 81 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6453 (mp0) REVERT: c 163 ARG cc_start: 0.6558 (OUTLIER) cc_final: 0.5084 (ptp-170) REVERT: c 168 ARG cc_start: 0.7189 (ttm110) cc_final: 0.6956 (ttp80) REVERT: c 184 ASN cc_start: 0.8295 (t0) cc_final: 0.7844 (t0) REVERT: d 76 LYS cc_start: 0.7564 (ttmt) cc_final: 0.6991 (mtpt) REVERT: e 127 TYR cc_start: 0.8651 (m-80) cc_final: 0.8406 (m-80) REVERT: e 131 ASN cc_start: 0.8840 (OUTLIER) cc_final: 0.8334 (t160) REVERT: e 155 LYS cc_start: 0.7977 (pttp) cc_final: 0.7698 (pttp) REVERT: f 55 HIS cc_start: 0.6639 (OUTLIER) cc_final: 0.6328 (m-70) REVERT: g 25 PHE cc_start: 0.8662 (t80) cc_final: 0.8372 (t80) REVERT: g 117 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7537 (tp) REVERT: h 26 MET cc_start: 0.7069 (OUTLIER) cc_final: 0.6434 (ptp) REVERT: i 31 GLN cc_start: 0.7921 (mp10) cc_final: 0.7439 (mp10) REVERT: i 118 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7830 (ttp80) REVERT: k 36 ARG cc_start: 0.7173 (mmm-85) cc_final: 0.6828 (mtt-85) REVERT: k 56 LYS cc_start: 0.8671 (ttpp) cc_final: 0.8400 (ttpp) REVERT: k 115 ILE cc_start: 0.8681 (mt) cc_final: 0.8353 (pt) REVERT: l 69 GLU cc_start: 0.6460 (mt-10) cc_final: 0.6163 (mt-10) REVERT: m 28 ARG cc_start: 0.6918 (tpt170) cc_final: 0.6613 (tmt-80) REVERT: n 43 ASN cc_start: 0.7443 (m-40) cc_final: 0.6990 (m110) REVERT: o 36 ASN cc_start: 0.8346 (m110) cc_final: 0.8107 (m-40) REVERT: o 72 LYS cc_start: 0.8361 (tttp) cc_final: 0.7867 (tttm) REVERT: p 5 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.6743 (ptt-90) REVERT: p 18 GLN cc_start: 0.7283 (OUTLIER) cc_final: 0.7047 (tp40) REVERT: p 56 ARG cc_start: 0.7521 (mmm-85) cc_final: 0.7157 (mmm160) REVERT: q 25 GLU cc_start: 0.7461 (pm20) cc_final: 0.7190 (mp0) REVERT: t 28 ARG cc_start: 0.7510 (OUTLIER) cc_final: 0.7256 (mtm110) REVERT: t 33 LYS cc_start: 0.8333 (tppp) cc_final: 0.8101 (ttpp) REVERT: v 133 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7760 (ttt90) outliers start: 345 outliers final: 277 residues processed: 1549 average time/residue: 1.3782 time to fit residues: 3611.4998 Evaluate side-chains 1626 residues out of total 5060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 298 poor density : 1328 time to evaluate : 6.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 238 ASN Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain D residue 184 ARG Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 145 ASP Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 50 ASP Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 71 LYS Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 86 CYS Chi-restraints excluded: chain F residue 134 GLN Chi-restraints excluded: chain F residue 139 GLU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 174 PHE Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 128 THR Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 90 GLU Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 53 MET Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 136 MET Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain P residue 9 GLN Chi-restraints excluded: chain P residue 36 LYS Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 65 ASN Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 113 LEU Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 103 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 92 ARG Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 91 GLN Chi-restraints excluded: chain U residue 92 VAL Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain V residue 48 MET Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 53 LYS Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 89 ILE Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 60 ASP Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain W residue 73 ARG Chi-restraints excluded: chain X residue 16 ASN Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 27 ASN Chi-restraints excluded: chain Y residue 39 GLN Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain Y residue 43 LEU Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 6 LYS Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 29 VAL Chi-restraints excluded: chain 0 residue 32 THR Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 1 residue 11 VAL Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 1 residue 43 ARG Chi-restraints excluded: chain 2 residue 9 VAL Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 5 residue 3 LEU Chi-restraints excluded: chain 5 residue 54 VAL Chi-restraints excluded: chain 5 residue 74 ASP Chi-restraints excluded: chain 5 residue 123 ILE Chi-restraints excluded: chain 6 residue 24 ILE Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain b residue 13 VAL Chi-restraints excluded: chain b residue 29 PHE Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 71 THR Chi-restraints excluded: chain b residue 108 GLN Chi-restraints excluded: chain b residue 127 LYS Chi-restraints excluded: chain b residue 139 GLU Chi-restraints excluded: chain b residue 163 ILE Chi-restraints excluded: chain b residue 166 ASP Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 182 VAL Chi-restraints excluded: chain b residue 220 VAL Chi-restraints excluded: chain b residue 222 GLU Chi-restraints excluded: chain c residue 54 ILE Chi-restraints excluded: chain c residue 63 ILE Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 102 ILE Chi-restraints excluded: chain c residue 163 ARG Chi-restraints excluded: chain c residue 164 THR Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 185 THR Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 20 LEU Chi-restraints excluded: chain d residue 27 ILE Chi-restraints excluded: chain d residue 116 LEU Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 137 SER Chi-restraints excluded: chain d residue 170 LEU Chi-restraints excluded: chain d residue 172 VAL Chi-restraints excluded: chain d residue 173 ASP Chi-restraints excluded: chain d residue 177 MET Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain e residue 10 LEU Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 55 VAL Chi-restraints excluded: chain e residue 105 ILE Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 131 ASN Chi-restraints excluded: chain e residue 133 ILE Chi-restraints excluded: chain e residue 152 VAL Chi-restraints excluded: chain f residue 5 GLU Chi-restraints excluded: chain f residue 26 THR Chi-restraints excluded: chain f residue 53 LYS Chi-restraints excluded: chain f residue 55 HIS Chi-restraints excluded: chain f residue 63 ASN Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 6 ILE Chi-restraints excluded: chain g residue 42 VAL Chi-restraints excluded: chain g residue 48 THR Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain h residue 2 MET Chi-restraints excluded: chain h residue 26 MET Chi-restraints excluded: chain h residue 38 VAL Chi-restraints excluded: chain h residue 45 ILE Chi-restraints excluded: chain h residue 54 THR Chi-restraints excluded: chain h residue 63 LYS Chi-restraints excluded: chain h residue 84 ILE Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 124 ILE Chi-restraints excluded: chain i residue 38 PHE Chi-restraints excluded: chain i residue 55 ASP Chi-restraints excluded: chain i residue 90 ASP Chi-restraints excluded: chain i residue 118 ARG Chi-restraints excluded: chain i residue 126 PHE Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 22 THR Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 52 LEU Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain j residue 71 LEU Chi-restraints excluded: chain j residue 91 ASP Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 31 VAL Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 54 SER Chi-restraints excluded: chain k residue 71 ASP Chi-restraints excluded: chain k residue 81 LEU Chi-restraints excluded: chain k residue 93 GLU Chi-restraints excluded: chain l residue 3 VAL Chi-restraints excluded: chain l residue 42 LYS Chi-restraints excluded: chain l residue 76 HIS Chi-restraints excluded: chain l residue 78 VAL Chi-restraints excluded: chain l residue 101 LEU Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 20 SER Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 59 VAL Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 71 GLU Chi-restraints excluded: chain m residue 75 SER Chi-restraints excluded: chain n residue 45 VAL Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain o residue 3 SER Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain p residue 3 THR Chi-restraints excluded: chain p residue 5 ARG Chi-restraints excluded: chain p residue 18 GLN Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain p residue 78 VAL Chi-restraints excluded: chain q residue 19 SER Chi-restraints excluded: chain q residue 28 VAL Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 47 ASP Chi-restraints excluded: chain q residue 75 VAL Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 14 LEU Chi-restraints excluded: chain s residue 24 SER Chi-restraints excluded: chain s residue 30 LEU Chi-restraints excluded: chain s residue 38 THR Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 28 ARG Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 43 GLU Chi-restraints excluded: chain u residue 52 VAL Chi-restraints excluded: chain v residue 126 LEU Chi-restraints excluded: chain v residue 133 ARG Chi-restraints excluded: chain v residue 162 ILE Chi-restraints excluded: chain v residue 209 LEU Chi-restraints excluded: chain v residue 224 ILE Chi-restraints excluded: chain v residue 226 THR Chi-restraints excluded: chain v residue 229 SER Chi-restraints excluded: chain v residue 333 MET Chi-restraints excluded: chain v residue 338 ASP Chi-restraints excluded: chain v residue 340 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1059 random chunks: chunk 987 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 chunk 583 optimal weight: 1.9990 chunk 748 optimal weight: 20.0000 chunk 579 optimal weight: 4.9990 chunk 862 optimal weight: 7.9990 chunk 572 optimal weight: 3.9990 chunk 1020 optimal weight: 0.8980 chunk 638 optimal weight: 0.0570 chunk 622 optimal weight: 2.9990 chunk 471 optimal weight: 2.9990 overall best weight: 1.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 18 GLN ** U 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 31 GLN 0 18 HIS 2 6 GLN ** 5 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 14 GLN f 17 GLN ** k 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 51 GLN ** m 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 73 HIS s 51 HIS v 235 GLN ** v 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 160601 Z= 0.168 Angle : 0.572 12.086 239844 Z= 0.298 Chirality : 0.035 0.369 30593 Planarity : 0.004 0.080 13157 Dihedral : 23.464 177.859 79343 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.10 % Favored : 90.77 % Rotamer: Outliers : 6.16 % Allowed : 20.93 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.10), residues: 6099 helix: -0.54 (0.12), residues: 1889 sheet: -1.86 (0.15), residues: 1109 loop : -2.25 (0.11), residues: 3101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP s 33 HIS 0.009 0.001 HIS f 11 PHE 0.026 0.002 PHE 2 18 TYR 0.020 0.001 TYR F 6 ARG 0.014 0.001 ARG r 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12198 Ramachandran restraints generated. 6099 Oldfield, 0 Emsley, 6099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12198 Ramachandran restraints generated. 6099 Oldfield, 0 Emsley, 6099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1686 residues out of total 5060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 310 poor density : 1376 time to evaluate : 6.492 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: C 131 MET cc_start: 0.7103 (mtm) cc_final: 0.6886 (mtm) REVERT: D 7 LYS cc_start: 0.8184 (ttmt) cc_final: 0.7754 (mtpp) REVERT: D 148 GLN cc_start: 0.8980 (mp10) cc_final: 0.8760 (mp10) REVERT: D 160 LYS cc_start: 0.8913 (mtmt) cc_final: 0.8682 (mtmt) REVERT: D 167 ASN cc_start: 0.8449 (t0) cc_final: 0.8062 (t0) REVERT: E 200 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7311 (mp) REVERT: F 16 MET cc_start: 0.6171 (mtp) cc_final: 0.5910 (mtm) REVERT: F 21 TYR cc_start: 0.5568 (m-80) cc_final: 0.5360 (m-10) REVERT: F 50 ASP cc_start: 0.6421 (OUTLIER) cc_final: 0.6134 (t0) REVERT: F 62 GLN cc_start: 0.8259 (pm20) cc_final: 0.7664 (pt0) REVERT: F 95 MET cc_start: 0.8306 (tmm) cc_final: 0.7902 (tmm) REVERT: F 174 PHE cc_start: 0.7078 (OUTLIER) cc_final: 0.6686 (m-80) REVERT: G 162 ARG cc_start: 0.7319 (ptp-170) cc_final: 0.6979 (mtm180) REVERT: G 167 VAL cc_start: 0.6750 (m) cc_final: 0.6509 (t) REVERT: I 2 LYS cc_start: 0.1539 (OUTLIER) cc_final: 0.0008 (ttmp) REVERT: J 80 HIS cc_start: 0.7863 (OUTLIER) cc_final: 0.6448 (t-90) REVERT: K 20 MET cc_start: 0.7854 (ttt) cc_final: 0.7653 (ttm) REVERT: K 31 ARG cc_start: 0.8117 (mmt90) cc_final: 0.7911 (mmt90) REVERT: K 66 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8152 (ttpt) REVERT: K 85 VAL cc_start: 0.9019 (OUTLIER) cc_final: 0.8801 (p) REVERT: L 69 ARG cc_start: 0.8403 (mtp85) cc_final: 0.8158 (mtt90) REVERT: L 99 ASN cc_start: 0.7725 (t0) cc_final: 0.6933 (t0) REVERT: M 18 ARG cc_start: 0.7407 (ttm110) cc_final: 0.6965 (mpt180) REVERT: N 102 PHE cc_start: 0.7949 (m-80) cc_final: 0.7727 (m-80) REVERT: O 62 LEU cc_start: 0.7238 (mt) cc_final: 0.6652 (pp) REVERT: O 80 GLU cc_start: 0.8177 (mp0) cc_final: 0.7850 (mm-30) REVERT: P 9 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.7496 (mp10) REVERT: P 28 LYS cc_start: 0.8794 (mttt) cc_final: 0.8353 (mtpp) REVERT: P 38 ARG cc_start: 0.8029 (mtm110) cc_final: 0.7814 (mtp85) REVERT: P 39 LEU cc_start: 0.7952 (mp) cc_final: 0.7589 (mp) REVERT: Q 12 ARG cc_start: 0.8070 (mtp85) cc_final: 0.7818 (ttm110) REVERT: Q 77 LYS cc_start: 0.8313 (mttt) cc_final: 0.8077 (mttt) REVERT: Q 94 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8514 (mt) REVERT: S 31 GLN cc_start: 0.8447 (pt0) cc_final: 0.8136 (pt0) REVERT: S 92 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.7158 (ttp80) REVERT: T 30 ILE cc_start: 0.8187 (tt) cc_final: 0.7976 (pt) REVERT: T 91 GLN cc_start: 0.5212 (OUTLIER) cc_final: 0.4265 (tt0) REVERT: U 27 VAL cc_start: 0.8573 (m) cc_final: 0.8233 (t) REVERT: U 86 PHE cc_start: 0.7424 (m-80) cc_final: 0.7104 (m-80) REVERT: W 21 ARG cc_start: 0.8175 (mmt90) cc_final: 0.7853 (mmt-90) REVERT: W 64 LYS cc_start: 0.8219 (tptm) cc_final: 0.7895 (ttpt) REVERT: Y 38 GLN cc_start: 0.7099 (tp40) cc_final: 0.6331 (pm20) REVERT: 1 24 LYS cc_start: 0.7181 (OUTLIER) cc_final: 0.6402 (tptp) REVERT: 2 1 MET cc_start: 0.5768 (ptm) cc_final: 0.4527 (ptm) REVERT: 2 22 MET cc_start: 0.8017 (tpt) cc_final: 0.7684 (mmm) REVERT: 5 1 MET cc_start: 0.1637 (tpt) cc_final: 0.1080 (mmm) REVERT: 5 74 ASP cc_start: 0.2439 (OUTLIER) cc_final: 0.2232 (m-30) REVERT: 5 86 MET cc_start: 0.1933 (mmm) cc_final: 0.1273 (pmm) REVERT: 6 34 LEU cc_start: 0.5961 (tp) cc_final: 0.5722 (tt) REVERT: 6 60 PHE cc_start: 0.7088 (t80) cc_final: 0.6804 (t80) REVERT: 6 63 ARG cc_start: 0.7198 (mtt180) cc_final: 0.5995 (mtp85) REVERT: b 8 MET cc_start: 0.7231 (ppp) cc_final: 0.6868 (ppp) REVERT: b 21 TYR cc_start: 0.7720 (OUTLIER) cc_final: 0.7214 (p90) REVERT: b 224 ARG cc_start: 0.5797 (mtm110) cc_final: 0.4705 (mmt180) REVERT: c 54 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7886 (mt) REVERT: c 81 GLU cc_start: 0.7303 (mm-30) cc_final: 0.6448 (mp0) REVERT: c 133 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7247 (ptm) REVERT: c 163 ARG cc_start: 0.6510 (OUTLIER) cc_final: 0.5064 (ptp-170) REVERT: d 76 LYS cc_start: 0.7551 (ttmt) cc_final: 0.7029 (mtpt) REVERT: e 68 ARG cc_start: 0.7768 (ptp90) cc_final: 0.7065 (ttp-110) REVERT: e 127 TYR cc_start: 0.8604 (m-80) cc_final: 0.8369 (m-80) REVERT: e 155 LYS cc_start: 0.7961 (pttp) cc_final: 0.7702 (pttp) REVERT: f 55 HIS cc_start: 0.6631 (OUTLIER) cc_final: 0.6321 (m-70) REVERT: g 25 PHE cc_start: 0.8609 (t80) cc_final: 0.8259 (t80) REVERT: g 117 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7490 (tp) REVERT: h 26 MET cc_start: 0.7075 (OUTLIER) cc_final: 0.6383 (ptp) REVERT: i 31 GLN cc_start: 0.7893 (mp10) cc_final: 0.7497 (mp10) REVERT: i 118 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7824 (ttp80) REVERT: k 56 LYS cc_start: 0.8670 (ttpp) cc_final: 0.8336 (tttp) REVERT: k 115 ILE cc_start: 0.8636 (mt) cc_final: 0.8323 (pt) REVERT: l 9 LYS cc_start: 0.8175 (ttpp) cc_final: 0.7901 (ptpt) REVERT: l 69 GLU cc_start: 0.6423 (mt-10) cc_final: 0.6123 (mt-10) REVERT: m 2 ARG cc_start: 0.6808 (OUTLIER) cc_final: 0.6490 (tpt90) REVERT: n 18 LYS cc_start: 0.8057 (tptt) cc_final: 0.7852 (tptt) REVERT: n 43 ASN cc_start: 0.7440 (m-40) cc_final: 0.6980 (m110) REVERT: n 90 ARG cc_start: 0.7318 (mtm110) cc_final: 0.6718 (mtm110) REVERT: n 92 GLU cc_start: 0.6776 (mt-10) cc_final: 0.6278 (mt-10) REVERT: o 36 ASN cc_start: 0.8302 (m110) cc_final: 0.8048 (m-40) REVERT: o 47 LYS cc_start: 0.7611 (mttp) cc_final: 0.7305 (mttp) REVERT: o 72 LYS cc_start: 0.8389 (tttp) cc_final: 0.7979 (tttm) REVERT: p 18 GLN cc_start: 0.7253 (OUTLIER) cc_final: 0.7036 (tp40) REVERT: p 56 ARG cc_start: 0.7487 (mmm-85) cc_final: 0.7116 (mmm160) REVERT: q 25 GLU cc_start: 0.7479 (pm20) cc_final: 0.7204 (mp0) REVERT: t 28 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.7257 (mtm110) REVERT: t 33 LYS cc_start: 0.8264 (tppp) cc_final: 0.8056 (ttpp) REVERT: v 159 TYR cc_start: 0.7352 (m-80) cc_final: 0.7090 (m-80) REVERT: v 309 THR cc_start: 0.8659 (t) cc_final: 0.8206 (m) outliers start: 310 outliers final: 239 residues processed: 1543 average time/residue: 1.4989 time to fit residues: 3975.7813 Evaluate side-chains 1592 residues out of total 5060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 263 poor density : 1329 time to evaluate : 5.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 238 ASN Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 50 ASP Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 86 CYS Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 134 GLN Chi-restraints excluded: chain F residue 139 GLU Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 157 THR Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 174 PHE Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain I residue 2 LYS Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 90 GLU Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 53 MET Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 136 MET Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain P residue 9 GLN Chi-restraints excluded: chain P residue 26 GLU Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 65 ASN Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 77 SER Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 113 LEU Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 92 ARG Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 91 GLN Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 92 VAL Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain V residue 48 MET Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 53 LYS Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 60 ASP Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain W residue 73 ARG Chi-restraints excluded: chain X residue 16 ASN Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 39 GLN Chi-restraints excluded: chain Y residue 40 SER Chi-restraints excluded: chain 0 residue 6 LYS Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 29 VAL Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 1 residue 11 VAL Chi-restraints excluded: chain 1 residue 24 LYS Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 1 residue 43 ARG Chi-restraints excluded: chain 2 residue 9 VAL Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 5 residue 3 LEU Chi-restraints excluded: chain 5 residue 54 VAL Chi-restraints excluded: chain 5 residue 74 ASP Chi-restraints excluded: chain 5 residue 123 ILE Chi-restraints excluded: chain 6 residue 24 ILE Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain b residue 13 VAL Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 29 PHE Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 71 THR Chi-restraints excluded: chain b residue 127 LYS Chi-restraints excluded: chain b residue 139 GLU Chi-restraints excluded: chain b residue 162 VAL Chi-restraints excluded: chain b residue 163 ILE Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 182 VAL Chi-restraints excluded: chain b residue 220 VAL Chi-restraints excluded: chain c residue 54 ILE Chi-restraints excluded: chain c residue 63 ILE Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 102 ILE Chi-restraints excluded: chain c residue 133 MET Chi-restraints excluded: chain c residue 163 ARG Chi-restraints excluded: chain c residue 164 THR Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 20 LEU Chi-restraints excluded: chain d residue 116 LEU Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 137 SER Chi-restraints excluded: chain d residue 170 LEU Chi-restraints excluded: chain d residue 177 MET Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain e residue 10 LEU Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 45 VAL Chi-restraints excluded: chain e residue 55 VAL Chi-restraints excluded: chain e residue 105 ILE Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain e residue 133 ILE Chi-restraints excluded: chain e residue 152 VAL Chi-restraints excluded: chain f residue 5 GLU Chi-restraints excluded: chain f residue 26 THR Chi-restraints excluded: chain f residue 30 THR Chi-restraints excluded: chain f residue 53 LYS Chi-restraints excluded: chain f residue 55 HIS Chi-restraints excluded: chain f residue 63 ASN Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 96 VAL Chi-restraints excluded: chain g residue 6 ILE Chi-restraints excluded: chain g residue 42 VAL Chi-restraints excluded: chain g residue 48 THR Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain h residue 2 MET Chi-restraints excluded: chain h residue 26 MET Chi-restraints excluded: chain h residue 38 VAL Chi-restraints excluded: chain h residue 45 ILE Chi-restraints excluded: chain h residue 54 THR Chi-restraints excluded: chain h residue 63 LYS Chi-restraints excluded: chain h residue 124 ILE Chi-restraints excluded: chain i residue 38 PHE Chi-restraints excluded: chain i residue 55 ASP Chi-restraints excluded: chain i residue 90 ASP Chi-restraints excluded: chain i residue 118 ARG Chi-restraints excluded: chain i residue 126 PHE Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 22 THR Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 71 LEU Chi-restraints excluded: chain j residue 91 ASP Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 54 SER Chi-restraints excluded: chain k residue 71 ASP Chi-restraints excluded: chain k residue 81 LEU Chi-restraints excluded: chain k residue 93 GLU Chi-restraints excluded: chain k residue 111 ASP Chi-restraints excluded: chain l residue 3 VAL Chi-restraints excluded: chain l residue 42 LYS Chi-restraints excluded: chain l residue 76 HIS Chi-restraints excluded: chain l residue 78 VAL Chi-restraints excluded: chain m residue 2 ARG Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 59 VAL Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain n residue 15 LEU Chi-restraints excluded: chain n residue 45 VAL Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain o residue 3 SER Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain p residue 3 THR Chi-restraints excluded: chain p residue 18 GLN Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain p residue 78 VAL Chi-restraints excluded: chain q residue 28 VAL Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain q residue 37 ILE Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 47 ASP Chi-restraints excluded: chain q residue 75 VAL Chi-restraints excluded: chain r residue 28 LEU Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 14 LEU Chi-restraints excluded: chain s residue 24 SER Chi-restraints excluded: chain s residue 30 LEU Chi-restraints excluded: chain s residue 38 THR Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 28 ARG Chi-restraints excluded: chain u residue 43 GLU Chi-restraints excluded: chain v residue 136 SER Chi-restraints excluded: chain v residue 162 ILE Chi-restraints excluded: chain v residue 209 LEU Chi-restraints excluded: chain v residue 224 ILE Chi-restraints excluded: chain v residue 226 THR Chi-restraints excluded: chain v residue 229 SER Chi-restraints excluded: chain v residue 329 LEU Chi-restraints excluded: chain v residue 333 MET Chi-restraints excluded: chain v residue 340 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1059 random chunks: chunk 631 optimal weight: 20.0000 chunk 407 optimal weight: 8.9990 chunk 609 optimal weight: 10.0000 chunk 307 optimal weight: 7.9990 chunk 200 optimal weight: 10.0000 chunk 197 optimal weight: 10.0000 chunk 648 optimal weight: 10.0000 chunk 695 optimal weight: 10.0000 chunk 504 optimal weight: 8.9990 chunk 95 optimal weight: 8.9990 chunk 802 optimal weight: 0.0370 overall best weight: 7.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 HIS ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 18 GLN ** U 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 15 ASN X 16 ASN Y 31 GLN 2 6 GLN ** c 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 14 GLN f 17 GLN ** f 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.099 160601 Z= 0.497 Angle : 0.852 12.832 239844 Z= 0.428 Chirality : 0.048 0.472 30593 Planarity : 0.007 0.094 13157 Dihedral : 23.651 177.556 79343 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.36 % Favored : 87.47 % Rotamer: Outliers : 7.31 % Allowed : 20.67 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.10), residues: 6099 helix: -1.12 (0.11), residues: 1879 sheet: -1.99 (0.15), residues: 1073 loop : -2.48 (0.10), residues: 3147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.110 0.004 TRP s 33 HIS 0.014 0.002 HIS S 102 PHE 0.029 0.003 PHE b 49 TYR 0.021 0.003 TYR d 64 ARG 0.026 0.001 ARG u 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12198 Ramachandran restraints generated. 6099 Oldfield, 0 Emsley, 6099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12198 Ramachandran restraints generated. 6099 Oldfield, 0 Emsley, 6099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1742 residues out of total 5060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 368 poor density : 1374 time to evaluate : 6.240 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: C 113 ASP cc_start: 0.7589 (m-30) cc_final: 0.7223 (m-30) REVERT: C 131 MET cc_start: 0.7188 (mtm) cc_final: 0.6947 (mtm) REVERT: D 131 ASP cc_start: 0.7803 (OUTLIER) cc_final: 0.7558 (t70) REVERT: D 167 ASN cc_start: 0.8644 (t0) cc_final: 0.8254 (t0) REVERT: E 171 ASP cc_start: 0.7683 (p0) cc_final: 0.7441 (p0) REVERT: E 200 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7461 (mp) REVERT: F 62 GLN cc_start: 0.8494 (pm20) cc_final: 0.8001 (pt0) REVERT: F 71 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7678 (pttm) REVERT: G 162 ARG cc_start: 0.7390 (ptp-170) cc_final: 0.6918 (mtm180) REVERT: I 2 LYS cc_start: 0.1610 (OUTLIER) cc_final: 0.0107 (ttmp) REVERT: J 80 HIS cc_start: 0.8094 (OUTLIER) cc_final: 0.6799 (t-90) REVERT: J 96 ARG cc_start: 0.7467 (mmm160) cc_final: 0.6921 (mmm160) REVERT: J 99 ARG cc_start: 0.7883 (mmm160) cc_final: 0.6783 (mmt90) REVERT: J 108 MET cc_start: 0.9013 (mtm) cc_final: 0.8764 (mtp) REVERT: K 32 TYR cc_start: 0.8840 (OUTLIER) cc_final: 0.7613 (p90) REVERT: K 66 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8294 (ttpt) REVERT: N 94 TYR cc_start: 0.8702 (m-80) cc_final: 0.8343 (m-10) REVERT: P 7 LEU cc_start: 0.9346 (mt) cc_final: 0.9026 (mt) REVERT: P 9 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.7504 (mp10) REVERT: P 38 ARG cc_start: 0.8078 (mtm110) cc_final: 0.7822 (mtp85) REVERT: P 39 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8049 (mp) REVERT: Q 12 ARG cc_start: 0.8094 (mtp85) cc_final: 0.7734 (ttm110) REVERT: Q 77 LYS cc_start: 0.8396 (mttt) cc_final: 0.8090 (mptt) REVERT: Q 94 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8715 (mt) REVERT: R 73 LYS cc_start: 0.7906 (ttpp) cc_final: 0.7685 (tttp) REVERT: S 31 GLN cc_start: 0.8584 (pt0) cc_final: 0.8262 (pt0) REVERT: T 15 HIS cc_start: 0.7629 (t-90) cc_final: 0.7412 (t-90) REVERT: T 30 ILE cc_start: 0.8188 (tt) cc_final: 0.7912 (pt) REVERT: W 64 LYS cc_start: 0.8280 (tptm) cc_final: 0.7892 (ttpt) REVERT: X 51 SER cc_start: 0.9068 (p) cc_final: 0.8738 (p) REVERT: Y 38 GLN cc_start: 0.7184 (tp40) cc_final: 0.6771 (mp10) REVERT: 1 24 LYS cc_start: 0.7355 (tttm) cc_final: 0.6789 (tttp) REVERT: 2 1 MET cc_start: 0.5966 (ptm) cc_final: 0.4359 (ptm) REVERT: 5 86 MET cc_start: 0.2482 (mmm) cc_final: 0.1733 (pmm) REVERT: 6 60 PHE cc_start: 0.7064 (t80) cc_final: 0.6774 (t80) REVERT: b 8 MET cc_start: 0.7633 (ppp) cc_final: 0.7410 (ppp) REVERT: b 21 TYR cc_start: 0.7710 (OUTLIER) cc_final: 0.7338 (p90) REVERT: b 30 ILE cc_start: 0.6380 (OUTLIER) cc_final: 0.5991 (pp) REVERT: b 108 GLN cc_start: 0.7095 (OUTLIER) cc_final: 0.6766 (pt0) REVERT: b 224 ARG cc_start: 0.5938 (mtm110) cc_final: 0.4825 (mmt180) REVERT: c 54 ILE cc_start: 0.8098 (OUTLIER) cc_final: 0.7791 (mt) REVERT: c 81 GLU cc_start: 0.6906 (mm-30) cc_final: 0.6593 (mp0) REVERT: c 113 LYS cc_start: 0.7925 (tptt) cc_final: 0.7611 (tptt) REVERT: c 163 ARG cc_start: 0.6607 (OUTLIER) cc_final: 0.4814 (ptp-170) REVERT: c 184 ASN cc_start: 0.8334 (t0) cc_final: 0.7567 (t0) REVERT: d 32 LYS cc_start: 0.7424 (mmmm) cc_final: 0.7161 (mmmm) REVERT: d 76 LYS cc_start: 0.7732 (ttmt) cc_final: 0.7235 (mtpt) REVERT: d 110 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7318 (mtm-85) REVERT: e 155 LYS cc_start: 0.7928 (pttp) cc_final: 0.7717 (pttp) REVERT: f 9 MET cc_start: 0.8494 (mtm) cc_final: 0.8180 (ptp) REVERT: f 55 HIS cc_start: 0.6795 (OUTLIER) cc_final: 0.6514 (m-70) REVERT: g 62 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7768 (tm-30) REVERT: g 117 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7528 (tp) REVERT: i 31 GLN cc_start: 0.8013 (mp10) cc_final: 0.7556 (mp10) REVERT: i 87 MET cc_start: 0.7997 (ppp) cc_final: 0.7112 (tpp) REVERT: i 118 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.8015 (ttp80) REVERT: k 56 LYS cc_start: 0.8680 (ttpp) cc_final: 0.8315 (tttp) REVERT: k 115 ILE cc_start: 0.8729 (mt) cc_final: 0.8436 (pt) REVERT: m 32 ILE cc_start: 0.8579 (mm) cc_final: 0.8298 (mt) REVERT: n 43 ASN cc_start: 0.7589 (m-40) cc_final: 0.7130 (m-40) REVERT: n 60 GLN cc_start: 0.7961 (mm-40) cc_final: 0.7717 (mm-40) REVERT: n 90 ARG cc_start: 0.7512 (mtm110) cc_final: 0.7155 (mtm110) REVERT: o 36 ASN cc_start: 0.8471 (m110) cc_final: 0.8224 (m-40) REVERT: o 72 LYS cc_start: 0.8396 (tttp) cc_final: 0.7927 (tttm) REVERT: p 56 ARG cc_start: 0.7628 (mmm-85) cc_final: 0.7167 (mmm160) REVERT: q 25 GLU cc_start: 0.7520 (pm20) cc_final: 0.7215 (mp0) REVERT: r 28 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8295 (mp) REVERT: t 33 LYS cc_start: 0.8481 (tppp) cc_final: 0.8159 (ttpp) REVERT: u 38 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7594 (tp30) REVERT: v 133 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7924 (ttt90) REVERT: v 159 TYR cc_start: 0.7646 (m-80) cc_final: 0.7352 (m-80) outliers start: 368 outliers final: 289 residues processed: 1569 average time/residue: 1.4033 time to fit residues: 3740.7443 Evaluate side-chains 1653 residues out of total 5060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 311 poor density : 1342 time to evaluate : 6.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 238 ASN Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 195 GLN Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 50 ASP Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 71 LYS Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 86 CYS Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 134 GLN Chi-restraints excluded: chain F residue 139 GLU Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 174 PHE Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain I residue 2 LYS Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 53 MET Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 136 MET Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain P residue 9 GLN Chi-restraints excluded: chain P residue 36 LYS Chi-restraints excluded: chain P residue 39 LEU Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 65 ASN Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 77 SER Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 73 ILE Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 103 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 92 VAL Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain V residue 48 MET Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 89 ILE Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain W residue 73 ARG Chi-restraints excluded: chain X residue 16 ASN Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 39 GLN Chi-restraints excluded: chain Y residue 43 LEU Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 6 LYS Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 29 VAL Chi-restraints excluded: chain 0 residue 32 THR Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 1 residue 11 VAL Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 1 residue 43 ARG Chi-restraints excluded: chain 2 residue 9 VAL Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 60 CYS Chi-restraints excluded: chain 5 residue 3 LEU Chi-restraints excluded: chain 5 residue 54 VAL Chi-restraints excluded: chain 5 residue 55 VAL Chi-restraints excluded: chain 5 residue 74 ASP Chi-restraints excluded: chain 5 residue 123 ILE Chi-restraints excluded: chain 6 residue 24 ILE Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain b residue 13 VAL Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 71 THR Chi-restraints excluded: chain b residue 108 GLN Chi-restraints excluded: chain b residue 127 LYS Chi-restraints excluded: chain b residue 139 GLU Chi-restraints excluded: chain b residue 163 ILE Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 182 VAL Chi-restraints excluded: chain c residue 54 ILE Chi-restraints excluded: chain c residue 63 ILE Chi-restraints excluded: chain c residue 102 ILE Chi-restraints excluded: chain c residue 163 ARG Chi-restraints excluded: chain c residue 164 THR Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 185 THR Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 20 LEU Chi-restraints excluded: chain d residue 110 ARG Chi-restraints excluded: chain d residue 116 LEU Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 137 SER Chi-restraints excluded: chain d residue 170 LEU Chi-restraints excluded: chain d residue 172 VAL Chi-restraints excluded: chain d residue 173 ASP Chi-restraints excluded: chain d residue 177 MET Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain e residue 10 LEU Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 55 VAL Chi-restraints excluded: chain e residue 60 GLN Chi-restraints excluded: chain e residue 75 LEU Chi-restraints excluded: chain e residue 105 ILE Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain e residue 133 ILE Chi-restraints excluded: chain e residue 152 VAL Chi-restraints excluded: chain f residue 5 GLU Chi-restraints excluded: chain f residue 17 GLN Chi-restraints excluded: chain f residue 26 THR Chi-restraints excluded: chain f residue 30 THR Chi-restraints excluded: chain f residue 53 LYS Chi-restraints excluded: chain f residue 55 HIS Chi-restraints excluded: chain f residue 63 ASN Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain g residue 6 ILE Chi-restraints excluded: chain g residue 48 THR Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain g residue 90 VAL Chi-restraints excluded: chain g residue 117 LEU Chi-restraints excluded: chain h residue 2 MET Chi-restraints excluded: chain h residue 26 MET Chi-restraints excluded: chain h residue 38 VAL Chi-restraints excluded: chain h residue 45 ILE Chi-restraints excluded: chain h residue 54 THR Chi-restraints excluded: chain h residue 63 LYS Chi-restraints excluded: chain h residue 84 ILE Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 104 SER Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 124 ILE Chi-restraints excluded: chain i residue 38 PHE Chi-restraints excluded: chain i residue 55 ASP Chi-restraints excluded: chain i residue 62 LEU Chi-restraints excluded: chain i residue 65 THR Chi-restraints excluded: chain i residue 90 ASP Chi-restraints excluded: chain i residue 97 LEU Chi-restraints excluded: chain i residue 118 ARG Chi-restraints excluded: chain i residue 126 PHE Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 22 THR Chi-restraints excluded: chain j residue 26 VAL Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 71 LEU Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 54 SER Chi-restraints excluded: chain k residue 71 ASP Chi-restraints excluded: chain k residue 111 ASP Chi-restraints excluded: chain k residue 124 LYS Chi-restraints excluded: chain l residue 3 VAL Chi-restraints excluded: chain l residue 76 HIS Chi-restraints excluded: chain l residue 78 VAL Chi-restraints excluded: chain l residue 101 LEU Chi-restraints excluded: chain m residue 2 ARG Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 18 LEU Chi-restraints excluded: chain m residue 20 SER Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 55 LEU Chi-restraints excluded: chain m residue 59 VAL Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 71 GLU Chi-restraints excluded: chain m residue 75 SER Chi-restraints excluded: chain n residue 15 LEU Chi-restraints excluded: chain n residue 45 VAL Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain o residue 3 SER Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain p residue 3 THR Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain p residue 78 VAL Chi-restraints excluded: chain q residue 19 SER Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 28 VAL Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain q residue 37 ILE Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 47 ASP Chi-restraints excluded: chain q residue 75 VAL Chi-restraints excluded: chain r residue 28 LEU Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 14 LEU Chi-restraints excluded: chain s residue 24 SER Chi-restraints excluded: chain s residue 30 LEU Chi-restraints excluded: chain s residue 38 THR Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 28 ARG Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 5 VAL Chi-restraints excluded: chain u residue 30 GLU Chi-restraints excluded: chain u residue 38 GLU Chi-restraints excluded: chain u residue 41 THR Chi-restraints excluded: chain u residue 43 GLU Chi-restraints excluded: chain u residue 52 VAL Chi-restraints excluded: chain v residue 133 ARG Chi-restraints excluded: chain v residue 136 SER Chi-restraints excluded: chain v residue 162 ILE Chi-restraints excluded: chain v residue 209 LEU Chi-restraints excluded: chain v residue 224 ILE Chi-restraints excluded: chain v residue 226 THR Chi-restraints excluded: chain v residue 229 SER Chi-restraints excluded: chain v residue 329 LEU Chi-restraints excluded: chain v residue 333 MET Chi-restraints excluded: chain v residue 338 ASP Chi-restraints excluded: chain v residue 340 LEU Chi-restraints excluded: chain z residue 8 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1059 random chunks: chunk 928 optimal weight: 0.5980 chunk 977 optimal weight: 1.9990 chunk 892 optimal weight: 5.9990 chunk 951 optimal weight: 4.9990 chunk 572 optimal weight: 3.9990 chunk 414 optimal weight: 2.9990 chunk 746 optimal weight: 10.0000 chunk 291 optimal weight: 10.0000 chunk 859 optimal weight: 3.9990 chunk 899 optimal weight: 4.9990 chunk 947 optimal weight: 8.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS ** I 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 HIS R 18 GLN ** U 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 31 GLN ** 5 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 14 GLN f 17 GLN f 68 GLN h 3 GLN ** h 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 99 GLN ** o 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 235 GLN ** v 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 160601 Z= 0.228 Angle : 0.636 12.128 239844 Z= 0.329 Chirality : 0.038 0.391 30593 Planarity : 0.005 0.088 13157 Dihedral : 23.552 178.839 79342 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.33 % Favored : 90.54 % Rotamer: Outliers : 5.90 % Allowed : 22.38 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.10), residues: 6099 helix: -0.75 (0.12), residues: 1889 sheet: -1.93 (0.14), residues: 1123 loop : -2.36 (0.11), residues: 3087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP P 30 HIS 0.011 0.001 HIS f 11 PHE 0.028 0.002 PHE 2 18 TYR 0.026 0.002 TYR d 64 ARG 0.013 0.001 ARG K 108 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12198 Ramachandran restraints generated. 6099 Oldfield, 0 Emsley, 6099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12198 Ramachandran restraints generated. 6099 Oldfield, 0 Emsley, 6099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1656 residues out of total 5060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 297 poor density : 1359 time to evaluate : 6.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 7 LYS cc_start: 0.8229 (ttmt) cc_final: 0.7758 (mtpp) REVERT: D 131 ASP cc_start: 0.7887 (OUTLIER) cc_final: 0.7677 (t70) REVERT: D 148 GLN cc_start: 0.9027 (mp10) cc_final: 0.8772 (mp10) REVERT: D 167 ASN cc_start: 0.8512 (t0) cc_final: 0.8158 (t0) REVERT: E 88 ARG cc_start: 0.7637 (mmm-85) cc_final: 0.6940 (tpp80) REVERT: E 200 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7335 (mp) REVERT: F 21 TYR cc_start: 0.5919 (m-80) cc_final: 0.5692 (m-10) REVERT: F 62 GLN cc_start: 0.8300 (pm20) cc_final: 0.7850 (pt0) REVERT: F 174 PHE cc_start: 0.7445 (OUTLIER) cc_final: 0.6554 (m-80) REVERT: G 63 GLN cc_start: 0.6473 (tm-30) cc_final: 0.6192 (tm-30) REVERT: G 162 ARG cc_start: 0.7343 (ptp-170) cc_final: 0.6960 (mtm180) REVERT: J 80 HIS cc_start: 0.7914 (OUTLIER) cc_final: 0.6497 (t-90) REVERT: J 99 ARG cc_start: 0.7706 (mmm160) cc_final: 0.7198 (tpp-160) REVERT: K 32 TYR cc_start: 0.8807 (OUTLIER) cc_final: 0.7590 (p90) REVERT: K 66 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.8105 (ttpt) REVERT: L 69 ARG cc_start: 0.8463 (mtp85) cc_final: 0.8183 (mtt90) REVERT: L 99 ASN cc_start: 0.7882 (t0) cc_final: 0.7642 (t0) REVERT: N 102 PHE cc_start: 0.7900 (m-80) cc_final: 0.7590 (m-80) REVERT: O 80 GLU cc_start: 0.8206 (mp0) cc_final: 0.7892 (mm-30) REVERT: P 9 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.7461 (mp10) REVERT: P 30 TRP cc_start: 0.8630 (m100) cc_final: 0.8348 (m100) REVERT: P 38 ARG cc_start: 0.7955 (mtm110) cc_final: 0.7696 (mtp85) REVERT: Q 12 ARG cc_start: 0.8089 (mtp85) cc_final: 0.7821 (ttm110) REVERT: Q 77 LYS cc_start: 0.8374 (mttt) cc_final: 0.8097 (mptt) REVERT: Q 94 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8592 (mt) REVERT: S 31 GLN cc_start: 0.8475 (pt0) cc_final: 0.8178 (pt0) REVERT: T 30 ILE cc_start: 0.8266 (tt) cc_final: 0.8002 (pt) REVERT: U 86 PHE cc_start: 0.7488 (m-80) cc_final: 0.7144 (m-80) REVERT: V 12 GLN cc_start: 0.6400 (pp30) cc_final: 0.6154 (pp30) REVERT: W 21 ARG cc_start: 0.8205 (mmt90) cc_final: 0.8004 (mmt-90) REVERT: W 64 LYS cc_start: 0.8263 (tptm) cc_final: 0.7935 (ttpt) REVERT: Y 38 GLN cc_start: 0.7105 (tp40) cc_final: 0.6333 (pm20) REVERT: 1 29 LYS cc_start: 0.8386 (mptt) cc_final: 0.6701 (ptmm) REVERT: 2 1 MET cc_start: 0.5665 (ptm) cc_final: 0.4341 (ptm) REVERT: 5 1 MET cc_start: 0.1918 (tpt) cc_final: 0.0571 (tpt) REVERT: 5 74 ASP cc_start: 0.2495 (OUTLIER) cc_final: 0.2274 (m-30) REVERT: 5 86 MET cc_start: 0.2078 (mmm) cc_final: 0.1388 (pmm) REVERT: 6 63 ARG cc_start: 0.7271 (mtt180) cc_final: 0.6049 (mtp85) REVERT: b 8 MET cc_start: 0.7621 (ppp) cc_final: 0.7416 (ppp) REVERT: b 21 TYR cc_start: 0.7715 (OUTLIER) cc_final: 0.7362 (p90) REVERT: b 35 ASN cc_start: 0.5937 (t0) cc_final: 0.5687 (t0) REVERT: b 108 GLN cc_start: 0.6989 (OUTLIER) cc_final: 0.6702 (pt0) REVERT: b 224 ARG cc_start: 0.6132 (mtm110) cc_final: 0.5909 (mtm-85) REVERT: c 54 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7749 (mt) REVERT: c 81 GLU cc_start: 0.7170 (mm-30) cc_final: 0.6454 (mp0) REVERT: c 163 ARG cc_start: 0.6527 (OUTLIER) cc_final: 0.5056 (ptp-170) REVERT: d 76 LYS cc_start: 0.7629 (ttmt) cc_final: 0.7066 (mtpt) REVERT: e 127 TYR cc_start: 0.8626 (m-80) cc_final: 0.8406 (m-80) REVERT: e 155 LYS cc_start: 0.7898 (pttp) cc_final: 0.7577 (pttp) REVERT: i 31 GLN cc_start: 0.7953 (mp10) cc_final: 0.7517 (mp10) REVERT: i 118 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7842 (ttp80) REVERT: k 56 LYS cc_start: 0.8614 (ttpp) cc_final: 0.8269 (tttp) REVERT: k 115 ILE cc_start: 0.8703 (mt) cc_final: 0.8382 (pt) REVERT: m 28 ARG cc_start: 0.6475 (OUTLIER) cc_final: 0.5988 (tmt-80) REVERT: n 18 LYS cc_start: 0.8123 (tptt) cc_final: 0.7883 (tptt) REVERT: n 43 ASN cc_start: 0.7483 (m-40) cc_final: 0.7059 (m110) REVERT: n 60 GLN cc_start: 0.7915 (mm-40) cc_final: 0.7669 (mm-40) REVERT: o 36 ASN cc_start: 0.8370 (m110) cc_final: 0.8148 (m-40) REVERT: o 72 LYS cc_start: 0.8474 (tttp) cc_final: 0.8035 (tttm) REVERT: p 18 GLN cc_start: 0.7281 (OUTLIER) cc_final: 0.6945 (tp-100) REVERT: p 56 ARG cc_start: 0.7473 (mmm-85) cc_final: 0.7192 (mmm160) REVERT: q 25 GLU cc_start: 0.7502 (pm20) cc_final: 0.7258 (mp0) REVERT: r 28 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8212 (mp) REVERT: t 33 LYS cc_start: 0.8349 (tppp) cc_final: 0.8121 (ttpp) REVERT: u 48 LYS cc_start: 0.7468 (mmtt) cc_final: 0.6991 (mmtm) REVERT: v 133 ARG cc_start: 0.8010 (OUTLIER) cc_final: 0.7768 (ttt90) REVERT: v 159 TYR cc_start: 0.7516 (m-80) cc_final: 0.7230 (m-80) REVERT: v 309 THR cc_start: 0.8705 (t) cc_final: 0.8185 (m) outliers start: 297 outliers final: 253 residues processed: 1507 average time/residue: 1.4042 time to fit residues: 3610.5554 Evaluate side-chains 1612 residues out of total 5060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 271 poor density : 1341 time to evaluate : 6.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 238 ASN Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 50 ASP Chi-restraints excluded: chain F residue 86 CYS Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 134 GLN Chi-restraints excluded: chain F residue 139 GLU Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 174 PHE Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 57 LEU Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 53 MET Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 136 MET Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain P residue 9 GLN Chi-restraints excluded: chain P residue 26 GLU Chi-restraints excluded: chain P residue 36 LYS Chi-restraints excluded: chain P residue 39 LEU Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 65 ASN Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 77 SER Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 92 VAL Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain V residue 48 MET Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain W residue 73 ARG Chi-restraints excluded: chain X residue 16 ASN Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 39 GLN Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 6 LYS Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 29 VAL Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 1 residue 11 VAL Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 1 residue 43 ARG Chi-restraints excluded: chain 2 residue 9 VAL Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 5 residue 3 LEU Chi-restraints excluded: chain 5 residue 54 VAL Chi-restraints excluded: chain 5 residue 55 VAL Chi-restraints excluded: chain 5 residue 74 ASP Chi-restraints excluded: chain 5 residue 123 ILE Chi-restraints excluded: chain 6 residue 24 ILE Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain b residue 13 VAL Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 58 LYS Chi-restraints excluded: chain b residue 71 THR Chi-restraints excluded: chain b residue 108 GLN Chi-restraints excluded: chain b residue 127 LYS Chi-restraints excluded: chain b residue 139 GLU Chi-restraints excluded: chain b residue 163 ILE Chi-restraints excluded: chain b residue 170 ILE Chi-restraints excluded: chain b residue 182 VAL Chi-restraints excluded: chain c residue 54 ILE Chi-restraints excluded: chain c residue 63 ILE Chi-restraints excluded: chain c residue 102 ILE Chi-restraints excluded: chain c residue 163 ARG Chi-restraints excluded: chain c residue 164 THR Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain d residue 16 THR Chi-restraints excluded: chain d residue 20 LEU Chi-restraints excluded: chain d residue 116 LEU Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 133 SER Chi-restraints excluded: chain d residue 137 SER Chi-restraints excluded: chain d residue 170 LEU Chi-restraints excluded: chain d residue 173 ASP Chi-restraints excluded: chain d residue 177 MET Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain e residue 10 LEU Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 55 VAL Chi-restraints excluded: chain e residue 105 ILE Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 133 ILE Chi-restraints excluded: chain e residue 152 VAL Chi-restraints excluded: chain f residue 5 GLU Chi-restraints excluded: chain f residue 26 THR Chi-restraints excluded: chain f residue 30 THR Chi-restraints excluded: chain f residue 53 LYS Chi-restraints excluded: chain f residue 63 ASN Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 6 ILE Chi-restraints excluded: chain g residue 48 THR Chi-restraints excluded: chain h residue 26 MET Chi-restraints excluded: chain h residue 38 VAL Chi-restraints excluded: chain h residue 45 ILE Chi-restraints excluded: chain h residue 54 THR Chi-restraints excluded: chain h residue 58 LEU Chi-restraints excluded: chain h residue 63 LYS Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 105 THR Chi-restraints excluded: chain h residue 124 ILE Chi-restraints excluded: chain i residue 38 PHE Chi-restraints excluded: chain i residue 55 ASP Chi-restraints excluded: chain i residue 65 THR Chi-restraints excluded: chain i residue 90 ASP Chi-restraints excluded: chain i residue 118 ARG Chi-restraints excluded: chain i residue 126 PHE Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 22 THR Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 71 LEU Chi-restraints excluded: chain j residue 91 ASP Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 54 SER Chi-restraints excluded: chain k residue 71 ASP Chi-restraints excluded: chain k residue 111 ASP Chi-restraints excluded: chain k residue 118 ASN Chi-restraints excluded: chain l residue 2 THR Chi-restraints excluded: chain l residue 3 VAL Chi-restraints excluded: chain l residue 76 HIS Chi-restraints excluded: chain l residue 78 VAL Chi-restraints excluded: chain l residue 101 LEU Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 20 SER Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 28 ARG Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 55 LEU Chi-restraints excluded: chain m residue 59 VAL Chi-restraints excluded: chain m residue 71 GLU Chi-restraints excluded: chain n residue 15 LEU Chi-restraints excluded: chain n residue 45 VAL Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 21 THR Chi-restraints excluded: chain p residue 3 THR Chi-restraints excluded: chain p residue 18 GLN Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain p residue 78 VAL Chi-restraints excluded: chain q residue 19 SER Chi-restraints excluded: chain q residue 28 VAL Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain q residue 37 ILE Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 47 ASP Chi-restraints excluded: chain q residue 75 VAL Chi-restraints excluded: chain r residue 28 LEU Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain s residue 24 SER Chi-restraints excluded: chain s residue 30 LEU Chi-restraints excluded: chain s residue 38 THR Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain t residue 28 ARG Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain u residue 43 GLU Chi-restraints excluded: chain u residue 52 VAL Chi-restraints excluded: chain v residue 133 ARG Chi-restraints excluded: chain v residue 136 SER Chi-restraints excluded: chain v residue 162 ILE Chi-restraints excluded: chain v residue 209 LEU Chi-restraints excluded: chain v residue 224 ILE Chi-restraints excluded: chain v residue 226 THR Chi-restraints excluded: chain v residue 229 SER Chi-restraints excluded: chain v residue 329 LEU Chi-restraints excluded: chain v residue 333 MET Chi-restraints excluded: chain v residue 338 ASP Chi-restraints excluded: chain v residue 340 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1059 random chunks: chunk 624 optimal weight: 0.0020 chunk 1005 optimal weight: 1.9990 chunk 613 optimal weight: 3.9990 chunk 477 optimal weight: 5.9990 chunk 699 optimal weight: 10.0000 chunk 1055 optimal weight: 10.0000 chunk 971 optimal weight: 0.7980 chunk 840 optimal weight: 0.8980 chunk 87 optimal weight: 10.0000 chunk 648 optimal weight: 9.9990 chunk 515 optimal weight: 7.9990 overall best weight: 1.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN ** I 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 18 GLN ** U 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 16 ASN Y 31 GLN ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 176 ASN c 189 HIS d 70 GLN ** d 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 14 GLN f 17 GLN ** f 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 121 ASN ** k 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 99 GLN ** p 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 160601 Z= 0.157 Angle : 0.570 12.425 239844 Z= 0.296 Chirality : 0.035 0.382 30593 Planarity : 0.005 0.092 13157 Dihedral : 23.415 177.406 79342 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.51 % Favored : 90.36 % Rotamer: Outliers : 4.97 % Allowed : 23.61 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.10), residues: 6099 helix: -0.43 (0.12), residues: 1889 sheet: -1.73 (0.15), residues: 1080 loop : -2.24 (0.11), residues: 3130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP P 30 HIS 0.008 0.001 HIS f 11 PHE 0.028 0.001 PHE 2 18 TYR 0.026 0.001 TYR d 64 ARG 0.012 0.001 ARG K 108 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12198 Ramachandran restraints generated. 6099 Oldfield, 0 Emsley, 6099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12198 Ramachandran restraints generated. 6099 Oldfield, 0 Emsley, 6099 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1610 residues out of total 5060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 1360 time to evaluate : 6.261 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: D 7 LYS cc_start: 0.8133 (ttmt) cc_final: 0.7696 (mtpp) REVERT: D 131 ASP cc_start: 0.7864 (OUTLIER) cc_final: 0.7635 (t70) REVERT: D 167 ASN cc_start: 0.8429 (t0) cc_final: 0.8039 (t0) REVERT: F 50 ASP cc_start: 0.6535 (OUTLIER) cc_final: 0.6314 (t0) REVERT: F 62 GLN cc_start: 0.8104 (pm20) cc_final: 0.7744 (pt0) REVERT: F 174 PHE cc_start: 0.7152 (OUTLIER) cc_final: 0.6325 (m-80) REVERT: G 162 ARG cc_start: 0.7367 (ptp-170) cc_final: 0.6910 (mtm180) REVERT: I 35 MET cc_start: 0.1233 (mpp) cc_final: 0.0985 (mpp) REVERT: J 80 HIS cc_start: 0.7848 (OUTLIER) cc_final: 0.6504 (t-90) REVERT: J 99 ARG cc_start: 0.7475 (mmm160) cc_final: 0.6937 (tpp-160) REVERT: K 20 MET cc_start: 0.7928 (ttt) cc_final: 0.7687 (ttm) REVERT: K 32 TYR cc_start: 0.8753 (OUTLIER) cc_final: 0.7498 (p90) REVERT: K 66 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.8174 (ttpt) REVERT: L 69 ARG cc_start: 0.8291 (mtp85) cc_final: 0.8040 (mtt90) REVERT: L 99 ASN cc_start: 0.7796 (t0) cc_final: 0.7569 (t0) REVERT: L 115 GLU cc_start: 0.6629 (mp0) cc_final: 0.6385 (pt0) REVERT: M 18 ARG cc_start: 0.7423 (ttm110) cc_final: 0.7035 (mpt180) REVERT: O 80 GLU cc_start: 0.8197 (mp0) cc_final: 0.7879 (mm-30) REVERT: P 9 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.7491 (mp10) REVERT: P 38 ARG cc_start: 0.7858 (mtm110) cc_final: 0.7502 (mtp85) REVERT: Q 12 ARG cc_start: 0.8028 (mtp85) cc_final: 0.7747 (ttm110) REVERT: Q 47 ARG cc_start: 0.8372 (ttp-170) cc_final: 0.8153 (ttp-170) REVERT: Q 94 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8414 (mt) REVERT: S 1 MET cc_start: 0.6549 (tmm) cc_final: 0.6201 (tmm) REVERT: T 6 ARG cc_start: 0.8230 (ptm160) cc_final: 0.7834 (ptm160) REVERT: U 86 PHE cc_start: 0.7394 (m-80) cc_final: 0.7027 (m-80) REVERT: V 12 GLN cc_start: 0.6431 (pp30) cc_final: 0.6153 (pp30) REVERT: W 64 LYS cc_start: 0.8245 (tptm) cc_final: 0.7964 (ttpt) REVERT: Z 36 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7337 (tt0) REVERT: 1 29 LYS cc_start: 0.8411 (mptt) cc_final: 0.6712 (ptmm) REVERT: 2 1 MET cc_start: 0.5773 (ptm) cc_final: 0.4512 (ptm) REVERT: 3 18 LYS cc_start: 0.8048 (mtmm) cc_final: 0.7784 (mtmt) REVERT: 5 1 MET cc_start: 0.1568 (tpt) cc_final: 0.1094 (mmm) REVERT: 5 86 MET cc_start: 0.1825 (mmm) cc_final: 0.1202 (pmm) REVERT: 6 63 ARG cc_start: 0.7199 (mtt180) cc_final: 0.5971 (mtp85) REVERT: b 21 TYR cc_start: 0.7655 (OUTLIER) cc_final: 0.7254 (p90) REVERT: b 30 ILE cc_start: 0.5838 (pp) cc_final: 0.5621 (pp) REVERT: b 44 LYS cc_start: 0.7131 (ttmt) cc_final: 0.6728 (ttmm) REVERT: b 207 ARG cc_start: 0.6107 (ttp80) cc_final: 0.5683 (tmm160) REVERT: b 224 ARG cc_start: 0.5996 (mtm110) cc_final: 0.4683 (mpt180) REVERT: c 54 ILE cc_start: 0.8050 (OUTLIER) cc_final: 0.7675 (mt) REVERT: c 81 GLU cc_start: 0.7333 (mm-30) cc_final: 0.6558 (mp0) REVERT: c 163 ARG cc_start: 0.6491 (OUTLIER) cc_final: 0.5010 (ptp-170) REVERT: d 76 LYS cc_start: 0.7614 (ttmt) cc_final: 0.6963 (mtpt) REVERT: e 68 ARG cc_start: 0.7781 (ptp90) cc_final: 0.7469 (ttm110) REVERT: e 155 LYS cc_start: 0.7880 (pttp) cc_final: 0.7603 (pttp) REVERT: h 26 MET cc_start: 0.7102 (OUTLIER) cc_final: 0.6638 (ptp) REVERT: i 31 GLN cc_start: 0.7902 (mp10) cc_final: 0.7405 (mp10) REVERT: i 87 MET cc_start: 0.7909 (ppp) cc_final: 0.7016 (tpp) REVERT: i 118 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7846 (ttp80) REVERT: j 88 MET cc_start: 0.5835 (tpp) cc_final: 0.4908 (mmm) REVERT: k 56 LYS cc_start: 0.8642 (ttpp) cc_final: 0.8302 (tttp) REVERT: l 4 ASN cc_start: 0.8235 (t0) cc_final: 0.7959 (t0) REVERT: l 69 GLU cc_start: 0.6149 (mt-10) cc_final: 0.5817 (mt-10) REVERT: l 85 ARG cc_start: 0.7495 (ptm-80) cc_final: 0.7275 (ptm160) REVERT: n 43 ASN cc_start: 0.7461 (m-40) cc_final: 0.7030 (m110) REVERT: n 60 GLN cc_start: 0.7768 (mm-40) cc_final: 0.7504 (mm-40) REVERT: o 36 ASN cc_start: 0.8233 (m110) cc_final: 0.7978 (m-40) REVERT: o 72 LYS cc_start: 0.8380 (tttp) cc_final: 0.7922 (tttm) REVERT: p 18 GLN cc_start: 0.7095 (OUTLIER) cc_final: 0.6700 (tp-100) REVERT: p 56 ARG cc_start: 0.7471 (mmm-85) cc_final: 0.7203 (mmm160) REVERT: t 33 LYS cc_start: 0.8255 (tppp) cc_final: 0.7976 (ttpp) REVERT: u 48 LYS cc_start: 0.7309 (mmtt) cc_final: 0.6881 (mmtm) REVERT: v 159 TYR cc_start: 0.7425 (m-80) cc_final: 0.7189 (m-80) REVERT: v 319 ASP cc_start: 0.7586 (t0) cc_final: 0.7274 (t0) outliers start: 250 outliers final: 209 residues processed: 1491 average time/residue: 1.4663 time to fit residues: 3745.9089 Evaluate side-chains 1524 residues out of total 5060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 1301 time to evaluate : 6.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 238 ASN Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 131 ASP Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 91 ASP Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 50 ASP Chi-restraints excluded: chain F residue 86 CYS Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 134 GLN Chi-restraints excluded: chain F residue 139 GLU Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 148 VAL Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 174 PHE Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 28 ASN Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 32 TYR Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 53 MET Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 136 MET Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain P residue 9 GLN Chi-restraints excluded: chain P residue 26 GLU Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 65 ASN Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 77 SER Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 113 LEU Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 92 VAL Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 17 LEU Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 67 VAL Chi-restraints excluded: chain X residue 16 ASN Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 39 GLN Chi-restraints excluded: chain 0 residue 6 LYS Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 29 VAL Chi-restraints excluded: chain 1 residue 7 LYS Chi-restraints excluded: chain 1 residue 11 VAL Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 1 residue 43 ARG Chi-restraints excluded: chain 1 residue 50 GLU Chi-restraints excluded: chain 2 residue 9 VAL Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 5 residue 3 LEU Chi-restraints excluded: chain 5 residue 54 VAL Chi-restraints excluded: chain 5 residue 123 ILE Chi-restraints excluded: chain 6 residue 24 ILE Chi-restraints excluded: chain 6 residue 53 THR Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 29 PHE Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 71 THR Chi-restraints excluded: chain b residue 127 LYS Chi-restraints excluded: chain b residue 139 GLU Chi-restraints excluded: chain b residue 163 ILE Chi-restraints excluded: chain b residue 182 VAL Chi-restraints excluded: chain c residue 54 ILE Chi-restraints excluded: chain c residue 63 ILE Chi-restraints excluded: chain c residue 102 ILE Chi-restraints excluded: chain c residue 163 ARG Chi-restraints excluded: chain c residue 164 THR Chi-restraints excluded: chain c residue 199 VAL Chi-restraints excluded: chain d residue 20 LEU Chi-restraints excluded: chain d residue 116 LEU Chi-restraints excluded: chain d residue 124 VAL Chi-restraints excluded: chain d residue 133 SER Chi-restraints excluded: chain d residue 137 SER Chi-restraints excluded: chain d residue 170 LEU Chi-restraints excluded: chain d residue 173 ASP Chi-restraints excluded: chain d residue 177 MET Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain e residue 10 LEU Chi-restraints excluded: chain e residue 31 SER Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 105 ILE Chi-restraints excluded: chain e residue 121 ASN Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 133 ILE Chi-restraints excluded: chain e residue 152 VAL Chi-restraints excluded: chain f residue 30 THR Chi-restraints excluded: chain f residue 53 LYS Chi-restraints excluded: chain f residue 63 ASN Chi-restraints excluded: chain f residue 92 THR Chi-restraints excluded: chain g residue 6 ILE Chi-restraints excluded: chain h residue 26 MET Chi-restraints excluded: chain h residue 38 VAL Chi-restraints excluded: chain h residue 54 THR Chi-restraints excluded: chain h residue 63 LYS Chi-restraints excluded: chain h residue 103 VAL Chi-restraints excluded: chain h residue 124 ILE Chi-restraints excluded: chain i residue 38 PHE Chi-restraints excluded: chain i residue 55 ASP Chi-restraints excluded: chain i residue 62 LEU Chi-restraints excluded: chain i residue 90 ASP Chi-restraints excluded: chain i residue 118 ARG Chi-restraints excluded: chain i residue 126 PHE Chi-restraints excluded: chain j residue 10 LEU Chi-restraints excluded: chain j residue 22 THR Chi-restraints excluded: chain j residue 71 LEU Chi-restraints excluded: chain j residue 91 ASP Chi-restraints excluded: chain k residue 30 ILE Chi-restraints excluded: chain k residue 39 ASN Chi-restraints excluded: chain k residue 54 SER Chi-restraints excluded: chain k residue 71 ASP Chi-restraints excluded: chain k residue 111 ASP Chi-restraints excluded: chain k residue 118 ASN Chi-restraints excluded: chain l residue 3 VAL Chi-restraints excluded: chain l residue 76 HIS Chi-restraints excluded: chain l residue 78 VAL Chi-restraints excluded: chain m residue 3 ILE Chi-restraints excluded: chain m residue 24 VAL Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 55 LEU Chi-restraints excluded: chain m residue 59 VAL Chi-restraints excluded: chain n residue 45 VAL Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain p residue 18 GLN Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain p residue 78 VAL Chi-restraints excluded: chain q residue 19 SER Chi-restraints excluded: chain q residue 28 VAL Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 47 ASP Chi-restraints excluded: chain q residue 75 VAL Chi-restraints excluded: chain r residue 28 LEU Chi-restraints excluded: chain s residue 10 ILE Chi-restraints excluded: chain s residue 24 SER Chi-restraints excluded: chain s residue 30 LEU Chi-restraints excluded: chain s residue 78 THR Chi-restraints excluded: chain u residue 34 ARG Chi-restraints excluded: chain u residue 52 VAL Chi-restraints excluded: chain v residue 136 SER Chi-restraints excluded: chain v residue 162 ILE Chi-restraints excluded: chain v residue 209 LEU Chi-restraints excluded: chain v residue 224 ILE Chi-restraints excluded: chain v residue 226 THR Chi-restraints excluded: chain v residue 229 SER Chi-restraints excluded: chain v residue 333 MET Chi-restraints excluded: chain v residue 340 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1059 random chunks: chunk 667 optimal weight: 10.0000 chunk 894 optimal weight: 0.7980 chunk 257 optimal weight: 10.0000 chunk 774 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 233 optimal weight: 10.0000 chunk 841 optimal weight: 4.9990 chunk 352 optimal weight: 3.9990 chunk 864 optimal weight: 2.9990 chunk 106 optimal weight: 20.0000 chunk 154 optimal weight: 10.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 ASN ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 GLN T 15 HIS ** U 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 15 ASN Y 31 GLN ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 14 GLN f 17 GLN ** f 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 74 HIS ** v 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.149038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.127184 restraints weight = 249420.874| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.21 r_work: 0.3278 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 160601 Z= 0.343 Angle : 0.703 12.463 239844 Z= 0.358 Chirality : 0.041 0.432 30593 Planarity : 0.006 0.089 13157 Dihedral : 23.476 179.902 79342 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.20 % Favored : 88.67 % Rotamer: Outliers : 5.31 % Allowed : 23.65 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.10), residues: 6099 helix: -0.71 (0.12), residues: 1896 sheet: -1.82 (0.15), residues: 1083 loop : -2.32 (0.10), residues: 3120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.082 0.003 TRP P 30 HIS 0.012 0.002 HIS f 11 PHE 0.022 0.002 PHE 2 18 TYR 0.033 0.002 TYR G 156 ARG 0.017 0.001 ARG h 113 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 49897.47 seconds wall clock time: 866 minutes 25.05 seconds (51985.05 seconds total)