Starting phenix.real_space_refine on Sat Mar 2 19:27:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kpx_8282/03_2024/5kpx_8282.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kpx_8282/03_2024/5kpx_8282.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kpx_8282/03_2024/5kpx_8282.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kpx_8282/03_2024/5kpx_8282.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kpx_8282/03_2024/5kpx_8282.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kpx_8282/03_2024/5kpx_8282.pdb" } resolution = 3.9 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= -0.006 sd= 0.043 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 4811 5.49 5 S 178 5.16 5 C 78209 2.51 5 N 28775 2.21 5 O 42630 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 13": "NH1" <-> "NH2" Residue "B ARG 33": "NH1" <-> "NH2" Residue "B TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 59": "NH1" <-> "NH2" Residue "B ARG 77": "NH1" <-> "NH2" Residue "B ARG 83": "NH1" <-> "NH2" Residue "B ARG 169": "NH1" <-> "NH2" Residue "B ARG 184": "NH1" <-> "NH2" Residue "C ARG 21": "NH1" <-> "NH2" Residue "C ARG 44": "NH1" <-> "NH2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "C ARG 61": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C ARG 102": "NH1" <-> "NH2" Residue "C ARG 162": "NH1" <-> "NH2" Residue "C ARG 170": "NH1" <-> "NH2" Residue "D PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 70": "NH1" <-> "NH2" Residue "D ARG 79": "NH1" <-> "NH2" Residue "D ARG 91": "NH1" <-> "NH2" Residue "D ARG 101": "NH1" <-> "NH2" Residue "D ARG 109": "NH1" <-> "NH2" Residue "D ARG 111": "NH1" <-> "NH2" Residue "D ARG 114": "NH1" <-> "NH2" Residue "D ARG 132": "NH1" <-> "NH2" Residue "E ARG 2": "NH1" <-> "NH2" Residue "E TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 152": "NH1" <-> "NH2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 169": "NH1" <-> "NH2" Residue "G TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 13": "NH1" <-> "NH2" Residue "I ARG 37": "NH1" <-> "NH2" Residue "I TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 96": "NH1" <-> "NH2" Residue "I ARG 120": "NH1" <-> "NH2" Residue "K ARG 21": "NH1" <-> "NH2" Residue "K ARG 33": "NH1" <-> "NH2" Residue "K ARG 41": "NH1" <-> "NH2" Residue "K ARG 47": "NH1" <-> "NH2" Residue "K ARG 60": "NH1" <-> "NH2" Residue "K PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 78": "NH1" <-> "NH2" Residue "K ARG 126": "NH1" <-> "NH2" Residue "L ARG 10": "NH1" <-> "NH2" Residue "L ARG 18": "NH1" <-> "NH2" Residue "L ARG 40": "NH1" <-> "NH2" Residue "L ARG 44": "NH1" <-> "NH2" Residue "L ARG 50": "NH1" <-> "NH2" Residue "L ARG 55": "NH1" <-> "NH2" Residue "L ARG 59": "NH1" <-> "NH2" Residue "L TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 114": "NH1" <-> "NH2" Residue "L PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 8": "NH1" <-> "NH2" Residue "M ARG 12": "NH1" <-> "NH2" Residue "M ARG 17": "NH1" <-> "NH2" Residue "M ARG 22": "NH1" <-> "NH2" Residue "M ARG 46": "NH1" <-> "NH2" Residue "M ARG 63": "NH1" <-> "NH2" Residue "M ARG 64": "NH1" <-> "NH2" Residue "M ARG 69": "NH1" <-> "NH2" Residue "M ARG 71": "NH1" <-> "NH2" Residue "M TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 96": "NH1" <-> "NH2" Residue "M ARG 118": "NH1" <-> "NH2" Residue "N ARG 10": "NH1" <-> "NH2" Residue "N ARG 16": "NH1" <-> "NH2" Residue "N ARG 25": "NH1" <-> "NH2" Residue "N TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 81": "NH1" <-> "NH2" Residue "N ARG 94": "NH1" <-> "NH2" Residue "N ARG 102": "NH1" <-> "NH2" Residue "N ARG 111": "NH1" <-> "NH2" Residue "O ARG 20": "NH1" <-> "NH2" Residue "O ARG 38": "NH1" <-> "NH2" Residue "O ARG 61": "NH1" <-> "NH2" Residue "O ARG 88": "NH1" <-> "NH2" Residue "O ARG 100": "NH1" <-> "NH2" Residue "O ARG 108": "NH1" <-> "NH2" Residue "P ARG 2": "NH1" <-> "NH2" Residue "P ARG 5": "NH1" <-> "NH2" Residue "P ARG 12": "NH1" <-> "NH2" Residue "P ARG 32": "NH1" <-> "NH2" Residue "P ARG 47": "NH1" <-> "NH2" Residue "P ARG 69": "NH1" <-> "NH2" Residue "P TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 21": "NH1" <-> "NH2" Residue "Q ARG 68": "NH1" <-> "NH2" Residue "Q ARG 78": "NH1" <-> "NH2" Residue "Q ARG 79": "NH1" <-> "NH2" Residue "Q ARG 84": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "R ARG 88": "NH1" <-> "NH2" Residue "R ARG 95": "NH1" <-> "NH2" Residue "R ARG 110": "NH1" <-> "NH2" Residue "S ARG 73": "NH1" <-> "NH2" Residue "T ARG 5": "NH1" <-> "NH2" Residue "T ARG 6": "NH1" <-> "NH2" Residue "T ARG 81": "NH1" <-> "NH2" Residue "T ARG 85": "NH1" <-> "NH2" Residue "T ARG 93": "NH1" <-> "NH2" Residue "U TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 29": "NH1" <-> "NH2" Residue "X ARG 47": "NH1" <-> "NH2" Residue "X ARG 52": "NH1" <-> "NH2" Residue "Y ARG 10": "NH1" <-> "NH2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 44": "NH1" <-> "NH2" Residue "Z ARG 49": "NH1" <-> "NH2" Residue "Z ARG 56": "NH1" <-> "NH2" Residue "1 ARG 9": "NH1" <-> "NH2" Residue "1 ARG 15": "NH1" <-> "NH2" Residue "1 ARG 39": "NH1" <-> "NH2" Residue "1 ARG 51": "NH1" <-> "NH2" Residue "2 ARG 43": "NH1" <-> "NH2" Residue "2 TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 3": "NH1" <-> "NH2" Residue "3 PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 12": "NH1" <-> "NH2" Residue "3 ARG 14": "NH1" <-> "NH2" Residue "3 ARG 19": "NH1" <-> "NH2" Residue "3 ARG 21": "NH1" <-> "NH2" Residue "3 ARG 33": "NH1" <-> "NH2" Residue "3 ARG 41": "NH1" <-> "NH2" Residue "4 ARG 12": "NH1" <-> "NH2" Residue "4 ARG 29": "NH1" <-> "NH2" Residue "4 ARG 39": "NH1" <-> "NH2" Residue "4 ARG 41": "NH1" <-> "NH2" Residue "5 ARG 12": "NH1" <-> "NH2" Residue "5 ARG 24": "NH1" <-> "NH2" Residue "6 PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 107": "NH1" <-> "NH2" Residue "6 PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 224": "NH1" <-> "NH2" Residue "7 ARG 106": "NH1" <-> "NH2" Residue "7 PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 130": "NH1" <-> "NH2" Residue "9 PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 156": "NH1" <-> "NH2" Residue "10 PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "13 ARG 123": "NH1" <-> "NH2" Residue "15 PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "16 TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "16 ARG 55": "NH1" <-> "NH2" Residue "16 TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "19 PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "19 TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "20 ARG 28": "NH1" <-> "NH2" Residue "25 PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "25 ARG 54": "NH1" <-> "NH2" Residue "25 ARG 61": "NH1" <-> "NH2" Residue "25 ARG 65": "NH1" <-> "NH2" Residue "25 ARG 66": "NH1" <-> "NH2" Residue "33 PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "33 TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "33 ARG 596": "NH1" <-> "NH2" Residue "33 ARG 611": "NH1" <-> "NH2" Residue "33 ARG 651": "NH1" <-> "NH2" Residue "33 TYR 717": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 154603 Number of models: 1 Model: "" Number of chains: 59 Chain: "A" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "B" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "C" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "D" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "E" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "F" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "G" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 988 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "H" 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: "I" 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: "J" 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: "K" 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: "L" 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: "M" 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: "N" 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: "O" 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: "P" 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: "Q" 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: "R" 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: "S" 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: "T" 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: "U" 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: "V" 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: "W" 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: "X" 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: "Y" 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: "Z" 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: "1" 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: "2" 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: "3" 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: "4" 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: "5" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "6" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1704 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "7" 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: "8" 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: "9" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1156 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "10" 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: "11" 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: "12" 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: "13" 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: "14" 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: "15" 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: "16" 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: "17" 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: "18" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "19" 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: "20" 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: "21" 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: "22" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 535 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "23" 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: "24" 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: "25" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 544 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "26" Number of atoms: 33016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33016 Classifications: {'RNA': 1539} Modifications used: {'p5*END': 1, 'rna2p_pur': 97, 'rna2p_pyr': 48, 'rna3p_pur': 777, 'rna3p_pyr': 617} Link IDs: {'rna2p': 145, 'rna3p': 1393} Chain: "27" Number of atoms: 62322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62322 Classifications: {'RNA': 2903} Modifications used: {'p5*END': 1, 'rna2p_pur': 218, 'rna2p_pyr': 96, 'rna3p_pur': 1456, 'rna3p_pyr': 1133} Link IDs: {'rna2p': 314, 'rna3p': 2588} Chain: "28" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2572 Classifications: {'RNA': 120} Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 62, 'rna3p_pyr': 53} Link IDs: {'rna2p': 5, 'rna3p': 114} Chain: "29" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 432 Classifications: {'RNA': 20} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 14, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 18} Chain: "30" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1623 Classifications: {'RNA': 76} Modifications used: {'p5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 4, 'rna3p_pur': 35, 'rna3p_pyr': 33} Link IDs: {'rna2p': 8, 'rna3p': 67} Chain: "31" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1644 Classifications: {'RNA': 77} Modifications used: {'p5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 34, 'rna3p_pyr': 34} Link IDs: {'rna2p': 9, 'rna3p': 67} Chain: "32" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1643 Classifications: {'RNA': 77} Modifications used: {'p5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 6, 'rna3p_pur': 34, 'rna3p_pyr': 32} Link IDs: {'rna2p': 11, 'rna3p': 65} Chain: "33" Number of atoms: 4911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 4911 Classifications: {'peptide': 675} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 119} Link IDs: {'CIS': 1, 'PTRANS': 25, 'TRANS': 648} Chain breaks: 5 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 470 Unresolved non-hydrogen angles: 600 Unresolved non-hydrogen dihedrals: 392 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 10, 'TRP:plan': 3, 'ASP:plan': 11, 'PHE:plan': 4, 'GLU:plan': 8, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 287 Time building chain proxies: 55.57, per 1000 atoms: 0.36 Number of scatterers: 154603 At special positions: 0 Unit cell: (275.52, 263.22, 238.62, 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 178 16.00 P 4811 15.00 O 42630 8.00 N 28775 7.00 C 78209 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS Z 18 " - pdb=" SG CYS Z 40 " distance=2.02 Simple disulfide: pdb=" SG CYS Z 37 " - pdb=" SG CYS Z 40 " distance=2.04 Simple disulfide: pdb=" SG CYS33 178 " - pdb=" SG CYS33 202 " distance=2.01 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: 73.82 Conformation dependent library (CDL) restraints added in 8.2 seconds 13018 Ramachandran restraints generated. 6509 Oldfield, 0 Emsley, 6509 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12182 Finding SS restraints... Secondary structure from input PDB file: 227 helices and 81 sheets defined 37.5% alpha, 13.0% beta 1567 base pairs and 2361 stacking pairs defined. Time for finding SS restraints: 54.05 Creating SS restraints... Processing helix chain 'A' and resid 29 through 31 No H-bonds generated for 'chain 'A' and resid 29 through 31' Processing helix chain 'A' and resid 196 through 202 removed outlier: 4.044A pdb=" N MET A 200 " --> pdb=" O ALA A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 212 removed outlier: 4.071A pdb=" N ALA A 210 " --> pdb=" O LYS A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 225 through 229 Processing helix chain 'B' and resid 61 through 72 Processing helix chain 'B' and resid 97 through 102 removed outlier: 3.537A pdb=" N LEU B 100 " --> pdb=" O SER B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'C' and resid 15 through 21 Processing helix chain 'C' and resid 24 through 40 removed outlier: 4.047A pdb=" N VAL C 28 " --> pdb=" O ASN C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 115 removed outlier: 3.571A pdb=" N ARG C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 141 removed outlier: 3.550A pdb=" N LEU C 134 " --> pdb=" O LYS C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 163 removed outlier: 3.937A pdb=" N PHE C 158 " --> pdb=" O ASP C 154 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASN C 163 " --> pdb=" O LEU C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 183 removed outlier: 3.776A pdb=" N PHE C 183 " --> pdb=" O SER C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 200 Processing helix chain 'D' and resid 2 through 9 Processing helix chain 'D' and resid 9 through 17 Processing helix chain 'D' and resid 23 through 27 Processing helix chain 'D' and resid 45 through 61 removed outlier: 4.121A pdb=" N LEU D 49 " --> pdb=" O ASP D 45 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP D 50 " --> pdb=" O LYS D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 77 Processing helix chain 'D' and resid 92 through 104 removed outlier: 3.527A pdb=" N TRP D 96 " --> pdb=" O GLY D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 110 Processing helix chain 'D' and resid 133 through 137 removed outlier: 3.942A pdb=" N ILE D 136 " --> pdb=" O GLU D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'E' and resid 59 through 80 removed outlier: 4.282A pdb=" N GLN E 63 " --> pdb=" O ASP E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 150 Processing helix chain 'F' and resid 22 through 28 removed outlier: 3.782A pdb=" N ALA F 26 " --> pdb=" O LYS F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 34 Processing helix chain 'F' and resid 40 through 51 removed outlier: 4.015A pdb=" N ALA F 49 " --> pdb=" O GLU F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 73 Processing helix chain 'F' and resid 95 through 107 removed outlier: 3.645A pdb=" N ALA F 105 " --> pdb=" O ASP F 101 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA F 106 " --> pdb=" O ALA F 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 18 Processing helix chain 'G' and resid 19 through 21 No H-bonds generated for 'chain 'G' and resid 19 through 21' Processing helix chain 'G' and resid 43 through 48 Processing helix chain 'G' and resid 62 through 67 removed outlier: 4.013A pdb=" N GLY G 66 " --> pdb=" O ARG G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 75 removed outlier: 4.054A pdb=" N ASP G 74 " --> pdb=" O CYS G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 104 removed outlier: 3.763A pdb=" N LYS G 97 " --> pdb=" O ALA G 93 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N PHE G 99 " --> pdb=" O LEU G 95 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA G 100 " --> pdb=" O PHE G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 115 removed outlier: 4.093A pdb=" N GLU G 114 " --> pdb=" O ALA G 110 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLY G 115 " --> pdb=" O ALA G 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 110 through 115' Processing helix chain 'H' and resid 23 through 29 removed outlier: 3.725A pdb=" N LEU H 27 " --> pdb=" O VAL H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 74 through 83 removed outlier: 3.795A pdb=" N ALA H 83 " --> pdb=" O LEU H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 111 Processing helix chain 'H' and resid 112 through 116 removed outlier: 4.100A pdb=" N MET H 116 " --> pdb=" O ALA H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 120 through 133 Processing helix chain 'I' and resid 24 through 37 Processing helix chain 'I' and resid 58 through 62 Processing helix chain 'I' and resid 67 through 72 Processing helix chain 'I' and resid 89 through 96 Processing helix chain 'I' and resid 96 through 107 removed outlier: 3.858A pdb=" N VAL I 100 " --> pdb=" O ARG I 96 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ILE I 101 " --> pdb=" O PRO I 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 120 removed outlier: 3.633A pdb=" N ARG I 120 " --> pdb=" O ARG I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 132 through 136 removed outlier: 3.600A pdb=" N GLN I 135 " --> pdb=" O HIS I 132 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 119 Processing helix chain 'K' and resid 22 through 26 Processing helix chain 'K' and resid 37 through 41 Processing helix chain 'K' and resid 56 through 61 Processing helix chain 'K' and resid 69 through 72 Processing helix chain 'K' and resid 78 through 83 removed outlier: 3.639A pdb=" N ALA K 83 " --> pdb=" O SER K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 128 through 138 removed outlier: 3.516A pdb=" N ALA K 138 " --> pdb=" O ALA K 134 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 57 removed outlier: 3.727A pdb=" N ALA L 56 " --> pdb=" O ALA L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 109 through 124 removed outlier: 3.801A pdb=" N LYS L 118 " --> pdb=" O ARG L 114 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU L 119 " --> pdb=" O GLU L 115 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 30 Processing helix chain 'M' and resid 38 through 56 removed outlier: 4.252A pdb=" N ARG M 46 " --> pdb=" O LYS M 42 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL M 47 " --> pdb=" O GLU M 43 " (cutoff:3.500A) Proline residue: M 50 - end of helix removed outlier: 3.516A pdb=" N LYS M 56 " --> pdb=" O ILE M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 69 Processing helix chain 'M' and resid 72 through 82 removed outlier: 4.066A pdb=" N PHE M 80 " --> pdb=" O VAL M 76 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN M 81 " --> pdb=" O ALA M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 82 through 87 Processing helix chain 'N' and resid 3 through 22 removed outlier: 4.134A pdb=" N ARG N 13 " --> pdb=" O ARG N 9 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ALA N 14 " --> pdb=" O ARG N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 60 Processing helix chain 'N' and resid 67 through 84 removed outlier: 3.634A pdb=" N ALA N 71 " --> pdb=" O ASN N 67 " (cutoff:3.500A) Processing helix chain 'N' and resid 101 through 115 removed outlier: 3.502A pdb=" N ALA N 105 " --> pdb=" O GLY N 101 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 9 Processing helix chain 'O' and resid 52 through 55 Processing helix chain 'O' and resid 96 through 101 removed outlier: 3.859A pdb=" N GLU O 101 " --> pdb=" O TYR O 97 " (cutoff:3.500A) Processing helix chain 'O' and resid 103 through 108 Processing helix chain 'P' and resid 6 through 19 Processing helix chain 'P' and resid 24 through 30 removed outlier: 3.568A pdb=" N ARG P 29 " --> pdb=" O GLY P 25 " (cutoff:3.500A) Processing helix chain 'P' and resid 30 through 70 removed outlier: 4.771A pdb=" N GLN P 36 " --> pdb=" O ARG P 32 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG P 50 " --> pdb=" O TYR P 46 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LYS P 53 " --> pdb=" O ARG P 49 " (cutoff:3.500A) Processing helix chain 'P' and resid 74 through 85 Processing helix chain 'P' and resid 90 through 100 Processing helix chain 'P' and resid 101 through 117 removed outlier: 3.545A pdb=" N ALA P 117 " --> pdb=" O LYS P 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 13 through 23 removed outlier: 3.907A pdb=" N LEU R 23 " --> pdb=" O LEU R 19 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 38 removed outlier: 3.550A pdb=" N ALA R 32 " --> pdb=" O LYS R 28 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 62 removed outlier: 3.536A pdb=" N ASP R 62 " --> pdb=" O ALA R 58 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 10 removed outlier: 3.951A pdb=" N LYS S 9 " --> pdb=" O GLU S 5 " (cutoff:3.500A) Processing helix chain 'S' and resid 17 through 27 Processing helix chain 'S' and resid 39 through 51 Processing helix chain 'U' and resid 13 through 22 Processing helix chain 'U' and resid 45 through 52 Processing helix chain 'U' and resid 53 through 58 Processing helix chain 'W' and resid 52 through 61 Processing helix chain 'W' and resid 62 through 74 Processing helix chain 'X' and resid 2 through 7 removed outlier: 4.491A pdb=" N ARG X 7 " --> pdb=" O ALA X 3 " (cutoff:3.500A) Processing helix chain 'X' and resid 9 through 22 Processing helix chain 'X' and resid 23 through 34 removed outlier: 3.741A pdb=" N ASN X 27 " --> pdb=" O ARG X 23 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER X 34 " --> pdb=" O MET X 30 " (cutoff:3.500A) Processing helix chain 'X' and resid 40 through 61 removed outlier: 3.660A pdb=" N LYS X 44 " --> pdb=" O SER X 40 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 27 Processing helix chain 'Y' and resid 40 through 51 Processing helix chain 'Z' and resid 55 through 62 removed outlier: 3.534A pdb=" N ARG Z 59 " --> pdb=" O GLY Z 55 " (cutoff:3.500A) Processing helix chain '1' and resid 8 through 17 removed outlier: 3.612A pdb=" N ARG 1 12 " --> pdb=" O THR 1 8 " (cutoff:3.500A) Processing helix chain '3' and resid 8 through 17 Processing helix chain '3' and resid 17 through 23 Processing helix chain '3' and resid 24 through 38 Processing helix chain '4' and resid 6 through 11 Processing helix chain '4' and resid 36 through 44 Processing helix chain '4' and resid 53 through 61 Processing helix chain '5' and resid 30 through 34 Processing helix chain '6' and resid 45 through 63 Processing helix chain '6' and resid 73 through 87 removed outlier: 3.755A pdb=" N GLU 6 77 " --> pdb=" O ARG 6 73 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA 6 78 " --> pdb=" O ALA 6 74 " (cutoff:3.500A) Processing helix chain '6' and resid 102 through 122 removed outlier: 5.901A pdb=" N GLN 6 108 " --> pdb=" O LYS 6 104 " (cutoff:3.500A) Processing helix chain '6' and resid 123 through 126 removed outlier: 4.543A pdb=" N ASP 6 126 " --> pdb=" O GLY 6 123 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 123 through 126' Processing helix chain '6' and resid 129 through 147 Processing helix chain '6' and resid 148 through 152 removed outlier: 3.795A pdb=" N ASP 6 152 " --> pdb=" O GLY 6 149 " (cutoff:3.500A) Processing helix chain '6' and resid 168 through 178 removed outlier: 3.892A pdb=" N LEU 6 178 " --> pdb=" O GLU 6 174 " (cutoff:3.500A) Processing helix chain '6' and resid 191 through 195 removed outlier: 4.060A pdb=" N GLY 6 194 " --> pdb=" O ASP 6 191 " (cutoff:3.500A) Processing helix chain '6' and resid 205 through 222 Processing helix chain '7' and resid 5 through 10 removed outlier: 3.628A pdb=" N ARG 7 10 " --> pdb=" O PRO 7 6 " (cutoff:3.500A) Processing helix chain '7' and resid 27 through 45 removed outlier: 3.715A pdb=" N ASN 7 31 " --> pdb=" O GLU 7 27 " (cutoff:3.500A) Processing helix chain '7' and resid 46 through 49 Processing helix chain '7' and resid 71 through 76 Processing helix chain '7' and resid 80 through 93 Processing helix chain '7' and resid 107 through 110 Processing helix chain '7' and resid 111 through 125 removed outlier: 3.859A pdb=" N VAL 7 115 " --> pdb=" O ASP 7 111 " (cutoff:3.500A) Processing helix chain '7' and resid 128 through 143 Processing helix chain '8' and resid 8 through 14 removed outlier: 3.686A pdb=" N ARG 8 12 " --> pdb=" O LEU 8 8 " (cutoff:3.500A) Processing helix chain '8' and resid 48 through 65 Processing helix chain '8' and resid 67 through 81 Processing helix chain '8' and resid 84 through 95 Processing helix chain '8' and resid 96 through 104 Processing helix chain '8' and resid 109 through 118 Processing helix chain '8' and resid 146 through 149 Processing helix chain '8' and resid 152 through 160 removed outlier: 4.129A pdb=" N ALA 8 156 " --> pdb=" O SER 8 152 " (cutoff:3.500A) Processing helix chain '8' and resid 161 through 163 No H-bonds generated for 'chain '8' and resid 161 through 163' Processing helix chain '8' and resid 195 through 205 removed outlier: 4.110A pdb=" N ILE 8 199 " --> pdb=" O ASN 8 195 " (cutoff:3.500A) Processing helix chain '9' and resid 54 through 68 removed outlier: 3.742A pdb=" N LYS 9 65 " --> pdb=" O LYS 9 61 " (cutoff:3.500A) Processing helix chain '9' and resid 109 through 118 Processing helix chain '9' and resid 132 through 146 Processing helix chain '9' and resid 148 through 153 Processing helix chain '9' and resid 159 through 164 Processing helix chain '10' and resid 11 through 16 Processing helix chain '10' and resid 18 through 32 Processing helix chain '10' and resid 67 through 81 Processing helix chain '11' and resid 19 through 28 removed outlier: 3.531A pdb=" N ALA11 23 " --> pdb=" O SER11 19 " (cutoff:3.500A) Processing helix chain '11' and resid 34 through 53 Processing helix chain '11' and resid 61 through 69 removed outlier: 4.035A pdb=" N ASN11 67 " --> pdb=" O VAL11 63 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL11 68 " --> pdb=" O ALA11 64 " (cutoff:3.500A) Processing helix chain '11' and resid 91 through 109 Processing helix chain '11' and resid 114 through 128 Processing helix chain '11' and resid 131 through 147 Processing helix chain '12' and resid 4 through 19 Processing helix chain '12' and resid 29 through 43 Processing helix chain '12' and resid 87 through 91 removed outlier: 3.962A pdb=" N LEU12 91 " --> pdb=" O LYS12 88 " (cutoff:3.500A) Processing helix chain '12' and resid 93 through 98 Processing helix chain '12' and resid 111 through 119 Processing helix chain '13' and resid 33 through 38 Processing helix chain '13' and resid 43 through 47 Processing helix chain '13' and resid 48 through 54 removed outlier: 3.517A pdb=" N VAL13 54 " --> pdb=" O PRO13 50 " (cutoff:3.500A) Processing helix chain '13' and resid 70 through 86 Processing helix chain '13' and resid 90 through 100 removed outlier: 3.997A pdb=" N ARG13 94 " --> pdb=" O ASP13 90 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N GLU13 96 " --> pdb=" O SER13 92 " (cutoff:3.500A) Processing helix chain '14' and resid 14 through 31 Processing helix chain '14' and resid 80 through 88 removed outlier: 3.809A pdb=" N ASP14 85 " --> pdb=" O GLU14 81 " (cutoff:3.500A) Processing helix chain '15' and resid 47 through 50 Processing helix chain '15' and resid 54 through 57 Processing helix chain '15' and resid 58 through 69 Processing helix chain '15' and resid 94 through 104 removed outlier: 3.675A pdb=" N GLY15 103 " --> pdb=" O LEU15 99 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE15 104 " --> pdb=" O ASN15 100 " (cutoff:3.500A) Processing helix chain '16' and resid 2 through 9 removed outlier: 3.552A pdb=" N LEU16 6 " --> pdb=" O THR16 2 " (cutoff:3.500A) Processing helix chain '17' and resid 13 through 20 Processing helix chain '17' and resid 25 through 37 Processing helix chain '17' and resid 48 through 60 removed outlier: 4.706A pdb=" N THR17 54 " --> pdb=" O GLY17 50 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA17 60 " --> pdb=" O ARG17 56 " (cutoff:3.500A) Processing helix chain '17' and resid 64 through 83 Processing helix chain '17' and resid 84 through 92 Processing helix chain '17' and resid 105 through 110 Processing helix chain '18' and resid 2 through 19 removed outlier: 3.561A pdb=" N LYS18 6 " --> pdb=" O LYS18 2 " (cutoff:3.500A) Processing helix chain '18' and resid 20 through 23 Processing helix chain '18' and resid 37 through 50 removed outlier: 3.644A pdb=" N TRP18 41 " --> pdb=" O ASP18 37 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N GLN18 48 " --> pdb=" O VAL18 44 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N THR18 49 " --> pdb=" O LEU18 45 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU18 50 " --> pdb=" O LYS18 46 " (cutoff:3.500A) Processing helix chain '18' and resid 55 through 59 Processing helix chain '18' and resid 79 through 88 Processing helix chain '19' and resid 3 through 15 Processing helix chain '19' and resid 23 through 44 removed outlier: 4.592A pdb=" N GLY19 40 " --> pdb=" O ASN19 36 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N HIS19 41 " --> pdb=" O HIS19 37 " (cutoff:3.500A) Processing helix chain '19' and resid 48 through 73 Processing helix chain '19' and resid 74 through 84 Processing helix chain '20' and resid 53 through 64 Processing helix chain '20' and resid 68 through 76 Processing helix chain '22' and resid 12 through 17 Processing helix chain '22' and resid 24 through 29 Processing helix chain '22' and resid 47 through 64 Processing helix chain '23' and resid 11 through 25 Processing helix chain '23' and resid 69 through 74 Processing helix chain '24' and resid 4 through 6 No H-bonds generated for 'chain '24' and resid 4 through 6' Processing helix chain '24' and resid 7 through 41 removed outlier: 4.025A pdb=" N ILE24 11 " --> pdb=" O LYS24 7 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N HIS24 19 " --> pdb=" O LYS24 15 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG24 23 " --> pdb=" O HIS24 19 " (cutoff:3.500A) Processing helix chain '24' and resid 42 through 52 Processing helix chain '24' and resid 53 through 64 Processing helix chain '24' and resid 68 through 86 Processing helix chain '25' and resid 24 through 32 removed outlier: 4.111A pdb=" N GLU25 30 " --> pdb=" O GLY25 26 " (cutoff:3.500A) Processing helix chain '25' and resid 38 through 59 removed outlier: 4.018A pdb=" N THR25 42 " --> pdb=" O GLU25 38 " (cutoff:3.500A) Processing helix chain '33' and resid 17 through 23 Processing helix chain '33' and resid 28 through 43 Processing helix chain '33' and resid 55 through 69 removed outlier: 4.249A pdb=" N GLY33 59 " --> pdb=" O LEU33 55 " (cutoff:3.500A) Processing helix chain '33' and resid 72 through 82 Processing helix chain '33' and resid 83 through 88 Processing helix chain '33' and resid 91 through 100 Processing helix chain '33' and resid 100 through 113 Processing helix chain '33' and resid 146 through 161 Processing helix chain '33' and resid 170 through 181 Processing helix chain '33' and resid 181 through 189 Processing helix chain '33' and resid 191 through 207 removed outlier: 3.521A pdb=" N GLU33 197 " --> pdb=" O GLN33 193 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TYR33 205 " --> pdb=" O TYR33 201 " (cutoff:3.500A) Processing helix chain '33' and resid 207 through 221 removed outlier: 3.802A pdb=" N HIS33 219 " --> pdb=" O ALA33 215 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU33 220 " --> pdb=" O LYS33 216 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ARG33 221 " --> pdb=" O LEU33 217 " (cutoff:3.500A) Processing helix chain '33' and resid 221 through 242 Processing helix chain '33' and resid 255 through 267 Processing helix chain '33' and resid 268 through 270 No H-bonds generated for 'chain '33' and resid 268 through 270' Processing helix chain '33' and resid 273 through 276 Processing helix chain '33' and resid 285 through 300 Processing helix chain '33' and resid 341 through 350 Processing helix chain '33' and resid 361 through 381 Processing helix chain '33' and resid 423 through 432 removed outlier: 3.579A pdb=" N ALA33 428 " --> pdb=" O PRO33 424 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR33 429 " --> pdb=" O LEU33 425 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N HIS33 430 " --> pdb=" O ASP33 426 " (cutoff:3.500A) Processing helix chain '33' and resid 432 through 438 Processing helix chain '33' and resid 470 through 474 removed outlier: 3.781A pdb=" N ARG33 473 " --> pdb=" O ASN33 470 " (cutoff:3.500A) Processing helix chain '33' and resid 476 through 480 Processing helix chain '33' and resid 488 through 519 removed outlier: 3.911A pdb=" N ILE33 492 " --> pdb=" O GLY33 488 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLN33 499 " --> pdb=" O TRP33 495 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP33 500 " --> pdb=" O PHE33 496 " (cutoff:3.500A) Processing helix chain '33' and resid 522 through 531 removed outlier: 3.590A pdb=" N ALA33 526 " --> pdb=" O SER33 522 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU33 530 " --> pdb=" O ALA33 526 " (cutoff:3.500A) Processing helix chain '33' and resid 538 through 543 Processing helix chain '33' and resid 555 through 561 Processing helix chain '33' and resid 569 through 579 Processing helix chain '33' and resid 586 through 591 Processing helix chain '33' and resid 598 through 602 removed outlier: 4.228A pdb=" N GLY33 601 " --> pdb=" O VAL33 598 " (cutoff:3.500A) Processing helix chain '33' and resid 638 through 646 removed outlier: 3.520A pdb=" N ARG33 645 " --> pdb=" O LEU33 641 " (cutoff:3.500A) Processing helix chain '33' and resid 647 through 652 removed outlier: 6.280A pdb=" N GLU33 650 " --> pdb=" O HIS33 647 " (cutoff:3.500A) Processing helix chain '33' and resid 678 through 688 removed outlier: 3.618A pdb=" N ILE33 686 " --> pdb=" O ASP33 682 " (cutoff:3.500A) Processing helix chain '33' and resid 689 through 691 No H-bonds generated for 'chain '33' and resid 689 through 691' Processing helix chain '33' and resid 718 through 730 removed outlier: 3.594A pdb=" N LEU33 722 " --> pdb=" O ASN33 718 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY33 723 " --> pdb=" O LEU33 719 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 4 Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 35 Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 104 removed outlier: 6.437A pdb=" N LEU A 94 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N VAL A 77 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA A 75 " --> pdb=" O ILE A 115 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 128 through 130 removed outlier: 6.487A pdb=" N THR A 172 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N ARG A 166 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N TYR A 170 " --> pdb=" O ARG A 166 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LYS A 182 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ILE A 266 " --> pdb=" O LYS A 182 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 4 through 15 removed outlier: 5.122A pdb=" N LYS B 8 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLU B 28 " --> pdb=" O LYS B 8 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N GLY B 10 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE B 27 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU B 186 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL B 180 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU B 188 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ASP B 176 " --> pdb=" O LYS B 190 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N THR B 171 " --> pdb=" O GLY B 111 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N GLY B 111 " --> pdb=" O THR B 171 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N GLN B 173 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL B 109 " --> pdb=" O GLN B 173 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N THR B 112 " --> pdb=" O ASP B 200 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASP B 200 " --> pdb=" O THR B 112 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 82 through 83 removed outlier: 3.654A pdb=" N GLN B 36 " --> pdb=" O GLN B 49 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N THR B 51 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N VAL B 34 " --> pdb=" O THR B 51 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 117 through 119 Processing sheet with id=AA8, first strand: chain 'C' and resid 118 through 121 removed outlier: 3.520A pdb=" N ILE C 149 " --> pdb=" O VAL C 187 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N ARG C 170 " --> pdb=" O VAL C 146 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE C 148 " --> pdb=" O ARG C 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 89 through 90 removed outlier: 6.841A pdb=" N THR D 156 " --> pdb=" O GLU D 31 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ILE D 33 " --> pdb=" O THR D 154 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N THR D 154 " --> pdb=" O ILE D 33 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU D 35 " --> pdb=" O ASP D 152 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ASP D 152 " --> pdb=" O LEU D 35 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU D 151 " --> pdb=" O VAL D 131 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL D 131 " --> pdb=" O LEU D 151 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 8 through 9 Processing sheet with id=AB2, first strand: chain 'E' and resid 17 through 19 removed outlier: 3.501A pdb=" N VAL E 22 " --> pdb=" O ASN E 19 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 120 through 123 Processing sheet with id=AB4, first strand: chain 'E' and resid 96 through 98 Processing sheet with id=AB5, first strand: chain 'F' and resid 4 through 5 Processing sheet with id=AB6, first strand: chain 'F' and resid 115 through 116 removed outlier: 3.573A pdb=" N SER F 131 " --> pdb=" O ARG F 116 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 24 through 25 Processing sheet with id=AB8, first strand: chain 'G' and resid 28 through 29 Processing sheet with id=AB9, first strand: chain 'H' and resid 12 through 13 Processing sheet with id=AC1, first strand: chain 'H' and resid 99 through 101 removed outlier: 5.337A pdb=" N ILE H 100 " --> pdb=" O GLU H 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'I' and resid 17 through 19 Processing sheet with id=AC3, first strand: chain 'I' and resid 73 through 75 Processing sheet with id=AC4, first strand: chain 'J' and resid 7 through 10 removed outlier: 7.010A pdb=" N LYS J 40 " --> pdb=" O ILE J 22 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N VAL J 24 " --> pdb=" O ILE J 38 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N ILE J 38 " --> pdb=" O VAL J 24 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA J 83 " --> pdb=" O VAL J 63 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N CYS J 84 " --> pdb=" O MET J 7 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ASN J 9 " --> pdb=" O CYS J 84 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N LEU J 86 " --> pdb=" O ASN J 9 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 69 through 70 Processing sheet with id=AC6, first strand: chain 'K' and resid 74 through 76 removed outlier: 6.199A pdb=" N ALA K 75 " --> pdb=" O LYS K 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'K' and resid 89 through 90 Processing sheet with id=AC8, first strand: chain 'L' and resid 100 through 101 Processing sheet with id=AC9, first strand: chain 'L' and resid 40 through 42 removed outlier: 5.611A pdb=" N VAL L 89 " --> pdb=" O GLU L 75 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLU L 75 " --> pdb=" O VAL L 89 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 62 through 65 Processing sheet with id=AD2, first strand: chain 'M' and resid 33 through 37 Processing sheet with id=AD3, first strand: chain 'N' and resid 25 through 28 removed outlier: 3.896A pdb=" N VAL N 49 " --> pdb=" O VAL N 39 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 69 through 74 removed outlier: 3.728A pdb=" N ALA O 48 " --> pdb=" O THR O 59 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ARG O 61 " --> pdb=" O VAL O 46 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N VAL O 46 " --> pdb=" O ARG O 61 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N TRP O 30 " --> pdb=" O VAL O 80 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL O 80 " --> pdb=" O TRP O 30 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Q' and resid 11 through 12 removed outlier: 6.603A pdb=" N GLN Q 6 " --> pdb=" O VAL Q 38 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL Q 38 " --> pdb=" O GLN Q 6 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Q' and resid 19 through 22 removed outlier: 6.286A pdb=" N ASP Q 95 " --> pdb=" O VAL Q 64 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Q' and resid 34 through 35 Processing sheet with id=AD8, first strand: chain 'Q' and resid 72 through 77 Processing sheet with id=AD9, first strand: chain 'R' and resid 4 through 10 removed outlier: 4.590A pdb=" N HIS R 9 " --> pdb=" O SER R 101 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N SER R 101 " --> pdb=" O HIS R 9 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'R' and resid 86 through 88 Processing sheet with id=AE2, first strand: chain 'S' and resid 11 through 14 removed outlier: 3.991A pdb=" N LYS S 81 " --> pdb=" O VAL S 34 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'T' and resid 64 through 65 removed outlier: 6.858A pdb=" N LYS T 32 " --> pdb=" O VAL T 27 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N VAL T 27 " --> pdb=" O LYS T 32 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE T 34 " --> pdb=" O LYS T 25 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'T' and resid 40 through 42 Processing sheet with id=AE5, first strand: chain 'T' and resid 82 through 87 Processing sheet with id=AE6, first strand: chain 'U' and resid 3 through 5 removed outlier: 6.304A pdb=" N ILE U 4 " --> pdb=" O VAL U 64 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ALA U 74 " --> pdb=" O VAL U 92 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL U 92 " --> pdb=" O ALA U 74 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP U 76 " --> pdb=" O ASP U 90 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS U 88 " --> pdb=" O GLN U 78 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N GLN U 87 " --> pdb=" O LYS U 25 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE U 89 " --> pdb=" O PRO U 27 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'V' and resid 26 through 27 Processing sheet with id=AE8, first strand: chain 'V' and resid 32 through 34 removed outlier: 6.555A pdb=" N ILE V 32 " --> pdb=" O ALA V 57 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ALA V 57 " --> pdb=" O ILE V 32 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'W' and resid 12 through 15 Processing sheet with id=AF1, first strand: chain 'W' and resid 32 through 39 Processing sheet with id=AF2, first strand: chain 'Y' and resid 34 through 38 Processing sheet with id=AF3, first strand: chain 'Z' and resid 11 through 12 Processing sheet with id=AF4, first strand: chain '1' and resid 47 through 48 Processing sheet with id=AF5, first strand: chain '2' and resid 19 through 23 removed outlier: 3.712A pdb=" N GLN 2 44 " --> pdb=" O ASP 2 39 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain '4' and resid 14 through 15 removed outlier: 3.746A pdb=" N LYS 4 14 " --> pdb=" O LYS 4 22 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain '5' and resid 15 through 17 Processing sheet with id=AF8, first strand: chain '6' and resid 30 through 32 Processing sheet with id=AF9, first strand: chain '6' and resid 89 through 91 removed outlier: 7.165A pdb=" N PHE 6 68 " --> pdb=" O VAL 6 91 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU 6 67 " --> pdb=" O PHE 6 161 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain '7' and resid 19 through 20 removed outlier: 6.600A pdb=" N HIS 7 68 " --> pdb=" O SER 7 52 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ILE 7 54 " --> pdb=" O THR 7 66 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N THR 7 66 " --> pdb=" O ILE 7 54 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ILE 7 56 " --> pdb=" O ARG 7 64 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ARG 7 64 " --> pdb=" O ILE 7 56 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ALA 7 103 " --> pdb=" O VAL 7 65 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ILE 7 67 " --> pdb=" O ALA 7 103 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain '7' and resid 163 through 170 Processing sheet with id=AG3, first strand: chain '7' and resid 163 through 170 Processing sheet with id=AG4, first strand: chain '8' and resid 122 through 124 Processing sheet with id=AG5, first strand: chain '9' and resid 12 through 13 Processing sheet with id=AG6, first strand: chain '9' and resid 17 through 20 Processing sheet with id=AG7, first strand: chain '9' and resid 84 through 85 Processing sheet with id=AG8, first strand: chain '10' and resid 2 through 3 Processing sheet with id=AG9, first strand: chain '10' and resid 43 through 45 removed outlier: 6.179A pdb=" N VAL10 7 " --> pdb=" O SER10 87 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N SER10 87 " --> pdb=" O VAL10 7 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N MET10 9 " --> pdb=" O ILE10 85 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain '11' and resid 72 through 73 Processing sheet with id=AH2, first strand: chain '12' and resid 23 through 27 removed outlier: 6.409A pdb=" N GLU12 59 " --> pdb=" O PHE12 48 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N PHE12 48 " --> pdb=" O GLU12 59 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N THR12 61 " --> pdb=" O GLU12 46 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain '12' and resid 73 through 76 removed outlier: 6.739A pdb=" N VAL12 102 " --> pdb=" O ILE12 125 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain '13' and resid 6 through 7 removed outlier: 6.250A pdb=" N VAL13 28 " --> pdb=" O ILE13 64 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N VAL13 66 " --> pdb=" O VAL13 28 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain '14' and resid 44 through 46 removed outlier: 3.688A pdb=" N ARG14 45 " --> pdb=" O THR14 69 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain '14' and resid 51 through 52 Processing sheet with id=AH7, first strand: chain '15' and resid 40 through 45 removed outlier: 6.245A pdb=" N LEU15 81 " --> pdb=" O ILE15 106 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASN15 108 " --> pdb=" O LEU15 81 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL25 5 " --> pdb=" O ILE15 109 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain '16' and resid 34 through 39 removed outlier: 4.593A pdb=" N VAL16 36 " --> pdb=" O VAL16 51 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL16 51 " --> pdb=" O VAL16 36 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR16 38 " --> pdb=" O ARG16 49 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ARG16 49 " --> pdb=" O THR16 38 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain '16' and resid 81 through 82 Processing sheet with id=AI1, first strand: chain '20' and resid 2 through 5 removed outlier: 3.614A pdb=" N GLU20 34 " --> pdb=" O VAL20 21 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain '20' and resid 37 through 39 Processing sheet with id=AI3, first strand: chain '21' and resid 10 through 16 removed outlier: 6.541A pdb=" N VAL21 21 " --> pdb=" O VAL21 12 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ASP21 14 " --> pdb=" O SER21 19 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N SER21 19 " --> pdb=" O ASP21 14 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP21 72 " --> pdb=" O HIS21 44 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N LEU21 74 " --> pdb=" O ARG21 61 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ARG21 61 " --> pdb=" O LEU21 74 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARG21 76 " --> pdb=" O GLU21 59 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASP21 56 " --> pdb=" O VAL21 11 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain '21' and resid 27 through 29 Processing sheet with id=AI5, first strand: chain '33' and resid 247 through 252 removed outlier: 3.957A pdb=" N ALA33 278 " --> pdb=" O ARG33 252 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain '33' and resid 405 through 409 removed outlier: 3.789A pdb=" N VAL33 408 " --> pdb=" O VAL33 416 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL33 416 " --> pdb=" O VAL33 408 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain '33' and resid 447 through 448 Processing sheet with id=AI8, first strand: chain '33' and resid 607 through 609 removed outlier: 6.163A pdb=" N HIS33 608 " --> pdb=" O VAL33 633 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILE33 621 " --> pdb=" O ALA33 655 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ALA33 655 " --> pdb=" O ILE33 621 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain '33' and resid 698 through 700 removed outlier: 3.696A pdb=" N ILE33 710 " --> pdb=" O VAL33 671 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG33 670 " --> pdb=" O ARG33 739 " (cutoff:3.500A) 2008 hydrogen bonds defined for protein. 5577 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3923 hydrogen bonds 6246 hydrogen bond angles 0 basepair planarities 1567 basepair parallelities 2361 stacking parallelities Total time for adding SS restraints: 239.56 Time building geometry restraints manager: 78.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 15828 1.32 - 1.46: 82056 1.46 - 1.60: 64677 1.60 - 1.74: 4812 1.74 - 1.88: 310 Bond restraints: 167683 Sorted by residual: bond pdb=" CZ ARG33 156 " pdb=" NH2 ARG33 156 " ideal model delta sigma weight residual 1.330 1.189 0.141 1.30e-02 5.92e+03 1.18e+02 bond pdb=" CA PRO33 17 " pdb=" CB PRO33 17 " ideal model delta sigma weight residual 1.534 1.386 0.148 1.49e-02 4.50e+03 9.84e+01 bond pdb=" NE1 TRP33 20 " pdb=" CE2 TRP33 20 " ideal model delta sigma weight residual 1.370 1.286 0.084 1.10e-02 8.26e+03 5.86e+01 bond pdb=" CD LYS33 152 " pdb=" CE LYS33 152 " ideal model delta sigma weight residual 1.520 1.314 0.206 3.00e-02 1.11e+03 4.73e+01 bond pdb=" CG HIS33 159 " pdb=" ND1 HIS33 159 " ideal model delta sigma weight residual 1.378 1.306 0.072 1.10e-02 8.26e+03 4.27e+01 ... (remaining 167678 not shown) Histogram of bond angle deviations from ideal: 88.62 - 98.00: 21 98.00 - 107.37: 36044 107.37 - 116.75: 114772 116.75 - 126.13: 83536 126.13 - 135.50: 15907 Bond angle restraints: 250280 Sorted by residual: angle pdb=" N ALA16 22 " pdb=" CA ALA16 22 " pdb=" C ALA16 22 " ideal model delta sigma weight residual 113.18 95.32 17.86 1.21e+00 6.83e-01 2.18e+02 angle pdb=" N ARG25 20 " pdb=" CA ARG25 20 " pdb=" C ARG25 20 " ideal model delta sigma weight residual 112.89 94.73 18.16 1.24e+00 6.50e-01 2.14e+02 angle pdb=" N GLN33 555 " pdb=" CA GLN33 555 " pdb=" C GLN33 555 " ideal model delta sigma weight residual 113.23 97.37 15.86 1.24e+00 6.50e-01 1.64e+02 angle pdb=" N PRO33 17 " pdb=" CA PRO33 17 " pdb=" CB PRO33 17 " ideal model delta sigma weight residual 103.33 89.93 13.40 1.10e+00 8.26e-01 1.48e+02 angle pdb=" NH1 ARG33 156 " pdb=" CZ ARG33 156 " pdb=" NH2 ARG33 156 " ideal model delta sigma weight residual 119.30 104.13 15.17 1.30e+00 5.92e-01 1.36e+02 ... (remaining 250275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.93: 94722 34.93 - 69.87: 11113 69.87 - 104.80: 1427 104.80 - 139.74: 16 139.74 - 174.67: 31 Dihedral angle restraints: 107309 sinusoidal: 88431 harmonic: 18878 Sorted by residual: dihedral pdb=" C5' C272712 " pdb=" C4' C272712 " pdb=" C3' C272712 " pdb=" O3' C272712 " ideal model delta sinusoidal sigma weight residual 147.00 74.35 72.65 1 8.00e+00 1.56e-02 1.05e+02 dihedral pdb=" C5' A271111 " pdb=" C4' A271111 " pdb=" C3' A271111 " pdb=" O3' A271111 " ideal model delta sinusoidal sigma weight residual 147.00 74.97 72.03 1 8.00e+00 1.56e-02 1.04e+02 dihedral pdb=" C PRO33 17 " pdb=" N PRO33 17 " pdb=" CA PRO33 17 " pdb=" CB PRO33 17 " ideal model delta harmonic sigma weight residual -120.70 -95.30 -25.40 0 2.50e+00 1.60e-01 1.03e+02 ... (remaining 107306 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 27524 0.130 - 0.260: 3998 0.260 - 0.391: 381 0.391 - 0.521: 22 0.521 - 0.651: 11 Chirality restraints: 31936 Sorted by residual: chirality pdb=" P G27 1 " pdb=" OP1 G27 1 " pdb=" OP2 G27 1 " pdb=" O5' G27 1 " both_signs ideal model delta sigma weight residual True 2.41 -3.06 -0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" P C31 1 " pdb=" OP1 C31 1 " pdb=" OP2 C31 1 " pdb=" O5' C31 1 " both_signs ideal model delta sigma weight residual True 2.41 -3.06 -0.64 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" P G30 1 " pdb=" OP1 G30 1 " pdb=" OP2 G30 1 " pdb=" O5' G30 1 " both_signs ideal model delta sigma weight residual True 2.41 -3.05 -0.64 2.00e-01 2.50e+01 1.03e+01 ... (remaining 31933 not shown) Planarity restraints: 13865 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G30 15 " -0.198 2.00e-02 2.50e+03 9.57e-02 2.75e+02 pdb=" N9 G30 15 " 0.003 2.00e-02 2.50e+03 pdb=" C8 G30 15 " 0.119 2.00e-02 2.50e+03 pdb=" N7 G30 15 " 0.126 2.00e-02 2.50e+03 pdb=" C5 G30 15 " 0.042 2.00e-02 2.50e+03 pdb=" C6 G30 15 " -0.040 2.00e-02 2.50e+03 pdb=" O6 G30 15 " -0.161 2.00e-02 2.50e+03 pdb=" N1 G30 15 " -0.024 2.00e-02 2.50e+03 pdb=" C2 G30 15 " 0.014 2.00e-02 2.50e+03 pdb=" N2 G30 15 " 0.100 2.00e-02 2.50e+03 pdb=" N3 G30 15 " -0.003 2.00e-02 2.50e+03 pdb=" C4 G30 15 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G26 898 " 0.193 2.00e-02 2.50e+03 8.29e-02 2.06e+02 pdb=" N9 G26 898 " -0.006 2.00e-02 2.50e+03 pdb=" C8 G26 898 " -0.095 2.00e-02 2.50e+03 pdb=" N7 G26 898 " -0.093 2.00e-02 2.50e+03 pdb=" C5 G26 898 " -0.035 2.00e-02 2.50e+03 pdb=" C6 G26 898 " 0.041 2.00e-02 2.50e+03 pdb=" O6 G26 898 " 0.123 2.00e-02 2.50e+03 pdb=" N1 G26 898 " 0.039 2.00e-02 2.50e+03 pdb=" C2 G26 898 " -0.018 2.00e-02 2.50e+03 pdb=" N2 G26 898 " -0.061 2.00e-02 2.50e+03 pdb=" N3 G26 898 " -0.043 2.00e-02 2.50e+03 pdb=" C4 G26 898 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP33 39 " -0.029 2.00e-02 2.50e+03 8.95e-02 2.00e+02 pdb=" CG TRP33 39 " 0.135 2.00e-02 2.50e+03 pdb=" CD1 TRP33 39 " 0.082 2.00e-02 2.50e+03 pdb=" CD2 TRP33 39 " 0.014 2.00e-02 2.50e+03 pdb=" NE1 TRP33 39 " -0.169 2.00e-02 2.50e+03 pdb=" CE2 TRP33 39 " -0.061 2.00e-02 2.50e+03 pdb=" CE3 TRP33 39 " -0.076 2.00e-02 2.50e+03 pdb=" CZ2 TRP33 39 " 0.064 2.00e-02 2.50e+03 pdb=" CZ3 TRP33 39 " -0.056 2.00e-02 2.50e+03 pdb=" CH2 TRP33 39 " 0.094 2.00e-02 2.50e+03 ... (remaining 13862 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 4769 2.65 - 3.21: 152263 3.21 - 3.77: 324559 3.77 - 4.34: 414772 4.34 - 4.90: 549935 Nonbonded interactions: 1446298 Sorted by model distance: nonbonded pdb=" NH1 ARG33 188 " pdb=" CA LEU33 377 " model vdw 2.087 3.550 nonbonded pdb=" O ASN K 93 " pdb=" N LEU K 95 " model vdw 2.182 2.520 nonbonded pdb=" OE1 GLN 5 37 " pdb=" O2' G271124 " model vdw 2.185 2.440 nonbonded pdb=" N ALA16 22 " pdb=" N LEU16 23 " model vdw 2.194 2.560 nonbonded pdb=" N GLN C 90 " pdb=" OE1 GLN C 90 " model vdw 2.226 2.520 ... (remaining 1446293 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain '31' and (resid 1 through 45 or resid 47 through 76)) selection = (chain '32' and (resid 1 through 45 or resid 47 through 76)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 26.990 Check model and map are aligned: 1.680 Set scattering table: 1.050 Process input model: 529.060 Find NCS groups from input model: 2.880 Set up NCS constraints: 0.370 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 570.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 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 : 0.008 0.206 167683 Z= 0.482 Angle : 1.184 22.177 250280 Z= 0.786 Chirality : 0.092 0.651 31936 Planarity : 0.014 0.292 13865 Dihedral : 22.842 174.674 95118 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 29.88 Ramachandran Plot: Outliers : 6.64 % Allowed : 13.21 % Favored : 80.15 % Rotamer: Outliers : 0.58 % Allowed : 3.05 % Favored : 96.36 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % 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: -4.56 (0.09), residues: 6509 helix: -3.14 (0.08), residues: 2103 sheet: -3.76 (0.13), residues: 987 loop : -2.68 (0.10), residues: 3419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.169 0.014 TRP33 39 HIS 0.042 0.001 HIS33 159 PHE 0.060 0.008 PHE33 274 TYR 0.151 0.011 TYR33 41 ARG 0.171 0.001 ARG33 156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13018 Ramachandran restraints generated. 6509 Oldfield, 0 Emsley, 6509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13018 Ramachandran restraints generated. 6509 Oldfield, 0 Emsley, 6509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1918 residues out of total 5423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 1887 time to evaluate : 6.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 195 GLN cc_start: 0.9631 (mm-40) cc_final: 0.9165 (mm110) REVERT: D 102 LEU cc_start: 0.9323 (tp) cc_final: 0.9116 (tt) REVERT: E 74 MET cc_start: 0.9193 (mtp) cc_final: 0.8830 (mtp) REVERT: E 130 ILE cc_start: 0.9192 (mt) cc_final: 0.8959 (mm) REVERT: F 2 GLN cc_start: 0.8900 (mp10) cc_final: 0.8412 (mp10) REVERT: F 28 ASN cc_start: 0.7741 (p0) cc_final: 0.7473 (p0) REVERT: F 135 HIS cc_start: 0.8644 (t-170) cc_final: 0.8370 (t70) REVERT: G 6 GLN cc_start: 0.9561 (mp10) cc_final: 0.9195 (mp10) REVERT: G 11 ILE cc_start: 0.8280 (mm) cc_final: 0.7896 (mm) REVERT: G 38 MET cc_start: 0.3498 (mtm) cc_final: 0.2781 (mtp) REVERT: G 52 MET cc_start: 0.1804 (ttt) cc_final: -0.1200 (mtt) REVERT: H 116 MET cc_start: 0.4192 (mtp) cc_final: 0.3519 (mtp) REVERT: I 120 ARG cc_start: 0.8772 (mtt90) cc_final: 0.8394 (mpt-90) REVERT: K 111 ILE cc_start: 0.8186 (mp) cc_final: 0.7906 (mp) REVERT: L 47 GLU cc_start: 0.9029 (tm-30) cc_final: 0.8612 (tp30) REVERT: M 51 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8682 (tt) REVERT: M 75 ILE cc_start: 0.9274 (mm) cc_final: 0.8773 (mm) REVERT: N 19 GLN cc_start: 0.9091 (tp40) cc_final: 0.8582 (tm-30) REVERT: N 89 ASP cc_start: 0.8894 (t70) cc_final: 0.8615 (t0) REVERT: O 15 ASP cc_start: 0.8489 (p0) cc_final: 0.8220 (p0) REVERT: O 113 LEU cc_start: 0.8681 (pp) cc_final: 0.8448 (pp) REVERT: Q 39 LEU cc_start: 0.8683 (tp) cc_final: 0.7998 (tp) REVERT: R 1 MET cc_start: 0.8688 (tpp) cc_final: 0.8480 (tpp) REVERT: R 109 ASP cc_start: 0.8273 (p0) cc_final: 0.7426 (p0) REVERT: U 56 PHE cc_start: 0.8883 (t80) cc_final: 0.8636 (t80) REVERT: U 57 TYR cc_start: 0.8394 (m-80) cc_final: 0.8152 (m-10) REVERT: U 60 VAL cc_start: 0.9234 (t) cc_final: 0.8958 (p) REVERT: W 47 THR cc_start: 0.8390 (m) cc_final: 0.8104 (t) REVERT: X 23 ARG cc_start: 0.8951 (mmt-90) cc_final: 0.8673 (mmp-170) REVERT: Y 3 THR cc_start: 0.9058 (p) cc_final: 0.8707 (t) REVERT: Y 36 GLU cc_start: 0.8441 (tm-30) cc_final: 0.8085 (tm-30) REVERT: Z 35 ASP cc_start: 0.8671 (p0) cc_final: 0.8191 (p0) REVERT: Z 50 ASP cc_start: 0.8421 (t70) cc_final: 0.8157 (t0) REVERT: 6 55 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8085 (mm-30) REVERT: 6 67 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8901 (mt) REVERT: 6 132 GLU cc_start: 0.8764 (tt0) cc_final: 0.8121 (pt0) REVERT: 6 207 ARG cc_start: 0.9250 (ttm170) cc_final: 0.8903 (ttm110) REVERT: 7 167 TYR cc_start: 0.7999 (m-80) cc_final: 0.7756 (m-80) REVERT: 10 13 ASP cc_start: 0.9045 (m-30) cc_final: 0.8708 (m-30) REVERT: 10 39 LEU cc_start: 0.9431 (mt) cc_final: 0.9162 (mp) REVERT: 11 105 GLU cc_start: 0.8949 (tp30) cc_final: 0.8737 (tm-30) REVERT: 12 9 MET cc_start: 0.9027 (ptm) cc_final: 0.8650 (ppp) REVERT: 12 127 TYR cc_start: 0.8770 (m-10) cc_final: 0.8531 (m-10) REVERT: 13 53 LEU cc_start: 0.9592 (tp) cc_final: 0.9255 (tp) REVERT: 14 15 HIS cc_start: 0.8985 (p-80) cc_final: 0.8564 (p-80) REVERT: 14 65 TYR cc_start: 0.7617 (m-80) cc_final: 0.6749 (m-80) REVERT: 14 101 SER cc_start: 0.8650 (m) cc_final: 0.8083 (t) REVERT: 15 104 PHE cc_start: 0.8236 (m-80) cc_final: 0.8023 (m-80) REVERT: 17 41 ASP cc_start: 0.9252 (p0) cc_final: 0.9005 (p0) REVERT: 17 43 LYS cc_start: 0.9420 (mptt) cc_final: 0.9168 (mmmt) REVERT: 17 62 PHE cc_start: 0.7580 (t80) cc_final: 0.7244 (t80) REVERT: 17 68 LEU cc_start: 0.9287 (tp) cc_final: 0.9058 (tp) REVERT: 18 30 ILE cc_start: 0.9323 (mt) cc_final: 0.8416 (mt) REVERT: 22 34 GLU cc_start: 0.8905 (tp30) cc_final: 0.8611 (tp30) REVERT: 25 7 GLU cc_start: 0.6976 (mm-30) cc_final: 0.6581 (mm-30) REVERT: 25 36 PHE cc_start: 0.8852 (p90) cc_final: 0.8621 (p90) REVERT: 25 48 LYS cc_start: 0.8891 (mmmt) cc_final: 0.8402 (mmtp) REVERT: 33 113 MET cc_start: 0.2736 (mmm) cc_final: 0.2167 (mtt) REVERT: 33 142 MET cc_start: 0.4034 (ptt) cc_final: 0.1622 (ptp) REVERT: 33 263 MET cc_start: 0.2743 (mtp) cc_final: 0.2507 (ptt) REVERT: 33 425 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8369 (pp) outliers start: 31 outliers final: 12 residues processed: 1913 average time/residue: 1.4851 time to fit residues: 4861.6018 Evaluate side-chains 1302 residues out of total 5423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 1287 time to evaluate : 6.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain Z residue 37 CYS Chi-restraints excluded: chain 3 residue 44 VAL Chi-restraints excluded: chain 6 residue 67 LEU Chi-restraints excluded: chain 7 residue 102 ILE Chi-restraints excluded: chain 8 residue 52 VAL Chi-restraints excluded: chain 9 residue 122 VAL Chi-restraints excluded: chain 9 residue 152 VAL Chi-restraints excluded: chain 13 residue 60 LEU Chi-restraints excluded: chain 13 residue 93 LEU Chi-restraints excluded: chain 33 residue 425 LEU Chi-restraints excluded: chain 33 residue 463 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1117 random chunks: chunk 943 optimal weight: 40.0000 chunk 846 optimal weight: 20.0000 chunk 469 optimal weight: 1.9990 chunk 289 optimal weight: 30.0000 chunk 571 optimal weight: 30.0000 chunk 452 optimal weight: 8.9990 chunk 875 optimal weight: 20.0000 chunk 338 optimal weight: 20.0000 chunk 532 optimal weight: 8.9990 chunk 651 optimal weight: 20.0000 chunk 1014 optimal weight: 20.0000 overall best weight: 11.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 238 ASN A 242 HIS ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN C 9 GLN C 62 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 4 HIS D 51 ASN D 62 GLN ** D 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 ASN E 110 HIS F 135 HIS ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 ASN ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 58 ASN ** I 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 35 HIS K 54 GLN K 104 GLN ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 22 GLN ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 ASN ** O 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 114 ASN Q 11 GLN ** Q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 15 HIS ** S 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 39 ASN ** T 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 49 ASN ** U 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 8 ASN V 72 ASN X 25 GLN X 58 ASN Z 20 ASN Z 61 ASN 1 4 GLN ** 1 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 14 HIS 6 35 ASN 6 57 ASN ** 7 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 35 GLN 8 53 GLN 8 84 ASN ** 8 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 125 ASN 8 151 GLN 9 42 ASN 10 3 HIS 10 63 ASN ** 11 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 121 ASN ** 12 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 30 ASN ** 13 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 14 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 14 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 15 27 ASN ** 15 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 16 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 16 28 GLN ** 16 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 18 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 19 39 GLN ** 19 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 19 49 HIS ** 20 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 20 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 20 63 GLN ** 20 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 23 68 HIS ** 24 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 25 63 ASN 33 88 ASN 33 108 HIS 33 320 GLN 33 430 HIS 33 437 HIS ** 33 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 33 604 ASN 33 614 GLN 33 693 ASN Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.113 167683 Z= 0.375 Angle : 0.830 16.166 250280 Z= 0.424 Chirality : 0.044 0.311 31936 Planarity : 0.006 0.154 13865 Dihedral : 23.996 177.755 82454 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 30.85 Ramachandran Plot: Outliers : 1.64 % Allowed : 11.95 % Favored : 86.40 % Rotamer: Outliers : 4.24 % Allowed : 15.82 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.25 (0.09), residues: 6509 helix: -1.48 (0.10), residues: 2183 sheet: -3.27 (0.13), residues: 1050 loop : -2.19 (0.10), residues: 3276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP C 78 HIS 0.012 0.002 HIS I 132 PHE 0.029 0.003 PHE D 174 TYR 0.045 0.003 TYR 8 74 ARG 0.012 0.001 ARG 6 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13018 Ramachandran restraints generated. 6509 Oldfield, 0 Emsley, 6509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13018 Ramachandran restraints generated. 6509 Oldfield, 0 Emsley, 6509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1724 residues out of total 5423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 1499 time to evaluate : 6.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ASP cc_start: 0.9049 (p0) cc_final: 0.8769 (p0) REVERT: C 195 GLN cc_start: 0.9585 (mm-40) cc_final: 0.9313 (mm110) REVERT: E 150 TYR cc_start: 0.8450 (m-80) cc_final: 0.7992 (m-80) REVERT: F 8 LYS cc_start: 0.8718 (tptp) cc_final: 0.8505 (tptp) REVERT: F 46 PHE cc_start: 0.9425 (m-10) cc_final: 0.9122 (m-10) REVERT: F 135 HIS cc_start: 0.8979 (t70) cc_final: 0.8442 (t70) REVERT: G 11 ILE cc_start: 0.8220 (mm) cc_final: 0.7993 (mm) REVERT: G 38 MET cc_start: 0.3301 (mtm) cc_final: 0.2547 (mtp) REVERT: G 52 MET cc_start: 0.0941 (ttt) cc_final: -0.1200 (mtt) REVERT: G 86 MET cc_start: 0.4896 (mmt) cc_final: 0.4657 (tpt) REVERT: H 120 ASP cc_start: 0.6056 (t0) cc_final: 0.5831 (t0) REVERT: H 124 MET cc_start: 0.3082 (mmp) cc_final: 0.2127 (mmt) REVERT: I 136 GLN cc_start: 0.8012 (mp10) cc_final: 0.7691 (mp10) REVERT: J 32 TYR cc_start: 0.8301 (m-80) cc_final: 0.7870 (m-80) REVERT: K 101 ILE cc_start: 0.8526 (pt) cc_final: 0.8295 (pt) REVERT: M 74 GLU cc_start: 0.8914 (tm-30) cc_final: 0.8652 (tm-30) REVERT: M 75 ILE cc_start: 0.8974 (mm) cc_final: 0.8770 (mm) REVERT: N 80 GLU cc_start: 0.9238 (mm-30) cc_final: 0.9035 (mm-30) REVERT: N 89 ASP cc_start: 0.8965 (t70) cc_final: 0.8723 (t0) REVERT: O 33 GLU cc_start: 0.7529 (mp0) cc_final: 0.6879 (mp0) REVERT: P 24 TYR cc_start: 0.6766 (t80) cc_final: 0.6546 (t80) REVERT: P 46 TYR cc_start: 0.8069 (t80) cc_final: 0.7807 (t80) REVERT: Q 39 LEU cc_start: 0.8564 (tp) cc_final: 0.8062 (tp) REVERT: Q 60 LYS cc_start: 0.9059 (mmmt) cc_final: 0.8832 (mmmt) REVERT: S 1 MET cc_start: 0.6045 (tpp) cc_final: 0.5064 (ppp) REVERT: S 69 ARG cc_start: 0.8458 (ttp80) cc_final: 0.7881 (ttp80) REVERT: T 6 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.7129 (tpp80) REVERT: T 26 ASN cc_start: 0.8911 (t0) cc_final: 0.8587 (t0) REVERT: W 37 PHE cc_start: 0.7669 (m-80) cc_final: 0.6823 (m-10) REVERT: W 47 THR cc_start: 0.8566 (m) cc_final: 0.8237 (t) REVERT: X 23 ARG cc_start: 0.8965 (mmt-90) cc_final: 0.8761 (mmp-170) REVERT: X 44 LYS cc_start: 0.9015 (tttp) cc_final: 0.8711 (tptp) REVERT: Y 4 ILE cc_start: 0.9236 (tt) cc_final: 0.8960 (tt) REVERT: Y 5 LYS cc_start: 0.8834 (mppt) cc_final: 0.8085 (mmtm) REVERT: Z 50 ASP cc_start: 0.8414 (t70) cc_final: 0.7955 (t0) REVERT: 6 21 TYR cc_start: 0.8418 (OUTLIER) cc_final: 0.7499 (p90) REVERT: 6 67 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8983 (mt) REVERT: 6 125 PHE cc_start: 0.8918 (p90) cc_final: 0.7931 (p90) REVERT: 6 153 MET cc_start: 0.8526 (tpt) cc_final: 0.7935 (tpp) REVERT: 6 207 ARG cc_start: 0.9097 (ttm170) cc_final: 0.8734 (ttm110) REVERT: 7 33 ASP cc_start: 0.8844 (t0) cc_final: 0.8333 (t0) REVERT: 7 117 ASP cc_start: 0.9388 (t0) cc_final: 0.9021 (p0) REVERT: 8 47 LEU cc_start: 0.9254 (tp) cc_final: 0.9042 (tt) REVERT: 10 16 GLU cc_start: 0.9011 (mp0) cc_final: 0.8749 (mp0) REVERT: 12 26 MET cc_start: 0.9057 (pmm) cc_final: 0.8834 (pmm) REVERT: 14 15 HIS cc_start: 0.8831 (p-80) cc_final: 0.8569 (p-80) REVERT: 14 63 ASP cc_start: 0.8507 (t0) cc_final: 0.8244 (t0) REVERT: 14 65 TYR cc_start: 0.7204 (m-80) cc_final: 0.6947 (m-80) REVERT: 14 81 GLU cc_start: 0.8737 (tm-30) cc_final: 0.8528 (tm-30) REVERT: 15 104 PHE cc_start: 0.8286 (m-80) cc_final: 0.8022 (m-80) REVERT: 17 71 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8473 (mm-30) REVERT: 20 1 MET cc_start: 0.8512 (ttp) cc_final: 0.8263 (tmm) REVERT: 22 34 GLU cc_start: 0.8841 (tp30) cc_final: 0.8489 (tp30) REVERT: 25 16 ARG cc_start: 0.7062 (ptm160) cc_final: 0.6795 (ptm-80) REVERT: 25 36 PHE cc_start: 0.8628 (p90) cc_final: 0.8307 (p90) REVERT: 33 113 MET cc_start: 0.2671 (mmm) cc_final: 0.2373 (mtt) REVERT: 33 142 MET cc_start: 0.2935 (ptt) cc_final: 0.2061 (ptp) REVERT: 33 425 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8393 (pp) REVERT: 33 451 PHE cc_start: 0.7819 (m-10) cc_final: 0.7541 (m-80) outliers start: 225 outliers final: 112 residues processed: 1600 average time/residue: 1.3933 time to fit residues: 3845.0605 Evaluate side-chains 1352 residues out of total 5423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 1236 time to evaluate : 6.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 268 ARG Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain H residue 91 LYS Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 80 ASP Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 80 SER Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain O residue 39 LEU Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 90 ASP Chi-restraints excluded: chain Q residue 70 GLU Chi-restraints excluded: chain R residue 110 ARG Chi-restraints excluded: chain S residue 32 LEU Chi-restraints excluded: chain T residue 6 ARG Chi-restraints excluded: chain U residue 8 VAL Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain V residue 54 THR Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain X residue 13 GLU Chi-restraints excluded: chain X residue 43 LEU Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain Z residue 4 ASP Chi-restraints excluded: chain Z residue 21 VAL Chi-restraints excluded: chain Z residue 37 CYS Chi-restraints excluded: chain Z residue 58 ASP Chi-restraints excluded: chain 1 residue 5 ASN Chi-restraints excluded: chain 3 residue 44 VAL Chi-restraints excluded: chain 4 residue 6 VAL Chi-restraints excluded: chain 4 residue 60 CYS Chi-restraints excluded: chain 5 residue 7 VAL Chi-restraints excluded: chain 5 residue 22 VAL Chi-restraints excluded: chain 6 residue 21 TYR Chi-restraints excluded: chain 6 residue 30 ILE Chi-restraints excluded: chain 6 residue 67 LEU Chi-restraints excluded: chain 6 residue 150 ILE Chi-restraints excluded: chain 6 residue 158 ASP Chi-restraints excluded: chain 6 residue 162 VAL Chi-restraints excluded: chain 7 residue 102 ILE Chi-restraints excluded: chain 7 residue 156 LEU Chi-restraints excluded: chain 8 residue 28 ASP Chi-restraints excluded: chain 8 residue 34 GLU Chi-restraints excluded: chain 8 residue 52 VAL Chi-restraints excluded: chain 8 residue 116 LEU Chi-restraints excluded: chain 8 residue 173 ASP Chi-restraints excluded: chain 8 residue 177 MET Chi-restraints excluded: chain 9 residue 29 ILE Chi-restraints excluded: chain 9 residue 121 ASN Chi-restraints excluded: chain 9 residue 122 VAL Chi-restraints excluded: chain 9 residue 130 THR Chi-restraints excluded: chain 9 residue 141 ASP Chi-restraints excluded: chain 9 residue 152 VAL Chi-restraints excluded: chain 10 residue 72 ASP Chi-restraints excluded: chain 10 residue 82 ASP Chi-restraints excluded: chain 11 residue 39 GLU Chi-restraints excluded: chain 12 residue 74 ILE Chi-restraints excluded: chain 12 residue 84 ILE Chi-restraints excluded: chain 12 residue 89 ASP Chi-restraints excluded: chain 13 residue 32 ARG Chi-restraints excluded: chain 13 residue 34 LEU Chi-restraints excluded: chain 13 residue 60 LEU Chi-restraints excluded: chain 14 residue 8 ILE Chi-restraints excluded: chain 14 residue 76 ILE Chi-restraints excluded: chain 15 residue 39 ASN Chi-restraints excluded: chain 15 residue 109 ILE Chi-restraints excluded: chain 16 residue 38 THR Chi-restraints excluded: chain 16 residue 40 THR Chi-restraints excluded: chain 16 residue 52 CYS Chi-restraints excluded: chain 16 residue 55 ARG Chi-restraints excluded: chain 17 residue 24 VAL Chi-restraints excluded: chain 17 residue 82 LEU Chi-restraints excluded: chain 18 residue 81 ILE Chi-restraints excluded: chain 18 residue 92 ILE Chi-restraints excluded: chain 18 residue 96 LYS Chi-restraints excluded: chain 20 residue 77 GLU Chi-restraints excluded: chain 21 residue 69 THR Chi-restraints excluded: chain 22 residue 41 SER Chi-restraints excluded: chain 23 residue 23 GLU Chi-restraints excluded: chain 23 residue 65 MET Chi-restraints excluded: chain 23 residue 66 VAL Chi-restraints excluded: chain 24 residue 78 LEU Chi-restraints excluded: chain 24 residue 85 LEU Chi-restraints excluded: chain 25 residue 12 ASP Chi-restraints excluded: chain 25 residue 18 PHE Chi-restraints excluded: chain 33 residue 108 HIS Chi-restraints excluded: chain 33 residue 425 LEU Chi-restraints excluded: chain 33 residue 613 CYS Chi-restraints excluded: chain 33 residue 654 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1117 random chunks: chunk 563 optimal weight: 5.9990 chunk 314 optimal weight: 40.0000 chunk 844 optimal weight: 20.0000 chunk 690 optimal weight: 20.0000 chunk 279 optimal weight: 30.0000 chunk 1016 optimal weight: 20.0000 chunk 1097 optimal weight: 50.0000 chunk 905 optimal weight: 20.0000 chunk 1007 optimal weight: 20.0000 chunk 346 optimal weight: 10.0000 chunk 815 optimal weight: 20.0000 overall best weight: 15.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 GLN B 134 HIS ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 87 GLN E 127 GLN ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 GLN ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 35 HIS ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 11 GLN O 14 GLN ** P 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 70 GLN ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 68 ASN ** T 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 44 HIS ** U 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 36 GLN ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 19 HIS ** 1 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 6 GLN ** 6 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 35 GLN ** 8 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 53 GLN ** 8 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 14 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 14 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 15 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 16 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 16 5 GLN 16 28 GLN ** 19 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 20 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 20 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 22 18 GLN ** 24 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 33 108 HIS ** 33 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 33 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 33 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.131 167683 Z= 0.435 Angle : 0.815 13.321 250280 Z= 0.419 Chirality : 0.043 0.325 31936 Planarity : 0.006 0.072 13865 Dihedral : 24.180 179.274 82447 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 36.69 Ramachandran Plot: Outliers : 1.32 % Allowed : 12.67 % Favored : 86.00 % Rotamer: Outliers : 5.96 % Allowed : 16.95 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.10), residues: 6509 helix: -1.04 (0.10), residues: 2182 sheet: -3.02 (0.13), residues: 1059 loop : -2.10 (0.11), residues: 3268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP C 78 HIS 0.033 0.002 HIS33 108 PHE 0.033 0.003 PHE C 85 TYR 0.041 0.003 TYR 8 74 ARG 0.023 0.001 ARG 9 68 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13018 Ramachandran restraints generated. 6509 Oldfield, 0 Emsley, 6509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13018 Ramachandran restraints generated. 6509 Oldfield, 0 Emsley, 6509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1633 residues out of total 5423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 316 poor density : 1317 time to evaluate : 6.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8821 (mm) REVERT: C 90 GLN cc_start: 0.9127 (pm20) cc_final: 0.8876 (pm20) REVERT: C 100 MET cc_start: 0.9132 (mmp) cc_final: 0.8851 (mmt) REVERT: C 195 GLN cc_start: 0.9586 (mm-40) cc_final: 0.9320 (mm110) REVERT: F 8 LYS cc_start: 0.8781 (tptp) cc_final: 0.8509 (tptp) REVERT: F 43 ASN cc_start: 0.9555 (m-40) cc_final: 0.9240 (p0) REVERT: F 132 PHE cc_start: 0.8365 (m-80) cc_final: 0.7959 (m-80) REVERT: F 135 HIS cc_start: 0.8963 (t70) cc_final: 0.8404 (t70) REVERT: F 141 LYS cc_start: 0.7878 (mmpt) cc_final: 0.7660 (mmmt) REVERT: G 6 GLN cc_start: 0.9397 (mp10) cc_final: 0.9155 (mp10) REVERT: G 38 MET cc_start: 0.3378 (mtm) cc_final: -0.0636 (mtp) REVERT: G 52 MET cc_start: 0.1154 (ttt) cc_final: -0.0925 (mtt) REVERT: H 117 THR cc_start: 0.0670 (OUTLIER) cc_final: -0.0301 (p) REVERT: H 120 ASP cc_start: 0.6765 (t0) cc_final: 0.6431 (t0) REVERT: H 124 MET cc_start: 0.3007 (mmp) cc_final: 0.1353 (tpp) REVERT: H 126 ARG cc_start: 0.8489 (ttm110) cc_final: 0.7986 (mtm-85) REVERT: K 77 ILE cc_start: 0.8489 (pt) cc_final: 0.8271 (mp) REVERT: K 81 ASP cc_start: 0.9280 (p0) cc_final: 0.8593 (t0) REVERT: K 105 ILE cc_start: 0.9336 (mt) cc_final: 0.8838 (mt) REVERT: L 136 MET cc_start: 0.7203 (tmm) cc_final: 0.6598 (tmm) REVERT: M 74 GLU cc_start: 0.9005 (tm-30) cc_final: 0.8799 (tm-30) REVERT: M 75 ILE cc_start: 0.9060 (mm) cc_final: 0.8812 (mm) REVERT: O 4 ILE cc_start: 0.9547 (tt) cc_final: 0.9275 (tt) REVERT: P 24 TYR cc_start: 0.6965 (t80) cc_final: 0.6700 (t80) REVERT: Q 39 LEU cc_start: 0.8491 (tp) cc_final: 0.7812 (tp) REVERT: Q 74 ILE cc_start: 0.8540 (mt) cc_final: 0.8233 (mt) REVERT: R 55 ILE cc_start: 0.9222 (mm) cc_final: 0.8981 (tt) REVERT: T 6 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.7746 (tpp80) REVERT: U 44 HIS cc_start: 0.7218 (t-90) cc_final: 0.6725 (t-90) REVERT: V 71 LYS cc_start: 0.8713 (mtmm) cc_final: 0.8484 (ptpp) REVERT: W 37 PHE cc_start: 0.7730 (m-80) cc_final: 0.6728 (m-10) REVERT: X 44 LYS cc_start: 0.8977 (tttp) cc_final: 0.8633 (tptp) REVERT: Z 50 ASP cc_start: 0.8367 (t70) cc_final: 0.6986 (t0) REVERT: 6 21 TYR cc_start: 0.8371 (OUTLIER) cc_final: 0.7510 (p90) REVERT: 6 24 PRO cc_start: 0.7036 (Cg_exo) cc_final: 0.6824 (Cg_endo) REVERT: 6 26 MET cc_start: 0.7975 (mtp) cc_final: 0.7595 (ttm) REVERT: 6 67 LEU cc_start: 0.9320 (tt) cc_final: 0.8901 (mt) REVERT: 6 153 MET cc_start: 0.8618 (tpt) cc_final: 0.8122 (tpp) REVERT: 6 207 ARG cc_start: 0.9027 (ttm170) cc_final: 0.8626 (ttm110) REVERT: 7 117 ASP cc_start: 0.9417 (t0) cc_final: 0.9072 (p0) REVERT: 7 133 MET cc_start: 0.9287 (mtp) cc_final: 0.8988 (mtm) REVERT: 7 167 TYR cc_start: 0.8290 (m-80) cc_final: 0.7768 (m-80) REVERT: 9 68 ARG cc_start: 0.8962 (mtm110) cc_final: 0.8643 (mtm-85) REVERT: 9 123 LEU cc_start: 0.9160 (mm) cc_final: 0.8891 (mm) REVERT: 10 59 TYR cc_start: 0.7482 (m-10) cc_final: 0.7136 (m-10) REVERT: 11 30 MET cc_start: 0.8301 (ttp) cc_final: 0.8051 (ttt) REVERT: 12 26 MET cc_start: 0.9129 (pmm) cc_final: 0.8730 (pmm) REVERT: 13 87 MET cc_start: 0.9585 (ppp) cc_final: 0.9214 (ppp) REVERT: 14 46 LYS cc_start: 0.8764 (mmmt) cc_final: 0.8191 (mmmm) REVERT: 14 65 TYR cc_start: 0.7525 (m-80) cc_final: 0.7183 (m-80) REVERT: 15 80 ASN cc_start: 0.7663 (OUTLIER) cc_final: 0.7439 (p0) REVERT: 16 5 GLN cc_start: 0.7818 (mt0) cc_final: 0.7414 (mt0) REVERT: 17 77 LYS cc_start: 0.9273 (tppt) cc_final: 0.8959 (tppt) REVERT: 20 69 ASP cc_start: 0.8953 (p0) cc_final: 0.8718 (p0) REVERT: 21 36 PHE cc_start: 0.7868 (m-80) cc_final: 0.7638 (m-10) REVERT: 21 42 LYS cc_start: 0.9307 (mtpt) cc_final: 0.9040 (ttpp) REVERT: 23 31 ARG cc_start: 0.9348 (mmm-85) cc_final: 0.9129 (tpp80) REVERT: 24 26 MET cc_start: 0.8864 (ppp) cc_final: 0.8506 (ppp) REVERT: 24 27 MET cc_start: 0.9512 (ppp) cc_final: 0.9294 (ppp) REVERT: 24 53 MET cc_start: 0.8997 (ppp) cc_final: 0.8559 (ppp) REVERT: 25 16 ARG cc_start: 0.7155 (ptm160) cc_final: 0.6816 (ptm-80) REVERT: 25 36 PHE cc_start: 0.8569 (p90) cc_final: 0.8227 (p90) REVERT: 25 48 LYS cc_start: 0.9006 (mmtt) cc_final: 0.8058 (tttt) REVERT: 33 142 MET cc_start: 0.3548 (ptt) cc_final: 0.2845 (ptp) REVERT: 33 425 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8405 (pp) outliers start: 316 outliers final: 210 residues processed: 1487 average time/residue: 1.3473 time to fit residues: 3450.1162 Evaluate side-chains 1386 residues out of total 5423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 1170 time to evaluate : 6.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 268 ARG Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 126 ASN Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 15 ASP Chi-restraints excluded: chain E residue 19 ASN Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 47 PHE Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 91 LYS Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 81 ILE Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain I residue 91 GLU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 37 ASP Chi-restraints excluded: chain J residue 51 LYS Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 80 ASP Chi-restraints excluded: chain J residue 89 ASN Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 80 SER Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 142 ILE Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain O residue 40 GLN Chi-restraints excluded: chain O residue 43 GLU Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 90 ASP Chi-restraints excluded: chain P residue 96 ASP Chi-restraints excluded: chain P residue 106 THR Chi-restraints excluded: chain Q residue 14 VAL Chi-restraints excluded: chain Q residue 55 ASP Chi-restraints excluded: chain Q residue 76 LYS Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 110 ARG Chi-restraints excluded: chain S residue 79 ASP Chi-restraints excluded: chain T residue 6 ARG Chi-restraints excluded: chain T residue 7 ASP Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 69 VAL Chi-restraints excluded: chain U residue 3 THR Chi-restraints excluded: chain U residue 8 VAL Chi-restraints excluded: chain U residue 35 GLU Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain V residue 54 THR Chi-restraints excluded: chain W residue 22 ASN Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain W residue 63 ILE Chi-restraints excluded: chain X residue 5 GLU Chi-restraints excluded: chain X residue 7 ARG Chi-restraints excluded: chain X residue 13 GLU Chi-restraints excluded: chain X residue 24 GLU Chi-restraints excluded: chain X residue 43 LEU Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain Y residue 54 VAL Chi-restraints excluded: chain Z residue 4 ASP Chi-restraints excluded: chain Z residue 18 CYS Chi-restraints excluded: chain Z residue 37 CYS Chi-restraints excluded: chain Z residue 58 ASP Chi-restraints excluded: chain 1 residue 5 ASN Chi-restraints excluded: chain 2 residue 13 SER Chi-restraints excluded: chain 2 residue 33 LEU Chi-restraints excluded: chain 3 residue 44 VAL Chi-restraints excluded: chain 4 residue 6 VAL Chi-restraints excluded: chain 4 residue 56 LEU Chi-restraints excluded: chain 4 residue 57 VAL Chi-restraints excluded: chain 5 residue 7 VAL Chi-restraints excluded: chain 5 residue 16 ILE Chi-restraints excluded: chain 5 residue 22 VAL Chi-restraints excluded: chain 5 residue 37 GLN Chi-restraints excluded: chain 6 residue 21 TYR Chi-restraints excluded: chain 6 residue 30 ILE Chi-restraints excluded: chain 6 residue 113 LEU Chi-restraints excluded: chain 6 residue 139 GLU Chi-restraints excluded: chain 6 residue 150 ILE Chi-restraints excluded: chain 6 residue 158 ASP Chi-restraints excluded: chain 6 residue 162 VAL Chi-restraints excluded: chain 6 residue 185 ILE Chi-restraints excluded: chain 6 residue 186 VAL Chi-restraints excluded: chain 6 residue 198 VAL Chi-restraints excluded: chain 7 residue 31 ASN Chi-restraints excluded: chain 7 residue 38 VAL Chi-restraints excluded: chain 7 residue 102 ILE Chi-restraints excluded: chain 7 residue 156 LEU Chi-restraints excluded: chain 8 residue 16 THR Chi-restraints excluded: chain 8 residue 28 ASP Chi-restraints excluded: chain 8 residue 34 GLU Chi-restraints excluded: chain 8 residue 50 TYR Chi-restraints excluded: chain 8 residue 52 VAL Chi-restraints excluded: chain 8 residue 92 LEU Chi-restraints excluded: chain 8 residue 116 LEU Chi-restraints excluded: chain 8 residue 170 LEU Chi-restraints excluded: chain 8 residue 173 ASP Chi-restraints excluded: chain 8 residue 177 MET Chi-restraints excluded: chain 9 residue 10 LEU Chi-restraints excluded: chain 9 residue 29 ILE Chi-restraints excluded: chain 9 residue 121 ASN Chi-restraints excluded: chain 9 residue 122 VAL Chi-restraints excluded: chain 9 residue 130 THR Chi-restraints excluded: chain 9 residue 141 ASP Chi-restraints excluded: chain 9 residue 152 VAL Chi-restraints excluded: chain 9 residue 155 LYS Chi-restraints excluded: chain 10 residue 7 VAL Chi-restraints excluded: chain 10 residue 13 ASP Chi-restraints excluded: chain 10 residue 72 ASP Chi-restraints excluded: chain 10 residue 82 ASP Chi-restraints excluded: chain 10 residue 94 HIS Chi-restraints excluded: chain 11 residue 39 GLU Chi-restraints excluded: chain 11 residue 44 SER Chi-restraints excluded: chain 12 residue 10 LEU Chi-restraints excluded: chain 12 residue 41 GLU Chi-restraints excluded: chain 12 residue 68 LYS Chi-restraints excluded: chain 12 residue 84 ILE Chi-restraints excluded: chain 12 residue 86 LYS Chi-restraints excluded: chain 12 residue 89 ASP Chi-restraints excluded: chain 13 residue 5 TYR Chi-restraints excluded: chain 13 residue 20 ILE Chi-restraints excluded: chain 13 residue 32 ARG Chi-restraints excluded: chain 13 residue 34 LEU Chi-restraints excluded: chain 13 residue 57 VAL Chi-restraints excluded: chain 13 residue 60 LEU Chi-restraints excluded: chain 13 residue 65 THR Chi-restraints excluded: chain 13 residue 90 ASP Chi-restraints excluded: chain 13 residue 108 ARG Chi-restraints excluded: chain 14 residue 8 ILE Chi-restraints excluded: chain 14 residue 17 LEU Chi-restraints excluded: chain 14 residue 32 THR Chi-restraints excluded: chain 14 residue 51 VAL Chi-restraints excluded: chain 14 residue 91 ASP Chi-restraints excluded: chain 14 residue 96 VAL Chi-restraints excluded: chain 14 residue 101 SER Chi-restraints excluded: chain 15 residue 39 ASN Chi-restraints excluded: chain 15 residue 45 THR Chi-restraints excluded: chain 15 residue 71 ASP Chi-restraints excluded: chain 15 residue 80 ASN Chi-restraints excluded: chain 15 residue 95 THR Chi-restraints excluded: chain 15 residue 109 ILE Chi-restraints excluded: chain 16 residue 28 GLN Chi-restraints excluded: chain 16 residue 33 CYS Chi-restraints excluded: chain 16 residue 38 THR Chi-restraints excluded: chain 16 residue 40 THR Chi-restraints excluded: chain 16 residue 52 CYS Chi-restraints excluded: chain 16 residue 56 LEU Chi-restraints excluded: chain 16 residue 75 GLU Chi-restraints excluded: chain 16 residue 77 SER Chi-restraints excluded: chain 16 residue 108 ASP Chi-restraints excluded: chain 17 residue 24 VAL Chi-restraints excluded: chain 18 residue 36 SER Chi-restraints excluded: chain 18 residue 79 SER Chi-restraints excluded: chain 18 residue 81 ILE Chi-restraints excluded: chain 18 residue 92 ILE Chi-restraints excluded: chain 19 residue 13 GLU Chi-restraints excluded: chain 20 residue 77 GLU Chi-restraints excluded: chain 21 residue 56 ASP Chi-restraints excluded: chain 21 residue 69 THR Chi-restraints excluded: chain 22 residue 11 ARG Chi-restraints excluded: chain 22 residue 41 SER Chi-restraints excluded: chain 22 residue 70 THR Chi-restraints excluded: chain 23 residue 18 VAL Chi-restraints excluded: chain 23 residue 23 GLU Chi-restraints excluded: chain 23 residue 28 LYS Chi-restraints excluded: chain 23 residue 39 ILE Chi-restraints excluded: chain 23 residue 42 ASN Chi-restraints excluded: chain 23 residue 59 VAL Chi-restraints excluded: chain 23 residue 65 MET Chi-restraints excluded: chain 23 residue 66 VAL Chi-restraints excluded: chain 24 residue 52 GLU Chi-restraints excluded: chain 24 residue 78 LEU Chi-restraints excluded: chain 25 residue 6 ARG Chi-restraints excluded: chain 25 residue 12 ASP Chi-restraints excluded: chain 25 residue 18 PHE Chi-restraints excluded: chain 25 residue 42 THR Chi-restraints excluded: chain 33 residue 63 VAL Chi-restraints excluded: chain 33 residue 425 LEU Chi-restraints excluded: chain 33 residue 463 ILE Chi-restraints excluded: chain 33 residue 613 CYS Chi-restraints excluded: chain 33 residue 654 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1117 random chunks: chunk 1004 optimal weight: 30.0000 chunk 764 optimal weight: 20.0000 chunk 527 optimal weight: 9.9990 chunk 112 optimal weight: 6.9990 chunk 484 optimal weight: 8.9990 chunk 682 optimal weight: 20.0000 chunk 1019 optimal weight: 20.0000 chunk 1079 optimal weight: 8.9990 chunk 532 optimal weight: 20.0000 chunk 966 optimal weight: 20.0000 chunk 290 optimal weight: 0.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 HIS ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 GLN ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 35 HIS ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 GLN ** P 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 189 HIS 8 53 GLN ** 8 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 36 GLN ** 14 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 14 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 16 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 16 19 ASN 18 3 GLN ** 20 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 20 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 21 49 ASN ** 21 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 33 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 33 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 33 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 167683 Z= 0.248 Angle : 0.685 13.319 250280 Z= 0.348 Chirality : 0.037 0.311 31936 Planarity : 0.005 0.075 13865 Dihedral : 24.188 179.017 82443 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 27.48 Ramachandran Plot: Outliers : 1.20 % Allowed : 10.66 % Favored : 88.14 % Rotamer: Outliers : 5.15 % Allowed : 19.74 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.10), residues: 6509 helix: -0.48 (0.10), residues: 2200 sheet: -2.68 (0.14), residues: 1032 loop : -1.97 (0.11), residues: 3277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 78 HIS 0.015 0.002 HIS I 80 PHE 0.034 0.002 PHE33 451 TYR 0.034 0.002 TYR I 75 ARG 0.015 0.001 ARG I 37 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13018 Ramachandran restraints generated. 6509 Oldfield, 0 Emsley, 6509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13018 Ramachandran restraints generated. 6509 Oldfield, 0 Emsley, 6509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1641 residues out of total 5423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 1368 time to evaluate : 8.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 PHE cc_start: 0.8097 (m-80) cc_final: 0.7879 (m-80) REVERT: F 8 LYS cc_start: 0.8669 (tptp) cc_final: 0.8416 (tptp) REVERT: F 43 ASN cc_start: 0.9568 (m-40) cc_final: 0.9174 (p0) REVERT: F 112 LYS cc_start: 0.6278 (mttt) cc_final: 0.5496 (mtmt) REVERT: F 132 PHE cc_start: 0.8564 (m-80) cc_final: 0.8160 (m-80) REVERT: F 135 HIS cc_start: 0.9008 (t70) cc_final: 0.8446 (t70) REVERT: F 141 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7614 (mmmt) REVERT: G 52 MET cc_start: 0.1256 (ttt) cc_final: -0.0786 (mtt) REVERT: H 120 ASP cc_start: 0.7038 (t0) cc_final: 0.6692 (t0) REVERT: H 124 MET cc_start: 0.2936 (mmp) cc_final: 0.1821 (mmt) REVERT: H 126 ARG cc_start: 0.8382 (ttm110) cc_final: 0.7870 (mtm-85) REVERT: I 37 ARG cc_start: 0.7801 (ttm170) cc_final: 0.7556 (ttp-170) REVERT: I 67 ASN cc_start: 0.8353 (t0) cc_final: 0.8074 (t0) REVERT: L 95 LEU cc_start: 0.9100 (tt) cc_final: 0.8889 (tp) REVERT: L 136 MET cc_start: 0.7270 (tmm) cc_final: 0.6497 (tmm) REVERT: M 74 GLU cc_start: 0.8947 (tm-30) cc_final: 0.8746 (tm-30) REVERT: M 75 ILE cc_start: 0.9021 (mm) cc_final: 0.8724 (mm) REVERT: P 24 TYR cc_start: 0.6814 (t80) cc_final: 0.6589 (t80) REVERT: Q 60 LYS cc_start: 0.8898 (mmtm) cc_final: 0.8341 (mmtm) REVERT: R 55 ILE cc_start: 0.9223 (mm) cc_final: 0.9013 (tt) REVERT: S 1 MET cc_start: 0.6081 (tpp) cc_final: 0.5266 (ppp) REVERT: S 57 VAL cc_start: 0.9194 (OUTLIER) cc_final: 0.8968 (p) REVERT: T 6 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7672 (tpp80) REVERT: T 40 LEU cc_start: 0.8909 (mm) cc_final: 0.8688 (mm) REVERT: U 44 HIS cc_start: 0.7180 (t-90) cc_final: 0.6695 (t-90) REVERT: W 37 PHE cc_start: 0.7408 (m-80) cc_final: 0.6796 (m-10) REVERT: W 67 LEU cc_start: 0.8921 (pp) cc_final: 0.8719 (pp) REVERT: X 23 ARG cc_start: 0.8876 (mmt-90) cc_final: 0.8539 (mmp-170) REVERT: X 24 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8455 (pm20) REVERT: Z 22 MET cc_start: 0.9327 (ttm) cc_final: 0.9003 (mtp) REVERT: 2 27 ARG cc_start: 0.8584 (ptp90) cc_final: 0.8382 (mtm-85) REVERT: 2 32 LYS cc_start: 0.8147 (tttm) cc_final: 0.7347 (tttp) REVERT: 6 21 TYR cc_start: 0.8343 (OUTLIER) cc_final: 0.7475 (p90) REVERT: 6 24 PRO cc_start: 0.6899 (Cg_exo) cc_final: 0.6685 (Cg_endo) REVERT: 6 26 MET cc_start: 0.8143 (mtp) cc_final: 0.7713 (ttm) REVERT: 6 108 GLN cc_start: 0.8209 (tm-30) cc_final: 0.7416 (pp30) REVERT: 6 153 MET cc_start: 0.8627 (tpt) cc_final: 0.8109 (tpp) REVERT: 6 167 HIS cc_start: 0.8799 (t-90) cc_final: 0.8490 (t-90) REVERT: 7 117 ASP cc_start: 0.9357 (t0) cc_final: 0.9078 (p0) REVERT: 7 133 MET cc_start: 0.9227 (mtp) cc_final: 0.9015 (mtp) REVERT: 8 47 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8839 (mp) REVERT: 9 123 LEU cc_start: 0.9145 (mm) cc_final: 0.8888 (mm) REVERT: 10 59 TYR cc_start: 0.7398 (m-10) cc_final: 0.7022 (m-10) REVERT: 11 30 MET cc_start: 0.8342 (ttp) cc_final: 0.8079 (ttt) REVERT: 12 26 MET cc_start: 0.9096 (pmm) cc_final: 0.8724 (pmm) REVERT: 13 35 GLU cc_start: 0.9099 (mp0) cc_final: 0.8576 (tp30) REVERT: 13 56 MET cc_start: 0.8660 (tmm) cc_final: 0.8253 (tmm) REVERT: 13 87 MET cc_start: 0.9487 (ppp) cc_final: 0.9137 (ppp) REVERT: 14 102 LEU cc_start: 0.8233 (tt) cc_final: 0.8026 (tp) REVERT: 16 58 ASN cc_start: 0.8838 (p0) cc_final: 0.8475 (p0) REVERT: 17 62 PHE cc_start: 0.8021 (t80) cc_final: 0.7316 (m-80) REVERT: 20 69 ASP cc_start: 0.8927 (p0) cc_final: 0.8640 (p0) REVERT: 23 31 ARG cc_start: 0.9317 (mmm-85) cc_final: 0.9111 (tpp80) REVERT: 24 26 MET cc_start: 0.8788 (ppp) cc_final: 0.8552 (ppp) REVERT: 24 27 MET cc_start: 0.9474 (ppp) cc_final: 0.9203 (ppp) REVERT: 24 53 MET cc_start: 0.8952 (ppp) cc_final: 0.8607 (ppp) REVERT: 25 7 GLU cc_start: 0.7049 (mm-30) cc_final: 0.6787 (mm-30) REVERT: 25 16 ARG cc_start: 0.7156 (ptm160) cc_final: 0.6834 (ptm-80) REVERT: 25 36 PHE cc_start: 0.8562 (p90) cc_final: 0.8267 (p90) REVERT: 25 42 THR cc_start: 0.9001 (OUTLIER) cc_final: 0.8497 (t) REVERT: 25 48 LYS cc_start: 0.8887 (mmtt) cc_final: 0.8499 (tttt) REVERT: 33 113 MET cc_start: 0.2449 (mtt) cc_final: 0.1543 (mtt) REVERT: 33 134 ASN cc_start: 0.8076 (m-40) cc_final: 0.7693 (m-40) REVERT: 33 138 MET cc_start: 0.6832 (ptt) cc_final: 0.6603 (ppp) REVERT: 33 425 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8321 (pp) outliers start: 273 outliers final: 170 residues processed: 1515 average time/residue: 1.4178 time to fit residues: 3731.8240 Evaluate side-chains 1390 residues out of total 5423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 1212 time to evaluate : 6.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 268 ARG Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 126 ASN Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain E residue 15 ASP Chi-restraints excluded: chain E residue 19 ASN Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 141 LYS Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 51 LYS Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 80 ASP Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 80 SER Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 113 ILE Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain O residue 39 LEU Chi-restraints excluded: chain O residue 99 LEU Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain P residue 90 ASP Chi-restraints excluded: chain P residue 96 ASP Chi-restraints excluded: chain Q residue 14 VAL Chi-restraints excluded: chain Q residue 76 LYS Chi-restraints excluded: chain Q residue 84 ARG Chi-restraints excluded: chain R residue 110 ARG Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 79 ASP Chi-restraints excluded: chain T residue 6 ARG Chi-restraints excluded: chain T residue 7 ASP Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain U residue 8 VAL Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain V residue 54 THR Chi-restraints excluded: chain W residue 22 ASN Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain W residue 63 ILE Chi-restraints excluded: chain X residue 5 GLU Chi-restraints excluded: chain X residue 24 GLU Chi-restraints excluded: chain X residue 43 LEU Chi-restraints excluded: chain Y residue 9 THR Chi-restraints excluded: chain Z residue 21 VAL Chi-restraints excluded: chain Z residue 37 CYS Chi-restraints excluded: chain Z residue 58 ASP Chi-restraints excluded: chain 1 residue 45 ASP Chi-restraints excluded: chain 2 residue 13 SER Chi-restraints excluded: chain 2 residue 33 LEU Chi-restraints excluded: chain 2 residue 42 VAL Chi-restraints excluded: chain 3 residue 44 VAL Chi-restraints excluded: chain 4 residue 6 VAL Chi-restraints excluded: chain 4 residue 25 HIS Chi-restraints excluded: chain 4 residue 56 LEU Chi-restraints excluded: chain 5 residue 7 VAL Chi-restraints excluded: chain 5 residue 16 ILE Chi-restraints excluded: chain 5 residue 22 VAL Chi-restraints excluded: chain 6 residue 14 HIS Chi-restraints excluded: chain 6 residue 21 TYR Chi-restraints excluded: chain 6 residue 30 ILE Chi-restraints excluded: chain 6 residue 113 LEU Chi-restraints excluded: chain 6 residue 139 GLU Chi-restraints excluded: chain 6 residue 150 ILE Chi-restraints excluded: chain 6 residue 162 VAL Chi-restraints excluded: chain 6 residue 185 ILE Chi-restraints excluded: chain 7 residue 102 ILE Chi-restraints excluded: chain 7 residue 156 LEU Chi-restraints excluded: chain 7 residue 206 ILE Chi-restraints excluded: chain 8 residue 16 THR Chi-restraints excluded: chain 8 residue 27 ILE Chi-restraints excluded: chain 8 residue 28 ASP Chi-restraints excluded: chain 8 residue 34 GLU Chi-restraints excluded: chain 8 residue 47 LEU Chi-restraints excluded: chain 8 residue 52 VAL Chi-restraints excluded: chain 8 residue 170 LEU Chi-restraints excluded: chain 8 residue 173 ASP Chi-restraints excluded: chain 8 residue 177 MET Chi-restraints excluded: chain 9 residue 10 LEU Chi-restraints excluded: chain 9 residue 14 LEU Chi-restraints excluded: chain 9 residue 29 ILE Chi-restraints excluded: chain 9 residue 121 ASN Chi-restraints excluded: chain 9 residue 122 VAL Chi-restraints excluded: chain 9 residue 141 ASP Chi-restraints excluded: chain 9 residue 152 VAL Chi-restraints excluded: chain 9 residue 155 LYS Chi-restraints excluded: chain 10 residue 7 VAL Chi-restraints excluded: chain 10 residue 13 ASP Chi-restraints excluded: chain 10 residue 82 ASP Chi-restraints excluded: chain 11 residue 26 VAL Chi-restraints excluded: chain 11 residue 39 GLU Chi-restraints excluded: chain 12 residue 68 LYS Chi-restraints excluded: chain 12 residue 73 SER Chi-restraints excluded: chain 12 residue 84 ILE Chi-restraints excluded: chain 12 residue 89 ASP Chi-restraints excluded: chain 12 residue 126 CYS Chi-restraints excluded: chain 13 residue 5 TYR Chi-restraints excluded: chain 13 residue 20 ILE Chi-restraints excluded: chain 13 residue 32 ARG Chi-restraints excluded: chain 13 residue 34 LEU Chi-restraints excluded: chain 13 residue 49 GLN Chi-restraints excluded: chain 13 residue 57 VAL Chi-restraints excluded: chain 13 residue 60 LEU Chi-restraints excluded: chain 13 residue 96 GLU Chi-restraints excluded: chain 13 residue 108 ARG Chi-restraints excluded: chain 14 residue 8 ILE Chi-restraints excluded: chain 14 residue 17 LEU Chi-restraints excluded: chain 14 residue 32 THR Chi-restraints excluded: chain 14 residue 51 VAL Chi-restraints excluded: chain 14 residue 91 ASP Chi-restraints excluded: chain 14 residue 96 VAL Chi-restraints excluded: chain 14 residue 101 SER Chi-restraints excluded: chain 15 residue 22 ILE Chi-restraints excluded: chain 15 residue 39 ASN Chi-restraints excluded: chain 15 residue 71 ASP Chi-restraints excluded: chain 15 residue 95 THR Chi-restraints excluded: chain 15 residue 96 ILE Chi-restraints excluded: chain 16 residue 19 ASN Chi-restraints excluded: chain 16 residue 20 VAL Chi-restraints excluded: chain 16 residue 33 CYS Chi-restraints excluded: chain 16 residue 40 THR Chi-restraints excluded: chain 16 residue 52 CYS Chi-restraints excluded: chain 16 residue 56 LEU Chi-restraints excluded: chain 16 residue 89 LEU Chi-restraints excluded: chain 16 residue 108 ASP Chi-restraints excluded: chain 17 residue 24 VAL Chi-restraints excluded: chain 18 residue 3 GLN Chi-restraints excluded: chain 18 residue 79 SER Chi-restraints excluded: chain 18 residue 81 ILE Chi-restraints excluded: chain 18 residue 92 ILE Chi-restraints excluded: chain 19 residue 13 GLU Chi-restraints excluded: chain 22 residue 11 ARG Chi-restraints excluded: chain 22 residue 54 LEU Chi-restraints excluded: chain 23 residue 12 LEU Chi-restraints excluded: chain 23 residue 23 GLU Chi-restraints excluded: chain 23 residue 24 SER Chi-restraints excluded: chain 23 residue 39 ILE Chi-restraints excluded: chain 23 residue 42 ASN Chi-restraints excluded: chain 23 residue 59 VAL Chi-restraints excluded: chain 23 residue 65 MET Chi-restraints excluded: chain 23 residue 66 VAL Chi-restraints excluded: chain 24 residue 52 GLU Chi-restraints excluded: chain 24 residue 78 LEU Chi-restraints excluded: chain 25 residue 12 ASP Chi-restraints excluded: chain 25 residue 18 PHE Chi-restraints excluded: chain 25 residue 42 THR Chi-restraints excluded: chain 33 residue 63 VAL Chi-restraints excluded: chain 33 residue 425 LEU Chi-restraints excluded: chain 33 residue 463 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1117 random chunks: chunk 899 optimal weight: 20.0000 chunk 612 optimal weight: 30.0000 chunk 15 optimal weight: 40.0000 chunk 803 optimal weight: 20.0000 chunk 445 optimal weight: 20.0000 chunk 921 optimal weight: 20.0000 chunk 746 optimal weight: 20.0000 chunk 1 optimal weight: 7.9990 chunk 551 optimal weight: 8.9990 chunk 969 optimal weight: 20.0000 chunk 272 optimal weight: 20.0000 overall best weight: 15.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 86 GLN K 35 HIS ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 20 ASN ** X 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 61 ASN ** 1 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 53 GLN ** 8 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 145 ASN ** 11 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 14 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 14 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 16 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 20 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 33 108 HIS ** 33 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 33 344 HIS ** 33 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 33 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.128 167683 Z= 0.448 Angle : 0.795 19.319 250280 Z= 0.405 Chirality : 0.042 0.339 31936 Planarity : 0.006 0.112 13865 Dihedral : 24.250 179.143 82443 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 39.49 Ramachandran Plot: Outliers : 1.04 % Allowed : 12.08 % Favored : 86.88 % Rotamer: Outliers : 6.56 % Allowed : 21.65 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.10), residues: 6509 helix: -0.60 (0.10), residues: 2207 sheet: -2.57 (0.15), residues: 995 loop : -2.07 (0.11), residues: 3307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 78 HIS 0.021 0.002 HIS I 80 PHE 0.023 0.002 PHE P 105 TYR 0.027 0.003 TYR13 5 ARG 0.023 0.001 ARG 6 112 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13018 Ramachandran restraints generated. 6509 Oldfield, 0 Emsley, 6509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13018 Ramachandran restraints generated. 6509 Oldfield, 0 Emsley, 6509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1568 residues out of total 5423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 348 poor density : 1220 time to evaluate : 6.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 8 LYS cc_start: 0.8747 (tptp) cc_final: 0.8500 (tptp) REVERT: F 43 ASN cc_start: 0.9582 (m-40) cc_final: 0.9207 (p0) REVERT: F 132 PHE cc_start: 0.8593 (m-80) cc_final: 0.8224 (m-80) REVERT: F 135 HIS cc_start: 0.8961 (t70) cc_final: 0.8432 (t70) REVERT: F 141 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.7601 (mmmt) REVERT: G 52 MET cc_start: 0.1237 (ttt) cc_final: 0.0165 (mtp) REVERT: H 120 ASP cc_start: 0.7223 (t0) cc_final: 0.6858 (t0) REVERT: H 124 MET cc_start: 0.2817 (mmp) cc_final: 0.1963 (mmt) REVERT: I 34 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.8671 (ptm-80) REVERT: I 37 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7564 (ttp-170) REVERT: I 67 ASN cc_start: 0.8425 (t0) cc_final: 0.8185 (t0) REVERT: L 136 MET cc_start: 0.7305 (tmm) cc_final: 0.6318 (tmm) REVERT: M 75 ILE cc_start: 0.9134 (mm) cc_final: 0.8866 (mm) REVERT: P 24 TYR cc_start: 0.6989 (t80) cc_final: 0.6689 (t80) REVERT: Q 74 ILE cc_start: 0.8576 (mt) cc_final: 0.8325 (mt) REVERT: S 1 MET cc_start: 0.6485 (tpp) cc_final: 0.5431 (ttt) REVERT: S 56 GLU cc_start: 0.8344 (tm-30) cc_final: 0.8094 (tm-30) REVERT: T 6 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8051 (tpp80) REVERT: U 44 HIS cc_start: 0.7153 (t-90) cc_final: 0.6861 (t-90) REVERT: U 57 TYR cc_start: 0.8039 (m-80) cc_final: 0.7535 (m-80) REVERT: W 67 LEU cc_start: 0.8993 (pp) cc_final: 0.8772 (pp) REVERT: Y 3 THR cc_start: 0.9122 (p) cc_final: 0.8749 (t) REVERT: Y 10 ARG cc_start: 0.8607 (mpp80) cc_final: 0.8407 (mpp80) REVERT: Y 43 ILE cc_start: 0.9445 (mm) cc_final: 0.9202 (tp) REVERT: Z 22 MET cc_start: 0.9307 (ttm) cc_final: 0.9000 (mtm) REVERT: Z 33 ASN cc_start: 0.9066 (OUTLIER) cc_final: 0.8841 (t0) REVERT: 6 153 MET cc_start: 0.8673 (tpt) cc_final: 0.8132 (tpp) REVERT: 7 117 ASP cc_start: 0.9406 (t0) cc_final: 0.9066 (p0) REVERT: 8 70 GLN cc_start: 0.8156 (tt0) cc_final: 0.7790 (tp-100) REVERT: 8 74 TYR cc_start: 0.8560 (m-80) cc_final: 0.7971 (m-80) REVERT: 9 65 LYS cc_start: 0.8986 (ptmm) cc_final: 0.8703 (ptmm) REVERT: 9 123 LEU cc_start: 0.9140 (mm) cc_final: 0.8929 (mm) REVERT: 9 146 MET cc_start: 0.8774 (tpp) cc_final: 0.8445 (ttt) REVERT: 9 156 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.6850 (ttp80) REVERT: 10 59 TYR cc_start: 0.7450 (m-10) cc_final: 0.7177 (m-10) REVERT: 12 26 MET cc_start: 0.9159 (pmm) cc_final: 0.8739 (pmm) REVERT: 12 42 GLU cc_start: 0.8908 (mm-30) cc_final: 0.7882 (mm-30) REVERT: 13 87 MET cc_start: 0.9572 (ppp) cc_final: 0.9224 (ppp) REVERT: 14 65 TYR cc_start: 0.7698 (m-80) cc_final: 0.7226 (m-80) REVERT: 14 66 GLU cc_start: 0.8065 (tp30) cc_final: 0.7211 (tp30) REVERT: 14 81 GLU cc_start: 0.8916 (tm-30) cc_final: 0.8682 (tm-30) REVERT: 20 69 ASP cc_start: 0.9041 (p0) cc_final: 0.8756 (p0) REVERT: 21 42 LYS cc_start: 0.9242 (mtpt) cc_final: 0.8958 (ttpp) REVERT: 23 31 ARG cc_start: 0.9388 (mmm-85) cc_final: 0.9163 (tpp80) REVERT: 24 26 MET cc_start: 0.8846 (ppp) cc_final: 0.8641 (ppp) REVERT: 24 27 MET cc_start: 0.9502 (ppp) cc_final: 0.9158 (ppp) REVERT: 24 53 MET cc_start: 0.9084 (ppp) cc_final: 0.8770 (ppp) REVERT: 25 7 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6886 (mm-30) REVERT: 25 36 PHE cc_start: 0.8624 (p90) cc_final: 0.8256 (p90) REVERT: 25 48 LYS cc_start: 0.8964 (mmtt) cc_final: 0.8530 (tptt) REVERT: 25 58 LYS cc_start: 0.8421 (pttt) cc_final: 0.8091 (pttm) REVERT: 33 62 MET cc_start: 0.5614 (tmm) cc_final: 0.4713 (ptp) REVERT: 33 71 MET cc_start: -0.2216 (tpp) cc_final: -0.2448 (tpp) REVERT: 33 113 MET cc_start: 0.2199 (mtt) cc_final: 0.1948 (mtt) REVERT: 33 425 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8392 (pp) outliers start: 348 outliers final: 253 residues processed: 1417 average time/residue: 1.3409 time to fit residues: 3302.9770 Evaluate side-chains 1401 residues out of total 5423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 1141 time to evaluate : 6.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 268 ARG Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 126 ASN Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 15 ASP Chi-restraints excluded: chain E residue 19 ASN Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 47 PHE Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 141 LYS Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 34 ARG Chi-restraints excluded: chain I residue 37 ARG Chi-restraints excluded: chain I residue 84 ILE Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 51 LYS Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 80 ASP Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 89 ASN Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 35 HIS Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 80 SER Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 91 ASP Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain M residue 113 ILE Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain O residue 43 GLU Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain P residue 90 ASP Chi-restraints excluded: chain P residue 96 ASP Chi-restraints excluded: chain P residue 106 THR Chi-restraints excluded: chain Q residue 14 VAL Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 76 LYS Chi-restraints excluded: chain Q residue 84 ARG Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 110 ARG Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 6 ARG Chi-restraints excluded: chain T residue 7 ASP Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 36 GLU Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain T residue 69 VAL Chi-restraints excluded: chain U residue 8 VAL Chi-restraints excluded: chain U residue 35 GLU Chi-restraints excluded: chain U residue 86 LEU Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain V residue 54 THR Chi-restraints excluded: chain V residue 78 ILE Chi-restraints excluded: chain W residue 22 ASN Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain W residue 63 ILE Chi-restraints excluded: chain X residue 5 GLU Chi-restraints excluded: chain X residue 7 ARG Chi-restraints excluded: chain X residue 13 GLU Chi-restraints excluded: chain X residue 43 LEU Chi-restraints excluded: chain Y residue 6 ILE Chi-restraints excluded: chain Y residue 9 THR Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain Z residue 18 CYS Chi-restraints excluded: chain Z residue 21 VAL Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain Z residue 33 ASN Chi-restraints excluded: chain Z residue 37 CYS Chi-restraints excluded: chain Z residue 58 ASP Chi-restraints excluded: chain 1 residue 5 ASN Chi-restraints excluded: chain 1 residue 26 SER Chi-restraints excluded: chain 1 residue 29 VAL Chi-restraints excluded: chain 1 residue 45 ASP Chi-restraints excluded: chain 2 residue 13 SER Chi-restraints excluded: chain 2 residue 33 LEU Chi-restraints excluded: chain 2 residue 42 VAL Chi-restraints excluded: chain 2 residue 52 LYS Chi-restraints excluded: chain 3 residue 43 THR Chi-restraints excluded: chain 3 residue 44 VAL Chi-restraints excluded: chain 4 residue 6 VAL Chi-restraints excluded: chain 4 residue 25 HIS Chi-restraints excluded: chain 4 residue 56 LEU Chi-restraints excluded: chain 4 residue 57 VAL Chi-restraints excluded: chain 5 residue 7 VAL Chi-restraints excluded: chain 5 residue 13 ASN Chi-restraints excluded: chain 5 residue 16 ILE Chi-restraints excluded: chain 5 residue 22 VAL Chi-restraints excluded: chain 5 residue 37 GLN Chi-restraints excluded: chain 6 residue 14 HIS Chi-restraints excluded: chain 6 residue 30 ILE Chi-restraints excluded: chain 6 residue 113 LEU Chi-restraints excluded: chain 6 residue 139 GLU Chi-restraints excluded: chain 6 residue 150 ILE Chi-restraints excluded: chain 6 residue 162 VAL Chi-restraints excluded: chain 6 residue 185 ILE Chi-restraints excluded: chain 6 residue 196 ASP Chi-restraints excluded: chain 6 residue 198 VAL Chi-restraints excluded: chain 7 residue 35 ASP Chi-restraints excluded: chain 7 residue 96 VAL Chi-restraints excluded: chain 7 residue 102 ILE Chi-restraints excluded: chain 7 residue 105 VAL Chi-restraints excluded: chain 7 residue 156 LEU Chi-restraints excluded: chain 8 residue 16 THR Chi-restraints excluded: chain 8 residue 28 ASP Chi-restraints excluded: chain 8 residue 34 GLU Chi-restraints excluded: chain 8 residue 50 TYR Chi-restraints excluded: chain 8 residue 52 VAL Chi-restraints excluded: chain 8 residue 81 LEU Chi-restraints excluded: chain 8 residue 128 VAL Chi-restraints excluded: chain 8 residue 139 ASN Chi-restraints excluded: chain 8 residue 170 LEU Chi-restraints excluded: chain 8 residue 173 ASP Chi-restraints excluded: chain 8 residue 177 MET Chi-restraints excluded: chain 9 residue 10 LEU Chi-restraints excluded: chain 9 residue 14 LEU Chi-restraints excluded: chain 9 residue 29 ILE Chi-restraints excluded: chain 9 residue 75 LEU Chi-restraints excluded: chain 9 residue 121 ASN Chi-restraints excluded: chain 9 residue 122 VAL Chi-restraints excluded: chain 9 residue 130 THR Chi-restraints excluded: chain 9 residue 141 ASP Chi-restraints excluded: chain 9 residue 151 MET Chi-restraints excluded: chain 9 residue 152 VAL Chi-restraints excluded: chain 9 residue 155 LYS Chi-restraints excluded: chain 9 residue 156 ARG Chi-restraints excluded: chain 10 residue 13 ASP Chi-restraints excluded: chain 10 residue 17 GLN Chi-restraints excluded: chain 10 residue 82 ASP Chi-restraints excluded: chain 11 residue 26 VAL Chi-restraints excluded: chain 11 residue 39 GLU Chi-restraints excluded: chain 12 residue 68 LYS Chi-restraints excluded: chain 12 residue 74 ILE Chi-restraints excluded: chain 12 residue 84 ILE Chi-restraints excluded: chain 12 residue 86 LYS Chi-restraints excluded: chain 12 residue 89 ASP Chi-restraints excluded: chain 12 residue 103 VAL Chi-restraints excluded: chain 12 residue 111 THR Chi-restraints excluded: chain 12 residue 126 CYS Chi-restraints excluded: chain 13 residue 5 TYR Chi-restraints excluded: chain 13 residue 20 ILE Chi-restraints excluded: chain 13 residue 34 LEU Chi-restraints excluded: chain 13 residue 38 PHE Chi-restraints excluded: chain 13 residue 49 GLN Chi-restraints excluded: chain 13 residue 57 VAL Chi-restraints excluded: chain 13 residue 60 LEU Chi-restraints excluded: chain 13 residue 65 THR Chi-restraints excluded: chain 13 residue 96 GLU Chi-restraints excluded: chain 13 residue 108 ARG Chi-restraints excluded: chain 14 residue 8 ILE Chi-restraints excluded: chain 14 residue 17 LEU Chi-restraints excluded: chain 14 residue 32 THR Chi-restraints excluded: chain 14 residue 51 VAL Chi-restraints excluded: chain 14 residue 91 ASP Chi-restraints excluded: chain 14 residue 96 VAL Chi-restraints excluded: chain 15 residue 22 ILE Chi-restraints excluded: chain 15 residue 39 ASN Chi-restraints excluded: chain 15 residue 45 THR Chi-restraints excluded: chain 15 residue 71 ASP Chi-restraints excluded: chain 15 residue 79 LYS Chi-restraints excluded: chain 15 residue 83 VAL Chi-restraints excluded: chain 15 residue 95 THR Chi-restraints excluded: chain 15 residue 96 ILE Chi-restraints excluded: chain 15 residue 109 ILE Chi-restraints excluded: chain 16 residue 20 VAL Chi-restraints excluded: chain 16 residue 33 CYS Chi-restraints excluded: chain 16 residue 38 THR Chi-restraints excluded: chain 16 residue 40 THR Chi-restraints excluded: chain 16 residue 52 CYS Chi-restraints excluded: chain 16 residue 56 LEU Chi-restraints excluded: chain 16 residue 57 THR Chi-restraints excluded: chain 16 residue 96 THR Chi-restraints excluded: chain 16 residue 108 ASP Chi-restraints excluded: chain 17 residue 24 VAL Chi-restraints excluded: chain 17 residue 73 SER Chi-restraints excluded: chain 18 residue 36 SER Chi-restraints excluded: chain 18 residue 63 CYS Chi-restraints excluded: chain 18 residue 78 LEU Chi-restraints excluded: chain 18 residue 79 SER Chi-restraints excluded: chain 18 residue 92 ILE Chi-restraints excluded: chain 19 residue 13 GLU Chi-restraints excluded: chain 19 residue 44 GLU Chi-restraints excluded: chain 20 residue 42 ILE Chi-restraints excluded: chain 20 residue 77 GLU Chi-restraints excluded: chain 21 residue 17 GLU Chi-restraints excluded: chain 21 residue 56 ASP Chi-restraints excluded: chain 21 residue 69 THR Chi-restraints excluded: chain 22 residue 11 ARG Chi-restraints excluded: chain 22 residue 41 SER Chi-restraints excluded: chain 22 residue 54 LEU Chi-restraints excluded: chain 22 residue 64 LEU Chi-restraints excluded: chain 23 residue 12 LEU Chi-restraints excluded: chain 23 residue 18 VAL Chi-restraints excluded: chain 23 residue 23 GLU Chi-restraints excluded: chain 23 residue 28 LYS Chi-restraints excluded: chain 23 residue 42 ASN Chi-restraints excluded: chain 23 residue 59 VAL Chi-restraints excluded: chain 23 residue 65 MET Chi-restraints excluded: chain 23 residue 66 VAL Chi-restraints excluded: chain 24 residue 12 GLN Chi-restraints excluded: chain 24 residue 52 GLU Chi-restraints excluded: chain 25 residue 12 ASP Chi-restraints excluded: chain 25 residue 18 PHE Chi-restraints excluded: chain 25 residue 37 TYR Chi-restraints excluded: chain 25 residue 42 THR Chi-restraints excluded: chain 33 residue 108 HIS Chi-restraints excluded: chain 33 residue 425 LEU Chi-restraints excluded: chain 33 residue 613 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1117 random chunks: chunk 363 optimal weight: 30.0000 chunk 972 optimal weight: 20.0000 chunk 213 optimal weight: 6.9990 chunk 633 optimal weight: 20.0000 chunk 266 optimal weight: 2.9990 chunk 1080 optimal weight: 50.0000 chunk 897 optimal weight: 20.0000 chunk 500 optimal weight: 0.9990 chunk 89 optimal weight: 7.9990 chunk 357 optimal weight: 30.0000 chunk 567 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 86 GLN ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 GLN O 114 ASN ** P 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 61 ASN 1 18 HIS ** 1 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 88 GLN ** 7 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 53 GLN ** 8 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 115 GLN ** 9 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 67 ASN ** 12 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 14 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 14 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 16 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 20 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 33 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 33 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 33 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 167683 Z= 0.215 Angle : 0.670 14.495 250280 Z= 0.338 Chirality : 0.036 0.430 31936 Planarity : 0.005 0.071 13865 Dihedral : 24.253 177.997 82443 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 27.29 Ramachandran Plot: Outliers : 1.06 % Allowed : 10.23 % Favored : 88.71 % Rotamer: Outliers : 5.00 % Allowed : 24.27 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.10), residues: 6509 helix: -0.22 (0.11), residues: 2203 sheet: -2.39 (0.15), residues: 992 loop : -1.93 (0.11), residues: 3314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 78 HIS 0.027 0.001 HIS I 80 PHE 0.029 0.002 PHE Z 64 TYR 0.028 0.002 TYR22 69 ARG 0.013 0.001 ARG 9 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13018 Ramachandran restraints generated. 6509 Oldfield, 0 Emsley, 6509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13018 Ramachandran restraints generated. 6509 Oldfield, 0 Emsley, 6509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1579 residues out of total 5423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 1314 time to evaluate : 6.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8773 (ptpp) REVERT: F 43 ASN cc_start: 0.9572 (m-40) cc_final: 0.9132 (p0) REVERT: F 112 LYS cc_start: 0.5996 (mttt) cc_final: 0.5756 (mtmt) REVERT: F 132 PHE cc_start: 0.8658 (m-80) cc_final: 0.8281 (m-80) REVERT: F 135 HIS cc_start: 0.8983 (t70) cc_final: 0.8466 (t70) REVERT: F 141 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7575 (mmmt) REVERT: G 52 MET cc_start: 0.1071 (ttt) cc_final: 0.0123 (mtp) REVERT: H 120 ASP cc_start: 0.7509 (t0) cc_final: 0.7080 (t0) REVERT: H 124 MET cc_start: 0.2497 (mmp) cc_final: 0.1674 (mmt) REVERT: H 126 ARG cc_start: 0.8388 (ttm110) cc_final: 0.8131 (mtm-85) REVERT: I 37 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.7475 (ttm-80) REVERT: I 67 ASN cc_start: 0.8398 (t0) cc_final: 0.8141 (t0) REVERT: I 80 HIS cc_start: 0.7453 (t-170) cc_final: 0.7226 (t-170) REVERT: I 92 MET cc_start: 0.9201 (mmm) cc_final: 0.8996 (tpt) REVERT: J 51 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8544 (pttm) REVERT: K 81 ASP cc_start: 0.9081 (p0) cc_final: 0.8831 (p0) REVERT: K 101 ILE cc_start: 0.8831 (pt) cc_final: 0.8568 (mm) REVERT: L 136 MET cc_start: 0.7353 (tmm) cc_final: 0.6392 (tmm) REVERT: M 3 HIS cc_start: 0.6902 (OUTLIER) cc_final: 0.6349 (m90) REVERT: M 20 MET cc_start: 0.8825 (mtp) cc_final: 0.8546 (mtm) REVERT: M 74 GLU cc_start: 0.8964 (tm-30) cc_final: 0.8736 (tm-30) REVERT: M 75 ILE cc_start: 0.9014 (mm) cc_final: 0.8720 (mm) REVERT: P 24 TYR cc_start: 0.6783 (t80) cc_final: 0.6525 (t80) REVERT: S 1 MET cc_start: 0.6069 (tpp) cc_final: 0.4736 (ttp) REVERT: T 6 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7620 (tpp80) REVERT: T 40 LEU cc_start: 0.8901 (mm) cc_final: 0.8681 (mm) REVERT: U 57 TYR cc_start: 0.8024 (m-80) cc_final: 0.7624 (m-80) REVERT: W 37 PHE cc_start: 0.7616 (m-80) cc_final: 0.7344 (m-80) REVERT: X 9 LYS cc_start: 0.9355 (tptp) cc_final: 0.9121 (ttpp) REVERT: X 12 GLU cc_start: 0.9332 (mp0) cc_final: 0.9051 (mp0) REVERT: X 23 ARG cc_start: 0.8850 (mmt-90) cc_final: 0.8531 (mmp-170) REVERT: X 24 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8441 (pm20) REVERT: Y 43 ILE cc_start: 0.9444 (mm) cc_final: 0.9157 (tp) REVERT: Y 53 MET cc_start: 0.8475 (ppp) cc_final: 0.8155 (ppp) REVERT: Z 22 MET cc_start: 0.9284 (ttm) cc_final: 0.8997 (mtm) REVERT: Z 62 LYS cc_start: 0.9435 (mmmt) cc_final: 0.9176 (mmmt) REVERT: 5 4 ARG cc_start: 0.8942 (mtm-85) cc_final: 0.8700 (ttm-80) REVERT: 6 136 ARG cc_start: 0.8107 (mmm-85) cc_final: 0.7873 (mmm-85) REVERT: 6 153 MET cc_start: 0.8569 (tpt) cc_final: 0.8111 (tpp) REVERT: 6 167 HIS cc_start: 0.8719 (t-90) cc_final: 0.8471 (t-90) REVERT: 7 117 ASP cc_start: 0.9331 (t0) cc_final: 0.9012 (p0) REVERT: 7 133 MET cc_start: 0.9240 (mtp) cc_final: 0.8980 (mtm) REVERT: 8 70 GLN cc_start: 0.8029 (tt0) cc_final: 0.7569 (tp-100) REVERT: 8 74 TYR cc_start: 0.8494 (m-80) cc_final: 0.7918 (m-80) REVERT: 8 104 MET cc_start: 0.8511 (tpt) cc_final: 0.8265 (tpt) REVERT: 9 65 LYS cc_start: 0.8979 (ptmm) cc_final: 0.8713 (ptmm) REVERT: 10 59 TYR cc_start: 0.7481 (m-10) cc_final: 0.7221 (m-10) REVERT: 10 91 ARG cc_start: 0.8082 (mpt180) cc_final: 0.7877 (mpt180) REVERT: 11 30 MET cc_start: 0.8160 (ttp) cc_final: 0.7936 (ttt) REVERT: 12 4 ASP cc_start: 0.8876 (t0) cc_final: 0.8379 (t0) REVERT: 12 26 MET cc_start: 0.9124 (pmm) cc_final: 0.8719 (pmm) REVERT: 12 42 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8361 (tp30) REVERT: 12 49 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8372 (mmtm) REVERT: 13 35 GLU cc_start: 0.9109 (mp0) cc_final: 0.8574 (tp30) REVERT: 13 87 MET cc_start: 0.9501 (ppp) cc_final: 0.9143 (ppp) REVERT: 13 119 LYS cc_start: 0.8055 (pttt) cc_final: 0.7533 (pttp) REVERT: 14 47 GLU cc_start: 0.8006 (mp0) cc_final: 0.7657 (mp0) REVERT: 14 65 TYR cc_start: 0.7528 (m-80) cc_final: 0.7220 (m-80) REVERT: 14 66 GLU cc_start: 0.7809 (tp30) cc_final: 0.7024 (tp30) REVERT: 16 58 ASN cc_start: 0.8808 (p0) cc_final: 0.8475 (p0) REVERT: 17 62 PHE cc_start: 0.8042 (t80) cc_final: 0.7447 (m-80) REVERT: 20 69 ASP cc_start: 0.8990 (p0) cc_final: 0.8686 (p0) REVERT: 22 50 TYR cc_start: 0.8464 (m-10) cc_final: 0.8241 (m-10) REVERT: 23 70 LEU cc_start: 0.8964 (mm) cc_final: 0.8492 (tp) REVERT: 23 73 PHE cc_start: 0.8713 (m-80) cc_final: 0.8488 (m-80) REVERT: 24 26 MET cc_start: 0.8820 (ppp) cc_final: 0.8609 (ppp) REVERT: 24 27 MET cc_start: 0.9471 (ppp) cc_final: 0.9177 (ppp) REVERT: 24 53 MET cc_start: 0.8999 (ppp) cc_final: 0.8762 (ppp) REVERT: 25 7 GLU cc_start: 0.6869 (mm-30) cc_final: 0.6609 (mm-30) REVERT: 25 35 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7517 (tp30) REVERT: 25 36 PHE cc_start: 0.8591 (p90) cc_final: 0.8194 (p90) REVERT: 25 43 GLU cc_start: 0.8759 (pt0) cc_final: 0.8231 (pt0) REVERT: 25 45 LYS cc_start: 0.9579 (mmmm) cc_final: 0.9370 (mmmt) REVERT: 25 48 LYS cc_start: 0.8944 (mmtt) cc_final: 0.8585 (tttt) REVERT: 33 425 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8233 (pp) outliers start: 265 outliers final: 200 residues processed: 1454 average time/residue: 1.3562 time to fit residues: 3416.3067 Evaluate side-chains 1396 residues out of total 5423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 1186 time to evaluate : 6.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 268 ARG Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 126 ASN Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 15 ASP Chi-restraints excluded: chain E residue 19 ASN Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 127 GLN Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 47 PHE Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 141 LYS Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 37 ARG Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 51 LYS Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 80 ASP Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 80 SER Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain L residue 24 THR Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 134 THR Chi-restraints excluded: chain M residue 3 HIS Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain M residue 113 ILE Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain O residue 39 LEU Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain P residue 90 ASP Chi-restraints excluded: chain P residue 96 ASP Chi-restraints excluded: chain P residue 99 VAL Chi-restraints excluded: chain P residue 106 THR Chi-restraints excluded: chain Q residue 14 VAL Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 76 LYS Chi-restraints excluded: chain Q residue 84 ARG Chi-restraints excluded: chain R residue 107 VAL Chi-restraints excluded: chain R residue 110 ARG Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 79 ASP Chi-restraints excluded: chain T residue 6 ARG Chi-restraints excluded: chain T residue 7 ASP Chi-restraints excluded: chain T residue 24 VAL Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain U residue 8 VAL Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain V residue 54 THR Chi-restraints excluded: chain V residue 78 ILE Chi-restraints excluded: chain W residue 22 ASN Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain W residue 50 VAL Chi-restraints excluded: chain X residue 5 GLU Chi-restraints excluded: chain X residue 7 ARG Chi-restraints excluded: chain X residue 24 GLU Chi-restraints excluded: chain X residue 43 LEU Chi-restraints excluded: chain Y residue 6 ILE Chi-restraints excluded: chain Z residue 18 CYS Chi-restraints excluded: chain Z residue 21 VAL Chi-restraints excluded: chain Z residue 37 CYS Chi-restraints excluded: chain 1 residue 45 ASP Chi-restraints excluded: chain 2 residue 42 VAL Chi-restraints excluded: chain 3 residue 44 VAL Chi-restraints excluded: chain 4 residue 6 VAL Chi-restraints excluded: chain 4 residue 25 HIS Chi-restraints excluded: chain 4 residue 43 LEU Chi-restraints excluded: chain 5 residue 7 VAL Chi-restraints excluded: chain 5 residue 16 ILE Chi-restraints excluded: chain 5 residue 22 VAL Chi-restraints excluded: chain 6 residue 14 HIS Chi-restraints excluded: chain 6 residue 30 ILE Chi-restraints excluded: chain 6 residue 113 LEU Chi-restraints excluded: chain 6 residue 139 GLU Chi-restraints excluded: chain 6 residue 150 ILE Chi-restraints excluded: chain 6 residue 162 VAL Chi-restraints excluded: chain 6 residue 198 VAL Chi-restraints excluded: chain 7 residue 18 ASN Chi-restraints excluded: chain 7 residue 28 PHE Chi-restraints excluded: chain 7 residue 35 ASP Chi-restraints excluded: chain 7 residue 48 LYS Chi-restraints excluded: chain 7 residue 96 VAL Chi-restraints excluded: chain 7 residue 102 ILE Chi-restraints excluded: chain 7 residue 105 VAL Chi-restraints excluded: chain 7 residue 128 MET Chi-restraints excluded: chain 7 residue 156 LEU Chi-restraints excluded: chain 7 residue 206 ILE Chi-restraints excluded: chain 8 residue 16 THR Chi-restraints excluded: chain 8 residue 28 ASP Chi-restraints excluded: chain 8 residue 34 GLU Chi-restraints excluded: chain 8 residue 52 VAL Chi-restraints excluded: chain 8 residue 80 ARG Chi-restraints excluded: chain 8 residue 115 GLN Chi-restraints excluded: chain 8 residue 139 ASN Chi-restraints excluded: chain 8 residue 170 LEU Chi-restraints excluded: chain 8 residue 173 ASP Chi-restraints excluded: chain 9 residue 10 LEU Chi-restraints excluded: chain 9 residue 14 LEU Chi-restraints excluded: chain 9 residue 29 ILE Chi-restraints excluded: chain 9 residue 63 MET Chi-restraints excluded: chain 9 residue 121 ASN Chi-restraints excluded: chain 9 residue 122 VAL Chi-restraints excluded: chain 9 residue 130 THR Chi-restraints excluded: chain 9 residue 141 ASP Chi-restraints excluded: chain 9 residue 152 VAL Chi-restraints excluded: chain 9 residue 155 LYS Chi-restraints excluded: chain 10 residue 7 VAL Chi-restraints excluded: chain 10 residue 17 GLN Chi-restraints excluded: chain 10 residue 82 ASP Chi-restraints excluded: chain 10 residue 85 ILE Chi-restraints excluded: chain 11 residue 39 GLU Chi-restraints excluded: chain 11 residue 44 SER Chi-restraints excluded: chain 12 residue 39 LEU Chi-restraints excluded: chain 12 residue 49 LYS Chi-restraints excluded: chain 12 residue 68 LYS Chi-restraints excluded: chain 12 residue 89 ASP Chi-restraints excluded: chain 12 residue 126 CYS Chi-restraints excluded: chain 13 residue 5 TYR Chi-restraints excluded: chain 13 residue 20 ILE Chi-restraints excluded: chain 13 residue 34 LEU Chi-restraints excluded: chain 13 residue 49 GLN Chi-restraints excluded: chain 13 residue 57 VAL Chi-restraints excluded: chain 13 residue 60 LEU Chi-restraints excluded: chain 14 residue 17 LEU Chi-restraints excluded: chain 14 residue 32 THR Chi-restraints excluded: chain 14 residue 51 VAL Chi-restraints excluded: chain 14 residue 90 LEU Chi-restraints excluded: chain 14 residue 91 ASP Chi-restraints excluded: chain 14 residue 96 VAL Chi-restraints excluded: chain 14 residue 102 LEU Chi-restraints excluded: chain 15 residue 22 ILE Chi-restraints excluded: chain 15 residue 39 ASN Chi-restraints excluded: chain 15 residue 71 ASP Chi-restraints excluded: chain 15 residue 85 VAL Chi-restraints excluded: chain 15 residue 86 LYS Chi-restraints excluded: chain 15 residue 95 THR Chi-restraints excluded: chain 16 residue 20 VAL Chi-restraints excluded: chain 16 residue 33 CYS Chi-restraints excluded: chain 16 residue 40 THR Chi-restraints excluded: chain 16 residue 56 LEU Chi-restraints excluded: chain 16 residue 108 ASP Chi-restraints excluded: chain 17 residue 24 VAL Chi-restraints excluded: chain 18 residue 78 LEU Chi-restraints excluded: chain 19 residue 44 GLU Chi-restraints excluded: chain 20 residue 42 ILE Chi-restraints excluded: chain 21 residue 17 GLU Chi-restraints excluded: chain 21 residue 62 GLU Chi-restraints excluded: chain 21 residue 69 THR Chi-restraints excluded: chain 22 residue 11 ARG Chi-restraints excluded: chain 22 residue 41 SER Chi-restraints excluded: chain 22 residue 42 ARG Chi-restraints excluded: chain 22 residue 54 LEU Chi-restraints excluded: chain 23 residue 12 LEU Chi-restraints excluded: chain 23 residue 23 GLU Chi-restraints excluded: chain 23 residue 39 ILE Chi-restraints excluded: chain 23 residue 42 ASN Chi-restraints excluded: chain 23 residue 59 VAL Chi-restraints excluded: chain 23 residue 66 VAL Chi-restraints excluded: chain 24 residue 52 GLU Chi-restraints excluded: chain 25 residue 6 ARG Chi-restraints excluded: chain 25 residue 12 ASP Chi-restraints excluded: chain 25 residue 18 PHE Chi-restraints excluded: chain 25 residue 35 GLU Chi-restraints excluded: chain 25 residue 42 THR Chi-restraints excluded: chain 33 residue 138 MET Chi-restraints excluded: chain 33 residue 425 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1117 random chunks: chunk 1041 optimal weight: 30.0000 chunk 121 optimal weight: 50.0000 chunk 615 optimal weight: 40.0000 chunk 789 optimal weight: 20.0000 chunk 611 optimal weight: 30.0000 chunk 909 optimal weight: 20.0000 chunk 603 optimal weight: 20.0000 chunk 1076 optimal weight: 10.0000 chunk 673 optimal weight: 30.0000 chunk 656 optimal weight: 30.0000 chunk 497 optimal weight: 10.0000 overall best weight: 16.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 86 GLN ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 GLN ** O 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 31 GLN ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 61 ASN ** 1 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 14 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 14 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 16 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 17 104 ASN ** 20 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 22 18 GLN ** 24 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 25 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 33 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 33 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 33 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 33 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 33 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.135 167683 Z= 0.459 Angle : 0.811 12.967 250280 Z= 0.412 Chirality : 0.042 0.390 31936 Planarity : 0.006 0.073 13865 Dihedral : 24.349 178.580 82443 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 42.78 Ramachandran Plot: Outliers : 1.01 % Allowed : 12.17 % Favored : 86.82 % Rotamer: Outliers : 5.83 % Allowed : 25.40 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.44 (0.10), residues: 6509 helix: -0.53 (0.11), residues: 2212 sheet: -2.51 (0.15), residues: 1009 loop : -2.08 (0.11), residues: 3288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 78 HIS 0.029 0.002 HIS25 55 PHE 0.024 0.003 PHE F 46 TYR 0.041 0.003 TYR 9 127 ARG 0.022 0.001 ARG17 91 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13018 Ramachandran restraints generated. 6509 Oldfield, 0 Emsley, 6509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13018 Ramachandran restraints generated. 6509 Oldfield, 0 Emsley, 6509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1487 residues out of total 5423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 309 poor density : 1178 time to evaluate : 6.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 43 ASN cc_start: 0.9586 (m-40) cc_final: 0.9154 (p0) REVERT: F 132 PHE cc_start: 0.8691 (m-80) cc_final: 0.8292 (m-80) REVERT: F 135 HIS cc_start: 0.8954 (t70) cc_final: 0.8433 (t70) REVERT: G 52 MET cc_start: 0.1545 (ttt) cc_final: 0.0548 (mtp) REVERT: H 120 ASP cc_start: 0.7550 (t0) cc_final: 0.7129 (t0) REVERT: H 124 MET cc_start: 0.2619 (mmp) cc_final: 0.1678 (mmt) REVERT: H 129 GLU cc_start: 0.9200 (pt0) cc_final: 0.8968 (pt0) REVERT: I 37 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7582 (ttm-80) REVERT: I 67 ASN cc_start: 0.8518 (t0) cc_final: 0.8293 (t0) REVERT: K 81 ASP cc_start: 0.9171 (p0) cc_final: 0.8952 (p0) REVERT: L 136 MET cc_start: 0.7440 (tmm) cc_final: 0.6445 (tmm) REVERT: M 20 MET cc_start: 0.8944 (mtp) cc_final: 0.8695 (mtm) REVERT: M 74 GLU cc_start: 0.9054 (tm-30) cc_final: 0.8709 (tm-30) REVERT: M 75 ILE cc_start: 0.9106 (mm) cc_final: 0.8640 (mm) REVERT: P 24 TYR cc_start: 0.7042 (t80) cc_final: 0.6600 (t80) REVERT: T 6 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8152 (tpp80) REVERT: U 57 TYR cc_start: 0.8065 (m-80) cc_final: 0.7714 (m-80) REVERT: V 17 LEU cc_start: 0.8752 (mp) cc_final: 0.8508 (mp) REVERT: W 69 GLU cc_start: 0.9237 (pt0) cc_final: 0.8999 (tm-30) REVERT: X 23 ARG cc_start: 0.8996 (mmt-90) cc_final: 0.8657 (mmp-170) REVERT: Y 46 MET cc_start: 0.8977 (mmm) cc_final: 0.8758 (mmm) REVERT: Z 22 MET cc_start: 0.9348 (ttm) cc_final: 0.9054 (mtm) REVERT: 2 26 LYS cc_start: 0.9210 (mmtm) cc_final: 0.8897 (mmtt) REVERT: 5 4 ARG cc_start: 0.8967 (mtm-85) cc_final: 0.8720 (ttm-80) REVERT: 6 153 MET cc_start: 0.8661 (tpt) cc_final: 0.8424 (tpt) REVERT: 7 117 ASP cc_start: 0.9384 (t0) cc_final: 0.9066 (p0) REVERT: 7 133 MET cc_start: 0.9274 (mtp) cc_final: 0.9059 (mtm) REVERT: 8 70 GLN cc_start: 0.8151 (tt0) cc_final: 0.7705 (tp40) REVERT: 8 74 TYR cc_start: 0.8488 (m-80) cc_final: 0.8090 (m-80) REVERT: 8 104 MET cc_start: 0.8649 (tpt) cc_final: 0.8401 (tpt) REVERT: 9 70 MET cc_start: 0.7696 (mmm) cc_final: 0.7032 (mmm) REVERT: 11 74 VAL cc_start: 0.9380 (OUTLIER) cc_final: 0.9163 (m) REVERT: 12 26 MET cc_start: 0.9190 (pmm) cc_final: 0.8765 (pmm) REVERT: 13 87 MET cc_start: 0.9594 (ppp) cc_final: 0.9230 (ppp) REVERT: 14 65 TYR cc_start: 0.7634 (m-80) cc_final: 0.7261 (m-80) REVERT: 14 66 GLU cc_start: 0.8074 (tp30) cc_final: 0.7112 (tp30) REVERT: 14 81 GLU cc_start: 0.8738 (tm-30) cc_final: 0.8468 (tm-30) REVERT: 17 62 PHE cc_start: 0.8171 (t80) cc_final: 0.7592 (m-80) REVERT: 20 69 ASP cc_start: 0.9103 (p0) cc_final: 0.8811 (p0) REVERT: 21 42 LYS cc_start: 0.9239 (mtpt) cc_final: 0.8992 (ttpp) REVERT: 24 27 MET cc_start: 0.9519 (ppp) cc_final: 0.9133 (ppp) REVERT: 24 53 MET cc_start: 0.9101 (ppp) cc_final: 0.8816 (ppp) REVERT: 25 7 GLU cc_start: 0.7112 (mm-30) cc_final: 0.6831 (mm-30) REVERT: 25 35 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7491 (tp30) REVERT: 25 36 PHE cc_start: 0.8617 (p90) cc_final: 0.8214 (p90) REVERT: 25 53 LYS cc_start: 0.9484 (pttt) cc_final: 0.9175 (pttm) REVERT: 33 71 MET cc_start: -0.1849 (tpp) cc_final: -0.2126 (tpp) REVERT: 33 113 MET cc_start: 0.2328 (mtt) cc_final: 0.1896 (mpp) outliers start: 309 outliers final: 261 residues processed: 1360 average time/residue: 1.4866 time to fit residues: 3547.5584 Evaluate side-chains 1384 residues out of total 5423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 1119 time to evaluate : 6.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 268 ARG Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 94 GLN Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 126 ASN Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 15 ASP Chi-restraints excluded: chain E residue 19 ASN Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 127 GLN Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 11 ASN Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 47 PHE Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 37 ARG Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 51 LYS Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 80 ASP Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 89 ASN Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 76 GLU Chi-restraints excluded: chain K residue 80 SER Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain L residue 134 THR Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain M residue 113 ILE Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain O residue 2 ASN Chi-restraints excluded: chain O residue 39 LEU Chi-restraints excluded: chain O residue 43 GLU Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain P residue 90 ASP Chi-restraints excluded: chain P residue 96 ASP Chi-restraints excluded: chain P residue 99 VAL Chi-restraints excluded: chain P residue 106 THR Chi-restraints excluded: chain Q residue 14 VAL Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 76 LYS Chi-restraints excluded: chain R residue 19 LEU Chi-restraints excluded: chain R residue 101 SER Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain R residue 110 ARG Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 79 ASP Chi-restraints excluded: chain T residue 6 ARG Chi-restraints excluded: chain T residue 7 ASP Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 33 VAL Chi-restraints excluded: chain T residue 36 GLU Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain U residue 8 VAL Chi-restraints excluded: chain U residue 35 GLU Chi-restraints excluded: chain U residue 86 LEU Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain V residue 54 THR Chi-restraints excluded: chain V residue 78 ILE Chi-restraints excluded: chain W residue 22 ASN Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 50 VAL Chi-restraints excluded: chain W residue 63 ILE Chi-restraints excluded: chain X residue 5 GLU Chi-restraints excluded: chain X residue 7 ARG Chi-restraints excluded: chain X residue 13 GLU Chi-restraints excluded: chain X residue 43 LEU Chi-restraints excluded: chain X residue 44 LYS Chi-restraints excluded: chain Y residue 6 ILE Chi-restraints excluded: chain Z residue 18 CYS Chi-restraints excluded: chain Z residue 21 VAL Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain Z residue 37 CYS Chi-restraints excluded: chain 1 residue 26 SER Chi-restraints excluded: chain 1 residue 45 ASP Chi-restraints excluded: chain 2 residue 42 VAL Chi-restraints excluded: chain 3 residue 43 THR Chi-restraints excluded: chain 3 residue 44 VAL Chi-restraints excluded: chain 4 residue 6 VAL Chi-restraints excluded: chain 4 residue 25 HIS Chi-restraints excluded: chain 4 residue 43 LEU Chi-restraints excluded: chain 5 residue 7 VAL Chi-restraints excluded: chain 5 residue 13 ASN Chi-restraints excluded: chain 5 residue 16 ILE Chi-restraints excluded: chain 5 residue 22 VAL Chi-restraints excluded: chain 5 residue 37 GLN Chi-restraints excluded: chain 6 residue 14 HIS Chi-restraints excluded: chain 6 residue 30 ILE Chi-restraints excluded: chain 6 residue 89 PHE Chi-restraints excluded: chain 6 residue 113 LEU Chi-restraints excluded: chain 6 residue 139 GLU Chi-restraints excluded: chain 6 residue 150 ILE Chi-restraints excluded: chain 6 residue 162 VAL Chi-restraints excluded: chain 6 residue 163 ILE Chi-restraints excluded: chain 6 residue 196 ASP Chi-restraints excluded: chain 6 residue 198 VAL Chi-restraints excluded: chain 7 residue 7 ASN Chi-restraints excluded: chain 7 residue 18 ASN Chi-restraints excluded: chain 7 residue 28 PHE Chi-restraints excluded: chain 7 residue 35 ASP Chi-restraints excluded: chain 7 residue 48 LYS Chi-restraints excluded: chain 7 residue 96 VAL Chi-restraints excluded: chain 7 residue 102 ILE Chi-restraints excluded: chain 7 residue 105 VAL Chi-restraints excluded: chain 7 residue 128 MET Chi-restraints excluded: chain 7 residue 156 LEU Chi-restraints excluded: chain 8 residue 16 THR Chi-restraints excluded: chain 8 residue 28 ASP Chi-restraints excluded: chain 8 residue 34 GLU Chi-restraints excluded: chain 8 residue 50 TYR Chi-restraints excluded: chain 8 residue 52 VAL Chi-restraints excluded: chain 8 residue 80 ARG Chi-restraints excluded: chain 8 residue 128 VAL Chi-restraints excluded: chain 8 residue 139 ASN Chi-restraints excluded: chain 8 residue 170 LEU Chi-restraints excluded: chain 8 residue 173 ASP Chi-restraints excluded: chain 8 residue 177 MET Chi-restraints excluded: chain 9 residue 10 LEU Chi-restraints excluded: chain 9 residue 14 LEU Chi-restraints excluded: chain 9 residue 29 ILE Chi-restraints excluded: chain 9 residue 63 MET Chi-restraints excluded: chain 9 residue 75 LEU Chi-restraints excluded: chain 9 residue 121 ASN Chi-restraints excluded: chain 9 residue 122 VAL Chi-restraints excluded: chain 9 residue 130 THR Chi-restraints excluded: chain 9 residue 141 ASP Chi-restraints excluded: chain 9 residue 151 MET Chi-restraints excluded: chain 9 residue 152 VAL Chi-restraints excluded: chain 9 residue 155 LYS Chi-restraints excluded: chain 10 residue 7 VAL Chi-restraints excluded: chain 10 residue 13 ASP Chi-restraints excluded: chain 10 residue 17 GLN Chi-restraints excluded: chain 10 residue 82 ASP Chi-restraints excluded: chain 10 residue 85 ILE Chi-restraints excluded: chain 11 residue 39 GLU Chi-restraints excluded: chain 11 residue 74 VAL Chi-restraints excluded: chain 12 residue 39 LEU Chi-restraints excluded: chain 12 residue 68 LYS Chi-restraints excluded: chain 12 residue 89 ASP Chi-restraints excluded: chain 12 residue 103 VAL Chi-restraints excluded: chain 12 residue 111 THR Chi-restraints excluded: chain 12 residue 126 CYS Chi-restraints excluded: chain 13 residue 5 TYR Chi-restraints excluded: chain 13 residue 20 ILE Chi-restraints excluded: chain 13 residue 34 LEU Chi-restraints excluded: chain 13 residue 38 PHE Chi-restraints excluded: chain 13 residue 42 THR Chi-restraints excluded: chain 13 residue 49 GLN Chi-restraints excluded: chain 13 residue 57 VAL Chi-restraints excluded: chain 13 residue 60 LEU Chi-restraints excluded: chain 13 residue 67 LYS Chi-restraints excluded: chain 13 residue 93 LEU Chi-restraints excluded: chain 14 residue 8 ILE Chi-restraints excluded: chain 14 residue 17 LEU Chi-restraints excluded: chain 14 residue 32 THR Chi-restraints excluded: chain 14 residue 51 VAL Chi-restraints excluded: chain 14 residue 90 LEU Chi-restraints excluded: chain 14 residue 91 ASP Chi-restraints excluded: chain 14 residue 96 VAL Chi-restraints excluded: chain 15 residue 22 ILE Chi-restraints excluded: chain 15 residue 39 ASN Chi-restraints excluded: chain 15 residue 58 THR Chi-restraints excluded: chain 15 residue 67 GLU Chi-restraints excluded: chain 15 residue 71 ASP Chi-restraints excluded: chain 15 residue 85 VAL Chi-restraints excluded: chain 15 residue 95 THR Chi-restraints excluded: chain 15 residue 96 ILE Chi-restraints excluded: chain 15 residue 109 ILE Chi-restraints excluded: chain 16 residue 20 VAL Chi-restraints excluded: chain 16 residue 33 CYS Chi-restraints excluded: chain 16 residue 38 THR Chi-restraints excluded: chain 16 residue 40 THR Chi-restraints excluded: chain 16 residue 56 LEU Chi-restraints excluded: chain 16 residue 89 LEU Chi-restraints excluded: chain 16 residue 108 ASP Chi-restraints excluded: chain 17 residue 24 VAL Chi-restraints excluded: chain 17 residue 27 THR Chi-restraints excluded: chain 18 residue 63 CYS Chi-restraints excluded: chain 18 residue 78 LEU Chi-restraints excluded: chain 19 residue 44 GLU Chi-restraints excluded: chain 20 residue 42 ILE Chi-restraints excluded: chain 21 residue 17 GLU Chi-restraints excluded: chain 21 residue 37 ILE Chi-restraints excluded: chain 21 residue 56 ASP Chi-restraints excluded: chain 21 residue 62 GLU Chi-restraints excluded: chain 21 residue 69 THR Chi-restraints excluded: chain 22 residue 41 SER Chi-restraints excluded: chain 22 residue 42 ARG Chi-restraints excluded: chain 22 residue 54 LEU Chi-restraints excluded: chain 22 residue 64 LEU Chi-restraints excluded: chain 23 residue 12 LEU Chi-restraints excluded: chain 23 residue 18 VAL Chi-restraints excluded: chain 23 residue 23 GLU Chi-restraints excluded: chain 23 residue 24 SER Chi-restraints excluded: chain 23 residue 39 ILE Chi-restraints excluded: chain 23 residue 42 ASN Chi-restraints excluded: chain 23 residue 59 VAL Chi-restraints excluded: chain 23 residue 65 MET Chi-restraints excluded: chain 23 residue 66 VAL Chi-restraints excluded: chain 23 residue 78 THR Chi-restraints excluded: chain 24 residue 52 GLU Chi-restraints excluded: chain 24 residue 57 VAL Chi-restraints excluded: chain 25 residue 6 ARG Chi-restraints excluded: chain 25 residue 12 ASP Chi-restraints excluded: chain 25 residue 18 PHE Chi-restraints excluded: chain 25 residue 35 GLU Chi-restraints excluded: chain 25 residue 37 TYR Chi-restraints excluded: chain 25 residue 42 THR Chi-restraints excluded: chain 33 residue 56 LEU Chi-restraints excluded: chain 33 residue 138 MET Chi-restraints excluded: chain 33 residue 425 LEU Chi-restraints excluded: chain 33 residue 599 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1117 random chunks: chunk 666 optimal weight: 20.0000 chunk 429 optimal weight: 30.0000 chunk 643 optimal weight: 20.0000 chunk 324 optimal weight: 8.9990 chunk 211 optimal weight: 0.0040 chunk 208 optimal weight: 8.9990 chunk 684 optimal weight: 20.0000 chunk 733 optimal weight: 20.0000 chunk 532 optimal weight: 6.9990 chunk 100 optimal weight: 30.0000 chunk 846 optimal weight: 20.0000 overall best weight: 9.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 GLN ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 86 GLN ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 GLN ** P 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 20 ASN Z 61 ASN ** 1 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 139 ASN ** 8 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 53 GLN ** 8 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 14 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 14 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 16 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 16 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 17 104 ASN ** 18 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 20 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 33 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 33 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 33 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 167683 Z= 0.281 Angle : 0.703 14.353 250280 Z= 0.356 Chirality : 0.037 0.437 31936 Planarity : 0.005 0.083 13865 Dihedral : 24.384 177.435 82443 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 32.33 Ramachandran Plot: Outliers : 1.01 % Allowed : 10.80 % Favored : 88.19 % Rotamer: Outliers : 4.83 % Allowed : 27.10 % Favored : 68.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.10), residues: 6509 helix: -0.30 (0.11), residues: 2202 sheet: -2.34 (0.15), residues: 1000 loop : -1.99 (0.11), residues: 3307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 78 HIS 0.038 0.002 HIS I 80 PHE 0.028 0.002 PHE F 46 TYR 0.027 0.002 TYR 9 127 ARG 0.012 0.001 ARG 9 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13018 Ramachandran restraints generated. 6509 Oldfield, 0 Emsley, 6509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13018 Ramachandran restraints generated. 6509 Oldfield, 0 Emsley, 6509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1469 residues out of total 5423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 256 poor density : 1213 time to evaluate : 7.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 43 ASN cc_start: 0.9581 (m-40) cc_final: 0.9148 (p0) REVERT: F 112 LYS cc_start: 0.6050 (mttt) cc_final: 0.5630 (mtmt) REVERT: F 132 PHE cc_start: 0.8797 (m-80) cc_final: 0.8363 (m-80) REVERT: F 135 HIS cc_start: 0.8960 (t70) cc_final: 0.8480 (t70) REVERT: G 31 ARG cc_start: 0.6997 (mtm-85) cc_final: 0.5893 (mtm-85) REVERT: G 52 MET cc_start: 0.1497 (ttt) cc_final: 0.0516 (mtp) REVERT: H 120 ASP cc_start: 0.7640 (t0) cc_final: 0.7145 (t0) REVERT: H 124 MET cc_start: 0.2846 (mmp) cc_final: 0.1682 (mmt) REVERT: H 126 ARG cc_start: 0.8381 (ttm110) cc_final: 0.7985 (mtm-85) REVERT: H 129 GLU cc_start: 0.9179 (pt0) cc_final: 0.8844 (pt0) REVERT: I 37 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7543 (ttp-170) REVERT: I 67 ASN cc_start: 0.8551 (t0) cc_final: 0.8267 (t0) REVERT: L 136 MET cc_start: 0.7465 (tmm) cc_final: 0.6486 (tmm) REVERT: M 20 MET cc_start: 0.8864 (mtp) cc_final: 0.8606 (mtm) REVERT: M 74 GLU cc_start: 0.9017 (tm-30) cc_final: 0.8651 (tm-30) REVERT: M 75 ILE cc_start: 0.9101 (mm) cc_final: 0.8560 (mm) REVERT: P 24 TYR cc_start: 0.6813 (t80) cc_final: 0.6523 (t80) REVERT: Q 40 MET cc_start: 0.9112 (tpt) cc_final: 0.8906 (tpt) REVERT: S 1 MET cc_start: 0.6377 (tpp) cc_final: 0.5640 (ppp) REVERT: T 6 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.7695 (tpp80) REVERT: U 57 TYR cc_start: 0.8030 (m-80) cc_final: 0.7760 (m-80) REVERT: V 17 LEU cc_start: 0.8729 (mp) cc_final: 0.8483 (mp) REVERT: W 59 ASP cc_start: 0.9228 (m-30) cc_final: 0.9026 (p0) REVERT: W 67 LEU cc_start: 0.8915 (pp) cc_final: 0.8676 (pp) REVERT: X 23 ARG cc_start: 0.8944 (mmt-90) cc_final: 0.8672 (mmp-170) REVERT: Z 22 MET cc_start: 0.9342 (ttm) cc_final: 0.9052 (mtm) REVERT: 2 27 ARG cc_start: 0.8702 (ptp90) cc_final: 0.8501 (mtm-85) REVERT: 5 4 ARG cc_start: 0.8984 (mtm-85) cc_final: 0.8701 (ttm-80) REVERT: 6 153 MET cc_start: 0.8603 (tpt) cc_final: 0.8310 (tpt) REVERT: 7 117 ASP cc_start: 0.9334 (t0) cc_final: 0.9067 (p0) REVERT: 7 133 MET cc_start: 0.9222 (mtp) cc_final: 0.9012 (mtm) REVERT: 8 70 GLN cc_start: 0.8111 (tt0) cc_final: 0.7704 (tp40) REVERT: 8 74 TYR cc_start: 0.8414 (m-80) cc_final: 0.8101 (m-80) REVERT: 8 104 MET cc_start: 0.8577 (tpt) cc_final: 0.8330 (tpt) REVERT: 9 70 MET cc_start: 0.7444 (mmm) cc_final: 0.6853 (mmm) REVERT: 10 59 TYR cc_start: 0.7481 (m-10) cc_final: 0.7216 (m-10) REVERT: 11 30 MET cc_start: 0.8401 (ttp) cc_final: 0.8134 (ttt) REVERT: 11 74 VAL cc_start: 0.9375 (OUTLIER) cc_final: 0.9156 (m) REVERT: 12 26 MET cc_start: 0.9167 (pmm) cc_final: 0.8712 (pmm) REVERT: 13 87 MET cc_start: 0.9545 (ppp) cc_final: 0.9165 (ppp) REVERT: 14 47 GLU cc_start: 0.8105 (mp0) cc_final: 0.7760 (mp0) REVERT: 14 65 TYR cc_start: 0.7509 (m-80) cc_final: 0.7258 (m-80) REVERT: 14 66 GLU cc_start: 0.7913 (tp30) cc_final: 0.7058 (tp30) REVERT: 16 58 ASN cc_start: 0.8766 (p0) cc_final: 0.8543 (p0) REVERT: 17 62 PHE cc_start: 0.8158 (t80) cc_final: 0.7712 (m-80) REVERT: 17 77 LYS cc_start: 0.9443 (tppt) cc_final: 0.9226 (tppt) REVERT: 20 69 ASP cc_start: 0.9015 (p0) cc_final: 0.8749 (p0) REVERT: 22 50 TYR cc_start: 0.8489 (m-10) cc_final: 0.8284 (m-10) REVERT: 24 53 MET cc_start: 0.9020 (ppp) cc_final: 0.8718 (ppp) REVERT: 25 7 GLU cc_start: 0.6932 (mm-30) cc_final: 0.6663 (mm-30) REVERT: 25 35 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7489 (tp30) REVERT: 25 36 PHE cc_start: 0.8541 (p90) cc_final: 0.8104 (p90) REVERT: 25 43 GLU cc_start: 0.8796 (pt0) cc_final: 0.8269 (pt0) REVERT: 33 71 MET cc_start: -0.1708 (tpp) cc_final: -0.1943 (tpp) REVERT: 33 113 MET cc_start: 0.2228 (mtt) cc_final: 0.1531 (ptp) outliers start: 256 outliers final: 217 residues processed: 1357 average time/residue: 1.4487 time to fit residues: 3462.8854 Evaluate side-chains 1361 residues out of total 5423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 1140 time to evaluate : 6.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 268 ARG Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 126 ASN Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 15 ASP Chi-restraints excluded: chain E residue 19 ASN Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 127 GLN Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 47 PHE Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 37 ARG Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain I residue 91 GLU Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 51 LYS Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 80 ASP Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 45 GLN Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 113 ILE Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain O residue 39 LEU Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain P residue 90 ASP Chi-restraints excluded: chain P residue 96 ASP Chi-restraints excluded: chain P residue 106 THR Chi-restraints excluded: chain Q residue 14 VAL Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 76 LYS Chi-restraints excluded: chain R residue 101 SER Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain R residue 110 ARG Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 79 ASP Chi-restraints excluded: chain T residue 6 ARG Chi-restraints excluded: chain T residue 7 ASP Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 36 GLU Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain U residue 8 VAL Chi-restraints excluded: chain U residue 86 LEU Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain V residue 54 THR Chi-restraints excluded: chain V residue 78 ILE Chi-restraints excluded: chain W residue 22 ASN Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain W residue 50 VAL Chi-restraints excluded: chain W residue 63 ILE Chi-restraints excluded: chain X residue 5 GLU Chi-restraints excluded: chain X residue 7 ARG Chi-restraints excluded: chain X residue 43 LEU Chi-restraints excluded: chain Y residue 6 ILE Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain Z residue 21 VAL Chi-restraints excluded: chain Z residue 37 CYS Chi-restraints excluded: chain 1 residue 26 SER Chi-restraints excluded: chain 1 residue 45 ASP Chi-restraints excluded: chain 2 residue 42 VAL Chi-restraints excluded: chain 3 residue 44 VAL Chi-restraints excluded: chain 4 residue 6 VAL Chi-restraints excluded: chain 4 residue 43 LEU Chi-restraints excluded: chain 5 residue 7 VAL Chi-restraints excluded: chain 5 residue 22 VAL Chi-restraints excluded: chain 5 residue 37 GLN Chi-restraints excluded: chain 6 residue 14 HIS Chi-restraints excluded: chain 6 residue 30 ILE Chi-restraints excluded: chain 6 residue 89 PHE Chi-restraints excluded: chain 6 residue 113 LEU Chi-restraints excluded: chain 6 residue 139 GLU Chi-restraints excluded: chain 6 residue 150 ILE Chi-restraints excluded: chain 6 residue 162 VAL Chi-restraints excluded: chain 6 residue 163 ILE Chi-restraints excluded: chain 7 residue 18 ASN Chi-restraints excluded: chain 7 residue 35 ASP Chi-restraints excluded: chain 7 residue 48 LYS Chi-restraints excluded: chain 7 residue 96 VAL Chi-restraints excluded: chain 7 residue 102 ILE Chi-restraints excluded: chain 7 residue 105 VAL Chi-restraints excluded: chain 7 residue 128 MET Chi-restraints excluded: chain 7 residue 185 THR Chi-restraints excluded: chain 8 residue 16 THR Chi-restraints excluded: chain 8 residue 28 ASP Chi-restraints excluded: chain 8 residue 34 GLU Chi-restraints excluded: chain 8 residue 50 TYR Chi-restraints excluded: chain 8 residue 52 VAL Chi-restraints excluded: chain 8 residue 80 ARG Chi-restraints excluded: chain 8 residue 128 VAL Chi-restraints excluded: chain 8 residue 139 ASN Chi-restraints excluded: chain 8 residue 170 LEU Chi-restraints excluded: chain 8 residue 173 ASP Chi-restraints excluded: chain 9 residue 10 LEU Chi-restraints excluded: chain 9 residue 14 LEU Chi-restraints excluded: chain 9 residue 29 ILE Chi-restraints excluded: chain 9 residue 63 MET Chi-restraints excluded: chain 9 residue 121 ASN Chi-restraints excluded: chain 9 residue 122 VAL Chi-restraints excluded: chain 9 residue 130 THR Chi-restraints excluded: chain 9 residue 141 ASP Chi-restraints excluded: chain 9 residue 152 VAL Chi-restraints excluded: chain 9 residue 155 LYS Chi-restraints excluded: chain 10 residue 10 VAL Chi-restraints excluded: chain 10 residue 17 GLN Chi-restraints excluded: chain 10 residue 82 ASP Chi-restraints excluded: chain 11 residue 11 ILE Chi-restraints excluded: chain 11 residue 26 VAL Chi-restraints excluded: chain 11 residue 39 GLU Chi-restraints excluded: chain 11 residue 74 VAL Chi-restraints excluded: chain 12 residue 41 GLU Chi-restraints excluded: chain 12 residue 68 LYS Chi-restraints excluded: chain 12 residue 89 ASP Chi-restraints excluded: chain 12 residue 111 THR Chi-restraints excluded: chain 12 residue 126 CYS Chi-restraints excluded: chain 13 residue 5 TYR Chi-restraints excluded: chain 13 residue 20 ILE Chi-restraints excluded: chain 13 residue 34 LEU Chi-restraints excluded: chain 13 residue 38 PHE Chi-restraints excluded: chain 13 residue 49 GLN Chi-restraints excluded: chain 13 residue 57 VAL Chi-restraints excluded: chain 13 residue 60 LEU Chi-restraints excluded: chain 13 residue 93 LEU Chi-restraints excluded: chain 14 residue 17 LEU Chi-restraints excluded: chain 14 residue 32 THR Chi-restraints excluded: chain 14 residue 51 VAL Chi-restraints excluded: chain 14 residue 90 LEU Chi-restraints excluded: chain 14 residue 91 ASP Chi-restraints excluded: chain 14 residue 96 VAL Chi-restraints excluded: chain 14 residue 102 LEU Chi-restraints excluded: chain 15 residue 22 ILE Chi-restraints excluded: chain 15 residue 39 ASN Chi-restraints excluded: chain 15 residue 58 THR Chi-restraints excluded: chain 15 residue 71 ASP Chi-restraints excluded: chain 15 residue 85 VAL Chi-restraints excluded: chain 15 residue 95 THR Chi-restraints excluded: chain 15 residue 109 ILE Chi-restraints excluded: chain 16 residue 20 VAL Chi-restraints excluded: chain 16 residue 33 CYS Chi-restraints excluded: chain 16 residue 38 THR Chi-restraints excluded: chain 16 residue 40 THR Chi-restraints excluded: chain 16 residue 56 LEU Chi-restraints excluded: chain 16 residue 89 LEU Chi-restraints excluded: chain 16 residue 108 ASP Chi-restraints excluded: chain 17 residue 24 VAL Chi-restraints excluded: chain 17 residue 27 THR Chi-restraints excluded: chain 18 residue 92 ILE Chi-restraints excluded: chain 19 residue 44 GLU Chi-restraints excluded: chain 20 residue 26 ASN Chi-restraints excluded: chain 20 residue 42 ILE Chi-restraints excluded: chain 21 residue 56 ASP Chi-restraints excluded: chain 21 residue 62 GLU Chi-restraints excluded: chain 21 residue 69 THR Chi-restraints excluded: chain 22 residue 9 PHE Chi-restraints excluded: chain 22 residue 41 SER Chi-restraints excluded: chain 22 residue 42 ARG Chi-restraints excluded: chain 22 residue 54 LEU Chi-restraints excluded: chain 23 residue 12 LEU Chi-restraints excluded: chain 23 residue 39 ILE Chi-restraints excluded: chain 23 residue 42 ASN Chi-restraints excluded: chain 23 residue 59 VAL Chi-restraints excluded: chain 23 residue 66 VAL Chi-restraints excluded: chain 24 residue 52 GLU Chi-restraints excluded: chain 25 residue 6 ARG Chi-restraints excluded: chain 25 residue 12 ASP Chi-restraints excluded: chain 25 residue 18 PHE Chi-restraints excluded: chain 25 residue 35 GLU Chi-restraints excluded: chain 25 residue 37 TYR Chi-restraints excluded: chain 25 residue 42 THR Chi-restraints excluded: chain 33 residue 425 LEU Chi-restraints excluded: chain 33 residue 613 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1117 random chunks: chunk 979 optimal weight: 20.0000 chunk 1031 optimal weight: 30.0000 chunk 941 optimal weight: 50.0000 chunk 1003 optimal weight: 30.0000 chunk 603 optimal weight: 20.0000 chunk 437 optimal weight: 50.0000 chunk 787 optimal weight: 30.0000 chunk 307 optimal weight: 20.0000 chunk 906 optimal weight: 20.0000 chunk 948 optimal weight: 20.0000 chunk 999 optimal weight: 30.0000 overall best weight: 20.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 104 GLN ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 24 ASN ** U 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 20 ASN Z 61 ASN ** 1 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 88 GLN ** 7 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 139 ASN ** 8 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 14 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 14 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 14 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 15 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 16 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 16 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 17 104 ASN ** 18 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 20 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 22 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 33 49 HIS ** 33 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 33 108 HIS 33 297 HIS ** 33 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 33 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 33 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 33 689 ASN 33 730 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.4836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.143 167683 Z= 0.549 Angle : 0.891 16.046 250280 Z= 0.450 Chirality : 0.046 0.400 31936 Planarity : 0.006 0.076 13865 Dihedral : 24.534 178.529 82443 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 49.80 Ramachandran Plot: Outliers : 0.95 % Allowed : 13.07 % Favored : 85.97 % Rotamer: Outliers : 5.49 % Allowed : 27.06 % Favored : 67.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 6509 helix: -0.84 (0.10), residues: 2214 sheet: -2.48 (0.15), residues: 1006 loop : -2.18 (0.11), residues: 3289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP C 78 HIS 0.037 0.003 HIS I 80 PHE 0.029 0.003 PHE24 30 TYR 0.027 0.003 TYR D 82 ARG 0.031 0.001 ARG 9 111 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13018 Ramachandran restraints generated. 6509 Oldfield, 0 Emsley, 6509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13018 Ramachandran restraints generated. 6509 Oldfield, 0 Emsley, 6509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1390 residues out of total 5423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 291 poor density : 1099 time to evaluate : 6.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 43 ASN cc_start: 0.9613 (m-40) cc_final: 0.9168 (p0) REVERT: F 132 PHE cc_start: 0.8778 (m-80) cc_final: 0.8322 (m-80) REVERT: F 135 HIS cc_start: 0.8974 (t70) cc_final: 0.8446 (t70) REVERT: G 31 ARG cc_start: 0.7485 (mtm-85) cc_final: 0.6381 (mtm-85) REVERT: G 52 MET cc_start: 0.1887 (ttt) cc_final: 0.0901 (mtp) REVERT: H 120 ASP cc_start: 0.7863 (t0) cc_final: 0.7410 (t0) REVERT: H 124 MET cc_start: 0.2934 (mmp) cc_final: 0.1726 (mmt) REVERT: H 129 GLU cc_start: 0.9163 (pt0) cc_final: 0.8938 (pt0) REVERT: I 34 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.8712 (ptm-80) REVERT: I 37 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7622 (ttp-170) REVERT: I 67 ASN cc_start: 0.8560 (t0) cc_final: 0.8343 (t0) REVERT: M 20 MET cc_start: 0.8958 (mtp) cc_final: 0.8749 (mtm) REVERT: M 74 GLU cc_start: 0.9142 (tm-30) cc_final: 0.8846 (tm-30) REVERT: M 75 ILE cc_start: 0.9183 (mm) cc_final: 0.8737 (mm) REVERT: P 24 TYR cc_start: 0.7018 (t80) cc_final: 0.6739 (t80) REVERT: T 6 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.7884 (tpp80) REVERT: U 12 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8677 (mm-40) REVERT: V 17 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8576 (mp) REVERT: W 67 LEU cc_start: 0.9040 (pp) cc_final: 0.8825 (pp) REVERT: X 23 ARG cc_start: 0.9131 (mmt-90) cc_final: 0.8746 (mmp-170) REVERT: X 24 GLU cc_start: 0.8942 (pt0) cc_final: 0.8641 (pm20) REVERT: 3 10 LEU cc_start: 0.8716 (tp) cc_final: 0.8480 (tt) REVERT: 4 48 MET cc_start: 0.9018 (tpp) cc_final: 0.8814 (tpp) REVERT: 5 4 ARG cc_start: 0.8991 (mtm-85) cc_final: 0.8756 (ttm-80) REVERT: 6 153 MET cc_start: 0.8601 (tpt) cc_final: 0.8239 (tpt) REVERT: 7 117 ASP cc_start: 0.9409 (t0) cc_final: 0.9127 (p0) REVERT: 8 70 GLN cc_start: 0.8597 (tt0) cc_final: 0.7779 (tp40) REVERT: 8 74 TYR cc_start: 0.8458 (m-80) cc_final: 0.8145 (m-80) REVERT: 8 104 MET cc_start: 0.8745 (tpt) cc_final: 0.8501 (tpt) REVERT: 10 59 TYR cc_start: 0.7598 (m-10) cc_final: 0.7377 (m-10) REVERT: 11 74 VAL cc_start: 0.9409 (OUTLIER) cc_final: 0.9198 (m) REVERT: 11 91 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8629 (ptp-110) REVERT: 12 26 MET cc_start: 0.9224 (pmm) cc_final: 0.8793 (pmm) REVERT: 13 87 MET cc_start: 0.9594 (ppp) cc_final: 0.9249 (ppp) REVERT: 14 47 GLU cc_start: 0.8362 (mp0) cc_final: 0.8042 (mp0) REVERT: 14 65 TYR cc_start: 0.7686 (m-80) cc_final: 0.7331 (m-80) REVERT: 14 66 GLU cc_start: 0.8128 (tp30) cc_final: 0.7207 (tp30) REVERT: 14 81 GLU cc_start: 0.8991 (tm-30) cc_final: 0.8777 (tm-30) REVERT: 17 62 PHE cc_start: 0.8145 (t80) cc_final: 0.7731 (m-80) REVERT: 20 69 ASP cc_start: 0.9112 (p0) cc_final: 0.8851 (p0) REVERT: 21 42 LYS cc_start: 0.9291 (mtpt) cc_final: 0.8992 (ttpp) REVERT: 24 53 MET cc_start: 0.9130 (ppp) cc_final: 0.8875 (ppp) REVERT: 25 43 GLU cc_start: 0.8922 (pt0) cc_final: 0.8480 (pt0) REVERT: 33 113 MET cc_start: 0.2665 (mtt) cc_final: 0.2216 (mpp) outliers start: 291 outliers final: 250 residues processed: 1274 average time/residue: 1.3312 time to fit residues: 2958.8089 Evaluate side-chains 1328 residues out of total 5423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 1071 time to evaluate : 6.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 268 ARG Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 126 ASN Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 148 GLN Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 15 ASP Chi-restraints excluded: chain E residue 19 ASN Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 127 GLN Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 47 PHE Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 34 ARG Chi-restraints excluded: chain I residue 37 ARG Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain I residue 91 GLU Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 51 LYS Chi-restraints excluded: chain J residue 56 ASP Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 80 ASP Chi-restraints excluded: chain J residue 89 ASN Chi-restraints excluded: chain J residue 92 GLU Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 104 GLN Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 45 GLN Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain L residue 134 THR Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 113 ILE Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain O residue 2 ASN Chi-restraints excluded: chain O residue 39 LEU Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain P residue 90 ASP Chi-restraints excluded: chain P residue 96 ASP Chi-restraints excluded: chain P residue 106 THR Chi-restraints excluded: chain Q residue 14 VAL Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 60 LYS Chi-restraints excluded: chain R residue 101 SER Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain R residue 110 ARG Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 79 ASP Chi-restraints excluded: chain T residue 6 ARG Chi-restraints excluded: chain T residue 7 ASP Chi-restraints excluded: chain T residue 27 VAL Chi-restraints excluded: chain T residue 36 GLU Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain U residue 8 VAL Chi-restraints excluded: chain U residue 12 GLN Chi-restraints excluded: chain U residue 35 GLU Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain U residue 86 LEU Chi-restraints excluded: chain V residue 17 LEU Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain V residue 54 THR Chi-restraints excluded: chain V residue 78 ILE Chi-restraints excluded: chain W residue 22 ASN Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 50 VAL Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain W residue 63 ILE Chi-restraints excluded: chain X residue 7 ARG Chi-restraints excluded: chain X residue 43 LEU Chi-restraints excluded: chain X residue 44 LYS Chi-restraints excluded: chain Y residue 6 ILE Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain Z residue 18 CYS Chi-restraints excluded: chain Z residue 21 VAL Chi-restraints excluded: chain Z residue 24 ILE Chi-restraints excluded: chain Z residue 37 CYS Chi-restraints excluded: chain 1 residue 5 ASN Chi-restraints excluded: chain 1 residue 26 SER Chi-restraints excluded: chain 1 residue 45 ASP Chi-restraints excluded: chain 2 residue 42 VAL Chi-restraints excluded: chain 3 residue 44 VAL Chi-restraints excluded: chain 4 residue 6 VAL Chi-restraints excluded: chain 4 residue 43 LEU Chi-restraints excluded: chain 5 residue 7 VAL Chi-restraints excluded: chain 5 residue 13 ASN Chi-restraints excluded: chain 5 residue 22 VAL Chi-restraints excluded: chain 5 residue 37 GLN Chi-restraints excluded: chain 6 residue 14 HIS Chi-restraints excluded: chain 6 residue 30 ILE Chi-restraints excluded: chain 6 residue 89 PHE Chi-restraints excluded: chain 6 residue 113 LEU Chi-restraints excluded: chain 6 residue 139 GLU Chi-restraints excluded: chain 6 residue 150 ILE Chi-restraints excluded: chain 6 residue 162 VAL Chi-restraints excluded: chain 6 residue 163 ILE Chi-restraints excluded: chain 6 residue 185 ILE Chi-restraints excluded: chain 6 residue 193 ASP Chi-restraints excluded: chain 7 residue 7 ASN Chi-restraints excluded: chain 7 residue 18 ASN Chi-restraints excluded: chain 7 residue 28 PHE Chi-restraints excluded: chain 7 residue 35 ASP Chi-restraints excluded: chain 7 residue 48 LYS Chi-restraints excluded: chain 7 residue 96 VAL Chi-restraints excluded: chain 7 residue 102 ILE Chi-restraints excluded: chain 7 residue 105 VAL Chi-restraints excluded: chain 7 residue 128 MET Chi-restraints excluded: chain 7 residue 185 THR Chi-restraints excluded: chain 8 residue 16 THR Chi-restraints excluded: chain 8 residue 28 ASP Chi-restraints excluded: chain 8 residue 34 GLU Chi-restraints excluded: chain 8 residue 50 TYR Chi-restraints excluded: chain 8 residue 52 VAL Chi-restraints excluded: chain 8 residue 80 ARG Chi-restraints excluded: chain 8 residue 124 VAL Chi-restraints excluded: chain 8 residue 128 VAL Chi-restraints excluded: chain 8 residue 139 ASN Chi-restraints excluded: chain 8 residue 170 LEU Chi-restraints excluded: chain 8 residue 173 ASP Chi-restraints excluded: chain 9 residue 10 LEU Chi-restraints excluded: chain 9 residue 14 LEU Chi-restraints excluded: chain 9 residue 29 ILE Chi-restraints excluded: chain 9 residue 63 MET Chi-restraints excluded: chain 9 residue 75 LEU Chi-restraints excluded: chain 9 residue 105 ILE Chi-restraints excluded: chain 9 residue 121 ASN Chi-restraints excluded: chain 9 residue 122 VAL Chi-restraints excluded: chain 9 residue 130 THR Chi-restraints excluded: chain 9 residue 141 ASP Chi-restraints excluded: chain 9 residue 151 MET Chi-restraints excluded: chain 9 residue 152 VAL Chi-restraints excluded: chain 9 residue 155 LYS Chi-restraints excluded: chain 10 residue 13 ASP Chi-restraints excluded: chain 10 residue 17 GLN Chi-restraints excluded: chain 10 residue 82 ASP Chi-restraints excluded: chain 11 residue 11 ILE Chi-restraints excluded: chain 11 residue 39 GLU Chi-restraints excluded: chain 11 residue 74 VAL Chi-restraints excluded: chain 11 residue 91 ARG Chi-restraints excluded: chain 12 residue 68 LYS Chi-restraints excluded: chain 12 residue 89 ASP Chi-restraints excluded: chain 12 residue 111 THR Chi-restraints excluded: chain 12 residue 126 CYS Chi-restraints excluded: chain 13 residue 5 TYR Chi-restraints excluded: chain 13 residue 20 ILE Chi-restraints excluded: chain 13 residue 34 LEU Chi-restraints excluded: chain 13 residue 38 PHE Chi-restraints excluded: chain 13 residue 57 VAL Chi-restraints excluded: chain 13 residue 60 LEU Chi-restraints excluded: chain 13 residue 67 LYS Chi-restraints excluded: chain 13 residue 93 LEU Chi-restraints excluded: chain 14 residue 32 THR Chi-restraints excluded: chain 14 residue 51 VAL Chi-restraints excluded: chain 14 residue 90 LEU Chi-restraints excluded: chain 14 residue 91 ASP Chi-restraints excluded: chain 14 residue 96 VAL Chi-restraints excluded: chain 15 residue 22 ILE Chi-restraints excluded: chain 15 residue 39 ASN Chi-restraints excluded: chain 15 residue 58 THR Chi-restraints excluded: chain 15 residue 67 GLU Chi-restraints excluded: chain 15 residue 71 ASP Chi-restraints excluded: chain 15 residue 85 VAL Chi-restraints excluded: chain 15 residue 95 THR Chi-restraints excluded: chain 15 residue 109 ILE Chi-restraints excluded: chain 16 residue 20 VAL Chi-restraints excluded: chain 16 residue 38 THR Chi-restraints excluded: chain 16 residue 40 THR Chi-restraints excluded: chain 16 residue 56 LEU Chi-restraints excluded: chain 16 residue 89 LEU Chi-restraints excluded: chain 16 residue 96 THR Chi-restraints excluded: chain 16 residue 108 ASP Chi-restraints excluded: chain 17 residue 24 VAL Chi-restraints excluded: chain 17 residue 27 THR Chi-restraints excluded: chain 18 residue 45 LEU Chi-restraints excluded: chain 18 residue 63 CYS Chi-restraints excluded: chain 18 residue 79 SER Chi-restraints excluded: chain 19 residue 44 GLU Chi-restraints excluded: chain 20 residue 20 VAL Chi-restraints excluded: chain 21 residue 10 ARG Chi-restraints excluded: chain 21 residue 37 ILE Chi-restraints excluded: chain 21 residue 56 ASP Chi-restraints excluded: chain 21 residue 62 GLU Chi-restraints excluded: chain 21 residue 69 THR Chi-restraints excluded: chain 22 residue 41 SER Chi-restraints excluded: chain 22 residue 42 ARG Chi-restraints excluded: chain 22 residue 54 LEU Chi-restraints excluded: chain 23 residue 12 LEU Chi-restraints excluded: chain 23 residue 39 ILE Chi-restraints excluded: chain 23 residue 42 ASN Chi-restraints excluded: chain 23 residue 59 VAL Chi-restraints excluded: chain 23 residue 65 MET Chi-restraints excluded: chain 23 residue 66 VAL Chi-restraints excluded: chain 23 residue 78 THR Chi-restraints excluded: chain 24 residue 52 GLU Chi-restraints excluded: chain 25 residue 6 ARG Chi-restraints excluded: chain 25 residue 12 ASP Chi-restraints excluded: chain 25 residue 18 PHE Chi-restraints excluded: chain 25 residue 35 GLU Chi-restraints excluded: chain 25 residue 37 TYR Chi-restraints excluded: chain 25 residue 42 THR Chi-restraints excluded: chain 33 residue 56 LEU Chi-restraints excluded: chain 33 residue 414 ASP Chi-restraints excluded: chain 33 residue 425 LEU Chi-restraints excluded: chain 33 residue 599 VAL Chi-restraints excluded: chain 33 residue 613 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1117 random chunks: chunk 658 optimal weight: 20.0000 chunk 1060 optimal weight: 40.0000 chunk 647 optimal weight: 10.0000 chunk 503 optimal weight: 6.9990 chunk 737 optimal weight: 20.0000 chunk 1112 optimal weight: 30.0000 chunk 1024 optimal weight: 10.0000 chunk 886 optimal weight: 10.0000 chunk 92 optimal weight: 8.9990 chunk 684 optimal weight: 20.0000 chunk 543 optimal weight: 10.0000 overall best weight: 9.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 86 GLN ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 GLN ** P 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 101 ASN ** 7 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 139 ASN ** 8 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 31 GLN ** 13 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 14 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 14 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 14 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 15 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 16 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 16 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 17 104 ASN ** 20 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 21 30 HIS ** 24 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 33 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.4811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 167683 Z= 0.295 Angle : 0.738 16.622 250280 Z= 0.372 Chirality : 0.038 0.406 31936 Planarity : 0.005 0.076 13865 Dihedral : 24.547 177.933 82443 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 34.58 Ramachandran Plot: Outliers : 0.98 % Allowed : 11.26 % Favored : 87.76 % Rotamer: Outliers : 4.70 % Allowed : 28.27 % Favored : 67.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.10), residues: 6509 helix: -0.57 (0.11), residues: 2230 sheet: -2.31 (0.15), residues: 978 loop : -2.04 (0.11), residues: 3301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP C 78 HIS 0.037 0.002 HIS I 80 PHE 0.068 0.002 PHE D 98 TYR 0.042 0.002 TYR U 57 ARG 0.013 0.001 ARG22 72 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13018 Ramachandran restraints generated. 6509 Oldfield, 0 Emsley, 6509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13018 Ramachandran restraints generated. 6509 Oldfield, 0 Emsley, 6509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1416 residues out of total 5423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 1167 time to evaluate : 6.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 43 ASN cc_start: 0.9588 (m-40) cc_final: 0.9073 (p0) REVERT: F 112 LYS cc_start: 0.5976 (mttt) cc_final: 0.5565 (mtmt) REVERT: F 132 PHE cc_start: 0.8791 (m-80) cc_final: 0.8326 (m-80) REVERT: F 135 HIS cc_start: 0.8975 (t70) cc_final: 0.8452 (t-90) REVERT: G 31 ARG cc_start: 0.7337 (mtm-85) cc_final: 0.6367 (mtm-85) REVERT: G 52 MET cc_start: 0.1746 (ttt) cc_final: 0.0702 (mtp) REVERT: H 120 ASP cc_start: 0.8088 (t0) cc_final: 0.7640 (t0) REVERT: H 124 MET cc_start: 0.2877 (mmp) cc_final: 0.1746 (mmt) REVERT: H 129 GLU cc_start: 0.9166 (pt0) cc_final: 0.8940 (pt0) REVERT: I 67 ASN cc_start: 0.8536 (t0) cc_final: 0.8265 (t0) REVERT: K 81 ASP cc_start: 0.9102 (p0) cc_final: 0.8849 (p0) REVERT: L 136 MET cc_start: 0.7414 (tmm) cc_final: 0.6530 (tmm) REVERT: M 20 MET cc_start: 0.8863 (mtp) cc_final: 0.8617 (mtm) REVERT: M 74 GLU cc_start: 0.9056 (tm-30) cc_final: 0.8770 (tm-30) REVERT: M 75 ILE cc_start: 0.9118 (mm) cc_final: 0.8673 (mm) REVERT: N 69 ASP cc_start: 0.9401 (OUTLIER) cc_final: 0.9189 (p0) REVERT: P 24 TYR cc_start: 0.6853 (t80) cc_final: 0.6499 (t80) REVERT: S 1 MET cc_start: 0.6617 (tpp) cc_final: 0.6213 (tmm) REVERT: T 6 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.7766 (tpp80) REVERT: T 40 LEU cc_start: 0.8862 (mm) cc_final: 0.8657 (mm) REVERT: U 57 TYR cc_start: 0.7972 (m-80) cc_final: 0.7622 (m-80) REVERT: V 68 LYS cc_start: 0.8168 (mmmt) cc_final: 0.7801 (mmmt) REVERT: W 59 ASP cc_start: 0.9239 (m-30) cc_final: 0.9029 (p0) REVERT: W 67 LEU cc_start: 0.8938 (pp) cc_final: 0.8738 (pp) REVERT: X 23 ARG cc_start: 0.9003 (mmt-90) cc_final: 0.8672 (mmp-170) REVERT: X 24 GLU cc_start: 0.8823 (pt0) cc_final: 0.8552 (pm20) REVERT: Z 22 MET cc_start: 0.9283 (mtm) cc_final: 0.8917 (mmm) REVERT: Z 30 HIS cc_start: 0.8730 (p-80) cc_final: 0.8364 (p-80) REVERT: 2 49 LYS cc_start: 0.8789 (mmtt) cc_final: 0.8558 (mmtm) REVERT: 3 10 LEU cc_start: 0.8584 (tp) cc_final: 0.8369 (tt) REVERT: 4 48 MET cc_start: 0.8949 (tpp) cc_final: 0.8723 (tpp) REVERT: 5 4 ARG cc_start: 0.8951 (mtm-85) cc_final: 0.8726 (ttm-80) REVERT: 6 26 MET cc_start: 0.7715 (mtp) cc_final: 0.7487 (ppp) REVERT: 6 153 MET cc_start: 0.8543 (tpt) cc_final: 0.8164 (tpt) REVERT: 7 101 ASN cc_start: 0.9279 (OUTLIER) cc_final: 0.8968 (m110) REVERT: 7 117 ASP cc_start: 0.9342 (t0) cc_final: 0.9077 (p0) REVERT: 8 70 GLN cc_start: 0.8395 (tt0) cc_final: 0.7654 (tp-100) REVERT: 8 74 TYR cc_start: 0.8351 (m-80) cc_final: 0.7905 (m-80) REVERT: 8 104 MET cc_start: 0.8637 (tpt) cc_final: 0.8412 (tpt) REVERT: 10 59 TYR cc_start: 0.7578 (m-10) cc_final: 0.7285 (m-10) REVERT: 11 30 MET cc_start: 0.8398 (ttp) cc_final: 0.8130 (ttt) REVERT: 11 74 VAL cc_start: 0.9398 (OUTLIER) cc_final: 0.9175 (m) REVERT: 11 91 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8571 (ptp-170) REVERT: 12 26 MET cc_start: 0.9191 (pmm) cc_final: 0.8740 (pmm) REVERT: 13 87 MET cc_start: 0.9508 (ppp) cc_final: 0.9150 (ppp) REVERT: 14 65 TYR cc_start: 0.7461 (m-80) cc_final: 0.7229 (m-80) REVERT: 14 66 GLU cc_start: 0.7867 (tp30) cc_final: 0.6996 (tp30) REVERT: 14 81 GLU cc_start: 0.8971 (tm-30) cc_final: 0.8761 (tm-30) REVERT: 15 112 VAL cc_start: 0.9400 (m) cc_final: 0.9098 (m) REVERT: 17 62 PHE cc_start: 0.8242 (t80) cc_final: 0.7877 (m-80) REVERT: 20 69 ASP cc_start: 0.8993 (p0) cc_final: 0.8742 (p0) REVERT: 24 53 MET cc_start: 0.9040 (ppp) cc_final: 0.8767 (ppp) REVERT: 25 7 GLU cc_start: 0.7067 (mm-30) cc_final: 0.6739 (mm-30) REVERT: 33 113 MET cc_start: 0.2644 (mtt) cc_final: 0.2292 (mpp) outliers start: 249 outliers final: 217 residues processed: 1317 average time/residue: 1.3253 time to fit residues: 3051.7295 Evaluate side-chains 1341 residues out of total 5423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 1119 time to evaluate : 6.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain A residue 155 ARG Chi-restraints excluded: chain A residue 156 SER Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 193 GLU Chi-restraints excluded: chain A residue 199 HIS Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 268 ARG Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 126 ASN Chi-restraints excluded: chain B residue 139 SER Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 15 ASP Chi-restraints excluded: chain E residue 19 ASN Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 127 GLN Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 11 ASN Chi-restraints excluded: chain F residue 40 THR Chi-restraints excluded: chain F residue 47 PHE Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain H residue 60 VAL Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 3 THR Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain I residue 91 GLU Chi-restraints excluded: chain J residue 28 SER Chi-restraints excluded: chain J residue 51 LYS Chi-restraints excluded: chain J residue 56 ASP Chi-restraints excluded: chain J residue 62 VAL Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 80 ASP Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 45 GLN Chi-restraints excluded: chain L residue 134 THR Chi-restraints excluded: chain M residue 2 ARG Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 113 ILE Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 54 VAL Chi-restraints excluded: chain N residue 69 ASP Chi-restraints excluded: chain N residue 115 LEU Chi-restraints excluded: chain O residue 39 LEU Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain P residue 90 ASP Chi-restraints excluded: chain P residue 96 ASP Chi-restraints excluded: chain P residue 106 THR Chi-restraints excluded: chain Q residue 14 VAL Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain R residue 101 SER Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain R residue 110 ARG Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 79 ASP Chi-restraints excluded: chain T residue 6 ARG Chi-restraints excluded: chain T residue 7 ASP Chi-restraints excluded: chain T residue 36 GLU Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain U residue 8 VAL Chi-restraints excluded: chain U residue 86 LEU Chi-restraints excluded: chain V residue 19 VAL Chi-restraints excluded: chain V residue 52 ASP Chi-restraints excluded: chain V residue 78 ILE Chi-restraints excluded: chain W residue 22 ASN Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 50 VAL Chi-restraints excluded: chain X residue 7 ARG Chi-restraints excluded: chain X residue 43 LEU Chi-restraints excluded: chain Y residue 6 ILE Chi-restraints excluded: chain Y residue 26 LEU Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain Z residue 18 CYS Chi-restraints excluded: chain Z residue 21 VAL Chi-restraints excluded: chain Z residue 37 CYS Chi-restraints excluded: chain 1 residue 5 ASN Chi-restraints excluded: chain 1 residue 26 SER Chi-restraints excluded: chain 1 residue 45 ASP Chi-restraints excluded: chain 2 residue 42 VAL Chi-restraints excluded: chain 3 residue 43 THR Chi-restraints excluded: chain 3 residue 44 VAL Chi-restraints excluded: chain 4 residue 6 VAL Chi-restraints excluded: chain 5 residue 7 VAL Chi-restraints excluded: chain 5 residue 13 ASN Chi-restraints excluded: chain 5 residue 22 VAL Chi-restraints excluded: chain 5 residue 37 GLN Chi-restraints excluded: chain 6 residue 14 HIS Chi-restraints excluded: chain 6 residue 30 ILE Chi-restraints excluded: chain 6 residue 89 PHE Chi-restraints excluded: chain 6 residue 113 LEU Chi-restraints excluded: chain 6 residue 139 GLU Chi-restraints excluded: chain 6 residue 150 ILE Chi-restraints excluded: chain 6 residue 158 ASP Chi-restraints excluded: chain 6 residue 163 ILE Chi-restraints excluded: chain 6 residue 185 ILE Chi-restraints excluded: chain 7 residue 18 ASN Chi-restraints excluded: chain 7 residue 35 ASP Chi-restraints excluded: chain 7 residue 48 LYS Chi-restraints excluded: chain 7 residue 96 VAL Chi-restraints excluded: chain 7 residue 101 ASN Chi-restraints excluded: chain 7 residue 105 VAL Chi-restraints excluded: chain 7 residue 128 MET Chi-restraints excluded: chain 8 residue 16 THR Chi-restraints excluded: chain 8 residue 28 ASP Chi-restraints excluded: chain 8 residue 34 GLU Chi-restraints excluded: chain 8 residue 52 VAL Chi-restraints excluded: chain 8 residue 80 ARG Chi-restraints excluded: chain 8 residue 128 VAL Chi-restraints excluded: chain 8 residue 139 ASN Chi-restraints excluded: chain 8 residue 170 LEU Chi-restraints excluded: chain 8 residue 173 ASP Chi-restraints excluded: chain 9 residue 10 LEU Chi-restraints excluded: chain 9 residue 14 LEU Chi-restraints excluded: chain 9 residue 29 ILE Chi-restraints excluded: chain 9 residue 63 MET Chi-restraints excluded: chain 9 residue 121 ASN Chi-restraints excluded: chain 9 residue 122 VAL Chi-restraints excluded: chain 9 residue 130 THR Chi-restraints excluded: chain 9 residue 141 ASP Chi-restraints excluded: chain 9 residue 152 VAL Chi-restraints excluded: chain 10 residue 10 VAL Chi-restraints excluded: chain 10 residue 13 ASP Chi-restraints excluded: chain 10 residue 82 ASP Chi-restraints excluded: chain 11 residue 11 ILE Chi-restraints excluded: chain 11 residue 39 GLU Chi-restraints excluded: chain 11 residue 74 VAL Chi-restraints excluded: chain 11 residue 91 ARG Chi-restraints excluded: chain 12 residue 68 LYS Chi-restraints excluded: chain 12 residue 89 ASP Chi-restraints excluded: chain 12 residue 111 THR Chi-restraints excluded: chain 12 residue 126 CYS Chi-restraints excluded: chain 13 residue 5 TYR Chi-restraints excluded: chain 13 residue 20 ILE Chi-restraints excluded: chain 13 residue 34 LEU Chi-restraints excluded: chain 13 residue 38 PHE Chi-restraints excluded: chain 13 residue 57 VAL Chi-restraints excluded: chain 13 residue 60 LEU Chi-restraints excluded: chain 14 residue 32 THR Chi-restraints excluded: chain 14 residue 51 VAL Chi-restraints excluded: chain 14 residue 90 LEU Chi-restraints excluded: chain 14 residue 91 ASP Chi-restraints excluded: chain 14 residue 96 VAL Chi-restraints excluded: chain 15 residue 39 ASN Chi-restraints excluded: chain 15 residue 58 THR Chi-restraints excluded: chain 15 residue 71 ASP Chi-restraints excluded: chain 15 residue 85 VAL Chi-restraints excluded: chain 15 residue 95 THR Chi-restraints excluded: chain 15 residue 109 ILE Chi-restraints excluded: chain 16 residue 32 VAL Chi-restraints excluded: chain 16 residue 38 THR Chi-restraints excluded: chain 16 residue 40 THR Chi-restraints excluded: chain 16 residue 56 LEU Chi-restraints excluded: chain 16 residue 89 LEU Chi-restraints excluded: chain 16 residue 108 ASP Chi-restraints excluded: chain 17 residue 24 VAL Chi-restraints excluded: chain 17 residue 27 THR Chi-restraints excluded: chain 18 residue 63 CYS Chi-restraints excluded: chain 18 residue 79 SER Chi-restraints excluded: chain 19 residue 44 GLU Chi-restraints excluded: chain 20 residue 20 VAL Chi-restraints excluded: chain 21 residue 56 ASP Chi-restraints excluded: chain 21 residue 62 GLU Chi-restraints excluded: chain 21 residue 69 THR Chi-restraints excluded: chain 22 residue 41 SER Chi-restraints excluded: chain 22 residue 42 ARG Chi-restraints excluded: chain 22 residue 54 LEU Chi-restraints excluded: chain 23 residue 12 LEU Chi-restraints excluded: chain 23 residue 39 ILE Chi-restraints excluded: chain 23 residue 42 ASN Chi-restraints excluded: chain 23 residue 59 VAL Chi-restraints excluded: chain 23 residue 65 MET Chi-restraints excluded: chain 23 residue 66 VAL Chi-restraints excluded: chain 23 residue 72 GLU Chi-restraints excluded: chain 23 residue 78 THR Chi-restraints excluded: chain 24 residue 52 GLU Chi-restraints excluded: chain 25 residue 6 ARG Chi-restraints excluded: chain 25 residue 12 ASP Chi-restraints excluded: chain 25 residue 18 PHE Chi-restraints excluded: chain 25 residue 35 GLU Chi-restraints excluded: chain 25 residue 37 TYR Chi-restraints excluded: chain 25 residue 42 THR Chi-restraints excluded: chain 33 residue 56 LEU Chi-restraints excluded: chain 33 residue 414 ASP Chi-restraints excluded: chain 33 residue 425 LEU Chi-restraints excluded: chain 33 residue 599 VAL Chi-restraints excluded: chain 33 residue 613 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1117 random chunks: chunk 703 optimal weight: 30.0000 chunk 943 optimal weight: 50.0000 chunk 271 optimal weight: 0.8980 chunk 817 optimal weight: 20.0000 chunk 130 optimal weight: 30.0000 chunk 246 optimal weight: 20.0000 chunk 887 optimal weight: 20.0000 chunk 371 optimal weight: 20.0000 chunk 911 optimal weight: 30.0000 chunk 112 optimal weight: 8.9990 chunk 163 optimal weight: 0.0070 overall best weight: 9.9808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 GLN ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 61 ASN ** 1 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 101 ASN ** 7 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 10 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 14 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 14 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 14 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 15 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 15 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 16 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 16 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 17 104 ASN ** 18 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 20 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 33 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.028784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2408 r_free = 0.2408 target = 0.020253 restraints weight = 1703762.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2422 r_free = 0.2422 target = 0.020624 restraints weight = 629880.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2438 r_free = 0.2438 target = 0.020968 restraints weight = 351434.050| |-----------------------------------------------------------------------------| r_work (final): 0.2420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9015 moved from start: 0.4822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.292 167683 Z= 0.336 Angle : 0.764 59.186 250280 Z= 0.391 Chirality : 0.039 0.612 31936 Planarity : 0.005 0.073 13865 Dihedral : 24.544 177.947 82441 Min Nonbonded Distance : 1.550 Molprobity Statistics. All-atom Clashscore : 36.46 Ramachandran Plot: Outliers : 0.98 % Allowed : 11.51 % Favored : 87.51 % Rotamer: Outliers : 4.58 % Allowed : 28.66 % Favored : 66.75 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.10), residues: 6509 helix: -0.55 (0.11), residues: 2229 sheet: -2.32 (0.15), residues: 983 loop : -2.03 (0.11), residues: 3297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 78 HIS 0.031 0.002 HIS I 80 PHE 0.055 0.002 PHE 7 129 TYR 0.038 0.003 TYR 9 127 ARG 0.062 0.001 ARG22 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 45617.82 seconds wall clock time: 800 minutes 13.73 seconds (48013.73 seconds total)