Starting phenix.real_space_refine on Sat Mar 2 08:15:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyp_8619/03_2024/5uyp_8619_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyp_8619/03_2024/5uyp_8619.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyp_8619/03_2024/5uyp_8619_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyp_8619/03_2024/5uyp_8619_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyp_8619/03_2024/5uyp_8619_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyp_8619/03_2024/5uyp_8619.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyp_8619/03_2024/5uyp_8619.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyp_8619/03_2024/5uyp_8619_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyp_8619/03_2024/5uyp_8619_updated.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= -0.332 sd= 1.036 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 4808 5.49 5 S 173 5.16 5 C 77715 2.51 5 N 28581 2.21 5 O 42503 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "05 ARG 13": "NH1" <-> "NH2" Residue "05 ARG 33": "NH1" <-> "NH2" Residue "05 ARG 59": "NH1" <-> "NH2" Residue "05 ARG 77": "NH1" <-> "NH2" Residue "05 ARG 83": "NH1" <-> "NH2" Residue "05 ARG 169": "NH1" <-> "NH2" Residue "05 ARG 184": "NH1" <-> "NH2" Residue "06 ARG 21": "NH1" <-> "NH2" Residue "06 ARG 44": "NH1" <-> "NH2" Residue "06 ARG 49": "NH1" <-> "NH2" Residue "06 ARG 61": "NH1" <-> "NH2" Residue "06 ARG 88": "NH1" <-> "NH2" Residue "06 ARG 102": "NH1" <-> "NH2" Residue "06 ARG 162": "NH1" <-> "NH2" Residue "06 ARG 170": "NH1" <-> "NH2" Residue "07 ARG 70": "NH1" <-> "NH2" Residue "07 ARG 79": "NH1" <-> "NH2" Residue "07 ARG 91": "NH1" <-> "NH2" Residue "07 ARG 101": "NH1" <-> "NH2" Residue "07 ARG 109": "NH1" <-> "NH2" Residue "07 ARG 111": "NH1" <-> "NH2" Residue "07 ARG 114": "NH1" <-> "NH2" Residue "07 ARG 132": "NH1" <-> "NH2" Residue "08 ARG 2": "NH1" <-> "NH2" Residue "08 ARG 152": "NH1" <-> "NH2" Residue "08 ARG 162": "NH1" <-> "NH2" Residue "08 ARG 169": "NH1" <-> "NH2" Residue "12 ARG 13": "NH1" <-> "NH2" Residue "12 ARG 37": "NH1" <-> "NH2" Residue "12 TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "12 ARG 96": "NH1" <-> "NH2" Residue "12 ARG 120": "NH1" <-> "NH2" Residue "13 TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "14 ARG 21": "NH1" <-> "NH2" Residue "14 ARG 33": "NH1" <-> "NH2" Residue "14 ARG 41": "NH1" <-> "NH2" Residue "14 ARG 47": "NH1" <-> "NH2" Residue "14 ARG 60": "NH1" <-> "NH2" Residue "14 ARG 78": "NH1" <-> "NH2" Residue "14 ARG 126": "NH1" <-> "NH2" Residue "15 ARG 10": "NH1" <-> "NH2" Residue "15 ARG 18": "NH1" <-> "NH2" Residue "15 ARG 40": "NH1" <-> "NH2" Residue "15 ARG 44": "NH1" <-> "NH2" Residue "15 ARG 50": "NH1" <-> "NH2" Residue "15 ARG 55": "NH1" <-> "NH2" Residue "15 ARG 59": "NH1" <-> "NH2" Residue "15 ARG 114": "NH1" <-> "NH2" Residue "16 ARG 8": "NH1" <-> "NH2" Residue "16 ARG 12": "NH1" <-> "NH2" Residue "16 ARG 17": "NH1" <-> "NH2" Residue "16 ARG 22": "NH1" <-> "NH2" Residue "16 ARG 46": "NH1" <-> "NH2" Residue "16 ARG 63": "NH1" <-> "NH2" Residue "16 ARG 64": "NH1" <-> "NH2" Residue "16 ARG 69": "NH1" <-> "NH2" Residue "16 ARG 71": "NH1" <-> "NH2" Residue "16 ARG 96": "NH1" <-> "NH2" Residue "16 ARG 118": "NH1" <-> "NH2" Residue "17 ARG 10": "NH1" <-> "NH2" Residue "17 ARG 16": "NH1" <-> "NH2" Residue "17 ARG 25": "NH1" <-> "NH2" Residue "17 TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "17 ARG 81": "NH1" <-> "NH2" Residue "17 ARG 94": "NH1" <-> "NH2" Residue "17 ARG 102": "NH1" <-> "NH2" Residue "17 ARG 111": "NH1" <-> "NH2" Residue "18 ARG 20": "NH1" <-> "NH2" Residue "18 ARG 38": "NH1" <-> "NH2" Residue "18 ARG 61": "NH1" <-> "NH2" Residue "18 ARG 88": "NH1" <-> "NH2" Residue "18 ARG 100": "NH1" <-> "NH2" Residue "18 ARG 108": "NH1" <-> "NH2" Residue "19 ARG 2": "NH1" <-> "NH2" Residue "19 ARG 5": "NH1" <-> "NH2" Residue "19 ARG 12": "NH1" <-> "NH2" Residue "19 ARG 32": "NH1" <-> "NH2" Residue "19 ARG 47": "NH1" <-> "NH2" Residue "19 PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "19 ARG 69": "NH1" <-> "NH2" Residue "20 ARG 21": "NH1" <-> "NH2" Residue "20 ARG 68": "NH1" <-> "NH2" Residue "20 ARG 78": "NH1" <-> "NH2" Residue "20 ARG 79": "NH1" <-> "NH2" Residue "20 ARG 84": "NH1" <-> "NH2" Residue "21 ARG 84": "NH1" <-> "NH2" Residue "21 ARG 88": "NH1" <-> "NH2" Residue "21 ARG 95": "NH1" <-> "NH2" Residue "21 ARG 110": "NH1" <-> "NH2" Residue "22 ARG 73": "NH1" <-> "NH2" Residue "23 ARG 5": "NH1" <-> "NH2" Residue "23 ARG 6": "NH1" <-> "NH2" Residue "23 ARG 81": "NH1" <-> "NH2" Residue "23 ARG 85": "NH1" <-> "NH2" Residue "23 ARG 93": "NH1" <-> "NH2" Residue "23 PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "24 TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "27 ARG 29": "NH1" <-> "NH2" Residue "27 ARG 47": "NH1" <-> "NH2" Residue "27 ARG 52": "NH1" <-> "NH2" Residue "28 ARG 10": "NH1" <-> "NH2" Residue "28 ARG 29": "NH1" <-> "NH2" Residue "28 ARG 44": "NH1" <-> "NH2" Residue "29 ARG 49": "NH1" <-> "NH2" Residue "29 ARG 56": "NH1" <-> "NH2" Residue "30 ARG 9": "NH1" <-> "NH2" Residue "30 ARG 15": "NH1" <-> "NH2" Residue "30 ARG 39": "NH1" <-> "NH2" Residue "30 ARG 51": "NH1" <-> "NH2" Residue "31 ARG 43": "NH1" <-> "NH2" Residue "31 TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "32 ARG 3": "NH1" <-> "NH2" Residue "32 ARG 12": "NH1" <-> "NH2" Residue "32 ARG 14": "NH1" <-> "NH2" Residue "32 ARG 19": "NH1" <-> "NH2" Residue "32 ARG 21": "NH1" <-> "NH2" Residue "32 ARG 33": "NH1" <-> "NH2" Residue "32 ARG 41": "NH1" <-> "NH2" Residue "33 ARG 12": "NH1" <-> "NH2" Residue "33 ARG 29": "NH1" <-> "NH2" Residue "33 ARG 39": "NH1" <-> "NH2" Residue "33 ARG 41": "NH1" <-> "NH2" Residue "34 ARG 12": "NH1" <-> "NH2" Residue "34 ARG 24": "NH1" <-> "NH2" Residue "B ARG 107": "NH1" <-> "NH2" Residue "B ARG 224": "NH1" <-> "NH2" Residue "C ARG 106": "NH1" <-> "NH2" Residue "C ARG 130": "NH1" <-> "NH2" Residue "E ARG 156": "NH1" <-> "NH2" Residue "I ARG 123": "NH1" <-> "NH2" Residue "L ARG 55": "NH1" <-> "NH2" Residue "P ARG 28": "NH1" <-> "NH2" Residue "P PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 11": "NH1" <-> "NH2" Residue "U ARG 66": "NH1" <-> "NH2" Residue "03 ARG 7": "NH1" <-> "NH2" Residue "03 ARG 12": "NH1" <-> "NH2" Residue "03 ARG 162": "NH1" <-> "NH2" Residue "03 TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 44": "NH1" <-> "NH2" Residue "Z ARG 223": "NH1" <-> "NH2" Residue "Z ARG 269": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 153780 Number of models: 1 Model: "" Number of chains: 63 Chain: "04" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2083 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "05" 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: "06" 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: "07" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1411 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "08" 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: "09" 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: "10" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 989 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "11" 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: "12" 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: "13" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 939 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "14" 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: "15" 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: "16" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 961 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "17" 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: "18" 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: "19" 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: "20" 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: "21" 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: "22" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 739 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "23" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 780 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "24" 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: "25" 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: "26" 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: "27" 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: "28" 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: "29" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 523 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "30" 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: "31" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 410 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "32" 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: "33" 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: "34" 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: "B" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1705 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "C" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1625 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1157 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "F" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 818 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "G" Number of atoms: 1182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1182 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "I" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 787 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "K" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 870 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "L" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "M" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 884 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "N" 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: "O" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Q" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 649 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "R" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 536 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "S" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 638 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "T" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "U" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 545 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "03" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1027 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain breaks: 1 Chain: "A" Number of atoms: 33012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33012 Classifications: {'RNA': 1539} Modifications used: {'5*END': 1, 'rna2p_pur': 89, 'rna2p_pyr': 47, 'rna3p_pur': 785, 'rna3p_pyr': 618} Link IDs: {'rna2p': 136, 'rna3p': 1402} Chain: "01" Number of atoms: 62317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62317 Classifications: {'RNA': 2903} Modifications used: {'5*END': 1, 'rna2p_pur': 207, 'rna2p_pyr': 91, 'rna3p_pur': 1467, 'rna3p_pyr': 1138} Link IDs: {'rna2p': 298, 'rna3p': 2604} Chain: "02" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2568 Classifications: {'RNA': 120} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 62, 'rna3p_pyr': 53} Link IDs: {'rna2p': 5, 'rna3p': 114} Chain: "X" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1640 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 5, 'rna3p_pur': 34, 'rna3p_pyr': 33} Link IDs: {'rna2p': 10, 'rna3p': 66} Chain: "V" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 417 Classifications: {'RNA': 19} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna3p_pur': 15, 'rna3p_pyr': 2} Link IDs: {'rna2p': 1, 'rna3p': 17} Chain: "W" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1640 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p_pur': 33, 'rna3p_pyr': 34} Link IDs: {'rna2p': 9, 'rna3p': 67} Chain: "Y" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1618 Classifications: {'RNA': 76} Modifications used: {'p5*END': 1, 'rna2p': 1, 'rna2p_pur': 8, 'rna2p_pyr': 7, 'rna3p_pur': 29, 'rna3p_pyr': 31} Link IDs: {'rna2p': 15, 'rna3p': 60} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "Z" Number of atoms: 3029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3029 Classifications: {'peptide': 392} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 371} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Y" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Chain: "Z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GCP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 57.97, per 1000 atoms: 0.38 Number of scatterers: 153780 At special positions: 0 Unit cell: (278.8, 266.5, 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 173 16.00 P 4808 15.00 O 42503 8.00 N 28581 7.00 C 77715 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 61.61 Conformation dependent library (CDL) restraints added in 7.1 seconds 12732 Ramachandran restraints generated. 6366 Oldfield, 0 Emsley, 6366 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11886 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 197 helices and 78 sheets defined 38.2% alpha, 18.3% beta 1427 base pairs and 2955 stacking pairs defined. Time for finding SS restraints: 78.49 Creating SS restraints... Processing helix chain '04' and resid 9 through 16 removed outlier: 7.813A pdb=" N HIS04 14 " --> pdb=" O PRO04 10 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N VAL04 15 " --> pdb=" O GLY04 11 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL04 16 " --> pdb=" O ARG04 12 " (cutoff:3.500A) Processing helix chain '04' and resid 29 through 34 removed outlier: 4.194A pdb=" N LEU04 33 " --> pdb=" O PHE04 29 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N GLU04 34 " --> pdb=" O ALA04 30 " (cutoff:3.500A) No H-bonds generated for 'chain '04' and resid 29 through 34' Processing helix chain '04' and resid 130 through 135 Proline residue: 04 135 - end of helix Processing helix chain '04' and resid 206 through 214 removed outlier: 4.203A pdb=" N ALA04 210 " --> pdb=" O LYS04 206 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG04 213 " --> pdb=" O ALA04 209 " (cutoff:3.500A) Processing helix chain '04' and resid 220 through 225 removed outlier: 4.322A pdb=" N MET04 224 " --> pdb=" O ARG04 220 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ASN04 225 " --> pdb=" O GLY04 221 " (cutoff:3.500A) No H-bonds generated for 'chain '04' and resid 220 through 225' Processing helix chain '04' and resid 259 through 267 removed outlier: 6.427A pdb=" N ASP04 263 " --> pdb=" O ASN04 259 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N LYS04 264 " --> pdb=" O LYS04 260 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N PHE04 265 " --> pdb=" O ARG04 261 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N VAL04 267 " --> pdb=" O ASP04 263 " (cutoff:3.500A) Processing helix chain '04' and resid 196 through 201 removed outlier: 4.286A pdb=" N MET04 200 " --> pdb=" O ALA04 197 " (cutoff:3.500A) Processing helix chain '05' and resid 61 through 72 removed outlier: 3.548A pdb=" N HIS05 67 " --> pdb=" O PRO05 63 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ALA05 71 " --> pdb=" O HIS05 67 " (cutoff:3.500A) Processing helix chain '05' and resid 120 through 125 Processing helix chain '05' and resid 39 through 44 Processing helix chain '06' and resid 24 through 40 removed outlier: 3.789A pdb=" N ARG06 40 " --> pdb=" O ALA06 36 " (cutoff:3.500A) Processing helix chain '06' and resid 48 through 53 removed outlier: 5.926A pdb=" N THR06 53 " --> pdb=" O ARG06 49 " (cutoff:3.500A) Processing helix chain '06' and resid 97 through 116 removed outlier: 3.521A pdb=" N LEU06 105 " --> pdb=" O TYR06 101 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG06 114 " --> pdb=" O SER06 110 " (cutoff:3.500A) Processing helix chain '06' and resid 130 through 142 removed outlier: 3.590A pdb=" N LYS06 137 " --> pdb=" O LEU06 133 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS06 139 " --> pdb=" O ALA06 135 " (cutoff:3.500A) Processing helix chain '06' and resid 154 through 163 removed outlier: 3.829A pdb=" N ALA06 160 " --> pdb=" O ASN06 156 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ASN06 163 " --> pdb=" O LEU06 159 " (cutoff:3.500A) Processing helix chain '06' and resid 176 through 182 removed outlier: 3.788A pdb=" N LEU06 180 " --> pdb=" O ASP06 176 " (cutoff:3.500A) Processing helix chain '06' and resid 189 through 201 removed outlier: 3.598A pdb=" N GLN06 195 " --> pdb=" O ASP06 191 " (cutoff:3.500A) Processing helix chain '06' and resid 15 through 21 removed outlier: 3.889A pdb=" N GLY06 20 " --> pdb=" O SER06 15 " (cutoff:3.500A) Processing helix chain '07' and resid 1 through 20 removed outlier: 3.563A pdb=" N VAL07 11 " --> pdb=" O TYR07 7 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N VAL07 12 " --> pdb=" O LYS07 8 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS07 13 " --> pdb=" O ASP07 9 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR07 17 " --> pdb=" O LYS07 13 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU07 18 " --> pdb=" O LYS07 14 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN07 20 " --> pdb=" O MET07 16 " (cutoff:3.500A) Processing helix chain '07' and resid 41 through 46 removed outlier: 3.534A pdb=" N ASP07 45 " --> pdb=" O GLU07 41 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS07 46 " --> pdb=" O ALA07 42 " (cutoff:3.500A) No H-bonds generated for 'chain '07' and resid 41 through 46' Processing helix chain '07' and resid 47 through 61 Processing helix chain '07' and resid 92 through 109 removed outlier: 4.420A pdb=" N TRP07 96 " --> pdb=" O GLY07 92 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE07 99 " --> pdb=" O MET07 95 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE07 105 " --> pdb=" O ARG07 101 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL07 107 " --> pdb=" O ILE07 103 " (cutoff:3.500A) Proline residue: 07 108 - end of helix Processing helix chain '07' and resid 133 through 138 removed outlier: 5.301A pdb=" N PHE07 137 " --> pdb=" O GLU07 133 " (cutoff:3.500A) Proline residue: 07 138 - end of helix No H-bonds generated for 'chain '07' and resid 133 through 138' Processing helix chain '07' and resid 161 through 173 removed outlier: 3.804A pdb=" N ALA07 167 " --> pdb=" O GLU07 163 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE07 172 " --> pdb=" O LEU07 168 " (cutoff:3.500A) Processing helix chain '08' and resid 1 through 6 removed outlier: 4.443A pdb=" N ALA08 6 " --> pdb=" O ARG08 2 " (cutoff:3.500A) Processing helix chain '08' and resid 59 through 80 removed outlier: 3.962A pdb=" N ALA08 69 " --> pdb=" O GLY08 65 " (cutoff:3.500A) Processing helix chain '08' and resid 136 through 152 removed outlier: 3.608A pdb=" N ALA08 149 " --> pdb=" O ALA08 145 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ARG08 151 " --> pdb=" O LEU08 147 " (cutoff:3.500A) Processing helix chain '09' and resid 22 through 27 Processing helix chain '09' and resid 29 through 34 removed outlier: 3.662A pdb=" N GLN09 33 " --> pdb=" O PHE09 29 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY09 34 " --> pdb=" O LEU09 30 " (cutoff:3.500A) No H-bonds generated for 'chain '09' and resid 29 through 34' Processing helix chain '09' and resid 40 through 50 removed outlier: 3.688A pdb=" N GLU09 48 " --> pdb=" O ILE09 44 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA09 49 " --> pdb=" O GLU09 45 " (cutoff:3.500A) Processing helix chain '09' and resid 53 through 74 removed outlier: 5.446A pdb=" N LYS09 57 " --> pdb=" O GLU09 53 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU09 62 " --> pdb=" O LEU09 58 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA09 67 " --> pdb=" O ALA09 63 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASN09 73 " --> pdb=" O ALA09 69 " (cutoff:3.500A) Processing helix chain '09' and resid 95 through 107 removed outlier: 3.500A pdb=" N ILE09 99 " --> pdb=" O GLY09 95 " (cutoff:3.500A) Processing helix chain '09' and resid 111 through 116 removed outlier: 3.993A pdb=" N VAL09 115 " --> pdb=" O ALA09 111 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ARG09 116 " --> pdb=" O LYS09 112 " (cutoff:3.500A) No H-bonds generated for 'chain '09' and resid 111 through 116' Processing helix chain '10' and resid 3 through 21 removed outlier: 3.909A pdb=" N LYS10 8 " --> pdb=" O ASN10 4 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU10 17 " --> pdb=" O ALA10 13 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS10 20 " --> pdb=" O SER10 16 " (cutoff:3.500A) Processing helix chain '10' and resid 33 through 48 removed outlier: 5.651A pdb=" N ARG10 42 " --> pdb=" O MET10 38 " (cutoff:3.500A) Processing helix chain '10' and resid 62 through 71 removed outlier: 3.929A pdb=" N GLY10 66 " --> pdb=" O ARG10 62 " (cutoff:3.500A) Proline residue: 10 68 - end of helix removed outlier: 4.244A pdb=" N CYS10 71 " --> pdb=" O THR10 67 " (cutoff:3.500A) Processing helix chain '10' and resid 94 through 106 removed outlier: 3.604A pdb=" N PHE10 99 " --> pdb=" O LEU10 95 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA10 104 " --> pdb=" O ALA10 100 " (cutoff:3.500A) Processing helix chain '10' and resid 72 through 78 removed outlier: 4.369A pdb=" N PHE10 76 " --> pdb=" O LYS10 73 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY10 78 " --> pdb=" O ALA10 75 " (cutoff:3.500A) Processing helix chain '11' and resid 21 through 31 Proline residue: 11 25 - end of helix removed outlier: 4.517A pdb=" N GLN11 30 " --> pdb=" O ALA11 26 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLY11 31 " --> pdb=" O LEU11 27 " (cutoff:3.500A) Processing helix chain '11' and resid 33 through 48 removed outlier: 3.649A pdb=" N PHE11 37 " --> pdb=" O ASN11 33 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA11 40 " --> pdb=" O GLU11 36 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER11 47 " --> pdb=" O ALA11 43 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ILE11 48 " --> pdb=" O LYS11 44 " (cutoff:3.500A) Processing helix chain '11' and resid 74 through 84 removed outlier: 3.934A pdb=" N LYS11 80 " --> pdb=" O ALA11 76 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA11 83 " --> pdb=" O LEU11 79 " (cutoff:3.500A) Processing helix chain '11' and resid 101 through 114 removed outlier: 4.128A pdb=" N GLU11 107 " --> pdb=" O ALA11 103 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA11 114 " --> pdb=" O GLN11 110 " (cutoff:3.500A) Processing helix chain '11' and resid 120 through 136 removed outlier: 3.968A pdb=" N MET11 124 " --> pdb=" O ASP11 120 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ARG11 126 " --> pdb=" O GLU11 122 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER11 127 " --> pdb=" O ALA11 123 " (cutoff:3.500A) Processing helix chain '12' and resid 24 through 38 removed outlier: 3.721A pdb=" N GLU12 31 " --> pdb=" O ARG12 27 " (cutoff:3.500A) Processing helix chain '12' and resid 67 through 72 Processing helix chain '12' and resid 88 through 96 removed outlier: 3.733A pdb=" N ALA12 94 " --> pdb=" O GLU12 90 " (cutoff:3.500A) Processing helix chain '12' and resid 97 through 110 removed outlier: 4.507A pdb=" N ILE12 101 " --> pdb=" O PRO12 97 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS12 106 " --> pdb=" O GLU12 102 " (cutoff:3.500A) Proline residue: 12 110 - end of helix Processing helix chain '12' and resid 112 through 123 removed outlier: 3.829A pdb=" N PHE12 119 " --> pdb=" O GLY12 115 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG12 120 " --> pdb=" O ARG12 116 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS12 121 " --> pdb=" O ALA12 117 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU12 122 " --> pdb=" O MET12 118 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N LYS12 123 " --> pdb=" O PHE12 119 " (cutoff:3.500A) Processing helix chain '13' and resid 112 through 120 removed outlier: 3.718A pdb=" N ILE13 116 " --> pdb=" O PHE13 112 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU13 118 " --> pdb=" O LYS13 114 " (cutoff:3.500A) Proline residue: 13 120 - end of helix Processing helix chain '13' and resid 104 through 109 removed outlier: 4.713A pdb=" N SER13 109 " --> pdb=" O GLU13 106 " (cutoff:3.500A) Processing helix chain '14' and resid 37 through 42 removed outlier: 5.888A pdb=" N SER14 42 " --> pdb=" O GLN14 38 " (cutoff:3.500A) Processing helix chain '14' and resid 56 through 62 Proline residue: 14 62 - end of helix Processing helix chain '14' and resid 68 through 75 removed outlier: 3.663A pdb=" N ALA14 72 " --> pdb=" O SER14 68 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE14 73 " --> pdb=" O ARG14 69 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR14 74 " --> pdb=" O LYS14 70 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ALA14 75 " --> pdb=" O ALA14 71 " (cutoff:3.500A) No H-bonds generated for 'chain '14' and resid 68 through 75' Processing helix chain '14' and resid 78 through 86 removed outlier: 3.750A pdb=" N LEU14 82 " --> pdb=" O ARG14 78 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA14 83 " --> pdb=" O LEU14 79 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS14 84 " --> pdb=" O SER14 80 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL14 85 " --> pdb=" O ASP14 81 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N GLU14 86 " --> pdb=" O LEU14 82 " (cutoff:3.500A) No H-bonds generated for 'chain '14' and resid 78 through 86' Processing helix chain '14' and resid 93 through 99 removed outlier: 5.700A pdb=" N ALA14 97 " --> pdb=" O ASN14 93 " (cutoff:3.500A) Processing helix chain '14' and resid 128 through 139 removed outlier: 3.681A pdb=" N ALA14 133 " --> pdb=" O LYS14 129 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA14 138 " --> pdb=" O ALA14 134 " (cutoff:3.500A) Processing helix chain '15' and resid 42 through 58 removed outlier: 4.231A pdb=" N ALA15 52 " --> pdb=" O ALA15 48 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL15 57 " --> pdb=" O MET15 53 " (cutoff:3.500A) Processing helix chain '15' and resid 109 through 125 removed outlier: 3.606A pdb=" N GLU15 115 " --> pdb=" O GLU15 111 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE15 117 " --> pdb=" O ALA15 113 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LYS15 118 " --> pdb=" O ARG15 114 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU15 119 " --> pdb=" O GLU15 115 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA15 120 " --> pdb=" O ALA15 116 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS15 123 " --> pdb=" O LEU15 119 " (cutoff:3.500A) Proline residue: 15 125 - end of helix Processing helix chain '16' and resid 13 through 32 removed outlier: 3.581A pdb=" N MET16 24 " --> pdb=" O MET16 20 " (cutoff:3.500A) Processing helix chain '16' and resid 38 through 57 removed outlier: 3.555A pdb=" N ARG16 45 " --> pdb=" O ALA16 41 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ARG16 46 " --> pdb=" O LYS16 42 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL16 47 " --> pdb=" O GLU16 43 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU16 49 " --> pdb=" O ARG16 45 " (cutoff:3.500A) Proline residue: 16 50 - end of helix removed outlier: 3.924A pdb=" N LYS16 56 " --> pdb=" O ILE16 52 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N THR16 57 " --> pdb=" O THR16 53 " (cutoff:3.500A) Processing helix chain '16' and resid 59 through 71 removed outlier: 3.884A pdb=" N ARG16 63 " --> pdb=" O SER16 59 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N THR16 70 " --> pdb=" O ALA16 66 " (cutoff:3.500A) Processing helix chain '16' and resid 72 through 81 removed outlier: 3.595A pdb=" N VAL16 76 " --> pdb=" O ASP16 72 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N PHE16 80 " --> pdb=" O VAL16 76 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASN16 81 " --> pdb=" O ALA16 77 " (cutoff:3.500A) Processing helix chain '16' and resid 82 through 89 removed outlier: 4.130A pdb=" N ARG16 86 " --> pdb=" O GLU16 82 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA16 88 " --> pdb=" O GLY16 84 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N SER16 89 " --> pdb=" O PRO16 85 " (cutoff:3.500A) Processing helix chain '17' and resid 3 through 22 removed outlier: 3.717A pdb=" N ARG17 7 " --> pdb=" O LYS17 3 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR17 12 " --> pdb=" O ILE17 8 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ARG17 13 " --> pdb=" O ARG17 9 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N ALA17 14 " --> pdb=" O ARG17 10 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG17 15 " --> pdb=" O ALA17 11 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LYS17 17 " --> pdb=" O ARG17 13 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY17 22 " --> pdb=" O LEU17 18 " (cutoff:3.500A) Processing helix chain '17' and resid 55 through 63 removed outlier: 3.611A pdb=" N GLU17 60 " --> pdb=" O LYS17 56 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N GLN17 61 " --> pdb=" O ALA17 57 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU17 62 " --> pdb=" O ILE17 58 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N LYS17 63 " --> pdb=" O ALA17 59 " (cutoff:3.500A) Processing helix chain '17' and resid 67 through 86 removed outlier: 3.524A pdb=" N VAL17 74 " --> pdb=" O ALA17 70 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY17 75 " --> pdb=" O ALA17 71 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS17 76 " --> pdb=" O ALA17 72 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU17 83 " --> pdb=" O ALA17 79 " (cutoff:3.500A) Processing helix chain '17' and resid 101 through 114 removed outlier: 3.575A pdb=" N GLU17 112 " --> pdb=" O ASP17 108 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA17 113 " --> pdb=" O ALA17 109 " (cutoff:3.500A) Processing helix chain '18' and resid 1 through 13 removed outlier: 3.732A pdb=" N GLU18 10 " --> pdb=" O GLN18 6 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N GLN18 11 " --> pdb=" O LEU18 7 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N MET18 12 " --> pdb=" O GLU18 8 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LYS18 13 " --> pdb=" O GLN18 9 " (cutoff:3.500A) Processing helix chain '18' and resid 96 through 103 removed outlier: 4.739A pdb=" N ARG18 100 " --> pdb=" O LEU18 96 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N GLU18 101 " --> pdb=" O TYR18 97 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ARG18 102 " --> pdb=" O TYR18 98 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N THR18 103 " --> pdb=" O LEU18 99 " (cutoff:3.500A) No H-bonds generated for 'chain '18' and resid 96 through 103' Processing helix chain '19' and resid 5 through 21 removed outlier: 3.841A pdb=" N ALA19 9 " --> pdb=" O ARG19 5 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN19 19 " --> pdb=" O LYS19 15 " (cutoff:3.500A) Processing helix chain '19' and resid 25 through 30 removed outlier: 3.708A pdb=" N ARG19 29 " --> pdb=" O GLY19 25 " (cutoff:3.500A) Processing helix chain '19' and resid 39 through 60 removed outlier: 3.574A pdb=" N ARG19 50 " --> pdb=" O TYR19 46 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LYS19 53 " --> pdb=" O ARG19 49 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG19 54 " --> pdb=" O ARG19 50 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG19 57 " --> pdb=" O LYS19 53 " (cutoff:3.500A) Processing helix chain '19' and resid 62 through 72 Processing helix chain '19' and resid 74 through 86 Processing helix chain '19' and resid 90 through 101 removed outlier: 3.893A pdb=" N ASP19 96 " --> pdb=" O LYS19 92 " (cutoff:3.500A) Processing helix chain '19' and resid 102 through 117 removed outlier: 3.680A pdb=" N ALA19 115 " --> pdb=" O LYS19 111 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU19 116 " --> pdb=" O ALA19 112 " (cutoff:3.500A) Processing helix chain '21' and resid 13 through 22 removed outlier: 3.548A pdb=" N LEU21 19 " --> pdb=" O GLN21 15 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL21 20 " --> pdb=" O LYS21 16 " (cutoff:3.500A) Processing helix chain '21' and resid 28 through 40 removed outlier: 4.012A pdb=" N ASP21 34 " --> pdb=" O SER21 30 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ASN21 40 " --> pdb=" O LEU21 36 " (cutoff:3.500A) Processing helix chain '21' and resid 41 through 60 removed outlier: 3.704A pdb=" N LYS21 48 " --> pdb=" O ALA21 44 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS21 49 " --> pdb=" O VAL21 45 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL21 50 " --> pdb=" O LEU21 46 " (cutoff:3.500A) Processing helix chain '22' and resid 2 through 11 removed outlier: 4.626A pdb=" N LYS22 9 " --> pdb=" O GLU22 5 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU22 11 " --> pdb=" O LEU22 7 " (cutoff:3.500A) Processing helix chain '22' and resid 17 through 26 Processing helix chain '22' and resid 39 through 51 Processing helix chain '23' and resid 35 through 40 removed outlier: 4.222A pdb=" N ASN23 39 " --> pdb=" O VAL23 35 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N LEU23 40 " --> pdb=" O GLU23 36 " (cutoff:3.500A) No H-bonds generated for 'chain '23' and resid 35 through 40' Processing helix chain '23' and resid 65 through 70 removed outlier: 4.267A pdb=" N VAL23 69 " --> pdb=" O GLN23 65 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ALA23 70 " --> pdb=" O VAL23 66 " (cutoff:3.500A) No H-bonds generated for 'chain '23' and resid 65 through 70' Processing helix chain '24' and resid 13 through 24 removed outlier: 3.559A pdb=" N ARG24 18 " --> pdb=" O LYS24 14 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG24 19 " --> pdb=" O GLY24 15 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASN24 24 " --> pdb=" O LEU24 20 " (cutoff:3.500A) Processing helix chain '24' and resid 44 through 54 removed outlier: 3.560A pdb=" N ALA24 52 " --> pdb=" O MET24 48 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS24 53 " --> pdb=" O ASN24 49 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N ALA24 54 " --> pdb=" O MET24 50 " (cutoff:3.500A) Processing helix chain '26' and resid 51 through 61 removed outlier: 3.522A pdb=" N MET26 55 " --> pdb=" O SER26 51 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ARG26 56 " --> pdb=" O ALA26 52 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL26 57 " --> pdb=" O LYS26 53 " (cutoff:3.500A) Processing helix chain '26' and resid 62 through 74 removed outlier: 3.944A pdb=" N LEU26 70 " --> pdb=" O VAL26 66 " (cutoff:3.500A) Processing helix chain '27' and resid 1 through 7 removed outlier: 3.625A pdb=" N GLU27 5 " --> pdb=" O MET27 1 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU27 6 " --> pdb=" O LYS27 2 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ARG27 7 " --> pdb=" O ALA27 3 " (cutoff:3.500A) No H-bonds generated for 'chain '27' and resid 1 through 7' Processing helix chain '27' and resid 9 through 35 removed outlier: 3.704A pdb=" N THR27 16 " --> pdb=" O GLU27 12 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG27 23 " --> pdb=" O LEU27 19 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLN27 25 " --> pdb=" O LEU27 21 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N PHE27 26 " --> pdb=" O LEU27 22 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU27 28 " --> pdb=" O GLU27 24 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ALA27 32 " --> pdb=" O LEU27 28 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER27 34 " --> pdb=" O MET27 30 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY27 35 " --> pdb=" O GLN27 31 " (cutoff:3.500A) Processing helix chain '27' and resid 40 through 62 removed outlier: 3.924A pdb=" N LYS27 44 " --> pdb=" O SER27 40 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN27 58 " --> pdb=" O LYS27 54 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLY27 62 " --> pdb=" O ASN27 58 " (cutoff:3.500A) Processing helix chain '28' and resid 16 through 27 removed outlier: 3.581A pdb=" N THR28 22 " --> pdb=" O LYS28 18 " (cutoff:3.500A) Processing helix chain '28' and resid 40 through 51 removed outlier: 3.817A pdb=" N MET28 46 " --> pdb=" O ALA28 42 " (cutoff:3.500A) Processing helix chain '29' and resid 43 through 51 removed outlier: 4.620A pdb=" N GLN29 48 " --> pdb=" O PHE29 44 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP29 50 " --> pdb=" O GLY29 46 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N VAL29 51 " --> pdb=" O LYS29 47 " (cutoff:3.500A) Processing helix chain '29' and resid 55 through 65 removed outlier: 5.438A pdb=" N ARG29 59 " --> pdb=" O GLY29 55 " (cutoff:3.500A) Processing helix chain '30' and resid 8 through 20 removed outlier: 4.559A pdb=" N HIS30 18 " --> pdb=" O MET30 14 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ASP30 19 " --> pdb=" O ARG30 15 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ALA30 20 " --> pdb=" O ARG30 16 " (cutoff:3.500A) Processing helix chain '32' and resid 8 through 16 Processing helix chain '32' and resid 17 through 24 removed outlier: 4.680A pdb=" N THR32 24 " --> pdb=" O ALA32 20 " (cutoff:3.500A) Processing helix chain '32' and resid 25 through 38 removed outlier: 3.993A pdb=" N ARG32 33 " --> pdb=" O GLN32 29 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG32 35 " --> pdb=" O LEU32 31 " (cutoff:3.500A) Processing helix chain '33' and resid 6 through 13 removed outlier: 3.620A pdb=" N ALA33 10 " --> pdb=" O VAL33 6 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LYS33 11 " --> pdb=" O ARG33 7 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ARG33 12 " --> pdb=" O GLY33 8 " (cutoff:3.500A) Processing helix chain '33' and resid 31 through 36 removed outlier: 5.036A pdb=" N LYS33 35 " --> pdb=" O ILE33 31 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ALA33 36 " --> pdb=" O LEU33 32 " (cutoff:3.500A) No H-bonds generated for 'chain '33' and resid 31 through 36' Processing helix chain '33' and resid 37 through 45 Proline residue: 33 45 - end of helix Processing helix chain '33' and resid 50 through 62 removed outlier: 4.043A pdb=" N GLY33 55 " --> pdb=" O LYS33 51 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N LEU33 56 " --> pdb=" O GLY33 52 " (cutoff:3.500A) Proline residue: 33 62 - end of helix Processing helix chain '34' and resid 30 through 35 removed outlier: 4.413A pdb=" N GLN34 35 " --> pdb=" O LYS34 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 63 removed outlier: 3.765A pdb=" N VAL B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Proline residue: B 47 - end of helix removed outlier: 3.669A pdb=" N ASN B 57 " --> pdb=" O LEU B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 86 removed outlier: 5.662A pdb=" N SER B 76 " --> pdb=" O LYS B 72 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N GLU B 77 " --> pdb=" O ARG B 73 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ALA B 78 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS B 80 " --> pdb=" O SER B 76 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 84 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N CYS B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 122 removed outlier: 4.281A pdb=" N GLN B 108 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR B 118 " --> pdb=" O LYS B 114 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER B 120 " --> pdb=" O LEU B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 147 removed outlier: 3.677A pdb=" N MET B 135 " --> pdb=" O LYS B 131 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ARG B 136 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 140 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU B 141 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 143 " --> pdb=" O GLU B 139 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN B 145 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N SER B 146 " --> pdb=" O LYS B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 154 removed outlier: 4.466A pdb=" N ASP B 152 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N MET B 153 " --> pdb=" O GLY B 149 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N GLY B 154 " --> pdb=" O ILE B 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 148 through 154' Processing helix chain 'B' and resid 168 through 179 removed outlier: 3.734A pdb=" N ILE B 172 " --> pdb=" O GLU B 168 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLY B 179 " --> pdb=" O ALA B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 225 removed outlier: 4.675A pdb=" N THR B 210 " --> pdb=" O ILE B 206 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU B 211 " --> pdb=" O ARG B 207 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA B 215 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N SER B 225 " --> pdb=" O ARG B 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 11 removed outlier: 3.557A pdb=" N ILE C 9 " --> pdb=" O HIS C 5 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG C 10 " --> pdb=" O PRO C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 47 removed outlier: 3.518A pdb=" N GLN C 40 " --> pdb=" O PHE C 36 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR C 41 " --> pdb=" O LYS C 37 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA C 47 " --> pdb=" O THR C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 77 removed outlier: 3.546A pdb=" N VAL C 75 " --> pdb=" O ARG C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 94 removed outlier: 4.113A pdb=" N GLU C 84 " --> pdb=" O GLY C 80 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA C 91 " --> pdb=" O ARG C 87 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE C 93 " --> pdb=" O VAL C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 112 removed outlier: 3.871A pdb=" N ASP C 111 " --> pdb=" O LYS C 107 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ALA C 112 " --> pdb=" O PRO C 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 107 through 112' Processing helix chain 'C' and resid 113 through 126 removed outlier: 4.167A pdb=" N ARG C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ARG C 126 " --> pdb=" O GLN C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 removed outlier: 3.553A pdb=" N ALA C 136 " --> pdb=" O ALA C 132 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N VAL C 137 " --> pdb=" O MET C 133 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU C 143 " --> pdb=" O ASN C 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 15 removed outlier: 4.462A pdb=" N LEU D 10 " --> pdb=" O PRO D 6 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N SER D 11 " --> pdb=" O LYS D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 65 Processing helix chain 'D' and resid 67 through 82 removed outlier: 5.578A pdb=" N LYS D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 96 removed outlier: 4.278A pdb=" N ARG D 96 " --> pdb=" O LEU D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 105 removed outlier: 3.596A pdb=" N GLY D 105 " --> pdb=" O VAL D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 120 removed outlier: 3.508A pdb=" N ARG D 114 " --> pdb=" O ARG D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 163 removed outlier: 6.561A pdb=" N LYS D 155 " --> pdb=" O GLN D 151 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA D 156 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU D 160 " --> pdb=" O ALA D 156 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N GLN D 163 " --> pdb=" O GLU D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 205 removed outlier: 4.623A pdb=" N ILE D 199 " --> pdb=" O ASN D 195 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL D 200 " --> pdb=" O GLU D 196 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU D 201 " --> pdb=" O HIS D 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 70 removed outlier: 4.075A pdb=" N GLU E 64 " --> pdb=" O GLN E 60 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS E 65 " --> pdb=" O LYS E 61 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N MET E 70 " --> pdb=" O ALA E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 118 removed outlier: 6.239A pdb=" N ALA E 112 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL E 113 " --> pdb=" O ALA E 109 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU E 114 " --> pdb=" O MET E 110 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL E 116 " --> pdb=" O ALA E 112 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA E 117 " --> pdb=" O VAL E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 147 removed outlier: 3.549A pdb=" N ILE E 140 " --> pdb=" O VAL E 136 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP E 141 " --> pdb=" O ARG E 137 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY E 142 " --> pdb=" O ALA E 138 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASN E 147 " --> pdb=" O LEU E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 156 Processing helix chain 'E' and resid 159 through 165 Processing helix chain 'F' and resid 14 through 33 removed outlier: 3.745A pdb=" N VAL F 18 " --> pdb=" O GLN F 14 " (cutoff:3.500A) Proline residue: F 19 - end of helix removed outlier: 3.816A pdb=" N ARG F 24 " --> pdb=" O GLY F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 81 removed outlier: 3.618A pdb=" N ASP F 72 " --> pdb=" O GLN F 68 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU F 73 " --> pdb=" O GLU F 69 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASN F 81 " --> pdb=" O THR F 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 30 removed outlier: 3.632A pdb=" N PHE G 25 " --> pdb=" O LEU G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 54 removed outlier: 3.827A pdb=" N SER G 40 " --> pdb=" O SER G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 69 removed outlier: 3.763A pdb=" N ALA G 60 " --> pdb=" O SER G 56 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL G 63 " --> pdb=" O GLU G 59 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ASN G 67 " --> pdb=" O VAL G 63 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N VAL G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 110 removed outlier: 4.077A pdb=" N ASN G 96 " --> pdb=" O PRO G 92 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ALA G 97 " --> pdb=" O VAL G 93 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TRP G 102 " --> pdb=" O LEU G 98 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ARG G 110 " --> pdb=" O ALA G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 129 Processing helix chain 'G' and resid 131 through 147 removed outlier: 3.554A pdb=" N ARG G 137 " --> pdb=" O ALA G 133 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLU G 145 " --> pdb=" O HIS G 141 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA G 146 " --> pdb=" O ARG G 142 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 20 removed outlier: 3.686A pdb=" N ALA H 18 " --> pdb=" O ARG H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 43 removed outlier: 3.627A pdb=" N GLY H 43 " --> pdb=" O LEU H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 119 removed outlier: 3.599A pdb=" N GLN H 117 " --> pdb=" O ARG H 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 38 removed outlier: 4.067A pdb=" N PHE I 38 " --> pdb=" O LEU I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 52 removed outlier: 4.534A pdb=" N ARG I 48 " --> pdb=" O ARG I 44 " (cutoff:3.500A) Proline residue: I 50 - end of helix Processing helix chain 'I' and resid 70 through 87 removed outlier: 3.585A pdb=" N GLN I 74 " --> pdb=" O GLY I 70 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA I 75 " --> pdb=" O ILE I 71 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY I 76 " --> pdb=" O SER I 72 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA I 77 " --> pdb=" O GLY I 73 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG I 79 " --> pdb=" O ALA I 75 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR I 83 " --> pdb=" O ARG I 79 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N MET I 87 " --> pdb=" O THR I 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 101 removed outlier: 3.918A pdb=" N ARG I 94 " --> pdb=" O ASP I 90 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLU I 96 " --> pdb=" O SER I 92 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS I 99 " --> pdb=" O SER I 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 31 removed outlier: 3.563A pdb=" N ALA J 23 " --> pdb=" O ASP J 19 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU J 24 " --> pdb=" O GLN J 20 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE J 25 " --> pdb=" O ALA J 21 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG J 31 " --> pdb=" O GLU J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 88 removed outlier: 3.946A pdb=" N VAL J 84 " --> pdb=" O THR J 80 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASP J 85 " --> pdb=" O GLU J 81 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ALA J 86 " --> pdb=" O LYS J 82 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N MET J 88 " --> pdb=" O VAL J 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 50 removed outlier: 3.569A pdb=" N SER K 49 " --> pdb=" O THR K 45 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLY K 50 " --> pdb=" O ALA K 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 45 through 50' Processing helix chain 'K' and resid 53 through 58 removed outlier: 3.693A pdb=" N SER K 57 " --> pdb=" O GLY K 53 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N THR K 58 " --> pdb=" O SER K 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 53 through 58' Processing helix chain 'K' and resid 59 through 75 removed outlier: 3.549A pdb=" N ASP K 71 " --> pdb=" O GLU K 67 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA K 72 " --> pdb=" O ARG K 68 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N VAL K 73 " --> pdb=" O CYS K 69 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LYS K 74 " --> pdb=" O ALA K 70 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N GLU K 75 " --> pdb=" O ASP K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 103 removed outlier: 5.438A pdb=" N THR K 95 " --> pdb=" O GLY K 91 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ILE K 96 " --> pdb=" O ARG K 92 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ARG K 97 " --> pdb=" O GLU K 93 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA K 98 " --> pdb=" O SER K 94 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU K 99 " --> pdb=" O THR K 95 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA K 101 " --> pdb=" O ARG K 97 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 10 removed outlier: 3.653A pdb=" N ARG L 8 " --> pdb=" O ASN L 4 " (cutoff:3.500A) Proline residue: L 10 - end of helix Processing helix chain 'L' and resid 21 through 26 removed outlier: 7.038A pdb=" N ALA L 25 " --> pdb=" O PRO L 21 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS L 26 " --> pdb=" O ALA L 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 21 through 26' Processing helix chain 'L' and resid 112 through 117 removed outlier: 4.828A pdb=" N TYR L 116 " --> pdb=" O ALA L 112 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLY L 117 " --> pdb=" O ARG L 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 112 through 117' Processing helix chain 'M' and resid 13 through 21 removed outlier: 3.702A pdb=" N SER M 20 " --> pdb=" O ILE M 16 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ILE M 21 " --> pdb=" O ALA M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 37 removed outlier: 3.505A pdb=" N ALA M 35 " --> pdb=" O ALA M 31 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 48 removed outlier: 5.407A pdb=" N SER M 48 " --> pdb=" O ILE M 44 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 63 removed outlier: 5.031A pdb=" N THR M 54 " --> pdb=" O GLY M 50 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU M 58 " --> pdb=" O THR M 54 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA M 60 " --> pdb=" O ARG M 56 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS M 61 " --> pdb=" O ASP M 57 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE M 62 " --> pdb=" O GLU M 58 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N VAL M 63 " --> pdb=" O VAL M 59 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 83 removed outlier: 4.341A pdb=" N ARG M 70 " --> pdb=" O GLY M 66 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N SER M 75 " --> pdb=" O GLU M 71 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 93 Processing helix chain 'M' and resid 105 through 110 Processing helix chain 'N' and resid 2 through 23 removed outlier: 3.510A pdb=" N TYR N 19 " --> pdb=" O LEU N 15 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ALA N 21 " --> pdb=" O ASP N 17 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LYS N 22 " --> pdb=" O LYS N 18 " (cutoff:3.500A) Processing helix chain 'N' and resid 24 through 29 Processing helix chain 'N' and resid 37 through 50 removed outlier: 4.902A pdb=" N GLN N 48 " --> pdb=" O VAL N 44 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N THR N 49 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU N 50 " --> pdb=" O LYS N 46 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 60 removed outlier: 5.152A pdb=" N ARG N 60 " --> pdb=" O PRO N 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 90 removed outlier: 3.882A pdb=" N GLU N 85 " --> pdb=" O ILE N 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 15 Processing helix chain 'O' and resid 23 through 46 removed outlier: 3.515A pdb=" N HIS O 41 " --> pdb=" O HIS O 37 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU O 44 " --> pdb=" O GLY O 40 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N HIS O 45 " --> pdb=" O HIS O 41 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LYS O 46 " --> pdb=" O PHE O 42 " (cutoff:3.500A) Processing helix chain 'O' and resid 48 through 73 removed outlier: 4.116A pdb=" N ARG O 53 " --> pdb=" O HIS O 49 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR O 68 " --> pdb=" O LYS O 64 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 85 removed outlier: 3.757A pdb=" N GLU O 82 " --> pdb=" O THR O 78 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY O 85 " --> pdb=" O ILE O 81 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 64 removed outlier: 3.708A pdb=" N ILE P 57 " --> pdb=" O ASP P 53 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLN P 63 " --> pdb=" O HIS P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 79 removed outlier: 3.544A pdb=" N LYS P 76 " --> pdb=" O ALA P 72 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN P 79 " --> pdb=" O ILE P 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 11 through 17 removed outlier: 6.843A pdb=" N GLU R 15 " --> pdb=" O ARG R 11 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY R 16 " --> pdb=" O PHE R 12 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N VAL R 17 " --> pdb=" O THR R 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 11 through 17' Processing helix chain 'R' and resid 24 through 33 removed outlier: 4.063A pdb=" N ASN R 30 " --> pdb=" O ALA R 26 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR R 31 " --> pdb=" O THR R 27 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE R 32 " --> pdb=" O LEU R 28 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N THR R 33 " --> pdb=" O LYS R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 45 removed outlier: 3.821A pdb=" N THR R 44 " --> pdb=" O PRO R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 47 through 65 removed outlier: 4.024A pdb=" N LEU R 64 " --> pdb=" O ARG R 60 " (cutoff:3.500A) Processing helix chain 'S' and resid 14 through 25 removed outlier: 3.988A pdb=" N GLU S 23 " --> pdb=" O GLU S 19 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER S 24 " --> pdb=" O LYS S 20 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 69 through 75 removed outlier: 4.490A pdb=" N PHE S 73 " --> pdb=" O LYS S 69 " (cutoff:3.500A) Proline residue: S 75 - end of helix Processing helix chain 'T' and resid 5 through 41 removed outlier: 4.949A pdb=" N ARG T 9 " --> pdb=" O SER T 5 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU T 14 " --> pdb=" O ALA T 10 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS T 18 " --> pdb=" O GLU T 14 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N HIS T 19 " --> pdb=" O LYS T 15 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA T 37 " --> pdb=" O LYS T 33 " (cutoff:3.500A) Processing helix chain 'T' and resid 42 through 64 removed outlier: 3.548A pdb=" N ALA T 46 " --> pdb=" O ASP T 42 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN T 47 " --> pdb=" O LYS T 43 " (cutoff:3.500A) Proline residue: T 55 - end of helix removed outlier: 3.891A pdb=" N GLN T 60 " --> pdb=" O ILE T 56 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA T 62 " --> pdb=" O ASP T 58 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS T 63 " --> pdb=" O ARG T 59 " (cutoff:3.500A) Processing helix chain 'T' and resid 67 through 86 removed outlier: 5.806A pdb=" N ALA T 71 " --> pdb=" O HIS T 67 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU T 78 " --> pdb=" O HIS T 74 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS T 84 " --> pdb=" O ALA T 80 " (cutoff:3.500A) Processing helix chain 'U' and resid 16 through 34 removed outlier: 4.086A pdb=" N ARG U 20 " --> pdb=" O ARG U 16 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N LYS U 24 " --> pdb=" O ARG U 20 " (cutoff:3.500A) removed outlier: 9.121A pdb=" N ALA U 25 " --> pdb=" O SER U 21 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLY U 26 " --> pdb=" O CYS U 22 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N VAL U 27 " --> pdb=" O GLU U 23 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LEU U 28 " --> pdb=" O LYS U 24 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N GLU U 30 " --> pdb=" O GLY U 26 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ARG U 33 " --> pdb=" O ALA U 29 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ARG U 34 " --> pdb=" O GLU U 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 36 through 61 Proline residue: U 40 - end of helix removed outlier: 3.619A pdb=" N ARG U 44 " --> pdb=" O PRO U 40 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N HIS U 55 " --> pdb=" O ALA U 51 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU U 59 " --> pdb=" O HIS U 55 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA U 60 " --> pdb=" O ALA U 56 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG U 61 " --> pdb=" O LYS U 57 " (cutoff:3.500A) Processing helix chain '03' and resid 5 through 14 removed outlier: 4.277A pdb=" N VAL03 10 " --> pdb=" O LYS03 6 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ARG03 12 " --> pdb=" O MET03 8 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU03 13 " --> pdb=" O ARG03 9 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LYS03 14 " --> pdb=" O VAL03 10 " (cutoff:3.500A) Processing helix chain '03' and resid 22 through 34 removed outlier: 3.617A pdb=" N ALA03 26 " --> pdb=" O ASP03 22 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE03 27 " --> pdb=" O ILE03 23 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ALA03 28 " --> pdb=" O ASN03 24 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU03 30 " --> pdb=" O ALA03 26 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LYS03 31 " --> pdb=" O ILE03 27 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU03 32 " --> pdb=" O ALA03 28 " (cutoff:3.500A) Processing helix chain '03' and resid 181 through 200 removed outlier: 3.940A pdb=" N ASN03 188 " --> pdb=" O LYS03 184 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA03 199 " --> pdb=" O ALA03 195 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS03 200 " --> pdb=" O LEU03 196 " (cutoff:3.500A) Processing helix chain 'Z' and resid 23 through 37 removed outlier: 3.661A pdb=" N THR Z 32 " --> pdb=" O THR Z 28 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU Z 35 " --> pdb=" O ILE Z 31 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LYS Z 37 " --> pdb=" O THR Z 33 " (cutoff:3.500A) Processing helix chain 'Z' and resid 45 through 51 removed outlier: 4.106A pdb=" N ASN Z 51 " --> pdb=" O ASP Z 47 " (cutoff:3.500A) Processing helix chain 'Z' and resid 52 through 59 Processing helix chain 'Z' and resid 85 through 96 removed outlier: 4.232A pdb=" N LYS Z 89 " --> pdb=" O ALA Z 85 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASN Z 90 " --> pdb=" O ASP Z 86 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR Z 93 " --> pdb=" O LYS Z 89 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLY Z 94 " --> pdb=" O ASN Z 90 " (cutoff:3.500A) Processing helix chain 'Z' and resid 112 through 126 removed outlier: 3.625A pdb=" N HIS Z 118 " --> pdb=" O GLN Z 114 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG Z 123 " --> pdb=" O ILE Z 119 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY Z 126 " --> pdb=" O GLY Z 122 " (cutoff:3.500A) Processing helix chain 'Z' and resid 136 through 141 removed outlier: 4.322A pdb=" N VAL Z 140 " --> pdb=" O LYS Z 136 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ASP Z 141 " --> pdb=" O CYS Z 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 136 through 141' Processing helix chain 'Z' and resid 142 through 161 removed outlier: 3.672A pdb=" N LEU Z 146 " --> pdb=" O ASP Z 142 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU Z 148 " --> pdb=" O GLU Z 144 " (cutoff:3.500A) Processing helix chain 'Z' and resid 173 through 180 removed outlier: 3.685A pdb=" N ALA Z 177 " --> pdb=" O SER Z 173 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY Z 180 " --> pdb=" O LYS Z 176 " (cutoff:3.500A) Processing helix chain 'Z' and resid 181 through 199 removed outlier: 3.522A pdb=" N LEU Z 191 " --> pdb=" O LYS Z 187 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP Z 196 " --> pdb=" O ALA Z 192 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ILE Z 199 " --> pdb=" O LEU Z 195 " (cutoff:3.500A) Processing helix chain 'Z' and resid 282 through 287 removed outlier: 3.876A pdb=" N ILE Z 286 " --> pdb=" O LYS Z 282 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N GLU Z 287 " --> pdb=" O ARG Z 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 282 through 287' Processing sheet with id= 1, first strand: chain '04' and resid 79 through 82 removed outlier: 6.896A pdb=" N LEU04 92 " --> pdb=" O GLU04 78 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASP04 113 " --> pdb=" O VAL04 77 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '04' and resid 161 through 164 removed outlier: 6.634A pdb=" N THR04 172 " --> pdb=" O VAL04 164 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU04 179 " --> pdb=" O LEU04 175 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '04' and resid 90 through 95 removed outlier: 4.020A pdb=" N GLU04 99 " --> pdb=" O TYR04 95 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '05' and resid 3 through 8 removed outlier: 4.442A pdb=" N SER05 199 " --> pdb=" O LYS05 8 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ASP05 200 " --> pdb=" O THR05 112 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N THR05 112 " --> pdb=" O ASP05 200 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL05 170 " --> pdb=" O GLY05 111 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain '05' and resid 11 through 16 removed outlier: 4.241A pdb=" N VAL05 20 " --> pdb=" O THR05 16 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG05 179 " --> pdb=" O LEU05 188 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain '05' and resid 79 through 84 removed outlier: 6.011A pdb=" N ARG05 46 " --> pdb=" O LEU05 84 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN05 49 " --> pdb=" O THR05 35 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL05 34 " --> pdb=" O GLN05 94 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLN05 94 " --> pdb=" O VAL05 34 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain '05' and resid 105 through 108 removed outlier: 6.515A pdb=" N LYS05 105 " --> pdb=" O VAL05 177 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain '06' and resid 1 through 5 removed outlier: 4.399A pdb=" N SER06 10 " --> pdb=" O LEU06 5 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain '06' and resid 117 through 120 removed outlier: 5.424A pdb=" N ARG06 117 " --> pdb=" O ASP06 184 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain '07' and resid 64 through 68 removed outlier: 3.590A pdb=" N CYS07 86 " --> pdb=" O MET07 37 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N GLY07 38 " --> pdb=" O GLY07 150 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N GLY07 150 " --> pdb=" O GLY07 38 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain '07' and resid 71 through 74 removed outlier: 5.039A pdb=" N SER07 72 " --> pdb=" O ARG07 79 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ARG07 79 " --> pdb=" O SER07 72 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA07 74 " --> pdb=" O LYS07 77 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain '08' and resid 7 through 10 removed outlier: 3.564A pdb=" N VAL08 8 " --> pdb=" O LEU08 49 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ASN08 47 " --> pdb=" O VAL08 10 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain '08' and resid 15 through 18 removed outlier: 3.669A pdb=" N LYS08 26 " --> pdb=" O ASP08 15 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS08 17 " --> pdb=" O THR08 24 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain '08' and resid 81 through 88 removed outlier: 3.777A pdb=" N GLY08 134 " --> pdb=" O PHE08 82 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N THR08 128 " --> pdb=" O LEU08 88 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS08 133 " --> pdb=" O THR08 121 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain '08' and resid 94 through 98 removed outlier: 3.671A pdb=" N ARG08 94 " --> pdb=" O SER08 105 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL08 101 " --> pdb=" O LYS08 98 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ASN08 100 " --> pdb=" O LEU08 116 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU08 116 " --> pdb=" O ASN08 100 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain '09' and resid 2 through 6 removed outlier: 6.951A pdb=" N GLN09 2 " --> pdb=" O ALA09 39 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N LYS09 35 " --> pdb=" O LEU09 6 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain '09' and resid 76 through 83 removed outlier: 5.502A pdb=" N GLU09 76 " --> pdb=" O LYS09 141 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN09 145 " --> pdb=" O VAL09 78 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain '10' and resid 22 through 28 No H-bonds generated for sheet with id= 18 Processing sheet with id= 19, first strand: chain '11' and resid 5 through 11 removed outlier: 3.783A pdb=" N LEU11 10 " --> pdb=" O VAL11 56 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL11 56 " --> pdb=" O LEU11 10 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N THR11 59 " --> pdb=" O THR11 67 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR11 67 " --> pdb=" O THR11 59 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain '12' and resid 52 through 57 removed outlier: 5.436A pdb=" N ASP12 19 " --> pdb=" O LEU12 140 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain '12' and resid 74 through 78 removed outlier: 3.732A pdb=" N ALA12 87 " --> pdb=" O TYR12 74 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS12 76 " --> pdb=" O LYS12 85 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N GLY12 83 " --> pdb=" O THR12 78 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain '13' and resid 17 through 21 removed outlier: 6.615A pdb=" N ARG13 17 " --> pdb=" O VAL13 10 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL13 10 " --> pdb=" O ARG13 17 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR13 6 " --> pdb=" O CYS13 21 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ASN13 82 " --> pdb=" O MET13 7 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain '15' and resid 37 through 40 removed outlier: 4.039A pdb=" N TYR15 91 " --> pdb=" O ILE15 73 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain '15' and resid 62 through 66 removed outlier: 5.722A pdb=" N LEU15 102 " --> pdb=" O ARG15 66 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR15 103 " --> pdb=" O LEU15 33 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N SER15 30 " --> pdb=" O LYS15 133 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LYS15 127 " --> pdb=" O VAL15 36 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain '17' and resid 49 through 52 removed outlier: 3.700A pdb=" N VAL17 49 " --> pdb=" O VAL17 39 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG17 25 " --> pdb=" O ILE17 40 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL17 28 " --> pdb=" O ASP17 93 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain '18' and resid 41 through 44 removed outlier: 6.229A pdb=" N THR18 24 " --> pdb=" O LYS18 86 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain '18' and resid 57 through 63 Processing sheet with id= 28, first strand: chain '20' and resid 11 through 14 removed outlier: 3.640A pdb=" N TYR20 2 " --> pdb=" O ALA20 42 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET20 40 " --> pdb=" O VAL20 4 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain '20' and resid 19 through 23 removed outlier: 6.595A pdb=" N ASP20 95 " --> pdb=" O VAL20 64 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N LYS20 60 " --> pdb=" O THR20 99 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL20 33 " --> pdb=" O ALA20 61 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain '20' and resid 57 through 60 removed outlier: 4.159A pdb=" N VAL20 58 " --> pdb=" O SER20 102 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER20 102 " --> pdb=" O VAL20 58 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain '20' and resid 65 through 69 removed outlier: 3.918A pdb=" N GLY20 67 " --> pdb=" O PHE20 93 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN20 91 " --> pdb=" O GLY20 69 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain '20' and resid 71 through 78 removed outlier: 4.266A pdb=" N TYR20 83 " --> pdb=" O ARG20 78 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain '21' and resid 2 through 8 removed outlier: 4.137A pdb=" N THR21 3 " --> pdb=" O VAL21 107 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL21 107 " --> pdb=" O THR21 3 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL21 106 " --> pdb=" O THR21 72 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain '21' and resid 73 through 79 removed outlier: 5.369A pdb=" N THR21 100 " --> pdb=" O GLY21 79 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain '21' and resid 80 through 88 Processing sheet with id= 36, first strand: chain '22' and resid 12 through 15 removed outlier: 5.077A pdb=" N VAL22 31 " --> pdb=" O HIS22 15 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ASN22 28 " --> pdb=" O LEU22 87 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LYS22 81 " --> pdb=" O VAL22 34 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N LYS22 66 " --> pdb=" O ARG22 77 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ASP22 79 " --> pdb=" O LYS22 64 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N LYS22 64 " --> pdb=" O ASP22 79 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LYS22 81 " --> pdb=" O VAL22 62 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N VAL22 62 " --> pdb=" O LYS22 81 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ALA22 83 " --> pdb=" O THR22 60 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR22 60 " --> pdb=" O ALA22 83 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N VAL22 85 " --> pdb=" O VAL22 58 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL22 58 " --> pdb=" O VAL22 85 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain '23' and resid 8 through 12 removed outlier: 5.213A pdb=" N ASP23 8 " --> pdb=" O VAL23 24 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N LYS23 20 " --> pdb=" O VAL23 12 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain '23' and resid 41 through 44 No H-bonds generated for sheet with id= 38 Processing sheet with id= 39, first strand: chain '23' and resid 81 through 86 removed outlier: 5.180A pdb=" N ARG23 81 " --> pdb=" O LYS23 96 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain '24' and resid 69 through 72 removed outlier: 3.652A pdb=" N VAL24 72 " --> pdb=" O LEU24 61 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ASN24 5 " --> pdb=" O ASP24 43 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ASP24 43 " --> pdb=" O ASN24 5 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ALA24 39 " --> pdb=" O ARG24 9 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE24 89 " --> pdb=" O PRO24 27 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain '25' and resid 47 through 50 removed outlier: 3.571A pdb=" N GLY25 48 " --> pdb=" O PHE25 56 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR25 54 " --> pdb=" O GLY25 50 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain '25' and resid 62 through 67 Processing sheet with id= 43, first strand: chain '26' and resid 15 through 18 removed outlier: 5.983A pdb=" N ASN26 16 " --> pdb=" O ALA26 23 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ALA26 23 " --> pdb=" O ASN26 16 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N SER26 18 " --> pdb=" O LEU26 21 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain '26' and resid 34 through 40 removed outlier: 3.698A pdb=" N HIS26 35 " --> pdb=" O LEU26 48 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain '28' and resid 34 through 38 removed outlier: 3.504A pdb=" N VAL28 35 " --> pdb=" O ILE28 6 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE28 6 " --> pdb=" O VAL28 35 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS28 5 " --> pdb=" O GLU28 57 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N MET28 53 " --> pdb=" O THR28 9 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain '29' and resid 11 through 15 Processing sheet with id= 47, first strand: chain '30' and resid 27 through 30 removed outlier: 6.294A pdb=" N SER30 28 " --> pdb=" O LYS30 36 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS30 36 " --> pdb=" O SER30 28 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ASP30 30 " --> pdb=" O GLY30 34 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain '31' and resid 19 through 23 removed outlier: 6.826A pdb=" N ILE31 47 " --> pdb=" O SER31 13 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU31 35 " --> pdb=" O TYR31 48 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain '33' and resid 21 through 24 removed outlier: 5.950A pdb=" N PHE33 21 " --> pdb=" O VAL33 49 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain '34' and resid 13 through 18 removed outlier: 8.051A pdb=" N ASN34 13 " --> pdb=" O SER34 28 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER34 28 " --> pdb=" O ASN34 13 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'B' and resid 66 through 70 removed outlier: 3.593A pdb=" N LEU B 67 " --> pdb=" O ALA B 159 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL B 162 " --> pdb=" O PHE B 183 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA B 184 " --> pdb=" O PHE B 197 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'C' and resid 53 through 58 removed outlier: 3.774A pdb=" N VAL C 65 " --> pdb=" O GLN C 99 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE C 67 " --> pdb=" O ASN C 101 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'C' and resid 164 through 168 removed outlier: 3.621A pdb=" N VAL C 152 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY C 147 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN C 184 " --> pdb=" O VAL C 199 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASP C 180 " --> pdb=" O LYS C 203 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'D' and resid 139 through 143 removed outlier: 3.670A pdb=" N ASP D 140 " --> pdb=" O PHE D 181 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N GLU D 178 " --> pdb=" O ASP D 173 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N TRP D 169 " --> pdb=" O LYS D 182 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'E' and resid 16 through 23 removed outlier: 3.726A pdb=" N ALA E 16 " --> pdb=" O LEU E 35 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU E 35 " --> pdb=" O ALA E 16 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ILE E 29 " --> pdb=" O LYS E 22 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLY E 50 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ARG E 44 " --> pdb=" O ASP E 40 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'E' and resid 83 through 87 removed outlier: 3.545A pdb=" N MET E 95 " --> pdb=" O VAL E 84 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL E 93 " --> pdb=" O GLY E 86 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG E 92 " --> pdb=" O TYR E 127 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N TYR E 127 " --> pdb=" O ARG E 92 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N PHE E 94 " --> pdb=" O LYS E 125 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'F' and resid 34 through 37 removed outlier: 3.667A pdb=" N LYS F 35 " --> pdb=" O GLU F 65 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N HIS F 37 " --> pdb=" O ASN F 63 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ASN F 63 " --> pdb=" O HIS F 37 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ILE F 6 " --> pdb=" O MET F 62 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL F 64 " --> pdb=" O TYR F 4 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N HIS F 3 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU F 5 " --> pdb=" O MET F 90 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N MET F 90 " --> pdb=" O GLU F 5 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET F 9 " --> pdb=" O ARG F 86 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ARG F 86 " --> pdb=" O MET F 9 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'F' and resid 38 through 42 removed outlier: 3.827A pdb=" N ARG F 38 " --> pdb=" O ASN F 63 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ASN F 63 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N TYR F 59 " --> pdb=" O TRP F 42 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'F' and resid 43 through 47 removed outlier: 3.590A pdb=" N GLY F 43 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N LEU F 47 " --> pdb=" O HIS F 55 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N HIS F 55 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'G' and resid 71 through 76 removed outlier: 7.168A pdb=" N THR G 71 " --> pdb=" O VAL G 90 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'H' and resid 22 through 28 removed outlier: 5.950A pdb=" N ALA H 22 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL H 24 " --> pdb=" O LEU H 60 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU H 59 " --> pdb=" O LYS H 49 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ASP H 47 " --> pdb=" O THR H 61 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'H' and resid 102 through 105 removed outlier: 7.104A pdb=" N VAL H 102 " --> pdb=" O ILE H 125 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'I' and resid 4 through 10 removed outlier: 3.658A pdb=" N THR I 65 " --> pdb=" O ARG I 17 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'J' and resid 44 through 52 removed outlier: 3.736A pdb=" N GLU J 47 " --> pdb=" O ILE J 67 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ILE J 8 " --> pdb=" O VAL J 74 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG J 7 " --> pdb=" O SER J 101 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'K' and resid 29 through 35 Processing sheet with id= 66, first strand: chain 'L' and resid 28 through 32 removed outlier: 5.242A pdb=" N LEU L 80 " --> pdb=" O VAL L 97 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG L 82 " --> pdb=" O HIS L 95 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'L' and resid 34 through 40 removed outlier: 4.802A pdb=" N ARG L 35 " --> pdb=" O ARG L 53 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N LYS L 50 " --> pdb=" O ILE L 66 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'P' and resid 4 through 11 removed outlier: 5.452A pdb=" N GLN P 18 " --> pdb=" O ALA P 7 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA P 11 " --> pdb=" O ARG P 14 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG P 14 " --> pdb=" O ALA P 11 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'P' and resid 37 through 40 removed outlier: 3.610A pdb=" N ARG P 51 " --> pdb=" O PHE P 38 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N GLY P 49 " --> pdb=" O ASN P 40 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'Q' and resid 6 through 10 removed outlier: 3.698A pdb=" N GLY Q 9 " --> pdb=" O VAL Q 58 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLU Q 59 " --> pdb=" O VAL Q 75 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'Q' and resid 18 through 27 No H-bonds generated for sheet with id= 71 Processing sheet with id= 72, first strand: chain 'S' and resid 46 through 51 removed outlier: 5.555A pdb=" N LEU S 46 " --> pdb=" O VAL S 61 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE S 48 " --> pdb=" O VAL S 59 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain '03' and resid 59 through 64 removed outlier: 5.667A pdb=" N VAL03 59 " --> pdb=" O ASN03 165 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain '03' and resid 169 through 176 removed outlier: 7.199A pdb=" N GLY03 169 " --> pdb=" O LEU03 48 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR03 173 " --> pdb=" O VAL03 44 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL03 42 " --> pdb=" O ILE03 175 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER03 215 " --> pdb=" O ASP03 43 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL03 212 " --> pdb=" O VAL03 224 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'Z' and resid 64 through 70 removed outlier: 3.585A pdb=" N VAL Z 67 " --> pdb=" O HIS Z 78 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY Z 15 " --> pdb=" O GLY Z 100 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE Z 102 " --> pdb=" O GLY Z 15 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE Z 17 " --> pdb=" O ILE Z 102 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N TYR Z 129 " --> pdb=" O ASP Z 99 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE Z 131 " --> pdb=" O ALA Z 101 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'Z' and resid 210 through 214 removed outlier: 5.854A pdb=" N PHE Z 210 " --> pdb=" O LYS Z 294 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N GLN Z 290 " --> pdb=" O ILE Z 214 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLU Z 240 " --> pdb=" O CYS Z 255 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'Z' and resid 216 through 219 removed outlier: 3.553A pdb=" N VAL Z 226 " --> pdb=" O PHE Z 218 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'Z' and resid 335 through 341 removed outlier: 3.634A pdb=" N THR Z 335 " --> pdb=" O PHE Z 332 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N PHE Z 332 " --> pdb=" O THR Z 335 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL Z 337 " --> pdb=" O PHE Z 330 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR Z 326 " --> pdb=" O ILE Z 341 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG Z 377 " --> pdb=" O GLN Z 329 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR Z 331 " --> pdb=" O ALA Z 375 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA Z 375 " --> pdb=" O TYR Z 331 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU Z 372 " --> pdb=" O VAL Z 387 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL Z 387 " --> pdb=" O LEU Z 372 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N PHE Z 374 " --> pdb=" O ALA Z 385 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ALA Z 385 " --> pdb=" O PHE Z 374 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ILE Z 376 " --> pdb=" O VAL Z 383 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP Z 354 " --> pdb=" O ILE Z 310 " (cutoff:3.500A) 1764 hydrogen bonds defined for protein. 5187 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3551 hydrogen bonds 5792 hydrogen bond angles 0 basepair planarities 1427 basepair parallelities 2955 stacking parallelities Total time for adding SS restraints: 256.13 Time building geometry restraints manager: 66.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 26625 1.33 - 1.46: 68980 1.46 - 1.58: 61320 1.58 - 1.71: 9613 1.71 - 1.83: 309 Bond restraints: 166847 Sorted by residual: bond pdb=" O3A GCP Z 401 " pdb=" PB GCP Z 401 " ideal model delta sigma weight residual 1.697 1.524 0.173 2.00e-02 2.50e+03 7.46e+01 bond pdb=" C5 U8U Y 34 " pdb=" C6 U8U Y 34 " ideal model delta sigma weight residual 1.506 1.365 0.141 2.00e-02 2.50e+03 4.99e+01 bond pdb=" O3A GCP Z 401 " pdb=" PA GCP Z 401 " ideal model delta sigma weight residual 1.621 1.516 0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" C1' GCP Z 401 " pdb=" N9 GCP Z 401 " ideal model delta sigma weight residual 1.463 1.559 -0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" C2 U8U Y 34 " pdb=" N3 U8U Y 34 " ideal model delta sigma weight residual 1.510 1.424 0.086 2.00e-02 2.50e+03 1.86e+01 ... (remaining 166842 not shown) Histogram of bond angle deviations from ideal: 93.31 - 104.98: 22389 104.98 - 116.65: 126607 116.65 - 128.32: 92393 128.32 - 139.98: 7725 139.98 - 151.65: 2 Bond angle restraints: 249116 Sorted by residual: angle pdb=" N LYS11 94 " pdb=" CA LYS11 94 " pdb=" C LYS11 94 " ideal model delta sigma weight residual 113.97 100.72 13.25 1.28e+00 6.10e-01 1.07e+02 angle pdb=" N ALA10 127 " pdb=" CA ALA10 127 " pdb=" C ALA10 127 " ideal model delta sigma weight residual 113.16 100.45 12.71 1.24e+00 6.50e-01 1.05e+02 angle pdb=" N GLU10 65 " pdb=" CA GLU10 65 " pdb=" C GLU10 65 " ideal model delta sigma weight residual 113.17 100.68 12.49 1.26e+00 6.30e-01 9.83e+01 angle pdb=" N SER B 85 " pdb=" CA SER B 85 " pdb=" C SER B 85 " ideal model delta sigma weight residual 112.89 100.97 11.92 1.24e+00 6.50e-01 9.24e+01 angle pdb=" N TYR I 89 " pdb=" CA TYR I 89 " pdb=" C TYR I 89 " ideal model delta sigma weight residual 110.65 98.74 11.91 1.26e+00 6.30e-01 8.94e+01 ... (remaining 249111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.70: 95039 35.70 - 71.41: 10480 71.41 - 107.11: 1266 107.11 - 142.82: 17 142.82 - 178.52: 23 Dihedral angle restraints: 106825 sinusoidal: 88393 harmonic: 18432 Sorted by residual: dihedral pdb=" C5' C A 280 " pdb=" C4' C A 280 " pdb=" C3' C A 280 " pdb=" O3' C A 280 " ideal model delta sinusoidal sigma weight residual 147.00 74.66 72.34 1 8.00e+00 1.56e-02 1.05e+02 dihedral pdb=" C4' C A 280 " pdb=" C3' C A 280 " pdb=" C2' C A 280 " pdb=" C1' C A 280 " ideal model delta sinusoidal sigma weight residual -35.00 33.09 -68.09 1 8.00e+00 1.56e-02 9.40e+01 dihedral pdb=" O4' C02 12 " pdb=" C1' C02 12 " pdb=" N1 C02 12 " pdb=" C2 C02 12 " ideal model delta sinusoidal sigma weight residual 200.00 27.18 172.82 1 1.50e+01 4.44e-03 8.50e+01 ... (remaining 106822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 27414 0.124 - 0.247: 4056 0.247 - 0.371: 293 0.371 - 0.494: 17 0.494 - 0.618: 7 Chirality restraints: 31787 Sorted by residual: chirality pdb=" C3' GCP Z 401 " pdb=" C2' GCP Z 401 " pdb=" C4' GCP Z 401 " pdb=" O3' GCP Z 401 " both_signs ideal model delta sigma weight residual False -2.57 -3.18 0.62 2.00e-01 2.50e+01 9.55e+00 chirality pdb=" P G Y 1 " pdb=" OP1 G Y 1 " pdb=" OP2 G Y 1 " pdb=" O5' G Y 1 " both_signs ideal model delta sigma weight residual True 2.41 3.02 -0.61 2.00e-01 2.50e+01 9.17e+00 chirality pdb=" C1' C011178 " pdb=" O4' C011178 " pdb=" C2' C011178 " pdb=" N1 C011178 " both_signs ideal model delta sigma weight residual False 2.47 1.86 0.61 2.00e-01 2.50e+01 9.17e+00 ... (remaining 31784 not shown) Planarity restraints: 13716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N FME W 101 " -0.242 2.00e-02 2.50e+03 1.97e-01 3.87e+02 pdb=" CA FME W 101 " 0.091 2.00e-02 2.50e+03 pdb=" CN FME W 101 " 0.271 2.00e-02 2.50e+03 pdb=" O1 FME W 101 " -0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U011647 " -0.093 2.00e-02 2.50e+03 5.19e-02 6.06e+01 pdb=" N1 U011647 " 0.002 2.00e-02 2.50e+03 pdb=" C2 U011647 " 0.017 2.00e-02 2.50e+03 pdb=" O2 U011647 " 0.037 2.00e-02 2.50e+03 pdb=" N3 U011647 " 0.016 2.00e-02 2.50e+03 pdb=" C4 U011647 " 0.019 2.00e-02 2.50e+03 pdb=" O4 U011647 " -0.093 2.00e-02 2.50e+03 pdb=" C5 U011647 " 0.052 2.00e-02 2.50e+03 pdb=" C6 U011647 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A011328 " -0.102 2.00e-02 2.50e+03 4.40e-02 5.32e+01 pdb=" N9 A011328 " 0.010 2.00e-02 2.50e+03 pdb=" C8 A011328 " 0.042 2.00e-02 2.50e+03 pdb=" N7 A011328 " 0.033 2.00e-02 2.50e+03 pdb=" C5 A011328 " 0.018 2.00e-02 2.50e+03 pdb=" C6 A011328 " -0.015 2.00e-02 2.50e+03 pdb=" N6 A011328 " -0.067 2.00e-02 2.50e+03 pdb=" N1 A011328 " -0.006 2.00e-02 2.50e+03 pdb=" C2 A011328 " 0.019 2.00e-02 2.50e+03 pdb=" N3 A011328 " 0.036 2.00e-02 2.50e+03 pdb=" C4 A011328 " 0.033 2.00e-02 2.50e+03 ... (remaining 13713 not shown) Histogram of nonbonded interaction distances: 1.32 - 2.03: 1 2.03 - 2.75: 16072 2.75 - 3.47: 203391 3.47 - 4.18: 501295 4.18 - 4.90: 672278 Nonbonded interactions: 1393037 Sorted by model distance: nonbonded pdb=" O3' A Y 76 " pdb=" C LYS Y 101 " model vdw 1.318 3.270 nonbonded pdb=" O3' A Y 76 " pdb=" O LYS Y 101 " model vdw 2.257 3.040 nonbonded pdb=" O2' A Y 69 " pdb=" O5' C Y 70 " model vdw 2.277 2.440 nonbonded pdb=" C3' A Y 76 " pdb=" C LYS Y 101 " model vdw 2.346 3.700 nonbonded pdb=" N ALA10 127 " pdb=" N THR10 128 " model vdw 2.350 2.560 ... (remaining 1393032 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 'W' and resid 1 through 76) selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.69 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: 6.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.090 Extract box with map and model: 26.630 Check model and map are aligned: 1.640 Set scattering table: 1.020 Process input model: 560.740 Find NCS groups from input model: 3.150 Set up NCS constraints: 0.450 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 603.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.173 166847 Z= 0.435 Angle : 1.071 26.882 249116 Z= 0.706 Chirality : 0.090 0.618 31787 Planarity : 0.009 0.197 13716 Dihedral : 22.430 178.523 94939 Min Nonbonded Distance : 1.318 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 3.06 % Allowed : 14.31 % Favored : 82.63 % Rotamer: Outliers : 1.57 % Allowed : 5.60 % Favored : 92.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.15 (0.08), residues: 6366 helix: -3.76 (0.07), residues: 1829 sheet: -3.26 (0.13), residues: 1059 loop : -3.33 (0.09), residues: 3478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.006 TRP05 80 HIS 0.002 0.000 HIS29 6 PHE 0.036 0.006 PHE U 36 TYR 0.067 0.008 TYR10 51 ARG 0.007 0.001 ARG07 91 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12732 Ramachandran restraints generated. 6366 Oldfield, 0 Emsley, 6366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12732 Ramachandran restraints generated. 6366 Oldfield, 0 Emsley, 6366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1901 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 1818 time to evaluate : 8.095 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: 04 47 ARG cc_start: 0.8555 (mtt180) cc_final: 0.8330 (ttm-80) REVERT: 04 250 GLN cc_start: 0.9076 (tp40) cc_final: 0.8673 (tm-30) REVERT: 05 131 ASP cc_start: 0.7336 (t70) cc_final: 0.6921 (m-30) REVERT: 06 1 MET cc_start: 0.8762 (tpp) cc_final: 0.8240 (ttt) REVERT: 06 2 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7757 (tp30) REVERT: 06 115 GLN cc_start: 0.8766 (mm-40) cc_final: 0.8442 (mm-40) REVERT: 07 31 GLU cc_start: 0.8316 (tt0) cc_final: 0.8035 (tt0) REVERT: 07 100 GLU cc_start: 0.9115 (tt0) cc_final: 0.8685 (mt-10) REVERT: 07 156 THR cc_start: 0.9057 (m) cc_final: 0.8795 (p) REVERT: 08 38 ASP cc_start: 0.8970 (t70) cc_final: 0.8438 (t0) REVERT: 08 146 ASP cc_start: 0.8962 (m-30) cc_final: 0.8224 (m-30) REVERT: 09 40 THR cc_start: 0.8523 (m) cc_final: 0.8156 (m) REVERT: 09 55 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8553 (pp20) REVERT: 09 89 LYS cc_start: 0.7531 (mmtm) cc_final: 0.6651 (tmtt) REVERT: 10 1 MET cc_start: 0.8137 (tpt) cc_final: 0.6700 (ptp) REVERT: 11 52 LEU cc_start: 0.7939 (tp) cc_final: 0.7475 (tp) REVERT: 11 67 THR cc_start: 0.5254 (OUTLIER) cc_final: 0.4830 (m) REVERT: 11 96 LYS cc_start: 0.8553 (mptt) cc_final: 0.8348 (tttm) REVERT: 11 107 GLU cc_start: 0.8546 (mt-10) cc_final: 0.7867 (pt0) REVERT: 11 108 ILE cc_start: 0.6975 (mt) cc_final: 0.6269 (mm) REVERT: 12 5 THR cc_start: 0.8561 (m) cc_final: 0.8196 (p) REVERT: 12 14 ASP cc_start: 0.8701 (t70) cc_final: 0.8073 (t70) REVERT: 12 16 TYR cc_start: 0.9072 (m-80) cc_final: 0.8829 (m-80) REVERT: 12 60 ASP cc_start: 0.8829 (p0) cc_final: 0.8602 (p0) REVERT: 12 67 ASN cc_start: 0.8894 (m-40) cc_final: 0.8691 (m-40) REVERT: 13 18 ARG cc_start: 0.8296 (tpp-160) cc_final: 0.7894 (mmm-85) REVERT: 13 21 CYS cc_start: 0.7532 (t) cc_final: 0.6917 (t) REVERT: 13 44 LYS cc_start: 0.8730 (mmmt) cc_final: 0.8144 (tttm) REVERT: 13 67 LYS cc_start: 0.7965 (tptt) cc_final: 0.7120 (tppt) REVERT: 13 69 VAL cc_start: 0.8606 (m) cc_final: 0.8361 (t) REVERT: 13 100 PHE cc_start: 0.8824 (m-80) cc_final: 0.8614 (m-80) REVERT: 16 18 GLN cc_start: 0.9018 (tt0) cc_final: 0.8804 (tt0) REVERT: 16 20 MET cc_start: 0.8902 (ptm) cc_final: 0.8652 (ptp) REVERT: 16 110 MET cc_start: 0.8620 (mmp) cc_final: 0.8051 (mmm) REVERT: 17 19 GLN cc_start: 0.9513 (pt0) cc_final: 0.9299 (pt0) REVERT: 17 26 LEU cc_start: 0.8384 (tp) cc_final: 0.8174 (mt) REVERT: 17 27 VAL cc_start: 0.8214 (t) cc_final: 0.7689 (t) REVERT: 17 28 VAL cc_start: 0.9286 (p) cc_final: 0.8967 (m) REVERT: 18 10 GLU cc_start: 0.8136 (pt0) cc_final: 0.7521 (pt0) REVERT: 20 76 LYS cc_start: 0.8787 (mmtp) cc_final: 0.8484 (mmtm) REVERT: 20 95 ASP cc_start: 0.7922 (m-30) cc_final: 0.7404 (m-30) REVERT: 20 99 THR cc_start: 0.7817 (p) cc_final: 0.7326 (t) REVERT: 21 15 GLN cc_start: 0.8820 (tt0) cc_final: 0.8590 (tt0) REVERT: 21 34 ASP cc_start: 0.9329 (m-30) cc_final: 0.8998 (p0) REVERT: 22 76 ARG cc_start: 0.8424 (ttp80) cc_final: 0.8195 (ptt-90) REVERT: 22 87 LEU cc_start: 0.8733 (mt) cc_final: 0.8502 (pp) REVERT: 23 99 SER cc_start: 0.8602 (OUTLIER) cc_final: 0.8209 (t) REVERT: 25 68 LYS cc_start: 0.8337 (mtpt) cc_final: 0.8108 (mmmt) REVERT: 26 28 PHE cc_start: 0.6546 (m-80) cc_final: 0.6159 (m-10) REVERT: 27 5 GLU cc_start: 0.8441 (mt-10) cc_final: 0.7696 (mm-30) REVERT: 27 13 GLU cc_start: 0.8546 (pt0) cc_final: 0.7981 (pt0) REVERT: 27 30 MET cc_start: 0.9496 (ttp) cc_final: 0.9145 (tmm) REVERT: 27 59 GLU cc_start: 0.9074 (tt0) cc_final: 0.8766 (tp30) REVERT: 28 43 ILE cc_start: 0.9471 (mm) cc_final: 0.9162 (tt) REVERT: 30 11 LYS cc_start: 0.9124 (tptm) cc_final: 0.8667 (tptt) REVERT: 30 14 MET cc_start: 0.8749 (mtm) cc_final: 0.8334 (mtm) REVERT: 33 3 ILE cc_start: 0.8567 (mt) cc_final: 0.8258 (mm) REVERT: 33 25 HIS cc_start: 0.8280 (OUTLIER) cc_final: 0.7928 (m-70) REVERT: 34 18 LYS cc_start: 0.8376 (tttm) cc_final: 0.8112 (ttmt) REVERT: 34 37 GLN cc_start: 0.8370 (tp-100) cc_final: 0.8016 (tt0) REVERT: B 14 HIS cc_start: 0.6405 (OUTLIER) cc_final: 0.4494 (p-80) REVERT: B 49 PHE cc_start: 0.9006 (p90) cc_final: 0.8713 (p90) REVERT: B 68 PHE cc_start: 0.8966 (m-80) cc_final: 0.8645 (m-10) REVERT: B 77 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7860 (mp0) REVERT: B 90 PHE cc_start: 0.8077 (p90) cc_final: 0.7809 (p90) REVERT: B 116 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.6928 (tt) REVERT: B 117 GLU cc_start: 0.9151 (pt0) cc_final: 0.8900 (pt0) REVERT: B 220 VAL cc_start: 0.9357 (t) cc_final: 0.8732 (t) REVERT: C 18 ASN cc_start: 0.8745 (m-40) cc_final: 0.7614 (p0) REVERT: C 24 ASN cc_start: 0.9202 (t0) cc_final: 0.8909 (t0) REVERT: C 50 SER cc_start: 0.9227 (m) cc_final: 0.8607 (m) REVERT: D 19 PHE cc_start: 0.8382 (m-80) cc_final: 0.8180 (m-10) REVERT: D 46 ARG cc_start: 0.8397 (tpp-160) cc_final: 0.8169 (tpt90) REVERT: D 68 GLU cc_start: 0.8546 (tp30) cc_final: 0.8306 (tp30) REVERT: D 77 GLU cc_start: 0.8369 (tp30) cc_final: 0.7964 (tp30) REVERT: D 104 MET cc_start: 0.8891 (mmt) cc_final: 0.8409 (mmt) REVERT: D 135 GLN cc_start: 0.8552 (tp-100) cc_final: 0.8114 (mm-40) REVERT: D 189 ASP cc_start: 0.7859 (m-30) cc_final: 0.7514 (m-30) REVERT: D 204 SER cc_start: 0.9017 (m) cc_final: 0.8769 (t) REVERT: E 10 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7823 (mp) REVERT: E 111 ARG cc_start: 0.8635 (ttm-80) cc_final: 0.8058 (ttm170) REVERT: F 11 HIS cc_start: 0.8692 (t70) cc_final: 0.8137 (t70) REVERT: F 70 VAL cc_start: 0.8645 (t) cc_final: 0.8342 (m) REVERT: F 73 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8237 (mp0) REVERT: F 78 PHE cc_start: 0.8982 (m-80) cc_final: 0.8476 (m-80) REVERT: G 19 SER cc_start: 0.8224 (t) cc_final: 0.7706 (p) REVERT: G 30 MET cc_start: 0.8256 (ttp) cc_final: 0.7945 (tmm) REVERT: G 48 THR cc_start: 0.8999 (p) cc_final: 0.8649 (t) REVERT: G 51 GLN cc_start: 0.9022 (tt0) cc_final: 0.8742 (tm-30) REVERT: G 85 GLN cc_start: 0.7317 (mm110) cc_final: 0.7055 (mm-40) REVERT: G 139 ASP cc_start: 0.9284 (m-30) cc_final: 0.8952 (m-30) REVERT: I 36 GLN cc_start: 0.8273 (pt0) cc_final: 0.7928 (tp-100) REVERT: I 63 TYR cc_start: 0.8070 (t80) cc_final: 0.7685 (t80) REVERT: J 49 PHE cc_start: 0.7374 (m-80) cc_final: 0.6724 (m-80) REVERT: J 66 GLU cc_start: 0.8634 (pt0) cc_final: 0.8395 (pm20) REVERT: J 88 MET cc_start: 0.8663 (mmm) cc_final: 0.8414 (ptm) REVERT: K 71 ASP cc_start: 0.9203 (p0) cc_final: 0.8986 (p0) REVERT: K 76 TYR cc_start: 0.8431 (m-80) cc_final: 0.7849 (m-80) REVERT: K 111 ASP cc_start: 0.8371 (t70) cc_final: 0.7960 (t0) REVERT: L 13 ARG cc_start: 0.8169 (tpt170) cc_final: 0.7887 (mpt180) REVERT: N 9 GLU cc_start: 0.9528 (tp30) cc_final: 0.9271 (tp30) REVERT: O 58 MET cc_start: 0.9148 (ptm) cc_final: 0.8559 (ptp) REVERT: Q 17 GLU cc_start: 0.8244 (tt0) cc_final: 0.7972 (tm-30) REVERT: R 9 PHE cc_start: 0.8774 (t80) cc_final: 0.8562 (t80) REVERT: S 43 MET cc_start: 0.8682 (mtp) cc_final: 0.8394 (mtp) REVERT: T 17 ARG cc_start: 0.8167 (ppt170) cc_final: 0.7908 (ptm-80) REVERT: T 81 GLN cc_start: 0.9108 (mm110) cc_final: 0.8810 (mp10) REVERT: U 4 LYS cc_start: 0.7652 (ttpp) cc_final: 0.7065 (ptmm) REVERT: U 9 GLU cc_start: 0.6515 (OUTLIER) cc_final: 0.6231 (tp30) REVERT: U 22 CYS cc_start: 0.8370 (t) cc_final: 0.7961 (m) REVERT: U 27 VAL cc_start: 0.8576 (m) cc_final: 0.8370 (p) REVERT: 03 216 THR cc_start: -0.2021 (OUTLIER) cc_final: -0.2483 (p) REVERT: Z 6 GLU cc_start: 0.7809 (tt0) cc_final: 0.6689 (mp0) REVERT: Z 98 MET cc_start: 0.7110 (ttm) cc_final: 0.6898 (ttm) REVERT: Z 173 SER cc_start: 0.4984 (t) cc_final: 0.4381 (p) REVERT: Z 285 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7571 (mp0) outliers start: 83 outliers final: 22 residues processed: 1878 average time/residue: 1.5340 time to fit residues: 4904.3775 Evaluate side-chains 1082 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 1052 time to evaluate : 6.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 10 residue 50 VAL Chi-restraints excluded: chain 10 residue 74 ASP Chi-restraints excluded: chain 11 residue 67 THR Chi-restraints excluded: chain 11 residue 97 VAL Chi-restraints excluded: chain 13 residue 54 LYS Chi-restraints excluded: chain 14 residue 96 LYS Chi-restraints excluded: chain 15 residue 70 ASP Chi-restraints excluded: chain 17 residue 78 VAL Chi-restraints excluded: chain 23 residue 99 SER Chi-restraints excluded: chain 29 residue 18 CYS Chi-restraints excluded: chain 33 residue 25 HIS Chi-restraints excluded: chain B residue 14 HIS Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain D residue 182 LYS Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 128 GLU Chi-restraints excluded: chain I residue 44 ARG Chi-restraints excluded: chain J residue 75 ASP Chi-restraints excluded: chain Q residue 18 LYS Chi-restraints excluded: chain R residue 11 ARG Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain U residue 9 GLU Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain 03 residue 216 THR Chi-restraints excluded: chain Z residue 125 VAL Chi-restraints excluded: chain Z residue 266 ASP Chi-restraints excluded: chain Z residue 334 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1101 random chunks: chunk 929 optimal weight: 20.0000 chunk 834 optimal weight: 20.0000 chunk 463 optimal weight: 6.9990 chunk 285 optimal weight: 8.9990 chunk 562 optimal weight: 9.9990 chunk 445 optimal weight: 5.9990 chunk 862 optimal weight: 20.0000 chunk 333 optimal weight: 20.0000 chunk 524 optimal weight: 20.0000 chunk 642 optimal weight: 20.0000 chunk 999 optimal weight: 20.0000 overall best weight: 10.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 04 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 04 36 ASN 04 44 ASN 04 127 ASN 04 225 ASN 04 259 ASN ** 05 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 05 134 HIS 06 94 GLN 06 165 HIS ** 08 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 114 HIS 08 142 GLN 09 33 GLN 09 119 ASN 09 135 HIS 10 103 ASN ** 11 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 12 131 ASN 13 5 GLN 13 29 HIS 13 88 ASN 14 4 ASN ** 14 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 15 17 ASN 16 9 GLN 16 18 GLN 16 23 ASN 18 6 GLN 18 14 GLN ** 18 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 18 65 ASN ** 19 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 20 86 GLN ** 20 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 22 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 23 68 ASN 23 73 ASN 24 49 ASN ** 24 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 24 75 GLN 24 87 GLN ** 25 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 26 15 ASN 26 19 HIS 27 58 ASN 28 19 HIS 29 20 ASN 29 61 ASN 34 35 GLN ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 HIS B 176 ASN B 177 ASN ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 ASN ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 ASN D 125 ASN D 130 ASN E 18 ASN F 55 HIS ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 129 ASN G 147 ASN H 20 ASN ** H 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 ASN I 36 GLN ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN K 39 ASN L 4 ASN ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 GLN L 45 ASN ** O 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 49 HIS O 61 GLN ** O 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 9 HIS P 79 ASN Q 30 HIS R 51 GLN ** R 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 20 ASN 03 20 GLN 03 24 ASN ** Z 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 84 HIS ** Z 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 290 GLN ** Z 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 69 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 166847 Z= 0.345 Angle : 0.821 17.557 249116 Z= 0.422 Chirality : 0.045 0.455 31787 Planarity : 0.007 0.164 13716 Dihedral : 23.358 178.065 82340 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 26.70 Ramachandran Plot: Outliers : 0.36 % Allowed : 11.69 % Favored : 87.95 % Rotamer: Outliers : 5.58 % Allowed : 15.19 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -3.80 (0.09), residues: 6366 helix: -2.03 (0.10), residues: 1934 sheet: -2.80 (0.14), residues: 1061 loop : -2.75 (0.10), residues: 3371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP B 103 HIS 0.013 0.002 HIS13 29 PHE 0.026 0.003 PHE09 47 TYR 0.022 0.003 TYR L 65 ARG 0.036 0.001 ARG12 99 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12732 Ramachandran restraints generated. 6366 Oldfield, 0 Emsley, 6366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12732 Ramachandran restraints generated. 6366 Oldfield, 0 Emsley, 6366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1459 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 295 poor density : 1164 time to evaluate : 6.639 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: 04 250 GLN cc_start: 0.9097 (tp40) cc_final: 0.8603 (tm-30) REVERT: 05 185 ASN cc_start: 0.8980 (t0) cc_final: 0.8635 (t0) REVERT: 06 1 MET cc_start: 0.8449 (tpp) cc_final: 0.7764 (ttt) REVERT: 06 90 GLN cc_start: 0.5330 (pt0) cc_final: 0.5067 (mt0) REVERT: 07 100 GLU cc_start: 0.9067 (tt0) cc_final: 0.8486 (tp30) REVERT: 07 156 THR cc_start: 0.9175 (m) cc_final: 0.8926 (p) REVERT: 08 38 ASP cc_start: 0.8859 (t70) cc_final: 0.8470 (t0) REVERT: 08 146 ASP cc_start: 0.9055 (m-30) cc_final: 0.8814 (m-30) REVERT: 09 55 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8445 (pp20) REVERT: 10 1 MET cc_start: 0.8101 (tpt) cc_final: 0.6743 (ptp) REVERT: 11 67 THR cc_start: 0.5139 (OUTLIER) cc_final: 0.4894 (m) REVERT: 11 107 GLU cc_start: 0.8644 (mt-10) cc_final: 0.7981 (tt0) REVERT: 11 116 MET cc_start: -0.0100 (mmt) cc_final: -0.0704 (mmt) REVERT: 11 140 GLU cc_start: 0.7938 (tp30) cc_final: 0.7603 (mm-30) REVERT: 12 5 THR cc_start: 0.8592 (m) cc_final: 0.8246 (p) REVERT: 12 28 LEU cc_start: 0.9508 (tp) cc_final: 0.9302 (tp) REVERT: 12 36 LEU cc_start: 0.8775 (mt) cc_final: 0.8513 (mt) REVERT: 12 60 ASP cc_start: 0.8851 (p0) cc_final: 0.8506 (p0) REVERT: 13 20 MET cc_start: 0.9235 (OUTLIER) cc_final: 0.9007 (tpp) REVERT: 13 44 LYS cc_start: 0.8701 (mmmt) cc_final: 0.8422 (ttmt) REVERT: 13 67 LYS cc_start: 0.7905 (tptt) cc_final: 0.7065 (tppt) REVERT: 13 100 PHE cc_start: 0.8856 (m-80) cc_final: 0.8598 (m-80) REVERT: 15 115 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8383 (mm-30) REVERT: 16 20 MET cc_start: 0.8757 (ptm) cc_final: 0.8408 (ptp) REVERT: 16 24 MET cc_start: 0.8751 (tpp) cc_final: 0.8422 (tpp) REVERT: 16 47 VAL cc_start: 0.8512 (t) cc_final: 0.8224 (p) REVERT: 16 110 MET cc_start: 0.8442 (mmp) cc_final: 0.8224 (mmm) REVERT: 18 9 GLN cc_start: 0.8932 (pm20) cc_final: 0.8591 (pm20) REVERT: 18 10 GLU cc_start: 0.8101 (pt0) cc_final: 0.7819 (pt0) REVERT: 18 73 PHE cc_start: 0.8147 (m-80) cc_final: 0.7925 (m-80) REVERT: 19 15 LYS cc_start: 0.9425 (mmtp) cc_final: 0.8583 (mmtp) REVERT: 19 51 GLN cc_start: 0.9154 (mt0) cc_final: 0.8407 (mp10) REVERT: 20 77 PHE cc_start: 0.8933 (t80) cc_final: 0.8713 (t80) REVERT: 22 24 MET cc_start: 0.9176 (tpt) cc_final: 0.8914 (tpp) REVERT: 22 87 LEU cc_start: 0.8807 (mt) cc_final: 0.8427 (pp) REVERT: 23 43 LYS cc_start: 0.8449 (tttp) cc_final: 0.8194 (tppt) REVERT: 24 49 ASN cc_start: 0.8613 (m110) cc_final: 0.8095 (m-40) REVERT: 25 68 LYS cc_start: 0.8441 (mtpt) cc_final: 0.8110 (mmmt) REVERT: 27 5 GLU cc_start: 0.8459 (mt-10) cc_final: 0.7758 (tp30) REVERT: 27 7 ARG cc_start: 0.7174 (OUTLIER) cc_final: 0.6706 (mtm-85) REVERT: 27 13 GLU cc_start: 0.8296 (pt0) cc_final: 0.7750 (pt0) REVERT: 29 48 GLN cc_start: 0.6520 (tt0) cc_final: 0.5770 (mp10) REVERT: 30 11 LYS cc_start: 0.9171 (tptm) cc_final: 0.8852 (tptp) REVERT: 30 14 MET cc_start: 0.8637 (mtm) cc_final: 0.8379 (mtm) REVERT: 31 27 ARG cc_start: 0.9331 (tpt90) cc_final: 0.9037 (tpt170) REVERT: 33 25 HIS cc_start: 0.8354 (OUTLIER) cc_final: 0.7809 (m-70) REVERT: 34 18 LYS cc_start: 0.8488 (tttm) cc_final: 0.8139 (ttmt) REVERT: 34 37 GLN cc_start: 0.8361 (tp-100) cc_final: 0.7953 (tt0) REVERT: B 26 MET cc_start: 0.7808 (mtp) cc_final: 0.7477 (mtt) REVERT: B 49 PHE cc_start: 0.8976 (p90) cc_final: 0.8753 (p90) REVERT: C 18 ASN cc_start: 0.8802 (m-40) cc_final: 0.7637 (p0) REVERT: C 24 ASN cc_start: 0.9433 (t0) cc_final: 0.9156 (t0) REVERT: C 48 LYS cc_start: 0.8963 (mptm) cc_final: 0.8744 (ttpp) REVERT: C 138 GLN cc_start: 0.9219 (mt0) cc_final: 0.8818 (mt0) REVERT: D 3 TYR cc_start: 0.8112 (t80) cc_final: 0.7907 (t80) REVERT: D 46 ARG cc_start: 0.8579 (tpp-160) cc_final: 0.8228 (tpt90) REVERT: D 74 TYR cc_start: 0.8273 (m-80) cc_final: 0.7898 (t80) REVERT: D 77 GLU cc_start: 0.8494 (tp30) cc_final: 0.8063 (tp30) REVERT: D 93 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8679 (mm) REVERT: D 104 MET cc_start: 0.8838 (mmt) cc_final: 0.8297 (mmt) REVERT: D 189 ASP cc_start: 0.7998 (m-30) cc_final: 0.7555 (m-30) REVERT: E 12 GLU cc_start: 0.8289 (pm20) cc_final: 0.7433 (pm20) REVERT: E 59 ILE cc_start: 0.8834 (pp) cc_final: 0.8562 (pp) REVERT: F 21 MET cc_start: 0.8819 (mtm) cc_final: 0.8133 (mpp) REVERT: F 73 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8444 (mt-10) REVERT: G 51 GLN cc_start: 0.9019 (tt0) cc_final: 0.8744 (tm-30) REVERT: G 85 GLN cc_start: 0.7539 (mm110) cc_final: 0.7295 (mm110) REVERT: G 139 ASP cc_start: 0.9282 (m-30) cc_final: 0.8711 (t0) REVERT: H 8 ASP cc_start: 0.8862 (m-30) cc_final: 0.8431 (t0) REVERT: I 26 LYS cc_start: 0.8711 (tptp) cc_final: 0.8384 (tptt) REVERT: I 31 GLN cc_start: 0.8871 (mp10) cc_final: 0.8522 (mp10) REVERT: I 56 MET cc_start: 0.7994 (ptm) cc_final: 0.7240 (tmm) REVERT: I 71 ILE cc_start: 0.9320 (mm) cc_final: 0.9078 (tp) REVERT: J 49 PHE cc_start: 0.7329 (m-80) cc_final: 0.6893 (m-80) REVERT: J 88 MET cc_start: 0.8674 (mmm) cc_final: 0.8412 (ptm) REVERT: J 89 ARG cc_start: 0.8361 (ptt-90) cc_final: 0.8133 (ptt90) REVERT: K 37 GLN cc_start: 0.8762 (mm110) cc_final: 0.7947 (tm-30) REVERT: K 76 TYR cc_start: 0.8500 (m-80) cc_final: 0.7854 (m-80) REVERT: K 111 ASP cc_start: 0.8462 (t70) cc_final: 0.8095 (t0) REVERT: L 65 TYR cc_start: 0.7988 (t80) cc_final: 0.7783 (t80) REVERT: N 9 GLU cc_start: 0.9501 (tp30) cc_final: 0.9258 (tp30) REVERT: N 85 GLU cc_start: 0.8780 (tp30) cc_final: 0.8526 (tp30) REVERT: O 61 GLN cc_start: 0.9380 (pt0) cc_final: 0.9133 (mm110) REVERT: Q 17 GLU cc_start: 0.8734 (tt0) cc_final: 0.8191 (tm-30) REVERT: Q 79 GLU cc_start: 0.8267 (mp0) cc_final: 0.8064 (mp0) REVERT: R 9 PHE cc_start: 0.8816 (t80) cc_final: 0.8559 (t80) REVERT: S 10 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8563 (pp) REVERT: S 43 MET cc_start: 0.8830 (mtp) cc_final: 0.8624 (mtp) REVERT: T 81 GLN cc_start: 0.8877 (mm110) cc_final: 0.8611 (mp10) REVERT: U 9 GLU cc_start: 0.6347 (OUTLIER) cc_final: 0.6139 (tp30) REVERT: U 32 ARG cc_start: 0.7980 (ptt180) cc_final: 0.7736 (ptm160) REVERT: Z 114 GLN cc_start: 0.3709 (tp40) cc_final: 0.2968 (tm-30) REVERT: Z 124 GLN cc_start: 0.5511 (mm110) cc_final: 0.5037 (mm-40) REVERT: Z 173 SER cc_start: 0.4156 (t) cc_final: 0.3773 (m) outliers start: 295 outliers final: 176 residues processed: 1337 average time/residue: 1.3607 time to fit residues: 3141.8086 Evaluate side-chains 1118 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 935 time to evaluate : 6.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 15 VAL Chi-restraints excluded: chain 04 residue 129 LEU Chi-restraints excluded: chain 04 residue 258 SER Chi-restraints excluded: chain 04 residue 263 ASP Chi-restraints excluded: chain 04 residue 271 SER Chi-restraints excluded: chain 05 residue 9 VAL Chi-restraints excluded: chain 05 residue 11 MET Chi-restraints excluded: chain 05 residue 22 ILE Chi-restraints excluded: chain 05 residue 26 VAL Chi-restraints excluded: chain 05 residue 181 ASP Chi-restraints excluded: chain 06 residue 19 PHE Chi-restraints excluded: chain 06 residue 73 ILE Chi-restraints excluded: chain 07 residue 141 ASP Chi-restraints excluded: chain 07 residue 148 VAL Chi-restraints excluded: chain 07 residue 169 LEU Chi-restraints excluded: chain 07 residue 173 ASP Chi-restraints excluded: chain 08 residue 10 VAL Chi-restraints excluded: chain 08 residue 88 LEU Chi-restraints excluded: chain 08 residue 102 ILE Chi-restraints excluded: chain 10 residue 5 LEU Chi-restraints excluded: chain 10 residue 50 VAL Chi-restraints excluded: chain 10 residue 74 ASP Chi-restraints excluded: chain 11 residue 59 THR Chi-restraints excluded: chain 11 residue 67 THR Chi-restraints excluded: chain 11 residue 97 VAL Chi-restraints excluded: chain 11 residue 100 ILE Chi-restraints excluded: chain 11 residue 138 VAL Chi-restraints excluded: chain 12 residue 80 HIS Chi-restraints excluded: chain 12 residue 81 ILE Chi-restraints excluded: chain 12 residue 84 ILE Chi-restraints excluded: chain 12 residue 105 VAL Chi-restraints excluded: chain 13 residue 8 LEU Chi-restraints excluded: chain 13 residue 20 MET Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 54 LYS Chi-restraints excluded: chain 13 residue 57 VAL Chi-restraints excluded: chain 13 residue 61 VAL Chi-restraints excluded: chain 13 residue 84 CYS Chi-restraints excluded: chain 13 residue 85 VAL Chi-restraints excluded: chain 13 residue 97 THR Chi-restraints excluded: chain 14 residue 96 LYS Chi-restraints excluded: chain 15 residue 54 THR Chi-restraints excluded: chain 15 residue 70 ASP Chi-restraints excluded: chain 16 residue 34 ILE Chi-restraints excluded: chain 16 residue 57 THR Chi-restraints excluded: chain 17 residue 5 SER Chi-restraints excluded: chain 17 residue 28 VAL Chi-restraints excluded: chain 17 residue 65 THR Chi-restraints excluded: chain 17 residue 69 ASP Chi-restraints excluded: chain 17 residue 78 VAL Chi-restraints excluded: chain 18 residue 3 ILE Chi-restraints excluded: chain 18 residue 8 GLU Chi-restraints excluded: chain 18 residue 15 ASP Chi-restraints excluded: chain 18 residue 65 ASN Chi-restraints excluded: chain 19 residue 33 VAL Chi-restraints excluded: chain 19 residue 94 LEU Chi-restraints excluded: chain 20 residue 51 VAL Chi-restraints excluded: chain 20 residue 58 VAL Chi-restraints excluded: chain 21 residue 76 VAL Chi-restraints excluded: chain 21 residue 77 ASP Chi-restraints excluded: chain 21 residue 81 SER Chi-restraints excluded: chain 22 residue 2 ILE Chi-restraints excluded: chain 22 residue 59 ASN Chi-restraints excluded: chain 23 residue 29 SER Chi-restraints excluded: chain 23 residue 88 ASP Chi-restraints excluded: chain 24 residue 64 VAL Chi-restraints excluded: chain 24 residue 66 ASP Chi-restraints excluded: chain 24 residue 89 ILE Chi-restraints excluded: chain 24 residue 92 VAL Chi-restraints excluded: chain 26 residue 19 HIS Chi-restraints excluded: chain 26 residue 22 ASN Chi-restraints excluded: chain 26 residue 33 HIS Chi-restraints excluded: chain 26 residue 39 VAL Chi-restraints excluded: chain 26 residue 57 VAL Chi-restraints excluded: chain 27 residue 7 ARG Chi-restraints excluded: chain 28 residue 24 LEU Chi-restraints excluded: chain 28 residue 40 THR Chi-restraints excluded: chain 29 residue 18 CYS Chi-restraints excluded: chain 29 residue 23 LYS Chi-restraints excluded: chain 30 residue 21 LEU Chi-restraints excluded: chain 31 residue 16 THR Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 33 residue 25 HIS Chi-restraints excluded: chain 33 residue 37 THR Chi-restraints excluded: chain 33 residue 53 ASP Chi-restraints excluded: chain B residue 14 HIS Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 21 TYR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 136 ARG Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 182 LYS Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 44 ARG Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 128 GLU Chi-restraints excluded: chain G residue 138 GLU Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 126 CYS Chi-restraints excluded: chain I residue 21 LYS Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 44 ARG Chi-restraints excluded: chain I residue 95 SER Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 75 ASP Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 76 HIS Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 102 ASP Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 71 GLU Chi-restraints excluded: chain M residue 72 ILE Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 37 ASP Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain O residue 1 SER Chi-restraints excluded: chain O residue 10 ILE Chi-restraints excluded: chain O residue 36 ASN Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain R residue 11 ARG Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain S residue 10 ILE Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain U residue 9 GLU Chi-restraints excluded: chain U residue 41 THR Chi-restraints excluded: chain 03 residue 50 ILE Chi-restraints excluded: chain 03 residue 190 GLU Chi-restraints excluded: chain 03 residue 209 ILE Chi-restraints excluded: chain Z residue 125 VAL Chi-restraints excluded: chain Z residue 148 LEU Chi-restraints excluded: chain Z residue 191 LEU Chi-restraints excluded: chain Z residue 238 VAL Chi-restraints excluded: chain Z residue 255 CYS Chi-restraints excluded: chain Z residue 266 ASP Chi-restraints excluded: chain Z residue 292 LEU Chi-restraints excluded: chain Z residue 326 TYR Chi-restraints excluded: chain Z residue 334 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1101 random chunks: chunk 555 optimal weight: 5.9990 chunk 310 optimal weight: 20.0000 chunk 832 optimal weight: 20.0000 chunk 680 optimal weight: 20.0000 chunk 275 optimal weight: 40.0000 chunk 1001 optimal weight: 20.0000 chunk 1082 optimal weight: 8.9990 chunk 892 optimal weight: 30.0000 chunk 993 optimal weight: 20.0000 chunk 341 optimal weight: 30.0000 chunk 803 optimal weight: 20.0000 overall best weight: 14.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 04 44 ASN ** 05 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 05 150 GLN ** 06 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 72 ASN ** 08 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 08 142 GLN 10 9 GLN ** 11 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 14 4 ASN 15 17 ASN 15 88 ASN ** 15 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 17 19 GLN 18 40 GLN ** 18 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 20 82 HIS ** 21 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 22 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 23 65 GLN 23 98 ASN ** 24 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 24 75 GLN ** 25 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 26 19 HIS 27 20 ASN 33 25 HIS ** 33 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 34 13 ASN ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 HIS ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 GLN L 45 ASN ** O 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 46 HIS ** R 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 81 GLN 03 57 GLN ** Z 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 301 HIS Z 355 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.126 166847 Z= 0.430 Angle : 0.852 12.648 249116 Z= 0.436 Chirality : 0.045 0.395 31787 Planarity : 0.007 0.143 13716 Dihedral : 23.813 178.094 82328 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 32.87 Ramachandran Plot: Outliers : 0.30 % Allowed : 14.37 % Favored : 85.33 % Rotamer: Outliers : 7.32 % Allowed : 18.10 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -3.67 (0.10), residues: 6366 helix: -1.85 (0.10), residues: 1952 sheet: -2.68 (0.14), residues: 1046 loop : -2.74 (0.10), residues: 3368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP15 64 HIS 0.019 0.002 HIS26 19 PHE 0.032 0.003 PHE09 46 TYR 0.029 0.003 TYR Z 87 ARG 0.027 0.001 ARG D 69 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12732 Ramachandran restraints generated. 6366 Oldfield, 0 Emsley, 6366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12732 Ramachandran restraints generated. 6366 Oldfield, 0 Emsley, 6366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1334 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 387 poor density : 947 time to evaluate : 6.706 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: 04 250 GLN cc_start: 0.9109 (tp40) cc_final: 0.8689 (tp40) REVERT: 05 42 ASN cc_start: 0.7969 (t0) cc_final: 0.7764 (t0) REVERT: 06 1 MET cc_start: 0.8475 (tpp) cc_final: 0.8088 (ttm) REVERT: 06 100 MET cc_start: 0.8861 (mmm) cc_final: 0.7989 (mmm) REVERT: 06 143 LEU cc_start: 0.8254 (mt) cc_final: 0.8048 (mt) REVERT: 07 16 MET cc_start: 0.7789 (mmt) cc_final: 0.7262 (mmt) REVERT: 07 100 GLU cc_start: 0.9040 (tt0) cc_final: 0.8698 (tp30) REVERT: 08 38 ASP cc_start: 0.8870 (t70) cc_final: 0.8606 (t70) REVERT: 08 138 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7617 (tp40) REVERT: 09 25 TYR cc_start: 0.9150 (t80) cc_final: 0.8920 (t80) REVERT: 09 89 LYS cc_start: 0.7813 (mmtm) cc_final: 0.7010 (tmtt) REVERT: 10 1 MET cc_start: 0.8018 (tpt) cc_final: 0.6610 (ptp) REVERT: 11 107 GLU cc_start: 0.8606 (mt-10) cc_final: 0.7931 (tt0) REVERT: 11 116 MET cc_start: 0.0539 (mmt) cc_final: -0.0039 (mmt) REVERT: 12 5 THR cc_start: 0.8732 (m) cc_final: 0.8354 (p) REVERT: 12 16 TYR cc_start: 0.8849 (m-80) cc_final: 0.8428 (m-10) REVERT: 12 52 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.6917 (t0) REVERT: 12 60 ASP cc_start: 0.8831 (p0) cc_final: 0.8488 (p0) REVERT: 13 1 MET cc_start: 0.8473 (ttt) cc_final: 0.8232 (ttp) REVERT: 13 20 MET cc_start: 0.9258 (ttp) cc_final: 0.9025 (tpp) REVERT: 13 44 LYS cc_start: 0.8806 (mmmt) cc_final: 0.8539 (ttmt) REVERT: 13 67 LYS cc_start: 0.8220 (tptt) cc_final: 0.7471 (tppt) REVERT: 13 93 GLN cc_start: 0.9428 (mp10) cc_final: 0.9023 (mp10) REVERT: 13 100 PHE cc_start: 0.8842 (m-80) cc_final: 0.8616 (m-80) REVERT: 14 100 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8787 (mm) REVERT: 16 20 MET cc_start: 0.8736 (ptm) cc_final: 0.8206 (ptp) REVERT: 16 24 MET cc_start: 0.8793 (tpp) cc_final: 0.8501 (tpp) REVERT: 17 56 LYS cc_start: 0.9272 (OUTLIER) cc_final: 0.8785 (ptpp) REVERT: 19 15 LYS cc_start: 0.9374 (mmtp) cc_final: 0.8389 (mmtp) REVERT: 20 77 PHE cc_start: 0.8935 (t80) cc_final: 0.8579 (t80) REVERT: 21 34 ASP cc_start: 0.9306 (m-30) cc_final: 0.8954 (p0) REVERT: 22 24 MET cc_start: 0.9166 (tpt) cc_final: 0.8938 (tpp) REVERT: 22 73 ARG cc_start: 0.7477 (tpp80) cc_final: 0.6811 (tpp80) REVERT: 22 87 LEU cc_start: 0.8888 (mt) cc_final: 0.8525 (pp) REVERT: 23 43 LYS cc_start: 0.8548 (tttp) cc_final: 0.8313 (tppt) REVERT: 25 68 LYS cc_start: 0.8480 (mtpt) cc_final: 0.8020 (mmmt) REVERT: 26 31 ASN cc_start: 0.8614 (t0) cc_final: 0.8402 (t0) REVERT: 27 5 GLU cc_start: 0.8451 (mt-10) cc_final: 0.7330 (mm-30) REVERT: 27 7 ARG cc_start: 0.7138 (OUTLIER) cc_final: 0.6613 (mtm-85) REVERT: 27 13 GLU cc_start: 0.8322 (pt0) cc_final: 0.7995 (mt-10) REVERT: 29 22 MET cc_start: 0.8561 (tmm) cc_final: 0.8286 (tmm) REVERT: 30 14 MET cc_start: 0.8791 (mtm) cc_final: 0.8572 (mtp) REVERT: 30 27 LEU cc_start: 0.8429 (tp) cc_final: 0.8065 (tp) REVERT: 31 27 ARG cc_start: 0.9322 (tpt90) cc_final: 0.9013 (tpt170) REVERT: 33 25 HIS cc_start: 0.8389 (OUTLIER) cc_final: 0.7765 (m170) REVERT: 34 18 LYS cc_start: 0.8716 (tttm) cc_final: 0.8335 (ttmt) REVERT: 34 37 GLN cc_start: 0.8513 (tp-100) cc_final: 0.7805 (tt0) REVERT: B 26 MET cc_start: 0.7873 (mtp) cc_final: 0.7560 (mtt) REVERT: B 34 ARG cc_start: 0.9068 (ptt-90) cc_final: 0.8228 (ptm160) REVERT: B 49 PHE cc_start: 0.9003 (p90) cc_final: 0.8698 (p90) REVERT: C 24 ASN cc_start: 0.9430 (t0) cc_final: 0.9166 (t0) REVERT: C 48 LYS cc_start: 0.9017 (mptm) cc_final: 0.8708 (ttpt) REVERT: C 138 GLN cc_start: 0.9219 (mt0) cc_final: 0.8819 (mt0) REVERT: C 151 GLU cc_start: 0.8345 (tt0) cc_final: 0.8058 (tm-30) REVERT: D 46 ARG cc_start: 0.8656 (tpp-160) cc_final: 0.8255 (tpt90) REVERT: D 68 GLU cc_start: 0.8534 (tp30) cc_final: 0.8199 (tp30) REVERT: D 74 TYR cc_start: 0.8206 (m-80) cc_final: 0.7714 (t80) REVERT: D 77 GLU cc_start: 0.8487 (tp30) cc_final: 0.8028 (tp30) REVERT: D 93 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8877 (mt) REVERT: D 104 MET cc_start: 0.8878 (mmt) cc_final: 0.8283 (mmt) REVERT: D 159 GLU cc_start: 0.7917 (tp30) cc_final: 0.7572 (tp30) REVERT: D 168 THR cc_start: 0.9266 (OUTLIER) cc_final: 0.8612 (p) REVERT: D 189 ASP cc_start: 0.8039 (m-30) cc_final: 0.7523 (m-30) REVERT: E 127 TYR cc_start: 0.8424 (m-80) cc_final: 0.8186 (m-80) REVERT: E 151 MET cc_start: 0.8783 (mtp) cc_final: 0.8489 (mpp) REVERT: F 1 MET cc_start: 0.8012 (ttm) cc_final: 0.7483 (ttp) REVERT: F 21 MET cc_start: 0.8772 (mtm) cc_final: 0.7885 (mpp) REVERT: F 73 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8268 (mt-10) REVERT: F 88 MET cc_start: 0.7437 (tmm) cc_final: 0.6828 (tmm) REVERT: G 139 ASP cc_start: 0.9340 (m-30) cc_final: 0.8680 (t0) REVERT: H 8 ASP cc_start: 0.8877 (m-30) cc_final: 0.8516 (t0) REVERT: I 45 MET cc_start: 0.6725 (ppp) cc_final: 0.6493 (ppp) REVERT: I 56 MET cc_start: 0.8254 (ptm) cc_final: 0.7530 (tmm) REVERT: J 88 MET cc_start: 0.8679 (mmm) cc_final: 0.8433 (ptm) REVERT: J 89 ARG cc_start: 0.8384 (ptt-90) cc_final: 0.8067 (ptt-90) REVERT: K 76 TYR cc_start: 0.8528 (m-80) cc_final: 0.7864 (m-80) REVERT: K 111 ASP cc_start: 0.8571 (t70) cc_final: 0.8229 (t0) REVERT: L 65 TYR cc_start: 0.8215 (t80) cc_final: 0.7813 (t80) REVERT: L 77 SER cc_start: 0.7147 (p) cc_final: 0.6632 (m) REVERT: N 85 GLU cc_start: 0.8781 (tp30) cc_final: 0.8432 (tp30) REVERT: O 61 GLN cc_start: 0.9339 (pt0) cc_final: 0.9054 (mm-40) REVERT: Q 16 MET cc_start: 0.8775 (ttp) cc_final: 0.8274 (mpp) REVERT: Q 17 GLU cc_start: 0.8513 (tt0) cc_final: 0.8084 (tm-30) REVERT: Q 79 GLU cc_start: 0.8412 (mp0) cc_final: 0.8189 (mp0) REVERT: R 9 PHE cc_start: 0.8845 (t80) cc_final: 0.8455 (t80) REVERT: S 43 MET cc_start: 0.8840 (mtp) cc_final: 0.8572 (mtp) REVERT: U 9 GLU cc_start: 0.6575 (OUTLIER) cc_final: 0.6097 (tp30) REVERT: Z 68 GLU cc_start: 0.8732 (pm20) cc_final: 0.8181 (mp0) REVERT: Z 84 HIS cc_start: 0.7251 (OUTLIER) cc_final: 0.6842 (t-90) REVERT: Z 114 GLN cc_start: 0.3206 (tp40) cc_final: 0.2427 (tm-30) REVERT: Z 124 GLN cc_start: 0.5896 (mm110) cc_final: 0.5558 (mm-40) REVERT: Z 237 LYS cc_start: 0.5519 (OUTLIER) cc_final: 0.5312 (pmmt) outliers start: 387 outliers final: 253 residues processed: 1200 average time/residue: 1.3040 time to fit residues: 2732.5100 Evaluate side-chains 1108 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 264 poor density : 844 time to evaluate : 6.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 15 VAL Chi-restraints excluded: chain 04 residue 81 GLU Chi-restraints excluded: chain 04 residue 219 VAL Chi-restraints excluded: chain 04 residue 258 SER Chi-restraints excluded: chain 04 residue 263 ASP Chi-restraints excluded: chain 04 residue 267 VAL Chi-restraints excluded: chain 04 residue 271 SER Chi-restraints excluded: chain 05 residue 9 VAL Chi-restraints excluded: chain 05 residue 11 MET Chi-restraints excluded: chain 05 residue 22 ILE Chi-restraints excluded: chain 05 residue 27 ILE Chi-restraints excluded: chain 05 residue 176 ASP Chi-restraints excluded: chain 05 residue 181 ASP Chi-restraints excluded: chain 06 residue 7 ASP Chi-restraints excluded: chain 06 residue 19 PHE Chi-restraints excluded: chain 06 residue 77 ILE Chi-restraints excluded: chain 06 residue 116 ASP Chi-restraints excluded: chain 07 residue 30 VAL Chi-restraints excluded: chain 07 residue 89 THR Chi-restraints excluded: chain 07 residue 95 MET Chi-restraints excluded: chain 07 residue 148 VAL Chi-restraints excluded: chain 07 residue 169 LEU Chi-restraints excluded: chain 08 residue 10 VAL Chi-restraints excluded: chain 08 residue 19 ASN Chi-restraints excluded: chain 08 residue 46 ASP Chi-restraints excluded: chain 08 residue 88 LEU Chi-restraints excluded: chain 08 residue 138 GLN Chi-restraints excluded: chain 10 residue 3 LEU Chi-restraints excluded: chain 10 residue 27 VAL Chi-restraints excluded: chain 10 residue 74 ASP Chi-restraints excluded: chain 10 residue 118 ILE Chi-restraints excluded: chain 10 residue 123 ILE Chi-restraints excluded: chain 10 residue 131 THR Chi-restraints excluded: chain 11 residue 8 VAL Chi-restraints excluded: chain 11 residue 59 THR Chi-restraints excluded: chain 11 residue 67 THR Chi-restraints excluded: chain 11 residue 97 VAL Chi-restraints excluded: chain 11 residue 100 ILE Chi-restraints excluded: chain 11 residue 104 GLN Chi-restraints excluded: chain 11 residue 128 ILE Chi-restraints excluded: chain 11 residue 138 VAL Chi-restraints excluded: chain 12 residue 52 ASP Chi-restraints excluded: chain 12 residue 80 HIS Chi-restraints excluded: chain 12 residue 81 ILE Chi-restraints excluded: chain 12 residue 84 ILE Chi-restraints excluded: chain 12 residue 105 VAL Chi-restraints excluded: chain 12 residue 122 LEU Chi-restraints excluded: chain 13 residue 8 LEU Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 54 LYS Chi-restraints excluded: chain 13 residue 57 VAL Chi-restraints excluded: chain 13 residue 61 VAL Chi-restraints excluded: chain 13 residue 84 CYS Chi-restraints excluded: chain 13 residue 97 THR Chi-restraints excluded: chain 13 residue 118 LEU Chi-restraints excluded: chain 14 residue 4 ASN Chi-restraints excluded: chain 14 residue 67 THR Chi-restraints excluded: chain 14 residue 82 LEU Chi-restraints excluded: chain 14 residue 89 VAL Chi-restraints excluded: chain 14 residue 96 LYS Chi-restraints excluded: chain 14 residue 100 ILE Chi-restraints excluded: chain 15 residue 54 THR Chi-restraints excluded: chain 15 residue 70 ASP Chi-restraints excluded: chain 15 residue 126 ILE Chi-restraints excluded: chain 16 residue 11 ASN Chi-restraints excluded: chain 16 residue 34 ILE Chi-restraints excluded: chain 16 residue 37 THR Chi-restraints excluded: chain 16 residue 47 VAL Chi-restraints excluded: chain 16 residue 57 THR Chi-restraints excluded: chain 16 residue 97 ILE Chi-restraints excluded: chain 17 residue 5 SER Chi-restraints excluded: chain 17 residue 27 VAL Chi-restraints excluded: chain 17 residue 28 VAL Chi-restraints excluded: chain 17 residue 55 GLU Chi-restraints excluded: chain 17 residue 56 LYS Chi-restraints excluded: chain 17 residue 65 THR Chi-restraints excluded: chain 17 residue 69 ASP Chi-restraints excluded: chain 17 residue 78 VAL Chi-restraints excluded: chain 17 residue 106 LEU Chi-restraints excluded: chain 18 residue 8 GLU Chi-restraints excluded: chain 18 residue 15 ASP Chi-restraints excluded: chain 18 residue 31 VAL Chi-restraints excluded: chain 18 residue 62 LYS Chi-restraints excluded: chain 19 residue 33 VAL Chi-restraints excluded: chain 19 residue 57 ARG Chi-restraints excluded: chain 19 residue 58 GLN Chi-restraints excluded: chain 19 residue 94 LEU Chi-restraints excluded: chain 20 residue 39 LEU Chi-restraints excluded: chain 20 residue 51 VAL Chi-restraints excluded: chain 20 residue 58 VAL Chi-restraints excluded: chain 20 residue 82 HIS Chi-restraints excluded: chain 21 residue 20 VAL Chi-restraints excluded: chain 21 residue 77 ASP Chi-restraints excluded: chain 21 residue 78 GLU Chi-restraints excluded: chain 21 residue 81 SER Chi-restraints excluded: chain 21 residue 86 MET Chi-restraints excluded: chain 21 residue 106 VAL Chi-restraints excluded: chain 22 residue 2 ILE Chi-restraints excluded: chain 22 residue 42 GLU Chi-restraints excluded: chain 22 residue 59 ASN Chi-restraints excluded: chain 23 residue 29 SER Chi-restraints excluded: chain 23 residue 33 VAL Chi-restraints excluded: chain 23 residue 48 VAL Chi-restraints excluded: chain 23 residue 88 ASP Chi-restraints excluded: chain 24 residue 64 VAL Chi-restraints excluded: chain 24 residue 65 VAL Chi-restraints excluded: chain 24 residue 66 ASP Chi-restraints excluded: chain 24 residue 92 VAL Chi-restraints excluded: chain 25 residue 13 GLU Chi-restraints excluded: chain 25 residue 27 VAL Chi-restraints excluded: chain 26 residue 12 VAL Chi-restraints excluded: chain 26 residue 19 HIS Chi-restraints excluded: chain 26 residue 22 ASN Chi-restraints excluded: chain 26 residue 33 HIS Chi-restraints excluded: chain 26 residue 39 VAL Chi-restraints excluded: chain 26 residue 63 ILE Chi-restraints excluded: chain 27 residue 7 ARG Chi-restraints excluded: chain 27 residue 11 VAL Chi-restraints excluded: chain 28 residue 6 ILE Chi-restraints excluded: chain 28 residue 24 LEU Chi-restraints excluded: chain 28 residue 40 THR Chi-restraints excluded: chain 29 residue 18 CYS Chi-restraints excluded: chain 29 residue 21 VAL Chi-restraints excluded: chain 29 residue 23 LYS Chi-restraints excluded: chain 30 residue 38 LEU Chi-restraints excluded: chain 31 residue 16 THR Chi-restraints excluded: chain 31 residue 46 VAL Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 33 residue 25 HIS Chi-restraints excluded: chain 33 residue 53 ASP Chi-restraints excluded: chain B residue 14 HIS Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 21 TYR Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 136 ARG Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 120 HIS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 44 ARG Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 138 GLU Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 126 CYS Chi-restraints excluded: chain I residue 21 LYS Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 38 PHE Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 44 ARG Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 64 GLN Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 75 ASP Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 71 ASP Chi-restraints excluded: chain K residue 75 GLU Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 43 LYS Chi-restraints excluded: chain L residue 64 SER Chi-restraints excluded: chain L residue 81 ILE Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 11 HIS Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 71 GLU Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain N residue 37 ASP Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain O residue 1 SER Chi-restraints excluded: chain O residue 10 ILE Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 36 ASN Chi-restraints excluded: chain O residue 37 HIS Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 63 CYS Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain S residue 65 MET Chi-restraints excluded: chain U residue 9 GLU Chi-restraints excluded: chain U residue 12 ASP Chi-restraints excluded: chain U residue 36 PHE Chi-restraints excluded: chain U residue 41 THR Chi-restraints excluded: chain 03 residue 29 LEU Chi-restraints excluded: chain 03 residue 35 THR Chi-restraints excluded: chain 03 residue 209 ILE Chi-restraints excluded: chain Z residue 13 ASN Chi-restraints excluded: chain Z residue 25 THR Chi-restraints excluded: chain Z residue 84 HIS Chi-restraints excluded: chain Z residue 92 ILE Chi-restraints excluded: chain Z residue 125 VAL Chi-restraints excluded: chain Z residue 148 LEU Chi-restraints excluded: chain Z residue 191 LEU Chi-restraints excluded: chain Z residue 235 ILE Chi-restraints excluded: chain Z residue 237 LYS Chi-restraints excluded: chain Z residue 238 VAL Chi-restraints excluded: chain Z residue 242 VAL Chi-restraints excluded: chain Z residue 244 ILE Chi-restraints excluded: chain Z residue 250 THR Chi-restraints excluded: chain Z residue 255 CYS Chi-restraints excluded: chain Z residue 266 ASP Chi-restraints excluded: chain Z residue 292 LEU Chi-restraints excluded: chain Z residue 326 TYR Chi-restraints excluded: chain Z residue 334 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1101 random chunks: chunk 989 optimal weight: 20.0000 chunk 753 optimal weight: 20.0000 chunk 519 optimal weight: 6.9990 chunk 110 optimal weight: 0.0170 chunk 478 optimal weight: 10.0000 chunk 672 optimal weight: 20.0000 chunk 1005 optimal weight: 20.0000 chunk 1064 optimal weight: 20.0000 chunk 525 optimal weight: 2.9990 chunk 952 optimal weight: 30.0000 chunk 286 optimal weight: 6.9990 overall best weight: 5.4028 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 04 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 05 150 GLN 08 29 ASN ** 08 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 72 ASN ** 08 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 11 GLN ** 12 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 12 131 ASN 14 4 ASN 15 17 ASN 15 88 ASN 18 65 ASN ** 19 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 22 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 24 75 GLN ** 25 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 26 19 HIS 27 31 GLN 34 13 ASN ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN J 99 GLN ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 ASN ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 79 GLN Q 8 GLN ** R 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 13 HIS 03 57 GLN ** Z 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 166847 Z= 0.197 Angle : 0.650 11.123 249116 Z= 0.336 Chirality : 0.037 0.419 31787 Planarity : 0.005 0.131 13716 Dihedral : 23.748 175.521 82314 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 22.24 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.82 % Favored : 88.97 % Rotamer: Outliers : 5.39 % Allowed : 20.79 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -3.14 (0.10), residues: 6366 helix: -1.24 (0.11), residues: 1950 sheet: -2.58 (0.14), residues: 1120 loop : -2.43 (0.11), residues: 3296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 103 HIS 0.018 0.001 HIS20 82 PHE 0.030 0.002 PHE09 46 TYR 0.030 0.002 TYR Z 87 ARG 0.008 0.001 ARG R 11 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12732 Ramachandran restraints generated. 6366 Oldfield, 0 Emsley, 6366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12732 Ramachandran restraints generated. 6366 Oldfield, 0 Emsley, 6366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1287 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 1002 time to evaluate : 6.643 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: 04 145 MET cc_start: 0.8963 (mmm) cc_final: 0.8712 (mmm) REVERT: 04 250 GLN cc_start: 0.9109 (tp40) cc_final: 0.8569 (tm-30) REVERT: 05 42 ASN cc_start: 0.7985 (t0) cc_final: 0.7712 (t0) REVERT: 05 128 ARG cc_start: 0.7529 (tmt170) cc_final: 0.7059 (tmt170) REVERT: 05 185 ASN cc_start: 0.8892 (t0) cc_final: 0.8560 (t0) REVERT: 06 115 GLN cc_start: 0.8624 (tp40) cc_final: 0.8342 (tp40) REVERT: 07 16 MET cc_start: 0.7771 (mmt) cc_final: 0.6988 (mmt) REVERT: 07 59 ILE cc_start: 0.8753 (mt) cc_final: 0.8552 (mm) REVERT: 07 100 GLU cc_start: 0.9017 (tt0) cc_final: 0.8606 (tp30) REVERT: 07 133 GLU cc_start: 0.7049 (mp0) cc_final: 0.6650 (pm20) REVERT: 08 138 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7572 (tp-100) REVERT: 09 1 MET cc_start: 0.8592 (mmm) cc_final: 0.8323 (mpp) REVERT: 09 89 LYS cc_start: 0.7670 (mmtm) cc_final: 0.6885 (tmtt) REVERT: 10 1 MET cc_start: 0.8069 (tpt) cc_final: 0.6691 (ptp) REVERT: 10 86 MET cc_start: 0.2481 (OUTLIER) cc_final: 0.1909 (ttt) REVERT: 11 59 THR cc_start: 0.6340 (OUTLIER) cc_final: 0.6047 (p) REVERT: 11 67 THR cc_start: 0.5092 (OUTLIER) cc_final: 0.4599 (m) REVERT: 11 107 GLU cc_start: 0.8497 (mt-10) cc_final: 0.7897 (tt0) REVERT: 11 116 MET cc_start: 0.0321 (mmt) cc_final: -0.0320 (mmt) REVERT: 12 5 THR cc_start: 0.8587 (m) cc_final: 0.8228 (p) REVERT: 12 16 TYR cc_start: 0.8778 (m-80) cc_final: 0.8492 (m-10) REVERT: 12 52 ASP cc_start: 0.7746 (OUTLIER) cc_final: 0.6719 (t0) REVERT: 12 54 ILE cc_start: 0.9404 (mm) cc_final: 0.9134 (mm) REVERT: 12 60 ASP cc_start: 0.8761 (p0) cc_final: 0.8478 (p0) REVERT: 13 20 MET cc_start: 0.9277 (ttp) cc_final: 0.9076 (tpp) REVERT: 13 44 LYS cc_start: 0.8707 (mmmt) cc_final: 0.8257 (tttm) REVERT: 13 67 LYS cc_start: 0.7965 (tptt) cc_final: 0.7184 (tppt) REVERT: 13 93 GLN cc_start: 0.9352 (mp10) cc_final: 0.8961 (mp10) REVERT: 13 100 PHE cc_start: 0.8826 (m-80) cc_final: 0.8535 (m-80) REVERT: 14 100 ILE cc_start: 0.8909 (pt) cc_final: 0.8672 (mm) REVERT: 15 103 TYR cc_start: 0.8725 (m-80) cc_final: 0.8501 (m-80) REVERT: 16 20 MET cc_start: 0.8713 (ptm) cc_final: 0.8195 (ptp) REVERT: 16 24 MET cc_start: 0.8782 (tpp) cc_final: 0.8437 (tpp) REVERT: 16 43 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7644 (mm-30) REVERT: 16 47 VAL cc_start: 0.8605 (t) cc_final: 0.8380 (p) REVERT: 17 67 ASN cc_start: 0.8259 (OUTLIER) cc_final: 0.7888 (p0) REVERT: 19 51 GLN cc_start: 0.9147 (mt0) cc_final: 0.8191 (mt0) REVERT: 20 77 PHE cc_start: 0.8845 (t80) cc_final: 0.8439 (t80) REVERT: 20 95 ASP cc_start: 0.7853 (m-30) cc_final: 0.7612 (m-30) REVERT: 21 15 GLN cc_start: 0.8480 (tt0) cc_final: 0.8234 (tt0) REVERT: 21 34 ASP cc_start: 0.9255 (m-30) cc_final: 0.8904 (p0) REVERT: 22 24 MET cc_start: 0.9095 (tpt) cc_final: 0.8789 (tpp) REVERT: 22 87 LEU cc_start: 0.8865 (mt) cc_final: 0.8529 (pp) REVERT: 25 68 LYS cc_start: 0.8430 (mtpt) cc_final: 0.8131 (mttm) REVERT: 27 5 GLU cc_start: 0.8453 (mt-10) cc_final: 0.7534 (mm-30) REVERT: 27 13 GLU cc_start: 0.8210 (pt0) cc_final: 0.7936 (mt-10) REVERT: 27 49 ASP cc_start: 0.9050 (m-30) cc_final: 0.8683 (p0) REVERT: 28 43 ILE cc_start: 0.9172 (mm) cc_final: 0.8957 (mm) REVERT: 29 22 MET cc_start: 0.8482 (tmm) cc_final: 0.8256 (tmm) REVERT: 30 11 LYS cc_start: 0.9209 (tptm) cc_final: 0.8663 (tppt) REVERT: 30 14 MET cc_start: 0.8689 (mtm) cc_final: 0.7914 (mtm) REVERT: 30 27 LEU cc_start: 0.8352 (tp) cc_final: 0.7995 (tp) REVERT: 30 36 LYS cc_start: 0.8989 (mmmm) cc_final: 0.8660 (mmmt) REVERT: 31 27 ARG cc_start: 0.9319 (tpt90) cc_final: 0.9030 (tpt170) REVERT: 33 25 HIS cc_start: 0.8255 (OUTLIER) cc_final: 0.7717 (m170) REVERT: 34 18 LYS cc_start: 0.8602 (tttm) cc_final: 0.8215 (ttmt) REVERT: 34 37 GLN cc_start: 0.8393 (tp-100) cc_final: 0.8022 (tt0) REVERT: B 26 MET cc_start: 0.7719 (mtp) cc_final: 0.7445 (mtt) REVERT: B 30 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8149 (tp) REVERT: B 34 ARG cc_start: 0.8978 (ptt-90) cc_final: 0.8086 (ptm160) REVERT: B 195 VAL cc_start: 0.8126 (t) cc_final: 0.7865 (p) REVERT: C 24 ASN cc_start: 0.9327 (t0) cc_final: 0.9083 (t0) REVERT: C 48 LYS cc_start: 0.9018 (mptm) cc_final: 0.8738 (ttpt) REVERT: C 102 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8780 (tt) REVERT: C 138 GLN cc_start: 0.9199 (mt0) cc_final: 0.8938 (mm-40) REVERT: C 151 GLU cc_start: 0.8323 (tt0) cc_final: 0.7998 (tm-30) REVERT: D 19 PHE cc_start: 0.8810 (m-80) cc_final: 0.8479 (m-10) REVERT: D 46 ARG cc_start: 0.8698 (tpp-160) cc_final: 0.8178 (tpt90) REVERT: D 68 GLU cc_start: 0.8515 (tp30) cc_final: 0.8178 (tp30) REVERT: D 74 TYR cc_start: 0.7903 (m-80) cc_final: 0.7569 (t80) REVERT: D 77 GLU cc_start: 0.8296 (tp30) cc_final: 0.7825 (tp30) REVERT: D 93 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8743 (mt) REVERT: D 104 MET cc_start: 0.8677 (mmt) cc_final: 0.8145 (mmt) REVERT: D 189 ASP cc_start: 0.7988 (m-30) cc_final: 0.7577 (m-30) REVERT: E 64 GLU cc_start: 0.9056 (mp0) cc_final: 0.8834 (mp0) REVERT: E 151 MET cc_start: 0.8737 (mtp) cc_final: 0.8447 (mpp) REVERT: F 11 HIS cc_start: 0.8318 (t70) cc_final: 0.7748 (t70) REVERT: F 21 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.8356 (mpp) REVERT: F 49 TYR cc_start: 0.7821 (p90) cc_final: 0.7606 (p90) REVERT: F 73 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8222 (mt-10) REVERT: F 88 MET cc_start: 0.7387 (tmm) cc_final: 0.6808 (tmm) REVERT: G 19 SER cc_start: 0.7595 (t) cc_final: 0.7228 (p) REVERT: G 110 ARG cc_start: 0.6408 (ttp80) cc_final: 0.6056 (ptm-80) REVERT: G 139 ASP cc_start: 0.9303 (m-30) cc_final: 0.8640 (t0) REVERT: H 8 ASP cc_start: 0.8859 (m-30) cc_final: 0.8507 (t0) REVERT: I 45 MET cc_start: 0.6556 (ppp) cc_final: 0.6349 (ppp) REVERT: I 56 MET cc_start: 0.8228 (ptm) cc_final: 0.7374 (tmm) REVERT: I 87 MET cc_start: 0.8743 (mmm) cc_final: 0.8448 (mmm) REVERT: J 49 PHE cc_start: 0.7413 (m-80) cc_final: 0.7034 (m-80) REVERT: J 88 MET cc_start: 0.8596 (mmm) cc_final: 0.8278 (ptm) REVERT: J 89 ARG cc_start: 0.8458 (ptt-90) cc_final: 0.7960 (ptt-90) REVERT: K 76 TYR cc_start: 0.8380 (m-80) cc_final: 0.7704 (m-80) REVERT: K 111 ASP cc_start: 0.8505 (t70) cc_final: 0.7858 (t0) REVERT: L 75 GLU cc_start: 0.8602 (tp30) cc_final: 0.8325 (tp30) REVERT: O 82 GLU cc_start: 0.8432 (mm-30) cc_final: 0.7970 (mp0) REVERT: Q 16 MET cc_start: 0.8475 (ttp) cc_final: 0.7951 (ttp) REVERT: Q 79 GLU cc_start: 0.8318 (mp0) cc_final: 0.8087 (mp0) REVERT: S 43 MET cc_start: 0.8731 (mtp) cc_final: 0.8517 (mtp) REVERT: U 4 LYS cc_start: 0.7494 (ttpp) cc_final: 0.5092 (mtmm) REVERT: U 9 GLU cc_start: 0.6241 (OUTLIER) cc_final: 0.5897 (tp30) REVERT: Z 68 GLU cc_start: 0.8729 (pm20) cc_final: 0.8236 (mm-30) REVERT: Z 98 MET cc_start: 0.8154 (tmm) cc_final: 0.7761 (ttp) REVERT: Z 114 GLN cc_start: 0.3598 (tp40) cc_final: 0.2960 (tm-30) REVERT: Z 124 GLN cc_start: 0.5530 (mm110) cc_final: 0.5013 (mm-40) outliers start: 285 outliers final: 177 residues processed: 1184 average time/residue: 1.3288 time to fit residues: 2757.2210 Evaluate side-chains 1075 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 886 time to evaluate : 6.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 15 VAL Chi-restraints excluded: chain 04 residue 59 GLN Chi-restraints excluded: chain 04 residue 89 ASN Chi-restraints excluded: chain 04 residue 129 LEU Chi-restraints excluded: chain 04 residue 219 VAL Chi-restraints excluded: chain 04 residue 258 SER Chi-restraints excluded: chain 04 residue 263 ASP Chi-restraints excluded: chain 04 residue 271 SER Chi-restraints excluded: chain 05 residue 1 MET Chi-restraints excluded: chain 05 residue 9 VAL Chi-restraints excluded: chain 05 residue 11 MET Chi-restraints excluded: chain 05 residue 22 ILE Chi-restraints excluded: chain 05 residue 27 ILE Chi-restraints excluded: chain 05 residue 104 VAL Chi-restraints excluded: chain 06 residue 19 PHE Chi-restraints excluded: chain 06 residue 146 VAL Chi-restraints excluded: chain 07 residue 30 VAL Chi-restraints excluded: chain 07 residue 141 ASP Chi-restraints excluded: chain 07 residue 148 VAL Chi-restraints excluded: chain 07 residue 169 LEU Chi-restraints excluded: chain 08 residue 10 VAL Chi-restraints excluded: chain 08 residue 19 ASN Chi-restraints excluded: chain 08 residue 88 LEU Chi-restraints excluded: chain 08 residue 138 GLN Chi-restraints excluded: chain 09 residue 110 VAL Chi-restraints excluded: chain 10 residue 5 LEU Chi-restraints excluded: chain 10 residue 27 VAL Chi-restraints excluded: chain 10 residue 74 ASP Chi-restraints excluded: chain 10 residue 86 MET Chi-restraints excluded: chain 10 residue 118 ILE Chi-restraints excluded: chain 11 residue 59 THR Chi-restraints excluded: chain 11 residue 67 THR Chi-restraints excluded: chain 11 residue 77 VAL Chi-restraints excluded: chain 11 residue 97 VAL Chi-restraints excluded: chain 11 residue 104 GLN Chi-restraints excluded: chain 11 residue 138 VAL Chi-restraints excluded: chain 12 residue 52 ASP Chi-restraints excluded: chain 12 residue 84 ILE Chi-restraints excluded: chain 12 residue 105 VAL Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 54 LYS Chi-restraints excluded: chain 13 residue 57 VAL Chi-restraints excluded: chain 13 residue 86 LEU Chi-restraints excluded: chain 14 residue 82 LEU Chi-restraints excluded: chain 15 residue 70 ASP Chi-restraints excluded: chain 15 residue 136 MET Chi-restraints excluded: chain 16 residue 11 ASN Chi-restraints excluded: chain 16 residue 34 ILE Chi-restraints excluded: chain 16 residue 37 THR Chi-restraints excluded: chain 16 residue 57 THR Chi-restraints excluded: chain 16 residue 97 ILE Chi-restraints excluded: chain 17 residue 5 SER Chi-restraints excluded: chain 17 residue 18 LEU Chi-restraints excluded: chain 17 residue 28 VAL Chi-restraints excluded: chain 17 residue 67 ASN Chi-restraints excluded: chain 17 residue 69 ASP Chi-restraints excluded: chain 17 residue 78 VAL Chi-restraints excluded: chain 18 residue 15 ASP Chi-restraints excluded: chain 18 residue 25 VAL Chi-restraints excluded: chain 18 residue 113 LEU Chi-restraints excluded: chain 19 residue 33 VAL Chi-restraints excluded: chain 19 residue 43 GLN Chi-restraints excluded: chain 19 residue 94 LEU Chi-restraints excluded: chain 20 residue 39 LEU Chi-restraints excluded: chain 20 residue 51 VAL Chi-restraints excluded: chain 20 residue 58 VAL Chi-restraints excluded: chain 20 residue 74 ILE Chi-restraints excluded: chain 21 residue 77 ASP Chi-restraints excluded: chain 22 residue 2 ILE Chi-restraints excluded: chain 22 residue 54 GLU Chi-restraints excluded: chain 22 residue 59 ASN Chi-restraints excluded: chain 23 residue 27 VAL Chi-restraints excluded: chain 23 residue 29 SER Chi-restraints excluded: chain 23 residue 88 ASP Chi-restraints excluded: chain 24 residue 64 VAL Chi-restraints excluded: chain 24 residue 65 VAL Chi-restraints excluded: chain 24 residue 66 ASP Chi-restraints excluded: chain 24 residue 86 LEU Chi-restraints excluded: chain 24 residue 92 VAL Chi-restraints excluded: chain 25 residue 17 LEU Chi-restraints excluded: chain 26 residue 3 VAL Chi-restraints excluded: chain 26 residue 12 VAL Chi-restraints excluded: chain 26 residue 19 HIS Chi-restraints excluded: chain 26 residue 22 ASN Chi-restraints excluded: chain 26 residue 33 HIS Chi-restraints excluded: chain 26 residue 39 VAL Chi-restraints excluded: chain 26 residue 57 VAL Chi-restraints excluded: chain 28 residue 48 ASN Chi-restraints excluded: chain 29 residue 18 CYS Chi-restraints excluded: chain 30 residue 38 LEU Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 33 residue 25 HIS Chi-restraints excluded: chain B residue 14 HIS Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 21 TYR Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 120 HIS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain F residue 24 ARG Chi-restraints excluded: chain F residue 44 ARG Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 138 GLU Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 21 LYS Chi-restraints excluded: chain I residue 32 ARG Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 38 PHE Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 44 ARG Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 75 ASP Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 43 LYS Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 81 ILE Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain N residue 37 ASP Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain O residue 1 SER Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain U residue 9 GLU Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 36 PHE Chi-restraints excluded: chain U residue 41 THR Chi-restraints excluded: chain 03 residue 29 LEU Chi-restraints excluded: chain 03 residue 35 THR Chi-restraints excluded: chain 03 residue 209 ILE Chi-restraints excluded: chain Z residue 13 ASN Chi-restraints excluded: chain Z residue 14 VAL Chi-restraints excluded: chain Z residue 125 VAL Chi-restraints excluded: chain Z residue 148 LEU Chi-restraints excluded: chain Z residue 191 LEU Chi-restraints excluded: chain Z residue 238 VAL Chi-restraints excluded: chain Z residue 255 CYS Chi-restraints excluded: chain Z residue 266 ASP Chi-restraints excluded: chain Z residue 292 LEU Chi-restraints excluded: chain Z residue 326 TYR Chi-restraints excluded: chain Z residue 334 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1101 random chunks: chunk 886 optimal weight: 30.0000 chunk 604 optimal weight: 30.0000 chunk 15 optimal weight: 2.9990 chunk 792 optimal weight: 30.0000 chunk 439 optimal weight: 10.0000 chunk 908 optimal weight: 20.0000 chunk 735 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 543 optimal weight: 9.9990 chunk 955 optimal weight: 50.0000 chunk 268 optimal weight: 8.9990 overall best weight: 10.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 04 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 05 126 ASN 06 94 GLN ** 08 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 72 ASN ** 08 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 89 ASN 15 17 ASN 15 22 GLN ** 15 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 22 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 24 51 GLN ** 25 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 26 19 HIS 32 6 GLN ** 33 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 34 13 ASN ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 GLN ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 21 HIS ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 61 GLN ** R 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 03 57 GLN ** Z 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 166847 Z= 0.314 Angle : 0.726 11.762 249116 Z= 0.373 Chirality : 0.040 0.392 31787 Planarity : 0.006 0.062 13716 Dihedral : 23.858 177.428 82310 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 29.02 Ramachandran Plot: Outliers : 0.20 % Allowed : 13.10 % Favored : 86.69 % Rotamer: Outliers : 6.81 % Allowed : 21.32 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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: -3.10 (0.10), residues: 6366 helix: -1.24 (0.11), residues: 1954 sheet: -2.50 (0.14), residues: 1108 loop : -2.42 (0.11), residues: 3304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 200 HIS 0.028 0.002 HIS26 19 PHE 0.041 0.002 PHE21 75 TYR 0.032 0.002 TYR07 142 ARG 0.013 0.001 ARG M 69 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12732 Ramachandran restraints generated. 6366 Oldfield, 0 Emsley, 6366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12732 Ramachandran restraints generated. 6366 Oldfield, 0 Emsley, 6366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1245 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 360 poor density : 885 time to evaluate : 6.822 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: 04 145 MET cc_start: 0.8954 (mmm) cc_final: 0.8743 (mmm) REVERT: 04 250 GLN cc_start: 0.9084 (tp40) cc_final: 0.8527 (tm-30) REVERT: 05 42 ASN cc_start: 0.8112 (t0) cc_final: 0.7809 (t0) REVERT: 05 128 ARG cc_start: 0.7619 (tmt170) cc_final: 0.7114 (tmt170) REVERT: 05 185 ASN cc_start: 0.8877 (t0) cc_final: 0.8582 (t0) REVERT: 06 100 MET cc_start: 0.8740 (mmm) cc_final: 0.8392 (mmm) REVERT: 07 16 MET cc_start: 0.7749 (mmt) cc_final: 0.7189 (mmt) REVERT: 07 31 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7878 (tm-30) REVERT: 07 59 ILE cc_start: 0.8772 (mt) cc_final: 0.8571 (mm) REVERT: 07 86 CYS cc_start: 0.7700 (p) cc_final: 0.7105 (p) REVERT: 07 133 GLU cc_start: 0.7152 (mp0) cc_final: 0.6515 (pm20) REVERT: 09 1 MET cc_start: 0.8508 (mmm) cc_final: 0.8244 (mpp) REVERT: 09 89 LYS cc_start: 0.7787 (mmtm) cc_final: 0.6960 (tmtt) REVERT: 10 1 MET cc_start: 0.7901 (tpt) cc_final: 0.6534 (ptp) REVERT: 10 86 MET cc_start: 0.2891 (OUTLIER) cc_final: 0.2049 (ttt) REVERT: 11 107 GLU cc_start: 0.8403 (mt-10) cc_final: 0.7883 (tt0) REVERT: 11 116 MET cc_start: 0.0851 (mmt) cc_final: 0.0230 (mmt) REVERT: 12 16 TYR cc_start: 0.8808 (m-80) cc_final: 0.8458 (m-10) REVERT: 12 36 LEU cc_start: 0.8763 (mm) cc_final: 0.8333 (mm) REVERT: 12 52 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.6840 (t0) REVERT: 12 60 ASP cc_start: 0.8799 (p0) cc_final: 0.8479 (p0) REVERT: 13 20 MET cc_start: 0.9336 (ttp) cc_final: 0.9018 (tpp) REVERT: 13 44 LYS cc_start: 0.8767 (mmmt) cc_final: 0.8509 (tppt) REVERT: 13 67 LYS cc_start: 0.8162 (tptt) cc_final: 0.7348 (tppt) REVERT: 13 93 GLN cc_start: 0.9369 (mp10) cc_final: 0.8957 (mp10) REVERT: 13 100 PHE cc_start: 0.8852 (m-80) cc_final: 0.8551 (m-80) REVERT: 14 100 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8741 (mm) REVERT: 16 20 MET cc_start: 0.8721 (ptm) cc_final: 0.8194 (ptp) REVERT: 16 24 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8368 (tpp) REVERT: 16 47 VAL cc_start: 0.8721 (OUTLIER) cc_final: 0.8431 (p) REVERT: 17 67 ASN cc_start: 0.8239 (OUTLIER) cc_final: 0.7921 (p0) REVERT: 18 73 PHE cc_start: 0.8126 (m-80) cc_final: 0.7910 (m-80) REVERT: 20 77 PHE cc_start: 0.8861 (t80) cc_final: 0.8524 (t80) REVERT: 20 83 TYR cc_start: 0.7682 (t80) cc_final: 0.7380 (t80) REVERT: 22 24 MET cc_start: 0.9105 (tpt) cc_final: 0.8815 (tpp) REVERT: 22 87 LEU cc_start: 0.8931 (mt) cc_final: 0.8555 (pp) REVERT: 23 43 LYS cc_start: 0.8456 (tttp) cc_final: 0.8253 (tppt) REVERT: 25 68 LYS cc_start: 0.8452 (mtpt) cc_final: 0.8058 (mttm) REVERT: 27 5 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8010 (mm-30) REVERT: 28 43 ILE cc_start: 0.9211 (mm) cc_final: 0.8988 (mm) REVERT: 29 22 MET cc_start: 0.8486 (tmm) cc_final: 0.8174 (tmm) REVERT: 30 14 MET cc_start: 0.8772 (mtm) cc_final: 0.8543 (mtp) REVERT: 30 36 LYS cc_start: 0.9009 (mmmm) cc_final: 0.8596 (mmmt) REVERT: 33 25 HIS cc_start: 0.8335 (OUTLIER) cc_final: 0.7904 (m170) REVERT: 34 18 LYS cc_start: 0.8761 (tttm) cc_final: 0.8309 (ttmt) REVERT: 34 37 GLN cc_start: 0.8696 (tp-100) cc_final: 0.8060 (tt0) REVERT: B 30 ILE cc_start: 0.8916 (OUTLIER) cc_final: 0.8255 (tp) REVERT: B 157 PRO cc_start: 0.8766 (Cg_endo) cc_final: 0.8532 (Cg_exo) REVERT: C 24 ASN cc_start: 0.9316 (t0) cc_final: 0.9062 (t0) REVERT: C 102 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8738 (tt) REVERT: C 138 GLN cc_start: 0.9229 (mt0) cc_final: 0.8953 (mm-40) REVERT: D 46 ARG cc_start: 0.8707 (tpp-160) cc_final: 0.8173 (tpt90) REVERT: D 68 GLU cc_start: 0.8479 (tp30) cc_final: 0.8122 (tp30) REVERT: D 104 MET cc_start: 0.8686 (mmt) cc_final: 0.8136 (mmt) REVERT: D 168 THR cc_start: 0.9263 (OUTLIER) cc_final: 0.8690 (p) REVERT: D 189 ASP cc_start: 0.7997 (m-30) cc_final: 0.7513 (m-30) REVERT: F 1 MET cc_start: 0.8081 (ttm) cc_final: 0.7872 (ttm) REVERT: F 11 HIS cc_start: 0.8340 (t70) cc_final: 0.8046 (t70) REVERT: F 21 MET cc_start: 0.8753 (mtm) cc_final: 0.8327 (mpp) REVERT: F 49 TYR cc_start: 0.8054 (p90) cc_final: 0.7833 (p90) REVERT: F 69 GLU cc_start: 0.8744 (mp0) cc_final: 0.8353 (pm20) REVERT: F 73 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8216 (mt-10) REVERT: F 88 MET cc_start: 0.7457 (tmm) cc_final: 0.6685 (tmm) REVERT: G 139 ASP cc_start: 0.9349 (m-30) cc_final: 0.8647 (t0) REVERT: G 143 MET cc_start: 0.8941 (mmp) cc_final: 0.8729 (mmp) REVERT: I 45 MET cc_start: 0.6410 (ppp) cc_final: 0.6077 (ppp) REVERT: J 88 MET cc_start: 0.8649 (mmm) cc_final: 0.8392 (ptm) REVERT: J 89 ARG cc_start: 0.8529 (ptt-90) cc_final: 0.8155 (ptt-90) REVERT: K 76 TYR cc_start: 0.8407 (m-80) cc_final: 0.7746 (m-80) REVERT: K 84 MET cc_start: 0.8478 (ppp) cc_final: 0.8188 (pmm) REVERT: K 111 ASP cc_start: 0.8562 (t70) cc_final: 0.7988 (t0) REVERT: L 13 ARG cc_start: 0.7922 (mpt180) cc_final: 0.7386 (mpt180) REVERT: L 75 GLU cc_start: 0.8708 (tp30) cc_final: 0.8418 (tp30) REVERT: L 102 ASP cc_start: 0.9058 (m-30) cc_final: 0.8738 (m-30) REVERT: O 61 GLN cc_start: 0.9301 (pt0) cc_final: 0.8833 (mm-40) REVERT: S 11 ASP cc_start: 0.7782 (t0) cc_final: 0.7465 (p0) REVERT: U 4 LYS cc_start: 0.7574 (ttpp) cc_final: 0.5143 (mtmm) REVERT: U 9 GLU cc_start: 0.6406 (OUTLIER) cc_final: 0.5969 (tp30) REVERT: Z 86 ASP cc_start: 0.8698 (OUTLIER) cc_final: 0.8294 (t0) REVERT: Z 98 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7744 (ttp) REVERT: Z 114 GLN cc_start: 0.3305 (tp40) cc_final: 0.2653 (tm-30) REVERT: Z 124 GLN cc_start: 0.5876 (mm110) cc_final: 0.5348 (mm-40) REVERT: Z 237 LYS cc_start: 0.5660 (OUTLIER) cc_final: 0.5456 (pmmt) REVERT: Z 260 MET cc_start: 0.7660 (mmt) cc_final: 0.7225 (tpp) REVERT: Y 101 LYS cc_start: 0.7272 (tppt) cc_final: 0.7072 (tptm) outliers start: 360 outliers final: 263 residues processed: 1124 average time/residue: 1.3028 time to fit residues: 2575.0822 Evaluate side-chains 1106 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 277 poor density : 829 time to evaluate : 6.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 15 VAL Chi-restraints excluded: chain 04 residue 59 GLN Chi-restraints excluded: chain 04 residue 89 ASN Chi-restraints excluded: chain 04 residue 129 LEU Chi-restraints excluded: chain 04 residue 134 ILE Chi-restraints excluded: chain 04 residue 167 ASP Chi-restraints excluded: chain 04 residue 219 VAL Chi-restraints excluded: chain 04 residue 222 THR Chi-restraints excluded: chain 04 residue 258 SER Chi-restraints excluded: chain 04 residue 263 ASP Chi-restraints excluded: chain 04 residue 267 VAL Chi-restraints excluded: chain 04 residue 271 SER Chi-restraints excluded: chain 05 residue 9 VAL Chi-restraints excluded: chain 05 residue 11 MET Chi-restraints excluded: chain 05 residue 22 ILE Chi-restraints excluded: chain 05 residue 27 ILE Chi-restraints excluded: chain 05 residue 104 VAL Chi-restraints excluded: chain 05 residue 176 ASP Chi-restraints excluded: chain 06 residue 19 PHE Chi-restraints excluded: chain 06 residue 116 ASP Chi-restraints excluded: chain 07 residue 17 THR Chi-restraints excluded: chain 07 residue 30 VAL Chi-restraints excluded: chain 07 residue 39 VAL Chi-restraints excluded: chain 07 residue 89 THR Chi-restraints excluded: chain 07 residue 95 MET Chi-restraints excluded: chain 07 residue 140 ILE Chi-restraints excluded: chain 07 residue 148 VAL Chi-restraints excluded: chain 07 residue 169 LEU Chi-restraints excluded: chain 08 residue 10 VAL Chi-restraints excluded: chain 08 residue 19 ASN Chi-restraints excluded: chain 08 residue 46 ASP Chi-restraints excluded: chain 08 residue 88 LEU Chi-restraints excluded: chain 08 residue 167 VAL Chi-restraints excluded: chain 09 residue 110 VAL Chi-restraints excluded: chain 10 residue 5 LEU Chi-restraints excluded: chain 10 residue 27 VAL Chi-restraints excluded: chain 10 residue 34 THR Chi-restraints excluded: chain 10 residue 74 ASP Chi-restraints excluded: chain 10 residue 86 MET Chi-restraints excluded: chain 10 residue 118 ILE Chi-restraints excluded: chain 11 residue 48 ILE Chi-restraints excluded: chain 11 residue 59 THR Chi-restraints excluded: chain 11 residue 77 VAL Chi-restraints excluded: chain 11 residue 85 ILE Chi-restraints excluded: chain 11 residue 97 VAL Chi-restraints excluded: chain 11 residue 138 VAL Chi-restraints excluded: chain 12 residue 14 ASP Chi-restraints excluded: chain 12 residue 52 ASP Chi-restraints excluded: chain 12 residue 81 ILE Chi-restraints excluded: chain 12 residue 84 ILE Chi-restraints excluded: chain 12 residue 93 ILE Chi-restraints excluded: chain 12 residue 118 MET Chi-restraints excluded: chain 13 residue 8 LEU Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 54 LYS Chi-restraints excluded: chain 13 residue 57 VAL Chi-restraints excluded: chain 13 residue 61 VAL Chi-restraints excluded: chain 13 residue 86 LEU Chi-restraints excluded: chain 13 residue 88 ASN Chi-restraints excluded: chain 13 residue 90 ASN Chi-restraints excluded: chain 13 residue 97 THR Chi-restraints excluded: chain 13 residue 104 THR Chi-restraints excluded: chain 14 residue 67 THR Chi-restraints excluded: chain 14 residue 82 LEU Chi-restraints excluded: chain 14 residue 100 ILE Chi-restraints excluded: chain 15 residue 22 GLN Chi-restraints excluded: chain 15 residue 54 THR Chi-restraints excluded: chain 15 residue 65 ILE Chi-restraints excluded: chain 15 residue 70 ASP Chi-restraints excluded: chain 15 residue 91 TYR Chi-restraints excluded: chain 15 residue 126 ILE Chi-restraints excluded: chain 15 residue 136 MET Chi-restraints excluded: chain 16 residue 11 ASN Chi-restraints excluded: chain 16 residue 24 MET Chi-restraints excluded: chain 16 residue 34 ILE Chi-restraints excluded: chain 16 residue 37 THR Chi-restraints excluded: chain 16 residue 47 VAL Chi-restraints excluded: chain 16 residue 57 THR Chi-restraints excluded: chain 16 residue 97 ILE Chi-restraints excluded: chain 17 residue 5 SER Chi-restraints excluded: chain 17 residue 27 VAL Chi-restraints excluded: chain 17 residue 28 VAL Chi-restraints excluded: chain 17 residue 65 THR Chi-restraints excluded: chain 17 residue 67 ASN Chi-restraints excluded: chain 17 residue 69 ASP Chi-restraints excluded: chain 17 residue 78 VAL Chi-restraints excluded: chain 17 residue 106 LEU Chi-restraints excluded: chain 18 residue 8 GLU Chi-restraints excluded: chain 18 residue 15 ASP Chi-restraints excluded: chain 18 residue 25 VAL Chi-restraints excluded: chain 18 residue 31 VAL Chi-restraints excluded: chain 18 residue 39 LEU Chi-restraints excluded: chain 18 residue 63 ILE Chi-restraints excluded: chain 18 residue 113 LEU Chi-restraints excluded: chain 19 residue 33 VAL Chi-restraints excluded: chain 19 residue 43 GLN Chi-restraints excluded: chain 20 residue 22 LEU Chi-restraints excluded: chain 20 residue 35 PHE Chi-restraints excluded: chain 20 residue 39 LEU Chi-restraints excluded: chain 20 residue 51 VAL Chi-restraints excluded: chain 20 residue 58 VAL Chi-restraints excluded: chain 20 residue 74 ILE Chi-restraints excluded: chain 20 residue 82 HIS Chi-restraints excluded: chain 21 residue 20 VAL Chi-restraints excluded: chain 21 residue 68 ASP Chi-restraints excluded: chain 21 residue 77 ASP Chi-restraints excluded: chain 22 residue 2 ILE Chi-restraints excluded: chain 22 residue 54 GLU Chi-restraints excluded: chain 22 residue 59 ASN Chi-restraints excluded: chain 23 residue 17 ASP Chi-restraints excluded: chain 23 residue 27 VAL Chi-restraints excluded: chain 23 residue 29 SER Chi-restraints excluded: chain 23 residue 48 VAL Chi-restraints excluded: chain 23 residue 88 ASP Chi-restraints excluded: chain 24 residue 64 VAL Chi-restraints excluded: chain 24 residue 65 VAL Chi-restraints excluded: chain 24 residue 66 ASP Chi-restraints excluded: chain 24 residue 86 LEU Chi-restraints excluded: chain 24 residue 92 VAL Chi-restraints excluded: chain 25 residue 26 SER Chi-restraints excluded: chain 25 residue 34 VAL Chi-restraints excluded: chain 26 residue 12 VAL Chi-restraints excluded: chain 26 residue 22 ASN Chi-restraints excluded: chain 26 residue 33 HIS Chi-restraints excluded: chain 26 residue 39 VAL Chi-restraints excluded: chain 26 residue 57 VAL Chi-restraints excluded: chain 28 residue 24 LEU Chi-restraints excluded: chain 28 residue 40 THR Chi-restraints excluded: chain 28 residue 48 ASN Chi-restraints excluded: chain 29 residue 18 CYS Chi-restraints excluded: chain 29 residue 33 ASN Chi-restraints excluded: chain 30 residue 38 LEU Chi-restraints excluded: chain 31 residue 8 ILE Chi-restraints excluded: chain 31 residue 16 THR Chi-restraints excluded: chain 32 residue 31 LEU Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 33 residue 25 HIS Chi-restraints excluded: chain 33 residue 58 ILE Chi-restraints excluded: chain B residue 14 HIS Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 21 TYR Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 120 HIS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 44 ARG Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 138 GLU Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 126 CYS Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 21 LYS Chi-restraints excluded: chain I residue 32 ARG Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 38 PHE Chi-restraints excluded: chain I residue 44 ARG Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 64 GLN Chi-restraints excluded: chain J residue 75 ASP Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 43 LYS Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 81 ILE Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 67 ASP Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain N residue 10 VAL Chi-restraints excluded: chain N residue 11 LYS Chi-restraints excluded: chain N residue 37 ASP Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain O residue 1 SER Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 36 ASN Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 43 LEU Chi-restraints excluded: chain Q residue 54 ILE Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 63 CYS Chi-restraints excluded: chain Q residue 69 THR Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 65 MET Chi-restraints excluded: chain U residue 9 GLU Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 36 PHE Chi-restraints excluded: chain U residue 41 THR Chi-restraints excluded: chain 03 residue 29 LEU Chi-restraints excluded: chain 03 residue 35 THR Chi-restraints excluded: chain 03 residue 209 ILE Chi-restraints excluded: chain Z residue 13 ASN Chi-restraints excluded: chain Z residue 14 VAL Chi-restraints excluded: chain Z residue 25 THR Chi-restraints excluded: chain Z residue 86 ASP Chi-restraints excluded: chain Z residue 98 MET Chi-restraints excluded: chain Z residue 125 VAL Chi-restraints excluded: chain Z residue 148 LEU Chi-restraints excluded: chain Z residue 165 ASP Chi-restraints excluded: chain Z residue 191 LEU Chi-restraints excluded: chain Z residue 235 ILE Chi-restraints excluded: chain Z residue 237 LYS Chi-restraints excluded: chain Z residue 238 VAL Chi-restraints excluded: chain Z residue 244 ILE Chi-restraints excluded: chain Z residue 250 THR Chi-restraints excluded: chain Z residue 255 CYS Chi-restraints excluded: chain Z residue 266 ASP Chi-restraints excluded: chain Z residue 292 LEU Chi-restraints excluded: chain Z residue 326 TYR Chi-restraints excluded: chain Z residue 334 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1101 random chunks: chunk 358 optimal weight: 2.9990 chunk 958 optimal weight: 20.0000 chunk 210 optimal weight: 10.0000 chunk 624 optimal weight: 30.0000 chunk 262 optimal weight: 20.0000 chunk 1065 optimal weight: 4.9990 chunk 884 optimal weight: 30.0000 chunk 493 optimal weight: 8.9990 chunk 88 optimal weight: 8.9990 chunk 352 optimal weight: 1.9990 chunk 559 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: 04 85 ASN ** 04 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 72 ASN ** 08 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 09 133 GLN 12 131 ASN ** 13 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 89 ASN 15 17 ASN ** 15 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 22 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 24 88 HIS 26 16 ASN 26 19 HIS ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 ASN ** I 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 8 GLN ** R 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.4522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 166847 Z= 0.197 Angle : 0.637 12.851 249116 Z= 0.328 Chirality : 0.036 0.380 31787 Planarity : 0.005 0.078 13716 Dihedral : 23.822 176.163 82309 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 23.16 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.56 % Favored : 89.27 % Rotamer: Outliers : 5.96 % Allowed : 23.08 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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: -2.78 (0.10), residues: 6366 helix: -0.92 (0.11), residues: 1958 sheet: -2.33 (0.14), residues: 1104 loop : -2.25 (0.11), residues: 3304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 200 HIS 0.014 0.001 HIS O 45 PHE 0.034 0.002 PHE09 46 TYR 0.023 0.002 TYR U 37 ARG 0.008 0.001 ARG G 101 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12732 Ramachandran restraints generated. 6366 Oldfield, 0 Emsley, 6366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12732 Ramachandran restraints generated. 6366 Oldfield, 0 Emsley, 6366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1238 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 315 poor density : 923 time to evaluate : 6.791 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: 04 250 GLN cc_start: 0.9096 (tp40) cc_final: 0.8559 (tm-30) REVERT: 05 42 ASN cc_start: 0.8117 (t0) cc_final: 0.7786 (t0) REVERT: 05 185 ASN cc_start: 0.8835 (t0) cc_final: 0.8515 (t0) REVERT: 06 100 MET cc_start: 0.8643 (mmm) cc_final: 0.8329 (mmm) REVERT: 07 16 MET cc_start: 0.7761 (mmt) cc_final: 0.7159 (mmt) REVERT: 07 31 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7882 (tm-30) REVERT: 07 59 ILE cc_start: 0.8706 (mt) cc_final: 0.8469 (mm) REVERT: 07 86 CYS cc_start: 0.7582 (p) cc_final: 0.7019 (p) REVERT: 07 100 GLU cc_start: 0.8990 (tt0) cc_final: 0.8603 (tp30) REVERT: 07 133 GLU cc_start: 0.7204 (mp0) cc_final: 0.6545 (pm20) REVERT: 09 89 LYS cc_start: 0.7663 (mmtm) cc_final: 0.6868 (tmtt) REVERT: 10 1 MET cc_start: 0.7988 (tpt) cc_final: 0.6608 (ptp) REVERT: 10 86 MET cc_start: 0.2907 (OUTLIER) cc_final: 0.2381 (ttt) REVERT: 11 59 THR cc_start: 0.6439 (OUTLIER) cc_final: 0.6046 (p) REVERT: 11 107 GLU cc_start: 0.8401 (mt-10) cc_final: 0.7904 (tt0) REVERT: 11 116 MET cc_start: 0.0985 (mmt) cc_final: 0.0031 (mmt) REVERT: 12 16 TYR cc_start: 0.8738 (m-80) cc_final: 0.8423 (m-10) REVERT: 12 36 LEU cc_start: 0.8676 (mm) cc_final: 0.8167 (mm) REVERT: 12 52 ASP cc_start: 0.7665 (OUTLIER) cc_final: 0.6643 (t0) REVERT: 12 60 ASP cc_start: 0.8743 (p0) cc_final: 0.8450 (p0) REVERT: 13 20 MET cc_start: 0.9336 (ttp) cc_final: 0.8997 (tpp) REVERT: 13 44 LYS cc_start: 0.8780 (mmmt) cc_final: 0.8519 (tppt) REVERT: 13 67 LYS cc_start: 0.8000 (tptt) cc_final: 0.7115 (tppt) REVERT: 13 93 GLN cc_start: 0.9321 (mp10) cc_final: 0.8900 (mp10) REVERT: 13 100 PHE cc_start: 0.8797 (m-80) cc_final: 0.8543 (m-80) REVERT: 14 100 ILE cc_start: 0.8871 (pt) cc_final: 0.8607 (mm) REVERT: 16 20 MET cc_start: 0.8694 (ptm) cc_final: 0.8196 (ptp) REVERT: 16 47 VAL cc_start: 0.8727 (t) cc_final: 0.8456 (p) REVERT: 16 110 MET cc_start: 0.8550 (mmm) cc_final: 0.8036 (mmm) REVERT: 17 67 ASN cc_start: 0.8163 (OUTLIER) cc_final: 0.7806 (p0) REVERT: 19 51 GLN cc_start: 0.9128 (mt0) cc_final: 0.8261 (mt0) REVERT: 20 77 PHE cc_start: 0.8844 (t80) cc_final: 0.8569 (t80) REVERT: 22 1 MET cc_start: 0.8001 (pmm) cc_final: 0.7241 (ppp) REVERT: 22 24 MET cc_start: 0.9081 (tpt) cc_final: 0.8751 (tpp) REVERT: 22 87 LEU cc_start: 0.8938 (mt) cc_final: 0.8586 (pp) REVERT: 25 68 LYS cc_start: 0.8404 (mtpt) cc_final: 0.8066 (mttm) REVERT: 27 5 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8056 (mm-30) REVERT: 27 49 ASP cc_start: 0.9079 (m-30) cc_final: 0.8782 (p0) REVERT: 28 43 ILE cc_start: 0.9163 (mm) cc_final: 0.8951 (mm) REVERT: 29 22 MET cc_start: 0.8465 (tmm) cc_final: 0.8202 (tmm) REVERT: 30 11 LYS cc_start: 0.9102 (tptm) cc_final: 0.8700 (tptt) REVERT: 30 14 MET cc_start: 0.8706 (mtm) cc_final: 0.8390 (mtm) REVERT: 30 36 LYS cc_start: 0.8980 (mmmm) cc_final: 0.8626 (mmmt) REVERT: 31 27 ARG cc_start: 0.9427 (tpt90) cc_final: 0.8989 (tpt170) REVERT: 33 25 HIS cc_start: 0.8267 (OUTLIER) cc_final: 0.7881 (m170) REVERT: 34 18 LYS cc_start: 0.8733 (tttm) cc_final: 0.8267 (ttmt) REVERT: 34 37 GLN cc_start: 0.8517 (tp-100) cc_final: 0.8036 (tt0) REVERT: B 26 MET cc_start: 0.7708 (mtp) cc_final: 0.7437 (mtt) REVERT: B 30 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8213 (tp) REVERT: B 157 PRO cc_start: 0.8776 (Cg_endo) cc_final: 0.8559 (Cg_exo) REVERT: C 24 ASN cc_start: 0.9192 (t0) cc_final: 0.8965 (t0) REVERT: C 36 PHE cc_start: 0.9396 (t80) cc_final: 0.8935 (t80) REVERT: C 102 ILE cc_start: 0.9136 (OUTLIER) cc_final: 0.8729 (tt) REVERT: C 138 GLN cc_start: 0.9218 (mt0) cc_final: 0.8936 (mm-40) REVERT: D 19 PHE cc_start: 0.8756 (m-80) cc_final: 0.8415 (m-10) REVERT: D 46 ARG cc_start: 0.8703 (tpp-160) cc_final: 0.8153 (tpt90) REVERT: D 68 GLU cc_start: 0.8486 (tp30) cc_final: 0.8130 (tp30) REVERT: D 74 TYR cc_start: 0.7844 (m-80) cc_final: 0.7583 (t80) REVERT: D 104 MET cc_start: 0.8622 (mmt) cc_final: 0.8170 (mmt) REVERT: D 168 THR cc_start: 0.9226 (OUTLIER) cc_final: 0.8674 (p) REVERT: D 189 ASP cc_start: 0.7907 (m-30) cc_final: 0.7416 (m-30) REVERT: E 9 GLU cc_start: 0.7411 (pm20) cc_final: 0.6586 (tt0) REVERT: F 11 HIS cc_start: 0.8172 (t70) cc_final: 0.7786 (t70) REVERT: F 21 MET cc_start: 0.8737 (mtm) cc_final: 0.8275 (mpp) REVERT: F 69 GLU cc_start: 0.8750 (mp0) cc_final: 0.8375 (pm20) REVERT: F 73 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8036 (mt-10) REVERT: F 88 MET cc_start: 0.7309 (tmm) cc_final: 0.6783 (tmm) REVERT: G 139 ASP cc_start: 0.9306 (m-30) cc_final: 0.8620 (t0) REVERT: I 45 MET cc_start: 0.6334 (ppp) cc_final: 0.6080 (ppp) REVERT: J 49 PHE cc_start: 0.7416 (m-80) cc_final: 0.7102 (m-80) REVERT: J 88 MET cc_start: 0.8569 (mmm) cc_final: 0.8233 (ptm) REVERT: J 89 ARG cc_start: 0.8465 (ptt-90) cc_final: 0.8142 (ptt-90) REVERT: K 76 TYR cc_start: 0.8385 (m-80) cc_final: 0.7681 (m-80) REVERT: K 111 ASP cc_start: 0.8484 (t70) cc_final: 0.8006 (t0) REVERT: L 13 ARG cc_start: 0.7924 (mpt180) cc_final: 0.7410 (mpt180) REVERT: L 75 GLU cc_start: 0.8582 (tp30) cc_final: 0.8320 (tp30) REVERT: M 62 PHE cc_start: 0.7546 (t80) cc_final: 0.7249 (m-80) REVERT: O 25 GLU cc_start: 0.8287 (pm20) cc_final: 0.7996 (pm20) REVERT: O 46 LYS cc_start: 0.9187 (mmmt) cc_final: 0.8961 (tppt) REVERT: O 61 GLN cc_start: 0.9279 (pt0) cc_final: 0.8794 (mm110) REVERT: U 4 LYS cc_start: 0.7463 (ttpp) cc_final: 0.5098 (mttp) REVERT: U 9 GLU cc_start: 0.6309 (OUTLIER) cc_final: 0.5698 (tp30) REVERT: Z 84 HIS cc_start: 0.7417 (OUTLIER) cc_final: 0.6994 (t70) REVERT: Z 86 ASP cc_start: 0.8600 (OUTLIER) cc_final: 0.8003 (t70) REVERT: Z 98 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7891 (ttp) REVERT: Z 114 GLN cc_start: 0.3374 (tp40) cc_final: 0.2765 (tm-30) REVERT: Z 124 GLN cc_start: 0.5695 (mm110) cc_final: 0.5202 (mm-40) REVERT: Z 130 ILE cc_start: 0.6505 (OUTLIER) cc_final: 0.6277 (mt) REVERT: Z 237 LYS cc_start: 0.5719 (OUTLIER) cc_final: 0.5464 (pmmt) REVERT: Z 260 MET cc_start: 0.7448 (OUTLIER) cc_final: 0.7021 (tpp) REVERT: Y 101 LYS cc_start: 0.7108 (tppt) cc_final: 0.6813 (tptm) outliers start: 315 outliers final: 235 residues processed: 1116 average time/residue: 1.2586 time to fit residues: 2475.6141 Evaluate side-chains 1102 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 852 time to evaluate : 6.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 59 GLN Chi-restraints excluded: chain 04 residue 66 PHE Chi-restraints excluded: chain 04 residue 89 ASN Chi-restraints excluded: chain 04 residue 129 LEU Chi-restraints excluded: chain 04 residue 167 ASP Chi-restraints excluded: chain 04 residue 219 VAL Chi-restraints excluded: chain 04 residue 239 PHE Chi-restraints excluded: chain 04 residue 258 SER Chi-restraints excluded: chain 04 residue 263 ASP Chi-restraints excluded: chain 04 residue 267 VAL Chi-restraints excluded: chain 04 residue 271 SER Chi-restraints excluded: chain 05 residue 1 MET Chi-restraints excluded: chain 05 residue 9 VAL Chi-restraints excluded: chain 05 residue 11 MET Chi-restraints excluded: chain 05 residue 22 ILE Chi-restraints excluded: chain 05 residue 27 ILE Chi-restraints excluded: chain 05 residue 104 VAL Chi-restraints excluded: chain 05 residue 181 ASP Chi-restraints excluded: chain 06 residue 19 PHE Chi-restraints excluded: chain 06 residue 77 ILE Chi-restraints excluded: chain 06 residue 146 VAL Chi-restraints excluded: chain 07 residue 17 THR Chi-restraints excluded: chain 07 residue 30 VAL Chi-restraints excluded: chain 07 residue 95 MET Chi-restraints excluded: chain 07 residue 140 ILE Chi-restraints excluded: chain 07 residue 141 ASP Chi-restraints excluded: chain 07 residue 146 ASP Chi-restraints excluded: chain 07 residue 148 VAL Chi-restraints excluded: chain 07 residue 169 LEU Chi-restraints excluded: chain 08 residue 10 VAL Chi-restraints excluded: chain 08 residue 19 ASN Chi-restraints excluded: chain 08 residue 46 ASP Chi-restraints excluded: chain 08 residue 88 LEU Chi-restraints excluded: chain 08 residue 121 THR Chi-restraints excluded: chain 08 residue 167 VAL Chi-restraints excluded: chain 09 residue 110 VAL Chi-restraints excluded: chain 10 residue 5 LEU Chi-restraints excluded: chain 10 residue 27 VAL Chi-restraints excluded: chain 10 residue 74 ASP Chi-restraints excluded: chain 10 residue 86 MET Chi-restraints excluded: chain 10 residue 118 ILE Chi-restraints excluded: chain 11 residue 48 ILE Chi-restraints excluded: chain 11 residue 59 THR Chi-restraints excluded: chain 11 residue 77 VAL Chi-restraints excluded: chain 11 residue 85 ILE Chi-restraints excluded: chain 11 residue 97 VAL Chi-restraints excluded: chain 11 residue 104 GLN Chi-restraints excluded: chain 11 residue 138 VAL Chi-restraints excluded: chain 12 residue 52 ASP Chi-restraints excluded: chain 12 residue 81 ILE Chi-restraints excluded: chain 12 residue 84 ILE Chi-restraints excluded: chain 12 residue 105 VAL Chi-restraints excluded: chain 12 residue 122 LEU Chi-restraints excluded: chain 12 residue 131 ASN Chi-restraints excluded: chain 13 residue 32 TYR Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 54 LYS Chi-restraints excluded: chain 13 residue 57 VAL Chi-restraints excluded: chain 13 residue 61 VAL Chi-restraints excluded: chain 13 residue 86 LEU Chi-restraints excluded: chain 13 residue 90 ASN Chi-restraints excluded: chain 14 residue 67 THR Chi-restraints excluded: chain 14 residue 82 LEU Chi-restraints excluded: chain 14 residue 110 VAL Chi-restraints excluded: chain 15 residue 24 THR Chi-restraints excluded: chain 15 residue 42 THR Chi-restraints excluded: chain 15 residue 54 THR Chi-restraints excluded: chain 15 residue 70 ASP Chi-restraints excluded: chain 15 residue 102 LEU Chi-restraints excluded: chain 15 residue 136 MET Chi-restraints excluded: chain 16 residue 11 ASN Chi-restraints excluded: chain 16 residue 34 ILE Chi-restraints excluded: chain 16 residue 37 THR Chi-restraints excluded: chain 16 residue 57 THR Chi-restraints excluded: chain 16 residue 97 ILE Chi-restraints excluded: chain 17 residue 5 SER Chi-restraints excluded: chain 17 residue 18 LEU Chi-restraints excluded: chain 17 residue 27 VAL Chi-restraints excluded: chain 17 residue 28 VAL Chi-restraints excluded: chain 17 residue 67 ASN Chi-restraints excluded: chain 17 residue 69 ASP Chi-restraints excluded: chain 17 residue 78 VAL Chi-restraints excluded: chain 18 residue 15 ASP Chi-restraints excluded: chain 18 residue 31 VAL Chi-restraints excluded: chain 18 residue 39 LEU Chi-restraints excluded: chain 18 residue 62 LYS Chi-restraints excluded: chain 18 residue 63 ILE Chi-restraints excluded: chain 18 residue 113 LEU Chi-restraints excluded: chain 19 residue 33 VAL Chi-restraints excluded: chain 20 residue 39 LEU Chi-restraints excluded: chain 20 residue 51 VAL Chi-restraints excluded: chain 20 residue 58 VAL Chi-restraints excluded: chain 20 residue 74 ILE Chi-restraints excluded: chain 20 residue 82 HIS Chi-restraints excluded: chain 21 residue 68 ASP Chi-restraints excluded: chain 21 residue 77 ASP Chi-restraints excluded: chain 22 residue 2 ILE Chi-restraints excluded: chain 22 residue 54 GLU Chi-restraints excluded: chain 22 residue 59 ASN Chi-restraints excluded: chain 23 residue 17 ASP Chi-restraints excluded: chain 23 residue 27 VAL Chi-restraints excluded: chain 23 residue 29 SER Chi-restraints excluded: chain 23 residue 48 VAL Chi-restraints excluded: chain 23 residue 88 ASP Chi-restraints excluded: chain 24 residue 20 LEU Chi-restraints excluded: chain 24 residue 64 VAL Chi-restraints excluded: chain 24 residue 66 ASP Chi-restraints excluded: chain 24 residue 86 LEU Chi-restraints excluded: chain 24 residue 92 VAL Chi-restraints excluded: chain 25 residue 17 LEU Chi-restraints excluded: chain 25 residue 34 VAL Chi-restraints excluded: chain 26 residue 12 VAL Chi-restraints excluded: chain 26 residue 19 HIS Chi-restraints excluded: chain 26 residue 22 ASN Chi-restraints excluded: chain 26 residue 33 HIS Chi-restraints excluded: chain 26 residue 39 VAL Chi-restraints excluded: chain 26 residue 63 ILE Chi-restraints excluded: chain 28 residue 18 LYS Chi-restraints excluded: chain 28 residue 24 LEU Chi-restraints excluded: chain 29 residue 18 CYS Chi-restraints excluded: chain 30 residue 38 LEU Chi-restraints excluded: chain 31 residue 8 ILE Chi-restraints excluded: chain 31 residue 16 THR Chi-restraints excluded: chain 31 residue 42 VAL Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 33 residue 25 HIS Chi-restraints excluded: chain B residue 14 HIS Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 21 TYR Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 120 HIS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 44 ARG Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 138 GLU Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 21 LYS Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 38 PHE Chi-restraints excluded: chain I residue 44 ARG Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 64 GLN Chi-restraints excluded: chain J residue 75 ASP Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 81 ILE Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain M residue 67 ASP Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain N residue 37 ASP Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain O residue 1 SER Chi-restraints excluded: chain O residue 13 GLU Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 36 ASN Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 54 ILE Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain S residue 62 THR Chi-restraints excluded: chain U residue 9 GLU Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 36 PHE Chi-restraints excluded: chain U residue 41 THR Chi-restraints excluded: chain 03 residue 29 LEU Chi-restraints excluded: chain 03 residue 35 THR Chi-restraints excluded: chain 03 residue 209 ILE Chi-restraints excluded: chain Z residue 13 ASN Chi-restraints excluded: chain Z residue 14 VAL Chi-restraints excluded: chain Z residue 25 THR Chi-restraints excluded: chain Z residue 84 HIS Chi-restraints excluded: chain Z residue 86 ASP Chi-restraints excluded: chain Z residue 98 MET Chi-restraints excluded: chain Z residue 125 VAL Chi-restraints excluded: chain Z residue 130 ILE Chi-restraints excluded: chain Z residue 148 LEU Chi-restraints excluded: chain Z residue 165 ASP Chi-restraints excluded: chain Z residue 191 LEU Chi-restraints excluded: chain Z residue 236 ILE Chi-restraints excluded: chain Z residue 237 LYS Chi-restraints excluded: chain Z residue 238 VAL Chi-restraints excluded: chain Z residue 244 ILE Chi-restraints excluded: chain Z residue 255 CYS Chi-restraints excluded: chain Z residue 260 MET Chi-restraints excluded: chain Z residue 266 ASP Chi-restraints excluded: chain Z residue 292 LEU Chi-restraints excluded: chain Z residue 326 TYR Chi-restraints excluded: chain Z residue 334 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1101 random chunks: chunk 1027 optimal weight: 30.0000 chunk 120 optimal weight: 30.0000 chunk 606 optimal weight: 30.0000 chunk 777 optimal weight: 20.0000 chunk 602 optimal weight: 30.0000 chunk 896 optimal weight: 30.0000 chunk 594 optimal weight: 30.0000 chunk 1061 optimal weight: 50.0000 chunk 664 optimal weight: 20.0000 chunk 646 optimal weight: 30.0000 chunk 489 optimal weight: 0.5980 overall best weight: 20.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 04 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 04 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 05 49 GLN ** 08 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 72 ASN ** 08 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 103 ASN ** 08 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 09 66 ASN 11 30 GLN ** 12 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 12 131 ASN ** 13 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 89 ASN 14 104 GLN ** 15 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 15 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 20 82 HIS 21 40 ASN ** 21 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 22 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 22 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 24 88 HIS ** 25 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 26 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 26 19 HIS ** 27 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 30 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 33 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 HIS ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 GLN ** E 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 8 GLN ** R 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 03 57 GLN ** Z 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.5162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.092 166847 Z= 0.556 Angle : 0.962 14.550 249116 Z= 0.481 Chirality : 0.049 0.385 31787 Planarity : 0.007 0.112 13716 Dihedral : 24.229 178.153 82309 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 42.30 Ramachandran Plot: Outliers : 0.27 % Allowed : 14.92 % Favored : 84.81 % Rotamer: Outliers : 7.34 % Allowed : 23.00 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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: -3.45 (0.10), residues: 6366 helix: -1.65 (0.10), residues: 1962 sheet: -2.50 (0.14), residues: 1079 loop : -2.63 (0.10), residues: 3325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP K 43 HIS 0.021 0.003 HIS12 132 PHE 0.033 0.003 PHE10 113 TYR 0.038 0.003 TYR E 127 ARG 0.014 0.001 ARG M 69 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12732 Ramachandran restraints generated. 6366 Oldfield, 0 Emsley, 6366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12732 Ramachandran restraints generated. 6366 Oldfield, 0 Emsley, 6366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1199 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 388 poor density : 811 time to evaluate : 6.142 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: 04 250 GLN cc_start: 0.9086 (tp40) cc_final: 0.8735 (tp40) REVERT: 05 42 ASN cc_start: 0.8286 (t0) cc_final: 0.7933 (t0) REVERT: 05 128 ARG cc_start: 0.7661 (tmt170) cc_final: 0.7120 (tmt170) REVERT: 07 16 MET cc_start: 0.7781 (mmt) cc_final: 0.7364 (mmt) REVERT: 07 86 CYS cc_start: 0.7695 (p) cc_final: 0.7083 (p) REVERT: 07 116 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8423 (mm) REVERT: 09 89 LYS cc_start: 0.7967 (mmtm) cc_final: 0.7148 (tmtt) REVERT: 10 1 MET cc_start: 0.7641 (tpt) cc_final: 0.6570 (ptp) REVERT: 10 86 MET cc_start: 0.3549 (OUTLIER) cc_final: 0.2863 (ttt) REVERT: 11 107 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7824 (tt0) REVERT: 11 116 MET cc_start: 0.1574 (mmt) cc_final: 0.0744 (mmt) REVERT: 12 16 TYR cc_start: 0.8878 (m-80) cc_final: 0.8431 (m-10) REVERT: 12 36 LEU cc_start: 0.8823 (mm) cc_final: 0.8306 (mm) REVERT: 12 52 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.6763 (t0) REVERT: 12 60 ASP cc_start: 0.8841 (p0) cc_final: 0.8449 (p0) REVERT: 13 20 MET cc_start: 0.9366 (ttp) cc_final: 0.9080 (tpp) REVERT: 13 44 LYS cc_start: 0.8961 (mmmt) cc_final: 0.8675 (tppt) REVERT: 13 67 LYS cc_start: 0.8504 (tptt) cc_final: 0.7803 (tppt) REVERT: 13 93 GLN cc_start: 0.9404 (mp10) cc_final: 0.9041 (mp10) REVERT: 13 100 PHE cc_start: 0.8867 (m-80) cc_final: 0.8528 (m-80) REVERT: 14 100 ILE cc_start: 0.9068 (pt) cc_final: 0.8748 (mm) REVERT: 16 20 MET cc_start: 0.8692 (ptm) cc_final: 0.8110 (ptp) REVERT: 16 24 MET cc_start: 0.8891 (tpp) cc_final: 0.8572 (tpp) REVERT: 19 23 TYR cc_start: 0.8234 (m-80) cc_final: 0.7967 (m-80) REVERT: 22 1 MET cc_start: 0.8075 (pmm) cc_final: 0.7245 (ppp) REVERT: 22 87 LEU cc_start: 0.8979 (mt) cc_final: 0.8694 (mt) REVERT: 24 48 MET cc_start: 0.9016 (tpp) cc_final: 0.8590 (mmm) REVERT: 25 68 LYS cc_start: 0.8474 (mtpt) cc_final: 0.7997 (mttm) REVERT: 26 16 ASN cc_start: 0.9591 (m-40) cc_final: 0.9053 (m110) REVERT: 26 21 LEU cc_start: 0.8802 (mp) cc_final: 0.8455 (tp) REVERT: 27 5 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8439 (tp30) REVERT: 29 22 MET cc_start: 0.8543 (tmm) cc_final: 0.8237 (tmm) REVERT: 30 14 MET cc_start: 0.8838 (mtm) cc_final: 0.8630 (mtp) REVERT: 33 25 HIS cc_start: 0.8497 (OUTLIER) cc_final: 0.8117 (m170) REVERT: 34 18 LYS cc_start: 0.8884 (tttm) cc_final: 0.8473 (ttmt) REVERT: 34 37 GLN cc_start: 0.8756 (tp-100) cc_final: 0.8133 (tt0) REVERT: B 48 MET cc_start: 0.8540 (pmm) cc_final: 0.8306 (pmm) REVERT: C 36 PHE cc_start: 0.9444 (t80) cc_final: 0.9189 (t80) REVERT: C 138 GLN cc_start: 0.9280 (mt0) cc_final: 0.8847 (mt0) REVERT: C 141 MET cc_start: 0.8763 (mmp) cc_final: 0.8422 (mmt) REVERT: D 46 ARG cc_start: 0.8780 (tpp-160) cc_final: 0.8208 (tpt90) REVERT: D 68 GLU cc_start: 0.8477 (tp30) cc_final: 0.8144 (tp30) REVERT: D 74 TYR cc_start: 0.8239 (m-80) cc_final: 0.7953 (t80) REVERT: D 104 MET cc_start: 0.8746 (mmt) cc_final: 0.8284 (mmt) REVERT: D 168 THR cc_start: 0.9301 (OUTLIER) cc_final: 0.8652 (p) REVERT: D 189 ASP cc_start: 0.8010 (m-30) cc_final: 0.7536 (m-30) REVERT: F 11 HIS cc_start: 0.8329 (t70) cc_final: 0.7676 (t70) REVERT: F 21 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8323 (mpp) REVERT: G 6 ILE cc_start: 0.7088 (OUTLIER) cc_final: 0.6814 (pt) REVERT: G 27 ASN cc_start: 0.9143 (m110) cc_final: 0.8885 (m110) REVERT: G 139 ASP cc_start: 0.9382 (m-30) cc_final: 0.8686 (t0) REVERT: H 88 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8635 (ttpp) REVERT: I 45 MET cc_start: 0.6253 (ppp) cc_final: 0.5845 (ppp) REVERT: I 87 MET cc_start: 0.8633 (mmm) cc_final: 0.8194 (mmm) REVERT: J 88 MET cc_start: 0.8639 (mmm) cc_final: 0.8338 (ptm) REVERT: J 89 ARG cc_start: 0.8547 (ptt-90) cc_final: 0.8219 (ptt-90) REVERT: J 97 ASP cc_start: 0.7543 (OUTLIER) cc_final: 0.7317 (m-30) REVERT: K 76 TYR cc_start: 0.8520 (m-80) cc_final: 0.7904 (m-80) REVERT: K 84 MET cc_start: 0.8461 (ppp) cc_final: 0.8179 (pmm) REVERT: K 111 ASP cc_start: 0.8544 (t70) cc_final: 0.8123 (t0) REVERT: L 65 TYR cc_start: 0.8176 (t80) cc_final: 0.7830 (t80) REVERT: L 102 ASP cc_start: 0.9008 (m-30) cc_final: 0.8714 (m-30) REVERT: N 17 ASP cc_start: 0.8828 (OUTLIER) cc_final: 0.8445 (p0) REVERT: O 61 GLN cc_start: 0.9372 (pt0) cc_final: 0.8935 (mm110) REVERT: U 9 GLU cc_start: 0.6259 (OUTLIER) cc_final: 0.5790 (tp30) REVERT: Z 84 HIS cc_start: 0.7594 (OUTLIER) cc_final: 0.7184 (t70) REVERT: Z 86 ASP cc_start: 0.8646 (OUTLIER) cc_final: 0.8119 (t0) REVERT: Z 114 GLN cc_start: 0.3281 (tp40) cc_final: 0.2806 (tm-30) REVERT: Z 124 GLN cc_start: 0.6364 (mm110) cc_final: 0.5852 (mm-40) REVERT: Z 218 PHE cc_start: 0.8238 (m-80) cc_final: 0.7951 (m-80) REVERT: Z 237 LYS cc_start: 0.5512 (OUTLIER) cc_final: 0.5291 (pmmt) REVERT: Z 260 MET cc_start: 0.7863 (OUTLIER) cc_final: 0.7426 (tpp) REVERT: Z 358 MET cc_start: 0.2325 (pmm) cc_final: 0.1995 (pmm) REVERT: Y 101 LYS cc_start: 0.7437 (tppt) cc_final: 0.7182 (tptm) outliers start: 388 outliers final: 302 residues processed: 1080 average time/residue: 1.3907 time to fit residues: 2678.0507 Evaluate side-chains 1087 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 317 poor density : 770 time to evaluate : 6.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 15 VAL Chi-restraints excluded: chain 04 residue 59 GLN Chi-restraints excluded: chain 04 residue 66 PHE Chi-restraints excluded: chain 04 residue 89 ASN Chi-restraints excluded: chain 04 residue 129 LEU Chi-restraints excluded: chain 04 residue 167 ASP Chi-restraints excluded: chain 04 residue 219 VAL Chi-restraints excluded: chain 04 residue 239 PHE Chi-restraints excluded: chain 04 residue 258 SER Chi-restraints excluded: chain 04 residue 263 ASP Chi-restraints excluded: chain 04 residue 267 VAL Chi-restraints excluded: chain 04 residue 271 SER Chi-restraints excluded: chain 05 residue 1 MET Chi-restraints excluded: chain 05 residue 9 VAL Chi-restraints excluded: chain 05 residue 11 MET Chi-restraints excluded: chain 05 residue 22 ILE Chi-restraints excluded: chain 05 residue 27 ILE Chi-restraints excluded: chain 05 residue 104 VAL Chi-restraints excluded: chain 05 residue 176 ASP Chi-restraints excluded: chain 05 residue 180 VAL Chi-restraints excluded: chain 05 residue 181 ASP Chi-restraints excluded: chain 06 residue 7 ASP Chi-restraints excluded: chain 06 residue 77 ILE Chi-restraints excluded: chain 06 residue 116 ASP Chi-restraints excluded: chain 06 residue 146 VAL Chi-restraints excluded: chain 07 residue 17 THR Chi-restraints excluded: chain 07 residue 27 VAL Chi-restraints excluded: chain 07 residue 30 VAL Chi-restraints excluded: chain 07 residue 39 VAL Chi-restraints excluded: chain 07 residue 95 MET Chi-restraints excluded: chain 07 residue 116 LEU Chi-restraints excluded: chain 07 residue 140 ILE Chi-restraints excluded: chain 07 residue 141 ASP Chi-restraints excluded: chain 07 residue 146 ASP Chi-restraints excluded: chain 07 residue 148 VAL Chi-restraints excluded: chain 07 residue 169 LEU Chi-restraints excluded: chain 07 residue 173 ASP Chi-restraints excluded: chain 08 residue 9 VAL Chi-restraints excluded: chain 08 residue 10 VAL Chi-restraints excluded: chain 08 residue 19 ASN Chi-restraints excluded: chain 08 residue 46 ASP Chi-restraints excluded: chain 08 residue 88 LEU Chi-restraints excluded: chain 08 residue 121 THR Chi-restraints excluded: chain 08 residue 167 VAL Chi-restraints excluded: chain 09 residue 40 THR Chi-restraints excluded: chain 09 residue 43 ASN Chi-restraints excluded: chain 09 residue 110 VAL Chi-restraints excluded: chain 10 residue 5 LEU Chi-restraints excluded: chain 10 residue 11 ILE Chi-restraints excluded: chain 10 residue 27 VAL Chi-restraints excluded: chain 10 residue 34 THR Chi-restraints excluded: chain 10 residue 74 ASP Chi-restraints excluded: chain 10 residue 86 MET Chi-restraints excluded: chain 10 residue 99 PHE Chi-restraints excluded: chain 10 residue 118 ILE Chi-restraints excluded: chain 11 residue 48 ILE Chi-restraints excluded: chain 11 residue 59 THR Chi-restraints excluded: chain 11 residue 77 VAL Chi-restraints excluded: chain 11 residue 85 ILE Chi-restraints excluded: chain 11 residue 97 VAL Chi-restraints excluded: chain 11 residue 104 GLN Chi-restraints excluded: chain 11 residue 138 VAL Chi-restraints excluded: chain 12 residue 14 ASP Chi-restraints excluded: chain 12 residue 52 ASP Chi-restraints excluded: chain 12 residue 81 ILE Chi-restraints excluded: chain 12 residue 84 ILE Chi-restraints excluded: chain 12 residue 93 ILE Chi-restraints excluded: chain 12 residue 122 LEU Chi-restraints excluded: chain 13 residue 7 MET Chi-restraints excluded: chain 13 residue 8 LEU Chi-restraints excluded: chain 13 residue 25 LEU Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 53 LYS Chi-restraints excluded: chain 13 residue 54 LYS Chi-restraints excluded: chain 13 residue 57 VAL Chi-restraints excluded: chain 13 residue 61 VAL Chi-restraints excluded: chain 13 residue 86 LEU Chi-restraints excluded: chain 13 residue 90 ASN Chi-restraints excluded: chain 13 residue 104 THR Chi-restraints excluded: chain 14 residue 46 VAL Chi-restraints excluded: chain 14 residue 82 LEU Chi-restraints excluded: chain 14 residue 89 VAL Chi-restraints excluded: chain 14 residue 110 VAL Chi-restraints excluded: chain 15 residue 24 THR Chi-restraints excluded: chain 15 residue 54 THR Chi-restraints excluded: chain 15 residue 70 ASP Chi-restraints excluded: chain 15 residue 102 LEU Chi-restraints excluded: chain 15 residue 112 LEU Chi-restraints excluded: chain 15 residue 126 ILE Chi-restraints excluded: chain 15 residue 129 THR Chi-restraints excluded: chain 16 residue 11 ASN Chi-restraints excluded: chain 16 residue 34 ILE Chi-restraints excluded: chain 16 residue 37 THR Chi-restraints excluded: chain 16 residue 57 THR Chi-restraints excluded: chain 16 residue 70 THR Chi-restraints excluded: chain 16 residue 97 ILE Chi-restraints excluded: chain 17 residue 5 SER Chi-restraints excluded: chain 17 residue 27 VAL Chi-restraints excluded: chain 17 residue 28 VAL Chi-restraints excluded: chain 17 residue 55 GLU Chi-restraints excluded: chain 17 residue 65 THR Chi-restraints excluded: chain 17 residue 67 ASN Chi-restraints excluded: chain 17 residue 69 ASP Chi-restraints excluded: chain 17 residue 78 VAL Chi-restraints excluded: chain 17 residue 106 LEU Chi-restraints excluded: chain 18 residue 8 GLU Chi-restraints excluded: chain 18 residue 15 ASP Chi-restraints excluded: chain 18 residue 31 VAL Chi-restraints excluded: chain 18 residue 39 LEU Chi-restraints excluded: chain 18 residue 113 LEU Chi-restraints excluded: chain 19 residue 33 VAL Chi-restraints excluded: chain 19 residue 94 LEU Chi-restraints excluded: chain 20 residue 35 PHE Chi-restraints excluded: chain 20 residue 39 LEU Chi-restraints excluded: chain 20 residue 51 VAL Chi-restraints excluded: chain 20 residue 58 VAL Chi-restraints excluded: chain 20 residue 74 ILE Chi-restraints excluded: chain 20 residue 82 HIS Chi-restraints excluded: chain 21 residue 20 VAL Chi-restraints excluded: chain 21 residue 35 ILE Chi-restraints excluded: chain 21 residue 68 ASP Chi-restraints excluded: chain 21 residue 77 ASP Chi-restraints excluded: chain 21 residue 78 GLU Chi-restraints excluded: chain 22 residue 2 ILE Chi-restraints excluded: chain 22 residue 54 GLU Chi-restraints excluded: chain 22 residue 59 ASN Chi-restraints excluded: chain 23 residue 17 ASP Chi-restraints excluded: chain 23 residue 23 LYS Chi-restraints excluded: chain 23 residue 27 VAL Chi-restraints excluded: chain 23 residue 29 SER Chi-restraints excluded: chain 23 residue 33 VAL Chi-restraints excluded: chain 23 residue 48 VAL Chi-restraints excluded: chain 23 residue 88 ASP Chi-restraints excluded: chain 24 residue 64 VAL Chi-restraints excluded: chain 24 residue 66 ASP Chi-restraints excluded: chain 24 residue 86 LEU Chi-restraints excluded: chain 25 residue 26 SER Chi-restraints excluded: chain 25 residue 34 VAL Chi-restraints excluded: chain 26 residue 12 VAL Chi-restraints excluded: chain 26 residue 22 ASN Chi-restraints excluded: chain 26 residue 33 HIS Chi-restraints excluded: chain 26 residue 39 VAL Chi-restraints excluded: chain 26 residue 57 VAL Chi-restraints excluded: chain 26 residue 63 ILE Chi-restraints excluded: chain 28 residue 24 LEU Chi-restraints excluded: chain 28 residue 40 THR Chi-restraints excluded: chain 28 residue 48 ASN Chi-restraints excluded: chain 29 residue 18 CYS Chi-restraints excluded: chain 29 residue 23 LYS Chi-restraints excluded: chain 30 residue 38 LEU Chi-restraints excluded: chain 31 residue 16 THR Chi-restraints excluded: chain 32 residue 31 LEU Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 33 residue 21 PHE Chi-restraints excluded: chain 33 residue 25 HIS Chi-restraints excluded: chain 33 residue 28 LEU Chi-restraints excluded: chain 33 residue 58 ILE Chi-restraints excluded: chain 33 residue 63 TYR Chi-restraints excluded: chain B residue 14 HIS Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 21 TYR Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain C residue 41 TYR Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 120 HIS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain F residue 44 ARG Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 138 GLU Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 88 LYS Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 126 CYS Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 21 LYS Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 38 PHE Chi-restraints excluded: chain I residue 44 ARG Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 64 GLN Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 75 ASP Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 97 ASP Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 71 ASP Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 81 ILE Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 103 CYS Chi-restraints excluded: chain M residue 11 HIS Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 67 ASP Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain N residue 17 ASP Chi-restraints excluded: chain N residue 37 ASP Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain O residue 1 SER Chi-restraints excluded: chain O residue 13 GLU Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 36 ASN Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 43 LEU Chi-restraints excluded: chain Q residue 54 ILE Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 63 CYS Chi-restraints excluded: chain Q residue 69 THR Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 62 THR Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain T residue 82 ILE Chi-restraints excluded: chain U residue 9 GLU Chi-restraints excluded: chain U residue 12 ASP Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 36 PHE Chi-restraints excluded: chain U residue 41 THR Chi-restraints excluded: chain 03 residue 29 LEU Chi-restraints excluded: chain 03 residue 35 THR Chi-restraints excluded: chain 03 residue 50 ILE Chi-restraints excluded: chain 03 residue 209 ILE Chi-restraints excluded: chain Z residue 13 ASN Chi-restraints excluded: chain Z residue 14 VAL Chi-restraints excluded: chain Z residue 25 THR Chi-restraints excluded: chain Z residue 84 HIS Chi-restraints excluded: chain Z residue 86 ASP Chi-restraints excluded: chain Z residue 92 ILE Chi-restraints excluded: chain Z residue 112 MET Chi-restraints excluded: chain Z residue 125 VAL Chi-restraints excluded: chain Z residue 148 LEU Chi-restraints excluded: chain Z residue 165 ASP Chi-restraints excluded: chain Z residue 178 LEU Chi-restraints excluded: chain Z residue 191 LEU Chi-restraints excluded: chain Z residue 235 ILE Chi-restraints excluded: chain Z residue 236 ILE Chi-restraints excluded: chain Z residue 237 LYS Chi-restraints excluded: chain Z residue 238 VAL Chi-restraints excluded: chain Z residue 242 VAL Chi-restraints excluded: chain Z residue 255 CYS Chi-restraints excluded: chain Z residue 260 MET Chi-restraints excluded: chain Z residue 266 ASP Chi-restraints excluded: chain Z residue 292 LEU Chi-restraints excluded: chain Z residue 326 TYR Chi-restraints excluded: chain Z residue 334 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1101 random chunks: chunk 656 optimal weight: 20.0000 chunk 423 optimal weight: 7.9990 chunk 633 optimal weight: 20.0000 chunk 319 optimal weight: 9.9990 chunk 208 optimal weight: 6.9990 chunk 205 optimal weight: 9.9990 chunk 674 optimal weight: 20.0000 chunk 722 optimal weight: 20.0000 chunk 524 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 834 optimal weight: 10.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 04 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 04 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 06 136 GLN ** 07 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 72 ASN 08 142 GLN 09 133 GLN ** 12 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 89 ASN ** 19 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 20 82 HIS 21 40 ASN ** 21 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 22 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 24 75 GLN 24 88 HIS ** 26 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 GLN ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 ASN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 GLN K 27 ASN ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.5062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 166847 Z= 0.258 Angle : 0.707 18.084 249116 Z= 0.362 Chirality : 0.039 0.356 31787 Planarity : 0.005 0.101 13716 Dihedral : 24.159 176.741 82309 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 28.08 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.56 % Favored : 88.23 % Rotamer: Outliers : 6.11 % Allowed : 24.91 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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: -3.04 (0.10), residues: 6366 helix: -1.17 (0.11), residues: 1926 sheet: -2.39 (0.14), residues: 1112 loop : -2.41 (0.10), residues: 3328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP07 96 HIS 0.011 0.002 HIS O 45 PHE 0.034 0.002 PHE09 46 TYR 0.053 0.002 TYR M 85 ARG 0.011 0.001 ARG C 135 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12732 Ramachandran restraints generated. 6366 Oldfield, 0 Emsley, 6366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12732 Ramachandran restraints generated. 6366 Oldfield, 0 Emsley, 6366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1192 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 323 poor density : 869 time to evaluate : 6.851 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: 04 145 MET cc_start: 0.8996 (mmm) cc_final: 0.8772 (mmm) REVERT: 04 250 GLN cc_start: 0.9089 (tp40) cc_final: 0.8887 (tp-100) REVERT: 05 42 ASN cc_start: 0.8313 (t0) cc_final: 0.7935 (t0) REVERT: 05 185 ASN cc_start: 0.8853 (t0) cc_final: 0.8568 (t0) REVERT: 07 16 MET cc_start: 0.7750 (mmt) cc_final: 0.7277 (mmt) REVERT: 07 86 CYS cc_start: 0.7451 (p) cc_final: 0.6854 (p) REVERT: 07 100 GLU cc_start: 0.9040 (tt0) cc_final: 0.8632 (tp30) REVERT: 09 89 LYS cc_start: 0.7794 (mmtm) cc_final: 0.6976 (tmtt) REVERT: 10 1 MET cc_start: 0.7734 (tpt) cc_final: 0.6486 (ptp) REVERT: 10 86 MET cc_start: 0.3076 (OUTLIER) cc_final: 0.2410 (ttt) REVERT: 11 59 THR cc_start: 0.6876 (OUTLIER) cc_final: 0.6463 (p) REVERT: 11 107 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7762 (tt0) REVERT: 11 124 MET cc_start: 0.0988 (mmt) cc_final: 0.0323 (mmm) REVERT: 12 16 TYR cc_start: 0.8797 (m-80) cc_final: 0.8465 (m-10) REVERT: 12 36 LEU cc_start: 0.8707 (mm) cc_final: 0.8177 (mm) REVERT: 12 52 ASP cc_start: 0.7670 (OUTLIER) cc_final: 0.6661 (t0) REVERT: 12 60 ASP cc_start: 0.8805 (p0) cc_final: 0.8498 (p0) REVERT: 13 20 MET cc_start: 0.9376 (ttp) cc_final: 0.9040 (tpp) REVERT: 13 44 LYS cc_start: 0.8840 (mmmt) cc_final: 0.8574 (tppt) REVERT: 13 67 LYS cc_start: 0.8310 (tptt) cc_final: 0.7493 (tppt) REVERT: 13 93 GLN cc_start: 0.9413 (mp10) cc_final: 0.9158 (mp10) REVERT: 13 100 PHE cc_start: 0.8794 (m-80) cc_final: 0.8537 (m-80) REVERT: 14 100 ILE cc_start: 0.8915 (pt) cc_final: 0.8615 (mm) REVERT: 16 20 MET cc_start: 0.8651 (ptm) cc_final: 0.7990 (ptp) REVERT: 16 110 MET cc_start: 0.8593 (mmm) cc_final: 0.8321 (mmm) REVERT: 19 23 TYR cc_start: 0.8066 (m-80) cc_final: 0.7849 (m-80) REVERT: 22 1 MET cc_start: 0.8016 (pmm) cc_final: 0.7190 (ppp) REVERT: 25 12 SER cc_start: 0.7269 (OUTLIER) cc_final: 0.6505 (p) REVERT: 25 68 LYS cc_start: 0.8320 (mtpt) cc_final: 0.7905 (mttm) REVERT: 26 16 ASN cc_start: 0.9595 (m-40) cc_final: 0.9106 (m110) REVERT: 28 43 ILE cc_start: 0.9223 (mm) cc_final: 0.9010 (mm) REVERT: 28 46 MET cc_start: 0.9016 (mtp) cc_final: 0.8587 (mtp) REVERT: 29 22 MET cc_start: 0.8579 (tmm) cc_final: 0.8290 (tmm) REVERT: 30 36 LYS cc_start: 0.9023 (mmmm) cc_final: 0.8640 (mmmt) REVERT: 33 25 HIS cc_start: 0.8357 (OUTLIER) cc_final: 0.8027 (m170) REVERT: 34 18 LYS cc_start: 0.8803 (tttm) cc_final: 0.8407 (ttmt) REVERT: 34 37 GLN cc_start: 0.8730 (tp-100) cc_final: 0.8182 (tt0) REVERT: B 26 MET cc_start: 0.7821 (mtp) cc_final: 0.7480 (mtt) REVERT: B 42 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8360 (mt) REVERT: B 48 MET cc_start: 0.8590 (pmm) cc_final: 0.8341 (pmm) REVERT: B 157 PRO cc_start: 0.8718 (Cg_endo) cc_final: 0.8470 (Cg_exo) REVERT: C 36 PHE cc_start: 0.9429 (t80) cc_final: 0.9155 (t80) REVERT: C 138 GLN cc_start: 0.9233 (mt0) cc_final: 0.8942 (mm-40) REVERT: C 141 MET cc_start: 0.8640 (mmp) cc_final: 0.8379 (mmt) REVERT: D 19 PHE cc_start: 0.8806 (m-80) cc_final: 0.8509 (m-10) REVERT: D 46 ARG cc_start: 0.8738 (tpp-160) cc_final: 0.8170 (tpt90) REVERT: D 68 GLU cc_start: 0.8475 (tp30) cc_final: 0.8094 (tp30) REVERT: D 104 MET cc_start: 0.8689 (mmt) cc_final: 0.8264 (mmt) REVERT: D 168 THR cc_start: 0.9233 (OUTLIER) cc_final: 0.8999 (p) REVERT: E 9 GLU cc_start: 0.7381 (pm20) cc_final: 0.7077 (mt-10) REVERT: E 77 ASN cc_start: 0.9411 (OUTLIER) cc_final: 0.9152 (p0) REVERT: E 158 LYS cc_start: 0.8368 (mmmt) cc_final: 0.7817 (mmtm) REVERT: F 1 MET cc_start: 0.7113 (ttt) cc_final: 0.5626 (ttt) REVERT: F 11 HIS cc_start: 0.8150 (OUTLIER) cc_final: 0.7739 (t70) REVERT: F 21 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8383 (mpp) REVERT: F 88 MET cc_start: 0.7368 (tmm) cc_final: 0.6711 (tmm) REVERT: G 6 ILE cc_start: 0.6815 (OUTLIER) cc_final: 0.6510 (pt) REVERT: G 27 ASN cc_start: 0.9050 (m110) cc_final: 0.8822 (m110) REVERT: G 84 TYR cc_start: 0.2323 (p90) cc_final: 0.1997 (p90) REVERT: G 139 ASP cc_start: 0.9360 (m-30) cc_final: 0.8655 (t0) REVERT: G 143 MET cc_start: 0.8928 (mmp) cc_final: 0.8695 (mmp) REVERT: I 45 MET cc_start: 0.6100 (OUTLIER) cc_final: 0.5767 (ppp) REVERT: J 49 PHE cc_start: 0.7454 (m-80) cc_final: 0.7132 (m-80) REVERT: J 88 MET cc_start: 0.8540 (mmm) cc_final: 0.8124 (ptm) REVERT: J 89 ARG cc_start: 0.8532 (ptt-90) cc_final: 0.8149 (ptt-90) REVERT: K 76 TYR cc_start: 0.8409 (m-80) cc_final: 0.7748 (m-80) REVERT: K 111 ASP cc_start: 0.8442 (t70) cc_final: 0.7984 (t0) REVERT: L 75 GLU cc_start: 0.8613 (tp30) cc_final: 0.8372 (tp30) REVERT: L 102 ASP cc_start: 0.9050 (m-30) cc_final: 0.8778 (m-30) REVERT: M 62 PHE cc_start: 0.7528 (t80) cc_final: 0.7260 (m-80) REVERT: O 61 GLN cc_start: 0.9342 (pt0) cc_final: 0.8792 (mm-40) REVERT: Q 16 MET cc_start: 0.7961 (ttp) cc_final: 0.7547 (tpp) REVERT: S 43 MET cc_start: 0.8857 (tpp) cc_final: 0.8593 (mmt) REVERT: U 9 GLU cc_start: 0.6210 (OUTLIER) cc_final: 0.5866 (tp30) REVERT: U 45 LYS cc_start: 0.9260 (tmtt) cc_final: 0.9033 (tttt) REVERT: Z 84 HIS cc_start: 0.7333 (OUTLIER) cc_final: 0.6951 (t70) REVERT: Z 86 ASP cc_start: 0.8677 (OUTLIER) cc_final: 0.8083 (t0) REVERT: Z 98 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.8065 (ttp) REVERT: Z 114 GLN cc_start: 0.3426 (tp40) cc_final: 0.2981 (tm-30) REVERT: Z 124 GLN cc_start: 0.6063 (mm110) cc_final: 0.5530 (mm-40) REVERT: Z 218 PHE cc_start: 0.8153 (m-80) cc_final: 0.7741 (m-80) REVERT: Z 237 LYS cc_start: 0.5597 (OUTLIER) cc_final: 0.5358 (pmmt) REVERT: Z 260 MET cc_start: 0.7609 (OUTLIER) cc_final: 0.7158 (tpp) REVERT: Z 358 MET cc_start: 0.1993 (pmm) cc_final: 0.1732 (pmm) REVERT: Z 368 MET cc_start: 0.4658 (ptp) cc_final: 0.4056 (ptp) REVERT: Y 101 LYS cc_start: 0.7402 (tppt) cc_final: 0.7174 (tptm) outliers start: 323 outliers final: 258 residues processed: 1078 average time/residue: 1.3956 time to fit residues: 2677.7446 Evaluate side-chains 1107 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 276 poor density : 831 time to evaluate : 6.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 15 VAL Chi-restraints excluded: chain 04 residue 59 GLN Chi-restraints excluded: chain 04 residue 66 PHE Chi-restraints excluded: chain 04 residue 89 ASN Chi-restraints excluded: chain 04 residue 129 LEU Chi-restraints excluded: chain 04 residue 167 ASP Chi-restraints excluded: chain 04 residue 186 ASP Chi-restraints excluded: chain 04 residue 219 VAL Chi-restraints excluded: chain 04 residue 222 THR Chi-restraints excluded: chain 04 residue 239 PHE Chi-restraints excluded: chain 04 residue 258 SER Chi-restraints excluded: chain 04 residue 263 ASP Chi-restraints excluded: chain 04 residue 267 VAL Chi-restraints excluded: chain 04 residue 271 SER Chi-restraints excluded: chain 05 residue 1 MET Chi-restraints excluded: chain 05 residue 9 VAL Chi-restraints excluded: chain 05 residue 11 MET Chi-restraints excluded: chain 05 residue 22 ILE Chi-restraints excluded: chain 05 residue 27 ILE Chi-restraints excluded: chain 05 residue 104 VAL Chi-restraints excluded: chain 05 residue 176 ASP Chi-restraints excluded: chain 05 residue 180 VAL Chi-restraints excluded: chain 05 residue 181 ASP Chi-restraints excluded: chain 06 residue 77 ILE Chi-restraints excluded: chain 06 residue 146 VAL Chi-restraints excluded: chain 07 residue 17 THR Chi-restraints excluded: chain 07 residue 27 VAL Chi-restraints excluded: chain 07 residue 30 VAL Chi-restraints excluded: chain 07 residue 95 MET Chi-restraints excluded: chain 07 residue 141 ASP Chi-restraints excluded: chain 07 residue 148 VAL Chi-restraints excluded: chain 07 residue 169 LEU Chi-restraints excluded: chain 08 residue 9 VAL Chi-restraints excluded: chain 08 residue 10 VAL Chi-restraints excluded: chain 08 residue 19 ASN Chi-restraints excluded: chain 08 residue 46 ASP Chi-restraints excluded: chain 08 residue 88 LEU Chi-restraints excluded: chain 08 residue 167 VAL Chi-restraints excluded: chain 09 residue 40 THR Chi-restraints excluded: chain 09 residue 110 VAL Chi-restraints excluded: chain 10 residue 5 LEU Chi-restraints excluded: chain 10 residue 11 ILE Chi-restraints excluded: chain 10 residue 27 VAL Chi-restraints excluded: chain 10 residue 34 THR Chi-restraints excluded: chain 10 residue 64 VAL Chi-restraints excluded: chain 10 residue 74 ASP Chi-restraints excluded: chain 10 residue 86 MET Chi-restraints excluded: chain 10 residue 118 ILE Chi-restraints excluded: chain 11 residue 48 ILE Chi-restraints excluded: chain 11 residue 59 THR Chi-restraints excluded: chain 11 residue 77 VAL Chi-restraints excluded: chain 11 residue 85 ILE Chi-restraints excluded: chain 11 residue 97 VAL Chi-restraints excluded: chain 11 residue 104 GLN Chi-restraints excluded: chain 11 residue 138 VAL Chi-restraints excluded: chain 12 residue 52 ASP Chi-restraints excluded: chain 12 residue 81 ILE Chi-restraints excluded: chain 12 residue 84 ILE Chi-restraints excluded: chain 12 residue 118 MET Chi-restraints excluded: chain 12 residue 122 LEU Chi-restraints excluded: chain 13 residue 7 MET Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 53 LYS Chi-restraints excluded: chain 13 residue 54 LYS Chi-restraints excluded: chain 13 residue 57 VAL Chi-restraints excluded: chain 13 residue 61 VAL Chi-restraints excluded: chain 13 residue 86 LEU Chi-restraints excluded: chain 13 residue 90 ASN Chi-restraints excluded: chain 13 residue 104 THR Chi-restraints excluded: chain 14 residue 82 LEU Chi-restraints excluded: chain 14 residue 110 VAL Chi-restraints excluded: chain 15 residue 24 THR Chi-restraints excluded: chain 15 residue 54 THR Chi-restraints excluded: chain 15 residue 70 ASP Chi-restraints excluded: chain 15 residue 102 LEU Chi-restraints excluded: chain 15 residue 112 LEU Chi-restraints excluded: chain 16 residue 11 ASN Chi-restraints excluded: chain 16 residue 34 ILE Chi-restraints excluded: chain 16 residue 37 THR Chi-restraints excluded: chain 16 residue 57 THR Chi-restraints excluded: chain 16 residue 97 ILE Chi-restraints excluded: chain 17 residue 5 SER Chi-restraints excluded: chain 17 residue 27 VAL Chi-restraints excluded: chain 17 residue 28 VAL Chi-restraints excluded: chain 17 residue 65 THR Chi-restraints excluded: chain 17 residue 67 ASN Chi-restraints excluded: chain 17 residue 69 ASP Chi-restraints excluded: chain 17 residue 78 VAL Chi-restraints excluded: chain 18 residue 8 GLU Chi-restraints excluded: chain 18 residue 15 ASP Chi-restraints excluded: chain 18 residue 31 VAL Chi-restraints excluded: chain 18 residue 39 LEU Chi-restraints excluded: chain 18 residue 113 LEU Chi-restraints excluded: chain 19 residue 33 VAL Chi-restraints excluded: chain 19 residue 56 PHE Chi-restraints excluded: chain 19 residue 94 LEU Chi-restraints excluded: chain 20 residue 35 PHE Chi-restraints excluded: chain 20 residue 39 LEU Chi-restraints excluded: chain 20 residue 51 VAL Chi-restraints excluded: chain 20 residue 58 VAL Chi-restraints excluded: chain 20 residue 74 ILE Chi-restraints excluded: chain 20 residue 82 HIS Chi-restraints excluded: chain 21 residue 20 VAL Chi-restraints excluded: chain 21 residue 68 ASP Chi-restraints excluded: chain 21 residue 76 VAL Chi-restraints excluded: chain 21 residue 77 ASP Chi-restraints excluded: chain 21 residue 78 GLU Chi-restraints excluded: chain 22 residue 2 ILE Chi-restraints excluded: chain 22 residue 54 GLU Chi-restraints excluded: chain 22 residue 59 ASN Chi-restraints excluded: chain 23 residue 17 ASP Chi-restraints excluded: chain 23 residue 27 VAL Chi-restraints excluded: chain 23 residue 29 SER Chi-restraints excluded: chain 23 residue 48 VAL Chi-restraints excluded: chain 23 residue 88 ASP Chi-restraints excluded: chain 24 residue 20 LEU Chi-restraints excluded: chain 24 residue 64 VAL Chi-restraints excluded: chain 24 residue 66 ASP Chi-restraints excluded: chain 24 residue 86 LEU Chi-restraints excluded: chain 24 residue 92 VAL Chi-restraints excluded: chain 25 residue 12 SER Chi-restraints excluded: chain 25 residue 13 GLU Chi-restraints excluded: chain 25 residue 34 VAL Chi-restraints excluded: chain 26 residue 12 VAL Chi-restraints excluded: chain 26 residue 22 ASN Chi-restraints excluded: chain 26 residue 33 HIS Chi-restraints excluded: chain 26 residue 39 VAL Chi-restraints excluded: chain 26 residue 63 ILE Chi-restraints excluded: chain 28 residue 24 LEU Chi-restraints excluded: chain 28 residue 40 THR Chi-restraints excluded: chain 28 residue 48 ASN Chi-restraints excluded: chain 29 residue 18 CYS Chi-restraints excluded: chain 30 residue 38 LEU Chi-restraints excluded: chain 31 residue 16 THR Chi-restraints excluded: chain 32 residue 31 LEU Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 33 residue 21 PHE Chi-restraints excluded: chain 33 residue 25 HIS Chi-restraints excluded: chain 33 residue 53 ASP Chi-restraints excluded: chain 33 residue 58 ILE Chi-restraints excluded: chain B residue 14 HIS Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 21 TYR Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 167 HIS Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 163 GLN Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 120 HIS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 11 HIS Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain F residue 44 ARG Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 138 GLU Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 88 LYS Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 21 LYS Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 38 PHE Chi-restraints excluded: chain I residue 44 ARG Chi-restraints excluded: chain I residue 45 MET Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 64 GLN Chi-restraints excluded: chain J residue 75 ASP Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 81 ILE Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain M residue 67 ASP Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 37 ASP Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain O residue 1 SER Chi-restraints excluded: chain O residue 13 GLU Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 36 ASN Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 43 LEU Chi-restraints excluded: chain Q residue 54 ILE Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 69 THR Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 62 THR Chi-restraints excluded: chain U residue 9 GLU Chi-restraints excluded: chain U residue 12 ASP Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 36 PHE Chi-restraints excluded: chain U residue 41 THR Chi-restraints excluded: chain 03 residue 29 LEU Chi-restraints excluded: chain 03 residue 35 THR Chi-restraints excluded: chain 03 residue 209 ILE Chi-restraints excluded: chain Z residue 13 ASN Chi-restraints excluded: chain Z residue 14 VAL Chi-restraints excluded: chain Z residue 25 THR Chi-restraints excluded: chain Z residue 84 HIS Chi-restraints excluded: chain Z residue 86 ASP Chi-restraints excluded: chain Z residue 98 MET Chi-restraints excluded: chain Z residue 112 MET Chi-restraints excluded: chain Z residue 148 LEU Chi-restraints excluded: chain Z residue 165 ASP Chi-restraints excluded: chain Z residue 191 LEU Chi-restraints excluded: chain Z residue 236 ILE Chi-restraints excluded: chain Z residue 237 LYS Chi-restraints excluded: chain Z residue 238 VAL Chi-restraints excluded: chain Z residue 242 VAL Chi-restraints excluded: chain Z residue 255 CYS Chi-restraints excluded: chain Z residue 260 MET Chi-restraints excluded: chain Z residue 266 ASP Chi-restraints excluded: chain Z residue 292 LEU Chi-restraints excluded: chain Z residue 326 TYR Chi-restraints excluded: chain Z residue 334 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1101 random chunks: chunk 965 optimal weight: 30.0000 chunk 1016 optimal weight: 20.0000 chunk 927 optimal weight: 20.0000 chunk 988 optimal weight: 20.0000 chunk 595 optimal weight: 20.0000 chunk 430 optimal weight: 0.5980 chunk 776 optimal weight: 20.0000 chunk 303 optimal weight: 0.6980 chunk 893 optimal weight: 30.0000 chunk 935 optimal weight: 30.0000 chunk 985 optimal weight: 20.0000 overall best weight: 12.2592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 04 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 04 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 72 ASN ** 12 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 89 ASN 15 22 GLN ** 19 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 20 82 HIS ** 21 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 22 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 26 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 33 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 8 GLN R 30 ASN ** R 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.5289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 166847 Z= 0.359 Angle : 0.775 15.967 249116 Z= 0.394 Chirality : 0.042 0.371 31787 Planarity : 0.006 0.099 13716 Dihedral : 24.224 179.252 82308 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 33.33 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.65 % Favored : 86.18 % Rotamer: Outliers : 6.17 % Allowed : 25.27 % Favored : 68.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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: -3.13 (0.10), residues: 6366 helix: -1.31 (0.11), residues: 1958 sheet: -2.38 (0.14), residues: 1083 loop : -2.47 (0.10), residues: 3325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 17 HIS 0.019 0.002 HIS T 19 PHE 0.048 0.003 PHE20 77 TYR 0.076 0.003 TYR M 85 ARG 0.012 0.001 ARG22 77 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12732 Ramachandran restraints generated. 6366 Oldfield, 0 Emsley, 6366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12732 Ramachandran restraints generated. 6366 Oldfield, 0 Emsley, 6366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1145 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 326 poor density : 819 time to evaluate : 6.676 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: 04 145 MET cc_start: 0.8989 (mmm) cc_final: 0.8747 (mmm) REVERT: 04 250 GLN cc_start: 0.9088 (tp40) cc_final: 0.8738 (tp40) REVERT: 05 42 ASN cc_start: 0.8392 (t0) cc_final: 0.7995 (t0) REVERT: 05 185 ASN cc_start: 0.8806 (t0) cc_final: 0.8534 (t0) REVERT: 07 16 MET cc_start: 0.7751 (mmt) cc_final: 0.7392 (mmt) REVERT: 07 100 GLU cc_start: 0.9034 (tt0) cc_final: 0.8635 (tp30) REVERT: 09 89 LYS cc_start: 0.7878 (mmtm) cc_final: 0.7065 (tmtt) REVERT: 10 1 MET cc_start: 0.7859 (tpt) cc_final: 0.6635 (ptp) REVERT: 10 86 MET cc_start: 0.3371 (OUTLIER) cc_final: 0.2683 (ttt) REVERT: 11 107 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7755 (tt0) REVERT: 11 116 MET cc_start: 0.2884 (mmt) cc_final: 0.1097 (mmt) REVERT: 12 16 TYR cc_start: 0.8820 (m-80) cc_final: 0.8448 (m-10) REVERT: 12 36 LEU cc_start: 0.8758 (mm) cc_final: 0.8187 (mm) REVERT: 12 52 ASP cc_start: 0.7646 (OUTLIER) cc_final: 0.6564 (t0) REVERT: 12 60 ASP cc_start: 0.8820 (p0) cc_final: 0.8494 (p0) REVERT: 13 20 MET cc_start: 0.9400 (ttp) cc_final: 0.9014 (tpp) REVERT: 13 44 LYS cc_start: 0.8887 (mmmt) cc_final: 0.8592 (tppt) REVERT: 13 67 LYS cc_start: 0.8420 (tptt) cc_final: 0.7480 (tppt) REVERT: 13 93 GLN cc_start: 0.9390 (mp10) cc_final: 0.9007 (mp10) REVERT: 13 100 PHE cc_start: 0.8852 (m-80) cc_final: 0.8573 (m-80) REVERT: 14 100 ILE cc_start: 0.8922 (pt) cc_final: 0.8602 (mm) REVERT: 16 20 MET cc_start: 0.8685 (ptm) cc_final: 0.8348 (ptp) REVERT: 16 110 MET cc_start: 0.8587 (mmm) cc_final: 0.8319 (mmm) REVERT: 19 23 TYR cc_start: 0.8350 (m-80) cc_final: 0.8149 (m-80) REVERT: 21 1 MET cc_start: 0.6968 (tpp) cc_final: 0.6692 (tpp) REVERT: 25 12 SER cc_start: 0.7121 (OUTLIER) cc_final: 0.6495 (p) REVERT: 25 68 LYS cc_start: 0.8367 (mtpt) cc_final: 0.7943 (mttm) REVERT: 25 79 GLU cc_start: 0.8891 (pm20) cc_final: 0.8683 (pm20) REVERT: 26 16 ASN cc_start: 0.9623 (m-40) cc_final: 0.9133 (m110) REVERT: 27 1 MET cc_start: 0.7399 (tpt) cc_final: 0.6770 (pmm) REVERT: 28 43 ILE cc_start: 0.9236 (mm) cc_final: 0.9027 (mm) REVERT: 29 22 MET cc_start: 0.8579 (tmm) cc_final: 0.8295 (tmm) REVERT: 30 14 MET cc_start: 0.8771 (mtm) cc_final: 0.8532 (mtp) REVERT: 30 36 LYS cc_start: 0.9072 (mmmm) cc_final: 0.8673 (mmmt) REVERT: 34 18 LYS cc_start: 0.8832 (tttm) cc_final: 0.8433 (ttmt) REVERT: 34 37 GLN cc_start: 0.8813 (tp-100) cc_final: 0.8208 (tt0) REVERT: B 42 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8363 (mt) REVERT: B 157 PRO cc_start: 0.8737 (Cg_endo) cc_final: 0.8476 (Cg_exo) REVERT: C 36 PHE cc_start: 0.9436 (t80) cc_final: 0.9158 (t80) REVERT: C 138 GLN cc_start: 0.9249 (mt0) cc_final: 0.8957 (mm-40) REVERT: C 141 MET cc_start: 0.8668 (mmp) cc_final: 0.8423 (mmt) REVERT: D 46 ARG cc_start: 0.8762 (tpp-160) cc_final: 0.8172 (tpt90) REVERT: D 68 GLU cc_start: 0.8494 (tp30) cc_final: 0.8123 (tp30) REVERT: D 104 MET cc_start: 0.8710 (mmt) cc_final: 0.8275 (mmt) REVERT: D 168 THR cc_start: 0.9287 (OUTLIER) cc_final: 0.9017 (p) REVERT: E 9 GLU cc_start: 0.7663 (pm20) cc_final: 0.7037 (mt-10) REVERT: E 77 ASN cc_start: 0.9470 (OUTLIER) cc_final: 0.9220 (p0) REVERT: E 158 LYS cc_start: 0.8354 (mmmt) cc_final: 0.7795 (mmtm) REVERT: F 1 MET cc_start: 0.7339 (OUTLIER) cc_final: 0.6044 (ttt) REVERT: F 11 HIS cc_start: 0.8151 (OUTLIER) cc_final: 0.7737 (t70) REVERT: F 21 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.8382 (mpp) REVERT: F 88 MET cc_start: 0.7431 (tmm) cc_final: 0.6737 (tmm) REVERT: G 6 ILE cc_start: 0.6959 (OUTLIER) cc_final: 0.6676 (pt) REVERT: G 139 ASP cc_start: 0.9355 (m-30) cc_final: 0.8654 (t0) REVERT: G 143 MET cc_start: 0.8956 (mmp) cc_final: 0.8726 (mmp) REVERT: I 45 MET cc_start: 0.6041 (OUTLIER) cc_final: 0.5663 (ppp) REVERT: I 87 MET cc_start: 0.8608 (mmm) cc_final: 0.8188 (mmm) REVERT: J 20 GLN cc_start: 0.9008 (mt0) cc_final: 0.8673 (mp10) REVERT: J 49 PHE cc_start: 0.7571 (m-80) cc_final: 0.7243 (m-80) REVERT: J 59 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7428 (tptm) REVERT: J 88 MET cc_start: 0.8528 (mmm) cc_final: 0.8193 (ptm) REVERT: J 89 ARG cc_start: 0.8459 (ptt-90) cc_final: 0.8000 (ptt-90) REVERT: K 76 TYR cc_start: 0.8453 (m-80) cc_final: 0.7822 (m-80) REVERT: K 111 ASP cc_start: 0.8444 (t70) cc_final: 0.8068 (t0) REVERT: L 75 GLU cc_start: 0.8667 (tp30) cc_final: 0.8447 (tp30) REVERT: L 102 ASP cc_start: 0.9076 (m-30) cc_final: 0.8799 (m-30) REVERT: M 16 ILE cc_start: 0.9243 (OUTLIER) cc_final: 0.8863 (tp) REVERT: M 62 PHE cc_start: 0.7461 (t80) cc_final: 0.7185 (m-80) REVERT: N 85 GLU cc_start: 0.8610 (tp30) cc_final: 0.8290 (tp30) REVERT: O 61 GLN cc_start: 0.9341 (pt0) cc_final: 0.8849 (mm110) REVERT: Q 16 MET cc_start: 0.8035 (ttp) cc_final: 0.7671 (tpp) REVERT: S 43 MET cc_start: 0.8831 (tpp) cc_final: 0.8611 (mmt) REVERT: T 23 ARG cc_start: 0.8712 (mmt180) cc_final: 0.8425 (mmt180) REVERT: U 4 LYS cc_start: 0.7464 (ttpp) cc_final: 0.5168 (mttm) REVERT: U 9 GLU cc_start: 0.6302 (OUTLIER) cc_final: 0.5945 (tp30) REVERT: Z 86 ASP cc_start: 0.8624 (OUTLIER) cc_final: 0.8149 (t0) REVERT: Z 98 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.8091 (ttp) REVERT: Z 114 GLN cc_start: 0.3338 (tp40) cc_final: 0.2866 (tm-30) REVERT: Z 124 GLN cc_start: 0.6104 (mm110) cc_final: 0.5628 (mm-40) REVERT: Z 218 PHE cc_start: 0.8183 (m-80) cc_final: 0.7809 (m-80) REVERT: Z 260 MET cc_start: 0.7622 (OUTLIER) cc_final: 0.7172 (tpp) REVERT: Z 368 MET cc_start: 0.4823 (ptp) cc_final: 0.4075 (ptp) REVERT: Y 101 LYS cc_start: 0.7348 (tppt) cc_final: 0.7051 (tptm) outliers start: 326 outliers final: 278 residues processed: 1028 average time/residue: 1.2989 time to fit residues: 2366.2421 Evaluate side-chains 1107 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 295 poor density : 812 time to evaluate : 6.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 15 VAL Chi-restraints excluded: chain 04 residue 59 GLN Chi-restraints excluded: chain 04 residue 66 PHE Chi-restraints excluded: chain 04 residue 89 ASN Chi-restraints excluded: chain 04 residue 129 LEU Chi-restraints excluded: chain 04 residue 167 ASP Chi-restraints excluded: chain 04 residue 219 VAL Chi-restraints excluded: chain 04 residue 222 THR Chi-restraints excluded: chain 04 residue 239 PHE Chi-restraints excluded: chain 04 residue 258 SER Chi-restraints excluded: chain 04 residue 263 ASP Chi-restraints excluded: chain 04 residue 267 VAL Chi-restraints excluded: chain 04 residue 271 SER Chi-restraints excluded: chain 05 residue 1 MET Chi-restraints excluded: chain 05 residue 9 VAL Chi-restraints excluded: chain 05 residue 11 MET Chi-restraints excluded: chain 05 residue 22 ILE Chi-restraints excluded: chain 05 residue 27 ILE Chi-restraints excluded: chain 05 residue 104 VAL Chi-restraints excluded: chain 05 residue 176 ASP Chi-restraints excluded: chain 05 residue 180 VAL Chi-restraints excluded: chain 05 residue 181 ASP Chi-restraints excluded: chain 06 residue 77 ILE Chi-restraints excluded: chain 06 residue 146 VAL Chi-restraints excluded: chain 07 residue 17 THR Chi-restraints excluded: chain 07 residue 27 VAL Chi-restraints excluded: chain 07 residue 30 VAL Chi-restraints excluded: chain 07 residue 95 MET Chi-restraints excluded: chain 07 residue 141 ASP Chi-restraints excluded: chain 07 residue 146 ASP Chi-restraints excluded: chain 07 residue 148 VAL Chi-restraints excluded: chain 07 residue 169 LEU Chi-restraints excluded: chain 08 residue 9 VAL Chi-restraints excluded: chain 08 residue 10 VAL Chi-restraints excluded: chain 08 residue 19 ASN Chi-restraints excluded: chain 08 residue 46 ASP Chi-restraints excluded: chain 08 residue 88 LEU Chi-restraints excluded: chain 08 residue 121 THR Chi-restraints excluded: chain 08 residue 167 VAL Chi-restraints excluded: chain 09 residue 40 THR Chi-restraints excluded: chain 09 residue 110 VAL Chi-restraints excluded: chain 10 residue 5 LEU Chi-restraints excluded: chain 10 residue 11 ILE Chi-restraints excluded: chain 10 residue 27 VAL Chi-restraints excluded: chain 10 residue 34 THR Chi-restraints excluded: chain 10 residue 74 ASP Chi-restraints excluded: chain 10 residue 86 MET Chi-restraints excluded: chain 10 residue 99 PHE Chi-restraints excluded: chain 10 residue 118 ILE Chi-restraints excluded: chain 11 residue 33 ASN Chi-restraints excluded: chain 11 residue 48 ILE Chi-restraints excluded: chain 11 residue 59 THR Chi-restraints excluded: chain 11 residue 77 VAL Chi-restraints excluded: chain 11 residue 85 ILE Chi-restraints excluded: chain 11 residue 97 VAL Chi-restraints excluded: chain 11 residue 104 GLN Chi-restraints excluded: chain 11 residue 138 VAL Chi-restraints excluded: chain 12 residue 52 ASP Chi-restraints excluded: chain 12 residue 81 ILE Chi-restraints excluded: chain 12 residue 84 ILE Chi-restraints excluded: chain 12 residue 118 MET Chi-restraints excluded: chain 12 residue 122 LEU Chi-restraints excluded: chain 13 residue 7 MET Chi-restraints excluded: chain 13 residue 8 LEU Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 53 LYS Chi-restraints excluded: chain 13 residue 54 LYS Chi-restraints excluded: chain 13 residue 57 VAL Chi-restraints excluded: chain 13 residue 61 VAL Chi-restraints excluded: chain 13 residue 86 LEU Chi-restraints excluded: chain 13 residue 90 ASN Chi-restraints excluded: chain 13 residue 104 THR Chi-restraints excluded: chain 13 residue 118 LEU Chi-restraints excluded: chain 14 residue 82 LEU Chi-restraints excluded: chain 14 residue 110 VAL Chi-restraints excluded: chain 15 residue 22 GLN Chi-restraints excluded: chain 15 residue 24 THR Chi-restraints excluded: chain 15 residue 54 THR Chi-restraints excluded: chain 15 residue 70 ASP Chi-restraints excluded: chain 15 residue 102 LEU Chi-restraints excluded: chain 15 residue 112 LEU Chi-restraints excluded: chain 15 residue 129 THR Chi-restraints excluded: chain 16 residue 11 ASN Chi-restraints excluded: chain 16 residue 37 THR Chi-restraints excluded: chain 16 residue 57 THR Chi-restraints excluded: chain 16 residue 97 ILE Chi-restraints excluded: chain 17 residue 5 SER Chi-restraints excluded: chain 17 residue 27 VAL Chi-restraints excluded: chain 17 residue 28 VAL Chi-restraints excluded: chain 17 residue 55 GLU Chi-restraints excluded: chain 17 residue 65 THR Chi-restraints excluded: chain 17 residue 67 ASN Chi-restraints excluded: chain 17 residue 69 ASP Chi-restraints excluded: chain 17 residue 78 VAL Chi-restraints excluded: chain 17 residue 106 LEU Chi-restraints excluded: chain 18 residue 8 GLU Chi-restraints excluded: chain 18 residue 15 ASP Chi-restraints excluded: chain 18 residue 31 VAL Chi-restraints excluded: chain 18 residue 39 LEU Chi-restraints excluded: chain 18 residue 113 LEU Chi-restraints excluded: chain 19 residue 33 VAL Chi-restraints excluded: chain 19 residue 94 LEU Chi-restraints excluded: chain 20 residue 35 PHE Chi-restraints excluded: chain 20 residue 39 LEU Chi-restraints excluded: chain 20 residue 51 VAL Chi-restraints excluded: chain 20 residue 55 ASP Chi-restraints excluded: chain 20 residue 58 VAL Chi-restraints excluded: chain 20 residue 74 ILE Chi-restraints excluded: chain 20 residue 82 HIS Chi-restraints excluded: chain 21 residue 20 VAL Chi-restraints excluded: chain 21 residue 68 ASP Chi-restraints excluded: chain 21 residue 77 ASP Chi-restraints excluded: chain 21 residue 78 GLU Chi-restraints excluded: chain 22 residue 2 ILE Chi-restraints excluded: chain 22 residue 54 GLU Chi-restraints excluded: chain 22 residue 59 ASN Chi-restraints excluded: chain 23 residue 17 ASP Chi-restraints excluded: chain 23 residue 27 VAL Chi-restraints excluded: chain 23 residue 29 SER Chi-restraints excluded: chain 23 residue 48 VAL Chi-restraints excluded: chain 23 residue 88 ASP Chi-restraints excluded: chain 24 residue 20 LEU Chi-restraints excluded: chain 24 residue 64 VAL Chi-restraints excluded: chain 24 residue 66 ASP Chi-restraints excluded: chain 24 residue 86 LEU Chi-restraints excluded: chain 24 residue 92 VAL Chi-restraints excluded: chain 25 residue 12 SER Chi-restraints excluded: chain 25 residue 13 GLU Chi-restraints excluded: chain 25 residue 34 VAL Chi-restraints excluded: chain 26 residue 12 VAL Chi-restraints excluded: chain 26 residue 22 ASN Chi-restraints excluded: chain 26 residue 33 HIS Chi-restraints excluded: chain 26 residue 39 VAL Chi-restraints excluded: chain 26 residue 63 ILE Chi-restraints excluded: chain 28 residue 24 LEU Chi-restraints excluded: chain 28 residue 40 THR Chi-restraints excluded: chain 28 residue 48 ASN Chi-restraints excluded: chain 28 residue 54 VAL Chi-restraints excluded: chain 29 residue 18 CYS Chi-restraints excluded: chain 30 residue 38 LEU Chi-restraints excluded: chain 31 residue 16 THR Chi-restraints excluded: chain 32 residue 31 LEU Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 33 residue 21 PHE Chi-restraints excluded: chain 33 residue 25 HIS Chi-restraints excluded: chain 33 residue 53 ASP Chi-restraints excluded: chain 33 residue 58 ILE Chi-restraints excluded: chain 33 residue 63 TYR Chi-restraints excluded: chain B residue 14 HIS Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 21 TYR Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 128 MET Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 120 HIS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 11 HIS Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain F residue 44 ARG Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 138 GLU Chi-restraints excluded: chain H residue 88 LYS Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 21 LYS Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 38 PHE Chi-restraints excluded: chain I residue 44 ARG Chi-restraints excluded: chain I residue 45 MET Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 64 GLN Chi-restraints excluded: chain J residue 75 ASP Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 71 ASP Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 81 ILE Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 67 ASP Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 37 ASP Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 50 LEU Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain N residue 92 ILE Chi-restraints excluded: chain O residue 1 SER Chi-restraints excluded: chain O residue 13 GLU Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 36 ASN Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 8 GLN Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 43 LEU Chi-restraints excluded: chain Q residue 54 ILE Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 63 CYS Chi-restraints excluded: chain Q residue 69 THR Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 62 THR Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 9 GLU Chi-restraints excluded: chain U residue 12 ASP Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 36 PHE Chi-restraints excluded: chain U residue 41 THR Chi-restraints excluded: chain 03 residue 29 LEU Chi-restraints excluded: chain 03 residue 35 THR Chi-restraints excluded: chain 03 residue 209 ILE Chi-restraints excluded: chain Z residue 13 ASN Chi-restraints excluded: chain Z residue 14 VAL Chi-restraints excluded: chain Z residue 25 THR Chi-restraints excluded: chain Z residue 86 ASP Chi-restraints excluded: chain Z residue 92 ILE Chi-restraints excluded: chain Z residue 98 MET Chi-restraints excluded: chain Z residue 112 MET Chi-restraints excluded: chain Z residue 148 LEU Chi-restraints excluded: chain Z residue 165 ASP Chi-restraints excluded: chain Z residue 178 LEU Chi-restraints excluded: chain Z residue 191 LEU Chi-restraints excluded: chain Z residue 238 VAL Chi-restraints excluded: chain Z residue 242 VAL Chi-restraints excluded: chain Z residue 255 CYS Chi-restraints excluded: chain Z residue 260 MET Chi-restraints excluded: chain Z residue 266 ASP Chi-restraints excluded: chain Z residue 292 LEU Chi-restraints excluded: chain Z residue 326 TYR Chi-restraints excluded: chain Z residue 334 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1101 random chunks: chunk 649 optimal weight: 20.0000 chunk 1045 optimal weight: 40.0000 chunk 638 optimal weight: 30.0000 chunk 496 optimal weight: 20.0000 chunk 726 optimal weight: 20.0000 chunk 1096 optimal weight: 30.0000 chunk 1009 optimal weight: 20.0000 chunk 873 optimal weight: 20.0000 chunk 90 optimal weight: 6.9990 chunk 674 optimal weight: 20.0000 chunk 535 optimal weight: 7.9990 overall best weight: 14.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 04 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 04 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 07 126 ASN ** 08 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 72 ASN ** 08 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 10 88 HIS ** 12 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 19 80 ASN ** 21 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 22 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 26 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 33 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.5577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.102 166847 Z= 0.425 Angle : 0.849 15.762 249116 Z= 0.430 Chirality : 0.045 0.386 31787 Planarity : 0.006 0.097 13716 Dihedral : 24.428 178.279 82308 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 37.86 Ramachandran Plot: Outliers : 0.20 % Allowed : 14.70 % Favored : 85.09 % Rotamer: Outliers : 6.17 % Allowed : 25.37 % Favored : 68.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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: -3.38 (0.10), residues: 6366 helix: -1.53 (0.11), residues: 1959 sheet: -2.52 (0.14), residues: 1089 loop : -2.60 (0.10), residues: 3318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP N 100 HIS 0.050 0.002 HIS20 82 PHE 0.051 0.003 PHE20 77 TYR 0.078 0.003 TYR M 85 ARG 0.011 0.001 ARG20 80 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12732 Ramachandran restraints generated. 6366 Oldfield, 0 Emsley, 6366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12732 Ramachandran restraints generated. 6366 Oldfield, 0 Emsley, 6366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1131 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 326 poor density : 805 time to evaluate : 6.074 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: 04 250 GLN cc_start: 0.9132 (tp40) cc_final: 0.8786 (tp40) REVERT: 05 42 ASN cc_start: 0.8552 (t0) cc_final: 0.8125 (t0) REVERT: 05 185 ASN cc_start: 0.8857 (t0) cc_final: 0.8600 (t0) REVERT: 07 16 MET cc_start: 0.7787 (mmt) cc_final: 0.7495 (mmt) REVERT: 07 100 GLU cc_start: 0.9047 (tt0) cc_final: 0.8641 (tp30) REVERT: 09 89 LYS cc_start: 0.7867 (mmtm) cc_final: 0.7047 (tmtt) REVERT: 10 1 MET cc_start: 0.7655 (tpt) cc_final: 0.6614 (ptp) REVERT: 10 52 MET cc_start: 0.1986 (ttp) cc_final: 0.1019 (ptm) REVERT: 10 86 MET cc_start: 0.3727 (OUTLIER) cc_final: 0.3121 (ttt) REVERT: 11 116 MET cc_start: 0.3070 (mmt) cc_final: 0.2457 (mmm) REVERT: 12 16 TYR cc_start: 0.8859 (m-80) cc_final: 0.8483 (m-10) REVERT: 12 36 LEU cc_start: 0.8776 (mm) cc_final: 0.8215 (mm) REVERT: 12 52 ASP cc_start: 0.7697 (OUTLIER) cc_final: 0.6664 (t0) REVERT: 12 60 ASP cc_start: 0.8848 (p0) cc_final: 0.8520 (p0) REVERT: 13 20 MET cc_start: 0.9405 (ttp) cc_final: 0.9002 (tpp) REVERT: 13 44 LYS cc_start: 0.8905 (mmmt) cc_final: 0.8616 (tppt) REVERT: 13 67 LYS cc_start: 0.8539 (tptt) cc_final: 0.7708 (tppt) REVERT: 13 93 GLN cc_start: 0.9423 (mp10) cc_final: 0.9028 (mp10) REVERT: 13 100 PHE cc_start: 0.8867 (m-80) cc_final: 0.8600 (m-80) REVERT: 14 100 ILE cc_start: 0.8996 (pt) cc_final: 0.8658 (mm) REVERT: 16 110 MET cc_start: 0.8607 (mmm) cc_final: 0.8320 (mmm) REVERT: 22 87 LEU cc_start: 0.8956 (mt) cc_final: 0.8727 (mt) REVERT: 25 68 LYS cc_start: 0.8383 (mtpt) cc_final: 0.7986 (mttm) REVERT: 26 16 ASN cc_start: 0.9632 (m-40) cc_final: 0.9159 (m110) REVERT: 27 44 LYS cc_start: 0.9245 (mtmm) cc_final: 0.9024 (mmmt) REVERT: 28 46 MET cc_start: 0.9141 (mtp) cc_final: 0.8723 (mtp) REVERT: 29 22 MET cc_start: 0.8592 (tmm) cc_final: 0.8310 (tmm) REVERT: 30 14 MET cc_start: 0.8807 (mtm) cc_final: 0.8569 (mtp) REVERT: 34 18 LYS cc_start: 0.8864 (tttm) cc_final: 0.8462 (ttmt) REVERT: 34 37 GLN cc_start: 0.8830 (tp-100) cc_final: 0.8161 (tt0) REVERT: B 42 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8387 (mt) REVERT: B 48 MET cc_start: 0.8603 (pmm) cc_final: 0.8403 (pmm) REVERT: B 157 PRO cc_start: 0.8738 (Cg_endo) cc_final: 0.8460 (Cg_exo) REVERT: C 36 PHE cc_start: 0.9432 (t80) cc_final: 0.9155 (t80) REVERT: C 138 GLN cc_start: 0.9289 (mt0) cc_final: 0.8805 (mt0) REVERT: C 141 MET cc_start: 0.8732 (mmp) cc_final: 0.8492 (mmt) REVERT: D 46 ARG cc_start: 0.8765 (tpp-160) cc_final: 0.8163 (tpt90) REVERT: D 89 LEU cc_start: 0.9375 (mt) cc_final: 0.8973 (mt) REVERT: D 93 LEU cc_start: 0.9156 (mp) cc_final: 0.8819 (pt) REVERT: D 104 MET cc_start: 0.8714 (mmt) cc_final: 0.8297 (mmt) REVERT: D 168 THR cc_start: 0.9246 (OUTLIER) cc_final: 0.8590 (p) REVERT: D 189 ASP cc_start: 0.8056 (m-30) cc_final: 0.7631 (m-30) REVERT: E 77 ASN cc_start: 0.9492 (OUTLIER) cc_final: 0.9235 (p0) REVERT: F 1 MET cc_start: 0.7391 (ttt) cc_final: 0.6132 (ttt) REVERT: F 11 HIS cc_start: 0.8160 (t70) cc_final: 0.7751 (t70) REVERT: F 21 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.8349 (mpp) REVERT: G 6 ILE cc_start: 0.7092 (OUTLIER) cc_final: 0.6802 (pt) REVERT: G 27 ASN cc_start: 0.9190 (m110) cc_final: 0.8939 (m110) REVERT: G 139 ASP cc_start: 0.9363 (m-30) cc_final: 0.8613 (t0) REVERT: G 143 MET cc_start: 0.8945 (mmp) cc_final: 0.8676 (mmp) REVERT: I 45 MET cc_start: 0.6096 (OUTLIER) cc_final: 0.5603 (ppp) REVERT: I 87 MET cc_start: 0.8670 (mmm) cc_final: 0.8272 (mmm) REVERT: I 111 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8237 (mt-10) REVERT: J 20 GLN cc_start: 0.9048 (mt0) cc_final: 0.8720 (mp10) REVERT: J 88 MET cc_start: 0.8525 (mmm) cc_final: 0.8222 (ptm) REVERT: J 99 GLN cc_start: 0.8304 (mt0) cc_final: 0.7742 (mp10) REVERT: K 111 ASP cc_start: 0.8452 (t70) cc_final: 0.8054 (t0) REVERT: L 102 ASP cc_start: 0.9065 (m-30) cc_final: 0.8758 (m-30) REVERT: M 16 ILE cc_start: 0.9298 (OUTLIER) cc_final: 0.8970 (tp) REVERT: O 61 GLN cc_start: 0.9363 (pt0) cc_final: 0.8878 (mm110) REVERT: Q 16 MET cc_start: 0.8082 (ttp) cc_final: 0.7834 (tpp) REVERT: U 4 LYS cc_start: 0.7564 (ttpp) cc_final: 0.5273 (mttm) REVERT: U 9 GLU cc_start: 0.6135 (OUTLIER) cc_final: 0.5896 (tp30) REVERT: Z 84 HIS cc_start: 0.7743 (OUTLIER) cc_final: 0.7386 (t70) REVERT: Z 86 ASP cc_start: 0.8711 (OUTLIER) cc_final: 0.8383 (t0) REVERT: Z 98 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.8044 (ttp) REVERT: Z 114 GLN cc_start: 0.3310 (tp40) cc_final: 0.2827 (tm-30) REVERT: Z 124 GLN cc_start: 0.6245 (mm110) cc_final: 0.5665 (mm-40) REVERT: Z 218 PHE cc_start: 0.8137 (m-80) cc_final: 0.7857 (m-10) REVERT: Z 260 MET cc_start: 0.7672 (OUTLIER) cc_final: 0.7221 (tpp) REVERT: Z 283 ARG cc_start: 0.7578 (tpt-90) cc_final: 0.6826 (tpp-160) outliers start: 326 outliers final: 288 residues processed: 1020 average time/residue: 1.2741 time to fit residues: 2299.1732 Evaluate side-chains 1090 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 302 poor density : 788 time to evaluate : 6.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 15 VAL Chi-restraints excluded: chain 04 residue 59 GLN Chi-restraints excluded: chain 04 residue 66 PHE Chi-restraints excluded: chain 04 residue 89 ASN Chi-restraints excluded: chain 04 residue 129 LEU Chi-restraints excluded: chain 04 residue 167 ASP Chi-restraints excluded: chain 04 residue 219 VAL Chi-restraints excluded: chain 04 residue 222 THR Chi-restraints excluded: chain 04 residue 239 PHE Chi-restraints excluded: chain 04 residue 258 SER Chi-restraints excluded: chain 04 residue 263 ASP Chi-restraints excluded: chain 04 residue 267 VAL Chi-restraints excluded: chain 04 residue 271 SER Chi-restraints excluded: chain 05 residue 1 MET Chi-restraints excluded: chain 05 residue 9 VAL Chi-restraints excluded: chain 05 residue 11 MET Chi-restraints excluded: chain 05 residue 22 ILE Chi-restraints excluded: chain 05 residue 27 ILE Chi-restraints excluded: chain 05 residue 104 VAL Chi-restraints excluded: chain 05 residue 176 ASP Chi-restraints excluded: chain 05 residue 180 VAL Chi-restraints excluded: chain 05 residue 181 ASP Chi-restraints excluded: chain 06 residue 77 ILE Chi-restraints excluded: chain 06 residue 146 VAL Chi-restraints excluded: chain 06 residue 173 THR Chi-restraints excluded: chain 06 residue 184 ASP Chi-restraints excluded: chain 07 residue 17 THR Chi-restraints excluded: chain 07 residue 27 VAL Chi-restraints excluded: chain 07 residue 30 VAL Chi-restraints excluded: chain 07 residue 39 VAL Chi-restraints excluded: chain 07 residue 95 MET Chi-restraints excluded: chain 07 residue 141 ASP Chi-restraints excluded: chain 07 residue 148 VAL Chi-restraints excluded: chain 07 residue 169 LEU Chi-restraints excluded: chain 08 residue 9 VAL Chi-restraints excluded: chain 08 residue 10 VAL Chi-restraints excluded: chain 08 residue 19 ASN Chi-restraints excluded: chain 08 residue 46 ASP Chi-restraints excluded: chain 08 residue 88 LEU Chi-restraints excluded: chain 08 residue 121 THR Chi-restraints excluded: chain 08 residue 167 VAL Chi-restraints excluded: chain 09 residue 110 VAL Chi-restraints excluded: chain 09 residue 121 VAL Chi-restraints excluded: chain 10 residue 5 LEU Chi-restraints excluded: chain 10 residue 27 VAL Chi-restraints excluded: chain 10 residue 34 THR Chi-restraints excluded: chain 10 residue 64 VAL Chi-restraints excluded: chain 10 residue 74 ASP Chi-restraints excluded: chain 10 residue 86 MET Chi-restraints excluded: chain 10 residue 99 PHE Chi-restraints excluded: chain 10 residue 118 ILE Chi-restraints excluded: chain 11 residue 48 ILE Chi-restraints excluded: chain 11 residue 59 THR Chi-restraints excluded: chain 11 residue 77 VAL Chi-restraints excluded: chain 11 residue 85 ILE Chi-restraints excluded: chain 11 residue 97 VAL Chi-restraints excluded: chain 11 residue 104 GLN Chi-restraints excluded: chain 11 residue 138 VAL Chi-restraints excluded: chain 12 residue 52 ASP Chi-restraints excluded: chain 12 residue 81 ILE Chi-restraints excluded: chain 12 residue 84 ILE Chi-restraints excluded: chain 12 residue 118 MET Chi-restraints excluded: chain 12 residue 122 LEU Chi-restraints excluded: chain 13 residue 7 MET Chi-restraints excluded: chain 13 residue 8 LEU Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 53 LYS Chi-restraints excluded: chain 13 residue 54 LYS Chi-restraints excluded: chain 13 residue 57 VAL Chi-restraints excluded: chain 13 residue 61 VAL Chi-restraints excluded: chain 13 residue 86 LEU Chi-restraints excluded: chain 13 residue 90 ASN Chi-restraints excluded: chain 13 residue 104 THR Chi-restraints excluded: chain 13 residue 118 LEU Chi-restraints excluded: chain 14 residue 82 LEU Chi-restraints excluded: chain 14 residue 89 VAL Chi-restraints excluded: chain 14 residue 110 VAL Chi-restraints excluded: chain 15 residue 24 THR Chi-restraints excluded: chain 15 residue 54 THR Chi-restraints excluded: chain 15 residue 70 ASP Chi-restraints excluded: chain 15 residue 75 GLU Chi-restraints excluded: chain 15 residue 102 LEU Chi-restraints excluded: chain 15 residue 112 LEU Chi-restraints excluded: chain 15 residue 126 ILE Chi-restraints excluded: chain 15 residue 128 THR Chi-restraints excluded: chain 15 residue 129 THR Chi-restraints excluded: chain 16 residue 11 ASN Chi-restraints excluded: chain 16 residue 34 ILE Chi-restraints excluded: chain 16 residue 37 THR Chi-restraints excluded: chain 16 residue 57 THR Chi-restraints excluded: chain 16 residue 97 ILE Chi-restraints excluded: chain 17 residue 5 SER Chi-restraints excluded: chain 17 residue 27 VAL Chi-restraints excluded: chain 17 residue 28 VAL Chi-restraints excluded: chain 17 residue 55 GLU Chi-restraints excluded: chain 17 residue 65 THR Chi-restraints excluded: chain 17 residue 67 ASN Chi-restraints excluded: chain 17 residue 69 ASP Chi-restraints excluded: chain 17 residue 78 VAL Chi-restraints excluded: chain 17 residue 106 LEU Chi-restraints excluded: chain 18 residue 8 GLU Chi-restraints excluded: chain 18 residue 15 ASP Chi-restraints excluded: chain 18 residue 31 VAL Chi-restraints excluded: chain 18 residue 39 LEU Chi-restraints excluded: chain 18 residue 113 LEU Chi-restraints excluded: chain 19 residue 33 VAL Chi-restraints excluded: chain 19 residue 44 TYR Chi-restraints excluded: chain 19 residue 94 LEU Chi-restraints excluded: chain 20 residue 35 PHE Chi-restraints excluded: chain 20 residue 39 LEU Chi-restraints excluded: chain 20 residue 51 VAL Chi-restraints excluded: chain 20 residue 55 ASP Chi-restraints excluded: chain 20 residue 58 VAL Chi-restraints excluded: chain 20 residue 74 ILE Chi-restraints excluded: chain 21 residue 20 VAL Chi-restraints excluded: chain 21 residue 68 ASP Chi-restraints excluded: chain 21 residue 77 ASP Chi-restraints excluded: chain 21 residue 78 GLU Chi-restraints excluded: chain 22 residue 2 ILE Chi-restraints excluded: chain 22 residue 24 MET Chi-restraints excluded: chain 22 residue 54 GLU Chi-restraints excluded: chain 22 residue 59 ASN Chi-restraints excluded: chain 23 residue 17 ASP Chi-restraints excluded: chain 23 residue 23 LYS Chi-restraints excluded: chain 23 residue 27 VAL Chi-restraints excluded: chain 23 residue 29 SER Chi-restraints excluded: chain 23 residue 33 VAL Chi-restraints excluded: chain 23 residue 48 VAL Chi-restraints excluded: chain 23 residue 88 ASP Chi-restraints excluded: chain 24 residue 20 LEU Chi-restraints excluded: chain 24 residue 64 VAL Chi-restraints excluded: chain 24 residue 66 ASP Chi-restraints excluded: chain 24 residue 86 LEU Chi-restraints excluded: chain 24 residue 92 VAL Chi-restraints excluded: chain 25 residue 13 GLU Chi-restraints excluded: chain 25 residue 34 VAL Chi-restraints excluded: chain 26 residue 12 VAL Chi-restraints excluded: chain 26 residue 22 ASN Chi-restraints excluded: chain 26 residue 33 HIS Chi-restraints excluded: chain 26 residue 39 VAL Chi-restraints excluded: chain 26 residue 63 ILE Chi-restraints excluded: chain 28 residue 24 LEU Chi-restraints excluded: chain 28 residue 40 THR Chi-restraints excluded: chain 28 residue 48 ASN Chi-restraints excluded: chain 29 residue 18 CYS Chi-restraints excluded: chain 30 residue 38 LEU Chi-restraints excluded: chain 31 residue 16 THR Chi-restraints excluded: chain 32 residue 31 LEU Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 33 residue 21 PHE Chi-restraints excluded: chain 33 residue 25 HIS Chi-restraints excluded: chain 33 residue 37 THR Chi-restraints excluded: chain 33 residue 53 ASP Chi-restraints excluded: chain 33 residue 58 ILE Chi-restraints excluded: chain 33 residue 63 TYR Chi-restraints excluded: chain B residue 14 HIS Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 21 TYR Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain C residue 78 LYS Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 184 LYS Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 99 SER Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 120 HIS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain F residue 6 ILE Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 21 MET Chi-restraints excluded: chain F residue 44 ARG Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 138 GLU Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain H residue 88 LYS Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 21 LYS Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 38 PHE Chi-restraints excluded: chain I residue 44 ARG Chi-restraints excluded: chain I residue 45 MET Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 64 GLN Chi-restraints excluded: chain J residue 75 ASP Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 71 ASP Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 81 ILE Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 88 LEU Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain N residue 17 ASP Chi-restraints excluded: chain N residue 20 PHE Chi-restraints excluded: chain N residue 37 ASP Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain N residue 92 ILE Chi-restraints excluded: chain O residue 1 SER Chi-restraints excluded: chain O residue 13 GLU Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 36 ASN Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain P residue 69 ASP Chi-restraints excluded: chain Q residue 27 PHE Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 43 LEU Chi-restraints excluded: chain Q residue 54 ILE Chi-restraints excluded: chain Q residue 63 CYS Chi-restraints excluded: chain Q residue 69 THR Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 62 THR Chi-restraints excluded: chain T residue 82 ILE Chi-restraints excluded: chain U residue 5 VAL Chi-restraints excluded: chain U residue 9 GLU Chi-restraints excluded: chain U residue 12 ASP Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 36 PHE Chi-restraints excluded: chain U residue 41 THR Chi-restraints excluded: chain 03 residue 29 LEU Chi-restraints excluded: chain 03 residue 35 THR Chi-restraints excluded: chain 03 residue 209 ILE Chi-restraints excluded: chain Z residue 13 ASN Chi-restraints excluded: chain Z residue 14 VAL Chi-restraints excluded: chain Z residue 25 THR Chi-restraints excluded: chain Z residue 84 HIS Chi-restraints excluded: chain Z residue 86 ASP Chi-restraints excluded: chain Z residue 98 MET Chi-restraints excluded: chain Z residue 112 MET Chi-restraints excluded: chain Z residue 148 LEU Chi-restraints excluded: chain Z residue 165 ASP Chi-restraints excluded: chain Z residue 178 LEU Chi-restraints excluded: chain Z residue 191 LEU Chi-restraints excluded: chain Z residue 238 VAL Chi-restraints excluded: chain Z residue 242 VAL Chi-restraints excluded: chain Z residue 255 CYS Chi-restraints excluded: chain Z residue 260 MET Chi-restraints excluded: chain Z residue 266 ASP Chi-restraints excluded: chain Z residue 292 LEU Chi-restraints excluded: chain Z residue 326 TYR Chi-restraints excluded: chain Z residue 334 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1101 random chunks: chunk 693 optimal weight: 20.0000 chunk 930 optimal weight: 20.0000 chunk 267 optimal weight: 9.9990 chunk 805 optimal weight: 20.0000 chunk 128 optimal weight: 30.0000 chunk 242 optimal weight: 7.9990 chunk 874 optimal weight: 20.0000 chunk 366 optimal weight: 10.0000 chunk 898 optimal weight: 20.0000 chunk 110 optimal weight: 0.0040 chunk 161 optimal weight: 9.9990 overall best weight: 7.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 04 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 04 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 07 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 72 ASN ** 09 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 3 GLN 13 89 ASN ** 19 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 22 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 24 75 GLN ** 26 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 51 HIS ** Z 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.042992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.036915 restraints weight = 1519379.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.037900 restraints weight = 628673.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.038471 restraints weight = 344875.070| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.5485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 166847 Z= 0.249 Angle : 0.703 15.806 249116 Z= 0.359 Chirality : 0.038 0.369 31787 Planarity : 0.005 0.092 13716 Dihedral : 24.298 178.034 82308 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 28.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.28 % Favored : 87.56 % Rotamer: Outliers : 5.35 % Allowed : 26.41 % Favored : 68.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.45 % 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: -3.02 (0.10), residues: 6366 helix: -1.15 (0.11), residues: 1947 sheet: -2.43 (0.14), residues: 1098 loop : -2.39 (0.11), residues: 3321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP07 96 HIS 0.010 0.002 HIS O 45 PHE 0.047 0.002 PHE20 77 TYR 0.066 0.002 TYR M 85 ARG 0.014 0.001 ARG09 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 39142.96 seconds wall clock time: 689 minutes 0.25 seconds (41340.25 seconds total)