Starting phenix.real_space_refine on Sat Mar 2 07:56:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyq_8620/03_2024/5uyq_8620_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyq_8620/03_2024/5uyq_8620.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyq_8620/03_2024/5uyq_8620_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyq_8620/03_2024/5uyq_8620_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyq_8620/03_2024/5uyq_8620_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyq_8620/03_2024/5uyq_8620.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyq_8620/03_2024/5uyq_8620.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyq_8620/03_2024/5uyq_8620_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyq_8620/03_2024/5uyq_8620_updated.pdb" } resolution = 3.8 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= -0.340 sd= 1.063 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: 6 Type Number sf(0) Gaussians P 4807 5.49 5 Mg 1 5.21 5 S 173 5.16 5 C 77705 2.51 5 N 28576 2.21 5 O 42497 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 "10 TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "12 ARG 13": "NH1" <-> "NH2" Residue "12 ARG 37": "NH1" <-> "NH2" Residue "12 ARG 96": "NH1" <-> "NH2" Residue "12 ARG 120": "NH1" <-> "NH2" 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 PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 "20 PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "24 TYR 82": "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 "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 PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 224": "NH1" <-> "NH2" Residue "C ARG 106": "NH1" <-> "NH2" Residue "C ARG 130": "NH1" <-> "NH2" Residue "E ARG 156": "NH1" <-> "NH2" Residue "F TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 123": "NH1" <-> "NH2" Residue "L ARG 55": "NH1" <-> "NH2" Residue "P ARG 28": "NH1" <-> "NH2" 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 "Z ARG 44": "NH1" <-> "NH2" Residue "Z TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 223": "NH1" <-> "NH2" Residue "Z ARG 269": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 153759 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': 91, 'rna2p_pyr': 47, 'rna3p_pur': 783, 'rna3p_pyr': 618} Link IDs: {'rna2p': 138, 'rna3p': 1400} 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': 213, 'rna2p_pyr': 97, 'rna3p_pur': 1461, 'rna3p_pyr': 1132} Link IDs: {'rna2p': 310, 'rna3p': 2592} 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: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 395 Classifications: {'RNA': 18} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 15, 'rna3p_pyr': 1} Link IDs: {'rna2p': 2, 'rna3p': 15} 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_pur': 8, 'rna2p_pyr': 7, 'rna3p': 1, 'rna3p_pur': 29, 'rna3p_pyr': 31} Link IDs: {'rna2p': 14, 'rna3p': 61} 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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GCP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 58.56, per 1000 atoms: 0.38 Number of scatterers: 153759 At special positions: 0 Unit cell: (277.16, 265.68, 238.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 173 16.00 P 4807 15.00 Mg 1 11.99 O 42497 8.00 N 28576 7.00 C 77705 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: 62.34 Conformation dependent library (CDL) restraints added in 7.4 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: 194 helices and 79 sheets defined 37.9% alpha, 18.6% beta 1394 base pairs and 2878 stacking pairs defined. Time for finding SS restraints: 79.02 Creating SS restraints... Processing helix chain '04' and resid 10 through 15 removed outlier: 7.720A pdb=" N HIS04 14 " --> pdb=" O PRO04 10 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N VAL04 15 " --> pdb=" O GLY04 11 " (cutoff:3.500A) No H-bonds generated for 'chain '04' and resid 10 through 15' Processing helix chain '04' and resid 29 through 34 removed outlier: 4.010A pdb=" N LEU04 33 " --> pdb=" O PHE04 29 " (cutoff:3.500A) removed outlier: 5.646A 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 206 through 214 removed outlier: 4.179A pdb=" N ALA04 210 " --> pdb=" O LYS04 206 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG04 213 " --> pdb=" O ALA04 209 " (cutoff:3.500A) Processing helix chain '04' and resid 220 through 225 removed outlier: 5.535A pdb=" N ASN04 225 " --> pdb=" O GLY04 221 " (cutoff:3.500A) Processing helix chain '04' and resid 259 through 267 removed outlier: 6.090A pdb=" N ASP04 263 " --> pdb=" O ASN04 259 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N LYS04 264 " --> pdb=" O LYS04 260 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N PHE04 265 " --> pdb=" O ARG04 261 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE04 266 " --> pdb=" O THR04 262 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N VAL04 267 " --> pdb=" O ASP04 263 " (cutoff:3.500A) No H-bonds generated for 'chain '04' and resid 259 through 267' Processing helix chain '05' and resid 61 through 72 Processing helix chain '05' and resid 98 through 105 removed outlier: 4.065A pdb=" N ALA05 102 " --> pdb=" O VAL05 98 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASP05 103 " --> pdb=" O GLU05 99 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL05 104 " --> pdb=" O LEU05 100 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N LYS05 105 " --> pdb=" O PHE05 101 " (cutoff:3.500A) No H-bonds generated for 'chain '05' and resid 98 through 105' Processing helix chain '05' and resid 120 through 126 removed outlier: 4.613A pdb=" N TRP05 125 " --> pdb=" O GLY05 120 " (cutoff:3.500A) Processing helix chain '06' and resid 24 through 41 removed outlier: 3.577A pdb=" N ALA06 39 " --> pdb=" O TYR06 35 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N GLN06 41 " --> pdb=" O ALA06 37 " (cutoff:3.500A) Processing helix chain '06' and resid 48 through 53 removed outlier: 7.754A pdb=" N THR06 53 " --> pdb=" O ARG06 49 " (cutoff:3.500A) Processing helix chain '06' and resid 97 through 116 Processing helix chain '06' and resid 130 through 142 removed outlier: 3.540A pdb=" N LEU06 134 " --> pdb=" O LYS06 130 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA06 142 " --> pdb=" O LEU06 138 " (cutoff:3.500A) Processing helix chain '06' and resid 155 through 163 removed outlier: 3.973A pdb=" N ALA06 160 " --> pdb=" O ASN06 156 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASN06 163 " --> pdb=" O LEU06 159 " (cutoff:3.500A) Processing helix chain '06' and resid 176 through 184 removed outlier: 3.518A pdb=" N ILE06 181 " --> pdb=" O PRO06 177 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE06 183 " --> pdb=" O SER06 179 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ASP06 184 " --> pdb=" O LEU06 180 " (cutoff:3.500A) Processing helix chain '06' and resid 189 through 201 removed outlier: 3.938A pdb=" N LYS06 194 " --> pdb=" O ALA06 190 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN06 195 " --> pdb=" O ASP06 191 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET06 199 " --> pdb=" O GLN06 195 " (cutoff:3.500A) Processing helix chain '06' and resid 15 through 20 removed outlier: 3.997A pdb=" N GLY06 20 " --> pdb=" O SER06 15 " (cutoff:3.500A) No H-bonds generated for 'chain '06' and resid 15 through 20' Processing helix chain '07' and resid 1 through 20 removed outlier: 3.562A pdb=" N ASP07 5 " --> pdb=" O ALA07 1 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N VAL07 12 " --> pdb=" O LYS07 8 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LYS07 13 " --> pdb=" O ASP07 9 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N GLU07 18 " --> pdb=" O LYS07 14 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN07 20 " --> pdb=" O MET07 16 " (cutoff:3.500A) Processing helix chain '07' and resid 41 through 46 removed outlier: 3.748A pdb=" N ASP07 45 " --> pdb=" O GLU07 41 " (cutoff:3.500A) removed outlier: 4.562A 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 60 removed outlier: 3.623A pdb=" N LEU07 56 " --> pdb=" O ALA07 52 " (cutoff:3.500A) Processing helix chain '07' and resid 92 through 110 removed outlier: 3.838A pdb=" N TRP07 96 " --> pdb=" O GLY07 92 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE07 105 " --> pdb=" O ARG07 101 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N VAL07 107 " --> pdb=" O ILE07 103 " (cutoff:3.500A) Proline residue: 07 108 - end of helix Processing helix chain '07' and resid 161 through 173 removed outlier: 3.689A pdb=" N ALA07 167 " --> pdb=" O GLU07 163 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA07 171 " --> pdb=" O ALA07 167 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE07 172 " --> pdb=" O LEU07 168 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ASP07 173 " --> pdb=" O LEU07 169 " (cutoff:3.500A) Processing helix chain '07' and resid 133 through 138 removed outlier: 3.738A pdb=" N ILE07 136 " --> pdb=" O GLU07 133 " (cutoff:3.500A) Proline residue: 07 138 - end of helix Processing helix chain '08' and resid 1 through 7 removed outlier: 4.555A pdb=" N ALA08 6 " --> pdb=" O ARG08 2 " (cutoff:3.500A) Proline residue: 08 7 - end of helix Processing helix chain '08' and resid 59 through 80 Processing helix chain '08' and resid 136 through 152 removed outlier: 4.041A pdb=" N ILE08 140 " --> pdb=" O ASP08 136 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR08 150 " --> pdb=" O ASP08 146 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ARG08 151 " --> pdb=" O LEU08 147 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG08 152 " --> pdb=" O ARG08 148 " (cutoff:3.500A) Processing helix chain '09' and resid 22 through 28 Processing helix chain '09' and resid 29 through 34 Processing helix chain '09' and resid 40 through 50 removed outlier: 3.970A pdb=" N ARG09 50 " --> pdb=" O PHE09 46 " (cutoff:3.500A) Processing helix chain '09' and resid 51 through 73 removed outlier: 4.444A pdb=" N ALA09 56 " --> pdb=" O ALA09 52 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LYS09 57 " --> pdb=" O GLU09 53 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU09 60 " --> pdb=" O ALA09 56 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL09 61 " --> pdb=" O LYS09 57 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU09 62 " --> pdb=" O LEU09 58 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA09 63 " --> pdb=" O ALA09 59 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA09 64 " --> pdb=" O GLU09 60 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ASN09 73 " --> pdb=" O ALA09 69 " (cutoff:3.500A) Processing helix chain '09' and resid 95 through 107 removed outlier: 3.606A pdb=" N ILE09 99 " --> pdb=" O GLY09 95 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR09 104 " --> pdb=" O ALA09 100 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA09 105 " --> pdb=" O ASP09 101 " (cutoff:3.500A) Processing helix chain '10' and resid 3 through 21 removed outlier: 3.712A pdb=" N ILE10 11 " --> pdb=" O ASP10 7 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU10 14 " --> pdb=" O ALA10 10 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU10 17 " --> pdb=" O ALA10 13 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA10 19 " --> pdb=" O VAL10 15 " (cutoff:3.500A) Processing helix chain '10' and resid 33 through 48 removed outlier: 3.680A pdb=" N THR10 39 " --> pdb=" O VAL10 35 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ARG10 42 " --> pdb=" O MET10 38 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA10 44 " --> pdb=" O GLU10 40 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU10 47 " --> pdb=" O LYS10 43 " (cutoff:3.500A) Processing helix chain '10' and resid 62 through 71 removed outlier: 3.757A pdb=" N GLY10 66 " --> pdb=" O ARG10 62 " (cutoff:3.500A) Proline residue: 10 68 - end of helix removed outlier: 4.339A pdb=" N CYS10 71 " --> pdb=" O THR10 67 " (cutoff:3.500A) Processing helix chain '10' and resid 74 through 79 removed outlier: 4.534A pdb=" N GLY10 78 " --> pdb=" O ASP10 74 " (cutoff:3.500A) Proline residue: 10 79 - end of helix No H-bonds generated for 'chain '10' and resid 74 through 79' Processing helix chain '10' and resid 94 through 106 removed outlier: 3.913A pdb=" N GLU10 98 " --> pdb=" O ARG10 94 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE10 99 " --> pdb=" O LEU10 95 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ALA10 100 " --> pdb=" O PHE10 96 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS10 101 " --> pdb=" O LYS10 97 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN10 103 " --> pdb=" O PHE10 99 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA10 104 " --> pdb=" O ALA10 100 " (cutoff:3.500A) Processing helix chain '10' and resid 109 through 114 removed outlier: 6.138A pdb=" N ALA10 112 " --> pdb=" O LYS10 109 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU10 114 " --> pdb=" O ALA10 111 " (cutoff:3.500A) Processing helix chain '11' and resid 23 through 31 removed outlier: 4.578A pdb=" N LEU11 27 " --> pdb=" O VAL11 23 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY11 28 " --> pdb=" O GLY11 24 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLN11 30 " --> pdb=" O ALA11 26 " (cutoff:3.500A) Processing helix chain '11' and resid 33 through 48 removed outlier: 3.640A pdb=" N LYS11 39 " --> pdb=" O MET11 35 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN11 42 " --> pdb=" O CYS11 38 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA11 43 " --> pdb=" O LYS11 39 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LYS11 44 " --> pdb=" O ALA11 40 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP11 46 " --> pdb=" O ASN11 42 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N SER11 47 " --> pdb=" O ALA11 43 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ILE11 48 " --> pdb=" O LYS11 44 " (cutoff:3.500A) Processing helix chain '11' and resid 74 through 82 removed outlier: 3.771A pdb=" N LYS11 80 " --> pdb=" O ALA11 76 " (cutoff:3.500A) Processing helix chain '11' and resid 103 through 113 removed outlier: 3.977A pdb=" N GLU11 107 " --> pdb=" O ALA11 103 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE11 108 " --> pdb=" O GLN11 104 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR11 111 " --> pdb=" O GLU11 107 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS11 112 " --> pdb=" O ILE11 108 " (cutoff:3.500A) Processing helix chain '11' and resid 120 through 136 removed outlier: 3.684A pdb=" N GLY11 136 " --> pdb=" O ALA11 132 " (cutoff:3.500A) Processing helix chain '12' and resid 24 through 38 removed outlier: 3.773A pdb=" N GLU12 31 " --> pdb=" O ARG12 27 " (cutoff:3.500A) Processing helix chain '12' and resid 88 through 96 Processing helix chain '12' and resid 97 through 110 removed outlier: 4.522A pdb=" N ILE12 101 " --> pdb=" O PRO12 97 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU12 102 " --> pdb=" O GLU12 98 " (cutoff:3.500A) Proline residue: 12 110 - end of helix Processing helix chain '12' and resid 112 through 122 removed outlier: 4.998A pdb=" N LYS12 121 " --> pdb=" O ALA12 117 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU12 122 " --> pdb=" O MET12 118 " (cutoff:3.500A) Processing helix chain '13' and resid 109 through 120 removed outlier: 6.451A pdb=" N MET13 113 " --> pdb=" O SER13 109 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N LYS13 114 " --> pdb=" O GLU13 110 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ILE13 115 " --> pdb=" O LYS13 111 " (cutoff:3.500A) Proline residue: 13 120 - end of helix 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: 4.092A pdb=" N ALA14 72 " --> pdb=" O SER14 68 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE14 73 " --> pdb=" O ARG14 69 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR14 74 " --> pdb=" O LYS14 70 " (cutoff:3.500A) removed outlier: 6.907A 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 85 removed outlier: 3.553A pdb=" N LEU14 82 " --> pdb=" O ARG14 78 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA14 83 " --> pdb=" O LEU14 79 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LYS14 84 " --> pdb=" O SER14 80 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N VAL14 85 " --> pdb=" O ASP14 81 " (cutoff:3.500A) No H-bonds generated for 'chain '14' and resid 78 through 85' Processing helix chain '14' and resid 93 through 99 removed outlier: 5.523A pdb=" N ALA14 97 " --> pdb=" O ASN14 93 " (cutoff:3.500A) Processing helix chain '14' and resid 128 through 139 removed outlier: 3.589A pdb=" N ALA14 133 " --> pdb=" O LYS14 129 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA14 134 " --> pdb=" O GLY14 130 " (cutoff:3.500A) Processing helix chain '15' and resid 42 through 58 removed outlier: 3.585A pdb=" N ILE15 46 " --> pdb=" O THR15 42 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA15 52 " --> pdb=" O ALA15 48 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ALA15 56 " --> pdb=" O ALA15 52 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL15 57 " --> pdb=" O MET15 53 " (cutoff:3.500A) Processing helix chain '15' and resid 109 through 125 removed outlier: 3.649A pdb=" N LYS15 118 " --> pdb=" O ARG15 114 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA15 122 " --> pdb=" O LYS15 118 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS15 123 " --> pdb=" O LEU15 119 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU15 124 " --> pdb=" O ALA15 120 " (cutoff:3.500A) Proline residue: 15 125 - end of helix Processing helix chain '16' and resid 13 through 32 removed outlier: 3.716A pdb=" N PHE16 21 " --> pdb=" O ARG16 17 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN16 23 " --> pdb=" O ALA16 19 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG16 30 " --> pdb=" O GLY16 26 " (cutoff:3.500A) Processing helix chain '16' and resid 37 through 58 removed outlier: 3.681A pdb=" N GLU16 43 " --> pdb=" O PRO16 39 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG16 45 " --> pdb=" O ALA16 41 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ARG16 46 " --> pdb=" O LYS16 42 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N VAL16 47 " --> pdb=" O GLU16 43 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU16 49 " --> pdb=" O ARG16 45 " (cutoff:3.500A) Proline residue: 16 50 - end of helix removed outlier: 3.689A pdb=" N LYS16 56 " --> pdb=" O ILE16 52 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N THR16 57 " --> pdb=" O THR16 53 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ASP16 58 " --> pdb=" O LEU16 54 " (cutoff:3.500A) Processing helix chain '16' and resid 59 through 71 removed outlier: 4.845A pdb=" N THR16 70 " --> pdb=" O ALA16 66 " (cutoff:3.500A) Processing helix chain '16' and resid 72 through 88 removed outlier: 4.448A pdb=" N PHE16 80 " --> pdb=" O VAL16 76 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN16 81 " --> pdb=" O ALA16 77 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N LEU16 83 " --> pdb=" O LEU16 79 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N GLY16 84 " --> pdb=" O PHE16 80 " (cutoff:3.500A) Proline residue: 16 85 - end of helix Processing helix chain '17' and resid 2 through 20 removed outlier: 3.676A pdb=" N ARG17 10 " --> pdb=" O ALA17 6 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG17 13 " --> pdb=" O ARG17 9 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA17 14 " --> pdb=" O ARG17 10 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU17 18 " --> pdb=" O ALA17 14 " (cutoff:3.500A) Processing helix chain '17' and resid 58 through 63 removed outlier: 4.381A pdb=" N LYS17 63 " --> pdb=" O ALA17 59 " (cutoff:3.500A) Processing helix chain '17' and resid 67 through 86 removed outlier: 3.674A pdb=" N ARG17 81 " --> pdb=" O ALA17 77 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU17 83 " --> pdb=" O ALA17 79 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU17 84 " --> pdb=" O GLU17 80 " (cutoff:3.500A) Processing helix chain '17' and resid 101 through 114 Processing helix chain '18' and resid 1 through 13 removed outlier: 3.696A pdb=" N GLU18 10 " --> pdb=" O GLN18 6 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLN18 11 " --> pdb=" O LEU18 7 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LYS18 13 " --> pdb=" O GLN18 9 " (cutoff:3.500A) Processing helix chain '18' and resid 96 through 103 removed outlier: 4.599A pdb=" N ARG18 100 " --> pdb=" O LEU18 96 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N GLU18 101 " --> pdb=" O TYR18 97 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG18 102 " --> pdb=" O TYR18 98 " (cutoff:3.500A) removed outlier: 5.836A 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 6 through 21 removed outlier: 3.643A pdb=" N ILE19 16 " --> pdb=" O ARG19 12 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN19 19 " --> pdb=" O LYS19 15 " (cutoff:3.500A) Processing helix chain '19' and resid 25 through 30 removed outlier: 3.710A pdb=" N ARG19 29 " --> pdb=" O GLY19 25 " (cutoff:3.500A) Processing helix chain '19' and resid 31 through 36 removed outlier: 4.187A pdb=" N GLN19 36 " --> pdb=" O ARG19 32 " (cutoff:3.500A) Processing helix chain '19' and resid 38 through 60 removed outlier: 3.628A pdb=" N ARG19 47 " --> pdb=" O GLN19 43 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG19 50 " --> pdb=" O TYR19 46 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LYS19 53 " --> pdb=" O ARG19 49 " (cutoff:3.500A) removed outlier: 3.927A 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 removed outlier: 3.666A pdb=" N ASN19 80 " --> pdb=" O SER19 76 " (cutoff:3.500A) Processing helix chain '19' and resid 90 through 101 removed outlier: 4.395A pdb=" N ASP19 96 " --> pdb=" O LYS19 92 " (cutoff:3.500A) Processing helix chain '19' and resid 102 through 117 removed outlier: 3.678A pdb=" N ALA19 107 " --> pdb=" O VAL19 103 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA19 117 " --> pdb=" O LYS19 113 " (cutoff:3.500A) Processing helix chain '21' and resid 13 through 23 removed outlier: 3.682A pdb=" N ARG21 18 " --> pdb=" O ALA21 14 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL21 20 " --> pdb=" O LYS21 16 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N LEU21 23 " --> pdb=" O LEU21 19 " (cutoff:3.500A) Processing helix chain '21' and resid 28 through 39 Processing helix chain '21' and resid 41 through 61 removed outlier: 3.555A pdb=" N VAL21 45 " --> pdb=" O LYS21 41 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N VAL21 50 " --> pdb=" O LEU21 46 " (cutoff:3.500A) Processing helix chain '22' and resid 1 through 11 removed outlier: 4.018A pdb=" N GLU22 5 " --> pdb=" O MET22 1 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU22 8 " --> pdb=" O GLU22 4 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS22 9 " --> pdb=" O GLU22 5 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU22 11 " --> pdb=" O LEU22 7 " (cutoff:3.500A) Processing helix chain '22' and resid 17 through 26 removed outlier: 3.509A pdb=" N SER22 21 " --> pdb=" O SER22 17 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR22 22 " --> pdb=" O GLU22 18 " (cutoff:3.500A) Processing helix chain '22' and resid 39 through 50 removed outlier: 3.521A pdb=" N LYS22 44 " --> pdb=" O LYS22 40 " (cutoff:3.500A) Processing helix chain '23' and resid 65 through 70 removed outlier: 4.098A pdb=" N VAL23 69 " --> pdb=" O GLN23 65 " (cutoff:3.500A) removed outlier: 5.318A 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: 3.538A pdb=" N SER24 17 " --> pdb=" O GLY24 13 " (cutoff:3.500A) Processing helix chain '24' and resid 43 through 52 removed outlier: 4.151A pdb=" N VAL24 47 " --> pdb=" O ASP24 43 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA24 52 " --> pdb=" O MET24 48 " (cutoff:3.500A) Processing helix chain '24' and resid 53 through 59 removed outlier: 4.103A pdb=" N TYR24 57 " --> pdb=" O LYS24 53 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER24 58 " --> pdb=" O ALA24 54 " (cutoff:3.500A) Processing helix chain '26' and resid 51 through 61 removed outlier: 3.516A pdb=" N MET26 55 " --> pdb=" O SER26 51 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG26 56 " --> pdb=" O ALA26 52 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL26 57 " --> pdb=" O LYS26 53 " (cutoff:3.500A) Processing helix chain '26' and resid 62 through 74 removed outlier: 3.570A pdb=" N ARG26 73 " --> pdb=" O GLU26 69 " (cutoff:3.500A) Processing helix chain '27' and resid 1 through 7 removed outlier: 3.867A pdb=" N LEU27 6 " --> pdb=" O LYS27 2 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ARG27 7 " --> pdb=" O ALA27 3 " (cutoff:3.500A) Processing helix chain '27' and resid 9 through 35 removed outlier: 3.590A pdb=" N GLU27 24 " --> pdb=" O ASN27 20 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLN27 25 " --> pdb=" O LEU27 21 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N PHE27 26 " --> pdb=" O LEU27 22 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG27 29 " --> pdb=" O GLN27 25 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN27 31 " --> pdb=" O ASN27 27 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA27 33 " --> pdb=" O ARG27 29 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER27 34 " --> pdb=" O MET27 30 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY27 35 " --> pdb=" O GLN27 31 " (cutoff:3.500A) Processing helix chain '27' and resid 40 through 62 removed outlier: 3.846A pdb=" N LYS27 44 " --> pdb=" O SER27 40 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA27 51 " --> pdb=" O ARG27 47 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLY27 62 " --> pdb=" O ASN27 58 " (cutoff:3.500A) Processing helix chain '28' and resid 16 through 27 Processing helix chain '28' and resid 40 through 51 removed outlier: 4.097A pdb=" N MET28 46 " --> pdb=" O ALA28 42 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER28 51 " --> pdb=" O ILE28 47 " (cutoff:3.500A) Processing helix chain '29' and resid 43 through 53 removed outlier: 4.526A pdb=" N GLN29 48 " --> pdb=" O PHE29 44 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP29 50 " --> pdb=" O GLY29 46 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL29 51 " --> pdb=" O LYS29 47 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ALA29 52 " --> pdb=" O GLN29 48 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR29 53 " --> pdb=" O ARG29 49 " (cutoff:3.500A) Processing helix chain '29' and resid 55 through 65 removed outlier: 4.516A pdb=" N ARG29 59 " --> pdb=" O GLY29 55 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG29 63 " --> pdb=" O ARG29 59 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE29 64 " --> pdb=" O PHE29 60 " (cutoff:3.500A) Processing helix chain '30' and resid 8 through 20 removed outlier: 4.644A pdb=" N HIS30 18 " --> pdb=" O MET30 14 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ASP30 19 " --> pdb=" O ARG30 15 " (cutoff:3.500A) removed outlier: 3.878A 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: 4.494A pdb=" N THR32 24 " --> pdb=" O ALA32 20 " (cutoff:3.500A) Processing helix chain '32' and resid 25 through 38 Processing helix chain '33' and resid 6 through 14 removed outlier: 4.257A pdb=" N ARG33 12 " --> pdb=" O GLY33 8 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE33 13 " --> pdb=" O ALA33 9 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LYS33 14 " --> pdb=" O ALA33 10 " (cutoff:3.500A) Processing helix chain '33' and resid 31 through 36 removed outlier: 5.318A pdb=" N LYS33 35 " --> pdb=" O ILE33 31 " (cutoff:3.500A) removed outlier: 4.952A 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 removed outlier: 3.546A pdb=" N ARG33 44 " --> pdb=" O LYS33 40 " (cutoff:3.500A) Proline residue: 33 45 - end of helix Processing helix chain '33' and resid 51 through 62 removed outlier: 4.225A pdb=" N GLY33 55 " --> pdb=" O LYS33 51 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N LEU33 56 " --> pdb=" O GLY33 52 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA33 59 " --> pdb=" O GLY33 55 " (cutoff:3.500A) Proline residue: 33 62 - end of helix Processing helix chain 'B' and resid 23 through 28 removed outlier: 4.060A pdb=" N LYS B 27 " --> pdb=" O ASN B 23 " (cutoff:3.500A) Proline residue: B 28 - end of helix No H-bonds generated for 'chain 'B' and resid 23 through 28' Processing helix chain 'B' and resid 41 through 63 Proline residue: B 47 - end of helix removed outlier: 3.529A pdb=" N SER B 61 " --> pdb=" O ASN B 57 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG B 62 " --> pdb=" O LYS B 58 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS B 63 " --> pdb=" O ILE B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 87 removed outlier: 3.834A pdb=" N SER B 76 " --> pdb=" O LYS B 72 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ALA B 78 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N CYS B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 122 removed outlier: 3.544A pdb=" N VAL B 106 " --> pdb=" O ASN B 102 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLN B 108 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER B 109 " --> pdb=" O THR B 105 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN B 121 " --> pdb=" O GLU B 117 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP B 122 " --> pdb=" O THR B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 147 removed outlier: 3.666A pdb=" N SER B 146 " --> pdb=" O LYS B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 169 removed outlier: 3.936A pdb=" N GLU B 168 " --> pdb=" O ASP B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 179 removed outlier: 3.677A pdb=" N LEU B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N GLY B 179 " --> pdb=" O ALA B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 225 removed outlier: 3.949A pdb=" N GLY B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA B 215 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N SER B 225 " --> pdb=" O ARG B 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 11 removed outlier: 3.853A pdb=" N ARG C 10 " --> pdb=" O PRO C 6 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU C 11 " --> pdb=" O ASN C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 47 removed outlier: 3.632A pdb=" N ASN C 31 " --> pdb=" O GLU C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 77 Processing helix chain 'C' and resid 80 through 95 removed outlier: 3.878A pdb=" N LYS C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE C 93 " --> pdb=" O VAL C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 112 removed outlier: 4.185A pdb=" N ASP C 111 " --> pdb=" O LYS C 107 " (cutoff:3.500A) removed outlier: 6.211A 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: 3.888A pdb=" N ARG C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 removed outlier: 3.509A pdb=" N ARG C 135 " --> pdb=" O ARG C 131 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL C 137 " --> pdb=" O MET C 133 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU C 143 " --> pdb=" O ASN C 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 15 removed outlier: 4.119A pdb=" N LEU D 10 " --> pdb=" O PRO D 6 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N SER D 11 " --> pdb=" O LYS D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 65 removed outlier: 3.573A pdb=" N GLU D 56 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE D 63 " --> pdb=" O LYS D 59 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR D 64 " --> pdb=" O VAL D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 removed outlier: 3.557A pdb=" N ASN D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU D 81 " --> pdb=" O GLU D 77 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N LYS D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 96 removed outlier: 3.588A pdb=" N ARG D 96 " --> pdb=" O LEU D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 105 removed outlier: 3.578A pdb=" N TYR D 102 " --> pdb=" O ASP D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 120 removed outlier: 4.106A pdb=" N LYS D 120 " --> pdb=" O LEU D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 164 removed outlier: 3.700A pdb=" N ALA D 156 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA D 157 " --> pdb=" O ARG D 153 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU D 160 " --> pdb=" O ALA D 156 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU D 162 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLN D 163 " --> pdb=" O GLU D 159 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ARG D 164 " --> pdb=" O LEU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 191 removed outlier: 3.543A pdb=" N LEU D 190 " --> pdb=" O GLU D 186 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N SER D 191 " --> pdb=" O ARG D 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 186 through 191' Processing helix chain 'D' and resid 195 through 205 removed outlier: 4.268A pdb=" N ILE D 199 " --> pdb=" O ASN D 195 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS D 205 " --> pdb=" O GLU D 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 70 removed outlier: 3.658A pdb=" N ILE E 59 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N GLU E 64 " --> pdb=" O GLN E 60 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LYS E 65 " --> pdb=" O LYS E 61 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG E 68 " --> pdb=" O GLU E 64 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N MET E 70 " --> pdb=" O ALA E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 118 removed outlier: 5.660A pdb=" N ALA E 112 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL E 113 " --> pdb=" O ALA E 109 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL E 116 " --> pdb=" O ALA E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 147 removed outlier: 3.567A pdb=" N ILE E 140 " --> pdb=" O VAL E 136 " (cutoff:3.500A) removed outlier: 3.678A 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: 5.566A 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 removed outlier: 4.159A pdb=" N LEU E 164 " --> pdb=" O VAL E 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 17 removed outlier: 3.566A pdb=" N SER F 15 " --> pdb=" O HIS F 11 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLU F 16 " --> pdb=" O PRO F 12 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N GLN F 17 " --> pdb=" O ASP F 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 11 through 17' Processing helix chain 'F' and resid 18 through 33 removed outlier: 3.684A pdb=" N GLU F 23 " --> pdb=" O PRO F 19 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA F 27 " --> pdb=" O GLU F 23 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA F 28 " --> pdb=" O ARG F 24 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY F 31 " --> pdb=" O ALA F 27 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA F 32 " --> pdb=" O ALA F 28 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU F 33 " --> pdb=" O ILE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 81 removed outlier: 3.789A pdb=" N ASP F 72 " --> pdb=" O GLN F 68 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU F 73 " --> pdb=" O GLU F 69 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU F 74 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR F 76 " --> pdb=" O ASP F 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 30 removed outlier: 3.574A pdb=" N ALA G 23 " --> pdb=" O SER G 19 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE G 25 " --> pdb=" O LEU G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 54 removed outlier: 3.638A pdb=" N SER G 44 " --> pdb=" O SER G 40 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU G 47 " --> pdb=" O TYR G 43 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR G 48 " --> pdb=" O SER G 44 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER G 53 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 69 removed outlier: 3.738A pdb=" N ALA G 60 " --> pdb=" O SER G 56 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU G 62 " --> pdb=" O LEU G 58 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASN G 67 " --> pdb=" O VAL G 63 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N VAL G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 111 removed outlier: 3.736A pdb=" N ASN G 96 " --> pdb=" O PRO G 92 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA G 97 " --> pdb=" O VAL G 93 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG G 101 " --> pdb=" O ALA G 97 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TRP G 102 " --> pdb=" O LEU G 98 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG G 110 " --> pdb=" O ALA G 106 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N GLY G 111 " --> pdb=" O ALA G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 129 removed outlier: 3.668A pdb=" N ALA G 126 " --> pdb=" O GLU G 122 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA G 127 " --> pdb=" O LEU G 123 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLU G 128 " --> pdb=" O SER G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 146 removed outlier: 3.646A pdb=" N LYS G 135 " --> pdb=" O GLY G 131 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU G 145 " --> pdb=" O HIS G 141 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA G 146 " --> pdb=" O ARG G 142 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 20 removed outlier: 3.558A pdb=" N ARG H 12 " --> pdb=" O ASP H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 43 removed outlier: 3.709A pdb=" N ALA H 34 " --> pdb=" O LYS H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 119 Processing helix chain 'I' and resid 33 through 38 removed outlier: 3.792A pdb=" N PHE I 38 " --> pdb=" O LEU I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 55 removed outlier: 4.921A pdb=" N ARG I 48 " --> pdb=" O ARG I 44 " (cutoff:3.500A) Proline residue: I 50 - end of helix removed outlier: 4.606A pdb=" N LEU I 53 " --> pdb=" O GLN I 49 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N VAL I 54 " --> pdb=" O PRO I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 87 removed outlier: 3.522A pdb=" N THR I 83 " --> pdb=" O ARG I 79 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N MET I 87 " --> pdb=" O THR I 83 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 101 removed outlier: 4.097A pdb=" N ARG I 94 " --> pdb=" O ASP I 90 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N GLU I 96 " --> pdb=" O SER I 92 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS I 99 " --> pdb=" O SER I 95 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA I 100 " --> pdb=" O GLU I 96 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY I 101 " --> pdb=" O LEU I 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 33 removed outlier: 3.703A pdb=" N ASP J 19 " --> pdb=" O HIS J 15 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE J 25 " --> pdb=" O ALA J 21 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA J 29 " --> pdb=" O ILE J 25 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS J 30 " --> pdb=" O VAL J 26 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N THR J 32 " --> pdb=" O THR J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 90 removed outlier: 4.151A pdb=" N MET J 88 " --> pdb=" O VAL J 84 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ARG J 89 " --> pdb=" O ASP J 85 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU J 90 " --> pdb=" O ALA J 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 50 Processing helix chain 'K' and resid 53 through 59 removed outlier: 4.712A pdb=" N SER K 57 " --> pdb=" O GLY K 53 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N THR K 58 " --> pdb=" O SER K 54 " (cutoff:3.500A) Proline residue: K 59 - end of helix No H-bonds generated for 'chain 'K' and resid 53 through 59' Processing helix chain 'K' and resid 60 through 73 removed outlier: 4.127A pdb=" N ASP K 71 " --> pdb=" O GLU K 67 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ALA K 72 " --> pdb=" O ARG K 68 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N VAL K 73 " --> pdb=" O CYS K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 103 removed outlier: 5.297A pdb=" N ILE K 96 " --> pdb=" O ARG K 92 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG K 97 " --> pdb=" O GLU K 93 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA K 98 " --> pdb=" O SER K 94 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU K 99 " --> pdb=" O THR K 95 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN K 100 " --> pdb=" O ILE K 96 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA K 101 " --> pdb=" O ARG K 97 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 9 Processing helix chain 'L' and resid 21 through 26 removed outlier: 6.048A pdb=" N ALA L 25 " --> pdb=" O PRO L 21 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 117 removed outlier: 5.175A pdb=" N TYR L 116 " --> pdb=" O ALA L 112 " (cutoff:3.500A) removed outlier: 3.877A 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 22 removed outlier: 3.724A pdb=" N THR M 19 " --> pdb=" O VAL M 15 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER M 20 " --> pdb=" O ILE M 16 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ILE M 21 " --> pdb=" O ALA M 17 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N TYR M 22 " --> pdb=" O LEU M 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 37 Processing helix chain 'M' and resid 43 through 48 removed outlier: 5.262A pdb=" N SER M 48 " --> pdb=" O ILE M 44 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 63 removed outlier: 3.647A pdb=" N ASP M 53 " --> pdb=" O GLU M 49 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR M 54 " --> pdb=" O GLY M 50 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU M 55 " --> pdb=" O GLN M 51 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU M 58 " --> pdb=" O THR M 54 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N LYS M 61 " --> pdb=" O ASP M 57 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE M 62 " --> pdb=" O GLU M 58 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N VAL M 63 " --> pdb=" O VAL M 59 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 83 removed outlier: 3.773A pdb=" N ARG M 70 " --> pdb=" O GLY M 66 " (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 20 removed outlier: 3.531A pdb=" N LYS N 11 " --> pdb=" O ALA N 7 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA N 14 " --> pdb=" O VAL N 10 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N TYR N 19 " --> pdb=" O LEU N 15 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE N 20 " --> pdb=" O ALA N 16 " (cutoff:3.500A) Processing helix chain 'N' and resid 23 through 33 removed outlier: 5.489A pdb=" N LYS N 27 " --> pdb=" O ARG N 23 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE N 29 " --> pdb=" O GLU N 25 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ILE N 30 " --> pdb=" O LEU N 26 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ASP N 32 " --> pdb=" O ALA N 28 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N VAL N 33 " --> pdb=" O ILE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 50 removed outlier: 3.757A pdb=" N ALA N 43 " --> pdb=" O ASP N 39 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL N 44 " --> pdb=" O ARG N 40 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N GLN N 48 " --> pdb=" O VAL N 44 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N THR N 49 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU N 50 " --> pdb=" O LYS N 46 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 90 removed outlier: 3.728A pdb=" N ARG N 84 " --> pdb=" O ARG N 80 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA N 87 " --> pdb=" O VAL N 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 15 removed outlier: 3.767A pdb=" N LYS O 9 " --> pdb=" O GLU O 5 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N SER O 12 " --> pdb=" O ALA O 8 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU O 13 " --> pdb=" O LYS O 9 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY O 15 " --> pdb=" O VAL O 11 " (cutoff:3.500A) Processing helix chain 'O' and resid 23 through 43 removed outlier: 3.563A pdb=" N ILE O 35 " --> pdb=" O LEU O 31 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLY O 40 " --> pdb=" O ASN O 36 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N HIS O 41 " --> pdb=" O HIS O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 73 removed outlier: 3.970A pdb=" N GLY O 54 " --> pdb=" O HIS O 50 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET O 58 " --> pdb=" O GLY O 54 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 84 removed outlier: 3.598A pdb=" N GLU O 82 " --> pdb=" O THR O 78 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG O 83 " --> pdb=" O GLN O 79 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 64 removed outlier: 3.612A pdb=" N GLN P 63 " --> pdb=" O HIS P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 79 removed outlier: 3.708A pdb=" N VAL P 78 " --> pdb=" O LEU P 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 33 removed outlier: 4.395A pdb=" N ASN R 30 " --> pdb=" O ALA R 26 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR R 31 " --> pdb=" O THR R 27 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ILE R 32 " --> pdb=" O LEU R 28 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N THR R 33 " --> pdb=" O LYS R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 45 removed outlier: 3.914A pdb=" N THR R 44 " --> pdb=" O PRO R 40 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY R 45 " --> pdb=" O SER R 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 40 through 45' Processing helix chain 'R' and resid 47 through 65 removed outlier: 3.604A pdb=" N LYS R 59 " --> pdb=" O ALA R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 12 through 17 removed outlier: 5.519A pdb=" N VAL R 17 " --> pdb=" O PHE R 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 12 through 17' Processing helix chain 'S' and resid 11 through 25 removed outlier: 3.612A pdb=" N LYS S 17 " --> pdb=" O HIS S 13 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLU S 23 " --> pdb=" O GLU S 19 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 69 through 75 removed outlier: 4.825A pdb=" N PHE S 73 " --> pdb=" O LYS S 69 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA S 74 " --> pdb=" O LEU S 70 " (cutoff:3.500A) Proline residue: S 75 - end of helix No H-bonds generated for 'chain 'S' and resid 69 through 75' Processing helix chain 'T' and resid 6 through 41 removed outlier: 4.748A pdb=" N ALA T 10 " --> pdb=" O ALA T 6 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS T 19 " --> pdb=" O LYS T 15 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER T 22 " --> pdb=" O LYS T 18 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA T 40 " --> pdb=" O ALA T 36 " (cutoff:3.500A) Processing helix chain 'T' and resid 44 through 64 Proline residue: T 55 - end of helix removed outlier: 3.548A pdb=" N ARG T 59 " --> pdb=" O PRO T 55 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY T 64 " --> pdb=" O GLN T 60 " (cutoff:3.500A) Processing helix chain 'T' and resid 67 through 86 removed outlier: 3.504A pdb=" N HIS T 74 " --> pdb=" O LYS T 70 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR T 79 " --> pdb=" O LYS T 75 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA T 80 " --> pdb=" O ALA T 76 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU T 85 " --> pdb=" O GLN T 81 " (cutoff:3.500A) Processing helix chain 'U' and resid 16 through 22 removed outlier: 3.909A pdb=" N ARG U 20 " --> pdb=" O ARG U 16 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER U 21 " --> pdb=" O ARG U 17 " (cutoff:3.500A) Processing helix chain 'U' and resid 24 through 34 removed outlier: 3.576A pdb=" N LEU U 28 " --> pdb=" O LYS U 24 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N GLU U 30 " --> pdb=" O GLY U 26 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ARG U 33 " --> pdb=" O ALA U 29 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ARG U 34 " --> pdb=" O GLU U 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 38 through 61 removed outlier: 3.688A pdb=" N THR U 42 " --> pdb=" O GLU U 38 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL U 52 " --> pdb=" O LYS U 48 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS U 57 " --> pdb=" O LYS U 53 " (cutoff:3.500A) Processing helix chain '03' and resid 6 through 16 removed outlier: 3.834A pdb=" N VAL03 10 " --> pdb=" O LYS03 6 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE03 11 " --> pdb=" O ARG03 7 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG03 12 " --> pdb=" O MET03 8 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS03 14 " --> pdb=" O VAL03 10 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL03 15 " --> pdb=" O ILE03 11 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASP03 16 " --> pdb=" O ARG03 12 " (cutoff:3.500A) Processing helix chain '03' and resid 22 through 35 removed outlier: 3.561A pdb=" N ALA03 28 " --> pdb=" O ASN03 24 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU03 30 " --> pdb=" O ALA03 26 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N LYS03 31 " --> pdb=" O ILE03 27 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU03 32 " --> pdb=" O ALA03 28 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU03 33 " --> pdb=" O LEU03 29 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA03 34 " --> pdb=" O LEU03 30 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N THR03 35 " --> pdb=" O LYS03 31 " (cutoff:3.500A) Processing helix chain '03' and resid 181 through 200 removed outlier: 4.105A pdb=" N GLU03 187 " --> pdb=" O ASP03 183 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN03 188 " --> pdb=" O LYS03 184 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU03 189 " --> pdb=" O LEU03 185 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU03 190 " --> pdb=" O LYS03 186 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU03 196 " --> pdb=" O LEU03 192 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS03 198 " --> pdb=" O VAL03 194 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA03 199 " --> pdb=" O ALA03 195 " (cutoff:3.500A) Processing helix chain 'Z' and resid 23 through 39 removed outlier: 3.871A pdb=" N LYS Z 37 " --> pdb=" O THR Z 33 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR Z 38 " --> pdb=" O VAL Z 34 " (cutoff:3.500A) Processing helix chain 'Z' and resid 45 through 51 removed outlier: 3.627A pdb=" N ASN Z 51 " --> pdb=" O ASP Z 47 " (cutoff:3.500A) Processing helix chain 'Z' and resid 52 through 59 removed outlier: 3.883A pdb=" N ALA Z 57 " --> pdb=" O PRO Z 53 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ARG Z 58 " --> pdb=" O GLU Z 54 " (cutoff:3.500A) Processing helix chain 'Z' and resid 87 through 99 removed outlier: 4.002A pdb=" N GLN Z 97 " --> pdb=" O THR Z 93 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N MET Z 98 " --> pdb=" O GLY Z 94 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ASP Z 99 " --> pdb=" O ALA Z 95 " (cutoff:3.500A) Processing helix chain 'Z' and resid 112 through 126 removed outlier: 3.541A pdb=" N VAL Z 125 " --> pdb=" O LEU Z 121 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLY Z 126 " --> pdb=" O GLY Z 122 " (cutoff:3.500A) Processing helix chain 'Z' and resid 136 through 141 removed outlier: 4.168A pdb=" N VAL Z 140 " --> pdb=" O LYS Z 136 " (cutoff:3.500A) removed outlier: 4.998A 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: 3.873A pdb=" N LEU Z 146 " --> pdb=" O ASP Z 142 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU Z 148 " --> pdb=" O GLU Z 144 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N TYR Z 160 " --> pdb=" O LEU Z 156 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP Z 161 " --> pdb=" O LEU Z 157 " (cutoff:3.500A) Processing helix chain 'Z' and resid 173 through 180 Processing helix chain 'Z' and resid 181 through 198 removed outlier: 3.734A pdb=" N LYS Z 187 " --> pdb=" O GLU Z 183 " (cutoff:3.500A) Processing helix chain 'Z' and resid 282 through 287 removed outlier: 3.844A pdb=" N ILE Z 286 " --> pdb=" O LYS Z 282 " (cutoff:3.500A) removed outlier: 5.136A 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 1 through 4 Processing sheet with id= 2, first strand: chain '04' and resid 72 through 78 removed outlier: 4.944A pdb=" N ILE04 73 " --> pdb=" O SER04 117 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N SER04 117 " --> pdb=" O ILE04 73 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP04 113 " --> pdb=" O VAL04 77 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '04' and resid 79 through 82 removed outlier: 3.739A pdb=" N ILE04 90 " --> pdb=" O GLU04 81 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ASN04 89 " --> pdb=" O ALA04 105 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '04' and resid 127 through 130 removed outlier: 4.817A pdb=" N ASN04 127 " --> pdb=" O LEU04 191 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain '04' and resid 137 through 140 removed outlier: 3.552A pdb=" N SER04 138 " --> pdb=" O ILE04 163 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N THR04 172 " --> pdb=" O VAL04 164 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLU04 179 " --> pdb=" O LEU04 175 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain '05' and resid 3 through 9 removed outlier: 4.287A pdb=" N SER05 199 " --> pdb=" O LYS05 8 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ASP05 200 " --> pdb=" O THR05 112 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N THR05 112 " --> pdb=" O ASP05 200 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain '05' and resid 11 through 16 removed outlier: 3.689A pdb=" N ILE05 22 " --> pdb=" O ILE05 14 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N VAL05 20 " --> pdb=" O THR05 16 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain '05' and resid 36 through 40 removed outlier: 6.400A pdb=" N GLN05 36 " --> pdb=" O ILE05 48 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ILE05 48 " --> pdb=" O GLN05 36 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LYS05 38 " --> pdb=" O ARG05 46 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ARG05 46 " --> pdb=" O LYS05 38 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N LEU05 40 " --> pdb=" O GLY05 44 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLN05 49 " --> pdb=" O THR05 35 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLN05 94 " --> pdb=" O VAL05 34 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain '05' and resid 46 through 51 removed outlier: 5.739A pdb=" N ARG05 46 " --> pdb=" O LEU05 84 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain '06' and resid 1 through 5 No H-bonds generated for sheet with id= 10 Processing sheet with id= 11, first strand: chain '06' and resid 117 through 120 removed outlier: 3.995A pdb=" N ASP06 168 " --> pdb=" O VAL06 146 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain '07' and resid 64 through 68 removed outlier: 3.599A pdb=" N LYS07 32 " --> pdb=" O THR07 156 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN07 36 " --> pdb=" O ASP07 152 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N GLY07 38 " --> pdb=" O GLY07 150 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N GLY07 150 " --> pdb=" O GLY07 38 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU07 151 " --> pdb=" O VAL07 131 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain '08' and resid 14 through 19 removed outlier: 7.035A pdb=" N GLN08 21 " --> pdb=" O LEU08 36 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU08 36 " --> pdb=" O GLN08 21 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE08 23 " --> pdb=" O ARG08 34 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG08 34 " --> pdb=" O ILE08 23 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N GLY08 30 " --> pdb=" O GLY08 27 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain '08' and resid 39 through 44 removed outlier: 7.650A pdb=" N ALA08 39 " --> pdb=" O ARG08 54 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain '08' and resid 81 through 88 removed outlier: 3.522A pdb=" N GLY08 134 " --> pdb=" O PHE08 82 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N THR08 128 " --> pdb=" O LEU08 88 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain '08' and resid 100 through 105 removed outlier: 6.685A pdb=" N ASN08 100 " --> pdb=" O LEU08 116 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain '09' and resid 76 through 83 removed outlier: 8.005A pdb=" N GLU09 76 " --> pdb=" O LYS09 141 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU09 149 " --> pdb=" O SER09 82 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain '10' and resid 24 through 28 removed outlier: 4.418A pdb=" N ALA10 25 " --> pdb=" O SER10 85 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain '11' and resid 7 through 10 removed outlier: 4.027A pdb=" N VAL11 57 " --> pdb=" O VAL11 69 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL11 69 " --> pdb=" O VAL11 57 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain '11' and resid 98 through 101 Processing sheet with id= 21, first strand: chain '12' and resid 52 through 57 removed outlier: 5.443A pdb=" N ASP12 19 " --> pdb=" O LEU12 140 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain '12' and resid 74 through 78 removed outlier: 7.340A pdb=" N GLY12 83 " --> pdb=" O THR12 78 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain '13' and resid 18 through 21 removed outlier: 3.646A pdb=" N THR13 6 " --> pdb=" O CYS13 21 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ASN13 82 " --> pdb=" O MET13 7 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain '15' and resid 37 through 40 removed outlier: 3.549A pdb=" N LYS15 71 " --> pdb=" O VAL15 93 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain '15' and resid 62 through 66 removed outlier: 6.236A 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: 3.605A pdb=" N MET15 105 " --> pdb=" O PHE15 31 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N SER15 30 " --> pdb=" O LYS15 133 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS15 133 " --> pdb=" O SER15 30 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LYS15 127 " --> pdb=" O VAL15 36 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain '16' and resid 33 through 36 removed outlier: 5.927A pdb=" N MET16 110 " --> pdb=" O CYS16 100 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR16 112 " --> pdb=" O LEU16 98 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU16 114 " --> pdb=" O ARG16 96 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N TYR16 94 " --> pdb=" O VAL16 116 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain '17' and resid 49 through 53 removed outlier: 3.886A pdb=" N VAL17 49 " --> pdb=" O VAL17 39 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE17 35 " --> pdb=" O THR17 53 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG17 25 " --> pdb=" O ILE17 40 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL17 28 " --> pdb=" O ASP17 93 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain '18' and resid 37 through 44 Processing sheet with id= 29, first strand: chain '18' and resid 48 through 51 removed outlier: 3.641A pdb=" N ALA18 48 " --> pdb=" O THR18 59 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N SER18 56 " --> pdb=" O THR18 75 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain '20' and resid 11 through 15 removed outlier: 3.609A pdb=" N VAL20 4 " --> pdb=" O MET20 40 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N MET20 40 " --> pdb=" O VAL20 4 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain '20' and resid 17 through 22 removed outlier: 6.465A pdb=" N ASP20 95 " --> pdb=" O VAL20 64 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LYS20 60 " --> pdb=" O THR20 99 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain '20' and resid 57 through 60 removed outlier: 4.332A pdb=" N VAL20 58 " --> pdb=" O SER20 102 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain '20' and resid 65 through 68 removed outlier: 3.774A pdb=" N ALA20 65 " --> pdb=" O ASP20 95 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLY20 67 " --> pdb=" O PHE20 93 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain '20' and resid 69 through 78 removed outlier: 5.297A pdb=" N GLU20 70 " --> pdb=" O GLN20 91 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLN20 91 " --> pdb=" O GLU20 70 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TYR20 83 " --> pdb=" O ARG20 78 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain '21' and resid 2 through 8 removed outlier: 4.720A pdb=" N THR21 3 " --> pdb=" O VAL21 107 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL21 107 " --> pdb=" O THR21 3 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain '22' and resid 28 through 34 removed outlier: 6.313A pdb=" N ASN22 28 " --> pdb=" O LEU22 87 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE22 30 " --> pdb=" O VAL22 85 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS22 81 " --> pdb=" O VAL22 34 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LYS22 66 " --> pdb=" O ARG22 77 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ASP22 79 " --> pdb=" O LYS22 64 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LYS22 64 " --> pdb=" O ASP22 79 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LYS22 81 " --> pdb=" O VAL22 62 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL22 62 " --> pdb=" O LYS22 81 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ALA22 83 " --> pdb=" O THR22 60 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N THR22 60 " --> pdb=" O ALA22 83 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL22 85 " --> pdb=" O VAL22 58 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL22 58 " --> pdb=" O VAL22 85 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain '23' and resid 39 through 44 removed outlier: 4.950A pdb=" N ASN23 39 " --> pdb=" O ALA23 62 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain '23' and resid 82 through 86 Processing sheet with id= 39, first strand: chain '24' and resid 2 through 5 Processing sheet with id= 40, first strand: chain '24' and resid 37 through 42 removed outlier: 3.789A pdb=" N ILE24 89 " --> pdb=" O PRO24 27 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain '25' and resid 46 through 50 removed outlier: 8.376A pdb=" N ASN25 46 " --> pdb=" O LYS25 58 " (cutoff:3.500A) removed outlier: 4.148A 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 removed outlier: 3.593A pdb=" N LYS25 62 " --> pdb=" O GLU25 79 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain '26' and resid 11 through 18 removed outlier: 3.536A pdb=" N VAL26 12 " --> pdb=" O PHE26 28 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER26 18 " --> pdb=" O ASN26 22 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ASN26 22 " --> pdb=" O SER26 18 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain '26' and resid 34 through 40 Processing sheet with id= 45, first strand: chain '28' and resid 34 through 38 removed outlier: 4.136A pdb=" N LYS28 5 " --> pdb=" O GLU28 57 " (cutoff:3.500A) removed outlier: 7.250A 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 '31' and resid 18 through 23 removed outlier: 6.473A pdb=" N HIS31 18 " --> pdb=" O SER31 12 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE31 47 " --> pdb=" O SER31 13 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU31 33 " --> pdb=" O GLU31 50 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain '34' and resid 13 through 19 removed outlier: 8.392A pdb=" N ASN34 13 " --> pdb=" O SER34 28 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER34 28 " --> pdb=" O ASN34 13 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE34 26 " --> pdb=" O LYS34 15 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N CYS34 27 " --> pdb=" O HIS34 33 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N HIS34 33 " --> pdb=" O CYS34 27 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'B' and resid 30 through 33 removed outlier: 4.320A pdb=" N VAL B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'B' and resid 88 through 91 removed outlier: 3.533A pdb=" N ILE B 185 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE B 197 " --> pdb=" O VAL B 182 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA B 184 " --> pdb=" O PHE B 197 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'C' and resid 18 through 21 removed outlier: 6.044A pdb=" N ASN C 18 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG C 58 " --> pdb=" O THR C 20 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG C 53 " --> pdb=" O HIS C 68 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL C 65 " --> pdb=" O GLN C 99 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'C' and resid 163 through 170 removed outlier: 3.508A pdb=" N GLY C 154 " --> pdb=" O ARG C 163 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE C 201 " --> pdb=" O ASP C 182 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ASP C 180 " --> pdb=" O LYS C 203 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N GLU C 205 " --> pdb=" O ARG C 178 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ARG C 178 " --> pdb=" O GLU C 205 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'D' and resid 140 through 143 removed outlier: 6.066A pdb=" N GLU D 178 " --> pdb=" O ASP D 173 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'E' and resid 10 through 15 removed outlier: 6.551A pdb=" N LEU E 35 " --> pdb=" O ILE E 15 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'E' and resid 82 through 87 removed outlier: 7.278A pdb=" N HIS E 82 " --> pdb=" O PRO E 97 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL E 93 " --> pdb=" O GLY E 86 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG E 92 " --> pdb=" O TYR E 127 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N TYR E 127 " --> pdb=" O ARG E 92 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU E 123 " --> pdb=" O GLN E 96 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'E' and resid 31 through 40 removed outlier: 4.618A pdb=" N GLY E 50 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ARG E 44 " --> pdb=" O ASP E 40 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'F' and resid 39 through 43 removed outlier: 3.776A pdb=" N LEU F 61 " --> pdb=" O GLU F 40 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TRP F 42 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TYR F 59 " --> pdb=" O TRP F 42 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ILE F 6 " --> pdb=" O MET F 62 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N HIS F 3 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR F 92 " --> pdb=" O HIS F 3 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLU F 5 " --> pdb=" O MET F 90 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'G' and resid 72 through 76 Processing sheet with id= 59, first strand: chain 'H' and resid 22 through 28 removed outlier: 5.956A pdb=" N ALA H 22 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLU H 51 " --> pdb=" O GLU H 57 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N THR H 61 " --> pdb=" O ASP H 47 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ASP H 47 " --> pdb=" O THR H 61 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'H' and resid 73 through 76 removed outlier: 4.417A pdb=" N SER H 73 " --> pdb=" O ALA H 129 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL H 102 " --> pdb=" O ILE H 125 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'I' and resid 4 through 10 removed outlier: 3.512A pdb=" N TYR I 5 " --> pdb=" O ILE I 20 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLY I 9 " --> pdb=" O ALA I 16 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS I 67 " --> pdb=" O ALA I 15 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE I 19 " --> pdb=" O TYR I 63 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYS I 26 " --> pdb=" O LEU I 60 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'J' and resid 35 through 38 removed outlier: 8.243A pdb=" N GLN J 35 " --> pdb=" O VAL J 77 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ASP J 75 " --> pdb=" O ARG J 37 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA J 12 " --> pdb=" O HIS J 70 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE J 8 " --> pdb=" O VAL J 74 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'J' and resid 39 through 42 removed outlier: 4.878A pdb=" N LEU J 42 " --> pdb=" O LEU J 71 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N LEU J 71 " --> pdb=" O LEU J 42 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'J' and resid 44 through 52 removed outlier: 6.623A pdb=" N GLU J 47 " --> pdb=" O ILE J 67 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'K' and resid 30 through 34 removed outlier: 6.360A pdb=" N ILE K 109 " --> pdb=" O LEU K 81 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL K 83 " --> pdb=" O ILE K 109 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ASP K 111 " --> pdb=" O VAL K 83 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N VAL K 85 " --> pdb=" O ASP K 111 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'L' and resid 28 through 31 removed outlier: 5.175A pdb=" N LEU L 80 " --> pdb=" O VAL L 97 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'L' and resid 35 through 40 removed outlier: 4.507A pdb=" N ARG L 35 " --> pdb=" O ARG L 53 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LYS L 50 " --> pdb=" O ILE L 66 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N CYS L 52 " --> pdb=" O SER L 64 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N PHE L 60 " --> pdb=" O LEU L 56 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'P' and resid 4 through 10 removed outlier: 3.687A pdb=" N ALA P 7 " --> pdb=" O GLN P 18 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLN P 18 " --> pdb=" O ALA P 7 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'P' and resid 37 through 40 No H-bonds generated for sheet with id= 69 Processing sheet with id= 70, first strand: chain 'Q' and resid 6 through 10 removed outlier: 3.520A pdb=" N GLY Q 9 " --> pdb=" O VAL Q 58 " (cutoff:3.500A) removed outlier: 6.989A 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 30 removed outlier: 4.896A pdb=" N LYS Q 18 " --> pdb=" O ASP Q 47 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LYS Q 35 " --> pdb=" O HIS Q 30 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'S' and resid 47 through 51 removed outlier: 3.707A pdb=" N ILE S 48 " --> pdb=" O VAL S 59 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL S 59 " --> pdb=" O ILE S 48 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain '03' and resid 60 through 64 removed outlier: 4.050A pdb=" N GLY03 61 " --> pdb=" O TYR03 163 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain '03' and resid 169 through 177 removed outlier: 5.655A pdb=" N GLY03 169 " --> pdb=" O LEU03 48 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL03 46 " --> pdb=" O ILE03 171 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N THR03 173 " --> pdb=" O VAL03 44 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL03 44 " --> pdb=" O THR03 173 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LYS03 177 " --> pdb=" O GLU03 40 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N GLU03 40 " --> pdb=" O LYS03 177 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS03 211 " --> pdb=" O ASN03 47 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL03 212 " --> pdb=" O VAL03 224 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'Z' and resid 64 through 71 removed outlier: 3.698A pdb=" N TYR Z 69 " --> pdb=" O TYR Z 76 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY Z 100 " --> pdb=" O ASN Z 13 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY Z 15 " --> pdb=" O GLY Z 100 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL Z 132 " --> pdb=" O PRO Z 168 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL Z 170 " --> pdb=" O VAL Z 132 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'Z' and resid 210 through 215 removed outlier: 7.193A pdb=" N PHE Z 210 " --> pdb=" O LYS Z 294 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS Z 294 " --> pdb=" O PHE Z 210 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU Z 212 " --> pdb=" O LEU Z 292 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLN Z 290 " --> pdb=" O ILE Z 214 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA Z 293 " --> pdb=" O GLU Z 243 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'Z' and resid 216 through 219 Processing sheet with id= 78, first strand: chain 'Z' and resid 328 through 332 removed outlier: 3.552A pdb=" N GLN Z 329 " --> pdb=" O ARG Z 377 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LEU Z 372 " --> pdb=" O VAL Z 388 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE Z 376 " --> pdb=" O GLY Z 384 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'Z' and resid 303 through 306 removed outlier: 4.220A pdb=" N LYS Z 303 " --> pdb=" O LEU Z 392 " (cutoff:3.500A) 1737 hydrogen bonds defined for protein. 5145 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3464 hydrogen bonds 5700 hydrogen bond angles 0 basepair planarities 1394 basepair parallelities 2878 stacking parallelities Total time for adding SS restraints: 238.04 Time building geometry restraints manager: 67.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 30536 1.34 - 1.47: 70995 1.47 - 1.59: 56374 1.59 - 1.72: 8608 1.72 - 1.85: 309 Bond restraints: 166822 Sorted by residual: bond pdb=" O3A GCP Z 402 " pdb=" PB GCP Z 402 " ideal model delta sigma weight residual 1.697 1.522 0.175 2.00e-02 2.50e+03 7.64e+01 bond pdb=" C5 U8U Y 34 " pdb=" C6 U8U Y 34 " ideal model delta sigma weight residual 1.506 1.360 0.146 2.00e-02 2.50e+03 5.36e+01 bond pdb=" O3A GCP Z 402 " pdb=" PA GCP Z 402 " ideal model delta sigma weight residual 1.621 1.528 0.093 2.00e-02 2.50e+03 2.18e+01 bond pdb=" C2 U8U Y 34 " pdb=" N3 U8U Y 34 " ideal model delta sigma weight residual 1.510 1.418 0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" N1 U8U Y 34 " pdb=" C2 U8U Y 34 " ideal model delta sigma weight residual 1.475 1.389 0.086 2.00e-02 2.50e+03 1.85e+01 ... (remaining 166817 not shown) Histogram of bond angle deviations from ideal: 93.27 - 104.98: 22291 104.98 - 116.69: 127123 116.69 - 128.40: 91967 128.40 - 140.11: 7694 140.11 - 151.82: 2 Bond angle restraints: 249077 Sorted by residual: angle pdb=" O3' A A 246 " pdb=" C3' A A 246 " pdb=" C2' A A 246 " ideal model delta sigma weight residual 109.50 127.11 -17.61 1.50e+00 4.44e-01 1.38e+02 angle pdb=" N LEU14 95 " pdb=" CA LEU14 95 " pdb=" C LEU14 95 " ideal model delta sigma weight residual 112.89 98.71 14.18 1.24e+00 6.50e-01 1.31e+02 angle pdb=" N VAL10 77 " pdb=" CA VAL10 77 " pdb=" C VAL10 77 " ideal model delta sigma weight residual 111.91 102.40 9.51 8.90e-01 1.26e+00 1.14e+02 angle pdb=" N MET Z 98 " pdb=" CA MET Z 98 " pdb=" C MET Z 98 " ideal model delta sigma weight residual 110.43 124.02 -13.59 1.31e+00 5.83e-01 1.08e+02 angle pdb=" N ARG04 12 " pdb=" CA ARG04 12 " pdb=" C ARG04 12 " ideal model delta sigma weight residual 112.88 100.03 12.85 1.29e+00 6.01e-01 9.92e+01 ... (remaining 249072 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 94830 35.73 - 71.45: 10680 71.45 - 107.18: 1270 107.18 - 142.90: 14 142.90 - 178.63: 19 Dihedral angle restraints: 106813 sinusoidal: 88381 harmonic: 18432 Sorted by residual: dihedral pdb=" C5' A A 246 " pdb=" C4' A A 246 " pdb=" C3' A A 246 " pdb=" O3' A A 246 " ideal model delta sinusoidal sigma weight residual 147.00 80.14 66.86 1 8.00e+00 1.56e-02 9.11e+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 29.35 170.65 1 1.50e+01 4.44e-03 8.48e+01 dihedral pdb=" O4' U011915 " pdb=" C1' U011915 " pdb=" N1 U011915 " pdb=" C2 U011915 " ideal model delta sinusoidal sigma weight residual 200.00 33.46 166.54 1 1.50e+01 4.44e-03 8.42e+01 ... (remaining 106810 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.396: 31768 0.396 - 0.793: 13 0.793 - 1.189: 0 1.189 - 1.585: 0 1.585 - 1.982: 1 Chirality restraints: 31782 Sorted by residual: chirality pdb=" C3' A A 246 " pdb=" C4' A A 246 " pdb=" O3' A A 246 " pdb=" C2' A A 246 " both_signs ideal model delta sigma weight residual False -2.74 -0.76 -1.98 2.00e-01 2.50e+01 9.82e+01 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 3.06 -0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" C3' GCP Z 402 " pdb=" C2' GCP Z 402 " pdb=" C4' GCP Z 402 " pdb=" O3' GCP Z 402 " both_signs ideal model delta sigma weight residual False -2.57 -3.21 0.65 2.00e-01 2.50e+01 1.05e+01 ... (remaining 31779 not shown) Planarity restraints: 13715 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N FME W 101 " -0.225 2.00e-02 2.50e+03 1.84e-01 3.38e+02 pdb=" CA FME W 101 " 0.088 2.00e-02 2.50e+03 pdb=" CN FME W 101 " 0.252 2.00e-02 2.50e+03 pdb=" O1 FME W 101 " -0.115 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C X 69 " -0.111 2.00e-02 2.50e+03 5.54e-02 6.90e+01 pdb=" N1 C X 69 " 0.012 2.00e-02 2.50e+03 pdb=" C2 C X 69 " 0.020 2.00e-02 2.50e+03 pdb=" O2 C X 69 " 0.049 2.00e-02 2.50e+03 pdb=" N3 C X 69 " 0.001 2.00e-02 2.50e+03 pdb=" C4 C X 69 " -0.005 2.00e-02 2.50e+03 pdb=" N4 C X 69 " -0.077 2.00e-02 2.50e+03 pdb=" C5 C X 69 " 0.048 2.00e-02 2.50e+03 pdb=" C6 C X 69 " 0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U01 562 " -0.095 2.00e-02 2.50e+03 5.32e-02 6.36e+01 pdb=" N1 U01 562 " 0.003 2.00e-02 2.50e+03 pdb=" C2 U01 562 " 0.019 2.00e-02 2.50e+03 pdb=" O2 U01 562 " 0.035 2.00e-02 2.50e+03 pdb=" N3 U01 562 " 0.020 2.00e-02 2.50e+03 pdb=" C4 U01 562 " 0.020 2.00e-02 2.50e+03 pdb=" O4 U01 562 " -0.097 2.00e-02 2.50e+03 pdb=" C5 U01 562 " 0.052 2.00e-02 2.50e+03 pdb=" C6 U01 562 " 0.043 2.00e-02 2.50e+03 ... (remaining 13712 not shown) Histogram of nonbonded interaction distances: 1.31 - 2.03: 1 2.03 - 2.75: 16027 2.75 - 3.47: 204690 3.47 - 4.18: 501348 4.18 - 4.90: 670873 Nonbonded interactions: 1392939 Sorted by model distance: nonbonded pdb=" O3' A Y 76 " pdb=" C LYS Y 101 " model vdw 1.314 3.270 nonbonded pdb=" O2' A Y 69 " pdb=" O5' C Y 70 " model vdw 2.250 2.440 nonbonded pdb=" O3' A Y 76 " pdb=" O LYS Y 101 " model vdw 2.253 3.040 nonbonded pdb=" O2' A Y 76 " pdb=" O LYS Y 101 " model vdw 2.253 2.440 nonbonded pdb=" O2' A Y 69 " pdb=" O4' C Y 70 " model vdw 2.328 2.440 ... (remaining 1392934 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: 7.800 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: 0.100 Extract box with map and model: 26.570 Check model and map are aligned: 1.680 Set scattering table: 1.020 Process input model: 543.310 Find NCS groups from input model: 3.180 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 586.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 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 0.175 166822 Z= 0.419 Angle : 1.047 27.051 249077 Z= 0.692 Chirality : 0.089 1.982 31782 Planarity : 0.009 0.184 13715 Dihedral : 22.525 178.629 94927 Min Nonbonded Distance : 1.314 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 2.72 % Allowed : 13.87 % Favored : 83.41 % Rotamer: Outliers : 1.29 % Allowed : 5.85 % Favored : 92.87 % 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: -5.24 (0.08), residues: 6366 helix: -3.68 (0.07), residues: 1829 sheet: -3.11 (0.14), residues: 1049 loop : -3.57 (0.08), residues: 3488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.006 TRP F 42 HIS 0.002 0.000 HIS B 14 PHE 0.035 0.005 PHE24 2 TYR 0.063 0.007 TYR Z 69 ARG 0.006 0.001 ARG G 9 *********************** 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 1882 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 1814 time to evaluate : 6.732 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: 04 78 GLU cc_start: 0.8501 (tt0) cc_final: 0.8263 (mm-30) REVERT: 04 179 GLU cc_start: 0.7263 (tt0) cc_final: 0.6917 (tt0) REVERT: 06 31 VAL cc_start: 0.8874 (t) cc_final: 0.8649 (m) REVERT: 06 199 MET cc_start: 0.8269 (ttp) cc_final: 0.7419 (mmm) REVERT: 07 21 TYR cc_start: 0.7472 (m-80) cc_final: 0.6145 (m-10) REVERT: 07 34 THR cc_start: 0.8900 (m) cc_final: 0.8484 (p) REVERT: 07 37 MET cc_start: 0.7707 (mtt) cc_final: 0.7211 (mtt) REVERT: 07 173 ASP cc_start: 0.7378 (m-30) cc_final: 0.6877 (t70) REVERT: 09 17 ASP cc_start: 0.8386 (m-30) cc_final: 0.8113 (m-30) REVERT: 09 29 PHE cc_start: 0.8544 (t80) cc_final: 0.8316 (t80) REVERT: 09 35 LYS cc_start: 0.9442 (mptp) cc_final: 0.9237 (mmtp) REVERT: 09 94 ILE cc_start: 0.6965 (mp) cc_final: 0.6479 (mp) REVERT: 09 114 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8309 (tt0) REVERT: 10 6 GLN cc_start: 0.8772 (mm110) cc_final: 0.8285 (tm-30) REVERT: 10 56 ARG cc_start: 0.4863 (mmt90) cc_final: 0.4384 (mmt180) REVERT: 11 105 LEU cc_start: 0.9084 (mt) cc_final: 0.8665 (tt) REVERT: 12 25 LEU cc_start: 0.8963 (tp) cc_final: 0.8730 (tt) REVERT: 12 81 ILE cc_start: 0.7852 (OUTLIER) cc_final: 0.7190 (tt) REVERT: 13 7 MET cc_start: 0.8162 (mmp) cc_final: 0.7886 (mmm) REVERT: 13 58 LEU cc_start: 0.8655 (pp) cc_final: 0.8447 (pt) REVERT: 14 36 LYS cc_start: 0.8323 (mttt) cc_final: 0.8054 (pttm) REVERT: 14 58 TYR cc_start: 0.8145 (p90) cc_final: 0.7456 (p90) REVERT: 14 90 VAL cc_start: 0.8357 (t) cc_final: 0.8085 (p) REVERT: 15 1 MET cc_start: 0.6784 (ttp) cc_final: 0.6581 (ttp) REVERT: 15 92 TRP cc_start: 0.8114 (m100) cc_final: 0.7771 (m100) REVERT: 16 98 LEU cc_start: 0.9076 (mt) cc_final: 0.8860 (mp) REVERT: 17 92 PHE cc_start: 0.8846 (t80) cc_final: 0.8418 (t80) REVERT: 17 104 GLN cc_start: 0.8177 (tt0) cc_final: 0.7832 (tp40) REVERT: 18 14 GLN cc_start: 0.7034 (OUTLIER) cc_final: 0.6803 (mp10) REVERT: 18 84 SER cc_start: 0.7600 (p) cc_final: 0.7378 (p) REVERT: 19 96 ASP cc_start: 0.7849 (t70) cc_final: 0.7306 (t0) REVERT: 20 11 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8273 (mp10) REVERT: 20 95 ASP cc_start: 0.7351 (m-30) cc_final: 0.7067 (m-30) REVERT: 21 4 ILE cc_start: 0.8854 (pt) cc_final: 0.8455 (mp) REVERT: 24 45 ASP cc_start: 0.8670 (m-30) cc_final: 0.8223 (m-30) REVERT: 24 64 VAL cc_start: 0.7775 (t) cc_final: 0.7570 (t) REVERT: 24 76 ASP cc_start: 0.7734 (t70) cc_final: 0.7419 (t0) REVERT: 25 22 PHE cc_start: 0.7089 (m-80) cc_final: 0.6405 (m-10) REVERT: 26 15 ASN cc_start: 0.8351 (m-40) cc_final: 0.7929 (m110) REVERT: 28 43 ILE cc_start: 0.9415 (mm) cc_final: 0.9160 (mm) REVERT: 29 33 ASN cc_start: 0.7563 (t0) cc_final: 0.7343 (t0) REVERT: 31 20 TYR cc_start: 0.6713 (m-80) cc_final: 0.6366 (m-80) REVERT: 32 10 LEU cc_start: 0.9038 (tp) cc_final: 0.8809 (tt) REVERT: 32 18 PHE cc_start: 0.8433 (t80) cc_final: 0.8188 (t80) REVERT: B 173 LYS cc_start: 0.9302 (tttt) cc_final: 0.9088 (tptp) REVERT: C 44 LYS cc_start: 0.9363 (tptm) cc_final: 0.9109 (mmtt) REVERT: C 124 GLU cc_start: 0.8463 (mt-10) cc_final: 0.7876 (pp20) REVERT: C 183 TYR cc_start: 0.8000 (t80) cc_final: 0.7725 (t80) REVERT: D 59 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8630 (ttmt) REVERT: D 102 TYR cc_start: 0.8579 (t80) cc_final: 0.8351 (t80) REVERT: D 104 MET cc_start: 0.7411 (mmm) cc_final: 0.7211 (mmt) REVERT: D 201 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8281 (tp30) REVERT: E 10 LEU cc_start: 0.6955 (OUTLIER) cc_final: 0.6049 (pp) REVERT: E 70 MET cc_start: 0.8265 (mmm) cc_final: 0.7478 (mmm) REVERT: E 123 LEU cc_start: 0.8399 (mt) cc_final: 0.7474 (mt) REVERT: F 16 GLU cc_start: 0.9220 (mm-30) cc_final: 0.8903 (mp0) REVERT: F 17 GLN cc_start: 0.9250 (mt0) cc_final: 0.9001 (tm-30) REVERT: F 52 ASN cc_start: 0.9465 (t0) cc_final: 0.9173 (t0) REVERT: F 72 ASP cc_start: 0.8871 (t70) cc_final: 0.8464 (t0) REVERT: F 73 GLU cc_start: 0.9197 (mt-10) cc_final: 0.8662 (mp0) REVERT: G 11 ILE cc_start: 0.8524 (pt) cc_final: 0.8242 (pt) REVERT: G 30 MET cc_start: 0.8898 (ppp) cc_final: 0.8644 (ppp) REVERT: H 57 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7681 (mm-30) REVERT: H 89 ASP cc_start: 0.7533 (p0) cc_final: 0.7013 (p0) REVERT: H 104 SER cc_start: 0.8820 (t) cc_final: 0.8546 (p) REVERT: I 8 THR cc_start: 0.8673 (m) cc_final: 0.8466 (m) REVERT: I 30 ASN cc_start: 0.7721 (t0) cc_final: 0.7319 (t0) REVERT: J 20 GLN cc_start: 0.8246 (pt0) cc_final: 0.7630 (tp-100) REVERT: K 63 GLN cc_start: 0.8124 (pt0) cc_final: 0.7879 (pt0) REVERT: L 71 HIS cc_start: 0.8179 (p90) cc_final: 0.7890 (p-80) REVERT: L 107 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.8114 (tptt) REVERT: M 71 GLU cc_start: 0.9103 (tm-30) cc_final: 0.8804 (tm-30) REVERT: N 11 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8644 (pttm) REVERT: N 52 ARG cc_start: 0.7747 (mmp80) cc_final: 0.7484 (mmp80) REVERT: O 68 TYR cc_start: 0.7900 (t80) cc_final: 0.7014 (t80) REVERT: O 77 TYR cc_start: 0.8178 (t80) cc_final: 0.7932 (t80) REVERT: P 1 MET cc_start: 0.8726 (ttp) cc_final: 0.8434 (tpp) REVERT: P 34 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8435 (pp20) REVERT: Q 42 LYS cc_start: 0.8467 (mtpt) cc_final: 0.7767 (mptt) REVERT: Q 66 LEU cc_start: 0.9196 (mt) cc_final: 0.8932 (mt) REVERT: R 50 TYR cc_start: 0.8451 (m-10) cc_final: 0.7992 (m-10) REVERT: S 13 HIS cc_start: 0.8745 (p90) cc_final: 0.8250 (p90) REVERT: S 20 LYS cc_start: 0.9275 (ttpm) cc_final: 0.8888 (pptt) REVERT: S 55 GLN cc_start: 0.7200 (mm110) cc_final: 0.6630 (mm110) REVERT: T 12 GLN cc_start: 0.8596 (tm-30) cc_final: 0.8378 (tm-30) REVERT: U 18 PHE cc_start: 0.7461 (t80) cc_final: 0.7074 (t80) REVERT: U 32 ARG cc_start: 0.8663 (ptt90) cc_final: 0.8340 (ttt180) REVERT: 03 5 THR cc_start: 0.4698 (OUTLIER) cc_final: 0.4367 (p) REVERT: 03 9 ARG cc_start: 0.8307 (mtp-110) cc_final: 0.8049 (ptt90) REVERT: 03 12 ARG cc_start: 0.7828 (ptp-170) cc_final: 0.7143 (tpt90) REVERT: 03 33 LEU cc_start: 0.3401 (pp) cc_final: 0.2991 (pp) REVERT: 03 37 LYS cc_start: 0.0330 (OUTLIER) cc_final: 0.0048 (tttm) REVERT: Z 39 TYR cc_start: 0.8147 (t80) cc_final: 0.7758 (t80) REVERT: Z 51 ASN cc_start: 0.8478 (p0) cc_final: 0.8026 (m-40) REVERT: Z 255 CYS cc_start: 0.8877 (m) cc_final: 0.8655 (t) REVERT: Z 358 MET cc_start: 0.7165 (pmm) cc_final: 0.6825 (pmm) REVERT: Z 359 VAL cc_start: 0.8548 (t) cc_final: 0.8254 (m) outliers start: 68 outliers final: 9 residues processed: 1865 average time/residue: 1.5566 time to fit residues: 4965.7030 Evaluate side-chains 1071 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 1052 time to evaluate : 7.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 05 residue 133 THR Chi-restraints excluded: chain 06 residue 163 ASN Chi-restraints excluded: chain 12 residue 81 ILE Chi-restraints excluded: chain 18 residue 14 GLN Chi-restraints excluded: chain 20 residue 11 GLN Chi-restraints excluded: chain 21 residue 97 LEU Chi-restraints excluded: chain 24 residue 44 HIS Chi-restraints excluded: chain 27 residue 7 ARG Chi-restraints excluded: chain 34 residue 36 ARG Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain H residue 66 GLN Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain L residue 113 ARG Chi-restraints excluded: chain N residue 11 LYS Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain 03 residue 5 THR Chi-restraints excluded: chain 03 residue 37 LYS 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: 2.9990 chunk 285 optimal weight: 20.0000 chunk 562 optimal weight: 1.9990 chunk 445 optimal weight: 20.0000 chunk 862 optimal weight: 20.0000 chunk 333 optimal weight: 30.0000 chunk 524 optimal weight: 6.9990 chunk 642 optimal weight: 20.0000 chunk 999 optimal weight: 20.0000 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 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 04 36 ASN ** 04 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 04 238 ASN 05 32 ASN ** 05 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 06 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 06 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 06 94 GLN 06 97 ASN ** 06 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 07 62 GLN 08 19 ASN 08 44 HIS 08 47 ASN ** 08 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 110 HIS 09 43 ASN 09 128 HIS 10 88 HIS 11 18 ASN ** 11 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 93 ASN 11 106 GLN ** 12 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 90 ASN 16 18 GLN ** 16 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 17 19 GLN 17 29 HIS 18 14 GLN 18 55 HIS 18 65 ASN 18 114 ASN 19 36 GLN ** 19 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 19 80 ASN 20 18 GLN 20 82 HIS 21 57 ASN 22 59 ASN 22 72 GLN 23 45 GLN 23 53 GLN 23 68 ASN 23 73 ASN ** 24 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 25 72 ASN 27 20 ASN 28 19 HIS ** 28 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 29 61 ASN 33 42 HIS 34 35 GLN B 23 ASN B 35 ASN B 41 ASN B 121 GLN B 177 ASN B 189 ASN C 2 GLN C 18 ASN C 24 ASN ** C 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 GLN D 125 ASN D 135 GLN D 151 GLN D 195 ASN E 134 ASN E 145 ASN F 11 HIS F 55 HIS F 58 HIS F 63 ASN F 68 GLN G 27 ASN ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 141 HIS H 3 GLN ** H 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 ASN I 31 GLN I 36 GLN I 74 GLN J 20 GLN K 21 HIS ** K 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 GLN L 4 ASN ** L 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 ASN L 111 GLN ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 34 ASN N 61 ASN O 61 GLN R 51 GLN ** R 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 55 GLN ** S 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 68 HIS ** T 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 54 GLN 03 168 ASN 03 188 ASN ** Z 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 114 GLN ** Z 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 329 GLN Total number of N/Q/H flips: 86 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 166822 Z= 0.335 Angle : 0.813 13.714 249077 Z= 0.418 Chirality : 0.044 0.292 31782 Planarity : 0.006 0.070 13715 Dihedral : 23.477 179.669 82318 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 24.46 Ramachandran Plot: Outliers : 0.44 % Allowed : 11.84 % Favored : 87.72 % Rotamer: Outliers : 5.09 % Allowed : 16.10 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.97 (0.09), residues: 6366 helix: -1.97 (0.10), residues: 1953 sheet: -2.64 (0.14), residues: 1160 loop : -3.09 (0.10), residues: 3253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP Q 72 HIS 0.012 0.002 HIS17 34 PHE 0.027 0.003 PHE U 11 TYR 0.022 0.003 TYR07 142 ARG 0.011 0.001 ARG B 136 *********************** 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 1416 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 269 poor density : 1147 time to evaluate : 6.924 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: 04 78 GLU cc_start: 0.8598 (tt0) cc_final: 0.8338 (mm-30) REVERT: 04 176 ARG cc_start: 0.8510 (tpt170) cc_final: 0.8199 (tpp80) REVERT: 04 254 LYS cc_start: 0.8321 (tppt) cc_final: 0.8030 (tmtt) REVERT: 06 199 MET cc_start: 0.8306 (ttp) cc_final: 0.7337 (mmm) REVERT: 07 22 ASN cc_start: 0.7687 (m-40) cc_final: 0.6987 (p0) REVERT: 07 31 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7901 (tm-30) REVERT: 07 173 ASP cc_start: 0.7675 (m-30) cc_final: 0.6908 (t70) REVERT: 09 12 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8088 (pp) REVERT: 09 29 PHE cc_start: 0.8363 (t80) cc_final: 0.7796 (t80) REVERT: 09 46 PHE cc_start: 0.8979 (m-80) cc_final: 0.8673 (t80) REVERT: 10 6 GLN cc_start: 0.8992 (mm110) cc_final: 0.8339 (tm-30) REVERT: 10 56 ARG cc_start: 0.4926 (mmt90) cc_final: 0.4356 (mmt180) REVERT: 10 123 ILE cc_start: 0.4200 (OUTLIER) cc_final: 0.3920 (pt) REVERT: 11 60 VAL cc_start: 0.6888 (OUTLIER) cc_final: 0.6594 (t) REVERT: 11 105 LEU cc_start: 0.9111 (mt) cc_final: 0.8853 (mt) REVERT: 11 129 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7763 (mm-30) REVERT: 11 133 ARG cc_start: 0.8125 (ttm110) cc_final: 0.7754 (ptp-110) REVERT: 12 25 LEU cc_start: 0.9008 (tp) cc_final: 0.8771 (tt) REVERT: 13 7 MET cc_start: 0.8188 (mmp) cc_final: 0.7731 (tpp) REVERT: 13 44 LYS cc_start: 0.8513 (mmmt) cc_final: 0.8266 (mmmt) REVERT: 13 90 ASN cc_start: 0.8467 (OUTLIER) cc_final: 0.7958 (p0) REVERT: 13 111 LYS cc_start: 0.8145 (pttp) cc_final: 0.7940 (pttp) REVERT: 14 23 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8346 (mp) REVERT: 14 36 LYS cc_start: 0.8377 (mttt) cc_final: 0.8087 (pttm) REVERT: 14 58 TYR cc_start: 0.8418 (p90) cc_final: 0.7564 (p90) REVERT: 15 91 TYR cc_start: 0.8409 (OUTLIER) cc_final: 0.8193 (p90) REVERT: 15 92 TRP cc_start: 0.8440 (m100) cc_final: 0.8122 (m100) REVERT: 16 98 LEU cc_start: 0.9240 (mt) cc_final: 0.8920 (mp) REVERT: 17 19 GLN cc_start: 0.8772 (pt0) cc_final: 0.8356 (tm-30) REVERT: 17 92 PHE cc_start: 0.8745 (t80) cc_final: 0.8345 (t80) REVERT: 17 104 GLN cc_start: 0.8042 (tt0) cc_final: 0.7552 (tp-100) REVERT: 18 114 ASN cc_start: 0.7588 (OUTLIER) cc_final: 0.7155 (m110) REVERT: 19 96 ASP cc_start: 0.7796 (t70) cc_final: 0.7545 (t70) REVERT: 20 54 VAL cc_start: 0.6644 (OUTLIER) cc_final: 0.6404 (m) REVERT: 21 4 ILE cc_start: 0.8568 (pt) cc_final: 0.8190 (mp) REVERT: 22 1 MET cc_start: 0.2731 (ptt) cc_final: 0.2499 (mpp) REVERT: 23 73 ASN cc_start: 0.7173 (OUTLIER) cc_final: 0.6700 (t0) REVERT: 24 75 GLN cc_start: 0.8569 (tp40) cc_final: 0.8366 (tp40) REVERT: 24 90 ASP cc_start: 0.6980 (m-30) cc_final: 0.6751 (m-30) REVERT: 25 72 ASN cc_start: 0.9081 (OUTLIER) cc_final: 0.8798 (t0) REVERT: 26 15 ASN cc_start: 0.8333 (m-40) cc_final: 0.7853 (m110) REVERT: 27 12 GLU cc_start: 0.8458 (tp30) cc_final: 0.7943 (tp30) REVERT: 27 27 ASN cc_start: 0.8840 (t0) cc_final: 0.8634 (t0) REVERT: 31 32 LYS cc_start: 0.7623 (mmmt) cc_final: 0.7402 (mmmt) REVERT: 31 45 HIS cc_start: 0.7840 (OUTLIER) cc_final: 0.6229 (m90) REVERT: 33 27 ASN cc_start: 0.8230 (t0) cc_final: 0.7906 (t0) REVERT: 33 61 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7454 (pp) REVERT: 34 37 GLN cc_start: 0.8631 (tp-100) cc_final: 0.8317 (tp-100) REVERT: B 116 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8369 (tp) REVERT: B 173 LYS cc_start: 0.9437 (tttt) cc_final: 0.9205 (tptp) REVERT: C 36 PHE cc_start: 0.8037 (t80) cc_final: 0.7424 (t80) REVERT: C 124 GLU cc_start: 0.8454 (mt-10) cc_final: 0.7985 (pp20) REVERT: D 59 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8735 (ttpt) REVERT: D 93 LEU cc_start: 0.9403 (mt) cc_final: 0.9172 (mm) REVERT: D 197 HIS cc_start: 0.9213 (m-70) cc_final: 0.8855 (m-70) REVERT: D 201 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8150 (tp30) REVERT: E 54 GLU cc_start: 0.6448 (tt0) cc_final: 0.6081 (tm-30) REVERT: E 115 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8633 (mt-10) REVERT: F 16 GLU cc_start: 0.9220 (mm-30) cc_final: 0.8917 (mp0) REVERT: F 52 ASN cc_start: 0.9461 (t0) cc_final: 0.9172 (t0) REVERT: G 84 TYR cc_start: 0.7888 (m-80) cc_final: 0.7643 (m-80) REVERT: H 2 MET cc_start: 0.8463 (mmp) cc_final: 0.8226 (mmp) REVERT: H 57 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7691 (mm-30) REVERT: H 82 LEU cc_start: 0.8871 (tp) cc_final: 0.8660 (tp) REVERT: H 84 ILE cc_start: 0.9067 (OUTLIER) cc_final: 0.8856 (mm) REVERT: H 104 SER cc_start: 0.8662 (t) cc_final: 0.8300 (p) REVERT: I 8 THR cc_start: 0.8047 (m) cc_final: 0.7824 (m) REVERT: I 30 ASN cc_start: 0.7775 (t0) cc_final: 0.7435 (t0) REVERT: I 106 ASP cc_start: 0.7485 (t0) cc_final: 0.7152 (t0) REVERT: J 63 ASP cc_start: 0.7502 (t70) cc_final: 0.6488 (t0) REVERT: J 65 TYR cc_start: 0.8811 (m-80) cc_final: 0.8524 (m-10) REVERT: J 75 ASP cc_start: 0.8063 (m-30) cc_final: 0.7341 (m-30) REVERT: K 31 VAL cc_start: 0.9273 (t) cc_final: 0.9050 (p) REVERT: M 57 ASP cc_start: 0.8664 (p0) cc_final: 0.8389 (p0) REVERT: M 71 GLU cc_start: 0.8993 (tm-30) cc_final: 0.8703 (tm-30) REVERT: O 36 ASN cc_start: 0.8364 (m110) cc_final: 0.7676 (m-40) REVERT: O 77 TYR cc_start: 0.8374 (t80) cc_final: 0.8062 (t80) REVERT: P 1 MET cc_start: 0.8861 (ttp) cc_final: 0.8629 (tpp) REVERT: Q 42 LYS cc_start: 0.8461 (mtpt) cc_final: 0.7568 (mptt) REVERT: Q 64 ARG cc_start: 0.8826 (ttp80) cc_final: 0.8621 (mmm160) REVERT: R 25 ILE cc_start: 0.9146 (pt) cc_final: 0.8596 (mp) REVERT: T 14 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7952 (mp0) REVERT: U 32 ARG cc_start: 0.8629 (ptt90) cc_final: 0.8349 (ttt180) REVERT: U 39 LYS cc_start: 0.8891 (mmtt) cc_final: 0.8431 (mmmt) REVERT: U 45 LYS cc_start: 0.8804 (tmtt) cc_final: 0.8538 (tptp) REVERT: U 46 ARG cc_start: 0.8796 (tpt170) cc_final: 0.8569 (ttm170) REVERT: 03 9 ARG cc_start: 0.8276 (mtp-110) cc_final: 0.8072 (ptt90) REVERT: 03 12 ARG cc_start: 0.7786 (ptp-170) cc_final: 0.7115 (tpt90) REVERT: 03 24 ASN cc_start: 0.6444 (OUTLIER) cc_final: 0.6015 (p0) REVERT: 03 196 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8162 (pt) REVERT: Z 39 TYR cc_start: 0.7958 (t80) cc_final: 0.7544 (t80) REVERT: Z 51 ASN cc_start: 0.8664 (p0) cc_final: 0.8028 (m-40) outliers start: 269 outliers final: 154 residues processed: 1308 average time/residue: 1.4390 time to fit residues: 3275.0209 Evaluate side-chains 1097 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 926 time to evaluate : 6.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 222 THR Chi-restraints excluded: chain 05 residue 14 ILE Chi-restraints excluded: chain 05 residue 27 ILE Chi-restraints excluded: chain 05 residue 126 ASN Chi-restraints excluded: chain 05 residue 133 THR Chi-restraints excluded: chain 05 residue 145 SER Chi-restraints excluded: chain 05 residue 180 VAL Chi-restraints excluded: chain 05 residue 186 LEU Chi-restraints excluded: chain 05 residue 197 THR Chi-restraints excluded: chain 06 residue 15 SER Chi-restraints excluded: chain 06 residue 22 ASP Chi-restraints excluded: chain 06 residue 72 SER Chi-restraints excluded: chain 06 residue 73 ILE Chi-restraints excluded: chain 06 residue 116 ASP Chi-restraints excluded: chain 06 residue 149 ILE Chi-restraints excluded: chain 06 residue 163 ASN Chi-restraints excluded: chain 07 residue 46 LYS Chi-restraints excluded: chain 07 residue 146 ASP Chi-restraints excluded: chain 08 residue 9 VAL Chi-restraints excluded: chain 08 residue 19 ASN Chi-restraints excluded: chain 08 residue 25 ILE Chi-restraints excluded: chain 08 residue 100 ASN Chi-restraints excluded: chain 08 residue 146 ASP Chi-restraints excluded: chain 09 residue 12 LEU Chi-restraints excluded: chain 09 residue 20 ASN Chi-restraints excluded: chain 09 residue 22 LYS Chi-restraints excluded: chain 09 residue 40 THR Chi-restraints excluded: chain 09 residue 137 GLU Chi-restraints excluded: chain 10 residue 123 ILE Chi-restraints excluded: chain 11 residue 7 TYR Chi-restraints excluded: chain 11 residue 12 VAL Chi-restraints excluded: chain 11 residue 34 ILE Chi-restraints excluded: chain 11 residue 60 VAL Chi-restraints excluded: chain 11 residue 124 MET Chi-restraints excluded: chain 11 residue 139 VAL Chi-restraints excluded: chain 13 residue 14 SER Chi-restraints excluded: chain 13 residue 25 LEU Chi-restraints excluded: chain 13 residue 56 ASP Chi-restraints excluded: chain 13 residue 61 VAL Chi-restraints excluded: chain 13 residue 69 VAL Chi-restraints excluded: chain 13 residue 90 ASN Chi-restraints excluded: chain 13 residue 92 GLU Chi-restraints excluded: chain 13 residue 107 LEU Chi-restraints excluded: chain 14 residue 5 THR Chi-restraints excluded: chain 14 residue 23 ILE Chi-restraints excluded: chain 14 residue 57 LEU Chi-restraints excluded: chain 14 residue 77 ILE Chi-restraints excluded: chain 14 residue 118 THR Chi-restraints excluded: chain 15 residue 42 THR Chi-restraints excluded: chain 15 residue 91 TYR Chi-restraints excluded: chain 16 residue 47 VAL Chi-restraints excluded: chain 16 residue 62 ASN Chi-restraints excluded: chain 16 residue 89 SER Chi-restraints excluded: chain 16 residue 97 ILE Chi-restraints excluded: chain 16 residue 113 ILE Chi-restraints excluded: chain 17 residue 18 LEU Chi-restraints excluded: chain 17 residue 106 LEU Chi-restraints excluded: chain 18 residue 114 ASN Chi-restraints excluded: chain 20 residue 19 THR Chi-restraints excluded: chain 20 residue 54 VAL Chi-restraints excluded: chain 21 residue 33 LEU Chi-restraints excluded: chain 21 residue 34 ASP Chi-restraints excluded: chain 21 residue 40 ASN Chi-restraints excluded: chain 21 residue 66 ILE Chi-restraints excluded: chain 21 residue 67 ASP Chi-restraints excluded: chain 21 residue 97 LEU Chi-restraints excluded: chain 22 residue 32 LEU Chi-restraints excluded: chain 23 residue 11 ILE Chi-restraints excluded: chain 23 residue 26 ASN Chi-restraints excluded: chain 23 residue 68 ASN Chi-restraints excluded: chain 23 residue 73 ASN Chi-restraints excluded: chain 24 residue 5 ASN Chi-restraints excluded: chain 24 residue 40 ILE Chi-restraints excluded: chain 24 residue 44 HIS Chi-restraints excluded: chain 24 residue 66 ASP Chi-restraints excluded: chain 24 residue 72 VAL Chi-restraints excluded: chain 25 residue 72 ASN Chi-restraints excluded: chain 25 residue 77 SER Chi-restraints excluded: chain 26 residue 3 VAL Chi-restraints excluded: chain 26 residue 24 THR Chi-restraints excluded: chain 26 residue 47 THR Chi-restraints excluded: chain 26 residue 57 VAL Chi-restraints excluded: chain 26 residue 65 THR Chi-restraints excluded: chain 27 residue 7 ARG Chi-restraints excluded: chain 27 residue 11 VAL Chi-restraints excluded: chain 27 residue 24 GLU Chi-restraints excluded: chain 28 residue 22 THR Chi-restraints excluded: chain 28 residue 40 THR Chi-restraints excluded: chain 29 residue 34 LEU Chi-restraints excluded: chain 29 residue 53 THR Chi-restraints excluded: chain 30 residue 24 VAL Chi-restraints excluded: chain 30 residue 31 LYS Chi-restraints excluded: chain 30 residue 35 GLU Chi-restraints excluded: chain 30 residue 38 LEU Chi-restraints excluded: chain 31 residue 10 LEU Chi-restraints excluded: chain 31 residue 11 VAL Chi-restraints excluded: chain 31 residue 45 HIS Chi-restraints excluded: chain 31 residue 47 ILE Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 33 residue 6 VAL Chi-restraints excluded: chain 33 residue 50 SER Chi-restraints excluded: chain 33 residue 61 LEU Chi-restraints excluded: chain 34 residue 36 ARG Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 151 GLN Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain F residue 8 PHE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 96 ASN Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 66 GLN Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 126 PHE Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 71 ASP Chi-restraints excluded: chain K residue 96 ILE Chi-restraints excluded: chain K residue 104 PHE Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain L residue 7 VAL Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain M residue 11 HIS Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 106 ARG Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 34 ASN Chi-restraints excluded: chain O residue 19 ASN Chi-restraints excluded: chain O residue 46 LYS Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain Q residue 52 CYS Chi-restraints excluded: chain Q residue 59 GLU Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain 03 residue 24 ASN Chi-restraints excluded: chain 03 residue 193 LEU Chi-restraints excluded: chain 03 residue 196 LEU Chi-restraints excluded: chain Z residue 47 ASP Chi-restraints excluded: chain Z residue 211 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1101 random chunks: chunk 555 optimal weight: 0.0370 chunk 310 optimal weight: 9.9990 chunk 832 optimal weight: 20.0000 chunk 680 optimal weight: 20.0000 chunk 275 optimal weight: 4.9990 chunk 1001 optimal weight: 20.0000 chunk 1082 optimal weight: 0.7980 chunk 892 optimal weight: 30.0000 chunk 993 optimal weight: 20.0000 chunk 341 optimal weight: 10.0000 chunk 803 optimal weight: 20.0000 overall best weight: 5.1666 ------------------------------------------------------------------------------- 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 ** 04 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 04 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 06 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 06 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 06 195 GLN ** 08 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 103 ASN 11 30 GLN ** 11 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 110 GLN ** 12 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 13 90 ASN 15 13 HIS ** 16 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 18 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 19 36 GLN 20 6 GLN 23 45 GLN 23 73 ASN ** 24 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 27 36 GLN ** 28 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 GLN ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 ASN F 68 GLN G 85 GLN ** G 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 35 GLN ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 ASN ** L 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 34 ASN O 36 ASN ** O 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 30 HIS ** R 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 51 HIS S 56 HIS ** T 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 114 GLN Z 273 ASN ** Z 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 319 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 166822 Z= 0.194 Angle : 0.651 13.683 249077 Z= 0.338 Chirality : 0.037 0.303 31782 Planarity : 0.005 0.067 13715 Dihedral : 23.557 178.882 82289 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 0.38 % Allowed : 11.18 % Favored : 88.44 % Rotamer: Outliers : 4.81 % Allowed : 18.88 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.10), residues: 6366 helix: -1.26 (0.11), residues: 1950 sheet: -2.43 (0.14), residues: 1161 loop : -2.74 (0.10), residues: 3255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 17 HIS 0.009 0.001 HIS17 34 PHE 0.025 0.002 PHE U 18 TYR 0.032 0.002 TYR N 19 ARG 0.010 0.001 ARG10 42 *********************** 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 1308 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 254 poor density : 1054 time to evaluate : 6.790 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 33 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8551 (pp) REVERT: 04 78 GLU cc_start: 0.8500 (tt0) cc_final: 0.8272 (mm-30) REVERT: 04 176 ARG cc_start: 0.8415 (tpt170) cc_final: 0.8172 (tpp80) REVERT: 04 184 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7372 (tm-30) REVERT: 04 254 LYS cc_start: 0.8285 (tppt) cc_final: 0.8009 (tmtt) REVERT: 05 123 LYS cc_start: 0.9391 (tttm) cc_final: 0.9067 (mmtt) REVERT: 06 199 MET cc_start: 0.8219 (ttp) cc_final: 0.7221 (mmm) REVERT: 07 22 ASN cc_start: 0.7552 (m-40) cc_final: 0.6968 (p0) REVERT: 07 31 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7771 (tm-30) REVERT: 07 56 LEU cc_start: 0.8530 (mt) cc_final: 0.8218 (mt) REVERT: 07 173 ASP cc_start: 0.7721 (m-30) cc_final: 0.6910 (t70) REVERT: 08 51 PHE cc_start: 0.5900 (OUTLIER) cc_final: 0.4488 (m-80) REVERT: 09 8 LYS cc_start: 0.8136 (mmmt) cc_final: 0.7733 (mttt) REVERT: 09 29 PHE cc_start: 0.8257 (t80) cc_final: 0.7625 (t80) REVERT: 09 41 LYS cc_start: 0.9018 (tmtt) cc_final: 0.8681 (tptt) REVERT: 09 46 PHE cc_start: 0.8931 (m-80) cc_final: 0.8604 (t80) REVERT: 09 109 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7543 (tp30) REVERT: 10 6 GLN cc_start: 0.9034 (mm110) cc_final: 0.8397 (tm-30) REVERT: 10 56 ARG cc_start: 0.5035 (mmt90) cc_final: 0.4548 (mmt180) REVERT: 10 123 ILE cc_start: 0.4079 (OUTLIER) cc_final: 0.3864 (pt) REVERT: 11 99 LYS cc_start: 0.5188 (mmtm) cc_final: 0.4099 (tptt) REVERT: 11 129 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7723 (mm-30) REVERT: 11 133 ARG cc_start: 0.8065 (ttm110) cc_final: 0.7757 (ptp-110) REVERT: 11 138 VAL cc_start: 0.3942 (OUTLIER) cc_final: 0.3299 (m) REVERT: 12 25 LEU cc_start: 0.8749 (tp) cc_final: 0.8473 (tt) REVERT: 13 7 MET cc_start: 0.8081 (mmp) cc_final: 0.7823 (mmm) REVERT: 13 67 LYS cc_start: 0.8821 (tptp) cc_final: 0.8621 (tptt) REVERT: 14 23 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8462 (mp) REVERT: 14 36 LYS cc_start: 0.8346 (mttt) cc_final: 0.7977 (pttm) REVERT: 14 58 TYR cc_start: 0.8335 (p90) cc_final: 0.7529 (p90) REVERT: 15 91 TYR cc_start: 0.8360 (OUTLIER) cc_final: 0.8018 (p90) REVERT: 15 115 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8564 (mm-30) REVERT: 16 9 GLN cc_start: 0.7968 (tt0) cc_final: 0.7675 (tt0) REVERT: 16 98 LEU cc_start: 0.9077 (mt) cc_final: 0.8753 (mp) REVERT: 17 18 LEU cc_start: 0.8505 (tp) cc_final: 0.8284 (pp) REVERT: 17 92 PHE cc_start: 0.8700 (t80) cc_final: 0.8315 (t80) REVERT: 18 12 MET cc_start: 0.8835 (tmm) cc_final: 0.8624 (tmm) REVERT: 19 96 ASP cc_start: 0.7870 (t70) cc_final: 0.7623 (t70) REVERT: 21 4 ILE cc_start: 0.8519 (pt) cc_final: 0.8209 (mp) REVERT: 22 1 MET cc_start: 0.3619 (ptt) cc_final: 0.2499 (mpp) REVERT: 24 41 GLU cc_start: 0.7329 (pt0) cc_final: 0.6754 (pt0) REVERT: 24 75 GLN cc_start: 0.8604 (tp40) cc_final: 0.8373 (tp40) REVERT: 25 72 ASN cc_start: 0.9121 (t0) cc_final: 0.8910 (m-40) REVERT: 26 15 ASN cc_start: 0.8090 (m-40) cc_final: 0.7686 (m110) REVERT: 26 47 THR cc_start: 0.8313 (OUTLIER) cc_final: 0.7956 (p) REVERT: 26 55 MET cc_start: 0.9133 (mmm) cc_final: 0.8650 (ppp) REVERT: 26 70 LEU cc_start: 0.9292 (tp) cc_final: 0.8910 (tp) REVERT: 31 45 HIS cc_start: 0.7721 (OUTLIER) cc_final: 0.6234 (m90) REVERT: 32 10 LEU cc_start: 0.9054 (tp) cc_final: 0.8777 (tt) REVERT: 33 27 ASN cc_start: 0.8286 (t0) cc_final: 0.7969 (t0) REVERT: 33 61 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7207 (pp) REVERT: B 73 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7809 (ttp-170) REVERT: B 116 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8432 (tp) REVERT: B 173 LYS cc_start: 0.9426 (tttt) cc_final: 0.9160 (tptp) REVERT: C 124 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8015 (pp20) REVERT: C 183 TYR cc_start: 0.7731 (t80) cc_final: 0.7358 (t80) REVERT: C 192 TYR cc_start: 0.7837 (m-80) cc_final: 0.7192 (m-80) REVERT: D 29 THR cc_start: 0.7292 (OUTLIER) cc_final: 0.6798 (p) REVERT: D 59 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8531 (ttpt) REVERT: D 197 HIS cc_start: 0.9116 (m-70) cc_final: 0.8788 (m170) REVERT: D 201 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8090 (tp30) REVERT: E 10 LEU cc_start: 0.6913 (OUTLIER) cc_final: 0.6393 (pp) REVERT: E 54 GLU cc_start: 0.6471 (tt0) cc_final: 0.6246 (tm-30) REVERT: F 16 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8853 (mp0) REVERT: F 23 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8274 (mp0) REVERT: F 52 ASN cc_start: 0.9469 (t0) cc_final: 0.9124 (t0) REVERT: F 72 ASP cc_start: 0.9072 (t0) cc_final: 0.8571 (t0) REVERT: G 84 TYR cc_start: 0.7949 (m-80) cc_final: 0.7696 (m-80) REVERT: H 57 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7662 (mm-30) REVERT: I 30 ASN cc_start: 0.7815 (t0) cc_final: 0.7439 (t0) REVERT: I 55 ASP cc_start: 0.8287 (OUTLIER) cc_final: 0.7934 (p0) REVERT: I 106 ASP cc_start: 0.7499 (t0) cc_final: 0.7161 (t0) REVERT: J 20 GLN cc_start: 0.8506 (pt0) cc_final: 0.7832 (tp-100) REVERT: J 65 TYR cc_start: 0.8813 (m-80) cc_final: 0.8350 (m-10) REVERT: J 75 ASP cc_start: 0.7996 (m-30) cc_final: 0.7688 (m-30) REVERT: K 73 VAL cc_start: 0.7708 (t) cc_final: 0.7431 (m) REVERT: K 76 TYR cc_start: 0.8768 (m-80) cc_final: 0.8498 (m-10) REVERT: O 36 ASN cc_start: 0.8190 (m-40) cc_final: 0.7721 (m-40) REVERT: O 77 TYR cc_start: 0.8292 (t80) cc_final: 0.8073 (t80) REVERT: P 1 MET cc_start: 0.8822 (ttp) cc_final: 0.8591 (tpp) REVERT: P 60 TRP cc_start: 0.8430 (m100) cc_final: 0.8077 (m100) REVERT: Q 42 LYS cc_start: 0.8451 (mtpt) cc_final: 0.7473 (mptt) REVERT: U 18 PHE cc_start: 0.7775 (t80) cc_final: 0.7391 (t80) REVERT: U 32 ARG cc_start: 0.8561 (ptt90) cc_final: 0.8334 (ttt180) REVERT: U 39 LYS cc_start: 0.8704 (mmtt) cc_final: 0.8376 (tptt) REVERT: U 45 LYS cc_start: 0.8794 (tmtt) cc_final: 0.8520 (tptp) REVERT: U 46 ARG cc_start: 0.8826 (tpt170) cc_final: 0.8620 (ttm170) REVERT: Z 39 TYR cc_start: 0.7951 (t80) cc_final: 0.7736 (t80) REVERT: Z 51 ASN cc_start: 0.8564 (p0) cc_final: 0.7964 (m-40) REVERT: Z 243 GLU cc_start: 0.7928 (tt0) cc_final: 0.7152 (pt0) REVERT: Z 358 MET cc_start: 0.6902 (pmm) cc_final: 0.6689 (pmm) outliers start: 254 outliers final: 148 residues processed: 1213 average time/residue: 1.3379 time to fit residues: 2828.8941 Evaluate side-chains 1090 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 927 time to evaluate : 6.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 33 LEU Chi-restraints excluded: chain 04 residue 222 THR Chi-restraints excluded: chain 05 residue 14 ILE Chi-restraints excluded: chain 05 residue 27 ILE Chi-restraints excluded: chain 05 residue 133 THR Chi-restraints excluded: chain 05 residue 142 VAL Chi-restraints excluded: chain 05 residue 186 LEU Chi-restraints excluded: chain 05 residue 197 THR Chi-restraints excluded: chain 06 residue 15 SER Chi-restraints excluded: chain 06 residue 72 SER Chi-restraints excluded: chain 06 residue 116 ASP Chi-restraints excluded: chain 06 residue 149 ILE Chi-restraints excluded: chain 06 residue 175 ILE Chi-restraints excluded: chain 07 residue 46 LYS Chi-restraints excluded: chain 07 residue 152 ASP Chi-restraints excluded: chain 07 residue 154 THR Chi-restraints excluded: chain 08 residue 19 ASN Chi-restraints excluded: chain 08 residue 25 ILE Chi-restraints excluded: chain 08 residue 51 PHE Chi-restraints excluded: chain 08 residue 100 ASN Chi-restraints excluded: chain 08 residue 146 ASP Chi-restraints excluded: chain 08 residue 161 VAL Chi-restraints excluded: chain 09 residue 20 ASN Chi-restraints excluded: chain 09 residue 22 LYS Chi-restraints excluded: chain 09 residue 31 VAL Chi-restraints excluded: chain 09 residue 40 THR Chi-restraints excluded: chain 09 residue 145 ASN Chi-restraints excluded: chain 10 residue 38 MET Chi-restraints excluded: chain 10 residue 99 PHE Chi-restraints excluded: chain 10 residue 117 LEU Chi-restraints excluded: chain 10 residue 123 ILE Chi-restraints excluded: chain 11 residue 7 TYR Chi-restraints excluded: chain 11 residue 34 ILE Chi-restraints excluded: chain 11 residue 67 THR Chi-restraints excluded: chain 11 residue 70 THR Chi-restraints excluded: chain 11 residue 138 VAL Chi-restraints excluded: chain 13 residue 25 LEU Chi-restraints excluded: chain 13 residue 69 VAL Chi-restraints excluded: chain 14 residue 5 THR Chi-restraints excluded: chain 14 residue 23 ILE Chi-restraints excluded: chain 14 residue 77 ILE Chi-restraints excluded: chain 14 residue 92 LEU Chi-restraints excluded: chain 14 residue 118 THR Chi-restraints excluded: chain 15 residue 42 THR Chi-restraints excluded: chain 15 residue 70 ASP Chi-restraints excluded: chain 15 residue 91 TYR Chi-restraints excluded: chain 16 residue 20 MET Chi-restraints excluded: chain 16 residue 47 VAL Chi-restraints excluded: chain 16 residue 89 SER Chi-restraints excluded: chain 16 residue 97 ILE Chi-restraints excluded: chain 16 residue 113 ILE Chi-restraints excluded: chain 17 residue 21 LEU Chi-restraints excluded: chain 17 residue 47 VAL Chi-restraints excluded: chain 17 residue 106 LEU Chi-restraints excluded: chain 18 residue 60 VAL Chi-restraints excluded: chain 18 residue 112 ARG Chi-restraints excluded: chain 19 residue 38 VAL Chi-restraints excluded: chain 20 residue 19 THR Chi-restraints excluded: chain 21 residue 33 LEU Chi-restraints excluded: chain 21 residue 40 ASN Chi-restraints excluded: chain 21 residue 66 ILE Chi-restraints excluded: chain 21 residue 67 ASP Chi-restraints excluded: chain 21 residue 97 LEU Chi-restraints excluded: chain 22 residue 32 LEU Chi-restraints excluded: chain 22 residue 93 LEU Chi-restraints excluded: chain 23 residue 10 VAL Chi-restraints excluded: chain 23 residue 26 ASN Chi-restraints excluded: chain 23 residue 48 VAL Chi-restraints excluded: chain 24 residue 5 ASN Chi-restraints excluded: chain 24 residue 40 ILE Chi-restraints excluded: chain 24 residue 56 PHE Chi-restraints excluded: chain 24 residue 65 VAL Chi-restraints excluded: chain 24 residue 89 ILE Chi-restraints excluded: chain 26 residue 47 THR Chi-restraints excluded: chain 26 residue 65 THR Chi-restraints excluded: chain 27 residue 7 ARG Chi-restraints excluded: chain 27 residue 11 VAL Chi-restraints excluded: chain 27 residue 17 GLU Chi-restraints excluded: chain 28 residue 2 LYS Chi-restraints excluded: chain 28 residue 40 THR Chi-restraints excluded: chain 28 residue 48 ASN Chi-restraints excluded: chain 29 residue 34 LEU Chi-restraints excluded: chain 29 residue 53 THR Chi-restraints excluded: chain 30 residue 31 LYS Chi-restraints excluded: chain 30 residue 38 LEU Chi-restraints excluded: chain 30 residue 53 VAL Chi-restraints excluded: chain 31 residue 45 HIS Chi-restraints excluded: chain 31 residue 47 ILE Chi-restraints excluded: chain 33 residue 6 VAL Chi-restraints excluded: chain 33 residue 50 SER Chi-restraints excluded: chain 33 residue 61 LEU Chi-restraints excluded: chain 34 residue 35 GLN Chi-restraints excluded: chain 34 residue 36 ARG Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 191 SER Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 96 ASN Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 66 GLN Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 71 ASP Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 96 ILE Chi-restraints excluded: chain K residue 104 PHE Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain L residue 102 ASP Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 106 ARG Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain O residue 19 ASN Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain Q residue 52 CYS Chi-restraints excluded: chain R residue 11 ARG Chi-restraints excluded: chain R residue 20 ILE Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain S residue 38 THR Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 64 GLU Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain T residue 5 SER Chi-restraints excluded: chain T residue 7 LYS Chi-restraints excluded: chain 03 residue 8 MET Chi-restraints excluded: chain 03 residue 10 VAL Chi-restraints excluded: chain Z residue 47 ASP Chi-restraints excluded: chain Z residue 140 VAL Chi-restraints excluded: chain Z residue 211 LEU Chi-restraints excluded: chain Z residue 228 THR Chi-restraints excluded: chain Z residue 255 CYS Chi-restraints excluded: chain Z residue 359 VAL 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: 30.0000 chunk 519 optimal weight: 20.0000 chunk 110 optimal weight: 30.0000 chunk 478 optimal weight: 4.9990 chunk 672 optimal weight: 30.0000 chunk 1005 optimal weight: 20.0000 chunk 1064 optimal weight: 6.9990 chunk 525 optimal weight: 20.0000 chunk 952 optimal weight: 40.0000 chunk 286 optimal weight: 6.9990 overall best weight: 11.7994 ------------------------------------------------------------------------------- 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 04 162 GLN ** 04 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 05 130 GLN 05 134 HIS ** 05 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 06 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 06 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 08 19 ASN 08 29 ASN ** 08 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 17 116 GLN ** 18 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 18 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 19 19 GLN 19 51 GLN ** 21 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 23 68 ASN ** 23 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 25 72 ASN 26 15 ASN ** 27 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 28 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 29 20 ASN 31 18 HIS ** 32 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 34 35 GLN ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN D 163 GLN E 76 ASN ** G 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 ASN I 80 HIS ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 ASN ** K 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 7 ASN M 13 HIS M 104 ASN ** O 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 03 160 GLN ** Z 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 166822 Z= 0.358 Angle : 0.777 15.454 249077 Z= 0.397 Chirality : 0.042 0.305 31782 Planarity : 0.006 0.073 13715 Dihedral : 23.865 178.910 82282 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 29.42 Ramachandran Plot: Outliers : 0.36 % Allowed : 13.29 % Favored : 86.35 % Rotamer: Outliers : 6.38 % Allowed : 20.24 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.10), residues: 6366 helix: -1.15 (0.11), residues: 1932 sheet: -2.44 (0.14), residues: 1145 loop : -2.71 (0.10), residues: 3289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP06 60 HIS 0.017 0.002 HIS24 44 PHE 0.023 0.003 PHE F 8 TYR 0.036 0.003 TYR N 19 ARG 0.015 0.001 ARG12 99 *********************** 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 1278 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 337 poor density : 941 time to evaluate : 7.076 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: 05 123 LYS cc_start: 0.9393 (tttm) cc_final: 0.9079 (mmtt) REVERT: 05 128 ARG cc_start: 0.8026 (mmp80) cc_final: 0.7718 (mmm-85) REVERT: 06 199 MET cc_start: 0.8365 (ttp) cc_final: 0.7474 (mmm) REVERT: 07 22 ASN cc_start: 0.7493 (m-40) cc_final: 0.6866 (p0) REVERT: 07 56 LEU cc_start: 0.8453 (mt) cc_final: 0.7552 (mt) REVERT: 07 173 ASP cc_start: 0.7594 (m-30) cc_final: 0.6846 (t0) REVERT: 08 51 PHE cc_start: 0.6257 (OUTLIER) cc_final: 0.4395 (m-80) REVERT: 09 41 LYS cc_start: 0.9048 (tmtt) cc_final: 0.8575 (tptt) REVERT: 09 46 PHE cc_start: 0.9022 (m-80) cc_final: 0.8319 (t80) REVERT: 09 109 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7605 (tp30) REVERT: 10 6 GLN cc_start: 0.9015 (mm110) cc_final: 0.8329 (tm-30) REVERT: 10 31 ARG cc_start: 0.7954 (tpt90) cc_final: 0.7493 (mmm160) REVERT: 10 56 ARG cc_start: 0.4902 (mmt90) cc_final: 0.4138 (mmt180) REVERT: 10 123 ILE cc_start: 0.4299 (OUTLIER) cc_final: 0.4087 (pt) REVERT: 11 45 THR cc_start: 0.6860 (OUTLIER) cc_final: 0.6627 (p) REVERT: 11 48 ILE cc_start: 0.1003 (OUTLIER) cc_final: 0.0296 (mt) REVERT: 12 25 LEU cc_start: 0.8865 (tp) cc_final: 0.8607 (tt) REVERT: 13 7 MET cc_start: 0.8054 (mmp) cc_final: 0.7826 (mmm) REVERT: 13 112 PHE cc_start: 0.8887 (m-80) cc_final: 0.8655 (m-80) REVERT: 14 23 ILE cc_start: 0.9010 (OUTLIER) cc_final: 0.8598 (mp) REVERT: 14 36 LYS cc_start: 0.8368 (mttt) cc_final: 0.7985 (pttm) REVERT: 14 58 TYR cc_start: 0.8555 (p90) cc_final: 0.7813 (p90) REVERT: 15 91 TYR cc_start: 0.8484 (OUTLIER) cc_final: 0.8062 (p90) REVERT: 15 136 MET cc_start: 0.8930 (tmm) cc_final: 0.8436 (tmm) REVERT: 16 24 MET cc_start: 0.9091 (mpp) cc_final: 0.8743 (mmt) REVERT: 16 74 GLU cc_start: 0.8515 (tt0) cc_final: 0.8233 (tm-30) REVERT: 17 17 LYS cc_start: 0.8759 (tppt) cc_final: 0.8306 (ptmt) REVERT: 17 92 PHE cc_start: 0.8642 (t80) cc_final: 0.8215 (t80) REVERT: 19 96 ASP cc_start: 0.7913 (t70) cc_final: 0.7705 (t70) REVERT: 20 83 TYR cc_start: 0.7726 (t80) cc_final: 0.7396 (t80) REVERT: 21 4 ILE cc_start: 0.8614 (pt) cc_final: 0.8172 (mp) REVERT: 25 12 SER cc_start: 0.6742 (OUTLIER) cc_final: 0.6188 (p) REVERT: 25 72 ASN cc_start: 0.9263 (t0) cc_final: 0.9036 (t0) REVERT: 26 15 ASN cc_start: 0.8235 (m110) cc_final: 0.7626 (m110) REVERT: 31 45 HIS cc_start: 0.7688 (OUTLIER) cc_final: 0.6647 (m90) REVERT: 33 61 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7402 (pp) REVERT: B 73 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7780 (ttp-170) REVERT: B 99 MET cc_start: 0.7712 (mtt) cc_final: 0.7504 (mtt) REVERT: B 116 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8480 (tp) REVERT: C 53 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7536 (ptt90) REVERT: C 124 GLU cc_start: 0.8388 (mt-10) cc_final: 0.7969 (pp20) REVERT: C 141 MET cc_start: 0.8963 (mmp) cc_final: 0.8678 (mmm) REVERT: C 183 TYR cc_start: 0.7901 (t80) cc_final: 0.7661 (t80) REVERT: C 192 TYR cc_start: 0.7975 (m-80) cc_final: 0.7583 (t80) REVERT: D 29 THR cc_start: 0.7631 (OUTLIER) cc_final: 0.7130 (p) REVERT: D 59 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8707 (ttpt) REVERT: D 102 TYR cc_start: 0.8534 (t80) cc_final: 0.8087 (t80) REVERT: E 10 LEU cc_start: 0.7198 (OUTLIER) cc_final: 0.6570 (pp) REVERT: E 104 ILE cc_start: 0.8884 (tp) cc_final: 0.8554 (pt) REVERT: F 1 MET cc_start: 0.8443 (ttp) cc_final: 0.8056 (tmm) REVERT: F 16 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8886 (mp0) REVERT: F 21 MET cc_start: 0.9182 (mtt) cc_final: 0.8868 (mmm) REVERT: F 52 ASN cc_start: 0.9505 (t0) cc_final: 0.9127 (t0) REVERT: F 72 ASP cc_start: 0.9018 (t0) cc_final: 0.8499 (t0) REVERT: F 78 PHE cc_start: 0.8863 (m-80) cc_final: 0.8597 (m-80) REVERT: G 27 ASN cc_start: 0.8847 (p0) cc_final: 0.8599 (p0) REVERT: G 36 SER cc_start: 0.8979 (OUTLIER) cc_final: 0.8507 (p) REVERT: H 2 MET cc_start: 0.8131 (mmp) cc_final: 0.7827 (mmp) REVERT: I 30 ASN cc_start: 0.7986 (t0) cc_final: 0.7620 (t0) REVERT: I 44 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.8162 (pmm150) REVERT: I 106 ASP cc_start: 0.7881 (t0) cc_final: 0.7513 (t0) REVERT: J 31 ARG cc_start: 0.7984 (ttp80) cc_final: 0.7600 (ttm110) REVERT: J 75 ASP cc_start: 0.7877 (m-30) cc_final: 0.7558 (m-30) REVERT: K 76 TYR cc_start: 0.8873 (m-80) cc_final: 0.8626 (m-10) REVERT: M 12 LYS cc_start: 0.8810 (mttt) cc_final: 0.8313 (mmtt) REVERT: O 36 ASN cc_start: 0.8241 (m-40) cc_final: 0.7859 (m-40) REVERT: O 77 TYR cc_start: 0.8292 (t80) cc_final: 0.8074 (t80) REVERT: P 54 LEU cc_start: 0.7795 (mt) cc_final: 0.7060 (pt) REVERT: Q 27 PHE cc_start: 0.8776 (t80) cc_final: 0.8574 (t80) REVERT: Q 42 LYS cc_start: 0.8676 (mtpt) cc_final: 0.7551 (mptt) REVERT: U 32 ARG cc_start: 0.8639 (ptt90) cc_final: 0.8327 (ttt180) REVERT: U 36 PHE cc_start: 0.8178 (OUTLIER) cc_final: 0.7850 (t80) REVERT: U 39 LYS cc_start: 0.8766 (mmtt) cc_final: 0.8486 (tptt) REVERT: U 45 LYS cc_start: 0.8805 (tmtt) cc_final: 0.8593 (tptp) REVERT: U 46 ARG cc_start: 0.8819 (tpt170) cc_final: 0.8607 (ttm170) REVERT: Z 39 TYR cc_start: 0.8154 (t80) cc_final: 0.7793 (t80) REVERT: Z 51 ASN cc_start: 0.8707 (p0) cc_final: 0.8054 (m-40) REVERT: Z 91 MET cc_start: 0.7942 (tmm) cc_final: 0.7614 (tpp) REVERT: Z 358 MET cc_start: 0.7154 (pmm) cc_final: 0.6946 (pmm) outliers start: 337 outliers final: 238 residues processed: 1161 average time/residue: 1.3328 time to fit residues: 2706.6728 Evaluate side-chains 1111 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 256 poor density : 855 time to evaluate : 6.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 33 LEU Chi-restraints excluded: chain 04 residue 129 LEU Chi-restraints excluded: chain 04 residue 143 VAL Chi-restraints excluded: chain 04 residue 222 THR Chi-restraints excluded: chain 04 residue 227 VAL Chi-restraints excluded: chain 05 residue 14 ILE Chi-restraints excluded: chain 05 residue 27 ILE Chi-restraints excluded: chain 05 residue 48 ILE Chi-restraints excluded: chain 05 residue 96 ILE Chi-restraints excluded: chain 05 residue 133 THR Chi-restraints excluded: chain 05 residue 145 SER Chi-restraints excluded: chain 05 residue 151 THR Chi-restraints excluded: chain 05 residue 180 VAL Chi-restraints excluded: chain 05 residue 186 LEU Chi-restraints excluded: chain 05 residue 188 LEU Chi-restraints excluded: chain 05 residue 197 THR Chi-restraints excluded: chain 06 residue 15 SER Chi-restraints excluded: chain 06 residue 22 ASP Chi-restraints excluded: chain 06 residue 48 THR Chi-restraints excluded: chain 06 residue 72 SER Chi-restraints excluded: chain 06 residue 73 ILE Chi-restraints excluded: chain 06 residue 116 ASP Chi-restraints excluded: chain 06 residue 149 ILE Chi-restraints excluded: chain 06 residue 175 ILE Chi-restraints excluded: chain 07 residue 46 LYS Chi-restraints excluded: chain 07 residue 146 ASP Chi-restraints excluded: chain 07 residue 152 ASP Chi-restraints excluded: chain 07 residue 154 THR Chi-restraints excluded: chain 08 residue 9 VAL Chi-restraints excluded: chain 08 residue 19 ASN Chi-restraints excluded: chain 08 residue 25 ILE Chi-restraints excluded: chain 08 residue 51 PHE Chi-restraints excluded: chain 08 residue 55 ASP Chi-restraints excluded: chain 08 residue 75 VAL Chi-restraints excluded: chain 08 residue 100 ASN Chi-restraints excluded: chain 08 residue 146 ASP Chi-restraints excluded: chain 08 residue 161 VAL Chi-restraints excluded: chain 09 residue 20 ASN Chi-restraints excluded: chain 09 residue 22 LYS Chi-restraints excluded: chain 09 residue 31 VAL Chi-restraints excluded: chain 09 residue 40 THR Chi-restraints excluded: chain 09 residue 145 ASN Chi-restraints excluded: chain 10 residue 8 LYS Chi-restraints excluded: chain 10 residue 27 VAL Chi-restraints excluded: chain 10 residue 38 MET Chi-restraints excluded: chain 10 residue 99 PHE Chi-restraints excluded: chain 10 residue 123 ILE Chi-restraints excluded: chain 11 residue 7 TYR Chi-restraints excluded: chain 11 residue 12 VAL Chi-restraints excluded: chain 11 residue 34 ILE Chi-restraints excluded: chain 11 residue 45 THR Chi-restraints excluded: chain 11 residue 48 ILE Chi-restraints excluded: chain 11 residue 67 THR Chi-restraints excluded: chain 11 residue 70 THR Chi-restraints excluded: chain 11 residue 72 THR Chi-restraints excluded: chain 11 residue 139 VAL Chi-restraints excluded: chain 12 residue 68 LYS Chi-restraints excluded: chain 12 residue 84 ILE Chi-restraints excluded: chain 13 residue 14 SER Chi-restraints excluded: chain 13 residue 25 LEU Chi-restraints excluded: chain 13 residue 61 VAL Chi-restraints excluded: chain 13 residue 65 THR Chi-restraints excluded: chain 13 residue 69 VAL Chi-restraints excluded: chain 13 residue 107 LEU Chi-restraints excluded: chain 14 residue 23 ILE Chi-restraints excluded: chain 14 residue 77 ILE Chi-restraints excluded: chain 14 residue 90 VAL Chi-restraints excluded: chain 14 residue 92 LEU Chi-restraints excluded: chain 14 residue 110 VAL Chi-restraints excluded: chain 14 residue 118 THR Chi-restraints excluded: chain 15 residue 36 VAL Chi-restraints excluded: chain 15 residue 42 THR Chi-restraints excluded: chain 15 residue 67 VAL Chi-restraints excluded: chain 15 residue 70 ASP Chi-restraints excluded: chain 15 residue 91 TYR Chi-restraints excluded: chain 15 residue 110 GLU Chi-restraints excluded: chain 16 residue 47 VAL Chi-restraints excluded: chain 16 residue 62 ASN Chi-restraints excluded: chain 16 residue 89 SER Chi-restraints excluded: chain 16 residue 97 ILE Chi-restraints excluded: chain 16 residue 113 ILE Chi-restraints excluded: chain 17 residue 18 LEU Chi-restraints excluded: chain 17 residue 21 LEU Chi-restraints excluded: chain 17 residue 27 VAL Chi-restraints excluded: chain 17 residue 69 ASP Chi-restraints excluded: chain 17 residue 106 LEU Chi-restraints excluded: chain 18 residue 49 ILE Chi-restraints excluded: chain 18 residue 60 VAL Chi-restraints excluded: chain 18 residue 84 SER Chi-restraints excluded: chain 18 residue 112 ARG Chi-restraints excluded: chain 19 residue 38 VAL Chi-restraints excluded: chain 20 residue 19 THR Chi-restraints excluded: chain 20 residue 26 ASP Chi-restraints excluded: chain 21 residue 33 LEU Chi-restraints excluded: chain 21 residue 34 ASP Chi-restraints excluded: chain 21 residue 40 ASN Chi-restraints excluded: chain 21 residue 66 ILE Chi-restraints excluded: chain 21 residue 67 ASP Chi-restraints excluded: chain 21 residue 82 MET Chi-restraints excluded: chain 21 residue 85 ILE Chi-restraints excluded: chain 21 residue 97 LEU Chi-restraints excluded: chain 22 residue 32 LEU Chi-restraints excluded: chain 22 residue 43 ILE Chi-restraints excluded: chain 22 residue 70 HIS Chi-restraints excluded: chain 22 residue 93 LEU Chi-restraints excluded: chain 23 residue 10 VAL Chi-restraints excluded: chain 23 residue 11 ILE Chi-restraints excluded: chain 23 residue 26 ASN Chi-restraints excluded: chain 23 residue 48 VAL Chi-restraints excluded: chain 23 residue 68 ASN Chi-restraints excluded: chain 24 residue 5 ASN Chi-restraints excluded: chain 24 residue 40 ILE Chi-restraints excluded: chain 24 residue 56 PHE Chi-restraints excluded: chain 24 residue 66 ASP Chi-restraints excluded: chain 24 residue 89 ILE Chi-restraints excluded: chain 25 residue 12 SER Chi-restraints excluded: chain 25 residue 77 SER Chi-restraints excluded: chain 26 residue 3 VAL Chi-restraints excluded: chain 26 residue 24 THR Chi-restraints excluded: chain 26 residue 47 THR Chi-restraints excluded: chain 26 residue 57 VAL Chi-restraints excluded: chain 26 residue 58 ILE Chi-restraints excluded: chain 26 residue 65 THR Chi-restraints excluded: chain 27 residue 2 LYS Chi-restraints excluded: chain 27 residue 11 VAL Chi-restraints excluded: chain 27 residue 17 GLU Chi-restraints excluded: chain 27 residue 50 VAL Chi-restraints excluded: chain 28 residue 2 LYS Chi-restraints excluded: chain 28 residue 22 THR Chi-restraints excluded: chain 28 residue 34 THR Chi-restraints excluded: chain 28 residue 40 THR Chi-restraints excluded: chain 28 residue 48 ASN Chi-restraints excluded: chain 29 residue 31 ASP Chi-restraints excluded: chain 29 residue 34 LEU Chi-restraints excluded: chain 29 residue 53 THR Chi-restraints excluded: chain 30 residue 24 VAL Chi-restraints excluded: chain 30 residue 31 LYS Chi-restraints excluded: chain 30 residue 38 LEU Chi-restraints excluded: chain 30 residue 53 VAL Chi-restraints excluded: chain 31 residue 11 VAL Chi-restraints excluded: chain 31 residue 28 THR Chi-restraints excluded: chain 31 residue 45 HIS Chi-restraints excluded: chain 31 residue 47 ILE Chi-restraints excluded: chain 32 residue 1 MET Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 33 residue 6 VAL Chi-restraints excluded: chain 33 residue 50 SER Chi-restraints excluded: chain 33 residue 53 ASP Chi-restraints excluded: chain 33 residue 61 LEU Chi-restraints excluded: chain 34 residue 36 ARG Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 108 GLN Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain C residue 53 ARG Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 191 SER Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain F residue 8 PHE Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 96 ASN Chi-restraints excluded: chain G residue 121 ASN Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 44 ARG Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 71 ASP Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 96 ILE Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 61 LYS Chi-restraints excluded: chain M residue 106 ARG Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain O residue 19 ASN Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 38 PHE Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain Q residue 20 ILE Chi-restraints excluded: chain Q residue 22 VAL Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 52 CYS Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain R residue 11 ARG Chi-restraints excluded: chain R residue 20 ILE Chi-restraints excluded: chain R residue 29 LYS Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain S residue 11 ASP Chi-restraints excluded: chain S residue 38 THR Chi-restraints excluded: chain S residue 43 MET Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 64 GLU Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain U residue 12 ASP Chi-restraints excluded: chain U residue 35 GLU Chi-restraints excluded: chain U residue 36 PHE Chi-restraints excluded: chain 03 residue 10 VAL Chi-restraints excluded: chain Z residue 20 VAL Chi-restraints excluded: chain Z residue 32 THR Chi-restraints excluded: chain Z residue 47 ASP Chi-restraints excluded: chain Z residue 140 VAL Chi-restraints excluded: chain Z residue 211 LEU Chi-restraints excluded: chain Z residue 228 THR Chi-restraints excluded: chain Z residue 255 CYS Chi-restraints excluded: chain Z residue 359 VAL 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: 30.0000 chunk 792 optimal weight: 20.0000 chunk 439 optimal weight: 6.9990 chunk 908 optimal weight: 20.0000 chunk 735 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 543 optimal weight: 20.0000 chunk 955 optimal weight: 50.0000 chunk 268 optimal weight: 0.0980 overall best weight: 11.4194 ------------------------------------------------------------------------------- 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** ** 04 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 19 ASN ** 08 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 09 11 ASN ** 09 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 33 ASN ** 11 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 13 3 GLN 16 18 GLN 17 19 GLN 18 114 ASN 19 19 GLN 19 51 GLN ** 24 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 28 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 29 20 ASN ** 32 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 ASN ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 HIS ** G 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 ASN ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 63 GLN ** L 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 166822 Z= 0.333 Angle : 0.741 15.502 249077 Z= 0.380 Chirality : 0.040 0.321 31782 Planarity : 0.006 0.070 13715 Dihedral : 24.021 179.731 82275 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 28.57 Ramachandran Plot: Outliers : 0.31 % Allowed : 12.96 % Favored : 86.73 % Rotamer: Outliers : 6.73 % Allowed : 21.68 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.10), residues: 6366 helix: -1.09 (0.11), residues: 1943 sheet: -2.44 (0.14), residues: 1168 loop : -2.67 (0.10), residues: 3255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K 43 HIS 0.008 0.002 HIS17 34 PHE 0.019 0.002 PHE R 12 TYR 0.034 0.003 TYR N 19 ARG 0.013 0.001 ARG16 2 *********************** 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 1258 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 356 poor density : 902 time to evaluate : 6.789 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: 04 78 GLU cc_start: 0.7821 (mt-10) cc_final: 0.6561 (mm-30) REVERT: 05 128 ARG cc_start: 0.8238 (mmp80) cc_final: 0.7727 (mmm-85) REVERT: 06 199 MET cc_start: 0.8435 (ttp) cc_final: 0.7523 (mmm) REVERT: 07 22 ASN cc_start: 0.7557 (m-40) cc_final: 0.7030 (p0) REVERT: 07 56 LEU cc_start: 0.8489 (mt) cc_final: 0.8022 (mt) REVERT: 08 51 PHE cc_start: 0.6324 (OUTLIER) cc_final: 0.4483 (m-80) REVERT: 08 151 ARG cc_start: 0.7196 (mtt-85) cc_final: 0.6200 (mtt-85) REVERT: 09 41 LYS cc_start: 0.9057 (tmtt) cc_final: 0.8562 (tptt) REVERT: 09 109 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7416 (tp30) REVERT: 10 6 GLN cc_start: 0.9024 (mm110) cc_final: 0.8289 (tm-30) REVERT: 10 123 ILE cc_start: 0.4192 (OUTLIER) cc_final: 0.3779 (mt) REVERT: 11 45 THR cc_start: 0.6916 (OUTLIER) cc_final: 0.6654 (p) REVERT: 11 48 ILE cc_start: 0.1276 (OUTLIER) cc_final: 0.0530 (mt) REVERT: 12 25 LEU cc_start: 0.8825 (tp) cc_final: 0.8579 (tt) REVERT: 12 118 MET cc_start: 0.8767 (tmm) cc_final: 0.8478 (ttp) REVERT: 14 23 ILE cc_start: 0.9010 (OUTLIER) cc_final: 0.8607 (mp) REVERT: 14 36 LYS cc_start: 0.8336 (mttt) cc_final: 0.7941 (pttm) REVERT: 14 58 TYR cc_start: 0.8514 (p90) cc_final: 0.7606 (p90) REVERT: 15 12 MET cc_start: 0.8391 (ppp) cc_final: 0.8168 (ppp) REVERT: 15 91 TYR cc_start: 0.8517 (OUTLIER) cc_final: 0.8121 (p90) REVERT: 15 136 MET cc_start: 0.8903 (tmm) cc_final: 0.8430 (tmm) REVERT: 16 1 MET cc_start: 0.6351 (OUTLIER) cc_final: 0.5972 (pmm) REVERT: 16 24 MET cc_start: 0.9093 (OUTLIER) cc_final: 0.8791 (mmt) REVERT: 17 17 LYS cc_start: 0.8749 (tppt) cc_final: 0.8314 (ptmt) REVERT: 17 92 PHE cc_start: 0.8671 (t80) cc_final: 0.8237 (t80) REVERT: 18 114 ASN cc_start: 0.8158 (OUTLIER) cc_final: 0.7497 (m110) REVERT: 19 96 ASP cc_start: 0.7947 (t70) cc_final: 0.7476 (t70) REVERT: 25 12 SER cc_start: 0.6708 (OUTLIER) cc_final: 0.5651 (t) REVERT: 25 72 ASN cc_start: 0.9287 (t0) cc_final: 0.9078 (t0) REVERT: 26 15 ASN cc_start: 0.8190 (m110) cc_final: 0.7919 (m110) REVERT: 31 32 LYS cc_start: 0.7968 (mmmt) cc_final: 0.7632 (mmmt) REVERT: 31 45 HIS cc_start: 0.7774 (OUTLIER) cc_final: 0.6815 (m90) REVERT: 33 61 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7523 (pp) REVERT: B 73 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7739 (ttp-170) REVERT: B 99 MET cc_start: 0.7848 (mtt) cc_final: 0.7602 (mtt) REVERT: B 116 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8579 (tp) REVERT: B 143 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8094 (mp) REVERT: C 53 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.6903 (ptt90) REVERT: C 124 GLU cc_start: 0.8347 (mt-10) cc_final: 0.7915 (pp20) REVERT: C 141 MET cc_start: 0.8893 (mmp) cc_final: 0.8675 (mmm) REVERT: C 183 TYR cc_start: 0.8023 (t80) cc_final: 0.7741 (t80) REVERT: C 192 TYR cc_start: 0.8009 (m-80) cc_final: 0.7643 (t80) REVERT: D 29 THR cc_start: 0.7716 (OUTLIER) cc_final: 0.7210 (p) REVERT: D 59 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8646 (ttpt) REVERT: D 102 TYR cc_start: 0.8563 (t80) cc_final: 0.8142 (t80) REVERT: E 10 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6694 (pp) REVERT: E 63 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.7617 (mmm) REVERT: E 104 ILE cc_start: 0.8909 (tp) cc_final: 0.8688 (pt) REVERT: F 16 GLU cc_start: 0.9133 (mm-30) cc_final: 0.8885 (mp0) REVERT: F 21 MET cc_start: 0.9267 (mtt) cc_final: 0.8866 (mmm) REVERT: F 24 ARG cc_start: 0.8079 (ptt90) cc_final: 0.7293 (ptt90) REVERT: F 46 GLN cc_start: 0.9144 (tp-100) cc_final: 0.8776 (tm-30) REVERT: F 52 ASN cc_start: 0.9493 (t0) cc_final: 0.9068 (t0) REVERT: F 78 PHE cc_start: 0.8856 (m-80) cc_final: 0.8421 (m-80) REVERT: G 27 ASN cc_start: 0.8873 (p0) cc_final: 0.8660 (p0) REVERT: G 36 SER cc_start: 0.8890 (OUTLIER) cc_final: 0.8382 (p) REVERT: H 2 MET cc_start: 0.8046 (mmp) cc_final: 0.7776 (mmp) REVERT: I 30 ASN cc_start: 0.8078 (t0) cc_final: 0.7722 (t0) REVERT: I 106 ASP cc_start: 0.7881 (t0) cc_final: 0.7544 (t0) REVERT: J 20 GLN cc_start: 0.8457 (pt0) cc_final: 0.7768 (tp-100) REVERT: J 31 ARG cc_start: 0.8190 (ttp80) cc_final: 0.7822 (ttm110) REVERT: J 65 TYR cc_start: 0.8659 (m-80) cc_final: 0.8257 (m-10) REVERT: J 75 ASP cc_start: 0.7937 (m-30) cc_final: 0.7711 (m-30) REVERT: K 73 VAL cc_start: 0.8074 (t) cc_final: 0.7825 (m) REVERT: K 76 TYR cc_start: 0.8827 (m-80) cc_final: 0.8563 (m-10) REVERT: M 12 LYS cc_start: 0.8749 (mttt) cc_final: 0.8242 (mmtt) REVERT: Q 61 ARG cc_start: 0.8774 (tmm160) cc_final: 0.8551 (tmm-80) REVERT: U 32 ARG cc_start: 0.8668 (ptt90) cc_final: 0.8315 (ttt180) REVERT: U 36 PHE cc_start: 0.8202 (OUTLIER) cc_final: 0.7876 (t80) REVERT: U 39 LYS cc_start: 0.8738 (mmtt) cc_final: 0.8465 (tptt) REVERT: U 45 LYS cc_start: 0.8807 (tmtt) cc_final: 0.8582 (tptp) REVERT: U 46 ARG cc_start: 0.8820 (tpt170) cc_final: 0.8604 (ttm170) REVERT: Z 51 ASN cc_start: 0.8708 (p0) cc_final: 0.8136 (m-40) REVERT: Z 243 GLU cc_start: 0.7990 (tt0) cc_final: 0.7660 (tp30) outliers start: 356 outliers final: 253 residues processed: 1145 average time/residue: 1.2915 time to fit residues: 2601.2661 Evaluate side-chains 1113 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 275 poor density : 838 time to evaluate : 6.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 33 LEU Chi-restraints excluded: chain 04 residue 143 VAL Chi-restraints excluded: chain 04 residue 222 THR Chi-restraints excluded: chain 04 residue 227 VAL Chi-restraints excluded: chain 05 residue 14 ILE Chi-restraints excluded: chain 05 residue 27 ILE Chi-restraints excluded: chain 05 residue 48 ILE Chi-restraints excluded: chain 05 residue 133 THR Chi-restraints excluded: chain 05 residue 145 SER Chi-restraints excluded: chain 05 residue 180 VAL Chi-restraints excluded: chain 05 residue 186 LEU Chi-restraints excluded: chain 05 residue 188 LEU Chi-restraints excluded: chain 05 residue 197 THR Chi-restraints excluded: chain 06 residue 15 SER Chi-restraints excluded: chain 06 residue 22 ASP Chi-restraints excluded: chain 06 residue 48 THR Chi-restraints excluded: chain 06 residue 72 SER Chi-restraints excluded: chain 06 residue 73 ILE Chi-restraints excluded: chain 06 residue 116 ASP Chi-restraints excluded: chain 06 residue 149 ILE Chi-restraints excluded: chain 06 residue 175 ILE Chi-restraints excluded: chain 07 residue 24 VAL Chi-restraints excluded: chain 07 residue 46 LYS Chi-restraints excluded: chain 07 residue 105 ILE Chi-restraints excluded: chain 07 residue 146 ASP Chi-restraints excluded: chain 07 residue 152 ASP Chi-restraints excluded: chain 07 residue 154 THR Chi-restraints excluded: chain 08 residue 9 VAL Chi-restraints excluded: chain 08 residue 25 ILE Chi-restraints excluded: chain 08 residue 51 PHE Chi-restraints excluded: chain 08 residue 75 VAL Chi-restraints excluded: chain 08 residue 100 ASN Chi-restraints excluded: chain 08 residue 146 ASP Chi-restraints excluded: chain 08 residue 161 VAL Chi-restraints excluded: chain 09 residue 20 ASN Chi-restraints excluded: chain 09 residue 22 LYS Chi-restraints excluded: chain 09 residue 28 ASN Chi-restraints excluded: chain 09 residue 31 VAL Chi-restraints excluded: chain 09 residue 40 THR Chi-restraints excluded: chain 09 residue 145 ASN Chi-restraints excluded: chain 10 residue 8 LYS Chi-restraints excluded: chain 10 residue 27 VAL Chi-restraints excluded: chain 10 residue 31 ARG Chi-restraints excluded: chain 10 residue 80 THR Chi-restraints excluded: chain 10 residue 88 HIS Chi-restraints excluded: chain 10 residue 99 PHE Chi-restraints excluded: chain 10 residue 117 LEU Chi-restraints excluded: chain 10 residue 123 ILE Chi-restraints excluded: chain 11 residue 7 TYR Chi-restraints excluded: chain 11 residue 34 ILE Chi-restraints excluded: chain 11 residue 45 THR Chi-restraints excluded: chain 11 residue 48 ILE Chi-restraints excluded: chain 11 residue 67 THR Chi-restraints excluded: chain 11 residue 70 THR Chi-restraints excluded: chain 11 residue 72 THR Chi-restraints excluded: chain 11 residue 105 LEU Chi-restraints excluded: chain 11 residue 110 GLN Chi-restraints excluded: chain 11 residue 138 VAL Chi-restraints excluded: chain 11 residue 139 VAL Chi-restraints excluded: chain 12 residue 68 LYS Chi-restraints excluded: chain 12 residue 76 HIS Chi-restraints excluded: chain 12 residue 101 ILE Chi-restraints excluded: chain 13 residue 25 LEU Chi-restraints excluded: chain 13 residue 43 ILE Chi-restraints excluded: chain 13 residue 69 VAL Chi-restraints excluded: chain 14 residue 23 ILE Chi-restraints excluded: chain 14 residue 46 VAL Chi-restraints excluded: chain 14 residue 92 LEU Chi-restraints excluded: chain 14 residue 118 THR Chi-restraints excluded: chain 14 residue 121 THR Chi-restraints excluded: chain 14 residue 129 LYS Chi-restraints excluded: chain 15 residue 25 ASP Chi-restraints excluded: chain 15 residue 42 THR Chi-restraints excluded: chain 15 residue 46 ILE Chi-restraints excluded: chain 15 residue 70 ASP Chi-restraints excluded: chain 15 residue 91 TYR Chi-restraints excluded: chain 15 residue 110 GLU Chi-restraints excluded: chain 15 residue 119 LEU Chi-restraints excluded: chain 16 residue 1 MET Chi-restraints excluded: chain 16 residue 24 MET Chi-restraints excluded: chain 16 residue 47 VAL Chi-restraints excluded: chain 16 residue 62 ASN Chi-restraints excluded: chain 16 residue 89 SER Chi-restraints excluded: chain 16 residue 97 ILE Chi-restraints excluded: chain 16 residue 113 ILE Chi-restraints excluded: chain 17 residue 18 LEU Chi-restraints excluded: chain 17 residue 21 LEU Chi-restraints excluded: chain 17 residue 27 VAL Chi-restraints excluded: chain 17 residue 55 GLU Chi-restraints excluded: chain 17 residue 69 ASP Chi-restraints excluded: chain 17 residue 106 LEU Chi-restraints excluded: chain 18 residue 49 ILE Chi-restraints excluded: chain 18 residue 60 VAL Chi-restraints excluded: chain 18 residue 83 ILE Chi-restraints excluded: chain 18 residue 112 ARG Chi-restraints excluded: chain 18 residue 114 ASN Chi-restraints excluded: chain 19 residue 38 VAL Chi-restraints excluded: chain 20 residue 19 THR Chi-restraints excluded: chain 20 residue 26 ASP Chi-restraints excluded: chain 21 residue 33 LEU Chi-restraints excluded: chain 21 residue 34 ASP Chi-restraints excluded: chain 21 residue 40 ASN Chi-restraints excluded: chain 21 residue 66 ILE Chi-restraints excluded: chain 21 residue 67 ASP Chi-restraints excluded: chain 21 residue 82 MET Chi-restraints excluded: chain 21 residue 85 ILE Chi-restraints excluded: chain 21 residue 97 LEU Chi-restraints excluded: chain 22 residue 32 LEU Chi-restraints excluded: chain 22 residue 43 ILE Chi-restraints excluded: chain 22 residue 70 HIS Chi-restraints excluded: chain 22 residue 93 LEU Chi-restraints excluded: chain 23 residue 10 VAL Chi-restraints excluded: chain 23 residue 11 ILE Chi-restraints excluded: chain 23 residue 26 ASN Chi-restraints excluded: chain 23 residue 48 VAL Chi-restraints excluded: chain 24 residue 5 ASN Chi-restraints excluded: chain 24 residue 40 ILE Chi-restraints excluded: chain 24 residue 56 PHE Chi-restraints excluded: chain 24 residue 65 VAL Chi-restraints excluded: chain 24 residue 89 ILE Chi-restraints excluded: chain 25 residue 12 SER Chi-restraints excluded: chain 25 residue 17 LEU Chi-restraints excluded: chain 25 residue 77 SER Chi-restraints excluded: chain 26 residue 24 THR Chi-restraints excluded: chain 26 residue 47 THR Chi-restraints excluded: chain 26 residue 58 ILE Chi-restraints excluded: chain 26 residue 65 THR Chi-restraints excluded: chain 27 residue 6 LEU Chi-restraints excluded: chain 27 residue 11 VAL Chi-restraints excluded: chain 27 residue 17 GLU Chi-restraints excluded: chain 27 residue 50 VAL Chi-restraints excluded: chain 28 residue 2 LYS Chi-restraints excluded: chain 28 residue 34 THR Chi-restraints excluded: chain 28 residue 40 THR Chi-restraints excluded: chain 28 residue 48 ASN Chi-restraints excluded: chain 29 residue 4 ASP Chi-restraints excluded: chain 29 residue 31 ASP Chi-restraints excluded: chain 29 residue 34 LEU Chi-restraints excluded: chain 29 residue 53 THR Chi-restraints excluded: chain 30 residue 24 VAL Chi-restraints excluded: chain 30 residue 31 LYS Chi-restraints excluded: chain 30 residue 38 LEU Chi-restraints excluded: chain 31 residue 11 VAL Chi-restraints excluded: chain 31 residue 28 THR Chi-restraints excluded: chain 31 residue 45 HIS Chi-restraints excluded: chain 31 residue 47 ILE Chi-restraints excluded: chain 32 residue 1 MET Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 33 residue 6 VAL Chi-restraints excluded: chain 33 residue 50 SER Chi-restraints excluded: chain 33 residue 61 LEU Chi-restraints excluded: chain 34 residue 36 ARG Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain C residue 53 ARG Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 19 PHE Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 191 SER Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 96 ASN Chi-restraints excluded: chain G residue 121 ASN Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 9 MET Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 63 GLN Chi-restraints excluded: chain K residue 71 ASP Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 96 ILE Chi-restraints excluded: chain K residue 104 PHE Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 102 ASP Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 11 HIS Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 61 LYS Chi-restraints excluded: chain M residue 106 ARG Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain O residue 19 ASN Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 38 PHE Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain Q residue 20 ILE Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 52 CYS Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain R residue 20 ILE Chi-restraints excluded: chain R residue 29 LYS Chi-restraints excluded: chain S residue 11 ASP Chi-restraints excluded: chain S residue 38 THR Chi-restraints excluded: chain S residue 43 MET Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 64 GLU Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain T residue 7 LYS Chi-restraints excluded: chain U residue 12 ASP Chi-restraints excluded: chain U residue 35 GLU Chi-restraints excluded: chain U residue 36 PHE Chi-restraints excluded: chain 03 residue 10 VAL Chi-restraints excluded: chain Z residue 32 THR Chi-restraints excluded: chain Z residue 47 ASP Chi-restraints excluded: chain Z residue 140 VAL Chi-restraints excluded: chain Z residue 156 LEU Chi-restraints excluded: chain Z residue 211 LEU Chi-restraints excluded: chain Z residue 228 THR Chi-restraints excluded: chain Z residue 254 THR Chi-restraints excluded: chain Z residue 255 CYS Chi-restraints excluded: chain Z residue 335 THR Chi-restraints excluded: chain Z residue 359 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1101 random chunks: chunk 358 optimal weight: 9.9990 chunk 958 optimal weight: 20.0000 chunk 210 optimal weight: 8.9990 chunk 624 optimal weight: 30.0000 chunk 262 optimal weight: 9.9990 chunk 1065 optimal weight: 8.9990 chunk 884 optimal weight: 30.0000 chunk 493 optimal weight: 4.9990 chunk 88 optimal weight: 20.0000 chunk 352 optimal weight: 9.9990 chunk 559 optimal weight: 3.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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** ** 04 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 103 ASN ** 09 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 19 19 GLN ** 24 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 25 8 ASN ** 27 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 28 48 ASN 29 20 ASN ** 32 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 GLN ** E 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 26 ASN ** R 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 166822 Z= 0.241 Angle : 0.666 16.066 249077 Z= 0.342 Chirality : 0.037 0.325 31782 Planarity : 0.005 0.081 13715 Dihedral : 23.984 179.226 82275 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 24.94 Ramachandran Plot: Outliers : 0.28 % Allowed : 12.14 % Favored : 87.57 % Rotamer: Outliers : 6.03 % Allowed : 23.38 % Favored : 70.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.10), residues: 6366 helix: -0.82 (0.11), residues: 1956 sheet: -2.29 (0.14), residues: 1136 loop : -2.54 (0.10), residues: 3274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP K 43 HIS 0.008 0.001 HIS B 14 PHE 0.023 0.002 PHE11 66 TYR 0.031 0.002 TYR N 19 ARG 0.007 0.001 ARG31 27 *********************** 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 1245 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 319 poor density : 926 time to evaluate : 6.898 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: 05 128 ARG cc_start: 0.8276 (mmp80) cc_final: 0.7752 (mmm-85) REVERT: 05 200 ASP cc_start: 0.8711 (p0) cc_final: 0.8421 (p0) REVERT: 06 199 MET cc_start: 0.8399 (ttp) cc_final: 0.7506 (mmm) REVERT: 07 22 ASN cc_start: 0.7482 (m-40) cc_final: 0.6927 (p0) REVERT: 07 56 LEU cc_start: 0.8439 (mt) cc_final: 0.7862 (mt) REVERT: 08 51 PHE cc_start: 0.6255 (OUTLIER) cc_final: 0.4450 (m-80) REVERT: 08 151 ARG cc_start: 0.7144 (mtt-85) cc_final: 0.6081 (mtt-85) REVERT: 09 41 LYS cc_start: 0.9086 (tmtt) cc_final: 0.8604 (tptt) REVERT: 09 46 PHE cc_start: 0.9160 (OUTLIER) cc_final: 0.8732 (t80) REVERT: 09 51 ARG cc_start: 0.7534 (mmt-90) cc_final: 0.7252 (mpt180) REVERT: 10 6 GLN cc_start: 0.8982 (mm110) cc_final: 0.8263 (tm-30) REVERT: 10 123 ILE cc_start: 0.4259 (OUTLIER) cc_final: 0.3738 (mt) REVERT: 11 122 GLU cc_start: 0.8372 (tm-30) cc_final: 0.8157 (pp20) REVERT: 13 111 LYS cc_start: 0.8437 (ttpp) cc_final: 0.7657 (ttpp) REVERT: 13 112 PHE cc_start: 0.8881 (m-80) cc_final: 0.8636 (m-10) REVERT: 14 23 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8533 (mp) REVERT: 14 36 LYS cc_start: 0.8298 (mttt) cc_final: 0.7896 (pttm) REVERT: 14 58 TYR cc_start: 0.8471 (p90) cc_final: 0.7783 (p90) REVERT: 15 91 TYR cc_start: 0.8437 (OUTLIER) cc_final: 0.8082 (p90) REVERT: 15 136 MET cc_start: 0.8891 (tmm) cc_final: 0.8341 (tmm) REVERT: 16 1 MET cc_start: 0.6276 (OUTLIER) cc_final: 0.5978 (pmm) REVERT: 16 20 MET cc_start: 0.7902 (tpp) cc_final: 0.7345 (tpp) REVERT: 16 24 MET cc_start: 0.8990 (OUTLIER) cc_final: 0.8604 (mmt) REVERT: 16 74 GLU cc_start: 0.8510 (tt0) cc_final: 0.8228 (tm-30) REVERT: 17 17 LYS cc_start: 0.8729 (tppt) cc_final: 0.8286 (ptmt) REVERT: 17 92 PHE cc_start: 0.8696 (t80) cc_final: 0.8210 (t80) REVERT: 19 96 ASP cc_start: 0.7987 (t70) cc_final: 0.7694 (t70) REVERT: 25 12 SER cc_start: 0.6718 (OUTLIER) cc_final: 0.5728 (t) REVERT: 25 72 ASN cc_start: 0.9269 (t0) cc_final: 0.9055 (t0) REVERT: 26 15 ASN cc_start: 0.8133 (m110) cc_final: 0.7847 (m110) REVERT: 31 32 LYS cc_start: 0.8013 (mmmt) cc_final: 0.7685 (mmmt) REVERT: 31 45 HIS cc_start: 0.7779 (OUTLIER) cc_final: 0.6753 (m90) REVERT: 33 61 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7555 (pp) REVERT: B 99 MET cc_start: 0.7811 (mtt) cc_final: 0.7370 (mtt) REVERT: B 116 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8566 (tp) REVERT: B 143 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8100 (mp) REVERT: C 24 ASN cc_start: 0.8535 (t0) cc_final: 0.8206 (t0) REVERT: C 53 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.6016 (ptt90) REVERT: C 183 TYR cc_start: 0.7899 (t80) cc_final: 0.7626 (t80) REVERT: C 192 TYR cc_start: 0.7965 (m-80) cc_final: 0.7732 (t80) REVERT: D 29 THR cc_start: 0.7572 (OUTLIER) cc_final: 0.7067 (p) REVERT: D 59 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8576 (ttpt) REVERT: D 102 TYR cc_start: 0.8556 (t80) cc_final: 0.8169 (t80) REVERT: E 10 LEU cc_start: 0.7129 (OUTLIER) cc_final: 0.6814 (pp) REVERT: E 63 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7511 (mmm) REVERT: E 137 ARG cc_start: 0.9023 (ttm-80) cc_final: 0.8805 (ttp-110) REVERT: F 16 GLU cc_start: 0.9134 (mm-30) cc_final: 0.8884 (mp0) REVERT: F 21 MET cc_start: 0.9249 (mtt) cc_final: 0.8852 (mmm) REVERT: F 24 ARG cc_start: 0.7964 (ptt90) cc_final: 0.7547 (ptt90) REVERT: F 52 ASN cc_start: 0.9458 (t0) cc_final: 0.9032 (t0) REVERT: G 36 SER cc_start: 0.8811 (OUTLIER) cc_final: 0.8270 (p) REVERT: H 2 MET cc_start: 0.7858 (mmp) cc_final: 0.7643 (mmp) REVERT: I 30 ASN cc_start: 0.8169 (t0) cc_final: 0.7817 (t0) REVERT: I 67 LYS cc_start: 0.8553 (tptt) cc_final: 0.7898 (mmtm) REVERT: I 106 ASP cc_start: 0.7823 (t0) cc_final: 0.7504 (t0) REVERT: J 20 GLN cc_start: 0.8443 (pt0) cc_final: 0.7764 (tp-100) REVERT: J 31 ARG cc_start: 0.8180 (ttp80) cc_final: 0.7819 (ttm110) REVERT: J 63 ASP cc_start: 0.7132 (t70) cc_final: 0.5888 (t0) REVERT: J 65 TYR cc_start: 0.8742 (m-80) cc_final: 0.8344 (m-10) REVERT: K 73 VAL cc_start: 0.7835 (t) cc_final: 0.7386 (m) REVERT: K 74 LYS cc_start: 0.8670 (mmmt) cc_final: 0.8357 (mmmt) REVERT: K 76 TYR cc_start: 0.8724 (m-80) cc_final: 0.8445 (m-10) REVERT: M 12 LYS cc_start: 0.8736 (mttt) cc_final: 0.8190 (mmtt) REVERT: Q 27 PHE cc_start: 0.8834 (t80) cc_final: 0.8566 (t80) REVERT: Q 42 LYS cc_start: 0.8556 (mtmt) cc_final: 0.7075 (mptt) REVERT: U 32 ARG cc_start: 0.8611 (ptt90) cc_final: 0.8278 (ttt180) REVERT: U 45 LYS cc_start: 0.8769 (tmtt) cc_final: 0.8536 (tptp) REVERT: U 46 ARG cc_start: 0.8820 (tpt170) cc_final: 0.8600 (ttm170) REVERT: Z 51 ASN cc_start: 0.8718 (p0) cc_final: 0.8192 (m-40) REVERT: Z 69 TYR cc_start: 0.7931 (p90) cc_final: 0.7707 (p90) REVERT: Z 206 ILE cc_start: 0.7636 (OUTLIER) cc_final: 0.7380 (pp) REVERT: Z 243 GLU cc_start: 0.7946 (tt0) cc_final: 0.7267 (pt0) REVERT: Z 358 MET cc_start: 0.7181 (pmm) cc_final: 0.6899 (pmm) outliers start: 319 outliers final: 240 residues processed: 1138 average time/residue: 1.3035 time to fit residues: 2609.3050 Evaluate side-chains 1107 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 848 time to evaluate : 6.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 33 LEU Chi-restraints excluded: chain 04 residue 143 VAL Chi-restraints excluded: chain 04 residue 163 ILE Chi-restraints excluded: chain 04 residue 222 THR Chi-restraints excluded: chain 04 residue 227 VAL Chi-restraints excluded: chain 05 residue 14 ILE Chi-restraints excluded: chain 05 residue 27 ILE Chi-restraints excluded: chain 05 residue 133 THR Chi-restraints excluded: chain 05 residue 180 VAL Chi-restraints excluded: chain 05 residue 186 LEU Chi-restraints excluded: chain 05 residue 188 LEU Chi-restraints excluded: chain 05 residue 197 THR Chi-restraints excluded: chain 06 residue 15 SER Chi-restraints excluded: chain 06 residue 22 ASP Chi-restraints excluded: chain 06 residue 72 SER Chi-restraints excluded: chain 06 residue 73 ILE Chi-restraints excluded: chain 06 residue 116 ASP Chi-restraints excluded: chain 06 residue 149 ILE Chi-restraints excluded: chain 07 residue 46 LYS Chi-restraints excluded: chain 07 residue 146 ASP Chi-restraints excluded: chain 07 residue 152 ASP Chi-restraints excluded: chain 07 residue 154 THR Chi-restraints excluded: chain 08 residue 9 VAL Chi-restraints excluded: chain 08 residue 25 ILE Chi-restraints excluded: chain 08 residue 51 PHE Chi-restraints excluded: chain 08 residue 100 ASN Chi-restraints excluded: chain 08 residue 146 ASP Chi-restraints excluded: chain 08 residue 161 VAL Chi-restraints excluded: chain 09 residue 20 ASN Chi-restraints excluded: chain 09 residue 22 LYS Chi-restraints excluded: chain 09 residue 31 VAL Chi-restraints excluded: chain 09 residue 40 THR Chi-restraints excluded: chain 09 residue 46 PHE Chi-restraints excluded: chain 09 residue 94 ILE Chi-restraints excluded: chain 09 residue 145 ASN Chi-restraints excluded: chain 10 residue 8 LYS Chi-restraints excluded: chain 10 residue 27 VAL Chi-restraints excluded: chain 10 residue 31 ARG Chi-restraints excluded: chain 10 residue 64 VAL Chi-restraints excluded: chain 10 residue 80 THR Chi-restraints excluded: chain 10 residue 99 PHE Chi-restraints excluded: chain 10 residue 117 LEU Chi-restraints excluded: chain 10 residue 123 ILE Chi-restraints excluded: chain 11 residue 7 TYR Chi-restraints excluded: chain 11 residue 34 ILE Chi-restraints excluded: chain 11 residue 67 THR Chi-restraints excluded: chain 11 residue 70 THR Chi-restraints excluded: chain 11 residue 72 THR Chi-restraints excluded: chain 11 residue 105 LEU Chi-restraints excluded: chain 11 residue 110 GLN Chi-restraints excluded: chain 11 residue 121 ILE Chi-restraints excluded: chain 11 residue 138 VAL Chi-restraints excluded: chain 11 residue 139 VAL Chi-restraints excluded: chain 12 residue 76 HIS Chi-restraints excluded: chain 12 residue 101 ILE Chi-restraints excluded: chain 13 residue 25 LEU Chi-restraints excluded: chain 13 residue 43 ILE Chi-restraints excluded: chain 13 residue 61 VAL Chi-restraints excluded: chain 13 residue 65 THR Chi-restraints excluded: chain 13 residue 69 VAL Chi-restraints excluded: chain 13 residue 114 LYS Chi-restraints excluded: chain 14 residue 23 ILE Chi-restraints excluded: chain 14 residue 46 VAL Chi-restraints excluded: chain 14 residue 92 LEU Chi-restraints excluded: chain 14 residue 118 THR Chi-restraints excluded: chain 14 residue 121 THR Chi-restraints excluded: chain 14 residue 129 LYS Chi-restraints excluded: chain 15 residue 20 LEU Chi-restraints excluded: chain 15 residue 36 VAL Chi-restraints excluded: chain 15 residue 70 ASP Chi-restraints excluded: chain 15 residue 91 TYR Chi-restraints excluded: chain 15 residue 119 LEU Chi-restraints excluded: chain 16 residue 1 MET Chi-restraints excluded: chain 16 residue 24 MET Chi-restraints excluded: chain 16 residue 47 VAL Chi-restraints excluded: chain 16 residue 89 SER Chi-restraints excluded: chain 16 residue 97 ILE Chi-restraints excluded: chain 16 residue 113 ILE Chi-restraints excluded: chain 17 residue 18 LEU Chi-restraints excluded: chain 17 residue 21 LEU Chi-restraints excluded: chain 17 residue 47 VAL Chi-restraints excluded: chain 17 residue 55 GLU Chi-restraints excluded: chain 17 residue 65 THR Chi-restraints excluded: chain 17 residue 69 ASP Chi-restraints excluded: chain 17 residue 106 LEU Chi-restraints excluded: chain 18 residue 4 ILE Chi-restraints excluded: chain 18 residue 49 ILE Chi-restraints excluded: chain 18 residue 60 VAL Chi-restraints excluded: chain 18 residue 112 ARG Chi-restraints excluded: chain 18 residue 114 ASN Chi-restraints excluded: chain 19 residue 38 VAL Chi-restraints excluded: chain 20 residue 19 THR Chi-restraints excluded: chain 20 residue 26 ASP Chi-restraints excluded: chain 20 residue 54 VAL Chi-restraints excluded: chain 21 residue 4 ILE Chi-restraints excluded: chain 21 residue 40 ASN Chi-restraints excluded: chain 21 residue 66 ILE Chi-restraints excluded: chain 21 residue 67 ASP Chi-restraints excluded: chain 21 residue 85 ILE Chi-restraints excluded: chain 21 residue 97 LEU Chi-restraints excluded: chain 22 residue 32 LEU Chi-restraints excluded: chain 22 residue 43 ILE Chi-restraints excluded: chain 22 residue 70 HIS Chi-restraints excluded: chain 22 residue 93 LEU Chi-restraints excluded: chain 23 residue 11 ILE Chi-restraints excluded: chain 23 residue 26 ASN Chi-restraints excluded: chain 23 residue 48 VAL Chi-restraints excluded: chain 24 residue 40 ILE Chi-restraints excluded: chain 24 residue 56 PHE Chi-restraints excluded: chain 24 residue 65 VAL Chi-restraints excluded: chain 24 residue 66 ASP Chi-restraints excluded: chain 24 residue 89 ILE Chi-restraints excluded: chain 25 residue 12 SER Chi-restraints excluded: chain 25 residue 77 SER Chi-restraints excluded: chain 26 residue 3 VAL Chi-restraints excluded: chain 26 residue 24 THR Chi-restraints excluded: chain 26 residue 47 THR Chi-restraints excluded: chain 26 residue 58 ILE Chi-restraints excluded: chain 26 residue 65 THR Chi-restraints excluded: chain 27 residue 6 LEU Chi-restraints excluded: chain 27 residue 11 VAL Chi-restraints excluded: chain 27 residue 17 GLU Chi-restraints excluded: chain 28 residue 2 LYS Chi-restraints excluded: chain 28 residue 22 THR Chi-restraints excluded: chain 28 residue 40 THR Chi-restraints excluded: chain 28 residue 48 ASN Chi-restraints excluded: chain 29 residue 31 ASP Chi-restraints excluded: chain 29 residue 33 ASN Chi-restraints excluded: chain 29 residue 34 LEU Chi-restraints excluded: chain 29 residue 53 THR Chi-restraints excluded: chain 30 residue 24 VAL Chi-restraints excluded: chain 30 residue 31 LYS Chi-restraints excluded: chain 30 residue 38 LEU Chi-restraints excluded: chain 31 residue 11 VAL Chi-restraints excluded: chain 31 residue 28 THR Chi-restraints excluded: chain 31 residue 45 HIS Chi-restraints excluded: chain 31 residue 47 ILE Chi-restraints excluded: chain 32 residue 1 MET Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 33 residue 6 VAL Chi-restraints excluded: chain 33 residue 50 SER Chi-restraints excluded: chain 33 residue 61 LEU Chi-restraints excluded: chain 34 residue 36 ARG Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 108 GLN Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain C residue 53 ARG Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 19 PHE Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 191 SER Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 152 VAL 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 84 VAL Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 96 ASN Chi-restraints excluded: chain G residue 121 ASN Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 71 ASP Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 96 ILE Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 102 ASP Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 61 LYS Chi-restraints excluded: chain M residue 94 LEU Chi-restraints excluded: chain M residue 106 ARG Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 29 ILE Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain O residue 19 ASN Chi-restraints excluded: chain O residue 42 PHE Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 38 PHE Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain Q residue 20 ILE Chi-restraints excluded: chain Q residue 52 CYS Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain R residue 20 ILE Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain S residue 11 ASP Chi-restraints excluded: chain S residue 38 THR Chi-restraints excluded: chain S residue 43 MET Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 64 GLU Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain U residue 12 ASP Chi-restraints excluded: chain U residue 35 GLU Chi-restraints excluded: chain U residue 36 PHE Chi-restraints excluded: chain 03 residue 10 VAL Chi-restraints excluded: chain Z residue 20 VAL Chi-restraints excluded: chain Z residue 47 ASP Chi-restraints excluded: chain Z residue 140 VAL Chi-restraints excluded: chain Z residue 142 ASP Chi-restraints excluded: chain Z residue 156 LEU Chi-restraints excluded: chain Z residue 206 ILE Chi-restraints excluded: chain Z residue 211 LEU Chi-restraints excluded: chain Z residue 228 THR Chi-restraints excluded: chain Z residue 255 CYS Chi-restraints excluded: chain Z residue 335 THR Chi-restraints excluded: chain Z residue 340 THR Chi-restraints excluded: chain Z residue 351 MET Chi-restraints excluded: chain Z residue 359 VAL 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: 3.9990 chunk 606 optimal weight: 40.0000 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: 40.0000 chunk 664 optimal weight: 20.0000 chunk 646 optimal weight: 30.0000 chunk 489 optimal weight: 40.0000 overall best weight: 20.7998 ------------------------------------------------------------------------------- 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** 04 162 GLN ** 04 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 19 ASN ** 08 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 110 HIS ** 09 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 10 122 GLN ** 11 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 15 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 29 48 GLN ** 32 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.5081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.095 166822 Z= 0.581 Angle : 1.011 16.866 249077 Z= 0.504 Chirality : 0.050 0.430 31782 Planarity : 0.007 0.100 13715 Dihedral : 24.486 179.624 82275 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 43.15 Ramachandran Plot: Outliers : 0.36 % Allowed : 16.10 % Favored : 83.54 % Rotamer: Outliers : 7.62 % Allowed : 23.59 % Favored : 68.79 % 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: -3.53 (0.10), residues: 6366 helix: -1.49 (0.11), residues: 1911 sheet: -2.52 (0.14), residues: 1104 loop : -2.84 (0.10), residues: 3351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP K 43 HIS 0.032 0.003 HIS24 44 PHE 0.031 0.004 PHE14 64 TYR 0.040 0.004 TYR07 142 ARG 0.012 0.001 ARG Q 26 *********************** 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 1213 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 403 poor density : 810 time to evaluate : 6.265 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: 05 123 LYS cc_start: 0.9400 (tttm) cc_final: 0.9095 (mmtt) REVERT: 05 200 ASP cc_start: 0.8970 (p0) cc_final: 0.8669 (p0) REVERT: 07 22 ASN cc_start: 0.7782 (m-40) cc_final: 0.7197 (p0) REVERT: 07 56 LEU cc_start: 0.8565 (mt) cc_final: 0.7702 (mt) REVERT: 07 173 ASP cc_start: 0.7603 (m-30) cc_final: 0.6943 (t0) REVERT: 09 41 LYS cc_start: 0.9107 (tmtt) cc_final: 0.8587 (tptt) REVERT: 09 104 THR cc_start: 0.8928 (p) cc_final: 0.8457 (p) REVERT: 09 109 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7220 (tp30) REVERT: 10 6 GLN cc_start: 0.8933 (mm110) cc_final: 0.8079 (tm-30) REVERT: 10 69 PHE cc_start: 0.8050 (t80) cc_final: 0.7620 (t80) REVERT: 13 112 PHE cc_start: 0.8895 (m-80) cc_final: 0.8566 (m-80) REVERT: 14 23 ILE cc_start: 0.9148 (OUTLIER) cc_final: 0.8750 (mp) REVERT: 14 36 LYS cc_start: 0.8357 (mttt) cc_final: 0.7990 (pttm) REVERT: 15 12 MET cc_start: 0.8561 (ppp) cc_final: 0.8323 (ppp) REVERT: 16 9 GLN cc_start: 0.8431 (tt0) cc_final: 0.8199 (tt0) REVERT: 16 20 MET cc_start: 0.8178 (tpp) cc_final: 0.7284 (tpp) REVERT: 16 24 MET cc_start: 0.9105 (OUTLIER) cc_final: 0.8767 (mmt) REVERT: 16 103 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7192 (mtm-85) REVERT: 17 2 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7939 (t70) REVERT: 17 92 PHE cc_start: 0.8727 (t80) cc_final: 0.8302 (t80) REVERT: 19 96 ASP cc_start: 0.8109 (t70) cc_final: 0.7795 (t70) REVERT: 27 24 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7687 (mp0) REVERT: 31 45 HIS cc_start: 0.7958 (OUTLIER) cc_final: 0.7428 (m90) REVERT: 32 22 MET cc_start: 0.8883 (tpp) cc_final: 0.8591 (tpp) REVERT: B 99 MET cc_start: 0.8196 (mtt) cc_final: 0.7786 (mtt) REVERT: B 116 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8636 (tp) REVERT: C 183 TYR cc_start: 0.8119 (t80) cc_final: 0.7911 (t80) REVERT: C 192 TYR cc_start: 0.8063 (m-80) cc_final: 0.7625 (t80) REVERT: E 10 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6893 (pp) REVERT: E 63 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7970 (mmm) REVERT: F 16 GLU cc_start: 0.9284 (mm-30) cc_final: 0.8956 (mp0) REVERT: F 33 GLU cc_start: 0.8658 (pm20) cc_final: 0.8426 (pm20) REVERT: F 52 ASN cc_start: 0.9508 (t0) cc_final: 0.9086 (t0) REVERT: F 72 ASP cc_start: 0.8976 (t0) cc_final: 0.8772 (t0) REVERT: G 36 SER cc_start: 0.9049 (OUTLIER) cc_final: 0.8578 (p) REVERT: H 72 GLU cc_start: 0.8881 (tm-30) cc_final: 0.8361 (tm-30) REVERT: I 30 ASN cc_start: 0.8335 (t0) cc_final: 0.7958 (t0) REVERT: J 20 GLN cc_start: 0.8485 (pt0) cc_final: 0.8017 (tp-100) REVERT: J 24 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8273 (tm-30) REVERT: J 31 ARG cc_start: 0.8307 (ttp80) cc_final: 0.7692 (ttm110) REVERT: J 65 TYR cc_start: 0.8840 (m-80) cc_final: 0.8323 (m-10) REVERT: K 74 LYS cc_start: 0.8860 (mmmt) cc_final: 0.8616 (mmmt) REVERT: K 76 TYR cc_start: 0.8954 (m-80) cc_final: 0.8677 (m-10) REVERT: K 126 ARG cc_start: 0.8384 (mmp-170) cc_final: 0.7999 (tpp-160) REVERT: M 12 LYS cc_start: 0.8744 (mttt) cc_final: 0.8105 (mmtt) REVERT: N 11 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8740 (pttp) REVERT: P 14 ARG cc_start: 0.8695 (ttt-90) cc_final: 0.8250 (ttt-90) REVERT: P 67 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8626 (tp) REVERT: Q 42 LYS cc_start: 0.8846 (mtmt) cc_final: 0.8539 (ttmt) REVERT: T 14 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8148 (mp0) REVERT: U 32 ARG cc_start: 0.8727 (ptt90) cc_final: 0.8352 (ttt180) REVERT: U 36 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.7929 (t80) REVERT: U 46 ARG cc_start: 0.8834 (tpt170) cc_final: 0.8563 (ttm170) REVERT: 03 180 PHE cc_start: 0.1173 (OUTLIER) cc_final: 0.0656 (m-80) REVERT: 03 192 LEU cc_start: 0.6777 (tt) cc_final: 0.6576 (mt) REVERT: Z 39 TYR cc_start: 0.8148 (t80) cc_final: 0.7886 (t80) REVERT: Z 51 ASN cc_start: 0.8878 (p0) cc_final: 0.8307 (m-40) REVERT: Z 142 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7504 (p0) REVERT: Z 206 ILE cc_start: 0.7585 (OUTLIER) cc_final: 0.7314 (pp) REVERT: Z 243 GLU cc_start: 0.8234 (tt0) cc_final: 0.7552 (pt0) REVERT: Z 358 MET cc_start: 0.7544 (pmm) cc_final: 0.7310 (pmm) REVERT: Z 368 MET cc_start: 0.7816 (mmm) cc_final: 0.7582 (tpt) outliers start: 403 outliers final: 302 residues processed: 1095 average time/residue: 1.2702 time to fit residues: 2467.5322 Evaluate side-chains 1091 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 318 poor density : 773 time to evaluate : 6.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 33 LEU Chi-restraints excluded: chain 04 residue 53 ILE Chi-restraints excluded: chain 04 residue 129 LEU Chi-restraints excluded: chain 04 residue 143 VAL Chi-restraints excluded: chain 04 residue 219 VAL Chi-restraints excluded: chain 04 residue 222 THR Chi-restraints excluded: chain 04 residue 227 VAL Chi-restraints excluded: chain 05 residue 14 ILE Chi-restraints excluded: chain 05 residue 27 ILE Chi-restraints excluded: chain 05 residue 48 ILE Chi-restraints excluded: chain 05 residue 96 ILE Chi-restraints excluded: chain 05 residue 133 THR Chi-restraints excluded: chain 05 residue 145 SER Chi-restraints excluded: chain 05 residue 151 THR Chi-restraints excluded: chain 05 residue 180 VAL Chi-restraints excluded: chain 05 residue 186 LEU Chi-restraints excluded: chain 05 residue 187 LEU Chi-restraints excluded: chain 05 residue 188 LEU Chi-restraints excluded: chain 05 residue 197 THR Chi-restraints excluded: chain 06 residue 15 SER Chi-restraints excluded: chain 06 residue 22 ASP Chi-restraints excluded: chain 06 residue 48 THR Chi-restraints excluded: chain 06 residue 72 SER Chi-restraints excluded: chain 06 residue 73 ILE Chi-restraints excluded: chain 06 residue 150 THR Chi-restraints excluded: chain 06 residue 175 ILE Chi-restraints excluded: chain 07 residue 24 VAL Chi-restraints excluded: chain 07 residue 46 LYS Chi-restraints excluded: chain 07 residue 105 ILE Chi-restraints excluded: chain 07 residue 146 ASP Chi-restraints excluded: chain 07 residue 154 THR Chi-restraints excluded: chain 08 residue 9 VAL Chi-restraints excluded: chain 08 residue 19 ASN Chi-restraints excluded: chain 08 residue 25 ILE Chi-restraints excluded: chain 08 residue 51 PHE Chi-restraints excluded: chain 08 residue 75 VAL Chi-restraints excluded: chain 08 residue 100 ASN Chi-restraints excluded: chain 08 residue 161 VAL Chi-restraints excluded: chain 09 residue 20 ASN Chi-restraints excluded: chain 09 residue 31 VAL Chi-restraints excluded: chain 09 residue 94 ILE Chi-restraints excluded: chain 09 residue 99 ILE Chi-restraints excluded: chain 09 residue 145 ASN Chi-restraints excluded: chain 10 residue 8 LYS Chi-restraints excluded: chain 10 residue 27 VAL Chi-restraints excluded: chain 10 residue 31 ARG Chi-restraints excluded: chain 10 residue 64 VAL Chi-restraints excluded: chain 10 residue 99 PHE Chi-restraints excluded: chain 10 residue 117 LEU Chi-restraints excluded: chain 10 residue 123 ILE Chi-restraints excluded: chain 11 residue 34 ILE Chi-restraints excluded: chain 11 residue 48 ILE Chi-restraints excluded: chain 11 residue 67 THR Chi-restraints excluded: chain 11 residue 70 THR Chi-restraints excluded: chain 11 residue 72 THR Chi-restraints excluded: chain 11 residue 77 VAL Chi-restraints excluded: chain 11 residue 110 GLN Chi-restraints excluded: chain 11 residue 121 ILE Chi-restraints excluded: chain 11 residue 138 VAL Chi-restraints excluded: chain 11 residue 139 VAL Chi-restraints excluded: chain 13 residue 25 LEU Chi-restraints excluded: chain 13 residue 43 ILE Chi-restraints excluded: chain 13 residue 58 LEU Chi-restraints excluded: chain 13 residue 61 VAL Chi-restraints excluded: chain 13 residue 69 VAL Chi-restraints excluded: chain 13 residue 88 ASN Chi-restraints excluded: chain 13 residue 114 LYS Chi-restraints excluded: chain 14 residue 23 ILE Chi-restraints excluded: chain 14 residue 46 VAL Chi-restraints excluded: chain 14 residue 92 LEU Chi-restraints excluded: chain 14 residue 103 ILE Chi-restraints excluded: chain 14 residue 118 THR Chi-restraints excluded: chain 14 residue 121 THR Chi-restraints excluded: chain 14 residue 129 LYS Chi-restraints excluded: chain 15 residue 20 LEU Chi-restraints excluded: chain 15 residue 25 ASP Chi-restraints excluded: chain 15 residue 36 VAL Chi-restraints excluded: chain 15 residue 41 LEU Chi-restraints excluded: chain 15 residue 46 ILE Chi-restraints excluded: chain 15 residue 70 ASP Chi-restraints excluded: chain 15 residue 91 TYR Chi-restraints excluded: chain 15 residue 119 LEU Chi-restraints excluded: chain 15 residue 124 LEU Chi-restraints excluded: chain 16 residue 1 MET Chi-restraints excluded: chain 16 residue 2 ARG Chi-restraints excluded: chain 16 residue 24 MET Chi-restraints excluded: chain 16 residue 47 VAL Chi-restraints excluded: chain 16 residue 62 ASN Chi-restraints excluded: chain 16 residue 65 LEU Chi-restraints excluded: chain 16 residue 89 SER Chi-restraints excluded: chain 16 residue 103 ARG Chi-restraints excluded: chain 16 residue 113 ILE Chi-restraints excluded: chain 17 residue 2 ASP Chi-restraints excluded: chain 17 residue 27 VAL Chi-restraints excluded: chain 17 residue 55 GLU Chi-restraints excluded: chain 17 residue 65 THR Chi-restraints excluded: chain 17 residue 69 ASP Chi-restraints excluded: chain 17 residue 106 LEU Chi-restraints excluded: chain 18 residue 49 ILE Chi-restraints excluded: chain 18 residue 60 VAL Chi-restraints excluded: chain 18 residue 83 ILE Chi-restraints excluded: chain 18 residue 84 SER Chi-restraints excluded: chain 18 residue 111 GLU Chi-restraints excluded: chain 19 residue 38 VAL Chi-restraints excluded: chain 20 residue 19 THR Chi-restraints excluded: chain 20 residue 26 ASP Chi-restraints excluded: chain 20 residue 54 VAL Chi-restraints excluded: chain 20 residue 95 ASP Chi-restraints excluded: chain 21 residue 4 ILE Chi-restraints excluded: chain 21 residue 20 VAL Chi-restraints excluded: chain 21 residue 34 ASP Chi-restraints excluded: chain 21 residue 40 ASN Chi-restraints excluded: chain 21 residue 66 ILE Chi-restraints excluded: chain 21 residue 67 ASP Chi-restraints excluded: chain 21 residue 82 MET Chi-restraints excluded: chain 21 residue 97 LEU Chi-restraints excluded: chain 22 residue 32 LEU Chi-restraints excluded: chain 22 residue 37 ASP Chi-restraints excluded: chain 22 residue 43 ILE Chi-restraints excluded: chain 22 residue 47 VAL Chi-restraints excluded: chain 22 residue 70 HIS Chi-restraints excluded: chain 22 residue 87 LEU Chi-restraints excluded: chain 22 residue 93 LEU Chi-restraints excluded: chain 23 residue 10 VAL Chi-restraints excluded: chain 23 residue 11 ILE Chi-restraints excluded: chain 23 residue 26 ASN Chi-restraints excluded: chain 23 residue 48 VAL Chi-restraints excluded: chain 24 residue 40 ILE Chi-restraints excluded: chain 24 residue 56 PHE Chi-restraints excluded: chain 24 residue 66 ASP Chi-restraints excluded: chain 24 residue 89 ILE Chi-restraints excluded: chain 25 residue 17 LEU Chi-restraints excluded: chain 25 residue 77 SER Chi-restraints excluded: chain 26 residue 3 VAL Chi-restraints excluded: chain 26 residue 24 THR Chi-restraints excluded: chain 26 residue 47 THR Chi-restraints excluded: chain 26 residue 58 ILE Chi-restraints excluded: chain 26 residue 65 THR Chi-restraints excluded: chain 27 residue 6 LEU Chi-restraints excluded: chain 27 residue 11 VAL Chi-restraints excluded: chain 27 residue 13 GLU Chi-restraints excluded: chain 27 residue 17 GLU Chi-restraints excluded: chain 27 residue 24 GLU Chi-restraints excluded: chain 27 residue 50 VAL Chi-restraints excluded: chain 28 residue 2 LYS Chi-restraints excluded: chain 28 residue 22 THR 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 4 ASP Chi-restraints excluded: chain 29 residue 31 ASP Chi-restraints excluded: chain 29 residue 34 LEU Chi-restraints excluded: chain 29 residue 53 THR Chi-restraints excluded: chain 30 residue 24 VAL Chi-restraints excluded: chain 30 residue 28 SER Chi-restraints excluded: chain 30 residue 38 LEU Chi-restraints excluded: chain 30 residue 53 VAL Chi-restraints excluded: chain 31 residue 10 LEU Chi-restraints excluded: chain 31 residue 11 VAL Chi-restraints excluded: chain 31 residue 28 THR Chi-restraints excluded: chain 31 residue 45 HIS Chi-restraints excluded: chain 31 residue 47 ILE Chi-restraints excluded: chain 32 residue 1 MET Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 33 residue 6 VAL Chi-restraints excluded: chain 33 residue 50 SER Chi-restraints excluded: chain 33 residue 53 ASP Chi-restraints excluded: chain 33 residue 61 LEU Chi-restraints excluded: chain 34 residue 26 ILE Chi-restraints excluded: chain 34 residue 36 ARG Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 108 GLN Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 53 ARG Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 19 PHE Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 191 SER Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain F residue 8 PHE Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 73 GLU Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 96 ASN Chi-restraints excluded: chain G residue 121 ASN Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 126 PHE Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 75 ASP Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain K residue 96 ILE Chi-restraints excluded: chain K residue 104 PHE Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 11 HIS Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 61 LYS Chi-restraints excluded: chain M residue 94 LEU Chi-restraints excluded: chain N residue 11 LYS Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 19 TYR Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain O residue 19 ASN Chi-restraints excluded: chain O residue 42 PHE Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 38 PHE Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 20 ILE Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain R residue 20 ILE Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 73 HIS Chi-restraints excluded: chain S residue 11 ASP Chi-restraints excluded: chain S residue 38 THR Chi-restraints excluded: chain S residue 43 MET Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 64 GLU Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain T residue 54 GLN Chi-restraints excluded: chain U residue 12 ASP Chi-restraints excluded: chain U residue 35 GLU Chi-restraints excluded: chain U residue 36 PHE Chi-restraints excluded: chain 03 residue 10 VAL Chi-restraints excluded: chain 03 residue 180 PHE Chi-restraints excluded: chain Z residue 32 THR Chi-restraints excluded: chain Z residue 47 ASP Chi-restraints excluded: chain Z residue 140 VAL Chi-restraints excluded: chain Z residue 142 ASP Chi-restraints excluded: chain Z residue 156 LEU Chi-restraints excluded: chain Z residue 206 ILE Chi-restraints excluded: chain Z residue 211 LEU Chi-restraints excluded: chain Z residue 228 THR Chi-restraints excluded: chain Z residue 254 THR Chi-restraints excluded: chain Z residue 255 CYS Chi-restraints excluded: chain Z residue 335 THR Chi-restraints excluded: chain Z residue 340 THR Chi-restraints excluded: chain Z residue 359 VAL 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: 9.9990 chunk 633 optimal weight: 20.0000 chunk 319 optimal weight: 7.9990 chunk 208 optimal weight: 9.9990 chunk 205 optimal weight: 10.0000 chunk 674 optimal weight: 10.0000 chunk 722 optimal weight: 20.0000 chunk 524 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 834 optimal weight: 5.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 04 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 04 162 GLN ** 04 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 19 ASN ** 08 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 10 103 ASN ** 11 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 18 114 ASN 19 19 GLN ** 24 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 28 33 HIS ** 32 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 63 GLN ** L 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 ASN O 79 GLN ** T 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 166822 Z= 0.246 Angle : 0.709 16.395 249077 Z= 0.363 Chirality : 0.039 0.343 31782 Planarity : 0.005 0.107 13715 Dihedral : 24.302 179.810 82271 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 27.72 Ramachandran Plot: Outliers : 0.30 % Allowed : 12.44 % Favored : 87.26 % Rotamer: Outliers : 5.68 % Allowed : 26.13 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.10), residues: 6366 helix: -1.04 (0.11), residues: 1936 sheet: -2.39 (0.14), residues: 1123 loop : -2.59 (0.10), residues: 3307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP K 43 HIS 0.012 0.001 HIS24 44 PHE 0.023 0.002 PHE29 64 TYR 0.037 0.002 TYR07 142 ARG 0.009 0.001 ARG B 73 *********************** 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 1164 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 300 poor density : 864 time to evaluate : 6.933 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: 05 123 LYS cc_start: 0.9381 (tttm) cc_final: 0.9112 (mmtt) REVERT: 05 200 ASP cc_start: 0.8841 (p0) cc_final: 0.8565 (p0) REVERT: 07 22 ASN cc_start: 0.7600 (m-40) cc_final: 0.7009 (p0) REVERT: 07 34 THR cc_start: 0.8759 (m) cc_final: 0.8372 (p) REVERT: 07 56 LEU cc_start: 0.8502 (mt) cc_final: 0.8081 (mt) REVERT: 08 51 PHE cc_start: 0.6371 (OUTLIER) cc_final: 0.4664 (m-80) REVERT: 09 41 LYS cc_start: 0.9067 (tmtt) cc_final: 0.8507 (tptt) REVERT: 09 46 PHE cc_start: 0.9221 (t80) cc_final: 0.8994 (t80) REVERT: 09 109 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7439 (tp30) REVERT: 10 6 GLN cc_start: 0.8865 (mm110) cc_final: 0.8146 (tm-30) REVERT: 10 56 ARG cc_start: 0.6125 (mpt180) cc_final: 0.5743 (mpt180) REVERT: 13 111 LYS cc_start: 0.8448 (ttpp) cc_final: 0.7772 (ttpp) REVERT: 13 112 PHE cc_start: 0.8851 (m-80) cc_final: 0.8632 (m-80) REVERT: 14 23 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8483 (mp) REVERT: 14 36 LYS cc_start: 0.8303 (mttt) cc_final: 0.7929 (pttm) REVERT: 14 58 TYR cc_start: 0.8510 (p90) cc_final: 0.7749 (p90) REVERT: 16 20 MET cc_start: 0.8021 (tpp) cc_final: 0.7555 (tpp) REVERT: 16 24 MET cc_start: 0.9017 (OUTLIER) cc_final: 0.8676 (mmt) REVERT: 16 74 GLU cc_start: 0.8493 (tt0) cc_final: 0.8262 (tm-30) REVERT: 17 17 LYS cc_start: 0.8663 (tptp) cc_final: 0.7843 (ptmt) REVERT: 17 25 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.8128 (ptt-90) REVERT: 17 92 PHE cc_start: 0.8766 (t80) cc_final: 0.8290 (t80) REVERT: 18 40 GLN cc_start: 0.7721 (OUTLIER) cc_final: 0.7307 (pt0) REVERT: 18 114 ASN cc_start: 0.8164 (OUTLIER) cc_final: 0.7740 (m110) REVERT: 19 96 ASP cc_start: 0.8116 (t70) cc_final: 0.7792 (t70) REVERT: 31 45 HIS cc_start: 0.7775 (OUTLIER) cc_final: 0.6780 (m90) REVERT: 33 61 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7612 (pp) REVERT: B 99 MET cc_start: 0.8069 (mtt) cc_final: 0.7586 (mtt) REVERT: B 116 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8539 (tp) REVERT: C 53 ARG cc_start: 0.7475 (OUTLIER) cc_final: 0.6083 (ptt90) REVERT: C 183 TYR cc_start: 0.8032 (t80) cc_final: 0.7667 (t80) REVERT: C 192 TYR cc_start: 0.8064 (m-80) cc_final: 0.7739 (t80) REVERT: D 102 TYR cc_start: 0.8511 (t80) cc_final: 0.8183 (t80) REVERT: E 63 MET cc_start: 0.7920 (OUTLIER) cc_final: 0.7671 (mmm) REVERT: F 16 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8914 (mp0) REVERT: F 52 ASN cc_start: 0.9479 (t0) cc_final: 0.9051 (t0) REVERT: G 36 SER cc_start: 0.8817 (OUTLIER) cc_final: 0.8285 (p) REVERT: G 139 ASP cc_start: 0.7944 (m-30) cc_final: 0.7676 (t70) REVERT: H 2 MET cc_start: 0.7836 (mmp) cc_final: 0.7354 (tpt) REVERT: H 57 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7638 (mm-30) REVERT: I 30 ASN cc_start: 0.8320 (t0) cc_final: 0.7962 (t0) REVERT: I 106 ASP cc_start: 0.7967 (t0) cc_final: 0.7684 (t0) REVERT: J 20 GLN cc_start: 0.8440 (pt0) cc_final: 0.7723 (tp-100) REVERT: J 31 ARG cc_start: 0.8257 (ttp80) cc_final: 0.7636 (ttm110) REVERT: J 63 ASP cc_start: 0.7213 (t70) cc_final: 0.6077 (t0) REVERT: J 65 TYR cc_start: 0.8833 (m-80) cc_final: 0.8347 (m-10) REVERT: K 74 LYS cc_start: 0.8817 (mmmt) cc_final: 0.8493 (mmmt) REVERT: K 76 TYR cc_start: 0.8794 (m-80) cc_final: 0.8495 (m-10) REVERT: K 126 ARG cc_start: 0.8231 (mmp-170) cc_final: 0.7731 (tpp-160) REVERT: M 12 LYS cc_start: 0.8674 (mttt) cc_final: 0.8030 (mmtt) REVERT: P 14 ARG cc_start: 0.8523 (ttt-90) cc_final: 0.8030 (ttt180) REVERT: P 67 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8454 (tp) REVERT: Q 42 LYS cc_start: 0.8666 (mtmt) cc_final: 0.8460 (ttmt) REVERT: U 32 ARG cc_start: 0.8657 (ptt90) cc_final: 0.8273 (ttt180) REVERT: U 36 PHE cc_start: 0.8216 (OUTLIER) cc_final: 0.7764 (t80) REVERT: U 39 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8593 (tptt) REVERT: 03 180 PHE cc_start: 0.1590 (OUTLIER) cc_final: 0.1146 (m-10) REVERT: Z 39 TYR cc_start: 0.8015 (t80) cc_final: 0.7748 (t80) REVERT: Z 51 ASN cc_start: 0.8812 (p0) cc_final: 0.8286 (m-40) REVERT: Z 142 ASP cc_start: 0.7570 (OUTLIER) cc_final: 0.7311 (p0) REVERT: Z 206 ILE cc_start: 0.7610 (OUTLIER) cc_final: 0.7356 (pp) REVERT: Z 243 GLU cc_start: 0.7999 (tt0) cc_final: 0.7348 (pt0) outliers start: 300 outliers final: 250 residues processed: 1073 average time/residue: 1.3280 time to fit residues: 2535.8675 Evaluate side-chains 1080 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 268 poor density : 812 time to evaluate : 6.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 33 LEU Chi-restraints excluded: chain 04 residue 143 VAL Chi-restraints excluded: chain 04 residue 163 ILE Chi-restraints excluded: chain 04 residue 219 VAL Chi-restraints excluded: chain 04 residue 222 THR Chi-restraints excluded: chain 04 residue 227 VAL Chi-restraints excluded: chain 05 residue 14 ILE Chi-restraints excluded: chain 05 residue 27 ILE Chi-restraints excluded: chain 05 residue 133 THR Chi-restraints excluded: chain 05 residue 180 VAL Chi-restraints excluded: chain 05 residue 186 LEU Chi-restraints excluded: chain 05 residue 188 LEU Chi-restraints excluded: chain 05 residue 197 THR Chi-restraints excluded: chain 06 residue 15 SER Chi-restraints excluded: chain 06 residue 22 ASP Chi-restraints excluded: chain 06 residue 48 THR Chi-restraints excluded: chain 06 residue 72 SER Chi-restraints excluded: chain 06 residue 73 ILE Chi-restraints excluded: chain 06 residue 149 ILE Chi-restraints excluded: chain 07 residue 3 LEU Chi-restraints excluded: chain 07 residue 24 VAL Chi-restraints excluded: chain 07 residue 46 LYS Chi-restraints excluded: chain 07 residue 146 ASP Chi-restraints excluded: chain 07 residue 154 THR Chi-restraints excluded: chain 08 residue 9 VAL Chi-restraints excluded: chain 08 residue 25 ILE Chi-restraints excluded: chain 08 residue 51 PHE Chi-restraints excluded: chain 08 residue 75 VAL Chi-restraints excluded: chain 08 residue 100 ASN Chi-restraints excluded: chain 08 residue 161 VAL Chi-restraints excluded: chain 09 residue 12 LEU Chi-restraints excluded: chain 09 residue 20 ASN Chi-restraints excluded: chain 09 residue 31 VAL Chi-restraints excluded: chain 09 residue 94 ILE Chi-restraints excluded: chain 09 residue 99 ILE Chi-restraints excluded: chain 09 residue 125 THR Chi-restraints excluded: chain 09 residue 145 ASN Chi-restraints excluded: chain 10 residue 8 LYS Chi-restraints excluded: chain 10 residue 27 VAL Chi-restraints excluded: chain 10 residue 31 ARG Chi-restraints excluded: chain 10 residue 64 VAL Chi-restraints excluded: chain 10 residue 99 PHE Chi-restraints excluded: chain 10 residue 117 LEU Chi-restraints excluded: chain 10 residue 123 ILE Chi-restraints excluded: chain 11 residue 7 TYR Chi-restraints excluded: chain 11 residue 34 ILE Chi-restraints excluded: chain 11 residue 48 ILE Chi-restraints excluded: chain 11 residue 67 THR Chi-restraints excluded: chain 11 residue 70 THR Chi-restraints excluded: chain 11 residue 72 THR Chi-restraints excluded: chain 11 residue 105 LEU Chi-restraints excluded: chain 11 residue 121 ILE Chi-restraints excluded: chain 11 residue 138 VAL Chi-restraints excluded: chain 11 residue 139 VAL Chi-restraints excluded: chain 13 residue 25 LEU Chi-restraints excluded: chain 13 residue 35 VAL Chi-restraints excluded: chain 13 residue 43 ILE Chi-restraints excluded: chain 13 residue 61 VAL Chi-restraints excluded: chain 13 residue 69 VAL Chi-restraints excluded: chain 13 residue 88 ASN Chi-restraints excluded: chain 13 residue 114 LYS Chi-restraints excluded: chain 14 residue 23 ILE Chi-restraints excluded: chain 14 residue 46 VAL Chi-restraints excluded: chain 14 residue 92 LEU Chi-restraints excluded: chain 14 residue 118 THR Chi-restraints excluded: chain 14 residue 121 THR Chi-restraints excluded: chain 15 residue 20 LEU Chi-restraints excluded: chain 15 residue 36 VAL Chi-restraints excluded: chain 15 residue 41 LEU Chi-restraints excluded: chain 15 residue 70 ASP Chi-restraints excluded: chain 15 residue 91 TYR Chi-restraints excluded: chain 15 residue 119 LEU Chi-restraints excluded: chain 16 residue 2 ARG Chi-restraints excluded: chain 16 residue 24 MET Chi-restraints excluded: chain 16 residue 47 VAL Chi-restraints excluded: chain 16 residue 89 SER Chi-restraints excluded: chain 16 residue 113 ILE Chi-restraints excluded: chain 17 residue 25 ARG Chi-restraints excluded: chain 17 residue 27 VAL Chi-restraints excluded: chain 17 residue 55 GLU Chi-restraints excluded: chain 17 residue 65 THR Chi-restraints excluded: chain 17 residue 69 ASP Chi-restraints excluded: chain 17 residue 106 LEU Chi-restraints excluded: chain 18 residue 40 GLN Chi-restraints excluded: chain 18 residue 49 ILE Chi-restraints excluded: chain 18 residue 60 VAL Chi-restraints excluded: chain 18 residue 83 ILE Chi-restraints excluded: chain 18 residue 114 ASN Chi-restraints excluded: chain 20 residue 19 THR Chi-restraints excluded: chain 20 residue 26 ASP Chi-restraints excluded: chain 20 residue 54 VAL Chi-restraints excluded: chain 21 residue 4 ILE Chi-restraints excluded: chain 21 residue 34 ASP Chi-restraints excluded: chain 21 residue 40 ASN Chi-restraints excluded: chain 21 residue 66 ILE Chi-restraints excluded: chain 21 residue 67 ASP Chi-restraints excluded: chain 21 residue 97 LEU Chi-restraints excluded: chain 21 residue 109 ASP Chi-restraints excluded: chain 22 residue 32 LEU Chi-restraints excluded: chain 22 residue 37 ASP Chi-restraints excluded: chain 22 residue 43 ILE Chi-restraints excluded: chain 22 residue 70 HIS Chi-restraints excluded: chain 22 residue 87 LEU Chi-restraints excluded: chain 22 residue 93 LEU Chi-restraints excluded: chain 23 residue 11 ILE Chi-restraints excluded: chain 23 residue 26 ASN Chi-restraints excluded: chain 23 residue 48 VAL Chi-restraints excluded: chain 24 residue 56 PHE Chi-restraints excluded: chain 24 residue 66 ASP Chi-restraints excluded: chain 24 residue 89 ILE Chi-restraints excluded: chain 25 residue 17 LEU Chi-restraints excluded: chain 25 residue 77 SER Chi-restraints excluded: chain 26 residue 3 VAL Chi-restraints excluded: chain 26 residue 24 THR Chi-restraints excluded: chain 26 residue 47 THR Chi-restraints excluded: chain 26 residue 58 ILE Chi-restraints excluded: chain 26 residue 65 THR Chi-restraints excluded: chain 27 residue 2 LYS Chi-restraints excluded: chain 27 residue 6 LEU Chi-restraints excluded: chain 27 residue 11 VAL Chi-restraints excluded: chain 27 residue 17 GLU Chi-restraints excluded: chain 28 residue 2 LYS Chi-restraints excluded: chain 28 residue 22 THR Chi-restraints excluded: chain 28 residue 40 THR Chi-restraints excluded: chain 28 residue 48 ASN Chi-restraints excluded: chain 29 residue 4 ASP Chi-restraints excluded: chain 29 residue 31 ASP Chi-restraints excluded: chain 29 residue 34 LEU Chi-restraints excluded: chain 29 residue 53 THR Chi-restraints excluded: chain 30 residue 24 VAL Chi-restraints excluded: chain 30 residue 28 SER Chi-restraints excluded: chain 30 residue 38 LEU Chi-restraints excluded: chain 31 residue 10 LEU Chi-restraints excluded: chain 31 residue 45 HIS Chi-restraints excluded: chain 32 residue 1 MET Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 33 residue 6 VAL Chi-restraints excluded: chain 33 residue 50 SER Chi-restraints excluded: chain 33 residue 53 ASP Chi-restraints excluded: chain 33 residue 61 LEU Chi-restraints excluded: chain 34 residue 20 ASP Chi-restraints excluded: chain 34 residue 36 ARG Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 108 GLN Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 53 ARG Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 19 PHE Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 191 SER Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 96 ASN Chi-restraints excluded: chain G residue 121 ASN Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 96 ILE Chi-restraints excluded: chain K residue 104 PHE Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 20 SER Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 61 LYS Chi-restraints excluded: chain M residue 94 LEU Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 19 TYR Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain O residue 19 ASN Chi-restraints excluded: chain O residue 42 PHE Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 38 PHE Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain Q residue 20 ILE Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain R residue 20 ILE Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain S residue 11 ASP Chi-restraints excluded: chain S residue 38 THR Chi-restraints excluded: chain S residue 43 MET Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 54 GLN Chi-restraints excluded: chain U residue 12 ASP Chi-restraints excluded: chain U residue 35 GLU Chi-restraints excluded: chain U residue 36 PHE Chi-restraints excluded: chain U residue 39 LYS Chi-restraints excluded: chain 03 residue 10 VAL Chi-restraints excluded: chain 03 residue 180 PHE Chi-restraints excluded: chain Z residue 32 THR Chi-restraints excluded: chain Z residue 47 ASP Chi-restraints excluded: chain Z residue 140 VAL Chi-restraints excluded: chain Z residue 142 ASP Chi-restraints excluded: chain Z residue 156 LEU Chi-restraints excluded: chain Z residue 206 ILE Chi-restraints excluded: chain Z residue 211 LEU Chi-restraints excluded: chain Z residue 228 THR Chi-restraints excluded: chain Z residue 255 CYS Chi-restraints excluded: chain Z residue 335 THR Chi-restraints excluded: chain Z residue 351 MET Chi-restraints excluded: chain Z residue 359 VAL Chi-restraints excluded: chain Z residue 391 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1101 random chunks: chunk 965 optimal weight: 20.0000 chunk 1016 optimal weight: 20.0000 chunk 927 optimal weight: 20.0000 chunk 988 optimal weight: 20.0000 chunk 595 optimal weight: 30.0000 chunk 430 optimal weight: 20.0000 chunk 776 optimal weight: 20.0000 chunk 303 optimal weight: 20.0000 chunk 893 optimal weight: 20.0000 chunk 935 optimal weight: 20.0000 chunk 985 optimal weight: 20.0000 overall best weight: 20.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 04 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 04 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 06 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 06 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 110 HIS ** 09 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 33 ASN ** 11 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 18 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 21 7 HIS ** 24 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 28 48 ASN ** 32 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 ASN ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 54 GLN ** Z 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.5323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.106 166822 Z= 0.560 Angle : 0.982 15.908 249077 Z= 0.491 Chirality : 0.050 0.410 31782 Planarity : 0.007 0.093 13715 Dihedral : 24.574 179.536 82271 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 42.73 Ramachandran Plot: Outliers : 0.28 % Allowed : 16.73 % Favored : 82.99 % Rotamer: Outliers : 6.36 % Allowed : 26.03 % Favored : 67.61 % 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: -3.58 (0.10), residues: 6366 helix: -1.53 (0.11), residues: 1913 sheet: -2.52 (0.14), residues: 1112 loop : -2.89 (0.10), residues: 3341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP P 60 HIS 0.025 0.003 HIS06 165 PHE 0.037 0.003 PHE F 8 TYR 0.044 0.004 TYR D 75 ARG 0.018 0.001 ARG09 51 *********************** 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 1114 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 336 poor density : 778 time to evaluate : 6.939 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: 05 123 LYS cc_start: 0.9424 (tttm) cc_final: 0.9109 (mmtt) REVERT: 05 200 ASP cc_start: 0.9000 (p0) cc_final: 0.8713 (p0) REVERT: 06 199 MET cc_start: 0.8048 (ttt) cc_final: 0.7104 (tpp) REVERT: 07 173 ASP cc_start: 0.7561 (m-30) cc_final: 0.6890 (t0) REVERT: 09 41 LYS cc_start: 0.9027 (tmtt) cc_final: 0.8464 (tptt) REVERT: 09 104 THR cc_start: 0.8953 (p) cc_final: 0.8482 (p) REVERT: 09 109 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7186 (tp30) REVERT: 10 69 PHE cc_start: 0.8009 (t80) cc_final: 0.7593 (t80) REVERT: 13 111 LYS cc_start: 0.8517 (ttpp) cc_final: 0.7862 (ttpp) REVERT: 13 112 PHE cc_start: 0.8918 (m-80) cc_final: 0.8593 (m-80) REVERT: 14 23 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8719 (mp) REVERT: 14 36 LYS cc_start: 0.8372 (mttt) cc_final: 0.7983 (pttm) REVERT: 15 12 MET cc_start: 0.8538 (ppp) cc_final: 0.8328 (ppp) REVERT: 16 20 MET cc_start: 0.8172 (tpp) cc_final: 0.7375 (tpp) REVERT: 16 24 MET cc_start: 0.9096 (OUTLIER) cc_final: 0.8832 (mmt) REVERT: 17 25 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.8163 (ptt-90) REVERT: 17 92 PHE cc_start: 0.8740 (t80) cc_final: 0.8277 (t80) REVERT: 18 40 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7480 (pt0) REVERT: 19 96 ASP cc_start: 0.8170 (t70) cc_final: 0.7925 (t70) REVERT: 26 15 ASN cc_start: 0.8382 (m110) cc_final: 0.8032 (m110) REVERT: 27 24 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7523 (mp0) REVERT: 31 45 HIS cc_start: 0.8134 (OUTLIER) cc_final: 0.7655 (m90) REVERT: B 99 MET cc_start: 0.8226 (mtt) cc_final: 0.7884 (mtt) REVERT: B 116 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8642 (tp) REVERT: C 183 TYR cc_start: 0.8148 (t80) cc_final: 0.7918 (t80) REVERT: C 192 TYR cc_start: 0.8072 (m-80) cc_final: 0.7568 (t80) REVERT: D 123 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8279 (tpp) REVERT: E 63 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.8026 (mmm) REVERT: E 85 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.6941 (mmmm) REVERT: F 16 GLU cc_start: 0.9288 (mm-30) cc_final: 0.8961 (mp0) REVERT: F 52 ASN cc_start: 0.9492 (t0) cc_final: 0.9052 (t0) REVERT: G 6 ILE cc_start: 0.6472 (OUTLIER) cc_final: 0.6198 (pp) REVERT: G 36 SER cc_start: 0.9081 (OUTLIER) cc_final: 0.8614 (p) REVERT: H 83 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.8078 (tpp80) REVERT: I 30 ASN cc_start: 0.8436 (t0) cc_final: 0.8102 (t0) REVERT: J 20 GLN cc_start: 0.8501 (pt0) cc_final: 0.8017 (tp-100) REVERT: J 24 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8249 (tm-30) REVERT: J 31 ARG cc_start: 0.8552 (ttp80) cc_final: 0.7870 (ttm110) REVERT: J 65 TYR cc_start: 0.8760 (m-80) cc_final: 0.8378 (m-10) REVERT: K 74 LYS cc_start: 0.8897 (mmmt) cc_final: 0.8682 (mmmt) REVERT: K 76 TYR cc_start: 0.8937 (m-80) cc_final: 0.8638 (m-10) REVERT: K 126 ARG cc_start: 0.8360 (mmp-170) cc_final: 0.7962 (tpp-160) REVERT: M 12 LYS cc_start: 0.8749 (mttt) cc_final: 0.8002 (mmtt) REVERT: P 14 ARG cc_start: 0.8661 (ttt-90) cc_final: 0.8289 (ttt180) REVERT: P 67 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8612 (tp) REVERT: Q 42 LYS cc_start: 0.8840 (mtmt) cc_final: 0.8537 (ttmt) REVERT: T 14 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8153 (mp0) REVERT: T 65 LEU cc_start: 0.9028 (tt) cc_final: 0.8825 (tp) REVERT: U 32 ARG cc_start: 0.8711 (ptt90) cc_final: 0.8319 (ttt180) REVERT: U 36 PHE cc_start: 0.8272 (OUTLIER) cc_final: 0.7841 (t80) REVERT: U 46 ARG cc_start: 0.8812 (tpt170) cc_final: 0.8573 (ttm170) REVERT: 03 180 PHE cc_start: 0.1548 (OUTLIER) cc_final: 0.0935 (m-80) REVERT: Z 39 TYR cc_start: 0.8156 (t80) cc_final: 0.7890 (t80) REVERT: Z 51 ASN cc_start: 0.8945 (p0) cc_final: 0.8406 (m-40) REVERT: Z 142 ASP cc_start: 0.7735 (OUTLIER) cc_final: 0.7519 (p0) REVERT: Z 206 ILE cc_start: 0.7541 (OUTLIER) cc_final: 0.7269 (pp) REVERT: Z 243 GLU cc_start: 0.8206 (tt0) cc_final: 0.7542 (pt0) outliers start: 336 outliers final: 296 residues processed: 1016 average time/residue: 1.3040 time to fit residues: 2348.6581 Evaluate side-chains 1072 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 314 poor density : 758 time to evaluate : 6.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 33 LEU Chi-restraints excluded: chain 04 residue 129 LEU Chi-restraints excluded: chain 04 residue 143 VAL Chi-restraints excluded: chain 04 residue 163 ILE Chi-restraints excluded: chain 04 residue 219 VAL Chi-restraints excluded: chain 04 residue 222 THR Chi-restraints excluded: chain 04 residue 227 VAL Chi-restraints excluded: chain 05 residue 14 ILE Chi-restraints excluded: chain 05 residue 27 ILE Chi-restraints excluded: chain 05 residue 48 ILE Chi-restraints excluded: chain 05 residue 133 THR Chi-restraints excluded: chain 05 residue 145 SER Chi-restraints excluded: chain 05 residue 151 THR Chi-restraints excluded: chain 05 residue 180 VAL Chi-restraints excluded: chain 05 residue 186 LEU Chi-restraints excluded: chain 05 residue 188 LEU Chi-restraints excluded: chain 05 residue 197 THR Chi-restraints excluded: chain 06 residue 15 SER Chi-restraints excluded: chain 06 residue 22 ASP Chi-restraints excluded: chain 06 residue 48 THR Chi-restraints excluded: chain 06 residue 72 SER Chi-restraints excluded: chain 06 residue 73 ILE Chi-restraints excluded: chain 06 residue 150 THR Chi-restraints excluded: chain 06 residue 175 ILE Chi-restraints excluded: chain 07 residue 3 LEU Chi-restraints excluded: chain 07 residue 24 VAL Chi-restraints excluded: chain 07 residue 46 LYS Chi-restraints excluded: chain 07 residue 146 ASP Chi-restraints excluded: chain 07 residue 154 THR Chi-restraints excluded: chain 08 residue 9 VAL Chi-restraints excluded: chain 08 residue 25 ILE Chi-restraints excluded: chain 08 residue 51 PHE Chi-restraints excluded: chain 08 residue 75 VAL Chi-restraints excluded: chain 08 residue 100 ASN Chi-restraints excluded: chain 08 residue 123 GLU Chi-restraints excluded: chain 08 residue 161 VAL Chi-restraints excluded: chain 09 residue 12 LEU Chi-restraints excluded: chain 09 residue 20 ASN Chi-restraints excluded: chain 09 residue 31 VAL Chi-restraints excluded: chain 09 residue 94 ILE Chi-restraints excluded: chain 09 residue 99 ILE Chi-restraints excluded: chain 09 residue 125 THR Chi-restraints excluded: chain 09 residue 145 ASN Chi-restraints excluded: chain 10 residue 8 LYS Chi-restraints excluded: chain 10 residue 27 VAL Chi-restraints excluded: chain 10 residue 31 ARG Chi-restraints excluded: chain 10 residue 64 VAL Chi-restraints excluded: chain 10 residue 80 THR Chi-restraints excluded: chain 10 residue 99 PHE Chi-restraints excluded: chain 10 residue 117 LEU Chi-restraints excluded: chain 10 residue 123 ILE Chi-restraints excluded: chain 11 residue 7 TYR Chi-restraints excluded: chain 11 residue 48 ILE Chi-restraints excluded: chain 11 residue 67 THR Chi-restraints excluded: chain 11 residue 70 THR Chi-restraints excluded: chain 11 residue 72 THR Chi-restraints excluded: chain 11 residue 77 VAL Chi-restraints excluded: chain 11 residue 110 GLN Chi-restraints excluded: chain 11 residue 121 ILE Chi-restraints excluded: chain 11 residue 138 VAL Chi-restraints excluded: chain 11 residue 139 VAL Chi-restraints excluded: chain 12 residue 111 LYS Chi-restraints excluded: chain 13 residue 25 LEU Chi-restraints excluded: chain 13 residue 43 ILE Chi-restraints excluded: chain 13 residue 58 LEU Chi-restraints excluded: chain 13 residue 61 VAL Chi-restraints excluded: chain 13 residue 88 ASN Chi-restraints excluded: chain 13 residue 114 LYS Chi-restraints excluded: chain 14 residue 23 ILE Chi-restraints excluded: chain 14 residue 46 VAL Chi-restraints excluded: chain 14 residue 92 LEU Chi-restraints excluded: chain 14 residue 117 THR Chi-restraints excluded: chain 14 residue 118 THR Chi-restraints excluded: chain 14 residue 121 THR Chi-restraints excluded: chain 15 residue 36 VAL Chi-restraints excluded: chain 15 residue 70 ASP Chi-restraints excluded: chain 15 residue 91 TYR Chi-restraints excluded: chain 15 residue 119 LEU Chi-restraints excluded: chain 15 residue 124 LEU Chi-restraints excluded: chain 16 residue 1 MET Chi-restraints excluded: chain 16 residue 2 ARG Chi-restraints excluded: chain 16 residue 24 MET Chi-restraints excluded: chain 16 residue 47 VAL Chi-restraints excluded: chain 16 residue 62 ASN Chi-restraints excluded: chain 16 residue 89 SER Chi-restraints excluded: chain 16 residue 113 ILE Chi-restraints excluded: chain 17 residue 21 LEU Chi-restraints excluded: chain 17 residue 25 ARG Chi-restraints excluded: chain 17 residue 27 VAL Chi-restraints excluded: chain 17 residue 55 GLU Chi-restraints excluded: chain 17 residue 65 THR Chi-restraints excluded: chain 17 residue 69 ASP Chi-restraints excluded: chain 17 residue 106 LEU Chi-restraints excluded: chain 18 residue 40 GLN Chi-restraints excluded: chain 18 residue 49 ILE Chi-restraints excluded: chain 18 residue 60 VAL Chi-restraints excluded: chain 18 residue 83 ILE Chi-restraints excluded: chain 19 residue 38 VAL Chi-restraints excluded: chain 20 residue 19 THR Chi-restraints excluded: chain 20 residue 26 ASP Chi-restraints excluded: chain 20 residue 54 VAL Chi-restraints excluded: chain 20 residue 95 ASP Chi-restraints excluded: chain 21 residue 4 ILE Chi-restraints excluded: chain 21 residue 34 ASP Chi-restraints excluded: chain 21 residue 40 ASN Chi-restraints excluded: chain 21 residue 66 ILE Chi-restraints excluded: chain 21 residue 67 ASP Chi-restraints excluded: chain 21 residue 82 MET Chi-restraints excluded: chain 21 residue 97 LEU Chi-restraints excluded: chain 21 residue 109 ASP Chi-restraints excluded: chain 22 residue 32 LEU Chi-restraints excluded: chain 22 residue 37 ASP Chi-restraints excluded: chain 22 residue 43 ILE Chi-restraints excluded: chain 22 residue 70 HIS Chi-restraints excluded: chain 22 residue 87 LEU Chi-restraints excluded: chain 23 residue 10 VAL Chi-restraints excluded: chain 23 residue 11 ILE Chi-restraints excluded: chain 23 residue 26 ASN Chi-restraints excluded: chain 23 residue 48 VAL Chi-restraints excluded: chain 24 residue 56 PHE Chi-restraints excluded: chain 24 residue 65 VAL Chi-restraints excluded: chain 24 residue 66 ASP Chi-restraints excluded: chain 24 residue 89 ILE Chi-restraints excluded: chain 25 residue 17 LEU Chi-restraints excluded: chain 25 residue 77 SER Chi-restraints excluded: chain 26 residue 3 VAL Chi-restraints excluded: chain 26 residue 24 THR Chi-restraints excluded: chain 26 residue 47 THR Chi-restraints excluded: chain 26 residue 58 ILE Chi-restraints excluded: chain 26 residue 65 THR Chi-restraints excluded: chain 27 residue 2 LYS Chi-restraints excluded: chain 27 residue 6 LEU Chi-restraints excluded: chain 27 residue 11 VAL Chi-restraints excluded: chain 27 residue 17 GLU Chi-restraints excluded: chain 27 residue 24 GLU Chi-restraints excluded: chain 27 residue 43 LEU Chi-restraints excluded: chain 27 residue 50 VAL Chi-restraints excluded: chain 28 residue 2 LYS Chi-restraints excluded: chain 28 residue 22 THR Chi-restraints excluded: chain 28 residue 40 THR Chi-restraints excluded: chain 28 residue 54 VAL Chi-restraints excluded: chain 29 residue 4 ASP Chi-restraints excluded: chain 29 residue 31 ASP Chi-restraints excluded: chain 29 residue 34 LEU Chi-restraints excluded: chain 29 residue 53 THR Chi-restraints excluded: chain 30 residue 24 VAL Chi-restraints excluded: chain 30 residue 31 LYS Chi-restraints excluded: chain 30 residue 38 LEU Chi-restraints excluded: chain 31 residue 10 LEU Chi-restraints excluded: chain 31 residue 11 VAL Chi-restraints excluded: chain 31 residue 28 THR Chi-restraints excluded: chain 31 residue 45 HIS Chi-restraints excluded: chain 32 residue 1 MET Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 33 residue 6 VAL Chi-restraints excluded: chain 33 residue 50 SER Chi-restraints excluded: chain 33 residue 53 ASP Chi-restraints excluded: chain 33 residue 61 LEU Chi-restraints excluded: chain 34 residue 20 ASP Chi-restraints excluded: chain 34 residue 36 ARG Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 108 GLN Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 53 ARG Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 19 PHE Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 49 ASP Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 191 SER Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain F residue 8 PHE Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 67 ASN Chi-restraints excluded: chain G residue 96 ASN Chi-restraints excluded: chain G residue 121 ASN Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 96 ILE Chi-restraints excluded: chain K residue 104 PHE Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 11 HIS Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 20 SER Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 61 LYS Chi-restraints excluded: chain M residue 94 LEU Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 19 TYR Chi-restraints excluded: chain N residue 41 TRP Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain O residue 19 ASN Chi-restraints excluded: chain O residue 37 HIS Chi-restraints excluded: chain O residue 42 PHE Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 38 PHE Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 20 ILE Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain Q residue 74 LEU Chi-restraints excluded: chain R residue 20 ILE Chi-restraints excluded: chain R residue 24 ASP Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain S residue 11 ASP Chi-restraints excluded: chain S residue 38 THR Chi-restraints excluded: chain S residue 43 MET Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 62 THR Chi-restraints excluded: chain S residue 64 GLU Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain U residue 12 ASP Chi-restraints excluded: chain U residue 35 GLU Chi-restraints excluded: chain U residue 36 PHE Chi-restraints excluded: chain 03 residue 10 VAL Chi-restraints excluded: chain 03 residue 180 PHE Chi-restraints excluded: chain Z residue 32 THR Chi-restraints excluded: chain Z residue 47 ASP Chi-restraints excluded: chain Z residue 140 VAL Chi-restraints excluded: chain Z residue 142 ASP Chi-restraints excluded: chain Z residue 156 LEU Chi-restraints excluded: chain Z residue 206 ILE Chi-restraints excluded: chain Z residue 211 LEU Chi-restraints excluded: chain Z residue 228 THR Chi-restraints excluded: chain Z residue 254 THR Chi-restraints excluded: chain Z residue 255 CYS Chi-restraints excluded: chain Z residue 335 THR Chi-restraints excluded: chain Z residue 340 THR Chi-restraints excluded: chain Z residue 351 MET Chi-restraints excluded: chain Z residue 359 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1101 random chunks: chunk 649 optimal weight: 10.0000 chunk 1045 optimal weight: 40.0000 chunk 638 optimal weight: 20.0000 chunk 496 optimal weight: 30.0000 chunk 726 optimal weight: 10.0000 chunk 1096 optimal weight: 5.9990 chunk 1009 optimal weight: 10.0000 chunk 873 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 674 optimal weight: 20.0000 chunk 535 optimal weight: 5.9990 overall best weight: 8.3994 ------------------------------------------------------------------------------- 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** ** 04 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 06 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 06 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 15 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 19 19 GLN ** 24 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 28 48 ASN ** 32 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 104 ASN ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.5156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 166822 Z= 0.270 Angle : 0.734 18.803 249077 Z= 0.374 Chirality : 0.040 0.348 31782 Planarity : 0.005 0.064 13715 Dihedral : 24.403 179.881 82271 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 29.24 Ramachandran Plot: Outliers : 0.24 % Allowed : 13.20 % Favored : 86.57 % Rotamer: Outliers : 5.51 % Allowed : 27.19 % Favored : 67.31 % 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: -3.19 (0.10), residues: 6366 helix: -1.16 (0.11), residues: 1917 sheet: -2.40 (0.14), residues: 1101 loop : -2.63 (0.10), residues: 3348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP K 43 HIS 0.011 0.001 HIS24 44 PHE 0.048 0.002 PHE H 65 TYR 0.035 0.002 TYR D 75 ARG 0.016 0.001 ARG09 51 ********************** 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 1123 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 291 poor density : 832 time to evaluate : 6.974 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: 05 123 LYS cc_start: 0.9351 (tttm) cc_final: 0.9085 (mmtt) REVERT: 05 200 ASP cc_start: 0.8878 (p0) cc_final: 0.8628 (p0) REVERT: 07 34 THR cc_start: 0.8724 (m) cc_final: 0.8382 (p) REVERT: 08 138 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7743 (tp40) REVERT: 09 41 LYS cc_start: 0.9065 (tmtt) cc_final: 0.8484 (tptt) REVERT: 10 6 GLN cc_start: 0.8850 (mm110) cc_final: 0.8036 (tm-30) REVERT: 13 66 LYS cc_start: 0.8576 (mmmm) cc_final: 0.8340 (mmmm) REVERT: 13 87 LEU cc_start: 0.8220 (mp) cc_final: 0.7787 (mp) REVERT: 13 111 LYS cc_start: 0.8536 (ttpp) cc_final: 0.7876 (ttpp) REVERT: 13 112 PHE cc_start: 0.8871 (m-80) cc_final: 0.8567 (m-80) REVERT: 14 23 ILE cc_start: 0.8906 (OUTLIER) cc_final: 0.8468 (mp) REVERT: 14 36 LYS cc_start: 0.8264 (mttt) cc_final: 0.7892 (pttm) REVERT: 16 20 MET cc_start: 0.8114 (tpp) cc_final: 0.7799 (tpp) REVERT: 16 24 MET cc_start: 0.9022 (OUTLIER) cc_final: 0.8718 (mmt) REVERT: 16 74 GLU cc_start: 0.8499 (tt0) cc_final: 0.8280 (tm-30) REVERT: 17 17 LYS cc_start: 0.8725 (tptp) cc_final: 0.7999 (pttp) REVERT: 17 25 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.8058 (ptt-90) REVERT: 17 92 PHE cc_start: 0.8761 (t80) cc_final: 0.8267 (t80) REVERT: 18 40 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.7364 (pt0) REVERT: 19 96 ASP cc_start: 0.8094 (t70) cc_final: 0.7798 (t70) REVERT: 22 1 MET cc_start: 0.5215 (ptt) cc_final: 0.4106 (mmt) REVERT: 26 15 ASN cc_start: 0.8149 (m110) cc_final: 0.7698 (m110) REVERT: 30 36 LYS cc_start: 0.9057 (mmtt) cc_final: 0.8833 (tptp) REVERT: 31 45 HIS cc_start: 0.8054 (OUTLIER) cc_final: 0.7301 (m90) REVERT: 32 22 MET cc_start: 0.8450 (tpp) cc_final: 0.8051 (tpp) REVERT: 33 61 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7636 (pp) REVERT: B 99 MET cc_start: 0.8132 (mtt) cc_final: 0.7782 (mtt) REVERT: B 116 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8549 (tp) REVERT: C 183 TYR cc_start: 0.8096 (t80) cc_final: 0.7831 (t80) REVERT: C 192 TYR cc_start: 0.8058 (m-80) cc_final: 0.7742 (t80) REVERT: D 123 MET cc_start: 0.8314 (tpp) cc_final: 0.8097 (tpp) REVERT: E 63 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7698 (mmm) REVERT: E 85 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.6565 (mmmm) REVERT: F 52 ASN cc_start: 0.9471 (t0) cc_final: 0.9022 (t0) REVERT: G 6 ILE cc_start: 0.6322 (OUTLIER) cc_final: 0.6050 (pp) REVERT: G 36 SER cc_start: 0.8799 (OUTLIER) cc_final: 0.8260 (p) REVERT: H 57 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7659 (mm-30) REVERT: I 30 ASN cc_start: 0.8399 (t0) cc_final: 0.8105 (t0) REVERT: I 67 LYS cc_start: 0.8522 (tptt) cc_final: 0.7888 (mmtm) REVERT: I 106 ASP cc_start: 0.8017 (t0) cc_final: 0.7787 (t0) REVERT: J 20 GLN cc_start: 0.8428 (pt0) cc_final: 0.7716 (tp-100) REVERT: J 31 ARG cc_start: 0.8389 (ttp80) cc_final: 0.7755 (ttm110) REVERT: J 65 TYR cc_start: 0.8810 (m-80) cc_final: 0.8304 (m-10) REVERT: K 74 LYS cc_start: 0.8854 (mmmt) cc_final: 0.8609 (mmmt) REVERT: K 76 TYR cc_start: 0.8777 (m-80) cc_final: 0.8471 (m-10) REVERT: K 126 ARG cc_start: 0.8246 (mmp-170) cc_final: 0.7728 (tpp-160) REVERT: L 53 ARG cc_start: 0.9034 (ttp-110) cc_final: 0.8830 (ttt90) REVERT: M 12 LYS cc_start: 0.8677 (mttt) cc_final: 0.7944 (mmtt) REVERT: P 14 ARG cc_start: 0.8550 (ttt-90) cc_final: 0.8161 (ttt180) REVERT: P 67 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8517 (tp) REVERT: Q 42 LYS cc_start: 0.8642 (mtmt) cc_final: 0.8438 (ttmt) REVERT: T 65 LEU cc_start: 0.8943 (tt) cc_final: 0.8710 (tp) REVERT: U 32 ARG cc_start: 0.8658 (ptt90) cc_final: 0.8267 (ttt180) REVERT: U 36 PHE cc_start: 0.8249 (OUTLIER) cc_final: 0.7757 (t80) REVERT: U 46 ARG cc_start: 0.8812 (tpt170) cc_final: 0.8562 (ttm170) REVERT: 03 12 ARG cc_start: 0.8045 (ptp-170) cc_final: 0.7574 (mmt180) REVERT: 03 180 PHE cc_start: 0.1427 (OUTLIER) cc_final: 0.1015 (m-10) REVERT: Z 39 TYR cc_start: 0.8060 (t80) cc_final: 0.7793 (t80) REVERT: Z 51 ASN cc_start: 0.8867 (p0) cc_final: 0.8309 (m-40) REVERT: Z 206 ILE cc_start: 0.7555 (OUTLIER) cc_final: 0.7288 (pp) REVERT: Z 243 GLU cc_start: 0.8018 (tt0) cc_final: 0.7400 (pt0) outliers start: 291 outliers final: 255 residues processed: 1037 average time/residue: 1.2986 time to fit residues: 2383.4904 Evaluate side-chains 1076 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 271 poor density : 805 time to evaluate : 6.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 33 LEU Chi-restraints excluded: chain 04 residue 143 VAL Chi-restraints excluded: chain 04 residue 163 ILE Chi-restraints excluded: chain 04 residue 219 VAL Chi-restraints excluded: chain 04 residue 227 VAL Chi-restraints excluded: chain 05 residue 14 ILE Chi-restraints excluded: chain 05 residue 27 ILE Chi-restraints excluded: chain 05 residue 133 THR Chi-restraints excluded: chain 05 residue 145 SER Chi-restraints excluded: chain 05 residue 180 VAL Chi-restraints excluded: chain 05 residue 186 LEU Chi-restraints excluded: chain 05 residue 188 LEU Chi-restraints excluded: chain 05 residue 197 THR Chi-restraints excluded: chain 06 residue 15 SER Chi-restraints excluded: chain 06 residue 22 ASP Chi-restraints excluded: chain 06 residue 48 THR Chi-restraints excluded: chain 06 residue 72 SER Chi-restraints excluded: chain 06 residue 73 ILE Chi-restraints excluded: chain 06 residue 149 ILE Chi-restraints excluded: chain 06 residue 150 THR Chi-restraints excluded: chain 07 residue 3 LEU Chi-restraints excluded: chain 07 residue 24 VAL Chi-restraints excluded: chain 07 residue 46 LYS Chi-restraints excluded: chain 07 residue 146 ASP Chi-restraints excluded: chain 07 residue 154 THR Chi-restraints excluded: chain 08 residue 9 VAL Chi-restraints excluded: chain 08 residue 25 ILE Chi-restraints excluded: chain 08 residue 51 PHE Chi-restraints excluded: chain 08 residue 75 VAL Chi-restraints excluded: chain 08 residue 100 ASN Chi-restraints excluded: chain 08 residue 123 GLU Chi-restraints excluded: chain 08 residue 138 GLN Chi-restraints excluded: chain 08 residue 161 VAL Chi-restraints excluded: chain 09 residue 20 ASN Chi-restraints excluded: chain 09 residue 31 VAL Chi-restraints excluded: chain 09 residue 94 ILE Chi-restraints excluded: chain 09 residue 99 ILE Chi-restraints excluded: chain 09 residue 125 THR Chi-restraints excluded: chain 09 residue 145 ASN Chi-restraints excluded: chain 10 residue 8 LYS Chi-restraints excluded: chain 10 residue 27 VAL Chi-restraints excluded: chain 10 residue 31 ARG Chi-restraints excluded: chain 10 residue 64 VAL Chi-restraints excluded: chain 10 residue 80 THR Chi-restraints excluded: chain 10 residue 99 PHE Chi-restraints excluded: chain 10 residue 117 LEU Chi-restraints excluded: chain 10 residue 123 ILE Chi-restraints excluded: chain 11 residue 7 TYR Chi-restraints excluded: chain 11 residue 67 THR Chi-restraints excluded: chain 11 residue 70 THR Chi-restraints excluded: chain 11 residue 72 THR Chi-restraints excluded: chain 11 residue 77 VAL Chi-restraints excluded: chain 11 residue 110 GLN Chi-restraints excluded: chain 11 residue 121 ILE Chi-restraints excluded: chain 11 residue 138 VAL Chi-restraints excluded: chain 11 residue 139 VAL Chi-restraints excluded: chain 13 residue 25 LEU Chi-restraints excluded: chain 13 residue 43 ILE Chi-restraints excluded: chain 13 residue 61 VAL Chi-restraints excluded: chain 13 residue 88 ASN Chi-restraints excluded: chain 13 residue 114 LYS Chi-restraints excluded: chain 14 residue 23 ILE Chi-restraints excluded: chain 14 residue 46 VAL Chi-restraints excluded: chain 14 residue 92 LEU Chi-restraints excluded: chain 14 residue 117 THR Chi-restraints excluded: chain 14 residue 118 THR Chi-restraints excluded: chain 14 residue 121 THR Chi-restraints excluded: chain 15 residue 36 VAL Chi-restraints excluded: chain 15 residue 70 ASP Chi-restraints excluded: chain 15 residue 91 TYR Chi-restraints excluded: chain 15 residue 119 LEU Chi-restraints excluded: chain 16 residue 2 ARG Chi-restraints excluded: chain 16 residue 24 MET Chi-restraints excluded: chain 16 residue 47 VAL Chi-restraints excluded: chain 16 residue 62 ASN Chi-restraints excluded: chain 16 residue 89 SER Chi-restraints excluded: chain 16 residue 113 ILE Chi-restraints excluded: chain 17 residue 21 LEU Chi-restraints excluded: chain 17 residue 25 ARG Chi-restraints excluded: chain 17 residue 27 VAL Chi-restraints excluded: chain 17 residue 55 GLU Chi-restraints excluded: chain 17 residue 65 THR Chi-restraints excluded: chain 17 residue 69 ASP Chi-restraints excluded: chain 17 residue 106 LEU Chi-restraints excluded: chain 18 residue 40 GLN Chi-restraints excluded: chain 18 residue 49 ILE Chi-restraints excluded: chain 18 residue 60 VAL Chi-restraints excluded: chain 18 residue 83 ILE Chi-restraints excluded: chain 20 residue 19 THR Chi-restraints excluded: chain 20 residue 26 ASP Chi-restraints excluded: chain 21 residue 4 ILE Chi-restraints excluded: chain 21 residue 34 ASP Chi-restraints excluded: chain 21 residue 40 ASN Chi-restraints excluded: chain 21 residue 66 ILE Chi-restraints excluded: chain 21 residue 67 ASP Chi-restraints excluded: chain 21 residue 97 LEU Chi-restraints excluded: chain 21 residue 109 ASP Chi-restraints excluded: chain 22 residue 32 LEU Chi-restraints excluded: chain 22 residue 37 ASP Chi-restraints excluded: chain 22 residue 43 ILE Chi-restraints excluded: chain 22 residue 70 HIS Chi-restraints excluded: chain 22 residue 87 LEU Chi-restraints excluded: chain 23 residue 11 ILE Chi-restraints excluded: chain 23 residue 26 ASN Chi-restraints excluded: chain 23 residue 48 VAL Chi-restraints excluded: chain 24 residue 40 ILE Chi-restraints excluded: chain 24 residue 56 PHE Chi-restraints excluded: chain 24 residue 66 ASP Chi-restraints excluded: chain 24 residue 89 ILE Chi-restraints excluded: chain 25 residue 17 LEU Chi-restraints excluded: chain 25 residue 77 SER Chi-restraints excluded: chain 26 residue 3 VAL Chi-restraints excluded: chain 26 residue 24 THR Chi-restraints excluded: chain 26 residue 47 THR Chi-restraints excluded: chain 26 residue 58 ILE Chi-restraints excluded: chain 26 residue 65 THR Chi-restraints excluded: chain 27 residue 2 LYS Chi-restraints excluded: chain 27 residue 6 LEU Chi-restraints excluded: chain 27 residue 11 VAL Chi-restraints excluded: chain 27 residue 17 GLU Chi-restraints excluded: chain 27 residue 43 LEU Chi-restraints excluded: chain 28 residue 2 LYS Chi-restraints excluded: chain 28 residue 22 THR Chi-restraints excluded: chain 28 residue 40 THR Chi-restraints excluded: chain 28 residue 48 ASN Chi-restraints excluded: chain 29 residue 4 ASP Chi-restraints excluded: chain 29 residue 31 ASP Chi-restraints excluded: chain 29 residue 34 LEU Chi-restraints excluded: chain 29 residue 53 THR Chi-restraints excluded: chain 30 residue 24 VAL Chi-restraints excluded: chain 30 residue 28 SER Chi-restraints excluded: chain 30 residue 31 LYS Chi-restraints excluded: chain 30 residue 38 LEU Chi-restraints excluded: chain 31 residue 10 LEU Chi-restraints excluded: chain 31 residue 45 HIS Chi-restraints excluded: chain 32 residue 1 MET Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 33 residue 6 VAL Chi-restraints excluded: chain 33 residue 50 SER Chi-restraints excluded: chain 33 residue 53 ASP Chi-restraints excluded: chain 33 residue 61 LEU Chi-restraints excluded: chain 34 residue 20 ASP Chi-restraints excluded: chain 34 residue 36 ARG Chi-restraints excluded: chain B residue 29 PHE Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 108 GLN Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 53 ARG Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 19 PHE Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 191 SER Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 63 MET Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 85 LYS Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 90 MET Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 96 ASN Chi-restraints excluded: chain G residue 121 ASN Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 120 LEU Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 75 ASP Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain K residue 15 VAL Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 78 ILE Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 96 ILE Chi-restraints excluded: chain K residue 104 PHE Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 95 HIS Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 53 ASP Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 61 LYS Chi-restraints excluded: chain M residue 94 LEU Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 19 TYR Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain O residue 19 ASN Chi-restraints excluded: chain O residue 42 PHE Chi-restraints excluded: chain O residue 56 LEU Chi-restraints excluded: chain O residue 86 LEU Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 38 PHE Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 67 ILE Chi-restraints excluded: chain Q residue 20 ILE Chi-restraints excluded: chain Q residue 66 LEU Chi-restraints excluded: chain Q residue 74 LEU Chi-restraints excluded: chain R residue 20 ILE Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain S residue 11 ASP Chi-restraints excluded: chain S residue 38 THR Chi-restraints excluded: chain S residue 43 MET Chi-restraints excluded: chain S residue 62 THR Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain U residue 12 ASP Chi-restraints excluded: chain U residue 35 GLU Chi-restraints excluded: chain U residue 36 PHE Chi-restraints excluded: chain 03 residue 10 VAL Chi-restraints excluded: chain 03 residue 180 PHE Chi-restraints excluded: chain Z residue 32 THR Chi-restraints excluded: chain Z residue 47 ASP Chi-restraints excluded: chain Z residue 156 LEU Chi-restraints excluded: chain Z residue 206 ILE Chi-restraints excluded: chain Z residue 211 LEU Chi-restraints excluded: chain Z residue 228 THR Chi-restraints excluded: chain Z residue 254 THR Chi-restraints excluded: chain Z residue 255 CYS Chi-restraints excluded: chain Z residue 335 THR Chi-restraints excluded: chain Z residue 340 THR Chi-restraints excluded: chain Z residue 351 MET Chi-restraints excluded: chain Z residue 359 VAL 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: 30.0000 chunk 267 optimal weight: 7.9990 chunk 805 optimal weight: 20.0000 chunk 128 optimal weight: 30.0000 chunk 242 optimal weight: 20.0000 chunk 874 optimal weight: 20.0000 chunk 366 optimal weight: 5.9990 chunk 898 optimal weight: 30.0000 chunk 110 optimal weight: 6.9990 chunk 161 optimal weight: 3.9990 overall best weight: 8.9992 ------------------------------------------------------------------------------- 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** ** 04 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 06 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 13 9 ASN ** 15 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 28 48 ASN ** 32 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.043338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.037595 restraints weight = 1505883.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.038522 restraints weight = 604681.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.039068 restraints weight = 322851.148| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.5163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.216 166822 Z= 0.297 Angle : 0.752 58.969 249077 Z= 0.388 Chirality : 0.040 1.016 31782 Planarity : 0.005 0.060 13715 Dihedral : 24.400 179.890 82271 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 30.27 Ramachandran Plot: Outliers : 0.22 % Allowed : 13.38 % Favored : 86.40 % Rotamer: Outliers : 5.51 % Allowed : 27.36 % Favored : 67.14 % Cbeta Deviations : 0.02 % 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: -3.16 (0.10), residues: 6366 helix: -1.13 (0.11), residues: 1920 sheet: -2.39 (0.14), residues: 1101 loop : -2.62 (0.10), residues: 3345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP K 43 HIS 0.009 0.001 HIS06 165 PHE 0.053 0.002 PHE09 46 TYR 0.032 0.002 TYR N 19 ARG 0.010 0.001 ARG Z 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 38938.42 seconds wall clock time: 685 minutes 56.67 seconds (41156.67 seconds total)