Starting phenix.real_space_refine on Sat Mar 2 07:20:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyl_8616/03_2024/5uyl_8616_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyl_8616/03_2024/5uyl_8616.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyl_8616/03_2024/5uyl_8616.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyl_8616/03_2024/5uyl_8616.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyl_8616/03_2024/5uyl_8616_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyl_8616/03_2024/5uyl_8616_updated.pdb" } resolution = 3.6 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= -0.407 sd= 1.298 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4806 5.49 5 S 172 5.16 5 C 77705 2.51 5 N 28575 2.21 5 O 42495 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "05 ARG 13": "NH1" <-> "NH2" Residue "05 ARG 33": "NH1" <-> "NH2" Residue "05 ARG 59": "NH1" <-> "NH2" Residue "05 ARG 77": "NH1" <-> "NH2" Residue "05 ARG 83": "NH1" <-> "NH2" Residue "05 ARG 169": "NH1" <-> "NH2" Residue "05 ARG 184": "NH1" <-> "NH2" Residue "06 ARG 21": "NH1" <-> "NH2" Residue "06 ARG 44": "NH1" <-> "NH2" Residue "06 ARG 49": "NH1" <-> "NH2" Residue "06 ARG 61": "NH1" <-> "NH2" Residue "06 ARG 88": "NH1" <-> "NH2" Residue "06 ARG 102": "NH1" <-> "NH2" Residue "06 ARG 162": "NH1" <-> "NH2" Residue "06 ARG 170": "NH1" <-> "NH2" Residue "07 ARG 70": "NH1" <-> "NH2" Residue "07 ARG 79": "NH1" <-> "NH2" Residue "07 ARG 91": "NH1" <-> "NH2" Residue "07 ARG 101": "NH1" <-> "NH2" Residue "07 ARG 109": "NH1" <-> "NH2" Residue "07 ARG 111": "NH1" <-> "NH2" Residue "07 ARG 114": "NH1" <-> "NH2" Residue "07 ARG 132": "NH1" <-> "NH2" Residue "08 ARG 2": "NH1" <-> "NH2" Residue "08 ARG 152": "NH1" <-> "NH2" Residue "08 ARG 162": "NH1" <-> "NH2" Residue "08 ARG 169": "NH1" <-> "NH2" Residue "12 ARG 13": "NH1" <-> "NH2" Residue "12 ARG 37": "NH1" <-> "NH2" Residue "12 TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "12 ARG 96": "NH1" <-> "NH2" Residue "12 ARG 120": "NH1" <-> "NH2" Residue "13 TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "14 ARG 21": "NH1" <-> "NH2" Residue "14 ARG 33": "NH1" <-> "NH2" Residue "14 ARG 41": "NH1" <-> "NH2" Residue "14 ARG 47": "NH1" <-> "NH2" Residue "14 ARG 60": "NH1" <-> "NH2" Residue "14 ARG 78": "NH1" <-> "NH2" Residue "14 ARG 126": "NH1" <-> "NH2" Residue "15 ARG 10": "NH1" <-> "NH2" Residue "15 ARG 18": "NH1" <-> "NH2" Residue "15 ARG 40": "NH1" <-> "NH2" Residue "15 ARG 44": "NH1" <-> "NH2" Residue "15 ARG 50": "NH1" <-> "NH2" Residue "15 ARG 55": "NH1" <-> "NH2" Residue "15 ARG 59": "NH1" <-> "NH2" Residue "15 ARG 114": "NH1" <-> "NH2" Residue "16 ARG 8": "NH1" <-> "NH2" Residue "16 ARG 12": "NH1" <-> "NH2" Residue "16 ARG 17": "NH1" <-> "NH2" Residue "16 ARG 22": "NH1" <-> "NH2" Residue "16 ARG 46": "NH1" <-> "NH2" Residue "16 ARG 63": "NH1" <-> "NH2" Residue "16 ARG 64": "NH1" <-> "NH2" Residue "16 ARG 69": "NH1" <-> "NH2" Residue "16 ARG 71": "NH1" <-> "NH2" Residue "16 ARG 96": "NH1" <-> "NH2" Residue "16 ARG 118": "NH1" <-> "NH2" Residue "17 ARG 10": "NH1" <-> "NH2" Residue "17 ARG 16": "NH1" <-> "NH2" Residue "17 ARG 25": "NH1" <-> "NH2" Residue "17 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 TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "20 ARG 21": "NH1" <-> "NH2" Residue "20 ARG 68": "NH1" <-> "NH2" Residue "20 ARG 78": "NH1" <-> "NH2" Residue "20 ARG 79": "NH1" <-> "NH2" Residue "20 ARG 84": "NH1" <-> "NH2" Residue "21 ARG 84": "NH1" <-> "NH2" Residue "21 ARG 88": "NH1" <-> "NH2" Residue "21 ARG 95": "NH1" <-> "NH2" Residue "21 ARG 110": "NH1" <-> "NH2" Residue "22 ARG 73": "NH1" <-> "NH2" Residue "22 TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "24 TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "27 ARG 29": "NH1" <-> "NH2" Residue "27 ARG 47": "NH1" <-> "NH2" Residue "27 ARG 52": "NH1" <-> "NH2" Residue "28 ARG 10": "NH1" <-> "NH2" Residue "28 ARG 29": "NH1" <-> "NH2" Residue "28 ARG 44": "NH1" <-> "NH2" Residue "29 ARG 49": "NH1" <-> "NH2" Residue "29 ARG 56": "NH1" <-> "NH2" Residue "30 ARG 9": "NH1" <-> "NH2" Residue "30 ARG 15": "NH1" <-> "NH2" Residue "30 ARG 39": "NH1" <-> "NH2" Residue "30 ARG 51": "NH1" <-> "NH2" Residue "31 ARG 43": "NH1" <-> "NH2" Residue "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 PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 107": "NH1" <-> "NH2" Residue "B ARG 224": "NH1" <-> "NH2" Residue "C ARG 106": "NH1" <-> "NH2" Residue "C ARG 130": "NH1" <-> "NH2" Residue "E ARG 156": "NH1" <-> "NH2" Residue "I ARG 123": "NH1" <-> "NH2" Residue "K TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "03 ARG 162": "NH1" <-> "NH2" Residue "03 TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 44": "NH1" <-> "NH2" Residue "Z TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 223": "NH1" <-> "NH2" Residue "Z PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 269": "NH1" <-> "NH2" Residue "Y PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 153753 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: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1026 Classifications: {'peptide': 134} 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': 90, 'rna2p_pyr': 48, 'rna3p_pur': 784, 'rna3p_pyr': 617} 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': 210, 'rna2p_pyr': 91, 'rna3p_pur': 1464, 'rna3p_pyr': 1138} Link IDs: {'rna2p': 301, 'rna3p': 2601} 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: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 388 Classifications: {'RNA': 18} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 12, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 16} 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: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1619 Classifications: {'RNA': 76} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 32, 'rna3p_pyr': 32} Link IDs: {'rna2p': 11, 'rna3p': 64} 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: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Classifications: {'peptide': 1} Chain: "Z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GCP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N PHE Y 101 " occ=0.94 ... (9 atoms not shown) pdb=" CZ PHE Y 101 " occ=0.75 Time building chain proxies: 59.20, per 1000 atoms: 0.39 Number of scatterers: 153753 At special positions: 0 Unit cell: (279.62, 268.96, 237.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 172 16.00 P 4806 15.00 O 42495 8.00 N 28575 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: 62.75 Conformation dependent library (CDL) restraints added in 7.5 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: 191 helices and 77 sheets defined 37.6% alpha, 17.6% beta 1476 base pairs and 2817 stacking pairs defined. Time for finding SS restraints: 83.29 Creating SS restraints... Processing helix chain '04' and resid 9 through 15 removed outlier: 7.959A pdb=" N HIS04 14 " --> pdb=" O PRO04 10 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N VAL04 15 " --> pdb=" O GLY04 11 " (cutoff:3.500A) Processing helix chain '04' and resid 29 through 34 removed outlier: 4.134A pdb=" N LEU04 33 " --> pdb=" O PHE04 29 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N GLU04 34 " --> pdb=" O ALA04 30 " (cutoff:3.500A) No H-bonds generated for 'chain '04' and resid 29 through 34' Processing helix chain '04' and resid 130 through 135 removed outlier: 4.128A pdb=" N ILE04 134 " --> pdb=" O PRO04 130 " (cutoff:3.500A) Proline residue: 04 135 - end of helix No H-bonds generated for 'chain '04' and resid 130 through 135' Processing helix chain '04' and resid 206 through 214 removed outlier: 4.797A pdb=" N ALA04 210 " --> pdb=" O LYS04 206 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ARG04 211 " --> pdb=" O ALA04 207 " (cutoff:3.500A) Processing helix chain '04' and resid 220 through 225 removed outlier: 4.073A pdb=" N MET04 224 " --> pdb=" O ARG04 220 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ASN04 225 " --> pdb=" O GLY04 221 " (cutoff:3.500A) No H-bonds generated for 'chain '04' and resid 220 through 225' Processing helix chain '04' and resid 259 through 267 removed outlier: 6.255A pdb=" N ASP04 263 " --> pdb=" O ASN04 259 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LYS04 264 " --> pdb=" O LYS04 260 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N PHE04 265 " --> pdb=" O ARG04 261 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE04 266 " --> pdb=" O THR04 262 " (cutoff:3.500A) removed outlier: 5.854A 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 '04' and resid 196 through 201 removed outlier: 4.019A pdb=" N MET04 200 " --> pdb=" O ALA04 197 " (cutoff:3.500A) Processing helix chain '05' and resid 56 through 61 removed outlier: 7.864A pdb=" N THR05 61 " --> pdb=" O ALA05 57 " (cutoff:3.500A) Processing helix chain '05' and resid 62 through 72 removed outlier: 3.629A pdb=" N HIS05 67 " --> pdb=" O PRO05 63 " (cutoff:3.500A) Processing helix chain '05' and resid 98 through 105 removed outlier: 4.165A pdb=" N ALA05 102 " --> pdb=" O VAL05 98 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ASP05 103 " --> pdb=" O GLU05 99 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N VAL05 104 " --> pdb=" O LEU05 100 " (cutoff:3.500A) removed outlier: 5.794A 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 125 Processing helix chain '06' and resid 15 through 20 removed outlier: 3.804A pdb=" N PHE06 19 " --> pdb=" O SER06 15 " (cutoff:3.500A) Processing helix chain '06' and resid 24 through 40 removed outlier: 3.525A pdb=" N ALA06 36 " --> pdb=" O VAL06 32 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG06 40 " --> pdb=" O ALA06 36 " (cutoff:3.500A) Processing helix chain '06' and resid 48 through 53 removed outlier: 3.521A pdb=" N VAL06 52 " --> pdb=" O THR06 48 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N THR06 53 " --> pdb=" O ARG06 49 " (cutoff:3.500A) No H-bonds generated for 'chain '06' and resid 48 through 53' Processing helix chain '06' and resid 97 through 116 Processing helix chain '06' and resid 130 through 142 Processing helix chain '06' and resid 154 through 163 removed outlier: 3.902A pdb=" N ALA06 160 " --> pdb=" O ASN06 156 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ASN06 163 " --> pdb=" O LEU06 159 " (cutoff:3.500A) Processing helix chain '06' and resid 176 through 183 removed outlier: 3.637A pdb=" N LEU06 180 " --> pdb=" O ASP06 176 " (cutoff:3.500A) Processing helix chain '06' and resid 189 through 201 Processing helix chain '07' and resid 1 through 20 removed outlier: 4.086A pdb=" N ASP07 5 " --> pdb=" O ALA07 1 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR07 6 " --> pdb=" O LYS07 2 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL07 11 " --> pdb=" O TYR07 7 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N VAL07 12 " --> pdb=" O LYS07 8 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS07 13 " --> pdb=" O ASP07 9 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET07 16 " --> pdb=" O VAL07 12 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR07 17 " --> pdb=" O LYS07 13 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU07 18 " --> pdb=" O LYS07 14 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE07 19 " --> pdb=" O LEU07 15 " (cutoff:3.500A) Processing helix chain '07' and resid 41 through 46 removed outlier: 3.835A pdb=" N ASP07 45 " --> pdb=" O GLU07 41 " (cutoff:3.500A) removed outlier: 4.320A 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: 3.545A pdb=" N ASP07 55 " --> pdb=" O ASN07 51 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU07 56 " --> pdb=" O ALA07 52 " (cutoff:3.500A) Processing helix chain '07' and resid 92 through 110 removed outlier: 4.175A pdb=" N TRP07 96 " --> pdb=" O GLY07 92 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE07 105 " --> pdb=" O ARG07 101 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N VAL07 107 " --> pdb=" O ILE07 103 " (cutoff:3.500A) Proline residue: 07 108 - end of helix Processing helix chain '07' and resid 141 through 146 removed outlier: 6.612A pdb=" N VAL07 145 " --> pdb=" O ASP07 141 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ASP07 146 " --> pdb=" O TYR07 142 " (cutoff:3.500A) No H-bonds generated for 'chain '07' and resid 141 through 146' Processing helix chain '07' and resid 161 through 173 removed outlier: 3.599A pdb=" N ALA07 171 " --> pdb=" O ALA07 167 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N PHE07 172 " --> pdb=" O LEU07 168 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASP07 173 " --> pdb=" O LEU07 169 " (cutoff:3.500A) Processing helix chain '08' and resid 1 through 6 removed outlier: 4.965A pdb=" N ALA08 6 " --> pdb=" O ARG08 2 " (cutoff:3.500A) Processing helix chain '08' and resid 59 through 80 Processing helix chain '08' and resid 136 through 152 removed outlier: 3.539A pdb=" N ILE08 140 " --> pdb=" O ASP08 136 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG08 148 " --> pdb=" O ALA08 144 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR08 150 " --> pdb=" O ASP08 146 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ARG08 151 " --> pdb=" O LEU08 147 " (cutoff:3.500A) Processing helix chain '09' and resid 22 through 29 Processing helix chain '09' and resid 40 through 50 removed outlier: 5.815A pdb=" N ILE09 44 " --> pdb=" O THR09 40 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLU09 45 " --> pdb=" O LYS09 41 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA09 49 " --> pdb=" O GLU09 45 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG09 50 " --> pdb=" O PHE09 46 " (cutoff:3.500A) Processing helix chain '09' and resid 53 through 74 removed outlier: 5.466A pdb=" N LYS09 57 " --> pdb=" O GLU09 53 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG09 68 " --> pdb=" O ALA09 64 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU09 70 " --> pdb=" O ASN09 66 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LYS09 71 " --> pdb=" O ALA09 67 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE09 72 " --> pdb=" O ARG09 68 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASN09 73 " --> pdb=" O ALA09 69 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA09 74 " --> pdb=" O GLU09 70 " (cutoff:3.500A) Processing helix chain '09' and resid 95 through 107 removed outlier: 4.670A pdb=" N ILE09 99 " --> pdb=" O GLY09 95 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA09 106 " --> pdb=" O ALA09 102 " (cutoff:3.500A) Processing helix chain '10' and resid 4 through 21 removed outlier: 3.997A pdb=" N GLN10 9 " --> pdb=" O LEU10 5 " (cutoff:3.500A) Processing helix chain '10' and resid 33 through 48 removed outlier: 3.700A pdb=" N LYS10 37 " --> pdb=" O VAL10 33 " (cutoff:3.500A) Processing helix chain '10' and resid 62 through 68 Proline residue: 10 68 - end of helix Processing helix chain '10' and resid 73 through 79 removed outlier: 4.355A pdb=" N VAL10 77 " --> pdb=" O LYS10 73 " (cutoff:3.500A) removed outlier: 3.517A 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 73 through 79' Processing helix chain '10' and resid 94 through 106 removed outlier: 4.003A pdb=" N PHE10 99 " --> pdb=" O LEU10 95 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA10 100 " --> pdb=" O PHE10 96 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA10 104 " --> pdb=" O ALA10 100 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N PHE10 106 " --> pdb=" O ALA10 102 " (cutoff:3.500A) Processing helix chain '10' and resid 109 through 114 removed outlier: 6.254A pdb=" N ALA10 112 " --> pdb=" O LYS10 109 " (cutoff:3.500A) Processing helix chain '11' and resid 23 through 31 removed outlier: 4.717A pdb=" N LEU11 27 " --> pdb=" O VAL11 23 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N GLN11 30 " --> pdb=" O ALA11 26 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N GLY11 31 " --> pdb=" O LEU11 27 " (cutoff:3.500A) Processing helix chain '11' and resid 35 through 49 removed outlier: 4.586A pdb=" N ALA11 40 " --> pdb=" O GLU11 36 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N SER11 47 " --> pdb=" O ALA11 43 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU11 49 " --> pdb=" O THR11 45 " (cutoff:3.500A) Processing helix chain '11' and resid 74 through 83 removed outlier: 3.641A pdb=" N LYS11 81 " --> pdb=" O VAL11 77 " (cutoff:3.500A) Processing helix chain '11' and resid 103 through 114 removed outlier: 3.821A pdb=" N GLU11 107 " --> pdb=" O ALA11 103 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE11 108 " --> pdb=" O GLN11 104 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR11 111 " --> pdb=" O GLU11 107 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS11 112 " --> pdb=" O ILE11 108 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA11 114 " --> pdb=" O GLN11 110 " (cutoff:3.500A) Processing helix chain '11' and resid 120 through 136 removed outlier: 3.531A pdb=" N ARG11 126 " --> pdb=" O GLU11 122 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER11 127 " --> pdb=" O ALA11 123 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE11 128 " --> pdb=" O MET11 124 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU11 129 " --> pdb=" O THR11 125 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR11 131 " --> pdb=" O SER11 127 " (cutoff:3.500A) Processing helix chain '12' and resid 24 through 38 Processing helix chain '12' and resid 88 through 96 removed outlier: 3.664A pdb=" N ALA12 94 " --> pdb=" O GLU12 90 " (cutoff:3.500A) Processing helix chain '12' and resid 97 through 110 removed outlier: 4.611A pdb=" N ILE12 101 " --> pdb=" O PRO12 97 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS12 106 " --> pdb=" O GLU12 102 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N MET12 108 " --> pdb=" O ALA12 104 " (cutoff:3.500A) Proline residue: 12 110 - end of helix Processing helix chain '12' and resid 112 through 122 removed outlier: 3.599A pdb=" N ARG12 120 " --> pdb=" O ARG12 116 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS12 121 " --> pdb=" O ALA12 117 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU12 122 " --> pdb=" O MET12 118 " (cutoff:3.500A) Processing helix chain '13' and resid 109 through 119 removed outlier: 6.068A pdb=" N MET13 113 " --> pdb=" O SER13 109 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N LYS13 114 " --> pdb=" O GLU13 110 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ILE13 115 " --> pdb=" O LYS13 111 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU13 118 " --> pdb=" O LYS13 114 " (cutoff:3.500A) Processing helix chain '14' and resid 37 through 42 removed outlier: 3.515A pdb=" N ARG14 41 " --> pdb=" O GLY14 37 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N SER14 42 " --> pdb=" O GLN14 38 " (cutoff:3.500A) No H-bonds generated for 'chain '14' and resid 37 through 42' Processing helix chain '14' and resid 56 through 62 removed outlier: 3.520A pdb=" N LEU14 61 " --> pdb=" O LEU14 57 " (cutoff:3.500A) Proline residue: 14 62 - end of helix Processing helix chain '14' and resid 68 through 75 removed outlier: 4.360A pdb=" N ALA14 72 " --> pdb=" O SER14 68 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE14 73 " --> pdb=" O ARG14 69 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR14 74 " --> pdb=" O LYS14 70 " (cutoff:3.500A) removed outlier: 5.481A 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 83 removed outlier: 4.342A pdb=" N ALA14 83 " --> pdb=" O LEU14 79 " (cutoff:3.500A) Processing helix chain '14' and resid 91 through 99 removed outlier: 4.585A pdb=" N LEU14 95 " --> pdb=" O ASP14 91 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LYS14 96 " --> pdb=" O LEU14 92 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ALA14 97 " --> pdb=" O ASN14 93 " (cutoff:3.500A) Processing helix chain '14' and resid 128 through 139 Processing helix chain '15' and resid 42 through 58 removed outlier: 3.797A pdb=" N ALA15 49 " --> pdb=" O GLN15 45 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N MET15 53 " --> pdb=" O ALA15 49 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG15 55 " --> pdb=" O ARG15 51 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ALA15 56 " --> pdb=" O ALA15 52 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL15 57 " --> pdb=" O MET15 53 " (cutoff:3.500A) Processing helix chain '15' and resid 109 through 125 removed outlier: 3.909A pdb=" N LYS15 118 " --> pdb=" O ARG15 114 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS15 123 " --> pdb=" O LEU15 119 " (cutoff:3.500A) Proline residue: 15 125 - end of helix Processing helix chain '16' and resid 13 through 32 removed outlier: 3.666A pdb=" N PHE16 21 " --> pdb=" O ARG16 17 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY16 26 " --> pdb=" O ARG16 22 " (cutoff:3.500A) Processing helix chain '16' and resid 38 through 57 removed outlier: 3.614A pdb=" N ARG16 45 " --> pdb=" O ALA16 41 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ARG16 46 " --> pdb=" O LYS16 42 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL16 47 " --> pdb=" O GLU16 43 " (cutoff:3.500A) Proline residue: 16 50 - end of helix removed outlier: 3.578A pdb=" N ALA16 55 " --> pdb=" O LEU16 51 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N THR16 57 " --> pdb=" O THR16 53 " (cutoff:3.500A) Processing helix chain '16' and resid 59 through 71 removed outlier: 3.826A pdb=" N ARG16 63 " --> pdb=" O SER16 59 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG16 64 " --> pdb=" O VAL16 60 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE16 67 " --> pdb=" O ARG16 63 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N THR16 70 " --> pdb=" O ALA16 66 " (cutoff:3.500A) Processing helix chain '16' and resid 72 through 82 removed outlier: 3.813A pdb=" N VAL16 76 " --> pdb=" O ASP16 72 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N PHE16 80 " --> pdb=" O VAL16 76 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ASN16 81 " --> pdb=" O ALA16 77 " (cutoff:3.500A) Processing helix chain '16' and resid 83 through 88 removed outlier: 3.708A pdb=" N PHE16 87 " --> pdb=" O LEU16 83 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ALA16 88 " --> pdb=" O GLY16 84 " (cutoff:3.500A) No H-bonds generated for 'chain '16' and resid 83 through 88' Processing helix chain '17' and resid 2 through 22 removed outlier: 3.691A pdb=" N ARG17 9 " --> pdb=" O SER17 5 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ARG17 13 " --> pdb=" O ARG17 9 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ALA17 14 " --> pdb=" O ARG17 10 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU17 18 " --> pdb=" O ALA17 14 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU17 20 " --> pdb=" O ARG17 16 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU17 21 " --> pdb=" O LYS17 17 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY17 22 " --> pdb=" O LEU17 18 " (cutoff:3.500A) Processing helix chain '17' and resid 55 through 62 removed outlier: 4.816A pdb=" N GLN17 61 " --> pdb=" O ALA17 57 " (cutoff:3.500A) Processing helix chain '17' and resid 67 through 86 removed outlier: 3.554A pdb=" N VAL17 74 " --> pdb=" O ALA17 70 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA17 79 " --> pdb=" O GLY17 75 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU17 83 " --> pdb=" O ALA17 79 " (cutoff:3.500A) Processing helix chain '17' and resid 101 through 114 removed outlier: 3.541A pdb=" N ALA17 110 " --> pdb=" O LEU17 106 " (cutoff:3.500A) Processing helix chain '18' and resid 1 through 12 removed outlier: 3.587A pdb=" N GLU18 10 " --> pdb=" O GLN18 6 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLN18 11 " --> pdb=" O LEU18 7 " (cutoff:3.500A) Processing helix chain '18' and resid 96 through 103 removed outlier: 4.384A pdb=" N ARG18 100 " --> pdb=" O LEU18 96 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N GLU18 101 " --> pdb=" O TYR18 97 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG18 102 " --> pdb=" O TYR18 98 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N THR18 103 " --> pdb=" O LEU18 99 " (cutoff:3.500A) No H-bonds generated for 'chain '18' and resid 96 through 103' Processing helix chain '19' and resid 5 through 21 removed outlier: 4.277A pdb=" N ALA19 9 " --> pdb=" O ARG19 5 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG19 10 " --> pdb=" O GLY19 6 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA19 11 " --> pdb=" O VAL19 7 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS19 15 " --> pdb=" O ALA19 11 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLN19 19 " --> pdb=" O LYS19 15 " (cutoff:3.500A) Processing helix chain '19' and resid 25 through 30 removed outlier: 4.221A pdb=" N ARG19 29 " --> pdb=" O GLY19 25 " (cutoff:3.500A) Processing helix chain '19' and resid 38 through 71 removed outlier: 4.226A pdb=" N ARG19 50 " --> pdb=" O TYR19 46 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN19 51 " --> pdb=" O ARG19 47 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LYS19 53 " --> pdb=" O ARG19 49 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG19 54 " --> pdb=" O ARG19 50 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG19 57 " --> pdb=" O LYS19 53 " (cutoff:3.500A) Processing helix chain '19' and resid 74 through 86 removed outlier: 3.762A pdb=" N ASN19 80 " --> pdb=" O SER19 76 " (cutoff:3.500A) Processing helix chain '19' and resid 90 through 101 Processing helix chain '19' and resid 102 through 117 removed outlier: 3.653A pdb=" N ALA19 107 " --> pdb=" O VAL19 103 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA19 112 " --> pdb=" O LEU19 108 " (cutoff:3.500A) Processing helix chain '21' and resid 13 through 25 removed outlier: 3.617A pdb=" N LEU21 19 " --> pdb=" O GLN21 15 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL21 20 " --> pdb=" O LYS21 16 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU21 23 " --> pdb=" O LEU21 19 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ILE21 24 " --> pdb=" O VAL21 20 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ARG21 25 " --> pdb=" O ALA21 21 " (cutoff:3.500A) Processing helix chain '21' and resid 28 through 39 Processing helix chain '21' and resid 41 through 60 removed outlier: 3.501A pdb=" N LYS21 49 " --> pdb=" O VAL21 45 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL21 50 " --> pdb=" O LEU21 46 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA21 58 " --> pdb=" O ALA21 54 " (cutoff:3.500A) Processing helix chain '22' and resid 1 through 11 removed outlier: 4.354A pdb=" N GLU22 5 " --> pdb=" O MET22 1 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU22 8 " --> pdb=" O GLU22 4 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LYS22 9 " --> pdb=" O GLU22 5 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL22 10 " --> pdb=" O ARG22 6 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N LEU22 11 " --> pdb=" O LEU22 7 " (cutoff:3.500A) Processing helix chain '22' and resid 17 through 26 removed outlier: 3.573A pdb=" N GLU22 25 " --> pdb=" O SER22 21 " (cutoff:3.500A) Processing helix chain '22' and resid 39 through 51 removed outlier: 3.624A pdb=" N GLN22 48 " --> pdb=" O LYS22 44 " (cutoff:3.500A) Processing helix chain '23' and resid 65 through 70 removed outlier: 4.248A pdb=" N VAL23 69 " --> pdb=" O GLN23 65 " (cutoff:3.500A) removed outlier: 5.224A 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: 3.504A pdb=" N ARG24 19 " --> pdb=" O GLY24 15 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASN24 24 " --> pdb=" O LEU24 20 " (cutoff:3.500A) Processing helix chain '24' and resid 43 through 53 removed outlier: 4.591A pdb=" N VAL24 47 " --> pdb=" O ASP24 43 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN24 49 " --> pdb=" O ASP24 45 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA24 52 " --> pdb=" O MET24 48 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LYS24 53 " --> pdb=" O ASN24 49 " (cutoff:3.500A) Processing helix chain '24' and resid 54 through 59 removed outlier: 4.737A pdb=" N SER24 58 " --> pdb=" O ALA24 54 " (cutoff:3.500A) Processing helix chain '26' and resid 51 through 61 removed outlier: 3.691A pdb=" N ILE26 58 " --> pdb=" O GLY26 54 " (cutoff:3.500A) Processing helix chain '26' and resid 62 through 74 Processing helix chain '27' and resid 1 through 7 removed outlier: 3.975A pdb=" N LEU27 6 " --> pdb=" O LYS27 2 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ARG27 7 " --> pdb=" O ALA27 3 " (cutoff:3.500A) Processing helix chain '27' and resid 9 through 35 removed outlier: 3.987A pdb=" N LEU27 14 " --> pdb=" O SER27 10 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR27 16 " --> pdb=" O GLU27 12 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ARG27 23 " --> pdb=" O LEU27 19 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU27 24 " --> pdb=" O ASN27 20 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLN27 25 " --> pdb=" O LEU27 21 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N PHE27 26 " --> pdb=" O LEU27 22 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN27 27 " --> pdb=" O ARG27 23 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG27 29 " --> pdb=" O GLN27 25 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA27 33 " --> pdb=" O ARG27 29 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER27 34 " --> pdb=" O MET27 30 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY27 35 " --> pdb=" O GLN27 31 " (cutoff:3.500A) Processing helix chain '27' and resid 40 through 62 removed outlier: 3.825A pdb=" N LYS27 44 " --> pdb=" O SER27 40 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N GLY27 62 " --> pdb=" O ASN27 58 " (cutoff:3.500A) Processing helix chain '28' and resid 16 through 27 removed outlier: 3.545A pdb=" N LYS28 20 " --> pdb=" O LEU28 16 " (cutoff:3.500A) Processing helix chain '28' and resid 40 through 51 Processing helix chain '29' and resid 43 through 52 removed outlier: 3.627A pdb=" N LYS29 47 " --> pdb=" O PHE29 43 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N GLN29 48 " --> pdb=" O PHE29 44 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP29 50 " --> pdb=" O GLY29 46 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL29 51 " --> pdb=" O LYS29 47 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ALA29 52 " --> pdb=" O GLN29 48 " (cutoff:3.500A) Processing helix chain '29' and resid 55 through 65 removed outlier: 4.469A pdb=" N ARG29 59 " --> pdb=" O GLY29 55 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG29 63 " --> pdb=" O ARG29 59 " (cutoff:3.500A) Processing helix chain '30' and resid 8 through 20 removed outlier: 3.643A pdb=" N ARG30 16 " --> pdb=" O ARG30 12 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER30 17 " --> pdb=" O GLY30 13 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N HIS30 18 " --> pdb=" O MET30 14 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ASP30 19 " --> pdb=" O ARG30 15 " (cutoff:3.500A) removed outlier: 3.785A 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: 4.481A pdb=" N THR32 24 " --> pdb=" O ALA32 20 " (cutoff:3.500A) Processing helix chain '32' and resid 25 through 38 removed outlier: 3.592A pdb=" N ARG32 34 " --> pdb=" O VAL32 30 " (cutoff:3.500A) Processing helix chain '33' and resid 6 through 13 removed outlier: 3.881A pdb=" N LYS33 11 " --> pdb=" O ARG33 7 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ARG33 12 " --> pdb=" O GLY33 8 " (cutoff:3.500A) Processing helix chain '33' and resid 36 through 45 removed outlier: 3.647A pdb=" N ARG33 44 " --> pdb=" O LYS33 40 " (cutoff:3.500A) Proline residue: 33 45 - end of helix Processing helix chain '33' and resid 50 through 62 removed outlier: 4.910A pdb=" N GLY33 55 " --> pdb=" O LYS33 51 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N LEU33 56 " --> pdb=" O GLY33 52 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL33 57 " --> pdb=" O ASP33 53 " (cutoff:3.500A) Proline residue: 33 62 - end of helix Processing helix chain 'B' and resid 43 through 63 Proline residue: B 47 - end of helix removed outlier: 3.519A pdb=" N ASN B 50 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER B 61 " --> pdb=" O ASN B 57 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG B 62 " --> pdb=" O LYS B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 4.227A pdb=" N ALA B 78 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL B 79 " --> pdb=" O ALA B 75 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N SER B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N CYS B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 123 removed outlier: 3.869A pdb=" N VAL B 106 " --> pdb=" O ASN B 102 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLN B 108 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER B 109 " --> pdb=" O THR B 105 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR B 118 " --> pdb=" O LYS B 114 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLN B 121 " --> pdb=" O GLU B 117 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASP B 122 " --> pdb=" O THR B 118 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY B 123 " --> pdb=" O GLN B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 147 removed outlier: 3.844A pdb=" N LEU B 134 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR B 137 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN B 145 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER B 146 " --> pdb=" O LYS B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 154 removed outlier: 4.815A pdb=" N ASP B 152 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N MET B 153 " --> pdb=" O GLY B 149 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLY B 154 " --> pdb=" O ILE B 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 148 through 154' Processing helix chain 'B' and resid 168 through 179 removed outlier: 3.503A pdb=" N ILE B 172 " --> pdb=" O GLU B 168 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N GLY B 179 " --> pdb=" O ALA B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 225 removed outlier: 3.585A pdb=" N THR B 210 " --> pdb=" O ILE B 206 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU B 211 " --> pdb=" O ARG B 207 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY B 223 " --> pdb=" O THR B 219 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ARG B 224 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N SER B 225 " --> pdb=" O ARG B 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 11 removed outlier: 3.792A pdb=" N ARG C 10 " --> pdb=" O PRO C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 46 removed outlier: 3.504A pdb=" N SER C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE C 36 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU C 42 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR C 43 " --> pdb=" O ARG C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 77 Processing helix chain 'C' and resid 80 through 95 removed outlier: 3.790A pdb=" N GLU C 84 " --> pdb=" O GLY C 80 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL C 89 " --> pdb=" O LYS C 85 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA C 91 " --> pdb=" O ARG C 87 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE C 93 " --> pdb=" O VAL C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 112 removed outlier: 5.286A pdb=" N ALA C 112 " --> pdb=" O PRO C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 126 removed outlier: 3.680A pdb=" N GLN C 122 " --> pdb=" O SER C 118 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU C 123 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU C 124 " --> pdb=" O THR C 120 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ARG C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG C 126 " --> pdb=" O GLN C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 removed outlier: 3.522A pdb=" N ALA C 136 " --> pdb=" O ALA C 132 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL C 137 " --> pdb=" O MET C 133 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN C 138 " --> pdb=" O LYS C 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 15 removed outlier: 3.811A pdb=" N LEU D 10 " --> pdb=" O PRO D 6 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N SER D 11 " --> pdb=" O LYS D 7 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG D 12 " --> pdb=" O LEU D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 65 removed outlier: 3.544A pdb=" N VAL D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE D 63 " --> pdb=" O LYS D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 removed outlier: 3.642A pdb=" N ARG D 80 " --> pdb=" O LYS D 76 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N LYS D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 96 removed outlier: 3.625A pdb=" N ARG D 96 " --> pdb=" O LEU D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 105 Processing helix chain 'D' and resid 109 through 120 removed outlier: 4.309A pdb=" N LYS D 120 " --> pdb=" O LEU D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 165 removed outlier: 6.198A pdb=" N LYS D 155 " --> pdb=" O GLN D 151 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ALA D 156 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU D 162 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLN D 163 " --> pdb=" O GLU D 159 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG D 164 " --> pdb=" O LEU D 160 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N GLU D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 191 removed outlier: 5.267A pdb=" N SER D 191 " --> pdb=" O ARG D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 205 removed outlier: 4.926A pdb=" N ILE D 199 " --> pdb=" O ASN D 195 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU D 201 " --> pdb=" O HIS D 197 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR D 203 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS D 205 " --> pdb=" O GLU D 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 70 removed outlier: 3.591A pdb=" N GLN E 60 " --> pdb=" O PRO E 56 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS E 65 " --> pdb=" O LYS E 61 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ARG E 68 " --> pdb=" O GLU E 64 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N MET E 70 " --> pdb=" O ALA E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 118 removed outlier: 6.142A pdb=" N ALA E 112 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL E 113 " --> pdb=" O ALA E 109 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL E 116 " --> pdb=" O ALA E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 147 removed outlier: 3.872A pdb=" N ILE E 140 " --> pdb=" O VAL E 136 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASP E 141 " --> pdb=" O ARG E 137 " (cutoff:3.500A) removed outlier: 5.672A 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: 3.670A pdb=" N GLY E 165 " --> pdb=" O GLU E 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 33 removed outlier: 4.228A pdb=" N VAL F 18 " --> pdb=" O GLN F 14 " (cutoff:3.500A) Proline residue: F 19 - end of helix removed outlier: 3.628A pdb=" N ARG F 24 " --> pdb=" O GLY F 20 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA F 28 " --> pdb=" O ARG F 24 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE F 29 " --> pdb=" O TYR F 25 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY F 31 " --> pdb=" O ALA F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 81 removed outlier: 3.592A pdb=" N ILE F 71 " --> pdb=" O PRO F 67 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP F 72 " --> pdb=" O GLN F 68 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU F 73 " --> pdb=" O GLU F 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 30 removed outlier: 3.586A pdb=" N ALA G 23 " --> pdb=" O SER G 19 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE G 28 " --> pdb=" O LYS G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 54 removed outlier: 3.713A pdb=" N THR G 48 " --> pdb=" O SER G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 69 removed outlier: 3.949A pdb=" N ALA G 60 " --> pdb=" O SER G 56 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL G 63 " --> pdb=" O GLU G 59 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN G 67 " --> pdb=" O VAL G 63 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 111 removed outlier: 3.758A pdb=" N ASN G 96 " --> pdb=" O PRO G 92 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA G 97 " --> pdb=" O VAL G 93 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG G 101 " --> pdb=" O ALA G 97 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TRP G 102 " --> pdb=" O LEU G 98 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ARG G 110 " --> pdb=" O ALA G 106 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N GLY G 111 " --> pdb=" O ALA G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 129 removed outlier: 3.536A pdb=" N ALA G 120 " --> pdb=" O ALA G 116 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU G 128 " --> pdb=" O SER G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 149 removed outlier: 3.857A pdb=" N LYS G 135 " --> pdb=" O GLY G 131 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N GLU G 145 " --> pdb=" O HIS G 141 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA G 146 " --> pdb=" O ARG G 142 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN G 147 " --> pdb=" O MET G 143 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LYS G 148 " --> pdb=" O ALA G 144 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ALA G 149 " --> pdb=" O GLU G 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 20 removed outlier: 3.549A pdb=" N ALA H 18 " --> pdb=" O ARG H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 43 Processing helix chain 'H' and resid 111 through 119 Processing helix chain 'I' and resid 33 through 38 removed outlier: 3.856A pdb=" N PHE I 38 " --> pdb=" O LEU I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 53 removed outlier: 4.814A pdb=" N ARG I 48 " --> pdb=" O ARG I 44 " (cutoff:3.500A) Proline residue: I 50 - end of helix removed outlier: 4.045A pdb=" N LEU I 53 " --> pdb=" O GLN I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 86 removed outlier: 3.907A pdb=" N THR I 83 " --> pdb=" O ARG I 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 99 removed outlier: 5.153A pdb=" N GLU I 96 " --> pdb=" O SER I 92 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU I 97 " --> pdb=" O LEU I 93 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS I 99 " --> pdb=" O SER I 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 33 removed outlier: 4.518A pdb=" N GLN J 20 " --> pdb=" O ARG J 16 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA J 21 " --> pdb=" O LEU J 17 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA J 23 " --> pdb=" O ASP J 19 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU J 24 " --> pdb=" O GLN J 20 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG J 31 " --> pdb=" O GLU J 27 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N THR J 32 " --> pdb=" O THR J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 90 removed outlier: 4.056A pdb=" N ALA J 86 " --> pdb=" O LYS J 82 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET J 88 " --> pdb=" O VAL J 84 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N ARG J 89 " --> pdb=" O ASP J 85 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU J 90 " --> pdb=" O ALA J 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 50 removed outlier: 3.569A pdb=" N SER K 49 " --> pdb=" O THR K 45 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLY K 50 " --> pdb=" O ALA K 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 45 through 50' Processing helix chain 'K' and resid 53 through 58 removed outlier: 4.207A pdb=" N SER K 57 " --> pdb=" O GLY K 53 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N THR K 58 " --> pdb=" O SER K 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 53 through 58' Processing helix chain 'K' and resid 59 through 74 removed outlier: 3.536A pdb=" N GLU K 67 " --> pdb=" O GLN K 63 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP K 71 " --> pdb=" O GLU K 67 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ALA K 72 " --> pdb=" O ARG K 68 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N VAL K 73 " --> pdb=" O CYS K 69 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS K 74 " --> pdb=" O ALA K 70 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 103 removed outlier: 5.488A pdb=" N THR K 95 " --> pdb=" O GLY K 91 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ILE K 96 " --> pdb=" O ARG K 92 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA K 98 " --> pdb=" O SER K 94 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU K 99 " --> pdb=" O THR K 95 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN K 100 " --> pdb=" O ILE K 96 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA K 101 " --> pdb=" O ARG K 97 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 10 Proline residue: L 10 - end of helix Processing helix chain 'L' and resid 112 through 117 removed outlier: 5.164A pdb=" N TYR L 116 " --> pdb=" O ALA L 112 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY L 117 " --> pdb=" O ARG L 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 112 through 117' Processing helix chain 'M' and resid 13 through 21 removed outlier: 3.564A pdb=" N THR M 19 " --> pdb=" O VAL M 15 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER M 20 " --> pdb=" O ILE M 16 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ILE M 21 " --> pdb=" O ALA M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 37 removed outlier: 3.640A pdb=" N SER M 29 " --> pdb=" O GLY M 25 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA M 35 " --> pdb=" O ALA M 31 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 63 removed outlier: 5.088A pdb=" N THR M 54 " --> pdb=" O GLY M 50 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU M 55 " --> pdb=" O GLN M 51 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG M 56 " --> pdb=" O ILE M 52 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP M 57 " --> pdb=" O ASP M 53 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU M 58 " --> pdb=" O THR M 54 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LYS M 61 " --> pdb=" O ASP M 57 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE M 62 " --> pdb=" O GLU M 58 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N VAL M 63 " --> pdb=" O VAL M 59 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 83 removed outlier: 3.587A pdb=" N ARG M 69 " --> pdb=" O GLU M 65 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG M 70 " --> pdb=" O GLY M 66 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY M 83 " --> pdb=" O LEU M 79 " (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: 3.641A pdb=" N LYS N 6 " --> pdb=" O LYS N 2 " (cutoff:3.500A) Processing helix chain 'N' and resid 23 through 29 removed outlier: 5.048A pdb=" N LYS N 27 " --> pdb=" O ARG N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 51 removed outlier: 3.723A pdb=" N TRP N 41 " --> pdb=" O ASP N 37 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL N 44 " --> pdb=" O ARG N 40 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLN N 48 " --> pdb=" O VAL N 44 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR N 49 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU N 50 " --> pdb=" O LYS N 46 " (cutoff:3.500A) Proline residue: N 51 - end of helix Processing helix chain 'N' and resid 55 through 60 removed outlier: 4.269A pdb=" N GLN N 59 " --> pdb=" O SER N 55 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ARG N 60 " --> pdb=" O PRO N 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 55 through 60' Processing helix chain 'N' and resid 79 through 90 removed outlier: 3.730A pdb=" N ARG N 84 " --> pdb=" O ARG N 80 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG N 89 " --> pdb=" O GLU N 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 15 Processing helix chain 'O' and resid 23 through 42 removed outlier: 4.384A pdb=" N GLY O 40 " --> pdb=" O ASN O 36 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N HIS O 41 " --> pdb=" O HIS O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 48 through 73 removed outlier: 3.726A pdb=" N GLY O 54 " --> pdb=" O HIS O 50 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 85 removed outlier: 3.539A pdb=" N GLU O 82 " --> pdb=" O THR O 78 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 64 removed outlier: 3.612A pdb=" N TRP P 60 " --> pdb=" O ARG P 56 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN P 63 " --> pdb=" O HIS P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 79 removed outlier: 3.570A pdb=" N LEU P 74 " --> pdb=" O ARG P 70 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS P 76 " --> pdb=" O ALA P 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 11 through 16 removed outlier: 6.761A pdb=" N GLU R 15 " --> pdb=" O ARG R 11 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY R 16 " --> pdb=" O PHE R 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 11 through 16' Processing helix chain 'R' and resid 24 through 33 removed outlier: 3.950A pdb=" N ASN R 30 " --> pdb=" O ALA R 26 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR R 31 " --> pdb=" O THR R 27 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE R 32 " --> pdb=" O LEU R 28 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N THR R 33 " --> pdb=" O LYS R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 45 removed outlier: 3.550A pdb=" N THR R 44 " --> pdb=" O PRO R 40 " (cutoff:3.500A) removed outlier: 3.527A 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: 3.551A pdb=" N GLN R 53 " --> pdb=" O LYS R 49 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR R 63 " --> pdb=" O LYS R 59 " (cutoff:3.500A) Processing helix chain 'S' and resid 11 through 25 removed outlier: 3.719A pdb=" N LYS S 17 " --> pdb=" O HIS S 13 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU S 23 " --> pdb=" O GLU S 19 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER S 24 " --> pdb=" O LYS S 20 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 69 through 75 removed outlier: 4.375A pdb=" N PHE S 73 " --> pdb=" O LYS S 69 " (cutoff:3.500A) removed outlier: 3.950A 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: 4.503A pdb=" N ALA T 10 " --> pdb=" O ALA T 6 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE T 11 " --> pdb=" O LYS T 7 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS T 15 " --> pdb=" O ILE T 11 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS T 18 " --> pdb=" O GLU T 14 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N HIS T 19 " --> pdb=" O LYS T 15 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG T 23 " --> pdb=" O HIS T 19 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE T 30 " --> pdb=" O MET T 26 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL T 34 " --> pdb=" O PHE T 30 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR T 35 " --> pdb=" O ILE T 31 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA T 37 " --> pdb=" O LYS T 33 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 64 removed outlier: 4.069A pdb=" N GLN T 47 " --> pdb=" O LYS T 43 " (cutoff:3.500A) Proline residue: T 55 - end of helix removed outlier: 3.545A pdb=" N GLN T 60 " --> pdb=" O ILE T 56 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLY T 64 " --> pdb=" O GLN T 60 " (cutoff:3.500A) Processing helix chain 'T' and resid 67 through 86 removed outlier: 5.962A pdb=" N ALA T 71 " --> pdb=" O HIS T 67 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR T 79 " --> pdb=" O LYS T 75 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS T 84 " --> pdb=" O ALA T 80 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU T 85 " --> pdb=" O GLN T 81 " (cutoff:3.500A) Processing helix chain 'U' and resid 16 through 23 removed outlier: 4.503A pdb=" N ARG U 20 " --> pdb=" O ARG U 16 " (cutoff:3.500A) Processing helix chain 'U' and resid 24 through 34 removed outlier: 5.435A pdb=" N LEU U 28 " --> pdb=" O LYS U 24 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLU U 30 " --> pdb=" O GLY U 26 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ARG U 33 " --> pdb=" O ALA U 29 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ARG U 34 " --> pdb=" O GLU U 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 38 through 61 removed outlier: 3.715A pdb=" N LYS U 57 " --> pdb=" O LYS U 53 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS U 58 " --> pdb=" O ARG U 54 " (cutoff:3.500A) Processing helix chain '03' and resid 5 through 16 removed outlier: 3.635A pdb=" N LYS03 14 " --> pdb=" O VAL03 10 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL03 15 " --> pdb=" O ILE03 11 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ASP03 16 " --> pdb=" O ARG03 12 " (cutoff:3.500A) Processing helix chain '03' and resid 23 through 35 removed outlier: 4.244A pdb=" N ALA03 28 " --> pdb=" O ASN03 24 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS03 31 " --> pdb=" O ILE03 27 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU03 32 " --> pdb=" O ALA03 28 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU03 33 " --> pdb=" O LEU03 29 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR03 35 " --> pdb=" O LYS03 31 " (cutoff:3.500A) Processing helix chain '03' and resid 183 through 200 removed outlier: 4.250A pdb=" N GLU03 187 " --> pdb=" O ASP03 183 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASN03 188 " --> pdb=" O LYS03 184 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA03 191 " --> pdb=" O GLU03 187 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS03 200 " --> pdb=" O LEU03 196 " (cutoff:3.500A) Processing helix chain 'Z' and resid 23 through 39 removed outlier: 4.184A pdb=" N LYS Z 37 " --> pdb=" O THR Z 33 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR Z 38 " --> pdb=" O VAL Z 34 " (cutoff:3.500A) Processing helix chain 'Z' and resid 45 through 51 Processing helix chain 'Z' and resid 52 through 59 removed outlier: 3.888A pdb=" N ALA Z 57 " --> pdb=" O PRO Z 53 " (cutoff:3.500A) Processing helix chain 'Z' and resid 87 through 98 removed outlier: 4.088A pdb=" N MET Z 91 " --> pdb=" O TYR Z 87 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA Z 96 " --> pdb=" O ILE Z 92 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N GLN Z 97 " --> pdb=" O THR Z 93 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N MET Z 98 " --> pdb=" O GLY Z 94 " (cutoff:3.500A) Processing helix chain 'Z' and resid 112 through 125 removed outlier: 3.595A pdb=" N GLU Z 117 " --> pdb=" O PRO Z 113 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE Z 119 " --> pdb=" O THR Z 115 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG Z 123 " --> pdb=" O ILE Z 119 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN Z 124 " --> pdb=" O LEU Z 120 " (cutoff:3.500A) Processing helix chain 'Z' and resid 142 through 161 removed outlier: 3.663A pdb=" N LEU Z 146 " --> pdb=" O ASP Z 142 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR Z 160 " --> pdb=" O LEU Z 156 " (cutoff:3.500A) removed outlier: 3.997A 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: 3.616A pdb=" N ALA Z 186 " --> pdb=" O ALA Z 182 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LYS Z 187 " --> pdb=" O GLU Z 183 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE Z 188 " --> pdb=" O TRP Z 184 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU Z 189 " --> pdb=" O GLU Z 185 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER Z 197 " --> pdb=" O GLY Z 193 " (cutoff:3.500A) Processing helix chain 'Z' and resid 282 through 287 removed outlier: 4.267A pdb=" N ILE Z 286 " --> pdb=" O LYS Z 282 " (cutoff:3.500A) removed outlier: 7.358A 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 removed outlier: 3.549A pdb=" N VAL04 3 " --> pdb=" O LYS04 17 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '04' and resid 79 through 82 removed outlier: 3.855A pdb=" N ILE04 90 " --> pdb=" O GLU04 81 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU04 92 " --> pdb=" O GLU04 78 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE04 73 " --> pdb=" O SER04 117 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER04 117 " --> pdb=" O ILE04 73 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ASP04 113 " --> pdb=" O VAL04 77 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '04' and resid 137 through 141 removed outlier: 3.984A pdb=" N SER04 138 " --> pdb=" O ILE04 163 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE04 163 " --> pdb=" O SER04 138 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N THR04 172 " --> pdb=" O VAL04 164 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLU04 179 " --> pdb=" O LEU04 175 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '04' and resid 89 through 95 removed outlier: 5.394A pdb=" N ASN04 89 " --> pdb=" O ALA04 105 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU04 99 " --> pdb=" O TYR04 95 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain '05' and resid 3 through 6 removed outlier: 3.574A pdb=" N LYS05 204 " --> pdb=" O ASP05 108 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain '05' and resid 11 through 16 removed outlier: 4.060A pdb=" N VAL05 20 " --> pdb=" O THR05 16 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL05 189 " --> pdb=" O THR05 25 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain '05' and resid 36 through 40 removed outlier: 3.827A pdb=" N ALA05 47 " --> pdb=" O LYS05 38 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU05 40 " --> pdb=" O TYR05 45 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N TYR05 45 " --> pdb=" O LEU05 40 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLN05 49 " --> pdb=" O THR05 35 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N GLN05 94 " --> pdb=" O VAL05 34 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain '05' and resid 46 through 51 removed outlier: 6.356A pdb=" N ARG05 46 " --> pdb=" O LEU05 84 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain '06' and resid 1 through 5 removed outlier: 3.617A pdb=" N MET06 1 " --> pdb=" O VAL06 14 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LEU06 5 " --> pdb=" O SER06 10 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N SER06 10 " --> pdb=" O LEU06 5 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain '06' and resid 117 through 120 removed outlier: 3.577A pdb=" N ASP06 168 " --> pdb=" O VAL06 146 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain '07' and resid 64 through 67 removed outlier: 3.636A pdb=" N GLY07 85 " --> pdb=" O THR07 67 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N GLY07 38 " --> pdb=" O GLY07 150 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLY07 150 " --> pdb=" O GLY07 38 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain '08' and resid 15 through 18 Processing sheet with id= 13, first strand: chain '08' and resid 81 through 88 removed outlier: 6.506A pdb=" N THR08 128 " --> pdb=" O LEU08 88 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain '08' and resid 94 through 97 removed outlier: 3.785A pdb=" N SER08 105 " --> pdb=" O ARG08 94 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain '09' and resid 2 through 6 removed outlier: 5.484A pdb=" N GLN09 2 " --> pdb=" O ALA09 39 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU09 6 " --> pdb=" O LYS09 35 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N LYS09 35 " --> pdb=" O LEU09 6 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain '09' and resid 76 through 81 removed outlier: 7.922A pdb=" N GLU09 76 " --> pdb=" O LYS09 141 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE09 143 " --> pdb=" O GLU09 76 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N VAL09 78 " --> pdb=" O ILE09 143 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ASN09 145 " --> pdb=" O VAL09 78 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA09 140 " --> pdb=" O PHE09 132 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N SER09 131 " --> pdb=" O ARG09 116 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLU09 114 " --> pdb=" O GLN09 133 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain '10' and resid 23 through 28 removed outlier: 4.256A pdb=" N LEU10 23 " --> pdb=" O GLU10 87 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA10 25 " --> pdb=" O SER10 85 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER10 85 " --> pdb=" O ALA10 25 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain '11' and resid 6 through 11 removed outlier: 4.118A pdb=" N ALA11 6 " --> pdb=" O VAL11 60 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N VAL11 60 " --> pdb=" O ALA11 6 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain '11' and resid 98 through 101 removed outlier: 3.506A pdb=" N VAL11 138 " --> pdb=" O GLY11 98 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE11 100 " --> pdb=" O VAL11 138 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain '12' and resid 14 through 19 removed outlier: 3.501A pdb=" N LEU12 57 " --> pdb=" O VAL12 18 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain '12' and resid 74 through 77 Processing sheet with id= 22, first strand: chain '13' and resid 18 through 21 removed outlier: 4.084A pdb=" N THR13 6 " --> pdb=" O CYS13 21 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ASN13 82 " --> pdb=" O MET13 7 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain '15' and resid 62 through 66 removed outlier: 7.081A pdb=" N LEU15 102 " --> pdb=" O ARG15 66 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N TYR15 103 " --> pdb=" O LEU15 33 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET15 105 " --> pdb=" O PHE15 31 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL15 131 " --> pdb=" O GLY15 32 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LYS15 127 " --> pdb=" O VAL15 36 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain '16' and resid 95 through 100 removed outlier: 3.875A pdb=" N MET16 110 " --> pdb=" O CYS16 100 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain '17' and resid 49 through 52 removed outlier: 4.145A pdb=" N VAL17 49 " --> pdb=" O VAL17 39 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA17 37 " --> pdb=" O ALA17 51 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL17 28 " --> pdb=" O ASP17 93 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain '18' and resid 37 through 44 removed outlier: 6.310A pdb=" N THR18 24 " --> pdb=" O LYS18 86 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain '18' and resid 56 through 63 removed outlier: 7.813A pdb=" N SER18 56 " --> pdb=" O THR18 75 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain '20' and resid 11 through 14 removed outlier: 3.664A pdb=" N TYR20 2 " --> pdb=" O ALA20 42 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET20 40 " --> pdb=" O VAL20 4 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain '20' and resid 18 through 21 removed outlier: 3.974A pdb=" N GLN20 18 " --> pdb=" O ILE20 98 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASP20 95 " --> pdb=" O VAL20 64 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain '20' and resid 57 through 60 removed outlier: 4.319A pdb=" N VAL20 58 " --> pdb=" O SER20 102 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain '20' and resid 65 through 68 Processing sheet with id= 32, first strand: chain '20' and resid 71 through 78 removed outlier: 4.235A pdb=" N TYR20 83 " --> pdb=" O ARG20 78 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain '21' and resid 2 through 8 removed outlier: 4.138A pdb=" N THR21 3 " --> pdb=" O VAL21 107 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL21 107 " --> pdb=" O THR21 3 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL21 105 " --> pdb=" O ALA21 5 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL21 106 " --> pdb=" O THR21 72 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain '21' and resid 73 through 79 removed outlier: 5.689A pdb=" N THR21 100 " --> pdb=" O GLY21 79 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain '21' and resid 80 through 88 removed outlier: 4.386A pdb=" N ARG21 92 " --> pdb=" O ARG21 88 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain '22' and resid 29 through 33 removed outlier: 5.284A pdb=" N LYS22 66 " --> pdb=" O ARG22 77 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ASP22 79 " --> pdb=" O LYS22 64 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LYS22 64 " --> pdb=" O ASP22 79 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LYS22 81 " --> pdb=" O VAL22 62 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL22 62 " --> pdb=" O LYS22 81 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ALA22 83 " --> pdb=" O THR22 60 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N THR22 60 " --> pdb=" O ALA22 83 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL22 85 " --> pdb=" O VAL22 58 " (cutoff:3.500A) removed outlier: 6.937A 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 No H-bonds generated for sheet with id= 37 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 69 through 72 removed outlier: 3.901A pdb=" N ILE24 4 " --> pdb=" O THR24 62 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ALA24 39 " --> pdb=" O ARG24 9 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE24 89 " --> pdb=" O PRO24 27 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain '25' and resid 47 through 50 removed outlier: 4.067A pdb=" N THR25 54 " --> pdb=" O GLY25 50 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain '25' and resid 63 through 67 Processing sheet with id= 42, first strand: chain '26' and resid 11 through 15 Processing sheet with id= 43, first strand: chain '26' and resid 34 through 38 Processing sheet with id= 44, first strand: chain '28' and resid 33 through 38 removed outlier: 4.289A pdb=" N HIS28 33 " --> pdb=" O GLN28 8 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN28 8 " --> pdb=" O HIS28 33 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS28 5 " --> pdb=" O GLU28 57 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR28 7 " --> pdb=" O LYS28 55 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N MET28 53 " --> pdb=" O THR28 9 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain '29' and resid 20 through 25 removed outlier: 4.666A pdb=" N ASN29 20 " --> pdb=" O CYS29 16 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N CYS29 16 " --> pdb=" O ASN29 20 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU29 32 " --> pdb=" O THR29 13 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER29 15 " --> pdb=" O LEU29 32 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain '30' and resid 27 through 30 removed outlier: 6.304A pdb=" N SER30 28 " --> pdb=" O LYS30 36 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS30 36 " --> pdb=" O SER30 28 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ASP30 30 " --> pdb=" O GLY30 34 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain '31' and resid 7 through 11 removed outlier: 3.683A pdb=" N THR31 22 " --> pdb=" O ILE31 8 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain '31' and resid 33 through 38 removed outlier: 6.751A pdb=" N LEU31 33 " --> pdb=" O GLU31 50 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU31 50 " --> pdb=" O LEU31 33 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU31 35 " --> pdb=" O TYR31 48 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain '33' and resid 21 through 24 No H-bonds generated for sheet with id= 49 Processing sheet with id= 50, first strand: chain '34' and resid 13 through 18 removed outlier: 8.048A pdb=" N ASN34 13 " --> pdb=" O SER34 28 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER34 28 " --> pdb=" O ASN34 13 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'B' and resid 29 through 33 removed outlier: 6.079A pdb=" N PHE B 29 " --> pdb=" O ASN B 41 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'B' and resid 66 through 70 removed outlier: 4.187A pdb=" N PHE B 183 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'C' and resid 53 through 58 removed outlier: 3.773A pdb=" N ARG C 53 " --> pdb=" O HIS C 68 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL C 65 " --> pdb=" O GLN C 99 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR C 69 " --> pdb=" O ALA C 103 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'C' and resid 163 through 168 removed outlier: 3.986A pdb=" N ARG C 163 " --> pdb=" O GLY C 154 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL C 152 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN C 184 " --> pdb=" O VAL C 199 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ASP C 180 " --> pdb=" O LYS C 203 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'D' and resid 139 through 143 removed outlier: 3.549A pdb=" N ASP D 140 " --> pdb=" O PHE D 181 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N GLU D 178 " --> pdb=" O ASP D 173 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N TRP D 169 " --> pdb=" O LYS D 182 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'E' and resid 11 through 15 removed outlier: 3.737A pdb=" N GLN E 11 " --> pdb=" O GLY E 39 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY E 39 " --> pdb=" O GLN E 11 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU E 35 " --> pdb=" O ILE E 15 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'E' and resid 83 through 87 removed outlier: 3.958A pdb=" N VAL E 93 " --> pdb=" O GLY E 86 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG E 92 " --> pdb=" O TYR E 127 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TYR E 127 " --> pdb=" O ARG E 92 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN E 96 " --> pdb=" O LEU E 123 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU E 123 " --> pdb=" O GLN E 96 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'F' and resid 39 through 42 removed outlier: 6.176A pdb=" N ILE F 6 " --> pdb=" O MET F 62 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N HIS F 3 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU F 5 " --> pdb=" O MET F 90 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N MET F 90 " --> pdb=" O GLU F 5 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N MET F 9 " --> pdb=" O ARG F 86 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ARG F 86 " --> pdb=" O MET F 9 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'G' and resid 72 through 76 Processing sheet with id= 60, first strand: chain 'H' and resid 22 through 27 removed outlier: 6.380A pdb=" N ALA H 22 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU H 51 " --> pdb=" O GLU H 57 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS H 49 " --> pdb=" O GLU H 59 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N THR H 61 " --> pdb=" O ASP H 47 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ASP H 47 " --> pdb=" O THR H 61 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'H' and resid 122 through 125 removed outlier: 6.777A pdb=" N VAL H 102 " --> pdb=" O ILE H 125 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS H 126 " --> pdb=" O VAL H 102 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'I' and resid 4 through 10 removed outlier: 4.428A pdb=" N GLY I 9 " --> pdb=" O ALA I 16 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS I 67 " --> pdb=" O ALA I 15 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N LYS I 26 " --> pdb=" O LEU I 60 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'J' and resid 44 through 52 removed outlier: 6.224A pdb=" N ILE J 8 " --> pdb=" O VAL J 74 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG J 7 " --> pdb=" O SER J 101 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'K' and resid 41 through 44 removed outlier: 3.512A pdb=" N GLY K 42 " --> pdb=" O ILE K 33 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA K 44 " --> pdb=" O VAL K 31 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL K 31 " --> pdb=" O ALA K 44 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY K 18 " --> pdb=" O ASN K 80 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ASN K 108 " --> pdb=" O LEU K 81 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N GLY K 87 " --> pdb=" O VAL K 112 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'L' and resid 28 through 31 removed outlier: 3.624A pdb=" N ILE L 79 " --> pdb=" O GLY L 31 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N LEU L 80 " --> pdb=" O VAL L 97 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'L' and resid 35 through 40 removed outlier: 4.691A pdb=" N ARG L 35 " --> pdb=" O ARG L 53 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N LYS L 50 " --> pdb=" O ILE L 66 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU L 56 " --> pdb=" O PHE L 60 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N PHE L 60 " --> pdb=" O LEU L 56 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'P' and resid 4 through 11 removed outlier: 5.761A pdb=" N GLN P 18 " --> pdb=" O ALA P 7 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL P 19 " --> pdb=" O GLY P 37 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLY P 37 " --> pdb=" O VAL P 19 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLY P 49 " --> pdb=" O ASN P 40 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'Q' and resid 6 through 10 removed outlier: 3.867A pdb=" N GLY Q 9 " --> pdb=" O VAL Q 58 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLU Q 59 " --> pdb=" O VAL Q 75 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'Q' and resid 18 through 29 No H-bonds generated for sheet with id= 69 Processing sheet with id= 70, first strand: chain 'S' and resid 46 through 51 removed outlier: 4.754A pdb=" N LEU S 46 " --> pdb=" O VAL S 61 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE S 48 " --> pdb=" O VAL S 59 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain '03' and resid 60 through 64 Processing sheet with id= 72, first strand: chain '03' and resid 169 through 174 removed outlier: 5.275A pdb=" N GLY03 169 " --> pdb=" O LEU03 48 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL03 44 " --> pdb=" O THR03 173 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL03 212 " --> pdb=" O VAL03 224 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'Z' and resid 64 through 71 removed outlier: 3.628A pdb=" N SER Z 65 " --> pdb=" O ASP Z 80 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR Z 69 " --> pdb=" O TYR Z 76 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG Z 74 " --> pdb=" O THR Z 71 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL Z 12 " --> pdb=" O HIS Z 75 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA Z 77 " --> pdb=" O VAL Z 12 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N GLY Z 18 " --> pdb=" O CYS Z 81 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLY Z 83 " --> pdb=" O GLY Z 18 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY Z 100 " --> pdb=" O ASN Z 13 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY Z 15 " --> pdb=" O GLY Z 100 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N HIS Z 19 " --> pdb=" O VAL Z 104 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ALA Z 106 " --> pdb=" O HIS Z 19 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR Z 129 " --> pdb=" O ASP Z 99 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL Z 170 " --> pdb=" O VAL Z 132 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'Z' and resid 210 through 214 removed outlier: 7.190A pdb=" N PHE Z 210 " --> pdb=" O LYS Z 294 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N GLN Z 290 " --> pdb=" O ILE Z 214 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU Z 240 " --> pdb=" O CYS Z 255 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN Z 251 " --> pdb=" O ILE Z 244 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'Z' and resid 216 through 220 removed outlier: 3.588A pdb=" N VAL Z 226 " --> pdb=" O PHE Z 218 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N THR Z 225 " --> pdb=" O LEU Z 278 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL Z 274 " --> pdb=" O GLY Z 229 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'Z' and resid 326 through 331 removed outlier: 5.070A pdb=" N TYR Z 326 " --> pdb=" O ILE Z 341 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE Z 341 " --> pdb=" O TYR Z 326 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'Z' and resid 354 through 359 removed outlier: 6.229A pdb=" N GLU Z 305 " --> pdb=" O ALA Z 389 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU Z 372 " --> pdb=" O VAL Z 388 " (cutoff:3.500A) 1737 hydrogen bonds defined for protein. 5124 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3699 hydrogen bonds 6040 hydrogen bond angles 0 basepair planarities 1476 basepair parallelities 2817 stacking parallelities Total time for adding SS restraints: 262.85 Time building geometry restraints manager: 68.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.39: 55360 1.39 - 1.56: 100633 1.56 - 1.74: 10515 1.74 - 1.92: 293 1.92 - 2.10: 16 Bond restraints: 166817 Sorted by residual: bond pdb=" SD MET Z 91 " pdb=" CE MET Z 91 " ideal model delta sigma weight residual 1.791 2.095 -0.304 2.50e-02 1.60e+03 1.48e+02 bond pdb=" SD MET Z 260 " pdb=" CE MET Z 260 " ideal model delta sigma weight residual 1.791 2.071 -0.280 2.50e-02 1.60e+03 1.26e+02 bond pdb=" SD MET03 218 " pdb=" CE MET03 218 " ideal model delta sigma weight residual 1.791 2.054 -0.263 2.50e-02 1.60e+03 1.11e+02 bond pdb=" SD MET Z 358 " pdb=" CE MET Z 358 " ideal model delta sigma weight residual 1.791 2.046 -0.255 2.50e-02 1.60e+03 1.04e+02 bond pdb=" C LEU B 160 " pdb=" N PHE B 161 " ideal model delta sigma weight residual 1.331 1.473 -0.143 1.44e-02 4.82e+03 9.81e+01 ... (remaining 166812 not shown) Histogram of bond angle deviations from ideal: 92.84 - 104.15: 17409 104.15 - 115.47: 122397 115.47 - 126.78: 96186 126.78 - 138.10: 13076 138.10 - 149.41: 2 Bond angle restraints: 249070 Sorted by residual: angle pdb=" N GLY H 67 " pdb=" CA GLY H 67 " pdb=" C GLY H 67 " ideal model delta sigma weight residual 114.85 98.10 16.75 1.35e+00 5.49e-01 1.54e+02 angle pdb=" N ARG F 91 " pdb=" CA ARG F 91 " pdb=" C ARG F 91 " ideal model delta sigma weight residual 110.41 123.02 -12.61 1.23e+00 6.61e-01 1.05e+02 angle pdb=" CA LEU B 160 " pdb=" C LEU B 160 " pdb=" N PHE B 161 " ideal model delta sigma weight residual 116.18 130.52 -14.34 1.41e+00 5.03e-01 1.03e+02 angle pdb=" N LEU10 117 " pdb=" CA LEU10 117 " pdb=" C LEU10 117 " ideal model delta sigma weight residual 107.75 125.86 -18.11 1.86e+00 2.89e-01 9.48e+01 angle pdb=" N ASP Z 99 " pdb=" CA ASP Z 99 " pdb=" C ASP Z 99 " ideal model delta sigma weight residual 111.69 100.03 11.66 1.23e+00 6.61e-01 8.99e+01 ... (remaining 249065 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 95079 35.76 - 71.52: 10489 71.52 - 107.29: 1232 107.29 - 143.05: 17 143.05 - 178.81: 16 Dihedral angle restraints: 106833 sinusoidal: 88401 harmonic: 18432 Sorted by residual: dihedral pdb=" C5' U A 438 " pdb=" C4' U A 438 " pdb=" C3' U A 438 " pdb=" O3' U A 438 " ideal model delta sinusoidal sigma weight residual 147.00 71.97 75.03 1 8.00e+00 1.56e-02 1.11e+02 dihedral pdb=" C5' A011070 " pdb=" C4' A011070 " pdb=" C3' A011070 " pdb=" O3' A011070 " ideal model delta sinusoidal sigma weight residual 147.00 72.74 74.26 1 8.00e+00 1.56e-02 1.09e+02 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 78.05 68.95 1 8.00e+00 1.56e-02 9.61e+01 ... (remaining 106830 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.143: 28233 0.143 - 0.286: 3201 0.286 - 0.429: 327 0.429 - 0.571: 20 0.571 - 0.714: 1 Chirality restraints: 31782 Sorted by residual: chirality pdb=" C3' GCP Z 401 " pdb=" C2' GCP Z 401 " pdb=" C4' GCP Z 401 " pdb=" O3' GCP Z 401 " both_signs ideal model delta sigma weight residual False -2.57 -3.28 0.71 2.00e-01 2.50e+01 1.28e+01 chirality pdb=" C3' G A1190 " pdb=" C4' G A1190 " pdb=" O3' G A1190 " pdb=" C2' G A1190 " both_signs ideal model delta sigma weight residual False -2.74 -2.18 -0.56 2.00e-01 2.50e+01 7.95e+00 chirality pdb=" CA PHE03 180 " pdb=" N PHE03 180 " pdb=" C PHE03 180 " pdb=" CB PHE03 180 " both_signs ideal model delta sigma weight residual False 2.51 3.05 -0.54 2.00e-01 2.50e+01 7.30e+00 ... (remaining 31779 not shown) Planarity restraints: 13715 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N FME W 101 " -0.239 2.00e-02 2.50e+03 1.95e-01 3.80e+02 pdb=" CA FME W 101 " 0.091 2.00e-02 2.50e+03 pdb=" CN FME W 101 " 0.269 2.00e-02 2.50e+03 pdb=" O1 FME W 101 " -0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U A1086 " 0.110 2.00e-02 2.50e+03 6.22e-02 8.72e+01 pdb=" N1 U A1086 " -0.002 2.00e-02 2.50e+03 pdb=" C2 U A1086 " -0.022 2.00e-02 2.50e+03 pdb=" O2 U A1086 " -0.038 2.00e-02 2.50e+03 pdb=" N3 U A1086 " -0.025 2.00e-02 2.50e+03 pdb=" C4 U A1086 " -0.027 2.00e-02 2.50e+03 pdb=" O4 U A1086 " 0.116 2.00e-02 2.50e+03 pdb=" C5 U A1086 " -0.062 2.00e-02 2.50e+03 pdb=" C6 U A1086 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U01 683 " -0.114 2.00e-02 2.50e+03 6.16e-02 8.53e+01 pdb=" N1 U01 683 " 0.004 2.00e-02 2.50e+03 pdb=" C2 U01 683 " 0.022 2.00e-02 2.50e+03 pdb=" O2 U01 683 " 0.044 2.00e-02 2.50e+03 pdb=" N3 U01 683 " 0.019 2.00e-02 2.50e+03 pdb=" C4 U01 683 " 0.017 2.00e-02 2.50e+03 pdb=" O4 U01 683 " -0.107 2.00e-02 2.50e+03 pdb=" C5 U01 683 " 0.060 2.00e-02 2.50e+03 pdb=" C6 U01 683 " 0.055 2.00e-02 2.50e+03 ... (remaining 13712 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.05: 1 2.05 - 2.76: 20887 2.76 - 3.48: 204240 3.48 - 4.19: 493757 4.19 - 4.90: 659884 Nonbonded interactions: 1378769 Sorted by model distance: nonbonded pdb=" O3' A Y 76 " pdb=" C PHE Y 101 " model vdw 1.339 3.270 nonbonded pdb=" N GLY H 67 " pdb=" N LYS H 68 " model vdw 2.260 2.560 nonbonded pdb=" O3' A Y 76 " pdb=" O PHE Y 101 " model vdw 2.278 3.040 nonbonded pdb=" O LEU L 101 " pdb=" N CYS L 103 " model vdw 2.295 2.520 nonbonded pdb=" O HIS O 45 " pdb=" N LYS O 47 " model vdw 2.307 2.520 ... (remaining 1378764 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.820 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: 0.110 Extract box with map and model: 26.630 Check model and map are aligned: 1.620 Set scattering table: 1.040 Process input model: 575.510 Find NCS groups from input model: 2.880 Set up NCS constraints: 0.400 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 615.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 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 : 0.010 0.304 166817 Z= 0.574 Angle : 1.061 24.639 249070 Z= 0.699 Chirality : 0.095 0.714 31782 Planarity : 0.010 0.195 13715 Dihedral : 22.372 178.810 94947 Min Nonbonded Distance : 1.339 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 2.21 % Allowed : 12.19 % Favored : 85.60 % Rotamer: Outliers : 1.12 % Allowed : 5.09 % Favored : 93.79 % 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: -4.96 (0.08), residues: 6366 helix: -3.75 (0.07), residues: 1836 sheet: -2.86 (0.14), residues: 1037 loop : -3.23 (0.09), residues: 3493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.006 TRP26 38 HIS 0.003 0.000 HIS Z 319 PHE 0.066 0.007 PHE Z 210 TYR 0.090 0.009 TYR Z 198 ARG 0.008 0.001 ARG20 80 *********************** 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 2110 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 2051 time to evaluate : 6.742 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 TARDY: cannot create tardy model for: "SER Z 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 04 29 PHE cc_start: 0.8840 (t80) cc_final: 0.8497 (t80) REVERT: 04 170 TYR cc_start: 0.8618 (m-10) cc_final: 0.8350 (m-10) REVERT: 06 15 SER cc_start: 0.8320 (m) cc_final: 0.7754 (p) REVERT: 06 152 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8409 (tm-30) REVERT: 07 97 GLU cc_start: 0.8570 (tp30) cc_final: 0.8339 (tm-30) REVERT: 07 99 PHE cc_start: 0.9118 (t80) cc_final: 0.8774 (t80) REVERT: 07 127 TYR cc_start: 0.8595 (t80) cc_final: 0.8194 (t80) REVERT: 07 142 TYR cc_start: 0.7462 (t80) cc_final: 0.7215 (t80) REVERT: 08 68 ARG cc_start: 0.8815 (tmt170) cc_final: 0.8574 (tmt-80) REVERT: 08 115 GLN cc_start: 0.8366 (tp-100) cc_final: 0.7970 (tm-30) REVERT: 09 77 THR cc_start: 0.4972 (t) cc_final: 0.4746 (m) REVERT: 09 91 PHE cc_start: 0.6985 (t80) cc_final: 0.6681 (t80) REVERT: 09 115 VAL cc_start: 0.9304 (t) cc_final: 0.9025 (m) REVERT: 09 128 HIS cc_start: 0.8035 (m-70) cc_final: 0.7470 (m-70) REVERT: 09 133 GLN cc_start: 0.8661 (mt0) cc_final: 0.8232 (tm-30) REVERT: 10 43 LYS cc_start: 0.5365 (ttpt) cc_final: 0.5114 (ttpt) REVERT: 11 37 PHE cc_start: 0.7888 (t80) cc_final: 0.7390 (t80) REVERT: 11 116 MET cc_start: 0.2954 (mmp) cc_final: 0.1001 (ptm) REVERT: 12 16 TYR cc_start: 0.8585 (m-80) cc_final: 0.8357 (m-80) REVERT: 12 75 TYR cc_start: 0.8014 (m-80) cc_final: 0.7727 (m-80) REVERT: 12 84 ILE cc_start: 0.8851 (tp) cc_final: 0.8581 (tt) REVERT: 13 40 LYS cc_start: 0.8810 (tptt) cc_final: 0.8571 (tttp) REVERT: 13 113 MET cc_start: 0.8983 (tpp) cc_final: 0.8599 (tpp) REVERT: 15 136 MET cc_start: 0.7981 (ttp) cc_final: 0.7710 (tmm) REVERT: 16 75 ILE cc_start: 0.8687 (mm) cc_final: 0.8377 (mm) REVERT: 16 106 ASP cc_start: 0.7805 (p0) cc_final: 0.7461 (p0) REVERT: 17 84 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8451 (mt-10) REVERT: 17 108 ASP cc_start: 0.9061 (m-30) cc_final: 0.8173 (m-30) REVERT: 18 7 LEU cc_start: 0.9332 (tt) cc_final: 0.9054 (tp) REVERT: 20 19 THR cc_start: 0.8667 (m) cc_final: 0.8362 (p) REVERT: 20 95 ASP cc_start: 0.7843 (m-30) cc_final: 0.7607 (m-30) REVERT: 21 1 MET cc_start: 0.8670 (tpp) cc_final: 0.8107 (tpp) REVERT: 21 30 SER cc_start: 0.9098 (p) cc_final: 0.8649 (p) REVERT: 22 1 MET cc_start: 0.6058 (ptm) cc_final: 0.5230 (ptp) REVERT: 22 7 LEU cc_start: 0.8505 (mt) cc_final: 0.8109 (mp) REVERT: 22 77 ARG cc_start: 0.8362 (mmt90) cc_final: 0.7598 (mmt90) REVERT: 23 61 GLU cc_start: 0.7354 (mp0) cc_final: 0.7108 (mm-30) REVERT: 24 45 ASP cc_start: 0.8784 (m-30) cc_final: 0.8533 (t0) REVERT: 24 55 GLU cc_start: 0.8991 (mp0) cc_final: 0.8738 (mp0) REVERT: 24 57 TYR cc_start: 0.7479 (m-80) cc_final: 0.7170 (m-10) REVERT: 24 76 ASP cc_start: 0.8754 (t0) cc_final: 0.8466 (t0) REVERT: 27 2 LYS cc_start: 0.8000 (pttt) cc_final: 0.7771 (pttt) REVERT: 27 5 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7602 (tm-30) REVERT: 27 7 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.8009 (tmm160) REVERT: 27 11 VAL cc_start: 0.9215 (t) cc_final: 0.8884 (p) REVERT: 27 26 PHE cc_start: 0.8843 (t80) cc_final: 0.8385 (t80) REVERT: 27 45 GLN cc_start: 0.8559 (pt0) cc_final: 0.8337 (tp-100) REVERT: 27 49 ASP cc_start: 0.9216 (m-30) cc_final: 0.9003 (m-30) REVERT: 30 14 MET cc_start: 0.8861 (mtm) cc_final: 0.8376 (mtm) REVERT: 30 15 ARG cc_start: 0.8673 (ttp-110) cc_final: 0.8389 (ttp80) REVERT: 32 33 ARG cc_start: 0.8627 (mtm-85) cc_final: 0.8422 (mtm-85) REVERT: 32 45 SER cc_start: 0.8207 (m) cc_final: 0.7971 (p) REVERT: B 141 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8592 (mt-10) REVERT: B 162 VAL cc_start: 0.9249 (t) cc_final: 0.8960 (t) REVERT: C 82 ASP cc_start: 0.8482 (m-30) cc_final: 0.8228 (m-30) REVERT: C 121 SER cc_start: 0.8881 (m) cc_final: 0.8579 (p) REVERT: C 129 PHE cc_start: 0.9258 (p90) cc_final: 0.9024 (p90) REVERT: D 97 LEU cc_start: 0.8847 (tp) cc_final: 0.8624 (tt) REVERT: E 10 LEU cc_start: 0.8923 (pp) cc_final: 0.8382 (pt) REVERT: E 129 SER cc_start: 0.9075 (t) cc_final: 0.8667 (p) REVERT: F 13 ASP cc_start: 0.8545 (p0) cc_final: 0.8220 (p0) REVERT: F 93 LYS cc_start: 0.7992 (mttt) cc_final: 0.7597 (mtmt) REVERT: G 36 SER cc_start: 0.9264 (m) cc_final: 0.9024 (p) REVERT: H 25 THR cc_start: 0.8375 (m) cc_final: 0.7337 (p) REVERT: I 18 VAL cc_start: 0.8897 (t) cc_final: 0.8646 (p) REVERT: I 30 ASN cc_start: 0.8193 (m110) cc_final: 0.7503 (m110) REVERT: I 35 GLU cc_start: 0.8323 (tp30) cc_final: 0.8059 (tp30) REVERT: I 61 ASP cc_start: 0.7882 (p0) cc_final: 0.7546 (p0) REVERT: J 85 ASP cc_start: 0.8109 (m-30) cc_final: 0.7811 (p0) REVERT: L 23 LEU cc_start: 0.8557 (tp) cc_final: 0.8307 (tp) REVERT: M 15 VAL cc_start: 0.9332 (m) cc_final: 0.9126 (p) REVERT: M 22 TYR cc_start: 0.8542 (t80) cc_final: 0.8276 (t80) REVERT: M 68 LEU cc_start: 0.8717 (tp) cc_final: 0.8107 (tp) REVERT: M 71 GLU cc_start: 0.8630 (tm-30) cc_final: 0.8214 (tm-30) REVERT: N 27 LYS cc_start: 0.8937 (pttp) cc_final: 0.8705 (ptmt) REVERT: N 42 ASN cc_start: 0.8559 (m-40) cc_final: 0.8359 (m110) REVERT: O 9 LYS cc_start: 0.9465 (mtpt) cc_final: 0.9229 (mttt) REVERT: O 19 ASN cc_start: 0.8673 (t0) cc_final: 0.8347 (t0) REVERT: Q 20 ILE cc_start: 0.8775 (tt) cc_final: 0.8482 (mm) REVERT: S 15 LEU cc_start: 0.8924 (tp) cc_final: 0.7850 (tt) REVERT: S 22 VAL cc_start: 0.8016 (t) cc_final: 0.7782 (m) REVERT: U 13 VAL cc_start: 0.7519 (p) cc_final: 0.7266 (m) REVERT: U 43 GLU cc_start: 0.8750 (pt0) cc_final: 0.8483 (tt0) REVERT: 03 4 LEU cc_start: 0.5519 (OUTLIER) cc_final: 0.5317 (mt) REVERT: 03 12 ARG cc_start: 0.7532 (ttm-80) cc_final: 0.7132 (mpt180) REVERT: 03 16 ASP cc_start: 0.7444 (t0) cc_final: 0.6818 (p0) REVERT: Z 17 ILE cc_start: 0.6479 (pp) cc_final: 0.6259 (pp) REVERT: Z 39 TYR cc_start: 0.8247 (t80) cc_final: 0.7882 (t80) REVERT: Z 114 GLN cc_start: 0.8120 (mp-120) cc_final: 0.7642 (mp10) REVERT: Z 197 SER cc_start: 0.8202 (t) cc_final: 0.7985 (p) REVERT: Z 215 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7345 (tm-30) REVERT: Z 252 LYS cc_start: 0.8640 (mttt) cc_final: 0.8203 (mttt) REVERT: Z 255 CYS cc_start: 0.9258 (t) cc_final: 0.8604 (p) REVERT: Z 305 GLU cc_start: 0.8534 (tt0) cc_final: 0.8200 (mt-10) REVERT: Z 368 MET cc_start: 0.5200 (mmm) cc_final: 0.4965 (mtm) outliers start: 59 outliers final: 17 residues processed: 2088 average time/residue: 1.3913 time to fit residues: 4935.8300 Evaluate side-chains 1289 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 1270 time to evaluate : 6.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 239 PHE Chi-restraints excluded: chain 11 residue 131 THR Chi-restraints excluded: chain 12 residue 57 LEU Chi-restraints excluded: chain 13 residue 61 VAL Chi-restraints excluded: chain 14 residue 110 VAL Chi-restraints excluded: chain 21 residue 3 THR Chi-restraints excluded: chain 22 residue 32 LEU Chi-restraints excluded: chain 27 residue 7 ARG Chi-restraints excluded: chain L residue 28 GLN Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain S residue 10 ILE Chi-restraints excluded: chain U residue 10 PRO Chi-restraints excluded: chain 03 residue 4 LEU Chi-restraints excluded: chain 03 residue 10 VAL Chi-restraints excluded: chain Z residue 98 MET Chi-restraints excluded: chain Z residue 225 THR Chi-restraints excluded: chain Z residue 236 ILE Chi-restraints excluded: chain Z residue 237 LYS Chi-restraints excluded: chain Z residue 358 MET 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: 5.9990 chunk 285 optimal weight: 20.0000 chunk 562 optimal weight: 4.9990 chunk 445 optimal weight: 20.0000 chunk 862 optimal weight: 20.0000 chunk 333 optimal weight: 8.9990 chunk 524 optimal weight: 5.9990 chunk 642 optimal weight: 10.0000 chunk 999 optimal weight: 10.0000 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 04 36 ASN 04 89 ASN ** 04 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 04 133 ASN 05 49 GLN ** 06 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 06 156 ASN 06 163 ASN 07 51 ASN 08 37 ASN 08 63 GLN 08 87 GLN ** 08 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 09 43 ASN ** 09 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 10 88 HIS 10 122 GLN 11 29 GLN 11 110 GLN 13 82 ASN ** 15 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 16 3 HIS 16 31 HIS 16 107 ASN 17 19 GLN 17 38 GLN 18 2 ASN ** 19 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 20 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 20 18 GLN 22 28 ASN 22 59 ASN 23 65 GLN 23 68 ASN 23 98 ASN 25 8 ASN 25 42 HIS 26 16 ASN 27 25 GLN 27 27 ASN 27 58 ASN ** 29 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 29 61 ASN 29 65 ASN 31 18 HIS B 23 ASN B 121 GLN ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 ASN D 139 ASN E 134 ASN F 52 ASN ** F 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 ASN G 129 ASN H 3 GLN ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 4 GLN I 30 ASN I 36 GLN I 80 HIS I 125 GLN J 58 ASN ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 ASN L 72 ASN ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 ASN N 48 GLN ** N 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 34 GLN ** O 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 41 HIS P 18 GLN ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 63 GLN Q 30 HIS S 55 GLN ** T 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 03 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 03 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 63 ASN ** Z 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 97 GLN ** Z 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 329 GLN Z 355 ASN Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 166817 Z= 0.283 Angle : 0.740 13.098 249070 Z= 0.384 Chirality : 0.041 0.415 31782 Planarity : 0.006 0.105 13715 Dihedral : 23.178 175.831 82325 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.49 % Allowed : 10.13 % Favored : 89.38 % Rotamer: Outliers : 4.46 % Allowed : 16.95 % Favored : 78.58 % 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: -3.56 (0.09), residues: 6366 helix: -1.67 (0.10), residues: 1916 sheet: -2.41 (0.14), residues: 1087 loop : -2.81 (0.10), residues: 3363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP04 212 HIS 0.010 0.001 HIS12 80 PHE 0.045 0.002 PHE U 36 TYR 0.031 0.003 TYR I 5 ARG 0.011 0.001 ARG20 13 *********************** 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 1635 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 1399 time to evaluate : 6.674 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 TARDY: cannot create tardy model for: "SER Z 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 04 29 PHE cc_start: 0.8850 (t80) cc_final: 0.8605 (t80) REVERT: 04 97 ASP cc_start: 0.7194 (p0) cc_final: 0.6859 (p0) REVERT: 04 162 GLN cc_start: 0.7991 (mm110) cc_final: 0.7496 (tp-100) REVERT: 04 200 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7841 (ttt) REVERT: 07 144 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7764 (mtmm) REVERT: 07 164 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8656 (pt0) REVERT: 07 174 PHE cc_start: 0.7422 (m-80) cc_final: 0.7145 (m-80) REVERT: 08 68 ARG cc_start: 0.8829 (tmt170) cc_final: 0.8614 (tmt-80) REVERT: 08 71 LEU cc_start: 0.9560 (OUTLIER) cc_final: 0.9108 (mm) REVERT: 09 97 ARG cc_start: 0.8878 (mmm-85) cc_final: 0.8653 (tpp80) REVERT: 09 128 HIS cc_start: 0.7712 (m-70) cc_final: 0.7375 (m90) REVERT: 09 133 GLN cc_start: 0.8901 (mt0) cc_final: 0.8314 (tm-30) REVERT: 11 18 ASN cc_start: 0.6992 (t0) cc_final: 0.6758 (t0) REVERT: 11 116 MET cc_start: 0.3692 (mmp) cc_final: 0.1308 (ptm) REVERT: 12 84 ILE cc_start: 0.9214 (tp) cc_final: 0.8935 (tt) REVERT: 15 60 GLN cc_start: 0.8086 (pt0) cc_final: 0.7882 (pt0) REVERT: 15 136 MET cc_start: 0.7961 (ttp) cc_final: 0.7741 (tmm) REVERT: 16 106 ASP cc_start: 0.7932 (p0) cc_final: 0.7653 (p0) REVERT: 17 27 VAL cc_start: 0.8743 (p) cc_final: 0.8539 (m) REVERT: 17 84 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8641 (pt0) REVERT: 20 19 THR cc_start: 0.8588 (m) cc_final: 0.8224 (p) REVERT: 20 95 ASP cc_start: 0.8187 (m-30) cc_final: 0.7820 (m-30) REVERT: 21 1 MET cc_start: 0.8502 (tpp) cc_final: 0.8027 (tpp) REVERT: 21 66 ILE cc_start: 0.8813 (mp) cc_final: 0.8366 (mt) REVERT: 22 1 MET cc_start: 0.6262 (ptm) cc_final: 0.5385 (ptp) REVERT: 22 25 GLU cc_start: 0.8414 (pp20) cc_final: 0.7683 (pp20) REVERT: 22 29 THR cc_start: 0.8904 (m) cc_final: 0.8326 (p) REVERT: 24 19 ARG cc_start: 0.8095 (ptp-110) cc_final: 0.7800 (ptp-170) REVERT: 24 45 ASP cc_start: 0.8837 (m-30) cc_final: 0.8493 (t0) REVERT: 24 57 TYR cc_start: 0.7513 (m-80) cc_final: 0.7257 (m-10) REVERT: 24 75 GLN cc_start: 0.8617 (tp40) cc_final: 0.8279 (tm-30) REVERT: 27 2 LYS cc_start: 0.7961 (pttt) cc_final: 0.7680 (pttt) REVERT: 27 7 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8411 (ptm-80) REVERT: 27 26 PHE cc_start: 0.8951 (t80) cc_final: 0.8433 (t80) REVERT: 27 45 GLN cc_start: 0.8582 (pt0) cc_final: 0.8073 (pp30) REVERT: 27 49 ASP cc_start: 0.9252 (m-30) cc_final: 0.8159 (m-30) REVERT: 30 15 ARG cc_start: 0.8631 (ttp-110) cc_final: 0.8391 (ttp80) REVERT: 30 36 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7870 (tppt) REVERT: 31 20 TYR cc_start: 0.7932 (m-10) cc_final: 0.7546 (m-10) REVERT: 31 24 LYS cc_start: 0.8779 (tppt) cc_final: 0.8408 (tppt) REVERT: 32 9 VAL cc_start: 0.8811 (t) cc_final: 0.8585 (p) REVERT: B 141 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8651 (mt-10) REVERT: C 33 ASP cc_start: 0.8275 (t70) cc_final: 0.7989 (t0) REVERT: C 129 PHE cc_start: 0.9334 (p90) cc_final: 0.8922 (p90) REVERT: D 53 GLN cc_start: 0.9211 (mt0) cc_final: 0.8984 (mt0) REVERT: D 93 LEU cc_start: 0.9423 (mt) cc_final: 0.9203 (mp) REVERT: D 97 LEU cc_start: 0.8868 (tp) cc_final: 0.8638 (tt) REVERT: D 170 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7905 (pp) REVERT: E 111 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7832 (ttp80) REVERT: E 129 SER cc_start: 0.9045 (t) cc_final: 0.8697 (p) REVERT: L 61 GLU cc_start: 0.8084 (tp30) cc_final: 0.7676 (tm-30) REVERT: L 72 ASN cc_start: 0.9027 (OUTLIER) cc_final: 0.8299 (p0) REVERT: M 10 ASP cc_start: 0.8077 (t70) cc_final: 0.7275 (t0) REVERT: M 22 TYR cc_start: 0.8736 (t80) cc_final: 0.8375 (t80) REVERT: M 33 LEU cc_start: 0.8838 (mp) cc_final: 0.8552 (mp) REVERT: M 65 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7718 (mm-30) REVERT: M 72 ILE cc_start: 0.9339 (pt) cc_final: 0.9090 (tp) REVERT: N 39 ASP cc_start: 0.9213 (OUTLIER) cc_final: 0.8865 (t0) REVERT: N 42 ASN cc_start: 0.8533 (m110) cc_final: 0.8276 (m110) REVERT: O 19 ASN cc_start: 0.8575 (t0) cc_final: 0.8286 (t0) REVERT: S 15 LEU cc_start: 0.8664 (tp) cc_final: 0.8304 (tt) REVERT: U 4 LYS cc_start: 0.8283 (tmmt) cc_final: 0.7970 (tptp) REVERT: U 30 GLU cc_start: 0.9385 (OUTLIER) cc_final: 0.9056 (pp20) REVERT: U 54 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.8055 (ttt180) REVERT: U 57 LYS cc_start: 0.8860 (mmpt) cc_final: 0.8621 (mtmt) REVERT: 03 16 ASP cc_start: 0.7555 (t0) cc_final: 0.7224 (t70) REVERT: 03 209 ILE cc_start: 0.8466 (pt) cc_final: 0.8142 (mm) REVERT: Z 13 ASN cc_start: 0.7753 (m110) cc_final: 0.7456 (m110) REVERT: Z 69 TYR cc_start: 0.5951 (p90) cc_final: 0.5686 (p90) REVERT: Z 70 ASP cc_start: 0.6929 (OUTLIER) cc_final: 0.6597 (p0) REVERT: Z 184 TRP cc_start: 0.6681 (m100) cc_final: 0.6478 (m100) REVERT: Z 215 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7107 (tm-30) REVERT: Z 255 CYS cc_start: 0.9056 (t) cc_final: 0.8226 (p) REVERT: Z 260 MET cc_start: 0.8673 (ppp) cc_final: 0.8452 (ppp) REVERT: Z 283 ARG cc_start: 0.7085 (mpp80) cc_final: 0.6821 (mpp80) outliers start: 236 outliers final: 145 residues processed: 1512 average time/residue: 1.3351 time to fit residues: 3533.0758 Evaluate side-chains 1287 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 1129 time to evaluate : 6.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 2 VAL Chi-restraints excluded: chain 04 residue 50 THR Chi-restraints excluded: chain 04 residue 80 LEU Chi-restraints excluded: chain 04 residue 156 SER Chi-restraints excluded: chain 04 residue 200 MET Chi-restraints excluded: chain 04 residue 258 SER Chi-restraints excluded: chain 04 residue 266 ILE Chi-restraints excluded: chain 05 residue 2 ILE Chi-restraints excluded: chain 05 residue 17 GLU Chi-restraints excluded: chain 05 residue 121 THR Chi-restraints excluded: chain 05 residue 137 SER Chi-restraints excluded: chain 05 residue 139 SER Chi-restraints excluded: chain 05 residue 199 SER Chi-restraints excluded: chain 06 residue 6 LYS Chi-restraints excluded: chain 06 residue 149 ILE Chi-restraints excluded: chain 06 residue 187 VAL Chi-restraints excluded: chain 07 residue 25 MET Chi-restraints excluded: chain 07 residue 30 VAL Chi-restraints excluded: chain 07 residue 144 LYS Chi-restraints excluded: chain 07 residue 164 GLU Chi-restraints excluded: chain 08 residue 15 ASP Chi-restraints excluded: chain 08 residue 19 ASN Chi-restraints excluded: chain 08 residue 59 ASP Chi-restraints excluded: chain 08 residue 71 LEU Chi-restraints excluded: chain 09 residue 40 THR Chi-restraints excluded: chain 09 residue 47 PHE Chi-restraints excluded: chain 10 residue 27 VAL Chi-restraints excluded: chain 10 residue 108 VAL Chi-restraints excluded: chain 11 residue 63 ASP Chi-restraints excluded: chain 11 residue 131 THR Chi-restraints excluded: chain 12 residue 12 LYS Chi-restraints excluded: chain 12 residue 50 THR Chi-restraints excluded: chain 12 residue 57 LEU Chi-restraints excluded: chain 13 residue 20 MET Chi-restraints excluded: chain 13 residue 21 CYS Chi-restraints excluded: chain 13 residue 28 SER Chi-restraints excluded: chain 13 residue 32 TYR Chi-restraints excluded: chain 13 residue 56 ASP Chi-restraints excluded: chain 13 residue 88 ASN Chi-restraints excluded: chain 13 residue 91 SER Chi-restraints excluded: chain 14 residue 5 THR Chi-restraints excluded: chain 14 residue 27 LEU Chi-restraints excluded: chain 14 residue 73 ILE Chi-restraints excluded: chain 14 residue 110 VAL Chi-restraints excluded: chain 15 residue 7 THR Chi-restraints excluded: chain 15 residue 42 THR Chi-restraints excluded: chain 15 residue 89 VAL Chi-restraints excluded: chain 15 residue 95 LEU Chi-restraints excluded: chain 15 residue 128 THR Chi-restraints excluded: chain 16 residue 53 THR Chi-restraints excluded: chain 16 residue 89 SER Chi-restraints excluded: chain 17 residue 35 ILE Chi-restraints excluded: chain 18 residue 1 SER Chi-restraints excluded: chain 18 residue 103 THR Chi-restraints excluded: chain 18 residue 109 ILE Chi-restraints excluded: chain 19 residue 61 ILE Chi-restraints excluded: chain 20 residue 99 THR Chi-restraints excluded: chain 21 residue 3 THR Chi-restraints excluded: chain 21 residue 4 ILE Chi-restraints excluded: chain 21 residue 12 SER Chi-restraints excluded: chain 21 residue 15 GLN Chi-restraints excluded: chain 21 residue 23 LEU Chi-restraints excluded: chain 21 residue 39 THR Chi-restraints excluded: chain 21 residue 81 SER Chi-restraints excluded: chain 22 residue 31 VAL Chi-restraints excluded: chain 22 residue 32 LEU Chi-restraints excluded: chain 22 residue 89 GLU Chi-restraints excluded: chain 22 residue 92 ASN Chi-restraints excluded: chain 24 residue 3 THR Chi-restraints excluded: chain 25 residue 25 GLU Chi-restraints excluded: chain 25 residue 26 SER Chi-restraints excluded: chain 25 residue 34 VAL Chi-restraints excluded: chain 26 residue 29 LEU Chi-restraints excluded: chain 26 residue 61 LYS Chi-restraints excluded: chain 26 residue 66 VAL Chi-restraints excluded: chain 27 residue 7 ARG Chi-restraints excluded: chain 27 residue 50 VAL Chi-restraints excluded: chain 28 residue 9 THR Chi-restraints excluded: chain 28 residue 24 LEU Chi-restraints excluded: chain 29 residue 23 LYS Chi-restraints excluded: chain 29 residue 58 ASP Chi-restraints excluded: chain 30 residue 10 SER Chi-restraints excluded: chain 30 residue 22 THR Chi-restraints excluded: chain 30 residue 36 LYS Chi-restraints excluded: chain 30 residue 45 ASP Chi-restraints excluded: chain 31 residue 8 ILE Chi-restraints excluded: chain 32 residue 15 SER Chi-restraints excluded: chain 33 residue 5 THR Chi-restraints excluded: chain 33 residue 57 VAL Chi-restraints excluded: chain 34 residue 17 VAL Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 111 ARG Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain K residue 17 ASP Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 44 ILE Chi-restraints excluded: chain M residue 77 LYS Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 79 SER Chi-restraints excluded: chain O residue 46 LYS Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain P residue 55 ASP Chi-restraints excluded: chain Q residue 21 VAL Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain S residue 10 ILE Chi-restraints excluded: chain S residue 11 ASP Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain T residue 43 LYS Chi-restraints excluded: chain U residue 30 GLU Chi-restraints excluded: chain U residue 54 ARG Chi-restraints excluded: chain 03 residue 14 LYS Chi-restraints excluded: chain Z residue 70 ASP Chi-restraints excluded: chain Z residue 236 ILE Chi-restraints excluded: chain Z residue 243 GLU Chi-restraints excluded: chain Z residue 314 ASP Chi-restraints excluded: chain Z residue 358 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1101 random chunks: chunk 555 optimal weight: 7.9990 chunk 310 optimal weight: 20.0000 chunk 832 optimal weight: 20.0000 chunk 680 optimal weight: 20.0000 chunk 275 optimal weight: 30.0000 chunk 1001 optimal weight: 20.0000 chunk 1082 optimal weight: 0.0970 chunk 892 optimal weight: 20.0000 chunk 993 optimal weight: 20.0000 chunk 341 optimal weight: 7.9990 chunk 803 optimal weight: 20.0000 overall best weight: 11.2190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 04 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 04 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 05 94 GLN 06 41 GLN ** 07 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 07 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 127 GLN ** 08 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 11 5 GLN 13 82 ASN 16 107 ASN 18 6 GLN 19 36 GLN 19 58 GLN 20 82 HIS 20 87 GLN 23 44 HIS 24 24 ASN ** 24 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 24 87 GLN ** 27 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 27 45 GLN 28 8 GLN ** 29 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 32 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 34 33 HIS B 18 GLN B 38 HIS B 119 GLN ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 GLN ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 8 GLN G 121 ASN I 30 ASN I 109 GLN L 4 ASN ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 34 ASN ** N 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 70 HIS ** O 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 45 HIS ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 63 ASN ** 03 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 03 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 166817 Z= 0.386 Angle : 0.759 14.539 249070 Z= 0.391 Chirality : 0.041 0.368 31782 Planarity : 0.006 0.079 13715 Dihedral : 23.550 179.392 82305 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 24.63 Ramachandran Plot: Outliers : 0.28 % Allowed : 12.27 % Favored : 87.45 % Rotamer: Outliers : 6.51 % Allowed : 18.60 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.11 (0.10), residues: 6366 helix: -1.16 (0.11), residues: 1938 sheet: -2.13 (0.14), residues: 1135 loop : -2.64 (0.10), residues: 3293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP P 60 HIS 0.010 0.002 HIS Z 84 PHE 0.034 0.003 PHE M 62 TYR 0.048 0.003 TYR07 21 ARG 0.010 0.001 ARG K 92 *********************** 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 1539 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 344 poor density : 1195 time to evaluate : 6.923 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 TARDY: cannot create tardy model for: "SER Z 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 04 29 PHE cc_start: 0.8876 (t80) cc_final: 0.8655 (t80) REVERT: 04 97 ASP cc_start: 0.7359 (p0) cc_final: 0.6923 (p0) REVERT: 04 200 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.7983 (ttt) REVERT: 07 127 TYR cc_start: 0.8466 (t80) cc_final: 0.8114 (t80) REVERT: 07 174 PHE cc_start: 0.7729 (m-80) cc_final: 0.7427 (m-80) REVERT: 08 100 ASN cc_start: 0.8150 (t0) cc_final: 0.7937 (t0) REVERT: 08 120 ILE cc_start: 0.8548 (mm) cc_final: 0.8287 (mt) REVERT: 09 11 ASN cc_start: 0.7654 (p0) cc_final: 0.7435 (p0) REVERT: 09 89 LYS cc_start: 0.8644 (mmtt) cc_final: 0.8011 (tmtt) REVERT: 09 97 ARG cc_start: 0.8893 (mmm-85) cc_final: 0.8663 (tpp80) REVERT: 09 133 GLN cc_start: 0.8996 (mt0) cc_final: 0.8387 (tm-30) REVERT: 09 141 LYS cc_start: 0.8257 (mmmt) cc_final: 0.7876 (mmmt) REVERT: 10 1 MET cc_start: 0.3763 (tpt) cc_final: 0.3485 (tpp) REVERT: 11 116 MET cc_start: 0.3643 (mmp) cc_final: 0.1500 (ttm) REVERT: 12 16 TYR cc_start: 0.8404 (m-80) cc_final: 0.8119 (m-10) REVERT: 13 117 SER cc_start: 0.9261 (m) cc_final: 0.9010 (p) REVERT: 14 81 ASP cc_start: 0.8815 (t0) cc_final: 0.8514 (t70) REVERT: 14 91 ASP cc_start: 0.7722 (m-30) cc_final: 0.7238 (p0) REVERT: 15 47 GLU cc_start: 0.8842 (tp30) cc_final: 0.8026 (tp30) REVERT: 15 136 MET cc_start: 0.7876 (ttp) cc_final: 0.7653 (tmm) REVERT: 16 106 ASP cc_start: 0.8077 (p0) cc_final: 0.7801 (p0) REVERT: 16 114 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8320 (pm20) REVERT: 17 80 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7060 (pt0) REVERT: 19 31 TYR cc_start: 0.8685 (t80) cc_final: 0.8387 (t80) REVERT: 20 19 THR cc_start: 0.8696 (m) cc_final: 0.8333 (p) REVERT: 20 95 ASP cc_start: 0.8080 (m-30) cc_final: 0.7832 (m-30) REVERT: 21 1 MET cc_start: 0.8630 (tpp) cc_final: 0.8153 (tpp) REVERT: 21 66 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8400 (mt) REVERT: 22 1 MET cc_start: 0.6079 (ptm) cc_final: 0.5359 (ptp) REVERT: 22 25 GLU cc_start: 0.8428 (pp20) cc_final: 0.7988 (pp20) REVERT: 23 72 PHE cc_start: 0.8607 (t80) cc_final: 0.8155 (t80) REVERT: 23 102 ILE cc_start: 0.7925 (OUTLIER) cc_final: 0.7434 (mp) REVERT: 24 57 TYR cc_start: 0.7489 (m-80) cc_final: 0.7192 (m-10) REVERT: 25 11 ASP cc_start: 0.8171 (t0) cc_final: 0.7864 (t0) REVERT: 26 71 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.8171 (mtp-110) REVERT: 27 23 ARG cc_start: 0.8847 (mmt90) cc_final: 0.8634 (mmt-90) REVERT: 27 26 PHE cc_start: 0.8974 (t80) cc_final: 0.8343 (t80) REVERT: 27 45 GLN cc_start: 0.8528 (pt0) cc_final: 0.8178 (pp30) REVERT: 27 49 ASP cc_start: 0.9293 (m-30) cc_final: 0.8337 (m-30) REVERT: 30 36 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.8008 (tppt) REVERT: 31 20 TYR cc_start: 0.8072 (m-10) cc_final: 0.7829 (m-10) REVERT: 32 26 ASN cc_start: 0.8712 (m-40) cc_final: 0.8414 (t0) REVERT: B 69 VAL cc_start: 0.8761 (t) cc_final: 0.8351 (p) REVERT: B 191 ASP cc_start: 0.8982 (t0) cc_final: 0.8610 (t0) REVERT: B 193 ASP cc_start: 0.8410 (m-30) cc_final: 0.8090 (m-30) REVERT: C 33 ASP cc_start: 0.8311 (t70) cc_final: 0.8056 (t0) REVERT: C 129 PHE cc_start: 0.9323 (p90) cc_final: 0.8968 (p90) REVERT: C 182 ASP cc_start: 0.8326 (t0) cc_final: 0.8122 (p0) REVERT: D 97 LEU cc_start: 0.9058 (tp) cc_final: 0.8798 (tt) REVERT: D 123 MET cc_start: 0.9055 (mtm) cc_final: 0.8802 (mmm) REVERT: E 129 SER cc_start: 0.9187 (t) cc_final: 0.8780 (p) REVERT: F 25 TYR cc_start: 0.8608 (m-80) cc_final: 0.8380 (m-80) REVERT: F 53 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8389 (mttp) REVERT: F 88 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.8340 (tmm) REVERT: H 82 LEU cc_start: 0.9161 (tp) cc_final: 0.8836 (tt) REVERT: I 58 GLU cc_start: 0.8361 (tp30) cc_final: 0.7477 (tp30) REVERT: K 57 SER cc_start: 0.9272 (m) cc_final: 0.9035 (m) REVERT: L 37 TYR cc_start: 0.8639 (p90) cc_final: 0.8394 (p90) REVERT: L 61 GLU cc_start: 0.7952 (tp30) cc_final: 0.7706 (tm-30) REVERT: M 10 ASP cc_start: 0.8156 (t70) cc_final: 0.7301 (t0) REVERT: M 15 VAL cc_start: 0.9608 (m) cc_final: 0.9261 (p) REVERT: M 16 ILE cc_start: 0.9182 (OUTLIER) cc_final: 0.8707 (tp) REVERT: N 26 LEU cc_start: 0.8083 (mp) cc_final: 0.7824 (mp) REVERT: S 15 LEU cc_start: 0.8821 (tp) cc_final: 0.8402 (tt) REVERT: U 30 GLU cc_start: 0.9366 (OUTLIER) cc_final: 0.8988 (pp20) REVERT: U 48 LYS cc_start: 0.8456 (tttt) cc_final: 0.8031 (pttt) REVERT: U 57 LYS cc_start: 0.9057 (mmpt) cc_final: 0.8564 (mtmt) REVERT: Z 13 ASN cc_start: 0.8381 (m110) cc_final: 0.8040 (m110) REVERT: Z 69 TYR cc_start: 0.6091 (p90) cc_final: 0.5747 (p90) REVERT: Z 70 ASP cc_start: 0.7156 (OUTLIER) cc_final: 0.6856 (m-30) REVERT: Z 114 GLN cc_start: 0.8169 (mm-40) cc_final: 0.7934 (mp10) REVERT: Z 215 GLU cc_start: 0.7542 (tm-30) cc_final: 0.7135 (tm-30) REVERT: Z 255 CYS cc_start: 0.9056 (t) cc_final: 0.8189 (p) REVERT: Z 368 MET cc_start: 0.5780 (mmm) cc_final: 0.5068 (mtt) outliers start: 344 outliers final: 239 residues processed: 1383 average time/residue: 1.2705 time to fit residues: 3088.0154 Evaluate side-chains 1311 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 1060 time to evaluate : 6.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 2 VAL Chi-restraints excluded: chain 04 residue 24 HIS Chi-restraints excluded: chain 04 residue 50 THR Chi-restraints excluded: chain 04 residue 80 LEU Chi-restraints excluded: chain 04 residue 113 ASP Chi-restraints excluded: chain 04 residue 156 SER Chi-restraints excluded: chain 04 residue 200 MET Chi-restraints excluded: chain 04 residue 249 VAL Chi-restraints excluded: chain 04 residue 258 SER Chi-restraints excluded: chain 05 residue 121 THR Chi-restraints excluded: chain 05 residue 137 SER Chi-restraints excluded: chain 05 residue 139 SER Chi-restraints excluded: chain 05 residue 199 SER Chi-restraints excluded: chain 06 residue 70 SER Chi-restraints excluded: chain 06 residue 73 ILE Chi-restraints excluded: chain 06 residue 83 VAL Chi-restraints excluded: chain 06 residue 187 VAL Chi-restraints excluded: chain 07 residue 22 ASN Chi-restraints excluded: chain 07 residue 25 MET Chi-restraints excluded: chain 07 residue 30 VAL Chi-restraints excluded: chain 07 residue 144 LYS Chi-restraints excluded: chain 07 residue 154 THR Chi-restraints excluded: chain 07 residue 164 GLU Chi-restraints excluded: chain 08 residue 9 VAL Chi-restraints excluded: chain 08 residue 15 ASP Chi-restraints excluded: chain 08 residue 19 ASN Chi-restraints excluded: chain 08 residue 55 ASP Chi-restraints excluded: chain 08 residue 59 ASP Chi-restraints excluded: chain 08 residue 161 VAL Chi-restraints excluded: chain 09 residue 40 THR Chi-restraints excluded: chain 09 residue 47 PHE Chi-restraints excluded: chain 09 residue 91 PHE Chi-restraints excluded: chain 09 residue 98 ASP Chi-restraints excluded: chain 09 residue 99 ILE Chi-restraints excluded: chain 09 residue 115 VAL Chi-restraints excluded: chain 09 residue 134 VAL Chi-restraints excluded: chain 10 residue 27 VAL Chi-restraints excluded: chain 10 residue 82 ILE Chi-restraints excluded: chain 10 residue 108 VAL Chi-restraints excluded: chain 11 residue 46 ASP Chi-restraints excluded: chain 11 residue 63 ASP Chi-restraints excluded: chain 12 residue 12 LYS Chi-restraints excluded: chain 12 residue 25 LEU Chi-restraints excluded: chain 12 residue 50 THR Chi-restraints excluded: chain 12 residue 57 LEU Chi-restraints excluded: chain 12 residue 131 ASN Chi-restraints excluded: chain 13 residue 13 ASN Chi-restraints excluded: chain 13 residue 21 CYS Chi-restraints excluded: chain 13 residue 25 LEU Chi-restraints excluded: chain 13 residue 28 SER Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 56 ASP Chi-restraints excluded: chain 13 residue 88 ASN Chi-restraints excluded: chain 13 residue 91 SER Chi-restraints excluded: chain 14 residue 5 THR Chi-restraints excluded: chain 14 residue 7 SER Chi-restraints excluded: chain 14 residue 27 LEU Chi-restraints excluded: chain 14 residue 67 THR Chi-restraints excluded: chain 14 residue 73 ILE Chi-restraints excluded: chain 15 residue 7 THR Chi-restraints excluded: chain 15 residue 42 THR Chi-restraints excluded: chain 15 residue 78 LEU Chi-restraints excluded: chain 15 residue 89 VAL Chi-restraints excluded: chain 15 residue 95 LEU Chi-restraints excluded: chain 15 residue 128 THR Chi-restraints excluded: chain 15 residue 129 THR Chi-restraints excluded: chain 16 residue 33 ILE Chi-restraints excluded: chain 16 residue 37 THR Chi-restraints excluded: chain 16 residue 76 VAL Chi-restraints excluded: chain 16 residue 83 LEU Chi-restraints excluded: chain 16 residue 89 SER Chi-restraints excluded: chain 16 residue 114 GLU Chi-restraints excluded: chain 17 residue 24 THR Chi-restraints excluded: chain 17 residue 28 VAL Chi-restraints excluded: chain 17 residue 35 ILE Chi-restraints excluded: chain 17 residue 47 VAL Chi-restraints excluded: chain 17 residue 80 GLU Chi-restraints excluded: chain 17 residue 87 ILE Chi-restraints excluded: chain 18 residue 24 THR Chi-restraints excluded: chain 18 residue 103 THR Chi-restraints excluded: chain 18 residue 109 ILE Chi-restraints excluded: chain 19 residue 7 VAL Chi-restraints excluded: chain 19 residue 38 VAL Chi-restraints excluded: chain 19 residue 61 ILE Chi-restraints excluded: chain 19 residue 79 ILE Chi-restraints excluded: chain 19 residue 82 LEU Chi-restraints excluded: chain 19 residue 103 VAL Chi-restraints excluded: chain 19 residue 108 LEU Chi-restraints excluded: chain 20 residue 98 ILE Chi-restraints excluded: chain 20 residue 102 SER Chi-restraints excluded: chain 21 residue 3 THR Chi-restraints excluded: chain 21 residue 4 ILE Chi-restraints excluded: chain 21 residue 12 SER Chi-restraints excluded: chain 21 residue 15 GLN Chi-restraints excluded: chain 21 residue 22 ASP Chi-restraints excluded: chain 21 residue 39 THR Chi-restraints excluded: chain 21 residue 57 ASN Chi-restraints excluded: chain 21 residue 66 ILE Chi-restraints excluded: chain 21 residue 81 SER Chi-restraints excluded: chain 21 residue 82 MET Chi-restraints excluded: chain 21 residue 94 ASP Chi-restraints excluded: chain 21 residue 96 ILE Chi-restraints excluded: chain 22 residue 31 VAL Chi-restraints excluded: chain 22 residue 32 LEU Chi-restraints excluded: chain 22 residue 39 THR Chi-restraints excluded: chain 22 residue 76 ARG Chi-restraints excluded: chain 22 residue 89 GLU Chi-restraints excluded: chain 22 residue 92 ASN Chi-restraints excluded: chain 23 residue 17 ASP Chi-restraints excluded: chain 23 residue 39 ASN Chi-restraints excluded: chain 23 residue 102 ILE Chi-restraints excluded: chain 24 residue 40 ILE Chi-restraints excluded: chain 25 residue 25 GLU Chi-restraints excluded: chain 25 residue 26 SER Chi-restraints excluded: chain 25 residue 27 VAL Chi-restraints excluded: chain 25 residue 34 VAL Chi-restraints excluded: chain 25 residue 63 VAL Chi-restraints excluded: chain 26 residue 58 ILE Chi-restraints excluded: chain 26 residue 71 ARG Chi-restraints excluded: chain 27 residue 7 ARG Chi-restraints excluded: chain 27 residue 13 GLU Chi-restraints excluded: chain 27 residue 15 ASN Chi-restraints excluded: chain 27 residue 50 VAL Chi-restraints excluded: chain 28 residue 9 THR Chi-restraints excluded: chain 28 residue 24 LEU Chi-restraints excluded: chain 29 residue 16 CYS Chi-restraints excluded: chain 29 residue 27 THR Chi-restraints excluded: chain 29 residue 58 ASP Chi-restraints excluded: chain 30 residue 24 VAL Chi-restraints excluded: chain 30 residue 36 LYS Chi-restraints excluded: chain 30 residue 45 ASP Chi-restraints excluded: chain 31 residue 8 ILE Chi-restraints excluded: chain 32 residue 15 SER Chi-restraints excluded: chain 33 residue 5 THR Chi-restraints excluded: chain 34 residue 17 VAL Chi-restraints excluded: chain 34 residue 22 VAL Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 8 GLN Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 61 PHE Chi-restraints excluded: chain G residue 115 MET Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 117 GLN Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain K residue 17 ASP Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 102 ASP Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 11 HIS Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 44 ILE Chi-restraints excluded: chain M residue 77 LYS Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 46 LYS Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 55 ASP Chi-restraints excluded: chain P residue 79 ASN Chi-restraints excluded: chain Q residue 21 VAL Chi-restraints excluded: chain Q residue 25 GLU Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain S residue 10 ILE Chi-restraints excluded: chain S residue 11 ASP Chi-restraints excluded: chain S residue 18 VAL Chi-restraints excluded: chain S residue 38 THR Chi-restraints excluded: chain S residue 42 ASN Chi-restraints excluded: chain S residue 62 THR Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 31 ILE Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain T residue 43 LYS Chi-restraints excluded: chain T residue 66 ILE Chi-restraints excluded: chain T residue 73 ARG Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 30 GLU Chi-restraints excluded: chain U residue 34 ARG Chi-restraints excluded: chain 03 residue 35 THR Chi-restraints excluded: chain 03 residue 189 LEU Chi-restraints excluded: chain 03 residue 216 THR Chi-restraints excluded: chain Z residue 70 ASP Chi-restraints excluded: chain Z residue 145 LEU Chi-restraints excluded: chain Z residue 216 ASP Chi-restraints excluded: chain Z residue 236 ILE Chi-restraints excluded: chain Z residue 291 VAL Chi-restraints excluded: chain Z residue 358 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1101 random chunks: chunk 989 optimal weight: 10.0000 chunk 753 optimal weight: 20.0000 chunk 519 optimal weight: 4.9990 chunk 110 optimal weight: 30.0000 chunk 478 optimal weight: 8.9990 chunk 672 optimal weight: 20.0000 chunk 1005 optimal weight: 10.0000 chunk 1064 optimal weight: 30.0000 chunk 525 optimal weight: 0.0060 chunk 952 optimal weight: 30.0000 chunk 286 optimal weight: 8.9990 overall best weight: 6.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 04 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 06 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 07 22 ASN 07 26 GLN ** 08 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 09 2 GLN ** 09 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 13 82 ASN ** 15 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 19 55 GLN 20 87 GLN ** 23 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 26 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 27 45 GLN ** 29 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 29 48 GLN 30 3 GLN ** C 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 GLN ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 8 GLN G 121 ASN ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 ASN ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 72 ASN ** O 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 03 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 03 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 251 GLN Z 319 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 166817 Z= 0.247 Angle : 0.654 13.789 249070 Z= 0.337 Chirality : 0.037 0.331 31782 Planarity : 0.005 0.075 13715 Dihedral : 23.560 179.463 82303 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 20.57 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.70 % Favored : 89.07 % Rotamer: Outliers : 5.77 % Allowed : 20.85 % Favored : 73.38 % 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: -2.71 (0.10), residues: 6366 helix: -0.69 (0.11), residues: 1941 sheet: -1.98 (0.15), residues: 1111 loop : -2.46 (0.10), residues: 3314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP P 60 HIS 0.011 0.001 HIS Z 319 PHE 0.035 0.002 PHE U 36 TYR 0.026 0.002 TYR R 22 ARG 0.010 0.001 ARG H 79 *********************** 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 1485 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 305 poor density : 1180 time to evaluate : 6.684 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 TARDY: cannot create tardy model for: "SER Z 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 04 29 PHE cc_start: 0.8875 (t80) cc_final: 0.8637 (t80) REVERT: 04 33 LEU cc_start: 0.8375 (mp) cc_final: 0.8083 (mt) REVERT: 04 97 ASP cc_start: 0.7440 (p0) cc_final: 0.7005 (p0) REVERT: 04 200 MET cc_start: 0.8215 (OUTLIER) cc_final: 0.7901 (ttt) REVERT: 07 37 MET cc_start: 0.9279 (ttm) cc_final: 0.8837 (tmm) REVERT: 07 127 TYR cc_start: 0.8255 (t80) cc_final: 0.7929 (t80) REVERT: 07 174 PHE cc_start: 0.7849 (m-10) cc_final: 0.7488 (m-10) REVERT: 09 46 PHE cc_start: 0.8487 (m-80) cc_final: 0.8096 (m-80) REVERT: 09 89 LYS cc_start: 0.8647 (mmtt) cc_final: 0.8042 (tmtt) REVERT: 09 97 ARG cc_start: 0.8911 (mmm-85) cc_final: 0.8678 (tpp80) REVERT: 09 133 GLN cc_start: 0.8979 (mt0) cc_final: 0.8388 (tm-30) REVERT: 10 1 MET cc_start: 0.3388 (tpt) cc_final: 0.3184 (tpp) REVERT: 11 116 MET cc_start: 0.3951 (mmp) cc_final: 0.1572 (ttm) REVERT: 12 14 ASP cc_start: 0.8311 (t0) cc_final: 0.8093 (t0) REVERT: 13 104 THR cc_start: 0.8693 (m) cc_final: 0.8466 (m) REVERT: 14 81 ASP cc_start: 0.8579 (t0) cc_final: 0.8309 (t70) REVERT: 14 91 ASP cc_start: 0.7693 (m-30) cc_final: 0.7162 (p0) REVERT: 14 136 GLU cc_start: 0.9079 (mm-30) cc_final: 0.8542 (pt0) REVERT: 16 2 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.7213 (ppp-140) REVERT: 16 106 ASP cc_start: 0.8087 (p0) cc_final: 0.7785 (p0) REVERT: 17 84 GLU cc_start: 0.8150 (pt0) cc_final: 0.7750 (mt-10) REVERT: 20 19 THR cc_start: 0.8678 (m) cc_final: 0.8317 (p) REVERT: 20 48 LYS cc_start: 0.8221 (ptpt) cc_final: 0.7494 (ptpt) REVERT: 20 86 GLN cc_start: 0.7997 (tt0) cc_final: 0.7738 (mt0) REVERT: 20 95 ASP cc_start: 0.8155 (m-30) cc_final: 0.7845 (m-30) REVERT: 21 1 MET cc_start: 0.8543 (tpp) cc_final: 0.8089 (tpp) REVERT: 21 66 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8397 (mt) REVERT: 22 1 MET cc_start: 0.6129 (ptm) cc_final: 0.5413 (ptp) REVERT: 22 24 MET cc_start: 0.8772 (mmm) cc_final: 0.8516 (mmm) REVERT: 22 25 GLU cc_start: 0.8414 (pp20) cc_final: 0.7994 (pp20) REVERT: 24 48 MET cc_start: 0.8986 (tpp) cc_final: 0.8728 (mpp) REVERT: 24 75 GLN cc_start: 0.8647 (tp40) cc_final: 0.8329 (tm-30) REVERT: 25 11 ASP cc_start: 0.8165 (t0) cc_final: 0.7853 (t0) REVERT: 27 2 LYS cc_start: 0.8183 (pttt) cc_final: 0.7840 (pttm) REVERT: 27 7 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8088 (tmm160) REVERT: 27 26 PHE cc_start: 0.8981 (t80) cc_final: 0.7560 (t80) REVERT: 27 45 GLN cc_start: 0.8493 (pt0) cc_final: 0.8121 (pp30) REVERT: 27 49 ASP cc_start: 0.9261 (m-30) cc_final: 0.8291 (m-30) REVERT: 29 62 LYS cc_start: 0.9252 (tppt) cc_final: 0.8825 (tptp) REVERT: 30 36 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7986 (tppt) REVERT: 31 20 TYR cc_start: 0.7999 (m-10) cc_final: 0.7757 (m-10) REVERT: 31 24 LYS cc_start: 0.8445 (tppt) cc_final: 0.8196 (tppt) REVERT: B 191 ASP cc_start: 0.8975 (t0) cc_final: 0.8550 (t0) REVERT: B 193 ASP cc_start: 0.8378 (m-30) cc_final: 0.8064 (m-30) REVERT: C 33 ASP cc_start: 0.8247 (t70) cc_final: 0.7979 (t0) REVERT: C 129 PHE cc_start: 0.9297 (p90) cc_final: 0.8927 (p90) REVERT: C 182 ASP cc_start: 0.8275 (t0) cc_final: 0.8064 (p0) REVERT: D 58 GLN cc_start: 0.8894 (mm110) cc_final: 0.8276 (mm-40) REVERT: D 170 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7775 (pp) REVERT: E 129 SER cc_start: 0.9114 (t) cc_final: 0.8780 (p) REVERT: F 21 MET cc_start: 0.8963 (mtt) cc_final: 0.8725 (mmm) REVERT: H 82 LEU cc_start: 0.9092 (tp) cc_final: 0.8879 (tt) REVERT: H 100 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8416 (mm) REVERT: H 117 GLN cc_start: 0.9159 (mt0) cc_final: 0.8877 (mp10) REVERT: H 128 VAL cc_start: 0.9033 (OUTLIER) cc_final: 0.8594 (t) REVERT: J 15 HIS cc_start: 0.9174 (OUTLIER) cc_final: 0.8973 (p-80) REVERT: L 61 GLU cc_start: 0.8056 (tp30) cc_final: 0.7732 (tm-30) REVERT: M 10 ASP cc_start: 0.8266 (t70) cc_final: 0.7495 (t0) REVERT: N 26 LEU cc_start: 0.8067 (mp) cc_final: 0.7861 (mp) REVERT: N 32 ASP cc_start: 0.8493 (OUTLIER) cc_final: 0.8102 (t0) REVERT: Q 39 ARG cc_start: 0.9170 (tpp80) cc_final: 0.8910 (tpp80) REVERT: U 30 GLU cc_start: 0.9362 (OUTLIER) cc_final: 0.9070 (pp20) REVERT: U 43 GLU cc_start: 0.8793 (tp30) cc_final: 0.8588 (tp30) REVERT: U 57 LYS cc_start: 0.9054 (mmpt) cc_final: 0.8547 (mtmt) REVERT: Z 21 ASP cc_start: 0.8120 (t70) cc_final: 0.7879 (t70) REVERT: Z 114 GLN cc_start: 0.8239 (mm-40) cc_final: 0.7996 (mp-120) REVERT: Z 215 GLU cc_start: 0.7551 (tm-30) cc_final: 0.7098 (tm-30) REVERT: Z 391 VAL cc_start: 0.6171 (OUTLIER) cc_final: 0.5818 (t) outliers start: 305 outliers final: 214 residues processed: 1338 average time/residue: 1.2832 time to fit residues: 3033.7490 Evaluate side-chains 1289 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 1063 time to evaluate : 6.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 2 VAL Chi-restraints excluded: chain 04 residue 24 HIS Chi-restraints excluded: chain 04 residue 113 ASP Chi-restraints excluded: chain 04 residue 133 ASN Chi-restraints excluded: chain 04 residue 156 SER Chi-restraints excluded: chain 04 residue 167 ASP Chi-restraints excluded: chain 04 residue 200 MET Chi-restraints excluded: chain 04 residue 249 VAL Chi-restraints excluded: chain 04 residue 258 SER Chi-restraints excluded: chain 05 residue 2 ILE Chi-restraints excluded: chain 05 residue 17 GLU Chi-restraints excluded: chain 05 residue 137 SER Chi-restraints excluded: chain 05 residue 139 SER Chi-restraints excluded: chain 05 residue 199 SER Chi-restraints excluded: chain 06 residue 70 SER Chi-restraints excluded: chain 06 residue 73 ILE Chi-restraints excluded: chain 06 residue 83 VAL Chi-restraints excluded: chain 06 residue 187 VAL Chi-restraints excluded: chain 07 residue 22 ASN Chi-restraints excluded: chain 07 residue 25 MET Chi-restraints excluded: chain 07 residue 30 VAL Chi-restraints excluded: chain 07 residue 144 LYS Chi-restraints excluded: chain 07 residue 164 GLU Chi-restraints excluded: chain 08 residue 9 VAL Chi-restraints excluded: chain 08 residue 15 ASP Chi-restraints excluded: chain 08 residue 19 ASN Chi-restraints excluded: chain 08 residue 59 ASP Chi-restraints excluded: chain 08 residue 126 THR Chi-restraints excluded: chain 08 residue 146 ASP Chi-restraints excluded: chain 08 residue 161 VAL Chi-restraints excluded: chain 09 residue 40 THR Chi-restraints excluded: chain 09 residue 47 PHE Chi-restraints excluded: chain 09 residue 99 ILE Chi-restraints excluded: chain 09 residue 115 VAL Chi-restraints excluded: chain 09 residue 134 VAL Chi-restraints excluded: chain 10 residue 27 VAL Chi-restraints excluded: chain 10 residue 82 ILE Chi-restraints excluded: chain 10 residue 106 PHE Chi-restraints excluded: chain 11 residue 46 ASP Chi-restraints excluded: chain 11 residue 63 ASP Chi-restraints excluded: chain 12 residue 12 LYS Chi-restraints excluded: chain 12 residue 25 LEU Chi-restraints excluded: chain 12 residue 57 LEU Chi-restraints excluded: chain 12 residue 131 ASN Chi-restraints excluded: chain 13 residue 28 SER Chi-restraints excluded: chain 13 residue 32 TYR Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 42 THR Chi-restraints excluded: chain 13 residue 56 ASP Chi-restraints excluded: chain 13 residue 87 LEU Chi-restraints excluded: chain 13 residue 90 ASN Chi-restraints excluded: chain 13 residue 91 SER Chi-restraints excluded: chain 14 residue 67 THR Chi-restraints excluded: chain 14 residue 85 VAL Chi-restraints excluded: chain 15 residue 7 THR Chi-restraints excluded: chain 15 residue 36 VAL Chi-restraints excluded: chain 15 residue 42 THR Chi-restraints excluded: chain 15 residue 95 LEU Chi-restraints excluded: chain 15 residue 128 THR Chi-restraints excluded: chain 15 residue 129 THR Chi-restraints excluded: chain 16 residue 2 ARG Chi-restraints excluded: chain 16 residue 33 ILE Chi-restraints excluded: chain 16 residue 34 ILE Chi-restraints excluded: chain 16 residue 76 VAL Chi-restraints excluded: chain 16 residue 89 SER Chi-restraints excluded: chain 17 residue 24 THR Chi-restraints excluded: chain 17 residue 28 VAL Chi-restraints excluded: chain 17 residue 35 ILE Chi-restraints excluded: chain 17 residue 47 VAL Chi-restraints excluded: chain 17 residue 87 ILE Chi-restraints excluded: chain 18 residue 103 THR Chi-restraints excluded: chain 18 residue 109 ILE Chi-restraints excluded: chain 19 residue 7 VAL Chi-restraints excluded: chain 19 residue 38 VAL Chi-restraints excluded: chain 19 residue 61 ILE Chi-restraints excluded: chain 19 residue 79 ILE Chi-restraints excluded: chain 19 residue 108 LEU Chi-restraints excluded: chain 20 residue 29 THR Chi-restraints excluded: chain 20 residue 99 THR Chi-restraints excluded: chain 21 residue 3 THR Chi-restraints excluded: chain 21 residue 4 ILE Chi-restraints excluded: chain 21 residue 12 SER Chi-restraints excluded: chain 21 residue 39 THR Chi-restraints excluded: chain 21 residue 66 ILE Chi-restraints excluded: chain 21 residue 67 ASP Chi-restraints excluded: chain 21 residue 81 SER Chi-restraints excluded: chain 21 residue 82 MET Chi-restraints excluded: chain 22 residue 31 VAL Chi-restraints excluded: chain 22 residue 32 LEU Chi-restraints excluded: chain 22 residue 39 THR Chi-restraints excluded: chain 22 residue 76 ARG Chi-restraints excluded: chain 22 residue 89 GLU Chi-restraints excluded: chain 22 residue 92 ASN Chi-restraints excluded: chain 25 residue 25 GLU Chi-restraints excluded: chain 25 residue 26 SER Chi-restraints excluded: chain 25 residue 27 VAL Chi-restraints excluded: chain 25 residue 34 VAL Chi-restraints excluded: chain 26 residue 24 THR Chi-restraints excluded: chain 26 residue 58 ILE Chi-restraints excluded: chain 26 residue 61 LYS Chi-restraints excluded: chain 26 residue 71 ARG Chi-restraints excluded: chain 27 residue 7 ARG Chi-restraints excluded: chain 27 residue 13 GLU Chi-restraints excluded: chain 27 residue 15 ASN Chi-restraints excluded: chain 28 residue 9 THR Chi-restraints excluded: chain 28 residue 24 LEU Chi-restraints excluded: chain 29 residue 27 THR Chi-restraints excluded: chain 29 residue 58 ASP Chi-restraints excluded: chain 30 residue 22 THR Chi-restraints excluded: chain 30 residue 24 VAL Chi-restraints excluded: chain 30 residue 28 SER Chi-restraints excluded: chain 30 residue 36 LYS Chi-restraints excluded: chain 30 residue 45 ASP Chi-restraints excluded: chain 33 residue 49 VAL Chi-restraints excluded: chain 33 residue 54 LEU Chi-restraints excluded: chain 34 residue 17 VAL Chi-restraints excluded: chain 34 residue 22 VAL Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain C residue 7 ASN Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 10 LYS Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 61 PHE Chi-restraints excluded: chain G residue 115 MET Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain J residue 15 HIS Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain K residue 17 ASP Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 102 ASP Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 11 HIS Chi-restraints excluded: chain M residue 77 LYS Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain N residue 32 ASP Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain O residue 10 ILE Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 46 LYS Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain P residue 55 ASP Chi-restraints excluded: chain Q residue 7 LEU Chi-restraints excluded: chain Q residue 21 VAL Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain S residue 10 ILE Chi-restraints excluded: chain S residue 42 ASN Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 31 ILE Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain T residue 43 LYS Chi-restraints excluded: chain T residue 66 ILE Chi-restraints excluded: chain T residue 73 ARG Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 30 GLU Chi-restraints excluded: chain U residue 34 ARG Chi-restraints excluded: chain 03 residue 18 THR Chi-restraints excluded: chain 03 residue 189 LEU Chi-restraints excluded: chain 03 residue 216 THR Chi-restraints excluded: chain Z residue 136 LYS Chi-restraints excluded: chain Z residue 145 LEU Chi-restraints excluded: chain Z residue 216 ASP Chi-restraints excluded: chain Z residue 221 SER Chi-restraints excluded: chain Z residue 236 ILE Chi-restraints excluded: chain Z residue 319 HIS Chi-restraints excluded: chain Z residue 358 MET Chi-restraints excluded: chain Z residue 391 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: 20.0000 chunk 792 optimal weight: 20.0000 chunk 439 optimal weight: 10.0000 chunk 908 optimal weight: 20.0000 chunk 735 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 543 optimal weight: 6.9990 chunk 955 optimal weight: 50.0000 chunk 268 optimal weight: 10.0000 overall best weight: 11.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 04 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 04 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 06 9 GLN ** 07 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 13 82 ASN ** 15 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 18 6 GLN 19 55 GLN 20 87 GLN ** 23 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 26 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 29 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 29 48 GLN 30 3 GLN 31 44 GLN C 18 ASN ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 ASN ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 HIS ** O 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 53 GLN ** T 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 03 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 03 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 63 ASN Z 90 ASN Z 251 GLN Z 319 HIS Z 329 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 166817 Z= 0.388 Angle : 0.741 13.166 249070 Z= 0.379 Chirality : 0.040 0.360 31782 Planarity : 0.006 0.071 13715 Dihedral : 23.703 178.609 82303 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 26.25 Ramachandran Plot: Outliers : 0.20 % Allowed : 12.50 % Favored : 87.29 % Rotamer: Outliers : 6.94 % Allowed : 21.59 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.10), residues: 6366 helix: -0.72 (0.11), residues: 1952 sheet: -1.92 (0.15), residues: 1128 loop : -2.46 (0.10), residues: 3286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP P 60 HIS 0.029 0.002 HIS Z 319 PHE 0.046 0.002 PHE B 49 TYR 0.033 0.002 TYR R 63 ARG 0.011 0.001 ARG D 127 *********************** 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 1440 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 367 poor density : 1073 time to evaluate : 8.595 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 TARDY: cannot create tardy model for: "SER Z 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: 04 29 PHE cc_start: 0.8912 (t80) cc_final: 0.8689 (t80) REVERT: 04 33 LEU cc_start: 0.8426 (mp) cc_final: 0.8222 (mt) REVERT: 04 97 ASP cc_start: 0.7646 (p0) cc_final: 0.7224 (p0) REVERT: 04 200 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.8001 (ttt) REVERT: 07 37 MET cc_start: 0.9286 (ttm) cc_final: 0.8783 (tmm) REVERT: 07 127 TYR cc_start: 0.8338 (t80) cc_final: 0.7841 (t80) REVERT: 07 174 PHE cc_start: 0.8052 (m-10) cc_final: 0.7757 (m-80) REVERT: 08 71 LEU cc_start: 0.9575 (OUTLIER) cc_final: 0.9363 (mm) REVERT: 09 86 ASP cc_start: 0.8600 (t0) cc_final: 0.8340 (t0) REVERT: 09 97 ARG cc_start: 0.8875 (mmm-85) cc_final: 0.8573 (tpp80) REVERT: 09 128 HIS cc_start: 0.7932 (m-70) cc_final: 0.7568 (m90) REVERT: 11 116 MET cc_start: 0.4063 (mmp) cc_final: 0.1763 (ttt) REVERT: 12 16 TYR cc_start: 0.8378 (m-80) cc_final: 0.8135 (m-10) REVERT: 12 108 MET cc_start: 0.7935 (mtt) cc_final: 0.7676 (mtt) REVERT: 14 81 ASP cc_start: 0.8537 (t0) cc_final: 0.8211 (t70) REVERT: 14 91 ASP cc_start: 0.7864 (m-30) cc_final: 0.7057 (p0) REVERT: 14 136 GLU cc_start: 0.9078 (mm-30) cc_final: 0.8591 (pt0) REVERT: 15 111 GLU cc_start: 0.8568 (tm-30) cc_final: 0.8274 (tm-30) REVERT: 16 2 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.7272 (ppp-140) REVERT: 16 106 ASP cc_start: 0.8197 (p0) cc_final: 0.7884 (p0) REVERT: 20 86 GLN cc_start: 0.7977 (tt0) cc_final: 0.7748 (mt0) REVERT: 21 1 MET cc_start: 0.8501 (tpp) cc_final: 0.8165 (mmm) REVERT: 21 66 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8404 (mt) REVERT: 22 1 MET cc_start: 0.6310 (ptm) cc_final: 0.5720 (ptp) REVERT: 22 24 MET cc_start: 0.8829 (mmm) cc_final: 0.8593 (mmm) REVERT: 23 102 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7607 (mp) REVERT: 25 11 ASP cc_start: 0.8281 (t0) cc_final: 0.7921 (t0) REVERT: 26 71 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8317 (mtp-110) REVERT: 27 7 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.8296 (tmm160) REVERT: 27 26 PHE cc_start: 0.8929 (t80) cc_final: 0.8264 (t80) REVERT: 27 45 GLN cc_start: 0.8533 (pt0) cc_final: 0.8146 (pp30) REVERT: 27 49 ASP cc_start: 0.9263 (m-30) cc_final: 0.8279 (m-30) REVERT: 29 62 LYS cc_start: 0.9263 (tppt) cc_final: 0.8946 (tptp) REVERT: 30 36 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8096 (tppt) REVERT: 31 20 TYR cc_start: 0.8145 (m-10) cc_final: 0.7875 (m-10) REVERT: B 191 ASP cc_start: 0.9003 (t0) cc_final: 0.8579 (t0) REVERT: B 193 ASP cc_start: 0.8398 (m-30) cc_final: 0.8072 (m-30) REVERT: C 33 ASP cc_start: 0.8219 (t70) cc_final: 0.7969 (t0) REVERT: C 129 PHE cc_start: 0.9289 (p90) cc_final: 0.9008 (p90) REVERT: C 182 ASP cc_start: 0.8355 (t0) cc_final: 0.8073 (p0) REVERT: D 97 LEU cc_start: 0.9141 (tp) cc_final: 0.8890 (tt) REVERT: D 177 MET cc_start: 0.8361 (mpp) cc_final: 0.8095 (mpp) REVERT: E 129 SER cc_start: 0.9135 (t) cc_final: 0.8778 (p) REVERT: H 128 VAL cc_start: 0.9011 (OUTLIER) cc_final: 0.8740 (t) REVERT: I 58 GLU cc_start: 0.8646 (tp30) cc_final: 0.7892 (tp30) REVERT: I 117 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8939 (tp) REVERT: K 57 SER cc_start: 0.9326 (m) cc_final: 0.9083 (m) REVERT: L 37 TYR cc_start: 0.8674 (p90) cc_final: 0.8371 (p90) REVERT: L 61 GLU cc_start: 0.8066 (tp30) cc_final: 0.7793 (tm-30) REVERT: M 10 ASP cc_start: 0.8346 (t70) cc_final: 0.7582 (t0) REVERT: N 88 MET cc_start: 0.8353 (mmt) cc_final: 0.8113 (mmt) REVERT: P 29 ASN cc_start: 0.8893 (OUTLIER) cc_final: 0.8550 (m-40) REVERT: U 30 GLU cc_start: 0.9365 (OUTLIER) cc_final: 0.9050 (pp20) REVERT: U 43 GLU cc_start: 0.8845 (tp30) cc_final: 0.8541 (tp30) REVERT: U 63 ASN cc_start: 0.7293 (m110) cc_final: 0.7046 (m110) REVERT: Z 21 ASP cc_start: 0.8120 (t70) cc_final: 0.7863 (t70) REVERT: Z 70 ASP cc_start: 0.7042 (OUTLIER) cc_final: 0.6766 (m-30) REVERT: Z 114 GLN cc_start: 0.8255 (mm-40) cc_final: 0.8050 (mp-120) REVERT: Z 160 TYR cc_start: 0.5728 (m-80) cc_final: 0.5304 (m-80) REVERT: Z 319 HIS cc_start: 0.5518 (OUTLIER) cc_final: 0.4898 (p-80) REVERT: Z 391 VAL cc_start: 0.6359 (OUTLIER) cc_final: 0.6005 (t) outliers start: 367 outliers final: 273 residues processed: 1288 average time/residue: 1.2888 time to fit residues: 2942.5785 Evaluate side-chains 1301 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 288 poor density : 1013 time to evaluate : 6.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 2 VAL Chi-restraints excluded: chain 04 residue 24 HIS Chi-restraints excluded: chain 04 residue 44 ASN Chi-restraints excluded: chain 04 residue 50 THR Chi-restraints excluded: chain 04 residue 113 ASP Chi-restraints excluded: chain 04 residue 133 ASN Chi-restraints excluded: chain 04 residue 156 SER Chi-restraints excluded: chain 04 residue 167 ASP Chi-restraints excluded: chain 04 residue 200 MET Chi-restraints excluded: chain 04 residue 249 VAL Chi-restraints excluded: chain 04 residue 258 SER Chi-restraints excluded: chain 04 residue 267 VAL Chi-restraints excluded: chain 05 residue 2 ILE Chi-restraints excluded: chain 05 residue 91 THR Chi-restraints excluded: chain 05 residue 104 VAL Chi-restraints excluded: chain 05 residue 137 SER Chi-restraints excluded: chain 05 residue 139 SER Chi-restraints excluded: chain 05 residue 186 LEU Chi-restraints excluded: chain 05 residue 199 SER Chi-restraints excluded: chain 06 residue 70 SER Chi-restraints excluded: chain 06 residue 73 ILE Chi-restraints excluded: chain 06 residue 83 VAL Chi-restraints excluded: chain 06 residue 97 ASN Chi-restraints excluded: chain 06 residue 187 VAL Chi-restraints excluded: chain 07 residue 25 MET Chi-restraints excluded: chain 07 residue 30 VAL Chi-restraints excluded: chain 07 residue 144 LYS Chi-restraints excluded: chain 07 residue 164 GLU Chi-restraints excluded: chain 08 residue 9 VAL Chi-restraints excluded: chain 08 residue 15 ASP Chi-restraints excluded: chain 08 residue 19 ASN Chi-restraints excluded: chain 08 residue 44 HIS Chi-restraints excluded: chain 08 residue 55 ASP Chi-restraints excluded: chain 08 residue 59 ASP Chi-restraints excluded: chain 08 residue 71 LEU Chi-restraints excluded: chain 08 residue 126 THR Chi-restraints excluded: chain 08 residue 146 ASP Chi-restraints excluded: chain 08 residue 161 VAL Chi-restraints excluded: chain 08 residue 167 VAL Chi-restraints excluded: chain 09 residue 40 THR Chi-restraints excluded: chain 09 residue 47 PHE Chi-restraints excluded: chain 09 residue 50 ARG Chi-restraints excluded: chain 09 residue 91 PHE Chi-restraints excluded: chain 09 residue 99 ILE Chi-restraints excluded: chain 09 residue 115 VAL Chi-restraints excluded: chain 09 residue 134 VAL Chi-restraints excluded: chain 10 residue 27 VAL Chi-restraints excluded: chain 10 residue 50 VAL Chi-restraints excluded: chain 10 residue 82 ILE Chi-restraints excluded: chain 10 residue 108 VAL Chi-restraints excluded: chain 10 residue 128 THR Chi-restraints excluded: chain 11 residue 46 ASP Chi-restraints excluded: chain 11 residue 63 ASP Chi-restraints excluded: chain 12 residue 12 LYS Chi-restraints excluded: chain 12 residue 25 LEU Chi-restraints excluded: chain 12 residue 50 THR Chi-restraints excluded: chain 12 residue 57 LEU Chi-restraints excluded: chain 12 residue 131 ASN Chi-restraints excluded: chain 13 residue 13 ASN Chi-restraints excluded: chain 13 residue 21 CYS Chi-restraints excluded: chain 13 residue 28 SER Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 56 ASP Chi-restraints excluded: chain 13 residue 87 LEU Chi-restraints excluded: chain 13 residue 90 ASN Chi-restraints excluded: chain 13 residue 91 SER Chi-restraints excluded: chain 14 residue 5 THR Chi-restraints excluded: chain 14 residue 27 LEU Chi-restraints excluded: chain 14 residue 67 THR Chi-restraints excluded: chain 14 residue 85 VAL Chi-restraints excluded: chain 15 residue 7 THR Chi-restraints excluded: chain 15 residue 36 VAL Chi-restraints excluded: chain 15 residue 42 THR Chi-restraints excluded: chain 15 residue 78 LEU Chi-restraints excluded: chain 15 residue 95 LEU Chi-restraints excluded: chain 15 residue 128 THR Chi-restraints excluded: chain 15 residue 129 THR Chi-restraints excluded: chain 16 residue 2 ARG Chi-restraints excluded: chain 16 residue 33 ILE Chi-restraints excluded: chain 16 residue 34 ILE Chi-restraints excluded: chain 16 residue 72 ASP Chi-restraints excluded: chain 16 residue 76 VAL Chi-restraints excluded: chain 16 residue 83 LEU Chi-restraints excluded: chain 16 residue 89 SER Chi-restraints excluded: chain 17 residue 28 VAL Chi-restraints excluded: chain 17 residue 35 ILE Chi-restraints excluded: chain 17 residue 47 VAL Chi-restraints excluded: chain 17 residue 87 ILE Chi-restraints excluded: chain 18 residue 31 VAL Chi-restraints excluded: chain 18 residue 43 GLU Chi-restraints excluded: chain 18 residue 47 ILE Chi-restraints excluded: chain 18 residue 59 THR Chi-restraints excluded: chain 18 residue 100 ARG Chi-restraints excluded: chain 18 residue 103 THR Chi-restraints excluded: chain 18 residue 109 ILE Chi-restraints excluded: chain 19 residue 7 VAL Chi-restraints excluded: chain 19 residue 38 VAL Chi-restraints excluded: chain 19 residue 61 ILE Chi-restraints excluded: chain 19 residue 79 ILE Chi-restraints excluded: chain 19 residue 103 VAL Chi-restraints excluded: chain 19 residue 108 LEU Chi-restraints excluded: chain 20 residue 10 LYS Chi-restraints excluded: chain 20 residue 29 THR Chi-restraints excluded: chain 20 residue 99 THR Chi-restraints excluded: chain 20 residue 102 SER Chi-restraints excluded: chain 21 residue 3 THR Chi-restraints excluded: chain 21 residue 4 ILE Chi-restraints excluded: chain 21 residue 12 SER Chi-restraints excluded: chain 21 residue 39 THR Chi-restraints excluded: chain 21 residue 66 ILE Chi-restraints excluded: chain 21 residue 81 SER Chi-restraints excluded: chain 21 residue 82 MET Chi-restraints excluded: chain 22 residue 31 VAL Chi-restraints excluded: chain 22 residue 32 LEU Chi-restraints excluded: chain 22 residue 39 THR Chi-restraints excluded: chain 22 residue 76 ARG Chi-restraints excluded: chain 22 residue 79 ASP Chi-restraints excluded: chain 22 residue 92 ASN Chi-restraints excluded: chain 23 residue 102 ILE Chi-restraints excluded: chain 24 residue 30 ILE Chi-restraints excluded: chain 25 residue 25 GLU Chi-restraints excluded: chain 25 residue 26 SER Chi-restraints excluded: chain 25 residue 34 VAL Chi-restraints excluded: chain 26 residue 24 THR Chi-restraints excluded: chain 26 residue 29 LEU Chi-restraints excluded: chain 26 residue 58 ILE Chi-restraints excluded: chain 26 residue 71 ARG Chi-restraints excluded: chain 27 residue 7 ARG Chi-restraints excluded: chain 27 residue 13 GLU Chi-restraints excluded: chain 27 residue 15 ASN Chi-restraints excluded: chain 27 residue 27 ASN Chi-restraints excluded: chain 27 residue 50 VAL Chi-restraints excluded: chain 28 residue 9 THR Chi-restraints excluded: chain 28 residue 24 LEU Chi-restraints excluded: chain 29 residue 16 CYS Chi-restraints excluded: chain 29 residue 20 ASN Chi-restraints excluded: chain 29 residue 27 THR Chi-restraints excluded: chain 29 residue 58 ASP Chi-restraints excluded: chain 30 residue 8 THR Chi-restraints excluded: chain 30 residue 22 THR Chi-restraints excluded: chain 30 residue 24 VAL Chi-restraints excluded: chain 30 residue 28 SER Chi-restraints excluded: chain 30 residue 36 LYS Chi-restraints excluded: chain 30 residue 45 ASP Chi-restraints excluded: chain 30 residue 53 VAL Chi-restraints excluded: chain 31 residue 8 ILE Chi-restraints excluded: chain 33 residue 5 THR Chi-restraints excluded: chain 33 residue 49 VAL Chi-restraints excluded: chain 34 residue 17 VAL Chi-restraints excluded: chain 34 residue 22 VAL Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain C residue 7 ASN Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 61 PHE Chi-restraints excluded: chain G residue 115 MET Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain I residue 21 LYS Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain I residue 117 LEU Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain K residue 17 ASP Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 102 ASP Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 11 HIS Chi-restraints excluded: chain M residue 22 TYR Chi-restraints excluded: chain M residue 44 ILE Chi-restraints excluded: chain M residue 61 LYS Chi-restraints excluded: chain M residue 77 LYS Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 79 SER Chi-restraints excluded: chain O residue 10 ILE Chi-restraints excluded: chain O residue 17 ASP Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 46 LYS Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 29 ASN Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain P residue 55 ASP Chi-restraints excluded: chain Q residue 21 VAL Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 60 ILE Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain S residue 10 ILE Chi-restraints excluded: chain S residue 11 ASP Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 42 ASN Chi-restraints excluded: chain S residue 70 LEU Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 31 ILE Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain T residue 43 LYS Chi-restraints excluded: chain T residue 66 ILE Chi-restraints excluded: chain T residue 73 ARG Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain U residue 12 ASP Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 30 GLU Chi-restraints excluded: chain U residue 34 ARG Chi-restraints excluded: chain 03 residue 16 ASP Chi-restraints excluded: chain 03 residue 18 THR Chi-restraints excluded: chain 03 residue 189 LEU Chi-restraints excluded: chain 03 residue 216 THR Chi-restraints excluded: chain Z residue 70 ASP Chi-restraints excluded: chain Z residue 136 LYS Chi-restraints excluded: chain Z residue 145 LEU Chi-restraints excluded: chain Z residue 216 ASP Chi-restraints excluded: chain Z residue 221 SER Chi-restraints excluded: chain Z residue 236 ILE Chi-restraints excluded: chain Z residue 244 ILE Chi-restraints excluded: chain Z residue 291 VAL Chi-restraints excluded: chain Z residue 319 HIS Chi-restraints excluded: chain Z residue 358 MET Chi-restraints excluded: chain Z residue 391 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1101 random chunks: chunk 358 optimal weight: 4.9990 chunk 958 optimal weight: 20.0000 chunk 210 optimal weight: 7.9990 chunk 624 optimal weight: 20.0000 chunk 262 optimal weight: 20.0000 chunk 1065 optimal weight: 50.0000 chunk 884 optimal weight: 20.0000 chunk 493 optimal weight: 20.0000 chunk 88 optimal weight: 20.0000 chunk 352 optimal weight: 9.9990 chunk 559 optimal weight: 5.9990 overall best weight: 9.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 04 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 04 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 06 165 HIS ** 07 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 09 133 GLN 09 135 HIS 13 82 ASN ** 15 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 17 116 GLN ** 18 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 19 36 GLN 19 55 GLN 20 87 GLN ** 23 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 27 45 GLN ** 29 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 29 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 30 3 GLN ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 56 HIS ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 03 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 251 GLN Z 319 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 166817 Z= 0.333 Angle : 0.700 13.474 249070 Z= 0.359 Chirality : 0.039 0.360 31782 Planarity : 0.005 0.072 13715 Dihedral : 23.767 179.540 82303 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 24.51 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.55 % Favored : 88.28 % Rotamer: Outliers : 6.73 % Allowed : 23.31 % Favored : 69.96 % 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: -2.59 (0.10), residues: 6366 helix: -0.60 (0.11), residues: 1969 sheet: -1.88 (0.15), residues: 1115 loop : -2.40 (0.10), residues: 3282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP P 60 HIS 0.024 0.002 HIS Z 319 PHE 0.038 0.002 PHE B 49 TYR 0.025 0.002 TYR M 85 ARG 0.014 0.001 ARG31 43 *********************** 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 1415 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 356 poor density : 1059 time to evaluate : 6.872 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: 04 29 PHE cc_start: 0.8927 (t80) cc_final: 0.8706 (t80) REVERT: 04 97 ASP cc_start: 0.7677 (p0) cc_final: 0.7219 (p0) REVERT: 04 200 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7956 (ttt) REVERT: 07 6 TYR cc_start: 0.8595 (t80) cc_final: 0.8324 (t80) REVERT: 07 37 MET cc_start: 0.9283 (ttm) cc_final: 0.8741 (tmm) REVERT: 07 99 PHE cc_start: 0.9160 (t80) cc_final: 0.8939 (t80) REVERT: 07 127 TYR cc_start: 0.8229 (t80) cc_final: 0.7768 (t80) REVERT: 07 174 PHE cc_start: 0.8074 (m-10) cc_final: 0.7819 (m-80) REVERT: 08 71 LEU cc_start: 0.9575 (OUTLIER) cc_final: 0.9367 (mm) REVERT: 08 87 GLN cc_start: 0.8628 (pm20) cc_final: 0.8189 (pm20) REVERT: 09 86 ASP cc_start: 0.8675 (t0) cc_final: 0.8423 (t0) REVERT: 09 97 ARG cc_start: 0.8887 (mmm-85) cc_final: 0.8566 (tpp80) REVERT: 09 133 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.8685 (tp-100) REVERT: 10 52 MET cc_start: 0.2663 (mtm) cc_final: 0.2397 (ptp) REVERT: 11 116 MET cc_start: 0.3998 (mmp) cc_final: 0.1622 (ttt) REVERT: 12 108 MET cc_start: 0.7951 (mtt) cc_final: 0.7668 (mtt) REVERT: 14 81 ASP cc_start: 0.8552 (t0) cc_final: 0.8323 (t70) REVERT: 14 136 GLU cc_start: 0.9073 (OUTLIER) cc_final: 0.8580 (pt0) REVERT: 16 2 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.7352 (ppp-140) REVERT: 16 106 ASP cc_start: 0.8188 (p0) cc_final: 0.7835 (p0) REVERT: 20 86 GLN cc_start: 0.8001 (tt0) cc_final: 0.7754 (mt0) REVERT: 21 1 MET cc_start: 0.8536 (tpp) cc_final: 0.8190 (mmm) REVERT: 21 66 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8386 (mt) REVERT: 22 1 MET cc_start: 0.6260 (ptm) cc_final: 0.5698 (ptp) REVERT: 22 24 MET cc_start: 0.8805 (mmm) cc_final: 0.8589 (mmm) REVERT: 23 102 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7726 (mp) REVERT: 25 11 ASP cc_start: 0.8258 (t0) cc_final: 0.7884 (t0) REVERT: 26 65 THR cc_start: 0.9225 (m) cc_final: 0.9021 (p) REVERT: 27 7 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8277 (tmm160) REVERT: 27 45 GLN cc_start: 0.8462 (pt0) cc_final: 0.8077 (pp30) REVERT: 27 49 ASP cc_start: 0.9232 (m-30) cc_final: 0.8223 (m-30) REVERT: 29 62 LYS cc_start: 0.9318 (tppt) cc_final: 0.9022 (tptp) REVERT: 30 36 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8081 (tppt) REVERT: 31 20 TYR cc_start: 0.8112 (m-10) cc_final: 0.7838 (m-10) REVERT: 31 24 LYS cc_start: 0.8442 (tppt) cc_final: 0.8203 (tppt) REVERT: 32 26 ASN cc_start: 0.8531 (t0) cc_final: 0.8302 (t0) REVERT: 33 48 MET cc_start: 0.8366 (mtt) cc_final: 0.8087 (mtt) REVERT: B 42 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8557 (pp) REVERT: B 191 ASP cc_start: 0.9047 (t0) cc_final: 0.8561 (t0) REVERT: B 193 ASP cc_start: 0.8370 (m-30) cc_final: 0.8028 (m-30) REVERT: C 33 ASP cc_start: 0.8171 (t70) cc_final: 0.7918 (t0) REVERT: C 129 PHE cc_start: 0.9285 (p90) cc_final: 0.8997 (p90) REVERT: C 182 ASP cc_start: 0.8342 (t0) cc_final: 0.8062 (p0) REVERT: D 97 LEU cc_start: 0.9131 (tp) cc_final: 0.8890 (tt) REVERT: D 177 MET cc_start: 0.8431 (mpp) cc_final: 0.8199 (mpp) REVERT: E 45 VAL cc_start: 0.8738 (OUTLIER) cc_final: 0.8504 (t) REVERT: E 67 ARG cc_start: 0.9059 (mmm160) cc_final: 0.8844 (mmm160) REVERT: E 129 SER cc_start: 0.9101 (t) cc_final: 0.8731 (p) REVERT: F 21 MET cc_start: 0.8703 (mmm) cc_final: 0.8433 (mmm) REVERT: F 62 MET cc_start: 0.9296 (mtp) cc_final: 0.9023 (tpp) REVERT: F 80 PHE cc_start: 0.8310 (m-80) cc_final: 0.8052 (m-80) REVERT: H 51 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8093 (pt0) REVERT: I 128 LYS cc_start: 0.8084 (ttmt) cc_final: 0.7879 (tttt) REVERT: J 30 LYS cc_start: 0.8610 (pttp) cc_final: 0.8380 (ttpp) REVERT: K 57 SER cc_start: 0.9351 (m) cc_final: 0.9112 (m) REVERT: L 61 GLU cc_start: 0.8001 (tp30) cc_final: 0.7764 (tm-30) REVERT: M 10 ASP cc_start: 0.8375 (t0) cc_final: 0.7546 (t0) REVERT: N 32 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.8105 (t0) REVERT: N 38 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8320 (tm-30) REVERT: P 29 ASN cc_start: 0.8883 (OUTLIER) cc_final: 0.8624 (m-40) REVERT: U 30 GLU cc_start: 0.9342 (OUTLIER) cc_final: 0.9044 (pp20) REVERT: U 43 GLU cc_start: 0.8861 (tp30) cc_final: 0.8496 (tp30) REVERT: U 57 LYS cc_start: 0.9098 (mmpt) cc_final: 0.8443 (mtmt) REVERT: Z 21 ASP cc_start: 0.8042 (t70) cc_final: 0.7782 (t70) REVERT: Z 39 TYR cc_start: 0.8032 (t80) cc_final: 0.7534 (t80) REVERT: Z 91 MET cc_start: 0.9065 (tpt) cc_final: 0.8731 (tpt) REVERT: Z 160 TYR cc_start: 0.5710 (m-80) cc_final: 0.5415 (m-80) REVERT: Z 391 VAL cc_start: 0.6353 (OUTLIER) cc_final: 0.6009 (t) outliers start: 356 outliers final: 279 residues processed: 1268 average time/residue: 1.2925 time to fit residues: 2906.4517 Evaluate side-chains 1308 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 295 poor density : 1013 time to evaluate : 5.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 2 VAL Chi-restraints excluded: chain 04 residue 24 HIS Chi-restraints excluded: chain 04 residue 44 ASN Chi-restraints excluded: chain 04 residue 99 GLU Chi-restraints excluded: chain 04 residue 113 ASP Chi-restraints excluded: chain 04 residue 133 ASN Chi-restraints excluded: chain 04 residue 167 ASP Chi-restraints excluded: chain 04 residue 200 MET Chi-restraints excluded: chain 04 residue 249 VAL Chi-restraints excluded: chain 04 residue 258 SER Chi-restraints excluded: chain 04 residue 263 ASP Chi-restraints excluded: chain 04 residue 267 VAL Chi-restraints excluded: chain 05 residue 2 ILE Chi-restraints excluded: chain 05 residue 91 THR Chi-restraints excluded: chain 05 residue 104 VAL Chi-restraints excluded: chain 05 residue 137 SER Chi-restraints excluded: chain 05 residue 139 SER Chi-restraints excluded: chain 05 residue 186 LEU Chi-restraints excluded: chain 05 residue 199 SER Chi-restraints excluded: chain 06 residue 70 SER Chi-restraints excluded: chain 06 residue 73 ILE Chi-restraints excluded: chain 06 residue 83 VAL Chi-restraints excluded: chain 06 residue 119 ILE Chi-restraints excluded: chain 06 residue 187 VAL Chi-restraints excluded: chain 07 residue 22 ASN Chi-restraints excluded: chain 07 residue 25 MET Chi-restraints excluded: chain 07 residue 30 VAL Chi-restraints excluded: chain 07 residue 144 LYS Chi-restraints excluded: chain 07 residue 146 ASP Chi-restraints excluded: chain 07 residue 164 GLU Chi-restraints excluded: chain 08 residue 9 VAL Chi-restraints excluded: chain 08 residue 15 ASP Chi-restraints excluded: chain 08 residue 19 ASN Chi-restraints excluded: chain 08 residue 44 HIS Chi-restraints excluded: chain 08 residue 55 ASP Chi-restraints excluded: chain 08 residue 59 ASP Chi-restraints excluded: chain 08 residue 71 LEU Chi-restraints excluded: chain 08 residue 126 THR Chi-restraints excluded: chain 08 residue 146 ASP Chi-restraints excluded: chain 08 residue 161 VAL Chi-restraints excluded: chain 08 residue 167 VAL Chi-restraints excluded: chain 09 residue 8 LYS Chi-restraints excluded: chain 09 residue 40 THR Chi-restraints excluded: chain 09 residue 47 PHE Chi-restraints excluded: chain 09 residue 91 PHE Chi-restraints excluded: chain 09 residue 99 ILE Chi-restraints excluded: chain 09 residue 115 VAL Chi-restraints excluded: chain 09 residue 133 GLN Chi-restraints excluded: chain 09 residue 134 VAL Chi-restraints excluded: chain 10 residue 27 VAL Chi-restraints excluded: chain 10 residue 50 VAL Chi-restraints excluded: chain 10 residue 77 VAL Chi-restraints excluded: chain 10 residue 82 ILE Chi-restraints excluded: chain 10 residue 118 ILE Chi-restraints excluded: chain 11 residue 41 PHE Chi-restraints excluded: chain 11 residue 46 ASP Chi-restraints excluded: chain 11 residue 63 ASP Chi-restraints excluded: chain 12 residue 12 LYS Chi-restraints excluded: chain 12 residue 25 LEU Chi-restraints excluded: chain 12 residue 50 THR Chi-restraints excluded: chain 12 residue 57 LEU Chi-restraints excluded: chain 12 residue 93 ILE Chi-restraints excluded: chain 12 residue 131 ASN Chi-restraints excluded: chain 13 residue 13 ASN Chi-restraints excluded: chain 13 residue 28 SER Chi-restraints excluded: chain 13 residue 32 TYR Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 56 ASP Chi-restraints excluded: chain 13 residue 87 LEU Chi-restraints excluded: chain 13 residue 90 ASN Chi-restraints excluded: chain 13 residue 91 SER Chi-restraints excluded: chain 14 residue 7 SER Chi-restraints excluded: chain 14 residue 27 LEU Chi-restraints excluded: chain 14 residue 67 THR Chi-restraints excluded: chain 14 residue 73 ILE Chi-restraints excluded: chain 14 residue 85 VAL Chi-restraints excluded: chain 14 residue 136 GLU Chi-restraints excluded: chain 15 residue 7 THR Chi-restraints excluded: chain 15 residue 36 VAL Chi-restraints excluded: chain 15 residue 42 THR Chi-restraints excluded: chain 15 residue 78 LEU Chi-restraints excluded: chain 15 residue 95 LEU Chi-restraints excluded: chain 15 residue 115 GLU Chi-restraints excluded: chain 15 residue 128 THR Chi-restraints excluded: chain 15 residue 129 THR Chi-restraints excluded: chain 16 residue 2 ARG Chi-restraints excluded: chain 16 residue 33 ILE Chi-restraints excluded: chain 16 residue 34 ILE Chi-restraints excluded: chain 16 residue 72 ASP Chi-restraints excluded: chain 16 residue 76 VAL Chi-restraints excluded: chain 16 residue 89 SER Chi-restraints excluded: chain 17 residue 28 VAL Chi-restraints excluded: chain 17 residue 35 ILE Chi-restraints excluded: chain 17 residue 47 VAL Chi-restraints excluded: chain 17 residue 87 ILE Chi-restraints excluded: chain 18 residue 31 VAL Chi-restraints excluded: chain 18 residue 43 GLU Chi-restraints excluded: chain 18 residue 47 ILE Chi-restraints excluded: chain 18 residue 59 THR Chi-restraints excluded: chain 18 residue 100 ARG Chi-restraints excluded: chain 18 residue 103 THR Chi-restraints excluded: chain 18 residue 109 ILE Chi-restraints excluded: chain 18 residue 114 ASN Chi-restraints excluded: chain 19 residue 7 VAL Chi-restraints excluded: chain 19 residue 38 VAL Chi-restraints excluded: chain 19 residue 61 ILE Chi-restraints excluded: chain 19 residue 79 ILE Chi-restraints excluded: chain 19 residue 103 VAL Chi-restraints excluded: chain 19 residue 108 LEU Chi-restraints excluded: chain 19 residue 110 GLU Chi-restraints excluded: chain 20 residue 29 THR Chi-restraints excluded: chain 20 residue 51 VAL Chi-restraints excluded: chain 20 residue 99 THR Chi-restraints excluded: chain 20 residue 102 SER Chi-restraints excluded: chain 21 residue 3 THR Chi-restraints excluded: chain 21 residue 4 ILE Chi-restraints excluded: chain 21 residue 12 SER Chi-restraints excluded: chain 21 residue 39 THR Chi-restraints excluded: chain 21 residue 66 ILE Chi-restraints excluded: chain 21 residue 67 ASP Chi-restraints excluded: chain 21 residue 81 SER Chi-restraints excluded: chain 21 residue 82 MET Chi-restraints excluded: chain 22 residue 31 VAL Chi-restraints excluded: chain 22 residue 32 LEU Chi-restraints excluded: chain 22 residue 39 THR Chi-restraints excluded: chain 22 residue 76 ARG Chi-restraints excluded: chain 22 residue 92 ASN Chi-restraints excluded: chain 23 residue 102 ILE Chi-restraints excluded: chain 24 residue 30 ILE Chi-restraints excluded: chain 25 residue 25 GLU Chi-restraints excluded: chain 25 residue 26 SER Chi-restraints excluded: chain 25 residue 34 VAL Chi-restraints excluded: chain 26 residue 24 THR Chi-restraints excluded: chain 26 residue 29 LEU Chi-restraints excluded: chain 26 residue 58 ILE Chi-restraints excluded: chain 26 residue 71 ARG Chi-restraints excluded: chain 27 residue 7 ARG Chi-restraints excluded: chain 27 residue 13 GLU Chi-restraints excluded: chain 27 residue 15 ASN Chi-restraints excluded: chain 27 residue 50 VAL Chi-restraints excluded: chain 28 residue 9 THR Chi-restraints excluded: chain 28 residue 24 LEU Chi-restraints excluded: chain 29 residue 16 CYS Chi-restraints excluded: chain 29 residue 27 THR Chi-restraints excluded: chain 29 residue 58 ASP Chi-restraints excluded: chain 30 residue 8 THR Chi-restraints excluded: chain 30 residue 22 THR Chi-restraints excluded: chain 30 residue 24 VAL Chi-restraints excluded: chain 30 residue 28 SER Chi-restraints excluded: chain 30 residue 36 LYS Chi-restraints excluded: chain 30 residue 45 ASP Chi-restraints excluded: chain 30 residue 53 VAL Chi-restraints excluded: chain 33 residue 54 LEU Chi-restraints excluded: chain 34 residue 17 VAL Chi-restraints excluded: chain 34 residue 22 VAL Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 7 ASN Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 61 PHE Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 115 MET Chi-restraints excluded: chain H residue 51 GLU Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 95 MET Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain I residue 21 LYS Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain J residue 15 HIS Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain K residue 17 ASP Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 102 ASP Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 11 HIS Chi-restraints excluded: chain M residue 19 THR Chi-restraints excluded: chain M residue 44 ILE Chi-restraints excluded: chain M residue 61 LYS Chi-restraints excluded: chain M residue 77 LYS Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 32 ASP Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 79 SER Chi-restraints excluded: chain O residue 10 ILE Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 46 LYS Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 29 ASN Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain P residue 55 ASP Chi-restraints excluded: chain Q residue 21 VAL Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 60 ILE Chi-restraints excluded: chain R residue 10 CYS Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain S residue 10 ILE Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 42 ASN Chi-restraints excluded: chain S residue 70 LEU Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 31 ILE Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain T residue 43 LYS Chi-restraints excluded: chain T residue 66 ILE Chi-restraints excluded: chain T residue 73 ARG Chi-restraints excluded: chain U residue 12 ASP Chi-restraints excluded: chain U residue 15 LEU Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 30 GLU Chi-restraints excluded: chain U residue 34 ARG Chi-restraints excluded: chain U residue 38 GLU Chi-restraints excluded: chain 03 residue 16 ASP Chi-restraints excluded: chain 03 residue 18 THR Chi-restraints excluded: chain 03 residue 189 LEU Chi-restraints excluded: chain 03 residue 216 THR Chi-restraints excluded: chain Z residue 136 LYS Chi-restraints excluded: chain Z residue 145 LEU Chi-restraints excluded: chain Z residue 221 SER Chi-restraints excluded: chain Z residue 236 ILE Chi-restraints excluded: chain Z residue 237 LYS Chi-restraints excluded: chain Z residue 358 MET Chi-restraints excluded: chain Z residue 391 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1101 random chunks: chunk 1027 optimal weight: 20.0000 chunk 120 optimal weight: 20.0000 chunk 606 optimal weight: 30.0000 chunk 777 optimal weight: 20.0000 chunk 602 optimal weight: 20.0000 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: 20.0000 chunk 489 optimal weight: 10.0000 overall best weight: 18.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 04 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 04 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 07 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 82 ASN ** 18 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 23 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 26 33 HIS ** 29 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 29 48 GLN ** 29 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 34 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 ASN ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 03 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 84 HIS ** Z 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.124 166817 Z= 0.575 Angle : 0.887 13.448 249070 Z= 0.447 Chirality : 0.046 0.380 31782 Planarity : 0.006 0.076 13715 Dihedral : 24.037 178.477 82303 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 33.93 Ramachandran Plot: Outliers : 0.19 % Allowed : 14.15 % Favored : 85.66 % Rotamer: Outliers : 7.62 % Allowed : 23.74 % Favored : 68.63 % 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: -3.01 (0.10), residues: 6366 helix: -1.10 (0.11), residues: 1965 sheet: -2.12 (0.15), residues: 1066 loop : -2.56 (0.10), residues: 3335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP26 38 HIS 0.011 0.002 HIS28 19 PHE 0.040 0.003 PHE B 49 TYR 0.032 0.003 TYR12 75 ARG 0.024 0.001 ARG10 46 *********************** 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 1388 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 403 poor density : 985 time to evaluate : 6.761 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: 04 97 ASP cc_start: 0.7752 (p0) cc_final: 0.7294 (p0) REVERT: 04 200 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.8050 (ttt) REVERT: 07 37 MET cc_start: 0.9310 (ttm) cc_final: 0.8749 (tmm) REVERT: 07 127 TYR cc_start: 0.8344 (t80) cc_final: 0.7744 (t80) REVERT: 07 174 PHE cc_start: 0.8256 (m-10) cc_final: 0.7971 (m-80) REVERT: 08 71 LEU cc_start: 0.9600 (OUTLIER) cc_final: 0.9383 (mm) REVERT: 09 97 ARG cc_start: 0.8885 (mmm-85) cc_final: 0.8573 (tpp80) REVERT: 09 133 GLN cc_start: 0.9055 (tt0) cc_final: 0.8666 (tp40) REVERT: 10 52 MET cc_start: 0.2874 (OUTLIER) cc_final: 0.2486 (ptp) REVERT: 10 84 TYR cc_start: 0.5118 (OUTLIER) cc_final: 0.3634 (m-80) REVERT: 12 108 MET cc_start: 0.8138 (mtt) cc_final: 0.7843 (mtt) REVERT: 13 32 TYR cc_start: 0.8546 (OUTLIER) cc_final: 0.7900 (p90) REVERT: 13 90 ASN cc_start: 0.8714 (OUTLIER) cc_final: 0.8208 (p0) REVERT: 14 81 ASP cc_start: 0.8705 (t0) cc_final: 0.8454 (t70) REVERT: 16 2 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.7396 (ppp-140) REVERT: 16 106 ASP cc_start: 0.8377 (p0) cc_final: 0.8072 (p0) REVERT: 21 1 MET cc_start: 0.8604 (tpp) cc_final: 0.8305 (mmm) REVERT: 21 66 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8789 (mp) REVERT: 22 1 MET cc_start: 0.6587 (ptm) cc_final: 0.6084 (ptp) REVERT: 23 102 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.7794 (mp) REVERT: 25 11 ASP cc_start: 0.8343 (t0) cc_final: 0.7908 (t0) REVERT: 27 7 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8400 (tmm160) REVERT: 28 53 MET cc_start: 0.8982 (ppp) cc_final: 0.8705 (ppp) REVERT: 29 62 LYS cc_start: 0.9324 (tppt) cc_final: 0.8998 (tptp) REVERT: 30 16 ARG cc_start: 0.8682 (mtt90) cc_final: 0.8413 (mtt90) REVERT: 30 36 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8163 (tppt) REVERT: 31 20 TYR cc_start: 0.8145 (m-10) cc_final: 0.7809 (m-10) REVERT: B 183 PHE cc_start: 0.8205 (OUTLIER) cc_final: 0.7656 (p90) REVERT: B 191 ASP cc_start: 0.9080 (t0) cc_final: 0.8641 (t0) REVERT: B 193 ASP cc_start: 0.8361 (m-30) cc_final: 0.8021 (m-30) REVERT: D 58 GLN cc_start: 0.8844 (mm110) cc_final: 0.8578 (mm110) REVERT: D 177 MET cc_start: 0.8667 (mpp) cc_final: 0.8407 (mpp) REVERT: E 129 SER cc_start: 0.9188 (t) cc_final: 0.8725 (p) REVERT: F 69 GLU cc_start: 0.8571 (pm20) cc_final: 0.8230 (pm20) REVERT: F 80 PHE cc_start: 0.8316 (m-80) cc_final: 0.8024 (m-80) REVERT: H 1 SER cc_start: 0.6788 (OUTLIER) cc_final: 0.6519 (m) REVERT: H 2 MET cc_start: 0.8357 (tpt) cc_final: 0.8140 (tpt) REVERT: H 128 VAL cc_start: 0.8912 (OUTLIER) cc_final: 0.8665 (t) REVERT: I 58 GLU cc_start: 0.8840 (mm-30) cc_final: 0.7918 (tp30) REVERT: I 88 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8109 (pm20) REVERT: K 57 SER cc_start: 0.9361 (m) cc_final: 0.9119 (m) REVERT: L 37 TYR cc_start: 0.8735 (p90) cc_final: 0.8487 (p90) REVERT: L 61 GLU cc_start: 0.7982 (tp30) cc_final: 0.7752 (tm-30) REVERT: M 10 ASP cc_start: 0.8422 (t0) cc_final: 0.7442 (t0) REVERT: M 46 GLU cc_start: 0.8684 (pt0) cc_final: 0.8240 (pp20) REVERT: N 32 ASP cc_start: 0.8435 (OUTLIER) cc_final: 0.8156 (t0) REVERT: N 34 ASN cc_start: 0.9104 (m110) cc_final: 0.8774 (m-40) REVERT: N 88 MET cc_start: 0.8352 (mmt) cc_final: 0.8007 (mmt) REVERT: P 29 ASN cc_start: 0.8998 (OUTLIER) cc_final: 0.8582 (m-40) REVERT: Q 48 GLU cc_start: 0.8686 (tp30) cc_final: 0.8272 (tp30) REVERT: Z 39 TYR cc_start: 0.8040 (t80) cc_final: 0.7748 (t80) REVERT: Z 70 ASP cc_start: 0.7193 (OUTLIER) cc_final: 0.5944 (m-30) REVERT: Z 91 MET cc_start: 0.9184 (tpt) cc_final: 0.8833 (tpt) outliers start: 403 outliers final: 320 residues processed: 1241 average time/residue: 1.3432 time to fit residues: 2958.3388 Evaluate side-chains 1293 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 338 poor density : 955 time to evaluate : 6.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 2 VAL Chi-restraints excluded: chain 04 residue 24 HIS Chi-restraints excluded: chain 04 residue 44 ASN Chi-restraints excluded: chain 04 residue 59 GLN Chi-restraints excluded: chain 04 residue 99 GLU Chi-restraints excluded: chain 04 residue 113 ASP Chi-restraints excluded: chain 04 residue 133 ASN Chi-restraints excluded: chain 04 residue 156 SER Chi-restraints excluded: chain 04 residue 167 ASP Chi-restraints excluded: chain 04 residue 200 MET Chi-restraints excluded: chain 04 residue 249 VAL Chi-restraints excluded: chain 04 residue 258 SER Chi-restraints excluded: chain 04 residue 263 ASP Chi-restraints excluded: chain 05 residue 91 THR Chi-restraints excluded: chain 05 residue 104 VAL Chi-restraints excluded: chain 05 residue 137 SER Chi-restraints excluded: chain 05 residue 139 SER Chi-restraints excluded: chain 05 residue 186 LEU Chi-restraints excluded: chain 05 residue 199 SER Chi-restraints excluded: chain 06 residue 70 SER Chi-restraints excluded: chain 06 residue 73 ILE Chi-restraints excluded: chain 06 residue 83 VAL Chi-restraints excluded: chain 06 residue 97 ASN Chi-restraints excluded: chain 06 residue 119 ILE Chi-restraints excluded: chain 06 residue 187 VAL Chi-restraints excluded: chain 07 residue 22 ASN Chi-restraints excluded: chain 07 residue 25 MET Chi-restraints excluded: chain 07 residue 30 VAL Chi-restraints excluded: chain 07 residue 60 SER Chi-restraints excluded: chain 07 residue 144 LYS Chi-restraints excluded: chain 07 residue 146 ASP Chi-restraints excluded: chain 07 residue 154 THR Chi-restraints excluded: chain 07 residue 164 GLU Chi-restraints excluded: chain 08 residue 9 VAL Chi-restraints excluded: chain 08 residue 15 ASP Chi-restraints excluded: chain 08 residue 19 ASN Chi-restraints excluded: chain 08 residue 44 HIS Chi-restraints excluded: chain 08 residue 55 ASP Chi-restraints excluded: chain 08 residue 71 LEU Chi-restraints excluded: chain 08 residue 120 ILE Chi-restraints excluded: chain 08 residue 126 THR Chi-restraints excluded: chain 08 residue 130 ILE Chi-restraints excluded: chain 08 residue 146 ASP Chi-restraints excluded: chain 08 residue 161 VAL Chi-restraints excluded: chain 08 residue 167 VAL Chi-restraints excluded: chain 09 residue 8 LYS Chi-restraints excluded: chain 09 residue 40 THR Chi-restraints excluded: chain 09 residue 47 PHE Chi-restraints excluded: chain 09 residue 50 ARG Chi-restraints excluded: chain 09 residue 91 PHE Chi-restraints excluded: chain 09 residue 99 ILE Chi-restraints excluded: chain 09 residue 108 VAL Chi-restraints excluded: chain 09 residue 115 VAL Chi-restraints excluded: chain 09 residue 134 VAL Chi-restraints excluded: chain 10 residue 27 VAL Chi-restraints excluded: chain 10 residue 50 VAL Chi-restraints excluded: chain 10 residue 52 MET Chi-restraints excluded: chain 10 residue 77 VAL Chi-restraints excluded: chain 10 residue 82 ILE Chi-restraints excluded: chain 10 residue 84 TYR Chi-restraints excluded: chain 11 residue 41 PHE Chi-restraints excluded: chain 11 residue 46 ASP Chi-restraints excluded: chain 11 residue 63 ASP Chi-restraints excluded: chain 12 residue 12 LYS Chi-restraints excluded: chain 12 residue 25 LEU Chi-restraints excluded: chain 12 residue 50 THR Chi-restraints excluded: chain 12 residue 57 LEU Chi-restraints excluded: chain 12 residue 62 VAL Chi-restraints excluded: chain 12 residue 67 ASN Chi-restraints excluded: chain 12 residue 93 ILE Chi-restraints excluded: chain 12 residue 131 ASN Chi-restraints excluded: chain 13 residue 8 LEU Chi-restraints excluded: chain 13 residue 13 ASN Chi-restraints excluded: chain 13 residue 28 SER Chi-restraints excluded: chain 13 residue 32 TYR Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 42 THR Chi-restraints excluded: chain 13 residue 56 ASP Chi-restraints excluded: chain 13 residue 69 VAL Chi-restraints excluded: chain 13 residue 87 LEU Chi-restraints excluded: chain 13 residue 90 ASN Chi-restraints excluded: chain 13 residue 91 SER Chi-restraints excluded: chain 14 residue 5 THR Chi-restraints excluded: chain 14 residue 7 SER Chi-restraints excluded: chain 14 residue 27 LEU Chi-restraints excluded: chain 14 residue 67 THR Chi-restraints excluded: chain 14 residue 73 ILE Chi-restraints excluded: chain 14 residue 85 VAL Chi-restraints excluded: chain 14 residue 136 GLU Chi-restraints excluded: chain 15 residue 7 THR Chi-restraints excluded: chain 15 residue 24 THR Chi-restraints excluded: chain 15 residue 36 VAL Chi-restraints excluded: chain 15 residue 42 THR Chi-restraints excluded: chain 15 residue 78 LEU Chi-restraints excluded: chain 15 residue 95 LEU Chi-restraints excluded: chain 15 residue 115 GLU Chi-restraints excluded: chain 15 residue 128 THR Chi-restraints excluded: chain 15 residue 129 THR Chi-restraints excluded: chain 16 residue 2 ARG Chi-restraints excluded: chain 16 residue 33 ILE Chi-restraints excluded: chain 16 residue 34 ILE Chi-restraints excluded: chain 16 residue 72 ASP Chi-restraints excluded: chain 16 residue 76 VAL Chi-restraints excluded: chain 16 residue 89 SER Chi-restraints excluded: chain 17 residue 28 VAL Chi-restraints excluded: chain 17 residue 35 ILE Chi-restraints excluded: chain 17 residue 47 VAL Chi-restraints excluded: chain 17 residue 87 ILE Chi-restraints excluded: chain 18 residue 1 SER Chi-restraints excluded: chain 18 residue 24 THR Chi-restraints excluded: chain 18 residue 31 VAL Chi-restraints excluded: chain 18 residue 43 GLU Chi-restraints excluded: chain 18 residue 47 ILE Chi-restraints excluded: chain 18 residue 59 THR Chi-restraints excluded: chain 18 residue 100 ARG Chi-restraints excluded: chain 18 residue 103 THR Chi-restraints excluded: chain 18 residue 109 ILE Chi-restraints excluded: chain 18 residue 114 ASN Chi-restraints excluded: chain 19 residue 7 VAL Chi-restraints excluded: chain 19 residue 30 VAL Chi-restraints excluded: chain 19 residue 38 VAL Chi-restraints excluded: chain 19 residue 61 ILE Chi-restraints excluded: chain 19 residue 79 ILE Chi-restraints excluded: chain 19 residue 82 LEU Chi-restraints excluded: chain 19 residue 103 VAL Chi-restraints excluded: chain 19 residue 108 LEU Chi-restraints excluded: chain 19 residue 110 GLU Chi-restraints excluded: chain 20 residue 29 THR Chi-restraints excluded: chain 20 residue 51 VAL Chi-restraints excluded: chain 20 residue 96 VAL Chi-restraints excluded: chain 20 residue 99 THR Chi-restraints excluded: chain 20 residue 102 SER Chi-restraints excluded: chain 21 residue 3 THR Chi-restraints excluded: chain 21 residue 4 ILE Chi-restraints excluded: chain 21 residue 12 SER Chi-restraints excluded: chain 21 residue 39 THR Chi-restraints excluded: chain 21 residue 66 ILE Chi-restraints excluded: chain 21 residue 67 ASP Chi-restraints excluded: chain 21 residue 81 SER Chi-restraints excluded: chain 22 residue 31 VAL Chi-restraints excluded: chain 22 residue 32 LEU Chi-restraints excluded: chain 22 residue 39 THR Chi-restraints excluded: chain 22 residue 76 ARG Chi-restraints excluded: chain 22 residue 92 ASN Chi-restraints excluded: chain 23 residue 39 ASN Chi-restraints excluded: chain 23 residue 102 ILE Chi-restraints excluded: chain 24 residue 30 ILE Chi-restraints excluded: chain 24 residue 40 ILE Chi-restraints excluded: chain 24 residue 90 ASP Chi-restraints excluded: chain 25 residue 25 GLU Chi-restraints excluded: chain 25 residue 26 SER Chi-restraints excluded: chain 25 residue 34 VAL Chi-restraints excluded: chain 26 residue 24 THR Chi-restraints excluded: chain 26 residue 29 LEU Chi-restraints excluded: chain 26 residue 58 ILE Chi-restraints excluded: chain 26 residue 71 ARG Chi-restraints excluded: chain 27 residue 7 ARG Chi-restraints excluded: chain 27 residue 13 GLU Chi-restraints excluded: chain 27 residue 15 ASN Chi-restraints excluded: chain 27 residue 47 ARG Chi-restraints excluded: chain 27 residue 50 VAL Chi-restraints excluded: chain 28 residue 9 THR Chi-restraints excluded: chain 28 residue 24 LEU Chi-restraints excluded: chain 28 residue 31 ILE Chi-restraints excluded: chain 29 residue 16 CYS Chi-restraints excluded: chain 29 residue 20 ASN Chi-restraints excluded: chain 29 residue 27 THR Chi-restraints excluded: chain 29 residue 32 LEU Chi-restraints excluded: chain 29 residue 58 ASP Chi-restraints excluded: chain 30 residue 3 GLN Chi-restraints excluded: chain 30 residue 8 THR Chi-restraints excluded: chain 30 residue 22 THR Chi-restraints excluded: chain 30 residue 24 VAL Chi-restraints excluded: chain 30 residue 28 SER Chi-restraints excluded: chain 30 residue 36 LYS Chi-restraints excluded: chain 30 residue 45 ASP Chi-restraints excluded: chain 30 residue 53 VAL Chi-restraints excluded: chain 31 residue 8 ILE Chi-restraints excluded: chain 31 residue 16 THR Chi-restraints excluded: chain 31 residue 42 VAL Chi-restraints excluded: chain 31 residue 49 LYS Chi-restraints excluded: chain 31 residue 52 LYS Chi-restraints excluded: chain 33 residue 5 THR Chi-restraints excluded: chain 33 residue 54 LEU Chi-restraints excluded: chain 34 residue 17 VAL Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 7 ASN Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 61 PHE Chi-restraints excluded: chain G residue 115 MET Chi-restraints excluded: chain H residue 1 SER Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 95 MET Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain I residue 21 LYS Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 88 GLU Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain J residue 15 HIS Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain K residue 17 ASP Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 102 ASP Chi-restraints excluded: chain L residue 108 ASP Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 11 HIS Chi-restraints excluded: chain M residue 19 THR Chi-restraints excluded: chain M residue 22 TYR Chi-restraints excluded: chain M residue 44 ILE Chi-restraints excluded: chain M residue 61 LYS Chi-restraints excluded: chain M residue 77 LYS Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 32 ASP Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain O residue 10 ILE Chi-restraints excluded: chain O residue 17 ASP Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 46 LYS Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 24 SER Chi-restraints excluded: chain P residue 29 ASN Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain P residue 55 ASP Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain Q residue 21 VAL Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 60 ILE Chi-restraints excluded: chain R residue 10 CYS Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain S residue 10 ILE Chi-restraints excluded: chain S residue 11 ASP Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 37 SER Chi-restraints excluded: chain S residue 42 ASN Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 70 LEU Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain T residue 43 LYS Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 66 ILE Chi-restraints excluded: chain T residue 73 ARG Chi-restraints excluded: chain U residue 12 ASP Chi-restraints excluded: chain U residue 15 LEU Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 34 ARG Chi-restraints excluded: chain U residue 38 GLU Chi-restraints excluded: chain 03 residue 16 ASP Chi-restraints excluded: chain 03 residue 18 THR Chi-restraints excluded: chain 03 residue 175 ILE Chi-restraints excluded: chain 03 residue 189 LEU Chi-restraints excluded: chain 03 residue 216 THR Chi-restraints excluded: chain Z residue 70 ASP Chi-restraints excluded: chain Z residue 145 LEU Chi-restraints excluded: chain Z residue 221 SER Chi-restraints excluded: chain Z residue 236 ILE Chi-restraints excluded: chain Z residue 237 LYS Chi-restraints excluded: chain Z residue 244 ILE Chi-restraints excluded: chain Z residue 269 ARG Chi-restraints excluded: chain Z residue 363 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1101 random chunks: chunk 656 optimal weight: 10.0000 chunk 423 optimal weight: 10.0000 chunk 633 optimal weight: 20.0000 chunk 319 optimal weight: 9.9990 chunk 208 optimal weight: 8.9990 chunk 205 optimal weight: 6.9990 chunk 674 optimal weight: 10.0000 chunk 722 optimal weight: 10.0000 chunk 524 optimal weight: 8.9990 chunk 98 optimal weight: 9.9990 chunk 834 optimal weight: 5.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 04 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 04 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 07 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 09 2 GLN ** 09 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 93 ASN 13 82 ASN ** 15 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 18 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 19 55 GLN ** 19 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 23 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 27 45 GLN ** 29 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 29 48 GLN ** 29 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 GLN ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 ASN O 34 GLN ** O 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 03 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 166817 Z= 0.290 Angle : 0.700 14.767 249070 Z= 0.357 Chirality : 0.038 0.369 31782 Planarity : 0.005 0.075 13715 Dihedral : 23.960 179.932 82300 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 24.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.69 % Favored : 88.16 % Rotamer: Outliers : 6.45 % Allowed : 25.29 % Favored : 68.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.64 (0.10), residues: 6366 helix: -0.70 (0.11), residues: 1971 sheet: -1.95 (0.15), residues: 1080 loop : -2.37 (0.10), residues: 3315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP P 60 HIS 0.008 0.001 HIS24 44 PHE 0.037 0.002 PHE U 36 TYR 0.038 0.002 TYR B 212 ARG 0.015 0.001 ARG H 79 *********************** 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 1399 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 341 poor density : 1058 time to evaluate : 6.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 04 97 ASP cc_start: 0.7704 (p0) cc_final: 0.7238 (p0) REVERT: 04 200 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7932 (ttt) REVERT: 05 4 LEU cc_start: 0.7796 (mt) cc_final: 0.7548 (mt) REVERT: 05 11 MET cc_start: 0.8832 (tpp) cc_final: 0.8630 (mmm) REVERT: 07 37 MET cc_start: 0.9292 (ttm) cc_final: 0.8734 (tmm) REVERT: 07 127 TYR cc_start: 0.8165 (t80) cc_final: 0.7554 (t80) REVERT: 07 174 PHE cc_start: 0.8136 (m-10) cc_final: 0.7792 (m-80) REVERT: 08 71 LEU cc_start: 0.9568 (OUTLIER) cc_final: 0.9344 (mm) REVERT: 09 86 ASP cc_start: 0.8856 (t0) cc_final: 0.8607 (t0) REVERT: 09 97 ARG cc_start: 0.8920 (mmm-85) cc_final: 0.8565 (tpp80) REVERT: 09 133 GLN cc_start: 0.9053 (tt0) cc_final: 0.8689 (tp40) REVERT: 10 52 MET cc_start: 0.2663 (OUTLIER) cc_final: 0.2350 (ptp) REVERT: 11 116 MET cc_start: 0.3454 (mmt) cc_final: 0.0963 (ttm) REVERT: 12 108 MET cc_start: 0.8010 (mtt) cc_final: 0.7740 (mtt) REVERT: 13 32 TYR cc_start: 0.8487 (OUTLIER) cc_final: 0.8094 (p90) REVERT: 13 90 ASN cc_start: 0.8651 (OUTLIER) cc_final: 0.8138 (p0) REVERT: 14 136 GLU cc_start: 0.9072 (OUTLIER) cc_final: 0.8636 (pt0) REVERT: 15 33 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8671 (mt) REVERT: 15 53 MET cc_start: 0.8212 (tpt) cc_final: 0.8004 (tpt) REVERT: 16 2 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.7403 (ppp-140) REVERT: 16 106 ASP cc_start: 0.8202 (p0) cc_final: 0.7863 (p0) REVERT: 16 110 MET cc_start: 0.8609 (mmm) cc_final: 0.7711 (mmm) REVERT: 20 86 GLN cc_start: 0.7942 (tt0) cc_final: 0.7679 (mt0) REVERT: 21 1 MET cc_start: 0.8587 (tpp) cc_final: 0.8239 (mmm) REVERT: 21 66 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8744 (mp) REVERT: 22 1 MET cc_start: 0.6407 (ptm) cc_final: 0.5916 (ptp) REVERT: 22 24 MET cc_start: 0.8795 (mmm) cc_final: 0.8429 (mmm) REVERT: 22 89 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.6994 (tp30) REVERT: 25 11 ASP cc_start: 0.8307 (t0) cc_final: 0.7905 (t0) REVERT: 26 65 THR cc_start: 0.9261 (m) cc_final: 0.9010 (p) REVERT: 27 7 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.8294 (tmm160) REVERT: 27 45 GLN cc_start: 0.8513 (pt0) cc_final: 0.8030 (pp30) REVERT: 27 49 ASP cc_start: 0.9253 (m-30) cc_final: 0.8152 (m-30) REVERT: 29 62 LYS cc_start: 0.9290 (tppt) cc_final: 0.9037 (tptp) REVERT: 30 16 ARG cc_start: 0.8595 (mtt90) cc_final: 0.8339 (mtt90) REVERT: 30 36 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8210 (tppt) REVERT: 31 20 TYR cc_start: 0.8089 (m-10) cc_final: 0.7779 (m-10) REVERT: B 191 ASP cc_start: 0.9073 (t0) cc_final: 0.8584 (t0) REVERT: B 193 ASP cc_start: 0.8384 (m-30) cc_final: 0.8058 (m-30) REVERT: D 35 GLN cc_start: 0.7947 (pp30) cc_final: 0.7625 (pp30) REVERT: D 58 GLN cc_start: 0.8757 (mm110) cc_final: 0.8538 (mm110) REVERT: D 97 LEU cc_start: 0.9154 (tp) cc_final: 0.8927 (tt) REVERT: D 177 MET cc_start: 0.8589 (mpp) cc_final: 0.8366 (mpp) REVERT: E 45 VAL cc_start: 0.8722 (OUTLIER) cc_final: 0.8508 (t) REVERT: E 111 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.8046 (ttp80) REVERT: E 129 SER cc_start: 0.9032 (t) cc_final: 0.8657 (p) REVERT: F 80 PHE cc_start: 0.8300 (m-80) cc_final: 0.8043 (m-80) REVERT: H 2 MET cc_start: 0.8275 (tpt) cc_final: 0.8061 (tpt) REVERT: H 128 VAL cc_start: 0.8799 (OUTLIER) cc_final: 0.8597 (t) REVERT: I 58 GLU cc_start: 0.8594 (mm-30) cc_final: 0.7505 (tp30) REVERT: J 30 LYS cc_start: 0.8613 (pttm) cc_final: 0.8325 (ttpp) REVERT: K 57 SER cc_start: 0.9364 (m) cc_final: 0.9127 (m) REVERT: L 61 GLU cc_start: 0.7960 (tp30) cc_final: 0.7727 (tm-30) REVERT: M 10 ASP cc_start: 0.8408 (t0) cc_final: 0.7368 (t0) REVERT: M 46 GLU cc_start: 0.8496 (pt0) cc_final: 0.8290 (pp20) REVERT: N 17 ASP cc_start: 0.8809 (p0) cc_final: 0.7944 (t0) REVERT: N 22 LYS cc_start: 0.8010 (mptt) cc_final: 0.7649 (mptt) REVERT: N 32 ASP cc_start: 0.8417 (OUTLIER) cc_final: 0.8155 (t0) REVERT: N 34 ASN cc_start: 0.9087 (m110) cc_final: 0.8749 (m-40) REVERT: N 38 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8275 (tm-30) REVERT: N 41 TRP cc_start: 0.8342 (t-100) cc_final: 0.8119 (t-100) REVERT: N 88 MET cc_start: 0.8206 (mmt) cc_final: 0.7883 (mmt) REVERT: O 9 LYS cc_start: 0.9143 (mttt) cc_final: 0.8908 (mttm) REVERT: P 29 ASN cc_start: 0.8891 (OUTLIER) cc_final: 0.8686 (m-40) REVERT: Q 48 GLU cc_start: 0.8598 (tp30) cc_final: 0.8346 (tp30) REVERT: S 42 ASN cc_start: 0.8729 (OUTLIER) cc_final: 0.8301 (p0) REVERT: Z 21 ASP cc_start: 0.8056 (t70) cc_final: 0.7779 (t70) REVERT: Z 39 TYR cc_start: 0.7978 (t80) cc_final: 0.7481 (t80) REVERT: Z 91 MET cc_start: 0.9185 (tpt) cc_final: 0.8870 (tpt) REVERT: Z 147 GLU cc_start: 0.8997 (mt-10) cc_final: 0.8720 (tm-30) outliers start: 341 outliers final: 270 residues processed: 1269 average time/residue: 1.3186 time to fit residues: 2958.7837 Evaluate side-chains 1285 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 288 poor density : 997 time to evaluate : 6.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 2 VAL Chi-restraints excluded: chain 04 residue 44 ASN Chi-restraints excluded: chain 04 residue 99 GLU Chi-restraints excluded: chain 04 residue 113 ASP Chi-restraints excluded: chain 04 residue 133 ASN Chi-restraints excluded: chain 04 residue 167 ASP Chi-restraints excluded: chain 04 residue 200 MET Chi-restraints excluded: chain 04 residue 249 VAL Chi-restraints excluded: chain 04 residue 258 SER Chi-restraints excluded: chain 04 residue 263 ASP Chi-restraints excluded: chain 04 residue 267 VAL Chi-restraints excluded: chain 05 residue 2 ILE Chi-restraints excluded: chain 05 residue 104 VAL Chi-restraints excluded: chain 05 residue 137 SER Chi-restraints excluded: chain 05 residue 139 SER Chi-restraints excluded: chain 05 residue 186 LEU Chi-restraints excluded: chain 05 residue 199 SER Chi-restraints excluded: chain 06 residue 70 SER Chi-restraints excluded: chain 06 residue 73 ILE Chi-restraints excluded: chain 06 residue 97 ASN Chi-restraints excluded: chain 06 residue 119 ILE Chi-restraints excluded: chain 06 residue 187 VAL Chi-restraints excluded: chain 07 residue 22 ASN Chi-restraints excluded: chain 07 residue 24 VAL Chi-restraints excluded: chain 07 residue 25 MET Chi-restraints excluded: chain 07 residue 30 VAL Chi-restraints excluded: chain 07 residue 60 SER Chi-restraints excluded: chain 07 residue 144 LYS Chi-restraints excluded: chain 07 residue 146 ASP Chi-restraints excluded: chain 07 residue 164 GLU Chi-restraints excluded: chain 08 residue 9 VAL Chi-restraints excluded: chain 08 residue 15 ASP Chi-restraints excluded: chain 08 residue 19 ASN Chi-restraints excluded: chain 08 residue 44 HIS Chi-restraints excluded: chain 08 residue 55 ASP Chi-restraints excluded: chain 08 residue 71 LEU Chi-restraints excluded: chain 08 residue 126 THR Chi-restraints excluded: chain 08 residue 130 ILE Chi-restraints excluded: chain 08 residue 146 ASP Chi-restraints excluded: chain 08 residue 161 VAL Chi-restraints excluded: chain 08 residue 167 VAL Chi-restraints excluded: chain 09 residue 40 THR Chi-restraints excluded: chain 09 residue 47 PHE Chi-restraints excluded: chain 09 residue 50 ARG Chi-restraints excluded: chain 09 residue 91 PHE Chi-restraints excluded: chain 09 residue 99 ILE Chi-restraints excluded: chain 09 residue 108 VAL Chi-restraints excluded: chain 09 residue 115 VAL Chi-restraints excluded: chain 09 residue 128 HIS Chi-restraints excluded: chain 09 residue 134 VAL Chi-restraints excluded: chain 10 residue 27 VAL Chi-restraints excluded: chain 10 residue 50 VAL Chi-restraints excluded: chain 10 residue 52 MET Chi-restraints excluded: chain 10 residue 77 VAL Chi-restraints excluded: chain 10 residue 82 ILE Chi-restraints excluded: chain 11 residue 16 MET Chi-restraints excluded: chain 11 residue 39 LYS Chi-restraints excluded: chain 11 residue 46 ASP Chi-restraints excluded: chain 11 residue 63 ASP Chi-restraints excluded: chain 11 residue 138 VAL Chi-restraints excluded: chain 12 residue 12 LYS Chi-restraints excluded: chain 12 residue 25 LEU Chi-restraints excluded: chain 12 residue 50 THR Chi-restraints excluded: chain 12 residue 57 LEU Chi-restraints excluded: chain 12 residue 62 VAL Chi-restraints excluded: chain 12 residue 67 ASN Chi-restraints excluded: chain 12 residue 81 ILE Chi-restraints excluded: chain 12 residue 131 ASN Chi-restraints excluded: chain 13 residue 13 ASN Chi-restraints excluded: chain 13 residue 28 SER Chi-restraints excluded: chain 13 residue 32 TYR Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 42 THR Chi-restraints excluded: chain 13 residue 56 ASP Chi-restraints excluded: chain 13 residue 87 LEU Chi-restraints excluded: chain 13 residue 90 ASN Chi-restraints excluded: chain 13 residue 91 SER Chi-restraints excluded: chain 14 residue 7 SER Chi-restraints excluded: chain 14 residue 27 LEU Chi-restraints excluded: chain 14 residue 67 THR Chi-restraints excluded: chain 14 residue 73 ILE Chi-restraints excluded: chain 14 residue 85 VAL Chi-restraints excluded: chain 14 residue 136 GLU Chi-restraints excluded: chain 15 residue 7 THR Chi-restraints excluded: chain 15 residue 33 LEU Chi-restraints excluded: chain 15 residue 36 VAL Chi-restraints excluded: chain 15 residue 42 THR Chi-restraints excluded: chain 15 residue 95 LEU Chi-restraints excluded: chain 15 residue 115 GLU Chi-restraints excluded: chain 15 residue 128 THR Chi-restraints excluded: chain 15 residue 129 THR Chi-restraints excluded: chain 16 residue 2 ARG Chi-restraints excluded: chain 16 residue 33 ILE Chi-restraints excluded: chain 16 residue 34 ILE Chi-restraints excluded: chain 16 residue 76 VAL Chi-restraints excluded: chain 16 residue 89 SER Chi-restraints excluded: chain 17 residue 28 VAL Chi-restraints excluded: chain 17 residue 35 ILE Chi-restraints excluded: chain 17 residue 47 VAL Chi-restraints excluded: chain 17 residue 87 ILE Chi-restraints excluded: chain 18 residue 31 VAL Chi-restraints excluded: chain 18 residue 43 GLU Chi-restraints excluded: chain 18 residue 59 THR Chi-restraints excluded: chain 18 residue 100 ARG Chi-restraints excluded: chain 18 residue 103 THR Chi-restraints excluded: chain 19 residue 7 VAL Chi-restraints excluded: chain 19 residue 38 VAL Chi-restraints excluded: chain 19 residue 61 ILE Chi-restraints excluded: chain 19 residue 79 ILE Chi-restraints excluded: chain 19 residue 82 LEU Chi-restraints excluded: chain 19 residue 103 VAL Chi-restraints excluded: chain 19 residue 108 LEU Chi-restraints excluded: chain 20 residue 29 THR Chi-restraints excluded: chain 20 residue 51 VAL Chi-restraints excluded: chain 20 residue 102 SER Chi-restraints excluded: chain 21 residue 3 THR Chi-restraints excluded: chain 21 residue 4 ILE Chi-restraints excluded: chain 21 residue 39 THR Chi-restraints excluded: chain 21 residue 66 ILE Chi-restraints excluded: chain 21 residue 67 ASP Chi-restraints excluded: chain 21 residue 81 SER Chi-restraints excluded: chain 22 residue 31 VAL Chi-restraints excluded: chain 22 residue 32 LEU Chi-restraints excluded: chain 22 residue 39 THR Chi-restraints excluded: chain 22 residue 61 LEU Chi-restraints excluded: chain 22 residue 76 ARG Chi-restraints excluded: chain 22 residue 79 ASP Chi-restraints excluded: chain 22 residue 89 GLU Chi-restraints excluded: chain 23 residue 39 ASN Chi-restraints excluded: chain 24 residue 30 ILE Chi-restraints excluded: chain 24 residue 90 ASP Chi-restraints excluded: chain 25 residue 26 SER Chi-restraints excluded: chain 25 residue 34 VAL Chi-restraints excluded: chain 26 residue 24 THR Chi-restraints excluded: chain 26 residue 29 LEU Chi-restraints excluded: chain 26 residue 58 ILE Chi-restraints excluded: chain 26 residue 61 LYS Chi-restraints excluded: chain 26 residue 71 ARG Chi-restraints excluded: chain 27 residue 7 ARG Chi-restraints excluded: chain 27 residue 13 GLU Chi-restraints excluded: chain 27 residue 15 ASN Chi-restraints excluded: chain 27 residue 47 ARG Chi-restraints excluded: chain 28 residue 9 THR Chi-restraints excluded: chain 28 residue 24 LEU Chi-restraints excluded: chain 28 residue 31 ILE Chi-restraints excluded: chain 29 residue 16 CYS Chi-restraints excluded: chain 29 residue 20 ASN Chi-restraints excluded: chain 29 residue 27 THR Chi-restraints excluded: chain 29 residue 32 LEU Chi-restraints excluded: chain 29 residue 58 ASP Chi-restraints excluded: chain 30 residue 3 GLN Chi-restraints excluded: chain 30 residue 8 THR Chi-restraints excluded: chain 30 residue 22 THR Chi-restraints excluded: chain 30 residue 24 VAL Chi-restraints excluded: chain 30 residue 28 SER Chi-restraints excluded: chain 30 residue 36 LYS Chi-restraints excluded: chain 30 residue 45 ASP Chi-restraints excluded: chain 30 residue 53 VAL Chi-restraints excluded: chain 31 residue 16 THR Chi-restraints excluded: chain 33 residue 6 VAL Chi-restraints excluded: chain 33 residue 54 LEU Chi-restraints excluded: chain 34 residue 17 VAL Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 7 ASN Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 111 ARG Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 61 PHE Chi-restraints excluded: chain G residue 115 MET Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain I residue 21 LYS Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain J residue 15 HIS Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain K residue 17 ASP Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 102 ASP Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 11 HIS Chi-restraints excluded: chain M residue 61 LYS Chi-restraints excluded: chain M residue 77 LYS Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 32 ASP Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain O residue 17 ASP Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 29 ASN Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain P residue 55 ASP Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain Q residue 21 VAL Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 60 ILE Chi-restraints excluded: chain R residue 10 CYS Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain S residue 10 ILE Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 42 ASN Chi-restraints excluded: chain S residue 70 LEU Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain T residue 43 LYS Chi-restraints excluded: chain T residue 66 ILE Chi-restraints excluded: chain T residue 73 ARG Chi-restraints excluded: chain U residue 11 PHE Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 34 ARG Chi-restraints excluded: chain U residue 38 GLU Chi-restraints excluded: chain 03 residue 16 ASP Chi-restraints excluded: chain 03 residue 18 THR Chi-restraints excluded: chain 03 residue 189 LEU Chi-restraints excluded: chain 03 residue 216 THR Chi-restraints excluded: chain Z residue 145 LEU Chi-restraints excluded: chain Z residue 221 SER Chi-restraints excluded: chain Z residue 236 ILE Chi-restraints excluded: chain Z residue 335 THR Chi-restraints excluded: chain Z residue 360 VAL Chi-restraints excluded: chain Z residue 363 ILE 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: 20.0000 chunk 430 optimal weight: 20.0000 chunk 776 optimal weight: 20.0000 chunk 303 optimal weight: 30.0000 chunk 893 optimal weight: 20.0000 chunk 935 optimal weight: 10.0000 chunk 985 optimal weight: 20.0000 overall best weight: 18.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 04 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 04 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 05 134 HIS ** 07 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 142 GLN ** 09 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 3 GLN 13 82 ASN ** 18 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 24 49 ASN ** 24 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 29 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 29 48 GLN ** 29 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 34 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 ASN ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 HIS ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 63 ASN ** 03 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.5084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.132 166817 Z= 0.579 Angle : 0.925 14.311 249070 Z= 0.464 Chirality : 0.047 0.377 31782 Planarity : 0.007 0.098 13715 Dihedral : 24.235 179.623 82300 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 36.83 Ramachandran Plot: Outliers : 0.17 % Allowed : 14.94 % Favored : 84.89 % Rotamer: Outliers : 7.32 % Allowed : 25.22 % Favored : 67.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.10), residues: 6366 helix: -1.26 (0.11), residues: 1979 sheet: -2.04 (0.15), residues: 1049 loop : -2.62 (0.10), residues: 3338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP26 38 HIS 0.014 0.002 HIS28 19 PHE 0.044 0.003 PHE U 36 TYR 0.043 0.003 TYR M 85 ARG 0.017 0.001 ARG10 46 *********************** 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 1341 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 387 poor density : 954 time to evaluate : 6.794 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: 04 97 ASP cc_start: 0.7756 (p0) cc_final: 0.7278 (p0) REVERT: 04 200 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.8064 (ttt) REVERT: 07 37 MET cc_start: 0.9312 (ttm) cc_final: 0.8731 (tmm) REVERT: 07 127 TYR cc_start: 0.8273 (t80) cc_final: 0.7752 (t80) REVERT: 07 129 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7763 (ppp) REVERT: 07 164 GLU cc_start: 0.9140 (OUTLIER) cc_final: 0.8834 (pt0) REVERT: 07 174 PHE cc_start: 0.8368 (m-10) cc_final: 0.8025 (m-80) REVERT: 09 86 ASP cc_start: 0.8812 (t0) cc_final: 0.8594 (t0) REVERT: 09 97 ARG cc_start: 0.8889 (mmm-85) cc_final: 0.8557 (tpp80) REVERT: 11 116 MET cc_start: 0.4030 (mmt) cc_final: 0.1067 (ttm) REVERT: 12 108 MET cc_start: 0.8141 (mtt) cc_final: 0.7865 (mtt) REVERT: 13 1 MET cc_start: 0.7713 (tpt) cc_final: 0.7324 (tpt) REVERT: 13 32 TYR cc_start: 0.8654 (OUTLIER) cc_final: 0.7631 (p90) REVERT: 13 90 ASN cc_start: 0.8848 (OUTLIER) cc_final: 0.8366 (p0) REVERT: 15 53 MET cc_start: 0.8411 (tpt) cc_final: 0.8199 (tpt) REVERT: 16 2 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.7617 (ppp-140) REVERT: 16 106 ASP cc_start: 0.8458 (p0) cc_final: 0.8156 (p0) REVERT: 16 114 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8116 (pm20) REVERT: 18 12 MET cc_start: 0.8598 (ptp) cc_final: 0.8107 (mtm) REVERT: 21 1 MET cc_start: 0.8571 (tpp) cc_final: 0.8342 (mmm) REVERT: 21 66 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8782 (mp) REVERT: 22 1 MET cc_start: 0.6750 (ptm) cc_final: 0.6322 (ptp) REVERT: 22 24 MET cc_start: 0.8854 (mmm) cc_final: 0.8512 (mmm) REVERT: 25 11 ASP cc_start: 0.8364 (t0) cc_final: 0.7894 (t0) REVERT: 28 53 MET cc_start: 0.9008 (ppp) cc_final: 0.8758 (ppp) REVERT: 29 62 LYS cc_start: 0.9308 (tppt) cc_final: 0.9075 (tptp) REVERT: 30 16 ARG cc_start: 0.8697 (mtt90) cc_final: 0.8443 (mtt90) REVERT: 30 36 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8228 (tppt) REVERT: 31 20 TYR cc_start: 0.8182 (m-10) cc_final: 0.7819 (m-10) REVERT: 33 48 MET cc_start: 0.8530 (mtt) cc_final: 0.8172 (mtt) REVERT: B 191 ASP cc_start: 0.9108 (t0) cc_final: 0.8675 (t0) REVERT: B 193 ASP cc_start: 0.8344 (m-30) cc_final: 0.8021 (m-30) REVERT: D 58 GLN cc_start: 0.8831 (mm110) cc_final: 0.8586 (mm110) REVERT: E 111 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8160 (ttp80) REVERT: F 69 GLU cc_start: 0.8568 (pm20) cc_final: 0.8227 (pm20) REVERT: F 80 PHE cc_start: 0.8342 (m-80) cc_final: 0.8073 (m-80) REVERT: H 1 SER cc_start: 0.6831 (OUTLIER) cc_final: 0.6494 (m) REVERT: H 128 VAL cc_start: 0.8865 (OUTLIER) cc_final: 0.8604 (t) REVERT: I 58 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8123 (tp30) REVERT: J 76 ILE cc_start: 0.6906 (OUTLIER) cc_final: 0.6643 (tp) REVERT: K 57 SER cc_start: 0.9387 (m) cc_final: 0.9154 (m) REVERT: L 61 GLU cc_start: 0.8009 (tp30) cc_final: 0.7795 (tm-30) REVERT: M 10 ASP cc_start: 0.8616 (t0) cc_final: 0.7548 (t0) REVERT: N 32 ASP cc_start: 0.8440 (OUTLIER) cc_final: 0.8223 (t0) REVERT: N 34 ASN cc_start: 0.9059 (m110) cc_final: 0.8754 (m-40) REVERT: N 88 MET cc_start: 0.8378 (mmt) cc_final: 0.8061 (mmt) REVERT: P 29 ASN cc_start: 0.9020 (OUTLIER) cc_final: 0.8624 (m-40) REVERT: Z 21 ASP cc_start: 0.8170 (t70) cc_final: 0.7896 (t70) REVERT: Z 39 TYR cc_start: 0.7991 (t80) cc_final: 0.7524 (t80) REVERT: Z 91 MET cc_start: 0.9248 (tpt) cc_final: 0.8874 (tpt) outliers start: 387 outliers final: 320 residues processed: 1203 average time/residue: 1.3955 time to fit residues: 2991.8520 Evaluate side-chains 1261 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 335 poor density : 926 time to evaluate : 6.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 2 VAL Chi-restraints excluded: chain 04 residue 24 HIS Chi-restraints excluded: chain 04 residue 44 ASN Chi-restraints excluded: chain 04 residue 99 GLU Chi-restraints excluded: chain 04 residue 113 ASP Chi-restraints excluded: chain 04 residue 133 ASN Chi-restraints excluded: chain 04 residue 156 SER Chi-restraints excluded: chain 04 residue 167 ASP Chi-restraints excluded: chain 04 residue 200 MET Chi-restraints excluded: chain 04 residue 228 ASP Chi-restraints excluded: chain 04 residue 249 VAL Chi-restraints excluded: chain 04 residue 258 SER Chi-restraints excluded: chain 04 residue 263 ASP Chi-restraints excluded: chain 04 residue 267 VAL Chi-restraints excluded: chain 05 residue 9 VAL Chi-restraints excluded: chain 05 residue 91 THR Chi-restraints excluded: chain 05 residue 104 VAL Chi-restraints excluded: chain 05 residue 121 THR Chi-restraints excluded: chain 05 residue 137 SER Chi-restraints excluded: chain 05 residue 139 SER Chi-restraints excluded: chain 05 residue 199 SER Chi-restraints excluded: chain 06 residue 70 SER Chi-restraints excluded: chain 06 residue 73 ILE Chi-restraints excluded: chain 06 residue 97 ASN Chi-restraints excluded: chain 06 residue 108 ILE Chi-restraints excluded: chain 06 residue 119 ILE Chi-restraints excluded: chain 06 residue 187 VAL Chi-restraints excluded: chain 07 residue 22 ASN Chi-restraints excluded: chain 07 residue 24 VAL Chi-restraints excluded: chain 07 residue 25 MET Chi-restraints excluded: chain 07 residue 30 VAL Chi-restraints excluded: chain 07 residue 60 SER Chi-restraints excluded: chain 07 residue 129 MET Chi-restraints excluded: chain 07 residue 144 LYS Chi-restraints excluded: chain 07 residue 146 ASP Chi-restraints excluded: chain 07 residue 154 THR Chi-restraints excluded: chain 07 residue 164 GLU Chi-restraints excluded: chain 08 residue 9 VAL Chi-restraints excluded: chain 08 residue 15 ASP Chi-restraints excluded: chain 08 residue 19 ASN Chi-restraints excluded: chain 08 residue 44 HIS Chi-restraints excluded: chain 08 residue 55 ASP Chi-restraints excluded: chain 08 residue 126 THR Chi-restraints excluded: chain 08 residue 130 ILE Chi-restraints excluded: chain 08 residue 146 ASP Chi-restraints excluded: chain 08 residue 161 VAL Chi-restraints excluded: chain 08 residue 167 VAL Chi-restraints excluded: chain 09 residue 40 THR Chi-restraints excluded: chain 09 residue 47 PHE Chi-restraints excluded: chain 09 residue 50 ARG Chi-restraints excluded: chain 09 residue 91 PHE Chi-restraints excluded: chain 09 residue 99 ILE Chi-restraints excluded: chain 09 residue 108 VAL Chi-restraints excluded: chain 09 residue 115 VAL Chi-restraints excluded: chain 09 residue 128 HIS Chi-restraints excluded: chain 09 residue 134 VAL Chi-restraints excluded: chain 10 residue 7 ASP Chi-restraints excluded: chain 10 residue 27 VAL Chi-restraints excluded: chain 10 residue 50 VAL Chi-restraints excluded: chain 10 residue 77 VAL Chi-restraints excluded: chain 10 residue 82 ILE Chi-restraints excluded: chain 10 residue 128 THR Chi-restraints excluded: chain 11 residue 41 PHE Chi-restraints excluded: chain 11 residue 46 ASP Chi-restraints excluded: chain 11 residue 63 ASP Chi-restraints excluded: chain 11 residue 138 VAL Chi-restraints excluded: chain 12 residue 12 LYS Chi-restraints excluded: chain 12 residue 17 VAL Chi-restraints excluded: chain 12 residue 25 LEU Chi-restraints excluded: chain 12 residue 50 THR Chi-restraints excluded: chain 12 residue 57 LEU Chi-restraints excluded: chain 12 residue 62 VAL Chi-restraints excluded: chain 12 residue 67 ASN Chi-restraints excluded: chain 12 residue 81 ILE Chi-restraints excluded: chain 12 residue 93 ILE Chi-restraints excluded: chain 12 residue 131 ASN Chi-restraints excluded: chain 13 residue 13 ASN Chi-restraints excluded: chain 13 residue 28 SER Chi-restraints excluded: chain 13 residue 32 TYR Chi-restraints excluded: chain 13 residue 35 VAL Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 42 THR Chi-restraints excluded: chain 13 residue 56 ASP Chi-restraints excluded: chain 13 residue 69 VAL Chi-restraints excluded: chain 13 residue 87 LEU Chi-restraints excluded: chain 13 residue 90 ASN Chi-restraints excluded: chain 13 residue 91 SER Chi-restraints excluded: chain 14 residue 5 THR Chi-restraints excluded: chain 14 residue 7 SER Chi-restraints excluded: chain 14 residue 27 LEU Chi-restraints excluded: chain 14 residue 67 THR Chi-restraints excluded: chain 14 residue 73 ILE Chi-restraints excluded: chain 14 residue 85 VAL Chi-restraints excluded: chain 14 residue 136 GLU Chi-restraints excluded: chain 15 residue 7 THR Chi-restraints excluded: chain 15 residue 33 LEU Chi-restraints excluded: chain 15 residue 36 VAL Chi-restraints excluded: chain 15 residue 42 THR Chi-restraints excluded: chain 15 residue 95 LEU Chi-restraints excluded: chain 15 residue 115 GLU Chi-restraints excluded: chain 15 residue 128 THR Chi-restraints excluded: chain 15 residue 129 THR Chi-restraints excluded: chain 16 residue 2 ARG Chi-restraints excluded: chain 16 residue 33 ILE Chi-restraints excluded: chain 16 residue 34 ILE Chi-restraints excluded: chain 16 residue 72 ASP Chi-restraints excluded: chain 16 residue 76 VAL Chi-restraints excluded: chain 16 residue 89 SER Chi-restraints excluded: chain 16 residue 114 GLU Chi-restraints excluded: chain 17 residue 28 VAL Chi-restraints excluded: chain 17 residue 35 ILE Chi-restraints excluded: chain 17 residue 47 VAL Chi-restraints excluded: chain 17 residue 87 ILE Chi-restraints excluded: chain 18 residue 1 SER Chi-restraints excluded: chain 18 residue 24 THR Chi-restraints excluded: chain 18 residue 31 VAL Chi-restraints excluded: chain 18 residue 43 GLU Chi-restraints excluded: chain 18 residue 47 ILE Chi-restraints excluded: chain 18 residue 59 THR Chi-restraints excluded: chain 18 residue 99 LEU Chi-restraints excluded: chain 18 residue 100 ARG Chi-restraints excluded: chain 18 residue 103 THR Chi-restraints excluded: chain 18 residue 114 ASN Chi-restraints excluded: chain 19 residue 7 VAL Chi-restraints excluded: chain 19 residue 38 VAL Chi-restraints excluded: chain 19 residue 61 ILE Chi-restraints excluded: chain 19 residue 79 ILE Chi-restraints excluded: chain 19 residue 82 LEU Chi-restraints excluded: chain 19 residue 103 VAL Chi-restraints excluded: chain 19 residue 108 LEU Chi-restraints excluded: chain 20 residue 29 THR Chi-restraints excluded: chain 20 residue 51 VAL Chi-restraints excluded: chain 20 residue 53 PHE Chi-restraints excluded: chain 20 residue 99 THR Chi-restraints excluded: chain 20 residue 102 SER Chi-restraints excluded: chain 21 residue 3 THR Chi-restraints excluded: chain 21 residue 4 ILE Chi-restraints excluded: chain 21 residue 12 SER Chi-restraints excluded: chain 21 residue 39 THR Chi-restraints excluded: chain 21 residue 66 ILE Chi-restraints excluded: chain 21 residue 67 ASP Chi-restraints excluded: chain 21 residue 81 SER Chi-restraints excluded: chain 22 residue 31 VAL Chi-restraints excluded: chain 22 residue 32 LEU Chi-restraints excluded: chain 22 residue 39 THR Chi-restraints excluded: chain 22 residue 76 ARG Chi-restraints excluded: chain 22 residue 79 ASP Chi-restraints excluded: chain 22 residue 89 GLU Chi-restraints excluded: chain 22 residue 92 ASN Chi-restraints excluded: chain 23 residue 39 ASN Chi-restraints excluded: chain 24 residue 30 ILE Chi-restraints excluded: chain 24 residue 40 ILE Chi-restraints excluded: chain 24 residue 90 ASP Chi-restraints excluded: chain 25 residue 26 SER Chi-restraints excluded: chain 25 residue 34 VAL Chi-restraints excluded: chain 26 residue 6 VAL Chi-restraints excluded: chain 26 residue 24 THR Chi-restraints excluded: chain 26 residue 29 LEU Chi-restraints excluded: chain 26 residue 66 VAL Chi-restraints excluded: chain 26 residue 71 ARG Chi-restraints excluded: chain 27 residue 7 ARG Chi-restraints excluded: chain 27 residue 13 GLU Chi-restraints excluded: chain 27 residue 15 ASN Chi-restraints excluded: chain 27 residue 47 ARG Chi-restraints excluded: chain 28 residue 9 THR Chi-restraints excluded: chain 28 residue 24 LEU Chi-restraints excluded: chain 28 residue 31 ILE Chi-restraints excluded: chain 29 residue 16 CYS Chi-restraints excluded: chain 29 residue 20 ASN Chi-restraints excluded: chain 29 residue 22 MET Chi-restraints excluded: chain 29 residue 27 THR Chi-restraints excluded: chain 29 residue 32 LEU Chi-restraints excluded: chain 29 residue 58 ASP Chi-restraints excluded: chain 30 residue 3 GLN Chi-restraints excluded: chain 30 residue 8 THR Chi-restraints excluded: chain 30 residue 22 THR Chi-restraints excluded: chain 30 residue 24 VAL Chi-restraints excluded: chain 30 residue 28 SER Chi-restraints excluded: chain 30 residue 36 LYS Chi-restraints excluded: chain 30 residue 45 ASP Chi-restraints excluded: chain 30 residue 53 VAL Chi-restraints excluded: chain 31 residue 8 ILE Chi-restraints excluded: chain 31 residue 16 THR Chi-restraints excluded: chain 31 residue 42 VAL Chi-restraints excluded: chain 33 residue 6 VAL Chi-restraints excluded: chain 33 residue 63 TYR Chi-restraints excluded: chain 34 residue 17 VAL Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 7 ASN Chi-restraints excluded: chain C residue 44 LYS Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 189 ASP Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 111 ARG Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 61 PHE Chi-restraints excluded: chain G residue 115 MET Chi-restraints excluded: chain H residue 1 SER Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain K residue 17 ASP Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 26 PHE Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 102 ASP Chi-restraints excluded: chain L residue 108 ASP Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 11 HIS Chi-restraints excluded: chain M residue 19 THR Chi-restraints excluded: chain M residue 22 TYR Chi-restraints excluded: chain M residue 44 ILE Chi-restraints excluded: chain M residue 61 LYS Chi-restraints excluded: chain M residue 77 LYS Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 32 ASP Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain N residue 79 SER Chi-restraints excluded: chain O residue 17 ASP Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 24 SER Chi-restraints excluded: chain P residue 29 ASN Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain P residue 53 ASP Chi-restraints excluded: chain P residue 55 ASP Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain Q residue 21 VAL Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 60 ILE Chi-restraints excluded: chain R residue 9 PHE Chi-restraints excluded: chain R residue 10 CYS Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain S residue 10 ILE Chi-restraints excluded: chain S residue 11 ASP Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 37 SER Chi-restraints excluded: chain S residue 38 THR Chi-restraints excluded: chain S residue 42 ASN Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 70 LEU Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 39 GLU Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain T residue 43 LYS Chi-restraints excluded: chain T residue 66 ILE Chi-restraints excluded: chain T residue 73 ARG Chi-restraints excluded: chain U residue 12 ASP Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 34 ARG Chi-restraints excluded: chain U residue 38 GLU Chi-restraints excluded: chain U residue 52 VAL Chi-restraints excluded: chain 03 residue 16 ASP Chi-restraints excluded: chain 03 residue 18 THR Chi-restraints excluded: chain 03 residue 189 LEU Chi-restraints excluded: chain 03 residue 216 THR Chi-restraints excluded: chain Z residue 35 LEU Chi-restraints excluded: chain Z residue 145 LEU Chi-restraints excluded: chain Z residue 167 THR Chi-restraints excluded: chain Z residue 221 SER Chi-restraints excluded: chain Z residue 236 ILE Chi-restraints excluded: chain Z residue 269 ARG Chi-restraints excluded: chain Z residue 286 ILE Chi-restraints excluded: chain Z residue 360 VAL Chi-restraints excluded: chain Z residue 363 ILE 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: 10.0000 chunk 496 optimal weight: 8.9990 chunk 726 optimal weight: 10.0000 chunk 1096 optimal weight: 30.0000 chunk 1009 optimal weight: 7.9990 chunk 873 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 674 optimal weight: 10.0000 chunk 535 optimal weight: 0.9980 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 04 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 04 238 ASN 04 250 GLN ** 05 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 07 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 09 133 GLN 13 3 GLN 13 82 ASN 13 93 GLN ** 15 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 18 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 19 55 GLN 19 80 ASN ** 23 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 27 45 GLN ** 29 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 29 48 GLN ** 29 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 32 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 HIS ** E 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 GLN ** O 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 03 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 159 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.4940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 166817 Z= 0.260 Angle : 0.705 14.720 249070 Z= 0.359 Chirality : 0.038 0.365 31782 Planarity : 0.005 0.079 13715 Dihedral : 24.085 179.846 82300 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 24.92 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.53 % Favored : 88.33 % Rotamer: Outliers : 5.54 % Allowed : 27.30 % Favored : 67.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.10), residues: 6366 helix: -0.75 (0.11), residues: 1966 sheet: -1.82 (0.16), residues: 1023 loop : -2.36 (0.10), residues: 3377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP18 30 HIS 0.008 0.001 HIS K 117 PHE 0.045 0.002 PHE U 36 TYR 0.040 0.002 TYR M 85 ARG 0.023 0.001 ARG E 67 ********************** 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 1329 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 293 poor density : 1036 time to evaluate : 6.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 04 97 ASP cc_start: 0.7697 (p0) cc_final: 0.7219 (p0) REVERT: 04 200 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7922 (ttt) REVERT: 05 4 LEU cc_start: 0.7710 (mt) cc_final: 0.7448 (mt) REVERT: 05 11 MET cc_start: 0.8840 (tpp) cc_final: 0.8507 (mmm) REVERT: 07 37 MET cc_start: 0.9291 (ttm) cc_final: 0.8742 (tmm) REVERT: 07 127 TYR cc_start: 0.8104 (t80) cc_final: 0.7742 (t80) REVERT: 07 174 PHE cc_start: 0.8196 (m-10) cc_final: 0.7863 (m-80) REVERT: 08 172 GLU cc_start: 0.7456 (tm-30) cc_final: 0.7137 (tm-30) REVERT: 09 86 ASP cc_start: 0.8805 (t0) cc_final: 0.8578 (t0) REVERT: 09 97 ARG cc_start: 0.8889 (mmm-85) cc_final: 0.8559 (tpp80) REVERT: 11 116 MET cc_start: 0.3539 (mmt) cc_final: 0.1029 (ttm) REVERT: 13 1 MET cc_start: 0.7458 (tpt) cc_final: 0.7114 (tpt) REVERT: 13 32 TYR cc_start: 0.8547 (OUTLIER) cc_final: 0.7563 (p90) REVERT: 13 90 ASN cc_start: 0.8641 (OUTLIER) cc_final: 0.8165 (p0) REVERT: 16 2 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.7427 (ppp-140) REVERT: 16 106 ASP cc_start: 0.8204 (p0) cc_final: 0.7867 (p0) REVERT: 16 110 MET cc_start: 0.8620 (mmm) cc_final: 0.7732 (mmm) REVERT: 18 12 MET cc_start: 0.8554 (ptp) cc_final: 0.8052 (mtm) REVERT: 21 1 MET cc_start: 0.8459 (tpp) cc_final: 0.8172 (mmm) REVERT: 21 66 ILE cc_start: 0.9026 (OUTLIER) cc_final: 0.8760 (mp) REVERT: 22 1 MET cc_start: 0.6492 (ptm) cc_final: 0.6011 (ptp) REVERT: 22 24 MET cc_start: 0.8800 (mmm) cc_final: 0.8475 (mmm) REVERT: 24 48 MET cc_start: 0.9268 (tpp) cc_final: 0.8913 (tpp) REVERT: 25 11 ASP cc_start: 0.8267 (t0) cc_final: 0.7852 (t0) REVERT: 27 49 ASP cc_start: 0.9189 (m-30) cc_final: 0.8645 (p0) REVERT: 29 62 LYS cc_start: 0.9286 (tppt) cc_final: 0.9056 (tptp) REVERT: 30 36 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8166 (tppt) REVERT: 31 20 TYR cc_start: 0.8047 (m-10) cc_final: 0.7768 (m-10) REVERT: 31 24 LYS cc_start: 0.8124 (tppt) cc_final: 0.7815 (tppt) REVERT: B 191 ASP cc_start: 0.9050 (t0) cc_final: 0.8553 (t0) REVERT: B 193 ASP cc_start: 0.8413 (m-30) cc_final: 0.8115 (m-30) REVERT: D 97 LEU cc_start: 0.9116 (tp) cc_final: 0.8891 (tt) REVERT: E 45 VAL cc_start: 0.8587 (OUTLIER) cc_final: 0.8366 (t) REVERT: E 111 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.8029 (ttp80) REVERT: F 69 GLU cc_start: 0.8662 (pm20) cc_final: 0.8438 (pm20) REVERT: F 80 PHE cc_start: 0.8303 (m-80) cc_final: 0.8048 (m-80) REVERT: H 128 VAL cc_start: 0.8702 (OUTLIER) cc_final: 0.8452 (t) REVERT: I 58 GLU cc_start: 0.8602 (mm-30) cc_final: 0.7501 (tp30) REVERT: J 30 LYS cc_start: 0.8613 (pttm) cc_final: 0.8200 (ttpp) REVERT: J 45 ARG cc_start: 0.8074 (tpt170) cc_final: 0.7575 (ttt90) REVERT: K 57 SER cc_start: 0.9366 (m) cc_final: 0.9131 (m) REVERT: L 61 GLU cc_start: 0.7897 (tp30) cc_final: 0.7697 (tm-30) REVERT: M 10 ASP cc_start: 0.8486 (t0) cc_final: 0.7353 (t0) REVERT: N 17 ASP cc_start: 0.8789 (p0) cc_final: 0.7890 (t0) REVERT: N 22 LYS cc_start: 0.8014 (mptt) cc_final: 0.7694 (mptt) REVERT: N 32 ASP cc_start: 0.8425 (OUTLIER) cc_final: 0.8182 (t0) REVERT: N 34 ASN cc_start: 0.9064 (m110) cc_final: 0.8762 (m-40) REVERT: N 88 MET cc_start: 0.8172 (mmt) cc_final: 0.7863 (mmt) REVERT: Q 16 MET cc_start: 0.8589 (tpp) cc_final: 0.8322 (tpp) REVERT: S 42 ASN cc_start: 0.8689 (OUTLIER) cc_final: 0.8269 (p0) REVERT: 03 218 MET cc_start: 0.5667 (mpp) cc_final: 0.4940 (mpp) REVERT: Z 21 ASP cc_start: 0.8148 (t70) cc_final: 0.7823 (t0) REVERT: Z 39 TYR cc_start: 0.7979 (t80) cc_final: 0.7498 (t80) REVERT: Z 147 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8753 (tm-30) REVERT: Z 368 MET cc_start: 0.6143 (mmm) cc_final: 0.5846 (mmp) outliers start: 293 outliers final: 264 residues processed: 1218 average time/residue: 1.2829 time to fit residues: 2755.8831 Evaluate side-chains 1258 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 275 poor density : 983 time to evaluate : 6.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 2 VAL Chi-restraints excluded: chain 04 residue 44 ASN Chi-restraints excluded: chain 04 residue 99 GLU Chi-restraints excluded: chain 04 residue 113 ASP Chi-restraints excluded: chain 04 residue 133 ASN Chi-restraints excluded: chain 04 residue 167 ASP Chi-restraints excluded: chain 04 residue 200 MET Chi-restraints excluded: chain 04 residue 249 VAL Chi-restraints excluded: chain 04 residue 250 GLN Chi-restraints excluded: chain 04 residue 263 ASP Chi-restraints excluded: chain 04 residue 267 VAL Chi-restraints excluded: chain 05 residue 2 ILE Chi-restraints excluded: chain 05 residue 104 VAL Chi-restraints excluded: chain 05 residue 137 SER Chi-restraints excluded: chain 05 residue 139 SER Chi-restraints excluded: chain 05 residue 186 LEU Chi-restraints excluded: chain 05 residue 199 SER Chi-restraints excluded: chain 06 residue 70 SER Chi-restraints excluded: chain 06 residue 73 ILE Chi-restraints excluded: chain 06 residue 97 ASN Chi-restraints excluded: chain 06 residue 119 ILE Chi-restraints excluded: chain 06 residue 149 ILE Chi-restraints excluded: chain 06 residue 187 VAL Chi-restraints excluded: chain 07 residue 22 ASN Chi-restraints excluded: chain 07 residue 24 VAL Chi-restraints excluded: chain 07 residue 25 MET Chi-restraints excluded: chain 07 residue 30 VAL Chi-restraints excluded: chain 07 residue 60 SER Chi-restraints excluded: chain 07 residue 144 LYS Chi-restraints excluded: chain 07 residue 146 ASP Chi-restraints excluded: chain 07 residue 164 GLU Chi-restraints excluded: chain 08 residue 9 VAL Chi-restraints excluded: chain 08 residue 15 ASP Chi-restraints excluded: chain 08 residue 19 ASN Chi-restraints excluded: chain 08 residue 44 HIS Chi-restraints excluded: chain 08 residue 55 ASP Chi-restraints excluded: chain 08 residue 126 THR Chi-restraints excluded: chain 08 residue 130 ILE Chi-restraints excluded: chain 08 residue 146 ASP Chi-restraints excluded: chain 08 residue 161 VAL Chi-restraints excluded: chain 08 residue 167 VAL Chi-restraints excluded: chain 09 residue 40 THR Chi-restraints excluded: chain 09 residue 47 PHE Chi-restraints excluded: chain 09 residue 91 PHE Chi-restraints excluded: chain 09 residue 99 ILE Chi-restraints excluded: chain 09 residue 115 VAL Chi-restraints excluded: chain 09 residue 128 HIS Chi-restraints excluded: chain 09 residue 133 GLN Chi-restraints excluded: chain 09 residue 134 VAL Chi-restraints excluded: chain 10 residue 27 VAL Chi-restraints excluded: chain 10 residue 50 VAL Chi-restraints excluded: chain 10 residue 77 VAL Chi-restraints excluded: chain 10 residue 82 ILE Chi-restraints excluded: chain 11 residue 46 ASP Chi-restraints excluded: chain 11 residue 63 ASP Chi-restraints excluded: chain 11 residue 138 VAL Chi-restraints excluded: chain 12 residue 12 LYS Chi-restraints excluded: chain 12 residue 17 VAL Chi-restraints excluded: chain 12 residue 25 LEU Chi-restraints excluded: chain 12 residue 50 THR Chi-restraints excluded: chain 12 residue 57 LEU Chi-restraints excluded: chain 12 residue 62 VAL Chi-restraints excluded: chain 12 residue 67 ASN Chi-restraints excluded: chain 12 residue 81 ILE Chi-restraints excluded: chain 12 residue 93 ILE Chi-restraints excluded: chain 12 residue 131 ASN Chi-restraints excluded: chain 13 residue 3 GLN Chi-restraints excluded: chain 13 residue 13 ASN Chi-restraints excluded: chain 13 residue 28 SER Chi-restraints excluded: chain 13 residue 32 TYR Chi-restraints excluded: chain 13 residue 35 VAL Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 56 ASP Chi-restraints excluded: chain 13 residue 69 VAL Chi-restraints excluded: chain 13 residue 87 LEU Chi-restraints excluded: chain 13 residue 90 ASN Chi-restraints excluded: chain 13 residue 91 SER Chi-restraints excluded: chain 14 residue 27 LEU Chi-restraints excluded: chain 14 residue 67 THR Chi-restraints excluded: chain 14 residue 73 ILE Chi-restraints excluded: chain 14 residue 85 VAL Chi-restraints excluded: chain 15 residue 7 THR Chi-restraints excluded: chain 15 residue 36 VAL Chi-restraints excluded: chain 15 residue 42 THR Chi-restraints excluded: chain 15 residue 78 LEU Chi-restraints excluded: chain 15 residue 95 LEU Chi-restraints excluded: chain 15 residue 115 GLU Chi-restraints excluded: chain 15 residue 128 THR Chi-restraints excluded: chain 15 residue 129 THR Chi-restraints excluded: chain 16 residue 2 ARG Chi-restraints excluded: chain 16 residue 33 ILE Chi-restraints excluded: chain 16 residue 76 VAL Chi-restraints excluded: chain 16 residue 89 SER Chi-restraints excluded: chain 17 residue 28 VAL Chi-restraints excluded: chain 17 residue 35 ILE Chi-restraints excluded: chain 17 residue 47 VAL Chi-restraints excluded: chain 17 residue 87 ILE Chi-restraints excluded: chain 18 residue 31 VAL Chi-restraints excluded: chain 18 residue 43 GLU Chi-restraints excluded: chain 18 residue 59 THR Chi-restraints excluded: chain 18 residue 100 ARG Chi-restraints excluded: chain 19 residue 7 VAL Chi-restraints excluded: chain 19 residue 38 VAL Chi-restraints excluded: chain 19 residue 61 ILE Chi-restraints excluded: chain 19 residue 79 ILE Chi-restraints excluded: chain 19 residue 82 LEU Chi-restraints excluded: chain 19 residue 103 VAL Chi-restraints excluded: chain 19 residue 108 LEU Chi-restraints excluded: chain 20 residue 29 THR Chi-restraints excluded: chain 20 residue 51 VAL Chi-restraints excluded: chain 20 residue 102 SER Chi-restraints excluded: chain 21 residue 3 THR Chi-restraints excluded: chain 21 residue 4 ILE Chi-restraints excluded: chain 21 residue 66 ILE Chi-restraints excluded: chain 21 residue 67 ASP Chi-restraints excluded: chain 21 residue 81 SER Chi-restraints excluded: chain 22 residue 31 VAL Chi-restraints excluded: chain 22 residue 32 LEU Chi-restraints excluded: chain 22 residue 39 THR Chi-restraints excluded: chain 22 residue 76 ARG Chi-restraints excluded: chain 22 residue 79 ASP Chi-restraints excluded: chain 24 residue 30 ILE Chi-restraints excluded: chain 24 residue 90 ASP Chi-restraints excluded: chain 25 residue 26 SER Chi-restraints excluded: chain 25 residue 34 VAL Chi-restraints excluded: chain 26 residue 24 THR Chi-restraints excluded: chain 26 residue 29 LEU Chi-restraints excluded: chain 26 residue 61 LYS Chi-restraints excluded: chain 26 residue 71 ARG Chi-restraints excluded: chain 27 residue 7 ARG Chi-restraints excluded: chain 27 residue 13 GLU Chi-restraints excluded: chain 27 residue 15 ASN Chi-restraints excluded: chain 28 residue 9 THR Chi-restraints excluded: chain 28 residue 24 LEU Chi-restraints excluded: chain 28 residue 31 ILE Chi-restraints excluded: chain 29 residue 16 CYS Chi-restraints excluded: chain 29 residue 20 ASN Chi-restraints excluded: chain 29 residue 27 THR Chi-restraints excluded: chain 29 residue 32 LEU Chi-restraints excluded: chain 29 residue 58 ASP Chi-restraints excluded: chain 30 residue 3 GLN Chi-restraints excluded: chain 30 residue 8 THR Chi-restraints excluded: chain 30 residue 22 THR Chi-restraints excluded: chain 30 residue 24 VAL Chi-restraints excluded: chain 30 residue 28 SER Chi-restraints excluded: chain 30 residue 36 LYS Chi-restraints excluded: chain 30 residue 45 ASP Chi-restraints excluded: chain 30 residue 53 VAL Chi-restraints excluded: chain 31 residue 16 THR Chi-restraints excluded: chain 31 residue 49 LYS Chi-restraints excluded: chain 33 residue 6 VAL Chi-restraints excluded: chain 33 residue 54 LEU Chi-restraints excluded: chain 34 residue 17 VAL Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain C residue 7 ASN Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 133 SER Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 111 ARG Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 61 PHE Chi-restraints excluded: chain G residue 115 MET Chi-restraints excluded: chain H residue 9 MET Chi-restraints excluded: chain H residue 53 ASP Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 95 MET Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 110 VAL Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain K residue 17 ASP Chi-restraints excluded: chain K residue 29 THR Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 108 ASP Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 11 HIS Chi-restraints excluded: chain M residue 44 ILE Chi-restraints excluded: chain M residue 61 LYS Chi-restraints excluded: chain M residue 77 LYS Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 32 ASP Chi-restraints excluded: chain O residue 17 ASP Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 47 GLU Chi-restraints excluded: chain P residue 55 ASP Chi-restraints excluded: chain Q residue 11 VAL Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain Q residue 21 VAL Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 60 ILE Chi-restraints excluded: chain R residue 9 PHE Chi-restraints excluded: chain R residue 10 CYS Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain S residue 10 ILE Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 37 SER Chi-restraints excluded: chain S residue 42 ASN Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 70 LEU Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain T residue 43 LYS Chi-restraints excluded: chain T residue 66 ILE Chi-restraints excluded: chain T residue 73 ARG Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 34 ARG Chi-restraints excluded: chain U residue 38 GLU Chi-restraints excluded: chain 03 residue 18 THR Chi-restraints excluded: chain 03 residue 42 VAL Chi-restraints excluded: chain 03 residue 189 LEU Chi-restraints excluded: chain 03 residue 216 THR Chi-restraints excluded: chain Z residue 145 LEU Chi-restraints excluded: chain Z residue 167 THR Chi-restraints excluded: chain Z residue 221 SER Chi-restraints excluded: chain Z residue 236 ILE Chi-restraints excluded: chain Z residue 269 ARG Chi-restraints excluded: chain Z residue 286 ILE Chi-restraints excluded: chain Z residue 363 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1101 random chunks: chunk 693 optimal weight: 20.0000 chunk 930 optimal weight: 20.0000 chunk 267 optimal weight: 0.7980 chunk 805 optimal weight: 20.0000 chunk 128 optimal weight: 9.9990 chunk 242 optimal weight: 20.0000 chunk 874 optimal weight: 20.0000 chunk 366 optimal weight: 0.9990 chunk 898 optimal weight: 20.0000 chunk 110 optimal weight: 9.9990 chunk 161 optimal weight: 0.0000 overall best weight: 4.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 04 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 04 250 GLN ** 05 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 07 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 10 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 13 3 GLN ** 13 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 93 GLN ** 15 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 18 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 23 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 29 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 29 48 GLN ** 29 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 32 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 03 67 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 159 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.042190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.034574 restraints weight = 1208952.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.035612 restraints weight = 398947.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.036209 restraints weight = 201717.446| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.4947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.316 166817 Z= 0.285 Angle : 0.747 59.151 249070 Z= 0.394 Chirality : 0.038 1.005 31782 Planarity : 0.005 0.122 13715 Dihedral : 24.083 179.832 82300 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 26.51 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.81 % Favored : 88.05 % Rotamer: Outliers : 5.71 % Allowed : 27.56 % Favored : 66.72 % Cbeta Deviations : 0.05 % 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: -2.59 (0.10), residues: 6366 helix: -0.73 (0.11), residues: 1966 sheet: -1.80 (0.16), residues: 1023 loop : -2.35 (0.10), residues: 3377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.091 0.003 TRP18 30 HIS 0.018 0.001 HIS S 68 PHE 0.043 0.002 PHE U 36 TYR 0.034 0.002 TYR B 212 ARG 0.014 0.001 ARG Q 76 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 42002.16 seconds wall clock time: 736 minutes 54.76 seconds (44214.76 seconds total)