Starting phenix.real_space_refine on Sat Mar 2 11:25:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uym_8617/03_2024/5uym_8617_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uym_8617/03_2024/5uym_8617.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uym_8617/03_2024/5uym_8617.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uym_8617/03_2024/5uym_8617.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uym_8617/03_2024/5uym_8617_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uym_8617/03_2024/5uym_8617_updated.pdb" } resolution = 3.2 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= -0.393 sd= 1.187 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 4806 5.49 5 Mg 383 5.21 5 S 172 5.16 5 C 77705 2.51 5 N 28575 2.21 5 O 42496 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 ARG 96": "NH1" <-> "NH2" Residue "12 ARG 120": "NH1" <-> "NH2" Residue "14 ARG 21": "NH1" <-> "NH2" Residue "14 ARG 33": "NH1" <-> "NH2" Residue "14 ARG 41": "NH1" <-> "NH2" Residue "14 ARG 47": "NH1" <-> "NH2" Residue "14 ARG 60": "NH1" <-> "NH2" Residue "14 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 ARG 21": "NH1" <-> "NH2" Residue "20 ARG 68": "NH1" <-> "NH2" Residue "20 ARG 78": "NH1" <-> "NH2" Residue "20 ARG 79": "NH1" <-> "NH2" Residue "20 ARG 84": "NH1" <-> "NH2" Residue "21 ARG 84": "NH1" <-> "NH2" Residue "21 ARG 88": "NH1" <-> "NH2" Residue "21 ARG 95": "NH1" <-> "NH2" Residue "21 ARG 110": "NH1" <-> "NH2" Residue "22 ARG 73": "NH1" <-> "NH2" Residue "23 ARG 5": "NH1" <-> "NH2" Residue "23 ARG 6": "NH1" <-> "NH2" Residue "23 ARG 81": "NH1" <-> "NH2" Residue "23 ARG 85": "NH1" <-> "NH2" Residue "23 ARG 93": "NH1" <-> "NH2" Residue "24 TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "27 ARG 29": "NH1" <-> "NH2" Residue "27 ARG 47": "NH1" <-> "NH2" Residue "27 ARG 52": "NH1" <-> "NH2" Residue "28 ARG 10": "NH1" <-> "NH2" Residue "28 ARG 29": "NH1" <-> "NH2" Residue "28 ARG 44": "NH1" <-> "NH2" Residue "29 ARG 49": "NH1" <-> "NH2" Residue "29 ARG 56": "NH1" <-> "NH2" Residue "30 ARG 9": "NH1" <-> "NH2" Residue "30 ARG 15": "NH1" <-> "NH2" Residue "30 ARG 39": "NH1" <-> "NH2" Residue "30 ARG 51": "NH1" <-> "NH2" Residue "31 ARG 43": "NH1" <-> "NH2" Residue "31 TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "32 ARG 3": "NH1" <-> "NH2" Residue "32 ARG 12": "NH1" <-> "NH2" Residue "32 ARG 14": "NH1" <-> "NH2" Residue "32 ARG 19": "NH1" <-> "NH2" Residue "32 ARG 21": "NH1" <-> "NH2" Residue "32 ARG 33": "NH1" <-> "NH2" Residue "32 ARG 41": "NH1" <-> "NH2" Residue "33 ARG 12": "NH1" <-> "NH2" Residue "33 ARG 29": "NH1" <-> "NH2" Residue "33 ARG 39": "NH1" <-> "NH2" Residue "33 ARG 41": "NH1" <-> "NH2" Residue "34 ARG 12": "NH1" <-> "NH2" Residue "34 ARG 24": "NH1" <-> "NH2" Residue "B ARG 107": "NH1" <-> "NH2" Residue "B ARG 224": "NH1" <-> "NH2" Residue "C ARG 106": "NH1" <-> "NH2" Residue "C ARG 130": "NH1" <-> "NH2" Residue "E ARG 156": "NH1" <-> "NH2" Residue "I ARG 123": "NH1" <-> "NH2" Residue "L ARG 55": "NH1" <-> "NH2" Residue "P ARG 28": "NH1" <-> "NH2" Residue "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 PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 44": "NH1" <-> "NH2" Residue "Z TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 223": "NH1" <-> "NH2" Residue "Z ARG 269": "NH1" <-> "NH2" Residue "Z PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 374": "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: 154139 Number of models: 1 Model: "" Number of chains: 72 Chain: "04" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2083 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "05" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "06" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "07" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1411 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "08" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "09" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "10" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 989 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "11" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1032 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "12" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "13" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 939 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "14" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "15" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "16" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 961 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "17" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "18" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "19" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "20" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "21" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "22" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 739 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "23" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 780 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "24" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "25" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "26" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "27" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "28" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "29" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 523 Classifications: {'peptide': 66} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "30" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "31" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 410 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "32" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "33" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "34" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "B" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1705 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "C" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1625 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1157 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "F" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 818 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "G" Number of atoms: 1182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1182 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "I" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 787 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "K" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 870 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "L" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "M" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 884 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "O" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Q" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 649 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "R" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 536 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "S" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 638 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "T" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "U" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 545 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "03" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1027 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain breaks: 1 Chain: "A" Number of atoms: 33012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33012 Classifications: {'RNA': 1539} Modifications used: {'5*END': 1, 'rna2p_pur': 90, 'rna2p_pyr': 49, 'rna3p_pur': 784, 'rna3p_pyr': 616} Link IDs: {'rna2p': 139, 'rna3p': 1399} 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': 211, 'rna2p_pyr': 96, 'rna3p_pur': 1463, 'rna3p_pyr': 1133} Link IDs: {'rna2p': 307, 'rna3p': 2595} 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': 4, 'rna2p_pyr': 2, 'rna3p_pur': 61, 'rna3p_pyr': 53} Link IDs: {'rna2p': 6, 'rna3p': 113} 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': 6, 'rna2p_pyr': 5, 'rna3p_pur': 33, 'rna3p_pyr': 33} Link IDs: {'rna2p': 11, 'rna3p': 65} 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': 8, 'rna2p_pyr': 4, 'rna3p_pur': 31, 'rna3p_pyr': 33} 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: "12" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "25" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "29" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "34" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 107 Unusual residues: {' MG': 107} Classifications: {'undetermined': 107} Link IDs: {None: 106} Chain: "01" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 263 Unusual residues: {' MG': 263} Classifications: {'undetermined': 263} Link IDs: {None: 262} Chain: "02" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' MG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "V" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 11 Unusual residues: {' MG': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GCP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 58.95, per 1000 atoms: 0.38 Number of scatterers: 154139 At special positions: 0 Unit cell: (280.44, 266.5, 240.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 172 16.00 P 4806 15.00 Mg 383 11.99 O 42496 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: 61.40 Conformation dependent library (CDL) restraints added in 7.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN34 101 " pdb="ZN ZN34 101 " - pdb=" ND1 HIS34 33 " 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: 190 helices and 81 sheets defined 37.7% alpha, 19.7% beta 1530 base pairs and 2903 stacking pairs defined. Time for finding SS restraints: 80.45 Creating SS restraints... Processing helix chain '04' and resid 9 through 15 removed outlier: 7.387A pdb=" N HIS04 14 " --> pdb=" O PRO04 10 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N VAL04 15 " --> pdb=" O GLY04 11 " (cutoff:3.500A) Processing helix chain '04' and resid 29 through 34 removed outlier: 4.115A pdb=" N LEU04 33 " --> pdb=" O PHE04 29 " (cutoff:3.500A) removed outlier: 5.733A 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: 3.634A 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: 4.267A pdb=" N ALA04 210 " --> pdb=" O LYS04 206 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG04 211 " --> pdb=" O ALA04 207 " (cutoff:3.500A) Processing helix chain '04' and resid 220 through 225 removed outlier: 3.859A pdb=" N MET04 224 " --> pdb=" O ARG04 220 " (cutoff:3.500A) removed outlier: 5.220A 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: 6.154A pdb=" N ASP04 263 " --> pdb=" O ASN04 259 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N LYS04 264 " --> pdb=" O LYS04 260 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N PHE04 265 " --> pdb=" O ARG04 261 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE04 266 " --> pdb=" O THR04 262 " (cutoff:3.500A) removed outlier: 5.658A 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: 4.391A pdb=" N MET04 200 " --> pdb=" O ALA04 197 " (cutoff:3.500A) Processing helix chain '05' and resid 61 through 72 removed outlier: 3.600A pdb=" N ALA05 71 " --> pdb=" O HIS05 67 " (cutoff:3.500A) Processing helix chain '05' and resid 120 through 125 Processing helix chain '05' and resid 97 through 103 removed outlier: 3.606A pdb=" N LEU05 100 " --> pdb=" O SER05 97 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE05 101 " --> pdb=" O VAL05 98 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N ASP05 103 " --> pdb=" O LEU05 100 " (cutoff:3.500A) Processing helix chain '06' and resid 15 through 20 Processing helix chain '06' and resid 24 through 40 removed outlier: 3.771A pdb=" N ALA06 34 " --> pdb=" O GLN06 30 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG06 40 " --> pdb=" O ALA06 36 " (cutoff:3.500A) Processing helix chain '06' and resid 97 through 116 removed outlier: 3.513A pdb=" N SER06 107 " --> pdb=" O GLY06 103 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER06 110 " --> pdb=" O LYS06 106 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL06 113 " --> pdb=" O LEU06 109 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG06 114 " --> pdb=" O SER06 110 " (cutoff:3.500A) Processing helix chain '06' and resid 130 through 142 removed outlier: 3.807A pdb=" N LEU06 134 " --> pdb=" O LYS06 130 " (cutoff:3.500A) Processing helix chain '06' and resid 154 through 163 removed outlier: 4.088A pdb=" N ARG06 162 " --> pdb=" O PHE06 158 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ASN06 163 " --> pdb=" O LEU06 159 " (cutoff:3.500A) Processing helix chain '06' and resid 176 through 184 removed outlier: 3.557A pdb=" N ILE06 181 " --> pdb=" O PRO06 177 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ASP06 184 " --> pdb=" O LEU06 180 " (cutoff:3.500A) Processing helix chain '06' and resid 189 through 201 removed outlier: 3.724A pdb=" N LYS06 194 " --> pdb=" O ALA06 190 " (cutoff:3.500A) Processing helix chain '07' and resid 1 through 20 removed outlier: 3.849A pdb=" N ASP07 5 " --> pdb=" O ALA07 1 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR07 6 " --> pdb=" O LYS07 2 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N VAL07 12 " --> pdb=" O LYS07 8 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LYS07 13 " --> pdb=" O ASP07 9 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLU07 18 " --> pdb=" O LYS07 14 " (cutoff:3.500A) Processing helix chain '07' and resid 41 through 46 removed outlier: 3.783A pdb=" N ASP07 45 " --> pdb=" O GLU07 41 " (cutoff:3.500A) removed outlier: 4.036A 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: 3.678A pdb=" N ALA07 54 " --> pdb=" O ASP07 50 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA07 57 " --> pdb=" O ALA07 53 " (cutoff:3.500A) Processing helix chain '07' and resid 92 through 110 removed outlier: 4.590A pdb=" N TRP07 96 " --> pdb=" O GLY07 92 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU07 97 " --> pdb=" O GLU07 93 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE07 98 " --> pdb=" O ARG07 94 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE07 105 " --> pdb=" O ARG07 101 " (cutoff:3.500A) removed outlier: 5.300A 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: 6.760A pdb=" N VAL07 145 " --> pdb=" O ASP07 141 " (cutoff:3.500A) removed outlier: 6.350A 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: 3.952A pdb=" N ALA07 167 " --> pdb=" O GLU07 163 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA07 171 " --> pdb=" O ALA07 167 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N PHE07 172 " --> pdb=" O LEU07 168 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASP07 173 " --> pdb=" O LEU07 169 " (cutoff:3.500A) Processing helix chain '07' and resid 133 through 138 removed outlier: 4.232A pdb=" N ILE07 136 " --> pdb=" O GLU07 133 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE07 137 " --> pdb=" O GLN07 134 " (cutoff:3.500A) Proline residue: 07 138 - end of helix No H-bonds generated for 'chain '07' and resid 133 through 138' Processing helix chain '08' and resid 1 through 7 removed outlier: 4.021A pdb=" N ALA08 6 " --> pdb=" O ARG08 2 " (cutoff:3.500A) Proline residue: 08 7 - end of helix Processing helix chain '08' and resid 59 through 80 removed outlier: 3.632A pdb=" N ALA08 69 " --> pdb=" O GLY08 65 " (cutoff:3.500A) Processing helix chain '08' and resid 136 through 152 removed outlier: 4.155A 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 54 removed outlier: 3.834A pdb=" N GLU09 45 " --> pdb=" O LYS09 41 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE09 46 " --> pdb=" O LYS09 42 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE09 47 " --> pdb=" O ASN09 43 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA09 49 " --> pdb=" O GLU09 45 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG09 50 " --> pdb=" O PHE09 46 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ALA09 52 " --> pdb=" O GLU09 48 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU09 53 " --> pdb=" O ALA09 49 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU09 54 " --> pdb=" O ARG09 50 " (cutoff:3.500A) Processing helix chain '09' and resid 55 through 72 removed outlier: 3.601A pdb=" N ALA09 59 " --> pdb=" O GLU09 55 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU09 60 " --> pdb=" O ALA09 56 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LYS09 71 " --> pdb=" O ALA09 67 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE09 72 " --> pdb=" O ARG09 68 " (cutoff:3.500A) Processing helix chain '09' and resid 95 through 107 removed outlier: 3.734A pdb=" N THR09 104 " --> pdb=" O ALA09 100 " (cutoff:3.500A) Processing helix chain '09' and resid 111 through 116 removed outlier: 3.957A pdb=" N VAL09 115 " --> pdb=" O ALA09 111 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ARG09 116 " --> pdb=" O LYS09 112 " (cutoff:3.500A) No H-bonds generated for 'chain '09' and resid 111 through 116' Processing helix chain '10' and resid 3 through 21 removed outlier: 3.598A pdb=" N GLN10 9 " --> pdb=" O LEU10 5 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU10 17 " --> pdb=" O ALA10 13 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA10 19 " --> pdb=" O VAL10 15 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LYS10 20 " --> pdb=" O SER10 16 " (cutoff:3.500A) Processing helix chain '10' and resid 33 through 48 removed outlier: 3.536A pdb=" N GLU10 40 " --> pdb=" O ASP10 36 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU10 41 " --> pdb=" O LYS10 37 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG10 42 " --> pdb=" O MET10 38 " (cutoff:3.500A) Processing helix chain '10' and resid 62 through 70 removed outlier: 4.665A pdb=" N GLY10 66 " --> pdb=" O ARG10 62 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR10 67 " --> pdb=" O ALA10 63 " (cutoff:3.500A) Proline residue: 10 68 - end of helix No H-bonds generated for 'chain '10' and resid 62 through 70' Processing helix chain '10' and resid 94 through 106 removed outlier: 3.752A pdb=" N PHE10 99 " --> pdb=" O LEU10 95 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA10 100 " --> pdb=" O PHE10 96 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LYS10 105 " --> pdb=" O LYS10 101 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE10 106 " --> pdb=" O ALA10 102 " (cutoff:3.500A) Processing helix chain '10' and resid 71 through 77 removed outlier: 3.711A pdb=" N ALA10 75 " --> pdb=" O LEU10 72 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE10 76 " --> pdb=" O LYS10 73 " (cutoff:3.500A) Processing helix chain '10' and resid 109 through 114 removed outlier: 6.081A pdb=" N ALA10 112 " --> pdb=" O LYS10 109 " (cutoff:3.500A) Processing helix chain '11' and resid 23 through 31 removed outlier: 4.857A pdb=" N LEU11 27 " --> pdb=" O VAL11 23 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N GLN11 30 " --> pdb=" O ALA11 26 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N GLY11 31 " --> pdb=" O LEU11 27 " (cutoff:3.500A) Processing helix chain '11' and resid 33 through 49 removed outlier: 3.634A pdb=" N LYS11 39 " --> pdb=" O MET11 35 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ALA11 43 " --> pdb=" O LYS11 39 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LYS11 44 " --> pdb=" O ALA11 40 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR11 45 " --> pdb=" O PHE11 41 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP11 46 " --> pdb=" O ASN11 42 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER11 47 " --> pdb=" O ALA11 43 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILE11 48 " --> pdb=" O LYS11 44 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU11 49 " --> pdb=" O THR11 45 " (cutoff:3.500A) Processing helix chain '11' and resid 74 through 83 removed outlier: 3.551A pdb=" N LYS11 80 " --> pdb=" O ALA11 76 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA11 83 " --> pdb=" O LEU11 79 " (cutoff:3.500A) Processing helix chain '11' and resid 103 through 114 removed outlier: 3.615A pdb=" N ALA11 114 " --> pdb=" O GLN11 110 " (cutoff:3.500A) Processing helix chain '11' and resid 120 through 136 removed outlier: 3.697A pdb=" N ARG11 126 " --> pdb=" O GLU11 122 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N SER11 127 " --> pdb=" O ALA11 123 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR11 131 " --> pdb=" O SER11 127 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA11 132 " --> pdb=" O ILE11 128 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER11 134 " --> pdb=" O GLY11 130 " (cutoff:3.500A) Processing helix chain '12' and resid 24 through 38 removed outlier: 3.622A pdb=" N GLU12 31 " --> pdb=" O ARG12 27 " (cutoff:3.500A) Processing helix chain '12' and resid 88 through 96 removed outlier: 3.691A pdb=" N ALA12 94 " --> pdb=" O GLU12 90 " (cutoff:3.500A) Processing helix chain '12' and resid 97 through 110 removed outlier: 4.729A pdb=" N ILE12 101 " --> pdb=" O PRO12 97 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS12 106 " --> pdb=" O GLU12 102 " (cutoff:3.500A) removed outlier: 3.735A 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 123 removed outlier: 3.525A pdb=" N PHE12 119 " --> pdb=" O GLY12 115 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG12 120 " --> pdb=" O ARG12 116 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS12 121 " --> pdb=" O ALA12 117 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LEU12 122 " --> pdb=" O MET12 118 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N LYS12 123 " --> pdb=" O PHE12 119 " (cutoff:3.500A) Processing helix chain '13' and resid 109 through 120 removed outlier: 6.425A pdb=" N MET13 113 " --> pdb=" O SER13 109 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LYS13 114 " --> pdb=" O GLU13 110 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ILE13 115 " --> pdb=" O LYS13 111 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU13 118 " --> pdb=" O LYS13 114 " (cutoff:3.500A) Proline residue: 13 120 - end of helix Processing helix chain '14' and resid 56 through 62 removed outlier: 3.540A 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: 4.548A pdb=" N ALA14 72 " --> pdb=" O SER14 68 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE14 73 " --> pdb=" O ARG14 69 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR14 74 " --> pdb=" O LYS14 70 " (cutoff:3.500A) removed outlier: 6.056A 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: 3.754A pdb=" N LEU14 82 " --> pdb=" O ARG14 78 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA14 83 " --> pdb=" O LEU14 79 " (cutoff:3.500A) No H-bonds generated for 'chain '14' and resid 78 through 83' Processing helix chain '14' and resid 91 through 99 removed outlier: 4.456A pdb=" N LEU14 95 " --> pdb=" O ASP14 91 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LYS14 96 " --> pdb=" O LEU14 92 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ALA14 97 " --> pdb=" O ASN14 93 " (cutoff:3.500A) Processing helix chain '14' and resid 128 through 139 removed outlier: 3.749A pdb=" N ALA14 138 " --> pdb=" O ALA14 134 " (cutoff:3.500A) Processing helix chain '15' and resid 42 through 58 removed outlier: 4.142A pdb=" N MET15 53 " --> pdb=" O ALA15 49 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ALA15 56 " --> pdb=" O ALA15 52 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL15 57 " --> pdb=" O MET15 53 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N LYS15 58 " --> pdb=" O THR15 54 " (cutoff:3.500A) Processing helix chain '15' and resid 109 through 125 removed outlier: 3.757A pdb=" N LYS15 118 " --> pdb=" O ARG15 114 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU15 119 " --> pdb=" O GLU15 115 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA15 122 " --> pdb=" O LYS15 118 " (cutoff:3.500A) removed outlier: 4.015A 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: 3.532A pdb=" N GLY16 26 " --> pdb=" O ARG16 22 " (cutoff:3.500A) Processing helix chain '16' and resid 38 through 58 removed outlier: 4.542A pdb=" N ARG16 46 " --> pdb=" O LYS16 42 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL16 47 " --> pdb=" O GLU16 43 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU16 49 " --> pdb=" O ARG16 45 " (cutoff:3.500A) Proline residue: 16 50 - end of helix removed outlier: 4.451A pdb=" N THR16 57 " --> pdb=" O THR16 53 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ASP16 58 " --> pdb=" O LEU16 54 " (cutoff:3.500A) Processing helix chain '16' and resid 59 through 71 removed outlier: 4.305A pdb=" N ARG16 63 " --> pdb=" O SER16 59 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG16 69 " --> pdb=" O LEU16 65 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N THR16 70 " --> pdb=" O ALA16 66 " (cutoff:3.500A) Processing helix chain '16' and resid 72 through 82 removed outlier: 4.325A pdb=" N PHE16 80 " --> pdb=" O VAL16 76 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ASN16 81 " --> pdb=" O ALA16 77 " (cutoff:3.500A) Processing helix chain '16' and resid 83 through 89 removed outlier: 3.620A pdb=" N PHE16 87 " --> pdb=" O LEU16 83 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA16 88 " --> pdb=" O GLY16 84 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N SER16 89 " --> pdb=" O PRO16 85 " (cutoff:3.500A) No H-bonds generated for 'chain '16' and resid 83 through 89' Processing helix chain '17' and resid 2 through 20 removed outlier: 3.713A pdb=" N ARG17 7 " --> pdb=" O LYS17 3 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG17 10 " --> pdb=" O ALA17 6 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG17 13 " --> pdb=" O ARG17 9 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ALA17 14 " --> pdb=" O ARG17 10 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS17 17 " --> pdb=" O ARG17 13 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU17 20 " --> pdb=" O ARG17 16 " (cutoff:3.500A) Processing helix chain '17' and resid 55 through 63 removed outlier: 5.175A pdb=" N GLN17 61 " --> pdb=" O ALA17 57 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU17 62 " --> pdb=" O ILE17 58 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N LYS17 63 " --> pdb=" O ALA17 59 " (cutoff:3.500A) Processing helix chain '17' and resid 67 through 86 removed outlier: 3.772A pdb=" N LEU17 83 " --> pdb=" O ALA17 79 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU17 84 " --> pdb=" O GLU17 80 " (cutoff:3.500A) Processing helix chain '17' and resid 101 through 114 removed outlier: 3.681A pdb=" N ALA17 107 " --> pdb=" O VAL17 103 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU17 112 " --> pdb=" O ASP17 108 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA17 113 " --> pdb=" O ALA17 109 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY17 114 " --> pdb=" O ALA17 110 " (cutoff:3.500A) Processing helix chain '18' and resid 1 through 13 removed outlier: 3.724A pdb=" N GLU18 10 " --> pdb=" O GLN18 6 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLN18 11 " --> pdb=" O LEU18 7 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LYS18 13 " --> pdb=" O GLN18 9 " (cutoff:3.500A) Processing helix chain '18' and resid 96 through 103 removed outlier: 4.943A pdb=" N ARG18 100 " --> pdb=" O LEU18 96 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N GLU18 101 " --> pdb=" O TYR18 97 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N THR18 103 " --> pdb=" O LEU18 99 " (cutoff:3.500A) Processing helix chain '19' and resid 5 through 21 removed outlier: 4.006A pdb=" N ALA19 9 " --> pdb=" O ARG19 5 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA19 11 " --> pdb=" O VAL19 7 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG19 12 " --> pdb=" O ILE19 8 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE19 16 " --> pdb=" O ARG19 12 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN19 19 " --> pdb=" O LYS19 15 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LYS19 21 " --> pdb=" O LEU19 17 " (cutoff:3.500A) Processing helix chain '19' and resid 25 through 30 removed outlier: 4.058A pdb=" N ARG19 29 " --> pdb=" O GLY19 25 " (cutoff:3.500A) Processing helix chain '19' and resid 38 through 72 removed outlier: 3.632A pdb=" N GLN19 43 " --> pdb=" O ILE19 39 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA19 45 " --> pdb=" O ALA19 41 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG19 49 " --> pdb=" O ALA19 45 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ARG19 50 " --> pdb=" O TYR19 46 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG19 52 " --> pdb=" O ASP19 48 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N LYS19 53 " --> pdb=" O ARG19 49 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG19 57 " --> pdb=" O LYS19 53 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA19 62 " --> pdb=" O GLN19 58 " (cutoff:3.500A) Processing helix chain '19' and resid 74 through 86 removed outlier: 3.922A 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: 3.534A pdb=" N THR19 106 " --> pdb=" O LYS19 102 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA19 117 " --> pdb=" O LYS19 113 " (cutoff:3.500A) Processing helix chain '21' and resid 13 through 25 removed outlier: 3.719A pdb=" N LEU21 19 " --> pdb=" O GLN21 15 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL21 20 " --> pdb=" O LYS21 16 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LEU21 23 " --> pdb=" O LEU21 19 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE21 24 " --> pdb=" O VAL21 20 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ARG21 25 " --> pdb=" O ALA21 21 " (cutoff:3.500A) Processing helix chain '21' and resid 28 through 39 removed outlier: 4.241A pdb=" N TYR21 38 " --> pdb=" O ASP21 34 " (cutoff:3.500A) Processing helix chain '21' and resid 41 through 61 removed outlier: 3.837A pdb=" N VAL21 45 " --> pdb=" O LYS21 41 " (cutoff:3.500A) Processing helix chain '22' and resid 1 through 11 removed outlier: 3.712A pdb=" N GLU22 5 " --> pdb=" O MET22 1 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU22 7 " --> pdb=" O ARG22 3 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LEU22 8 " --> pdb=" O GLU22 4 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS22 9 " --> pdb=" O GLU22 5 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL22 10 " --> pdb=" O ARG22 6 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU22 11 " --> pdb=" O LEU22 7 " (cutoff:3.500A) Processing helix chain '22' and resid 17 through 26 Processing helix chain '22' and resid 39 through 50 removed outlier: 3.557A pdb=" N ALA22 46 " --> pdb=" O GLU22 42 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS22 49 " --> pdb=" O ALA22 45 " (cutoff:3.500A) Processing helix chain '23' and resid 65 through 70 removed outlier: 4.033A pdb=" N VAL23 69 " --> pdb=" O GLN23 65 " (cutoff:3.500A) removed outlier: 5.177A 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: 3.906A pdb=" N LEU24 20 " --> pdb=" O ALA24 16 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ALA24 23 " --> pdb=" O ARG24 19 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASN24 24 " --> pdb=" O LEU24 20 " (cutoff:3.500A) Processing helix chain '24' and resid 43 through 54 removed outlier: 4.225A pdb=" N VAL24 47 " --> pdb=" O ASP24 43 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN24 49 " --> pdb=" O ASP24 45 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA24 52 " --> pdb=" O MET24 48 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS24 53 " --> pdb=" O ASN24 49 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ALA24 54 " --> pdb=" O MET24 50 " (cutoff:3.500A) Processing helix chain '26' and resid 51 through 62 removed outlier: 3.782A pdb=" N ARG26 56 " --> pdb=" O ALA26 52 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLY26 62 " --> pdb=" O ILE26 58 " (cutoff:3.500A) Processing helix chain '26' and resid 63 through 74 Processing helix chain '27' and resid 1 through 6 removed outlier: 3.724A pdb=" N LEU27 6 " --> pdb=" O LYS27 2 " (cutoff:3.500A) Processing helix chain '27' and resid 9 through 35 removed outlier: 3.509A pdb=" N LEU27 14 " --> pdb=" O SER27 10 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASN27 15 " --> pdb=" O VAL27 11 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR27 16 " --> pdb=" O GLU27 12 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ARG27 23 " --> pdb=" O LEU27 19 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU27 24 " --> pdb=" O ASN27 20 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLN27 25 " --> pdb=" O LEU27 21 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N PHE27 26 " --> pdb=" O LEU27 22 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN27 31 " --> pdb=" O ASN27 27 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA27 33 " --> pdb=" O ARG27 29 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER27 34 " --> pdb=" O MET27 30 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY27 35 " --> pdb=" O GLN27 31 " (cutoff:3.500A) Processing helix chain '27' and resid 40 through 61 removed outlier: 4.061A pdb=" N LYS27 44 " --> pdb=" O SER27 40 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU27 56 " --> pdb=" O ARG27 52 " (cutoff:3.500A) Processing helix chain '28' and resid 16 through 27 removed outlier: 3.742A pdb=" N THR28 22 " --> pdb=" O LYS28 18 " (cutoff:3.500A) Processing helix chain '28' and resid 40 through 51 removed outlier: 3.537A pdb=" N MET28 46 " --> pdb=" O ALA28 42 " (cutoff:3.500A) Processing helix chain '29' and resid 42 through 52 removed outlier: 4.044A pdb=" N LYS29 47 " --> pdb=" O PHE29 43 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N GLN29 48 " --> pdb=" O PHE29 44 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG29 49 " --> pdb=" O THR29 45 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ASP29 50 " --> pdb=" O GLY29 46 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA29 52 " --> pdb=" O GLN29 48 " (cutoff:3.500A) Processing helix chain '29' and resid 55 through 65 removed outlier: 4.627A pdb=" N ARG29 59 " --> pdb=" O GLY29 55 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS29 62 " --> pdb=" O ASP29 58 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ARG29 63 " --> pdb=" O ARG29 59 " (cutoff:3.500A) Processing helix chain '30' and resid 8 through 20 removed outlier: 3.519A pdb=" N ARG30 16 " --> pdb=" O ARG30 12 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N HIS30 18 " --> pdb=" O MET30 14 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ASP30 19 " --> pdb=" O ARG30 15 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA30 20 " --> pdb=" O ARG30 16 " (cutoff:3.500A) Processing helix chain '32' and resid 8 through 16 removed outlier: 3.526A pdb=" N SER32 15 " --> pdb=" O LYS32 11 " (cutoff:3.500A) Processing helix chain '32' and resid 17 through 24 removed outlier: 4.417A pdb=" N THR32 24 " --> pdb=" O ALA32 20 " (cutoff:3.500A) Processing helix chain '32' and resid 25 through 38 Processing helix chain '33' and resid 6 through 13 removed outlier: 3.579A pdb=" N LYS33 11 " --> pdb=" O ARG33 7 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG33 12 " --> pdb=" O GLY33 8 " (cutoff:3.500A) Processing helix chain '33' and resid 36 through 45 Proline residue: 33 45 - end of helix Processing helix chain '33' and resid 51 through 62 removed outlier: 4.334A pdb=" N GLY33 55 " --> pdb=" O LYS33 51 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LEU33 56 " --> pdb=" O GLY33 52 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS33 60 " --> pdb=" O LEU33 56 " (cutoff:3.500A) Proline residue: 33 62 - end of helix Processing helix chain 'B' and resid 41 through 63 removed outlier: 3.658A pdb=" N THR B 45 " --> pdb=" O ASN B 41 " (cutoff:3.500A) Proline residue: B 47 - end of helix removed outlier: 3.976A pdb=" N GLU B 55 " --> pdb=" O GLU B 51 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N SER B 61 " --> pdb=" O ASN B 57 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS B 63 " --> pdb=" O ILE B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 87 removed outlier: 6.126A pdb=" N SER B 76 " --> pdb=" O LYS B 72 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N GLU B 77 " --> pdb=" O ARG B 73 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA B 78 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS B 80 " --> pdb=" O SER B 76 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASP B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 122 removed outlier: 3.546A pdb=" N VAL B 106 " --> pdb=" O ASN B 102 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLN B 108 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N SER B 109 " --> pdb=" O THR B 105 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG B 112 " --> pdb=" O GLN B 108 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR B 118 " --> pdb=" O LYS B 114 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN B 121 " --> pdb=" O GLU B 117 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP B 122 " --> pdb=" O THR B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 147 removed outlier: 3.587A pdb=" N LYS B 142 " --> pdb=" O ARG B 138 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN B 145 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER B 146 " --> pdb=" O LYS B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 179 removed outlier: 3.513A pdb=" N ILE B 172 " --> pdb=" O GLU B 168 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU B 174 " --> pdb=" O ILE B 170 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN B 177 " --> pdb=" O LYS B 173 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLY B 179 " --> pdb=" O ALA B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 224 removed outlier: 3.752A pdb=" N LEU B 211 " --> pdb=" O ARG B 207 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG B 221 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ARG B 224 " --> pdb=" O VAL B 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 11 removed outlier: 3.702A pdb=" N ARG C 10 " --> pdb=" O PRO C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 47 removed outlier: 3.537A pdb=" N LEU C 42 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 77 Processing helix chain 'C' and resid 80 through 95 removed outlier: 3.725A pdb=" N GLU C 84 " --> pdb=" O GLY C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 112 removed outlier: 3.973A pdb=" N ASP C 111 " --> pdb=" O LYS C 107 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ALA C 112 " --> pdb=" O PRO C 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 107 through 112' Processing helix chain 'C' and resid 113 through 126 removed outlier: 3.690A pdb=" N GLU C 124 " --> pdb=" O THR C 120 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ARG C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG C 126 " --> pdb=" O GLN C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 removed outlier: 3.584A pdb=" N VAL C 137 " --> pdb=" O MET C 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 15 removed outlier: 4.112A pdb=" N LEU D 10 " --> pdb=" O PRO D 6 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N SER D 11 " --> pdb=" O LYS D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 65 removed outlier: 3.527A pdb=" N VAL D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 removed outlier: 3.516A pdb=" N ASN D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG D 80 " --> pdb=" O LYS D 76 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N LYS D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 96 removed outlier: 3.641A pdb=" N ARG D 96 " --> pdb=" O LEU D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 105 removed outlier: 3.516A pdb=" N TYR D 102 " --> pdb=" O ASP D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 120 removed outlier: 4.131A pdb=" N LYS D 120 " --> pdb=" O LEU D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 165 removed outlier: 5.870A pdb=" N LYS D 155 " --> pdb=" O GLN D 151 " (cutoff:3.500A) removed outlier: 4.485A 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: 4.277A pdb=" N GLN D 163 " --> pdb=" O GLU D 159 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG D 164 " --> pdb=" O LEU D 160 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N GLU D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 191 removed outlier: 5.326A pdb=" N SER D 191 " --> pdb=" O ARG D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 205 removed outlier: 4.251A pdb=" N ILE D 199 " --> pdb=" O ASN D 195 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL D 200 " --> pdb=" O GLU D 196 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS D 205 " --> pdb=" O GLU D 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 70 removed outlier: 3.695A pdb=" N LYS E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU E 64 " --> pdb=" O GLN E 60 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS E 65 " --> pdb=" O LYS E 61 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG E 68 " --> pdb=" O GLU E 64 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN E 69 " --> pdb=" O LYS E 65 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N MET E 70 " --> pdb=" O ALA E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 118 removed outlier: 6.433A pdb=" N ALA E 112 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL E 113 " --> pdb=" O ALA E 109 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL E 116 " --> pdb=" O ALA E 112 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA E 117 " --> pdb=" O VAL E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 146 removed outlier: 3.642A pdb=" N ILE E 140 " --> pdb=" O VAL E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 156 removed outlier: 3.852A pdb=" N LYS E 155 " --> pdb=" O MET E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 165 removed outlier: 4.135A pdb=" N LEU E 164 " --> pdb=" O VAL E 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 19 removed outlier: 4.918A pdb=" N GLU F 16 " --> pdb=" O PRO F 12 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N GLN F 17 " --> pdb=" O ASP F 13 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL F 18 " --> pdb=" O GLN F 14 " (cutoff:3.500A) Proline residue: F 19 - end of helix Processing helix chain 'F' and resid 20 through 33 removed outlier: 3.707A pdb=" N ARG F 24 " --> pdb=" O GLY F 20 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA F 32 " --> pdb=" O ALA F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 82 removed outlier: 3.553A pdb=" N PHE F 78 " --> pdb=" O LEU F 74 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG F 79 " --> pdb=" O GLU F 75 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE F 80 " --> pdb=" O THR F 76 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASN F 81 " --> pdb=" O THR F 77 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ASP F 82 " --> pdb=" O PHE F 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 30 Processing helix chain 'G' and resid 34 through 54 removed outlier: 3.717A pdb=" N ALA G 38 " --> pdb=" O LYS G 34 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER G 44 " --> pdb=" O SER G 40 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR G 48 " --> pdb=" O SER G 44 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG G 52 " --> pdb=" O THR G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 69 removed outlier: 3.557A pdb=" N ALA G 60 " --> pdb=" O SER G 56 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASN G 67 " --> pdb=" O VAL G 63 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 111 removed outlier: 3.749A pdb=" N ASN G 96 " --> pdb=" O PRO G 92 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA G 97 " --> pdb=" O VAL G 93 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE G 103 " --> pdb=" O ALA G 99 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS G 109 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG G 110 " --> pdb=" O ALA G 106 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLY G 111 " --> pdb=" O ALA G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 129 removed outlier: 3.704A pdb=" N ALA G 127 " --> pdb=" O LEU G 123 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU G 128 " --> pdb=" O SER G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 148 removed outlier: 3.756A pdb=" N LYS G 135 " --> pdb=" O GLY G 131 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASN G 147 " --> pdb=" O MET G 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 20 Processing helix chain 'H' and resid 29 through 43 Processing helix chain 'H' and resid 111 through 119 removed outlier: 3.515A pdb=" N GLN H 117 " --> pdb=" O ARG H 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 38 removed outlier: 3.634A pdb=" N PHE I 38 " --> pdb=" O LEU I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 53 removed outlier: 4.823A pdb=" N ARG I 48 " --> pdb=" O ARG I 44 " (cutoff:3.500A) Proline residue: I 50 - end of helix removed outlier: 3.761A pdb=" N LEU I 53 " --> pdb=" O GLN I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 86 Processing helix chain 'I' and resid 90 through 101 removed outlier: 5.323A pdb=" N GLU I 96 " --> pdb=" O SER I 92 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS I 99 " --> pdb=" O SER I 95 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA I 100 " --> pdb=" O GLU I 96 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLY I 101 " --> pdb=" O LEU I 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 33 removed outlier: 4.791A pdb=" N GLN J 20 " --> pdb=" O ARG J 16 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA J 23 " --> pdb=" O ASP J 19 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA J 29 " --> pdb=" O ILE J 25 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N THR J 32 " --> pdb=" O THR J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 90 removed outlier: 3.658A pdb=" N VAL J 84 " --> pdb=" O THR J 80 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASP J 85 " --> pdb=" O GLU J 81 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ALA J 86 " --> pdb=" O LYS J 82 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET J 88 " --> pdb=" O VAL J 84 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG J 89 " --> pdb=" O ASP J 85 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N LEU J 90 " --> pdb=" O ALA J 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 50 removed outlier: 3.550A pdb=" N SER K 49 " --> pdb=" O THR K 45 " (cutoff:3.500A) removed outlier: 4.921A 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: 4.177A pdb=" N SER K 57 " --> pdb=" O GLY K 53 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N THR K 58 " --> pdb=" O SER K 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 53 through 58' Processing helix chain 'K' and resid 59 through 75 removed outlier: 3.869A pdb=" N ASP K 71 " --> pdb=" O GLU K 67 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ALA K 72 " --> pdb=" O ARG K 68 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N VAL K 73 " --> pdb=" O CYS K 69 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS K 74 " --> pdb=" O ALA K 70 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N GLU K 75 " --> pdb=" O ASP K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 103 removed outlier: 5.329A pdb=" N THR K 95 " --> pdb=" O GLY K 91 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ILE K 96 " --> pdb=" O ARG K 92 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG K 97 " --> pdb=" O GLU K 93 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA K 98 " --> pdb=" O SER K 94 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLY K 103 " --> pdb=" O LEU K 99 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 10 removed outlier: 3.709A pdb=" N LEU L 6 " --> pdb=" O THR L 2 " (cutoff:3.500A) Proline residue: L 10 - end of helix Processing helix chain 'L' and resid 112 through 117 removed outlier: 4.707A pdb=" N TYR L 116 " --> pdb=" O ALA L 112 " (cutoff:3.500A) removed outlier: 4.009A 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 20 removed outlier: 3.788A pdb=" N THR M 19 " --> pdb=" O VAL M 15 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N SER M 20 " --> pdb=" O ILE M 16 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 37 removed outlier: 3.724A pdb=" N SER M 29 " --> pdb=" O GLY M 25 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA M 31 " --> pdb=" O THR M 27 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 48 removed outlier: 5.046A pdb=" N SER M 48 " --> pdb=" O ILE M 44 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 63 removed outlier: 4.752A pdb=" N THR M 54 " --> pdb=" O GLY M 50 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP M 57 " --> pdb=" O ASP M 53 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU M 58 " --> pdb=" O THR M 54 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS M 61 " --> pdb=" O ASP M 57 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N PHE M 62 " --> pdb=" O GLU M 58 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N VAL M 63 " --> pdb=" O VAL M 59 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 83 removed outlier: 3.526A pdb=" N ARG M 70 " --> pdb=" O GLY M 66 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 93 Processing helix chain 'M' and resid 105 through 110 removed outlier: 3.662A pdb=" N LYS M 109 " --> pdb=" O ALA M 105 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 20 removed outlier: 3.529A pdb=" N LYS N 6 " --> pdb=" O LYS N 2 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE N 20 " --> pdb=" O ALA N 16 " (cutoff:3.500A) Processing helix chain 'N' and resid 23 through 28 removed outlier: 5.250A pdb=" N LYS N 27 " --> pdb=" O ARG N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 51 removed outlier: 5.710A pdb=" N GLN N 48 " --> pdb=" O VAL N 44 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR N 49 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 3.673A 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 79 through 90 removed outlier: 3.697A pdb=" N ARG N 84 " --> pdb=" O ARG N 80 " (cutoff:3.500A) removed outlier: 3.696A 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 43 removed outlier: 3.574A pdb=" N GLN O 34 " --> pdb=" O LEU O 30 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLY O 40 " --> pdb=" O ASN O 36 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N HIS O 41 " --> pdb=" O HIS O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 48 through 73 removed outlier: 3.604A pdb=" N GLY O 54 " --> pdb=" O HIS O 50 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 85 removed outlier: 3.559A pdb=" N GLN O 79 " --> pdb=" O ALA O 75 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU O 82 " --> pdb=" O THR O 78 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY O 85 " --> pdb=" O ILE O 81 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 64 Processing helix chain 'P' and resid 68 through 79 removed outlier: 3.524A pdb=" N LEU P 74 " --> pdb=" O ARG P 70 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS P 76 " --> pdb=" O ALA P 72 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASN P 79 " --> pdb=" O ILE P 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 12 through 17 removed outlier: 4.082A pdb=" N GLY R 16 " --> pdb=" O PHE R 12 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 33 removed outlier: 4.184A pdb=" N ASN R 30 " --> pdb=" O ALA R 26 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TYR R 31 " --> pdb=" O THR R 27 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE R 32 " --> pdb=" O LEU R 28 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N THR R 33 " --> pdb=" O LYS R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 45 Processing helix chain 'R' and resid 47 through 65 removed outlier: 3.791A pdb=" N ARG R 52 " --> pdb=" O ALA R 48 " (cutoff:3.500A) Processing helix chain 'S' and resid 11 through 25 removed outlier: 3.736A pdb=" N GLU S 23 " --> pdb=" O GLU S 19 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER S 24 " --> pdb=" O LYS S 20 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 69 through 75 removed outlier: 4.845A pdb=" N PHE S 73 " --> pdb=" O LYS S 69 " (cutoff:3.500A) removed outlier: 4.076A 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: 4.735A pdb=" N ALA T 10 " --> pdb=" O ALA T 6 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE T 11 " --> pdb=" O LYS T 7 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS T 18 " --> pdb=" O GLU T 14 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N HIS T 19 " --> pdb=" O LYS T 15 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER T 22 " --> pdb=" O LYS T 18 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE T 30 " --> pdb=" O MET T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 64 removed outlier: 3.703A pdb=" N GLN T 47 " --> pdb=" O LYS T 43 " (cutoff:3.500A) Proline residue: T 55 - end of helix removed outlier: 3.742A pdb=" N GLN T 60 " --> pdb=" O ILE T 56 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA T 61 " --> pdb=" O VAL T 57 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA T 62 " --> pdb=" O ASP T 58 " (cutoff:3.500A) Processing helix chain 'T' and resid 67 through 86 removed outlier: 5.955A pdb=" N ALA T 71 " --> pdb=" O HIS T 67 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR T 79 " --> pdb=" O LYS T 75 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS T 84 " --> pdb=" O ALA T 80 " (cutoff:3.500A) Processing helix chain 'U' and resid 16 through 22 removed outlier: 4.951A pdb=" N ARG U 20 " --> pdb=" O ARG U 16 " (cutoff:3.500A) Processing helix chain 'U' and resid 24 through 34 removed outlier: 3.658A pdb=" N LEU U 28 " --> pdb=" O LYS U 24 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLU U 30 " --> pdb=" O GLY U 26 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL U 31 " --> pdb=" O VAL U 27 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ARG U 33 " --> pdb=" O ALA U 29 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N ARG U 34 " --> pdb=" O GLU U 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 36 through 61 Proline residue: U 40 - end of helix removed outlier: 3.858A pdb=" N LYS U 53 " --> pdb=" O ALA U 49 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS U 58 " --> pdb=" O ARG U 54 " (cutoff:3.500A) Processing helix chain '03' and resid 6 through 16 removed outlier: 3.743A pdb=" N VAL03 10 " --> pdb=" O LYS03 6 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG03 12 " --> pdb=" O MET03 8 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL03 15 " --> pdb=" O ILE03 11 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ASP03 16 " --> pdb=" O ARG03 12 " (cutoff:3.500A) Processing helix chain '03' and resid 22 through 35 removed outlier: 3.856A pdb=" N ILE03 27 " --> pdb=" O ILE03 23 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ALA03 28 " --> pdb=" O ASN03 24 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU03 30 " --> pdb=" O ALA03 26 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N LYS03 31 " --> pdb=" O ILE03 27 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N GLU03 32 " --> pdb=" O ALA03 28 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU03 33 " --> pdb=" O LEU03 29 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N THR03 35 " --> pdb=" O LYS03 31 " (cutoff:3.500A) Processing helix chain '03' and resid 181 through 200 Processing helix chain 'Z' and resid 23 through 39 removed outlier: 3.521A pdb=" N THR Z 32 " --> pdb=" O THR Z 28 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS Z 37 " --> pdb=" O THR Z 33 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N THR Z 38 " --> pdb=" O VAL Z 34 " (cutoff:3.500A) Processing helix chain 'Z' and resid 45 through 51 removed outlier: 3.524A pdb=" N ILE Z 49 " --> pdb=" O ALA Z 45 " (cutoff:3.500A) Processing helix chain 'Z' and resid 52 through 58 Processing helix chain 'Z' and resid 87 through 99 removed outlier: 3.569A pdb=" N MET Z 91 " --> pdb=" O TYR Z 87 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN Z 97 " --> pdb=" O THR Z 93 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ASP Z 99 " --> pdb=" O ALA Z 95 " (cutoff:3.500A) Processing helix chain 'Z' and resid 112 through 126 Processing helix chain 'Z' and resid 136 through 141 removed outlier: 3.877A pdb=" N VAL Z 140 " --> pdb=" O LYS Z 136 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ASP Z 141 " --> pdb=" O CYS Z 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 136 through 141' Processing helix chain 'Z' and resid 142 through 161 Processing helix chain 'Z' and resid 173 through 180 removed outlier: 3.732A pdb=" N GLU Z 179 " --> pdb=" O LEU Z 175 " (cutoff:3.500A) Processing helix chain 'Z' and resid 181 through 198 removed outlier: 4.172A pdb=" N LYS Z 187 " --> pdb=" O GLU Z 183 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE Z 188 " --> pdb=" O TRP Z 184 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU Z 189 " --> pdb=" O GLU Z 185 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE Z 194 " --> pdb=" O GLU Z 190 " (cutoff:3.500A) Processing helix chain 'Z' and resid 282 through 287 removed outlier: 4.676A pdb=" N GLU Z 287 " --> pdb=" O ARG Z 283 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '04' and resid 1 through 4 Processing sheet with id= 2, first strand: chain '04' and resid 79 through 82 removed outlier: 3.859A pdb=" N ILE04 90 " --> pdb=" O GLU04 81 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU04 92 " --> pdb=" O GLU04 78 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ILE04 73 " --> pdb=" O SER04 117 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N SER04 117 " --> pdb=" O ILE04 73 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ASP04 113 " --> pdb=" O VAL04 77 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N GLY04 126 " --> pdb=" O GLN04 114 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N GLN04 116 " --> pdb=" O GLY04 126 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '04' and resid 137 through 141 removed outlier: 4.059A pdb=" N SER04 138 " --> pdb=" O ILE04 163 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N THR04 172 " --> pdb=" O VAL04 164 " (cutoff:3.500A) removed outlier: 3.956A 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: 5.439A pdb=" N ASN04 89 " --> pdb=" O ALA04 105 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLU04 99 " --> pdb=" O TYR04 95 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain '05' and resid 3 through 9 removed outlier: 3.546A pdb=" N LYS05 8 " --> pdb=" O SER05 199 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N SER05 199 " --> pdb=" O LYS05 8 " (cutoff:3.500A) removed outlier: 12.994A pdb=" N GLY05 198 " --> pdb=" O LYS05 114 " (cutoff:3.500A) removed outlier: 10.866A pdb=" N LYS05 114 " --> pdb=" O GLY05 198 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASP05 200 " --> pdb=" O THR05 112 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N THR05 112 " --> pdb=" O ASP05 200 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU05 168 " --> pdb=" O SER05 113 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain '05' and resid 10 through 16 removed outlier: 4.062A pdb=" N GLY05 10 " --> pdb=" O VAL05 26 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N VAL05 20 " --> pdb=" O THR05 16 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain '05' and resid 32 through 35 removed outlier: 6.666A pdb=" N GLN05 49 " --> pdb=" O THR05 35 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain '05' and resid 46 through 51 removed outlier: 6.013A pdb=" N ARG05 46 " --> pdb=" O LEU05 84 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain '05' and resid 105 through 108 removed outlier: 6.375A pdb=" N LYS05 105 " --> pdb=" O VAL05 177 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain '06' and resid 117 through 120 Processing sheet with id= 11, first strand: chain '07' and resid 64 through 68 removed outlier: 5.898A pdb=" N GLY07 38 " --> pdb=" O GLY07 150 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N GLY07 150 " --> pdb=" O GLY07 38 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N THR07 157 " --> pdb=" O GLY07 125 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLY07 125 " --> pdb=" O THR07 157 " (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 40 through 44 Processing sheet with id= 14, first strand: chain '08' and resid 93 through 97 Processing sheet with id= 15, first strand: chain '08' and resid 120 through 124 removed outlier: 5.963A pdb=" N THR08 128 " --> pdb=" O LEU08 88 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain '09' and resid 2 through 5 removed outlier: 6.324A pdb=" N GLN09 2 " --> pdb=" O ALA09 39 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALA09 39 " --> pdb=" O GLN09 2 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain '09' and resid 76 through 81 removed outlier: 8.019A pdb=" N GLU09 76 " --> pdb=" O LYS09 141 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE09 143 " --> pdb=" O GLU09 76 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL09 78 " --> pdb=" O ILE09 143 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN09 145 " --> pdb=" O VAL09 78 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL09 142 " --> pdb=" O VAL09 130 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain '10' and resid 24 through 28 removed outlier: 3.816A pdb=" N ALA10 25 " --> pdb=" O SER10 85 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain '11' and resid 6 through 11 removed outlier: 4.103A pdb=" N ALA11 6 " --> pdb=" O VAL11 60 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL11 8 " --> pdb=" O ILE11 58 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS11 71 " --> pdb=" O PRO11 55 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain '11' and resid 98 through 101 removed outlier: 3.636A pdb=" N ILE11 100 " --> pdb=" O VAL11 138 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain '12' and resid 52 through 57 removed outlier: 3.723A pdb=" N GLN12 138 " --> pdb=" O TRP12 15 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ASP12 19 " --> pdb=" O LEU12 140 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain '12' and resid 74 through 78 removed outlier: 7.095A pdb=" N GLY12 83 " --> pdb=" O THR12 78 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain '13' and resid 18 through 21 removed outlier: 3.748A pdb=" N THR13 6 " --> pdb=" O CYS13 21 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ASN13 82 " --> pdb=" O MET13 7 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N GLY13 81 " --> pdb=" O LYS13 66 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N LYS13 66 " --> pdb=" O GLY13 81 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG13 64 " --> pdb=" O ALA13 83 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain '13' and resid 68 through 71 removed outlier: 3.511A pdb=" N VAL13 69 " --> pdb=" O ILE13 77 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER13 75 " --> pdb=" O ARG13 71 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain '15' and resid 37 through 40 No H-bonds generated for sheet with id= 25 Processing sheet with id= 26, first strand: chain '15' and resid 62 through 65 removed outlier: 4.073A pdb=" N TYR15 103 " --> pdb=" O LEU15 33 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU15 33 " --> pdb=" O LEU15 102 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS15 100 " --> pdb=" O ALA15 35 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain '15' and resid 30 through 36 removed outlier: 7.338A pdb=" N SER15 30 " --> pdb=" O LYS15 133 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LYS15 127 " --> pdb=" O VAL15 36 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain '16' and resid 33 through 37 removed outlier: 5.497A pdb=" N ALA16 108 " --> pdb=" O PHE16 102 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N PHE16 102 " --> pdb=" O ALA16 108 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N MET16 110 " --> pdb=" O CYS16 100 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain '17' and resid 49 through 52 removed outlier: 3.518A pdb=" N VAL17 49 " --> pdb=" O VAL17 39 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA17 37 " --> pdb=" O ALA17 51 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL17 28 " --> pdb=" O ASP17 93 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain '18' and resid 48 through 52 removed outlier: 4.109A pdb=" N ALA18 48 " --> pdb=" O THR18 59 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N ARG18 52 " --> pdb=" O HIS18 55 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N THR18 59 " --> pdb=" O ILE18 47 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR18 24 " --> pdb=" O LYS18 86 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER18 84 " --> pdb=" O GLU18 26 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER18 82 " --> pdb=" O LYS18 28 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain '18' and resid 56 through 63 removed outlier: 7.967A pdb=" N SER18 56 " --> pdb=" O THR18 75 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain '20' and resid 11 through 14 removed outlier: 3.552A pdb=" N TYR20 2 " --> pdb=" O ALA20 42 " (cutoff:3.500A) removed outlier: 8.969A pdb=" N LEU20 39 " --> pdb=" O ILE20 49 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE20 49 " --> pdb=" O LEU20 39 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain '20' and resid 19 through 22 removed outlier: 3.510A pdb=" N VAL20 96 " --> pdb=" O VAL20 20 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLY20 67 " --> pdb=" O PHE20 93 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA20 65 " --> pdb=" O ASP20 95 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain '20' and resid 32 through 36 removed outlier: 3.709A pdb=" N VAL20 58 " --> pdb=" O SER20 102 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain '20' and resid 71 through 78 removed outlier: 3.884A pdb=" N TYR20 83 " --> pdb=" O ARG20 78 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain '21' and resid 2 through 8 removed outlier: 4.153A pdb=" N THR21 3 " --> pdb=" O VAL21 107 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N THR21 100 " --> pdb=" O GLY21 79 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain '22' and resid 12 through 15 removed outlier: 5.137A pdb=" N VAL22 31 " --> pdb=" O HIS22 15 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS22 81 " --> pdb=" O VAL22 34 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG22 77 " --> pdb=" O LYS22 66 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LYS22 66 " --> pdb=" O ARG22 77 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ASP22 79 " --> pdb=" O LYS22 64 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LYS22 64 " --> pdb=" O ASP22 79 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LYS22 81 " --> pdb=" O VAL22 62 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL22 62 " --> pdb=" O LYS22 81 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ALA22 83 " --> pdb=" O THR22 60 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N THR22 60 " --> pdb=" O ALA22 83 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL22 85 " --> pdb=" O VAL22 58 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL22 58 " --> pdb=" O VAL22 85 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain '23' and resid 39 through 44 removed outlier: 4.487A pdb=" N ASN23 39 " --> pdb=" O ALA23 62 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL23 41 " --> pdb=" O LYS23 60 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain '23' and resid 81 through 86 removed outlier: 5.258A pdb=" N ARG23 81 " --> pdb=" O LYS23 96 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ARG23 93 " --> pdb=" O ILE23 102 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE23 95 " --> pdb=" O GLU23 100 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU23 100 " --> pdb=" O PHE23 95 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain '24' and resid 69 through 72 removed outlier: 3.655A pdb=" N ALA24 6 " --> pdb=" O VAL24 64 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ALA24 39 " --> pdb=" O ARG24 9 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE24 89 " --> pdb=" O PRO24 27 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain '25' and resid 47 through 50 removed outlier: 3.604A pdb=" N PHE25 56 " --> pdb=" O GLY25 48 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N THR25 54 " --> pdb=" O GLY25 50 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain '25' and resid 62 through 67 Processing sheet with id= 43, first strand: chain '26' and resid 11 through 18 removed outlier: 3.974A pdb=" N THR26 24 " --> pdb=" O ASN26 16 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER26 18 " --> pdb=" O ASN26 22 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ASN26 22 " --> pdb=" O SER26 18 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain '26' and resid 34 through 40 Processing sheet with id= 45, first strand: chain '28' and resid 34 through 38 removed outlier: 3.564A pdb=" N THR28 7 " --> pdb=" O LYS28 55 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N MET28 53 " --> pdb=" O THR28 9 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain '29' and resid 20 through 25 removed outlier: 4.211A pdb=" N ASN29 20 " --> pdb=" O CYS29 16 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N CYS29 16 " --> pdb=" O ASN29 20 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER29 15 " --> pdb=" O LEU29 32 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain '30' and resid 27 through 30 removed outlier: 6.468A pdb=" N SER30 28 " --> pdb=" O LYS30 36 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS30 36 " --> pdb=" O SER30 28 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ASP30 30 " --> pdb=" O GLY30 34 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain '31' and resid 7 through 11 Processing sheet with id= 49, first strand: chain '31' and resid 33 through 38 removed outlier: 6.872A pdb=" N LEU31 33 " --> pdb=" O GLU31 50 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU31 50 " --> pdb=" O LEU31 33 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU31 35 " --> pdb=" O TYR31 48 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain '33' and resid 21 through 24 removed outlier: 5.978A pdb=" N PHE33 21 " --> pdb=" O VAL33 49 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain '34' and resid 13 through 18 removed outlier: 8.412A pdb=" N ASN34 13 " --> pdb=" O SER34 28 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER34 28 " --> pdb=" O ASN34 13 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ILE34 23 " --> pdb=" O GLN34 37 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'B' and resid 30 through 33 removed outlier: 4.475A pdb=" N VAL B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'B' and resid 88 through 91 removed outlier: 3.657A pdb=" N ILE B 185 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE B 197 " --> pdb=" O VAL B 182 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA B 184 " --> pdb=" O PHE B 197 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'C' and resid 52 through 58 Processing sheet with id= 55, first strand: chain 'C' and resid 163 through 170 removed outlier: 3.515A pdb=" N VAL C 152 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY C 193 " --> pdb=" O THR C 190 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL C 199 " --> pdb=" O ASN C 184 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN C 184 " --> pdb=" O VAL C 199 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'D' and resid 139 through 143 removed outlier: 6.378A pdb=" N GLU D 178 " --> pdb=" O ASP D 173 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N TRP D 169 " --> pdb=" O LYS D 182 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'E' and resid 10 through 15 removed outlier: 3.838A pdb=" N GLN E 11 " --> pdb=" O GLY E 39 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY E 39 " --> pdb=" O GLN E 11 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU E 35 " --> pdb=" O ILE E 15 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'E' and resid 82 through 87 removed outlier: 7.626A pdb=" N HIS E 82 " --> pdb=" O PRO E 97 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL E 93 " --> pdb=" O GLY E 86 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N TYR E 127 " --> pdb=" O ARG E 92 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'E' and resid 31 through 40 removed outlier: 4.578A pdb=" N GLY E 50 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ARG E 44 " --> pdb=" O ASP E 40 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'F' and resid 39 through 42 removed outlier: 3.529A pdb=" N TRP F 42 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N TYR F 59 " --> pdb=" O TRP F 42 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ILE F 6 " --> pdb=" O MET F 62 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N HIS F 3 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLU F 5 " --> pdb=" O MET F 90 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N MET F 90 " --> pdb=" O GLU F 5 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'F' and resid 43 through 47 removed outlier: 3.839A pdb=" N GLY F 43 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LEU F 47 " --> pdb=" O HIS F 55 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N HIS F 55 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'G' and resid 72 through 76 Processing sheet with id= 63, first strand: chain 'H' and resid 22 through 28 removed outlier: 6.454A pdb=" N ALA H 22 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU H 57 " --> pdb=" O GLU H 51 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLU H 51 " --> pdb=" O GLU H 57 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N THR H 61 " --> pdb=" O ASP H 47 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ASP H 47 " --> pdb=" O THR H 61 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'H' and resid 73 through 76 removed outlier: 6.754A pdb=" N VAL H 102 " --> pdb=" O ILE H 125 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'I' and resid 4 through 10 removed outlier: 4.393A pdb=" N GLY I 9 " --> pdb=" O ALA I 16 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA I 15 " --> pdb=" O LYS I 67 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N LYS I 26 " --> pdb=" O LEU I 60 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'J' and resid 36 through 40 removed outlier: 3.957A pdb=" N LEU J 10 " --> pdb=" O ARG J 72 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE J 8 " --> pdb=" O VAL J 74 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'J' and resid 44 through 52 Processing sheet with id= 68, first strand: chain 'K' and resid 41 through 44 removed outlier: 3.636A pdb=" N GLY K 18 " --> pdb=" O ASN K 80 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'L' and resid 28 through 32 removed outlier: 5.233A pdb=" N LEU L 80 " --> pdb=" O VAL L 97 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'L' and resid 34 through 40 removed outlier: 4.832A pdb=" N ARG L 35 " --> pdb=" O ARG L 53 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N LYS L 50 " --> pdb=" O ILE L 66 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N PHE L 60 " --> pdb=" O LEU L 56 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'P' and resid 4 through 10 removed outlier: 3.656A pdb=" N VAL P 19 " --> pdb=" O GLY P 37 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLY P 37 " --> pdb=" O VAL P 19 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG P 51 " --> pdb=" O PHE P 38 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLY P 49 " --> pdb=" O ASN P 40 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'Q' and resid 6 through 10 removed outlier: 7.130A pdb=" N GLU Q 59 " --> pdb=" O VAL Q 75 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'Q' and resid 18 through 29 No H-bonds generated for sheet with id= 73 Processing sheet with id= 74, first strand: chain 'S' and resid 29 through 33 removed outlier: 4.371A pdb=" N LEU S 30 " --> pdb=" O THR S 47 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N LEU S 46 " --> pdb=" O VAL S 61 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE S 48 " --> pdb=" O VAL S 59 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain '03' and resid 41 through 48 No H-bonds generated for sheet with id= 75 Processing sheet with id= 76, first strand: chain '03' and resid 60 through 65 removed outlier: 3.878A pdb=" N LEU03 65 " --> pdb=" O GLY03 159 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N GLY03 159 " --> pdb=" O LEU03 65 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'Z' and resid 64 through 71 removed outlier: 4.004A pdb=" N SER Z 65 " --> pdb=" O ASP Z 80 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR Z 71 " --> pdb=" O ARG Z 74 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA Z 101 " --> pdb=" O TYR Z 129 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'Z' and resid 210 through 213 removed outlier: 6.717A pdb=" N PHE Z 210 " --> pdb=" O LYS Z 294 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLU Z 240 " --> pdb=" O CYS Z 255 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'Z' and resid 216 through 220 removed outlier: 4.226A pdb=" N ASP Z 216 " --> pdb=" O THR Z 228 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N THR Z 225 " --> pdb=" O LEU Z 278 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY Z 257 " --> pdb=" O LEU Z 277 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'Z' and resid 234 through 237 removed outlier: 7.285A pdb=" N GLY Z 234 " --> pdb=" O ALA Z 270 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'Z' and resid 335 through 340 removed outlier: 3.821A pdb=" N PHE Z 332 " --> pdb=" O THR Z 335 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE Z 304 " --> pdb=" O VAL Z 360 " (cutoff:3.500A) 1825 hydrogen bonds defined for protein. 5376 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3830 hydrogen bonds 6130 hydrogen bond angles 0 basepair planarities 1530 basepair parallelities 2903 stacking parallelities Total time for adding SS restraints: 282.98 Time building geometry restraints manager: 66.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.37: 43180 1.37 - 1.53: 109158 1.53 - 1.69: 14171 1.69 - 1.85: 283 1.85 - 2.01: 26 Bond restraints: 166818 Sorted by residual: bond pdb=" O3A GCP Z 402 " pdb=" PB GCP Z 402 " ideal model delta sigma weight residual 1.697 1.514 0.183 2.00e-02 2.50e+03 8.40e+01 bond pdb=" SD MET Z 151 " pdb=" CE MET Z 151 " ideal model delta sigma weight residual 1.791 2.012 -0.221 2.50e-02 1.60e+03 7.84e+01 bond pdb=" SD MET Z 260 " pdb=" CE MET Z 260 " ideal model delta sigma weight residual 1.791 2.007 -0.216 2.50e-02 1.60e+03 7.49e+01 bond pdb=" SD MET03 8 " pdb=" CE MET03 8 " ideal model delta sigma weight residual 1.791 2.005 -0.214 2.50e-02 1.60e+03 7.33e+01 bond pdb=" SD MET Z 112 " pdb=" CE MET Z 112 " ideal model delta sigma weight residual 1.791 1.998 -0.207 2.50e-02 1.60e+03 6.83e+01 ... (remaining 166813 not shown) Histogram of bond angle deviations from ideal: 92.53 - 103.86: 14497 103.86 - 115.18: 124269 115.18 - 126.51: 96082 126.51 - 137.84: 14222 137.84 - 149.17: 2 Bond angle restraints: 249072 Sorted by residual: angle pdb=" N SER L 114 " pdb=" CA SER L 114 " pdb=" C SER L 114 " ideal model delta sigma weight residual 111.14 99.09 12.05 1.08e+00 8.57e-01 1.25e+02 angle pdb=" N THR Z 71 " pdb=" CA THR Z 71 " pdb=" C THR Z 71 " ideal model delta sigma weight residual 110.29 95.66 14.63 1.38e+00 5.25e-01 1.12e+02 angle pdb=" N ALA N 24 " pdb=" CA ALA N 24 " pdb=" C ALA N 24 " ideal model delta sigma weight residual 113.28 101.58 11.70 1.22e+00 6.72e-01 9.20e+01 angle pdb=" N PHE03 180 " pdb=" CA PHE03 180 " pdb=" C PHE03 180 " ideal model delta sigma weight residual 110.50 97.96 12.54 1.41e+00 5.03e-01 7.92e+01 angle pdb=" N HIS B 17 " pdb=" CA HIS B 17 " pdb=" C HIS B 17 " ideal model delta sigma weight residual 108.24 119.96 -11.72 1.32e+00 5.74e-01 7.89e+01 ... (remaining 249067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.54: 95273 35.54 - 71.08: 10225 71.08 - 106.63: 1303 106.63 - 142.17: 13 142.17 - 177.71: 20 Dihedral angle restraints: 106834 sinusoidal: 88402 harmonic: 18432 Sorted by residual: dihedral pdb=" C4' U012296 " pdb=" C3' U012296 " pdb=" C2' U012296 " pdb=" C1' U012296 " ideal model delta sinusoidal sigma weight residual -35.00 33.77 -68.77 1 8.00e+00 1.56e-02 9.57e+01 dihedral pdb=" C5' U011130 " pdb=" C4' U011130 " pdb=" C3' U011130 " pdb=" O3' U011130 " ideal model delta sinusoidal sigma weight residual 147.00 80.15 66.85 1 8.00e+00 1.56e-02 9.10e+01 dihedral pdb=" C4' U011130 " pdb=" C3' U011130 " pdb=" C2' U011130 " pdb=" C1' U011130 " ideal model delta sinusoidal sigma weight residual -35.00 31.45 -66.45 1 8.00e+00 1.56e-02 9.01e+01 ... (remaining 106831 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.148: 29561 0.148 - 0.296: 2091 0.296 - 0.444: 122 0.444 - 0.592: 7 0.592 - 0.740: 1 Chirality restraints: 31782 Sorted by residual: chirality pdb=" C3' GCP Z 402 " pdb=" C2' GCP Z 402 " pdb=" C4' GCP Z 402 " pdb=" O3' GCP Z 402 " both_signs ideal model delta sigma weight residual False -2.57 -3.31 0.74 2.00e-01 2.50e+01 1.37e+01 chirality pdb=" CA THR Z 71 " pdb=" N THR Z 71 " pdb=" C THR Z 71 " pdb=" CB THR Z 71 " both_signs ideal model delta sigma weight residual False 2.53 3.03 -0.51 2.00e-01 2.50e+01 6.45e+00 chirality pdb=" CA LYS L 43 " pdb=" N LYS L 43 " pdb=" C LYS L 43 " pdb=" CB LYS L 43 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.22e+00 ... (remaining 31779 not shown) Planarity restraints: 13716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N FME W 101 " -0.221 2.00e-02 2.50e+03 1.81e-01 3.26e+02 pdb=" CA FME W 101 " 0.087 2.00e-02 2.50e+03 pdb=" CN FME W 101 " 0.247 2.00e-02 2.50e+03 pdb=" O1 FME W 101 " -0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G01 775 " 0.136 2.00e-02 2.50e+03 5.69e-02 9.70e+01 pdb=" N9 G01 775 " -0.007 2.00e-02 2.50e+03 pdb=" C8 G01 775 " -0.059 2.00e-02 2.50e+03 pdb=" N7 G01 775 " -0.057 2.00e-02 2.50e+03 pdb=" C5 G01 775 " -0.028 2.00e-02 2.50e+03 pdb=" C6 G01 775 " 0.027 2.00e-02 2.50e+03 pdb=" O6 G01 775 " 0.083 2.00e-02 2.50e+03 pdb=" N1 G01 775 " 0.029 2.00e-02 2.50e+03 pdb=" C2 G01 775 " -0.012 2.00e-02 2.50e+03 pdb=" N2 G01 775 " -0.031 2.00e-02 2.50e+03 pdb=" N3 G01 775 " -0.039 2.00e-02 2.50e+03 pdb=" C4 G01 775 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U012629 " 0.122 2.00e-02 2.50e+03 6.53e-02 9.59e+01 pdb=" N1 U012629 " -0.009 2.00e-02 2.50e+03 pdb=" C2 U012629 " -0.025 2.00e-02 2.50e+03 pdb=" O2 U012629 " -0.044 2.00e-02 2.50e+03 pdb=" N3 U012629 " -0.021 2.00e-02 2.50e+03 pdb=" C4 U012629 " -0.018 2.00e-02 2.50e+03 pdb=" O4 U012629 " 0.113 2.00e-02 2.50e+03 pdb=" C5 U012629 " -0.060 2.00e-02 2.50e+03 pdb=" C6 U012629 " -0.060 2.00e-02 2.50e+03 ... (remaining 13713 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 1 2.04 - 2.76: 19819 2.76 - 3.47: 197369 3.47 - 4.19: 495775 4.19 - 4.90: 681576 Nonbonded interactions: 1394540 Sorted by model distance: nonbonded pdb=" O3' A Y 76 " pdb=" C PHE Y 101 " model vdw 1.331 3.270 nonbonded pdb=" O HIS O 45 " pdb=" N LYS O 47 " model vdw 2.197 2.520 nonbonded pdb=" O LYS14 29 " pdb=" OG1 THR14 30 " model vdw 2.218 2.440 nonbonded pdb=" O2' U011130 " pdb=" OP1 G011131 " model vdw 2.253 2.440 nonbonded pdb=" O3' A Y 76 " pdb=" O PHE Y 101 " model vdw 2.267 3.040 ... (remaining 1394535 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.590 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: 27.640 Check model and map are aligned: 1.780 Set scattering table: 1.110 Process input model: 608.140 Find NCS groups from input model: 3.040 Set up NCS constraints: 0.450 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 652.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.221 166818 Z= 0.451 Angle : 1.002 24.397 249072 Z= 0.663 Chirality : 0.085 0.740 31782 Planarity : 0.008 0.181 13716 Dihedral : 22.187 177.710 94948 Min Nonbonded Distance : 1.331 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 2.04 % Allowed : 11.45 % Favored : 86.51 % Rotamer: Outliers : 1.17 % Allowed : 4.24 % Favored : 94.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.21 (0.08), residues: 6366 helix: -4.06 (0.06), residues: 1926 sheet: -3.03 (0.14), residues: 1081 loop : -3.24 (0.09), residues: 3359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.006 TRP04 212 HIS 0.003 0.000 HIS03 172 PHE 0.057 0.005 PHE03 38 TYR 0.123 0.008 TYR Z 309 ARG 0.011 0.001 ARG Z 7 *********************** 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 2109 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 2047 time to evaluate : 6.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 07 142 TYR cc_start: 0.8601 (t80) cc_final: 0.8359 (t80) REVERT: 09 51 ARG cc_start: 0.8921 (mtt180) cc_final: 0.7874 (ttp-110) REVERT: 09 112 LYS cc_start: 0.8043 (ttpp) cc_final: 0.7732 (mttt) REVERT: 09 132 PHE cc_start: 0.8595 (m-80) cc_final: 0.8305 (m-80) REVERT: 10 5 LEU cc_start: 0.9260 (mt) cc_final: 0.8988 (pp) REVERT: 10 24 SER cc_start: 0.7152 (m) cc_final: 0.6865 (m) REVERT: 10 34 THR cc_start: 0.7080 (p) cc_final: 0.6420 (p) REVERT: 11 33 ASN cc_start: 0.9161 (m-40) cc_final: 0.8378 (m110) REVERT: 11 36 GLU cc_start: 0.8277 (mt-10) cc_final: 0.7744 (mt-10) REVERT: 11 111 THR cc_start: 0.9343 (p) cc_final: 0.8821 (p) REVERT: 11 133 ARG cc_start: 0.9364 (ttm110) cc_final: 0.8996 (ttm170) REVERT: 12 49 ASP cc_start: 0.7796 (t0) cc_final: 0.7557 (t70) REVERT: 13 14 SER cc_start: 0.8524 (p) cc_final: 0.8315 (m) REVERT: 13 106 GLU cc_start: 0.8338 (mp0) cc_final: 0.8081 (mp0) REVERT: 16 72 ASP cc_start: 0.8583 (t70) cc_final: 0.8153 (t0) REVERT: 16 75 ILE cc_start: 0.9257 (mm) cc_final: 0.8735 (mm) REVERT: 21 86 MET cc_start: 0.9376 (tpt) cc_final: 0.8915 (tpt) REVERT: 21 109 ASP cc_start: 0.8681 (p0) cc_final: 0.8420 (p0) REVERT: 22 3 ARG cc_start: 0.8263 (tpt90) cc_final: 0.7707 (tpp80) REVERT: 24 41 GLU cc_start: 0.7468 (tm-30) cc_final: 0.7237 (tm-30) REVERT: 24 75 GLN cc_start: 0.9286 (tp40) cc_final: 0.8795 (tp-100) REVERT: 26 42 GLU cc_start: 0.8379 (mp0) cc_final: 0.8051 (mp0) REVERT: 31 24 LYS cc_start: 0.8614 (ttpt) cc_final: 0.8335 (tttt) REVERT: 34 37 GLN cc_start: 0.8404 (mm110) cc_final: 0.8176 (mm-40) REVERT: B 35 ASN cc_start: 0.8187 (t0) cc_final: 0.7986 (t0) REVERT: B 48 MET cc_start: 0.9302 (mmm) cc_final: 0.8959 (tpp) REVERT: B 160 LEU cc_start: 0.9143 (tp) cc_final: 0.8905 (tt) REVERT: C 139 ASN cc_start: 0.8651 (m110) cc_final: 0.8428 (m110) REVERT: C 141 MET cc_start: 0.8692 (mmm) cc_final: 0.6873 (mmt) REVERT: D 47 LEU cc_start: 0.9190 (tp) cc_final: 0.8987 (pp) REVERT: D 197 HIS cc_start: 0.8171 (t70) cc_final: 0.7865 (t70) REVERT: E 63 MET cc_start: 0.8228 (mmt) cc_final: 0.7951 (mmm) REVERT: E 76 ASN cc_start: 0.8986 (t0) cc_final: 0.8680 (t0) REVERT: E 102 THR cc_start: 0.8357 (m) cc_final: 0.7984 (p) REVERT: E 159 SER cc_start: 0.8625 (m) cc_final: 0.7890 (t) REVERT: H 89 ASP cc_start: 0.8342 (p0) cc_final: 0.7660 (p0) REVERT: H 112 ASP cc_start: 0.8091 (p0) cc_final: 0.7749 (p0) REVERT: J 28 THR cc_start: 0.9034 (m) cc_final: 0.8718 (t) REVERT: J 53 ILE cc_start: 0.8047 (tt) cc_final: 0.7681 (tt) REVERT: J 63 ASP cc_start: 0.7540 (m-30) cc_final: 0.7325 (m-30) REVERT: J 77 VAL cc_start: 0.9276 (t) cc_final: 0.8899 (t) REVERT: L 2 THR cc_start: 0.7576 (m) cc_final: 0.7058 (m) REVERT: L 72 ASN cc_start: 0.8398 (p0) cc_final: 0.7982 (p0) REVERT: M 65 GLU cc_start: 0.8118 (tp30) cc_final: 0.7785 (tp30) REVERT: N 19 TYR cc_start: 0.8395 (m-80) cc_final: 0.7734 (m-10) REVERT: N 49 THR cc_start: 0.9006 (m) cc_final: 0.8541 (m) REVERT: N 81 ILE cc_start: 0.8591 (mt) cc_final: 0.8104 (mt) REVERT: Q 16 MET cc_start: 0.8197 (ptm) cc_final: 0.7856 (ptm) REVERT: S 5 LYS cc_start: 0.6946 (ptmt) cc_final: 0.6669 (pttm) REVERT: S 26 ASP cc_start: 0.8418 (t70) cc_final: 0.8026 (t0) REVERT: T 31 ILE cc_start: 0.8913 (mt) cc_final: 0.8574 (mt) REVERT: T 35 TYR cc_start: 0.8500 (m-80) cc_final: 0.8267 (m-80) REVERT: T 82 ILE cc_start: 0.9329 (pt) cc_final: 0.9049 (mt) REVERT: U 32 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7634 (ptp90) REVERT: 03 203 GLN cc_start: 0.8774 (mp-120) cc_final: 0.8427 (mp10) REVERT: 03 218 MET cc_start: 0.5385 (mtt) cc_final: 0.4190 (ttt) REVERT: Z 160 TYR cc_start: 0.8013 (m-10) cc_final: 0.7254 (m-10) REVERT: Z 358 MET cc_start: 0.7138 (pmm) cc_final: 0.6575 (pmm) outliers start: 62 outliers final: 17 residues processed: 2087 average time/residue: 1.5469 time to fit residues: 5564.9614 Evaluate side-chains 1459 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 1441 time to evaluate : 6.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 07 residue 140 ILE Chi-restraints excluded: chain 10 residue 118 ILE Chi-restraints excluded: chain 10 residue 119 PRO Chi-restraints excluded: chain 12 residue 101 ILE Chi-restraints excluded: chain 18 residue 3 ILE Chi-restraints excluded: chain 21 residue 62 ASP Chi-restraints excluded: chain 32 residue 1 MET Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain U residue 32 ARG Chi-restraints excluded: chain Z residue 20 VAL Chi-restraints excluded: chain Z residue 134 LEU Chi-restraints excluded: chain Z residue 191 LEU Chi-restraints excluded: chain Z residue 236 ILE Chi-restraints excluded: chain Z residue 292 LEU Chi-restraints excluded: chain Z residue 332 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1101 random chunks: chunk 929 optimal weight: 10.0000 chunk 834 optimal weight: 10.0000 chunk 463 optimal weight: 30.0000 chunk 285 optimal weight: 9.9990 chunk 562 optimal weight: 7.9990 chunk 445 optimal weight: 10.0000 chunk 862 optimal weight: 10.0000 chunk 333 optimal weight: 9.9990 chunk 524 optimal weight: 9.9990 chunk 642 optimal weight: 10.0000 chunk 999 optimal weight: 10.0000 overall best weight: 9.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 04 24 HIS 04 36 ASN 04 45 ASN 04 52 HIS 04 85 ASN ** 04 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 04 127 ASN 04 196 ASN 04 238 ASN 04 259 ASN 05 49 GLN 05 185 ASN 06 30 GLN 06 92 HIS 06 94 GLN 06 97 ASN 06 163 ASN 07 51 ASN 07 134 GLN 08 21 GLN 08 37 ASN ** 08 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 138 GLN 09 2 GLN ** 09 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 09 66 ASN ** 09 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 10 103 ASN 11 18 ASN 11 42 ASN ** 11 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 12 58 ASN 12 128 ASN 14 4 ASN 14 38 GLN 15 17 ASN 16 62 ASN 17 29 HIS 17 38 GLN 17 104 GLN 18 6 GLN 18 11 GLN 18 51 ASN 19 80 ASN 20 12 HIS 20 18 GLN ** 21 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 21 40 ASN 22 59 ASN 22 92 ASN ** 23 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 23 65 GLN 23 68 ASN 23 73 ASN 24 49 ASN 27 31 GLN ** 27 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 28 19 HIS 29 61 ASN ** 30 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 31 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 33 27 ASN B 35 ASN B 121 GLN B 176 ASN ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN C 40 GLN ** C 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 GLN D 73 ASN ** D 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 ASN E 81 GLN E 120 HIS F 52 ASN F 55 HIS G 27 ASN G 121 ASN ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 GLN ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 14 GLN L 4 ASN L 45 ASN ** L 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN N 59 GLN N 65 GLN ** O 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 36 ASN P 26 ASN Q 30 HIS R 51 GLN R 53 GLN S 51 HIS S 68 HIS T 2 ASN ** T 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 69 ASN 03 58 ASN Z 66 HIS ** Z 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 251 GLN Z 364 HIS Total number of N/Q/H flips: 86 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 166818 Z= 0.382 Angle : 0.730 13.423 249072 Z= 0.377 Chirality : 0.040 0.337 31782 Planarity : 0.006 0.171 13716 Dihedral : 23.065 179.716 82327 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.08 % Favored : 90.56 % Rotamer: Outliers : 5.01 % Allowed : 15.78 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.49 (0.09), residues: 6366 helix: -1.72 (0.10), residues: 1960 sheet: -2.52 (0.14), residues: 1106 loop : -2.62 (0.10), residues: 3300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP04 212 HIS 0.014 0.001 HIS B 17 PHE 0.037 0.002 PHE U 36 TYR 0.029 0.002 TYR O 77 ARG 0.015 0.001 ARG F 24 *********************** 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 1803 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 1538 time to evaluate : 6.433 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: 06 30 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.8449 (tp40) REVERT: 07 112 ASP cc_start: 0.7661 (OUTLIER) cc_final: 0.7337 (t70) REVERT: 08 57 TYR cc_start: 0.8283 (m-80) cc_final: 0.7805 (m-10) REVERT: 08 127 GLN cc_start: 0.7958 (mm-40) cc_final: 0.7571 (tm-30) REVERT: 09 8 LYS cc_start: 0.8674 (tptp) cc_final: 0.8358 (tptp) REVERT: 09 129 GLU cc_start: 0.8657 (tt0) cc_final: 0.8131 (tp30) REVERT: 09 133 GLN cc_start: 0.9349 (tt0) cc_final: 0.8968 (tp-100) REVERT: 09 135 HIS cc_start: 0.7821 (t70) cc_final: 0.7043 (t70) REVERT: 09 139 PHE cc_start: 0.9132 (m-80) cc_final: 0.8474 (m-80) REVERT: 10 37 LYS cc_start: 0.8652 (pttt) cc_final: 0.7948 (mttp) REVERT: 11 30 GLN cc_start: 0.8415 (mp10) cc_final: 0.7526 (mp10) REVERT: 11 33 ASN cc_start: 0.9293 (m-40) cc_final: 0.8765 (m110) REVERT: 11 124 MET cc_start: 0.8620 (mmm) cc_final: 0.8236 (mmm) REVERT: 13 12 ASP cc_start: 0.7915 (p0) cc_final: 0.7439 (p0) REVERT: 13 13 ASN cc_start: 0.8929 (p0) cc_final: 0.8681 (p0) REVERT: 13 106 GLU cc_start: 0.8519 (mp0) cc_final: 0.8021 (mp0) REVERT: 16 72 ASP cc_start: 0.8749 (t70) cc_final: 0.8254 (t0) REVERT: 16 75 ILE cc_start: 0.9279 (mm) cc_final: 0.8972 (mm) REVERT: 17 16 ARG cc_start: 0.9007 (mmp80) cc_final: 0.8800 (mmp80) REVERT: 17 76 LYS cc_start: 0.9180 (tppt) cc_final: 0.8766 (tppt) REVERT: 17 80 GLU cc_start: 0.8474 (pt0) cc_final: 0.8249 (pt0) REVERT: 18 6 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.8531 (tp-100) REVERT: 18 9 GLN cc_start: 0.8543 (pp30) cc_final: 0.7908 (pp30) REVERT: 18 10 GLU cc_start: 0.8134 (pt0) cc_final: 0.7692 (pt0) REVERT: 18 98 TYR cc_start: 0.8483 (p90) cc_final: 0.8241 (p90) REVERT: 20 1 MET cc_start: 0.8506 (tpt) cc_final: 0.8033 (tpt) REVERT: 21 109 ASP cc_start: 0.8786 (p0) cc_final: 0.8441 (p0) REVERT: 22 4 GLU cc_start: 0.8063 (mp0) cc_final: 0.7714 (mp0) REVERT: 28 18 LYS cc_start: 0.8797 (mmmt) cc_final: 0.8586 (mmmt) REVERT: 29 12 ILE cc_start: 0.9399 (OUTLIER) cc_final: 0.8936 (mt) REVERT: 29 23 LYS cc_start: 0.8555 (mmmt) cc_final: 0.8222 (tptp) REVERT: 29 24 ILE cc_start: 0.9273 (tp) cc_final: 0.8670 (tp) REVERT: 30 14 MET cc_start: 0.8027 (mtm) cc_final: 0.7819 (mtm) REVERT: 30 35 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.6359 (pt0) REVERT: 34 37 GLN cc_start: 0.8116 (mm110) cc_final: 0.7721 (mm-40) REVERT: B 18 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8261 (mp10) REVERT: B 160 LEU cc_start: 0.9253 (tp) cc_final: 0.9000 (tt) REVERT: C 35 ASP cc_start: 0.8555 (t0) cc_final: 0.8231 (t0) REVERT: E 60 GLN cc_start: 0.8166 (tp40) cc_final: 0.7853 (tp40) REVERT: E 64 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7732 (mm-30) REVERT: E 76 ASN cc_start: 0.9222 (t0) cc_final: 0.9012 (t0) REVERT: F 14 GLN cc_start: 0.9213 (mp10) cc_final: 0.8930 (mp10) REVERT: F 16 GLU cc_start: 0.9025 (pm20) cc_final: 0.8779 (pm20) REVERT: F 21 MET cc_start: 0.9174 (tpt) cc_final: 0.8861 (tpt) REVERT: F 59 TYR cc_start: 0.8613 (m-10) cc_final: 0.8393 (m-10) REVERT: G 143 MET cc_start: 0.9186 (mmt) cc_final: 0.8894 (mmp) REVERT: H 62 LEU cc_start: 0.9179 (mp) cc_final: 0.8904 (mp) REVERT: H 89 ASP cc_start: 0.8056 (p0) cc_final: 0.7574 (p0) REVERT: I 87 MET cc_start: 0.9092 (ptt) cc_final: 0.8783 (ppp) REVERT: J 24 GLU cc_start: 0.8957 (pp20) cc_final: 0.8726 (pp20) REVERT: J 59 LYS cc_start: 0.8670 (tptm) cc_final: 0.8449 (tptm) REVERT: J 65 TYR cc_start: 0.8137 (m-80) cc_final: 0.7733 (m-80) REVERT: M 43 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8387 (mtpp) REVERT: N 46 LYS cc_start: 0.9253 (tppt) cc_final: 0.9022 (tppt) REVERT: N 49 THR cc_start: 0.8892 (m) cc_final: 0.8614 (m) REVERT: N 91 GLU cc_start: 0.8706 (mp0) cc_final: 0.8504 (mp0) REVERT: P 1 MET cc_start: 0.8627 (tpt) cc_final: 0.8203 (tmm) REVERT: Q 16 MET cc_start: 0.8605 (ptm) cc_final: 0.8139 (ptm) REVERT: S 16 LYS cc_start: 0.8899 (mtmm) cc_final: 0.8582 (mtmm) REVERT: S 63 ASP cc_start: 0.7918 (t0) cc_final: 0.7648 (t0) REVERT: S 64 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7868 (mm-30) REVERT: 03 8 MET cc_start: 0.7355 (mpp) cc_final: 0.7117 (mmt) REVERT: 03 218 MET cc_start: 0.5612 (mtt) cc_final: 0.5235 (mmt) REVERT: Z 160 TYR cc_start: 0.8500 (m-10) cc_final: 0.8044 (m-10) REVERT: Z 273 ASN cc_start: 0.8175 (t0) cc_final: 0.7883 (t0) outliers start: 265 outliers final: 161 residues processed: 1656 average time/residue: 1.4047 time to fit residues: 4073.1127 Evaluate side-chains 1485 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 1317 time to evaluate : 7.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 37 SER Chi-restraints excluded: chain 04 residue 117 SER Chi-restraints excluded: chain 04 residue 144 GLU Chi-restraints excluded: chain 04 residue 156 SER Chi-restraints excluded: chain 05 residue 22 ILE Chi-restraints excluded: chain 05 residue 95 SER Chi-restraints excluded: chain 05 residue 97 SER Chi-restraints excluded: chain 05 residue 103 ASP Chi-restraints excluded: chain 05 residue 108 ASP Chi-restraints excluded: chain 05 residue 139 SER Chi-restraints excluded: chain 05 residue 165 MET Chi-restraints excluded: chain 05 residue 199 SER Chi-restraints excluded: chain 05 residue 200 ASP Chi-restraints excluded: chain 06 residue 7 ASP Chi-restraints excluded: chain 06 residue 30 GLN Chi-restraints excluded: chain 06 residue 187 VAL Chi-restraints excluded: chain 07 residue 30 VAL Chi-restraints excluded: chain 07 residue 95 MET Chi-restraints excluded: chain 07 residue 112 ASP Chi-restraints excluded: chain 08 residue 9 VAL Chi-restraints excluded: chain 08 residue 55 ASP Chi-restraints excluded: chain 08 residue 130 ILE Chi-restraints excluded: chain 08 residue 154 GLU Chi-restraints excluded: chain 09 residue 42 LYS Chi-restraints excluded: chain 09 residue 54 LEU Chi-restraints excluded: chain 09 residue 91 PHE Chi-restraints excluded: chain 10 residue 76 PHE Chi-restraints excluded: chain 10 residue 123 ILE Chi-restraints excluded: chain 11 residue 85 ILE Chi-restraints excluded: chain 11 residue 121 ILE Chi-restraints excluded: chain 12 residue 81 ILE Chi-restraints excluded: chain 13 residue 21 CYS Chi-restraints excluded: chain 13 residue 65 THR Chi-restraints excluded: chain 13 residue 69 VAL Chi-restraints excluded: chain 13 residue 97 THR Chi-restraints excluded: chain 14 residue 42 SER Chi-restraints excluded: chain 14 residue 80 SER Chi-restraints excluded: chain 14 residue 103 ILE Chi-restraints excluded: chain 14 residue 110 VAL Chi-restraints excluded: chain 14 residue 122 VAL Chi-restraints excluded: chain 15 residue 74 THR Chi-restraints excluded: chain 15 residue 102 LEU Chi-restraints excluded: chain 16 residue 15 SER Chi-restraints excluded: chain 16 residue 20 MET Chi-restraints excluded: chain 16 residue 27 SER Chi-restraints excluded: chain 16 residue 36 THR Chi-restraints excluded: chain 16 residue 47 VAL Chi-restraints excluded: chain 16 residue 106 ASP Chi-restraints excluded: chain 17 residue 2 ASP Chi-restraints excluded: chain 17 residue 18 LEU Chi-restraints excluded: chain 17 residue 28 VAL Chi-restraints excluded: chain 17 residue 69 ASP Chi-restraints excluded: chain 18 residue 6 GLN Chi-restraints excluded: chain 18 residue 45 VAL Chi-restraints excluded: chain 18 residue 81 ASP Chi-restraints excluded: chain 19 residue 7 VAL Chi-restraints excluded: chain 19 residue 80 ASN Chi-restraints excluded: chain 19 residue 86 SER Chi-restraints excluded: chain 20 residue 15 SER Chi-restraints excluded: chain 20 residue 98 ILE Chi-restraints excluded: chain 21 residue 62 ASP Chi-restraints excluded: chain 21 residue 96 ILE Chi-restraints excluded: chain 21 residue 101 SER Chi-restraints excluded: chain 22 residue 5 GLU Chi-restraints excluded: chain 22 residue 37 ASP Chi-restraints excluded: chain 22 residue 78 SER Chi-restraints excluded: chain 23 residue 59 GLU Chi-restraints excluded: chain 23 residue 97 SER Chi-restraints excluded: chain 24 residue 58 SER Chi-restraints excluded: chain 24 residue 65 VAL Chi-restraints excluded: chain 25 residue 12 SER Chi-restraints excluded: chain 26 residue 59 ASP Chi-restraints excluded: chain 27 residue 55 THR Chi-restraints excluded: chain 28 residue 9 THR Chi-restraints excluded: chain 28 residue 16 LEU Chi-restraints excluded: chain 28 residue 31 ILE Chi-restraints excluded: chain 29 residue 12 ILE Chi-restraints excluded: chain 29 residue 44 PHE Chi-restraints excluded: chain 29 residue 57 VAL Chi-restraints excluded: chain 30 residue 8 THR Chi-restraints excluded: chain 30 residue 26 SER Chi-restraints excluded: chain 30 residue 29 VAL Chi-restraints excluded: chain 30 residue 35 GLU Chi-restraints excluded: chain 31 residue 35 LEU Chi-restraints excluded: chain 32 residue 1 MET Chi-restraints excluded: chain 32 residue 4 THR Chi-restraints excluded: chain 32 residue 10 LEU Chi-restraints excluded: chain 32 residue 30 VAL Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 32 residue 44 VAL Chi-restraints excluded: chain 33 residue 53 ASP Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 108 GLN Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 212 TYR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 156 LEU 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 E residue 29 ILE Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain F residue 65 GLU Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain G residue 125 ASP Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain I residue 72 SER Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain K residue 17 ASP Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 71 ASP Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 43 LYS Chi-restraints excluded: chain M residue 57 ASP Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 67 ASP Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain R residue 32 ILE Chi-restraints excluded: chain R residue 41 SER Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain U residue 8 ASN Chi-restraints excluded: chain U residue 12 ASP Chi-restraints excluded: chain U residue 18 PHE Chi-restraints excluded: chain U residue 43 GLU Chi-restraints excluded: chain U residue 48 LYS Chi-restraints excluded: chain 03 residue 35 THR Chi-restraints excluded: chain Z residue 20 VAL Chi-restraints excluded: chain Z residue 90 ASN Chi-restraints excluded: chain Z residue 134 LEU Chi-restraints excluded: chain Z residue 227 VAL Chi-restraints excluded: chain Z residue 236 ILE Chi-restraints excluded: chain Z residue 237 LYS Chi-restraints excluded: chain Z residue 292 LEU Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 332 PHE Chi-restraints excluded: chain Z residue 356 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1101 random chunks: chunk 555 optimal weight: 20.0000 chunk 310 optimal weight: 10.0000 chunk 832 optimal weight: 10.0000 chunk 680 optimal weight: 10.0000 chunk 275 optimal weight: 6.9990 chunk 1001 optimal weight: 10.0000 chunk 1082 optimal weight: 8.9990 chunk 892 optimal weight: 20.0000 chunk 993 optimal weight: 10.0000 chunk 341 optimal weight: 20.0000 chunk 803 optimal weight: 20.0000 overall best weight: 9.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 04 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 05 150 GLN 06 30 GLN ** 07 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 114 HIS ** 08 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 42 ASN ** 12 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 12 128 ASN 14 4 ASN 14 38 GLN ** 16 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 18 6 GLN 18 114 ASN 19 19 GLN ** 19 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 20 89 HIS ** 21 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 29 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 29 65 ASN ** 31 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 GLN B 202 ASN ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN D 197 HIS ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN I 74 GLN L 4 ASN L 76 HIS ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 ASN N 65 GLN ** O 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 53 GLN S 68 HIS ** T 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 135 ASN ** Z 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 251 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 166818 Z= 0.359 Angle : 0.664 16.327 249072 Z= 0.345 Chirality : 0.038 0.337 31782 Planarity : 0.005 0.118 13716 Dihedral : 23.267 179.262 82306 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.80 % Favored : 89.92 % Rotamer: Outliers : 6.32 % Allowed : 17.39 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.10), residues: 6366 helix: -0.73 (0.11), residues: 1952 sheet: -2.23 (0.15), residues: 1110 loop : -2.24 (0.10), residues: 3304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP04 212 HIS 0.014 0.002 HIS B 17 PHE 0.043 0.002 PHE U 36 TYR 0.036 0.002 TYR O 77 ARG 0.016 0.001 ARG F 44 *********************** 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 1730 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 334 poor density : 1396 time to evaluate : 6.975 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: 06 115 GLN cc_start: 0.8859 (mm-40) cc_final: 0.8654 (mp10) REVERT: 07 112 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7233 (t70) REVERT: 07 135 ILE cc_start: 0.9443 (OUTLIER) cc_final: 0.8974 (tp) REVERT: 08 57 TYR cc_start: 0.8399 (m-80) cc_final: 0.8057 (m-10) REVERT: 08 146 ASP cc_start: 0.7703 (OUTLIER) cc_final: 0.7436 (p0) REVERT: 09 91 PHE cc_start: 0.8126 (OUTLIER) cc_final: 0.7748 (m-80) REVERT: 09 133 GLN cc_start: 0.9321 (tt0) cc_final: 0.8840 (tp40) REVERT: 09 135 HIS cc_start: 0.8097 (t70) cc_final: 0.7143 (t70) REVERT: 10 37 LYS cc_start: 0.8579 (pttt) cc_final: 0.7610 (mttp) REVERT: 11 33 ASN cc_start: 0.9283 (m-40) cc_final: 0.8881 (m110) REVERT: 11 140 GLU cc_start: 0.7397 (pt0) cc_final: 0.6682 (mt-10) REVERT: 13 12 ASP cc_start: 0.7918 (p0) cc_final: 0.7618 (p0) REVERT: 13 13 ASN cc_start: 0.8867 (p0) cc_final: 0.8627 (p0) REVERT: 16 72 ASP cc_start: 0.8725 (t70) cc_final: 0.8100 (t0) REVERT: 16 75 ILE cc_start: 0.9268 (mm) cc_final: 0.8829 (mm) REVERT: 17 76 LYS cc_start: 0.9083 (tppt) cc_final: 0.8634 (tppt) REVERT: 18 6 GLN cc_start: 0.8775 (pt0) cc_final: 0.8556 (pt0) REVERT: 21 109 ASP cc_start: 0.8856 (p0) cc_final: 0.8555 (p0) REVERT: 22 1 MET cc_start: 0.6981 (ptt) cc_final: 0.6719 (ptp) REVERT: 22 4 GLU cc_start: 0.8441 (mp0) cc_final: 0.8075 (mp0) REVERT: 23 21 ARG cc_start: 0.8631 (mtm-85) cc_final: 0.8416 (mtm-85) REVERT: 24 51 GLN cc_start: 0.9022 (pp30) cc_final: 0.8728 (pp30) REVERT: 27 20 ASN cc_start: 0.8953 (m-40) cc_final: 0.8689 (m110) REVERT: 28 18 LYS cc_start: 0.8824 (mmmt) cc_final: 0.8600 (mmmt) REVERT: 29 9 TYR cc_start: 0.7533 (OUTLIER) cc_final: 0.7189 (t80) REVERT: 29 50 ASP cc_start: 0.8085 (t0) cc_final: 0.7882 (t0) REVERT: 30 14 MET cc_start: 0.7873 (mtm) cc_final: 0.7616 (mtm) REVERT: 31 6 GLU cc_start: 0.8304 (pm20) cc_final: 0.8100 (pm20) REVERT: B 48 MET cc_start: 0.9321 (tpp) cc_final: 0.8922 (mmt) REVERT: B 160 LEU cc_start: 0.9228 (tp) cc_final: 0.9001 (tt) REVERT: D 131 ILE cc_start: 0.8989 (mp) cc_final: 0.8775 (mm) REVERT: E 60 GLN cc_start: 0.8169 (tp40) cc_final: 0.7898 (tp40) REVERT: F 13 ASP cc_start: 0.8987 (p0) cc_final: 0.8687 (p0) REVERT: F 14 GLN cc_start: 0.9306 (mp10) cc_final: 0.9036 (mp10) REVERT: F 59 TYR cc_start: 0.8523 (m-10) cc_final: 0.8323 (m-10) REVERT: G 143 MET cc_start: 0.9172 (mmt) cc_final: 0.8929 (mmp) REVERT: H 89 ASP cc_start: 0.8165 (p0) cc_final: 0.7726 (p0) REVERT: I 87 MET cc_start: 0.9118 (ptt) cc_final: 0.8870 (ppp) REVERT: J 24 GLU cc_start: 0.9076 (pp20) cc_final: 0.8841 (pp20) REVERT: L 74 GLN cc_start: 0.9123 (pm20) cc_final: 0.8909 (pm20) REVERT: M 43 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8535 (mtpp) REVERT: O 77 TYR cc_start: 0.8555 (t80) cc_final: 0.8248 (t80) REVERT: Q 16 MET cc_start: 0.8786 (ptm) cc_final: 0.8495 (ptm) REVERT: S 12 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8653 (tp) REVERT: S 63 ASP cc_start: 0.8077 (t0) cc_final: 0.7796 (t0) REVERT: S 64 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7860 (mm-30) REVERT: U 45 LYS cc_start: 0.9071 (tppt) cc_final: 0.8857 (tppt) REVERT: 03 8 MET cc_start: 0.7517 (mpp) cc_final: 0.7311 (mmt) REVERT: 03 170 ILE cc_start: 0.8518 (mt) cc_final: 0.8287 (pt) REVERT: Z 160 TYR cc_start: 0.8531 (m-10) cc_final: 0.8162 (m-10) REVERT: Z 273 ASN cc_start: 0.8189 (t0) cc_final: 0.7986 (t0) outliers start: 334 outliers final: 214 residues processed: 1551 average time/residue: 1.3229 time to fit residues: 3591.2311 Evaluate side-chains 1497 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 1276 time to evaluate : 6.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 37 SER Chi-restraints excluded: chain 04 residue 117 SER Chi-restraints excluded: chain 04 residue 156 SER Chi-restraints excluded: chain 04 residue 200 MET Chi-restraints excluded: chain 04 residue 263 ASP Chi-restraints excluded: chain 05 residue 22 ILE Chi-restraints excluded: chain 05 residue 97 SER Chi-restraints excluded: chain 05 residue 103 ASP Chi-restraints excluded: chain 05 residue 108 ASP Chi-restraints excluded: chain 05 residue 139 SER Chi-restraints excluded: chain 05 residue 176 ASP Chi-restraints excluded: chain 05 residue 200 ASP Chi-restraints excluded: chain 06 residue 7 ASP Chi-restraints excluded: chain 06 residue 187 VAL Chi-restraints excluded: chain 07 residue 30 VAL Chi-restraints excluded: chain 07 residue 73 VAL Chi-restraints excluded: chain 07 residue 95 MET Chi-restraints excluded: chain 07 residue 112 ASP Chi-restraints excluded: chain 07 residue 135 ILE Chi-restraints excluded: chain 07 residue 154 THR Chi-restraints excluded: chain 08 residue 9 VAL Chi-restraints excluded: chain 08 residue 10 VAL Chi-restraints excluded: chain 08 residue 55 ASP Chi-restraints excluded: chain 08 residue 130 ILE Chi-restraints excluded: chain 08 residue 146 ASP Chi-restraints excluded: chain 08 residue 154 GLU Chi-restraints excluded: chain 09 residue 17 ASP Chi-restraints excluded: chain 09 residue 54 LEU Chi-restraints excluded: chain 09 residue 91 PHE Chi-restraints excluded: chain 10 residue 24 SER Chi-restraints excluded: chain 10 residue 76 PHE Chi-restraints excluded: chain 10 residue 123 ILE Chi-restraints excluded: chain 11 residue 67 THR Chi-restraints excluded: chain 11 residue 85 ILE Chi-restraints excluded: chain 11 residue 95 ASP Chi-restraints excluded: chain 11 residue 120 ASP Chi-restraints excluded: chain 12 residue 32 LEU Chi-restraints excluded: chain 12 residue 52 ASP Chi-restraints excluded: chain 12 residue 67 ASN Chi-restraints excluded: chain 12 residue 81 ILE Chi-restraints excluded: chain 12 residue 111 LYS Chi-restraints excluded: chain 12 residue 128 ASN Chi-restraints excluded: chain 13 residue 21 CYS Chi-restraints excluded: chain 13 residue 65 THR Chi-restraints excluded: chain 14 residue 4 ASN Chi-restraints excluded: chain 14 residue 42 SER Chi-restraints excluded: chain 14 residue 67 THR Chi-restraints excluded: chain 14 residue 85 VAL Chi-restraints excluded: chain 14 residue 103 ILE Chi-restraints excluded: chain 14 residue 110 VAL Chi-restraints excluded: chain 14 residue 122 VAL Chi-restraints excluded: chain 15 residue 12 MET Chi-restraints excluded: chain 15 residue 42 THR Chi-restraints excluded: chain 15 residue 74 THR Chi-restraints excluded: chain 15 residue 132 THR Chi-restraints excluded: chain 16 residue 2 ARG Chi-restraints excluded: chain 16 residue 9 GLN Chi-restraints excluded: chain 16 residue 15 SER Chi-restraints excluded: chain 16 residue 20 MET Chi-restraints excluded: chain 16 residue 27 SER Chi-restraints excluded: chain 16 residue 36 THR Chi-restraints excluded: chain 16 residue 57 THR Chi-restraints excluded: chain 16 residue 106 ASP Chi-restraints excluded: chain 17 residue 2 ASP Chi-restraints excluded: chain 17 residue 28 VAL Chi-restraints excluded: chain 17 residue 69 ASP Chi-restraints excluded: chain 17 residue 87 ILE Chi-restraints excluded: chain 18 residue 35 SER Chi-restraints excluded: chain 18 residue 45 VAL Chi-restraints excluded: chain 18 residue 51 ASN Chi-restraints excluded: chain 18 residue 72 VAL Chi-restraints excluded: chain 18 residue 81 ASP Chi-restraints excluded: chain 18 residue 96 LEU Chi-restraints excluded: chain 19 residue 7 VAL Chi-restraints excluded: chain 19 residue 16 ILE Chi-restraints excluded: chain 19 residue 79 ILE Chi-restraints excluded: chain 19 residue 82 LEU Chi-restraints excluded: chain 19 residue 86 SER Chi-restraints excluded: chain 20 residue 15 SER Chi-restraints excluded: chain 20 residue 51 VAL Chi-restraints excluded: chain 20 residue 98 ILE Chi-restraints excluded: chain 21 residue 39 THR Chi-restraints excluded: chain 21 residue 96 ILE Chi-restraints excluded: chain 21 residue 101 SER Chi-restraints excluded: chain 21 residue 104 THR Chi-restraints excluded: chain 22 residue 5 GLU Chi-restraints excluded: chain 22 residue 78 SER Chi-restraints excluded: chain 22 residue 93 LEU Chi-restraints excluded: chain 23 residue 14 THR Chi-restraints excluded: chain 23 residue 17 ASP Chi-restraints excluded: chain 23 residue 27 VAL Chi-restraints excluded: chain 23 residue 59 GLU Chi-restraints excluded: chain 24 residue 8 VAL Chi-restraints excluded: chain 24 residue 58 SER Chi-restraints excluded: chain 24 residue 61 LEU Chi-restraints excluded: chain 24 residue 65 VAL Chi-restraints excluded: chain 26 residue 24 THR Chi-restraints excluded: chain 26 residue 32 LEU Chi-restraints excluded: chain 26 residue 59 ASP Chi-restraints excluded: chain 27 residue 7 ARG Chi-restraints excluded: chain 27 residue 55 THR Chi-restraints excluded: chain 28 residue 9 THR Chi-restraints excluded: chain 28 residue 16 LEU Chi-restraints excluded: chain 28 residue 56 VAL Chi-restraints excluded: chain 29 residue 1 MET Chi-restraints excluded: chain 29 residue 9 TYR Chi-restraints excluded: chain 29 residue 12 ILE Chi-restraints excluded: chain 29 residue 33 ASN Chi-restraints excluded: chain 29 residue 34 LEU Chi-restraints excluded: chain 29 residue 39 LYS Chi-restraints excluded: chain 29 residue 44 PHE Chi-restraints excluded: chain 30 residue 22 THR Chi-restraints excluded: chain 30 residue 26 SER Chi-restraints excluded: chain 30 residue 29 VAL Chi-restraints excluded: chain 30 residue 36 LYS Chi-restraints excluded: chain 32 residue 1 MET Chi-restraints excluded: chain 32 residue 4 THR Chi-restraints excluded: chain 32 residue 10 LEU Chi-restraints excluded: chain 32 residue 30 VAL Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 32 residue 44 VAL Chi-restraints excluded: chain 33 residue 53 ASP Chi-restraints excluded: chain 33 residue 54 LEU Chi-restraints excluded: chain 34 residue 37 GLN Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 108 GLN Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain D residue 16 THR 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 191 SER Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 156 ARG Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 75 GLN Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain I residue 95 SER Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 36 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 76 ILE Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 69 CYS Chi-restraints excluded: chain K residue 71 ASP Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 43 LYS Chi-restraints excluded: chain M residue 67 ASP Chi-restraints excluded: chain M residue 72 ILE Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain Q residue 48 GLU Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain R residue 20 ILE Chi-restraints excluded: chain R residue 32 ILE Chi-restraints excluded: chain R residue 41 SER Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain U residue 4 LYS Chi-restraints excluded: chain U residue 8 ASN Chi-restraints excluded: chain U residue 12 ASP Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 36 PHE Chi-restraints excluded: chain U residue 48 LYS Chi-restraints excluded: chain 03 residue 35 THR Chi-restraints excluded: chain 03 residue 47 ASN Chi-restraints excluded: chain Z residue 20 VAL Chi-restraints excluded: chain Z residue 90 ASN Chi-restraints excluded: chain Z residue 134 LEU Chi-restraints excluded: chain Z residue 197 SER Chi-restraints excluded: chain Z residue 227 VAL Chi-restraints excluded: chain Z residue 236 ILE Chi-restraints excluded: chain Z residue 237 LYS Chi-restraints excluded: chain Z residue 255 CYS Chi-restraints excluded: chain Z residue 292 LEU Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 332 PHE Chi-restraints excluded: chain Z residue 362 LEU 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: 10.0000 chunk 110 optimal weight: 30.0000 chunk 478 optimal weight: 20.0000 chunk 672 optimal weight: 10.0000 chunk 1005 optimal weight: 10.0000 chunk 1064 optimal weight: 5.9990 chunk 525 optimal weight: 20.0000 chunk 952 optimal weight: 30.0000 chunk 286 optimal weight: 8.9990 overall best weight: 8.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 04 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 07 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 09 33 GLN ** 09 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 29 HIS 14 4 ASN 14 38 GLN ** 16 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 20 82 HIS ** 21 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 29 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 31 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 GLN ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 56 HIS J 99 GLN L 4 ASN ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 ASN O 34 GLN R 53 GLN ** T 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 03 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 159 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 166818 Z= 0.353 Angle : 0.654 16.838 249072 Z= 0.338 Chirality : 0.037 0.310 31782 Planarity : 0.005 0.118 13716 Dihedral : 23.333 178.547 82304 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.52 % Favored : 90.25 % Rotamer: Outliers : 6.58 % Allowed : 19.13 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.10), residues: 6366 helix: -0.28 (0.12), residues: 1981 sheet: -2.02 (0.15), residues: 1098 loop : -2.13 (0.10), residues: 3287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP04 212 HIS 0.010 0.001 HIS L 76 PHE 0.043 0.002 PHE U 36 TYR 0.029 0.002 TYR C 41 ARG 0.011 0.001 ARG26 44 *********************** 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 1684 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 348 poor density : 1336 time to evaluate : 6.912 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: 04 99 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7562 (pt0) REVERT: 07 112 ASP cc_start: 0.7789 (OUTLIER) cc_final: 0.7388 (t70) REVERT: 07 135 ILE cc_start: 0.9432 (OUTLIER) cc_final: 0.8973 (tp) REVERT: 08 57 TYR cc_start: 0.8405 (m-80) cc_final: 0.8111 (m-10) REVERT: 09 91 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.8036 (m-80) REVERT: 09 133 GLN cc_start: 0.9285 (tt0) cc_final: 0.8912 (tp-100) REVERT: 09 135 HIS cc_start: 0.8081 (t70) cc_final: 0.7186 (t70) REVERT: 10 1 MET cc_start: 0.7476 (tmm) cc_final: 0.6250 (tpp) REVERT: 10 38 MET cc_start: 0.8909 (mmp) cc_final: 0.8618 (mtt) REVERT: 10 42 ARG cc_start: 0.8250 (tpp-160) cc_final: 0.7961 (tpp-160) REVERT: 10 52 MET cc_start: -0.0110 (tpt) cc_final: -0.0322 (tpt) REVERT: 11 33 ASN cc_start: 0.9268 (m-40) cc_final: 0.8871 (m110) REVERT: 11 63 ASP cc_start: 0.6364 (OUTLIER) cc_final: 0.5790 (p0) REVERT: 12 80 HIS cc_start: 0.7778 (OUTLIER) cc_final: 0.7184 (t-90) REVERT: 12 114 LEU cc_start: 0.8968 (tp) cc_final: 0.8760 (tp) REVERT: 13 12 ASP cc_start: 0.7846 (p0) cc_final: 0.7528 (p0) REVERT: 16 72 ASP cc_start: 0.8719 (t70) cc_final: 0.8434 (t0) REVERT: 16 75 ILE cc_start: 0.9285 (mm) cc_final: 0.8914 (mm) REVERT: 17 58 ILE cc_start: 0.9249 (OUTLIER) cc_final: 0.8957 (mt) REVERT: 17 76 LYS cc_start: 0.9066 (tppt) cc_final: 0.8628 (tppt) REVERT: 18 9 GLN cc_start: 0.8715 (pp30) cc_final: 0.8183 (pp30) REVERT: 18 26 GLU cc_start: 0.8276 (tp30) cc_final: 0.7922 (tp30) REVERT: 18 43 GLU cc_start: 0.8466 (tp30) cc_final: 0.7913 (tp30) REVERT: 19 116 LEU cc_start: 0.9152 (tp) cc_final: 0.8895 (tt) REVERT: 21 65 ASP cc_start: 0.7952 (t0) cc_final: 0.7741 (t0) REVERT: 21 109 ASP cc_start: 0.8828 (p0) cc_final: 0.8461 (p0) REVERT: 22 1 MET cc_start: 0.6868 (ptt) cc_final: 0.6588 (ptp) REVERT: 22 4 GLU cc_start: 0.8476 (mp0) cc_final: 0.8000 (mp0) REVERT: 24 51 GLN cc_start: 0.8999 (pp30) cc_final: 0.8724 (pp30) REVERT: 28 18 LYS cc_start: 0.8761 (mmmt) cc_final: 0.8543 (mmmt) REVERT: 29 12 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8728 (mp) REVERT: 29 23 LYS cc_start: 0.8838 (mmmt) cc_final: 0.8599 (mmmt) REVERT: 29 53 THR cc_start: 0.7171 (OUTLIER) cc_final: 0.6381 (t) REVERT: 30 14 MET cc_start: 0.7904 (mtm) cc_final: 0.7683 (mtm) REVERT: 32 1 MET cc_start: 0.6965 (OUTLIER) cc_final: 0.6744 (ptm) REVERT: B 18 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8093 (mp10) REVERT: B 135 MET cc_start: 0.8876 (tmm) cc_final: 0.8570 (ppp) REVERT: B 160 LEU cc_start: 0.9203 (tp) cc_final: 0.8980 (tt) REVERT: E 60 GLN cc_start: 0.8245 (tp40) cc_final: 0.7991 (tp40) REVERT: E 70 MET cc_start: 0.7936 (mmm) cc_final: 0.7666 (tpp) REVERT: F 21 MET cc_start: 0.9219 (tpt) cc_final: 0.8996 (tpt) REVERT: F 70 VAL cc_start: 0.9353 (OUTLIER) cc_final: 0.8840 (m) REVERT: G 143 MET cc_start: 0.9182 (mmt) cc_final: 0.8946 (mmp) REVERT: H 53 ASP cc_start: 0.8040 (p0) cc_final: 0.7757 (p0) REVERT: H 89 ASP cc_start: 0.8224 (p0) cc_final: 0.7877 (p0) REVERT: I 45 MET cc_start: 0.9394 (ppp) cc_final: 0.9033 (ppp) REVERT: I 87 MET cc_start: 0.9107 (ptt) cc_final: 0.8887 (ppp) REVERT: J 24 GLU cc_start: 0.9114 (pp20) cc_final: 0.8875 (pp20) REVERT: L 74 GLN cc_start: 0.9162 (pm20) cc_final: 0.8893 (pm20) REVERT: Q 16 MET cc_start: 0.8754 (ptm) cc_final: 0.8420 (ptm) REVERT: S 16 LYS cc_start: 0.8900 (mtmm) cc_final: 0.8684 (mttp) REVERT: S 63 ASP cc_start: 0.8100 (t0) cc_final: 0.7801 (t0) REVERT: S 64 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7783 (mm-30) REVERT: U 8 ASN cc_start: 0.8385 (OUTLIER) cc_final: 0.7568 (p0) REVERT: U 45 LYS cc_start: 0.9050 (tppt) cc_final: 0.8824 (tppt) REVERT: Z 160 TYR cc_start: 0.8531 (m-10) cc_final: 0.8119 (m-10) outliers start: 348 outliers final: 242 residues processed: 1514 average time/residue: 1.3192 time to fit residues: 3505.4271 Evaluate side-chains 1500 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 1245 time to evaluate : 6.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 37 SER Chi-restraints excluded: chain 04 residue 44 ASN Chi-restraints excluded: chain 04 residue 99 GLU Chi-restraints excluded: chain 04 residue 117 SER Chi-restraints excluded: chain 04 residue 144 GLU Chi-restraints excluded: chain 04 residue 156 SER Chi-restraints excluded: chain 04 residue 159 THR Chi-restraints excluded: chain 04 residue 200 MET Chi-restraints excluded: chain 05 residue 22 ILE Chi-restraints excluded: chain 05 residue 97 SER Chi-restraints excluded: chain 05 residue 103 ASP Chi-restraints excluded: chain 05 residue 139 SER Chi-restraints excluded: chain 05 residue 177 VAL Chi-restraints excluded: chain 05 residue 200 ASP Chi-restraints excluded: chain 06 residue 7 ASP Chi-restraints excluded: chain 06 residue 187 VAL Chi-restraints excluded: chain 07 residue 30 VAL Chi-restraints excluded: chain 07 residue 73 VAL Chi-restraints excluded: chain 07 residue 95 MET Chi-restraints excluded: chain 07 residue 112 ASP Chi-restraints excluded: chain 07 residue 135 ILE Chi-restraints excluded: chain 08 residue 9 VAL Chi-restraints excluded: chain 08 residue 10 VAL 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 154 GLU Chi-restraints excluded: chain 09 residue 17 ASP Chi-restraints excluded: chain 09 residue 42 LYS Chi-restraints excluded: chain 09 residue 43 ASN Chi-restraints excluded: chain 09 residue 54 LEU Chi-restraints excluded: chain 09 residue 77 THR Chi-restraints excluded: chain 09 residue 91 PHE Chi-restraints excluded: chain 10 residue 24 SER Chi-restraints excluded: chain 10 residue 76 PHE Chi-restraints excluded: chain 10 residue 82 ILE Chi-restraints excluded: chain 10 residue 123 ILE Chi-restraints excluded: chain 11 residue 63 ASP Chi-restraints excluded: chain 11 residue 67 THR Chi-restraints excluded: chain 11 residue 70 THR Chi-restraints excluded: chain 11 residue 85 ILE Chi-restraints excluded: chain 11 residue 120 ASP Chi-restraints excluded: chain 11 residue 121 ILE Chi-restraints excluded: chain 12 residue 14 ASP Chi-restraints excluded: chain 12 residue 52 ASP Chi-restraints excluded: chain 12 residue 80 HIS Chi-restraints excluded: chain 12 residue 81 ILE Chi-restraints excluded: chain 12 residue 111 LYS Chi-restraints excluded: chain 13 residue 21 CYS Chi-restraints excluded: chain 13 residue 29 HIS Chi-restraints excluded: chain 13 residue 65 THR Chi-restraints excluded: chain 13 residue 84 CYS Chi-restraints excluded: chain 13 residue 97 THR Chi-restraints excluded: chain 13 residue 114 LYS Chi-restraints excluded: chain 14 residue 42 SER Chi-restraints excluded: chain 14 residue 67 THR Chi-restraints excluded: chain 14 residue 85 VAL Chi-restraints excluded: chain 14 residue 103 ILE Chi-restraints excluded: chain 14 residue 110 VAL Chi-restraints excluded: chain 14 residue 122 VAL Chi-restraints excluded: chain 15 residue 12 MET Chi-restraints excluded: chain 15 residue 42 THR Chi-restraints excluded: chain 15 residue 54 THR Chi-restraints excluded: chain 15 residue 74 THR Chi-restraints excluded: chain 15 residue 102 LEU Chi-restraints excluded: chain 15 residue 132 THR Chi-restraints excluded: chain 16 residue 20 MET Chi-restraints excluded: chain 16 residue 27 SER Chi-restraints excluded: chain 16 residue 36 THR Chi-restraints excluded: chain 16 residue 37 THR Chi-restraints excluded: chain 16 residue 57 THR Chi-restraints excluded: chain 16 residue 89 SER Chi-restraints excluded: chain 16 residue 106 ASP Chi-restraints excluded: chain 17 residue 2 ASP Chi-restraints excluded: chain 17 residue 18 LEU Chi-restraints excluded: chain 17 residue 28 VAL Chi-restraints excluded: chain 17 residue 54 VAL Chi-restraints excluded: chain 17 residue 58 ILE Chi-restraints excluded: chain 17 residue 69 ASP Chi-restraints excluded: chain 17 residue 87 ILE Chi-restraints excluded: chain 18 residue 45 VAL Chi-restraints excluded: chain 18 residue 51 ASN Chi-restraints excluded: chain 18 residue 72 VAL Chi-restraints excluded: chain 18 residue 81 ASP Chi-restraints excluded: chain 18 residue 96 LEU Chi-restraints excluded: chain 19 residue 7 VAL Chi-restraints excluded: chain 19 residue 16 ILE Chi-restraints excluded: chain 19 residue 82 LEU Chi-restraints excluded: chain 19 residue 86 SER Chi-restraints excluded: chain 20 residue 37 GLU Chi-restraints excluded: chain 20 residue 43 ASN Chi-restraints excluded: chain 20 residue 51 VAL Chi-restraints excluded: chain 20 residue 98 ILE Chi-restraints excluded: chain 21 residue 39 THR Chi-restraints excluded: chain 21 residue 81 SER Chi-restraints excluded: chain 21 residue 101 SER Chi-restraints excluded: chain 21 residue 104 THR Chi-restraints excluded: chain 22 residue 32 LEU Chi-restraints excluded: chain 22 residue 78 SER Chi-restraints excluded: chain 23 residue 7 ASP Chi-restraints excluded: chain 23 residue 14 THR Chi-restraints excluded: chain 23 residue 27 VAL Chi-restraints excluded: chain 23 residue 59 GLU Chi-restraints excluded: chain 24 residue 8 VAL Chi-restraints excluded: chain 26 residue 32 LEU Chi-restraints excluded: chain 26 residue 39 VAL Chi-restraints excluded: chain 26 residue 46 VAL Chi-restraints excluded: chain 26 residue 48 LEU Chi-restraints excluded: chain 26 residue 59 ASP Chi-restraints excluded: chain 26 residue 64 ASP Chi-restraints excluded: chain 27 residue 7 ARG Chi-restraints excluded: chain 27 residue 55 THR Chi-restraints excluded: chain 28 residue 2 LYS Chi-restraints excluded: chain 28 residue 9 THR Chi-restraints excluded: chain 28 residue 16 LEU Chi-restraints excluded: chain 28 residue 31 ILE Chi-restraints excluded: chain 28 residue 56 VAL Chi-restraints excluded: chain 29 residue 1 MET Chi-restraints excluded: chain 29 residue 12 ILE Chi-restraints excluded: chain 29 residue 33 ASN Chi-restraints excluded: chain 29 residue 39 LYS Chi-restraints excluded: chain 29 residue 44 PHE Chi-restraints excluded: chain 29 residue 53 THR Chi-restraints excluded: chain 30 residue 8 THR Chi-restraints excluded: chain 30 residue 10 SER Chi-restraints excluded: chain 30 residue 22 THR Chi-restraints excluded: chain 30 residue 24 VAL Chi-restraints excluded: chain 30 residue 26 SER Chi-restraints excluded: chain 30 residue 27 LEU Chi-restraints excluded: chain 32 residue 1 MET Chi-restraints excluded: chain 32 residue 4 THR Chi-restraints excluded: chain 32 residue 10 LEU Chi-restraints excluded: chain 32 residue 30 VAL Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 32 residue 44 VAL Chi-restraints excluded: chain 33 residue 53 ASP Chi-restraints excluded: chain 33 residue 54 LEU Chi-restraints excluded: chain 34 residue 37 GLN Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 108 GLN Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 19 PHE 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 191 SER Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain E residue 156 ARG Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain G residue 125 ASP Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 75 GLN Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 95 SER Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain K residue 17 ASP Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 57 SER Chi-restraints excluded: chain K residue 69 CYS Chi-restraints excluded: chain K residue 71 ASP Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain L residue 5 GLN Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 57 ASP Chi-restraints excluded: chain M residue 61 LYS Chi-restraints excluded: chain M residue 67 ASP Chi-restraints excluded: chain M residue 72 ILE Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 49 THR Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 34 GLN Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain R residue 20 ILE Chi-restraints excluded: chain R residue 41 SER Chi-restraints excluded: chain S residue 11 ASP Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain U residue 8 ASN Chi-restraints excluded: chain U residue 12 ASP Chi-restraints excluded: chain U residue 18 PHE Chi-restraints excluded: chain U residue 32 ARG Chi-restraints excluded: chain U residue 35 GLU Chi-restraints excluded: chain U residue 36 PHE Chi-restraints excluded: chain U residue 43 GLU Chi-restraints excluded: chain U residue 48 LYS Chi-restraints excluded: chain 03 residue 5 THR Chi-restraints excluded: chain 03 residue 35 THR Chi-restraints excluded: chain 03 residue 47 ASN Chi-restraints excluded: chain Z residue 20 VAL Chi-restraints excluded: chain Z residue 90 ASN Chi-restraints excluded: chain Z residue 134 LEU Chi-restraints excluded: chain Z residue 197 SER Chi-restraints excluded: chain Z residue 206 ILE Chi-restraints excluded: chain Z residue 227 VAL Chi-restraints excluded: chain Z residue 236 ILE Chi-restraints excluded: chain Z residue 237 LYS Chi-restraints excluded: chain Z residue 292 LEU Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 332 PHE Chi-restraints excluded: chain Z residue 356 ILE Chi-restraints excluded: chain Z residue 362 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1101 random chunks: chunk 886 optimal weight: 20.0000 chunk 604 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 792 optimal weight: 20.0000 chunk 439 optimal weight: 5.9990 chunk 908 optimal weight: 10.0000 chunk 735 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 543 optimal weight: 20.0000 chunk 955 optimal weight: 50.0000 chunk 268 optimal weight: 20.0000 overall best weight: 8.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 04 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 07 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 115 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 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 42 ASN ** 12 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 14 38 GLN 15 88 ASN ** 16 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 19 19 GLN ** 21 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 22 15 HIS ** 23 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 29 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 31 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 GLN ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 GLN ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 GLN I 49 GLN J 56 HIS J 99 GLN ** O 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 53 GLN T 47 GLN T 51 ASN ** Z 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 251 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 166818 Z= 0.338 Angle : 0.641 16.646 249072 Z= 0.331 Chirality : 0.037 0.303 31782 Planarity : 0.005 0.110 13716 Dihedral : 23.374 178.959 82304 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.93 % Favored : 89.85 % Rotamer: Outliers : 6.55 % Allowed : 20.89 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.10), residues: 6366 helix: -0.03 (0.12), residues: 1979 sheet: -1.88 (0.15), residues: 1125 loop : -2.01 (0.10), residues: 3262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP04 212 HIS 0.039 0.001 HIS13 29 PHE 0.041 0.002 PHE U 36 TYR 0.032 0.002 TYR C 41 ARG 0.014 0.001 ARG29 25 *********************** 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 1661 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 346 poor density : 1315 time to evaluate : 7.093 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: 04 224 MET cc_start: 0.8267 (mtm) cc_final: 0.8037 (mtm) REVERT: 07 135 ILE cc_start: 0.9437 (OUTLIER) cc_final: 0.8979 (tp) REVERT: 08 57 TYR cc_start: 0.8424 (m-80) cc_final: 0.8219 (m-10) REVERT: 09 91 PHE cc_start: 0.8176 (OUTLIER) cc_final: 0.7887 (m-80) REVERT: 09 133 GLN cc_start: 0.9296 (tt0) cc_final: 0.8943 (tp-100) REVERT: 09 135 HIS cc_start: 0.8240 (t70) cc_final: 0.7333 (t70) REVERT: 10 1 MET cc_start: 0.7345 (tmm) cc_final: 0.5242 (tpp) REVERT: 10 38 MET cc_start: 0.9038 (mmp) cc_final: 0.8727 (mtt) REVERT: 10 42 ARG cc_start: 0.8224 (tpp-160) cc_final: 0.7957 (tpp-160) REVERT: 10 52 MET cc_start: 0.0158 (tpt) cc_final: -0.0175 (tpt) REVERT: 11 33 ASN cc_start: 0.9254 (m-40) cc_final: 0.8876 (m110) REVERT: 11 63 ASP cc_start: 0.6372 (OUTLIER) cc_final: 0.5927 (p0) REVERT: 12 80 HIS cc_start: 0.7764 (OUTLIER) cc_final: 0.7235 (t-90) REVERT: 12 114 LEU cc_start: 0.8953 (tp) cc_final: 0.8739 (tt) REVERT: 12 118 MET cc_start: 0.9145 (ptp) cc_final: 0.8909 (ptp) REVERT: 13 12 ASP cc_start: 0.7837 (p0) cc_final: 0.7564 (p0) REVERT: 16 72 ASP cc_start: 0.8736 (t70) cc_final: 0.8436 (t0) REVERT: 16 74 GLU cc_start: 0.9101 (tm-30) cc_final: 0.8865 (tm-30) REVERT: 16 75 ILE cc_start: 0.9294 (mm) cc_final: 0.8931 (mm) REVERT: 18 26 GLU cc_start: 0.8251 (tp30) cc_final: 0.7470 (tp30) REVERT: 18 43 GLU cc_start: 0.8384 (tp30) cc_final: 0.8046 (tp30) REVERT: 19 116 LEU cc_start: 0.9161 (tp) cc_final: 0.8947 (tt) REVERT: 21 65 ASP cc_start: 0.7983 (t0) cc_final: 0.7772 (t0) REVERT: 21 86 MET cc_start: 0.9347 (tpt) cc_final: 0.9072 (ttt) REVERT: 22 1 MET cc_start: 0.6970 (ptt) cc_final: 0.6558 (ptp) REVERT: 22 4 GLU cc_start: 0.8526 (mp0) cc_final: 0.7983 (mp0) REVERT: 24 50 MET cc_start: 0.8954 (mtt) cc_final: 0.8631 (ttm) REVERT: 26 70 LEU cc_start: 0.9369 (mm) cc_final: 0.9057 (mm) REVERT: 29 12 ILE cc_start: 0.9240 (OUTLIER) cc_final: 0.8606 (mp) REVERT: 29 53 THR cc_start: 0.7184 (OUTLIER) cc_final: 0.6421 (t) REVERT: 30 51 ARG cc_start: 0.8422 (mtm110) cc_final: 0.8126 (ttp80) REVERT: B 48 MET cc_start: 0.9341 (tpp) cc_final: 0.9011 (mtp) REVERT: B 135 MET cc_start: 0.8959 (tmm) cc_final: 0.8633 (ppp) REVERT: B 160 LEU cc_start: 0.9204 (tp) cc_final: 0.8988 (tt) REVERT: B 163 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8572 (tp) REVERT: E 60 GLN cc_start: 0.8280 (tp40) cc_final: 0.8065 (tp40) REVERT: F 1 MET cc_start: 0.8045 (tpt) cc_final: 0.7318 (tpp) REVERT: F 21 MET cc_start: 0.9291 (tpt) cc_final: 0.9026 (tpp) REVERT: F 70 VAL cc_start: 0.9247 (OUTLIER) cc_final: 0.8973 (m) REVERT: H 53 ASP cc_start: 0.8063 (p0) cc_final: 0.7789 (p0) REVERT: H 89 ASP cc_start: 0.8203 (p0) cc_final: 0.7861 (p0) REVERT: I 45 MET cc_start: 0.9404 (ppp) cc_final: 0.9060 (ppp) REVERT: I 87 MET cc_start: 0.9082 (ptt) cc_final: 0.8871 (ppp) REVERT: J 24 GLU cc_start: 0.9164 (pp20) cc_final: 0.8919 (pp20) REVERT: J 65 TYR cc_start: 0.7921 (m-80) cc_final: 0.7435 (m-80) REVERT: K 86 LYS cc_start: 0.9002 (ttmm) cc_final: 0.8779 (ttmm) REVERT: L 74 GLN cc_start: 0.9187 (pm20) cc_final: 0.8878 (pm20) REVERT: Q 16 MET cc_start: 0.8755 (ptm) cc_final: 0.8389 (ptm) REVERT: S 16 LYS cc_start: 0.8910 (mtmm) cc_final: 0.8699 (mttp) REVERT: S 63 ASP cc_start: 0.8068 (t0) cc_final: 0.7758 (t0) REVERT: S 64 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7760 (mm-30) REVERT: U 4 LYS cc_start: 0.8800 (tptp) cc_final: 0.8586 (tptt) REVERT: U 8 ASN cc_start: 0.8349 (OUTLIER) cc_final: 0.7555 (p0) REVERT: U 45 LYS cc_start: 0.9043 (tppt) cc_final: 0.8831 (tppt) REVERT: U 55 HIS cc_start: 0.8652 (t-90) cc_final: 0.8446 (t-90) REVERT: 03 5 THR cc_start: 0.7737 (OUTLIER) cc_final: 0.7533 (t) REVERT: Z 160 TYR cc_start: 0.8569 (m-10) cc_final: 0.8360 (m-80) outliers start: 346 outliers final: 259 residues processed: 1484 average time/residue: 1.2872 time to fit residues: 3359.5386 Evaluate side-chains 1507 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 269 poor density : 1238 time to evaluate : 6.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 37 SER Chi-restraints excluded: chain 04 residue 117 SER Chi-restraints excluded: chain 04 residue 144 GLU Chi-restraints excluded: chain 04 residue 156 SER Chi-restraints excluded: chain 04 residue 159 THR Chi-restraints excluded: chain 04 residue 200 MET Chi-restraints excluded: chain 05 residue 22 ILE Chi-restraints excluded: chain 05 residue 97 SER Chi-restraints excluded: chain 05 residue 103 ASP Chi-restraints excluded: chain 05 residue 108 ASP Chi-restraints excluded: chain 05 residue 139 SER Chi-restraints excluded: chain 05 residue 176 ASP Chi-restraints excluded: chain 05 residue 177 VAL Chi-restraints excluded: chain 05 residue 200 ASP Chi-restraints excluded: chain 06 residue 7 ASP Chi-restraints excluded: chain 06 residue 187 VAL Chi-restraints excluded: chain 07 residue 30 VAL Chi-restraints excluded: chain 07 residue 73 VAL Chi-restraints excluded: chain 07 residue 95 MET Chi-restraints excluded: chain 07 residue 135 ILE Chi-restraints excluded: chain 07 residue 154 THR Chi-restraints excluded: chain 08 residue 9 VAL Chi-restraints excluded: chain 08 residue 10 VAL Chi-restraints excluded: chain 08 residue 55 ASP Chi-restraints excluded: chain 08 residue 126 THR Chi-restraints excluded: chain 08 residue 154 GLU Chi-restraints excluded: chain 09 residue 17 ASP Chi-restraints excluded: chain 09 residue 43 ASN Chi-restraints excluded: chain 09 residue 54 LEU Chi-restraints excluded: chain 09 residue 77 THR Chi-restraints excluded: chain 09 residue 91 PHE Chi-restraints excluded: chain 10 residue 24 SER Chi-restraints excluded: chain 10 residue 76 PHE Chi-restraints excluded: chain 10 residue 82 ILE Chi-restraints excluded: chain 10 residue 123 ILE Chi-restraints excluded: chain 11 residue 12 VAL Chi-restraints excluded: chain 11 residue 63 ASP Chi-restraints excluded: chain 11 residue 67 THR Chi-restraints excluded: chain 11 residue 85 ILE Chi-restraints excluded: chain 11 residue 120 ASP Chi-restraints excluded: chain 12 residue 14 ASP Chi-restraints excluded: chain 12 residue 32 LEU Chi-restraints excluded: chain 12 residue 52 ASP Chi-restraints excluded: chain 12 residue 67 ASN Chi-restraints excluded: chain 12 residue 80 HIS Chi-restraints excluded: chain 12 residue 81 ILE Chi-restraints excluded: chain 12 residue 109 LEU Chi-restraints excluded: chain 12 residue 111 LYS Chi-restraints excluded: chain 13 residue 21 CYS Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 65 THR Chi-restraints excluded: chain 13 residue 97 THR Chi-restraints excluded: chain 14 residue 42 SER Chi-restraints excluded: chain 14 residue 46 VAL Chi-restraints excluded: chain 14 residue 51 GLU Chi-restraints excluded: chain 14 residue 67 THR Chi-restraints excluded: chain 14 residue 80 SER Chi-restraints excluded: chain 14 residue 85 VAL Chi-restraints excluded: chain 14 residue 103 ILE Chi-restraints excluded: chain 14 residue 110 VAL Chi-restraints excluded: chain 14 residue 122 VAL Chi-restraints excluded: chain 15 residue 12 MET Chi-restraints excluded: chain 15 residue 42 THR Chi-restraints excluded: chain 15 residue 54 THR Chi-restraints excluded: chain 15 residue 74 THR Chi-restraints excluded: chain 15 residue 102 LEU Chi-restraints excluded: chain 15 residue 124 LEU Chi-restraints excluded: chain 15 residue 132 THR Chi-restraints excluded: chain 16 residue 20 MET Chi-restraints excluded: chain 16 residue 27 SER Chi-restraints excluded: chain 16 residue 36 THR Chi-restraints excluded: chain 16 residue 37 THR Chi-restraints excluded: chain 16 residue 57 THR Chi-restraints excluded: chain 16 residue 106 ASP Chi-restraints excluded: chain 16 residue 113 ILE Chi-restraints excluded: chain 17 residue 2 ASP Chi-restraints excluded: chain 17 residue 18 LEU Chi-restraints excluded: chain 17 residue 28 VAL Chi-restraints excluded: chain 17 residue 39 VAL Chi-restraints excluded: chain 17 residue 47 VAL Chi-restraints excluded: chain 17 residue 53 THR Chi-restraints excluded: chain 17 residue 54 VAL Chi-restraints excluded: chain 17 residue 69 ASP Chi-restraints excluded: chain 17 residue 87 ILE Chi-restraints excluded: chain 18 residue 45 VAL Chi-restraints excluded: chain 18 residue 51 ASN Chi-restraints excluded: chain 18 residue 72 VAL Chi-restraints excluded: chain 18 residue 81 ASP Chi-restraints excluded: chain 18 residue 96 LEU Chi-restraints excluded: chain 19 residue 7 VAL Chi-restraints excluded: chain 19 residue 16 ILE Chi-restraints excluded: chain 19 residue 82 LEU Chi-restraints excluded: chain 19 residue 86 SER Chi-restraints excluded: chain 19 residue 94 LEU Chi-restraints excluded: chain 19 residue 96 ASP Chi-restraints excluded: chain 20 residue 29 THR Chi-restraints excluded: chain 20 residue 37 GLU Chi-restraints excluded: chain 20 residue 43 ASN Chi-restraints excluded: chain 20 residue 51 VAL Chi-restraints excluded: chain 20 residue 98 ILE Chi-restraints excluded: chain 21 residue 22 ASP Chi-restraints excluded: chain 21 residue 39 THR Chi-restraints excluded: chain 21 residue 66 ILE Chi-restraints excluded: chain 21 residue 74 ILE Chi-restraints excluded: chain 21 residue 96 ILE Chi-restraints excluded: chain 21 residue 101 SER Chi-restraints excluded: chain 21 residue 104 THR Chi-restraints excluded: chain 22 residue 5 GLU Chi-restraints excluded: chain 22 residue 32 LEU Chi-restraints excluded: chain 22 residue 78 SER Chi-restraints excluded: chain 23 residue 7 ASP Chi-restraints excluded: chain 23 residue 27 VAL Chi-restraints excluded: chain 23 residue 59 GLU Chi-restraints excluded: chain 24 residue 8 VAL Chi-restraints excluded: chain 26 residue 24 THR Chi-restraints excluded: chain 26 residue 32 LEU Chi-restraints excluded: chain 26 residue 46 VAL Chi-restraints excluded: chain 26 residue 48 LEU Chi-restraints excluded: chain 26 residue 59 ASP Chi-restraints excluded: chain 27 residue 7 ARG Chi-restraints excluded: chain 27 residue 11 VAL Chi-restraints excluded: chain 27 residue 23 ARG Chi-restraints excluded: chain 27 residue 55 THR Chi-restraints excluded: chain 28 residue 2 LYS Chi-restraints excluded: chain 28 residue 9 THR Chi-restraints excluded: chain 28 residue 31 ILE Chi-restraints excluded: chain 28 residue 56 VAL Chi-restraints excluded: chain 29 residue 1 MET Chi-restraints excluded: chain 29 residue 12 ILE Chi-restraints excluded: chain 29 residue 25 ARG Chi-restraints excluded: chain 29 residue 33 ASN Chi-restraints excluded: chain 29 residue 39 LYS Chi-restraints excluded: chain 29 residue 44 PHE Chi-restraints excluded: chain 29 residue 53 THR Chi-restraints excluded: chain 29 residue 57 VAL Chi-restraints excluded: chain 30 residue 8 THR Chi-restraints excluded: chain 30 residue 10 SER Chi-restraints excluded: chain 30 residue 22 THR Chi-restraints excluded: chain 30 residue 24 VAL Chi-restraints excluded: chain 30 residue 26 SER Chi-restraints excluded: chain 30 residue 27 LEU Chi-restraints excluded: chain 30 residue 42 ILE Chi-restraints excluded: chain 32 residue 4 THR Chi-restraints excluded: chain 32 residue 10 LEU Chi-restraints excluded: chain 32 residue 30 VAL Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 32 residue 44 VAL Chi-restraints excluded: chain 33 residue 53 ASP Chi-restraints excluded: chain 33 residue 54 LEU Chi-restraints excluded: chain 34 residue 13 ASN Chi-restraints excluded: chain 34 residue 37 GLN Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain C residue 30 ASP 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 156 LEU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 19 PHE Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 124 VAL 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 191 SER Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 156 ARG Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain H residue 26 MET Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 88 GLU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 57 SER Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain K residue 69 CYS Chi-restraints excluded: chain K residue 71 ASP Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain L residue 5 GLN Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 61 LYS Chi-restraints excluded: chain M residue 67 ASP Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain O residue 34 GLN Chi-restraints excluded: chain O residue 59 VAL Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain R residue 41 SER Chi-restraints excluded: chain S residue 6 LYS Chi-restraints excluded: chain S residue 11 ASP Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain U residue 8 ASN Chi-restraints excluded: chain U residue 12 ASP Chi-restraints excluded: chain U residue 18 PHE Chi-restraints excluded: chain U residue 30 GLU Chi-restraints excluded: chain U residue 36 PHE Chi-restraints excluded: chain U residue 43 GLU Chi-restraints excluded: chain U residue 48 LYS Chi-restraints excluded: chain 03 residue 5 THR Chi-restraints excluded: chain 03 residue 23 ILE Chi-restraints excluded: chain 03 residue 35 THR Chi-restraints excluded: chain 03 residue 47 ASN Chi-restraints excluded: chain Z residue 20 VAL Chi-restraints excluded: chain Z residue 90 ASN Chi-restraints excluded: chain Z residue 130 ILE Chi-restraints excluded: chain Z residue 134 LEU Chi-restraints excluded: chain Z residue 197 SER Chi-restraints excluded: chain Z residue 227 VAL Chi-restraints excluded: chain Z residue 236 ILE Chi-restraints excluded: chain Z residue 237 LYS Chi-restraints excluded: chain Z residue 292 LEU Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 332 PHE Chi-restraints excluded: chain Z residue 362 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1101 random chunks: chunk 358 optimal weight: 7.9990 chunk 958 optimal weight: 20.0000 chunk 210 optimal weight: 4.9990 chunk 624 optimal weight: 10.0000 chunk 262 optimal weight: 20.0000 chunk 1065 optimal weight: 5.9990 chunk 884 optimal weight: 20.0000 chunk 493 optimal weight: 5.9990 chunk 88 optimal weight: 20.0000 chunk 352 optimal weight: 2.9990 chunk 559 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 04 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 04 152 GLN ** 05 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 07 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 09 135 HIS ** 11 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 18 ASN ** 12 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 13 13 ASN 13 29 HIS 14 38 GLN 16 3 HIS 21 15 GLN 21 40 ASN ** 27 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 29 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 30 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 31 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 GLN C 2 GLN ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 GLN ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 GLN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 49 GLN J 56 HIS J 99 GLN ** O 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 45 HIS R 53 GLN T 69 ASN ** Z 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 251 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 166818 Z= 0.241 Angle : 0.605 16.897 249072 Z= 0.311 Chirality : 0.035 0.339 31782 Planarity : 0.004 0.079 13716 Dihedral : 23.380 177.980 82301 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.21 % Favored : 90.57 % Rotamer: Outliers : 6.34 % Allowed : 22.19 % Favored : 71.47 % 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: -1.83 (0.10), residues: 6366 helix: 0.14 (0.12), residues: 1984 sheet: -1.72 (0.15), residues: 1130 loop : -1.91 (0.11), residues: 3252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP04 212 HIS 0.009 0.001 HIS16 31 PHE 0.043 0.001 PHE U 36 TYR 0.029 0.002 TYR Z 129 ARG 0.012 0.001 ARG29 25 *********************** 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 1683 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 335 poor density : 1348 time to evaluate : 6.673 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: 04 224 MET cc_start: 0.8239 (mtm) cc_final: 0.8003 (mtm) REVERT: 07 112 ASP cc_start: 0.7724 (OUTLIER) cc_final: 0.7275 (t70) REVERT: 07 135 ILE cc_start: 0.9440 (OUTLIER) cc_final: 0.8990 (tp) REVERT: 09 91 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7929 (m-80) REVERT: 09 133 GLN cc_start: 0.9298 (tt0) cc_final: 0.8950 (tp-100) REVERT: 09 135 HIS cc_start: 0.7922 (t-90) cc_final: 0.7258 (t70) REVERT: 10 1 MET cc_start: 0.7182 (tmm) cc_final: 0.6594 (tmm) REVERT: 10 38 MET cc_start: 0.9090 (mmp) cc_final: 0.8761 (mtt) REVERT: 10 42 ARG cc_start: 0.8140 (tpp-160) cc_final: 0.7899 (tpp-160) REVERT: 10 52 MET cc_start: 0.0337 (tpt) cc_final: -0.0068 (tpt) REVERT: 11 33 ASN cc_start: 0.9238 (m-40) cc_final: 0.8723 (m110) REVERT: 12 80 HIS cc_start: 0.7632 (OUTLIER) cc_final: 0.7214 (t-90) REVERT: 12 102 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8293 (mt-10) REVERT: 12 114 LEU cc_start: 0.8920 (tp) cc_final: 0.8405 (tt) REVERT: 12 118 MET cc_start: 0.9135 (ptp) cc_final: 0.8795 (ptp) REVERT: 13 12 ASP cc_start: 0.7989 (p0) cc_final: 0.7638 (p0) REVERT: 15 45 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8548 (mt0) REVERT: 16 72 ASP cc_start: 0.8644 (t70) cc_final: 0.8288 (t0) REVERT: 16 74 GLU cc_start: 0.9013 (tm-30) cc_final: 0.8755 (tm-30) REVERT: 16 75 ILE cc_start: 0.9306 (mm) cc_final: 0.8941 (mm) REVERT: 17 58 ILE cc_start: 0.9222 (OUTLIER) cc_final: 0.8967 (mt) REVERT: 17 76 LYS cc_start: 0.8895 (tppt) cc_final: 0.8679 (tppt) REVERT: 18 26 GLU cc_start: 0.8214 (tp30) cc_final: 0.7517 (tp30) REVERT: 18 43 GLU cc_start: 0.8330 (tp30) cc_final: 0.7680 (tp30) REVERT: 21 1 MET cc_start: 0.6897 (tpp) cc_final: 0.6485 (tpt) REVERT: 21 67 ASP cc_start: 0.9029 (OUTLIER) cc_final: 0.8771 (t70) REVERT: 21 86 MET cc_start: 0.9350 (tpt) cc_final: 0.9081 (ttt) REVERT: 22 1 MET cc_start: 0.6784 (ptt) cc_final: 0.6438 (ptp) REVERT: 22 4 GLU cc_start: 0.8600 (mp0) cc_final: 0.8059 (mp0) REVERT: 29 12 ILE cc_start: 0.9176 (OUTLIER) cc_final: 0.8759 (mp) REVERT: 29 53 THR cc_start: 0.7009 (OUTLIER) cc_final: 0.6353 (t) REVERT: B 48 MET cc_start: 0.9327 (tpp) cc_final: 0.9022 (mtp) REVERT: B 135 MET cc_start: 0.9005 (tmm) cc_final: 0.8650 (ppp) REVERT: B 163 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8492 (tp) REVERT: E 13 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7671 (ptmt) REVERT: E 60 GLN cc_start: 0.8318 (tp40) cc_final: 0.7937 (tp40) REVERT: E 70 MET cc_start: 0.7941 (mmm) cc_final: 0.7509 (tpp) REVERT: F 1 MET cc_start: 0.7947 (tpt) cc_final: 0.7241 (tpp) REVERT: F 21 MET cc_start: 0.9199 (tpt) cc_final: 0.8930 (tpt) REVERT: F 70 VAL cc_start: 0.9226 (OUTLIER) cc_final: 0.8982 (m) REVERT: H 53 ASP cc_start: 0.8041 (p0) cc_final: 0.7741 (p0) REVERT: H 89 ASP cc_start: 0.8131 (p0) cc_final: 0.7729 (p0) REVERT: I 45 MET cc_start: 0.9372 (ppp) cc_final: 0.9050 (ppp) REVERT: I 87 MET cc_start: 0.9059 (ptt) cc_final: 0.8768 (ppp) REVERT: I 88 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.6736 (pm20) REVERT: J 24 GLU cc_start: 0.9166 (pp20) cc_final: 0.8911 (pp20) REVERT: K 86 LYS cc_start: 0.8996 (ttmm) cc_final: 0.8741 (ttmm) REVERT: L 74 GLN cc_start: 0.9178 (pm20) cc_final: 0.8833 (pm20) REVERT: M 96 VAL cc_start: 0.9234 (m) cc_final: 0.8894 (t) REVERT: Q 3 LYS cc_start: 0.8518 (tppt) cc_final: 0.7743 (ttpt) REVERT: Q 16 MET cc_start: 0.8736 (ptm) cc_final: 0.8367 (ptm) REVERT: S 63 ASP cc_start: 0.8102 (t0) cc_final: 0.7888 (t0) REVERT: S 64 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7794 (mm-30) REVERT: U 4 LYS cc_start: 0.8732 (tptp) cc_final: 0.8508 (tptt) REVERT: U 8 ASN cc_start: 0.8288 (OUTLIER) cc_final: 0.7542 (p0) REVERT: 03 8 MET cc_start: 0.5793 (mmp) cc_final: 0.5512 (mmp) REVERT: 03 218 MET cc_start: 0.5962 (mtt) cc_final: 0.5602 (mmt) REVERT: Z 160 TYR cc_start: 0.8494 (OUTLIER) cc_final: 0.8215 (m-10) outliers start: 335 outliers final: 244 residues processed: 1513 average time/residue: 1.2749 time to fit residues: 3392.4714 Evaluate side-chains 1520 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 1260 time to evaluate : 6.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 37 SER Chi-restraints excluded: chain 04 residue 44 ASN Chi-restraints excluded: chain 04 residue 117 SER Chi-restraints excluded: chain 04 residue 144 GLU Chi-restraints excluded: chain 04 residue 156 SER Chi-restraints excluded: chain 04 residue 159 THR Chi-restraints excluded: chain 05 residue 22 ILE Chi-restraints excluded: chain 05 residue 97 SER Chi-restraints excluded: chain 05 residue 103 ASP Chi-restraints excluded: chain 05 residue 108 ASP Chi-restraints excluded: chain 05 residue 139 SER Chi-restraints excluded: chain 05 residue 176 ASP Chi-restraints excluded: chain 05 residue 177 VAL Chi-restraints excluded: chain 05 residue 200 ASP Chi-restraints excluded: chain 06 residue 7 ASP Chi-restraints excluded: chain 06 residue 187 VAL Chi-restraints excluded: chain 07 residue 16 MET Chi-restraints excluded: chain 07 residue 30 VAL Chi-restraints excluded: chain 07 residue 73 VAL Chi-restraints excluded: chain 07 residue 95 MET Chi-restraints excluded: chain 07 residue 112 ASP Chi-restraints excluded: chain 07 residue 135 ILE Chi-restraints excluded: chain 07 residue 154 THR Chi-restraints excluded: chain 08 residue 10 VAL Chi-restraints excluded: chain 08 residue 55 ASP Chi-restraints excluded: chain 08 residue 126 THR Chi-restraints excluded: chain 08 residue 154 GLU Chi-restraints excluded: chain 09 residue 17 ASP Chi-restraints excluded: chain 09 residue 54 LEU Chi-restraints excluded: chain 09 residue 77 THR Chi-restraints excluded: chain 09 residue 91 PHE Chi-restraints excluded: chain 10 residue 76 PHE Chi-restraints excluded: chain 10 residue 82 ILE Chi-restraints excluded: chain 10 residue 123 ILE Chi-restraints excluded: chain 11 residue 12 VAL Chi-restraints excluded: chain 11 residue 70 THR Chi-restraints excluded: chain 11 residue 85 ILE Chi-restraints excluded: chain 11 residue 120 ASP Chi-restraints excluded: chain 12 residue 14 ASP Chi-restraints excluded: chain 12 residue 32 LEU Chi-restraints excluded: chain 12 residue 67 ASN Chi-restraints excluded: chain 12 residue 80 HIS Chi-restraints excluded: chain 12 residue 81 ILE Chi-restraints excluded: chain 12 residue 102 GLU Chi-restraints excluded: chain 12 residue 109 LEU Chi-restraints excluded: chain 12 residue 111 LYS Chi-restraints excluded: chain 13 residue 29 HIS Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 65 THR Chi-restraints excluded: chain 13 residue 97 THR Chi-restraints excluded: chain 14 residue 42 SER Chi-restraints excluded: chain 14 residue 51 GLU Chi-restraints excluded: chain 14 residue 110 VAL Chi-restraints excluded: chain 14 residue 122 VAL Chi-restraints excluded: chain 15 residue 12 MET Chi-restraints excluded: chain 15 residue 42 THR Chi-restraints excluded: chain 15 residue 45 GLN Chi-restraints excluded: chain 15 residue 74 THR Chi-restraints excluded: chain 15 residue 124 LEU Chi-restraints excluded: chain 16 residue 9 GLN Chi-restraints excluded: chain 16 residue 20 MET Chi-restraints excluded: chain 16 residue 36 THR Chi-restraints excluded: chain 16 residue 37 THR Chi-restraints excluded: chain 16 residue 57 THR Chi-restraints excluded: chain 16 residue 106 ASP Chi-restraints excluded: chain 16 residue 113 ILE Chi-restraints excluded: chain 17 residue 2 ASP Chi-restraints excluded: chain 17 residue 18 LEU Chi-restraints excluded: chain 17 residue 35 ILE Chi-restraints excluded: chain 17 residue 39 VAL Chi-restraints excluded: chain 17 residue 47 VAL Chi-restraints excluded: chain 17 residue 53 THR Chi-restraints excluded: chain 17 residue 54 VAL Chi-restraints excluded: chain 17 residue 58 ILE Chi-restraints excluded: chain 17 residue 69 ASP Chi-restraints excluded: chain 17 residue 87 ILE Chi-restraints excluded: chain 17 residue 91 SER Chi-restraints excluded: chain 18 residue 35 SER Chi-restraints excluded: chain 18 residue 51 ASN Chi-restraints excluded: chain 18 residue 72 VAL Chi-restraints excluded: chain 18 residue 81 ASP Chi-restraints excluded: chain 18 residue 96 LEU Chi-restraints excluded: chain 19 residue 7 VAL Chi-restraints excluded: chain 19 residue 82 LEU Chi-restraints excluded: chain 19 residue 86 SER Chi-restraints excluded: chain 19 residue 94 LEU Chi-restraints excluded: chain 19 residue 96 ASP Chi-restraints excluded: chain 20 residue 29 THR Chi-restraints excluded: chain 20 residue 37 GLU Chi-restraints excluded: chain 20 residue 51 VAL Chi-restraints excluded: chain 20 residue 96 VAL Chi-restraints excluded: chain 20 residue 98 ILE Chi-restraints excluded: chain 21 residue 22 ASP Chi-restraints excluded: chain 21 residue 39 THR Chi-restraints excluded: chain 21 residue 67 ASP Chi-restraints excluded: chain 21 residue 74 ILE Chi-restraints excluded: chain 21 residue 81 SER Chi-restraints excluded: chain 21 residue 96 ILE Chi-restraints excluded: chain 21 residue 101 SER Chi-restraints excluded: chain 21 residue 104 THR Chi-restraints excluded: chain 22 residue 6 ARG Chi-restraints excluded: chain 22 residue 32 LEU Chi-restraints excluded: chain 23 residue 7 ASP Chi-restraints excluded: chain 23 residue 27 VAL Chi-restraints excluded: chain 23 residue 59 GLU Chi-restraints excluded: chain 23 residue 97 SER Chi-restraints excluded: chain 24 residue 8 VAL Chi-restraints excluded: chain 24 residue 48 MET Chi-restraints excluded: chain 24 residue 49 ASN Chi-restraints excluded: chain 24 residue 58 SER Chi-restraints excluded: chain 25 residue 63 VAL Chi-restraints excluded: chain 26 residue 24 THR Chi-restraints excluded: chain 26 residue 32 LEU Chi-restraints excluded: chain 26 residue 46 VAL Chi-restraints excluded: chain 26 residue 48 LEU Chi-restraints excluded: chain 26 residue 59 ASP Chi-restraints excluded: chain 26 residue 64 ASP Chi-restraints excluded: chain 27 residue 7 ARG Chi-restraints excluded: chain 27 residue 23 ARG Chi-restraints excluded: chain 27 residue 55 THR Chi-restraints excluded: chain 28 residue 2 LYS Chi-restraints excluded: chain 28 residue 9 THR Chi-restraints excluded: chain 28 residue 31 ILE Chi-restraints excluded: chain 28 residue 56 VAL Chi-restraints excluded: chain 29 residue 1 MET Chi-restraints excluded: chain 29 residue 12 ILE Chi-restraints excluded: chain 29 residue 33 ASN Chi-restraints excluded: chain 29 residue 39 LYS Chi-restraints excluded: chain 29 residue 44 PHE Chi-restraints excluded: chain 29 residue 53 THR Chi-restraints excluded: chain 29 residue 57 VAL Chi-restraints excluded: chain 30 residue 8 THR Chi-restraints excluded: chain 30 residue 10 SER Chi-restraints excluded: chain 30 residue 26 SER Chi-restraints excluded: chain 30 residue 27 LEU Chi-restraints excluded: chain 30 residue 42 ILE Chi-restraints excluded: chain 32 residue 10 LEU Chi-restraints excluded: chain 32 residue 30 VAL Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 32 residue 44 VAL Chi-restraints excluded: chain 33 residue 53 ASP Chi-restraints excluded: chain 33 residue 54 LEU Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain D residue 19 PHE Chi-restraints excluded: chain D residue 124 VAL 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 191 SER Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain E residue 13 LYS Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 156 ARG Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 88 GLU Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 59 LYS Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain K residue 17 ASP Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 57 SER Chi-restraints excluded: chain K residue 69 CYS Chi-restraints excluded: chain K residue 71 ASP Chi-restraints excluded: chain K residue 95 THR Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain L residue 5 GLN Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 61 LYS Chi-restraints excluded: chain M residue 67 ASP Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 81 ILE Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain R residue 41 SER Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain S residue 6 LYS Chi-restraints excluded: chain S residue 11 ASP Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 14 GLU Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain U residue 8 ASN Chi-restraints excluded: chain U residue 12 ASP Chi-restraints excluded: chain U residue 18 PHE Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 30 GLU Chi-restraints excluded: chain U residue 36 PHE Chi-restraints excluded: chain U residue 43 GLU Chi-restraints excluded: chain U residue 48 LYS Chi-restraints excluded: chain 03 residue 16 ASP Chi-restraints excluded: chain 03 residue 23 ILE Chi-restraints excluded: chain 03 residue 35 THR Chi-restraints excluded: chain 03 residue 47 ASN Chi-restraints excluded: chain Z residue 20 VAL Chi-restraints excluded: chain Z residue 90 ASN Chi-restraints excluded: chain Z residue 134 LEU Chi-restraints excluded: chain Z residue 160 TYR Chi-restraints excluded: chain Z residue 197 SER Chi-restraints excluded: chain Z residue 227 VAL Chi-restraints excluded: chain Z residue 236 ILE Chi-restraints excluded: chain Z residue 237 LYS Chi-restraints excluded: chain Z residue 292 LEU Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 332 PHE Chi-restraints excluded: chain Z residue 362 LEU Chi-restraints excluded: chain Z residue 387 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: 8.9990 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: 20.0000 chunk 664 optimal weight: 10.0000 chunk 646 optimal weight: 20.0000 chunk 489 optimal weight: 0.0470 overall best weight: 11.8092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 04 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 07 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 5 GLN ** 11 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 13 29 HIS 14 38 GLN 16 23 ASN 19 19 GLN ** 19 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 21 40 ASN 23 65 GLN 25 8 ASN ** 27 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 29 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 GLN ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 129 ASN ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 56 HIS O 34 GLN ** O 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 53 GLN ** T 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 69 ASN ** Z 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 251 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.110 166818 Z= 0.453 Angle : 0.698 15.905 249072 Z= 0.358 Chirality : 0.039 0.363 31782 Planarity : 0.005 0.069 13716 Dihedral : 23.440 179.078 82301 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 19.72 Ramachandran Plot: Outliers : 0.22 % Allowed : 10.56 % Favored : 89.22 % Rotamer: Outliers : 6.41 % Allowed : 22.78 % Favored : 70.81 % 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: -1.96 (0.10), residues: 6366 helix: -0.01 (0.11), residues: 1989 sheet: -1.77 (0.15), residues: 1166 loop : -1.95 (0.11), residues: 3211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP04 212 HIS 0.025 0.001 HIS20 82 PHE 0.041 0.002 PHE U 36 TYR 0.034 0.002 TYR Z 129 ARG 0.022 0.001 ARG13 30 *********************** 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 1581 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 339 poor density : 1242 time to evaluate : 6.917 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: 04 224 MET cc_start: 0.8332 (mtm) cc_final: 0.8077 (mtm) REVERT: 09 91 PHE cc_start: 0.8171 (OUTLIER) cc_final: 0.7898 (m-80) REVERT: 09 97 ARG cc_start: 0.8377 (mtm180) cc_final: 0.7921 (mtt-85) REVERT: 09 135 HIS cc_start: 0.8185 (t-90) cc_final: 0.7728 (t70) REVERT: 10 1 MET cc_start: 0.7120 (tmm) cc_final: 0.5376 (tpp) REVERT: 10 38 MET cc_start: 0.9158 (mmp) cc_final: 0.8781 (tmm) REVERT: 10 52 MET cc_start: 0.0891 (tpt) cc_final: 0.0425 (tpt) REVERT: 11 33 ASN cc_start: 0.9229 (m-40) cc_final: 0.8994 (m110) REVERT: 11 63 ASP cc_start: 0.6347 (OUTLIER) cc_final: 0.5678 (p0) REVERT: 11 64 ARG cc_start: 0.7730 (tpt90) cc_final: 0.6927 (mmm160) REVERT: 12 80 HIS cc_start: 0.7860 (OUTLIER) cc_final: 0.7232 (t-90) REVERT: 12 98 GLU cc_start: 0.9216 (pm20) cc_final: 0.8827 (pm20) REVERT: 12 102 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8332 (mt-10) REVERT: 13 12 ASP cc_start: 0.8012 (p0) cc_final: 0.7677 (p0) REVERT: 16 72 ASP cc_start: 0.8761 (t70) cc_final: 0.8427 (t0) REVERT: 16 74 GLU cc_start: 0.9135 (tm-30) cc_final: 0.8881 (tm-30) REVERT: 16 75 ILE cc_start: 0.9372 (mm) cc_final: 0.8986 (mm) REVERT: 17 58 ILE cc_start: 0.9238 (OUTLIER) cc_final: 0.9031 (mt) REVERT: 18 43 GLU cc_start: 0.8374 (tp30) cc_final: 0.8093 (tp30) REVERT: 21 67 ASP cc_start: 0.9093 (m-30) cc_final: 0.8833 (t0) REVERT: 21 86 MET cc_start: 0.9370 (tpt) cc_final: 0.9078 (ttt) REVERT: 22 1 MET cc_start: 0.6860 (ptt) cc_final: 0.6451 (ptp) REVERT: 22 4 GLU cc_start: 0.8637 (mp0) cc_final: 0.8074 (mp0) REVERT: 24 50 MET cc_start: 0.8983 (mtt) cc_final: 0.8688 (ttm) REVERT: 26 70 LEU cc_start: 0.9271 (mm) cc_final: 0.9035 (mm) REVERT: 26 75 GLU cc_start: 0.8540 (pm20) cc_final: 0.8200 (pm20) REVERT: 29 12 ILE cc_start: 0.9122 (OUTLIER) cc_final: 0.8713 (mp) REVERT: 29 50 ASP cc_start: 0.8305 (t0) cc_final: 0.7987 (t0) REVERT: 29 53 THR cc_start: 0.7073 (OUTLIER) cc_final: 0.6349 (t) REVERT: B 48 MET cc_start: 0.9354 (tpp) cc_final: 0.8910 (mtp) REVERT: B 135 MET cc_start: 0.9039 (tmm) cc_final: 0.8662 (ppp) REVERT: B 163 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8526 (tp) REVERT: F 21 MET cc_start: 0.9176 (tpt) cc_final: 0.8920 (tpt) REVERT: H 53 ASP cc_start: 0.8059 (p0) cc_final: 0.7761 (p0) REVERT: H 89 ASP cc_start: 0.8224 (p0) cc_final: 0.7913 (p0) REVERT: I 38 PHE cc_start: 0.9014 (OUTLIER) cc_final: 0.8644 (p90) REVERT: I 87 MET cc_start: 0.9092 (ptt) cc_final: 0.8813 (ppp) REVERT: I 88 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.6921 (pm20) REVERT: J 24 GLU cc_start: 0.9219 (pp20) cc_final: 0.8950 (pp20) REVERT: L 74 GLN cc_start: 0.9241 (pm20) cc_final: 0.8907 (pm20) REVERT: Q 16 MET cc_start: 0.8784 (ptm) cc_final: 0.8407 (ptm) REVERT: S 63 ASP cc_start: 0.8136 (t0) cc_final: 0.7809 (t0) REVERT: S 64 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7808 (mm-30) REVERT: U 8 ASN cc_start: 0.8350 (OUTLIER) cc_final: 0.7592 (p0) REVERT: U 45 LYS cc_start: 0.9152 (tppt) cc_final: 0.8936 (tppt) REVERT: U 55 HIS cc_start: 0.8627 (t-90) cc_final: 0.8415 (t-90) REVERT: 03 8 MET cc_start: 0.5841 (mmp) cc_final: 0.5606 (mmp) REVERT: 03 218 MET cc_start: 0.6028 (mtt) cc_final: 0.5413 (mmt) REVERT: Z 160 TYR cc_start: 0.8629 (OUTLIER) cc_final: 0.8373 (m-10) outliers start: 339 outliers final: 272 residues processed: 1410 average time/residue: 1.2947 time to fit residues: 3215.6196 Evaluate side-chains 1487 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 284 poor density : 1203 time to evaluate : 6.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 37 SER Chi-restraints excluded: chain 04 residue 44 ASN Chi-restraints excluded: chain 04 residue 117 SER Chi-restraints excluded: chain 04 residue 144 GLU Chi-restraints excluded: chain 04 residue 156 SER Chi-restraints excluded: chain 04 residue 159 THR Chi-restraints excluded: chain 04 residue 200 MET Chi-restraints excluded: chain 05 residue 1 MET Chi-restraints excluded: chain 05 residue 22 ILE Chi-restraints excluded: chain 05 residue 97 SER Chi-restraints excluded: chain 05 residue 103 ASP Chi-restraints excluded: chain 05 residue 108 ASP Chi-restraints excluded: chain 05 residue 139 SER Chi-restraints excluded: chain 05 residue 176 ASP Chi-restraints excluded: chain 05 residue 177 VAL Chi-restraints excluded: chain 05 residue 200 ASP Chi-restraints excluded: chain 06 residue 7 ASP Chi-restraints excluded: chain 06 residue 146 VAL Chi-restraints excluded: chain 06 residue 187 VAL Chi-restraints excluded: chain 07 residue 16 MET Chi-restraints excluded: chain 07 residue 30 VAL Chi-restraints excluded: chain 07 residue 73 VAL Chi-restraints excluded: chain 07 residue 95 MET Chi-restraints excluded: chain 07 residue 135 ILE Chi-restraints excluded: chain 07 residue 154 THR Chi-restraints excluded: chain 08 residue 9 VAL Chi-restraints excluded: chain 08 residue 10 VAL Chi-restraints excluded: chain 08 residue 55 ASP Chi-restraints excluded: chain 08 residue 126 THR Chi-restraints excluded: chain 08 residue 154 GLU Chi-restraints excluded: chain 09 residue 14 SER Chi-restraints excluded: chain 09 residue 17 ASP Chi-restraints excluded: chain 09 residue 54 LEU Chi-restraints excluded: chain 09 residue 91 PHE Chi-restraints excluded: chain 10 residue 76 PHE Chi-restraints excluded: chain 10 residue 82 ILE Chi-restraints excluded: chain 10 residue 123 ILE Chi-restraints excluded: chain 11 residue 12 VAL Chi-restraints excluded: chain 11 residue 63 ASP Chi-restraints excluded: chain 11 residue 85 ILE Chi-restraints excluded: chain 11 residue 120 ASP Chi-restraints excluded: chain 12 residue 14 ASP Chi-restraints excluded: chain 12 residue 32 LEU Chi-restraints excluded: chain 12 residue 52 ASP Chi-restraints excluded: chain 12 residue 67 ASN Chi-restraints excluded: chain 12 residue 80 HIS Chi-restraints excluded: chain 12 residue 81 ILE Chi-restraints excluded: chain 12 residue 102 GLU Chi-restraints excluded: chain 12 residue 109 LEU Chi-restraints excluded: chain 12 residue 111 LYS Chi-restraints excluded: chain 13 residue 21 CYS Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 61 VAL Chi-restraints excluded: chain 13 residue 65 THR Chi-restraints excluded: chain 13 residue 97 THR Chi-restraints excluded: chain 14 residue 42 SER Chi-restraints excluded: chain 14 residue 51 GLU Chi-restraints excluded: chain 14 residue 67 THR Chi-restraints excluded: chain 14 residue 85 VAL Chi-restraints excluded: chain 14 residue 103 ILE Chi-restraints excluded: chain 14 residue 110 VAL Chi-restraints excluded: chain 14 residue 122 VAL Chi-restraints excluded: chain 15 residue 12 MET Chi-restraints excluded: chain 15 residue 28 PHE Chi-restraints excluded: chain 15 residue 30 SER Chi-restraints excluded: chain 15 residue 42 THR Chi-restraints excluded: chain 15 residue 54 THR Chi-restraints excluded: chain 15 residue 74 THR Chi-restraints excluded: chain 15 residue 124 LEU Chi-restraints excluded: chain 15 residue 132 THR Chi-restraints excluded: chain 16 residue 9 GLN Chi-restraints excluded: chain 16 residue 20 MET Chi-restraints excluded: chain 16 residue 27 SER Chi-restraints excluded: chain 16 residue 36 THR Chi-restraints excluded: chain 16 residue 37 THR Chi-restraints excluded: chain 16 residue 57 THR Chi-restraints excluded: chain 16 residue 106 ASP Chi-restraints excluded: chain 16 residue 113 ILE Chi-restraints excluded: chain 17 residue 2 ASP Chi-restraints excluded: chain 17 residue 18 LEU Chi-restraints excluded: chain 17 residue 35 ILE Chi-restraints excluded: chain 17 residue 47 VAL Chi-restraints excluded: chain 17 residue 58 ILE Chi-restraints excluded: chain 17 residue 69 ASP Chi-restraints excluded: chain 17 residue 87 ILE Chi-restraints excluded: chain 17 residue 91 SER Chi-restraints excluded: chain 18 residue 35 SER Chi-restraints excluded: chain 18 residue 51 ASN Chi-restraints excluded: chain 18 residue 72 VAL Chi-restraints excluded: chain 18 residue 81 ASP Chi-restraints excluded: chain 18 residue 96 LEU Chi-restraints excluded: chain 19 residue 16 ILE Chi-restraints excluded: chain 19 residue 82 LEU Chi-restraints excluded: chain 19 residue 86 SER Chi-restraints excluded: chain 19 residue 94 LEU Chi-restraints excluded: chain 20 residue 29 THR Chi-restraints excluded: chain 20 residue 37 GLU Chi-restraints excluded: chain 20 residue 43 ASN Chi-restraints excluded: chain 20 residue 51 VAL Chi-restraints excluded: chain 20 residue 96 VAL Chi-restraints excluded: chain 20 residue 98 ILE Chi-restraints excluded: chain 21 residue 22 ASP Chi-restraints excluded: chain 21 residue 39 THR Chi-restraints excluded: chain 21 residue 74 ILE Chi-restraints excluded: chain 21 residue 96 ILE Chi-restraints excluded: chain 21 residue 101 SER Chi-restraints excluded: chain 21 residue 104 THR Chi-restraints excluded: chain 22 residue 5 GLU Chi-restraints excluded: chain 22 residue 32 LEU Chi-restraints excluded: chain 22 residue 78 SER Chi-restraints excluded: chain 23 residue 7 ASP Chi-restraints excluded: chain 23 residue 27 VAL Chi-restraints excluded: chain 23 residue 59 GLU Chi-restraints excluded: chain 23 residue 97 SER Chi-restraints excluded: chain 24 residue 8 VAL Chi-restraints excluded: chain 24 residue 48 MET Chi-restraints excluded: chain 24 residue 49 ASN Chi-restraints excluded: chain 24 residue 86 LEU Chi-restraints excluded: chain 25 residue 63 VAL Chi-restraints excluded: chain 26 residue 24 THR Chi-restraints excluded: chain 26 residue 32 LEU Chi-restraints excluded: chain 26 residue 46 VAL Chi-restraints excluded: chain 26 residue 48 LEU Chi-restraints excluded: chain 26 residue 59 ASP Chi-restraints excluded: chain 27 residue 7 ARG Chi-restraints excluded: chain 28 residue 2 LYS Chi-restraints excluded: chain 28 residue 9 THR Chi-restraints excluded: chain 28 residue 31 ILE Chi-restraints excluded: chain 28 residue 56 VAL Chi-restraints excluded: chain 29 residue 12 ILE Chi-restraints excluded: chain 29 residue 25 ARG Chi-restraints excluded: chain 29 residue 33 ASN Chi-restraints excluded: chain 29 residue 34 LEU Chi-restraints excluded: chain 29 residue 39 LYS Chi-restraints excluded: chain 29 residue 44 PHE Chi-restraints excluded: chain 29 residue 53 THR Chi-restraints excluded: chain 30 residue 8 THR Chi-restraints excluded: chain 30 residue 10 SER Chi-restraints excluded: chain 30 residue 24 VAL Chi-restraints excluded: chain 30 residue 26 SER Chi-restraints excluded: chain 30 residue 27 LEU Chi-restraints excluded: chain 30 residue 42 ILE Chi-restraints excluded: chain 31 residue 16 THR Chi-restraints excluded: chain 32 residue 4 THR Chi-restraints excluded: chain 32 residue 10 LEU Chi-restraints excluded: chain 32 residue 30 VAL Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 32 residue 44 VAL Chi-restraints excluded: chain 33 residue 53 ASP Chi-restraints excluded: chain 33 residue 54 LEU Chi-restraints excluded: chain 34 residue 37 GLN Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 19 PHE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 124 VAL 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 191 SER Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 156 ARG Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain I residue 24 ASN Chi-restraints excluded: chain I residue 38 PHE Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 88 GLU Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain K residue 17 ASP Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 67 GLU Chi-restraints excluded: chain K residue 69 CYS Chi-restraints excluded: chain K residue 71 ASP Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain L residue 5 GLN Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 81 ILE Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 57 ASP Chi-restraints excluded: chain M residue 61 LYS Chi-restraints excluded: chain M residue 67 ASP Chi-restraints excluded: chain M residue 72 ILE Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 59 VAL Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain R residue 41 SER Chi-restraints excluded: chain S residue 6 LYS Chi-restraints excluded: chain S residue 11 ASP Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 14 GLU Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 38 ILE Chi-restraints excluded: chain U residue 8 ASN Chi-restraints excluded: chain U residue 12 ASP Chi-restraints excluded: chain U residue 18 PHE Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 30 GLU Chi-restraints excluded: chain U residue 36 PHE Chi-restraints excluded: chain U residue 43 GLU Chi-restraints excluded: chain 03 residue 16 ASP Chi-restraints excluded: chain 03 residue 23 ILE Chi-restraints excluded: chain 03 residue 30 LEU Chi-restraints excluded: chain 03 residue 35 THR Chi-restraints excluded: chain 03 residue 47 ASN Chi-restraints excluded: chain Z residue 90 ASN Chi-restraints excluded: chain Z residue 130 ILE Chi-restraints excluded: chain Z residue 134 LEU Chi-restraints excluded: chain Z residue 160 TYR Chi-restraints excluded: chain Z residue 197 SER Chi-restraints excluded: chain Z residue 227 VAL Chi-restraints excluded: chain Z residue 236 ILE Chi-restraints excluded: chain Z residue 237 LYS Chi-restraints excluded: chain Z residue 292 LEU Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 332 PHE Chi-restraints excluded: chain Z residue 362 LEU 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: 9.9990 chunk 633 optimal weight: 20.0000 chunk 319 optimal weight: 3.9990 chunk 208 optimal weight: 20.0000 chunk 205 optimal weight: 0.0870 chunk 674 optimal weight: 10.0000 chunk 722 optimal weight: 10.0000 chunk 524 optimal weight: 5.9990 chunk 98 optimal weight: 9.9990 chunk 834 optimal weight: 10.0000 overall best weight: 6.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 04 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 07 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 10 103 ASN ** 11 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 18 ASN ** 12 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 13 13 ASN ** 15 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 16 107 ASN ** 19 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 21 9 HIS 21 40 ASN ** 27 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 29 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 GLN ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 GLN ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 20 GLN J 56 HIS J 99 GLN R 53 GLN ** T 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 69 ASN ** Z 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 84 HIS ** Z 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 251 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 166818 Z= 0.260 Angle : 0.628 16.626 249072 Z= 0.322 Chirality : 0.035 0.344 31782 Planarity : 0.005 0.074 13716 Dihedral : 23.469 178.836 82300 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.22 % Allowed : 9.52 % Favored : 90.26 % Rotamer: Outliers : 5.64 % Allowed : 24.20 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.10), residues: 6366 helix: 0.14 (0.12), residues: 1987 sheet: -1.68 (0.15), residues: 1155 loop : -1.84 (0.11), residues: 3224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP04 212 HIS 0.009 0.001 HIS L 76 PHE 0.039 0.002 PHE U 36 TYR 0.031 0.002 TYR O 77 ARG 0.010 0.001 ARG R 72 *********************** 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 1592 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 298 poor density : 1294 time to evaluate : 6.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 04 224 MET cc_start: 0.8285 (mtm) cc_final: 0.8024 (mtm) REVERT: 09 91 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.7899 (m-80) REVERT: 09 97 ARG cc_start: 0.8389 (mtm180) cc_final: 0.8116 (mtt-85) REVERT: 09 135 HIS cc_start: 0.8342 (t-90) cc_final: 0.7885 (t70) REVERT: 10 1 MET cc_start: 0.7110 (tmm) cc_final: 0.5485 (tpp) REVERT: 10 38 MET cc_start: 0.9137 (mmp) cc_final: 0.8815 (tmm) REVERT: 10 52 MET cc_start: 0.0763 (tpt) cc_final: 0.0356 (tpt) REVERT: 11 33 ASN cc_start: 0.9237 (m-40) cc_final: 0.8910 (m110) REVERT: 11 35 MET cc_start: 0.9300 (mmp) cc_final: 0.9034 (tmm) REVERT: 11 63 ASP cc_start: 0.6504 (OUTLIER) cc_final: 0.5915 (p0) REVERT: 11 64 ARG cc_start: 0.7654 (tpt90) cc_final: 0.6867 (mmp80) REVERT: 12 80 HIS cc_start: 0.7687 (OUTLIER) cc_final: 0.7239 (t-90) REVERT: 12 98 GLU cc_start: 0.9179 (pm20) cc_final: 0.8800 (pm20) REVERT: 13 12 ASP cc_start: 0.8005 (p0) cc_final: 0.7640 (p0) REVERT: 13 87 LEU cc_start: 0.8829 (mt) cc_final: 0.8582 (mt) REVERT: 15 73 ILE cc_start: 0.8759 (mm) cc_final: 0.8493 (mt) REVERT: 15 136 MET cc_start: 0.8387 (ppp) cc_final: 0.8051 (ppp) REVERT: 16 72 ASP cc_start: 0.8703 (t70) cc_final: 0.8372 (t0) REVERT: 16 74 GLU cc_start: 0.9107 (tm-30) cc_final: 0.8853 (tm-30) REVERT: 16 75 ILE cc_start: 0.9345 (mm) cc_final: 0.8989 (mm) REVERT: 17 58 ILE cc_start: 0.9227 (OUTLIER) cc_final: 0.9010 (mt) REVERT: 21 67 ASP cc_start: 0.9031 (m-30) cc_final: 0.8769 (t0) REVERT: 21 86 MET cc_start: 0.9357 (tpt) cc_final: 0.9079 (ttt) REVERT: 22 1 MET cc_start: 0.6752 (ptt) cc_final: 0.6404 (ptp) REVERT: 22 4 GLU cc_start: 0.8692 (mp0) cc_final: 0.8092 (mp0) REVERT: 24 50 MET cc_start: 0.8947 (mtt) cc_final: 0.8641 (ttm) REVERT: 29 10 GLU cc_start: 0.8225 (pm20) cc_final: 0.7870 (pp20) REVERT: 29 53 THR cc_start: 0.7085 (OUTLIER) cc_final: 0.6487 (t) REVERT: 31 4 ILE cc_start: 0.8679 (mm) cc_final: 0.8457 (mt) REVERT: B 48 MET cc_start: 0.9325 (tpp) cc_final: 0.8810 (mtt) REVERT: B 135 MET cc_start: 0.9053 (tmm) cc_final: 0.8661 (ppp) REVERT: B 163 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8460 (tp) REVERT: E 151 MET cc_start: 0.9237 (ptp) cc_final: 0.9020 (ptp) REVERT: F 21 MET cc_start: 0.9126 (tpt) cc_final: 0.8878 (tpt) REVERT: F 56 LYS cc_start: 0.8938 (ptmm) cc_final: 0.8606 (ptmm) REVERT: G 115 MET cc_start: 0.9055 (tpt) cc_final: 0.8697 (ttm) REVERT: H 53 ASP cc_start: 0.8042 (p0) cc_final: 0.7731 (p0) REVERT: I 87 MET cc_start: 0.9083 (ptt) cc_final: 0.8801 (ppp) REVERT: I 88 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.6681 (pm20) REVERT: J 24 GLU cc_start: 0.9200 (pp20) cc_final: 0.8978 (pp20) REVERT: K 86 LYS cc_start: 0.8980 (ttmm) cc_final: 0.8562 (ttmm) REVERT: L 74 GLN cc_start: 0.9221 (pm20) cc_final: 0.8940 (pm20) REVERT: M 61 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8568 (pttm) REVERT: O 88 ARG cc_start: 0.6652 (OUTLIER) cc_final: 0.6361 (mmp80) REVERT: Q 3 LYS cc_start: 0.8599 (tppt) cc_final: 0.7673 (ttpt) REVERT: Q 16 MET cc_start: 0.8742 (ptm) cc_final: 0.8349 (ptm) REVERT: Q 39 ARG cc_start: 0.8705 (mmp-170) cc_final: 0.8458 (mmp-170) REVERT: U 8 ASN cc_start: 0.8299 (OUTLIER) cc_final: 0.7555 (p0) REVERT: 03 218 MET cc_start: 0.6025 (mtt) cc_final: 0.5394 (mmt) REVERT: Z 51 ASN cc_start: 0.8696 (p0) cc_final: 0.8386 (p0) REVERT: Z 160 TYR cc_start: 0.8545 (OUTLIER) cc_final: 0.8301 (m-10) outliers start: 298 outliers final: 251 residues processed: 1438 average time/residue: 1.3937 time to fit residues: 3557.6351 Evaluate side-chains 1499 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 1237 time to evaluate : 6.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 44 ASN Chi-restraints excluded: chain 04 residue 117 SER Chi-restraints excluded: chain 04 residue 156 SER Chi-restraints excluded: chain 04 residue 159 THR Chi-restraints excluded: chain 04 residue 200 MET Chi-restraints excluded: chain 05 residue 1 MET Chi-restraints excluded: chain 05 residue 22 ILE Chi-restraints excluded: chain 05 residue 97 SER Chi-restraints excluded: chain 05 residue 103 ASP Chi-restraints excluded: chain 05 residue 108 ASP Chi-restraints excluded: chain 05 residue 139 SER Chi-restraints excluded: chain 05 residue 176 ASP Chi-restraints excluded: chain 05 residue 177 VAL Chi-restraints excluded: chain 05 residue 200 ASP Chi-restraints excluded: chain 06 residue 7 ASP Chi-restraints excluded: chain 06 residue 187 VAL Chi-restraints excluded: chain 07 residue 16 MET Chi-restraints excluded: chain 07 residue 30 VAL Chi-restraints excluded: chain 07 residue 73 VAL Chi-restraints excluded: chain 07 residue 95 MET Chi-restraints excluded: chain 07 residue 135 ILE Chi-restraints excluded: chain 07 residue 154 THR Chi-restraints excluded: chain 08 residue 9 VAL Chi-restraints excluded: chain 08 residue 10 VAL Chi-restraints excluded: chain 08 residue 55 ASP Chi-restraints excluded: chain 08 residue 126 THR Chi-restraints excluded: chain 08 residue 154 GLU Chi-restraints excluded: chain 09 residue 14 SER Chi-restraints excluded: chain 09 residue 17 ASP Chi-restraints excluded: chain 09 residue 54 LEU Chi-restraints excluded: chain 09 residue 91 PHE Chi-restraints excluded: chain 10 residue 76 PHE Chi-restraints excluded: chain 10 residue 82 ILE Chi-restraints excluded: chain 10 residue 123 ILE Chi-restraints excluded: chain 11 residue 12 VAL Chi-restraints excluded: chain 11 residue 46 ASP Chi-restraints excluded: chain 11 residue 63 ASP Chi-restraints excluded: chain 11 residue 85 ILE Chi-restraints excluded: chain 11 residue 120 ASP Chi-restraints excluded: chain 11 residue 135 MET Chi-restraints excluded: chain 12 residue 14 ASP Chi-restraints excluded: chain 12 residue 32 LEU Chi-restraints excluded: chain 12 residue 52 ASP Chi-restraints excluded: chain 12 residue 67 ASN Chi-restraints excluded: chain 12 residue 80 HIS Chi-restraints excluded: chain 12 residue 81 ILE Chi-restraints excluded: chain 12 residue 109 LEU Chi-restraints excluded: chain 12 residue 111 LYS Chi-restraints excluded: chain 13 residue 61 VAL Chi-restraints excluded: chain 13 residue 65 THR Chi-restraints excluded: chain 13 residue 97 THR Chi-restraints excluded: chain 14 residue 42 SER Chi-restraints excluded: chain 14 residue 51 GLU Chi-restraints excluded: chain 14 residue 67 THR Chi-restraints excluded: chain 14 residue 110 VAL Chi-restraints excluded: chain 14 residue 122 VAL Chi-restraints excluded: chain 15 residue 12 MET Chi-restraints excluded: chain 15 residue 30 SER Chi-restraints excluded: chain 15 residue 74 THR Chi-restraints excluded: chain 15 residue 124 LEU Chi-restraints excluded: chain 15 residue 132 THR Chi-restraints excluded: chain 16 residue 20 MET Chi-restraints excluded: chain 16 residue 27 SER Chi-restraints excluded: chain 16 residue 36 THR Chi-restraints excluded: chain 16 residue 37 THR Chi-restraints excluded: chain 16 residue 57 THR Chi-restraints excluded: chain 16 residue 106 ASP Chi-restraints excluded: chain 16 residue 113 ILE Chi-restraints excluded: chain 17 residue 2 ASP Chi-restraints excluded: chain 17 residue 18 LEU Chi-restraints excluded: chain 17 residue 39 VAL Chi-restraints excluded: chain 17 residue 47 VAL Chi-restraints excluded: chain 17 residue 58 ILE Chi-restraints excluded: chain 17 residue 69 ASP Chi-restraints excluded: chain 17 residue 87 ILE Chi-restraints excluded: chain 18 residue 35 SER Chi-restraints excluded: chain 18 residue 45 VAL Chi-restraints excluded: chain 18 residue 51 ASN Chi-restraints excluded: chain 18 residue 72 VAL Chi-restraints excluded: chain 18 residue 81 ASP Chi-restraints excluded: chain 18 residue 96 LEU Chi-restraints excluded: chain 19 residue 82 LEU Chi-restraints excluded: chain 19 residue 86 SER Chi-restraints excluded: chain 19 residue 94 LEU Chi-restraints excluded: chain 20 residue 29 THR Chi-restraints excluded: chain 20 residue 37 GLU Chi-restraints excluded: chain 20 residue 51 VAL Chi-restraints excluded: chain 20 residue 96 VAL Chi-restraints excluded: chain 20 residue 98 ILE Chi-restraints excluded: chain 21 residue 22 ASP Chi-restraints excluded: chain 21 residue 34 ASP Chi-restraints excluded: chain 21 residue 74 ILE Chi-restraints excluded: chain 21 residue 96 ILE Chi-restraints excluded: chain 21 residue 101 SER Chi-restraints excluded: chain 21 residue 104 THR Chi-restraints excluded: chain 22 residue 2 ILE Chi-restraints excluded: chain 22 residue 32 LEU Chi-restraints excluded: chain 22 residue 78 SER Chi-restraints excluded: chain 23 residue 7 ASP Chi-restraints excluded: chain 23 residue 27 VAL Chi-restraints excluded: chain 23 residue 59 GLU Chi-restraints excluded: chain 23 residue 97 SER Chi-restraints excluded: chain 24 residue 8 VAL Chi-restraints excluded: chain 24 residue 48 MET Chi-restraints excluded: chain 24 residue 49 ASN Chi-restraints excluded: chain 25 residue 63 VAL Chi-restraints excluded: chain 26 residue 24 THR Chi-restraints excluded: chain 26 residue 32 LEU Chi-restraints excluded: chain 26 residue 46 VAL Chi-restraints excluded: chain 26 residue 48 LEU Chi-restraints excluded: chain 26 residue 59 ASP Chi-restraints excluded: chain 27 residue 7 ARG Chi-restraints excluded: chain 28 residue 9 THR Chi-restraints excluded: chain 28 residue 31 ILE Chi-restraints excluded: chain 28 residue 56 VAL Chi-restraints excluded: chain 29 residue 33 ASN Chi-restraints excluded: chain 29 residue 39 LYS Chi-restraints excluded: chain 29 residue 44 PHE Chi-restraints excluded: chain 29 residue 53 THR Chi-restraints excluded: chain 30 residue 8 THR Chi-restraints excluded: chain 30 residue 10 SER Chi-restraints excluded: chain 30 residue 24 VAL Chi-restraints excluded: chain 30 residue 26 SER Chi-restraints excluded: chain 30 residue 27 LEU Chi-restraints excluded: chain 30 residue 42 ILE Chi-restraints excluded: chain 31 residue 16 THR Chi-restraints excluded: chain 32 residue 4 THR Chi-restraints excluded: chain 32 residue 10 LEU Chi-restraints excluded: chain 32 residue 30 VAL Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 32 residue 44 VAL Chi-restraints excluded: chain 33 residue 53 ASP Chi-restraints excluded: chain 33 residue 54 LEU Chi-restraints excluded: chain 34 residue 22 VAL Chi-restraints excluded: chain 34 residue 37 GLN Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain D residue 19 PHE Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 128 VAL 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 191 SER Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 156 ARG Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain I residue 24 ASN Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 88 GLU 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 96 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 69 CYS Chi-restraints excluded: chain K residue 71 ASP Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain L residue 5 GLN Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 57 ASP Chi-restraints excluded: chain M residue 61 LYS Chi-restraints excluded: chain M residue 67 ASP Chi-restraints excluded: chain M residue 72 ILE Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain N residue 85 GLU Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 88 ARG Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain R residue 41 SER Chi-restraints excluded: chain S residue 6 LYS Chi-restraints excluded: chain S residue 11 ASP Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 14 GLU Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain U residue 8 ASN Chi-restraints excluded: chain U residue 12 ASP Chi-restraints excluded: chain U residue 18 PHE Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 30 GLU Chi-restraints excluded: chain U residue 36 PHE Chi-restraints excluded: chain U residue 43 GLU Chi-restraints excluded: chain 03 residue 13 GLU Chi-restraints excluded: chain 03 residue 16 ASP Chi-restraints excluded: chain 03 residue 23 ILE Chi-restraints excluded: chain 03 residue 30 LEU Chi-restraints excluded: chain 03 residue 35 THR Chi-restraints excluded: chain 03 residue 47 ASN Chi-restraints excluded: chain Z residue 25 THR Chi-restraints excluded: chain Z residue 90 ASN Chi-restraints excluded: chain Z residue 130 ILE Chi-restraints excluded: chain Z residue 134 LEU Chi-restraints excluded: chain Z residue 160 TYR Chi-restraints excluded: chain Z residue 197 SER Chi-restraints excluded: chain Z residue 227 VAL Chi-restraints excluded: chain Z residue 236 ILE Chi-restraints excluded: chain Z residue 237 LYS Chi-restraints excluded: chain Z residue 292 LEU Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 332 PHE Chi-restraints excluded: chain Z residue 357 LYS Chi-restraints excluded: chain Z residue 362 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1101 random chunks: chunk 965 optimal weight: 10.0000 chunk 1016 optimal weight: 20.0000 chunk 927 optimal weight: 10.0000 chunk 988 optimal weight: 10.0000 chunk 595 optimal weight: 20.0000 chunk 430 optimal weight: 0.9990 chunk 776 optimal weight: 10.0000 chunk 303 optimal weight: 20.0000 chunk 893 optimal weight: 20.0000 chunk 935 optimal weight: 10.0000 chunk 985 optimal weight: 10.0000 overall best weight: 8.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 04 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 06 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 07 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 18 ASN ** 12 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 13 29 HIS ** 15 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 16 23 ASN 19 19 GLN ** 19 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 21 40 ASN ** 27 39 GLN ** 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 65 ASN 32 13 ASN B 121 GLN ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 49 GLN ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 56 HIS ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 53 GLN ** T 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 69 ASN ** Z 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 166818 Z= 0.328 Angle : 0.651 16.453 249072 Z= 0.334 Chirality : 0.036 0.374 31782 Planarity : 0.005 0.066 13716 Dihedral : 23.462 179.640 82300 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 18.83 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.13 % Favored : 89.63 % Rotamer: Outliers : 5.69 % Allowed : 24.56 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.10), residues: 6366 helix: 0.08 (0.11), residues: 1997 sheet: -1.63 (0.15), residues: 1161 loop : -1.82 (0.11), residues: 3208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP04 212 HIS 0.019 0.001 HIS L 76 PHE 0.041 0.002 PHE U 36 TYR 0.033 0.002 TYR Z 129 ARG 0.010 0.001 ARG R 72 *********************** 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 1565 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 301 poor density : 1264 time to evaluate : 7.007 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: 04 224 MET cc_start: 0.8309 (mtm) cc_final: 0.7998 (mtm) REVERT: 07 142 TYR cc_start: 0.8428 (t80) cc_final: 0.8135 (t80) REVERT: 09 91 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.7936 (m-80) REVERT: 09 97 ARG cc_start: 0.8398 (mtm180) cc_final: 0.8191 (ttm170) REVERT: 09 135 HIS cc_start: 0.8464 (t-90) cc_final: 0.7946 (t70) REVERT: 10 1 MET cc_start: 0.7114 (tmm) cc_final: 0.5646 (tpp) REVERT: 10 38 MET cc_start: 0.9156 (mmp) cc_final: 0.8830 (tmm) REVERT: 10 52 MET cc_start: 0.1122 (tpt) cc_final: 0.0701 (tpt) REVERT: 11 33 ASN cc_start: 0.9232 (m-40) cc_final: 0.8911 (m110) REVERT: 11 35 MET cc_start: 0.9296 (mmp) cc_final: 0.9051 (tmm) REVERT: 11 63 ASP cc_start: 0.6574 (OUTLIER) cc_final: 0.5907 (p0) REVERT: 11 64 ARG cc_start: 0.7747 (tpt90) cc_final: 0.6868 (mmp80) REVERT: 11 107 GLU cc_start: 0.9223 (pp20) cc_final: 0.8726 (pp20) REVERT: 12 80 HIS cc_start: 0.7768 (OUTLIER) cc_final: 0.7252 (t-90) REVERT: 13 12 ASP cc_start: 0.8074 (p0) cc_final: 0.7722 (p0) REVERT: 13 87 LEU cc_start: 0.8812 (mt) cc_final: 0.8552 (mt) REVERT: 15 73 ILE cc_start: 0.8779 (mm) cc_final: 0.8520 (mt) REVERT: 16 72 ASP cc_start: 0.8739 (t70) cc_final: 0.8408 (t0) REVERT: 16 74 GLU cc_start: 0.9110 (tm-30) cc_final: 0.8845 (tm-30) REVERT: 16 75 ILE cc_start: 0.9346 (mm) cc_final: 0.8937 (mm) REVERT: 18 6 GLN cc_start: 0.8775 (tp-100) cc_final: 0.8563 (tp-100) REVERT: 18 26 GLU cc_start: 0.8334 (tp30) cc_final: 0.7707 (tp30) REVERT: 18 43 GLU cc_start: 0.8352 (tp30) cc_final: 0.8040 (tp30) REVERT: 21 67 ASP cc_start: 0.9074 (m-30) cc_final: 0.8853 (t0) REVERT: 21 86 MET cc_start: 0.9363 (tpt) cc_final: 0.9080 (ttt) REVERT: 22 1 MET cc_start: 0.6734 (ptt) cc_final: 0.6342 (ptp) REVERT: 22 4 GLU cc_start: 0.8681 (mp0) cc_final: 0.8057 (mp0) REVERT: 24 50 MET cc_start: 0.8957 (mtt) cc_final: 0.8653 (ttm) REVERT: 29 10 GLU cc_start: 0.8221 (pm20) cc_final: 0.7940 (pp20) REVERT: 29 53 THR cc_start: 0.7073 (OUTLIER) cc_final: 0.6516 (t) REVERT: B 48 MET cc_start: 0.9327 (tpp) cc_final: 0.8832 (mtt) REVERT: B 135 MET cc_start: 0.9077 (tmm) cc_final: 0.8687 (ppp) REVERT: B 163 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8447 (tp) REVERT: C 99 GLN cc_start: 0.8173 (tm-30) cc_final: 0.7842 (pp30) REVERT: E 150 GLU cc_start: 0.8516 (pm20) cc_final: 0.7948 (pm20) REVERT: E 151 MET cc_start: 0.9226 (ptp) cc_final: 0.8946 (ptp) REVERT: F 21 MET cc_start: 0.9135 (tpt) cc_final: 0.8878 (tpt) REVERT: F 56 LYS cc_start: 0.8958 (ptmm) cc_final: 0.8646 (ptmm) REVERT: G 115 MET cc_start: 0.9074 (tpt) cc_final: 0.8698 (ttm) REVERT: H 53 ASP cc_start: 0.8093 (p0) cc_final: 0.7790 (p0) REVERT: I 87 MET cc_start: 0.9114 (ptt) cc_final: 0.8838 (ppp) REVERT: I 88 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.6876 (pm20) REVERT: J 24 GLU cc_start: 0.9219 (pp20) cc_final: 0.8959 (pp20) REVERT: L 74 GLN cc_start: 0.9341 (pm20) cc_final: 0.8920 (pm20) REVERT: L 75 GLU cc_start: 0.9008 (tm-30) cc_final: 0.8775 (tm-30) REVERT: M 96 VAL cc_start: 0.9245 (m) cc_final: 0.8903 (t) REVERT: O 88 ARG cc_start: 0.6636 (OUTLIER) cc_final: 0.6344 (mmp80) REVERT: Q 3 LYS cc_start: 0.8617 (tppt) cc_final: 0.7738 (ttpt) REVERT: U 8 ASN cc_start: 0.8333 (OUTLIER) cc_final: 0.7640 (p0) REVERT: U 38 GLU cc_start: 0.7730 (tm-30) cc_final: 0.7264 (tm-30) REVERT: U 55 HIS cc_start: 0.8560 (t-90) cc_final: 0.8301 (t-90) REVERT: 03 218 MET cc_start: 0.6061 (mtt) cc_final: 0.5488 (mmt) REVERT: Z 51 ASN cc_start: 0.8687 (p0) cc_final: 0.8402 (p0) REVERT: Z 160 TYR cc_start: 0.8563 (OUTLIER) cc_final: 0.8355 (m-10) outliers start: 301 outliers final: 267 residues processed: 1412 average time/residue: 1.2696 time to fit residues: 3163.2498 Evaluate side-chains 1509 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 276 poor density : 1233 time to evaluate : 6.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 37 SER Chi-restraints excluded: chain 04 residue 44 ASN Chi-restraints excluded: chain 04 residue 117 SER Chi-restraints excluded: chain 04 residue 156 SER Chi-restraints excluded: chain 04 residue 159 THR Chi-restraints excluded: chain 04 residue 200 MET Chi-restraints excluded: chain 05 residue 1 MET Chi-restraints excluded: chain 05 residue 22 ILE Chi-restraints excluded: chain 05 residue 97 SER Chi-restraints excluded: chain 05 residue 103 ASP Chi-restraints excluded: chain 05 residue 108 ASP Chi-restraints excluded: chain 05 residue 139 SER Chi-restraints excluded: chain 05 residue 176 ASP Chi-restraints excluded: chain 05 residue 177 VAL Chi-restraints excluded: chain 05 residue 200 ASP Chi-restraints excluded: chain 06 residue 7 ASP Chi-restraints excluded: chain 06 residue 187 VAL Chi-restraints excluded: chain 07 residue 16 MET Chi-restraints excluded: chain 07 residue 30 VAL Chi-restraints excluded: chain 07 residue 37 MET Chi-restraints excluded: chain 07 residue 95 MET Chi-restraints excluded: chain 07 residue 135 ILE Chi-restraints excluded: chain 07 residue 154 THR Chi-restraints excluded: chain 08 residue 9 VAL Chi-restraints excluded: chain 08 residue 10 VAL Chi-restraints excluded: chain 08 residue 55 ASP Chi-restraints excluded: chain 08 residue 126 THR Chi-restraints excluded: chain 08 residue 154 GLU Chi-restraints excluded: chain 09 residue 14 SER Chi-restraints excluded: chain 09 residue 17 ASP Chi-restraints excluded: chain 09 residue 54 LEU Chi-restraints excluded: chain 09 residue 91 PHE Chi-restraints excluded: chain 10 residue 24 SER Chi-restraints excluded: chain 10 residue 76 PHE Chi-restraints excluded: chain 10 residue 82 ILE Chi-restraints excluded: chain 10 residue 123 ILE Chi-restraints excluded: chain 11 residue 46 ASP Chi-restraints excluded: chain 11 residue 63 ASP Chi-restraints excluded: chain 11 residue 85 ILE Chi-restraints excluded: chain 11 residue 120 ASP Chi-restraints excluded: chain 12 residue 14 ASP Chi-restraints excluded: chain 12 residue 32 LEU Chi-restraints excluded: chain 12 residue 52 ASP Chi-restraints excluded: chain 12 residue 67 ASN Chi-restraints excluded: chain 12 residue 80 HIS Chi-restraints excluded: chain 12 residue 81 ILE Chi-restraints excluded: chain 12 residue 111 LYS Chi-restraints excluded: chain 13 residue 29 HIS Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 61 VAL Chi-restraints excluded: chain 13 residue 65 THR Chi-restraints excluded: chain 13 residue 97 THR Chi-restraints excluded: chain 13 residue 104 THR Chi-restraints excluded: chain 14 residue 42 SER Chi-restraints excluded: chain 14 residue 51 GLU Chi-restraints excluded: chain 14 residue 67 THR Chi-restraints excluded: chain 14 residue 103 ILE Chi-restraints excluded: chain 14 residue 110 VAL Chi-restraints excluded: chain 14 residue 122 VAL Chi-restraints excluded: chain 15 residue 12 MET Chi-restraints excluded: chain 15 residue 30 SER Chi-restraints excluded: chain 15 residue 74 THR Chi-restraints excluded: chain 15 residue 124 LEU Chi-restraints excluded: chain 15 residue 132 THR Chi-restraints excluded: chain 16 residue 20 MET Chi-restraints excluded: chain 16 residue 27 SER Chi-restraints excluded: chain 16 residue 36 THR Chi-restraints excluded: chain 16 residue 37 THR Chi-restraints excluded: chain 16 residue 57 THR Chi-restraints excluded: chain 16 residue 89 SER Chi-restraints excluded: chain 16 residue 106 ASP Chi-restraints excluded: chain 16 residue 113 ILE Chi-restraints excluded: chain 17 residue 2 ASP Chi-restraints excluded: chain 17 residue 18 LEU Chi-restraints excluded: chain 17 residue 35 ILE Chi-restraints excluded: chain 17 residue 39 VAL Chi-restraints excluded: chain 17 residue 47 VAL Chi-restraints excluded: chain 17 residue 53 THR Chi-restraints excluded: chain 17 residue 69 ASP Chi-restraints excluded: chain 17 residue 87 ILE Chi-restraints excluded: chain 18 residue 35 SER Chi-restraints excluded: chain 18 residue 51 ASN Chi-restraints excluded: chain 18 residue 72 VAL Chi-restraints excluded: chain 18 residue 81 ASP Chi-restraints excluded: chain 18 residue 96 LEU Chi-restraints excluded: chain 19 residue 82 LEU Chi-restraints excluded: chain 19 residue 86 SER Chi-restraints excluded: chain 19 residue 94 LEU Chi-restraints excluded: chain 20 residue 29 THR Chi-restraints excluded: chain 20 residue 37 GLU Chi-restraints excluded: chain 20 residue 43 ASN Chi-restraints excluded: chain 20 residue 51 VAL Chi-restraints excluded: chain 20 residue 96 VAL Chi-restraints excluded: chain 20 residue 98 ILE Chi-restraints excluded: chain 21 residue 22 ASP Chi-restraints excluded: chain 21 residue 34 ASP Chi-restraints excluded: chain 21 residue 74 ILE Chi-restraints excluded: chain 21 residue 96 ILE Chi-restraints excluded: chain 21 residue 101 SER Chi-restraints excluded: chain 21 residue 104 THR Chi-restraints excluded: chain 22 residue 32 LEU Chi-restraints excluded: chain 22 residue 78 SER Chi-restraints excluded: chain 23 residue 7 ASP Chi-restraints excluded: chain 23 residue 27 VAL Chi-restraints excluded: chain 23 residue 59 GLU Chi-restraints excluded: chain 23 residue 97 SER Chi-restraints excluded: chain 24 residue 8 VAL Chi-restraints excluded: chain 24 residue 48 MET Chi-restraints excluded: chain 24 residue 49 ASN Chi-restraints excluded: chain 25 residue 63 VAL Chi-restraints excluded: chain 26 residue 24 THR Chi-restraints excluded: chain 26 residue 32 LEU Chi-restraints excluded: chain 26 residue 46 VAL Chi-restraints excluded: chain 26 residue 48 LEU Chi-restraints excluded: chain 26 residue 59 ASP Chi-restraints excluded: chain 26 residue 63 ILE Chi-restraints excluded: chain 27 residue 7 ARG Chi-restraints excluded: chain 28 residue 2 LYS Chi-restraints excluded: chain 28 residue 9 THR Chi-restraints excluded: chain 28 residue 31 ILE Chi-restraints excluded: chain 28 residue 56 VAL Chi-restraints excluded: chain 29 residue 25 ARG Chi-restraints excluded: chain 29 residue 32 LEU Chi-restraints excluded: chain 29 residue 33 ASN Chi-restraints excluded: chain 29 residue 39 LYS Chi-restraints excluded: chain 29 residue 44 PHE Chi-restraints excluded: chain 29 residue 53 THR Chi-restraints excluded: chain 30 residue 8 THR Chi-restraints excluded: chain 30 residue 10 SER Chi-restraints excluded: chain 30 residue 24 VAL Chi-restraints excluded: chain 30 residue 26 SER Chi-restraints excluded: chain 30 residue 27 LEU Chi-restraints excluded: chain 30 residue 42 ILE Chi-restraints excluded: chain 31 residue 16 THR Chi-restraints excluded: chain 32 residue 4 THR Chi-restraints excluded: chain 32 residue 10 LEU Chi-restraints excluded: chain 32 residue 30 VAL Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 32 residue 44 VAL Chi-restraints excluded: chain 33 residue 53 ASP Chi-restraints excluded: chain 33 residue 54 LEU Chi-restraints excluded: chain 34 residue 22 VAL Chi-restraints excluded: chain 34 residue 37 GLN Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 19 PHE Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 128 VAL 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 191 SER Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 156 ARG Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain H residue 26 MET Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain I residue 24 ASN Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 88 GLU 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 96 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 69 CYS Chi-restraints excluded: chain K residue 71 ASP Chi-restraints excluded: chain K residue 99 LEU Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain L residue 5 GLN Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 81 ILE Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 61 LYS Chi-restraints excluded: chain M residue 67 ASP Chi-restraints excluded: chain M residue 72 ILE Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 88 ARG Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain R residue 20 ILE Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain R residue 41 SER Chi-restraints excluded: chain S residue 6 LYS Chi-restraints excluded: chain S residue 11 ASP Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 14 GLU Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 38 ILE Chi-restraints excluded: chain U residue 8 ASN Chi-restraints excluded: chain U residue 12 ASP Chi-restraints excluded: chain U residue 18 PHE Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 30 GLU Chi-restraints excluded: chain U residue 43 GLU Chi-restraints excluded: chain 03 residue 13 GLU Chi-restraints excluded: chain 03 residue 16 ASP Chi-restraints excluded: chain 03 residue 23 ILE Chi-restraints excluded: chain 03 residue 30 LEU Chi-restraints excluded: chain 03 residue 35 THR Chi-restraints excluded: chain 03 residue 47 ASN Chi-restraints excluded: chain Z residue 25 THR Chi-restraints excluded: chain Z residue 90 ASN Chi-restraints excluded: chain Z residue 130 ILE Chi-restraints excluded: chain Z residue 134 LEU Chi-restraints excluded: chain Z residue 160 TYR Chi-restraints excluded: chain Z residue 197 SER Chi-restraints excluded: chain Z residue 227 VAL Chi-restraints excluded: chain Z residue 236 ILE Chi-restraints excluded: chain Z residue 237 LYS Chi-restraints excluded: chain Z residue 292 LEU Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 332 PHE Chi-restraints excluded: chain Z residue 357 LYS Chi-restraints excluded: chain Z residue 362 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1101 random chunks: chunk 649 optimal weight: 20.0000 chunk 1045 optimal weight: 50.0000 chunk 638 optimal weight: 10.0000 chunk 496 optimal weight: 7.9990 chunk 726 optimal weight: 10.0000 chunk 1096 optimal weight: 2.9990 chunk 1009 optimal weight: 10.0000 chunk 873 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 674 optimal weight: 10.0000 chunk 535 optimal weight: 9.9990 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 04 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 07 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 18 ASN ** 11 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 13 13 ASN ** 15 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 15 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 16 9 GLN ** 19 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 21 40 ASN 24 87 GLN ** 27 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 29 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 32 13 ASN ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 GLN I 36 GLN I 49 GLN J 56 HIS J 58 ASN ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 53 GLN ** T 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 69 ASN ** Z 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 166818 Z= 0.315 Angle : 0.651 16.602 249072 Z= 0.334 Chirality : 0.036 0.390 31782 Planarity : 0.005 0.066 13716 Dihedral : 23.482 179.968 82300 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.96 % Favored : 89.87 % Rotamer: Outliers : 5.66 % Allowed : 24.90 % Favored : 69.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.10), residues: 6366 helix: 0.07 (0.12), residues: 2000 sheet: -1.58 (0.15), residues: 1163 loop : -1.80 (0.11), residues: 3203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP04 212 HIS 0.031 0.001 HIS13 29 PHE 0.043 0.002 PHE U 36 TYR 0.032 0.002 TYR Z 129 ARG 0.015 0.001 ARG31 27 ********************** 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 1557 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 299 poor density : 1258 time to evaluate : 6.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 04 224 MET cc_start: 0.8286 (mtm) cc_final: 0.7982 (mtm) REVERT: 07 142 TYR cc_start: 0.8446 (t80) cc_final: 0.8161 (t80) REVERT: 09 91 PHE cc_start: 0.8235 (OUTLIER) cc_final: 0.7942 (m-80) REVERT: 10 1 MET cc_start: 0.6718 (tmm) cc_final: 0.6062 (tpp) REVERT: 10 38 MET cc_start: 0.9163 (mmp) cc_final: 0.8865 (tmm) REVERT: 10 52 MET cc_start: 0.1168 (tpt) cc_final: 0.0780 (tpt) REVERT: 11 33 ASN cc_start: 0.9235 (m-40) cc_final: 0.8905 (m110) REVERT: 11 35 MET cc_start: 0.9298 (mmp) cc_final: 0.9047 (tmm) REVERT: 11 63 ASP cc_start: 0.6487 (OUTLIER) cc_final: 0.5864 (p0) REVERT: 11 64 ARG cc_start: 0.7862 (tpt90) cc_final: 0.6948 (mmp80) REVERT: 11 106 GLN cc_start: 0.8503 (tm-30) cc_final: 0.8158 (tm-30) REVERT: 11 107 GLU cc_start: 0.9067 (pp20) cc_final: 0.8795 (pp20) REVERT: 12 80 HIS cc_start: 0.7739 (OUTLIER) cc_final: 0.7258 (t-90) REVERT: 12 98 GLU cc_start: 0.9058 (pm20) cc_final: 0.8749 (pm20) REVERT: 13 12 ASP cc_start: 0.8029 (p0) cc_final: 0.7666 (p0) REVERT: 13 87 LEU cc_start: 0.8820 (mt) cc_final: 0.8575 (mt) REVERT: 15 73 ILE cc_start: 0.8774 (mm) cc_final: 0.8525 (mt) REVERT: 16 72 ASP cc_start: 0.8734 (t70) cc_final: 0.8424 (t0) REVERT: 16 74 GLU cc_start: 0.9115 (tm-30) cc_final: 0.8853 (tm-30) REVERT: 16 75 ILE cc_start: 0.9347 (mm) cc_final: 0.8938 (mm) REVERT: 18 26 GLU cc_start: 0.8329 (tp30) cc_final: 0.7671 (tp30) REVERT: 18 43 GLU cc_start: 0.8344 (tp30) cc_final: 0.8043 (tp30) REVERT: 21 86 MET cc_start: 0.9361 (tpt) cc_final: 0.9076 (ttt) REVERT: 22 1 MET cc_start: 0.6668 (ptt) cc_final: 0.6296 (ptp) REVERT: 22 4 GLU cc_start: 0.8705 (mp0) cc_final: 0.8068 (mp0) REVERT: 24 50 MET cc_start: 0.8954 (mtt) cc_final: 0.8669 (ttm) REVERT: 28 20 LYS cc_start: 0.8480 (mptt) cc_final: 0.8209 (mptt) REVERT: 29 10 GLU cc_start: 0.8186 (pm20) cc_final: 0.7928 (pp20) REVERT: 29 50 ASP cc_start: 0.8363 (t0) cc_final: 0.7082 (p0) REVERT: 29 53 THR cc_start: 0.7119 (OUTLIER) cc_final: 0.6450 (t) REVERT: B 48 MET cc_start: 0.9325 (tpp) cc_final: 0.8830 (mtt) REVERT: B 135 MET cc_start: 0.9096 (tmm) cc_final: 0.8702 (ppp) REVERT: B 163 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8464 (tp) REVERT: C 99 GLN cc_start: 0.8153 (tm-30) cc_final: 0.7847 (pp30) REVERT: E 150 GLU cc_start: 0.8500 (pm20) cc_final: 0.7896 (pm20) REVERT: E 151 MET cc_start: 0.9234 (ptp) cc_final: 0.8883 (ptp) REVERT: F 56 LYS cc_start: 0.8935 (ptmm) cc_final: 0.8673 (ptmm) REVERT: G 115 MET cc_start: 0.9068 (tpt) cc_final: 0.8709 (ttm) REVERT: H 53 ASP cc_start: 0.8077 (p0) cc_final: 0.7758 (p0) REVERT: I 87 MET cc_start: 0.9125 (ptt) cc_final: 0.8851 (ppp) REVERT: I 88 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.6990 (pm20) REVERT: J 24 GLU cc_start: 0.9230 (pp20) cc_final: 0.9018 (pp20) REVERT: J 27 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8456 (tm-30) REVERT: L 74 GLN cc_start: 0.9284 (pm20) cc_final: 0.8927 (pm20) REVERT: M 96 VAL cc_start: 0.9234 (m) cc_final: 0.8885 (t) REVERT: O 88 ARG cc_start: 0.6759 (OUTLIER) cc_final: 0.6451 (mmp80) REVERT: Q 3 LYS cc_start: 0.8652 (tppt) cc_final: 0.7788 (ttpt) REVERT: U 8 ASN cc_start: 0.8252 (OUTLIER) cc_final: 0.7594 (p0) REVERT: U 55 HIS cc_start: 0.8587 (t-90) cc_final: 0.8366 (t-90) REVERT: 03 218 MET cc_start: 0.6096 (mtt) cc_final: 0.5494 (mmt) REVERT: Z 51 ASN cc_start: 0.8708 (p0) cc_final: 0.8453 (p0) REVERT: Z 160 TYR cc_start: 0.8560 (OUTLIER) cc_final: 0.8356 (m-10) outliers start: 299 outliers final: 263 residues processed: 1405 average time/residue: 1.2833 time to fit residues: 3185.9269 Evaluate side-chains 1498 residues out of total 5287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 272 poor density : 1226 time to evaluate : 6.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 37 SER Chi-restraints excluded: chain 04 residue 44 ASN Chi-restraints excluded: chain 04 residue 117 SER Chi-restraints excluded: chain 04 residue 156 SER Chi-restraints excluded: chain 04 residue 159 THR Chi-restraints excluded: chain 04 residue 200 MET Chi-restraints excluded: chain 05 residue 1 MET Chi-restraints excluded: chain 05 residue 22 ILE Chi-restraints excluded: chain 05 residue 97 SER Chi-restraints excluded: chain 05 residue 103 ASP Chi-restraints excluded: chain 05 residue 108 ASP Chi-restraints excluded: chain 05 residue 139 SER Chi-restraints excluded: chain 05 residue 176 ASP Chi-restraints excluded: chain 05 residue 177 VAL Chi-restraints excluded: chain 05 residue 200 ASP Chi-restraints excluded: chain 06 residue 7 ASP Chi-restraints excluded: chain 07 residue 16 MET Chi-restraints excluded: chain 07 residue 30 VAL Chi-restraints excluded: chain 07 residue 37 MET Chi-restraints excluded: chain 07 residue 95 MET Chi-restraints excluded: chain 07 residue 135 ILE Chi-restraints excluded: chain 07 residue 154 THR Chi-restraints excluded: chain 08 residue 9 VAL Chi-restraints excluded: chain 08 residue 10 VAL Chi-restraints excluded: chain 08 residue 55 ASP Chi-restraints excluded: chain 08 residue 126 THR Chi-restraints excluded: chain 08 residue 154 GLU Chi-restraints excluded: chain 09 residue 14 SER Chi-restraints excluded: chain 09 residue 17 ASP Chi-restraints excluded: chain 09 residue 54 LEU Chi-restraints excluded: chain 09 residue 77 THR Chi-restraints excluded: chain 09 residue 91 PHE Chi-restraints excluded: chain 10 residue 24 SER Chi-restraints excluded: chain 10 residue 76 PHE Chi-restraints excluded: chain 10 residue 82 ILE Chi-restraints excluded: chain 10 residue 123 ILE Chi-restraints excluded: chain 11 residue 46 ASP Chi-restraints excluded: chain 11 residue 63 ASP Chi-restraints excluded: chain 11 residue 85 ILE Chi-restraints excluded: chain 11 residue 120 ASP Chi-restraints excluded: chain 11 residue 135 MET Chi-restraints excluded: chain 12 residue 14 ASP Chi-restraints excluded: chain 12 residue 52 ASP Chi-restraints excluded: chain 12 residue 67 ASN Chi-restraints excluded: chain 12 residue 80 HIS Chi-restraints excluded: chain 12 residue 81 ILE Chi-restraints excluded: chain 12 residue 111 LYS Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 61 VAL Chi-restraints excluded: chain 13 residue 65 THR Chi-restraints excluded: chain 13 residue 97 THR Chi-restraints excluded: chain 14 residue 42 SER Chi-restraints excluded: chain 14 residue 51 GLU Chi-restraints excluded: chain 14 residue 67 THR Chi-restraints excluded: chain 14 residue 80 SER Chi-restraints excluded: chain 14 residue 110 VAL Chi-restraints excluded: chain 14 residue 122 VAL Chi-restraints excluded: chain 15 residue 12 MET Chi-restraints excluded: chain 15 residue 28 PHE Chi-restraints excluded: chain 15 residue 30 SER Chi-restraints excluded: chain 15 residue 54 THR Chi-restraints excluded: chain 15 residue 74 THR Chi-restraints excluded: chain 15 residue 124 LEU Chi-restraints excluded: chain 15 residue 132 THR Chi-restraints excluded: chain 16 residue 20 MET Chi-restraints excluded: chain 16 residue 27 SER Chi-restraints excluded: chain 16 residue 36 THR Chi-restraints excluded: chain 16 residue 37 THR Chi-restraints excluded: chain 16 residue 57 THR Chi-restraints excluded: chain 16 residue 89 SER Chi-restraints excluded: chain 16 residue 106 ASP Chi-restraints excluded: chain 16 residue 113 ILE Chi-restraints excluded: chain 17 residue 2 ASP Chi-restraints excluded: chain 17 residue 18 LEU Chi-restraints excluded: chain 17 residue 35 ILE Chi-restraints excluded: chain 17 residue 39 VAL Chi-restraints excluded: chain 17 residue 47 VAL Chi-restraints excluded: chain 17 residue 53 THR Chi-restraints excluded: chain 17 residue 69 ASP Chi-restraints excluded: chain 17 residue 87 ILE Chi-restraints excluded: chain 18 residue 35 SER Chi-restraints excluded: chain 18 residue 51 ASN Chi-restraints excluded: chain 18 residue 72 VAL Chi-restraints excluded: chain 18 residue 81 ASP Chi-restraints excluded: chain 18 residue 96 LEU Chi-restraints excluded: chain 19 residue 16 ILE Chi-restraints excluded: chain 19 residue 82 LEU Chi-restraints excluded: chain 19 residue 86 SER Chi-restraints excluded: chain 19 residue 94 LEU Chi-restraints excluded: chain 20 residue 29 THR Chi-restraints excluded: chain 20 residue 37 GLU Chi-restraints excluded: chain 20 residue 43 ASN Chi-restraints excluded: chain 20 residue 51 VAL Chi-restraints excluded: chain 20 residue 98 ILE Chi-restraints excluded: chain 21 residue 22 ASP Chi-restraints excluded: chain 21 residue 34 ASP Chi-restraints excluded: chain 21 residue 74 ILE Chi-restraints excluded: chain 21 residue 96 ILE Chi-restraints excluded: chain 21 residue 101 SER Chi-restraints excluded: chain 21 residue 104 THR Chi-restraints excluded: chain 22 residue 2 ILE Chi-restraints excluded: chain 22 residue 32 LEU Chi-restraints excluded: chain 22 residue 78 SER Chi-restraints excluded: chain 23 residue 7 ASP Chi-restraints excluded: chain 23 residue 27 VAL Chi-restraints excluded: chain 23 residue 59 GLU Chi-restraints excluded: chain 23 residue 97 SER Chi-restraints excluded: chain 24 residue 8 VAL Chi-restraints excluded: chain 24 residue 48 MET Chi-restraints excluded: chain 24 residue 49 ASN Chi-restraints excluded: chain 24 residue 87 GLN Chi-restraints excluded: chain 25 residue 63 VAL Chi-restraints excluded: chain 26 residue 24 THR Chi-restraints excluded: chain 26 residue 32 LEU Chi-restraints excluded: chain 26 residue 46 VAL Chi-restraints excluded: chain 26 residue 48 LEU Chi-restraints excluded: chain 26 residue 59 ASP Chi-restraints excluded: chain 26 residue 63 ILE Chi-restraints excluded: chain 27 residue 7 ARG Chi-restraints excluded: chain 28 residue 2 LYS Chi-restraints excluded: chain 28 residue 9 THR Chi-restraints excluded: chain 28 residue 31 ILE Chi-restraints excluded: chain 28 residue 56 VAL Chi-restraints excluded: chain 29 residue 25 ARG Chi-restraints excluded: chain 29 residue 33 ASN Chi-restraints excluded: chain 29 residue 39 LYS Chi-restraints excluded: chain 29 residue 44 PHE Chi-restraints excluded: chain 29 residue 53 THR Chi-restraints excluded: chain 30 residue 8 THR Chi-restraints excluded: chain 30 residue 10 SER Chi-restraints excluded: chain 30 residue 24 VAL Chi-restraints excluded: chain 30 residue 26 SER Chi-restraints excluded: chain 30 residue 27 LEU Chi-restraints excluded: chain 30 residue 42 ILE Chi-restraints excluded: chain 31 residue 16 THR Chi-restraints excluded: chain 32 residue 4 THR Chi-restraints excluded: chain 32 residue 10 LEU Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 32 residue 44 VAL Chi-restraints excluded: chain 33 residue 53 ASP Chi-restraints excluded: chain 33 residue 54 LEU Chi-restraints excluded: chain 34 residue 22 VAL Chi-restraints excluded: chain 34 residue 37 GLN Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 49 PHE Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain D residue 19 PHE Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 128 VAL 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 191 SER Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 156 ARG Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 162 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain H residue 58 LEU Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 88 GLU Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 69 CYS Chi-restraints excluded: chain K residue 71 ASP Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain L residue 5 GLN Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 81 ILE Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 8 ILE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 57 ASP Chi-restraints excluded: chain M residue 61 LYS Chi-restraints excluded: chain M residue 67 ASP Chi-restraints excluded: chain M residue 72 ILE Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 47 LEU Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 88 ARG Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 24 ILE Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain R residue 25 ILE Chi-restraints excluded: chain S residue 6 LYS Chi-restraints excluded: chain S residue 11 ASP Chi-restraints excluded: chain S residue 12 LEU Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain T residue 11 ILE Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 38 ILE Chi-restraints excluded: chain U residue 8 ASN Chi-restraints excluded: chain U residue 12 ASP Chi-restraints excluded: chain U residue 18 PHE Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 30 GLU Chi-restraints excluded: chain U residue 43 GLU Chi-restraints excluded: chain 03 residue 13 GLU Chi-restraints excluded: chain 03 residue 16 ASP Chi-restraints excluded: chain 03 residue 23 ILE Chi-restraints excluded: chain 03 residue 35 THR Chi-restraints excluded: chain 03 residue 47 ASN Chi-restraints excluded: chain Z residue 25 THR Chi-restraints excluded: chain Z residue 61 THR Chi-restraints excluded: chain Z residue 90 ASN Chi-restraints excluded: chain Z residue 130 ILE Chi-restraints excluded: chain Z residue 134 LEU Chi-restraints excluded: chain Z residue 160 TYR Chi-restraints excluded: chain Z residue 197 SER Chi-restraints excluded: chain Z residue 227 VAL Chi-restraints excluded: chain Z residue 236 ILE Chi-restraints excluded: chain Z residue 237 LYS Chi-restraints excluded: chain Z residue 292 LEU Chi-restraints excluded: chain Z residue 308 VAL Chi-restraints excluded: chain Z residue 332 PHE Chi-restraints excluded: chain Z residue 357 LYS Chi-restraints excluded: chain Z residue 362 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1101 random chunks: chunk 693 optimal weight: 10.0000 chunk 930 optimal weight: 10.0000 chunk 267 optimal weight: 7.9990 chunk 805 optimal weight: 10.0000 chunk 128 optimal weight: 30.0000 chunk 242 optimal weight: 20.0000 chunk 874 optimal weight: 10.0000 chunk 366 optimal weight: 10.0000 chunk 898 optimal weight: 10.0000 chunk 110 optimal weight: 0.0970 chunk 161 optimal weight: 10.0000 overall best weight: 7.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 04 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 07 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 09 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 10 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 18 ASN ** 11 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 15 17 ASN ** 15 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 15 88 ASN 16 23 ASN ** 18 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 21 40 ASN ** 29 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 32 13 ASN ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 ASN ** C 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 17 GLN I 49 GLN ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 53 GLN ** T 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 69 ASN ** Z 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.038417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.029374 restraints weight = 1033972.600| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 2.17 r_work: 0.2551 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2546 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2546 r_free = 0.2546 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2545 r_free = 0.2545 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2545 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 166818 Z= 0.310 Angle : 0.653 16.673 249072 Z= 0.333 Chirality : 0.036 0.397 31782 Planarity : 0.005 0.065 13716 Dihedral : 23.486 179.701 82300 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.13 % Favored : 89.70 % Rotamer: Outliers : 5.39 % Allowed : 25.35 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.10), residues: 6366 helix: 0.06 (0.12), residues: 2007 sheet: -1.60 (0.15), residues: 1181 loop : -1.80 (0.11), residues: 3178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP04 212 HIS 0.009 0.001 HIS L 76 PHE 0.035 0.002 PHE U 36 TYR 0.035 0.002 TYR O 77 ARG 0.012 0.001 ARG31 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 50861.88 seconds wall clock time: 885 minutes 44.30 seconds (53144.30 seconds total)