Starting phenix.real_space_refine on Sat Mar 2 12:12:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyk_8615/03_2024/5uyk_8615_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyk_8615/03_2024/5uyk_8615.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyk_8615/03_2024/5uyk_8615.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyk_8615/03_2024/5uyk_8615.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyk_8615/03_2024/5uyk_8615_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5uyk_8615/03_2024/5uyk_8615_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.407 sd= 1.292 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4808 5.49 5 S 175 5.16 5 C 78104 2.51 5 N 28699 2.21 5 O 42626 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 "20 PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "21 ARG 84": "NH1" <-> "NH2" Residue "21 ARG 88": "NH1" <-> "NH2" Residue "21 ARG 95": "NH1" <-> "NH2" Residue "21 ARG 110": "NH1" <-> "NH2" Residue "22 ARG 73": "NH1" <-> "NH2" Residue "23 ARG 5": "NH1" <-> "NH2" Residue "23 ARG 6": "NH1" <-> "NH2" Residue "23 ARG 81": "NH1" <-> "NH2" Residue "23 ARG 85": "NH1" <-> "NH2" Residue "23 ARG 93": "NH1" <-> "NH2" Residue "27 ARG 29": "NH1" <-> "NH2" Residue "27 ARG 47": "NH1" <-> "NH2" Residue "27 ARG 52": "NH1" <-> "NH2" Residue "28 ARG 10": "NH1" <-> "NH2" Residue "28 ARG 29": "NH1" <-> "NH2" Residue "28 ARG 44": "NH1" <-> "NH2" Residue "29 ARG 49": "NH1" <-> "NH2" Residue "29 ARG 56": "NH1" <-> "NH2" Residue "30 ARG 9": "NH1" <-> "NH2" Residue "30 ARG 15": "NH1" <-> "NH2" Residue "30 ARG 39": "NH1" <-> "NH2" Residue "30 ARG 51": "NH1" <-> "NH2" Residue "31 ARG 43": "NH1" <-> "NH2" Residue "32 ARG 3": "NH1" <-> "NH2" Residue "32 ARG 12": "NH1" <-> "NH2" Residue "32 ARG 14": "NH1" <-> "NH2" Residue "32 ARG 19": "NH1" <-> "NH2" Residue "32 ARG 21": "NH1" <-> "NH2" Residue "32 ARG 33": "NH1" <-> "NH2" Residue "32 ARG 41": "NH1" <-> "NH2" Residue "33 ARG 12": "NH1" <-> "NH2" Residue "33 ARG 29": "NH1" <-> "NH2" Residue "33 ARG 39": "NH1" <-> "NH2" Residue "33 ARG 41": "NH1" <-> "NH2" Residue "34 ARG 12": "NH1" <-> "NH2" Residue "34 ARG 24": "NH1" <-> "NH2" Residue "B ARG 107": "NH1" <-> "NH2" Residue "B ARG 224": "NH1" <-> "NH2" Residue "C ARG 106": "NH1" <-> "NH2" Residue "C ARG 130": "NH1" <-> "NH2" Residue "E PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 156": "NH1" <-> "NH2" Residue "G TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 123": "NH1" <-> "NH2" Residue "L ARG 55": "NH1" <-> "NH2" Residue "M TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 28": "NH1" <-> "NH2" Residue "R ARG 11": "NH1" <-> "NH2" Residue "U ARG 66": "NH1" <-> "NH2" Residue "03 ARG 7": "NH1" <-> "NH2" Residue "03 ARG 12": "NH1" <-> "NH2" Residue "03 ARG 71": "NH1" <-> "NH2" Residue "03 ARG 74": "NH1" <-> "NH2" Residue "03 ARG 122": "NH1" <-> "NH2" Residue "03 ARG 162": "NH1" <-> "NH2" Residue "03 TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 44": "NH1" <-> "NH2" Residue "Z ARG 223": "NH1" <-> "NH2" Residue "Z ARG 269": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 154412 Number of models: 1 Model: "" Number of chains: 60 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: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1662 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 215} Chain: "A" Number of atoms: 33012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33012 Classifications: {'RNA': 1539} Modifications used: {'5*END': 1, 'rna2p_pur': 89, 'rna2p_pyr': 44, 'rna3p_pur': 785, 'rna3p_pyr': 621} Link IDs: {'rna2p': 133, 'rna3p': 1405} 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': 208, 'rna2p_pyr': 91, 'rna3p_pur': 1466, 'rna3p_pyr': 1138} Link IDs: {'rna2p': 299, 'rna3p': 2603} Chain: "02" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2568 Classifications: {'RNA': 120} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 62, 'rna3p_pyr': 53} Link IDs: {'rna2p': 5, 'rna3p': 114} Chain: "X" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1640 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 33, 'rna3p_pyr': 33} Link IDs: {'rna2p': 11, 'rna3p': 65} Chain: "V" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 432 Classifications: {'RNA': 20} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 14, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 18} Chain: "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': 5, 'rna2p_pyr': 4, 'rna3p_pur': 34, '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': 5, 'rna3p_pur': 31, 'rna3p_pyr': 32} Link IDs: {'rna2p': 12, 'rna3p': 63} Chain: "Z" Number of atoms: 3061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3061 Unusual residues: {'GCP': 1} Inner-chain residues flagged as termini: ['pdbres="LEU Z 392 "'] Classifications: {'peptide': 392, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 371, None: 1} Not linked: pdbres="LEU Z 392 " pdbres="GCP Z 401 " 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 Time building chain proxies: 58.29, per 1000 atoms: 0.38 Number of scatterers: 154412 At special positions: 0 Unit cell: (280.44, 268.96, 238.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 175 16.00 P 4808 15.00 O 42626 8.00 N 28699 7.00 C 78104 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=0, symmetry=0 Time building additional restraints: 60.55 Conformation dependent library (CDL) restraints added in 7.3 seconds 12914 Ramachandran restraints generated. 6457 Oldfield, 0 Emsley, 6457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12040 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: 201 helices and 73 sheets defined 38.3% alpha, 17.4% beta 1459 base pairs and 2890 stacking pairs defined. Time for finding SS restraints: 77.02 Creating SS restraints... Processing helix chain '04' and resid 10 through 16 removed outlier: 7.443A pdb=" N HIS04 14 " --> pdb=" O PRO04 10 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL04 15 " --> pdb=" O GLY04 11 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL04 16 " --> pdb=" O ARG04 12 " (cutoff:3.500A) No H-bonds generated for 'chain '04' and resid 10 through 16' Processing helix chain '04' and resid 29 through 34 removed outlier: 4.418A pdb=" N LEU04 33 " --> pdb=" O PHE04 29 " (cutoff:3.500A) removed outlier: 5.500A 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: 3.901A 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: 4.960A pdb=" N ALA04 210 " --> pdb=" O LYS04 206 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG04 211 " --> pdb=" O ALA04 207 " (cutoff:3.500A) Processing helix chain '04' and resid 220 through 225 removed outlier: 3.803A pdb=" N MET04 224 " --> pdb=" O ARG04 220 " (cutoff:3.500A) removed outlier: 5.346A 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: 6.416A pdb=" N ASP04 263 " --> pdb=" O ASN04 259 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N LYS04 264 " --> pdb=" O LYS04 260 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N PHE04 265 " --> pdb=" O ARG04 261 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N VAL04 267 " --> pdb=" O ASP04 263 " (cutoff:3.500A) Processing helix chain '04' and resid 196 through 201 removed outlier: 4.104A pdb=" N MET04 200 " --> pdb=" O ALA04 197 " (cutoff:3.500A) Processing helix chain '05' and resid 56 through 61 removed outlier: 7.944A pdb=" N THR05 61 " --> pdb=" O ALA05 57 " (cutoff:3.500A) Processing helix chain '05' and resid 62 through 72 removed outlier: 3.562A pdb=" N HIS05 67 " --> pdb=" O PRO05 63 " (cutoff:3.500A) Processing helix chain '05' and resid 98 through 105 removed outlier: 4.124A pdb=" N ALA05 102 " --> pdb=" O VAL05 98 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP05 103 " --> pdb=" O GLU05 99 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N VAL05 104 " --> pdb=" O LEU05 100 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LYS05 105 " --> pdb=" O PHE05 101 " (cutoff:3.500A) No H-bonds generated for 'chain '05' and resid 98 through 105' Processing helix chain '05' and resid 120 through 125 Processing helix chain '05' and resid 39 through 44 Processing helix chain '06' and resid 15 through 20 Processing helix chain '06' and resid 24 through 41 removed outlier: 3.561A pdb=" N ALA06 39 " --> pdb=" O TYR06 35 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG06 40 " --> pdb=" O ALA06 36 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N GLN06 41 " --> pdb=" O ALA06 37 " (cutoff:3.500A) Processing helix chain '06' and resid 97 through 116 removed outlier: 3.646A pdb=" N ARG06 114 " --> pdb=" O SER06 110 " (cutoff:3.500A) Processing helix chain '06' and resid 130 through 142 removed outlier: 3.616A pdb=" N GLN06 136 " --> pdb=" O LYS06 132 " (cutoff:3.500A) Processing helix chain '06' and resid 154 through 163 removed outlier: 3.752A pdb=" N ARG06 162 " --> pdb=" O PHE06 158 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ASN06 163 " --> pdb=" O LEU06 159 " (cutoff:3.500A) Processing helix chain '06' and resid 176 through 184 removed outlier: 3.830A pdb=" N LEU06 180 " --> pdb=" O ASP06 176 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE06 181 " --> pdb=" O PRO06 177 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ASP06 184 " --> pdb=" O LEU06 180 " (cutoff:3.500A) Processing helix chain '06' and resid 189 through 201 removed outlier: 3.647A pdb=" N LYS06 194 " --> pdb=" O ALA06 190 " (cutoff:3.500A) Processing helix chain '07' and resid 1 through 20 removed outlier: 3.749A pdb=" N ASP07 9 " --> pdb=" O ASP07 5 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N VAL07 12 " --> pdb=" O LYS07 8 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS07 13 " --> pdb=" O ASP07 9 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR07 17 " --> pdb=" O LYS07 13 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU07 18 " --> pdb=" O LYS07 14 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE07 19 " --> pdb=" O LEU07 15 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN07 20 " --> pdb=" O MET07 16 " (cutoff:3.500A) Processing helix chain '07' and resid 41 through 46 removed outlier: 3.609A pdb=" N ASP07 45 " --> pdb=" O GLU07 41 " (cutoff:3.500A) removed outlier: 3.923A 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: 3.721A pdb=" N LEU07 56 " --> pdb=" O ALA07 52 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA07 58 " --> pdb=" O ALA07 54 " (cutoff:3.500A) Processing helix chain '07' and resid 92 through 110 removed outlier: 4.226A pdb=" N TRP07 96 " --> pdb=" O GLY07 92 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE07 105 " --> pdb=" O ARG07 101 " (cutoff:3.500A) removed outlier: 4.741A 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: 6.621A pdb=" N VAL07 145 " --> pdb=" O ASP07 141 " (cutoff:3.500A) removed outlier: 5.840A 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: 3.954A pdb=" N ALA07 167 " --> pdb=" O GLU07 163 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU07 168 " --> pdb=" O GLU07 164 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU07 169 " --> pdb=" O GLY07 165 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA07 171 " --> pdb=" O ALA07 167 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N PHE07 172 " --> pdb=" O LEU07 168 " (cutoff:3.500A) Processing helix chain '07' and resid 133 through 138 removed outlier: 3.848A pdb=" N ILE07 136 " --> pdb=" O GLU07 133 " (cutoff:3.500A) Proline residue: 07 138 - end of helix Processing helix chain '08' and resid 1 through 7 removed outlier: 4.266A 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: 3.543A pdb=" N ALA08 64 " --> pdb=" O GLY08 60 " (cutoff:3.500A) Processing helix chain '08' and resid 136 through 152 removed outlier: 3.657A pdb=" N GLN08 142 " --> pdb=" O GLN08 138 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR08 150 " --> pdb=" O ASP08 146 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ARG08 151 " --> pdb=" O LEU08 147 " (cutoff:3.500A) Processing helix chain '09' and resid 22 through 29 removed outlier: 3.564A pdb=" N PHE09 29 " --> pdb=" O TYR09 25 " (cutoff:3.500A) Processing helix chain '09' and resid 40 through 50 removed outlier: 3.564A pdb=" N GLU09 45 " --> pdb=" O LYS09 41 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ALA09 49 " --> pdb=" O GLU09 45 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG09 50 " --> pdb=" O PHE09 46 " (cutoff:3.500A) Processing helix chain '09' and resid 53 through 72 removed outlier: 5.599A pdb=" N LYS09 57 " --> pdb=" O GLU09 53 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA09 59 " --> pdb=" O GLU09 55 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL09 61 " --> pdb=" O LYS09 57 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU09 70 " --> pdb=" O ASN09 66 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS09 71 " --> pdb=" O ALA09 67 " (cutoff:3.500A) Processing helix chain '09' and resid 95 through 107 removed outlier: 3.918A pdb=" N ILE09 99 " --> pdb=" O GLY09 95 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA09 102 " --> pdb=" O ASP09 98 " (cutoff:3.500A) Processing helix chain '10' and resid 3 through 21 removed outlier: 3.719A pdb=" N GLN10 9 " --> pdb=" O LEU10 5 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU10 17 " --> pdb=" O ALA10 13 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL10 18 " --> pdb=" O GLU10 14 " (cutoff:3.500A) Processing helix chain '10' and resid 33 through 48 removed outlier: 3.541A pdb=" N GLU10 40 " --> pdb=" O ASP10 36 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU10 41 " --> pdb=" O LYS10 37 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ARG10 42 " --> pdb=" O MET10 38 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA10 44 " --> pdb=" O GLU10 40 " (cutoff:3.500A) Processing helix chain '10' and resid 62 through 68 removed outlier: 4.061A pdb=" N GLY10 66 " --> pdb=" O ARG10 62 " (cutoff:3.500A) Proline residue: 10 68 - end of helix Processing helix chain '10' and resid 73 through 79 removed outlier: 4.656A pdb=" N VAL10 77 " --> pdb=" O LYS10 73 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY10 78 " --> pdb=" O ASP10 74 " (cutoff:3.500A) Proline residue: 10 79 - end of helix No H-bonds generated for 'chain '10' and resid 73 through 79' Processing helix chain '10' and resid 95 through 106 removed outlier: 4.543A pdb=" N PHE10 99 " --> pdb=" O LEU10 95 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ALA10 100 " --> pdb=" O PHE10 96 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ASN10 103 " --> pdb=" O PHE10 99 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ALA10 104 " --> pdb=" O ALA10 100 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS10 105 " --> pdb=" O LYS10 101 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE10 106 " --> pdb=" O ALA10 102 " (cutoff:3.500A) Processing helix chain '10' and resid 109 through 114 removed outlier: 6.689A pdb=" N ALA10 112 " --> pdb=" O LYS10 109 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE10 113 " --> pdb=" O ALA10 110 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU10 114 " --> pdb=" O ALA10 111 " (cutoff:3.500A) No H-bonds generated for 'chain '10' and resid 109 through 114' Processing helix chain '11' and resid 23 through 31 removed outlier: 4.824A pdb=" N LEU11 27 " --> pdb=" O VAL11 23 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N GLN11 30 " --> pdb=" O ALA11 26 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY11 31 " --> pdb=" O LEU11 27 " (cutoff:3.500A) Processing helix chain '11' and resid 35 through 48 removed outlier: 4.805A pdb=" N ALA11 40 " --> pdb=" O GLU11 36 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN11 42 " --> pdb=" O CYS11 38 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA11 43 " --> pdb=" O LYS11 39 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR11 45 " --> pdb=" O PHE11 41 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER11 47 " --> pdb=" O ALA11 43 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ILE11 48 " --> pdb=" O LYS11 44 " (cutoff:3.500A) Processing helix chain '11' and resid 74 through 83 removed outlier: 3.548A pdb=" N LYS11 80 " --> pdb=" O ALA11 76 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS11 81 " --> pdb=" O VAL11 77 " (cutoff:3.500A) Processing helix chain '11' and resid 101 through 114 removed outlier: 3.967A pdb=" N THR11 111 " --> pdb=" O GLU11 107 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA11 114 " --> pdb=" O GLN11 110 " (cutoff:3.500A) Processing helix chain '11' and resid 120 through 136 removed outlier: 4.004A pdb=" N SER11 127 " --> pdb=" O ALA11 123 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG11 133 " --> pdb=" O GLU11 129 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER11 134 " --> pdb=" O GLY11 130 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET11 135 " --> pdb=" O THR11 131 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY11 136 " --> pdb=" O ALA11 132 " (cutoff:3.500A) Processing helix chain '12' and resid 7 through 12 removed outlier: 5.928A pdb=" N LYS12 12 " --> pdb=" O PRO12 8 " (cutoff:3.500A) Processing helix chain '12' and resid 24 through 38 removed outlier: 3.647A pdb=" N GLU12 31 " --> pdb=" O ARG12 27 " (cutoff:3.500A) Processing helix chain '12' and resid 88 through 96 Processing helix chain '12' and resid 97 through 109 removed outlier: 4.523A pdb=" N ILE12 101 " --> pdb=" O PRO12 97 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS12 106 " --> pdb=" O GLU12 102 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N MET12 108 " --> pdb=" O ALA12 104 " (cutoff:3.500A) Processing helix chain '12' and resid 112 through 123 removed outlier: 3.553A pdb=" N ARG12 120 " --> pdb=" O ARG12 116 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS12 121 " --> pdb=" O ALA12 117 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU12 122 " --> pdb=" O MET12 118 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N LYS12 123 " --> pdb=" O PHE12 119 " (cutoff:3.500A) Processing helix chain '12' and resid 67 through 72 removed outlier: 4.307A pdb=" N LYS12 72 " --> pdb=" O ASN12 67 " (cutoff:3.500A) No H-bonds generated for 'chain '12' and resid 67 through 72' Processing helix chain '13' and resid 109 through 120 removed outlier: 6.382A pdb=" N MET13 113 " --> pdb=" O SER13 109 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N LYS13 114 " --> pdb=" O GLU13 110 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE13 115 " --> pdb=" O LYS13 111 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE13 116 " --> pdb=" O PHE13 112 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER13 117 " --> pdb=" O MET13 113 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU13 118 " --> pdb=" O LYS13 114 " (cutoff:3.500A) Proline residue: 13 120 - end of helix Processing helix chain '14' and resid 37 through 42 removed outlier: 3.741A pdb=" N ARG14 41 " --> pdb=" O GLY14 37 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N SER14 42 " --> pdb=" O GLN14 38 " (cutoff:3.500A) No H-bonds generated for 'chain '14' and resid 37 through 42' Processing helix chain '14' and resid 56 through 61 removed outlier: 3.630A pdb=" N LEU14 61 " --> pdb=" O LEU14 57 " (cutoff:3.500A) Processing helix chain '14' and resid 68 through 75 removed outlier: 3.837A pdb=" N ALA14 72 " --> pdb=" O SER14 68 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE14 73 " --> pdb=" O ARG14 69 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR14 74 " --> pdb=" O LYS14 70 " (cutoff:3.500A) removed outlier: 5.611A 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: 3.965A pdb=" N LEU14 82 " --> pdb=" O ARG14 78 " (cutoff:3.500A) removed outlier: 4.635A 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 93 through 99 removed outlier: 6.846A pdb=" N ALA14 97 " --> pdb=" O ASN14 93 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA14 98 " --> pdb=" O THR14 94 " (cutoff:3.500A) Processing helix chain '14' and resid 128 through 139 removed outlier: 3.860A pdb=" N ALA14 133 " --> pdb=" O LYS14 129 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA14 134 " --> pdb=" O GLY14 130 " (cutoff:3.500A) Processing helix chain '15' and resid 42 through 58 removed outlier: 3.648A pdb=" N ALA15 56 " --> pdb=" O ALA15 52 " (cutoff:3.500A) Processing helix chain '15' and resid 110 through 125 removed outlier: 3.826A pdb=" N GLU15 115 " --> pdb=" O GLU15 111 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS15 118 " --> pdb=" O ARG15 114 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS15 123 " --> pdb=" O LEU15 119 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU15 124 " --> pdb=" O ALA15 120 " (cutoff:3.500A) Proline residue: 15 125 - end of helix Processing helix chain '16' and resid 13 through 32 removed outlier: 3.686A pdb=" N PHE16 21 " --> pdb=" O ARG16 17 " (cutoff:3.500A) Processing helix chain '16' and resid 38 through 58 removed outlier: 3.640A pdb=" N GLU16 43 " --> pdb=" O PRO16 39 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG16 45 " --> pdb=" O ALA16 41 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ARG16 46 " --> pdb=" O LYS16 42 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL16 47 " --> pdb=" O GLU16 43 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU16 49 " --> pdb=" O ARG16 45 " (cutoff:3.500A) Proline residue: 16 50 - end of helix removed outlier: 4.940A pdb=" N THR16 57 " --> pdb=" O THR16 53 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ASP16 58 " --> pdb=" O LEU16 54 " (cutoff:3.500A) Processing helix chain '16' and resid 59 through 71 removed outlier: 4.001A pdb=" N ARG16 63 " --> pdb=" O SER16 59 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N THR16 70 " --> pdb=" O ALA16 66 " (cutoff:3.500A) Processing helix chain '16' and resid 72 through 88 removed outlier: 3.799A pdb=" N VAL16 76 " --> pdb=" O ASP16 72 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N PHE16 80 " --> pdb=" O VAL16 76 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASN16 81 " --> pdb=" O ALA16 77 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N LEU16 83 " --> pdb=" O LEU16 79 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N GLY16 84 " --> pdb=" O PHE16 80 " (cutoff:3.500A) Proline residue: 16 85 - end of helix removed outlier: 3.714A pdb=" N ALA16 88 " --> pdb=" O GLY16 84 " (cutoff:3.500A) Processing helix chain '17' and resid 2 through 22 removed outlier: 3.597A pdb=" N ARG17 7 " --> pdb=" O LYS17 3 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ARG17 13 " --> pdb=" O ARG17 9 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ALA17 14 " --> pdb=" O ARG17 10 " (cutoff:3.500A) Processing helix chain '17' and resid 55 through 62 removed outlier: 5.007A pdb=" N GLN17 61 " --> pdb=" O ALA17 57 " (cutoff:3.500A) Processing helix chain '17' and resid 67 through 86 removed outlier: 3.550A pdb=" N VAL17 74 " --> pdb=" O ALA17 70 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU17 83 " --> pdb=" O ALA17 79 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY17 86 " --> pdb=" O ALA17 82 " (cutoff:3.500A) Processing helix chain '17' and resid 101 through 114 removed outlier: 3.830A pdb=" N ALA17 113 " --> pdb=" O ALA17 109 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY17 114 " --> pdb=" O ALA17 110 " (cutoff:3.500A) Processing helix chain '18' and resid 1 through 12 removed outlier: 3.681A pdb=" N GLN18 6 " --> pdb=" O ASN18 2 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU18 10 " --> pdb=" O GLN18 6 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLN18 11 " --> pdb=" O LEU18 7 " (cutoff:3.500A) Processing helix chain '18' and resid 96 through 103 removed outlier: 4.359A pdb=" N ARG18 100 " --> pdb=" O LEU18 96 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLU18 101 " --> pdb=" O TYR18 97 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG18 102 " --> pdb=" O TYR18 98 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N THR18 103 " --> pdb=" O LEU18 99 " (cutoff:3.500A) No H-bonds generated for 'chain '18' and resid 96 through 103' Processing helix chain '18' and resid 104 through 109 removed outlier: 6.012A pdb=" N ILE18 109 " --> pdb=" O LYS18 105 " (cutoff:3.500A) Processing helix chain '19' and resid 5 through 21 removed outlier: 4.563A pdb=" N ALA19 9 " --> pdb=" O ARG19 5 " (cutoff:3.500A) Processing helix chain '19' and resid 25 through 30 removed outlier: 4.023A pdb=" N ARG19 29 " --> pdb=" O GLY19 25 " (cutoff:3.500A) Processing helix chain '19' and resid 38 through 72 removed outlier: 3.661A pdb=" N ARG19 49 " --> pdb=" O ALA19 45 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ARG19 50 " --> pdb=" O TYR19 46 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LYS19 53 " --> pdb=" O ARG19 49 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG19 54 " --> pdb=" O ARG19 50 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG19 57 " --> pdb=" O LYS19 53 " (cutoff:3.500A) Processing helix chain '19' and resid 74 through 86 removed outlier: 3.545A pdb=" N ASN19 80 " --> pdb=" O SER19 76 " (cutoff:3.500A) Processing helix chain '19' and resid 90 through 101 removed outlier: 3.599A pdb=" N PHE19 100 " --> pdb=" O ASP19 96 " (cutoff:3.500A) Processing helix chain '19' and resid 102 through 117 removed outlier: 3.504A pdb=" N ALA19 107 " --> pdb=" O VAL19 103 " (cutoff:3.500A) Processing helix chain '21' and resid 13 through 25 removed outlier: 4.030A pdb=" N VAL21 17 " --> pdb=" O SER21 13 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL21 20 " --> pdb=" O LYS21 16 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU21 23 " --> pdb=" O LEU21 19 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE21 24 " --> pdb=" O VAL21 20 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG21 25 " --> pdb=" O ALA21 21 " (cutoff:3.500A) Processing helix chain '21' and resid 28 through 39 removed outlier: 3.815A pdb=" N ASP21 34 " --> pdb=" O SER21 30 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE21 35 " --> pdb=" O GLN21 31 " (cutoff:3.500A) Processing helix chain '21' and resid 41 through 62 removed outlier: 3.587A pdb=" N VAL21 45 " --> pdb=" O LYS21 41 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS21 49 " --> pdb=" O VAL21 45 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN21 61 " --> pdb=" O ASN21 57 " (cutoff:3.500A) Processing helix chain '22' and resid 1 through 11 removed outlier: 4.105A pdb=" N LEU22 7 " --> pdb=" O ARG22 3 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU22 8 " --> pdb=" O GLU22 4 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LYS22 9 " --> pdb=" O GLU22 5 " (cutoff:3.500A) removed outlier: 4.162A 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: 3.582A pdb=" N LYS22 49 " --> pdb=" O ALA22 45 " (cutoff:3.500A) Processing helix chain '23' and resid 65 through 70 removed outlier: 3.802A pdb=" N VAL23 69 " --> pdb=" O GLN23 65 " (cutoff:3.500A) removed outlier: 5.245A 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: 3.550A pdb=" N SER24 17 " --> pdb=" O GLY24 13 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA24 23 " --> pdb=" O ARG24 19 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ASN24 24 " --> pdb=" O LEU24 20 " (cutoff:3.500A) Processing helix chain '24' and resid 43 through 52 removed outlier: 4.137A pdb=" N VAL24 47 " --> pdb=" O ASP24 43 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ALA24 52 " --> pdb=" O MET24 48 " (cutoff:3.500A) Processing helix chain '24' and resid 53 through 59 removed outlier: 4.102A pdb=" N TYR24 57 " --> pdb=" O LYS24 53 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER24 58 " --> pdb=" O ALA24 54 " (cutoff:3.500A) Processing helix chain '26' and resid 51 through 61 removed outlier: 3.711A pdb=" N MET26 55 " --> pdb=" O SER26 51 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG26 56 " --> pdb=" O ALA26 52 " (cutoff:3.500A) Processing helix chain '26' and resid 62 through 74 removed outlier: 3.616A pdb=" N ARG26 71 " --> pdb=" O LEU26 67 " (cutoff:3.500A) Processing helix chain '27' and resid 1 through 7 removed outlier: 4.151A pdb=" N LEU27 6 " --> pdb=" O LYS27 2 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ARG27 7 " --> pdb=" O ALA27 3 " (cutoff:3.500A) Processing helix chain '27' and resid 9 through 35 removed outlier: 3.802A pdb=" N ARG27 23 " --> pdb=" O LEU27 19 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU27 24 " --> pdb=" O ASN27 20 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLN27 25 " --> pdb=" O LEU27 21 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N PHE27 26 " --> pdb=" O LEU27 22 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU27 28 " --> pdb=" O GLU27 24 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG27 29 " --> pdb=" O GLN27 25 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN27 31 " --> pdb=" O ASN27 27 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER27 34 " --> pdb=" O MET27 30 " (cutoff:3.500A) Processing helix chain '27' and resid 40 through 62 removed outlier: 3.509A pdb=" N LYS27 44 " --> pdb=" O SER27 40 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN27 45 " --> pdb=" O HIS27 41 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG27 47 " --> pdb=" O LEU27 43 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLY27 62 " --> pdb=" O ASN27 58 " (cutoff:3.500A) Processing helix chain '28' and resid 16 through 27 Processing helix chain '28' and resid 40 through 51 Processing helix chain '29' and resid 43 through 52 removed outlier: 5.317A pdb=" N GLN29 48 " --> pdb=" O PHE29 44 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP29 50 " --> pdb=" O GLY29 46 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL29 51 " --> pdb=" O LYS29 47 " (cutoff:3.500A) Processing helix chain '29' and resid 55 through 65 removed outlier: 5.654A pdb=" N ARG29 59 " --> pdb=" O GLY29 55 " (cutoff:3.500A) Processing helix chain '30' and resid 8 through 20 removed outlier: 3.506A pdb=" N ARG30 16 " --> pdb=" O ARG30 12 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N HIS30 18 " --> pdb=" O MET30 14 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ASP30 19 " --> pdb=" O ARG30 15 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA30 20 " --> pdb=" O ARG30 16 " (cutoff:3.500A) Processing helix chain '32' and resid 8 through 16 Processing helix chain '32' and resid 17 through 24 removed outlier: 3.626A pdb=" N ALA32 23 " --> pdb=" O ARG32 19 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N THR32 24 " --> pdb=" O ALA32 20 " (cutoff:3.500A) Processing helix chain '32' and resid 25 through 38 removed outlier: 3.594A pdb=" N GLN32 29 " --> pdb=" O LYS32 25 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG32 35 " --> pdb=" O LEU32 31 " (cutoff:3.500A) Processing helix chain '33' and resid 6 through 14 removed outlier: 3.824A pdb=" N LYS33 11 " --> pdb=" O ARG33 7 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ARG33 12 " --> pdb=" O GLY33 8 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LYS33 14 " --> pdb=" O ALA33 10 " (cutoff:3.500A) Processing helix chain '33' and resid 31 through 36 removed outlier: 5.230A pdb=" N LYS33 35 " --> pdb=" O ILE33 31 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ALA33 36 " --> pdb=" O LEU33 32 " (cutoff:3.500A) No H-bonds generated for 'chain '33' and resid 31 through 36' Processing helix chain '33' and resid 37 through 45 Proline residue: 33 45 - end of helix Processing helix chain '33' and resid 50 through 62 removed outlier: 4.410A pdb=" N GLY33 55 " --> pdb=" O LYS33 51 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LEU33 56 " --> pdb=" O GLY33 52 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL33 57 " --> pdb=" O ASP33 53 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA33 59 " --> pdb=" O GLY33 55 " (cutoff:3.500A) Proline residue: 33 62 - end of helix Processing helix chain '34' and resid 30 through 35 removed outlier: 4.198A pdb=" N LYS34 34 " --> pdb=" O GLU34 30 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N GLN34 35 " --> pdb=" O PRO34 31 " (cutoff:3.500A) No H-bonds generated for 'chain '34' and resid 30 through 35' Processing helix chain 'B' and resid 42 through 63 Proline residue: B 47 - end of helix removed outlier: 3.585A pdb=" N ASN B 50 " --> pdb=" O VAL B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 87 removed outlier: 5.871A pdb=" N SER B 76 " --> pdb=" O LYS B 72 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N GLU B 77 " --> pdb=" O ARG B 73 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ALA B 78 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 79 " --> pdb=" O ALA B 75 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS B 80 " --> pdb=" O SER B 76 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N CYS B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 122 removed outlier: 3.901A pdb=" N GLN B 108 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER B 109 " --> pdb=" O THR B 105 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR B 118 " --> pdb=" O LYS B 114 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN B 121 " --> pdb=" O GLU B 117 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASP B 122 " --> pdb=" O THR B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 147 removed outlier: 3.516A pdb=" N LYS B 142 " --> pdb=" O ARG B 138 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN B 145 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N SER B 146 " --> pdb=" O LYS B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 178 removed outlier: 4.890A pdb=" N LEU B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 225 removed outlier: 3.524A pdb=" N THR B 210 " --> pdb=" O ILE B 206 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU B 211 " --> pdb=" O ARG B 207 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG B 221 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N SER B 225 " --> pdb=" O ARG B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 153 removed outlier: 3.660A pdb=" N LYS B 151 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP B 152 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 11 removed outlier: 3.737A pdb=" N ARG C 10 " --> pdb=" O PRO C 6 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU C 11 " --> pdb=" O ASN C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 47 removed outlier: 4.684A pdb=" N ALA C 29 " --> pdb=" O THR C 25 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N ASP C 30 " --> pdb=" O LYS C 26 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP C 33 " --> pdb=" O ALA C 29 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA C 47 " --> pdb=" O THR C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 77 Processing helix chain 'C' and resid 80 through 94 removed outlier: 3.557A pdb=" N LYS C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE C 93 " --> pdb=" O VAL C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 126 removed outlier: 3.745A pdb=" N GLN C 122 " --> pdb=" O SER C 118 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU C 124 " --> pdb=" O THR C 120 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG C 126 " --> pdb=" O GLN C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 removed outlier: 3.651A pdb=" N LEU C 143 " --> pdb=" O ASN C 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 15 removed outlier: 4.088A pdb=" N LEU D 10 " --> pdb=" O PRO D 6 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N SER D 11 " --> pdb=" O LYS D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 65 removed outlier: 3.689A pdb=" N GLU D 56 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG D 61 " --> pdb=" O LYS D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 removed outlier: 3.548A pdb=" N ASN D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG D 80 " --> pdb=" O LYS D 76 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LYS D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 96 removed outlier: 3.997A pdb=" N LEU D 90 " --> pdb=" O GLY D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 105 removed outlier: 3.536A pdb=" N MET D 104 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY D 105 " --> pdb=" O VAL D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 120 removed outlier: 4.110A pdb=" N LYS D 120 " --> pdb=" O LEU D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 165 removed outlier: 6.375A pdb=" N LYS D 155 " --> pdb=" O GLN D 151 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ALA D 156 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU D 160 " --> pdb=" O ALA D 156 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ALA D 161 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU D 162 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN D 163 " --> pdb=" O GLU D 159 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N GLU D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 191 removed outlier: 5.368A pdb=" N SER D 191 " --> pdb=" O ARG D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 205 removed outlier: 4.670A pdb=" N ILE D 199 " --> pdb=" O ASN D 195 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU D 201 " --> pdb=" O HIS D 197 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS D 205 " --> pdb=" O GLU D 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 70 removed outlier: 3.656A pdb=" N GLN E 60 " --> pdb=" O PRO E 56 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU E 64 " --> pdb=" O GLN E 60 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS E 65 " --> pdb=" O LYS E 61 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA E 66 " --> pdb=" O ALA E 62 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG E 68 " --> pdb=" O GLU E 64 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET E 70 " --> pdb=" O ALA E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 118 removed outlier: 6.307A pdb=" N ALA E 112 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL E 113 " --> pdb=" O ALA E 109 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL E 116 " --> pdb=" O ALA E 112 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA E 117 " --> pdb=" O VAL E 113 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY E 118 " --> pdb=" O LEU E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 147 removed outlier: 3.518A pdb=" N VAL E 136 " --> pdb=" O PRO E 132 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA E 138 " --> pdb=" O ASN E 134 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP E 141 " --> pdb=" O ARG E 137 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ASN E 147 " --> pdb=" O LEU E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 156 removed outlier: 3.542A pdb=" N VAL E 152 " --> pdb=" O SER E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 165 removed outlier: 4.020A pdb=" N LEU E 164 " --> pdb=" O VAL E 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 19 removed outlier: 4.406A pdb=" N GLU F 16 " --> pdb=" O PRO F 12 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N GLN F 17 " --> pdb=" O ASP F 13 " (cutoff:3.500A) Proline residue: F 19 - end of helix Processing helix chain 'F' and resid 20 through 33 removed outlier: 3.662A pdb=" N GLU F 33 " --> pdb=" O ILE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 81 removed outlier: 3.615A pdb=" N ILE F 71 " --> pdb=" O PRO F 67 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR F 76 " --> pdb=" O ASP F 72 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG F 79 " --> pdb=" O GLU F 75 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASN F 81 " --> pdb=" O THR F 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 30 removed outlier: 3.758A pdb=" N ALA G 23 " --> pdb=" O SER G 19 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS G 24 " --> pdb=" O GLU G 20 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE G 25 " --> pdb=" O LEU G 21 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN G 27 " --> pdb=" O ALA G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 54 removed outlier: 3.693A pdb=" N ILE G 41 " --> pdb=" O THR G 37 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR G 43 " --> pdb=" O GLU G 39 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU G 46 " --> pdb=" O VAL G 42 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLN G 51 " --> pdb=" O GLU G 47 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG G 52 " --> pdb=" O THR G 48 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY G 54 " --> pdb=" O ALA G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 69 removed outlier: 3.661A pdb=" N VAL G 63 " --> pdb=" O GLU G 59 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ALA G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASN G 67 " --> pdb=" O VAL G 63 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 111 removed outlier: 4.137A pdb=" N ALA G 97 " --> pdb=" O VAL G 93 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TRP G 102 " --> pdb=" O LEU G 98 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE G 103 " --> pdb=" O ALA G 99 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS G 109 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG G 110 " --> pdb=" O ALA G 106 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N GLY G 111 " --> pdb=" O ALA G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 129 removed outlier: 3.604A pdb=" N ALA G 120 " --> pdb=" O ALA G 116 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU G 128 " --> pdb=" O SER G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 147 removed outlier: 4.731A pdb=" N GLU G 145 " --> pdb=" O HIS G 141 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA G 146 " --> pdb=" O ARG G 142 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 20 Processing helix chain 'H' and resid 29 through 43 removed outlier: 3.845A pdb=" N GLU H 41 " --> pdb=" O ASN H 37 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU H 42 " --> pdb=" O VAL H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 119 removed outlier: 3.714A pdb=" N GLN H 117 " --> pdb=" O ARG H 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 38 removed outlier: 4.230A pdb=" N PHE I 38 " --> pdb=" O LEU I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 53 Proline residue: I 50 - end of helix removed outlier: 3.881A pdb=" N LEU I 53 " --> pdb=" O GLN I 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 46 through 53' Processing helix chain 'I' and resid 70 through 86 removed outlier: 3.633A pdb=" N ILE I 78 " --> pdb=" O GLN I 74 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR I 83 " --> pdb=" O ARG I 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 101 removed outlier: 5.417A pdb=" N GLU I 96 " --> pdb=" O SER I 92 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS I 99 " --> pdb=" O SER I 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 30 removed outlier: 3.813A pdb=" N ASP J 19 " --> pdb=" O HIS J 15 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN J 20 " --> pdb=" O ARG J 16 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA J 21 " --> pdb=" O LEU J 17 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE J 25 " --> pdb=" O ALA J 21 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA J 29 " --> pdb=" O ILE J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 88 removed outlier: 4.014A pdb=" N ASP J 85 " --> pdb=" O GLU J 81 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ALA J 86 " --> pdb=" O LYS J 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 50 removed outlier: 3.993A pdb=" N GLY K 50 " --> pdb=" O ALA K 46 " (cutoff:3.500A) Processing helix chain 'K' and resid 53 through 58 removed outlier: 4.294A pdb=" N SER K 57 " --> pdb=" O GLY K 53 " (cutoff:3.500A) removed outlier: 4.858A 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 73 removed outlier: 3.527A pdb=" N ASP K 71 " --> pdb=" O GLU K 67 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ALA K 72 " --> pdb=" O ARG K 68 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N VAL K 73 " --> pdb=" O CYS K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 103 removed outlier: 5.610A pdb=" N THR K 95 " --> pdb=" O GLY K 91 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ILE K 96 " --> pdb=" O ARG K 92 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG K 97 " --> pdb=" O GLU K 93 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA K 98 " --> pdb=" O SER K 94 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU K 99 " --> pdb=" O THR K 95 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLY K 103 " --> pdb=" O LEU K 99 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 10 Proline residue: L 10 - end of helix Processing helix chain 'L' and resid 112 through 117 removed outlier: 5.038A pdb=" N TYR L 116 " --> pdb=" O ALA L 112 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 20 removed outlier: 4.143A pdb=" N THR M 19 " --> pdb=" O VAL M 15 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER M 20 " --> pdb=" O ILE M 16 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 37 removed outlier: 3.516A pdb=" N SER M 29 " --> pdb=" O GLY M 25 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA M 35 " --> pdb=" O ALA M 31 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA M 36 " --> pdb=" O ILE M 32 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 48 removed outlier: 5.097A pdb=" N SER M 48 " --> pdb=" O ILE M 44 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 63 removed outlier: 3.597A pdb=" N ASP M 53 " --> pdb=" O GLU M 49 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N THR M 54 " --> pdb=" O GLY M 50 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP M 57 " --> pdb=" O ASP M 53 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU M 58 " --> pdb=" O THR M 54 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS M 61 " --> pdb=" O ASP M 57 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N PHE M 62 " --> pdb=" O GLU M 58 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N VAL M 63 " --> pdb=" O VAL M 59 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 83 removed outlier: 3.634A pdb=" N ARG M 69 " --> pdb=" O GLU M 65 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG M 70 " --> pdb=" O GLY M 66 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER M 75 " --> pdb=" O GLU M 71 " (cutoff:3.500A) Processing helix chain 'M' and resid 84 through 93 Processing helix chain 'M' and resid 105 through 110 Processing helix chain 'N' and resid 2 through 20 removed outlier: 3.542A pdb=" N ALA N 14 " --> pdb=" O VAL N 10 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR N 19 " --> pdb=" O LEU N 15 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE N 20 " --> pdb=" O ALA N 16 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 50 removed outlier: 5.126A pdb=" N GLN N 48 " --> pdb=" O VAL N 44 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THR N 49 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU N 50 " --> pdb=" O LYS N 46 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 90 removed outlier: 3.758A pdb=" N ARG N 84 " --> pdb=" O ARG N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 25 through 30 Processing helix chain 'O' and resid 3 through 15 removed outlier: 3.557A pdb=" N ILE O 10 " --> pdb=" O ALA O 6 " (cutoff:3.500A) Processing helix chain 'O' and resid 23 through 43 removed outlier: 3.629A pdb=" N ALA O 29 " --> pdb=" O GLU O 25 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY O 40 " --> pdb=" O ASN O 36 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N HIS O 41 " --> pdb=" O HIS O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 48 through 73 Processing helix chain 'O' and resid 74 through 85 removed outlier: 3.566A pdb=" N GLU O 82 " --> pdb=" O THR O 78 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG O 83 " --> pdb=" O GLN O 79 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 64 removed outlier: 3.506A pdb=" N GLN P 63 " --> pdb=" O HIS P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 79 Processing helix chain 'R' and resid 24 through 33 removed outlier: 4.241A pdb=" N LEU R 28 " --> pdb=" O ASP R 24 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN R 30 " --> pdb=" O ALA R 26 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N TYR R 31 " --> pdb=" O THR R 27 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE R 32 " --> pdb=" O LEU R 28 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N THR R 33 " --> pdb=" O LYS R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 45 removed outlier: 3.572A pdb=" N THR R 44 " --> pdb=" O PRO R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 47 through 65 Processing helix chain 'S' and resid 11 through 25 removed outlier: 3.525A pdb=" N GLU S 23 " --> pdb=" O GLU S 19 " (cutoff:3.500A) Processing helix chain 'S' and resid 69 through 75 removed outlier: 4.212A pdb=" N PHE S 73 " --> pdb=" O LYS S 69 " (cutoff:3.500A) Proline residue: S 75 - end of helix Processing helix chain 'T' and resid 6 through 41 removed outlier: 4.072A pdb=" N ALA T 10 " --> pdb=" O ALA T 6 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N HIS T 19 " --> pdb=" O LYS T 15 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE T 30 " --> pdb=" O MET T 26 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA T 40 " --> pdb=" O ALA T 36 " (cutoff:3.500A) Processing helix chain 'T' and resid 42 through 64 removed outlier: 3.747A pdb=" N GLN T 47 " --> pdb=" O LYS T 43 " (cutoff:3.500A) Proline residue: T 55 - end of helix removed outlier: 3.560A pdb=" N ARG T 59 " --> pdb=" O PRO T 55 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN T 60 " --> pdb=" O ILE T 56 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA T 61 " --> pdb=" O VAL T 57 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLY T 64 " --> pdb=" O GLN T 60 " (cutoff:3.500A) Processing helix chain 'T' and resid 67 through 86 removed outlier: 5.939A pdb=" N ALA T 71 " --> pdb=" O HIS T 67 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ALA T 72 " --> pdb=" O LYS T 68 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU T 78 " --> pdb=" O HIS T 74 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS T 84 " --> pdb=" O ALA T 80 " (cutoff:3.500A) Processing helix chain 'U' and resid 16 through 23 removed outlier: 4.045A pdb=" N ARG U 20 " --> pdb=" O ARG U 16 " (cutoff:3.500A) Processing helix chain 'U' and resid 25 through 33 removed outlier: 4.278A pdb=" N GLU U 30 " --> pdb=" O GLY U 26 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL U 31 " --> pdb=" O VAL U 27 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ARG U 33 " --> pdb=" O ALA U 29 " (cutoff:3.500A) Processing helix chain 'U' and resid 36 through 61 Proline residue: U 40 - end of helix removed outlier: 3.628A pdb=" N ALA U 47 " --> pdb=" O GLU U 43 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS U 53 " --> pdb=" O ALA U 49 " (cutoff:3.500A) Processing helix chain '03' and resid 7 through 16 removed outlier: 3.618A pdb=" N ILE03 11 " --> pdb=" O ARG03 7 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ARG03 12 " --> pdb=" O MET03 8 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ASP03 16 " --> pdb=" O ARG03 12 " (cutoff:3.500A) Processing helix chain '03' and resid 22 through 34 removed outlier: 3.761A pdb=" N ILE03 27 " --> pdb=" O ILE03 23 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ALA03 28 " --> pdb=" O ASN03 24 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU03 29 " --> pdb=" O GLU03 25 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU03 30 " --> pdb=" O ALA03 26 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LYS03 31 " --> pdb=" O ILE03 27 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU03 32 " --> pdb=" O ALA03 28 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU03 33 " --> pdb=" O LEU03 29 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ALA03 34 " --> pdb=" O LEU03 30 " (cutoff:3.500A) Processing helix chain '03' and resid 81 through 91 removed outlier: 3.942A pdb=" N ALA03 86 " --> pdb=" O ALA03 82 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA03 87 " --> pdb=" O ASN03 83 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LYS03 88 " --> pdb=" O ALA03 84 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ALA03 89 " --> pdb=" O GLU03 85 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA03 90 " --> pdb=" O ALA03 86 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY03 91 " --> pdb=" O ALA03 87 " (cutoff:3.500A) Processing helix chain '03' and resid 100 through 107 removed outlier: 3.963A pdb=" N ILE03 104 " --> pdb=" O LEU03 100 " (cutoff:3.500A) Processing helix chain '03' and resid 117 through 125 removed outlier: 3.832A pdb=" N MET03 121 " --> pdb=" O SER03 117 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ARG03 122 " --> pdb=" O PRO03 118 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N VAL03 123 " --> pdb=" O ASP03 119 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL03 124 " --> pdb=" O ALA03 120 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLY03 125 " --> pdb=" O MET03 121 " (cutoff:3.500A) No H-bonds generated for 'chain '03' and resid 117 through 125' Processing helix chain '03' and resid 126 through 135 removed outlier: 5.088A pdb=" N VAL03 130 " --> pdb=" O GLN03 126 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY03 132 " --> pdb=" O GLY03 128 " (cutoff:3.500A) Proline residue: 03 133 - end of helix Processing helix chain '03' and resid 148 through 159 removed outlier: 4.053A pdb=" N LYS03 154 " --> pdb=" O ALA03 150 " (cutoff:3.500A) Processing helix chain '03' and resid 181 through 200 removed outlier: 3.718A pdb=" N ALA03 191 " --> pdb=" O GLU03 187 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL03 194 " --> pdb=" O GLU03 190 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA03 195 " --> pdb=" O ALA03 191 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA03 199 " --> pdb=" O ALA03 195 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS03 200 " --> pdb=" O LEU03 196 " (cutoff:3.500A) Processing helix chain 'Z' and resid 23 through 39 removed outlier: 3.839A pdb=" N THR Z 32 " --> pdb=" O THR Z 28 " (cutoff:3.500A) Processing helix chain 'Z' and resid 45 through 51 removed outlier: 3.635A pdb=" N ASP Z 50 " --> pdb=" O PHE Z 46 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ASN Z 51 " --> pdb=" O ASP Z 47 " (cutoff:3.500A) Processing helix chain 'Z' and resid 52 through 59 Processing helix chain 'Z' and resid 87 through 99 removed outlier: 4.370A pdb=" N GLN Z 97 " --> pdb=" O THR Z 93 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET Z 98 " --> pdb=" O GLY Z 94 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ASP Z 99 " --> pdb=" O ALA Z 95 " (cutoff:3.500A) Processing helix chain 'Z' and resid 112 through 126 removed outlier: 3.685A pdb=" N GLY Z 122 " --> pdb=" O HIS Z 118 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY Z 126 " --> pdb=" O GLY Z 122 " (cutoff:3.500A) Processing helix chain 'Z' and resid 136 through 141 removed outlier: 3.731A pdb=" N VAL Z 140 " --> pdb=" O LYS Z 136 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ASP Z 141 " --> pdb=" O CYS Z 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 136 through 141' Processing helix chain 'Z' and resid 142 through 161 removed outlier: 3.511A pdb=" N GLU Z 152 " --> pdb=" O LEU Z 148 " (cutoff:3.500A) Processing helix chain 'Z' and resid 173 through 180 removed outlier: 3.854A pdb=" N ALA Z 177 " --> pdb=" O SER Z 173 " (cutoff:3.500A) Processing helix chain 'Z' and resid 182 through 198 removed outlier: 4.556A pdb=" N ALA Z 186 " --> pdb=" O ALA Z 182 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LYS Z 187 " --> pdb=" O GLU Z 183 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU Z 191 " --> pdb=" O LYS Z 187 " (cutoff:3.500A) Processing helix chain 'Z' and resid 282 through 287 removed outlier: 3.948A pdb=" N ILE Z 286 " --> pdb=" O LYS Z 282 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N GLU Z 287 " --> pdb=" O ARG Z 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 282 through 287' Processing sheet with id= 1, first strand: chain '04' and resid 79 through 82 removed outlier: 6.899A pdb=" N LEU04 92 " --> pdb=" O GLU04 78 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ILE04 73 " --> pdb=" O SER04 117 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N SER04 117 " --> pdb=" O ILE04 73 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP04 113 " --> pdb=" O VAL04 77 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '04' and resid 125 through 129 No H-bonds generated for sheet with id= 2 Processing sheet with id= 3, first strand: chain '04' and resid 137 through 140 removed outlier: 4.064A pdb=" N SER04 138 " --> pdb=" O ILE04 163 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE04 163 " --> pdb=" O SER04 138 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN04 162 " --> pdb=" O ARG04 174 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N THR04 172 " --> pdb=" O VAL04 164 " (cutoff:3.500A) removed outlier: 4.232A 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: 5.342A pdb=" N ASN04 89 " --> pdb=" O ALA04 105 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N GLU04 99 " --> pdb=" O TYR04 95 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain '05' and resid 3 through 6 Processing sheet with id= 6, first strand: chain '05' and resid 10 through 16 removed outlier: 4.389A pdb=" N GLY05 10 " --> pdb=" O VAL05 26 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N VAL05 20 " --> pdb=" O THR05 16 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG05 179 " --> pdb=" O LEU05 188 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain '05' and resid 79 through 84 removed outlier: 6.646A pdb=" N ARG05 46 " --> pdb=" O LEU05 84 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLN05 49 " --> pdb=" O THR05 35 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLN05 94 " --> pdb=" O VAL05 34 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain '06' and resid 1 through 5 removed outlier: 3.704A pdb=" N MET06 1 " --> pdb=" O VAL06 14 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N LEU06 5 " --> pdb=" O SER06 10 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N SER06 10 " --> pdb=" O LEU06 5 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain '06' and resid 117 through 120 removed outlier: 4.036A pdb=" N ASP06 168 " --> pdb=" O VAL06 146 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain '07' and resid 64 through 67 removed outlier: 3.603A pdb=" N GLY07 85 " --> pdb=" O THR07 67 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS07 32 " --> pdb=" O THR07 156 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLY07 38 " --> pdb=" O GLY07 150 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N GLY07 150 " --> pdb=" O GLY07 38 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU07 151 " --> pdb=" O VAL07 131 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain '08' and resid 15 through 18 removed outlier: 3.664A pdb=" N ARG08 34 " --> pdb=" O ILE08 23 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain '08' and resid 81 through 88 removed outlier: 6.429A pdb=" N THR08 128 " --> pdb=" O LEU08 88 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain '08' and resid 93 through 97 Processing sheet with id= 14, first strand: chain '09' and resid 2 through 6 removed outlier: 5.624A pdb=" N GLN09 2 " --> pdb=" O ALA09 39 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA09 39 " --> pdb=" O GLN09 2 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LYS09 35 " --> pdb=" O LEU09 6 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain '09' and resid 76 through 83 removed outlier: 5.750A pdb=" N GLU09 76 " --> pdb=" O LYS09 141 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE09 80 " --> pdb=" O ASN09 145 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain '10' and resid 24 through 28 removed outlier: 4.289A pdb=" N ALA10 25 " --> pdb=" O SER10 85 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER10 85 " --> pdb=" O ALA10 25 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL10 27 " --> pdb=" O ALA10 83 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain '11' and resid 6 through 12 removed outlier: 4.960A pdb=" N ALA11 6 " --> pdb=" O VAL11 60 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL11 60 " --> pdb=" O ALA11 6 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL11 56 " --> pdb=" O LEU11 10 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL11 12 " --> pdb=" O ILE11 54 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE11 54 " --> pdb=" O VAL11 12 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N THR11 67 " --> pdb=" O THR11 59 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain '12' and resid 52 through 56 Processing sheet with id= 19, first strand: chain '12' and resid 74 through 78 removed outlier: 3.596A pdb=" N LYS12 85 " --> pdb=" O HIS12 76 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N GLY12 83 " --> pdb=" O THR12 78 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain '13' and resid 18 through 21 removed outlier: 4.028A pdb=" N THR13 6 " --> pdb=" O CYS13 21 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ASN13 82 " --> pdb=" O MET13 7 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain '15' and resid 62 through 65 removed outlier: 4.272A pdb=" N TYR15 103 " --> pdb=" O LEU15 33 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU15 33 " --> pdb=" O LEU15 102 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS15 100 " --> pdb=" O ALA15 35 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain '15' and resid 30 through 36 removed outlier: 6.766A pdb=" N SER15 30 " --> pdb=" O LYS15 133 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LYS15 127 " --> pdb=" O VAL15 36 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain '16' and resid 33 through 37 removed outlier: 4.448A pdb=" N MET16 110 " --> pdb=" O CYS16 100 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain '17' and resid 35 through 41 removed outlier: 4.074A pdb=" N VAL17 28 " --> pdb=" O ASP17 93 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain '18' and resid 37 through 44 removed outlier: 6.220A pdb=" N THR18 24 " --> pdb=" O LYS18 86 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER18 82 " --> pdb=" O LYS18 28 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain '18' and resid 56 through 63 removed outlier: 7.962A pdb=" N SER18 56 " --> pdb=" O THR18 75 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain '20' and resid 11 through 15 removed outlier: 3.604A pdb=" N PHE20 5 " --> pdb=" O HIS20 12 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N TYR20 2 " --> pdb=" O ALA20 42 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain '20' and resid 18 through 22 removed outlier: 4.660A pdb=" N GLN20 18 " --> pdb=" O ILE20 98 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL20 96 " --> pdb=" O VAL20 20 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASP20 95 " --> pdb=" O VAL20 64 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LYS20 60 " --> pdb=" O THR20 99 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N VAL20 63 " --> pdb=" O GLU20 31 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLU20 31 " --> pdb=" O VAL20 63 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain '20' and resid 65 through 72 removed outlier: 3.663A pdb=" N ALA20 65 " --> pdb=" O ASP20 95 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLY20 67 " --> pdb=" O PHE20 93 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N GLN20 91 " --> pdb=" O GLY20 69 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N LYS20 71 " --> pdb=" O HIS20 89 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N HIS20 89 " --> pdb=" O LYS20 71 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain '21' and resid 4 through 8 removed outlier: 5.144A pdb=" N THR21 100 " --> pdb=" O GLY21 79 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain '21' and resid 80 through 88 removed outlier: 4.654A pdb=" N ARG21 92 " --> pdb=" O ARG21 88 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain '22' and resid 29 through 33 removed outlier: 3.606A pdb=" N VAL22 57 " --> pdb=" O THR22 86 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain '23' and resid 39 through 44 removed outlier: 4.551A pdb=" N ASN23 39 " --> pdb=" O ALA23 62 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain '23' and resid 82 through 86 Processing sheet with id= 35, first strand: chain '24' and resid 69 through 73 removed outlier: 6.739A pdb=" N PHE24 2 " --> pdb=" O VAL24 60 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA24 6 " --> pdb=" O VAL24 64 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ALA24 39 " --> pdb=" O ARG24 9 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU24 42 " --> pdb=" O PHE24 26 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE24 89 " --> pdb=" O PRO24 27 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain '25' and resid 41 through 44 removed outlier: 3.524A pdb=" N HIS25 42 " --> pdb=" O LYS25 74 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE25 78 " --> pdb=" O GLY25 44 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain '25' and resid 46 through 50 removed outlier: 7.092A pdb=" N ASN25 46 " --> pdb=" O LYS25 58 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR25 54 " --> pdb=" O GLY25 50 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain '26' and resid 11 through 15 Processing sheet with id= 39, first strand: chain '26' and resid 34 through 40 Processing sheet with id= 40, first strand: chain '28' and resid 32 through 38 removed outlier: 4.511A pdb=" N HIS28 33 " --> pdb=" O GLN28 8 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N MET28 53 " --> pdb=" O THR28 9 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain '29' and resid 12 through 16 removed outlier: 3.970A pdb=" N THR29 13 " --> pdb=" O HIS29 30 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER29 15 " --> pdb=" O LEU29 32 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain '31' and resid 7 through 12 removed outlier: 6.217A pdb=" N HIS31 18 " --> pdb=" O SER31 12 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain '31' and resid 33 through 38 removed outlier: 7.009A pdb=" N LEU31 33 " --> pdb=" O GLU31 50 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLU31 50 " --> pdb=" O LEU31 33 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LEU31 35 " --> pdb=" O TYR31 48 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain '33' and resid 21 through 24 No H-bonds generated for sheet with id= 44 Processing sheet with id= 45, first strand: chain '34' and resid 13 through 19 removed outlier: 8.233A pdb=" N ASN34 13 " --> pdb=" O SER34 28 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER34 28 " --> pdb=" O ASN34 13 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG34 19 " --> pdb=" O VAL34 22 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'B' and resid 29 through 33 removed outlier: 7.208A pdb=" N PHE B 29 " --> pdb=" O ASN B 41 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N VAL B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'B' and resid 88 through 91 removed outlier: 3.661A pdb=" N LEU B 67 " --> pdb=" O ALA B 159 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL B 69 " --> pdb=" O PHE B 161 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE B 183 " --> pdb=" O LEU B 160 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL B 162 " --> pdb=" O PHE B 183 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'C' and resid 52 through 58 removed outlier: 3.657A pdb=" N ARG C 53 " --> pdb=" O HIS C 68 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL C 65 " --> pdb=" O GLN C 99 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'C' and resid 164 through 170 removed outlier: 3.740A pdb=" N GLY C 147 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ASP C 180 " --> pdb=" O LYS C 203 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'D' and resid 139 through 143 removed outlier: 6.006A pdb=" N GLU D 178 " --> pdb=" O ASP D 173 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS D 182 " --> pdb=" O TRP D 169 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N TRP D 169 " --> pdb=" O LYS D 182 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'E' and resid 11 through 15 removed outlier: 3.778A pdb=" N GLN E 11 " --> pdb=" O GLY E 39 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY E 39 " --> pdb=" O GLN E 11 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LEU E 35 " --> pdb=" O ILE E 15 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ILE E 29 " --> pdb=" O LYS E 22 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA E 16 " --> pdb=" O LEU E 35 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'E' and resid 82 through 87 removed outlier: 6.896A pdb=" N HIS E 82 " --> pdb=" O PRO E 97 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET E 95 " --> pdb=" O VAL E 84 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL E 93 " --> pdb=" O GLY E 86 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR E 127 " --> pdb=" O ARG E 92 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'E' and resid 31 through 39 removed outlier: 3.535A pdb=" N ALA E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLY E 50 " --> pdb=" O ALA E 34 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'F' and resid 38 through 42 removed outlier: 6.089A pdb=" N ILE F 6 " --> pdb=" O MET F 62 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N HIS F 3 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLU F 5 " --> pdb=" O MET F 90 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N MET F 90 " --> pdb=" O GLU F 5 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'G' and resid 72 through 76 Processing sheet with id= 56, first strand: chain 'H' and resid 22 through 27 removed outlier: 6.024A pdb=" N ALA H 22 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLU H 51 " --> pdb=" O GLU H 57 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU H 59 " --> pdb=" O LYS H 49 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS H 49 " --> pdb=" O GLU H 59 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR H 61 " --> pdb=" O ASP H 47 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASP H 47 " --> pdb=" O THR H 61 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'H' and resid 122 through 125 removed outlier: 6.729A pdb=" N VAL H 102 " --> pdb=" O ILE H 125 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE H 100 " --> pdb=" O VAL H 128 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N CYS H 126 " --> pdb=" O VAL H 102 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'I' and resid 4 through 10 removed outlier: 4.326A pdb=" N GLY I 9 " --> pdb=" O ALA I 16 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR I 65 " --> pdb=" O ARG I 17 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'J' and resid 44 through 52 removed outlier: 3.529A pdb=" N ARG J 45 " --> pdb=" O THR J 69 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU J 47 " --> pdb=" O ILE J 67 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE J 67 " --> pdb=" O GLU J 47 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE J 8 " --> pdb=" O VAL J 74 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN J 99 " --> pdb=" O ARG J 9 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'K' and resid 41 through 44 removed outlier: 4.114A pdb=" N GLY K 42 " --> pdb=" O ILE K 33 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'L' and resid 28 through 32 removed outlier: 5.283A pdb=" N LEU L 80 " --> pdb=" O VAL L 97 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG L 82 " --> pdb=" O HIS L 95 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'L' and resid 36 through 40 removed outlier: 5.231A pdb=" N LYS L 50 " --> pdb=" O ILE L 66 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'P' and resid 4 through 10 removed outlier: 6.135A pdb=" N GLN P 18 " --> pdb=" O ALA P 7 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL P 19 " --> pdb=" O GLY P 37 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLY P 37 " --> pdb=" O VAL P 19 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'Q' and resid 19 through 30 No H-bonds generated for sheet with id= 64 Processing sheet with id= 65, first strand: chain 'Q' and resid 59 through 62 removed outlier: 6.997A pdb=" N GLU Q 59 " --> pdb=" O VAL Q 75 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'S' and resid 29 through 33 removed outlier: 3.863A pdb=" N LEU S 30 " --> pdb=" O THR S 47 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N LEU S 46 " --> pdb=" O VAL S 61 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain '03' and resid 60 through 64 removed outlier: 3.997A pdb=" N THR03 63 " --> pdb=" O VAL03 161 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain '03' and resid 93 through 98 removed outlier: 3.711A pdb=" N LEU03 94 " --> pdb=" O VAL03 75 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR03 79 " --> pdb=" O GLY03 96 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE03 115 " --> pdb=" O ALA03 76 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE03 78 " --> pdb=" O ILE03 115 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain '03' and resid 170 through 174 Processing sheet with id= 70, first strand: chain 'Z' and resid 64 through 71 removed outlier: 3.526A pdb=" N TYR Z 69 " --> pdb=" O TYR Z 76 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG Z 74 " --> pdb=" O THR Z 71 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY Z 15 " --> pdb=" O GLY Z 100 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE Z 131 " --> pdb=" O ALA Z 101 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'Z' and resid 210 through 214 removed outlier: 7.246A pdb=" N PHE Z 210 " --> pdb=" O LYS Z 294 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N GLN Z 290 " --> pdb=" O ILE Z 214 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA Z 293 " --> pdb=" O GLU Z 243 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLU Z 240 " --> pdb=" O CYS Z 255 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'Z' and resid 216 through 220 removed outlier: 3.896A pdb=" N ASP Z 216 " --> pdb=" O THR Z 228 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N THR Z 225 " --> pdb=" O LEU Z 278 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL Z 274 " --> pdb=" O GLY Z 229 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'Z' and resid 335 through 343 removed outlier: 3.592A pdb=" N THR Z 335 " --> pdb=" O PHE Z 332 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY Z 339 " --> pdb=" O PRO Z 328 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE Z 341 " --> pdb=" O TYR Z 326 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N TYR Z 326 " --> pdb=" O ILE Z 341 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N LEU Z 343 " --> pdb=" O LYS Z 324 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LYS Z 324 " --> pdb=" O LEU Z 343 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU Z 372 " --> pdb=" O VAL Z 388 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA Z 385 " --> pdb=" O TYR Z 309 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLU Z 305 " --> pdb=" O ALA Z 389 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE Z 356 " --> pdb=" O VAL Z 308 " (cutoff:3.500A) 1754 hydrogen bonds defined for protein. 5184 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3645 hydrogen bonds 5946 hydrogen bond angles 0 basepair planarities 1459 basepair parallelities 2890 stacking parallelities Total time for adding SS restraints: 266.99 Time building geometry restraints manager: 65.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.38: 43866 1.38 - 1.53: 107490 1.53 - 1.69: 15820 1.69 - 1.85: 284 1.85 - 2.01: 31 Bond restraints: 167491 Sorted by residual: bond pdb=" SD MET03 137 " pdb=" CE MET03 137 " ideal model delta sigma weight residual 1.791 2.011 -0.220 2.50e-02 1.60e+03 7.77e+01 bond pdb=" O3A GCP Z 401 " pdb=" PB GCP Z 401 " ideal model delta sigma weight residual 1.697 1.535 0.162 2.00e-02 2.50e+03 6.54e+01 bond pdb=" SD MET Z 368 " pdb=" CE MET Z 368 " ideal model delta sigma weight residual 1.791 1.989 -0.198 2.50e-02 1.60e+03 6.27e+01 bond pdb=" SD MET Z 91 " pdb=" CE MET Z 91 " ideal model delta sigma weight residual 1.791 1.974 -0.183 2.50e-02 1.60e+03 5.34e+01 bond pdb=" SD MET03 121 " pdb=" CE MET03 121 " ideal model delta sigma weight residual 1.791 1.971 -0.180 2.50e-02 1.60e+03 5.18e+01 ... (remaining 167486 not shown) Histogram of bond angle deviations from ideal: 93.32 - 104.68: 21804 104.68 - 116.03: 122232 116.03 - 127.38: 95763 127.38 - 138.74: 10199 138.74 - 150.09: 2 Bond angle restraints: 250000 Sorted by residual: angle pdb=" N HIS B 17 " pdb=" CA HIS B 17 " pdb=" C HIS B 17 " ideal model delta sigma weight residual 109.18 125.52 -16.34 1.42e+00 4.96e-01 1.32e+02 angle pdb=" N ARG G 142 " pdb=" CA ARG G 142 " pdb=" C ARG G 142 " ideal model delta sigma weight residual 113.41 101.91 11.50 1.22e+00 6.72e-01 8.89e+01 angle pdb=" N GLY H 67 " pdb=" CA GLY H 67 " pdb=" C GLY H 67 " ideal model delta sigma weight residual 113.37 100.85 12.52 1.34e+00 5.57e-01 8.73e+01 angle pdb=" O3' A A1201 " pdb=" C3' A A1201 " pdb=" C2' A A1201 " ideal model delta sigma weight residual 109.50 123.05 -13.55 1.50e+00 4.44e-01 8.16e+01 angle pdb=" O LEU B 160 " pdb=" C LEU B 160 " pdb=" N PHE B 161 " ideal model delta sigma weight residual 123.12 111.65 11.47 1.32e+00 5.74e-01 7.56e+01 ... (remaining 249995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.47: 95578 35.47 - 70.95: 10340 70.95 - 106.42: 1300 106.42 - 141.90: 17 141.90 - 177.37: 16 Dihedral angle restraints: 107251 sinusoidal: 88575 harmonic: 18676 Sorted by residual: dihedral pdb=" C5' A A 246 " pdb=" C4' A A 246 " pdb=" C3' A A 246 " pdb=" O3' A A 246 " ideal model delta sinusoidal sigma weight residual 147.00 76.49 70.51 1 8.00e+00 1.56e-02 1.00e+02 dihedral pdb=" O4' C02 12 " pdb=" C1' C02 12 " pdb=" N1 C02 12 " pdb=" C2 C02 12 " ideal model delta sinusoidal sigma weight residual 200.00 38.98 161.02 1 1.50e+01 4.44e-03 8.30e+01 dihedral pdb=" O4' U W 55 " pdb=" C1' U W 55 " pdb=" N1 U W 55 " pdb=" C2 U W 55 " ideal model delta sinusoidal sigma weight residual 200.00 43.95 156.05 1 1.50e+01 4.44e-03 8.17e+01 ... (remaining 107248 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.138: 28161 0.138 - 0.277: 3510 0.277 - 0.415: 209 0.415 - 0.554: 10 0.554 - 0.692: 2 Chirality restraints: 31892 Sorted by residual: chirality pdb=" C3' GCP Z 401 " pdb=" C2' GCP Z 401 " pdb=" C4' GCP Z 401 " pdb=" O3' GCP Z 401 " both_signs ideal model delta sigma weight residual False -2.57 -3.26 0.69 2.00e-01 2.50e+01 1.20e+01 chirality pdb=" C3' A011378 " pdb=" C4' A011378 " pdb=" O3' A011378 " pdb=" C2' A011378 " both_signs ideal model delta sigma weight residual False -2.74 -2.15 -0.60 2.00e-01 2.50e+01 8.92e+00 chirality pdb=" C3' G A1190 " pdb=" C4' G A1190 " pdb=" O3' G A1190 " pdb=" C2' G A1190 " both_signs ideal model delta sigma weight residual False -2.74 -2.19 -0.55 2.00e-01 2.50e+01 7.56e+00 ... (remaining 31889 not shown) Planarity restraints: 13835 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G01 512 " 0.118 2.00e-02 2.50e+03 4.88e-02 7.15e+01 pdb=" N9 G01 512 " -0.007 2.00e-02 2.50e+03 pdb=" C8 G01 512 " -0.047 2.00e-02 2.50e+03 pdb=" N7 G01 512 " -0.042 2.00e-02 2.50e+03 pdb=" C5 G01 512 " -0.024 2.00e-02 2.50e+03 pdb=" C6 G01 512 " 0.020 2.00e-02 2.50e+03 pdb=" O6 G01 512 " 0.075 2.00e-02 2.50e+03 pdb=" N1 G01 512 " 0.015 2.00e-02 2.50e+03 pdb=" C2 G01 512 " -0.014 2.00e-02 2.50e+03 pdb=" N2 G01 512 " -0.012 2.00e-02 2.50e+03 pdb=" N3 G01 512 " -0.042 2.00e-02 2.50e+03 pdb=" C4 G01 512 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U A1086 " 0.093 2.00e-02 2.50e+03 5.40e-02 6.57e+01 pdb=" N1 U A1086 " -0.001 2.00e-02 2.50e+03 pdb=" C2 U A1086 " -0.019 2.00e-02 2.50e+03 pdb=" O2 U A1086 " -0.031 2.00e-02 2.50e+03 pdb=" N3 U A1086 " -0.025 2.00e-02 2.50e+03 pdb=" C4 U A1086 " -0.026 2.00e-02 2.50e+03 pdb=" O4 U A1086 " 0.103 2.00e-02 2.50e+03 pdb=" C5 U A1086 " -0.053 2.00e-02 2.50e+03 pdb=" C6 U A1086 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U012689 " 0.092 2.00e-02 2.50e+03 5.32e-02 6.37e+01 pdb=" N1 U012689 " -0.001 2.00e-02 2.50e+03 pdb=" C2 U012689 " -0.019 2.00e-02 2.50e+03 pdb=" O2 U012689 " -0.031 2.00e-02 2.50e+03 pdb=" N3 U012689 " -0.025 2.00e-02 2.50e+03 pdb=" C4 U012689 " -0.026 2.00e-02 2.50e+03 pdb=" O4 U012689 " 0.101 2.00e-02 2.50e+03 pdb=" C5 U012689 " -0.052 2.00e-02 2.50e+03 pdb=" C6 U012689 " -0.040 2.00e-02 2.50e+03 ... (remaining 13832 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 8758 2.71 - 3.26: 138470 3.26 - 3.80: 302209 3.80 - 4.35: 397673 4.35 - 4.90: 529263 Nonbonded interactions: 1376373 Sorted by model distance: nonbonded pdb=" O2' A A 532 " pdb=" OP1 A A 533 " model vdw 2.162 2.440 nonbonded pdb=" O LEU L 101 " pdb=" N CYS L 103 " model vdw 2.223 2.520 nonbonded pdb=" O2' A A 246 " pdb=" O5' G A 247 " model vdw 2.305 2.440 nonbonded pdb=" OG1 THR F 92 " pdb=" N LYS F 93 " model vdw 2.336 2.520 nonbonded pdb=" O ASP N 53 " pdb=" OG SER N 54 " model vdw 2.353 2.440 ... (remaining 1376368 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' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.110 Extract box with map and model: 26.660 Check model and map are aligned: 1.700 Set scattering table: 1.030 Process input model: 570.970 Find NCS groups from input model: 3.300 Set up NCS constraints: 0.520 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 613.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.220 167491 Z= 0.508 Angle : 1.030 25.321 250000 Z= 0.680 Chirality : 0.091 0.692 31892 Planarity : 0.009 0.085 13835 Dihedral : 22.223 177.374 95211 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 1.72 % Allowed : 11.85 % Favored : 86.43 % Rotamer: Outliers : 0.88 % Allowed : 4.26 % Favored : 94.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.85 (0.08), residues: 6457 helix: -3.62 (0.07), residues: 1871 sheet: -2.76 (0.15), residues: 967 loop : -3.21 (0.09), residues: 3619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.005 TRP04 247 HIS 0.003 0.000 HIS03 172 PHE 0.038 0.005 PHE03 38 TYR 0.067 0.008 TYR Z 76 ARG 0.008 0.001 ARG Z 204 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12914 Ramachandran restraints generated. 6457 Oldfield, 0 Emsley, 6457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12914 Ramachandran restraints generated. 6457 Oldfield, 0 Emsley, 6457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2125 residues out of total 5350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 2078 time to evaluate : 6.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 04 63 ILE cc_start: 0.8639 (mt) cc_final: 0.8230 (mt) REVERT: 04 67 LYS cc_start: 0.8490 (tttt) cc_final: 0.8233 (tptt) REVERT: 04 87 SER cc_start: 0.8062 (p) cc_final: 0.7662 (p) REVERT: 04 160 TYR cc_start: 0.9116 (p90) cc_final: 0.8905 (p90) REVERT: 04 186 ASP cc_start: 0.8724 (m-30) cc_final: 0.7888 (t0) REVERT: 05 108 ASP cc_start: 0.6866 (m-30) cc_final: 0.6652 (m-30) REVERT: 05 131 ASP cc_start: 0.8824 (t70) cc_final: 0.8539 (t0) REVERT: 06 9 GLN cc_start: 0.7846 (tt0) cc_final: 0.7410 (mp-120) REVERT: 06 30 GLN cc_start: 0.9349 (tp40) cc_final: 0.8957 (tm-30) REVERT: 06 183 PHE cc_start: 0.8317 (m-80) cc_final: 0.7634 (m-80) REVERT: 06 195 GLN cc_start: 0.9451 (mt0) cc_final: 0.9020 (tm-30) REVERT: 07 22 ASN cc_start: 0.8915 (m-40) cc_final: 0.8514 (p0) REVERT: 07 51 ASN cc_start: 0.8796 (m110) cc_final: 0.8517 (t0) REVERT: 07 120 SER cc_start: 0.8188 (m) cc_final: 0.7792 (m) REVERT: 07 174 PHE cc_start: 0.8403 (t80) cc_final: 0.8125 (t80) REVERT: 08 114 HIS cc_start: 0.7772 (t70) cc_final: 0.7542 (t-170) REVERT: 08 142 GLN cc_start: 0.8576 (tp40) cc_final: 0.8161 (mm-40) REVERT: 08 146 ASP cc_start: 0.9116 (m-30) cc_final: 0.8535 (p0) REVERT: 09 33 GLN cc_start: 0.8555 (mt0) cc_final: 0.8317 (mt0) REVERT: 09 42 LYS cc_start: 0.8969 (mttt) cc_final: 0.8580 (tptp) REVERT: 09 46 PHE cc_start: 0.8038 (m-80) cc_final: 0.7807 (m-80) REVERT: 09 119 ASN cc_start: 0.8126 (t0) cc_final: 0.7806 (p0) REVERT: 09 123 ARG cc_start: 0.6324 (mtt180) cc_final: 0.5908 (mtt180) REVERT: 09 129 GLU cc_start: 0.9006 (tt0) cc_final: 0.8793 (tm-30) REVERT: 09 132 PHE cc_start: 0.8362 (m-80) cc_final: 0.8114 (m-80) REVERT: 10 17 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7673 (tt0) REVERT: 10 65 GLU cc_start: 0.7686 (tm-30) cc_final: 0.6885 (tp30) REVERT: 10 69 PHE cc_start: 0.8394 (t80) cc_final: 0.8110 (m-80) REVERT: 10 86 MET cc_start: 0.5259 (mmm) cc_final: 0.4972 (mmt) REVERT: 11 79 LEU cc_start: 0.7028 (mt) cc_final: 0.6798 (pp) REVERT: 11 95 ASP cc_start: 0.6917 (OUTLIER) cc_final: 0.6695 (p0) REVERT: 11 135 MET cc_start: 0.6324 (mmt) cc_final: 0.6102 (mmm) REVERT: 12 16 TYR cc_start: 0.9077 (m-80) cc_final: 0.8856 (m-80) REVERT: 13 7 MET cc_start: 0.8636 (mmt) cc_final: 0.8418 (mmm) REVERT: 13 73 ASP cc_start: 0.8415 (p0) cc_final: 0.8196 (p0) REVERT: 13 104 THR cc_start: 0.8702 (m) cc_final: 0.8494 (t) REVERT: 13 106 GLU cc_start: 0.8683 (mp0) cc_final: 0.8084 (mp0) REVERT: 14 115 GLU cc_start: 0.7951 (mp0) cc_final: 0.7733 (mp0) REVERT: 14 121 THR cc_start: 0.8804 (m) cc_final: 0.8546 (t) REVERT: 15 1 MET cc_start: 0.7354 (mtp) cc_final: 0.7124 (pmm) REVERT: 15 17 ASN cc_start: 0.8654 (t0) cc_final: 0.8207 (t0) REVERT: 15 30 SER cc_start: 0.9095 (m) cc_final: 0.8699 (m) REVERT: 15 68 PHE cc_start: 0.8283 (t80) cc_final: 0.8070 (t80) REVERT: 15 112 LEU cc_start: 0.9244 (tp) cc_final: 0.9030 (tp) REVERT: 16 20 MET cc_start: 0.9130 (ppp) cc_final: 0.8769 (tmm) REVERT: 16 43 GLU cc_start: 0.9186 (tp30) cc_final: 0.8949 (tp30) REVERT: 16 100 CYS cc_start: 0.8300 (p) cc_final: 0.7638 (t) REVERT: 16 120 GLU cc_start: 0.6631 (mm-30) cc_final: 0.6097 (pm20) REVERT: 17 56 LYS cc_start: 0.8904 (pttp) cc_final: 0.8137 (ttpp) REVERT: 17 76 LYS cc_start: 0.9494 (tttt) cc_final: 0.9246 (tptp) REVERT: 18 8 GLU cc_start: 0.9181 (mt-10) cc_final: 0.8965 (tt0) REVERT: 18 10 GLU cc_start: 0.8726 (pt0) cc_final: 0.8340 (pt0) REVERT: 18 26 GLU cc_start: 0.8418 (tm-30) cc_final: 0.7774 (tm-30) REVERT: 18 40 GLN cc_start: 0.9000 (pt0) cc_final: 0.8660 (tt0) REVERT: 18 74 GLN cc_start: 0.7643 (mm-40) cc_final: 0.7404 (mm-40) REVERT: 19 8 ILE cc_start: 0.9045 (pp) cc_final: 0.8713 (mt) REVERT: 19 23 TYR cc_start: 0.8065 (m-10) cc_final: 0.7760 (m-80) REVERT: 19 60 TRP cc_start: 0.9238 (m-10) cc_final: 0.8734 (m-90) REVERT: 20 11 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.8812 (mm-40) REVERT: 20 76 LYS cc_start: 0.9421 (mmmm) cc_final: 0.9139 (mtmt) REVERT: 20 83 TYR cc_start: 0.8569 (t80) cc_final: 0.8270 (t80) REVERT: 21 36 LEU cc_start: 0.9394 (mt) cc_final: 0.9007 (mt) REVERT: 21 40 ASN cc_start: 0.8854 (m-40) cc_final: 0.8540 (m-40) REVERT: 22 11 LEU cc_start: 0.9222 (mt) cc_final: 0.8825 (tt) REVERT: 22 25 GLU cc_start: 0.8728 (pt0) cc_final: 0.8259 (pp20) REVERT: 23 9 GLU cc_start: 0.8023 (tp30) cc_final: 0.7773 (tp30) REVERT: 23 40 LEU cc_start: 0.8936 (mt) cc_final: 0.8728 (mp) REVERT: 23 84 PHE cc_start: 0.8443 (m-80) cc_final: 0.8131 (m-10) REVERT: 24 3 THR cc_start: 0.9207 (m) cc_final: 0.8993 (p) REVERT: 24 41 GLU cc_start: 0.8396 (tm-30) cc_final: 0.8021 (tt0) REVERT: 25 35 ARG cc_start: 0.8827 (mmm-85) cc_final: 0.8564 (mtp-110) REVERT: 25 71 LYS cc_start: 0.9255 (mtmm) cc_final: 0.8531 (mtmt) REVERT: 25 73 ARG cc_start: 0.8368 (ptp-170) cc_final: 0.8110 (mtt180) REVERT: 26 16 ASN cc_start: 0.8908 (t0) cc_final: 0.8458 (t0) REVERT: 26 21 LEU cc_start: 0.9324 (mt) cc_final: 0.9091 (mp) REVERT: 26 55 MET cc_start: 0.9097 (mtp) cc_final: 0.8494 (tpp) REVERT: 27 16 THR cc_start: 0.9272 (m) cc_final: 0.8966 (p) REVERT: 27 26 PHE cc_start: 0.8915 (t80) cc_final: 0.8378 (t80) REVERT: 29 48 GLN cc_start: 0.8753 (tp40) cc_final: 0.8326 (mp10) REVERT: 30 26 SER cc_start: 0.8939 (m) cc_final: 0.8617 (p) REVERT: 30 27 LEU cc_start: 0.8541 (tp) cc_final: 0.8336 (tp) REVERT: 30 31 LYS cc_start: 0.9039 (tppp) cc_final: 0.8836 (mmtp) REVERT: 31 8 ILE cc_start: 0.9413 (pt) cc_final: 0.9205 (pt) REVERT: 31 42 VAL cc_start: 0.8984 (t) cc_final: 0.8754 (p) REVERT: 32 11 LYS cc_start: 0.9198 (mtpp) cc_final: 0.8978 (ttmm) REVERT: 32 14 ARG cc_start: 0.9117 (mmt90) cc_final: 0.8662 (ttm110) REVERT: 33 60 CYS cc_start: 0.9301 (p) cc_final: 0.9048 (p) REVERT: B 48 MET cc_start: 0.9459 (mmm) cc_final: 0.9225 (tpp) REVERT: C 5 HIS cc_start: 0.8786 (t-90) cc_final: 0.8563 (t70) REVERT: C 33 ASP cc_start: 0.8826 (t70) cc_final: 0.8530 (t0) REVERT: C 82 ASP cc_start: 0.8092 (m-30) cc_final: 0.7785 (m-30) REVERT: C 134 LYS cc_start: 0.9343 (tttt) cc_final: 0.8624 (mttp) REVERT: C 152 VAL cc_start: 0.9078 (m) cc_final: 0.8861 (p) REVERT: C 177 LEU cc_start: 0.9441 (mt) cc_final: 0.9136 (pp) REVERT: D 49 ASP cc_start: 0.8885 (t70) cc_final: 0.8667 (p0) REVERT: D 104 MET cc_start: 0.9079 (mmm) cc_final: 0.8719 (mmm) REVERT: D 195 ASN cc_start: 0.8857 (t0) cc_final: 0.8620 (t0) REVERT: E 49 TYR cc_start: 0.9086 (t80) cc_final: 0.8881 (t80) REVERT: E 65 LYS cc_start: 0.8900 (mttm) cc_final: 0.8568 (mtmt) REVERT: E 122 VAL cc_start: 0.8484 (m) cc_final: 0.8077 (m) REVERT: E 123 LEU cc_start: 0.9091 (mt) cc_final: 0.8283 (mt) REVERT: E 129 SER cc_start: 0.9399 (t) cc_final: 0.9101 (p) REVERT: F 47 LEU cc_start: 0.8667 (mt) cc_final: 0.8164 (mp) REVERT: F 61 LEU cc_start: 0.9130 (tp) cc_final: 0.8888 (mm) REVERT: F 87 SER cc_start: 0.8776 (p) cc_final: 0.8543 (m) REVERT: G 30 MET cc_start: 0.9016 (ttp) cc_final: 0.8517 (tmm) REVERT: G 117 LEU cc_start: 0.8928 (tp) cc_final: 0.8640 (tt) REVERT: H 83 ARG cc_start: 0.8920 (mmt180) cc_final: 0.8657 (mmt-90) REVERT: I 96 GLU cc_start: 0.8765 (mp0) cc_final: 0.8455 (mp0) REVERT: J 16 ARG cc_start: 0.8164 (ptt180) cc_final: 0.7714 (tpp-160) REVERT: J 31 ARG cc_start: 0.7566 (ttp80) cc_final: 0.7098 (tpp80) REVERT: J 64 GLN cc_start: 0.8921 (mt0) cc_final: 0.8616 (mt0) REVERT: J 84 VAL cc_start: 0.8115 (p) cc_final: 0.7898 (m) REVERT: J 89 ARG cc_start: 0.7747 (ptt-90) cc_final: 0.7031 (tpt90) REVERT: J 97 ASP cc_start: 0.8224 (t70) cc_final: 0.7468 (t0) REVERT: K 32 THR cc_start: 0.9520 (m) cc_final: 0.9229 (p) REVERT: K 41 LEU cc_start: 0.9440 (mt) cc_final: 0.9236 (mp) REVERT: K 67 GLU cc_start: 0.9059 (mt-10) cc_final: 0.8822 (mt-10) REVERT: K 96 ILE cc_start: 0.9387 (pt) cc_final: 0.9015 (pt) REVERT: K 112 VAL cc_start: 0.9045 (m) cc_final: 0.8730 (m) REVERT: K 114 PRO cc_start: 0.8393 (Cg_endo) cc_final: 0.8047 (Cg_exo) REVERT: L 2 THR cc_start: 0.8107 (m) cc_final: 0.7841 (m) REVERT: L 60 PHE cc_start: 0.9135 (m-80) cc_final: 0.8841 (m-80) REVERT: L 61 GLU cc_start: 0.8541 (tp30) cc_final: 0.8071 (tp30) REVERT: L 73 LEU cc_start: 0.8149 (mp) cc_final: 0.7859 (mt) REVERT: M 22 TYR cc_start: 0.8455 (t80) cc_final: 0.8056 (t80) REVERT: M 32 ILE cc_start: 0.9254 (mm) cc_final: 0.8996 (mm) REVERT: M 67 ASP cc_start: 0.8946 (m-30) cc_final: 0.8698 (m-30) REVERT: M 90 HIS cc_start: 0.9199 (m-70) cc_final: 0.8722 (m170) REVERT: N 5 MET cc_start: 0.9519 (mmm) cc_final: 0.9051 (mmt) REVERT: N 64 ARG cc_start: 0.9027 (mtt180) cc_final: 0.8709 (mtt-85) REVERT: N 66 THR cc_start: 0.8278 (p) cc_final: 0.7790 (t) REVERT: P 67 ILE cc_start: 0.9008 (mp) cc_final: 0.8741 (tt) REVERT: Q 64 ARG cc_start: 0.9028 (ttp-110) cc_final: 0.8651 (ptt90) REVERT: R 62 ARG cc_start: 0.9210 (mtt180) cc_final: 0.8827 (tpp80) REVERT: S 15 LEU cc_start: 0.9225 (tp) cc_final: 0.8864 (tp) REVERT: S 40 PHE cc_start: 0.8797 (m-80) cc_final: 0.8412 (m-80) REVERT: S 43 MET cc_start: 0.9044 (mtp) cc_final: 0.8643 (tpt) REVERT: S 61 VAL cc_start: 0.8544 (t) cc_final: 0.7470 (t) REVERT: S 72 GLU cc_start: 0.8457 (mm-30) cc_final: 0.7814 (mm-30) REVERT: T 15 LYS cc_start: 0.9508 (tttm) cc_final: 0.9245 (tppt) REVERT: T 24 ARG cc_start: 0.9132 (ttp-110) cc_final: 0.8696 (ttm110) REVERT: T 85 LEU cc_start: 0.6271 (tp) cc_final: 0.5852 (tt) REVERT: U 44 ARG cc_start: 0.8963 (tpp-160) cc_final: 0.8687 (ttm170) REVERT: 03 197 LYS cc_start: 0.7384 (mttp) cc_final: 0.6989 (mmmt) REVERT: Z 44 ARG cc_start: 0.6364 (mmt-90) cc_final: 0.6062 (mtm-85) REVERT: Z 98 MET cc_start: 0.6296 (mtm) cc_final: 0.5559 (mtt) REVERT: Z 116 ARG cc_start: 0.6686 (ttt180) cc_final: 0.6101 (ttp-170) REVERT: Z 159 GLN cc_start: 0.8972 (tt0) cc_final: 0.8768 (tt0) REVERT: Z 217 VAL cc_start: 0.7870 (t) cc_final: 0.7154 (t) REVERT: Z 312 SER cc_start: 0.3702 (p) cc_final: 0.3330 (t) outliers start: 47 outliers final: 9 residues processed: 2105 average time/residue: 1.4305 time to fit residues: 5070.1339 Evaluate side-chains 1189 residues out of total 5350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1178 time to evaluate : 6.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 07 residue 151 LEU Chi-restraints excluded: chain 11 residue 95 ASP Chi-restraints excluded: chain 20 residue 11 GLN Chi-restraints excluded: chain 22 residue 59 ASN Chi-restraints excluded: chain 27 residue 7 ARG Chi-restraints excluded: chain 27 residue 29 ARG Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain S residue 10 ILE Chi-restraints excluded: chain 03 residue 21 TYR Chi-restraints excluded: chain Z residue 359 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1111 random chunks: chunk 938 optimal weight: 20.0000 chunk 842 optimal weight: 20.0000 chunk 467 optimal weight: 2.9990 chunk 287 optimal weight: 30.0000 chunk 568 optimal weight: 0.9990 chunk 449 optimal weight: 9.9990 chunk 870 optimal weight: 20.0000 chunk 336 optimal weight: 7.9990 chunk 529 optimal weight: 30.0000 chunk 648 optimal weight: 20.0000 chunk 1008 optimal weight: 20.0000 overall best weight: 8.3992 ------------------------------------------------------------------------------- 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** 04 133 ASN 05 134 HIS 05 150 GLN 06 92 HIS 06 94 GLN 06 97 ASN 06 163 ASN 06 165 HIS 07 51 ASN 08 29 ASN ** 08 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 09 43 ASN ** 09 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 09 133 GLN 10 6 GLN ** 10 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 11 18 ASN 11 30 GLN 12 128 ASN ** 12 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 3 GLN ** 14 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 16 3 HIS ** 16 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 16 81 ASN 16 107 ASN 17 38 GLN 18 6 GLN 18 14 GLN 19 36 GLN ** 19 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 20 18 GLN ** 21 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 23 53 GLN 23 73 ASN 24 87 GLN 25 42 HIS 27 20 ASN ** 27 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 27 58 ASN 28 19 HIS 29 48 GLN 29 61 ASN 30 41 HIS ** 31 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 31 45 HIS 34 35 GLN ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 ASN B 167 HIS C 31 ASN C 138 GLN C 139 ASN D 139 ASN ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 HIS F 68 GLN G 27 ASN G 129 ASN ** G 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 ASN I 24 ASN I 74 GLN I 109 GLN I 125 GLN K 100 ASN L 45 ASN M 99 GLN ** N 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 59 GLN ** N 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 36 ASN ** P 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 8 GLN Q 30 HIS R 51 GLN S 68 HIS T 2 ASN T 12 GLN T 20 ASN T 51 ASN ** 03 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 03 148 ASN ** 03 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 03 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 124 GLN ** Z 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 167491 Z= 0.301 Angle : 0.757 17.365 250000 Z= 0.389 Chirality : 0.042 0.352 31892 Planarity : 0.006 0.072 13835 Dihedral : 23.143 179.272 82430 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 21.20 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.77 % Favored : 89.92 % Rotamer: Outliers : 5.09 % Allowed : 15.44 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.09), residues: 6457 helix: -1.70 (0.10), residues: 1976 sheet: -2.33 (0.14), residues: 1113 loop : -2.76 (0.10), residues: 3368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 103 HIS 0.014 0.002 HIS19 13 PHE 0.036 0.002 PHE U 36 TYR 0.027 0.002 TYR Z 309 ARG 0.010 0.001 ARG U 33 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12914 Ramachandran restraints generated. 6457 Oldfield, 0 Emsley, 6457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12914 Ramachandran restraints generated. 6457 Oldfield, 0 Emsley, 6457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1579 residues out of total 5350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 272 poor density : 1307 time to evaluate : 6.955 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: 04 67 LYS cc_start: 0.8584 (tttt) cc_final: 0.8175 (tptt) REVERT: 04 87 SER cc_start: 0.8044 (p) cc_final: 0.7659 (p) REVERT: 04 186 ASP cc_start: 0.8690 (m-30) cc_final: 0.7855 (t0) REVERT: 05 131 ASP cc_start: 0.8842 (t70) cc_final: 0.8620 (t0) REVERT: 06 1 MET cc_start: 0.8405 (tpp) cc_final: 0.8099 (tpp) REVERT: 06 9 GLN cc_start: 0.8016 (tt0) cc_final: 0.7512 (mp10) REVERT: 06 195 GLN cc_start: 0.9270 (mt0) cc_final: 0.8942 (mp10) REVERT: 07 22 ASN cc_start: 0.8934 (m-40) cc_final: 0.8440 (p0) REVERT: 07 176 PHE cc_start: 0.8651 (m-80) cc_final: 0.8233 (m-10) REVERT: 08 74 MET cc_start: 0.8984 (mtp) cc_final: 0.8756 (ptp) REVERT: 08 142 GLN cc_start: 0.8510 (tp40) cc_final: 0.7856 (tp-100) REVERT: 08 146 ASP cc_start: 0.9079 (m-30) cc_final: 0.8362 (m-30) REVERT: 09 123 ARG cc_start: 0.6089 (mtt180) cc_final: 0.5777 (mtt180) REVERT: 09 129 GLU cc_start: 0.8796 (tt0) cc_final: 0.8359 (tp30) REVERT: 10 1 MET cc_start: 0.7298 (tpt) cc_final: 0.6323 (tpt) REVERT: 10 17 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7431 (tt0) REVERT: 10 65 GLU cc_start: 0.7861 (tm-30) cc_final: 0.6788 (mm-30) REVERT: 10 69 PHE cc_start: 0.8429 (t80) cc_final: 0.8135 (m-80) REVERT: 10 94 ARG cc_start: 0.6594 (ttp-110) cc_final: 0.6251 (ttp80) REVERT: 11 106 GLN cc_start: 0.8545 (tt0) cc_final: 0.7979 (tp40) REVERT: 12 98 GLU cc_start: 0.8991 (mp0) cc_final: 0.8707 (mm-30) REVERT: 12 106 LYS cc_start: 0.8902 (ttmm) cc_final: 0.8667 (tppt) REVERT: 13 7 MET cc_start: 0.8451 (mmt) cc_final: 0.8190 (mmp) REVERT: 14 115 GLU cc_start: 0.8026 (mp0) cc_final: 0.7799 (mp0) REVERT: 15 1 MET cc_start: 0.7589 (mtp) cc_final: 0.7013 (pmm) REVERT: 15 17 ASN cc_start: 0.8646 (t0) cc_final: 0.8421 (t0) REVERT: 15 60 GLN cc_start: 0.8623 (pm20) cc_final: 0.8295 (pm20) REVERT: 15 95 LEU cc_start: 0.9330 (mt) cc_final: 0.8912 (pp) REVERT: 15 112 LEU cc_start: 0.9137 (tp) cc_final: 0.8753 (tp) REVERT: 16 1 MET cc_start: 0.8735 (pmm) cc_final: 0.8507 (pmm) REVERT: 16 20 MET cc_start: 0.9191 (ppp) cc_final: 0.8919 (tmm) REVERT: 16 44 LEU cc_start: 0.9445 (tp) cc_final: 0.9118 (tt) REVERT: 16 100 CYS cc_start: 0.8774 (p) cc_final: 0.8201 (t) REVERT: 16 120 GLU cc_start: 0.6476 (mm-30) cc_final: 0.5977 (pm20) REVERT: 17 76 LYS cc_start: 0.9338 (tttt) cc_final: 0.8685 (tptp) REVERT: 17 104 GLN cc_start: 0.9150 (tm-30) cc_final: 0.8911 (tp-100) REVERT: 18 9 GLN cc_start: 0.9424 (tp40) cc_final: 0.9152 (tp40) REVERT: 18 33 GLU cc_start: 0.7754 (pm20) cc_final: 0.7120 (pm20) REVERT: 18 40 GLN cc_start: 0.9064 (pt0) cc_final: 0.8804 (tt0) REVERT: 19 8 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8470 (mt) REVERT: 19 36 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8054 (mm-40) REVERT: 19 39 ILE cc_start: 0.9487 (mt) cc_final: 0.8972 (tt) REVERT: 20 12 HIS cc_start: 0.8951 (m90) cc_final: 0.8236 (m90) REVERT: 20 76 LYS cc_start: 0.9425 (mmmm) cc_final: 0.9120 (mtmt) REVERT: 20 78 ARG cc_start: 0.8972 (tpp-160) cc_final: 0.8744 (tpp-160) REVERT: 21 24 ILE cc_start: 0.9157 (mp) cc_final: 0.8926 (mm) REVERT: 21 52 GLU cc_start: 0.8877 (tp30) cc_final: 0.8477 (tm-30) REVERT: 21 69 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8417 (mt) REVERT: 22 25 GLU cc_start: 0.8941 (pt0) cc_final: 0.8541 (pp20) REVERT: 23 21 ARG cc_start: 0.7392 (mtm110) cc_final: 0.6972 (mtm180) REVERT: 23 84 PHE cc_start: 0.8640 (m-80) cc_final: 0.8362 (m-10) REVERT: 25 67 VAL cc_start: 0.9288 (OUTLIER) cc_final: 0.8702 (t) REVERT: 25 71 LYS cc_start: 0.9233 (mtmm) cc_final: 0.8894 (mtmt) REVERT: 25 73 ARG cc_start: 0.8648 (ptp-170) cc_final: 0.8362 (mtt180) REVERT: 26 15 ASN cc_start: 0.8883 (m-40) cc_final: 0.8633 (t0) REVERT: 26 16 ASN cc_start: 0.8978 (t0) cc_final: 0.8525 (t0) REVERT: 26 55 MET cc_start: 0.9067 (mtp) cc_final: 0.8681 (mmt) REVERT: 26 61 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8618 (mtpp) REVERT: 26 75 GLU cc_start: 0.6637 (mm-30) cc_final: 0.5991 (mm-30) REVERT: 27 16 THR cc_start: 0.9051 (m) cc_final: 0.8845 (p) REVERT: 28 2 LYS cc_start: 0.8597 (tppt) cc_final: 0.8023 (mmmt) REVERT: 29 9 TYR cc_start: 0.7442 (t80) cc_final: 0.5862 (t80) REVERT: 29 48 GLN cc_start: 0.8782 (tp-100) cc_final: 0.8252 (mp10) REVERT: 30 26 SER cc_start: 0.8963 (m) cc_final: 0.8555 (p) REVERT: 30 27 LEU cc_start: 0.8624 (tp) cc_final: 0.8383 (tp) REVERT: 30 31 LYS cc_start: 0.9015 (tppp) cc_final: 0.8741 (mmtp) REVERT: 30 53 VAL cc_start: 0.9263 (m) cc_final: 0.9030 (m) REVERT: 33 7 ARG cc_start: 0.7895 (mmm-85) cc_final: 0.7593 (mmm-85) REVERT: 33 27 ASN cc_start: 0.8676 (t0) cc_final: 0.8339 (t0) REVERT: 34 23 ILE cc_start: 0.9671 (mt) cc_final: 0.9377 (tt) REVERT: B 48 MET cc_start: 0.9464 (mmm) cc_final: 0.9122 (tpp) REVERT: B 181 PRO cc_start: 0.8887 (Cg_exo) cc_final: 0.8684 (Cg_endo) REVERT: C 33 ASP cc_start: 0.8813 (t70) cc_final: 0.8581 (t70) REVERT: C 82 ASP cc_start: 0.8205 (m-30) cc_final: 0.7997 (m-30) REVERT: C 177 LEU cc_start: 0.9536 (mt) cc_final: 0.9207 (pp) REVERT: C 181 ILE cc_start: 0.9428 (OUTLIER) cc_final: 0.9204 (mm) REVERT: D 102 TYR cc_start: 0.8613 (t80) cc_final: 0.8210 (t80) REVERT: E 49 TYR cc_start: 0.8937 (t80) cc_final: 0.8734 (t80) REVERT: E 65 LYS cc_start: 0.9003 (mttm) cc_final: 0.8728 (mtmt) REVERT: E 70 MET cc_start: 0.8529 (mmm) cc_final: 0.8209 (ttm) REVERT: E 121 ASN cc_start: 0.8277 (OUTLIER) cc_final: 0.7916 (p0) REVERT: E 122 VAL cc_start: 0.8142 (OUTLIER) cc_final: 0.7848 (t) REVERT: E 129 SER cc_start: 0.9458 (t) cc_final: 0.9163 (p) REVERT: F 62 MET cc_start: 0.9093 (mmm) cc_final: 0.8791 (mmm) REVERT: H 83 ARG cc_start: 0.8832 (mmt180) cc_final: 0.8507 (mmt-90) REVERT: I 4 GLN cc_start: 0.7716 (tt0) cc_final: 0.7035 (tp-100) REVERT: I 34 LEU cc_start: 0.8735 (tt) cc_final: 0.8534 (tp) REVERT: J 64 GLN cc_start: 0.8769 (mt0) cc_final: 0.8497 (mt0) REVERT: J 89 ARG cc_start: 0.7666 (ptt-90) cc_final: 0.7130 (tpt90) REVERT: K 35 ASP cc_start: 0.8183 (p0) cc_final: 0.7559 (p0) REVERT: K 41 LEU cc_start: 0.9506 (mt) cc_final: 0.9272 (mp) REVERT: K 51 PHE cc_start: 0.7203 (m-80) cc_final: 0.6901 (m-80) REVERT: M 22 TYR cc_start: 0.8712 (t80) cc_final: 0.8263 (t80) REVERT: M 67 ASP cc_start: 0.8765 (m-30) cc_final: 0.8376 (m-30) REVERT: N 5 MET cc_start: 0.9380 (mmm) cc_final: 0.8997 (mmt) REVERT: N 45 LEU cc_start: 0.9145 (tt) cc_final: 0.8905 (mt) REVERT: N 64 ARG cc_start: 0.9044 (mtt180) cc_final: 0.8512 (tpp-160) REVERT: N 95 LEU cc_start: 0.9037 (tt) cc_final: 0.8824 (tp) REVERT: O 57 ARG cc_start: 0.8931 (ttp80) cc_final: 0.8605 (ttp80) REVERT: Q 16 MET cc_start: 0.8515 (ptm) cc_final: 0.7990 (tmm) REVERT: Q 54 ILE cc_start: 0.6670 (OUTLIER) cc_final: 0.6429 (tp) REVERT: R 62 ARG cc_start: 0.9328 (mtt180) cc_final: 0.8784 (tpp80) REVERT: S 11 ASP cc_start: 0.7949 (m-30) cc_final: 0.7630 (m-30) REVERT: S 20 LYS cc_start: 0.9142 (ttpp) cc_final: 0.8940 (ttpp) REVERT: S 43 MET cc_start: 0.8948 (mtp) cc_final: 0.8622 (tpt) REVERT: S 61 VAL cc_start: 0.8561 (t) cc_final: 0.7698 (t) REVERT: S 72 GLU cc_start: 0.8373 (mm-30) cc_final: 0.7600 (mm-30) REVERT: T 15 LYS cc_start: 0.9537 (tttm) cc_final: 0.9267 (tppt) REVERT: T 20 ASN cc_start: 0.9120 (t0) cc_final: 0.8717 (t0) REVERT: 03 197 LYS cc_start: 0.7305 (mttp) cc_final: 0.7049 (mmmt) REVERT: 03 201 PRO cc_start: 0.2577 (Cg_exo) cc_final: 0.2347 (Cg_endo) REVERT: Z 114 GLN cc_start: 0.7684 (mm-40) cc_final: 0.7299 (tt0) REVERT: Z 349 MET cc_start: 0.7768 (ptm) cc_final: 0.7295 (ttt) outliers start: 272 outliers final: 147 residues processed: 1454 average time/residue: 1.4557 time to fit residues: 3689.9597 Evaluate side-chains 1204 residues out of total 5350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1048 time to evaluate : 6.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 156 SER Chi-restraints excluded: chain 04 residue 179 GLU Chi-restraints excluded: chain 04 residue 200 MET Chi-restraints excluded: chain 05 residue 2 ILE Chi-restraints excluded: chain 05 residue 27 ILE Chi-restraints excluded: chain 05 residue 109 VAL Chi-restraints excluded: chain 05 residue 137 SER Chi-restraints excluded: chain 05 residue 139 SER Chi-restraints excluded: chain 06 residue 140 ASP Chi-restraints excluded: chain 07 residue 15 LEU Chi-restraints excluded: chain 07 residue 151 LEU Chi-restraints excluded: chain 08 residue 15 ASP Chi-restraints excluded: chain 09 residue 117 LEU Chi-restraints excluded: chain 09 residue 145 ASN Chi-restraints excluded: chain 10 residue 6 GLN Chi-restraints excluded: chain 10 residue 29 ASP Chi-restraints excluded: chain 10 residue 131 THR Chi-restraints excluded: chain 11 residue 121 ILE Chi-restraints excluded: chain 12 residue 14 ASP Chi-restraints excluded: chain 12 residue 84 ILE Chi-restraints excluded: chain 13 residue 21 CYS Chi-restraints excluded: chain 13 residue 22 ILE Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 56 ASP Chi-restraints excluded: chain 13 residue 61 VAL Chi-restraints excluded: chain 13 residue 65 THR Chi-restraints excluded: chain 13 residue 75 SER Chi-restraints excluded: chain 13 residue 88 ASN Chi-restraints excluded: chain 14 residue 25 SER Chi-restraints excluded: chain 14 residue 46 VAL Chi-restraints excluded: chain 16 residue 6 SER Chi-restraints excluded: chain 16 residue 36 THR Chi-restraints excluded: chain 16 residue 47 VAL Chi-restraints excluded: chain 17 residue 47 VAL Chi-restraints excluded: chain 17 residue 54 VAL Chi-restraints excluded: chain 17 residue 61 GLN Chi-restraints excluded: chain 17 residue 91 SER Chi-restraints excluded: chain 18 residue 14 GLN Chi-restraints excluded: chain 18 residue 15 ASP Chi-restraints excluded: chain 19 residue 8 ILE Chi-restraints excluded: chain 19 residue 16 ILE Chi-restraints excluded: chain 19 residue 36 GLN Chi-restraints excluded: chain 20 residue 53 PHE Chi-restraints excluded: chain 20 residue 58 VAL Chi-restraints excluded: chain 21 residue 30 SER Chi-restraints excluded: chain 21 residue 62 ASP Chi-restraints excluded: chain 21 residue 69 LEU Chi-restraints excluded: chain 21 residue 101 SER Chi-restraints excluded: chain 21 residue 107 VAL Chi-restraints excluded: chain 22 residue 1 MET Chi-restraints excluded: chain 22 residue 37 ASP Chi-restraints excluded: chain 22 residue 50 LEU Chi-restraints excluded: chain 22 residue 79 ASP Chi-restraints excluded: chain 23 residue 13 LEU Chi-restraints excluded: chain 23 residue 34 ILE Chi-restraints excluded: chain 23 residue 43 LYS Chi-restraints excluded: chain 23 residue 71 ILE Chi-restraints excluded: chain 24 residue 10 LYS Chi-restraints excluded: chain 24 residue 34 LYS Chi-restraints excluded: chain 24 residue 60 VAL Chi-restraints excluded: chain 25 residue 12 SER Chi-restraints excluded: chain 25 residue 34 VAL Chi-restraints excluded: chain 25 residue 67 VAL Chi-restraints excluded: chain 26 residue 6 VAL Chi-restraints excluded: chain 26 residue 41 SER Chi-restraints excluded: chain 26 residue 57 VAL Chi-restraints excluded: chain 26 residue 61 LYS Chi-restraints excluded: chain 27 residue 7 ARG Chi-restraints excluded: chain 29 residue 32 LEU Chi-restraints excluded: chain 30 residue 2 VAL Chi-restraints excluded: chain 30 residue 8 THR Chi-restraints excluded: chain 31 residue 24 LYS Chi-restraints excluded: chain 31 residue 45 HIS Chi-restraints excluded: chain 32 residue 9 VAL Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 33 residue 3 ILE Chi-restraints excluded: chain 33 residue 5 THR Chi-restraints excluded: chain 33 residue 57 VAL Chi-restraints excluded: chain 34 residue 28 SER Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 120 HIS Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 67 ASN Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 141 HIS Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain I residue 24 ASN Chi-restraints excluded: chain I residue 30 ASN Chi-restraints excluded: chain I residue 109 GLN Chi-restraints excluded: chain I residue 127 SER Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 120 CYS Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain M residue 20 SER Chi-restraints excluded: chain M residue 48 SER Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain N residue 37 ASP Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain P residue 19 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 29 ASN Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 49 ASN Chi-restraints excluded: chain Q residue 54 ILE Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain R residue 21 ASP Chi-restraints excluded: chain S residue 10 ILE Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain U residue 50 SER Chi-restraints excluded: chain Z residue 32 THR Chi-restraints excluded: chain Z residue 235 ILE Chi-restraints excluded: chain Z residue 245 VAL Chi-restraints excluded: chain Z residue 255 CYS Chi-restraints excluded: chain Z residue 311 LEU Chi-restraints excluded: chain Z residue 335 THR Chi-restraints excluded: chain Z residue 359 VAL Chi-restraints excluded: chain Z residue 369 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1111 random chunks: chunk 560 optimal weight: 20.0000 chunk 313 optimal weight: 3.9990 chunk 839 optimal weight: 20.0000 chunk 687 optimal weight: 20.0000 chunk 278 optimal weight: 20.0000 chunk 1010 optimal weight: 20.0000 chunk 1091 optimal weight: 20.0000 chunk 900 optimal weight: 30.0000 chunk 1002 optimal weight: 20.0000 chunk 344 optimal weight: 30.0000 chunk 810 optimal weight: 20.0000 overall best weight: 16.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 04 14 HIS ** 04 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 04 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 04 225 ASN ** 05 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 05 67 HIS 05 130 GLN 05 150 GLN ** 06 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 06 97 ASN ** 08 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 44 HIS ** 08 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 09 33 GLN ** 09 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 10 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 10 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 16 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 16 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 16 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 17 19 GLN ** 17 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 18 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 19 36 GLN ** 19 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 21 15 GLN 21 40 ASN ** 23 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 24 49 ASN ** 24 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 26 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 29 33 ASN 31 45 HIS 32 29 GLN 33 27 ASN ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 HIS C 7 ASN ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 GLN ** K 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 95 HIS ** N 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 49 HIS ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 03 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 03 160 GLN ** 03 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 03 172 HIS ** 03 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 66 HIS Z 84 HIS Z 90 ASN ** Z 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 301 HIS ** Z 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.120 167491 Z= 0.523 Angle : 0.923 16.328 250000 Z= 0.466 Chirality : 0.047 0.334 31892 Planarity : 0.007 0.085 13835 Dihedral : 23.837 178.808 82417 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 35.72 Ramachandran Plot: Outliers : 0.29 % Allowed : 13.24 % Favored : 86.46 % Rotamer: Outliers : 7.35 % Allowed : 17.57 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -3.41 (0.09), residues: 6457 helix: -1.49 (0.10), residues: 1995 sheet: -2.24 (0.15), residues: 1101 loop : -2.80 (0.10), residues: 3361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP B 95 HIS 0.042 0.003 HIS31 45 PHE 0.038 0.003 PHE C 129 TYR 0.033 0.003 TYR I 5 ARG 0.023 0.001 ARG07 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12914 Ramachandran restraints generated. 6457 Oldfield, 0 Emsley, 6457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12914 Ramachandran restraints generated. 6457 Oldfield, 0 Emsley, 6457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1419 residues out of total 5350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 393 poor density : 1026 time to evaluate : 6.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 04 67 LYS cc_start: 0.8451 (tttt) cc_final: 0.7845 (tptt) REVERT: 05 130 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8292 (mm110) REVERT: 05 165 MET cc_start: 0.8863 (ttt) cc_final: 0.8621 (ttt) REVERT: 06 1 MET cc_start: 0.8637 (tpp) cc_final: 0.8360 (tpp) REVERT: 06 9 GLN cc_start: 0.8139 (tt0) cc_final: 0.7618 (mp10) REVERT: 06 30 GLN cc_start: 0.9427 (tm-30) cc_final: 0.9076 (tm-30) REVERT: 06 195 GLN cc_start: 0.9376 (mt0) cc_final: 0.8946 (mm-40) REVERT: 07 129 MET cc_start: 0.8928 (ppp) cc_final: 0.8548 (ppp) REVERT: 07 176 PHE cc_start: 0.8802 (m-80) cc_final: 0.8082 (m-10) REVERT: 08 142 GLN cc_start: 0.8603 (tp40) cc_final: 0.8105 (mm110) REVERT: 10 1 MET cc_start: 0.6082 (tpt) cc_final: 0.5818 (tpt) REVERT: 10 69 PHE cc_start: 0.8460 (t80) cc_final: 0.8129 (m-80) REVERT: 10 94 ARG cc_start: 0.6927 (OUTLIER) cc_final: 0.6671 (ttp80) REVERT: 10 123 ILE cc_start: 0.7796 (OUTLIER) cc_final: 0.7467 (mt) REVERT: 11 35 MET cc_start: 0.7876 (ttp) cc_final: 0.7307 (ptm) REVERT: 11 52 LEU cc_start: 0.8210 (tp) cc_final: 0.7866 (pp) REVERT: 11 106 GLN cc_start: 0.8589 (tt0) cc_final: 0.7979 (tp40) REVERT: 12 53 TYR cc_start: 0.8872 (m-80) cc_final: 0.8521 (m-80) REVERT: 13 7 MET cc_start: 0.8568 (mmt) cc_final: 0.8319 (mmm) REVERT: 13 45 GLU cc_start: 0.8467 (tp30) cc_final: 0.8236 (tm-30) REVERT: 14 38 GLN cc_start: 0.9024 (tm-30) cc_final: 0.8756 (tp-100) REVERT: 14 76 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8261 (mt-10) REVERT: 14 85 VAL cc_start: 0.8783 (m) cc_final: 0.8342 (p) REVERT: 15 1 MET cc_start: 0.7805 (mtp) cc_final: 0.7146 (pmm) REVERT: 15 17 ASN cc_start: 0.8648 (t0) cc_final: 0.8181 (t0) REVERT: 15 33 LEU cc_start: 0.8844 (tp) cc_final: 0.8512 (tt) REVERT: 15 95 LEU cc_start: 0.9416 (mt) cc_final: 0.9068 (pp) REVERT: 16 20 MET cc_start: 0.9232 (OUTLIER) cc_final: 0.8976 (tmm) REVERT: 16 110 MET cc_start: 0.9548 (mmp) cc_final: 0.9000 (mmm) REVERT: 16 120 GLU cc_start: 0.7210 (mm-30) cc_final: 0.6375 (pm20) REVERT: 18 33 GLU cc_start: 0.7671 (pm20) cc_final: 0.7252 (pm20) REVERT: 19 8 ILE cc_start: 0.9098 (OUTLIER) cc_final: 0.8682 (mt) REVERT: 19 39 ILE cc_start: 0.9495 (mt) cc_final: 0.9278 (tt) REVERT: 20 48 LYS cc_start: 0.8397 (ttmm) cc_final: 0.8146 (ttpp) REVERT: 20 76 LYS cc_start: 0.9478 (mmmm) cc_final: 0.9061 (mtmt) REVERT: 21 52 GLU cc_start: 0.9056 (tp30) cc_final: 0.8691 (tm-30) REVERT: 21 78 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8081 (tm-30) REVERT: 22 25 GLU cc_start: 0.9026 (pt0) cc_final: 0.8721 (pt0) REVERT: 22 73 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7629 (mmm-85) REVERT: 23 84 PHE cc_start: 0.8618 (m-80) cc_final: 0.8397 (m-10) REVERT: 24 34 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.7889 (pttm) REVERT: 24 55 GLU cc_start: 0.8682 (pm20) cc_final: 0.8372 (pm20) REVERT: 24 56 PHE cc_start: 0.8153 (t80) cc_final: 0.7900 (t80) REVERT: 25 51 ARG cc_start: 0.8216 (ptm160) cc_final: 0.7848 (ttp80) REVERT: 25 71 LYS cc_start: 0.9336 (mtmm) cc_final: 0.9067 (mtmt) REVERT: 26 15 ASN cc_start: 0.8884 (m-40) cc_final: 0.8515 (t0) REVERT: 26 16 ASN cc_start: 0.9158 (t0) cc_final: 0.8746 (t0) REVERT: 26 55 MET cc_start: 0.9140 (mtp) cc_final: 0.8673 (mmm) REVERT: 27 17 GLU cc_start: 0.8952 (pt0) cc_final: 0.8752 (pt0) REVERT: 28 53 MET cc_start: 0.9187 (OUTLIER) cc_final: 0.8942 (ppp) REVERT: 28 57 GLU cc_start: 0.7174 (pm20) cc_final: 0.6351 (pp20) REVERT: 29 44 PHE cc_start: 0.8479 (OUTLIER) cc_final: 0.7633 (p90) REVERT: 29 48 GLN cc_start: 0.8749 (tp-100) cc_final: 0.8077 (mp10) REVERT: 31 47 ILE cc_start: 0.9294 (OUTLIER) cc_final: 0.8842 (tp) REVERT: 33 27 ASN cc_start: 0.8723 (t160) cc_final: 0.8400 (t0) REVERT: B 48 MET cc_start: 0.9499 (mmm) cc_final: 0.8965 (tpp) REVERT: B 181 PRO cc_start: 0.8821 (Cg_exo) cc_final: 0.8555 (Cg_endo) REVERT: C 33 ASP cc_start: 0.8937 (t70) cc_final: 0.8544 (t0) REVERT: E 60 GLN cc_start: 0.8982 (tp-100) cc_final: 0.8752 (tp-100) REVERT: E 92 ARG cc_start: 0.8928 (mmm-85) cc_final: 0.8698 (mmm-85) REVERT: E 129 SER cc_start: 0.9550 (t) cc_final: 0.9097 (p) REVERT: F 21 MET cc_start: 0.8936 (mtt) cc_final: 0.8644 (mpp) REVERT: H 26 MET cc_start: 0.9088 (ptp) cc_final: 0.8695 (pmm) REVERT: H 83 ARG cc_start: 0.8984 (mmt180) cc_final: 0.8547 (mmt-90) REVERT: J 64 GLN cc_start: 0.8691 (mt0) cc_final: 0.8457 (mt0) REVERT: J 88 MET cc_start: 0.8799 (mmm) cc_final: 0.8366 (mmm) REVERT: K 63 GLN cc_start: 0.9408 (tp40) cc_final: 0.9147 (tp-100) REVERT: L 56 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8602 (mm) REVERT: M 22 TYR cc_start: 0.8793 (t80) cc_final: 0.8203 (t80) REVERT: M 58 GLU cc_start: 0.8243 (tp30) cc_final: 0.7902 (tp30) REVERT: N 5 MET cc_start: 0.9390 (mmm) cc_final: 0.9045 (mmt) REVERT: N 45 LEU cc_start: 0.9176 (tt) cc_final: 0.8947 (mt) REVERT: N 85 GLU cc_start: 0.9278 (tp30) cc_final: 0.8590 (tm-30) REVERT: Q 10 ARG cc_start: 0.8728 (tmm-80) cc_final: 0.8458 (tmm-80) REVERT: Q 15 LYS cc_start: 0.9078 (ptpp) cc_final: 0.8703 (ptpp) REVERT: Q 27 PHE cc_start: 0.8812 (m-80) cc_final: 0.8174 (m-10) REVERT: Q 79 GLU cc_start: 0.9382 (tt0) cc_final: 0.8743 (tm-30) REVERT: R 63 TYR cc_start: 0.9447 (t80) cc_final: 0.9118 (t80) REVERT: S 11 ASP cc_start: 0.8174 (m-30) cc_final: 0.7930 (m-30) REVERT: S 31 ARG cc_start: 0.8938 (ttm-80) cc_final: 0.8600 (mtp-110) REVERT: S 72 GLU cc_start: 0.8447 (mm-30) cc_final: 0.7590 (mm-30) REVERT: 03 109 MET cc_start: 0.4004 (mmm) cc_final: 0.3770 (mmt) REVERT: Z 114 GLN cc_start: 0.7730 (mm-40) cc_final: 0.7336 (tt0) REVERT: Z 244 ILE cc_start: 0.8954 (mp) cc_final: 0.8685 (mp) REVERT: Z 349 MET cc_start: 0.7614 (ptm) cc_final: 0.7272 (ttm) outliers start: 393 outliers final: 257 residues processed: 1289 average time/residue: 1.3350 time to fit residues: 3042.1335 Evaluate side-chains 1163 residues out of total 5350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 269 poor density : 894 time to evaluate : 6.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 156 SER Chi-restraints excluded: chain 04 residue 179 GLU Chi-restraints excluded: chain 04 residue 219 VAL Chi-restraints excluded: chain 04 residue 245 THR Chi-restraints excluded: chain 04 residue 249 VAL Chi-restraints excluded: chain 05 residue 2 ILE Chi-restraints excluded: chain 05 residue 22 ILE Chi-restraints excluded: chain 05 residue 27 ILE Chi-restraints excluded: chain 05 residue 42 ASN Chi-restraints excluded: chain 05 residue 109 VAL Chi-restraints excluded: chain 05 residue 130 GLN Chi-restraints excluded: chain 05 residue 137 SER Chi-restraints excluded: chain 05 residue 139 SER Chi-restraints excluded: chain 05 residue 142 VAL Chi-restraints excluded: chain 05 residue 151 THR Chi-restraints excluded: chain 06 residue 140 ASP Chi-restraints excluded: chain 07 residue 49 LEU Chi-restraints excluded: chain 07 residue 104 THR Chi-restraints excluded: chain 07 residue 143 ASP Chi-restraints excluded: chain 07 residue 151 LEU Chi-restraints excluded: chain 08 residue 10 VAL Chi-restraints excluded: chain 08 residue 15 ASP Chi-restraints excluded: chain 08 residue 28 LYS Chi-restraints excluded: chain 08 residue 44 HIS Chi-restraints excluded: chain 09 residue 12 LEU Chi-restraints excluded: chain 09 residue 145 ASN Chi-restraints excluded: chain 10 residue 7 ASP Chi-restraints excluded: chain 10 residue 29 ASP Chi-restraints excluded: chain 10 residue 41 LEU Chi-restraints excluded: chain 10 residue 94 ARG Chi-restraints excluded: chain 10 residue 123 ILE Chi-restraints excluded: chain 10 residue 131 THR Chi-restraints excluded: chain 11 residue 41 PHE Chi-restraints excluded: chain 11 residue 56 VAL Chi-restraints excluded: chain 11 residue 121 ILE Chi-restraints excluded: chain 11 residue 126 ARG Chi-restraints excluded: chain 11 residue 135 MET Chi-restraints excluded: chain 12 residue 14 ASP Chi-restraints excluded: chain 12 residue 101 ILE Chi-restraints excluded: chain 13 residue 22 ILE Chi-restraints excluded: chain 13 residue 32 TYR Chi-restraints excluded: chain 13 residue 35 VAL Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 52 VAL Chi-restraints excluded: chain 13 residue 56 ASP Chi-restraints excluded: chain 13 residue 61 VAL Chi-restraints excluded: chain 13 residue 65 THR Chi-restraints excluded: chain 13 residue 75 SER Chi-restraints excluded: chain 13 residue 88 ASN Chi-restraints excluded: chain 13 residue 90 ASN Chi-restraints excluded: chain 13 residue 104 THR Chi-restraints excluded: chain 13 residue 107 LEU Chi-restraints excluded: chain 13 residue 110 GLU Chi-restraints excluded: chain 13 residue 118 LEU Chi-restraints excluded: chain 14 residue 25 SER Chi-restraints excluded: chain 14 residue 27 LEU Chi-restraints excluded: chain 14 residue 46 VAL Chi-restraints excluded: chain 14 residue 76 GLU Chi-restraints excluded: chain 14 residue 80 SER Chi-restraints excluded: chain 15 residue 7 THR Chi-restraints excluded: chain 15 residue 24 THR Chi-restraints excluded: chain 15 residue 42 THR Chi-restraints excluded: chain 16 residue 6 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 37 THR Chi-restraints excluded: chain 16 residue 115 LEU Chi-restraints excluded: chain 17 residue 16 ARG Chi-restraints excluded: chain 17 residue 43 ASN Chi-restraints excluded: chain 17 residue 49 VAL Chi-restraints excluded: chain 17 residue 54 VAL Chi-restraints excluded: chain 17 residue 61 GLN Chi-restraints excluded: chain 17 residue 74 VAL Chi-restraints excluded: chain 17 residue 80 GLU Chi-restraints excluded: chain 17 residue 108 ASP Chi-restraints excluded: chain 18 residue 8 GLU Chi-restraints excluded: chain 18 residue 27 VAL Chi-restraints excluded: chain 18 residue 49 ILE Chi-restraints excluded: chain 18 residue 64 SER Chi-restraints excluded: chain 18 residue 75 THR Chi-restraints excluded: chain 18 residue 91 VAL Chi-restraints excluded: chain 19 residue 8 ILE Chi-restraints excluded: chain 19 residue 16 ILE Chi-restraints excluded: chain 19 residue 33 VAL Chi-restraints excluded: chain 19 residue 99 VAL Chi-restraints excluded: chain 20 residue 31 GLU Chi-restraints excluded: chain 20 residue 53 PHE Chi-restraints excluded: chain 20 residue 58 VAL Chi-restraints excluded: chain 21 residue 20 VAL Chi-restraints excluded: chain 21 residue 45 VAL Chi-restraints excluded: chain 21 residue 53 SER Chi-restraints excluded: chain 21 residue 62 ASP Chi-restraints excluded: chain 21 residue 69 LEU Chi-restraints excluded: chain 21 residue 101 SER Chi-restraints excluded: chain 21 residue 107 VAL Chi-restraints excluded: chain 22 residue 32 LEU Chi-restraints excluded: chain 22 residue 37 ASP Chi-restraints excluded: chain 22 residue 50 LEU Chi-restraints excluded: chain 22 residue 73 ARG Chi-restraints excluded: chain 22 residue 79 ASP Chi-restraints excluded: chain 23 residue 9 GLU Chi-restraints excluded: chain 23 residue 13 LEU Chi-restraints excluded: chain 23 residue 26 ASN Chi-restraints excluded: chain 23 residue 34 ILE Chi-restraints excluded: chain 23 residue 43 LYS Chi-restraints excluded: chain 23 residue 71 ILE Chi-restraints excluded: chain 24 residue 3 THR Chi-restraints excluded: chain 24 residue 10 LYS Chi-restraints excluded: chain 24 residue 34 LYS Chi-restraints excluded: chain 24 residue 61 LEU Chi-restraints excluded: chain 24 residue 65 VAL Chi-restraints excluded: chain 24 residue 86 LEU Chi-restraints excluded: chain 24 residue 87 GLN Chi-restraints excluded: chain 25 residue 12 SER Chi-restraints excluded: chain 25 residue 34 VAL Chi-restraints excluded: chain 25 residue 52 ASP Chi-restraints excluded: chain 25 residue 60 ASP Chi-restraints excluded: chain 25 residue 67 VAL Chi-restraints excluded: chain 26 residue 22 ASN Chi-restraints excluded: chain 26 residue 41 SER Chi-restraints excluded: chain 26 residue 57 VAL Chi-restraints excluded: chain 27 residue 7 ARG Chi-restraints excluded: chain 27 residue 11 VAL Chi-restraints excluded: chain 28 residue 53 MET Chi-restraints excluded: chain 29 residue 32 LEU Chi-restraints excluded: chain 29 residue 39 LYS Chi-restraints excluded: chain 29 residue 44 PHE Chi-restraints excluded: chain 30 residue 2 VAL Chi-restraints excluded: chain 30 residue 8 THR Chi-restraints excluded: chain 31 residue 16 THR Chi-restraints excluded: chain 31 residue 23 THR Chi-restraints excluded: chain 31 residue 42 VAL Chi-restraints excluded: chain 31 residue 47 ILE Chi-restraints excluded: chain 32 residue 9 VAL Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 33 residue 5 THR Chi-restraints excluded: chain 33 residue 6 VAL Chi-restraints excluded: chain 34 residue 10 LEU Chi-restraints excluded: chain 34 residue 28 SER Chi-restraints excluded: chain 34 residue 35 GLN Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 120 HIS Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 23 GLU Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 67 ASN Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 129 ASN Chi-restraints excluded: chain G residue 141 HIS Chi-restraints excluded: chain H residue 20 ASN Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 73 SER Chi-restraints excluded: chain I residue 30 ASN Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 109 GLN Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 127 SER Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 56 HIS Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 96 ILE Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 120 CYS Chi-restraints excluded: chain L residue 14 LYS Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 48 SER Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain N residue 92 ILE Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain P residue 3 THR Chi-restraints excluded: chain P residue 6 LEU Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 29 ASN Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 49 ASN Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain R residue 21 ASP Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 71 ASP Chi-restraints excluded: chain S residue 10 ILE Chi-restraints excluded: chain S residue 14 LEU Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 36 PHE Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain 03 residue 79 THR Chi-restraints excluded: chain 03 residue 202 THR Chi-restraints excluded: chain 03 residue 215 SER Chi-restraints excluded: chain Z residue 20 VAL Chi-restraints excluded: chain Z residue 32 THR Chi-restraints excluded: chain Z residue 156 LEU Chi-restraints excluded: chain Z residue 189 LEU Chi-restraints excluded: chain Z residue 194 PHE Chi-restraints excluded: chain Z residue 195 LEU Chi-restraints excluded: chain Z residue 215 GLU Chi-restraints excluded: chain Z residue 235 ILE Chi-restraints excluded: chain Z residue 245 VAL Chi-restraints excluded: chain Z residue 311 LEU Chi-restraints excluded: chain Z residue 335 THR Chi-restraints excluded: chain Z residue 336 ASP Chi-restraints excluded: chain Z residue 359 VAL Chi-restraints excluded: chain Z residue 362 LEU Chi-restraints excluded: chain Z residue 369 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1111 random chunks: chunk 998 optimal weight: 10.0000 chunk 759 optimal weight: 10.0000 chunk 524 optimal weight: 9.9990 chunk 111 optimal weight: 6.9990 chunk 482 optimal weight: 5.9990 chunk 678 optimal weight: 30.0000 chunk 1014 optimal weight: 10.0000 chunk 1073 optimal weight: 8.9990 chunk 529 optimal weight: 10.0000 chunk 961 optimal weight: 30.0000 chunk 289 optimal weight: 5.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 04 14 HIS ** 04 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 04 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 05 130 GLN 06 97 ASN 08 19 ASN ** 08 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 44 HIS 08 138 GLN 09 20 ASN 09 33 GLN ** 09 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 10 4 ASN ** 10 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 14 35 HIS ** 16 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 16 23 ASN 17 19 GLN ** 18 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 24 49 ASN ** 24 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 33 42 HIS 34 35 GLN ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 GLN ** L 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 42 ASN ** N 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 18 GLN ** S 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 03 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 03 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 03 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 97 GLN ** Z 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 167491 Z= 0.259 Angle : 0.673 17.727 250000 Z= 0.345 Chirality : 0.038 0.332 31892 Planarity : 0.005 0.067 13835 Dihedral : 23.754 177.322 82417 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 22.39 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.11 % Favored : 89.69 % Rotamer: Outliers : 5.83 % Allowed : 20.60 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.10), residues: 6457 helix: -0.93 (0.11), residues: 2002 sheet: -2.12 (0.15), residues: 1112 loop : -2.53 (0.10), residues: 3343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 103 HIS 0.026 0.001 HIS08 44 PHE 0.043 0.002 PHE S 73 TYR 0.029 0.002 TYR07 142 ARG 0.011 0.001 ARG N 89 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12914 Ramachandran restraints generated. 6457 Oldfield, 0 Emsley, 6457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12914 Ramachandran restraints generated. 6457 Oldfield, 0 Emsley, 6457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1352 residues out of total 5350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 312 poor density : 1040 time to evaluate : 6.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 04 67 LYS cc_start: 0.8400 (tttt) cc_final: 0.7750 (tptt) REVERT: 05 165 MET cc_start: 0.8844 (ttt) cc_final: 0.8598 (ttt) REVERT: 06 1 MET cc_start: 0.8421 (tpp) cc_final: 0.8148 (tpp) REVERT: 06 9 GLN cc_start: 0.8105 (tt0) cc_final: 0.7538 (mp10) REVERT: 06 30 GLN cc_start: 0.9399 (tm-30) cc_final: 0.9003 (tm-30) REVERT: 07 129 MET cc_start: 0.8905 (ppp) cc_final: 0.8511 (ppp) REVERT: 07 176 PHE cc_start: 0.8879 (m-80) cc_final: 0.8245 (m-80) REVERT: 08 114 HIS cc_start: 0.7753 (t-170) cc_final: 0.6822 (t-90) REVERT: 08 146 ASP cc_start: 0.9113 (m-30) cc_final: 0.8585 (p0) REVERT: 10 6 GLN cc_start: 0.9208 (mm-40) cc_final: 0.9006 (tm-30) REVERT: 10 69 PHE cc_start: 0.8467 (t80) cc_final: 0.8172 (m-80) REVERT: 10 123 ILE cc_start: 0.7663 (OUTLIER) cc_final: 0.7441 (mt) REVERT: 11 52 LEU cc_start: 0.8152 (tp) cc_final: 0.7794 (pp) REVERT: 11 124 MET cc_start: 0.6720 (mmm) cc_final: 0.6506 (mpp) REVERT: 11 129 GLU cc_start: 0.8867 (pp20) cc_final: 0.8634 (pp20) REVERT: 12 53 TYR cc_start: 0.8867 (m-80) cc_final: 0.8457 (m-80) REVERT: 13 7 MET cc_start: 0.8553 (mmt) cc_final: 0.8194 (mmm) REVERT: 13 20 MET cc_start: 0.9400 (tpp) cc_final: 0.9172 (tpt) REVERT: 15 1 MET cc_start: 0.7705 (mtp) cc_final: 0.6955 (pmm) REVERT: 15 17 ASN cc_start: 0.8652 (t0) cc_final: 0.8357 (t0) REVERT: 15 33 LEU cc_start: 0.8630 (tp) cc_final: 0.8341 (tt) REVERT: 15 95 LEU cc_start: 0.9363 (mt) cc_final: 0.9124 (pp) REVERT: 16 110 MET cc_start: 0.9509 (mmp) cc_final: 0.8981 (mmm) REVERT: 16 112 TYR cc_start: 0.8541 (m-80) cc_final: 0.8167 (m-10) REVERT: 16 120 GLU cc_start: 0.6982 (mm-30) cc_final: 0.6120 (pm20) REVERT: 18 33 GLU cc_start: 0.7814 (pm20) cc_final: 0.7473 (pm20) REVERT: 18 87 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.8520 (ttt90) REVERT: 19 8 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8630 (mt) REVERT: 19 60 TRP cc_start: 0.9310 (m-10) cc_final: 0.8399 (m-90) REVERT: 20 40 MET cc_start: 0.8884 (tmm) cc_final: 0.8399 (tmm) REVERT: 20 48 LYS cc_start: 0.8412 (ttmm) cc_final: 0.8173 (ttpp) REVERT: 20 76 LYS cc_start: 0.9422 (mmmm) cc_final: 0.9028 (mtmt) REVERT: 21 1 MET cc_start: 0.7631 (tpp) cc_final: 0.7207 (tpp) REVERT: 21 52 GLU cc_start: 0.8975 (tp30) cc_final: 0.8614 (tm-30) REVERT: 21 59 GLU cc_start: 0.8727 (tp30) cc_final: 0.8381 (tm-30) REVERT: 21 69 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8455 (mt) REVERT: 21 77 ASP cc_start: 0.7025 (t0) cc_final: 0.6736 (t0) REVERT: 21 78 GLU cc_start: 0.8321 (tm-30) cc_final: 0.8014 (tm-30) REVERT: 22 25 GLU cc_start: 0.8914 (pt0) cc_final: 0.8597 (pp20) REVERT: 23 53 GLN cc_start: 0.9222 (tm-30) cc_final: 0.8062 (mp10) REVERT: 24 1 MET cc_start: 0.8228 (tmm) cc_final: 0.7954 (ppp) REVERT: 24 34 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.7823 (pttm) REVERT: 24 46 LYS cc_start: 0.8893 (ptmt) cc_final: 0.8440 (mtmt) REVERT: 25 17 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8655 (tp) REVERT: 25 51 ARG cc_start: 0.8182 (ptm160) cc_final: 0.7779 (ttp80) REVERT: 25 71 LYS cc_start: 0.9282 (mtmm) cc_final: 0.9046 (mtmt) REVERT: 26 15 ASN cc_start: 0.8915 (m-40) cc_final: 0.8518 (t0) REVERT: 26 16 ASN cc_start: 0.9101 (t0) cc_final: 0.8682 (t0) REVERT: 26 55 MET cc_start: 0.9041 (mtp) cc_final: 0.8655 (mmm) REVERT: 28 53 MET cc_start: 0.8973 (ptm) cc_final: 0.8737 (tmm) REVERT: 30 26 SER cc_start: 0.8945 (m) cc_final: 0.8714 (p) REVERT: 30 27 LEU cc_start: 0.8682 (tp) cc_final: 0.8459 (tp) REVERT: 32 13 ASN cc_start: 0.9263 (m-40) cc_final: 0.8321 (t0) REVERT: 32 14 ARG cc_start: 0.9262 (mmt90) cc_final: 0.8864 (tpp80) REVERT: B 48 MET cc_start: 0.9508 (mmm) cc_final: 0.8966 (tpp) REVERT: B 181 PRO cc_start: 0.8793 (Cg_exo) cc_final: 0.8491 (Cg_endo) REVERT: C 138 GLN cc_start: 0.9292 (mt0) cc_final: 0.9064 (mp10) REVERT: C 177 LEU cc_start: 0.9613 (mt) cc_final: 0.9324 (pp) REVERT: D 102 TYR cc_start: 0.8559 (t80) cc_final: 0.8324 (t80) REVERT: E 60 GLN cc_start: 0.8961 (tp-100) cc_final: 0.8744 (tp-100) REVERT: E 129 SER cc_start: 0.9516 (t) cc_final: 0.9164 (p) REVERT: F 1 MET cc_start: 0.8508 (ttt) cc_final: 0.8257 (ttt) REVERT: F 21 MET cc_start: 0.8880 (mtt) cc_final: 0.8563 (mpp) REVERT: F 61 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8482 (pp) REVERT: H 26 MET cc_start: 0.9091 (ptp) cc_final: 0.8718 (pmm) REVERT: H 41 GLU cc_start: 0.8954 (mt-10) cc_final: 0.8553 (pm20) REVERT: H 83 ARG cc_start: 0.8794 (mmt180) cc_final: 0.8517 (mmt-90) REVERT: I 4 GLN cc_start: 0.8121 (tt0) cc_final: 0.7403 (tp40) REVERT: J 64 GLN cc_start: 0.8711 (mt0) cc_final: 0.8469 (mt0) REVERT: K 63 GLN cc_start: 0.9346 (tp40) cc_final: 0.9003 (tp40) REVERT: L 23 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7793 (tt) REVERT: M 22 TYR cc_start: 0.8668 (t80) cc_final: 0.8312 (t80) REVERT: N 45 LEU cc_start: 0.9150 (tt) cc_final: 0.8946 (mt) REVERT: N 85 GLU cc_start: 0.9219 (tp30) cc_final: 0.8645 (tm-30) REVERT: N 89 ARG cc_start: 0.8845 (tpp80) cc_final: 0.8463 (ttm-80) REVERT: O 57 ARG cc_start: 0.9059 (ttp80) cc_final: 0.8147 (ttp80) REVERT: O 58 MET cc_start: 0.9225 (ppp) cc_final: 0.8511 (ppp) REVERT: O 61 GLN cc_start: 0.9189 (OUTLIER) cc_final: 0.8921 (pt0) REVERT: Q 10 ARG cc_start: 0.8567 (tmm-80) cc_final: 0.8262 (tpp80) REVERT: Q 17 GLU cc_start: 0.8489 (tt0) cc_final: 0.7824 (tm-30) REVERT: Q 27 PHE cc_start: 0.8651 (m-80) cc_final: 0.8340 (m-10) REVERT: Q 79 GLU cc_start: 0.9242 (tt0) cc_final: 0.8523 (tm-30) REVERT: R 12 PHE cc_start: 0.7207 (m-80) cc_final: 0.6563 (m-80) REVERT: R 63 TYR cc_start: 0.9385 (t80) cc_final: 0.9043 (t80) REVERT: S 11 ASP cc_start: 0.7989 (m-30) cc_final: 0.7748 (m-30) REVERT: T 14 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8475 (mm-30) REVERT: U 44 ARG cc_start: 0.7986 (ttm-80) cc_final: 0.7670 (ttt180) REVERT: Z 87 TYR cc_start: 0.6516 (m-80) cc_final: 0.6273 (m-80) REVERT: Z 114 GLN cc_start: 0.7750 (mm-40) cc_final: 0.7300 (tt0) REVERT: Z 244 ILE cc_start: 0.8963 (mp) cc_final: 0.8693 (mp) REVERT: Z 322 PHE cc_start: 0.3740 (OUTLIER) cc_final: 0.3204 (p90) REVERT: Z 349 MET cc_start: 0.7613 (ptm) cc_final: 0.7210 (ttm) outliers start: 312 outliers final: 223 residues processed: 1230 average time/residue: 1.3265 time to fit residues: 2869.0546 Evaluate side-chains 1157 residues out of total 5350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 924 time to evaluate : 6.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 2 VAL Chi-restraints excluded: chain 04 residue 156 SER Chi-restraints excluded: chain 04 residue 179 GLU Chi-restraints excluded: chain 05 residue 2 ILE Chi-restraints excluded: chain 05 residue 27 ILE Chi-restraints excluded: chain 05 residue 42 ASN Chi-restraints excluded: chain 05 residue 109 VAL Chi-restraints excluded: chain 05 residue 137 SER Chi-restraints excluded: chain 05 residue 139 SER Chi-restraints excluded: chain 05 residue 186 LEU Chi-restraints excluded: chain 05 residue 201 LEU Chi-restraints excluded: chain 06 residue 140 ASP Chi-restraints excluded: chain 07 residue 49 LEU Chi-restraints excluded: chain 07 residue 143 ASP Chi-restraints excluded: chain 07 residue 151 LEU Chi-restraints excluded: chain 08 residue 10 VAL Chi-restraints excluded: chain 08 residue 15 ASP Chi-restraints excluded: chain 08 residue 19 ASN Chi-restraints excluded: chain 08 residue 113 ASP Chi-restraints excluded: chain 08 residue 167 VAL Chi-restraints excluded: chain 09 residue 12 LEU Chi-restraints excluded: chain 09 residue 145 ASN Chi-restraints excluded: chain 10 residue 29 ASP Chi-restraints excluded: chain 10 residue 41 LEU Chi-restraints excluded: chain 10 residue 123 ILE Chi-restraints excluded: chain 10 residue 131 THR Chi-restraints excluded: chain 11 residue 41 PHE Chi-restraints excluded: chain 11 residue 56 VAL Chi-restraints excluded: chain 11 residue 111 THR Chi-restraints excluded: chain 11 residue 121 ILE Chi-restraints excluded: chain 11 residue 126 ARG Chi-restraints excluded: chain 11 residue 135 MET Chi-restraints excluded: chain 12 residue 14 ASP Chi-restraints excluded: chain 12 residue 84 ILE Chi-restraints excluded: chain 12 residue 118 MET Chi-restraints excluded: chain 13 residue 22 ILE Chi-restraints excluded: chain 13 residue 32 TYR Chi-restraints excluded: chain 13 residue 35 VAL Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 56 ASP Chi-restraints excluded: chain 13 residue 61 VAL Chi-restraints excluded: chain 13 residue 65 THR Chi-restraints excluded: chain 13 residue 88 ASN Chi-restraints excluded: chain 13 residue 104 THR Chi-restraints excluded: chain 13 residue 110 GLU Chi-restraints excluded: chain 14 residue 25 SER Chi-restraints excluded: chain 14 residue 27 LEU Chi-restraints excluded: chain 14 residue 80 SER Chi-restraints excluded: chain 15 residue 7 THR Chi-restraints excluded: chain 15 residue 65 ILE Chi-restraints excluded: chain 16 residue 1 MET Chi-restraints excluded: chain 16 residue 36 THR Chi-restraints excluded: chain 16 residue 47 VAL Chi-restraints excluded: chain 16 residue 98 LEU Chi-restraints excluded: chain 16 residue 115 LEU Chi-restraints excluded: chain 17 residue 16 ARG Chi-restraints excluded: chain 17 residue 35 ILE Chi-restraints excluded: chain 17 residue 47 VAL Chi-restraints excluded: chain 17 residue 49 VAL Chi-restraints excluded: chain 17 residue 54 VAL Chi-restraints excluded: chain 17 residue 61 GLN Chi-restraints excluded: chain 18 residue 15 ASP Chi-restraints excluded: chain 18 residue 24 THR Chi-restraints excluded: chain 18 residue 40 GLN Chi-restraints excluded: chain 18 residue 49 ILE Chi-restraints excluded: chain 18 residue 87 ARG Chi-restraints excluded: chain 18 residue 91 VAL Chi-restraints excluded: chain 18 residue 103 THR Chi-restraints excluded: chain 19 residue 8 ILE Chi-restraints excluded: chain 19 residue 16 ILE Chi-restraints excluded: chain 19 residue 108 LEU Chi-restraints excluded: chain 20 residue 38 VAL Chi-restraints excluded: chain 20 residue 53 PHE Chi-restraints excluded: chain 20 residue 58 VAL Chi-restraints excluded: chain 20 residue 81 LYS Chi-restraints excluded: chain 20 residue 99 THR Chi-restraints excluded: chain 21 residue 45 VAL Chi-restraints excluded: chain 21 residue 53 SER Chi-restraints excluded: chain 21 residue 62 ASP Chi-restraints excluded: chain 21 residue 69 LEU Chi-restraints excluded: chain 21 residue 101 SER Chi-restraints excluded: chain 21 residue 107 VAL Chi-restraints excluded: chain 22 residue 37 ASP Chi-restraints excluded: chain 22 residue 50 LEU Chi-restraints excluded: chain 22 residue 73 ARG Chi-restraints excluded: chain 22 residue 74 ILE Chi-restraints excluded: chain 22 residue 79 ASP Chi-restraints excluded: chain 23 residue 9 GLU Chi-restraints excluded: chain 23 residue 12 VAL Chi-restraints excluded: chain 23 residue 13 LEU Chi-restraints excluded: chain 23 residue 14 THR Chi-restraints excluded: chain 23 residue 26 ASN Chi-restraints excluded: chain 23 residue 34 ILE Chi-restraints excluded: chain 23 residue 43 LYS Chi-restraints excluded: chain 23 residue 71 ILE Chi-restraints excluded: chain 24 residue 3 THR Chi-restraints excluded: chain 24 residue 10 LYS Chi-restraints excluded: chain 24 residue 34 LYS Chi-restraints excluded: chain 24 residue 65 VAL Chi-restraints excluded: chain 24 residue 87 GLN Chi-restraints excluded: chain 25 residue 7 ARG Chi-restraints excluded: chain 25 residue 12 SER Chi-restraints excluded: chain 25 residue 17 LEU Chi-restraints excluded: chain 25 residue 34 VAL Chi-restraints excluded: chain 25 residue 67 VAL Chi-restraints excluded: chain 26 residue 41 SER Chi-restraints excluded: chain 26 residue 57 VAL Chi-restraints excluded: chain 27 residue 7 ARG Chi-restraints excluded: chain 28 residue 26 LEU Chi-restraints excluded: chain 28 residue 31 ILE Chi-restraints excluded: chain 29 residue 5 ILE Chi-restraints excluded: chain 29 residue 32 LEU Chi-restraints excluded: chain 29 residue 39 LYS Chi-restraints excluded: chain 29 residue 53 THR Chi-restraints excluded: chain 30 residue 2 VAL Chi-restraints excluded: chain 30 residue 8 THR Chi-restraints excluded: chain 31 residue 23 THR Chi-restraints excluded: chain 31 residue 42 VAL Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 33 residue 5 THR Chi-restraints excluded: chain 33 residue 6 VAL Chi-restraints excluded: chain 34 residue 10 LEU Chi-restraints excluded: chain 34 residue 28 SER Chi-restraints excluded: chain 34 residue 35 GLN Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 120 HIS Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 67 ASN Chi-restraints excluded: chain G residue 98 LEU Chi-restraints excluded: chain G residue 129 ASN Chi-restraints excluded: chain G residue 141 HIS Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain I residue 24 ASN Chi-restraints excluded: chain I residue 30 ASN Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 127 SER Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 120 CYS Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 23 LEU Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 102 ASP Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 61 GLN Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 29 ASN Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 49 ASN Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain Q residue 74 LEU Chi-restraints excluded: chain R residue 21 ASP Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain S residue 10 ILE Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 36 PHE Chi-restraints excluded: chain U residue 50 SER Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain 03 residue 215 SER Chi-restraints excluded: chain Z residue 27 LEU Chi-restraints excluded: chain Z residue 32 THR Chi-restraints excluded: chain Z residue 156 LEU Chi-restraints excluded: chain Z residue 215 GLU Chi-restraints excluded: chain Z residue 235 ILE Chi-restraints excluded: chain Z residue 245 VAL Chi-restraints excluded: chain Z residue 311 LEU Chi-restraints excluded: chain Z residue 322 PHE Chi-restraints excluded: chain Z residue 335 THR Chi-restraints excluded: chain Z residue 359 VAL Chi-restraints excluded: chain Z residue 369 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1111 random chunks: chunk 894 optimal weight: 20.0000 chunk 609 optimal weight: 30.0000 chunk 15 optimal weight: 20.0000 chunk 799 optimal weight: 20.0000 chunk 443 optimal weight: 30.0000 chunk 916 optimal weight: 20.0000 chunk 742 optimal weight: 20.0000 chunk 1 optimal weight: 4.9990 chunk 548 optimal weight: 20.0000 chunk 963 optimal weight: 50.0000 chunk 270 optimal weight: 0.0070 overall best weight: 13.0012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 04 14 HIS ** 04 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 06 97 ASN 08 19 ASN ** 08 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 44 HIS 08 72 ASN 08 103 ASN 09 20 ASN 09 33 GLN ** 09 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 10 4 ASN ** 10 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 14 35 HIS ** 14 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 16 23 ASN ** 18 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 22 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 23 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 24 78 GLN ** 24 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 24 88 HIS ** 27 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 29 20 ASN ** 32 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 33 27 ASN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 ASN I 109 GLN ** L 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 18 GLN ** S 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 03 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 03 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 03 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.4760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.138 167491 Z= 0.417 Angle : 0.785 15.855 250000 Z= 0.399 Chirality : 0.042 0.355 31892 Planarity : 0.006 0.073 13835 Dihedral : 23.893 179.079 82417 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 30.87 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.84 % Favored : 86.99 % Rotamer: Outliers : 7.22 % Allowed : 22.04 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.10), residues: 6457 helix: -1.02 (0.11), residues: 1998 sheet: -2.12 (0.14), residues: 1148 loop : -2.60 (0.10), residues: 3311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 103 HIS 0.009 0.002 HIS04 52 PHE 0.028 0.003 PHE32 18 TYR 0.032 0.002 TYR07 142 ARG 0.013 0.001 ARG I 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12914 Ramachandran restraints generated. 6457 Oldfield, 0 Emsley, 6457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12914 Ramachandran restraints generated. 6457 Oldfield, 0 Emsley, 6457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1324 residues out of total 5350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 386 poor density : 938 time to evaluate : 6.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 04 67 LYS cc_start: 0.8416 (tttt) cc_final: 0.7699 (tptt) REVERT: 05 165 MET cc_start: 0.8851 (ttt) cc_final: 0.8622 (ttt) REVERT: 06 1 MET cc_start: 0.8534 (tpp) cc_final: 0.8231 (tpp) REVERT: 06 9 GLN cc_start: 0.8171 (tt0) cc_final: 0.7651 (mp10) REVERT: 06 30 GLN cc_start: 0.9446 (tm-30) cc_final: 0.9091 (tm-30) REVERT: 07 129 MET cc_start: 0.8878 (ppp) cc_final: 0.8440 (ppp) REVERT: 07 176 PHE cc_start: 0.8881 (m-80) cc_final: 0.8186 (m-80) REVERT: 08 114 HIS cc_start: 0.7753 (t-170) cc_final: 0.7023 (t-90) REVERT: 08 146 ASP cc_start: 0.9244 (m-30) cc_final: 0.8769 (p0) REVERT: 08 174 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7285 (pttm) REVERT: 10 69 PHE cc_start: 0.8474 (t80) cc_final: 0.8175 (m-80) REVERT: 10 123 ILE cc_start: 0.7857 (OUTLIER) cc_final: 0.7641 (mt) REVERT: 12 44 TYR cc_start: 0.8925 (t80) cc_final: 0.8718 (t80) REVERT: 12 53 TYR cc_start: 0.8890 (m-80) cc_final: 0.8496 (m-80) REVERT: 13 7 MET cc_start: 0.8594 (mmt) cc_final: 0.8191 (mmm) REVERT: 13 20 MET cc_start: 0.9467 (tpp) cc_final: 0.9158 (tpp) REVERT: 13 45 GLU cc_start: 0.8324 (tm-30) cc_final: 0.7792 (tm-30) REVERT: 14 76 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8145 (mt-10) REVERT: 14 85 VAL cc_start: 0.8789 (m) cc_final: 0.8537 (p) REVERT: 15 1 MET cc_start: 0.7914 (mtp) cc_final: 0.7042 (pmm) REVERT: 15 14 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8768 (ttmm) REVERT: 15 17 ASN cc_start: 0.8692 (t0) cc_final: 0.8339 (t0) REVERT: 15 33 LEU cc_start: 0.8722 (tp) cc_final: 0.8372 (tt) REVERT: 15 47 GLU cc_start: 0.9100 (tm-30) cc_final: 0.8870 (tm-30) REVERT: 15 95 LEU cc_start: 0.9354 (mt) cc_final: 0.9076 (pp) REVERT: 16 20 MET cc_start: 0.9211 (ppp) cc_final: 0.8848 (ppp) REVERT: 16 110 MET cc_start: 0.9564 (mmp) cc_final: 0.8947 (mmm) REVERT: 16 112 TYR cc_start: 0.8672 (m-80) cc_final: 0.8323 (m-10) REVERT: 16 120 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6356 (pm20) REVERT: 19 8 ILE cc_start: 0.9069 (OUTLIER) cc_final: 0.8688 (mt) REVERT: 19 60 TRP cc_start: 0.9313 (m-10) cc_final: 0.8410 (m-90) REVERT: 19 108 LEU cc_start: 0.9762 (OUTLIER) cc_final: 0.9298 (tt) REVERT: 20 10 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8851 (ptmm) REVERT: 20 40 MET cc_start: 0.8945 (tmm) cc_final: 0.8569 (tmm) REVERT: 20 48 LYS cc_start: 0.8542 (ttmm) cc_final: 0.8131 (ttpp) REVERT: 20 76 LYS cc_start: 0.9439 (mmmm) cc_final: 0.9067 (mtmt) REVERT: 21 52 GLU cc_start: 0.9024 (tp30) cc_final: 0.8674 (tm-30) REVERT: 21 69 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8388 (mt) REVERT: 21 77 ASP cc_start: 0.7110 (t0) cc_final: 0.6745 (t0) REVERT: 21 78 GLU cc_start: 0.8319 (tm-30) cc_final: 0.8052 (tm-30) REVERT: 22 51 PHE cc_start: 0.8270 (OUTLIER) cc_final: 0.8045 (m-80) REVERT: 22 73 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7519 (mmm-85) REVERT: 24 34 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.7909 (pttm) REVERT: 25 51 ARG cc_start: 0.8200 (ptm160) cc_final: 0.7855 (ttp80) REVERT: 26 15 ASN cc_start: 0.8910 (m-40) cc_final: 0.8585 (t0) REVERT: 26 16 ASN cc_start: 0.9136 (t0) cc_final: 0.8856 (t0) REVERT: 26 55 MET cc_start: 0.9074 (mtp) cc_final: 0.8725 (mmm) REVERT: 28 53 MET cc_start: 0.9093 (ptm) cc_final: 0.8741 (tmm) REVERT: 29 1 MET cc_start: 0.8934 (OUTLIER) cc_final: 0.8200 (tmm) REVERT: 29 48 GLN cc_start: 0.8867 (tp-100) cc_final: 0.8282 (mp10) REVERT: 32 14 ARG cc_start: 0.9404 (mmt90) cc_final: 0.8781 (ttm110) REVERT: 33 27 ASN cc_start: 0.8954 (OUTLIER) cc_final: 0.8579 (t0) REVERT: B 48 MET cc_start: 0.9487 (mmm) cc_final: 0.9151 (tpp) REVERT: B 181 PRO cc_start: 0.8888 (Cg_exo) cc_final: 0.8592 (Cg_endo) REVERT: C 133 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.8753 (ptm) REVERT: C 177 LEU cc_start: 0.9612 (mt) cc_final: 0.9167 (tp) REVERT: C 189 HIS cc_start: 0.8909 (OUTLIER) cc_final: 0.8615 (m90) REVERT: E 60 GLN cc_start: 0.9013 (tp-100) cc_final: 0.8788 (tp-100) REVERT: F 21 MET cc_start: 0.8912 (mtt) cc_final: 0.8584 (mpp) REVERT: F 90 MET cc_start: 0.8813 (ttm) cc_final: 0.8220 (ttt) REVERT: H 26 MET cc_start: 0.9055 (ptp) cc_final: 0.8673 (pmm) REVERT: H 83 ARG cc_start: 0.8916 (mmt180) cc_final: 0.8360 (mmt-90) REVERT: J 64 GLN cc_start: 0.8736 (mt0) cc_final: 0.8474 (mt0) REVERT: J 85 ASP cc_start: 0.9011 (t0) cc_final: 0.8665 (t0) REVERT: K 63 GLN cc_start: 0.9368 (tp40) cc_final: 0.9081 (tp40) REVERT: L 75 GLU cc_start: 0.9004 (tp30) cc_final: 0.8801 (tp30) REVERT: M 22 TYR cc_start: 0.8728 (t80) cc_final: 0.8394 (t80) REVERT: M 67 ASP cc_start: 0.8915 (m-30) cc_final: 0.8523 (m-30) REVERT: N 5 MET cc_start: 0.9046 (mmm) cc_final: 0.8834 (mmt) REVERT: N 30 ILE cc_start: 0.9212 (tt) cc_final: 0.8914 (mm) REVERT: N 85 GLU cc_start: 0.9168 (tp30) cc_final: 0.8958 (tm-30) REVERT: O 58 MET cc_start: 0.9205 (ppp) cc_final: 0.8607 (ppp) REVERT: O 61 GLN cc_start: 0.9242 (OUTLIER) cc_final: 0.8955 (pt0) REVERT: R 62 ARG cc_start: 0.9252 (mtt180) cc_final: 0.8793 (tpp80) REVERT: R 63 TYR cc_start: 0.9414 (t80) cc_final: 0.9097 (t80) REVERT: S 11 ASP cc_start: 0.8073 (m-30) cc_final: 0.7855 (m-30) REVERT: T 14 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8437 (mm-30) REVERT: T 35 TYR cc_start: 0.8902 (OUTLIER) cc_final: 0.8676 (m-10) REVERT: U 44 ARG cc_start: 0.8091 (ttm-80) cc_final: 0.7737 (ttt180) REVERT: Z 87 TYR cc_start: 0.6659 (m-80) cc_final: 0.6178 (m-80) REVERT: Z 114 GLN cc_start: 0.7739 (mm-40) cc_final: 0.7292 (tt0) REVERT: Z 244 ILE cc_start: 0.8995 (mp) cc_final: 0.8761 (mp) REVERT: Z 322 PHE cc_start: 0.3777 (OUTLIER) cc_final: 0.3476 (p90) REVERT: Z 349 MET cc_start: 0.7615 (ptm) cc_final: 0.7377 (ptm) REVERT: Z 358 MET cc_start: 0.6392 (OUTLIER) cc_final: 0.6119 (pmm) outliers start: 386 outliers final: 289 residues processed: 1190 average time/residue: 1.4100 time to fit residues: 2974.2132 Evaluate side-chains 1179 residues out of total 5350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 308 poor density : 871 time to evaluate : 6.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 2 VAL Chi-restraints excluded: chain 04 residue 156 SER Chi-restraints excluded: chain 04 residue 179 GLU Chi-restraints excluded: chain 04 residue 267 VAL Chi-restraints excluded: chain 05 residue 2 ILE Chi-restraints excluded: chain 05 residue 22 ILE Chi-restraints excluded: chain 05 residue 27 ILE Chi-restraints excluded: chain 05 residue 42 ASN Chi-restraints excluded: chain 05 residue 107 VAL Chi-restraints excluded: chain 05 residue 109 VAL Chi-restraints excluded: chain 05 residue 137 SER Chi-restraints excluded: chain 05 residue 139 SER Chi-restraints excluded: chain 05 residue 151 THR Chi-restraints excluded: chain 05 residue 186 LEU Chi-restraints excluded: chain 06 residue 7 ASP Chi-restraints excluded: chain 06 residue 48 THR Chi-restraints excluded: chain 06 residue 140 ASP Chi-restraints excluded: chain 07 residue 39 VAL Chi-restraints excluded: chain 07 residue 49 LEU Chi-restraints excluded: chain 07 residue 143 ASP Chi-restraints excluded: chain 07 residue 151 LEU Chi-restraints excluded: chain 08 residue 10 VAL Chi-restraints excluded: chain 08 residue 15 ASP Chi-restraints excluded: chain 08 residue 167 VAL Chi-restraints excluded: chain 08 residue 174 LYS Chi-restraints excluded: chain 09 residue 12 LEU Chi-restraints excluded: chain 09 residue 89 LYS Chi-restraints excluded: chain 09 residue 101 ASP Chi-restraints excluded: chain 09 residue 145 ASN Chi-restraints excluded: chain 10 residue 29 ASP Chi-restraints excluded: chain 10 residue 41 LEU Chi-restraints excluded: chain 10 residue 116 GLU Chi-restraints excluded: chain 10 residue 123 ILE Chi-restraints excluded: chain 10 residue 131 THR Chi-restraints excluded: chain 11 residue 41 PHE Chi-restraints excluded: chain 11 residue 56 VAL Chi-restraints excluded: chain 11 residue 93 ASN Chi-restraints excluded: chain 11 residue 111 THR Chi-restraints excluded: chain 11 residue 121 ILE Chi-restraints excluded: chain 11 residue 126 ARG Chi-restraints excluded: chain 11 residue 135 MET Chi-restraints excluded: chain 12 residue 14 ASP Chi-restraints excluded: chain 12 residue 84 ILE Chi-restraints excluded: chain 12 residue 118 MET Chi-restraints excluded: chain 12 residue 131 ASN Chi-restraints excluded: chain 13 residue 21 CYS Chi-restraints excluded: chain 13 residue 22 ILE Chi-restraints excluded: chain 13 residue 32 TYR Chi-restraints excluded: chain 13 residue 35 VAL Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 52 VAL Chi-restraints excluded: chain 13 residue 56 ASP Chi-restraints excluded: chain 13 residue 61 VAL Chi-restraints excluded: chain 13 residue 65 THR Chi-restraints excluded: chain 13 residue 75 SER Chi-restraints excluded: chain 13 residue 88 ASN Chi-restraints excluded: chain 13 residue 90 ASN Chi-restraints excluded: chain 13 residue 104 THR Chi-restraints excluded: chain 13 residue 110 GLU Chi-restraints excluded: chain 13 residue 118 LEU Chi-restraints excluded: chain 14 residue 25 SER Chi-restraints excluded: chain 14 residue 27 LEU Chi-restraints excluded: chain 14 residue 46 VAL Chi-restraints excluded: chain 14 residue 76 GLU Chi-restraints excluded: chain 14 residue 80 SER Chi-restraints excluded: chain 14 residue 92 LEU Chi-restraints excluded: chain 14 residue 129 LYS Chi-restraints excluded: chain 15 residue 7 THR Chi-restraints excluded: chain 15 residue 14 LYS Chi-restraints excluded: chain 16 residue 1 MET Chi-restraints excluded: chain 16 residue 36 THR Chi-restraints excluded: chain 16 residue 37 THR Chi-restraints excluded: chain 16 residue 48 VAL Chi-restraints excluded: chain 16 residue 63 ARG Chi-restraints excluded: chain 16 residue 76 VAL Chi-restraints excluded: chain 16 residue 114 GLU Chi-restraints excluded: chain 17 residue 16 ARG Chi-restraints excluded: chain 17 residue 19 GLN Chi-restraints excluded: chain 17 residue 35 ILE Chi-restraints excluded: chain 17 residue 43 ASN Chi-restraints excluded: chain 17 residue 47 VAL Chi-restraints excluded: chain 17 residue 49 VAL Chi-restraints excluded: chain 17 residue 54 VAL Chi-restraints excluded: chain 17 residue 61 GLN Chi-restraints excluded: chain 17 residue 74 VAL Chi-restraints excluded: chain 18 residue 7 LEU Chi-restraints excluded: chain 18 residue 15 ASP Chi-restraints excluded: chain 18 residue 40 GLN Chi-restraints excluded: chain 18 residue 49 ILE Chi-restraints excluded: chain 18 residue 91 VAL Chi-restraints excluded: chain 18 residue 103 THR Chi-restraints excluded: chain 19 residue 8 ILE Chi-restraints excluded: chain 19 residue 16 ILE Chi-restraints excluded: chain 19 residue 33 VAL Chi-restraints excluded: chain 19 residue 108 LEU Chi-restraints excluded: chain 20 residue 10 LYS Chi-restraints excluded: chain 20 residue 38 VAL Chi-restraints excluded: chain 20 residue 53 PHE Chi-restraints excluded: chain 20 residue 58 VAL Chi-restraints excluded: chain 20 residue 81 LYS Chi-restraints excluded: chain 20 residue 85 LYS Chi-restraints excluded: chain 20 residue 99 THR Chi-restraints excluded: chain 21 residue 3 THR Chi-restraints excluded: chain 21 residue 45 VAL Chi-restraints excluded: chain 21 residue 53 SER Chi-restraints excluded: chain 21 residue 62 ASP Chi-restraints excluded: chain 21 residue 69 LEU Chi-restraints excluded: chain 21 residue 72 THR Chi-restraints excluded: chain 21 residue 101 SER Chi-restraints excluded: chain 21 residue 107 VAL Chi-restraints excluded: chain 22 residue 37 ASP Chi-restraints excluded: chain 22 residue 50 LEU Chi-restraints excluded: chain 22 residue 51 PHE Chi-restraints excluded: chain 22 residue 73 ARG Chi-restraints excluded: chain 22 residue 74 ILE Chi-restraints excluded: chain 22 residue 79 ASP Chi-restraints excluded: chain 23 residue 9 GLU Chi-restraints excluded: chain 23 residue 12 VAL Chi-restraints excluded: chain 23 residue 13 LEU Chi-restraints excluded: chain 23 residue 14 THR Chi-restraints excluded: chain 23 residue 17 ASP Chi-restraints excluded: chain 23 residue 26 ASN Chi-restraints excluded: chain 23 residue 33 VAL Chi-restraints excluded: chain 23 residue 34 ILE Chi-restraints excluded: chain 23 residue 43 LYS Chi-restraints excluded: chain 23 residue 45 GLN Chi-restraints excluded: chain 24 residue 3 THR Chi-restraints excluded: chain 24 residue 10 LYS Chi-restraints excluded: chain 24 residue 34 LYS Chi-restraints excluded: chain 24 residue 38 LEU Chi-restraints excluded: chain 24 residue 65 VAL Chi-restraints excluded: chain 24 residue 87 GLN Chi-restraints excluded: chain 25 residue 7 ARG Chi-restraints excluded: chain 25 residue 12 SER Chi-restraints excluded: chain 25 residue 17 LEU Chi-restraints excluded: chain 25 residue 19 VAL Chi-restraints excluded: chain 25 residue 20 LYS Chi-restraints excluded: chain 25 residue 34 VAL Chi-restraints excluded: chain 25 residue 52 ASP Chi-restraints excluded: chain 25 residue 67 VAL Chi-restraints excluded: chain 26 residue 22 ASN Chi-restraints excluded: chain 26 residue 41 SER Chi-restraints excluded: chain 26 residue 57 VAL Chi-restraints excluded: chain 26 residue 66 VAL Chi-restraints excluded: chain 27 residue 7 ARG Chi-restraints excluded: chain 27 residue 11 VAL Chi-restraints excluded: chain 27 residue 50 VAL Chi-restraints excluded: chain 27 residue 59 GLU Chi-restraints excluded: chain 28 residue 26 LEU Chi-restraints excluded: chain 28 residue 31 ILE Chi-restraints excluded: chain 28 residue 39 ASP Chi-restraints excluded: chain 29 residue 1 MET 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 2 VAL Chi-restraints excluded: chain 30 residue 8 THR Chi-restraints excluded: chain 31 residue 23 THR Chi-restraints excluded: chain 31 residue 31 GLU Chi-restraints excluded: chain 31 residue 42 VAL Chi-restraints excluded: chain 31 residue 47 ILE Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 33 residue 5 THR Chi-restraints excluded: chain 33 residue 6 VAL Chi-restraints excluded: chain 33 residue 27 ASN Chi-restraints excluded: chain 33 residue 57 VAL Chi-restraints excluded: chain 34 residue 10 LEU Chi-restraints excluded: chain 34 residue 28 SER Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 112 ARG Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 56 ILE Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 189 HIS Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 120 HIS Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 67 ASN Chi-restraints excluded: chain G residue 129 ASN Chi-restraints excluded: chain G residue 141 HIS Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 57 GLU Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 24 ASN Chi-restraints excluded: chain I residue 30 ASN Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 127 SER Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 56 HIS Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 32 THR Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 84 MET Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 120 CYS Chi-restraints excluded: chain K residue 124 LYS Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 102 ASP Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 61 GLN Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 29 ASN Chi-restraints excluded: chain P residue 42 ILE Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain Q residue 59 GLU Chi-restraints excluded: chain Q residue 74 LEU Chi-restraints excluded: chain R residue 21 ASP Chi-restraints excluded: chain S residue 10 ILE Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 35 TYR Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 83 ASN Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain U residue 36 PHE Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain 03 residue 79 THR Chi-restraints excluded: chain 03 residue 215 SER Chi-restraints excluded: chain Z residue 22 HIS Chi-restraints excluded: chain Z residue 27 LEU Chi-restraints excluded: chain Z residue 32 THR Chi-restraints excluded: chain Z residue 156 LEU Chi-restraints excluded: chain Z residue 215 GLU Chi-restraints excluded: chain Z residue 235 ILE Chi-restraints excluded: chain Z residue 245 VAL Chi-restraints excluded: chain Z residue 311 LEU Chi-restraints excluded: chain Z residue 322 PHE Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 335 THR Chi-restraints excluded: chain Z residue 336 ASP Chi-restraints excluded: chain Z residue 358 MET Chi-restraints excluded: chain Z residue 359 VAL Chi-restraints excluded: chain Z residue 362 LEU Chi-restraints excluded: chain Z residue 369 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1111 random chunks: chunk 361 optimal weight: 7.9990 chunk 967 optimal weight: 20.0000 chunk 212 optimal weight: 6.9990 chunk 630 optimal weight: 20.0000 chunk 265 optimal weight: 5.9990 chunk 1074 optimal weight: 10.0000 chunk 892 optimal weight: 20.0000 chunk 497 optimal weight: 20.0000 chunk 89 optimal weight: 9.9990 chunk 355 optimal weight: 0.5980 chunk 564 optimal weight: 0.0470 overall best weight: 4.3284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 04 14 HIS 04 85 ASN ** 04 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 44 HIS 09 20 ASN 09 33 GLN ** 09 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 10 4 ASN ** 10 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 14 35 HIS 16 23 ASN 16 31 HIS 18 74 GLN ** 19 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 21 15 GLN ** 22 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 32 13 ASN ** 32 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 33 27 ASN 34 35 GLN ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 65 GLN R 18 GLN S 68 HIS ** 03 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 03 165 ASN ** 03 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 48 GLN ** Z 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.4686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 167491 Z= 0.186 Angle : 0.619 15.961 250000 Z= 0.316 Chirality : 0.035 0.309 31892 Planarity : 0.005 0.060 13835 Dihedral : 23.764 178.586 82415 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 20.52 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.57 % Favored : 90.31 % Rotamer: Outliers : 5.29 % Allowed : 24.25 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.10), residues: 6457 helix: -0.63 (0.11), residues: 1997 sheet: -2.03 (0.14), residues: 1128 loop : -2.36 (0.10), residues: 3332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP04 247 HIS 0.007 0.001 HIS04 52 PHE 0.029 0.002 PHE11 37 TYR 0.029 0.002 TYR U 37 ARG 0.018 0.001 ARG J 31 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12914 Ramachandran restraints generated. 6457 Oldfield, 0 Emsley, 6457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12914 Ramachandran restraints generated. 6457 Oldfield, 0 Emsley, 6457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1316 residues out of total 5350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 283 poor density : 1033 time to evaluate : 6.776 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 67 LYS cc_start: 0.8351 (tttt) cc_final: 0.7614 (tptt) REVERT: 05 165 MET cc_start: 0.8866 (ttt) cc_final: 0.8612 (ttt) REVERT: 06 1 MET cc_start: 0.8320 (tpp) cc_final: 0.8029 (tpp) REVERT: 06 9 GLN cc_start: 0.8092 (tt0) cc_final: 0.7557 (mp10) REVERT: 06 30 GLN cc_start: 0.9400 (tm-30) cc_final: 0.9023 (tm-30) REVERT: 07 129 MET cc_start: 0.8838 (ppp) cc_final: 0.8414 (ppp) REVERT: 07 176 PHE cc_start: 0.8920 (m-80) cc_final: 0.8211 (m-80) REVERT: 08 146 ASP cc_start: 0.9149 (m-30) cc_final: 0.8788 (m-30) REVERT: 08 174 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7260 (pttm) REVERT: 10 69 PHE cc_start: 0.8481 (t80) cc_final: 0.8205 (m-80) REVERT: 10 82 ILE cc_start: 0.6423 (mm) cc_final: 0.6151 (tp) REVERT: 10 123 ILE cc_start: 0.7915 (OUTLIER) cc_final: 0.7700 (mt) REVERT: 12 44 TYR cc_start: 0.8870 (t80) cc_final: 0.8658 (t80) REVERT: 13 7 MET cc_start: 0.8486 (mmt) cc_final: 0.8119 (mmm) REVERT: 13 20 MET cc_start: 0.9385 (tpp) cc_final: 0.9100 (tpt) REVERT: 13 116 ILE cc_start: 0.9289 (OUTLIER) cc_final: 0.9081 (pt) REVERT: 15 1 MET cc_start: 0.7717 (mtp) cc_final: 0.6916 (pmm) REVERT: 15 17 ASN cc_start: 0.8688 (t0) cc_final: 0.8367 (t0) REVERT: 15 33 LEU cc_start: 0.8524 (tp) cc_final: 0.8237 (tt) REVERT: 15 53 MET cc_start: 0.8897 (tpp) cc_final: 0.8670 (tpp) REVERT: 16 1 MET cc_start: 0.8483 (pmm) cc_final: 0.8273 (pmm) REVERT: 16 20 MET cc_start: 0.9123 (ppp) cc_final: 0.8842 (ptm) REVERT: 16 43 GLU cc_start: 0.9271 (tp30) cc_final: 0.8844 (mt-10) REVERT: 16 110 MET cc_start: 0.9492 (mmp) cc_final: 0.8905 (mmm) REVERT: 16 112 TYR cc_start: 0.8491 (m-80) cc_final: 0.8166 (m-10) REVERT: 16 120 GLU cc_start: 0.6955 (mm-30) cc_final: 0.6190 (pm20) REVERT: 19 8 ILE cc_start: 0.8874 (OUTLIER) cc_final: 0.8523 (mt) REVERT: 19 60 TRP cc_start: 0.9322 (m-10) cc_final: 0.8383 (m-90) REVERT: 20 40 MET cc_start: 0.8935 (tmm) cc_final: 0.8506 (tmm) REVERT: 20 48 LYS cc_start: 0.8527 (ttmm) cc_final: 0.8325 (ttpp) REVERT: 20 76 LYS cc_start: 0.9334 (mmmm) cc_final: 0.9008 (mtmt) REVERT: 21 52 GLU cc_start: 0.8964 (tp30) cc_final: 0.8455 (tm-30) REVERT: 21 77 ASP cc_start: 0.7244 (t0) cc_final: 0.6828 (t0) REVERT: 22 25 GLU cc_start: 0.8884 (pt0) cc_final: 0.8518 (pp20) REVERT: 22 51 PHE cc_start: 0.8166 (OUTLIER) cc_final: 0.7867 (m-80) REVERT: 24 34 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.7872 (pttm) REVERT: 25 17 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8326 (tp) REVERT: 25 62 LYS cc_start: 0.8659 (mmpt) cc_final: 0.8417 (mmmt) REVERT: 26 15 ASN cc_start: 0.8910 (m-40) cc_final: 0.8581 (t0) REVERT: 26 16 ASN cc_start: 0.9108 (t0) cc_final: 0.8841 (t0) REVERT: 26 55 MET cc_start: 0.9061 (mtp) cc_final: 0.8816 (mmm) REVERT: 30 27 LEU cc_start: 0.8538 (tp) cc_final: 0.8287 (tp) REVERT: 33 27 ASN cc_start: 0.8941 (OUTLIER) cc_final: 0.8566 (t0) REVERT: 34 35 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8639 (mp10) REVERT: B 48 MET cc_start: 0.9505 (mmm) cc_final: 0.9282 (tpp) REVERT: B 181 PRO cc_start: 0.8863 (Cg_exo) cc_final: 0.8570 (Cg_endo) REVERT: C 5 HIS cc_start: 0.8884 (t-90) cc_final: 0.8547 (t-170) REVERT: C 133 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.8701 (ptm) REVERT: C 141 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8381 (ttt) REVERT: C 177 LEU cc_start: 0.9633 (mt) cc_final: 0.9332 (pp) REVERT: D 102 TYR cc_start: 0.8572 (t80) cc_final: 0.8211 (t80) REVERT: E 60 GLN cc_start: 0.8941 (tp-100) cc_final: 0.8712 (tp-100) REVERT: E 163 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8170 (pt) REVERT: F 21 MET cc_start: 0.8825 (mtt) cc_final: 0.8507 (mpp) REVERT: F 61 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8333 (pp) REVERT: H 26 MET cc_start: 0.8969 (ptp) cc_final: 0.8768 (pmm) REVERT: H 41 GLU cc_start: 0.8865 (mp0) cc_final: 0.8568 (pm20) REVERT: H 83 ARG cc_start: 0.8884 (mmt180) cc_final: 0.8634 (mmt-90) REVERT: J 64 GLN cc_start: 0.8729 (mt0) cc_final: 0.8477 (mt0) REVERT: K 37 GLN cc_start: 0.9130 (mp10) cc_final: 0.8807 (mp10) REVERT: K 63 GLN cc_start: 0.9323 (tp40) cc_final: 0.9001 (tp40) REVERT: M 22 TYR cc_start: 0.8597 (t80) cc_final: 0.8269 (t80) REVERT: M 67 ASP cc_start: 0.8706 (m-30) cc_final: 0.8280 (m-30) REVERT: M 96 VAL cc_start: 0.9435 (OUTLIER) cc_final: 0.9072 (p) REVERT: N 3 GLN cc_start: 0.9266 (mm110) cc_final: 0.8963 (mp10) REVERT: N 30 ILE cc_start: 0.9097 (tt) cc_final: 0.8782 (mm) REVERT: O 57 ARG cc_start: 0.9104 (ttp80) cc_final: 0.8109 (ttp80) REVERT: O 58 MET cc_start: 0.9214 (ppp) cc_final: 0.8393 (ppp) REVERT: O 61 GLN cc_start: 0.9166 (tt0) cc_final: 0.8913 (pt0) REVERT: Q 17 GLU cc_start: 0.8376 (tt0) cc_final: 0.7698 (tm-30) REVERT: R 12 PHE cc_start: 0.8075 (m-80) cc_final: 0.7756 (m-10) REVERT: R 63 TYR cc_start: 0.9362 (t80) cc_final: 0.9052 (t80) REVERT: S 11 ASP cc_start: 0.7910 (m-30) cc_final: 0.7560 (m-30) REVERT: S 60 PHE cc_start: 0.8158 (t80) cc_final: 0.7299 (t80) REVERT: S 69 LYS cc_start: 0.8350 (mttm) cc_final: 0.7687 (mtmt) REVERT: S 72 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8004 (mm-30) REVERT: Z 87 TYR cc_start: 0.6530 (m-80) cc_final: 0.6149 (m-80) REVERT: Z 114 GLN cc_start: 0.7708 (mm-40) cc_final: 0.7264 (tt0) REVERT: Z 151 MET cc_start: 0.8742 (mtt) cc_final: 0.8297 (tpt) REVERT: Z 322 PHE cc_start: 0.3635 (OUTLIER) cc_final: 0.3254 (p90) REVERT: Z 358 MET cc_start: 0.6334 (OUTLIER) cc_final: 0.6031 (pmm) outliers start: 283 outliers final: 196 residues processed: 1206 average time/residue: 1.2953 time to fit residues: 2748.7218 Evaluate side-chains 1131 residues out of total 5350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 918 time to evaluate : 6.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 2 VAL Chi-restraints excluded: chain 04 residue 156 SER Chi-restraints excluded: chain 04 residue 179 GLU Chi-restraints excluded: chain 04 residue 219 VAL Chi-restraints excluded: chain 05 residue 2 ILE Chi-restraints excluded: chain 05 residue 27 ILE Chi-restraints excluded: chain 05 residue 107 VAL Chi-restraints excluded: chain 05 residue 137 SER Chi-restraints excluded: chain 05 residue 139 SER Chi-restraints excluded: chain 05 residue 201 LEU Chi-restraints excluded: chain 06 residue 48 THR Chi-restraints excluded: chain 07 residue 27 VAL Chi-restraints excluded: chain 07 residue 39 VAL Chi-restraints excluded: chain 07 residue 49 LEU Chi-restraints excluded: chain 07 residue 133 GLU Chi-restraints excluded: chain 07 residue 151 LEU Chi-restraints excluded: chain 08 residue 10 VAL Chi-restraints excluded: chain 08 residue 102 ILE Chi-restraints excluded: chain 08 residue 174 LYS Chi-restraints excluded: chain 09 residue 12 LEU Chi-restraints excluded: chain 09 residue 89 LYS Chi-restraints excluded: chain 09 residue 145 ASN Chi-restraints excluded: chain 10 residue 29 ASP Chi-restraints excluded: chain 10 residue 41 LEU Chi-restraints excluded: chain 10 residue 123 ILE Chi-restraints excluded: chain 11 residue 35 MET Chi-restraints excluded: chain 11 residue 41 PHE Chi-restraints excluded: chain 11 residue 56 VAL Chi-restraints excluded: chain 11 residue 111 THR Chi-restraints excluded: chain 11 residue 121 ILE Chi-restraints excluded: chain 11 residue 135 MET Chi-restraints excluded: chain 12 residue 14 ASP Chi-restraints excluded: chain 12 residue 84 ILE Chi-restraints excluded: chain 12 residue 118 MET Chi-restraints excluded: chain 12 residue 131 ASN Chi-restraints excluded: chain 13 residue 32 TYR Chi-restraints excluded: chain 13 residue 35 VAL Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 56 ASP Chi-restraints excluded: chain 13 residue 61 VAL Chi-restraints excluded: chain 13 residue 65 THR Chi-restraints excluded: chain 13 residue 88 ASN Chi-restraints excluded: chain 13 residue 104 THR Chi-restraints excluded: chain 13 residue 116 ILE Chi-restraints excluded: chain 14 residue 25 SER Chi-restraints excluded: chain 14 residue 27 LEU Chi-restraints excluded: chain 14 residue 46 VAL Chi-restraints excluded: chain 14 residue 122 VAL Chi-restraints excluded: chain 14 residue 129 LYS Chi-restraints excluded: chain 15 residue 7 THR Chi-restraints excluded: chain 16 residue 36 THR Chi-restraints excluded: chain 17 residue 35 ILE Chi-restraints excluded: chain 17 residue 47 VAL Chi-restraints excluded: chain 17 residue 54 VAL Chi-restraints excluded: chain 18 residue 15 ASP Chi-restraints excluded: chain 18 residue 24 THR Chi-restraints excluded: chain 18 residue 40 GLN Chi-restraints excluded: chain 18 residue 49 ILE Chi-restraints excluded: chain 18 residue 103 THR Chi-restraints excluded: chain 19 residue 8 ILE Chi-restraints excluded: chain 19 residue 16 ILE Chi-restraints excluded: chain 19 residue 108 LEU Chi-restraints excluded: chain 20 residue 53 PHE Chi-restraints excluded: chain 20 residue 58 VAL Chi-restraints excluded: chain 20 residue 85 LYS Chi-restraints excluded: chain 20 residue 99 THR Chi-restraints excluded: chain 21 residue 3 THR Chi-restraints excluded: chain 21 residue 53 SER Chi-restraints excluded: chain 21 residue 62 ASP Chi-restraints excluded: chain 21 residue 101 SER Chi-restraints excluded: chain 22 residue 37 ASP Chi-restraints excluded: chain 22 residue 50 LEU Chi-restraints excluded: chain 22 residue 51 PHE Chi-restraints excluded: chain 22 residue 73 ARG Chi-restraints excluded: chain 22 residue 74 ILE Chi-restraints excluded: chain 22 residue 79 ASP Chi-restraints excluded: chain 23 residue 9 GLU Chi-restraints excluded: chain 23 residue 12 VAL Chi-restraints excluded: chain 23 residue 13 LEU Chi-restraints excluded: chain 23 residue 14 THR Chi-restraints excluded: chain 23 residue 26 ASN Chi-restraints excluded: chain 23 residue 33 VAL Chi-restraints excluded: chain 23 residue 34 ILE Chi-restraints excluded: chain 23 residue 43 LYS Chi-restraints excluded: chain 23 residue 71 ILE Chi-restraints excluded: chain 24 residue 3 THR Chi-restraints excluded: chain 24 residue 10 LYS Chi-restraints excluded: chain 24 residue 34 LYS Chi-restraints excluded: chain 24 residue 38 LEU Chi-restraints excluded: chain 24 residue 65 VAL Chi-restraints excluded: chain 24 residue 87 GLN Chi-restraints excluded: chain 25 residue 7 ARG Chi-restraints excluded: chain 25 residue 12 SER Chi-restraints excluded: chain 25 residue 17 LEU Chi-restraints excluded: chain 25 residue 19 VAL Chi-restraints excluded: chain 25 residue 67 VAL Chi-restraints excluded: chain 26 residue 41 SER Chi-restraints excluded: chain 27 residue 48 ARG Chi-restraints excluded: chain 28 residue 40 THR Chi-restraints excluded: chain 29 residue 5 ILE Chi-restraints excluded: chain 29 residue 44 PHE Chi-restraints excluded: chain 29 residue 53 THR Chi-restraints excluded: chain 30 residue 2 VAL Chi-restraints excluded: chain 31 residue 42 VAL Chi-restraints excluded: chain 31 residue 47 ILE Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 33 residue 5 THR Chi-restraints excluded: chain 33 residue 27 ASN Chi-restraints excluded: chain 34 residue 10 LEU Chi-restraints excluded: chain 34 residue 28 SER Chi-restraints excluded: chain 34 residue 35 GLN Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 120 HIS Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 67 ASN Chi-restraints excluded: chain G residue 129 ASN Chi-restraints excluded: chain G residue 141 HIS Chi-restraints excluded: chain I residue 24 ASN Chi-restraints excluded: chain I residue 30 ASN Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 105 ARG Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 96 ILE Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 120 CYS Chi-restraints excluded: chain K residue 124 LYS Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 74 GLN Chi-restraints excluded: chain L residue 102 ASP Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 29 ASN Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain R residue 21 ASP Chi-restraints excluded: chain R residue 35 SER Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 71 ASP Chi-restraints excluded: chain S residue 10 ILE Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain S residue 72 GLU Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain U residue 36 PHE Chi-restraints excluded: chain 03 residue 79 THR Chi-restraints excluded: chain 03 residue 215 SER Chi-restraints excluded: chain Z residue 20 VAL Chi-restraints excluded: chain Z residue 27 LEU Chi-restraints excluded: chain Z residue 32 THR Chi-restraints excluded: chain Z residue 156 LEU Chi-restraints excluded: chain Z residue 245 VAL Chi-restraints excluded: chain Z residue 311 LEU Chi-restraints excluded: chain Z residue 322 PHE Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 335 THR Chi-restraints excluded: chain Z residue 336 ASP Chi-restraints excluded: chain Z residue 358 MET Chi-restraints excluded: chain Z residue 359 VAL Chi-restraints excluded: chain Z residue 369 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1111 random chunks: chunk 1036 optimal weight: 20.0000 chunk 121 optimal weight: 0.0980 chunk 612 optimal weight: 20.0000 chunk 784 optimal weight: 20.0000 chunk 608 optimal weight: 20.0000 chunk 904 optimal weight: 20.0000 chunk 600 optimal weight: 20.0000 chunk 1070 optimal weight: 50.0000 chunk 670 optimal weight: 20.0000 chunk 652 optimal weight: 20.0000 chunk 494 optimal weight: 20.0000 overall best weight: 16.0196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 04 14 HIS ** 04 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 04 133 ASN ** 05 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 06 94 GLN ** 08 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 44 HIS 09 20 ASN ** 09 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 10 4 ASN ** 10 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 12 128 ASN ** 12 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 9 ASN 14 35 HIS ** 14 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 16 23 ASN 16 31 HIS ** 19 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 22 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 32 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 33 27 ASN 34 35 GLN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 ASN ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 30 ASN ** 03 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 03 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 03 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 159 GLN ** Z 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.5194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.105 167491 Z= 0.500 Angle : 0.858 15.821 250000 Z= 0.431 Chirality : 0.044 0.362 31892 Planarity : 0.006 0.086 13835 Dihedral : 24.006 179.959 82411 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 35.55 Ramachandran Plot: Outliers : 0.14 % Allowed : 13.41 % Favored : 86.45 % Rotamer: Outliers : 7.18 % Allowed : 23.93 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.10), residues: 6457 helix: -1.00 (0.11), residues: 1993 sheet: -2.12 (0.14), residues: 1170 loop : -2.56 (0.10), residues: 3294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 103 HIS 0.022 0.002 HIS Z 22 PHE 0.038 0.003 PHE04 239 TYR 0.033 0.003 TYR S 79 ARG 0.015 0.001 ARG27 7 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12914 Ramachandran restraints generated. 6457 Oldfield, 0 Emsley, 6457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12914 Ramachandran restraints generated. 6457 Oldfield, 0 Emsley, 6457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1260 residues out of total 5350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 384 poor density : 876 time to evaluate : 7.194 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: 05 165 MET cc_start: 0.8843 (ttt) cc_final: 0.8634 (ttt) REVERT: 06 9 GLN cc_start: 0.8175 (tt0) cc_final: 0.7664 (mp10) REVERT: 06 30 GLN cc_start: 0.9447 (tm-30) cc_final: 0.9132 (tm-30) REVERT: 07 129 MET cc_start: 0.8921 (ppp) cc_final: 0.8638 (ppp) REVERT: 07 174 PHE cc_start: 0.9205 (OUTLIER) cc_final: 0.8814 (t80) REVERT: 07 176 PHE cc_start: 0.8907 (m-80) cc_final: 0.8162 (m-80) REVERT: 08 57 TYR cc_start: 0.8647 (m-10) cc_final: 0.8388 (m-10) REVERT: 08 146 ASP cc_start: 0.9137 (m-30) cc_final: 0.8778 (p0) REVERT: 08 174 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7373 (pttm) REVERT: 08 176 LYS cc_start: 0.5375 (tppt) cc_final: 0.4845 (mptt) REVERT: 10 6 GLN cc_start: 0.9223 (mm-40) cc_final: 0.9011 (tm-30) REVERT: 10 69 PHE cc_start: 0.8414 (t80) cc_final: 0.8098 (m-80) REVERT: 12 53 TYR cc_start: 0.8927 (m-80) cc_final: 0.8565 (m-80) REVERT: 13 20 MET cc_start: 0.9471 (tpp) cc_final: 0.9147 (tpp) REVERT: 13 116 ILE cc_start: 0.9329 (OUTLIER) cc_final: 0.9112 (pt) REVERT: 14 76 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8225 (mt-10) REVERT: 15 1 MET cc_start: 0.7919 (mtp) cc_final: 0.6928 (pmm) REVERT: 15 17 ASN cc_start: 0.8603 (t0) cc_final: 0.8165 (t0) REVERT: 15 33 LEU cc_start: 0.8763 (tp) cc_final: 0.8399 (tt) REVERT: 16 110 MET cc_start: 0.9567 (mmp) cc_final: 0.9280 (mmm) REVERT: 16 112 TYR cc_start: 0.8706 (m-80) cc_final: 0.8302 (m-10) REVERT: 16 120 GLU cc_start: 0.7125 (mm-30) cc_final: 0.6420 (pm20) REVERT: 19 8 ILE cc_start: 0.9118 (OUTLIER) cc_final: 0.8708 (mt) REVERT: 19 60 TRP cc_start: 0.9342 (m-10) cc_final: 0.8435 (m-90) REVERT: 19 108 LEU cc_start: 0.9774 (OUTLIER) cc_final: 0.9347 (tt) REVERT: 20 10 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8821 (ptmm) REVERT: 20 40 MET cc_start: 0.8990 (tmm) cc_final: 0.8640 (tmm) REVERT: 20 48 LYS cc_start: 0.8502 (ttmm) cc_final: 0.8146 (ttpp) REVERT: 20 76 LYS cc_start: 0.9468 (mmmm) cc_final: 0.9078 (mtmt) REVERT: 20 78 ARG cc_start: 0.9192 (mmm-85) cc_final: 0.8590 (mtt-85) REVERT: 21 52 GLU cc_start: 0.9066 (tp30) cc_final: 0.8547 (tm-30) REVERT: 21 69 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8437 (mt) REVERT: 21 77 ASP cc_start: 0.7393 (t0) cc_final: 0.6940 (t0) REVERT: 21 109 ASP cc_start: 0.8139 (p0) cc_final: 0.7869 (p0) REVERT: 22 51 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.8082 (m-80) REVERT: 24 34 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.7908 (pttm) REVERT: 26 15 ASN cc_start: 0.8912 (m-40) cc_final: 0.8638 (t0) REVERT: 26 16 ASN cc_start: 0.9146 (t0) cc_final: 0.8917 (t0) REVERT: 26 55 MET cc_start: 0.9127 (mtp) cc_final: 0.8828 (mmm) REVERT: 27 17 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8725 (pt0) REVERT: 27 29 ARG cc_start: 0.8863 (OUTLIER) cc_final: 0.7766 (ptp90) REVERT: 28 53 MET cc_start: 0.9177 (ptm) cc_final: 0.8919 (tmm) REVERT: 29 48 GLN cc_start: 0.8857 (tp-100) cc_final: 0.8229 (mp10) REVERT: 31 24 LYS cc_start: 0.8613 (pttp) cc_final: 0.8305 (ptmt) REVERT: 33 27 ASN cc_start: 0.8966 (OUTLIER) cc_final: 0.8650 (t0) REVERT: B 48 MET cc_start: 0.9492 (mmm) cc_final: 0.9169 (tpp) REVERT: B 181 PRO cc_start: 0.8942 (Cg_exo) cc_final: 0.8652 (Cg_endo) REVERT: C 133 MET cc_start: 0.9033 (OUTLIER) cc_final: 0.8690 (ptm) REVERT: C 141 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8309 (ttt) REVERT: C 177 LEU cc_start: 0.9642 (mt) cc_final: 0.9236 (tp) REVERT: E 23 THR cc_start: 0.8647 (OUTLIER) cc_final: 0.8128 (p) REVERT: E 60 GLN cc_start: 0.9043 (tp-100) cc_final: 0.8821 (tp-100) REVERT: F 21 MET cc_start: 0.8935 (mtt) cc_final: 0.8611 (mpp) REVERT: H 26 MET cc_start: 0.9035 (ptp) cc_final: 0.8712 (pmm) REVERT: H 83 ARG cc_start: 0.8886 (mmt180) cc_final: 0.8682 (mmt90) REVERT: J 64 GLN cc_start: 0.8773 (mt0) cc_final: 0.8481 (mt0) REVERT: K 63 GLN cc_start: 0.9361 (tp40) cc_final: 0.9046 (tp40) REVERT: L 75 GLU cc_start: 0.8989 (tp30) cc_final: 0.8761 (tp30) REVERT: M 7 ASN cc_start: 0.8553 (t0) cc_final: 0.8320 (t0) REVERT: M 22 TYR cc_start: 0.8662 (t80) cc_final: 0.8334 (t80) REVERT: N 3 GLN cc_start: 0.9237 (mm110) cc_final: 0.8971 (mp10) REVERT: N 30 ILE cc_start: 0.9241 (tt) cc_final: 0.8980 (mm) REVERT: N 45 LEU cc_start: 0.9156 (mt) cc_final: 0.8943 (mt) REVERT: O 34 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8608 (tp-100) REVERT: O 58 MET cc_start: 0.9281 (ppp) cc_final: 0.8684 (ppp) REVERT: O 61 GLN cc_start: 0.9245 (OUTLIER) cc_final: 0.8990 (pt0) REVERT: R 63 TYR cc_start: 0.9460 (t80) cc_final: 0.9163 (t80) REVERT: S 11 ASP cc_start: 0.8122 (m-30) cc_final: 0.7885 (m-30) REVERT: S 60 PHE cc_start: 0.8131 (t80) cc_final: 0.7391 (t80) REVERT: S 69 LYS cc_start: 0.8501 (mttm) cc_final: 0.7853 (mtmt) REVERT: T 35 TYR cc_start: 0.8898 (OUTLIER) cc_final: 0.8697 (m-10) REVERT: Z 87 TYR cc_start: 0.6618 (m-80) cc_final: 0.6128 (m-80) REVERT: Z 98 MET cc_start: 0.5289 (mtm) cc_final: 0.4965 (mtt) REVERT: Z 159 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8530 (pt0) REVERT: Z 322 PHE cc_start: 0.3832 (OUTLIER) cc_final: 0.3480 (p90) REVERT: Z 349 MET cc_start: 0.7509 (OUTLIER) cc_final: 0.7278 (ttm) REVERT: Z 358 MET cc_start: 0.6487 (OUTLIER) cc_final: 0.6228 (pmm) outliers start: 384 outliers final: 294 residues processed: 1122 average time/residue: 1.3730 time to fit residues: 2741.5796 Evaluate side-chains 1158 residues out of total 5350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 317 poor density : 841 time to evaluate : 6.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 2 VAL Chi-restraints excluded: chain 04 residue 156 SER Chi-restraints excluded: chain 04 residue 179 GLU Chi-restraints excluded: chain 04 residue 219 VAL Chi-restraints excluded: chain 04 residue 267 VAL Chi-restraints excluded: chain 05 residue 2 ILE Chi-restraints excluded: chain 05 residue 11 MET Chi-restraints excluded: chain 05 residue 22 ILE Chi-restraints excluded: chain 05 residue 27 ILE Chi-restraints excluded: chain 05 residue 42 ASN Chi-restraints excluded: chain 05 residue 107 VAL Chi-restraints excluded: chain 05 residue 109 VAL Chi-restraints excluded: chain 05 residue 137 SER Chi-restraints excluded: chain 05 residue 139 SER Chi-restraints excluded: chain 05 residue 151 THR Chi-restraints excluded: chain 05 residue 170 VAL Chi-restraints excluded: chain 05 residue 186 LEU Chi-restraints excluded: chain 05 residue 201 LEU Chi-restraints excluded: chain 06 residue 7 ASP Chi-restraints excluded: chain 06 residue 48 THR Chi-restraints excluded: chain 06 residue 140 ASP Chi-restraints excluded: chain 07 residue 39 VAL Chi-restraints excluded: chain 07 residue 49 LEU Chi-restraints excluded: chain 07 residue 65 LEU Chi-restraints excluded: chain 07 residue 89 THR Chi-restraints excluded: chain 07 residue 133 GLU Chi-restraints excluded: chain 07 residue 143 ASP Chi-restraints excluded: chain 07 residue 148 VAL Chi-restraints excluded: chain 07 residue 151 LEU Chi-restraints excluded: chain 07 residue 174 PHE Chi-restraints excluded: chain 08 residue 10 VAL Chi-restraints excluded: chain 08 residue 15 ASP Chi-restraints excluded: chain 08 residue 35 THR Chi-restraints excluded: chain 08 residue 102 ILE Chi-restraints excluded: chain 08 residue 167 VAL Chi-restraints excluded: chain 08 residue 174 LYS Chi-restraints excluded: chain 09 residue 12 LEU Chi-restraints excluded: chain 09 residue 89 LYS Chi-restraints excluded: chain 09 residue 145 ASN Chi-restraints excluded: chain 10 residue 29 ASP Chi-restraints excluded: chain 10 residue 41 LEU Chi-restraints excluded: chain 10 residue 131 THR Chi-restraints excluded: chain 11 residue 35 MET Chi-restraints excluded: chain 11 residue 41 PHE Chi-restraints excluded: chain 11 residue 56 VAL Chi-restraints excluded: chain 11 residue 111 THR Chi-restraints excluded: chain 11 residue 121 ILE Chi-restraints excluded: chain 11 residue 126 ARG Chi-restraints excluded: chain 11 residue 135 MET Chi-restraints excluded: chain 12 residue 14 ASP Chi-restraints excluded: chain 12 residue 118 MET Chi-restraints excluded: chain 12 residue 124 VAL Chi-restraints excluded: chain 12 residue 131 ASN Chi-restraints excluded: chain 13 residue 22 ILE Chi-restraints excluded: chain 13 residue 32 TYR Chi-restraints excluded: chain 13 residue 35 VAL Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 52 VAL Chi-restraints excluded: chain 13 residue 56 ASP Chi-restraints excluded: chain 13 residue 57 VAL Chi-restraints excluded: chain 13 residue 61 VAL Chi-restraints excluded: chain 13 residue 65 THR Chi-restraints excluded: chain 13 residue 75 SER Chi-restraints excluded: chain 13 residue 88 ASN Chi-restraints excluded: chain 13 residue 104 THR Chi-restraints excluded: chain 13 residue 110 GLU Chi-restraints excluded: chain 13 residue 116 ILE Chi-restraints excluded: chain 13 residue 117 SER Chi-restraints excluded: chain 13 residue 118 LEU Chi-restraints excluded: chain 14 residue 25 SER Chi-restraints excluded: chain 14 residue 27 LEU Chi-restraints excluded: chain 14 residue 46 VAL Chi-restraints excluded: chain 14 residue 76 GLU Chi-restraints excluded: chain 14 residue 80 SER Chi-restraints excluded: chain 14 residue 92 LEU Chi-restraints excluded: chain 14 residue 111 ILE Chi-restraints excluded: chain 14 residue 122 VAL Chi-restraints excluded: chain 14 residue 129 LYS Chi-restraints excluded: chain 15 residue 7 THR Chi-restraints excluded: chain 15 residue 42 THR Chi-restraints excluded: chain 15 residue 73 ILE Chi-restraints excluded: chain 15 residue 102 LEU Chi-restraints excluded: chain 16 residue 1 MET Chi-restraints excluded: chain 16 residue 36 THR Chi-restraints excluded: chain 16 residue 63 ARG Chi-restraints excluded: chain 16 residue 97 ILE Chi-restraints excluded: chain 16 residue 114 GLU Chi-restraints excluded: chain 17 residue 16 ARG Chi-restraints excluded: chain 17 residue 19 GLN Chi-restraints excluded: chain 17 residue 35 ILE Chi-restraints excluded: chain 17 residue 43 ASN Chi-restraints excluded: chain 17 residue 47 VAL Chi-restraints excluded: chain 17 residue 54 VAL Chi-restraints excluded: chain 18 residue 15 ASP Chi-restraints excluded: chain 18 residue 40 GLN Chi-restraints excluded: chain 18 residue 49 ILE Chi-restraints excluded: chain 18 residue 96 LEU Chi-restraints excluded: chain 18 residue 103 THR Chi-restraints excluded: chain 19 residue 8 ILE Chi-restraints excluded: chain 19 residue 39 ILE Chi-restraints excluded: chain 19 residue 108 LEU Chi-restraints excluded: chain 20 residue 10 LYS Chi-restraints excluded: chain 20 residue 38 VAL Chi-restraints excluded: chain 20 residue 53 PHE Chi-restraints excluded: chain 20 residue 58 VAL Chi-restraints excluded: chain 20 residue 85 LYS Chi-restraints excluded: chain 20 residue 99 THR Chi-restraints excluded: chain 21 residue 3 THR Chi-restraints excluded: chain 21 residue 19 LEU Chi-restraints excluded: chain 21 residue 45 VAL Chi-restraints excluded: chain 21 residue 53 SER Chi-restraints excluded: chain 21 residue 62 ASP Chi-restraints excluded: chain 21 residue 69 LEU Chi-restraints excluded: chain 21 residue 72 THR Chi-restraints excluded: chain 21 residue 78 GLU Chi-restraints excluded: chain 21 residue 107 VAL Chi-restraints excluded: chain 22 residue 37 ASP Chi-restraints excluded: chain 22 residue 50 LEU Chi-restraints excluded: chain 22 residue 51 PHE Chi-restraints excluded: chain 22 residue 62 VAL Chi-restraints excluded: chain 22 residue 74 ILE Chi-restraints excluded: chain 22 residue 79 ASP Chi-restraints excluded: chain 23 residue 12 VAL Chi-restraints excluded: chain 23 residue 13 LEU Chi-restraints excluded: chain 23 residue 14 THR Chi-restraints excluded: chain 23 residue 26 ASN Chi-restraints excluded: chain 23 residue 33 VAL Chi-restraints excluded: chain 23 residue 34 ILE Chi-restraints excluded: chain 23 residue 40 LEU Chi-restraints excluded: chain 23 residue 43 LYS Chi-restraints excluded: chain 23 residue 45 GLN Chi-restraints excluded: chain 23 residue 59 GLU Chi-restraints excluded: chain 23 residue 71 ILE Chi-restraints excluded: chain 24 residue 3 THR Chi-restraints excluded: chain 24 residue 10 LYS Chi-restraints excluded: chain 24 residue 34 LYS Chi-restraints excluded: chain 24 residue 38 LEU Chi-restraints excluded: chain 24 residue 65 VAL Chi-restraints excluded: chain 24 residue 87 GLN Chi-restraints excluded: chain 25 residue 12 SER Chi-restraints excluded: chain 25 residue 17 LEU Chi-restraints excluded: chain 25 residue 19 VAL Chi-restraints excluded: chain 25 residue 60 ASP Chi-restraints excluded: chain 25 residue 67 VAL Chi-restraints excluded: chain 26 residue 13 THR Chi-restraints excluded: chain 26 residue 41 SER Chi-restraints excluded: chain 26 residue 57 VAL Chi-restraints excluded: chain 27 residue 7 ARG Chi-restraints excluded: chain 27 residue 17 GLU Chi-restraints excluded: chain 27 residue 29 ARG Chi-restraints excluded: chain 27 residue 48 ARG Chi-restraints excluded: chain 27 residue 50 VAL Chi-restraints excluded: chain 28 residue 26 LEU Chi-restraints excluded: chain 28 residue 40 THR Chi-restraints excluded: chain 29 residue 5 ILE 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 31 residue 31 GLU Chi-restraints excluded: chain 31 residue 42 VAL Chi-restraints excluded: chain 31 residue 47 ILE Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 33 residue 5 THR Chi-restraints excluded: chain 33 residue 6 VAL Chi-restraints excluded: chain 33 residue 27 ASN Chi-restraints excluded: chain 33 residue 57 VAL Chi-restraints excluded: chain 34 residue 10 LEU Chi-restraints excluded: chain 34 residue 28 SER Chi-restraints excluded: chain 34 residue 35 GLN Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 120 HIS Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain E residue 158 LYS Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 17 PHE Chi-restraints excluded: chain G residue 67 ASN Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 125 ASP Chi-restraints excluded: chain G residue 129 ASN Chi-restraints excluded: chain G residue 141 HIS Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 37 ASN Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain I residue 24 ASN Chi-restraints excluded: chain I residue 30 ASN Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 105 ARG Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 127 SER Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 56 HIS Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 96 ILE Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 120 CYS Chi-restraints excluded: chain K residue 124 LYS Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 74 GLN Chi-restraints excluded: chain L residue 102 ASP Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 61 LYS Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain N residue 79 SER Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 34 GLN Chi-restraints excluded: chain O residue 61 GLN Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 29 ASN Chi-restraints excluded: chain P residue 42 ILE Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain Q residue 15 LYS Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain Q residue 59 GLU Chi-restraints excluded: chain R residue 21 ASP Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 71 ASP Chi-restraints excluded: chain S residue 10 ILE Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain S residue 72 GLU Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 35 TYR Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain U residue 36 PHE Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain 03 residue 79 THR Chi-restraints excluded: chain 03 residue 202 THR Chi-restraints excluded: chain 03 residue 215 SER Chi-restraints excluded: chain Z residue 2 LYS Chi-restraints excluded: chain Z residue 20 VAL Chi-restraints excluded: chain Z residue 27 LEU Chi-restraints excluded: chain Z residue 32 THR Chi-restraints excluded: chain Z residue 156 LEU Chi-restraints excluded: chain Z residue 159 GLN Chi-restraints excluded: chain Z residue 215 GLU Chi-restraints excluded: chain Z residue 245 VAL Chi-restraints excluded: chain Z residue 311 LEU Chi-restraints excluded: chain Z residue 322 PHE Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 335 THR Chi-restraints excluded: chain Z residue 336 ASP Chi-restraints excluded: chain Z residue 349 MET Chi-restraints excluded: chain Z residue 358 MET Chi-restraints excluded: chain Z residue 359 VAL Chi-restraints excluded: chain Z residue 369 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1111 random chunks: chunk 662 optimal weight: 20.0000 chunk 427 optimal weight: 8.9990 chunk 639 optimal weight: 20.0000 chunk 322 optimal weight: 20.0000 chunk 210 optimal weight: 8.9990 chunk 207 optimal weight: 20.0000 chunk 680 optimal weight: 10.0000 chunk 729 optimal weight: 20.0000 chunk 529 optimal weight: 9.9990 chunk 99 optimal weight: 0.9990 chunk 841 optimal weight: 10.0000 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 14 HIS ** 04 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 04 133 ASN ** 05 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 44 HIS 09 20 ASN ** 09 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 10 4 ASN ** 10 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 12 128 ASN ** 12 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 14 35 HIS ** 14 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 16 23 ASN ** 16 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 21 15 GLN ** 22 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 23 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 29 20 ASN ** 32 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 33 27 ASN 34 35 GLN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 ASN ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 03 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 03 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 03 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 159 GLN ** Z 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.5129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 167491 Z= 0.267 Angle : 0.679 16.482 250000 Z= 0.346 Chirality : 0.038 0.332 31892 Planarity : 0.005 0.063 13835 Dihedral : 23.958 177.259 82411 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 25.10 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.12 % Favored : 88.76 % Rotamer: Outliers : 5.98 % Allowed : 25.52 % Favored : 68.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.10), residues: 6457 helix: -0.75 (0.11), residues: 2020 sheet: -1.95 (0.15), residues: 1145 loop : -2.45 (0.10), residues: 3292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 103 HIS 0.008 0.001 HIS04 52 PHE 0.029 0.002 PHE06 23 TYR 0.032 0.002 TYR U 37 ARG 0.011 0.001 ARG34 36 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12914 Ramachandran restraints generated. 6457 Oldfield, 0 Emsley, 6457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12914 Ramachandran restraints generated. 6457 Oldfield, 0 Emsley, 6457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1235 residues out of total 5350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 320 poor density : 915 time to evaluate : 6.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 04 67 LYS cc_start: 0.8357 (tttt) cc_final: 0.7610 (tptt) REVERT: 05 165 MET cc_start: 0.8846 (ttt) cc_final: 0.8617 (ttt) REVERT: 06 9 GLN cc_start: 0.8151 (tt0) cc_final: 0.7631 (mp10) REVERT: 06 30 GLN cc_start: 0.9425 (tm-30) cc_final: 0.9067 (tm-30) REVERT: 07 129 MET cc_start: 0.8908 (ppp) cc_final: 0.8420 (ppp) REVERT: 07 176 PHE cc_start: 0.8919 (m-80) cc_final: 0.8188 (m-80) REVERT: 08 146 ASP cc_start: 0.9129 (m-30) cc_final: 0.8902 (m-30) REVERT: 08 174 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7333 (pttm) REVERT: 08 176 LYS cc_start: 0.5449 (tppt) cc_final: 0.4994 (mptt) REVERT: 10 69 PHE cc_start: 0.8411 (t80) cc_final: 0.8109 (m-80) REVERT: 11 49 GLU cc_start: 0.6924 (tt0) cc_final: 0.6426 (tm-30) REVERT: 11 116 MET cc_start: 0.1735 (mmt) cc_final: 0.1186 (mmt) REVERT: 12 44 TYR cc_start: 0.8920 (t80) cc_final: 0.8651 (t80) REVERT: 13 7 MET cc_start: 0.8178 (mmm) cc_final: 0.7831 (mmm) REVERT: 13 116 ILE cc_start: 0.9303 (OUTLIER) cc_final: 0.9102 (pt) REVERT: 14 76 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8149 (mt-10) REVERT: 14 85 VAL cc_start: 0.9143 (m) cc_final: 0.8571 (p) REVERT: 15 1 MET cc_start: 0.7730 (mtp) cc_final: 0.6863 (pmm) REVERT: 15 12 MET cc_start: 0.9399 (ppp) cc_final: 0.8921 (tmm) REVERT: 15 17 ASN cc_start: 0.8539 (t0) cc_final: 0.8216 (t0) REVERT: 15 33 LEU cc_start: 0.8568 (tp) cc_final: 0.8252 (tt) REVERT: 16 23 ASN cc_start: 0.9375 (m-40) cc_final: 0.9078 (t0) REVERT: 16 31 HIS cc_start: 0.8884 (m170) cc_final: 0.8671 (m170) REVERT: 16 110 MET cc_start: 0.9544 (mmp) cc_final: 0.8918 (mmm) REVERT: 16 112 TYR cc_start: 0.8599 (m-80) cc_final: 0.8236 (m-10) REVERT: 16 120 GLU cc_start: 0.7058 (mm-30) cc_final: 0.6401 (pm20) REVERT: 17 104 GLN cc_start: 0.9236 (tp-100) cc_final: 0.9011 (tp-100) REVERT: 19 8 ILE cc_start: 0.8951 (OUTLIER) cc_final: 0.8568 (mt) REVERT: 19 108 LEU cc_start: 0.9761 (OUTLIER) cc_final: 0.9265 (tt) REVERT: 20 10 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8618 (ptmm) REVERT: 20 40 MET cc_start: 0.8991 (tmm) cc_final: 0.8601 (tmm) REVERT: 20 48 LYS cc_start: 0.8525 (ttmm) cc_final: 0.8155 (ttpp) REVERT: 20 76 LYS cc_start: 0.9410 (mmmm) cc_final: 0.9007 (mtmt) REVERT: 21 52 GLU cc_start: 0.9012 (tp30) cc_final: 0.8498 (tm-30) REVERT: 21 77 ASP cc_start: 0.7436 (t0) cc_final: 0.6950 (t0) REVERT: 22 25 GLU cc_start: 0.8906 (pt0) cc_final: 0.8376 (pp20) REVERT: 22 51 PHE cc_start: 0.8244 (OUTLIER) cc_final: 0.7992 (m-80) REVERT: 24 34 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.7852 (pttm) REVERT: 26 15 ASN cc_start: 0.8915 (m-40) cc_final: 0.8633 (t0) REVERT: 26 16 ASN cc_start: 0.9122 (t0) cc_final: 0.8907 (t0) REVERT: 26 55 MET cc_start: 0.9050 (mtp) cc_final: 0.8746 (mmm) REVERT: 27 29 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.7714 (ptp90) REVERT: 28 57 GLU cc_start: 0.6962 (mp0) cc_final: 0.5846 (pp20) REVERT: 29 48 GLN cc_start: 0.8820 (tp-100) cc_final: 0.8228 (mp10) REVERT: 30 27 LEU cc_start: 0.8621 (tp) cc_final: 0.8388 (tp) REVERT: 32 1 MET cc_start: 0.6290 (ptm) cc_final: 0.6037 (ptm) REVERT: 32 13 ASN cc_start: 0.9226 (m110) cc_final: 0.8369 (t0) REVERT: 33 27 ASN cc_start: 0.8989 (OUTLIER) cc_final: 0.8594 (t0) REVERT: B 181 PRO cc_start: 0.8901 (Cg_exo) cc_final: 0.8609 (Cg_endo) REVERT: C 133 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8673 (ptm) REVERT: C 141 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8365 (ttt) REVERT: C 177 LEU cc_start: 0.9647 (mt) cc_final: 0.9195 (tp) REVERT: E 23 THR cc_start: 0.8578 (OUTLIER) cc_final: 0.8051 (p) REVERT: F 21 MET cc_start: 0.8921 (mtt) cc_final: 0.8621 (mpp) REVERT: H 26 MET cc_start: 0.9011 (ptp) cc_final: 0.8734 (pmm) REVERT: H 83 ARG cc_start: 0.8859 (mmt180) cc_final: 0.8619 (mmt90) REVERT: I 21 LYS cc_start: 0.8571 (tppt) cc_final: 0.8087 (tppt) REVERT: J 64 GLN cc_start: 0.8758 (mt0) cc_final: 0.8491 (mt0) REVERT: K 63 GLN cc_start: 0.9342 (tp40) cc_final: 0.8992 (tp40) REVERT: L 107 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8483 (tptt) REVERT: M 22 TYR cc_start: 0.8443 (t80) cc_final: 0.8143 (t80) REVERT: N 3 GLN cc_start: 0.9206 (mm110) cc_final: 0.8926 (mp10) REVERT: N 30 ILE cc_start: 0.9131 (tt) cc_final: 0.8835 (mm) REVERT: N 45 LEU cc_start: 0.9154 (mt) cc_final: 0.8953 (mt) REVERT: N 85 GLU cc_start: 0.9379 (tp30) cc_final: 0.9130 (tm-30) REVERT: O 57 ARG cc_start: 0.9198 (ttp80) cc_final: 0.8258 (ttp80) REVERT: O 58 MET cc_start: 0.9241 (ppp) cc_final: 0.8461 (ppp) REVERT: O 61 GLN cc_start: 0.9207 (tt0) cc_final: 0.8962 (pt0) REVERT: R 63 TYR cc_start: 0.9406 (t80) cc_final: 0.9105 (t80) REVERT: S 11 ASP cc_start: 0.8017 (m-30) cc_final: 0.7686 (m-30) REVERT: S 60 PHE cc_start: 0.8137 (t80) cc_final: 0.7893 (t80) REVERT: S 65 MET cc_start: 0.9039 (tpt) cc_final: 0.8627 (tpp) REVERT: S 69 LYS cc_start: 0.8395 (mttm) cc_final: 0.7676 (mtmt) REVERT: T 53 MET cc_start: 0.8917 (tmm) cc_final: 0.8673 (tmm) REVERT: U 20 ARG cc_start: 0.7587 (ptt-90) cc_final: 0.7085 (ptt-90) REVERT: 03 109 MET cc_start: 0.4275 (mmt) cc_final: 0.4042 (mmt) REVERT: Z 87 TYR cc_start: 0.6555 (m-80) cc_final: 0.6105 (m-80) REVERT: Z 98 MET cc_start: 0.5092 (mtm) cc_final: 0.4840 (mtt) REVERT: Z 151 MET cc_start: 0.8769 (mtt) cc_final: 0.8386 (tpt) REVERT: Z 322 PHE cc_start: 0.3747 (OUTLIER) cc_final: 0.3434 (p90) REVERT: Z 358 MET cc_start: 0.6485 (OUTLIER) cc_final: 0.6181 (pmm) outliers start: 320 outliers final: 242 residues processed: 1121 average time/residue: 1.3431 time to fit residues: 2657.1145 Evaluate side-chains 1135 residues out of total 5350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 877 time to evaluate : 6.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 2 VAL Chi-restraints excluded: chain 04 residue 156 SER Chi-restraints excluded: chain 04 residue 179 GLU Chi-restraints excluded: chain 04 residue 219 VAL Chi-restraints excluded: chain 04 residue 224 MET Chi-restraints excluded: chain 04 residue 267 VAL Chi-restraints excluded: chain 05 residue 2 ILE Chi-restraints excluded: chain 05 residue 107 VAL Chi-restraints excluded: chain 05 residue 109 VAL Chi-restraints excluded: chain 05 residue 137 SER Chi-restraints excluded: chain 05 residue 139 SER Chi-restraints excluded: chain 05 residue 186 LEU Chi-restraints excluded: chain 05 residue 201 LEU Chi-restraints excluded: chain 06 residue 7 ASP Chi-restraints excluded: chain 06 residue 48 THR Chi-restraints excluded: chain 06 residue 73 ILE Chi-restraints excluded: chain 07 residue 27 VAL Chi-restraints excluded: chain 07 residue 39 VAL Chi-restraints excluded: chain 07 residue 65 LEU Chi-restraints excluded: chain 07 residue 133 GLU Chi-restraints excluded: chain 07 residue 143 ASP Chi-restraints excluded: chain 07 residue 148 VAL Chi-restraints excluded: chain 07 residue 151 LEU Chi-restraints excluded: chain 08 residue 10 VAL Chi-restraints excluded: chain 08 residue 15 ASP Chi-restraints excluded: chain 08 residue 22 VAL Chi-restraints excluded: chain 08 residue 35 THR Chi-restraints excluded: chain 08 residue 102 ILE Chi-restraints excluded: chain 08 residue 167 VAL Chi-restraints excluded: chain 08 residue 174 LYS Chi-restraints excluded: chain 09 residue 12 LEU Chi-restraints excluded: chain 09 residue 89 LYS Chi-restraints excluded: chain 09 residue 145 ASN Chi-restraints excluded: chain 10 residue 29 ASP Chi-restraints excluded: chain 10 residue 41 LEU Chi-restraints excluded: chain 10 residue 131 THR Chi-restraints excluded: chain 11 residue 35 MET Chi-restraints excluded: chain 11 residue 41 PHE Chi-restraints excluded: chain 11 residue 56 VAL Chi-restraints excluded: chain 11 residue 111 THR Chi-restraints excluded: chain 11 residue 121 ILE Chi-restraints excluded: chain 11 residue 126 ARG Chi-restraints excluded: chain 11 residue 135 MET Chi-restraints excluded: chain 12 residue 14 ASP Chi-restraints excluded: chain 12 residue 118 MET Chi-restraints excluded: chain 12 residue 124 VAL Chi-restraints excluded: chain 12 residue 131 ASN Chi-restraints excluded: chain 13 residue 32 TYR Chi-restraints excluded: chain 13 residue 35 VAL Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 56 ASP Chi-restraints excluded: chain 13 residue 61 VAL Chi-restraints excluded: chain 13 residue 65 THR Chi-restraints excluded: chain 13 residue 75 SER Chi-restraints excluded: chain 13 residue 88 ASN Chi-restraints excluded: chain 13 residue 104 THR Chi-restraints excluded: chain 13 residue 116 ILE Chi-restraints excluded: chain 14 residue 25 SER Chi-restraints excluded: chain 14 residue 27 LEU Chi-restraints excluded: chain 14 residue 46 VAL Chi-restraints excluded: chain 14 residue 76 GLU Chi-restraints excluded: chain 14 residue 92 LEU Chi-restraints excluded: chain 14 residue 122 VAL Chi-restraints excluded: chain 14 residue 129 LYS Chi-restraints excluded: chain 15 residue 7 THR Chi-restraints excluded: chain 16 residue 36 THR Chi-restraints excluded: chain 16 residue 63 ARG Chi-restraints excluded: chain 16 residue 97 ILE Chi-restraints excluded: chain 17 residue 16 ARG Chi-restraints excluded: chain 17 residue 19 GLN Chi-restraints excluded: chain 17 residue 35 ILE Chi-restraints excluded: chain 17 residue 54 VAL Chi-restraints excluded: chain 18 residue 7 LEU Chi-restraints excluded: chain 18 residue 15 ASP Chi-restraints excluded: chain 18 residue 40 GLN Chi-restraints excluded: chain 18 residue 49 ILE Chi-restraints excluded: chain 18 residue 103 THR Chi-restraints excluded: chain 19 residue 8 ILE Chi-restraints excluded: chain 19 residue 16 ILE Chi-restraints excluded: chain 19 residue 99 VAL Chi-restraints excluded: chain 19 residue 108 LEU Chi-restraints excluded: chain 20 residue 10 LYS Chi-restraints excluded: chain 20 residue 38 VAL Chi-restraints excluded: chain 20 residue 53 PHE Chi-restraints excluded: chain 20 residue 58 VAL Chi-restraints excluded: chain 20 residue 85 LYS Chi-restraints excluded: chain 20 residue 99 THR Chi-restraints excluded: chain 21 residue 3 THR Chi-restraints excluded: chain 21 residue 45 VAL Chi-restraints excluded: chain 21 residue 53 SER Chi-restraints excluded: chain 21 residue 62 ASP Chi-restraints excluded: chain 21 residue 107 VAL Chi-restraints excluded: chain 22 residue 37 ASP Chi-restraints excluded: chain 22 residue 50 LEU Chi-restraints excluded: chain 22 residue 51 PHE Chi-restraints excluded: chain 22 residue 62 VAL Chi-restraints excluded: chain 22 residue 79 ASP Chi-restraints excluded: chain 23 residue 12 VAL Chi-restraints excluded: chain 23 residue 13 LEU Chi-restraints excluded: chain 23 residue 14 THR Chi-restraints excluded: chain 23 residue 17 ASP Chi-restraints excluded: chain 23 residue 26 ASN Chi-restraints excluded: chain 23 residue 33 VAL Chi-restraints excluded: chain 23 residue 34 ILE Chi-restraints excluded: chain 23 residue 43 LYS Chi-restraints excluded: chain 23 residue 71 ILE Chi-restraints excluded: chain 24 residue 3 THR Chi-restraints excluded: chain 24 residue 10 LYS Chi-restraints excluded: chain 24 residue 34 LYS Chi-restraints excluded: chain 24 residue 38 LEU Chi-restraints excluded: chain 24 residue 65 VAL Chi-restraints excluded: chain 24 residue 87 GLN Chi-restraints excluded: chain 24 residue 90 ASP Chi-restraints excluded: chain 25 residue 7 ARG Chi-restraints excluded: chain 25 residue 12 SER Chi-restraints excluded: chain 25 residue 17 LEU Chi-restraints excluded: chain 25 residue 19 VAL Chi-restraints excluded: chain 25 residue 67 VAL Chi-restraints excluded: chain 26 residue 13 THR Chi-restraints excluded: chain 26 residue 41 SER Chi-restraints excluded: chain 26 residue 58 ILE Chi-restraints excluded: chain 27 residue 29 ARG Chi-restraints excluded: chain 27 residue 48 ARG Chi-restraints excluded: chain 28 residue 40 THR Chi-restraints excluded: chain 29 residue 5 ILE 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 2 VAL Chi-restraints excluded: chain 31 residue 23 THR Chi-restraints excluded: chain 31 residue 42 VAL Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 33 residue 5 THR Chi-restraints excluded: chain 33 residue 6 VAL Chi-restraints excluded: chain 33 residue 27 ASN Chi-restraints excluded: chain 33 residue 28 LEU Chi-restraints excluded: chain 34 residue 10 LEU Chi-restraints excluded: chain 34 residue 28 SER Chi-restraints excluded: chain B residue 34 ARG Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 120 HIS Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 17 PHE Chi-restraints excluded: chain G residue 67 ASN Chi-restraints excluded: chain G residue 129 ASN Chi-restraints excluded: chain G residue 141 HIS Chi-restraints excluded: chain H residue 37 ASN Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain I residue 24 ASN Chi-restraints excluded: chain I residue 30 ASN Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 105 ARG Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 96 ILE Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 120 CYS Chi-restraints excluded: chain K residue 124 LYS Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 102 ASP Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 29 ASN Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain Q residue 15 LYS Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain R residue 21 ASP Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 41 SER Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 71 ASP Chi-restraints excluded: chain S residue 10 ILE Chi-restraints excluded: chain S residue 48 ILE Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain U residue 36 PHE Chi-restraints excluded: chain 03 residue 79 THR Chi-restraints excluded: chain 03 residue 202 THR Chi-restraints excluded: chain 03 residue 215 SER Chi-restraints excluded: chain Z residue 20 VAL Chi-restraints excluded: chain Z residue 27 LEU Chi-restraints excluded: chain Z residue 32 THR Chi-restraints excluded: chain Z residue 156 LEU Chi-restraints excluded: chain Z residue 245 VAL Chi-restraints excluded: chain Z residue 311 LEU Chi-restraints excluded: chain Z residue 322 PHE Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 335 THR Chi-restraints excluded: chain Z residue 336 ASP Chi-restraints excluded: chain Z residue 358 MET Chi-restraints excluded: chain Z residue 359 VAL Chi-restraints excluded: chain Z residue 369 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1111 random chunks: chunk 974 optimal weight: 20.0000 chunk 1025 optimal weight: 20.0000 chunk 935 optimal weight: 20.0000 chunk 997 optimal weight: 20.0000 chunk 600 optimal weight: 20.0000 chunk 434 optimal weight: 5.9990 chunk 783 optimal weight: 30.0000 chunk 306 optimal weight: 10.0000 chunk 901 optimal weight: 30.0000 chunk 943 optimal weight: 20.0000 chunk 994 optimal weight: 20.0000 overall best weight: 15.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 04 14 HIS ** 04 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 04 133 ASN ** 05 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 44 HIS 09 20 ASN ** 09 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 10 4 ASN ** 10 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 12 128 ASN ** 12 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 14 35 HIS ** 14 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 19 36 GLN 19 55 GLN ** 22 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 23 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 32 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 03 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 03 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 03 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 03 129 GLN ** 03 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.5483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.098 167491 Z= 0.461 Angle : 0.831 15.971 250000 Z= 0.418 Chirality : 0.043 0.365 31892 Planarity : 0.006 0.071 13835 Dihedral : 24.143 179.750 82411 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 34.39 Ramachandran Plot: Outliers : 0.15 % Allowed : 13.86 % Favored : 85.98 % Rotamer: Outliers : 6.23 % Allowed : 25.46 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.10), residues: 6457 helix: -1.01 (0.11), residues: 1998 sheet: -2.10 (0.14), residues: 1141 loop : -2.53 (0.10), residues: 3318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 103 HIS 0.010 0.002 HIS Q 46 PHE 0.049 0.003 PHE04 239 TYR 0.038 0.003 TYR07 142 ARG 0.009 0.001 ARG08 169 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12914 Ramachandran restraints generated. 6457 Oldfield, 0 Emsley, 6457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12914 Ramachandran restraints generated. 6457 Oldfield, 0 Emsley, 6457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1209 residues out of total 5350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 333 poor density : 876 time to evaluate : 6.705 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: 05 165 MET cc_start: 0.8806 (ttt) cc_final: 0.8605 (ttt) REVERT: 05 173 GLN cc_start: 0.7427 (tt0) cc_final: 0.7118 (tt0) REVERT: 06 1 MET cc_start: 0.8457 (tpt) cc_final: 0.8180 (tpp) REVERT: 06 9 GLN cc_start: 0.8131 (tt0) cc_final: 0.7622 (mp10) REVERT: 06 30 GLN cc_start: 0.9453 (tm-30) cc_final: 0.9120 (tm-30) REVERT: 07 129 MET cc_start: 0.8949 (ppp) cc_final: 0.8680 (ppp) REVERT: 07 176 PHE cc_start: 0.8898 (m-80) cc_final: 0.8141 (m-80) REVERT: 08 146 ASP cc_start: 0.9226 (m-30) cc_final: 0.8963 (m-30) REVERT: 08 174 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7398 (pttm) REVERT: 08 176 LYS cc_start: 0.5524 (tppt) cc_final: 0.4984 (mptt) REVERT: 10 69 PHE cc_start: 0.8383 (t80) cc_final: 0.8083 (m-80) REVERT: 11 116 MET cc_start: 0.1772 (mmt) cc_final: 0.1162 (mmt) REVERT: 12 53 TYR cc_start: 0.8915 (m-80) cc_final: 0.8563 (m-80) REVERT: 13 7 MET cc_start: 0.8358 (mmm) cc_final: 0.8109 (mmm) REVERT: 13 116 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.9114 (pt) REVERT: 14 76 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8264 (mt-10) REVERT: 15 1 MET cc_start: 0.7868 (mtp) cc_final: 0.6804 (pmm) REVERT: 15 17 ASN cc_start: 0.8513 (t0) cc_final: 0.8210 (t0) REVERT: 15 33 LEU cc_start: 0.8669 (tp) cc_final: 0.8307 (tt) REVERT: 15 53 MET cc_start: 0.9007 (tpp) cc_final: 0.8705 (tpp) REVERT: 16 31 HIS cc_start: 0.8991 (m170) cc_final: 0.8768 (m170) REVERT: 16 110 MET cc_start: 0.9569 (mmp) cc_final: 0.8923 (mmm) REVERT: 16 112 TYR cc_start: 0.8698 (m-80) cc_final: 0.8266 (m-10) REVERT: 16 120 GLU cc_start: 0.7341 (mm-30) cc_final: 0.6490 (pm20) REVERT: 18 12 MET cc_start: 0.8189 (mmm) cc_final: 0.7981 (tpp) REVERT: 19 8 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8699 (mt) REVERT: 19 108 LEU cc_start: 0.9769 (OUTLIER) cc_final: 0.9330 (tt) REVERT: 20 6 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8175 (tm-30) REVERT: 20 40 MET cc_start: 0.9006 (tmm) cc_final: 0.8731 (tmm) REVERT: 20 48 LYS cc_start: 0.8510 (ttmm) cc_final: 0.8153 (ttpp) REVERT: 20 76 LYS cc_start: 0.9416 (mmmm) cc_final: 0.9002 (mtmt) REVERT: 20 78 ARG cc_start: 0.9261 (mmm-85) cc_final: 0.9058 (mtt-85) REVERT: 21 52 GLU cc_start: 0.9073 (tp30) cc_final: 0.8566 (tm-30) REVERT: 21 69 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8450 (mt) REVERT: 21 77 ASP cc_start: 0.7322 (t0) cc_final: 0.6842 (t0) REVERT: 22 25 GLU cc_start: 0.8964 (pt0) cc_final: 0.8369 (pp20) REVERT: 22 51 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.8074 (m-80) REVERT: 24 34 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.7882 (pttm) REVERT: 24 50 MET cc_start: 0.8821 (tpt) cc_final: 0.8338 (tpt) REVERT: 26 15 ASN cc_start: 0.8891 (m-40) cc_final: 0.8659 (t0) REVERT: 26 55 MET cc_start: 0.9086 (mtp) cc_final: 0.8797 (mmm) REVERT: 27 29 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.8015 (ptp90) REVERT: 28 57 GLU cc_start: 0.7055 (mp0) cc_final: 0.6026 (pp20) REVERT: 31 24 LYS cc_start: 0.8370 (pttp) cc_final: 0.8153 (ptmt) REVERT: 32 1 MET cc_start: 0.6483 (ptm) cc_final: 0.6217 (ptm) REVERT: 33 27 ASN cc_start: 0.8881 (t0) cc_final: 0.8487 (t0) REVERT: B 48 MET cc_start: 0.9427 (tpp) cc_final: 0.9052 (tpp) REVERT: B 181 PRO cc_start: 0.8967 (Cg_exo) cc_final: 0.8684 (Cg_endo) REVERT: C 109 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8001 (mm-30) REVERT: C 133 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.8713 (ptm) REVERT: C 141 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8317 (ttt) REVERT: C 177 LEU cc_start: 0.9646 (mt) cc_final: 0.9256 (tp) REVERT: E 33 THR cc_start: 0.9093 (p) cc_final: 0.8843 (p) REVERT: F 21 MET cc_start: 0.8974 (mtt) cc_final: 0.8663 (mpp) REVERT: G 30 MET cc_start: 0.8348 (tpp) cc_final: 0.8085 (tpp) REVERT: H 26 MET cc_start: 0.9037 (ptp) cc_final: 0.8734 (pmm) REVERT: I 24 ASN cc_start: 0.9025 (OUTLIER) cc_final: 0.8637 (p0) REVERT: J 64 GLN cc_start: 0.8776 (mt0) cc_final: 0.8465 (mt0) REVERT: K 63 GLN cc_start: 0.9344 (tp40) cc_final: 0.9008 (tp40) REVERT: L 107 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8477 (tptt) REVERT: N 3 GLN cc_start: 0.9187 (mm110) cc_final: 0.8953 (mp10) REVERT: N 30 ILE cc_start: 0.9153 (tt) cc_final: 0.8891 (mm) REVERT: O 58 MET cc_start: 0.9270 (ppp) cc_final: 0.8653 (ppp) REVERT: O 61 GLN cc_start: 0.9247 (OUTLIER) cc_final: 0.9012 (pt0) REVERT: R 63 TYR cc_start: 0.9464 (t80) cc_final: 0.9168 (t80) REVERT: S 11 ASP cc_start: 0.8095 (m-30) cc_final: 0.7868 (m-30) REVERT: S 20 LYS cc_start: 0.9134 (ttpp) cc_final: 0.8833 (ptpt) REVERT: S 60 PHE cc_start: 0.8188 (t80) cc_final: 0.7940 (t80) REVERT: S 69 LYS cc_start: 0.8440 (mttm) cc_final: 0.7776 (mtmt) REVERT: U 8 ASN cc_start: 0.7459 (m-40) cc_final: 0.7070 (p0) REVERT: U 20 ARG cc_start: 0.7712 (ptt-90) cc_final: 0.7219 (ptt-90) REVERT: Z 87 TYR cc_start: 0.6545 (m-80) cc_final: 0.6298 (m-80) REVERT: Z 358 MET cc_start: 0.6547 (OUTLIER) cc_final: 0.6278 (pmm) outliers start: 333 outliers final: 284 residues processed: 1093 average time/residue: 1.2659 time to fit residues: 2449.6085 Evaluate side-chains 1155 residues out of total 5350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 300 poor density : 855 time to evaluate : 6.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 2 VAL Chi-restraints excluded: chain 04 residue 8 THR Chi-restraints excluded: chain 04 residue 156 SER Chi-restraints excluded: chain 04 residue 179 GLU Chi-restraints excluded: chain 04 residue 219 VAL Chi-restraints excluded: chain 04 residue 224 MET Chi-restraints excluded: chain 04 residue 267 VAL Chi-restraints excluded: chain 05 residue 2 ILE Chi-restraints excluded: chain 05 residue 22 ILE Chi-restraints excluded: chain 05 residue 107 VAL Chi-restraints excluded: chain 05 residue 109 VAL Chi-restraints excluded: chain 05 residue 137 SER Chi-restraints excluded: chain 05 residue 139 SER Chi-restraints excluded: chain 05 residue 151 THR Chi-restraints excluded: chain 05 residue 170 VAL Chi-restraints excluded: chain 05 residue 186 LEU Chi-restraints excluded: chain 05 residue 201 LEU Chi-restraints excluded: chain 06 residue 7 ASP Chi-restraints excluded: chain 06 residue 48 THR Chi-restraints excluded: chain 06 residue 73 ILE Chi-restraints excluded: chain 06 residue 140 ASP Chi-restraints excluded: chain 07 residue 27 VAL Chi-restraints excluded: chain 07 residue 39 VAL Chi-restraints excluded: chain 07 residue 49 LEU Chi-restraints excluded: chain 07 residue 65 LEU Chi-restraints excluded: chain 07 residue 89 THR Chi-restraints excluded: chain 07 residue 133 GLU Chi-restraints excluded: chain 07 residue 143 ASP Chi-restraints excluded: chain 07 residue 148 VAL Chi-restraints excluded: chain 07 residue 151 LEU Chi-restraints excluded: chain 08 residue 10 VAL Chi-restraints excluded: chain 08 residue 15 ASP Chi-restraints excluded: chain 08 residue 22 VAL Chi-restraints excluded: chain 08 residue 102 ILE Chi-restraints excluded: chain 08 residue 167 VAL Chi-restraints excluded: chain 08 residue 174 LYS Chi-restraints excluded: chain 09 residue 12 LEU Chi-restraints excluded: chain 09 residue 89 LYS Chi-restraints excluded: chain 09 residue 145 ASN Chi-restraints excluded: chain 10 residue 29 ASP Chi-restraints excluded: chain 10 residue 41 LEU Chi-restraints excluded: chain 10 residue 103 ASN Chi-restraints excluded: chain 10 residue 117 LEU Chi-restraints excluded: chain 10 residue 131 THR Chi-restraints excluded: chain 11 residue 35 MET Chi-restraints excluded: chain 11 residue 41 PHE Chi-restraints excluded: chain 11 residue 56 VAL Chi-restraints excluded: chain 11 residue 111 THR Chi-restraints excluded: chain 11 residue 121 ILE Chi-restraints excluded: chain 11 residue 126 ARG Chi-restraints excluded: chain 11 residue 135 MET Chi-restraints excluded: chain 12 residue 14 ASP Chi-restraints excluded: chain 12 residue 118 MET Chi-restraints excluded: chain 12 residue 124 VAL Chi-restraints excluded: chain 12 residue 131 ASN Chi-restraints excluded: chain 13 residue 21 CYS Chi-restraints excluded: chain 13 residue 22 ILE Chi-restraints excluded: chain 13 residue 32 TYR Chi-restraints excluded: chain 13 residue 35 VAL Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 56 ASP Chi-restraints excluded: chain 13 residue 57 VAL Chi-restraints excluded: chain 13 residue 61 VAL Chi-restraints excluded: chain 13 residue 65 THR Chi-restraints excluded: chain 13 residue 75 SER Chi-restraints excluded: chain 13 residue 88 ASN Chi-restraints excluded: chain 13 residue 104 THR Chi-restraints excluded: chain 13 residue 110 GLU Chi-restraints excluded: chain 13 residue 116 ILE Chi-restraints excluded: chain 14 residue 25 SER Chi-restraints excluded: chain 14 residue 27 LEU Chi-restraints excluded: chain 14 residue 46 VAL Chi-restraints excluded: chain 14 residue 76 GLU Chi-restraints excluded: chain 14 residue 92 LEU Chi-restraints excluded: chain 14 residue 122 VAL Chi-restraints excluded: chain 14 residue 129 LYS Chi-restraints excluded: chain 15 residue 7 THR Chi-restraints excluded: chain 15 residue 30 SER Chi-restraints excluded: chain 15 residue 73 ILE Chi-restraints excluded: chain 15 residue 102 LEU Chi-restraints excluded: chain 15 residue 128 THR Chi-restraints excluded: chain 16 residue 36 THR Chi-restraints excluded: chain 16 residue 37 THR Chi-restraints excluded: chain 16 residue 47 VAL Chi-restraints excluded: chain 16 residue 63 ARG Chi-restraints excluded: chain 16 residue 97 ILE Chi-restraints excluded: chain 16 residue 114 GLU Chi-restraints excluded: chain 17 residue 16 ARG Chi-restraints excluded: chain 17 residue 19 GLN Chi-restraints excluded: chain 17 residue 35 ILE Chi-restraints excluded: chain 17 residue 47 VAL Chi-restraints excluded: chain 17 residue 54 VAL Chi-restraints excluded: chain 18 residue 4 ILE Chi-restraints excluded: chain 18 residue 7 LEU Chi-restraints excluded: chain 18 residue 15 ASP Chi-restraints excluded: chain 18 residue 40 GLN Chi-restraints excluded: chain 18 residue 49 ILE Chi-restraints excluded: chain 18 residue 96 LEU Chi-restraints excluded: chain 18 residue 103 THR Chi-restraints excluded: chain 19 residue 8 ILE Chi-restraints excluded: chain 19 residue 99 VAL Chi-restraints excluded: chain 19 residue 108 LEU Chi-restraints excluded: chain 20 residue 6 GLN Chi-restraints excluded: chain 20 residue 38 VAL Chi-restraints excluded: chain 20 residue 53 PHE Chi-restraints excluded: chain 20 residue 58 VAL Chi-restraints excluded: chain 20 residue 85 LYS Chi-restraints excluded: chain 20 residue 99 THR Chi-restraints excluded: chain 21 residue 3 THR Chi-restraints excluded: chain 21 residue 19 LEU Chi-restraints excluded: chain 21 residue 45 VAL Chi-restraints excluded: chain 21 residue 53 SER Chi-restraints excluded: chain 21 residue 62 ASP Chi-restraints excluded: chain 21 residue 69 LEU Chi-restraints excluded: chain 21 residue 74 ILE Chi-restraints excluded: chain 21 residue 107 VAL Chi-restraints excluded: chain 22 residue 37 ASP Chi-restraints excluded: chain 22 residue 50 LEU Chi-restraints excluded: chain 22 residue 51 PHE Chi-restraints excluded: chain 22 residue 62 VAL Chi-restraints excluded: chain 22 residue 79 ASP Chi-restraints excluded: chain 23 residue 12 VAL Chi-restraints excluded: chain 23 residue 13 LEU Chi-restraints excluded: chain 23 residue 14 THR Chi-restraints excluded: chain 23 residue 17 ASP Chi-restraints excluded: chain 23 residue 26 ASN Chi-restraints excluded: chain 23 residue 33 VAL Chi-restraints excluded: chain 23 residue 34 ILE Chi-restraints excluded: chain 23 residue 43 LYS Chi-restraints excluded: chain 23 residue 45 GLN Chi-restraints excluded: chain 23 residue 71 ILE Chi-restraints excluded: chain 24 residue 3 THR Chi-restraints excluded: chain 24 residue 10 LYS Chi-restraints excluded: chain 24 residue 34 LYS Chi-restraints excluded: chain 24 residue 38 LEU Chi-restraints excluded: chain 24 residue 65 VAL Chi-restraints excluded: chain 24 residue 87 GLN Chi-restraints excluded: chain 24 residue 90 ASP Chi-restraints excluded: chain 25 residue 12 SER Chi-restraints excluded: chain 25 residue 17 LEU Chi-restraints excluded: chain 25 residue 19 VAL Chi-restraints excluded: chain 25 residue 52 ASP Chi-restraints excluded: chain 25 residue 67 VAL Chi-restraints excluded: chain 26 residue 13 THR Chi-restraints excluded: chain 26 residue 41 SER Chi-restraints excluded: chain 26 residue 58 ILE Chi-restraints excluded: chain 27 residue 7 ARG Chi-restraints excluded: chain 27 residue 29 ARG Chi-restraints excluded: chain 27 residue 48 ARG Chi-restraints excluded: chain 28 residue 40 THR Chi-restraints excluded: chain 29 residue 5 ILE 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 31 residue 16 THR Chi-restraints excluded: chain 31 residue 23 THR Chi-restraints excluded: chain 31 residue 31 GLU Chi-restraints excluded: chain 31 residue 42 VAL Chi-restraints excluded: chain 32 residue 24 THR Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 33 residue 5 THR Chi-restraints excluded: chain 33 residue 6 VAL Chi-restraints excluded: chain 33 residue 28 LEU Chi-restraints excluded: chain 34 residue 10 LEU Chi-restraints excluded: chain 34 residue 28 SER Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 120 HIS Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 17 PHE Chi-restraints excluded: chain G residue 67 ASN Chi-restraints excluded: chain G residue 129 ASN Chi-restraints excluded: chain G residue 141 HIS Chi-restraints excluded: chain H residue 37 ASN Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain I residue 24 ASN Chi-restraints excluded: chain I residue 30 ASN Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 105 ARG Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 56 HIS Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 96 ILE Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 120 CYS Chi-restraints excluded: chain K residue 124 LYS Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 74 GLN Chi-restraints excluded: chain L residue 102 ASP Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 81 ASP Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain N residue 79 SER Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 61 GLN Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 29 ASN Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain Q residue 15 LYS Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain Q residue 59 GLU Chi-restraints excluded: chain R residue 21 ASP Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 41 SER Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 71 ASP Chi-restraints excluded: chain S residue 10 ILE Chi-restraints excluded: chain S residue 48 ILE Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain S residue 72 GLU Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain U residue 36 PHE Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain 03 residue 79 THR Chi-restraints excluded: chain 03 residue 202 THR Chi-restraints excluded: chain 03 residue 215 SER Chi-restraints excluded: chain Z residue 2 LYS Chi-restraints excluded: chain Z residue 20 VAL Chi-restraints excluded: chain Z residue 27 LEU Chi-restraints excluded: chain Z residue 32 THR Chi-restraints excluded: chain Z residue 156 LEU Chi-restraints excluded: chain Z residue 245 VAL Chi-restraints excluded: chain Z residue 311 LEU Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 335 THR Chi-restraints excluded: chain Z residue 336 ASP Chi-restraints excluded: chain Z residue 358 MET Chi-restraints excluded: chain Z residue 359 VAL Chi-restraints excluded: chain Z residue 369 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1111 random chunks: chunk 655 optimal weight: 20.0000 chunk 1055 optimal weight: 40.0000 chunk 644 optimal weight: 20.0000 chunk 500 optimal weight: 1.9990 chunk 733 optimal weight: 20.0000 chunk 1106 optimal weight: 4.9990 chunk 1018 optimal weight: 10.0000 chunk 881 optimal weight: 20.0000 chunk 91 optimal weight: 6.9990 chunk 680 optimal weight: 10.0000 chunk 540 optimal weight: 7.9990 overall best weight: 6.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 04 14 HIS ** 04 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 04 133 ASN ** 05 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 44 HIS 09 20 ASN 09 73 ASN ** 09 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 10 4 ASN ** 10 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 14 35 HIS ** 14 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 16 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 21 15 GLN ** 22 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 23 53 GLN ** 24 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 32 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 27 GLN ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 03 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 03 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 03 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.5367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 167491 Z= 0.236 Angle : 0.673 16.790 250000 Z= 0.342 Chirality : 0.037 0.336 31892 Planarity : 0.005 0.066 13835 Dihedral : 24.010 178.155 82411 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 24.34 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.95 % Favored : 88.93 % Rotamer: Outliers : 5.38 % Allowed : 26.42 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.10), residues: 6457 helix: -0.70 (0.11), residues: 2022 sheet: -1.87 (0.15), residues: 1102 loop : -2.41 (0.10), residues: 3333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP04 247 HIS 0.008 0.001 HIS19 13 PHE 0.046 0.002 PHE C 129 TYR 0.044 0.002 TYR07 142 ARG 0.015 0.001 ARG08 169 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12914 Ramachandran restraints generated. 6457 Oldfield, 0 Emsley, 6457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12914 Ramachandran restraints generated. 6457 Oldfield, 0 Emsley, 6457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1215 residues out of total 5350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 288 poor density : 927 time to evaluate : 6.858 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: 05 165 MET cc_start: 0.8833 (ttt) cc_final: 0.8620 (ttt) REVERT: 05 173 GLN cc_start: 0.7322 (tt0) cc_final: 0.7031 (tt0) REVERT: 06 9 GLN cc_start: 0.8142 (tt0) cc_final: 0.7614 (mp10) REVERT: 06 30 GLN cc_start: 0.9417 (tm-30) cc_final: 0.9062 (tm-30) REVERT: 07 129 MET cc_start: 0.8898 (ppp) cc_final: 0.8405 (ppp) REVERT: 07 176 PHE cc_start: 0.8883 (m-80) cc_final: 0.8113 (m-80) REVERT: 08 146 ASP cc_start: 0.9199 (m-30) cc_final: 0.8864 (m-30) REVERT: 08 174 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7277 (pttm) REVERT: 08 176 LYS cc_start: 0.5482 (tppt) cc_final: 0.4906 (mptt) REVERT: 09 123 ARG cc_start: 0.6493 (mtt180) cc_final: 0.6273 (mmt90) REVERT: 10 69 PHE cc_start: 0.8436 (t80) cc_final: 0.8136 (m-80) REVERT: 11 49 GLU cc_start: 0.6990 (tt0) cc_final: 0.6490 (tm-30) REVERT: 11 116 MET cc_start: 0.1894 (mmt) cc_final: 0.1207 (mmt) REVERT: 12 43 GLU cc_start: 0.8638 (pm20) cc_final: 0.8437 (pm20) REVERT: 13 116 ILE cc_start: 0.9307 (OUTLIER) cc_final: 0.8952 (pt) REVERT: 13 117 SER cc_start: 0.9153 (OUTLIER) cc_final: 0.8587 (p) REVERT: 14 76 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8145 (mt-10) REVERT: 15 1 MET cc_start: 0.7692 (mtp) cc_final: 0.6761 (pmm) REVERT: 15 12 MET cc_start: 0.9062 (tmm) cc_final: 0.8473 (tmm) REVERT: 15 17 ASN cc_start: 0.8660 (t0) cc_final: 0.8319 (t0) REVERT: 15 33 LEU cc_start: 0.8483 (tp) cc_final: 0.8151 (tt) REVERT: 15 53 MET cc_start: 0.9007 (tpp) cc_final: 0.8720 (tpp) REVERT: 16 23 ASN cc_start: 0.9375 (m-40) cc_final: 0.9036 (t0) REVERT: 16 110 MET cc_start: 0.9538 (mmp) cc_final: 0.8895 (mmm) REVERT: 16 112 TYR cc_start: 0.8543 (m-80) cc_final: 0.8146 (m-10) REVERT: 16 120 GLU cc_start: 0.7319 (mm-30) cc_final: 0.6528 (pm20) REVERT: 17 60 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7817 (tm-30) REVERT: 17 104 GLN cc_start: 0.9237 (tp-100) cc_final: 0.9029 (tp-100) REVERT: 18 12 MET cc_start: 0.8147 (mmm) cc_final: 0.7624 (tpp) REVERT: 19 8 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8563 (mt) REVERT: 20 40 MET cc_start: 0.8980 (tmm) cc_final: 0.8647 (tmm) REVERT: 20 76 LYS cc_start: 0.9315 (mmmm) cc_final: 0.8951 (mtmt) REVERT: 20 78 ARG cc_start: 0.9204 (mmm-85) cc_final: 0.8728 (mtt-85) REVERT: 21 52 GLU cc_start: 0.9006 (tp30) cc_final: 0.8499 (tm-30) REVERT: 21 69 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8484 (mt) REVERT: 21 77 ASP cc_start: 0.7373 (t0) cc_final: 0.6873 (t0) REVERT: 21 78 GLU cc_start: 0.8536 (tp30) cc_final: 0.8261 (tp30) REVERT: 22 25 GLU cc_start: 0.8902 (pt0) cc_final: 0.8335 (pp20) REVERT: 22 51 PHE cc_start: 0.8315 (OUTLIER) cc_final: 0.8005 (m-80) REVERT: 24 34 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.7800 (pttm) REVERT: 25 76 ILE cc_start: 0.9033 (mm) cc_final: 0.8832 (mm) REVERT: 26 15 ASN cc_start: 0.8892 (m-40) cc_final: 0.8661 (t0) REVERT: 26 55 MET cc_start: 0.9018 (mtp) cc_final: 0.8781 (mmm) REVERT: 27 29 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.7787 (ptp90) REVERT: 28 53 MET cc_start: 0.8983 (ppp) cc_final: 0.8673 (tmm) REVERT: 28 57 GLU cc_start: 0.7012 (mp0) cc_final: 0.6124 (pp20) REVERT: 29 32 LEU cc_start: 0.8527 (mt) cc_final: 0.8293 (mt) REVERT: 30 27 LEU cc_start: 0.8613 (tp) cc_final: 0.8367 (tp) REVERT: 31 24 LYS cc_start: 0.8245 (pttp) cc_final: 0.8011 (ptmt) REVERT: 32 1 MET cc_start: 0.6237 (ptm) cc_final: 0.5988 (ptm) REVERT: 32 13 ASN cc_start: 0.9200 (m110) cc_final: 0.8365 (t0) REVERT: 32 14 ARG cc_start: 0.9385 (mmt90) cc_final: 0.9019 (tpp80) REVERT: 33 27 ASN cc_start: 0.8882 (t0) cc_final: 0.8408 (t0) REVERT: B 8 MET cc_start: 0.8005 (tmm) cc_final: 0.7695 (tmm) REVERT: B 48 MET cc_start: 0.9422 (tpp) cc_final: 0.9064 (tpp) REVERT: B 181 PRO cc_start: 0.8929 (Cg_exo) cc_final: 0.8641 (Cg_endo) REVERT: C 109 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7621 (mm-30) REVERT: C 133 MET cc_start: 0.8970 (OUTLIER) cc_final: 0.8685 (ptm) REVERT: C 141 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8305 (ttt) REVERT: C 177 LEU cc_start: 0.9641 (mt) cc_final: 0.9175 (tp) REVERT: E 33 THR cc_start: 0.9024 (p) cc_final: 0.8783 (p) REVERT: F 21 MET cc_start: 0.8933 (mtt) cc_final: 0.8644 (mpp) REVERT: H 26 MET cc_start: 0.8961 (ptp) cc_final: 0.8727 (pmm) REVERT: H 41 GLU cc_start: 0.8793 (mp0) cc_final: 0.8526 (pm20) REVERT: H 75 GLN cc_start: 0.8886 (pp30) cc_final: 0.8441 (pp30) REVERT: J 64 GLN cc_start: 0.8753 (mt0) cc_final: 0.8483 (mt0) REVERT: K 63 GLN cc_start: 0.9331 (tp40) cc_final: 0.8968 (tp40) REVERT: L 107 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8468 (tptt) REVERT: M 22 TYR cc_start: 0.8670 (t80) cc_final: 0.8298 (t80) REVERT: N 3 GLN cc_start: 0.9201 (mm110) cc_final: 0.8929 (mp10) REVERT: N 30 ILE cc_start: 0.9087 (tt) cc_final: 0.8796 (mm) REVERT: O 57 ARG cc_start: 0.9220 (ttp80) cc_final: 0.8232 (ttp80) REVERT: O 58 MET cc_start: 0.9248 (ppp) cc_final: 0.8414 (ppp) REVERT: O 61 GLN cc_start: 0.9185 (OUTLIER) cc_final: 0.8927 (pt0) REVERT: R 63 TYR cc_start: 0.9375 (t80) cc_final: 0.9079 (t80) REVERT: S 20 LYS cc_start: 0.9124 (ttpp) cc_final: 0.8814 (ptpt) REVERT: S 65 MET cc_start: 0.9021 (tpt) cc_final: 0.8522 (tpp) REVERT: U 20 ARG cc_start: 0.7619 (ptt-90) cc_final: 0.7117 (ptt-90) REVERT: Z 87 TYR cc_start: 0.6525 (m-80) cc_final: 0.6199 (m-80) REVERT: Z 151 MET cc_start: 0.8767 (mtt) cc_final: 0.8337 (tpt) REVERT: Z 297 THR cc_start: 0.2809 (t) cc_final: 0.2441 (m) REVERT: Z 358 MET cc_start: 0.6497 (OUTLIER) cc_final: 0.6185 (pmm) REVERT: Z 368 MET cc_start: 0.6703 (mmm) cc_final: 0.6503 (mmm) outliers start: 288 outliers final: 252 residues processed: 1117 average time/residue: 1.2642 time to fit residues: 2493.8878 Evaluate side-chains 1152 residues out of total 5350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 886 time to evaluate : 6.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 2 VAL Chi-restraints excluded: chain 04 residue 8 THR Chi-restraints excluded: chain 04 residue 156 SER Chi-restraints excluded: chain 04 residue 179 GLU Chi-restraints excluded: chain 04 residue 219 VAL Chi-restraints excluded: chain 04 residue 224 MET Chi-restraints excluded: chain 04 residue 267 VAL Chi-restraints excluded: chain 05 residue 2 ILE Chi-restraints excluded: chain 05 residue 27 ILE Chi-restraints excluded: chain 05 residue 107 VAL Chi-restraints excluded: chain 05 residue 109 VAL Chi-restraints excluded: chain 05 residue 137 SER Chi-restraints excluded: chain 05 residue 139 SER Chi-restraints excluded: chain 05 residue 186 LEU Chi-restraints excluded: chain 05 residue 201 LEU Chi-restraints excluded: chain 06 residue 7 ASP Chi-restraints excluded: chain 06 residue 48 THR Chi-restraints excluded: chain 06 residue 148 ILE Chi-restraints excluded: chain 07 residue 27 VAL Chi-restraints excluded: chain 07 residue 39 VAL Chi-restraints excluded: chain 07 residue 65 LEU Chi-restraints excluded: chain 07 residue 89 THR Chi-restraints excluded: chain 07 residue 133 GLU Chi-restraints excluded: chain 07 residue 143 ASP Chi-restraints excluded: chain 07 residue 148 VAL Chi-restraints excluded: chain 07 residue 151 LEU Chi-restraints excluded: chain 08 residue 10 VAL Chi-restraints excluded: chain 08 residue 15 ASP Chi-restraints excluded: chain 08 residue 22 VAL Chi-restraints excluded: chain 08 residue 102 ILE Chi-restraints excluded: chain 08 residue 167 VAL Chi-restraints excluded: chain 08 residue 174 LYS Chi-restraints excluded: chain 09 residue 12 LEU Chi-restraints excluded: chain 09 residue 73 ASN Chi-restraints excluded: chain 09 residue 89 LYS Chi-restraints excluded: chain 09 residue 145 ASN Chi-restraints excluded: chain 10 residue 29 ASP Chi-restraints excluded: chain 10 residue 41 LEU Chi-restraints excluded: chain 10 residue 131 THR Chi-restraints excluded: chain 11 residue 4 VAL Chi-restraints excluded: chain 11 residue 41 PHE Chi-restraints excluded: chain 11 residue 56 VAL Chi-restraints excluded: chain 11 residue 111 THR Chi-restraints excluded: chain 11 residue 121 ILE Chi-restraints excluded: chain 11 residue 135 MET Chi-restraints excluded: chain 12 residue 14 ASP Chi-restraints excluded: chain 12 residue 118 MET Chi-restraints excluded: chain 12 residue 131 ASN Chi-restraints excluded: chain 13 residue 22 ILE Chi-restraints excluded: chain 13 residue 32 TYR Chi-restraints excluded: chain 13 residue 35 VAL Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 56 ASP Chi-restraints excluded: chain 13 residue 57 VAL Chi-restraints excluded: chain 13 residue 61 VAL Chi-restraints excluded: chain 13 residue 65 THR Chi-restraints excluded: chain 13 residue 75 SER Chi-restraints excluded: chain 13 residue 88 ASN Chi-restraints excluded: chain 13 residue 104 THR Chi-restraints excluded: chain 13 residue 116 ILE Chi-restraints excluded: chain 13 residue 117 SER Chi-restraints excluded: chain 14 residue 25 SER Chi-restraints excluded: chain 14 residue 27 LEU Chi-restraints excluded: chain 14 residue 46 VAL Chi-restraints excluded: chain 14 residue 76 GLU Chi-restraints excluded: chain 14 residue 80 SER Chi-restraints excluded: chain 14 residue 92 LEU Chi-restraints excluded: chain 14 residue 122 VAL Chi-restraints excluded: chain 14 residue 129 LYS Chi-restraints excluded: chain 15 residue 7 THR Chi-restraints excluded: chain 15 residue 102 LEU Chi-restraints excluded: chain 16 residue 36 THR Chi-restraints excluded: chain 16 residue 63 ARG Chi-restraints excluded: chain 16 residue 76 VAL Chi-restraints excluded: chain 17 residue 16 ARG Chi-restraints excluded: chain 17 residue 19 GLN Chi-restraints excluded: chain 17 residue 35 ILE Chi-restraints excluded: chain 17 residue 47 VAL Chi-restraints excluded: chain 17 residue 54 VAL Chi-restraints excluded: chain 18 residue 4 ILE Chi-restraints excluded: chain 18 residue 7 LEU Chi-restraints excluded: chain 18 residue 15 ASP Chi-restraints excluded: chain 18 residue 40 GLN Chi-restraints excluded: chain 18 residue 49 ILE Chi-restraints excluded: chain 18 residue 103 THR Chi-restraints excluded: chain 19 residue 8 ILE Chi-restraints excluded: chain 19 residue 108 LEU Chi-restraints excluded: chain 20 residue 38 VAL Chi-restraints excluded: chain 20 residue 53 PHE Chi-restraints excluded: chain 20 residue 58 VAL Chi-restraints excluded: chain 20 residue 85 LYS Chi-restraints excluded: chain 20 residue 99 THR Chi-restraints excluded: chain 21 residue 3 THR Chi-restraints excluded: chain 21 residue 53 SER Chi-restraints excluded: chain 21 residue 62 ASP Chi-restraints excluded: chain 21 residue 69 LEU Chi-restraints excluded: chain 21 residue 107 VAL Chi-restraints excluded: chain 22 residue 37 ASP Chi-restraints excluded: chain 22 residue 50 LEU Chi-restraints excluded: chain 22 residue 51 PHE Chi-restraints excluded: chain 22 residue 62 VAL Chi-restraints excluded: chain 22 residue 79 ASP Chi-restraints excluded: chain 23 residue 12 VAL Chi-restraints excluded: chain 23 residue 13 LEU Chi-restraints excluded: chain 23 residue 14 THR Chi-restraints excluded: chain 23 residue 17 ASP Chi-restraints excluded: chain 23 residue 26 ASN Chi-restraints excluded: chain 23 residue 33 VAL Chi-restraints excluded: chain 23 residue 34 ILE Chi-restraints excluded: chain 23 residue 43 LYS Chi-restraints excluded: chain 23 residue 45 GLN Chi-restraints excluded: chain 23 residue 71 ILE Chi-restraints excluded: chain 24 residue 3 THR Chi-restraints excluded: chain 24 residue 10 LYS Chi-restraints excluded: chain 24 residue 34 LYS Chi-restraints excluded: chain 24 residue 38 LEU Chi-restraints excluded: chain 24 residue 65 VAL Chi-restraints excluded: chain 24 residue 87 GLN Chi-restraints excluded: chain 24 residue 90 ASP Chi-restraints excluded: chain 25 residue 12 SER Chi-restraints excluded: chain 25 residue 17 LEU Chi-restraints excluded: chain 25 residue 19 VAL Chi-restraints excluded: chain 25 residue 60 ASP Chi-restraints excluded: chain 25 residue 67 VAL Chi-restraints excluded: chain 26 residue 13 THR Chi-restraints excluded: chain 26 residue 41 SER Chi-restraints excluded: chain 27 residue 7 ARG Chi-restraints excluded: chain 27 residue 29 ARG Chi-restraints excluded: chain 27 residue 48 ARG Chi-restraints excluded: chain 28 residue 40 THR Chi-restraints excluded: chain 29 residue 5 ILE 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 31 residue 23 THR Chi-restraints excluded: chain 31 residue 42 VAL Chi-restraints excluded: chain 32 residue 24 THR Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 33 residue 5 THR Chi-restraints excluded: chain 33 residue 6 VAL Chi-restraints excluded: chain 34 residue 10 LEU Chi-restraints excluded: chain 34 residue 28 SER Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 105 VAL Chi-restraints excluded: chain C residue 133 MET Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 120 HIS Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 53 LYS Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 94 HIS Chi-restraints excluded: chain F residue 97 THR Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 17 PHE Chi-restraints excluded: chain G residue 67 ASN Chi-restraints excluded: chain G residue 129 ASN Chi-restraints excluded: chain G residue 141 HIS Chi-restraints excluded: chain H residue 37 ASN Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain I residue 24 ASN Chi-restraints excluded: chain I residue 30 ASN Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 67 LYS Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 105 ARG Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 88 MET Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 96 ILE Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain K residue 120 CYS Chi-restraints excluded: chain K residue 124 LYS Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 102 ASP Chi-restraints excluded: chain L residue 107 LYS Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 55 LEU Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 96 VAL Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain O residue 21 THR Chi-restraints excluded: chain O residue 26 VAL Chi-restraints excluded: chain O residue 61 GLN Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 29 ASN Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain Q residue 15 LYS Chi-restraints excluded: chain Q residue 40 THR Chi-restraints excluded: chain Q residue 56 ASP Chi-restraints excluded: chain R residue 21 ASP Chi-restraints excluded: chain R residue 27 THR Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 71 ASP Chi-restraints excluded: chain S residue 10 ILE Chi-restraints excluded: chain S residue 48 ILE Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain S residue 72 GLU Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 79 THR Chi-restraints excluded: chain U residue 36 PHE Chi-restraints excluded: chain U residue 50 SER Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain 03 residue 79 THR Chi-restraints excluded: chain 03 residue 215 SER Chi-restraints excluded: chain Z residue 20 VAL Chi-restraints excluded: chain Z residue 27 LEU Chi-restraints excluded: chain Z residue 32 THR Chi-restraints excluded: chain Z residue 156 LEU Chi-restraints excluded: chain Z residue 238 VAL Chi-restraints excluded: chain Z residue 245 VAL Chi-restraints excluded: chain Z residue 311 LEU Chi-restraints excluded: chain Z residue 334 THR Chi-restraints excluded: chain Z residue 335 THR Chi-restraints excluded: chain Z residue 336 ASP Chi-restraints excluded: chain Z residue 358 MET Chi-restraints excluded: chain Z residue 359 VAL Chi-restraints excluded: chain Z residue 369 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1111 random chunks: chunk 700 optimal weight: 20.0000 chunk 938 optimal weight: 30.0000 chunk 270 optimal weight: 6.9990 chunk 812 optimal weight: 30.0000 chunk 130 optimal weight: 7.9990 chunk 244 optimal weight: 20.0000 chunk 882 optimal weight: 20.0000 chunk 369 optimal weight: 3.9990 chunk 906 optimal weight: 20.0000 chunk 111 optimal weight: 30.0000 chunk 162 optimal weight: 20.0000 overall best weight: 11.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 04 14 HIS ** 04 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 04 133 ASN ** 05 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 44 HIS 09 20 ASN ** 09 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 10 4 ASN ** 10 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 12 128 ASN ** 12 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 14 35 HIS ** 14 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 20 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 22 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 32 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 03 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 03 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 03 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.044017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.035977 restraints weight = 1291218.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.037026 restraints weight = 459763.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.037618 restraints weight = 242182.946| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.5378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.249 167491 Z= 0.354 Angle : 0.711 59.189 250000 Z= 0.366 Chirality : 0.039 0.540 31892 Planarity : 0.005 0.155 13835 Dihedral : 24.001 178.160 82411 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 25.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.24 % Favored : 88.63 % Rotamer: Outliers : 5.59 % Allowed : 26.38 % Favored : 68.03 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.10), residues: 6457 helix: -0.67 (0.11), residues: 2022 sheet: -1.86 (0.15), residues: 1102 loop : -2.40 (0.10), residues: 3333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP04 212 HIS 0.028 0.002 HIS29 6 PHE 0.043 0.002 PHE C 129 TYR 0.037 0.002 TYR07 142 ARG 0.014 0.001 ARG H 113 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 41041.44 seconds wall clock time: 720 minutes 22.82 seconds (43222.82 seconds total)