Starting phenix.real_space_refine on Wed Mar 27 22:39:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bu8_7289/03_2024/6bu8_7289_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bu8_7289/03_2024/6bu8_7289.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bu8_7289/03_2024/6bu8_7289.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bu8_7289/03_2024/6bu8_7289.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bu8_7289/03_2024/6bu8_7289_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bu8_7289/03_2024/6bu8_7289_updated.pdb" } resolution = 3.5 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= -0.001 sd= 0.005 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 4804 5.49 5 S 161 5.16 5 C 76683 2.51 5 N 28308 2.21 5 O 42195 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "05 ARG 13": "NH1" <-> "NH2" Residue "05 ARG 33": "NH1" <-> "NH2" Residue "05 ARG 59": "NH1" <-> "NH2" Residue "05 ARG 77": "NH1" <-> "NH2" Residue "05 ARG 83": "NH1" <-> "NH2" Residue "05 ARG 169": "NH1" <-> "NH2" Residue "05 ARG 184": "NH1" <-> "NH2" Residue "06 ARG 21": "NH1" <-> "NH2" Residue "06 ARG 44": "NH1" <-> "NH2" Residue "06 ARG 49": "NH1" <-> "NH2" Residue "06 ARG 61": "NH1" <-> "NH2" Residue "06 ARG 88": "NH1" <-> "NH2" Residue "06 ARG 102": "NH1" <-> "NH2" Residue "06 ARG 162": "NH1" <-> "NH2" Residue "06 ARG 170": "NH1" <-> "NH2" Residue "07 ARG 70": "NH1" <-> "NH2" Residue "07 ARG 79": "NH1" <-> "NH2" Residue "07 ARG 91": "NH1" <-> "NH2" Residue "07 ARG 101": "NH1" <-> "NH2" Residue "07 ARG 109": "NH1" <-> "NH2" Residue "07 ARG 111": "NH1" <-> "NH2" Residue "07 ARG 114": "NH1" <-> "NH2" Residue "07 ARG 132": "NH1" <-> "NH2" Residue "08 ARG 2": "NH1" <-> "NH2" Residue "08 ARG 152": "NH1" <-> "NH2" Residue "08 ARG 162": "NH1" <-> "NH2" Residue "08 ARG 169": "NH1" <-> "NH2" Residue "12 ARG 13": "NH1" <-> "NH2" Residue "12 ARG 37": "NH1" <-> "NH2" Residue "12 ARG 96": "NH1" <-> "NH2" Residue "12 ARG 120": "NH1" <-> "NH2" Residue "14 ARG 21": "NH1" <-> "NH2" Residue "14 ARG 33": "NH1" <-> "NH2" Residue "14 ARG 41": "NH1" <-> "NH2" Residue "14 ARG 47": "NH1" <-> "NH2" Residue "14 ARG 60": "NH1" <-> "NH2" Residue "14 ARG 78": "NH1" <-> "NH2" Residue "14 ARG 126": "NH1" <-> "NH2" Residue "15 ARG 10": "NH1" <-> "NH2" Residue "15 ARG 18": "NH1" <-> "NH2" Residue "15 ARG 40": "NH1" <-> "NH2" Residue "15 ARG 44": "NH1" <-> "NH2" Residue "15 ARG 50": "NH1" <-> "NH2" Residue "15 ARG 55": "NH1" <-> "NH2" Residue "15 ARG 59": "NH1" <-> "NH2" Residue "15 ARG 114": "NH1" <-> "NH2" Residue "16 ARG 8": "NH1" <-> "NH2" Residue "16 ARG 12": "NH1" <-> "NH2" Residue "16 ARG 17": "NH1" <-> "NH2" Residue "16 ARG 22": "NH1" <-> "NH2" Residue "16 ARG 46": "NH1" <-> "NH2" Residue "16 ARG 63": "NH1" <-> "NH2" Residue "16 ARG 64": "NH1" <-> "NH2" Residue "16 ARG 69": "NH1" <-> "NH2" Residue "16 ARG 71": "NH1" <-> "NH2" Residue "16 ARG 96": "NH1" <-> "NH2" Residue "16 ARG 118": "NH1" <-> "NH2" Residue "17 ARG 10": "NH1" <-> "NH2" Residue "17 ARG 16": "NH1" <-> "NH2" Residue "17 ARG 25": "NH1" <-> "NH2" Residue "17 ARG 81": "NH1" <-> "NH2" Residue "17 ARG 94": "NH1" <-> "NH2" Residue "17 ARG 102": "NH1" <-> "NH2" Residue "17 ARG 111": "NH1" <-> "NH2" Residue "18 ARG 20": "NH1" <-> "NH2" Residue "18 ARG 38": "NH1" <-> "NH2" Residue "18 ARG 61": "NH1" <-> "NH2" Residue "18 ARG 88": "NH1" <-> "NH2" Residue "18 ARG 100": "NH1" <-> "NH2" Residue "18 ARG 108": "NH1" <-> "NH2" Residue "19 ARG 2": "NH1" <-> "NH2" Residue "19 ARG 5": "NH1" <-> "NH2" Residue "19 ARG 12": "NH1" <-> "NH2" Residue "19 ARG 32": "NH1" <-> "NH2" Residue "19 ARG 47": "NH1" <-> "NH2" Residue "19 ARG 69": "NH1" <-> "NH2" Residue "20 ARG 21": "NH1" <-> "NH2" Residue "20 ARG 68": "NH1" <-> "NH2" Residue "20 ARG 78": "NH1" <-> "NH2" Residue "20 ARG 79": "NH1" <-> "NH2" Residue "20 ARG 84": "NH1" <-> "NH2" Residue "21 ARG 84": "NH1" <-> "NH2" Residue "21 ARG 88": "NH1" <-> "NH2" Residue "21 ARG 95": "NH1" <-> "NH2" Residue "21 ARG 110": "NH1" <-> "NH2" Residue "22 ARG 73": "NH1" <-> "NH2" Residue "23 ARG 5": "NH1" <-> "NH2" Residue "23 ARG 6": "NH1" <-> "NH2" Residue "23 ARG 81": "NH1" <-> "NH2" Residue "23 ARG 85": "NH1" <-> "NH2" Residue "23 ARG 93": "NH1" <-> "NH2" Residue "25 PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "27 ARG 29": "NH1" <-> "NH2" Residue "27 ARG 47": "NH1" <-> "NH2" Residue "27 ARG 52": "NH1" <-> "NH2" Residue "28 ARG 10": "NH1" <-> "NH2" Residue "28 ARG 29": "NH1" <-> "NH2" Residue "28 ARG 44": "NH1" <-> "NH2" Residue "28 PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 224": "NH1" <-> "NH2" Residue "C ARG 106": "NH1" <-> "NH2" Residue "C ARG 130": "NH1" <-> "NH2" Residue "E PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 156": "NH1" <-> "NH2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "F ARG 112": "NH1" <-> "NH2" Residue "F ARG 113": "NH1" <-> "NH2" Residue "F GLU 119": "OE1" <-> "OE2" Residue "F GLU 125": "OE1" <-> "OE2" Residue "I ARG 123": "NH1" <-> "NH2" Residue "L ARG 55": "NH1" <-> "NH2" Residue "P ARG 28": "NH1" <-> "NH2" Residue "R ARG 11": "NH1" <-> "NH2" Residue "R TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 66": "NH1" <-> "NH2" Residue "03 ARG 7": "NH1" <-> "NH2" Residue "03 ARG 12": "NH1" <-> "NH2" Residue "03 PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "03 ARG 162": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 152151 Number of models: 1 Model: "" Number of chains: 61 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: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1757 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 217} 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: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1028 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "G" Number of atoms: 1182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1182 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "I" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 787 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "K" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 870 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "L" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "M" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 884 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "O" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Q" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 649 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "R" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 536 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "S" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 638 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "T" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "U" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 545 Classifications: {'peptide': 65} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "03" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1027 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain breaks: 1 Chain: "A" Number of atoms: 33012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33012 Classifications: {'RNA': 1539} Modifications used: {'5*END': 1, 'rna2p_pur': 90, 'rna2p_pyr': 49, 'rna3p_pur': 784, 'rna3p_pyr': 616} Link IDs: {'rna2p': 139, 'rna3p': 1399} Chain: "01" Number of atoms: 62317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62317 Classifications: {'RNA': 2903} Modifications used: {'5*END': 1, 'rna2p_pur': 211, 'rna2p_pyr': 92, 'rna3p_pur': 1463, 'rna3p_pyr': 1137} Link IDs: {'rna2p': 303, 'rna3p': 2599} Chain: "02" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2568 Classifications: {'RNA': 120} Modifications used: {'5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 61, 'rna3p_pyr': 53} Link IDs: {'rna2p': 6, 'rna3p': 113} Chain: "X" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1640 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 33, 'rna3p_pyr': 33} Link IDs: {'rna2p': 11, 'rna3p': 65} Chain: "V" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 388 Classifications: {'RNA': 18} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 12, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "W" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1640 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p_pur': 33, 'rna3p_pyr': 34} Link IDs: {'rna2p': 9, 'rna3p': 67} Chain: "Y" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1622 Classifications: {'RNA': 76} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 33, 'rna3p_pyr': 31} Link IDs: {'rna2p': 12, 'rna3p': 63} Chain: "Z" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1204 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 152} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "W" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N GLN Z 52 " occ=0.58 ... (7 atoms not shown) pdb=" NE2 GLN Z 52 " occ=0.58 Time building chain proxies: 57.57, per 1000 atoms: 0.38 Number of scatterers: 152151 At special positions: 0 Unit cell: (282.08, 267.32, 251.74, 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 161 16.00 P 4804 15.00 O 42195 8.00 N 28308 7.00 C 76683 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS34 11 " - pdb=" SG CYS34 14 " distance=2.95 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 60.06 Conformation dependent library (CDL) restraints added in 6.9 seconds 12318 Ramachandran restraints generated. 6159 Oldfield, 0 Emsley, 6159 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11538 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: 192 helices and 73 sheets defined 38.6% alpha, 17.4% beta 1453 base pairs and 2733 stacking pairs defined. Time for finding SS restraints: 73.46 Creating SS restraints... Processing helix chain '04' and resid 29 through 34 removed outlier: 4.156A pdb=" N LEU04 33 " --> pdb=" O PHE04 29 " (cutoff:3.500A) removed outlier: 5.482A 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: 3.817A 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: 4.140A pdb=" N ALA04 210 " --> pdb=" O LYS04 206 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG04 211 " --> pdb=" O ALA04 207 " (cutoff:3.500A) Processing helix chain '04' and resid 259 through 267 removed outlier: 6.047A pdb=" N ASP04 263 " --> pdb=" O ASN04 259 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LYS04 264 " --> pdb=" O LYS04 260 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N PHE04 265 " --> pdb=" O ARG04 261 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE04 266 " --> pdb=" O THR04 262 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N VAL04 267 " --> pdb=" O ASP04 263 " (cutoff:3.500A) No H-bonds generated for 'chain '04' and resid 259 through 267' Processing helix chain '05' and resid 56 through 61 removed outlier: 3.581A pdb=" N VAL05 60 " --> pdb=" O LYS05 56 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N THR05 61 " --> pdb=" O ALA05 57 " (cutoff:3.500A) No H-bonds generated for 'chain '05' and resid 56 through 61' Processing helix chain '05' and resid 62 through 72 removed outlier: 4.242A pdb=" N ALA05 71 " --> pdb=" O HIS05 67 " (cutoff:3.500A) Processing helix chain '05' and resid 98 through 105 removed outlier: 4.172A pdb=" N ALA05 102 " --> pdb=" O VAL05 98 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ASP05 103 " --> pdb=" O GLU05 99 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL05 104 " --> pdb=" O LEU05 100 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LYS05 105 " --> pdb=" O PHE05 101 " (cutoff:3.500A) No H-bonds generated for 'chain '05' and resid 98 through 105' Processing helix chain '05' and resid 120 through 125 Processing helix chain '06' and resid 15 through 20 removed outlier: 3.894A pdb=" N PHE06 19 " --> pdb=" O SER06 15 " (cutoff:3.500A) Processing helix chain '06' and resid 24 through 40 removed outlier: 3.686A pdb=" N GLN06 30 " --> pdb=" O ALA06 26 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL06 31 " --> pdb=" O LEU06 27 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG06 40 " --> pdb=" O ALA06 36 " (cutoff:3.500A) Processing helix chain '06' and resid 97 through 116 removed outlier: 3.666A pdb=" N ARG06 114 " --> pdb=" O SER06 110 " (cutoff:3.500A) Processing helix chain '06' and resid 130 through 142 removed outlier: 4.125A pdb=" N LEU06 134 " --> pdb=" O LYS06 130 " (cutoff:3.500A) Processing helix chain '06' and resid 154 through 163 removed outlier: 3.529A pdb=" N PHE06 158 " --> pdb=" O ASP06 154 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG06 162 " --> pdb=" O PHE06 158 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ASN06 163 " --> pdb=" O LEU06 159 " (cutoff:3.500A) Processing helix chain '06' and resid 176 through 183 removed outlier: 3.569A pdb=" N LEU06 180 " --> pdb=" O ASP06 176 " (cutoff:3.500A) Processing helix chain '06' and resid 189 through 201 removed outlier: 3.749A pdb=" N GLN06 195 " --> pdb=" O ASP06 191 " (cutoff:3.500A) Processing helix chain '07' and resid 1 through 20 removed outlier: 4.186A pdb=" N ASP07 5 " --> pdb=" O ALA07 1 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR07 6 " --> pdb=" O LYS07 2 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL07 11 " --> pdb=" O TYR07 7 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N VAL07 12 " --> pdb=" O LYS07 8 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR07 17 " --> pdb=" O LYS07 13 " (cutoff:3.500A) Processing helix chain '07' and resid 45 through 61 removed outlier: 4.222A pdb=" N LEU07 49 " --> pdb=" O ASP07 45 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASP07 50 " --> pdb=" O LYS07 46 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA07 58 " --> pdb=" O ALA07 54 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE07 59 " --> pdb=" O ASP07 55 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N GLY07 61 " --> pdb=" O ALA07 57 " (cutoff:3.500A) Processing helix chain '07' and resid 92 through 110 removed outlier: 3.548A pdb=" N TRP07 96 " --> pdb=" O GLY07 92 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ILE07 105 " --> pdb=" O ARG07 101 " (cutoff:3.500A) removed outlier: 4.976A 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: 6.330A pdb=" N VAL07 145 " --> pdb=" O ASP07 141 " (cutoff:3.500A) removed outlier: 5.980A 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: 4.362A pdb=" N ALA07 167 " --> pdb=" O GLU07 163 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA07 171 " --> pdb=" O ALA07 167 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N PHE07 172 " --> pdb=" O LEU07 168 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP07 173 " --> pdb=" O LEU07 169 " (cutoff:3.500A) Processing helix chain '07' and resid 39 through 44 removed outlier: 5.029A pdb=" N ALA07 42 " --> pdb=" O VAL07 39 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ILE07 43 " --> pdb=" O GLY07 40 " (cutoff:3.500A) Processing helix chain '08' and resid 1 through 6 removed outlier: 5.575A pdb=" N ALA08 6 " --> pdb=" O ARG08 2 " (cutoff:3.500A) Processing helix chain '08' and resid 59 through 80 removed outlier: 3.632A pdb=" N ILE08 76 " --> pdb=" O ASN08 72 " (cutoff:3.500A) Processing helix chain '08' and resid 136 through 152 removed outlier: 3.515A pdb=" N ILE08 140 " --> pdb=" O ASP08 136 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY08 141 " --> pdb=" O LYS08 137 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN08 142 " --> pdb=" O GLN08 138 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG08 148 " --> pdb=" O ALA08 144 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG08 151 " --> pdb=" O LEU08 147 " (cutoff:3.500A) Processing helix chain '09' and resid 22 through 28 removed outlier: 3.609A pdb=" N ALA09 26 " --> pdb=" O LYS09 22 " (cutoff:3.500A) Processing helix chain '09' and resid 29 through 34 Processing helix chain '09' and resid 40 through 54 removed outlier: 3.677A pdb=" N ILE09 44 " --> pdb=" O THR09 40 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA09 49 " --> pdb=" O GLU09 45 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG09 50 " --> pdb=" O PHE09 46 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ALA09 52 " --> pdb=" O GLU09 48 " (cutoff:3.500A) Processing helix chain '09' and resid 55 through 73 removed outlier: 3.867A pdb=" N ALA09 59 " --> pdb=" O GLU09 55 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA09 64 " --> pdb=" O GLU09 60 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA09 69 " --> pdb=" O ALA09 65 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU09 70 " --> pdb=" O ASN09 66 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS09 71 " --> pdb=" O ALA09 67 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE09 72 " --> pdb=" O ARG09 68 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ASN09 73 " --> pdb=" O ALA09 69 " (cutoff:3.500A) Processing helix chain '09' and resid 95 through 107 removed outlier: 4.305A pdb=" N ILE09 99 " --> pdb=" O GLY09 95 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA09 105 " --> pdb=" O ASP09 101 " (cutoff:3.500A) Processing helix chain '09' and resid 111 through 116 removed outlier: 3.604A pdb=" N VAL09 115 " --> pdb=" O ALA09 111 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N ARG09 116 " --> pdb=" O LYS09 112 " (cutoff:3.500A) No H-bonds generated for 'chain '09' and resid 111 through 116' Processing helix chain '10' and resid 3 through 21 removed outlier: 3.556A pdb=" N ALA10 10 " --> pdb=" O GLN10 6 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE10 11 " --> pdb=" O ASP10 7 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER10 16 " --> pdb=" O VAL10 12 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS10 20 " --> pdb=" O SER10 16 " (cutoff:3.500A) Processing helix chain '10' and resid 33 through 48 removed outlier: 3.830A pdb=" N LYS10 37 " --> pdb=" O VAL10 33 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET10 38 " --> pdb=" O THR10 34 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR10 39 " --> pdb=" O VAL10 35 " (cutoff:3.500A) removed outlier: 4.512A 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) removed outlier: 3.587A pdb=" N GLY10 45 " --> pdb=" O LEU10 41 " (cutoff:3.500A) Processing helix chain '10' and resid 62 through 71 removed outlier: 3.763A pdb=" N GLY10 66 " --> pdb=" O ARG10 62 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR10 67 " --> pdb=" O ALA10 63 " (cutoff:3.500A) Proline residue: 10 68 - end of helix removed outlier: 4.400A pdb=" N CYS10 71 " --> pdb=" O THR10 67 " (cutoff:3.500A) No H-bonds generated for 'chain '10' and resid 62 through 71' Processing helix chain '10' and resid 94 through 106 removed outlier: 3.735A pdb=" N ALA10 100 " --> pdb=" O PHE10 96 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA10 104 " --> pdb=" O ALA10 100 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE10 106 " --> pdb=" O ALA10 102 " (cutoff:3.500A) Processing helix chain '10' and resid 109 through 114 removed outlier: 7.301A pdb=" N PHE10 113 " --> pdb=" O LYS10 109 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N GLU10 114 " --> pdb=" O ALA10 110 " (cutoff:3.500A) No H-bonds generated for 'chain '10' and resid 109 through 114' Processing helix chain '10' and resid 72 through 79 removed outlier: 3.726A pdb=" N GLY10 78 " --> pdb=" O ALA10 75 " (cutoff:3.500A) Proline residue: 10 79 - end of helix Processing helix chain '11' and resid 19 through 24 Processing helix chain '11' and resid 25 through 31 removed outlier: 5.420A pdb=" N GLN11 30 " --> pdb=" O ALA11 26 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLY11 31 " --> pdb=" O LEU11 27 " (cutoff:3.500A) Processing helix chain '11' and resid 33 through 49 removed outlier: 3.669A pdb=" N PHE11 41 " --> pdb=" O PHE11 37 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP11 46 " --> pdb=" O ASN11 42 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N SER11 47 " --> pdb=" O ALA11 43 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE11 48 " --> pdb=" O LYS11 44 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLU11 49 " --> pdb=" O THR11 45 " (cutoff:3.500A) Processing helix chain '11' and resid 74 through 84 Processing helix chain '11' and resid 101 through 114 Processing helix chain '11' and resid 120 through 136 removed outlier: 3.746A pdb=" N SER11 127 " --> pdb=" O ALA11 123 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE11 128 " --> pdb=" O MET11 124 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY11 136 " --> pdb=" O ALA11 132 " (cutoff:3.500A) Processing helix chain '12' and resid 24 through 38 Processing helix chain '12' and resid 67 through 72 Processing helix chain '12' and resid 88 through 96 Processing helix chain '12' and resid 97 through 110 removed outlier: 4.818A pdb=" N ILE12 101 " --> pdb=" O PRO12 97 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU12 102 " --> pdb=" O GLU12 98 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N MET12 108 " --> pdb=" O ALA12 104 " (cutoff:3.500A) Proline residue: 12 110 - end of helix Processing helix chain '12' and resid 112 through 122 removed outlier: 3.525A pdb=" N ARG12 120 " --> pdb=" O ARG12 116 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LYS12 121 " --> pdb=" O ALA12 117 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU12 122 " --> pdb=" O MET12 118 " (cutoff:3.500A) Processing helix chain '13' and resid 109 through 120 removed outlier: 6.223A pdb=" N MET13 113 " --> pdb=" O SER13 109 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N LYS13 114 " --> pdb=" O GLU13 110 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE13 115 " --> pdb=" O LYS13 111 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE13 116 " --> pdb=" O PHE13 112 " (cutoff:3.500A) Proline residue: 13 120 - end of helix Processing helix chain '14' and resid 37 through 42 removed outlier: 3.746A pdb=" N ARG14 41 " --> pdb=" O GLY14 37 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N SER14 42 " --> pdb=" O GLN14 38 " (cutoff:3.500A) No H-bonds generated for 'chain '14' and resid 37 through 42' Processing helix chain '14' and resid 56 through 62 Proline residue: 14 62 - end of helix Processing helix chain '14' and resid 68 through 74 removed outlier: 4.443A pdb=" N ALA14 72 " --> pdb=" O SER14 68 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE14 73 " --> pdb=" O ARG14 69 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR14 74 " --> pdb=" O LYS14 70 " (cutoff:3.500A) No H-bonds generated for 'chain '14' and resid 68 through 74' Processing helix chain '14' and resid 78 through 83 removed outlier: 3.818A pdb=" N ALA14 83 " --> pdb=" O LEU14 79 " (cutoff:3.500A) Processing helix chain '14' and resid 93 through 99 removed outlier: 6.299A pdb=" N ALA14 97 " --> pdb=" O ASN14 93 " (cutoff:3.500A) Processing helix chain '14' and resid 128 through 139 removed outlier: 3.746A pdb=" N ALA14 134 " --> pdb=" O GLY14 130 " (cutoff:3.500A) Processing helix chain '15' and resid 42 through 58 removed outlier: 4.368A pdb=" N ALA15 56 " --> pdb=" O ALA15 52 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL15 57 " --> pdb=" O MET15 53 " (cutoff:3.500A) Processing helix chain '15' and resid 109 through 125 removed outlier: 3.807A pdb=" N LEU15 119 " --> pdb=" O GLU15 115 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA15 120 " --> pdb=" O ALA15 116 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA15 122 " --> pdb=" O LYS15 118 " (cutoff:3.500A) Proline residue: 15 125 - end of helix Processing helix chain '16' and resid 13 through 32 removed outlier: 3.617A pdb=" N ALA16 25 " --> pdb=" O PHE16 21 " (cutoff:3.500A) Processing helix chain '16' and resid 38 through 56 removed outlier: 4.607A pdb=" N ARG16 46 " --> pdb=" O LYS16 42 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL16 47 " --> pdb=" O GLU16 43 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU16 49 " --> pdb=" O ARG16 45 " (cutoff:3.500A) Proline residue: 16 50 - end of helix Processing helix chain '16' and resid 59 through 71 removed outlier: 5.823A pdb=" N ARG16 63 " --> pdb=" O SER16 59 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG16 69 " --> pdb=" O LEU16 65 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR16 70 " --> pdb=" O ALA16 66 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG16 71 " --> pdb=" O PHE16 67 " (cutoff:3.500A) Processing helix chain '16' and resid 72 through 82 removed outlier: 4.368A pdb=" N PHE16 80 " --> pdb=" O VAL16 76 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASN16 81 " --> pdb=" O ALA16 77 " (cutoff:3.500A) Processing helix chain '16' and resid 83 through 88 Processing helix chain '17' and resid 2 through 20 removed outlier: 4.095A pdb=" N ARG17 13 " --> pdb=" O ARG17 9 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ALA17 14 " --> pdb=" O ARG17 10 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS17 17 " --> pdb=" O ARG17 13 " (cutoff:3.500A) Processing helix chain '17' and resid 55 through 63 removed outlier: 4.251A pdb=" N GLN17 61 " --> pdb=" O ALA17 57 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N LYS17 63 " --> pdb=" O ALA17 59 " (cutoff:3.500A) Processing helix chain '17' and resid 67 through 86 removed outlier: 3.905A pdb=" N ALA17 71 " --> pdb=" O ASN17 67 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS17 85 " --> pdb=" O ARG17 81 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY17 86 " --> pdb=" O ALA17 82 " (cutoff:3.500A) Processing helix chain '17' and resid 101 through 114 removed outlier: 3.627A pdb=" N ALA17 110 " --> pdb=" O LEU17 106 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY17 114 " --> pdb=" O ALA17 110 " (cutoff:3.500A) Processing helix chain '18' and resid 1 through 13 removed outlier: 3.530A pdb=" N GLN18 9 " --> pdb=" O LYS18 5 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU18 10 " --> pdb=" O GLN18 6 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLN18 11 " --> pdb=" O LEU18 7 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N LYS18 13 " --> pdb=" O GLN18 9 " (cutoff:3.500A) Processing helix chain '18' and resid 96 through 103 removed outlier: 4.834A pdb=" N ARG18 100 " --> pdb=" O LEU18 96 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLU18 101 " --> pdb=" O TYR18 97 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ARG18 102 " --> pdb=" O TYR18 98 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N THR18 103 " --> pdb=" O LEU18 99 " (cutoff:3.500A) No H-bonds generated for 'chain '18' and resid 96 through 103' Processing helix chain '19' and resid 5 through 21 removed outlier: 4.957A pdb=" N ALA19 9 " --> pdb=" O ARG19 5 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG19 10 " --> pdb=" O GLY19 6 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS19 15 " --> pdb=" O ALA19 11 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS19 21 " --> pdb=" O LEU19 17 " (cutoff:3.500A) Processing helix chain '19' and resid 25 through 30 removed outlier: 4.854A pdb=" N ARG19 29 " --> pdb=" O GLY19 25 " (cutoff:3.500A) Processing helix chain '19' and resid 42 through 60 removed outlier: 3.878A pdb=" N ARG19 50 " --> pdb=" O TYR19 46 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LYS19 53 " --> pdb=" O ARG19 49 " (cutoff:3.500A) Processing helix chain '19' and resid 62 through 72 Processing helix chain '19' and resid 74 through 86 Processing helix chain '19' and resid 90 through 101 removed outlier: 3.647A pdb=" N LEU19 94 " --> pdb=" O ASP19 90 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE19 100 " --> pdb=" O ASP19 96 " (cutoff:3.500A) Processing helix chain '19' and resid 102 through 117 removed outlier: 3.610A pdb=" N ALA19 117 " --> pdb=" O LYS19 113 " (cutoff:3.500A) Processing helix chain '21' and resid 13 through 25 removed outlier: 3.535A pdb=" N VAL21 17 " --> pdb=" O SER21 13 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL21 20 " --> pdb=" O LYS21 16 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU21 23 " --> pdb=" O LEU21 19 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ILE21 24 " --> pdb=" O VAL21 20 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG21 25 " --> pdb=" O ALA21 21 " (cutoff:3.500A) Processing helix chain '21' and resid 28 through 39 removed outlier: 4.096A pdb=" N TYR21 38 " --> pdb=" O ASP21 34 " (cutoff:3.500A) Processing helix chain '21' and resid 41 through 61 removed outlier: 3.907A pdb=" N VAL21 45 " --> pdb=" O LYS21 41 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL21 50 " --> pdb=" O LEU21 46 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN21 61 " --> pdb=" O ASN21 57 " (cutoff:3.500A) Processing helix chain '22' and resid 1 through 11 removed outlier: 4.162A pdb=" N GLU22 5 " --> pdb=" O MET22 1 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL22 10 " --> pdb=" O ARG22 6 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU22 11 " --> pdb=" O LEU22 7 " (cutoff:3.500A) Processing helix chain '22' and resid 17 through 26 removed outlier: 3.552A pdb=" N THR22 22 " --> pdb=" O GLU22 18 " (cutoff:3.500A) Processing helix chain '22' and resid 39 through 51 Processing helix chain '23' and resid 65 through 70 removed outlier: 3.818A pdb=" N VAL23 69 " --> pdb=" O GLN23 65 " (cutoff:3.500A) removed outlier: 5.125A 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: 3.541A pdb=" N SER24 17 " --> pdb=" O GLY24 13 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA24 23 " --> pdb=" O ARG24 19 " (cutoff:3.500A) Processing helix chain '24' and resid 43 through 53 removed outlier: 3.997A pdb=" N VAL24 47 " --> pdb=" O ASP24 43 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA24 52 " --> pdb=" O MET24 48 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LYS24 53 " --> pdb=" O ASN24 49 " (cutoff:3.500A) Processing helix chain '26' and resid 51 through 62 removed outlier: 3.813A pdb=" N ARG26 56 " --> pdb=" O ALA26 52 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLY26 62 " --> pdb=" O ILE26 58 " (cutoff:3.500A) Processing helix chain '26' and resid 63 through 74 removed outlier: 3.604A pdb=" N ARG26 73 " --> pdb=" O GLU26 69 " (cutoff:3.500A) Processing helix chain '27' and resid 2 through 7 removed outlier: 4.685A pdb=" N ARG27 7 " --> pdb=" O ALA27 3 " (cutoff:3.500A) Processing helix chain '27' and resid 9 through 35 removed outlier: 3.776A pdb=" N LEU27 18 " --> pdb=" O LEU27 14 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU27 19 " --> pdb=" O ASN27 15 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN27 20 " --> pdb=" O THR27 16 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU27 24 " --> pdb=" O ASN27 20 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLN27 25 " --> pdb=" O LEU27 21 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N PHE27 26 " --> pdb=" O LEU27 22 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN27 27 " --> pdb=" O ARG27 23 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER27 34 " --> pdb=" O MET27 30 " (cutoff:3.500A) Processing helix chain '27' and resid 40 through 63 removed outlier: 3.699A pdb=" N LYS27 44 " --> pdb=" O SER27 40 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA27 51 " --> pdb=" O ARG27 47 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N GLY27 62 " --> pdb=" O ASN27 58 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA27 63 " --> pdb=" O GLU27 59 " (cutoff:3.500A) Processing helix chain '28' and resid 16 through 27 removed outlier: 3.546A pdb=" N LYS28 20 " --> pdb=" O LEU28 16 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA28 21 " --> pdb=" O PRO28 17 " (cutoff:3.500A) Processing helix chain '28' and resid 40 through 51 Processing helix chain '29' and resid 42 through 50 removed outlier: 4.987A pdb=" N GLN29 48 " --> pdb=" O PHE29 44 " (cutoff:3.500A) Processing helix chain '29' and resid 55 through 65 removed outlier: 4.178A pdb=" N ARG29 59 " --> pdb=" O GLY29 55 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS29 62 " --> pdb=" O ASP29 58 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG29 63 " --> pdb=" O ARG29 59 " (cutoff:3.500A) Processing helix chain '30' and resid 8 through 18 removed outlier: 3.612A pdb=" N ARG30 16 " --> pdb=" O ARG30 12 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N HIS30 18 " --> pdb=" O MET30 14 " (cutoff:3.500A) Processing helix chain '32' and resid 8 through 16 Processing helix chain '32' and resid 17 through 25 removed outlier: 4.061A pdb=" N THR32 24 " --> pdb=" O ALA32 20 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N LYS32 25 " --> pdb=" O ARG32 21 " (cutoff:3.500A) Processing helix chain '32' and resid 26 through 38 Processing helix chain '33' and resid 6 through 13 removed outlier: 3.593A pdb=" N LYS33 11 " --> pdb=" O ARG33 7 " (cutoff:3.500A) Processing helix chain '33' and resid 31 through 36 removed outlier: 5.270A pdb=" N LYS33 35 " --> pdb=" O ILE33 31 " (cutoff:3.500A) removed outlier: 5.677A 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: 4.552A pdb=" N GLY33 55 " --> pdb=" O LYS33 51 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LEU33 56 " --> pdb=" O GLY33 52 " (cutoff:3.500A) Proline residue: 33 62 - end of helix Processing helix chain 'B' and resid 4 through 12 Processing helix chain 'B' and resid 41 through 63 removed outlier: 3.866A pdb=" N THR B 45 " --> pdb=" O ASN B 41 " (cutoff:3.500A) Proline residue: B 47 - end of helix removed outlier: 3.699A pdb=" N LYS B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE B 59 " --> pdb=" O GLU B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 87 removed outlier: 3.772A pdb=" N LYS B 80 " --> pdb=" O SER B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 123 removed outlier: 5.017A pdb=" N GLN B 108 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER B 109 " --> pdb=" O THR B 105 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR B 118 " --> pdb=" O LYS B 114 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER B 120 " --> pdb=" O LEU B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 129 removed outlier: 3.525A pdb=" N LEU B 128 " --> pdb=" O THR B 124 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N THR B 129 " --> pdb=" O PHE B 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 124 through 129' Processing helix chain 'B' and resid 130 through 147 removed outlier: 3.728A pdb=" N SER B 146 " --> pdb=" O LYS B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 169 Processing helix chain 'B' and resid 170 through 179 Processing helix chain 'B' and resid 205 through 225 removed outlier: 3.703A pdb=" N SER B 225 " --> pdb=" O ARG B 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 12 removed outlier: 4.084A pdb=" N ARG C 10 " --> pdb=" O PRO C 6 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLY C 12 " --> pdb=" O GLY C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 47 removed outlier: 3.574A pdb=" N VAL C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 77 Processing helix chain 'C' and resid 80 through 95 removed outlier: 3.680A pdb=" N LYS C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL C 89 " --> pdb=" O LYS C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 112 removed outlier: 5.654A pdb=" N ALA C 112 " --> pdb=" O PRO C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 126 removed outlier: 3.595A pdb=" N GLN C 122 " --> pdb=" O SER C 118 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU C 124 " --> pdb=" O THR C 120 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG C 126 " --> pdb=" O GLN C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 removed outlier: 3.550A pdb=" N VAL C 137 " --> pdb=" O MET C 133 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU C 143 " --> pdb=" O ASN C 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 15 removed outlier: 4.175A pdb=" N LEU D 10 " --> pdb=" O PRO D 6 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N SER D 11 " --> pdb=" O LYS D 7 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG D 12 " --> pdb=" O LEU D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 65 Processing helix chain 'D' and resid 67 through 81 removed outlier: 3.844A pdb=" N LEU D 81 " --> pdb=" O GLU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 96 removed outlier: 3.884A pdb=" N LEU D 90 " --> pdb=" O GLY D 86 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU D 92 " --> pdb=" O ASN D 88 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG D 96 " --> pdb=" O LEU D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 105 Processing helix chain 'D' and resid 109 through 120 removed outlier: 4.341A pdb=" N HIS D 119 " --> pdb=" O GLN D 115 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LYS D 120 " --> pdb=" O LEU D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 165 removed outlier: 5.631A pdb=" N LYS D 155 " --> pdb=" O GLN D 151 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA D 156 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU D 159 " --> pdb=" O LYS D 155 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU D 162 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLN D 163 " --> pdb=" O GLU D 159 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG D 164 " --> pdb=" O LEU D 160 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLU D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 191 removed outlier: 3.845A pdb=" N LEU D 190 " --> pdb=" O GLU D 186 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N SER D 191 " --> pdb=" O ARG D 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 186 through 191' Processing helix chain 'D' and resid 195 through 205 removed outlier: 4.345A pdb=" N ILE D 199 " --> pdb=" O ASN D 195 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU D 201 " --> pdb=" O HIS D 197 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU D 202 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR D 203 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER D 204 " --> pdb=" O VAL D 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 70 removed outlier: 3.589A pdb=" N GLN E 60 " --> pdb=" O PRO E 56 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU E 64 " --> pdb=" O GLN E 60 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS E 65 " --> pdb=" O LYS E 61 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET E 70 " --> pdb=" O ALA E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 118 removed outlier: 5.760A pdb=" N ALA E 112 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL E 113 " --> pdb=" O ALA E 109 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL E 116 " --> pdb=" O ALA E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 147 removed outlier: 3.779A pdb=" N ARG E 137 " --> pdb=" O ILE E 133 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ASN E 147 " --> pdb=" O LEU E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 156 Processing helix chain 'E' and resid 159 through 165 Processing helix chain 'F' and resid 12 through 33 removed outlier: 4.138A pdb=" N GLU F 16 " --> pdb=" O PRO F 12 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLN F 17 " --> pdb=" O ASP F 13 " (cutoff:3.500A) Proline residue: F 19 - end of helix removed outlier: 3.588A pdb=" N ALA F 28 " --> pdb=" O ARG F 24 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE F 29 " --> pdb=" O TYR F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 81 removed outlier: 3.621A pdb=" N ILE F 71 " --> pdb=" O PRO F 67 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP F 72 " --> pdb=" O GLN F 68 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR F 77 " --> pdb=" O GLU F 73 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N PHE F 78 " --> pdb=" O LEU F 74 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG F 79 " --> pdb=" O GLU F 75 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN F 81 " --> pdb=" O THR F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 126 removed outlier: 4.896A pdb=" N ALA F 105 " --> pdb=" O PRO F 101 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS F 106 " --> pdb=" O MET F 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 31 removed outlier: 5.289A pdb=" N VAL G 31 " --> pdb=" O ASN G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 54 removed outlier: 3.597A pdb=" N ALA G 38 " --> pdb=" O LYS G 34 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU G 47 " --> pdb=" O TYR G 43 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR G 48 " --> pdb=" O SER G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 70 removed outlier: 3.708A pdb=" N VAL G 63 " --> pdb=" O GLU G 59 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASN G 67 " --> pdb=" O VAL G 63 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N VAL G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) Proline residue: G 70 - end of helix Processing helix chain 'G' and resid 91 through 111 removed outlier: 3.760A pdb=" N ASN G 96 " --> pdb=" O PRO G 92 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA G 97 " --> pdb=" O VAL G 93 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA G 99 " --> pdb=" O ARG G 95 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG G 110 " --> pdb=" O ALA G 106 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N GLY G 111 " --> pdb=" O ALA G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 129 removed outlier: 3.963A pdb=" N GLU G 128 " --> pdb=" O SER G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 148 removed outlier: 3.666A pdb=" N LYS G 135 " --> pdb=" O GLY G 131 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG G 142 " --> pdb=" O GLU G 138 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA G 146 " --> pdb=" O ARG G 142 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN G 147 " --> pdb=" O MET G 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 20 Processing helix chain 'H' and resid 29 through 43 Processing helix chain 'H' and resid 111 through 119 removed outlier: 4.397A pdb=" N GLN H 117 " --> pdb=" O ARG H 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 38 removed outlier: 3.522A pdb=" N PHE I 38 " --> pdb=" O LEU I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 55 Proline residue: I 50 - end of helix removed outlier: 3.885A pdb=" N LEU I 53 " --> pdb=" O GLN I 49 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL I 54 " --> pdb=" O PRO I 50 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASP I 55 " --> pdb=" O LEU I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 86 Processing helix chain 'I' and resid 91 through 101 removed outlier: 5.502A pdb=" N GLU I 96 " --> pdb=" O SER I 92 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ALA I 100 " --> pdb=" O GLU I 96 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLY I 101 " --> pdb=" O LEU I 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 33 removed outlier: 5.064A pdb=" N GLN J 20 " --> pdb=" O ARG J 16 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N THR J 32 " --> pdb=" O THR J 28 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLY J 33 " --> pdb=" O ALA J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 90 removed outlier: 4.492A pdb=" N ASP J 85 " --> pdb=" O GLU J 81 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA J 86 " --> pdb=" O LYS J 82 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ARG J 89 " --> pdb=" O ASP J 85 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU J 90 " --> pdb=" O ALA J 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 50 removed outlier: 3.574A pdb=" N SER K 49 " --> pdb=" O THR K 45 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLY K 50 " --> pdb=" O ALA K 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 45 through 50' Processing helix chain 'K' and resid 53 through 59 removed outlier: 3.533A pdb=" N SER K 57 " --> pdb=" O GLY K 53 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N THR K 58 " --> pdb=" O SER K 54 " (cutoff:3.500A) Proline residue: K 59 - end of helix No H-bonds generated for 'chain 'K' and resid 53 through 59' Processing helix chain 'K' and resid 60 through 74 removed outlier: 4.177A pdb=" N ALA K 72 " --> pdb=" O ARG K 68 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL K 73 " --> pdb=" O CYS K 69 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N LYS K 74 " --> pdb=" O ALA K 70 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 103 removed outlier: 4.035A pdb=" N ILE K 96 " --> pdb=" O ARG K 92 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ARG K 97 " --> pdb=" O GLU K 93 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA K 98 " --> pdb=" O SER K 94 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLY K 103 " --> pdb=" O LEU K 99 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 10 removed outlier: 3.779A pdb=" N LEU L 6 " --> pdb=" O THR L 2 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL L 7 " --> pdb=" O VAL L 3 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG L 8 " --> pdb=" O ASN L 4 " (cutoff:3.500A) Proline residue: L 10 - end of helix Processing helix chain 'L' and resid 112 through 117 removed outlier: 5.402A pdb=" N TYR L 116 " --> pdb=" O ALA L 112 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 21 removed outlier: 3.565A pdb=" N THR M 19 " --> pdb=" O VAL M 15 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N SER M 20 " --> pdb=" O ILE M 16 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE M 21 " --> pdb=" O ALA M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 25 through 37 removed outlier: 3.540A pdb=" N LEU M 33 " --> pdb=" O SER M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 63 removed outlier: 5.205A pdb=" N THR M 54 " --> pdb=" O GLY M 50 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP M 57 " --> pdb=" O ASP M 53 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LYS M 61 " --> pdb=" O ASP M 57 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N PHE M 62 " --> pdb=" O GLU M 58 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N VAL M 63 " --> pdb=" O VAL M 59 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 83 Processing helix chain 'M' and resid 84 through 93 Processing helix chain 'M' and resid 105 through 110 Processing helix chain 'N' and resid 2 through 23 removed outlier: 3.709A pdb=" N LYS N 6 " --> pdb=" O LYS N 2 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE N 20 " --> pdb=" O ALA N 16 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ALA N 21 " --> pdb=" O ASP N 17 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N LYS N 22 " --> pdb=" O LYS N 18 " (cutoff:3.500A) Processing helix chain 'N' and resid 24 through 29 Processing helix chain 'N' and resid 37 through 50 removed outlier: 3.617A pdb=" N TRP N 41 " --> pdb=" O ASP N 37 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLN N 48 " --> pdb=" O VAL N 44 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N THR N 49 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU N 50 " --> pdb=" O LYS N 46 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 60 removed outlier: 3.998A pdb=" N GLN N 59 " --> pdb=" O SER N 55 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ARG N 60 " --> pdb=" O PRO N 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 55 through 60' Processing helix chain 'N' and resid 79 through 90 Processing helix chain 'O' and resid 3 through 15 Processing helix chain 'O' and resid 23 through 43 removed outlier: 4.530A pdb=" N GLY O 40 " --> pdb=" O ASN O 36 " (cutoff:3.500A) removed outlier: 4.821A 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 Processing helix chain 'P' and resid 53 through 64 removed outlier: 3.567A pdb=" N ILE P 57 " --> pdb=" O ASP P 53 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA P 58 " --> pdb=" O LEU P 54 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 79 removed outlier: 3.536A pdb=" N LEU P 74 " --> pdb=" O ARG P 70 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS P 76 " --> pdb=" O ALA P 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 12 through 17 removed outlier: 4.353A pdb=" N GLY R 16 " --> pdb=" O PHE R 12 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 33 removed outlier: 4.194A pdb=" N LEU R 28 " --> pdb=" O ASP R 24 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ASN R 30 " --> pdb=" O ALA R 26 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N TYR R 31 " --> pdb=" O THR R 27 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ILE R 32 " --> pdb=" O LEU R 28 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N THR R 33 " --> pdb=" O LYS R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 45 removed outlier: 3.636A pdb=" N THR R 44 " --> pdb=" O PRO R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 47 through 65 removed outlier: 3.631A pdb=" N GLN R 53 " --> pdb=" O LYS R 49 " (cutoff:3.500A) Processing helix chain 'S' and resid 11 through 25 removed outlier: 3.541A pdb=" N SER S 24 " --> pdb=" O LYS S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 70 through 75 removed outlier: 4.329A pdb=" N ALA S 74 " --> pdb=" O LEU S 70 " (cutoff:3.500A) Proline residue: S 75 - end of helix No H-bonds generated for 'chain 'S' and resid 70 through 75' Processing helix chain 'T' and resid 6 through 41 removed outlier: 4.085A pdb=" N ALA T 10 " --> pdb=" O ALA T 6 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS T 15 " --> pdb=" O ILE T 11 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N HIS T 19 " --> pdb=" O LYS T 15 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA T 21 " --> pdb=" O ARG T 17 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG T 23 " --> pdb=" O HIS T 19 " (cutoff:3.500A) Processing helix chain 'T' and resid 42 through 64 Proline residue: T 55 - end of helix Processing helix chain 'T' and resid 67 through 86 removed outlier: 5.926A pdb=" N ALA T 71 " --> pdb=" O HIS T 67 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR T 79 " --> pdb=" O LYS T 75 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN T 83 " --> pdb=" O THR T 79 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA T 86 " --> pdb=" O ILE T 82 " (cutoff:3.500A) Processing helix chain 'U' and resid 17 through 23 Processing helix chain 'U' and resid 24 through 32 removed outlier: 3.829A pdb=" N LEU U 28 " --> pdb=" O LYS U 24 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU U 30 " --> pdb=" O GLY U 26 " (cutoff:3.500A) Processing helix chain 'U' and resid 36 through 61 Proline residue: U 40 - end of helix removed outlier: 3.547A pdb=" N LYS U 48 " --> pdb=" O ARG U 44 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS U 53 " --> pdb=" O ALA U 49 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS U 58 " --> pdb=" O ARG U 54 " (cutoff:3.500A) Processing helix chain '03' and resid 5 through 16 removed outlier: 3.800A pdb=" N VAL03 15 " --> pdb=" O ILE03 11 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ASP03 16 " --> pdb=" O ARG03 12 " (cutoff:3.500A) Processing helix chain '03' and resid 23 through 35 removed outlier: 4.835A pdb=" N ALA03 28 " --> pdb=" O ASN03 24 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LYS03 31 " --> pdb=" O ILE03 27 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU03 32 " --> pdb=" O ALA03 28 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU03 33 " --> pdb=" O LEU03 29 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N THR03 35 " --> pdb=" O LYS03 31 " (cutoff:3.500A) Processing helix chain '03' and resid 181 through 200 removed outlier: 3.810A pdb=" N ASN03 188 " --> pdb=" O LYS03 184 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL03 194 " --> pdb=" O GLU03 190 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA03 195 " --> pdb=" O ALA03 191 " (cutoff:3.500A) Processing helix chain 'Z' and resid 4 through 16 removed outlier: 3.647A pdb=" N LEU Z 8 " --> pdb=" O SER Z 4 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE Z 9 " --> pdb=" O PHE Z 5 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LYS Z 14 " --> pdb=" O GLU Z 10 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU Z 15 " --> pdb=" O GLU Z 11 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE Z 16 " --> pdb=" O SER Z 12 " (cutoff:3.500A) Processing helix chain 'Z' and resid 49 through 54 removed outlier: 4.460A pdb=" N PHE Z 53 " --> pdb=" O PRO Z 49 " (cutoff:3.500A) Processing helix chain 'Z' and resid 89 through 99 removed outlier: 4.541A pdb=" N GLU Z 93 " --> pdb=" O ALA Z 89 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ILE Z 96 " --> pdb=" O HIS Z 92 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N THR Z 97 " --> pdb=" O GLU Z 93 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU Z 98 " --> pdb=" O ALA Z 94 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU Z 99 " --> pdb=" O TRP Z 95 " (cutoff:3.500A) Processing helix chain 'Z' and resid 100 through 105 removed outlier: 5.022A pdb=" N ASP Z 104 " --> pdb=" O LYS Z 100 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA Z 105 " --> pdb=" O ALA Z 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 100 through 105' Processing helix chain 'Z' and resid 172 through 178 removed outlier: 5.019A pdb=" N ASN Z 178 " --> pdb=" O ILE Z 174 " (cutoff:3.500A) Processing helix chain 'Z' and resid 144 through 149 removed outlier: 4.840A pdb=" N LEU Z 147 " --> pdb=" O THR Z 144 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLU Z 148 " --> pdb=" O LEU Z 145 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N GLY Z 149 " --> pdb=" O HIS Z 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 144 through 149' Processing sheet with id= 1, first strand: chain '04' and resid 1 through 7 removed outlier: 3.559A pdb=" N CYS04 5 " --> pdb=" O VAL04 15 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL04 15 " --> pdb=" O CYS04 5 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ARG04 13 " --> pdb=" O PRO04 7 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '04' and resid 72 through 77 removed outlier: 4.825A pdb=" N ILE04 73 " --> pdb=" O SER04 117 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N SER04 117 " --> pdb=" O ILE04 73 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ASP04 113 " --> pdb=" O VAL04 77 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '04' and resid 79 through 82 removed outlier: 6.049A pdb=" N ASN04 89 " --> pdb=" O ALA04 105 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '04' and resid 126 through 129 removed outlier: 3.947A pdb=" N ASN04 127 " --> pdb=" O LEU04 191 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain '04' and resid 137 through 141 removed outlier: 4.603A pdb=" N SER04 138 " --> pdb=" O ILE04 163 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN04 162 " --> pdb=" O ARG04 174 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR04 172 " --> pdb=" O VAL04 164 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU04 179 " --> pdb=" O LEU04 175 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain '05' and resid 3 through 8 removed outlier: 4.149A pdb=" N SER05 199 " --> pdb=" O LYS05 8 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS05 204 " --> pdb=" O ASP05 108 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain '05' and resid 11 through 16 removed outlier: 3.725A pdb=" N VAL05 20 " --> pdb=" O THR05 16 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ARG05 179 " --> pdb=" O LEU05 188 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain '05' and resid 36 through 40 removed outlier: 3.679A pdb=" N LEU05 40 " --> pdb=" O TYR05 45 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N TYR05 45 " --> pdb=" O LEU05 40 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLN05 49 " --> pdb=" O THR05 35 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR05 51 " --> pdb=" O ARG05 33 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLN05 94 " --> pdb=" O VAL05 34 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain '05' and resid 47 through 51 Processing sheet with id= 10, first strand: chain '06' and resid 1 through 5 No H-bonds generated for sheet with id= 10 Processing sheet with id= 11, first strand: chain '06' and resid 117 through 120 removed outlier: 5.755A pdb=" N ARG06 117 " --> pdb=" O ASP06 184 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS06 185 " --> pdb=" O ASP06 145 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP06 168 " --> pdb=" O VAL06 146 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR06 150 " --> pdb=" O ARG06 170 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain '07' and resid 64 through 68 removed outlier: 3.650A pdb=" N ILE07 33 " --> pdb=" O LEU07 90 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS07 32 " --> pdb=" O THR07 156 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N GLY07 38 " --> pdb=" O GLY07 150 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N GLY07 150 " --> pdb=" O GLY07 38 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU07 151 " --> pdb=" O VAL07 131 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain '08' and resid 15 through 18 removed outlier: 3.514A pdb=" N LYS08 26 " --> pdb=" O ASP08 15 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain '08' and resid 40 through 44 Processing sheet with id= 15, first strand: chain '08' and resid 81 through 88 removed outlier: 3.557A pdb=" N LYS08 84 " --> pdb=" O LEU08 132 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU08 132 " --> pdb=" O LYS08 84 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N THR08 128 " --> pdb=" O LEU08 88 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR08 121 " --> pdb=" O LYS08 133 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain '08' and resid 93 through 97 removed outlier: 3.664A pdb=" N SER08 105 " --> pdb=" O ARG08 94 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL08 112 " --> pdb=" O LEU08 104 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain '09' and resid 76 through 81 removed outlier: 6.950A pdb=" N GLU09 76 " --> pdb=" O LYS09 141 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N HIS09 128 " --> pdb=" O VAL09 144 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain '10' and resid 22 through 28 removed outlier: 4.005A pdb=" N LEU10 23 " --> pdb=" O GLU10 87 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA10 25 " --> pdb=" O SER10 85 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain '11' and resid 6 through 13 removed outlier: 5.139A pdb=" N ALA11 6 " --> pdb=" O VAL11 60 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N VAL11 60 " --> pdb=" O ALA11 6 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL11 8 " --> pdb=" O ILE11 58 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL11 12 " --> pdb=" O ILE11 54 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain '12' and resid 52 through 57 removed outlier: 4.339A pdb=" N GLN12 138 " --> pdb=" O TRP12 15 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL12 17 " --> pdb=" O GLN12 138 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ASP12 19 " --> pdb=" O LEU12 140 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain '12' and resid 74 through 77 Processing sheet with id= 22, first strand: chain '13' and resid 6 through 9 removed outlier: 4.045A pdb=" N THR13 6 " --> pdb=" O CYS13 21 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain '15' and resid 38 through 41 removed outlier: 3.886A pdb=" N TYR15 91 " --> pdb=" O ILE15 73 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain '15' and resid 62 through 65 removed outlier: 3.622A pdb=" N ASP15 106 " --> pdb=" O LYS15 62 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU15 104 " --> pdb=" O TRP15 64 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TYR15 103 " --> pdb=" O LEU15 33 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU15 33 " --> pdb=" O LEU15 102 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS15 100 " --> pdb=" O ALA15 35 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain '15' and resid 31 through 36 removed outlier: 3.562A pdb=" N LYS15 34 " --> pdb=" O THR15 129 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LYS15 127 " --> pdb=" O VAL15 36 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain '16' and resid 33 through 37 removed outlier: 5.407A pdb=" N ARG16 103 " --> pdb=" O ASN16 107 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLY16 101 " --> pdb=" O PRO16 109 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA16 111 " --> pdb=" O LYS16 99 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LYS16 99 " --> pdb=" O ALA16 111 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE16 113 " --> pdb=" O ILE16 97 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ILE16 97 " --> pdb=" O ILE16 113 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU16 115 " --> pdb=" O THR16 95 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N THR16 95 " --> pdb=" O LEU16 115 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain '17' and resid 49 through 52 removed outlier: 3.823A pdb=" N VAL17 49 " --> pdb=" O VAL17 39 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA17 37 " --> pdb=" O ALA17 51 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER17 91 " --> pdb=" O THR17 24 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL17 28 " --> pdb=" O ASP17 93 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain '18' and resid 37 through 44 removed outlier: 6.677A pdb=" N THR18 24 " --> pdb=" O LYS18 86 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER18 84 " --> pdb=" O GLU18 26 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain '18' and resid 56 through 63 removed outlier: 7.806A pdb=" N SER18 56 " --> pdb=" O THR18 75 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain '20' and resid 19 through 23 removed outlier: 6.883A pdb=" N ASP20 95 " --> pdb=" O VAL20 64 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N LYS20 60 " --> pdb=" O THR20 99 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N GLU20 31 " --> pdb=" O VAL20 63 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain '20' and resid 71 through 78 removed outlier: 4.192A pdb=" N TYR20 83 " --> pdb=" O ARG20 78 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain '21' and resid 2 through 8 removed outlier: 4.827A pdb=" N THR21 3 " --> pdb=" O VAL21 107 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL21 107 " --> pdb=" O THR21 3 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL21 106 " --> pdb=" O THR21 72 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain '21' and resid 73 through 79 removed outlier: 4.755A pdb=" N THR21 100 " --> pdb=" O GLY21 79 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain '21' and resid 80 through 87 Processing sheet with id= 35, first strand: chain '22' and resid 12 through 15 removed outlier: 5.253A pdb=" N LYS22 66 " --> pdb=" O ARG22 77 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ASP22 79 " --> pdb=" O LYS22 64 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N LYS22 64 " --> pdb=" O ASP22 79 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LYS22 81 " --> pdb=" O VAL22 62 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL22 62 " --> pdb=" O LYS22 81 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ALA22 83 " --> pdb=" O THR22 60 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N THR22 60 " --> pdb=" O ALA22 83 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL22 85 " --> pdb=" O VAL22 58 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL22 58 " --> pdb=" O VAL22 85 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain '23' and resid 39 through 43 removed outlier: 6.471A pdb=" N ASN23 39 " --> pdb=" O GLU23 61 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL23 41 " --> pdb=" O GLU23 59 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLU23 59 " --> pdb=" O VAL23 41 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LYS23 43 " --> pdb=" O ILE23 57 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE23 57 " --> pdb=" O LYS23 43 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain '23' and resid 81 through 85 removed outlier: 5.621A pdb=" N ARG23 81 " --> pdb=" O LYS23 96 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE23 94 " --> pdb=" O GLY23 83 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain '24' and resid 6 through 9 removed outlier: 3.790A pdb=" N ILE24 89 " --> pdb=" O PRO24 27 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain '24' and resid 61 through 64 removed outlier: 3.539A pdb=" N ILE24 63 " --> pdb=" O ILE24 70 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE24 70 " --> pdb=" O ILE24 63 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain '25' and resid 30 through 33 removed outlier: 3.796A pdb=" N SER25 31 " --> pdb=" O ALA25 57 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU25 55 " --> pdb=" O ILE25 33 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR25 54 " --> pdb=" O GLY25 50 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain '26' and resid 11 through 18 removed outlier: 3.729A pdb=" N THR26 24 " --> pdb=" O ASN26 16 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ASN26 22 " --> pdb=" O SER26 18 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain '26' and resid 34 through 39 Processing sheet with id= 43, first strand: chain '28' and resid 34 through 38 removed outlier: 7.402A pdb=" N MET28 53 " --> pdb=" O THR28 9 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain '29' and resid 12 through 16 No H-bonds generated for sheet with id= 44 Processing sheet with id= 45, first strand: chain '30' and resid 27 through 30 No H-bonds generated for sheet with id= 45 Processing sheet with id= 46, first strand: chain '31' and resid 18 through 23 removed outlier: 6.067A pdb=" N HIS31 18 " --> pdb=" O SER31 12 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ILE31 47 " --> pdb=" O SER31 13 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU31 50 " --> pdb=" O LEU31 33 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LEU31 33 " --> pdb=" O GLU31 50 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain '34' and resid 13 through 18 removed outlier: 8.052A pdb=" N ASN34 13 " --> pdb=" O SER34 28 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE34 23 " --> pdb=" O GLN34 37 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'B' and resid 88 through 92 removed outlier: 3.547A pdb=" N ILE B 163 " --> pdb=" O VAL B 69 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'C' and resid 18 through 21 removed outlier: 7.139A pdb=" N ASN C 18 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE C 56 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG C 58 " --> pdb=" O THR C 20 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG C 53 " --> pdb=" O HIS C 68 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'C' and resid 166 through 169 removed outlier: 3.838A pdb=" N GLY C 147 " --> pdb=" O PHE C 202 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'D' and resid 139 through 143 removed outlier: 6.067A pdb=" N GLU D 178 " --> pdb=" O ASP D 173 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS D 182 " --> pdb=" O TRP D 169 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N TRP D 169 " --> pdb=" O LYS D 182 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'E' and resid 10 through 15 removed outlier: 4.190A pdb=" N GLN E 11 " --> pdb=" O GLY E 39 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU E 35 " --> pdb=" O ILE E 15 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'E' and resid 82 through 86 removed outlier: 7.781A pdb=" N HIS E 82 " --> pdb=" O PRO E 97 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N MET E 95 " --> pdb=" O VAL E 84 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N VAL E 93 " --> pdb=" O GLY E 86 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N TYR E 127 " --> pdb=" O ARG E 92 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'E' and resid 31 through 39 removed outlier: 4.263A pdb=" N GLY E 50 " --> pdb=" O ALA E 34 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'F' and resid 39 through 42 removed outlier: 3.852A pdb=" N GLU F 40 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TRP F 42 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N TYR F 59 " --> pdb=" O TRP F 42 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS F 58 " --> pdb=" O VAL F 10 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE F 8 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ILE F 6 " --> pdb=" O MET F 62 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N HIS F 3 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR F 92 " --> pdb=" O HIS F 3 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N GLU F 5 " --> pdb=" O MET F 90 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET F 90 " --> pdb=" O GLU F 5 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'F' and resid 43 through 47 removed outlier: 4.060A pdb=" N GLY F 43 " --> pdb=" O TYR F 59 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N LEU F 47 " --> pdb=" O HIS F 55 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N HIS F 55 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'G' and resid 72 through 79 removed outlier: 3.803A pdb=" N LYS G 75 " --> pdb=" O VAL G 86 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG G 77 " --> pdb=" O TYR G 84 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N TYR G 84 " --> pdb=" O ARG G 77 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N SER G 82 " --> pdb=" O VAL G 79 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'H' and resid 22 through 28 removed outlier: 6.711A pdb=" N ALA H 22 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU H 51 " --> pdb=" O GLU H 57 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR H 61 " --> pdb=" O ASP H 47 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ASP H 47 " --> pdb=" O THR H 61 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'H' and resid 73 through 76 removed outlier: 7.046A pdb=" N VAL H 102 " --> pdb=" O ILE H 125 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'I' and resid 4 through 10 removed outlier: 4.478A pdb=" N GLY I 9 " --> pdb=" O ALA I 16 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA I 16 " --> pdb=" O GLY I 9 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'J' and resid 44 through 52 removed outlier: 3.513A pdb=" N ARG J 45 " --> pdb=" O THR J 69 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU J 47 " --> pdb=" O ILE J 67 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE J 8 " --> pdb=" O VAL J 74 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG J 9 " --> pdb=" O GLN J 99 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'K' and resid 29 through 35 Processing sheet with id= 63, first strand: chain 'L' and resid 28 through 31 removed outlier: 5.252A pdb=" N LEU L 80 " --> pdb=" O VAL L 97 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'L' and resid 35 through 40 removed outlier: 4.839A pdb=" N ARG L 35 " --> pdb=" O ARG L 53 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N LYS L 50 " --> pdb=" O ILE L 66 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'P' and resid 4 through 10 removed outlier: 3.744A pdb=" N PHE P 16 " --> pdb=" O HIS P 9 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLY P 37 " --> pdb=" O VAL P 19 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLY P 49 " --> pdb=" O ASN P 40 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'Q' and resid 6 through 9 removed outlier: 3.723A pdb=" N GLY Q 9 " --> pdb=" O VAL Q 58 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N GLU Q 59 " --> pdb=" O VAL Q 75 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'Q' and resid 18 through 27 removed outlier: 5.602A pdb=" N LYS Q 18 " --> pdb=" O ASP Q 47 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ASP Q 47 " --> pdb=" O LYS Q 18 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'S' and resid 29 through 33 removed outlier: 4.749A pdb=" N LEU S 30 " --> pdb=" O THR S 47 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS S 51 " --> pdb=" O THR S 32 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LEU S 46 " --> pdb=" O VAL S 61 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE S 48 " --> pdb=" O VAL S 59 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain '03' and resid 59 through 64 removed outlier: 5.486A pdb=" N VAL03 59 " --> pdb=" O ASN03 165 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain '03' and resid 169 through 174 removed outlier: 5.813A pdb=" N GLY03 169 " --> pdb=" O LEU03 48 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS03 211 " --> pdb=" O ASN03 47 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N VAL03 212 " --> pdb=" O VAL03 224 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'Z' and resid 23 through 28 removed outlier: 4.604A pdb=" N ASP Z 66 " --> pdb=" O VAL Z 28 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'Z' and resid 36 through 39 Processing sheet with id= 73, first strand: chain 'Z' and resid 119 through 123 removed outlier: 3.638A pdb=" N VAL Z 122 " --> pdb=" O ALA Z 129 " (cutoff:3.500A) 1735 hydrogen bonds defined for protein. 5130 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3621 hydrogen bonds 5924 hydrogen bond angles 0 basepair planarities 1453 basepair parallelities 2733 stacking parallelities Total time for adding SS restraints: 234.00 Time building geometry restraints manager: 65.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 28931 1.34 - 1.46: 70853 1.46 - 1.59: 55492 1.59 - 1.72: 9606 1.72 - 1.84: 288 Bond restraints: 165170 Sorted by residual: bond pdb=" CA THR Z 144 " pdb=" CB THR Z 144 " ideal model delta sigma weight residual 1.523 1.580 -0.057 1.27e-02 6.20e+03 1.98e+01 bond pdb=" CA VAL Z 166 " pdb=" CB VAL Z 166 " ideal model delta sigma weight residual 1.532 1.565 -0.033 1.08e-02 8.57e+03 9.29e+00 bond pdb=" CA ILE Z 127 " pdb=" CB ILE Z 127 " ideal model delta sigma weight residual 1.539 1.573 -0.034 1.18e-02 7.18e+03 8.52e+00 bond pdb=" CA VAL08 9 " pdb=" CB VAL08 9 " ideal model delta sigma weight residual 1.530 1.560 -0.030 1.05e-02 9.07e+03 7.93e+00 bond pdb=" CA THR Z 121 " pdb=" CB THR Z 121 " ideal model delta sigma weight residual 1.527 1.562 -0.034 1.30e-02 5.92e+03 6.98e+00 ... (remaining 165165 not shown) Histogram of bond angle deviations from ideal: 98.73 - 105.78: 25671 105.78 - 112.83: 94103 112.83 - 119.88: 58677 119.88 - 126.93: 56150 126.93 - 133.98: 12221 Bond angle restraints: 246822 Sorted by residual: angle pdb=" N VAL08 10 " pdb=" CA VAL08 10 " pdb=" C VAL08 10 " ideal model delta sigma weight residual 107.73 118.06 -10.33 1.14e+00 7.69e-01 8.21e+01 angle pdb=" N SER L 114 " pdb=" CA SER L 114 " pdb=" C SER L 114 " ideal model delta sigma weight residual 111.07 101.83 9.24 1.07e+00 8.73e-01 7.46e+01 angle pdb=" N VAL G 5 " pdb=" CA VAL G 5 " pdb=" C VAL G 5 " ideal model delta sigma weight residual 112.29 105.06 7.23 9.40e-01 1.13e+00 5.92e+01 angle pdb=" N LEU10 117 " pdb=" CA LEU10 117 " pdb=" C LEU10 117 " ideal model delta sigma weight residual 109.15 120.23 -11.08 1.44e+00 4.82e-01 5.92e+01 angle pdb=" N GLY G 80 " pdb=" CA GLY G 80 " pdb=" C GLY G 80 " ideal model delta sigma weight residual 114.37 105.13 9.24 1.26e+00 6.30e-01 5.37e+01 ... (remaining 246817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.57: 94588 35.57 - 71.14: 10000 71.14 - 106.71: 1238 106.71 - 142.28: 15 142.28 - 177.85: 18 Dihedral angle restraints: 105859 sinusoidal: 87989 harmonic: 17870 Sorted by residual: dihedral pdb=" O4' U012552 " pdb=" C1' U012552 " pdb=" N1 U012552 " pdb=" C2 U012552 " ideal model delta sinusoidal sigma weight residual 200.00 39.97 160.03 1 1.50e+01 4.44e-03 8.28e+01 dihedral pdb=" O4' U011915 " pdb=" C1' U011915 " pdb=" N1 U011915 " pdb=" C2 U011915 " ideal model delta sinusoidal sigma weight residual 200.00 40.09 159.91 1 1.50e+01 4.44e-03 8.27e+01 dihedral pdb=" O4' C02 12 " pdb=" C1' C02 12 " pdb=" N1 C02 12 " pdb=" C2 C02 12 " ideal model delta sinusoidal sigma weight residual 200.00 41.68 158.32 1 1.50e+01 4.44e-03 8.23e+01 ... (remaining 105856 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 27788 0.121 - 0.241: 3657 0.241 - 0.362: 87 0.362 - 0.483: 1 0.483 - 0.604: 1 Chirality restraints: 31534 Sorted by residual: chirality pdb=" P G Y 1 " pdb=" OP1 G Y 1 " pdb=" OP2 G Y 1 " pdb=" O5' G Y 1 " both_signs ideal model delta sigma weight residual True 2.41 3.01 -0.60 2.00e-01 2.50e+01 9.11e+00 chirality pdb=" C3' A011020 " pdb=" C4' A011020 " pdb=" O3' A011020 " pdb=" C2' A011020 " both_signs ideal model delta sigma weight residual False -2.74 -2.37 -0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" C1' G A 413 " pdb=" O4' G A 413 " pdb=" C2' G A 413 " pdb=" N9 G A 413 " both_signs ideal model delta sigma weight residual False 2.46 2.10 0.36 2.00e-01 2.50e+01 3.21e+00 ... (remaining 31531 not shown) Planarity restraints: 13429 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G012061 " -0.087 2.00e-02 2.50e+03 3.63e-02 3.95e+01 pdb=" N9 G012061 " 0.005 2.00e-02 2.50e+03 pdb=" C8 G012061 " 0.040 2.00e-02 2.50e+03 pdb=" N7 G012061 " 0.036 2.00e-02 2.50e+03 pdb=" C5 G012061 " 0.016 2.00e-02 2.50e+03 pdb=" C6 G012061 " -0.017 2.00e-02 2.50e+03 pdb=" O6 G012061 " -0.054 2.00e-02 2.50e+03 pdb=" N1 G012061 " -0.015 2.00e-02 2.50e+03 pdb=" C2 G012061 " 0.008 2.00e-02 2.50e+03 pdb=" N2 G012061 " 0.020 2.00e-02 2.50e+03 pdb=" N3 G012061 " 0.023 2.00e-02 2.50e+03 pdb=" C4 G012061 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 413 " 0.088 2.00e-02 2.50e+03 3.61e-02 3.91e+01 pdb=" N9 G A 413 " -0.008 2.00e-02 2.50e+03 pdb=" C8 G A 413 " -0.039 2.00e-02 2.50e+03 pdb=" N7 G A 413 " -0.034 2.00e-02 2.50e+03 pdb=" C5 G A 413 " -0.015 2.00e-02 2.50e+03 pdb=" C6 G A 413 " 0.016 2.00e-02 2.50e+03 pdb=" O6 G A 413 " 0.055 2.00e-02 2.50e+03 pdb=" N1 G A 413 " 0.012 2.00e-02 2.50e+03 pdb=" C2 G A 413 " -0.009 2.00e-02 2.50e+03 pdb=" N2 G A 413 " -0.017 2.00e-02 2.50e+03 pdb=" N3 G A 413 " -0.023 2.00e-02 2.50e+03 pdb=" C4 G A 413 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U01 810 " 0.066 2.00e-02 2.50e+03 4.03e-02 3.66e+01 pdb=" N1 U01 810 " -0.002 2.00e-02 2.50e+03 pdb=" C2 U01 810 " -0.015 2.00e-02 2.50e+03 pdb=" O2 U01 810 " -0.016 2.00e-02 2.50e+03 pdb=" N3 U01 810 " -0.025 2.00e-02 2.50e+03 pdb=" C4 U01 810 " -0.026 2.00e-02 2.50e+03 pdb=" O4 U01 810 " 0.080 2.00e-02 2.50e+03 pdb=" C5 U01 810 " -0.035 2.00e-02 2.50e+03 pdb=" C6 U01 810 " -0.028 2.00e-02 2.50e+03 ... (remaining 13426 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 24519 2.77 - 3.30: 139088 3.30 - 3.84: 300477 3.84 - 4.37: 366630 4.37 - 4.90: 497125 Nonbonded interactions: 1327839 Sorted by model distance: nonbonded pdb=" O THR M 54 " pdb=" OD1 ASP M 57 " model vdw 2.239 3.040 nonbonded pdb=" O ILE M 72 " pdb=" OG SER M 75 " model vdw 2.264 2.440 nonbonded pdb=" O ARG16 69 " pdb=" OG1 THR16 70 " model vdw 2.282 2.440 nonbonded pdb=" O VAL09 37 " pdb=" N ALA09 39 " model vdw 2.282 2.520 nonbonded pdb=" O2' G012391 " pdb=" O5' A012392 " model vdw 2.287 2.440 ... (remaining 1327834 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'W' and resid 1 through 76) selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.47 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: 5.550 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: 0.140 Extract box with map and model: 27.020 Check model and map are aligned: 1.980 Set scattering table: 1.040 Process input model: 531.930 Find NCS groups from input model: 3.090 Set up NCS constraints: 0.410 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 573.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 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 : 0.006 0.057 165170 Z= 0.360 Angle : 0.908 14.454 246822 Z= 0.606 Chirality : 0.079 0.604 31534 Planarity : 0.006 0.065 13429 Dihedral : 21.952 177.853 94318 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 3.36 % Allowed : 14.81 % Favored : 81.83 % Rotamer: Outliers : 0.70 % Allowed : 2.60 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.26 (0.08), residues: 6159 helix: -4.12 (0.07), residues: 1811 sheet: -2.54 (0.14), residues: 1035 loop : -3.50 (0.09), residues: 3313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.008 TRP S 33 HIS 0.001 0.000 HIS12 47 PHE 0.034 0.005 PHE B 15 TYR 0.046 0.007 TYR I 5 ARG 0.005 0.001 ARG30 51 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12318 Ramachandran restraints generated. 6159 Oldfield, 0 Emsley, 6159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12318 Ramachandran restraints generated. 6159 Oldfield, 0 Emsley, 6159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1931 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 1895 time to evaluate : 6.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 04 94 LEU cc_start: 0.9589 (tp) cc_final: 0.9356 (pp) REVERT: 04 145 MET cc_start: 0.9257 (mmm) cc_final: 0.8865 (ptt) REVERT: 04 170 TYR cc_start: 0.8919 (m-80) cc_final: 0.8594 (m-10) REVERT: 04 186 ASP cc_start: 0.9175 (m-30) cc_final: 0.8962 (m-30) REVERT: 04 193 GLU cc_start: 0.8997 (mt-10) cc_final: 0.8739 (mp0) REVERT: 05 81 GLU cc_start: 0.8857 (tt0) cc_final: 0.8430 (tm-30) REVERT: 05 174 SER cc_start: 0.9417 (m) cc_final: 0.9124 (p) REVERT: 06 9 GLN cc_start: 0.9447 (mt0) cc_final: 0.9204 (tm-30) REVERT: 06 35 TYR cc_start: 0.8768 (t80) cc_final: 0.8564 (t80) REVERT: 06 100 MET cc_start: 0.9556 (mtp) cc_final: 0.9209 (mtp) REVERT: 07 82 TYR cc_start: 0.8446 (t80) cc_final: 0.8155 (t80) REVERT: 07 86 CYS cc_start: 0.8517 (p) cc_final: 0.8133 (p) REVERT: 07 95 MET cc_start: 0.9107 (ptm) cc_final: 0.8397 (ptm) REVERT: 07 127 TYR cc_start: 0.9117 (t80) cc_final: 0.8853 (t80) REVERT: 07 152 ASP cc_start: 0.8677 (p0) cc_final: 0.8263 (m-30) REVERT: 08 19 ASN cc_start: 0.9005 (t0) cc_final: 0.8782 (p0) REVERT: 08 23 ILE cc_start: 0.9051 (mt) cc_final: 0.8746 (mp) REVERT: 08 98 LYS cc_start: 0.9497 (mtmm) cc_final: 0.9285 (pttt) REVERT: 08 123 GLU cc_start: 0.9276 (mm-30) cc_final: 0.9043 (mp0) REVERT: 08 146 ASP cc_start: 0.9504 (m-30) cc_final: 0.9250 (p0) REVERT: 09 33 GLN cc_start: 0.9494 (mt0) cc_final: 0.9156 (mt0) REVERT: 09 71 LYS cc_start: 0.8827 (mtmt) cc_final: 0.8606 (tppt) REVERT: 09 128 HIS cc_start: 0.8150 (m-70) cc_final: 0.7479 (m-70) REVERT: 11 16 MET cc_start: 0.7302 (mmp) cc_final: 0.7099 (ptm) REVERT: 11 27 LEU cc_start: 0.2408 (pp) cc_final: 0.1932 (pp) REVERT: 11 135 MET cc_start: 0.4433 (mmp) cc_final: 0.3905 (mtt) REVERT: 11 139 VAL cc_start: 0.7742 (p) cc_final: 0.7091 (t) REVERT: 12 14 ASP cc_start: 0.8851 (t70) cc_final: 0.7935 (t0) REVERT: 12 16 TYR cc_start: 0.8886 (m-80) cc_final: 0.8532 (m-80) REVERT: 12 37 ARG cc_start: 0.9265 (ttt90) cc_final: 0.9057 (ttm-80) REVERT: 12 44 TYR cc_start: 0.8840 (t80) cc_final: 0.8549 (t80) REVERT: 12 86 GLN cc_start: 0.9474 (pt0) cc_final: 0.8690 (pp30) REVERT: 12 91 GLU cc_start: 0.9583 (mt-10) cc_final: 0.9255 (tm-30) REVERT: 12 92 MET cc_start: 0.9510 (tpp) cc_final: 0.9037 (tpt) REVERT: 12 98 GLU cc_start: 0.9268 (mt-10) cc_final: 0.8800 (pm20) REVERT: 12 99 ARG cc_start: 0.9613 (mmm160) cc_final: 0.9222 (tpp80) REVERT: 12 103 ILE cc_start: 0.9746 (mt) cc_final: 0.9545 (mt) REVERT: 12 114 LEU cc_start: 0.9816 (tp) cc_final: 0.9610 (tt) REVERT: 12 118 MET cc_start: 0.9540 (ptp) cc_final: 0.9263 (ptp) REVERT: 13 12 ASP cc_start: 0.8627 (p0) cc_final: 0.8079 (p0) REVERT: 13 17 ARG cc_start: 0.9403 (tpp80) cc_final: 0.8869 (tpt90) REVERT: 13 20 MET cc_start: 0.9367 (ttp) cc_final: 0.9115 (ttp) REVERT: 13 38 ILE cc_start: 0.8655 (mm) cc_final: 0.8400 (tp) REVERT: 13 44 LYS cc_start: 0.9301 (mmmt) cc_final: 0.8899 (mmmm) REVERT: 13 59 LYS cc_start: 0.9437 (mttt) cc_final: 0.9121 (mtpp) REVERT: 13 73 ASP cc_start: 0.9215 (p0) cc_final: 0.8747 (p0) REVERT: 13 88 ASN cc_start: 0.9056 (t0) cc_final: 0.8565 (t0) REVERT: 14 38 GLN cc_start: 0.8813 (tt0) cc_final: 0.8587 (tt0) REVERT: 14 86 GLU cc_start: 0.9476 (tt0) cc_final: 0.9266 (pp20) REVERT: 15 45 GLN cc_start: 0.9568 (mt0) cc_final: 0.9303 (mt0) REVERT: 15 53 MET cc_start: 0.9474 (ttp) cc_final: 0.9254 (tmm) REVERT: 15 74 THR cc_start: 0.8900 (p) cc_final: 0.8650 (t) REVERT: 15 82 MET cc_start: 0.9287 (mmp) cc_final: 0.9072 (mmm) REVERT: 15 111 GLU cc_start: 0.9675 (tp30) cc_final: 0.9415 (tm-30) REVERT: 15 112 LEU cc_start: 0.9457 (tp) cc_final: 0.9216 (tp) REVERT: 16 1 MET cc_start: 0.9385 (ptp) cc_final: 0.8897 (mtm) REVERT: 16 34 ILE cc_start: 0.9327 (pt) cc_final: 0.9004 (mm) REVERT: 16 49 GLU cc_start: 0.9145 (mt-10) cc_final: 0.8840 (mt-10) REVERT: 17 36 TYR cc_start: 0.8735 (m-80) cc_final: 0.8386 (m-10) REVERT: 17 43 ASN cc_start: 0.9178 (p0) cc_final: 0.8172 (p0) REVERT: 17 45 SER cc_start: 0.8729 (t) cc_final: 0.8341 (p) REVERT: 17 46 GLU cc_start: 0.9052 (pt0) cc_final: 0.8802 (pm20) REVERT: 17 48 LEU cc_start: 0.9422 (mt) cc_final: 0.9061 (mp) REVERT: 17 80 GLU cc_start: 0.9380 (mt-10) cc_final: 0.8767 (mt-10) REVERT: 17 89 ASP cc_start: 0.8625 (t70) cc_final: 0.8240 (t0) REVERT: 17 104 GLN cc_start: 0.9762 (tt0) cc_final: 0.9451 (tp40) REVERT: 17 108 ASP cc_start: 0.9553 (m-30) cc_final: 0.9248 (m-30) REVERT: 18 83 ILE cc_start: 0.9109 (mt) cc_final: 0.8745 (mm) REVERT: 18 105 LYS cc_start: 0.8931 (mmmt) cc_final: 0.8697 (mmtm) REVERT: 18 111 GLU cc_start: 0.8641 (tp30) cc_final: 0.8126 (tp30) REVERT: 19 35 PHE cc_start: 0.9678 (t80) cc_final: 0.9381 (t80) REVERT: 19 40 LYS cc_start: 0.9514 (ttmm) cc_final: 0.9088 (tptm) REVERT: 19 44 TYR cc_start: 0.9372 (m-80) cc_final: 0.9036 (m-80) REVERT: 19 90 ASP cc_start: 0.7893 (p0) cc_final: 0.7528 (p0) REVERT: 19 110 GLU cc_start: 0.9629 (mm-30) cc_final: 0.9315 (mm-30) REVERT: 20 1 MET cc_start: 0.9240 (tpp) cc_final: 0.8971 (tmm) REVERT: 20 32 THR cc_start: 0.9361 (t) cc_final: 0.9092 (t) REVERT: 20 37 GLU cc_start: 0.9290 (mm-30) cc_final: 0.8979 (mm-30) REVERT: 20 40 MET cc_start: 0.9557 (ttp) cc_final: 0.9025 (tmm) REVERT: 20 60 LYS cc_start: 0.9463 (mtmm) cc_final: 0.9196 (ttmm) REVERT: 21 1 MET cc_start: 0.7117 (tpp) cc_final: 0.6845 (ppp) REVERT: 21 3 THR cc_start: 0.9482 (m) cc_final: 0.8922 (p) REVERT: 21 4 ILE cc_start: 0.9654 (pt) cc_final: 0.8922 (pt) REVERT: 21 66 ILE cc_start: 0.9299 (mm) cc_final: 0.9078 (mm) REVERT: 21 77 ASP cc_start: 0.8065 (p0) cc_final: 0.7683 (p0) REVERT: 21 84 ARG cc_start: 0.8574 (mmt-90) cc_final: 0.8182 (mmt-90) REVERT: 21 96 ILE cc_start: 0.9514 (pt) cc_final: 0.9293 (mm) REVERT: 21 97 LEU cc_start: 0.9549 (mp) cc_final: 0.8811 (mt) REVERT: 21 100 THR cc_start: 0.9090 (p) cc_final: 0.8772 (p) REVERT: 22 8 LEU cc_start: 0.9629 (mt) cc_final: 0.8868 (mt) REVERT: 22 11 LEU cc_start: 0.9510 (mt) cc_final: 0.9120 (mm) REVERT: 22 48 GLN cc_start: 0.9351 (mm110) cc_final: 0.8622 (mt0) REVERT: 22 50 LEU cc_start: 0.9346 (mp) cc_final: 0.8865 (mm) REVERT: 23 57 ILE cc_start: 0.9152 (mt) cc_final: 0.8856 (tp) REVERT: 24 48 MET cc_start: 0.9508 (tpt) cc_final: 0.9265 (tpt) REVERT: 24 55 GLU cc_start: 0.9544 (mt-10) cc_final: 0.9219 (tm-30) REVERT: 24 71 LYS cc_start: 0.9254 (mtpp) cc_final: 0.8996 (mtpp) REVERT: 24 78 GLN cc_start: 0.9118 (mt0) cc_final: 0.8803 (mt0) REVERT: 24 86 LEU cc_start: 0.9373 (mt) cc_final: 0.8828 (mt) REVERT: 25 68 LYS cc_start: 0.9440 (mtmt) cc_final: 0.9088 (mtpt) REVERT: 25 75 PHE cc_start: 0.9137 (m-80) cc_final: 0.8930 (m-10) REVERT: 25 76 ILE cc_start: 0.9644 (mt) cc_final: 0.9419 (mt) REVERT: 26 2 ARG cc_start: 0.9277 (mtt90) cc_final: 0.8987 (mtt90) REVERT: 26 16 ASN cc_start: 0.9573 (t0) cc_final: 0.9349 (t0) REVERT: 26 36 ARG cc_start: 0.9318 (ttp-170) cc_final: 0.8857 (ttp80) REVERT: 26 47 THR cc_start: 0.9592 (m) cc_final: 0.9356 (p) REVERT: 26 55 MET cc_start: 0.9353 (mtp) cc_final: 0.9054 (mtp) REVERT: 27 13 GLU cc_start: 0.9195 (pt0) cc_final: 0.8746 (pt0) REVERT: 27 31 GLN cc_start: 0.9566 (tt0) cc_final: 0.9288 (tt0) REVERT: 27 39 GLN cc_start: 0.9412 (mt0) cc_final: 0.9042 (pm20) REVERT: 27 59 GLU cc_start: 0.9325 (tt0) cc_final: 0.9102 (tp30) REVERT: 27 60 LYS cc_start: 0.9171 (mmmt) cc_final: 0.8829 (ptmt) REVERT: 28 5 LYS cc_start: 0.9292 (mtpp) cc_final: 0.8731 (mmmt) REVERT: 28 10 ARG cc_start: 0.9357 (mtt90) cc_final: 0.9029 (tpp80) REVERT: 28 20 LYS cc_start: 0.9489 (mttp) cc_final: 0.9206 (mptt) REVERT: 28 46 MET cc_start: 0.8996 (mtp) cc_final: 0.8602 (mtp) REVERT: 29 22 MET cc_start: 0.9075 (ttp) cc_final: 0.8870 (ppp) REVERT: 30 21 LEU cc_start: 0.8666 (mt) cc_final: 0.8369 (pp) REVERT: 30 36 LYS cc_start: 0.9425 (mmtp) cc_final: 0.9106 (mmmm) REVERT: 31 4 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8024 (tt) REVERT: 31 6 GLU cc_start: 0.9252 (pt0) cc_final: 0.8676 (pm20) REVERT: 31 7 LYS cc_start: 0.9360 (ptpt) cc_final: 0.9146 (pttt) REVERT: 31 8 ILE cc_start: 0.8987 (pt) cc_final: 0.8679 (pt) REVERT: 31 19 PHE cc_start: 0.9312 (p90) cc_final: 0.8972 (p90) REVERT: 31 24 LYS cc_start: 0.8831 (ttpt) cc_final: 0.8452 (ttpp) REVERT: 31 27 ARG cc_start: 0.9082 (mtp180) cc_final: 0.8745 (mmm160) REVERT: 31 32 LYS cc_start: 0.9193 (mtmm) cc_final: 0.8715 (mttt) REVERT: 31 47 ILE cc_start: 0.9357 (mp) cc_final: 0.9136 (pt) REVERT: 31 48 TYR cc_start: 0.8743 (m-80) cc_final: 0.8312 (m-80) REVERT: 32 1 MET cc_start: 0.7807 (ptm) cc_final: 0.7024 (ppp) REVERT: 32 6 GLN cc_start: 0.9464 (mm-40) cc_final: 0.9095 (mp10) REVERT: 32 9 VAL cc_start: 0.9644 (t) cc_final: 0.9394 (m) REVERT: 32 10 LEU cc_start: 0.9304 (tp) cc_final: 0.8936 (tt) REVERT: 32 13 ASN cc_start: 0.9417 (m-40) cc_final: 0.8520 (t0) REVERT: 32 28 ARG cc_start: 0.9353 (mtm-85) cc_final: 0.9128 (mtm-85) REVERT: 32 37 LYS cc_start: 0.9459 (tttt) cc_final: 0.9105 (tmtt) REVERT: 33 21 PHE cc_start: 0.8864 (m-80) cc_final: 0.8596 (m-10) REVERT: 33 39 ARG cc_start: 0.8991 (ttt180) cc_final: 0.8701 (ttt-90) REVERT: 34 18 LYS cc_start: 0.9536 (tttt) cc_final: 0.9315 (ttmt) REVERT: 34 22 VAL cc_start: 0.9432 (t) cc_final: 0.9213 (t) REVERT: 34 36 ARG cc_start: 0.9336 (ptm-80) cc_final: 0.8759 (ttp-170) REVERT: 34 37 GLN cc_start: 0.9216 (tp-100) cc_final: 0.8879 (tp-100) REVERT: B 99 MET cc_start: 0.9355 (mtp) cc_final: 0.9088 (mtp) REVERT: B 108 GLN cc_start: 0.9543 (mm110) cc_final: 0.9322 (mp10) REVERT: C 2 GLN cc_start: 0.8403 (pt0) cc_final: 0.7563 (pt0) REVERT: C 33 ASP cc_start: 0.9655 (t70) cc_final: 0.9160 (t0) REVERT: C 141 MET cc_start: 0.9131 (mmm) cc_final: 0.8756 (mmt) REVERT: C 169 GLU cc_start: 0.9278 (tp30) cc_final: 0.9025 (tp30) REVERT: D 39 GLN cc_start: 0.8262 (tt0) cc_final: 0.7966 (tm-30) REVERT: D 50 TYR cc_start: 0.9249 (t80) cc_final: 0.8785 (t80) REVERT: D 73 ASN cc_start: 0.9295 (m-40) cc_final: 0.9076 (m110) REVERT: D 139 ASN cc_start: 0.8969 (t0) cc_final: 0.8726 (p0) REVERT: E 63 MET cc_start: 0.9258 (mmt) cc_final: 0.8819 (mmt) REVERT: E 67 ARG cc_start: 0.9582 (mmt90) cc_final: 0.9180 (mmt90) REVERT: E 96 GLN cc_start: 0.9240 (tt0) cc_final: 0.8568 (mt0) REVERT: E 141 ASP cc_start: 0.9478 (m-30) cc_final: 0.8976 (p0) REVERT: F 1 MET cc_start: 0.9228 (mtm) cc_final: 0.8176 (mtm) REVERT: F 25 TYR cc_start: 0.9175 (m-80) cc_final: 0.8831 (m-80) REVERT: F 59 TYR cc_start: 0.8781 (m-80) cc_final: 0.7966 (m-80) REVERT: F 65 GLU cc_start: 0.9011 (tt0) cc_final: 0.8441 (tm-30) REVERT: F 72 ASP cc_start: 0.9599 (m-30) cc_final: 0.9341 (m-30) REVERT: F 89 VAL cc_start: 0.9358 (t) cc_final: 0.8996 (t) REVERT: F 98 GLU cc_start: 0.9003 (mm-30) cc_final: 0.8730 (mm-30) REVERT: G 4 ARG cc_start: 0.8774 (mmt-90) cc_final: 0.8503 (mmp80) REVERT: G 11 ILE cc_start: 0.8867 (pt) cc_final: 0.8353 (pt) REVERT: G 30 MET cc_start: 0.9362 (ttp) cc_final: 0.9064 (ttt) REVERT: G 32 ASP cc_start: 0.8546 (m-30) cc_final: 0.8044 (t0) REVERT: G 105 GLU cc_start: 0.9463 (tp30) cc_final: 0.9178 (tm-30) REVERT: G 115 MET cc_start: 0.9476 (tpt) cc_final: 0.9096 (ttt) REVERT: H 8 ASP cc_start: 0.9344 (t70) cc_final: 0.9123 (t0) REVERT: H 58 LEU cc_start: 0.9372 (tp) cc_final: 0.9122 (tp) REVERT: H 65 PHE cc_start: 0.9142 (t80) cc_final: 0.8852 (t80) REVERT: H 84 ILE cc_start: 0.9600 (mt) cc_final: 0.9227 (tp) REVERT: H 95 MET cc_start: 0.9417 (mtp) cc_final: 0.9176 (mtt) REVERT: H 110 MET cc_start: 0.9354 (ptp) cc_final: 0.9009 (ptp) REVERT: H 112 ASP cc_start: 0.9616 (p0) cc_final: 0.8927 (t0) REVERT: H 117 GLN cc_start: 0.9189 (mt0) cc_final: 0.8897 (mp10) REVERT: I 32 ARG cc_start: 0.9468 (mmt-90) cc_final: 0.9152 (mtm-85) REVERT: I 106 ASP cc_start: 0.8955 (t70) cc_final: 0.8731 (t70) REVERT: I 117 LEU cc_start: 0.9454 (mp) cc_final: 0.9217 (mp) REVERT: J 11 LYS cc_start: 0.9592 (ptpt) cc_final: 0.9262 (pttt) REVERT: J 24 GLU cc_start: 0.9549 (mt-10) cc_final: 0.9289 (pp20) REVERT: J 47 GLU cc_start: 0.7654 (mp0) cc_final: 0.7380 (mm-30) REVERT: J 63 ASP cc_start: 0.8636 (t0) cc_final: 0.8110 (t0) REVERT: J 65 TYR cc_start: 0.8614 (m-80) cc_final: 0.8381 (m-80) REVERT: J 97 ASP cc_start: 0.9062 (t70) cc_final: 0.8620 (p0) REVERT: J 99 GLN cc_start: 0.8514 (mt0) cc_final: 0.8080 (mt0) REVERT: K 67 GLU cc_start: 0.9252 (mt-10) cc_final: 0.9034 (tm-30) REVERT: K 124 LYS cc_start: 0.8643 (pttp) cc_final: 0.8397 (pttt) REVERT: L 2 THR cc_start: 0.9006 (m) cc_final: 0.8635 (m) REVERT: L 19 ASN cc_start: 0.9392 (m-40) cc_final: 0.9139 (t0) REVERT: L 28 GLN cc_start: 0.9627 (mp10) cc_final: 0.9405 (mp10) REVERT: M 11 HIS cc_start: 0.9249 (m-70) cc_final: 0.8849 (t-170) REVERT: M 32 ILE cc_start: 0.9460 (mm) cc_final: 0.9225 (mm) REVERT: M 51 GLN cc_start: 0.9594 (mt0) cc_final: 0.9241 (tm-30) REVERT: M 63 VAL cc_start: 0.9661 (t) cc_final: 0.9250 (p) REVERT: M 82 LEU cc_start: 0.9365 (tp) cc_final: 0.9097 (tt) REVERT: N 18 LYS cc_start: 0.8601 (ttpt) cc_final: 0.8395 (ttmt) REVERT: N 25 GLU cc_start: 0.9288 (pt0) cc_final: 0.8948 (tm-30) REVERT: N 49 THR cc_start: 0.9595 (m) cc_final: 0.9311 (m) REVERT: N 65 GLN cc_start: 0.9370 (mt0) cc_final: 0.9090 (mt0) REVERT: O 37 HIS cc_start: 0.9533 (t70) cc_final: 0.9156 (t-170) REVERT: O 47 LYS cc_start: 0.9452 (mmmt) cc_final: 0.9086 (mptt) REVERT: O 61 GLN cc_start: 0.9738 (tp40) cc_final: 0.9497 (tt0) REVERT: O 78 THR cc_start: 0.9577 (p) cc_final: 0.8701 (p) REVERT: P 14 ARG cc_start: 0.9209 (mmm-85) cc_final: 0.8965 (mmm160) REVERT: Q 6 THR cc_start: 0.9091 (t) cc_final: 0.8782 (m) REVERT: Q 8 GLN cc_start: 0.9213 (mm-40) cc_final: 0.8648 (mm-40) REVERT: Q 14 ASP cc_start: 0.7958 (t70) cc_final: 0.7713 (t0) REVERT: Q 16 MET cc_start: 0.8498 (ptm) cc_final: 0.7888 (tmm) REVERT: Q 41 THR cc_start: 0.7673 (m) cc_final: 0.7157 (m) REVERT: Q 51 GLU cc_start: 0.9187 (pt0) cc_final: 0.8959 (pm20) REVERT: Q 59 GLU cc_start: 0.8434 (mm-30) cc_final: 0.7854 (mm-30) REVERT: Q 62 GLU cc_start: 0.8415 (tp30) cc_final: 0.8081 (tp30) REVERT: Q 68 LYS cc_start: 0.9512 (tttp) cc_final: 0.9271 (ttmt) REVERT: T 26 MET cc_start: 0.9322 (ttp) cc_final: 0.8841 (tpp) REVERT: U 3 ILE cc_start: 0.8767 (mm) cc_final: 0.8324 (mm) REVERT: U 8 ASN cc_start: 0.9157 (m110) cc_final: 0.8440 (p0) REVERT: U 44 ARG cc_start: 0.9139 (tpp-160) cc_final: 0.8893 (tmm160) REVERT: U 45 LYS cc_start: 0.9471 (tptt) cc_final: 0.9148 (tppt) REVERT: U 48 LYS cc_start: 0.9380 (ttmm) cc_final: 0.9124 (tppp) REVERT: U 55 HIS cc_start: 0.8085 (t70) cc_final: 0.7830 (t-90) REVERT: 03 209 ILE cc_start: 0.7571 (pt) cc_final: 0.7309 (mt) REVERT: Z 23 ILE cc_start: 0.6739 (tp) cc_final: 0.6381 (mm) outliers start: 36 outliers final: 13 residues processed: 1922 average time/residue: 1.4276 time to fit residues: 4629.1336 Evaluate side-chains 1180 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1166 time to evaluate : 6.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 07 residue 140 ILE Chi-restraints excluded: chain 12 residue 84 ILE Chi-restraints excluded: chain 14 residue 23 ILE Chi-restraints excluded: chain 14 residue 111 ILE Chi-restraints excluded: chain 18 residue 3 ILE Chi-restraints excluded: chain 23 residue 4 ILE Chi-restraints excluded: chain 31 residue 4 ILE Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain E residue 15 ILE Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain N residue 92 ILE Chi-restraints excluded: chain P residue 29 ASN Chi-restraints excluded: chain Z residue 100 LYS Chi-restraints excluded: chain Z residue 162 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1080 random chunks: chunk 911 optimal weight: 20.0000 chunk 818 optimal weight: 20.0000 chunk 454 optimal weight: 30.0000 chunk 279 optimal weight: 10.0000 chunk 552 optimal weight: 20.0000 chunk 437 optimal weight: 20.0000 chunk 846 optimal weight: 40.0000 chunk 327 optimal weight: 20.0000 chunk 514 optimal weight: 10.0000 chunk 630 optimal weight: 30.0000 chunk 980 optimal weight: 20.0000 overall best weight: 16.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 04 44 ASN 04 45 ASN 04 52 HIS 04 85 ASN 04 89 ASN ** 04 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 04 133 ASN 04 238 ASN 06 24 ASN 06 94 GLN 06 97 ASN 08 21 GLN 08 37 ASN 08 44 HIS 08 87 GLN 08 138 GLN ** 09 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 10 4 ASN 10 9 GLN 10 57 ASN 10 88 HIS 11 93 ASN 12 58 ASN 12 80 HIS ** 12 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 88 ASN 14 38 GLN 16 81 ASN ** 16 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 19 36 GLN 19 51 GLN 19 55 GLN 20 18 GLN ** 20 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 21 9 HIS ** 21 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 22 59 ASN ** 23 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 23 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 23 68 ASN 23 73 ASN 24 12 GLN 26 22 ASN 27 27 ASN ** 27 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 28 19 HIS 29 61 ASN 30 18 HIS 31 18 HIS ** 31 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 34 13 ASN B 17 HIS B 50 ASN B 176 ASN ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 2 GLN ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN D 73 ASN ** D 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 GLN D 195 ASN D 197 HIS E 81 GLN ** E 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 11 HIS ** F 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 GLN G 27 ASN ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 121 ASN G 129 ASN ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 ASN ** J 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN ** K 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 45 ASN M 7 ASN M 104 ASN ** N 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 59 GLN N 61 ASN ** O 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 51 GLN T 19 HIS T 47 GLN T 51 ASN ** T 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 03 20 GLN 03 203 GLN Z 7 GLN Z 92 HIS Z 165 ASN Z 178 ASN Total number of N/Q/H flips: 73 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.135 165170 Z= 0.514 Angle : 0.923 12.662 246822 Z= 0.464 Chirality : 0.046 0.269 31534 Planarity : 0.008 0.129 13429 Dihedral : 23.406 176.496 82065 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 31.73 Ramachandran Plot: Outliers : 0.36 % Allowed : 11.19 % Favored : 88.46 % Rotamer: Outliers : 5.80 % Allowed : 14.03 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.88 (0.09), residues: 6159 helix: -2.39 (0.10), residues: 1926 sheet: -2.23 (0.14), residues: 1095 loop : -2.83 (0.10), residues: 3138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP04 247 HIS 0.014 0.003 HIS20 89 PHE 0.028 0.003 PHE F 116 TYR 0.034 0.004 TYR I 5 ARG 0.017 0.001 ARG20 90 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12318 Ramachandran restraints generated. 6159 Oldfield, 0 Emsley, 6159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12318 Ramachandran restraints generated. 6159 Oldfield, 0 Emsley, 6159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1546 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 297 poor density : 1249 time to evaluate : 6.600 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: 04 35 LYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8770 (ttpt) REVERT: 04 145 MET cc_start: 0.9532 (mmm) cc_final: 0.9057 (ptt) REVERT: 04 224 MET cc_start: 0.9305 (mtp) cc_final: 0.8711 (mtm) REVERT: 04 250 GLN cc_start: 0.9351 (tp-100) cc_final: 0.9136 (tp-100) REVERT: 05 149 ASN cc_start: 0.8667 (t0) cc_final: 0.8452 (t0) REVERT: 06 9 GLN cc_start: 0.9423 (mt0) cc_final: 0.9103 (tm-30) REVERT: 06 94 GLN cc_start: 0.9394 (pt0) cc_final: 0.9058 (pt0) REVERT: 07 89 THR cc_start: 0.9263 (OUTLIER) cc_final: 0.9008 (p) REVERT: 07 127 TYR cc_start: 0.8990 (t80) cc_final: 0.8786 (t80) REVERT: 08 98 LYS cc_start: 0.9557 (mtmm) cc_final: 0.9290 (pttt) REVERT: 08 123 GLU cc_start: 0.9339 (mm-30) cc_final: 0.8870 (mp0) REVERT: 08 127 GLN cc_start: 0.7464 (tp-100) cc_final: 0.7153 (tp-100) REVERT: 08 142 GLN cc_start: 0.9057 (tp40) cc_final: 0.8830 (tp40) REVERT: 08 146 ASP cc_start: 0.9510 (m-30) cc_final: 0.9307 (m-30) REVERT: 09 33 GLN cc_start: 0.9436 (mt0) cc_final: 0.9194 (mt0) REVERT: 09 43 ASN cc_start: 0.9156 (m-40) cc_final: 0.8657 (t0) REVERT: 09 68 ARG cc_start: 0.8890 (tmm160) cc_final: 0.7899 (ttp80) REVERT: 09 71 LYS cc_start: 0.8845 (mtmt) cc_final: 0.8587 (tppt) REVERT: 09 128 HIS cc_start: 0.7722 (m-70) cc_final: 0.7013 (m90) REVERT: 10 1 MET cc_start: 0.6998 (mmt) cc_final: 0.6234 (mmt) REVERT: 10 96 PHE cc_start: 0.4796 (t80) cc_final: 0.4584 (t80) REVERT: 11 16 MET cc_start: 0.7149 (mmp) cc_final: 0.6935 (ptm) REVERT: 11 116 MET cc_start: 0.2745 (tpt) cc_final: 0.2251 (tpt) REVERT: 12 14 ASP cc_start: 0.8434 (t70) cc_final: 0.8001 (t0) REVERT: 12 16 TYR cc_start: 0.8768 (m-80) cc_final: 0.8536 (m-80) REVERT: 12 86 GLN cc_start: 0.9250 (pt0) cc_final: 0.8638 (pp30) REVERT: 12 98 GLU cc_start: 0.9197 (mt-10) cc_final: 0.8678 (pm20) REVERT: 12 99 ARG cc_start: 0.9514 (mmm160) cc_final: 0.9203 (tpp80) REVERT: 12 114 LEU cc_start: 0.9821 (tp) cc_final: 0.9608 (tt) REVERT: 12 118 MET cc_start: 0.9564 (ptp) cc_final: 0.9328 (ptp) REVERT: 13 12 ASP cc_start: 0.8528 (p0) cc_final: 0.8143 (p0) REVERT: 13 59 LYS cc_start: 0.9443 (mttt) cc_final: 0.9230 (mtpp) REVERT: 13 67 LYS cc_start: 0.9132 (tptt) cc_final: 0.8721 (tppt) REVERT: 13 73 ASP cc_start: 0.9217 (p0) cc_final: 0.8892 (p0) REVERT: 14 38 GLN cc_start: 0.9222 (tt0) cc_final: 0.8264 (tm-30) REVERT: 14 81 ASP cc_start: 0.9393 (p0) cc_final: 0.9152 (t0) REVERT: 14 86 GLU cc_start: 0.9484 (tt0) cc_final: 0.9236 (pm20) REVERT: 14 104 GLN cc_start: 0.9497 (mm-40) cc_final: 0.9171 (tp-100) REVERT: 15 10 ARG cc_start: 0.9616 (ptm160) cc_final: 0.9108 (mmm160) REVERT: 15 28 PHE cc_start: 0.9448 (m-80) cc_final: 0.9210 (m-80) REVERT: 15 41 LEU cc_start: 0.9348 (mm) cc_final: 0.9029 (mm) REVERT: 15 45 GLN cc_start: 0.9612 (mt0) cc_final: 0.9278 (mt0) REVERT: 15 53 MET cc_start: 0.9268 (ttp) cc_final: 0.8981 (tmm) REVERT: 15 73 ILE cc_start: 0.9291 (mm) cc_final: 0.9054 (mm) REVERT: 15 74 THR cc_start: 0.8768 (p) cc_final: 0.8565 (p) REVERT: 15 75 GLU cc_start: 0.8990 (mm-30) cc_final: 0.8691 (mm-30) REVERT: 15 82 MET cc_start: 0.9485 (mmp) cc_final: 0.9064 (mmm) REVERT: 15 88 ASN cc_start: 0.9219 (m-40) cc_final: 0.8869 (m-40) REVERT: 16 1 MET cc_start: 0.9398 (ptp) cc_final: 0.8999 (mtm) REVERT: 16 34 ILE cc_start: 0.9467 (pt) cc_final: 0.9132 (mm) REVERT: 16 49 GLU cc_start: 0.9082 (mt-10) cc_final: 0.8770 (mt-10) REVERT: 16 72 ASP cc_start: 0.9082 (m-30) cc_final: 0.8763 (m-30) REVERT: 17 43 ASN cc_start: 0.9084 (p0) cc_final: 0.7871 (p0) REVERT: 17 45 SER cc_start: 0.9076 (t) cc_final: 0.8628 (p) REVERT: 17 46 GLU cc_start: 0.9230 (pt0) cc_final: 0.8889 (pm20) REVERT: 17 60 GLU cc_start: 0.9163 (mm-30) cc_final: 0.8566 (pp20) REVERT: 17 76 LYS cc_start: 0.9681 (ttpt) cc_final: 0.9081 (tppt) REVERT: 17 80 GLU cc_start: 0.9353 (mt-10) cc_final: 0.9116 (mm-30) REVERT: 17 92 PHE cc_start: 0.8841 (t80) cc_final: 0.8287 (t80) REVERT: 17 104 GLN cc_start: 0.9733 (tt0) cc_final: 0.9302 (tp-100) REVERT: 17 108 ASP cc_start: 0.9527 (m-30) cc_final: 0.9101 (m-30) REVERT: 17 112 GLU cc_start: 0.8942 (pp20) cc_final: 0.8693 (pp20) REVERT: 18 8 GLU cc_start: 0.9349 (pt0) cc_final: 0.9101 (pp20) REVERT: 18 43 GLU cc_start: 0.9157 (tp30) cc_final: 0.8939 (tp30) REVERT: 18 49 ILE cc_start: 0.9095 (mt) cc_final: 0.8840 (mp) REVERT: 18 51 ASN cc_start: 0.8891 (OUTLIER) cc_final: 0.8382 (p0) REVERT: 18 83 ILE cc_start: 0.9204 (mt) cc_final: 0.8828 (mm) REVERT: 18 105 LYS cc_start: 0.9167 (mmmt) cc_final: 0.8694 (mmtm) REVERT: 18 111 GLU cc_start: 0.8511 (tp30) cc_final: 0.8260 (tp30) REVERT: 19 27 ARG cc_start: 0.9335 (mtt-85) cc_final: 0.9036 (mmm-85) REVERT: 19 82 LEU cc_start: 0.9417 (mm) cc_final: 0.9194 (mm) REVERT: 19 88 GLU cc_start: 0.9042 (mp0) cc_final: 0.8834 (mp0) REVERT: 19 116 LEU cc_start: 0.9729 (tt) cc_final: 0.9386 (mt) REVERT: 20 37 GLU cc_start: 0.9318 (mm-30) cc_final: 0.8887 (mm-30) REVERT: 20 40 MET cc_start: 0.9425 (ttp) cc_final: 0.8953 (tmm) REVERT: 20 60 LYS cc_start: 0.9570 (mtmm) cc_final: 0.9344 (ttpp) REVERT: 20 76 LYS cc_start: 0.9324 (mmtp) cc_final: 0.9014 (mmtp) REVERT: 21 77 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.7526 (p0) REVERT: 21 78 GLU cc_start: 0.8829 (pm20) cc_final: 0.8581 (pm20) REVERT: 21 84 ARG cc_start: 0.8857 (mmt-90) cc_final: 0.8157 (mmt90) REVERT: 22 76 ARG cc_start: 0.9427 (mtp-110) cc_final: 0.9093 (mtp85) REVERT: 24 55 GLU cc_start: 0.9618 (mt-10) cc_final: 0.9286 (pm20) REVERT: 25 68 LYS cc_start: 0.9316 (mtmt) cc_final: 0.9010 (mttt) REVERT: 25 76 ILE cc_start: 0.9565 (mt) cc_final: 0.9356 (pt) REVERT: 26 25 LYS cc_start: 0.9245 (mmtp) cc_final: 0.8874 (mmmt) REVERT: 26 67 LEU cc_start: 0.9738 (mm) cc_final: 0.9500 (mm) REVERT: 26 70 LEU cc_start: 0.9621 (mt) cc_final: 0.9216 (tp) REVERT: 26 75 GLU cc_start: 0.8453 (mm-30) cc_final: 0.7805 (mp0) REVERT: 27 39 GLN cc_start: 0.9534 (mt0) cc_final: 0.9234 (mp10) REVERT: 27 44 LYS cc_start: 0.9756 (OUTLIER) cc_final: 0.9479 (tptp) REVERT: 28 20 LYS cc_start: 0.9559 (mttp) cc_final: 0.9189 (mtmm) REVERT: 30 9 ARG cc_start: 0.8682 (mtt90) cc_final: 0.8475 (mtt180) REVERT: 30 36 LYS cc_start: 0.9452 (mmtp) cc_final: 0.9043 (mmmt) REVERT: 31 6 GLU cc_start: 0.8911 (pt0) cc_final: 0.8498 (pm20) REVERT: 31 24 LYS cc_start: 0.8554 (ttpt) cc_final: 0.8197 (tmmt) REVERT: 31 35 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8505 (tp) REVERT: 31 48 TYR cc_start: 0.8928 (m-80) cc_final: 0.8553 (m-80) REVERT: 32 1 MET cc_start: 0.7882 (ptm) cc_final: 0.7628 (ppp) REVERT: 32 2 LYS cc_start: 0.9502 (ttmt) cc_final: 0.9000 (ttpt) REVERT: 32 6 GLN cc_start: 0.9278 (mm-40) cc_final: 0.8849 (mm110) REVERT: 32 13 ASN cc_start: 0.9312 (m-40) cc_final: 0.8390 (t0) REVERT: 32 29 GLN cc_start: 0.9487 (mp10) cc_final: 0.9142 (mp10) REVERT: 32 37 LYS cc_start: 0.9574 (tttt) cc_final: 0.9133 (tttp) REVERT: 34 2 LYS cc_start: 0.8829 (mmtt) cc_final: 0.8595 (mttt) REVERT: 34 10 LEU cc_start: 0.9587 (OUTLIER) cc_final: 0.9279 (tp) REVERT: 34 18 LYS cc_start: 0.9520 (tttt) cc_final: 0.9199 (ttpt) REVERT: B 21 TYR cc_start: 0.9483 (m-80) cc_final: 0.9045 (m-80) REVERT: B 48 MET cc_start: 0.9416 (mtm) cc_final: 0.9140 (ptm) REVERT: B 99 MET cc_start: 0.9452 (mtp) cc_final: 0.9132 (mtp) REVERT: B 119 GLN cc_start: 0.9618 (OUTLIER) cc_final: 0.9393 (pt0) REVERT: C 2 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7047 (pt0) REVERT: D 50 TYR cc_start: 0.9069 (t80) cc_final: 0.8719 (t80) REVERT: E 12 GLU cc_start: 0.7263 (mt-10) cc_final: 0.7059 (mt-10) REVERT: E 63 MET cc_start: 0.9426 (mmt) cc_final: 0.8974 (mmt) REVERT: E 64 GLU cc_start: 0.9721 (mm-30) cc_final: 0.9251 (mm-30) REVERT: E 127 TYR cc_start: 0.8894 (m-10) cc_final: 0.8637 (m-10) REVERT: E 141 ASP cc_start: 0.9321 (m-30) cc_final: 0.8915 (t0) REVERT: F 4 TYR cc_start: 0.8929 (m-10) cc_final: 0.8529 (m-10) REVERT: F 9 MET cc_start: 0.9365 (mtt) cc_final: 0.9119 (mpp) REVERT: G 32 ASP cc_start: 0.8877 (m-30) cc_final: 0.8184 (t0) REVERT: G 139 ASP cc_start: 0.9343 (m-30) cc_final: 0.8277 (t0) REVERT: G 142 ARG cc_start: 0.9587 (mmt90) cc_final: 0.9101 (mtm-85) REVERT: H 9 MET cc_start: 0.9628 (tmm) cc_final: 0.9351 (tmm) REVERT: H 26 MET cc_start: 0.8641 (ptp) cc_final: 0.8378 (ppp) REVERT: H 41 GLU cc_start: 0.9457 (tm-30) cc_final: 0.9235 (pp20) REVERT: H 48 PHE cc_start: 0.9013 (p90) cc_final: 0.8499 (p90) REVERT: H 84 ILE cc_start: 0.9383 (mt) cc_final: 0.9160 (tp) REVERT: H 90 GLU cc_start: 0.9540 (tt0) cc_final: 0.9253 (tt0) REVERT: H 112 ASP cc_start: 0.9541 (p0) cc_final: 0.8839 (t0) REVERT: H 123 GLU cc_start: 0.8345 (tm-30) cc_final: 0.8078 (tm-30) REVERT: I 34 LEU cc_start: 0.9679 (OUTLIER) cc_final: 0.9465 (pt) REVERT: I 45 MET cc_start: 0.9524 (ppp) cc_final: 0.9225 (ppp) REVERT: I 106 ASP cc_start: 0.8840 (t70) cc_final: 0.8467 (t0) REVERT: I 117 LEU cc_start: 0.9448 (mp) cc_final: 0.9175 (mp) REVERT: I 128 LYS cc_start: 0.9041 (tptm) cc_final: 0.8657 (tptm) REVERT: J 24 GLU cc_start: 0.9562 (mt-10) cc_final: 0.9353 (pp20) REVERT: J 59 LYS cc_start: 0.9216 (tttm) cc_final: 0.8640 (ttmt) REVERT: J 63 ASP cc_start: 0.8217 (t0) cc_final: 0.7768 (t0) REVERT: J 65 TYR cc_start: 0.8220 (m-80) cc_final: 0.7803 (m-80) REVERT: K 39 ASN cc_start: 0.9227 (m-40) cc_final: 0.8913 (t0) REVERT: K 110 THR cc_start: 0.9149 (p) cc_final: 0.8549 (p) REVERT: L 19 ASN cc_start: 0.9451 (m-40) cc_final: 0.9208 (t0) REVERT: M 80 MET cc_start: 0.9237 (mtm) cc_final: 0.8926 (ttp) REVERT: N 25 GLU cc_start: 0.9283 (pt0) cc_final: 0.8842 (tm-30) REVERT: N 26 LEU cc_start: 0.9599 (OUTLIER) cc_final: 0.9375 (mm) REVERT: N 73 LEU cc_start: 0.9447 (mt) cc_final: 0.9238 (mp) REVERT: N 85 GLU cc_start: 0.9564 (tp30) cc_final: 0.9188 (mm-30) REVERT: O 47 LYS cc_start: 0.9505 (mmmt) cc_final: 0.8900 (ttpt) REVERT: O 88 ARG cc_start: 0.7936 (tpp-160) cc_final: 0.6643 (mmt90) REVERT: P 14 ARG cc_start: 0.9313 (mmm-85) cc_final: 0.8921 (mmm-85) REVERT: Q 17 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7716 (tm-30) REVERT: Q 30 HIS cc_start: 0.9028 (t-90) cc_final: 0.8805 (t-90) REVERT: Q 42 LYS cc_start: 0.9338 (mttt) cc_final: 0.9035 (mtmm) REVERT: Q 51 GLU cc_start: 0.9246 (pt0) cc_final: 0.8977 (pm20) REVERT: R 56 ARG cc_start: 0.9393 (ttm110) cc_final: 0.9183 (mtp-110) REVERT: T 26 MET cc_start: 0.9113 (ttp) cc_final: 0.8704 (tpp) REVERT: T 39 GLU cc_start: 0.9288 (mm-30) cc_final: 0.8812 (mp0) REVERT: U 18 PHE cc_start: 0.8988 (t80) cc_final: 0.8544 (t80) REVERT: U 33 ARG cc_start: 0.8620 (ptm-80) cc_final: 0.8231 (ptm-80) REVERT: U 44 ARG cc_start: 0.9045 (tpp-160) cc_final: 0.8576 (ttp80) REVERT: U 45 LYS cc_start: 0.9351 (tptt) cc_final: 0.9149 (tppt) REVERT: 03 12 ARG cc_start: 0.7323 (mpt180) cc_final: 0.7045 (mpt180) REVERT: 03 25 GLU cc_start: 0.8362 (mt-10) cc_final: 0.8044 (mt-10) REVERT: 03 203 GLN cc_start: 0.8303 (tp40) cc_final: 0.8058 (tp40) REVERT: Z 91 ARG cc_start: 0.7688 (mmp80) cc_final: 0.6662 (pmt-80) outliers start: 297 outliers final: 188 residues processed: 1418 average time/residue: 1.2941 time to fit residues: 3168.4829 Evaluate side-chains 1232 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 1033 time to evaluate : 6.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 35 LYS Chi-restraints excluded: chain 04 residue 131 MET Chi-restraints excluded: chain 04 residue 138 SER Chi-restraints excluded: chain 04 residue 163 ILE Chi-restraints excluded: chain 04 residue 199 HIS Chi-restraints excluded: chain 04 residue 215 VAL Chi-restraints excluded: chain 04 residue 249 VAL Chi-restraints excluded: chain 04 residue 258 SER Chi-restraints excluded: chain 05 residue 48 ILE Chi-restraints excluded: chain 05 residue 112 THR Chi-restraints excluded: chain 05 residue 126 ASN Chi-restraints excluded: chain 05 residue 138 LEU Chi-restraints excluded: chain 05 residue 145 SER Chi-restraints excluded: chain 05 residue 177 VAL Chi-restraints excluded: chain 05 residue 201 LEU Chi-restraints excluded: chain 06 residue 175 ILE Chi-restraints excluded: chain 06 residue 199 MET Chi-restraints excluded: chain 07 residue 9 ASP Chi-restraints excluded: chain 07 residue 46 LYS Chi-restraints excluded: chain 07 residue 66 ILE Chi-restraints excluded: chain 07 residue 89 THR Chi-restraints excluded: chain 07 residue 143 ASP Chi-restraints excluded: chain 07 residue 148 VAL Chi-restraints excluded: chain 07 residue 156 THR Chi-restraints excluded: chain 07 residue 157 THR Chi-restraints excluded: chain 08 residue 9 VAL Chi-restraints excluded: chain 08 residue 15 ASP Chi-restraints excluded: chain 08 residue 154 GLU Chi-restraints excluded: chain 09 residue 77 THR Chi-restraints excluded: chain 10 residue 123 ILE Chi-restraints excluded: chain 11 residue 58 ILE Chi-restraints excluded: chain 11 residue 70 THR Chi-restraints excluded: chain 11 residue 102 ARG Chi-restraints excluded: chain 12 residue 25 LEU Chi-restraints excluded: chain 12 residue 52 ASP Chi-restraints excluded: chain 12 residue 55 ILE Chi-restraints excluded: chain 12 residue 84 ILE Chi-restraints excluded: chain 12 residue 139 VAL Chi-restraints excluded: chain 13 residue 22 ILE Chi-restraints excluded: chain 13 residue 39 ILE Chi-restraints excluded: chain 13 residue 58 LEU Chi-restraints excluded: chain 13 residue 65 THR Chi-restraints excluded: chain 13 residue 80 ASP Chi-restraints excluded: chain 13 residue 91 SER Chi-restraints excluded: chain 14 residue 35 HIS Chi-restraints excluded: chain 14 residue 89 VAL Chi-restraints excluded: chain 14 residue 91 ASP Chi-restraints excluded: chain 14 residue 120 VAL Chi-restraints excluded: chain 15 residue 24 THR Chi-restraints excluded: chain 15 residue 30 SER Chi-restraints excluded: chain 15 residue 42 THR Chi-restraints excluded: chain 15 residue 105 MET Chi-restraints excluded: chain 15 residue 129 THR Chi-restraints excluded: chain 15 residue 134 THR Chi-restraints excluded: chain 16 residue 6 SER Chi-restraints excluded: chain 16 residue 32 GLU Chi-restraints excluded: chain 16 residue 37 THR Chi-restraints excluded: chain 16 residue 48 VAL Chi-restraints excluded: chain 16 residue 57 THR Chi-restraints excluded: chain 17 residue 28 VAL Chi-restraints excluded: chain 18 residue 10 GLU Chi-restraints excluded: chain 18 residue 51 ASN Chi-restraints excluded: chain 19 residue 8 ILE Chi-restraints excluded: chain 19 residue 17 LEU Chi-restraints excluded: chain 19 residue 30 VAL Chi-restraints excluded: chain 19 residue 58 GLN Chi-restraints excluded: chain 20 residue 58 VAL Chi-restraints excluded: chain 21 residue 12 SER Chi-restraints excluded: chain 21 residue 51 LEU Chi-restraints excluded: chain 21 residue 62 ASP Chi-restraints excluded: chain 21 residue 67 ASP Chi-restraints excluded: chain 21 residue 77 ASP Chi-restraints excluded: chain 21 residue 109 ASP Chi-restraints excluded: chain 22 residue 30 ILE Chi-restraints excluded: chain 22 residue 79 ASP Chi-restraints excluded: chain 23 residue 8 ASP Chi-restraints excluded: chain 23 residue 17 ASP Chi-restraints excluded: chain 23 residue 64 ILE Chi-restraints excluded: chain 24 residue 3 THR Chi-restraints excluded: chain 24 residue 4 ILE Chi-restraints excluded: chain 24 residue 24 ASN Chi-restraints excluded: chain 24 residue 42 LEU Chi-restraints excluded: chain 24 residue 89 ILE Chi-restraints excluded: chain 25 residue 8 ASN Chi-restraints excluded: chain 26 residue 1 SER Chi-restraints excluded: chain 26 residue 15 ASN Chi-restraints excluded: chain 26 residue 46 VAL Chi-restraints excluded: chain 27 residue 11 VAL Chi-restraints excluded: chain 27 residue 15 ASN Chi-restraints excluded: chain 27 residue 17 GLU Chi-restraints excluded: chain 27 residue 44 LYS Chi-restraints excluded: chain 28 residue 56 VAL Chi-restraints excluded: chain 29 residue 34 LEU Chi-restraints excluded: chain 29 residue 58 ASP Chi-restraints excluded: chain 30 residue 2 VAL Chi-restraints excluded: chain 30 residue 32 THR Chi-restraints excluded: chain 30 residue 35 GLU Chi-restraints excluded: chain 31 residue 21 THR Chi-restraints excluded: chain 31 residue 23 THR Chi-restraints excluded: chain 31 residue 35 LEU Chi-restraints excluded: chain 31 residue 46 VAL Chi-restraints excluded: chain 33 residue 49 VAL Chi-restraints excluded: chain 33 residue 50 SER Chi-restraints excluded: chain 33 residue 58 ILE Chi-restraints excluded: chain 34 residue 10 LEU Chi-restraints excluded: chain 34 residue 13 ASN Chi-restraints excluded: chain 34 residue 17 VAL Chi-restraints excluded: chain 34 residue 20 ASP Chi-restraints excluded: chain 34 residue 26 ILE Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 169 HIS Chi-restraints excluded: chain C residue 2 GLN Chi-restraints excluded: chain C residue 40 GLN Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 124 VAL Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 196 GLU Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 155 LYS Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain H residue 20 ASN Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 109 GLN Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 125 GLN Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 51 PHE Chi-restraints excluded: chain K residue 69 CYS Chi-restraints excluded: chain K residue 80 ASN Chi-restraints excluded: chain K residue 86 LYS Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 74 GLN Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 67 ASP Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain N residue 26 LEU Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain O residue 12 SER Chi-restraints excluded: chain O residue 46 LYS Chi-restraints excluded: chain P residue 31 ARG Chi-restraints excluded: chain P residue 54 LEU Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 76 ARG Chi-restraints excluded: chain S residue 11 ASP Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain T residue 20 ASN Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain 03 residue 18 THR Chi-restraints excluded: chain 03 residue 43 ASP Chi-restraints excluded: chain 03 residue 56 ASP Chi-restraints excluded: chain Z residue 42 LEU Chi-restraints excluded: chain Z residue 100 LYS Chi-restraints excluded: chain Z residue 162 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1080 random chunks: chunk 545 optimal weight: 5.9990 chunk 304 optimal weight: 20.0000 chunk 816 optimal weight: 10.0000 chunk 667 optimal weight: 10.0000 chunk 270 optimal weight: 0.1980 chunk 982 optimal weight: 10.0000 chunk 1061 optimal weight: 20.0000 chunk 875 optimal weight: 20.0000 chunk 974 optimal weight: 10.0000 chunk 334 optimal weight: 6.9990 chunk 788 optimal weight: 10.0000 overall best weight: 6.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 04 59 GLN ** 04 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 05 150 GLN 11 106 GLN 12 128 ASN ** 12 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 9 ASN ** 13 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 14 4 ASN 16 62 ASN 16 107 ASN 18 9 GLN 19 36 GLN 19 51 GLN 19 58 GLN 19 80 ASN 20 89 HIS ** 21 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 23 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 23 44 HIS 24 88 HIS 27 31 GLN ** 27 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 31 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 32 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 34 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 GLN ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 ASN D 115 GLN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 GLN D 197 HIS E 96 GLN ** E 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 4 GLN ** J 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 11 HIS N 42 ASN ** O 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 29 ASN ** T 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 55 HIS Z 7 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 165170 Z= 0.219 Angle : 0.616 10.081 246822 Z= 0.320 Chirality : 0.035 0.278 31534 Planarity : 0.005 0.078 13429 Dihedral : 23.389 176.753 82044 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 19.14 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.21 % Favored : 90.52 % Rotamer: Outliers : 4.87 % Allowed : 16.90 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.10), residues: 6159 helix: -1.03 (0.11), residues: 1945 sheet: -1.89 (0.14), residues: 1110 loop : -2.23 (0.11), residues: 3104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP04 212 HIS 0.017 0.001 HIS T 67 PHE 0.029 0.002 PHE G 61 TYR 0.023 0.002 TYR I 5 ARG 0.011 0.001 ARG22 69 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12318 Ramachandran restraints generated. 6159 Oldfield, 0 Emsley, 6159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12318 Ramachandran restraints generated. 6159 Oldfield, 0 Emsley, 6159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1453 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 1204 time to evaluate : 6.697 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: 04 33 LEU cc_start: 0.9618 (OUTLIER) cc_final: 0.9387 (mm) REVERT: 04 131 MET cc_start: 0.9736 (mtp) cc_final: 0.9378 (mpp) REVERT: 04 145 MET cc_start: 0.9514 (mmm) cc_final: 0.9021 (ptt) REVERT: 04 159 THR cc_start: 0.9432 (OUTLIER) cc_final: 0.9081 (p) REVERT: 04 224 MET cc_start: 0.9259 (mtp) cc_final: 0.9016 (mtp) REVERT: 04 228 ASP cc_start: 0.8964 (p0) cc_final: 0.8522 (p0) REVERT: 05 164 GLN cc_start: 0.8875 (tp40) cc_final: 0.8473 (tm-30) REVERT: 05 165 MET cc_start: 0.9155 (ttt) cc_final: 0.8874 (ttm) REVERT: 06 9 GLN cc_start: 0.9329 (mt0) cc_final: 0.9040 (tm-30) REVERT: 06 62 GLN cc_start: 0.8940 (tp40) cc_final: 0.8727 (tp40) REVERT: 06 94 GLN cc_start: 0.9292 (pt0) cc_final: 0.9006 (pt0) REVERT: 06 100 MET cc_start: 0.9418 (mtp) cc_final: 0.9157 (ptp) REVERT: 07 95 MET cc_start: 0.9235 (ptm) cc_final: 0.8995 (ttp) REVERT: 08 74 MET cc_start: 0.8688 (tpp) cc_final: 0.8484 (tpp) REVERT: 08 87 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8235 (tm-30) REVERT: 08 123 GLU cc_start: 0.9289 (mm-30) cc_final: 0.9050 (mm-30) REVERT: 09 5 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.9203 (pp) REVERT: 09 33 GLN cc_start: 0.9469 (mt0) cc_final: 0.8756 (mt0) REVERT: 09 35 LYS cc_start: 0.9240 (mmmm) cc_final: 0.8906 (mptt) REVERT: 09 68 ARG cc_start: 0.8785 (tmm160) cc_final: 0.7875 (ttp80) REVERT: 09 71 LYS cc_start: 0.8719 (mtmt) cc_final: 0.8377 (tppt) REVERT: 09 89 LYS cc_start: 0.8265 (mmmm) cc_final: 0.7178 (pttm) REVERT: 09 128 HIS cc_start: 0.7579 (m-70) cc_final: 0.6943 (m90) REVERT: 09 135 HIS cc_start: 0.9292 (t70) cc_final: 0.8946 (t-170) REVERT: 09 141 LYS cc_start: 0.8900 (mttt) cc_final: 0.8669 (mmmt) REVERT: 10 1 MET cc_start: 0.6610 (mmt) cc_final: 0.6313 (mmt) REVERT: 10 96 PHE cc_start: 0.4818 (t80) cc_final: 0.4518 (t80) REVERT: 10 99 PHE cc_start: 0.6048 (OUTLIER) cc_final: 0.5372 (m-10) REVERT: 11 16 MET cc_start: 0.7124 (mmp) cc_final: 0.6821 (ptm) REVERT: 11 116 MET cc_start: 0.2377 (tpt) cc_final: 0.1787 (tpt) REVERT: 12 14 ASP cc_start: 0.8552 (t70) cc_final: 0.8111 (t0) REVERT: 12 31 GLU cc_start: 0.9034 (tp30) cc_final: 0.8771 (tp30) REVERT: 12 37 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8689 (ttp80) REVERT: 12 86 GLN cc_start: 0.9293 (pt0) cc_final: 0.8595 (pp30) REVERT: 12 96 ARG cc_start: 0.9211 (mtp85) cc_final: 0.8725 (mtm180) REVERT: 12 98 GLU cc_start: 0.9076 (mt-10) cc_final: 0.8525 (pm20) REVERT: 12 99 ARG cc_start: 0.9456 (mmm160) cc_final: 0.8964 (mmm160) REVERT: 13 4 GLU cc_start: 0.9490 (mm-30) cc_final: 0.9222 (mm-30) REVERT: 13 12 ASP cc_start: 0.8555 (p0) cc_final: 0.8123 (t70) REVERT: 13 73 ASP cc_start: 0.9169 (p0) cc_final: 0.8749 (p0) REVERT: 13 88 ASN cc_start: 0.9191 (t0) cc_final: 0.8385 (t0) REVERT: 13 100 PHE cc_start: 0.8874 (m-10) cc_final: 0.8660 (m-10) REVERT: 14 38 GLN cc_start: 0.9086 (tt0) cc_final: 0.8713 (tt0) REVERT: 14 104 GLN cc_start: 0.9350 (mm-40) cc_final: 0.8995 (tp-100) REVERT: 14 106 GLU cc_start: 0.8959 (mm-30) cc_final: 0.8758 (mm-30) REVERT: 15 1 MET cc_start: 0.6248 (tpt) cc_final: 0.5659 (tpt) REVERT: 15 10 ARG cc_start: 0.9584 (ptm160) cc_final: 0.8977 (mmp80) REVERT: 15 28 PHE cc_start: 0.9400 (m-80) cc_final: 0.9157 (m-80) REVERT: 15 45 GLN cc_start: 0.9579 (mt0) cc_final: 0.9206 (mt0) REVERT: 15 53 MET cc_start: 0.9242 (ttp) cc_final: 0.8898 (tmm) REVERT: 15 73 ILE cc_start: 0.9126 (mm) cc_final: 0.8908 (mm) REVERT: 15 74 THR cc_start: 0.8796 (p) cc_final: 0.8483 (t) REVERT: 15 88 ASN cc_start: 0.9196 (m-40) cc_final: 0.8853 (m-40) REVERT: 15 103 TYR cc_start: 0.8916 (m-80) cc_final: 0.8715 (m-80) REVERT: 15 136 MET cc_start: 0.8932 (ptt) cc_final: 0.8526 (ppp) REVERT: 16 1 MET cc_start: 0.9338 (ptp) cc_final: 0.8943 (mtm) REVERT: 16 34 ILE cc_start: 0.9453 (pt) cc_final: 0.9094 (mm) REVERT: 16 49 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8335 (mm-30) REVERT: 16 72 ASP cc_start: 0.8826 (m-30) cc_final: 0.8617 (m-30) REVERT: 17 18 LEU cc_start: 0.9652 (tp) cc_final: 0.9432 (pp) REVERT: 17 36 TYR cc_start: 0.8858 (m-10) cc_final: 0.8349 (m-10) REVERT: 17 43 ASN cc_start: 0.9106 (p0) cc_final: 0.7705 (p0) REVERT: 17 45 SER cc_start: 0.9124 (t) cc_final: 0.8575 (m) REVERT: 17 46 GLU cc_start: 0.9300 (pt0) cc_final: 0.8881 (pm20) REVERT: 17 60 GLU cc_start: 0.9152 (mm-30) cc_final: 0.8612 (pp20) REVERT: 17 62 LEU cc_start: 0.6935 (pp) cc_final: 0.6597 (pp) REVERT: 17 76 LYS cc_start: 0.9690 (ttpt) cc_final: 0.9322 (tppt) REVERT: 17 80 GLU cc_start: 0.9421 (mt-10) cc_final: 0.8891 (mt-10) REVERT: 17 92 PHE cc_start: 0.8896 (t80) cc_final: 0.8334 (t80) REVERT: 17 104 GLN cc_start: 0.9725 (tt0) cc_final: 0.9312 (tp-100) REVERT: 17 108 ASP cc_start: 0.9503 (m-30) cc_final: 0.9061 (m-30) REVERT: 18 9 GLN cc_start: 0.9540 (tp-100) cc_final: 0.9324 (tp-100) REVERT: 18 26 GLU cc_start: 0.9409 (tp30) cc_final: 0.8331 (tp30) REVERT: 18 43 GLU cc_start: 0.9256 (tp30) cc_final: 0.8750 (tp30) REVERT: 18 49 ILE cc_start: 0.8975 (mt) cc_final: 0.8713 (mp) REVERT: 18 51 ASN cc_start: 0.8908 (OUTLIER) cc_final: 0.8405 (p0) REVERT: 18 83 ILE cc_start: 0.9259 (mt) cc_final: 0.8841 (mm) REVERT: 18 105 LYS cc_start: 0.9148 (mmmt) cc_final: 0.8772 (mmtm) REVERT: 18 111 GLU cc_start: 0.8601 (tp30) cc_final: 0.8332 (tp30) REVERT: 19 27 ARG cc_start: 0.9233 (mtt-85) cc_final: 0.8818 (mmm-85) REVERT: 19 88 GLU cc_start: 0.9088 (mp0) cc_final: 0.8851 (mp0) REVERT: 19 116 LEU cc_start: 0.9710 (tt) cc_final: 0.9308 (mt) REVERT: 20 13 ARG cc_start: 0.9077 (ttt-90) cc_final: 0.8782 (ttt180) REVERT: 20 37 GLU cc_start: 0.9327 (mm-30) cc_final: 0.9003 (mm-30) REVERT: 20 40 MET cc_start: 0.9490 (ttp) cc_final: 0.8987 (tmm) REVERT: 20 76 LYS cc_start: 0.9286 (mmtp) cc_final: 0.8984 (mmtp) REVERT: 20 78 ARG cc_start: 0.9318 (tpp80) cc_final: 0.8475 (tpp80) REVERT: 21 4 ILE cc_start: 0.9668 (OUTLIER) cc_final: 0.9368 (mt) REVERT: 21 53 SER cc_start: 0.9024 (t) cc_final: 0.8735 (p) REVERT: 21 77 ASP cc_start: 0.8400 (p0) cc_final: 0.7546 (p0) REVERT: 21 78 GLU cc_start: 0.8587 (pm20) cc_final: 0.8382 (pm20) REVERT: 21 94 ASP cc_start: 0.8851 (m-30) cc_final: 0.8593 (m-30) REVERT: 21 97 LEU cc_start: 0.9504 (mt) cc_final: 0.9303 (mt) REVERT: 22 8 LEU cc_start: 0.9564 (mt) cc_final: 0.9280 (tt) REVERT: 24 42 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8734 (mp) REVERT: 24 48 MET cc_start: 0.9503 (tpt) cc_final: 0.9302 (tpt) REVERT: 24 55 GLU cc_start: 0.9595 (mt-10) cc_final: 0.9216 (pm20) REVERT: 25 20 LYS cc_start: 0.8997 (mptt) cc_final: 0.7870 (tppt) REVERT: 25 68 LYS cc_start: 0.9324 (mtmt) cc_final: 0.8978 (mttt) REVERT: 26 25 LYS cc_start: 0.9205 (mmtp) cc_final: 0.8828 (mmmt) REVERT: 26 70 LEU cc_start: 0.9582 (mt) cc_final: 0.9270 (tp) REVERT: 26 75 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7784 (mp0) REVERT: 27 39 GLN cc_start: 0.9521 (mt0) cc_final: 0.9182 (mp10) REVERT: 27 44 LYS cc_start: 0.9748 (OUTLIER) cc_final: 0.9484 (tptp) REVERT: 27 49 ASP cc_start: 0.9454 (m-30) cc_final: 0.9172 (m-30) REVERT: 28 20 LYS cc_start: 0.9519 (mttp) cc_final: 0.9238 (mtmm) REVERT: 28 53 MET cc_start: 0.9540 (ttm) cc_final: 0.9213 (ttt) REVERT: 30 36 LYS cc_start: 0.9347 (mmtp) cc_final: 0.9012 (mmmm) REVERT: 31 6 GLU cc_start: 0.8827 (pt0) cc_final: 0.8332 (pm20) REVERT: 31 19 PHE cc_start: 0.8901 (p90) cc_final: 0.8409 (p90) REVERT: 31 24 LYS cc_start: 0.8634 (ttpt) cc_final: 0.8281 (tmmt) REVERT: 31 35 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8685 (tp) REVERT: 32 1 MET cc_start: 0.7897 (ptm) cc_final: 0.7599 (ppp) REVERT: 32 2 LYS cc_start: 0.9531 (ttmt) cc_final: 0.9024 (ttpt) REVERT: 32 6 GLN cc_start: 0.9218 (mm-40) cc_final: 0.8716 (mm110) REVERT: 32 13 ASN cc_start: 0.9294 (m-40) cc_final: 0.8378 (t0) REVERT: 32 37 LYS cc_start: 0.9463 (tttt) cc_final: 0.8953 (tttp) REVERT: 34 10 LEU cc_start: 0.9522 (OUTLIER) cc_final: 0.9186 (tp) REVERT: 34 18 LYS cc_start: 0.9511 (tttt) cc_final: 0.9206 (ttmt) REVERT: 34 34 LYS cc_start: 0.9492 (tttt) cc_final: 0.9105 (ttpt) REVERT: B 21 TYR cc_start: 0.9452 (m-80) cc_final: 0.9034 (m-80) REVERT: B 48 MET cc_start: 0.9375 (mtm) cc_final: 0.8949 (ptm) REVERT: B 93 HIS cc_start: 0.9066 (t-90) cc_final: 0.8713 (t-90) REVERT: B 99 MET cc_start: 0.9443 (mtp) cc_final: 0.9152 (mtp) REVERT: B 119 GLN cc_start: 0.9577 (mp10) cc_final: 0.9367 (pt0) REVERT: C 2 GLN cc_start: 0.8392 (pt0) cc_final: 0.7391 (pt0) REVERT: D 47 LEU cc_start: 0.9024 (tp) cc_final: 0.8604 (pp) REVERT: D 50 TYR cc_start: 0.8956 (t80) cc_final: 0.8662 (t80) REVERT: D 131 ILE cc_start: 0.8425 (mt) cc_final: 0.8139 (tt) REVERT: E 11 GLN cc_start: 0.8487 (tt0) cc_final: 0.8115 (tt0) REVERT: E 54 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8517 (tm-30) REVERT: E 94 PHE cc_start: 0.9470 (t80) cc_final: 0.9234 (t80) REVERT: F 21 MET cc_start: 0.9263 (mtt) cc_final: 0.8876 (mtt) REVERT: F 25 TYR cc_start: 0.8970 (m-10) cc_final: 0.8680 (m-10) REVERT: F 59 TYR cc_start: 0.8092 (m-80) cc_final: 0.7778 (m-80) REVERT: F 72 ASP cc_start: 0.9455 (OUTLIER) cc_final: 0.9014 (p0) REVERT: F 78 PHE cc_start: 0.9580 (m-80) cc_final: 0.8850 (m-80) REVERT: G 139 ASP cc_start: 0.9349 (m-30) cc_final: 0.8986 (t0) REVERT: H 26 MET cc_start: 0.8564 (ptp) cc_final: 0.8340 (ppp) REVERT: H 41 GLU cc_start: 0.9459 (tm-30) cc_final: 0.9220 (pp20) REVERT: H 48 PHE cc_start: 0.8870 (p90) cc_final: 0.8419 (p90) REVERT: H 59 GLU cc_start: 0.8947 (pm20) cc_final: 0.7210 (pm20) REVERT: H 90 GLU cc_start: 0.9541 (tt0) cc_final: 0.9231 (tt0) REVERT: H 112 ASP cc_start: 0.9445 (p0) cc_final: 0.8783 (t0) REVERT: H 123 GLU cc_start: 0.8357 (tm-30) cc_final: 0.8063 (tm-30) REVERT: I 45 MET cc_start: 0.9589 (ppp) cc_final: 0.9249 (ppp) REVERT: I 106 ASP cc_start: 0.8844 (t70) cc_final: 0.8465 (t0) REVERT: J 59 LYS cc_start: 0.9123 (tttm) cc_final: 0.8580 (ttpt) REVERT: J 63 ASP cc_start: 0.8142 (t0) cc_final: 0.7769 (t0) REVERT: J 65 TYR cc_start: 0.8142 (m-80) cc_final: 0.7745 (m-80) REVERT: K 37 GLN cc_start: 0.9324 (mp10) cc_final: 0.8940 (mp10) REVERT: L 19 ASN cc_start: 0.9435 (m-40) cc_final: 0.9196 (t0) REVERT: M 11 HIS cc_start: 0.9295 (m90) cc_final: 0.8991 (p-80) REVERT: M 65 GLU cc_start: 0.9271 (tp30) cc_final: 0.9038 (tp30) REVERT: M 80 MET cc_start: 0.9262 (mtm) cc_final: 0.8975 (ttp) REVERT: N 25 GLU cc_start: 0.9243 (pt0) cc_final: 0.8762 (tm-30) REVERT: N 85 GLU cc_start: 0.9583 (tp30) cc_final: 0.9179 (mm-30) REVERT: N 91 GLU cc_start: 0.9150 (mm-30) cc_final: 0.8730 (mm-30) REVERT: O 13 GLU cc_start: 0.9603 (tt0) cc_final: 0.9348 (pt0) REVERT: O 47 LYS cc_start: 0.9476 (mmmt) cc_final: 0.9262 (mmmm) REVERT: Q 16 MET cc_start: 0.8343 (ttm) cc_final: 0.8098 (ttm) REVERT: Q 17 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7699 (tm-30) REVERT: Q 29 LYS cc_start: 0.9432 (OUTLIER) cc_final: 0.9159 (tptp) REVERT: Q 42 LYS cc_start: 0.9221 (mttt) cc_final: 0.8921 (mtmm) REVERT: Q 51 GLU cc_start: 0.9208 (pt0) cc_final: 0.8926 (pm20) REVERT: R 28 LEU cc_start: 0.9600 (mm) cc_final: 0.9355 (mt) REVERT: R 34 GLU cc_start: 0.9211 (pm20) cc_final: 0.8924 (pm20) REVERT: R 37 LYS cc_start: 0.9673 (mtpp) cc_final: 0.9470 (mmmm) REVERT: R 47 ARG cc_start: 0.9539 (mmm160) cc_final: 0.8824 (mpp-170) REVERT: R 60 ARG cc_start: 0.9581 (OUTLIER) cc_final: 0.9300 (mtp180) REVERT: S 20 LYS cc_start: 0.9627 (mtmm) cc_final: 0.9230 (pmtt) REVERT: T 26 MET cc_start: 0.9123 (ttp) cc_final: 0.8694 (tpp) REVERT: T 53 MET cc_start: 0.9407 (ppp) cc_final: 0.9085 (ppp) REVERT: U 18 PHE cc_start: 0.8940 (t80) cc_final: 0.8508 (t80) REVERT: U 33 ARG cc_start: 0.8640 (ptm-80) cc_final: 0.8259 (ptm-80) REVERT: U 36 PHE cc_start: 0.8620 (m-80) cc_final: 0.8396 (m-80) REVERT: U 44 ARG cc_start: 0.8973 (tpp-160) cc_final: 0.8761 (ttp80) REVERT: U 45 LYS cc_start: 0.9347 (tptt) cc_final: 0.8856 (tppt) REVERT: 03 25 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8058 (mt-10) REVERT: 03 203 GLN cc_start: 0.8115 (tp40) cc_final: 0.7867 (tp-100) REVERT: Z 7 GLN cc_start: 0.9273 (tt0) cc_final: 0.9007 (tp40) REVERT: Z 91 ARG cc_start: 0.7710 (mmp80) cc_final: 0.6803 (pmt-80) outliers start: 249 outliers final: 160 residues processed: 1337 average time/residue: 1.3163 time to fit residues: 3055.3176 Evaluate side-chains 1221 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 1046 time to evaluate : 6.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 33 LEU Chi-restraints excluded: chain 04 residue 37 SER Chi-restraints excluded: chain 04 residue 159 THR Chi-restraints excluded: chain 04 residue 163 ILE Chi-restraints excluded: chain 04 residue 199 HIS Chi-restraints excluded: chain 04 residue 215 VAL Chi-restraints excluded: chain 05 residue 2 ILE Chi-restraints excluded: chain 05 residue 103 ASP Chi-restraints excluded: chain 05 residue 126 ASN Chi-restraints excluded: chain 05 residue 137 SER Chi-restraints excluded: chain 05 residue 146 ILE Chi-restraints excluded: chain 05 residue 201 LEU Chi-restraints excluded: chain 06 residue 148 ILE Chi-restraints excluded: chain 06 residue 175 ILE Chi-restraints excluded: chain 07 residue 46 LYS Chi-restraints excluded: chain 07 residue 86 CYS Chi-restraints excluded: chain 07 residue 112 ASP Chi-restraints excluded: chain 07 residue 148 VAL Chi-restraints excluded: chain 07 residue 157 THR Chi-restraints excluded: chain 07 residue 161 SER Chi-restraints excluded: chain 08 residue 9 VAL Chi-restraints excluded: chain 08 residue 10 VAL Chi-restraints excluded: chain 08 residue 87 GLN Chi-restraints excluded: chain 08 residue 154 GLU Chi-restraints excluded: chain 09 residue 4 ILE Chi-restraints excluded: chain 09 residue 5 LEU Chi-restraints excluded: chain 09 residue 77 THR Chi-restraints excluded: chain 10 residue 99 PHE Chi-restraints excluded: chain 10 residue 123 ILE Chi-restraints excluded: chain 11 residue 7 TYR Chi-restraints excluded: chain 11 residue 27 LEU Chi-restraints excluded: chain 11 residue 58 ILE Chi-restraints excluded: chain 11 residue 70 THR Chi-restraints excluded: chain 11 residue 102 ARG Chi-restraints excluded: chain 12 residue 25 LEU Chi-restraints excluded: chain 12 residue 37 ARG Chi-restraints excluded: chain 12 residue 84 ILE Chi-restraints excluded: chain 13 residue 17 ARG Chi-restraints excluded: chain 13 residue 25 LEU Chi-restraints excluded: chain 13 residue 47 ILE Chi-restraints excluded: chain 13 residue 54 LYS Chi-restraints excluded: chain 13 residue 58 LEU Chi-restraints excluded: chain 13 residue 65 THR Chi-restraints excluded: chain 13 residue 80 ASP Chi-restraints excluded: chain 13 residue 91 SER Chi-restraints excluded: chain 13 residue 104 THR Chi-restraints excluded: chain 14 residue 35 HIS Chi-restraints excluded: chain 14 residue 89 VAL Chi-restraints excluded: chain 14 residue 91 ASP Chi-restraints excluded: chain 15 residue 24 THR Chi-restraints excluded: chain 15 residue 30 SER Chi-restraints excluded: chain 15 residue 42 THR Chi-restraints excluded: chain 15 residue 134 THR Chi-restraints excluded: chain 16 residue 6 SER Chi-restraints excluded: chain 16 residue 32 GLU Chi-restraints excluded: chain 16 residue 37 THR Chi-restraints excluded: chain 16 residue 48 VAL Chi-restraints excluded: chain 18 residue 10 GLU Chi-restraints excluded: chain 18 residue 51 ASN Chi-restraints excluded: chain 19 residue 8 ILE Chi-restraints excluded: chain 19 residue 17 LEU Chi-restraints excluded: chain 19 residue 51 GLN Chi-restraints excluded: chain 19 residue 89 ILE Chi-restraints excluded: chain 19 residue 90 ASP Chi-restraints excluded: chain 20 residue 43 ASN Chi-restraints excluded: chain 21 residue 4 ILE Chi-restraints excluded: chain 21 residue 62 ASP Chi-restraints excluded: chain 21 residue 67 ASP Chi-restraints excluded: chain 21 residue 109 ASP Chi-restraints excluded: chain 22 residue 11 LEU Chi-restraints excluded: chain 23 residue 8 ASP Chi-restraints excluded: chain 23 residue 17 ASP Chi-restraints excluded: chain 23 residue 27 VAL Chi-restraints excluded: chain 24 residue 4 ILE Chi-restraints excluded: chain 24 residue 24 ASN Chi-restraints excluded: chain 24 residue 42 LEU Chi-restraints excluded: chain 24 residue 66 ASP Chi-restraints excluded: chain 24 residue 89 ILE Chi-restraints excluded: chain 26 residue 34 SER Chi-restraints excluded: chain 26 residue 63 ILE Chi-restraints excluded: chain 27 residue 11 VAL Chi-restraints excluded: chain 27 residue 15 ASN Chi-restraints excluded: chain 27 residue 17 GLU Chi-restraints excluded: chain 27 residue 31 GLN Chi-restraints excluded: chain 27 residue 36 GLN Chi-restraints excluded: chain 27 residue 44 LYS Chi-restraints excluded: chain 27 residue 55 THR Chi-restraints excluded: chain 28 residue 56 VAL Chi-restraints excluded: chain 29 residue 27 THR Chi-restraints excluded: chain 30 residue 2 VAL Chi-restraints excluded: chain 30 residue 35 GLU Chi-restraints excluded: chain 31 residue 10 LEU Chi-restraints excluded: chain 31 residue 35 LEU Chi-restraints excluded: chain 31 residue 46 VAL Chi-restraints excluded: chain 33 residue 3 ILE Chi-restraints excluded: chain 33 residue 49 VAL Chi-restraints excluded: chain 33 residue 50 SER Chi-restraints excluded: chain 33 residue 58 ILE Chi-restraints excluded: chain 34 residue 10 LEU Chi-restraints excluded: chain 34 residue 26 ILE Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain H residue 20 ASN Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 125 GLN Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 51 PHE Chi-restraints excluded: chain K residue 57 SER Chi-restraints excluded: chain K residue 69 CYS Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain K residue 80 ASN Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 67 ASP Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain P residue 66 THR Chi-restraints excluded: chain P residue 75 ILE Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain Q residue 21 VAL Chi-restraints excluded: chain Q residue 29 LYS Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain R residue 60 ARG Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain T residue 20 ASN Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain U residue 37 TYR Chi-restraints excluded: chain 03 residue 18 THR Chi-restraints excluded: chain 03 residue 56 ASP Chi-restraints excluded: chain Z residue 42 LEU Chi-restraints excluded: chain Z residue 100 LYS Chi-restraints excluded: chain Z residue 162 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1080 random chunks: chunk 970 optimal weight: 20.0000 chunk 738 optimal weight: 20.0000 chunk 509 optimal weight: 3.9990 chunk 108 optimal weight: 50.0000 chunk 468 optimal weight: 20.0000 chunk 659 optimal weight: 20.0000 chunk 986 optimal weight: 20.0000 chunk 1043 optimal weight: 50.0000 chunk 515 optimal weight: 7.9990 chunk 934 optimal weight: 20.0000 chunk 281 optimal weight: 20.0000 overall best weight: 14.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 04 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 05 150 GLN 06 62 GLN ** 06 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 06 136 GLN ** 07 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 08 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 14 4 ASN ** 15 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 16 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 16 107 ASN 17 67 ASN 18 114 ASN 19 19 GLN 19 36 GLN 19 58 GLN ** 20 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 23 52 ASN 24 75 GLN ** 27 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 29 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 31 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 32 6 GLN ** 32 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 ASN ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 111 GLN N 70 HIS O 34 GLN ** O 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 60 GLN ** T 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 63 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.108 165170 Z= 0.436 Angle : 0.765 12.432 246822 Z= 0.391 Chirality : 0.040 0.355 31534 Planarity : 0.006 0.085 13429 Dihedral : 23.716 179.839 82044 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 30.80 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.70 % Favored : 88.98 % Rotamer: Outliers : 6.80 % Allowed : 18.27 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.10), residues: 6159 helix: -0.93 (0.11), residues: 1943 sheet: -1.82 (0.15), residues: 1031 loop : -2.20 (0.10), residues: 3185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP S 33 HIS 0.011 0.002 HIS T 67 PHE 0.026 0.003 PHE07 113 TYR 0.030 0.003 TYR F 4 ARG 0.020 0.001 ARG P 14 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12318 Ramachandran restraints generated. 6159 Oldfield, 0 Emsley, 6159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12318 Ramachandran restraints generated. 6159 Oldfield, 0 Emsley, 6159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1410 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 348 poor density : 1062 time to evaluate : 6.710 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: 04 33 LEU cc_start: 0.9609 (OUTLIER) cc_final: 0.9404 (mm) REVERT: 04 145 MET cc_start: 0.9541 (mmm) cc_final: 0.9054 (ptt) REVERT: 04 159 THR cc_start: 0.9506 (OUTLIER) cc_final: 0.8994 (p) REVERT: 04 250 GLN cc_start: 0.9326 (tp-100) cc_final: 0.9067 (tp-100) REVERT: 05 200 ASP cc_start: 0.9128 (m-30) cc_final: 0.8922 (m-30) REVERT: 06 9 GLN cc_start: 0.9286 (mt0) cc_final: 0.9006 (tm-30) REVERT: 06 62 GLN cc_start: 0.9129 (OUTLIER) cc_final: 0.8883 (tp40) REVERT: 06 94 GLN cc_start: 0.9289 (pt0) cc_final: 0.8959 (pt0) REVERT: 06 188 MET cc_start: 0.9510 (mmm) cc_final: 0.9183 (mmm) REVERT: 08 87 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.8408 (tm-30) REVERT: 08 123 GLU cc_start: 0.9315 (mm-30) cc_final: 0.9109 (mm-30) REVERT: 09 43 ASN cc_start: 0.8987 (t0) cc_final: 0.8674 (t0) REVERT: 09 46 PHE cc_start: 0.9387 (t80) cc_final: 0.9021 (t80) REVERT: 09 128 HIS cc_start: 0.7285 (m-70) cc_final: 0.6663 (m90) REVERT: 09 141 LYS cc_start: 0.8925 (mttt) cc_final: 0.8522 (mmtt) REVERT: 10 96 PHE cc_start: 0.4940 (t80) cc_final: 0.4736 (t80) REVERT: 10 99 PHE cc_start: 0.6181 (OUTLIER) cc_final: 0.5577 (m-10) REVERT: 11 16 MET cc_start: 0.7054 (mmp) cc_final: 0.6784 (ptm) REVERT: 11 116 MET cc_start: 0.3476 (tpt) cc_final: 0.2783 (tpt) REVERT: 12 14 ASP cc_start: 0.8553 (t70) cc_final: 0.8228 (t0) REVERT: 12 31 GLU cc_start: 0.9096 (tp30) cc_final: 0.8844 (tp30) REVERT: 12 86 GLN cc_start: 0.9231 (pt0) cc_final: 0.8603 (pp30) REVERT: 12 96 ARG cc_start: 0.9165 (mtp85) cc_final: 0.8711 (mtm110) REVERT: 12 98 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8393 (mt-10) REVERT: 12 99 ARG cc_start: 0.9442 (mmm160) cc_final: 0.9138 (mmp80) REVERT: 12 118 MET cc_start: 0.9502 (ptp) cc_final: 0.9142 (mtm) REVERT: 13 20 MET cc_start: 0.9337 (ttt) cc_final: 0.9044 (ttt) REVERT: 13 73 ASP cc_start: 0.9092 (p0) cc_final: 0.8798 (p0) REVERT: 13 100 PHE cc_start: 0.8882 (m-10) cc_final: 0.8629 (m-10) REVERT: 14 38 GLN cc_start: 0.9191 (tt0) cc_final: 0.8857 (tt0) REVERT: 14 76 GLU cc_start: 0.8979 (pt0) cc_final: 0.8625 (mt-10) REVERT: 14 104 GLN cc_start: 0.9338 (mm-40) cc_final: 0.8893 (tp-100) REVERT: 14 106 GLU cc_start: 0.8915 (mm-30) cc_final: 0.8698 (mm-30) REVERT: 15 10 ARG cc_start: 0.9622 (ptm160) cc_final: 0.9024 (mmp80) REVERT: 15 28 PHE cc_start: 0.9392 (m-80) cc_final: 0.9181 (m-80) REVERT: 15 45 GLN cc_start: 0.9626 (mt0) cc_final: 0.9311 (mt0) REVERT: 15 53 MET cc_start: 0.9180 (ttp) cc_final: 0.8860 (ppp) REVERT: 15 82 MET cc_start: 0.9424 (mmm) cc_final: 0.9139 (mmm) REVERT: 15 88 ASN cc_start: 0.9175 (m-40) cc_final: 0.8794 (m-40) REVERT: 15 136 MET cc_start: 0.9014 (ptt) cc_final: 0.8550 (ppp) REVERT: 16 1 MET cc_start: 0.9432 (ptp) cc_final: 0.9138 (mtm) REVERT: 16 34 ILE cc_start: 0.9409 (pt) cc_final: 0.9190 (mm) REVERT: 16 49 GLU cc_start: 0.9089 (mt-10) cc_final: 0.8282 (mp0) REVERT: 16 72 ASP cc_start: 0.9062 (m-30) cc_final: 0.8847 (m-30) REVERT: 17 43 ASN cc_start: 0.9012 (p0) cc_final: 0.7887 (p0) REVERT: 17 45 SER cc_start: 0.9097 (t) cc_final: 0.8726 (p) REVERT: 17 46 GLU cc_start: 0.9289 (pt0) cc_final: 0.8909 (pm20) REVERT: 17 76 LYS cc_start: 0.9725 (ttpt) cc_final: 0.9505 (mtpp) REVERT: 17 80 GLU cc_start: 0.9443 (mt-10) cc_final: 0.9021 (mt-10) REVERT: 17 92 PHE cc_start: 0.8925 (t80) cc_final: 0.8381 (t80) REVERT: 17 104 GLN cc_start: 0.9741 (tt0) cc_final: 0.9368 (tp-100) REVERT: 17 108 ASP cc_start: 0.9446 (m-30) cc_final: 0.8990 (m-30) REVERT: 17 112 GLU cc_start: 0.9122 (pp20) cc_final: 0.8900 (pp20) REVERT: 18 6 GLN cc_start: 0.8885 (mt0) cc_final: 0.8627 (mp10) REVERT: 18 26 GLU cc_start: 0.8932 (tp30) cc_final: 0.8616 (tp30) REVERT: 18 49 ILE cc_start: 0.9123 (mt) cc_final: 0.8909 (mp) REVERT: 18 51 ASN cc_start: 0.8822 (OUTLIER) cc_final: 0.8250 (p0) REVERT: 18 83 ILE cc_start: 0.9079 (OUTLIER) cc_final: 0.8657 (mm) REVERT: 18 105 LYS cc_start: 0.9172 (mmmt) cc_final: 0.8754 (mmtm) REVERT: 18 114 ASN cc_start: 0.5594 (OUTLIER) cc_final: 0.5253 (t0) REVERT: 19 51 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8529 (tp40) REVERT: 19 88 GLU cc_start: 0.9074 (mp0) cc_final: 0.8814 (mp0) REVERT: 19 116 LEU cc_start: 0.9671 (tt) cc_final: 0.9270 (tp) REVERT: 20 13 ARG cc_start: 0.9122 (ttt-90) cc_final: 0.8863 (ttt180) REVERT: 20 40 MET cc_start: 0.9534 (ttp) cc_final: 0.9020 (tmm) REVERT: 20 78 ARG cc_start: 0.9408 (tpp80) cc_final: 0.8765 (tpp80) REVERT: 21 53 SER cc_start: 0.9167 (t) cc_final: 0.8117 (p) REVERT: 21 77 ASP cc_start: 0.8425 (OUTLIER) cc_final: 0.7571 (p0) REVERT: 21 78 GLU cc_start: 0.8851 (pm20) cc_final: 0.8557 (pm20) REVERT: 22 69 ARG cc_start: 0.7857 (mmm160) cc_final: 0.7651 (mmm160) REVERT: 24 55 GLU cc_start: 0.9599 (mt-10) cc_final: 0.9139 (mp0) REVERT: 25 20 LYS cc_start: 0.9055 (mptt) cc_final: 0.8375 (tppt) REVERT: 25 68 LYS cc_start: 0.9322 (mtmt) cc_final: 0.8895 (mttt) REVERT: 26 25 LYS cc_start: 0.9266 (mmtp) cc_final: 0.8933 (mmmm) REVERT: 26 70 LEU cc_start: 0.9560 (mt) cc_final: 0.9154 (tp) REVERT: 26 75 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7282 (mp0) REVERT: 27 39 GLN cc_start: 0.9523 (mt0) cc_final: 0.9120 (mp10) REVERT: 27 44 LYS cc_start: 0.9762 (OUTLIER) cc_final: 0.9484 (tptp) REVERT: 27 49 ASP cc_start: 0.9384 (m-30) cc_final: 0.9081 (m-30) REVERT: 29 8 LYS cc_start: 0.9223 (mmtp) cc_final: 0.8851 (tmmt) REVERT: 30 36 LYS cc_start: 0.9434 (mmtp) cc_final: 0.9036 (mmmm) REVERT: 31 6 GLU cc_start: 0.8701 (pt0) cc_final: 0.8123 (pm20) REVERT: 31 19 PHE cc_start: 0.8923 (p90) cc_final: 0.8480 (p90) REVERT: 31 24 LYS cc_start: 0.8668 (ttpt) cc_final: 0.8191 (tmmt) REVERT: 32 1 MET cc_start: 0.7907 (ptm) cc_final: 0.7545 (ppp) REVERT: 32 2 LYS cc_start: 0.9519 (ttmt) cc_final: 0.8954 (ttpt) REVERT: 32 6 GLN cc_start: 0.8998 (mm110) cc_final: 0.8539 (mm110) REVERT: 32 13 ASN cc_start: 0.9299 (m-40) cc_final: 0.8352 (t0) REVERT: 34 1 MET cc_start: 0.9301 (OUTLIER) cc_final: 0.8306 (mmm) REVERT: 34 10 LEU cc_start: 0.9554 (OUTLIER) cc_final: 0.9292 (tp) REVERT: 34 18 LYS cc_start: 0.9511 (tttt) cc_final: 0.9186 (ttpt) REVERT: B 48 MET cc_start: 0.9393 (mtm) cc_final: 0.9014 (ptp) REVERT: B 93 HIS cc_start: 0.9247 (t-90) cc_final: 0.8968 (t-170) REVERT: B 99 MET cc_start: 0.9344 (mtp) cc_final: 0.9074 (mtp) REVERT: B 119 GLN cc_start: 0.9624 (OUTLIER) cc_final: 0.9344 (pt0) REVERT: C 2 GLN cc_start: 0.8280 (pt0) cc_final: 0.7225 (pt0) REVERT: D 39 GLN cc_start: 0.8940 (tm-30) cc_final: 0.8640 (tm-30) REVERT: D 50 TYR cc_start: 0.8999 (t80) cc_final: 0.8618 (t80) REVERT: D 131 ILE cc_start: 0.8362 (mt) cc_final: 0.8119 (tt) REVERT: E 11 GLN cc_start: 0.8139 (tt0) cc_final: 0.7780 (tt0) REVERT: E 12 GLU cc_start: 0.8421 (tt0) cc_final: 0.8038 (tt0) REVERT: E 54 GLU cc_start: 0.8777 (tm-30) cc_final: 0.8524 (tm-30) REVERT: E 67 ARG cc_start: 0.8903 (mmt90) cc_final: 0.8571 (mmt90) REVERT: E 141 ASP cc_start: 0.9143 (t0) cc_final: 0.8865 (t0) REVERT: F 21 MET cc_start: 0.9193 (mtt) cc_final: 0.8778 (mtt) REVERT: F 25 TYR cc_start: 0.9060 (m-10) cc_final: 0.8795 (m-10) REVERT: F 72 ASP cc_start: 0.9527 (OUTLIER) cc_final: 0.9129 (p0) REVERT: F 78 PHE cc_start: 0.9628 (m-80) cc_final: 0.8937 (m-80) REVERT: F 81 ASN cc_start: 0.9152 (t0) cc_final: 0.8873 (t0) REVERT: F 90 MET cc_start: 0.9156 (mmt) cc_final: 0.8803 (mmt) REVERT: G 142 ARG cc_start: 0.9623 (mmt90) cc_final: 0.9226 (ttm170) REVERT: H 48 PHE cc_start: 0.8939 (p90) cc_final: 0.8404 (p90) REVERT: H 90 GLU cc_start: 0.9502 (tt0) cc_final: 0.9201 (tt0) REVERT: H 112 ASP cc_start: 0.9483 (p0) cc_final: 0.8832 (t0) REVERT: I 45 MET cc_start: 0.9655 (ppp) cc_final: 0.9266 (ppp) REVERT: I 96 GLU cc_start: 0.9072 (mp0) cc_final: 0.8857 (mp0) REVERT: I 106 ASP cc_start: 0.8873 (t70) cc_final: 0.8486 (t0) REVERT: I 128 LYS cc_start: 0.9014 (tptm) cc_final: 0.8735 (tptm) REVERT: J 59 LYS cc_start: 0.9203 (tttm) cc_final: 0.8607 (ttmt) REVERT: J 65 TYR cc_start: 0.8506 (m-80) cc_final: 0.8068 (m-80) REVERT: J 81 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7643 (mm-30) REVERT: J 82 LYS cc_start: 0.9560 (mptt) cc_final: 0.9335 (tppt) REVERT: J 87 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8840 (mt) REVERT: K 37 GLN cc_start: 0.9381 (mp10) cc_final: 0.9172 (mp10) REVERT: K 39 ASN cc_start: 0.9129 (m-40) cc_final: 0.8792 (t0) REVERT: L 19 ASN cc_start: 0.9464 (m-40) cc_final: 0.9144 (t0) REVERT: M 6 ILE cc_start: 0.8938 (OUTLIER) cc_final: 0.8411 (mm) REVERT: M 16 ILE cc_start: 0.9552 (OUTLIER) cc_final: 0.9257 (mm) REVERT: M 85 TYR cc_start: 0.9338 (t80) cc_final: 0.9032 (t80) REVERT: N 25 GLU cc_start: 0.9173 (pt0) cc_final: 0.8653 (tm-30) REVERT: O 27 GLN cc_start: 0.9126 (OUTLIER) cc_final: 0.8783 (mp10) REVERT: O 88 ARG cc_start: 0.8223 (tpp-160) cc_final: 0.6861 (mmt-90) REVERT: Q 16 MET cc_start: 0.7782 (ttm) cc_final: 0.7496 (tpp) REVERT: Q 29 LYS cc_start: 0.9464 (OUTLIER) cc_final: 0.9240 (tptp) REVERT: Q 42 LYS cc_start: 0.9154 (mttt) cc_final: 0.8914 (mtmm) REVERT: Q 51 GLU cc_start: 0.9121 (pt0) cc_final: 0.8917 (pm20) REVERT: R 47 ARG cc_start: 0.9555 (mmm160) cc_final: 0.8858 (mpp-170) REVERT: T 26 MET cc_start: 0.9162 (ttp) cc_final: 0.8653 (tpp) REVERT: T 39 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8682 (mp0) REVERT: T 53 MET cc_start: 0.9454 (ppp) cc_final: 0.9194 (ppp) REVERT: U 33 ARG cc_start: 0.8914 (ptm-80) cc_final: 0.8299 (ptm-80) REVERT: U 36 PHE cc_start: 0.8688 (m-80) cc_final: 0.8445 (m-80) REVERT: U 44 ARG cc_start: 0.8986 (tpp-160) cc_final: 0.8658 (ttp80) REVERT: U 45 LYS cc_start: 0.9302 (tptt) cc_final: 0.9000 (tppt) REVERT: 03 25 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7998 (mt-10) REVERT: 03 203 GLN cc_start: 0.8126 (tp40) cc_final: 0.7863 (tp-100) REVERT: Z 7 GLN cc_start: 0.9216 (tt0) cc_final: 0.8950 (tp40) REVERT: Z 91 ARG cc_start: 0.8071 (mmp80) cc_final: 0.6963 (pmt-80) outliers start: 348 outliers final: 250 residues processed: 1273 average time/residue: 1.4129 time to fit residues: 3175.2550 Evaluate side-chains 1263 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 270 poor density : 993 time to evaluate : 6.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 33 LEU Chi-restraints excluded: chain 04 residue 37 SER Chi-restraints excluded: chain 04 residue 63 ILE Chi-restraints excluded: chain 04 residue 159 THR Chi-restraints excluded: chain 04 residue 199 HIS Chi-restraints excluded: chain 04 residue 215 VAL Chi-restraints excluded: chain 04 residue 227 VAL Chi-restraints excluded: chain 04 residue 263 ASP Chi-restraints excluded: chain 05 residue 103 ASP Chi-restraints excluded: chain 05 residue 112 THR Chi-restraints excluded: chain 05 residue 126 ASN Chi-restraints excluded: chain 05 residue 145 SER Chi-restraints excluded: chain 05 residue 146 ILE Chi-restraints excluded: chain 05 residue 177 VAL Chi-restraints excluded: chain 05 residue 201 LEU Chi-restraints excluded: chain 06 residue 62 GLN Chi-restraints excluded: chain 06 residue 84 THR Chi-restraints excluded: chain 06 residue 148 ILE Chi-restraints excluded: chain 06 residue 175 ILE Chi-restraints excluded: chain 06 residue 199 MET Chi-restraints excluded: chain 07 residue 9 ASP Chi-restraints excluded: chain 07 residue 46 LYS Chi-restraints excluded: chain 07 residue 51 ASN Chi-restraints excluded: chain 07 residue 86 CYS Chi-restraints excluded: chain 07 residue 143 ASP Chi-restraints excluded: chain 07 residue 148 VAL Chi-restraints excluded: chain 07 residue 156 THR Chi-restraints excluded: chain 07 residue 157 THR Chi-restraints excluded: chain 07 residue 174 PHE Chi-restraints excluded: chain 07 residue 177 ARG Chi-restraints excluded: chain 08 residue 9 VAL Chi-restraints excluded: chain 08 residue 10 VAL Chi-restraints excluded: chain 08 residue 87 GLN Chi-restraints excluded: chain 08 residue 154 GLU Chi-restraints excluded: chain 09 residue 4 ILE Chi-restraints excluded: chain 09 residue 77 THR Chi-restraints excluded: chain 10 residue 27 VAL Chi-restraints excluded: chain 10 residue 99 PHE Chi-restraints excluded: chain 10 residue 123 ILE Chi-restraints excluded: chain 11 residue 7 TYR Chi-restraints excluded: chain 11 residue 27 LEU Chi-restraints excluded: chain 11 residue 58 ILE Chi-restraints excluded: chain 11 residue 70 THR Chi-restraints excluded: chain 11 residue 102 ARG Chi-restraints excluded: chain 12 residue 25 LEU Chi-restraints excluded: chain 12 residue 52 ASP Chi-restraints excluded: chain 12 residue 57 LEU Chi-restraints excluded: chain 12 residue 81 ILE Chi-restraints excluded: chain 12 residue 84 ILE Chi-restraints excluded: chain 12 residue 139 VAL Chi-restraints excluded: chain 13 residue 1 MET Chi-restraints excluded: chain 13 residue 25 LEU Chi-restraints excluded: chain 13 residue 39 ILE Chi-restraints excluded: chain 13 residue 54 LYS Chi-restraints excluded: chain 13 residue 58 LEU Chi-restraints excluded: chain 13 residue 65 THR Chi-restraints excluded: chain 13 residue 80 ASP Chi-restraints excluded: chain 13 residue 91 SER Chi-restraints excluded: chain 13 residue 104 THR Chi-restraints excluded: chain 14 residue 35 HIS Chi-restraints excluded: chain 14 residue 89 VAL Chi-restraints excluded: chain 14 residue 91 ASP Chi-restraints excluded: chain 14 residue 103 ILE Chi-restraints excluded: chain 15 residue 24 THR Chi-restraints excluded: chain 15 residue 30 SER Chi-restraints excluded: chain 15 residue 42 THR Chi-restraints excluded: chain 15 residue 111 GLU Chi-restraints excluded: chain 15 residue 129 THR Chi-restraints excluded: chain 15 residue 134 THR Chi-restraints excluded: chain 16 residue 6 SER Chi-restraints excluded: chain 16 residue 32 GLU Chi-restraints excluded: chain 16 residue 37 THR Chi-restraints excluded: chain 16 residue 48 VAL Chi-restraints excluded: chain 16 residue 57 THR Chi-restraints excluded: chain 17 residue 19 GLN Chi-restraints excluded: chain 17 residue 53 THR Chi-restraints excluded: chain 17 residue 91 SER Chi-restraints excluded: chain 18 residue 10 GLU Chi-restraints excluded: chain 18 residue 23 ASP Chi-restraints excluded: chain 18 residue 51 ASN Chi-restraints excluded: chain 18 residue 83 ILE Chi-restraints excluded: chain 18 residue 114 ASN Chi-restraints excluded: chain 19 residue 8 ILE Chi-restraints excluded: chain 19 residue 16 ILE Chi-restraints excluded: chain 19 residue 17 LEU Chi-restraints excluded: chain 19 residue 51 GLN Chi-restraints excluded: chain 19 residue 89 ILE Chi-restraints excluded: chain 19 residue 90 ASP Chi-restraints excluded: chain 19 residue 106 THR Chi-restraints excluded: chain 20 residue 6 GLN Chi-restraints excluded: chain 20 residue 27 ILE Chi-restraints excluded: chain 20 residue 43 ASN Chi-restraints excluded: chain 20 residue 58 VAL Chi-restraints excluded: chain 21 residue 4 ILE Chi-restraints excluded: chain 21 residue 37 THR Chi-restraints excluded: chain 21 residue 51 LEU Chi-restraints excluded: chain 21 residue 62 ASP Chi-restraints excluded: chain 21 residue 67 ASP Chi-restraints excluded: chain 21 residue 72 THR Chi-restraints excluded: chain 21 residue 77 ASP Chi-restraints excluded: chain 21 residue 100 THR Chi-restraints excluded: chain 21 residue 109 ASP Chi-restraints excluded: chain 22 residue 11 LEU Chi-restraints excluded: chain 22 residue 32 LEU Chi-restraints excluded: chain 23 residue 8 ASP Chi-restraints excluded: chain 23 residue 17 ASP Chi-restraints excluded: chain 23 residue 27 VAL Chi-restraints excluded: chain 23 residue 64 ILE Chi-restraints excluded: chain 24 residue 4 ILE Chi-restraints excluded: chain 24 residue 24 ASN Chi-restraints excluded: chain 24 residue 42 LEU Chi-restraints excluded: chain 24 residue 66 ASP Chi-restraints excluded: chain 24 residue 89 ILE Chi-restraints excluded: chain 25 residue 8 ASN Chi-restraints excluded: chain 25 residue 17 LEU Chi-restraints excluded: chain 25 residue 60 ASP Chi-restraints excluded: chain 25 residue 63 VAL Chi-restraints excluded: chain 26 residue 3 VAL Chi-restraints excluded: chain 26 residue 6 VAL Chi-restraints excluded: chain 26 residue 15 ASN Chi-restraints excluded: chain 26 residue 34 SER Chi-restraints excluded: chain 26 residue 46 VAL Chi-restraints excluded: chain 26 residue 63 ILE Chi-restraints excluded: chain 27 residue 11 VAL Chi-restraints excluded: chain 27 residue 15 ASN Chi-restraints excluded: chain 27 residue 17 GLU Chi-restraints excluded: chain 27 residue 44 LYS Chi-restraints excluded: chain 27 residue 50 VAL Chi-restraints excluded: chain 27 residue 55 THR Chi-restraints excluded: chain 28 residue 4 ILE Chi-restraints excluded: chain 28 residue 56 VAL Chi-restraints excluded: chain 29 residue 34 LEU Chi-restraints excluded: chain 29 residue 58 ASP Chi-restraints excluded: chain 29 residue 59 ARG Chi-restraints excluded: chain 30 residue 2 VAL Chi-restraints excluded: chain 30 residue 32 THR Chi-restraints excluded: chain 30 residue 35 GLU Chi-restraints excluded: chain 31 residue 23 THR Chi-restraints excluded: chain 31 residue 33 LEU Chi-restraints excluded: chain 31 residue 46 VAL Chi-restraints excluded: chain 32 residue 44 VAL Chi-restraints excluded: chain 33 residue 49 VAL Chi-restraints excluded: chain 33 residue 50 SER Chi-restraints excluded: chain 33 residue 58 ILE Chi-restraints excluded: chain 34 residue 1 MET Chi-restraints excluded: chain 34 residue 10 LEU Chi-restraints excluded: chain 34 residue 13 ASN Chi-restraints excluded: chain 34 residue 17 VAL Chi-restraints excluded: chain 34 residue 20 ASP Chi-restraints excluded: chain 34 residue 26 ILE Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 84 ASN Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 116 PHE Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 32 ASP Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 20 ASN Chi-restraints excluded: chain H residue 26 MET Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 109 GLN Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 125 GLN Chi-restraints excluded: chain J residue 18 ILE Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 49 PHE Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 51 PHE Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 69 CYS Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain K residue 80 ASN Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 118 ASN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 74 GLN Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 67 ASP Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain N residue 83 VAL Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 27 GLN Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain P residue 75 ILE Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 21 VAL Chi-restraints excluded: chain Q residue 29 LYS Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain S residue 11 ASP Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain T residue 20 ASN Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain U residue 37 TYR Chi-restraints excluded: chain U residue 43 GLU Chi-restraints excluded: chain 03 residue 18 THR Chi-restraints excluded: chain 03 residue 43 ASP Chi-restraints excluded: chain 03 residue 50 ILE Chi-restraints excluded: chain 03 residue 56 ASP Chi-restraints excluded: chain 03 residue 218 MET Chi-restraints excluded: chain Z residue 42 LEU Chi-restraints excluded: chain Z residue 96 ILE Chi-restraints excluded: chain Z residue 97 THR Chi-restraints excluded: chain Z residue 100 LYS Chi-restraints excluded: chain Z residue 162 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1080 random chunks: chunk 869 optimal weight: 20.0000 chunk 592 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 chunk 777 optimal weight: 20.0000 chunk 430 optimal weight: 0.9990 chunk 890 optimal weight: 20.0000 chunk 721 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 533 optimal weight: 5.9990 chunk 937 optimal weight: 10.0000 chunk 263 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 04 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 06 115 GLN 07 4 HIS ** 11 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 9 ASN ** 13 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 15 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 16 62 ASN 16 107 ASN 19 36 GLN 19 51 GLN 20 6 GLN ** 21 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 27 31 GLN 27 38 GLN ** 27 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 29 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 31 18 HIS ** 31 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 32 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 HIS ** E 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 2 ASN ** T 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.5013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 165170 Z= 0.219 Angle : 0.609 12.617 246822 Z= 0.313 Chirality : 0.034 0.282 31534 Planarity : 0.005 0.060 13429 Dihedral : 23.691 176.468 82044 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 21.16 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.43 % Favored : 91.26 % Rotamer: Outliers : 5.39 % Allowed : 20.40 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.10), residues: 6159 helix: -0.43 (0.11), residues: 1953 sheet: -1.64 (0.15), residues: 1078 loop : -1.91 (0.11), residues: 3128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP P 60 HIS 0.011 0.001 HIS T 67 PHE 0.034 0.002 PHE G 61 TYR 0.025 0.002 TYR I 5 ARG 0.023 0.001 ARG09 50 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12318 Ramachandran restraints generated. 6159 Oldfield, 0 Emsley, 6159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12318 Ramachandran restraints generated. 6159 Oldfield, 0 Emsley, 6159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1402 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 276 poor density : 1126 time to evaluate : 6.552 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: 04 131 MET cc_start: 0.9722 (mtp) cc_final: 0.9352 (mpp) REVERT: 04 145 MET cc_start: 0.9521 (mmm) cc_final: 0.9024 (ptt) REVERT: 04 159 THR cc_start: 0.9466 (OUTLIER) cc_final: 0.9177 (p) REVERT: 05 200 ASP cc_start: 0.9096 (m-30) cc_final: 0.8830 (m-30) REVERT: 06 9 GLN cc_start: 0.9274 (mt0) cc_final: 0.8998 (tm-30) REVERT: 06 94 GLN cc_start: 0.9238 (pt0) cc_final: 0.8923 (pt0) REVERT: 07 95 MET cc_start: 0.9293 (ttp) cc_final: 0.8960 (ttp) REVERT: 08 74 MET cc_start: 0.8550 (tpp) cc_final: 0.8228 (tpp) REVERT: 08 87 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8358 (tm-30) REVERT: 08 123 GLU cc_start: 0.9254 (mm-30) cc_final: 0.8845 (mp0) REVERT: 08 127 GLN cc_start: 0.7379 (tp-100) cc_final: 0.7172 (tp40) REVERT: 09 33 GLN cc_start: 0.9389 (mt0) cc_final: 0.9064 (tt0) REVERT: 09 43 ASN cc_start: 0.8920 (t0) cc_final: 0.8582 (t0) REVERT: 09 89 LYS cc_start: 0.8223 (mmmm) cc_final: 0.7130 (pttm) REVERT: 09 128 HIS cc_start: 0.7117 (m-70) cc_final: 0.6675 (m-70) REVERT: 09 135 HIS cc_start: 0.9369 (t70) cc_final: 0.8825 (t70) REVERT: 09 141 LYS cc_start: 0.8967 (mttt) cc_final: 0.8553 (mmtt) REVERT: 10 37 LYS cc_start: 0.5231 (pttp) cc_final: 0.4949 (pttp) REVERT: 10 99 PHE cc_start: 0.6226 (OUTLIER) cc_final: 0.5604 (m-10) REVERT: 11 16 MET cc_start: 0.7028 (mmp) cc_final: 0.6799 (ptm) REVERT: 12 31 GLU cc_start: 0.9105 (tp30) cc_final: 0.8884 (tp30) REVERT: 12 35 ARG cc_start: 0.9704 (mmt180) cc_final: 0.9462 (mmt-90) REVERT: 12 75 TYR cc_start: 0.9420 (m-10) cc_final: 0.9112 (m-10) REVERT: 12 86 GLN cc_start: 0.9335 (pt0) cc_final: 0.8443 (pp30) REVERT: 12 98 GLU cc_start: 0.8966 (mt-10) cc_final: 0.8325 (mt-10) REVERT: 12 99 ARG cc_start: 0.9433 (mmm160) cc_final: 0.9082 (mmp80) REVERT: 12 118 MET cc_start: 0.9430 (ptp) cc_final: 0.9091 (mtm) REVERT: 12 131 ASN cc_start: 0.9177 (p0) cc_final: 0.8809 (p0) REVERT: 13 1 MET cc_start: 0.8456 (ttm) cc_final: 0.8132 (mtp) REVERT: 13 4 GLU cc_start: 0.9519 (mm-30) cc_final: 0.9268 (mm-30) REVERT: 13 7 MET cc_start: 0.9262 (mmp) cc_final: 0.9034 (mmp) REVERT: 13 20 MET cc_start: 0.9266 (ttt) cc_final: 0.8996 (ttm) REVERT: 13 73 ASP cc_start: 0.9105 (p0) cc_final: 0.8635 (p0) REVERT: 13 100 PHE cc_start: 0.8929 (m-10) cc_final: 0.8707 (m-10) REVERT: 14 38 GLN cc_start: 0.9089 (tt0) cc_final: 0.8737 (tt0) REVERT: 14 76 GLU cc_start: 0.8884 (pt0) cc_final: 0.8576 (mt-10) REVERT: 14 104 GLN cc_start: 0.9270 (mm-40) cc_final: 0.8910 (mm110) REVERT: 15 1 MET cc_start: 0.6086 (tpt) cc_final: 0.5650 (tpt) REVERT: 15 10 ARG cc_start: 0.9585 (ptm160) cc_final: 0.8965 (mmp80) REVERT: 15 45 GLN cc_start: 0.9589 (mt0) cc_final: 0.9301 (mt0) REVERT: 15 82 MET cc_start: 0.9378 (mmm) cc_final: 0.8874 (mmm) REVERT: 15 88 ASN cc_start: 0.9123 (m-40) cc_final: 0.8899 (m-40) REVERT: 15 103 TYR cc_start: 0.9021 (m-80) cc_final: 0.8807 (m-80) REVERT: 15 136 MET cc_start: 0.8983 (ptt) cc_final: 0.8607 (ppp) REVERT: 16 1 MET cc_start: 0.9352 (ptp) cc_final: 0.8980 (mtm) REVERT: 16 27 SER cc_start: 0.9424 (m) cc_final: 0.9051 (p) REVERT: 16 43 GLU cc_start: 0.9137 (tp30) cc_final: 0.8858 (mm-30) REVERT: 16 49 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8253 (mp0) REVERT: 17 36 TYR cc_start: 0.8912 (m-10) cc_final: 0.8477 (m-10) REVERT: 17 43 ASN cc_start: 0.9032 (p0) cc_final: 0.7767 (p0) REVERT: 17 45 SER cc_start: 0.9074 (t) cc_final: 0.8647 (p) REVERT: 17 46 GLU cc_start: 0.9336 (pt0) cc_final: 0.8922 (pm20) REVERT: 17 76 LYS cc_start: 0.9725 (ttpt) cc_final: 0.9354 (tppt) REVERT: 17 80 GLU cc_start: 0.9449 (mt-10) cc_final: 0.8958 (mt-10) REVERT: 17 92 PHE cc_start: 0.8911 (t80) cc_final: 0.8345 (t80) REVERT: 17 104 GLN cc_start: 0.9722 (tt0) cc_final: 0.9356 (tp-100) REVERT: 17 108 ASP cc_start: 0.9444 (m-30) cc_final: 0.8897 (m-30) REVERT: 18 12 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.7754 (mmm) REVERT: 18 83 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8599 (mm) REVERT: 18 86 LYS cc_start: 0.9212 (mmtp) cc_final: 0.9008 (mmtm) REVERT: 18 105 LYS cc_start: 0.9098 (mmmt) cc_final: 0.8515 (mmtm) REVERT: 19 88 GLU cc_start: 0.9085 (mp0) cc_final: 0.8839 (mp0) REVERT: 20 13 ARG cc_start: 0.9062 (ttt-90) cc_final: 0.8732 (ttt-90) REVERT: 20 40 MET cc_start: 0.9513 (ttp) cc_final: 0.8875 (tmm) REVERT: 21 4 ILE cc_start: 0.9632 (OUTLIER) cc_final: 0.9404 (mt) REVERT: 21 53 SER cc_start: 0.8605 (t) cc_final: 0.8086 (p) REVERT: 21 77 ASP cc_start: 0.8460 (OUTLIER) cc_final: 0.7610 (p0) REVERT: 21 78 GLU cc_start: 0.8613 (pm20) cc_final: 0.8347 (pm20) REVERT: 22 69 ARG cc_start: 0.7901 (mmm160) cc_final: 0.7646 (mmm160) REVERT: 24 48 MET cc_start: 0.9508 (tpt) cc_final: 0.9281 (tpt) REVERT: 24 55 GLU cc_start: 0.9584 (mt-10) cc_final: 0.9093 (mp0) REVERT: 25 20 LYS cc_start: 0.9034 (mptt) cc_final: 0.8328 (tppt) REVERT: 25 68 LYS cc_start: 0.9363 (mtmt) cc_final: 0.8908 (mttt) REVERT: 26 25 LYS cc_start: 0.9196 (mmtp) cc_final: 0.8672 (mmmm) REVERT: 26 70 LEU cc_start: 0.9528 (mt) cc_final: 0.9170 (tp) REVERT: 26 75 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7314 (mp0) REVERT: 27 1 MET cc_start: 0.8808 (mmm) cc_final: 0.8507 (mmm) REVERT: 27 39 GLN cc_start: 0.9499 (mt0) cc_final: 0.9122 (mp10) REVERT: 27 44 LYS cc_start: 0.9751 (OUTLIER) cc_final: 0.9528 (tptp) REVERT: 27 49 ASP cc_start: 0.9411 (m-30) cc_final: 0.9097 (m-30) REVERT: 29 8 LYS cc_start: 0.9190 (mmtp) cc_final: 0.8760 (tmmt) REVERT: 30 11 LYS cc_start: 0.9188 (tppp) cc_final: 0.8872 (tppp) REVERT: 30 36 LYS cc_start: 0.9398 (mmtp) cc_final: 0.9024 (mmmm) REVERT: 31 19 PHE cc_start: 0.8907 (p90) cc_final: 0.8484 (p90) REVERT: 31 34 GLU cc_start: 0.8852 (tm-30) cc_final: 0.8633 (tm-30) REVERT: 31 35 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8676 (tp) REVERT: 32 1 MET cc_start: 0.7778 (ptm) cc_final: 0.7378 (ppp) REVERT: 32 2 LYS cc_start: 0.9516 (ttmt) cc_final: 0.8931 (ttpp) REVERT: 32 6 GLN cc_start: 0.9023 (mm110) cc_final: 0.8579 (mp10) REVERT: 32 22 MET cc_start: 0.9325 (OUTLIER) cc_final: 0.9074 (tpt) REVERT: 32 28 ARG cc_start: 0.9118 (mtm-85) cc_final: 0.8832 (mtt180) REVERT: 32 37 LYS cc_start: 0.9385 (tttt) cc_final: 0.8917 (tttp) REVERT: 34 10 LEU cc_start: 0.9544 (OUTLIER) cc_final: 0.9304 (tp) REVERT: 34 18 LYS cc_start: 0.9507 (tttt) cc_final: 0.9211 (ttpt) REVERT: B 21 TYR cc_start: 0.9382 (m-80) cc_final: 0.9039 (m-80) REVERT: B 48 MET cc_start: 0.9392 (mtm) cc_final: 0.9004 (ptp) REVERT: B 93 HIS cc_start: 0.9211 (t-90) cc_final: 0.8939 (t-170) REVERT: B 99 MET cc_start: 0.9361 (mtp) cc_final: 0.9077 (mtp) REVERT: B 119 GLN cc_start: 0.9572 (OUTLIER) cc_final: 0.9319 (pt0) REVERT: C 2 GLN cc_start: 0.8317 (pt0) cc_final: 0.7220 (pt0) REVERT: D 47 LEU cc_start: 0.9042 (tp) cc_final: 0.8564 (pp) REVERT: D 50 TYR cc_start: 0.8935 (t80) cc_final: 0.8677 (t80) REVERT: D 131 ILE cc_start: 0.8431 (mt) cc_final: 0.8212 (tt) REVERT: D 144 ILE cc_start: 0.8582 (mp) cc_final: 0.8303 (mp) REVERT: D 177 MET cc_start: 0.6696 (mtm) cc_final: 0.5885 (mtt) REVERT: E 12 GLU cc_start: 0.8176 (tt0) cc_final: 0.7694 (tt0) REVERT: E 54 GLU cc_start: 0.8838 (tm-30) cc_final: 0.8538 (tm-30) REVERT: E 67 ARG cc_start: 0.8900 (mmt90) cc_final: 0.8626 (mmt90) REVERT: E 141 ASP cc_start: 0.8992 (t0) cc_final: 0.8670 (t0) REVERT: F 72 ASP cc_start: 0.9504 (OUTLIER) cc_final: 0.9053 (p0) REVERT: F 78 PHE cc_start: 0.9615 (m-80) cc_final: 0.8957 (m-80) REVERT: F 81 ASN cc_start: 0.9122 (t0) cc_final: 0.8836 (t0) REVERT: G 139 ASP cc_start: 0.9404 (m-30) cc_final: 0.9007 (t0) REVERT: H 41 GLU cc_start: 0.9454 (tm-30) cc_final: 0.9137 (pp20) REVERT: H 48 PHE cc_start: 0.8960 (p90) cc_final: 0.8468 (p90) REVERT: H 90 GLU cc_start: 0.9513 (tt0) cc_final: 0.9229 (tt0) REVERT: H 112 ASP cc_start: 0.9413 (p0) cc_final: 0.8821 (t0) REVERT: I 45 MET cc_start: 0.9652 (ppp) cc_final: 0.9269 (ppp) REVERT: I 96 GLU cc_start: 0.9034 (mp0) cc_final: 0.8777 (mp0) REVERT: I 106 ASP cc_start: 0.8827 (t70) cc_final: 0.8413 (t0) REVERT: J 46 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8552 (mmmm) REVERT: J 59 LYS cc_start: 0.9061 (tttm) cc_final: 0.8481 (ttmt) REVERT: J 63 ASP cc_start: 0.8433 (t0) cc_final: 0.8090 (t0) REVERT: J 65 TYR cc_start: 0.8601 (m-80) cc_final: 0.8398 (m-80) REVERT: J 66 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7814 (tm-30) REVERT: J 87 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8863 (mt) REVERT: K 37 GLN cc_start: 0.9457 (mp10) cc_final: 0.9192 (mp10) REVERT: K 39 ASN cc_start: 0.9081 (m-40) cc_final: 0.8722 (t0) REVERT: L 19 ASN cc_start: 0.9408 (m-40) cc_final: 0.9138 (t0) REVERT: M 6 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8304 (mm) REVERT: N 25 GLU cc_start: 0.9155 (pt0) cc_final: 0.8532 (tm-30) REVERT: O 13 GLU cc_start: 0.9616 (tt0) cc_final: 0.9287 (pt0) REVERT: O 27 GLN cc_start: 0.9078 (OUTLIER) cc_final: 0.8701 (mp10) REVERT: O 47 LYS cc_start: 0.9410 (mmmm) cc_final: 0.8723 (ttpt) REVERT: O 88 ARG cc_start: 0.8060 (tpp-160) cc_final: 0.6858 (mmt-90) REVERT: P 6 LEU cc_start: 0.8467 (tp) cc_final: 0.8196 (tp) REVERT: Q 42 LYS cc_start: 0.9102 (mttt) cc_final: 0.8813 (mtmm) REVERT: Q 51 GLU cc_start: 0.9180 (pt0) cc_final: 0.8927 (pm20) REVERT: R 28 LEU cc_start: 0.9636 (mm) cc_final: 0.9378 (mt) REVERT: R 47 ARG cc_start: 0.9533 (mmm160) cc_final: 0.8837 (mpp-170) REVERT: S 20 LYS cc_start: 0.9643 (mtmm) cc_final: 0.9251 (pttt) REVERT: T 26 MET cc_start: 0.9158 (ttp) cc_final: 0.8650 (tpp) REVERT: T 53 MET cc_start: 0.9484 (ppp) cc_final: 0.9164 (ppp) REVERT: U 33 ARG cc_start: 0.8731 (ptm-80) cc_final: 0.8213 (ptm-80) REVERT: U 44 ARG cc_start: 0.8858 (tpp-160) cc_final: 0.8499 (ttp80) REVERT: U 45 LYS cc_start: 0.9285 (tptt) cc_final: 0.8981 (tppt) REVERT: 03 25 GLU cc_start: 0.8328 (mt-10) cc_final: 0.8032 (mt-10) REVERT: 03 203 GLN cc_start: 0.8059 (tp40) cc_final: 0.7750 (tp-100) REVERT: Z 7 GLN cc_start: 0.9237 (tt0) cc_final: 0.8973 (tp40) REVERT: Z 59 GLU cc_start: 0.6783 (mm-30) cc_final: 0.6467 (pm20) REVERT: Z 91 ARG cc_start: 0.7803 (mmp80) cc_final: 0.6870 (pmt-80) outliers start: 276 outliers final: 198 residues processed: 1285 average time/residue: 1.2362 time to fit residues: 2778.5265 Evaluate side-chains 1243 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 1028 time to evaluate : 6.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 159 THR Chi-restraints excluded: chain 04 residue 163 ILE Chi-restraints excluded: chain 04 residue 199 HIS Chi-restraints excluded: chain 04 residue 215 VAL Chi-restraints excluded: chain 04 residue 227 VAL Chi-restraints excluded: chain 05 residue 2 ILE Chi-restraints excluded: chain 05 residue 103 ASP Chi-restraints excluded: chain 05 residue 126 ASN Chi-restraints excluded: chain 05 residue 146 ILE Chi-restraints excluded: chain 05 residue 177 VAL Chi-restraints excluded: chain 05 residue 201 LEU Chi-restraints excluded: chain 06 residue 73 ILE Chi-restraints excluded: chain 06 residue 148 ILE Chi-restraints excluded: chain 06 residue 149 ILE Chi-restraints excluded: chain 06 residue 164 LEU Chi-restraints excluded: chain 06 residue 199 MET Chi-restraints excluded: chain 07 residue 46 LYS Chi-restraints excluded: chain 07 residue 86 CYS Chi-restraints excluded: chain 07 residue 112 ASP Chi-restraints excluded: chain 07 residue 135 ILE Chi-restraints excluded: chain 07 residue 148 VAL Chi-restraints excluded: chain 07 residue 157 THR Chi-restraints excluded: chain 07 residue 161 SER Chi-restraints excluded: chain 07 residue 177 ARG Chi-restraints excluded: chain 08 residue 9 VAL Chi-restraints excluded: chain 08 residue 10 VAL Chi-restraints excluded: chain 08 residue 87 GLN Chi-restraints excluded: chain 08 residue 154 GLU Chi-restraints excluded: chain 08 residue 167 VAL Chi-restraints excluded: chain 09 residue 77 THR Chi-restraints excluded: chain 10 residue 99 PHE Chi-restraints excluded: chain 10 residue 123 ILE Chi-restraints excluded: chain 11 residue 7 TYR Chi-restraints excluded: chain 11 residue 27 LEU Chi-restraints excluded: chain 11 residue 58 ILE Chi-restraints excluded: chain 11 residue 70 THR Chi-restraints excluded: chain 11 residue 102 ARG Chi-restraints excluded: chain 11 residue 107 GLU Chi-restraints excluded: chain 12 residue 25 LEU Chi-restraints excluded: chain 12 residue 57 LEU Chi-restraints excluded: chain 12 residue 81 ILE Chi-restraints excluded: chain 12 residue 84 ILE Chi-restraints excluded: chain 13 residue 12 ASP Chi-restraints excluded: chain 13 residue 25 LEU Chi-restraints excluded: chain 13 residue 58 LEU Chi-restraints excluded: chain 13 residue 65 THR Chi-restraints excluded: chain 13 residue 80 ASP Chi-restraints excluded: chain 13 residue 104 THR Chi-restraints excluded: chain 14 residue 35 HIS Chi-restraints excluded: chain 14 residue 89 VAL Chi-restraints excluded: chain 14 residue 91 ASP Chi-restraints excluded: chain 15 residue 24 THR Chi-restraints excluded: chain 15 residue 30 SER Chi-restraints excluded: chain 15 residue 42 THR Chi-restraints excluded: chain 15 residue 134 THR Chi-restraints excluded: chain 16 residue 6 SER Chi-restraints excluded: chain 16 residue 32 GLU Chi-restraints excluded: chain 16 residue 37 THR Chi-restraints excluded: chain 17 residue 19 GLN Chi-restraints excluded: chain 17 residue 53 THR Chi-restraints excluded: chain 18 residue 10 GLU Chi-restraints excluded: chain 18 residue 12 MET Chi-restraints excluded: chain 18 residue 51 ASN Chi-restraints excluded: chain 18 residue 83 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 89 ILE Chi-restraints excluded: chain 19 residue 90 ASP Chi-restraints excluded: chain 20 residue 27 ILE Chi-restraints excluded: chain 20 residue 43 ASN Chi-restraints excluded: chain 20 residue 58 VAL Chi-restraints excluded: chain 21 residue 4 ILE Chi-restraints excluded: chain 21 residue 62 ASP Chi-restraints excluded: chain 21 residue 67 ASP Chi-restraints excluded: chain 21 residue 77 ASP Chi-restraints excluded: chain 21 residue 107 VAL Chi-restraints excluded: chain 21 residue 109 ASP Chi-restraints excluded: chain 23 residue 8 ASP Chi-restraints excluded: chain 23 residue 27 VAL Chi-restraints excluded: chain 23 residue 33 VAL Chi-restraints excluded: chain 23 residue 48 VAL Chi-restraints excluded: chain 24 residue 4 ILE Chi-restraints excluded: chain 24 residue 24 ASN Chi-restraints excluded: chain 24 residue 42 LEU Chi-restraints excluded: chain 24 residue 66 ASP Chi-restraints excluded: chain 25 residue 7 ARG Chi-restraints excluded: chain 25 residue 8 ASN Chi-restraints excluded: chain 25 residue 60 ASP Chi-restraints excluded: chain 25 residue 63 VAL Chi-restraints excluded: chain 26 residue 6 VAL Chi-restraints excluded: chain 26 residue 15 ASN Chi-restraints excluded: chain 26 residue 34 SER Chi-restraints excluded: chain 26 residue 41 SER Chi-restraints excluded: chain 26 residue 63 ILE Chi-restraints excluded: chain 27 residue 11 VAL Chi-restraints excluded: chain 27 residue 15 ASN Chi-restraints excluded: chain 27 residue 44 LYS Chi-restraints excluded: chain 27 residue 55 THR Chi-restraints excluded: chain 28 residue 56 VAL Chi-restraints excluded: chain 29 residue 24 ILE Chi-restraints excluded: chain 30 residue 2 VAL Chi-restraints excluded: chain 30 residue 35 GLU Chi-restraints excluded: chain 31 residue 33 LEU Chi-restraints excluded: chain 31 residue 35 LEU Chi-restraints excluded: chain 32 residue 22 MET Chi-restraints excluded: chain 32 residue 44 VAL Chi-restraints excluded: chain 33 residue 6 VAL Chi-restraints excluded: chain 33 residue 49 VAL Chi-restraints excluded: chain 34 residue 1 MET Chi-restraints excluded: chain 34 residue 3 VAL Chi-restraints excluded: chain 34 residue 10 LEU Chi-restraints excluded: chain 34 residue 13 ASN Chi-restraints excluded: chain 34 residue 26 ILE Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 197 HIS Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 20 ASN Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 125 GLN Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 49 PHE Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 51 PHE Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 69 CYS Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain K residue 80 ASN Chi-restraints excluded: chain K residue 118 ASN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 74 GLN Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 119 LYS Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 11 HIS Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 38 ILE Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 67 ASP Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain N residue 85 GLU Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain O residue 27 GLN Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain P residue 29 ASN Chi-restraints excluded: chain P residue 75 ILE Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain S residue 65 MET Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain T residue 20 ASN Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain U residue 37 TYR Chi-restraints excluded: chain U residue 41 THR Chi-restraints excluded: chain U residue 43 GLU Chi-restraints excluded: chain 03 residue 18 THR Chi-restraints excluded: chain 03 residue 50 ILE Chi-restraints excluded: chain 03 residue 56 ASP Chi-restraints excluded: chain 03 residue 63 THR Chi-restraints excluded: chain 03 residue 218 MET Chi-restraints excluded: chain Z residue 16 ILE Chi-restraints excluded: chain Z residue 42 LEU Chi-restraints excluded: chain Z residue 100 LYS Chi-restraints excluded: chain Z residue 162 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1080 random chunks: chunk 351 optimal weight: 10.0000 chunk 940 optimal weight: 20.0000 chunk 206 optimal weight: 10.0000 chunk 612 optimal weight: 20.0000 chunk 257 optimal weight: 10.0000 chunk 1044 optimal weight: 50.0000 chunk 867 optimal weight: 20.0000 chunk 483 optimal weight: 20.0000 chunk 86 optimal weight: 0.0030 chunk 345 optimal weight: 0.5980 chunk 548 optimal weight: 20.0000 overall best weight: 6.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 04 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 06 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 09 11 ASN 09 133 GLN ** 11 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 106 GLN ** 12 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 9 ASN ** 13 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 82 ASN ** 13 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 15 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 15 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 16 107 ASN 19 36 GLN 19 51 GLN ** 21 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 29 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 31 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 32 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 ASN ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.5159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 165170 Z= 0.215 Angle : 0.600 14.020 246822 Z= 0.307 Chirality : 0.034 0.264 31534 Planarity : 0.005 0.061 13429 Dihedral : 23.656 176.140 82044 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 21.47 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.99 % Favored : 90.70 % Rotamer: Outliers : 5.73 % Allowed : 21.46 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.11), residues: 6159 helix: -0.14 (0.12), residues: 1954 sheet: -1.56 (0.15), residues: 1078 loop : -1.79 (0.11), residues: 3127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP P 60 HIS 0.018 0.001 HIS D 197 PHE 0.035 0.002 PHE C 129 TYR 0.025 0.002 TYR20 83 ARG 0.009 0.001 ARG07 177 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12318 Ramachandran restraints generated. 6159 Oldfield, 0 Emsley, 6159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12318 Ramachandran restraints generated. 6159 Oldfield, 0 Emsley, 6159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1365 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 293 poor density : 1072 time to evaluate : 6.658 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: 04 71 ASP cc_start: 0.8773 (m-30) cc_final: 0.8333 (m-30) REVERT: 04 131 MET cc_start: 0.9721 (mtp) cc_final: 0.9353 (mpp) REVERT: 04 145 MET cc_start: 0.9516 (mmm) cc_final: 0.9020 (ptt) REVERT: 04 159 THR cc_start: 0.9469 (OUTLIER) cc_final: 0.9144 (p) REVERT: 05 101 PHE cc_start: 0.9044 (m-10) cc_final: 0.8780 (m-80) REVERT: 05 200 ASP cc_start: 0.9096 (m-30) cc_final: 0.8814 (m-30) REVERT: 06 9 GLN cc_start: 0.9275 (mt0) cc_final: 0.8994 (tm-30) REVERT: 06 94 GLN cc_start: 0.9206 (pt0) cc_final: 0.8880 (pt0) REVERT: 06 100 MET cc_start: 0.9401 (ptm) cc_final: 0.9200 (ptp) REVERT: 07 95 MET cc_start: 0.9355 (ttp) cc_final: 0.8985 (ttp) REVERT: 07 156 THR cc_start: 0.9139 (m) cc_final: 0.8781 (p) REVERT: 08 74 MET cc_start: 0.8494 (tpp) cc_final: 0.8193 (tpp) REVERT: 08 123 GLU cc_start: 0.9232 (mm-30) cc_final: 0.8862 (mp0) REVERT: 08 127 GLN cc_start: 0.7375 (tp-100) cc_final: 0.7155 (tp40) REVERT: 09 33 GLN cc_start: 0.9356 (mt0) cc_final: 0.9016 (tt0) REVERT: 09 43 ASN cc_start: 0.8974 (t0) cc_final: 0.8593 (t0) REVERT: 09 89 LYS cc_start: 0.8290 (mmmm) cc_final: 0.7178 (pttm) REVERT: 09 128 HIS cc_start: 0.7016 (m-70) cc_final: 0.6561 (m-70) REVERT: 09 141 LYS cc_start: 0.9010 (mttt) cc_final: 0.8580 (mmtt) REVERT: 10 96 PHE cc_start: 0.5068 (t80) cc_final: 0.4654 (t80) REVERT: 10 99 PHE cc_start: 0.6277 (OUTLIER) cc_final: 0.5699 (m-10) REVERT: 11 16 MET cc_start: 0.6901 (mmp) cc_final: 0.6691 (ptm) REVERT: 11 116 MET cc_start: 0.1806 (tpt) cc_final: 0.1449 (tpt) REVERT: 12 14 ASP cc_start: 0.8399 (t0) cc_final: 0.8197 (t0) REVERT: 12 31 GLU cc_start: 0.9104 (tp30) cc_final: 0.8858 (tp30) REVERT: 12 35 ARG cc_start: 0.9701 (mmt180) cc_final: 0.9431 (mmt-90) REVERT: 12 75 TYR cc_start: 0.9424 (m-10) cc_final: 0.9130 (m-10) REVERT: 12 86 GLN cc_start: 0.9342 (pt0) cc_final: 0.8449 (pp30) REVERT: 12 98 GLU cc_start: 0.8948 (mt-10) cc_final: 0.8305 (mt-10) REVERT: 12 99 ARG cc_start: 0.9426 (mmm160) cc_final: 0.9074 (mmp80) REVERT: 12 108 MET cc_start: 0.9121 (tpp) cc_final: 0.8898 (tpp) REVERT: 12 118 MET cc_start: 0.9406 (ptp) cc_final: 0.9048 (mtm) REVERT: 12 131 ASN cc_start: 0.9195 (p0) cc_final: 0.8819 (p0) REVERT: 13 4 GLU cc_start: 0.9529 (mm-30) cc_final: 0.9315 (mm-30) REVERT: 13 7 MET cc_start: 0.9241 (mmp) cc_final: 0.8959 (mmp) REVERT: 13 20 MET cc_start: 0.9269 (ttt) cc_final: 0.8986 (ttm) REVERT: 13 73 ASP cc_start: 0.9100 (p0) cc_final: 0.8669 (p0) REVERT: 13 100 PHE cc_start: 0.8953 (m-10) cc_final: 0.8726 (m-10) REVERT: 14 38 GLN cc_start: 0.9070 (tt0) cc_final: 0.8739 (tt0) REVERT: 14 76 GLU cc_start: 0.8896 (pt0) cc_final: 0.8571 (mt-10) REVERT: 14 104 GLN cc_start: 0.9231 (mm-40) cc_final: 0.8918 (mm110) REVERT: 15 1 MET cc_start: 0.6024 (tpt) cc_final: 0.5813 (tpt) REVERT: 15 2 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8768 (tp) REVERT: 15 10 ARG cc_start: 0.9587 (ptm160) cc_final: 0.8972 (mmp80) REVERT: 15 45 GLN cc_start: 0.9593 (mt0) cc_final: 0.9204 (mt0) REVERT: 15 75 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8403 (mm-30) REVERT: 15 82 MET cc_start: 0.9364 (mmm) cc_final: 0.8946 (mmm) REVERT: 15 103 TYR cc_start: 0.9007 (m-80) cc_final: 0.8770 (m-80) REVERT: 15 119 LEU cc_start: 0.9441 (mt) cc_final: 0.9136 (pp) REVERT: 15 136 MET cc_start: 0.8970 (ptt) cc_final: 0.8563 (ppp) REVERT: 16 1 MET cc_start: 0.9366 (ptp) cc_final: 0.9014 (mtm) REVERT: 16 27 SER cc_start: 0.9396 (m) cc_final: 0.9033 (p) REVERT: 16 49 GLU cc_start: 0.9057 (mt-10) cc_final: 0.8233 (mp0) REVERT: 17 36 TYR cc_start: 0.8919 (m-10) cc_final: 0.8496 (m-10) REVERT: 17 43 ASN cc_start: 0.9001 (p0) cc_final: 0.7975 (p0) REVERT: 17 45 SER cc_start: 0.9077 (t) cc_final: 0.8731 (p) REVERT: 17 46 GLU cc_start: 0.9331 (pt0) cc_final: 0.9040 (pm20) REVERT: 17 76 LYS cc_start: 0.9716 (ttpt) cc_final: 0.9382 (tppt) REVERT: 17 80 GLU cc_start: 0.9451 (mt-10) cc_final: 0.8977 (mt-10) REVERT: 17 92 PHE cc_start: 0.8887 (t80) cc_final: 0.8312 (t80) REVERT: 17 104 GLN cc_start: 0.9710 (tt0) cc_final: 0.9356 (tp-100) REVERT: 17 108 ASP cc_start: 0.9409 (m-30) cc_final: 0.8870 (m-30) REVERT: 17 112 GLU cc_start: 0.9117 (pp20) cc_final: 0.8765 (pp20) REVERT: 18 6 GLN cc_start: 0.8783 (mt0) cc_final: 0.8541 (mp10) REVERT: 18 12 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.7603 (mmm) REVERT: 18 51 ASN cc_start: 0.8838 (OUTLIER) cc_final: 0.8228 (p0) REVERT: 18 83 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8455 (mm) REVERT: 18 105 LYS cc_start: 0.9029 (mmmt) cc_final: 0.8430 (mmtm) REVERT: 19 88 GLU cc_start: 0.9066 (mp0) cc_final: 0.8832 (mp0) REVERT: 20 10 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8410 (mttm) REVERT: 20 13 ARG cc_start: 0.9068 (ttt-90) cc_final: 0.8697 (ttt-90) REVERT: 20 37 GLU cc_start: 0.9251 (mm-30) cc_final: 0.8846 (mm-30) REVERT: 20 40 MET cc_start: 0.9479 (ttp) cc_final: 0.8847 (tmm) REVERT: 21 4 ILE cc_start: 0.9584 (OUTLIER) cc_final: 0.9346 (mt) REVERT: 21 53 SER cc_start: 0.8508 (t) cc_final: 0.8099 (p) REVERT: 21 77 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.7697 (p0) REVERT: 22 8 LEU cc_start: 0.9577 (mt) cc_final: 0.9375 (pp) REVERT: 22 69 ARG cc_start: 0.7878 (mmm160) cc_final: 0.7612 (mmm160) REVERT: 24 55 GLU cc_start: 0.9578 (mt-10) cc_final: 0.9075 (mp0) REVERT: 25 20 LYS cc_start: 0.9056 (mptt) cc_final: 0.8113 (tppt) REVERT: 25 37 ARG cc_start: 0.9271 (tpm170) cc_final: 0.9063 (tpm170) REVERT: 25 68 LYS cc_start: 0.9330 (mtmt) cc_final: 0.8918 (mttt) REVERT: 26 25 LYS cc_start: 0.9178 (mmtp) cc_final: 0.8684 (mmmm) REVERT: 27 1 MET cc_start: 0.8718 (mmm) cc_final: 0.8298 (mmm) REVERT: 27 30 MET cc_start: 0.9491 (ttp) cc_final: 0.9204 (mmp) REVERT: 27 39 GLN cc_start: 0.9475 (mt0) cc_final: 0.9112 (mp10) REVERT: 29 4 ASP cc_start: 0.9198 (m-30) cc_final: 0.8900 (p0) REVERT: 29 8 LYS cc_start: 0.9202 (mmtp) cc_final: 0.8803 (tmmt) REVERT: 30 11 LYS cc_start: 0.9158 (tppp) cc_final: 0.8825 (tppp) REVERT: 30 36 LYS cc_start: 0.9400 (mmtp) cc_final: 0.9021 (mmmm) REVERT: 31 19 PHE cc_start: 0.8860 (p90) cc_final: 0.8448 (p90) REVERT: 31 35 LEU cc_start: 0.8932 (tp) cc_final: 0.8695 (tp) REVERT: 32 1 MET cc_start: 0.7704 (ptm) cc_final: 0.7320 (ppp) REVERT: 32 2 LYS cc_start: 0.9527 (ttmt) cc_final: 0.8965 (ttpt) REVERT: 32 6 GLN cc_start: 0.9053 (mm110) cc_final: 0.8589 (mp10) REVERT: 32 37 LYS cc_start: 0.9379 (tttt) cc_final: 0.8888 (tptp) REVERT: 34 10 LEU cc_start: 0.9535 (OUTLIER) cc_final: 0.9326 (tp) REVERT: 34 18 LYS cc_start: 0.9506 (tttt) cc_final: 0.9211 (ttpt) REVERT: B 21 TYR cc_start: 0.9407 (m-80) cc_final: 0.9068 (m-80) REVERT: B 26 MET cc_start: 0.9179 (mtp) cc_final: 0.8877 (mtt) REVERT: B 48 MET cc_start: 0.9392 (mtm) cc_final: 0.8978 (ptm) REVERT: B 93 HIS cc_start: 0.9222 (t-90) cc_final: 0.8944 (t-170) REVERT: B 99 MET cc_start: 0.9354 (mtp) cc_final: 0.9089 (mtp) REVERT: B 119 GLN cc_start: 0.9555 (OUTLIER) cc_final: 0.9309 (pt0) REVERT: C 2 GLN cc_start: 0.8300 (pt0) cc_final: 0.7235 (pt0) REVERT: D 50 TYR cc_start: 0.9023 (t80) cc_final: 0.8667 (t80) REVERT: E 12 GLU cc_start: 0.7960 (tt0) cc_final: 0.7635 (tt0) REVERT: E 54 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8473 (tm-30) REVERT: E 67 ARG cc_start: 0.8878 (mmt90) cc_final: 0.8640 (mmt90) REVERT: E 104 ILE cc_start: 0.8904 (mt) cc_final: 0.8593 (mm) REVERT: E 141 ASP cc_start: 0.8999 (t0) cc_final: 0.8680 (t0) REVERT: F 21 MET cc_start: 0.9142 (mtt) cc_final: 0.8862 (mtm) REVERT: F 72 ASP cc_start: 0.9511 (OUTLIER) cc_final: 0.9032 (p0) REVERT: F 78 PHE cc_start: 0.9637 (m-80) cc_final: 0.9018 (m-80) REVERT: F 81 ASN cc_start: 0.9108 (t0) cc_final: 0.8823 (t0) REVERT: G 139 ASP cc_start: 0.9425 (m-30) cc_final: 0.9025 (t0) REVERT: H 26 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8336 (ppp) REVERT: H 41 GLU cc_start: 0.9444 (tm-30) cc_final: 0.9121 (pp20) REVERT: H 48 PHE cc_start: 0.8915 (p90) cc_final: 0.8577 (p90) REVERT: H 90 GLU cc_start: 0.9465 (tt0) cc_final: 0.9248 (tt0) REVERT: H 110 MET cc_start: 0.9111 (ptp) cc_final: 0.8752 (mpp) REVERT: H 112 ASP cc_start: 0.9434 (p0) cc_final: 0.8771 (t0) REVERT: I 45 MET cc_start: 0.9665 (ppp) cc_final: 0.9298 (ppp) REVERT: I 96 GLU cc_start: 0.9033 (mp0) cc_final: 0.8832 (mp0) REVERT: I 106 ASP cc_start: 0.8850 (t70) cc_final: 0.8430 (t0) REVERT: J 59 LYS cc_start: 0.9157 (tttm) cc_final: 0.8628 (ttmt) REVERT: J 63 ASP cc_start: 0.8486 (t0) cc_final: 0.8054 (t0) REVERT: J 65 TYR cc_start: 0.8555 (m-80) cc_final: 0.8280 (m-80) REVERT: J 87 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8836 (mt) REVERT: K 37 GLN cc_start: 0.9507 (mp10) cc_final: 0.9264 (mp10) REVERT: K 39 ASN cc_start: 0.9086 (m-40) cc_final: 0.8722 (t0) REVERT: L 19 ASN cc_start: 0.9429 (m-40) cc_final: 0.9124 (t0) REVERT: M 6 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8302 (mm) REVERT: N 25 GLU cc_start: 0.9174 (pt0) cc_final: 0.8506 (tm-30) REVERT: O 13 GLU cc_start: 0.9632 (tt0) cc_final: 0.9297 (pt0) REVERT: O 27 GLN cc_start: 0.9128 (OUTLIER) cc_final: 0.8712 (mp10) REVERT: O 88 ARG cc_start: 0.8048 (tpp-160) cc_final: 0.6885 (mmt-90) REVERT: P 6 LEU cc_start: 0.8445 (tp) cc_final: 0.8182 (tp) REVERT: Q 42 LYS cc_start: 0.9102 (mttt) cc_final: 0.8803 (mtmm) REVERT: Q 51 GLU cc_start: 0.9150 (pt0) cc_final: 0.8908 (pm20) REVERT: R 28 LEU cc_start: 0.9635 (mm) cc_final: 0.9378 (mt) REVERT: R 47 ARG cc_start: 0.9528 (mmm160) cc_final: 0.8874 (mpp-170) REVERT: R 60 ARG cc_start: 0.9476 (mpp80) cc_final: 0.9054 (mtm-85) REVERT: S 20 LYS cc_start: 0.9641 (mtmm) cc_final: 0.9244 (pttt) REVERT: T 26 MET cc_start: 0.9160 (ttp) cc_final: 0.8636 (tpp) REVERT: T 53 MET cc_start: 0.9481 (ppp) cc_final: 0.9195 (ppp) REVERT: U 18 PHE cc_start: 0.9026 (OUTLIER) cc_final: 0.8338 (t80) REVERT: U 30 GLU cc_start: 0.9610 (mm-30) cc_final: 0.9400 (mm-30) REVERT: 03 25 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8071 (mt-10) REVERT: Z 7 GLN cc_start: 0.9242 (tt0) cc_final: 0.8977 (tp40) REVERT: Z 59 GLU cc_start: 0.6846 (mm-30) cc_final: 0.6541 (pm20) REVERT: Z 100 LYS cc_start: 0.4092 (OUTLIER) cc_final: 0.3810 (tptp) outliers start: 293 outliers final: 216 residues processed: 1247 average time/residue: 1.2083 time to fit residues: 2630.9898 Evaluate side-chains 1248 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 1014 time to evaluate : 5.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 63 ILE Chi-restraints excluded: chain 04 residue 159 THR Chi-restraints excluded: chain 04 residue 163 ILE Chi-restraints excluded: chain 04 residue 215 VAL Chi-restraints excluded: chain 04 residue 227 VAL Chi-restraints excluded: chain 05 residue 2 ILE Chi-restraints excluded: chain 05 residue 103 ASP Chi-restraints excluded: chain 05 residue 112 THR Chi-restraints excluded: chain 05 residue 126 ASN Chi-restraints excluded: chain 05 residue 137 SER Chi-restraints excluded: chain 05 residue 146 ILE Chi-restraints excluded: chain 05 residue 175 LEU Chi-restraints excluded: chain 05 residue 177 VAL Chi-restraints excluded: chain 05 residue 201 LEU Chi-restraints excluded: chain 06 residue 73 ILE Chi-restraints excluded: chain 06 residue 148 ILE Chi-restraints excluded: chain 06 residue 149 ILE Chi-restraints excluded: chain 06 residue 164 LEU Chi-restraints excluded: chain 06 residue 175 ILE Chi-restraints excluded: chain 07 residue 9 ASP Chi-restraints excluded: chain 07 residue 46 LYS Chi-restraints excluded: chain 07 residue 65 LEU Chi-restraints excluded: chain 07 residue 86 CYS Chi-restraints excluded: chain 07 residue 112 ASP Chi-restraints excluded: chain 07 residue 135 ILE Chi-restraints excluded: chain 07 residue 148 VAL Chi-restraints excluded: chain 07 residue 157 THR Chi-restraints excluded: chain 07 residue 161 SER Chi-restraints excluded: chain 07 residue 177 ARG Chi-restraints excluded: chain 08 residue 9 VAL Chi-restraints excluded: chain 08 residue 10 VAL Chi-restraints excluded: chain 08 residue 154 GLU Chi-restraints excluded: chain 08 residue 167 VAL Chi-restraints excluded: chain 09 residue 6 LEU Chi-restraints excluded: chain 09 residue 68 ARG Chi-restraints excluded: chain 09 residue 77 THR Chi-restraints excluded: chain 09 residue 110 VAL Chi-restraints excluded: chain 10 residue 27 VAL Chi-restraints excluded: chain 10 residue 99 PHE Chi-restraints excluded: chain 10 residue 123 ILE Chi-restraints excluded: chain 11 residue 7 TYR Chi-restraints excluded: chain 11 residue 27 LEU Chi-restraints excluded: chain 11 residue 58 ILE Chi-restraints excluded: chain 11 residue 70 THR Chi-restraints excluded: chain 12 residue 25 LEU Chi-restraints excluded: chain 12 residue 52 ASP Chi-restraints excluded: chain 12 residue 57 LEU Chi-restraints excluded: chain 12 residue 81 ILE Chi-restraints excluded: chain 12 residue 84 ILE Chi-restraints excluded: chain 12 residue 139 VAL Chi-restraints excluded: chain 13 residue 1 MET Chi-restraints excluded: chain 13 residue 12 ASP Chi-restraints excluded: chain 13 residue 25 LEU Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 39 ILE Chi-restraints excluded: chain 13 residue 58 LEU Chi-restraints excluded: chain 13 residue 65 THR Chi-restraints excluded: chain 13 residue 80 ASP Chi-restraints excluded: chain 13 residue 104 THR Chi-restraints excluded: chain 14 residue 35 HIS Chi-restraints excluded: chain 14 residue 89 VAL Chi-restraints excluded: chain 14 residue 91 ASP Chi-restraints excluded: chain 14 residue 103 ILE Chi-restraints excluded: chain 15 residue 2 LEU Chi-restraints excluded: chain 15 residue 24 THR Chi-restraints excluded: chain 15 residue 30 SER Chi-restraints excluded: chain 15 residue 42 THR Chi-restraints excluded: chain 15 residue 105 MET Chi-restraints excluded: chain 15 residue 129 THR Chi-restraints excluded: chain 15 residue 134 THR Chi-restraints excluded: chain 16 residue 6 SER Chi-restraints excluded: chain 16 residue 21 PHE Chi-restraints excluded: chain 16 residue 32 GLU Chi-restraints excluded: chain 16 residue 37 THR Chi-restraints excluded: chain 16 residue 48 VAL Chi-restraints excluded: chain 17 residue 19 GLN Chi-restraints excluded: chain 17 residue 53 THR Chi-restraints excluded: chain 18 residue 10 GLU Chi-restraints excluded: chain 18 residue 12 MET Chi-restraints excluded: chain 18 residue 24 THR Chi-restraints excluded: chain 18 residue 51 ASN Chi-restraints excluded: chain 18 residue 83 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 51 GLN Chi-restraints excluded: chain 19 residue 89 ILE Chi-restraints excluded: chain 19 residue 90 ASP Chi-restraints excluded: chain 20 residue 10 LYS Chi-restraints excluded: chain 20 residue 27 ILE Chi-restraints excluded: chain 20 residue 43 ASN Chi-restraints excluded: chain 20 residue 53 PHE Chi-restraints excluded: chain 20 residue 58 VAL Chi-restraints excluded: chain 21 residue 4 ILE Chi-restraints excluded: chain 21 residue 62 ASP Chi-restraints excluded: chain 21 residue 67 ASP Chi-restraints excluded: chain 21 residue 77 ASP Chi-restraints excluded: chain 21 residue 109 ASP Chi-restraints excluded: chain 22 residue 11 LEU Chi-restraints excluded: chain 23 residue 8 ASP Chi-restraints excluded: chain 23 residue 17 ASP Chi-restraints excluded: chain 23 residue 27 VAL Chi-restraints excluded: chain 23 residue 33 VAL Chi-restraints excluded: chain 23 residue 48 VAL Chi-restraints excluded: chain 24 residue 4 ILE Chi-restraints excluded: chain 24 residue 24 ASN Chi-restraints excluded: chain 24 residue 42 LEU Chi-restraints excluded: chain 24 residue 66 ASP Chi-restraints excluded: chain 25 residue 7 ARG Chi-restraints excluded: chain 25 residue 8 ASN Chi-restraints excluded: chain 25 residue 17 LEU Chi-restraints excluded: chain 25 residue 60 ASP Chi-restraints excluded: chain 25 residue 63 VAL Chi-restraints excluded: chain 26 residue 3 VAL Chi-restraints excluded: chain 26 residue 6 VAL Chi-restraints excluded: chain 26 residue 41 SER Chi-restraints excluded: chain 26 residue 63 ILE Chi-restraints excluded: chain 27 residue 11 VAL Chi-restraints excluded: chain 27 residue 15 ASN Chi-restraints excluded: chain 27 residue 36 GLN Chi-restraints excluded: chain 27 residue 55 THR Chi-restraints excluded: chain 28 residue 56 VAL Chi-restraints excluded: chain 29 residue 24 ILE Chi-restraints excluded: chain 29 residue 58 ASP Chi-restraints excluded: chain 29 residue 59 ARG Chi-restraints excluded: chain 30 residue 2 VAL Chi-restraints excluded: chain 30 residue 35 GLU Chi-restraints excluded: chain 31 residue 21 THR Chi-restraints excluded: chain 32 residue 44 VAL Chi-restraints excluded: chain 33 residue 6 VAL Chi-restraints excluded: chain 33 residue 49 VAL Chi-restraints excluded: chain 34 residue 1 MET Chi-restraints excluded: chain 34 residue 3 VAL Chi-restraints excluded: chain 34 residue 10 LEU Chi-restraints excluded: chain 34 residue 13 ASN Chi-restraints excluded: chain 34 residue 26 ILE Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 116 PHE Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain H residue 26 MET Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 125 GLN Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 49 PHE Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 51 PHE Chi-restraints excluded: chain K residue 69 CYS Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain K residue 80 ASN Chi-restraints excluded: chain K residue 118 ASN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 74 GLN Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 119 LYS Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 38 ILE Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 67 ASP Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain O residue 27 GLN Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain P residue 29 ASN Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain T residue 20 ASN Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain U residue 13 VAL Chi-restraints excluded: chain U residue 18 PHE Chi-restraints excluded: chain U residue 37 TYR Chi-restraints excluded: chain U residue 41 THR Chi-restraints excluded: chain 03 residue 18 THR Chi-restraints excluded: chain 03 residue 43 ASP Chi-restraints excluded: chain 03 residue 50 ILE Chi-restraints excluded: chain 03 residue 56 ASP Chi-restraints excluded: chain 03 residue 63 THR Chi-restraints excluded: chain 03 residue 218 MET Chi-restraints excluded: chain Z residue 42 LEU Chi-restraints excluded: chain Z residue 97 THR Chi-restraints excluded: chain Z residue 100 LYS Chi-restraints excluded: chain Z residue 162 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1080 random chunks: chunk 1007 optimal weight: 20.0000 chunk 117 optimal weight: 0.0370 chunk 595 optimal weight: 40.0000 chunk 763 optimal weight: 20.0000 chunk 591 optimal weight: 30.0000 chunk 879 optimal weight: 20.0000 chunk 583 optimal weight: 20.0000 chunk 1040 optimal weight: 20.0000 chunk 651 optimal weight: 20.0000 chunk 634 optimal weight: 30.0000 chunk 480 optimal weight: 50.0000 overall best weight: 16.0074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 04 44 ASN ** 04 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 29 ASN ** 09 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 9 ASN ** 13 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 15 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 16 107 ASN 18 51 ASN ** 19 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 23 98 ASN ** 27 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 29 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 31 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 32 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 HIS ** E 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 34 ASN ** O 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.5834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.119 165170 Z= 0.482 Angle : 0.816 13.914 246822 Z= 0.411 Chirality : 0.042 0.371 31534 Planarity : 0.006 0.092 13429 Dihedral : 24.009 178.878 82044 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 35.57 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.63 % Favored : 88.03 % Rotamer: Outliers : 6.84 % Allowed : 22.02 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.10), residues: 6159 helix: -0.64 (0.11), residues: 1951 sheet: -1.68 (0.16), residues: 1026 loop : -2.00 (0.11), residues: 3182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP S 33 HIS 0.015 0.002 HIS O 49 PHE 0.044 0.003 PHE G 61 TYR 0.032 0.003 TYR20 83 ARG 0.016 0.001 ARG I 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12318 Ramachandran restraints generated. 6159 Oldfield, 0 Emsley, 6159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12318 Ramachandran restraints generated. 6159 Oldfield, 0 Emsley, 6159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1331 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 350 poor density : 981 time to evaluate : 8.322 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: 04 145 MET cc_start: 0.9524 (mmm) cc_final: 0.9058 (ptt) REVERT: 04 159 THR cc_start: 0.9497 (OUTLIER) cc_final: 0.8964 (p) REVERT: 04 250 GLN cc_start: 0.9325 (tp-100) cc_final: 0.9069 (tp-100) REVERT: 05 84 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8719 (mm) REVERT: 05 200 ASP cc_start: 0.9109 (m-30) cc_final: 0.8830 (m-30) REVERT: 07 95 MET cc_start: 0.9393 (ttp) cc_final: 0.9071 (ttp) REVERT: 08 29 ASN cc_start: 0.9057 (OUTLIER) cc_final: 0.8573 (m110) REVERT: 08 74 MET cc_start: 0.8601 (tpp) cc_final: 0.8223 (tpp) REVERT: 08 127 GLN cc_start: 0.7397 (tp-100) cc_final: 0.7075 (tp-100) REVERT: 09 17 ASP cc_start: 0.9123 (m-30) cc_final: 0.8898 (m-30) REVERT: 09 58 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8892 (pp) REVERT: 09 128 HIS cc_start: 0.6806 (m-70) cc_final: 0.6387 (m-70) REVERT: 09 141 LYS cc_start: 0.9048 (mttt) cc_final: 0.8609 (mmtt) REVERT: 10 99 PHE cc_start: 0.6466 (OUTLIER) cc_final: 0.5918 (m-10) REVERT: 12 14 ASP cc_start: 0.8797 (t0) cc_final: 0.8585 (t0) REVERT: 12 31 GLU cc_start: 0.9120 (tp30) cc_final: 0.8824 (tp30) REVERT: 12 75 TYR cc_start: 0.9361 (m-10) cc_final: 0.9042 (m-10) REVERT: 12 86 GLN cc_start: 0.9278 (pt0) cc_final: 0.8407 (pp30) REVERT: 12 98 GLU cc_start: 0.8965 (mt-10) cc_final: 0.8369 (mt-10) REVERT: 12 99 ARG cc_start: 0.9408 (mmm160) cc_final: 0.9002 (mmp80) REVERT: 12 108 MET cc_start: 0.9149 (tpp) cc_final: 0.8830 (tpp) REVERT: 12 131 ASN cc_start: 0.9263 (p0) cc_final: 0.8877 (p0) REVERT: 13 1 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8293 (mtp) REVERT: 13 4 GLU cc_start: 0.9500 (mm-30) cc_final: 0.9227 (mm-30) REVERT: 13 7 MET cc_start: 0.9284 (mmp) cc_final: 0.9061 (mmp) REVERT: 13 73 ASP cc_start: 0.9072 (p0) cc_final: 0.8871 (p0) REVERT: 13 100 PHE cc_start: 0.8924 (m-10) cc_final: 0.8691 (m-10) REVERT: 14 38 GLN cc_start: 0.9198 (tt0) cc_final: 0.8964 (tt0) REVERT: 14 76 GLU cc_start: 0.8921 (pt0) cc_final: 0.8565 (mt-10) REVERT: 14 104 GLN cc_start: 0.9299 (mm-40) cc_final: 0.9074 (mm110) REVERT: 15 2 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8620 (tp) REVERT: 15 10 ARG cc_start: 0.9621 (ptm160) cc_final: 0.9028 (mmp80) REVERT: 15 45 GLN cc_start: 0.9635 (mt0) cc_final: 0.9323 (mt0) REVERT: 15 68 PHE cc_start: 0.7996 (t80) cc_final: 0.7785 (t80) REVERT: 15 75 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8424 (mm-30) REVERT: 15 82 MET cc_start: 0.9343 (mmm) cc_final: 0.9008 (mmm) REVERT: 15 136 MET cc_start: 0.8909 (ptt) cc_final: 0.8429 (ppp) REVERT: 16 27 SER cc_start: 0.9443 (m) cc_final: 0.9016 (p) REVERT: 16 49 GLU cc_start: 0.9099 (mt-10) cc_final: 0.8251 (mp0) REVERT: 17 43 ASN cc_start: 0.8893 (p0) cc_final: 0.7533 (p0) REVERT: 17 45 SER cc_start: 0.9106 (t) cc_final: 0.8666 (m) REVERT: 17 46 GLU cc_start: 0.9260 (pt0) cc_final: 0.8759 (pm20) REVERT: 17 76 LYS cc_start: 0.9731 (ttpt) cc_final: 0.9515 (mtpp) REVERT: 17 80 GLU cc_start: 0.9483 (mt-10) cc_final: 0.9065 (mt-10) REVERT: 17 92 PHE cc_start: 0.8958 (t80) cc_final: 0.8322 (t80) REVERT: 17 112 GLU cc_start: 0.9115 (pp20) cc_final: 0.8880 (pp20) REVERT: 18 12 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.7607 (mmm) REVERT: 18 83 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8594 (mm) REVERT: 18 105 LYS cc_start: 0.9115 (mmmt) cc_final: 0.8655 (mmtm) REVERT: 19 88 GLU cc_start: 0.9036 (mp0) cc_final: 0.8795 (mp0) REVERT: 20 13 ARG cc_start: 0.8934 (ttt-90) cc_final: 0.8728 (ttt-90) REVERT: 20 37 GLU cc_start: 0.9258 (mm-30) cc_final: 0.8798 (mm-30) REVERT: 20 40 MET cc_start: 0.9500 (ttp) cc_final: 0.8967 (tmm) REVERT: 21 53 SER cc_start: 0.8718 (t) cc_final: 0.8269 (p) REVERT: 21 77 ASP cc_start: 0.8375 (OUTLIER) cc_final: 0.7440 (p0) REVERT: 22 69 ARG cc_start: 0.7840 (mmm160) cc_final: 0.7602 (mmm160) REVERT: 24 55 GLU cc_start: 0.9576 (mt-10) cc_final: 0.9126 (mp0) REVERT: 25 20 LYS cc_start: 0.9060 (mptt) cc_final: 0.8369 (tppt) REVERT: 25 68 LYS cc_start: 0.9308 (mtmt) cc_final: 0.8887 (mttt) REVERT: 26 25 LYS cc_start: 0.9257 (mmtp) cc_final: 0.8896 (mmmm) REVERT: 26 70 LEU cc_start: 0.9650 (tp) cc_final: 0.9389 (tp) REVERT: 26 75 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8185 (mp0) REVERT: 27 1 MET cc_start: 0.8778 (mmm) cc_final: 0.8445 (mmm) REVERT: 29 1 MET cc_start: 0.9317 (tpp) cc_final: 0.8790 (tpp) REVERT: 29 8 LYS cc_start: 0.9280 (mmtp) cc_final: 0.8885 (ttpp) REVERT: 30 36 LYS cc_start: 0.9449 (mmtp) cc_final: 0.9048 (mmmm) REVERT: 31 6 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8315 (pm20) REVERT: 31 19 PHE cc_start: 0.8946 (p90) cc_final: 0.8603 (p90) REVERT: 31 20 TYR cc_start: 0.9142 (OUTLIER) cc_final: 0.8454 (m-80) REVERT: 32 1 MET cc_start: 0.7886 (ptm) cc_final: 0.7512 (ppp) REVERT: 32 2 LYS cc_start: 0.9502 (ttmt) cc_final: 0.8900 (ttpp) REVERT: 32 6 GLN cc_start: 0.8962 (mm110) cc_final: 0.8526 (mp10) REVERT: 32 13 ASN cc_start: 0.9339 (m-40) cc_final: 0.8471 (t0) REVERT: 32 37 LYS cc_start: 0.9361 (tttt) cc_final: 0.8816 (tptp) REVERT: 34 10 LEU cc_start: 0.9532 (OUTLIER) cc_final: 0.9319 (tp) REVERT: 34 18 LYS cc_start: 0.9472 (tttt) cc_final: 0.9208 (ttpt) REVERT: 34 23 ILE cc_start: 0.9301 (mp) cc_final: 0.9059 (mt) REVERT: B 21 TYR cc_start: 0.9414 (m-80) cc_final: 0.9071 (m-80) REVERT: B 48 MET cc_start: 0.9392 (mtm) cc_final: 0.8920 (ptm) REVERT: B 91 VAL cc_start: 0.9429 (OUTLIER) cc_final: 0.9129 (m) REVERT: B 93 HIS cc_start: 0.9288 (t-90) cc_final: 0.8977 (t-170) REVERT: B 99 MET cc_start: 0.9337 (mtp) cc_final: 0.9075 (mtp) REVERT: B 119 GLN cc_start: 0.9612 (OUTLIER) cc_final: 0.9299 (pt0) REVERT: B 153 MET cc_start: 0.8431 (tmm) cc_final: 0.7813 (tmm) REVERT: D 47 LEU cc_start: 0.9165 (tp) cc_final: 0.8615 (pp) REVERT: D 131 ILE cc_start: 0.8396 (mt) cc_final: 0.8078 (tt) REVERT: D 147 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8015 (pptt) REVERT: E 54 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8487 (tm-30) REVERT: E 67 ARG cc_start: 0.8915 (mmt90) cc_final: 0.8615 (mmt90) REVERT: E 92 ARG cc_start: 0.9248 (mmp80) cc_final: 0.9014 (mmp80) REVERT: E 141 ASP cc_start: 0.9019 (t0) cc_final: 0.8662 (t0) REVERT: F 74 LEU cc_start: 0.9689 (OUTLIER) cc_final: 0.9385 (tt) REVERT: F 78 PHE cc_start: 0.9681 (m-80) cc_final: 0.9121 (m-80) REVERT: F 81 ASN cc_start: 0.9078 (t0) cc_final: 0.8768 (t0) REVERT: G 139 ASP cc_start: 0.9464 (m-30) cc_final: 0.9033 (t0) REVERT: H 48 PHE cc_start: 0.9002 (p90) cc_final: 0.8801 (p90) REVERT: H 59 GLU cc_start: 0.8767 (pm20) cc_final: 0.8524 (pm20) REVERT: H 110 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8600 (mpp) REVERT: H 112 ASP cc_start: 0.9497 (p0) cc_final: 0.8830 (t0) REVERT: I 45 MET cc_start: 0.9675 (ppp) cc_final: 0.9316 (ppp) REVERT: I 96 GLU cc_start: 0.9096 (mp0) cc_final: 0.8886 (mp0) REVERT: I 106 ASP cc_start: 0.8823 (t70) cc_final: 0.8414 (t0) REVERT: J 46 LYS cc_start: 0.9033 (OUTLIER) cc_final: 0.8507 (mmmm) REVERT: J 59 LYS cc_start: 0.9048 (tttm) cc_final: 0.8508 (ttmt) REVERT: J 63 ASP cc_start: 0.8712 (t0) cc_final: 0.8273 (t0) REVERT: J 65 TYR cc_start: 0.8658 (m-80) cc_final: 0.8349 (m-80) REVERT: J 66 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7868 (tm-30) REVERT: J 87 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8895 (mt) REVERT: K 37 GLN cc_start: 0.9505 (mp10) cc_final: 0.9195 (mp10) REVERT: K 39 ASN cc_start: 0.9130 (m-40) cc_final: 0.8893 (t0) REVERT: K 86 LYS cc_start: 0.9422 (OUTLIER) cc_final: 0.9080 (pptt) REVERT: L 19 ASN cc_start: 0.9460 (m-40) cc_final: 0.9121 (t0) REVERT: N 25 GLU cc_start: 0.9187 (pt0) cc_final: 0.8479 (tm-30) REVERT: O 27 GLN cc_start: 0.9109 (OUTLIER) cc_final: 0.8780 (mp10) REVERT: O 47 LYS cc_start: 0.9517 (mmmm) cc_final: 0.8680 (ttpt) REVERT: P 6 LEU cc_start: 0.8730 (tp) cc_final: 0.8514 (tp) REVERT: Q 42 LYS cc_start: 0.9142 (mttt) cc_final: 0.8931 (mtmm) REVERT: Q 51 GLU cc_start: 0.9059 (pt0) cc_final: 0.8813 (pm20) REVERT: Q 56 ASP cc_start: 0.9137 (p0) cc_final: 0.8756 (p0) REVERT: R 47 ARG cc_start: 0.9545 (mmm160) cc_final: 0.8884 (mpp-170) REVERT: R 60 ARG cc_start: 0.9533 (OUTLIER) cc_final: 0.9312 (mtm-85) REVERT: T 26 MET cc_start: 0.9206 (ttp) cc_final: 0.8672 (tpp) REVERT: T 53 MET cc_start: 0.9512 (ppp) cc_final: 0.9244 (ppp) REVERT: U 36 PHE cc_start: 0.8712 (m-80) cc_final: 0.8496 (m-80) REVERT: 03 25 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7970 (mt-10) REVERT: Z 100 LYS cc_start: 0.3732 (OUTLIER) cc_final: 0.3341 (tptp) outliers start: 350 outliers final: 266 residues processed: 1202 average time/residue: 1.1595 time to fit residues: 2433.6644 Evaluate side-chains 1227 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 291 poor density : 936 time to evaluate : 5.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 63 ILE Chi-restraints excluded: chain 04 residue 159 THR Chi-restraints excluded: chain 04 residue 190 THR Chi-restraints excluded: chain 04 residue 199 HIS Chi-restraints excluded: chain 04 residue 215 VAL Chi-restraints excluded: chain 04 residue 227 VAL Chi-restraints excluded: chain 04 residue 258 SER Chi-restraints excluded: chain 05 residue 2 ILE Chi-restraints excluded: chain 05 residue 84 LEU Chi-restraints excluded: chain 05 residue 103 ASP Chi-restraints excluded: chain 05 residue 126 ASN Chi-restraints excluded: chain 05 residue 145 SER Chi-restraints excluded: chain 05 residue 177 VAL Chi-restraints excluded: chain 05 residue 201 LEU Chi-restraints excluded: chain 06 residue 148 ILE Chi-restraints excluded: chain 06 residue 164 LEU Chi-restraints excluded: chain 06 residue 175 ILE Chi-restraints excluded: chain 06 residue 199 MET Chi-restraints excluded: chain 07 residue 9 ASP Chi-restraints excluded: chain 07 residue 13 LYS Chi-restraints excluded: chain 07 residue 26 GLN Chi-restraints excluded: chain 07 residue 46 LYS Chi-restraints excluded: chain 07 residue 51 ASN Chi-restraints excluded: chain 07 residue 86 CYS Chi-restraints excluded: chain 07 residue 135 ILE Chi-restraints excluded: chain 07 residue 143 ASP Chi-restraints excluded: chain 07 residue 148 VAL Chi-restraints excluded: chain 07 residue 156 THR Chi-restraints excluded: chain 07 residue 157 THR Chi-restraints excluded: chain 07 residue 177 ARG Chi-restraints excluded: chain 08 residue 9 VAL Chi-restraints excluded: chain 08 residue 10 VAL Chi-restraints excluded: chain 08 residue 29 ASN Chi-restraints excluded: chain 08 residue 154 GLU Chi-restraints excluded: chain 08 residue 167 VAL Chi-restraints excluded: chain 09 residue 4 ILE Chi-restraints excluded: chain 09 residue 6 LEU Chi-restraints excluded: chain 09 residue 58 LEU Chi-restraints excluded: chain 09 residue 68 ARG Chi-restraints excluded: chain 09 residue 110 VAL Chi-restraints excluded: chain 10 residue 27 VAL Chi-restraints excluded: chain 10 residue 84 TYR Chi-restraints excluded: chain 10 residue 99 PHE Chi-restraints excluded: chain 10 residue 123 ILE Chi-restraints excluded: chain 11 residue 7 TYR Chi-restraints excluded: chain 11 residue 27 LEU Chi-restraints excluded: chain 11 residue 58 ILE Chi-restraints excluded: chain 11 residue 70 THR Chi-restraints excluded: chain 11 residue 107 GLU Chi-restraints excluded: chain 12 residue 25 LEU Chi-restraints excluded: chain 12 residue 52 ASP Chi-restraints excluded: chain 12 residue 57 LEU Chi-restraints excluded: chain 12 residue 84 ILE Chi-restraints excluded: chain 12 residue 101 ILE Chi-restraints excluded: chain 12 residue 139 VAL Chi-restraints excluded: chain 13 residue 1 MET Chi-restraints excluded: chain 13 residue 12 ASP Chi-restraints excluded: chain 13 residue 25 LEU Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 39 ILE Chi-restraints excluded: chain 13 residue 47 ILE Chi-restraints excluded: chain 13 residue 54 LYS Chi-restraints excluded: chain 13 residue 58 LEU Chi-restraints excluded: chain 13 residue 65 THR Chi-restraints excluded: chain 13 residue 80 ASP Chi-restraints excluded: chain 13 residue 104 THR Chi-restraints excluded: chain 14 residue 35 HIS Chi-restraints excluded: chain 14 residue 89 VAL Chi-restraints excluded: chain 14 residue 91 ASP Chi-restraints excluded: chain 14 residue 103 ILE Chi-restraints excluded: chain 14 residue 120 VAL Chi-restraints excluded: chain 15 residue 2 LEU Chi-restraints excluded: chain 15 residue 24 THR Chi-restraints excluded: chain 15 residue 28 PHE Chi-restraints excluded: chain 15 residue 30 SER Chi-restraints excluded: chain 15 residue 42 THR Chi-restraints excluded: chain 15 residue 93 VAL Chi-restraints excluded: chain 15 residue 105 MET Chi-restraints excluded: chain 15 residue 129 THR Chi-restraints excluded: chain 15 residue 134 THR Chi-restraints excluded: chain 16 residue 6 SER 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 17 residue 19 GLN Chi-restraints excluded: chain 17 residue 53 THR Chi-restraints excluded: chain 17 residue 67 ASN Chi-restraints excluded: chain 17 residue 91 SER Chi-restraints excluded: chain 18 residue 10 GLU Chi-restraints excluded: chain 18 residue 12 MET Chi-restraints excluded: chain 18 residue 51 ASN Chi-restraints excluded: chain 18 residue 83 ILE Chi-restraints excluded: chain 19 residue 8 ILE Chi-restraints excluded: chain 19 residue 16 ILE Chi-restraints excluded: chain 19 residue 28 SER Chi-restraints excluded: chain 19 residue 89 ILE Chi-restraints excluded: chain 19 residue 90 ASP Chi-restraints excluded: chain 19 residue 106 THR Chi-restraints excluded: chain 20 residue 27 ILE Chi-restraints excluded: chain 20 residue 43 ASN Chi-restraints excluded: chain 20 residue 58 VAL Chi-restraints excluded: chain 21 residue 4 ILE Chi-restraints excluded: chain 21 residue 33 LEU Chi-restraints excluded: chain 21 residue 51 LEU Chi-restraints excluded: chain 21 residue 62 ASP Chi-restraints excluded: chain 21 residue 67 ASP Chi-restraints excluded: chain 21 residue 77 ASP Chi-restraints excluded: chain 21 residue 97 LEU Chi-restraints excluded: chain 21 residue 100 THR Chi-restraints excluded: chain 21 residue 109 ASP Chi-restraints excluded: chain 22 residue 11 LEU Chi-restraints excluded: chain 23 residue 8 ASP Chi-restraints excluded: chain 23 residue 27 VAL Chi-restraints excluded: chain 23 residue 33 VAL Chi-restraints excluded: chain 23 residue 64 ILE Chi-restraints excluded: chain 24 residue 3 THR Chi-restraints excluded: chain 24 residue 4 ILE Chi-restraints excluded: chain 24 residue 24 ASN Chi-restraints excluded: chain 24 residue 42 LEU Chi-restraints excluded: chain 24 residue 66 ASP Chi-restraints excluded: chain 25 residue 8 ASN Chi-restraints excluded: chain 25 residue 17 LEU Chi-restraints excluded: chain 25 residue 60 ASP Chi-restraints excluded: chain 25 residue 63 VAL Chi-restraints excluded: chain 26 residue 3 VAL Chi-restraints excluded: chain 26 residue 6 VAL Chi-restraints excluded: chain 26 residue 34 SER Chi-restraints excluded: chain 26 residue 41 SER Chi-restraints excluded: chain 26 residue 46 VAL Chi-restraints excluded: chain 26 residue 60 LYS Chi-restraints excluded: chain 26 residue 63 ILE Chi-restraints excluded: chain 26 residue 75 GLU Chi-restraints excluded: chain 27 residue 11 VAL Chi-restraints excluded: chain 27 residue 15 ASN Chi-restraints excluded: chain 27 residue 36 GLN Chi-restraints excluded: chain 27 residue 50 VAL Chi-restraints excluded: chain 27 residue 55 THR Chi-restraints excluded: chain 28 residue 56 VAL Chi-restraints excluded: chain 29 residue 24 ILE Chi-restraints excluded: chain 29 residue 27 THR Chi-restraints excluded: chain 29 residue 34 LEU Chi-restraints excluded: chain 29 residue 58 ASP Chi-restraints excluded: chain 29 residue 59 ARG Chi-restraints excluded: chain 30 residue 2 VAL Chi-restraints excluded: chain 30 residue 21 LEU Chi-restraints excluded: chain 30 residue 35 GLU Chi-restraints excluded: chain 31 residue 6 GLU Chi-restraints excluded: chain 31 residue 10 LEU Chi-restraints excluded: chain 31 residue 20 TYR Chi-restraints excluded: chain 31 residue 21 THR Chi-restraints excluded: chain 31 residue 23 THR Chi-restraints excluded: chain 31 residue 46 VAL Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 32 residue 44 VAL Chi-restraints excluded: chain 33 residue 6 VAL Chi-restraints excluded: chain 33 residue 49 VAL Chi-restraints excluded: chain 34 residue 1 MET Chi-restraints excluded: chain 34 residue 3 VAL Chi-restraints excluded: chain 34 residue 10 LEU Chi-restraints excluded: chain 34 residue 13 ASN Chi-restraints excluded: chain 34 residue 17 VAL Chi-restraints excluded: chain 34 residue 20 ASP Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 116 PHE Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 26 MET Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 110 MET Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 109 GLN Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 125 GLN Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 49 PHE Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 51 PHE Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 69 CYS Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain K residue 80 ASN Chi-restraints excluded: chain K residue 86 LYS Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 118 ASN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 74 GLN Chi-restraints excluded: chain L residue 87 LYS Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 119 LYS Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 11 HIS Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 38 ILE Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 67 ASP Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain N residue 85 GLU Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 27 GLN Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain P residue 29 ASN Chi-restraints excluded: chain P residue 75 ILE Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 69 THR Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain R residue 60 ARG Chi-restraints excluded: chain S residue 11 ASP Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain T residue 20 ASN Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain U residue 37 TYR Chi-restraints excluded: chain U residue 41 THR Chi-restraints excluded: chain 03 residue 18 THR Chi-restraints excluded: chain 03 residue 43 ASP Chi-restraints excluded: chain 03 residue 50 ILE Chi-restraints excluded: chain 03 residue 56 ASP Chi-restraints excluded: chain 03 residue 63 THR Chi-restraints excluded: chain 03 residue 209 ILE Chi-restraints excluded: chain 03 residue 218 MET Chi-restraints excluded: chain Z residue 42 LEU Chi-restraints excluded: chain Z residue 97 THR Chi-restraints excluded: chain Z residue 100 LYS Chi-restraints excluded: chain Z residue 144 THR Chi-restraints excluded: chain Z residue 162 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1080 random chunks: chunk 643 optimal weight: 10.0000 chunk 415 optimal weight: 9.9990 chunk 621 optimal weight: 20.0000 chunk 313 optimal weight: 20.0000 chunk 204 optimal weight: 10.0000 chunk 201 optimal weight: 5.9990 chunk 661 optimal weight: 10.0000 chunk 709 optimal weight: 20.0000 chunk 514 optimal weight: 20.0000 chunk 97 optimal weight: 20.0000 chunk 818 optimal weight: 10.0000 overall best weight: 9.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 04 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 106 GLN ** 12 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 9 ASN ** 13 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 14 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 15 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 15 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 18 51 ASN ** 20 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 24 75 GLN ** 27 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 29 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 31 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 32 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 HIS ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 75 GLN ** I 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 14 GLN ** K 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.5794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 165170 Z= 0.288 Angle : 0.667 14.955 246822 Z= 0.340 Chirality : 0.037 0.307 31534 Planarity : 0.005 0.061 13429 Dihedral : 23.984 176.801 82044 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 26.10 Ramachandran Plot: Outliers : 0.31 % Allowed : 9.68 % Favored : 90.01 % Rotamer: Outliers : 5.61 % Allowed : 23.96 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.11), residues: 6159 helix: -0.39 (0.11), residues: 1968 sheet: -1.59 (0.16), residues: 1035 loop : -1.88 (0.11), residues: 3156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP P 60 HIS 0.007 0.001 HIS T 67 PHE 0.028 0.002 PHE12 89 TYR 0.030 0.002 TYR F 59 ARG 0.010 0.001 ARG07 177 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12318 Ramachandran restraints generated. 6159 Oldfield, 0 Emsley, 6159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12318 Ramachandran restraints generated. 6159 Oldfield, 0 Emsley, 6159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1297 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 287 poor density : 1010 time to evaluate : 5.866 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: 04 131 MET cc_start: 0.9750 (mtp) cc_final: 0.9360 (mpp) REVERT: 04 145 MET cc_start: 0.9555 (mmm) cc_final: 0.9067 (ptt) REVERT: 04 159 THR cc_start: 0.9470 (OUTLIER) cc_final: 0.9146 (p) REVERT: 05 200 ASP cc_start: 0.9120 (m-30) cc_final: 0.8794 (m-30) REVERT: 06 94 GLN cc_start: 0.9189 (pt0) cc_final: 0.8891 (pt0) REVERT: 07 95 MET cc_start: 0.9370 (ttp) cc_final: 0.9000 (ttp) REVERT: 09 17 ASP cc_start: 0.9082 (m-30) cc_final: 0.8879 (m-30) REVERT: 09 43 ASN cc_start: 0.8871 (t0) cc_final: 0.8487 (t0) REVERT: 09 58 LEU cc_start: 0.9093 (mp) cc_final: 0.8830 (pp) REVERT: 09 89 LYS cc_start: 0.8195 (mmmm) cc_final: 0.7103 (pttm) REVERT: 09 128 HIS cc_start: 0.6803 (m-70) cc_final: 0.6380 (m-70) REVERT: 09 141 LYS cc_start: 0.9061 (mttt) cc_final: 0.8607 (mmtt) REVERT: 10 1 MET cc_start: 0.6832 (mpp) cc_final: 0.6520 (mpp) REVERT: 10 99 PHE cc_start: 0.6448 (OUTLIER) cc_final: 0.5882 (m-10) REVERT: 12 31 GLU cc_start: 0.9145 (tp30) cc_final: 0.8862 (tp30) REVERT: 12 75 TYR cc_start: 0.9410 (m-10) cc_final: 0.9100 (m-10) REVERT: 12 86 GLN cc_start: 0.9321 (pt0) cc_final: 0.8404 (pp30) REVERT: 12 98 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8343 (mt-10) REVERT: 12 99 ARG cc_start: 0.9405 (mmm160) cc_final: 0.9002 (mmp80) REVERT: 12 118 MET cc_start: 0.9397 (OUTLIER) cc_final: 0.8987 (mtm) REVERT: 12 131 ASN cc_start: 0.9249 (p0) cc_final: 0.8873 (p0) REVERT: 13 1 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8262 (mtp) REVERT: 13 4 GLU cc_start: 0.9428 (mm-30) cc_final: 0.9194 (mm-30) REVERT: 13 73 ASP cc_start: 0.9079 (p0) cc_final: 0.8801 (p0) REVERT: 13 100 PHE cc_start: 0.8931 (m-10) cc_final: 0.8706 (m-10) REVERT: 14 38 GLN cc_start: 0.9153 (tt0) cc_final: 0.8910 (tt0) REVERT: 14 76 GLU cc_start: 0.8899 (pt0) cc_final: 0.8525 (mt-10) REVERT: 14 104 GLN cc_start: 0.9351 (mm-40) cc_final: 0.9020 (mm110) REVERT: 15 2 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8650 (tp) REVERT: 15 10 ARG cc_start: 0.9621 (ptm160) cc_final: 0.9009 (mmp80) REVERT: 15 45 GLN cc_start: 0.9614 (mt0) cc_final: 0.9284 (mt0) REVERT: 15 75 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8456 (mm-30) REVERT: 15 82 MET cc_start: 0.9307 (mmm) cc_final: 0.8933 (mmm) REVERT: 15 136 MET cc_start: 0.8921 (ptt) cc_final: 0.8468 (ppp) REVERT: 16 27 SER cc_start: 0.9380 (m) cc_final: 0.8974 (p) REVERT: 16 49 GLU cc_start: 0.9060 (mt-10) cc_final: 0.8213 (mp0) REVERT: 17 43 ASN cc_start: 0.8911 (p0) cc_final: 0.7858 (p0) REVERT: 17 45 SER cc_start: 0.9142 (t) cc_final: 0.8821 (p) REVERT: 17 46 GLU cc_start: 0.9319 (pt0) cc_final: 0.9022 (pm20) REVERT: 17 76 LYS cc_start: 0.9728 (ttpt) cc_final: 0.9407 (tppt) REVERT: 17 80 GLU cc_start: 0.9484 (mt-10) cc_final: 0.9031 (mt-10) REVERT: 17 92 PHE cc_start: 0.8906 (t80) cc_final: 0.8311 (t80) REVERT: 17 112 GLU cc_start: 0.9091 (pp20) cc_final: 0.8774 (pp20) REVERT: 18 51 ASN cc_start: 0.9094 (OUTLIER) cc_final: 0.8797 (p0) REVERT: 18 83 ILE cc_start: 0.8950 (OUTLIER) cc_final: 0.8361 (mm) REVERT: 18 105 LYS cc_start: 0.9055 (mmmt) cc_final: 0.8575 (mmtm) REVERT: 19 51 GLN cc_start: 0.8894 (mm110) cc_final: 0.8483 (mm-40) REVERT: 19 58 GLN cc_start: 0.9647 (tt0) cc_final: 0.9090 (tp40) REVERT: 19 88 GLU cc_start: 0.9067 (mp0) cc_final: 0.8788 (mp0) REVERT: 20 13 ARG cc_start: 0.8894 (ttt-90) cc_final: 0.8668 (ttt-90) REVERT: 20 16 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8707 (mm-30) REVERT: 20 37 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8843 (mm-30) REVERT: 20 40 MET cc_start: 0.9482 (ttp) cc_final: 0.8867 (tmm) REVERT: 21 53 SER cc_start: 0.8631 (t) cc_final: 0.8202 (p) REVERT: 21 77 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.7432 (p0) REVERT: 21 78 GLU cc_start: 0.8665 (pm20) cc_final: 0.8377 (pm20) REVERT: 22 69 ARG cc_start: 0.7909 (mmm160) cc_final: 0.7647 (mmm160) REVERT: 24 55 GLU cc_start: 0.9578 (mt-10) cc_final: 0.9125 (mp0) REVERT: 25 37 ARG cc_start: 0.9246 (tpm170) cc_final: 0.8987 (tpm170) REVERT: 25 68 LYS cc_start: 0.9261 (mtmt) cc_final: 0.8844 (mttt) REVERT: 26 25 LYS cc_start: 0.9201 (mmtp) cc_final: 0.8755 (mmmm) REVERT: 26 67 LEU cc_start: 0.9769 (mm) cc_final: 0.9496 (mm) REVERT: 26 70 LEU cc_start: 0.9627 (tp) cc_final: 0.9356 (tp) REVERT: 26 75 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8146 (mp0) REVERT: 27 1 MET cc_start: 0.8714 (mmm) cc_final: 0.8324 (mmm) REVERT: 27 30 MET cc_start: 0.9522 (mtp) cc_final: 0.9218 (mmp) REVERT: 29 1 MET cc_start: 0.9185 (tpp) cc_final: 0.8509 (tpp) REVERT: 29 8 LYS cc_start: 0.9273 (mmtp) cc_final: 0.8885 (ttpp) REVERT: 30 36 LYS cc_start: 0.9458 (mmtp) cc_final: 0.9057 (mmmm) REVERT: 31 6 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8279 (pm20) REVERT: 31 19 PHE cc_start: 0.8938 (p90) cc_final: 0.8625 (p90) REVERT: 32 1 MET cc_start: 0.7754 (ptm) cc_final: 0.7479 (ppp) REVERT: 32 2 LYS cc_start: 0.9511 (ttmt) cc_final: 0.8924 (tttm) REVERT: 32 6 GLN cc_start: 0.9021 (mm110) cc_final: 0.8495 (mp10) REVERT: 32 37 LYS cc_start: 0.9339 (tttt) cc_final: 0.8918 (tptp) REVERT: 34 1 MET cc_start: 0.9406 (OUTLIER) cc_final: 0.8581 (mmm) REVERT: 34 10 LEU cc_start: 0.9533 (OUTLIER) cc_final: 0.9280 (tp) REVERT: 34 18 LYS cc_start: 0.9470 (tttt) cc_final: 0.9201 (ttpt) REVERT: 34 23 ILE cc_start: 0.9317 (mp) cc_final: 0.9091 (mt) REVERT: B 21 TYR cc_start: 0.9396 (m-80) cc_final: 0.9054 (m-80) REVERT: B 48 MET cc_start: 0.9403 (mtm) cc_final: 0.9122 (mtm) REVERT: B 91 VAL cc_start: 0.9382 (OUTLIER) cc_final: 0.9080 (m) REVERT: B 93 HIS cc_start: 0.9279 (t-90) cc_final: 0.8976 (t-170) REVERT: B 99 MET cc_start: 0.9340 (mtp) cc_final: 0.9064 (mtp) REVERT: B 119 GLN cc_start: 0.9602 (OUTLIER) cc_final: 0.9299 (pt0) REVERT: B 153 MET cc_start: 0.8434 (mmm) cc_final: 0.7793 (tmm) REVERT: C 61 LYS cc_start: 0.9283 (tptp) cc_final: 0.8871 (ptpp) REVERT: D 47 LEU cc_start: 0.9092 (tp) cc_final: 0.8593 (pp) REVERT: D 131 ILE cc_start: 0.8341 (mt) cc_final: 0.8039 (tt) REVERT: E 54 GLU cc_start: 0.8843 (tm-30) cc_final: 0.8515 (tm-30) REVERT: E 67 ARG cc_start: 0.8860 (mmt90) cc_final: 0.8635 (mmt90) REVERT: E 104 ILE cc_start: 0.9040 (mt) cc_final: 0.8708 (mm) REVERT: E 141 ASP cc_start: 0.9021 (t0) cc_final: 0.8655 (t0) REVERT: F 2 ARG cc_start: 0.9266 (OUTLIER) cc_final: 0.8425 (mmm-85) REVERT: F 72 ASP cc_start: 0.9546 (OUTLIER) cc_final: 0.9095 (p0) REVERT: F 78 PHE cc_start: 0.9665 (m-80) cc_final: 0.9027 (m-80) REVERT: F 81 ASN cc_start: 0.9057 (t0) cc_final: 0.8764 (t0) REVERT: G 139 ASP cc_start: 0.9434 (m-30) cc_final: 0.8909 (t0) REVERT: G 142 ARG cc_start: 0.9632 (mmt90) cc_final: 0.9213 (ttm170) REVERT: H 41 GLU cc_start: 0.9408 (tm-30) cc_final: 0.9119 (pp20) REVERT: H 48 PHE cc_start: 0.8961 (p90) cc_final: 0.8404 (p90) REVERT: H 110 MET cc_start: 0.8986 (ptp) cc_final: 0.8626 (mpp) REVERT: H 112 ASP cc_start: 0.9445 (p0) cc_final: 0.8763 (t0) REVERT: I 45 MET cc_start: 0.9678 (ppp) cc_final: 0.9329 (ppp) REVERT: I 96 GLU cc_start: 0.9066 (mp0) cc_final: 0.8860 (mp0) REVERT: I 106 ASP cc_start: 0.8787 (t70) cc_final: 0.8365 (t0) REVERT: J 46 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8535 (mmmm) REVERT: J 59 LYS cc_start: 0.9042 (tttm) cc_final: 0.8454 (ttmt) REVERT: J 63 ASP cc_start: 0.8650 (t0) cc_final: 0.8187 (t0) REVERT: J 65 TYR cc_start: 0.8520 (m-80) cc_final: 0.8244 (m-80) REVERT: J 66 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7876 (tm-30) REVERT: J 87 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8890 (mt) REVERT: K 37 GLN cc_start: 0.9555 (mp10) cc_final: 0.9262 (mp10) REVERT: K 86 LYS cc_start: 0.9395 (OUTLIER) cc_final: 0.9059 (pptt) REVERT: L 19 ASN cc_start: 0.9426 (m-40) cc_final: 0.9138 (t0) REVERT: N 25 GLU cc_start: 0.9185 (pt0) cc_final: 0.8477 (tm-30) REVERT: N 91 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8712 (mm-30) REVERT: O 27 GLN cc_start: 0.9060 (OUTLIER) cc_final: 0.8680 (mp10) REVERT: O 47 LYS cc_start: 0.9491 (mmmm) cc_final: 0.8733 (ttpt) REVERT: O 88 ARG cc_start: 0.8217 (tpp-160) cc_final: 0.7059 (mmp80) REVERT: P 6 LEU cc_start: 0.8716 (tp) cc_final: 0.8468 (tp) REVERT: Q 16 MET cc_start: 0.7934 (tpp) cc_final: 0.7262 (mmm) REVERT: Q 42 LYS cc_start: 0.9104 (mttt) cc_final: 0.8805 (mtmm) REVERT: Q 51 GLU cc_start: 0.9044 (pt0) cc_final: 0.8808 (pm20) REVERT: R 28 LEU cc_start: 0.9669 (mm) cc_final: 0.9381 (mt) REVERT: R 37 LYS cc_start: 0.9475 (mmmm) cc_final: 0.9118 (tppt) REVERT: R 47 ARG cc_start: 0.9533 (mmm160) cc_final: 0.8886 (mpp-170) REVERT: R 60 ARG cc_start: 0.9405 (mpp80) cc_final: 0.8991 (mtm-85) REVERT: S 20 LYS cc_start: 0.9643 (mtmm) cc_final: 0.9248 (pttt) REVERT: T 26 MET cc_start: 0.9184 (ttp) cc_final: 0.8617 (tpp) REVERT: T 53 MET cc_start: 0.9521 (ppp) cc_final: 0.9245 (ppp) REVERT: U 18 PHE cc_start: 0.9061 (OUTLIER) cc_final: 0.8465 (t80) REVERT: 03 25 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7975 (mt-10) REVERT: Z 91 ARG cc_start: 0.7819 (mmp-170) cc_final: 0.6616 (pmt-80) REVERT: Z 100 LYS cc_start: 0.3747 (OUTLIER) cc_final: 0.3291 (tptp) outliers start: 287 outliers final: 233 residues processed: 1191 average time/residue: 1.1369 time to fit residues: 2368.4758 Evaluate side-chains 1210 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 254 poor density : 956 time to evaluate : 5.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 63 ILE Chi-restraints excluded: chain 04 residue 159 THR Chi-restraints excluded: chain 04 residue 190 THR Chi-restraints excluded: chain 04 residue 199 HIS Chi-restraints excluded: chain 04 residue 215 VAL Chi-restraints excluded: chain 04 residue 227 VAL Chi-restraints excluded: chain 04 residue 258 SER Chi-restraints excluded: chain 05 residue 2 ILE Chi-restraints excluded: chain 05 residue 103 ASP Chi-restraints excluded: chain 05 residue 126 ASN Chi-restraints excluded: chain 05 residue 145 SER Chi-restraints excluded: chain 05 residue 177 VAL Chi-restraints excluded: chain 05 residue 201 LEU Chi-restraints excluded: chain 06 residue 73 ILE Chi-restraints excluded: chain 06 residue 148 ILE Chi-restraints excluded: chain 06 residue 149 ILE Chi-restraints excluded: chain 06 residue 164 LEU Chi-restraints excluded: chain 06 residue 175 ILE Chi-restraints excluded: chain 06 residue 199 MET Chi-restraints excluded: chain 07 residue 9 ASP Chi-restraints excluded: chain 07 residue 46 LYS Chi-restraints excluded: chain 07 residue 51 ASN Chi-restraints excluded: chain 07 residue 86 CYS Chi-restraints excluded: chain 07 residue 135 ILE Chi-restraints excluded: chain 07 residue 148 VAL Chi-restraints excluded: chain 07 residue 156 THR Chi-restraints excluded: chain 07 residue 157 THR Chi-restraints excluded: chain 07 residue 177 ARG Chi-restraints excluded: chain 08 residue 9 VAL Chi-restraints excluded: chain 08 residue 10 VAL Chi-restraints excluded: chain 08 residue 113 ASP Chi-restraints excluded: chain 08 residue 154 GLU Chi-restraints excluded: chain 08 residue 167 VAL Chi-restraints excluded: chain 09 residue 4 ILE Chi-restraints excluded: chain 09 residue 6 LEU Chi-restraints excluded: chain 09 residue 68 ARG Chi-restraints excluded: chain 09 residue 110 VAL Chi-restraints excluded: chain 10 residue 27 VAL Chi-restraints excluded: chain 10 residue 84 TYR Chi-restraints excluded: chain 10 residue 99 PHE Chi-restraints excluded: chain 10 residue 123 ILE Chi-restraints excluded: chain 11 residue 7 TYR Chi-restraints excluded: chain 11 residue 27 LEU Chi-restraints excluded: chain 11 residue 58 ILE Chi-restraints excluded: chain 11 residue 70 THR Chi-restraints excluded: chain 11 residue 107 GLU Chi-restraints excluded: chain 12 residue 25 LEU Chi-restraints excluded: chain 12 residue 52 ASP Chi-restraints excluded: chain 12 residue 57 LEU Chi-restraints excluded: chain 12 residue 81 ILE Chi-restraints excluded: chain 12 residue 84 ILE Chi-restraints excluded: chain 12 residue 118 MET Chi-restraints excluded: chain 12 residue 139 VAL Chi-restraints excluded: chain 13 residue 1 MET Chi-restraints excluded: chain 13 residue 12 ASP Chi-restraints excluded: chain 13 residue 25 LEU Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 39 ILE Chi-restraints excluded: chain 13 residue 47 ILE Chi-restraints excluded: chain 13 residue 58 LEU Chi-restraints excluded: chain 13 residue 65 THR Chi-restraints excluded: chain 13 residue 80 ASP Chi-restraints excluded: chain 13 residue 91 SER Chi-restraints excluded: chain 13 residue 104 THR Chi-restraints excluded: chain 14 residue 35 HIS Chi-restraints excluded: chain 14 residue 89 VAL Chi-restraints excluded: chain 14 residue 91 ASP Chi-restraints excluded: chain 14 residue 103 ILE Chi-restraints excluded: chain 15 residue 2 LEU Chi-restraints excluded: chain 15 residue 24 THR Chi-restraints excluded: chain 15 residue 28 PHE Chi-restraints excluded: chain 15 residue 30 SER Chi-restraints excluded: chain 15 residue 42 THR Chi-restraints excluded: chain 15 residue 93 VAL Chi-restraints excluded: chain 15 residue 105 MET Chi-restraints excluded: chain 15 residue 129 THR Chi-restraints excluded: chain 15 residue 134 THR Chi-restraints excluded: chain 16 residue 6 SER 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 17 residue 19 GLN Chi-restraints excluded: chain 17 residue 53 THR Chi-restraints excluded: chain 17 residue 67 ASN Chi-restraints excluded: chain 18 residue 10 GLU Chi-restraints excluded: chain 18 residue 51 ASN Chi-restraints excluded: chain 18 residue 83 ILE Chi-restraints excluded: chain 19 residue 8 ILE Chi-restraints excluded: chain 19 residue 16 ILE Chi-restraints excluded: chain 19 residue 89 ILE Chi-restraints excluded: chain 19 residue 90 ASP Chi-restraints excluded: chain 19 residue 106 THR Chi-restraints excluded: chain 20 residue 27 ILE Chi-restraints excluded: chain 20 residue 43 ASN Chi-restraints excluded: chain 20 residue 58 VAL Chi-restraints excluded: chain 21 residue 4 ILE Chi-restraints excluded: chain 21 residue 62 ASP Chi-restraints excluded: chain 21 residue 67 ASP Chi-restraints excluded: chain 21 residue 77 ASP Chi-restraints excluded: chain 21 residue 100 THR Chi-restraints excluded: chain 21 residue 107 VAL Chi-restraints excluded: chain 21 residue 109 ASP Chi-restraints excluded: chain 22 residue 11 LEU Chi-restraints excluded: chain 23 residue 8 ASP Chi-restraints excluded: chain 23 residue 17 ASP Chi-restraints excluded: chain 23 residue 27 VAL Chi-restraints excluded: chain 23 residue 33 VAL Chi-restraints excluded: chain 23 residue 64 ILE Chi-restraints excluded: chain 24 residue 4 ILE Chi-restraints excluded: chain 24 residue 24 ASN Chi-restraints excluded: chain 24 residue 42 LEU Chi-restraints excluded: chain 24 residue 66 ASP Chi-restraints excluded: chain 25 residue 8 ASN Chi-restraints excluded: chain 25 residue 60 ASP Chi-restraints excluded: chain 25 residue 63 VAL Chi-restraints excluded: chain 26 residue 3 VAL Chi-restraints excluded: chain 26 residue 6 VAL Chi-restraints excluded: chain 26 residue 34 SER Chi-restraints excluded: chain 26 residue 41 SER Chi-restraints excluded: chain 26 residue 63 ILE Chi-restraints excluded: chain 27 residue 11 VAL Chi-restraints excluded: chain 27 residue 15 ASN Chi-restraints excluded: chain 27 residue 55 THR Chi-restraints excluded: chain 28 residue 56 VAL Chi-restraints excluded: chain 29 residue 24 ILE Chi-restraints excluded: chain 29 residue 27 THR Chi-restraints excluded: chain 29 residue 34 LEU Chi-restraints excluded: chain 29 residue 58 ASP Chi-restraints excluded: chain 29 residue 59 ARG Chi-restraints excluded: chain 30 residue 2 VAL Chi-restraints excluded: chain 30 residue 35 GLU Chi-restraints excluded: chain 31 residue 6 GLU Chi-restraints excluded: chain 31 residue 10 LEU Chi-restraints excluded: chain 31 residue 21 THR Chi-restraints excluded: chain 31 residue 46 VAL Chi-restraints excluded: chain 32 residue 44 VAL Chi-restraints excluded: chain 33 residue 6 VAL Chi-restraints excluded: chain 33 residue 49 VAL Chi-restraints excluded: chain 34 residue 1 MET Chi-restraints excluded: chain 34 residue 3 VAL Chi-restraints excluded: chain 34 residue 10 LEU Chi-restraints excluded: chain 34 residue 13 ASN Chi-restraints excluded: chain 34 residue 17 VAL Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain F residue 2 ARG Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 116 PHE Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain H residue 26 MET Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 125 GLN Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 49 PHE Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 51 PHE Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 69 CYS Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain K residue 80 ASN Chi-restraints excluded: chain K residue 86 LYS Chi-restraints excluded: chain K residue 118 ASN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 74 GLN Chi-restraints excluded: chain L residue 87 LYS Chi-restraints excluded: chain L residue 119 LYS Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 11 HIS Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 38 ILE Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 67 ASP Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 85 GLU Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain O residue 27 GLN Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain T residue 20 ASN Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain U residue 18 PHE Chi-restraints excluded: chain U residue 37 TYR Chi-restraints excluded: chain U residue 41 THR Chi-restraints excluded: chain 03 residue 18 THR Chi-restraints excluded: chain 03 residue 43 ASP Chi-restraints excluded: chain 03 residue 50 ILE Chi-restraints excluded: chain 03 residue 56 ASP Chi-restraints excluded: chain 03 residue 218 MET Chi-restraints excluded: chain Z residue 42 LEU Chi-restraints excluded: chain Z residue 97 THR Chi-restraints excluded: chain Z residue 100 LYS Chi-restraints excluded: chain Z residue 144 THR Chi-restraints excluded: chain Z residue 162 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1080 random chunks: chunk 946 optimal weight: 20.0000 chunk 997 optimal weight: 20.0000 chunk 909 optimal weight: 20.0000 chunk 970 optimal weight: 20.0000 chunk 996 optimal weight: 20.0000 chunk 583 optimal weight: 30.0000 chunk 422 optimal weight: 7.9990 chunk 761 optimal weight: 20.0000 chunk 297 optimal weight: 30.0000 chunk 876 optimal weight: 20.0000 chunk 917 optimal weight: 20.0000 overall best weight: 17.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 04 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 08 29 ASN ** 09 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 9 ASN ** 13 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 14 38 GLN ** 15 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 18 51 ASN ** 19 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 23 52 ASN 24 75 GLN ** 27 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 29 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 31 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 32 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 GLN ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN D 197 HIS ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 125 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.6260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.127 165170 Z= 0.520 Angle : 0.854 15.203 246822 Z= 0.428 Chirality : 0.044 0.361 31534 Planarity : 0.006 0.083 13429 Dihedral : 24.214 179.581 82044 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 37.76 Ramachandran Plot: Outliers : 0.29 % Allowed : 12.73 % Favored : 86.98 % Rotamer: Outliers : 6.16 % Allowed : 24.12 % Favored : 69.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.10), residues: 6159 helix: -0.77 (0.11), residues: 1942 sheet: -1.76 (0.16), residues: 1026 loop : -2.09 (0.11), residues: 3191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP S 33 HIS 0.010 0.002 HIS24 44 PHE 0.049 0.003 PHE15 68 TYR 0.032 0.003 TYR R 63 ARG 0.013 0.001 ARG05 169 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12318 Ramachandran restraints generated. 6159 Oldfield, 0 Emsley, 6159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12318 Ramachandran restraints generated. 6159 Oldfield, 0 Emsley, 6159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1252 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 315 poor density : 937 time to evaluate : 6.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 04 145 MET cc_start: 0.9540 (mmm) cc_final: 0.9087 (ptt) REVERT: 04 159 THR cc_start: 0.9498 (OUTLIER) cc_final: 0.9010 (p) REVERT: 05 11 MET cc_start: 0.8702 (mtm) cc_final: 0.8367 (mpp) REVERT: 05 200 ASP cc_start: 0.9123 (m-30) cc_final: 0.8866 (m-30) REVERT: 07 95 MET cc_start: 0.9367 (ttp) cc_final: 0.9020 (ttp) REVERT: 08 29 ASN cc_start: 0.9042 (OUTLIER) cc_final: 0.8665 (m-40) REVERT: 09 17 ASP cc_start: 0.9225 (m-30) cc_final: 0.9000 (m-30) REVERT: 09 43 ASN cc_start: 0.8862 (t0) cc_final: 0.8445 (t0) REVERT: 09 128 HIS cc_start: 0.6777 (m-70) cc_final: 0.6385 (m-70) REVERT: 10 37 LYS cc_start: 0.5503 (pttp) cc_final: 0.5101 (pttp) REVERT: 10 38 MET cc_start: 0.2087 (mtt) cc_final: 0.1642 (mpt) REVERT: 10 99 PHE cc_start: 0.6821 (OUTLIER) cc_final: 0.6272 (m-10) REVERT: 12 31 GLU cc_start: 0.9155 (tp30) cc_final: 0.8874 (tp30) REVERT: 12 75 TYR cc_start: 0.9319 (m-10) cc_final: 0.8981 (m-10) REVERT: 12 86 GLN cc_start: 0.9292 (pt0) cc_final: 0.8413 (pp30) REVERT: 12 98 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8301 (mt-10) REVERT: 12 99 ARG cc_start: 0.9388 (mmm160) cc_final: 0.9011 (mmp80) REVERT: 12 118 MET cc_start: 0.9472 (OUTLIER) cc_final: 0.9230 (mtm) REVERT: 12 131 ASN cc_start: 0.9314 (p0) cc_final: 0.8944 (p0) REVERT: 13 1 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8307 (mtp) REVERT: 13 4 GLU cc_start: 0.9430 (mm-30) cc_final: 0.9204 (mm-30) REVERT: 13 73 ASP cc_start: 0.9079 (p0) cc_final: 0.8877 (p0) REVERT: 13 93 GLN cc_start: 0.9454 (tp40) cc_final: 0.9078 (mp10) REVERT: 13 100 PHE cc_start: 0.8848 (m-10) cc_final: 0.8616 (m-10) REVERT: 14 76 GLU cc_start: 0.8918 (pt0) cc_final: 0.8498 (mt-10) REVERT: 14 104 GLN cc_start: 0.9371 (mm-40) cc_final: 0.9046 (mm110) REVERT: 15 2 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8772 (tp) REVERT: 15 45 GLN cc_start: 0.9637 (mt0) cc_final: 0.9321 (mt0) REVERT: 15 75 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8473 (mm-30) REVERT: 15 82 MET cc_start: 0.9346 (mmm) cc_final: 0.9009 (mmm) REVERT: 15 119 LEU cc_start: 0.9455 (mt) cc_final: 0.9166 (pp) REVERT: 15 136 MET cc_start: 0.8914 (ptt) cc_final: 0.8457 (ppp) REVERT: 16 27 SER cc_start: 0.9446 (m) cc_final: 0.9042 (p) REVERT: 16 49 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8245 (mp0) REVERT: 17 43 ASN cc_start: 0.8899 (p0) cc_final: 0.7780 (p0) REVERT: 17 45 SER cc_start: 0.9064 (t) cc_final: 0.8791 (p) REVERT: 17 46 GLU cc_start: 0.9291 (pt0) cc_final: 0.8928 (pm20) REVERT: 17 76 LYS cc_start: 0.9731 (ttpt) cc_final: 0.9441 (tptm) REVERT: 17 80 GLU cc_start: 0.9494 (mt-10) cc_final: 0.9046 (mt-10) REVERT: 17 92 PHE cc_start: 0.8980 (t80) cc_final: 0.8310 (t80) REVERT: 18 12 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.7700 (mmm) REVERT: 18 51 ASN cc_start: 0.8944 (OUTLIER) cc_final: 0.8542 (p0) REVERT: 18 83 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8496 (mm) REVERT: 19 51 GLN cc_start: 0.8987 (mm110) cc_final: 0.8652 (mm-40) REVERT: 19 88 GLU cc_start: 0.9003 (mp0) cc_final: 0.8755 (mp0) REVERT: 19 116 LEU cc_start: 0.9555 (tt) cc_final: 0.9107 (mt) REVERT: 20 16 GLU cc_start: 0.9131 (mt-10) cc_final: 0.8645 (mm-30) REVERT: 20 37 GLU cc_start: 0.9227 (mm-30) cc_final: 0.8828 (mm-30) REVERT: 20 40 MET cc_start: 0.9508 (ttp) cc_final: 0.8973 (tmm) REVERT: 21 53 SER cc_start: 0.8786 (t) cc_final: 0.8394 (p) REVERT: 21 77 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.7364 (p0) REVERT: 22 69 ARG cc_start: 0.7824 (mmm160) cc_final: 0.7576 (mmm160) REVERT: 24 48 MET cc_start: 0.9530 (tpt) cc_final: 0.9274 (mmt) REVERT: 24 55 GLU cc_start: 0.9581 (mt-10) cc_final: 0.9121 (mp0) REVERT: 25 20 LYS cc_start: 0.9049 (mptt) cc_final: 0.8371 (tppt) REVERT: 25 37 ARG cc_start: 0.9211 (tpm170) cc_final: 0.8914 (tpm170) REVERT: 25 68 LYS cc_start: 0.9330 (mtmt) cc_final: 0.8854 (mttt) REVERT: 26 25 LYS cc_start: 0.9262 (mmtp) cc_final: 0.8901 (mmmm) REVERT: 26 67 LEU cc_start: 0.9769 (mm) cc_final: 0.9487 (mm) REVERT: 26 70 LEU cc_start: 0.9647 (tp) cc_final: 0.9183 (tp) REVERT: 26 75 GLU cc_start: 0.8515 (mm-30) cc_final: 0.7776 (mp0) REVERT: 27 1 MET cc_start: 0.8804 (mmm) cc_final: 0.8478 (mmm) REVERT: 27 30 MET cc_start: 0.9525 (mtp) cc_final: 0.9242 (mmp) REVERT: 29 1 MET cc_start: 0.9098 (tpp) cc_final: 0.8735 (tpp) REVERT: 29 8 LYS cc_start: 0.9332 (mmtp) cc_final: 0.8950 (ttpp) REVERT: 30 36 LYS cc_start: 0.9459 (mmtp) cc_final: 0.9042 (mmmm) REVERT: 31 6 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8245 (pm20) REVERT: 31 19 PHE cc_start: 0.8945 (p90) cc_final: 0.8628 (p90) REVERT: 32 1 MET cc_start: 0.8056 (ptm) cc_final: 0.7642 (ppp) REVERT: 32 2 LYS cc_start: 0.9512 (ttmt) cc_final: 0.8936 (tttm) REVERT: 32 6 GLN cc_start: 0.8975 (mm110) cc_final: 0.8492 (mp10) REVERT: 32 13 ASN cc_start: 0.9383 (m-40) cc_final: 0.8589 (t0) REVERT: 32 37 LYS cc_start: 0.9348 (tttt) cc_final: 0.8830 (tptp) REVERT: 34 10 LEU cc_start: 0.9537 (OUTLIER) cc_final: 0.9321 (tp) REVERT: 34 18 LYS cc_start: 0.9473 (tttt) cc_final: 0.9224 (ttmt) REVERT: B 21 TYR cc_start: 0.9423 (m-80) cc_final: 0.9092 (m-80) REVERT: B 48 MET cc_start: 0.9412 (mtm) cc_final: 0.8810 (ptm) REVERT: B 91 VAL cc_start: 0.9402 (OUTLIER) cc_final: 0.9113 (m) REVERT: B 93 HIS cc_start: 0.9376 (t-90) cc_final: 0.9071 (t-170) REVERT: B 99 MET cc_start: 0.9299 (mtp) cc_final: 0.9019 (mtp) REVERT: B 119 GLN cc_start: 0.9624 (OUTLIER) cc_final: 0.9289 (pt0) REVERT: B 153 MET cc_start: 0.8422 (mmm) cc_final: 0.7798 (tmm) REVERT: D 131 ILE cc_start: 0.8519 (mt) cc_final: 0.8220 (tt) REVERT: D 147 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.7956 (pptt) REVERT: E 54 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8457 (tm-30) REVERT: E 67 ARG cc_start: 0.8914 (mmt90) cc_final: 0.8621 (mmt90) REVERT: E 110 MET cc_start: 0.9613 (ttp) cc_final: 0.9381 (ppp) REVERT: E 141 ASP cc_start: 0.9009 (t0) cc_final: 0.8685 (t0) REVERT: F 2 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.8307 (mmm-85) REVERT: F 78 PHE cc_start: 0.9673 (m-80) cc_final: 0.9155 (m-80) REVERT: F 81 ASN cc_start: 0.9050 (t0) cc_final: 0.8756 (t0) REVERT: G 32 ASP cc_start: 0.8701 (m-30) cc_final: 0.8143 (t0) REVERT: G 139 ASP cc_start: 0.9450 (m-30) cc_final: 0.9019 (t0) REVERT: H 41 GLU cc_start: 0.9413 (tm-30) cc_final: 0.9154 (pp20) REVERT: H 48 PHE cc_start: 0.9041 (p90) cc_final: 0.8505 (p90) REVERT: H 59 GLU cc_start: 0.8767 (pm20) cc_final: 0.8545 (pm20) REVERT: I 45 MET cc_start: 0.9677 (ppp) cc_final: 0.9281 (ppp) REVERT: I 52 GLU cc_start: 0.9485 (mm-30) cc_final: 0.9227 (mm-30) REVERT: I 87 MET cc_start: 0.9259 (ppp) cc_final: 0.8862 (ppp) REVERT: I 96 GLU cc_start: 0.9088 (mp0) cc_final: 0.8875 (mp0) REVERT: I 106 ASP cc_start: 0.8795 (t70) cc_final: 0.8398 (t0) REVERT: J 46 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8540 (mmmm) REVERT: J 59 LYS cc_start: 0.9092 (tttm) cc_final: 0.8521 (ttmt) REVERT: J 63 ASP cc_start: 0.8776 (t0) cc_final: 0.8295 (t0) REVERT: J 65 TYR cc_start: 0.8625 (m-80) cc_final: 0.8266 (m-80) REVERT: J 66 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7928 (tm-30) REVERT: J 87 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8898 (mt) REVERT: K 37 GLN cc_start: 0.9546 (mp10) cc_final: 0.9261 (mp10) REVERT: K 39 ASN cc_start: 0.9151 (t0) cc_final: 0.8871 (t0) REVERT: L 19 ASN cc_start: 0.9443 (m-40) cc_final: 0.9164 (t0) REVERT: N 25 GLU cc_start: 0.9205 (pt0) cc_final: 0.8518 (tm-30) REVERT: N 91 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8637 (mm-30) REVERT: O 47 LYS cc_start: 0.9505 (mmmm) cc_final: 0.8749 (ttpt) REVERT: P 6 LEU cc_start: 0.9009 (tp) cc_final: 0.8803 (tp) REVERT: Q 5 ARG cc_start: 0.8989 (tpt90) cc_final: 0.8586 (tpt90) REVERT: Q 16 MET cc_start: 0.7823 (tpp) cc_final: 0.7223 (mmm) REVERT: Q 42 LYS cc_start: 0.9143 (mttt) cc_final: 0.8879 (mtmm) REVERT: Q 47 ASP cc_start: 0.6442 (OUTLIER) cc_final: 0.5396 (p0) REVERT: R 37 LYS cc_start: 0.9494 (mmmm) cc_final: 0.9150 (tppt) REVERT: R 47 ARG cc_start: 0.9540 (mmm160) cc_final: 0.8877 (mpp-170) REVERT: R 60 ARG cc_start: 0.9485 (mpp80) cc_final: 0.9108 (mtm-85) REVERT: T 26 MET cc_start: 0.9245 (ttp) cc_final: 0.8737 (tpp) REVERT: T 53 MET cc_start: 0.9528 (ppp) cc_final: 0.9303 (ppp) REVERT: 03 25 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7896 (mt-10) REVERT: Z 43 LYS cc_start: 0.6312 (mtpt) cc_final: 0.5832 (mtmm) REVERT: Z 100 LYS cc_start: 0.3590 (OUTLIER) cc_final: 0.2938 (tptp) outliers start: 315 outliers final: 265 residues processed: 1144 average time/residue: 1.1043 time to fit residues: 2225.0981 Evaluate side-chains 1194 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 909 time to evaluate : 8.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 63 ILE Chi-restraints excluded: chain 04 residue 159 THR Chi-restraints excluded: chain 04 residue 190 THR Chi-restraints excluded: chain 04 residue 199 HIS Chi-restraints excluded: chain 04 residue 215 VAL Chi-restraints excluded: chain 04 residue 227 VAL Chi-restraints excluded: chain 04 residue 258 SER Chi-restraints excluded: chain 05 residue 2 ILE Chi-restraints excluded: chain 05 residue 103 ASP Chi-restraints excluded: chain 05 residue 126 ASN Chi-restraints excluded: chain 05 residue 145 SER Chi-restraints excluded: chain 05 residue 177 VAL Chi-restraints excluded: chain 05 residue 201 LEU Chi-restraints excluded: chain 06 residue 73 ILE Chi-restraints excluded: chain 06 residue 148 ILE Chi-restraints excluded: chain 06 residue 149 ILE Chi-restraints excluded: chain 06 residue 164 LEU Chi-restraints excluded: chain 06 residue 175 ILE Chi-restraints excluded: chain 06 residue 199 MET Chi-restraints excluded: chain 07 residue 9 ASP Chi-restraints excluded: chain 07 residue 26 GLN Chi-restraints excluded: chain 07 residue 46 LYS Chi-restraints excluded: chain 07 residue 51 ASN Chi-restraints excluded: chain 07 residue 65 LEU Chi-restraints excluded: chain 07 residue 86 CYS Chi-restraints excluded: chain 07 residue 128 SER Chi-restraints excluded: chain 07 residue 135 ILE Chi-restraints excluded: chain 07 residue 143 ASP Chi-restraints excluded: chain 07 residue 148 VAL Chi-restraints excluded: chain 07 residue 156 THR Chi-restraints excluded: chain 07 residue 157 THR Chi-restraints excluded: chain 07 residue 177 ARG Chi-restraints excluded: chain 08 residue 9 VAL Chi-restraints excluded: chain 08 residue 10 VAL Chi-restraints excluded: chain 08 residue 29 ASN Chi-restraints excluded: chain 08 residue 38 ASP Chi-restraints excluded: chain 08 residue 113 ASP Chi-restraints excluded: chain 08 residue 154 GLU Chi-restraints excluded: chain 08 residue 167 VAL Chi-restraints excluded: chain 09 residue 4 ILE Chi-restraints excluded: chain 09 residue 6 LEU Chi-restraints excluded: chain 09 residue 28 ASN Chi-restraints excluded: chain 09 residue 68 ARG Chi-restraints excluded: chain 09 residue 110 VAL Chi-restraints excluded: chain 10 residue 27 VAL Chi-restraints excluded: chain 10 residue 99 PHE Chi-restraints excluded: chain 10 residue 123 ILE Chi-restraints excluded: chain 11 residue 7 TYR Chi-restraints excluded: chain 11 residue 27 LEU Chi-restraints excluded: chain 11 residue 58 ILE Chi-restraints excluded: chain 11 residue 70 THR Chi-restraints excluded: chain 11 residue 107 GLU Chi-restraints excluded: chain 12 residue 25 LEU Chi-restraints excluded: chain 12 residue 52 ASP Chi-restraints excluded: chain 12 residue 57 LEU Chi-restraints excluded: chain 12 residue 84 ILE Chi-restraints excluded: chain 12 residue 118 MET Chi-restraints excluded: chain 13 residue 1 MET Chi-restraints excluded: chain 13 residue 12 ASP Chi-restraints excluded: chain 13 residue 25 LEU Chi-restraints excluded: chain 13 residue 37 ASP Chi-restraints excluded: chain 13 residue 39 ILE Chi-restraints excluded: chain 13 residue 47 ILE Chi-restraints excluded: chain 13 residue 54 LYS Chi-restraints excluded: chain 13 residue 58 LEU Chi-restraints excluded: chain 13 residue 65 THR Chi-restraints excluded: chain 13 residue 80 ASP Chi-restraints excluded: chain 13 residue 91 SER Chi-restraints excluded: chain 13 residue 104 THR Chi-restraints excluded: chain 14 residue 35 HIS Chi-restraints excluded: chain 14 residue 91 ASP Chi-restraints excluded: chain 14 residue 103 ILE Chi-restraints excluded: chain 14 residue 120 VAL Chi-restraints excluded: chain 15 residue 2 LEU Chi-restraints excluded: chain 15 residue 24 THR Chi-restraints excluded: chain 15 residue 28 PHE Chi-restraints excluded: chain 15 residue 30 SER Chi-restraints excluded: chain 15 residue 42 THR Chi-restraints excluded: chain 15 residue 93 VAL Chi-restraints excluded: chain 15 residue 105 MET Chi-restraints excluded: chain 15 residue 129 THR Chi-restraints excluded: chain 15 residue 134 THR Chi-restraints excluded: chain 16 residue 6 SER 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 48 VAL Chi-restraints excluded: chain 17 residue 19 GLN Chi-restraints excluded: chain 17 residue 53 THR Chi-restraints excluded: chain 17 residue 67 ASN Chi-restraints excluded: chain 18 residue 10 GLU Chi-restraints excluded: chain 18 residue 12 MET Chi-restraints excluded: chain 18 residue 51 ASN Chi-restraints excluded: chain 18 residue 83 ILE Chi-restraints excluded: chain 19 residue 8 ILE Chi-restraints excluded: chain 19 residue 19 GLN Chi-restraints excluded: chain 19 residue 28 SER Chi-restraints excluded: chain 19 residue 89 ILE Chi-restraints excluded: chain 19 residue 90 ASP Chi-restraints excluded: chain 19 residue 106 THR Chi-restraints excluded: chain 20 residue 27 ILE Chi-restraints excluded: chain 20 residue 43 ASN Chi-restraints excluded: chain 20 residue 53 PHE Chi-restraints excluded: chain 20 residue 58 VAL Chi-restraints excluded: chain 21 residue 4 ILE Chi-restraints excluded: chain 21 residue 33 LEU Chi-restraints excluded: chain 21 residue 51 LEU Chi-restraints excluded: chain 21 residue 62 ASP Chi-restraints excluded: chain 21 residue 67 ASP Chi-restraints excluded: chain 21 residue 77 ASP Chi-restraints excluded: chain 21 residue 109 ASP Chi-restraints excluded: chain 22 residue 11 LEU Chi-restraints excluded: chain 23 residue 8 ASP Chi-restraints excluded: chain 23 residue 17 ASP Chi-restraints excluded: chain 23 residue 27 VAL Chi-restraints excluded: chain 23 residue 33 VAL Chi-restraints excluded: chain 23 residue 64 ILE Chi-restraints excluded: chain 23 residue 71 ILE Chi-restraints excluded: chain 24 residue 4 ILE Chi-restraints excluded: chain 24 residue 24 ASN Chi-restraints excluded: chain 24 residue 42 LEU Chi-restraints excluded: chain 24 residue 66 ASP Chi-restraints excluded: chain 25 residue 8 ASN Chi-restraints excluded: chain 25 residue 60 ASP Chi-restraints excluded: chain 25 residue 63 VAL Chi-restraints excluded: chain 26 residue 3 VAL Chi-restraints excluded: chain 26 residue 6 VAL Chi-restraints excluded: chain 26 residue 34 SER Chi-restraints excluded: chain 26 residue 46 VAL Chi-restraints excluded: chain 26 residue 63 ILE Chi-restraints excluded: chain 27 residue 11 VAL Chi-restraints excluded: chain 27 residue 15 ASN Chi-restraints excluded: chain 27 residue 36 GLN Chi-restraints excluded: chain 27 residue 50 VAL Chi-restraints excluded: chain 27 residue 55 THR Chi-restraints excluded: chain 28 residue 56 VAL Chi-restraints excluded: chain 29 residue 24 ILE Chi-restraints excluded: chain 29 residue 27 THR Chi-restraints excluded: chain 29 residue 34 LEU Chi-restraints excluded: chain 29 residue 58 ASP Chi-restraints excluded: chain 29 residue 59 ARG Chi-restraints excluded: chain 30 residue 2 VAL Chi-restraints excluded: chain 30 residue 22 THR Chi-restraints excluded: chain 30 residue 35 GLU Chi-restraints excluded: chain 31 residue 6 GLU Chi-restraints excluded: chain 31 residue 10 LEU Chi-restraints excluded: chain 31 residue 21 THR Chi-restraints excluded: chain 31 residue 46 VAL Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 32 residue 44 VAL Chi-restraints excluded: chain 33 residue 6 VAL Chi-restraints excluded: chain 33 residue 49 VAL Chi-restraints excluded: chain 34 residue 1 MET Chi-restraints excluded: chain 34 residue 3 VAL Chi-restraints excluded: chain 34 residue 10 LEU Chi-restraints excluded: chain 34 residue 13 ASN Chi-restraints excluded: chain 34 residue 17 VAL Chi-restraints excluded: chain 34 residue 20 ASP Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 2 ARG Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 116 PHE Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain H residue 26 MET Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain I residue 29 ILE Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 109 GLN Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 125 GLN Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 87 LEU Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 51 PHE Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 69 CYS Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain K residue 80 ASN Chi-restraints excluded: chain K residue 86 LYS Chi-restraints excluded: chain K residue 118 ASN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 5 GLN Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 74 GLN Chi-restraints excluded: chain L residue 87 LYS Chi-restraints excluded: chain L residue 119 LYS Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 11 HIS Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 67 ASP Chi-restraints excluded: chain M residue 79 LEU Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 85 GLU Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 47 ASP Chi-restraints excluded: chain Q residue 69 THR Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain S residue 62 THR Chi-restraints excluded: chain S residue 68 HIS Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain T residue 20 ASN Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain U residue 20 ARG Chi-restraints excluded: chain U residue 41 THR Chi-restraints excluded: chain U residue 43 GLU Chi-restraints excluded: chain 03 residue 18 THR Chi-restraints excluded: chain 03 residue 43 ASP Chi-restraints excluded: chain 03 residue 50 ILE Chi-restraints excluded: chain 03 residue 56 ASP Chi-restraints excluded: chain 03 residue 209 ILE Chi-restraints excluded: chain 03 residue 218 MET Chi-restraints excluded: chain Z residue 16 ILE Chi-restraints excluded: chain Z residue 42 LEU Chi-restraints excluded: chain Z residue 97 THR Chi-restraints excluded: chain Z residue 100 LYS Chi-restraints excluded: chain Z residue 144 THR Chi-restraints excluded: chain Z residue 162 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1080 random chunks: chunk 966 optimal weight: 10.0000 chunk 636 optimal weight: 20.0000 chunk 1025 optimal weight: 10.0000 chunk 626 optimal weight: 20.0000 chunk 486 optimal weight: 0.9990 chunk 713 optimal weight: 20.0000 chunk 1075 optimal weight: 7.9990 chunk 990 optimal weight: 10.0000 chunk 856 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 661 optimal weight: 10.0000 overall best weight: 6.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 04 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 05 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 9 ASN ** 13 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 14 4 ASN 14 38 GLN ** 15 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 15 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 24 75 GLN ** 27 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 29 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 31 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 32 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 122 GLN ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 HIS ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 ASN ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 GLN ** K 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 03 57 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.6090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 165170 Z= 0.243 Angle : 0.662 16.379 246822 Z= 0.335 Chirality : 0.036 0.313 31534 Planarity : 0.005 0.085 13429 Dihedral : 24.099 179.511 82044 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 24.87 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.83 % Favored : 90.88 % Rotamer: Outliers : 4.91 % Allowed : 25.70 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.10), residues: 6159 helix: -0.43 (0.11), residues: 1978 sheet: -1.63 (0.16), residues: 1022 loop : -1.91 (0.11), residues: 3159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP04 212 HIS 0.008 0.001 HIS12 40 PHE 0.045 0.002 PHE G 61 TYR 0.031 0.002 TYR U 37 ARG 0.015 0.001 ARG12 37 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12318 Ramachandran restraints generated. 6159 Oldfield, 0 Emsley, 6159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12318 Ramachandran restraints generated. 6159 Oldfield, 0 Emsley, 6159 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1251 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 1000 time to evaluate : 5.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 04 131 MET cc_start: 0.9764 (mtp) cc_final: 0.9379 (mpp) REVERT: 04 145 MET cc_start: 0.9557 (mmm) cc_final: 0.9073 (ptt) REVERT: 05 11 MET cc_start: 0.8564 (mtm) cc_final: 0.8261 (mpp) REVERT: 05 200 ASP cc_start: 0.9116 (m-30) cc_final: 0.8778 (m-30) REVERT: 06 94 GLN cc_start: 0.9142 (pt0) cc_final: 0.8846 (pt0) REVERT: 07 95 MET cc_start: 0.9348 (ttp) cc_final: 0.8970 (ttp) REVERT: 09 43 ASN cc_start: 0.8873 (t0) cc_final: 0.8465 (t0) REVERT: 09 123 ARG cc_start: 0.7082 (mtt180) cc_final: 0.6865 (mtp180) REVERT: 09 128 HIS cc_start: 0.6762 (m-70) cc_final: 0.6357 (m-70) REVERT: 10 37 LYS cc_start: 0.4977 (pttp) cc_final: 0.4672 (pttp) REVERT: 10 38 MET cc_start: 0.1821 (mtt) cc_final: 0.1422 (mpt) REVERT: 10 99 PHE cc_start: 0.6748 (OUTLIER) cc_final: 0.6203 (m-10) REVERT: 12 31 GLU cc_start: 0.9145 (tp30) cc_final: 0.8833 (tp30) REVERT: 12 35 ARG cc_start: 0.9632 (mmt180) cc_final: 0.9337 (mmt-90) REVERT: 12 75 TYR cc_start: 0.9384 (m-10) cc_final: 0.9057 (m-10) REVERT: 12 86 GLN cc_start: 0.9341 (pt0) cc_final: 0.8390 (pp30) REVERT: 12 98 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8323 (mt-10) REVERT: 12 99 ARG cc_start: 0.9409 (mmm160) cc_final: 0.9012 (mmp80) REVERT: 12 118 MET cc_start: 0.9370 (OUTLIER) cc_final: 0.8993 (mtp) REVERT: 12 131 ASN cc_start: 0.9235 (p0) cc_final: 0.8867 (p0) REVERT: 13 1 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8261 (mtp) REVERT: 13 4 GLU cc_start: 0.9471 (mm-30) cc_final: 0.9264 (mm-30) REVERT: 13 100 PHE cc_start: 0.8935 (m-10) cc_final: 0.8717 (m-10) REVERT: 14 76 GLU cc_start: 0.8875 (pt0) cc_final: 0.8481 (mt-10) REVERT: 14 104 GLN cc_start: 0.9305 (mm-40) cc_final: 0.8985 (mm110) REVERT: 15 2 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8898 (tp) REVERT: 15 10 ARG cc_start: 0.9575 (ptm160) cc_final: 0.8993 (mmp80) REVERT: 15 75 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8475 (mm-30) REVERT: 15 82 MET cc_start: 0.9256 (mmm) cc_final: 0.8882 (mmm) REVERT: 15 103 TYR cc_start: 0.9068 (m-80) cc_final: 0.8849 (m-80) REVERT: 15 119 LEU cc_start: 0.9402 (mt) cc_final: 0.9118 (pp) REVERT: 15 136 MET cc_start: 0.8916 (ptt) cc_final: 0.8513 (ppp) REVERT: 16 27 SER cc_start: 0.9319 (m) cc_final: 0.8923 (p) REVERT: 16 49 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8180 (mp0) REVERT: 17 43 ASN cc_start: 0.8938 (p0) cc_final: 0.7891 (p0) REVERT: 17 45 SER cc_start: 0.9081 (t) cc_final: 0.8833 (p) REVERT: 17 46 GLU cc_start: 0.9346 (pt0) cc_final: 0.9078 (pm20) REVERT: 17 80 GLU cc_start: 0.9476 (mt-10) cc_final: 0.9099 (mt-10) REVERT: 17 92 PHE cc_start: 0.8901 (t80) cc_final: 0.8322 (t80) REVERT: 17 116 GLN cc_start: 0.9349 (tp40) cc_final: 0.9088 (tm-30) REVERT: 18 12 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.7607 (mmm) REVERT: 18 51 ASN cc_start: 0.9023 (OUTLIER) cc_final: 0.8753 (p0) REVERT: 18 83 ILE cc_start: 0.9018 (OUTLIER) cc_final: 0.8520 (mm) REVERT: 19 51 GLN cc_start: 0.8884 (mm110) cc_final: 0.8525 (mm-40) REVERT: 19 58 GLN cc_start: 0.9596 (tt0) cc_final: 0.9104 (tp40) REVERT: 19 88 GLU cc_start: 0.9049 (mp0) cc_final: 0.8754 (mp0) REVERT: 20 16 GLU cc_start: 0.9235 (mt-10) cc_final: 0.8793 (mm-30) REVERT: 20 40 MET cc_start: 0.9455 (ttp) cc_final: 0.8792 (tmm) REVERT: 21 34 ASP cc_start: 0.9585 (m-30) cc_final: 0.9298 (p0) REVERT: 21 53 SER cc_start: 0.8644 (t) cc_final: 0.8284 (p) REVERT: 21 77 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.7446 (p0) REVERT: 21 78 GLU cc_start: 0.8508 (pm20) cc_final: 0.8240 (pm20) REVERT: 22 8 LEU cc_start: 0.9539 (mt) cc_final: 0.9316 (pp) REVERT: 22 69 ARG cc_start: 0.7863 (mmm160) cc_final: 0.7582 (mmm160) REVERT: 24 55 GLU cc_start: 0.9568 (mt-10) cc_final: 0.9109 (mp0) REVERT: 25 68 LYS cc_start: 0.9256 (mtmt) cc_final: 0.8813 (mttt) REVERT: 26 25 LYS cc_start: 0.9174 (mmtp) cc_final: 0.8774 (mmmm) REVERT: 26 70 LEU cc_start: 0.9634 (tp) cc_final: 0.9392 (tp) REVERT: 26 75 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8063 (mp0) REVERT: 27 1 MET cc_start: 0.8760 (mmm) cc_final: 0.8404 (mmm) REVERT: 27 30 MET cc_start: 0.9505 (mtp) cc_final: 0.9217 (mmp) REVERT: 29 1 MET cc_start: 0.9195 (tpp) cc_final: 0.8603 (tpp) REVERT: 29 8 LYS cc_start: 0.9262 (mmtp) cc_final: 0.8863 (ttpp) REVERT: 30 36 LYS cc_start: 0.9447 (mmtp) cc_final: 0.9052 (mmmm) REVERT: 31 6 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8253 (pm20) REVERT: 31 19 PHE cc_start: 0.8899 (p90) cc_final: 0.8572 (p90) REVERT: 31 35 LEU cc_start: 0.8871 (tp) cc_final: 0.8594 (tp) REVERT: 32 1 MET cc_start: 0.7738 (ptm) cc_final: 0.7490 (ppp) REVERT: 32 6 GLN cc_start: 0.9023 (mm110) cc_final: 0.8600 (mp10) REVERT: 32 37 LYS cc_start: 0.9334 (tttt) cc_final: 0.8770 (tptp) REVERT: 34 1 MET cc_start: 0.9425 (OUTLIER) cc_final: 0.8662 (mmm) REVERT: 34 18 LYS cc_start: 0.9476 (tttt) cc_final: 0.9196 (ttmt) REVERT: B 21 TYR cc_start: 0.9365 (m-80) cc_final: 0.9049 (m-80) REVERT: B 91 VAL cc_start: 0.9345 (OUTLIER) cc_final: 0.9046 (m) REVERT: B 93 HIS cc_start: 0.9276 (t-90) cc_final: 0.8983 (t-170) REVERT: B 99 MET cc_start: 0.9320 (mtp) cc_final: 0.9031 (mtp) REVERT: B 119 GLN cc_start: 0.9588 (OUTLIER) cc_final: 0.9246 (pt0) REVERT: B 153 MET cc_start: 0.8334 (mmm) cc_final: 0.7625 (tmm) REVERT: D 47 LEU cc_start: 0.9029 (tp) cc_final: 0.8544 (pp) REVERT: D 131 ILE cc_start: 0.8406 (mt) cc_final: 0.8090 (tt) REVERT: D 147 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7920 (pptt) REVERT: E 54 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8436 (tm-30) REVERT: E 67 ARG cc_start: 0.8820 (mmt90) cc_final: 0.8603 (mmt90) REVERT: E 104 ILE cc_start: 0.9009 (mt) cc_final: 0.8689 (mm) REVERT: E 110 MET cc_start: 0.9570 (ttp) cc_final: 0.9292 (ppp) REVERT: E 141 ASP cc_start: 0.9004 (t0) cc_final: 0.8700 (t0) REVERT: F 72 ASP cc_start: 0.9546 (OUTLIER) cc_final: 0.9093 (p0) REVERT: F 78 PHE cc_start: 0.9664 (m-80) cc_final: 0.9156 (m-80) REVERT: F 81 ASN cc_start: 0.9013 (t0) cc_final: 0.8738 (t0) REVERT: G 139 ASP cc_start: 0.9388 (m-30) cc_final: 0.8981 (t0) REVERT: H 41 GLU cc_start: 0.9444 (tm-30) cc_final: 0.9132 (pp20) REVERT: H 48 PHE cc_start: 0.8947 (p90) cc_final: 0.8646 (p90) REVERT: H 110 MET cc_start: 0.8966 (ptp) cc_final: 0.8601 (mpp) REVERT: H 112 ASP cc_start: 0.9458 (p0) cc_final: 0.8605 (t0) REVERT: I 45 MET cc_start: 0.9679 (ppp) cc_final: 0.9348 (ppp) REVERT: I 87 MET cc_start: 0.9291 (ppp) cc_final: 0.8875 (ppp) REVERT: I 106 ASP cc_start: 0.8765 (t70) cc_final: 0.8358 (t0) REVERT: J 63 ASP cc_start: 0.8660 (t0) cc_final: 0.8154 (t0) REVERT: J 65 TYR cc_start: 0.8430 (m-80) cc_final: 0.8135 (m-80) REVERT: K 37 GLN cc_start: 0.9543 (mp10) cc_final: 0.9274 (mp10) REVERT: K 39 ASN cc_start: 0.9092 (t0) cc_final: 0.8808 (t0) REVERT: K 86 LYS cc_start: 0.9441 (pttt) cc_final: 0.9086 (pptt) REVERT: L 19 ASN cc_start: 0.9417 (m-40) cc_final: 0.9198 (t0) REVERT: M 85 TYR cc_start: 0.9329 (t80) cc_final: 0.8927 (t80) REVERT: N 25 GLU cc_start: 0.9179 (pt0) cc_final: 0.8486 (tm-30) REVERT: N 89 ARG cc_start: 0.9504 (ttm110) cc_final: 0.8890 (ptp-170) REVERT: N 91 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8702 (mm-30) REVERT: O 47 LYS cc_start: 0.9454 (mmmm) cc_final: 0.8785 (ttpt) REVERT: O 88 ARG cc_start: 0.8283 (tpp-160) cc_final: 0.7092 (mmt-90) REVERT: Q 16 MET cc_start: 0.7986 (tpp) cc_final: 0.7233 (mmm) REVERT: Q 42 LYS cc_start: 0.9048 (mttt) cc_final: 0.8733 (mtmm) REVERT: R 28 LEU cc_start: 0.9677 (mm) cc_final: 0.9373 (mt) REVERT: R 37 LYS cc_start: 0.9497 (mmmm) cc_final: 0.9270 (mmmt) REVERT: R 47 ARG cc_start: 0.9526 (mmm160) cc_final: 0.8908 (mpp-170) REVERT: S 20 LYS cc_start: 0.9634 (mtmm) cc_final: 0.9249 (pttt) REVERT: S 72 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8229 (mm-30) REVERT: T 26 MET cc_start: 0.9185 (ttp) cc_final: 0.8605 (tpp) REVERT: T 53 MET cc_start: 0.9530 (ppp) cc_final: 0.9257 (ppp) REVERT: U 18 PHE cc_start: 0.9067 (OUTLIER) cc_final: 0.8448 (t80) REVERT: 03 25 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7939 (mt-10) REVERT: 03 198 LYS cc_start: 0.7604 (pttt) cc_final: 0.7308 (mmmt) REVERT: Z 9 PHE cc_start: 0.9035 (t80) cc_final: 0.8776 (m-80) REVERT: Z 100 LYS cc_start: 0.3814 (OUTLIER) cc_final: 0.3090 (tptp) outliers start: 251 outliers final: 215 residues processed: 1158 average time/residue: 1.1098 time to fit residues: 2255.4452 Evaluate side-chains 1184 residues out of total 5120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 953 time to evaluate : 5.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 04 residue 63 ILE Chi-restraints excluded: chain 04 residue 227 VAL Chi-restraints excluded: chain 04 residue 258 SER Chi-restraints excluded: chain 05 residue 2 ILE Chi-restraints excluded: chain 05 residue 103 ASP Chi-restraints excluded: chain 05 residue 126 ASN Chi-restraints excluded: chain 05 residue 177 VAL Chi-restraints excluded: chain 05 residue 201 LEU Chi-restraints excluded: chain 06 residue 73 ILE Chi-restraints excluded: chain 06 residue 148 ILE Chi-restraints excluded: chain 06 residue 164 LEU Chi-restraints excluded: chain 07 residue 9 ASP Chi-restraints excluded: chain 07 residue 46 LYS Chi-restraints excluded: chain 07 residue 51 ASN Chi-restraints excluded: chain 07 residue 65 LEU Chi-restraints excluded: chain 07 residue 82 TYR Chi-restraints excluded: chain 07 residue 86 CYS Chi-restraints excluded: chain 07 residue 128 SER Chi-restraints excluded: chain 07 residue 135 ILE Chi-restraints excluded: chain 07 residue 148 VAL Chi-restraints excluded: chain 07 residue 156 THR Chi-restraints excluded: chain 07 residue 157 THR Chi-restraints excluded: chain 07 residue 177 ARG Chi-restraints excluded: chain 08 residue 9 VAL Chi-restraints excluded: chain 08 residue 10 VAL Chi-restraints excluded: chain 08 residue 38 ASP Chi-restraints excluded: chain 08 residue 154 GLU Chi-restraints excluded: chain 08 residue 167 VAL Chi-restraints excluded: chain 09 residue 6 LEU Chi-restraints excluded: chain 09 residue 68 ARG Chi-restraints excluded: chain 09 residue 110 VAL Chi-restraints excluded: chain 10 residue 27 VAL Chi-restraints excluded: chain 10 residue 84 TYR Chi-restraints excluded: chain 10 residue 99 PHE Chi-restraints excluded: chain 10 residue 123 ILE Chi-restraints excluded: chain 11 residue 7 TYR Chi-restraints excluded: chain 11 residue 27 LEU Chi-restraints excluded: chain 11 residue 58 ILE Chi-restraints excluded: chain 12 residue 25 LEU Chi-restraints excluded: chain 12 residue 52 ASP Chi-restraints excluded: chain 12 residue 57 LEU Chi-restraints excluded: chain 12 residue 84 ILE Chi-restraints excluded: chain 12 residue 118 MET Chi-restraints excluded: chain 13 residue 1 MET Chi-restraints excluded: chain 13 residue 12 ASP Chi-restraints excluded: chain 13 residue 25 LEU Chi-restraints excluded: chain 13 residue 39 ILE Chi-restraints excluded: chain 13 residue 47 ILE Chi-restraints excluded: chain 13 residue 54 LYS Chi-restraints excluded: chain 13 residue 58 LEU Chi-restraints excluded: chain 13 residue 65 THR Chi-restraints excluded: chain 13 residue 80 ASP Chi-restraints excluded: chain 13 residue 91 SER Chi-restraints excluded: chain 13 residue 104 THR Chi-restraints excluded: chain 14 residue 35 HIS Chi-restraints excluded: chain 14 residue 91 ASP Chi-restraints excluded: chain 14 residue 103 ILE Chi-restraints excluded: chain 15 residue 2 LEU Chi-restraints excluded: chain 15 residue 24 THR Chi-restraints excluded: chain 15 residue 28 PHE Chi-restraints excluded: chain 15 residue 30 SER Chi-restraints excluded: chain 15 residue 42 THR Chi-restraints excluded: chain 15 residue 93 VAL Chi-restraints excluded: chain 15 residue 105 MET Chi-restraints excluded: chain 15 residue 129 THR Chi-restraints excluded: chain 15 residue 134 THR Chi-restraints excluded: chain 16 residue 6 SER Chi-restraints excluded: chain 16 residue 37 THR Chi-restraints excluded: chain 16 residue 48 VAL Chi-restraints excluded: chain 17 residue 19 GLN Chi-restraints excluded: chain 17 residue 53 THR Chi-restraints excluded: chain 17 residue 67 ASN Chi-restraints excluded: chain 18 residue 10 GLU Chi-restraints excluded: chain 18 residue 12 MET Chi-restraints excluded: chain 18 residue 51 ASN Chi-restraints excluded: chain 18 residue 83 ILE Chi-restraints excluded: chain 19 residue 8 ILE Chi-restraints excluded: chain 19 residue 89 ILE Chi-restraints excluded: chain 19 residue 90 ASP Chi-restraints excluded: chain 19 residue 106 THR Chi-restraints excluded: chain 20 residue 27 ILE Chi-restraints excluded: chain 20 residue 43 ASN Chi-restraints excluded: chain 20 residue 58 VAL Chi-restraints excluded: chain 21 residue 4 ILE Chi-restraints excluded: chain 21 residue 62 ASP Chi-restraints excluded: chain 21 residue 67 ASP Chi-restraints excluded: chain 21 residue 77 ASP Chi-restraints excluded: chain 21 residue 97 LEU Chi-restraints excluded: chain 21 residue 109 ASP Chi-restraints excluded: chain 23 residue 8 ASP Chi-restraints excluded: chain 23 residue 17 ASP Chi-restraints excluded: chain 23 residue 27 VAL Chi-restraints excluded: chain 23 residue 33 VAL Chi-restraints excluded: chain 23 residue 71 ILE Chi-restraints excluded: chain 24 residue 24 ASN Chi-restraints excluded: chain 24 residue 42 LEU Chi-restraints excluded: chain 24 residue 66 ASP Chi-restraints excluded: chain 25 residue 8 ASN Chi-restraints excluded: chain 25 residue 17 LEU Chi-restraints excluded: chain 25 residue 60 ASP Chi-restraints excluded: chain 25 residue 63 VAL Chi-restraints excluded: chain 26 residue 3 VAL Chi-restraints excluded: chain 26 residue 6 VAL Chi-restraints excluded: chain 26 residue 34 SER Chi-restraints excluded: chain 26 residue 63 ILE Chi-restraints excluded: chain 27 residue 11 VAL Chi-restraints excluded: chain 27 residue 15 ASN Chi-restraints excluded: chain 28 residue 56 VAL Chi-restraints excluded: chain 29 residue 24 ILE Chi-restraints excluded: chain 29 residue 27 THR Chi-restraints excluded: chain 29 residue 59 ARG Chi-restraints excluded: chain 30 residue 2 VAL Chi-restraints excluded: chain 30 residue 22 THR Chi-restraints excluded: chain 30 residue 35 GLU Chi-restraints excluded: chain 31 residue 6 GLU Chi-restraints excluded: chain 31 residue 10 LEU Chi-restraints excluded: chain 31 residue 46 VAL Chi-restraints excluded: chain 32 residue 43 THR Chi-restraints excluded: chain 32 residue 44 VAL Chi-restraints excluded: chain 33 residue 6 VAL Chi-restraints excluded: chain 33 residue 49 VAL Chi-restraints excluded: chain 34 residue 1 MET Chi-restraints excluded: chain 34 residue 3 VAL Chi-restraints excluded: chain 34 residue 13 ASN Chi-restraints excluded: chain 34 residue 17 VAL Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 87 ASP Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 119 GLN Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 141 MET Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 98 ASP Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 147 LYS Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain E residue 17 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 42 ASN Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain F residue 2 ARG Chi-restraints excluded: chain F residue 13 ASP Chi-restraints excluded: chain F residue 55 HIS Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 75 GLU Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 116 PHE Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 14 ASP Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain H residue 26 MET Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 103 VAL Chi-restraints excluded: chain H residue 124 ILE Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 125 GLN Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain K residue 30 ILE Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 51 PHE Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 69 CYS Chi-restraints excluded: chain K residue 79 LYS Chi-restraints excluded: chain K residue 80 ASN Chi-restraints excluded: chain K residue 118 ASN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 62 VAL Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 74 GLN Chi-restraints excluded: chain L residue 119 LYS Chi-restraints excluded: chain M residue 6 ILE Chi-restraints excluded: chain M residue 11 HIS Chi-restraints excluded: chain M residue 16 ILE Chi-restraints excluded: chain M residue 24 VAL Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 41 ASP Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 63 VAL Chi-restraints excluded: chain M residue 67 ASP Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 85 GLU Chi-restraints excluded: chain O residue 4 THR Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain Q residue 69 THR Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain S residue 68 HIS Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 65 LEU Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain U residue 18 PHE Chi-restraints excluded: chain U residue 20 ARG Chi-restraints excluded: chain U residue 41 THR Chi-restraints excluded: chain 03 residue 43 ASP Chi-restraints excluded: chain 03 residue 50 ILE Chi-restraints excluded: chain 03 residue 56 ASP Chi-restraints excluded: chain Z residue 16 ILE Chi-restraints excluded: chain Z residue 42 LEU Chi-restraints excluded: chain Z residue 97 THR Chi-restraints excluded: chain Z residue 100 LYS Chi-restraints excluded: chain Z residue 144 THR Chi-restraints excluded: chain Z residue 162 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1080 random chunks: chunk 525 optimal weight: 7.9990 chunk 680 optimal weight: 20.0000 chunk 912 optimal weight: 20.0000 chunk 262 optimal weight: 5.9990 chunk 790 optimal weight: 20.0000 chunk 126 optimal weight: 30.0000 chunk 238 optimal weight: 0.9980 chunk 858 optimal weight: 30.0000 chunk 359 optimal weight: 7.9990 chunk 881 optimal weight: 30.0000 chunk 108 optimal weight: 0.9980 overall best weight: 4.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 04 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 05 167 ASN 07 26 GLN ** 09 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 9 ASN ** 13 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 14 38 GLN ** 15 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 15 60 GLN ** 21 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 22 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 27 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 29 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 31 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 32 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 HIS ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 75 GLN ** I 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 109 GLN ** K 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 26 ASN R 30 ASN ** T 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.036837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.029391 restraints weight = 1391534.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.030321 restraints weight = 474832.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.030893 restraints weight = 249892.363| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2951 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2951 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.6064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 165170 Z= 0.193 Angle : 0.621 16.269 246822 Z= 0.314 Chirality : 0.034 0.402 31534 Planarity : 0.005 0.094 13429 Dihedral : 23.905 179.759 82044 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 21.91 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.21 % Favored : 90.47 % Rotamer: Outliers : 4.36 % Allowed : 26.60 % Favored : 69.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.11), residues: 6159 helix: -0.18 (0.12), residues: 1963 sheet: -1.41 (0.16), residues: 995 loop : -1.75 (0.11), residues: 3201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP P 60 HIS 0.009 0.001 HIS T 67 PHE 0.027 0.002 PHE15 68 TYR 0.029 0.002 TYR U 37 ARG 0.013 0.001 ARG34 12 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 40519.26 seconds wall clock time: 708 minutes 56.34 seconds (42536.34 seconds total)