Starting phenix.real_space_refine on Sat Mar 2 18:32:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kpw_8281/03_2024/5kpw_8281.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kpw_8281/03_2024/5kpw_8281.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kpw_8281/03_2024/5kpw_8281.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kpw_8281/03_2024/5kpw_8281.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kpw_8281/03_2024/5kpw_8281.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kpw_8281/03_2024/5kpw_8281.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.006 sd= 0.041 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 4811 5.49 5 S 178 5.16 5 C 78209 2.51 5 N 28775 2.21 5 O 42630 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 13": "NH1" <-> "NH2" Residue "B ARG 33": "NH1" <-> "NH2" Residue "B TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 59": "NH1" <-> "NH2" Residue "B ARG 77": "NH1" <-> "NH2" Residue "B ARG 83": "NH1" <-> "NH2" Residue "B ARG 169": "NH1" <-> "NH2" Residue "B ARG 184": "NH1" <-> "NH2" Residue "C ARG 21": "NH1" <-> "NH2" Residue "C ARG 44": "NH1" <-> "NH2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "C ARG 61": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C ARG 102": "NH1" <-> "NH2" Residue "C ARG 162": "NH1" <-> "NH2" Residue "C ARG 170": "NH1" <-> "NH2" Residue "D ARG 70": "NH1" <-> "NH2" Residue "D ARG 79": "NH1" <-> "NH2" Residue "D ARG 91": "NH1" <-> "NH2" Residue "D ARG 101": "NH1" <-> "NH2" Residue "D ARG 109": "NH1" <-> "NH2" Residue "D ARG 111": "NH1" <-> "NH2" Residue "D ARG 114": "NH1" <-> "NH2" Residue "D ARG 132": "NH1" <-> "NH2" Residue "E ARG 2": "NH1" <-> "NH2" Residue "E ARG 152": "NH1" <-> "NH2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 169": "NH1" <-> "NH2" Residue "F PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 13": "NH1" <-> "NH2" Residue "I ARG 37": "NH1" <-> "NH2" Residue "I TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 96": "NH1" <-> "NH2" Residue "I ARG 120": "NH1" <-> "NH2" Residue "K ARG 21": "NH1" <-> "NH2" Residue "K ARG 33": "NH1" <-> "NH2" Residue "K ARG 41": "NH1" <-> "NH2" Residue "K ARG 47": "NH1" <-> "NH2" Residue "K ARG 60": "NH1" <-> "NH2" Residue "K PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 78": "NH1" <-> "NH2" Residue "K ARG 126": "NH1" <-> "NH2" Residue "L ARG 10": "NH1" <-> "NH2" Residue "L ARG 18": "NH1" <-> "NH2" Residue "L ARG 40": "NH1" <-> "NH2" Residue "L ARG 44": "NH1" <-> "NH2" Residue "L ARG 50": "NH1" <-> "NH2" Residue "L ARG 55": "NH1" <-> "NH2" Residue "L ARG 59": "NH1" <-> "NH2" Residue "L ARG 114": "NH1" <-> "NH2" Residue "M ARG 8": "NH1" <-> "NH2" Residue "M ARG 12": "NH1" <-> "NH2" Residue "M ARG 17": "NH1" <-> "NH2" Residue "M ARG 22": "NH1" <-> "NH2" Residue "M ARG 46": "NH1" <-> "NH2" Residue "M ARG 63": "NH1" <-> "NH2" Residue "M ARG 64": "NH1" <-> "NH2" Residue "M ARG 69": "NH1" <-> "NH2" Residue "M ARG 71": "NH1" <-> "NH2" Residue "M ARG 96": "NH1" <-> "NH2" Residue "M ARG 118": "NH1" <-> "NH2" Residue "N ARG 10": "NH1" <-> "NH2" Residue "N ARG 16": "NH1" <-> "NH2" Residue "N ARG 25": "NH1" <-> "NH2" Residue "N TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 81": "NH1" <-> "NH2" Residue "N ARG 94": "NH1" <-> "NH2" Residue "N ARG 102": "NH1" <-> "NH2" Residue "N ARG 111": "NH1" <-> "NH2" Residue "O ARG 20": "NH1" <-> "NH2" Residue "O ARG 38": "NH1" <-> "NH2" Residue "O ARG 61": "NH1" <-> "NH2" Residue "O ARG 88": "NH1" <-> "NH2" Residue "O ARG 100": "NH1" <-> "NH2" Residue "O ARG 108": "NH1" <-> "NH2" Residue "P ARG 2": "NH1" <-> "NH2" Residue "P ARG 5": "NH1" <-> "NH2" Residue "P ARG 12": "NH1" <-> "NH2" Residue "P ARG 32": "NH1" <-> "NH2" Residue "P ARG 47": "NH1" <-> "NH2" Residue "P ARG 69": "NH1" <-> "NH2" Residue "Q PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 21": "NH1" <-> "NH2" Residue "Q ARG 68": "NH1" <-> "NH2" Residue "Q ARG 78": "NH1" <-> "NH2" Residue "Q ARG 79": "NH1" <-> "NH2" Residue "Q ARG 84": "NH1" <-> "NH2" Residue "R PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "R ARG 88": "NH1" <-> "NH2" Residue "R ARG 95": "NH1" <-> "NH2" Residue "R ARG 110": "NH1" <-> "NH2" Residue "S ARG 73": "NH1" <-> "NH2" Residue "T ARG 5": "NH1" <-> "NH2" Residue "T ARG 6": "NH1" <-> "NH2" Residue "T ARG 81": "NH1" <-> "NH2" Residue "T ARG 85": "NH1" <-> "NH2" Residue "T ARG 93": "NH1" <-> "NH2" Residue "U PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 29": "NH1" <-> "NH2" Residue "X ARG 47": "NH1" <-> "NH2" Residue "X ARG 52": "NH1" <-> "NH2" Residue "Y ARG 10": "NH1" <-> "NH2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 44": "NH1" <-> "NH2" Residue "Z PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 49": "NH1" <-> "NH2" Residue "Z ARG 56": "NH1" <-> "NH2" Residue "1 ARG 9": "NH1" <-> "NH2" Residue "1 ARG 15": "NH1" <-> "NH2" Residue "1 ARG 39": "NH1" <-> "NH2" Residue "1 ARG 51": "NH1" <-> "NH2" Residue "2 ARG 43": "NH1" <-> "NH2" Residue "3 ARG 3": "NH1" <-> "NH2" Residue "3 ARG 12": "NH1" <-> "NH2" Residue "3 ARG 14": "NH1" <-> "NH2" Residue "3 ARG 19": "NH1" <-> "NH2" Residue "3 ARG 21": "NH1" <-> "NH2" Residue "3 ARG 33": "NH1" <-> "NH2" Residue "3 ARG 41": "NH1" <-> "NH2" Residue "4 ARG 12": "NH1" <-> "NH2" Residue "4 ARG 29": "NH1" <-> "NH2" Residue "4 ARG 39": "NH1" <-> "NH2" Residue "4 ARG 41": "NH1" <-> "NH2" Residue "5 ARG 12": "NH1" <-> "NH2" Residue "5 ARG 24": "NH1" <-> "NH2" Residue "6 PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 107": "NH1" <-> "NH2" Residue "6 PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 224": "NH1" <-> "NH2" Residue "7 ARG 106": "NH1" <-> "NH2" Residue "7 ARG 130": "NH1" <-> "NH2" Residue "7 TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 156": "NH1" <-> "NH2" Residue "13 ARG 123": "NH1" <-> "NH2" Residue "16 TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "16 ARG 55": "NH1" <-> "NH2" Residue "18 ASP 37": "OD1" <-> "OD2" Residue "18 GLU 38": "OE1" <-> "OE2" Residue "18 PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "20 ARG 28": "NH1" <-> "NH2" Residue "22 TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "22 TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "25 PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "25 ARG 54": "NH1" <-> "NH2" Residue "25 ARG 61": "NH1" <-> "NH2" Residue "25 ARG 65": "NH1" <-> "NH2" Residue "25 ARG 66": "NH1" <-> "NH2" Residue "33 PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "33 ARG 596": "NH1" <-> "NH2" Residue "33 ARG 611": "NH1" <-> "NH2" Residue "33 ARG 651": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 154603 Number of models: 1 Model: "" Number of chains: 59 Chain: "A" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "B" 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: "C" 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: "D" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "E" 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: "F" 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: "G" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 988 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "H" 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: "I" 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: "J" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "K" 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: "L" 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: "M" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "N" 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: "O" 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: "P" 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: "Q" 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: "R" 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: "S" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "T" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "U" 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: "V" 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: "W" 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: "X" 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: "Y" 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: "Z" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "1" 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: "2" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 409 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "3" 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: "4" 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: "5" 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: "6" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1704 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "7" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "8" 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: "9" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1156 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "10" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 817 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "11" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "12" 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: "13" 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: "14" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "15" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 869 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 7, 'TRANS': 108} Chain: "16" 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: "17" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "18" 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: "19" 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: "20" 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: "21" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "22" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 535 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "23" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "24" 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: "25" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 544 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "26" Number of atoms: 33016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33016 Classifications: {'RNA': 1539} Modifications used: {'p5*END': 1, 'rna2p_pur': 93, 'rna2p_pyr': 52, 'rna3p_pur': 781, 'rna3p_pyr': 613} Link IDs: {'rna2p': 145, 'rna3p': 1393} Chain: "27" Number of atoms: 62322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62322 Classifications: {'RNA': 2903} Modifications used: {'p5*END': 1, 'rna2p_pur': 219, 'rna2p_pyr': 95, 'rna3p_pur': 1455, 'rna3p_pyr': 1134} Link IDs: {'rna2p': 314, 'rna3p': 2588} Chain: "28" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2572 Classifications: {'RNA': 120} Modifications used: {'p5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 61, 'rna3p_pyr': 53} Link IDs: {'rna2p': 6, 'rna3p': 113} Chain: "29" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 432 Classifications: {'RNA': 20} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 14, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 18} Chain: "30" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1623 Classifications: {'RNA': 76} Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p_pur': 36, 'rna3p_pyr': 33} Link IDs: {'rna2p': 7, 'rna3p': 68} Chain: "31" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1644 Classifications: {'RNA': 77} Modifications used: {'p5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 34, 'rna3p_pyr': 34} Link IDs: {'rna2p': 9, 'rna3p': 67} Chain: "32" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1643 Classifications: {'RNA': 77} Modifications used: {'p5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 6, 'rna3p_pur': 34, 'rna3p_pyr': 32} Link IDs: {'rna2p': 11, 'rna3p': 65} Chain: "33" Number of atoms: 4911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 4911 Classifications: {'peptide': 675} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 119} Link IDs: {'CIS': 1, 'PTRANS': 25, 'TRANS': 648} Chain breaks: 5 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 470 Unresolved non-hydrogen angles: 600 Unresolved non-hydrogen dihedrals: 392 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 10, 'TRP:plan': 3, 'ASP:plan': 11, 'PHE:plan': 4, 'GLU:plan': 8, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 287 Time building chain proxies: 57.53, per 1000 atoms: 0.37 Number of scatterers: 154603 At special positions: 0 Unit cell: (277.16, 265.68, 239.44, 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 178 16.00 P 4811 15.00 O 42630 8.00 N 28775 7.00 C 78209 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS Z 18 " - pdb=" SG CYS Z 40 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 37 " - pdb=" SG CYS Z 40 " distance=2.03 Simple disulfide: pdb=" SG CYS33 178 " - pdb=" SG CYS33 202 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 63.81 Conformation dependent library (CDL) restraints added in 7.8 seconds 13018 Ramachandran restraints generated. 6509 Oldfield, 0 Emsley, 6509 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12182 Finding SS restraints... Secondary structure from input PDB file: 222 helices and 79 sheets defined 37.8% alpha, 12.5% beta 1552 base pairs and 2554 stacking pairs defined. Time for finding SS restraints: 57.39 Creating SS restraints... Processing helix chain 'A' and resid 29 through 31 No H-bonds generated for 'chain 'A' and resid 29 through 31' Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 196 through 202 removed outlier: 4.231A pdb=" N MET A 200 " --> pdb=" O ALA A 197 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG A 202 " --> pdb=" O HIS A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 213 removed outlier: 3.795A pdb=" N ALA A 210 " --> pdb=" O LYS A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 229 Processing helix chain 'B' and resid 61 through 72 Processing helix chain 'B' and resid 98 through 102 Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'C' and resid 15 through 20 Processing helix chain 'C' and resid 24 through 40 Processing helix chain 'C' and resid 97 through 115 Processing helix chain 'C' and resid 130 through 141 removed outlier: 3.949A pdb=" N LEU C 134 " --> pdb=" O LYS C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 159 Processing helix chain 'C' and resid 176 through 183 Processing helix chain 'C' and resid 190 through 201 Processing helix chain 'D' and resid 2 through 17 removed outlier: 4.666A pdb=" N VAL D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 27 Processing helix chain 'D' and resid 40 through 44 removed outlier: 4.168A pdb=" N ILE D 43 " --> pdb=" O GLY D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 60 removed outlier: 3.722A pdb=" N LEU D 49 " --> pdb=" O ASP D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 77 Processing helix chain 'D' and resid 92 through 104 Processing helix chain 'D' and resid 105 through 110 removed outlier: 3.679A pdb=" N ARG D 109 " --> pdb=" O ILE D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 121 removed outlier: 3.895A pdb=" N SER D 120 " --> pdb=" O SER D 117 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N PHE D 121 " --> pdb=" O ALA D 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 117 through 121' Processing helix chain 'D' and resid 133 through 137 removed outlier: 3.544A pdb=" N PHE D 137 " --> pdb=" O GLN D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 145 removed outlier: 3.551A pdb=" N LYS D 144 " --> pdb=" O ASP D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 170 Processing helix chain 'D' and resid 171 through 173 No H-bonds generated for 'chain 'D' and resid 171 through 173' Processing helix chain 'E' and resid 59 through 78 removed outlier: 3.792A pdb=" N GLN E 63 " --> pdb=" O ASP E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 150 removed outlier: 3.575A pdb=" N ILE E 140 " --> pdb=" O ASP E 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 29 Processing helix chain 'F' and resid 41 through 48 Processing helix chain 'F' and resid 54 through 74 Processing helix chain 'F' and resid 95 through 105 removed outlier: 3.579A pdb=" N ILE F 99 " --> pdb=" O GLY F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 113 No H-bonds generated for 'chain 'F' and resid 111 through 113' Processing helix chain 'G' and resid 3 through 20 removed outlier: 3.822A pdb=" N LYS G 20 " --> pdb=" O SER G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 45 Processing helix chain 'G' and resid 73 through 78 removed outlier: 3.882A pdb=" N VAL G 77 " --> pdb=" O LYS G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 96 Processing helix chain 'G' and resid 97 through 103 Processing helix chain 'H' and resid 22 through 29 removed outlier: 4.059A pdb=" N LEU H 27 " --> pdb=" O VAL H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 33 through 45 Processing helix chain 'H' and resid 74 through 84 removed outlier: 3.655A pdb=" N LEU H 78 " --> pdb=" O PRO H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 113 Processing helix chain 'H' and resid 120 through 135 Processing helix chain 'I' and resid 24 through 37 Processing helix chain 'I' and resid 58 through 62 Processing helix chain 'I' and resid 67 through 72 Processing helix chain 'I' and resid 88 through 96 Processing helix chain 'I' and resid 96 through 107 removed outlier: 4.004A pdb=" N VAL I 100 " --> pdb=" O ARG I 96 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE I 101 " --> pdb=" O PRO I 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 120 Processing helix chain 'J' and resid 104 through 108 Processing helix chain 'J' and resid 112 through 119 removed outlier: 3.625A pdb=" N ILE J 116 " --> pdb=" O PHE J 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 56 through 61 Processing helix chain 'K' and resid 69 through 74 removed outlier: 3.895A pdb=" N ILE K 73 " --> pdb=" O ARG K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 97 Processing helix chain 'K' and resid 128 through 138 Processing helix chain 'L' and resid 43 through 58 removed outlier: 4.350A pdb=" N ALA L 56 " --> pdb=" O ALA L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 109 through 124 Processing helix chain 'M' and resid 13 through 32 Processing helix chain 'M' and resid 38 through 56 removed outlier: 3.845A pdb=" N ARG M 46 " --> pdb=" O LYS M 42 " (cutoff:3.500A) Proline residue: M 50 - end of helix Processing helix chain 'M' and resid 60 through 69 Processing helix chain 'M' and resid 72 through 82 removed outlier: 4.433A pdb=" N PHE M 80 " --> pdb=" O VAL M 76 " (cutoff:3.500A) Processing helix chain 'M' and resid 82 through 87 Processing helix chain 'N' and resid 3 through 22 removed outlier: 4.416A pdb=" N ARG N 13 " --> pdb=" O ARG N 9 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ALA N 14 " --> pdb=" O ARG N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 60 Processing helix chain 'N' and resid 67 through 85 Processing helix chain 'N' and resid 101 through 113 Processing helix chain 'O' and resid 2 through 12 removed outlier: 3.781A pdb=" N GLN O 11 " --> pdb=" O LEU O 7 " (cutoff:3.500A) Processing helix chain 'O' and resid 52 through 55 Processing helix chain 'O' and resid 96 through 101 Processing helix chain 'O' and resid 103 through 108 removed outlier: 3.736A pdb=" N ARG O 108 " --> pdb=" O GLY O 104 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 18 Processing helix chain 'P' and resid 19 through 21 No H-bonds generated for 'chain 'P' and resid 19 through 21' Processing helix chain 'P' and resid 24 through 29 Processing helix chain 'P' and resid 30 through 71 removed outlier: 4.385A pdb=" N GLN P 36 " --> pdb=" O ARG P 32 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG P 50 " --> pdb=" O TYR P 46 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LYS P 53 " --> pdb=" O ARG P 49 " (cutoff:3.500A) Processing helix chain 'P' and resid 74 through 85 Processing helix chain 'P' and resid 90 through 100 removed outlier: 3.530A pdb=" N ASP P 96 " --> pdb=" O LYS P 92 " (cutoff:3.500A) Processing helix chain 'P' and resid 101 through 116 Processing helix chain 'R' and resid 13 through 22 Processing helix chain 'R' and resid 28 through 38 removed outlier: 3.983A pdb=" N TYR R 38 " --> pdb=" O ASP R 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 60 removed outlier: 3.926A pdb=" N VAL R 50 " --> pdb=" O LEU R 46 " (cutoff:3.500A) Processing helix chain 'R' and resid 89 through 91 No H-bonds generated for 'chain 'R' and resid 89 through 91' Processing helix chain 'S' and resid 2 through 11 removed outlier: 4.928A pdb=" N LYS S 9 " --> pdb=" O GLU S 5 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU S 11 " --> pdb=" O LEU S 7 " (cutoff:3.500A) Processing helix chain 'S' and resid 17 through 27 Processing helix chain 'S' and resid 39 through 51 Processing helix chain 'U' and resid 13 through 22 Processing helix chain 'U' and resid 43 through 51 removed outlier: 4.219A pdb=" N VAL U 47 " --> pdb=" O ASP U 43 " (cutoff:3.500A) Processing helix chain 'U' and resid 54 through 59 removed outlier: 3.504A pdb=" N SER U 58 " --> pdb=" O ALA U 54 " (cutoff:3.500A) Processing helix chain 'W' and resid 52 through 61 Processing helix chain 'W' and resid 62 through 73 Processing helix chain 'X' and resid 9 through 24 Processing helix chain 'X' and resid 24 through 34 Processing helix chain 'X' and resid 39 through 61 removed outlier: 3.724A pdb=" N LEU X 43 " --> pdb=" O GLN X 39 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 26 Processing helix chain 'Y' and resid 40 through 50 Processing helix chain 'Z' and resid 56 through 63 Processing helix chain '1' and resid 8 through 17 Processing helix chain '1' and resid 18 through 20 No H-bonds generated for 'chain '1' and resid 18 through 20' Processing helix chain '3' and resid 9 through 15 Processing helix chain '3' and resid 17 through 23 Processing helix chain '3' and resid 24 through 37 Processing helix chain '4' and resid 6 through 11 removed outlier: 3.735A pdb=" N ALA 4 10 " --> pdb=" O VAL 4 6 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS 4 11 " --> pdb=" O ARG 4 7 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 6 through 11' Processing helix chain '4' and resid 36 through 44 Processing helix chain '4' and resid 50 through 61 removed outlier: 4.009A pdb=" N GLY 4 55 " --> pdb=" O LYS 4 51 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N LEU 4 56 " --> pdb=" O GLY 4 52 " (cutoff:3.500A) Processing helix chain '5' and resid 18 through 22 removed outlier: 4.131A pdb=" N GLY 5 21 " --> pdb=" O LYS 5 18 " (cutoff:3.500A) Processing helix chain '5' and resid 30 through 34 Processing helix chain '6' and resid 23 through 27 Processing helix chain '6' and resid 41 through 62 removed outlier: 3.604A pdb=" N THR 6 45 " --> pdb=" O ASN 6 41 " (cutoff:3.500A) Proline residue: 6 47 - end of helix Processing helix chain '6' and resid 73 through 86 removed outlier: 4.129A pdb=" N GLU 6 77 " --> pdb=" O ARG 6 73 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA 6 78 " --> pdb=" O ALA 6 74 " (cutoff:3.500A) Processing helix chain '6' and resid 102 through 122 removed outlier: 3.551A pdb=" N VAL 6 106 " --> pdb=" O ASN 6 102 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N GLN 6 108 " --> pdb=" O LYS 6 104 " (cutoff:3.500A) Processing helix chain '6' and resid 124 through 128 removed outlier: 3.537A pdb=" N LEU 6 128 " --> pdb=" O PHE 6 125 " (cutoff:3.500A) Processing helix chain '6' and resid 129 through 146 Processing helix chain '6' and resid 168 through 178 removed outlier: 3.647A pdb=" N LEU 6 178 " --> pdb=" O GLU 6 174 " (cutoff:3.500A) Processing helix chain '6' and resid 205 through 223 removed outlier: 4.016A pdb=" N VAL 6 209 " --> pdb=" O ALA 6 205 " (cutoff:3.500A) Processing helix chain '7' and resid 5 through 10 removed outlier: 3.540A pdb=" N ILE 7 9 " --> pdb=" O HIS 7 5 " (cutoff:3.500A) Processing helix chain '7' and resid 27 through 46 Processing helix chain '7' and resid 71 through 77 Processing helix chain '7' and resid 80 through 95 removed outlier: 3.753A pdb=" N GLU 7 84 " --> pdb=" O GLY 7 80 " (cutoff:3.500A) Processing helix chain '7' and resid 111 through 125 Processing helix chain '7' and resid 128 through 144 removed outlier: 3.692A pdb=" N ALA 7 132 " --> pdb=" O MET 7 128 " (cutoff:3.500A) Processing helix chain '8' and resid 6 through 15 removed outlier: 3.821A pdb=" N LEU 8 10 " --> pdb=" O PRO 8 6 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER 8 11 " --> pdb=" O LYS 8 7 " (cutoff:3.500A) Processing helix chain '8' and resid 39 through 43 removed outlier: 3.859A pdb=" N ALA 8 42 " --> pdb=" O GLN 8 39 " (cutoff:3.500A) Processing helix chain '8' and resid 48 through 64 Processing helix chain '8' and resid 67 through 81 Processing helix chain '8' and resid 84 through 96 removed outlier: 3.562A pdb=" N ARG 8 96 " --> pdb=" O LEU 8 92 " (cutoff:3.500A) Processing helix chain '8' and resid 96 through 105 Processing helix chain '8' and resid 109 through 119 Processing helix chain '8' and resid 152 through 162 Processing helix chain '8' and resid 174 through 177 Processing helix chain '8' and resid 196 through 205 Processing helix chain '9' and resid 54 through 68 removed outlier: 3.847A pdb=" N LYS 9 65 " --> pdb=" O LYS 9 61 " (cutoff:3.500A) Processing helix chain '9' and resid 109 through 118 removed outlier: 3.602A pdb=" N VAL 9 113 " --> pdb=" O ALA 9 109 " (cutoff:3.500A) Processing helix chain '9' and resid 131 through 146 Processing helix chain '9' and resid 148 through 156 Processing helix chain '9' and resid 159 through 165 removed outlier: 3.635A pdb=" N ILE 9 163 " --> pdb=" O SER 9 159 " (cutoff:3.500A) Processing helix chain '10' and resid 11 through 16 removed outlier: 3.536A pdb=" N GLU10 16 " --> pdb=" O PRO10 12 " (cutoff:3.500A) Processing helix chain '10' and resid 17 through 32 removed outlier: 3.661A pdb=" N MET10 21 " --> pdb=" O GLN10 17 " (cutoff:3.500A) Processing helix chain '10' and resid 67 through 81 removed outlier: 3.523A pdb=" N PHE10 80 " --> pdb=" O THR10 76 " (cutoff:3.500A) Processing helix chain '11' and resid 19 through 30 Processing helix chain '11' and resid 34 through 54 Processing helix chain '11' and resid 56 through 67 removed outlier: 3.941A pdb=" N ASN11 67 " --> pdb=" O VAL11 63 " (cutoff:3.500A) Processing helix chain '11' and resid 91 through 109 removed outlier: 3.663A pdb=" N LYS11 109 " --> pdb=" O GLU11 105 " (cutoff:3.500A) Processing helix chain '11' and resid 114 through 128 removed outlier: 3.695A pdb=" N GLU11 128 " --> pdb=" O SER11 124 " (cutoff:3.500A) Processing helix chain '11' and resid 131 through 146 Processing helix chain '12' and resid 4 through 19 Processing helix chain '12' and resid 29 through 42 Processing helix chain '12' and resid 87 through 91 Processing helix chain '12' and resid 93 through 98 Processing helix chain '12' and resid 111 through 119 Processing helix chain '13' and resid 33 through 38 Processing helix chain '13' and resid 44 through 54 removed outlier: 3.799A pdb=" N ARG13 48 " --> pdb=" O ARG13 44 " (cutoff:3.500A) Proline residue: 13 50 - end of helix removed outlier: 3.562A pdb=" N LEU13 53 " --> pdb=" O GLN13 49 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL13 54 " --> pdb=" O PRO13 50 " (cutoff:3.500A) Processing helix chain '13' and resid 70 through 86 Processing helix chain '13' and resid 90 through 101 removed outlier: 4.922A pdb=" N GLU13 96 " --> pdb=" O SER13 92 " (cutoff:3.500A) Processing helix chain '14' and resid 14 through 32 removed outlier: 3.695A pdb=" N GLN14 20 " --> pdb=" O ARG14 16 " (cutoff:3.500A) Processing helix chain '14' and resid 80 through 88 removed outlier: 3.570A pdb=" N ASP14 85 " --> pdb=" O GLU14 81 " (cutoff:3.500A) Processing helix chain '15' and resid 46 through 50 removed outlier: 3.739A pdb=" N GLY15 50 " --> pdb=" O GLY15 47 " (cutoff:3.500A) Processing helix chain '15' and resid 52 through 57 removed outlier: 3.805A pdb=" N ARG15 55 " --> pdb=" O ARG15 52 " (cutoff:3.500A) Processing helix chain '15' and resid 58 through 71 Processing helix chain '15' and resid 73 through 77 Processing helix chain '15' and resid 94 through 102 Processing helix chain '16' and resid 2 through 9 removed outlier: 3.525A pdb=" N LEU16 6 " --> pdb=" O THR16 2 " (cutoff:3.500A) Processing helix chain '17' and resid 2 through 6 Processing helix chain '17' and resid 13 through 18 Processing helix chain '17' and resid 25 through 36 Processing helix chain '17' and resid 48 through 60 removed outlier: 4.686A pdb=" N THR17 54 " --> pdb=" O GLY17 50 " (cutoff:3.500A) Processing helix chain '17' and resid 64 through 83 Processing helix chain '17' and resid 84 through 92 Processing helix chain '17' and resid 105 through 110 Processing helix chain '18' and resid 2 through 19 Processing helix chain '18' and resid 28 through 32 removed outlier: 3.620A pdb=" N ASP18 32 " --> pdb=" O ILE18 29 " (cutoff:3.500A) Processing helix chain '18' and resid 37 through 50 removed outlier: 3.944A pdb=" N TRP18 41 " --> pdb=" O ASP18 37 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N GLN18 48 " --> pdb=" O VAL18 44 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR18 49 " --> pdb=" O LEU18 45 " (cutoff:3.500A) Processing helix chain '18' and resid 55 through 59 Processing helix chain '18' and resid 79 through 90 Processing helix chain '19' and resid 3 through 15 Processing helix chain '19' and resid 23 through 44 removed outlier: 4.464A pdb=" N GLY19 40 " --> pdb=" O ASN19 36 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N HIS19 41 " --> pdb=" O HIS19 37 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU19 44 " --> pdb=" O GLY19 40 " (cutoff:3.500A) Processing helix chain '19' and resid 48 through 73 Processing helix chain '19' and resid 73 through 85 removed outlier: 3.519A pdb=" N TYR19 77 " --> pdb=" O ASP19 73 " (cutoff:3.500A) Processing helix chain '20' and resid 40 through 44 removed outlier: 4.516A pdb=" N SER20 44 " --> pdb=" O PRO20 41 " (cutoff:3.500A) Processing helix chain '20' and resid 53 through 62 removed outlier: 3.899A pdb=" N ILE20 57 " --> pdb=" O ASP20 53 " (cutoff:3.500A) Processing helix chain '20' and resid 68 through 79 Processing helix chain '22' and resid 11 through 15 removed outlier: 3.924A pdb=" N ALA22 14 " --> pdb=" O ARG22 11 " (cutoff:3.500A) Processing helix chain '22' and resid 24 through 30 removed outlier: 3.756A pdb=" N ASN22 30 " --> pdb=" O ALA22 26 " (cutoff:3.500A) Processing helix chain '22' and resid 40 through 45 removed outlier: 3.592A pdb=" N THR22 44 " --> pdb=" O PRO22 40 " (cutoff:3.500A) Processing helix chain '22' and resid 47 through 64 Processing helix chain '23' and resid 11 through 23 Processing helix chain '23' and resid 40 through 44 Processing helix chain '23' and resid 69 through 74 Processing helix chain '24' and resid 6 through 41 Processing helix chain '24' and resid 42 through 63 Proline residue: 24 55 - end of helix Processing helix chain '24' and resid 67 through 85 removed outlier: 3.656A pdb=" N ALA24 71 " --> pdb=" O HIS24 67 " (cutoff:3.500A) Processing helix chain '25' and resid 24 through 32 removed outlier: 4.429A pdb=" N GLU25 30 " --> pdb=" O GLY25 26 " (cutoff:3.500A) Processing helix chain '25' and resid 38 through 58 removed outlier: 4.044A pdb=" N THR25 42 " --> pdb=" O GLU25 38 " (cutoff:3.500A) Processing helix chain '33' and resid 17 through 23 Processing helix chain '33' and resid 28 through 43 Processing helix chain '33' and resid 55 through 69 removed outlier: 4.249A pdb=" N GLY33 59 " --> pdb=" O LEU33 55 " (cutoff:3.500A) Processing helix chain '33' and resid 72 through 82 Processing helix chain '33' and resid 83 through 88 Processing helix chain '33' and resid 91 through 100 Processing helix chain '33' and resid 100 through 113 Processing helix chain '33' and resid 146 through 161 Processing helix chain '33' and resid 170 through 181 Processing helix chain '33' and resid 181 through 189 Processing helix chain '33' and resid 191 through 207 removed outlier: 3.522A pdb=" N GLU33 197 " --> pdb=" O GLN33 193 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR33 205 " --> pdb=" O TYR33 201 " (cutoff:3.500A) Processing helix chain '33' and resid 207 through 221 removed outlier: 3.802A pdb=" N HIS33 219 " --> pdb=" O ALA33 215 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU33 220 " --> pdb=" O LYS33 216 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ARG33 221 " --> pdb=" O LEU33 217 " (cutoff:3.500A) Processing helix chain '33' and resid 221 through 242 Processing helix chain '33' and resid 255 through 267 Processing helix chain '33' and resid 268 through 270 No H-bonds generated for 'chain '33' and resid 268 through 270' Processing helix chain '33' and resid 273 through 276 Processing helix chain '33' and resid 285 through 300 Processing helix chain '33' and resid 341 through 350 Processing helix chain '33' and resid 361 through 381 Processing helix chain '33' and resid 423 through 432 Processing helix chain '33' and resid 432 through 438 Processing helix chain '33' and resid 485 through 517 removed outlier: 4.415A pdb=" N ARG33 489 " --> pdb=" O THR33 485 " (cutoff:3.500A) Processing helix chain '33' and resid 522 through 530 Processing helix chain '33' and resid 538 through 547 removed outlier: 3.684A pdb=" N LEU33 543 " --> pdb=" O VAL33 539 " (cutoff:3.500A) Processing helix chain '33' and resid 554 through 561 Processing helix chain '33' and resid 568 through 579 removed outlier: 3.851A pdb=" N LEU33 577 " --> pdb=" O ASP33 573 " (cutoff:3.500A) Processing helix chain '33' and resid 598 through 602 Processing helix chain '33' and resid 638 through 645 Processing helix chain '33' and resid 679 through 687 removed outlier: 3.854A pdb=" N ILE33 683 " --> pdb=" O LEU33 679 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE33 686 " --> pdb=" O ASP33 682 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU33 687 " --> pdb=" O ILE33 683 " (cutoff:3.500A) Processing helix chain '33' and resid 718 through 732 removed outlier: 3.630A pdb=" N GLY33 723 " --> pdb=" O LEU33 719 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY33 727 " --> pdb=" O GLY33 723 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N LYS33 728 " --> pdb=" O ARG33 724 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU33 729 " --> pdb=" O VAL33 725 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL33 732 " --> pdb=" O LYS33 728 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 4 Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 34 Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 104 Processing sheet with id=AA4, first strand: chain 'A' and resid 128 through 130 removed outlier: 3.811A pdb=" N GLN A 162 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR A 172 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ARG A 166 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N TYR A 170 " --> pdb=" O ARG A 166 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LYS A 182 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ILE A 266 " --> pdb=" O LYS A 182 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 169 through 170 removed outlier: 4.051A pdb=" N THR B 112 " --> pdb=" O ASP B 200 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ASP B 200 " --> pdb=" O THR B 112 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LYS B 7 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL B 26 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N MET B 11 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N VAL B 24 " --> pdb=" O MET B 11 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ARG B 13 " --> pdb=" O ILE B 22 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ILE B 22 " --> pdb=" O ARG B 13 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N PHE B 15 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL B 20 " --> pdb=" O PHE B 15 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 80 through 83 removed outlier: 6.638A pdb=" N THR B 51 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N VAL B 34 " --> pdb=" O THR B 51 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 117 through 119 Processing sheet with id=AA8, first strand: chain 'C' and resid 118 through 121 removed outlier: 7.738A pdb=" N LYS C 185 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ILE C 149 " --> pdb=" O LYS C 185 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL C 187 " --> pdb=" O ILE C 149 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 65 through 68 removed outlier: 3.746A pdb=" N GLY D 85 " --> pdb=" O THR D 67 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU D 90 " --> pdb=" O ILE D 33 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS D 32 " --> pdb=" O THR D 156 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 15 through 19 Processing sheet with id=AB2, first strand: chain 'E' and resid 41 through 43 Processing sheet with id=AB3, first strand: chain 'E' and resid 120 through 121 Processing sheet with id=AB4, first strand: chain 'E' and resid 93 through 96 Processing sheet with id=AB5, first strand: chain 'F' and resid 4 through 5 Processing sheet with id=AB6, first strand: chain 'F' and resid 77 through 80 removed outlier: 6.712A pdb=" N VAL F 78 " --> pdb=" O ASN F 145 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 10 through 13 Processing sheet with id=AB8, first strand: chain 'I' and resid 55 through 57 removed outlier: 6.543A pdb=" N TYR I 16 " --> pdb=" O ILE I 55 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N LEU I 57 " --> pdb=" O TYR I 16 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL I 18 " --> pdb=" O LEU I 57 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 74 through 77 Processing sheet with id=AC1, first strand: chain 'J' and resid 92 through 94 removed outlier: 4.707A pdb=" N GLN J 93 " --> pdb=" O ASN J 88 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA J 83 " --> pdb=" O VAL J 63 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LYS J 59 " --> pdb=" O LEU J 87 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ILE J 41 " --> pdb=" O ILE J 22 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE J 22 " --> pdb=" O ILE J 41 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ILE J 43 " --> pdb=" O MET J 20 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N MET J 20 " --> pdb=" O ILE J 43 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N CYS J 84 " --> pdb=" O MET J 7 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASN J 9 " --> pdb=" O CYS J 84 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N LEU J 86 " --> pdb=" O ASN J 9 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 69 through 70 Processing sheet with id=AC3, first strand: chain 'K' and resid 89 through 91 removed outlier: 6.618A pdb=" N VAL K 90 " --> pdb=" O ARG K 123 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 31 through 35 removed outlier: 3.846A pdb=" N GLY L 32 " --> pdb=" O VAL L 131 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 39 through 42 removed outlier: 6.969A pdb=" N ILE L 73 " --> pdb=" O GLU L 90 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N TRP L 92 " --> pdb=" O LYS L 71 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LYS L 71 " --> pdb=" O TRP L 92 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 62 through 64 Processing sheet with id=AC7, first strand: chain 'M' and resid 33 through 37 Processing sheet with id=AC8, first strand: chain 'N' and resid 47 through 51 removed outlier: 4.025A pdb=" N VAL N 49 " --> pdb=" O VAL N 39 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'O' and resid 72 through 74 removed outlier: 3.728A pdb=" N ALA O 48 " --> pdb=" O THR O 59 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ARG O 61 " --> pdb=" O VAL O 46 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N VAL O 46 " --> pdb=" O ARG O 61 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N THR O 24 " --> pdb=" O VAL O 85 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N VAL O 85 " --> pdb=" O THR O 24 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLU O 26 " --> pdb=" O ILE O 83 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ILE O 83 " --> pdb=" O GLU O 26 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LYS O 28 " --> pdb=" O ASP O 81 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'O' and resid 31 through 33 removed outlier: 3.592A pdb=" N LYS O 36 " --> pdb=" O GLU O 33 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Q' and resid 3 through 5 removed outlier: 6.320A pdb=" N VAL Q 4 " --> pdb=" O LEU Q 39 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE Q 41 " --> pdb=" O VAL Q 47 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Q' and resid 19 through 22 removed outlier: 6.746A pdb=" N ASP Q 95 " --> pdb=" O VAL Q 64 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LYS Q 60 " --> pdb=" O THR Q 99 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Q' and resid 74 through 78 removed outlier: 3.947A pdb=" N TYR Q 83 " --> pdb=" O ARG Q 78 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'R' and resid 7 through 10 removed outlier: 4.824A pdb=" N ARG R 8 " --> pdb=" O ILE R 103 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE R 103 " --> pdb=" O ARG R 8 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LYS R 98 " --> pdb=" O SER R 81 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N SER R 81 " --> pdb=" O LYS R 98 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N THR R 100 " --> pdb=" O GLY R 79 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'R' and resid 85 through 87 Processing sheet with id=AD7, first strand: chain 'S' and resid 13 through 14 Processing sheet with id=AD8, first strand: chain 'T' and resid 64 through 65 removed outlier: 3.895A pdb=" N ASN T 26 " --> pdb=" O ILE T 34 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ASP T 8 " --> pdb=" O VAL T 24 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'T' and resid 40 through 43 Processing sheet with id=AE1, first strand: chain 'T' and resid 82 through 87 Processing sheet with id=AE2, first strand: chain 'U' and resid 5 through 8 removed outlier: 8.595A pdb=" N PHE U 91 " --> pdb=" O PRO U 27 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE U 29 " --> pdb=" O PHE U 91 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ARG U 93 " --> pdb=" O ILE U 29 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N TYR U 31 " --> pdb=" O ARG U 93 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ASP U 90 " --> pdb=" O GLN U 75 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'V' and resid 47 through 49 Processing sheet with id=AE4, first strand: chain 'V' and resid 62 through 66 Processing sheet with id=AE5, first strand: chain 'W' and resid 12 through 15 Processing sheet with id=AE6, first strand: chain 'W' and resid 32 through 33 Processing sheet with id=AE7, first strand: chain 'W' and resid 36 through 39 Processing sheet with id=AE8, first strand: chain 'Y' and resid 34 through 36 removed outlier: 3.716A pdb=" N LYS Y 5 " --> pdb=" O GLU Y 57 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Z' and resid 10 through 12 Processing sheet with id=AF1, first strand: chain '2' and resid 19 through 24 Processing sheet with id=AF2, first strand: chain '2' and resid 38 through 39 removed outlier: 3.731A pdb=" N ASP 2 39 " --> pdb=" O GLN 2 44 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain '4' and resid 13 through 15 Processing sheet with id=AF4, first strand: chain '5' and resid 14 through 16 Processing sheet with id=AF5, first strand: chain '6' and resid 89 through 91 removed outlier: 6.660A pdb=" N ILE 6 66 " --> pdb=" O PHE 6 89 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL 6 91 " --> pdb=" O ILE 6 66 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N PHE 6 68 " --> pdb=" O VAL 6 91 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N LEU 6 160 " --> pdb=" O PHE 6 183 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain '7' and resid 19 through 20 removed outlier: 5.696A pdb=" N VAL 7 65 " --> pdb=" O ASN 7 101 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ALA 7 103 " --> pdb=" O VAL 7 65 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ILE 7 67 " --> pdb=" O ALA 7 103 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain '7' and resid 163 through 169 Processing sheet with id=AF8, first strand: chain '8' and resid 127 through 128 Processing sheet with id=AF9, first strand: chain '8' and resid 171 through 172 Processing sheet with id=AG1, first strand: chain '9' and resid 13 through 18 removed outlier: 5.492A pdb=" N LEU 9 14 " --> pdb=" O VAL 9 37 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL 9 37 " --> pdb=" O LEU 9 14 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain '9' and resid 13 through 18 removed outlier: 5.492A pdb=" N LEU 9 14 " --> pdb=" O VAL 9 37 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL 9 37 " --> pdb=" O LEU 9 14 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain '9' and resid 84 through 85 Processing sheet with id=AG4, first strand: chain '10' and resid 2 through 4 Processing sheet with id=AG5, first strand: chain '10' and resid 7 through 10 Processing sheet with id=AG6, first strand: chain '11' and resid 72 through 73 Processing sheet with id=AG7, first strand: chain '11' and resid 76 through 77 Processing sheet with id=AG8, first strand: chain '12' and resid 24 through 27 removed outlier: 4.333A pdb=" N ASP12 47 " --> pdb=" O THR12 61 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain '12' and resid 75 through 76 Processing sheet with id=AH1, first strand: chain '12' and resid 75 through 76 removed outlier: 6.831A pdb=" N VAL12 102 " --> pdb=" O ILE12 125 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain '13' and resid 14 through 21 removed outlier: 5.808A pdb=" N LYS13 26 " --> pdb=" O LEU13 62 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE13 64 " --> pdb=" O LYS13 26 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL13 28 " --> pdb=" O ILE13 64 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N VAL13 66 " --> pdb=" O VAL13 28 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain '14' and resid 70 through 73 Processing sheet with id=AH4, first strand: chain '14' and resid 48 through 52 Processing sheet with id=AH5, first strand: chain '15' and resid 40 through 44 removed outlier: 3.739A pdb=" N GLY15 42 " --> pdb=" O ILE15 33 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU15 81 " --> pdb=" O ASN15 108 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N THR15 110 " --> pdb=" O LEU15 81 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N VAL15 83 " --> pdb=" O THR15 110 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain '16' and resid 29 through 31 removed outlier: 7.086A pdb=" N TYR16 65 " --> pdb=" O THR16 96 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain '16' and resid 34 through 39 removed outlier: 4.833A pdb=" N ARG16 35 " --> pdb=" O ARG16 53 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG16 49 " --> pdb=" O THR16 39 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N PHE16 60 " --> pdb=" O LEU16 56 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain '20' and resid 34 through 35 Processing sheet with id=AH9, first strand: chain '21' and resid 11 through 13 removed outlier: 6.903A pdb=" N VAL21 21 " --> pdb=" O VAL21 12 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N HIS21 44 " --> pdb=" O LYS21 70 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N TRP21 72 " --> pdb=" O HIS21 44 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N SER21 71 " --> pdb=" O CYS21 63 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N GLU21 59 " --> pdb=" O VAL21 75 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain '22' and resid 32 through 33 removed outlier: 3.821A pdb=" N LYS22 37 " --> pdb=" O THR22 33 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain '23' and resid 31 through 32 Processing sheet with id=AI3, first strand: chain '33' and resid 247 through 252 removed outlier: 3.956A pdb=" N ALA33 278 " --> pdb=" O ARG33 252 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain '33' and resid 406 through 410 removed outlier: 3.827A pdb=" N ASP33 414 " --> pdb=" O THR33 410 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain '33' and resid 447 through 449 removed outlier: 4.447A pdb=" N ALA33 442 " --> pdb=" O VAL33 449 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain '33' and resid 631 through 633 Processing sheet with id=AI7, first strand: chain '33' and resid 697 through 698 removed outlier: 3.955A pdb=" N ILE33 710 " --> pdb=" O VAL33 671 " (cutoff:3.500A) 2028 hydrogen bonds defined for protein. 5643 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3903 hydrogen bonds 6276 hydrogen bond angles 0 basepair planarities 1552 basepair parallelities 2554 stacking parallelities Total time for adding SS restraints: 232.83 Time building geometry restraints manager: 68.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 15182 1.31 - 1.45: 72986 1.45 - 1.58: 69587 1.58 - 1.72: 9618 1.72 - 1.85: 310 Bond restraints: 167683 Sorted by residual: bond pdb=" CZ ARG33 156 " pdb=" NH2 ARG33 156 " ideal model delta sigma weight residual 1.330 1.188 0.142 1.30e-02 5.92e+03 1.20e+02 bond pdb=" CA PRO33 17 " pdb=" CB PRO33 17 " ideal model delta sigma weight residual 1.534 1.386 0.148 1.49e-02 4.50e+03 9.83e+01 bond pdb=" NE1 TRP33 20 " pdb=" CE2 TRP33 20 " ideal model delta sigma weight residual 1.370 1.285 0.085 1.10e-02 8.26e+03 5.94e+01 bond pdb=" CD LYS33 152 " pdb=" CE LYS33 152 " ideal model delta sigma weight residual 1.520 1.314 0.206 3.00e-02 1.11e+03 4.71e+01 bond pdb=" CG HIS33 159 " pdb=" ND1 HIS33 159 " ideal model delta sigma weight residual 1.378 1.307 0.071 1.10e-02 8.26e+03 4.16e+01 ... (remaining 167678 not shown) Histogram of bond angle deviations from ideal: 88.66 - 98.04: 17 98.04 - 107.41: 35369 107.41 - 116.79: 115613 116.79 - 126.17: 83610 126.17 - 135.54: 15671 Bond angle restraints: 250280 Sorted by residual: angle pdb=" N VAL M 60 " pdb=" CA VAL M 60 " pdb=" C VAL M 60 " ideal model delta sigma weight residual 112.12 99.86 12.26 8.40e-01 1.42e+00 2.13e+02 angle pdb=" N SER33 490 " pdb=" CA SER33 490 " pdb=" C SER33 490 " ideal model delta sigma weight residual 111.03 96.30 14.73 1.11e+00 8.12e-01 1.76e+02 angle pdb=" N GLU G 107 " pdb=" CA GLU G 107 " pdb=" C GLU G 107 " ideal model delta sigma weight residual 113.28 97.24 16.04 1.22e+00 6.72e-01 1.73e+02 angle pdb=" N PRO33 17 " pdb=" CA PRO33 17 " pdb=" CB PRO33 17 " ideal model delta sigma weight residual 103.33 89.87 13.46 1.10e+00 8.26e-01 1.50e+02 angle pdb=" NH1 ARG33 156 " pdb=" CZ ARG33 156 " pdb=" NH2 ARG33 156 " ideal model delta sigma weight residual 119.30 104.26 15.04 1.30e+00 5.92e-01 1.34e+02 ... (remaining 250275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 95329 35.98 - 71.97: 10775 71.97 - 107.95: 1164 107.95 - 143.93: 20 143.93 - 179.91: 21 Dihedral angle restraints: 107309 sinusoidal: 88431 harmonic: 18878 Sorted by residual: dihedral pdb=" C5' C272712 " pdb=" C4' C272712 " pdb=" C3' C272712 " pdb=" O3' C272712 " ideal model delta sinusoidal sigma weight residual 147.00 73.57 73.43 1 8.00e+00 1.56e-02 1.07e+02 dihedral pdb=" C PRO33 17 " pdb=" N PRO33 17 " pdb=" CA PRO33 17 " pdb=" CB PRO33 17 " ideal model delta harmonic sigma weight residual -120.70 -95.21 -25.49 0 2.50e+00 1.60e-01 1.04e+02 dihedral pdb=" C4' C272712 " pdb=" C3' C272712 " pdb=" C2' C272712 " pdb=" C1' C272712 " ideal model delta sinusoidal sigma weight residual -35.00 34.63 -69.63 1 8.00e+00 1.56e-02 9.78e+01 ... (remaining 107306 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 28201 0.133 - 0.266: 3453 0.266 - 0.400: 255 0.400 - 0.533: 18 0.533 - 0.666: 9 Chirality restraints: 31936 Sorted by residual: chirality pdb=" P C31 1 " pdb=" OP1 C31 1 " pdb=" OP2 C31 1 " pdb=" O5' C31 1 " both_signs ideal model delta sigma weight residual True 2.41 -3.08 -0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" P C32 1 " pdb=" OP1 C32 1 " pdb=" OP2 C32 1 " pdb=" O5' C32 1 " both_signs ideal model delta sigma weight residual True 2.41 3.04 -0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" P U28 1 " pdb=" OP1 U28 1 " pdb=" OP2 U28 1 " pdb=" O5' U28 1 " both_signs ideal model delta sigma weight residual True 2.41 3.04 -0.63 2.00e-01 2.50e+01 9.80e+00 ... (remaining 31933 not shown) Planarity restraints: 13865 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G261182 " -0.212 2.00e-02 2.50e+03 8.73e-02 2.29e+02 pdb=" N9 G261182 " 0.017 2.00e-02 2.50e+03 pdb=" C8 G261182 " 0.098 2.00e-02 2.50e+03 pdb=" N7 G261182 " 0.082 2.00e-02 2.50e+03 pdb=" C5 G261182 " 0.035 2.00e-02 2.50e+03 pdb=" C6 G261182 " -0.042 2.00e-02 2.50e+03 pdb=" O6 G261182 " -0.127 2.00e-02 2.50e+03 pdb=" N1 G261182 " -0.036 2.00e-02 2.50e+03 pdb=" C2 G261182 " 0.022 2.00e-02 2.50e+03 pdb=" N2 G261182 " 0.043 2.00e-02 2.50e+03 pdb=" N3 G261182 " 0.060 2.00e-02 2.50e+03 pdb=" C4 G261182 " 0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP33 39 " -0.029 2.00e-02 2.50e+03 8.93e-02 1.99e+02 pdb=" CG TRP33 39 " 0.134 2.00e-02 2.50e+03 pdb=" CD1 TRP33 39 " 0.082 2.00e-02 2.50e+03 pdb=" CD2 TRP33 39 " 0.015 2.00e-02 2.50e+03 pdb=" NE1 TRP33 39 " -0.169 2.00e-02 2.50e+03 pdb=" CE2 TRP33 39 " -0.060 2.00e-02 2.50e+03 pdb=" CE3 TRP33 39 " -0.076 2.00e-02 2.50e+03 pdb=" CZ2 TRP33 39 " 0.064 2.00e-02 2.50e+03 pdb=" CZ3 TRP33 39 " -0.056 2.00e-02 2.50e+03 pdb=" CH2 TRP33 39 " 0.094 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G30 15 " -0.167 2.00e-02 2.50e+03 8.13e-02 1.98e+02 pdb=" N9 G30 15 " 0.003 2.00e-02 2.50e+03 pdb=" C8 G30 15 " 0.096 2.00e-02 2.50e+03 pdb=" N7 G30 15 " 0.109 2.00e-02 2.50e+03 pdb=" C5 G30 15 " 0.038 2.00e-02 2.50e+03 pdb=" C6 G30 15 " -0.034 2.00e-02 2.50e+03 pdb=" O6 G30 15 " -0.138 2.00e-02 2.50e+03 pdb=" N1 G30 15 " -0.022 2.00e-02 2.50e+03 pdb=" C2 G30 15 " 0.011 2.00e-02 2.50e+03 pdb=" N2 G30 15 " 0.087 2.00e-02 2.50e+03 pdb=" N3 G30 15 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G30 15 " 0.021 2.00e-02 2.50e+03 ... (remaining 13862 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 16397 2.73 - 3.27: 155043 3.27 - 3.82: 325573 3.82 - 4.36: 404106 4.36 - 4.90: 533558 Nonbonded interactions: 1434677 Sorted by model distance: nonbonded pdb=" O ASN K 93 " pdb=" N LEU K 95 " model vdw 2.191 2.520 nonbonded pdb=" N ARG T 6 " pdb=" OP1 G27 85 " model vdw 2.201 2.520 nonbonded pdb=" O GLU25 35 " pdb=" N TYR25 37 " model vdw 2.207 2.520 nonbonded pdb=" O2' A26 246 " pdb=" O5' G26 247 " model vdw 2.211 2.440 nonbonded pdb=" O ASP 8 28 " pdb=" N LYS 8 30 " model vdw 2.240 2.520 ... (remaining 1434672 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 '31' and (resid 1 through 45 or resid 47 through 76)) selection = (chain '32' and (resid 1 through 45 or resid 47 through 76)) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.140 Extract box with map and model: 26.370 Check model and map are aligned: 1.660 Set scattering table: 1.050 Process input model: 515.880 Find NCS groups from input model: 3.080 Set up NCS constraints: 0.350 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:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 558.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.206 167683 Z= 0.401 Angle : 1.110 22.140 250280 Z= 0.739 Chirality : 0.088 0.666 31936 Planarity : 0.012 0.292 13865 Dihedral : 22.509 179.914 95118 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 24.08 Ramachandran Plot: Outliers : 5.67 % Allowed : 12.92 % Favored : 81.41 % Rotamer: Outliers : 0.79 % Allowed : 3.05 % Favored : 96.15 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.53 (0.09), residues: 6509 helix: -3.31 (0.07), residues: 2209 sheet: -3.58 (0.14), residues: 919 loop : -2.57 (0.10), residues: 3381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.169 0.011 TRP33 39 HIS 0.041 0.001 HIS33 159 PHE 0.060 0.007 PHE33 274 TYR 0.151 0.010 TYR33 41 ARG 0.170 0.001 ARG33 156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13018 Ramachandran restraints generated. 6509 Oldfield, 0 Emsley, 6509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13018 Ramachandran restraints generated. 6509 Oldfield, 0 Emsley, 6509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1848 residues out of total 5423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 1806 time to evaluate : 6.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 MET cc_start: 0.8369 (ttp) cc_final: 0.8068 (tmm) REVERT: B 173 GLN cc_start: 0.8111 (pt0) cc_final: 0.7863 (pt0) REVERT: C 16 GLU cc_start: 0.8901 (tt0) cc_final: 0.8395 (tt0) REVERT: D 82 TYR cc_start: 0.8605 (t80) cc_final: 0.7565 (t80) REVERT: D 95 MET cc_start: 0.8916 (ptm) cc_final: 0.8679 (ptm) REVERT: F 94 ILE cc_start: 0.8573 (mt) cc_final: 0.8290 (mm) REVERT: F 123 ARG cc_start: 0.8839 (mtt180) cc_final: 0.7731 (mmt90) REVERT: G 4 ASN cc_start: 0.9250 (t0) cc_final: 0.9046 (p0) REVERT: G 29 ASP cc_start: 0.5068 (m-30) cc_final: 0.4536 (m-30) REVERT: H 37 PHE cc_start: 0.8883 (t80) cc_final: 0.8377 (t80) REVERT: H 106 GLN cc_start: 0.9619 (mt0) cc_final: 0.9382 (mt0) REVERT: I 14 ASP cc_start: 0.8640 (t70) cc_final: 0.8246 (t70) REVERT: I 118 MET cc_start: 0.9157 (ptp) cc_final: 0.8798 (ptp) REVERT: K 106 GLU cc_start: 0.9218 (tp30) cc_final: 0.8982 (mm-30) REVERT: M 33 ILE cc_start: 0.9094 (tt) cc_final: 0.8683 (tt) REVERT: O 9 GLN cc_start: 0.9465 (tp40) cc_final: 0.8954 (tp40) REVERT: O 12 MET cc_start: 0.8817 (mtp) cc_final: 0.8493 (mtp) REVERT: O 114 ASN cc_start: 0.7505 (p0) cc_final: 0.7230 (t0) REVERT: Q 27 ILE cc_start: 0.9322 (mm) cc_final: 0.9043 (mm) REVERT: R 19 LEU cc_start: 0.9190 (tp) cc_final: 0.8696 (tp) REVERT: R 82 MET cc_start: 0.8331 (mtm) cc_final: 0.8104 (mtm) REVERT: S 1 MET cc_start: 0.1238 (ptp) cc_final: 0.0025 (mtm) REVERT: S 37 ASP cc_start: 0.8794 (p0) cc_final: 0.8576 (p0) REVERT: T 9 GLU cc_start: 0.8138 (tt0) cc_final: 0.7025 (tp30) REVERT: U 61 LEU cc_start: 0.8632 (mp) cc_final: 0.8285 (tt) REVERT: V 75 PHE cc_start: 0.8524 (m-80) cc_final: 0.8219 (m-10) REVERT: Y 48 ASN cc_start: 0.9115 (t0) cc_final: 0.8903 (t0) REVERT: Z 32 LEU cc_start: 0.9483 (tp) cc_final: 0.9275 (tt) REVERT: 1 21 LEU cc_start: 0.9274 (mt) cc_final: 0.8916 (mt) REVERT: 1 27 LEU cc_start: 0.9012 (tp) cc_final: 0.8663 (tt) REVERT: 6 162 VAL cc_start: 0.8713 (t) cc_final: 0.8486 (t) REVERT: 6 191 ASP cc_start: 0.9035 (m-30) cc_final: 0.8716 (m-30) REVERT: 6 212 TYR cc_start: 0.9508 (m-80) cc_final: 0.8950 (m-80) REVERT: 10 21 MET cc_start: 0.9764 (mtt) cc_final: 0.9489 (mpp) REVERT: 11 30 MET cc_start: 0.9119 (ttp) cc_final: 0.8581 (ptm) REVERT: 12 20 ASN cc_start: 0.9125 (m110) cc_final: 0.8895 (m-40) REVERT: 15 51 PHE cc_start: 0.8674 (m-80) cc_final: 0.8247 (m-80) REVERT: 17 71 GLU cc_start: 0.9249 (tm-30) cc_final: 0.8918 (tm-30) REVERT: 17 72 ILE cc_start: 0.9706 (mt) cc_final: 0.9499 (mm) REVERT: 17 82 LEU cc_start: 0.9361 (tp) cc_final: 0.8851 (tp) REVERT: 17 103 THR cc_start: 0.9074 (m) cc_final: 0.8807 (m) REVERT: 17 114 PRO cc_start: 0.7041 (OUTLIER) cc_final: 0.6840 (Cg_endo) REVERT: 18 82 LYS cc_start: 0.9238 (mmmt) cc_final: 0.8507 (mmmm) REVERT: 23 65 MET cc_start: 0.8994 (ptp) cc_final: 0.8607 (ptp) REVERT: 25 43 GLU cc_start: 0.9390 (tt0) cc_final: 0.8659 (tt0) outliers start: 42 outliers final: 7 residues processed: 1836 average time/residue: 1.5204 time to fit residues: 4811.3851 Evaluate side-chains 1198 residues out of total 5423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1190 time to evaluate : 6.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain S residue 32 LEU Chi-restraints excluded: chain Z residue 37 CYS Chi-restraints excluded: chain 3 residue 44 VAL Chi-restraints excluded: chain 12 residue 103 VAL Chi-restraints excluded: chain 17 residue 114 PRO Chi-restraints excluded: chain 18 residue 81 ILE Chi-restraints excluded: chain 33 residue 267 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1117 random chunks: chunk 943 optimal weight: 40.0000 chunk 846 optimal weight: 20.0000 chunk 469 optimal weight: 7.9990 chunk 289 optimal weight: 8.9990 chunk 571 optimal weight: 0.7980 chunk 452 optimal weight: 6.9990 chunk 875 optimal weight: 30.0000 chunk 338 optimal weight: 9.9990 chunk 532 optimal weight: 20.0000 chunk 651 optimal weight: 20.0000 chunk 1014 optimal weight: 20.0000 overall best weight: 6.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 116 GLN A 127 ASN B 49 GLN B 140 HIS ** B 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 GLN ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 ASN F 133 GLN ** G 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 GLN H 11 GLN H 29 GLN H 30 GLN H 42 ASN ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN K 99 ASN M 9 GLN ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 62 ASN N 38 GLN ** N 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 11 GLN O 14 GLN O 51 ASN O 65 ASN P 43 GLN ** P 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 18 GLN Q 43 ASN Q 89 HIS R 31 GLN ** S 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 20 ASN X 58 ASN Z 48 GLN Z 61 ASN ** 1 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 13 ASN 4 27 ASN 6 17 HIS 6 18 GLN 6 167 HIS 6 177 ASN 7 18 ASN 7 122 GLN 7 139 ASN 8 40 HIS ** 8 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 42 ASN 9 134 ASN ** 10 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 10 37 HIS 11 27 ASN 11 129 ASN ** 11 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 12 20 ASN ** 13 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 36 GLN 13 49 GLN 13 74 GLN 14 58 ASN ** 15 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 15 39 ASN 16 45 ASN 16 111 GLN 18 42 ASN 19 19 ASN ** 19 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 20 26 ASN ** 20 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 20 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 21 30 HIS 22 18 GLN 22 51 GLN 22 73 HIS 23 68 HIS 24 51 ASN 24 69 ASN 24 83 ASN 33 88 ASN 33 267 ASN ** 33 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 33 437 HIS ** 33 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 33 604 ASN 33 614 GLN 33 730 ASN Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 167683 Z= 0.257 Angle : 0.750 14.177 250280 Z= 0.386 Chirality : 0.040 0.330 31936 Planarity : 0.006 0.113 13865 Dihedral : 23.666 175.458 82444 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 23.49 Ramachandran Plot: Outliers : 1.46 % Allowed : 10.45 % Favored : 88.09 % Rotamer: Outliers : 3.45 % Allowed : 15.44 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.10), residues: 6509 helix: -1.38 (0.10), residues: 2262 sheet: -3.04 (0.14), residues: 956 loop : -1.94 (0.11), residues: 3291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP 6 95 HIS 0.009 0.001 HIS15 117 PHE 0.028 0.003 PHE25 11 TYR 0.036 0.003 TYR10 25 ARG 0.014 0.001 ARG 5 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13018 Ramachandran restraints generated. 6509 Oldfield, 0 Emsley, 6509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13018 Ramachandran restraints generated. 6509 Oldfield, 0 Emsley, 6509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1609 residues out of total 5423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 1426 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 173 GLN cc_start: 0.7916 (pt0) cc_final: 0.7684 (pt0) REVERT: D 6 TYR cc_start: 0.8974 (t80) cc_final: 0.8677 (t80) REVERT: D 37 MET cc_start: 0.8748 (ttm) cc_final: 0.8508 (ttp) REVERT: D 148 VAL cc_start: 0.8963 (OUTLIER) cc_final: 0.8714 (p) REVERT: E 100 ASN cc_start: 0.8847 (p0) cc_final: 0.8532 (p0) REVERT: F 68 ARG cc_start: 0.9419 (mtt90) cc_final: 0.9118 (tpt90) REVERT: F 79 THR cc_start: 0.9312 (t) cc_final: 0.9070 (m) REVERT: F 91 PHE cc_start: 0.8772 (t80) cc_final: 0.8339 (m-80) REVERT: F 94 ILE cc_start: 0.8357 (mt) cc_final: 0.8133 (mm) REVERT: F 116 ARG cc_start: 0.9429 (tpp-160) cc_final: 0.9113 (tpp-160) REVERT: F 123 ARG cc_start: 0.8682 (mtt180) cc_final: 0.8410 (mtt-85) REVERT: G 1 MET cc_start: 0.7563 (tmm) cc_final: 0.7322 (tpt) REVERT: G 4 ASN cc_start: 0.9177 (t0) cc_final: 0.8786 (p0) REVERT: G 105 LYS cc_start: 0.8834 (mtpt) cc_final: 0.8562 (ptpt) REVERT: H 35 MET cc_start: 0.9262 (ptm) cc_final: 0.8917 (ppp) REVERT: H 37 PHE cc_start: 0.8742 (t80) cc_final: 0.8319 (t80) REVERT: I 16 TYR cc_start: 0.8295 (m-80) cc_final: 0.8034 (m-80) REVERT: I 60 ASP cc_start: 0.9117 (p0) cc_final: 0.8883 (p0) REVERT: J 12 ASP cc_start: 0.8575 (p0) cc_final: 0.8231 (p0) REVERT: J 32 TYR cc_start: 0.8019 (m-10) cc_final: 0.7816 (m-10) REVERT: L 65 ILE cc_start: 0.9309 (mm) cc_final: 0.9092 (mm) REVERT: L 136 MET cc_start: 0.7679 (tmm) cc_final: 0.7439 (tmm) REVERT: M 43 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8528 (mt-10) REVERT: N 19 GLN cc_start: 0.9097 (pp30) cc_final: 0.8868 (pp30) REVERT: Q 22 LEU cc_start: 0.8248 (mt) cc_final: 0.7955 (tp) REVERT: R 19 LEU cc_start: 0.9216 (tp) cc_final: 0.8887 (tp) REVERT: R 38 TYR cc_start: 0.8849 (m-80) cc_final: 0.8647 (m-10) REVERT: R 69 LEU cc_start: 0.8908 (tp) cc_final: 0.8589 (mt) REVERT: S 1 MET cc_start: 0.1080 (ptp) cc_final: 0.0323 (mtm) REVERT: V 35 ARG cc_start: 0.8266 (ttm-80) cc_final: 0.7868 (mtt-85) REVERT: V 75 PHE cc_start: 0.8577 (m-80) cc_final: 0.8205 (m-10) REVERT: W 67 LEU cc_start: 0.9427 (mp) cc_final: 0.9124 (mp) REVERT: W 76 LYS cc_start: 0.9186 (mmtt) cc_final: 0.8959 (mmtm) REVERT: Y 50 VAL cc_start: 0.8852 (m) cc_final: 0.8635 (m) REVERT: Z 32 LEU cc_start: 0.9525 (tp) cc_final: 0.9271 (mp) REVERT: 6 95 TRP cc_start: 0.8468 (t60) cc_final: 0.7990 (t60) REVERT: 6 103 TRP cc_start: 0.8701 (t60) cc_final: 0.7951 (t60) REVERT: 6 152 ASP cc_start: 0.8352 (p0) cc_final: 0.8069 (p0) REVERT: 6 212 TYR cc_start: 0.9279 (m-80) cc_final: 0.8878 (m-80) REVERT: 9 60 GLN cc_start: 0.8607 (tm-30) cc_final: 0.8374 (tm-30) REVERT: 10 13 ASP cc_start: 0.8706 (m-30) cc_final: 0.8371 (t0) REVERT: 10 21 MET cc_start: 0.9510 (mtt) cc_final: 0.9110 (mpp) REVERT: 10 25 TYR cc_start: 0.8694 (m-80) cc_final: 0.7643 (m-80) REVERT: 10 52 ASN cc_start: 0.9122 (t0) cc_final: 0.8811 (t0) REVERT: 12 20 ASN cc_start: 0.9239 (m-40) cc_final: 0.9014 (m110) REVERT: 12 26 MET cc_start: 0.7989 (ptp) cc_final: 0.7659 (ptp) REVERT: 12 79 ARG cc_start: 0.8930 (mtm110) cc_final: 0.8726 (mtm-85) REVERT: 12 89 ASP cc_start: 0.8856 (p0) cc_final: 0.8455 (p0) REVERT: 13 24 ASN cc_start: 0.9352 (t0) cc_final: 0.8898 (t0) REVERT: 13 51 LEU cc_start: 0.9528 (mt) cc_final: 0.9272 (mm) REVERT: 14 10 LEU cc_start: 0.8661 (pp) cc_final: 0.8426 (pp) REVERT: 14 40 ILE cc_start: 0.8975 (mt) cc_final: 0.8745 (mm) REVERT: 14 102 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.5980 (mp) REVERT: 15 51 PHE cc_start: 0.8625 (m-80) cc_final: 0.8401 (m-80) REVERT: 15 112 VAL cc_start: 0.9043 (t) cc_final: 0.8778 (m) REVERT: 17 77 LYS cc_start: 0.8942 (tppt) cc_final: 0.8723 (tptt) REVERT: 20 35 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.8084 (ttt180) REVERT: 23 64 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8451 (tm-30) REVERT: 24 27 MET cc_start: 0.9438 (mmm) cc_final: 0.9106 (tpt) outliers start: 183 outliers final: 90 residues processed: 1512 average time/residue: 1.3549 time to fit residues: 3553.2579 Evaluate side-chains 1226 residues out of total 5423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 1133 time to evaluate : 6.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain C residue 60 TRP Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 165 ASP Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 133 GLN Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 88 HIS Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain I residue 55 ILE Chi-restraints excluded: chain J residue 37 ASP Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 73 ASP Chi-restraints excluded: chain J residue 80 ASP Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 28 PHE Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 88 ASN Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 106 LEU Chi-restraints excluded: chain O residue 49 ILE Chi-restraints excluded: chain O residue 65 ASN Chi-restraints excluded: chain P residue 16 ILE Chi-restraints excluded: chain R residue 39 THR Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain S residue 32 LEU Chi-restraints excluded: chain T residue 88 ASP Chi-restraints excluded: chain U residue 66 ASP Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain V residue 54 THR Chi-restraints excluded: chain Z residue 30 HIS Chi-restraints excluded: chain Z residue 37 CYS Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 1 residue 53 VAL Chi-restraints excluded: chain 2 residue 28 THR Chi-restraints excluded: chain 2 residue 41 VAL Chi-restraints excluded: chain 3 residue 44 VAL Chi-restraints excluded: chain 4 residue 50 SER Chi-restraints excluded: chain 4 residue 54 LEU Chi-restraints excluded: chain 6 residue 124 THR Chi-restraints excluded: chain 7 residue 68 HIS Chi-restraints excluded: chain 8 residue 16 THR Chi-restraints excluded: chain 8 residue 142 VAL Chi-restraints excluded: chain 8 residue 190 LEU Chi-restraints excluded: chain 9 residue 80 LEU Chi-restraints excluded: chain 9 residue 130 THR Chi-restraints excluded: chain 9 residue 164 LEU Chi-restraints excluded: chain 10 residue 7 VAL Chi-restraints excluded: chain 10 residue 74 LEU Chi-restraints excluded: chain 11 residue 44 SER Chi-restraints excluded: chain 11 residue 112 ASP Chi-restraints excluded: chain 12 residue 103 VAL Chi-restraints excluded: chain 13 residue 47 VAL Chi-restraints excluded: chain 14 residue 89 ARG Chi-restraints excluded: chain 14 residue 102 LEU Chi-restraints excluded: chain 15 residue 33 ILE Chi-restraints excluded: chain 15 residue 74 LYS Chi-restraints excluded: chain 15 residue 115 ILE Chi-restraints excluded: chain 16 residue 33 CYS Chi-restraints excluded: chain 16 residue 55 ARG Chi-restraints excluded: chain 16 residue 111 GLN Chi-restraints excluded: chain 17 residue 18 LEU Chi-restraints excluded: chain 17 residue 24 VAL Chi-restraints excluded: chain 17 residue 42 VAL Chi-restraints excluded: chain 17 residue 48 SER Chi-restraints excluded: chain 17 residue 67 ASP Chi-restraints excluded: chain 17 residue 73 SER Chi-restraints excluded: chain 18 residue 22 LYS Chi-restraints excluded: chain 19 residue 24 THR Chi-restraints excluded: chain 20 residue 35 ARG Chi-restraints excluded: chain 21 residue 49 ASN Chi-restraints excluded: chain 22 residue 25 ILE Chi-restraints excluded: chain 23 residue 50 VAL Chi-restraints excluded: chain 33 residue 240 MET Chi-restraints excluded: chain 33 residue 621 ILE Chi-restraints excluded: chain 33 residue 631 ILE Chi-restraints excluded: chain 33 residue 685 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1117 random chunks: chunk 563 optimal weight: 5.9990 chunk 314 optimal weight: 5.9990 chunk 844 optimal weight: 20.0000 chunk 690 optimal weight: 20.0000 chunk 279 optimal weight: 8.9990 chunk 1016 optimal weight: 20.0000 chunk 1097 optimal weight: 0.0070 chunk 905 optimal weight: 20.0000 chunk 1007 optimal weight: 20.0000 chunk 346 optimal weight: 2.9990 chunk 815 optimal weight: 20.0000 overall best weight: 4.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 148 GLN C 30 GLN ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 HIS E 63 GLN ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 136 GLN ** L 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 9 GLN N 116 GLN O 11 GLN ** O 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 31 GLN ** S 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 88 GLN ** 10 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 10 94 HIS 11 27 ASN ** 11 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 49 GLN 14 99 GLN ** 15 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 18 61 ASN ** 20 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 22 53 GLN ** 33 594 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 167683 Z= 0.195 Angle : 0.660 15.938 250280 Z= 0.339 Chirality : 0.036 0.316 31936 Planarity : 0.005 0.057 13865 Dihedral : 23.676 177.940 82437 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 21.23 Ramachandran Plot: Outliers : 1.09 % Allowed : 10.60 % Favored : 88.31 % Rotamer: Outliers : 4.02 % Allowed : 17.54 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.45 % 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: -2.25 (0.10), residues: 6509 helix: -0.58 (0.10), residues: 2220 sheet: -2.61 (0.15), residues: 1007 loop : -1.71 (0.11), residues: 3282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP21 72 HIS 0.006 0.001 HIS N 29 PHE 0.032 0.002 PHE U 91 TYR 0.027 0.002 TYR16 65 ARG 0.017 0.001 ARG S 76 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13018 Ramachandran restraints generated. 6509 Oldfield, 0 Emsley, 6509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13018 Ramachandran restraints generated. 6509 Oldfield, 0 Emsley, 6509 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1531 residues out of total 5423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 1318 time to evaluate : 6.846 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: A 145 MET cc_start: 0.8127 (ttp) cc_final: 0.7918 (tmm) REVERT: D 6 TYR cc_start: 0.8963 (t80) cc_final: 0.8697 (t80) REVERT: D 174 PHE cc_start: 0.8325 (t80) cc_final: 0.7955 (t80) REVERT: E 100 ASN cc_start: 0.8848 (p0) cc_final: 0.8627 (p0) REVERT: F 68 ARG cc_start: 0.9379 (mtt90) cc_final: 0.9073 (tpt90) REVERT: F 79 THR cc_start: 0.9236 (t) cc_final: 0.9014 (m) REVERT: F 91 PHE cc_start: 0.8830 (t80) cc_final: 0.8498 (m-80) REVERT: F 94 ILE cc_start: 0.8407 (mt) cc_final: 0.7881 (mm) REVERT: G 4 ASN cc_start: 0.9116 (t0) cc_final: 0.8641 (p0) REVERT: G 38 MET cc_start: 0.9073 (mmp) cc_final: 0.8836 (mmt) REVERT: H 37 PHE cc_start: 0.8726 (t80) cc_final: 0.8307 (t80) REVERT: H 116 MET cc_start: 0.2844 (ttt) cc_final: 0.2085 (tpt) REVERT: I 60 ASP cc_start: 0.9125 (p0) cc_final: 0.8891 (p0) REVERT: J 12 ASP cc_start: 0.8663 (p0) cc_final: 0.8369 (p0) REVERT: L 12 MET cc_start: 0.9032 (ppp) cc_final: 0.8787 (ppp) REVERT: L 136 MET cc_start: 0.7568 (tmm) cc_final: 0.7158 (tmm) REVERT: M 43 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8436 (mt-10) REVERT: N 67 ASN cc_start: 0.7622 (OUTLIER) cc_final: 0.7402 (p0) REVERT: R 52 GLU cc_start: 0.8250 (tt0) cc_final: 0.8038 (tm-30) REVERT: R 69 LEU cc_start: 0.8739 (tp) cc_final: 0.8464 (mt) REVERT: S 1 MET cc_start: 0.1535 (ptp) cc_final: 0.0805 (mtm) REVERT: S 5 GLU cc_start: 0.8468 (mp0) cc_final: 0.8116 (mp0) REVERT: U 61 LEU cc_start: 0.8469 (tt) cc_final: 0.8258 (tt) REVERT: V 75 PHE cc_start: 0.8513 (m-80) cc_final: 0.8187 (m-80) REVERT: W 73 ARG cc_start: 0.9070 (ttm110) cc_final: 0.8816 (ttm110) REVERT: X 5 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8107 (mt-10) REVERT: Y 6 ILE cc_start: 0.8429 (mm) cc_final: 0.8178 (mm) REVERT: Z 10 GLU cc_start: 0.8703 (tp30) cc_final: 0.8478 (tp30) REVERT: Z 23 LYS cc_start: 0.8978 (mmtm) cc_final: 0.8702 (mmtm) REVERT: Z 32 LEU cc_start: 0.9424 (tp) cc_final: 0.9197 (tt) REVERT: 2 9 LYS cc_start: 0.8816 (pttt) cc_final: 0.8610 (pttm) REVERT: 2 34 GLU cc_start: 0.9285 (mm-30) cc_final: 0.9007 (mm-30) REVERT: 2 50 GLU cc_start: 0.7511 (tt0) cc_final: 0.7213 (tt0) REVERT: 6 18 GLN cc_start: 0.7203 (tp-100) cc_final: 0.6934 (tp40) REVERT: 6 103 TRP cc_start: 0.8752 (t60) cc_final: 0.8158 (t60) REVERT: 6 152 ASP cc_start: 0.8236 (p0) cc_final: 0.7917 (p0) REVERT: 6 191 ASP cc_start: 0.9087 (m-30) cc_final: 0.8678 (t0) REVERT: 6 212 TYR cc_start: 0.9196 (m-10) cc_final: 0.8959 (m-80) REVERT: 7 129 PHE cc_start: 0.8798 (p90) cc_final: 0.8270 (p90) REVERT: 9 60 GLN cc_start: 0.8808 (tm-30) cc_final: 0.8513 (tm-30) REVERT: 9 61 LYS cc_start: 0.8508 (mmtt) cc_final: 0.8303 (mmtp) REVERT: 10 13 ASP cc_start: 0.8746 (m-30) cc_final: 0.8435 (t0) REVERT: 10 69 GLU cc_start: 0.9298 (pm20) cc_final: 0.8761 (pm20) REVERT: 10 70 VAL cc_start: 0.9298 (m) cc_final: 0.8792 (m) REVERT: 11 30 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.8539 (ptt) REVERT: 11 134 VAL cc_start: 0.9395 (OUTLIER) cc_final: 0.9195 (p) REVERT: 12 20 ASN cc_start: 0.9244 (m-40) cc_final: 0.9013 (m110) REVERT: 12 89 ASP cc_start: 0.9014 (p0) cc_final: 0.8651 (p0) REVERT: 12 90 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8816 (mm-30) REVERT: 13 24 ASN cc_start: 0.9377 (t0) cc_final: 0.9029 (t0) REVERT: 13 35 GLU cc_start: 0.9418 (mp0) cc_final: 0.9092 (mp0) REVERT: 14 102 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.6733 (mt) REVERT: 15 51 PHE cc_start: 0.8682 (m-80) cc_final: 0.8369 (m-80) REVERT: 17 51 GLN cc_start: 0.9558 (OUTLIER) cc_final: 0.9272 (mp10) REVERT: 17 77 LYS cc_start: 0.8941 (tppt) cc_final: 0.8509 (tppt) REVERT: 18 50 LEU cc_start: 0.9339 (tp) cc_final: 0.9126 (tt) REVERT: 19 47 LYS cc_start: 0.9006 (mmmm) cc_final: 0.8783 (mmmm) REVERT: 20 35 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.7890 (ttt180) REVERT: 22 17 VAL cc_start: 0.8703 (OUTLIER) cc_final: 0.8306 (m) REVERT: 33 280 ARG cc_start: 0.4608 (ttm170) cc_final: 0.4317 (ttm170) outliers start: 213 outliers final: 102 residues processed: 1423 average time/residue: 1.3333 time to fit residues: 3313.4506 Evaluate side-chains 1247 residues out of total 5423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 1138 time to evaluate : 6.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 SER Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain C residue 60 TRP Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 165 ASP Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain G residue 31 ARG Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 50 VAL Chi-restraints excluded: chain G residue 88 HIS Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain I residue 55 ILE Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 73 ASP Chi-restraints excluded: chain J residue 80 ASP Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 73 ILE Chi-restraints excluded: chain K residue 121 THR Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 28 PHE Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 88 ASN Chi-restraints excluded: chain L residue 126 ILE Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 67 ASN Chi-restraints excluded: chain N residue 116 GLN Chi-restraints excluded: chain O residue 49 ILE Chi-restraints excluded: chain Q residue 85 LYS Chi-restraints excluded: chain R residue 31 GLN Chi-restraints excluded: chain R residue 39 THR Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 103 ILE Chi-restraints excluded: chain S residue 32 LEU Chi-restraints excluded: chain S residue 78 SER Chi-restraints excluded: chain U residue 66 ASP Chi-restraints excluded: chain U residue 92 VAL Chi-restraints excluded: chain V residue 54 THR Chi-restraints excluded: chain V residue 76 ILE Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain Y residue 56 VAL Chi-restraints excluded: chain Z residue 30 HIS Chi-restraints excluded: chain Z residue 37 CYS Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 1 residue 53 VAL Chi-restraints excluded: chain 2 residue 11 VAL Chi-restraints excluded: chain 2 residue 41 VAL Chi-restraints excluded: chain 3 residue 44 VAL Chi-restraints excluded: chain 4 residue 16 THR Chi-restraints excluded: chain 4 residue 31 ILE Chi-restraints excluded: chain 4 residue 50 SER Chi-restraints excluded: chain 6 residue 67 LEU Chi-restraints excluded: chain 6 residue 124 THR Chi-restraints excluded: chain 7 residue 123 LEU Chi-restraints excluded: chain 8 residue 142 VAL Chi-restraints excluded: chain 8 residue 170 LEU Chi-restraints excluded: chain 9 residue 130 THR Chi-restraints excluded: chain 9 residue 160 VAL Chi-restraints excluded: chain 9 residue 164 LEU Chi-restraints excluded: chain 10 residue 7 VAL Chi-restraints excluded: chain 10 residue 74 LEU Chi-restraints excluded: chain 11 residue 4 ARG Chi-restraints excluded: chain 11 residue 21 LEU Chi-restraints excluded: chain 11 residue 30 MET Chi-restraints excluded: chain 11 residue 72 VAL Chi-restraints excluded: chain 11 residue 112 ASP Chi-restraints excluded: chain 11 residue 129 ASN Chi-restraints excluded: chain 11 residue 134 VAL Chi-restraints excluded: chain 12 residue 103 VAL Chi-restraints excluded: chain 13 residue 47 VAL Chi-restraints excluded: chain 14 residue 89 ARG Chi-restraints excluded: chain 14 residue 102 LEU Chi-restraints excluded: chain 15 residue 31 VAL Chi-restraints excluded: chain 15 residue 33 ILE Chi-restraints excluded: chain 15 residue 74 LYS Chi-restraints excluded: chain 16 residue 28 GLN Chi-restraints excluded: chain 16 residue 33 CYS Chi-restraints excluded: chain 17 residue 18 LEU Chi-restraints excluded: chain 17 residue 24 VAL Chi-restraints excluded: chain 17 residue 48 SER Chi-restraints excluded: chain 17 residue 51 GLN Chi-restraints excluded: chain 17 residue 67 ASP Chi-restraints excluded: chain 17 residue 73 SER Chi-restraints excluded: chain 18 residue 22 LYS Chi-restraints excluded: chain 19 residue 13 GLU Chi-restraints excluded: chain 19 residue 24 THR Chi-restraints excluded: chain 20 residue 35 ARG Chi-restraints excluded: chain 21 residue 49 ASN Chi-restraints excluded: chain 22 residue 17 VAL Chi-restraints excluded: chain 23 residue 50 VAL Chi-restraints excluded: chain 24 residue 69 ASN Chi-restraints excluded: chain 25 residue 18 PHE Chi-restraints excluded: chain 33 residue 27 THR Chi-restraints excluded: chain 33 residue 142 MET Chi-restraints excluded: chain 33 residue 240 MET Chi-restraints excluded: chain 33 residue 621 ILE Chi-restraints excluded: chain 33 residue 631 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/iotbx/cli_parser.py", line 939, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.7931 > 50: distance: 8 - 12: 6.550 distance: 12 - 13: 7.578 distance: 13 - 14: 6.861 distance: 13 - 16: 4.306 distance: 14 - 15: 8.617 distance: 14 - 23: 14.460 distance: 16 - 17: 3.885 distance: 17 - 18: 4.293 distance: 23 - 24: 17.680 distance: 24 - 25: 10.295 distance: 25 - 26: 12.948 distance: 25 - 31: 10.806 distance: 27 - 28: 6.008 distance: 28 - 29: 6.361 distance: 28 - 30: 4.901 distance: 31 - 32: 14.750 distance: 32 - 33: 32.504 distance: 33 - 34: 21.973 distance: 33 - 35: 11.213 distance: 35 - 36: 10.256 distance: 36 - 37: 6.905 distance: 36 - 39: 10.029 distance: 37 - 38: 19.759 distance: 37 - 42: 8.020 distance: 39 - 40: 15.402 distance: 39 - 41: 11.920 distance: 42 - 43: 12.019 distance: 43 - 44: 8.045 distance: 43 - 46: 8.395 distance: 44 - 51: 11.200 distance: 46 - 47: 11.020 distance: 47 - 48: 3.919 distance: 51 - 52: 7.402 distance: 52 - 53: 19.551 distance: 52 - 55: 9.540 distance: 53 - 54: 14.932 distance: 53 - 62: 26.355 distance: 55 - 56: 5.753 distance: 62 - 63: 19.372 distance: 63 - 64: 22.204 distance: 63 - 66: 21.642 distance: 64 - 65: 13.452 distance: 64 - 73: 15.763 distance: 66 - 67: 14.257 distance: 67 - 69: 8.388 distance: 70 - 72: 6.658 distance: 71 - 72: 5.982 distance: 73 - 74: 55.950 distance: 74 - 75: 36.963 distance: 75 - 76: 36.630 distance: 75 - 77: 10.815 distance: 77 - 78: 13.070 distance: 78 - 79: 14.905 distance: 79 - 80: 19.107 distance: 79 - 81: 6.866 distance: 81 - 82: 17.580 distance: 82 - 83: 14.036 distance: 82 - 85: 4.927 distance: 83 - 84: 8.490 distance: 83 - 90: 3.919 distance: 85 - 86: 19.228 distance: 86 - 87: 4.009 distance: 87 - 88: 8.955