Starting phenix.real_space_refine on Sat Mar 2 19:03:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kpv_8280/03_2024/5kpv_8280.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kpv_8280/03_2024/5kpv_8280.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kpv_8280/03_2024/5kpv_8280.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kpv_8280/03_2024/5kpv_8280.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kpv_8280/03_2024/5kpv_8280.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kpv_8280/03_2024/5kpv_8280.pdb" } resolution = 4.1 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= 0.042 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 "A TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "G TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 13": "NH1" <-> "NH2" Residue "I ARG 37": "NH1" <-> "NH2" 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 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 TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "Q PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "S TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "T PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 56": "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 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 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 107": "NH1" <-> "NH2" Residue "6 ARG 224": "NH1" <-> "NH2" Residue "7 ARG 106": "NH1" <-> "NH2" Residue "7 PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 130": "NH1" <-> "NH2" Residue "9 PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 156": "NH1" <-> "NH2" Residue "10 PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "13 PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "13 ARG 123": "NH1" <-> "NH2" Residue "16 ARG 55": "NH1" <-> "NH2" Residue "18 ASP 37": "OD1" <-> "OD2" Residue "18 GLU 38": "OE1" <-> "OE2" Residue "20 ARG 28": "NH1" <-> "NH2" Residue "21 PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "22 TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "23 PHE 40": "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 TYR 407": "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': 94, 'rna2p_pyr': 49, 'rna3p_pur': 780, 'rna3p_pyr': 616} Link IDs: {'rna2p': 143, 'rna3p': 1395} 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': 218, 'rna2p_pyr': 98, 'rna3p_pur': 1456, 'rna3p_pyr': 1131} Link IDs: {'rna2p': 316, 'rna3p': 2586} 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: 57.61, per 1000 atoms: 0.37 Number of scatterers: 154603 At special positions: 0 Unit cell: (276.34, 264.86, 241.9, 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=4, symmetry=0 Simple disulfide: pdb=" SG CYS Z 18 " - pdb=" SG CYS Z 37 " distance=2.87 Simple disulfide: pdb=" SG CYS Z 18 " - pdb=" SG CYS Z 40 " distance=2.04 Simple disulfide: pdb=" SG CYS Z 37 " - pdb=" SG CYS Z 40 " distance=2.04 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: 70.57 Conformation dependent library (CDL) restraints added in 7.9 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: 223 helices and 84 sheets defined 37.5% alpha, 13.7% beta 1581 base pairs and 2373 stacking pairs defined. Time for finding SS restraints: 56.48 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 196 through 202 removed outlier: 3.572A pdb=" N MET A 200 " --> pdb=" O ALA A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 213 removed outlier: 4.102A pdb=" N ALA A 210 " --> pdb=" O LYS A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 225 through 229 Processing helix chain 'B' and resid 39 through 44 Processing helix chain 'B' and resid 61 through 71 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 181 through 185 Processing helix chain 'C' and resid 15 through 21 removed outlier: 3.532A pdb=" N PHE C 19 " --> pdb=" O SER C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 40 removed outlier: 3.611A pdb=" N ARG C 40 " --> pdb=" O ALA C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 115 Processing helix chain 'C' and resid 130 through 141 removed outlier: 3.507A pdb=" N LEU C 134 " --> pdb=" O LYS C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 161 removed outlier: 4.040A pdb=" N ALA C 160 " --> pdb=" O ASN C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 183 Processing helix chain 'C' and resid 190 through 200 Processing helix chain 'D' and resid 2 through 9 Processing helix chain 'D' and resid 9 through 19 Processing helix chain 'D' and resid 23 through 27 Processing helix chain 'D' and resid 45 through 61 removed outlier: 3.884A pdb=" N LEU D 49 " --> pdb=" O ASP D 45 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASP D 50 " --> pdb=" O LYS D 46 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN D 51 " --> pdb=" O LYS D 47 " (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 133 through 137 removed outlier: 3.528A pdb=" N ILE D 136 " --> pdb=" O GLU D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 172 removed outlier: 3.798A pdb=" N PHE D 172 " --> pdb=" O LEU D 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 6 removed outlier: 3.915A pdb=" N ALA E 6 " --> pdb=" O ARG E 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2 through 6' Processing helix chain 'E' and resid 59 through 79 removed outlier: 3.707A pdb=" N GLN E 63 " --> pdb=" O ASP E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 150 removed outlier: 3.605A pdb=" N ILE E 140 " --> pdb=" O ASP E 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 28 Processing helix chain 'F' and resid 29 through 34 Processing helix chain 'F' and resid 41 through 48 Processing helix chain 'F' and resid 54 through 71 Processing helix chain 'F' and resid 95 through 106 removed outlier: 3.538A pdb=" N ALA F 106 " --> pdb=" O ALA F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 115 Processing helix chain 'G' and resid 6 through 19 removed outlier: 3.557A pdb=" N ALA G 10 " --> pdb=" O GLN G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 48 removed outlier: 3.989A pdb=" N LYS G 37 " --> pdb=" O VAL G 33 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA G 48 " --> pdb=" O ALA G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 67 Processing helix chain 'G' and resid 71 through 77 removed outlier: 3.840A pdb=" N PHE G 76 " --> pdb=" O LYS G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 104 Processing helix chain 'H' and resid 24 through 29 Processing helix chain 'H' and resid 33 through 46 Processing helix chain 'H' and resid 76 through 83 Processing helix chain 'H' and resid 101 through 108 Processing helix chain 'H' and resid 108 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: 3.772A pdb=" N VAL I 100 " --> pdb=" O ARG I 96 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE I 101 " --> pdb=" O PRO I 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 120 removed outlier: 3.743A pdb=" N GLY I 115 " --> pdb=" O LYS I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 132 through 136 Processing helix chain 'J' and resid 104 through 108 Processing helix chain 'J' and resid 112 through 118 Processing helix chain 'K' and resid 22 through 26 Processing helix chain 'K' and resid 36 through 41 removed outlier: 3.512A pdb=" N SER K 40 " --> pdb=" O LYS K 36 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG K 41 " --> pdb=" O GLY K 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 36 through 41' Processing helix chain 'K' and resid 56 through 61 Processing helix chain 'K' and resid 69 through 74 removed outlier: 3.589A pdb=" N THR K 74 " --> pdb=" O ALA K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 96 removed outlier: 3.943A pdb=" N LEU K 95 " --> pdb=" O ASP K 91 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS K 96 " --> pdb=" O LEU K 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 91 through 96' Processing helix chain 'K' and resid 128 through 137 Processing helix chain 'L' and resid 43 through 55 Processing helix chain 'L' and resid 56 through 58 No H-bonds generated for 'chain 'L' and resid 56 through 58' Processing helix chain 'L' and resid 109 through 124 removed outlier: 3.547A pdb=" N LEU L 119 " --> pdb=" O GLU L 115 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 30 Processing helix chain 'M' and resid 38 through 57 removed outlier: 4.450A pdb=" N ARG M 46 " --> pdb=" O LYS M 42 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL M 47 " --> pdb=" O GLU M 43 " (cutoff:3.500A) Proline residue: M 50 - end of helix removed outlier: 4.283A pdb=" N THR M 57 " --> pdb=" O THR M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 69 Processing helix chain 'M' and resid 72 through 82 removed outlier: 4.159A 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 21 removed outlier: 4.095A pdb=" N ARG N 13 " --> pdb=" O ARG N 9 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ALA N 14 " --> pdb=" O ARG N 10 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU N 21 " --> pdb=" O LYS N 17 " (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 removed outlier: 3.755A pdb=" N ALA N 113 " --> pdb=" O ALA N 109 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 7 Processing helix chain 'O' and resid 52 through 55 Processing helix chain 'O' and resid 96 through 100 Processing helix chain 'O' and resid 103 through 108 Processing helix chain 'P' and resid 6 through 20 Processing helix chain 'P' and resid 30 through 71 removed outlier: 3.996A pdb=" N GLN P 36 " --> pdb=" O ARG P 32 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG P 50 " --> pdb=" O TYR P 46 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS P 53 " --> pdb=" O ARG P 49 " (cutoff:3.500A) Processing helix chain 'P' and resid 74 through 83 Processing helix chain 'P' and resid 90 through 100 Processing helix chain 'P' and resid 101 through 117 Processing helix chain 'R' and resid 13 through 22 removed outlier: 3.546A pdb=" N VAL R 17 " --> pdb=" O SER R 13 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 37 Processing helix chain 'R' and resid 41 through 62 removed outlier: 3.602A pdb=" N ASP R 62 " --> pdb=" O ALA R 58 " (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 10 removed outlier: 3.508A pdb=" N LEU S 8 " --> pdb=" O GLU S 4 " (cutoff:3.500A) Processing helix chain 'S' and resid 17 through 28 Processing helix chain 'S' and resid 39 through 51 removed outlier: 3.545A pdb=" N LEU S 50 " --> pdb=" O ALA S 46 " (cutoff:3.500A) Processing helix chain 'U' and resid 13 through 23 Processing helix chain 'U' and resid 44 through 53 removed outlier: 4.456A pdb=" N LYS U 53 " --> pdb=" O ASN U 49 " (cutoff:3.500A) Processing helix chain 'U' and resid 54 through 58 Processing helix chain 'W' and resid 52 through 61 Processing helix chain 'W' and resid 62 through 74 Processing helix chain 'X' and resid 9 through 22 Processing helix chain 'X' and resid 23 through 31 Processing helix chain 'X' and resid 39 through 60 removed outlier: 4.140A 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 51 Processing helix chain 'Z' and resid 45 through 52 removed outlier: 3.918A pdb=" N ARG Z 49 " --> pdb=" O THR Z 45 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA Z 52 " --> pdb=" O GLN Z 48 " (cutoff:3.500A) Processing helix chain 'Z' and resid 55 through 63 removed outlier: 3.691A pdb=" N ARG Z 59 " --> pdb=" O GLY Z 55 " (cutoff:3.500A) Processing helix chain '1' and resid 8 through 16 Processing helix chain '3' and resid 8 through 17 Processing helix chain '3' and resid 17 through 22 Processing helix chain '3' and resid 24 through 38 Processing helix chain '4' and resid 6 through 11 removed outlier: 3.744A pdb=" N ALA 4 10 " --> pdb=" O VAL 4 6 " (cutoff:3.500A) removed outlier: 3.517A 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: 4.138A pdb=" N GLY 4 55 " --> pdb=" O LYS 4 51 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LEU 4 56 " --> pdb=" O GLY 4 52 " (cutoff:3.500A) Processing helix chain '5' and resid 18 through 22 Processing helix chain '6' and resid 23 through 27 Processing helix chain '6' and resid 41 through 61 removed outlier: 3.571A pdb=" N THR 6 45 " --> pdb=" O ASN 6 41 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL 6 46 " --> pdb=" O LEU 6 42 " (cutoff:3.500A) Proline residue: 6 47 - end of helix Processing helix chain '6' and resid 72 through 85 removed outlier: 3.910A pdb=" N GLU 6 77 " --> pdb=" O ARG 6 73 " (cutoff:3.500A) Processing helix chain '6' and resid 102 through 123 removed outlier: 4.454A pdb=" N GLN 6 108 " --> pdb=" O LYS 6 104 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER 6 109 " --> pdb=" O THR 6 105 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN 6 121 " --> pdb=" O GLU 6 117 " (cutoff:3.500A) Processing helix chain '6' and resid 129 through 148 Processing helix chain '6' and resid 164 through 177 removed outlier: 6.763A pdb=" N ILE 6 170 " --> pdb=" O ASP 6 166 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ALA 6 171 " --> pdb=" O HIS 6 167 " (cutoff:3.500A) Processing helix chain '6' and resid 206 through 225 removed outlier: 3.611A pdb=" N ARG 6 221 " --> pdb=" O ALA 6 217 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU 6 222 " --> pdb=" O ALA 6 218 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG 6 224 " --> pdb=" O VAL 6 220 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N SER 6 225 " --> pdb=" O ARG 6 221 " (cutoff:3.500A) Processing helix chain '7' and resid 5 through 11 Processing helix chain '7' and resid 24 through 46 removed outlier: 4.550A pdb=" N ALA 7 29 " --> pdb=" O THR 7 25 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ASP 7 30 " --> pdb=" O LYS 7 26 " (cutoff:3.500A) Processing helix chain '7' and resid 71 through 77 Processing helix chain '7' and resid 80 through 95 Processing helix chain '7' and resid 111 through 125 removed outlier: 3.732A pdb=" N VAL 7 115 " --> pdb=" O ASP 7 111 " (cutoff:3.500A) Processing helix chain '7' and resid 128 through 143 removed outlier: 3.507A pdb=" N ALA 7 132 " --> pdb=" O MET 7 128 " (cutoff:3.500A) Processing helix chain '7' and resid 155 through 159 Processing helix chain '8' and resid 8 through 15 Processing helix chain '8' and resid 48 through 65 Processing helix chain '8' and resid 67 through 81 Processing helix chain '8' and resid 84 through 95 removed outlier: 3.922A pdb=" N LEU 8 90 " --> pdb=" O GLY 8 86 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY 8 95 " --> pdb=" O ALA 8 91 " (cutoff:3.500A) Processing helix chain '8' and resid 96 through 104 Processing helix chain '8' and resid 110 through 119 Processing helix chain '8' and resid 151 through 162 removed outlier: 3.628A pdb=" N LYS 8 155 " --> pdb=" O GLN 8 151 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU 8 162 " --> pdb=" O LEU 8 158 " (cutoff:3.500A) Processing helix chain '8' and resid 196 through 203 Processing helix chain '9' and resid 54 through 69 Processing helix chain '9' and resid 109 through 116 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: 3.806A pdb=" N GLY 9 165 " --> pdb=" O GLU 9 161 " (cutoff:3.500A) Processing helix chain '10' and resid 17 through 31 removed outlier: 4.007A pdb=" N MET10 21 " --> pdb=" O GLN10 17 " (cutoff:3.500A) Processing helix chain '10' and resid 67 through 81 removed outlier: 3.761A pdb=" N ILE10 71 " --> pdb=" O PRO10 67 " (cutoff:3.500A) Processing helix chain '11' and resid 19 through 28 removed outlier: 3.543A pdb=" N ILE11 28 " --> pdb=" O LYS11 24 " (cutoff:3.500A) Processing helix chain '11' and resid 34 through 54 Processing helix chain '11' and resid 61 through 69 Processing helix chain '11' and resid 91 through 109 Processing helix chain '11' and resid 114 through 128 Processing helix chain '11' and resid 132 through 146 Processing helix chain '12' and resid 4 through 20 Processing helix chain '12' and resid 29 through 42 Processing helix chain '12' and resid 87 through 91 removed outlier: 3.570A pdb=" N LEU12 91 " --> pdb=" O LYS12 88 " (cutoff:3.500A) Processing helix chain '12' and resid 111 through 118 removed outlier: 3.946A pdb=" N GLN12 117 " --> pdb=" O ARG12 113 " (cutoff:3.500A) Processing helix chain '13' and resid 33 through 39 Processing helix chain '13' and resid 44 through 53 removed outlier: 3.946A pdb=" N ARG13 48 " --> pdb=" O ARG13 44 " (cutoff:3.500A) Proline residue: 13 50 - end of helix removed outlier: 4.087A pdb=" N LEU13 53 " --> pdb=" O GLN13 49 " (cutoff:3.500A) Processing helix chain '13' and resid 70 through 86 Processing helix chain '13' and resid 90 through 101 removed outlier: 6.500A pdb=" N GLU13 96 " --> pdb=" O SER13 92 " (cutoff:3.500A) Processing helix chain '14' and resid 14 through 31 removed outlier: 4.121A pdb=" N GLN14 20 " --> pdb=" O ARG14 16 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA14 29 " --> pdb=" O ILE14 25 " (cutoff:3.500A) Processing helix chain '14' and resid 83 through 88 removed outlier: 3.551A pdb=" N MET14 88 " --> pdb=" O VAL14 84 " (cutoff:3.500A) Processing helix chain '15' and resid 52 through 57 removed outlier: 4.412A 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 91 through 102 removed outlier: 3.910A pdb=" N THR15 95 " --> pdb=" O GLY15 91 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE15 96 " --> pdb=" O ARG15 92 " (cutoff:3.500A) Processing helix chain '16' and resid 2 through 9 Processing helix chain '17' and resid 13 through 20 removed outlier: 3.842A pdb=" N SER17 20 " --> pdb=" O ILE17 16 " (cutoff:3.500A) Processing helix chain '17' and resid 25 through 36 Processing helix chain '17' and resid 48 through 60 removed outlier: 4.498A 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 24 through 29 Processing helix chain '18' and resid 37 through 50 removed outlier: 3.988A pdb=" N TRP18 41 " --> pdb=" O ASP18 37 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N GLN18 48 " --> pdb=" O VAL18 44 " (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 13 Processing helix chain '19' and resid 19 through 22 removed outlier: 4.091A pdb=" N GLY19 22 " --> pdb=" O ASN19 19 " (cutoff:3.500A) No H-bonds generated for 'chain '19' and resid 19 through 22' Processing helix chain '19' and resid 23 through 44 removed outlier: 3.901A pdb=" N GLY19 40 " --> pdb=" O ASN19 36 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N HIS19 41 " --> pdb=" O HIS19 37 " (cutoff:3.500A) Processing helix chain '19' and resid 48 through 73 Processing helix chain '19' and resid 73 through 84 Processing helix chain '20' and resid 53 through 62 Processing helix chain '20' and resid 68 through 76 Processing helix chain '22' and resid 24 through 29 removed outlier: 3.815A pdb=" N LEU22 28 " --> pdb=" O ASP22 24 " (cutoff:3.500A) Processing helix chain '22' and resid 30 through 32 No H-bonds generated for 'chain '22' and resid 30 through 32' Processing helix chain '22' and resid 40 through 45 removed outlier: 3.509A pdb=" N GLY22 45 " --> pdb=" O SER22 41 " (cutoff:3.500A) Processing helix chain '22' and resid 47 through 64 Processing helix chain '23' and resid 11 through 24 Processing helix chain '23' and resid 40 through 44 Processing helix chain '23' and resid 69 through 74 Processing helix chain '24' and resid 4 through 6 No H-bonds generated for 'chain '24' and resid 4 through 6' Processing helix chain '24' and resid 7 through 41 removed outlier: 4.150A pdb=" N ILE24 11 " --> pdb=" O LYS24 7 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N HIS24 19 " --> pdb=" O LYS24 15 " (cutoff:3.500A) Processing helix chain '24' and resid 42 through 63 Proline residue: 24 55 - end of helix Processing helix chain '24' and resid 68 through 86 Processing helix chain '25' and resid 16 through 22 removed outlier: 3.800A pdb=" N LYS25 19 " --> pdb=" O ARG25 16 " (cutoff:3.500A) Processing helix chain '25' and resid 25 through 31 Processing helix chain '25' and resid 38 through 60 removed outlier: 3.552A 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: 3.521A pdb=" N GLU33 197 " --> pdb=" O GLN33 193 " (cutoff:3.500A) removed outlier: 3.862A 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: 4.277A 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 369 removed outlier: 3.537A pdb=" N ARG33 367 " --> pdb=" O ALA33 363 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY33 369 " --> pdb=" O GLY33 365 " (cutoff:3.500A) Processing helix chain '33' and resid 376 through 381 Processing helix chain '33' and resid 423 through 432 removed outlier: 4.571A pdb=" N TYR33 429 " --> pdb=" O LEU33 425 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N HIS33 430 " --> pdb=" O ASP33 426 " (cutoff:3.500A) Processing helix chain '33' and resid 432 through 438 Processing helix chain '33' and resid 472 through 476 Processing helix chain '33' and resid 486 through 519 Processing helix chain '33' and resid 522 through 529 Processing helix chain '33' and resid 539 through 549 removed outlier: 3.583A pdb=" N ALA33 545 " --> pdb=" O GLU33 541 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE33 546 " --> pdb=" O LEU33 542 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N GLY33 547 " --> pdb=" O LEU33 543 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY33 548 " --> pdb=" O ALA33 544 " (cutoff:3.500A) Processing helix chain '33' and resid 554 through 561 Processing helix chain '33' and resid 566 through 577 removed outlier: 3.598A pdb=" N GLN33 572 " --> pdb=" O SER33 568 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA33 575 " --> pdb=" O GLU33 571 " (cutoff:3.500A) Processing helix chain '33' and resid 585 through 589 Processing helix chain '33' and resid 638 through 647 removed outlier: 3.993A pdb=" N ARG33 645 " --> pdb=" O LEU33 641 " (cutoff:3.500A) Processing helix chain '33' and resid 648 through 652 Processing helix chain '33' and resid 680 through 690 Processing helix chain '33' and resid 718 through 730 removed outlier: 3.955A pdb=" N LEU33 722 " --> pdb=" O ASN33 718 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLY33 723 " --> pdb=" O LEU33 719 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG33 724 " --> pdb=" O GLN33 720 " (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 35 Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 104 removed outlier: 3.601A pdb=" N GLU A 81 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU A 94 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N VAL A 77 " --> pdb=" O LEU A 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 128 through 130 removed outlier: 3.912A pdb=" N GLN A 162 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N THR A 172 " --> pdb=" O VAL A 164 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 21 through 28 removed outlier: 6.046A pdb=" N ILE B 22 " --> pdb=" O ARG B 13 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ARG B 13 " --> pdb=" O ILE B 22 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL B 24 " --> pdb=" O MET B 11 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N MET B 11 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N VAL B 26 " --> pdb=" O VAL B 9 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ASP B 200 " --> pdb=" O THR B 112 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N THR B 112 " --> pdb=" O ASP B 200 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL B 109 " --> pdb=" O GLN B 173 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N GLN B 173 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N GLY B 111 " --> pdb=" O THR B 171 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N THR B 171 " --> pdb=" O GLY B 111 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 80 through 83 removed outlier: 6.975A pdb=" N THR B 51 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N VAL B 34 " --> pdb=" O THR B 51 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 115 through 119 Processing sheet with id=AA8, first strand: chain 'C' and resid 118 through 121 removed outlier: 5.841A pdb=" N LEU C 147 " --> pdb=" O VAL C 187 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N THR C 189 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N ILE C 149 " --> pdb=" O THR C 189 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 65 through 68 removed outlier: 4.214A pdb=" N LYS D 32 " --> pdb=" O THR D 156 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 18 through 19 Processing sheet with id=AB2, first strand: chain 'E' and resid 40 through 41 Processing sheet with id=AB3, first strand: chain 'E' and resid 82 through 84 Processing sheet with id=AB4, first strand: chain 'E' and resid 86 through 89 removed outlier: 3.656A pdb=" N VAL E 89 " --> pdb=" O GLY E 160 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 94 through 98 Processing sheet with id=AB6, first strand: chain 'F' and resid 4 through 5 Processing sheet with id=AB7, first strand: chain 'F' and resid 77 through 79 removed outlier: 6.724A pdb=" N VAL F 78 " --> pdb=" O ASN F 145 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 56 through 60 Processing sheet with id=AB9, first strand: chain 'I' and resid 122 through 124 removed outlier: 6.214A pdb=" N ILE I 54 " --> pdb=" O LYS I 123 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N TYR I 16 " --> pdb=" O ILE I 55 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N LEU I 57 " --> pdb=" O TYR I 16 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL I 18 " --> pdb=" O LEU I 57 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 92 through 94 removed outlier: 4.771A pdb=" N GLN J 93 " --> pdb=" O ASN J 88 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA J 83 " --> pdb=" O VAL J 63 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LYS J 59 " --> pdb=" O LEU J 87 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LYS J 40 " --> pdb=" O ILE J 22 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR J 6 " --> pdb=" O CYS J 21 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N CYS J 84 " --> pdb=" O MET J 7 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ASN J 9 " --> pdb=" O CYS J 84 " (cutoff:3.500A) removed outlier: 7.921A 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 90 Processing sheet with id=AC4, first strand: chain 'L' and resid 33 through 35 Processing sheet with id=AC5, first strand: chain 'L' and resid 39 through 42 removed outlier: 5.842A pdb=" N VAL L 89 " --> pdb=" O GLU L 75 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLU L 75 " --> pdb=" O VAL L 89 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 62 through 65 Processing sheet with id=AC7, first strand: chain 'M' and resid 34 through 37 Processing sheet with id=AC8, first strand: chain 'N' and resid 25 through 30 removed outlier: 3.980A pdb=" N VAL N 49 " --> pdb=" O VAL N 39 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'O' and resid 36 through 45 removed outlier: 6.531A pdb=" N THR O 24 " --> pdb=" O LYS O 86 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER O 82 " --> pdb=" O LYS O 28 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N TRP O 30 " --> pdb=" O VAL O 80 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL O 80 " --> pdb=" O TRP O 30 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'O' and resid 49 through 50 Processing sheet with id=AD2, first strand: chain 'Q' and resid 11 through 14 removed outlier: 6.139A pdb=" N VAL Q 4 " --> pdb=" O LEU Q 39 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Q' and resid 19 through 23 removed outlier: 7.056A pdb=" N THR Q 94 " --> pdb=" O HIS Q 66 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N HIS Q 66 " --> pdb=" O THR Q 94 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL Q 96 " --> pdb=" O VAL Q 64 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N VAL Q 64 " --> pdb=" O VAL Q 96 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N ILE Q 98 " --> pdb=" O GLU Q 62 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLU Q 62 " --> pdb=" O ILE Q 98 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Q' and resid 72 through 78 removed outlier: 4.004A pdb=" N TYR Q 83 " --> pdb=" O ARG Q 78 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'R' and resid 4 through 10 removed outlier: 5.561A pdb=" N ILE R 4 " --> pdb=" O VAL R 107 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N VAL R 107 " --> pdb=" O ILE R 4 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N LYS R 6 " --> pdb=" O VAL R 105 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL R 105 " --> pdb=" O LYS R 6 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ARG R 8 " --> pdb=" O ILE R 103 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ILE R 103 " --> pdb=" O ARG R 8 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N LYS R 98 " --> pdb=" O PRO R 80 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N THR R 100 " --> pdb=" O GLU R 78 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLU R 78 " --> pdb=" O THR R 100 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N HIS R 102 " --> pdb=" O VAL R 76 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL R 76 " --> pdb=" O HIS R 102 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N THR R 104 " --> pdb=" O ILE R 74 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE R 74 " --> pdb=" O THR R 104 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N VAL R 106 " --> pdb=" O THR R 72 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'R' and resid 86 through 87 Processing sheet with id=AD7, first strand: chain 'S' and resid 11 through 14 removed outlier: 4.748A pdb=" N LYS S 81 " --> pdb=" O VAL S 34 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N TRP S 80 " --> pdb=" O VAL S 62 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N VAL S 62 " --> pdb=" O TRP S 80 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LYS S 82 " --> pdb=" O THR S 60 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N THR S 60 " --> pdb=" O LYS S 82 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N TYR S 84 " --> pdb=" O VAL S 58 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N VAL S 58 " --> pdb=" O TYR S 84 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR S 86 " --> pdb=" O GLU S 56 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'S' and resid 67 through 68 Processing sheet with id=AD9, first strand: chain 'T' and resid 21 through 22 Processing sheet with id=AE1, first strand: chain 'T' and resid 24 through 27 removed outlier: 3.591A pdb=" N ASN T 26 " --> pdb=" O ILE T 34 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'T' and resid 39 through 42 removed outlier: 4.225A pdb=" N ASN T 39 " --> pdb=" O ALA T 62 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'T' and resid 82 through 87 Processing sheet with id=AE4, first strand: chain 'U' and resid 3 through 4 removed outlier: 6.727A pdb=" N ILE U 4 " --> pdb=" O VAL U 64 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'U' and resid 7 through 8 Processing sheet with id=AE6, first strand: chain 'U' and resid 7 through 8 removed outlier: 6.260A pdb=" N VAL U 92 " --> pdb=" O ALA U 74 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N ALA U 74 " --> pdb=" O VAL U 92 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'V' and resid 18 through 19 removed outlier: 4.145A pdb=" N GLY V 18 " --> pdb=" O ARG V 35 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE V 32 " --> pdb=" O ALA V 57 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA V 57 " --> pdb=" O ILE V 32 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'V' and resid 26 through 27 Processing sheet with id=AE9, first strand: chain 'W' and resid 12 through 15 Processing sheet with id=AF1, first strand: chain 'W' and resid 32 through 35 Processing sheet with id=AF2, first strand: chain 'W' and resid 38 through 39 Processing sheet with id=AF3, first strand: chain 'Y' and resid 35 through 37 removed outlier: 3.932A pdb=" N LYS Y 5 " --> pdb=" O GLU Y 57 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Z' and resid 21 through 26 Processing sheet with id=AF5, first strand: chain '1' and resid 28 through 29 Processing sheet with id=AF6, first strand: chain '1' and resid 47 through 48 Processing sheet with id=AF7, first strand: chain '2' and resid 19 through 24 Processing sheet with id=AF8, first strand: chain '4' and resid 14 through 15 removed outlier: 3.646A pdb=" N LYS 4 22 " --> pdb=" O LYS 4 14 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain '5' and resid 14 through 15 Processing sheet with id=AG1, first strand: chain '6' and resid 31 through 32 Processing sheet with id=AG2, first strand: chain '6' and resid 89 through 91 removed outlier: 3.732A pdb=" N PHE 6 89 " --> pdb=" O ILE 6 66 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LEU 6 67 " --> pdb=" O PHE 6 161 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain '6' and resid 184 through 186 removed outlier: 7.199A pdb=" N ALA 6 184 " --> pdb=" O ILE 6 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain '7' and resid 51 through 57 removed outlier: 6.611A pdb=" N HIS 7 68 " --> pdb=" O SER 7 52 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ILE 7 54 " --> pdb=" O THR 7 66 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N THR 7 66 " --> pdb=" O ILE 7 54 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ILE 7 56 " --> pdb=" O ARG 7 64 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ARG 7 64 " --> pdb=" O ILE 7 56 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE 7 63 " --> pdb=" O GLN 7 99 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ASN 7 101 " --> pdb=" O ILE 7 63 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N VAL 7 65 " --> pdb=" O ASN 7 101 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N ALA 7 103 " --> pdb=" O VAL 7 65 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE 7 67 " --> pdb=" O ALA 7 103 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain '7' and resid 165 through 170 Processing sheet with id=AG6, first strand: chain '8' and resid 127 through 128 Processing sheet with id=AG7, first strand: chain '9' and resid 12 through 20 removed outlier: 6.775A pdb=" N LEU 9 35 " --> pdb=" O ILE 9 15 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL 9 17 " --> pdb=" O THR 9 33 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N THR 9 33 " --> pdb=" O VAL 9 17 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG 9 19 " --> pdb=" O SER 9 31 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N SER 9 31 " --> pdb=" O ARG 9 19 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain '9' and resid 94 through 96 Processing sheet with id=AG9, first strand: chain '10' and resid 2 through 4 Processing sheet with id=AH1, first strand: chain '10' and resid 60 through 61 Processing sheet with id=AH2, first strand: chain '11' and resid 72 through 75 Processing sheet with id=AH3, first strand: chain '12' and resid 23 through 27 removed outlier: 6.896A pdb=" N GLU12 59 " --> pdb=" O PHE12 48 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N PHE12 48 " --> pdb=" O GLU12 59 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THR12 61 " --> pdb=" O GLU12 46 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain '12' and resid 74 through 76 removed outlier: 3.725A pdb=" N GLY12 122 " --> pdb=" O LYS12 86 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS12 86 " --> pdb=" O GLY12 122 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain '12' and resid 74 through 76 removed outlier: 6.751A pdb=" N VAL12 102 " --> pdb=" O ILE12 125 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain '13' and resid 5 through 7 Processing sheet with id=AH7, first strand: chain '14' and resid 45 through 52 removed outlier: 3.953A pdb=" N GLU14 47 " --> pdb=" O ILE14 67 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain '14' and resid 45 through 52 removed outlier: 3.953A pdb=" N GLU14 47 " --> pdb=" O ILE14 67 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain '15' and resid 40 through 44 removed outlier: 3.791A pdb=" N GLY15 42 " --> pdb=" O ILE15 33 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LEU15 81 " --> pdb=" O ILE15 106 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain '16' and resid 29 through 31 removed outlier: 8.064A pdb=" N THR16 96 " --> pdb=" O THR16 63 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N TYR16 65 " --> pdb=" O THR16 96 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE16 66 " --> pdb=" O LYS16 50 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N LYS16 50 " --> pdb=" O ILE16 66 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ARG16 49 " --> pdb=" O THR16 38 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N THR16 38 " --> pdb=" O ARG16 49 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N VAL16 51 " --> pdb=" O VAL16 36 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N VAL16 36 " --> pdb=" O VAL16 51 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain '20' and resid 2 through 5 removed outlier: 3.729A pdb=" N GLU20 34 " --> pdb=" O VAL20 21 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain '20' and resid 10 through 11 Processing sheet with id=AI4, first strand: chain '21' and resid 10 through 13 removed outlier: 6.545A pdb=" N VAL21 21 " --> pdb=" O VAL21 12 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain '21' and resid 26 through 29 Processing sheet with id=AI6, first strand: chain '21' and resid 59 through 62 removed outlier: 6.484A pdb=" N GLU21 59 " --> pdb=" O VAL21 75 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain '23' and resid 30 through 32 removed outlier: 5.470A pdb=" N LEU23 30 " --> pdb=" O ALA23 49 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N HIS23 51 " --> pdb=" O LEU23 30 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N THR23 32 " --> pdb=" O HIS23 51 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain '33' and resid 247 through 252 removed outlier: 3.957A pdb=" N ALA33 278 " --> pdb=" O ARG33 252 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain '33' and resid 407 through 409 Processing sheet with id=AJ1, first strand: chain '33' and resid 441 through 444 removed outlier: 3.831A pdb=" N GLU33 462 " --> pdb=" O LYS33 443 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain '33' and resid 624 through 625 Processing sheet with id=AJ3, first strand: chain '33' and resid 694 through 700 removed outlier: 3.889A pdb=" N GLY33 696 " --> pdb=" O THR33 713 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ASN33 674 " --> pdb=" O VAL33 735 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N VAL33 735 " --> pdb=" O ASN33 674 " (cutoff:3.500A) 2028 hydrogen bonds defined for protein. 5592 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3971 hydrogen bonds 6306 hydrogen bond angles 0 basepair planarities 1581 basepair parallelities 2373 stacking parallelities Total time for adding SS restraints: 221.53 Time building geometry restraints manager: 74.82 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: 14902 1.31 - 1.45: 72885 1.45 - 1.58: 69969 1.58 - 1.72: 9617 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 1.187 0.143 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 9.86e+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 5.92e+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 4.72e+01 bond pdb=" CG HIS33 159 " pdb=" ND1 HIS33 159 " ideal model delta sigma weight residual 1.378 1.306 0.072 1.10e-02 8.26e+03 4.30e+01 ... (remaining 167678 not shown) Histogram of bond angle deviations from ideal: 88.63 - 98.00: 22 98.00 - 107.37: 35092 107.37 - 116.75: 115832 116.75 - 126.12: 83490 126.12 - 135.49: 15844 Bond angle restraints: 250280 Sorted by residual: angle pdb=" N SER M 119 " pdb=" CA SER M 119 " pdb=" C SER M 119 " ideal model delta sigma weight residual 112.54 94.35 18.19 1.22e+00 6.72e-01 2.22e+02 angle pdb=" N VAL16 20 " pdb=" CA VAL16 20 " pdb=" C VAL16 20 " ideal model delta sigma weight residual 107.60 122.41 -14.81 1.07e+00 8.73e-01 1.92e+02 angle pdb=" N LEU G 60 " pdb=" CA LEU G 60 " pdb=" C LEU G 60 " ideal model delta sigma weight residual 113.20 96.16 17.04 1.36e+00 5.41e-01 1.57e+02 angle pdb=" N PRO33 17 " pdb=" CA PRO33 17 " pdb=" CB PRO33 17 " ideal model delta sigma weight residual 103.33 89.90 13.43 1.10e+00 8.26e-01 1.49e+02 angle pdb=" N MET13 87 " pdb=" CA MET13 87 " pdb=" C MET13 87 " ideal model delta sigma weight residual 113.38 98.56 14.82 1.23e+00 6.61e-01 1.45e+02 ... (remaining 250275 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.59: 94793 35.59 - 71.19: 11134 71.19 - 106.78: 1334 106.78 - 142.37: 26 142.37 - 177.97: 25 Dihedral angle restraints: 107312 sinusoidal: 88434 harmonic: 18878 Sorted by residual: 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 -95.27 -25.43 0 2.50e+00 1.60e-01 1.03e+02 dihedral pdb=" C4' U26 421 " pdb=" C3' U26 421 " pdb=" C2' U26 421 " pdb=" C1' U26 421 " ideal model delta sinusoidal sigma weight residual -35.00 33.63 -68.63 1 8.00e+00 1.56e-02 9.53e+01 dihedral pdb=" C4' U272296 " pdb=" C3' U272296 " pdb=" C2' U272296 " pdb=" C1' U272296 " ideal model delta sinusoidal sigma weight residual -35.00 32.03 -67.03 1 8.00e+00 1.56e-02 9.15e+01 ... (remaining 107309 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 27572 0.133 - 0.266: 4014 0.266 - 0.399: 321 0.399 - 0.532: 19 0.532 - 0.665: 10 Chirality restraints: 31936 Sorted by residual: 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 3.07 -0.66 2.00e-01 2.50e+01 1.10e+01 chirality pdb=" P G30 1 " pdb=" OP1 G30 1 " pdb=" OP2 G30 1 " pdb=" O5' G30 1 " both_signs ideal model delta sigma weight residual True 2.41 -3.06 -0.65 2.00e-01 2.50e+01 1.07e+01 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 -3.04 -0.63 2.00e-01 2.50e+01 9.77e+00 ... (remaining 31933 not shown) Planarity restraints: 13865 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G27 512 " 0.229 2.00e-02 2.50e+03 9.34e-02 2.62e+02 pdb=" N9 G27 512 " -0.014 2.00e-02 2.50e+03 pdb=" C8 G27 512 " -0.089 2.00e-02 2.50e+03 pdb=" N7 G27 512 " -0.079 2.00e-02 2.50e+03 pdb=" C5 G27 512 " -0.043 2.00e-02 2.50e+03 pdb=" C6 G27 512 " 0.044 2.00e-02 2.50e+03 pdb=" O6 G27 512 " 0.128 2.00e-02 2.50e+03 pdb=" N1 G27 512 " 0.045 2.00e-02 2.50e+03 pdb=" C2 G27 512 " -0.025 2.00e-02 2.50e+03 pdb=" N2 G27 512 " -0.027 2.00e-02 2.50e+03 pdb=" N3 G27 512 " -0.089 2.00e-02 2.50e+03 pdb=" C4 G27 512 " -0.080 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 8.94e-02 2.00e+02 pdb=" CG TRP33 39 " 0.135 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 " -0.168 2.00e-02 2.50e+03 pdb=" CE2 TRP33 39 " -0.061 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' U27 683 " -0.158 2.00e-02 2.50e+03 8.41e-02 1.59e+02 pdb=" N1 U27 683 " 0.007 2.00e-02 2.50e+03 pdb=" C2 U27 683 " 0.029 2.00e-02 2.50e+03 pdb=" O2 U27 683 " 0.067 2.00e-02 2.50e+03 pdb=" N3 U27 683 " 0.016 2.00e-02 2.50e+03 pdb=" C4 U27 683 " 0.018 2.00e-02 2.50e+03 pdb=" O4 U27 683 " -0.140 2.00e-02 2.50e+03 pdb=" C5 U27 683 " 0.085 2.00e-02 2.50e+03 pdb=" C6 U27 683 " 0.076 2.00e-02 2.50e+03 ... (remaining 13862 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 4436 2.64 - 3.20: 152760 3.20 - 3.77: 332923 3.77 - 4.33: 419360 4.33 - 4.90: 548794 Nonbonded interactions: 1458273 Sorted by model distance: nonbonded pdb=" O ASP 8 28 " pdb=" N LYS 8 30 " model vdw 2.074 2.520 nonbonded pdb=" O2' A26 246 " pdb=" O5' G26 247 " model vdw 2.083 2.440 nonbonded pdb=" O2' U271130 " pdb=" OP1 G271131 " model vdw 2.170 2.440 nonbonded pdb=" OD2 ASP P 48 " pdb=" O2' U27 534 " model vdw 2.180 2.440 nonbonded pdb=" O ALA15 40 " pdb=" O2' U26 684 " model vdw 2.191 2.440 ... (remaining 1458268 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: 8.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.130 Extract box with map and model: 27.470 Check model and map are aligned: 1.680 Set scattering table: 1.050 Process input model: 513.650 Find NCS groups from input model: 3.070 Set up NCS constraints: 0.380 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:2.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 558.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.206 167683 Z= 0.458 Angle : 1.184 22.171 250280 Z= 0.787 Chirality : 0.093 0.665 31936 Planarity : 0.013 0.292 13865 Dihedral : 22.931 177.968 95118 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 34.60 Ramachandran Plot: Outliers : 6.21 % Allowed : 13.50 % Favored : 80.29 % Rotamer: Outliers : 0.66 % Allowed : 3.83 % Favored : 95.51 % 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: -4.67 (0.09), residues: 6509 helix: -3.28 (0.08), residues: 2165 sheet: -3.33 (0.14), residues: 990 loop : -2.87 (0.10), residues: 3354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.168 0.013 TRP33 39 HIS 0.042 0.001 HIS33 159 PHE 0.069 0.008 PHE13 38 TYR 0.151 0.011 TYR33 41 ARG 0.171 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 1857 residues out of total 5423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 1822 time to evaluate : 6.930 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: 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clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 109 LEU cc_start: 0.8807 (tp) cc_final: 0.8567 (tt) REVERT: A 228 ASP cc_start: 0.8916 (m-30) cc_final: 0.8716 (m-30) REVERT: A 239 PHE cc_start: 0.7873 (t80) cc_final: 0.7564 (t80) REVERT: B 90 PHE cc_start: 0.8503 (m-80) cc_final: 0.8033 (m-80) REVERT: C 46 GLN cc_start: 0.8689 (mp10) cc_final: 0.8413 (mp10) REVERT: C 78 TRP cc_start: 0.7758 (m-10) cc_final: 0.7428 (m-10) REVERT: D 82 TYR cc_start: 0.8992 (t80) cc_final: 0.8604 (t80) REVERT: D 97 GLU cc_start: 0.9400 (tp30) cc_final: 0.8907 (tp30) REVERT: F 2 GLN cc_start: 0.9157 (mm-40) cc_final: 0.8934 (mm-40) REVERT: F 6 LEU cc_start: 0.9354 (tt) cc_final: 0.9123 (tt) REVERT: F 15 LEU cc_start: 0.9387 (tp) cc_final: 0.9177 (tp) REVERT: F 89 LYS cc_start: 0.8407 (mptt) cc_final: 0.7835 (mtmm) REVERT: F 135 HIS cc_start: 0.9175 (t-170) cc_final: 0.8474 (t-90) REVERT: H 5 GLN cc_start: 0.8057 (tt0) cc_final: 0.7756 (pp30) REVERT: H 64 ARG cc_start: 0.5949 (tpt90) cc_final: 0.5250 (mmp80) REVERT: I 69 ARG cc_start: 0.8004 (tpp80) cc_final: 0.7762 (tpp80) REVERT: I 118 MET cc_start: 0.8988 (ptp) cc_final: 0.8665 (ptp) REVERT: K 142 ILE cc_start: 0.9009 (mp) cc_final: 0.8594 (mp) REVERT: L 54 THR cc_start: 0.9494 (m) cc_final: 0.9167 (m) REVERT: L 63 ILE cc_start: 0.8897 (mt) cc_final: 0.8693 (mm) REVERT: L 112 LEU cc_start: 0.8989 (tp) cc_final: 0.8666 (tp) REVERT: L 136 MET cc_start: 0.8575 (ttp) cc_final: 0.7733 (tmm) REVERT: M 112 TYR cc_start: 0.8003 (m-80) cc_final: 0.7745 (m-80) REVERT: N 45 SER cc_start: 0.9153 (t) cc_final: 0.8916 (p) REVERT: N 92 PHE cc_start: 0.8753 (t80) cc_final: 0.8516 (t80) REVERT: O 54 LEU cc_start: 0.9200 (tp) cc_final: 0.8967 (tt) REVERT: P 82 LEU cc_start: 0.9048 (mt) cc_final: 0.8798 (tt) REVERT: S 42 GLU cc_start: 0.9329 (tt0) cc_final: 0.9107 (tt0) REVERT: S 87 LEU cc_start: 0.8758 (mp) cc_final: 0.8546 (mt) REVERT: U 46 LYS cc_start: 0.9589 (mptt) cc_final: 0.9389 (mmtm) REVERT: V 19 VAL cc_start: 0.8683 (t) cc_final: 0.8337 (t) REVERT: V 20 LYS cc_start: 0.8552 (mmtm) cc_final: 0.8238 (mmpt) REVERT: V 28 LEU cc_start: 0.9260 (mt) cc_final: 0.8886 (mm) REVERT: W 34 SER cc_start: 0.9166 (m) cc_final: 0.8928 (p) REVERT: W 48 LEU cc_start: 0.8559 (mt) cc_final: 0.8162 (mt) REVERT: Y 3 THR cc_start: 0.8390 (p) cc_final: 0.7804 (p) REVERT: Y 36 GLU cc_start: 0.8377 (tt0) cc_final: 0.7493 (tt0) REVERT: 1 27 LEU cc_start: 0.8850 (tp) cc_final: 0.8273 (tp) REVERT: 3 15 SER cc_start: 0.8934 (p) cc_final: 0.8655 (m) REVERT: 4 39 ARG cc_start: 0.8638 (ttt180) cc_final: 0.8400 (ttt-90) REVERT: 6 95 TRP cc_start: 0.8883 (t60) cc_final: 0.8432 (t60) REVERT: 6 170 ILE cc_start: 0.9332 (pt) cc_final: 0.8865 (pt) REVERT: 7 156 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8953 (pp) REVERT: 8 177 MET cc_start: 0.9213 (mmm) cc_final: 0.8922 (mmp) REVERT: 9 14 LEU cc_start: 0.9046 (tp) cc_final: 0.8728 (tt) REVERT: 9 35 LEU cc_start: 0.9053 (tp) cc_final: 0.8845 (tp) REVERT: 9 59 ILE cc_start: 0.9632 (pt) cc_final: 0.9405 (pt) REVERT: 10 52 ASN cc_start: 0.9054 (t0) cc_final: 0.8629 (t0) REVERT: 12 82 LEU cc_start: 0.8373 (tp) cc_final: 0.8155 (tt) REVERT: 13 24 ASN cc_start: 0.9041 (t0) cc_final: 0.8545 (t0) REVERT: 13 35 GLU cc_start: 0.9463 (mp0) cc_final: 0.9025 (mm-30) REVERT: 14 10 LEU cc_start: 0.8816 (pp) cc_final: 0.8478 (pp) REVERT: 15 41 LEU cc_start: 0.7913 (mt) cc_final: 0.7607 (tp) REVERT: 15 49 SER cc_start: 0.8619 (m) cc_final: 0.8359 (p) REVERT: 15 51 PHE cc_start: 0.8284 (m-10) cc_final: 0.8051 (m-10) REVERT: 16 33 CYS cc_start: 0.8543 (t) cc_final: 0.7951 (t) REVERT: 17 20 SER cc_start: 0.9639 (m) cc_final: 0.9151 (t) REVERT: 17 77 LYS cc_start: 0.9263 (tptm) cc_final: 0.8731 (tptt) REVERT: 17 81 ASP cc_start: 0.8598 (m-30) cc_final: 0.7823 (m-30) REVERT: 18 17 ASP cc_start: 0.8748 (t70) cc_final: 0.8515 (t0) REVERT: 18 46 LYS cc_start: 0.9391 (mptt) cc_final: 0.9170 (mmmt) REVERT: 18 49 THR cc_start: 0.9315 (m) cc_final: 0.8885 (m) REVERT: 19 77 TYR cc_start: 0.8736 (t80) cc_final: 0.8421 (t80) REVERT: 19 79 GLN cc_start: 0.9315 (tp-100) cc_final: 0.9109 (tm-30) REVERT: 21 62 GLU cc_start: 0.8688 (tt0) cc_final: 0.8205 (tt0) REVERT: 22 50 TYR cc_start: 0.8832 (m-80) cc_final: 0.8545 (m-10) REVERT: 24 5 SER cc_start: 0.8872 (m) cc_final: 0.8660 (t) REVERT: 24 60 GLN cc_start: 0.8830 (mm-40) cc_final: 0.8524 (mm-40) outliers start: 35 outliers final: 16 residues processed: 1845 average time/residue: 1.4247 time to fit residues: 4458.1541 Evaluate side-chains 1251 residues out of total 5423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 1234 time to evaluate : 6.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 289 optimal weight: 7.9990 chunk 571 optimal weight: 30.0000 chunk 452 optimal weight: 7.9990 chunk 875 optimal weight: 30.0000 chunk 338 optimal weight: 20.0000 chunk 532 optimal weight: 4.9990 chunk 651 optimal weight: 20.0000 chunk 1014 optimal weight: 20.0000 overall best weight: 9.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 44 ASN A 57 HIS A 89 ASN ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 GLN A 225 ASN ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 ASN D 62 GLN D 80 GLN ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 HIS E 142 GLN ** F 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 GLN F 28 ASN F 135 HIS ** G 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 ASN ** H 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 58 ASN I 128 ASN J 82 ASN K 104 GLN ** L 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 23 ASN N 29 HIS N 104 GLN O 55 HIS P 43 GLN Q 43 ASN ** R 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 59 ASN ** T 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 20 ASN X 25 GLN ** Y 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 19 HIS ** 6 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 18 GLN 6 41 ASN ** 6 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 2 GLN 7 18 ASN 7 139 ASN 8 70 GLN ** 8 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 125 ASN 8 151 GLN ** 9 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 134 ASN ** 10 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 10 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 27 ASN 11 121 ASN ** 11 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 12 66 GLN ** 13 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 109 GLN ** 13 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 14 35 GLN ** 14 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 15 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 16 5 GLN 17 13 HIS 18 3 GLN 18 42 ASN 19 34 GLN 19 49 HIS 19 61 GLN ** 21 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 22 51 GLN ** 23 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 23 68 HIS 24 47 GLN 24 51 ASN ** 25 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 33 88 ASN ** 33 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 33 614 GLN ** 33 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 33 730 ASN Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 167683 Z= 0.319 Angle : 0.801 13.704 250280 Z= 0.410 Chirality : 0.043 0.413 31936 Planarity : 0.006 0.141 13865 Dihedral : 24.074 179.743 82431 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 27.51 Ramachandran Plot: Outliers : 1.57 % Allowed : 11.55 % Favored : 86.88 % Rotamer: Outliers : 0.21 % Allowed : 4.28 % Favored : 95.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.10), residues: 6509 helix: -1.53 (0.10), residues: 2201 sheet: -2.98 (0.14), residues: 1071 loop : -2.20 (0.11), residues: 3237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A 212 HIS 0.016 0.002 HIS I 132 PHE 0.034 0.003 PHE G 69 TYR 0.033 0.003 TYR H 7 ARG 0.023 0.001 ARG E 148 *********************** 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 1604 residues out of total 5423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1593 time to evaluate : 7.024 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: B 1 MET cc_start: 0.7694 (ptt) cc_final: 0.7401 (ptt) REVERT: B 82 PHE cc_start: 0.7569 (m-80) cc_final: 0.7240 (m-80) REVERT: C 19 PHE cc_start: 0.8763 (m-80) cc_final: 0.8325 (m-10) REVERT: C 78 TRP cc_start: 0.7691 (m-10) cc_final: 0.7360 (m-10) REVERT: D 37 MET cc_start: 0.9145 (mtm) cc_final: 0.8849 (mtm) REVERT: D 82 TYR cc_start: 0.8852 (t80) cc_final: 0.8630 (t80) REVERT: F 2 GLN cc_start: 0.9217 (mm-40) cc_final: 0.8983 (mm-40) REVERT: F 6 LEU cc_start: 0.9364 (tt) cc_final: 0.9091 (tt) REVERT: F 28 ASN cc_start: 0.8064 (m110) cc_final: 0.7841 (m110) REVERT: F 117 LEU cc_start: 0.8772 (pp) cc_final: 0.8382 (pp) REVERT: F 135 HIS cc_start: 0.9235 (t70) cc_final: 0.8985 (t70) REVERT: F 141 LYS cc_start: 0.8772 (pttm) cc_final: 0.8441 (tptp) REVERT: H 5 GLN cc_start: 0.8339 (tt0) cc_final: 0.7864 (pp30) REVERT: I 118 MET cc_start: 0.8886 (ptp) cc_final: 0.8659 (ptp) REVERT: I 140 LEU cc_start: 0.8519 (tp) cc_final: 0.8049 (tt) REVERT: J 80 ASP cc_start: 0.8971 (m-30) cc_final: 0.8654 (p0) REVERT: L 59 ARG cc_start: 0.8335 (mtt90) cc_final: 0.8085 (mmt90) REVERT: L 74 THR cc_start: 0.8811 (p) cc_final: 0.8468 (p) REVERT: M 28 LEU cc_start: 0.9212 (tp) cc_final: 0.8971 (tp) REVERT: M 44 LEU cc_start: 0.9187 (tp) cc_final: 0.8507 (tp) REVERT: M 112 TYR cc_start: 0.8135 (m-80) cc_final: 0.7866 (m-80) REVERT: N 16 ARG cc_start: 0.9351 (mmp80) cc_final: 0.9148 (mmp80) REVERT: N 19 GLN cc_start: 0.9468 (pp30) cc_final: 0.9139 (pp30) REVERT: N 45 SER cc_start: 0.9168 (t) cc_final: 0.8930 (p) REVERT: O 6 GLN cc_start: 0.9471 (tt0) cc_final: 0.9121 (tp-100) REVERT: Q 95 ASP cc_start: 0.8537 (m-30) cc_final: 0.8229 (m-30) REVERT: U 86 LEU cc_start: 0.8779 (mt) cc_final: 0.8441 (mt) REVERT: V 8 ASN cc_start: 0.8038 (p0) cc_final: 0.7815 (p0) REVERT: V 11 ASP cc_start: 0.8682 (t0) cc_final: 0.8220 (t0) REVERT: V 20 LYS cc_start: 0.8567 (mmtm) cc_final: 0.8356 (mmmt) REVERT: V 28 LEU cc_start: 0.9225 (mt) cc_final: 0.8875 (mm) REVERT: W 34 SER cc_start: 0.9122 (m) cc_final: 0.8893 (p) REVERT: W 41 SER cc_start: 0.9358 (p) cc_final: 0.9131 (p) REVERT: X 4 LYS cc_start: 0.9075 (ptpp) cc_final: 0.8826 (ptmm) REVERT: X 25 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8421 (tp-100) REVERT: 1 27 LEU cc_start: 0.8297 (tp) cc_final: 0.7876 (tp) REVERT: 2 20 TYR cc_start: 0.7616 (m-80) cc_final: 0.7362 (m-10) REVERT: 3 15 SER cc_start: 0.8754 (p) cc_final: 0.8425 (m) REVERT: 6 48 MET cc_start: 0.9109 (mmp) cc_final: 0.8874 (mmp) REVERT: 7 99 GLN cc_start: 0.9097 (tm-30) cc_final: 0.8868 (tm-30) REVERT: 7 183 TYR cc_start: 0.8202 (t80) cc_final: 0.7975 (t80) REVERT: 8 53 GLN cc_start: 0.8882 (mt0) cc_final: 0.8389 (tt0) REVERT: 9 95 MET cc_start: 0.8890 (pmm) cc_final: 0.8689 (pmm) REVERT: 9 114 LEU cc_start: 0.9126 (mp) cc_final: 0.8904 (mp) REVERT: 9 155 LYS cc_start: 0.9115 (mtmm) cc_final: 0.8899 (ptpp) REVERT: 10 24 ARG cc_start: 0.9332 (mmm160) cc_final: 0.9113 (tpm170) REVERT: 12 17 GLN cc_start: 0.8496 (mm-40) cc_final: 0.8143 (mm-40) REVERT: 12 65 PHE cc_start: 0.8636 (t80) cc_final: 0.8141 (t80) REVERT: 13 12 LYS cc_start: 0.8087 (mttt) cc_final: 0.7884 (mttt) REVERT: 13 36 GLN cc_start: 0.8915 (pt0) cc_final: 0.8371 (pm20) REVERT: 14 24 GLU cc_start: 0.8957 (pp20) cc_final: 0.8665 (pp20) REVERT: 16 58 ASN cc_start: 0.9030 (p0) cc_final: 0.8811 (p0) REVERT: 17 20 SER cc_start: 0.9574 (m) cc_final: 0.9103 (t) REVERT: 18 76 PHE cc_start: 0.8633 (m-10) cc_final: 0.8369 (m-10) REVERT: 19 77 TYR cc_start: 0.8682 (t80) cc_final: 0.8259 (t80) REVERT: 21 8 GLN cc_start: 0.8924 (tp-100) cc_final: 0.8666 (tp-100) REVERT: 21 62 GLU cc_start: 0.8823 (tt0) cc_final: 0.8274 (tt0) REVERT: 22 50 TYR cc_start: 0.8749 (m-10) cc_final: 0.8434 (m-10) REVERT: 24 5 SER cc_start: 0.8737 (m) cc_final: 0.8435 (t) outliers start: 11 outliers final: 6 residues processed: 1599 average time/residue: 1.4070 time to fit residues: 3876.8323 Evaluate side-chains 1198 residues out of total 5423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1191 time to evaluate : 6.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 844 optimal weight: 20.0000 chunk 690 optimal weight: 20.0000 chunk 279 optimal weight: 40.0000 chunk 1016 optimal weight: 20.0000 chunk 1097 optimal weight: 40.0000 chunk 905 optimal weight: 20.0000 chunk 1007 optimal weight: 20.0000 chunk 346 optimal weight: 30.0000 chunk 815 optimal weight: 20.0000 overall best weight: 13.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 ASN ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 ASN ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 GLN ** F 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 ASN ** G 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 128 ASN ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 ASN M 9 GLN P 55 GLN ** R 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 48 GLN 5 35 GLN 6 14 HIS 6 17 HIS ** 6 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 2 GLN ** 7 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 10 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 10 94 HIS ** 11 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 36 GLN ** 13 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 15 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 15 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 22 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 23 68 HIS ** 24 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 24 47 GLN 24 69 ASN 25 55 HIS ** 33 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 33 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 167683 Z= 0.400 Angle : 0.793 13.283 250280 Z= 0.409 Chirality : 0.042 0.367 31936 Planarity : 0.006 0.123 13865 Dihedral : 24.258 178.751 82431 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 35.49 Ramachandran Plot: Outliers : 1.38 % Allowed : 12.55 % Favored : 86.07 % Rotamer: Outliers : 0.38 % Allowed : 5.71 % Favored : 93.91 % 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: -2.73 (0.10), residues: 6509 helix: -0.93 (0.10), residues: 2208 sheet: -2.70 (0.14), residues: 1088 loop : -2.07 (0.11), residues: 3213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A 212 HIS 0.023 0.002 HIS O 76 PHE 0.036 0.003 PHE E 51 TYR 0.035 0.003 TYR22 69 ARG 0.024 0.001 ARG J 17 *********************** 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 1468 residues out of total 5423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 1448 time to evaluate : 6.810 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: A 228 ASP cc_start: 0.9036 (m-30) cc_final: 0.8797 (m-30) REVERT: B 82 PHE cc_start: 0.7740 (m-80) cc_final: 0.7393 (m-80) REVERT: C 78 TRP cc_start: 0.7675 (m-10) cc_final: 0.7434 (m-10) REVERT: C 149 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8380 (tp) REVERT: C 199 MET cc_start: 0.9198 (ppp) cc_final: 0.8812 (ppp) REVERT: D 174 PHE cc_start: 0.9088 (t80) cc_final: 0.8845 (t80) REVERT: F 2 GLN cc_start: 0.9322 (mm-40) cc_final: 0.8988 (mm-40) REVERT: F 117 LEU cc_start: 0.8838 (pp) cc_final: 0.8491 (pp) REVERT: F 135 HIS cc_start: 0.9244 (t70) cc_final: 0.8889 (t-90) REVERT: F 141 LYS cc_start: 0.8688 (pttm) cc_final: 0.8476 (tptp) REVERT: G 8 LYS cc_start: 0.9535 (mtpp) cc_final: 0.9297 (mtpp) REVERT: H 5 GLN cc_start: 0.8418 (tt0) cc_final: 0.8181 (mt0) REVERT: I 93 ILE cc_start: 0.9284 (mm) cc_final: 0.8963 (mm) REVERT: I 140 LEU cc_start: 0.8651 (tp) cc_final: 0.8450 (tp) REVERT: J 80 ASP cc_start: 0.8943 (m-30) cc_final: 0.8658 (p0) REVERT: L 74 THR cc_start: 0.8787 (p) cc_final: 0.8558 (p) REVERT: M 21 PHE cc_start: 0.8831 (m-80) cc_final: 0.8474 (m-80) REVERT: M 75 ILE cc_start: 0.9066 (mm) cc_final: 0.8796 (mm) REVERT: M 112 TYR cc_start: 0.8189 (m-80) cc_final: 0.7800 (m-80) REVERT: N 16 ARG cc_start: 0.9370 (mmp80) cc_final: 0.9119 (mmp80) REVERT: N 45 SER cc_start: 0.9255 (t) cc_final: 0.8969 (p) REVERT: N 92 PHE cc_start: 0.8712 (t80) cc_final: 0.8245 (t80) REVERT: O 6 GLN cc_start: 0.9484 (tt0) cc_final: 0.9088 (tp-100) REVERT: P 78 PHE cc_start: 0.8999 (t80) cc_final: 0.8723 (t80) REVERT: P 116 LEU cc_start: 0.9337 (pp) cc_final: 0.9001 (tt) REVERT: Q 19 THR cc_start: 0.9237 (m) cc_final: 0.8809 (p) REVERT: Q 86 GLN cc_start: 0.8075 (pp30) cc_final: 0.7575 (pp30) REVERT: Q 95 ASP cc_start: 0.8558 (m-30) cc_final: 0.8268 (m-30) REVERT: S 1 MET cc_start: 0.6336 (ptm) cc_final: 0.4991 (mtm) REVERT: V 8 ASN cc_start: 0.8216 (p0) cc_final: 0.7940 (p0) REVERT: V 11 ASP cc_start: 0.8753 (t0) cc_final: 0.8546 (t0) REVERT: V 28 LEU cc_start: 0.9254 (mt) cc_final: 0.8937 (mm) REVERT: V 35 ARG cc_start: 0.8138 (mtt180) cc_final: 0.7794 (mtm180) REVERT: W 70 LEU cc_start: 0.9461 (tp) cc_final: 0.9205 (tp) REVERT: W 77 TYR cc_start: 0.8591 (p90) cc_final: 0.8273 (p90) REVERT: X 25 GLN cc_start: 0.8637 (tp40) cc_final: 0.8381 (tp40) REVERT: 3 15 SER cc_start: 0.8886 (p) cc_final: 0.8586 (m) REVERT: 6 90 PHE cc_start: 0.8444 (p90) cc_final: 0.8117 (p90) REVERT: 6 169 HIS cc_start: 0.9097 (p-80) cc_final: 0.8769 (p-80) REVERT: 6 173 LYS cc_start: 0.9116 (tttt) cc_final: 0.8881 (tmtt) REVERT: 8 195 ASN cc_start: 0.8356 (m-40) cc_final: 0.8083 (m-40) REVERT: 10 21 MET cc_start: 0.9648 (mtp) cc_final: 0.9237 (mpp) REVERT: 10 24 ARG cc_start: 0.9396 (mmm160) cc_final: 0.9092 (tpm170) REVERT: 10 52 ASN cc_start: 0.8831 (t0) cc_final: 0.8612 (t0) REVERT: 10 59 TYR cc_start: 0.7108 (m-10) cc_final: 0.6825 (m-10) REVERT: 10 88 MET cc_start: 0.8970 (ptm) cc_final: 0.8243 (ptm) REVERT: 11 28 ILE cc_start: 0.9274 (mm) cc_final: 0.8994 (tt) REVERT: 12 58 LEU cc_start: 0.8867 (tp) cc_final: 0.8581 (tp) REVERT: 12 65 PHE cc_start: 0.8592 (t80) cc_final: 0.8380 (t80) REVERT: 12 82 LEU cc_start: 0.8538 (tp) cc_final: 0.8256 (tt) REVERT: 13 12 LYS cc_start: 0.8472 (mttt) cc_final: 0.8034 (mttt) REVERT: 13 62 LEU cc_start: 0.8443 (mm) cc_final: 0.8062 (mm) REVERT: 14 24 GLU cc_start: 0.8966 (pp20) cc_final: 0.8761 (pp20) REVERT: 14 52 LEU cc_start: 0.8932 (mm) cc_final: 0.8678 (mt) REVERT: 15 71 ASP cc_start: 0.9197 (p0) cc_final: 0.8922 (p0) REVERT: 16 58 ASN cc_start: 0.9173 (p0) cc_final: 0.8956 (p0) REVERT: 17 40 GLU cc_start: 0.6912 (mp0) cc_final: 0.6363 (mp0) REVERT: 18 81 ILE cc_start: 0.9196 (mt) cc_final: 0.8879 (tt) REVERT: 19 77 TYR cc_start: 0.8722 (t80) cc_final: 0.8289 (t80) REVERT: 20 78 VAL cc_start: 0.8972 (p) cc_final: 0.8690 (p) REVERT: 21 62 GLU cc_start: 0.8895 (tt0) cc_final: 0.8672 (tm-30) REVERT: 22 50 TYR cc_start: 0.8694 (m-10) cc_final: 0.8266 (m-10) REVERT: 23 17 LYS cc_start: 0.8979 (mtmm) cc_final: 0.8400 (mmtm) REVERT: 33 142 MET cc_start: 0.5395 (ppp) cc_final: 0.4397 (ppp) REVERT: 33 440 ILE cc_start: 0.8821 (pt) cc_final: 0.8560 (mm) outliers start: 20 outliers final: 9 residues processed: 1460 average time/residue: 1.3645 time to fit residues: 3426.0537 Evaluate side-chains 1154 residues out of total 5423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1144 time to evaluate : 6.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1117 random chunks: chunk 1004 optimal weight: 30.0000 chunk 764 optimal weight: 30.0000 chunk 527 optimal weight: 5.9990 chunk 112 optimal weight: 8.9990 chunk 484 optimal weight: 6.9990 chunk 682 optimal weight: 20.0000 chunk 1019 optimal weight: 20.0000 chunk 1079 optimal weight: 0.9980 chunk 532 optimal weight: 9.9990 chunk 966 optimal weight: 20.0000 chunk 290 optimal weight: 20.0000 overall best weight: 6.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 GLN ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 HIS F 28 ASN F 73 ASN ** G 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN J 82 ASN ** K 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 104 GLN ** O 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 12 GLN ** U 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 2 GLN ** 8 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 14 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 15 23 HIS ** 15 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 22 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 23 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 24 69 ASN ** 33 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 33 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 33 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 167683 Z= 0.229 Angle : 0.661 10.856 250280 Z= 0.340 Chirality : 0.036 0.337 31936 Planarity : 0.005 0.123 13865 Dihedral : 24.245 178.260 82431 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 26.39 Ramachandran Plot: Outliers : 1.21 % Allowed : 10.23 % Favored : 88.55 % Rotamer: Outliers : 0.02 % Allowed : 3.17 % Favored : 96.81 % 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: -2.25 (0.10), residues: 6509 helix: -0.43 (0.11), residues: 2234 sheet: -2.50 (0.14), residues: 1066 loop : -1.87 (0.11), residues: 3209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 212 HIS 0.018 0.001 HIS M 3 PHE 0.029 0.002 PHE J 79 TYR 0.029 0.002 TYR17 22 ARG 0.010 0.001 ARG E 148 *********************** REFINEMENT MACRO_CYCLE 4 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 1490 residues out of total 5423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1489 time to evaluate : 7.047 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: A 228 ASP cc_start: 0.9081 (m-30) cc_final: 0.8688 (m-30) REVERT: B 82 PHE cc_start: 0.7608 (m-80) cc_final: 0.7244 (m-80) REVERT: C 73 ILE cc_start: 0.8713 (mp) cc_final: 0.8425 (mp) REVERT: C 199 MET cc_start: 0.9161 (ppp) cc_final: 0.8794 (ppp) REVERT: D 97 GLU cc_start: 0.8946 (tp30) cc_final: 0.8530 (tp30) REVERT: F 2 GLN cc_start: 0.9286 (mm-40) cc_final: 0.8917 (mm-40) REVERT: F 43 ASN cc_start: 0.9563 (m110) cc_final: 0.9253 (m110) REVERT: F 117 LEU cc_start: 0.8676 (pp) cc_final: 0.8333 (pp) REVERT: F 133 GLN cc_start: 0.8884 (pm20) cc_final: 0.7872 (pm20) REVERT: F 135 HIS cc_start: 0.9214 (t70) cc_final: 0.8823 (t70) REVERT: F 141 LYS cc_start: 0.8676 (pttm) cc_final: 0.8464 (tptp) REVERT: G 8 LYS cc_start: 0.9576 (mtpp) cc_final: 0.9319 (mtpp) REVERT: H 5 GLN cc_start: 0.8171 (tt0) cc_final: 0.7893 (mt0) REVERT: I 118 MET cc_start: 0.8967 (ptm) cc_final: 0.8330 (ptm) REVERT: J 80 ASP cc_start: 0.8829 (m-30) cc_final: 0.8591 (p0) REVERT: K 23 ILE cc_start: 0.8911 (mt) cc_final: 0.8245 (mt) REVERT: M 24 MET cc_start: 0.8699 (tpp) cc_final: 0.8350 (tpp) REVERT: M 35 LYS cc_start: 0.8330 (ttmm) cc_final: 0.8123 (ttmm) REVERT: M 54 LEU cc_start: 0.9185 (tp) cc_final: 0.8929 (tp) REVERT: M 75 ILE cc_start: 0.9082 (mm) cc_final: 0.8727 (mm) REVERT: M 112 TYR cc_start: 0.8201 (m-80) cc_final: 0.7727 (m-80) REVERT: N 16 ARG cc_start: 0.9372 (mmp80) cc_final: 0.9058 (mmp80) REVERT: N 19 GLN cc_start: 0.9493 (pp30) cc_final: 0.9258 (pp30) REVERT: N 45 SER cc_start: 0.9226 (t) cc_final: 0.8977 (p) REVERT: N 76 LYS cc_start: 0.9675 (ttpt) cc_final: 0.9407 (ptmm) REVERT: N 80 GLU cc_start: 0.9248 (mt-10) cc_final: 0.8860 (mt-10) REVERT: N 92 PHE cc_start: 0.8733 (t80) cc_final: 0.8304 (t80) REVERT: O 6 GLN cc_start: 0.9507 (tt0) cc_final: 0.9099 (tp-100) REVERT: P 78 PHE cc_start: 0.8921 (t80) cc_final: 0.8607 (t80) REVERT: P 116 LEU cc_start: 0.9340 (pp) cc_final: 0.9036 (tt) REVERT: Q 95 ASP cc_start: 0.8456 (m-30) cc_final: 0.8197 (m-30) REVERT: S 50 LEU cc_start: 0.9537 (mp) cc_final: 0.9063 (mt) REVERT: T 38 ILE cc_start: 0.9417 (mm) cc_final: 0.9159 (mm) REVERT: U 61 LEU cc_start: 0.9118 (mp) cc_final: 0.8833 (mt) REVERT: U 90 ASP cc_start: 0.8259 (m-30) cc_final: 0.7077 (m-30) REVERT: V 20 LYS cc_start: 0.8838 (mmmt) cc_final: 0.8587 (mmtt) REVERT: V 28 LEU cc_start: 0.9207 (mt) cc_final: 0.8876 (mm) REVERT: W 43 LYS cc_start: 0.9301 (mppt) cc_final: 0.9093 (mppt) REVERT: W 66 VAL cc_start: 0.9149 (t) cc_final: 0.8344 (p) REVERT: W 77 TYR cc_start: 0.8432 (p90) cc_final: 0.8121 (p90) REVERT: X 25 GLN cc_start: 0.8620 (tp40) cc_final: 0.8319 (tp-100) REVERT: Z 32 LEU cc_start: 0.9357 (tp) cc_final: 0.9140 (tt) REVERT: 2 32 LYS cc_start: 0.9318 (mmmm) cc_final: 0.9023 (mmmm) REVERT: 3 15 SER cc_start: 0.8819 (p) cc_final: 0.8538 (m) REVERT: 5 2 LYS cc_start: 0.7891 (tttm) cc_final: 0.7423 (mtmt) REVERT: 6 169 HIS cc_start: 0.9069 (p-80) cc_final: 0.8845 (p-80) REVERT: 6 173 LYS cc_start: 0.9053 (tttt) cc_final: 0.8781 (tmtt) REVERT: 7 18 ASN cc_start: 0.8399 (t0) cc_final: 0.8172 (t0) REVERT: 7 99 GLN cc_start: 0.9205 (tm-30) cc_final: 0.8987 (tm-30) REVERT: 8 64 TYR cc_start: 0.8146 (m-80) cc_final: 0.7888 (m-80) REVERT: 9 114 LEU cc_start: 0.9217 (mm) cc_final: 0.8970 (mm) REVERT: 10 21 MET cc_start: 0.9695 (mtp) cc_final: 0.9172 (mpp) REVERT: 10 59 TYR cc_start: 0.7074 (m-10) cc_final: 0.6756 (m-10) REVERT: 11 28 ILE cc_start: 0.9232 (mm) cc_final: 0.8925 (tt) REVERT: 12 58 LEU cc_start: 0.8885 (tp) cc_final: 0.8598 (tp) REVERT: 13 12 LYS cc_start: 0.8420 (mttt) cc_final: 0.8003 (mttt) REVERT: 13 35 GLU cc_start: 0.9411 (mp0) cc_final: 0.9161 (mm-30) REVERT: 13 49 GLN cc_start: 0.9366 (tt0) cc_final: 0.9110 (tt0) REVERT: 14 52 LEU cc_start: 0.8929 (mm) cc_final: 0.8692 (mt) REVERT: 15 19 VAL cc_start: 0.7965 (t) cc_final: 0.7675 (t) REVERT: 16 58 ASN cc_start: 0.9106 (p0) cc_final: 0.8623 (p0) REVERT: 17 41 ASP cc_start: 0.9267 (p0) cc_final: 0.8788 (t0) REVERT: 17 82 LEU cc_start: 0.9424 (tp) cc_final: 0.9215 (tp) REVERT: 19 77 TYR cc_start: 0.8608 (t80) cc_final: 0.7667 (t80) REVERT: 22 50 TYR cc_start: 0.8377 (m-10) cc_final: 0.7994 (m-10) REVERT: 23 17 LYS cc_start: 0.8978 (mtmm) cc_final: 0.8354 (mmtm) REVERT: 23 72 GLU cc_start: 0.8242 (pp20) cc_final: 0.8022 (pp20) REVERT: 33 142 MET cc_start: 0.5579 (ppp) cc_final: 0.4871 (ppp) REVERT: 33 440 ILE cc_start: 0.8831 (pt) cc_final: 0.8586 (mm) outliers start: 1 outliers final: 0 residues processed: 1489 average time/residue: 1.3683 time to fit residues: 3531.4596 Evaluate side-chains 1141 residues out of total 5423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1141 time to evaluate : 6.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1117 random chunks: chunk 899 optimal weight: 20.0000 chunk 612 optimal weight: 30.0000 chunk 15 optimal weight: 50.0000 chunk 803 optimal weight: 20.0000 chunk 445 optimal weight: 20.0000 chunk 921 optimal weight: 20.0000 chunk 746 optimal weight: 20.0000 chunk 1 optimal weight: 30.0000 chunk 551 optimal weight: 20.0000 chunk 969 optimal weight: 20.0000 chunk 272 optimal weight: 20.0000 overall best weight: 20.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 ASN ** F 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 ASN ** F 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 ASN ** F 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 80 HIS ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN J 82 ASN K 104 GLN O 11 GLN P 58 GLN P 70 GLN ** R 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 2 GLN ** 7 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 15 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 16 95 HIS ** 18 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 22 30 ASN ** 22 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 23 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 23 68 HIS ** 24 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 33 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 33 108 HIS ** 33 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 33 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 33 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 33 706 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.109 167683 Z= 0.556 Angle : 0.907 15.620 250280 Z= 0.460 Chirality : 0.047 0.376 31936 Planarity : 0.007 0.108 13865 Dihedral : 24.457 178.095 82431 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 47.53 Ramachandran Plot: Outliers : 1.09 % Allowed : 12.83 % Favored : 86.08 % Rotamer: Outliers : 0.06 % Allowed : 5.07 % Favored : 94.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.10), residues: 6509 helix: -0.88 (0.10), residues: 2235 sheet: -2.57 (0.14), residues: 1059 loop : -2.15 (0.11), residues: 3215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP C 78 HIS 0.017 0.002 HIS 8 197 PHE 0.043 0.004 PHE16 60 TYR 0.033 0.003 TYR22 69 ARG 0.021 0.001 ARG22 11 *********************** REFINEMENT MACRO_CYCLE 5 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 1348 residues out of total 5423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1345 time to evaluate : 7.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 120 ASP cc_start: 0.8970 (p0) cc_final: 0.8717 (p0) REVERT: B 82 PHE cc_start: 0.7850 (m-80) cc_final: 0.7578 (m-80) REVERT: C 199 MET cc_start: 0.9240 (ppp) cc_final: 0.8944 (ppp) REVERT: D 127 TYR cc_start: 0.8552 (t80) cc_final: 0.8309 (t80) REVERT: D 174 PHE cc_start: 0.9141 (t80) cc_final: 0.8925 (t80) REVERT: F 2 GLN cc_start: 0.9388 (mm-40) cc_final: 0.9040 (mm-40) REVERT: F 89 LYS cc_start: 0.8557 (mptt) cc_final: 0.8034 (mtmm) REVERT: F 117 LEU cc_start: 0.8796 (pp) cc_final: 0.8420 (pp) REVERT: F 135 HIS cc_start: 0.9297 (t70) cc_final: 0.8886 (t-90) REVERT: G 8 LYS cc_start: 0.9559 (mtpp) cc_final: 0.9312 (mtpp) REVERT: H 5 GLN cc_start: 0.8259 (tt0) cc_final: 0.7813 (mt0) REVERT: I 118 MET cc_start: 0.9032 (ptm) cc_final: 0.8675 (ptm) REVERT: J 80 ASP cc_start: 0.9134 (m-30) cc_final: 0.8579 (p0) REVERT: L 136 MET cc_start: 0.8643 (tmm) cc_final: 0.7586 (tmm) REVERT: M 28 LEU cc_start: 0.9159 (tp) cc_final: 0.8887 (tt) REVERT: M 75 ILE cc_start: 0.9140 (mm) cc_final: 0.8833 (mm) REVERT: M 112 TYR cc_start: 0.8244 (m-80) cc_final: 0.7842 (m-80) REVERT: N 92 PHE cc_start: 0.8817 (t80) cc_final: 0.8361 (t80) REVERT: O 6 GLN cc_start: 0.9481 (tt0) cc_final: 0.9187 (tp-100) REVERT: P 3 VAL cc_start: 0.9065 (t) cc_final: 0.8841 (p) REVERT: P 78 PHE cc_start: 0.9085 (t80) cc_final: 0.8832 (t80) REVERT: Q 27 ILE cc_start: 0.9301 (tp) cc_final: 0.8927 (tp) REVERT: Q 86 GLN cc_start: 0.7953 (pp30) cc_final: 0.7224 (pp30) REVERT: Q 87 GLN cc_start: 0.8507 (tm-30) cc_final: 0.8291 (tm-30) REVERT: Q 95 ASP cc_start: 0.8637 (m-30) cc_final: 0.8436 (m-30) REVERT: R 95 ARG cc_start: 0.7835 (ttp80) cc_final: 0.7409 (ttp80) REVERT: S 5 GLU cc_start: 0.9189 (pp20) cc_final: 0.8886 (pp20) REVERT: T 17 ASP cc_start: 0.8220 (p0) cc_final: 0.7937 (p0) REVERT: U 61 LEU cc_start: 0.9218 (mp) cc_final: 0.8959 (mp) REVERT: U 76 ASP cc_start: 0.9169 (p0) cc_final: 0.8041 (p0) REVERT: V 11 ASP cc_start: 0.8930 (t70) cc_final: 0.8587 (t0) REVERT: V 28 LEU cc_start: 0.9216 (mt) cc_final: 0.8796 (mm) REVERT: W 43 LYS cc_start: 0.9420 (mppt) cc_final: 0.9196 (mppt) REVERT: Z 32 LEU cc_start: 0.9439 (tp) cc_final: 0.9176 (tt) REVERT: 2 6 GLU cc_start: 0.8388 (pp20) cc_final: 0.7806 (pp20) REVERT: 2 8 ILE cc_start: 0.8614 (pt) cc_final: 0.8410 (pt) REVERT: 2 32 LYS cc_start: 0.9246 (mmmm) cc_final: 0.9042 (mmmm) REVERT: 2 34 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8488 (mm-30) REVERT: 3 15 SER cc_start: 0.9012 (p) cc_final: 0.8729 (m) REVERT: 6 153 MET cc_start: 0.8347 (mtp) cc_final: 0.8040 (mtp) REVERT: 6 161 PHE cc_start: 0.7630 (t80) cc_final: 0.7388 (t80) REVERT: 6 169 HIS cc_start: 0.9219 (p-80) cc_final: 0.8974 (p-80) REVERT: 7 18 ASN cc_start: 0.8682 (t0) cc_final: 0.8394 (t0) REVERT: 8 64 TYR cc_start: 0.8220 (m-80) cc_final: 0.7916 (m-80) REVERT: 9 95 MET cc_start: 0.9103 (pmm) cc_final: 0.8828 (pmm) REVERT: 9 96 GLN cc_start: 0.8955 (pp30) cc_final: 0.8731 (pp30) REVERT: 10 21 MET cc_start: 0.9685 (mtp) cc_final: 0.9165 (mpp) REVERT: 10 24 ARG cc_start: 0.9411 (mmm160) cc_final: 0.9140 (tpm170) REVERT: 10 52 ASN cc_start: 0.8953 (t0) cc_final: 0.8735 (t0) REVERT: 10 62 MET cc_start: 0.9219 (mpp) cc_final: 0.8917 (mpp) REVERT: 10 80 PHE cc_start: 0.9133 (m-80) cc_final: 0.8899 (m-80) REVERT: 11 30 MET cc_start: 0.8646 (tpp) cc_final: 0.8374 (tpp) REVERT: 12 58 LEU cc_start: 0.8941 (tp) cc_final: 0.8734 (tp) REVERT: 14 20 GLN cc_start: 0.9314 (pp30) cc_final: 0.8985 (pp30) REVERT: 14 46 LYS cc_start: 0.8709 (mmmm) cc_final: 0.8282 (mmmm) REVERT: 14 50 THR cc_start: 0.9134 (m) cc_final: 0.8801 (p) REVERT: 14 52 LEU cc_start: 0.8923 (mm) cc_final: 0.8682 (mt) REVERT: 19 77 TYR cc_start: 0.8815 (t80) cc_final: 0.7943 (t80) REVERT: 22 50 TYR cc_start: 0.8395 (m-10) cc_final: 0.8070 (m-10) REVERT: 23 17 LYS cc_start: 0.9058 (mtmm) cc_final: 0.8491 (mmtm) REVERT: 23 65 MET cc_start: 0.8855 (mtt) cc_final: 0.8629 (tpp) REVERT: 24 14 GLU cc_start: 0.8324 (tp30) cc_final: 0.8097 (tp30) REVERT: 25 48 LYS cc_start: 0.8976 (ttpt) cc_final: 0.8571 (ttpt) outliers start: 3 outliers final: 0 residues processed: 1347 average time/residue: 1.3337 time to fit residues: 3122.5671 Evaluate side-chains 1044 residues out of total 5423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1044 time to evaluate : 6.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1117 random chunks: chunk 363 optimal weight: 20.0000 chunk 972 optimal weight: 20.0000 chunk 213 optimal weight: 20.0000 chunk 633 optimal weight: 20.0000 chunk 266 optimal weight: 6.9990 chunk 1080 optimal weight: 8.9990 chunk 897 optimal weight: 20.0000 chunk 500 optimal weight: 0.7980 chunk 89 optimal weight: 6.9990 chunk 357 optimal weight: 5.9990 chunk 567 optimal weight: 0.9980 overall best weight: 4.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 ASN ** A 238 ASN ** 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 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 ASN ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 ASN F 73 ASN ** G 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 29 GLN ** H 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 80 HIS ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN ** J 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 35 HIS K 104 GLN ** L 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 ASN P 43 GLN P 58 GLN ** U 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 25 GLN ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 2 GLN ** 8 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 135 GLN ** 9 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 10 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 10 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 27 ASN ** 12 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 36 GLN ** 13 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 15 23 HIS ** 15 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 18 3 GLN 19 34 GLN 20 59 HIS 21 30 HIS 22 51 GLN ** 22 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 23 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 24 69 ASN ** 33 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 33 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 33 608 HIS 33 674 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 167683 Z= 0.194 Angle : 0.656 17.653 250280 Z= 0.333 Chirality : 0.035 0.365 31936 Planarity : 0.005 0.156 13865 Dihedral : 24.413 179.353 82431 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 25.48 Ramachandran Plot: Outliers : 1.12 % Allowed : 9.59 % Favored : 89.29 % Rotamer: Outliers : 0.02 % Allowed : 2.41 % Favored : 97.57 % 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: -2.08 (0.10), residues: 6509 helix: -0.23 (0.11), residues: 2248 sheet: -2.30 (0.15), residues: 1050 loop : -1.87 (0.11), residues: 3211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 212 HIS 0.018 0.001 HIS M 3 PHE 0.027 0.002 PHE16 60 TYR 0.033 0.002 TYR K 58 ARG 0.032 0.001 ARG33 596 *********************** REFINEMENT MACRO_CYCLE 6 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 1486 residues out of total 5423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1485 time to evaluate : 6.807 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: A 120 ASP cc_start: 0.8754 (p0) cc_final: 0.8465 (p0) REVERT: A 170 TYR cc_start: 0.7874 (m-10) cc_final: 0.7601 (m-10) REVERT: B 82 PHE cc_start: 0.7611 (m-80) cc_final: 0.7264 (m-80) REVERT: B 146 ILE cc_start: 0.8294 (pt) cc_final: 0.8087 (pt) REVERT: C 35 TYR cc_start: 0.8846 (t80) cc_final: 0.8621 (t80) REVERT: C 199 MET cc_start: 0.9087 (ppp) cc_final: 0.8813 (ppp) REVERT: D 98 PHE cc_start: 0.8914 (t80) cc_final: 0.8660 (t80) REVERT: D 139 GLU cc_start: 0.8890 (pm20) cc_final: 0.8689 (pm20) REVERT: F 2 GLN cc_start: 0.9300 (mm-40) cc_final: 0.9018 (mm-40) REVERT: F 117 LEU cc_start: 0.8602 (pp) cc_final: 0.8398 (pp) REVERT: F 135 HIS cc_start: 0.9105 (t70) cc_final: 0.8168 (t-90) REVERT: F 141 LYS cc_start: 0.9142 (tptp) cc_final: 0.8891 (tptp) REVERT: G 5 LEU cc_start: 0.9685 (tp) cc_final: 0.9443 (pp) REVERT: G 8 LYS cc_start: 0.9605 (mtpp) cc_final: 0.9389 (mtpp) REVERT: G 56 ARG cc_start: 0.8831 (mmt90) cc_final: 0.8168 (mmt-90) REVERT: G 88 HIS cc_start: 0.8605 (t70) cc_final: 0.8192 (t70) REVERT: H 102 ARG cc_start: 0.8628 (ttp80) cc_final: 0.8174 (ttp80) REVERT: H 116 MET cc_start: 0.2155 (ptt) cc_final: 0.1750 (ptt) REVERT: H 124 MET cc_start: 0.7720 (mmm) cc_final: 0.7308 (mmp) REVERT: J 32 TYR cc_start: 0.8751 (p90) cc_final: 0.8400 (p90) REVERT: J 104 THR cc_start: 0.8457 (t) cc_final: 0.8224 (p) REVERT: L 136 MET cc_start: 0.8726 (tmm) cc_final: 0.7821 (tmm) REVERT: M 28 LEU cc_start: 0.8934 (tp) cc_final: 0.8588 (tt) REVERT: M 75 ILE cc_start: 0.9063 (mm) cc_final: 0.8793 (mm) REVERT: M 112 TYR cc_start: 0.8160 (m-80) cc_final: 0.7729 (m-80) REVERT: N 3 LYS cc_start: 0.9095 (ptpt) cc_final: 0.8346 (pttt) REVERT: N 19 GLN cc_start: 0.9484 (pp30) cc_final: 0.9234 (pp30) REVERT: N 80 GLU cc_start: 0.9259 (mt-10) cc_final: 0.8940 (mt-10) REVERT: O 6 GLN cc_start: 0.9411 (tt0) cc_final: 0.9116 (tp-100) REVERT: P 78 PHE cc_start: 0.8936 (t80) cc_final: 0.8634 (t80) REVERT: P 116 LEU cc_start: 0.9330 (pp) cc_final: 0.9028 (tt) REVERT: Q 86 GLN cc_start: 0.7848 (pp30) cc_final: 0.7341 (pp30) REVERT: Q 95 ASP cc_start: 0.8576 (m-30) cc_final: 0.8245 (m-30) REVERT: S 1 MET cc_start: 0.6107 (mtp) cc_final: 0.4331 (ttp) REVERT: S 5 GLU cc_start: 0.8998 (pp20) cc_final: 0.8707 (pp20) REVERT: S 50 LEU cc_start: 0.9396 (mp) cc_final: 0.9121 (mp) REVERT: U 8 VAL cc_start: 0.9315 (t) cc_final: 0.9015 (p) REVERT: U 61 LEU cc_start: 0.9199 (mp) cc_final: 0.8957 (mt) REVERT: U 86 LEU cc_start: 0.8679 (mm) cc_final: 0.8386 (mm) REVERT: U 87 GLN cc_start: 0.8165 (tm-30) cc_final: 0.7908 (tm-30) REVERT: V 11 ASP cc_start: 0.8803 (t70) cc_final: 0.8539 (t0) REVERT: V 20 LYS cc_start: 0.8924 (mmtt) cc_final: 0.8687 (mmtt) REVERT: V 28 LEU cc_start: 0.9065 (mt) cc_final: 0.8545 (mm) REVERT: W 43 LYS cc_start: 0.9276 (mppt) cc_final: 0.9048 (mppt) REVERT: W 48 LEU cc_start: 0.8227 (mt) cc_final: 0.7926 (mp) REVERT: Z 32 LEU cc_start: 0.9329 (tp) cc_final: 0.9029 (tt) REVERT: 2 6 GLU cc_start: 0.8027 (pp20) cc_final: 0.7815 (pp20) REVERT: 3 15 SER cc_start: 0.8836 (p) cc_final: 0.8558 (m) REVERT: 6 67 LEU cc_start: 0.9176 (tt) cc_final: 0.8932 (mt) REVERT: 6 161 PHE cc_start: 0.7793 (t80) cc_final: 0.7589 (t80) REVERT: 7 99 GLN cc_start: 0.9241 (tm-30) cc_final: 0.8981 (tm-30) REVERT: 7 133 MET cc_start: 0.9236 (ttt) cc_final: 0.9012 (ttt) REVERT: 8 53 GLN cc_start: 0.8730 (mt0) cc_final: 0.8315 (tt0) REVERT: 8 64 TYR cc_start: 0.8132 (m-80) cc_final: 0.7895 (m-80) REVERT: 9 96 GLN cc_start: 0.8887 (pp30) cc_final: 0.8656 (pp30) REVERT: 9 114 LEU cc_start: 0.9190 (mm) cc_final: 0.8958 (mm) REVERT: 10 21 MET cc_start: 0.9647 (mtp) cc_final: 0.9231 (mpp) REVERT: 10 52 ASN cc_start: 0.8923 (t0) cc_final: 0.8721 (t0) REVERT: 10 62 MET cc_start: 0.9031 (mpp) cc_final: 0.8773 (mpp) REVERT: 10 76 THR cc_start: 0.9522 (p) cc_final: 0.9287 (p) REVERT: 10 80 PHE cc_start: 0.9040 (m-80) cc_final: 0.8792 (m-80) REVERT: 10 88 MET cc_start: 0.8881 (ptm) cc_final: 0.8241 (ttp) REVERT: 11 30 MET cc_start: 0.8697 (tpp) cc_final: 0.8212 (tpp) REVERT: 11 102 TRP cc_start: 0.8266 (m-10) cc_final: 0.7923 (m-10) REVERT: 11 115 MET cc_start: 0.8720 (tpt) cc_final: 0.8444 (tpt) REVERT: 12 58 LEU cc_start: 0.8881 (tp) cc_final: 0.8678 (tp) REVERT: 13 29 ILE cc_start: 0.8849 (pt) cc_final: 0.8558 (mp) REVERT: 13 49 GLN cc_start: 0.9270 (tt0) cc_final: 0.9028 (tt0) REVERT: 13 90 ASP cc_start: 0.8709 (p0) cc_final: 0.8430 (p0) REVERT: 14 52 LEU cc_start: 0.9024 (mm) cc_final: 0.8821 (mt) REVERT: 16 2 THR cc_start: 0.7510 (m) cc_final: 0.7041 (m) REVERT: 16 58 ASN cc_start: 0.9195 (p0) cc_final: 0.8913 (p0) REVERT: 17 41 ASP cc_start: 0.9285 (p0) cc_final: 0.8552 (t0) REVERT: 19 25 GLU cc_start: 0.9033 (pp20) cc_final: 0.8242 (pp20) REVERT: 19 77 TYR cc_start: 0.8573 (t80) cc_final: 0.7865 (t80) REVERT: 23 17 LYS cc_start: 0.8969 (mtmm) cc_final: 0.8442 (mmtm) REVERT: 33 440 ILE cc_start: 0.8866 (pt) cc_final: 0.8639 (mm) outliers start: 1 outliers final: 1 residues processed: 1486 average time/residue: 1.3506 time to fit residues: 3482.4249 Evaluate side-chains 1144 residues out of total 5423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1143 time to evaluate : 6.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1117 random chunks: chunk 1041 optimal weight: 30.0000 chunk 121 optimal weight: 7.9990 chunk 615 optimal weight: 40.0000 chunk 789 optimal weight: 30.0000 chunk 611 optimal weight: 30.0000 chunk 909 optimal weight: 20.0000 chunk 603 optimal weight: 20.0000 chunk 1076 optimal weight: 10.0000 chunk 673 optimal weight: 20.0000 chunk 656 optimal weight: 30.0000 chunk 497 optimal weight: 0.2980 overall best weight: 11.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 ASN A 238 ASN ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 GLN B 167 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 ASN ** F 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 80 HIS ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 ASN K 104 GLN ** M 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 58 GLN S 28 ASN U 12 GLN ** U 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 25 GLN 1 4 GLN ** 6 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 2 GLN ** 8 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 135 GLN ** 9 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 27 ASN ** 11 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 36 GLN ** 13 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 15 23 HIS ** 15 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 19 36 ASN ** 22 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 23 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 24 69 ASN ** 33 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 33 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 33 604 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.115 167683 Z= 0.347 Angle : 0.716 13.282 250280 Z= 0.367 Chirality : 0.039 0.378 31936 Planarity : 0.006 0.215 13865 Dihedral : 24.360 179.076 82431 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 34.73 Ramachandran Plot: Outliers : 1.08 % Allowed : 11.05 % Favored : 87.88 % Rotamer: Outliers : 0.02 % Allowed : 2.06 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.10), residues: 6509 helix: -0.23 (0.11), residues: 2234 sheet: -2.30 (0.15), residues: 1066 loop : -1.92 (0.11), residues: 3209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP A 212 HIS 0.012 0.002 HIS M 3 PHE 0.038 0.002 PHE F 46 TYR 0.026 0.002 TYR I 75 ARG 0.018 0.001 ARG Z 25 *********************** REFINEMENT MACRO_CYCLE 7 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 1391 residues out of total 5423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1390 time to evaluate : 6.842 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: A 228 ASP cc_start: 0.8930 (m-30) cc_final: 0.8722 (m-30) REVERT: B 82 PHE cc_start: 0.7775 (m-80) cc_final: 0.7455 (m-80) REVERT: C 124 PHE cc_start: 0.8225 (t80) cc_final: 0.7982 (t80) REVERT: C 199 MET cc_start: 0.9104 (ppp) cc_final: 0.8854 (ppp) REVERT: D 25 MET cc_start: 0.9333 (ptp) cc_final: 0.9013 (pmm) REVERT: D 37 MET cc_start: 0.8791 (mmm) cc_final: 0.8405 (mmm) REVERT: D 98 PHE cc_start: 0.8943 (t80) cc_final: 0.8719 (t80) REVERT: D 127 TYR cc_start: 0.8510 (t80) cc_final: 0.8297 (t80) REVERT: D 174 PHE cc_start: 0.9072 (t80) cc_final: 0.8773 (t80) REVERT: F 2 GLN cc_start: 0.9361 (mm-40) cc_final: 0.9016 (mm-40) REVERT: F 135 HIS cc_start: 0.9150 (t70) cc_final: 0.8530 (t70) REVERT: F 141 LYS cc_start: 0.9098 (tptp) cc_final: 0.8778 (tptp) REVERT: G 56 ARG cc_start: 0.8792 (mmt90) cc_final: 0.8122 (mmt-90) REVERT: H 5 GLN cc_start: 0.8176 (tt0) cc_final: 0.7759 (mt0) REVERT: H 102 ARG cc_start: 0.8612 (ttp80) cc_final: 0.8181 (tpt90) REVERT: H 122 GLU cc_start: 0.9278 (tp30) cc_final: 0.8914 (tp30) REVERT: I 93 ILE cc_start: 0.9278 (mm) cc_final: 0.9071 (mm) REVERT: J 45 GLU cc_start: 0.8603 (pp20) cc_final: 0.7996 (tm-30) REVERT: L 136 MET cc_start: 0.8725 (tmm) cc_final: 0.7789 (tmm) REVERT: M 24 MET cc_start: 0.8932 (tpp) cc_final: 0.8669 (tpp) REVERT: M 35 LYS cc_start: 0.8351 (ttmm) cc_final: 0.7921 (ttmt) REVERT: M 75 ILE cc_start: 0.9120 (mm) cc_final: 0.8780 (mm) REVERT: M 112 TYR cc_start: 0.8265 (m-80) cc_final: 0.7970 (m-80) REVERT: N 19 GLN cc_start: 0.9526 (pp30) cc_final: 0.9239 (pp30) REVERT: N 80 GLU cc_start: 0.9283 (mt-10) cc_final: 0.8947 (mt-10) REVERT: N 92 PHE cc_start: 0.8905 (t80) cc_final: 0.8447 (t80) REVERT: O 6 GLN cc_start: 0.9446 (tt0) cc_final: 0.9169 (tp-100) REVERT: P 78 PHE cc_start: 0.8980 (t80) cc_final: 0.8716 (t80) REVERT: R 95 ARG cc_start: 0.7799 (ttp80) cc_final: 0.7331 (ttp80) REVERT: S 1 MET cc_start: 0.6340 (mtp) cc_final: 0.5979 (mtt) REVERT: S 5 GLU cc_start: 0.9084 (pp20) cc_final: 0.8834 (pp20) REVERT: S 50 LEU cc_start: 0.9486 (mp) cc_final: 0.9225 (mp) REVERT: T 17 ASP cc_start: 0.8085 (p0) cc_final: 0.7850 (p0) REVERT: U 61 LEU cc_start: 0.9204 (mp) cc_final: 0.8952 (mt) REVERT: V 11 ASP cc_start: 0.8850 (t70) cc_final: 0.8627 (t0) REVERT: V 28 LEU cc_start: 0.9095 (mt) cc_final: 0.8550 (mm) REVERT: W 63 ILE cc_start: 0.8994 (tt) cc_final: 0.8725 (tt) REVERT: Y 43 ILE cc_start: 0.9168 (mp) cc_final: 0.8908 (mp) REVERT: Z 32 LEU cc_start: 0.9352 (tp) cc_final: 0.9090 (tt) REVERT: 3 15 SER cc_start: 0.8905 (p) cc_final: 0.8591 (p) REVERT: 6 67 LEU cc_start: 0.9172 (tt) cc_final: 0.8903 (mt) REVERT: 6 153 MET cc_start: 0.8411 (mtp) cc_final: 0.7994 (mtp) REVERT: 7 22 PHE cc_start: 0.8570 (t80) cc_final: 0.7968 (t80) REVERT: 7 24 ASN cc_start: 0.8868 (m-40) cc_final: 0.8625 (m-40) REVERT: 7 99 GLN cc_start: 0.9290 (tm-30) cc_final: 0.9025 (tm-30) REVERT: 7 133 MET cc_start: 0.9263 (ttt) cc_final: 0.9059 (ttt) REVERT: 8 104 MET cc_start: 0.8697 (mmm) cc_final: 0.8352 (mmm) REVERT: 9 96 GLN cc_start: 0.8911 (pp30) cc_final: 0.8653 (pp30) REVERT: 9 155 LYS cc_start: 0.9285 (ptpp) cc_final: 0.9079 (pttm) REVERT: 10 24 ARG cc_start: 0.9374 (mmm160) cc_final: 0.9157 (tpm170) REVERT: 10 52 ASN cc_start: 0.8970 (t0) cc_final: 0.8749 (t0) REVERT: 10 62 MET cc_start: 0.9112 (mpp) cc_final: 0.8880 (mpp) REVERT: 10 76 THR cc_start: 0.9568 (p) cc_final: 0.9298 (p) REVERT: 10 80 PHE cc_start: 0.9126 (m-80) cc_final: 0.8834 (m-80) REVERT: 11 102 TRP cc_start: 0.8280 (m-10) cc_final: 0.7957 (m-10) REVERT: 11 115 MET cc_start: 0.8713 (tpt) cc_final: 0.8394 (tpt) REVERT: 12 8 ASP cc_start: 0.8884 (m-30) cc_final: 0.8658 (m-30) REVERT: 13 29 ILE cc_start: 0.8912 (pt) cc_final: 0.8630 (mp) REVERT: 13 49 GLN cc_start: 0.9296 (tt0) cc_final: 0.9046 (tt0) REVERT: 13 90 ASP cc_start: 0.8733 (p0) cc_final: 0.8520 (p0) REVERT: 14 20 GLN cc_start: 0.9342 (pp30) cc_final: 0.8968 (pp30) REVERT: 14 50 THR cc_start: 0.9051 (m) cc_final: 0.8691 (p) REVERT: 16 58 ASN cc_start: 0.9373 (p0) cc_final: 0.9063 (p0) REVERT: 17 22 TYR cc_start: 0.8278 (t80) cc_final: 0.7788 (t80) REVERT: 17 68 LEU cc_start: 0.9549 (tp) cc_final: 0.9141 (tt) REVERT: 19 77 TYR cc_start: 0.8711 (t80) cc_final: 0.7852 (t80) REVERT: 23 17 LYS cc_start: 0.9043 (mtmm) cc_final: 0.8512 (mmtm) REVERT: 24 14 GLU cc_start: 0.8346 (tp30) cc_final: 0.8014 (tp30) outliers start: 1 outliers final: 0 residues processed: 1391 average time/residue: 1.3244 time to fit residues: 3216.2527 Evaluate side-chains 1092 residues out of total 5423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1092 time to evaluate : 6.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1117 random chunks: chunk 666 optimal weight: 20.0000 chunk 429 optimal weight: 0.6980 chunk 643 optimal weight: 20.0000 chunk 324 optimal weight: 20.0000 chunk 211 optimal weight: 6.9990 chunk 208 optimal weight: 6.9990 chunk 684 optimal weight: 30.0000 chunk 733 optimal weight: 20.0000 chunk 532 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 chunk 846 optimal weight: 20.0000 overall best weight: 6.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 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 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 ASN ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 2 GLN ** G 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 80 HIS ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN ** J 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 ASN K 35 HIS K 104 GLN N 104 GLN ** P 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 75 GLN U 78 GLN U 87 GLN ** V 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 25 GLN 6 41 ASN ** 6 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 2 GLN ** 8 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 135 GLN 9 42 ASN ** 9 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 27 ASN ** 11 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 36 GLN ** 13 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 15 23 HIS ** 15 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 22 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 23 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 23 68 HIS 24 69 ASN 24 81 GLN ** 33 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 33 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 33 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 33 604 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 167683 Z= 0.212 Angle : 0.638 11.815 250280 Z= 0.327 Chirality : 0.035 0.376 31936 Planarity : 0.005 0.127 13865 Dihedral : 24.337 177.573 82431 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 27.07 Ramachandran Plot: Outliers : 1.01 % Allowed : 9.82 % Favored : 89.17 % Rotamer: Outliers : 0.02 % Allowed : 1.32 % Favored : 98.66 % 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: -1.91 (0.10), residues: 6509 helix: -0.05 (0.11), residues: 2248 sheet: -2.11 (0.15), residues: 1059 loop : -1.83 (0.11), residues: 3202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A 212 HIS 0.017 0.001 HIS V 42 PHE 0.026 0.002 PHE P 35 TYR 0.026 0.002 TYR I 75 ARG 0.023 0.001 ARG24 24 *********************** REFINEMENT MACRO_CYCLE 8 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 1443 residues out of total 5423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1442 time to evaluate : 6.990 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: B 82 PHE cc_start: 0.7698 (m-80) cc_final: 0.7277 (m-80) REVERT: B 146 ILE cc_start: 0.8396 (pt) cc_final: 0.8164 (pt) REVERT: D 25 MET cc_start: 0.9377 (ptp) cc_final: 0.9121 (pmm) REVERT: D 37 MET cc_start: 0.8713 (mmm) cc_final: 0.8198 (mmm) REVERT: D 127 TYR cc_start: 0.8466 (t80) cc_final: 0.8222 (t80) REVERT: D 133 GLU cc_start: 0.8994 (pm20) cc_final: 0.8660 (pm20) REVERT: D 139 GLU cc_start: 0.8872 (pm20) cc_final: 0.8654 (pm20) REVERT: F 2 GLN cc_start: 0.9294 (mm110) cc_final: 0.9090 (mm-40) REVERT: F 135 HIS cc_start: 0.8897 (t70) cc_final: 0.8117 (t70) REVERT: F 141 LYS cc_start: 0.9063 (tptp) cc_final: 0.8831 (tptp) REVERT: G 5 LEU cc_start: 0.9625 (tp) cc_final: 0.9336 (pp) REVERT: H 116 MET cc_start: 0.1519 (ptt) cc_final: 0.0199 (ptt) REVERT: H 122 GLU cc_start: 0.9280 (tp30) cc_final: 0.9035 (tp30) REVERT: H 124 MET cc_start: 0.7363 (mmm) cc_final: 0.7151 (mmp) REVERT: J 45 GLU cc_start: 0.7942 (pp20) cc_final: 0.7718 (pp20) REVERT: J 104 THR cc_start: 0.8629 (t) cc_final: 0.8259 (p) REVERT: J 114 LYS cc_start: 0.9055 (mppt) cc_final: 0.8802 (mtmt) REVERT: K 104 GLN cc_start: 0.9464 (mm110) cc_final: 0.9186 (mp10) REVERT: L 17 ASN cc_start: 0.7375 (t0) cc_final: 0.6881 (t0) REVERT: L 136 MET cc_start: 0.8775 (tmm) cc_final: 0.7850 (tmm) REVERT: M 24 MET cc_start: 0.8924 (tpp) cc_final: 0.8688 (tpp) REVERT: M 28 LEU cc_start: 0.8878 (tp) cc_final: 0.8523 (tt) REVERT: M 35 LYS cc_start: 0.8350 (ttmm) cc_final: 0.7926 (ttmt) REVERT: M 75 ILE cc_start: 0.9094 (mm) cc_final: 0.8836 (mm) REVERT: M 112 TYR cc_start: 0.8220 (m-80) cc_final: 0.7887 (m-80) REVERT: N 3 LYS cc_start: 0.9083 (ptpt) cc_final: 0.8364 (pttt) REVERT: N 19 GLN cc_start: 0.9495 (pp30) cc_final: 0.9286 (pp30) REVERT: N 80 GLU cc_start: 0.9244 (mt-10) cc_final: 0.8944 (mt-10) REVERT: O 6 GLN cc_start: 0.9424 (tt0) cc_final: 0.9183 (tp-100) REVERT: P 78 PHE cc_start: 0.8928 (t80) cc_final: 0.8650 (t80) REVERT: S 1 MET cc_start: 0.6015 (mtp) cc_final: 0.5710 (mtt) REVERT: S 5 GLU cc_start: 0.9060 (pp20) cc_final: 0.8822 (pp20) REVERT: T 17 ASP cc_start: 0.7917 (p0) cc_final: 0.7708 (p0) REVERT: U 61 LEU cc_start: 0.9146 (mp) cc_final: 0.8731 (mt) REVERT: V 11 ASP cc_start: 0.8770 (t70) cc_final: 0.8569 (t0) REVERT: V 28 LEU cc_start: 0.8995 (mt) cc_final: 0.8421 (mm) REVERT: W 40 GLU cc_start: 0.9022 (tp30) cc_final: 0.8313 (tp30) REVERT: W 43 LYS cc_start: 0.9113 (mppt) cc_final: 0.8829 (mptt) REVERT: W 48 LEU cc_start: 0.8223 (mt) cc_final: 0.7926 (mp) REVERT: Z 32 LEU cc_start: 0.9325 (tp) cc_final: 0.9063 (tt) REVERT: 3 15 SER cc_start: 0.8875 (p) cc_final: 0.8604 (p) REVERT: 3 18 PHE cc_start: 0.8698 (t80) cc_final: 0.8200 (t80) REVERT: 7 22 PHE cc_start: 0.8617 (t80) cc_final: 0.8406 (t80) REVERT: 7 24 ASN cc_start: 0.8813 (m-40) cc_final: 0.8587 (m-40) REVERT: 7 99 GLN cc_start: 0.9293 (tm-30) cc_final: 0.9034 (tm-30) REVERT: 9 114 LEU cc_start: 0.9145 (mm) cc_final: 0.8919 (mm) REVERT: 10 52 ASN cc_start: 0.8930 (t0) cc_final: 0.8710 (t0) REVERT: 10 62 MET cc_start: 0.9110 (mpp) cc_final: 0.8835 (mpp) REVERT: 10 76 THR cc_start: 0.9503 (p) cc_final: 0.9191 (p) REVERT: 10 80 PHE cc_start: 0.9059 (m-80) cc_final: 0.8784 (m-80) REVERT: 11 102 TRP cc_start: 0.8218 (m-10) cc_final: 0.7905 (m-10) REVERT: 11 115 MET cc_start: 0.8677 (tpt) cc_final: 0.8340 (mmm) REVERT: 11 139 ASP cc_start: 0.8828 (m-30) cc_final: 0.8547 (m-30) REVERT: 13 8 THR cc_start: 0.8884 (m) cc_final: 0.8659 (m) REVERT: 13 12 LYS cc_start: 0.8324 (mttt) cc_final: 0.7930 (mttt) REVERT: 13 29 ILE cc_start: 0.8936 (pt) cc_final: 0.8664 (mp) REVERT: 13 90 ASP cc_start: 0.8629 (p0) cc_final: 0.8391 (p0) REVERT: 14 20 GLN cc_start: 0.9340 (pp30) cc_final: 0.9011 (pp30) REVERT: 14 50 THR cc_start: 0.9079 (m) cc_final: 0.8702 (p) REVERT: 14 67 ILE cc_start: 0.8462 (mp) cc_final: 0.8144 (mp) REVERT: 16 58 ASN cc_start: 0.9251 (p0) cc_final: 0.8917 (p0) REVERT: 17 22 TYR cc_start: 0.8256 (t80) cc_final: 0.7707 (t80) REVERT: 17 41 ASP cc_start: 0.9234 (p0) cc_final: 0.8599 (t0) REVERT: 19 77 TYR cc_start: 0.8571 (t80) cc_final: 0.7909 (t80) REVERT: 22 22 TYR cc_start: 0.9174 (p90) cc_final: 0.8952 (p90) REVERT: 23 72 GLU cc_start: 0.7988 (pm20) cc_final: 0.7647 (pm20) REVERT: 24 14 GLU cc_start: 0.8580 (tp30) cc_final: 0.8274 (tp30) REVERT: 24 18 LYS cc_start: 0.9078 (mtmm) cc_final: 0.8501 (mtmm) REVERT: 24 26 MET cc_start: 0.8962 (ppp) cc_final: 0.8601 (ppp) outliers start: 1 outliers final: 0 residues processed: 1443 average time/residue: 1.3462 time to fit residues: 3389.7512 Evaluate side-chains 1123 residues out of total 5423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1123 time to evaluate : 6.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1117 random chunks: chunk 979 optimal weight: 30.0000 chunk 1031 optimal weight: 40.0000 chunk 941 optimal weight: 50.0000 chunk 1003 optimal weight: 30.0000 chunk 603 optimal weight: 20.0000 chunk 437 optimal weight: 30.0000 chunk 787 optimal weight: 30.0000 chunk 307 optimal weight: 5.9990 chunk 906 optimal weight: 30.0000 chunk 948 optimal weight: 30.0000 chunk 999 optimal weight: 30.0000 overall best weight: 23.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 GLN ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 ASN ** F 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 80 HIS ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82 ASN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 87 GLN ** V 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 46 ASN X 25 GLN ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 2 GLN ** 7 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 10 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 10 46 GLN 11 27 ASN ** 11 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 36 GLN ** 13 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 15 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 18 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 22 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 22 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 23 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 23 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 24 69 ASN 33 49 HIS ** 33 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 33 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 33 689 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.140 167683 Z= 0.640 Angle : 0.975 15.474 250280 Z= 0.491 Chirality : 0.050 0.401 31936 Planarity : 0.007 0.188 13865 Dihedral : 24.606 178.144 82431 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 53.75 Ramachandran Plot: Outliers : 1.06 % Allowed : 12.84 % Favored : 86.10 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.10), residues: 6509 helix: -0.84 (0.10), residues: 2206 sheet: -2.35 (0.15), residues: 1099 loop : -2.18 (0.11), residues: 3204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A 212 HIS 0.020 0.003 HIS V 42 PHE 0.036 0.003 PHE P 35 TYR 0.035 0.003 TYR22 69 ARG 0.014 0.001 ARG S 6 *********************** REFINEMENT MACRO_CYCLE 9 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 1269 residues out of total 5423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1269 time to evaluate : 6.738 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: A 120 ASP cc_start: 0.8944 (p0) cc_final: 0.8694 (p0) REVERT: B 27 ILE cc_start: 0.8840 (mm) cc_final: 0.8616 (mm) REVERT: B 175 LEU cc_start: 0.8259 (mm) cc_final: 0.8048 (mm) REVERT: D 25 MET cc_start: 0.9469 (ptp) cc_final: 0.9146 (ptm) REVERT: D 37 MET cc_start: 0.8701 (mmm) cc_final: 0.8258 (mmm) REVERT: D 127 TYR cc_start: 0.8641 (t80) cc_final: 0.8436 (t80) REVERT: E 100 ASN cc_start: 0.9358 (p0) cc_final: 0.9146 (p0) REVERT: E 115 GLN cc_start: 0.9417 (pp30) cc_final: 0.9061 (pp30) REVERT: E 172 GLU cc_start: 0.8497 (tm-30) cc_final: 0.8150 (tm-30) REVERT: F 2 GLN cc_start: 0.9431 (mm110) cc_final: 0.9202 (mm-40) REVERT: F 89 LYS cc_start: 0.8636 (mptt) cc_final: 0.8103 (mtmm) REVERT: F 135 HIS cc_start: 0.9264 (t70) cc_final: 0.8543 (t-90) REVERT: F 141 LYS cc_start: 0.8984 (tptp) cc_final: 0.8766 (tptp) REVERT: G 56 ARG cc_start: 0.8489 (mmt180) cc_final: 0.8089 (mmt180) REVERT: G 73 LYS cc_start: 0.8636 (mttm) cc_final: 0.8424 (mtmt) REVERT: H 5 GLN cc_start: 0.8522 (tt0) cc_final: 0.8016 (mt0) REVERT: I 93 ILE cc_start: 0.9305 (mm) cc_final: 0.8934 (mm) REVERT: J 5 GLN cc_start: 0.8162 (mt0) cc_final: 0.7899 (mt0) REVERT: J 45 GLU cc_start: 0.8066 (pp20) cc_final: 0.7788 (pp20) REVERT: L 136 MET cc_start: 0.8711 (tmm) cc_final: 0.7738 (tmm) REVERT: M 24 MET cc_start: 0.9163 (tpp) cc_final: 0.8962 (tpp) REVERT: M 28 LEU cc_start: 0.9154 (tp) cc_final: 0.8949 (tt) REVERT: M 75 ILE cc_start: 0.9161 (mm) cc_final: 0.8836 (mm) REVERT: M 112 TYR cc_start: 0.8282 (m-80) cc_final: 0.7935 (m-80) REVERT: N 92 PHE cc_start: 0.8928 (t80) cc_final: 0.8607 (t80) REVERT: S 1 MET cc_start: 0.7206 (mtp) cc_final: 0.6795 (mtt) REVERT: T 17 ASP cc_start: 0.8389 (p0) cc_final: 0.8053 (p0) REVERT: U 61 LEU cc_start: 0.9157 (mp) cc_final: 0.8880 (mt) REVERT: V 11 ASP cc_start: 0.8915 (t70) cc_final: 0.8484 (t0) REVERT: V 28 LEU cc_start: 0.9167 (mt) cc_final: 0.8625 (mm) REVERT: 2 26 LYS cc_start: 0.8909 (mmtm) cc_final: 0.8593 (mmtm) REVERT: 6 160 LEU cc_start: 0.8673 (tp) cc_final: 0.8307 (tt) REVERT: 8 35 GLN cc_start: 0.8036 (tm-30) cc_final: 0.7796 (tm-30) REVERT: 9 95 MET cc_start: 0.9135 (pmm) cc_final: 0.8891 (pmm) REVERT: 9 146 MET cc_start: 0.9433 (tmm) cc_final: 0.8797 (tmm) REVERT: 10 62 MET cc_start: 0.9159 (mpp) cc_final: 0.8872 (mpp) REVERT: 10 80 PHE cc_start: 0.9283 (m-80) cc_final: 0.9016 (m-80) REVERT: 11 102 TRP cc_start: 0.8369 (m-10) cc_final: 0.8155 (m-10) REVERT: 14 50 THR cc_start: 0.9081 (m) cc_final: 0.8833 (p) REVERT: 16 61 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8510 (mm-30) REVERT: 16 69 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7986 (mm-30) REVERT: 19 77 TYR cc_start: 0.8869 (t80) cc_final: 0.8011 (t80) REVERT: 24 14 GLU cc_start: 0.8765 (tp30) cc_final: 0.8409 (tp30) REVERT: 24 18 LYS cc_start: 0.9321 (mtmm) cc_final: 0.9002 (mttp) REVERT: 25 48 LYS cc_start: 0.8734 (ttpt) cc_final: 0.8464 (ttpt) outliers start: 0 outliers final: 0 residues processed: 1269 average time/residue: 1.3124 time to fit residues: 2902.6469 Evaluate side-chains 990 residues out of total 5423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 990 time to evaluate : 9.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1117 random chunks: chunk 658 optimal weight: 10.0000 chunk 1060 optimal weight: 9.9990 chunk 647 optimal weight: 5.9990 chunk 503 optimal weight: 10.0000 chunk 737 optimal weight: 10.0000 chunk 1112 optimal weight: 20.0000 chunk 1024 optimal weight: 10.0000 chunk 886 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 684 optimal weight: 20.0000 chunk 543 optimal weight: 6.9990 overall best weight: 8.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 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** C 30 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 GLN F 73 ASN ** F 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN K 35 HIS K 104 GLN ** P 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 78 GLN ** V 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 25 GLN ** 3 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 25 HIS ** 6 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 2 GLN ** 7 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 135 GLN ** 9 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 27 ASN ** 11 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 36 GLN ** 13 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 15 23 HIS ** 15 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 22 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 23 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 23 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 24 69 ASN ** 33 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 33 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 167683 Z= 0.279 Angle : 0.699 12.209 250280 Z= 0.358 Chirality : 0.037 0.512 31936 Planarity : 0.005 0.156 13865 Dihedral : 24.604 178.468 82431 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 33.26 Ramachandran Plot: Outliers : 0.97 % Allowed : 10.66 % Favored : 88.37 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.10), residues: 6509 helix: -0.41 (0.10), residues: 2244 sheet: -2.18 (0.15), residues: 1072 loop : -2.01 (0.11), residues: 3193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A 212 HIS 0.014 0.001 HIS V 42 PHE 0.030 0.002 PHE 8 106 TYR 0.040 0.002 TYR H 7 ARG 0.025 0.001 ARG24 24 ********************** REFINEMENT MACRO_CYCLE 10 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 1349 residues out of total 5423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1349 time to evaluate : 6.919 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: A 120 ASP cc_start: 0.8789 (p0) cc_final: 0.8527 (p0) REVERT: B 82 PHE cc_start: 0.7773 (m-80) cc_final: 0.7400 (m-80) REVERT: B 146 ILE cc_start: 0.8495 (pt) cc_final: 0.8259 (pt) REVERT: B 175 LEU cc_start: 0.8166 (mm) cc_final: 0.7918 (mm) REVERT: D 37 MET cc_start: 0.8670 (mmm) cc_final: 0.8251 (mmm) REVERT: D 139 GLU cc_start: 0.8847 (pm20) cc_final: 0.8568 (pm20) REVERT: D 174 PHE cc_start: 0.9046 (t80) cc_final: 0.8804 (t80) REVERT: E 115 GLN cc_start: 0.9383 (pp30) cc_final: 0.9171 (pp30) REVERT: E 172 GLU cc_start: 0.8458 (tm-30) cc_final: 0.8243 (tm-30) REVERT: F 117 LEU cc_start: 0.8517 (pp) cc_final: 0.8289 (pp) REVERT: F 135 HIS cc_start: 0.9192 (t70) cc_final: 0.8529 (t-90) REVERT: F 141 LYS cc_start: 0.8971 (tptp) cc_final: 0.8752 (tptp) REVERT: G 1 MET cc_start: 0.7710 (tmm) cc_final: 0.7508 (tmm) REVERT: G 38 MET cc_start: 0.4078 (mmp) cc_final: 0.3751 (mmm) REVERT: K 104 GLN cc_start: 0.9491 (mm110) cc_final: 0.9180 (mp10) REVERT: L 136 MET cc_start: 0.8762 (tmm) cc_final: 0.7818 (tmm) REVERT: M 24 MET cc_start: 0.9025 (tpp) cc_final: 0.8738 (tpp) REVERT: M 28 LEU cc_start: 0.9014 (tp) cc_final: 0.8716 (tt) REVERT: M 35 LYS cc_start: 0.8279 (ttmm) cc_final: 0.7928 (ttmt) REVERT: M 75 ILE cc_start: 0.9073 (mm) cc_final: 0.8836 (mm) REVERT: M 112 TYR cc_start: 0.8185 (m-80) cc_final: 0.7898 (m-80) REVERT: N 19 GLN cc_start: 0.9498 (pp30) cc_final: 0.9264 (pp30) REVERT: N 84 GLU cc_start: 0.9449 (pt0) cc_final: 0.9246 (pt0) REVERT: O 6 GLN cc_start: 0.9452 (tt0) cc_final: 0.9195 (tp-100) REVERT: P 78 PHE cc_start: 0.8989 (t80) cc_final: 0.8659 (t80) REVERT: Q 55 ASP cc_start: 0.8842 (p0) cc_final: 0.8635 (p0) REVERT: S 1 MET cc_start: 0.6654 (mtp) cc_final: 0.6161 (mtt) REVERT: S 5 GLU cc_start: 0.9180 (pp20) cc_final: 0.8977 (pp20) REVERT: S 50 LEU cc_start: 0.9499 (mp) cc_final: 0.9297 (mp) REVERT: V 11 ASP cc_start: 0.8911 (t70) cc_final: 0.8669 (t0) REVERT: V 28 LEU cc_start: 0.9077 (mt) cc_final: 0.8469 (mm) REVERT: W 40 GLU cc_start: 0.9025 (tp30) cc_final: 0.8579 (tp30) REVERT: 3 15 SER cc_start: 0.8967 (p) cc_final: 0.8700 (p) REVERT: 6 90 PHE cc_start: 0.8434 (p90) cc_final: 0.8146 (p90) REVERT: 6 160 LEU cc_start: 0.8743 (tp) cc_final: 0.8305 (tt) REVERT: 6 162 VAL cc_start: 0.9135 (t) cc_final: 0.8931 (t) REVERT: 7 99 GLN cc_start: 0.9297 (tm-30) cc_final: 0.9067 (tm-30) REVERT: 8 46 ARG cc_start: 0.8841 (tpm170) cc_final: 0.8639 (mmm160) REVERT: 9 146 MET cc_start: 0.9377 (tmm) cc_final: 0.8885 (tmm) REVERT: 10 21 MET cc_start: 0.9576 (mtp) cc_final: 0.9185 (mpp) REVERT: 10 62 MET cc_start: 0.9142 (mpp) cc_final: 0.8828 (mpp) REVERT: 10 71 ILE cc_start: 0.9346 (mp) cc_final: 0.8851 (mp) REVERT: 10 75 GLU cc_start: 0.9343 (mm-30) cc_final: 0.9083 (mm-30) REVERT: 10 76 THR cc_start: 0.9531 (p) cc_final: 0.9246 (p) REVERT: 10 80 PHE cc_start: 0.9187 (m-80) cc_final: 0.8857 (m-80) REVERT: 10 90 MET cc_start: 0.8534 (mpp) cc_final: 0.8316 (mpp) REVERT: 11 102 TRP cc_start: 0.8311 (m-10) cc_final: 0.7958 (m-10) REVERT: 11 139 ASP cc_start: 0.8883 (m-30) cc_final: 0.8626 (m-30) REVERT: 13 8 THR cc_start: 0.8949 (m) cc_final: 0.8710 (m) REVERT: 13 12 LYS cc_start: 0.8304 (mttt) cc_final: 0.7946 (mmtt) REVERT: 13 24 ASN cc_start: 0.8563 (t0) cc_final: 0.8196 (t0) REVERT: 13 29 ILE cc_start: 0.8996 (pt) cc_final: 0.8664 (mp) REVERT: 13 90 ASP cc_start: 0.8710 (p0) cc_final: 0.8359 (p0) REVERT: 14 20 GLN cc_start: 0.9354 (pp30) cc_final: 0.8995 (pp30) REVERT: 14 50 THR cc_start: 0.9156 (m) cc_final: 0.8835 (p) REVERT: 16 23 LEU cc_start: 0.9304 (mp) cc_final: 0.9067 (mp) REVERT: 17 53 ASP cc_start: 0.9512 (p0) cc_final: 0.9295 (p0) REVERT: 19 77 TYR cc_start: 0.8666 (t80) cc_final: 0.7720 (t80) REVERT: 24 14 GLU cc_start: 0.8634 (tp30) cc_final: 0.8425 (tp30) REVERT: 24 18 LYS cc_start: 0.9211 (mtmm) cc_final: 0.8669 (mtmm) REVERT: 24 26 MET cc_start: 0.9010 (ppp) cc_final: 0.8789 (ppp) REVERT: 33 62 MET cc_start: -0.0037 (ttm) cc_final: -0.1235 (mmt) outliers start: 0 outliers final: 0 residues processed: 1349 average time/residue: 1.3138 time to fit residues: 3109.0361 Evaluate side-chains 1064 residues out of total 5423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1064 time to evaluate : 5.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1117 random chunks: chunk 703 optimal weight: 30.0000 chunk 943 optimal weight: 40.0000 chunk 271 optimal weight: 0.4980 chunk 817 optimal weight: 20.0000 chunk 130 optimal weight: 6.9990 chunk 246 optimal weight: 50.0000 chunk 887 optimal weight: 20.0000 chunk 371 optimal weight: 9.9990 chunk 911 optimal weight: 30.0000 chunk 112 optimal weight: 5.9990 chunk 163 optimal weight: 8.9990 overall best weight: 6.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 ASN ** F 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 80 HIS ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN J 5 GLN ** P 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 78 GLN ** V 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 25 GLN ** 6 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 2 GLN ** 8 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 11 GLN ** 9 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 10 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 27 ASN ** 12 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 36 GLN ** 13 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 15 23 HIS ** 15 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 18 34 ASN ** 23 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 23 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 24 69 ASN 33 105 ASN ** 33 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 33 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.028151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2386 r_free = 0.2386 target = 0.020287 restraints weight = 1772271.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2418 r_free = 0.2418 target = 0.020987 restraints weight = 642847.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2435 r_free = 0.2435 target = 0.021331 restraints weight = 356568.925| |-----------------------------------------------------------------------------| r_work (final): 0.2419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 0.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 167683 Z= 0.236 Angle : 0.657 12.241 250280 Z= 0.336 Chirality : 0.036 0.451 31936 Planarity : 0.005 0.111 13865 Dihedral : 24.448 177.144 82431 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 29.54 Ramachandran Plot: Outliers : 0.94 % Allowed : 10.89 % Favored : 88.17 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: -1.99 (0.10), residues: 6509 helix: -0.19 (0.11), residues: 2249 sheet: -2.07 (0.15), residues: 1051 loop : -1.86 (0.11), residues: 3209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 212 HIS 0.011 0.001 HIS V 42 PHE 0.025 0.002 PHE16 60 TYR 0.027 0.002 TYR O 98 ARG 0.040 0.001 ARG 9 111 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 45535.46 seconds wall clock time: 801 minutes 51.84 seconds (48111.84 seconds total)