Starting phenix.real_space_refine on Mon Mar 25 15:45:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kps_8279/03_2024/5kps_8279.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kps_8279/03_2024/5kps_8279.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kps_8279/03_2024/5kps_8279.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kps_8279/03_2024/5kps_8279.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kps_8279/03_2024/5kps_8279.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5kps_8279/03_2024/5kps_8279.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.006 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4733 5.49 5 S 161 5.16 5 C 75081 2.51 5 N 27780 2.21 5 O 41373 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 596": "NH1" <-> "NH2" Residue "A ARG 611": "NH1" <-> "NH2" Residue "A ARG 651": "NH1" <-> "NH2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C ARG 33": "NH1" <-> "NH2" Residue "C TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 59": "NH1" <-> "NH2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C ARG 83": "NH1" <-> "NH2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C ARG 184": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 44": "NH1" <-> "NH2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "D ARG 61": "NH1" <-> "NH2" Residue "D PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 88": "NH1" <-> "NH2" Residue "D ARG 102": "NH1" <-> "NH2" Residue "D ARG 162": "NH1" <-> "NH2" Residue "D ARG 170": "NH1" <-> "NH2" Residue "E PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 70": "NH1" <-> "NH2" Residue "E ARG 79": "NH1" <-> "NH2" Residue "E ARG 91": "NH1" <-> "NH2" Residue "E ARG 101": "NH1" <-> "NH2" Residue "E ARG 109": "NH1" <-> "NH2" Residue "E ARG 111": "NH1" <-> "NH2" Residue "E ARG 114": "NH1" <-> "NH2" Residue "E ARG 132": "NH1" <-> "NH2" Residue "F ARG 2": "NH1" <-> "NH2" Residue "F ARG 152": "NH1" <-> "NH2" Residue "F ARG 162": "NH1" <-> "NH2" Residue "F ARG 169": "NH1" <-> "NH2" Residue "H PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M ARG 40": "NH1" <-> "NH2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M ARG 59": "NH1" <-> "NH2" Residue "M ARG 114": "NH1" <-> "NH2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "N ARG 17": "NH1" <-> "NH2" Residue "N ARG 22": "NH1" <-> "NH2" Residue "N ARG 46": "NH1" <-> "NH2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N ARG 71": "NH1" <-> "NH2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "O ARG 10": "NH1" <-> "NH2" Residue "O ARG 16": "NH1" <-> "NH2" Residue "O ARG 25": "NH1" <-> "NH2" Residue "O ARG 81": "NH1" <-> "NH2" Residue "O ARG 94": "NH1" <-> "NH2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P ARG 61": "NH1" <-> "NH2" Residue "P ARG 88": "NH1" <-> "NH2" Residue "P ARG 100": "NH1" <-> "NH2" Residue "P ARG 108": "NH1" <-> "NH2" Residue "Q ARG 2": "NH1" <-> "NH2" Residue "Q ARG 5": "NH1" <-> "NH2" Residue "Q ARG 12": "NH1" <-> "NH2" Residue "Q ARG 32": "NH1" <-> "NH2" Residue "Q ARG 47": "NH1" <-> "NH2" Residue "Q ARG 69": "NH1" <-> "NH2" Residue "R PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "S PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 95": "NH1" <-> "NH2" Residue "S ARG 110": "NH1" <-> "NH2" Residue "T ARG 73": "NH1" <-> "NH2" Residue "U ARG 5": "NH1" <-> "NH2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U ARG 81": "NH1" <-> "NH2" Residue "U ARG 85": "NH1" <-> "NH2" Residue "U ARG 93": "NH1" <-> "NH2" Residue "V TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 10": "NH1" <-> "NH2" Residue "Z ARG 29": "NH1" <-> "NH2" Residue "Z ARG 44": "NH1" <-> "NH2" Residue "1 PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 49": "NH1" <-> "NH2" Residue "1 ARG 56": "NH1" <-> "NH2" Residue "2 ARG 9": "NH1" <-> "NH2" Residue "2 ARG 15": "NH1" <-> "NH2" Residue "2 ARG 39": "NH1" <-> "NH2" Residue "2 ARG 51": "NH1" <-> "NH2" Residue "3 ARG 43": "NH1" <-> "NH2" Residue "4 ARG 3": "NH1" <-> "NH2" Residue "4 ARG 12": "NH1" <-> "NH2" Residue "4 ARG 14": "NH1" <-> "NH2" Residue "4 ARG 19": "NH1" <-> "NH2" Residue "4 ARG 21": "NH1" <-> "NH2" Residue "4 ARG 33": "NH1" <-> "NH2" Residue "4 ARG 41": "NH1" <-> "NH2" Residue "5 ARG 12": "NH1" <-> "NH2" Residue "5 ARG 29": "NH1" <-> "NH2" Residue "5 ARG 39": "NH1" <-> "NH2" Residue "5 ARG 41": "NH1" <-> "NH2" Residue "6 ARG 12": "NH1" <-> "NH2" Residue "6 ARG 24": "NH1" <-> "NH2" Residue "7 PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 107": "NH1" <-> "NH2" Residue "7 ARG 224": "NH1" <-> "NH2" Residue "8 ARG 106": "NH1" <-> "NH2" Residue "8 PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 130": "NH1" <-> "NH2" Residue "10 PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "10 ARG 156": "NH1" <-> "NH2" Residue "11 PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "13 TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "14 PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "14 ARG 123": "NH1" <-> "NH2" Residue "16 PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "17 TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "17 ARG 55": "NH1" <-> "NH2" Residue "19 PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "21 ARG 28": "NH1" <-> "NH2" Residue "25 TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "26 PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "26 TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "26 ARG 54": "NH1" <-> "NH2" Residue "26 ARG 61": "NH1" <-> "NH2" Residue "26 ARG 65": "NH1" <-> "NH2" Residue "26 ARG 66": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 149128 Number of models: 1 Model: "" Number of chains: 58 Chain: "A" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1103 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain breaks: 1 Chain: "B" 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: "C" 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: "D" 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: "E" 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: "F" 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: "G" 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: "H" 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: "I" 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: "J" 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: "K" 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: "L" 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: "M" 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: "N" 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: "O" 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: "P" 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: "Q" 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: "R" 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: "S" 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: "T" 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: "U" 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: "V" 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: "W" 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: "X" 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: "Y" 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: "Z" 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: "1" 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: "2" 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: "3" 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: "4" 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: "5" 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: "6" 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: "7" 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: "8" 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: "9" 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: "10" 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: "11" 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: "12" 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: "13" 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: "14" 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: "15" 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: "16" 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: "17" 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: "18" 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: "19" 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: "20" 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: "21" 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: "22" 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: "23" 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: "24" 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: "25" 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: "26" 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: "27" Number of atoms: 33016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33016 Classifications: {'RNA': 1539} Modifications used: {'p5*END': 1, 'rna2p_pur': 93, 'rna2p_pyr': 46, 'rna3p_pur': 781, 'rna3p_pyr': 619} Link IDs: {'rna2p': 139, 'rna3p': 1399} Chain: "28" 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': 214, 'rna2p_pyr': 95, 'rna3p_pur': 1460, 'rna3p_pyr': 1134} Link IDs: {'rna2p': 309, 'rna3p': 2593} Chain: "29" 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: "30" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 388 Classifications: {'RNA': 18} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 12, 'rna3p_pyr': 5} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "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} Time building chain proxies: 56.88, per 1000 atoms: 0.38 Number of scatterers: 149128 At special positions: 0 Unit cell: (273.88, 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 161 16.00 P 4733 15.00 O 41373 8.00 N 27780 7.00 C 75081 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS 1 16 " - pdb=" SG CYS 1 37 " distance=2.99 Simple disulfide: pdb=" SG CYS 1 18 " - pdb=" SG CYS 1 40 " distance=1.97 Simple disulfide: pdb=" SG CYS 1 37 " - pdb=" SG CYS 1 40 " distance=2.00 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: 74.67 Conformation dependent library (CDL) restraints added in 6.9 seconds 11970 Ramachandran restraints generated. 5985 Oldfield, 0 Emsley, 5985 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11192 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 79 sheets defined 37.1% alpha, 15.0% beta 1588 base pairs and 2468 stacking pairs defined. Time for finding SS restraints: 58.23 Creating SS restraints... Processing helix chain 'A' and resid 598 through 602 Processing helix chain 'A' and resid 638 through 648 Processing helix chain 'A' and resid 678 through 690 removed outlier: 4.038A pdb=" N ASN A 689 " --> pdb=" O THR A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 731 Processing helix chain 'B' and resid 29 through 33 Processing helix chain 'B' and resid 132 through 134 No H-bonds generated for 'chain 'B' and resid 132 through 134' Processing helix chain 'B' and resid 196 through 202 removed outlier: 3.786A pdb=" N MET B 200 " --> pdb=" O ALA B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 213 removed outlier: 4.153A pdb=" N ALA B 210 " --> pdb=" O LYS B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 224 Processing helix chain 'C' and resid 39 through 44 Processing helix chain 'C' and resid 61 through 72 Processing helix chain 'C' and resid 97 through 102 removed outlier: 3.701A pdb=" N LEU C 100 " --> pdb=" O SER C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 181 through 184 Processing helix chain 'D' and resid 15 through 21 Processing helix chain 'D' and resid 24 through 40 Processing helix chain 'D' and resid 97 through 115 removed outlier: 3.505A pdb=" N ARG D 114 " --> pdb=" O SER D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 142 Processing helix chain 'D' and resid 154 through 163 removed outlier: 3.735A pdb=" N ALA D 160 " --> pdb=" O ASN D 156 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ASN D 163 " --> pdb=" O LEU D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 175 No H-bonds generated for 'chain 'D' and resid 173 through 175' Processing helix chain 'D' and resid 176 through 183 Processing helix chain 'D' and resid 190 through 200 Processing helix chain 'E' and resid 2 through 9 Processing helix chain 'E' and resid 9 through 20 removed outlier: 3.568A pdb=" N THR E 17 " --> pdb=" O LYS E 13 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU E 18 " --> pdb=" O LYS E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 27 Processing helix chain 'E' and resid 45 through 61 removed outlier: 3.697A pdb=" N LEU E 49 " --> pdb=" O ASP E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 104 Processing helix chain 'E' and resid 106 through 110 Processing helix chain 'E' and resid 133 through 137 Processing helix chain 'E' and resid 161 through 172 removed outlier: 3.702A pdb=" N PHE E 172 " --> pdb=" O LEU E 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 6 removed outlier: 3.652A pdb=" N ALA F 6 " --> pdb=" O VAL F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 80 Processing helix chain 'F' and resid 136 through 149 Processing helix chain 'G' and resid 22 through 29 Processing helix chain 'G' and resid 40 through 49 Processing helix chain 'G' and resid 54 through 72 Processing helix chain 'G' and resid 95 through 106 removed outlier: 3.730A pdb=" N ILE G 99 " --> pdb=" O GLY G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 115 Processing helix chain 'H' and resid 3 through 20 removed outlier: 4.078A pdb=" N LYS H 20 " --> pdb=" O SER H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 33 through 48 removed outlier: 4.168A pdb=" N THR H 39 " --> pdb=" O VAL H 35 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ARG H 42 " --> pdb=" O MET H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 67 Processing helix chain 'H' and resid 71 through 75 Processing helix chain 'H' and resid 94 through 104 removed outlier: 3.888A pdb=" N PHE H 99 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA H 100 " --> pdb=" O PHE H 96 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 29 Processing helix chain 'I' and resid 33 through 46 Processing helix chain 'I' and resid 74 through 83 Processing helix chain 'I' and resid 102 through 115 Processing helix chain 'I' and resid 120 through 136 Processing helix chain 'J' and resid 24 through 38 Processing helix chain 'J' and resid 58 through 62 Processing helix chain 'J' and resid 65 through 71 removed outlier: 3.713A pdb=" N LYS J 68 " --> pdb=" O THR J 65 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ARG J 69 " --> pdb=" O GLY J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 96 Processing helix chain 'J' and resid 96 through 107 removed outlier: 3.693A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 120 Processing helix chain 'J' and resid 132 through 136 Processing helix chain 'K' and resid 104 through 108 Processing helix chain 'K' and resid 112 through 119 Processing helix chain 'L' and resid 22 through 26 Processing helix chain 'L' and resid 37 through 41 Processing helix chain 'L' and resid 56 through 61 Processing helix chain 'L' and resid 68 through 73 Processing helix chain 'L' and resid 78 through 83 removed outlier: 4.111A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) Processing helix chain 'L' and resid 129 through 138 Processing helix chain 'M' and resid 43 through 58 Processing helix chain 'M' and resid 109 through 124 Processing helix chain 'N' and resid 13 through 32 Processing helix chain 'N' and resid 38 through 56 removed outlier: 4.698A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 59 through 69 Processing helix chain 'N' and resid 72 through 82 removed outlier: 4.375A pdb=" N PHE N 80 " --> pdb=" O VAL N 76 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 87 Processing helix chain 'O' and resid 3 through 22 removed outlier: 3.878A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 60 Processing helix chain 'O' and resid 67 through 85 Processing helix chain 'O' and resid 101 through 113 Processing helix chain 'P' and resid 2 through 10 Processing helix chain 'P' and resid 52 through 55 Processing helix chain 'P' and resid 96 through 101 Processing helix chain 'P' and resid 103 through 108 Processing helix chain 'Q' and resid 5 through 21 removed outlier: 3.633A pdb=" N ALA Q 9 " --> pdb=" O ARG Q 5 " (cutoff:3.500A) Processing helix chain 'Q' and resid 24 through 29 Processing helix chain 'Q' and resid 30 through 71 removed outlier: 4.566A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 85 Processing helix chain 'Q' and resid 90 through 100 Processing helix chain 'Q' and resid 101 through 117 Processing helix chain 'S' and resid 13 through 22 Processing helix chain 'S' and resid 28 through 39 removed outlier: 3.839A pdb=" N TYR S 38 " --> pdb=" O ASP S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 62 Processing helix chain 'S' and resid 89 through 91 No H-bonds generated for 'chain 'S' and resid 89 through 91' Processing helix chain 'T' and resid 2 through 10 removed outlier: 4.640A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 28 Processing helix chain 'T' and resid 39 through 51 Processing helix chain 'U' and resid 14 through 18 removed outlier: 4.117A pdb=" N ASP U 17 " --> pdb=" O THR U 14 " (cutoff:3.500A) Processing helix chain 'V' and resid 13 through 22 Processing helix chain 'V' and resid 44 through 51 Processing helix chain 'V' and resid 52 through 58 removed outlier: 6.255A pdb=" N GLU V 55 " --> pdb=" O ALA V 52 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 61 Processing helix chain 'X' and resid 62 through 74 Processing helix chain 'Y' and resid 2 through 6 Processing helix chain 'Y' and resid 9 through 34 removed outlier: 3.842A pdb=" N GLU Y 24 " --> pdb=" O ASN Y 20 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN Y 25 " --> pdb=" O LEU Y 21 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 61 Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 40 through 50 Processing helix chain '1' and resid 45 through 52 removed outlier: 4.023A pdb=" N ALA 1 52 " --> pdb=" O GLN 1 48 " (cutoff:3.500A) Processing helix chain '1' and resid 55 through 65 removed outlier: 4.345A pdb=" N ARG 1 59 " --> pdb=" O GLY 1 55 " (cutoff:3.500A) Processing helix chain '2' and resid 8 through 17 Processing helix chain '2' and resid 18 through 20 No H-bonds generated for 'chain '2' and resid 18 through 20' Processing helix chain '4' and resid 8 through 16 Processing helix chain '4' and resid 17 through 23 Processing helix chain '4' and resid 24 through 38 Processing helix chain '5' and resid 6 through 11 Processing helix chain '5' and resid 36 through 44 Processing helix chain '5' and resid 50 through 61 removed outlier: 4.011A pdb=" N GLY 5 55 " --> pdb=" O LYS 5 51 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU 5 56 " --> pdb=" O GLY 5 52 " (cutoff:3.500A) Processing helix chain '6' and resid 18 through 22 Processing helix chain '6' and resid 30 through 34 Processing helix chain '7' and resid 41 through 44 Processing helix chain '7' and resid 45 through 62 Processing helix chain '7' and resid 72 through 74 No H-bonds generated for 'chain '7' and resid 72 through 74' Processing helix chain '7' and resid 75 through 84 Processing helix chain '7' and resid 102 through 120 removed outlier: 3.532A pdb=" N VAL 7 106 " --> pdb=" O ASN 7 102 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN 7 108 " --> pdb=" O LYS 7 104 " (cutoff:3.500A) Processing helix chain '7' and resid 129 through 147 Processing helix chain '7' and resid 148 through 153 Processing helix chain '7' and resid 168 through 176 Processing helix chain '7' and resid 205 through 224 Processing helix chain '8' and resid 5 through 11 Processing helix chain '8' and resid 24 through 46 removed outlier: 4.595A pdb=" N ALA 8 29 " --> pdb=" O THR 8 25 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ASP 8 30 " --> pdb=" O LYS 8 26 " (cutoff:3.500A) Processing helix chain '8' and resid 47 through 49 No H-bonds generated for 'chain '8' and resid 47 through 49' Processing helix chain '8' and resid 71 through 77 Processing helix chain '8' and resid 80 through 95 Processing helix chain '8' and resid 107 through 110 Processing helix chain '8' and resid 111 through 124 Processing helix chain '8' and resid 128 through 144 Processing helix chain '9' and resid 6 through 15 removed outlier: 3.805A pdb=" N LEU 9 10 " --> pdb=" O PRO 9 6 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER 9 11 " --> pdb=" O LYS 9 7 " (cutoff:3.500A) Processing helix chain '9' and resid 48 through 65 Processing helix chain '9' and resid 67 through 81 Processing helix chain '9' and resid 84 through 96 removed outlier: 4.107A pdb=" N LEU 9 90 " --> pdb=" O GLY 9 86 " (cutoff:3.500A) Processing helix chain '9' and resid 96 through 105 Processing helix chain '9' and resid 109 through 119 Processing helix chain '9' and resid 152 through 162 removed outlier: 3.667A pdb=" N GLU 9 162 " --> pdb=" O LEU 9 158 " (cutoff:3.500A) Processing helix chain '9' and resid 174 through 176 No H-bonds generated for 'chain '9' and resid 174 through 176' Processing helix chain '9' and resid 186 through 190 Processing helix chain '9' and resid 195 through 205 removed outlier: 3.835A pdb=" N ILE 9 199 " --> pdb=" O ASN 9 195 " (cutoff:3.500A) Processing helix chain '10' and resid 54 through 69 removed outlier: 3.794A pdb=" N GLU10 64 " --> pdb=" O GLN10 60 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS10 65 " --> pdb=" O LYS10 61 " (cutoff:3.500A) Processing helix chain '10' and resid 109 through 118 Processing helix chain '10' and resid 131 through 145 Processing helix chain '10' and resid 148 through 153 Processing helix chain '10' and resid 159 through 165 Processing helix chain '11' and resid 11 through 17 Processing helix chain '11' and resid 18 through 31 Processing helix chain '11' and resid 67 through 81 Processing helix chain '12' and resid 19 through 30 Processing helix chain '12' and resid 34 through 54 Processing helix chain '12' and resid 57 through 66 Processing helix chain '12' and resid 91 through 109 removed outlier: 3.601A pdb=" N ALA12 97 " --> pdb=" O VAL12 93 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS12 109 " --> pdb=" O GLU12 105 " (cutoff:3.500A) Processing helix chain '12' and resid 114 through 128 removed outlier: 3.948A pdb=" N GLU12 128 " --> pdb=" O SER12 124 " (cutoff:3.500A) Processing helix chain '12' and resid 131 through 147 Processing helix chain '13' and resid 4 through 20 Processing helix chain '13' and resid 29 through 43 Processing helix chain '13' and resid 87 through 91 Processing helix chain '13' and resid 112 through 119 Processing helix chain '14' and resid 33 through 38 Processing helix chain '14' and resid 43 through 47 removed outlier: 3.691A pdb=" N VAL14 47 " --> pdb=" O ARG14 44 " (cutoff:3.500A) Processing helix chain '14' and resid 48 through 55 removed outlier: 3.883A pdb=" N VAL14 54 " --> pdb=" O PRO14 50 " (cutoff:3.500A) Processing helix chain '14' and resid 70 through 86 Processing helix chain '14' and resid 87 through 89 No H-bonds generated for 'chain '14' and resid 87 through 89' Processing helix chain '14' and resid 90 through 100 removed outlier: 5.316A pdb=" N GLU14 96 " --> pdb=" O SER14 92 " (cutoff:3.500A) Processing helix chain '15' and resid 14 through 33 removed outlier: 3.623A pdb=" N GLN15 20 " --> pdb=" O ARG15 16 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA15 29 " --> pdb=" O ILE15 25 " (cutoff:3.500A) Processing helix chain '15' and resid 80 through 88 removed outlier: 3.598A pdb=" N ALA15 86 " --> pdb=" O LYS15 82 " (cutoff:3.500A) Processing helix chain '16' and resid 46 through 50 Processing helix chain '16' and resid 53 through 57 Processing helix chain '16' and resid 58 through 71 Processing helix chain '16' and resid 73 through 77 Processing helix chain '16' and resid 91 through 101 removed outlier: 3.952A pdb=" N ILE16 96 " --> pdb=" O ARG16 92 " (cutoff:3.500A) Processing helix chain '17' and resid 2 through 9 Processing helix chain '17' and resid 114 through 118 removed outlier: 4.075A pdb=" N GLY17 117 " --> pdb=" O SER17 114 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL17 118 " --> pdb=" O LYS17 115 " (cutoff:3.500A) No H-bonds generated for 'chain '17' and resid 114 through 118' Processing helix chain '18' and resid 13 through 20 Processing helix chain '18' and resid 25 through 37 Processing helix chain '18' and resid 48 through 61 removed outlier: 4.435A pdb=" N THR18 54 " --> pdb=" O GLY18 50 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS18 61 " --> pdb=" O ASP18 57 " (cutoff:3.500A) Processing helix chain '18' and resid 64 through 83 Processing helix chain '18' and resid 84 through 92 Processing helix chain '18' and resid 105 through 110 Processing helix chain '19' and resid 2 through 19 Processing helix chain '19' and resid 24 through 30 Processing helix chain '19' and resid 37 through 50 removed outlier: 3.701A pdb=" N TRP19 41 " --> pdb=" O ASP19 37 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLN19 48 " --> pdb=" O VAL19 44 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR19 49 " --> pdb=" O LEU19 45 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU19 50 " --> pdb=" O LYS19 46 " (cutoff:3.500A) Processing helix chain '19' and resid 55 through 59 Processing helix chain '19' and resid 79 through 90 Processing helix chain '20' and resid 3 through 15 Processing helix chain '20' and resid 23 through 44 removed outlier: 4.306A pdb=" N GLY20 40 " --> pdb=" O ASN20 36 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N HIS20 41 " --> pdb=" O HIS20 37 " (cutoff:3.500A) Processing helix chain '20' and resid 48 through 73 Processing helix chain '20' and resid 73 through 85 Processing helix chain '21' and resid 53 through 62 Processing helix chain '21' and resid 68 through 78 Processing helix chain '23' and resid 12 through 17 Processing helix chain '23' and resid 24 through 31 removed outlier: 3.768A pdb=" N LEU23 28 " --> pdb=" O ASP23 24 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN23 30 " --> pdb=" O ALA23 26 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR23 31 " --> pdb=" O THR23 27 " (cutoff:3.500A) Processing helix chain '23' and resid 40 through 45 Processing helix chain '23' and resid 47 through 64 Processing helix chain '24' and resid 11 through 25 Processing helix chain '24' and resid 40 through 44 Processing helix chain '24' and resid 69 through 74 Processing helix chain '25' and resid 5 through 41 removed outlier: 3.705A pdb=" N ARG25 9 " --> pdb=" O SER25 5 " (cutoff:3.500A) Processing helix chain '25' and resid 42 through 63 Proline residue: 25 55 - end of helix Processing helix chain '25' and resid 68 through 86 Processing helix chain '26' and resid 17 through 22 Processing helix chain '26' and resid 24 through 32 removed outlier: 4.240A pdb=" N GLU26 30 " --> pdb=" O GLY26 26 " (cutoff:3.500A) Processing helix chain '26' and resid 37 through 59 removed outlier: 4.101A pdb=" N THR26 41 " --> pdb=" O TYR26 37 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 607 through 609 Processing sheet with id=AA2, first strand: chain 'A' and resid 699 through 700 removed outlier: 7.508A pdb=" N ASN A 674 " --> pdb=" O VAL A 735 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N VAL A 735 " --> pdb=" O ASN A 674 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 4 Processing sheet with id=AA4, first strand: chain 'B' and resid 99 through 104 removed outlier: 6.863A pdb=" N ILE B 90 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N LEU B 80 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU B 92 " --> pdb=" O GLU B 78 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 128 through 130 removed outlier: 5.670A pdb=" N ILE B 163 " --> pdb=" O ARG B 174 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ARG B 174 " --> pdb=" O ILE B 163 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 169 through 176 removed outlier: 5.643A pdb=" N THR C 171 " --> pdb=" O GLY C 111 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N GLY C 111 " --> pdb=" O THR C 171 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLN C 173 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL C 109 " --> pdb=" O GLN C 173 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N THR C 112 " --> pdb=" O ASP C 200 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ASP C 200 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL C 26 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N MET C 11 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL C 24 " --> pdb=" O MET C 11 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ARG C 13 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ILE C 22 " --> pdb=" O ARG C 13 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 33 through 38 removed outlier: 5.451A pdb=" N VAL C 34 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR C 51 " --> pdb=" O VAL C 34 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'D' and resid 2 through 3 Processing sheet with id=AB1, first strand: chain 'D' and resid 118 through 121 Processing sheet with id=AB2, first strand: chain 'D' and resid 148 through 150 removed outlier: 6.564A pdb=" N ILE D 148 " --> pdb=" O ARG D 170 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 65 through 68 removed outlier: 3.671A pdb=" N GLY E 85 " --> pdb=" O THR E 67 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N THR E 156 " --> pdb=" O GLU E 31 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE E 33 " --> pdb=" O THR E 154 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N THR E 154 " --> pdb=" O ILE E 33 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU E 35 " --> pdb=" O ASP E 152 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASP E 152 " --> pdb=" O LEU E 35 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 8 through 9 Processing sheet with id=AB5, first strand: chain 'F' and resid 15 through 19 Processing sheet with id=AB6, first strand: chain 'F' and resid 121 through 126 removed outlier: 7.031A pdb=" N GLU F 129 " --> pdb=" O PRO F 125 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 94 through 98 Processing sheet with id=AB8, first strand: chain 'G' and resid 4 through 5 Processing sheet with id=AB9, first strand: chain 'G' and resid 77 through 82 Processing sheet with id=AC1, first strand: chain 'H' and resid 25 through 27 removed outlier: 4.126A pdb=" N VAL H 27 " --> pdb=" O ALA H 83 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 9 through 11 Processing sheet with id=AC3, first strand: chain 'I' and resid 99 through 101 removed outlier: 5.022A pdb=" N ILE I 100 " --> pdb=" O GLU I 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'J' and resid 122 through 124 removed outlier: 6.850A pdb=" N ILE J 54 " --> pdb=" O LYS J 123 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N TYR J 16 " --> pdb=" O ILE J 55 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N LEU J 57 " --> pdb=" O TYR J 16 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL J 18 " --> pdb=" O LEU J 57 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN J 138 " --> pdb=" O TRP J 15 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 73 through 77 Processing sheet with id=AC6, first strand: chain 'K' and resid 7 through 10 removed outlier: 6.505A pdb=" N ARG K 17 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLU K 45 " --> pdb=" O ARG K 17 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL K 19 " --> pdb=" O ILE K 43 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ILE K 43 " --> pdb=" O VAL K 19 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N CYS K 21 " --> pdb=" O ILE K 41 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE K 41 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LYS K 23 " --> pdb=" O ILE K 39 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ILE K 39 " --> pdb=" O LYS K 23 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N CYS K 84 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ASN K 9 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N LEU K 86 " --> pdb=" O ASN K 9 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 69 through 70 removed outlier: 4.545A pdb=" N VAL K 76 " --> pdb=" O VAL P 72 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA P 48 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ARG P 61 " --> pdb=" O VAL P 46 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N VAL P 46 " --> pdb=" O ARG P 61 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N ILE P 63 " --> pdb=" O GLY P 44 " (cutoff:3.500A) removed outlier: 8.357A pdb=" N GLY P 44 " --> pdb=" O ILE P 63 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS P 36 " --> pdb=" O GLU P 33 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 74 through 76 Processing sheet with id=AC9, first strand: chain 'L' and resid 89 through 90 Processing sheet with id=AD1, first strand: chain 'M' and resid 62 through 65 removed outlier: 5.724A pdb=" N VAL M 101 " --> pdb=" O ALA M 35 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ALA M 35 " --> pdb=" O VAL M 101 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 39 through 42 removed outlier: 5.490A pdb=" N VAL M 89 " --> pdb=" O GLU M 75 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLU M 75 " --> pdb=" O VAL M 89 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 33 through 37 removed outlier: 3.947A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 47 through 52 removed outlier: 3.978A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'R' and resid 3 through 5 removed outlier: 6.446A pdb=" N VAL R 4 " --> pdb=" O LEU R 39 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'R' and resid 19 through 23 removed outlier: 6.166A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'R' and resid 74 through 78 removed outlier: 4.255A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'S' and resid 4 through 10 removed outlier: 4.344A pdb=" N HIS S 9 " --> pdb=" O SER S 101 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N SER S 101 " --> pdb=" O HIS S 9 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'S' and resid 84 through 88 Processing sheet with id=AE1, first strand: chain 'T' and resid 11 through 14 removed outlier: 3.946A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N TRP T 80 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N VAL T 62 " --> pdb=" O TRP T 80 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LYS T 82 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N THR T 60 " --> pdb=" O LYS T 82 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N TYR T 84 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N VAL T 58 " --> pdb=" O TYR T 84 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N THR T 86 " --> pdb=" O GLU T 56 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'T' and resid 67 through 70 Processing sheet with id=AE3, first strand: chain 'U' and resid 64 through 65 removed outlier: 6.821A pdb=" N LYS U 32 " --> pdb=" O VAL U 27 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N VAL U 27 " --> pdb=" O LYS U 32 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE U 34 " --> pdb=" O LYS U 25 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'U' and resid 40 through 42 Processing sheet with id=AE5, first strand: chain 'U' and resid 82 through 84 Processing sheet with id=AE6, first strand: chain 'V' and resid 3 through 5 removed outlier: 6.413A pdb=" N ILE V 4 " --> pdb=" O VAL V 64 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'V' and resid 7 through 8 removed outlier: 8.813A pdb=" N LYS V 25 " --> pdb=" O GLN V 87 " (cutoff:3.500A) removed outlier: 10.304A pdb=" N ILE V 89 " --> pdb=" O LYS V 25 " (cutoff:3.500A) removed outlier: 9.088A pdb=" N PHE V 91 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE V 29 " --> pdb=" O PHE V 91 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ARG V 93 " --> pdb=" O ILE V 29 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N TYR V 31 " --> pdb=" O ARG V 93 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N VAL V 92 " --> pdb=" O ALA V 74 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ALA V 74 " --> pdb=" O VAL V 92 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'W' and resid 18 through 19 removed outlier: 6.736A pdb=" N LEU W 55 " --> pdb=" O ILE W 33 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'W' and resid 26 through 27 removed outlier: 6.996A pdb=" N HIS W 42 " --> pdb=" O ILE W 76 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N ILE W 78 " --> pdb=" O HIS W 42 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'X' and resid 12 through 15 Processing sheet with id=AF2, first strand: chain 'X' and resid 32 through 39 Processing sheet with id=AF3, first strand: chain 'Z' and resid 34 through 38 Processing sheet with id=AF4, first strand: chain '1' and resid 22 through 26 removed outlier: 4.066A pdb=" N LEU 1 32 " --> pdb=" O THR 1 13 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain '2' and resid 28 through 29 Processing sheet with id=AF6, first strand: chain '3' and resid 19 through 24 Processing sheet with id=AF7, first strand: chain '5' and resid 14 through 15 Processing sheet with id=AF8, first strand: chain '6' and resid 14 through 17 Processing sheet with id=AF9, first strand: chain '7' and resid 16 through 17 removed outlier: 3.534A pdb=" N HIS 7 38 " --> pdb=" O HIS 7 17 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain '7' and resid 89 through 91 removed outlier: 6.014A pdb=" N ILE 7 66 " --> pdb=" O PHE 7 89 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N VAL 7 91 " --> pdb=" O ILE 7 66 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N PHE 7 68 " --> pdb=" O VAL 7 91 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU 7 67 " --> pdb=" O PHE 7 161 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain '7' and resid 184 through 186 Processing sheet with id=AG3, first strand: chain '8' and resid 19 through 20 removed outlier: 6.645A pdb=" N HIS 8 68 " --> pdb=" O SER 8 52 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ILE 8 54 " --> pdb=" O THR 8 66 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N THR 8 66 " --> pdb=" O ILE 8 54 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ILE 8 56 " --> pdb=" O ARG 8 64 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ARG 8 64 " --> pdb=" O ILE 8 56 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE 8 63 " --> pdb=" O GLN 8 99 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain '8' and resid 165 through 170 removed outlier: 4.442A pdb=" N VAL 8 194 " --> pdb=" O THR 8 190 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N THR 8 190 " --> pdb=" O VAL 8 194 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N GLY 8 196 " --> pdb=" O ALA 8 188 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ALA 8 188 " --> pdb=" O GLY 8 196 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N LYS 8 198 " --> pdb=" O SER 8 186 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N SER 8 186 " --> pdb=" O LYS 8 198 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N TRP 8 200 " --> pdb=" O ASN 8 184 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ASN 8 184 " --> pdb=" O TRP 8 200 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N PHE 8 202 " --> pdb=" O ASP 8 182 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ASP 8 182 " --> pdb=" O PHE 8 202 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain '9' and resid 127 through 128 Processing sheet with id=AG6, first strand: chain '10' and resid 12 through 20 removed outlier: 6.821A pdb=" N LEU10 35 " --> pdb=" O ILE10 15 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL10 17 " --> pdb=" O THR10 33 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N THR10 33 " --> pdb=" O VAL10 17 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG10 19 " --> pdb=" O SER10 31 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N SER10 31 " --> pdb=" O ARG10 19 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain '10' and resid 12 through 20 removed outlier: 6.821A pdb=" N LEU10 35 " --> pdb=" O ILE10 15 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL10 17 " --> pdb=" O THR10 33 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N THR10 33 " --> pdb=" O VAL10 17 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG10 19 " --> pdb=" O SER10 31 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N SER10 31 " --> pdb=" O ARG10 19 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain '10' and resid 84 through 85 Processing sheet with id=AG9, first strand: chain '11' and resid 2 through 3 Processing sheet with id=AH1, first strand: chain '11' and resid 43 through 45 removed outlier: 4.592A pdb=" N ARG11 86 " --> pdb=" O MET11 9 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain '12' and resid 72 through 75 Processing sheet with id=AH3, first strand: chain '13' and resid 23 through 27 removed outlier: 3.981A pdb=" N THR13 61 " --> pdb=" O ASP13 47 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ASP13 47 " --> pdb=" O THR13 61 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain '13' and resid 75 through 76 removed outlier: 5.161A pdb=" N ILE13 124 " --> pdb=" O SER13 104 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N SER13 104 " --> pdb=" O ILE13 124 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE13 100 " --> pdb=" O VAL13 128 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain '14' and resid 5 through 7 Processing sheet with id=AH6, first strand: chain '15' and resid 7 through 8 Processing sheet with id=AH7, first strand: chain '15' and resid 10 through 12 removed outlier: 3.863A pdb=" N GLU15 47 " --> pdb=" O ILE15 67 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain '15' and resid 10 through 12 removed outlier: 3.508A pdb=" N LYS19 96 " --> pdb=" O GLU15 66 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain '16' and resid 40 through 44 removed outlier: 7.270A pdb=" N LEU16 81 " --> pdb=" O ASN16 108 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N THR16 110 " --> pdb=" O LEU16 81 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N VAL16 83 " --> pdb=" O THR16 110 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain '17' and resid 29 through 31 Processing sheet with id=AI2, first strand: chain '17' and resid 36 through 39 Processing sheet with id=AI3, first strand: chain '17' and resid 54 through 55 Processing sheet with id=AI4, first strand: chain '21' and resid 2 through 5 Processing sheet with id=AI5, first strand: chain '22' and resid 11 through 13 removed outlier: 6.485A pdb=" N HIS22 44 " --> pdb=" O TRP22 72 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LEU22 74 " --> pdb=" O HIS22 44 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N HIS22 46 " --> pdb=" O LEU22 74 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain '22' and resid 26 through 29 Processing sheet with id=AI7, first strand: chain '24' and resid 31 through 32 removed outlier: 7.849A pdb=" N THR24 32 " --> pdb=" O HIS24 51 " (cutoff:3.500A) 1927 hydrogen bonds defined for protein. 5286 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3998 hydrogen bonds 6302 hydrogen bond angles 0 basepair planarities 1588 basepair parallelities 2468 stacking parallelities Total time for adding SS restraints: 271.00 Time building geometry restraints manager: 79.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 30375 1.34 - 1.48: 71172 1.48 - 1.62: 60069 1.62 - 1.76: 49 1.76 - 1.90: 285 Bond restraints: 161950 Sorted by residual: bond pdb=" C THR A 684 " pdb=" O THR A 684 " ideal model delta sigma weight residual 1.236 1.338 -0.102 1.15e-02 7.56e+03 7.86e+01 bond pdb=" C ARG H 94 " pdb=" O ARG H 94 " ideal model delta sigma weight residual 1.235 1.303 -0.068 1.38e-02 5.25e+03 2.45e+01 bond pdb=" CA VAL A 598 " pdb=" CB VAL A 598 " ideal model delta sigma weight residual 1.540 1.606 -0.066 1.36e-02 5.41e+03 2.36e+01 bond pdb=" N ALA A 688 " pdb=" CA ALA A 688 " ideal model delta sigma weight residual 1.459 1.517 -0.058 1.23e-02 6.61e+03 2.24e+01 bond pdb=" C ALA 8 91 " pdb=" O ALA 8 91 " ideal model delta sigma weight residual 1.236 1.291 -0.055 1.18e-02 7.18e+03 2.20e+01 ... (remaining 161945 not shown) Histogram of bond angle deviations from ideal: 94.89 - 103.47: 12410 103.47 - 112.05: 97087 112.05 - 120.62: 79107 120.62 - 129.20: 49313 129.20 - 137.77: 4199 Bond angle restraints: 242116 Sorted by residual: angle pdb=" N GLY10 101 " pdb=" CA GLY10 101 " pdb=" C GLY10 101 " ideal model delta sigma weight residual 114.67 99.65 15.02 1.10e+00 8.26e-01 1.86e+02 angle pdb=" N GLY A 678 " pdb=" CA GLY A 678 " pdb=" C GLY A 678 " ideal model delta sigma weight residual 113.79 127.41 -13.62 1.17e+00 7.31e-01 1.36e+02 angle pdb=" N ARG A 681 " pdb=" CA ARG A 681 " pdb=" C ARG A 681 " ideal model delta sigma weight residual 111.36 98.67 12.69 1.09e+00 8.42e-01 1.36e+02 angle pdb=" N VAL D 120 " pdb=" CA VAL D 120 " pdb=" C VAL D 120 " ideal model delta sigma weight residual 107.73 124.76 -17.03 1.56e+00 4.11e-01 1.19e+02 angle pdb=" N SER 7 85 " pdb=" CA SER 7 85 " pdb=" C SER 7 85 " ideal model delta sigma weight residual 111.82 99.24 12.58 1.16e+00 7.43e-01 1.18e+02 ... (remaining 242111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 91844 35.73 - 71.46: 10608 71.46 - 107.19: 1275 107.19 - 142.92: 19 142.92 - 178.65: 22 Dihedral angle restraints: 103768 sinusoidal: 86423 harmonic: 17345 Sorted by residual: dihedral pdb=" C4' U281130 " pdb=" C3' U281130 " pdb=" C2' U281130 " pdb=" C1' U281130 " ideal model delta sinusoidal sigma weight residual -35.00 31.33 -66.33 1 8.00e+00 1.56e-02 8.98e+01 dihedral pdb=" C4' U282296 " pdb=" C3' U282296 " pdb=" C2' U282296 " pdb=" C1' U282296 " ideal model delta sinusoidal sigma weight residual -35.00 31.32 -66.32 1 8.00e+00 1.56e-02 8.98e+01 dihedral pdb=" C5' U281130 " pdb=" C4' U281130 " pdb=" C3' U281130 " pdb=" O3' U281130 " ideal model delta sinusoidal sigma weight residual 147.00 81.15 65.85 1 8.00e+00 1.56e-02 8.86e+01 ... (remaining 103765 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 27780 0.129 - 0.257: 2905 0.257 - 0.386: 229 0.386 - 0.515: 20 0.515 - 0.643: 5 Chirality restraints: 30939 Sorted by residual: chirality pdb=" P C32 1 " pdb=" OP1 C32 1 " pdb=" OP2 C32 1 " pdb=" O5' C32 1 " both_signs ideal model delta sigma weight residual True 2.41 3.05 -0.64 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" P U29 1 " pdb=" OP1 U29 1 " pdb=" OP2 U29 1 " pdb=" O5' U29 1 " both_signs ideal model delta sigma weight residual True 2.41 3.05 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" P A27 2 " pdb=" OP1 A27 2 " pdb=" OP2 A27 2 " pdb=" O5' A27 2 " both_signs ideal model delta sigma weight residual True 2.41 -3.04 -0.63 2.00e-01 2.50e+01 9.92e+00 ... (remaining 30936 not shown) Planarity restraints: 13091 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G28 512 " 0.210 2.00e-02 2.50e+03 8.73e-02 2.28e+02 pdb=" N9 G28 512 " -0.012 2.00e-02 2.50e+03 pdb=" C8 G28 512 " -0.093 2.00e-02 2.50e+03 pdb=" N7 G28 512 " -0.084 2.00e-02 2.50e+03 pdb=" C5 G28 512 " -0.040 2.00e-02 2.50e+03 pdb=" C6 G28 512 " 0.040 2.00e-02 2.50e+03 pdb=" O6 G28 512 " 0.131 2.00e-02 2.50e+03 pdb=" N1 G28 512 " 0.035 2.00e-02 2.50e+03 pdb=" C2 G28 512 " -0.022 2.00e-02 2.50e+03 pdb=" N2 G28 512 " -0.042 2.00e-02 2.50e+03 pdb=" N3 G28 512 " -0.061 2.00e-02 2.50e+03 pdb=" C4 G28 512 " -0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G281171 " 0.200 2.00e-02 2.50e+03 8.43e-02 2.13e+02 pdb=" N9 G281171 " -0.012 2.00e-02 2.50e+03 pdb=" C8 G281171 " -0.093 2.00e-02 2.50e+03 pdb=" N7 G281171 " -0.085 2.00e-02 2.50e+03 pdb=" C5 G281171 " -0.038 2.00e-02 2.50e+03 pdb=" C6 G281171 " 0.037 2.00e-02 2.50e+03 pdb=" O6 G281171 " 0.134 2.00e-02 2.50e+03 pdb=" N1 G281171 " 0.026 2.00e-02 2.50e+03 pdb=" C2 G281171 " -0.022 2.00e-02 2.50e+03 pdb=" N2 G281171 " -0.044 2.00e-02 2.50e+03 pdb=" N3 G281171 " -0.049 2.00e-02 2.50e+03 pdb=" C4 G281171 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A281328 " -0.179 2.00e-02 2.50e+03 7.81e-02 1.68e+02 pdb=" N9 A281328 " 0.009 2.00e-02 2.50e+03 pdb=" C8 A281328 " 0.067 2.00e-02 2.50e+03 pdb=" N7 A281328 " 0.063 2.00e-02 2.50e+03 pdb=" C5 A281328 " 0.039 2.00e-02 2.50e+03 pdb=" C6 A281328 " -0.026 2.00e-02 2.50e+03 pdb=" N6 A281328 " -0.121 2.00e-02 2.50e+03 pdb=" N1 A281328 " -0.014 2.00e-02 2.50e+03 pdb=" C2 A281328 " 0.033 2.00e-02 2.50e+03 pdb=" N3 A281328 " 0.068 2.00e-02 2.50e+03 pdb=" C4 A281328 " 0.062 2.00e-02 2.50e+03 ... (remaining 13088 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 764 2.52 - 3.11: 114010 3.11 - 3.71: 313219 3.71 - 4.30: 428482 4.30 - 4.90: 558932 Nonbonded interactions: 1415407 Sorted by model distance: nonbonded pdb=" O ARG11 38 " pdb=" O MET11 62 " model vdw 1.923 3.040 nonbonded pdb=" O LEU19 45 " pdb=" OE1 GLN19 48 " model vdw 2.038 3.040 nonbonded pdb=" O LYS T 88 " pdb=" N GLY T 90 " model vdw 2.106 2.520 nonbonded pdb=" O2' A27 246 " pdb=" O5' G27 247 " model vdw 2.130 2.440 nonbonded pdb=" O PRO I 92 " pdb=" O2' C281076 " model vdw 2.137 2.440 ... (remaining 1415402 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain '31' and (resid 1 through 45 or resid 47 through 76)) selection = (chain '32' and (resid 1 through 45 or resid 47 through 76)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.150 Extract box with map and model: 26.650 Check model and map are aligned: 1.610 Set scattering table: 1.010 Process input model: 569.660 Find NCS groups from input model: 3.230 Set up NCS constraints: 0.460 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 612.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 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 0.102 161950 Z= 0.463 Angle : 1.106 17.028 242116 Z= 0.732 Chirality : 0.085 0.643 30939 Planarity : 0.012 0.087 13091 Dihedral : 22.560 178.646 92567 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 27.29 Ramachandran Plot: Outliers : 4.64 % Allowed : 12.51 % Favored : 82.84 % Rotamer: Outliers : 0.32 % Allowed : 1.71 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.23 (0.09), residues: 5985 helix: -3.24 (0.08), residues: 1963 sheet: -3.76 (0.12), residues: 988 loop : -2.04 (0.11), residues: 3034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.011 TRP22 72 HIS 0.004 0.001 HIS 8 189 PHE 0.085 0.011 PHE I 37 TYR 0.091 0.011 TYR S 38 ARG 0.016 0.001 ARG A 681 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11970 Ramachandran restraints generated. 5985 Oldfield, 0 Emsley, 5985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11970 Ramachandran restraints generated. 5985 Oldfield, 0 Emsley, 5985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1880 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 1864 time to evaluate : 6.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 ASP cc_start: 0.8819 (t0) cc_final: 0.8593 (t0) REVERT: D 136 GLN cc_start: 0.9038 (tp-100) cc_final: 0.8799 (tp-100) REVERT: D 199 MET cc_start: 0.9172 (ttm) cc_final: 0.8966 (tpp) REVERT: F 25 ILE cc_start: 0.8890 (mt) cc_final: 0.8614 (mm) REVERT: F 150 TYR cc_start: 0.8748 (m-80) cc_final: 0.8515 (m-80) REVERT: G 40 THR cc_start: 0.9417 (m) cc_final: 0.9120 (p) REVERT: G 43 ASN cc_start: 0.9657 (m-40) cc_final: 0.9313 (m110) REVERT: G 135 HIS cc_start: 0.8161 (t-90) cc_final: 0.7790 (t-90) REVERT: H 1 MET cc_start: 0.4277 (ttm) cc_final: 0.1817 (tmm) REVERT: H 3 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7686 (pp) REVERT: I 35 MET cc_start: 0.7080 (ptm) cc_final: 0.6474 (mpp) REVERT: J 16 TYR cc_start: 0.8412 (m-80) cc_final: 0.7868 (m-80) REVERT: J 120 ARG cc_start: 0.8971 (mtt90) cc_final: 0.8586 (mtt90) REVERT: K 73 ASP cc_start: 0.8956 (p0) cc_final: 0.8398 (p0) REVERT: P 81 ASP cc_start: 0.8920 (t70) cc_final: 0.8662 (t0) REVERT: R 95 ASP cc_start: 0.8361 (m-30) cc_final: 0.8128 (m-30) REVERT: S 97 LEU cc_start: 0.8732 (pp) cc_final: 0.8507 (pp) REVERT: T 37 ASP cc_start: 0.9268 (p0) cc_final: 0.9016 (p0) REVERT: U 17 ASP cc_start: 0.8612 (m-30) cc_final: 0.8172 (m-30) REVERT: V 46 LYS cc_start: 0.9410 (mptt) cc_final: 0.9026 (mmtm) REVERT: V 57 TYR cc_start: 0.8608 (m-80) cc_final: 0.7988 (m-80) REVERT: W 11 ASP cc_start: 0.8302 (t70) cc_final: 0.7781 (t0) REVERT: W 16 ARG cc_start: 0.7631 (mmt-90) cc_final: 0.7198 (mmt-90) REVERT: X 67 LEU cc_start: 0.9525 (mp) cc_final: 0.9317 (mm) REVERT: X 70 LEU cc_start: 0.9556 (mt) cc_final: 0.9290 (mt) REVERT: Y 5 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8513 (pt0) REVERT: Z 28 LEU cc_start: 0.8580 (mt) cc_final: 0.7956 (mp) REVERT: 7 25 LYS cc_start: 0.7599 (mmtt) cc_final: 0.7319 (ptpp) REVERT: 7 26 MET cc_start: 0.8470 (mtp) cc_final: 0.8257 (mtm) REVERT: 7 34 ARG cc_start: 0.8575 (mmt-90) cc_final: 0.8197 (tpm170) REVERT: 7 86 CYS cc_start: 0.8232 (t) cc_final: 0.7557 (t) REVERT: 7 89 PHE cc_start: 0.8532 (m-80) cc_final: 0.8246 (m-80) REVERT: 7 138 ARG cc_start: 0.6699 (ttt90) cc_final: 0.6310 (ttt180) REVERT: 7 158 ASP cc_start: 0.9196 (t70) cc_final: 0.8888 (t0) REVERT: 8 7 ASN cc_start: 0.8784 (t0) cc_final: 0.8543 (t0) REVERT: 8 114 LEU cc_start: 0.9273 (mt) cc_final: 0.8701 (mt) REVERT: 9 70 GLN cc_start: 0.8408 (tt0) cc_final: 0.8110 (tt0) REVERT: 11 14 GLN cc_start: 0.8872 (mp10) cc_final: 0.8585 (tp40) REVERT: 11 25 TYR cc_start: 0.8829 (m-80) cc_final: 0.7724 (m-80) REVERT: 12 30 MET cc_start: 0.8867 (ttp) cc_final: 0.8572 (ttp) REVERT: 13 25 THR cc_start: 0.8535 (m) cc_final: 0.8225 (t) REVERT: 13 42 GLU cc_start: 0.8883 (tp30) cc_final: 0.8520 (tp30) REVERT: 14 54 VAL cc_start: 0.9445 (m) cc_final: 0.8457 (p) REVERT: 15 58 ASN cc_start: 0.8953 (m110) cc_final: 0.8627 (m110) REVERT: 16 76 TYR cc_start: 0.9066 (m-10) cc_final: 0.8321 (m-10) REVERT: 16 104 PHE cc_start: 0.7688 (m-80) cc_final: 0.7474 (m-80) REVERT: 18 22 TYR cc_start: 0.8425 (t80) cc_final: 0.8167 (t80) REVERT: 18 81 ASP cc_start: 0.9287 (m-30) cc_final: 0.8627 (m-30) REVERT: 22 62 GLU cc_start: 0.8747 (tt0) cc_final: 0.8524 (pp20) REVERT: 24 40 PHE cc_start: 0.8437 (m-80) cc_final: 0.7956 (m-10) REVERT: 24 58 PRO cc_start: 0.8701 (Cg_exo) cc_final: 0.8461 (Cg_endo) REVERT: 24 61 VAL cc_start: 0.8943 (t) cc_final: 0.8326 (t) REVERT: 26 38 GLU cc_start: 0.6909 (pt0) cc_final: 0.6172 (pp20) outliers start: 16 outliers final: 7 residues processed: 1875 average time/residue: 1.4514 time to fit residues: 4688.3052 Evaluate side-chains 1177 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1169 time to evaluate : 6.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain 1 residue 37 CYS Chi-restraints excluded: chain 4 residue 44 VAL Chi-restraints excluded: chain 9 residue 4 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1056 random chunks: chunk 891 optimal weight: 20.0000 chunk 800 optimal weight: 20.0000 chunk 444 optimal weight: 8.9990 chunk 273 optimal weight: 6.9990 chunk 539 optimal weight: 0.9980 chunk 427 optimal weight: 30.0000 chunk 827 optimal weight: 30.0000 chunk 320 optimal weight: 8.9990 chunk 503 optimal weight: 2.9990 chunk 616 optimal weight: 20.0000 chunk 958 optimal weight: 20.0000 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 674 ASN A 705 GLN A 706 GLN A 730 ASN B 89 ASN B 199 HIS C 32 ASN C 42 ASN C 49 GLN C 150 GLN D 29 HIS ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN F 44 HIS F 138 GLN G 66 ASN G 119 ASN J 130 HIS J 136 GLN K 88 ASN N 81 ASN P 2 ASN P 11 GLN P 74 GLN ** P 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 HIS R 91 GLN T 28 ASN ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 73 ASN V 24 ASN W 8 ASN ** Y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 58 ASN Z 19 HIS 2 4 GLN 2 5 ASN 6 35 GLN 7 17 HIS 7 38 HIS 7 50 ASN 7 169 HIS 8 7 ASN 8 138 GLN 8 139 ASN ** 9 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 130 ASN 9 139 ASN 9 151 GLN 10 42 ASN 10 121 ASN 10 134 ASN ** 11 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 12 51 GLN ** 12 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 3 GLN ** 13 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 14 3 ASN 14 4 GLN 14 30 ASN 14 36 GLN 14 125 GLN 15 56 HIS 16 14 GLN 16 80 ASN 16 118 ASN ** 17 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 17 45 ASN 17 76 HIS ** 18 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 19 59 GLN 20 34 GLN ** 21 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 22 8 GLN 22 30 HIS 23 51 GLN 24 55 GLN Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 161950 Z= 0.232 Angle : 0.709 13.541 242116 Z= 0.366 Chirality : 0.040 0.416 30939 Planarity : 0.006 0.067 13091 Dihedral : 23.826 176.197 80648 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 23.22 Ramachandran Plot: Outliers : 1.20 % Allowed : 9.04 % Favored : 89.76 % Rotamer: Outliers : 3.82 % Allowed : 13.88 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.10), residues: 5985 helix: -1.14 (0.10), residues: 1998 sheet: -3.20 (0.13), residues: 1055 loop : -1.51 (0.12), residues: 2932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 212 HIS 0.009 0.002 HIS 5 30 PHE 0.033 0.003 PHE H 113 TYR 0.054 0.003 TYR 7 212 ARG 0.008 0.001 ARG11 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11970 Ramachandran restraints generated. 5985 Oldfield, 0 Emsley, 5985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11970 Ramachandran restraints generated. 5985 Oldfield, 0 Emsley, 5985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1610 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 1420 time to evaluate : 6.430 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: B 59 GLN cc_start: 0.8696 (pt0) cc_final: 0.8430 (pt0) REVERT: D 90 GLN cc_start: 0.9008 (pm20) cc_final: 0.8787 (pm20) REVERT: D 100 MET cc_start: 0.8559 (mtt) cc_final: 0.8307 (mtt) REVERT: D 136 GLN cc_start: 0.8796 (tp-100) cc_final: 0.8543 (tp-100) REVERT: E 16 MET cc_start: 0.9296 (mmm) cc_final: 0.8926 (mmm) REVERT: E 25 MET cc_start: 0.9485 (mmm) cc_final: 0.8640 (tpp) REVERT: E 51 ASN cc_start: 0.9595 (m110) cc_final: 0.9323 (m110) REVERT: F 57 TYR cc_start: 0.8188 (m-80) cc_final: 0.7943 (m-10) REVERT: G 40 THR cc_start: 0.9602 (m) cc_final: 0.9266 (p) REVERT: G 135 HIS cc_start: 0.8364 (t-90) cc_final: 0.7911 (t-90) REVERT: H 1 MET cc_start: 0.4844 (ttm) cc_final: 0.2294 (tmm) REVERT: H 6 GLN cc_start: 0.7752 (mp10) cc_final: 0.7430 (mp10) REVERT: H 38 MET cc_start: -0.0704 (mmt) cc_final: -0.1130 (mmt) REVERT: I 35 MET cc_start: 0.7422 (ptm) cc_final: 0.6773 (mpp) REVERT: I 124 MET cc_start: 0.6582 (mmt) cc_final: 0.6292 (mmt) REVERT: J 16 TYR cc_start: 0.8414 (m-80) cc_final: 0.8153 (m-10) REVERT: J 19 ASP cc_start: 0.8509 (t70) cc_final: 0.8308 (t0) REVERT: J 138 GLN cc_start: 0.8139 (pp30) cc_final: 0.7862 (pp30) REVERT: K 73 ASP cc_start: 0.9002 (p0) cc_final: 0.8572 (p0) REVERT: L 23 ILE cc_start: 0.8961 (mp) cc_final: 0.8689 (mp) REVERT: N 75 ILE cc_start: 0.8990 (mm) cc_final: 0.8618 (mm) REVERT: P 81 ASP cc_start: 0.9140 (t70) cc_final: 0.8801 (t0) REVERT: R 1 MET cc_start: 0.8838 (tpp) cc_final: 0.8435 (tpp) REVERT: S 11 ARG cc_start: 0.8381 (mmm160) cc_final: 0.7983 (tpt-90) REVERT: S 68 ASP cc_start: 0.8547 (p0) cc_final: 0.8070 (p0) REVERT: T 37 ASP cc_start: 0.9100 (p0) cc_final: 0.8852 (p0) REVERT: U 21 ARG cc_start: 0.7252 (mtm110) cc_final: 0.6792 (mtp-110) REVERT: V 40 ILE cc_start: 0.9201 (tp) cc_final: 0.8934 (mm) REVERT: W 11 ASP cc_start: 0.8308 (t70) cc_final: 0.7705 (t0) REVERT: Y 5 GLU cc_start: 0.8865 (mt-10) cc_final: 0.8601 (pt0) REVERT: Z 4 ILE cc_start: 0.9144 (OUTLIER) cc_final: 0.8903 (tt) REVERT: Z 28 LEU cc_start: 0.8603 (mt) cc_final: 0.8098 (mp) REVERT: 1 35 ASP cc_start: 0.9267 (p0) cc_final: 0.8960 (p0) REVERT: 1 50 ASP cc_start: 0.5930 (t70) cc_final: 0.5680 (t0) REVERT: 2 36 LYS cc_start: 0.8917 (mmmt) cc_final: 0.8663 (mmmt) REVERT: 3 6 GLU cc_start: 0.8656 (pm20) cc_final: 0.7953 (pm20) REVERT: 3 34 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7726 (mm-30) REVERT: 5 48 MET cc_start: 0.9038 (tpp) cc_final: 0.8799 (tpp) REVERT: 7 34 ARG cc_start: 0.8512 (mmt-90) cc_final: 0.8297 (tpm170) REVERT: 7 158 ASP cc_start: 0.9124 (t70) cc_final: 0.8846 (t0) REVERT: 7 202 ASN cc_start: 0.7916 (p0) cc_final: 0.7659 (p0) REVERT: 8 40 GLN cc_start: 0.9052 (tm-30) cc_final: 0.8815 (pp30) REVERT: 9 139 ASN cc_start: 0.8947 (OUTLIER) cc_final: 0.8716 (p0) REVERT: 10 123 LEU cc_start: 0.8492 (mt) cc_final: 0.8143 (tp) REVERT: 10 141 ASP cc_start: 0.8618 (t0) cc_final: 0.8141 (t70) REVERT: 11 14 GLN cc_start: 0.8724 (mp10) cc_final: 0.7991 (tp40) REVERT: 12 30 MET cc_start: 0.8761 (ttp) cc_final: 0.7806 (tmm) REVERT: 12 139 ASP cc_start: 0.9286 (p0) cc_final: 0.8623 (t0) REVERT: 13 10 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8218 (mm) REVERT: 13 37 ASN cc_start: 0.8211 (t0) cc_final: 0.7773 (t0) REVERT: 13 72 GLU cc_start: 0.8715 (mp0) cc_final: 0.8475 (mp0) REVERT: 13 73 SER cc_start: 0.9171 (OUTLIER) cc_final: 0.8913 (p) REVERT: 13 74 ILE cc_start: 0.8932 (pt) cc_final: 0.8510 (pt) REVERT: 14 31 GLN cc_start: 0.9308 (mp10) cc_final: 0.8901 (mp10) REVERT: 14 45 MET cc_start: 0.9477 (ppp) cc_final: 0.8696 (ppp) REVERT: 14 49 GLN cc_start: 0.8807 (mm110) cc_final: 0.8559 (mm110) REVERT: 14 114 LYS cc_start: 0.8490 (mttm) cc_final: 0.8237 (mttp) REVERT: 15 58 ASN cc_start: 0.9106 (m110) cc_final: 0.8730 (m110) REVERT: 15 63 ASP cc_start: 0.7619 (p0) cc_final: 0.6708 (p0) REVERT: 15 97 ASP cc_start: 0.7697 (t0) cc_final: 0.7393 (t0) REVERT: 16 80 ASN cc_start: 0.8136 (m-40) cc_final: 0.7702 (p0) REVERT: 19 53 ASP cc_start: 0.8539 (OUTLIER) cc_final: 0.7677 (t70) REVERT: 22 27 PHE cc_start: 0.8736 (m-10) cc_final: 0.8519 (m-80) REVERT: 24 27 LYS cc_start: 0.8605 (ptpp) cc_final: 0.8350 (mtmm) REVERT: 24 28 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.7750 (ttmt) REVERT: 24 61 VAL cc_start: 0.8938 (t) cc_final: 0.8479 (t) outliers start: 190 outliers final: 99 residues processed: 1501 average time/residue: 1.3156 time to fit residues: 3451.0548 Evaluate side-chains 1253 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 1148 time to evaluate : 5.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain B residue 5 CYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain F residue 19 ASN Chi-restraints excluded: chain F residue 166 GLU Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain G residue 149 GLU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 130 HIS Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 144 GLU Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 82 GLU Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 74 GLN Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain S residue 31 GLN Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain U residue 26 ASN Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain W residue 27 VAL Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 48 LEU Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain Z residue 4 ILE Chi-restraints excluded: chain 1 residue 18 CYS Chi-restraints excluded: chain 1 residue 37 CYS Chi-restraints excluded: chain 1 residue 65 ASN Chi-restraints excluded: chain 2 residue 2 VAL Chi-restraints excluded: chain 2 residue 4 GLN Chi-restraints excluded: chain 2 residue 35 GLU Chi-restraints excluded: chain 4 residue 4 THR Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 5 residue 27 ASN Chi-restraints excluded: chain 5 residue 28 LEU Chi-restraints excluded: chain 5 residue 50 SER Chi-restraints excluded: chain 5 residue 53 ASP Chi-restraints excluded: chain 6 residue 22 VAL Chi-restraints excluded: chain 7 residue 15 PHE Chi-restraints excluded: chain 7 residue 39 ILE Chi-restraints excluded: chain 7 residue 66 ILE Chi-restraints excluded: chain 7 residue 160 LEU Chi-restraints excluded: chain 7 residue 170 ILE Chi-restraints excluded: chain 8 residue 101 ASN Chi-restraints excluded: chain 8 residue 122 GLN Chi-restraints excluded: chain 8 residue 180 ASP Chi-restraints excluded: chain 9 residue 16 THR Chi-restraints excluded: chain 9 residue 52 VAL Chi-restraints excluded: chain 9 residue 98 ASP Chi-restraints excluded: chain 9 residue 139 ASN Chi-restraints excluded: chain 10 residue 29 ILE Chi-restraints excluded: chain 11 residue 6 ILE Chi-restraints excluded: chain 11 residue 13 ASP Chi-restraints excluded: chain 12 residue 48 THR Chi-restraints excluded: chain 13 residue 10 LEU Chi-restraints excluded: chain 13 residue 73 SER Chi-restraints excluded: chain 14 residue 34 LEU Chi-restraints excluded: chain 14 residue 36 GLN Chi-restraints excluded: chain 14 residue 71 ILE Chi-restraints excluded: chain 15 residue 17 LEU Chi-restraints excluded: chain 15 residue 22 THR Chi-restraints excluded: chain 15 residue 24 GLU Chi-restraints excluded: chain 15 residue 26 VAL Chi-restraints excluded: chain 16 residue 84 MET Chi-restraints excluded: chain 17 residue 34 THR Chi-restraints excluded: chain 17 residue 40 THR Chi-restraints excluded: chain 18 residue 11 HIS Chi-restraints excluded: chain 18 residue 58 GLU Chi-restraints excluded: chain 18 residue 101 THR Chi-restraints excluded: chain 19 residue 17 ASP Chi-restraints excluded: chain 19 residue 53 ASP Chi-restraints excluded: chain 22 residue 6 THR Chi-restraints excluded: chain 22 residue 37 ILE Chi-restraints excluded: chain 22 residue 56 ASP Chi-restraints excluded: chain 24 residue 28 LYS Chi-restraints excluded: chain 24 residue 78 THR Chi-restraints excluded: chain 25 residue 56 ILE Chi-restraints excluded: chain 26 residue 18 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1056 random chunks: chunk 532 optimal weight: 30.0000 chunk 297 optimal weight: 5.9990 chunk 798 optimal weight: 20.0000 chunk 652 optimal weight: 20.0000 chunk 264 optimal weight: 20.0000 chunk 960 optimal weight: 20.0000 chunk 1037 optimal weight: 20.0000 chunk 855 optimal weight: 20.0000 chunk 952 optimal weight: 50.0000 chunk 327 optimal weight: 20.0000 chunk 770 optimal weight: 30.0000 overall best weight: 17.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 GLN B 238 ASN B 259 ASN C 173 GLN ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 4 HIS I 33 ASN J 130 HIS L 54 GLN ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 62 ASN ** O 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 74 GLN P 114 ASN ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN R 18 GLN ** R 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 ASN V 75 GLN X 15 ASN ** Y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 13 ASN 6 35 GLN ** 7 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 35 ASN ** 7 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 7 ASN ** 8 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 10 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 14 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 16 63 GLN ** 16 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 18 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 19 3 GLN ** 19 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 20 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 21 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 25 60 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.112 161950 Z= 0.493 Angle : 0.833 14.431 242116 Z= 0.428 Chirality : 0.044 0.330 30939 Planarity : 0.006 0.106 13091 Dihedral : 24.061 177.916 80643 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 40.18 Ramachandran Plot: Outliers : 1.00 % Allowed : 11.38 % Favored : 87.62 % Rotamer: Outliers : 5.49 % Allowed : 17.12 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.10), residues: 5985 helix: -0.82 (0.11), residues: 1992 sheet: -3.03 (0.13), residues: 1099 loop : -1.56 (0.12), residues: 2894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 247 HIS 0.018 0.002 HIS J 130 PHE 0.038 0.003 PHE26 36 TYR 0.050 0.003 TYR 9 74 ARG 0.015 0.001 ARG F 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11970 Ramachandran restraints generated. 5985 Oldfield, 0 Emsley, 5985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11970 Ramachandran restraints generated. 5985 Oldfield, 0 Emsley, 5985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1460 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 1187 time to evaluate : 6.393 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: B 66 PHE cc_start: 0.8957 (m-80) cc_final: 0.8740 (m-80) REVERT: D 97 ASN cc_start: 0.7858 (OUTLIER) cc_final: 0.6510 (p0) REVERT: D 100 MET cc_start: 0.8709 (mtt) cc_final: 0.8413 (mtt) REVERT: D 136 GLN cc_start: 0.8855 (tp-100) cc_final: 0.8618 (tp-100) REVERT: E 25 MET cc_start: 0.9439 (mmm) cc_final: 0.8604 (tpp) REVERT: E 51 ASN cc_start: 0.9543 (m110) cc_final: 0.9294 (m-40) REVERT: G 7 ASP cc_start: 0.8635 (t0) cc_final: 0.7858 (t0) REVERT: G 135 HIS cc_start: 0.8395 (t-90) cc_final: 0.7945 (t-90) REVERT: H 1 MET cc_start: 0.5213 (ttm) cc_final: 0.2941 (tmm) REVERT: H 86 MET cc_start: 0.2192 (tpt) cc_final: 0.1986 (tpt) REVERT: K 4 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8192 (mm-30) REVERT: K 73 ASP cc_start: 0.9087 (p0) cc_final: 0.8774 (p0) REVERT: K 98 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7937 (ttm-80) REVERT: N 5 LYS cc_start: 0.8814 (mmmt) cc_final: 0.8504 (mmmm) REVERT: P 81 ASP cc_start: 0.9201 (t70) cc_final: 0.8935 (t0) REVERT: P 101 GLU cc_start: 0.8944 (pp20) cc_final: 0.8592 (pp20) REVERT: R 1 MET cc_start: 0.8926 (tpp) cc_final: 0.8571 (tpp) REVERT: S 65 ASP cc_start: 0.8431 (t0) cc_final: 0.8164 (t0) REVERT: S 78 GLU cc_start: 0.8016 (pm20) cc_final: 0.7753 (pm20) REVERT: T 1 MET cc_start: 0.5305 (ttt) cc_final: 0.5022 (ttt) REVERT: T 25 GLU cc_start: 0.8806 (pp20) cc_final: 0.8109 (pp20) REVERT: T 37 ASP cc_start: 0.9137 (p0) cc_final: 0.8815 (p0) REVERT: W 11 ASP cc_start: 0.8446 (t70) cc_final: 0.8095 (t0) REVERT: Y 30 MET cc_start: 0.9059 (mmm) cc_final: 0.8817 (mmt) REVERT: Z 28 LEU cc_start: 0.8750 (mt) cc_final: 0.8331 (mp) REVERT: Z 46 MET cc_start: 0.9305 (mmm) cc_final: 0.9078 (mmm) REVERT: 1 30 HIS cc_start: 0.8371 (p-80) cc_final: 0.8063 (p-80) REVERT: 3 6 GLU cc_start: 0.8808 (pm20) cc_final: 0.8518 (pm20) REVERT: 7 158 ASP cc_start: 0.9225 (t70) cc_final: 0.9017 (t0) REVERT: 9 123 MET cc_start: 0.8987 (mmp) cc_final: 0.8753 (mmp) REVERT: 10 30 PHE cc_start: 0.8570 (m-80) cc_final: 0.8266 (m-80) REVERT: 10 123 LEU cc_start: 0.8641 (mt) cc_final: 0.8383 (tp) REVERT: 11 21 MET cc_start: 0.9182 (ttp) cc_final: 0.8812 (mpp) REVERT: 12 30 MET cc_start: 0.8852 (ttp) cc_final: 0.8395 (tmm) REVERT: 13 26 MET cc_start: 0.8689 (ptp) cc_final: 0.8307 (ptp) REVERT: 13 37 ASN cc_start: 0.8355 (t0) cc_final: 0.8145 (t0) REVERT: 13 89 ASP cc_start: 0.8206 (p0) cc_final: 0.7734 (p0) REVERT: 14 45 MET cc_start: 0.9523 (OUTLIER) cc_final: 0.9253 (ppp) REVERT: 14 62 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8280 (mm) REVERT: 15 58 ASN cc_start: 0.9111 (m110) cc_final: 0.8831 (m110) REVERT: 16 80 ASN cc_start: 0.8214 (m-40) cc_final: 0.7794 (p0) REVERT: 17 61 GLU cc_start: 0.8974 (tp30) cc_final: 0.8447 (tp30) REVERT: 18 77 LYS cc_start: 0.9174 (tppt) cc_final: 0.8898 (tppt) REVERT: 24 65 MET cc_start: 0.9275 (ptm) cc_final: 0.8802 (ppp) REVERT: 25 27 MET cc_start: 0.9429 (tmm) cc_final: 0.9196 (tmm) outliers start: 273 outliers final: 193 residues processed: 1323 average time/residue: 1.3900 time to fit residues: 3257.1460 Evaluate side-chains 1231 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 1034 time to evaluate : 5.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain B residue 5 CYS Chi-restraints excluded: chain B residue 110 LYS Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 19 ASN Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 146 ASP Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 59 THR Chi-restraints excluded: chain K residue 37 ASP Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 56 ASP Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 98 ARG Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 144 GLU Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 9 GLN Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 82 GLU Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 80 GLU Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain O residue 108 ASP Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 18 SER Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 74 GLN Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 55 ASP Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain S residue 22 ASP Chi-restraints excluded: chain S residue 31 GLN Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain U residue 26 ASN Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 72 ASN Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 48 LEU Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain Y residue 15 ASN Chi-restraints excluded: chain Z residue 2 LYS Chi-restraints excluded: chain Z residue 13 ILE Chi-restraints excluded: chain 1 residue 18 CYS Chi-restraints excluded: chain 1 residue 37 CYS Chi-restraints excluded: chain 1 residue 39 LYS Chi-restraints excluded: chain 1 residue 63 ARG Chi-restraints excluded: chain 1 residue 65 ASN Chi-restraints excluded: chain 2 residue 2 VAL Chi-restraints excluded: chain 2 residue 21 LEU Chi-restraints excluded: chain 2 residue 35 GLU Chi-restraints excluded: chain 2 residue 41 HIS Chi-restraints excluded: chain 2 residue 45 ASP Chi-restraints excluded: chain 2 residue 53 VAL Chi-restraints excluded: chain 3 residue 33 LEU Chi-restraints excluded: chain 4 residue 4 THR Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 4 residue 44 VAL Chi-restraints excluded: chain 5 residue 6 VAL Chi-restraints excluded: chain 5 residue 27 ASN Chi-restraints excluded: chain 5 residue 28 LEU Chi-restraints excluded: chain 5 residue 49 VAL Chi-restraints excluded: chain 5 residue 50 SER Chi-restraints excluded: chain 5 residue 53 ASP Chi-restraints excluded: chain 5 residue 54 LEU Chi-restraints excluded: chain 5 residue 57 VAL Chi-restraints excluded: chain 6 residue 22 VAL Chi-restraints excluded: chain 6 residue 26 ILE Chi-restraints excluded: chain 7 residue 15 PHE Chi-restraints excluded: chain 7 residue 19 THR Chi-restraints excluded: chain 7 residue 39 ILE Chi-restraints excluded: chain 7 residue 66 ILE Chi-restraints excluded: chain 7 residue 67 LEU Chi-restraints excluded: chain 7 residue 103 TRP Chi-restraints excluded: chain 7 residue 105 THR Chi-restraints excluded: chain 7 residue 160 LEU Chi-restraints excluded: chain 7 residue 163 ILE Chi-restraints excluded: chain 7 residue 170 ILE Chi-restraints excluded: chain 7 residue 185 ILE Chi-restraints excluded: chain 7 residue 196 ASP Chi-restraints excluded: chain 8 residue 51 VAL Chi-restraints excluded: chain 8 residue 82 ASP Chi-restraints excluded: chain 8 residue 92 ASP Chi-restraints excluded: chain 8 residue 101 ASN Chi-restraints excluded: chain 8 residue 122 GLN Chi-restraints excluded: chain 8 residue 180 ASP Chi-restraints excluded: chain 8 residue 199 VAL Chi-restraints excluded: chain 9 residue 4 LEU Chi-restraints excluded: chain 9 residue 16 THR Chi-restraints excluded: chain 9 residue 52 VAL Chi-restraints excluded: chain 9 residue 98 ASP Chi-restraints excluded: chain 9 residue 170 LEU Chi-restraints excluded: chain 10 residue 14 LEU Chi-restraints excluded: chain 10 residue 29 ILE Chi-restraints excluded: chain 10 residue 63 MET Chi-restraints excluded: chain 10 residue 75 LEU Chi-restraints excluded: chain 11 residue 6 ILE Chi-restraints excluded: chain 11 residue 13 ASP Chi-restraints excluded: chain 12 residue 48 THR Chi-restraints excluded: chain 12 residue 84 TYR Chi-restraints excluded: chain 12 residue 103 ILE Chi-restraints excluded: chain 13 residue 73 SER Chi-restraints excluded: chain 13 residue 103 VAL Chi-restraints excluded: chain 14 residue 5 TYR Chi-restraints excluded: chain 14 residue 45 MET Chi-restraints excluded: chain 14 residue 62 LEU Chi-restraints excluded: chain 14 residue 71 ILE Chi-restraints excluded: chain 15 residue 17 LEU Chi-restraints excluded: chain 15 residue 22 THR Chi-restraints excluded: chain 15 residue 24 GLU Chi-restraints excluded: chain 15 residue 26 VAL Chi-restraints excluded: chain 15 residue 36 VAL Chi-restraints excluded: chain 15 residue 101 SER Chi-restraints excluded: chain 16 residue 15 VAL Chi-restraints excluded: chain 16 residue 31 VAL Chi-restraints excluded: chain 16 residue 56 LYS Chi-restraints excluded: chain 16 residue 64 VAL Chi-restraints excluded: chain 16 residue 84 MET Chi-restraints excluded: chain 16 residue 107 THR Chi-restraints excluded: chain 17 residue 19 ASN Chi-restraints excluded: chain 17 residue 34 THR Chi-restraints excluded: chain 17 residue 40 THR Chi-restraints excluded: chain 18 residue 8 ILE Chi-restraints excluded: chain 18 residue 24 VAL Chi-restraints excluded: chain 18 residue 82 LEU Chi-restraints excluded: chain 18 residue 101 THR Chi-restraints excluded: chain 19 residue 17 ASP Chi-restraints excluded: chain 19 residue 34 ASN Chi-restraints excluded: chain 19 residue 57 SER Chi-restraints excluded: chain 19 residue 85 GLU Chi-restraints excluded: chain 20 residue 56 LEU Chi-restraints excluded: chain 21 residue 1 MET Chi-restraints excluded: chain 21 residue 66 THR Chi-restraints excluded: chain 22 residue 6 THR Chi-restraints excluded: chain 22 residue 19 SER Chi-restraints excluded: chain 22 residue 37 ILE Chi-restraints excluded: chain 22 residue 56 ASP Chi-restraints excluded: chain 23 residue 32 ILE Chi-restraints excluded: chain 23 residue 64 LEU Chi-restraints excluded: chain 23 residue 70 THR Chi-restraints excluded: chain 24 residue 14 LEU Chi-restraints excluded: chain 24 residue 18 VAL Chi-restraints excluded: chain 24 residue 28 LYS Chi-restraints excluded: chain 24 residue 78 THR Chi-restraints excluded: chain 25 residue 56 ILE Chi-restraints excluded: chain 26 residue 12 ASP Chi-restraints excluded: chain 26 residue 18 PHE Chi-restraints excluded: chain 26 residue 42 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1056 random chunks: chunk 949 optimal weight: 40.0000 chunk 722 optimal weight: 20.0000 chunk 498 optimal weight: 30.0000 chunk 106 optimal weight: 40.0000 chunk 458 optimal weight: 8.9990 chunk 645 optimal weight: 10.0000 chunk 964 optimal weight: 20.0000 chunk 1020 optimal weight: 20.0000 chunk 503 optimal weight: 10.0000 chunk 913 optimal weight: 20.0000 chunk 275 optimal weight: 20.0000 overall best weight: 13.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 ASN ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 GLN ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN N 62 ASN ** O 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 104 GLN P 74 GLN P 114 ASN ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 91 GLN V 49 ASN W 42 HIS ** Y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 7 ASN ** 9 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 10 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 10 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 3 HIS ** 11 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 14 36 GLN 16 118 ASN ** 17 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 18 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 20 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 23 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 161950 Z= 0.379 Angle : 0.733 15.106 242116 Z= 0.377 Chirality : 0.040 0.296 30939 Planarity : 0.006 0.114 13091 Dihedral : 24.304 179.132 80642 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 34.81 Ramachandran Plot: Outliers : 0.89 % Allowed : 10.09 % Favored : 89.02 % Rotamer: Outliers : 5.53 % Allowed : 19.21 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.11), residues: 5985 helix: -0.52 (0.11), residues: 1987 sheet: -2.78 (0.13), residues: 1122 loop : -1.53 (0.12), residues: 2876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP 8 17 HIS 0.011 0.002 HIS Z 33 PHE 0.027 0.003 PHE25 30 TYR 0.044 0.003 TYR 7 212 ARG 0.015 0.001 ARG K 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11970 Ramachandran restraints generated. 5985 Oldfield, 0 Emsley, 5985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11970 Ramachandran restraints generated. 5985 Oldfield, 0 Emsley, 5985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1414 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 275 poor density : 1139 time to evaluate : 6.408 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: B 23 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8864 (mm) REVERT: B 66 PHE cc_start: 0.8915 (m-80) cc_final: 0.8651 (m-80) REVERT: D 97 ASN cc_start: 0.7857 (OUTLIER) cc_final: 0.6308 (p0) REVERT: D 100 MET cc_start: 0.8729 (mtt) cc_final: 0.8429 (mtt) REVERT: E 16 MET cc_start: 0.9313 (mmm) cc_final: 0.8928 (mmm) REVERT: E 25 MET cc_start: 0.9481 (mmm) cc_final: 0.8628 (tpp) REVERT: E 51 ASN cc_start: 0.9559 (m110) cc_final: 0.9320 (m-40) REVERT: G 7 ASP cc_start: 0.8504 (t0) cc_final: 0.8251 (t0) REVERT: G 135 HIS cc_start: 0.8456 (t-90) cc_final: 0.8033 (t-90) REVERT: H 1 MET cc_start: 0.5495 (ttm) cc_final: 0.2970 (tmm) REVERT: H 38 MET cc_start: -0.0286 (mmt) cc_final: -0.0493 (mmt) REVERT: I 35 MET cc_start: 0.7594 (ptm) cc_final: 0.6892 (mpp) REVERT: K 4 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8206 (mm-30) REVERT: K 53 LYS cc_start: 0.9264 (OUTLIER) cc_final: 0.8983 (mmtt) REVERT: K 73 ASP cc_start: 0.9066 (p0) cc_final: 0.8680 (p0) REVERT: K 98 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.8014 (ttm-80) REVERT: M 1 MET cc_start: 0.7227 (mmm) cc_final: 0.6742 (mmm) REVERT: M 75 GLU cc_start: 0.8248 (tt0) cc_final: 0.7895 (tt0) REVERT: O 76 LYS cc_start: 0.9113 (mmmt) cc_final: 0.8775 (mmmt) REVERT: P 81 ASP cc_start: 0.9256 (t70) cc_final: 0.9019 (t0) REVERT: P 101 GLU cc_start: 0.8917 (pp20) cc_final: 0.8562 (pp20) REVERT: R 1 MET cc_start: 0.8976 (tpp) cc_final: 0.8700 (tpp) REVERT: S 11 ARG cc_start: 0.8693 (mmm160) cc_final: 0.8315 (tpt-90) REVERT: S 95 ARG cc_start: 0.7794 (ttp80) cc_final: 0.7581 (ttp80) REVERT: T 1 MET cc_start: 0.5680 (ttt) cc_final: 0.5390 (ttt) REVERT: T 25 GLU cc_start: 0.8835 (pp20) cc_final: 0.8280 (pp20) REVERT: T 37 ASP cc_start: 0.9117 (p0) cc_final: 0.8715 (p0) REVERT: V 11 GLU cc_start: 0.8944 (OUTLIER) cc_final: 0.8732 (mm-30) REVERT: X 75 GLU cc_start: 0.7090 (mm-30) cc_final: 0.6616 (mm-30) REVERT: Y 30 MET cc_start: 0.9072 (mmm) cc_final: 0.8810 (mmt) REVERT: Z 28 LEU cc_start: 0.8801 (mt) cc_final: 0.8272 (mp) REVERT: Z 46 MET cc_start: 0.9315 (mmm) cc_final: 0.9111 (mmm) REVERT: 2 27 LEU cc_start: 0.8570 (tp) cc_final: 0.8058 (tp) REVERT: 2 36 LYS cc_start: 0.9067 (mmmt) cc_final: 0.8669 (mmmt) REVERT: 3 35 LEU cc_start: 0.7963 (tp) cc_final: 0.7742 (tp) REVERT: 5 48 MET cc_start: 0.9095 (tpp) cc_final: 0.8867 (tpp) REVERT: 7 67 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8913 (mm) REVERT: 7 68 PHE cc_start: 0.8638 (m-80) cc_final: 0.8426 (m-80) REVERT: 8 40 GLN cc_start: 0.9196 (pp30) cc_final: 0.8353 (pp30) REVERT: 10 30 PHE cc_start: 0.8563 (m-80) cc_final: 0.8103 (m-80) REVERT: 10 63 MET cc_start: 0.9148 (mmm) cc_final: 0.8743 (mmm) REVERT: 10 70 MET cc_start: 0.9024 (tpp) cc_final: 0.8608 (tpp) REVERT: 10 146 MET cc_start: 0.8793 (ttp) cc_final: 0.8572 (tmm) REVERT: 11 21 MET cc_start: 0.9224 (ttp) cc_final: 0.9005 (mtm) REVERT: 13 10 LEU cc_start: 0.8862 (mm) cc_final: 0.8578 (mm) REVERT: 13 47 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7542 (p0) REVERT: 14 36 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8550 (pp30) REVERT: 14 45 MET cc_start: 0.9623 (ppp) cc_final: 0.8802 (ppp) REVERT: 14 62 LEU cc_start: 0.8646 (mm) cc_final: 0.8388 (mm) REVERT: 15 58 ASN cc_start: 0.9080 (m110) cc_final: 0.8815 (m110) REVERT: 16 124 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7882 (tptp) REVERT: 18 77 LYS cc_start: 0.9245 (tppt) cc_final: 0.9044 (tppt) REVERT: 22 16 MET cc_start: 0.8888 (ppp) cc_final: 0.8526 (ppp) REVERT: 24 62 THR cc_start: 0.9350 (OUTLIER) cc_final: 0.8948 (p) REVERT: 24 65 MET cc_start: 0.9187 (ptm) cc_final: 0.8663 (ppp) outliers start: 275 outliers final: 185 residues processed: 1295 average time/residue: 1.4005 time to fit residues: 3230.9184 Evaluate side-chains 1217 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 1022 time to evaluate : 6.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 110 LYS Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 19 ASN Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 146 ASP Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain G residue 46 PHE Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 56 ASP Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 98 ARG Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 144 GLU Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 9 GLN Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 82 GLU Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 67 ASN Chi-restraints excluded: chain O residue 80 GLU Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 18 SER Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 114 ASN Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain S residue 31 GLN Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 76 ARG Chi-restraints excluded: chain U residue 26 ASN Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain V residue 11 GLU Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain W residue 19 VAL Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 15 ASN Chi-restraints excluded: chain X residue 48 LEU Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain Y residue 15 ASN Chi-restraints excluded: chain Z residue 2 LYS Chi-restraints excluded: chain Z residue 13 ILE Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain 1 residue 22 MET Chi-restraints excluded: chain 1 residue 37 CYS Chi-restraints excluded: chain 1 residue 39 LYS Chi-restraints excluded: chain 1 residue 65 ASN Chi-restraints excluded: chain 2 residue 2 VAL Chi-restraints excluded: chain 2 residue 5 ASN Chi-restraints excluded: chain 2 residue 21 LEU Chi-restraints excluded: chain 2 residue 35 GLU Chi-restraints excluded: chain 2 residue 41 HIS Chi-restraints excluded: chain 2 residue 45 ASP Chi-restraints excluded: chain 3 residue 26 LYS Chi-restraints excluded: chain 3 residue 33 LEU Chi-restraints excluded: chain 4 residue 4 THR Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 4 residue 44 VAL Chi-restraints excluded: chain 5 residue 6 VAL Chi-restraints excluded: chain 5 residue 27 ASN Chi-restraints excluded: chain 5 residue 28 LEU Chi-restraints excluded: chain 5 residue 49 VAL Chi-restraints excluded: chain 5 residue 50 SER Chi-restraints excluded: chain 5 residue 53 ASP Chi-restraints excluded: chain 5 residue 54 LEU Chi-restraints excluded: chain 5 residue 57 VAL Chi-restraints excluded: chain 6 residue 26 ILE Chi-restraints excluded: chain 7 residue 15 PHE Chi-restraints excluded: chain 7 residue 19 THR Chi-restraints excluded: chain 7 residue 39 ILE Chi-restraints excluded: chain 7 residue 66 ILE Chi-restraints excluded: chain 7 residue 67 LEU Chi-restraints excluded: chain 7 residue 153 MET Chi-restraints excluded: chain 7 residue 160 LEU Chi-restraints excluded: chain 7 residue 166 ASP Chi-restraints excluded: chain 7 residue 170 ILE Chi-restraints excluded: chain 7 residue 185 ILE Chi-restraints excluded: chain 7 residue 196 ASP Chi-restraints excluded: chain 7 residue 204 ASP Chi-restraints excluded: chain 7 residue 224 ARG Chi-restraints excluded: chain 8 residue 92 ASP Chi-restraints excluded: chain 8 residue 101 ASN Chi-restraints excluded: chain 8 residue 122 GLN Chi-restraints excluded: chain 8 residue 180 ASP Chi-restraints excluded: chain 8 residue 199 VAL Chi-restraints excluded: chain 9 residue 16 THR Chi-restraints excluded: chain 9 residue 52 VAL Chi-restraints excluded: chain 9 residue 98 ASP Chi-restraints excluded: chain 10 residue 29 ILE Chi-restraints excluded: chain 10 residue 75 LEU Chi-restraints excluded: chain 11 residue 6 ILE Chi-restraints excluded: chain 11 residue 13 ASP Chi-restraints excluded: chain 11 residue 36 ILE Chi-restraints excluded: chain 11 residue 70 VAL Chi-restraints excluded: chain 11 residue 96 VAL Chi-restraints excluded: chain 12 residue 5 VAL Chi-restraints excluded: chain 12 residue 48 THR Chi-restraints excluded: chain 12 residue 103 ILE Chi-restraints excluded: chain 13 residue 47 ASP Chi-restraints excluded: chain 13 residue 73 SER Chi-restraints excluded: chain 13 residue 100 ILE Chi-restraints excluded: chain 13 residue 103 VAL Chi-restraints excluded: chain 14 residue 34 LEU Chi-restraints excluded: chain 14 residue 36 GLN Chi-restraints excluded: chain 14 residue 71 ILE Chi-restraints excluded: chain 14 residue 115 VAL Chi-restraints excluded: chain 15 residue 17 LEU Chi-restraints excluded: chain 15 residue 22 THR Chi-restraints excluded: chain 15 residue 24 GLU Chi-restraints excluded: chain 15 residue 26 VAL Chi-restraints excluded: chain 15 residue 36 VAL Chi-restraints excluded: chain 15 residue 51 VAL Chi-restraints excluded: chain 16 residue 31 VAL Chi-restraints excluded: chain 16 residue 56 LYS Chi-restraints excluded: chain 16 residue 64 VAL Chi-restraints excluded: chain 16 residue 99 LEU Chi-restraints excluded: chain 16 residue 124 LYS Chi-restraints excluded: chain 17 residue 34 THR Chi-restraints excluded: chain 17 residue 40 THR Chi-restraints excluded: chain 18 residue 8 ILE Chi-restraints excluded: chain 18 residue 24 VAL Chi-restraints excluded: chain 18 residue 101 THR Chi-restraints excluded: chain 18 residue 103 THR Chi-restraints excluded: chain 19 residue 17 ASP Chi-restraints excluded: chain 19 residue 34 ASN Chi-restraints excluded: chain 19 residue 83 VAL Chi-restraints excluded: chain 21 residue 1 MET Chi-restraints excluded: chain 21 residue 19 VAL Chi-restraints excluded: chain 21 residue 74 LEU Chi-restraints excluded: chain 22 residue 6 THR Chi-restraints excluded: chain 22 residue 19 SER Chi-restraints excluded: chain 22 residue 37 ILE Chi-restraints excluded: chain 22 residue 56 ASP Chi-restraints excluded: chain 23 residue 32 ILE Chi-restraints excluded: chain 23 residue 70 THR Chi-restraints excluded: chain 24 residue 14 LEU Chi-restraints excluded: chain 24 residue 17 LYS Chi-restraints excluded: chain 24 residue 18 VAL Chi-restraints excluded: chain 24 residue 28 LYS Chi-restraints excluded: chain 24 residue 62 THR Chi-restraints excluded: chain 24 residue 78 THR Chi-restraints excluded: chain 25 residue 12 GLN Chi-restraints excluded: chain 26 residue 12 ASP Chi-restraints excluded: chain 26 residue 18 PHE Chi-restraints excluded: chain 26 residue 42 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1056 random chunks: chunk 850 optimal weight: 30.0000 chunk 579 optimal weight: 20.0000 chunk 14 optimal weight: 0.5980 chunk 760 optimal weight: 20.0000 chunk 421 optimal weight: 20.0000 chunk 871 optimal weight: 20.0000 chunk 705 optimal weight: 20.0000 chunk 1 optimal weight: 50.0000 chunk 521 optimal weight: 9.9990 chunk 916 optimal weight: 20.0000 chunk 257 optimal weight: 8.9990 overall best weight: 11.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 11 GLN K 3 GLN ** O 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 98 GLN O 104 GLN P 2 ASN ** P 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 70 GLN ** V 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 108 GLN ** 7 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 10 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 10 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 14 36 GLN ** 16 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 18 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 19 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 20 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 23 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 25 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 25 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 26 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 161950 Z= 0.346 Angle : 0.713 16.909 242116 Z= 0.365 Chirality : 0.039 0.299 30939 Planarity : 0.006 0.107 13091 Dihedral : 24.332 179.071 80642 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 34.88 Ramachandran Plot: Outliers : 0.92 % Allowed : 10.66 % Favored : 88.42 % Rotamer: Outliers : 5.83 % Allowed : 20.68 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.11), residues: 5985 helix: -0.42 (0.11), residues: 1994 sheet: -2.58 (0.13), residues: 1122 loop : -1.56 (0.12), residues: 2869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP 8 166 HIS 0.013 0.002 HIS26 55 PHE 0.030 0.002 PHE26 36 TYR 0.046 0.003 TYR 7 212 ARG 0.014 0.001 ARG16 121 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11970 Ramachandran restraints generated. 5985 Oldfield, 0 Emsley, 5985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11970 Ramachandran restraints generated. 5985 Oldfield, 0 Emsley, 5985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1423 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 290 poor density : 1133 time to evaluate : 6.436 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: B 23 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8769 (mm) REVERT: D 97 ASN cc_start: 0.7844 (OUTLIER) cc_final: 0.6205 (p0) REVERT: D 100 MET cc_start: 0.8716 (mtt) cc_final: 0.8401 (mtt) REVERT: E 25 MET cc_start: 0.9470 (mmm) cc_final: 0.8661 (tpp) REVERT: E 37 MET cc_start: 0.9215 (OUTLIER) cc_final: 0.8875 (mtp) REVERT: E 51 ASN cc_start: 0.9563 (m110) cc_final: 0.9340 (m-40) REVERT: E 173 ASP cc_start: 0.9164 (OUTLIER) cc_final: 0.8922 (t0) REVERT: F 73 SER cc_start: 0.8989 (t) cc_final: 0.8697 (p) REVERT: G 135 HIS cc_start: 0.8510 (t-90) cc_final: 0.8124 (t-90) REVERT: H 1 MET cc_start: 0.5510 (ttm) cc_final: 0.3119 (tmm) REVERT: H 38 MET cc_start: -0.0170 (mmt) cc_final: -0.0751 (mmp) REVERT: I 35 MET cc_start: 0.7658 (ptm) cc_final: 0.6964 (mpp) REVERT: J 118 MET cc_start: 0.8760 (ppp) cc_final: 0.8067 (ppp) REVERT: K 4 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8259 (mm-30) REVERT: K 73 ASP cc_start: 0.9062 (p0) cc_final: 0.8588 (p0) REVERT: M 1 MET cc_start: 0.7105 (mmm) cc_final: 0.6656 (mmm) REVERT: M 75 GLU cc_start: 0.8162 (tt0) cc_final: 0.7840 (tt0) REVERT: O 76 LYS cc_start: 0.9030 (mmmt) cc_final: 0.8772 (mmmm) REVERT: P 81 ASP cc_start: 0.9272 (t70) cc_final: 0.9046 (t0) REVERT: P 101 GLU cc_start: 0.8955 (pp20) cc_final: 0.8604 (pp20) REVERT: P 114 ASN cc_start: 0.8363 (OUTLIER) cc_final: 0.8000 (p0) REVERT: S 11 ARG cc_start: 0.8722 (mmm160) cc_final: 0.8282 (tpt-90) REVERT: T 1 MET cc_start: 0.5779 (ttt) cc_final: 0.5349 (ttt) REVERT: T 37 ASP cc_start: 0.9105 (p0) cc_final: 0.8739 (p0) REVERT: Z 28 LEU cc_start: 0.8818 (mt) cc_final: 0.8337 (mp) REVERT: Z 46 MET cc_start: 0.9312 (mmm) cc_final: 0.9046 (mmm) REVERT: 2 27 LEU cc_start: 0.8656 (tp) cc_final: 0.8136 (tp) REVERT: 2 36 LYS cc_start: 0.9049 (mmmt) cc_final: 0.8643 (mmmt) REVERT: 3 32 LYS cc_start: 0.8458 (mtmt) cc_final: 0.8159 (mtmt) REVERT: 7 67 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8836 (mm) REVERT: 9 123 MET cc_start: 0.8873 (mmp) cc_final: 0.8605 (mmp) REVERT: 10 63 MET cc_start: 0.9115 (mmm) cc_final: 0.8195 (tpp) REVERT: 10 67 ARG cc_start: 0.8612 (mtt-85) cc_final: 0.8082 (mtt-85) REVERT: 10 70 MET cc_start: 0.8944 (tpp) cc_final: 0.8658 (tpp) REVERT: 11 21 MET cc_start: 0.9102 (ttp) cc_final: 0.8883 (mtp) REVERT: 12 30 MET cc_start: 0.8688 (ttp) cc_final: 0.7568 (tmm) REVERT: 12 102 TRP cc_start: 0.8658 (m-10) cc_final: 0.8409 (m-10) REVERT: 14 45 MET cc_start: 0.9574 (ppp) cc_final: 0.8844 (ppp) REVERT: 14 62 LEU cc_start: 0.8610 (mm) cc_final: 0.8241 (mm) REVERT: 15 58 ASN cc_start: 0.9100 (m110) cc_final: 0.8829 (m110) REVERT: 15 63 ASP cc_start: 0.7690 (p0) cc_final: 0.7305 (p0) REVERT: 15 74 VAL cc_start: 0.9182 (t) cc_final: 0.8960 (t) REVERT: 16 124 LYS cc_start: 0.8199 (pttt) cc_final: 0.7893 (pttt) REVERT: 17 61 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8596 (mm-30) REVERT: 19 95 LEU cc_start: 0.8624 (tp) cc_final: 0.8287 (mt) REVERT: 20 13 GLU cc_start: 0.8919 (pt0) cc_final: 0.8546 (pt0) REVERT: 24 28 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.7963 (ttmt) REVERT: 24 62 THR cc_start: 0.9324 (OUTLIER) cc_final: 0.8834 (p) REVERT: 24 65 MET cc_start: 0.9180 (ptm) cc_final: 0.8668 (ppp) REVERT: 25 60 GLN cc_start: 0.8812 (mm110) cc_final: 0.8601 (mm-40) REVERT: 26 53 LYS cc_start: 0.9473 (pttm) cc_final: 0.9154 (pttm) REVERT: 26 57 LYS cc_start: 0.8433 (pttp) cc_final: 0.7772 (pttm) outliers start: 290 outliers final: 210 residues processed: 1293 average time/residue: 1.2845 time to fit residues: 2942.3854 Evaluate side-chains 1257 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 1039 time to evaluate : 6.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 110 LYS Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 97 ASN Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 20 ASN Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 173 ASP Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 19 ASN Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 146 ASP Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain K residue 37 ASP Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 56 ASP Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 144 GLU Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 9 GLN Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 82 GLU Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain O residue 80 GLU Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 114 ASN Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 55 ASP Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain R residue 95 ASP Chi-restraints excluded: chain S residue 31 GLN Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 76 ARG Chi-restraints excluded: chain U residue 26 ASN Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 39 ASN Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 53 GLN Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain W residue 19 VAL Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain X residue 15 ASN Chi-restraints excluded: chain X residue 48 LEU Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain Y residue 15 ASN Chi-restraints excluded: chain Z residue 2 LYS Chi-restraints excluded: chain Z residue 13 ILE Chi-restraints excluded: chain 1 residue 18 CYS Chi-restraints excluded: chain 1 residue 22 MET Chi-restraints excluded: chain 1 residue 37 CYS Chi-restraints excluded: chain 1 residue 39 LYS Chi-restraints excluded: chain 1 residue 63 ARG Chi-restraints excluded: chain 1 residue 65 ASN Chi-restraints excluded: chain 2 residue 2 VAL Chi-restraints excluded: chain 2 residue 5 ASN Chi-restraints excluded: chain 2 residue 21 LEU Chi-restraints excluded: chain 2 residue 35 GLU Chi-restraints excluded: chain 2 residue 41 HIS Chi-restraints excluded: chain 2 residue 45 ASP Chi-restraints excluded: chain 3 residue 33 LEU Chi-restraints excluded: chain 4 residue 4 THR Chi-restraints excluded: chain 4 residue 25 LYS Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 4 residue 44 VAL Chi-restraints excluded: chain 5 residue 6 VAL Chi-restraints excluded: chain 5 residue 27 ASN Chi-restraints excluded: chain 5 residue 28 LEU Chi-restraints excluded: chain 5 residue 49 VAL Chi-restraints excluded: chain 5 residue 50 SER Chi-restraints excluded: chain 5 residue 53 ASP Chi-restraints excluded: chain 5 residue 54 LEU Chi-restraints excluded: chain 5 residue 57 VAL Chi-restraints excluded: chain 6 residue 26 ILE Chi-restraints excluded: chain 7 residue 15 PHE Chi-restraints excluded: chain 7 residue 19 THR Chi-restraints excluded: chain 7 residue 39 ILE Chi-restraints excluded: chain 7 residue 66 ILE Chi-restraints excluded: chain 7 residue 67 LEU Chi-restraints excluded: chain 7 residue 105 THR Chi-restraints excluded: chain 7 residue 108 GLN Chi-restraints excluded: chain 7 residue 153 MET Chi-restraints excluded: chain 7 residue 160 LEU Chi-restraints excluded: chain 7 residue 163 ILE Chi-restraints excluded: chain 7 residue 185 ILE Chi-restraints excluded: chain 7 residue 198 VAL Chi-restraints excluded: chain 7 residue 204 ASP Chi-restraints excluded: chain 7 residue 224 ARG Chi-restraints excluded: chain 8 residue 51 VAL Chi-restraints excluded: chain 8 residue 82 ASP Chi-restraints excluded: chain 8 residue 92 ASP Chi-restraints excluded: chain 8 residue 101 ASN Chi-restraints excluded: chain 8 residue 122 GLN Chi-restraints excluded: chain 8 residue 150 VAL Chi-restraints excluded: chain 8 residue 180 ASP Chi-restraints excluded: chain 8 residue 199 VAL Chi-restraints excluded: chain 9 residue 4 LEU Chi-restraints excluded: chain 9 residue 16 THR Chi-restraints excluded: chain 9 residue 52 VAL Chi-restraints excluded: chain 9 residue 98 ASP Chi-restraints excluded: chain 9 residue 125 ASN Chi-restraints excluded: chain 10 residue 14 LEU Chi-restraints excluded: chain 10 residue 29 ILE Chi-restraints excluded: chain 10 residue 75 LEU Chi-restraints excluded: chain 11 residue 6 ILE Chi-restraints excluded: chain 11 residue 13 ASP Chi-restraints excluded: chain 11 residue 30 THR Chi-restraints excluded: chain 11 residue 70 VAL Chi-restraints excluded: chain 11 residue 94 HIS Chi-restraints excluded: chain 11 residue 96 VAL Chi-restraints excluded: chain 12 residue 5 VAL Chi-restraints excluded: chain 12 residue 48 THR Chi-restraints excluded: chain 12 residue 103 ILE Chi-restraints excluded: chain 13 residue 73 SER Chi-restraints excluded: chain 13 residue 100 ILE Chi-restraints excluded: chain 13 residue 103 VAL Chi-restraints excluded: chain 14 residue 5 TYR Chi-restraints excluded: chain 14 residue 26 LYS Chi-restraints excluded: chain 14 residue 34 LEU Chi-restraints excluded: chain 14 residue 40 ARG Chi-restraints excluded: chain 14 residue 71 ILE Chi-restraints excluded: chain 15 residue 17 LEU Chi-restraints excluded: chain 15 residue 22 THR Chi-restraints excluded: chain 15 residue 24 GLU Chi-restraints excluded: chain 15 residue 26 VAL Chi-restraints excluded: chain 15 residue 36 VAL Chi-restraints excluded: chain 15 residue 51 VAL Chi-restraints excluded: chain 15 residue 102 LEU Chi-restraints excluded: chain 16 residue 15 VAL Chi-restraints excluded: chain 16 residue 30 ILE Chi-restraints excluded: chain 16 residue 31 VAL Chi-restraints excluded: chain 16 residue 45 THR Chi-restraints excluded: chain 16 residue 56 LYS Chi-restraints excluded: chain 16 residue 64 VAL Chi-restraints excluded: chain 17 residue 19 ASN Chi-restraints excluded: chain 17 residue 34 THR Chi-restraints excluded: chain 17 residue 40 THR Chi-restraints excluded: chain 18 residue 8 ILE Chi-restraints excluded: chain 18 residue 24 VAL Chi-restraints excluded: chain 18 residue 101 THR Chi-restraints excluded: chain 18 residue 103 THR Chi-restraints excluded: chain 19 residue 17 ASP Chi-restraints excluded: chain 19 residue 34 ASN Chi-restraints excluded: chain 19 residue 47 LEU Chi-restraints excluded: chain 21 residue 1 MET Chi-restraints excluded: chain 22 residue 6 THR Chi-restraints excluded: chain 22 residue 19 SER Chi-restraints excluded: chain 22 residue 28 VAL Chi-restraints excluded: chain 22 residue 37 ILE Chi-restraints excluded: chain 22 residue 56 ASP Chi-restraints excluded: chain 23 residue 17 VAL Chi-restraints excluded: chain 23 residue 32 ILE Chi-restraints excluded: chain 23 residue 70 THR Chi-restraints excluded: chain 24 residue 14 LEU Chi-restraints excluded: chain 24 residue 17 LYS Chi-restraints excluded: chain 24 residue 28 LYS Chi-restraints excluded: chain 24 residue 62 THR Chi-restraints excluded: chain 24 residue 70 LEU Chi-restraints excluded: chain 24 residue 78 THR Chi-restraints excluded: chain 25 residue 12 GLN Chi-restraints excluded: chain 26 residue 12 ASP Chi-restraints excluded: chain 26 residue 18 PHE Chi-restraints excluded: chain 26 residue 42 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1056 random chunks: chunk 343 optimal weight: 20.0000 chunk 919 optimal weight: 20.0000 chunk 201 optimal weight: 2.9990 chunk 599 optimal weight: 20.0000 chunk 251 optimal weight: 0.8980 chunk 1021 optimal weight: 20.0000 chunk 848 optimal weight: 50.0000 chunk 473 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 337 optimal weight: 7.9990 chunk 536 optimal weight: 4.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 HIS ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 29 ASN ** G 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 ASN ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 HIS N 62 ASN O 104 GLN ** P 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 74 GLN P 114 ASN Q 36 GLN ** V 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 57 ASN 7 108 GLN 7 119 GLN ** 7 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 139 ASN ** 9 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 130 ASN ** 10 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 16 14 GLN 16 118 ASN ** 17 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 18 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 19 42 ASN ** 23 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 23 73 HIS ** 24 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 25 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 161950 Z= 0.191 Angle : 0.645 17.143 242116 Z= 0.326 Chirality : 0.035 0.379 30939 Planarity : 0.005 0.090 13091 Dihedral : 24.254 179.628 80642 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 25.96 Ramachandran Plot: Outliers : 0.87 % Allowed : 8.65 % Favored : 90.48 % Rotamer: Outliers : 4.32 % Allowed : 23.63 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.11), residues: 5985 helix: -0.20 (0.11), residues: 1989 sheet: -2.29 (0.14), residues: 1109 loop : -1.46 (0.12), residues: 2887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP 8 166 HIS 0.008 0.001 HIS V 44 PHE 0.027 0.002 PHE R 77 TYR 0.047 0.002 TYR 7 212 ARG 0.012 0.001 ARG 6 4 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11970 Ramachandran restraints generated. 5985 Oldfield, 0 Emsley, 5985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11970 Ramachandran restraints generated. 5985 Oldfield, 0 Emsley, 5985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1434 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 1219 time to evaluate : 6.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 621 ILE cc_start: 0.6577 (mm) cc_final: 0.6248 (mp) REVERT: B 23 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8765 (mm) REVERT: B 59 GLN cc_start: 0.8727 (pt0) cc_final: 0.8455 (pt0) REVERT: D 186 VAL cc_start: 0.9117 (t) cc_final: 0.8811 (p) REVERT: D 188 MET cc_start: 0.8726 (mpp) cc_final: 0.8454 (mpp) REVERT: E 25 MET cc_start: 0.9462 (mmm) cc_final: 0.8690 (tpp) REVERT: E 51 ASN cc_start: 0.9572 (m110) cc_final: 0.9357 (m-40) REVERT: F 73 SER cc_start: 0.8929 (t) cc_final: 0.8678 (p) REVERT: G 135 HIS cc_start: 0.8578 (t-90) cc_final: 0.8137 (t-90) REVERT: G 141 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8236 (pptt) REVERT: H 1 MET cc_start: 0.5797 (ttm) cc_final: 0.3593 (tmm) REVERT: H 38 MET cc_start: -0.0382 (mmt) cc_final: -0.0591 (mmt) REVERT: I 10 LEU cc_start: 0.4191 (OUTLIER) cc_final: 0.3960 (mp) REVERT: I 27 LEU cc_start: 0.7093 (pp) cc_final: 0.6461 (mt) REVERT: I 35 MET cc_start: 0.7747 (ptm) cc_final: 0.7227 (mpp) REVERT: J 36 LEU cc_start: 0.8746 (mm) cc_final: 0.8456 (mp) REVERT: J 118 MET cc_start: 0.8828 (ppp) cc_final: 0.8212 (ppp) REVERT: K 4 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8140 (mm-30) REVERT: K 53 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8811 (mmtm) REVERT: K 73 ASP cc_start: 0.8990 (p0) cc_final: 0.8456 (p0) REVERT: M 1 MET cc_start: 0.7026 (mmm) cc_final: 0.6605 (mmm) REVERT: M 75 GLU cc_start: 0.8046 (tt0) cc_final: 0.7804 (tt0) REVERT: P 81 ASP cc_start: 0.9254 (t70) cc_final: 0.9037 (t0) REVERT: P 101 GLU cc_start: 0.8910 (pp20) cc_final: 0.8607 (pp20) REVERT: S 11 ARG cc_start: 0.8603 (mmm160) cc_final: 0.8307 (tpt-90) REVERT: S 69 LEU cc_start: 0.8769 (tp) cc_final: 0.8434 (mm) REVERT: T 1 MET cc_start: 0.5558 (ttt) cc_final: 0.4911 (ttt) REVERT: T 4 GLU cc_start: 0.9172 (pm20) cc_final: 0.8368 (pm20) REVERT: T 25 GLU cc_start: 0.8734 (pp20) cc_final: 0.8243 (pp20) REVERT: T 37 ASP cc_start: 0.8995 (p0) cc_final: 0.8662 (p0) REVERT: X 13 THR cc_start: 0.8982 (p) cc_final: 0.8779 (t) REVERT: Z 46 MET cc_start: 0.9302 (mmm) cc_final: 0.9028 (mmm) REVERT: 1 35 ASP cc_start: 0.9119 (p0) cc_final: 0.8908 (p0) REVERT: 2 27 LEU cc_start: 0.8616 (tp) cc_final: 0.8230 (tp) REVERT: 2 36 LYS cc_start: 0.9036 (mmmt) cc_final: 0.8805 (mmmt) REVERT: 3 34 GLU cc_start: 0.8447 (mm-30) cc_final: 0.7772 (mm-30) REVERT: 5 48 MET cc_start: 0.8963 (tpp) cc_final: 0.8712 (tpp) REVERT: 7 67 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8786 (mm) REVERT: 7 168 GLU cc_start: 0.8699 (mp0) cc_final: 0.8359 (mp0) REVERT: 9 71 PHE cc_start: 0.8276 (t80) cc_final: 0.8067 (t80) REVERT: 10 30 PHE cc_start: 0.8490 (m-80) cc_final: 0.8121 (m-80) REVERT: 10 70 MET cc_start: 0.8899 (tpp) cc_final: 0.8643 (tpp) REVERT: 10 115 GLU cc_start: 0.9198 (pp20) cc_final: 0.8914 (pp20) REVERT: 10 146 MET cc_start: 0.8710 (ttp) cc_final: 0.8227 (tmm) REVERT: 12 25 PHE cc_start: 0.8915 (t80) cc_final: 0.8673 (t80) REVERT: 12 102 TRP cc_start: 0.8556 (m-10) cc_final: 0.8277 (m-10) REVERT: 14 45 MET cc_start: 0.9569 (ppp) cc_final: 0.8921 (ppp) REVERT: 14 62 LEU cc_start: 0.8589 (mm) cc_final: 0.8241 (mm) REVERT: 15 58 ASN cc_start: 0.9102 (m110) cc_final: 0.8872 (m110) REVERT: 15 63 ASP cc_start: 0.7681 (p0) cc_final: 0.7460 (p0) REVERT: 16 93 GLU cc_start: 0.8543 (pp20) cc_final: 0.8341 (tm-30) REVERT: 18 8 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.8118 (mp) REVERT: 18 77 LYS cc_start: 0.9196 (tppt) cc_final: 0.8858 (tppt) REVERT: 18 81 ASP cc_start: 0.9345 (p0) cc_final: 0.9095 (p0) REVERT: 20 88 ARG cc_start: 0.6155 (mmt-90) cc_final: 0.4719 (mmp80) REVERT: 21 78 VAL cc_start: 0.9620 (OUTLIER) cc_final: 0.9325 (p) REVERT: 24 28 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8471 (ttmt) REVERT: 24 62 THR cc_start: 0.9300 (OUTLIER) cc_final: 0.8783 (p) REVERT: 24 65 MET cc_start: 0.9177 (ptm) cc_final: 0.8773 (ppp) REVERT: 25 60 GLN cc_start: 0.8696 (mm110) cc_final: 0.8444 (mm-40) REVERT: 25 85 LEU cc_start: 0.8570 (pp) cc_final: 0.8255 (tt) outliers start: 215 outliers final: 153 residues processed: 1335 average time/residue: 1.2862 time to fit residues: 3028.3541 Evaluate side-chains 1234 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 1072 time to evaluate : 6.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 110 LYS Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 19 ASN Chi-restraints excluded: chain F residue 146 ASP Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain G residue 94 ILE Chi-restraints excluded: chain G residue 141 LYS Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 144 GLU Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 9 GLN Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain O residue 80 GLU Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain Q residue 43 GLN Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain T residue 76 ARG Chi-restraints excluded: chain U residue 6 ARG Chi-restraints excluded: chain U residue 26 ASN Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain V residue 10 LYS Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain W residue 19 VAL Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain X residue 48 LEU Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain 1 residue 18 CYS Chi-restraints excluded: chain 1 residue 27 THR Chi-restraints excluded: chain 1 residue 37 CYS Chi-restraints excluded: chain 1 residue 65 ASN Chi-restraints excluded: chain 2 residue 2 VAL Chi-restraints excluded: chain 2 residue 5 ASN Chi-restraints excluded: chain 2 residue 35 GLU Chi-restraints excluded: chain 2 residue 38 LEU Chi-restraints excluded: chain 2 residue 41 HIS Chi-restraints excluded: chain 2 residue 45 ASP Chi-restraints excluded: chain 2 residue 53 VAL Chi-restraints excluded: chain 4 residue 4 THR Chi-restraints excluded: chain 4 residue 44 VAL Chi-restraints excluded: chain 5 residue 6 VAL Chi-restraints excluded: chain 5 residue 27 ASN Chi-restraints excluded: chain 5 residue 50 SER Chi-restraints excluded: chain 5 residue 53 ASP Chi-restraints excluded: chain 7 residue 15 PHE Chi-restraints excluded: chain 7 residue 19 THR Chi-restraints excluded: chain 7 residue 66 ILE Chi-restraints excluded: chain 7 residue 67 LEU Chi-restraints excluded: chain 7 residue 160 LEU Chi-restraints excluded: chain 7 residue 163 ILE Chi-restraints excluded: chain 7 residue 166 ASP Chi-restraints excluded: chain 7 residue 185 ILE Chi-restraints excluded: chain 7 residue 224 ARG Chi-restraints excluded: chain 8 residue 51 VAL Chi-restraints excluded: chain 8 residue 92 ASP Chi-restraints excluded: chain 8 residue 101 ASN Chi-restraints excluded: chain 8 residue 122 GLN Chi-restraints excluded: chain 8 residue 180 ASP Chi-restraints excluded: chain 8 residue 199 VAL Chi-restraints excluded: chain 9 residue 4 LEU Chi-restraints excluded: chain 9 residue 16 THR Chi-restraints excluded: chain 9 residue 98 ASP Chi-restraints excluded: chain 10 residue 29 ILE Chi-restraints excluded: chain 10 residue 75 LEU Chi-restraints excluded: chain 11 residue 6 ILE Chi-restraints excluded: chain 11 residue 13 ASP Chi-restraints excluded: chain 11 residue 30 THR Chi-restraints excluded: chain 11 residue 36 ILE Chi-restraints excluded: chain 12 residue 5 VAL Chi-restraints excluded: chain 12 residue 48 THR Chi-restraints excluded: chain 12 residue 71 THR Chi-restraints excluded: chain 12 residue 103 ILE Chi-restraints excluded: chain 13 residue 100 ILE Chi-restraints excluded: chain 13 residue 103 VAL Chi-restraints excluded: chain 14 residue 34 LEU Chi-restraints excluded: chain 14 residue 61 ASP Chi-restraints excluded: chain 14 residue 71 ILE Chi-restraints excluded: chain 15 residue 17 LEU Chi-restraints excluded: chain 15 residue 24 GLU Chi-restraints excluded: chain 15 residue 36 VAL Chi-restraints excluded: chain 15 residue 51 VAL Chi-restraints excluded: chain 15 residue 52 LEU Chi-restraints excluded: chain 15 residue 101 SER Chi-restraints excluded: chain 16 residue 30 ILE Chi-restraints excluded: chain 16 residue 31 VAL Chi-restraints excluded: chain 16 residue 99 LEU Chi-restraints excluded: chain 17 residue 34 THR Chi-restraints excluded: chain 17 residue 40 THR Chi-restraints excluded: chain 18 residue 8 ILE Chi-restraints excluded: chain 18 residue 24 VAL Chi-restraints excluded: chain 18 residue 101 THR Chi-restraints excluded: chain 18 residue 103 THR Chi-restraints excluded: chain 19 residue 17 ASP Chi-restraints excluded: chain 19 residue 34 ASN Chi-restraints excluded: chain 21 residue 1 MET Chi-restraints excluded: chain 21 residue 78 VAL Chi-restraints excluded: chain 22 residue 6 THR Chi-restraints excluded: chain 22 residue 19 SER Chi-restraints excluded: chain 22 residue 28 VAL Chi-restraints excluded: chain 22 residue 37 ILE Chi-restraints excluded: chain 22 residue 52 CYS Chi-restraints excluded: chain 22 residue 56 ASP Chi-restraints excluded: chain 23 residue 17 VAL Chi-restraints excluded: chain 23 residue 24 ASP Chi-restraints excluded: chain 24 residue 28 LYS Chi-restraints excluded: chain 24 residue 31 ARG Chi-restraints excluded: chain 24 residue 62 THR Chi-restraints excluded: chain 25 residue 12 GLN Chi-restraints excluded: chain 26 residue 3 ILE Chi-restraints excluded: chain 26 residue 18 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1056 random chunks: chunk 985 optimal weight: 30.0000 chunk 115 optimal weight: 7.9990 chunk 582 optimal weight: 9.9990 chunk 746 optimal weight: 30.0000 chunk 578 optimal weight: 20.0000 chunk 860 optimal weight: 20.0000 chunk 570 optimal weight: 40.0000 chunk 1017 optimal weight: 30.0000 chunk 636 optimal weight: 30.0000 chunk 620 optimal weight: 20.0000 chunk 469 optimal weight: 30.0000 overall best weight: 15.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 26 GLN ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 35 HIS N 62 ASN ** O 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 104 GLN ** P 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 114 ASN ** T 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 ASN ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 35 GLN 6 37 GLN ** 7 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 10 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 10 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 13 75 GLN ** 16 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 16 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 18 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 20 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 23 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 25 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.112 161950 Z= 0.430 Angle : 0.759 17.023 242116 Z= 0.387 Chirality : 0.040 0.316 30939 Planarity : 0.006 0.064 13091 Dihedral : 24.319 179.593 80642 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 39.17 Ramachandran Plot: Outliers : 0.90 % Allowed : 10.94 % Favored : 88.15 % Rotamer: Outliers : 5.43 % Allowed : 25.30 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.11), residues: 5985 helix: -0.46 (0.11), residues: 1995 sheet: -2.26 (0.14), residues: 1110 loop : -1.54 (0.12), residues: 2880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 78 HIS 0.014 0.002 HIS 1 6 PHE 0.043 0.003 PHE26 36 TYR 0.053 0.003 TYR G 25 ARG 0.015 0.001 ARG 9 46 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11970 Ramachandran restraints generated. 5985 Oldfield, 0 Emsley, 5985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11970 Ramachandran restraints generated. 5985 Oldfield, 0 Emsley, 5985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1317 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 270 poor density : 1047 time to evaluate : 6.443 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: D 188 MET cc_start: 0.8779 (mpp) cc_final: 0.8433 (mpp) REVERT: E 25 MET cc_start: 0.9442 (mmm) cc_final: 0.8724 (tpp) REVERT: E 51 ASN cc_start: 0.9555 (m110) cc_final: 0.9335 (m-40) REVERT: E 173 ASP cc_start: 0.9191 (OUTLIER) cc_final: 0.8928 (t0) REVERT: G 135 HIS cc_start: 0.8567 (t-90) cc_final: 0.8159 (t-90) REVERT: G 141 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8097 (pptt) REVERT: H 1 MET cc_start: 0.5726 (ttm) cc_final: 0.3646 (tmm) REVERT: H 38 MET cc_start: -0.0081 (mmt) cc_final: -0.0656 (mmp) REVERT: H 94 ARG cc_start: 0.4550 (OUTLIER) cc_final: 0.3870 (mmt-90) REVERT: I 35 MET cc_start: 0.7756 (ptm) cc_final: 0.7132 (mpp) REVERT: J 118 MET cc_start: 0.9018 (ppp) cc_final: 0.8649 (ppp) REVERT: K 4 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8353 (mm-30) REVERT: K 53 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.9008 (mmtt) REVERT: K 73 ASP cc_start: 0.9109 (p0) cc_final: 0.8660 (p0) REVERT: M 1 MET cc_start: 0.7161 (mmm) cc_final: 0.6766 (mmm) REVERT: M 75 GLU cc_start: 0.8204 (tt0) cc_final: 0.7949 (tt0) REVERT: N 5 LYS cc_start: 0.8841 (mmmt) cc_final: 0.8531 (mmmt) REVERT: P 67 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7863 (tm-30) REVERT: P 81 ASP cc_start: 0.9292 (t70) cc_final: 0.9080 (t0) REVERT: P 101 GLU cc_start: 0.8966 (pp20) cc_final: 0.8643 (pp20) REVERT: S 11 ARG cc_start: 0.8749 (mmm160) cc_final: 0.8361 (tpt-90) REVERT: T 1 MET cc_start: 0.5487 (ttt) cc_final: 0.5274 (ttt) REVERT: T 37 ASP cc_start: 0.9124 (p0) cc_final: 0.8741 (p0) REVERT: V 48 MET cc_start: 0.8894 (mmm) cc_final: 0.8524 (mmm) REVERT: Z 46 MET cc_start: 0.9320 (mmm) cc_final: 0.9070 (mmm) REVERT: 2 27 LEU cc_start: 0.8681 (tp) cc_final: 0.8256 (tp) REVERT: 5 48 MET cc_start: 0.9133 (tpp) cc_final: 0.8910 (tpp) REVERT: 7 67 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.9048 (mm) REVERT: 7 202 ASN cc_start: 0.8142 (p0) cc_final: 0.7764 (p0) REVERT: 10 30 PHE cc_start: 0.8558 (m-80) cc_final: 0.8120 (m-10) REVERT: 10 63 MET cc_start: 0.9125 (OUTLIER) cc_final: 0.8832 (mmm) REVERT: 10 70 MET cc_start: 0.9078 (tpp) cc_final: 0.8839 (tpp) REVERT: 12 102 TRP cc_start: 0.8701 (m-10) cc_final: 0.8379 (m-10) REVERT: 12 115 MET cc_start: 0.9010 (ttt) cc_final: 0.8711 (mtp) REVERT: 14 45 MET cc_start: 0.9627 (ppp) cc_final: 0.9155 (ppp) REVERT: 14 62 LEU cc_start: 0.8638 (mm) cc_final: 0.8208 (mm) REVERT: 15 58 ASN cc_start: 0.9163 (m110) cc_final: 0.8920 (m110) REVERT: 17 61 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8805 (mm-30) REVERT: 18 77 LYS cc_start: 0.9307 (tppt) cc_final: 0.8946 (tppt) REVERT: 18 81 ASP cc_start: 0.9370 (p0) cc_final: 0.9105 (p0) REVERT: 24 28 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8357 (ttmm) REVERT: 24 62 THR cc_start: 0.9420 (OUTLIER) cc_final: 0.8855 (p) REVERT: 24 65 MET cc_start: 0.9192 (ptm) cc_final: 0.8686 (ppp) REVERT: 25 26 MET cc_start: 0.8939 (ppp) cc_final: 0.8652 (ppp) REVERT: 25 60 GLN cc_start: 0.8850 (mm110) cc_final: 0.8647 (mm-40) REVERT: 25 85 LEU cc_start: 0.8726 (pp) cc_final: 0.8399 (tt) outliers start: 270 outliers final: 225 residues processed: 1195 average time/residue: 1.4587 time to fit residues: 3109.3529 Evaluate side-chains 1244 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 1011 time to evaluate : 5.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 110 LYS Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 162 GLN Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 20 ASN Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 173 ASP Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 19 ASN Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 146 ASP Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain G residue 25 TYR Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain G residue 141 LYS Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 56 ASP Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 121 GLU Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 144 GLU Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 9 GLN Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 82 GLU Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 67 ASN Chi-restraints excluded: chain O residue 80 GLU Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 18 SER Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 114 ASN Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 43 GLN Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 69 LEU Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 76 ARG Chi-restraints excluded: chain U residue 26 ASN Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 39 ASN Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 53 GLN Chi-restraints excluded: chain V residue 10 LYS Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain W residue 19 VAL Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain X residue 15 ASN Chi-restraints excluded: chain X residue 48 LEU Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain Y residue 13 GLU Chi-restraints excluded: chain Z residue 2 LYS Chi-restraints excluded: chain Z residue 16 LEU Chi-restraints excluded: chain Z residue 23 LEU Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain 1 residue 18 CYS Chi-restraints excluded: chain 1 residue 24 ILE Chi-restraints excluded: chain 1 residue 27 THR Chi-restraints excluded: chain 1 residue 37 CYS Chi-restraints excluded: chain 1 residue 39 LYS Chi-restraints excluded: chain 1 residue 63 ARG Chi-restraints excluded: chain 1 residue 65 ASN Chi-restraints excluded: chain 2 residue 2 VAL Chi-restraints excluded: chain 2 residue 5 ASN Chi-restraints excluded: chain 2 residue 21 LEU Chi-restraints excluded: chain 2 residue 35 GLU Chi-restraints excluded: chain 2 residue 38 LEU Chi-restraints excluded: chain 2 residue 41 HIS Chi-restraints excluded: chain 2 residue 45 ASP Chi-restraints excluded: chain 2 residue 53 VAL Chi-restraints excluded: chain 3 residue 33 LEU Chi-restraints excluded: chain 4 residue 4 THR Chi-restraints excluded: chain 4 residue 29 GLN Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 4 residue 44 VAL Chi-restraints excluded: chain 5 residue 6 VAL Chi-restraints excluded: chain 5 residue 27 ASN Chi-restraints excluded: chain 5 residue 50 SER Chi-restraints excluded: chain 5 residue 53 ASP Chi-restraints excluded: chain 6 residue 26 ILE Chi-restraints excluded: chain 7 residue 15 PHE Chi-restraints excluded: chain 7 residue 19 THR Chi-restraints excluded: chain 7 residue 66 ILE Chi-restraints excluded: chain 7 residue 67 LEU Chi-restraints excluded: chain 7 residue 141 GLU Chi-restraints excluded: chain 7 residue 160 LEU Chi-restraints excluded: chain 7 residue 163 ILE Chi-restraints excluded: chain 7 residue 166 ASP Chi-restraints excluded: chain 7 residue 185 ILE Chi-restraints excluded: chain 7 residue 204 ASP Chi-restraints excluded: chain 7 residue 224 ARG Chi-restraints excluded: chain 8 residue 7 ASN Chi-restraints excluded: chain 8 residue 51 VAL Chi-restraints excluded: chain 8 residue 82 ASP Chi-restraints excluded: chain 8 residue 92 ASP Chi-restraints excluded: chain 8 residue 101 ASN Chi-restraints excluded: chain 8 residue 122 GLN Chi-restraints excluded: chain 8 residue 150 VAL Chi-restraints excluded: chain 8 residue 180 ASP Chi-restraints excluded: chain 8 residue 199 VAL Chi-restraints excluded: chain 9 residue 4 LEU Chi-restraints excluded: chain 9 residue 16 THR Chi-restraints excluded: chain 9 residue 34 GLU Chi-restraints excluded: chain 9 residue 52 VAL Chi-restraints excluded: chain 9 residue 98 ASP Chi-restraints excluded: chain 9 residue 125 ASN Chi-restraints excluded: chain 10 residue 29 ILE Chi-restraints excluded: chain 10 residue 63 MET Chi-restraints excluded: chain 10 residue 75 LEU Chi-restraints excluded: chain 10 residue 100 GLU Chi-restraints excluded: chain 11 residue 6 ILE Chi-restraints excluded: chain 11 residue 13 ASP Chi-restraints excluded: chain 11 residue 21 MET Chi-restraints excluded: chain 11 residue 36 ILE Chi-restraints excluded: chain 11 residue 47 LEU Chi-restraints excluded: chain 11 residue 96 VAL Chi-restraints excluded: chain 12 residue 5 VAL Chi-restraints excluded: chain 12 residue 48 THR Chi-restraints excluded: chain 12 residue 71 THR Chi-restraints excluded: chain 12 residue 103 ILE Chi-restraints excluded: chain 13 residue 100 ILE Chi-restraints excluded: chain 13 residue 103 VAL Chi-restraints excluded: chain 14 residue 5 TYR Chi-restraints excluded: chain 14 residue 26 LYS Chi-restraints excluded: chain 14 residue 34 LEU Chi-restraints excluded: chain 14 residue 61 ASP Chi-restraints excluded: chain 14 residue 71 ILE Chi-restraints excluded: chain 14 residue 86 LEU Chi-restraints excluded: chain 14 residue 115 VAL Chi-restraints excluded: chain 15 residue 17 LEU Chi-restraints excluded: chain 15 residue 22 THR Chi-restraints excluded: chain 15 residue 24 GLU Chi-restraints excluded: chain 15 residue 36 VAL Chi-restraints excluded: chain 15 residue 51 VAL Chi-restraints excluded: chain 15 residue 101 SER Chi-restraints excluded: chain 16 residue 30 ILE Chi-restraints excluded: chain 16 residue 31 VAL Chi-restraints excluded: chain 16 residue 45 THR Chi-restraints excluded: chain 16 residue 64 VAL Chi-restraints excluded: chain 16 residue 67 GLU Chi-restraints excluded: chain 16 residue 81 LEU Chi-restraints excluded: chain 16 residue 99 LEU Chi-restraints excluded: chain 17 residue 19 ASN Chi-restraints excluded: chain 17 residue 34 THR Chi-restraints excluded: chain 17 residue 40 THR Chi-restraints excluded: chain 18 residue 8 ILE Chi-restraints excluded: chain 18 residue 11 HIS Chi-restraints excluded: chain 18 residue 24 VAL Chi-restraints excluded: chain 18 residue 101 THR Chi-restraints excluded: chain 18 residue 103 THR Chi-restraints excluded: chain 19 residue 13 VAL Chi-restraints excluded: chain 19 residue 17 ASP Chi-restraints excluded: chain 19 residue 34 ASN Chi-restraints excluded: chain 20 residue 84 LEU Chi-restraints excluded: chain 21 residue 1 MET Chi-restraints excluded: chain 22 residue 6 THR Chi-restraints excluded: chain 22 residue 19 SER Chi-restraints excluded: chain 22 residue 28 VAL Chi-restraints excluded: chain 22 residue 32 ILE Chi-restraints excluded: chain 22 residue 37 ILE Chi-restraints excluded: chain 22 residue 52 CYS Chi-restraints excluded: chain 22 residue 56 ASP Chi-restraints excluded: chain 22 residue 61 ARG Chi-restraints excluded: chain 23 residue 17 VAL Chi-restraints excluded: chain 23 residue 24 ASP Chi-restraints excluded: chain 23 residue 29 LYS Chi-restraints excluded: chain 23 residue 30 ASN Chi-restraints excluded: chain 24 residue 14 LEU Chi-restraints excluded: chain 24 residue 28 LYS Chi-restraints excluded: chain 24 residue 31 ARG Chi-restraints excluded: chain 24 residue 62 THR Chi-restraints excluded: chain 25 residue 9 ARG Chi-restraints excluded: chain 25 residue 38 ILE Chi-restraints excluded: chain 25 residue 56 ILE Chi-restraints excluded: chain 26 residue 18 PHE Chi-restraints excluded: chain 26 residue 42 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1056 random chunks: chunk 629 optimal weight: 30.0000 chunk 406 optimal weight: 0.9980 chunk 607 optimal weight: 30.0000 chunk 306 optimal weight: 40.0000 chunk 199 optimal weight: 8.9990 chunk 197 optimal weight: 10.0000 chunk 647 optimal weight: 20.0000 chunk 693 optimal weight: 20.0000 chunk 503 optimal weight: 7.9990 chunk 94 optimal weight: 9.9990 chunk 800 optimal weight: 20.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN ** B 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN L 35 HIS N 62 ASN ** O 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 104 GLN ** P 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 114 ASN ** V 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 19 HIS ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 10 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 10 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 16 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 18 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 20 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 23 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 25 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.4231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 161950 Z= 0.248 Angle : 0.676 15.188 242116 Z= 0.343 Chirality : 0.036 0.318 30939 Planarity : 0.005 0.082 13091 Dihedral : 24.345 179.544 80642 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 30.60 Ramachandran Plot: Outliers : 0.84 % Allowed : 9.46 % Favored : 89.71 % Rotamer: Outliers : 4.73 % Allowed : 26.25 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.11), residues: 5985 helix: -0.37 (0.11), residues: 2003 sheet: -2.14 (0.14), residues: 1135 loop : -1.51 (0.12), residues: 2847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP D 78 HIS 0.017 0.002 HIS J 80 PHE 0.029 0.002 PHE13 44 TYR 0.051 0.002 TYR 7 212 ARG 0.012 0.001 ARG P 112 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11970 Ramachandran restraints generated. 5985 Oldfield, 0 Emsley, 5985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11970 Ramachandran restraints generated. 5985 Oldfield, 0 Emsley, 5985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1336 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 1101 time to evaluate : 6.486 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: B 23 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8658 (mm) REVERT: B 59 GLN cc_start: 0.8772 (pt0) cc_final: 0.8472 (pt0) REVERT: D 188 MET cc_start: 0.8778 (mpp) cc_final: 0.8427 (mpp) REVERT: E 25 MET cc_start: 0.9397 (mmm) cc_final: 0.8793 (tpp) REVERT: E 51 ASN cc_start: 0.9558 (m110) cc_final: 0.9342 (m-40) REVERT: F 73 SER cc_start: 0.8925 (t) cc_final: 0.8633 (p) REVERT: G 51 ARG cc_start: 0.8770 (mtt-85) cc_final: 0.8322 (ptp-110) REVERT: G 135 HIS cc_start: 0.8579 (t-90) cc_final: 0.8162 (t-90) REVERT: G 141 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8107 (pptt) REVERT: H 1 MET cc_start: 0.5825 (ttm) cc_final: 0.3827 (tmm) REVERT: H 38 MET cc_start: -0.0288 (mmt) cc_final: -0.0881 (mmp) REVERT: H 94 ARG cc_start: 0.4492 (OUTLIER) cc_final: 0.3760 (mmt-90) REVERT: I 35 MET cc_start: 0.7706 (ptm) cc_final: 0.7223 (mpp) REVERT: J 118 MET cc_start: 0.8943 (ppp) cc_final: 0.8691 (ppp) REVERT: K 4 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8399 (mm-30) REVERT: K 5 GLN cc_start: 0.7629 (pt0) cc_final: 0.7149 (pt0) REVERT: K 53 LYS cc_start: 0.9203 (OUTLIER) cc_final: 0.8998 (mmtt) REVERT: K 73 ASP cc_start: 0.9052 (p0) cc_final: 0.8570 (p0) REVERT: M 75 GLU cc_start: 0.8123 (tt0) cc_final: 0.7889 (tt0) REVERT: P 67 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7679 (tm-30) REVERT: P 81 ASP cc_start: 0.9273 (t70) cc_final: 0.9065 (t0) REVERT: P 101 GLU cc_start: 0.8944 (pp20) cc_final: 0.8631 (pp20) REVERT: R 74 ILE cc_start: 0.8825 (mp) cc_final: 0.8489 (mm) REVERT: S 11 ARG cc_start: 0.8699 (mmm160) cc_final: 0.8314 (tpt-90) REVERT: S 69 LEU cc_start: 0.8819 (tp) cc_final: 0.8401 (mm) REVERT: T 1 MET cc_start: 0.5175 (ttt) cc_final: 0.4940 (ttt) REVERT: T 25 GLU cc_start: 0.8757 (pp20) cc_final: 0.8319 (pp20) REVERT: T 37 ASP cc_start: 0.9052 (p0) cc_final: 0.8697 (p0) REVERT: V 48 MET cc_start: 0.8922 (mmm) cc_final: 0.8543 (mmm) REVERT: X 13 THR cc_start: 0.8962 (p) cc_final: 0.8755 (t) REVERT: Z 46 MET cc_start: 0.9318 (mmm) cc_final: 0.9029 (mmm) REVERT: 3 24 LYS cc_start: 0.9071 (ptmm) cc_final: 0.7962 (ptmm) REVERT: 3 34 GLU cc_start: 0.8575 (mm-30) cc_final: 0.7817 (mm-30) REVERT: 7 67 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8891 (mm) REVERT: 7 90 PHE cc_start: 0.8607 (p90) cc_final: 0.8365 (p90) REVERT: 7 153 MET cc_start: 0.8262 (mmm) cc_final: 0.7680 (mmm) REVERT: 7 168 GLU cc_start: 0.8722 (mp0) cc_final: 0.8397 (mp0) REVERT: 7 183 PHE cc_start: 0.7963 (m-10) cc_final: 0.7308 (m-80) REVERT: 7 202 ASN cc_start: 0.8096 (p0) cc_final: 0.7707 (p0) REVERT: 9 123 MET cc_start: 0.8552 (mmp) cc_final: 0.8263 (mmm) REVERT: 10 30 PHE cc_start: 0.8551 (m-80) cc_final: 0.8195 (m-80) REVERT: 10 70 MET cc_start: 0.9042 (tpp) cc_final: 0.8841 (tpp) REVERT: 12 102 TRP cc_start: 0.8637 (m-10) cc_final: 0.8262 (m-10) REVERT: 12 115 MET cc_start: 0.8987 (ttt) cc_final: 0.8659 (mtp) REVERT: 14 45 MET cc_start: 0.9622 (ppp) cc_final: 0.9126 (ppp) REVERT: 14 62 LEU cc_start: 0.8623 (mm) cc_final: 0.8210 (mm) REVERT: 15 58 ASN cc_start: 0.9159 (m110) cc_final: 0.8940 (m110) REVERT: 17 61 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8725 (mm-30) REVERT: 18 8 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.8254 (mp) REVERT: 18 77 LYS cc_start: 0.9290 (tppt) cc_final: 0.8850 (tppt) REVERT: 18 81 ASP cc_start: 0.9337 (p0) cc_final: 0.9133 (p0) REVERT: 24 28 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.7886 (ttmt) REVERT: 24 62 THR cc_start: 0.9398 (OUTLIER) cc_final: 0.8870 (p) REVERT: 24 65 MET cc_start: 0.9164 (ptm) cc_final: 0.8739 (ppp) REVERT: 25 60 GLN cc_start: 0.8751 (mm110) cc_final: 0.8524 (mm-40) REVERT: 25 85 LEU cc_start: 0.8716 (pp) cc_final: 0.8370 (tt) outliers start: 235 outliers final: 188 residues processed: 1231 average time/residue: 1.3450 time to fit residues: 2952.9117 Evaluate side-chains 1233 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 1037 time to evaluate : 6.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 110 LYS Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 19 ASN Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 146 ASP Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain G residue 46 PHE Chi-restraints excluded: chain G residue 141 LYS Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 67 ASN Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 56 ASP Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 121 GLU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 144 GLU Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 9 GLN Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 67 ASN Chi-restraints excluded: chain O residue 80 GLU Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 18 SER Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 113 LEU Chi-restraints excluded: chain P residue 114 ASN Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 43 GLN Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 76 ARG Chi-restraints excluded: chain U residue 26 ASN Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 39 ASN Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain V residue 10 LYS Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain W residue 19 VAL Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 66 GLU Chi-restraints excluded: chain X residue 48 LEU Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 69 GLU Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 18 CYS Chi-restraints excluded: chain 1 residue 37 CYS Chi-restraints excluded: chain 1 residue 63 ARG Chi-restraints excluded: chain 1 residue 65 ASN Chi-restraints excluded: chain 2 residue 2 VAL Chi-restraints excluded: chain 2 residue 5 ASN Chi-restraints excluded: chain 2 residue 21 LEU Chi-restraints excluded: chain 2 residue 35 GLU Chi-restraints excluded: chain 2 residue 41 HIS Chi-restraints excluded: chain 2 residue 45 ASP Chi-restraints excluded: chain 2 residue 53 VAL Chi-restraints excluded: chain 3 residue 33 LEU Chi-restraints excluded: chain 4 residue 4 THR Chi-restraints excluded: chain 4 residue 29 GLN Chi-restraints excluded: chain 4 residue 44 VAL Chi-restraints excluded: chain 5 residue 6 VAL Chi-restraints excluded: chain 5 residue 27 ASN Chi-restraints excluded: chain 5 residue 28 LEU Chi-restraints excluded: chain 5 residue 53 ASP Chi-restraints excluded: chain 7 residue 15 PHE Chi-restraints excluded: chain 7 residue 19 THR Chi-restraints excluded: chain 7 residue 39 ILE Chi-restraints excluded: chain 7 residue 66 ILE Chi-restraints excluded: chain 7 residue 67 LEU Chi-restraints excluded: chain 7 residue 140 LEU Chi-restraints excluded: chain 7 residue 160 LEU Chi-restraints excluded: chain 7 residue 163 ILE Chi-restraints excluded: chain 7 residue 166 ASP Chi-restraints excluded: chain 7 residue 204 ASP Chi-restraints excluded: chain 7 residue 224 ARG Chi-restraints excluded: chain 8 residue 51 VAL Chi-restraints excluded: chain 8 residue 92 ASP Chi-restraints excluded: chain 8 residue 101 ASN Chi-restraints excluded: chain 8 residue 122 GLN Chi-restraints excluded: chain 8 residue 180 ASP Chi-restraints excluded: chain 8 residue 199 VAL Chi-restraints excluded: chain 9 residue 4 LEU Chi-restraints excluded: chain 9 residue 16 THR Chi-restraints excluded: chain 9 residue 34 GLU Chi-restraints excluded: chain 9 residue 52 VAL Chi-restraints excluded: chain 9 residue 98 ASP Chi-restraints excluded: chain 9 residue 125 ASN Chi-restraints excluded: chain 10 residue 29 ILE Chi-restraints excluded: chain 10 residue 63 MET Chi-restraints excluded: chain 10 residue 75 LEU Chi-restraints excluded: chain 11 residue 6 ILE Chi-restraints excluded: chain 11 residue 13 ASP Chi-restraints excluded: chain 11 residue 21 MET Chi-restraints excluded: chain 11 residue 92 THR Chi-restraints excluded: chain 11 residue 94 HIS Chi-restraints excluded: chain 12 residue 5 VAL Chi-restraints excluded: chain 12 residue 48 THR Chi-restraints excluded: chain 12 residue 71 THR Chi-restraints excluded: chain 12 residue 103 ILE Chi-restraints excluded: chain 13 residue 47 ASP Chi-restraints excluded: chain 13 residue 100 ILE Chi-restraints excluded: chain 13 residue 103 VAL Chi-restraints excluded: chain 14 residue 5 TYR Chi-restraints excluded: chain 14 residue 26 LYS Chi-restraints excluded: chain 14 residue 34 LEU Chi-restraints excluded: chain 14 residue 61 ASP Chi-restraints excluded: chain 14 residue 71 ILE Chi-restraints excluded: chain 15 residue 17 LEU Chi-restraints excluded: chain 15 residue 24 GLU Chi-restraints excluded: chain 15 residue 36 VAL Chi-restraints excluded: chain 15 residue 52 LEU Chi-restraints excluded: chain 15 residue 101 SER Chi-restraints excluded: chain 16 residue 30 ILE Chi-restraints excluded: chain 16 residue 31 VAL Chi-restraints excluded: chain 16 residue 45 THR Chi-restraints excluded: chain 16 residue 99 LEU Chi-restraints excluded: chain 17 residue 19 ASN Chi-restraints excluded: chain 17 residue 34 THR Chi-restraints excluded: chain 17 residue 40 THR Chi-restraints excluded: chain 18 residue 8 ILE Chi-restraints excluded: chain 18 residue 24 VAL Chi-restraints excluded: chain 18 residue 82 LEU Chi-restraints excluded: chain 18 residue 101 THR Chi-restraints excluded: chain 18 residue 103 THR Chi-restraints excluded: chain 19 residue 17 ASP Chi-restraints excluded: chain 19 residue 34 ASN Chi-restraints excluded: chain 20 residue 84 LEU Chi-restraints excluded: chain 21 residue 1 MET Chi-restraints excluded: chain 22 residue 6 THR Chi-restraints excluded: chain 22 residue 19 SER Chi-restraints excluded: chain 22 residue 28 VAL Chi-restraints excluded: chain 22 residue 37 ILE Chi-restraints excluded: chain 22 residue 52 CYS Chi-restraints excluded: chain 22 residue 56 ASP Chi-restraints excluded: chain 23 residue 17 VAL Chi-restraints excluded: chain 23 residue 24 ASP Chi-restraints excluded: chain 24 residue 28 LYS Chi-restraints excluded: chain 24 residue 55 GLN Chi-restraints excluded: chain 24 residue 62 THR Chi-restraints excluded: chain 24 residue 78 THR Chi-restraints excluded: chain 25 residue 9 ARG Chi-restraints excluded: chain 26 residue 3 ILE Chi-restraints excluded: chain 26 residue 18 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1056 random chunks: chunk 925 optimal weight: 30.0000 chunk 975 optimal weight: 20.0000 chunk 889 optimal weight: 30.0000 chunk 948 optimal weight: 30.0000 chunk 974 optimal weight: 20.0000 chunk 570 optimal weight: 5.9990 chunk 413 optimal weight: 40.0000 chunk 744 optimal weight: 20.0000 chunk 291 optimal weight: 20.0000 chunk 857 optimal weight: 20.0000 chunk 897 optimal weight: 30.0000 overall best weight: 17.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 35 HIS L 104 GLN N 62 ASN ** O 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 104 GLN P 114 ASN ** V 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 19 HIS ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 10 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 16 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 18 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 20 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 20 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 23 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 24 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 25 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.111 161950 Z= 0.472 Angle : 0.820 17.743 242116 Z= 0.416 Chirality : 0.043 0.346 30939 Planarity : 0.006 0.073 13091 Dihedral : 24.475 179.286 80642 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 44.64 Ramachandran Plot: Outliers : 0.82 % Allowed : 11.41 % Favored : 87.77 % Rotamer: Outliers : 5.39 % Allowed : 25.93 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.11), residues: 5985 helix: -0.66 (0.11), residues: 1983 sheet: -2.28 (0.14), residues: 1103 loop : -1.67 (0.12), residues: 2899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.003 TRP D 78 HIS 0.031 0.002 HIS J 80 PHE 0.041 0.003 PHE R 77 TYR 0.055 0.003 TYR 7 212 ARG 0.023 0.001 ARG16 12 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11970 Ramachandran restraints generated. 5985 Oldfield, 0 Emsley, 5985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11970 Ramachandran restraints generated. 5985 Oldfield, 0 Emsley, 5985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1274 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 268 poor density : 1006 time to evaluate : 6.482 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: B 23 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8709 (mm) REVERT: B 224 MET cc_start: 0.7934 (mmt) cc_final: 0.7466 (mmt) REVERT: D 100 MET cc_start: 0.8695 (mtt) cc_final: 0.8293 (mtt) REVERT: D 188 MET cc_start: 0.8830 (mpp) cc_final: 0.8471 (mpp) REVERT: E 25 MET cc_start: 0.9390 (mmm) cc_final: 0.8762 (tpp) REVERT: E 173 ASP cc_start: 0.9216 (OUTLIER) cc_final: 0.8905 (t0) REVERT: G 135 HIS cc_start: 0.8567 (t-90) cc_final: 0.8179 (t-90) REVERT: G 141 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.7939 (pptt) REVERT: H 1 MET cc_start: 0.5871 (ttm) cc_final: 0.3742 (tmm) REVERT: H 38 MET cc_start: 0.0116 (mmt) cc_final: -0.0881 (mmt) REVERT: H 94 ARG cc_start: 0.4686 (OUTLIER) cc_final: 0.3882 (mmt-90) REVERT: I 35 MET cc_start: 0.7752 (ptm) cc_final: 0.7105 (mpp) REVERT: J 14 ASP cc_start: 0.8392 (p0) cc_final: 0.8133 (p0) REVERT: J 16 TYR cc_start: 0.8698 (m-80) cc_final: 0.8456 (m-80) REVERT: J 67 ASN cc_start: 0.9029 (OUTLIER) cc_final: 0.8689 (p0) REVERT: K 4 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8538 (mm-30) REVERT: K 53 LYS cc_start: 0.9324 (OUTLIER) cc_final: 0.9029 (mmtt) REVERT: K 73 ASP cc_start: 0.9158 (p0) cc_final: 0.8693 (p0) REVERT: M 75 GLU cc_start: 0.8267 (tt0) cc_final: 0.8027 (tt0) REVERT: P 67 GLU cc_start: 0.8259 (tm-30) cc_final: 0.8049 (tm-30) REVERT: P 101 GLU cc_start: 0.8982 (pp20) cc_final: 0.8644 (pp20) REVERT: P 114 ASN cc_start: 0.8202 (OUTLIER) cc_final: 0.7972 (p0) REVERT: R 74 ILE cc_start: 0.8881 (mp) cc_final: 0.8469 (mm) REVERT: S 11 ARG cc_start: 0.8779 (mmm160) cc_final: 0.8410 (tpt-90) REVERT: T 1 MET cc_start: 0.5633 (ttt) cc_final: 0.5051 (ttt) REVERT: T 37 ASP cc_start: 0.9167 (p0) cc_final: 0.8795 (p0) REVERT: V 48 MET cc_start: 0.8939 (mmm) cc_final: 0.8626 (mmm) REVERT: X 67 LEU cc_start: 0.9325 (mm) cc_final: 0.9112 (tp) REVERT: 3 6 GLU cc_start: 0.8670 (pm20) cc_final: 0.8428 (pm20) REVERT: 3 24 LYS cc_start: 0.8677 (ptmm) cc_final: 0.8380 (pptt) REVERT: 3 26 LYS cc_start: 0.9436 (mmmt) cc_final: 0.9132 (mmtp) REVERT: 3 32 LYS cc_start: 0.9054 (mmmm) cc_final: 0.8758 (mmmm) REVERT: 7 67 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8940 (mm) REVERT: 7 90 PHE cc_start: 0.8581 (p90) cc_final: 0.8357 (p90) REVERT: 7 153 MET cc_start: 0.8378 (mmm) cc_final: 0.7988 (mmm) REVERT: 7 168 GLU cc_start: 0.8773 (mp0) cc_final: 0.8462 (mp0) REVERT: 10 30 PHE cc_start: 0.8612 (m-80) cc_final: 0.8347 (m-80) REVERT: 12 102 TRP cc_start: 0.8741 (m-10) cc_final: 0.8436 (m-10) REVERT: 14 45 MET cc_start: 0.9671 (OUTLIER) cc_final: 0.9243 (ppp) REVERT: 14 87 MET cc_start: 0.9321 (ppp) cc_final: 0.8932 (ppp) REVERT: 15 58 ASN cc_start: 0.9208 (m110) cc_final: 0.8990 (m110) REVERT: 17 61 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8745 (mm-30) REVERT: 18 77 LYS cc_start: 0.9347 (tppt) cc_final: 0.8958 (tppt) REVERT: 18 81 ASP cc_start: 0.9344 (p0) cc_final: 0.9100 (p0) REVERT: 24 28 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8329 (ttmt) REVERT: 24 62 THR cc_start: 0.9464 (OUTLIER) cc_final: 0.8874 (p) REVERT: 24 65 MET cc_start: 0.9182 (ptm) cc_final: 0.8692 (ppp) REVERT: 25 26 MET cc_start: 0.8941 (ppp) cc_final: 0.8672 (ppp) REVERT: 25 85 LEU cc_start: 0.8776 (pp) cc_final: 0.8376 (tt) outliers start: 268 outliers final: 227 residues processed: 1163 average time/residue: 1.3044 time to fit residues: 2695.8802 Evaluate side-chains 1223 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 985 time to evaluate : 6.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 110 LYS Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 162 GLN Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 20 ASN Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 173 ASP Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 19 ASN Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 146 ASP Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain G residue 46 PHE Chi-restraints excluded: chain G residue 141 LYS Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 67 ASN Chi-restraints excluded: chain J residue 91 GLU Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 56 ASP Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 121 GLU Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 144 GLU Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 82 GLU Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 67 ASN Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain O residue 80 GLU Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 10 GLU Chi-restraints excluded: chain P residue 18 SER Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 114 ASN Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 43 GLN Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 76 ARG Chi-restraints excluded: chain U residue 26 ASN Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 39 ASN Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 53 GLN Chi-restraints excluded: chain V residue 10 LYS Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain W residue 19 VAL Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain W residue 46 ASN Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 66 GLU Chi-restraints excluded: chain W residue 72 ASN Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain X residue 48 LEU Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 69 GLU Chi-restraints excluded: chain Z residue 2 LYS Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 18 CYS Chi-restraints excluded: chain 1 residue 24 ILE Chi-restraints excluded: chain 1 residue 27 THR Chi-restraints excluded: chain 1 residue 34 LEU Chi-restraints excluded: chain 1 residue 37 CYS Chi-restraints excluded: chain 1 residue 63 ARG Chi-restraints excluded: chain 1 residue 65 ASN Chi-restraints excluded: chain 2 residue 2 VAL Chi-restraints excluded: chain 2 residue 5 ASN Chi-restraints excluded: chain 2 residue 21 LEU Chi-restraints excluded: chain 2 residue 35 GLU Chi-restraints excluded: chain 2 residue 41 HIS Chi-restraints excluded: chain 2 residue 45 ASP Chi-restraints excluded: chain 2 residue 53 VAL Chi-restraints excluded: chain 3 residue 11 VAL Chi-restraints excluded: chain 3 residue 33 LEU Chi-restraints excluded: chain 4 residue 4 THR Chi-restraints excluded: chain 4 residue 29 GLN Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 4 residue 44 VAL Chi-restraints excluded: chain 5 residue 6 VAL Chi-restraints excluded: chain 5 residue 27 ASN Chi-restraints excluded: chain 5 residue 53 ASP Chi-restraints excluded: chain 6 residue 26 ILE Chi-restraints excluded: chain 7 residue 15 PHE Chi-restraints excluded: chain 7 residue 19 THR Chi-restraints excluded: chain 7 residue 39 ILE Chi-restraints excluded: chain 7 residue 66 ILE Chi-restraints excluded: chain 7 residue 67 LEU Chi-restraints excluded: chain 7 residue 140 LEU Chi-restraints excluded: chain 7 residue 160 LEU Chi-restraints excluded: chain 7 residue 163 ILE Chi-restraints excluded: chain 7 residue 166 ASP Chi-restraints excluded: chain 7 residue 198 VAL Chi-restraints excluded: chain 7 residue 204 ASP Chi-restraints excluded: chain 7 residue 224 ARG Chi-restraints excluded: chain 8 residue 7 ASN Chi-restraints excluded: chain 8 residue 51 VAL Chi-restraints excluded: chain 8 residue 92 ASP Chi-restraints excluded: chain 8 residue 101 ASN Chi-restraints excluded: chain 8 residue 122 GLN Chi-restraints excluded: chain 8 residue 150 VAL Chi-restraints excluded: chain 8 residue 180 ASP Chi-restraints excluded: chain 8 residue 189 HIS Chi-restraints excluded: chain 8 residue 199 VAL Chi-restraints excluded: chain 9 residue 4 LEU Chi-restraints excluded: chain 9 residue 16 THR Chi-restraints excluded: chain 9 residue 34 GLU Chi-restraints excluded: chain 9 residue 52 VAL Chi-restraints excluded: chain 9 residue 98 ASP Chi-restraints excluded: chain 9 residue 125 ASN Chi-restraints excluded: chain 10 residue 29 ILE Chi-restraints excluded: chain 10 residue 63 MET Chi-restraints excluded: chain 10 residue 75 LEU Chi-restraints excluded: chain 10 residue 100 GLU Chi-restraints excluded: chain 10 residue 140 ILE Chi-restraints excluded: chain 11 residue 6 ILE Chi-restraints excluded: chain 11 residue 13 ASP Chi-restraints excluded: chain 11 residue 30 THR Chi-restraints excluded: chain 11 residue 47 LEU Chi-restraints excluded: chain 11 residue 92 THR Chi-restraints excluded: chain 11 residue 94 HIS Chi-restraints excluded: chain 12 residue 5 VAL Chi-restraints excluded: chain 12 residue 48 THR Chi-restraints excluded: chain 12 residue 71 THR Chi-restraints excluded: chain 12 residue 103 ILE Chi-restraints excluded: chain 13 residue 100 ILE Chi-restraints excluded: chain 13 residue 103 VAL Chi-restraints excluded: chain 14 residue 5 TYR Chi-restraints excluded: chain 14 residue 26 LYS Chi-restraints excluded: chain 14 residue 34 LEU Chi-restraints excluded: chain 14 residue 45 MET Chi-restraints excluded: chain 14 residue 61 ASP Chi-restraints excluded: chain 14 residue 71 ILE Chi-restraints excluded: chain 14 residue 86 LEU Chi-restraints excluded: chain 14 residue 115 VAL Chi-restraints excluded: chain 15 residue 17 LEU Chi-restraints excluded: chain 15 residue 22 THR Chi-restraints excluded: chain 15 residue 24 GLU Chi-restraints excluded: chain 15 residue 36 VAL Chi-restraints excluded: chain 15 residue 101 SER Chi-restraints excluded: chain 16 residue 14 GLN Chi-restraints excluded: chain 16 residue 30 ILE Chi-restraints excluded: chain 16 residue 31 VAL Chi-restraints excluded: chain 16 residue 45 THR Chi-restraints excluded: chain 16 residue 67 GLU Chi-restraints excluded: chain 16 residue 81 LEU Chi-restraints excluded: chain 16 residue 96 ILE Chi-restraints excluded: chain 16 residue 99 LEU Chi-restraints excluded: chain 17 residue 19 ASN Chi-restraints excluded: chain 17 residue 34 THR Chi-restraints excluded: chain 17 residue 40 THR Chi-restraints excluded: chain 18 residue 8 ILE Chi-restraints excluded: chain 18 residue 11 HIS Chi-restraints excluded: chain 18 residue 24 VAL Chi-restraints excluded: chain 18 residue 82 LEU Chi-restraints excluded: chain 18 residue 101 THR Chi-restraints excluded: chain 18 residue 103 THR Chi-restraints excluded: chain 19 residue 17 ASP Chi-restraints excluded: chain 19 residue 34 ASN Chi-restraints excluded: chain 20 residue 84 LEU Chi-restraints excluded: chain 21 residue 1 MET Chi-restraints excluded: chain 22 residue 6 THR Chi-restraints excluded: chain 22 residue 17 GLU Chi-restraints excluded: chain 22 residue 19 SER Chi-restraints excluded: chain 22 residue 28 VAL Chi-restraints excluded: chain 22 residue 32 ILE Chi-restraints excluded: chain 22 residue 37 ILE Chi-restraints excluded: chain 22 residue 52 CYS Chi-restraints excluded: chain 22 residue 56 ASP Chi-restraints excluded: chain 22 residue 61 ARG Chi-restraints excluded: chain 23 residue 17 VAL Chi-restraints excluded: chain 23 residue 24 ASP Chi-restraints excluded: chain 23 residue 70 THR Chi-restraints excluded: chain 24 residue 14 LEU Chi-restraints excluded: chain 24 residue 28 LYS Chi-restraints excluded: chain 24 residue 55 GLN Chi-restraints excluded: chain 24 residue 62 THR Chi-restraints excluded: chain 24 residue 70 LEU Chi-restraints excluded: chain 24 residue 78 THR Chi-restraints excluded: chain 25 residue 9 ARG Chi-restraints excluded: chain 25 residue 12 GLN Chi-restraints excluded: chain 25 residue 38 ILE Chi-restraints excluded: chain 26 residue 3 ILE Chi-restraints excluded: chain 26 residue 5 VAL Chi-restraints excluded: chain 26 residue 12 ASP Chi-restraints excluded: chain 26 residue 18 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1056 random chunks: chunk 945 optimal weight: 20.0000 chunk 622 optimal weight: 20.0000 chunk 1002 optimal weight: 20.0000 chunk 612 optimal weight: 20.0000 chunk 475 optimal weight: 8.9990 chunk 697 optimal weight: 20.0000 chunk 1052 optimal weight: 40.0000 chunk 968 optimal weight: 20.0000 chunk 837 optimal weight: 20.0000 chunk 86 optimal weight: 6.9990 chunk 647 optimal weight: 20.0000 overall best weight: 15.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 104 GLN P 114 ASN ** V 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 19 HIS ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 50 ASN ** 7 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 10 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 16 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 18 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 19 3 GLN ** 20 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 23 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 25 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.098 161950 Z= 0.416 Angle : 0.782 16.256 242116 Z= 0.397 Chirality : 0.041 0.362 30939 Planarity : 0.006 0.086 13091 Dihedral : 24.593 179.175 80642 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 41.40 Ramachandran Plot: Outliers : 0.82 % Allowed : 11.09 % Favored : 88.09 % Rotamer: Outliers : 5.15 % Allowed : 26.27 % Favored : 68.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.10), residues: 5985 helix: -0.72 (0.11), residues: 1986 sheet: -2.22 (0.14), residues: 1122 loop : -1.74 (0.12), residues: 2877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.003 TRP D 78 HIS 0.011 0.002 HIS 1 6 PHE 0.032 0.003 PHE R 53 TYR 0.058 0.003 TYR 7 212 ARG 0.017 0.001 ARG P 112 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11970 Ramachandran restraints generated. 5985 Oldfield, 0 Emsley, 5985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11970 Ramachandran restraints generated. 5985 Oldfield, 0 Emsley, 5985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1266 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 256 poor density : 1010 time to evaluate : 6.348 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: A 621 ILE cc_start: 0.6676 (mm) cc_final: 0.6444 (mm) REVERT: B 23 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8826 (mm) REVERT: B 224 MET cc_start: 0.7939 (mmt) cc_final: 0.7490 (mmt) REVERT: D 100 MET cc_start: 0.8677 (mtt) cc_final: 0.8314 (mtt) REVERT: D 188 MET cc_start: 0.8823 (mpp) cc_final: 0.8446 (mpp) REVERT: E 25 MET cc_start: 0.9390 (mmm) cc_final: 0.8759 (tpp) REVERT: E 37 MET cc_start: 0.9293 (mmm) cc_final: 0.9087 (mmm) REVERT: E 173 ASP cc_start: 0.9205 (OUTLIER) cc_final: 0.8912 (t0) REVERT: F 73 SER cc_start: 0.8875 (t) cc_final: 0.8616 (p) REVERT: G 135 HIS cc_start: 0.8560 (t-90) cc_final: 0.8172 (t-90) REVERT: G 141 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.7960 (pptt) REVERT: H 1 MET cc_start: 0.5875 (ttm) cc_final: 0.3752 (tmm) REVERT: H 38 MET cc_start: -0.0061 (mmt) cc_final: -0.1107 (mmt) REVERT: H 94 ARG cc_start: 0.4550 (OUTLIER) cc_final: 0.3765 (mmt-90) REVERT: I 35 MET cc_start: 0.7767 (ptm) cc_final: 0.7165 (mpp) REVERT: J 67 ASN cc_start: 0.8994 (OUTLIER) cc_final: 0.8677 (p0) REVERT: J 80 HIS cc_start: 0.8020 (t70) cc_final: 0.7800 (t70) REVERT: K 4 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8517 (mm-30) REVERT: K 53 LYS cc_start: 0.9296 (OUTLIER) cc_final: 0.8985 (mmtm) REVERT: K 73 ASP cc_start: 0.9114 (p0) cc_final: 0.8607 (p0) REVERT: M 75 GLU cc_start: 0.8226 (tt0) cc_final: 0.7981 (tt0) REVERT: P 67 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7910 (tm-30) REVERT: P 101 GLU cc_start: 0.8998 (pp20) cc_final: 0.8639 (pp20) REVERT: R 74 ILE cc_start: 0.8887 (mp) cc_final: 0.8478 (mm) REVERT: S 11 ARG cc_start: 0.8787 (mmm160) cc_final: 0.8400 (tpt-90) REVERT: T 1 MET cc_start: 0.5711 (ttt) cc_final: 0.5293 (ttt) REVERT: T 37 ASP cc_start: 0.9133 (p0) cc_final: 0.8774 (p0) REVERT: V 48 MET cc_start: 0.8951 (mmm) cc_final: 0.8700 (mmm) REVERT: X 10 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.8765 (ptm-80) REVERT: Z 46 MET cc_start: 0.9332 (mmm) cc_final: 0.8988 (mmm) REVERT: 7 67 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8946 (mm) REVERT: 7 90 PHE cc_start: 0.8612 (p90) cc_final: 0.8308 (p90) REVERT: 7 153 MET cc_start: 0.8316 (mmm) cc_final: 0.7797 (mmm) REVERT: 7 183 PHE cc_start: 0.7799 (m-80) cc_final: 0.7102 (m-80) REVERT: 11 21 MET cc_start: 0.8769 (ptp) cc_final: 0.8424 (ptp) REVERT: 11 25 TYR cc_start: 0.8306 (m-80) cc_final: 0.8017 (m-80) REVERT: 12 30 MET cc_start: 0.8720 (ttp) cc_final: 0.8488 (tpp) REVERT: 12 102 TRP cc_start: 0.8693 (m-10) cc_final: 0.8413 (m-10) REVERT: 12 115 MET cc_start: 0.8953 (ttt) cc_final: 0.8542 (mtp) REVERT: 13 47 ASP cc_start: 0.7503 (OUTLIER) cc_final: 0.7295 (p0) REVERT: 14 45 MET cc_start: 0.9678 (OUTLIER) cc_final: 0.9256 (ppp) REVERT: 14 87 MET cc_start: 0.9322 (ppp) cc_final: 0.9032 (ppp) REVERT: 15 58 ASN cc_start: 0.9167 (m110) cc_final: 0.8952 (m110) REVERT: 17 61 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8739 (mm-30) REVERT: 18 77 LYS cc_start: 0.9333 (tppt) cc_final: 0.8926 (tppt) REVERT: 18 81 ASP cc_start: 0.9342 (p0) cc_final: 0.9083 (p0) REVERT: 24 28 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8313 (ttmt) REVERT: 24 62 THR cc_start: 0.9408 (OUTLIER) cc_final: 0.8798 (p) REVERT: 24 65 MET cc_start: 0.9143 (ptm) cc_final: 0.8728 (ppp) REVERT: 25 85 LEU cc_start: 0.8796 (pp) cc_final: 0.8365 (tt) outliers start: 256 outliers final: 222 residues processed: 1155 average time/residue: 1.2693 time to fit residues: 2601.6492 Evaluate side-chains 1215 residues out of total 4972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 981 time to evaluate : 6.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 616 ILE Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 686 ILE Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 110 LYS Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 165 MET Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 116 ASP Chi-restraints excluded: chain D residue 148 ILE Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 20 ASN Chi-restraints excluded: chain E residue 22 ASN Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 173 ASP Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 19 ASN Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 146 ASP Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 40 THR Chi-restraints excluded: chain G residue 43 ASN Chi-restraints excluded: chain G residue 46 PHE Chi-restraints excluded: chain G residue 141 LYS Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 41 PHE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 67 ASN Chi-restraints excluded: chain J residue 103 ILE Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 56 ASP Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 144 GLU Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 126 ILE Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 67 ASN Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain O residue 80 GLU Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain P residue 10 GLU Chi-restraints excluded: chain P residue 18 SER Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 113 LEU Chi-restraints excluded: chain Q residue 33 VAL Chi-restraints excluded: chain Q residue 43 GLN Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 76 ARG Chi-restraints excluded: chain U residue 26 ASN Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 39 ASN Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 53 GLN Chi-restraints excluded: chain V residue 10 LYS Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain W residue 19 VAL Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain W residue 46 ASN Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 66 GLU Chi-restraints excluded: chain W residue 72 ASN Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain X residue 10 ARG Chi-restraints excluded: chain X residue 15 ASN Chi-restraints excluded: chain X residue 48 LEU Chi-restraints excluded: chain X residue 57 VAL Chi-restraints excluded: chain X residue 69 GLU Chi-restraints excluded: chain Z residue 2 LYS Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 1 residue 18 CYS Chi-restraints excluded: chain 1 residue 24 ILE Chi-restraints excluded: chain 1 residue 34 LEU Chi-restraints excluded: chain 1 residue 37 CYS Chi-restraints excluded: chain 1 residue 63 ARG Chi-restraints excluded: chain 1 residue 65 ASN Chi-restraints excluded: chain 2 residue 2 VAL Chi-restraints excluded: chain 2 residue 5 ASN Chi-restraints excluded: chain 2 residue 21 LEU Chi-restraints excluded: chain 2 residue 35 GLU Chi-restraints excluded: chain 2 residue 41 HIS Chi-restraints excluded: chain 2 residue 45 ASP Chi-restraints excluded: chain 2 residue 53 VAL Chi-restraints excluded: chain 3 residue 33 LEU Chi-restraints excluded: chain 4 residue 4 THR Chi-restraints excluded: chain 4 residue 29 GLN Chi-restraints excluded: chain 4 residue 43 THR Chi-restraints excluded: chain 4 residue 44 VAL Chi-restraints excluded: chain 5 residue 6 VAL Chi-restraints excluded: chain 5 residue 27 ASN Chi-restraints excluded: chain 5 residue 53 ASP Chi-restraints excluded: chain 6 residue 26 ILE Chi-restraints excluded: chain 7 residue 15 PHE Chi-restraints excluded: chain 7 residue 19 THR Chi-restraints excluded: chain 7 residue 39 ILE Chi-restraints excluded: chain 7 residue 66 ILE Chi-restraints excluded: chain 7 residue 67 LEU Chi-restraints excluded: chain 7 residue 140 LEU Chi-restraints excluded: chain 7 residue 160 LEU Chi-restraints excluded: chain 7 residue 163 ILE Chi-restraints excluded: chain 7 residue 166 ASP Chi-restraints excluded: chain 7 residue 198 VAL Chi-restraints excluded: chain 7 residue 204 ASP Chi-restraints excluded: chain 7 residue 224 ARG Chi-restraints excluded: chain 8 residue 7 ASN Chi-restraints excluded: chain 8 residue 51 VAL Chi-restraints excluded: chain 8 residue 92 ASP Chi-restraints excluded: chain 8 residue 101 ASN Chi-restraints excluded: chain 8 residue 122 GLN Chi-restraints excluded: chain 8 residue 180 ASP Chi-restraints excluded: chain 8 residue 189 HIS Chi-restraints excluded: chain 8 residue 199 VAL Chi-restraints excluded: chain 9 residue 4 LEU Chi-restraints excluded: chain 9 residue 16 THR Chi-restraints excluded: chain 9 residue 34 GLU Chi-restraints excluded: chain 9 residue 52 VAL Chi-restraints excluded: chain 9 residue 98 ASP Chi-restraints excluded: chain 9 residue 123 MET Chi-restraints excluded: chain 10 residue 29 ILE Chi-restraints excluded: chain 10 residue 63 MET Chi-restraints excluded: chain 10 residue 75 LEU Chi-restraints excluded: chain 11 residue 6 ILE Chi-restraints excluded: chain 11 residue 30 THR Chi-restraints excluded: chain 11 residue 36 ILE Chi-restraints excluded: chain 11 residue 47 LEU Chi-restraints excluded: chain 11 residue 92 THR Chi-restraints excluded: chain 11 residue 94 HIS Chi-restraints excluded: chain 12 residue 5 VAL Chi-restraints excluded: chain 12 residue 48 THR Chi-restraints excluded: chain 12 residue 71 THR Chi-restraints excluded: chain 12 residue 84 TYR Chi-restraints excluded: chain 12 residue 103 ILE Chi-restraints excluded: chain 13 residue 47 ASP Chi-restraints excluded: chain 13 residue 100 ILE Chi-restraints excluded: chain 13 residue 103 VAL Chi-restraints excluded: chain 14 residue 5 TYR Chi-restraints excluded: chain 14 residue 20 ILE Chi-restraints excluded: chain 14 residue 26 LYS Chi-restraints excluded: chain 14 residue 34 LEU Chi-restraints excluded: chain 14 residue 45 MET Chi-restraints excluded: chain 14 residue 61 ASP Chi-restraints excluded: chain 14 residue 71 ILE Chi-restraints excluded: chain 14 residue 86 LEU Chi-restraints excluded: chain 15 residue 17 LEU Chi-restraints excluded: chain 15 residue 22 THR Chi-restraints excluded: chain 15 residue 24 GLU Chi-restraints excluded: chain 15 residue 36 VAL Chi-restraints excluded: chain 15 residue 101 SER Chi-restraints excluded: chain 16 residue 30 ILE Chi-restraints excluded: chain 16 residue 31 VAL Chi-restraints excluded: chain 16 residue 45 THR Chi-restraints excluded: chain 16 residue 67 GLU Chi-restraints excluded: chain 16 residue 81 LEU Chi-restraints excluded: chain 16 residue 96 ILE Chi-restraints excluded: chain 16 residue 99 LEU Chi-restraints excluded: chain 17 residue 19 ASN Chi-restraints excluded: chain 17 residue 34 THR Chi-restraints excluded: chain 17 residue 40 THR Chi-restraints excluded: chain 18 residue 8 ILE Chi-restraints excluded: chain 18 residue 11 HIS Chi-restraints excluded: chain 18 residue 24 VAL Chi-restraints excluded: chain 18 residue 42 VAL Chi-restraints excluded: chain 18 residue 82 LEU Chi-restraints excluded: chain 18 residue 101 THR Chi-restraints excluded: chain 18 residue 103 THR Chi-restraints excluded: chain 19 residue 17 ASP Chi-restraints excluded: chain 19 residue 34 ASN Chi-restraints excluded: chain 20 residue 84 LEU Chi-restraints excluded: chain 21 residue 1 MET Chi-restraints excluded: chain 22 residue 19 SER Chi-restraints excluded: chain 22 residue 28 VAL Chi-restraints excluded: chain 22 residue 32 ILE Chi-restraints excluded: chain 22 residue 37 ILE Chi-restraints excluded: chain 22 residue 52 CYS Chi-restraints excluded: chain 22 residue 56 ASP Chi-restraints excluded: chain 23 residue 17 VAL Chi-restraints excluded: chain 23 residue 24 ASP Chi-restraints excluded: chain 23 residue 70 THR Chi-restraints excluded: chain 24 residue 14 LEU Chi-restraints excluded: chain 24 residue 28 LYS Chi-restraints excluded: chain 24 residue 55 GLN Chi-restraints excluded: chain 24 residue 62 THR Chi-restraints excluded: chain 24 residue 70 LEU Chi-restraints excluded: chain 24 residue 78 THR Chi-restraints excluded: chain 25 residue 9 ARG Chi-restraints excluded: chain 25 residue 12 GLN Chi-restraints excluded: chain 25 residue 38 ILE Chi-restraints excluded: chain 26 residue 12 ASP Chi-restraints excluded: chain 26 residue 18 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1056 random chunks: chunk 513 optimal weight: 9.9990 chunk 665 optimal weight: 20.0000 chunk 892 optimal weight: 40.0000 chunk 256 optimal weight: 0.4980 chunk 772 optimal weight: 20.0000 chunk 123 optimal weight: 50.0000 chunk 232 optimal weight: 8.9990 chunk 839 optimal weight: 20.0000 chunk 351 optimal weight: 7.9990 chunk 861 optimal weight: 20.0000 chunk 106 optimal weight: 9.9990 overall best weight: 7.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 HIS ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 35 HIS N 62 ASN ** O 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 19 HIS ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 50 ASN ** 7 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 10 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 11 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 12 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 13 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 16 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 17 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 17 74 GLN 17 111 GLN ** 18 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 20 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 23 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 25 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.024106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.2335 r_free = 0.2335 target = 0.017480 restraints weight = 1885204.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.2364 r_free = 0.2364 target = 0.018081 restraints weight = 688147.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 71)----------------| | r_work = 0.2377 r_free = 0.2377 target = 0.018423 restraints weight = 392143.676| |-----------------------------------------------------------------------------| r_work (final): 0.2366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9031 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 161950 Z= 0.245 Angle : 0.696 17.397 242116 Z= 0.350 Chirality : 0.036 0.371 30939 Planarity : 0.005 0.092 13091 Dihedral : 24.485 179.555 80642 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 31.03 Ramachandran Plot: Outliers : 0.75 % Allowed : 10.13 % Favored : 89.12 % Rotamer: Outliers : 4.36 % Allowed : 27.33 % Favored : 68.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.11), residues: 5985 helix: -0.51 (0.11), residues: 1978 sheet: -2.06 (0.15), residues: 1103 loop : -1.59 (0.12), residues: 2904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP D 78 HIS 0.010 0.001 HIS 1 6 PHE 0.028 0.002 PHE10 47 TYR 0.056 0.002 TYR 7 212 ARG 0.013 0.001 ARG 1 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 42213.27 seconds wall clock time: 740 minutes 41.73 seconds (44441.73 seconds total)