Starting phenix.real_space_refine on Sun Mar 24 03:52:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcd_6549/03_2024/3jcd_6549_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcd_6549/03_2024/3jcd_6549.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcd_6549/03_2024/3jcd_6549.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcd_6549/03_2024/3jcd_6549.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcd_6549/03_2024/3jcd_6549_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcd_6549/03_2024/3jcd_6549_neut.pdb" } resolution = 3.7 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= -0.000 sd= 0.002 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 4715 5.49 5 S 154 5.16 5 C 74337 2.51 5 N 27525 2.21 5 O 41084 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "c ARG 131": "NH1" <-> "NH2" Residue "c TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 124": "NH1" <-> "NH2" Residue "l ARG 56": "NH1" <-> "NH2" Residue "p ARG 28": "NH1" <-> "NH2" Residue "p PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 9": "NH1" <-> "NH2" Residue "0 ARG 15": "NH1" <-> "NH2" Residue "0 ARG 51": "NH1" <-> "NH2" Residue "1 PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 43": "NH1" <-> "NH2" Residue "2 ARG 3": "NH1" <-> "NH2" Residue "2 ARG 12": "NH1" <-> "NH2" Residue "2 ARG 14": "NH1" <-> "NH2" Residue "2 ARG 19": "NH1" <-> "NH2" Residue "2 ARG 21": "NH1" <-> "NH2" Residue "2 ARG 33": "NH1" <-> "NH2" Residue "2 ARG 41": "NH1" <-> "NH2" Residue "3 ARG 12": "NH1" <-> "NH2" Residue "3 ARG 29": "NH1" <-> "NH2" Residue "3 ARG 39": "NH1" <-> "NH2" Residue "3 ARG 41": "NH1" <-> "NH2" Residue "4 ARG 24": "NH1" <-> "NH2" Residue "C ARG 51": "NH1" <-> "NH2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 132": "NH1" <-> "NH2" Residue "C ARG 166": "NH1" <-> "NH2" Residue "C ARG 176": "NH1" <-> "NH2" Residue "C ARG 181": "NH1" <-> "NH2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "C ARG 202": "NH1" <-> "NH2" Residue "C ARG 211": "NH1" <-> "NH2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "F ARG 70": "NH1" <-> "NH2" Residue "F ARG 79": "NH1" <-> "NH2" Residue "F ARG 91": "NH1" <-> "NH2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F ARG 111": "NH1" <-> "NH2" Residue "F ARG 114": "NH1" <-> "NH2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "G ARG 2": "NH1" <-> "NH2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G ARG 162": "NH1" <-> "NH2" Residue "G ARG 169": "NH1" <-> "NH2" Residue "H ARG 27": "NH1" <-> "NH2" Residue "H PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 139": "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 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 50": "NH1" <-> "NH2" Residue "P PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 61": "NH1" <-> "NH2" Residue "P ARG 88": "NH1" <-> "NH2" Residue "P TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 38": "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 93": "NH1" <-> "NH2" Residue "U PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 19": "NH1" <-> "NH2" Residue "W ARG 76": "NH1" <-> "NH2" Residue "X ARG 2": "NH1" <-> "NH2" Residue "X ARG 10": "NH1" <-> "NH2" Residue "X ARG 17": "NH1" <-> "NH2" Residue "X ARG 36": "NH1" <-> "NH2" Residue "X ARG 49": "NH1" <-> "NH2" Residue "X ARG 56": "NH1" <-> "NH2" Residue "X ARG 73": "NH1" <-> "NH2" 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 "x TYR 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ARG 560": "NH1" <-> "NH2" Residue "x ARG 574": "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: 147815 Number of models: 1 Model: "" Number of chains: 57 Chain: "b" 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: "c" 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: "d" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "e" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1105 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain: "f" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 832 Classifications: {'peptide': 102} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 96} Chain: "g" 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: "h" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "i" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "j" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "k" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "l" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "m" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "n" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 774 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain breaks: 1 Chain: "o" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "p" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "r" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 455 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "s" 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: "t" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "u" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "0" 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: "1" 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: "2" 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: "3" 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: "4" 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: "5" Number of atoms: 1733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1733 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 6, 'TRANS': 225} Chain: "C" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2076 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 17, 'TRANS': 252} Chain: "D" 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: "E" 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: "F" 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: "G" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 166} Chain: "H" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 2, 'TRANS': 144} 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: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 596 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} 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: "x" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 214 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Chain: "a" Number of atoms: 32895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1533, 32895 Classifications: {'RNA': 1533} Modifications used: {'rna2p_pur': 112, 'rna2p_pyr': 76, 'rna3p_pur': 762, 'rna3p_pyr': 583} Link IDs: {'rna2p': 188, 'rna3p': 1344} Chain: "A" Number of atoms: 62320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62320 Classifications: {'RNA': 2903} Modifications used: {'rna2p_pur': 275, 'rna2p_pyr': 149, 'rna3p_pur': 1399, 'rna3p_pyr': 1080} Link IDs: {'rna2p': 424, 'rna3p': 2478} Chain: "B" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2529 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 6, 'rna3p_pur': 56, 'rna3p_pyr': 48} Link IDs: {'rna2p': 14, 'rna3p': 103} Chain: "7" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 191 Classifications: {'RNA': 9} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 3} Link IDs: {'rna2p': 2, 'rna3p': 6} Chain: "8" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1623 Classifications: {'RNA': 76} Modifications used: {'p5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 4, 'rna3p_pur': 31, 'rna3p_pyr': 33} Link IDs: {'rna2p': 11, 'rna3p': 64} Chain: "9" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1623 Classifications: {'RNA': 76} Modifications used: {'p5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 4, 'rna3p_pur': 32, 'rna3p_pyr': 33} Link IDs: {'rna2p': 10, 'rna3p': 65} Time building chain proxies: 56.12, per 1000 atoms: 0.38 Number of scatterers: 147815 At special positions: 0 Unit cell: (261.36, 233.64, 270.6, 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 154 16.00 P 4715 15.00 O 41084 8.00 N 27525 7.00 C 74337 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS 4 11 " - pdb=" SG CYS 4 14 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 11 " - pdb=" SG CYS 4 27 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 14 " - pdb=" SG CYS 4 27 " distance=2.03 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: 68.03 Conformation dependent library (CDL) restraints added in 6.7 seconds 11756 Ramachandran restraints generated. 5878 Oldfield, 0 Emsley, 5878 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10978 Finding SS restraints... Secondary structure from input PDB file: 205 helices and 69 sheets defined 34.7% alpha, 10.9% beta 1299 base pairs and 1980 stacking pairs defined. Time for finding SS restraints: 50.97 Creating SS restraints... Processing helix chain 'b' and resid 23 through 30 Proline residue: b 28 - end of helix Processing helix chain 'b' and resid 33 through 37 removed outlier: 3.549A pdb=" N LYS b 36 " --> pdb=" O ALA b 33 " (cutoff:3.500A) Processing helix chain 'b' and resid 41 through 46 Processing helix chain 'b' and resid 47 through 50 Processing helix chain 'b' and resid 52 through 61 Processing helix chain 'b' and resid 71 through 80 removed outlier: 4.500A pdb=" N ALA b 75 " --> pdb=" O THR b 71 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N GLU b 77 " --> pdb=" O ARG b 73 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA b 78 " --> pdb=" O ALA b 74 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LYS b 80 " --> pdb=" O SER b 76 " (cutoff:3.500A) Processing helix chain 'b' and resid 102 through 119 removed outlier: 5.134A pdb=" N GLN b 108 " --> pdb=" O LYS b 104 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER b 109 " --> pdb=" O THR b 105 " (cutoff:3.500A) Processing helix chain 'b' and resid 123 through 127 removed outlier: 4.135A pdb=" N ASP b 126 " --> pdb=" O GLY b 123 " (cutoff:3.500A) Processing helix chain 'b' and resid 129 through 148 removed outlier: 4.119A pdb=" N ARG b 136 " --> pdb=" O GLU b 132 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLU b 139 " --> pdb=" O MET b 135 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU b 141 " --> pdb=" O THR b 137 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N SER b 146 " --> pdb=" O LYS b 142 " (cutoff:3.500A) Processing helix chain 'b' and resid 149 through 151 No H-bonds generated for 'chain 'b' and resid 149 through 151' Processing helix chain 'b' and resid 165 through 167 No H-bonds generated for 'chain 'b' and resid 165 through 167' Processing helix chain 'b' and resid 168 through 179 removed outlier: 3.716A pdb=" N ILE b 172 " --> pdb=" O GLU b 168 " (cutoff:3.500A) Processing helix chain 'b' and resid 191 through 195 removed outlier: 3.984A pdb=" N GLY b 194 " --> pdb=" O ASP b 191 " (cutoff:3.500A) Processing helix chain 'b' and resid 207 through 221 removed outlier: 3.578A pdb=" N LEU b 211 " --> pdb=" O ARG b 207 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N THR b 219 " --> pdb=" O ALA b 215 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N VAL b 220 " --> pdb=" O VAL b 216 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ARG b 221 " --> pdb=" O ALA b 217 " (cutoff:3.500A) Processing helix chain 'b' and resid 222 through 225 Processing helix chain 'c' and resid 6 through 11 removed outlier: 3.905A pdb=" N ILE c 10 " --> pdb=" O HIS c 6 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ARG c 11 " --> pdb=" O PRO c 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 6 through 11' Processing helix chain 'c' and resid 25 through 47 removed outlier: 4.826A pdb=" N ALA c 30 " --> pdb=" O THR c 26 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N ASP c 31 " --> pdb=" O LYS c 27 " (cutoff:3.500A) Processing helix chain 'c' and resid 48 through 50 No H-bonds generated for 'chain 'c' and resid 48 through 50' Processing helix chain 'c' and resid 72 through 78 removed outlier: 4.176A pdb=" N VAL c 76 " --> pdb=" O ARG c 72 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY c 78 " --> pdb=" O GLY c 74 " (cutoff:3.500A) Processing helix chain 'c' and resid 81 through 96 Processing helix chain 'c' and resid 108 through 111 Processing helix chain 'c' and resid 112 through 125 Processing helix chain 'c' and resid 129 through 144 removed outlier: 3.957A pdb=" N LEU c 144 " --> pdb=" O ASN c 140 " (cutoff:3.500A) Processing helix chain 'c' and resid 156 through 160 removed outlier: 3.564A pdb=" N GLY c 159 " --> pdb=" O ARG c 156 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 16 Processing helix chain 'd' and resid 49 through 66 removed outlier: 3.501A pdb=" N VAL d 53 " --> pdb=" O SER d 49 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN d 54 " --> pdb=" O ASP d 50 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS d 58 " --> pdb=" O GLN d 54 " (cutoff:3.500A) Processing helix chain 'd' and resid 68 through 82 Processing helix chain 'd' and resid 85 through 96 removed outlier: 3.560A pdb=" N ASN d 89 " --> pdb=" O ASN d 85 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU d 91 " --> pdb=" O GLY d 87 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 105 Processing helix chain 'd' and resid 110 through 120 Processing helix chain 'd' and resid 153 through 161 Processing helix chain 'd' and resid 162 through 165 removed outlier: 3.789A pdb=" N ARG d 165 " --> pdb=" O ALA d 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 162 through 165' Processing helix chain 'd' and resid 198 through 203 Processing helix chain 'd' and resid 204 through 206 No H-bonds generated for 'chain 'd' and resid 204 through 206' Processing helix chain 'e' and resid 55 through 69 removed outlier: 3.978A pdb=" N ARG e 69 " --> pdb=" O GLU e 65 " (cutoff:3.500A) Processing helix chain 'e' and resid 111 through 119 Processing helix chain 'e' and resid 132 through 146 removed outlier: 3.626A pdb=" N ARG e 138 " --> pdb=" O ILE e 134 " (cutoff:3.500A) Processing helix chain 'e' and resid 149 through 154 Processing helix chain 'f' and resid 12 through 16 removed outlier: 5.152A pdb=" N GLU f 16 " --> pdb=" O ASP f 13 " (cutoff:3.500A) Processing helix chain 'f' and resid 17 through 30 removed outlier: 3.676A pdb=" N THR f 26 " --> pdb=" O ILE f 22 " (cutoff:3.500A) Processing helix chain 'f' and resid 31 through 33 No H-bonds generated for 'chain 'f' and resid 31 through 33' Processing helix chain 'f' and resid 67 through 81 removed outlier: 4.155A pdb=" N ILE f 71 " --> pdb=" O PRO f 67 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR f 76 " --> pdb=" O ASP f 72 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 31 removed outlier: 3.598A pdb=" N ALA g 24 " --> pdb=" O SER g 20 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 55 Processing helix chain 'g' and resid 58 through 68 removed outlier: 3.591A pdb=" N PHE g 62 " --> pdb=" O GLU g 58 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 111 removed outlier: 3.543A pdb=" N ASN g 97 " --> pdb=" O PRO g 93 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 129 removed outlier: 3.703A pdb=" N GLU g 129 " --> pdb=" O SER g 125 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 145 Processing helix chain 'g' and resid 148 through 152 Processing helix chain 'h' and resid 5 through 20 Processing helix chain 'h' and resid 30 through 43 Processing helix chain 'h' and resid 113 through 119 Processing helix chain 'i' and resid 34 through 39 removed outlier: 3.950A pdb=" N TYR i 38 " --> pdb=" O SER i 34 " (cutoff:3.500A) Processing helix chain 'i' and resid 42 through 46 removed outlier: 4.192A pdb=" N MET i 46 " --> pdb=" O THR i 43 " (cutoff:3.500A) Processing helix chain 'i' and resid 49 through 55 removed outlier: 4.033A pdb=" N LEU i 54 " --> pdb=" O GLN i 50 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL i 55 " --> pdb=" O PRO i 51 " (cutoff:3.500A) Processing helix chain 'i' and resid 73 through 87 removed outlier: 3.549A pdb=" N THR i 84 " --> pdb=" O ARG i 80 " (cutoff:3.500A) Processing helix chain 'i' and resid 93 through 98 Processing helix chain 'i' and resid 99 through 102 Processing helix chain 'j' and resid 16 through 32 removed outlier: 3.991A pdb=" N GLN j 20 " --> pdb=" O ARG j 16 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU j 24 " --> pdb=" O GLN j 20 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ILE j 25 " --> pdb=" O ALA j 21 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LYS j 30 " --> pdb=" O VAL j 26 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR j 32 " --> pdb=" O THR j 28 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 88 removed outlier: 3.526A pdb=" N VAL j 84 " --> pdb=" O THR j 80 " (cutoff:3.500A) Processing helix chain 'k' and resid 47 through 51 removed outlier: 3.652A pdb=" N GLY k 51 " --> pdb=" O GLY k 48 " (cutoff:3.500A) Processing helix chain 'k' and resid 53 through 58 removed outlier: 3.870A pdb=" N LYS k 57 " --> pdb=" O GLY k 54 " (cutoff:3.500A) Processing helix chain 'k' and resid 59 through 71 removed outlier: 3.527A pdb=" N ALA k 63 " --> pdb=" O THR k 59 " (cutoff:3.500A) Processing helix chain 'k' and resid 74 through 78 Processing helix chain 'k' and resid 94 through 103 removed outlier: 3.668A pdb=" N ARG k 98 " --> pdb=" O GLU k 94 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA k 99 " --> pdb=" O SER k 95 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 10 Processing helix chain 'l' and resid 23 through 27 removed outlier: 3.913A pdb=" N ALA l 26 " --> pdb=" O ALA l 23 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N CYS l 27 " --> pdb=" O LEU l 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 23 through 27' Processing helix chain 'l' and resid 115 through 119 removed outlier: 4.523A pdb=" N VAL l 119 " --> pdb=" O LYS l 116 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 22 removed outlier: 3.581A pdb=" N LEU m 19 " --> pdb=" O ALA m 15 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N THR m 20 " --> pdb=" O VAL m 16 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE m 22 " --> pdb=" O ALA m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 removed outlier: 3.941A pdb=" N ALA m 36 " --> pdb=" O ALA m 32 " (cutoff:3.500A) Processing helix chain 'm' and resid 52 through 60 removed outlier: 3.611A pdb=" N LEU m 56 " --> pdb=" O GLN m 52 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU m 59 " --> pdb=" O THR m 55 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL m 60 " --> pdb=" O LEU m 56 " (cutoff:3.500A) Processing helix chain 'm' and resid 65 through 81 Processing helix chain 'm' and resid 85 through 94 Processing helix chain 'm' and resid 106 through 111 Processing helix chain 'n' and resid 3 through 20 removed outlier: 3.756A pdb=" N LYS n 7 " --> pdb=" O LYS n 3 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASP n 18 " --> pdb=" O VAL n 14 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR n 20 " --> pdb=" O LEU n 16 " (cutoff:3.500A) Processing helix chain 'n' and resid 24 through 33 removed outlier: 6.215A pdb=" N ILE n 30 " --> pdb=" O LEU n 27 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ILE n 31 " --> pdb=" O LYS n 28 " (cutoff:3.500A) Processing helix chain 'n' and resid 42 through 51 removed outlier: 3.566A pdb=" N VAL n 45 " --> pdb=" O TRP n 42 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LEU n 48 " --> pdb=" O VAL n 45 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N GLN n 49 " --> pdb=" O LEU n 46 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR n 50 " --> pdb=" O LYS n 47 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 60 Processing helix chain 'n' and resid 80 through 90 removed outlier: 3.763A pdb=" N ARG n 90 " --> pdb=" O GLU n 86 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 16 removed outlier: 3.577A pdb=" N GLY o 16 " --> pdb=" O VAL o 12 " (cutoff:3.500A) Processing helix chain 'o' and resid 24 through 43 removed outlier: 4.245A pdb=" N GLY o 41 " --> pdb=" O ASN o 37 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N HIS o 42 " --> pdb=" O HIS o 38 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 73 removed outlier: 3.546A pdb=" N ARG o 53 " --> pdb=" O ASP o 49 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY o 55 " --> pdb=" O HIS o 51 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 86 removed outlier: 3.557A pdb=" N THR o 79 " --> pdb=" O VAL o 75 " (cutoff:3.500A) Processing helix chain 'p' and resid 53 through 62 Processing helix chain 'p' and resid 68 through 79 Processing helix chain 'r' and resid 25 through 30 Processing helix chain 'r' and resid 41 through 46 removed outlier: 3.637A pdb=" N THR r 45 " --> pdb=" O PRO r 41 " (cutoff:3.500A) Processing helix chain 'r' and resid 48 through 65 removed outlier: 3.996A pdb=" N GLN r 54 " --> pdb=" O LYS r 50 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 23 removed outlier: 4.274A pdb=" N VAL s 23 " --> pdb=" O VAL s 19 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 45 Processing helix chain 's' and resid 63 through 69 removed outlier: 4.266A pdb=" N GLY s 68 " --> pdb=" O GLU s 65 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 75 Processing helix chain 't' and resid 7 through 42 removed outlier: 3.970A pdb=" N ALA t 11 " --> pdb=" O ALA t 7 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS t 16 " --> pdb=" O ILE t 12 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N HIS t 20 " --> pdb=" O LYS t 16 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER t 23 " --> pdb=" O LYS t 19 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG t 29 " --> pdb=" O ARG t 25 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS t 34 " --> pdb=" O THR t 30 " (cutoff:3.500A) Processing helix chain 't' and resid 43 through 64 Proline residue: t 56 - end of helix Processing helix chain 't' and resid 68 through 87 removed outlier: 3.675A pdb=" N ALA t 72 " --> pdb=" O HIS t 68 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS t 85 " --> pdb=" O ALA t 81 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU t 86 " --> pdb=" O GLN t 82 " (cutoff:3.500A) Processing helix chain 'u' and resid 18 through 23 removed outlier: 3.842A pdb=" N SER u 22 " --> pdb=" O ARG u 18 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N CYS u 23 " --> pdb=" O PHE u 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 18 through 23' Processing helix chain 'u' and resid 24 through 32 removed outlier: 4.761A pdb=" N LEU u 29 " --> pdb=" O ALA u 26 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA u 30 " --> pdb=" O GLY u 27 " (cutoff:3.500A) Processing helix chain 'u' and resid 40 through 51 removed outlier: 3.515A pdb=" N SER u 51 " --> pdb=" O ARG u 47 " (cutoff:3.500A) Processing helix chain '0' and resid 8 through 16 Processing helix chain '2' and resid 8 through 17 Processing helix chain '2' and resid 17 through 22 Processing helix chain '2' and resid 24 through 37 Processing helix chain '3' and resid 6 through 11 Processing helix chain '3' and resid 31 through 35 removed outlier: 3.811A pdb=" N LYS 3 34 " --> pdb=" O ILE 3 31 " (cutoff:3.500A) Processing helix chain '3' and resid 36 through 44 removed outlier: 3.510A pdb=" N LYS 3 40 " --> pdb=" O ALA 3 36 " (cutoff:3.500A) Processing helix chain '3' and resid 53 through 61 removed outlier: 3.698A pdb=" N VAL 3 57 " --> pdb=" O ASP 3 53 " (cutoff:3.500A) Processing helix chain '4' and resid 30 through 34 removed outlier: 3.614A pdb=" N HIS 4 33 " --> pdb=" O GLU 4 30 " (cutoff:3.500A) Processing helix chain '5' and resid 5 through 15 removed outlier: 3.949A pdb=" N ARG 5 9 " --> pdb=" O THR 5 5 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL 5 15 " --> pdb=" O ILE 5 11 " (cutoff:3.500A) Processing helix chain '5' and resid 22 through 27 removed outlier: 4.077A pdb=" N ILE 5 27 " --> pdb=" O ILE 5 23 " (cutoff:3.500A) Processing helix chain '5' and resid 81 through 86 removed outlier: 4.135A pdb=" N ALA 5 86 " --> pdb=" O ALA 5 82 " (cutoff:3.500A) Processing helix chain '5' and resid 101 through 105 removed outlier: 3.725A pdb=" N ILE 5 104 " --> pdb=" O ALA 5 101 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS 5 105 " --> pdb=" O ASP 5 102 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 101 through 105' Processing helix chain '5' and resid 117 through 122 removed outlier: 3.681A pdb=" N MET 5 121 " --> pdb=" O SER 5 117 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG 5 122 " --> pdb=" O PRO 5 118 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 117 through 122' Processing helix chain '5' and resid 148 through 155 Processing helix chain '5' and resid 181 through 198 Processing helix chain 'C' and resid 198 through 202 removed outlier: 3.745A pdb=" N ARG C 202 " --> pdb=" O HIS C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 212 removed outlier: 3.729A pdb=" N ALA C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 224 Processing helix chain 'C' and resid 225 through 229 removed outlier: 3.679A pdb=" N HIS C 229 " --> pdb=" O PRO C 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 70 Processing helix chain 'D' and resid 97 through 104 removed outlier: 4.304A pdb=" N ASP D 103 " --> pdb=" O LEU D 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 37 Processing helix chain 'E' and resid 97 through 115 Processing helix chain 'E' and resid 130 through 141 removed outlier: 4.005A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET E 141 " --> pdb=" O LYS E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 160 Processing helix chain 'E' and resid 171 through 175 Processing helix chain 'E' and resid 176 through 183 removed outlier: 3.612A pdb=" N PHE E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 200 Processing helix chain 'F' and resid 3 through 10 Processing helix chain 'F' and resid 11 through 19 Processing helix chain 'F' and resid 46 through 60 Processing helix chain 'F' and resid 91 through 105 removed outlier: 3.906A pdb=" N ILE F 105 " --> pdb=" O ARG F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 110 Processing helix chain 'F' and resid 133 through 137 removed outlier: 3.564A pdb=" N ILE F 136 " --> pdb=" O GLU F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 172 removed outlier: 3.793A pdb=" N GLY F 165 " --> pdb=" O SER F 161 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE F 172 " --> pdb=" O LEU F 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 6 Processing helix chain 'G' and resid 61 through 78 Processing helix chain 'G' and resid 136 through 150 removed outlier: 4.130A pdb=" N TYR G 150 " --> pdb=" O ASP G 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 34 Processing helix chain 'H' and resid 43 through 58 removed outlier: 4.124A pdb=" N ALA H 52 " --> pdb=" O GLU H 48 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLU H 53 " --> pdb=" O ALA H 49 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ALA H 56 " --> pdb=" O ALA H 52 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU H 58 " --> pdb=" O LEU H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 65 removed outlier: 3.585A pdb=" N ALA H 63 " --> pdb=" O GLU H 60 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA H 65 " --> pdb=" O LEU H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 73 Processing helix chain 'H' and resid 95 through 99 Processing helix chain 'H' and resid 103 through 107 removed outlier: 3.539A pdb=" N GLY H 107 " --> pdb=" O THR H 104 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 48 removed outlier: 3.561A pdb=" N PHE I 37 " --> pdb=" O ASN I 33 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N LYS I 39 " --> pdb=" O MET I 35 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASN I 42 " --> pdb=" O CYS I 38 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ALA I 43 " --> pdb=" O LYS I 39 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LYS I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE I 48 " --> pdb=" O LYS I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 84 removed outlier: 3.625A pdb=" N LEU I 78 " --> pdb=" O PRO I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 113 Processing helix chain 'I' and resid 120 through 135 removed outlier: 3.815A pdb=" N MET I 135 " --> pdb=" O THR I 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 11 removed outlier: 3.676A pdb=" N VAL J 11 " --> pdb=" O PRO J 8 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 37 Processing helix chain 'J' and resid 58 through 62 removed outlier: 3.539A pdb=" N LYS J 61 " --> pdb=" O ASN J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 removed outlier: 3.628A pdb=" N LYS J 72 " --> pdb=" O LYS J 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 95 removed outlier: 3.562A pdb=" N ARG J 95 " --> pdb=" O GLU J 91 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 107 removed outlier: 3.904A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA J 104 " --> pdb=" O VAL J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 120 removed outlier: 3.655A pdb=" N ARG J 116 " --> pdb=" O GLY J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 136 removed outlier: 4.287A pdb=" N ALA J 134 " --> pdb=" O ASN J 131 " (cutoff:3.500A) Processing helix chain 'K' and resid 104 through 108 Processing helix chain 'K' and resid 112 through 117 Processing helix chain 'L' and resid 2 through 6 removed outlier: 3.867A pdb=" N LEU L 6 " --> pdb=" O LEU L 3 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 26 removed outlier: 3.543A pdb=" N SER L 25 " --> pdb=" O GLY L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 61 removed outlier: 3.990A pdb=" N LEU L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 74 Processing helix chain 'L' and resid 94 through 99 Processing helix chain 'L' and resid 128 through 138 Processing helix chain 'M' and resid 43 through 58 removed outlier: 4.601A pdb=" N ALA M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VAL M 57 " --> pdb=" O MET M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 121 Processing helix chain 'N' and resid 13 through 32 Processing helix chain 'N' and resid 38 through 56 removed outlier: 4.369A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.970A 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: 4.657A pdb=" N PHE N 80 " --> pdb=" O VAL N 76 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN N 81 " --> pdb=" O ALA N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 87 removed outlier: 3.846A pdb=" N PHE N 87 " --> pdb=" O LEU N 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 22 removed outlier: 4.700A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 60 removed outlier: 3.756A pdb=" N ALA O 59 " --> pdb=" O GLU O 55 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU O 60 " --> pdb=" O LYS O 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 55 through 60' Processing helix chain 'O' and resid 67 through 84 removed outlier: 3.552A pdb=" N ALA O 71 " --> pdb=" O ASN O 67 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU O 84 " --> pdb=" O GLU O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 103 through 108 removed outlier: 3.886A pdb=" N ALA O 107 " --> pdb=" O VAL O 103 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP O 108 " --> pdb=" O GLN O 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 103 through 108' Processing helix chain 'O' and resid 108 through 113 removed outlier: 3.639A pdb=" N GLU O 112 " --> pdb=" O ASP O 108 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA O 113 " --> pdb=" O ALA O 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 108 through 113' Processing helix chain 'P' and resid 5 through 10 removed outlier: 3.875A pdb=" N GLU P 10 " --> pdb=" O GLN P 6 " (cutoff:3.500A) Processing helix chain 'P' and resid 77 through 81 Processing helix chain 'P' and resid 96 through 101 removed outlier: 3.680A pdb=" N LEU P 99 " --> pdb=" O LEU P 96 " (cutoff:3.500A) Processing helix chain 'P' and resid 103 through 108 removed outlier: 4.025A pdb=" N ARG P 108 " --> pdb=" O LYS P 105 " (cutoff:3.500A) Processing helix chain 'Q' and resid 8 through 20 removed outlier: 3.696A pdb=" N GLN Q 19 " --> pdb=" O LYS Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 24 through 29 removed outlier: 3.516A pdb=" N ARG Q 27 " --> pdb=" O TYR Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 30 through 71 removed outlier: 4.288A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 85 Processing helix chain 'Q' and resid 91 through 99 Processing helix chain 'Q' and resid 101 through 117 removed outlier: 3.889A pdb=" N PHE Q 105 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) Processing helix chain 'S' and resid 16 through 25 removed outlier: 4.458A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA S 21 " --> pdb=" O VAL S 17 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ASP S 22 " --> pdb=" O ARG S 18 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 16 through 25' Processing helix chain 'S' and resid 28 through 39 Processing helix chain 'S' and resid 41 through 61 removed outlier: 3.604A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) 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 17 through 20 Processing helix chain 'T' and resid 21 through 26 removed outlier: 3.507A pdb=" N LYS T 26 " --> pdb=" O THR T 22 " (cutoff:3.500A) Processing helix chain 'T' and resid 40 through 49 removed outlier: 3.828A pdb=" N ALA T 46 " --> pdb=" O GLU T 42 " (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: 6.148A pdb=" N GLU V 55 " --> pdb=" O ALA V 52 " (cutoff:3.500A) Processing helix chain 'X' and resid 53 through 62 removed outlier: 3.578A pdb=" N GLY X 62 " --> pdb=" O ILE X 58 " (cutoff:3.500A) Processing helix chain 'X' and resid 62 through 69 removed outlier: 3.642A pdb=" N GLU X 69 " --> pdb=" O THR X 65 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 24 Processing helix chain 'Y' and resid 24 through 34 Processing helix chain 'Y' and resid 40 through 45 removed outlier: 3.844A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) Processing helix chain 'Y' and resid 46 through 54 Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 40 through 50 removed outlier: 3.525A pdb=" N VAL Z 50 " --> pdb=" O MET Z 46 " (cutoff:3.500A) Processing helix chain 'x' and resid 558 through 578 removed outlier: 3.801A pdb=" N LYS x 563 " --> pdb=" O SER x 559 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N LEU x 564 " --> pdb=" O ARG x 560 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS x 572 " --> pdb=" O GLN x 568 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG x 574 " --> pdb=" O GLU x 570 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN x 577 " --> pdb=" O LYS x 573 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'b' and resid 68 through 69 removed outlier: 5.992A pdb=" N PHE b 68 " --> pdb=" O VAL b 91 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'b' and resid 161 through 162 removed outlier: 3.676A pdb=" N ILE b 185 " --> pdb=" O VAL b 162 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N ALA b 184 " --> pdb=" O ILE b 199 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'c' and resid 52 through 56 removed outlier: 6.863A pdb=" N HIS c 69 " --> pdb=" O SER c 53 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ILE c 55 " --> pdb=" O THR c 67 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N THR c 67 " --> pdb=" O ILE c 55 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR c 70 " --> pdb=" O ALA c 104 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'c' and resid 166 through 171 removed outlier: 3.786A pdb=" N GLY c 194 " --> pdb=" O THR c 191 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'd' and resid 123 through 124 Processing sheet with id= F, first strand: chain 'e' and resid 14 through 22 removed outlier: 5.604A pdb=" N LEU e 15 " --> pdb=" O VAL e 38 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL e 38 " --> pdb=" O LEU e 15 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'e' and resid 14 through 22 removed outlier: 5.604A pdb=" N LEU e 15 " --> pdb=" O VAL e 38 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL e 38 " --> pdb=" O LEU e 15 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'e' and resid 85 through 89 Processing sheet with id= I, first strand: chain 'f' and resid 43 through 45 removed outlier: 3.712A pdb=" N GLY f 43 " --> pdb=" O TYR f 59 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL f 7 " --> pdb=" O SER f 87 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N SER f 87 " --> pdb=" O VAL f 7 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N MET f 9 " --> pdb=" O ILE f 85 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE f 85 " --> pdb=" O MET f 9 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'g' and resid 73 through 77 Processing sheet with id= K, first strand: chain 'h' and resid 25 through 28 Processing sheet with id= L, first strand: chain 'h' and resid 74 through 77 removed outlier: 3.894A pdb=" N CYS h 127 " --> pdb=" O VAL h 103 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'i' and resid 11 through 12 Processing sheet with id= N, first strand: chain 'j' and resid 45 through 51 removed outlier: 3.799A pdb=" N ARG j 45 " --> pdb=" O THR j 69 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'k' and resid 41 through 44 removed outlier: 6.709A pdb=" N ILE k 34 " --> pdb=" O LEU k 42 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY k 19 " --> pdb=" O ASN k 81 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'l' and resid 30 through 32 Processing sheet with id= Q, first strand: chain 'l' and resid 36 through 40 Processing sheet with id= R, first strand: chain 'p' and resid 34 through 35 removed outlier: 3.583A pdb=" N GLU p 34 " --> pdb=" O VAL p 21 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL p 2 " --> pdb=" O THR p 66 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'p' and resid 38 through 39 Processing sheet with id= T, first strand: chain 'q' and resid 21 through 23 removed outlier: 4.552A pdb=" N TRP q 73 " --> pdb=" O HIS q 45 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLU q 60 " --> pdb=" O VAL q 76 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N VAL q 78 " --> pdb=" O VAL q 58 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL q 58 " --> pdb=" O VAL q 78 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'q' and resid 29 through 30 Processing sheet with id= V, first strand: chain 's' and resid 51 through 52 Processing sheet with id= W, first strand: chain '0' and resid 28 through 29 Processing sheet with id= X, first strand: chain '0' and resid 47 through 48 removed outlier: 3.569A pdb=" N ARG 0 51 " --> pdb=" O TYR 0 48 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain '1' and resid 19 through 24 removed outlier: 3.596A pdb=" N VAL 1 11 " --> pdb=" O LYS 1 49 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain '4' and resid 17 through 19 Processing sheet with id= AA, first strand: chain '5' and resid 44 through 46 removed outlier: 4.097A pdb=" N HIS 5 172 " --> pdb=" O ARG 5 164 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ARG 5 164 " --> pdb=" O HIS 5 172 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 3 through 4 removed outlier: 3.546A pdb=" N LYS C 17 " --> pdb=" O VAL C 3 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 33 through 34 removed outlier: 3.551A pdb=" N GLU C 34 " --> pdb=" O TYR C 61 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR C 61 " --> pdb=" O GLU C 34 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'C' and resid 75 through 76 Processing sheet with id= AE, first strand: chain 'C' and resid 80 through 81 Processing sheet with id= AF, first strand: chain 'C' and resid 128 through 130 removed outlier: 3.579A pdb=" N GLN C 162 " --> pdb=" O ARG C 174 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N THR C 172 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N MET C 180 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'D' and resid 12 through 16 Processing sheet with id= AH, first strand: chain 'D' and resid 12 through 16 Processing sheet with id= AI, first strand: chain 'D' and resid 34 through 36 removed outlier: 6.589A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'F' and resid 86 through 90 removed outlier: 6.947A pdb=" N THR F 156 " --> pdb=" O GLU F 31 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'F' and resid 129 through 130 Processing sheet with id= AL, first strand: chain 'G' and resid 18 through 19 Processing sheet with id= AM, first strand: chain 'G' and resid 40 through 43 Processing sheet with id= AN, first strand: chain 'G' and resid 123 through 126 removed outlier: 3.539A pdb=" N VAL G 131 " --> pdb=" O GLU G 123 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N GLU G 129 " --> pdb=" O PRO G 125 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'H' and resid 3 through 4 removed outlier: 3.609A pdb=" N VAL H 19 " --> pdb=" O VAL H 3 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'I' and resid 12 through 13 Processing sheet with id= AQ, first strand: chain 'I' and resid 56 through 60 Processing sheet with id= AR, first strand: chain 'J' and resid 53 through 57 Processing sheet with id= AS, first strand: chain 'K' and resid 5 through 10 removed outlier: 4.985A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS K 21 " --> pdb=" O THR K 6 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N VAL K 24 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N ILE K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS K 59 " --> pdb=" O LEU K 87 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N CYS K 84 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ASN K 9 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N LEU K 86 " --> pdb=" O ASN K 9 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'L' and resid 122 through 123 removed outlier: 6.479A pdb=" N VAL L 122 " --> pdb=" O GLU L 143 " (cutoff:3.500A) No H-bonds generated for sheet with id= AT Processing sheet with id= AU, first strand: chain 'M' and resid 63 through 65 removed outlier: 6.393A pdb=" N LEU M 33 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLU M 104 " --> pdb=" O PHE M 31 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N PHE M 31 " --> pdb=" O GLU M 104 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'M' and resid 39 through 42 Processing sheet with id= AW, first strand: chain 'N' and resid 34 through 37 Processing sheet with id= AX, first strand: chain 'O' and resid 47 through 52 removed outlier: 6.723A pdb=" N VAL O 39 " --> pdb=" O LEU O 48 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ALA O 50 " --> pdb=" O ALA O 37 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ALA O 37 " --> pdb=" O ALA O 50 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'P' and resid 37 through 43 removed outlier: 5.871A pdb=" N THR P 24 " --> pdb=" O LYS P 86 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LYS P 86 " --> pdb=" O THR P 24 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER P 82 " --> pdb=" O LYS P 28 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'P' and resid 45 through 46 Processing sheet with id= BA, first strand: chain 'R' and resid 11 through 15 removed outlier: 6.673A pdb=" N TYR R 2 " --> pdb=" O ILE R 41 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ILE R 41 " --> pdb=" O TYR R 2 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL R 4 " --> pdb=" O LEU R 39 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE R 41 " --> pdb=" O VAL R 47 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'R' and resid 20 through 22 removed outlier: 4.414A pdb=" N ALA R 65 " --> pdb=" O ASP R 95 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'R' and resid 72 through 78 removed outlier: 4.124A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'S' and resid 4 through 10 removed outlier: 4.034A pdb=" N ILE S 103 " --> pdb=" O HIS S 7 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N SER S 101 " --> pdb=" O HIS S 9 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'S' and resid 82 through 83 Processing sheet with id= BF, first strand: chain 'S' and resid 86 through 87 Processing sheet with id= BG, first strand: chain 'T' and resid 13 through 14 removed outlier: 3.910A pdb=" N ALA T 13 " --> pdb=" O LYS T 33 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'T' and resid 61 through 63 Processing sheet with id= BI, first strand: chain 'T' and resid 67 through 68 removed outlier: 3.656A pdb=" N LYS T 68 " --> pdb=" O GLY T 75 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY T 75 " --> pdb=" O LYS T 68 " (cutoff:3.500A) No H-bonds generated for sheet with id= BI Processing sheet with id= BJ, first strand: chain 'U' and resid 21 through 23 Processing sheet with id= BK, first strand: chain 'U' and resid 32 through 33 Processing sheet with id= BL, first strand: chain 'U' and resid 40 through 43 Processing sheet with id= BM, first strand: chain 'V' and resid 38 through 43 removed outlier: 8.289A pdb=" N LYS V 25 " --> pdb=" O GLN V 87 " (cutoff:3.500A) removed outlier: 9.803A pdb=" N ILE V 89 " --> pdb=" O LYS V 25 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N PHE V 91 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE V 29 " --> pdb=" O PHE V 91 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N ARG V 93 " --> pdb=" O ILE V 29 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N TYR V 31 " --> pdb=" O ARG V 93 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N HIS V 88 " --> pdb=" O GLN V 78 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP V 76 " --> pdb=" O ASP V 90 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N VAL V 92 " --> pdb=" O ALA V 74 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ALA V 74 " --> pdb=" O VAL V 92 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'W' and resid 64 through 66 Processing sheet with id= BO, first strand: chain 'X' and resid 12 through 15 Processing sheet with id= BP, first strand: chain 'X' and resid 37 through 38 Processing sheet with id= BQ, first strand: chain 'Z' and resid 35 through 37 1503 hydrogen bonds defined for protein. 4002 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3218 hydrogen bonds 5066 hydrogen bond angles 0 basepair planarities 1299 basepair parallelities 1980 stacking parallelities Total time for adding SS restraints: 213.79 Time building geometry restraints manager: 73.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 19386 1.33 - 1.45: 68607 1.45 - 1.57: 62871 1.57 - 1.70: 9425 1.70 - 1.82: 279 Bond restraints: 160568 Sorted by residual: bond pdb=" CA PRO I 73 " pdb=" C PRO I 73 " ideal model delta sigma weight residual 1.514 1.537 -0.022 5.50e-03 3.31e+04 1.64e+01 bond pdb=" CA ALA d 193 " pdb=" CB ALA d 193 " ideal model delta sigma weight residual 1.542 1.512 0.030 8.90e-03 1.26e+04 1.17e+01 bond pdb=" CA ALA E 45 " pdb=" CB ALA E 45 " ideal model delta sigma weight residual 1.530 1.477 0.053 1.69e-02 3.50e+03 9.74e+00 bond pdb=" CA PRO I 21 " pdb=" C PRO I 21 " ideal model delta sigma weight residual 1.517 1.543 -0.025 9.30e-03 1.16e+04 7.48e+00 bond pdb=" CA TYR e 50 " pdb=" C TYR e 50 " ideal model delta sigma weight residual 1.520 1.533 -0.013 4.80e-03 4.34e+04 7.33e+00 ... (remaining 160563 not shown) Histogram of bond angle deviations from ideal: 98.51 - 106.27: 27461 106.27 - 114.03: 102059 114.03 - 121.79: 73585 121.79 - 129.55: 33864 129.55 - 137.31: 3174 Bond angle restraints: 240143 Sorted by residual: angle pdb=" C THR D 151 " pdb=" N PRO D 152 " pdb=" CA PRO D 152 " ideal model delta sigma weight residual 119.84 109.42 10.42 1.25e+00 6.40e-01 6.94e+01 angle pdb=" C GLY J 112 " pdb=" N PRO J 113 " pdb=" CA PRO J 113 " ideal model delta sigma weight residual 119.84 129.70 -9.86 1.25e+00 6.40e-01 6.22e+01 angle pdb=" C ARG g 70 " pdb=" N PRO g 71 " pdb=" CA PRO g 71 " ideal model delta sigma weight residual 119.85 127.81 -7.96 1.01e+00 9.80e-01 6.21e+01 angle pdb=" C MET L 55 " pdb=" N PRO L 56 " pdb=" CA PRO L 56 " ideal model delta sigma weight residual 119.78 127.81 -8.03 1.03e+00 9.43e-01 6.07e+01 angle pdb=" C ARG k 122 " pdb=" N PRO k 123 " pdb=" CA PRO k 123 " ideal model delta sigma weight residual 119.66 125.01 -5.35 7.30e-01 1.88e+00 5.37e+01 ... (remaining 240138 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 91107 35.91 - 71.83: 10414 71.83 - 107.74: 1349 107.74 - 143.66: 28 143.66 - 179.57: 21 Dihedral angle restraints: 102919 sinusoidal: 85897 harmonic: 17022 Sorted by residual: dihedral pdb=" C4' U 8 20 " pdb=" C3' U 8 20 " pdb=" C2' U 8 20 " pdb=" C1' U 8 20 " ideal model delta sinusoidal sigma weight residual -35.00 33.88 -68.88 1 8.00e+00 1.56e-02 9.60e+01 dihedral pdb=" C5' U 8 20 " pdb=" C4' U 8 20 " pdb=" C3' U 8 20 " pdb=" O3' U 8 20 " ideal model delta sinusoidal sigma weight residual 147.00 78.41 68.59 1 8.00e+00 1.56e-02 9.52e+01 dihedral pdb=" O4' C A2165 " pdb=" C1' C A2165 " pdb=" N1 C A2165 " pdb=" C2 C A2165 " ideal model delta sinusoidal sigma weight residual 200.00 34.52 165.48 1 1.50e+01 4.44e-03 8.40e+01 ... (remaining 102916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 26849 0.053 - 0.106: 3377 0.106 - 0.159: 410 0.159 - 0.212: 58 0.212 - 0.265: 11 Chirality restraints: 30705 Sorted by residual: chirality pdb=" C3' A a 913 " pdb=" C4' A a 913 " pdb=" O3' A a 913 " pdb=" C2' A a 913 " both_signs ideal model delta sigma weight residual False -2.74 -2.48 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" C3' U 8 20 " pdb=" C4' U 8 20 " pdb=" O3' U 8 20 " pdb=" C2' U 8 20 " both_signs ideal model delta sigma weight residual False -2.74 -2.49 -0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CB VAL D 107 " pdb=" CA VAL D 107 " pdb=" CG1 VAL D 107 " pdb=" CG2 VAL D 107 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 30702 not shown) Planarity restraints: 12903 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 212 " 0.026 2.00e-02 2.50e+03 2.13e-02 1.13e+01 pdb=" CG TRP C 212 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP C 212 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP C 212 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 212 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 212 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 212 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 212 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 212 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 212 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN I 18 " -0.049 5.00e-02 4.00e+02 7.42e-02 8.81e+00 pdb=" N PRO I 19 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO I 19 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO I 19 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO I 21 " 0.043 5.00e-02 4.00e+02 6.47e-02 6.71e+00 pdb=" N PRO I 22 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO I 22 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO I 22 " 0.037 5.00e-02 4.00e+02 ... (remaining 12900 not shown) Histogram of nonbonded interaction distances: 1.29 - 2.01: 15 2.01 - 2.73: 19847 2.73 - 3.46: 212465 3.46 - 4.18: 456084 4.18 - 4.90: 632881 Nonbonded interactions: 1321292 Sorted by model distance: nonbonded pdb=" N7 A 8 21 " pdb=" C6 G 8 46 " model vdw 1.289 3.340 nonbonded pdb=" C8 A 8 21 " pdb=" O6 G 8 46 " model vdw 1.310 3.260 nonbonded pdb=" C2 A 8 21 " pdb=" C4 C 8 48 " model vdw 1.460 3.560 nonbonded pdb=" O6 G A 271 " pdb=" C5 G A 367 " model vdw 1.620 2.608 nonbonded pdb=" C2 A 8 21 " pdb=" N3 C 8 48 " model vdw 1.645 3.420 ... (remaining 1321287 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 '8' selection = chain '9' } 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: 2.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.160 Extract box with map and model: 12.820 Check model and map are aligned: 1.590 Set scattering table: 1.030 Process input model: 494.150 Find NCS groups from input model: 3.150 Set up NCS constraints: 0.520 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.040 Load rotamer database and sin/cos tables:2.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 518.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0379 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 160568 Z= 0.348 Angle : 0.835 12.314 240143 Z= 0.516 Chirality : 0.036 0.265 30705 Planarity : 0.004 0.074 12903 Dihedral : 22.771 179.571 91932 Min Nonbonded Distance : 1.289 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 4.53 % Allowed : 9.65 % Favored : 85.83 % Rotamer: Outliers : 0.02 % Allowed : 0.94 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.05 % Twisted Proline : 0.50 % 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: -2.43 (0.11), residues: 5878 helix: -2.88 (0.08), residues: 1685 sheet: -3.76 (0.14), residues: 848 loop : -0.11 (0.12), residues: 3345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP C 212 HIS 0.012 0.002 HIS M 13 PHE 0.025 0.002 PHE U 86 TYR 0.030 0.002 TYR J 44 ARG 0.017 0.001 ARG k 122 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11756 Ramachandran restraints generated. 5878 Oldfield, 0 Emsley, 5878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11756 Ramachandran restraints generated. 5878 Oldfield, 0 Emsley, 5878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 592 time to evaluate : 6.134 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: b 26 MET cc_start: -0.0622 (mmp) cc_final: -0.1568 (mmm) REVERT: b 135 MET cc_start: -0.0923 (tpt) cc_final: -0.2133 (tpt) REVERT: t 28 MET cc_start: 0.0093 (ptm) cc_final: -0.0273 (ptp) REVERT: 2 1 MET cc_start: -0.2555 (tpt) cc_final: -0.3008 (mpp) REVERT: 2 22 MET cc_start: 0.0128 (mmm) cc_final: -0.1296 (mmm) REVERT: 5 137 MET cc_start: -0.3899 (mmt) cc_final: -0.4595 (mmt) REVERT: E 100 MET cc_start: 0.1257 (mtp) cc_final: 0.0852 (mtt) REVERT: E 199 MET cc_start: -0.4608 (ttp) cc_final: -0.6441 (mmt) REVERT: F 129 MET cc_start: -0.3261 (ptm) cc_final: -0.5818 (tpt) REVERT: H 1 MET cc_start: 0.1414 (ttt) cc_final: 0.0198 (ptp) REVERT: I 116 MET cc_start: 0.1420 (mtp) cc_final: 0.0269 (tpp) REVERT: P 12 MET cc_start: -0.0788 (mtp) cc_final: -0.2045 (mmm) REVERT: Y 1 MET cc_start: -0.3776 (ttt) cc_final: -0.4121 (tmm) outliers start: 1 outliers final: 0 residues processed: 593 average time/residue: 1.4933 time to fit residues: 1451.4486 Evaluate side-chains 276 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 5.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1043 random chunks: chunk 880 optimal weight: 20.0000 chunk 790 optimal weight: 20.0000 chunk 438 optimal weight: 9.9990 chunk 270 optimal weight: 50.0000 chunk 533 optimal weight: 9.9990 chunk 422 optimal weight: 5.9990 chunk 817 optimal weight: 30.0000 chunk 316 optimal weight: 0.0270 chunk 497 optimal weight: 6.9990 chunk 608 optimal weight: 10.0000 chunk 947 optimal weight: 20.0000 overall best weight: 6.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 3 HIS f 55 HIS f 63 ASN ** i 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 81 HIS j 56 HIS j 64 GLN k 22 HIS ** k 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 28 GLN o 35 GLN ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 59 HIS q 45 HIS q 51 ASN r 52 GLN s 57 HIS t 48 GLN 0 18 HIS ** 3 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 25 HIS 4 37 GLN 5 155 ASN 5 165 ASN ** 5 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 HIS ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 ASN D 32 ASN ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 21 GLN G 103 ASN G 110 HIS ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 135 HIS ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 47 HIS ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 34 HIS ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 44 HIS U 65 GLN V 80 HIS ** W 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 ASN ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 45 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0784 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 160568 Z= 0.291 Angle : 0.894 19.210 240143 Z= 0.439 Chirality : 0.043 0.407 30705 Planarity : 0.007 0.098 12903 Dihedral : 23.786 179.417 80207 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 20.31 Ramachandran Plot: Outliers : 1.67 % Allowed : 9.08 % Favored : 89.25 % Rotamer: Outliers : 1.42 % Allowed : 6.53 % Favored : 92.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.05 % Twisted Proline : 0.50 % Twisted General : 0.17 % 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: -2.39 (0.10), residues: 5878 helix: -1.59 (0.11), residues: 1732 sheet: -3.28 (0.15), residues: 833 loop : -1.01 (0.11), residues: 3313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP q 73 HIS 0.023 0.003 HIS N 3 PHE 0.040 0.003 PHE U 86 TYR 0.054 0.003 TYR J 44 ARG 0.036 0.001 ARG E 170 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11756 Ramachandran restraints generated. 5878 Oldfield, 0 Emsley, 5878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11756 Ramachandran restraints generated. 5878 Oldfield, 0 Emsley, 5878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 317 time to evaluate : 5.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 26 MET cc_start: 0.0114 (mmp) cc_final: -0.0755 (mmm) REVERT: b 135 MET cc_start: -0.1016 (tpt) cc_final: -0.1416 (tpt) REVERT: f 56 LYS cc_start: 0.1995 (OUTLIER) cc_final: 0.1794 (pttm) REVERT: g 101 MET cc_start: -0.0827 (mmt) cc_final: -0.1029 (mmt) REVERT: l 110 ARG cc_start: 0.2610 (OUTLIER) cc_final: 0.2262 (tpp80) REVERT: o 59 MET cc_start: -0.3369 (mtt) cc_final: -0.4286 (mmt) REVERT: t 28 MET cc_start: -0.0283 (ptm) cc_final: -0.0567 (ptp) REVERT: 2 1 MET cc_start: -0.2709 (tpt) cc_final: -0.3268 (mpp) REVERT: 2 22 MET cc_start: 0.0051 (mmm) cc_final: -0.0149 (mmm) REVERT: 5 137 MET cc_start: -0.3850 (mmt) cc_final: -0.4124 (mmt) REVERT: C 141 HIS cc_start: 0.3318 (OUTLIER) cc_final: 0.2921 (p-80) REVERT: C 200 MET cc_start: -0.2798 (tmm) cc_final: -0.3224 (ttp) REVERT: D 165 MET cc_start: -0.3103 (ttt) cc_final: -0.3380 (tpp) REVERT: E 199 MET cc_start: -0.4159 (ttp) cc_final: -0.6116 (mmt) REVERT: F 129 MET cc_start: -0.2727 (ptm) cc_final: -0.5451 (tpt) REVERT: H 1 MET cc_start: 0.0825 (ttt) cc_final: -0.0341 (ptp) REVERT: I 124 MET cc_start: 0.2431 (mtp) cc_final: 0.1658 (tmm) REVERT: I 135 MET cc_start: 0.0630 (mmm) cc_final: -0.0255 (mpp) REVERT: J 39 LYS cc_start: -0.2549 (OUTLIER) cc_final: -0.3163 (mptt) outliers start: 69 outliers final: 33 residues processed: 363 average time/residue: 1.4199 time to fit residues: 877.5696 Evaluate side-chains 297 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 260 time to evaluate : 6.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 198 VAL Chi-restraints excluded: chain c residue 49 LYS Chi-restraints excluded: chain d residue 130 VAL Chi-restraints excluded: chain e residue 96 MET Chi-restraints excluded: chain e residue 111 MET Chi-restraints excluded: chain f residue 56 LYS Chi-restraints excluded: chain i residue 57 MET Chi-restraints excluded: chain i residue 72 ILE Chi-restraints excluded: chain j residue 15 HIS Chi-restraints excluded: chain l residue 110 ARG Chi-restraints excluded: chain m residue 19 LEU Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain p residue 59 HIS Chi-restraints excluded: chain t residue 54 MET Chi-restraints excluded: chain 0 residue 18 HIS Chi-restraints excluded: chain 2 residue 29 GLN Chi-restraints excluded: chain 5 residue 97 MET Chi-restraints excluded: chain 5 residue 117 SER Chi-restraints excluded: chain 5 residue 153 VAL Chi-restraints excluded: chain C residue 24 HIS Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain F residue 21 TYR Chi-restraints excluded: chain F residue 22 ASN Chi-restraints excluded: chain G residue 150 TYR Chi-restraints excluded: chain J residue 39 LYS Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain S residue 48 LYS Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain X residue 4 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1043 random chunks: chunk 526 optimal weight: 6.9990 chunk 293 optimal weight: 7.9990 chunk 788 optimal weight: 20.0000 chunk 644 optimal weight: 20.0000 chunk 261 optimal weight: 9.9990 chunk 948 optimal weight: 20.0000 chunk 1025 optimal weight: 20.0000 chunk 845 optimal weight: 10.0000 chunk 940 optimal weight: 40.0000 chunk 323 optimal weight: 9.9990 chunk 761 optimal weight: 20.0000 overall best weight: 8.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 28 ASN ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 16 ASN ** i 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 112 GLN o 28 GLN o 40 GLN o 50 HIS t 55 GLN ** 0 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 29 GLN ** 3 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 67 HIS 5 155 ASN 5 234 ASN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 45 ASN ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 GLN ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN F 4 HIS ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 35 HIS N 3 HIS ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 HIS ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 39 GLN W 45 HIS ** Y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 33 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1422 moved from start: 0.7323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.243 160568 Z= 0.396 Angle : 1.134 18.817 240143 Z= 0.565 Chirality : 0.054 0.441 30705 Planarity : 0.009 0.164 12903 Dihedral : 24.580 177.118 80207 Min Nonbonded Distance : 1.666 Molprobity Statistics. All-atom Clashscore : 43.73 Ramachandran Plot: Outliers : 1.46 % Allowed : 12.28 % Favored : 86.25 % Rotamer: Outliers : 3.82 % Allowed : 9.38 % Favored : 86.80 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.05 % Twisted Proline : 0.50 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.10), residues: 5878 helix: -1.80 (0.11), residues: 1713 sheet: -2.86 (0.16), residues: 800 loop : -1.88 (0.10), residues: 3365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.004 TRP p 60 HIS 0.080 0.005 HIS p 59 PHE 0.052 0.004 PHE D 90 TYR 0.036 0.004 TYR r 64 ARG 0.071 0.002 ARG m 92 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11756 Ramachandran restraints generated. 5878 Oldfield, 0 Emsley, 5878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11756 Ramachandran restraints generated. 5878 Oldfield, 0 Emsley, 5878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 311 time to evaluate : 6.148 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: b 26 MET cc_start: 0.1251 (mmp) cc_final: 0.0356 (mmm) REVERT: d 123 ILE cc_start: 0.3402 (tp) cc_final: 0.3048 (tt) REVERT: f 62 MET cc_start: -0.2088 (ttt) cc_final: -0.2323 (ttt) REVERT: f 88 MET cc_start: -0.0637 (mmm) cc_final: -0.1212 (mtt) REVERT: g 101 MET cc_start: -0.0935 (mmt) cc_final: -0.1227 (mmt) REVERT: m 81 MET cc_start: -0.1941 (tmm) cc_final: -0.2278 (ttp) REVERT: o 59 MET cc_start: -0.2485 (mtt) cc_final: -0.3085 (tpp) REVERT: t 28 MET cc_start: 0.0879 (ptm) cc_final: 0.0476 (ptm) REVERT: t 68 HIS cc_start: -0.2875 (OUTLIER) cc_final: -0.3939 (t70) REVERT: 2 1 MET cc_start: -0.2783 (tpt) cc_final: -0.3778 (mtp) REVERT: 3 48 MET cc_start: 0.2765 (mmt) cc_final: 0.1861 (mmt) REVERT: 5 137 MET cc_start: -0.3381 (mmt) cc_final: -0.3815 (mmt) REVERT: C 141 HIS cc_start: 0.3456 (OUTLIER) cc_final: 0.2602 (p-80) REVERT: E 199 MET cc_start: -0.2911 (ttp) cc_final: -0.5004 (mmt) REVERT: F 112 ASP cc_start: -0.3225 (OUTLIER) cc_final: -0.3716 (m-30) REVERT: F 129 MET cc_start: -0.1863 (ptm) cc_final: -0.3905 (tpt) REVERT: H 1 MET cc_start: 0.1707 (ttt) cc_final: -0.0542 (ptp) REVERT: H 46 PHE cc_start: -0.0109 (OUTLIER) cc_final: -0.0397 (m-10) REVERT: I 124 MET cc_start: 0.1999 (mtp) cc_final: 0.1667 (tmm) REVERT: J 3 THR cc_start: 0.0146 (OUTLIER) cc_final: -0.0138 (p) REVERT: J 12 LYS cc_start: -0.1928 (OUTLIER) cc_final: -0.2134 (pttm) REVERT: L 111 ILE cc_start: 0.1812 (OUTLIER) cc_final: 0.1612 (mt) REVERT: M 12 MET cc_start: -0.0170 (OUTLIER) cc_final: -0.1830 (mmt) REVERT: M 82 MET cc_start: -0.1790 (mmt) cc_final: -0.2021 (mmt) REVERT: Q 111 LYS cc_start: -0.1683 (OUTLIER) cc_final: -0.1990 (pttt) outliers start: 186 outliers final: 74 residues processed: 456 average time/residue: 1.3222 time to fit residues: 1038.2555 Evaluate side-chains 333 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 250 time to evaluate : 5.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 8 MET Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain b residue 219 THR Chi-restraints excluded: chain c residue 55 ILE Chi-restraints excluded: chain c residue 93 ASP Chi-restraints excluded: chain d residue 130 VAL Chi-restraints excluded: chain e residue 96 MET Chi-restraints excluded: chain e residue 115 LEU Chi-restraints excluded: chain f residue 2 ARG Chi-restraints excluded: chain f residue 56 LYS Chi-restraints excluded: chain h residue 14 ILE Chi-restraints excluded: chain h residue 34 VAL Chi-restraints excluded: chain j residue 15 HIS Chi-restraints excluded: chain k residue 119 ASN Chi-restraints excluded: chain l residue 63 VAL Chi-restraints excluded: chain l residue 82 ILE Chi-restraints excluded: chain l residue 107 VAL Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 25 THR Chi-restraints excluded: chain p residue 1 MET Chi-restraints excluded: chain p residue 50 THR Chi-restraints excluded: chain p residue 59 HIS Chi-restraints excluded: chain q residue 76 VAL Chi-restraints excluded: chain t residue 54 MET Chi-restraints excluded: chain t residue 68 HIS Chi-restraints excluded: chain 0 residue 3 GLN Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain 4 residue 3 VAL Chi-restraints excluded: chain 5 residue 97 MET Chi-restraints excluded: chain 5 residue 111 PHE Chi-restraints excluded: chain 5 residue 184 LYS Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain F residue 21 TYR Chi-restraints excluded: chain F residue 22 ASN Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 150 TYR Chi-restraints excluded: chain H residue 46 PHE Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 69 ARG Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 107 PHE Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 73 ASN Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 51 ASN Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 83 ILE Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 111 LYS Chi-restraints excluded: chain S residue 48 LYS Chi-restraints excluded: chain U residue 17 ASP Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 38 ARG Chi-restraints excluded: chain Y residue 27 ASN Chi-restraints excluded: chain Z residue 56 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1043 random chunks: chunk 937 optimal weight: 20.0000 chunk 713 optimal weight: 20.0000 chunk 492 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 452 optimal weight: 4.9990 chunk 637 optimal weight: 20.0000 chunk 952 optimal weight: 20.0000 chunk 1008 optimal weight: 20.0000 chunk 497 optimal weight: 20.0000 chunk 902 optimal weight: 20.0000 chunk 271 optimal weight: 4.9990 overall best weight: 9.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 57 ASN ** b 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 167 HIS ** c 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 16 ASN ** h 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 110 GLN j 35 GLN k 15 GLN k 28 ASN ** k 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 101 ASN m 91 HIS m 105 ASN ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 55 GLN t 75 HIS 0 4 GLN 0 18 HIS ** 3 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 27 ASN ** 3 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 HIS ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 HIS ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN F 51 ASN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 HIS ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 5 GLN L 38 GLN ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 74 GLN R 87 GLN ** S 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 45 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1590 moved from start: 0.9314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.166 160568 Z= 0.362 Angle : 1.016 16.662 240143 Z= 0.513 Chirality : 0.050 0.732 30705 Planarity : 0.008 0.200 12903 Dihedral : 24.810 176.501 80207 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 37.15 Ramachandran Plot: Outliers : 1.46 % Allowed : 10.48 % Favored : 88.06 % Rotamer: Outliers : 3.88 % Allowed : 12.09 % Favored : 84.03 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.05 % Twisted Proline : 0.50 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.20 (0.10), residues: 5878 helix: -1.86 (0.11), residues: 1700 sheet: -2.81 (0.16), residues: 797 loop : -2.10 (0.10), residues: 3381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.005 TRP p 60 HIS 0.094 0.004 HIS p 59 PHE 0.056 0.004 PHE N 21 TYR 0.047 0.004 TYR 5 21 ARG 0.041 0.002 ARG O 15 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11756 Ramachandran restraints generated. 5878 Oldfield, 0 Emsley, 5878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11756 Ramachandran restraints generated. 5878 Oldfield, 0 Emsley, 5878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 306 time to evaluate : 5.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 26 MET cc_start: -0.0154 (mmp) cc_final: -0.0762 (tpt) REVERT: b 135 MET cc_start: -0.2403 (tpp) cc_final: -0.2777 (tpt) REVERT: b 199 ILE cc_start: -0.1019 (OUTLIER) cc_final: -0.1548 (tp) REVERT: f 90 MET cc_start: -0.2908 (mtt) cc_final: -0.3128 (mtt) REVERT: g 31 MET cc_start: 0.1154 (ppp) cc_final: 0.0732 (ppp) REVERT: i 57 MET cc_start: -0.2241 (OUTLIER) cc_final: -0.2688 (ttp) REVERT: k 85 MET cc_start: -0.0043 (mtp) cc_final: -0.0452 (mtp) REVERT: m 81 MET cc_start: -0.1870 (tmm) cc_final: -0.2123 (ttp) REVERT: m 93 ARG cc_start: 0.3456 (OUTLIER) cc_final: 0.3174 (tpm170) REVERT: n 6 MET cc_start: -0.2530 (mmt) cc_final: -0.2911 (mmt) REVERT: o 59 MET cc_start: -0.2340 (mtt) cc_final: -0.2838 (tpp) REVERT: o 84 ARG cc_start: 0.2295 (ttt180) cc_final: 0.0261 (mmp80) REVERT: t 28 MET cc_start: 0.0778 (ptm) cc_final: 0.0438 (ptm) REVERT: 0 19 ASP cc_start: 0.4048 (OUTLIER) cc_final: 0.3615 (m-30) REVERT: 2 1 MET cc_start: -0.2961 (tpt) cc_final: -0.4156 (mpp) REVERT: 3 48 MET cc_start: 0.3170 (mmt) cc_final: 0.2058 (mmt) REVERT: 5 137 MET cc_start: -0.4128 (mmt) cc_final: -0.4417 (mmt) REVERT: 5 200 LYS cc_start: 0.2304 (OUTLIER) cc_final: 0.1297 (tmtt) REVERT: C 141 HIS cc_start: 0.2744 (OUTLIER) cc_final: 0.2142 (p-80) REVERT: C 176 ARG cc_start: -0.0833 (OUTLIER) cc_final: -0.3367 (mmm-85) REVERT: E 176 ASP cc_start: -0.0973 (OUTLIER) cc_final: -0.1607 (m-30) REVERT: E 199 MET cc_start: -0.2515 (ttp) cc_final: -0.4255 (mmt) REVERT: F 129 MET cc_start: -0.2338 (ptm) cc_final: -0.4144 (tpt) REVERT: H 1 MET cc_start: 0.1805 (ttt) cc_final: -0.0143 (mtm) REVERT: N 33 ILE cc_start: -0.3425 (OUTLIER) cc_final: -0.3699 (pt) REVERT: N 37 THR cc_start: -0.2993 (OUTLIER) cc_final: -0.3230 (p) REVERT: P 12 MET cc_start: 0.0159 (ttt) cc_final: -0.1223 (tpp) REVERT: P 69 VAL cc_start: -0.1699 (OUTLIER) cc_final: -0.2071 (p) REVERT: T 15 HIS cc_start: -0.1448 (OUTLIER) cc_final: -0.3048 (m90) REVERT: V 45 ASP cc_start: 0.5201 (OUTLIER) cc_final: 0.4090 (m-30) outliers start: 189 outliers final: 76 residues processed: 455 average time/residue: 1.3281 time to fit residues: 1044.3548 Evaluate side-chains 346 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 257 time to evaluate : 6.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 8 MET Chi-restraints excluded: chain b residue 17 HIS Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 44 LYS Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 199 ILE Chi-restraints excluded: chain b residue 213 LEU Chi-restraints excluded: chain c residue 55 ILE Chi-restraints excluded: chain d residue 48 LEU Chi-restraints excluded: chain d residue 132 ILE Chi-restraints excluded: chain d residue 152 GLN Chi-restraints excluded: chain e residue 96 MET Chi-restraints excluded: chain f residue 51 ILE Chi-restraints excluded: chain f residue 56 LYS Chi-restraints excluded: chain i residue 30 ILE Chi-restraints excluded: chain i residue 57 MET Chi-restraints excluded: chain i residue 100 LYS Chi-restraints excluded: chain j residue 15 HIS Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain k residue 65 VAL Chi-restraints excluded: chain l residue 109 ASP Chi-restraints excluded: chain m residue 9 ILE Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain m residue 93 ARG Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 67 LEU Chi-restraints excluded: chain p residue 50 THR Chi-restraints excluded: chain s residue 14 HIS Chi-restraints excluded: chain u residue 10 GLU Chi-restraints excluded: chain 0 residue 19 ASP Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain 3 residue 27 ASN Chi-restraints excluded: chain 4 residue 3 VAL Chi-restraints excluded: chain 5 residue 97 MET Chi-restraints excluded: chain 5 residue 111 PHE Chi-restraints excluded: chain 5 residue 121 MET Chi-restraints excluded: chain 5 residue 200 LYS Chi-restraints excluded: chain 5 residue 217 THR Chi-restraints excluded: chain 5 residue 222 VAL Chi-restraints excluded: chain C residue 24 HIS Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain C residue 176 ARG Chi-restraints excluded: chain C residue 242 HIS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 118 PHE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain F residue 21 TYR Chi-restraints excluded: chain F residue 22 ASN Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain G residue 61 TRP Chi-restraints excluded: chain G residue 150 TYR Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 60 ARG Chi-restraints excluded: chain L residue 69 ARG Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 107 PHE Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 83 TYR Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 48 LYS Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain T residue 15 HIS Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain W residue 22 VAL Chi-restraints excluded: chain Y residue 27 ASN Chi-restraints excluded: chain Z residue 4 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1043 random chunks: chunk 839 optimal weight: 30.0000 chunk 572 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 750 optimal weight: 30.0000 chunk 415 optimal weight: 8.9990 chunk 860 optimal weight: 20.0000 chunk 696 optimal weight: 30.0000 chunk 1 optimal weight: 3.9990 chunk 514 optimal weight: 6.9990 chunk 904 optimal weight: 20.0000 chunk 254 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 139 GLN ** d 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 60 GLN o 40 GLN ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 5 ASN ** 3 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 35 GLN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 HIS ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 ASN D 167 ASN F 51 ASN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 HIS N 3 HIS ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 51 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1642 moved from start: 1.0468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.131 160568 Z= 0.272 Angle : 0.867 17.591 240143 Z= 0.440 Chirality : 0.044 0.286 30705 Planarity : 0.007 0.114 12903 Dihedral : 24.817 179.795 80207 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 34.63 Ramachandran Plot: Outliers : 1.36 % Allowed : 12.16 % Favored : 86.47 % Rotamer: Outliers : 3.65 % Allowed : 14.02 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.10), residues: 5878 helix: -1.69 (0.11), residues: 1706 sheet: -2.61 (0.17), residues: 804 loop : -2.07 (0.10), residues: 3368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.004 TRP p 60 HIS 0.039 0.003 HIS p 59 PHE 0.027 0.003 PHE c 130 TYR 0.043 0.003 TYR Q 23 ARG 0.019 0.001 ARG J 99 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11756 Ramachandran restraints generated. 5878 Oldfield, 0 Emsley, 5878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11756 Ramachandran restraints generated. 5878 Oldfield, 0 Emsley, 5878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 282 time to evaluate : 6.098 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: e 147 MET cc_start: 0.0066 (mmm) cc_final: -0.0199 (mmt) REVERT: f 1 MET cc_start: 0.2347 (mmp) cc_final: 0.2138 (mmp) REVERT: f 21 MET cc_start: 0.0259 (OUTLIER) cc_final: -0.0329 (ptm) REVERT: f 56 LYS cc_start: 0.3001 (OUTLIER) cc_final: 0.2703 (pttm) REVERT: f 62 MET cc_start: -0.1420 (ttt) cc_final: -0.2130 (ttt) REVERT: f 88 MET cc_start: 0.0000 (OUTLIER) cc_final: -0.0815 (ttp) REVERT: g 31 MET cc_start: 0.1285 (ppp) cc_final: 0.0772 (ppp) REVERT: g 131 LYS cc_start: -0.2769 (OUTLIER) cc_final: -0.5021 (ttmm) REVERT: i 120 LYS cc_start: 0.1819 (OUTLIER) cc_final: 0.1451 (mmtp) REVERT: k 85 MET cc_start: -0.0128 (mtp) cc_final: -0.0395 (mtt) REVERT: m 93 ARG cc_start: 0.2741 (OUTLIER) cc_final: 0.2373 (tpm170) REVERT: o 59 MET cc_start: -0.1708 (mtt) cc_final: -0.2223 (tpp) REVERT: o 84 ARG cc_start: 0.2354 (ttt180) cc_final: 0.0721 (mmp80) REVERT: s 37 ARG cc_start: -0.0707 (OUTLIER) cc_final: -0.1748 (tpp80) REVERT: 2 1 MET cc_start: -0.3591 (tpt) cc_final: -0.3990 (mpp) REVERT: 3 48 MET cc_start: 0.3443 (mmt) cc_final: 0.2489 (mmt) REVERT: 5 137 MET cc_start: -0.4140 (mmt) cc_final: -0.4624 (mmt) REVERT: C 45 ASN cc_start: -0.0910 (OUTLIER) cc_final: -0.1157 (m110) REVERT: C 167 ASP cc_start: -0.4273 (OUTLIER) cc_final: -0.4802 (m-30) REVERT: D 43 ASP cc_start: 0.2201 (OUTLIER) cc_final: 0.1915 (m-30) REVERT: E 69 ARG cc_start: 0.0538 (OUTLIER) cc_final: -0.0087 (ttm170) REVERT: E 199 MET cc_start: -0.2673 (ttp) cc_final: -0.4446 (mmt) REVERT: H 1 MET cc_start: 0.1786 (ttt) cc_final: 0.0320 (mpp) REVERT: I 135 MET cc_start: -0.0953 (mmp) cc_final: -0.1402 (mmt) REVERT: K 23 LYS cc_start: -0.1070 (OUTLIER) cc_final: -0.1285 (tptt) REVERT: L 111 ILE cc_start: 0.0721 (OUTLIER) cc_final: 0.0315 (mt) REVERT: O 30 ARG cc_start: 0.0347 (OUTLIER) cc_final: -0.1318 (ttt180) outliers start: 178 outliers final: 99 residues processed: 426 average time/residue: 1.3416 time to fit residues: 987.1375 Evaluate side-chains 366 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 253 time to evaluate : 6.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 8 MET Chi-restraints excluded: chain b residue 19 THR Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 44 LYS Chi-restraints excluded: chain b residue 106 VAL Chi-restraints excluded: chain b residue 153 MET Chi-restraints excluded: chain c residue 55 ILE Chi-restraints excluded: chain c residue 69 HIS Chi-restraints excluded: chain c residue 93 ASP Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain d residue 48 LEU Chi-restraints excluded: chain d residue 132 ILE Chi-restraints excluded: chain d residue 152 GLN Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 96 MET Chi-restraints excluded: chain f residue 2 ARG Chi-restraints excluded: chain f residue 21 MET Chi-restraints excluded: chain f residue 26 THR Chi-restraints excluded: chain f residue 51 ILE Chi-restraints excluded: chain f residue 56 LYS Chi-restraints excluded: chain f residue 88 MET Chi-restraints excluded: chain g residue 131 LYS Chi-restraints excluded: chain h residue 14 ILE Chi-restraints excluded: chain i residue 72 ILE Chi-restraints excluded: chain i residue 88 MET Chi-restraints excluded: chain i residue 107 ASP Chi-restraints excluded: chain i residue 111 VAL Chi-restraints excluded: chain i residue 120 LYS Chi-restraints excluded: chain j residue 15 HIS Chi-restraints excluded: chain k residue 17 SER Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain l residue 82 ILE Chi-restraints excluded: chain m residue 9 ILE Chi-restraints excluded: chain m residue 93 ARG Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 75 VAL Chi-restraints excluded: chain p residue 1 MET Chi-restraints excluded: chain p residue 50 THR Chi-restraints excluded: chain q residue 23 VAL Chi-restraints excluded: chain s residue 14 HIS Chi-restraints excluded: chain s residue 37 ARG Chi-restraints excluded: chain t residue 68 HIS Chi-restraints excluded: chain u residue 10 GLU Chi-restraints excluded: chain 4 residue 3 VAL Chi-restraints excluded: chain 5 residue 97 MET Chi-restraints excluded: chain 5 residue 111 PHE Chi-restraints excluded: chain 5 residue 121 MET Chi-restraints excluded: chain 5 residue 184 LYS Chi-restraints excluded: chain C residue 24 HIS Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 118 PHE Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain F residue 21 TYR Chi-restraints excluded: chain F residue 22 ASN Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 61 TRP Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 150 TYR Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 108 MET Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 23 LYS Chi-restraints excluded: chain K residue 64 ARG Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 60 ARG Chi-restraints excluded: chain L residue 69 ARG Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 107 PHE Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain N residue 34 ILE Chi-restraints excluded: chain N residue 73 ASN Chi-restraints excluded: chain O residue 30 ARG Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 97 PHE Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 83 ILE Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain R residue 83 TYR Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 48 LYS Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 106 VAL Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 14 ASP Chi-restraints excluded: chain Y residue 27 ASN Chi-restraints excluded: chain Z residue 4 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1043 random chunks: chunk 339 optimal weight: 0.8980 chunk 907 optimal weight: 20.0000 chunk 199 optimal weight: 8.9990 chunk 591 optimal weight: 20.0000 chunk 248 optimal weight: 7.9990 chunk 1009 optimal weight: 20.0000 chunk 837 optimal weight: 40.0000 chunk 467 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 333 optimal weight: 0.0050 chunk 529 optimal weight: 0.9980 overall best weight: 3.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 139 GLN ** d 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 120 HIS ** f 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 43 ASN t 48 GLN ** 3 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 35 GLN 5 155 ASN 5 160 GLN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 71 ASN ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1578 moved from start: 1.0847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.113 160568 Z= 0.198 Angle : 0.741 14.305 240143 Z= 0.377 Chirality : 0.039 0.309 30705 Planarity : 0.005 0.079 12903 Dihedral : 24.643 179.684 80207 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 28.16 Ramachandran Plot: Outliers : 1.21 % Allowed : 10.38 % Favored : 88.41 % Rotamer: Outliers : 3.02 % Allowed : 15.11 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.10), residues: 5878 helix: -1.37 (0.12), residues: 1702 sheet: -2.34 (0.17), residues: 781 loop : -2.07 (0.10), residues: 3395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP G 61 HIS 0.017 0.002 HIS C 229 PHE 0.037 0.002 PHE V 56 TYR 0.023 0.002 TYR d 76 ARG 0.012 0.001 ARG J 99 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11756 Ramachandran restraints generated. 5878 Oldfield, 0 Emsley, 5878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11756 Ramachandran restraints generated. 5878 Oldfield, 0 Emsley, 5878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 281 time to evaluate : 6.062 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: c 134 MET cc_start: 0.0473 (OUTLIER) cc_final: -0.0384 (pmm) REVERT: d 152 GLN cc_start: -0.1111 (OUTLIER) cc_final: -0.1578 (mt0) REVERT: e 147 MET cc_start: -0.0251 (mmm) cc_final: -0.0531 (mtt) REVERT: f 21 MET cc_start: 0.0101 (ttp) cc_final: -0.0595 (ptm) REVERT: f 56 LYS cc_start: 0.3708 (OUTLIER) cc_final: 0.3508 (pttm) REVERT: f 62 MET cc_start: -0.0413 (ttt) cc_final: -0.1726 (ttt) REVERT: f 88 MET cc_start: 0.0072 (OUTLIER) cc_final: -0.0670 (ttp) REVERT: g 31 MET cc_start: 0.1564 (ppp) cc_final: 0.1194 (ppp) REVERT: j 48 ARG cc_start: 0.3964 (OUTLIER) cc_final: 0.3204 (ptp90) REVERT: m 93 ARG cc_start: 0.3107 (OUTLIER) cc_final: 0.2564 (tpm170) REVERT: n 43 ASN cc_start: -0.1801 (OUTLIER) cc_final: -0.2693 (m-40) REVERT: o 59 MET cc_start: -0.1619 (mtt) cc_final: -0.2103 (tpp) REVERT: o 84 ARG cc_start: 0.2778 (ttt180) cc_final: 0.1602 (mmp80) REVERT: s 37 ARG cc_start: -0.0669 (OUTLIER) cc_final: -0.1855 (tpp80) REVERT: 0 14 MET cc_start: -0.1043 (ptt) cc_final: -0.1418 (ptt) REVERT: 2 1 MET cc_start: -0.3360 (tpt) cc_final: -0.3986 (mpp) REVERT: 2 22 MET cc_start: -0.1425 (mmm) cc_final: -0.1785 (mmm) REVERT: 3 48 MET cc_start: 0.3152 (mmt) cc_final: 0.2279 (mmt) REVERT: 5 137 MET cc_start: -0.4111 (mmt) cc_final: -0.4691 (mmt) REVERT: C 141 HIS cc_start: 0.2873 (OUTLIER) cc_final: 0.2099 (p-80) REVERT: C 176 ARG cc_start: -0.0700 (OUTLIER) cc_final: -0.2573 (mmm-85) REVERT: D 43 ASP cc_start: 0.1933 (OUTLIER) cc_final: 0.1672 (m-30) REVERT: D 161 MET cc_start: 0.4103 (mmm) cc_final: 0.3863 (mmm) REVERT: E 176 ASP cc_start: -0.2323 (OUTLIER) cc_final: -0.2935 (m-30) REVERT: E 199 MET cc_start: -0.2551 (ttp) cc_final: -0.4522 (mmt) REVERT: F 129 MET cc_start: -0.2009 (ptm) cc_final: -0.4870 (tpt) REVERT: H 1 MET cc_start: 0.1425 (ttt) cc_final: 0.0173 (mpp) REVERT: I 135 MET cc_start: -0.1557 (mmp) cc_final: -0.2762 (mtp) REVERT: L 21 ARG cc_start: 0.1395 (OUTLIER) cc_final: 0.1175 (mtt-85) REVERT: L 111 ILE cc_start: 0.0899 (OUTLIER) cc_final: 0.0572 (mt) REVERT: O 30 ARG cc_start: 0.0349 (OUTLIER) cc_final: -0.1278 (ttt-90) REVERT: P 12 MET cc_start: 0.0340 (OUTLIER) cc_final: -0.0503 (tpp) REVERT: R 1 MET cc_start: -0.0187 (mmm) cc_final: -0.1518 (mpp) REVERT: R 89 HIS cc_start: 0.1865 (OUTLIER) cc_final: 0.1076 (m-70) outliers start: 147 outliers final: 76 residues processed: 399 average time/residue: 1.3583 time to fit residues: 938.8455 Evaluate side-chains 344 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 251 time to evaluate : 5.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 8 MET Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 153 MET Chi-restraints excluded: chain c residue 55 ILE Chi-restraints excluded: chain c residue 134 MET Chi-restraints excluded: chain d residue 48 LEU Chi-restraints excluded: chain d residue 132 ILE Chi-restraints excluded: chain d residue 142 VAL Chi-restraints excluded: chain d residue 152 GLN Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 96 MET Chi-restraints excluded: chain f residue 2 ARG Chi-restraints excluded: chain f residue 51 ILE Chi-restraints excluded: chain f residue 56 LYS Chi-restraints excluded: chain f residue 88 MET Chi-restraints excluded: chain h residue 38 ASN Chi-restraints excluded: chain i residue 72 ILE Chi-restraints excluded: chain j residue 48 ARG Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain k residue 17 SER Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain m residue 9 ILE Chi-restraints excluded: chain m residue 93 ARG Chi-restraints excluded: chain n residue 43 ASN Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain s residue 14 HIS Chi-restraints excluded: chain s residue 37 ARG Chi-restraints excluded: chain t residue 40 GLU Chi-restraints excluded: chain u residue 10 GLU Chi-restraints excluded: chain 5 residue 97 MET Chi-restraints excluded: chain 5 residue 111 PHE Chi-restraints excluded: chain 5 residue 155 ASN Chi-restraints excluded: chain 5 residue 184 LYS Chi-restraints excluded: chain 5 residue 217 THR Chi-restraints excluded: chain C residue 24 HIS Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain C residue 176 ARG Chi-restraints excluded: chain C residue 242 HIS Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 118 PHE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain F residue 21 TYR Chi-restraints excluded: chain F residue 22 ASN Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 61 TRP Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 150 TYR Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain I residue 35 MET Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain J residue 108 MET Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain L residue 21 ARG Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 60 ARG Chi-restraints excluded: chain L residue 69 ARG Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 107 PHE Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain O residue 30 ARG Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 12 MET Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 83 TYR Chi-restraints excluded: chain R residue 89 HIS Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain Y residue 27 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1043 random chunks: chunk 972 optimal weight: 30.0000 chunk 113 optimal weight: 7.9990 chunk 574 optimal weight: 20.0000 chunk 736 optimal weight: 20.0000 chunk 570 optimal weight: 6.9990 chunk 849 optimal weight: 20.0000 chunk 563 optimal weight: 20.0000 chunk 1005 optimal weight: 20.0000 chunk 629 optimal weight: 40.0000 chunk 612 optimal weight: 30.0000 chunk 464 optimal weight: 10.0000 overall best weight: 12.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 139 GLN ** d 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 37 GLN 5 83 ASN ** 5 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 ASN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 93 ASN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 72 GLN ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 44 HIS ** X 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 45 GLN ** Z 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2212 moved from start: 1.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.282 160568 Z= 0.522 Angle : 1.425 22.437 240143 Z= 0.698 Chirality : 0.067 0.802 30705 Planarity : 0.011 0.140 12903 Dihedral : 26.026 179.682 80207 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 66.23 Ramachandran Plot: Outliers : 1.41 % Allowed : 15.45 % Favored : 83.14 % Rotamer: Outliers : 4.62 % Allowed : 15.83 % Favored : 79.55 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.05 % Twisted Proline : 0.50 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.82 (0.10), residues: 5878 helix: -2.32 (0.11), residues: 1636 sheet: -2.65 (0.18), residues: 707 loop : -2.71 (0.10), residues: 3535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.129 0.006 TRP Q 60 HIS 0.032 0.005 HIS C 229 PHE 0.060 0.005 PHE n 21 TYR 0.049 0.005 TYR r 51 ARG 0.071 0.002 ARG F 101 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11756 Ramachandran restraints generated. 5878 Oldfield, 0 Emsley, 5878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11756 Ramachandran restraints generated. 5878 Oldfield, 0 Emsley, 5878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 310 time to evaluate : 6.148 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: c 134 MET cc_start: 0.1371 (OUTLIER) cc_final: 0.0272 (pmm) REVERT: d 132 ILE cc_start: -0.0466 (OUTLIER) cc_final: -0.0683 (pt) REVERT: f 21 MET cc_start: -0.0241 (ttp) cc_final: -0.1151 (ptm) REVERT: f 56 LYS cc_start: 0.3631 (OUTLIER) cc_final: 0.2990 (pttm) REVERT: f 62 MET cc_start: -0.0327 (ttt) cc_final: -0.1360 (ttt) REVERT: g 5 ARG cc_start: -0.1374 (OUTLIER) cc_final: -0.3093 (ttt180) REVERT: j 48 ARG cc_start: 0.3961 (OUTLIER) cc_final: 0.3581 (ptp90) REVERT: k 85 MET cc_start: 0.0243 (mtp) cc_final: -0.0162 (mtp) REVERT: k 108 THR cc_start: -0.0656 (OUTLIER) cc_final: -0.0881 (t) REVERT: m 81 MET cc_start: -0.2567 (ttt) cc_final: -0.2796 (ttt) REVERT: o 84 ARG cc_start: 0.3373 (ttt180) cc_final: 0.3057 (mmp80) REVERT: s 37 ARG cc_start: 0.0644 (OUTLIER) cc_final: -0.0723 (tpp80) REVERT: u 4 ILE cc_start: 0.0987 (mm) cc_final: 0.0561 (mm) REVERT: 0 14 MET cc_start: 0.0076 (ptt) cc_final: -0.0562 (ptt) REVERT: 0 19 ASP cc_start: 0.5917 (OUTLIER) cc_final: 0.5214 (m-30) REVERT: 2 1 MET cc_start: -0.2999 (tpt) cc_final: -0.4661 (ptm) REVERT: 3 48 MET cc_start: 0.3845 (mmt) cc_final: 0.2917 (mmt) REVERT: 5 137 MET cc_start: -0.3771 (mmt) cc_final: -0.4366 (mmt) REVERT: C 141 HIS cc_start: 0.2694 (OUTLIER) cc_final: 0.1914 (p-80) REVERT: C 224 MET cc_start: 0.2255 (ttm) cc_final: 0.1909 (tpp) REVERT: C 229 HIS cc_start: 0.2328 (OUTLIER) cc_final: 0.2113 (m170) REVERT: D 161 MET cc_start: 0.4622 (mmm) cc_final: 0.4290 (mmp) REVERT: E 176 ASP cc_start: -0.1748 (OUTLIER) cc_final: -0.2017 (m-30) REVERT: E 199 MET cc_start: -0.1490 (ttp) cc_final: -0.3580 (mmt) REVERT: F 16 MET cc_start: -0.2055 (mmt) cc_final: -0.3056 (mmt) REVERT: F 25 MET cc_start: 0.3925 (tpt) cc_final: 0.3224 (mmp) REVERT: I 135 MET cc_start: -0.2463 (mmp) cc_final: -0.2770 (mmt) REVERT: L 21 ARG cc_start: 0.2882 (OUTLIER) cc_final: 0.2645 (mtt-85) REVERT: L 59 ARG cc_start: 0.5240 (OUTLIER) cc_final: 0.4967 (mmm-85) REVERT: L 111 ILE cc_start: 0.0792 (OUTLIER) cc_final: 0.0461 (mt) REVERT: O 94 ARG cc_start: -0.0481 (OUTLIER) cc_final: -0.2055 (ptp90) REVERT: Q 91 ARG cc_start: 0.0716 (OUTLIER) cc_final: 0.0460 (mpt180) REVERT: R 1 MET cc_start: 0.1612 (mmm) cc_final: 0.0683 (mpp) REVERT: U 86 PHE cc_start: 0.0406 (OUTLIER) cc_final: -0.1633 (t80) REVERT: U 93 ARG cc_start: 0.3585 (mtm180) cc_final: 0.3219 (mtm180) REVERT: V 45 ASP cc_start: 0.6365 (OUTLIER) cc_final: 0.6037 (m-30) REVERT: Y 1 MET cc_start: 0.0664 (ttt) cc_final: -0.0158 (ttt) REVERT: Z 53 MET cc_start: -0.0074 (mtp) cc_final: -0.0655 (mtp) outliers start: 225 outliers final: 121 residues processed: 489 average time/residue: 1.3697 time to fit residues: 1152.2368 Evaluate side-chains 407 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 268 time to evaluate : 6.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 8 MET Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 106 VAL Chi-restraints excluded: chain b residue 150 ILE Chi-restraints excluded: chain b residue 153 MET Chi-restraints excluded: chain b residue 219 THR Chi-restraints excluded: chain c residue 55 ILE Chi-restraints excluded: chain c residue 77 ILE Chi-restraints excluded: chain c residue 93 ASP Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 134 MET Chi-restraints excluded: chain c residue 172 ARG Chi-restraints excluded: chain c residue 193 TYR Chi-restraints excluded: chain d residue 48 LEU Chi-restraints excluded: chain d residue 132 ILE Chi-restraints excluded: chain d residue 152 GLN Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain f residue 2 ARG Chi-restraints excluded: chain f residue 51 ILE Chi-restraints excluded: chain f residue 56 LYS Chi-restraints excluded: chain f residue 65 GLU Chi-restraints excluded: chain f residue 88 MET Chi-restraints excluded: chain g residue 5 ARG Chi-restraints excluded: chain g residue 120 LEU Chi-restraints excluded: chain h residue 14 ILE Chi-restraints excluded: chain h residue 38 ASN Chi-restraints excluded: chain i residue 72 ILE Chi-restraints excluded: chain i residue 88 MET Chi-restraints excluded: chain j residue 48 ARG Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain j residue 63 ASP Chi-restraints excluded: chain k residue 108 THR Chi-restraints excluded: chain l residue 82 ILE Chi-restraints excluded: chain l residue 119 VAL Chi-restraints excluded: chain n residue 6 MET Chi-restraints excluded: chain n residue 48 LEU Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain p residue 1 MET Chi-restraints excluded: chain p residue 42 ILE Chi-restraints excluded: chain q residue 29 VAL Chi-restraints excluded: chain q residue 65 ARG Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain s residue 14 HIS Chi-restraints excluded: chain s residue 37 ARG Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain 0 residue 19 ASP Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 5 residue 97 MET Chi-restraints excluded: chain 5 residue 121 MET Chi-restraints excluded: chain 5 residue 153 VAL Chi-restraints excluded: chain 5 residue 184 LYS Chi-restraints excluded: chain 5 residue 217 THR Chi-restraints excluded: chain C residue 24 HIS Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 141 HIS Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 229 HIS Chi-restraints excluded: chain C residue 242 HIS Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 118 PHE Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain F residue 21 TYR Chi-restraints excluded: chain F residue 22 ASN Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 61 TRP Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 150 TYR Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain L residue 21 ARG Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 59 ARG Chi-restraints excluded: chain L residue 60 ARG Chi-restraints excluded: chain L residue 69 ARG Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 107 PHE Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 73 ASN Chi-restraints excluded: chain O residue 76 LYS Chi-restraints excluded: chain O residue 94 ARG Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 67 GLU Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 73 PHE Chi-restraints excluded: chain P residue 77 SER Chi-restraints excluded: chain P residue 98 TYR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain Q residue 91 ARG Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 83 TYR Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 69 LEU Chi-restraints excluded: chain S residue 75 PHE Chi-restraints excluded: chain S residue 106 VAL Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 48 GLN Chi-restraints excluded: chain T residue 51 PHE Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 86 PHE Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 72 VAL Chi-restraints excluded: chain W residue 44 PHE Chi-restraints excluded: chain W residue 55 ASP Chi-restraints excluded: chain X residue 3 VAL Chi-restraints excluded: chain X residue 71 ARG Chi-restraints excluded: chain Y residue 27 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1043 random chunks: chunk 621 optimal weight: 20.0000 chunk 401 optimal weight: 0.9980 chunk 600 optimal weight: 9.9990 chunk 302 optimal weight: 8.9990 chunk 197 optimal weight: 4.9990 chunk 194 optimal weight: 8.9990 chunk 639 optimal weight: 20.0000 chunk 684 optimal weight: 20.0000 chunk 497 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 790 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: ** b 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 139 GLN ** d 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 196 ASN ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 64 GLN ** j 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 14 HIS ** m 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 83 ASN 5 110 ASN ** 5 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 ASN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 HIS ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 26 ASN ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 44 HIS ** W 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 33 HIS ** Z 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1949 moved from start: 1.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 160568 Z= 0.249 Angle : 0.913 14.069 240143 Z= 0.460 Chirality : 0.047 0.361 30705 Planarity : 0.006 0.070 12903 Dihedral : 25.562 179.102 80207 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 37.07 Ramachandran Plot: Outliers : 1.29 % Allowed : 11.82 % Favored : 86.88 % Rotamer: Outliers : 3.02 % Allowed : 17.96 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.10), residues: 5878 helix: -1.89 (0.11), residues: 1671 sheet: -2.45 (0.18), residues: 760 loop : -2.61 (0.10), residues: 3447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.005 TRP Q 60 HIS 0.023 0.002 HIS p 59 PHE 0.031 0.003 PHE U 86 TYR 0.032 0.003 TYR R 2 ARG 0.013 0.001 ARG N 103 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11756 Ramachandran restraints generated. 5878 Oldfield, 0 Emsley, 5878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11756 Ramachandran restraints generated. 5878 Oldfield, 0 Emsley, 5878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 297 time to evaluate : 6.112 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: c 134 MET cc_start: 0.1072 (OUTLIER) cc_final: 0.0386 (pmm) REVERT: d 22 LYS cc_start: -0.0551 (mmmt) cc_final: -0.0860 (tttt) REVERT: d 41 HIS cc_start: 0.0911 (m-70) cc_final: 0.0086 (t-90) REVERT: d 132 ILE cc_start: -0.0961 (OUTLIER) cc_final: -0.1265 (pt) REVERT: d 152 GLN cc_start: -0.1164 (OUTLIER) cc_final: -0.1814 (mt0) REVERT: f 56 LYS cc_start: 0.2874 (OUTLIER) cc_final: 0.2628 (pttm) REVERT: f 62 MET cc_start: -0.0393 (ttt) cc_final: -0.0770 (ttt) REVERT: k 85 MET cc_start: -0.0435 (mtp) cc_final: -0.0789 (mtp) REVERT: u 4 ILE cc_start: -0.0218 (mm) cc_final: -0.0558 (mm) REVERT: 0 14 MET cc_start: 0.0223 (ptt) cc_final: -0.0021 (ptt) REVERT: 2 22 MET cc_start: -0.1830 (mmm) cc_final: -0.2350 (tpt) REVERT: 3 48 MET cc_start: 0.3497 (mmt) cc_final: 0.2567 (mmt) REVERT: 5 137 MET cc_start: -0.3791 (mmt) cc_final: -0.4318 (mmt) REVERT: 5 200 LYS cc_start: 0.1775 (OUTLIER) cc_final: 0.0809 (tmtt) REVERT: D 161 MET cc_start: 0.3943 (mmm) cc_final: 0.3499 (mmp) REVERT: E 199 MET cc_start: -0.2024 (ttp) cc_final: -0.4079 (mmt) REVERT: F 16 MET cc_start: -0.1881 (mmt) cc_final: -0.3176 (mmt) REVERT: F 25 MET cc_start: 0.4752 (tpt) cc_final: 0.3556 (mmp) REVERT: F 129 MET cc_start: -0.1019 (ptm) cc_final: -0.1418 (tmm) REVERT: H 1 MET cc_start: 0.2848 (mpp) cc_final: 0.2399 (mpp) REVERT: I 135 MET cc_start: -0.1733 (mmp) cc_final: -0.2322 (mmp) REVERT: J 12 LYS cc_start: -0.1369 (OUTLIER) cc_final: -0.2744 (mttm) REVERT: L 69 ARG cc_start: 0.3023 (OUTLIER) cc_final: 0.2473 (mtt90) REVERT: O 94 ARG cc_start: 0.0196 (OUTLIER) cc_final: -0.1054 (ptp90) REVERT: P 12 MET cc_start: 0.1711 (mmm) cc_final: 0.1499 (mmm) REVERT: R 1 MET cc_start: 0.1962 (mmm) cc_final: 0.1556 (mpp) REVERT: U 51 LEU cc_start: 0.2390 (OUTLIER) cc_final: 0.1799 (tp) REVERT: U 86 PHE cc_start: 0.0014 (OUTLIER) cc_final: -0.1937 (t80) REVERT: Y 1 MET cc_start: 0.0147 (ttt) cc_final: -0.0650 (ttt) REVERT: Z 46 MET cc_start: -0.0809 (ptt) cc_final: -0.1012 (ptt) REVERT: Z 53 MET cc_start: -0.0433 (mtp) cc_final: -0.1011 (mtp) outliers start: 147 outliers final: 103 residues processed: 413 average time/residue: 1.3251 time to fit residues: 931.8147 Evaluate side-chains 378 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 265 time to evaluate : 5.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 8 MET Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 150 ILE Chi-restraints excluded: chain b residue 153 MET Chi-restraints excluded: chain b residue 213 LEU Chi-restraints excluded: chain b residue 219 THR Chi-restraints excluded: chain c residue 77 ILE Chi-restraints excluded: chain c residue 134 MET Chi-restraints excluded: chain c residue 157 LEU Chi-restraints excluded: chain c residue 193 TYR Chi-restraints excluded: chain d residue 48 LEU Chi-restraints excluded: chain d residue 132 ILE Chi-restraints excluded: chain d residue 152 GLN Chi-restraints excluded: chain d residue 196 ASN Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain f residue 2 ARG Chi-restraints excluded: chain f residue 51 ILE Chi-restraints excluded: chain f residue 56 LYS Chi-restraints excluded: chain h residue 107 SER Chi-restraints excluded: chain i residue 27 LYS Chi-restraints excluded: chain i residue 72 ILE Chi-restraints excluded: chain i residue 88 MET Chi-restraints excluded: chain j residue 48 ARG Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain l residue 82 ILE Chi-restraints excluded: chain l residue 119 VAL Chi-restraints excluded: chain m residue 9 ILE Chi-restraints excluded: chain n residue 6 MET Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain p residue 59 HIS Chi-restraints excluded: chain q residue 25 ILE Chi-restraints excluded: chain s residue 14 HIS Chi-restraints excluded: chain s residue 37 ARG Chi-restraints excluded: chain 2 residue 41 ARG Chi-restraints excluded: chain 5 residue 1 MET Chi-restraints excluded: chain 5 residue 97 MET Chi-restraints excluded: chain 5 residue 153 VAL Chi-restraints excluded: chain 5 residue 173 THR Chi-restraints excluded: chain 5 residue 184 LYS Chi-restraints excluded: chain 5 residue 200 LYS Chi-restraints excluded: chain 5 residue 217 THR Chi-restraints excluded: chain C residue 24 HIS Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 242 HIS Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 118 PHE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 101 TYR Chi-restraints excluded: chain E residue 117 ARG Chi-restraints excluded: chain F residue 21 TYR Chi-restraints excluded: chain F residue 22 ASN Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 61 TRP Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 150 TYR Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain K residue 20 MET Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 23 LYS Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 60 ARG Chi-restraints excluded: chain L residue 69 ARG Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 107 PHE Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 102 PHE Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 94 ARG Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 67 GLU Chi-restraints excluded: chain P residue 98 TYR Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain Q residue 60 TRP Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 83 TYR Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 75 PHE Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 86 PHE Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain X residue 71 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1043 random chunks: chunk 914 optimal weight: 20.0000 chunk 963 optimal weight: 20.0000 chunk 878 optimal weight: 10.0000 chunk 936 optimal weight: 20.0000 chunk 962 optimal weight: 30.0000 chunk 563 optimal weight: 7.9990 chunk 408 optimal weight: 8.9990 chunk 735 optimal weight: 20.0000 chunk 287 optimal weight: 20.0000 chunk 846 optimal weight: 20.0000 chunk 886 optimal weight: 20.0000 overall best weight: 13.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 116 GLN ** d 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 67 GLN ** i 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 75 GLN ** m 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 51 HIS ** p 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 5 ASN ** 3 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 27 ASN ** 5 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 ASN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 ASN Y 38 GLN Y 45 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2547 moved from start: 1.8068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.283 160568 Z= 0.555 Angle : 1.628 24.086 240143 Z= 0.787 Chirality : 0.074 0.677 30705 Planarity : 0.013 0.229 12903 Dihedral : 26.846 178.599 80207 Min Nonbonded Distance : 1.718 Molprobity Statistics. All-atom Clashscore : 80.30 Ramachandran Plot: Outliers : 1.70 % Allowed : 17.86 % Favored : 80.44 % Rotamer: Outliers : 3.90 % Allowed : 18.09 % Favored : 78.01 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.05 % Twisted Proline : 1.51 % Twisted General : 0.42 % 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: -4.46 (0.09), residues: 5878 helix: -2.80 (0.10), residues: 1632 sheet: -2.89 (0.18), residues: 706 loop : -3.20 (0.09), residues: 3540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.110 0.009 TRP b 22 HIS 0.071 0.005 HIS d 198 PHE 0.096 0.006 PHE W 59 TYR 0.051 0.006 TYR K 32 ARG 0.085 0.002 ARG F 91 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11756 Ramachandran restraints generated. 5878 Oldfield, 0 Emsley, 5878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11756 Ramachandran restraints generated. 5878 Oldfield, 0 Emsley, 5878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 323 time to evaluate : 6.126 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: b 135 MET cc_start: -0.1509 (mmt) cc_final: -0.2398 (mmp) REVERT: c 3 GLN cc_start: 0.3695 (OUTLIER) cc_final: 0.3359 (tp40) REVERT: c 134 MET cc_start: 0.0767 (OUTLIER) cc_final: 0.0018 (pmm) REVERT: d 22 LYS cc_start: 0.0325 (mmmt) cc_final: -0.0878 (tttt) REVERT: d 132 ILE cc_start: 0.0188 (OUTLIER) cc_final: -0.0085 (pt) REVERT: f 62 MET cc_start: 0.0004 (ttt) cc_final: -0.0877 (ttt) REVERT: f 78 PHE cc_start: -0.2297 (OUTLIER) cc_final: -0.2994 (t80) REVERT: g 31 MET cc_start: 0.0094 (OUTLIER) cc_final: -0.0287 (ppp) REVERT: g 116 MET cc_start: 0.1958 (tmm) cc_final: 0.1275 (ttp) REVERT: p 59 HIS cc_start: 0.4072 (OUTLIER) cc_final: 0.3852 (p-80) REVERT: u 4 ILE cc_start: 0.1863 (mm) cc_final: 0.1409 (mm) REVERT: 0 14 MET cc_start: 0.0366 (ptt) cc_final: 0.0039 (ptt) REVERT: 2 1 MET cc_start: -0.2600 (tpt) cc_final: -0.4957 (ptt) REVERT: 3 48 MET cc_start: 0.3981 (mmt) cc_final: 0.2864 (mmt) REVERT: 5 137 MET cc_start: -0.3965 (mmt) cc_final: -0.4645 (mmt) REVERT: C 180 MET cc_start: -0.1328 (mtt) cc_final: -0.1833 (mtt) REVERT: C 224 MET cc_start: 0.2658 (OUTLIER) cc_final: 0.2326 (ttm) REVERT: E 199 MET cc_start: -0.1698 (ttp) cc_final: -0.3449 (tpt) REVERT: F 16 MET cc_start: -0.2256 (mmt) cc_final: -0.3210 (mmt) REVERT: F 25 MET cc_start: 0.4710 (tpt) cc_final: 0.3891 (mmp) REVERT: F 129 MET cc_start: -0.1491 (ptm) cc_final: -0.1895 (ptm) REVERT: H 4 ILE cc_start: -0.2818 (OUTLIER) cc_final: -0.3123 (mt) REVERT: I 16 MET cc_start: 0.2992 (OUTLIER) cc_final: 0.2379 (mtp) REVERT: I 124 MET cc_start: 0.0441 (mmp) cc_final: -0.0033 (tpt) REVERT: I 135 MET cc_start: -0.1956 (mmp) cc_final: -0.2590 (mmp) REVERT: J 118 MET cc_start: 0.4967 (ppp) cc_final: 0.4564 (ppp) REVERT: L 59 ARG cc_start: 0.5509 (OUTLIER) cc_final: 0.5168 (mmm-85) REVERT: O 94 ARG cc_start: 0.0051 (OUTLIER) cc_final: -0.1432 (ptp90) REVERT: P 113 LEU cc_start: 0.1392 (OUTLIER) cc_final: 0.0883 (tp) REVERT: Q 91 ARG cc_start: 0.0707 (OUTLIER) cc_final: 0.0397 (mpt180) REVERT: R 83 TYR cc_start: 0.2855 (OUTLIER) cc_final: 0.1872 (t80) REVERT: R 89 HIS cc_start: 0.3474 (OUTLIER) cc_final: 0.2028 (m-70) REVERT: V 45 ASP cc_start: 0.6008 (OUTLIER) cc_final: 0.5801 (m-30) outliers start: 190 outliers final: 125 residues processed: 473 average time/residue: 1.3580 time to fit residues: 1098.9301 Evaluate side-chains 426 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 285 time to evaluate : 5.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 8 MET Chi-restraints excluded: chain b residue 17 HIS Chi-restraints excluded: chain b residue 21 TYR Chi-restraints excluded: chain b residue 44 LYS Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain b residue 150 ILE Chi-restraints excluded: chain b residue 153 MET Chi-restraints excluded: chain b residue 213 LEU Chi-restraints excluded: chain b residue 219 THR Chi-restraints excluded: chain c residue 3 GLN Chi-restraints excluded: chain c residue 77 ILE Chi-restraints excluded: chain c residue 93 ASP Chi-restraints excluded: chain c residue 134 MET Chi-restraints excluded: chain c residue 157 LEU Chi-restraints excluded: chain c residue 193 TYR Chi-restraints excluded: chain d residue 48 LEU Chi-restraints excluded: chain d residue 98 LEU Chi-restraints excluded: chain d residue 99 ASP Chi-restraints excluded: chain d residue 132 ILE Chi-restraints excluded: chain d residue 152 GLN Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain f residue 2 ARG Chi-restraints excluded: chain f residue 51 ILE Chi-restraints excluded: chain f residue 56 LYS Chi-restraints excluded: chain f residue 65 GLU Chi-restraints excluded: chain f residue 78 PHE Chi-restraints excluded: chain g residue 31 MET Chi-restraints excluded: chain h residue 10 MET Chi-restraints excluded: chain h residue 38 ASN Chi-restraints excluded: chain h residue 107 SER Chi-restraints excluded: chain i residue 72 ILE Chi-restraints excluded: chain i residue 88 MET Chi-restraints excluded: chain i residue 100 LYS Chi-restraints excluded: chain i residue 104 VAL Chi-restraints excluded: chain i residue 111 VAL Chi-restraints excluded: chain j residue 48 ARG Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain l residue 82 ILE Chi-restraints excluded: chain l residue 110 ARG Chi-restraints excluded: chain l residue 119 VAL Chi-restraints excluded: chain m residue 85 CYS Chi-restraints excluded: chain n residue 6 MET Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain p residue 59 HIS Chi-restraints excluded: chain q residue 65 ARG Chi-restraints excluded: chain s residue 14 HIS Chi-restraints excluded: chain s residue 37 ARG Chi-restraints excluded: chain s residue 62 VAL Chi-restraints excluded: chain 2 residue 41 ARG Chi-restraints excluded: chain 3 residue 58 ILE Chi-restraints excluded: chain 5 residue 23 ILE Chi-restraints excluded: chain 5 residue 97 MET Chi-restraints excluded: chain 5 residue 121 MET Chi-restraints excluded: chain 5 residue 146 THR Chi-restraints excluded: chain 5 residue 153 VAL Chi-restraints excluded: chain 5 residue 173 THR Chi-restraints excluded: chain 5 residue 184 LYS Chi-restraints excluded: chain 5 residue 217 THR Chi-restraints excluded: chain C residue 24 HIS Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 95 TYR Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 118 PHE Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 5 LEU Chi-restraints excluded: chain E residue 117 ARG Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain F residue 21 TYR Chi-restraints excluded: chain F residue 22 ASN Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 119 LYS Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 61 TRP Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 150 TYR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 59 ARG Chi-restraints excluded: chain L residue 60 ARG Chi-restraints excluded: chain L residue 69 ARG Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 107 PHE Chi-restraints excluded: chain L residue 109 LYS Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 73 ASN Chi-restraints excluded: chain N residue 102 PHE Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 80 GLU Chi-restraints excluded: chain O residue 94 ARG Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 51 ASN Chi-restraints excluded: chain P residue 67 GLU Chi-restraints excluded: chain P residue 73 PHE Chi-restraints excluded: chain P residue 98 TYR Chi-restraints excluded: chain P residue 113 LEU Chi-restraints excluded: chain Q residue 51 GLN Chi-restraints excluded: chain Q residue 60 TRP Chi-restraints excluded: chain Q residue 91 ARG Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 83 TYR Chi-restraints excluded: chain R residue 89 HIS Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 75 PHE Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 51 PHE Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain V residue 45 ASP Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain X residue 22 ASN Chi-restraints excluded: chain X residue 71 ARG Chi-restraints excluded: chain Y residue 27 ASN Chi-restraints excluded: chain Y residue 45 GLN Chi-restraints excluded: chain Y residue 50 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1043 random chunks: chunk 933 optimal weight: 20.0000 chunk 615 optimal weight: 20.0000 chunk 990 optimal weight: 20.0000 chunk 604 optimal weight: 9.9990 chunk 469 optimal weight: 9.9990 chunk 688 optimal weight: 20.0000 chunk 1039 optimal weight: 20.0000 chunk 956 optimal weight: 10.0000 chunk 827 optimal weight: 5.9990 chunk 85 optimal weight: 30.0000 chunk 639 optimal weight: 20.0000 overall best weight: 11.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 119 GLN ** b 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 75 GLN i 126 GLN ** j 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 8 ASN ** m 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 83 ASN ** 5 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 GLN C 133 ASN ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 HIS ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 27 ASN Y 58 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2427 moved from start: 1.8915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.242 160568 Z= 0.379 Angle : 1.186 23.544 240143 Z= 0.593 Chirality : 0.058 0.924 30705 Planarity : 0.009 0.129 12903 Dihedral : 26.657 179.393 80207 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 54.27 Ramachandran Plot: Outliers : 1.31 % Allowed : 16.01 % Favored : 82.68 % Rotamer: Outliers : 2.77 % Allowed : 19.81 % Favored : 77.42 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.05 % Twisted Proline : 0.50 % Twisted General : 0.37 % 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: -4.28 (0.09), residues: 5878 helix: -2.50 (0.10), residues: 1653 sheet: -2.74 (0.18), residues: 677 loop : -3.18 (0.09), residues: 3548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.006 TRP Q 60 HIS 0.020 0.003 HIS j 70 PHE 0.080 0.004 PHE W 59 TYR 0.062 0.004 TYR C 170 ARG 0.032 0.002 ARG g 92 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11756 Ramachandran restraints generated. 5878 Oldfield, 0 Emsley, 5878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11756 Ramachandran restraints generated. 5878 Oldfield, 0 Emsley, 5878 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 311 time to evaluate : 6.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 132 ARG cc_start: 0.5716 (mtt180) cc_final: 0.5369 (mtt-85) REVERT: c 134 MET cc_start: 0.0616 (OUTLIER) cc_final: 0.0144 (pmm) REVERT: d 22 LYS cc_start: -0.0188 (mmmt) cc_final: -0.0853 (tttt) REVERT: d 132 ILE cc_start: -0.0011 (OUTLIER) cc_final: -0.0435 (pt) REVERT: d 196 ASN cc_start: 0.3020 (p0) cc_final: 0.2734 (p0) REVERT: f 56 LYS cc_start: 0.4359 (OUTLIER) cc_final: 0.3872 (pttm) REVERT: f 62 MET cc_start: 0.0361 (ttt) cc_final: -0.0019 (ttt) REVERT: g 116 MET cc_start: 0.1626 (tmm) cc_final: 0.1047 (ttp) REVERT: t 80 THR cc_start: 0.2304 (OUTLIER) cc_final: 0.1504 (m) REVERT: 2 1 MET cc_start: -0.2216 (tpt) cc_final: -0.4403 (ptm) REVERT: 3 48 MET cc_start: 0.3319 (mmt) cc_final: 0.2391 (mmt) REVERT: 5 137 MET cc_start: -0.4001 (mmt) cc_final: -0.4752 (mmt) REVERT: C 259 ASN cc_start: 0.0264 (t160) cc_final: -0.0161 (m-40) REVERT: E 97 ASN cc_start: 0.3243 (OUTLIER) cc_final: 0.2991 (m-40) REVERT: E 188 MET cc_start: -0.1087 (tpt) cc_final: -0.1593 (tpt) REVERT: E 199 MET cc_start: -0.2265 (ttp) cc_final: -0.3585 (tpt) REVERT: F 16 MET cc_start: -0.1931 (mmt) cc_final: -0.2971 (mmt) REVERT: F 25 MET cc_start: 0.4947 (tpt) cc_final: 0.4439 (mmp) REVERT: I 16 MET cc_start: 0.3504 (OUTLIER) cc_final: 0.2896 (mtp) REVERT: I 135 MET cc_start: -0.1006 (mmp) cc_final: -0.1864 (mmt) REVERT: L 69 ARG cc_start: 0.2797 (OUTLIER) cc_final: 0.2272 (mpt-90) REVERT: N 102 PHE cc_start: 0.2669 (OUTLIER) cc_final: 0.2248 (p90) REVERT: O 94 ARG cc_start: 0.0096 (OUTLIER) cc_final: -0.1431 (ptp90) REVERT: R 83 TYR cc_start: 0.2210 (OUTLIER) cc_final: 0.1361 (t80) REVERT: R 89 HIS cc_start: 0.2594 (OUTLIER) cc_final: 0.1307 (m170) REVERT: Y 1 MET cc_start: 0.0775 (ttt) cc_final: -0.0123 (ttt) outliers start: 135 outliers final: 94 residues processed: 414 average time/residue: 1.3798 time to fit residues: 982.5241 Evaluate side-chains 396 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 291 time to evaluate : 5.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 106 VAL Chi-restraints excluded: chain b residue 150 ILE Chi-restraints excluded: chain b residue 213 LEU Chi-restraints excluded: chain b residue 219 THR Chi-restraints excluded: chain c residue 77 ILE Chi-restraints excluded: chain c residue 134 MET Chi-restraints excluded: chain d residue 48 LEU Chi-restraints excluded: chain d residue 98 LEU Chi-restraints excluded: chain d residue 132 ILE Chi-restraints excluded: chain d residue 152 GLN Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 112 ARG Chi-restraints excluded: chain f residue 2 ARG Chi-restraints excluded: chain f residue 56 LYS Chi-restraints excluded: chain f residue 65 GLU Chi-restraints excluded: chain h residue 107 SER Chi-restraints excluded: chain i residue 72 ILE Chi-restraints excluded: chain i residue 88 MET Chi-restraints excluded: chain i residue 100 LYS Chi-restraints excluded: chain j residue 48 ARG Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain l residue 82 ILE Chi-restraints excluded: chain l residue 110 ARG Chi-restraints excluded: chain m residue 85 CYS Chi-restraints excluded: chain n residue 6 MET Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 42 HIS Chi-restraints excluded: chain p residue 59 HIS Chi-restraints excluded: chain q residue 65 ARG Chi-restraints excluded: chain r residue 72 ASP Chi-restraints excluded: chain s residue 14 HIS Chi-restraints excluded: chain s residue 37 ARG Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain t residue 27 MET Chi-restraints excluded: chain t residue 48 GLN Chi-restraints excluded: chain t residue 54 MET Chi-restraints excluded: chain t residue 80 THR Chi-restraints excluded: chain 2 residue 41 ARG Chi-restraints excluded: chain 5 residue 97 MET Chi-restraints excluded: chain 5 residue 109 MET Chi-restraints excluded: chain 5 residue 173 THR Chi-restraints excluded: chain 5 residue 184 LYS Chi-restraints excluded: chain 5 residue 217 THR Chi-restraints excluded: chain C residue 24 HIS Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 59 GLN Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 118 PHE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 117 ARG Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain F residue 21 TYR Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 61 TRP Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 150 TYR Chi-restraints excluded: chain I residue 16 MET Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain L residue 60 ARG Chi-restraints excluded: chain L residue 69 ARG Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 107 PHE Chi-restraints excluded: chain L residue 109 LYS Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 102 PHE Chi-restraints excluded: chain O residue 94 ARG Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 51 ASN Chi-restraints excluded: chain P residue 73 PHE Chi-restraints excluded: chain Q residue 60 TRP Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 83 TYR Chi-restraints excluded: chain R residue 89 HIS Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 75 PHE Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 51 PHE Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 64 VAL Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain X residue 71 ARG Chi-restraints excluded: chain Y residue 50 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1043 random chunks: chunk 507 optimal weight: 2.9990 chunk 657 optimal weight: 20.0000 chunk 881 optimal weight: 20.0000 chunk 253 optimal weight: 10.0000 chunk 762 optimal weight: 20.0000 chunk 122 optimal weight: 0.9990 chunk 229 optimal weight: 4.9990 chunk 828 optimal weight: 20.0000 chunk 346 optimal weight: 5.9990 chunk 850 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 57 ASN b 167 HIS ** d 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 75 GLN m 8 ASN m 12 HIS ** m 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 40 GLN ** 3 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 83 ASN ** 5 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 ASN ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 ASN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 ASN H 145 ASN J 40 HIS ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 HIS ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 HIS ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 58 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.120039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.110117 restraints weight = 1251042.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.111895 restraints weight = 826933.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.113069 restraints weight = 589801.588| |-----------------------------------------------------------------------------| r_work (final): 0.4509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4007 moved from start: 1.8924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.273 160568 Z= 0.259 Angle : 0.956 17.248 240143 Z= 0.476 Chirality : 0.048 0.437 30705 Planarity : 0.007 0.125 12903 Dihedral : 26.244 177.039 80207 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 38.21 Ramachandran Plot: Outliers : 1.29 % Allowed : 13.85 % Favored : 84.86 % Rotamer: Outliers : 2.09 % Allowed : 20.53 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.81 (0.10), residues: 5878 helix: -1.96 (0.11), residues: 1674 sheet: -2.40 (0.18), residues: 707 loop : -2.98 (0.09), residues: 3497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.004 TRP Q 60 HIS 0.099 0.003 HIS R 89 PHE 0.044 0.003 PHE O 97 TYR 0.029 0.003 TYR J 75 ARG 0.037 0.001 ARG S 25 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21277.31 seconds wall clock time: 385 minutes 38.93 seconds (23138.93 seconds total)