Starting phenix.real_space_refine (version: dev) on Fri May 20 18:01:40 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcd_6549/05_2022/3jcd_6549_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcd_6549/05_2022/3jcd_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_6549/05_2022/3jcd_6549.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcd_6549/05_2022/3jcd_6549.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcd_6549/05_2022/3jcd_6549_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jcd_6549/05_2022/3jcd_6549_neut.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/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: {'PTRANS': 4, 'TRANS': 96, 'PCIS': 1} 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, 'PTRANS': 6, 'TRANS': 225, 'PCIS': 1} 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: {'PTRANS': 8, 'CIS': 1, '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: {'PTRANS': 2, 'CIS': 1, 'TRANS': 144, 'PCIS': 1} 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: {'rna3p_pyr': 583, 'rna2p_pur': 112, 'rna3p_pur': 762, 'rna2p_pyr': 76} Link IDs: {'rna3p': 1344, 'rna2p': 188} Chain: "A" Number of atoms: 62320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62320 Classifications: {'RNA': 2903} Modifications used: {'rna3p_pyr': 1080, 'rna2p_pur': 275, 'rna3p_pur': 1399, 'rna2p_pyr': 149} Link IDs: {'rna3p': 2478, 'rna2p': 424} Chain: "B" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2529 Classifications: {'RNA': 118} Modifications used: {'rna3p_pyr': 48, 'rna2p_pur': 8, 'rna3p_pur': 56, 'rna2p_pyr': 6} Link IDs: {'rna3p': 103, 'rna2p': 14} Chain: "7" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 191 Classifications: {'RNA': 9} Modifications used: {'rna3p_pyr': 3, 'rna2p_pur': 1, 'rna3p_pur': 4, 'rna2p_pyr': 1} Link IDs: {'rna3p': 6, 'rna2p': 2} Chain: "8" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1623 Classifications: {'RNA': 76} Modifications used: {'rna2p_pyr': 4, 'rna3p_pyr': 33, 'p5*END': 1, 'rna3p_pur': 31, 'rna2p_pur': 8} Link IDs: {'rna3p': 64, 'rna2p': 11} Chain: "9" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1623 Classifications: {'RNA': 76} Modifications used: {'rna2p_pyr': 4, 'rna3p_pyr': 33, 'p5*END': 1, 'rna3p_pur': 32, 'rna2p_pur': 7} Link IDs: {'rna3p': 65, 'rna2p': 10} Time building chain proxies: 61.16, per 1000 atoms: 0.41 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: 59.55 Conformation dependent library (CDL) restraints added in 5.7 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: 45.48 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: 223.69 Time building geometry restraints manager: 65.58 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: 82754 35.91 - 71.83: 2818 71.83 - 107.74: 284 107.74 - 143.66: 28 143.66 - 179.57: 21 Dihedral angle restraints: 85905 sinusoidal: 68883 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 85902 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 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. 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: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.140 Extract box with map and model: 17.050 Check model and map are aligned: 1.660 Convert atoms to be neutral: 0.930 Process input model: 495.530 Find NCS groups from input model: 3.180 Set up NCS constraints: 0.510 Set refine NCS operators: 0.000 Set scattering table: 0.050 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 523.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0388 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 : 0.834 12.314 240143 Z= 0.516 Chirality : 0.036 0.265 30705 Planarity : 0.004 0.074 12903 Dihedral : 14.688 179.571 74918 Min Nonbonded Distance : 1.289 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 4.53 % Allowed : 9.65 % Favored : 85.83 % Rotamer Outliers : 0.02 % 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 *********************** 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 : 6.222 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 outliers start: 1 outliers final: 0 residues processed: 593 average time/residue: 1.5400 time to fit residues: 1511.4619 Evaluate side-chains 275 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 6.156 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.9076 ------------------------------------------------------------------------------- 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: 10.0000 chunk 270 optimal weight: 50.0000 chunk 533 optimal weight: 9.9990 chunk 422 optimal weight: 5.9990 chunk 817 optimal weight: 40.0000 chunk 316 optimal weight: 0.0270 chunk 497 optimal weight: 6.9990 chunk 608 optimal weight: 9.9990 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 ** 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 t 75 HIS 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 ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 ASN 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: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0797 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.241 160568 Z= 0.302 Angle : 0.891 20.326 240143 Z= 0.439 Chirality : 0.042 0.439 30705 Planarity : 0.007 0.099 12903 Dihedral : 15.243 179.594 63193 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 21.36 Ramachandran Plot: Outliers : 1.67 % Allowed : 9.25 % Favored : 89.08 % Rotamer Outliers : 1.50 % Cbeta Deviations : 0.00 % 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: -2.41 (0.10), residues: 5878 helix: -1.61 (0.11), residues: 1734 sheet: -3.35 (0.15), residues: 822 loop : -1.02 (0.11), residues: 3322 *********************** 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 388 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 315 time to evaluate : 6.070 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 outliers start: 73 outliers final: 32 residues processed: 361 average time/residue: 1.4352 time to fit residues: 886.6427 Evaluate side-chains 286 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 254 time to evaluate : 6.186 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 1.1922 time to fit residues: 77.3364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 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: 8.9990 chunk 940 optimal weight: 40.0000 chunk 323 optimal weight: 10.0000 chunk 761 optimal weight: 20.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- 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** c 139 GLN ** d 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 83 HIS ** f 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 6 GLN o 40 GLN o 80 GLN ** t 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 55 GLN ** 3 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 67 HIS ** 5 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 GLN ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN D 173 GLN E 97 ASN F 4 HIS G 44 HIS ** H 18 GLN ** 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 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 35 HIS ** N 9 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 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 9 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 Z 33 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1301 moved from start: 0.6678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.257 160568 Z= 0.358 Angle : 1.020 23.024 240143 Z= 0.509 Chirality : 0.049 0.676 30705 Planarity : 0.008 0.134 12903 Dihedral : 16.473 177.826 63193 Min Nonbonded Distance : 1.674 Molprobity Statistics. All-atom Clashscore : 37.14 Ramachandran Plot: Outliers : 1.48 % Allowed : 11.76 % Favored : 86.76 % Rotamer Outliers : 3.16 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.05 % Twisted Proline : 0.00 % 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: -2.80 (0.10), residues: 5878 helix: -1.54 (0.11), residues: 1724 sheet: -2.86 (0.16), residues: 816 loop : -1.75 (0.10), residues: 3338 *********************** 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 466 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 312 time to evaluate : 6.227 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 outliers start: 154 outliers final: 55 residues processed: 439 average time/residue: 1.4013 time to fit residues: 1071.1997 Evaluate side-chains 302 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 247 time to evaluate : 6.285 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 0 residues processed: 55 average time/residue: 1.2463 time to fit residues: 131.5438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 105 optimal weight: 5.9990 chunk 452 optimal weight: 5.9990 chunk 637 optimal weight: 20.0000 chunk 952 optimal weight: 20.0000 chunk 1008 optimal weight: 20.0000 chunk 497 optimal weight: 9.9990 chunk 902 optimal weight: 20.0000 chunk 271 optimal weight: 20.0000 overall best weight: 9.5992 ------------------------------------------------------------------------------- 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 ** b 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 167 HIS ** c 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 110 GLN j 35 GLN k 15 GLN k 28 ASN k 29 ASN ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 101 ASN l 6 GLN l 112 GLN o 28 GLN ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 4 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 83 ASN ** 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 152 GLN C 199 HIS ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN ** D 136 ASN ** 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** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** 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 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** ** R 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 87 GLN R 89 HIS ** 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** ** W 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1603 moved from start: 0.9179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.280 160568 Z= 0.387 Angle : 1.106 27.691 240143 Z= 0.549 Chirality : 0.052 0.559 30705 Planarity : 0.009 0.260 12903 Dihedral : 17.536 177.832 63193 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 41.05 Ramachandran Plot: Outliers : 1.50 % Allowed : 10.31 % Favored : 88.19 % Rotamer Outliers : 3.86 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.05 % Twisted Proline : 1.01 % 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: -3.23 (0.10), residues: 5878 helix: -1.88 (0.11), residues: 1714 sheet: -2.81 (0.16), residues: 784 loop : -2.14 (0.10), residues: 3380 *********************** 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 490 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 302 time to evaluate : 5.541 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 outliers start: 188 outliers final: 80 residues processed: 441 average time/residue: 1.3453 time to fit residues: 1032.4349 Evaluate side-chains 335 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 255 time to evaluate : 6.235 Switching outliers to nearest non-outliers outliers start: 80 outliers final: 0 residues processed: 80 average time/residue: 1.1920 time to fit residues: 181.2404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 14 optimal weight: 10.0000 chunk 750 optimal weight: 30.0000 chunk 415 optimal weight: 10.0000 chunk 860 optimal weight: 20.0000 chunk 696 optimal weight: 30.0000 chunk 1 optimal weight: 10.0000 chunk 514 optimal weight: 6.9990 chunk 904 optimal weight: 20.0000 chunk 254 optimal weight: 0.9990 overall best weight: 5.9994 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 28 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** ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 91 HIS o 40 GLN ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 50 HIS o 80 GLN t 55 GLN 0 5 ASN ** 3 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 83 ASN 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 152 GLN C 229 HIS ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 ASN F 51 ASN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 HIS ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 93 ASN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 HIS ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 74 GLN ** R 66 HIS ** 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 V 87 GLN ** W 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 45 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1571 moved from start: 0.9935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.218 160568 Z= 0.261 Angle : 0.817 16.144 240143 Z= 0.416 Chirality : 0.042 0.291 30705 Planarity : 0.006 0.109 12903 Dihedral : 17.361 179.342 63193 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 31.12 Ramachandran Plot: Outliers : 1.34 % Allowed : 11.36 % Favored : 87.29 % Rotamer Outliers : 2.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.97 (0.10), residues: 5878 helix: -1.54 (0.11), residues: 1714 sheet: -2.61 (0.17), residues: 780 loop : -2.06 (0.10), residues: 3384 *********************** 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 403 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 299 time to evaluate : 6.219 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 outliers start: 104 outliers final: 46 residues processed: 378 average time/residue: 1.3659 time to fit residues: 897.1320 Evaluate side-chains 306 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 260 time to evaluate : 5.915 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 46 outliers final: 1 residues processed: 46 average time/residue: 1.1150 time to fit residues: 102.0204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1043 random chunks: chunk 339 optimal weight: 10.0000 chunk 907 optimal weight: 20.0000 chunk 199 optimal weight: 30.0000 chunk 591 optimal weight: 20.0000 chunk 248 optimal weight: 4.9990 chunk 1009 optimal weight: 20.0000 chunk 837 optimal weight: 50.0000 chunk 467 optimal weight: 8.9990 chunk 83 optimal weight: 9.9990 chunk 333 optimal weight: 10.0000 chunk 529 optimal weight: 2.9990 overall best weight: 7.3992 ------------------------------------------------------------------------------- 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** ** d 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 43 ASN n 60 GLN ** o 46 HIS ** 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 ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 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 80 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 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 48 GLN ** T 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 44 HIS ** W 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1852 moved from start: 1.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.202 160568 Z= 0.351 Angle : 1.050 19.133 240143 Z= 0.521 Chirality : 0.050 0.394 30705 Planarity : 0.008 0.127 12903 Dihedral : 18.141 176.694 63193 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 44.80 Ramachandran Plot: Outliers : 1.26 % Allowed : 11.69 % Favored : 87.05 % Rotamer Outliers : 2.59 % Cbeta Deviations : 0.00 % 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: -3.30 (0.10), residues: 5878 helix: -1.88 (0.11), residues: 1709 sheet: -2.48 (0.18), residues: 767 loop : -2.33 (0.10), residues: 3402 *********************** 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 440 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 314 time to evaluate : 6.495 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 outliers start: 126 outliers final: 44 residues processed: 415 average time/residue: 1.4385 time to fit residues: 1044.1725 Evaluate side-chains 312 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 268 time to evaluate : 6.285 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 1.1804 time to fit residues: 105.2802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 574 optimal weight: 20.0000 chunk 736 optimal weight: 20.0000 chunk 570 optimal weight: 0.9980 chunk 849 optimal weight: 20.0000 chunk 563 optimal weight: 8.9990 chunk 1005 optimal weight: 20.0000 chunk 629 optimal weight: 40.0000 chunk 612 optimal weight: 20.0000 chunk 464 optimal weight: 9.9990 overall best weight: 9.9990 ------------------------------------------------------------------------------- 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 41 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 ** both conformations clash, **PLEASE CHECK MANUALLY** d 120 HIS ** e 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 16 ASN ** 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** ** m 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 59 HIS ** t 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 114 GLN ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 HIS ** L 38 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 71 ASN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 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 ** both conformations clash, **PLEASE CHECK MANUALLY** U 26 ASN ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2056 moved from start: 1.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.668 160568 Z= 0.442 Angle : 1.131 36.122 240143 Z= 0.567 Chirality : 0.054 0.547 30705 Planarity : 0.009 0.183 12903 Dihedral : 19.214 178.280 63193 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 49.79 Ramachandran Plot: Outliers : 1.43 % Allowed : 14.04 % Favored : 84.54 % Rotamer Outliers : 2.30 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.05 % Twisted Proline : 0.50 % 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: -3.69 (0.10), residues: 5878 helix: -2.17 (0.11), residues: 1696 sheet: -2.69 (0.18), residues: 726 loop : -2.62 (0.10), residues: 3456 *********************** 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 419 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 307 time to evaluate : 5.820 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 outliers start: 112 outliers final: 56 residues processed: 389 average time/residue: 1.4718 time to fit residues: 982.9163 Evaluate side-chains 321 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 265 time to evaluate : 6.325 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 0 residues processed: 56 average time/residue: 1.3354 time to fit residues: 139.4863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1043 random chunks: chunk 621 optimal weight: 30.0000 chunk 401 optimal weight: 3.9990 chunk 600 optimal weight: 9.9990 chunk 302 optimal weight: 6.9990 chunk 197 optimal weight: 6.9990 chunk 194 optimal weight: 10.0000 chunk 639 optimal weight: 30.0000 chunk 684 optimal weight: 20.0000 chunk 497 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 790 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 57 ASN ** b 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 139 GLN d 196 ASN ** g 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 16 ASN ** i 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 15 GLN ** 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** ** n 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 59 HIS 5 83 ASN ** 5 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 GLN ** 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 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** 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 80 HIS ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** 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 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 48 GLN ** T 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 53 GLN ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 33 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2005 moved from start: 1.4800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.321 160568 Z= 0.277 Angle : 0.929 23.147 240143 Z= 0.467 Chirality : 0.047 0.367 30705 Planarity : 0.007 0.130 12903 Dihedral : 18.943 178.752 63193 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 39.63 Ramachandran Plot: Outliers : 1.22 % Allowed : 11.30 % Favored : 87.48 % Rotamer Outliers : 1.23 % 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: -3.43 (0.10), residues: 5878 helix: -1.84 (0.11), residues: 1722 sheet: -2.49 (0.18), residues: 735 loop : -2.53 (0.10), residues: 3421 *********************** 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 353 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 293 time to evaluate : 6.213 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 outliers start: 60 outliers final: 25 residues processed: 337 average time/residue: 1.3886 time to fit residues: 806.7223 Evaluate side-chains 286 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 261 time to evaluate : 6.315 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 1.2054 time to fit residues: 62.2795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 20.0000 chunk 936 optimal weight: 20.0000 chunk 962 optimal weight: 30.0000 chunk 563 optimal weight: 6.9990 chunk 408 optimal weight: 9.9990 chunk 735 optimal weight: 20.0000 chunk 287 optimal weight: 5.9990 chunk 846 optimal weight: 20.0000 chunk 886 optimal weight: 20.0000 overall best weight: 12.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 28 ASN ** 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 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 31 ASN ** 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 40 ASN ** 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** ** n 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 23 HIS ** 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 114 GLN ** 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 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 ASN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 73 ASN ** 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** ** P 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 GLN ** 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 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 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 38 GLN ** Z 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2424 moved from start: 1.7079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.638 160568 Z= 0.509 Angle : 1.416 73.899 240143 Z= 0.693 Chirality : 0.065 0.658 30705 Planarity : 0.011 0.186 12903 Dihedral : 20.343 179.302 63193 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 72.47 Ramachandran Plot: Outliers : 1.50 % Allowed : 16.94 % Favored : 81.56 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.11 % 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: -4.19 (0.09), residues: 5878 helix: -2.49 (0.10), residues: 1664 sheet: -2.83 (0.18), residues: 697 loop : -3.05 (0.09), residues: 3517 *********************** 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 382 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 295 time to evaluate : 6.234 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 outliers start: 87 outliers final: 45 residues processed: 358 average time/residue: 1.4160 time to fit residues: 877.6263 Evaluate side-chains 314 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 269 time to evaluate : 6.338 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 1.2094 time to fit residues: 107.3275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 469 optimal weight: 2.9990 chunk 688 optimal weight: 20.0000 chunk 1039 optimal weight: 20.0000 chunk 956 optimal weight: 20.0000 chunk 827 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 639 optimal weight: 20.0000 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 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 69 HIS ** c 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 196 ASN ** e 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 28 ASN ** 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 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 67 GLN ** i 31 ASN ** 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 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** ** n 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 23 HIS ** 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 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 HIS ** 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 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 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** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 116 GLN ** 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 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 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2372 moved from start: 1.7117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 1.118 160568 Z= 0.478 Angle : 1.278 106.098 240143 Z= 0.630 Chirality : 0.059 0.759 30705 Planarity : 0.010 0.241 12903 Dihedral : 20.250 178.931 63193 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 62.94 Ramachandran Plot: Outliers : 1.36 % Allowed : 15.77 % Favored : 82.87 % Rotamer Outliers : 0.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -4.20 (0.09), residues: 5878 helix: -2.49 (0.11), residues: 1663 sheet: -2.78 (0.18), residues: 707 loop : -3.07 (0.09), residues: 3508 ********************** 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 317 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 280 time to evaluate : 6.063 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 outliers start: 37 outliers final: 18 residues processed: 309 average time/residue: 1.3891 time to fit residues: 744.8964 Evaluate side-chains 286 residues out of total 4871 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 268 time to evaluate : 6.319 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 1.1118 time to fit residues: 45.4127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1043 random chunks: chunk 507 optimal weight: 4.9990 chunk 657 optimal weight: 20.0000 chunk 881 optimal weight: 20.0000 chunk 253 optimal weight: 30.0000 chunk 762 optimal weight: 20.0000 chunk 122 optimal weight: 9.9990 chunk 229 optimal weight: 4.9990 chunk 828 optimal weight: 9.9990 chunk 346 optimal weight: 20.0000 chunk 850 optimal weight: 10.0000 chunk 104 optimal weight: 9.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 28 ASN ** 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 38 ASN ** 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 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** ** n 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 23 HIS ** 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 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 HIS ** 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 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 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** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** 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 55 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** ** 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 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.118512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.108661 restraints weight = 1187169.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.110471 restraints weight = 786208.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.111653 restraints weight = 561200.282| |-----------------------------------------------------------------------------| r_work (final): 0.4477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4005 moved from start: 1.7142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.726 160568 Z= 0.406 Angle : 1.213 73.840 240143 Z= 0.601 Chirality : 0.057 0.610 30705 Planarity : 0.009 0.197 12903 Dihedral : 20.199 178.378 63193 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 58.45 Ramachandran Plot: Outliers : 1.28 % Allowed : 16.42 % Favored : 82.31 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.05 % Twisted Proline : 0.50 % Twisted General : 0.26 % 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: -4.16 (0.09), residues: 5878 helix: -2.40 (0.11), residues: 1668 sheet: -2.81 (0.18), residues: 698 loop : -3.06 (0.09), residues: 3512 =============================================================================== Job complete usr+sys time: 21007.72 seconds wall clock time: 376 minutes 53.85 seconds (22613.85 seconds total)