Starting phenix.real_space_refine on Tue Mar 19 06:58:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwn_21422/03_2024/6vwn_21422.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwn_21422/03_2024/6vwn_21422.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwn_21422/03_2024/6vwn_21422.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwn_21422/03_2024/6vwn_21422.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwn_21422/03_2024/6vwn_21422.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwn_21422/03_2024/6vwn_21422.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.203 sd= 1.100 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4577 5.49 5 Mg 55 5.21 5 S 133 5.16 5 C 69976 2.51 5 N 26084 2.21 5 O 39211 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 62": "NH1" <-> "NH2" Residue "A ARG 68": "NH1" <-> "NH2" Residue "A ARG 86": "NH1" <-> "NH2" Residue "A ARG 166": "NH1" <-> "NH2" Residue "A ARG 257": "NH1" <-> "NH2" Residue "A ARG 268": "NH1" <-> "NH2" Residue "B ARG 13": "NH1" <-> "NH2" Residue "B ARG 59": "NH1" <-> "NH2" Residue "B GLU 64": "OE1" <-> "OE2" Residue "B ARG 77": "NH1" <-> "NH2" Residue "B PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 83": "NH1" <-> "NH2" Residue "B PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 169": "NH1" <-> "NH2" Residue "B ARG 184": "NH1" <-> "NH2" Residue "C ARG 21": "NH1" <-> "NH2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "C ARG 61": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C ARG 102": "NH1" <-> "NH2" Residue "C GLU 122": "OE1" <-> "OE2" Residue "C ARG 162": "NH1" <-> "NH2" Residue "C ARG 170": "NH1" <-> "NH2" Residue "C PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 184": "OD1" <-> "OD2" Residue "C ASP 191": "OD1" <-> "OD2" Residue "D GLU 18": "OE1" <-> "OE2" Residue "D PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 31": "OE1" <-> "OE2" Residue "D ASP 55": "OD1" <-> "OD2" Residue "D ARG 70": "NH1" <-> "NH2" Residue "D ARG 79": "NH1" <-> "NH2" Residue "D ARG 91": "NH1" <-> "NH2" Residue "D GLU 97": "OE1" <-> "OE2" Residue "D ARG 101": "NH1" <-> "NH2" Residue "D ARG 109": "NH1" <-> "NH2" Residue "D ARG 111": "NH1" <-> "NH2" Residue "D ASP 112": "OD1" <-> "OD2" Residue "D ARG 114": "NH1" <-> "NH2" Residue "D ARG 132": "NH1" <-> "NH2" Residue "D GLU 139": "OE1" <-> "OE2" Residue "D GLU 164": "OE1" <-> "OE2" Residue "D ASP 173": "OD1" <-> "OD2" Residue "D PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 46": "OD1" <-> "OD2" Residue "E PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 80": "OE1" <-> "OE2" Residue "E ARG 152": "NH1" <-> "NH2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 169": "NH1" <-> "NH2" Residue "F ASP 17": "OD1" <-> "OD2" Residue "F GLU 45": "OE1" <-> "OE2" Residue "G ARG 37": "NH1" <-> "NH2" Residue "G TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 96": "NH1" <-> "NH2" Residue "G ARG 99": "NH1" <-> "NH2" Residue "G ARG 120": "NH1" <-> "NH2" Residue "G TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 4": "OE1" <-> "OE2" Residue "I ARG 31": "NH1" <-> "NH2" Residue "I ARG 71": "NH1" <-> "NH2" Residue "I ARG 108": "NH1" <-> "NH2" Residue "J ARG 41": "NH1" <-> "NH2" Residue "J ARG 47": "NH1" <-> "NH2" Residue "J GLU 51": "OE1" <-> "OE2" Residue "J ARG 60": "NH1" <-> "NH2" Residue "J ARG 69": "NH1" <-> "NH2" Residue "J ARG 78": "NH1" <-> "NH2" Residue "J ARG 126": "NH1" <-> "NH2" Residue "J GLU 136": "OE1" <-> "OE2" Residue "K ARG 10": "NH1" <-> "NH2" Residue "K ARG 18": "NH1" <-> "NH2" Residue "K PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 40": "NH1" <-> "NH2" Residue "K ARG 50": "NH1" <-> "NH2" Residue "K ARG 51": "NH1" <-> "NH2" Residue "K GLU 111": "OE1" <-> "OE2" Residue "K ARG 114": "NH1" <-> "NH2" Residue "K GLU 115": "OE1" <-> "OE2" Residue "L ARG 2": "NH1" <-> "NH2" Residue "L ARG 8": "NH1" <-> "NH2" Residue "L ARG 12": "NH1" <-> "NH2" Residue "L ARG 17": "NH1" <-> "NH2" Residue "L ARG 22": "NH1" <-> "NH2" Residue "L ARG 30": "NH1" <-> "NH2" Residue "L ARG 45": "NH1" <-> "NH2" Residue "L ARG 46": "NH1" <-> "NH2" Residue "L ARG 63": "NH1" <-> "NH2" Residue "L ARG 64": "NH1" <-> "NH2" Residue "L ARG 69": "NH1" <-> "NH2" Residue "L ARG 71": "NH1" <-> "NH2" Residue "L GLU 82": "OE1" <-> "OE2" Residue "L ARG 96": "NH1" <-> "NH2" Residue "M ARG 7": "NH1" <-> "NH2" Residue "M ARG 16": "NH1" <-> "NH2" Residue "M ARG 25": "NH1" <-> "NH2" Residue "M ARG 81": "NH1" <-> "NH2" Residue "M ARG 102": "NH1" <-> "NH2" Residue "M ARG 111": "NH1" <-> "NH2" Residue "M GLU 112": "OE1" <-> "OE2" Residue "N ARG 20": "NH1" <-> "NH2" Residue "N ARG 61": "NH1" <-> "NH2" Residue "N ARG 88": "NH1" <-> "NH2" Residue "N ARG 100": "NH1" <-> "NH2" Residue "N ARG 102": "NH1" <-> "NH2" Residue "N ARG 108": "NH1" <-> "NH2" Residue "O ARG 2": "NH1" <-> "NH2" Residue "O ARG 5": "NH1" <-> "NH2" Residue "O ARG 12": "NH1" <-> "NH2" Residue "O ARG 32": "NH1" <-> "NH2" Residue "O ARG 47": "NH1" <-> "NH2" Residue "O ARG 52": "NH1" <-> "NH2" Residue "O PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 69": "NH1" <-> "NH2" Residue "O ASP 90": "OD1" <-> "OD2" Residue "O GLU 110": "OE1" <-> "OE2" Residue "P TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 16": "OE1" <-> "OE2" Residue "P ARG 21": "NH1" <-> "NH2" Residue "P ARG 68": "NH1" <-> "NH2" Residue "P ARG 78": "NH1" <-> "NH2" Residue "P ARG 79": "NH1" <-> "NH2" Residue "P ARG 84": "NH1" <-> "NH2" Residue "Q GLU 78": "OE1" <-> "OE2" Residue "Q ARG 84": "NH1" <-> "NH2" Residue "Q ARG 88": "NH1" <-> "NH2" Residue "Q ASP 94": "OD1" <-> "OD2" Residue "Q ARG 95": "NH1" <-> "NH2" Residue "Q ARG 110": "NH1" <-> "NH2" Residue "R GLU 25": "OE1" <-> "OE2" Residue "R GLU 56": "OE1" <-> "OE2" Residue "R ARG 69": "NH1" <-> "NH2" Residue "R ARG 73": "NH1" <-> "NH2" Residue "S ARG 5": "NH1" <-> "NH2" Residue "S GLU 9": "OE1" <-> "OE2" Residue "S ARG 81": "NH1" <-> "NH2" Residue "S ARG 85": "NH1" <-> "NH2" Residue "S GLU 87": "OE1" <-> "OE2" Residue "S ARG 93": "NH1" <-> "NH2" Residue "T TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 59": "OE1" <-> "OE2" Residue "T TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 7": "NH1" <-> "NH2" Residue "U PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 8": "OE1" <-> "OE2" Residue "W ARG 23": "NH1" <-> "NH2" Residue "W ARG 29": "NH1" <-> "NH2" Residue "W ARG 47": "NH1" <-> "NH2" Residue "W ARG 52": "NH1" <-> "NH2" Residue "X ARG 10": "NH1" <-> "NH2" Residue "X ARG 29": "NH1" <-> "NH2" Residue "X GLU 38": "OE1" <-> "OE2" Residue "X PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 9": "NH1" <-> "NH2" Residue "Y ARG 15": "NH1" <-> "NH2" Residue "Y ARG 39": "NH1" <-> "NH2" Residue "Y ARG 51": "NH1" <-> "NH2" Residue "Z PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 39": "OD1" <-> "OD2" Residue "Z ARG 43": "NH1" <-> "NH2" Residue "Z GLU 50": "OE1" <-> "OE2" Residue "AA ARG 3": "NH1" <-> "NH2" Residue "AA ARG 12": "NH1" <-> "NH2" Residue "AA ARG 14": "NH1" <-> "NH2" Residue "AA ARG 19": "NH1" <-> "NH2" Residue "AA ARG 21": "NH1" <-> "NH2" Residue "AA ARG 33": "NH1" <-> "NH2" Residue "AA ARG 41": "NH1" <-> "NH2" Residue "AB ARG 12": "NH1" <-> "NH2" Residue "AB ARG 29": "NH1" <-> "NH2" Residue "AB ARG 41": "NH1" <-> "NH2" Residue "AC ARG 4": "NH1" <-> "NH2" Residue "AC ARG 12": "NH1" <-> "NH2" Residue "AC ARG 24": "NH1" <-> "NH2" Residue "a GLU 51": "OE1" <-> "OE2" Residue "a ARG 73": "NH1" <-> "NH2" Residue "a GLU 77": "OE1" <-> "OE2" Residue "a ARG 94": "NH1" <-> "NH2" Residue "a ASP 122": "OD1" <-> "OD2" Residue "a ASP 158": "OD1" <-> "OD2" Residue "a ASP 193": "OD1" <-> "OD2" Residue "a ASP 203": "OD1" <-> "OD2" Residue "b ASP 33": "OD1" <-> "OD2" Residue "b TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 64": "NH1" <-> "NH2" Residue "b ARG 71": "NH1" <-> "NH2" Residue "b ASP 92": "OD1" <-> "OD2" Residue "b ASP 111": "OD1" <-> "OD2" Residue "b ASP 117": "OD1" <-> "OD2" Residue "b PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 169": "OE1" <-> "OE2" Residue "b GLU 187": "OE1" <-> "OE2" Residue "c TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 55": "NH1" <-> "NH2" Residue "c ARG 61": "NH1" <-> "NH2" Residue "c ARG 62": "NH1" <-> "NH2" Residue "c TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 87": "OE1" <-> "OE2" Residue "c ARG 96": "NH1" <-> "NH2" Residue "c TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 110": "NH1" <-> "NH2" Residue "c GLU 112": "OE1" <-> "OE2" Residue "c ARG 153": "NH1" <-> "NH2" Residue "c GLU 165": "OE1" <-> "OE2" Residue "c ARG 187": "NH1" <-> "NH2" Residue "d PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 156": "NH1" <-> "NH2" Residue "e ARG 44": "NH1" <-> "NH2" Residue "e TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 75": "OE1" <-> "OE2" Residue "f PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 91": "NH1" <-> "NH2" Residue "f ARG 94": "NH1" <-> "NH2" Residue "f ASP 112": "OD1" <-> "OD2" Residue "g GLU 42": "OE1" <-> "OE2" Residue "g ASP 53": "OD1" <-> "OD2" Residue "g ASP 89": "OD1" <-> "OD2" Residue "h TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 94": "NH1" <-> "NH2" Residue "h GLU 96": "OE1" <-> "OE2" Residue "h ASP 106": "OD1" <-> "OD2" Residue "h ARG 112": "NH1" <-> "NH2" Residue "i ARG 7": "NH1" <-> "NH2" Residue "i GLU 27": "OE1" <-> "OE2" Residue "i ARG 45": "NH1" <-> "NH2" Residue "i ASP 60": "OD1" <-> "OD2" Residue "i ASP 85": "OD1" <-> "OD2" Residue "j ARG 12": "NH1" <-> "NH2" Residue "j ASP 71": "OD1" <-> "OD2" Residue "k GLU 24": "OE1" <-> "OE2" Residue "k ARG 55": "NH1" <-> "NH2" Residue "k GLU 69": "OE1" <-> "OE2" Residue "l TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 39": "OD1" <-> "OD2" Residue "o ARG 28": "NH1" <-> "NH2" Residue "p PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ASP 26": "OD1" <-> "OD2" Residue "r ARG 80": "NH1" <-> "NH2" Residue "s TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 39": "OE1" <-> "OE2" Residue "t GLU 9": "OE1" <-> "OE2" Residue "t PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t GLU 43": "OE1" <-> "OE2" Residue "t GLU 62": "OE1" <-> "OE2" Residue "t ARG 66": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 140036 Number of models: 1 Model: "" Number of chains: 57 Chain: "3" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2568 Classifications: {'RNA': 120} Modifications used: {'5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 5, 'rna3p_pur': 61, 'rna3p_pyr': 50} Link IDs: {'rna2p': 9, 'rna3p': 110} Chain: "5" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1619 Classifications: {'RNA': 76} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 4, 'rna3p_pur': 31, 'rna3p_pyr': 33} Link IDs: {'rna2p': 11, 'rna3p': 64} Chain: "A" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "B" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "C" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "D" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "E" Number of atoms: 1298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1298 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "F" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 368 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "G" 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: "I" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 947 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "J" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1043 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "K" 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: "L" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 951 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "M" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 875 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain: "N" 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: "O" 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: "P" 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: "Q" 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: "R" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 714 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "S" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 735 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain breaks: 1 Chain: "T" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 745 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain: "U" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "V" 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: "W" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 491 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "X" 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: "Y" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 434 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "Z" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 396 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "AA" 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: "AB" 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: "AC" 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: "2" Number of atoms: 60819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2833, 60819 Classifications: {'RNA': 2833} Modifications used: {'5*END': 1, 'rna2p_pur': 248, 'rna2p_pyr': 129, 'rna3p_pur': 1386, 'rna3p_pyr': 1070} Link IDs: {'rna2p': 377, 'rna3p': 2455} Chain breaks: 1 Chain: "a" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1672 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 7, 'TRANS': 212} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "b" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1502 Classifications: {'peptide': 197} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 189} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 41 Chain: "c" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1273 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 155} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "d" Number of atoms: 1146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1146 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 151} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "e" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 824 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "f" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 742 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "g" 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: "h" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 950 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 117} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "i" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 726 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain breaks: 1 Chain: "j" 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: "k" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 867 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain breaks: 1 Chain: "l" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 859 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "m" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "n" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 702 Classifications: {'peptide': 87} Link IDs: {'TRANS': 86} Chain: "o" 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: "p" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 632 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 2, 'TRANS': 75} Chain: "q" Number of atoms: 443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 443 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "r" 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: "s" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 655 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "t" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 566 Classifications: {'peptide': 68} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 65} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "1" Number of atoms: 32365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1508, 32365 Classifications: {'RNA': 1508} Modifications used: {'rna2p_pur': 95, 'rna2p_pyr': 64, 'rna3p_pur': 767, 'rna3p_pyr': 582} Link IDs: {'rna2p': 159, 'rna3p': 1348} Chain breaks: 2 Chain: "4" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 926 Classifications: {'RNA': 43} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 23, 'rna3p_pyr': 16} Link IDs: {'rna2p': 3, 'rna3p': 39} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Unusual residues: {' MG': 45} Classifications: {'undetermined': 45} Link IDs: {None: 44} Chain: "1" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' MG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Time building chain proxies: 52.66, per 1000 atoms: 0.38 Number of scatterers: 140036 At special positions: 0 Unit cell: (267.65, 279.77, 223.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 133 16.00 P 4577 15.00 Mg 55 11.99 O 39211 8.00 N 26084 7.00 C 69976 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS k 33 " - pdb=" SG CYS k 52 " 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: 57.23 Conformation dependent library (CDL) restraints added in 7.2 seconds 10470 Ramachandran restraints generated. 5235 Oldfield, 0 Emsley, 5235 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9810 Finding SS restraints... Secondary structure from input PDB file: 159 helices and 70 sheets defined 36.5% alpha, 18.8% beta 1584 base pairs and 2390 stacking pairs defined. Time for finding SS restraints: 49.50 Creating SS restraints... Processing helix chain 'A' and resid 29 through 31 No H-bonds generated for 'chain 'A' and resid 29 through 31' Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 196 through 202 removed outlier: 4.256A pdb=" N MET A 200 " --> pdb=" O ALA A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 214 removed outlier: 3.939A pdb=" N ALA A 210 " --> pdb=" O LYS A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 259 through 266 Processing helix chain 'B' and resid 61 through 72 Processing helix chain 'B' and resid 98 through 103 Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'C' and resid 15 through 20 Processing helix chain 'C' and resid 24 through 39 Processing helix chain 'C' and resid 97 through 115 Processing helix chain 'C' and resid 130 through 141 Processing helix chain 'C' and resid 154 through 164 Processing helix chain 'C' and resid 176 through 183 removed outlier: 3.786A pdb=" N PHE C 183 " --> pdb=" O SER C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 201 Processing helix chain 'D' and resid 3 through 19 removed outlier: 3.724A pdb=" N ASP D 9 " --> pdb=" O ASP D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 60 Processing helix chain 'D' and resid 73 through 77 removed outlier: 3.593A pdb=" N PHE D 76 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS D 77 " --> pdb=" O ALA D 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 73 through 77' Processing helix chain 'D' and resid 93 through 106 removed outlier: 3.759A pdb=" N ILE D 105 " --> pdb=" O ARG D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 137 removed outlier: 3.550A pdb=" N ILE D 136 " --> pdb=" O GLU D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 172 removed outlier: 3.654A pdb=" N ALA D 171 " --> pdb=" O ALA D 167 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE D 172 " --> pdb=" O LEU D 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 80 Processing helix chain 'E' and resid 136 through 151 Processing helix chain 'F' and resid 22 through 31 Processing helix chain 'F' and resid 40 through 48 Processing helix chain 'G' and resid 24 through 38 Processing helix chain 'G' and resid 58 through 62 removed outlier: 3.686A pdb=" N VAL G 62 " --> pdb=" O ALA G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 72 Processing helix chain 'G' and resid 89 through 96 Processing helix chain 'G' and resid 98 through 109 Processing helix chain 'G' and resid 112 through 121 Processing helix chain 'G' and resid 132 through 136 removed outlier: 3.507A pdb=" N GLN G 135 " --> pdb=" O HIS G 132 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN G 136 " --> pdb=" O ALA G 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 132 through 136' Processing helix chain 'I' and resid 104 through 108 removed outlier: 3.881A pdb=" N LEU I 107 " --> pdb=" O THR I 104 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ARG I 108 " --> pdb=" O ARG I 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 104 through 108' Processing helix chain 'I' and resid 112 through 119 Processing helix chain 'J' and resid 1 through 5 removed outlier: 4.442A pdb=" N ASN J 4 " --> pdb=" O MET J 1 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'J' and resid 68 through 73 Processing helix chain 'J' and resid 78 through 85 Processing helix chain 'J' and resid 91 through 99 Processing helix chain 'J' and resid 128 through 139 Processing helix chain 'K' and resid 43 through 58 Processing helix chain 'K' and resid 109 through 124 Processing helix chain 'L' and resid 13 through 32 Processing helix chain 'L' and resid 38 through 55 Proline residue: L 50 - end of helix Processing helix chain 'L' and resid 59 through 71 Processing helix chain 'L' and resid 72 through 84 Processing helix chain 'M' and resid 5 through 22 Processing helix chain 'M' and resid 55 through 62 Processing helix chain 'M' and resid 67 through 86 Processing helix chain 'M' and resid 101 through 114 Processing helix chain 'N' and resid 2 through 12 Processing helix chain 'N' and resid 52 through 55 removed outlier: 3.585A pdb=" N HIS N 55 " --> pdb=" O ARG N 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 52 through 55' Processing helix chain 'N' and resid 98 through 103 removed outlier: 3.864A pdb=" N THR N 103 " --> pdb=" O LEU N 99 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 108 Processing helix chain 'O' and resid 6 through 20 Processing helix chain 'O' and resid 24 through 29 removed outlier: 3.623A pdb=" N SER O 28 " --> pdb=" O GLY O 25 " (cutoff:3.500A) Processing helix chain 'O' and resid 30 through 71 removed outlier: 4.581A pdb=" N GLN O 36 " --> pdb=" O ARG O 32 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ARG O 54 " --> pdb=" O ARG O 50 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ARG O 57 " --> pdb=" O LYS O 53 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 85 Processing helix chain 'O' and resid 90 through 101 Processing helix chain 'O' and resid 101 through 117 Processing helix chain 'Q' and resid 13 through 22 Processing helix chain 'Q' and resid 28 through 39 Processing helix chain 'Q' and resid 41 through 61 removed outlier: 4.364A pdb=" N VAL Q 45 " --> pdb=" O LYS Q 41 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU Q 46 " --> pdb=" O LYS Q 42 " (cutoff:3.500A) Processing helix chain 'Q' and resid 89 through 91 No H-bonds generated for 'chain 'Q' and resid 89 through 91' Processing helix chain 'R' and resid 4 through 10 Processing helix chain 'R' and resid 17 through 27 Processing helix chain 'R' and resid 39 through 51 Processing helix chain 'T' and resid 13 through 23 Processing helix chain 'T' and resid 44 through 52 removed outlier: 3.587A pdb=" N ALA T 52 " --> pdb=" O MET T 48 " (cutoff:3.500A) Processing helix chain 'T' and resid 53 through 57 removed outlier: 4.359A pdb=" N TYR T 57 " --> pdb=" O ALA T 54 " (cutoff:3.500A) Processing helix chain 'V' and resid 51 through 62 Processing helix chain 'V' and resid 62 through 74 Processing helix chain 'W' and resid 3 through 9 Processing helix chain 'W' and resid 10 through 35 Processing helix chain 'W' and resid 40 through 61 removed outlier: 4.170A pdb=" N LYS W 44 " --> pdb=" O SER W 40 " (cutoff:3.500A) Processing helix chain 'X' and resid 16 through 27 Processing helix chain 'X' and resid 40 through 50 Processing helix chain 'Y' and resid 8 through 17 Processing helix chain 'AA' and resid 8 through 17 Processing helix chain 'AA' and resid 17 through 24 removed outlier: 4.241A pdb=" N THRAA 24 " --> pdb=" O ALAAA 20 " (cutoff:3.500A) Processing helix chain 'AA' and resid 24 through 38 removed outlier: 3.598A pdb=" N ARGAA 28 " --> pdb=" O THRAA 24 " (cutoff:3.500A) Processing helix chain 'AB' and resid 6 through 13 Processing helix chain 'AB' and resid 36 through 44 Processing helix chain 'AB' and resid 50 through 61 Processing helix chain 'a' and resid 44 through 63 removed outlier: 3.998A pdb=" N MET a 48 " --> pdb=" O LYS a 44 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN a 50 " --> pdb=" O VAL a 46 " (cutoff:3.500A) Processing helix chain 'a' and resid 76 through 86 removed outlier: 4.160A pdb=" N LYS a 80 " --> pdb=" O SER a 76 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP a 81 " --> pdb=" O GLU a 77 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA a 82 " --> pdb=" O ALA a 78 " (cutoff:3.500A) Processing helix chain 'a' and resid 102 through 123 Processing helix chain 'a' and resid 129 through 147 Processing helix chain 'a' and resid 168 through 179 removed outlier: 3.754A pdb=" N ILE a 172 " --> pdb=" O GLU a 168 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN a 177 " --> pdb=" O LYS a 173 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU a 178 " --> pdb=" O GLU a 174 " (cutoff:3.500A) Processing helix chain 'a' and resid 205 through 225 Processing helix chain 'b' and resid 5 through 10 Processing helix chain 'b' and resid 24 through 46 Processing helix chain 'b' and resid 88 through 94 Processing helix chain 'b' and resid 111 through 125 Processing helix chain 'b' and resid 128 through 143 removed outlier: 3.501A pdb=" N LEU b 143 " --> pdb=" O ASN b 139 " (cutoff:3.500A) Processing helix chain 'c' and resid 49 through 65 removed outlier: 4.016A pdb=" N LYS c 57 " --> pdb=" O GLN c 53 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL c 60 " --> pdb=" O GLU c 56 " (cutoff:3.500A) Processing helix chain 'c' and resid 67 through 81 Processing helix chain 'c' and resid 85 through 95 Processing helix chain 'c' and resid 96 through 105 Processing helix chain 'c' and resid 109 through 119 Processing helix chain 'c' and resid 146 through 150 removed outlier: 3.560A pdb=" N LYS c 149 " --> pdb=" O GLU c 146 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS c 150 " --> pdb=" O LYS c 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 146 through 150' Processing helix chain 'c' and resid 152 through 165 Processing helix chain 'c' and resid 196 through 203 Processing helix chain 'd' and resid 54 through 69 Processing helix chain 'd' and resid 108 through 118 Processing helix chain 'd' and resid 131 through 146 Processing helix chain 'd' and resid 148 through 157 Processing helix chain 'd' and resid 159 through 165 Processing helix chain 'e' and resid 17 through 32 Processing helix chain 'e' and resid 67 through 80 Processing helix chain 'f' and resid 19 through 29 Processing helix chain 'f' and resid 30 through 33 Processing helix chain 'f' and resid 34 through 50 removed outlier: 3.548A pdb=" N ALA f 38 " --> pdb=" O LYS f 34 " (cutoff:3.500A) Processing helix chain 'f' and resid 92 through 109 Processing helix chain 'f' and resid 113 through 127 removed outlier: 5.220A pdb=" N LEU f 119 " --> pdb=" O MET f 115 " (cutoff:3.500A) Processing helix chain 'g' and resid 4 through 20 Processing helix chain 'g' and resid 29 through 43 Processing helix chain 'g' and resid 87 through 91 removed outlier: 3.519A pdb=" N GLU g 90 " --> pdb=" O ARG g 87 " (cutoff:3.500A) Processing helix chain 'g' and resid 93 through 98 Processing helix chain 'g' and resid 112 through 119 Processing helix chain 'h' and resid 34 through 38 Processing helix chain 'h' and resid 42 through 53 Proline residue: h 50 - end of helix removed outlier: 4.106A pdb=" N LEU h 53 " --> pdb=" O GLN h 49 " (cutoff:3.500A) Processing helix chain 'h' and resid 71 through 90 Processing helix chain 'h' and resid 91 through 100 Processing helix chain 'i' and resid 14 through 33 Processing helix chain 'i' and resid 80 through 88 Processing helix chain 'j' and resid 46 through 50 Processing helix chain 'j' and resid 58 through 75 removed outlier: 3.796A pdb=" N ARG j 68 " --> pdb=" O VAL j 64 " (cutoff:3.500A) Processing helix chain 'j' and resid 91 through 102 Processing helix chain 'k' and resid 2 through 9 Processing helix chain 'k' and resid 114 through 118 removed outlier: 3.745A pdb=" N GLY k 117 " --> pdb=" O SER k 114 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL k 118 " --> pdb=" O LYS k 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 114 through 118' Processing helix chain 'l' and resid 13 through 19 removed outlier: 3.542A pdb=" N THR l 19 " --> pdb=" O VAL l 15 " (cutoff:3.500A) Processing helix chain 'l' and resid 25 through 37 Processing helix chain 'l' and resid 48 through 61 removed outlier: 3.664A pdb=" N ILE l 52 " --> pdb=" O SER l 48 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR l 54 " --> pdb=" O GLY l 50 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP l 57 " --> pdb=" O ASP l 53 " (cutoff:3.500A) Processing helix chain 'l' and resid 64 through 83 Processing helix chain 'l' and resid 84 through 93 Processing helix chain 'l' and resid 105 through 110 Processing helix chain 'm' and resid 2 through 19 Processing helix chain 'm' and resid 19 through 32 removed outlier: 3.589A pdb=" N ARG m 23 " --> pdb=" O TYR m 19 " (cutoff:3.500A) Processing helix chain 'm' and resid 36 through 50 Processing helix chain 'm' and resid 79 through 90 Processing helix chain 'n' and resid 3 through 15 Processing helix chain 'n' and resid 23 through 43 Processing helix chain 'n' and resid 48 through 73 removed outlier: 3.601A pdb=" N ARG n 52 " --> pdb=" O ASP n 48 " (cutoff:3.500A) Processing helix chain 'n' and resid 73 through 85 Processing helix chain 'o' and resid 53 through 64 Processing helix chain 'o' and resid 68 through 82 Processing helix chain 'q' and resid 24 through 31 Processing helix chain 'q' and resid 40 through 45 Processing helix chain 'q' and resid 49 through 64 Processing helix chain 'r' and resid 11 through 24 Processing helix chain 'r' and resid 62 through 66 Processing helix chain 's' and resid 3 through 39 Processing helix chain 's' and resid 44 through 63 Proline residue: s 55 - end of helix removed outlier: 3.509A pdb=" N ASP s 58 " --> pdb=" O GLN s 54 " (cutoff:3.500A) Processing helix chain 's' and resid 67 through 85 Processing helix chain 't' and resid 11 through 26 Processing helix chain 't' and resid 27 through 35 Processing helix chain 't' and resid 39 through 67 removed outlier: 4.032A pdb=" N GLU t 43 " --> pdb=" O LYS t 39 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG t 44 " --> pdb=" O PRO t 40 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 4 Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 34 Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 104 removed outlier: 6.654A pdb=" N ILE A 90 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N LEU A 80 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU A 92 " --> pdb=" O GLU A 78 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 129 through 130 removed outlier: 7.268A pdb=" N ARG A 188 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N VAL A 143 " --> pdb=" O ARG A 188 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N VAL A 143 " --> pdb=" O GLN A 152 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 129 through 130 removed outlier: 7.268A pdb=" N ARG A 188 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N VAL A 143 " --> pdb=" O ARG A 188 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N THR A 172 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ARG A 166 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N TYR A 170 " --> pdb=" O ARG A 166 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 4 through 15 removed outlier: 5.542A pdb=" N LYS B 8 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLU B 28 " --> pdb=" O LYS B 8 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY B 10 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU B 186 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N VAL B 180 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU B 188 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASP B 176 " --> pdb=" O LYS B 190 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N THR B 171 " --> pdb=" O GLY B 111 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N GLY B 111 " --> pdb=" O THR B 171 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N GLN B 173 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL B 109 " --> pdb=" O GLN B 173 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N THR B 112 " --> pdb=" O ASP B 200 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ASP B 200 " --> pdb=" O THR B 112 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 79 through 83 removed outlier: 3.923A pdb=" N GLN B 36 " --> pdb=" O GLN B 49 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR B 51 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N VAL B 34 " --> pdb=" O THR B 51 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 115 through 119 removed outlier: 3.544A pdb=" N GLY B 117 " --> pdb=" O MET B 165 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 118 through 121 removed outlier: 5.810A pdb=" N LEU C 147 " --> pdb=" O VAL C 187 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N THR C 189 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N ILE C 149 " --> pdb=" O THR C 189 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 65 through 67 removed outlier: 6.743A pdb=" N THR D 156 " --> pdb=" O GLU D 31 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ILE D 33 " --> pdb=" O THR D 154 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N THR D 154 " --> pdb=" O ILE D 33 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU D 35 " --> pdb=" O ASP D 152 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ASP D 152 " --> pdb=" O LEU D 35 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 8 through 9 Processing sheet with id=AB3, first strand: chain 'E' and resid 15 through 19 removed outlier: 3.535A pdb=" N VAL E 22 " --> pdb=" O ASN E 19 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 121 through 123 removed outlier: 3.519A pdb=" N VAL E 89 " --> pdb=" O GLY E 160 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 94 through 98 Processing sheet with id=AB6, first strand: chain 'F' and resid 17 through 20 removed outlier: 3.697A pdb=" N VAL F 37 " --> pdb=" O ILE F 4 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 122 through 124 removed outlier: 6.034A pdb=" N ILE G 54 " --> pdb=" O LYS G 123 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TYR G 16 " --> pdb=" O ILE G 55 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N LEU G 57 " --> pdb=" O TYR G 16 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL G 18 " --> pdb=" O LEU G 57 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TRP G 15 " --> pdb=" O GLN G 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'G' and resid 73 through 75 Processing sheet with id=AB9, first strand: chain 'I' and resid 6 through 10 removed outlier: 3.724A pdb=" N THR I 6 " --> pdb=" O CYS I 21 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL I 19 " --> pdb=" O LEU I 8 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL I 10 " --> pdb=" O ARG I 17 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ARG I 17 " --> pdb=" O VAL I 10 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ALA I 16 " --> pdb=" O ALA I 46 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ALA I 46 " --> pdb=" O ALA I 16 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ARG I 18 " --> pdb=" O LYS I 44 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LYS I 40 " --> pdb=" O ILE I 22 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N VAL I 24 " --> pdb=" O ILE I 38 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N ILE I 38 " --> pdb=" O VAL I 24 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL I 63 " --> pdb=" O ALA I 83 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ALA I 83 " --> pdb=" O VAL I 63 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N CYS I 84 " --> pdb=" O MET I 7 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ASN I 9 " --> pdb=" O CYS I 84 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU I 86 " --> pdb=" O ASN I 9 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 77 through 79 removed outlier: 6.827A pdb=" N ALA N 57 " --> pdb=" O ILE N 49 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ILE N 49 " --> pdb=" O ALA N 57 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N THR N 59 " --> pdb=" O ILE N 47 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N THR N 24 " --> pdb=" O LYS N 86 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N TRP N 30 " --> pdb=" O VAL N 80 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N VAL N 80 " --> pdb=" O TRP N 30 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 74 through 77 removed outlier: 6.695A pdb=" N ALA J 108 " --> pdb=" O ARG J 126 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 89 through 90 removed outlier: 3.569A pdb=" N VAL J 122 " --> pdb=" O LYS J 141 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 62 through 65 removed outlier: 6.484A pdb=" N LEU K 33 " --> pdb=" O LEU K 102 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLU K 104 " --> pdb=" O PHE K 31 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N PHE K 31 " --> pdb=" O GLU K 104 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 39 through 42 removed outlier: 3.694A pdb=" N ILE K 96 " --> pdb=" O GLY K 39 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TYR K 91 " --> pdb=" O ILE K 73 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE K 73 " --> pdb=" O TYR K 91 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 33 through 37 removed outlier: 6.874A pdb=" N MET L 110 " --> pdb=" O CYS L 100 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 49 through 52 removed outlier: 4.677A pdb=" N VAL M 49 " --> pdb=" O VAL M 39 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL M 28 " --> pdb=" O ASP M 93 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'P' and resid 10 through 15 removed outlier: 6.685A pdb=" N TYR P 2 " --> pdb=" O ILE P 41 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ILE P 41 " --> pdb=" O TYR P 2 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL P 4 " --> pdb=" O LEU P 39 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU P 46 " --> pdb=" O ASN P 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'P' and resid 19 through 23 removed outlier: 6.721A pdb=" N PHE P 93 " --> pdb=" O HIS P 66 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N HIS P 66 " --> pdb=" O PHE P 93 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ASP P 95 " --> pdb=" O VAL P 64 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LYS P 60 " --> pdb=" O THR P 99 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ILE P 101 " --> pdb=" O VAL P 58 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL P 58 " --> pdb=" O ILE P 101 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'P' and resid 72 through 78 removed outlier: 4.135A pdb=" N TYR P 83 " --> pdb=" O ARG P 78 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Q' and resid 3 through 10 removed outlier: 4.060A pdb=" N HIS Q 9 " --> pdb=" O SER Q 101 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N SER Q 101 " --> pdb=" O HIS Q 9 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS Q 73 " --> pdb=" O VAL Q 106 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N SER Q 108 " --> pdb=" O VAL Q 71 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N VAL Q 71 " --> pdb=" O SER Q 108 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Q' and resid 82 through 87 Processing sheet with id=AD4, first strand: chain 'R' and resid 11 through 14 removed outlier: 4.936A pdb=" N VAL R 57 " --> pdb=" O THR R 86 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'R' and resid 67 through 70 removed outlier: 3.701A pdb=" N ARG R 73 " --> pdb=" O HIS R 70 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'S' and resid 64 through 65 removed outlier: 3.786A pdb=" N LYS S 32 " --> pdb=" O LEU S 28 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N GLU S 9 " --> pdb=" O PHE S 72 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE S 71 " --> pdb=" O ASP S 80 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'S' and resid 40 through 45 Processing sheet with id=AD8, first strand: chain 'S' and resid 82 through 87 Processing sheet with id=AD9, first strand: chain 'T' and resid 3 through 5 removed outlier: 6.476A pdb=" N ILE T 4 " --> pdb=" O VAL T 64 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ALA T 74 " --> pdb=" O PHE T 91 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N PHE T 91 " --> pdb=" O ALA T 74 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ASP T 76 " --> pdb=" O ILE T 89 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE T 89 " --> pdb=" O ASP T 76 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLN T 78 " --> pdb=" O GLN T 87 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLN T 87 " --> pdb=" O LYS T 25 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE T 89 " --> pdb=" O PRO T 27 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'U' and resid 18 through 19 removed outlier: 7.076A pdb=" N LEU U 55 " --> pdb=" O ILE U 33 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'U' and resid 26 through 27 Processing sheet with id=AE3, first strand: chain 'V' and resid 12 through 15 Processing sheet with id=AE4, first strand: chain 'V' and resid 33 through 39 Processing sheet with id=AE5, first strand: chain 'X' and resid 34 through 38 Processing sheet with id=AE6, first strand: chain 'Y' and resid 27 through 29 Processing sheet with id=AE7, first strand: chain 'Y' and resid 47 through 48 Processing sheet with id=AE8, first strand: chain 'Z' and resid 19 through 24 removed outlier: 4.003A pdb=" N LYS Z 9 " --> pdb=" O ALA Z 51 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN Z 44 " --> pdb=" O ASP Z 39 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'AB' and resid 14 through 15 Processing sheet with id=AF1, first strand: chain 'AC' and resid 14 through 19 removed outlier: 3.532A pdb=" N ARGAC 19 " --> pdb=" O VALAC 22 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VALAC 22 " --> pdb=" O ARGAC 19 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'a' and resid 33 through 34 removed outlier: 3.577A pdb=" N VAL a 37 " --> pdb=" O ARG a 34 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'a' and resid 66 through 69 Processing sheet with id=AF4, first strand: chain 'a' and resid 185 through 186 Processing sheet with id=AF5, first strand: chain 'b' and resid 19 through 20 Processing sheet with id=AF6, first strand: chain 'b' and resid 164 through 170 removed outlier: 3.523A pdb=" N GLU b 169 " --> pdb=" O ILE b 148 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ILE b 148 " --> pdb=" O GLU b 169 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ASP b 180 " --> pdb=" O LYS b 203 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'c' and resid 127 through 128 removed outlier: 3.757A pdb=" N GLU c 178 " --> pdb=" O ASP c 173 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP c 173 " --> pdb=" O GLU c 178 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'd' and resid 14 through 24 removed outlier: 5.446A pdb=" N LEU d 14 " --> pdb=" O VAL d 37 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL d 37 " --> pdb=" O LEU d 14 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'd' and resid 84 through 87 Processing sheet with id=AG1, first strand: chain 'e' and resid 38 through 46 removed outlier: 3.616A pdb=" N ARG e 44 " --> pdb=" O ALA e 57 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ALA e 57 " --> pdb=" O ARG e 44 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARG e 86 " --> pdb=" O MET e 9 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'g' and resid 23 through 24 Processing sheet with id=AG3, first strand: chain 'g' and resid 64 through 65 Processing sheet with id=AG4, first strand: chain 'g' and resid 73 through 76 removed outlier: 6.880A pdb=" N VAL g 102 " --> pdb=" O ILE g 125 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N TYR g 127 " --> pdb=" O ILE g 100 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE g 100 " --> pdb=" O TYR g 127 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'h' and resid 9 through 10 Processing sheet with id=AG6, first strand: chain 'h' and resid 28 through 29 Processing sheet with id=AG7, first strand: chain 'i' and resid 40 through 46 removed outlier: 4.670A pdb=" N LEU i 71 " --> pdb=" O LEU i 42 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N THR i 44 " --> pdb=" O THR i 69 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N THR i 69 " --> pdb=" O THR i 44 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'i' and resid 49 through 52 removed outlier: 4.134A pdb=" N PHE i 49 " --> pdb=" O TYR i 65 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N TYR i 65 " --> pdb=" O PHE i 49 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL i 51 " --> pdb=" O ASP i 63 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'j' and resid 40 through 45 removed outlier: 3.783A pdb=" N GLY j 42 " --> pdb=" O ILE j 33 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE j 30 " --> pdb=" O HIS j 23 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ALA j 20 " --> pdb=" O MET j 84 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N LYS j 86 " --> pdb=" O ALA j 20 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE j 22 " --> pdb=" O LYS j 86 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N LEU j 81 " --> pdb=" O ILE j 106 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ASN j 108 " --> pdb=" O LEU j 81 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR j 110 " --> pdb=" O VAL j 83 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL j 85 " --> pdb=" O THR j 110 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'k' and resid 31 through 37 removed outlier: 3.535A pdb=" N ARG k 55 " --> pdb=" O VAL k 32 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL k 36 " --> pdb=" O VAL k 51 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL k 51 " --> pdb=" O VAL k 36 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'k' and resid 81 through 82 Processing sheet with id=AH3, first strand: chain 'o' and resid 32 through 35 removed outlier: 3.570A pdb=" N ILE o 33 " --> pdb=" O VAL o 21 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N VAL o 21 " --> pdb=" O ILE o 33 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ARG o 35 " --> pdb=" O VAL o 19 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N VAL o 19 " --> pdb=" O ARG o 35 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA o 22 " --> pdb=" O THR o 3 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'o' and resid 9 through 11 Processing sheet with id=AH5, first strand: chain 'o' and resid 38 through 39 Processing sheet with id=AH6, first strand: chain 'p' and resid 36 through 45 removed outlier: 7.700A pdb=" N VAL p 21 " --> pdb=" O VAL p 12 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLU p 25 " --> pdb=" O GLN p 8 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N GLN p 8 " --> pdb=" O GLU p 25 " (cutoff:3.500A) removed outlier: 14.451A pdb=" N PHE p 27 " --> pdb=" O THR p 6 " (cutoff:3.500A) removed outlier: 17.836A pdb=" N THR p 6 " --> pdb=" O PHE p 27 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N VAL p 57 " --> pdb=" O VAL p 77 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N VAL p 77 " --> pdb=" O VAL p 57 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLU p 59 " --> pdb=" O VAL p 75 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N SER p 71 " --> pdb=" O CYS p 63 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'r' and resid 30 through 32 removed outlier: 3.966A pdb=" N LEU r 30 " --> pdb=" O THR r 47 " (cutoff:3.500A) 1838 hydrogen bonds defined for protein. 5229 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3974 hydrogen bonds 6164 hydrogen bond angles 0 basepair planarities 1584 basepair parallelities 2390 stacking parallelities Total time for adding SS restraints: 224.40 Time building geometry restraints manager: 62.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 21083 1.33 - 1.46: 66847 1.46 - 1.58: 55020 1.58 - 1.71: 9149 1.71 - 1.83: 240 Bond restraints: 152339 Sorted by residual: bond pdb=" C VAL h 54 " pdb=" N ASP h 55 " ideal model delta sigma weight residual 1.332 1.383 -0.050 1.40e-02 5.10e+03 1.30e+01 bond pdb=" C ILE b 195 " pdb=" N GLY b 196 " ideal model delta sigma weight residual 1.332 1.322 0.011 5.00e-03 4.00e+04 4.43e+00 bond pdb=" CA VAL h 54 " pdb=" C VAL h 54 " ideal model delta sigma weight residual 1.524 1.499 0.025 1.19e-02 7.06e+03 4.36e+00 bond pdb=" C LYS d 85 " pdb=" N GLY d 86 " ideal model delta sigma weight residual 1.332 1.342 -0.010 5.00e-03 4.00e+04 3.62e+00 bond pdb=" C LYS r 28 " pdb=" N PRO r 29 " ideal model delta sigma weight residual 1.340 1.391 -0.051 2.76e-02 1.31e+03 3.36e+00 ... (remaining 152334 not shown) Histogram of bond angle deviations from ideal: 99.68 - 106.79: 27890 106.79 - 113.89: 94609 113.89 - 121.00: 63983 121.00 - 128.11: 34358 128.11 - 135.22: 7566 Bond angle restraints: 228406 Sorted by residual: angle pdb=" C3' A 2 265 " pdb=" O3' A 2 265 " pdb=" P G 2 266 " ideal model delta sigma weight residual 120.20 126.86 -6.66 1.50e+00 4.44e-01 1.97e+01 angle pdb=" C3' A 11201 " pdb=" O3' A 11201 " pdb=" P U 11202 " ideal model delta sigma weight residual 120.20 126.79 -6.59 1.50e+00 4.44e-01 1.93e+01 angle pdb=" N VAL K 36 " pdb=" CA VAL K 36 " pdb=" C VAL K 36 " ideal model delta sigma weight residual 113.42 108.35 5.07 1.17e+00 7.31e-01 1.88e+01 angle pdb=" P A 2 63 " pdb=" O5' A 2 63 " pdb=" C5' A 2 63 " ideal model delta sigma weight residual 120.90 126.82 -5.92 1.50e+00 4.44e-01 1.56e+01 angle pdb=" CA LEU h 53 " pdb=" CB LEU h 53 " pdb=" CG LEU h 53 " ideal model delta sigma weight residual 116.30 129.80 -13.50 3.50e+00 8.16e-02 1.49e+01 ... (remaining 228401 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 85420 35.97 - 71.93: 10889 71.93 - 107.90: 1279 107.90 - 143.86: 7 143.86 - 179.83: 28 Dihedral angle restraints: 97623 sinusoidal: 82420 harmonic: 15203 Sorted by residual: dihedral pdb=" O4' U 21176 " pdb=" C1' U 21176 " pdb=" N1 U 21176 " pdb=" C2 U 21176 " ideal model delta sinusoidal sigma weight residual 200.00 22.77 177.23 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 1 516 " pdb=" C1' U 1 516 " pdb=" N1 U 1 516 " pdb=" C2 U 1 516 " ideal model delta sinusoidal sigma weight residual -160.00 10.24 -170.24 1 1.50e+01 4.44e-03 8.47e+01 dihedral pdb=" O4' U 2 92 " pdb=" C1' U 2 92 " pdb=" N1 U 2 92 " pdb=" C2 U 2 92 " ideal model delta sinusoidal sigma weight residual 200.00 41.71 158.29 1 1.50e+01 4.44e-03 8.23e+01 ... (remaining 97620 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 26882 0.055 - 0.110: 2087 0.110 - 0.165: 265 0.165 - 0.220: 22 0.220 - 0.275: 11 Chirality restraints: 29267 Sorted by residual: chirality pdb=" C3' A 2 265 " pdb=" C4' A 2 265 " pdb=" O3' A 2 265 " pdb=" C2' A 2 265 " both_signs ideal model delta sigma weight residual False -2.74 -2.47 -0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C3' G 2 859 " pdb=" C4' G 2 859 " pdb=" O3' G 2 859 " pdb=" C2' G 2 859 " both_signs ideal model delta sigma weight residual False -2.48 -2.22 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" C3' A 11201 " pdb=" C4' A 11201 " pdb=" O3' A 11201 " pdb=" C2' A 11201 " both_signs ideal model delta sigma weight residual False -2.74 -2.49 -0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 29264 not shown) Planarity restraints: 11889 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C 2 268 " 0.003 2.00e-02 2.50e+03 2.73e-02 1.68e+01 pdb=" N1 C 2 268 " 0.000 2.00e-02 2.50e+03 pdb=" C2 C 2 268 " 0.063 2.00e-02 2.50e+03 pdb=" O2 C 2 268 " -0.044 2.00e-02 2.50e+03 pdb=" N3 C 2 268 " -0.004 2.00e-02 2.50e+03 pdb=" C4 C 2 268 " 0.017 2.00e-02 2.50e+03 pdb=" N4 C 2 268 " -0.010 2.00e-02 2.50e+03 pdb=" C5 C 2 268 " -0.011 2.00e-02 2.50e+03 pdb=" C6 C 2 268 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C 1 624 " -0.009 2.00e-02 2.50e+03 2.15e-02 1.04e+01 pdb=" N1 C 1 624 " 0.005 2.00e-02 2.50e+03 pdb=" C2 C 1 624 " 0.056 2.00e-02 2.50e+03 pdb=" O2 C 1 624 " -0.025 2.00e-02 2.50e+03 pdb=" N3 C 1 624 " -0.016 2.00e-02 2.50e+03 pdb=" C4 C 1 624 " -0.003 2.00e-02 2.50e+03 pdb=" N4 C 1 624 " 0.002 2.00e-02 2.50e+03 pdb=" C5 C 1 624 " -0.008 2.00e-02 2.50e+03 pdb=" C6 C 1 624 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U 22580 " -0.039 2.00e-02 2.50e+03 2.03e-02 9.26e+00 pdb=" N1 U 22580 " 0.043 2.00e-02 2.50e+03 pdb=" C2 U 22580 " 0.002 2.00e-02 2.50e+03 pdb=" O2 U 22580 " 0.004 2.00e-02 2.50e+03 pdb=" N3 U 22580 " -0.000 2.00e-02 2.50e+03 pdb=" C4 U 22580 " -0.006 2.00e-02 2.50e+03 pdb=" O4 U 22580 " -0.013 2.00e-02 2.50e+03 pdb=" C5 U 22580 " 0.003 2.00e-02 2.50e+03 pdb=" C6 U 22580 " 0.007 2.00e-02 2.50e+03 ... (remaining 11886 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 1048 2.54 - 3.13: 95970 3.13 - 3.72: 280236 3.72 - 4.31: 380715 4.31 - 4.90: 512701 Nonbonded interactions: 1270670 Sorted by model distance: nonbonded pdb=" O4 U 1 13 " pdb=" O4 U 1 20 " model vdw 1.951 3.040 nonbonded pdb=" OP2 C 21315 " pdb="MG MG 23019 " model vdw 1.963 2.170 nonbonded pdb=" OP1 G 21332 " pdb="MG MG 23019 " model vdw 2.028 2.170 nonbonded pdb=" OP1 G 22592 " pdb="MG MG 23025 " model vdw 2.085 2.170 nonbonded pdb=" OP2 G 21824 " pdb="MG MG A 301 " model vdw 2.094 2.170 ... (remaining 1270665 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 16.200 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: 0.110 Extract box with map and model: 57.660 Check model and map are aligned: 1.480 Set scattering table: 0.940 Process input model: 479.540 Find NCS groups from input model: 2.550 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 561.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 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 : 0.002 0.051 152339 Z= 0.138 Angle : 0.582 13.497 228406 Z= 0.293 Chirality : 0.031 0.275 29267 Planarity : 0.004 0.049 11889 Dihedral : 23.323 179.826 87810 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.85 % Allowed : 9.06 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.10), residues: 5235 helix: -1.43 (0.10), residues: 1808 sheet: -1.67 (0.16), residues: 930 loop : -2.75 (0.10), residues: 2497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP b 200 HIS 0.009 0.001 HIS i 56 PHE 0.019 0.001 PHE r 40 TYR 0.014 0.001 TYR R 84 ARG 0.005 0.000 ARG i 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10470 Ramachandran restraints generated. 5235 Oldfield, 0 Emsley, 5235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10470 Ramachandran restraints generated. 5235 Oldfield, 0 Emsley, 5235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1733 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 1566 time to evaluate : 5.733 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: A 145 MET cc_start: 0.7836 (mmm) cc_final: 0.7536 (mmm) REVERT: B 145 SER cc_start: 0.8537 (t) cc_final: 0.8331 (m) REVERT: C 4 VAL cc_start: 0.8885 (m) cc_final: 0.8665 (t) REVERT: D 14 LYS cc_start: 0.8223 (mttm) cc_final: 0.7821 (pptt) REVERT: D 22 ASN cc_start: 0.7922 (p0) cc_final: 0.7666 (p0) REVERT: D 97 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7745 (pt0) REVERT: D 127 TYR cc_start: 0.7692 (t80) cc_final: 0.7062 (t80) REVERT: D 158 THR cc_start: 0.7501 (OUTLIER) cc_final: 0.6865 (p) REVERT: E 63 GLN cc_start: 0.7036 (tp40) cc_final: 0.6215 (pm20) REVERT: E 103 ASN cc_start: 0.7681 (m-40) cc_final: 0.6661 (t0) REVERT: E 115 GLN cc_start: 0.7263 (tp40) cc_final: 0.6538 (tp40) REVERT: G 16 TYR cc_start: 0.8206 (m-10) cc_final: 0.7575 (m-80) REVERT: G 92 MET cc_start: 0.8792 (tpp) cc_final: 0.8483 (tpp) REVERT: G 131 ASN cc_start: 0.7537 (m-40) cc_final: 0.7231 (p0) REVERT: J 105 ILE cc_start: 0.8882 (mm) cc_final: 0.8533 (mm) REVERT: K 30 SER cc_start: 0.8339 (p) cc_final: 0.8138 (p) REVERT: K 31 PHE cc_start: 0.8752 (m-80) cc_final: 0.7939 (m-80) REVERT: K 92 TRP cc_start: 0.8234 (m100) cc_final: 0.8006 (m100) REVERT: K 104 GLU cc_start: 0.7297 (mm-30) cc_final: 0.7091 (mm-30) REVERT: L 117 ASP cc_start: 0.7916 (p0) cc_final: 0.7695 (p0) REVERT: M 31 THR cc_start: 0.9107 (OUTLIER) cc_final: 0.8839 (t) REVERT: M 62 LEU cc_start: 0.9006 (pp) cc_final: 0.8706 (pp) REVERT: M 64 TYR cc_start: 0.7285 (t80) cc_final: 0.7028 (t80) REVERT: M 83 LEU cc_start: 0.9178 (mm) cc_final: 0.8858 (pp) REVERT: M 112 GLU cc_start: 0.8617 (pp20) cc_final: 0.8415 (pp20) REVERT: O 48 ASP cc_start: 0.7870 (m-30) cc_final: 0.7587 (m-30) REVERT: O 65 ASN cc_start: 0.9184 (t0) cc_final: 0.8981 (t0) REVERT: O 87 VAL cc_start: 0.9359 (t) cc_final: 0.9153 (m) REVERT: R 7 LEU cc_start: 0.9326 (mt) cc_final: 0.8890 (mt) REVERT: R 32 LEU cc_start: 0.8655 (mm) cc_final: 0.8370 (mm) REVERT: S 101 THR cc_start: 0.8996 (t) cc_final: 0.8763 (t) REVERT: T 26 PHE cc_start: 0.8133 (p90) cc_final: 0.7879 (p90) REVERT: T 43 ASP cc_start: 0.7907 (m-30) cc_final: 0.7679 (m-30) REVERT: T 50 MET cc_start: 0.7373 (ttm) cc_final: 0.7066 (tpt) REVERT: T 71 LYS cc_start: 0.8614 (ttmt) cc_final: 0.7987 (tptp) REVERT: U 64 LYS cc_start: 0.8441 (tptm) cc_final: 0.7848 (ttpt) REVERT: Z 25 ASN cc_start: 0.8160 (p0) cc_final: 0.7347 (p0) REVERT: AB 53 ASP cc_start: 0.7068 (OUTLIER) cc_final: 0.6790 (p0) REVERT: AC 16 ILE cc_start: 0.8632 (pp) cc_final: 0.7924 (mt) REVERT: AC 20 ASP cc_start: 0.7760 (t0) cc_final: 0.7508 (t0) REVERT: AC 35 GLN cc_start: 0.8581 (mp10) cc_final: 0.8345 (mt0) REVERT: a 15 PHE cc_start: 0.6445 (m-80) cc_final: 0.6185 (m-10) REVERT: b 129 PHE cc_start: 0.7855 (m-80) cc_final: 0.7527 (m-10) REVERT: b 169 GLU cc_start: 0.7962 (tp30) cc_final: 0.7412 (mm-30) REVERT: c 70 GLN cc_start: 0.9026 (mt0) cc_final: 0.8805 (tt0) REVERT: c 124 VAL cc_start: 0.8780 (t) cc_final: 0.8538 (p) REVERT: c 125 ASN cc_start: 0.8785 (t0) cc_final: 0.8313 (t0) REVERT: c 155 LYS cc_start: 0.5250 (mmtp) cc_final: 0.4287 (ptpt) REVERT: d 71 ILE cc_start: 0.7560 (tp) cc_final: 0.7118 (tp) REVERT: d 125 LYS cc_start: 0.8421 (tptp) cc_final: 0.7472 (mttt) REVERT: d 127 TYR cc_start: 0.8651 (m-80) cc_final: 0.8377 (m-80) REVERT: d 134 ASN cc_start: 0.7621 (m-40) cc_final: 0.7270 (m-40) REVERT: d 159 SER cc_start: 0.8123 (p) cc_final: 0.7546 (p) REVERT: e 81 ASN cc_start: 0.8171 (t0) cc_final: 0.7823 (t0) REVERT: f 35 LYS cc_start: 0.7155 (tttt) cc_final: 0.6845 (tptm) REVERT: f 122 GLU cc_start: 0.6424 (tm-30) cc_final: 0.6170 (tt0) REVERT: g 51 GLU cc_start: 0.7717 (mp0) cc_final: 0.7498 (mp0) REVERT: g 66 GLN cc_start: 0.7990 (mt0) cc_final: 0.7511 (tm-30) REVERT: g 84 ILE cc_start: 0.8772 (mm) cc_final: 0.8539 (pt) REVERT: g 123 GLU cc_start: 0.7895 (tt0) cc_final: 0.7685 (tt0) REVERT: h 21 LYS cc_start: 0.2793 (OUTLIER) cc_final: 0.2209 (ptpt) REVERT: h 35 GLU cc_start: 0.6089 (mm-30) cc_final: 0.5694 (tt0) REVERT: h 128 LYS cc_start: 0.6396 (pptt) cc_final: 0.5935 (mtmt) REVERT: i 5 ARG cc_start: 0.5327 (tpt170) cc_final: 0.5007 (ttm170) REVERT: i 53 ILE cc_start: 0.6774 (mm) cc_final: 0.6535 (mm) REVERT: j 19 VAL cc_start: 0.6686 (m) cc_final: 0.6032 (t) REVERT: k 36 VAL cc_start: 0.5048 (OUTLIER) cc_final: 0.4693 (t) REVERT: k 110 LYS cc_start: 0.7685 (tmtt) cc_final: 0.7462 (mtmm) REVERT: l 72 ILE cc_start: 0.8609 (mt) cc_final: 0.8270 (mm) REVERT: l 80 MET cc_start: 0.6816 (mtt) cc_final: 0.6012 (ttt) REVERT: m 6 LYS cc_start: 0.8146 (mmmt) cc_final: 0.7761 (tptt) REVERT: m 9 GLU cc_start: 0.8359 (mm-30) cc_final: 0.7880 (tp30) REVERT: m 73 LEU cc_start: 0.8727 (mt) cc_final: 0.8315 (tp) REVERT: n 68 TYR cc_start: 0.8717 (t80) cc_final: 0.8431 (t80) REVERT: o 14 ARG cc_start: 0.8184 (mtp85) cc_final: 0.7912 (ttt-90) REVERT: o 76 LYS cc_start: 0.6331 (ttmt) cc_final: 0.5890 (ttpt) REVERT: q 67 LEU cc_start: 0.8656 (mm) cc_final: 0.8324 (mt) REVERT: r 9 PHE cc_start: 0.6984 (t80) cc_final: 0.6709 (t80) REVERT: r 10 ILE cc_start: 0.7467 (tp) cc_final: 0.7044 (tp) REVERT: r 39 ILE cc_start: 0.3592 (OUTLIER) cc_final: 0.3376 (pt) REVERT: r 51 HIS cc_start: 0.5908 (t-170) cc_final: 0.5256 (t70) REVERT: r 69 LYS cc_start: 0.5175 (tptm) cc_final: 0.4291 (mptt) REVERT: s 31 ILE cc_start: 0.9272 (mt) cc_final: 0.9049 (pt) REVERT: s 50 PHE cc_start: 0.8602 (t80) cc_final: 0.8363 (t80) REVERT: t 11 PHE cc_start: 0.6621 (t80) cc_final: 0.6262 (m-80) REVERT: t 62 GLU cc_start: 0.6791 (mm-30) cc_final: 0.6432 (tm-30) outliers start: 167 outliers final: 74 residues processed: 1683 average time/residue: 1.4079 time to fit residues: 4064.2961 Evaluate side-chains 1017 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 936 time to evaluate : 5.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain D residue 6 TYR Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 28 VAL Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 71 VAL Chi-restraints excluded: chain Q residue 77 ASP Chi-restraints excluded: chain R residue 16 VAL Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain S residue 27 VAL Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain T residue 8 VAL Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain V residue 15 ASN Chi-restraints excluded: chain V residue 29 LEU Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain AB residue 30 HIS Chi-restraints excluded: chain AB residue 53 ASP Chi-restraints excluded: chain AC residue 3 VAL Chi-restraints excluded: chain AC residue 25 VAL Chi-restraints excluded: chain a residue 186 VAL Chi-restraints excluded: chain a residue 198 VAL Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 75 VAL Chi-restraints excluded: chain c residue 85 THR Chi-restraints excluded: chain e residue 18 VAL Chi-restraints excluded: chain e residue 61 LEU Chi-restraints excluded: chain g residue 103 VAL Chi-restraints excluded: chain g residue 126 CYS Chi-restraints excluded: chain h residue 21 LYS Chi-restraints excluded: chain h residue 28 VAL Chi-restraints excluded: chain h residue 55 ASP Chi-restraints excluded: chain h residue 57 VAL Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 32 VAL Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain k residue 113 ARG Chi-restraints excluded: chain k residue 118 VAL Chi-restraints excluded: chain l residue 6 ILE Chi-restraints excluded: chain m residue 33 VAL Chi-restraints excluded: chain n residue 69 LEU Chi-restraints excluded: chain n residue 84 LEU Chi-restraints excluded: chain o residue 2 VAL Chi-restraints excluded: chain p residue 45 VAL Chi-restraints excluded: chain p residue 57 VAL Chi-restraints excluded: chain p residue 77 VAL Chi-restraints excluded: chain q residue 28 LEU Chi-restraints excluded: chain r residue 35 ARG Chi-restraints excluded: chain r residue 39 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 816 optimal weight: 20.0000 chunk 732 optimal weight: 7.9990 chunk 406 optimal weight: 9.9990 chunk 250 optimal weight: 0.7980 chunk 494 optimal weight: 10.0000 chunk 391 optimal weight: 10.0000 chunk 757 optimal weight: 8.9990 chunk 293 optimal weight: 3.9990 chunk 460 optimal weight: 20.0000 chunk 564 optimal weight: 10.0000 chunk 878 optimal weight: 10.0000 overall best weight: 6.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 GLN B 32 ASN B 136 ASN B 150 GLN B 164 GLN D 4 HIS D 36 ASN D 62 GLN ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 40 HIS ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 22 GLN L 18 GLN L 31 HIS M 38 GLN O 36 GLN O 43 GLN O 71 ASN P 12 HIS ** P 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 57 ASN Q 61 ASN R 48 GLN S 44 HIS S 65 GLN S 68 ASN T 12 GLN U 53 HIS AB 30 HIS ** a 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 108 GLN ** a 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 101 ASN b 139 ASN b 175 HIS ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 42 ASN ** d 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 17 GLN e 37 HIS e 55 HIS f 27 ASN g 3 GLN g 20 ASN ** h 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 5 GLN ** k 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 111 GLN ** l 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 65 GLN ** n 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 19 HIS ** s 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 63 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.143 152339 Z= 0.412 Angle : 0.712 9.764 228406 Z= 0.362 Chirality : 0.039 0.311 29267 Planarity : 0.006 0.062 11889 Dihedral : 24.024 179.888 77501 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.73 % Favored : 94.25 % Rotamer: Outliers : 6.06 % Allowed : 17.10 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.11), residues: 5235 helix: 0.03 (0.12), residues: 1811 sheet: -1.24 (0.17), residues: 904 loop : -2.33 (0.11), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP N 30 HIS 0.008 0.002 HIS k 95 PHE 0.027 0.002 PHE o 39 TYR 0.039 0.003 TYR n 77 ARG 0.017 0.001 ARG K 16 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10470 Ramachandran restraints generated. 5235 Oldfield, 0 Emsley, 5235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10470 Ramachandran restraints generated. 5235 Oldfield, 0 Emsley, 5235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1202 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 263 poor density : 939 time to evaluate : 5.828 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: A 162 GLN cc_start: 0.8060 (tp-100) cc_final: 0.7777 (tp40) REVERT: B 131 ASP cc_start: 0.8090 (OUTLIER) cc_final: 0.7699 (p0) REVERT: D 14 LYS cc_start: 0.8171 (mttm) cc_final: 0.7871 (pptt) REVERT: D 25 MET cc_start: 0.5301 (ttm) cc_final: 0.5002 (ttm) REVERT: D 129 MET cc_start: 0.7770 (ppp) cc_final: 0.6987 (ptp) REVERT: F 1 MET cc_start: 0.6008 (tpt) cc_final: 0.5228 (ttp) REVERT: G 16 TYR cc_start: 0.8624 (m-80) cc_final: 0.7985 (m-80) REVERT: G 108 MET cc_start: 0.8500 (mtt) cc_final: 0.8036 (mmt) REVERT: I 86 LEU cc_start: 0.9135 (mm) cc_final: 0.8899 (mm) REVERT: K 104 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7220 (mm-30) REVERT: L 72 ASP cc_start: 0.8712 (t0) cc_final: 0.7711 (t0) REVERT: M 31 THR cc_start: 0.9039 (OUTLIER) cc_final: 0.8776 (t) REVERT: M 85 LYS cc_start: 0.8941 (mmmm) cc_final: 0.8733 (mmmm) REVERT: M 98 GLN cc_start: 0.8230 (tp40) cc_final: 0.8009 (mm110) REVERT: M 116 GLN cc_start: 0.6873 (tm-30) cc_final: 0.6540 (tm-30) REVERT: O 48 ASP cc_start: 0.8210 (m-30) cc_final: 0.7954 (m-30) REVERT: O 101 ASP cc_start: 0.7868 (t0) cc_final: 0.7582 (t70) REVERT: R 7 LEU cc_start: 0.9350 (mt) cc_final: 0.8987 (mt) REVERT: S 9 GLU cc_start: 0.7282 (tp30) cc_final: 0.6927 (tp30) REVERT: S 61 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7287 (mt-10) REVERT: T 11 GLU cc_start: 0.7240 (pt0) cc_final: 0.7023 (pt0) REVERT: T 26 PHE cc_start: 0.8634 (p90) cc_final: 0.8110 (p90) REVERT: T 45 ASP cc_start: 0.8454 (OUTLIER) cc_final: 0.8240 (p0) REVERT: T 55 GLU cc_start: 0.8699 (pm20) cc_final: 0.8323 (pm20) REVERT: U 68 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8225 (mmtm) REVERT: V 37 PHE cc_start: 0.8939 (m-80) cc_final: 0.8585 (m-80) REVERT: V 75 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7893 (tm-30) REVERT: W 17 GLU cc_start: 0.7992 (tp30) cc_final: 0.7780 (tp30) REVERT: Z 25 ASN cc_start: 0.8678 (p0) cc_final: 0.8424 (p0) REVERT: AA 1 MET cc_start: 0.7948 (ptp) cc_final: 0.7472 (ptp) REVERT: AB 53 ASP cc_start: 0.7341 (OUTLIER) cc_final: 0.6940 (p0) REVERT: AC 20 ASP cc_start: 0.8164 (t0) cc_final: 0.7776 (t0) REVERT: AC 32 LYS cc_start: 0.9165 (mtpt) cc_final: 0.8916 (mtpt) REVERT: a 15 PHE cc_start: 0.6758 (m-80) cc_final: 0.6290 (m-10) REVERT: a 158 ASP cc_start: 0.8110 (t70) cc_final: 0.7896 (t0) REVERT: a 212 TYR cc_start: 0.8413 (m-80) cc_final: 0.8096 (m-80) REVERT: b 139 ASN cc_start: 0.7569 (m-40) cc_final: 0.7239 (m110) REVERT: b 151 GLU cc_start: 0.8370 (tt0) cc_final: 0.8027 (mp0) REVERT: b 200 TRP cc_start: 0.8150 (m-90) cc_final: 0.7671 (m-90) REVERT: c 104 MET cc_start: 0.7127 (mmm) cc_final: 0.6714 (mmt) REVERT: c 155 LYS cc_start: 0.4916 (mmtp) cc_final: 0.4017 (ptpt) REVERT: c 203 TYR cc_start: 0.6912 (OUTLIER) cc_final: 0.5902 (t80) REVERT: d 125 LYS cc_start: 0.8737 (tptp) cc_final: 0.7795 (mttt) REVERT: d 159 SER cc_start: 0.8399 (p) cc_final: 0.8061 (m) REVERT: e 5 GLU cc_start: 0.7547 (tm-30) cc_final: 0.7337 (tm-30) REVERT: e 11 HIS cc_start: 0.8583 (t-90) cc_final: 0.8253 (t-90) REVERT: e 81 ASN cc_start: 0.8227 (t0) cc_final: 0.7854 (t0) REVERT: f 35 LYS cc_start: 0.7068 (tttt) cc_final: 0.6789 (tptm) REVERT: g 3 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7502 (mt0) REVERT: g 66 GLN cc_start: 0.8206 (mt0) cc_final: 0.7565 (tm-30) REVERT: h 35 GLU cc_start: 0.6246 (mm-30) cc_final: 0.5327 (tt0) REVERT: i 5 ARG cc_start: 0.5331 (tpt170) cc_final: 0.5126 (ttm170) REVERT: i 47 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7629 (mp0) REVERT: i 99 GLN cc_start: 0.7350 (mm-40) cc_final: 0.7146 (tt0) REVERT: j 19 VAL cc_start: 0.7513 (m) cc_final: 0.7169 (t) REVERT: j 124 LYS cc_start: 0.8717 (pttt) cc_final: 0.8462 (pttt) REVERT: k 110 LYS cc_start: 0.7887 (tmtt) cc_final: 0.7609 (mmmt) REVERT: l 7 ASN cc_start: 0.6322 (t0) cc_final: 0.5883 (m-40) REVERT: l 12 LYS cc_start: 0.5477 (mttt) cc_final: 0.5204 (mmmt) REVERT: l 55 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7879 (mm) REVERT: l 77 LYS cc_start: 0.7965 (pttp) cc_final: 0.7688 (ptmt) REVERT: l 94 LEU cc_start: 0.7215 (mm) cc_final: 0.6996 (mt) REVERT: m 9 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8171 (tp30) REVERT: m 22 LYS cc_start: 0.7135 (pttm) cc_final: 0.6605 (mmtm) REVERT: m 41 TRP cc_start: 0.7790 (t-100) cc_final: 0.7502 (t60) REVERT: m 48 GLN cc_start: 0.6883 (mm-40) cc_final: 0.6520 (tm-30) REVERT: m 73 LEU cc_start: 0.8789 (mt) cc_final: 0.8336 (tp) REVERT: n 44 GLU cc_start: 0.8062 (pm20) cc_final: 0.7813 (pm20) REVERT: o 5 ARG cc_start: 0.5064 (ptp-170) cc_final: 0.4491 (ttm110) REVERT: o 63 GLN cc_start: 0.7368 (mm-40) cc_final: 0.6999 (mm-40) REVERT: p 17 GLU cc_start: 0.6972 (tm-30) cc_final: 0.6681 (tm-30) REVERT: p 32 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8236 (tp) REVERT: q 64 LEU cc_start: 0.9281 (mm) cc_final: 0.9013 (mm) REVERT: q 67 LEU cc_start: 0.8726 (mm) cc_final: 0.8490 (mt) REVERT: r 15 LEU cc_start: 0.6811 (mt) cc_final: 0.6548 (mp) REVERT: r 39 ILE cc_start: 0.3755 (OUTLIER) cc_final: 0.3526 (pt) REVERT: r 43 MET cc_start: 0.7637 (ttt) cc_final: 0.6486 (mmt) REVERT: r 69 LYS cc_start: 0.5838 (tptm) cc_final: 0.4744 (mptt) REVERT: t 62 GLU cc_start: 0.6712 (mm-30) cc_final: 0.6301 (tm-30) REVERT: t 63 ASN cc_start: 0.4948 (m-40) cc_final: 0.4591 (m110) outliers start: 263 outliers final: 165 residues processed: 1126 average time/residue: 1.1730 time to fit residues: 2349.9200 Evaluate side-chains 999 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 823 time to evaluate : 5.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain D residue 6 TYR Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 46 PHE Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain K residue 2 LEU Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 59 ARG Chi-restraints excluded: chain M residue 19 GLN Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 28 VAL Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain M residue 36 TYR Chi-restraints excluded: chain M residue 38 GLN Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 26 ASP Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain Q residue 3 THR Chi-restraints excluded: chain Q residue 13 SER Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 67 ASP Chi-restraints excluded: chain Q residue 71 VAL Chi-restraints excluded: chain Q residue 77 ASP Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain R residue 16 VAL Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 27 VAL Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain T residue 8 VAL Chi-restraints excluded: chain T residue 45 ASP Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 34 VAL Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain U residue 68 LYS Chi-restraints excluded: chain V residue 15 ASN Chi-restraints excluded: chain V residue 29 LEU Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain V residue 34 SER Chi-restraints excluded: chain V residue 59 ASP Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 75 GLU Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 56 VAL Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 33 SER Chi-restraints excluded: chain Z residue 46 VAL Chi-restraints excluded: chain AB residue 3 ILE Chi-restraints excluded: chain AB residue 5 THR Chi-restraints excluded: chain AB residue 53 ASP Chi-restraints excluded: chain AC residue 3 VAL Chi-restraints excluded: chain AC residue 25 VAL Chi-restraints excluded: chain a residue 18 GLN Chi-restraints excluded: chain a residue 45 THR Chi-restraints excluded: chain a residue 59 ILE Chi-restraints excluded: chain a residue 108 GLN Chi-restraints excluded: chain a residue 147 LEU Chi-restraints excluded: chain a residue 178 LEU Chi-restraints excluded: chain a residue 185 ILE Chi-restraints excluded: chain a residue 186 VAL Chi-restraints excluded: chain a residue 190 SER Chi-restraints excluded: chain a residue 198 VAL Chi-restraints excluded: chain a residue 199 ILE Chi-restraints excluded: chain b residue 63 ILE Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 75 VAL Chi-restraints excluded: chain b residue 118 SER Chi-restraints excluded: chain b residue 182 ASP Chi-restraints excluded: chain b residue 195 ILE Chi-restraints excluded: chain c residue 85 THR Chi-restraints excluded: chain c residue 101 VAL Chi-restraints excluded: chain c residue 154 VAL Chi-restraints excluded: chain c residue 203 TYR Chi-restraints excluded: chain d residue 84 VAL Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain e residue 2 ARG Chi-restraints excluded: chain e residue 18 VAL Chi-restraints excluded: chain e residue 55 HIS Chi-restraints excluded: chain e residue 61 LEU Chi-restraints excluded: chain e residue 64 VAL Chi-restraints excluded: chain e residue 77 THR Chi-restraints excluded: chain e residue 96 VAL Chi-restraints excluded: chain f residue 17 PHE Chi-restraints excluded: chain f residue 21 LEU Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain g residue 3 GLN Chi-restraints excluded: chain g residue 39 LEU Chi-restraints excluded: chain g residue 74 ILE Chi-restraints excluded: chain g residue 91 LEU Chi-restraints excluded: chain g residue 100 ILE Chi-restraints excluded: chain g residue 102 VAL Chi-restraints excluded: chain g residue 103 VAL Chi-restraints excluded: chain g residue 112 ASP Chi-restraints excluded: chain h residue 28 VAL Chi-restraints excluded: chain h residue 57 VAL Chi-restraints excluded: chain i residue 10 LEU Chi-restraints excluded: chain i residue 49 PHE Chi-restraints excluded: chain i residue 63 ASP Chi-restraints excluded: chain j residue 22 ILE Chi-restraints excluded: chain j residue 29 THR Chi-restraints excluded: chain j residue 45 THR Chi-restraints excluded: chain j residue 58 THR Chi-restraints excluded: chain j residue 115 ILE Chi-restraints excluded: chain k residue 32 VAL Chi-restraints excluded: chain k residue 56 LEU Chi-restraints excluded: chain k residue 81 ILE Chi-restraints excluded: chain l residue 6 ILE Chi-restraints excluded: chain l residue 19 THR Chi-restraints excluded: chain l residue 55 LEU Chi-restraints excluded: chain m residue 33 VAL Chi-restraints excluded: chain m residue 45 LEU Chi-restraints excluded: chain n residue 21 THR Chi-restraints excluded: chain n residue 84 LEU Chi-restraints excluded: chain o residue 2 VAL Chi-restraints excluded: chain o residue 23 ASP Chi-restraints excluded: chain o residue 60 TRP Chi-restraints excluded: chain p residue 32 ILE Chi-restraints excluded: chain p residue 45 VAL Chi-restraints excluded: chain p residue 49 ASN Chi-restraints excluded: chain p residue 59 GLU Chi-restraints excluded: chain p residue 77 VAL Chi-restraints excluded: chain q residue 28 LEU Chi-restraints excluded: chain r residue 39 ILE Chi-restraints excluded: chain r residue 40 PHE Chi-restraints excluded: chain r residue 42 ASN Chi-restraints excluded: chain s residue 54 GLN Chi-restraints excluded: chain t residue 21 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 488 optimal weight: 5.9990 chunk 272 optimal weight: 0.9980 chunk 730 optimal weight: 6.9990 chunk 597 optimal weight: 10.0000 chunk 242 optimal weight: 6.9990 chunk 879 optimal weight: 10.0000 chunk 950 optimal weight: 10.0000 chunk 783 optimal weight: 10.0000 chunk 872 optimal weight: 10.0000 chunk 299 optimal weight: 10.0000 chunk 705 optimal weight: 40.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN ** A 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 GLN E 142 GLN ** F 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 58 ASN ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 9 GLN M 38 GLN ** P 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 49 ASN Y 4 GLN ** Z 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AB 30 HIS ** a 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 108 GLN ** a 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 84 ASN ** c 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 121 ASN g 3 GLN h 49 GLN ** i 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 100 ASN ** k 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 37 HIS ** n 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.126 152339 Z= 0.388 Angle : 0.689 11.527 228406 Z= 0.351 Chirality : 0.039 0.338 29267 Planarity : 0.005 0.069 11889 Dihedral : 24.114 179.848 77465 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.77 % Favored : 94.19 % Rotamer: Outliers : 6.94 % Allowed : 18.76 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.11), residues: 5235 helix: 0.20 (0.12), residues: 1808 sheet: -1.26 (0.16), residues: 962 loop : -2.17 (0.11), residues: 2465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP p 72 HIS 0.059 0.002 HIS e 55 PHE 0.031 0.002 PHE e 78 TYR 0.045 0.003 TYR c 74 ARG 0.016 0.001 ARGAC 12 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10470 Ramachandran restraints generated. 5235 Oldfield, 0 Emsley, 5235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10470 Ramachandran restraints generated. 5235 Oldfield, 0 Emsley, 5235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1205 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 301 poor density : 904 time to evaluate : 5.849 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: B 130 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8135 (mp10) REVERT: C 30 GLN cc_start: 0.9171 (OUTLIER) cc_final: 0.8863 (tt0) REVERT: C 73 ILE cc_start: 0.9284 (OUTLIER) cc_final: 0.8954 (mt) REVERT: D 14 LYS cc_start: 0.8050 (mttm) cc_final: 0.7798 (pptt) REVERT: D 16 MET cc_start: 0.7111 (mmt) cc_final: 0.6789 (mmp) REVERT: D 25 MET cc_start: 0.5279 (ttm) cc_final: 0.4843 (ttm) REVERT: E 100 ASN cc_start: 0.7429 (p0) cc_final: 0.7228 (p0) REVERT: G 108 MET cc_start: 0.8552 (mtt) cc_final: 0.8149 (mtt) REVERT: I 86 LEU cc_start: 0.9131 (mm) cc_final: 0.8927 (mm) REVERT: K 28 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.8124 (p90) REVERT: K 63 ILE cc_start: 0.9128 (pt) cc_final: 0.8901 (mt) REVERT: K 104 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7388 (mm-30) REVERT: L 49 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8040 (mm-30) REVERT: M 31 THR cc_start: 0.9034 (OUTLIER) cc_final: 0.8765 (t) REVERT: M 80 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8565 (mt-10) REVERT: M 85 LYS cc_start: 0.9091 (mmmm) cc_final: 0.8880 (mmmm) REVERT: O 48 ASP cc_start: 0.8211 (m-30) cc_final: 0.7911 (m-30) REVERT: O 101 ASP cc_start: 0.7881 (t0) cc_final: 0.7447 (t70) REVERT: Q 13 SER cc_start: 0.8808 (OUTLIER) cc_final: 0.8590 (p) REVERT: R 7 LEU cc_start: 0.9272 (mt) cc_final: 0.8859 (mt) REVERT: S 61 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7149 (mt-10) REVERT: S 81 ARG cc_start: 0.8813 (mtm110) cc_final: 0.8487 (mtm110) REVERT: S 96 LYS cc_start: 0.8487 (mtpt) cc_final: 0.8057 (mtpt) REVERT: T 4 ILE cc_start: 0.7726 (mm) cc_final: 0.7403 (mm) REVERT: T 25 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8485 (mtpt) REVERT: T 26 PHE cc_start: 0.8545 (p90) cc_final: 0.8083 (p90) REVERT: T 45 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.8167 (p0) REVERT: U 11 ASP cc_start: 0.8041 (t0) cc_final: 0.7788 (t0) REVERT: U 35 ARG cc_start: 0.8446 (mtp-110) cc_final: 0.8087 (mtm180) REVERT: V 75 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7846 (tm-30) REVERT: Z 16 THR cc_start: 0.7167 (OUTLIER) cc_final: 0.6821 (p) REVERT: Z 25 ASN cc_start: 0.8799 (OUTLIER) cc_final: 0.8212 (p0) REVERT: AA 1 MET cc_start: 0.7814 (ptp) cc_final: 0.7261 (ptp) REVERT: AB 53 ASP cc_start: 0.7269 (OUTLIER) cc_final: 0.6916 (p0) REVERT: AC 20 ASP cc_start: 0.8212 (t0) cc_final: 0.7854 (t0) REVERT: a 8 MET cc_start: 0.8052 (mmm) cc_final: 0.7798 (mmm) REVERT: a 15 PHE cc_start: 0.6886 (m-80) cc_final: 0.6382 (m-10) REVERT: a 158 ASP cc_start: 0.8234 (t70) cc_final: 0.7929 (t0) REVERT: c 71 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.8202 (m-10) REVERT: c 104 MET cc_start: 0.7124 (mmm) cc_final: 0.6804 (tpt) REVERT: c 155 LYS cc_start: 0.5056 (mmtp) cc_final: 0.4178 (ptpt) REVERT: c 203 TYR cc_start: 0.6943 (OUTLIER) cc_final: 0.5933 (t80) REVERT: d 125 LYS cc_start: 0.8703 (tptp) cc_final: 0.7852 (mttt) REVERT: d 161 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7966 (mp0) REVERT: e 5 GLU cc_start: 0.7614 (tm-30) cc_final: 0.7192 (tm-30) REVERT: e 74 LEU cc_start: 0.9310 (tp) cc_final: 0.8896 (tp) REVERT: e 78 PHE cc_start: 0.8840 (m-80) cc_final: 0.8427 (m-80) REVERT: e 81 ASN cc_start: 0.8329 (t0) cc_final: 0.7991 (t0) REVERT: f 17 PHE cc_start: 0.2236 (OUTLIER) cc_final: 0.1863 (m-80) REVERT: f 39 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8164 (pt0) REVERT: f 103 ILE cc_start: 0.8846 (pt) cc_final: 0.8616 (mm) REVERT: f 105 GLU cc_start: 0.7662 (tp30) cc_final: 0.7381 (tp30) REVERT: g 66 GLN cc_start: 0.8211 (mt0) cc_final: 0.7461 (tm-30) REVERT: g 110 MET cc_start: 0.7178 (ptp) cc_final: 0.6814 (ptt) REVERT: h 35 GLU cc_start: 0.6507 (mm-30) cc_final: 0.5411 (tt0) REVERT: i 5 ARG cc_start: 0.5192 (tpt170) cc_final: 0.4951 (ttm170) REVERT: i 18 ILE cc_start: 0.8145 (tp) cc_final: 0.7932 (pt) REVERT: i 56 HIS cc_start: 0.7738 (OUTLIER) cc_final: 0.7505 (m-70) REVERT: i 99 GLN cc_start: 0.7550 (mm-40) cc_final: 0.7303 (mm-40) REVERT: j 19 VAL cc_start: 0.7745 (m) cc_final: 0.7187 (t) REVERT: j 124 LYS cc_start: 0.8897 (pttt) cc_final: 0.8696 (pttt) REVERT: l 12 LYS cc_start: 0.5751 (mttt) cc_final: 0.5503 (mmmt) REVERT: l 77 LYS cc_start: 0.7960 (pttp) cc_final: 0.7676 (pttp) REVERT: l 80 MET cc_start: 0.6865 (mtt) cc_final: 0.5905 (ttt) REVERT: l 81 ASP cc_start: 0.7234 (m-30) cc_final: 0.6968 (m-30) REVERT: m 9 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8254 (tp30) REVERT: m 41 TRP cc_start: 0.7763 (t-100) cc_final: 0.7253 (t60) REVERT: m 48 GLN cc_start: 0.6948 (mm-40) cc_final: 0.6421 (tm-30) REVERT: m 72 PHE cc_start: 0.5620 (t80) cc_final: 0.5222 (t80) REVERT: m 73 LEU cc_start: 0.8759 (mt) cc_final: 0.7991 (tp) REVERT: n 84 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8561 (mt) REVERT: o 5 ARG cc_start: 0.5037 (ptp-170) cc_final: 0.4378 (ttm110) REVERT: p 76 ARG cc_start: 0.7925 (mtm-85) cc_final: 0.7176 (mtm-85) REVERT: r 15 LEU cc_start: 0.7028 (mt) cc_final: 0.6681 (mt) REVERT: r 43 MET cc_start: 0.7615 (ttt) cc_final: 0.6382 (mmt) REVERT: r 69 LYS cc_start: 0.6153 (tptm) cc_final: 0.5101 (mptt) REVERT: t 24 LYS cc_start: 0.9189 (mmmt) cc_final: 0.8910 (mmmt) REVERT: t 43 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7462 (mm-30) REVERT: t 62 GLU cc_start: 0.6558 (mm-30) cc_final: 0.6117 (tm-30) REVERT: t 63 ASN cc_start: 0.5192 (m-40) cc_final: 0.4888 (m110) outliers start: 301 outliers final: 208 residues processed: 1118 average time/residue: 1.1553 time to fit residues: 2304.2098 Evaluate side-chains 1037 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 811 time to evaluate : 5.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 130 GLN Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 30 GLN Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain D residue 6 TYR Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 15 ASP Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 131 ASN Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 28 VAL Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain N residue 4 ILE Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain N residue 103 THR Chi-restraints excluded: chain N residue 113 LEU Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 26 ASP Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 101 ILE Chi-restraints excluded: chain Q residue 3 THR Chi-restraints excluded: chain Q residue 13 SER Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 40 ASN Chi-restraints excluded: chain Q residue 61 ASN Chi-restraints excluded: chain Q residue 67 ASP Chi-restraints excluded: chain Q residue 71 VAL Chi-restraints excluded: chain Q residue 77 ASP Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain R residue 16 VAL Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain S residue 10 VAL Chi-restraints excluded: chain S residue 27 VAL Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain T residue 2 PHE Chi-restraints excluded: chain T residue 5 ASN Chi-restraints excluded: chain T residue 8 VAL Chi-restraints excluded: chain T residue 25 LYS Chi-restraints excluded: chain T residue 45 ASP Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 34 VAL Chi-restraints excluded: chain V residue 15 ASN Chi-restraints excluded: chain V residue 29 LEU Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain V residue 34 SER Chi-restraints excluded: chain V residue 47 THR Chi-restraints excluded: chain V residue 59 ASP Chi-restraints excluded: chain V residue 75 GLU Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain Y residue 2 VAL Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 22 THR Chi-restraints excluded: chain Z residue 16 THR Chi-restraints excluded: chain Z residue 25 ASN Chi-restraints excluded: chain Z residue 41 VAL Chi-restraints excluded: chain Z residue 46 VAL Chi-restraints excluded: chain AA residue 24 THR Chi-restraints excluded: chain AA residue 30 VAL Chi-restraints excluded: chain AB residue 5 THR Chi-restraints excluded: chain AB residue 53 ASP Chi-restraints excluded: chain AC residue 3 VAL Chi-restraints excluded: chain AC residue 25 VAL Chi-restraints excluded: chain a residue 18 GLN Chi-restraints excluded: chain a residue 30 ILE Chi-restraints excluded: chain a residue 45 THR Chi-restraints excluded: chain a residue 59 ILE Chi-restraints excluded: chain a residue 147 LEU Chi-restraints excluded: chain a residue 178 LEU Chi-restraints excluded: chain a residue 183 PHE Chi-restraints excluded: chain a residue 185 ILE Chi-restraints excluded: chain a residue 186 VAL Chi-restraints excluded: chain a residue 190 SER Chi-restraints excluded: chain a residue 198 VAL Chi-restraints excluded: chain a residue 199 ILE Chi-restraints excluded: chain b residue 63 ILE Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 74 ILE Chi-restraints excluded: chain b residue 75 VAL Chi-restraints excluded: chain b residue 118 SER Chi-restraints excluded: chain b residue 133 MET Chi-restraints excluded: chain b residue 156 LEU Chi-restraints excluded: chain b residue 195 ILE Chi-restraints excluded: chain b residue 206 ILE Chi-restraints excluded: chain c residue 71 PHE Chi-restraints excluded: chain c residue 85 THR Chi-restraints excluded: chain c residue 125 ASN Chi-restraints excluded: chain c residue 154 VAL Chi-restraints excluded: chain c residue 168 THR Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 203 TYR Chi-restraints excluded: chain d residue 84 VAL Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain d residue 163 ILE Chi-restraints excluded: chain e residue 18 VAL Chi-restraints excluded: chain e residue 61 LEU Chi-restraints excluded: chain e residue 77 THR Chi-restraints excluded: chain f residue 17 PHE Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain g residue 39 LEU Chi-restraints excluded: chain g residue 74 ILE Chi-restraints excluded: chain g residue 91 LEU Chi-restraints excluded: chain g residue 100 ILE Chi-restraints excluded: chain g residue 102 VAL Chi-restraints excluded: chain g residue 103 VAL Chi-restraints excluded: chain g residue 111 THR Chi-restraints excluded: chain g residue 112 ASP Chi-restraints excluded: chain g residue 125 ILE Chi-restraints excluded: chain h residue 28 VAL Chi-restraints excluded: chain h residue 57 VAL Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain h residue 110 VAL Chi-restraints excluded: chain i residue 10 LEU Chi-restraints excluded: chain i residue 17 LEU Chi-restraints excluded: chain i residue 49 PHE Chi-restraints excluded: chain i residue 56 HIS Chi-restraints excluded: chain i residue 63 ASP Chi-restraints excluded: chain i residue 73 LEU Chi-restraints excluded: chain i residue 74 VAL Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain i residue 102 LEU Chi-restraints excluded: chain j residue 22 ILE Chi-restraints excluded: chain j residue 41 LEU Chi-restraints excluded: chain j residue 45 THR Chi-restraints excluded: chain j residue 58 THR Chi-restraints excluded: chain j residue 64 VAL Chi-restraints excluded: chain j residue 115 ILE Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain k residue 56 LEU Chi-restraints excluded: chain l residue 6 ILE Chi-restraints excluded: chain l residue 19 THR Chi-restraints excluded: chain l residue 52 ILE Chi-restraints excluded: chain l residue 82 LEU Chi-restraints excluded: chain m residue 29 ILE Chi-restraints excluded: chain m residue 33 VAL Chi-restraints excluded: chain m residue 45 LEU Chi-restraints excluded: chain m residue 49 THR Chi-restraints excluded: chain m residue 53 ASP Chi-restraints excluded: chain n residue 21 THR Chi-restraints excluded: chain n residue 84 LEU Chi-restraints excluded: chain o residue 2 VAL Chi-restraints excluded: chain o residue 13 LYS Chi-restraints excluded: chain o residue 23 ASP Chi-restraints excluded: chain o residue 52 LEU Chi-restraints excluded: chain o residue 60 TRP Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain p residue 20 ILE Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 37 ILE Chi-restraints excluded: chain p residue 45 VAL Chi-restraints excluded: chain p residue 46 HIS Chi-restraints excluded: chain p residue 57 VAL Chi-restraints excluded: chain p residue 77 VAL Chi-restraints excluded: chain q residue 28 LEU Chi-restraints excluded: chain r residue 39 ILE Chi-restraints excluded: chain r residue 40 PHE Chi-restraints excluded: chain r residue 42 ASN Chi-restraints excluded: chain r residue 61 VAL Chi-restraints excluded: chain s residue 29 THR Chi-restraints excluded: chain t residue 27 VAL Chi-restraints excluded: chain t residue 42 THR Chi-restraints excluded: chain t residue 43 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 869 optimal weight: 10.0000 chunk 661 optimal weight: 10.0000 chunk 456 optimal weight: 20.0000 chunk 97 optimal weight: 8.9990 chunk 419 optimal weight: 10.0000 chunk 590 optimal weight: 10.0000 chunk 882 optimal weight: 10.0000 chunk 934 optimal weight: 20.0000 chunk 461 optimal weight: 10.0000 chunk 836 optimal weight: 10.0000 chunk 251 optimal weight: 4.9990 overall best weight: 8.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 ASN ** F 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 29 HIS M 38 GLN M 98 GLN O 36 GLN ** O 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 55 GLN ** P 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 48 GLN T 49 ASN T 51 GLN U 42 HIS ** Z 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AB 27 ASN AB 30 HIS a 14 HIS a 102 ASN ** a 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 55 HIS g 3 GLN ** i 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 61 ASN n 39 GLN ** n 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 26 ASN ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 30 HIS p 49 ASN ** q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 81 GLN t 8 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.4682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.174 152339 Z= 0.544 Angle : 0.858 13.442 228406 Z= 0.432 Chirality : 0.047 0.390 29267 Planarity : 0.007 0.074 11889 Dihedral : 24.384 179.426 77460 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 22.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.37 % Favored : 91.61 % Rotamer: Outliers : 8.71 % Allowed : 19.56 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.11), residues: 5235 helix: -0.19 (0.12), residues: 1796 sheet: -1.50 (0.16), residues: 949 loop : -2.19 (0.11), residues: 2490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP N 30 HIS 0.020 0.002 HIS e 55 PHE 0.042 0.003 PHE G 89 TYR 0.050 0.003 TYR a 212 ARG 0.017 0.001 ARGAC 12 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10470 Ramachandran restraints generated. 5235 Oldfield, 0 Emsley, 5235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10470 Ramachandran restraints generated. 5235 Oldfield, 0 Emsley, 5235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1221 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 378 poor density : 843 time to evaluate : 5.776 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: A 97 ASP cc_start: 0.8272 (p0) cc_final: 0.7916 (p0) REVERT: A 116 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7574 (tm130) REVERT: B 130 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8175 (mp10) REVERT: B 131 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7854 (p0) REVERT: C 30 GLN cc_start: 0.9244 (OUTLIER) cc_final: 0.8959 (tt0) REVERT: D 14 LYS cc_start: 0.7964 (mttm) cc_final: 0.7673 (pptt) REVERT: F 1 MET cc_start: 0.6690 (tpt) cc_final: 0.5988 (ptt) REVERT: G 108 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8249 (mtt) REVERT: I 56 ASP cc_start: 0.7979 (OUTLIER) cc_final: 0.7692 (p0) REVERT: K 28 PHE cc_start: 0.8484 (OUTLIER) cc_final: 0.8200 (p90) REVERT: K 110 GLU cc_start: 0.8442 (tp30) cc_final: 0.8125 (tp30) REVERT: L 49 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8063 (mm-30) REVERT: L 94 TYR cc_start: 0.9240 (m-80) cc_final: 0.8733 (m-80) REVERT: M 31 THR cc_start: 0.9061 (OUTLIER) cc_final: 0.8838 (t) REVERT: M 36 TYR cc_start: 0.8506 (OUTLIER) cc_final: 0.8273 (m-80) REVERT: O 48 ASP cc_start: 0.8343 (m-30) cc_final: 0.8004 (m-30) REVERT: O 101 ASP cc_start: 0.8126 (t0) cc_final: 0.7737 (t0) REVERT: Q 86 MET cc_start: 0.7567 (OUTLIER) cc_final: 0.7349 (ttt) REVERT: R 54 GLU cc_start: 0.6841 (tm-30) cc_final: 0.6244 (tm-30) REVERT: R 88 LYS cc_start: 0.8219 (tptp) cc_final: 0.7507 (tptp) REVERT: S 9 GLU cc_start: 0.7357 (tp30) cc_final: 0.7114 (tp30) REVERT: S 61 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7219 (mt-10) REVERT: S 96 LYS cc_start: 0.8538 (mtpt) cc_final: 0.8244 (mtpt) REVERT: T 55 GLU cc_start: 0.8450 (pm20) cc_final: 0.8194 (pm20) REVERT: U 8 ASN cc_start: 0.9053 (OUTLIER) cc_final: 0.8853 (p0) REVERT: U 11 ASP cc_start: 0.8203 (t0) cc_final: 0.7887 (t0) REVERT: U 22 PHE cc_start: 0.8570 (m-10) cc_final: 0.8369 (m-10) REVERT: V 75 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7795 (tm-30) REVERT: W 49 ASP cc_start: 0.8805 (m-30) cc_final: 0.8554 (m-30) REVERT: Z 25 ASN cc_start: 0.8879 (OUTLIER) cc_final: 0.8290 (p0) REVERT: AA 1 MET cc_start: 0.7715 (ptp) cc_final: 0.7214 (ptp) REVERT: AB 53 ASP cc_start: 0.7477 (OUTLIER) cc_final: 0.6913 (p0) REVERT: AC 20 ASP cc_start: 0.8316 (t0) cc_final: 0.7974 (t0) REVERT: a 15 PHE cc_start: 0.6929 (m-80) cc_final: 0.6513 (m-10) REVERT: a 38 HIS cc_start: 0.7234 (m90) cc_final: 0.6977 (m90) REVERT: a 68 PHE cc_start: 0.5950 (m-80) cc_final: 0.5634 (m-80) REVERT: a 158 ASP cc_start: 0.8296 (t70) cc_final: 0.7962 (t0) REVERT: a 207 ARG cc_start: 0.6554 (mtm180) cc_final: 0.5870 (mpt180) REVERT: b 133 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.6985 (ttp) REVERT: c 71 PHE cc_start: 0.8642 (OUTLIER) cc_final: 0.8343 (m-80) REVERT: c 155 LYS cc_start: 0.5095 (mmtp) cc_final: 0.4291 (ptpt) REVERT: c 203 TYR cc_start: 0.7133 (OUTLIER) cc_final: 0.5941 (t80) REVERT: d 47 PHE cc_start: 0.8361 (OUTLIER) cc_final: 0.8144 (p90) REVERT: d 63 MET cc_start: 0.8378 (mtm) cc_final: 0.8047 (mtm) REVERT: d 125 LYS cc_start: 0.8717 (tptp) cc_final: 0.7923 (mttt) REVERT: e 5 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7456 (tm-30) REVERT: e 14 GLN cc_start: 0.8334 (tp-100) cc_final: 0.8057 (tp-100) REVERT: e 36 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8286 (mt) REVERT: e 78 PHE cc_start: 0.8980 (m-80) cc_final: 0.8725 (m-80) REVERT: e 81 ASN cc_start: 0.8510 (t0) cc_final: 0.8227 (t0) REVERT: f 17 PHE cc_start: 0.2128 (OUTLIER) cc_final: 0.1825 (m-80) REVERT: f 108 ARG cc_start: 0.8302 (ptm160) cc_final: 0.7952 (mtt180) REVERT: g 47 ASP cc_start: 0.8166 (t70) cc_final: 0.7907 (t70) REVERT: g 66 GLN cc_start: 0.8303 (mt0) cc_final: 0.7549 (tm-30) REVERT: g 110 MET cc_start: 0.7596 (ptp) cc_final: 0.7152 (ptt) REVERT: h 59 LYS cc_start: 0.5839 (mtmm) cc_final: 0.5637 (tptp) REVERT: i 5 ARG cc_start: 0.5008 (tpt170) cc_final: 0.4798 (ttm170) REVERT: i 56 HIS cc_start: 0.8218 (OUTLIER) cc_final: 0.7199 (m90) REVERT: j 14 GLN cc_start: 0.7959 (tm-30) cc_final: 0.7541 (tm-30) REVERT: l 12 LYS cc_start: 0.6338 (mttt) cc_final: 0.5977 (mmtp) REVERT: l 46 GLU cc_start: 0.3832 (OUTLIER) cc_final: 0.3483 (mm-30) REVERT: l 51 GLN cc_start: 0.7768 (pm20) cc_final: 0.7504 (pm20) REVERT: l 85 TYR cc_start: 0.7313 (OUTLIER) cc_final: 0.7032 (m-80) REVERT: l 102 LYS cc_start: 0.7448 (tttp) cc_final: 0.7221 (ttpp) REVERT: m 22 LYS cc_start: 0.7137 (OUTLIER) cc_final: 0.6518 (mttt) REVERT: m 72 PHE cc_start: 0.5660 (t80) cc_final: 0.5448 (t80) REVERT: m 73 LEU cc_start: 0.8803 (mt) cc_final: 0.8124 (tp) REVERT: n 34 GLN cc_start: 0.8209 (tp-100) cc_final: 0.7891 (mm-40) REVERT: n 84 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8430 (mt) REVERT: o 5 ARG cc_start: 0.5206 (ptp-170) cc_final: 0.4454 (ttm110) REVERT: o 45 GLU cc_start: 0.7534 (pm20) cc_final: 0.6781 (pm20) REVERT: o 46 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7609 (mptt) REVERT: o 63 GLN cc_start: 0.7585 (mm-40) cc_final: 0.6961 (mt0) REVERT: p 17 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7327 (tm-30) REVERT: p 76 ARG cc_start: 0.7908 (mtm-85) cc_final: 0.7185 (mtm-85) REVERT: r 36 ARG cc_start: 0.6202 (OUTLIER) cc_final: 0.5785 (ptm160) REVERT: r 69 LYS cc_start: 0.6693 (tptm) cc_final: 0.5799 (mptt) REVERT: s 2 ASN cc_start: 0.7167 (OUTLIER) cc_final: 0.6710 (t0) REVERT: s 3 ILE cc_start: 0.7511 (mm) cc_final: 0.6904 (mm) REVERT: t 43 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7546 (mm-30) REVERT: t 62 GLU cc_start: 0.6442 (mm-30) cc_final: 0.5942 (tm-30) outliers start: 378 outliers final: 262 residues processed: 1108 average time/residue: 1.1663 time to fit residues: 2299.3908 Evaluate side-chains 1057 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 291 poor density : 766 time to evaluate : 5.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 130 GLN Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 30 GLN Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 15 ASP Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 108 MET Chi-restraints excluded: chain G residue 131 ASN Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 59 ARG Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 28 VAL Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain M residue 36 TYR Chi-restraints excluded: chain M residue 38 GLN Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain M residue 84 GLU Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain N residue 103 THR Chi-restraints excluded: chain N residue 113 LEU Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 61 ILE Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 101 ILE Chi-restraints excluded: chain Q residue 3 THR Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 40 ASN Chi-restraints excluded: chain Q residue 61 ASN Chi-restraints excluded: chain Q residue 67 ASP Chi-restraints excluded: chain Q residue 74 ILE Chi-restraints excluded: chain Q residue 77 ASP Chi-restraints excluded: chain Q residue 86 MET Chi-restraints excluded: chain Q residue 94 ASP Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain R residue 16 VAL Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 86 THR Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 10 VAL Chi-restraints excluded: chain S residue 27 VAL Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 87 GLU Chi-restraints excluded: chain T residue 5 ASN Chi-restraints excluded: chain T residue 8 VAL Chi-restraints excluded: chain T residue 20 LEU Chi-restraints excluded: chain T residue 49 ASN Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 65 VAL Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain U residue 8 ASN Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 34 VAL Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain V residue 15 ASN Chi-restraints excluded: chain V residue 29 LEU Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain V residue 34 SER Chi-restraints excluded: chain V residue 47 THR Chi-restraints excluded: chain V residue 59 ASP Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 75 GLU Chi-restraints excluded: chain W residue 13 GLU Chi-restraints excluded: chain W residue 45 GLN Chi-restraints excluded: chain X residue 23 LEU Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain Y residue 2 VAL Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 22 THR Chi-restraints excluded: chain Y residue 33 SER Chi-restraints excluded: chain Y residue 54 ILE Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 25 ASN Chi-restraints excluded: chain Z residue 41 VAL Chi-restraints excluded: chain Z residue 46 VAL Chi-restraints excluded: chain AA residue 24 THR Chi-restraints excluded: chain AA residue 30 VAL Chi-restraints excluded: chain AA residue 44 VAL Chi-restraints excluded: chain AB residue 5 THR Chi-restraints excluded: chain AB residue 53 ASP Chi-restraints excluded: chain AC residue 3 VAL Chi-restraints excluded: chain AC residue 7 VAL Chi-restraints excluded: chain AC residue 16 ILE Chi-restraints excluded: chain AC residue 25 VAL Chi-restraints excluded: chain a residue 18 GLN Chi-restraints excluded: chain a residue 30 ILE Chi-restraints excluded: chain a residue 45 THR Chi-restraints excluded: chain a residue 59 ILE Chi-restraints excluded: chain a residue 147 LEU Chi-restraints excluded: chain a residue 178 LEU Chi-restraints excluded: chain a residue 185 ILE Chi-restraints excluded: chain a residue 186 VAL Chi-restraints excluded: chain a residue 190 SER Chi-restraints excluded: chain a residue 198 VAL Chi-restraints excluded: chain b residue 24 ASN Chi-restraints excluded: chain b residue 63 ILE Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 74 ILE Chi-restraints excluded: chain b residue 75 VAL Chi-restraints excluded: chain b residue 111 ASP Chi-restraints excluded: chain b residue 118 SER Chi-restraints excluded: chain b residue 133 MET Chi-restraints excluded: chain b residue 156 LEU Chi-restraints excluded: chain b residue 182 ASP Chi-restraints excluded: chain b residue 195 ILE Chi-restraints excluded: chain c residue 49 ASP Chi-restraints excluded: chain c residue 71 PHE Chi-restraints excluded: chain c residue 85 THR Chi-restraints excluded: chain c residue 125 ASN Chi-restraints excluded: chain c residue 154 VAL Chi-restraints excluded: chain c residue 168 THR Chi-restraints excluded: chain c residue 203 TYR Chi-restraints excluded: chain d residue 29 ILE Chi-restraints excluded: chain d residue 47 PHE Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain d residue 139 THR Chi-restraints excluded: chain d residue 163 ILE Chi-restraints excluded: chain e residue 3 HIS Chi-restraints excluded: chain e residue 13 ASP Chi-restraints excluded: chain e residue 18 VAL Chi-restraints excluded: chain e residue 36 ILE Chi-restraints excluded: chain e residue 61 LEU Chi-restraints excluded: chain e residue 64 VAL Chi-restraints excluded: chain e residue 77 THR Chi-restraints excluded: chain e residue 90 MET Chi-restraints excluded: chain f residue 17 PHE Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 58 LEU Chi-restraints excluded: chain f residue 98 LEU Chi-restraints excluded: chain f residue 123 LEU Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain g residue 39 LEU Chi-restraints excluded: chain g residue 58 LEU Chi-restraints excluded: chain g residue 74 ILE Chi-restraints excluded: chain g residue 91 LEU Chi-restraints excluded: chain g residue 100 ILE Chi-restraints excluded: chain g residue 102 VAL Chi-restraints excluded: chain g residue 103 VAL Chi-restraints excluded: chain g residue 111 THR Chi-restraints excluded: chain g residue 112 ASP Chi-restraints excluded: chain g residue 125 ILE Chi-restraints excluded: chain h residue 28 VAL Chi-restraints excluded: chain h residue 57 VAL Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain h residue 105 ARG Chi-restraints excluded: chain h residue 110 VAL Chi-restraints excluded: chain i residue 8 ILE Chi-restraints excluded: chain i residue 10 LEU Chi-restraints excluded: chain i residue 17 LEU Chi-restraints excluded: chain i residue 49 PHE Chi-restraints excluded: chain i residue 56 HIS Chi-restraints excluded: chain i residue 63 ASP Chi-restraints excluded: chain i residue 72 ARG Chi-restraints excluded: chain i residue 73 LEU Chi-restraints excluded: chain i residue 102 LEU Chi-restraints excluded: chain j residue 22 ILE Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 41 LEU Chi-restraints excluded: chain j residue 45 THR Chi-restraints excluded: chain j residue 58 THR Chi-restraints excluded: chain j residue 92 ARG Chi-restraints excluded: chain j residue 115 ILE Chi-restraints excluded: chain j residue 118 ASN Chi-restraints excluded: chain k residue 7 VAL Chi-restraints excluded: chain l residue 6 ILE Chi-restraints excluded: chain l residue 19 THR Chi-restraints excluded: chain l residue 46 GLU Chi-restraints excluded: chain l residue 52 ILE Chi-restraints excluded: chain l residue 85 TYR Chi-restraints excluded: chain m residue 22 LYS Chi-restraints excluded: chain m residue 29 ILE Chi-restraints excluded: chain m residue 33 VAL Chi-restraints excluded: chain m residue 45 LEU Chi-restraints excluded: chain m residue 53 ASP Chi-restraints excluded: chain m residue 81 ILE Chi-restraints excluded: chain n residue 21 THR Chi-restraints excluded: chain n residue 30 LEU Chi-restraints excluded: chain n residue 53 ARG Chi-restraints excluded: chain n residue 61 GLN Chi-restraints excluded: chain n residue 84 LEU Chi-restraints excluded: chain n residue 86 LEU Chi-restraints excluded: chain o residue 13 LYS Chi-restraints excluded: chain o residue 23 ASP Chi-restraints excluded: chain o residue 46 LYS Chi-restraints excluded: chain o residue 60 TRP Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain p residue 20 ILE Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 24 ILE Chi-restraints excluded: chain p residue 32 ILE Chi-restraints excluded: chain p residue 37 ILE Chi-restraints excluded: chain p residue 45 VAL Chi-restraints excluded: chain p residue 57 VAL Chi-restraints excluded: chain p residue 59 GLU Chi-restraints excluded: chain p residue 77 VAL Chi-restraints excluded: chain q residue 28 LEU Chi-restraints excluded: chain r residue 4 LEU Chi-restraints excluded: chain r residue 36 ARG Chi-restraints excluded: chain r residue 39 ILE Chi-restraints excluded: chain r residue 40 PHE Chi-restraints excluded: chain r residue 42 ASN Chi-restraints excluded: chain r residue 78 THR Chi-restraints excluded: chain s residue 2 ASN Chi-restraints excluded: chain s residue 25 SER Chi-restraints excluded: chain s residue 29 THR Chi-restraints excluded: chain t residue 21 SER Chi-restraints excluded: chain t residue 27 VAL Chi-restraints excluded: chain t residue 43 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 778 optimal weight: 0.8980 chunk 530 optimal weight: 10.0000 chunk 13 optimal weight: 30.0000 chunk 695 optimal weight: 10.0000 chunk 385 optimal weight: 2.9990 chunk 797 optimal weight: 30.0000 chunk 646 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 477 optimal weight: 6.9990 chunk 838 optimal weight: 10.0000 chunk 235 optimal weight: 1.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 GLN ** E 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 ASN ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 36 GLN ** P 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 49 ASN X 19 HIS Z 45 HIS AB 30 HIS a 17 HIS a 102 ASN a 108 GLN ** b 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 125 ASN ** c 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 55 HIS ** j 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 95 HIS m 42 ASN n 39 GLN ** n 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 51 GLN ** r 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.4503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 152339 Z= 0.262 Angle : 0.633 13.133 228406 Z= 0.325 Chirality : 0.037 0.334 29267 Planarity : 0.005 0.052 11889 Dihedral : 24.241 179.067 77455 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.73 % Favored : 94.25 % Rotamer: Outliers : 6.45 % Allowed : 22.81 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.11), residues: 5235 helix: 0.29 (0.12), residues: 1807 sheet: -1.27 (0.16), residues: 948 loop : -2.01 (0.12), residues: 2480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP N 30 HIS 0.011 0.001 HIS p 46 PHE 0.026 0.002 PHE s 50 TYR 0.043 0.002 TYR F 25 ARG 0.009 0.001 ARG Y 51 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10470 Ramachandran restraints generated. 5235 Oldfield, 0 Emsley, 5235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10470 Ramachandran restraints generated. 5235 Oldfield, 0 Emsley, 5235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1168 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 280 poor density : 888 time to evaluate : 5.590 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: A 97 ASP cc_start: 0.8267 (p0) cc_final: 0.7911 (p0) REVERT: A 224 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8521 (mmt) REVERT: B 130 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8077 (mp10) REVERT: C 30 GLN cc_start: 0.9149 (OUTLIER) cc_final: 0.8839 (tt0) REVERT: C 73 ILE cc_start: 0.9270 (OUTLIER) cc_final: 0.8933 (mt) REVERT: C 156 ASN cc_start: 0.8540 (OUTLIER) cc_final: 0.8238 (m-40) REVERT: D 7 TYR cc_start: 0.7642 (OUTLIER) cc_final: 0.6957 (t80) REVERT: D 14 LYS cc_start: 0.8079 (mttm) cc_final: 0.7810 (pptt) REVERT: D 172 PHE cc_start: 0.6839 (m-10) cc_final: 0.6268 (m-10) REVERT: E 138 GLN cc_start: 0.8493 (tm130) cc_final: 0.7940 (pp30) REVERT: G 108 MET cc_start: 0.8558 (mtt) cc_final: 0.7954 (mmt) REVERT: K 104 GLU cc_start: 0.7639 (mm-30) cc_final: 0.6935 (mt-10) REVERT: K 110 GLU cc_start: 0.8410 (tp30) cc_final: 0.8072 (tp30) REVERT: L 49 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8005 (mm-30) REVERT: L 94 TYR cc_start: 0.9148 (m-80) cc_final: 0.8811 (m-80) REVERT: M 31 THR cc_start: 0.9057 (OUTLIER) cc_final: 0.8822 (t) REVERT: N 59 THR cc_start: 0.9417 (m) cc_final: 0.9175 (t) REVERT: O 48 ASP cc_start: 0.8164 (m-30) cc_final: 0.7815 (m-30) REVERT: O 101 ASP cc_start: 0.8160 (t0) cc_final: 0.7756 (t0) REVERT: P 1 MET cc_start: 0.6770 (tpp) cc_final: 0.6337 (tpt) REVERT: R 54 GLU cc_start: 0.6669 (tm-30) cc_final: 0.6174 (tm-30) REVERT: R 88 LYS cc_start: 0.8047 (tptp) cc_final: 0.7467 (tptp) REVERT: S 61 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7059 (mt-10) REVERT: T 26 PHE cc_start: 0.8547 (p90) cc_final: 0.8262 (p90) REVERT: T 51 GLN cc_start: 0.7728 (tm130) cc_final: 0.7403 (tp40) REVERT: T 55 GLU cc_start: 0.8557 (pm20) cc_final: 0.8310 (pm20) REVERT: U 11 ASP cc_start: 0.8152 (t0) cc_final: 0.7894 (t0) REVERT: U 22 PHE cc_start: 0.8406 (m-10) cc_final: 0.8187 (m-10) REVERT: V 75 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7807 (tm-30) REVERT: W 58 ASN cc_start: 0.8828 (t0) cc_final: 0.8619 (t0) REVERT: Y 47 TYR cc_start: 0.8507 (m-80) cc_final: 0.8271 (m-10) REVERT: Z 25 ASN cc_start: 0.8702 (OUTLIER) cc_final: 0.8173 (p0) REVERT: AA 1 MET cc_start: 0.7691 (ptp) cc_final: 0.7409 (ptp) REVERT: AB 53 ASP cc_start: 0.7171 (OUTLIER) cc_final: 0.6892 (p0) REVERT: AC 20 ASP cc_start: 0.8212 (t0) cc_final: 0.7912 (t0) REVERT: a 15 PHE cc_start: 0.6982 (m-80) cc_final: 0.6565 (m-10) REVERT: a 68 PHE cc_start: 0.6064 (m-80) cc_final: 0.5723 (m-80) REVERT: a 158 ASP cc_start: 0.8233 (t70) cc_final: 0.7691 (m-30) REVERT: b 133 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.6964 (ttp) REVERT: c 71 PHE cc_start: 0.8640 (OUTLIER) cc_final: 0.8314 (m-80) REVERT: c 104 MET cc_start: 0.7451 (mmm) cc_final: 0.7038 (mmt) REVERT: c 155 LYS cc_start: 0.5074 (mmtp) cc_final: 0.4277 (ptpt) REVERT: c 203 TYR cc_start: 0.7128 (OUTLIER) cc_final: 0.5908 (t80) REVERT: d 125 LYS cc_start: 0.8607 (tptp) cc_final: 0.7885 (mttp) REVERT: e 5 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7570 (tm-30) REVERT: e 35 LYS cc_start: 0.8313 (mtmm) cc_final: 0.8015 (mppt) REVERT: e 36 ILE cc_start: 0.8674 (mp) cc_final: 0.8333 (mt) REVERT: e 81 ASN cc_start: 0.8381 (t0) cc_final: 0.8140 (t0) REVERT: f 17 PHE cc_start: 0.1887 (OUTLIER) cc_final: 0.1565 (m-80) REVERT: f 108 ARG cc_start: 0.8335 (ptm160) cc_final: 0.7946 (mtt180) REVERT: g 42 GLU cc_start: 0.8070 (tp30) cc_final: 0.7818 (tp30) REVERT: g 47 ASP cc_start: 0.8266 (t70) cc_final: 0.7987 (t70) REVERT: g 66 GLN cc_start: 0.8202 (mt0) cc_final: 0.7569 (tm-30) REVERT: g 110 MET cc_start: 0.7439 (ptp) cc_final: 0.7089 (ptt) REVERT: j 124 LYS cc_start: 0.8975 (pttt) cc_final: 0.8753 (pttt) REVERT: l 12 LYS cc_start: 0.6283 (mttt) cc_final: 0.5925 (mmmt) REVERT: l 40 GLU cc_start: 0.2001 (OUTLIER) cc_final: 0.1457 (mm-30) REVERT: l 55 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7928 (mm) REVERT: m 72 PHE cc_start: 0.5476 (t80) cc_final: 0.5264 (t80) REVERT: m 73 LEU cc_start: 0.8785 (mt) cc_final: 0.8051 (tp) REVERT: n 13 GLU cc_start: 0.8296 (pt0) cc_final: 0.7165 (pt0) REVERT: n 68 TYR cc_start: 0.9026 (t80) cc_final: 0.8711 (t80) REVERT: n 84 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8512 (mt) REVERT: o 5 ARG cc_start: 0.4942 (ptp-170) cc_final: 0.4355 (ttm170) REVERT: o 45 GLU cc_start: 0.7518 (pm20) cc_final: 0.6898 (pm20) REVERT: o 46 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7673 (mptt) REVERT: o 63 GLN cc_start: 0.7719 (mm-40) cc_final: 0.7235 (mt0) REVERT: p 17 GLU cc_start: 0.7525 (tm-30) cc_final: 0.7231 (tm-30) REVERT: p 32 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8286 (tp) REVERT: p 76 ARG cc_start: 0.7888 (mtm-85) cc_final: 0.7649 (mtm-85) REVERT: q 42 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8087 (ppt170) REVERT: q 63 TYR cc_start: 0.7975 (t80) cc_final: 0.7721 (t80) REVERT: r 69 LYS cc_start: 0.6379 (tptm) cc_final: 0.5448 (mptt) REVERT: s 3 ILE cc_start: 0.7706 (mm) cc_final: 0.7440 (mm) REVERT: t 24 LYS cc_start: 0.9193 (mmmt) cc_final: 0.8949 (mmmt) REVERT: t 43 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7546 (mm-30) REVERT: t 62 GLU cc_start: 0.6470 (mm-30) cc_final: 0.6083 (tm-30) outliers start: 280 outliers final: 197 residues processed: 1085 average time/residue: 1.2234 time to fit residues: 2381.1145 Evaluate side-chains 1033 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 815 time to evaluate : 5.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 130 GLN Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 30 GLN Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 156 ASN Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain D residue 7 TYR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 15 ASP Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 131 ASN Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain K residue 59 ARG Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain M residue 38 GLN Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain M residue 84 GLU Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain N residue 30 TRP Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain N residue 103 THR Chi-restraints excluded: chain N residue 114 ASN Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 101 ILE Chi-restraints excluded: chain Q residue 3 THR Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 40 ASN Chi-restraints excluded: chain Q residue 67 ASP Chi-restraints excluded: chain Q residue 71 VAL Chi-restraints excluded: chain Q residue 77 ASP Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain R residue 16 VAL Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain S residue 10 VAL Chi-restraints excluded: chain S residue 27 VAL Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 87 GLU Chi-restraints excluded: chain T residue 5 ASN Chi-restraints excluded: chain T residue 43 ASP Chi-restraints excluded: chain T residue 62 THR Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 34 VAL Chi-restraints excluded: chain V residue 15 ASN Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain V residue 34 SER Chi-restraints excluded: chain V residue 59 ASP Chi-restraints excluded: chain V residue 75 GLU Chi-restraints excluded: chain X residue 23 LEU Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain Y residue 2 VAL Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 22 THR Chi-restraints excluded: chain Y residue 54 ILE Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 25 ASN Chi-restraints excluded: chain Z residue 41 VAL Chi-restraints excluded: chain Z residue 46 VAL Chi-restraints excluded: chain AA residue 44 VAL Chi-restraints excluded: chain AB residue 5 THR Chi-restraints excluded: chain AB residue 50 SER Chi-restraints excluded: chain AB residue 53 ASP Chi-restraints excluded: chain AC residue 3 VAL Chi-restraints excluded: chain AC residue 25 VAL Chi-restraints excluded: chain a residue 30 ILE Chi-restraints excluded: chain a residue 45 THR Chi-restraints excluded: chain a residue 59 ILE Chi-restraints excluded: chain a residue 108 GLN Chi-restraints excluded: chain a residue 147 LEU Chi-restraints excluded: chain a residue 183 PHE Chi-restraints excluded: chain a residue 186 VAL Chi-restraints excluded: chain a residue 190 SER Chi-restraints excluded: chain a residue 198 VAL Chi-restraints excluded: chain a residue 199 ILE Chi-restraints excluded: chain a residue 212 TYR Chi-restraints excluded: chain b residue 63 ILE Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 74 ILE Chi-restraints excluded: chain b residue 75 VAL Chi-restraints excluded: chain b residue 133 MET Chi-restraints excluded: chain b residue 156 LEU Chi-restraints excluded: chain b residue 195 ILE Chi-restraints excluded: chain c residue 71 PHE Chi-restraints excluded: chain c residue 85 THR Chi-restraints excluded: chain c residue 154 VAL Chi-restraints excluded: chain c residue 203 TYR Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain d residue 163 ILE Chi-restraints excluded: chain e residue 13 ASP Chi-restraints excluded: chain e residue 18 VAL Chi-restraints excluded: chain e residue 61 LEU Chi-restraints excluded: chain e residue 96 VAL Chi-restraints excluded: chain f residue 17 PHE Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 123 LEU Chi-restraints excluded: chain g residue 9 MET Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 39 LEU Chi-restraints excluded: chain g residue 74 ILE Chi-restraints excluded: chain g residue 89 ASP Chi-restraints excluded: chain g residue 91 LEU Chi-restraints excluded: chain g residue 100 ILE Chi-restraints excluded: chain g residue 102 VAL Chi-restraints excluded: chain g residue 103 VAL Chi-restraints excluded: chain g residue 111 THR Chi-restraints excluded: chain g residue 112 ASP Chi-restraints excluded: chain g residue 125 ILE Chi-restraints excluded: chain h residue 28 VAL Chi-restraints excluded: chain h residue 57 VAL Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain i residue 8 ILE Chi-restraints excluded: chain i residue 10 LEU Chi-restraints excluded: chain i residue 17 LEU Chi-restraints excluded: chain i residue 44 THR Chi-restraints excluded: chain i residue 49 PHE Chi-restraints excluded: chain i residue 63 ASP Chi-restraints excluded: chain i residue 73 LEU Chi-restraints excluded: chain i residue 102 LEU Chi-restraints excluded: chain j residue 22 ILE Chi-restraints excluded: chain j residue 41 LEU Chi-restraints excluded: chain j residue 58 THR Chi-restraints excluded: chain j residue 115 ILE Chi-restraints excluded: chain k residue 38 THR Chi-restraints excluded: chain k residue 56 LEU Chi-restraints excluded: chain l residue 6 ILE Chi-restraints excluded: chain l residue 40 GLU Chi-restraints excluded: chain l residue 52 ILE Chi-restraints excluded: chain l residue 55 LEU Chi-restraints excluded: chain m residue 29 ILE Chi-restraints excluded: chain m residue 33 VAL Chi-restraints excluded: chain m residue 45 LEU Chi-restraints excluded: chain m residue 53 ASP Chi-restraints excluded: chain m residue 63 CYS Chi-restraints excluded: chain n residue 53 ARG Chi-restraints excluded: chain n residue 84 LEU Chi-restraints excluded: chain n residue 86 LEU Chi-restraints excluded: chain o residue 2 VAL Chi-restraints excluded: chain o residue 13 LYS Chi-restraints excluded: chain o residue 46 LYS Chi-restraints excluded: chain o residue 60 TRP Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 20 ILE Chi-restraints excluded: chain p residue 24 ILE Chi-restraints excluded: chain p residue 32 ILE Chi-restraints excluded: chain p residue 45 VAL Chi-restraints excluded: chain p residue 77 VAL Chi-restraints excluded: chain q residue 28 LEU Chi-restraints excluded: chain q residue 42 ARG Chi-restraints excluded: chain r residue 40 PHE Chi-restraints excluded: chain r residue 42 ASN Chi-restraints excluded: chain r residue 61 VAL Chi-restraints excluded: chain r residue 78 THR Chi-restraints excluded: chain s residue 29 THR Chi-restraints excluded: chain s residue 38 ILE Chi-restraints excluded: chain s residue 58 ASP Chi-restraints excluded: chain t residue 21 SER Chi-restraints excluded: chain t residue 27 VAL Chi-restraints excluded: chain t residue 28 LEU Chi-restraints excluded: chain t residue 42 THR Chi-restraints excluded: chain t residue 43 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 314 optimal weight: 5.9990 chunk 841 optimal weight: 10.0000 chunk 184 optimal weight: 0.7980 chunk 548 optimal weight: 10.0000 chunk 230 optimal weight: 3.9990 chunk 935 optimal weight: 30.0000 chunk 776 optimal weight: 20.0000 chunk 433 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 309 optimal weight: 0.9990 chunk 491 optimal weight: 8.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 ASN ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 GLN ** P 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 49 ASN AB 30 HIS a 108 GLN ** b 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 184 ASN ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 88 HIS ** d 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 56 HIS ** j 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 34 GLN ** n 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 51 GLN ** r 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 2 ASN ** s 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.4574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 152339 Z= 0.259 Angle : 0.616 14.380 228406 Z= 0.317 Chirality : 0.036 0.345 29267 Planarity : 0.004 0.052 11889 Dihedral : 24.129 179.907 77446 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.76 % Favored : 93.22 % Rotamer: Outliers : 6.52 % Allowed : 23.39 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.11), residues: 5235 helix: 0.41 (0.12), residues: 1803 sheet: -1.12 (0.17), residues: 932 loop : -1.91 (0.12), residues: 2500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP N 30 HIS 0.010 0.001 HIS p 46 PHE 0.031 0.002 PHE e 78 TYR 0.047 0.002 TYR F 25 ARG 0.019 0.001 ARG G 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10470 Ramachandran restraints generated. 5235 Oldfield, 0 Emsley, 5235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10470 Ramachandran restraints generated. 5235 Oldfield, 0 Emsley, 5235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1134 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 283 poor density : 851 time to evaluate : 5.824 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: A 97 ASP cc_start: 0.8260 (p0) cc_final: 0.7909 (p0) REVERT: A 116 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7743 (tt0) REVERT: A 224 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8483 (mmt) REVERT: B 131 ASP cc_start: 0.8106 (OUTLIER) cc_final: 0.7822 (p0) REVERT: D 7 TYR cc_start: 0.7603 (OUTLIER) cc_final: 0.6931 (t80) REVERT: D 14 LYS cc_start: 0.8003 (mttm) cc_final: 0.7771 (pptt) REVERT: F 1 MET cc_start: 0.6106 (tpt) cc_final: 0.5094 (ttp) REVERT: G 108 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8099 (mtt) REVERT: K 110 GLU cc_start: 0.8368 (tp30) cc_final: 0.8052 (tp30) REVERT: L 49 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8096 (mm-30) REVERT: L 72 ASP cc_start: 0.8742 (t0) cc_final: 0.8413 (t0) REVERT: L 94 TYR cc_start: 0.9169 (m-80) cc_final: 0.8828 (m-80) REVERT: M 31 THR cc_start: 0.9046 (OUTLIER) cc_final: 0.8829 (t) REVERT: O 48 ASP cc_start: 0.8152 (m-30) cc_final: 0.7802 (m-30) REVERT: O 101 ASP cc_start: 0.8119 (t0) cc_final: 0.7714 (t0) REVERT: Q 95 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7826 (mtm-85) REVERT: R 52 GLU cc_start: 0.8444 (mp0) cc_final: 0.8190 (mp0) REVERT: R 54 GLU cc_start: 0.6737 (tm-30) cc_final: 0.6230 (tm-30) REVERT: R 88 LYS cc_start: 0.7929 (tptp) cc_final: 0.7181 (tptp) REVERT: S 61 GLU cc_start: 0.7456 (mt-10) cc_final: 0.7105 (mt-10) REVERT: T 26 PHE cc_start: 0.8481 (p90) cc_final: 0.8220 (p90) REVERT: T 55 GLU cc_start: 0.8571 (pm20) cc_final: 0.8321 (pm20) REVERT: U 8 ASN cc_start: 0.8908 (OUTLIER) cc_final: 0.8660 (p0) REVERT: U 11 ASP cc_start: 0.8118 (t0) cc_final: 0.7816 (t0) REVERT: U 22 PHE cc_start: 0.8408 (m-10) cc_final: 0.8192 (m-10) REVERT: V 75 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7734 (tm-30) REVERT: W 58 ASN cc_start: 0.8838 (t0) cc_final: 0.8621 (t0) REVERT: Y 47 TYR cc_start: 0.8493 (m-80) cc_final: 0.8245 (m-80) REVERT: Z 25 ASN cc_start: 0.8677 (OUTLIER) cc_final: 0.8154 (p0) REVERT: AA 1 MET cc_start: 0.7726 (ptp) cc_final: 0.7213 (ptp) REVERT: AB 53 ASP cc_start: 0.7175 (OUTLIER) cc_final: 0.6869 (p0) REVERT: AC 20 ASP cc_start: 0.8177 (t0) cc_final: 0.7869 (t0) REVERT: a 15 PHE cc_start: 0.7027 (m-80) cc_final: 0.6558 (m-10) REVERT: a 68 PHE cc_start: 0.5968 (m-80) cc_final: 0.5655 (m-80) REVERT: a 89 PHE cc_start: 0.6430 (m-80) cc_final: 0.6101 (m-80) REVERT: a 95 TRP cc_start: 0.6727 (t-100) cc_final: 0.6130 (t-100) REVERT: a 158 ASP cc_start: 0.8283 (t70) cc_final: 0.7726 (m-30) REVERT: b 133 MET cc_start: 0.7744 (OUTLIER) cc_final: 0.6925 (ttp) REVERT: c 71 PHE cc_start: 0.8680 (OUTLIER) cc_final: 0.8375 (m-80) REVERT: c 125 ASN cc_start: 0.8590 (m110) cc_final: 0.7372 (t0) REVERT: c 155 LYS cc_start: 0.5028 (mmtp) cc_final: 0.4245 (ptpt) REVERT: c 203 TYR cc_start: 0.7157 (OUTLIER) cc_final: 0.5974 (t80) REVERT: d 125 LYS cc_start: 0.8628 (tptp) cc_final: 0.7908 (mttp) REVERT: e 5 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7592 (tm-30) REVERT: e 36 ILE cc_start: 0.8692 (mp) cc_final: 0.8390 (mt) REVERT: e 81 ASN cc_start: 0.8295 (t0) cc_final: 0.8075 (t0) REVERT: f 17 PHE cc_start: 0.1814 (OUTLIER) cc_final: 0.1449 (m-80) REVERT: f 39 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8156 (pt0) REVERT: g 42 GLU cc_start: 0.8025 (tp30) cc_final: 0.7767 (tp30) REVERT: g 59 GLU cc_start: 0.7652 (tp30) cc_final: 0.7300 (tp30) REVERT: g 66 GLN cc_start: 0.8192 (mt0) cc_final: 0.7600 (tm-30) REVERT: h 111 GLU cc_start: 0.7114 (pt0) cc_final: 0.6465 (mp0) REVERT: i 20 GLN cc_start: 0.7363 (pp30) cc_final: 0.7009 (mm-40) REVERT: i 99 GLN cc_start: 0.5604 (mm-40) cc_final: 0.4159 (tt0) REVERT: j 124 LYS cc_start: 0.8924 (pttt) cc_final: 0.8719 (pttt) REVERT: l 12 LYS cc_start: 0.6254 (mttt) cc_final: 0.5860 (mmmt) REVERT: l 40 GLU cc_start: 0.2069 (OUTLIER) cc_final: 0.1516 (mm-30) REVERT: l 46 GLU cc_start: 0.4027 (OUTLIER) cc_final: 0.3594 (mm-30) REVERT: m 41 TRP cc_start: 0.7456 (t-100) cc_final: 0.7022 (t60) REVERT: m 72 PHE cc_start: 0.5526 (t80) cc_final: 0.5297 (t80) REVERT: m 73 LEU cc_start: 0.8799 (mt) cc_final: 0.8052 (tp) REVERT: n 62 ARG cc_start: 0.9193 (tmm-80) cc_final: 0.8824 (ttm-80) REVERT: n 84 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8356 (mt) REVERT: o 5 ARG cc_start: 0.4983 (ptp-170) cc_final: 0.3883 (ttm110) REVERT: o 63 GLN cc_start: 0.7750 (mm-40) cc_final: 0.7321 (mt0) REVERT: p 17 GLU cc_start: 0.7574 (tm-30) cc_final: 0.7210 (tm-30) REVERT: p 32 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8203 (tp) REVERT: q 42 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8044 (ppt170) REVERT: r 15 LEU cc_start: 0.7174 (tt) cc_final: 0.6820 (tt) REVERT: r 69 LYS cc_start: 0.6498 (tptm) cc_final: 0.5529 (mptt) REVERT: s 3 ILE cc_start: 0.7601 (mm) cc_final: 0.7305 (mm) REVERT: t 24 LYS cc_start: 0.9167 (mmmt) cc_final: 0.8932 (mmmt) REVERT: t 43 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7601 (mm-30) REVERT: t 62 GLU cc_start: 0.6508 (mm-30) cc_final: 0.6243 (tm-30) outliers start: 283 outliers final: 216 residues processed: 1051 average time/residue: 1.1436 time to fit residues: 2148.0854 Evaluate side-chains 1032 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 795 time to evaluate : 5.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain D residue 7 TYR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain E residue 15 ASP Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 108 MET Chi-restraints excluded: chain G residue 131 ASN Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 59 ARG Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 28 VAL Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain M residue 38 GLN Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain M residue 84 GLU Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 103 THR Chi-restraints excluded: chain N residue 113 LEU Chi-restraints excluded: chain N residue 114 ASN Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 101 ILE Chi-restraints excluded: chain Q residue 3 THR Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 40 ASN Chi-restraints excluded: chain Q residue 67 ASP Chi-restraints excluded: chain Q residue 71 VAL Chi-restraints excluded: chain Q residue 77 ASP Chi-restraints excluded: chain Q residue 95 ARG Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain R residue 16 VAL Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain S residue 10 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 27 VAL Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 87 GLU Chi-restraints excluded: chain T residue 43 ASP Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 62 THR Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain U residue 8 ASN Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 34 VAL Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain V residue 15 ASN Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain V residue 34 SER Chi-restraints excluded: chain V residue 47 THR Chi-restraints excluded: chain V residue 59 ASP Chi-restraints excluded: chain V residue 75 GLU Chi-restraints excluded: chain W residue 45 GLN Chi-restraints excluded: chain X residue 23 LEU Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain Y residue 2 VAL Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 22 THR Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 25 ASN Chi-restraints excluded: chain Z residue 41 VAL Chi-restraints excluded: chain Z residue 46 VAL Chi-restraints excluded: chain AA residue 44 VAL Chi-restraints excluded: chain AB residue 5 THR Chi-restraints excluded: chain AB residue 53 ASP Chi-restraints excluded: chain AC residue 3 VAL Chi-restraints excluded: chain AC residue 25 VAL Chi-restraints excluded: chain a residue 18 GLN Chi-restraints excluded: chain a residue 30 ILE Chi-restraints excluded: chain a residue 45 THR Chi-restraints excluded: chain a residue 59 ILE Chi-restraints excluded: chain a residue 71 THR Chi-restraints excluded: chain a residue 147 LEU Chi-restraints excluded: chain a residue 186 VAL Chi-restraints excluded: chain a residue 190 SER Chi-restraints excluded: chain a residue 198 VAL Chi-restraints excluded: chain a residue 199 ILE Chi-restraints excluded: chain b residue 51 VAL Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 75 VAL Chi-restraints excluded: chain b residue 133 MET Chi-restraints excluded: chain b residue 156 LEU Chi-restraints excluded: chain b residue 195 ILE Chi-restraints excluded: chain c residue 71 PHE Chi-restraints excluded: chain c residue 85 THR Chi-restraints excluded: chain c residue 136 VAL Chi-restraints excluded: chain c residue 154 VAL Chi-restraints excluded: chain c residue 190 LEU Chi-restraints excluded: chain c residue 203 TYR Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain d residue 139 THR Chi-restraints excluded: chain d residue 163 ILE Chi-restraints excluded: chain e residue 13 ASP Chi-restraints excluded: chain e residue 18 VAL Chi-restraints excluded: chain e residue 61 LEU Chi-restraints excluded: chain e residue 73 GLU Chi-restraints excluded: chain e residue 96 VAL Chi-restraints excluded: chain f residue 17 PHE Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 123 LEU Chi-restraints excluded: chain g residue 9 MET Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain g residue 39 LEU Chi-restraints excluded: chain g residue 74 ILE Chi-restraints excluded: chain g residue 89 ASP Chi-restraints excluded: chain g residue 91 LEU Chi-restraints excluded: chain g residue 100 ILE Chi-restraints excluded: chain g residue 102 VAL Chi-restraints excluded: chain g residue 103 VAL Chi-restraints excluded: chain g residue 111 THR Chi-restraints excluded: chain g residue 112 ASP Chi-restraints excluded: chain g residue 113 ARG Chi-restraints excluded: chain g residue 125 ILE Chi-restraints excluded: chain h residue 28 VAL Chi-restraints excluded: chain h residue 57 VAL Chi-restraints excluded: chain h residue 64 ILE Chi-restraints excluded: chain h residue 97 LEU Chi-restraints excluded: chain h residue 110 VAL Chi-restraints excluded: chain i residue 8 ILE Chi-restraints excluded: chain i residue 10 LEU Chi-restraints excluded: chain i residue 17 LEU Chi-restraints excluded: chain i residue 49 PHE Chi-restraints excluded: chain i residue 63 ASP Chi-restraints excluded: chain i residue 72 ARG Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain i residue 102 LEU Chi-restraints excluded: chain j residue 22 ILE Chi-restraints excluded: chain j residue 58 THR Chi-restraints excluded: chain j residue 64 VAL Chi-restraints excluded: chain j residue 92 ARG Chi-restraints excluded: chain j residue 115 ILE Chi-restraints excluded: chain k residue 56 LEU Chi-restraints excluded: chain k residue 63 THR Chi-restraints excluded: chain l residue 6 ILE Chi-restraints excluded: chain l residue 21 ILE Chi-restraints excluded: chain l residue 40 GLU Chi-restraints excluded: chain l residue 46 GLU Chi-restraints excluded: chain l residue 52 ILE Chi-restraints excluded: chain m residue 29 ILE Chi-restraints excluded: chain m residue 33 VAL Chi-restraints excluded: chain m residue 45 LEU Chi-restraints excluded: chain m residue 53 ASP Chi-restraints excluded: chain m residue 63 CYS Chi-restraints excluded: chain n residue 21 THR Chi-restraints excluded: chain n residue 53 ARG Chi-restraints excluded: chain n residue 84 LEU Chi-restraints excluded: chain o residue 2 VAL Chi-restraints excluded: chain o residue 13 LYS Chi-restraints excluded: chain o residue 46 LYS Chi-restraints excluded: chain o residue 60 TRP Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 20 ILE Chi-restraints excluded: chain p residue 24 ILE Chi-restraints excluded: chain p residue 32 ILE Chi-restraints excluded: chain p residue 37 ILE Chi-restraints excluded: chain p residue 45 VAL Chi-restraints excluded: chain p residue 57 VAL Chi-restraints excluded: chain p residue 77 VAL Chi-restraints excluded: chain q residue 28 LEU Chi-restraints excluded: chain q residue 42 ARG Chi-restraints excluded: chain r residue 40 PHE Chi-restraints excluded: chain r residue 42 ASN Chi-restraints excluded: chain r residue 78 THR Chi-restraints excluded: chain s residue 29 THR Chi-restraints excluded: chain s residue 38 ILE Chi-restraints excluded: chain s residue 56 ILE Chi-restraints excluded: chain s residue 58 ASP Chi-restraints excluded: chain s residue 65 LEU Chi-restraints excluded: chain t residue 21 SER Chi-restraints excluded: chain t residue 27 VAL Chi-restraints excluded: chain t residue 28 LEU Chi-restraints excluded: chain t residue 42 THR Chi-restraints excluded: chain t residue 43 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 902 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 chunk 533 optimal weight: 8.9990 chunk 683 optimal weight: 5.9990 chunk 529 optimal weight: 10.0000 chunk 787 optimal weight: 2.9990 chunk 522 optimal weight: 40.0000 chunk 932 optimal weight: 20.0000 chunk 583 optimal weight: 10.0000 chunk 568 optimal weight: 8.9990 chunk 430 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 GLN C 163 ASN ** E 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 28 ASN ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 54 GLN M 38 GLN ** P 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 49 ASN AB 30 HIS a 108 GLN ** b 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 139 ASN ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 39 GLN ** n 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.4900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.132 152339 Z= 0.401 Angle : 0.708 13.732 228406 Z= 0.360 Chirality : 0.040 0.317 29267 Planarity : 0.005 0.052 11889 Dihedral : 24.181 179.496 77442 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 18.91 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.66 % Favored : 92.32 % Rotamer: Outliers : 7.28 % Allowed : 23.46 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.11), residues: 5235 helix: 0.25 (0.12), residues: 1800 sheet: -1.31 (0.16), residues: 952 loop : -1.95 (0.12), residues: 2483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP N 30 HIS 0.011 0.002 HIS p 46 PHE 0.046 0.002 PHE e 78 TYR 0.052 0.002 TYR F 25 ARG 0.018 0.001 ARG N 108 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10470 Ramachandran restraints generated. 5235 Oldfield, 0 Emsley, 5235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10470 Ramachandran restraints generated. 5235 Oldfield, 0 Emsley, 5235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1120 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 316 poor density : 804 time to evaluate : 7.732 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: A 97 ASP cc_start: 0.8227 (p0) cc_final: 0.7911 (p0) REVERT: A 116 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7481 (tm130) REVERT: A 224 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.8523 (mmt) REVERT: B 130 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8165 (mp10) REVERT: B 131 ASP cc_start: 0.8135 (OUTLIER) cc_final: 0.7851 (p0) REVERT: C 30 GLN cc_start: 0.9206 (OUTLIER) cc_final: 0.8887 (tt0) REVERT: D 7 TYR cc_start: 0.7668 (OUTLIER) cc_final: 0.6892 (t80) REVERT: D 14 LYS cc_start: 0.7993 (mttm) cc_final: 0.7766 (pttp) REVERT: F 1 MET cc_start: 0.6192 (tpt) cc_final: 0.5457 (ttp) REVERT: G 16 TYR cc_start: 0.8891 (m-80) cc_final: 0.8407 (m-80) REVERT: G 108 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8132 (mtt) REVERT: K 110 GLU cc_start: 0.8440 (tp30) cc_final: 0.8088 (tp30) REVERT: L 49 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8071 (mm-30) REVERT: L 82 GLU cc_start: 0.7997 (mp0) cc_final: 0.7758 (mp0) REVERT: L 94 TYR cc_start: 0.9210 (m-80) cc_final: 0.8807 (m-80) REVERT: M 31 THR cc_start: 0.9049 (OUTLIER) cc_final: 0.8834 (t) REVERT: M 46 GLU cc_start: 0.7486 (pt0) cc_final: 0.6955 (pt0) REVERT: O 48 ASP cc_start: 0.8193 (m-30) cc_final: 0.7883 (m-30) REVERT: O 101 ASP cc_start: 0.8237 (t0) cc_final: 0.7801 (t0) REVERT: Q 95 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7810 (mtm-85) REVERT: R 7 LEU cc_start: 0.9087 (mp) cc_final: 0.8716 (mt) REVERT: R 52 GLU cc_start: 0.8397 (mp0) cc_final: 0.8106 (mp0) REVERT: R 54 GLU cc_start: 0.6805 (tm-30) cc_final: 0.6391 (tm-30) REVERT: S 61 GLU cc_start: 0.7369 (mt-10) cc_final: 0.6955 (mt-10) REVERT: T 26 PHE cc_start: 0.8619 (p90) cc_final: 0.8263 (p90) REVERT: T 55 GLU cc_start: 0.8496 (pm20) cc_final: 0.8274 (pm20) REVERT: U 8 ASN cc_start: 0.9021 (OUTLIER) cc_final: 0.8800 (p0) REVERT: U 11 ASP cc_start: 0.8170 (t0) cc_final: 0.7915 (t0) REVERT: U 22 PHE cc_start: 0.8481 (m-10) cc_final: 0.8258 (m-10) REVERT: U 68 LYS cc_start: 0.8904 (mtmm) cc_final: 0.8614 (mtmm) REVERT: V 75 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7747 (tm-30) REVERT: W 58 ASN cc_start: 0.8886 (t0) cc_final: 0.8664 (t0) REVERT: Y 47 TYR cc_start: 0.8578 (m-80) cc_final: 0.8138 (m-80) REVERT: Z 25 ASN cc_start: 0.8699 (OUTLIER) cc_final: 0.8115 (p0) REVERT: AA 1 MET cc_start: 0.7759 (ptp) cc_final: 0.7278 (ptp) REVERT: AB 53 ASP cc_start: 0.7315 (OUTLIER) cc_final: 0.7081 (p0) REVERT: AC 20 ASP cc_start: 0.8288 (t0) cc_final: 0.7908 (t0) REVERT: a 15 PHE cc_start: 0.7058 (m-80) cc_final: 0.6699 (m-10) REVERT: a 20 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7849 (ptm-80) REVERT: a 95 TRP cc_start: 0.6744 (t-100) cc_final: 0.6358 (t-100) REVERT: a 158 ASP cc_start: 0.8189 (t70) cc_final: 0.7664 (m-30) REVERT: b 133 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.6992 (ttp) REVERT: c 71 PHE cc_start: 0.8699 (OUTLIER) cc_final: 0.8408 (m-80) REVERT: c 104 MET cc_start: 0.7068 (mmm) cc_final: 0.6825 (mmt) REVERT: c 203 TYR cc_start: 0.7252 (OUTLIER) cc_final: 0.6138 (t80) REVERT: d 125 LYS cc_start: 0.8633 (tptp) cc_final: 0.7925 (mttp) REVERT: e 36 ILE cc_start: 0.8719 (mp) cc_final: 0.8387 (mt) REVERT: e 53 LYS cc_start: 0.7771 (pttm) cc_final: 0.6912 (mmtp) REVERT: e 81 ASN cc_start: 0.8344 (t0) cc_final: 0.8107 (t0) REVERT: f 17 PHE cc_start: 0.1938 (OUTLIER) cc_final: 0.1573 (m-80) REVERT: f 30 MET cc_start: 0.7041 (tmm) cc_final: 0.6631 (tmm) REVERT: g 42 GLU cc_start: 0.8038 (tp30) cc_final: 0.7765 (tp30) REVERT: g 47 ASP cc_start: 0.7936 (t70) cc_final: 0.7732 (t0) REVERT: g 59 GLU cc_start: 0.7598 (tp30) cc_final: 0.7266 (tp30) REVERT: g 66 GLN cc_start: 0.8190 (mt0) cc_final: 0.7554 (tm-30) REVERT: h 105 ARG cc_start: 0.5827 (OUTLIER) cc_final: 0.4745 (tpm170) REVERT: i 20 GLN cc_start: 0.7412 (pp30) cc_final: 0.7137 (mm-40) REVERT: i 56 HIS cc_start: 0.8339 (OUTLIER) cc_final: 0.7408 (m-70) REVERT: j 124 LYS cc_start: 0.8958 (pttt) cc_final: 0.8749 (pttt) REVERT: l 12 LYS cc_start: 0.6247 (mttt) cc_final: 0.5864 (mmmt) REVERT: l 40 GLU cc_start: 0.2270 (OUTLIER) cc_final: 0.1703 (mm-30) REVERT: l 46 GLU cc_start: 0.3851 (OUTLIER) cc_final: 0.3514 (mm-30) REVERT: l 85 TYR cc_start: 0.7257 (OUTLIER) cc_final: 0.6892 (m-80) REVERT: m 41 TRP cc_start: 0.7374 (t-100) cc_final: 0.7134 (t60) REVERT: m 72 PHE cc_start: 0.5729 (t80) cc_final: 0.5420 (t80) REVERT: m 73 LEU cc_start: 0.8815 (mt) cc_final: 0.8070 (tp) REVERT: o 63 GLN cc_start: 0.7759 (mm-40) cc_final: 0.7288 (mt0) REVERT: p 17 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7236 (tm-30) REVERT: p 76 ARG cc_start: 0.8042 (mtm-85) cc_final: 0.7791 (mtm-85) REVERT: q 42 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.8186 (ppt170) REVERT: r 69 LYS cc_start: 0.6727 (tptm) cc_final: 0.5939 (mptt) REVERT: s 3 ILE cc_start: 0.7694 (mm) cc_final: 0.7383 (mm) REVERT: t 11 PHE cc_start: 0.6348 (t80) cc_final: 0.5963 (t80) REVERT: t 24 LYS cc_start: 0.9173 (mmmt) cc_final: 0.8939 (mmmt) REVERT: t 62 GLU cc_start: 0.6521 (mm-30) cc_final: 0.6237 (tm-30) outliers start: 316 outliers final: 245 residues processed: 1031 average time/residue: 1.1632 time to fit residues: 2138.7806 Evaluate side-chains 1037 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 269 poor density : 768 time to evaluate : 5.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 116 GLN Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 130 GLN Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 30 GLN Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain D residue 7 TYR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain E residue 15 ASP Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 108 MET Chi-restraints excluded: chain G residue 131 ASN Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 59 ARG Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain M residue 84 GLU Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain N residue 103 THR Chi-restraints excluded: chain N residue 113 LEU Chi-restraints excluded: chain N residue 114 ASN Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 101 ILE Chi-restraints excluded: chain Q residue 3 THR Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 40 ASN Chi-restraints excluded: chain Q residue 61 ASN Chi-restraints excluded: chain Q residue 67 ASP Chi-restraints excluded: chain Q residue 77 ASP Chi-restraints excluded: chain Q residue 94 ASP Chi-restraints excluded: chain Q residue 95 ARG Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain R residue 16 VAL Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 84 TYR Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain S residue 10 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 27 VAL Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 87 GLU Chi-restraints excluded: chain T residue 5 ASN Chi-restraints excluded: chain T residue 8 VAL Chi-restraints excluded: chain T residue 20 LEU Chi-restraints excluded: chain T residue 43 ASP Chi-restraints excluded: chain T residue 49 ASN Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 62 THR Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain U residue 8 ASN Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 34 VAL Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain V residue 34 SER Chi-restraints excluded: chain V residue 46 VAL Chi-restraints excluded: chain V residue 47 THR Chi-restraints excluded: chain V residue 59 ASP Chi-restraints excluded: chain V residue 75 GLU Chi-restraints excluded: chain W residue 45 GLN Chi-restraints excluded: chain X residue 23 LEU Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain Y residue 2 VAL Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 22 THR Chi-restraints excluded: chain Y residue 33 SER Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 25 ASN Chi-restraints excluded: chain Z residue 41 VAL Chi-restraints excluded: chain Z residue 46 VAL Chi-restraints excluded: chain AA residue 24 THR Chi-restraints excluded: chain AA residue 44 VAL Chi-restraints excluded: chain AB residue 5 THR Chi-restraints excluded: chain AB residue 28 LEU Chi-restraints excluded: chain AB residue 50 SER Chi-restraints excluded: chain AB residue 53 ASP Chi-restraints excluded: chain AC residue 3 VAL Chi-restraints excluded: chain AC residue 16 ILE Chi-restraints excluded: chain AC residue 25 VAL Chi-restraints excluded: chain a residue 18 GLN Chi-restraints excluded: chain a residue 20 ARG Chi-restraints excluded: chain a residue 30 ILE Chi-restraints excluded: chain a residue 45 THR Chi-restraints excluded: chain a residue 59 ILE Chi-restraints excluded: chain a residue 71 THR Chi-restraints excluded: chain a residue 108 GLN Chi-restraints excluded: chain a residue 147 LEU Chi-restraints excluded: chain a residue 178 LEU Chi-restraints excluded: chain a residue 185 ILE Chi-restraints excluded: chain a residue 186 VAL Chi-restraints excluded: chain a residue 190 SER Chi-restraints excluded: chain a residue 212 TYR Chi-restraints excluded: chain b residue 51 VAL Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 75 VAL Chi-restraints excluded: chain b residue 133 MET Chi-restraints excluded: chain b residue 156 LEU Chi-restraints excluded: chain b residue 190 THR Chi-restraints excluded: chain b residue 195 ILE Chi-restraints excluded: chain c residue 71 PHE Chi-restraints excluded: chain c residue 85 THR Chi-restraints excluded: chain c residue 136 VAL Chi-restraints excluded: chain c residue 154 VAL Chi-restraints excluded: chain c residue 190 LEU Chi-restraints excluded: chain c residue 203 TYR Chi-restraints excluded: chain d residue 29 ILE Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain d residue 139 THR Chi-restraints excluded: chain d residue 163 ILE Chi-restraints excluded: chain e residue 13 ASP Chi-restraints excluded: chain e residue 18 VAL Chi-restraints excluded: chain e residue 61 LEU Chi-restraints excluded: chain e residue 73 GLU Chi-restraints excluded: chain f residue 17 PHE Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 123 LEU Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 35 ILE Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain g residue 39 LEU Chi-restraints excluded: chain g residue 74 ILE Chi-restraints excluded: chain g residue 89 ASP Chi-restraints excluded: chain g residue 91 LEU Chi-restraints excluded: chain g residue 100 ILE Chi-restraints excluded: chain g residue 102 VAL Chi-restraints excluded: chain g residue 103 VAL Chi-restraints excluded: chain g residue 111 THR Chi-restraints excluded: chain g residue 112 ASP Chi-restraints excluded: chain g residue 113 ARG Chi-restraints excluded: chain g residue 125 ILE Chi-restraints excluded: chain h residue 28 VAL Chi-restraints excluded: chain h residue 57 VAL Chi-restraints excluded: chain h residue 64 ILE Chi-restraints excluded: chain h residue 72 SER Chi-restraints excluded: chain h residue 105 ARG Chi-restraints excluded: chain h residue 110 VAL Chi-restraints excluded: chain i residue 8 ILE Chi-restraints excluded: chain i residue 10 LEU Chi-restraints excluded: chain i residue 17 LEU Chi-restraints excluded: chain i residue 44 THR Chi-restraints excluded: chain i residue 49 PHE Chi-restraints excluded: chain i residue 56 HIS Chi-restraints excluded: chain i residue 63 ASP Chi-restraints excluded: chain i residue 72 ARG Chi-restraints excluded: chain i residue 102 LEU Chi-restraints excluded: chain j residue 41 LEU Chi-restraints excluded: chain j residue 58 THR Chi-restraints excluded: chain j residue 64 VAL Chi-restraints excluded: chain j residue 92 ARG Chi-restraints excluded: chain j residue 115 ILE Chi-restraints excluded: chain j residue 118 ASN Chi-restraints excluded: chain k residue 56 LEU Chi-restraints excluded: chain k residue 71 HIS Chi-restraints excluded: chain l residue 6 ILE Chi-restraints excluded: chain l residue 21 ILE Chi-restraints excluded: chain l residue 40 GLU Chi-restraints excluded: chain l residue 46 GLU Chi-restraints excluded: chain l residue 52 ILE Chi-restraints excluded: chain l residue 85 TYR Chi-restraints excluded: chain m residue 29 ILE Chi-restraints excluded: chain m residue 33 VAL Chi-restraints excluded: chain m residue 45 LEU Chi-restraints excluded: chain m residue 53 ASP Chi-restraints excluded: chain m residue 63 CYS Chi-restraints excluded: chain m residue 92 ILE Chi-restraints excluded: chain n residue 21 THR Chi-restraints excluded: chain n residue 53 ARG Chi-restraints excluded: chain n residue 61 GLN Chi-restraints excluded: chain n residue 84 LEU Chi-restraints excluded: chain o residue 2 VAL Chi-restraints excluded: chain o residue 13 LYS Chi-restraints excluded: chain o residue 46 LYS Chi-restraints excluded: chain o residue 60 TRP Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 20 ILE Chi-restraints excluded: chain p residue 24 ILE Chi-restraints excluded: chain p residue 32 ILE Chi-restraints excluded: chain p residue 37 ILE Chi-restraints excluded: chain p residue 45 VAL Chi-restraints excluded: chain p residue 57 VAL Chi-restraints excluded: chain p residue 77 VAL Chi-restraints excluded: chain q residue 28 LEU Chi-restraints excluded: chain q residue 42 ARG Chi-restraints excluded: chain r residue 16 LYS Chi-restraints excluded: chain r residue 40 PHE Chi-restraints excluded: chain r residue 42 ASN Chi-restraints excluded: chain r residue 78 THR Chi-restraints excluded: chain s residue 25 SER Chi-restraints excluded: chain s residue 29 THR Chi-restraints excluded: chain s residue 38 ILE Chi-restraints excluded: chain s residue 58 ASP Chi-restraints excluded: chain s residue 65 LEU Chi-restraints excluded: chain t residue 21 SER Chi-restraints excluded: chain t residue 27 VAL Chi-restraints excluded: chain t residue 42 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 576 optimal weight: 8.9990 chunk 372 optimal weight: 5.9990 chunk 556 optimal weight: 10.0000 chunk 280 optimal weight: 7.9990 chunk 183 optimal weight: 0.9980 chunk 180 optimal weight: 0.9990 chunk 592 optimal weight: 10.0000 chunk 634 optimal weight: 6.9990 chunk 460 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 732 optimal weight: 6.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 ASN ** E 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 GLN ** P 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 49 ASN Y 5 ASN AB 30 HIS a 108 GLN ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 51 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.4904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 152339 Z= 0.277 Angle : 0.634 14.105 228406 Z= 0.324 Chirality : 0.036 0.319 29267 Planarity : 0.005 0.060 11889 Dihedral : 24.153 179.788 77439 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.61 % Favored : 93.37 % Rotamer: Outliers : 6.59 % Allowed : 24.33 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.11), residues: 5235 helix: 0.34 (0.12), residues: 1798 sheet: -1.21 (0.16), residues: 958 loop : -1.87 (0.12), residues: 2479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP N 30 HIS 0.013 0.001 HIS b 5 PHE 0.044 0.002 PHE e 78 TYR 0.040 0.002 TYR F 25 ARG 0.014 0.001 ARG a 107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10470 Ramachandran restraints generated. 5235 Oldfield, 0 Emsley, 5235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10470 Ramachandran restraints generated. 5235 Oldfield, 0 Emsley, 5235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1116 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 286 poor density : 830 time to evaluate : 5.979 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: A 97 ASP cc_start: 0.8180 (p0) cc_final: 0.7836 (p0) REVERT: A 224 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8442 (mmt) REVERT: B 130 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.8125 (mp10) REVERT: B 131 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7830 (p0) REVERT: C 30 GLN cc_start: 0.9150 (OUTLIER) cc_final: 0.8822 (tt0) REVERT: D 7 TYR cc_start: 0.7656 (OUTLIER) cc_final: 0.6907 (t80) REVERT: D 14 LYS cc_start: 0.8047 (mttm) cc_final: 0.7744 (pptt) REVERT: F 1 MET cc_start: 0.6234 (tpt) cc_final: 0.5428 (ttp) REVERT: G 16 TYR cc_start: 0.8856 (m-80) cc_final: 0.8367 (m-80) REVERT: G 108 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8106 (mtt) REVERT: K 104 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7190 (mt-10) REVERT: K 110 GLU cc_start: 0.8344 (tp30) cc_final: 0.8018 (tp30) REVERT: L 49 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8050 (mm-30) REVERT: L 82 GLU cc_start: 0.7921 (mp0) cc_final: 0.7697 (mp0) REVERT: L 94 TYR cc_start: 0.9162 (m-80) cc_final: 0.8801 (m-80) REVERT: M 31 THR cc_start: 0.9070 (OUTLIER) cc_final: 0.8858 (t) REVERT: M 46 GLU cc_start: 0.7441 (pt0) cc_final: 0.6883 (pt0) REVERT: O 48 ASP cc_start: 0.8163 (m-30) cc_final: 0.7809 (m-30) REVERT: O 101 ASP cc_start: 0.8068 (t0) cc_final: 0.7664 (t0) REVERT: Q 95 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7852 (mtm-85) REVERT: R 32 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8881 (mm) REVERT: R 52 GLU cc_start: 0.8403 (mp0) cc_final: 0.8120 (mp0) REVERT: R 54 GLU cc_start: 0.6886 (tm-30) cc_final: 0.6477 (tm-30) REVERT: S 61 GLU cc_start: 0.7350 (mt-10) cc_final: 0.6903 (mt-10) REVERT: T 26 PHE cc_start: 0.8605 (p90) cc_final: 0.8313 (p90) REVERT: T 55 GLU cc_start: 0.8556 (pm20) cc_final: 0.8283 (pm20) REVERT: U 11 ASP cc_start: 0.8113 (t0) cc_final: 0.7830 (t0) REVERT: U 22 PHE cc_start: 0.8415 (m-10) cc_final: 0.8167 (m-10) REVERT: V 75 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7742 (tm-30) REVERT: W 58 ASN cc_start: 0.8851 (t0) cc_final: 0.8630 (t0) REVERT: Y 47 TYR cc_start: 0.8442 (m-80) cc_final: 0.8240 (m-10) REVERT: Z 21 THR cc_start: 0.8621 (OUTLIER) cc_final: 0.8189 (m) REVERT: Z 25 ASN cc_start: 0.8660 (OUTLIER) cc_final: 0.8332 (p0) REVERT: AA 1 MET cc_start: 0.7766 (ptp) cc_final: 0.7269 (ptp) REVERT: AB 53 ASP cc_start: 0.7207 (OUTLIER) cc_final: 0.6965 (p0) REVERT: AC 20 ASP cc_start: 0.8258 (t0) cc_final: 0.7914 (t0) REVERT: a 15 PHE cc_start: 0.7116 (m-80) cc_final: 0.6788 (m-10) REVERT: a 20 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7759 (ptm-80) REVERT: a 68 PHE cc_start: 0.5739 (m-80) cc_final: 0.5371 (m-80) REVERT: a 95 TRP cc_start: 0.6666 (t-100) cc_final: 0.6424 (t-100) REVERT: a 158 ASP cc_start: 0.8201 (t70) cc_final: 0.7713 (m-30) REVERT: b 133 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.6984 (ttp) REVERT: c 71 PHE cc_start: 0.8701 (OUTLIER) cc_final: 0.8414 (m-80) REVERT: c 104 MET cc_start: 0.7082 (mmm) cc_final: 0.6842 (mmt) REVERT: c 124 VAL cc_start: 0.8946 (t) cc_final: 0.8728 (p) REVERT: c 203 TYR cc_start: 0.7212 (OUTLIER) cc_final: 0.6073 (t80) REVERT: d 125 LYS cc_start: 0.8544 (tptp) cc_final: 0.7891 (mttp) REVERT: e 36 ILE cc_start: 0.8680 (mp) cc_final: 0.8368 (mt) REVERT: e 53 LYS cc_start: 0.7748 (pttm) cc_final: 0.6931 (mmtp) REVERT: e 81 ASN cc_start: 0.8356 (t0) cc_final: 0.8120 (t0) REVERT: f 17 PHE cc_start: 0.1945 (OUTLIER) cc_final: 0.1616 (m-80) REVERT: g 42 GLU cc_start: 0.7997 (tp30) cc_final: 0.7700 (tp30) REVERT: g 47 ASP cc_start: 0.8035 (t70) cc_final: 0.7812 (t0) REVERT: g 59 GLU cc_start: 0.7662 (tp30) cc_final: 0.7336 (tp30) REVERT: g 66 GLN cc_start: 0.8160 (mt0) cc_final: 0.7616 (tm-30) REVERT: h 105 ARG cc_start: 0.5999 (OUTLIER) cc_final: 0.4904 (tpm170) REVERT: i 20 GLN cc_start: 0.7488 (pp30) cc_final: 0.7264 (mm-40) REVERT: i 56 HIS cc_start: 0.8220 (OUTLIER) cc_final: 0.7708 (t-90) REVERT: j 67 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7686 (tm-30) REVERT: j 124 LYS cc_start: 0.8954 (pttt) cc_final: 0.8738 (pttt) REVERT: k 23 LEU cc_start: 0.7288 (mp) cc_final: 0.7053 (mp) REVERT: l 12 LYS cc_start: 0.6260 (mttt) cc_final: 0.5868 (mmmt) REVERT: l 40 GLU cc_start: 0.2379 (OUTLIER) cc_final: 0.1828 (mm-30) REVERT: l 46 GLU cc_start: 0.3947 (OUTLIER) cc_final: 0.3511 (mm-30) REVERT: l 77 LYS cc_start: 0.7823 (pttp) cc_final: 0.7319 (mtpp) REVERT: l 80 MET cc_start: 0.6942 (mmt) cc_final: 0.5602 (ttt) REVERT: m 41 TRP cc_start: 0.7320 (t-100) cc_final: 0.7107 (t60) REVERT: m 72 PHE cc_start: 0.5699 (t80) cc_final: 0.5442 (t80) REVERT: m 73 LEU cc_start: 0.8800 (mt) cc_final: 0.8088 (tp) REVERT: n 62 ARG cc_start: 0.9216 (tmm-80) cc_final: 0.8860 (ttm-80) REVERT: n 68 TYR cc_start: 0.8962 (t80) cc_final: 0.8632 (t80) REVERT: o 46 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7603 (mptt) REVERT: o 63 GLN cc_start: 0.7721 (mm-40) cc_final: 0.7375 (mt0) REVERT: p 17 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7374 (tm-30) REVERT: p 59 GLU cc_start: 0.6368 (OUTLIER) cc_final: 0.6099 (pt0) REVERT: q 42 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8013 (ppt170) REVERT: r 69 LYS cc_start: 0.6677 (tptm) cc_final: 0.6207 (mptt) REVERT: s 3 ILE cc_start: 0.7677 (mm) cc_final: 0.7331 (mm) REVERT: t 11 PHE cc_start: 0.6435 (t80) cc_final: 0.6046 (t80) REVERT: t 24 LYS cc_start: 0.9150 (mmmt) cc_final: 0.8943 (mmmt) REVERT: t 62 GLU cc_start: 0.6492 (mm-30) cc_final: 0.6272 (tm-30) outliers start: 286 outliers final: 228 residues processed: 1031 average time/residue: 1.1877 time to fit residues: 2191.2577 Evaluate side-chains 1048 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 795 time to evaluate : 5.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 130 GLN Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 30 GLN Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain D residue 7 TYR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain E residue 15 ASP Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 108 MET Chi-restraints excluded: chain G residue 131 ASN Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 59 ARG Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain M residue 36 TYR Chi-restraints excluded: chain M residue 38 GLN Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain M residue 84 GLU Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain N residue 103 THR Chi-restraints excluded: chain N residue 113 LEU Chi-restraints excluded: chain N residue 114 ASN Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 101 ILE Chi-restraints excluded: chain Q residue 3 THR Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 40 ASN Chi-restraints excluded: chain Q residue 67 ASP Chi-restraints excluded: chain Q residue 71 VAL Chi-restraints excluded: chain Q residue 77 ASP Chi-restraints excluded: chain Q residue 95 ARG Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain R residue 16 VAL Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain S residue 10 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 27 VAL Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 87 GLU Chi-restraints excluded: chain T residue 5 ASN Chi-restraints excluded: chain T residue 8 VAL Chi-restraints excluded: chain T residue 43 ASP Chi-restraints excluded: chain T residue 49 ASN Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 62 THR Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 34 VAL Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain V residue 34 SER Chi-restraints excluded: chain V residue 47 THR Chi-restraints excluded: chain V residue 59 ASP Chi-restraints excluded: chain V residue 75 GLU Chi-restraints excluded: chain W residue 45 GLN Chi-restraints excluded: chain X residue 23 LEU Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain Y residue 2 VAL Chi-restraints excluded: chain Y residue 5 ASN Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 22 THR Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 25 ASN Chi-restraints excluded: chain Z residue 41 VAL Chi-restraints excluded: chain Z residue 46 VAL Chi-restraints excluded: chain AA residue 24 THR Chi-restraints excluded: chain AA residue 44 VAL Chi-restraints excluded: chain AB residue 5 THR Chi-restraints excluded: chain AB residue 28 LEU Chi-restraints excluded: chain AB residue 50 SER Chi-restraints excluded: chain AB residue 53 ASP Chi-restraints excluded: chain AC residue 3 VAL Chi-restraints excluded: chain AC residue 25 VAL Chi-restraints excluded: chain a residue 18 GLN Chi-restraints excluded: chain a residue 20 ARG Chi-restraints excluded: chain a residue 30 ILE Chi-restraints excluded: chain a residue 45 THR Chi-restraints excluded: chain a residue 59 ILE Chi-restraints excluded: chain a residue 71 THR Chi-restraints excluded: chain a residue 108 GLN Chi-restraints excluded: chain a residue 147 LEU Chi-restraints excluded: chain a residue 185 ILE Chi-restraints excluded: chain a residue 186 VAL Chi-restraints excluded: chain a residue 190 SER Chi-restraints excluded: chain b residue 51 VAL Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 75 VAL Chi-restraints excluded: chain b residue 133 MET Chi-restraints excluded: chain b residue 156 LEU Chi-restraints excluded: chain b residue 195 ILE Chi-restraints excluded: chain c residue 71 PHE Chi-restraints excluded: chain c residue 85 THR Chi-restraints excluded: chain c residue 136 VAL Chi-restraints excluded: chain c residue 190 LEU Chi-restraints excluded: chain c residue 203 TYR Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain d residue 139 THR Chi-restraints excluded: chain d residue 163 ILE Chi-restraints excluded: chain e residue 13 ASP Chi-restraints excluded: chain e residue 18 VAL Chi-restraints excluded: chain e residue 61 LEU Chi-restraints excluded: chain e residue 73 GLU Chi-restraints excluded: chain f residue 17 PHE Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain f residue 58 LEU Chi-restraints excluded: chain f residue 123 LEU Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain g residue 39 LEU Chi-restraints excluded: chain g residue 74 ILE Chi-restraints excluded: chain g residue 89 ASP Chi-restraints excluded: chain g residue 91 LEU Chi-restraints excluded: chain g residue 100 ILE Chi-restraints excluded: chain g residue 102 VAL Chi-restraints excluded: chain g residue 103 VAL Chi-restraints excluded: chain g residue 111 THR Chi-restraints excluded: chain g residue 112 ASP Chi-restraints excluded: chain g residue 113 ARG Chi-restraints excluded: chain g residue 117 GLN Chi-restraints excluded: chain g residue 125 ILE Chi-restraints excluded: chain h residue 28 VAL Chi-restraints excluded: chain h residue 57 VAL Chi-restraints excluded: chain h residue 64 ILE Chi-restraints excluded: chain h residue 104 THR Chi-restraints excluded: chain h residue 105 ARG Chi-restraints excluded: chain h residue 110 VAL Chi-restraints excluded: chain i residue 8 ILE Chi-restraints excluded: chain i residue 10 LEU Chi-restraints excluded: chain i residue 17 LEU Chi-restraints excluded: chain i residue 44 THR Chi-restraints excluded: chain i residue 49 PHE Chi-restraints excluded: chain i residue 56 HIS Chi-restraints excluded: chain i residue 63 ASP Chi-restraints excluded: chain i residue 72 ARG Chi-restraints excluded: chain j residue 41 LEU Chi-restraints excluded: chain j residue 58 THR Chi-restraints excluded: chain j residue 92 ARG Chi-restraints excluded: chain j residue 115 ILE Chi-restraints excluded: chain k residue 56 LEU Chi-restraints excluded: chain k residue 71 HIS Chi-restraints excluded: chain l residue 6 ILE Chi-restraints excluded: chain l residue 21 ILE Chi-restraints excluded: chain l residue 40 GLU Chi-restraints excluded: chain l residue 46 GLU Chi-restraints excluded: chain l residue 52 ILE Chi-restraints excluded: chain m residue 29 ILE Chi-restraints excluded: chain m residue 33 VAL Chi-restraints excluded: chain m residue 45 LEU Chi-restraints excluded: chain m residue 53 ASP Chi-restraints excluded: chain m residue 63 CYS Chi-restraints excluded: chain m residue 92 ILE Chi-restraints excluded: chain n residue 21 THR Chi-restraints excluded: chain n residue 53 ARG Chi-restraints excluded: chain n residue 84 LEU Chi-restraints excluded: chain o residue 2 VAL Chi-restraints excluded: chain o residue 13 LYS Chi-restraints excluded: chain o residue 46 LYS Chi-restraints excluded: chain o residue 52 LEU Chi-restraints excluded: chain o residue 60 TRP Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 20 ILE Chi-restraints excluded: chain p residue 32 ILE Chi-restraints excluded: chain p residue 37 ILE Chi-restraints excluded: chain p residue 45 VAL Chi-restraints excluded: chain p residue 57 VAL Chi-restraints excluded: chain p residue 59 GLU Chi-restraints excluded: chain p residue 77 VAL Chi-restraints excluded: chain q residue 28 LEU Chi-restraints excluded: chain q residue 42 ARG Chi-restraints excluded: chain r residue 40 PHE Chi-restraints excluded: chain r residue 42 ASN Chi-restraints excluded: chain r residue 78 THR Chi-restraints excluded: chain s residue 25 SER Chi-restraints excluded: chain s residue 29 THR Chi-restraints excluded: chain s residue 38 ILE Chi-restraints excluded: chain s residue 58 ASP Chi-restraints excluded: chain s residue 65 LEU Chi-restraints excluded: chain t residue 21 SER Chi-restraints excluded: chain t residue 27 VAL Chi-restraints excluded: chain t residue 28 LEU Chi-restraints excluded: chain t residue 42 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 847 optimal weight: 10.0000 chunk 892 optimal weight: 10.0000 chunk 814 optimal weight: 10.0000 chunk 868 optimal weight: 9.9990 chunk 522 optimal weight: 40.0000 chunk 378 optimal weight: 10.0000 chunk 682 optimal weight: 6.9990 chunk 266 optimal weight: 10.0000 chunk 784 optimal weight: 8.9990 chunk 821 optimal weight: 20.0000 chunk 865 optimal weight: 20.0000 overall best weight: 9.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 GLN O 36 GLN ** P 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 30 HIS a 108 GLN ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 39 GLN ** n 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.5451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.179 152339 Z= 0.557 Angle : 0.853 14.905 228406 Z= 0.429 Chirality : 0.046 0.303 29267 Planarity : 0.006 0.069 11889 Dihedral : 24.325 177.981 77437 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 22.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.04 % Favored : 90.95 % Rotamer: Outliers : 7.10 % Allowed : 24.29 % Favored : 68.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.11), residues: 5235 helix: -0.15 (0.12), residues: 1791 sheet: -1.41 (0.16), residues: 958 loop : -2.10 (0.11), residues: 2486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP r 33 HIS 0.016 0.002 HIS r 51 PHE 0.045 0.003 PHE K 28 TYR 0.074 0.003 TYR F 25 ARG 0.013 0.001 ARG S 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10470 Ramachandran restraints generated. 5235 Oldfield, 0 Emsley, 5235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10470 Ramachandran restraints generated. 5235 Oldfield, 0 Emsley, 5235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1074 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 308 poor density : 766 time to evaluate : 5.824 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: A 97 ASP cc_start: 0.8186 (p0) cc_final: 0.7857 (p0) REVERT: A 224 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.8532 (mmt) REVERT: B 130 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.8192 (mp10) REVERT: B 131 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7895 (p0) REVERT: C 30 GLN cc_start: 0.9243 (OUTLIER) cc_final: 0.8979 (tt0) REVERT: D 7 TYR cc_start: 0.7741 (OUTLIER) cc_final: 0.6977 (t80) REVERT: D 25 MET cc_start: 0.6368 (OUTLIER) cc_final: 0.5989 (ppp) REVERT: D 127 TYR cc_start: 0.7525 (t80) cc_final: 0.7316 (t80) REVERT: E 138 GLN cc_start: 0.8525 (tm130) cc_final: 0.8102 (pp30) REVERT: F 1 MET cc_start: 0.6514 (tpt) cc_final: 0.5768 (ptt) REVERT: G 16 TYR cc_start: 0.8927 (m-80) cc_final: 0.8323 (m-80) REVERT: G 108 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.8194 (mtt) REVERT: K 110 GLU cc_start: 0.8447 (tp30) cc_final: 0.8080 (tp30) REVERT: L 49 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8077 (mm-30) REVERT: L 94 TYR cc_start: 0.9217 (m-80) cc_final: 0.8857 (m-80) REVERT: M 31 THR cc_start: 0.8945 (OUTLIER) cc_final: 0.8703 (t) REVERT: M 36 TYR cc_start: 0.8457 (OUTLIER) cc_final: 0.8227 (m-10) REVERT: M 43 ASN cc_start: 0.8103 (p0) cc_final: 0.7854 (p0) REVERT: M 46 GLU cc_start: 0.7302 (pt0) cc_final: 0.6991 (pt0) REVERT: O 48 ASP cc_start: 0.8308 (m-30) cc_final: 0.7980 (m-30) REVERT: O 101 ASP cc_start: 0.8331 (t0) cc_final: 0.7873 (t0) REVERT: R 7 LEU cc_start: 0.9143 (mp) cc_final: 0.8788 (mt) REVERT: R 52 GLU cc_start: 0.8402 (mp0) cc_final: 0.8064 (mp0) REVERT: R 54 GLU cc_start: 0.7029 (tm-30) cc_final: 0.6610 (tm-30) REVERT: S 61 GLU cc_start: 0.7364 (mt-10) cc_final: 0.6996 (mt-10) REVERT: T 26 PHE cc_start: 0.8689 (p90) cc_final: 0.8267 (p90) REVERT: U 8 ASN cc_start: 0.9101 (OUTLIER) cc_final: 0.8894 (p0) REVERT: U 11 ASP cc_start: 0.8191 (t0) cc_final: 0.7907 (t0) REVERT: U 22 PHE cc_start: 0.8548 (m-10) cc_final: 0.8287 (m-10) REVERT: V 75 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7695 (tm-30) REVERT: W 9 LYS cc_start: 0.8470 (tppt) cc_final: 0.8239 (ttmt) REVERT: W 17 GLU cc_start: 0.8246 (tp30) cc_final: 0.8016 (tp30) REVERT: X 26 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.9073 (mp) REVERT: Y 47 TYR cc_start: 0.8576 (m-80) cc_final: 0.8219 (m-10) REVERT: Z 25 ASN cc_start: 0.8682 (OUTLIER) cc_final: 0.8244 (p0) REVERT: AA 1 MET cc_start: 0.7763 (ptp) cc_final: 0.7315 (ptp) REVERT: AB 53 ASP cc_start: 0.7492 (OUTLIER) cc_final: 0.7203 (p0) REVERT: AC 20 ASP cc_start: 0.8355 (t0) cc_final: 0.8084 (t0) REVERT: a 15 PHE cc_start: 0.7270 (m-80) cc_final: 0.7030 (m-10) REVERT: a 26 MET cc_start: 0.8335 (tpp) cc_final: 0.8128 (mmt) REVERT: a 158 ASP cc_start: 0.8201 (t70) cc_final: 0.7854 (t0) REVERT: b 133 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.7035 (ttp) REVERT: c 71 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.8374 (m-80) REVERT: d 125 LYS cc_start: 0.8581 (tptp) cc_final: 0.7859 (mttp) REVERT: e 36 ILE cc_start: 0.8776 (mp) cc_final: 0.8446 (mt) REVERT: e 81 ASN cc_start: 0.8496 (t0) cc_final: 0.8267 (t0) REVERT: f 17 PHE cc_start: 0.1912 (OUTLIER) cc_final: 0.1499 (m-80) REVERT: f 30 MET cc_start: 0.7082 (tmm) cc_final: 0.6787 (tmm) REVERT: g 47 ASP cc_start: 0.7907 (t70) cc_final: 0.7666 (t0) REVERT: g 59 GLU cc_start: 0.7681 (tp30) cc_final: 0.7459 (tp30) REVERT: g 66 GLN cc_start: 0.8204 (mt0) cc_final: 0.7526 (tm-30) REVERT: h 105 ARG cc_start: 0.5827 (OUTLIER) cc_final: 0.4648 (tpm170) REVERT: i 20 GLN cc_start: 0.7389 (pp30) cc_final: 0.7183 (mm-40) REVERT: j 67 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7801 (tm-30) REVERT: k 23 LEU cc_start: 0.7401 (mp) cc_final: 0.7126 (mp) REVERT: k 110 LYS cc_start: 0.8201 (tppt) cc_final: 0.7684 (mtmm) REVERT: l 12 LYS cc_start: 0.6475 (mttt) cc_final: 0.6071 (mmmt) REVERT: l 40 GLU cc_start: 0.2600 (OUTLIER) cc_final: 0.1713 (mm-30) REVERT: l 46 GLU cc_start: 0.4005 (OUTLIER) cc_final: 0.3670 (mm-30) REVERT: l 80 MET cc_start: 0.7080 (mmt) cc_final: 0.5829 (ttt) REVERT: l 85 TYR cc_start: 0.7083 (OUTLIER) cc_final: 0.6524 (m-80) REVERT: m 41 TRP cc_start: 0.7433 (t-100) cc_final: 0.7060 (t60) REVERT: m 73 LEU cc_start: 0.8845 (mt) cc_final: 0.8340 (tp) REVERT: o 46 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7634 (mptt) REVERT: o 63 GLN cc_start: 0.7589 (mm-40) cc_final: 0.7227 (mt0) REVERT: p 17 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7260 (tm-30) REVERT: p 59 GLU cc_start: 0.6417 (OUTLIER) cc_final: 0.6177 (pt0) REVERT: r 36 ARG cc_start: 0.5754 (OUTLIER) cc_final: 0.5514 (ptm160) REVERT: r 69 LYS cc_start: 0.6954 (tptm) cc_final: 0.6527 (mptt) REVERT: s 3 ILE cc_start: 0.7833 (mm) cc_final: 0.7482 (mm) REVERT: t 62 GLU cc_start: 0.6520 (mm-30) cc_final: 0.6103 (tm-30) outliers start: 308 outliers final: 255 residues processed: 984 average time/residue: 1.1678 time to fit residues: 2048.8900 Evaluate side-chains 1022 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 279 poor density : 743 time to evaluate : 5.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 52 HIS Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 130 GLN Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 30 GLN Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain D residue 7 TYR Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 15 ASP Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 108 MET Chi-restraints excluded: chain G residue 131 ASN Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 27 SER Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 59 ARG Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain M residue 36 TYR Chi-restraints excluded: chain M residue 38 GLN Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain M residue 84 GLU Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain N residue 4 ILE Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain N residue 103 THR Chi-restraints excluded: chain N residue 113 LEU Chi-restraints excluded: chain N residue 114 ASN Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 101 ILE Chi-restraints excluded: chain Q residue 3 THR Chi-restraints excluded: chain Q residue 20 VAL Chi-restraints excluded: chain Q residue 40 ASN Chi-restraints excluded: chain Q residue 61 ASN Chi-restraints excluded: chain Q residue 67 ASP Chi-restraints excluded: chain Q residue 77 ASP Chi-restraints excluded: chain Q residue 94 ASP Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain Q residue 107 VAL Chi-restraints excluded: chain R residue 16 VAL Chi-restraints excluded: chain R residue 55 VAL Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain S residue 10 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 27 VAL Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain T residue 5 ASN Chi-restraints excluded: chain T residue 20 LEU Chi-restraints excluded: chain T residue 43 ASP Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 62 THR Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain T residue 65 VAL Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain U residue 8 ASN Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 34 VAL Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain V residue 34 SER Chi-restraints excluded: chain V residue 46 VAL Chi-restraints excluded: chain V residue 47 THR Chi-restraints excluded: chain V residue 59 ASP Chi-restraints excluded: chain V residue 75 GLU Chi-restraints excluded: chain W residue 45 GLN Chi-restraints excluded: chain X residue 23 LEU Chi-restraints excluded: chain X residue 26 LEU Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain Y residue 5 ASN Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 22 THR Chi-restraints excluded: chain Y residue 33 SER Chi-restraints excluded: chain Z residue 21 THR Chi-restraints excluded: chain Z residue 25 ASN Chi-restraints excluded: chain Z residue 41 VAL Chi-restraints excluded: chain Z residue 46 VAL Chi-restraints excluded: chain AA residue 24 THR Chi-restraints excluded: chain AA residue 44 VAL Chi-restraints excluded: chain AB residue 5 THR Chi-restraints excluded: chain AB residue 28 LEU Chi-restraints excluded: chain AB residue 50 SER Chi-restraints excluded: chain AB residue 53 ASP Chi-restraints excluded: chain AC residue 3 VAL Chi-restraints excluded: chain AC residue 16 ILE Chi-restraints excluded: chain AC residue 25 VAL Chi-restraints excluded: chain a residue 18 GLN Chi-restraints excluded: chain a residue 30 ILE Chi-restraints excluded: chain a residue 45 THR Chi-restraints excluded: chain a residue 59 ILE Chi-restraints excluded: chain a residue 71 THR Chi-restraints excluded: chain a residue 102 ASN Chi-restraints excluded: chain a residue 108 GLN Chi-restraints excluded: chain a residue 147 LEU Chi-restraints excluded: chain a residue 185 ILE Chi-restraints excluded: chain a residue 186 VAL Chi-restraints excluded: chain a residue 190 SER Chi-restraints excluded: chain a residue 212 TYR Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 75 VAL Chi-restraints excluded: chain b residue 133 MET Chi-restraints excluded: chain b residue 156 LEU Chi-restraints excluded: chain b residue 190 THR Chi-restraints excluded: chain b residue 195 ILE Chi-restraints excluded: chain c residue 71 PHE Chi-restraints excluded: chain c residue 85 THR Chi-restraints excluded: chain c residue 136 VAL Chi-restraints excluded: chain c residue 169 TRP Chi-restraints excluded: chain c residue 190 LEU Chi-restraints excluded: chain d residue 29 ILE Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain d residue 139 THR Chi-restraints excluded: chain d residue 163 ILE Chi-restraints excluded: chain e residue 13 ASP Chi-restraints excluded: chain e residue 18 VAL Chi-restraints excluded: chain e residue 61 LEU Chi-restraints excluded: chain e residue 64 VAL Chi-restraints excluded: chain e residue 73 GLU Chi-restraints excluded: chain f residue 17 PHE Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain f residue 58 LEU Chi-restraints excluded: chain f residue 123 LEU Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain g residue 39 LEU Chi-restraints excluded: chain g residue 74 ILE Chi-restraints excluded: chain g residue 89 ASP Chi-restraints excluded: chain g residue 91 LEU Chi-restraints excluded: chain g residue 100 ILE Chi-restraints excluded: chain g residue 102 VAL Chi-restraints excluded: chain g residue 103 VAL Chi-restraints excluded: chain g residue 111 THR Chi-restraints excluded: chain g residue 112 ASP Chi-restraints excluded: chain g residue 113 ARG Chi-restraints excluded: chain g residue 117 GLN Chi-restraints excluded: chain g residue 125 ILE Chi-restraints excluded: chain h residue 28 VAL Chi-restraints excluded: chain h residue 57 VAL Chi-restraints excluded: chain h residue 64 ILE Chi-restraints excluded: chain h residue 72 SER Chi-restraints excluded: chain h residue 104 THR Chi-restraints excluded: chain h residue 105 ARG Chi-restraints excluded: chain h residue 110 VAL Chi-restraints excluded: chain i residue 10 LEU Chi-restraints excluded: chain i residue 17 LEU Chi-restraints excluded: chain i residue 32 THR Chi-restraints excluded: chain i residue 44 THR Chi-restraints excluded: chain i residue 49 PHE Chi-restraints excluded: chain i residue 63 ASP Chi-restraints excluded: chain i residue 72 ARG Chi-restraints excluded: chain j residue 41 LEU Chi-restraints excluded: chain j residue 58 THR Chi-restraints excluded: chain j residue 92 ARG Chi-restraints excluded: chain j residue 115 ILE Chi-restraints excluded: chain k residue 24 GLU Chi-restraints excluded: chain k residue 56 LEU Chi-restraints excluded: chain k residue 71 HIS Chi-restraints excluded: chain l residue 6 ILE Chi-restraints excluded: chain l residue 21 ILE Chi-restraints excluded: chain l residue 40 GLU Chi-restraints excluded: chain l residue 46 GLU Chi-restraints excluded: chain l residue 49 GLU Chi-restraints excluded: chain l residue 52 ILE Chi-restraints excluded: chain l residue 85 TYR Chi-restraints excluded: chain m residue 29 ILE Chi-restraints excluded: chain m residue 33 VAL Chi-restraints excluded: chain m residue 45 LEU Chi-restraints excluded: chain m residue 53 ASP Chi-restraints excluded: chain m residue 63 CYS Chi-restraints excluded: chain m residue 79 SER Chi-restraints excluded: chain m residue 92 ILE Chi-restraints excluded: chain n residue 2 LEU Chi-restraints excluded: chain n residue 21 THR Chi-restraints excluded: chain n residue 53 ARG Chi-restraints excluded: chain n residue 61 GLN Chi-restraints excluded: chain n residue 84 LEU Chi-restraints excluded: chain o residue 2 VAL Chi-restraints excluded: chain o residue 13 LYS Chi-restraints excluded: chain o residue 46 LYS Chi-restraints excluded: chain o residue 52 LEU Chi-restraints excluded: chain o residue 60 TRP Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 20 ILE Chi-restraints excluded: chain p residue 32 ILE Chi-restraints excluded: chain p residue 37 ILE Chi-restraints excluded: chain p residue 45 VAL Chi-restraints excluded: chain p residue 57 VAL Chi-restraints excluded: chain p residue 59 GLU Chi-restraints excluded: chain p residue 77 VAL Chi-restraints excluded: chain q residue 28 LEU Chi-restraints excluded: chain q residue 42 ARG Chi-restraints excluded: chain r residue 16 LYS Chi-restraints excluded: chain r residue 36 ARG Chi-restraints excluded: chain r residue 40 PHE Chi-restraints excluded: chain r residue 42 ASN Chi-restraints excluded: chain r residue 78 THR Chi-restraints excluded: chain s residue 25 SER Chi-restraints excluded: chain s residue 29 THR Chi-restraints excluded: chain s residue 38 ILE Chi-restraints excluded: chain s residue 56 ILE Chi-restraints excluded: chain s residue 58 ASP Chi-restraints excluded: chain s residue 65 LEU Chi-restraints excluded: chain t residue 21 SER Chi-restraints excluded: chain t residue 27 VAL Chi-restraints excluded: chain t residue 28 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 570 optimal weight: 0.7980 chunk 918 optimal weight: 10.0000 chunk 560 optimal weight: 0.7980 chunk 435 optimal weight: 0.7980 chunk 638 optimal weight: 20.0000 chunk 963 optimal weight: 10.0000 chunk 886 optimal weight: 10.0000 chunk 767 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 592 optimal weight: 7.9990 chunk 470 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 69 ASN A 133 ASN A 242 HIS ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 GLN ** E 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 ASN M 38 GLN O 36 GLN O 55 GLN ** P 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 49 ASN Y 5 ASN AB 30 HIS b 24 ASN ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 51 GLN ** r 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.5065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.101 152339 Z= 0.153 Angle : 0.607 14.726 228406 Z= 0.309 Chirality : 0.034 0.392 29267 Planarity : 0.004 0.049 11889 Dihedral : 24.190 179.596 77437 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.01 % Allowed : 27.47 % Favored : 68.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.11), residues: 5235 helix: 0.39 (0.12), residues: 1789 sheet: -1.10 (0.17), residues: 940 loop : -1.83 (0.12), residues: 2506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.112 0.002 TRP r 33 HIS 0.015 0.001 HIS r 51 PHE 0.029 0.002 PHE e 78 TYR 0.037 0.002 TYR a 212 ARG 0.025 0.001 ARG a 107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10470 Ramachandran restraints generated. 5235 Oldfield, 0 Emsley, 5235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10470 Ramachandran restraints generated. 5235 Oldfield, 0 Emsley, 5235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1053 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 879 time to evaluate : 5.818 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: A 97 ASP cc_start: 0.8118 (p0) cc_final: 0.7763 (p0) REVERT: A 224 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8420 (mmt) REVERT: A 265 PHE cc_start: 0.7869 (m-80) cc_final: 0.7046 (m-80) REVERT: D 7 TYR cc_start: 0.7629 (OUTLIER) cc_final: 0.6891 (t80) REVERT: D 129 MET cc_start: 0.7786 (tmm) cc_final: 0.6786 (ptp) REVERT: D 161 SER cc_start: 0.8234 (t) cc_final: 0.7539 (p) REVERT: E 138 GLN cc_start: 0.8336 (tm130) cc_final: 0.7811 (pp30) REVERT: F 1 MET cc_start: 0.6200 (tpt) cc_final: 0.5491 (tmm) REVERT: G 16 TYR cc_start: 0.8712 (m-80) cc_final: 0.8377 (m-80) REVERT: G 91 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7272 (mt-10) REVERT: G 108 MET cc_start: 0.8574 (mtt) cc_final: 0.7908 (mmt) REVERT: I 92 GLU cc_start: 0.7942 (pt0) cc_final: 0.7393 (pt0) REVERT: K 110 GLU cc_start: 0.8256 (tp30) cc_final: 0.7959 (tp30) REVERT: L 49 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8004 (mm-30) REVERT: L 56 LYS cc_start: 0.8897 (mttt) cc_final: 0.8675 (mttt) REVERT: L 94 TYR cc_start: 0.9053 (m-80) cc_final: 0.8637 (m-80) REVERT: M 31 THR cc_start: 0.9158 (OUTLIER) cc_final: 0.8954 (t) REVERT: M 46 GLU cc_start: 0.7300 (pt0) cc_final: 0.6733 (pt0) REVERT: O 48 ASP cc_start: 0.8022 (m-30) cc_final: 0.7643 (m-30) REVERT: O 101 ASP cc_start: 0.8066 (t0) cc_final: 0.7686 (t0) REVERT: P 46 GLU cc_start: 0.7745 (pp20) cc_final: 0.7507 (pp20) REVERT: R 32 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8721 (mm) REVERT: R 52 GLU cc_start: 0.8362 (mp0) cc_final: 0.8031 (mp0) REVERT: R 88 LYS cc_start: 0.7806 (tptp) cc_final: 0.7461 (tppt) REVERT: S 61 GLU cc_start: 0.7355 (mt-10) cc_final: 0.7062 (mt-10) REVERT: U 11 ASP cc_start: 0.8074 (t0) cc_final: 0.7825 (t0) REVERT: U 22 PHE cc_start: 0.8314 (m-10) cc_final: 0.7992 (m-10) REVERT: W 9 LYS cc_start: 0.8362 (tppt) cc_final: 0.8139 (ttmt) REVERT: Z 25 ASN cc_start: 0.8521 (OUTLIER) cc_final: 0.8217 (p0) REVERT: Z 43 ARG cc_start: 0.7559 (mtt180) cc_final: 0.7325 (mtt90) REVERT: AA 1 MET cc_start: 0.7712 (ptp) cc_final: 0.7177 (ptp) REVERT: AA 29 GLN cc_start: 0.7680 (mt0) cc_final: 0.7419 (mt0) REVERT: AC 20 ASP cc_start: 0.8213 (t0) cc_final: 0.7867 (t0) REVERT: a 15 PHE cc_start: 0.7057 (m-80) cc_final: 0.6832 (m-10) REVERT: a 26 MET cc_start: 0.8200 (tpp) cc_final: 0.7814 (mmt) REVERT: a 68 PHE cc_start: 0.5976 (m-80) cc_final: 0.5667 (m-80) REVERT: a 89 PHE cc_start: 0.5911 (m-80) cc_final: 0.5694 (m-80) REVERT: a 108 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7759 (mp10) REVERT: a 158 ASP cc_start: 0.8184 (t70) cc_final: 0.7729 (m-30) REVERT: b 133 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.6930 (ttp) REVERT: c 71 PHE cc_start: 0.8689 (OUTLIER) cc_final: 0.8207 (m-10) REVERT: c 74 TYR cc_start: 0.8307 (m-80) cc_final: 0.7881 (m-80) REVERT: c 104 MET cc_start: 0.7030 (mmm) cc_final: 0.6781 (mmm) REVERT: c 123 MET cc_start: 0.4854 (mmm) cc_final: 0.4599 (mmm) REVERT: d 125 LYS cc_start: 0.8437 (tptp) cc_final: 0.7664 (mttp) REVERT: e 13 ASP cc_start: 0.8462 (OUTLIER) cc_final: 0.8067 (p0) REVERT: e 36 ILE cc_start: 0.8669 (mp) cc_final: 0.8387 (mt) REVERT: e 42 TRP cc_start: 0.6407 (m100) cc_final: 0.6105 (m100) REVERT: e 53 LYS cc_start: 0.7679 (pttm) cc_final: 0.6811 (mmtp) REVERT: e 81 ASN cc_start: 0.8415 (t0) cc_final: 0.8200 (t0) REVERT: f 30 MET cc_start: 0.6870 (tmm) cc_final: 0.6496 (tmm) REVERT: f 105 GLU cc_start: 0.7634 (tp30) cc_final: 0.7356 (tp30) REVERT: g 37 ASN cc_start: 0.7922 (m-40) cc_final: 0.7408 (m-40) REVERT: g 47 ASP cc_start: 0.8011 (t70) cc_final: 0.7791 (t0) REVERT: g 59 GLU cc_start: 0.7677 (tp30) cc_final: 0.7338 (tp30) REVERT: g 66 GLN cc_start: 0.8125 (mt0) cc_final: 0.7599 (tm-30) REVERT: h 64 ILE cc_start: 0.6690 (OUTLIER) cc_final: 0.6408 (mm) REVERT: h 111 GLU cc_start: 0.7002 (pt0) cc_final: 0.6552 (mp0) REVERT: j 14 GLN cc_start: 0.7825 (tm-30) cc_final: 0.7222 (pp30) REVERT: j 67 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7734 (tm-30) REVERT: k 23 LEU cc_start: 0.7205 (mp) cc_final: 0.7005 (mp) REVERT: l 12 LYS cc_start: 0.6223 (mttt) cc_final: 0.5827 (mmmt) REVERT: l 40 GLU cc_start: 0.2607 (OUTLIER) cc_final: 0.2178 (mm-30) REVERT: l 46 GLU cc_start: 0.3912 (OUTLIER) cc_final: 0.3476 (mm-30) REVERT: l 77 LYS cc_start: 0.7799 (pttp) cc_final: 0.7337 (mtpp) REVERT: l 80 MET cc_start: 0.7019 (mmt) cc_final: 0.5421 (ttt) REVERT: m 41 TRP cc_start: 0.7319 (t-100) cc_final: 0.7072 (t60) REVERT: m 48 GLN cc_start: 0.7027 (mm-40) cc_final: 0.6565 (tm-30) REVERT: m 72 PHE cc_start: 0.5700 (t80) cc_final: 0.5394 (t80) REVERT: m 73 LEU cc_start: 0.8797 (mt) cc_final: 0.8055 (tp) REVERT: n 62 ARG cc_start: 0.9147 (tmm-80) cc_final: 0.8793 (ttm-80) REVERT: o 63 GLN cc_start: 0.7774 (mm-40) cc_final: 0.7563 (mt0) REVERT: p 17 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7345 (tm-30) REVERT: p 59 GLU cc_start: 0.6280 (OUTLIER) cc_final: 0.6007 (pt0) REVERT: r 69 LYS cc_start: 0.6488 (tptm) cc_final: 0.5867 (mptt) REVERT: s 3 ILE cc_start: 0.7581 (mm) cc_final: 0.7220 (mm) REVERT: t 11 PHE cc_start: 0.6467 (t80) cc_final: 0.6146 (t80) REVERT: t 24 LYS cc_start: 0.9155 (mmmt) cc_final: 0.8919 (mmmt) REVERT: t 43 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7918 (mm-30) outliers start: 174 outliers final: 131 residues processed: 996 average time/residue: 1.0974 time to fit residues: 1960.7241 Evaluate side-chains 952 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 807 time to evaluate : 5.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 HIS Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 120 ASP Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 130 GLN Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain D residue 7 TYR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 15 ASP Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 161 VAL Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 5 LEU Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 131 ASN Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain M residue 36 TYR Chi-restraints excluded: chain M residue 38 GLN Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 69 ASP Chi-restraints excluded: chain M residue 84 GLU Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain N residue 103 THR Chi-restraints excluded: chain N residue 113 LEU Chi-restraints excluded: chain O residue 3 VAL Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 51 VAL Chi-restraints excluded: chain Q residue 40 ASN Chi-restraints excluded: chain Q residue 67 ASP Chi-restraints excluded: chain Q residue 77 ASP Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain R residue 16 VAL Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain S residue 10 VAL Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain T residue 5 ASN Chi-restraints excluded: chain T residue 49 ASN Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 62 THR Chi-restraints excluded: chain T residue 64 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain V residue 34 SER Chi-restraints excluded: chain W residue 45 GLN Chi-restraints excluded: chain X residue 23 LEU Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain Y residue 5 ASN Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 22 THR Chi-restraints excluded: chain Z residue 25 ASN Chi-restraints excluded: chain Z residue 41 VAL Chi-restraints excluded: chain AA residue 44 VAL Chi-restraints excluded: chain AB residue 53 ASP Chi-restraints excluded: chain AC residue 3 VAL Chi-restraints excluded: chain AC residue 25 VAL Chi-restraints excluded: chain a residue 30 ILE Chi-restraints excluded: chain a residue 108 GLN Chi-restraints excluded: chain a residue 186 VAL Chi-restraints excluded: chain a residue 190 SER Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 75 VAL Chi-restraints excluded: chain b residue 133 MET Chi-restraints excluded: chain b residue 156 LEU Chi-restraints excluded: chain b residue 195 ILE Chi-restraints excluded: chain c residue 71 PHE Chi-restraints excluded: chain c residue 85 THR Chi-restraints excluded: chain c residue 169 TRP Chi-restraints excluded: chain d residue 163 ILE Chi-restraints excluded: chain e residue 13 ASP Chi-restraints excluded: chain e residue 18 VAL Chi-restraints excluded: chain e residue 61 LEU Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 42 VAL Chi-restraints excluded: chain f residue 123 LEU Chi-restraints excluded: chain g residue 9 MET Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain g residue 74 ILE Chi-restraints excluded: chain g residue 91 LEU Chi-restraints excluded: chain g residue 102 VAL Chi-restraints excluded: chain g residue 103 VAL Chi-restraints excluded: chain g residue 111 THR Chi-restraints excluded: chain g residue 113 ARG Chi-restraints excluded: chain g residue 117 GLN Chi-restraints excluded: chain h residue 28 VAL Chi-restraints excluded: chain h residue 57 VAL Chi-restraints excluded: chain h residue 64 ILE Chi-restraints excluded: chain h residue 110 VAL Chi-restraints excluded: chain i residue 10 LEU Chi-restraints excluded: chain i residue 44 THR Chi-restraints excluded: chain i residue 49 PHE Chi-restraints excluded: chain j residue 41 LEU Chi-restraints excluded: chain j residue 58 THR Chi-restraints excluded: chain j residue 115 ILE Chi-restraints excluded: chain k residue 56 LEU Chi-restraints excluded: chain l residue 6 ILE Chi-restraints excluded: chain l residue 21 ILE Chi-restraints excluded: chain l residue 40 GLU Chi-restraints excluded: chain l residue 46 GLU Chi-restraints excluded: chain m residue 33 VAL Chi-restraints excluded: chain m residue 45 LEU Chi-restraints excluded: chain m residue 53 ASP Chi-restraints excluded: chain m residue 79 SER Chi-restraints excluded: chain n residue 53 ARG Chi-restraints excluded: chain n residue 84 LEU Chi-restraints excluded: chain o residue 2 VAL Chi-restraints excluded: chain o residue 52 LEU Chi-restraints excluded: chain p residue 4 ILE Chi-restraints excluded: chain p residue 45 VAL Chi-restraints excluded: chain p residue 57 VAL Chi-restraints excluded: chain p residue 59 GLU Chi-restraints excluded: chain q residue 28 LEU Chi-restraints excluded: chain r residue 40 PHE Chi-restraints excluded: chain s residue 56 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 967 random chunks: chunk 609 optimal weight: 6.9990 chunk 817 optimal weight: 20.0000 chunk 235 optimal weight: 0.9990 chunk 707 optimal weight: 30.0000 chunk 113 optimal weight: 0.9980 chunk 213 optimal weight: 3.9990 chunk 768 optimal weight: 1.9990 chunk 321 optimal weight: 10.0000 chunk 788 optimal weight: 0.0770 chunk 97 optimal weight: 7.9990 chunk 141 optimal weight: 3.9990 overall best weight: 1.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 GLN ** E 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 GLN O 71 ASN ** P 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 72 GLN T 49 ASN Y 5 ASN AB 30 HIS AC 13 ASN a 108 GLN b 139 ASN ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 121 ASN ** d 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 51 GLN ** r 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.070581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.050351 restraints weight = 701132.618| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.63 r_work: 0.2991 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.5015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 152339 Z= 0.162 Angle : 0.581 14.690 228406 Z= 0.297 Chirality : 0.033 0.347 29267 Planarity : 0.004 0.049 11889 Dihedral : 24.048 179.895 77431 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.59 % Allowed : 28.29 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.11), residues: 5235 helix: 0.53 (0.12), residues: 1795 sheet: -0.94 (0.17), residues: 968 loop : -1.73 (0.12), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.104 0.002 TRP r 33 HIS 0.023 0.001 HIS r 51 PHE 0.042 0.002 PHE s 50 TYR 0.041 0.002 TYR F 25 ARG 0.012 0.000 ARG S 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 38042.35 seconds wall clock time: 663 minutes 39.24 seconds (39819.24 seconds total)