Starting phenix.real_space_refine on Tue Mar 19 08:15:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwm_21421/03_2024/6vwm_21421.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwm_21421/03_2024/6vwm_21421.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/6vwm_21421/03_2024/6vwm_21421.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwm_21421/03_2024/6vwm_21421.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwm_21421/03_2024/6vwm_21421.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwm_21421/03_2024/6vwm_21421.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= 0.187 sd= 1.136 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 53 5.21 5 S 133 5.16 5 C 69982 2.51 5 N 26087 2.21 5 O 39212 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 GLU 184": "OE1" <-> "OE2" 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 ARG 77": "NH1" <-> "NH2" Residue "B PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 83": "NH1" <-> "NH2" Residue "B GLU 99": "OE1" <-> "OE2" 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 ASP 91": "OD1" <-> "OD2" Residue "C ARG 102": "NH1" <-> "NH2" 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 "D PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 31": "OE1" <-> "OE2" Residue "D ARG 70": "NH1" <-> "NH2" Residue "D ARG 79": "NH1" <-> "NH2" Residue "D ARG 91": "NH1" <-> "NH2" Residue "D ARG 101": "NH1" <-> "NH2" Residue "D ARG 109": "NH1" <-> "NH2" Residue "D ARG 111": "NH1" <-> "NH2" Residue "D ASP 112": "OD1" <-> "OD2" Residue "D ARG 114": "NH1" <-> "NH2" Residue "D ARG 132": "NH1" <-> "NH2" Residue "D GLU 139": "OE1" <-> "OE2" Residue "D ASP 141": "OD1" <-> "OD2" Residue "D PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 152": "NH1" <-> "NH2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 169": "NH1" <-> "NH2" Residue "H ARG 37": "NH1" <-> "NH2" Residue "H TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 96": "NH1" <-> "NH2" Residue "H ARG 99": "NH1" <-> "NH2" Residue "H ARG 120": "NH1" <-> "NH2" Residue "H TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 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 "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 ARG 69": "NH1" <-> "NH2" Residue "O ASP 90": "OD1" <-> "OD2" Residue "P TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 21": "NH1" <-> "NH2" Residue "P GLU 34": "OE1" <-> "OE2" 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 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 ARG 69": "NH1" <-> "NH2" Residue "R ARG 73": "NH1" <-> "NH2" Residue "S ARG 5": "NH1" <-> "NH2" Residue "S ARG 81": "NH1" <-> "NH2" Residue "S ARG 85": "NH1" <-> "NH2" Residue "S ARG 93": "NH1" <-> "NH2" Residue "T TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 7": "NH1" <-> "NH2" Residue "U ASP 52": "OD1" <-> "OD2" Residue "U PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 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 TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 51": "NH1" <-> "NH2" Residue "Z GLU 31": "OE1" <-> "OE2" Residue "Z PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 43": "NH1" <-> "NH2" 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 ARG 73": "NH1" <-> "NH2" Residue "a PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 94": "NH1" <-> "NH2" Residue "a ASP 122": "OD1" <-> "OD2" Residue "a ASP 193": "OD1" <-> "OD2" Residue "b ASP 33": "OD1" <-> "OD2" Residue "b TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 57": "OE1" <-> "OE2" Residue "b ARG 64": "NH1" <-> "NH2" Residue "b ARG 71": "NH1" <-> "NH2" 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 77": "OE1" <-> "OE2" Residue "c ARG 96": "NH1" <-> "NH2" Residue "c ARG 110": "NH1" <-> "NH2" Residue "c GLU 112": "OE1" <-> "OE2" Residue "c GLU 146": "OE1" <-> "OE2" Residue "c ARG 153": "NH1" <-> "NH2" Residue "c GLU 159": "OE1" <-> "OE2" Residue "c GLU 162": "OE1" <-> "OE2" Residue "c GLU 186": "OE1" <-> "OE2" Residue "c ARG 187": "NH1" <-> "NH2" Residue "d PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 156": "NH1" <-> "NH2" Residue "e TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 44": "NH1" <-> "NH2" Residue "e TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 91": "NH1" <-> "NH2" Residue "f ARG 94": "NH1" <-> "NH2" Residue "h ASP 55": "OD1" <-> "OD2" Residue "h TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 94": "NH1" <-> "NH2" Residue "h GLU 96": "OE1" <-> "OE2" Residue "h ARG 112": "NH1" <-> "NH2" Residue "i ARG 7": "NH1" <-> "NH2" Residue "i ARG 45": "NH1" <-> "NH2" Residue "i PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 85": "OD1" <-> "OD2" Residue "j ARG 12": "NH1" <-> "NH2" Residue "k TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 55": "NH1" <-> "NH2" Residue "k GLU 69": "OE1" <-> "OE2" Residue "k TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 10": "OD1" <-> "OD2" Residue "l TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 81": "OD1" <-> "OD2" Residue "m ASP 17": "OD1" <-> "OD2" Residue "m GLU 85": "OE1" <-> "OE2" Residue "o ARG 28": "NH1" <-> "NH2" Residue "p PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 23": "OE1" <-> "OE2" Residue "r ARG 80": "NH1" <-> "NH2" Residue "s GLU 39": "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: 140044 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: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1622 Classifications: {'RNA': 76} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 3, '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: "G" 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: "H" 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: 1280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1280 Classifications: {'peptide': 160} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 156} 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': 2, 'rna2p_pyr': 1, 'rna3p_pur': 24, 'rna3p_pyr': 16} Link IDs: {'rna2p': 2, 'rna3p': 40} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 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: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' MG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 51.85, per 1000 atoms: 0.37 Number of scatterers: 140044 At special positions: 0 Unit cell: (267.65, 279.77, 224.22, 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 53 11.99 O 39212 8.00 N 26087 7.00 C 69982 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: 57.60 Conformation dependent library (CDL) restraints added in 7.7 seconds 10472 Ramachandran restraints generated. 5236 Oldfield, 0 Emsley, 5236 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9812 Finding SS restraints... Secondary structure from input PDB file: 157 helices and 70 sheets defined 36.4% alpha, 18.7% beta 1590 base pairs and 2394 stacking pairs defined. Time for finding SS restraints: 52.80 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 198 through 202 Processing helix chain 'A' and resid 206 through 214 removed outlier: 4.010A pdb=" N ALA A 210 " --> pdb=" O LYS A 206 " (cutoff:3.500A) 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 40 Processing helix chain 'C' and resid 97 through 115 Processing helix chain 'C' and resid 130 through 142 Processing helix chain 'C' and resid 154 through 164 Processing helix chain 'C' and resid 176 through 183 removed outlier: 3.825A 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: 3.658A pdb=" N ASP D 9 " --> pdb=" O ASP D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 60 Processing helix chain 'D' and resid 73 through 77 removed outlier: 4.105A pdb=" N PHE D 76 " --> pdb=" O VAL D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 106 removed outlier: 3.865A pdb=" N ILE D 105 " --> pdb=" O ARG D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 137 removed outlier: 3.556A pdb=" N ILE D 136 " --> pdb=" O GLU D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 172 removed outlier: 3.705A pdb=" N ALA D 171 " --> pdb=" O ALA D 167 " (cutoff:3.500A) removed outlier: 3.722A 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 'G' and resid 22 through 31 Processing helix chain 'G' and resid 40 through 48 Processing helix chain 'H' and resid 24 through 38 Processing helix chain 'H' and resid 58 through 62 removed outlier: 3.613A pdb=" N VAL H 62 " --> pdb=" O ALA H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 72 Processing helix chain 'H' and resid 89 through 96 Processing helix chain 'H' and resid 98 through 109 Processing helix chain 'H' and resid 112 through 121 Processing helix chain 'H' and resid 132 through 136 removed outlier: 3.593A pdb=" N GLN H 135 " --> pdb=" O HIS H 132 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN H 136 " --> pdb=" O ALA H 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 132 through 136' Processing helix chain 'I' and resid 104 through 108 removed outlier: 3.719A pdb=" N LEU I 107 " --> pdb=" O THR I 104 " (cutoff:3.500A) removed outlier: 3.883A 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: 4.407A 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 87 Proline residue: L 85 - end of helix 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: 3.785A 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 97 through 101 Processing helix chain 'N' and resid 104 through 108 removed outlier: 3.545A pdb=" N ARG N 108 " --> pdb=" O LYS N 105 " (cutoff:3.500A) 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: 4.493A pdb=" N GLN O 36 " --> pdb=" O ARG O 32 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA O 37 " --> pdb=" O VAL O 33 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG O 54 " --> pdb=" O ARG O 50 " (cutoff:3.500A) removed outlier: 4.332A 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: 4.358A pdb=" N VAL Q 45 " --> pdb=" O LYS Q 41 " (cutoff:3.500A) removed outlier: 4.054A 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: 3.657A pdb=" N ALA T 52 " --> pdb=" O MET T 48 " (cutoff:3.500A) Processing helix chain 'V' and resid 52 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: 4.224A 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: 4.181A pdb=" N THRAA 24 " --> pdb=" O ALAAA 20 " (cutoff:3.500A) Processing helix chain 'AA' and resid 24 through 38 removed outlier: 3.604A pdb=" N ARGAA 28 " --> pdb=" O THRAA 24 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALAAA 32 " --> pdb=" O ARGAA 28 " (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 62 removed outlier: 4.037A pdb=" N MET a 48 " --> pdb=" O LYS a 44 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN a 50 " --> pdb=" O VAL a 46 " (cutoff:3.500A) Processing helix chain 'a' and resid 75 through 86 removed outlier: 3.887A pdb=" N LYS a 80 " --> pdb=" O SER a 76 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASP a 81 " --> pdb=" O GLU a 77 " (cutoff:3.500A) Processing helix chain 'a' and resid 102 through 123 Processing helix chain 'a' and resid 129 through 148 Processing helix chain 'a' and resid 168 through 179 removed outlier: 3.876A pdb=" N ILE a 172 " --> pdb=" O GLU a 168 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASN a 177 " --> pdb=" O LYS a 173 " (cutoff:3.500A) removed outlier: 4.116A 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 47 through 49 No H-bonds generated for 'chain 'b' and resid 47 through 49' 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 142 Processing helix chain 'c' and resid 48 through 65 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: 4.026A pdb=" N LYS c 150 " --> pdb=" O LYS c 147 " (cutoff:3.500A) Processing helix chain 'c' and resid 152 through 165 Processing helix chain 'c' and resid 195 through 204 removed outlier: 3.973A pdb=" N ILE c 199 " --> pdb=" O ASN c 195 " (cutoff:3.500A) 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: 3.684A 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: 5.168A 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 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 54 Proline residue: h 50 - end of helix removed outlier: 3.737A pdb=" N LEU h 53 " --> pdb=" O GLN h 49 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL h 54 " --> pdb=" O PRO h 50 " (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 Processing helix chain 'j' and resid 90 through 102 removed outlier: 4.458A pdb=" N SER j 94 " --> pdb=" O PRO j 90 " (cutoff:3.500A) Processing helix chain 'k' and resid 2 through 9 Processing helix chain 'l' and resid 13 through 19 removed outlier: 3.524A 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: 3.719A pdb=" N ILE l 52 " --> pdb=" O SER l 48 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR l 54 " --> pdb=" O GLY l 50 " (cutoff:3.500A) removed outlier: 4.390A 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 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 removed outlier: 3.675A pdb=" N ASN n 36 " --> pdb=" O THR n 32 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N HIS n 37 " --> pdb=" O ALA n 33 " (cutoff:3.500A) Processing helix chain 'n' and resid 49 through 73 Processing helix chain 'n' and resid 73 through 85 removed outlier: 3.501A pdb=" N TYR n 77 " --> pdb=" O ASP n 73 " (cutoff:3.500A) 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 removed outlier: 3.520A pdb=" N VAL r 66 " --> pdb=" O ASP r 63 " (cutoff:3.500A) Processing helix chain 'r' and resid 69 through 73 removed outlier: 3.755A pdb=" N PHE r 73 " --> pdb=" O LEU r 70 " (cutoff:3.500A) 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 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: 4.222A pdb=" N GLU t 43 " --> pdb=" O LYS t 39 " (cutoff:3.500A) removed outlier: 3.625A 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: 6.716A pdb=" N ILE A 90 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU A 80 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 6.739A 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: 5.687A pdb=" N ARG A 188 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR A 190 " --> pdb=" O ASN A 142 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ASN A 142 " --> pdb=" O THR A 190 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 129 through 130 removed outlier: 5.687A pdb=" N ARG A 188 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR A 190 " --> pdb=" O ASN A 142 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ASN A 142 " --> pdb=" O THR A 190 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N ILE A 163 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ARG A 174 " --> pdb=" O ILE A 163 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 4 through 15 removed outlier: 5.549A pdb=" N LYS B 8 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLU B 28 " --> pdb=" O LYS B 8 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY B 10 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 189 " --> pdb=" O THR B 25 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU B 186 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N VAL B 180 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU B 188 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ASP B 176 " --> pdb=" O LYS B 190 " (cutoff:3.500A) removed outlier: 5.785A 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: 5.110A pdb=" N GLN B 173 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL B 109 " --> pdb=" O GLN B 173 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N THR B 112 " --> pdb=" O ASP B 200 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ASP B 200 " --> pdb=" O THR B 112 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 78 through 83 removed outlier: 4.335A pdb=" N GLY B 78 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N THR B 52 " --> pdb=" O GLY B 78 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN B 36 " --> pdb=" O GLN B 49 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N THR B 51 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VAL B 34 " --> pdb=" O THR B 51 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'C' and resid 118 through 121 removed outlier: 5.718A pdb=" N LEU C 147 " --> pdb=" O VAL C 187 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N THR C 189 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ILE C 149 " --> pdb=" O THR C 189 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N ARG C 170 " --> pdb=" O VAL C 146 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE C 148 " --> pdb=" O ARG C 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 65 through 67 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: 3.597A pdb=" N VAL E 22 " --> pdb=" O ASN E 19 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 120 through 123 removed outlier: 3.523A 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 'G' and resid 17 through 20 removed outlier: 3.501A pdb=" N ILE G 4 " --> pdb=" O VAL G 37 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL G 37 " --> pdb=" O ILE G 4 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 122 through 124 removed outlier: 6.057A pdb=" N ILE H 54 " --> pdb=" O LYS H 123 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N TYR H 16 " --> pdb=" O ILE H 55 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N LEU H 57 " --> pdb=" O TYR H 16 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL H 18 " --> pdb=" O LEU H 57 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TRP H 15 " --> pdb=" O GLN H 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'H' and resid 73 through 75 Processing sheet with id=AB9, first strand: chain 'I' and resid 6 through 9 removed outlier: 3.713A pdb=" N THR I 6 " --> pdb=" O CYS I 21 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLU I 45 " --> pdb=" O ARG I 17 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL I 19 " --> pdb=" O ILE I 43 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ILE I 43 " --> pdb=" O VAL I 19 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N CYS I 21 " --> pdb=" O ILE I 41 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE I 41 " --> pdb=" O CYS I 21 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LYS I 23 " --> pdb=" O ILE I 39 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ILE I 39 " --> pdb=" O LYS I 23 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL I 63 " --> pdb=" O ALA I 83 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA I 83 " --> pdb=" O VAL I 63 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 77 through 79 removed outlier: 6.835A pdb=" N ALA N 57 " --> pdb=" O ILE N 49 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ILE N 49 " --> pdb=" O ALA N 57 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR N 59 " --> pdb=" O ILE N 47 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N THR N 24 " --> pdb=" O LYS N 86 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N TRP N 30 " --> pdb=" O VAL N 80 " (cutoff:3.500A) removed outlier: 6.000A 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: 6.782A 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: 3.519A 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: 6.455A pdb=" N LEU K 33 " --> pdb=" O LEU K 102 " (cutoff:3.500A) removed outlier: 4.569A 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: 3.723A pdb=" N ILE K 96 " --> pdb=" O GLY K 39 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TYR K 91 " --> pdb=" O ILE K 73 " (cutoff:3.500A) removed outlier: 3.540A 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: 6.983A pdb=" N MET L 110 " --> pdb=" O CYS L 100 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 50 through 52 removed outlier: 3.548A pdb=" N HIS M 34 " --> pdb=" O THR M 31 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'P' and resid 10 through 15 removed outlier: 6.693A pdb=" N TYR P 2 " --> pdb=" O ILE P 41 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ILE P 41 " --> pdb=" O TYR P 2 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL P 4 " --> pdb=" O LEU P 39 " (cutoff:3.500A) removed outlier: 4.074A 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: 3.611A pdb=" N ALA P 65 " --> pdb=" O ASP P 95 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LYS P 97 " --> pdb=" O VAL P 63 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N VAL P 63 " --> pdb=" O LYS P 97 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N THR P 99 " --> pdb=" O ALA P 61 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ALA P 61 " --> pdb=" O THR P 99 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE P 101 " --> pdb=" O ILE P 59 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ILE P 59 " --> pdb=" O ILE P 101 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'P' and resid 72 through 78 removed outlier: 4.144A pdb=" N TYR P 83 " --> pdb=" O ARG P 78 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Q' and resid 2 through 10 removed outlier: 5.570A pdb=" N ILE Q 4 " --> pdb=" O VAL Q 107 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL Q 107 " --> pdb=" O ILE Q 4 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N LYS Q 6 " --> pdb=" O VAL Q 105 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N VAL Q 105 " --> pdb=" O LYS Q 6 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ARG Q 8 " --> pdb=" O ILE Q 103 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE Q 103 " --> pdb=" O ARG Q 8 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS Q 73 " --> pdb=" O VAL Q 106 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N SER Q 108 " --> pdb=" O VAL Q 71 " (cutoff:3.500A) removed outlier: 5.000A 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 Processing sheet with id=AD5, first strand: chain 'R' and resid 67 through 70 removed outlier: 3.630A 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: 3.733A pdb=" N LYS S 32 " --> pdb=" O LEU S 28 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N GLU S 9 " --> pdb=" O PHE S 72 " (cutoff:3.500A) removed outlier: 3.631A 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 removed outlier: 3.842A pdb=" N GLU S 100 " --> pdb=" O PHE S 95 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'T' and resid 3 through 5 removed outlier: 6.480A pdb=" N ALA T 74 " --> pdb=" O PHE T 91 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N PHE T 91 " --> pdb=" O ALA T 74 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ASP T 76 " --> pdb=" O ILE T 89 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ILE T 89 " --> pdb=" O ASP T 76 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLN T 78 " --> pdb=" O GLN T 87 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N GLN T 87 " --> pdb=" O LYS T 25 " (cutoff:3.500A) removed outlier: 3.797A 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: 6.885A 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 32 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: 4.439A pdb=" N LYS Z 9 " --> pdb=" O ALA Z 51 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS Z 49 " --> pdb=" O VAL Z 11 " (cutoff:3.500A) removed outlier: 3.697A 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: 3.757A 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 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 removed outlier: 6.384A pdb=" N ILE b 63 " --> pdb=" O GLN b 99 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ASN b 101 " --> pdb=" O ILE b 63 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N VAL b 65 " --> pdb=" O ASN b 101 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ALA b 103 " --> pdb=" O VAL b 65 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILE b 67 " --> pdb=" O ALA b 103 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'b' and resid 164 through 170 removed outlier: 3.522A pdb=" N ILE b 148 " --> pdb=" O GLU b 169 " (cutoff:3.500A) removed outlier: 6.943A 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: 3.827A pdb=" N GLU c 178 " --> pdb=" O ASP c 173 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP c 173 " --> pdb=" O GLU c 178 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR c 180 " --> pdb=" O GLU c 171 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU c 171 " --> pdb=" O THR c 180 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'd' and resid 11 through 24 removed outlier: 6.442A pdb=" N GLU d 12 " --> pdb=" O GLY d 39 " (cutoff:3.500A) removed outlier: 8.806A pdb=" N GLY d 39 " --> pdb=" O GLU d 12 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LEU d 14 " --> pdb=" O VAL d 37 " (cutoff:3.500A) removed outlier: 6.484A 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: 3.593A pdb=" N ARG e 44 " --> pdb=" O ALA e 57 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ALA e 57 " --> pdb=" O ARG e 44 " (cutoff:3.500A) removed outlier: 4.019A 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: 6.675A pdb=" N VAL g 102 " --> pdb=" O ILE g 125 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N TYR g 127 " --> pdb=" O ILE g 100 " (cutoff:3.500A) removed outlier: 6.898A 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 removed outlier: 3.512A pdb=" N GLY h 9 " --> pdb=" O ALA h 16 " (cutoff:3.500A) 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 41 removed outlier: 3.512A pdb=" N LEU i 73 " --> pdb=" O ILE i 40 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR i 69 " --> pdb=" O ARG i 45 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ARG i 45 " --> pdb=" O THR i 69 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'i' and resid 40 through 41 removed outlier: 3.512A pdb=" N LEU i 73 " --> pdb=" O ILE i 40 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'i' and resid 49 through 52 removed outlier: 4.193A pdb=" N PHE i 49 " --> pdb=" O TYR i 65 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N TYR i 65 " --> pdb=" O PHE i 49 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL i 51 " --> pdb=" O ASP i 63 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASP i 63 " --> pdb=" O VAL i 51 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'j' and resid 40 through 45 removed outlier: 4.012A pdb=" N GLY j 42 " --> pdb=" O ILE j 33 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE j 30 " --> pdb=" O HIS j 23 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLY j 18 " --> pdb=" O GLU j 82 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N MET j 84 " --> pdb=" O GLY j 18 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ALA j 20 " --> pdb=" O MET j 84 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LYS j 86 " --> pdb=" O ALA j 20 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE j 22 " --> pdb=" O LYS j 86 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N LEU j 81 " --> pdb=" O ILE j 106 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ASN j 108 " --> pdb=" O LEU j 81 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR j 110 " --> pdb=" O VAL j 83 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL j 85 " --> pdb=" O THR j 110 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'k' and resid 32 through 34 removed outlier: 3.644A pdb=" N ARG k 55 " --> pdb=" O VAL k 32 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N THR k 63 " --> pdb=" O TYR k 94 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N THR k 96 " --> pdb=" O THR k 63 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N TYR k 65 " --> pdb=" O THR k 96 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'o' and resid 9 through 11 Processing sheet with id=AH4, first strand: chain 'o' and resid 9 through 11 Processing sheet with id=AH5, first strand: chain 'p' and resid 41 through 45 removed outlier: 7.539A pdb=" N VAL p 21 " --> pdb=" O VAL p 12 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N VAL p 57 " --> pdb=" O VAL p 77 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N VAL p 77 " --> pdb=" O VAL p 57 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLU p 59 " --> pdb=" O VAL p 75 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N SER p 71 " --> pdb=" O CYS p 63 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'p' and resid 27 through 29 Processing sheet with id=AH7, first strand: chain 'r' and resid 30 through 32 removed outlier: 6.035A pdb=" N LEU r 30 " --> pdb=" O ALA r 49 " (cutoff:3.500A) 1826 hydrogen bonds defined for protein. 5193 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3985 hydrogen bonds 6166 hydrogen bond angles 0 basepair planarities 1590 basepair parallelities 2394 stacking parallelities Total time for adding SS restraints: 221.69 Time building geometry restraints manager: 62.51 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: 24404 1.33 - 1.46: 66318 1.46 - 1.59: 52242 1.59 - 1.71: 9147 1.71 - 1.84: 240 Bond restraints: 152351 Sorted by residual: bond pdb=" N3 U 1 13 " pdb=" C4 U 1 13 " ideal model delta sigma weight residual 1.380 1.345 0.035 2.00e-02 2.50e+03 3.14e+00 bond pdb=" C LYS r 28 " pdb=" N PRO r 29 " ideal model delta sigma weight residual 1.340 1.388 -0.048 2.76e-02 1.31e+03 3.06e+00 bond pdb=" C3' A 2 265 " pdb=" O3' A 2 265 " ideal model delta sigma weight residual 1.427 1.451 -0.024 1.50e-02 4.44e+03 2.60e+00 bond pdb=" C3' A 11201 " pdb=" O3' A 11201 " ideal model delta sigma weight residual 1.427 1.451 -0.024 1.50e-02 4.44e+03 2.48e+00 bond pdb=" C3' G 11300 " pdb=" O3' G 11300 " ideal model delta sigma weight residual 1.417 1.440 -0.023 1.50e-02 4.44e+03 2.31e+00 ... (remaining 152346 not shown) Histogram of bond angle deviations from ideal: 99.69 - 106.85: 27935 106.85 - 114.00: 95474 114.00 - 121.15: 64883 121.15 - 128.30: 33202 128.30 - 135.45: 6930 Bond angle restraints: 228424 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 120.20 127.09 -6.89 1.50e+00 4.44e-01 2.11e+01 angle pdb=" C3' A 11201 " pdb=" O3' A 11201 " pdb=" P U 11202 " ideal model delta sigma weight residual 120.20 126.93 -6.73 1.50e+00 4.44e-01 2.02e+01 angle pdb=" N VAL j 15 " pdb=" CA VAL j 15 " pdb=" C VAL j 15 " ideal model delta sigma weight residual 113.71 110.08 3.63 9.50e-01 1.11e+00 1.46e+01 angle pdb=" C3' G 11300 " pdb=" O3' G 11300 " pdb=" P U 11301 " ideal model delta sigma weight residual 120.20 125.88 -5.68 1.50e+00 4.44e-01 1.43e+01 angle pdb=" C3' G 11190 " pdb=" O3' G 11190 " pdb=" P A 11191 " ideal model delta sigma weight residual 120.20 125.83 -5.63 1.50e+00 4.44e-01 1.41e+01 ... (remaining 228419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 85562 35.94 - 71.89: 10749 71.89 - 107.83: 1285 107.83 - 143.77: 7 143.77 - 179.72: 28 Dihedral angle restraints: 97631 sinusoidal: 82425 harmonic: 15206 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 20.40 179.60 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 200.00 23.30 176.70 1 1.50e+01 4.44e-03 8.53e+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 41.70 158.30 1 1.50e+01 4.44e-03 8.23e+01 ... (remaining 97628 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 27018 0.058 - 0.115: 2008 0.115 - 0.173: 215 0.173 - 0.230: 19 0.230 - 0.288: 8 Chirality restraints: 29268 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 -2.46 -0.29 2.00e-01 2.50e+01 2.07e+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 -2.20 -0.28 2.00e-01 2.50e+01 1.90e+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 1.63e+00 ... (remaining 29265 not shown) Planarity restraints: 11890 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C 2 268 " 0.002 2.00e-02 2.50e+03 2.76e-02 1.71e+01 pdb=" N1 C 2 268 " -0.000 2.00e-02 2.50e+03 pdb=" C2 C 2 268 " 0.064 2.00e-02 2.50e+03 pdb=" O2 C 2 268 " -0.044 2.00e-02 2.50e+03 pdb=" N3 C 2 268 " -0.005 2.00e-02 2.50e+03 pdb=" C4 C 2 268 " 0.018 2.00e-02 2.50e+03 pdb=" N4 C 2 268 " -0.010 2.00e-02 2.50e+03 pdb=" C5 C 2 268 " -0.012 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 " -0.007 2.00e-02 2.50e+03 2.15e-02 1.04e+01 pdb=" N1 C 1 624 " 0.004 2.00e-02 2.50e+03 pdb=" C2 C 1 624 " 0.055 2.00e-02 2.50e+03 pdb=" O2 C 1 624 " -0.025 2.00e-02 2.50e+03 pdb=" N3 C 1 624 " -0.017 2.00e-02 2.50e+03 pdb=" C4 C 1 624 " -0.002 2.00e-02 2.50e+03 pdb=" N4 C 1 624 " 0.003 2.00e-02 2.50e+03 pdb=" C5 C 1 624 " -0.009 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' G 2 425 " 0.003 2.00e-02 2.50e+03 1.69e-02 8.61e+00 pdb=" N9 G 2 425 " 0.003 2.00e-02 2.50e+03 pdb=" C8 G 2 425 " 0.003 2.00e-02 2.50e+03 pdb=" N7 G 2 425 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G 2 425 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G 2 425 " -0.020 2.00e-02 2.50e+03 pdb=" O6 G 2 425 " 0.016 2.00e-02 2.50e+03 pdb=" N1 G 2 425 " 0.005 2.00e-02 2.50e+03 pdb=" C2 G 2 425 " -0.043 2.00e-02 2.50e+03 pdb=" N2 G 2 425 " 0.030 2.00e-02 2.50e+03 pdb=" N3 G 2 425 " 0.000 2.00e-02 2.50e+03 pdb=" C4 G 2 425 " -0.000 2.00e-02 2.50e+03 ... (remaining 11887 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 1109 2.55 - 3.14: 97340 3.14 - 3.73: 279847 3.73 - 4.31: 378074 4.31 - 4.90: 511352 Nonbonded interactions: 1267722 Sorted by model distance: nonbonded pdb=" O4 U 1 13 " pdb=" O4 U 1 20 " model vdw 1.963 3.040 nonbonded pdb=" OP2 C 21315 " pdb="MG MG 23019 " model vdw 2.062 2.170 nonbonded pdb=" OP2 G 11505 " pdb="MG MG 11604 " model vdw 2.064 2.170 nonbonded pdb=" OP2 C 2 731 " pdb="MG MG 23014 " model vdw 2.065 2.170 nonbonded pdb=" OP2 C 21314 " pdb="MG MG 23019 " model vdw 2.072 2.170 ... (remaining 1267717 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: 10.260 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: 0.100 Extract box with map and model: 57.090 Check model and map are aligned: 1.500 Set scattering table: 0.920 Process input model: 484.750 Find NCS groups from input model: 2.560 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: 0.020 Load rotamer database and sin/cos tables:2.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 559.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 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 : 0.003 0.048 152351 Z= 0.152 Angle : 0.593 11.635 228424 Z= 0.296 Chirality : 0.032 0.288 29268 Planarity : 0.004 0.052 11890 Dihedral : 23.194 179.716 87816 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.73 % Allowed : 8.85 % Favored : 89.43 % 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: -3.11 (0.10), residues: 5236 helix: -1.43 (0.10), residues: 1829 sheet: -1.67 (0.16), residues: 890 loop : -2.70 (0.10), residues: 2517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP e 42 HIS 0.004 0.001 HIS r 13 PHE 0.024 0.001 PHE r 40 TYR 0.014 0.001 TYR D 6 ARG 0.004 0.000 ARG i 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10472 Ramachandran restraints generated. 5236 Oldfield, 0 Emsley, 5236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10472 Ramachandran restraints generated. 5236 Oldfield, 0 Emsley, 5236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1478 residues out of total 4375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 1403 time to evaluate : 5.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 124 PHE cc_start: 0.8729 (t80) cc_final: 0.8454 (t80) REVERT: C 139 LYS cc_start: 0.8617 (tttt) cc_final: 0.8412 (tptt) REVERT: D 47 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7629 (tptt) REVERT: D 56 LEU cc_start: 0.8350 (tp) cc_final: 0.7898 (tp) REVERT: D 64 PRO cc_start: 0.8127 (Cg_endo) cc_final: 0.7885 (Cg_exo) REVERT: D 156 THR cc_start: 0.8628 (m) cc_final: 0.8297 (m) REVERT: D 166 ARG cc_start: 0.7995 (ttp-170) cc_final: 0.7758 (ttp80) REVERT: E 32 LEU cc_start: 0.6662 (tp) cc_final: 0.6440 (pp) REVERT: E 33 THR cc_start: 0.7198 (p) cc_final: 0.6554 (t) REVERT: E 148 ARG cc_start: 0.7806 (ttt-90) cc_final: 0.7404 (ttt-90) REVERT: G 3 VAL cc_start: 0.7001 (t) cc_final: 0.6489 (p) REVERT: G 44 ILE cc_start: 0.6849 (mt) cc_final: 0.6511 (tt) REVERT: H 13 ARG cc_start: 0.8616 (mmt90) cc_final: 0.8398 (mmt90) REVERT: J 1 MET cc_start: 0.7641 (mtp) cc_final: 0.7440 (mtm) REVERT: K 47 GLU cc_start: 0.7970 (tp30) cc_final: 0.7659 (tp30) REVERT: L 112 TYR cc_start: 0.8485 (m-80) cc_final: 0.8128 (m-80) REVERT: L 117 ASP cc_start: 0.7052 (p0) cc_final: 0.6675 (p0) REVERT: N 54 LEU cc_start: 0.8975 (tp) cc_final: 0.8751 (tp) REVERT: N 81 ASP cc_start: 0.8653 (OUTLIER) cc_final: 0.8331 (p0) REVERT: P 1 MET cc_start: 0.7441 (tpt) cc_final: 0.7011 (tpp) REVERT: R 6 ARG cc_start: 0.7453 (tpt-90) cc_final: 0.6402 (tpt170) REVERT: S 21 ARG cc_start: 0.8361 (mtp-110) cc_final: 0.8112 (mtp85) REVERT: S 45 GLN cc_start: 0.8492 (tp-100) cc_final: 0.8233 (tp40) REVERT: T 21 ARG cc_start: 0.8381 (mtt90) cc_final: 0.8038 (mtt90) REVERT: U 74 LYS cc_start: 0.8875 (mppt) cc_final: 0.8652 (mttm) REVERT: U 79 GLU cc_start: 0.7675 (tt0) cc_final: 0.7462 (tm-30) REVERT: X 24 LEU cc_start: 0.9094 (tp) cc_final: 0.8809 (tp) REVERT: X 44 ARG cc_start: 0.8701 (mmt180) cc_final: 0.8213 (tpp-160) REVERT: X 48 ASN cc_start: 0.8602 (t0) cc_final: 0.8358 (t0) REVERT: Y 54 ILE cc_start: 0.8659 (mm) cc_final: 0.8452 (mm) REVERT: Z 46 VAL cc_start: 0.7844 (t) cc_final: 0.7641 (p) REVERT: Z 49 LYS cc_start: 0.7863 (mttt) cc_final: 0.7495 (pttm) REVERT: a 15 PHE cc_start: 0.5983 (m-80) cc_final: 0.4525 (t80) REVERT: a 47 PRO cc_start: 0.6917 (Cg_exo) cc_final: 0.6663 (Cg_endo) REVERT: a 48 MET cc_start: 0.7029 (mmt) cc_final: 0.6062 (mtt) REVERT: a 73 ARG cc_start: 0.6618 (OUTLIER) cc_final: 0.6164 (mtt180) REVERT: a 95 TRP cc_start: 0.7747 (t-100) cc_final: 0.7386 (t-100) REVERT: a 112 ARG cc_start: 0.7332 (tmt170) cc_final: 0.6515 (ttt180) REVERT: b 24 ASN cc_start: 0.7484 (m-40) cc_final: 0.6975 (p0) REVERT: b 41 TYR cc_start: 0.8067 (t80) cc_final: 0.7678 (t80) REVERT: b 42 LEU cc_start: 0.8501 (tt) cc_final: 0.8268 (pp) REVERT: c 74 TYR cc_start: 0.8870 (m-10) cc_final: 0.8569 (m-10) REVERT: c 104 MET cc_start: 0.6847 (mtt) cc_final: 0.6315 (tpp) REVERT: d 65 LYS cc_start: 0.9171 (mmtp) cc_final: 0.8754 (mptt) REVERT: d 125 LYS cc_start: 0.8255 (tptp) cc_final: 0.7095 (mmtt) REVERT: e 65 GLU cc_start: 0.3783 (mm-30) cc_final: 0.1869 (tt0) REVERT: f 25 PHE cc_start: 0.6943 (m-80) cc_final: 0.6625 (m-10) REVERT: f 27 ASN cc_start: 0.5990 (m110) cc_final: 0.5728 (m-40) REVERT: g 2 MET cc_start: 0.7854 (tpp) cc_final: 0.7558 (tpp) REVERT: g 17 GLN cc_start: 0.8413 (mm-40) cc_final: 0.8173 (mm-40) REVERT: g 25 THR cc_start: 0.8281 (p) cc_final: 0.8063 (m) REVERT: g 89 ASP cc_start: 0.7511 (m-30) cc_final: 0.7210 (t0) REVERT: g 95 MET cc_start: 0.8760 (mtp) cc_final: 0.8281 (mtm) REVERT: i 25 ILE cc_start: 0.7326 (mm) cc_final: 0.7098 (tp) REVERT: j 64 VAL cc_start: 0.7431 (t) cc_final: 0.7134 (p) REVERT: j 75 GLU cc_start: 0.4953 (tm-30) cc_final: 0.4499 (mt-10) REVERT: k 17 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8475 (ttpt) REVERT: k 38 THR cc_start: 0.5221 (t) cc_final: 0.4337 (p) REVERT: k 118 VAL cc_start: 0.5885 (OUTLIER) cc_final: 0.5254 (m) REVERT: l 58 GLU cc_start: 0.5337 (tp30) cc_final: 0.4429 (mt-10) REVERT: m 3 GLN cc_start: 0.8118 (mp10) cc_final: 0.7622 (pp30) REVERT: m 37 ASP cc_start: 0.7383 (p0) cc_final: 0.7132 (m-30) REVERT: m 42 ASN cc_start: 0.7962 (m-40) cc_final: 0.7710 (m-40) REVERT: m 65 GLN cc_start: 0.5808 (pt0) cc_final: 0.5433 (tp-100) REVERT: m 76 PHE cc_start: 0.8469 (m-10) cc_final: 0.7661 (m-10) REVERT: n 9 LYS cc_start: 0.8965 (pttt) cc_final: 0.8706 (ttpt) REVERT: n 11 VAL cc_start: 0.7832 (m) cc_final: 0.7537 (m) REVERT: n 26 VAL cc_start: 0.9163 (m) cc_final: 0.8927 (p) REVERT: n 47 LYS cc_start: 0.8297 (mmmm) cc_final: 0.7460 (mtmt) REVERT: o 12 LYS cc_start: 0.7848 (ttpp) cc_final: 0.7414 (tttm) REVERT: o 16 PHE cc_start: 0.7494 (t80) cc_final: 0.7190 (t80) REVERT: o 60 TRP cc_start: 0.8371 (m100) cc_final: 0.8166 (m100) REVERT: o 77 GLU cc_start: 0.6604 (mt-10) cc_final: 0.5861 (tm-30) REVERT: p 10 ARG cc_start: 0.8046 (ttm110) cc_final: 0.7739 (ttm-80) REVERT: p 45 VAL cc_start: 0.7896 (t) cc_final: 0.7145 (m) REVERT: q 59 LYS cc_start: 0.7808 (mmtt) cc_final: 0.7349 (mttt) REVERT: q 62 ARG cc_start: 0.8461 (mtt180) cc_final: 0.8205 (mtt90) REVERT: q 66 LEU cc_start: 0.8405 (mp) cc_final: 0.8027 (tp) REVERT: r 9 PHE cc_start: 0.7365 (t80) cc_final: 0.6969 (t80) REVERT: r 11 ASP cc_start: 0.7848 (t0) cc_final: 0.7426 (t70) REVERT: r 43 MET cc_start: 0.5107 (OUTLIER) cc_final: 0.4697 (mmm) REVERT: s 47 GLN cc_start: 0.8672 (tp40) cc_final: 0.8393 (tp-100) REVERT: s 51 ASN cc_start: 0.8677 (m-40) cc_final: 0.8355 (m110) REVERT: s 73 ARG cc_start: 0.7736 (ptm160) cc_final: 0.7471 (ptm160) outliers start: 75 outliers final: 17 residues processed: 1453 average time/residue: 1.3239 time to fit residues: 3318.8988 Evaluate side-chains 938 residues out of total 4375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 915 time to evaluate : 5.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 7 TYR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 81 ASP Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 27 VAL Chi-restraints excluded: chain T residue 92 VAL Chi-restraints excluded: chain AB residue 5 THR Chi-restraints excluded: chain AB residue 6 VAL Chi-restraints excluded: chain a residue 73 ARG Chi-restraints excluded: chain c residue 69 ARG Chi-restraints excluded: chain c residue 71 PHE Chi-restraints excluded: chain d residue 42 ASN Chi-restraints excluded: chain h residue 106 ASP Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain k residue 17 LYS Chi-restraints excluded: chain k residue 118 VAL Chi-restraints excluded: chain o residue 20 VAL Chi-restraints excluded: chain r residue 35 ARG Chi-restraints excluded: chain r residue 43 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 817 optimal weight: 10.0000 chunk 733 optimal weight: 9.9990 chunk 407 optimal weight: 10.0000 chunk 250 optimal weight: 10.0000 chunk 494 optimal weight: 10.0000 chunk 391 optimal weight: 10.0000 chunk 758 optimal weight: 10.0000 chunk 293 optimal weight: 0.9980 chunk 461 optimal weight: 20.0000 chunk 564 optimal weight: 10.0000 chunk 879 optimal weight: 10.0000 overall best weight: 8.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 45 ASN A 162 GLN A 250 GLN ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN ** C 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 ASN ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 ASN E 103 ASN ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 ASN ** H 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 ASN J 93 ASN K 13 HIS L 18 GLN L 31 HIS L 62 ASN M 38 GLN O 36 GLN O 43 GLN ** O 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 31 GLN Q 61 ASN R 48 GLN R 70 HIS S 45 GLN S 65 GLN U 53 HIS V 16 ASN Y 18 HIS ** a 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 88 GLN a 102 ASN ** a 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 135 GLN ** c 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 197 HIS ** d 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 134 ASN d 145 ASN f 27 ASN h 31 GLN h 125 GLN j 118 ASN ** l 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 59 GLN ** n 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 45 HIS ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 30 HIS p 44 HIS p 50 ASN ** q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 2 ASN s 19 HIS s 47 GLN s 69 ASN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.175 152351 Z= 0.469 Angle : 0.773 16.415 228424 Z= 0.388 Chirality : 0.041 0.295 29268 Planarity : 0.006 0.073 11890 Dihedral : 24.156 179.985 77438 Min Nonbonded Distance : 1.684 Molprobity Statistics. All-atom Clashscore : 19.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.63 % Favored : 93.33 % Rotamer: Outliers : 5.62 % Allowed : 16.01 % Favored : 78.37 % 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: -2.12 (0.11), residues: 5236 helix: -0.13 (0.12), residues: 1829 sheet: -1.43 (0.17), residues: 914 loop : -2.42 (0.11), residues: 2493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP b 21 HIS 0.008 0.002 HIS p 30 PHE 0.023 0.003 PHE T 91 TYR 0.022 0.003 TYR d 127 ARG 0.068 0.001 ARG f 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10472 Ramachandran restraints generated. 5236 Oldfield, 0 Emsley, 5236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10472 Ramachandran restraints generated. 5236 Oldfield, 0 Emsley, 5236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1147 residues out of total 4375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 903 time to evaluate : 5.699 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: A 86 ARG cc_start: 0.7158 (mpt180) cc_final: 0.6849 (mpt180) REVERT: C 124 PHE cc_start: 0.8839 (t80) cc_final: 0.8608 (t80) REVERT: D 6 TYR cc_start: 0.6707 (OUTLIER) cc_final: 0.4899 (t80) REVERT: D 126 ASN cc_start: 0.8208 (m-40) cc_final: 0.7947 (t0) REVERT: D 141 ASP cc_start: 0.7999 (OUTLIER) cc_final: 0.7425 (t70) REVERT: D 166 ARG cc_start: 0.8294 (ttp-170) cc_final: 0.7037 (mtp85) REVERT: G 8 LYS cc_start: 0.8408 (tmmt) cc_final: 0.8168 (tptm) REVERT: J 115 GLU cc_start: 0.7175 (pm20) cc_final: 0.6877 (pm20) REVERT: M 31 THR cc_start: 0.8814 (OUTLIER) cc_final: 0.8584 (t) REVERT: M 84 GLU cc_start: 0.7780 (pp20) cc_final: 0.7315 (pp20) REVERT: P 49 ILE cc_start: 0.8720 (mt) cc_final: 0.8407 (mt) REVERT: P 70 GLU cc_start: 0.8300 (pm20) cc_final: 0.8069 (pm20) REVERT: R 6 ARG cc_start: 0.7564 (tpt-90) cc_final: 0.7293 (tpt170) REVERT: R 7 LEU cc_start: 0.9485 (mt) cc_final: 0.9179 (mt) REVERT: Z 29 LYS cc_start: 0.7641 (mmmt) cc_final: 0.7345 (ttmt) REVERT: Z 49 LYS cc_start: 0.7667 (mttt) cc_final: 0.7115 (pttm) REVERT: a 15 PHE cc_start: 0.6256 (m-80) cc_final: 0.4470 (t80) REVERT: a 20 ARG cc_start: 0.8606 (ttp-110) cc_final: 0.8395 (ttp-110) REVERT: a 84 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7845 (mm) REVERT: a 95 TRP cc_start: 0.7971 (t-100) cc_final: 0.7586 (t-100) REVERT: a 112 ARG cc_start: 0.7513 (tmt170) cc_final: 0.6941 (ttt180) REVERT: b 41 TYR cc_start: 0.8100 (t80) cc_final: 0.7780 (t80) REVERT: b 45 GLU cc_start: 0.6423 (pt0) cc_final: 0.5241 (tt0) REVERT: b 122 GLN cc_start: 0.8515 (mt0) cc_final: 0.8293 (mt0) REVERT: b 180 ASP cc_start: 0.6677 (m-30) cc_final: 0.6165 (m-30) REVERT: c 123 MET cc_start: 0.7184 (OUTLIER) cc_final: 0.6725 (ttm) REVERT: c 177 MET cc_start: 0.1148 (mmm) cc_final: 0.0940 (mmt) REVERT: d 63 MET cc_start: 0.8057 (mmm) cc_final: 0.7848 (mmm) REVERT: d 65 LYS cc_start: 0.9299 (mmtp) cc_final: 0.8936 (mptt) REVERT: e 8 PHE cc_start: 0.8629 (p90) cc_final: 0.8198 (p90) REVERT: e 79 ARG cc_start: 0.7375 (ptm-80) cc_final: 0.6442 (ptm-80) REVERT: e 88 MET cc_start: 0.7598 (tpt) cc_final: 0.7296 (tpt) REVERT: f 30 MET cc_start: 0.6366 (tmm) cc_final: 0.6057 (tmm) REVERT: f 39 GLU cc_start: 0.6274 (tp30) cc_final: 0.5951 (tp30) REVERT: f 102 TRP cc_start: 0.7165 (m100) cc_final: 0.6729 (m-10) REVERT: g 15 ASN cc_start: 0.7364 (m-40) cc_final: 0.6663 (p0) REVERT: g 17 GLN cc_start: 0.8522 (mm-40) cc_final: 0.8260 (mm-40) REVERT: g 42 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8394 (mm-30) REVERT: g 79 ARG cc_start: 0.8731 (mtm-85) cc_final: 0.8499 (ttp80) REVERT: g 85 TYR cc_start: 0.8019 (m-10) cc_final: 0.6709 (m-10) REVERT: g 89 ASP cc_start: 0.7954 (m-30) cc_final: 0.7363 (t0) REVERT: g 95 MET cc_start: 0.8920 (mtp) cc_final: 0.8696 (mtm) REVERT: g 123 GLU cc_start: 0.7290 (tt0) cc_final: 0.6971 (tt0) REVERT: h 36 GLN cc_start: 0.8299 (tm-30) cc_final: 0.8092 (tm-30) REVERT: i 15 HIS cc_start: 0.8341 (p90) cc_final: 0.8127 (p90) REVERT: k 28 GLN cc_start: 0.8660 (mp10) cc_final: 0.8450 (mp10) REVERT: l 61 LYS cc_start: 0.8610 (ttpt) cc_final: 0.8285 (mtpt) REVERT: l 102 LYS cc_start: 0.8063 (tptm) cc_final: 0.7731 (tptp) REVERT: m 37 ASP cc_start: 0.7067 (p0) cc_final: 0.6814 (m-30) REVERT: n 47 LYS cc_start: 0.8386 (mmmm) cc_final: 0.7615 (mtmt) REVERT: o 12 LYS cc_start: 0.7636 (ttpp) cc_final: 0.7333 (tttm) REVERT: o 17 TYR cc_start: 0.8377 (m-80) cc_final: 0.7957 (m-80) REVERT: o 60 TRP cc_start: 0.8570 (m100) cc_final: 0.8181 (m100) REVERT: p 10 ARG cc_start: 0.8224 (ttm110) cc_final: 0.7925 (ttm-80) REVERT: q 59 LYS cc_start: 0.7788 (mmtt) cc_final: 0.7201 (mttt) REVERT: r 9 PHE cc_start: 0.7676 (t80) cc_final: 0.7292 (t80) REVERT: r 11 ASP cc_start: 0.7873 (t0) cc_final: 0.7495 (t70) REVERT: r 43 MET cc_start: 0.4833 (OUTLIER) cc_final: 0.4585 (mmt) REVERT: r 60 PHE cc_start: 0.6748 (OUTLIER) cc_final: 0.6494 (t80) REVERT: s 25 SER cc_start: 0.8999 (t) cc_final: 0.8631 (p) REVERT: s 31 ILE cc_start: 0.9269 (mm) cc_final: 0.9067 (mt) REVERT: t 70 TYR cc_start: 0.5330 (p90) cc_final: 0.4773 (m-10) outliers start: 244 outliers final: 153 residues processed: 1043 average time/residue: 1.1826 time to fit residues: 2158.2829 Evaluate side-chains 966 residues out of total 4375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 806 time to evaluate : 6.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 123 LYS Chi-restraints excluded: chain C residue 156 ASN Chi-restraints excluded: chain C residue 165 HIS Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain D residue 5 ASP Chi-restraints excluded: chain D residue 6 TYR Chi-restraints excluded: chain D residue 7 TYR Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 47 ILE Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 84 CYS Chi-restraints excluded: chain I residue 90 ASN Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 60 VAL 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 39 VAL Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain N residue 103 THR Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain Q residue 53 SER Chi-restraints excluded: chain Q residue 71 VAL Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 27 VAL Chi-restraints excluded: chain S residue 39 ASN Chi-restraints excluded: chain S residue 80 ASP Chi-restraints excluded: chain T residue 5 ASN Chi-restraints excluded: chain T residue 35 GLU Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain T residue 92 VAL Chi-restraints excluded: chain U residue 55 LEU Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain X residue 4 ILE Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Z residue 8 ILE Chi-restraints excluded: chain Z residue 12 SER Chi-restraints excluded: chain Z residue 42 VAL Chi-restraints excluded: chain AA residue 1 MET Chi-restraints excluded: chain AA residue 30 VAL Chi-restraints excluded: chain AA residue 42 LEU Chi-restraints excluded: chain AB residue 5 THR Chi-restraints excluded: chain AB residue 6 VAL Chi-restraints excluded: chain AB residue 50 SER Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 81 ASP Chi-restraints excluded: chain a residue 84 LEU Chi-restraints excluded: chain a residue 92 ASN Chi-restraints excluded: chain a residue 109 SER Chi-restraints excluded: chain a residue 196 ASP Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 33 ASP Chi-restraints excluded: chain c residue 48 SER Chi-restraints excluded: chain c residue 71 PHE Chi-restraints excluded: chain c residue 123 MET Chi-restraints excluded: chain c residue 140 ASP Chi-restraints excluded: chain c residue 154 VAL Chi-restraints excluded: chain c residue 190 LEU Chi-restraints excluded: chain c residue 191 SER Chi-restraints excluded: chain d residue 10 LEU Chi-restraints excluded: chain d residue 21 SER Chi-restraints excluded: chain d residue 33 THR Chi-restraints excluded: chain d residue 42 ASN Chi-restraints excluded: chain d residue 45 VAL Chi-restraints excluded: chain d residue 71 ILE Chi-restraints excluded: chain d residue 151 MET Chi-restraints excluded: chain d residue 162 GLU Chi-restraints excluded: chain e residue 11 HIS Chi-restraints excluded: chain e residue 15 SER Chi-restraints excluded: chain e residue 18 VAL Chi-restraints excluded: chain e residue 26 THR Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 96 VAL Chi-restraints excluded: chain f residue 68 VAL Chi-restraints excluded: chain g residue 45 ILE Chi-restraints excluded: chain g residue 46 GLU Chi-restraints excluded: chain g residue 77 VAL Chi-restraints excluded: chain h residue 106 ASP Chi-restraints excluded: chain i residue 28 THR Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain j residue 19 VAL Chi-restraints excluded: chain j residue 41 LEU Chi-restraints excluded: chain j residue 107 THR Chi-restraints excluded: chain k residue 17 LYS Chi-restraints excluded: chain k residue 60 PHE Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 96 THR Chi-restraints excluded: chain k residue 118 VAL Chi-restraints excluded: chain l residue 103 THR Chi-restraints excluded: chain m residue 5 MET Chi-restraints excluded: chain m residue 26 LEU Chi-restraints excluded: chain m residue 49 THR Chi-restraints excluded: chain m residue 53 ASP Chi-restraints excluded: chain n residue 7 THR Chi-restraints excluded: chain n residue 19 ASN Chi-restraints excluded: chain n residue 24 THR Chi-restraints excluded: chain o residue 19 VAL Chi-restraints excluded: chain o residue 20 VAL Chi-restraints excluded: chain o residue 48 GLU Chi-restraints excluded: chain p residue 19 SER Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 57 VAL Chi-restraints excluded: chain q residue 28 LEU Chi-restraints excluded: chain q residue 44 THR Chi-restraints excluded: chain r residue 12 LEU Chi-restraints excluded: chain r residue 14 LEU Chi-restraints excluded: chain r residue 32 THR Chi-restraints excluded: chain r residue 43 MET Chi-restraints excluded: chain r residue 60 PHE Chi-restraints excluded: chain s residue 11 ILE Chi-restraints excluded: chain s residue 29 THR Chi-restraints excluded: chain s residue 38 ILE Chi-restraints excluded: chain t residue 18 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 488 optimal weight: 5.9990 chunk 272 optimal weight: 1.9990 chunk 731 optimal weight: 7.9990 chunk 598 optimal weight: 10.0000 chunk 242 optimal weight: 6.9990 chunk 880 optimal weight: 20.0000 chunk 951 optimal weight: 10.0000 chunk 784 optimal weight: 6.9990 chunk 873 optimal weight: 10.0000 chunk 300 optimal weight: 0.8980 chunk 706 optimal weight: 0.8980 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 9 GLN ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 HIS ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 HIS I 88 ASN N 40 GLN O 71 ASN ** P 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 7 HIS Q 57 ASN S 45 GLN ** W 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 37 GLN ** a 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 130 ASN c 151 GLN ** d 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 11 HIS g 117 GLN j 39 ASN j 118 ASN l 99 GLN ** n 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 51 GLN r 55 GLN ** s 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 152351 Z= 0.218 Angle : 0.573 13.924 228424 Z= 0.292 Chirality : 0.033 0.264 29268 Planarity : 0.004 0.065 11890 Dihedral : 24.064 178.922 77419 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 4.56 % Allowed : 18.91 % Favored : 76.53 % 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: -1.63 (0.11), residues: 5236 helix: 0.40 (0.12), residues: 1834 sheet: -1.17 (0.17), residues: 903 loop : -2.23 (0.11), residues: 2499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 30 HIS 0.005 0.001 HIS b 5 PHE 0.020 0.002 PHE r 40 TYR 0.024 0.001 TYR M 64 ARG 0.007 0.000 ARG b 58 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10472 Ramachandran restraints generated. 5236 Oldfield, 0 Emsley, 5236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10472 Ramachandran restraints generated. 5236 Oldfield, 0 Emsley, 5236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1088 residues out of total 4375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 890 time to evaluate : 5.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 124 PHE cc_start: 0.8777 (t80) cc_final: 0.8415 (t80) REVERT: C 137 LYS cc_start: 0.8187 (tttt) cc_final: 0.7945 (tttt) REVERT: D 5 ASP cc_start: 0.6983 (OUTLIER) cc_final: 0.6392 (t0) REVERT: D 6 TYR cc_start: 0.6660 (OUTLIER) cc_final: 0.5007 (t80) REVERT: D 96 TRP cc_start: 0.7010 (m100) cc_final: 0.6787 (m100) REVERT: D 99 PHE cc_start: 0.8874 (t80) cc_final: 0.8485 (t80) REVERT: E 5 LYS cc_start: 0.7303 (pttt) cc_final: 0.6647 (tppp) REVERT: E 151 ARG cc_start: 0.8050 (tpt170) cc_final: 0.7786 (tpt170) REVERT: G 8 LYS cc_start: 0.8353 (tmmt) cc_final: 0.8095 (tptm) REVERT: I 73 ASP cc_start: 0.8498 (p0) cc_final: 0.8282 (p0) REVERT: J 115 GLU cc_start: 0.7169 (pm20) cc_final: 0.6902 (pm20) REVERT: K 47 GLU cc_start: 0.7927 (tp30) cc_final: 0.7721 (tp30) REVERT: K 95 LEU cc_start: 0.9263 (mt) cc_final: 0.8960 (mt) REVERT: M 84 GLU cc_start: 0.7831 (pp20) cc_final: 0.7378 (pp20) REVERT: N 10 GLU cc_start: 0.8064 (pt0) cc_final: 0.7784 (pt0) REVERT: N 81 ASP cc_start: 0.8963 (OUTLIER) cc_final: 0.8474 (p0) REVERT: P 10 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8418 (mtmm) REVERT: P 49 ILE cc_start: 0.8691 (mt) cc_final: 0.8389 (mt) REVERT: S 45 GLN cc_start: 0.8497 (tp40) cc_final: 0.8266 (tp40) REVERT: T 55 GLU cc_start: 0.7477 (pm20) cc_final: 0.7234 (pm20) REVERT: Y 31 LYS cc_start: 0.9148 (ptpt) cc_final: 0.8925 (ptpt) REVERT: Y 47 TYR cc_start: 0.8320 (m-80) cc_final: 0.8109 (m-80) REVERT: AB 31 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8489 (tp) REVERT: a 15 PHE cc_start: 0.6267 (m-80) cc_final: 0.4535 (t80) REVERT: a 20 ARG cc_start: 0.8574 (ttp-110) cc_final: 0.8373 (ttp-110) REVERT: a 26 MET cc_start: 0.7627 (ttp) cc_final: 0.7341 (ptm) REVERT: a 31 PHE cc_start: 0.6925 (t80) cc_final: 0.6314 (t80) REVERT: a 95 TRP cc_start: 0.7861 (t-100) cc_final: 0.7621 (t-100) REVERT: a 102 ASN cc_start: 0.6154 (OUTLIER) cc_final: 0.5930 (m110) REVERT: a 112 ARG cc_start: 0.7557 (tmt170) cc_final: 0.6866 (ttt180) REVERT: b 28 PHE cc_start: 0.8798 (t80) cc_final: 0.8524 (t80) REVERT: b 41 TYR cc_start: 0.8097 (t80) cc_final: 0.7831 (t80) REVERT: b 45 GLU cc_start: 0.6361 (pt0) cc_final: 0.5535 (tt0) REVERT: b 180 ASP cc_start: 0.6611 (m-30) cc_final: 0.6213 (m-30) REVERT: b 183 TYR cc_start: 0.7013 (t80) cc_final: 0.6775 (t80) REVERT: c 123 MET cc_start: 0.7246 (OUTLIER) cc_final: 0.7030 (ttm) REVERT: d 65 LYS cc_start: 0.9241 (mmtp) cc_final: 0.8857 (mptt) REVERT: e 24 ARG cc_start: 0.8242 (mtp85) cc_final: 0.7827 (mtm180) REVERT: e 79 ARG cc_start: 0.7394 (ptm-80) cc_final: 0.6547 (ptm-80) REVERT: e 88 MET cc_start: 0.7411 (tpt) cc_final: 0.7180 (tpt) REVERT: f 39 GLU cc_start: 0.6777 (tp30) cc_final: 0.6554 (tp30) REVERT: f 101 ARG cc_start: 0.8314 (ttm110) cc_final: 0.7766 (tpp-160) REVERT: f 102 TRP cc_start: 0.7097 (m100) cc_final: 0.6735 (m-10) REVERT: g 15 ASN cc_start: 0.7286 (m-40) cc_final: 0.6548 (p0) REVERT: g 17 GLN cc_start: 0.8501 (mm-40) cc_final: 0.8286 (mm-40) REVERT: g 42 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8402 (mm-30) REVERT: g 79 ARG cc_start: 0.8724 (mtm-85) cc_final: 0.8402 (ttp-110) REVERT: g 85 TYR cc_start: 0.8048 (m-10) cc_final: 0.7715 (m-10) REVERT: g 89 ASP cc_start: 0.7909 (m-30) cc_final: 0.7345 (t0) REVERT: g 95 MET cc_start: 0.8815 (mtp) cc_final: 0.8567 (mtm) REVERT: g 113 ARG cc_start: 0.8667 (tpp-160) cc_final: 0.8455 (tpp-160) REVERT: h 119 LYS cc_start: 0.7303 (mtmm) cc_final: 0.6972 (ptpp) REVERT: j 39 ASN cc_start: 0.8028 (OUTLIER) cc_final: 0.7618 (t0) REVERT: l 16 ILE cc_start: 0.4946 (mp) cc_final: 0.4130 (mm) REVERT: l 102 LYS cc_start: 0.8128 (tptm) cc_final: 0.7847 (tptp) REVERT: n 47 LYS cc_start: 0.8481 (mmmm) cc_final: 0.7731 (mtmt) REVERT: o 17 TYR cc_start: 0.8313 (m-80) cc_final: 0.7825 (m-80) REVERT: o 60 TRP cc_start: 0.8586 (m100) cc_final: 0.8216 (m100) REVERT: p 10 ARG cc_start: 0.8229 (ttm110) cc_final: 0.7850 (ttm-80) REVERT: q 59 LYS cc_start: 0.7778 (mmtt) cc_final: 0.7152 (mttt) REVERT: r 9 PHE cc_start: 0.7538 (t80) cc_final: 0.7062 (t80) REVERT: r 11 ASP cc_start: 0.8027 (t0) cc_final: 0.7641 (t70) REVERT: r 60 PHE cc_start: 0.6736 (OUTLIER) cc_final: 0.6495 (t80) REVERT: s 31 ILE cc_start: 0.9148 (mm) cc_final: 0.8896 (mt) outliers start: 198 outliers final: 125 residues processed: 1008 average time/residue: 1.1897 time to fit residues: 2107.1114 Evaluate side-chains 958 residues out of total 4375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 824 time to evaluate : 5.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain C residue 123 LYS Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 156 ASN Chi-restraints excluded: chain C residue 165 HIS Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain D residue 5 ASP Chi-restraints excluded: chain D residue 6 TYR Chi-restraints excluded: chain D residue 7 TYR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 47 ILE Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain J residue 81 ASP Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 25 ASP Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain K residue 136 MET Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 116 GLN Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 81 ASP Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain O residue 99 VAL Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 10 LYS Chi-restraints excluded: chain Q residue 53 SER Chi-restraints excluded: chain Q residue 71 VAL Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain S residue 10 VAL Chi-restraints excluded: chain S residue 27 VAL Chi-restraints excluded: chain S residue 39 ASN Chi-restraints excluded: chain S residue 80 ASP Chi-restraints excluded: chain T residue 5 ASN Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain U residue 26 SER Chi-restraints excluded: chain U residue 67 VAL Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain AA residue 1 MET Chi-restraints excluded: chain AB residue 31 ILE Chi-restraints excluded: chain AB residue 50 SER Chi-restraints excluded: chain a residue 81 ASP Chi-restraints excluded: chain a residue 92 ASN Chi-restraints excluded: chain a residue 102 ASN Chi-restraints excluded: chain a residue 109 SER Chi-restraints excluded: chain a residue 196 ASP Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 69 THR Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain c residue 71 PHE Chi-restraints excluded: chain c residue 84 ASN Chi-restraints excluded: chain c residue 92 LEU Chi-restraints excluded: chain c residue 123 MET Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 190 LEU Chi-restraints excluded: chain c residue 191 SER Chi-restraints excluded: chain d residue 10 LEU Chi-restraints excluded: chain d residue 21 SER Chi-restraints excluded: chain d residue 42 ASN Chi-restraints excluded: chain d residue 45 VAL Chi-restraints excluded: chain d residue 130 THR Chi-restraints excluded: chain d residue 151 MET Chi-restraints excluded: chain d residue 162 GLU Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 18 VAL Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 64 VAL Chi-restraints excluded: chain e residue 96 VAL Chi-restraints excluded: chain g residue 45 ILE Chi-restraints excluded: chain g residue 77 VAL Chi-restraints excluded: chain h residue 28 VAL Chi-restraints excluded: chain h residue 106 ASP Chi-restraints excluded: chain h residue 115 VAL Chi-restraints excluded: chain i residue 25 ILE Chi-restraints excluded: chain i residue 28 THR Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 56 HIS Chi-restraints excluded: chain j residue 39 ASN Chi-restraints excluded: chain k residue 17 LYS Chi-restraints excluded: chain k residue 38 THR Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 96 THR Chi-restraints excluded: chain l residue 41 ASP Chi-restraints excluded: chain m residue 26 LEU Chi-restraints excluded: chain m residue 49 THR Chi-restraints excluded: chain m residue 53 ASP Chi-restraints excluded: chain n residue 7 THR Chi-restraints excluded: chain o residue 19 VAL Chi-restraints excluded: chain o residue 48 GLU Chi-restraints excluded: chain p residue 6 THR Chi-restraints excluded: chain p residue 20 ILE Chi-restraints excluded: chain p residue 28 VAL Chi-restraints excluded: chain p residue 46 HIS Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 57 VAL Chi-restraints excluded: chain q residue 28 LEU Chi-restraints excluded: chain q residue 44 THR Chi-restraints excluded: chain r residue 12 LEU Chi-restraints excluded: chain r residue 14 LEU Chi-restraints excluded: chain r residue 32 THR Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain r residue 57 VAL Chi-restraints excluded: chain r residue 60 PHE Chi-restraints excluded: chain s residue 12 GLN Chi-restraints excluded: chain s residue 29 THR Chi-restraints excluded: chain t residue 18 PHE Chi-restraints excluded: chain t residue 41 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 870 optimal weight: 10.0000 chunk 662 optimal weight: 20.0000 chunk 457 optimal weight: 30.0000 chunk 97 optimal weight: 20.0000 chunk 420 optimal weight: 10.0000 chunk 591 optimal weight: 10.0000 chunk 883 optimal weight: 20.0000 chunk 935 optimal weight: 30.0000 chunk 461 optimal weight: 20.0000 chunk 837 optimal weight: 20.0000 chunk 252 optimal weight: 3.9990 overall best weight: 10.7998 ------------------------------------------------------------------------------- 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** ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 HIS ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 135 GLN ** H 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 ASN L 81 ASN M 38 GLN N 74 GLN O 51 GLN ** O 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 12 HIS ** P 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 57 ASN U 8 ASN ** W 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 5 ASN AB 27 ASN ** a 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 18 ASN ** d 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 99 GLN m 42 ASN m 61 ASN m 70 HIS ** n 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 37 HIS ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 44 HIS ** q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 13 HIS ** s 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 81 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.196 152351 Z= 0.619 Angle : 0.904 14.471 228424 Z= 0.448 Chirality : 0.047 0.312 29268 Planarity : 0.006 0.094 11890 Dihedral : 24.401 178.416 77408 Min Nonbonded Distance : 1.699 Molprobity Statistics. All-atom Clashscore : 23.16 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.21 % Favored : 91.77 % Rotamer: Outliers : 7.21 % Allowed : 19.17 % Favored : 73.62 % 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: -2.11 (0.11), residues: 5236 helix: -0.21 (0.11), residues: 1824 sheet: -1.28 (0.17), residues: 954 loop : -2.41 (0.11), residues: 2458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP N 30 HIS 0.008 0.002 HIS C 92 PHE 0.032 0.003 PHE K 31 TYR 0.033 0.003 TYR M 64 ARG 0.010 0.001 ARG A 12 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10472 Ramachandran restraints generated. 5236 Oldfield, 0 Emsley, 5236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10472 Ramachandran restraints generated. 5236 Oldfield, 0 Emsley, 5236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1130 residues out of total 4375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 313 poor density : 817 time to evaluate : 5.721 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: C 168 ASP cc_start: 0.6563 (t0) cc_final: 0.6285 (t0) REVERT: D 6 TYR cc_start: 0.6565 (OUTLIER) cc_final: 0.5134 (t80) REVERT: D 7 TYR cc_start: 0.7626 (OUTLIER) cc_final: 0.7323 (p90) REVERT: D 166 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.6727 (mtp85) REVERT: G 8 LYS cc_start: 0.8403 (tmmt) cc_final: 0.8193 (tptm) REVERT: I 73 ASP cc_start: 0.8705 (p0) cc_final: 0.8453 (p0) REVERT: J 115 GLU cc_start: 0.7331 (pm20) cc_final: 0.7045 (pm20) REVERT: K 31 PHE cc_start: 0.7786 (m-10) cc_final: 0.7496 (m-10) REVERT: K 47 GLU cc_start: 0.7975 (tp30) cc_final: 0.7740 (tp30) REVERT: K 53 MET cc_start: 0.8510 (mmm) cc_final: 0.8308 (mmp) REVERT: K 110 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8111 (tp30) REVERT: M 25 ARG cc_start: 0.9099 (OUTLIER) cc_final: 0.8710 (ptm160) REVERT: M 55 GLU cc_start: 0.6991 (mm-30) cc_final: 0.6767 (mm-30) REVERT: M 84 GLU cc_start: 0.7899 (pp20) cc_final: 0.7460 (pp20) REVERT: N 12 MET cc_start: 0.8401 (mtm) cc_final: 0.8086 (ttm) REVERT: N 67 GLU cc_start: 0.6845 (tt0) cc_final: 0.6565 (tt0) REVERT: P 10 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8600 (mtmm) REVERT: P 49 ILE cc_start: 0.8792 (mt) cc_final: 0.8484 (mt) REVERT: Y 31 LYS cc_start: 0.9282 (ptpt) cc_final: 0.9012 (ptpt) REVERT: Z 24 LYS cc_start: 0.7247 (mmtm) cc_final: 0.6936 (mmtm) REVERT: Z 36 LYS cc_start: 0.7456 (mtpp) cc_final: 0.6794 (mtpp) REVERT: Z 49 LYS cc_start: 0.7768 (mttt) cc_final: 0.7248 (pttm) REVERT: AB 31 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8727 (tp) REVERT: a 20 ARG cc_start: 0.8744 (ttp-110) cc_final: 0.8447 (ttp-110) REVERT: a 26 MET cc_start: 0.8033 (ttp) cc_final: 0.7701 (ptm) REVERT: a 31 PHE cc_start: 0.7199 (t80) cc_final: 0.6712 (t80) REVERT: a 112 ARG cc_start: 0.7791 (tmt170) cc_final: 0.7151 (ttt180) REVERT: b 41 TYR cc_start: 0.8275 (t80) cc_final: 0.7566 (t80) REVERT: b 45 GLU cc_start: 0.6744 (pt0) cc_final: 0.6140 (pt0) REVERT: b 107 LYS cc_start: 0.8409 (mmtt) cc_final: 0.7951 (mmtt) REVERT: b 111 ASP cc_start: 0.7509 (t0) cc_final: 0.7308 (t0) REVERT: b 122 GLN cc_start: 0.8658 (mt0) cc_final: 0.8390 (mt0) REVERT: b 143 LEU cc_start: 0.7564 (tp) cc_final: 0.7178 (tp) REVERT: b 180 ASP cc_start: 0.6616 (m-30) cc_final: 0.6141 (m-30) REVERT: c 123 MET cc_start: 0.7096 (OUTLIER) cc_final: 0.6793 (ttm) REVERT: d 21 SER cc_start: 0.8616 (OUTLIER) cc_final: 0.8268 (m) REVERT: d 65 LYS cc_start: 0.9351 (mmtp) cc_final: 0.8967 (mptt) REVERT: e 88 MET cc_start: 0.7696 (tpt) cc_final: 0.7414 (tpt) REVERT: f 39 GLU cc_start: 0.7085 (tp30) cc_final: 0.6685 (pt0) REVERT: f 102 TRP cc_start: 0.7140 (m100) cc_final: 0.6806 (m-10) REVERT: g 15 ASN cc_start: 0.7624 (m-40) cc_final: 0.6795 (p0) REVERT: g 42 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8274 (mm-30) REVERT: i 14 ASP cc_start: 0.7898 (t0) cc_final: 0.7690 (t0) REVERT: l 102 LYS cc_start: 0.8237 (tptm) cc_final: 0.7879 (tptp) REVERT: n 47 LYS cc_start: 0.8736 (mmmm) cc_final: 0.7887 (mtmt) REVERT: o 3 THR cc_start: 0.7986 (m) cc_final: 0.7359 (p) REVERT: p 10 ARG cc_start: 0.8272 (ttm110) cc_final: 0.7976 (ttm-80) REVERT: q 59 LYS cc_start: 0.7813 (mmtt) cc_final: 0.7127 (mttt) REVERT: r 11 ASP cc_start: 0.7983 (t0) cc_final: 0.7675 (t70) REVERT: s 25 SER cc_start: 0.9151 (t) cc_final: 0.8824 (p) REVERT: s 31 ILE cc_start: 0.9312 (mm) cc_final: 0.9089 (mt) outliers start: 313 outliers final: 223 residues processed: 1007 average time/residue: 1.1450 time to fit residues: 2039.6033 Evaluate side-chains 999 residues out of total 4375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 767 time to evaluate : 5.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 123 LYS Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 156 ASN Chi-restraints excluded: chain C residue 165 HIS Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain D residue 5 ASP Chi-restraints excluded: chain D residue 6 TYR Chi-restraints excluded: chain D residue 7 TYR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 46 PHE Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 47 ILE Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 84 CYS Chi-restraints excluded: chain I residue 90 ASN Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 107 PHE Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 25 ASP Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain K residue 136 MET Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 106 ASP Chi-restraints excluded: chain M residue 25 ARG Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 38 GLN Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain O residue 61 ILE Chi-restraints excluded: chain O residue 97 ILE Chi-restraints excluded: chain O residue 99 VAL Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 10 LYS Chi-restraints excluded: chain P residue 102 SER Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 53 SER Chi-restraints excluded: chain Q residue 71 VAL Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain Q residue 77 ASP Chi-restraints excluded: chain R residue 7 LEU Chi-restraints excluded: chain R residue 10 VAL Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain S residue 10 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 26 ASN Chi-restraints excluded: chain S residue 27 VAL Chi-restraints excluded: chain S residue 39 ASN Chi-restraints excluded: chain S residue 40 LEU Chi-restraints excluded: chain S residue 80 ASP Chi-restraints excluded: chain T residue 5 ASN Chi-restraints excluded: chain T residue 35 GLU Chi-restraints excluded: chain T residue 47 VAL Chi-restraints excluded: chain T residue 63 ILE Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain U residue 26 SER Chi-restraints excluded: chain U residue 33 ILE Chi-restraints excluded: chain U residue 39 THR Chi-restraints excluded: chain U residue 67 VAL Chi-restraints excluded: chain V residue 7 THR Chi-restraints excluded: chain V residue 29 LEU Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain X residue 4 ILE Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 16 LEU Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Z residue 12 SER Chi-restraints excluded: chain Z residue 42 VAL Chi-restraints excluded: chain Z residue 46 VAL Chi-restraints excluded: chain AA residue 1 MET Chi-restraints excluded: chain AA residue 24 THR Chi-restraints excluded: chain AA residue 30 VAL Chi-restraints excluded: chain AA residue 42 LEU Chi-restraints excluded: chain AA residue 43 THR Chi-restraints excluded: chain AA residue 44 VAL Chi-restraints excluded: chain AB residue 5 THR Chi-restraints excluded: chain AB residue 31 ILE Chi-restraints excluded: chain AB residue 50 SER Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 81 ASP Chi-restraints excluded: chain a residue 109 SER Chi-restraints excluded: chain a residue 170 ILE Chi-restraints excluded: chain a residue 178 LEU Chi-restraints excluded: chain a residue 196 ASP Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 33 ASP Chi-restraints excluded: chain b residue 69 THR Chi-restraints excluded: chain c residue 71 PHE Chi-restraints excluded: chain c residue 84 ASN Chi-restraints excluded: chain c residue 92 LEU Chi-restraints excluded: chain c residue 123 MET Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 140 ASP Chi-restraints excluded: chain c residue 141 VAL Chi-restraints excluded: chain c residue 154 VAL Chi-restraints excluded: chain c residue 190 LEU Chi-restraints excluded: chain c residue 191 SER Chi-restraints excluded: chain c residue 201 GLU Chi-restraints excluded: chain d residue 10 LEU Chi-restraints excluded: chain d residue 21 SER Chi-restraints excluded: chain d residue 42 ASN Chi-restraints excluded: chain d residue 45 VAL Chi-restraints excluded: chain d residue 130 THR Chi-restraints excluded: chain d residue 151 MET Chi-restraints excluded: chain d residue 162 GLU Chi-restraints excluded: chain e residue 13 ASP Chi-restraints excluded: chain e residue 18 VAL Chi-restraints excluded: chain e residue 26 THR Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 64 VAL Chi-restraints excluded: chain e residue 71 ILE Chi-restraints excluded: chain e residue 78 PHE Chi-restraints excluded: chain e residue 96 VAL Chi-restraints excluded: chain f residue 22 LEU Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 103 ILE Chi-restraints excluded: chain g residue 31 LEU Chi-restraints excluded: chain g residue 45 ILE Chi-restraints excluded: chain g residue 46 GLU Chi-restraints excluded: chain g residue 77 VAL Chi-restraints excluded: chain i residue 22 THR Chi-restraints excluded: chain i residue 25 ILE Chi-restraints excluded: chain i residue 28 THR Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 56 HIS Chi-restraints excluded: chain i residue 58 ASN Chi-restraints excluded: chain j residue 19 VAL Chi-restraints excluded: chain j residue 22 ILE Chi-restraints excluded: chain j residue 31 VAL Chi-restraints excluded: chain j residue 35 ASP Chi-restraints excluded: chain j residue 41 LEU Chi-restraints excluded: chain j residue 58 THR Chi-restraints excluded: chain j residue 84 MET Chi-restraints excluded: chain j residue 96 ILE Chi-restraints excluded: chain k residue 17 LYS Chi-restraints excluded: chain k residue 33 CYS Chi-restraints excluded: chain k residue 38 THR Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 96 THR Chi-restraints excluded: chain l residue 41 ASP Chi-restraints excluded: chain l residue 88 LEU Chi-restraints excluded: chain l residue 101 THR Chi-restraints excluded: chain l residue 103 THR Chi-restraints excluded: chain m residue 26 LEU Chi-restraints excluded: chain m residue 32 ASP Chi-restraints excluded: chain m residue 49 THR Chi-restraints excluded: chain m residue 53 ASP Chi-restraints excluded: chain n residue 7 THR Chi-restraints excluded: chain n residue 19 ASN Chi-restraints excluded: chain n residue 24 THR Chi-restraints excluded: chain o residue 19 VAL Chi-restraints excluded: chain o residue 20 VAL Chi-restraints excluded: chain o residue 48 GLU Chi-restraints excluded: chain o residue 54 LEU Chi-restraints excluded: chain o residue 71 VAL Chi-restraints excluded: chain p residue 6 THR Chi-restraints excluded: chain p residue 19 SER Chi-restraints excluded: chain p residue 20 ILE Chi-restraints excluded: chain p residue 28 VAL Chi-restraints excluded: chain p residue 46 HIS Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 57 VAL Chi-restraints excluded: chain p residue 73 THR Chi-restraints excluded: chain p residue 78 VAL Chi-restraints excluded: chain q residue 28 LEU Chi-restraints excluded: chain q residue 44 THR Chi-restraints excluded: chain r residue 12 LEU Chi-restraints excluded: chain r residue 14 LEU Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain r residue 57 VAL Chi-restraints excluded: chain r residue 60 PHE Chi-restraints excluded: chain s residue 12 GLN Chi-restraints excluded: chain s residue 27 MET Chi-restraints excluded: chain s residue 29 THR Chi-restraints excluded: chain s residue 33 LYS Chi-restraints excluded: chain s residue 38 ILE Chi-restraints excluded: chain t residue 18 PHE Chi-restraints excluded: chain t residue 41 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 779 optimal weight: 7.9990 chunk 531 optimal weight: 6.9990 chunk 13 optimal weight: 20.0000 chunk 696 optimal weight: 10.0000 chunk 386 optimal weight: 4.9990 chunk 798 optimal weight: 0.9980 chunk 646 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 477 optimal weight: 5.9990 chunk 839 optimal weight: 10.0000 chunk 236 optimal weight: 0.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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** C 163 ASN ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 HIS ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 135 GLN I 88 ASN M 38 GLN N 40 GLN ** O 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 45 GLN ** W 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 102 ASN ** a 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 125 GLN j 39 ASN ** n 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 51 GLN ** s 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 81 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 152351 Z= 0.249 Angle : 0.622 15.096 228424 Z= 0.317 Chirality : 0.036 0.256 29268 Planarity : 0.004 0.057 11890 Dihedral : 24.227 179.317 77406 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 5.76 % Allowed : 21.88 % Favored : 72.36 % 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: 5236 helix: 0.37 (0.12), residues: 1808 sheet: -1.14 (0.17), residues: 895 loop : -2.12 (0.11), residues: 2533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP N 30 HIS 0.007 0.001 HIS i 15 PHE 0.031 0.002 PHE Z 38 TYR 0.030 0.002 TYR M 64 ARG 0.009 0.000 ARG f 101 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10472 Ramachandran restraints generated. 5236 Oldfield, 0 Emsley, 5236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10472 Ramachandran restraints generated. 5236 Oldfield, 0 Emsley, 5236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1116 residues out of total 4375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 866 time to evaluate : 5.894 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: C 124 PHE cc_start: 0.8917 (t80) cc_final: 0.8626 (t80) REVERT: C 137 LYS cc_start: 0.8372 (tttt) cc_final: 0.8152 (tttt) REVERT: C 168 ASP cc_start: 0.6518 (t0) cc_final: 0.6260 (t0) REVERT: D 6 TYR cc_start: 0.6524 (OUTLIER) cc_final: 0.5104 (t80) REVERT: D 7 TYR cc_start: 0.7440 (OUTLIER) cc_final: 0.7234 (p90) REVERT: D 153 ILE cc_start: 0.9063 (mt) cc_final: 0.8819 (pt) REVERT: D 166 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.6570 (mtp85) REVERT: G 8 LYS cc_start: 0.8378 (tmmt) cc_final: 0.8138 (tptm) REVERT: I 73 ASP cc_start: 0.8561 (p0) cc_final: 0.8360 (p0) REVERT: J 115 GLU cc_start: 0.7446 (pm20) cc_final: 0.7131 (pm20) REVERT: K 47 GLU cc_start: 0.7908 (tp30) cc_final: 0.7613 (tp30) REVERT: M 55 GLU cc_start: 0.7013 (mm-30) cc_final: 0.6562 (mm-30) REVERT: M 84 GLU cc_start: 0.7903 (pp20) cc_final: 0.7520 (pp20) REVERT: P 1 MET cc_start: 0.8317 (tpt) cc_final: 0.8071 (tpt) REVERT: P 2 TYR cc_start: 0.9057 (p90) cc_final: 0.8708 (p90) REVERT: P 10 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8488 (mtmm) REVERT: P 23 GLU cc_start: 0.8001 (pm20) cc_final: 0.7634 (pm20) REVERT: P 49 ILE cc_start: 0.8748 (mt) cc_final: 0.8452 (mt) REVERT: R 52 GLU cc_start: 0.8698 (mp0) cc_final: 0.8427 (mp0) REVERT: S 39 ASN cc_start: 0.8880 (OUTLIER) cc_final: 0.8648 (m-40) REVERT: S 45 GLN cc_start: 0.8453 (tp40) cc_final: 0.8226 (tp40) REVERT: Z 36 LYS cc_start: 0.7370 (mtpp) cc_final: 0.6937 (mmtt) REVERT: Z 49 LYS cc_start: 0.7654 (mttt) cc_final: 0.7122 (pttm) REVERT: AB 31 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8612 (tp) REVERT: a 20 ARG cc_start: 0.8646 (ttp-110) cc_final: 0.8358 (ttp-110) REVERT: a 94 ARG cc_start: 0.4352 (ttt-90) cc_final: 0.4113 (tpt170) REVERT: a 95 TRP cc_start: 0.7999 (t-100) cc_final: 0.7504 (t-100) REVERT: a 112 ARG cc_start: 0.7848 (tmt170) cc_final: 0.7220 (ttt180) REVERT: a 113 LEU cc_start: 0.7844 (mt) cc_final: 0.7598 (mt) REVERT: b 41 TYR cc_start: 0.8189 (t80) cc_final: 0.7552 (t80) REVERT: b 45 GLU cc_start: 0.6645 (pt0) cc_final: 0.6423 (pt0) REVERT: b 107 LYS cc_start: 0.8441 (mmtt) cc_final: 0.7943 (mmtt) REVERT: b 122 GLN cc_start: 0.8632 (mt0) cc_final: 0.8264 (mt0) REVERT: b 143 LEU cc_start: 0.7421 (tp) cc_final: 0.6947 (tp) REVERT: b 180 ASP cc_start: 0.6706 (m-30) cc_final: 0.6323 (m-30) REVERT: c 123 MET cc_start: 0.7239 (OUTLIER) cc_final: 0.7001 (ttm) REVERT: d 21 SER cc_start: 0.8462 (OUTLIER) cc_final: 0.8224 (m) REVERT: d 65 LYS cc_start: 0.9270 (mmtp) cc_final: 0.8849 (mptt) REVERT: e 24 ARG cc_start: 0.8266 (mtp85) cc_final: 0.7873 (mmp-170) REVERT: f 39 GLU cc_start: 0.7181 (tp30) cc_final: 0.6858 (pt0) REVERT: f 102 TRP cc_start: 0.7122 (m100) cc_final: 0.6910 (m-10) REVERT: g 9 MET cc_start: 0.9297 (ttp) cc_final: 0.9079 (tmm) REVERT: g 15 ASN cc_start: 0.7442 (m-40) cc_final: 0.6461 (p0) REVERT: g 42 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8339 (mm-30) REVERT: g 89 ASP cc_start: 0.7885 (m-30) cc_final: 0.7313 (t0) REVERT: g 113 ARG cc_start: 0.8785 (tpp-160) cc_final: 0.8584 (tpp-160) REVERT: h 56 MET cc_start: 0.6448 (tpt) cc_final: 0.6015 (tmm) REVERT: h 119 LYS cc_start: 0.7526 (mtmm) cc_final: 0.7081 (ptpp) REVERT: i 14 ASP cc_start: 0.7895 (t0) cc_final: 0.7666 (t0) REVERT: l 16 ILE cc_start: 0.5122 (mp) cc_final: 0.4624 (tp) REVERT: l 102 LYS cc_start: 0.8234 (tptm) cc_final: 0.7876 (tptp) REVERT: n 47 LYS cc_start: 0.8685 (mmmm) cc_final: 0.7832 (mtmt) REVERT: p 10 ARG cc_start: 0.8210 (ttm110) cc_final: 0.7891 (ttm-80) REVERT: q 59 LYS cc_start: 0.7759 (mmtt) cc_final: 0.7110 (mttt) REVERT: r 11 ASP cc_start: 0.7888 (t0) cc_final: 0.7633 (t70) REVERT: s 9 ARG cc_start: 0.9035 (mmt180) cc_final: 0.8819 (mmm-85) REVERT: s 25 SER cc_start: 0.8936 (t) cc_final: 0.8592 (p) REVERT: s 31 ILE cc_start: 0.9186 (mm) cc_final: 0.8891 (mt) REVERT: t 30 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7407 (mp0) outliers start: 250 outliers final: 191 residues processed: 1010 average time/residue: 1.1975 time to fit residues: 2153.7731 Evaluate side-chains 1008 residues out of total 4375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 808 time to evaluate : 5.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 123 LYS Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 156 ASN Chi-restraints excluded: chain C residue 165 HIS Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain D residue 5 ASP Chi-restraints excluded: chain D residue 6 TYR Chi-restraints excluded: chain D residue 7 TYR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 47 ILE Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 90 ASN Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 68 SER Chi-restraints excluded: chain J residue 81 ASP Chi-restraints excluded: chain J residue 107 PHE Chi-restraints excluded: chain J residue 117 THR Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 25 ASP Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 106 ASP Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 115 LEU Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain O residue 76 SER Chi-restraints excluded: chain O residue 99 VAL Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 10 LYS Chi-restraints excluded: chain P residue 102 SER Chi-restraints excluded: chain Q residue 53 SER Chi-restraints excluded: chain Q residue 71 VAL Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain R residue 7 LEU Chi-restraints excluded: chain R residue 10 VAL Chi-restraints excluded: chain R residue 57 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 39 ASN Chi-restraints excluded: chain S residue 98 ASN Chi-restraints excluded: chain T residue 5 ASN Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain U residue 26 SER Chi-restraints excluded: chain U residue 67 VAL Chi-restraints excluded: chain V residue 7 THR Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 36 GLU Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain AA residue 1 MET Chi-restraints excluded: chain AA residue 24 THR Chi-restraints excluded: chain AA residue 42 LEU Chi-restraints excluded: chain AA residue 44 VAL Chi-restraints excluded: chain AB residue 5 THR Chi-restraints excluded: chain AB residue 31 ILE Chi-restraints excluded: chain AB residue 50 SER Chi-restraints excluded: chain a residue 56 LEU Chi-restraints excluded: chain a residue 81 ASP Chi-restraints excluded: chain a residue 100 LEU Chi-restraints excluded: chain a residue 109 SER Chi-restraints excluded: chain a residue 170 ILE Chi-restraints excluded: chain a residue 178 LEU Chi-restraints excluded: chain a residue 196 ASP Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 69 THR Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain c residue 71 PHE Chi-restraints excluded: chain c residue 84 ASN Chi-restraints excluded: chain c residue 85 THR Chi-restraints excluded: chain c residue 92 LEU Chi-restraints excluded: chain c residue 123 MET Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 140 ASP Chi-restraints excluded: chain c residue 141 VAL Chi-restraints excluded: chain c residue 190 LEU Chi-restraints excluded: chain c residue 191 SER Chi-restraints excluded: chain c residue 201 GLU Chi-restraints excluded: chain d residue 10 LEU Chi-restraints excluded: chain d residue 21 SER Chi-restraints excluded: chain d residue 42 ASN Chi-restraints excluded: chain d residue 45 VAL Chi-restraints excluded: chain d residue 130 THR Chi-restraints excluded: chain d residue 151 MET Chi-restraints excluded: chain d residue 162 GLU Chi-restraints excluded: chain e residue 11 HIS Chi-restraints excluded: chain e residue 18 VAL Chi-restraints excluded: chain e residue 26 THR Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 62 MET Chi-restraints excluded: chain e residue 71 ILE Chi-restraints excluded: chain e residue 79 ARG Chi-restraints excluded: chain e residue 96 VAL Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 68 VAL Chi-restraints excluded: chain f residue 115 MET Chi-restraints excluded: chain g residue 31 LEU Chi-restraints excluded: chain g residue 45 ILE Chi-restraints excluded: chain g residue 46 GLU Chi-restraints excluded: chain g residue 77 VAL Chi-restraints excluded: chain h residue 115 VAL Chi-restraints excluded: chain i residue 24 GLU Chi-restraints excluded: chain i residue 25 ILE Chi-restraints excluded: chain i residue 28 THR Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 51 VAL Chi-restraints excluded: chain i residue 56 HIS Chi-restraints excluded: chain j residue 19 VAL Chi-restraints excluded: chain j residue 30 ILE Chi-restraints excluded: chain j residue 31 VAL Chi-restraints excluded: chain j residue 58 THR Chi-restraints excluded: chain k residue 33 CYS Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 96 THR Chi-restraints excluded: chain k residue 118 VAL Chi-restraints excluded: chain l residue 41 ASP Chi-restraints excluded: chain l residue 88 LEU Chi-restraints excluded: chain l residue 101 THR Chi-restraints excluded: chain l residue 103 THR Chi-restraints excluded: chain m residue 26 LEU Chi-restraints excluded: chain m residue 32 ASP Chi-restraints excluded: chain m residue 53 ASP Chi-restraints excluded: chain n residue 7 THR Chi-restraints excluded: chain n residue 24 THR Chi-restraints excluded: chain o residue 19 VAL Chi-restraints excluded: chain o residue 48 GLU Chi-restraints excluded: chain p residue 6 THR Chi-restraints excluded: chain p residue 20 ILE Chi-restraints excluded: chain p residue 46 HIS Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 57 VAL Chi-restraints excluded: chain p residue 67 SER Chi-restraints excluded: chain q residue 28 LEU Chi-restraints excluded: chain q residue 39 VAL Chi-restraints excluded: chain q residue 44 THR Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain r residue 57 VAL Chi-restraints excluded: chain r residue 60 PHE Chi-restraints excluded: chain s residue 12 GLN Chi-restraints excluded: chain s residue 19 HIS Chi-restraints excluded: chain s residue 27 MET Chi-restraints excluded: chain s residue 29 THR Chi-restraints excluded: chain s residue 33 LYS Chi-restraints excluded: chain t residue 18 PHE Chi-restraints excluded: chain t residue 30 GLU Chi-restraints excluded: chain t residue 41 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 314 optimal weight: 6.9990 chunk 842 optimal weight: 10.0000 chunk 184 optimal weight: 0.7980 chunk 549 optimal weight: 10.0000 chunk 230 optimal weight: 8.9990 chunk 936 optimal weight: 20.0000 chunk 777 optimal weight: 20.0000 chunk 433 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 309 optimal weight: 8.9990 chunk 491 optimal weight: 10.0000 overall best weight: 6.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 40 GLN O 51 GLN P 66 HIS ** P 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 7 HIS ** W 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 135 GLN c 195 ASN ** d 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 20 ASN ** h 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 125 GLN ** n 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 74 HIS ** s 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.131 152351 Z= 0.386 Angle : 0.719 16.720 228424 Z= 0.362 Chirality : 0.039 0.351 29268 Planarity : 0.005 0.081 11890 Dihedral : 24.292 179.285 77402 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 19.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.04 % Favored : 91.94 % Rotamer: Outliers : 6.86 % Allowed : 22.16 % Favored : 70.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.11), residues: 5236 helix: 0.27 (0.12), residues: 1799 sheet: -1.13 (0.17), residues: 901 loop : -2.14 (0.11), residues: 2536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP N 30 HIS 0.008 0.001 HIS i 15 PHE 0.029 0.002 PHE K 31 TYR 0.028 0.002 TYR M 64 ARG 0.006 0.001 ARG f 101 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10472 Ramachandran restraints generated. 5236 Oldfield, 0 Emsley, 5236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10472 Ramachandran restraints generated. 5236 Oldfield, 0 Emsley, 5236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1108 residues out of total 4375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 298 poor density : 810 time to evaluate : 5.966 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: A 86 ARG cc_start: 0.7269 (OUTLIER) cc_final: 0.6791 (mpt180) REVERT: C 168 ASP cc_start: 0.6562 (t0) cc_final: 0.6275 (t0) REVERT: D 6 TYR cc_start: 0.6405 (OUTLIER) cc_final: 0.5157 (t80) REVERT: D 7 TYR cc_start: 0.7595 (OUTLIER) cc_final: 0.7314 (p90) REVERT: D 153 ILE cc_start: 0.9051 (mt) cc_final: 0.8790 (pt) REVERT: G 8 LYS cc_start: 0.8403 (tmmt) cc_final: 0.8181 (tptm) REVERT: I 73 ASP cc_start: 0.8594 (p0) cc_final: 0.8390 (p0) REVERT: I 116 ILE cc_start: 0.9343 (OUTLIER) cc_final: 0.8900 (mt) REVERT: J 76 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7849 (tp30) REVERT: J 115 GLU cc_start: 0.7359 (pm20) cc_final: 0.7050 (pm20) REVERT: K 110 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8293 (tp30) REVERT: M 55 GLU cc_start: 0.7041 (mm-30) cc_final: 0.6592 (mm-30) REVERT: M 84 GLU cc_start: 0.7915 (pp20) cc_final: 0.7531 (pp20) REVERT: N 12 MET cc_start: 0.8357 (mtm) cc_final: 0.8037 (ttm) REVERT: N 38 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.7176 (ptp-170) REVERT: P 10 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8548 (mtmm) REVERT: P 49 ILE cc_start: 0.8788 (mt) cc_final: 0.8500 (mt) REVERT: S 9 GLU cc_start: 0.8518 (tp30) cc_final: 0.8301 (tp30) REVERT: S 45 GLN cc_start: 0.8493 (tp40) cc_final: 0.8186 (tp40) REVERT: Y 48 TYR cc_start: 0.8895 (t80) cc_final: 0.8038 (t80) REVERT: Z 31 GLU cc_start: 0.7370 (pm20) cc_final: 0.7153 (mp0) REVERT: Z 36 LYS cc_start: 0.7311 (mtpp) cc_final: 0.6879 (mmtt) REVERT: Z 49 LYS cc_start: 0.7757 (mttt) cc_final: 0.7157 (pttm) REVERT: AB 31 ILE cc_start: 0.8964 (OUTLIER) cc_final: 0.8686 (tp) REVERT: a 20 ARG cc_start: 0.8682 (ttp-110) cc_final: 0.8368 (ttp-110) REVERT: a 94 ARG cc_start: 0.4531 (tpt-90) cc_final: 0.4023 (tpt170) REVERT: a 95 TRP cc_start: 0.8106 (t-100) cc_final: 0.7691 (t-100) REVERT: a 112 ARG cc_start: 0.7862 (tmt170) cc_final: 0.7280 (ttt180) REVERT: a 113 LEU cc_start: 0.7839 (mt) cc_final: 0.7582 (mt) REVERT: a 207 ARG cc_start: 0.8422 (mtm110) cc_final: 0.7789 (ttp-170) REVERT: b 21 TRP cc_start: 0.7309 (p-90) cc_final: 0.7075 (p-90) REVERT: b 41 TYR cc_start: 0.8271 (t80) cc_final: 0.7662 (t80) REVERT: b 45 GLU cc_start: 0.6648 (pt0) cc_final: 0.6360 (pt0) REVERT: b 107 LYS cc_start: 0.8508 (mmtt) cc_final: 0.8182 (mmtt) REVERT: b 143 LEU cc_start: 0.7464 (tp) cc_final: 0.6952 (tp) REVERT: b 180 ASP cc_start: 0.6663 (m-30) cc_final: 0.6216 (m-30) REVERT: d 21 SER cc_start: 0.8536 (OUTLIER) cc_final: 0.8246 (m) REVERT: d 65 LYS cc_start: 0.9319 (mmtp) cc_final: 0.8907 (mptt) REVERT: e 24 ARG cc_start: 0.8277 (mtp85) cc_final: 0.7878 (mmp-170) REVERT: f 39 GLU cc_start: 0.7239 (tp30) cc_final: 0.6878 (pt0) REVERT: g 15 ASN cc_start: 0.7452 (m-40) cc_final: 0.6531 (p0) REVERT: g 42 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8333 (mm-30) REVERT: h 96 GLU cc_start: 0.8213 (tt0) cc_final: 0.7346 (mm-30) REVERT: h 119 LYS cc_start: 0.7482 (mtmm) cc_final: 0.7084 (ptpp) REVERT: i 49 PHE cc_start: 0.6806 (OUTLIER) cc_final: 0.4129 (p90) REVERT: k 71 HIS cc_start: 0.5250 (OUTLIER) cc_final: 0.4784 (t-90) REVERT: l 16 ILE cc_start: 0.5232 (mp) cc_final: 0.4808 (tp) REVERT: l 65 GLU cc_start: 0.5941 (OUTLIER) cc_final: 0.5630 (pt0) REVERT: l 102 LYS cc_start: 0.8198 (tptm) cc_final: 0.7853 (tptp) REVERT: n 47 LYS cc_start: 0.8754 (mmmm) cc_final: 0.7931 (mtmt) REVERT: p 10 ARG cc_start: 0.8227 (ttm110) cc_final: 0.7957 (ttm-80) REVERT: p 16 MET cc_start: 0.7443 (mmm) cc_final: 0.7132 (mmm) REVERT: q 59 LYS cc_start: 0.7822 (mmtt) cc_final: 0.7145 (mttt) REVERT: r 11 ASP cc_start: 0.7856 (t0) cc_final: 0.7569 (t70) REVERT: r 12 LEU cc_start: 0.5403 (OUTLIER) cc_final: 0.5192 (mt) REVERT: r 18 VAL cc_start: 0.4265 (p) cc_final: 0.3761 (p) REVERT: r 43 MET cc_start: 0.4719 (mmt) cc_final: 0.4354 (mpp) REVERT: s 9 ARG cc_start: 0.9126 (mmt180) cc_final: 0.8903 (mmm-85) REVERT: s 25 SER cc_start: 0.9035 (t) cc_final: 0.8697 (p) REVERT: s 31 ILE cc_start: 0.9272 (mm) cc_final: 0.8996 (mt) REVERT: t 30 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7352 (mp0) outliers start: 298 outliers final: 223 residues processed: 1006 average time/residue: 1.1558 time to fit residues: 2064.5226 Evaluate side-chains 1018 residues out of total 4375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 781 time to evaluate : 5.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 123 LYS Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 156 ASN Chi-restraints excluded: chain C residue 165 HIS Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain D residue 5 ASP Chi-restraints excluded: chain D residue 6 TYR Chi-restraints excluded: chain D residue 7 TYR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 47 ILE Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 84 CYS Chi-restraints excluded: chain I residue 90 ASN Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 116 ILE Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 68 SER Chi-restraints excluded: chain J residue 81 ASP Chi-restraints excluded: chain J residue 107 PHE Chi-restraints excluded: chain J residue 117 THR Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 25 ASP Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 106 ASP Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 115 LEU Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain O residue 99 VAL Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 10 LYS Chi-restraints excluded: chain Q residue 53 SER Chi-restraints excluded: chain Q residue 71 VAL Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain R residue 7 LEU Chi-restraints excluded: chain R residue 10 VAL Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain S residue 7 ASP Chi-restraints excluded: chain S residue 10 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 26 ASN Chi-restraints excluded: chain S residue 27 VAL Chi-restraints excluded: chain S residue 80 ASP Chi-restraints excluded: chain S residue 98 ASN Chi-restraints excluded: chain T residue 5 ASN Chi-restraints excluded: chain T residue 63 ILE Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain U residue 26 SER Chi-restraints excluded: chain U residue 39 THR Chi-restraints excluded: chain U residue 67 VAL Chi-restraints excluded: chain V residue 7 THR Chi-restraints excluded: chain V residue 29 LEU Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain W residue 29 ARG Chi-restraints excluded: chain X residue 4 ILE Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 36 GLU Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Z residue 12 SER Chi-restraints excluded: chain Z residue 42 VAL Chi-restraints excluded: chain AA residue 1 MET Chi-restraints excluded: chain AA residue 24 THR Chi-restraints excluded: chain AA residue 30 VAL Chi-restraints excluded: chain AA residue 42 LEU Chi-restraints excluded: chain AA residue 44 VAL Chi-restraints excluded: chain AB residue 5 THR Chi-restraints excluded: chain AB residue 31 ILE Chi-restraints excluded: chain AB residue 50 SER Chi-restraints excluded: chain AB residue 61 LEU Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 81 ASP Chi-restraints excluded: chain a residue 92 ASN Chi-restraints excluded: chain a residue 100 LEU Chi-restraints excluded: chain a residue 109 SER Chi-restraints excluded: chain a residue 170 ILE Chi-restraints excluded: chain a residue 178 LEU Chi-restraints excluded: chain a residue 196 ASP Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 69 THR Chi-restraints excluded: chain b residue 191 THR Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain c residue 71 PHE Chi-restraints excluded: chain c residue 84 ASN Chi-restraints excluded: chain c residue 92 LEU Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 141 VAL Chi-restraints excluded: chain c residue 190 LEU Chi-restraints excluded: chain c residue 191 SER Chi-restraints excluded: chain c residue 201 GLU Chi-restraints excluded: chain d residue 10 LEU Chi-restraints excluded: chain d residue 20 VAL Chi-restraints excluded: chain d residue 21 SER Chi-restraints excluded: chain d residue 42 ASN Chi-restraints excluded: chain d residue 45 VAL Chi-restraints excluded: chain d residue 130 THR Chi-restraints excluded: chain d residue 151 MET Chi-restraints excluded: chain d residue 162 GLU Chi-restraints excluded: chain e residue 11 HIS Chi-restraints excluded: chain e residue 13 ASP Chi-restraints excluded: chain e residue 26 THR Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 71 ILE Chi-restraints excluded: chain e residue 79 ARG Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain e residue 96 VAL Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 68 VAL Chi-restraints excluded: chain f residue 115 MET Chi-restraints excluded: chain g residue 31 LEU Chi-restraints excluded: chain g residue 33 VAL Chi-restraints excluded: chain g residue 45 ILE Chi-restraints excluded: chain g residue 46 GLU Chi-restraints excluded: chain g residue 50 VAL Chi-restraints excluded: chain g residue 79 ARG Chi-restraints excluded: chain g residue 89 ASP Chi-restraints excluded: chain h residue 115 VAL Chi-restraints excluded: chain i residue 22 THR Chi-restraints excluded: chain i residue 24 GLU Chi-restraints excluded: chain i residue 25 ILE Chi-restraints excluded: chain i residue 28 THR Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 49 PHE Chi-restraints excluded: chain i residue 51 VAL Chi-restraints excluded: chain i residue 56 HIS Chi-restraints excluded: chain i residue 58 ASN Chi-restraints excluded: chain j residue 19 VAL Chi-restraints excluded: chain j residue 26 PHE Chi-restraints excluded: chain j residue 27 ASN Chi-restraints excluded: chain j residue 30 ILE Chi-restraints excluded: chain j residue 31 VAL Chi-restraints excluded: chain j residue 58 THR Chi-restraints excluded: chain j residue 84 MET Chi-restraints excluded: chain k residue 33 CYS Chi-restraints excluded: chain k residue 38 THR Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 71 HIS Chi-restraints excluded: chain k residue 96 THR Chi-restraints excluded: chain k residue 118 VAL Chi-restraints excluded: chain l residue 8 ILE Chi-restraints excluded: chain l residue 41 ASP Chi-restraints excluded: chain l residue 65 GLU Chi-restraints excluded: chain l residue 88 LEU Chi-restraints excluded: chain l residue 101 THR Chi-restraints excluded: chain l residue 103 THR Chi-restraints excluded: chain m residue 5 MET Chi-restraints excluded: chain m residue 26 LEU Chi-restraints excluded: chain m residue 32 ASP Chi-restraints excluded: chain m residue 49 THR Chi-restraints excluded: chain m residue 53 ASP Chi-restraints excluded: chain n residue 7 THR Chi-restraints excluded: chain n residue 24 THR Chi-restraints excluded: chain o residue 19 VAL Chi-restraints excluded: chain o residue 71 VAL Chi-restraints excluded: chain p residue 6 THR Chi-restraints excluded: chain p residue 11 VAL Chi-restraints excluded: chain p residue 19 SER Chi-restraints excluded: chain p residue 46 HIS Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 57 VAL Chi-restraints excluded: chain p residue 67 SER Chi-restraints excluded: chain q residue 28 LEU Chi-restraints excluded: chain q residue 44 THR Chi-restraints excluded: chain r residue 12 LEU Chi-restraints excluded: chain r residue 14 LEU Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain r residue 57 VAL Chi-restraints excluded: chain r residue 60 PHE Chi-restraints excluded: chain s residue 12 GLN Chi-restraints excluded: chain s residue 19 HIS Chi-restraints excluded: chain s residue 27 MET Chi-restraints excluded: chain s residue 29 THR Chi-restraints excluded: chain s residue 33 LYS Chi-restraints excluded: chain t residue 18 PHE Chi-restraints excluded: chain t residue 30 GLU Chi-restraints excluded: chain t residue 41 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 902 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 533 optimal weight: 7.9990 chunk 683 optimal weight: 20.0000 chunk 529 optimal weight: 10.0000 chunk 788 optimal weight: 2.9990 chunk 522 optimal weight: 50.0000 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: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 HIS ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 GLN N 40 GLN O 51 GLN Q 7 HIS R 70 HIS ** W 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 65 GLN ** n 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.132 152351 Z= 0.415 Angle : 0.744 17.843 228424 Z= 0.375 Chirality : 0.041 0.274 29268 Planarity : 0.005 0.069 11890 Dihedral : 24.362 179.452 77402 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 20.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 7.12 % Allowed : 22.67 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.11), residues: 5236 helix: 0.13 (0.12), residues: 1801 sheet: -1.20 (0.17), residues: 897 loop : -2.16 (0.11), residues: 2538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.089 0.003 TRP N 30 HIS 0.009 0.001 HIS i 15 PHE 0.026 0.002 PHE Z 38 TYR 0.032 0.002 TYR M 64 ARG 0.012 0.001 ARG Z 43 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10472 Ramachandran restraints generated. 5236 Oldfield, 0 Emsley, 5236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10472 Ramachandran restraints generated. 5236 Oldfield, 0 Emsley, 5236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1104 residues out of total 4375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 309 poor density : 795 time to evaluate : 5.934 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: A 86 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.6814 (mpt180) REVERT: C 168 ASP cc_start: 0.6552 (t0) cc_final: 0.6260 (t0) REVERT: D 6 TYR cc_start: 0.6343 (OUTLIER) cc_final: 0.5310 (t80) REVERT: D 7 TYR cc_start: 0.7593 (OUTLIER) cc_final: 0.7279 (p90) REVERT: D 127 TYR cc_start: 0.7316 (t80) cc_final: 0.6195 (t80) REVERT: D 153 ILE cc_start: 0.9099 (mt) cc_final: 0.8818 (pt) REVERT: D 166 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.6860 (mtp85) REVERT: G 8 LYS cc_start: 0.8373 (tmmt) cc_final: 0.8162 (tptm) REVERT: I 113 MET cc_start: 0.7874 (mmm) cc_final: 0.7665 (mmm) REVERT: I 116 ILE cc_start: 0.9274 (OUTLIER) cc_final: 0.8991 (mt) REVERT: J 115 GLU cc_start: 0.7450 (pm20) cc_final: 0.7151 (pm20) REVERT: K 53 MET cc_start: 0.8523 (mmp) cc_final: 0.8320 (mmp) REVERT: K 110 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8311 (tp30) REVERT: M 25 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.8799 (ptm-80) REVERT: M 55 GLU cc_start: 0.7056 (mm-30) cc_final: 0.6617 (mm-30) REVERT: M 84 GLU cc_start: 0.7925 (pp20) cc_final: 0.7540 (pp20) REVERT: N 12 MET cc_start: 0.8390 (mtm) cc_final: 0.8093 (ttm) REVERT: N 30 TRP cc_start: 0.8217 (m-90) cc_final: 0.7785 (m-90) REVERT: N 38 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.7187 (ptp-170) REVERT: N 114 ASN cc_start: 0.5195 (OUTLIER) cc_final: 0.4833 (t0) REVERT: P 10 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8562 (mtmm) REVERT: P 49 ILE cc_start: 0.8797 (mt) cc_final: 0.8508 (mt) REVERT: S 45 GLN cc_start: 0.8495 (tp40) cc_final: 0.8218 (tp40) REVERT: Z 24 LYS cc_start: 0.7207 (mmtm) cc_final: 0.6997 (mmtm) REVERT: Z 31 GLU cc_start: 0.7316 (pm20) cc_final: 0.7104 (mp0) REVERT: Z 36 LYS cc_start: 0.7279 (mtpp) cc_final: 0.6819 (mmtt) REVERT: Z 43 ARG cc_start: 0.7468 (mtt180) cc_final: 0.7143 (mmt180) REVERT: Z 49 LYS cc_start: 0.7812 (mttt) cc_final: 0.7192 (pttm) REVERT: AB 31 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8722 (tp) REVERT: a 26 MET cc_start: 0.8240 (ptm) cc_final: 0.8023 (ptt) REVERT: a 94 ARG cc_start: 0.4519 (tpt-90) cc_final: 0.4007 (tpt170) REVERT: a 95 TRP cc_start: 0.8148 (t-100) cc_final: 0.7629 (t-100) REVERT: a 112 ARG cc_start: 0.7898 (tmt170) cc_final: 0.7286 (ttt180) REVERT: a 113 LEU cc_start: 0.7819 (mt) cc_final: 0.7557 (mt) REVERT: b 41 TYR cc_start: 0.8307 (t80) cc_final: 0.7702 (t80) REVERT: b 45 GLU cc_start: 0.6813 (pt0) cc_final: 0.6581 (pt0) REVERT: b 107 LYS cc_start: 0.8579 (mmtt) cc_final: 0.8284 (mmtt) REVERT: b 143 LEU cc_start: 0.7483 (tp) cc_final: 0.7058 (tp) REVERT: b 180 ASP cc_start: 0.6669 (m-30) cc_final: 0.6209 (m-30) REVERT: d 21 SER cc_start: 0.8550 (OUTLIER) cc_final: 0.8275 (m) REVERT: d 65 LYS cc_start: 0.9309 (mmtp) cc_final: 0.8904 (mptt) REVERT: e 73 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7550 (mp0) REVERT: f 39 GLU cc_start: 0.7343 (tp30) cc_final: 0.6952 (pt0) REVERT: g 15 ASN cc_start: 0.7370 (m-40) cc_final: 0.6447 (p0) REVERT: g 42 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8316 (mm-30) REVERT: g 123 GLU cc_start: 0.6975 (tt0) cc_final: 0.6627 (tt0) REVERT: h 96 GLU cc_start: 0.8235 (tt0) cc_final: 0.7397 (mm-30) REVERT: h 105 ARG cc_start: 0.6209 (OUTLIER) cc_final: 0.5855 (tpm170) REVERT: i 49 PHE cc_start: 0.6684 (OUTLIER) cc_final: 0.4174 (p90) REVERT: k 60 PHE cc_start: 0.6842 (OUTLIER) cc_final: 0.5970 (m-80) REVERT: k 71 HIS cc_start: 0.5322 (OUTLIER) cc_final: 0.4825 (t-90) REVERT: k 101 LEU cc_start: 0.8259 (pt) cc_final: 0.8029 (pt) REVERT: l 16 ILE cc_start: 0.5550 (mp) cc_final: 0.5197 (tp) REVERT: l 65 GLU cc_start: 0.6071 (OUTLIER) cc_final: 0.5654 (pt0) REVERT: l 102 LYS cc_start: 0.8285 (tptm) cc_final: 0.7931 (tptp) REVERT: n 47 LYS cc_start: 0.8766 (mmmm) cc_final: 0.7948 (mtmt) REVERT: n 83 ARG cc_start: 0.7843 (ttm170) cc_final: 0.7599 (ttp-110) REVERT: o 17 TYR cc_start: 0.8375 (m-10) cc_final: 0.8105 (m-80) REVERT: p 10 ARG cc_start: 0.8245 (ttm110) cc_final: 0.7991 (ttm-80) REVERT: q 59 LYS cc_start: 0.7787 (mmtt) cc_final: 0.7089 (mttt) REVERT: r 12 LEU cc_start: 0.5397 (OUTLIER) cc_final: 0.5115 (mt) REVERT: s 9 ARG cc_start: 0.9162 (mmt180) cc_final: 0.8926 (mmm-85) REVERT: s 25 SER cc_start: 0.9081 (t) cc_final: 0.8741 (p) REVERT: s 31 ILE cc_start: 0.9283 (mm) cc_final: 0.9034 (mt) REVERT: t 30 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7420 (mp0) outliers start: 309 outliers final: 238 residues processed: 1001 average time/residue: 1.1357 time to fit residues: 2020.3390 Evaluate side-chains 1035 residues out of total 4375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 778 time to evaluate : 5.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ARG Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 123 LYS Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 156 ASN Chi-restraints excluded: chain C residue 165 HIS Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain D residue 5 ASP Chi-restraints excluded: chain D residue 6 TYR Chi-restraints excluded: chain D residue 7 TYR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 47 ILE Chi-restraints excluded: chain I residue 62 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 90 ASN Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 116 ILE Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 68 SER Chi-restraints excluded: chain J residue 81 ASP Chi-restraints excluded: chain J residue 107 PHE Chi-restraints excluded: chain J residue 117 THR Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 25 ASP Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 106 ASP Chi-restraints excluded: chain L residue 113 ILE Chi-restraints excluded: chain M residue 25 ARG Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 115 LEU Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain N residue 114 ASN Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain O residue 99 VAL Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 10 LYS Chi-restraints excluded: chain P residue 60 LYS Chi-restraints excluded: chain P residue 102 SER Chi-restraints excluded: chain Q residue 45 VAL Chi-restraints excluded: chain Q residue 53 SER Chi-restraints excluded: chain Q residue 71 VAL Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain Q residue 77 ASP Chi-restraints excluded: chain R residue 7 LEU Chi-restraints excluded: chain R residue 10 VAL Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain S residue 7 ASP Chi-restraints excluded: chain S residue 10 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 26 ASN Chi-restraints excluded: chain S residue 27 VAL Chi-restraints excluded: chain S residue 80 ASP Chi-restraints excluded: chain S residue 98 ASN Chi-restraints excluded: chain T residue 5 ASN Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain U residue 26 SER Chi-restraints excluded: chain U residue 39 THR Chi-restraints excluded: chain U residue 67 VAL Chi-restraints excluded: chain V residue 7 THR Chi-restraints excluded: chain V residue 29 LEU Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain W residue 29 ARG Chi-restraints excluded: chain X residue 4 ILE Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 36 GLU Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Z residue 8 ILE Chi-restraints excluded: chain Z residue 10 LEU Chi-restraints excluded: chain Z residue 12 SER Chi-restraints excluded: chain AA residue 1 MET Chi-restraints excluded: chain AA residue 24 THR Chi-restraints excluded: chain AA residue 30 VAL Chi-restraints excluded: chain AA residue 42 LEU Chi-restraints excluded: chain AA residue 44 VAL Chi-restraints excluded: chain AB residue 5 THR Chi-restraints excluded: chain AB residue 31 ILE Chi-restraints excluded: chain AB residue 50 SER Chi-restraints excluded: chain AB residue 61 LEU Chi-restraints excluded: chain a residue 30 ILE Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 51 GLU Chi-restraints excluded: chain a residue 81 ASP Chi-restraints excluded: chain a residue 92 ASN Chi-restraints excluded: chain a residue 109 SER Chi-restraints excluded: chain a residue 170 ILE Chi-restraints excluded: chain a residue 178 LEU Chi-restraints excluded: chain a residue 196 ASP Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 69 THR Chi-restraints excluded: chain b residue 90 VAL Chi-restraints excluded: chain b residue 191 THR Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain c residue 71 PHE Chi-restraints excluded: chain c residue 84 ASN Chi-restraints excluded: chain c residue 85 THR Chi-restraints excluded: chain c residue 92 LEU Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 141 VAL Chi-restraints excluded: chain c residue 169 TRP Chi-restraints excluded: chain c residue 190 LEU Chi-restraints excluded: chain c residue 191 SER Chi-restraints excluded: chain d residue 20 VAL Chi-restraints excluded: chain d residue 21 SER Chi-restraints excluded: chain d residue 42 ASN Chi-restraints excluded: chain d residue 45 VAL Chi-restraints excluded: chain d residue 130 THR Chi-restraints excluded: chain d residue 151 MET Chi-restraints excluded: chain d residue 162 GLU Chi-restraints excluded: chain e residue 13 ASP Chi-restraints excluded: chain e residue 26 THR Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 62 MET Chi-restraints excluded: chain e residue 79 ARG Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain e residue 96 VAL Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 68 VAL Chi-restraints excluded: chain f residue 115 MET Chi-restraints excluded: chain g residue 31 LEU Chi-restraints excluded: chain g residue 33 VAL Chi-restraints excluded: chain g residue 45 ILE Chi-restraints excluded: chain g residue 46 GLU Chi-restraints excluded: chain g residue 50 VAL Chi-restraints excluded: chain g residue 79 ARG Chi-restraints excluded: chain g residue 89 ASP Chi-restraints excluded: chain h residue 105 ARG Chi-restraints excluded: chain h residue 115 VAL Chi-restraints excluded: chain i residue 14 ASP Chi-restraints excluded: chain i residue 22 THR Chi-restraints excluded: chain i residue 24 GLU Chi-restraints excluded: chain i residue 25 ILE Chi-restraints excluded: chain i residue 28 THR Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 49 PHE Chi-restraints excluded: chain i residue 56 HIS Chi-restraints excluded: chain j residue 19 VAL Chi-restraints excluded: chain j residue 26 PHE Chi-restraints excluded: chain j residue 27 ASN Chi-restraints excluded: chain j residue 30 ILE Chi-restraints excluded: chain j residue 31 VAL Chi-restraints excluded: chain j residue 58 THR Chi-restraints excluded: chain j residue 84 MET Chi-restraints excluded: chain k residue 33 CYS Chi-restraints excluded: chain k residue 38 THR Chi-restraints excluded: chain k residue 60 PHE Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 71 HIS Chi-restraints excluded: chain k residue 96 THR Chi-restraints excluded: chain k residue 118 VAL Chi-restraints excluded: chain l residue 8 ILE Chi-restraints excluded: chain l residue 41 ASP Chi-restraints excluded: chain l residue 65 GLU Chi-restraints excluded: chain l residue 88 LEU Chi-restraints excluded: chain l residue 101 THR Chi-restraints excluded: chain l residue 103 THR Chi-restraints excluded: chain m residue 26 LEU Chi-restraints excluded: chain m residue 32 ASP Chi-restraints excluded: chain m residue 49 THR Chi-restraints excluded: chain m residue 53 ASP Chi-restraints excluded: chain n residue 7 THR Chi-restraints excluded: chain n residue 19 ASN Chi-restraints excluded: chain n residue 24 THR Chi-restraints excluded: chain o residue 19 VAL Chi-restraints excluded: chain o residue 20 VAL Chi-restraints excluded: chain o residue 36 VAL Chi-restraints excluded: chain o residue 54 LEU Chi-restraints excluded: chain o residue 71 VAL Chi-restraints excluded: chain p residue 6 THR Chi-restraints excluded: chain p residue 11 VAL Chi-restraints excluded: chain p residue 19 SER Chi-restraints excluded: chain p residue 28 VAL Chi-restraints excluded: chain p residue 46 HIS Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 57 VAL Chi-restraints excluded: chain p residue 67 SER Chi-restraints excluded: chain p residue 73 THR Chi-restraints excluded: chain p residue 78 VAL Chi-restraints excluded: chain q residue 28 LEU Chi-restraints excluded: chain q residue 39 VAL Chi-restraints excluded: chain q residue 44 THR Chi-restraints excluded: chain r residue 12 LEU Chi-restraints excluded: chain r residue 14 LEU Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain r residue 57 VAL Chi-restraints excluded: chain r residue 60 PHE Chi-restraints excluded: chain s residue 12 GLN Chi-restraints excluded: chain s residue 26 MET Chi-restraints excluded: chain s residue 27 MET Chi-restraints excluded: chain s residue 29 THR Chi-restraints excluded: chain s residue 33 LYS Chi-restraints excluded: chain t residue 18 PHE Chi-restraints excluded: chain t residue 30 GLU Chi-restraints excluded: chain t residue 41 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 577 optimal weight: 7.9990 chunk 372 optimal weight: 5.9990 chunk 557 optimal weight: 8.9990 chunk 281 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 180 optimal weight: 0.9980 chunk 593 optimal weight: 10.0000 chunk 635 optimal weight: 5.9990 chunk 461 optimal weight: 20.0000 chunk 86 optimal weight: 2.9990 chunk 733 optimal weight: 7.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 GLN M 43 ASN N 40 GLN N 74 GLN ** O 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 7 HIS R 48 GLN ** W 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 38 HIS ** a 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 46 GLN h 125 GLN ** m 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 152351 Z= 0.194 Angle : 0.593 18.634 228424 Z= 0.300 Chirality : 0.034 0.304 29268 Planarity : 0.004 0.053 11890 Dihedral : 24.178 179.567 77402 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 5.30 % Allowed : 24.67 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.11), residues: 5236 helix: 0.54 (0.12), residues: 1820 sheet: -0.96 (0.18), residues: 872 loop : -1.95 (0.12), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP N 30 HIS 0.006 0.001 HIS i 15 PHE 0.023 0.002 PHE Z 38 TYR 0.029 0.002 TYR M 64 ARG 0.008 0.000 ARG E 169 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10472 Ramachandran restraints generated. 5236 Oldfield, 0 Emsley, 5236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10472 Ramachandran restraints generated. 5236 Oldfield, 0 Emsley, 5236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1070 residues out of total 4375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 840 time to evaluate : 5.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 124 PHE cc_start: 0.8818 (t80) cc_final: 0.8486 (t80) REVERT: C 137 LYS cc_start: 0.8346 (tttt) cc_final: 0.8071 (tttt) REVERT: C 168 ASP cc_start: 0.6572 (t0) cc_final: 0.6338 (t0) REVERT: C 188 MET cc_start: 0.8405 (ttt) cc_final: 0.8199 (ttt) REVERT: D 6 TYR cc_start: 0.6481 (OUTLIER) cc_final: 0.5132 (t80) REVERT: D 153 ILE cc_start: 0.9039 (mt) cc_final: 0.8790 (pt) REVERT: G 7 ASP cc_start: 0.7535 (p0) cc_final: 0.6975 (p0) REVERT: G 8 LYS cc_start: 0.8360 (tmmt) cc_final: 0.8113 (tptm) REVERT: G 19 VAL cc_start: 0.7938 (t) cc_final: 0.7497 (t) REVERT: G 35 LYS cc_start: 0.8071 (mmtt) cc_final: 0.7620 (mmtt) REVERT: I 116 ILE cc_start: 0.9266 (OUTLIER) cc_final: 0.8975 (mt) REVERT: J 115 GLU cc_start: 0.7540 (pm20) cc_final: 0.7231 (pm20) REVERT: M 55 GLU cc_start: 0.6871 (mm-30) cc_final: 0.6463 (mm-30) REVERT: M 84 GLU cc_start: 0.7938 (pp20) cc_final: 0.7613 (pp20) REVERT: N 12 MET cc_start: 0.8291 (mtm) cc_final: 0.8052 (ttm) REVERT: N 38 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.7182 (ptp-170) REVERT: N 114 ASN cc_start: 0.5330 (OUTLIER) cc_final: 0.4917 (t0) REVERT: P 1 MET cc_start: 0.8531 (tpt) cc_final: 0.7623 (tpt) REVERT: S 45 GLN cc_start: 0.8469 (tp40) cc_final: 0.8236 (tp40) REVERT: Z 43 ARG cc_start: 0.7433 (mtt180) cc_final: 0.7232 (mmt90) REVERT: Z 49 LYS cc_start: 0.7727 (mttt) cc_final: 0.7140 (pttm) REVERT: AB 31 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8588 (tp) REVERT: a 20 ARG cc_start: 0.8564 (ttp-110) cc_final: 0.8311 (ttp-110) REVERT: a 94 ARG cc_start: 0.4425 (tpt-90) cc_final: 0.4169 (tpt-90) REVERT: a 95 TRP cc_start: 0.8129 (t-100) cc_final: 0.7740 (t-100) REVERT: a 112 ARG cc_start: 0.7869 (tmt170) cc_final: 0.7277 (ttt180) REVERT: b 41 TYR cc_start: 0.8277 (t80) cc_final: 0.7610 (t80) REVERT: b 45 GLU cc_start: 0.6716 (pt0) cc_final: 0.6501 (pt0) REVERT: b 107 LYS cc_start: 0.8578 (mmtt) cc_final: 0.8280 (mmtt) REVERT: b 143 LEU cc_start: 0.7392 (tp) cc_final: 0.6966 (tp) REVERT: b 180 ASP cc_start: 0.6759 (m-30) cc_final: 0.6353 (m-30) REVERT: d 65 LYS cc_start: 0.9239 (mmtp) cc_final: 0.8790 (mptt) REVERT: e 73 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7593 (mp0) REVERT: f 39 GLU cc_start: 0.7419 (tp30) cc_final: 0.6844 (pt0) REVERT: f 102 TRP cc_start: 0.6905 (m-10) cc_final: 0.6574 (m100) REVERT: g 15 ASN cc_start: 0.6969 (m-40) cc_final: 0.6239 (p0) REVERT: g 42 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8402 (mm-30) REVERT: h 41 GLU cc_start: 0.5253 (pm20) cc_final: 0.4419 (pm20) REVERT: h 96 GLU cc_start: 0.8219 (tt0) cc_final: 0.7328 (mm-30) REVERT: l 16 ILE cc_start: 0.5630 (mp) cc_final: 0.5286 (tp) REVERT: l 102 LYS cc_start: 0.8385 (tptm) cc_final: 0.8022 (tptp) REVERT: n 47 LYS cc_start: 0.8694 (mmmm) cc_final: 0.7883 (mtmt) REVERT: o 17 TYR cc_start: 0.8230 (m-10) cc_final: 0.7908 (m-80) REVERT: p 10 ARG cc_start: 0.8104 (ttm110) cc_final: 0.7824 (ttm-80) REVERT: q 59 LYS cc_start: 0.7702 (mmtt) cc_final: 0.7047 (mttt) REVERT: r 60 PHE cc_start: 0.6540 (OUTLIER) cc_final: 0.6288 (t80) REVERT: s 9 ARG cc_start: 0.9063 (mmt180) cc_final: 0.8847 (mmm-85) REVERT: s 25 SER cc_start: 0.8874 (t) cc_final: 0.8490 (p) outliers start: 230 outliers final: 182 residues processed: 990 average time/residue: 1.2528 time to fit residues: 2215.2484 Evaluate side-chains 981 residues out of total 4375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 793 time to evaluate : 5.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 123 LYS Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 156 ASN Chi-restraints excluded: chain C residue 165 HIS Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain D residue 5 ASP Chi-restraints excluded: chain D residue 6 TYR Chi-restraints excluded: chain D residue 7 TYR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 47 ILE Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 90 ASN Chi-restraints excluded: chain I residue 116 ILE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 68 SER Chi-restraints excluded: chain J residue 81 ASP Chi-restraints excluded: chain J residue 107 PHE Chi-restraints excluded: chain J residue 117 THR Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 25 ASP Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 113 ILE Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 115 LEU Chi-restraints excluded: chain M residue 116 GLN Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 67 GLU Chi-restraints excluded: chain N residue 114 ASN Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain O residue 99 VAL Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 85 LYS Chi-restraints excluded: chain Q residue 53 SER Chi-restraints excluded: chain Q residue 71 VAL Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain Q residue 77 ASP Chi-restraints excluded: chain R residue 7 LEU Chi-restraints excluded: chain R residue 10 VAL Chi-restraints excluded: chain R residue 57 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 T residue 5 ASN Chi-restraints excluded: chain T residue 63 ILE Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain U residue 26 SER Chi-restraints excluded: chain U residue 67 VAL Chi-restraints excluded: chain V residue 7 THR Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 36 GLU Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Z residue 8 ILE Chi-restraints excluded: chain Z residue 46 VAL Chi-restraints excluded: chain AA residue 1 MET Chi-restraints excluded: chain AA residue 24 THR Chi-restraints excluded: chain AA residue 42 LEU Chi-restraints excluded: chain AB residue 5 THR Chi-restraints excluded: chain AB residue 31 ILE Chi-restraints excluded: chain AB residue 50 SER Chi-restraints excluded: chain AB residue 61 LEU Chi-restraints excluded: chain a residue 30 ILE Chi-restraints excluded: chain a residue 38 HIS Chi-restraints excluded: chain a residue 81 ASP Chi-restraints excluded: chain a residue 92 ASN Chi-restraints excluded: chain a residue 100 LEU Chi-restraints excluded: chain a residue 109 SER Chi-restraints excluded: chain a residue 178 LEU Chi-restraints excluded: chain a residue 196 ASP Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain c residue 71 PHE Chi-restraints excluded: chain c residue 85 THR Chi-restraints excluded: chain c residue 92 LEU Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 140 ASP Chi-restraints excluded: chain c residue 141 VAL Chi-restraints excluded: chain c residue 190 LEU Chi-restraints excluded: chain c residue 191 SER Chi-restraints excluded: chain d residue 42 ASN Chi-restraints excluded: chain d residue 45 VAL Chi-restraints excluded: chain d residue 151 MET Chi-restraints excluded: chain d residue 162 GLU Chi-restraints excluded: chain e residue 11 HIS Chi-restraints excluded: chain e residue 18 VAL Chi-restraints excluded: chain e residue 26 THR Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 70 VAL Chi-restraints excluded: chain e residue 79 ARG Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain e residue 96 VAL Chi-restraints excluded: chain f residue 22 LEU Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 68 VAL Chi-restraints excluded: chain f residue 115 MET Chi-restraints excluded: chain g residue 31 LEU Chi-restraints excluded: chain g residue 33 VAL Chi-restraints excluded: chain g residue 45 ILE Chi-restraints excluded: chain g residue 46 GLU Chi-restraints excluded: chain g residue 111 THR Chi-restraints excluded: chain h residue 115 VAL Chi-restraints excluded: chain i residue 28 THR Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 56 HIS Chi-restraints excluded: chain i residue 58 ASN Chi-restraints excluded: chain j residue 27 ASN Chi-restraints excluded: chain j residue 30 ILE Chi-restraints excluded: chain j residue 31 VAL Chi-restraints excluded: chain j residue 58 THR Chi-restraints excluded: chain k residue 33 CYS Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 76 HIS Chi-restraints excluded: chain k residue 96 THR Chi-restraints excluded: chain k residue 118 VAL Chi-restraints excluded: chain l residue 8 ILE Chi-restraints excluded: chain l residue 41 ASP Chi-restraints excluded: chain l residue 88 LEU Chi-restraints excluded: chain l residue 101 THR Chi-restraints excluded: chain l residue 103 THR Chi-restraints excluded: chain m residue 49 THR Chi-restraints excluded: chain m residue 53 ASP Chi-restraints excluded: chain n residue 7 THR Chi-restraints excluded: chain n residue 19 ASN Chi-restraints excluded: chain n residue 32 THR Chi-restraints excluded: chain o residue 19 VAL Chi-restraints excluded: chain o residue 20 VAL Chi-restraints excluded: chain p residue 6 THR Chi-restraints excluded: chain p residue 46 HIS Chi-restraints excluded: chain p residue 57 VAL Chi-restraints excluded: chain p residue 67 SER Chi-restraints excluded: chain p residue 78 VAL Chi-restraints excluded: chain q residue 28 LEU Chi-restraints excluded: chain q residue 44 THR Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain r residue 57 VAL Chi-restraints excluded: chain r residue 60 PHE Chi-restraints excluded: chain s residue 12 GLN Chi-restraints excluded: chain s residue 27 MET Chi-restraints excluded: chain s residue 29 THR Chi-restraints excluded: chain s residue 33 LYS Chi-restraints excluded: chain t residue 18 PHE Chi-restraints excluded: chain t residue 41 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 848 optimal weight: 10.0000 chunk 893 optimal weight: 10.0000 chunk 815 optimal weight: 10.0000 chunk 869 optimal weight: 10.0000 chunk 523 optimal weight: 40.0000 chunk 378 optimal weight: 10.0000 chunk 682 optimal weight: 10.0000 chunk 266 optimal weight: 3.9990 chunk 785 optimal weight: 7.9990 chunk 822 optimal weight: 20.0000 chunk 866 optimal weight: 20.0000 overall best weight: 8.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 142 GLN G 20 ASN H 135 GLN ** H 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 40 GLN N 74 GLN O 51 GLN ** O 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 48 GLN ** W 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 30 ASN ** q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.146 152351 Z= 0.480 Angle : 0.791 19.139 228424 Z= 0.396 Chirality : 0.043 0.284 29268 Planarity : 0.006 0.076 11890 Dihedral : 24.358 178.190 77402 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 21.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 6.08 % Allowed : 24.35 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.11), residues: 5236 helix: 0.12 (0.12), residues: 1800 sheet: -1.13 (0.17), residues: 913 loop : -2.11 (0.12), residues: 2523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.111 0.003 TRP N 30 HIS 0.033 0.002 HIS a 38 PHE 0.032 0.002 PHE D 19 TYR 0.035 0.002 TYR c 134 ARG 0.008 0.001 ARG Z 43 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10472 Ramachandran restraints generated. 5236 Oldfield, 0 Emsley, 5236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10472 Ramachandran restraints generated. 5236 Oldfield, 0 Emsley, 5236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1041 residues out of total 4375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 264 poor density : 777 time to evaluate : 5.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 168 ASP cc_start: 0.6577 (t0) cc_final: 0.6268 (t0) REVERT: D 6 TYR cc_start: 0.6358 (OUTLIER) cc_final: 0.5321 (t80) REVERT: D 7 TYR cc_start: 0.7648 (OUTLIER) cc_final: 0.7329 (p90) REVERT: D 127 TYR cc_start: 0.7542 (t80) cc_final: 0.7202 (t80) REVERT: D 153 ILE cc_start: 0.9103 (mt) cc_final: 0.8852 (pt) REVERT: D 166 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.6799 (mtp85) REVERT: G 8 LYS cc_start: 0.8400 (tmmt) cc_final: 0.8180 (tptm) REVERT: G 20 ASN cc_start: 0.7341 (OUTLIER) cc_final: 0.6911 (m110) REVERT: I 116 ILE cc_start: 0.9297 (OUTLIER) cc_final: 0.9005 (mt) REVERT: J 115 GLU cc_start: 0.7435 (pm20) cc_final: 0.7164 (pm20) REVERT: M 25 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.8777 (ptm-80) REVERT: M 55 GLU cc_start: 0.7025 (mm-30) cc_final: 0.6613 (mm-30) REVERT: M 84 GLU cc_start: 0.7934 (pp20) cc_final: 0.7565 (pp20) REVERT: M 100 HIS cc_start: 0.7185 (OUTLIER) cc_final: 0.6904 (t-90) REVERT: N 12 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.8079 (ttm) REVERT: N 38 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7161 (ptp-170) REVERT: N 114 ASN cc_start: 0.5258 (OUTLIER) cc_final: 0.4635 (t0) REVERT: P 10 LYS cc_start: 0.9133 (OUTLIER) cc_final: 0.8587 (mtmm) REVERT: P 49 ILE cc_start: 0.8783 (mt) cc_final: 0.8513 (mt) REVERT: S 45 GLN cc_start: 0.8551 (tp40) cc_final: 0.8250 (tp40) REVERT: Z 43 ARG cc_start: 0.7871 (mtt180) cc_final: 0.7499 (mmt180) REVERT: Z 49 LYS cc_start: 0.7995 (mttt) cc_final: 0.7339 (pttm) REVERT: a 38 HIS cc_start: 0.7793 (OUTLIER) cc_final: 0.7044 (m-70) REVERT: a 94 ARG cc_start: 0.4484 (tpt-90) cc_final: 0.4156 (tpt-90) REVERT: a 95 TRP cc_start: 0.8177 (t-100) cc_final: 0.7634 (t-100) REVERT: a 112 ARG cc_start: 0.7957 (tmt170) cc_final: 0.7314 (ttt180) REVERT: b 41 TYR cc_start: 0.8306 (t80) cc_final: 0.7712 (t80) REVERT: b 45 GLU cc_start: 0.6806 (pt0) cc_final: 0.6563 (pt0) REVERT: b 107 LYS cc_start: 0.8606 (mmtt) cc_final: 0.8334 (mmtt) REVERT: b 109 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7468 (mt-10) REVERT: b 143 LEU cc_start: 0.7474 (tp) cc_final: 0.7007 (tp) REVERT: b 180 ASP cc_start: 0.6743 (m-30) cc_final: 0.6318 (m-30) REVERT: d 65 LYS cc_start: 0.9314 (mmtp) cc_final: 0.8904 (mptt) REVERT: e 73 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7684 (mp0) REVERT: f 39 GLU cc_start: 0.7410 (tp30) cc_final: 0.7075 (pt0) REVERT: g 15 ASN cc_start: 0.7226 (m-40) cc_final: 0.6334 (p0) REVERT: g 42 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8248 (mm-30) REVERT: h 96 GLU cc_start: 0.8308 (tt0) cc_final: 0.7534 (mm-30) REVERT: i 49 PHE cc_start: 0.6694 (OUTLIER) cc_final: 0.4443 (p90) REVERT: k 71 HIS cc_start: 0.5237 (OUTLIER) cc_final: 0.4709 (t-90) REVERT: k 101 LEU cc_start: 0.8328 (pt) cc_final: 0.8086 (pt) REVERT: l 16 ILE cc_start: 0.5935 (mp) cc_final: 0.5640 (tp) REVERT: l 102 LYS cc_start: 0.8293 (tptm) cc_final: 0.7882 (tptp) REVERT: n 47 LYS cc_start: 0.8777 (mmmm) cc_final: 0.7950 (mtmt) REVERT: o 17 TYR cc_start: 0.8392 (m-10) cc_final: 0.8154 (m-80) REVERT: p 10 ARG cc_start: 0.8246 (ttm110) cc_final: 0.7990 (ttm-80) REVERT: q 59 LYS cc_start: 0.7811 (mmtt) cc_final: 0.7090 (mttt) REVERT: r 60 PHE cc_start: 0.6478 (OUTLIER) cc_final: 0.6240 (t80) REVERT: s 25 SER cc_start: 0.9145 (t) cc_final: 0.8807 (p) REVERT: s 31 ILE cc_start: 0.9289 (mm) cc_final: 0.9038 (mt) outliers start: 264 outliers final: 228 residues processed: 949 average time/residue: 1.1312 time to fit residues: 1901.4502 Evaluate side-chains 1003 residues out of total 4375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 760 time to evaluate : 5.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 123 LYS Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 165 HIS Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain D residue 5 ASP Chi-restraints excluded: chain D residue 6 TYR Chi-restraints excluded: chain D residue 7 TYR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 140 ILE Chi-restraints excluded: chain E residue 142 GLN Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 47 ILE Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 90 ASN Chi-restraints excluded: chain I residue 116 ILE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 68 SER Chi-restraints excluded: chain J residue 107 PHE Chi-restraints excluded: chain J residue 117 THR Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 25 ASP Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 106 ASP Chi-restraints excluded: chain L residue 113 ILE Chi-restraints excluded: chain M residue 25 ARG Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 43 ASN Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 100 HIS Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 115 LEU Chi-restraints excluded: chain N residue 12 MET Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 67 GLU Chi-restraints excluded: chain N residue 114 ASN Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain O residue 61 ILE Chi-restraints excluded: chain O residue 97 ILE Chi-restraints excluded: chain O residue 99 VAL Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 10 LYS Chi-restraints excluded: chain P residue 14 VAL Chi-restraints excluded: chain P residue 25 LEU Chi-restraints excluded: chain P residue 102 SER Chi-restraints excluded: chain Q residue 53 SER Chi-restraints excluded: chain Q residue 71 VAL Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain Q residue 77 ASP Chi-restraints excluded: chain R residue 7 LEU Chi-restraints excluded: chain R residue 10 VAL Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain S residue 7 ASP 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 98 ASN Chi-restraints excluded: chain T residue 5 ASN Chi-restraints excluded: chain T residue 63 ILE Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain U residue 26 SER Chi-restraints excluded: chain U residue 55 LEU Chi-restraints excluded: chain U residue 67 VAL Chi-restraints excluded: chain V residue 7 THR Chi-restraints excluded: chain V residue 29 LEU Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain V residue 71 ARG Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 36 GLU Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Z residue 8 ILE Chi-restraints excluded: chain Z residue 10 LEU Chi-restraints excluded: chain Z residue 12 SER Chi-restraints excluded: chain Z residue 46 VAL Chi-restraints excluded: chain AA residue 1 MET Chi-restraints excluded: chain AA residue 24 THR Chi-restraints excluded: chain AA residue 42 LEU 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 61 LEU Chi-restraints excluded: chain a residue 30 ILE Chi-restraints excluded: chain a residue 38 HIS Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 81 ASP Chi-restraints excluded: chain a residue 92 ASN Chi-restraints excluded: chain a residue 109 SER Chi-restraints excluded: chain a residue 118 THR Chi-restraints excluded: chain a residue 170 ILE Chi-restraints excluded: chain a residue 178 LEU Chi-restraints excluded: chain a residue 196 ASP Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 69 THR Chi-restraints excluded: chain b residue 90 VAL Chi-restraints excluded: chain b residue 191 THR Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain c residue 71 PHE Chi-restraints excluded: chain c residue 85 THR Chi-restraints excluded: chain c residue 92 LEU Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 141 VAL Chi-restraints excluded: chain c residue 190 LEU Chi-restraints excluded: chain c residue 191 SER Chi-restraints excluded: chain d residue 20 VAL Chi-restraints excluded: chain d residue 42 ASN Chi-restraints excluded: chain d residue 45 VAL Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain d residue 130 THR Chi-restraints excluded: chain d residue 151 MET Chi-restraints excluded: chain d residue 162 GLU Chi-restraints excluded: chain e residue 13 ASP Chi-restraints excluded: chain e residue 26 THR Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 63 ASN Chi-restraints excluded: chain e residue 79 ARG Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain e residue 96 VAL Chi-restraints excluded: chain f residue 22 LEU Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 58 LEU Chi-restraints excluded: chain f residue 68 VAL Chi-restraints excluded: chain f residue 115 MET Chi-restraints excluded: chain g residue 31 LEU Chi-restraints excluded: chain g residue 33 VAL Chi-restraints excluded: chain g residue 45 ILE Chi-restraints excluded: chain g residue 46 GLU Chi-restraints excluded: chain g residue 50 VAL Chi-restraints excluded: chain g residue 79 ARG Chi-restraints excluded: chain g residue 89 ASP Chi-restraints excluded: chain g residue 111 THR Chi-restraints excluded: chain h residue 115 VAL Chi-restraints excluded: chain i residue 14 ASP Chi-restraints excluded: chain i residue 22 THR Chi-restraints excluded: chain i residue 24 GLU Chi-restraints excluded: chain i residue 28 THR Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 49 PHE Chi-restraints excluded: chain i residue 56 HIS Chi-restraints excluded: chain i residue 58 ASN Chi-restraints excluded: chain j residue 26 PHE Chi-restraints excluded: chain j residue 27 ASN Chi-restraints excluded: chain j residue 30 ILE Chi-restraints excluded: chain j residue 31 VAL Chi-restraints excluded: chain j residue 58 THR Chi-restraints excluded: chain j residue 84 MET Chi-restraints excluded: chain k residue 33 CYS Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 71 HIS Chi-restraints excluded: chain k residue 96 THR Chi-restraints excluded: chain k residue 118 VAL Chi-restraints excluded: chain l residue 8 ILE Chi-restraints excluded: chain l residue 41 ASP Chi-restraints excluded: chain l residue 88 LEU Chi-restraints excluded: chain l residue 101 THR Chi-restraints excluded: chain l residue 103 THR Chi-restraints excluded: chain m residue 5 MET Chi-restraints excluded: chain m residue 32 ASP Chi-restraints excluded: chain m residue 44 VAL Chi-restraints excluded: chain m residue 53 ASP Chi-restraints excluded: chain n residue 7 THR Chi-restraints excluded: chain n residue 19 ASN Chi-restraints excluded: chain n residue 24 THR Chi-restraints excluded: chain o residue 19 VAL Chi-restraints excluded: chain o residue 20 VAL Chi-restraints excluded: chain p residue 6 THR Chi-restraints excluded: chain p residue 46 HIS Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 57 VAL Chi-restraints excluded: chain p residue 67 SER Chi-restraints excluded: chain p residue 73 THR Chi-restraints excluded: chain p residue 78 VAL Chi-restraints excluded: chain q residue 28 LEU Chi-restraints excluded: chain q residue 44 THR Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain r residue 57 VAL Chi-restraints excluded: chain r residue 60 PHE Chi-restraints excluded: chain s residue 12 GLN Chi-restraints excluded: chain s residue 26 MET Chi-restraints excluded: chain s residue 27 MET Chi-restraints excluded: chain s residue 29 THR Chi-restraints excluded: chain s residue 33 LYS Chi-restraints excluded: chain t residue 18 PHE Chi-restraints excluded: chain t residue 41 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 570 optimal weight: 3.9990 chunk 919 optimal weight: 10.0000 chunk 561 optimal weight: 7.9990 chunk 436 optimal weight: 6.9990 chunk 639 optimal weight: 6.9990 chunk 964 optimal weight: 10.0000 chunk 887 optimal weight: 10.0000 chunk 767 optimal weight: 0.9980 chunk 79 optimal weight: 10.0000 chunk 593 optimal weight: 8.9990 chunk 470 optimal weight: 6.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 GLN H 135 GLN M 61 GLN ** N 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 7 HIS ** W 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 152351 Z= 0.315 Angle : 0.679 18.371 228424 Z= 0.344 Chirality : 0.038 0.299 29268 Planarity : 0.005 0.052 11890 Dihedral : 24.321 179.054 77402 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 5.46 % Allowed : 25.06 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.11), residues: 5236 helix: 0.25 (0.12), residues: 1807 sheet: -1.08 (0.17), residues: 928 loop : -2.05 (0.12), residues: 2501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.103 0.003 TRP N 30 HIS 0.010 0.001 HIS a 38 PHE 0.040 0.002 PHE Z 38 TYR 0.036 0.002 TYR M 64 ARG 0.007 0.001 ARG s 28 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10472 Ramachandran restraints generated. 5236 Oldfield, 0 Emsley, 5236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10472 Ramachandran restraints generated. 5236 Oldfield, 0 Emsley, 5236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1016 residues out of total 4375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 779 time to evaluate : 5.853 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: C 168 ASP cc_start: 0.6602 (t0) cc_final: 0.6305 (t0) REVERT: D 6 TYR cc_start: 0.6379 (OUTLIER) cc_final: 0.5196 (t80) REVERT: D 7 TYR cc_start: 0.7614 (OUTLIER) cc_final: 0.7320 (p90) REVERT: D 153 ILE cc_start: 0.9085 (mt) cc_final: 0.8811 (pt) REVERT: D 166 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.6764 (mtp85) REVERT: G 8 LYS cc_start: 0.8392 (tmmt) cc_final: 0.8155 (tptm) REVERT: G 35 LYS cc_start: 0.8081 (mmtt) cc_final: 0.7880 (mmtm) REVERT: I 116 ILE cc_start: 0.9246 (OUTLIER) cc_final: 0.8978 (mt) REVERT: J 115 GLU cc_start: 0.7453 (pm20) cc_final: 0.7168 (pm20) REVERT: K 110 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8254 (tp30) REVERT: M 55 GLU cc_start: 0.6884 (mm-30) cc_final: 0.6448 (mm-30) REVERT: M 84 GLU cc_start: 0.7946 (pp20) cc_final: 0.7575 (pp20) REVERT: N 12 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.8090 (ttm) REVERT: N 38 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.7167 (ptp-170) REVERT: N 114 ASN cc_start: 0.5155 (OUTLIER) cc_final: 0.4549 (t0) REVERT: P 49 ILE cc_start: 0.8778 (mt) cc_final: 0.8504 (mt) REVERT: S 45 GLN cc_start: 0.8508 (tp40) cc_final: 0.8271 (tp40) REVERT: Z 39 ASP cc_start: 0.8684 (m-30) cc_final: 0.8365 (m-30) REVERT: Z 43 ARG cc_start: 0.7881 (mtt180) cc_final: 0.7437 (mmt180) REVERT: Z 49 LYS cc_start: 0.7963 (mttt) cc_final: 0.7308 (pttm) REVERT: a 94 ARG cc_start: 0.4417 (tpt-90) cc_final: 0.4112 (tpt-90) REVERT: a 95 TRP cc_start: 0.8124 (t-100) cc_final: 0.7634 (t-100) REVERT: a 112 ARG cc_start: 0.7885 (tmt170) cc_final: 0.7293 (ttt180) REVERT: a 207 ARG cc_start: 0.8419 (mtm110) cc_final: 0.7816 (ttp-170) REVERT: b 36 PHE cc_start: 0.8629 (OUTLIER) cc_final: 0.7932 (m-80) REVERT: b 41 TYR cc_start: 0.8298 (t80) cc_final: 0.7685 (t80) REVERT: b 45 GLU cc_start: 0.6777 (pt0) cc_final: 0.6557 (pt0) REVERT: b 107 LYS cc_start: 0.8588 (mmtt) cc_final: 0.8292 (mmtt) REVERT: b 109 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7613 (mt-10) REVERT: b 143 LEU cc_start: 0.7486 (tp) cc_final: 0.7050 (tp) REVERT: b 180 ASP cc_start: 0.6692 (m-30) cc_final: 0.6263 (m-30) REVERT: d 65 LYS cc_start: 0.9259 (mmtp) cc_final: 0.8824 (mptt) REVERT: d 123 LEU cc_start: 0.8182 (mt) cc_final: 0.7981 (pp) REVERT: e 73 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7712 (mp0) REVERT: e 88 MET cc_start: 0.7766 (mmm) cc_final: 0.7355 (mmm) REVERT: f 30 MET cc_start: 0.5738 (tmm) cc_final: 0.3086 (ttm) REVERT: f 39 GLU cc_start: 0.7393 (tp30) cc_final: 0.6945 (pt0) REVERT: f 102 TRP cc_start: 0.7207 (m-10) cc_final: 0.6550 (m100) REVERT: g 15 ASN cc_start: 0.7134 (m-40) cc_final: 0.6314 (p0) REVERT: g 42 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8315 (mm-30) REVERT: h 41 GLU cc_start: 0.5219 (pm20) cc_final: 0.4449 (pm20) REVERT: h 96 GLU cc_start: 0.8383 (tt0) cc_final: 0.7574 (mm-30) REVERT: i 66 GLU cc_start: 0.7033 (pt0) cc_final: 0.6706 (pm20) REVERT: k 101 LEU cc_start: 0.8269 (pt) cc_final: 0.8045 (pt) REVERT: l 16 ILE cc_start: 0.5943 (mp) cc_final: 0.5585 (tp) REVERT: l 102 LYS cc_start: 0.8450 (tptm) cc_final: 0.8032 (tptp) REVERT: n 47 LYS cc_start: 0.8746 (mmmm) cc_final: 0.7924 (mtmt) REVERT: o 17 TYR cc_start: 0.8296 (m-10) cc_final: 0.8029 (m-80) REVERT: p 10 ARG cc_start: 0.8105 (ttm110) cc_final: 0.7871 (ttm-80) REVERT: q 59 LYS cc_start: 0.7709 (mmtt) cc_final: 0.6998 (mttt) REVERT: r 60 PHE cc_start: 0.6583 (OUTLIER) cc_final: 0.6316 (t80) REVERT: s 25 SER cc_start: 0.9069 (t) cc_final: 0.8716 (p) outliers start: 237 outliers final: 209 residues processed: 936 average time/residue: 1.1495 time to fit residues: 1913.8895 Evaluate side-chains 980 residues out of total 4375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 761 time to evaluate : 5.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 200 MET Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain B residue 14 ILE Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 123 LYS Chi-restraints excluded: chain C residue 145 ASP Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 156 ASN Chi-restraints excluded: chain C residue 165 HIS Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain D residue 5 ASP Chi-restraints excluded: chain D residue 6 TYR Chi-restraints excluded: chain D residue 7 TYR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 166 ARG Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 71 LEU Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 52 ASP Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 142 ILE Chi-restraints excluded: chain I residue 14 SER Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 47 ILE Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 90 ASN Chi-restraints excluded: chain I residue 97 THR Chi-restraints excluded: chain I residue 116 ILE Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 23 ILE Chi-restraints excluded: chain J residue 68 SER Chi-restraints excluded: chain J residue 107 PHE Chi-restraints excluded: chain J residue 117 THR Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 25 ASP Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain K residue 41 LEU Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 106 ASP Chi-restraints excluded: chain L residue 113 ILE Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 61 GLN Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 106 LEU Chi-restraints excluded: chain M residue 115 LEU Chi-restraints excluded: chain N residue 12 MET Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 67 GLU Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain N residue 114 ASN Chi-restraints excluded: chain O residue 33 VAL Chi-restraints excluded: chain O residue 99 VAL Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 25 LEU Chi-restraints excluded: chain P residue 85 LYS Chi-restraints excluded: chain P residue 102 SER Chi-restraints excluded: chain Q residue 53 SER Chi-restraints excluded: chain Q residue 71 VAL Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain Q residue 77 ASP Chi-restraints excluded: chain R residue 7 LEU Chi-restraints excluded: chain R residue 10 VAL Chi-restraints excluded: chain R residue 57 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 63 ILE Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain U residue 26 SER Chi-restraints excluded: chain U residue 55 LEU Chi-restraints excluded: chain U residue 67 VAL Chi-restraints excluded: chain V residue 7 THR Chi-restraints excluded: chain V residue 29 LEU Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 36 GLU Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Z residue 8 ILE Chi-restraints excluded: chain Z residue 10 LEU Chi-restraints excluded: chain Z residue 46 VAL Chi-restraints excluded: chain AA residue 1 MET Chi-restraints excluded: chain AA residue 24 THR Chi-restraints excluded: chain AA residue 42 LEU 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 61 LEU Chi-restraints excluded: chain a residue 30 ILE Chi-restraints excluded: chain a residue 81 ASP Chi-restraints excluded: chain a residue 92 ASN Chi-restraints excluded: chain a residue 109 SER Chi-restraints excluded: chain a residue 118 THR Chi-restraints excluded: chain a residue 178 LEU Chi-restraints excluded: chain a residue 196 ASP Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 36 PHE Chi-restraints excluded: chain b residue 69 THR Chi-restraints excluded: chain b residue 191 THR Chi-restraints excluded: chain c residue 71 PHE Chi-restraints excluded: chain c residue 85 THR Chi-restraints excluded: chain c residue 92 LEU Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 141 VAL Chi-restraints excluded: chain c residue 190 LEU Chi-restraints excluded: chain c residue 191 SER Chi-restraints excluded: chain d residue 42 ASN Chi-restraints excluded: chain d residue 45 VAL Chi-restraints excluded: chain d residue 114 LEU Chi-restraints excluded: chain d residue 130 THR Chi-restraints excluded: chain d residue 151 MET Chi-restraints excluded: chain d residue 162 GLU Chi-restraints excluded: chain e residue 13 ASP Chi-restraints excluded: chain e residue 26 THR Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 79 ARG Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain e residue 96 VAL Chi-restraints excluded: chain f residue 22 LEU Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 58 LEU Chi-restraints excluded: chain f residue 68 VAL Chi-restraints excluded: chain f residue 115 MET Chi-restraints excluded: chain g residue 31 LEU Chi-restraints excluded: chain g residue 33 VAL Chi-restraints excluded: chain g residue 45 ILE Chi-restraints excluded: chain g residue 46 GLU Chi-restraints excluded: chain g residue 50 VAL Chi-restraints excluded: chain g residue 111 THR Chi-restraints excluded: chain h residue 115 VAL Chi-restraints excluded: chain i residue 14 ASP Chi-restraints excluded: chain i residue 22 THR Chi-restraints excluded: chain i residue 24 GLU Chi-restraints excluded: chain i residue 28 THR Chi-restraints excluded: chain i residue 36 VAL Chi-restraints excluded: chain i residue 56 HIS Chi-restraints excluded: chain i residue 58 ASN Chi-restraints excluded: chain j residue 27 ASN Chi-restraints excluded: chain j residue 30 ILE Chi-restraints excluded: chain j residue 31 VAL Chi-restraints excluded: chain j residue 58 THR Chi-restraints excluded: chain j residue 94 SER Chi-restraints excluded: chain k residue 33 CYS Chi-restraints excluded: chain k residue 62 VAL Chi-restraints excluded: chain k residue 76 HIS Chi-restraints excluded: chain k residue 96 THR Chi-restraints excluded: chain k residue 118 VAL Chi-restraints excluded: chain l residue 8 ILE Chi-restraints excluded: chain l residue 41 ASP Chi-restraints excluded: chain l residue 88 LEU Chi-restraints excluded: chain l residue 101 THR Chi-restraints excluded: chain l residue 103 THR Chi-restraints excluded: chain m residue 32 ASP Chi-restraints excluded: chain m residue 44 VAL Chi-restraints excluded: chain m residue 53 ASP Chi-restraints excluded: chain n residue 7 THR Chi-restraints excluded: chain n residue 19 ASN Chi-restraints excluded: chain n residue 24 THR Chi-restraints excluded: chain n residue 32 THR Chi-restraints excluded: chain o residue 19 VAL Chi-restraints excluded: chain o residue 20 VAL Chi-restraints excluded: chain o residue 36 VAL Chi-restraints excluded: chain p residue 6 THR Chi-restraints excluded: chain p residue 46 HIS Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 57 VAL Chi-restraints excluded: chain p residue 67 SER Chi-restraints excluded: chain p residue 73 THR Chi-restraints excluded: chain p residue 78 VAL Chi-restraints excluded: chain q residue 28 LEU Chi-restraints excluded: chain q residue 44 THR Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain r residue 57 VAL Chi-restraints excluded: chain r residue 60 PHE Chi-restraints excluded: chain s residue 12 GLN Chi-restraints excluded: chain s residue 26 MET Chi-restraints excluded: chain s residue 27 MET Chi-restraints excluded: chain s residue 29 THR Chi-restraints excluded: chain s residue 33 LYS Chi-restraints excluded: chain t residue 18 PHE Chi-restraints excluded: chain t residue 41 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 609 optimal weight: 0.6980 chunk 818 optimal weight: 10.0000 chunk 235 optimal weight: 2.9990 chunk 708 optimal weight: 0.0470 chunk 113 optimal weight: 20.0000 chunk 213 optimal weight: 0.9980 chunk 769 optimal weight: 7.9990 chunk 321 optimal weight: 10.0000 chunk 789 optimal weight: 0.8980 chunk 97 optimal weight: 0.0470 chunk 141 optimal weight: 5.9990 overall best weight: 0.5376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 142 GLN L 62 ASN M 61 GLN ** O 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 7 HIS R 48 GLN W 15 ASN ** W 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 13 ASN ** AC 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 38 HIS ** a 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 69 ASN ** d 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 51 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.070721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.052421 restraints weight = 733182.371| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.72 r_work: 0.3120 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.099 152351 Z= 0.138 Angle : 0.577 17.855 228424 Z= 0.289 Chirality : 0.033 0.836 29268 Planarity : 0.004 0.055 11890 Dihedral : 24.063 179.393 77402 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.43 % Allowed : 27.23 % Favored : 69.34 % 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: -1.22 (0.11), residues: 5236 helix: 0.59 (0.12), residues: 1814 sheet: -0.89 (0.18), residues: 862 loop : -1.84 (0.12), residues: 2560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.002 TRP N 30 HIS 0.005 0.001 HIS b 5 PHE 0.035 0.002 PHE r 40 TYR 0.018 0.001 TYR D 127 ARG 0.008 0.000 ARG s 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 37141.41 seconds wall clock time: 648 minutes 59.14 seconds (38939.14 seconds total)