Starting phenix.real_space_refine on Sat Apr 13 17:45:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mlc_3525/04_2024/5mlc_3525.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mlc_3525/04_2024/5mlc_3525.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mlc_3525/04_2024/5mlc_3525.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mlc_3525/04_2024/5mlc_3525.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mlc_3525/04_2024/5mlc_3525.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mlc_3525/04_2024/5mlc_3525.pdb" } resolution = 3.6 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= 0.005 sd= 0.068 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2963 5.49 5 S 99 5.16 5 C 45416 2.51 5 N 16983 2.21 5 O 25186 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 34": "NH1" <-> "NH2" Residue "D ARG 39": "NH1" <-> "NH2" Residue "D ARG 42": "NH1" <-> "NH2" Residue "D ARG 50": "NH1" <-> "NH2" Residue "D ARG 56": "NH1" <-> "NH2" Residue "D ARG 64": "NH1" <-> "NH2" Residue "D ASP 94": "OD1" <-> "OD2" Residue "D GLU 96": "OE1" <-> "OE2" Residue "D ARG 104": "NH1" <-> "NH2" Residue "D ARG 146": "NH1" <-> "NH2" Residue "D GLU 164": "OE1" <-> "OE2" Residue "D ARG 200": "NH1" <-> "NH2" Residue "D ARG 203": "NH1" <-> "NH2" Residue "D ARG 239": "NH1" <-> "NH2" Residue "D ARG 253": "NH1" <-> "NH2" Residue "D ARG 254": "NH1" <-> "NH2" Residue "D ARG 258": "NH1" <-> "NH2" Residue "D ASP 263": "OD1" <-> "OD2" Residue "D PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 87": "OD1" <-> "OD2" Residue "E PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 132": "OD1" <-> "OD2" Residue "E ARG 143": "NH1" <-> "NH2" Residue "E ARG 154": "NH1" <-> "NH2" Residue "E ARG 172": "NH1" <-> "NH2" Residue "E ASP 177": "OD1" <-> "OD2" Residue "E ASP 178": "OD1" <-> "OD2" Residue "E PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 214": "NH1" <-> "NH2" Residue "E ARG 219": "NH1" <-> "NH2" Residue "E ARG 291": "NH1" <-> "NH2" Residue "F PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 67": "OE1" <-> "OE2" Residue "F ARG 81": "NH1" <-> "NH2" Residue "F ARG 86": "NH1" <-> "NH2" Residue "F ARG 97": "NH1" <-> "NH2" Residue "F ARG 105": "NH1" <-> "NH2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F ARG 113": "NH1" <-> "NH2" Residue "F TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 126": "NH1" <-> "NH2" Residue "F ARG 134": "NH1" <-> "NH2" Residue "F ARG 146": "NH1" <-> "NH2" Residue "F ARG 157": "NH1" <-> "NH2" Residue "F ARG 158": "NH1" <-> "NH2" Residue "F GLU 180": "OE1" <-> "OE2" Residue "F PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 196": "NH1" <-> "NH2" Residue "F GLU 203": "OE1" <-> "OE2" Residue "F PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 211": "OD1" <-> "OD2" Residue "F ARG 221": "NH1" <-> "NH2" Residue "F ARG 224": "NH1" <-> "NH2" Residue "F ARG 232": "NH1" <-> "NH2" Residue "F GLU 243": "OE1" <-> "OE2" Residue "F ARG 258": "NH1" <-> "NH2" Residue "G GLU 33": "OE1" <-> "OE2" Residue "G GLU 34": "OE1" <-> "OE2" Residue "G ARG 117": "NH1" <-> "NH2" Residue "G ARG 148": "NH1" <-> "NH2" Residue "G ASP 168": "OD1" <-> "OD2" Residue "G ARG 193": "NH1" <-> "NH2" Residue "H GLU 71": "OE1" <-> "OE2" Residue "H TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 83": "OE1" <-> "OE2" Residue "H TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 195": "OE1" <-> "OE2" Residue "I ARG 49": "NH1" <-> "NH2" Residue "I ASP 68": "OD1" <-> "OD2" Residue "I ARG 70": "NH1" <-> "NH2" Residue "L TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 136": "NH1" <-> "NH2" Residue "L TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 174": "NH1" <-> "NH2" Residue "L ARG 175": "NH1" <-> "NH2" Residue "L PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 205": "NH1" <-> "NH2" Residue "L ARG 212": "NH1" <-> "NH2" Residue "L ASP 238": "OD1" <-> "OD2" Residue "L GLU 249": "OE1" <-> "OE2" Residue "M ARG 23": "NH1" <-> "NH2" Residue "M TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 34": "NH1" <-> "NH2" Residue "M GLU 53": "OE1" <-> "OE2" Residue "M ARG 54": "NH1" <-> "NH2" Residue "M ARG 59": "NH1" <-> "NH2" Residue "M GLU 68": "OE1" <-> "OE2" Residue "M TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 97": "NH1" <-> "NH2" Residue "M ARG 107": "NH1" <-> "NH2" Residue "M PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 79": "NH1" <-> "NH2" Residue "N TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 163": "NH1" <-> "NH2" Residue "N GLU 166": "OE1" <-> "OE2" Residue "N PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 238": "NH1" <-> "NH2" Residue "N TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 244": "OE1" <-> "OE2" Residue "N ARG 252": "NH1" <-> "NH2" Residue "N ASP 254": "OD1" <-> "OD2" Residue "N TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 8": "NH1" <-> "NH2" Residue "O ARG 10": "NH1" <-> "NH2" Residue "O ARG 14": "NH1" <-> "NH2" Residue "O ARG 26": "NH1" <-> "NH2" Residue "O ARG 31": "NH1" <-> "NH2" Residue "O ARG 45": "NH1" <-> "NH2" Residue "O ARG 51": "NH1" <-> "NH2" Residue "O ARG 56": "NH1" <-> "NH2" Residue "O ARG 59": "NH1" <-> "NH2" Residue "O ARG 60": "NH1" <-> "NH2" Residue "O ARG 77": "NH1" <-> "NH2" Residue "O GLU 80": "OE1" <-> "OE2" Residue "O TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 101": "NH1" <-> "NH2" Residue "O ARG 115": "NH1" <-> "NH2" Residue "O ARG 128": "NH1" <-> "NH2" Residue "P ARG 15": "NH1" <-> "NH2" Residue "P ARG 19": "NH1" <-> "NH2" Residue "P ARG 22": "NH1" <-> "NH2" Residue "P ARG 27": "NH1" <-> "NH2" Residue "P ARG 28": "NH1" <-> "NH2" Residue "P ARG 32": "NH1" <-> "NH2" Residue "P ARG 43": "NH1" <-> "NH2" Residue "P ARG 48": "NH1" <-> "NH2" Residue "P TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 73": "NH1" <-> "NH2" Residue "P ARG 74": "NH1" <-> "NH2" Residue "P PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 106": "NH1" <-> "NH2" Residue "P ARG 109": "NH1" <-> "NH2" Residue "Q ARG 49": "NH1" <-> "NH2" Residue "Q ARG 50": "NH1" <-> "NH2" Residue "Q GLU 69": "OE1" <-> "OE2" Residue "Q ARG 70": "NH1" <-> "NH2" Residue "Q ARG 72": "NH1" <-> "NH2" Residue "Q ASP 142": "OD1" <-> "OD2" Residue "Q ARG 143": "NH1" <-> "NH2" Residue "Q ARG 151": "NH1" <-> "NH2" Residue "Q ARG 160": "NH1" <-> "NH2" Residue "Q PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 138": "NH1" <-> "NH2" Residue "R ARG 144": "NH1" <-> "NH2" Residue "R ASP 147": "OD1" <-> "OD2" Residue "R ARG 152": "NH1" <-> "NH2" Residue "R ARG 160": "NH1" <-> "NH2" Residue "R ARG 172": "NH1" <-> "NH2" Residue "R ARG 182": "NH1" <-> "NH2" Residue "R ARG 184": "NH1" <-> "NH2" Residue "R ARG 185": "NH1" <-> "NH2" Residue "R PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 212": "NH1" <-> "NH2" Residue "R ARG 218": "NH1" <-> "NH2" Residue "R TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 223": "NH1" <-> "NH2" Residue "S ARG 3": "NH1" <-> "NH2" Residue "S ARG 6": "NH1" <-> "NH2" Residue "S ARG 12": "NH1" <-> "NH2" Residue "S ARG 13": "NH1" <-> "NH2" Residue "S ARG 14": "NH1" <-> "NH2" Residue "S ARG 18": "NH1" <-> "NH2" Residue "S ARG 25": "NH1" <-> "NH2" Residue "S ARG 33": "NH1" <-> "NH2" Residue "S ARG 41": "NH1" <-> "NH2" Residue "S ARG 48": "NH1" <-> "NH2" Residue "S ASP 51": "OD1" <-> "OD2" Residue "S ARG 52": "NH1" <-> "NH2" Residue "S ARG 59": "NH1" <-> "NH2" Residue "S ARG 70": "NH1" <-> "NH2" Residue "S ARG 72": "NH1" <-> "NH2" Residue "S TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 132": "NH1" <-> "NH2" Residue "T TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 140": "NH1" <-> "NH2" Residue "T ARG 146": "NH1" <-> "NH2" Residue "T PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 207": "NH1" <-> "NH2" Residue "T ARG 208": "NH1" <-> "NH2" Residue "T ARG 218": "NH1" <-> "NH2" Residue "U ARG 35": "NH1" <-> "NH2" Residue "U TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 48": "NH1" <-> "NH2" Residue "U ARG 56": "NH1" <-> "NH2" Residue "U ARG 71": "NH1" <-> "NH2" Residue "U PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 117": "NH1" <-> "NH2" Residue "U ARG 119": "NH1" <-> "NH2" Residue "U ARG 127": "NH1" <-> "NH2" Residue "U ARG 137": "NH1" <-> "NH2" Residue "U GLU 150": "OE1" <-> "OE2" Residue "V TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 106": "NH1" <-> "NH2" Residue "V ARG 107": "NH1" <-> "NH2" Residue "V TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 141": "NH1" <-> "NH2" Residue "V ARG 148": "NH1" <-> "NH2" Residue "V PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 160": "NH1" <-> "NH2" Residue "V ARG 167": "NH1" <-> "NH2" Residue "V TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 47": "NH1" <-> "NH2" Residue "W ARG 146": "NH1" <-> "NH2" Residue "W ARG 156": "NH1" <-> "NH2" Residue "W ARG 159": "NH1" <-> "NH2" Residue "X PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 155": "NH1" <-> "NH2" Residue "X ARG 162": "NH1" <-> "NH2" Residue "Y ARG 120": "NH1" <-> "NH2" Residue "Y ARG 146": "NH1" <-> "NH2" Residue "Z PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 111": "NH1" <-> "NH2" Residue "Z ARG 131": "NH1" <-> "NH2" Residue "Z ARG 147": "NH1" <-> "NH2" Residue "2 ARG 7": "NH1" <-> "NH2" Residue "2 TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 20": "NH1" <-> "NH2" Residue "3 ARG 28": "NH1" <-> "NH2" Residue "3 ARG 32": "NH1" <-> "NH2" Residue "3 TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 39": "NH1" <-> "NH2" Residue "3 ARG 45": "NH1" <-> "NH2" Residue "3 ARG 49": "NH1" <-> "NH2" Residue "4 ARG 103": "NH1" <-> "NH2" Residue "4 ARG 105": "NH1" <-> "NH2" Residue "4 ARG 110": "NH1" <-> "NH2" Residue "4 PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 115": "NH1" <-> "NH2" Residue "4 ARG 117": "NH1" <-> "NH2" Residue "4 ARG 129": "NH1" <-> "NH2" Residue "4 ARG 149": "NH1" <-> "NH2" Residue "5 ARG 103": "NH1" <-> "NH2" Residue "5 ARG 112": "NH1" <-> "NH2" Residue "5 ARG 114": "NH1" <-> "NH2" Residue "5 ARG 128": "NH1" <-> "NH2" Residue "5 ARG 131": "NH1" <-> "NH2" Residue "5 ARG 140": "NH1" <-> "NH2" Residue "5 TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 157": "NH1" <-> "NH2" Residue "6 ARG 8": "NH1" <-> "NH2" Residue "6 ARG 15": "NH1" <-> "NH2" Residue "6 ARG 18": "NH1" <-> "NH2" Residue "6 ARG 20": "NH1" <-> "NH2" Residue "6 ARG 22": "NH1" <-> "NH2" Residue "9 ARG 98": "NH1" <-> "NH2" Residue "9 ARG 107": "NH1" <-> "NH2" Residue "9 ARG 114": "NH1" <-> "NH2" Residue "9 ARG 195": "NH1" <-> "NH2" Residue "9 ARG 196": "NH1" <-> "NH2" Residue "9 ARG 215": "NH1" <-> "NH2" Residue "9 ARG 219": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 90647 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 59074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2750, 59074 Classifications: {'RNA': 2750} Modifications used: {'rna2p_pur': 246, 'rna2p_pyr': 112, 'rna3p_pur': 1355, 'rna3p_pyr': 1037} Link IDs: {'rna2p': 358, 'rna3p': 2391} Chain breaks: 5 Chain: "B" Number of atoms: 2564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2564 Classifications: {'RNA': 120} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 2, 'rna3p_pur': 59, 'rna3p_pyr': 53} Link IDs: {'rna2p': 8, 'rna3p': 111} Chain: "C" Number of atoms: 2001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 2001 Classifications: {'RNA': 93} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 2, 'rna3p_pur': 51, 'rna3p_pyr': 35} Link IDs: {'rna2p': 7, 'rna3p': 85} Chain breaks: 1 Chain: "D" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1895 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 13, 'TRANS': 232} Chain: "E" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1669 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 10, 'TRANS': 208} Chain: "F" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1617 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 11, 'TRANS': 193} Chain: "G" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1387 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 8, 'TRANS': 170} Chain: "H" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1386 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 9, 'TRANS': 168} Chain: "I" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "L" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1489 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 12, 'TRANS': 183} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TRP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 66 Chain: "M" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 934 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "N" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1385 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 10, 'TRANS': 171} Chain: "O" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1075 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "P" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 945 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "Q" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 931 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "R" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 915 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "S" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 1003 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 1, 'TRANS': 114} Chain: "T" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1017 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 9, 'TRANS': 124} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "U" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1165 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 6, 'TRANS': 145} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 24 Chain: "V" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 734 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Chain: "W" Number of atoms: 1018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1018 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 125} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "X" Number of atoms: 866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 866 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "Y" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 616 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "Z" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 788 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "2" Number of atoms: 341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 341 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "3" Number of atoms: 489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 489 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "4" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 471 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 2, 'TRANS': 58} Chain: "5" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 575 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "6" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 305 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 34} Chain: "9" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 881 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'TRANS': 106} Chain breaks: 1 Chain: "7" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 378 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "8" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 374 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 8, 'TRANS': 38} Time building chain proxies: 34.81, per 1000 atoms: 0.38 Number of scatterers: 90647 At special positions: 0 Unit cell: (207.956, 213.261, 217.505, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 99 16.00 P 2963 15.00 O 25186 8.00 N 16983 7.00 C 45416 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS 6 11 " - pdb=" SG CYS 6 14 " distance=2.03 Simple disulfide: pdb=" SG CYS 6 11 " - pdb=" SG CYS 6 27 " distance=2.04 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: 35.50 Conformation dependent library (CDL) restraints added in 3.9 seconds 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6278 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 37 sheets defined 31.8% alpha, 14.0% beta 855 base pairs and 1446 stacking pairs defined. Time for finding SS restraints: 30.77 Creating SS restraints... Processing helix chain 'D' and resid 203 through 209 removed outlier: 3.892A pdb=" N LYS D 207 " --> pdb=" O ARG D 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 161 removed outlier: 3.889A pdb=" N ALA E 160 " --> pdb=" O HIS E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 216 Processing helix chain 'F' and resid 81 through 96 Processing helix chain 'F' and resid 153 through 169 removed outlier: 3.604A pdb=" N ARG F 157 " --> pdb=" O ASN F 153 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE F 165 " --> pdb=" O LEU F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 198 removed outlier: 3.559A pdb=" N PHE F 190 " --> pdb=" O LYS F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 222 removed outlier: 4.496A pdb=" N ASN F 222 " --> pdb=" O LYS F 218 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 242 removed outlier: 3.586A pdb=" N VAL F 239 " --> pdb=" O ASN F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 259 Processing helix chain 'G' and resid 17 through 26 removed outlier: 3.684A pdb=" N ASN G 22 " --> pdb=" O ARG G 18 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU G 25 " --> pdb=" O THR G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 36 Processing helix chain 'G' and resid 56 through 60 removed outlier: 3.721A pdb=" N SER G 59 " --> pdb=" O GLY G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 74 Processing helix chain 'G' and resid 108 through 121 removed outlier: 3.663A pdb=" N TYR G 112 " --> pdb=" O GLY G 108 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE G 119 " --> pdb=" O LEU G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 Processing helix chain 'G' and resid 177 through 189 removed outlier: 3.743A pdb=" N ALA G 181 " --> pdb=" O THR G 177 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR G 182 " --> pdb=" O ASP G 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 104 Processing helix chain 'H' and resid 104 through 121 removed outlier: 3.938A pdb=" N THR H 110 " --> pdb=" O GLY H 106 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR H 112 " --> pdb=" O PHE H 108 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP H 113 " --> pdb=" O ARG H 109 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN H 114 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL H 116 " --> pdb=" O THR H 112 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL H 117 " --> pdb=" O ASP H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 178 through 192 removed outlier: 4.034A pdb=" N PHE H 184 " --> pdb=" O VAL H 180 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE H 188 " --> pdb=" O PHE H 184 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TRP H 191 " --> pdb=" O THR H 187 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ARG H 192 " --> pdb=" O ILE H 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 213 through 217 removed outlier: 3.645A pdb=" N ALA H 216 " --> pdb=" O GLU H 213 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 77 removed outlier: 4.104A pdb=" N LEU I 74 " --> pdb=" O ARG I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 82 removed outlier: 3.863A pdb=" N LEU I 81 " --> pdb=" O PHE I 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 74 removed outlier: 3.657A pdb=" N VAL L 68 " --> pdb=" O LEU L 64 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA L 73 " --> pdb=" O LYS L 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 137 removed outlier: 3.663A pdb=" N THR L 130 " --> pdb=" O ARG L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 157 through 161 Processing helix chain 'L' and resid 166 through 171 Processing helix chain 'L' and resid 188 through 195 removed outlier: 3.709A pdb=" N ARG L 194 " --> pdb=" O GLN L 190 " (cutoff:3.500A) Processing helix chain 'L' and resid 196 through 206 removed outlier: 4.003A pdb=" N ILE L 200 " --> pdb=" O PRO L 196 " (cutoff:3.500A) Processing helix chain 'L' and resid 211 through 217 removed outlier: 3.645A pdb=" N TYR L 216 " --> pdb=" O ARG L 212 " (cutoff:3.500A) Processing helix chain 'M' and resid 103 through 108 removed outlier: 3.650A pdb=" N LEU M 106 " --> pdb=" O ALA M 103 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN M 108 " --> pdb=" O GLU M 105 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 116 removed outlier: 3.830A pdb=" N VAL M 114 " --> pdb=" O PHE M 110 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU M 116 " --> pdb=" O LYS M 112 " (cutoff:3.500A) Processing helix chain 'N' and resid 135 through 139 Processing helix chain 'N' and resid 161 through 166 removed outlier: 3.546A pdb=" N GLU N 166 " --> pdb=" O LEU N 162 " (cutoff:3.500A) Processing helix chain 'N' and resid 177 through 184 removed outlier: 3.590A pdb=" N LYS N 182 " --> pdb=" O LEU N 178 " (cutoff:3.500A) Processing helix chain 'N' and resid 191 through 196 Processing helix chain 'N' and resid 218 through 229 removed outlier: 3.816A pdb=" N GLU N 223 " --> pdb=" O GLY N 219 " (cutoff:3.500A) Processing helix chain 'N' and resid 243 through 259 Processing helix chain 'O' and resid 22 through 26 removed outlier: 3.676A pdb=" N ASN O 25 " --> pdb=" O TYR O 22 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG O 26 " --> pdb=" O ARG O 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 22 through 26' Processing helix chain 'O' and resid 44 through 57 removed outlier: 3.759A pdb=" N ASN O 57 " --> pdb=" O ALA O 53 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 125 removed outlier: 3.505A pdb=" N ARG O 116 " --> pdb=" O ASN O 112 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE O 120 " --> pdb=" O ARG O 116 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET O 125 " --> pdb=" O ALA O 121 " (cutoff:3.500A) Processing helix chain 'P' and resid 23 through 42 removed outlier: 3.765A pdb=" N ARG P 28 " --> pdb=" O ALA P 24 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA P 29 " --> pdb=" O ASP P 25 " (cutoff:3.500A) Processing helix chain 'P' and resid 48 through 53 Processing helix chain 'P' and resid 54 through 65 Processing helix chain 'P' and resid 69 through 81 removed outlier: 3.505A pdb=" N ARG P 74 " --> pdb=" O LEU P 70 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE P 79 " --> pdb=" O GLN P 75 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TYR P 81 " --> pdb=" O LEU P 77 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 87 removed outlier: 3.666A pdb=" N VAL P 86 " --> pdb=" O GLU P 82 " (cutoff:3.500A) Processing helix chain 'P' and resid 87 through 92 removed outlier: 4.171A pdb=" N ALA P 91 " --> pdb=" O HIS P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 92 through 97 Processing helix chain 'P' and resid 113 through 117 removed outlier: 3.870A pdb=" N ASP P 116 " --> pdb=" O ARG P 113 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASN P 117 " --> pdb=" O ARG P 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 113 through 117' Processing helix chain 'Q' and resid 50 through 65 removed outlier: 3.692A pdb=" N THR Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA Q 55 " --> pdb=" O GLU Q 51 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE Q 60 " --> pdb=" O ARG Q 56 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS Q 63 " --> pdb=" O ARG Q 59 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 107 removed outlier: 3.853A pdb=" N SER Q 106 " --> pdb=" O GLN Q 102 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLU Q 107 " --> pdb=" O LYS Q 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 102 through 107' Processing helix chain 'Q' and resid 116 through 135 removed outlier: 3.640A pdb=" N GLU Q 125 " --> pdb=" O GLN Q 121 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA Q 128 " --> pdb=" O GLY Q 124 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N CYS Q 131 " --> pdb=" O ILE Q 127 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU Q 132 " --> pdb=" O ALA Q 128 " (cutoff:3.500A) Processing helix chain 'Q' and resid 150 through 163 removed outlier: 4.184A pdb=" N GLY Q 163 " --> pdb=" O ALA Q 159 " (cutoff:3.500A) Processing helix chain 'R' and resid 121 through 138 removed outlier: 3.571A pdb=" N ALA R 134 " --> pdb=" O ALA R 130 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 178 Processing helix chain 'R' and resid 219 through 225 removed outlier: 3.776A pdb=" N LYS R 225 " --> pdb=" O LEU R 222 " (cutoff:3.500A) Processing helix chain 'S' and resid 6 through 9 Processing helix chain 'S' and resid 10 through 22 removed outlier: 4.155A pdb=" N LYS S 16 " --> pdb=" O ARG S 12 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA S 21 " --> pdb=" O ILE S 17 " (cutoff:3.500A) Processing helix chain 'S' and resid 26 through 30 Processing helix chain 'S' and resid 31 through 70 removed outlier: 4.060A pdb=" N ILE S 40 " --> pdb=" O ALA S 36 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG S 41 " --> pdb=" O GLN S 37 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP S 51 " --> pdb=" O HIS S 47 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS S 54 " --> pdb=" O ARG S 50 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG S 55 " --> pdb=" O ASP S 51 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG S 58 " --> pdb=" O LYS S 54 " (cutoff:3.500A) Processing helix chain 'S' and resid 77 through 88 removed outlier: 3.607A pdb=" N HIS S 83 " --> pdb=" O SER S 79 " (cutoff:3.500A) Processing helix chain 'S' and resid 93 through 104 Processing helix chain 'S' and resid 104 through 117 removed outlier: 3.728A pdb=" N ILE S 108 " --> pdb=" O ASN S 104 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE S 116 " --> pdb=" O TYR S 112 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS S 117 " --> pdb=" O ASN S 113 " (cutoff:3.500A) Processing helix chain 'T' and resid 102 through 111 removed outlier: 4.217A pdb=" N ILE T 107 " --> pdb=" O TYR T 103 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN T 108 " --> pdb=" O ASN T 104 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 51 removed outlier: 4.118A pdb=" N VAL U 49 " --> pdb=" O LYS U 45 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP U 51 " --> pdb=" O ARG U 47 " (cutoff:3.500A) Processing helix chain 'U' and resid 57 through 68 removed outlier: 3.843A pdb=" N LEU U 67 " --> pdb=" O MET U 63 " (cutoff:3.500A) Processing helix chain 'U' and resid 72 through 90 removed outlier: 3.839A pdb=" N ILE U 76 " --> pdb=" O ALA U 72 " (cutoff:3.500A) Processing helix chain 'U' and resid 118 through 120 No H-bonds generated for 'chain 'U' and resid 118 through 120' Processing helix chain 'U' and resid 142 through 149 removed outlier: 3.532A pdb=" N PHE U 148 " --> pdb=" O SER U 144 " (cutoff:3.500A) Processing helix chain 'V' and resid 121 through 132 removed outlier: 3.515A pdb=" N LYS V 126 " --> pdb=" O GLU V 122 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA V 129 " --> pdb=" O ILE V 125 " (cutoff:3.500A) Processing helix chain 'V' and resid 143 through 156 Processing helix chain 'V' and resid 183 through 190 Processing helix chain 'X' and resid 149 through 166 Processing helix chain 'Y' and resid 122 through 132 removed outlier: 3.694A pdb=" N LEU Y 126 " --> pdb=" O SER Y 122 " (cutoff:3.500A) Processing helix chain 'Y' and resid 133 through 139 removed outlier: 3.810A pdb=" N VAL Y 137 " --> pdb=" O GLY Y 133 " (cutoff:3.500A) Processing helix chain 'Z' and resid 61 through 68 removed outlier: 4.528A pdb=" N LEU Z 65 " --> pdb=" O LYS Z 61 " (cutoff:3.500A) Processing helix chain 'Z' and resid 72 through 89 removed outlier: 4.341A pdb=" N ASN Z 77 " --> pdb=" O ASN Z 73 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY Z 85 " --> pdb=" O LEU Z 81 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLU Z 86 " --> pdb=" O GLN Z 82 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N LEU Z 87 " --> pdb=" O LEU Z 83 " (cutoff:3.500A) Processing helix chain 'Z' and resid 102 through 127 removed outlier: 3.580A pdb=" N GLY Z 106 " --> pdb=" O PRO Z 102 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL Z 118 " --> pdb=" O ARG Z 114 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU Z 125 " --> pdb=" O GLU Z 121 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN Z 126 " --> pdb=" O ARG Z 122 " (cutoff:3.500A) Processing helix chain 'Z' and resid 131 through 143 Processing helix chain '2' and resid 11 through 39 removed outlier: 3.705A pdb=" N ILE 2 19 " --> pdb=" O ILE 2 15 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TRP 2 20 " --> pdb=" O ARG 2 16 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA 2 35 " --> pdb=" O ALA 2 31 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS 2 36 " --> pdb=" O PHE 2 32 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER 2 37 " --> pdb=" O SER 2 33 " (cutoff:3.500A) Processing helix chain '4' and resid 104 through 113 Processing helix chain '4' and resid 113 through 120 removed outlier: 3.634A pdb=" N SER 4 119 " --> pdb=" O ARG 4 115 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR 4 120 " --> pdb=" O LEU 4 116 " (cutoff:3.500A) Processing helix chain '4' and resid 120 through 134 removed outlier: 3.666A pdb=" N LEU 4 126 " --> pdb=" O SER 4 122 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU 4 127 " --> pdb=" O GLY 4 123 " (cutoff:3.500A) Processing helix chain '5' and resid 98 through 102 Processing helix chain '5' and resid 125 through 134 removed outlier: 3.658A pdb=" N LYS 5 129 " --> pdb=" O ASN 5 125 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN 5 130 " --> pdb=" O THR 5 126 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG 5 131 " --> pdb=" O LYS 5 127 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS 5 134 " --> pdb=" O ASN 5 130 " (cutoff:3.500A) Processing helix chain '5' and resid 142 through 150 Processing helix chain '9' and resid 90 through 113 removed outlier: 3.868A pdb=" N ASN 9 94 " --> pdb=" O LEU 9 90 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG 9 98 " --> pdb=" O ASN 9 94 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N MET 9 99 " --> pdb=" O THR 9 95 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU 9 100 " --> pdb=" O LYS 9 96 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS 9 101 " --> pdb=" O GLN 9 97 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER 9 112 " --> pdb=" O SER 9 108 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL 9 113 " --> pdb=" O ASN 9 109 " (cutoff:3.500A) Processing helix chain '9' and resid 194 through 231 removed outlier: 3.917A pdb=" N GLU 9 198 " --> pdb=" O ASP 9 194 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU 9 199 " --> pdb=" O ARG 9 195 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA 9 200 " --> pdb=" O ARG 9 196 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS 9 201 " --> pdb=" O LYS 9 197 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL 9 202 " --> pdb=" O GLU 9 198 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS 9 205 " --> pdb=" O LYS 9 201 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE 9 217 " --> pdb=" O ALA 9 213 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG 9 218 " --> pdb=" O VAL 9 214 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS 9 227 " --> pdb=" O LYS 9 223 " (cutoff:3.500A) Processing helix chain '9' and resid 237 through 253 Processing helix chain '9' and resid 253 through 270 removed outlier: 3.658A pdb=" N GLU 9 267 " --> pdb=" O GLN 9 263 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU 9 268 " --> pdb=" O LYS 9 264 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N MET 9 269 " --> pdb=" O GLU 9 265 " (cutoff:3.500A) Processing helix chain '7' and resid 100 through 128 removed outlier: 3.815A pdb=" N LYS 7 105 " --> pdb=" O GLU 7 101 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS 7 107 " --> pdb=" O LYS 7 103 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N MET 7 108 " --> pdb=" O ILE 7 104 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU 7 125 " --> pdb=" O ALA 7 121 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG 7 128 " --> pdb=" O SER 7 124 " (cutoff:3.500A) Processing helix chain '7' and resid 132 through 139 removed outlier: 3.878A pdb=" N MET 7 136 " --> pdb=" O PRO 7 132 " (cutoff:3.500A) Processing helix chain '8' and resid 55 through 62 removed outlier: 3.875A pdb=" N HIS 8 59 " --> pdb=" O GLY 8 55 " (cutoff:3.500A) Processing helix chain '8' and resid 68 through 73 removed outlier: 3.548A pdb=" N LYS 8 73 " --> pdb=" O ARG 8 69 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 29 through 30 Processing sheet with id=AA2, first strand: chain 'D' and resid 97 through 101 removed outlier: 6.714A pdb=" N ILE D 87 " --> pdb=" O ILE D 77 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE D 77 " --> pdb=" O ILE D 87 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU D 89 " --> pdb=" O VAL D 75 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 125 through 127 removed outlier: 5.511A pdb=" N LEU D 160 " --> pdb=" O LYS D 171 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LYS D 171 " --> pdb=" O LEU D 160 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 261 through 264 removed outlier: 4.920A pdb=" N ARG E 262 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE E 199 " --> pdb=" O ARG E 262 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N LYS E 96 " --> pdb=" O GLY E 116 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N GLY E 116 " --> pdb=" O LYS E 96 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLY E 98 " --> pdb=" O VAL E 114 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL E 275 " --> pdb=" O ILE E 269 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ILE E 269 " --> pdb=" O VAL E 275 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N MET E 277 " --> pdb=" O MET E 267 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 123 through 127 removed outlier: 6.623A pdb=" N GLN E 138 " --> pdb=" O THR E 124 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N VAL E 126 " --> pdb=" O ALA E 136 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA E 136 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR E 141 " --> pdb=" O HIS E 167 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N HIS E 167 " --> pdb=" O TYR E 141 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ARG E 143 " --> pdb=" O MET E 165 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N MET E 165 " --> pdb=" O ARG E 143 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 205 through 209 removed outlier: 3.680A pdb=" N GLY E 207 " --> pdb=" O MET E 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 174 through 175 removed outlier: 3.685A pdb=" N THR F 248 " --> pdb=" O PHE F 208 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N LEU F 229 " --> pdb=" O SER F 205 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE F 207 " --> pdb=" O LEU F 229 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 81 through 84 removed outlier: 3.717A pdb=" N GLY G 101 " --> pdb=" O THR G 83 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 170 through 173 Processing sheet with id=AB1, first strand: chain 'H' and resid 135 through 138 removed outlier: 3.647A pdb=" N ARG H 135 " --> pdb=" O SER H 146 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 51 through 53 Processing sheet with id=AB3, first strand: chain 'L' and resid 221 through 222 Processing sheet with id=AB4, first strand: chain 'L' and resid 172 through 176 Processing sheet with id=AB5, first strand: chain 'M' and resid 7 through 10 removed outlier: 3.736A pdb=" N VAL M 10 " --> pdb=" O ARG M 17 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ARG M 17 " --> pdb=" O VAL M 10 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ALA M 16 " --> pdb=" O ALA M 46 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ALA M 46 " --> pdb=" O ALA M 16 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLU M 18 " --> pdb=" O LYS M 44 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL M 40 " --> pdb=" O ILE M 22 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ILE M 24 " --> pdb=" O VAL M 38 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N VAL M 38 " --> pdb=" O ILE M 24 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N VAL M 62 " --> pdb=" O VAL M 85 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N VAL M 85 " --> pdb=" O VAL M 62 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ALA M 84 " --> pdb=" O HIS M 7 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ASN M 9 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 69 through 70 removed outlier: 3.636A pdb=" N LEU M 69 " --> pdb=" O ILE M 77 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N THR R 180 " --> pdb=" O ARG R 172 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ARG R 172 " --> pdb=" O THR R 180 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ARG R 182 " --> pdb=" O ILE R 170 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE R 186 " --> pdb=" O LYS R 166 " (cutoff:3.500A) removed outlier: 8.904A pdb=" N LYS R 166 " --> pdb=" O ILE R 186 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER R 163 " --> pdb=" O LEU R 153 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU R 153 " --> pdb=" O SER R 163 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ASP R 147 " --> pdb=" O VAL R 169 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ILE R 148 " --> pdb=" O VAL R 208 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N VAL R 208 " --> pdb=" O ILE R 148 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N GLN R 150 " --> pdb=" O ILE R 206 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ILE R 206 " --> pdb=" O GLN R 150 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ARG R 152 " --> pdb=" O LYS R 204 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 211 through 214 Processing sheet with id=AB8, first strand: chain 'O' and resid 63 through 66 removed outlier: 6.669A pdb=" N LEU O 34 " --> pdb=" O LEU O 103 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLU O 105 " --> pdb=" O TYR O 32 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N TYR O 32 " --> pdb=" O GLU O 105 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'O' and resid 40 through 43 removed outlier: 3.644A pdb=" N TYR O 92 " --> pdb=" O VAL O 74 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'P' and resid 43 through 47 Processing sheet with id=AC2, first strand: chain 'Q' and resid 94 through 99 removed outlier: 3.977A pdb=" N ALA Q 96 " --> pdb=" O VAL Q 86 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU Q 73 " --> pdb=" O ASP Q 142 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'T' and resid 133 through 136 removed outlier: 3.688A pdb=" N LEU T 163 " --> pdb=" O VAL T 126 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N VAL T 128 " --> pdb=" O VAL T 161 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N VAL T 161 " --> pdb=" O VAL T 128 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'T' and resid 140 through 145 removed outlier: 3.551A pdb=" N ARG T 140 " --> pdb=" O ILE T 221 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ARG T 218 " --> pdb=" O GLU T 187 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N HIS T 183 " --> pdb=" O THR T 222 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASP T 154 " --> pdb=" O VAL T 186 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'T' and resid 195 through 201 removed outlier: 4.515A pdb=" N TYR T 206 " --> pdb=" O LYS T 201 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'U' and resid 32 through 34 removed outlier: 3.773A pdb=" N ILE U 32 " --> pdb=" O LEU U 136 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU U 136 " --> pdb=" O ILE U 32 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N CYS U 130 " --> pdb=" O SER U 38 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'U' and resid 32 through 34 removed outlier: 3.773A pdb=" N ILE U 32 " --> pdb=" O LEU U 136 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU U 136 " --> pdb=" O ILE U 32 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ARG U 137 " --> pdb=" O ILE U 100 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ILE U 100 " --> pdb=" O ARG U 137 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'U' and resid 111 through 116 Processing sheet with id=AC9, first strand: chain 'V' and resid 117 through 118 removed outlier: 3.667A pdb=" N THR V 171 " --> pdb=" O ARG V 167 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG V 167 " --> pdb=" O THR V 171 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS V 161 " --> pdb=" O MET V 177 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'W' and resid 129 through 130 removed outlier: 3.624A pdb=" N LYS W 91 " --> pdb=" O ILE W 100 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'W' and resid 110 through 111 removed outlier: 3.681A pdb=" N VAL W 111 " --> pdb=" O GLN W 121 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'W' and resid 148 through 151 Processing sheet with id=AD4, first strand: chain 'X' and resid 78 through 79 removed outlier: 6.684A pdb=" N ILE X 115 " --> pdb=" O ILE X 93 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'X' and resid 101 through 103 Processing sheet with id=AD6, first strand: chain 'Y' and resid 83 through 85 Processing sheet with id=AD7, first strand: chain 'Y' and resid 104 through 109 Processing sheet with id=AD8, first strand: chain '3' and resid 8 through 13 Processing sheet with id=AD9, first strand: chain '3' and resid 47 through 49 removed outlier: 3.954A pdb=" N LEU 3 48 " --> pdb=" O HIS 3 61 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain '5' and resid 103 through 104 857 hydrogen bonds defined for protein. 2400 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2184 hydrogen bonds 3692 hydrogen bond angles 0 basepair planarities 855 basepair parallelities 1446 stacking parallelities Total time for adding SS restraints: 127.58 Time building geometry restraints manager: 38.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 17039 1.34 - 1.48: 44548 1.48 - 1.61: 36410 1.61 - 1.75: 534 1.75 - 1.89: 171 Bond restraints: 98702 Sorted by residual: bond pdb=" C ILE U 158 " pdb=" N ALA U 159 " ideal model delta sigma weight residual 1.333 1.845 -0.512 1.26e-02 6.30e+03 1.65e+03 bond pdb=" O3' C A1554 " pdb=" P G A1555 " ideal model delta sigma weight residual 1.607 1.330 0.277 1.50e-02 4.44e+03 3.41e+02 bond pdb=" C ASP W 169 " pdb=" N THR W 170 " ideal model delta sigma weight residual 1.331 1.580 -0.249 1.35e-02 5.49e+03 3.39e+02 bond pdb=" C PRO T 118 " pdb=" N PRO T 119 " ideal model delta sigma weight residual 1.334 1.709 -0.375 2.34e-02 1.83e+03 2.57e+02 bond pdb=" O3' U A1435 " pdb=" P U A1436 " ideal model delta sigma weight residual 1.607 1.439 0.168 1.50e-02 4.44e+03 1.25e+02 ... (remaining 98697 not shown) Histogram of bond angle deviations from ideal: 91.95 - 101.34: 2056 101.34 - 110.73: 50954 110.73 - 120.12: 57759 120.12 - 129.50: 35231 129.50 - 138.89: 1908 Bond angle restraints: 147908 Sorted by residual: angle pdb=" O3' A A 763 " pdb=" C3' A A 763 " pdb=" C2' A A 763 " ideal model delta sigma weight residual 109.50 128.71 -19.21 1.50e+00 4.44e-01 1.64e+02 angle pdb=" O3' G A 50 " pdb=" C3' G A 50 " pdb=" C2' G A 50 " ideal model delta sigma weight residual 109.50 126.57 -17.07 1.50e+00 4.44e-01 1.29e+02 angle pdb=" O3' G A1260 " pdb=" C3' G A1260 " pdb=" C2' G A1260 " ideal model delta sigma weight residual 113.70 98.75 14.95 1.50e+00 4.44e-01 9.94e+01 angle pdb=" N PRO T 117 " pdb=" CA PRO T 117 " pdb=" C PRO T 117 " ideal model delta sigma weight residual 110.70 122.86 -12.16 1.22e+00 6.72e-01 9.93e+01 angle pdb=" C4' A A1399 " pdb=" C3' A A1399 " pdb=" O3' A A1399 " ideal model delta sigma weight residual 109.40 124.13 -14.73 1.50e+00 4.44e-01 9.64e+01 ... (remaining 147903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 54963 35.98 - 71.97: 7270 71.97 - 107.95: 901 107.95 - 143.94: 26 143.94 - 179.92: 58 Dihedral angle restraints: 63218 sinusoidal: 53453 harmonic: 9765 Sorted by residual: dihedral pdb=" C5' U A1241 " pdb=" C4' U A1241 " pdb=" C3' U A1241 " pdb=" O3' U A1241 " ideal model delta sinusoidal sigma weight residual 147.00 80.06 66.94 1 8.00e+00 1.56e-02 9.13e+01 dihedral pdb=" O4' U A2090 " pdb=" C1' U A2090 " pdb=" N1 U A2090 " pdb=" C2 U A2090 " ideal model delta sinusoidal sigma weight residual 200.00 30.39 169.61 1 1.50e+01 4.44e-03 8.46e+01 dihedral pdb=" O4' C A 557 " pdb=" C1' C A 557 " pdb=" N1 C A 557 " pdb=" C2 C A 557 " ideal model delta sinusoidal sigma weight residual 200.00 35.61 164.39 1 1.50e+01 4.44e-03 8.38e+01 ... (remaining 63215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.167: 16134 0.167 - 0.334: 2679 0.334 - 0.501: 35 0.501 - 0.667: 17 0.667 - 0.834: 8 Chirality restraints: 18873 Sorted by residual: chirality pdb=" C3' G A1050 " pdb=" C4' G A1050 " pdb=" O3' G A1050 " pdb=" C2' G A1050 " both_signs ideal model delta sigma weight residual False -2.74 -1.91 -0.83 2.00e-01 2.50e+01 1.74e+01 chirality pdb=" C3' G A 50 " pdb=" C4' G A 50 " pdb=" O3' G A 50 " pdb=" C2' G A 50 " both_signs ideal model delta sigma weight residual False -2.74 -1.92 -0.83 2.00e-01 2.50e+01 1.71e+01 chirality pdb=" C3' C A1048 " pdb=" C4' C A1048 " pdb=" O3' C A1048 " pdb=" C2' C A1048 " both_signs ideal model delta sigma weight residual False -2.74 -1.94 -0.81 2.00e-01 2.50e+01 1.63e+01 ... (remaining 18870 not shown) Planarity restraints: 7648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U A2665 " 0.061 2.00e-02 2.50e+03 4.14e-02 3.86e+01 pdb=" N1 U A2665 " -0.036 2.00e-02 2.50e+03 pdb=" C2 U A2665 " -0.002 2.00e-02 2.50e+03 pdb=" O2 U A2665 " 0.014 2.00e-02 2.50e+03 pdb=" N3 U A2665 " -0.068 2.00e-02 2.50e+03 pdb=" C4 U A2665 " -0.002 2.00e-02 2.50e+03 pdb=" O4 U A2665 " 0.070 2.00e-02 2.50e+03 pdb=" C5 U A2665 " -0.016 2.00e-02 2.50e+03 pdb=" C6 U A2665 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY Z 129 " -0.027 2.00e-02 2.50e+03 5.25e-02 2.76e+01 pdb=" C GLY Z 129 " 0.091 2.00e-02 2.50e+03 pdb=" O GLY Z 129 " -0.033 2.00e-02 2.50e+03 pdb=" N LYS Z 130 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A2707 " 0.067 2.00e-02 2.50e+03 3.03e-02 2.52e+01 pdb=" N9 A A2707 " -0.070 2.00e-02 2.50e+03 pdb=" C8 A A2707 " -0.009 2.00e-02 2.50e+03 pdb=" N7 A A2707 " 0.007 2.00e-02 2.50e+03 pdb=" C5 A A2707 " 0.003 2.00e-02 2.50e+03 pdb=" C6 A A2707 " 0.006 2.00e-02 2.50e+03 pdb=" N6 A A2707 " 0.017 2.00e-02 2.50e+03 pdb=" N1 A A2707 " 0.003 2.00e-02 2.50e+03 pdb=" C2 A A2707 " -0.005 2.00e-02 2.50e+03 pdb=" N3 A A2707 " -0.010 2.00e-02 2.50e+03 pdb=" C4 A A2707 " -0.009 2.00e-02 2.50e+03 ... (remaining 7645 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.13: 17 2.13 - 2.83: 22277 2.83 - 3.52: 117873 3.52 - 4.21: 287491 4.21 - 4.90: 375258 Nonbonded interactions: 802916 Sorted by model distance: nonbonded pdb=" O4 U A 219 " pdb=" N1 A A 442 " model vdw 1.443 2.496 nonbonded pdb=" O2' A A 263 " pdb=" OP1 A A 265 " model vdw 1.445 2.440 nonbonded pdb=" O2' G A 49 " pdb=" CD LYS Z 130 " model vdw 1.554 3.440 nonbonded pdb=" O2' G A1438 " pdb=" O2' A A1623 " model vdw 1.694 2.440 nonbonded pdb=" N2 G A 81 " pdb=" O4 U A 102 " model vdw 1.707 2.520 ... (remaining 802911 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 13.510 Check model and map are aligned: 0.980 Set scattering table: 0.690 Process input model: 289.770 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.210 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:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 313.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.512 98702 Z= 0.479 Angle : 1.223 19.211 147908 Z= 0.810 Chirality : 0.105 0.834 18873 Planarity : 0.007 0.074 7648 Dihedral : 24.860 179.924 56934 Min Nonbonded Distance : 1.443 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 3.00 % Allowed : 11.51 % Favored : 85.48 % Rotamer: Outliers : 6.93 % Allowed : 10.80 % Favored : 82.27 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.19 (0.11), residues: 3362 helix: -1.94 (0.14), residues: 909 sheet: -2.63 (0.22), residues: 446 loop : -3.40 (0.11), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP Y 109 HIS 0.013 0.002 HIS M 7 PHE 0.032 0.003 PHE Z 100 TYR 0.040 0.003 TYR U 37 ARG 0.022 0.002 ARG P 96 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1112 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 915 time to evaluate : 3.799 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: D 58 TYR cc_start: 0.8185 (t80) cc_final: 0.7723 (t80) REVERT: D 60 LYS cc_start: 0.8477 (mttt) cc_final: 0.8154 (mtpt) REVERT: D 159 LYS cc_start: 0.7937 (ttpt) cc_final: 0.7678 (ttpp) REVERT: D 187 THR cc_start: 0.8641 (m) cc_final: 0.8277 (p) REVERT: D 193 ASN cc_start: 0.8526 (t0) cc_final: 0.8311 (t0) REVERT: D 213 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7890 (mtp-110) REVERT: E 102 PHE cc_start: 0.8782 (t80) cc_final: 0.8547 (t80) REVERT: E 118 LYS cc_start: 0.8107 (mttt) cc_final: 0.7732 (mttm) REVERT: E 153 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7989 (mt-10) REVERT: E 154 ARG cc_start: 0.8019 (mtp85) cc_final: 0.7681 (mtp180) REVERT: E 183 GLN cc_start: 0.8552 (tt0) cc_final: 0.8283 (tt0) REVERT: E 190 LEU cc_start: 0.8160 (tp) cc_final: 0.7936 (tt) REVERT: E 222 MET cc_start: 0.8144 (mmt) cc_final: 0.7943 (mmm) REVERT: E 230 ARG cc_start: 0.8601 (mtp85) cc_final: 0.8355 (mtp180) REVERT: E 292 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8676 (mp) REVERT: F 93 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7887 (mt0) REVERT: F 139 VAL cc_start: 0.9091 (t) cc_final: 0.8830 (p) REVERT: F 171 ASN cc_start: 0.8101 (m110) cc_final: 0.7582 (m110) REVERT: F 186 LYS cc_start: 0.8044 (mmtt) cc_final: 0.7587 (mttt) REVERT: F 188 LYS cc_start: 0.8136 (tttp) cc_final: 0.7859 (tttp) REVERT: F 204 LYS cc_start: 0.8558 (mtmt) cc_final: 0.8162 (mtpp) REVERT: F 213 VAL cc_start: 0.8079 (t) cc_final: 0.7792 (p) REVERT: F 222 ASN cc_start: 0.9146 (t0) cc_final: 0.8387 (t0) REVERT: F 254 TYR cc_start: 0.7739 (t80) cc_final: 0.7492 (t80) REVERT: G 106 LEU cc_start: 0.7096 (mt) cc_final: 0.6363 (tp) REVERT: G 159 GLU cc_start: 0.0371 (OUTLIER) cc_final: 0.0114 (pm20) REVERT: G 178 ASP cc_start: 0.4560 (OUTLIER) cc_final: 0.4040 (m-30) REVERT: G 190 MET cc_start: 0.5452 (tpt) cc_final: 0.5210 (tpt) REVERT: H 109 ARG cc_start: 0.5185 (mtt180) cc_final: 0.3890 (ptp-110) REVERT: H 200 LYS cc_start: 0.7638 (mtpt) cc_final: 0.7423 (ttpt) REVERT: L 112 LYS cc_start: 0.8794 (mttt) cc_final: 0.8542 (mtmm) REVERT: L 176 HIS cc_start: 0.8303 (t-90) cc_final: 0.8053 (t-170) REVERT: L 225 LYS cc_start: 0.8166 (tttm) cc_final: 0.7948 (tptp) REVERT: L 232 GLN cc_start: 0.8640 (mt0) cc_final: 0.8220 (mp10) REVERT: L 245 ARG cc_start: 0.7745 (mpt-90) cc_final: 0.7334 (mpt-90) REVERT: M 23 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8401 (mmm160) REVERT: M 68 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7187 (pm20) REVERT: M 78 ARG cc_start: 0.8190 (mtm180) cc_final: 0.7919 (mtm180) REVERT: M 97 ARG cc_start: 0.7796 (ttm170) cc_final: 0.7522 (ttm170) REVERT: M 105 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8476 (mm-30) REVERT: M 108 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8563 (mt0) REVERT: M 112 LYS cc_start: 0.8180 (tptt) cc_final: 0.7422 (tptm) REVERT: N 79 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7537 (ptm-80) REVERT: N 115 ARG cc_start: 0.8324 (mtt180) cc_final: 0.8081 (mtt90) REVERT: N 170 PHE cc_start: 0.4381 (OUTLIER) cc_final: 0.3950 (p90) REVERT: N 182 LYS cc_start: 0.8554 (ttpp) cc_final: 0.8331 (ttpt) REVERT: O 32 TYR cc_start: 0.7159 (m-80) cc_final: 0.6851 (m-80) REVERT: O 41 TRP cc_start: 0.8146 (m-10) cc_final: 0.7794 (m-10) REVERT: O 71 ASP cc_start: 0.8972 (OUTLIER) cc_final: 0.8525 (p0) REVERT: O 111 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7049 (tm-30) REVERT: P 25 ASP cc_start: 0.7923 (m-30) cc_final: 0.7569 (m-30) REVERT: P 55 ARG cc_start: 0.8557 (mtm180) cc_final: 0.8263 (mtm110) REVERT: P 64 LEU cc_start: 0.9019 (tp) cc_final: 0.8783 (tp) REVERT: P 119 PRO cc_start: 0.9426 (Cg_exo) cc_final: 0.9208 (Cg_endo) REVERT: P 120 MET cc_start: 0.8526 (tpt) cc_final: 0.8290 (mmt) REVERT: Q 102 GLN cc_start: 0.4530 (OUTLIER) cc_final: 0.4017 (pp30) REVERT: Q 157 ASP cc_start: 0.6150 (m-30) cc_final: 0.5779 (m-30) REVERT: R 193 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7858 (mt-10) REVERT: S 45 SER cc_start: 0.9078 (t) cc_final: 0.8826 (t) REVERT: S 56 ASP cc_start: 0.7459 (OUTLIER) cc_final: 0.6969 (t70) REVERT: S 97 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8093 (tt) REVERT: S 113 ASN cc_start: 0.7107 (OUTLIER) cc_final: 0.6765 (m-40) REVERT: T 138 PRO cc_start: 0.9087 (Cg_endo) cc_final: 0.8789 (Cg_exo) REVERT: T 213 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.8101 (mtp85) REVERT: U 32 ILE cc_start: 0.8489 (tt) cc_final: 0.8185 (tt) REVERT: U 41 MET cc_start: 0.6799 (tpp) cc_final: 0.6460 (tpt) REVERT: V 185 SER cc_start: 0.8462 (m) cc_final: 0.8165 (t) REVERT: V 191 ILE cc_start: 0.8445 (mt) cc_final: 0.8191 (mm) REVERT: W 70 LYS cc_start: 0.8264 (ptmt) cc_final: 0.7980 (ptpt) REVERT: W 91 LYS cc_start: 0.8247 (tttp) cc_final: 0.8028 (mttt) REVERT: W 98 THR cc_start: 0.8612 (p) cc_final: 0.8382 (t) REVERT: W 169 ASP cc_start: 0.6940 (OUTLIER) cc_final: 0.6471 (t70) REVERT: X 86 VAL cc_start: 0.8646 (p) cc_final: 0.8249 (m) REVERT: X 106 ASN cc_start: 0.7113 (m-40) cc_final: 0.6807 (m110) REVERT: X 124 LYS cc_start: 0.8705 (tptm) cc_final: 0.8384 (ttmt) REVERT: Y 75 CYS cc_start: 0.8691 (t) cc_final: 0.8375 (t) REVERT: Y 81 LYS cc_start: 0.8668 (mttp) cc_final: 0.8410 (mmtt) REVERT: Y 93 HIS cc_start: 0.7377 (m-70) cc_final: 0.7071 (m-70) REVERT: Y 104 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.6960 (mt0) REVERT: Y 134 LEU cc_start: 0.8298 (mt) cc_final: 0.7664 (mp) REVERT: Z 88 PHE cc_start: 0.8054 (t80) cc_final: 0.7815 (t80) REVERT: Z 89 MET cc_start: 0.7579 (mmm) cc_final: 0.7257 (mmm) REVERT: Z 104 ASP cc_start: 0.8528 (m-30) cc_final: 0.8311 (m-30) REVERT: Z 115 MET cc_start: 0.8611 (mmm) cc_final: 0.8306 (tpp) REVERT: Z 116 LEU cc_start: 0.9247 (mt) cc_final: 0.8980 (mt) REVERT: Z 147 ARG cc_start: 0.7538 (ptp-170) cc_final: 0.7327 (ptp90) REVERT: 2 42 ASN cc_start: 0.7118 (m-40) cc_final: 0.6838 (m-40) REVERT: 3 7 VAL cc_start: 0.8165 (m) cc_final: 0.7747 (t) REVERT: 3 14 GLU cc_start: 0.7078 (mt-10) cc_final: 0.6732 (mt-10) REVERT: 3 32 ARG cc_start: 0.7901 (ttm170) cc_final: 0.7552 (mtt180) REVERT: 4 124 ARG cc_start: 0.7925 (ttp-110) cc_final: 0.7540 (mtp85) REVERT: 4 141 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7698 (mmmm) REVERT: 4 149 ARG cc_start: 0.7702 (mmt-90) cc_final: 0.7013 (mpt180) REVERT: 6 36 GLN cc_start: 0.8310 (tp40) cc_final: 0.8071 (tp40) REVERT: 7 138 LYS cc_start: 0.8292 (ttpt) cc_final: 0.7963 (ttmm) REVERT: 7 140 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.7605 (ptmm) REVERT: 8 89 TRP cc_start: 0.8167 (p-90) cc_final: 0.7746 (p-90) outliers start: 197 outliers final: 44 residues processed: 1043 average time/residue: 1.0106 time to fit residues: 1670.5329 Evaluate side-chains 816 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 748 time to evaluate : 3.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 213 ARG Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 292 LEU Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain G residue 178 ASP Chi-restraints excluded: chain H residue 151 HIS Chi-restraints excluded: chain I residue 73 PHE Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain M residue 23 ARG Chi-restraints excluded: chain M residue 68 GLU Chi-restraints excluded: chain M residue 105 GLU Chi-restraints excluded: chain M residue 108 GLN Chi-restraints excluded: chain N residue 79 ARG Chi-restraints excluded: chain N residue 170 PHE Chi-restraints excluded: chain N residue 186 ILE Chi-restraints excluded: chain N residue 242 ILE Chi-restraints excluded: chain N residue 244 GLU Chi-restraints excluded: chain O residue 44 SER Chi-restraints excluded: chain O residue 71 ASP Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain O residue 111 GLU Chi-restraints excluded: chain P residue 11 MET Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain Q residue 102 GLN Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 193 GLU Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 56 ASP Chi-restraints excluded: chain S residue 83 HIS Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain S residue 107 CYS Chi-restraints excluded: chain S residue 113 ASN Chi-restraints excluded: chain T residue 128 VAL Chi-restraints excluded: chain T residue 133 GLN Chi-restraints excluded: chain T residue 136 VAL Chi-restraints excluded: chain T residue 157 VAL Chi-restraints excluded: chain T residue 171 TYR Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 213 ARG Chi-restraints excluded: chain U residue 31 GLU Chi-restraints excluded: chain U residue 110 THR Chi-restraints excluded: chain W residue 56 CYS Chi-restraints excluded: chain W residue 108 THR Chi-restraints excluded: chain W residue 132 SER Chi-restraints excluded: chain W residue 169 ASP Chi-restraints excluded: chain Y residue 104 GLN Chi-restraints excluded: chain Y residue 120 ARG Chi-restraints excluded: chain Y residue 121 LEU Chi-restraints excluded: chain 2 residue 9 SER Chi-restraints excluded: chain 2 residue 11 TYR Chi-restraints excluded: chain 3 residue 30 VAL Chi-restraints excluded: chain 4 residue 96 LEU Chi-restraints excluded: chain 4 residue 98 LEU Chi-restraints excluded: chain 4 residue 141 LYS Chi-restraints excluded: chain 4 residue 143 ASN Chi-restraints excluded: chain 5 residue 155 VAL Chi-restraints excluded: chain 6 residue 7 VAL Chi-restraints excluded: chain 7 residue 140 LYS Chi-restraints excluded: chain 7 residue 141 ASN Chi-restraints excluded: chain 8 residue 50 ARG Chi-restraints excluded: chain 8 residue 54 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 526 optimal weight: 2.9990 chunk 472 optimal weight: 4.9990 chunk 262 optimal weight: 10.0000 chunk 161 optimal weight: 6.9990 chunk 319 optimal weight: 0.4980 chunk 252 optimal weight: 6.9990 chunk 489 optimal weight: 1.9990 chunk 189 optimal weight: 7.9990 chunk 297 optimal weight: 6.9990 chunk 364 optimal weight: 7.9990 chunk 566 optimal weight: 6.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 ASN D 102 HIS E 301 ASN F 93 GLN G 22 ASN G 109 ASN H 53 ASN L 97 ASN ** L 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN M 9 ASN N 117 GLN N 133 GLN N 211 GLN O 12 GLN O 35 GLN P 26 GLN P 87 HIS P 101 ASN P 117 ASN Q 93 HIS Q 108 ASN ** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 99 GLN S 106 ASN T 212 HIS U 97 ASN ** V 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 179 ASN W 59 ASN W 93 HIS W 95 HIS W 133 ASN X 68 ASN X 75 GLN X 85 GLN X 143 GLN Y 83 ASN 3 61 HIS ** 4 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 95 HIS 5 118 GLN 9 97 GLN 9 109 ASN ** 7 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.112 98702 Z= 0.349 Angle : 0.831 18.618 147908 Z= 0.420 Chirality : 0.046 0.360 18873 Planarity : 0.007 0.092 7648 Dihedral : 24.717 179.862 50087 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 1.01 % Allowed : 8.92 % Favored : 90.07 % Rotamer: Outliers : 6.86 % Allowed : 16.71 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.06 % 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: -3.18 (0.13), residues: 3362 helix: -0.60 (0.16), residues: 908 sheet: -2.48 (0.20), residues: 554 loop : -2.87 (0.13), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP Y 109 HIS 0.018 0.002 HIS P 87 PHE 0.030 0.002 PHE G 192 TYR 0.027 0.002 TYR P 104 ARG 0.017 0.001 ARG W 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1001 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 806 time to evaluate : 3.848 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: D 60 LYS cc_start: 0.8454 (mttt) cc_final: 0.8203 (mtpt) REVERT: D 97 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7710 (mttt) REVERT: D 193 ASN cc_start: 0.8569 (t0) cc_final: 0.8314 (t0) REVERT: D 213 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7899 (mtp-110) REVERT: E 118 LYS cc_start: 0.8028 (mttt) cc_final: 0.7591 (mtmm) REVERT: E 153 GLU cc_start: 0.8526 (mt-10) cc_final: 0.7998 (mt-10) REVERT: E 154 ARG cc_start: 0.8073 (mtp85) cc_final: 0.7705 (mtp180) REVERT: E 183 GLN cc_start: 0.8665 (tt0) cc_final: 0.8415 (tt0) REVERT: F 99 THR cc_start: 0.9028 (p) cc_final: 0.8808 (p) REVERT: F 204 LYS cc_start: 0.8427 (mtmt) cc_final: 0.8220 (mtpp) REVERT: F 222 ASN cc_start: 0.9233 (t0) cc_final: 0.8593 (t0) REVERT: G 20 LYS cc_start: 0.8061 (tttm) cc_final: 0.7645 (tptp) REVERT: G 98 MET cc_start: 0.3392 (ttm) cc_final: 0.3003 (ttm) REVERT: G 106 LEU cc_start: 0.7144 (mt) cc_final: 0.6479 (tp) REVERT: H 58 MET cc_start: 0.6770 (mmm) cc_final: 0.6364 (mmm) REVERT: H 90 LEU cc_start: 0.2609 (mt) cc_final: 0.2192 (tt) REVERT: H 100 ARG cc_start: 0.6841 (mtm180) cc_final: 0.6531 (ttp-170) REVERT: H 104 MET cc_start: 0.6463 (mtp) cc_final: 0.6050 (ttm) REVERT: H 109 ARG cc_start: 0.5003 (mtt180) cc_final: 0.4282 (ptp-110) REVERT: H 130 VAL cc_start: 0.6612 (t) cc_final: 0.6409 (p) REVERT: L 108 VAL cc_start: 0.8787 (m) cc_final: 0.8537 (m) REVERT: L 112 LYS cc_start: 0.8826 (mttt) cc_final: 0.8526 (mtmm) REVERT: L 152 PHE cc_start: 0.8340 (OUTLIER) cc_final: 0.8003 (m-80) REVERT: L 186 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7289 (pm20) REVERT: L 195 ILE cc_start: 0.9012 (mm) cc_final: 0.8455 (tt) REVERT: L 225 LYS cc_start: 0.8207 (tttm) cc_final: 0.7913 (tptp) REVERT: M 12 ASP cc_start: 0.8885 (OUTLIER) cc_final: 0.8616 (p0) REVERT: M 13 ASN cc_start: 0.8772 (p0) cc_final: 0.8369 (p0) REVERT: M 45 GLU cc_start: 0.8429 (pm20) cc_final: 0.7953 (pm20) REVERT: M 86 ILE cc_start: 0.9369 (mt) cc_final: 0.9148 (mp) REVERT: M 97 ARG cc_start: 0.7790 (ttm170) cc_final: 0.7479 (ttm170) REVERT: M 112 LYS cc_start: 0.8267 (tptt) cc_final: 0.7431 (tptm) REVERT: N 134 MET cc_start: 0.8360 (tpp) cc_final: 0.8131 (tpp) REVERT: N 170 PHE cc_start: 0.4674 (OUTLIER) cc_final: 0.3566 (p90) REVERT: N 182 LYS cc_start: 0.8629 (ttpp) cc_final: 0.8233 (ttpt) REVERT: O 17 MET cc_start: 0.7790 (mtm) cc_final: 0.7390 (mpp) REVERT: O 41 TRP cc_start: 0.8237 (m-10) cc_final: 0.7642 (m-10) REVERT: O 63 LYS cc_start: 0.7088 (tttt) cc_final: 0.6875 (tttt) REVERT: O 87 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8227 (mmtm) REVERT: O 111 GLU cc_start: 0.6646 (OUTLIER) cc_final: 0.6389 (tm-30) REVERT: P 25 ASP cc_start: 0.7692 (m-30) cc_final: 0.7457 (m-30) REVERT: P 31 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8190 (mp) REVERT: P 113 ARG cc_start: 0.8846 (ttm-80) cc_final: 0.8494 (ttp80) REVERT: Q 61 ARG cc_start: 0.7428 (tpp-160) cc_final: 0.6644 (tpp-160) REVERT: Q 121 GLN cc_start: 0.6305 (OUTLIER) cc_final: 0.6042 (mm110) REVERT: R 157 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6789 (pt0) REVERT: R 193 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7518 (mt-10) REVERT: R 228 ARG cc_start: 0.8200 (mtp-110) cc_final: 0.7969 (mtp-110) REVERT: S 6 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.8008 (ptp-170) REVERT: S 25 ARG cc_start: 0.8048 (ttt90) cc_final: 0.7781 (mtp-110) REVERT: S 56 ASP cc_start: 0.7440 (OUTLIER) cc_final: 0.6305 (t70) REVERT: S 84 ASP cc_start: 0.7380 (m-30) cc_final: 0.7106 (m-30) REVERT: S 85 LEU cc_start: 0.8428 (mt) cc_final: 0.8086 (tt) REVERT: S 113 ASN cc_start: 0.6974 (OUTLIER) cc_final: 0.6599 (m-40) REVERT: T 183 HIS cc_start: 0.8461 (m-70) cc_final: 0.8077 (m-70) REVERT: T 205 ASN cc_start: 0.8229 (m-40) cc_final: 0.8011 (m-40) REVERT: U 31 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7637 (pm20) REVERT: U 51 ASP cc_start: 0.8115 (m-30) cc_final: 0.7883 (m-30) REVERT: U 93 PHE cc_start: 0.5696 (OUTLIER) cc_final: 0.4790 (p90) REVERT: U 147 LYS cc_start: 0.8665 (ttmm) cc_final: 0.8253 (ttmm) REVERT: V 132 ASN cc_start: 0.8354 (t0) cc_final: 0.7824 (t0) REVERT: V 185 SER cc_start: 0.8480 (OUTLIER) cc_final: 0.8214 (t) REVERT: W 52 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7775 (mt-10) REVERT: W 70 LYS cc_start: 0.8400 (ptmt) cc_final: 0.8194 (ptmt) REVERT: W 98 THR cc_start: 0.9014 (p) cc_final: 0.8517 (t) REVERT: X 100 LYS cc_start: 0.8659 (mttt) cc_final: 0.8284 (mtpp) REVERT: X 106 ASN cc_start: 0.6912 (m-40) cc_final: 0.6667 (m110) REVERT: X 124 LYS cc_start: 0.8678 (tptm) cc_final: 0.8188 (tptm) REVERT: Y 75 CYS cc_start: 0.8692 (t) cc_final: 0.8365 (t) REVERT: Y 97 ARG cc_start: 0.7552 (ptp-170) cc_final: 0.7342 (ptp-170) REVERT: Y 104 GLN cc_start: 0.7181 (OUTLIER) cc_final: 0.6732 (mt0) REVERT: Z 89 MET cc_start: 0.7242 (mmm) cc_final: 0.6953 (mmm) REVERT: Z 104 ASP cc_start: 0.8476 (m-30) cc_final: 0.8097 (m-30) REVERT: Z 147 ARG cc_start: 0.7697 (ptp-170) cc_final: 0.7465 (ptp90) REVERT: 3 10 LYS cc_start: 0.8468 (pttm) cc_final: 0.7723 (mmtm) REVERT: 3 32 ARG cc_start: 0.8038 (ttm170) cc_final: 0.7517 (mtt180) REVERT: 4 136 LYS cc_start: 0.9002 (ttmt) cc_final: 0.8775 (ttpt) REVERT: 4 149 ARG cc_start: 0.8057 (mmt-90) cc_final: 0.7283 (mpt180) REVERT: 6 22 ARG cc_start: 0.8093 (mmt-90) cc_final: 0.7596 (mmt-90) REVERT: 6 36 GLN cc_start: 0.8276 (tp40) cc_final: 0.7862 (tp40) REVERT: 9 269 MET cc_start: 0.1139 (mmm) cc_final: 0.0895 (mmm) REVERT: 7 138 LYS cc_start: 0.8277 (ttpt) cc_final: 0.8021 (ttmm) REVERT: 7 140 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7620 (ptmm) REVERT: 8 88 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7715 (mp0) outliers start: 195 outliers final: 122 residues processed: 917 average time/residue: 0.9769 time to fit residues: 1450.2595 Evaluate side-chains 861 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 719 time to evaluate : 3.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 97 LYS Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 213 ARG Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 259 ASN Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 191 ILE Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain H residue 151 HIS Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 73 PHE Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 111 ASP Chi-restraints excluded: chain L residue 133 ILE Chi-restraints excluded: chain L residue 139 ASN Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain L residue 166 LYS Chi-restraints excluded: chain L residue 186 GLU Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 12 ASP Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 66 CYS Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 91 SER Chi-restraints excluded: chain N residue 125 ILE Chi-restraints excluded: chain N residue 154 LEU Chi-restraints excluded: chain N residue 170 PHE Chi-restraints excluded: chain N residue 175 GLU Chi-restraints excluded: chain N residue 186 ILE Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain N residue 218 SER Chi-restraints excluded: chain N residue 235 LEU Chi-restraints excluded: chain N residue 242 ILE Chi-restraints excluded: chain N residue 244 GLU Chi-restraints excluded: chain N residue 250 LEU Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 71 ASP Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain O residue 87 LYS Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain O residue 96 VAL Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain O residue 111 GLU Chi-restraints excluded: chain P residue 11 MET Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain P residue 31 LEU Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 63 THR Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 75 GLN Chi-restraints excluded: chain P residue 93 VAL Chi-restraints excluded: chain Q residue 121 GLN Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain R residue 143 ILE Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 157 GLU Chi-restraints excluded: chain R residue 193 GLU Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain S residue 6 ARG Chi-restraints excluded: chain S residue 9 ILE Chi-restraints excluded: chain S residue 56 ASP Chi-restraints excluded: chain S residue 83 HIS Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain S residue 107 CYS Chi-restraints excluded: chain S residue 113 ASN Chi-restraints excluded: chain T residue 133 GLN Chi-restraints excluded: chain T residue 136 VAL Chi-restraints excluded: chain T residue 142 ILE Chi-restraints excluded: chain T residue 157 VAL Chi-restraints excluded: chain T residue 159 ASN Chi-restraints excluded: chain T residue 161 VAL Chi-restraints excluded: chain T residue 171 TYR Chi-restraints excluded: chain T residue 174 THR Chi-restraints excluded: chain T residue 176 ILE Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 210 ILE Chi-restraints excluded: chain T residue 234 THR Chi-restraints excluded: chain U residue 30 ASP Chi-restraints excluded: chain U residue 31 GLU Chi-restraints excluded: chain U residue 93 PHE Chi-restraints excluded: chain U residue 104 GLU Chi-restraints excluded: chain U residue 110 THR Chi-restraints excluded: chain U residue 139 ILE Chi-restraints excluded: chain U residue 157 LEU Chi-restraints excluded: chain V residue 112 TYR Chi-restraints excluded: chain V residue 143 ASP Chi-restraints excluded: chain V residue 162 VAL Chi-restraints excluded: chain V residue 163 ASN Chi-restraints excluded: chain V residue 179 ASN Chi-restraints excluded: chain V residue 185 SER Chi-restraints excluded: chain W residue 56 CYS Chi-restraints excluded: chain W residue 108 THR Chi-restraints excluded: chain W residue 122 ILE Chi-restraints excluded: chain W residue 169 ASP Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 120 ASP Chi-restraints excluded: chain Y residue 89 SER Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Y residue 104 GLN Chi-restraints excluded: chain Y residue 120 ARG Chi-restraints excluded: chain Y residue 121 LEU Chi-restraints excluded: chain Z residue 81 LEU Chi-restraints excluded: chain Z residue 117 THR Chi-restraints excluded: chain 2 residue 9 SER Chi-restraints excluded: chain 2 residue 11 TYR Chi-restraints excluded: chain 2 residue 22 LYS Chi-restraints excluded: chain 3 residue 31 SER Chi-restraints excluded: chain 4 residue 96 LEU Chi-restraints excluded: chain 4 residue 98 LEU Chi-restraints excluded: chain 4 residue 120 THR Chi-restraints excluded: chain 4 residue 121 THR Chi-restraints excluded: chain 4 residue 143 ASN Chi-restraints excluded: chain 5 residue 126 THR Chi-restraints excluded: chain 6 residue 28 SER Chi-restraints excluded: chain 7 residue 112 ILE Chi-restraints excluded: chain 7 residue 140 LYS Chi-restraints excluded: chain 8 residue 50 ARG Chi-restraints excluded: chain 8 residue 72 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 314 optimal weight: 5.9990 chunk 175 optimal weight: 7.9990 chunk 471 optimal weight: 0.5980 chunk 385 optimal weight: 9.9990 chunk 156 optimal weight: 20.0000 chunk 567 optimal weight: 0.9990 chunk 613 optimal weight: 3.9990 chunk 505 optimal weight: 0.0980 chunk 562 optimal weight: 9.9990 chunk 193 optimal weight: 6.9990 chunk 455 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 301 ASN G 60 GLN G 70 ASN L 157 ASN L 220 HIS O 12 GLN ** P 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 202 ASN S 83 HIS ** S 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 59 ASN ** X 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 93 HIS ** 4 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 98702 Z= 0.214 Angle : 0.668 17.909 147908 Z= 0.345 Chirality : 0.039 0.298 18873 Planarity : 0.005 0.094 7648 Dihedral : 24.443 179.922 50035 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.80 % Allowed : 8.77 % Favored : 90.42 % Rotamer: Outliers : 6.58 % Allowed : 19.87 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.14), residues: 3362 helix: -0.15 (0.16), residues: 936 sheet: -2.21 (0.21), residues: 529 loop : -2.56 (0.13), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP T 141 HIS 0.011 0.001 HIS E 215 PHE 0.017 0.002 PHE Z 100 TYR 0.032 0.002 TYR P 104 ARG 0.014 0.001 ARG R 223 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 966 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 779 time to evaluate : 3.772 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: D 131 MET cc_start: 0.9209 (mmm) cc_final: 0.8967 (tpp) REVERT: D 193 ASN cc_start: 0.8448 (t0) cc_final: 0.8115 (t0) REVERT: D 208 ARG cc_start: 0.8706 (mmm-85) cc_final: 0.8475 (mmm160) REVERT: D 209 TRP cc_start: 0.8630 (p90) cc_final: 0.8136 (p90) REVERT: E 118 LYS cc_start: 0.7991 (mttt) cc_final: 0.7664 (mttm) REVERT: E 153 GLU cc_start: 0.8506 (mt-10) cc_final: 0.7928 (mt-10) REVERT: E 183 GLN cc_start: 0.8733 (tt0) cc_final: 0.8506 (tt0) REVERT: F 129 GLN cc_start: 0.8620 (mm-40) cc_final: 0.8171 (mm-40) REVERT: F 152 MET cc_start: 0.7928 (ttt) cc_final: 0.7659 (ttt) REVERT: F 214 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7947 (tm-30) REVERT: F 222 ASN cc_start: 0.9115 (t0) cc_final: 0.8347 (t0) REVERT: G 20 LYS cc_start: 0.8025 (tttm) cc_final: 0.7514 (tttm) REVERT: G 49 ILE cc_start: 0.6297 (mt) cc_final: 0.5790 (mp) REVERT: G 98 MET cc_start: 0.3004 (ttm) cc_final: 0.2534 (ttm) REVERT: G 106 LEU cc_start: 0.7159 (mt) cc_final: 0.6239 (tp) REVERT: G 111 MET cc_start: 0.4377 (OUTLIER) cc_final: 0.3112 (ttp) REVERT: H 58 MET cc_start: 0.6845 (mmm) cc_final: 0.6475 (mmm) REVERT: H 90 LEU cc_start: 0.2721 (mt) cc_final: 0.2210 (tt) REVERT: H 109 ARG cc_start: 0.5320 (mtt180) cc_final: 0.4125 (ptp-110) REVERT: H 155 MET cc_start: 0.6469 (mmm) cc_final: 0.5994 (mtt) REVERT: I 43 LYS cc_start: 0.6801 (OUTLIER) cc_final: 0.6477 (pmmt) REVERT: L 94 ASP cc_start: 0.8138 (t0) cc_final: 0.7909 (t70) REVERT: L 186 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7075 (pm20) REVERT: L 195 ILE cc_start: 0.9009 (mm) cc_final: 0.8448 (tt) REVERT: L 207 MET cc_start: 0.8138 (mmt) cc_final: 0.7696 (mmt) REVERT: L 225 LYS cc_start: 0.8116 (tttm) cc_final: 0.7880 (tptp) REVERT: M 12 ASP cc_start: 0.8772 (OUTLIER) cc_final: 0.8525 (p0) REVERT: M 13 ASN cc_start: 0.8704 (p0) cc_final: 0.8418 (p0) REVERT: M 45 GLU cc_start: 0.8307 (pm20) cc_final: 0.7847 (pm20) REVERT: M 97 ARG cc_start: 0.7735 (ttm170) cc_final: 0.7480 (ttm170) REVERT: M 112 LYS cc_start: 0.8274 (tptt) cc_final: 0.7437 (tptm) REVERT: N 134 MET cc_start: 0.8298 (tpp) cc_final: 0.7917 (tpp) REVERT: N 170 PHE cc_start: 0.4515 (OUTLIER) cc_final: 0.3344 (p90) REVERT: N 182 LYS cc_start: 0.8554 (ttpp) cc_final: 0.8162 (ttpt) REVERT: P 84 GLN cc_start: 0.8243 (mm-40) cc_final: 0.7898 (mt0) REVERT: R 193 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7615 (mt-10) REVERT: R 216 LYS cc_start: 0.8641 (ttmm) cc_final: 0.8279 (mttp) REVERT: R 228 ARG cc_start: 0.8105 (mtp-110) cc_final: 0.7801 (mtp-110) REVERT: S 6 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.7733 (ptp-170) REVERT: S 56 ASP cc_start: 0.7249 (OUTLIER) cc_final: 0.6219 (t70) REVERT: S 84 ASP cc_start: 0.7497 (m-30) cc_final: 0.7168 (m-30) REVERT: S 85 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8135 (tt) REVERT: S 88 ARG cc_start: 0.7417 (mmm160) cc_final: 0.7074 (tpt90) REVERT: S 113 ASN cc_start: 0.6961 (OUTLIER) cc_final: 0.6634 (m-40) REVERT: T 121 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7422 (tm-30) REVERT: U 31 GLU cc_start: 0.7636 (pm20) cc_final: 0.7270 (pm20) REVERT: U 51 ASP cc_start: 0.8162 (m-30) cc_final: 0.7865 (m-30) REVERT: U 70 TYR cc_start: 0.8626 (m-80) cc_final: 0.8413 (m-10) REVERT: U 93 PHE cc_start: 0.5229 (OUTLIER) cc_final: 0.4081 (p90) REVERT: V 132 ASN cc_start: 0.8436 (t0) cc_final: 0.7937 (t0) REVERT: V 185 SER cc_start: 0.8499 (OUTLIER) cc_final: 0.8247 (t) REVERT: W 49 LYS cc_start: 0.7765 (mttt) cc_final: 0.7515 (mttm) REVERT: W 96 ASN cc_start: 0.7522 (m-40) cc_final: 0.7304 (m-40) REVERT: W 98 THR cc_start: 0.9009 (p) cc_final: 0.8560 (t) REVERT: W 129 ILE cc_start: 0.9040 (tt) cc_final: 0.8754 (pt) REVERT: X 123 VAL cc_start: 0.9245 (OUTLIER) cc_final: 0.8996 (m) REVERT: X 124 LYS cc_start: 0.8653 (tptm) cc_final: 0.8277 (tptm) REVERT: Y 104 GLN cc_start: 0.6857 (OUTLIER) cc_final: 0.6653 (mt0) REVERT: Y 109 TRP cc_start: 0.6983 (t-100) cc_final: 0.6739 (t-100) REVERT: Z 88 PHE cc_start: 0.7568 (t80) cc_final: 0.7315 (t80) REVERT: Z 89 MET cc_start: 0.7247 (mmm) cc_final: 0.6949 (mmm) REVERT: Z 147 ARG cc_start: 0.7670 (ptp-170) cc_final: 0.7295 (ptp-110) REVERT: 2 11 TYR cc_start: 0.8248 (OUTLIER) cc_final: 0.6613 (p90) REVERT: 2 22 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7876 (mmtt) REVERT: 3 32 ARG cc_start: 0.7909 (ttm170) cc_final: 0.7429 (mtt180) REVERT: 4 149 ARG cc_start: 0.7955 (mmt-90) cc_final: 0.7707 (mpt180) REVERT: 9 269 MET cc_start: 0.1303 (mmm) cc_final: 0.0982 (mmm) REVERT: 7 140 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.6998 (ptmm) REVERT: 8 69 ARG cc_start: 0.8311 (ttt90) cc_final: 0.7974 (ttt180) REVERT: 8 88 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7641 (mt-10) outliers start: 187 outliers final: 112 residues processed: 884 average time/residue: 1.0312 time to fit residues: 1494.3484 Evaluate side-chains 860 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 730 time to evaluate : 3.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 259 ASN Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain F residue 191 ILE Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 110 LEU Chi-restraints excluded: chain G residue 111 MET Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 73 PHE Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 133 ILE Chi-restraints excluded: chain L residue 139 ASN Chi-restraints excluded: chain L residue 186 GLU Chi-restraints excluded: chain M residue 12 ASP Chi-restraints excluded: chain M residue 29 ASN Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 66 CYS Chi-restraints excluded: chain N residue 91 SER Chi-restraints excluded: chain N residue 125 ILE Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 170 PHE Chi-restraints excluded: chain N residue 175 GLU Chi-restraints excluded: chain N residue 186 ILE Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain N residue 218 SER Chi-restraints excluded: chain N residue 234 VAL Chi-restraints excluded: chain N residue 242 ILE Chi-restraints excluded: chain N residue 244 GLU Chi-restraints excluded: chain O residue 68 ILE Chi-restraints excluded: chain O residue 71 ASP Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain O residue 96 VAL Chi-restraints excluded: chain P residue 11 MET Chi-restraints excluded: chain P residue 31 LEU Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 75 GLN Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain R residue 143 ILE Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 193 GLU Chi-restraints excluded: chain R residue 194 ILE Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain S residue 6 ARG Chi-restraints excluded: chain S residue 9 ILE Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 56 ASP Chi-restraints excluded: chain S residue 69 ILE Chi-restraints excluded: chain S residue 83 HIS Chi-restraints excluded: chain S residue 85 LEU Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain S residue 113 ASN Chi-restraints excluded: chain T residue 142 ILE Chi-restraints excluded: chain T residue 157 VAL Chi-restraints excluded: chain T residue 159 ASN Chi-restraints excluded: chain T residue 161 VAL Chi-restraints excluded: chain T residue 171 TYR Chi-restraints excluded: chain T residue 174 THR Chi-restraints excluded: chain T residue 176 ILE Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 210 ILE Chi-restraints excluded: chain T residue 234 THR Chi-restraints excluded: chain U residue 29 CYS Chi-restraints excluded: chain U residue 79 LEU Chi-restraints excluded: chain U residue 93 PHE Chi-restraints excluded: chain U residue 104 GLU Chi-restraints excluded: chain U residue 110 THR Chi-restraints excluded: chain U residue 139 ILE Chi-restraints excluded: chain U residue 157 LEU Chi-restraints excluded: chain V residue 112 TYR Chi-restraints excluded: chain V residue 143 ASP Chi-restraints excluded: chain V residue 163 ASN Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 SER Chi-restraints excluded: chain W residue 56 CYS Chi-restraints excluded: chain W residue 108 THR Chi-restraints excluded: chain W residue 122 ILE Chi-restraints excluded: chain W residue 132 SER Chi-restraints excluded: chain W residue 145 ASP Chi-restraints excluded: chain W residue 151 ILE Chi-restraints excluded: chain W residue 169 ASP Chi-restraints excluded: chain X residue 72 SER Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 120 ASP Chi-restraints excluded: chain X residue 123 VAL Chi-restraints excluded: chain Y residue 82 SER Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Y residue 104 GLN Chi-restraints excluded: chain Y residue 120 ARG Chi-restraints excluded: chain Z residue 81 LEU Chi-restraints excluded: chain Z residue 117 THR Chi-restraints excluded: chain 2 residue 11 TYR Chi-restraints excluded: chain 2 residue 22 LYS Chi-restraints excluded: chain 3 residue 19 VAL Chi-restraints excluded: chain 3 residue 23 VAL Chi-restraints excluded: chain 3 residue 31 SER Chi-restraints excluded: chain 3 residue 58 HIS Chi-restraints excluded: chain 3 residue 64 ILE Chi-restraints excluded: chain 4 residue 96 LEU Chi-restraints excluded: chain 4 residue 98 LEU Chi-restraints excluded: chain 4 residue 143 ASN Chi-restraints excluded: chain 6 residue 7 VAL Chi-restraints excluded: chain 6 residue 28 SER Chi-restraints excluded: chain 7 residue 140 LYS Chi-restraints excluded: chain 8 residue 50 ARG Chi-restraints excluded: chain 8 residue 72 ILE Chi-restraints excluded: chain 8 residue 88 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 560 optimal weight: 8.9990 chunk 426 optimal weight: 7.9990 chunk 294 optimal weight: 8.9990 chunk 62 optimal weight: 8.9990 chunk 270 optimal weight: 20.0000 chunk 381 optimal weight: 9.9990 chunk 569 optimal weight: 2.9990 chunk 603 optimal weight: 6.9990 chunk 297 optimal weight: 0.3980 chunk 539 optimal weight: 1.9990 chunk 162 optimal weight: 7.9990 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 102 HIS L 170 GLN N 211 GLN O 12 GLN ** P 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 174 ASN R 202 ASN S 53 GLN ** S 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 104 ASN ** T 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 59 ASN ** X 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 137 GLN ** 6 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.125 98702 Z= 0.387 Angle : 0.803 15.276 147908 Z= 0.403 Chirality : 0.045 0.369 18873 Planarity : 0.006 0.085 7648 Dihedral : 24.434 179.718 50006 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.77 % Allowed : 10.59 % Favored : 88.64 % Rotamer: Outliers : 8.27 % Allowed : 20.58 % Favored : 71.16 % 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: -2.72 (0.13), residues: 3362 helix: -0.31 (0.16), residues: 929 sheet: -2.15 (0.21), residues: 551 loop : -2.57 (0.13), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP W 51 HIS 0.011 0.002 HIS P 87 PHE 0.023 0.002 PHE 3 51 TYR 0.028 0.002 TYR P 104 ARG 0.011 0.001 ARG Z 131 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 992 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 757 time to evaluate : 3.664 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: D 131 MET cc_start: 0.9302 (mmm) cc_final: 0.8912 (mpp) REVERT: D 193 ASN cc_start: 0.8578 (t0) cc_final: 0.8259 (t0) REVERT: D 209 TRP cc_start: 0.8594 (p90) cc_final: 0.8153 (p90) REVERT: E 153 GLU cc_start: 0.8572 (mt-10) cc_final: 0.7949 (mt-10) REVERT: E 154 ARG cc_start: 0.8100 (mtp85) cc_final: 0.7615 (mtt180) REVERT: E 193 GLU cc_start: 0.7675 (tp30) cc_final: 0.7441 (tp30) REVERT: F 154 LYS cc_start: 0.8398 (mttt) cc_final: 0.8080 (mttp) REVERT: F 161 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8773 (tt) REVERT: F 214 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7531 (tm-30) REVERT: F 222 ASN cc_start: 0.9177 (t0) cc_final: 0.8394 (t0) REVERT: G 20 LYS cc_start: 0.7970 (tttm) cc_final: 0.7445 (tttm) REVERT: G 27 MET cc_start: 0.5137 (ptt) cc_final: 0.4732 (ptt) REVERT: G 30 LEU cc_start: 0.6735 (mp) cc_final: 0.6192 (pp) REVERT: G 49 ILE cc_start: 0.6378 (mt) cc_final: 0.5814 (mp) REVERT: G 106 LEU cc_start: 0.7056 (mt) cc_final: 0.6053 (tp) REVERT: G 111 MET cc_start: 0.4211 (OUTLIER) cc_final: 0.2926 (ttp) REVERT: H 58 MET cc_start: 0.6484 (mmm) cc_final: 0.6140 (mmm) REVERT: H 109 ARG cc_start: 0.5159 (mtt180) cc_final: 0.2793 (mtt180) REVERT: H 200 LYS cc_start: 0.7650 (mtpt) cc_final: 0.7103 (ttpt) REVERT: H 203 ARG cc_start: 0.6992 (mtp180) cc_final: 0.6678 (mtp180) REVERT: H 213 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7579 (pm20) REVERT: I 43 LYS cc_start: 0.6763 (OUTLIER) cc_final: 0.6065 (pmmt) REVERT: I 44 LYS cc_start: 0.7358 (tptp) cc_final: 0.7148 (tptp) REVERT: I 63 LYS cc_start: 0.7096 (mtpp) cc_final: 0.6783 (mtpp) REVERT: L 94 ASP cc_start: 0.8157 (t0) cc_final: 0.7942 (t70) REVERT: L 186 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7229 (pm20) REVERT: L 195 ILE cc_start: 0.9070 (mm) cc_final: 0.8543 (tt) REVERT: L 207 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7643 (mmt) REVERT: L 225 LYS cc_start: 0.8156 (tttm) cc_final: 0.7880 (tptp) REVERT: M 12 ASP cc_start: 0.8899 (OUTLIER) cc_final: 0.8624 (p0) REVERT: M 13 ASN cc_start: 0.8773 (p0) cc_final: 0.8514 (p0) REVERT: M 45 GLU cc_start: 0.8391 (pm20) cc_final: 0.7919 (pm20) REVERT: M 78 ARG cc_start: 0.7635 (mtm180) cc_final: 0.7427 (ttm170) REVERT: M 97 ARG cc_start: 0.7723 (ttm170) cc_final: 0.7475 (ttm170) REVERT: M 112 LYS cc_start: 0.8297 (tptt) cc_final: 0.7502 (tptm) REVERT: N 170 PHE cc_start: 0.4711 (OUTLIER) cc_final: 0.3247 (p90) REVERT: N 182 LYS cc_start: 0.8609 (ttpp) cc_final: 0.8222 (ttpt) REVERT: N 186 ILE cc_start: 0.8054 (OUTLIER) cc_final: 0.7719 (mt) REVERT: N 193 GLU cc_start: 0.8084 (pm20) cc_final: 0.7867 (pm20) REVERT: O 63 LYS cc_start: 0.7089 (tttt) cc_final: 0.6851 (tttt) REVERT: Q 81 HIS cc_start: 0.7240 (m-70) cc_final: 0.6762 (t-90) REVERT: Q 121 GLN cc_start: 0.6103 (OUTLIER) cc_final: 0.5724 (mm110) REVERT: R 207 LYS cc_start: 0.7730 (tttt) cc_final: 0.7321 (mtpp) REVERT: R 216 LYS cc_start: 0.8759 (ttmm) cc_final: 0.8431 (mttp) REVERT: R 228 ARG cc_start: 0.8157 (mtp-110) cc_final: 0.7888 (mtp-110) REVERT: S 6 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8112 (ptp-170) REVERT: S 56 ASP cc_start: 0.7462 (OUTLIER) cc_final: 0.7056 (t70) REVERT: S 84 ASP cc_start: 0.7774 (m-30) cc_final: 0.7310 (m-30) REVERT: S 85 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8171 (tt) REVERT: S 113 ASN cc_start: 0.7056 (OUTLIER) cc_final: 0.6764 (m-40) REVERT: T 121 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7508 (tm-30) REVERT: T 123 ILE cc_start: 0.8346 (pt) cc_final: 0.7698 (pp) REVERT: U 31 GLU cc_start: 0.7631 (pm20) cc_final: 0.7260 (pm20) REVERT: U 91 LYS cc_start: 0.7965 (mttm) cc_final: 0.7603 (mttm) REVERT: U 93 PHE cc_start: 0.5527 (OUTLIER) cc_final: 0.4341 (p90) REVERT: V 132 ASN cc_start: 0.8733 (t0) cc_final: 0.8222 (t0) REVERT: V 185 SER cc_start: 0.8603 (OUTLIER) cc_final: 0.8394 (t) REVERT: W 70 LYS cc_start: 0.8559 (ptmt) cc_final: 0.8253 (mtpt) REVERT: W 96 ASN cc_start: 0.7679 (m-40) cc_final: 0.7447 (m-40) REVERT: W 98 THR cc_start: 0.9030 (p) cc_final: 0.8502 (t) REVERT: X 124 LYS cc_start: 0.8697 (tptm) cc_final: 0.8314 (tptm) REVERT: Y 104 GLN cc_start: 0.7134 (OUTLIER) cc_final: 0.6858 (mt0) REVERT: Y 109 TRP cc_start: 0.7200 (t-100) cc_final: 0.6895 (t-100) REVERT: Z 88 PHE cc_start: 0.7718 (t80) cc_final: 0.7507 (t80) REVERT: Z 89 MET cc_start: 0.7344 (mmm) cc_final: 0.6899 (mmm) REVERT: Z 116 LEU cc_start: 0.9098 (mt) cc_final: 0.8867 (mm) REVERT: Z 147 ARG cc_start: 0.7805 (ptp-170) cc_final: 0.7448 (ptp-110) REVERT: 3 10 LYS cc_start: 0.8474 (pttm) cc_final: 0.7677 (mmtm) REVERT: 3 32 ARG cc_start: 0.7938 (ttm170) cc_final: 0.7455 (mtt180) REVERT: 4 136 LYS cc_start: 0.9099 (ttpt) cc_final: 0.8807 (ttpt) REVERT: 4 149 ARG cc_start: 0.7955 (mmt-90) cc_final: 0.7737 (mpt180) REVERT: 5 90 TYR cc_start: 0.7384 (OUTLIER) cc_final: 0.7017 (t80) REVERT: 9 269 MET cc_start: 0.1252 (mmm) cc_final: 0.0942 (mmm) REVERT: 7 140 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7113 (ptmm) REVERT: 8 69 ARG cc_start: 0.8481 (ttt90) cc_final: 0.8204 (ttt180) REVERT: 8 88 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7664 (mp0) REVERT: 8 89 TRP cc_start: 0.7969 (p-90) cc_final: 0.7599 (p90) outliers start: 235 outliers final: 166 residues processed: 883 average time/residue: 0.9781 time to fit residues: 1417.7140 Evaluate side-chains 917 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 732 time to evaluate : 3.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 163 LYS Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 259 ASN Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain F residue 191 ILE Chi-restraints excluded: chain F residue 200 ASP Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 110 LEU Chi-restraints excluded: chain G residue 111 MET Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 73 PHE Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 133 ILE Chi-restraints excluded: chain L residue 139 ASN Chi-restraints excluded: chain L residue 186 GLU Chi-restraints excluded: chain L residue 207 MET Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 12 ASP Chi-restraints excluded: chain M residue 25 ILE Chi-restraints excluded: chain M residue 29 ASN Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 66 CYS Chi-restraints excluded: chain M residue 73 ASN Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain N residue 91 SER Chi-restraints excluded: chain N residue 154 LEU Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 170 PHE Chi-restraints excluded: chain N residue 175 GLU Chi-restraints excluded: chain N residue 186 ILE Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain N residue 218 SER Chi-restraints excluded: chain N residue 234 VAL Chi-restraints excluded: chain N residue 235 LEU Chi-restraints excluded: chain N residue 242 ILE Chi-restraints excluded: chain N residue 244 GLU Chi-restraints excluded: chain O residue 32 TYR Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 68 ILE Chi-restraints excluded: chain O residue 71 ASP Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain O residue 96 VAL Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain O residue 127 ILE Chi-restraints excluded: chain P residue 11 MET Chi-restraints excluded: chain P residue 31 LEU Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 63 THR Chi-restraints excluded: chain P residue 67 GLU Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 75 GLN Chi-restraints excluded: chain P residue 111 LEU Chi-restraints excluded: chain P residue 123 ILE Chi-restraints excluded: chain Q residue 121 GLN Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain R residue 143 ILE Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 180 THR Chi-restraints excluded: chain R residue 194 ILE Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain S residue 6 ARG Chi-restraints excluded: chain S residue 9 ILE Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 53 GLN Chi-restraints excluded: chain S residue 56 ASP Chi-restraints excluded: chain S residue 62 ILE Chi-restraints excluded: chain S residue 83 HIS Chi-restraints excluded: chain S residue 85 LEU Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain S residue 113 ASN Chi-restraints excluded: chain T residue 136 VAL Chi-restraints excluded: chain T residue 142 ILE Chi-restraints excluded: chain T residue 159 ASN Chi-restraints excluded: chain T residue 161 VAL Chi-restraints excluded: chain T residue 171 TYR Chi-restraints excluded: chain T residue 176 ILE Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 210 ILE Chi-restraints excluded: chain T residue 234 THR Chi-restraints excluded: chain U residue 29 CYS Chi-restraints excluded: chain U residue 30 ASP Chi-restraints excluded: chain U residue 32 ILE Chi-restraints excluded: chain U residue 38 SER Chi-restraints excluded: chain U residue 79 LEU Chi-restraints excluded: chain U residue 93 PHE Chi-restraints excluded: chain U residue 104 GLU Chi-restraints excluded: chain U residue 110 THR Chi-restraints excluded: chain U residue 139 ILE Chi-restraints excluded: chain U residue 149 LEU Chi-restraints excluded: chain U residue 157 LEU Chi-restraints excluded: chain V residue 112 TYR Chi-restraints excluded: chain V residue 143 ASP Chi-restraints excluded: chain V residue 162 VAL Chi-restraints excluded: chain V residue 163 ASN Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 SER Chi-restraints excluded: chain W residue 56 CYS Chi-restraints excluded: chain W residue 108 THR Chi-restraints excluded: chain W residue 122 ILE Chi-restraints excluded: chain W residue 132 SER Chi-restraints excluded: chain W residue 145 ASP Chi-restraints excluded: chain W residue 151 ILE Chi-restraints excluded: chain W residue 169 ASP Chi-restraints excluded: chain X residue 72 SER Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 120 ASP Chi-restraints excluded: chain X residue 123 VAL Chi-restraints excluded: chain X residue 160 LEU Chi-restraints excluded: chain Y residue 72 ARG Chi-restraints excluded: chain Y residue 82 SER Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Y residue 104 GLN Chi-restraints excluded: chain Y residue 120 ARG Chi-restraints excluded: chain Y residue 129 ILE Chi-restraints excluded: chain Z residue 76 LEU Chi-restraints excluded: chain Z residue 81 LEU Chi-restraints excluded: chain Z residue 117 THR Chi-restraints excluded: chain Z residue 138 LYS Chi-restraints excluded: chain 2 residue 11 TYR Chi-restraints excluded: chain 2 residue 22 LYS Chi-restraints excluded: chain 2 residue 29 LEU Chi-restraints excluded: chain 3 residue 19 VAL Chi-restraints excluded: chain 3 residue 23 VAL Chi-restraints excluded: chain 3 residue 31 SER Chi-restraints excluded: chain 3 residue 58 HIS Chi-restraints excluded: chain 4 residue 96 LEU Chi-restraints excluded: chain 4 residue 98 LEU Chi-restraints excluded: chain 4 residue 143 ASN Chi-restraints excluded: chain 5 residue 90 TYR Chi-restraints excluded: chain 5 residue 126 THR Chi-restraints excluded: chain 5 residue 135 LEU Chi-restraints excluded: chain 5 residue 150 LEU Chi-restraints excluded: chain 6 residue 3 ILE Chi-restraints excluded: chain 6 residue 7 VAL Chi-restraints excluded: chain 7 residue 112 ILE Chi-restraints excluded: chain 7 residue 140 LYS Chi-restraints excluded: chain 7 residue 141 ASN Chi-restraints excluded: chain 8 residue 50 ARG Chi-restraints excluded: chain 8 residue 72 ILE Chi-restraints excluded: chain 8 residue 88 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 502 optimal weight: 1.9990 chunk 342 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 449 optimal weight: 2.9990 chunk 248 optimal weight: 10.0000 chunk 514 optimal weight: 4.9990 chunk 416 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 307 optimal weight: 2.9990 chunk 541 optimal weight: 6.9990 chunk 152 optimal weight: 10.0000 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 288 ASN G 52 ASN O 12 GLN R 202 ASN ** S 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 59 ASN ** 4 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 137 GLN ** 6 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 98702 Z= 0.264 Angle : 0.703 18.675 147908 Z= 0.358 Chirality : 0.040 0.374 18873 Planarity : 0.006 0.086 7648 Dihedral : 24.378 179.830 50002 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.71 % Allowed : 9.96 % Favored : 89.32 % Rotamer: Outliers : 7.35 % Allowed : 22.86 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.14), residues: 3362 helix: -0.09 (0.17), residues: 921 sheet: -2.15 (0.20), residues: 567 loop : -2.42 (0.13), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP T 141 HIS 0.009 0.001 HIS H 105 PHE 0.018 0.002 PHE Z 100 TYR 0.025 0.002 TYR D 261 ARG 0.008 0.001 ARG S 11 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 957 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 748 time to evaluate : 3.715 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: D 131 MET cc_start: 0.9242 (mmm) cc_final: 0.8923 (mpp) REVERT: D 182 LYS cc_start: 0.8107 (pttt) cc_final: 0.7724 (ptmm) REVERT: D 188 VAL cc_start: 0.8405 (p) cc_final: 0.8132 (m) REVERT: D 193 ASN cc_start: 0.8501 (t0) cc_final: 0.8211 (t0) REVERT: D 209 TRP cc_start: 0.8567 (p90) cc_final: 0.8044 (p90) REVERT: E 153 GLU cc_start: 0.8528 (mt-10) cc_final: 0.7908 (mt-10) REVERT: E 154 ARG cc_start: 0.8076 (mtp85) cc_final: 0.7537 (mtt180) REVERT: E 193 GLU cc_start: 0.7715 (tp30) cc_final: 0.7453 (tp30) REVERT: F 67 GLU cc_start: 0.6957 (OUTLIER) cc_final: 0.6637 (pt0) REVERT: F 152 MET cc_start: 0.7992 (ttt) cc_final: 0.7617 (ttt) REVERT: F 214 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7542 (tm-30) REVERT: F 222 ASN cc_start: 0.9158 (t0) cc_final: 0.8396 (t0) REVERT: G 20 LYS cc_start: 0.8003 (tttm) cc_final: 0.7418 (tptt) REVERT: G 49 ILE cc_start: 0.6306 (mt) cc_final: 0.4778 (mp) REVERT: G 98 MET cc_start: 0.3202 (ttm) cc_final: 0.2693 (ttm) REVERT: G 106 LEU cc_start: 0.7051 (mt) cc_final: 0.6509 (tp) REVERT: G 111 MET cc_start: 0.3996 (OUTLIER) cc_final: 0.2037 (tmm) REVERT: H 58 MET cc_start: 0.6356 (mmm) cc_final: 0.6049 (mmm) REVERT: H 100 ARG cc_start: 0.6554 (ttp-170) cc_final: 0.6254 (ttp-170) REVERT: H 109 ARG cc_start: 0.5270 (mtt180) cc_final: 0.2844 (mtt180) REVERT: H 200 LYS cc_start: 0.7538 (mtpt) cc_final: 0.6885 (ttpt) REVERT: H 213 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7634 (pm20) REVERT: I 43 LYS cc_start: 0.6785 (OUTLIER) cc_final: 0.6231 (pmmt) REVERT: I 44 LYS cc_start: 0.7368 (tptp) cc_final: 0.7165 (tptp) REVERT: I 63 LYS cc_start: 0.6969 (mtpp) cc_final: 0.6628 (mtpp) REVERT: L 94 ASP cc_start: 0.8177 (t0) cc_final: 0.7974 (t70) REVERT: L 186 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7177 (pm20) REVERT: L 195 ILE cc_start: 0.9067 (mm) cc_final: 0.8535 (tt) REVERT: L 207 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7664 (mmt) REVERT: L 225 LYS cc_start: 0.8143 (tttm) cc_final: 0.7848 (tptp) REVERT: M 12 ASP cc_start: 0.8878 (OUTLIER) cc_final: 0.8593 (p0) REVERT: M 13 ASN cc_start: 0.8751 (p0) cc_final: 0.8520 (p0) REVERT: M 45 GLU cc_start: 0.8318 (pm20) cc_final: 0.7855 (pm20) REVERT: M 97 ARG cc_start: 0.7751 (ttm170) cc_final: 0.7471 (ttm170) REVERT: M 112 LYS cc_start: 0.8261 (tptt) cc_final: 0.7469 (tptm) REVERT: N 170 PHE cc_start: 0.4655 (OUTLIER) cc_final: 0.3105 (p90) REVERT: N 182 LYS cc_start: 0.8580 (ttpp) cc_final: 0.8190 (ttpt) REVERT: Q 121 GLN cc_start: 0.6031 (OUTLIER) cc_final: 0.5682 (mm110) REVERT: R 185 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.8005 (ttt90) REVERT: R 216 LYS cc_start: 0.8750 (ttmm) cc_final: 0.8460 (mttp) REVERT: R 228 ARG cc_start: 0.8127 (mtp-110) cc_final: 0.7886 (mtp-110) REVERT: S 6 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.7873 (ptp-170) REVERT: S 56 ASP cc_start: 0.7269 (OUTLIER) cc_final: 0.6940 (t70) REVERT: S 84 ASP cc_start: 0.7687 (m-30) cc_final: 0.7334 (m-30) REVERT: S 113 ASN cc_start: 0.6979 (OUTLIER) cc_final: 0.6468 (m-40) REVERT: T 121 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7477 (tm-30) REVERT: T 123 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.7846 (pp) REVERT: U 31 GLU cc_start: 0.7526 (pm20) cc_final: 0.7193 (pm20) REVERT: U 70 TYR cc_start: 0.8636 (m-80) cc_final: 0.8418 (m-80) REVERT: U 93 PHE cc_start: 0.5435 (OUTLIER) cc_final: 0.4209 (p90) REVERT: U 97 ASN cc_start: 0.8169 (OUTLIER) cc_final: 0.7903 (t0) REVERT: V 132 ASN cc_start: 0.8756 (t0) cc_final: 0.8205 (t0) REVERT: V 162 VAL cc_start: 0.8468 (OUTLIER) cc_final: 0.8143 (p) REVERT: V 185 SER cc_start: 0.8573 (OUTLIER) cc_final: 0.8369 (t) REVERT: W 70 LYS cc_start: 0.8467 (ptmt) cc_final: 0.8142 (mtpt) REVERT: X 124 LYS cc_start: 0.8669 (tptm) cc_final: 0.8288 (tptm) REVERT: Y 109 TRP cc_start: 0.7315 (t-100) cc_final: 0.6993 (t-100) REVERT: Z 66 LYS cc_start: 0.8182 (mttt) cc_final: 0.7558 (mmmt) REVERT: Z 88 PHE cc_start: 0.7663 (t80) cc_final: 0.7440 (t80) REVERT: Z 89 MET cc_start: 0.7408 (mmm) cc_final: 0.6898 (mmm) REVERT: Z 147 ARG cc_start: 0.7791 (ptp-170) cc_final: 0.7440 (ptp-110) REVERT: 2 11 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.6683 (p90) REVERT: 2 22 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.8021 (mmtt) REVERT: 3 10 LYS cc_start: 0.8453 (pttm) cc_final: 0.7661 (mmtm) REVERT: 3 32 ARG cc_start: 0.7910 (ttm170) cc_final: 0.7436 (mtt180) REVERT: 4 149 ARG cc_start: 0.7978 (mmt-90) cc_final: 0.7535 (mpt180) REVERT: 9 269 MET cc_start: 0.0928 (mmm) cc_final: 0.0659 (mmm) REVERT: 7 140 LYS cc_start: 0.7616 (OUTLIER) cc_final: 0.6889 (ptmm) REVERT: 8 69 ARG cc_start: 0.8463 (ttt90) cc_final: 0.8071 (ttt180) REVERT: 8 88 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7614 (mp0) outliers start: 209 outliers final: 157 residues processed: 853 average time/residue: 0.9570 time to fit residues: 1330.7226 Evaluate side-chains 898 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 720 time to evaluate : 3.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 259 ASN Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 191 ILE Chi-restraints excluded: chain F residue 200 ASP Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 110 LEU Chi-restraints excluded: chain G residue 111 MET Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 73 PHE Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 133 ILE Chi-restraints excluded: chain L residue 139 ASN Chi-restraints excluded: chain L residue 186 GLU Chi-restraints excluded: chain L residue 207 MET Chi-restraints excluded: chain M residue 12 ASP Chi-restraints excluded: chain M residue 25 ILE Chi-restraints excluded: chain M residue 29 ASN Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 66 CYS Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 73 ASN Chi-restraints excluded: chain M residue 102 ILE Chi-restraints excluded: chain N residue 91 SER Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 170 PHE Chi-restraints excluded: chain N residue 175 GLU Chi-restraints excluded: chain N residue 186 ILE Chi-restraints excluded: chain N residue 190 SER Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain N residue 234 VAL Chi-restraints excluded: chain N residue 235 LEU Chi-restraints excluded: chain N residue 242 ILE Chi-restraints excluded: chain N residue 244 GLU Chi-restraints excluded: chain O residue 32 TYR Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 68 ILE Chi-restraints excluded: chain O residue 71 ASP Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain O residue 96 VAL Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain O residue 127 ILE Chi-restraints excluded: chain P residue 11 MET Chi-restraints excluded: chain P residue 31 LEU Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 63 THR Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 75 GLN Chi-restraints excluded: chain P residue 105 THR Chi-restraints excluded: chain P residue 123 ILE Chi-restraints excluded: chain Q residue 121 GLN Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain R residue 143 ILE Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 185 ARG Chi-restraints excluded: chain R residue 194 ILE Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain R residue 225 LYS Chi-restraints excluded: chain S residue 6 ARG Chi-restraints excluded: chain S residue 9 ILE Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 56 ASP Chi-restraints excluded: chain S residue 83 HIS Chi-restraints excluded: chain S residue 85 LEU Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain S residue 113 ASN Chi-restraints excluded: chain T residue 123 ILE Chi-restraints excluded: chain T residue 142 ILE Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain T residue 155 LYS Chi-restraints excluded: chain T residue 159 ASN Chi-restraints excluded: chain T residue 161 VAL Chi-restraints excluded: chain T residue 171 TYR Chi-restraints excluded: chain T residue 176 ILE Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 210 ILE Chi-restraints excluded: chain T residue 234 THR Chi-restraints excluded: chain U residue 32 ILE Chi-restraints excluded: chain U residue 38 SER Chi-restraints excluded: chain U residue 79 LEU Chi-restraints excluded: chain U residue 93 PHE Chi-restraints excluded: chain U residue 97 ASN Chi-restraints excluded: chain U residue 104 GLU Chi-restraints excluded: chain U residue 110 THR Chi-restraints excluded: chain U residue 130 CYS Chi-restraints excluded: chain U residue 137 ARG Chi-restraints excluded: chain U residue 139 ILE Chi-restraints excluded: chain U residue 149 LEU Chi-restraints excluded: chain U residue 157 LEU Chi-restraints excluded: chain V residue 112 TYR Chi-restraints excluded: chain V residue 143 ASP Chi-restraints excluded: chain V residue 162 VAL Chi-restraints excluded: chain V residue 163 ASN Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain V residue 185 SER Chi-restraints excluded: chain W residue 56 CYS Chi-restraints excluded: chain W residue 90 SER Chi-restraints excluded: chain W residue 108 THR Chi-restraints excluded: chain W residue 122 ILE Chi-restraints excluded: chain W residue 132 SER Chi-restraints excluded: chain W residue 145 ASP Chi-restraints excluded: chain W residue 151 ILE Chi-restraints excluded: chain W residue 169 ASP Chi-restraints excluded: chain X residue 72 SER Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 120 ASP Chi-restraints excluded: chain X residue 123 VAL Chi-restraints excluded: chain X residue 160 LEU Chi-restraints excluded: chain Y residue 82 SER Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Z residue 81 LEU Chi-restraints excluded: chain Z residue 117 THR Chi-restraints excluded: chain 2 residue 11 TYR Chi-restraints excluded: chain 2 residue 22 LYS Chi-restraints excluded: chain 2 residue 29 LEU Chi-restraints excluded: chain 3 residue 23 VAL Chi-restraints excluded: chain 3 residue 31 SER Chi-restraints excluded: chain 3 residue 58 HIS Chi-restraints excluded: chain 3 residue 64 ILE Chi-restraints excluded: chain 4 residue 96 LEU Chi-restraints excluded: chain 4 residue 98 LEU Chi-restraints excluded: chain 4 residue 120 THR Chi-restraints excluded: chain 4 residue 143 ASN Chi-restraints excluded: chain 5 residue 126 THR Chi-restraints excluded: chain 5 residue 133 SER Chi-restraints excluded: chain 5 residue 135 LEU Chi-restraints excluded: chain 5 residue 150 LEU Chi-restraints excluded: chain 6 residue 3 ILE Chi-restraints excluded: chain 6 residue 7 VAL Chi-restraints excluded: chain 7 residue 140 LYS Chi-restraints excluded: chain 7 residue 141 ASN Chi-restraints excluded: chain 8 residue 50 ARG Chi-restraints excluded: chain 8 residue 60 MET Chi-restraints excluded: chain 8 residue 72 ILE Chi-restraints excluded: chain 8 residue 78 VAL Chi-restraints excluded: chain 8 residue 88 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 202 optimal weight: 6.9990 chunk 543 optimal weight: 0.7980 chunk 119 optimal weight: 7.9990 chunk 354 optimal weight: 6.9990 chunk 148 optimal weight: 9.9990 chunk 603 optimal weight: 7.9990 chunk 501 optimal weight: 3.9990 chunk 279 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 199 optimal weight: 7.9990 chunk 316 optimal weight: 5.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 12 GLN P 87 HIS R 202 ASN ** S 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 59 ASN ** X 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 137 GLN ** 6 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.148 98702 Z= 0.431 Angle : 0.852 19.326 147908 Z= 0.423 Chirality : 0.046 0.409 18873 Planarity : 0.007 0.085 7648 Dihedral : 24.421 179.777 49995 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.71 % Allowed : 12.40 % Favored : 86.88 % Rotamer: Outliers : 9.25 % Allowed : 22.76 % Favored : 67.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.81 (0.13), residues: 3362 helix: -0.40 (0.17), residues: 918 sheet: -2.29 (0.20), residues: 548 loop : -2.58 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP Y 110 HIS 0.023 0.002 HIS P 87 PHE 0.024 0.003 PHE E 171 TYR 0.029 0.003 TYR P 81 ARG 0.008 0.001 ARG N 97 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1012 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 263 poor density : 749 time to evaluate : 3.659 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: D 131 MET cc_start: 0.9330 (mmm) cc_final: 0.9030 (tpp) REVERT: D 188 VAL cc_start: 0.8486 (p) cc_final: 0.8227 (m) REVERT: D 193 ASN cc_start: 0.8664 (t0) cc_final: 0.8357 (t0) REVERT: D 209 TRP cc_start: 0.8607 (p90) cc_final: 0.7849 (p90) REVERT: E 153 GLU cc_start: 0.8606 (mt-10) cc_final: 0.7972 (mt-10) REVERT: E 154 ARG cc_start: 0.8123 (mtp85) cc_final: 0.7503 (mtt180) REVERT: F 154 LYS cc_start: 0.8345 (mttt) cc_final: 0.8054 (mttp) REVERT: F 161 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8778 (tt) REVERT: F 214 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7420 (tm-30) REVERT: F 222 ASN cc_start: 0.9203 (t0) cc_final: 0.8468 (t0) REVERT: F 234 LEU cc_start: 0.9153 (tp) cc_final: 0.8848 (tp) REVERT: G 20 LYS cc_start: 0.8020 (tttm) cc_final: 0.7558 (tptt) REVERT: G 106 LEU cc_start: 0.6922 (mt) cc_final: 0.6541 (mm) REVERT: G 111 MET cc_start: 0.4020 (OUTLIER) cc_final: 0.3287 (ttp) REVERT: G 167 MET cc_start: 0.5799 (ptp) cc_final: 0.5152 (ptp) REVERT: H 58 MET cc_start: 0.6345 (mmm) cc_final: 0.6010 (mmm) REVERT: H 100 ARG cc_start: 0.6782 (ttp-170) cc_final: 0.6468 (ttp-170) REVERT: H 109 ARG cc_start: 0.5134 (mtt180) cc_final: 0.2919 (mtt180) REVERT: H 200 LYS cc_start: 0.7615 (mtpt) cc_final: 0.7276 (ttpt) REVERT: H 213 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7656 (pm20) REVERT: I 43 LYS cc_start: 0.6816 (OUTLIER) cc_final: 0.5916 (pmmt) REVERT: L 186 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7313 (pm20) REVERT: L 195 ILE cc_start: 0.9109 (mm) cc_final: 0.8574 (tt) REVERT: L 207 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7810 (mmt) REVERT: L 225 LYS cc_start: 0.8049 (tttm) cc_final: 0.7705 (tptp) REVERT: M 12 ASP cc_start: 0.8882 (OUTLIER) cc_final: 0.8575 (p0) REVERT: M 13 ASN cc_start: 0.8800 (p0) cc_final: 0.8553 (p0) REVERT: M 45 GLU cc_start: 0.8424 (pm20) cc_final: 0.7904 (pm20) REVERT: M 97 ARG cc_start: 0.7739 (ttm170) cc_final: 0.7479 (ttm170) REVERT: M 112 LYS cc_start: 0.8337 (tptt) cc_final: 0.7507 (tptm) REVERT: N 142 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7543 (ptpt) REVERT: N 170 PHE cc_start: 0.4944 (OUTLIER) cc_final: 0.2825 (p90) REVERT: N 182 LYS cc_start: 0.8614 (ttpp) cc_final: 0.8368 (ttpt) REVERT: N 186 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7755 (mt) REVERT: N 193 GLU cc_start: 0.8202 (pm20) cc_final: 0.7820 (pm20) REVERT: N 252 ARG cc_start: 0.6650 (tpt90) cc_final: 0.6282 (ttt180) REVERT: O 16 ARG cc_start: 0.8904 (OUTLIER) cc_final: 0.7662 (ptm-80) REVERT: O 48 GLU cc_start: 0.7910 (tp30) cc_final: 0.7642 (tp30) REVERT: O 63 LYS cc_start: 0.7098 (tttt) cc_final: 0.6881 (tttt) REVERT: Q 81 HIS cc_start: 0.7335 (m-70) cc_final: 0.6761 (t-90) REVERT: Q 121 GLN cc_start: 0.6044 (OUTLIER) cc_final: 0.5638 (mm110) REVERT: R 185 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.7937 (ttt90) REVERT: R 207 LYS cc_start: 0.7841 (tttt) cc_final: 0.7381 (mtpp) REVERT: R 216 LYS cc_start: 0.8822 (ttmm) cc_final: 0.8346 (mtpp) REVERT: R 228 ARG cc_start: 0.8189 (mtp-110) cc_final: 0.7944 (mtp-110) REVERT: S 6 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8168 (ptp-170) REVERT: S 56 ASP cc_start: 0.7324 (OUTLIER) cc_final: 0.6233 (t70) REVERT: S 83 HIS cc_start: 0.8287 (OUTLIER) cc_final: 0.7843 (t-90) REVERT: S 84 ASP cc_start: 0.7902 (m-30) cc_final: 0.7371 (m-30) REVERT: S 94 ARG cc_start: 0.8776 (mtt90) cc_final: 0.8380 (mmt-90) REVERT: S 113 ASN cc_start: 0.7025 (OUTLIER) cc_final: 0.6574 (m-40) REVERT: T 121 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7495 (tm-30) REVERT: T 123 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.7826 (pp) REVERT: U 31 GLU cc_start: 0.7616 (pm20) cc_final: 0.7314 (pm20) REVERT: U 57 SER cc_start: 0.8844 (t) cc_final: 0.8589 (m) REVERT: U 93 PHE cc_start: 0.5720 (OUTLIER) cc_final: 0.4518 (p90) REVERT: U 97 ASN cc_start: 0.8274 (OUTLIER) cc_final: 0.8004 (t0) REVERT: V 132 ASN cc_start: 0.8882 (t0) cc_final: 0.8350 (t0) REVERT: W 70 LYS cc_start: 0.8581 (ptmt) cc_final: 0.8282 (mtpt) REVERT: W 116 GLU cc_start: 0.3706 (OUTLIER) cc_final: 0.3448 (pm20) REVERT: X 92 ILE cc_start: 0.9017 (mt) cc_final: 0.8749 (tt) REVERT: X 124 LYS cc_start: 0.8732 (tptm) cc_final: 0.8386 (tptm) REVERT: Y 109 TRP cc_start: 0.7398 (t-100) cc_final: 0.6962 (t-100) REVERT: Z 66 LYS cc_start: 0.8237 (mttt) cc_final: 0.7655 (mmmt) REVERT: Z 79 GLU cc_start: 0.8470 (tt0) cc_final: 0.8252 (tt0) REVERT: Z 88 PHE cc_start: 0.7776 (t80) cc_final: 0.7500 (t80) REVERT: Z 89 MET cc_start: 0.7463 (mmm) cc_final: 0.6903 (mmm) REVERT: Z 147 ARG cc_start: 0.7741 (ptp-170) cc_final: 0.7337 (ptp-110) REVERT: 3 10 LYS cc_start: 0.8511 (pttm) cc_final: 0.7747 (mmtt) REVERT: 3 32 ARG cc_start: 0.7935 (ttm170) cc_final: 0.7406 (mtt180) REVERT: 4 149 ARG cc_start: 0.7955 (mmt-90) cc_final: 0.7567 (mpt180) REVERT: 5 90 TYR cc_start: 0.7356 (OUTLIER) cc_final: 0.7135 (t80) REVERT: 9 206 LEU cc_start: 0.6945 (mt) cc_final: 0.6733 (mt) REVERT: 9 269 MET cc_start: 0.0893 (mmm) cc_final: 0.0645 (mmm) REVERT: 7 140 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7161 (ptmm) REVERT: 8 69 ARG cc_start: 0.8557 (ttt90) cc_final: 0.8222 (ttt180) REVERT: 8 88 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7738 (mt-10) REVERT: 8 89 TRP cc_start: 0.7921 (p-90) cc_final: 0.7463 (p90) outliers start: 263 outliers final: 194 residues processed: 892 average time/residue: 1.0290 time to fit residues: 1513.6442 Evaluate side-chains 951 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 734 time to evaluate : 3.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 163 LYS Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 259 ASN Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 99 THR Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 102 THR Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 191 ILE Chi-restraints excluded: chain F residue 200 ASP Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 110 LEU Chi-restraints excluded: chain G residue 111 MET Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 73 PHE Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 133 ILE Chi-restraints excluded: chain L residue 139 ASN Chi-restraints excluded: chain L residue 186 GLU Chi-restraints excluded: chain L residue 207 MET Chi-restraints excluded: chain L residue 237 ILE Chi-restraints excluded: chain L residue 248 VAL Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 12 ASP Chi-restraints excluded: chain M residue 25 ILE Chi-restraints excluded: chain M residue 29 ASN Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 42 VAL Chi-restraints excluded: chain M residue 66 CYS Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 73 ASN Chi-restraints excluded: chain N residue 85 LEU Chi-restraints excluded: chain N residue 91 SER Chi-restraints excluded: chain N residue 142 LYS Chi-restraints excluded: chain N residue 154 LEU Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 170 PHE Chi-restraints excluded: chain N residue 175 GLU Chi-restraints excluded: chain N residue 186 ILE Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain N residue 234 VAL Chi-restraints excluded: chain N residue 235 LEU Chi-restraints excluded: chain N residue 242 ILE Chi-restraints excluded: chain N residue 244 GLU Chi-restraints excluded: chain N residue 250 LEU Chi-restraints excluded: chain O residue 16 ARG Chi-restraints excluded: chain O residue 32 TYR Chi-restraints excluded: chain O residue 55 THR Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 68 ILE Chi-restraints excluded: chain O residue 71 ASP Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain O residue 96 VAL Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain O residue 120 ILE Chi-restraints excluded: chain O residue 127 ILE Chi-restraints excluded: chain P residue 11 MET Chi-restraints excluded: chain P residue 31 LEU Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 63 THR Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 75 GLN Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 105 THR Chi-restraints excluded: chain P residue 110 THR Chi-restraints excluded: chain P residue 111 LEU Chi-restraints excluded: chain P residue 123 ILE Chi-restraints excluded: chain Q residue 121 GLN Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 143 ARG Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 137 LEU Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain R residue 143 ILE Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 180 THR Chi-restraints excluded: chain R residue 185 ARG Chi-restraints excluded: chain R residue 194 ILE Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 225 LYS Chi-restraints excluded: chain S residue 6 ARG Chi-restraints excluded: chain S residue 9 ILE Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 29 SER Chi-restraints excluded: chain S residue 56 ASP Chi-restraints excluded: chain S residue 83 HIS Chi-restraints excluded: chain S residue 85 LEU Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain S residue 113 ASN Chi-restraints excluded: chain T residue 123 ILE Chi-restraints excluded: chain T residue 136 VAL Chi-restraints excluded: chain T residue 142 ILE Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain T residue 155 LYS Chi-restraints excluded: chain T residue 159 ASN Chi-restraints excluded: chain T residue 161 VAL Chi-restraints excluded: chain T residue 170 THR Chi-restraints excluded: chain T residue 171 TYR Chi-restraints excluded: chain T residue 176 ILE Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 210 ILE Chi-restraints excluded: chain T residue 234 THR Chi-restraints excluded: chain U residue 29 CYS Chi-restraints excluded: chain U residue 30 ASP Chi-restraints excluded: chain U residue 32 ILE Chi-restraints excluded: chain U residue 38 SER Chi-restraints excluded: chain U residue 58 TYR Chi-restraints excluded: chain U residue 79 LEU Chi-restraints excluded: chain U residue 86 ASN Chi-restraints excluded: chain U residue 88 SER Chi-restraints excluded: chain U residue 93 PHE Chi-restraints excluded: chain U residue 97 ASN Chi-restraints excluded: chain U residue 104 GLU Chi-restraints excluded: chain U residue 110 THR Chi-restraints excluded: chain U residue 130 CYS Chi-restraints excluded: chain U residue 139 ILE Chi-restraints excluded: chain U residue 149 LEU Chi-restraints excluded: chain U residue 157 LEU Chi-restraints excluded: chain V residue 112 TYR Chi-restraints excluded: chain V residue 143 ASP Chi-restraints excluded: chain V residue 162 VAL Chi-restraints excluded: chain V residue 163 ASN Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain W residue 56 CYS Chi-restraints excluded: chain W residue 90 SER Chi-restraints excluded: chain W residue 96 ASN Chi-restraints excluded: chain W residue 98 THR Chi-restraints excluded: chain W residue 108 THR Chi-restraints excluded: chain W residue 116 GLU Chi-restraints excluded: chain W residue 122 ILE Chi-restraints excluded: chain W residue 132 SER Chi-restraints excluded: chain W residue 138 LEU Chi-restraints excluded: chain W residue 145 ASP Chi-restraints excluded: chain W residue 159 ARG Chi-restraints excluded: chain W residue 169 ASP Chi-restraints excluded: chain X residue 72 SER Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 120 ASP Chi-restraints excluded: chain X residue 123 VAL Chi-restraints excluded: chain X residue 160 LEU Chi-restraints excluded: chain Y residue 72 ARG Chi-restraints excluded: chain Y residue 82 SER Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Z residue 76 LEU Chi-restraints excluded: chain Z residue 81 LEU Chi-restraints excluded: chain Z residue 117 THR Chi-restraints excluded: chain 2 residue 11 TYR Chi-restraints excluded: chain 2 residue 22 LYS Chi-restraints excluded: chain 2 residue 29 LEU Chi-restraints excluded: chain 3 residue 19 VAL Chi-restraints excluded: chain 3 residue 23 VAL Chi-restraints excluded: chain 3 residue 31 SER Chi-restraints excluded: chain 3 residue 58 HIS Chi-restraints excluded: chain 3 residue 64 ILE Chi-restraints excluded: chain 4 residue 96 LEU Chi-restraints excluded: chain 4 residue 120 THR Chi-restraints excluded: chain 4 residue 143 ASN Chi-restraints excluded: chain 5 residue 90 TYR Chi-restraints excluded: chain 5 residue 126 THR Chi-restraints excluded: chain 5 residue 135 LEU Chi-restraints excluded: chain 5 residue 150 LEU Chi-restraints excluded: chain 6 residue 3 ILE Chi-restraints excluded: chain 6 residue 7 VAL Chi-restraints excluded: chain 7 residue 112 ILE Chi-restraints excluded: chain 7 residue 140 LYS Chi-restraints excluded: chain 7 residue 141 ASN Chi-restraints excluded: chain 8 residue 50 ARG Chi-restraints excluded: chain 8 residue 54 LYS Chi-restraints excluded: chain 8 residue 67 THR Chi-restraints excluded: chain 8 residue 72 ILE Chi-restraints excluded: chain 8 residue 78 VAL Chi-restraints excluded: chain 8 residue 88 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 582 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 343 optimal weight: 0.7980 chunk 440 optimal weight: 0.0770 chunk 341 optimal weight: 0.0980 chunk 508 optimal weight: 0.7980 chunk 337 optimal weight: 6.9990 chunk 601 optimal weight: 2.9990 chunk 376 optimal weight: 6.9990 chunk 366 optimal weight: 6.9990 chunk 277 optimal weight: 20.0000 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 215 ASN ** N 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 12 GLN Q 85 GLN ** S 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 104 ASN ** V 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 59 ASN 4 143 ASN 5 125 ASN 5 137 GLN ** 6 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 98702 Z= 0.148 Angle : 0.632 20.106 147908 Z= 0.323 Chirality : 0.036 0.379 18873 Planarity : 0.005 0.086 7648 Dihedral : 24.311 179.954 49993 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.59 % Allowed : 8.06 % Favored : 91.34 % Rotamer: Outliers : 5.73 % Allowed : 26.17 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.14), residues: 3362 helix: 0.15 (0.17), residues: 927 sheet: -2.01 (0.21), residues: 521 loop : -2.27 (0.13), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP T 141 HIS 0.009 0.001 HIS H 105 PHE 0.012 0.001 PHE E 208 TYR 0.025 0.001 TYR D 261 ARG 0.007 0.001 ARG O 128 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 913 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 750 time to evaluate : 3.751 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: D 71 TYR cc_start: 0.7472 (OUTLIER) cc_final: 0.6626 (m-80) REVERT: D 131 MET cc_start: 0.9208 (mmm) cc_final: 0.8970 (tpp) REVERT: D 188 VAL cc_start: 0.8345 (p) cc_final: 0.8086 (m) REVERT: E 153 GLU cc_start: 0.8415 (mt-10) cc_final: 0.7776 (mt-10) REVERT: F 67 GLU cc_start: 0.6685 (OUTLIER) cc_final: 0.6472 (pt0) REVERT: F 125 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.6696 (ptt-90) REVERT: F 161 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8661 (tt) REVERT: F 214 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7530 (tm-30) REVERT: F 222 ASN cc_start: 0.9160 (t0) cc_final: 0.8478 (t0) REVERT: F 258 ARG cc_start: 0.8177 (mmm160) cc_final: 0.7943 (mtm110) REVERT: G 20 LYS cc_start: 0.7951 (tttm) cc_final: 0.7373 (tptt) REVERT: G 48 LYS cc_start: 0.6958 (pttt) cc_final: 0.6578 (ptpt) REVERT: G 49 ILE cc_start: 0.6158 (mp) cc_final: 0.5800 (mp) REVERT: G 106 LEU cc_start: 0.6965 (mt) cc_final: 0.6495 (tp) REVERT: G 167 MET cc_start: 0.5767 (ptp) cc_final: 0.5203 (ptp) REVERT: H 58 MET cc_start: 0.6438 (mmm) cc_final: 0.6194 (mmm) REVERT: H 100 ARG cc_start: 0.6780 (ttp-170) cc_final: 0.6188 (ttp-170) REVERT: H 104 MET cc_start: 0.5721 (ttm) cc_final: 0.5493 (tmm) REVERT: H 109 ARG cc_start: 0.5202 (mtt180) cc_final: 0.2861 (mtt180) REVERT: H 141 LYS cc_start: 0.5399 (ttpp) cc_final: 0.5104 (tmmt) REVERT: H 200 LYS cc_start: 0.7455 (mtpt) cc_final: 0.6769 (ttpt) REVERT: H 213 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7495 (pm20) REVERT: I 44 LYS cc_start: 0.7083 (tptp) cc_final: 0.6866 (mppt) REVERT: L 140 LEU cc_start: 0.9103 (mt) cc_final: 0.8784 (mp) REVERT: L 186 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.7149 (pm20) REVERT: L 195 ILE cc_start: 0.9038 (mm) cc_final: 0.8513 (tt) REVERT: L 207 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7669 (mmt) REVERT: L 225 LYS cc_start: 0.8075 (tttm) cc_final: 0.7764 (tptp) REVERT: M 12 ASP cc_start: 0.8753 (OUTLIER) cc_final: 0.8523 (p0) REVERT: M 13 ASN cc_start: 0.8676 (p0) cc_final: 0.8414 (p0) REVERT: M 97 ARG cc_start: 0.7729 (ttm170) cc_final: 0.7473 (ttm170) REVERT: M 112 LYS cc_start: 0.8243 (tptt) cc_final: 0.7453 (tptm) REVERT: N 97 ARG cc_start: 0.7750 (ptm-80) cc_final: 0.7293 (ptm-80) REVERT: N 134 MET cc_start: 0.7849 (tpp) cc_final: 0.7470 (tpp) REVERT: N 170 PHE cc_start: 0.4597 (OUTLIER) cc_final: 0.3264 (p90) REVERT: N 182 LYS cc_start: 0.8496 (ttpp) cc_final: 0.8087 (ttpt) REVERT: N 186 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7756 (mt) REVERT: N 252 ARG cc_start: 0.6707 (tpt90) cc_final: 0.6476 (ttt180) REVERT: O 16 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.7476 (ptm-80) REVERT: O 63 LYS cc_start: 0.7017 (tttt) cc_final: 0.6767 (tttt) REVERT: Q 56 ARG cc_start: 0.7060 (OUTLIER) cc_final: 0.6736 (mtt180) REVERT: R 228 ARG cc_start: 0.8133 (mtp-110) cc_final: 0.7854 (mtp-110) REVERT: S 6 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7445 (ptp-170) REVERT: S 56 ASP cc_start: 0.7006 (OUTLIER) cc_final: 0.6064 (t70) REVERT: S 84 ASP cc_start: 0.7644 (m-30) cc_final: 0.7341 (m-30) REVERT: S 113 ASN cc_start: 0.6945 (OUTLIER) cc_final: 0.6624 (m-40) REVERT: T 121 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7782 (tm-30) REVERT: T 122 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7898 (mp0) REVERT: T 123 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.7729 (pp) REVERT: U 31 GLU cc_start: 0.7485 (pm20) cc_final: 0.7115 (pm20) REVERT: U 35 ARG cc_start: 0.7662 (mtp180) cc_final: 0.7120 (mmm-85) REVERT: V 132 ASN cc_start: 0.8735 (t0) cc_final: 0.8143 (t0) REVERT: V 149 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7844 (tt0) REVERT: W 70 LYS cc_start: 0.8231 (ptmt) cc_final: 0.8018 (mtpt) REVERT: X 124 LYS cc_start: 0.8646 (tptm) cc_final: 0.8287 (tptm) REVERT: Z 89 MET cc_start: 0.7429 (mmm) cc_final: 0.6839 (mmm) REVERT: Z 147 ARG cc_start: 0.7590 (ptp-170) cc_final: 0.7303 (ptp-110) REVERT: 2 11 TYR cc_start: 0.8280 (OUTLIER) cc_final: 0.6897 (p90) REVERT: 2 22 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7887 (mmtt) REVERT: 3 10 LYS cc_start: 0.8442 (pttm) cc_final: 0.7769 (mmtt) REVERT: 3 32 ARG cc_start: 0.7817 (ttm170) cc_final: 0.7532 (mtt90) REVERT: 4 149 ARG cc_start: 0.7889 (mmt-90) cc_final: 0.7374 (mpt180) REVERT: 7 140 LYS cc_start: 0.7301 (OUTLIER) cc_final: 0.6535 (ptmm) REVERT: 8 69 ARG cc_start: 0.8408 (ttt90) cc_final: 0.8154 (ttt180) REVERT: 8 88 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7548 (mt-10) outliers start: 163 outliers final: 117 residues processed: 838 average time/residue: 0.9443 time to fit residues: 1291.9525 Evaluate side-chains 858 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 722 time to evaluate : 3.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 TYR Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 259 ASN Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 125 ARG Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 162 SER Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 111 MET Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 73 PHE Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 133 ILE Chi-restraints excluded: chain L residue 139 ASN Chi-restraints excluded: chain L residue 186 GLU Chi-restraints excluded: chain L residue 207 MET Chi-restraints excluded: chain L residue 248 VAL Chi-restraints excluded: chain M residue 12 ASP Chi-restraints excluded: chain M residue 25 ILE Chi-restraints excluded: chain M residue 66 CYS Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 73 ASN Chi-restraints excluded: chain N residue 91 SER Chi-restraints excluded: chain N residue 125 ILE Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 170 PHE Chi-restraints excluded: chain N residue 186 ILE Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain N residue 218 SER Chi-restraints excluded: chain N residue 234 VAL Chi-restraints excluded: chain N residue 242 ILE Chi-restraints excluded: chain N residue 250 LEU Chi-restraints excluded: chain O residue 16 ARG Chi-restraints excluded: chain O residue 71 ASP Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain O residue 96 VAL Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain O residue 127 ILE Chi-restraints excluded: chain P residue 11 MET Chi-restraints excluded: chain P residue 30 LEU Chi-restraints excluded: chain P residue 31 LEU Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 63 THR Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 75 GLN Chi-restraints excluded: chain P residue 105 THR Chi-restraints excluded: chain P residue 111 LEU Chi-restraints excluded: chain P residue 123 ILE Chi-restraints excluded: chain Q residue 56 ARG Chi-restraints excluded: chain Q residue 86 VAL Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain R residue 123 MET Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 194 ILE Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain R residue 225 LYS Chi-restraints excluded: chain S residue 6 ARG Chi-restraints excluded: chain S residue 9 ILE Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 29 SER Chi-restraints excluded: chain S residue 56 ASP Chi-restraints excluded: chain S residue 83 HIS Chi-restraints excluded: chain S residue 87 LYS Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain S residue 113 ASN Chi-restraints excluded: chain T residue 123 ILE Chi-restraints excluded: chain T residue 142 ILE Chi-restraints excluded: chain T residue 155 LYS Chi-restraints excluded: chain T residue 159 ASN Chi-restraints excluded: chain T residue 161 VAL Chi-restraints excluded: chain T residue 171 TYR Chi-restraints excluded: chain T residue 176 ILE Chi-restraints excluded: chain T residue 210 ILE Chi-restraints excluded: chain T residue 234 THR Chi-restraints excluded: chain U residue 30 ASP Chi-restraints excluded: chain U residue 32 ILE Chi-restraints excluded: chain U residue 104 GLU Chi-restraints excluded: chain U residue 110 THR Chi-restraints excluded: chain U residue 149 LEU Chi-restraints excluded: chain V residue 143 ASP Chi-restraints excluded: chain V residue 163 ASN Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain W residue 56 CYS Chi-restraints excluded: chain W residue 90 SER Chi-restraints excluded: chain W residue 98 THR Chi-restraints excluded: chain W residue 108 THR Chi-restraints excluded: chain W residue 122 ILE Chi-restraints excluded: chain W residue 145 ASP Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 120 ASP Chi-restraints excluded: chain Y residue 82 SER Chi-restraints excluded: chain Z residue 81 LEU Chi-restraints excluded: chain Z residue 133 SER Chi-restraints excluded: chain 2 residue 11 TYR Chi-restraints excluded: chain 2 residue 22 LYS Chi-restraints excluded: chain 3 residue 23 VAL Chi-restraints excluded: chain 3 residue 31 SER Chi-restraints excluded: chain 3 residue 58 HIS Chi-restraints excluded: chain 3 residue 64 ILE Chi-restraints excluded: chain 4 residue 96 LEU Chi-restraints excluded: chain 5 residue 133 SER Chi-restraints excluded: chain 5 residue 143 TYR Chi-restraints excluded: chain 5 residue 150 LEU Chi-restraints excluded: chain 6 residue 3 ILE Chi-restraints excluded: chain 6 residue 7 VAL Chi-restraints excluded: chain 7 residue 140 LYS Chi-restraints excluded: chain 7 residue 141 ASN Chi-restraints excluded: chain 8 residue 50 ARG Chi-restraints excluded: chain 8 residue 60 MET Chi-restraints excluded: chain 8 residue 72 ILE Chi-restraints excluded: chain 8 residue 78 VAL Chi-restraints excluded: chain 8 residue 88 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 372 optimal weight: 0.0980 chunk 240 optimal weight: 6.9990 chunk 359 optimal weight: 0.6980 chunk 181 optimal weight: 10.0000 chunk 118 optimal weight: 7.9990 chunk 116 optimal weight: 9.9990 chunk 382 optimal weight: 0.0000 chunk 409 optimal weight: 8.9990 chunk 297 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 472 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN L 170 GLN O 12 GLN Q 85 GLN R 202 ASN ** S 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 59 ASN 5 137 GLN ** 6 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 98702 Z= 0.205 Angle : 0.651 20.065 147908 Z= 0.330 Chirality : 0.037 0.390 18873 Planarity : 0.005 0.084 7648 Dihedral : 24.248 179.994 49980 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.99 % Favored : 89.53 % Rotamer: Outliers : 6.51 % Allowed : 25.85 % Favored : 67.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.14), residues: 3362 helix: 0.19 (0.17), residues: 924 sheet: -2.00 (0.21), residues: 514 loop : -2.27 (0.14), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP Y 109 HIS 0.010 0.001 HIS P 87 PHE 0.023 0.002 PHE N 129 TYR 0.031 0.002 TYR D 261 ARG 0.013 0.001 ARG M 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 918 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 733 time to evaluate : 3.775 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: D 71 TYR cc_start: 0.7432 (OUTLIER) cc_final: 0.6658 (m-80) REVERT: D 131 MET cc_start: 0.9241 (mmm) cc_final: 0.9000 (tpp) REVERT: D 188 VAL cc_start: 0.8366 (p) cc_final: 0.8103 (m) REVERT: E 153 GLU cc_start: 0.8481 (mt-10) cc_final: 0.7851 (mt-10) REVERT: E 199 ILE cc_start: 0.8978 (mp) cc_final: 0.8747 (mm) REVERT: F 67 GLU cc_start: 0.6875 (OUTLIER) cc_final: 0.6624 (pt0) REVERT: F 125 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.6717 (ptt-90) REVERT: F 161 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8729 (tt) REVERT: F 214 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7498 (tm-30) REVERT: F 222 ASN cc_start: 0.9130 (t0) cc_final: 0.8378 (t0) REVERT: G 20 LYS cc_start: 0.7975 (tttm) cc_final: 0.7409 (tttm) REVERT: G 30 LEU cc_start: 0.6520 (mp) cc_final: 0.5944 (pt) REVERT: G 48 LYS cc_start: 0.6942 (pttt) cc_final: 0.6548 (ptpt) REVERT: G 49 ILE cc_start: 0.5867 (mp) cc_final: 0.5416 (mp) REVERT: G 106 LEU cc_start: 0.7025 (mt) cc_final: 0.6526 (tp) REVERT: G 167 MET cc_start: 0.5764 (ptp) cc_final: 0.5181 (ptp) REVERT: H 58 MET cc_start: 0.6432 (mmm) cc_final: 0.6193 (mmm) REVERT: H 100 ARG cc_start: 0.6778 (ttp-170) cc_final: 0.6553 (ttp-170) REVERT: H 109 ARG cc_start: 0.5124 (mtt180) cc_final: 0.2827 (mtt180) REVERT: H 200 LYS cc_start: 0.7452 (mtpt) cc_final: 0.7042 (ttpt) REVERT: H 213 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7556 (pm20) REVERT: I 43 LYS cc_start: 0.6763 (OUTLIER) cc_final: 0.5796 (pmmt) REVERT: I 53 LEU cc_start: 0.6509 (mp) cc_final: 0.6226 (tp) REVERT: I 63 LYS cc_start: 0.6947 (mtpp) cc_final: 0.6349 (mtpp) REVERT: L 140 LEU cc_start: 0.9078 (mt) cc_final: 0.8759 (mp) REVERT: L 186 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7201 (pm20) REVERT: L 195 ILE cc_start: 0.9049 (mm) cc_final: 0.8522 (tt) REVERT: L 207 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.7663 (mmt) REVERT: L 225 LYS cc_start: 0.8103 (tttm) cc_final: 0.7779 (tptp) REVERT: M 12 ASP cc_start: 0.8822 (OUTLIER) cc_final: 0.8542 (p0) REVERT: M 13 ASN cc_start: 0.8706 (p0) cc_final: 0.8478 (p0) REVERT: M 97 ARG cc_start: 0.7721 (ttm170) cc_final: 0.7453 (ttm170) REVERT: M 112 LYS cc_start: 0.8292 (tptt) cc_final: 0.7464 (tptm) REVERT: N 97 ARG cc_start: 0.7810 (ptm-80) cc_final: 0.7342 (ptm-80) REVERT: N 134 MET cc_start: 0.7889 (tpp) cc_final: 0.7499 (tpp) REVERT: N 170 PHE cc_start: 0.4570 (OUTLIER) cc_final: 0.3283 (p90) REVERT: N 182 LYS cc_start: 0.8502 (ttpp) cc_final: 0.8127 (ttpt) REVERT: N 186 ILE cc_start: 0.8188 (OUTLIER) cc_final: 0.7797 (mt) REVERT: N 252 ARG cc_start: 0.6608 (tpt90) cc_final: 0.6327 (ttt180) REVERT: O 16 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.7429 (ptm-80) REVERT: O 48 GLU cc_start: 0.7758 (tp30) cc_final: 0.7484 (tp30) REVERT: O 63 LYS cc_start: 0.7052 (tttt) cc_final: 0.6774 (tttt) REVERT: Q 56 ARG cc_start: 0.7111 (OUTLIER) cc_final: 0.6772 (mtt180) REVERT: Q 81 HIS cc_start: 0.7411 (m-70) cc_final: 0.6816 (t-90) REVERT: R 185 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.7983 (ttt90) REVERT: R 228 ARG cc_start: 0.8157 (mtp-110) cc_final: 0.7887 (mtp-110) REVERT: S 56 ASP cc_start: 0.7098 (OUTLIER) cc_final: 0.6115 (t70) REVERT: S 84 ASP cc_start: 0.7673 (m-30) cc_final: 0.7390 (m-30) REVERT: S 113 ASN cc_start: 0.6940 (OUTLIER) cc_final: 0.6606 (m-40) REVERT: T 121 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7815 (tm-30) REVERT: T 123 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.7904 (pp) REVERT: U 31 GLU cc_start: 0.7542 (pm20) cc_final: 0.7184 (pm20) REVERT: U 35 ARG cc_start: 0.7701 (mtp180) cc_final: 0.7212 (mmm-85) REVERT: V 132 ASN cc_start: 0.8750 (t0) cc_final: 0.8181 (t0) REVERT: V 149 GLU cc_start: 0.8387 (tm-30) cc_final: 0.7994 (tt0) REVERT: W 70 LYS cc_start: 0.8313 (ptmt) cc_final: 0.8070 (mtpt) REVERT: X 124 LYS cc_start: 0.8667 (tptm) cc_final: 0.8325 (tptm) REVERT: Z 66 LYS cc_start: 0.8162 (mttt) cc_final: 0.7741 (mmmt) REVERT: Z 89 MET cc_start: 0.7362 (mmm) cc_final: 0.6809 (mmm) REVERT: Z 147 ARG cc_start: 0.7582 (ptp-170) cc_final: 0.7302 (ptp-110) REVERT: 2 11 TYR cc_start: 0.8371 (OUTLIER) cc_final: 0.6817 (p90) REVERT: 2 22 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7973 (mmtt) REVERT: 3 10 LYS cc_start: 0.8444 (pttm) cc_final: 0.7772 (mmtt) REVERT: 3 32 ARG cc_start: 0.7833 (ttm170) cc_final: 0.7310 (mtt180) REVERT: 4 149 ARG cc_start: 0.7886 (mmt-90) cc_final: 0.7415 (mpt180) REVERT: 8 69 ARG cc_start: 0.8438 (ttt90) cc_final: 0.8184 (ttt180) REVERT: 8 88 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7584 (mt-10) outliers start: 185 outliers final: 142 residues processed: 829 average time/residue: 0.9538 time to fit residues: 1291.1757 Evaluate side-chains 885 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 724 time to evaluate : 3.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 71 TYR Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 259 ASN Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 125 ARG Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 111 MET Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 73 PHE Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 127 MET Chi-restraints excluded: chain L residue 133 ILE Chi-restraints excluded: chain L residue 139 ASN Chi-restraints excluded: chain L residue 186 GLU Chi-restraints excluded: chain L residue 207 MET Chi-restraints excluded: chain L residue 237 ILE Chi-restraints excluded: chain M residue 12 ASP Chi-restraints excluded: chain M residue 25 ILE Chi-restraints excluded: chain M residue 29 ASN Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 66 CYS Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 73 ASN Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 78 ARG Chi-restraints excluded: chain N residue 91 SER Chi-restraints excluded: chain N residue 125 ILE Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 170 PHE Chi-restraints excluded: chain N residue 186 ILE Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain N residue 218 SER Chi-restraints excluded: chain N residue 234 VAL Chi-restraints excluded: chain N residue 242 ILE Chi-restraints excluded: chain N residue 250 LEU Chi-restraints excluded: chain O residue 16 ARG Chi-restraints excluded: chain O residue 32 TYR Chi-restraints excluded: chain O residue 68 ILE Chi-restraints excluded: chain O residue 71 ASP Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain O residue 96 VAL Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain O residue 120 ILE Chi-restraints excluded: chain O residue 127 ILE Chi-restraints excluded: chain P residue 11 MET Chi-restraints excluded: chain P residue 30 LEU Chi-restraints excluded: chain P residue 31 LEU Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 63 THR Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 75 GLN Chi-restraints excluded: chain P residue 105 THR Chi-restraints excluded: chain P residue 111 LEU Chi-restraints excluded: chain P residue 116 ASP Chi-restraints excluded: chain P residue 123 ILE Chi-restraints excluded: chain Q residue 56 ARG Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 185 ARG Chi-restraints excluded: chain R residue 194 ILE Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain R residue 225 LYS Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 29 SER Chi-restraints excluded: chain S residue 56 ASP Chi-restraints excluded: chain S residue 83 HIS Chi-restraints excluded: chain S residue 85 LEU Chi-restraints excluded: chain S residue 87 LYS Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain S residue 113 ASN Chi-restraints excluded: chain T residue 123 ILE Chi-restraints excluded: chain T residue 142 ILE Chi-restraints excluded: chain T residue 155 LYS Chi-restraints excluded: chain T residue 159 ASN Chi-restraints excluded: chain T residue 161 VAL Chi-restraints excluded: chain T residue 170 THR Chi-restraints excluded: chain T residue 171 TYR Chi-restraints excluded: chain T residue 176 ILE Chi-restraints excluded: chain T residue 210 ILE Chi-restraints excluded: chain T residue 234 THR Chi-restraints excluded: chain U residue 30 ASP Chi-restraints excluded: chain U residue 32 ILE Chi-restraints excluded: chain U residue 79 LEU Chi-restraints excluded: chain U residue 88 SER Chi-restraints excluded: chain U residue 104 GLU Chi-restraints excluded: chain U residue 130 CYS Chi-restraints excluded: chain U residue 139 ILE Chi-restraints excluded: chain U residue 149 LEU Chi-restraints excluded: chain U residue 157 LEU Chi-restraints excluded: chain V residue 143 ASP Chi-restraints excluded: chain V residue 163 ASN Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain W residue 56 CYS Chi-restraints excluded: chain W residue 90 SER Chi-restraints excluded: chain W residue 98 THR Chi-restraints excluded: chain W residue 108 THR Chi-restraints excluded: chain W residue 122 ILE Chi-restraints excluded: chain W residue 129 ILE Chi-restraints excluded: chain W residue 145 ASP Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 120 ASP Chi-restraints excluded: chain X residue 122 LEU Chi-restraints excluded: chain Y residue 82 SER Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Y residue 129 ILE Chi-restraints excluded: chain Z residue 76 LEU Chi-restraints excluded: chain Z residue 81 LEU Chi-restraints excluded: chain Z residue 83 LEU Chi-restraints excluded: chain Z residue 133 SER Chi-restraints excluded: chain 2 residue 11 TYR Chi-restraints excluded: chain 2 residue 22 LYS Chi-restraints excluded: chain 2 residue 29 LEU Chi-restraints excluded: chain 3 residue 31 SER Chi-restraints excluded: chain 3 residue 58 HIS Chi-restraints excluded: chain 3 residue 59 THR Chi-restraints excluded: chain 3 residue 64 ILE Chi-restraints excluded: chain 4 residue 96 LEU Chi-restraints excluded: chain 5 residue 133 SER Chi-restraints excluded: chain 5 residue 143 TYR Chi-restraints excluded: chain 5 residue 150 LEU Chi-restraints excluded: chain 6 residue 3 ILE Chi-restraints excluded: chain 6 residue 7 VAL Chi-restraints excluded: chain 7 residue 141 ASN Chi-restraints excluded: chain 8 residue 50 ARG Chi-restraints excluded: chain 8 residue 72 ILE Chi-restraints excluded: chain 8 residue 78 VAL Chi-restraints excluded: chain 8 residue 88 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 547 optimal weight: 0.0070 chunk 576 optimal weight: 3.9990 chunk 525 optimal weight: 0.9990 chunk 560 optimal weight: 3.9990 chunk 337 optimal weight: 0.9980 chunk 244 optimal weight: 8.9990 chunk 440 optimal weight: 4.9990 chunk 171 optimal weight: 7.9990 chunk 506 optimal weight: 20.0000 chunk 530 optimal weight: 5.9990 chunk 558 optimal weight: 5.9990 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 170 GLN O 12 GLN P 87 HIS Q 85 GLN R 202 ASN ** S 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 59 ASN 5 137 GLN ** 6 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 98702 Z= 0.210 Angle : 0.651 20.076 147908 Z= 0.330 Chirality : 0.037 0.393 18873 Planarity : 0.005 0.099 7648 Dihedral : 24.227 179.919 49975 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.54 % Allowed : 9.82 % Favored : 89.65 % Rotamer: Outliers : 6.09 % Allowed : 26.24 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.14), residues: 3362 helix: 0.20 (0.17), residues: 929 sheet: -1.96 (0.21), residues: 509 loop : -2.26 (0.14), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP T 141 HIS 0.011 0.001 HIS P 87 PHE 0.037 0.002 PHE Z 88 TYR 0.030 0.002 TYR D 261 ARG 0.010 0.001 ARG V 106 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 899 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 726 time to evaluate : 3.714 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: D 71 TYR cc_start: 0.7435 (OUTLIER) cc_final: 0.6626 (m-80) REVERT: D 188 VAL cc_start: 0.8355 (p) cc_final: 0.8118 (m) REVERT: E 153 GLU cc_start: 0.8480 (mt-10) cc_final: 0.7851 (mt-10) REVERT: F 60 PHE cc_start: 0.7590 (OUTLIER) cc_final: 0.7198 (m-80) REVERT: F 67 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6719 (pt0) REVERT: F 125 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.6718 (ptt-90) REVERT: F 161 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8719 (tt) REVERT: F 214 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7514 (tm-30) REVERT: F 222 ASN cc_start: 0.9119 (t0) cc_final: 0.8396 (t0) REVERT: F 258 ARG cc_start: 0.8193 (mmm160) cc_final: 0.7915 (mtm110) REVERT: G 20 LYS cc_start: 0.7982 (tttm) cc_final: 0.7341 (tttm) REVERT: G 30 LEU cc_start: 0.6471 (mp) cc_final: 0.5769 (pp) REVERT: G 48 LYS cc_start: 0.6948 (pttt) cc_final: 0.6550 (ptpt) REVERT: G 49 ILE cc_start: 0.5817 (mp) cc_final: 0.5358 (mp) REVERT: G 106 LEU cc_start: 0.7023 (mt) cc_final: 0.6510 (tp) REVERT: G 167 MET cc_start: 0.5759 (ptp) cc_final: 0.5187 (ptp) REVERT: H 58 MET cc_start: 0.6374 (mmm) cc_final: 0.6173 (mmm) REVERT: H 109 ARG cc_start: 0.5075 (mtt180) cc_final: 0.2830 (mtt180) REVERT: H 200 LYS cc_start: 0.7442 (mtpt) cc_final: 0.7023 (ttpt) REVERT: H 213 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7551 (pm20) REVERT: I 63 LYS cc_start: 0.6900 (mtpp) cc_final: 0.6502 (mtpp) REVERT: L 131 ILE cc_start: 0.9201 (mm) cc_final: 0.8986 (tt) REVERT: L 140 LEU cc_start: 0.9079 (mt) cc_final: 0.8762 (mp) REVERT: L 186 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7164 (pm20) REVERT: L 195 ILE cc_start: 0.9055 (mm) cc_final: 0.8520 (tt) REVERT: L 207 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7650 (mmt) REVERT: L 225 LYS cc_start: 0.8091 (tttm) cc_final: 0.7763 (tptp) REVERT: M 12 ASP cc_start: 0.8804 (OUTLIER) cc_final: 0.8532 (p0) REVERT: M 13 ASN cc_start: 0.8692 (p0) cc_final: 0.8456 (p0) REVERT: M 45 GLU cc_start: 0.8239 (pm20) cc_final: 0.7941 (pm20) REVERT: M 97 ARG cc_start: 0.7697 (ttm170) cc_final: 0.7449 (ttm170) REVERT: M 112 LYS cc_start: 0.8294 (tptt) cc_final: 0.7470 (tptm) REVERT: N 97 ARG cc_start: 0.7820 (ptm-80) cc_final: 0.7337 (ptm-80) REVERT: N 170 PHE cc_start: 0.4593 (OUTLIER) cc_final: 0.3314 (p90) REVERT: N 182 LYS cc_start: 0.8518 (ttpp) cc_final: 0.8309 (ttpt) REVERT: N 186 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7851 (mt) REVERT: N 252 ARG cc_start: 0.6627 (tpt90) cc_final: 0.6332 (ttt180) REVERT: O 16 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.7435 (ptm-80) REVERT: O 48 GLU cc_start: 0.7760 (tp30) cc_final: 0.7478 (tp30) REVERT: O 63 LYS cc_start: 0.7050 (tttt) cc_final: 0.6760 (tttt) REVERT: Q 56 ARG cc_start: 0.7094 (OUTLIER) cc_final: 0.6750 (mtt180) REVERT: Q 81 HIS cc_start: 0.7357 (m-70) cc_final: 0.6694 (t-90) REVERT: R 185 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.7979 (ttt90) REVERT: R 228 ARG cc_start: 0.8164 (mtp-110) cc_final: 0.7912 (mtp-110) REVERT: S 6 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7647 (ptp-170) REVERT: S 56 ASP cc_start: 0.7082 (OUTLIER) cc_final: 0.6099 (t70) REVERT: S 84 ASP cc_start: 0.7682 (m-30) cc_final: 0.7390 (m-30) REVERT: S 113 ASN cc_start: 0.6939 (OUTLIER) cc_final: 0.6618 (m-40) REVERT: U 31 GLU cc_start: 0.7506 (pm20) cc_final: 0.7157 (pm20) REVERT: U 35 ARG cc_start: 0.7703 (mtp180) cc_final: 0.7222 (mmm-85) REVERT: V 132 ASN cc_start: 0.8761 (t0) cc_final: 0.8187 (t0) REVERT: V 149 GLU cc_start: 0.8383 (tm-30) cc_final: 0.8000 (tt0) REVERT: W 70 LYS cc_start: 0.8326 (ptmt) cc_final: 0.8081 (mtpt) REVERT: X 124 LYS cc_start: 0.8687 (tptm) cc_final: 0.8353 (tptm) REVERT: X 155 ARG cc_start: 0.8688 (ttm170) cc_final: 0.7973 (ttm170) REVERT: Z 66 LYS cc_start: 0.8183 (mttt) cc_final: 0.7783 (mmmt) REVERT: Z 89 MET cc_start: 0.7402 (mmm) cc_final: 0.6785 (mmm) REVERT: Z 147 ARG cc_start: 0.7608 (ptp-170) cc_final: 0.7316 (ptp-110) REVERT: 2 11 TYR cc_start: 0.8367 (OUTLIER) cc_final: 0.6954 (p90) REVERT: 2 22 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7983 (mmtt) REVERT: 3 10 LYS cc_start: 0.8440 (pttm) cc_final: 0.7770 (mmtt) REVERT: 3 32 ARG cc_start: 0.7824 (ttm170) cc_final: 0.7379 (mtt180) REVERT: 4 149 ARG cc_start: 0.7882 (mmt-90) cc_final: 0.7421 (mpt180) REVERT: 7 140 LYS cc_start: 0.7466 (OUTLIER) cc_final: 0.6685 (ptmm) REVERT: 8 69 ARG cc_start: 0.8461 (ttt90) cc_final: 0.8205 (ttt180) REVERT: 8 88 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7568 (mp0) outliers start: 173 outliers final: 140 residues processed: 817 average time/residue: 1.0373 time to fit residues: 1397.4214 Evaluate side-chains 879 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 719 time to evaluate : 3.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 71 TYR Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 259 ASN Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain F residue 60 PHE Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 125 ARG Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 111 MET Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 73 PHE Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 127 MET Chi-restraints excluded: chain L residue 133 ILE Chi-restraints excluded: chain L residue 139 ASN Chi-restraints excluded: chain L residue 186 GLU Chi-restraints excluded: chain L residue 207 MET Chi-restraints excluded: chain L residue 237 ILE Chi-restraints excluded: chain M residue 12 ASP Chi-restraints excluded: chain M residue 25 ILE Chi-restraints excluded: chain M residue 29 ASN Chi-restraints excluded: chain M residue 66 CYS Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 73 ASN Chi-restraints excluded: chain N residue 91 SER Chi-restraints excluded: chain N residue 125 ILE Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 170 PHE Chi-restraints excluded: chain N residue 175 GLU Chi-restraints excluded: chain N residue 186 ILE Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain N residue 218 SER Chi-restraints excluded: chain N residue 234 VAL Chi-restraints excluded: chain N residue 242 ILE Chi-restraints excluded: chain N residue 250 LEU Chi-restraints excluded: chain O residue 7 THR Chi-restraints excluded: chain O residue 12 GLN Chi-restraints excluded: chain O residue 16 ARG Chi-restraints excluded: chain O residue 32 TYR Chi-restraints excluded: chain O residue 68 ILE Chi-restraints excluded: chain O residue 71 ASP Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain O residue 96 VAL Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain O residue 120 ILE Chi-restraints excluded: chain O residue 127 ILE Chi-restraints excluded: chain P residue 11 MET Chi-restraints excluded: chain P residue 30 LEU Chi-restraints excluded: chain P residue 31 LEU Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 61 MET Chi-restraints excluded: chain P residue 63 THR Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 75 GLN Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 105 THR Chi-restraints excluded: chain P residue 111 LEU Chi-restraints excluded: chain P residue 116 ASP Chi-restraints excluded: chain P residue 123 ILE Chi-restraints excluded: chain Q residue 56 ARG Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 185 ARG Chi-restraints excluded: chain R residue 194 ILE Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain R residue 225 LYS Chi-restraints excluded: chain S residue 6 ARG Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 29 SER Chi-restraints excluded: chain S residue 56 ASP Chi-restraints excluded: chain S residue 83 HIS Chi-restraints excluded: chain S residue 85 LEU Chi-restraints excluded: chain S residue 87 LYS Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain S residue 113 ASN Chi-restraints excluded: chain T residue 142 ILE Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain T residue 155 LYS Chi-restraints excluded: chain T residue 159 ASN Chi-restraints excluded: chain T residue 161 VAL Chi-restraints excluded: chain T residue 171 TYR Chi-restraints excluded: chain T residue 176 ILE Chi-restraints excluded: chain T residue 210 ILE Chi-restraints excluded: chain T residue 234 THR Chi-restraints excluded: chain U residue 30 ASP Chi-restraints excluded: chain U residue 32 ILE Chi-restraints excluded: chain U residue 88 SER Chi-restraints excluded: chain U residue 94 ASN Chi-restraints excluded: chain U residue 104 GLU Chi-restraints excluded: chain U residue 110 THR Chi-restraints excluded: chain U residue 130 CYS Chi-restraints excluded: chain U residue 139 ILE Chi-restraints excluded: chain U residue 149 LEU Chi-restraints excluded: chain U residue 157 LEU Chi-restraints excluded: chain V residue 143 ASP Chi-restraints excluded: chain V residue 163 ASN Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain W residue 56 CYS Chi-restraints excluded: chain W residue 90 SER Chi-restraints excluded: chain W residue 98 THR Chi-restraints excluded: chain W residue 108 THR Chi-restraints excluded: chain W residue 122 ILE Chi-restraints excluded: chain W residue 129 ILE Chi-restraints excluded: chain W residue 145 ASP Chi-restraints excluded: chain X residue 72 SER Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 120 ASP Chi-restraints excluded: chain Y residue 82 SER Chi-restraints excluded: chain Z residue 81 LEU Chi-restraints excluded: chain Z residue 133 SER Chi-restraints excluded: chain 2 residue 11 TYR Chi-restraints excluded: chain 2 residue 22 LYS Chi-restraints excluded: chain 2 residue 29 LEU Chi-restraints excluded: chain 3 residue 31 SER Chi-restraints excluded: chain 3 residue 58 HIS Chi-restraints excluded: chain 3 residue 64 ILE Chi-restraints excluded: chain 4 residue 96 LEU Chi-restraints excluded: chain 5 residue 133 SER Chi-restraints excluded: chain 5 residue 143 TYR Chi-restraints excluded: chain 5 residue 150 LEU Chi-restraints excluded: chain 6 residue 3 ILE Chi-restraints excluded: chain 6 residue 7 VAL Chi-restraints excluded: chain 7 residue 140 LYS Chi-restraints excluded: chain 7 residue 141 ASN Chi-restraints excluded: chain 8 residue 50 ARG Chi-restraints excluded: chain 8 residue 72 ILE Chi-restraints excluded: chain 8 residue 78 VAL Chi-restraints excluded: chain 8 residue 88 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 368 optimal weight: 20.0000 chunk 592 optimal weight: 4.9990 chunk 361 optimal weight: 0.6980 chunk 281 optimal weight: 20.0000 chunk 411 optimal weight: 4.9990 chunk 621 optimal weight: 4.9990 chunk 572 optimal weight: 1.9990 chunk 495 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 382 optimal weight: 0.0020 chunk 303 optimal weight: 5.9990 overall best weight: 2.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 85 GLN R 202 ASN ** S 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 59 ASN ** X 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 137 GLN ** 6 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 98702 Z= 0.247 Angle : 0.672 20.081 147908 Z= 0.339 Chirality : 0.038 0.395 18873 Planarity : 0.006 0.190 7648 Dihedral : 24.210 179.964 49975 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.51 % Allowed : 10.38 % Favored : 89.11 % Rotamer: Outliers : 6.09 % Allowed : 26.38 % Favored : 67.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.14), residues: 3362 helix: 0.09 (0.17), residues: 939 sheet: -1.96 (0.21), residues: 516 loop : -2.28 (0.14), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP T 141 HIS 0.009 0.001 HIS P 87 PHE 0.032 0.002 PHE Z 88 TYR 0.029 0.002 TYR D 261 ARG 0.014 0.001 ARG V 106 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6724 Ramachandran restraints generated. 3362 Oldfield, 0 Emsley, 3362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 899 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 726 time to evaluate : 3.666 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: D 71 TYR cc_start: 0.7447 (OUTLIER) cc_final: 0.6646 (m-80) REVERT: D 188 VAL cc_start: 0.8370 (p) cc_final: 0.8134 (m) REVERT: E 153 GLU cc_start: 0.8489 (mt-10) cc_final: 0.7860 (mt-10) REVERT: F 60 PHE cc_start: 0.7629 (OUTLIER) cc_final: 0.7232 (m-80) REVERT: F 67 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6697 (pt0) REVERT: F 125 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.6710 (ptt-90) REVERT: F 161 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8694 (tt) REVERT: F 214 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7514 (tm-30) REVERT: F 222 ASN cc_start: 0.9127 (t0) cc_final: 0.8403 (t0) REVERT: F 258 ARG cc_start: 0.8209 (mmm160) cc_final: 0.7920 (mtm110) REVERT: G 20 LYS cc_start: 0.8021 (tttm) cc_final: 0.7407 (tttm) REVERT: G 30 LEU cc_start: 0.6512 (mp) cc_final: 0.5839 (pp) REVERT: G 48 LYS cc_start: 0.6946 (pttt) cc_final: 0.6545 (ptpt) REVERT: G 49 ILE cc_start: 0.5816 (mp) cc_final: 0.5344 (mp) REVERT: G 106 LEU cc_start: 0.7007 (mt) cc_final: 0.6456 (tp) REVERT: G 167 MET cc_start: 0.5878 (ptp) cc_final: 0.5328 (ptp) REVERT: H 109 ARG cc_start: 0.5104 (mtt180) cc_final: 0.2845 (mtt180) REVERT: H 200 LYS cc_start: 0.7506 (mtpt) cc_final: 0.7073 (ttpt) REVERT: H 213 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7555 (pm20) REVERT: I 43 LYS cc_start: 0.6378 (OUTLIER) cc_final: 0.5860 (pmmt) REVERT: I 53 LEU cc_start: 0.6620 (mp) cc_final: 0.6407 (tp) REVERT: I 63 LYS cc_start: 0.6909 (mtpp) cc_final: 0.6252 (mtpp) REVERT: L 131 ILE cc_start: 0.9205 (mm) cc_final: 0.8990 (tt) REVERT: L 140 LEU cc_start: 0.9079 (mt) cc_final: 0.8758 (mp) REVERT: L 186 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.7175 (pm20) REVERT: L 195 ILE cc_start: 0.9058 (mm) cc_final: 0.8526 (tt) REVERT: L 207 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7670 (mmt) REVERT: L 225 LYS cc_start: 0.8094 (tttm) cc_final: 0.7767 (tptp) REVERT: M 12 ASP cc_start: 0.8816 (OUTLIER) cc_final: 0.8534 (p0) REVERT: M 13 ASN cc_start: 0.8704 (p0) cc_final: 0.8451 (p0) REVERT: M 45 GLU cc_start: 0.8274 (pm20) cc_final: 0.7972 (pm20) REVERT: M 97 ARG cc_start: 0.7699 (ttm170) cc_final: 0.7459 (ttm170) REVERT: M 112 LYS cc_start: 0.8305 (tptt) cc_final: 0.7476 (tptm) REVERT: N 97 ARG cc_start: 0.7836 (ptm-80) cc_final: 0.7345 (ptm-80) REVERT: N 134 MET cc_start: 0.7901 (tpp) cc_final: 0.7552 (tpp) REVERT: N 170 PHE cc_start: 0.4599 (OUTLIER) cc_final: 0.3258 (p90) REVERT: N 182 LYS cc_start: 0.8525 (ttpp) cc_final: 0.8320 (ttpt) REVERT: N 186 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.7846 (mt) REVERT: N 252 ARG cc_start: 0.6627 (tpt90) cc_final: 0.6325 (ttt180) REVERT: O 16 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.7461 (ptm-80) REVERT: O 48 GLU cc_start: 0.7784 (tp30) cc_final: 0.7507 (tp30) REVERT: O 63 LYS cc_start: 0.7064 (tttt) cc_final: 0.6768 (tttt) REVERT: O 81 THR cc_start: 0.8712 (m) cc_final: 0.8504 (m) REVERT: Q 56 ARG cc_start: 0.7129 (OUTLIER) cc_final: 0.6766 (mtt180) REVERT: Q 81 HIS cc_start: 0.7371 (m-70) cc_final: 0.6717 (t-90) REVERT: R 185 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.8019 (ttt90) REVERT: S 6 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7658 (ptp-170) REVERT: S 56 ASP cc_start: 0.7082 (OUTLIER) cc_final: 0.6062 (t70) REVERT: S 63 THR cc_start: 0.8792 (m) cc_final: 0.8575 (m) REVERT: S 84 ASP cc_start: 0.7749 (m-30) cc_final: 0.7437 (m-30) REVERT: S 113 ASN cc_start: 0.6955 (OUTLIER) cc_final: 0.6623 (m-40) REVERT: T 122 GLU cc_start: 0.8258 (mp0) cc_final: 0.7978 (mp0) REVERT: U 31 GLU cc_start: 0.7503 (pm20) cc_final: 0.7143 (pm20) REVERT: U 35 ARG cc_start: 0.7714 (mtp180) cc_final: 0.7243 (mmm-85) REVERT: U 93 PHE cc_start: 0.5623 (OUTLIER) cc_final: 0.4643 (p90) REVERT: V 132 ASN cc_start: 0.8783 (t0) cc_final: 0.8203 (t0) REVERT: W 70 LYS cc_start: 0.8348 (ptmt) cc_final: 0.8106 (mtpt) REVERT: X 124 LYS cc_start: 0.8692 (tptm) cc_final: 0.8356 (tptm) REVERT: X 155 ARG cc_start: 0.8699 (ttm170) cc_final: 0.7972 (ttm170) REVERT: Z 66 LYS cc_start: 0.8193 (mttt) cc_final: 0.7735 (mmmt) REVERT: Z 89 MET cc_start: 0.7390 (mmm) cc_final: 0.6778 (mmm) REVERT: Z 147 ARG cc_start: 0.7632 (ptp-170) cc_final: 0.7355 (ptp-110) REVERT: 2 11 TYR cc_start: 0.8388 (OUTLIER) cc_final: 0.6840 (p90) REVERT: 2 22 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.8010 (mmtt) REVERT: 3 10 LYS cc_start: 0.8443 (pttm) cc_final: 0.7789 (mmtt) REVERT: 3 32 ARG cc_start: 0.7831 (ttm170) cc_final: 0.7380 (mtt180) REVERT: 4 149 ARG cc_start: 0.7896 (mmt-90) cc_final: 0.7433 (mpt180) REVERT: 5 135 LEU cc_start: 0.8970 (pp) cc_final: 0.8735 (pt) REVERT: 7 140 LYS cc_start: 0.7617 (OUTLIER) cc_final: 0.6779 (ptmm) REVERT: 8 69 ARG cc_start: 0.8475 (ttt90) cc_final: 0.8208 (ttt180) REVERT: 8 88 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7587 (mp0) outliers start: 173 outliers final: 148 residues processed: 816 average time/residue: 0.9554 time to fit residues: 1269.0339 Evaluate side-chains 893 residues out of total 2908 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 723 time to evaluate : 3.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 71 TYR Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 187 THR Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 259 ASN Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 190 LEU Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain F residue 60 PHE Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 81 ARG Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 125 ARG Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain G residue 111 MET Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 73 PHE Chi-restraints excluded: chain L residue 104 SER Chi-restraints excluded: chain L residue 127 MET Chi-restraints excluded: chain L residue 133 ILE Chi-restraints excluded: chain L residue 139 ASN Chi-restraints excluded: chain L residue 186 GLU Chi-restraints excluded: chain L residue 207 MET Chi-restraints excluded: chain L residue 237 ILE Chi-restraints excluded: chain M residue 12 ASP Chi-restraints excluded: chain M residue 25 ILE Chi-restraints excluded: chain M residue 29 ASN Chi-restraints excluded: chain M residue 66 CYS Chi-restraints excluded: chain M residue 69 LEU Chi-restraints excluded: chain M residue 73 ASN Chi-restraints excluded: chain N residue 91 SER Chi-restraints excluded: chain N residue 125 ILE Chi-restraints excluded: chain N residue 165 ILE Chi-restraints excluded: chain N residue 170 PHE Chi-restraints excluded: chain N residue 175 GLU Chi-restraints excluded: chain N residue 186 ILE Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain N residue 218 SER Chi-restraints excluded: chain N residue 234 VAL Chi-restraints excluded: chain N residue 242 ILE Chi-restraints excluded: chain N residue 250 LEU Chi-restraints excluded: chain O residue 7 THR Chi-restraints excluded: chain O residue 16 ARG Chi-restraints excluded: chain O residue 32 TYR Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 68 ILE Chi-restraints excluded: chain O residue 71 ASP Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain O residue 96 VAL Chi-restraints excluded: chain O residue 109 VAL Chi-restraints excluded: chain O residue 120 ILE Chi-restraints excluded: chain O residue 127 ILE Chi-restraints excluded: chain P residue 11 MET Chi-restraints excluded: chain P residue 16 LYS Chi-restraints excluded: chain P residue 30 LEU Chi-restraints excluded: chain P residue 31 LEU Chi-restraints excluded: chain P residue 52 SER Chi-restraints excluded: chain P residue 61 MET Chi-restraints excluded: chain P residue 63 THR Chi-restraints excluded: chain P residue 70 LEU Chi-restraints excluded: chain P residue 75 GLN Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 105 THR Chi-restraints excluded: chain P residue 111 LEU Chi-restraints excluded: chain P residue 116 ASP Chi-restraints excluded: chain P residue 123 ILE Chi-restraints excluded: chain Q residue 56 ARG Chi-restraints excluded: chain Q residue 152 VAL Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 185 ARG Chi-restraints excluded: chain R residue 194 ILE Chi-restraints excluded: chain R residue 195 VAL Chi-restraints excluded: chain R residue 222 LEU Chi-restraints excluded: chain R residue 225 LYS Chi-restraints excluded: chain S residue 6 ARG Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 29 SER Chi-restraints excluded: chain S residue 56 ASP Chi-restraints excluded: chain S residue 83 HIS Chi-restraints excluded: chain S residue 85 LEU Chi-restraints excluded: chain S residue 87 LYS Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 108 ILE Chi-restraints excluded: chain S residue 113 ASN Chi-restraints excluded: chain T residue 142 ILE Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain T residue 155 LYS Chi-restraints excluded: chain T residue 159 ASN Chi-restraints excluded: chain T residue 161 VAL Chi-restraints excluded: chain T residue 170 THR Chi-restraints excluded: chain T residue 171 TYR Chi-restraints excluded: chain T residue 176 ILE Chi-restraints excluded: chain T residue 210 ILE Chi-restraints excluded: chain T residue 234 THR Chi-restraints excluded: chain U residue 30 ASP Chi-restraints excluded: chain U residue 32 ILE Chi-restraints excluded: chain U residue 88 SER Chi-restraints excluded: chain U residue 93 PHE Chi-restraints excluded: chain U residue 94 ASN Chi-restraints excluded: chain U residue 104 GLU Chi-restraints excluded: chain U residue 110 THR Chi-restraints excluded: chain U residue 130 CYS Chi-restraints excluded: chain U residue 138 ASP Chi-restraints excluded: chain U residue 139 ILE Chi-restraints excluded: chain U residue 149 LEU Chi-restraints excluded: chain U residue 157 LEU Chi-restraints excluded: chain V residue 143 ASP Chi-restraints excluded: chain V residue 163 ASN Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain W residue 56 CYS Chi-restraints excluded: chain W residue 90 SER Chi-restraints excluded: chain W residue 98 THR Chi-restraints excluded: chain W residue 108 THR Chi-restraints excluded: chain W residue 122 ILE Chi-restraints excluded: chain W residue 129 ILE Chi-restraints excluded: chain W residue 145 ASP Chi-restraints excluded: chain X residue 72 SER Chi-restraints excluded: chain X residue 107 VAL Chi-restraints excluded: chain X residue 120 ASP Chi-restraints excluded: chain Y residue 82 SER Chi-restraints excluded: chain Y residue 95 THR Chi-restraints excluded: chain Z residue 76 LEU Chi-restraints excluded: chain Z residue 81 LEU Chi-restraints excluded: chain Z residue 83 LEU Chi-restraints excluded: chain Z residue 133 SER Chi-restraints excluded: chain 2 residue 11 TYR Chi-restraints excluded: chain 2 residue 22 LYS Chi-restraints excluded: chain 2 residue 29 LEU Chi-restraints excluded: chain 3 residue 31 SER Chi-restraints excluded: chain 3 residue 58 HIS Chi-restraints excluded: chain 3 residue 59 THR Chi-restraints excluded: chain 3 residue 64 ILE Chi-restraints excluded: chain 4 residue 96 LEU Chi-restraints excluded: chain 5 residue 133 SER Chi-restraints excluded: chain 5 residue 143 TYR Chi-restraints excluded: chain 5 residue 150 LEU Chi-restraints excluded: chain 6 residue 3 ILE Chi-restraints excluded: chain 6 residue 7 VAL Chi-restraints excluded: chain 7 residue 140 LYS Chi-restraints excluded: chain 7 residue 141 ASN Chi-restraints excluded: chain 8 residue 50 ARG Chi-restraints excluded: chain 8 residue 72 ILE Chi-restraints excluded: chain 8 residue 78 VAL Chi-restraints excluded: chain 8 residue 88 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 393 optimal weight: 7.9990 chunk 527 optimal weight: 2.9990 chunk 151 optimal weight: 20.0000 chunk 456 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 137 optimal weight: 8.9990 chunk 495 optimal weight: 4.9990 chunk 207 optimal weight: 40.0000 chunk 509 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 12 GLN R 202 ASN ** S 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 104 ASN W 59 ASN 3 61 HIS 5 137 GLN ** 6 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.150963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.118399 restraints weight = 151250.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.121490 restraints weight = 51206.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.121883 restraints weight = 26327.973| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.147 98702 Z= 0.469 Angle : 0.894 18.898 147908 Z= 0.442 Chirality : 0.048 0.416 18873 Planarity : 0.007 0.111 7648 Dihedral : 24.434 179.954 49975 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.57 % Allowed : 13.06 % Favored : 86.38 % Rotamer: Outliers : 6.61 % Allowed : 26.13 % Favored : 67.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.14), residues: 3362 helix: -0.49 (0.16), residues: 931 sheet: -2.11 (0.21), residues: 510 loop : -2.43 (0.13), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP Y 110 HIS 0.010 0.002 HIS P 87 PHE 0.036 0.003 PHE Z 88 TYR 0.036 0.003 TYR D 261 ARG 0.010 0.001 ARG V 106 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19695.39 seconds wall clock time: 346 minutes 48.31 seconds (20808.31 seconds total)