Starting phenix.real_space_refine on Wed Feb 21 02:14:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x8t_6711/02_2024/5x8t_6711.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x8t_6711/02_2024/5x8t_6711.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x8t_6711/02_2024/5x8t_6711.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x8t_6711/02_2024/5x8t_6711.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x8t_6711/02_2024/5x8t_6711.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x8t_6711/02_2024/5x8t_6711.pdb" } resolution = 3.3 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= 0.001 sd= 0.018 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 3028 5.49 5 S 102 5.16 5 C 45887 2.51 5 N 17144 2.21 5 O 25553 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 ARG 20": "NH1" <-> "NH2" Residue "2 ARG 28": "NH1" <-> "NH2" Residue "2 ARG 32": "NH1" <-> "NH2" Residue "2 ARG 39": "NH1" <-> "NH2" Residue "2 ARG 45": "NH1" <-> "NH2" Residue "3 ARG 112": "NH1" <-> "NH2" Residue "3 ARG 114": "NH1" <-> "NH2" Residue "3 ARG 121": "NH1" <-> "NH2" Residue "3 ARG 126": "NH1" <-> "NH2" Residue "3 ARG 127": "NH1" <-> "NH2" Residue "3 ARG 132": "NH1" <-> "NH2" Residue "3 ARG 146": "NH1" <-> "NH2" Residue "4 ARG 101": "NH1" <-> "NH2" Residue "4 ARG 103": "NH1" <-> "NH2" Residue "4 ARG 112": "NH1" <-> "NH2" Residue "4 ARG 113": "NH1" <-> "NH2" Residue "4 ARG 114": "NH1" <-> "NH2" Residue "4 ARG 128": "NH1" <-> "NH2" Residue "4 ARG 131": "NH1" <-> "NH2" Residue "5 ARG 4": "NH1" <-> "NH2" Residue "5 ARG 8": "NH1" <-> "NH2" Residue "5 ARG 15": "NH1" <-> "NH2" Residue "5 ARG 18": "NH1" <-> "NH2" Residue "5 ARG 20": "NH1" <-> "NH2" Residue "5 ARG 22": "NH1" <-> "NH2" Residue "7 ARG 50": "NH1" <-> "NH2" Residue "7 ARG 63": "NH1" <-> "NH2" Residue "7 ARG 69": "NH1" <-> "NH2" Residue "7 ARG 74": "NH1" <-> "NH2" Residue "C ARG 33": "NH1" <-> "NH2" Residue "C ARG 48": "NH1" <-> "NH2" Residue "C ARG 50": "NH1" <-> "NH2" Residue "C ARG 59": "NH1" <-> "NH2" Residue "C ARG 64": "NH1" <-> "NH2" Residue "C ARG 83": "NH1" <-> "NH2" Residue "C ARG 98": "NH1" <-> "NH2" Residue "C ARG 104": "NH1" <-> "NH2" Residue "C ARG 146": "NH1" <-> "NH2" Residue "C ARG 152": "NH1" <-> "NH2" Residue "C ARG 178": "NH1" <-> "NH2" Residue "C ARG 200": "NH1" <-> "NH2" Residue "C ARG 208": "NH1" <-> "NH2" Residue "C ARG 213": "NH1" <-> "NH2" Residue "C ARG 217": "NH1" <-> "NH2" Residue "C ARG 234": "NH1" <-> "NH2" Residue "C ARG 239": "NH1" <-> "NH2" Residue "C ARG 253": "NH1" <-> "NH2" Residue "C ARG 254": "NH1" <-> "NH2" Residue "C ARG 268": "NH1" <-> "NH2" Residue "D ARG 143": "NH1" <-> "NH2" Residue "D ARG 145": "NH1" <-> "NH2" Residue "D ARG 147": "NH1" <-> "NH2" Residue "D ARG 154": "NH1" <-> "NH2" Residue "D ARG 166": "NH1" <-> "NH2" Residue "D ARG 172": "NH1" <-> "NH2" Residue "D ARG 214": "NH1" <-> "NH2" Residue "D ARG 219": "NH1" <-> "NH2" Residue "D ARG 253": "NH1" <-> "NH2" Residue "D ARG 262": "NH1" <-> "NH2" Residue "D ARG 274": "NH1" <-> "NH2" Residue "D ARG 291": "NH1" <-> "NH2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "E ARG 96": "NH1" <-> "NH2" Residue "E ARG 97": "NH1" <-> "NH2" Residue "E ARG 109": "NH1" <-> "NH2" Residue "E TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 125": "NH1" <-> "NH2" Residue "E ARG 126": "NH1" <-> "NH2" Residue "E ARG 134": "NH1" <-> "NH2" Residue "E ARG 146": "NH1" <-> "NH2" Residue "E ARG 158": "NH1" <-> "NH2" Residue "E ARG 221": "NH1" <-> "NH2" Residue "E ARG 224": "NH1" <-> "NH2" Residue "E ARG 232": "NH1" <-> "NH2" Residue "E ARG 258": "NH1" <-> "NH2" Residue "F ARG 56": "NH1" <-> "NH2" Residue "F ARG 117": "NH1" <-> "NH2" Residue "F ARG 133": "NH1" <-> "NH2" Residue "F ARG 145": "NH1" <-> "NH2" Residue "F ARG 155": "NH1" <-> "NH2" Residue "F ARG 163": "NH1" <-> "NH2" Residue "F ARG 165": "NH1" <-> "NH2" Residue "F PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 203": "NH1" <-> "NH2" Residue "G ARG 42": "NH1" <-> "NH2" Residue "G ARG 78": "NH1" <-> "NH2" Residue "G ARG 91": "NH1" <-> "NH2" Residue "G ARG 93": "NH1" <-> "NH2" Residue "G ARG 99": "NH1" <-> "NH2" Residue "G ARG 100": "NH1" <-> "NH2" Residue "G ARG 109": "NH1" <-> "NH2" Residue "G ARG 135": "NH1" <-> "NH2" Residue "G ARG 154": "NH1" <-> "NH2" Residue "G ARG 176": "NH1" <-> "NH2" Residue "G ARG 189": "NH1" <-> "NH2" Residue "G ARG 192": "NH1" <-> "NH2" Residue "G ARG 203": "NH1" <-> "NH2" Residue "G ARG 210": "NH1" <-> "NH2" Residue "H ARG 49": "NH1" <-> "NH2" Residue "K ARG 126": "NH1" <-> "NH2" Residue "K ARG 168": "NH1" <-> "NH2" Residue "K ARG 174": "NH1" <-> "NH2" Residue "K ARG 175": "NH1" <-> "NH2" Residue "K ARG 179": "NH1" <-> "NH2" Residue "K ARG 194": "NH1" <-> "NH2" Residue "K ARG 198": "NH1" <-> "NH2" Residue "K ARG 205": "NH1" <-> "NH2" Residue "K ARG 212": "NH1" <-> "NH2" Residue "K ARG 242": "NH1" <-> "NH2" Residue "L ARG 17": "NH1" <-> "NH2" Residue "L ARG 30": "NH1" <-> "NH2" Residue "L ARG 31": "NH1" <-> "NH2" Residue "L ARG 34": "NH1" <-> "NH2" Residue "L ARG 54": "NH1" <-> "NH2" Residue "L ARG 59": "NH1" <-> "NH2" Residue "L ARG 64": "NH1" <-> "NH2" Residue "L ARG 71": "NH1" <-> "NH2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L ARG 97": "NH1" <-> "NH2" Residue "L ARG 104": "NH1" <-> "NH2" Residue "L ARG 107": "NH1" <-> "NH2" Residue "M ARG 81": "NH1" <-> "NH2" Residue "M ARG 97": "NH1" <-> "NH2" Residue "M ARG 100": "NH1" <-> "NH2" Residue "M ARG 127": "NH1" <-> "NH2" Residue "M TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 192": "NH1" <-> "NH2" Residue "M ARG 252": "NH1" <-> "NH2" Residue "N ARG 6": "NH1" <-> "NH2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 14": "NH1" <-> "NH2" Residue "N ARG 31": "NH1" <-> "NH2" Residue "N ARG 51": "NH1" <-> "NH2" Residue "N ARG 52": "NH1" <-> "NH2" Residue "N ARG 56": "NH1" <-> "NH2" Residue "N ARG 59": "NH1" <-> "NH2" Residue "N ARG 60": "NH1" <-> "NH2" Residue "N ARG 67": "NH1" <-> "NH2" Residue "N TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 101": "NH1" <-> "NH2" Residue "N ARG 115": "NH1" <-> "NH2" Residue "N ARG 116": "NH1" <-> "NH2" Residue "N ARG 128": "NH1" <-> "NH2" Residue "O ARG 15": "NH1" <-> "NH2" Residue "O ARG 19": "NH1" <-> "NH2" Residue "O ARG 27": "NH1" <-> "NH2" Residue "O ARG 28": "NH1" <-> "NH2" Residue "O ARG 32": "NH1" <-> "NH2" Residue "O ARG 43": "NH1" <-> "NH2" Residue "O ARG 48": "NH1" <-> "NH2" Residue "O ARG 73": "NH1" <-> "NH2" Residue "O ARG 74": "NH1" <-> "NH2" Residue "O PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 96": "NH1" <-> "NH2" Residue "O ARG 106": "NH1" <-> "NH2" Residue "O ARG 109": "NH1" <-> "NH2" Residue "O ARG 113": "NH1" <-> "NH2" Residue "O ARG 114": "NH1" <-> "NH2" Residue "P ARG 49": "NH1" <-> "NH2" Residue "P ARG 77": "NH1" <-> "NH2" Residue "P ARG 143": "NH1" <-> "NH2" Residue "P ARG 151": "NH1" <-> "NH2" Residue "P ARG 160": "NH1" <-> "NH2" Residue "Q ARG 116": "NH1" <-> "NH2" Residue "Q ARG 138": "NH1" <-> "NH2" Residue "Q ARG 144": "NH1" <-> "NH2" Residue "Q ARG 152": "NH1" <-> "NH2" Residue "Q ARG 160": "NH1" <-> "NH2" Residue "Q ARG 161": "NH1" <-> "NH2" Residue "Q ARG 172": "NH1" <-> "NH2" Residue "Q ARG 182": "NH1" <-> "NH2" Residue "Q ARG 184": "NH1" <-> "NH2" Residue "Q ARG 185": "NH1" <-> "NH2" Residue "Q ARG 228": "NH1" <-> "NH2" Residue "Q PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 6": "NH1" <-> "NH2" Residue "R ARG 12": "NH1" <-> "NH2" Residue "R ARG 18": "NH1" <-> "NH2" Residue "R PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 25": "NH1" <-> "NH2" Residue "R ARG 30": "NH1" <-> "NH2" Residue "R ARG 33": "NH1" <-> "NH2" Residue "R ARG 48": "NH1" <-> "NH2" Residue "R ARG 50": "NH1" <-> "NH2" Residue "R ARG 52": "NH1" <-> "NH2" Residue "R ARG 55": "NH1" <-> "NH2" Residue "R ARG 58": "NH1" <-> "NH2" Residue "R ARG 59": "NH1" <-> "NH2" Residue "R ARG 64": "NH1" <-> "NH2" Residue "R ARG 70": "NH1" <-> "NH2" Residue "R ARG 72": "NH1" <-> "NH2" Residue "R ARG 88": "NH1" <-> "NH2" Residue "S ARG 140": "NH1" <-> "NH2" Residue "S ARG 207": "NH1" <-> "NH2" Residue "S ARG 213": "NH1" <-> "NH2" Residue "S ARG 218": "NH1" <-> "NH2" Residue "T ARG 35": "NH1" <-> "NH2" Residue "T ARG 47": "NH1" <-> "NH2" Residue "T ARG 48": "NH1" <-> "NH2" Residue "T ARG 54": "NH1" <-> "NH2" Residue "T ARG 119": "NH1" <-> "NH2" Residue "T ARG 121": "NH1" <-> "NH2" Residue "T ARG 127": "NH1" <-> "NH2" Residue "T ARG 137": "NH1" <-> "NH2" Residue "U ARG 106": "NH1" <-> "NH2" Residue "U ARG 148": "NH1" <-> "NH2" Residue "U ARG 160": "NH1" <-> "NH2" Residue "U ARG 167": "NH1" <-> "NH2" Residue "V ARG 146": "NH1" <-> "NH2" Residue "V ARG 156": "NH1" <-> "NH2" Residue "V ARG 159": "NH1" <-> "NH2" Residue "V ARG 173": "NH1" <-> "NH2" Residue "X ARG 70": "NH1" <-> "NH2" Residue "X ARG 76": "NH1" <-> "NH2" Residue "X ARG 95": "NH1" <-> "NH2" Residue "X ARG 97": "NH1" <-> "NH2" Residue "X ARG 151": "NH1" <-> "NH2" Residue "Y ARG 73": "NH1" <-> "NH2" Residue "Y ARG 97": "NH1" <-> "NH2" Residue "Y ARG 115": "NH1" <-> "NH2" Residue "Y ARG 120": "NH1" <-> "NH2" Residue "Z ARG 69": "NH1" <-> "NH2" Residue "Z ARG 107": "NH1" <-> "NH2" Residue "Z ARG 111": "NH1" <-> "NH2" Residue "Z ARG 114": "NH1" <-> "NH2" Residue "Z ARG 131": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 91714 Number of models: 1 Model: "" Number of chains: 32 Chain: "1" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 378 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "2" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 415 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "3" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 445 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "4" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 563 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "5" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 304 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 2, 'TRANS': 34} Chain: "6" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 422 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "7" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 368 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 8, 'TRANS': 37} Chain: "B" Number of atoms: 2500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2500 Classifications: {'RNA': 117} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 5, 'rna3p_pur': 59, 'rna3p_pyr': 49} Link IDs: {'rna2p': 9, 'rna3p': 107} Chain: "C" Number of atoms: 1904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1904 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 14, 'TRANS': 232} Chain: "D" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1620 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 9, 'TRANS': 202} Chain: "E" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1655 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 13, 'TRANS': 196} Chain: "F" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1351 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain: "G" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1353 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 9, 'TRANS': 163} Chain: "H" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 423 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 3, 'TRANS': 49} Chain: "K" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1568 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 12, 'TRANS': 180} Chain: "L" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 942 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "M" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1342 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 10, 'TRANS': 166} Chain: "N" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1067 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 8, 'TRANS': 125} Chain: "O" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 944 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "P" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 947 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "Q" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 953 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain: "R" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 996 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 1, 'TRANS': 113} Chain: "S" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1171 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 13, 'TRANS': 133} Chain: "T" Number of atoms: 1149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1149 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 5, 'TRANS': 138} Chain: "U" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 740 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain: "V" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 993 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "W" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 2187 Classifications: {'RNA': 102} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 53, 'rna3p_pyr': 36} Link IDs: {'rna2p': 13, 'rna3p': 88} Chain: "X" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 810 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "Y" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 605 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "Z" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 754 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain: "A" Number of atoms: 60324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2809, 60324 Classifications: {'RNA': 2809} Modifications used: {'rna2p_pur': 279, 'rna2p_pyr': 120, 'rna3p_pur': 1352, 'rna3p_pyr': 1058} Link IDs: {'rna2p': 399, 'rna3p': 2409} Chain: "0" Number of atoms: 521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 521 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Time building chain proxies: 34.65, per 1000 atoms: 0.38 Number of scatterers: 91714 At special positions: 0 Unit cell: (201.6, 238.35, 224.7, 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 102 16.00 P 3028 15.00 O 25553 8.00 N 17144 7.00 C 45887 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 5 11 " - pdb=" SG CYS 5 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: 35.80 Conformation dependent library (CDL) restraints added in 4.5 seconds 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6146 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 42 sheets defined 27.7% alpha, 14.5% beta 1010 base pairs and 1682 stacking pairs defined. Time for finding SS restraints: 37.69 Creating SS restraints... Processing helix chain '1' and resid 9 through 26 Processing helix chain '1' and resid 28 through 38 Processing helix chain '3' and resid 101 through 109 removed outlier: 3.520A pdb=" N THR 3 108 " --> pdb=" O SER 3 104 " (cutoff:3.500A) Processing helix chain '3' and resid 110 through 116 Processing helix chain '3' and resid 117 through 131 Processing helix chain '4' and resid 95 through 100 Processing helix chain '4' and resid 125 through 132 Processing helix chain '4' and resid 140 through 145 Processing helix chain '5' and resid 29 through 33 removed outlier: 3.696A pdb=" N LYS 5 33 " --> pdb=" O PRO 5 30 " (cutoff:3.500A) Processing helix chain '6' and resid 95 through 128 Processing helix chain '6' and resid 132 through 138 Processing helix chain '7' and resid 68 through 73 removed outlier: 3.755A pdb=" N LYS 7 73 " --> pdb=" O ARG 7 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 198 removed outlier: 3.886A pdb=" N VAL C 196 " --> pdb=" O ASN C 193 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN C 198 " --> pdb=" O GLY C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 210 removed outlier: 3.609A pdb=" N TRP C 209 " --> pdb=" O GLY C 205 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU C 210 " --> pdb=" O SER C 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 205 through 210' Processing helix chain 'D' and resid 145 through 149 Processing helix chain 'D' and resid 150 through 160 removed outlier: 3.816A pdb=" N ALA D 160 " --> pdb=" O HIS D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 215 removed outlier: 3.800A pdb=" N HIS D 215 " --> pdb=" O GLY D 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 95 removed outlier: 3.546A pdb=" N VAL E 83 " --> pdb=" O LYS E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 169 removed outlier: 3.611A pdb=" N LEU E 159 " --> pdb=" O LYS E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 197 removed outlier: 3.671A pdb=" N ILE E 191 " --> pdb=" O THR E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 221 removed outlier: 3.645A pdb=" N GLU E 217 " --> pdb=" O VAL E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 259 Processing helix chain 'F' and resid 57 through 63 removed outlier: 4.023A pdb=" N GLU F 63 " --> pdb=" O THR F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 73 Processing helix chain 'F' and resid 99 through 114 Processing helix chain 'F' and resid 146 through 160 removed outlier: 3.699A pdb=" N TYR F 150 " --> pdb=" O GLY F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 217 through 226 Processing helix chain 'G' and resid 98 through 121 removed outlier: 3.605A pdb=" N ASN G 102 " --> pdb=" O THR G 98 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY G 106 " --> pdb=" O ASN G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 190 Processing helix chain 'H' and resid 70 through 77 Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'K' and resid 55 through 73 Processing helix chain 'K' and resid 123 through 137 removed outlier: 3.825A pdb=" N HIS K 134 " --> pdb=" O THR K 130 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY K 137 " --> pdb=" O ILE K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 157 through 161 removed outlier: 3.610A pdb=" N LYS K 160 " --> pdb=" O ASN K 157 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL K 161 " --> pdb=" O ALA K 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 157 through 161' Processing helix chain 'K' and resid 166 through 171 Processing helix chain 'K' and resid 187 through 195 Processing helix chain 'K' and resid 198 through 206 removed outlier: 3.617A pdb=" N ARG K 205 " --> pdb=" O GLU K 201 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLY K 206 " --> pdb=" O HIS K 202 " (cutoff:3.500A) Processing helix chain 'L' and resid 104 through 109 Processing helix chain 'L' and resid 110 through 116 removed outlier: 3.798A pdb=" N VAL L 114 " --> pdb=" O PHE L 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 143 through 149 Processing helix chain 'M' and resid 162 through 167 removed outlier: 3.597A pdb=" N VAL M 167 " --> pdb=" O ARG M 163 " (cutoff:3.500A) Processing helix chain 'M' and resid 177 through 184 Processing helix chain 'M' and resid 218 through 228 Processing helix chain 'M' and resid 243 through 253 removed outlier: 3.566A pdb=" N ALA M 253 " --> pdb=" O ASN M 249 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 59 Processing helix chain 'N' and resid 110 through 121 Processing helix chain 'N' and resid 122 through 124 No H-bonds generated for 'chain 'N' and resid 122 through 124' Processing helix chain 'O' and resid 23 through 42 Processing helix chain 'O' and resid 48 through 65 removed outlier: 3.919A pdb=" N TYR O 57 " --> pdb=" O ALA O 53 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA O 65 " --> pdb=" O MET O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 69 through 80 removed outlier: 3.571A pdb=" N ARG O 73 " --> pdb=" O SER O 69 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 87 removed outlier: 4.205A pdb=" N VAL O 86 " --> pdb=" O GLU O 82 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N HIS O 87 " --> pdb=" O LYS O 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 82 through 87' Processing helix chain 'O' and resid 92 through 97 Processing helix chain 'P' and resid 48 through 62 Processing helix chain 'P' and resid 100 through 104 Processing helix chain 'P' and resid 116 through 131 removed outlier: 3.906A pdb=" N CYS P 131 " --> pdb=" O ILE P 127 " (cutoff:3.500A) Processing helix chain 'P' and resid 150 through 161 removed outlier: 4.373A pdb=" N ALA P 154 " --> pdb=" O GLY P 150 " (cutoff:3.500A) Processing helix chain 'Q' and resid 122 through 138 Processing helix chain 'Q' and resid 175 through 178 Processing helix chain 'Q' and resid 226 through 230 Processing helix chain 'R' and resid 8 through 21 removed outlier: 3.606A pdb=" N ARG R 12 " --> pdb=" O TYR R 8 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE R 17 " --> pdb=" O ARG R 13 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 70 removed outlier: 4.872A pdb=" N GLN R 37 " --> pdb=" O ARG R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 71 through 73 No H-bonds generated for 'chain 'R' and resid 71 through 73' Processing helix chain 'R' and resid 77 through 87 removed outlier: 3.667A pdb=" N PHE R 81 " --> pdb=" O ASN R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 99 through 104 Processing helix chain 'R' and resid 104 through 117 removed outlier: 3.892A pdb=" N LYS R 117 " --> pdb=" O ASN R 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 106 through 111 Processing helix chain 'T' and resid 42 through 53 removed outlier: 3.601A pdb=" N ALA T 46 " --> pdb=" O SER T 42 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE T 53 " --> pdb=" O VAL T 49 " (cutoff:3.500A) Processing helix chain 'T' and resid 57 through 65 Processing helix chain 'T' and resid 72 through 90 removed outlier: 3.930A pdb=" N ILE T 76 " --> pdb=" O ALA T 72 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN T 86 " --> pdb=" O SER T 82 " (cutoff:3.500A) Processing helix chain 'T' and resid 153 through 161 removed outlier: 4.643A pdb=" N ALA T 159 " --> pdb=" O LYS T 155 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU T 161 " --> pdb=" O LEU T 157 " (cutoff:3.500A) Processing helix chain 'U' and resid 110 through 113 Processing helix chain 'U' and resid 121 through 132 removed outlier: 3.517A pdb=" N ILE U 125 " --> pdb=" O THR U 121 " (cutoff:3.500A) Processing helix chain 'U' and resid 145 through 150 removed outlier: 3.563A pdb=" N GLU U 149 " --> pdb=" O LYS U 145 " (cutoff:3.500A) Processing helix chain 'U' and resid 183 through 189 removed outlier: 3.514A pdb=" N LEU U 187 " --> pdb=" O ASN U 183 " (cutoff:3.500A) Processing helix chain 'V' and resid 50 through 54 removed outlier: 3.745A pdb=" N LYS V 54 " --> pdb=" O TRP V 51 " (cutoff:3.500A) Processing helix chain 'V' and resid 57 through 61 removed outlier: 3.857A pdb=" N SER V 60 " --> pdb=" O LYS V 57 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU V 61 " --> pdb=" O PRO V 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 57 through 61' Processing helix chain 'X' and resid 149 through 165 removed outlier: 3.526A pdb=" N ARG X 153 " --> pdb=" O SER X 149 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS X 165 " --> pdb=" O GLN X 161 " (cutoff:3.500A) Processing helix chain 'Y' and resid 122 through 132 Processing helix chain 'Y' and resid 133 through 142 removed outlier: 3.602A pdb=" N VAL Y 137 " --> pdb=" O GLY Y 133 " (cutoff:3.500A) Processing helix chain 'Z' and resid 65 through 70 removed outlier: 3.843A pdb=" N LEU Z 68 " --> pdb=" O LEU Z 65 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG Z 69 " --> pdb=" O LYS Z 66 " (cutoff:3.500A) Processing helix chain 'Z' and resid 72 through 96 Processing helix chain 'Z' and resid 101 through 125 removed outlier: 3.506A pdb=" N PHE Z 105 " --> pdb=" O LYS Z 101 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG Z 109 " --> pdb=" O PHE Z 105 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG Z 114 " --> pdb=" O LYS Z 110 " (cutoff:3.500A) Processing helix chain 'Z' and resid 129 through 142 removed outlier: 3.537A pdb=" N ARG Z 142 " --> pdb=" O LYS Z 138 " (cutoff:3.500A) Processing helix chain '0' and resid 81 through 86 Processing helix chain '0' and resid 94 through 99 removed outlier: 3.571A pdb=" N LYS 0 99 " --> pdb=" O GLU 0 95 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '2' and resid 13 through 16 Processing sheet with id=AA2, first strand: chain '4' and resid 102 through 104 Processing sheet with id=AA3, first strand: chain '5' and resid 15 through 19 Processing sheet with id=AA4, first strand: chain '7' and resid 90 through 91 removed outlier: 7.008A pdb=" N ALA S 181 " --> pdb=" O ILE S 224 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE S 224 " --> pdb=" O ALA S 181 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N HIS S 183 " --> pdb=" O THR S 222 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ARG S 218 " --> pdb=" O GLU S 187 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N GLN S 189 " --> pdb=" O ILE S 216 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ILE S 216 " --> pdb=" O GLN S 189 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 74 through 78 removed outlier: 3.776A pdb=" N THR C 76 " --> pdb=" O LEU C 89 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 125 through 127 removed outlier: 3.801A pdb=" N ASN C 139 " --> pdb=" O THR C 187 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 159 through 163 removed outlier: 4.390A pdb=" N THR C 169 " --> pdb=" O ILE C 161 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N LYS C 163 " --> pdb=" O SER C 167 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N SER C 167 " --> pdb=" O LYS C 163 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 258 through 264 removed outlier: 5.620A pdb=" N LYS D 260 " --> pdb=" O GLY D 201 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N GLY D 201 " --> pdb=" O LYS D 260 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ARG D 262 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE D 199 " --> pdb=" O ARG D 262 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N THR D 202 " --> pdb=" O LEU D 289 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU D 289 " --> pdb=" O THR D 202 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL D 114 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N MET D 99 " --> pdb=" O VAL D 112 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL D 112 " --> pdb=" O MET D 99 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N SER D 101 " --> pdb=" O VAL D 110 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N VAL D 110 " --> pdb=" O SER D 101 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL D 275 " --> pdb=" O ASP D 270 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYS D 268 " --> pdb=" O MET D 277 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LYS D 279 " --> pdb=" O ILE D 266 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE D 266 " --> pdb=" O LYS D 279 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 165 through 172 removed outlier: 6.847A pdb=" N GLU D 142 " --> pdb=" O ARG D 166 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LEU D 168 " --> pdb=" O GLY D 140 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLY D 140 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLU D 170 " --> pdb=" O GLN D 138 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLN D 138 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ARG D 172 " --> pdb=" O ALA D 136 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ALA D 136 " --> pdb=" O ARG D 172 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ALA D 136 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N VAL D 126 " --> pdb=" O ALA D 136 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLN D 138 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE D 122 " --> pdb=" O GLY D 140 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL D 123 " --> pdb=" O LYS D 184 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LYS D 184 " --> pdb=" O VAL D 123 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 208 through 209 Processing sheet with id=AB2, first strand: chain 'E' and resid 228 through 229 removed outlier: 7.373A pdb=" N PHE E 207 " --> pdb=" O LEU E 229 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL E 246 " --> pdb=" O LEU E 206 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE E 208 " --> pdb=" O VAL E 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'F' and resid 119 through 120 removed outlier: 3.578A pdb=" N LEU F 144 " --> pdb=" O ILE F 87 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE F 87 " --> pdb=" O LEU F 144 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 48 through 49 removed outlier: 3.754A pdb=" N LEU G 90 " --> pdb=" O ILE G 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 55 through 59 Processing sheet with id=AB6, first strand: chain 'G' and resid 161 through 164 Processing sheet with id=AB7, first strand: chain 'G' and resid 135 through 139 Processing sheet with id=AB8, first strand: chain 'H' and resid 51 through 53 Processing sheet with id=AB9, first strand: chain 'K' and resid 221 through 223 removed outlier: 6.163A pdb=" N TYR K 115 " --> pdb=" O ILE K 154 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL K 156 " --> pdb=" O TYR K 115 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL K 117 " --> pdb=" O VAL K 156 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N TRP K 114 " --> pdb=" O ILE K 237 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 7 through 10 removed outlier: 7.369A pdb=" N ARG L 17 " --> pdb=" O VAL L 10 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ALA L 16 " --> pdb=" O ALA L 46 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ALA L 46 " --> pdb=" O ALA L 16 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLU L 18 " --> pdb=" O LYS L 44 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS L 44 " --> pdb=" O GLU L 18 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ARG L 59 " --> pdb=" O ILE L 87 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ALA L 83 " --> pdb=" O VAL L 63 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ALA L 84 " --> pdb=" O HIS L 7 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASN L 9 " --> pdb=" O ALA L 84 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ILE L 86 " --> pdb=" O ASN L 9 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 76 through 78 removed outlier: 3.609A pdb=" N ILE L 76 " --> pdb=" O VAL Q 195 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ARG Q 182 " --> pdb=" O ILE Q 170 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU Q 153 " --> pdb=" O SER Q 163 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ASP Q 147 " --> pdb=" O VAL Q 169 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE Q 148 " --> pdb=" O VAL Q 208 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N VAL Q 208 " --> pdb=" O ILE Q 148 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N GLN Q 150 " --> pdb=" O ILE Q 206 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE Q 206 " --> pdb=" O GLN Q 150 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ARG Q 152 " --> pdb=" O LYS Q 204 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 159 through 160 Processing sheet with id=AC4, first strand: chain 'M' and resid 175 through 176 Processing sheet with id=AC5, first strand: chain 'N' and resid 63 through 66 removed outlier: 6.391A pdb=" N ILE N 102 " --> pdb=" O ALA N 36 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA N 36 " --> pdb=" O ILE N 102 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR N 104 " --> pdb=" O LEU N 34 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 40 through 43 removed outlier: 3.695A pdb=" N LYS N 72 " --> pdb=" O VAL N 94 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'O' and resid 44 through 47 Processing sheet with id=AC8, first strand: chain 'P' and resid 93 through 99 removed outlier: 6.542A pdb=" N VAL P 86 " --> pdb=" O LEU P 95 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ALA P 97 " --> pdb=" O VAL P 84 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL P 84 " --> pdb=" O ALA P 97 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N SER P 99 " --> pdb=" O LEU P 82 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU P 82 " --> pdb=" O SER P 99 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU P 73 " --> pdb=" O ALA P 140 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'S' and resid 132 through 136 Processing sheet with id=AD1, first strand: chain 'S' and resid 164 through 165 Processing sheet with id=AD2, first strand: chain 'S' and resid 197 through 200 Processing sheet with id=AD3, first strand: chain 'T' and resid 31 through 34 Processing sheet with id=AD4, first strand: chain 'T' and resid 31 through 34 Processing sheet with id=AD5, first strand: chain 'T' and resid 111 through 117 Processing sheet with id=AD6, first strand: chain 'U' and resid 115 through 118 Processing sheet with id=AD7, first strand: chain 'V' and resid 129 through 130 removed outlier: 7.595A pdb=" N THR V 98 " --> pdb=" O ILE V 92 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ILE V 92 " --> pdb=" O THR V 98 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ILE V 100 " --> pdb=" O SER V 90 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'V' and resid 107 through 110 Processing sheet with id=AD9, first strand: chain 'V' and resid 149 through 151 Processing sheet with id=AE1, first strand: chain 'X' and resid 78 through 79 removed outlier: 6.430A pdb=" N ILE X 92 " --> pdb=" O ALA X 117 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA X 117 " --> pdb=" O ILE X 92 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'X' and resid 122 through 124 Processing sheet with id=AE3, first strand: chain 'Y' and resid 83 through 84 Processing sheet with id=AE4, first strand: chain 'Y' and resid 87 through 88 removed outlier: 3.787A pdb=" N ARG Y 87 " --> pdb=" O THR Y 95 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR Y 95 " --> pdb=" O ARG Y 87 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'Y' and resid 104 through 110 Processing sheet with id=AE6, first strand: chain '0' and resid 58 through 63 removed outlier: 4.894A pdb=" N GLY 0 63 " --> pdb=" O GLU 0 47 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLU 0 47 " --> pdb=" O GLY 0 63 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N TYR 0 68 " --> pdb=" O ASP 0 48 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LYS 0 50 " --> pdb=" O TYR 0 68 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL 0 70 " --> pdb=" O LYS 0 50 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TYR 0 52 " --> pdb=" O VAL 0 70 " (cutoff:3.500A) 819 hydrogen bonds defined for protein. 2274 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2540 hydrogen bonds 3930 hydrogen bond angles 0 basepair planarities 1010 basepair parallelities 1682 stacking parallelities Total time for adding SS restraints: 162.98 Time building geometry restraints manager: 38.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 11768 1.33 - 1.46: 45740 1.46 - 1.58: 36231 1.58 - 1.71: 6053 1.71 - 1.84: 175 Bond restraints: 99967 Sorted by residual: bond pdb=" C LYS N 98 " pdb=" N PRO N 99 " ideal model delta sigma weight residual 1.330 1.368 -0.038 1.22e-02 6.72e+03 9.92e+00 bond pdb=" C LYS D 285 " pdb=" N PRO D 286 " ideal model delta sigma weight residual 1.332 1.362 -0.030 1.12e-02 7.97e+03 7.09e+00 bond pdb=" C CYS 2 52 " pdb=" N PRO 2 53 " ideal model delta sigma weight residual 1.333 1.363 -0.030 1.20e-02 6.94e+03 6.24e+00 bond pdb=" CB ASP Q 224 " pdb=" CG ASP Q 224 " ideal model delta sigma weight residual 1.516 1.572 -0.056 2.50e-02 1.60e+03 4.93e+00 bond pdb=" CD LYS R 5 " pdb=" CE LYS R 5 " ideal model delta sigma weight residual 1.520 1.460 0.060 3.00e-02 1.11e+03 3.99e+00 ... (remaining 99962 not shown) Histogram of bond angle deviations from ideal: 97.26 - 105.42: 15105 105.42 - 113.59: 62727 113.59 - 121.75: 48657 121.75 - 129.91: 21697 129.91 - 138.08: 1783 Bond angle restraints: 149969 Sorted by residual: angle pdb=" C ARG Q 223 " pdb=" N ASP Q 224 " pdb=" CA ASP Q 224 " ideal model delta sigma weight residual 124.82 134.91 -10.09 1.78e+00 3.16e-01 3.22e+01 angle pdb=" C GLY 7 55 " pdb=" N THR 7 56 " pdb=" CA THR 7 56 " ideal model delta sigma weight residual 121.54 132.18 -10.64 1.91e+00 2.74e-01 3.10e+01 angle pdb=" N LYS X 134 " pdb=" CA LYS X 134 " pdb=" C LYS X 134 " ideal model delta sigma weight residual 110.91 117.41 -6.50 1.17e+00 7.31e-01 3.09e+01 angle pdb=" C VAL G 205 " pdb=" N ASP G 206 " pdb=" CA ASP G 206 " ideal model delta sigma weight residual 122.46 130.20 -7.74 1.41e+00 5.03e-01 3.01e+01 angle pdb=" CA LEU Y 103 " pdb=" CB LEU Y 103 " pdb=" CG LEU Y 103 " ideal model delta sigma weight residual 116.30 134.02 -17.72 3.50e+00 8.16e-02 2.56e+01 ... (remaining 149964 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 56158 35.78 - 71.57: 6957 71.57 - 107.35: 863 107.35 - 143.13: 11 143.13 - 178.92: 12 Dihedral angle restraints: 64001 sinusoidal: 54433 harmonic: 9568 Sorted by residual: dihedral pdb=" CA THR S 174 " pdb=" C THR S 174 " pdb=" N PRO S 175 " pdb=" CA PRO S 175 " ideal model delta harmonic sigma weight residual -180.00 -117.80 -62.20 0 5.00e+00 4.00e-02 1.55e+02 dihedral pdb=" C4' U B 57 " pdb=" C3' U B 57 " pdb=" C2' U B 57 " pdb=" C1' U B 57 " ideal model delta sinusoidal sigma weight residual -35.00 32.08 -67.08 1 8.00e+00 1.56e-02 9.16e+01 dihedral pdb=" C5' U B 57 " pdb=" C4' U B 57 " pdb=" C3' U B 57 " pdb=" O3' U B 57 " ideal model delta sinusoidal sigma weight residual 147.00 81.62 65.38 1 8.00e+00 1.56e-02 8.75e+01 ... (remaining 63998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 17611 0.073 - 0.145: 1344 0.145 - 0.218: 152 0.218 - 0.290: 21 0.290 - 0.363: 6 Chirality restraints: 19134 Sorted by residual: chirality pdb=" C3' U B 57 " pdb=" C4' U B 57 " pdb=" O3' U B 57 " pdb=" C2' U B 57 " both_signs ideal model delta sigma weight residual False -2.74 -2.38 -0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CB ILE D 278 " pdb=" CA ILE D 278 " pdb=" CG1 ILE D 278 " pdb=" CG2 ILE D 278 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" CB ILE P 109 " pdb=" CA ILE P 109 " pdb=" CG1 ILE P 109 " pdb=" CG2 ILE P 109 " both_signs ideal model delta sigma weight residual False 2.64 2.29 0.35 2.00e-01 2.50e+01 3.08e+00 ... (remaining 19131 not shown) Planarity restraints: 7664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C A2709 " -0.011 2.00e-02 2.50e+03 2.68e-02 1.62e+01 pdb=" N1 C A2709 " 0.014 2.00e-02 2.50e+03 pdb=" C2 C A2709 " -0.062 2.00e-02 2.50e+03 pdb=" O2 C A2709 " 0.044 2.00e-02 2.50e+03 pdb=" N3 C A2709 " 0.001 2.00e-02 2.50e+03 pdb=" C4 C A2709 " -0.010 2.00e-02 2.50e+03 pdb=" N4 C A2709 " 0.003 2.00e-02 2.50e+03 pdb=" C5 C A2709 " 0.014 2.00e-02 2.50e+03 pdb=" C6 C A2709 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A2736 " -0.008 2.00e-02 2.50e+03 2.22e-02 1.48e+01 pdb=" N9 G A2736 " 0.004 2.00e-02 2.50e+03 pdb=" C8 G A2736 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G A2736 " -0.006 2.00e-02 2.50e+03 pdb=" C5 G A2736 " 0.004 2.00e-02 2.50e+03 pdb=" C6 G A2736 " 0.015 2.00e-02 2.50e+03 pdb=" O6 G A2736 " -0.016 2.00e-02 2.50e+03 pdb=" N1 G A2736 " -0.007 2.00e-02 2.50e+03 pdb=" C2 G A2736 " 0.060 2.00e-02 2.50e+03 pdb=" N2 G A2736 " -0.040 2.00e-02 2.50e+03 pdb=" N3 G A2736 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G A2736 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A1987 " -0.014 2.00e-02 2.50e+03 2.15e-02 1.39e+01 pdb=" N9 G A1987 " 0.011 2.00e-02 2.50e+03 pdb=" C8 G A1987 " 0.003 2.00e-02 2.50e+03 pdb=" N7 G A1987 " -0.007 2.00e-02 2.50e+03 pdb=" C5 G A1987 " -0.005 2.00e-02 2.50e+03 pdb=" C6 G A1987 " -0.005 2.00e-02 2.50e+03 pdb=" O6 G A1987 " 0.004 2.00e-02 2.50e+03 pdb=" N1 G A1987 " -0.017 2.00e-02 2.50e+03 pdb=" C2 G A1987 " 0.061 2.00e-02 2.50e+03 pdb=" N2 G A1987 " -0.034 2.00e-02 2.50e+03 pdb=" N3 G A1987 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G A1987 " -0.000 2.00e-02 2.50e+03 ... (remaining 7661 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 5827 2.70 - 3.25: 74807 3.25 - 3.80: 183644 3.80 - 4.35: 238853 4.35 - 4.90: 318053 Nonbonded interactions: 821184 Sorted by model distance: nonbonded pdb=" O4 U A2764 " pdb=" O4 U A2774 " model vdw 2.145 3.040 nonbonded pdb=" O2' C A 17 " pdb=" OP1 U A 564 " model vdw 2.211 2.440 nonbonded pdb=" O2' A A1112 " pdb=" O2' U A1133 " model vdw 2.216 2.440 nonbonded pdb=" OP2 G A 423 " pdb=" O2' A A2423 " model vdw 2.238 2.440 nonbonded pdb=" O2 U A2300 " pdb=" O6 G A2342 " model vdw 2.242 2.432 ... (remaining 821179 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 2.700 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: 14.030 Check model and map are aligned: 0.960 Set scattering table: 0.610 Process input model: 333.290 Find NCS groups from input model: 1.490 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:2.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 355.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 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 : 0.004 0.063 99967 Z= 0.225 Angle : 0.850 17.717 149969 Z= 0.417 Chirality : 0.041 0.363 19134 Planarity : 0.006 0.084 7664 Dihedral : 23.087 178.917 57852 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.89 % Favored : 90.02 % Rotamer: Outliers : 0.53 % Allowed : 4.07 % Favored : 95.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: -4.87 (0.11), residues: 3296 helix: -3.91 (0.10), residues: 850 sheet: -2.90 (0.21), residues: 475 loop : -3.11 (0.11), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP R 61 HIS 0.013 0.002 HIS V 68 PHE 0.032 0.003 PHE E 208 TYR 0.034 0.003 TYR S 230 ARG 0.012 0.001 ARG L 31 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 990 residues out of total 2847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 975 time to evaluate : 3.726 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: 4 136 ILE cc_start: 0.8693 (pt) cc_final: 0.8451 (tt) REVERT: 6 99 LYS cc_start: 0.6555 (mtpm) cc_final: 0.6153 (tmtt) REVERT: 7 49 SER cc_start: 0.8131 (t) cc_final: 0.7845 (p) REVERT: 7 71 ASP cc_start: 0.7168 (t0) cc_final: 0.6941 (t0) REVERT: C 73 LYS cc_start: 0.7797 (mtpp) cc_final: 0.7484 (mtpt) REVERT: C 234 ARG cc_start: 0.7562 (mpt-90) cc_final: 0.7305 (mmt180) REVERT: D 144 LEU cc_start: 0.7991 (mt) cc_final: 0.7544 (mt) REVERT: F 195 LYS cc_start: 0.4765 (tttp) cc_final: 0.4331 (ttpt) REVERT: K 91 THR cc_start: 0.7134 (m) cc_final: 0.6925 (p) REVERT: L 69 LEU cc_start: 0.8592 (tp) cc_final: 0.8264 (tp) REVERT: Q 226 LEU cc_start: 0.7585 (tm) cc_final: 0.7259 (tm) REVERT: S 143 TYR cc_start: 0.6833 (m-80) cc_final: 0.6628 (m-10) REVERT: S 230 TYR cc_start: 0.6101 (p90) cc_final: 0.5421 (p90) REVERT: Y 84 LYS cc_start: 0.8176 (ttpp) cc_final: 0.7866 (ptmt) outliers start: 15 outliers final: 4 residues processed: 986 average time/residue: 1.0340 time to fit residues: 1617.8506 Evaluate side-chains 664 residues out of total 2847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 660 time to evaluate : 3.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 48 LEU Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain M residue 196 LEU Chi-restraints excluded: chain Y residue 103 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 526 optimal weight: 10.0000 chunk 472 optimal weight: 7.9990 chunk 262 optimal weight: 0.7980 chunk 161 optimal weight: 0.6980 chunk 319 optimal weight: 0.9990 chunk 252 optimal weight: 3.9990 chunk 489 optimal weight: 20.0000 chunk 189 optimal weight: 0.9980 chunk 297 optimal weight: 4.9990 chunk 364 optimal weight: 9.9990 chunk 566 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 36 GLN 4 95 HIS ** 4 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 145 ASN ** C 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 HIS ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN D 229 HIS E 71 ASN E 93 GLN E 153 ASN E 222 ASN F 77 ASN ** F 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 188 GLN G 103 GLN K 97 ASN K 139 ASN K 220 HIS L 3 GLN ** L 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 82 ASN M 102 HIS M 161 ASN ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 87 HIS Q 211 HIS ** R 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 47 HIS R 66 ASN R 93 ASN ** R 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 113 ASN ** S 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 89 HIS T 106 ASN U 132 ASN V 93 HIS V 95 HIS V 130 HIS V 133 ASN X 102 HIS X 106 ASN X 113 HIS Y 104 GLN 0 76 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.113 99967 Z= 0.199 Angle : 0.623 12.611 149969 Z= 0.316 Chirality : 0.035 0.248 19134 Planarity : 0.005 0.070 7664 Dihedral : 23.945 179.033 50867 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.07 % Favored : 90.84 % Rotamer: Outliers : 4.18 % Allowed : 11.87 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: -3.76 (0.12), residues: 3296 helix: -2.29 (0.14), residues: 895 sheet: -2.27 (0.22), residues: 469 loop : -2.75 (0.12), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP Y 110 HIS 0.009 0.001 HIS T 89 PHE 0.021 0.002 PHE F 152 TYR 0.023 0.002 TYR L 32 ARG 0.012 0.001 ARG G 203 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 2847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 704 time to evaluate : 3.756 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: 5 18 ARG cc_start: 0.7889 (ttm170) cc_final: 0.7651 (ttm170) REVERT: 6 99 LYS cc_start: 0.6433 (mtpm) cc_final: 0.6149 (tmtt) REVERT: 7 49 SER cc_start: 0.8235 (t) cc_final: 0.7778 (p) REVERT: C 159 LYS cc_start: 0.7237 (tttm) cc_final: 0.6807 (ttpp) REVERT: C 234 ARG cc_start: 0.7785 (mpt-90) cc_final: 0.7411 (mmt180) REVERT: D 267 MET cc_start: 0.6871 (mmm) cc_final: 0.6632 (mmm) REVERT: E 218 LYS cc_start: 0.7522 (tttm) cc_final: 0.6485 (mmtp) REVERT: E 232 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.8069 (tpt90) REVERT: G 155 MET cc_start: 0.6609 (OUTLIER) cc_final: 0.6320 (mtm) REVERT: M 134 MET cc_start: 0.7528 (tpt) cc_final: 0.7243 (tpt) REVERT: N 133 ILE cc_start: 0.7776 (pp) cc_final: 0.7572 (pt) REVERT: Q 226 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.8014 (tp) REVERT: S 143 TYR cc_start: 0.6815 (m-80) cc_final: 0.6507 (m-80) REVERT: S 171 TYR cc_start: 0.7790 (m-80) cc_final: 0.7303 (m-80) REVERT: S 204 LYS cc_start: 0.8548 (mmtp) cc_final: 0.8224 (mptt) REVERT: S 230 TYR cc_start: 0.6339 (p90) cc_final: 0.5834 (p90) REVERT: T 54 ARG cc_start: 0.8254 (ttm170) cc_final: 0.8044 (ttm110) REVERT: T 115 LYS cc_start: 0.7885 (tttm) cc_final: 0.7313 (mmmt) REVERT: U 102 LEU cc_start: 0.6551 (tp) cc_final: 0.6215 (tt) REVERT: Y 84 LYS cc_start: 0.8018 (ttpp) cc_final: 0.7728 (ptmt) REVERT: Z 78 GLU cc_start: 0.7024 (tp30) cc_final: 0.6637 (tp30) REVERT: Z 130 LYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7573 (tttt) REVERT: Z 136 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7235 (mt) outliers start: 119 outliers final: 58 residues processed: 760 average time/residue: 0.9599 time to fit residues: 1206.6400 Evaluate side-chains 695 residues out of total 2847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 632 time to evaluate : 3.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 26 TRP Chi-restraints excluded: chain 2 residue 11 VAL Chi-restraints excluded: chain 2 residue 14 GLU Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 35 THR Chi-restraints excluded: chain 2 residue 48 LEU Chi-restraints excluded: chain 3 residue 95 LEU Chi-restraints excluded: chain 3 residue 134 ILE Chi-restraints excluded: chain 5 residue 25 VAL Chi-restraints excluded: chain 6 residue 120 MET Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 123 ARG Chi-restraints excluded: chain E residue 125 ARG Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 232 ARG Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain G residue 155 MET Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain K residue 187 THR Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 171 LYS Chi-restraints excluded: chain M residue 193 GLU Chi-restraints excluded: chain M residue 196 LEU Chi-restraints excluded: chain M residue 210 LEU Chi-restraints excluded: chain M residue 234 VAL Chi-restraints excluded: chain N residue 2 LEU Chi-restraints excluded: chain N residue 123 SER Chi-restraints excluded: chain N residue 131 PHE Chi-restraints excluded: chain Q residue 208 VAL Chi-restraints excluded: chain Q residue 226 LEU Chi-restraints excluded: chain R residue 51 ASP Chi-restraints excluded: chain S residue 121 GLU Chi-restraints excluded: chain S residue 128 VAL Chi-restraints excluded: chain S residue 141 TRP Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain S residue 179 ASN Chi-restraints excluded: chain S residue 200 TYR Chi-restraints excluded: chain S residue 203 LYS Chi-restraints excluded: chain T residue 50 ILE Chi-restraints excluded: chain V residue 97 SER Chi-restraints excluded: chain V residue 108 THR Chi-restraints excluded: chain V residue 109 LYS Chi-restraints excluded: chain Y residue 103 LEU Chi-restraints excluded: chain Z residue 90 LEU Chi-restraints excluded: chain Z residue 130 LYS Chi-restraints excluded: chain Z residue 133 SER Chi-restraints excluded: chain Z residue 136 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 314 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 chunk 471 optimal weight: 8.9990 chunk 385 optimal weight: 5.9990 chunk 156 optimal weight: 0.0670 chunk 567 optimal weight: 6.9990 chunk 613 optimal weight: 7.9990 chunk 505 optimal weight: 7.9990 chunk 562 optimal weight: 7.9990 chunk 193 optimal weight: 6.9990 chunk 455 optimal weight: 6.9990 overall best weight: 4.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 119 HIS C 26 ASN C 49 HIS C 82 ASN ** C 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 GLN ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 HIS D 167 HIS ** E 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 ASN ** F 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 134 HIS ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 173 GLN Q 178 HIS Q 211 HIS R 28 HIS R 93 ASN ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 113 ASN S 189 GLN S 205 ASN ** S 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 106 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 99967 Z= 0.428 Angle : 0.795 15.650 149969 Z= 0.396 Chirality : 0.043 0.303 19134 Planarity : 0.007 0.075 7664 Dihedral : 23.957 177.849 50867 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.62 % Favored : 89.26 % Rotamer: Outliers : 6.32 % Allowed : 14.40 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: -3.43 (0.13), residues: 3296 helix: -1.62 (0.15), residues: 896 sheet: -2.38 (0.21), residues: 512 loop : -2.65 (0.13), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP Y 110 HIS 0.014 0.002 HIS R 83 PHE 0.032 0.003 PHE H 73 TYR 0.032 0.003 TYR X 128 ARG 0.012 0.001 ARG N 115 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 2847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 689 time to evaluate : 3.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 13 LYS cc_start: 0.8077 (ttpt) cc_final: 0.7823 (ttpp) REVERT: 4 118 GLN cc_start: 0.8036 (pp30) cc_final: 0.7772 (pp30) REVERT: 6 99 LYS cc_start: 0.6773 (mtpm) cc_final: 0.6349 (tmtt) REVERT: 7 49 SER cc_start: 0.8695 (t) cc_final: 0.8198 (p) REVERT: 7 50 ARG cc_start: 0.8593 (mmt90) cc_final: 0.8389 (mmt90) REVERT: C 159 LYS cc_start: 0.7224 (tttm) cc_final: 0.6881 (tttm) REVERT: C 209 TRP cc_start: 0.6308 (m100) cc_final: 0.6045 (m100) REVERT: D 170 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7520 (pt0) REVERT: D 261 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7761 (pt) REVERT: E 218 LYS cc_start: 0.7491 (tttm) cc_final: 0.6465 (mmtp) REVERT: E 232 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8396 (tpt170) REVERT: E 254 TYR cc_start: 0.7598 (t80) cc_final: 0.7206 (t80) REVERT: G 74 ILE cc_start: 0.4903 (OUTLIER) cc_final: 0.4323 (mt) REVERT: H 95 MET cc_start: 0.4333 (ppp) cc_final: 0.1694 (mmm) REVERT: K 184 LYS cc_start: 0.7259 (tttm) cc_final: 0.6854 (tttp) REVERT: M 93 LYS cc_start: 0.8293 (ttmm) cc_final: 0.7786 (ttpt) REVERT: M 213 LYS cc_start: 0.6664 (ptpp) cc_final: 0.5936 (tttm) REVERT: M 248 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7719 (mtpp) REVERT: N 32 TYR cc_start: 0.7989 (m-80) cc_final: 0.7477 (m-80) REVERT: N 91 GLU cc_start: 0.6199 (tm-30) cc_final: 0.5926 (tp30) REVERT: N 120 ILE cc_start: 0.7761 (OUTLIER) cc_final: 0.7422 (mt) REVERT: P 127 ILE cc_start: 0.8131 (tp) cc_final: 0.7815 (tt) REVERT: Q 170 ILE cc_start: 0.9250 (mm) cc_final: 0.9009 (mm) REVERT: R 86 TYR cc_start: 0.8881 (m-10) cc_final: 0.8392 (m-80) REVERT: R 94 ARG cc_start: 0.7040 (mmt180) cc_final: 0.6587 (mmt180) REVERT: R 113 ASN cc_start: 0.7626 (m-40) cc_final: 0.7349 (m110) REVERT: S 230 TYR cc_start: 0.6582 (p90) cc_final: 0.6086 (p90) REVERT: V 159 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.8125 (mpp80) REVERT: X 134 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.8158 (ttpt) REVERT: Y 84 LYS cc_start: 0.8039 (ttpp) cc_final: 0.7688 (ptmt) REVERT: Z 78 GLU cc_start: 0.7285 (tp30) cc_final: 0.6990 (tp30) REVERT: Z 125 GLU cc_start: 0.6810 (OUTLIER) cc_final: 0.6536 (mt-10) outliers start: 180 outliers final: 112 residues processed: 781 average time/residue: 0.9149 time to fit residues: 1192.0221 Evaluate side-chains 747 residues out of total 2847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 626 time to evaluate : 3.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 8 THR Chi-restraints excluded: chain 1 residue 37 SER Chi-restraints excluded: chain 2 residue 11 VAL Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 34 ILE Chi-restraints excluded: chain 2 residue 35 THR Chi-restraints excluded: chain 2 residue 48 LEU Chi-restraints excluded: chain 4 residue 142 ASP Chi-restraints excluded: chain 5 residue 3 ILE Chi-restraints excluded: chain 5 residue 25 VAL Chi-restraints excluded: chain 6 residue 142 VAL Chi-restraints excluded: chain 7 residue 91 ILE Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 282 VAL Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 232 ARG Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 149 MET Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 194 ILE Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain G residue 43 ILE Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 104 MET Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 187 THR Chi-restraints excluded: chain K residue 238 ASP Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 9 ASN Chi-restraints excluded: chain L residue 18 GLU Chi-restraints excluded: chain L residue 24 ILE Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 193 GLU Chi-restraints excluded: chain M residue 196 LEU Chi-restraints excluded: chain M residue 234 VAL Chi-restraints excluded: chain M residue 248 LYS Chi-restraints excluded: chain N residue 2 LEU Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain N residue 120 ILE Chi-restraints excluded: chain N residue 123 SER Chi-restraints excluded: chain N residue 131 PHE Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 54 MET Chi-restraints excluded: chain P residue 54 THR Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain Q residue 163 SER Chi-restraints excluded: chain Q residue 178 HIS Chi-restraints excluded: chain Q residue 208 VAL Chi-restraints excluded: chain Q residue 226 LEU Chi-restraints excluded: chain R residue 29 SER Chi-restraints excluded: chain R residue 51 ASP Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 100 ILE Chi-restraints excluded: chain S residue 121 GLU Chi-restraints excluded: chain S residue 124 PHE Chi-restraints excluded: chain S residue 136 VAL Chi-restraints excluded: chain S residue 141 TRP Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain S residue 164 VAL Chi-restraints excluded: chain S residue 166 THR Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 179 ASN Chi-restraints excluded: chain S residue 185 VAL Chi-restraints excluded: chain S residue 200 TYR Chi-restraints excluded: chain S residue 203 LYS Chi-restraints excluded: chain S residue 205 ASN Chi-restraints excluded: chain T residue 124 MET Chi-restraints excluded: chain T residue 132 ILE Chi-restraints excluded: chain U residue 133 SER Chi-restraints excluded: chain U residue 159 VAL Chi-restraints excluded: chain V residue 69 VAL Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain V residue 108 THR Chi-restraints excluded: chain V residue 125 ILE Chi-restraints excluded: chain V residue 129 ILE Chi-restraints excluded: chain V residue 159 ARG Chi-restraints excluded: chain V residue 162 ILE Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain X residue 134 LYS Chi-restraints excluded: chain Y residue 91 SER Chi-restraints excluded: chain Y residue 100 PHE Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Z residue 90 LEU Chi-restraints excluded: chain Z residue 125 GLU Chi-restraints excluded: chain Z residue 130 LYS Chi-restraints excluded: chain Z residue 133 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 560 optimal weight: 10.0000 chunk 426 optimal weight: 10.0000 chunk 294 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 270 optimal weight: 0.0570 chunk 381 optimal weight: 7.9990 chunk 569 optimal weight: 10.0000 chunk 603 optimal weight: 5.9990 chunk 297 optimal weight: 2.9990 chunk 539 optimal weight: 4.9990 chunk 162 optimal weight: 0.0030 overall best weight: 1.5712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 119 HIS ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 ASN ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 42 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 99967 Z= 0.196 Angle : 0.614 13.633 149969 Z= 0.312 Chirality : 0.035 0.256 19134 Planarity : 0.005 0.087 7664 Dihedral : 23.867 176.616 50865 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.41 % Favored : 90.50 % Rotamer: Outliers : 5.76 % Allowed : 17.39 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: -2.89 (0.13), residues: 3296 helix: -1.09 (0.16), residues: 905 sheet: -1.90 (0.23), residues: 453 loop : -2.43 (0.13), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP 0 73 HIS 0.028 0.002 HIS Q 178 PHE 0.013 0.002 PHE F 152 TYR 0.031 0.002 TYR O 122 ARG 0.006 0.000 ARG F 203 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 2847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 657 time to evaluate : 3.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 7 ARG cc_start: 0.7751 (ptm160) cc_final: 0.7390 (ptm160) REVERT: 6 99 LYS cc_start: 0.6672 (mtpm) cc_final: 0.6309 (tmtt) REVERT: 7 49 SER cc_start: 0.8701 (t) cc_final: 0.8154 (p) REVERT: C 159 LYS cc_start: 0.7185 (tttm) cc_final: 0.6894 (tttm) REVERT: C 164 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6466 (tt0) REVERT: D 170 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7373 (pt0) REVERT: D 190 LEU cc_start: 0.6617 (OUTLIER) cc_final: 0.5961 (pt) REVERT: E 89 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8212 (tp) REVERT: E 158 ARG cc_start: 0.7792 (mpt-90) cc_final: 0.7531 (mtt180) REVERT: E 218 LYS cc_start: 0.7330 (tttm) cc_final: 0.6418 (mmtp) REVERT: E 228 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7725 (mt) REVERT: E 254 TYR cc_start: 0.7643 (t80) cc_final: 0.7192 (t80) REVERT: G 74 ILE cc_start: 0.5015 (OUTLIER) cc_final: 0.4591 (mt) REVERT: K 212 ARG cc_start: 0.8153 (mtt-85) cc_final: 0.7746 (mtt-85) REVERT: M 93 LYS cc_start: 0.8093 (ttmm) cc_final: 0.7575 (ttpt) REVERT: N 120 ILE cc_start: 0.7916 (OUTLIER) cc_final: 0.7618 (mt) REVERT: O 97 TYR cc_start: 0.7185 (m-80) cc_final: 0.6567 (m-80) REVERT: P 127 ILE cc_start: 0.8137 (tp) cc_final: 0.7820 (tt) REVERT: Q 205 GLU cc_start: 0.7761 (pm20) cc_final: 0.7252 (pm20) REVERT: R 75 TYR cc_start: 0.5755 (m-10) cc_final: 0.5392 (m-10) REVERT: R 86 TYR cc_start: 0.8695 (m-10) cc_final: 0.8356 (m-80) REVERT: R 94 ARG cc_start: 0.6877 (mmt180) cc_final: 0.6057 (mmt180) REVERT: S 124 PHE cc_start: 0.7407 (OUTLIER) cc_final: 0.6721 (t80) REVERT: S 204 LYS cc_start: 0.8573 (mmtp) cc_final: 0.8331 (mptt) REVERT: S 230 TYR cc_start: 0.6408 (p90) cc_final: 0.5751 (p90) REVERT: T 32 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8126 (tp) REVERT: T 115 LYS cc_start: 0.7824 (tttm) cc_final: 0.7203 (mmmt) REVERT: U 146 MET cc_start: 0.6984 (mtm) cc_final: 0.6756 (mtp) REVERT: V 82 GLU cc_start: 0.7323 (pm20) cc_final: 0.7087 (pm20) REVERT: Z 78 GLU cc_start: 0.7157 (tp30) cc_final: 0.6911 (tp30) REVERT: Z 125 GLU cc_start: 0.6882 (OUTLIER) cc_final: 0.6614 (mt-10) REVERT: Z 130 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7875 (tttt) REVERT: Z 136 LEU cc_start: 0.7738 (tt) cc_final: 0.7258 (mt) outliers start: 164 outliers final: 97 residues processed: 748 average time/residue: 0.9077 time to fit residues: 1129.5400 Evaluate side-chains 730 residues out of total 2847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 622 time to evaluate : 3.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 37 SER Chi-restraints excluded: chain 2 residue 11 VAL Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 34 ILE Chi-restraints excluded: chain 2 residue 35 THR Chi-restraints excluded: chain 2 residue 48 LEU Chi-restraints excluded: chain 3 residue 95 LEU Chi-restraints excluded: chain 4 residue 142 ASP Chi-restraints excluded: chain 5 residue 3 ILE Chi-restraints excluded: chain 5 residue 25 VAL Chi-restraints excluded: chain 7 residue 91 ILE Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 125 ARG Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 249 GLU Chi-restraints excluded: chain E residue 256 ASN Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 149 MET Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain G residue 43 ILE Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 187 THR Chi-restraints excluded: chain K residue 238 ASP Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 9 ASN Chi-restraints excluded: chain L residue 18 GLU Chi-restraints excluded: chain L residue 21 CYS Chi-restraints excluded: chain L residue 24 ILE Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 193 GLU Chi-restraints excluded: chain M residue 196 LEU Chi-restraints excluded: chain M residue 234 VAL Chi-restraints excluded: chain N residue 2 LEU Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain N residue 120 ILE Chi-restraints excluded: chain N residue 123 SER Chi-restraints excluded: chain N residue 131 PHE Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 54 MET Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 90 THR Chi-restraints excluded: chain Q residue 208 VAL Chi-restraints excluded: chain Q residue 226 LEU Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain R residue 100 ILE Chi-restraints excluded: chain S residue 121 GLU Chi-restraints excluded: chain S residue 124 PHE Chi-restraints excluded: chain S residue 128 VAL Chi-restraints excluded: chain S residue 136 VAL Chi-restraints excluded: chain S residue 141 TRP Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain S residue 164 VAL Chi-restraints excluded: chain S residue 185 VAL Chi-restraints excluded: chain S residue 200 TYR Chi-restraints excluded: chain S residue 203 LYS Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 33 THR Chi-restraints excluded: chain T residue 124 MET Chi-restraints excluded: chain U residue 133 SER Chi-restraints excluded: chain V residue 108 THR Chi-restraints excluded: chain V residue 109 LYS Chi-restraints excluded: chain V residue 125 ILE Chi-restraints excluded: chain V residue 129 ILE Chi-restraints excluded: chain V residue 162 ILE Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain Y residue 91 SER Chi-restraints excluded: chain Y residue 100 PHE Chi-restraints excluded: chain Z residue 90 LEU Chi-restraints excluded: chain Z residue 125 GLU Chi-restraints excluded: chain Z residue 130 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 502 optimal weight: 6.9990 chunk 342 optimal weight: 8.9990 chunk 8 optimal weight: 0.0770 chunk 449 optimal weight: 20.0000 chunk 248 optimal weight: 1.9990 chunk 514 optimal weight: 8.9990 chunk 416 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 307 optimal weight: 10.0000 chunk 541 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 overall best weight: 3.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 119 HIS C 102 HIS ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 ASN D 138 GLN F 90 ASN N 13 HIS ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 113 ASN S 189 GLN S 205 ASN ** S 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 42 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.119 99967 Z= 0.349 Angle : 0.707 15.345 149969 Z= 0.354 Chirality : 0.040 0.285 19134 Planarity : 0.006 0.063 7664 Dihedral : 23.857 175.644 50865 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.07 % Favored : 88.83 % Rotamer: Outliers : 6.85 % Allowed : 17.95 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: -2.89 (0.13), residues: 3296 helix: -1.04 (0.16), residues: 907 sheet: -1.99 (0.22), residues: 497 loop : -2.42 (0.13), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP 1 20 HIS 0.009 0.002 HIS C 226 PHE 0.023 0.002 PHE H 73 TYR 0.031 0.002 TYR O 122 ARG 0.010 0.001 ARG F 117 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 835 residues out of total 2847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 640 time to evaluate : 3.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 118 GLN cc_start: 0.8204 (pp30) cc_final: 0.7742 (pp30) REVERT: 6 99 LYS cc_start: 0.6755 (mtpm) cc_final: 0.6313 (tmtt) REVERT: 7 49 SER cc_start: 0.8688 (t) cc_final: 0.8213 (p) REVERT: C 126 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.7960 (pp) REVERT: C 164 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6690 (tt0) REVERT: D 170 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7467 (pt0) REVERT: D 190 LEU cc_start: 0.6848 (mm) cc_final: 0.6162 (pt) REVERT: D 222 MET cc_start: 0.8546 (mmm) cc_final: 0.7699 (mmm) REVERT: D 261 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7883 (pt) REVERT: E 89 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8365 (tp) REVERT: E 218 LYS cc_start: 0.7440 (tttm) cc_final: 0.6512 (mmtp) REVERT: E 228 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.7986 (mt) REVERT: E 254 TYR cc_start: 0.7652 (t80) cc_final: 0.7205 (t80) REVERT: K 184 LYS cc_start: 0.7265 (tttm) cc_final: 0.6848 (tttp) REVERT: M 93 LYS cc_start: 0.8212 (ttmm) cc_final: 0.7676 (ttpt) REVERT: M 205 GLU cc_start: 0.6402 (mm-30) cc_final: 0.6176 (mm-30) REVERT: N 32 TYR cc_start: 0.7841 (m-80) cc_final: 0.7272 (m-80) REVERT: O 122 TYR cc_start: 0.7455 (t80) cc_final: 0.7254 (t80) REVERT: P 127 ILE cc_start: 0.8268 (tp) cc_final: 0.7963 (tt) REVERT: Q 205 GLU cc_start: 0.7848 (pm20) cc_final: 0.7330 (pm20) REVERT: R 75 TYR cc_start: 0.5677 (m-10) cc_final: 0.5389 (m-10) REVERT: R 86 TYR cc_start: 0.8779 (m-10) cc_final: 0.8333 (m-80) REVERT: R 94 ARG cc_start: 0.7091 (mmt180) cc_final: 0.6810 (mmt180) REVERT: S 124 PHE cc_start: 0.7584 (OUTLIER) cc_final: 0.7026 (t80) REVERT: S 204 LYS cc_start: 0.8713 (mmtp) cc_final: 0.8367 (mptt) REVERT: S 230 TYR cc_start: 0.6500 (p90) cc_final: 0.5881 (p90) REVERT: V 82 GLU cc_start: 0.7474 (pm20) cc_final: 0.7129 (pm20) REVERT: V 159 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7954 (mpp80) REVERT: X 97 ARG cc_start: 0.8506 (tpp-160) cc_final: 0.8277 (tpp-160) REVERT: Y 72 ARG cc_start: 0.7353 (mtm-85) cc_final: 0.6917 (mtm-85) REVERT: Y 84 LYS cc_start: 0.8032 (ttpp) cc_final: 0.7666 (ptmt) REVERT: Z 125 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6635 (mt-10) REVERT: Z 136 LEU cc_start: 0.7919 (tt) cc_final: 0.7400 (mt) outliers start: 195 outliers final: 137 residues processed: 749 average time/residue: 0.9030 time to fit residues: 1136.3821 Evaluate side-chains 755 residues out of total 2847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 609 time to evaluate : 3.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 8 THR Chi-restraints excluded: chain 1 residue 37 SER Chi-restraints excluded: chain 2 residue 11 VAL Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 34 ILE Chi-restraints excluded: chain 2 residue 35 THR Chi-restraints excluded: chain 3 residue 95 LEU Chi-restraints excluded: chain 3 residue 136 CYS Chi-restraints excluded: chain 4 residue 142 ASP Chi-restraints excluded: chain 5 residue 3 ILE Chi-restraints excluded: chain 5 residue 10 ILE Chi-restraints excluded: chain 5 residue 25 VAL Chi-restraints excluded: chain 7 residue 91 ILE Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 126 LEU Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 125 ARG Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 149 MET Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 171 ASN Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain G residue 43 ILE Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 187 THR Chi-restraints excluded: chain K residue 189 ASP Chi-restraints excluded: chain K residue 238 ASP Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 9 ASN Chi-restraints excluded: chain L residue 18 GLU Chi-restraints excluded: chain L residue 21 CYS Chi-restraints excluded: chain L residue 24 ILE Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain L residue 75 MET Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 193 GLU Chi-restraints excluded: chain M residue 196 LEU Chi-restraints excluded: chain M residue 234 VAL Chi-restraints excluded: chain N residue 2 LEU Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain N residue 123 SER Chi-restraints excluded: chain N residue 131 PHE Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 54 MET Chi-restraints excluded: chain P residue 54 THR Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain Q residue 163 SER Chi-restraints excluded: chain Q residue 178 HIS Chi-restraints excluded: chain Q residue 181 ILE Chi-restraints excluded: chain Q residue 208 VAL Chi-restraints excluded: chain Q residue 222 LEU Chi-restraints excluded: chain Q residue 226 LEU Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain R residue 100 ILE Chi-restraints excluded: chain S residue 124 PHE Chi-restraints excluded: chain S residue 128 VAL Chi-restraints excluded: chain S residue 136 VAL Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain S residue 164 VAL Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 177 VAL Chi-restraints excluded: chain S residue 179 ASN Chi-restraints excluded: chain S residue 185 VAL Chi-restraints excluded: chain S residue 200 TYR Chi-restraints excluded: chain S residue 203 LYS Chi-restraints excluded: chain S residue 205 ASN Chi-restraints excluded: chain T residue 33 THR Chi-restraints excluded: chain T residue 80 ILE Chi-restraints excluded: chain T residue 124 MET Chi-restraints excluded: chain U residue 133 SER Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain V residue 101 ILE Chi-restraints excluded: chain V residue 108 THR Chi-restraints excluded: chain V residue 125 ILE Chi-restraints excluded: chain V residue 129 ILE Chi-restraints excluded: chain V residue 137 ILE Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain V residue 159 ARG Chi-restraints excluded: chain V residue 162 ILE Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain Y residue 91 SER Chi-restraints excluded: chain Y residue 100 PHE Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Z residue 90 LEU Chi-restraints excluded: chain Z residue 125 GLU Chi-restraints excluded: chain Z residue 130 LYS Chi-restraints excluded: chain Z residue 133 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 202 optimal weight: 0.8980 chunk 543 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 chunk 354 optimal weight: 7.9990 chunk 148 optimal weight: 10.0000 chunk 603 optimal weight: 6.9990 chunk 501 optimal weight: 7.9990 chunk 279 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 199 optimal weight: 0.8980 chunk 316 optimal weight: 3.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 102 HIS ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 ASN D 138 GLN E 222 ASN F 90 ASN ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 79 ASN Q 178 HIS ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 113 ASN S 205 ASN ** S 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 99967 Z= 0.234 Angle : 0.631 14.554 149969 Z= 0.318 Chirality : 0.036 0.263 19134 Planarity : 0.005 0.057 7664 Dihedral : 23.828 176.395 50863 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.04 % Favored : 89.90 % Rotamer: Outliers : 6.78 % Allowed : 19.32 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: -2.66 (0.14), residues: 3296 helix: -0.79 (0.16), residues: 914 sheet: -1.90 (0.22), residues: 480 loop : -2.29 (0.13), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP 0 73 HIS 0.017 0.002 HIS N 13 PHE 0.024 0.002 PHE P 76 TYR 0.024 0.002 TYR O 122 ARG 0.007 0.001 ARG F 117 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 2847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 619 time to evaluate : 3.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 7 ARG cc_start: 0.8064 (ptm160) cc_final: 0.7689 (ptm160) REVERT: 4 118 GLN cc_start: 0.8239 (pp30) cc_final: 0.7771 (pp30) REVERT: 5 2 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8258 (mtpp) REVERT: 6 99 LYS cc_start: 0.6758 (mtpm) cc_final: 0.6290 (tmtt) REVERT: 7 49 SER cc_start: 0.8740 (t) cc_final: 0.8273 (p) REVERT: C 84 ASN cc_start: 0.7815 (t0) cc_final: 0.7566 (t0) REVERT: C 164 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6686 (tt0) REVERT: D 170 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7445 (pt0) REVERT: D 190 LEU cc_start: 0.6693 (mm) cc_final: 0.6095 (pt) REVERT: E 89 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8272 (tp) REVERT: E 180 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.5434 (mp0) REVERT: E 218 LYS cc_start: 0.7391 (tttm) cc_final: 0.6443 (mmtp) REVERT: E 228 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7956 (mt) REVERT: E 254 TYR cc_start: 0.7763 (t80) cc_final: 0.7302 (t80) REVERT: L 87 ILE cc_start: 0.7667 (OUTLIER) cc_final: 0.7302 (tp) REVERT: M 93 LYS cc_start: 0.8180 (ttmm) cc_final: 0.7653 (ttpt) REVERT: M 205 GLU cc_start: 0.6379 (mm-30) cc_final: 0.6156 (mm-30) REVERT: M 244 GLU cc_start: 0.7096 (mm-30) cc_final: 0.6516 (mm-30) REVERT: M 247 ARG cc_start: 0.6935 (ttp80) cc_final: 0.6609 (ttm110) REVERT: N 32 TYR cc_start: 0.7784 (m-80) cc_final: 0.7170 (m-80) REVERT: P 127 ILE cc_start: 0.8315 (tp) cc_final: 0.8005 (tt) REVERT: Q 205 GLU cc_start: 0.7630 (pm20) cc_final: 0.7196 (pm20) REVERT: R 75 TYR cc_start: 0.5626 (m-10) cc_final: 0.5330 (m-10) REVERT: R 86 TYR cc_start: 0.8678 (m-10) cc_final: 0.8319 (m-80) REVERT: S 124 PHE cc_start: 0.7388 (OUTLIER) cc_final: 0.6647 (t80) REVERT: S 204 LYS cc_start: 0.8647 (mmtp) cc_final: 0.8323 (mptt) REVERT: S 230 TYR cc_start: 0.6429 (p90) cc_final: 0.5749 (p90) REVERT: T 32 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8020 (tp) REVERT: U 146 MET cc_start: 0.6987 (mtm) cc_final: 0.6691 (mtp) REVERT: V 82 GLU cc_start: 0.7420 (pm20) cc_final: 0.7094 (pm20) REVERT: V 159 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7997 (mpp80) REVERT: Y 72 ARG cc_start: 0.7372 (mtm-85) cc_final: 0.6998 (mtm-85) REVERT: Y 84 LYS cc_start: 0.7993 (ttpp) cc_final: 0.7645 (ptmt) REVERT: Z 136 LEU cc_start: 0.7931 (tt) cc_final: 0.7441 (mt) outliers start: 193 outliers final: 141 residues processed: 728 average time/residue: 0.9089 time to fit residues: 1111.3277 Evaluate side-chains 755 residues out of total 2847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 604 time to evaluate : 3.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 8 THR Chi-restraints excluded: chain 1 residue 26 TRP Chi-restraints excluded: chain 1 residue 37 SER Chi-restraints excluded: chain 2 residue 11 VAL Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 34 ILE Chi-restraints excluded: chain 2 residue 35 THR Chi-restraints excluded: chain 3 residue 95 LEU Chi-restraints excluded: chain 3 residue 136 CYS Chi-restraints excluded: chain 3 residue 138 LYS Chi-restraints excluded: chain 4 residue 142 ASP Chi-restraints excluded: chain 5 residue 2 LYS Chi-restraints excluded: chain 5 residue 3 ILE Chi-restraints excluded: chain 5 residue 25 VAL Chi-restraints excluded: chain 7 residue 91 ILE Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 125 ARG Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 249 GLU Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 149 MET Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 171 ASN Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain G residue 43 ILE Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 133 ILE Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 187 THR Chi-restraints excluded: chain K residue 189 ASP Chi-restraints excluded: chain K residue 238 ASP Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 9 ASN Chi-restraints excluded: chain L residue 21 CYS Chi-restraints excluded: chain L residue 24 ILE Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 193 GLU Chi-restraints excluded: chain M residue 196 LEU Chi-restraints excluded: chain M residue 210 LEU Chi-restraints excluded: chain N residue 2 LEU Chi-restraints excluded: chain N residue 64 ILE Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain N residue 123 SER Chi-restraints excluded: chain N residue 131 PHE Chi-restraints excluded: chain N residue 134 SER Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 54 MET Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain Q residue 171 SER Chi-restraints excluded: chain Q residue 178 HIS Chi-restraints excluded: chain Q residue 181 ILE Chi-restraints excluded: chain Q residue 208 VAL Chi-restraints excluded: chain Q residue 222 LEU Chi-restraints excluded: chain Q residue 226 LEU Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain R residue 83 HIS Chi-restraints excluded: chain R residue 100 ILE Chi-restraints excluded: chain S residue 121 GLU Chi-restraints excluded: chain S residue 124 PHE Chi-restraints excluded: chain S residue 128 VAL Chi-restraints excluded: chain S residue 136 VAL Chi-restraints excluded: chain S residue 141 TRP Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 164 VAL Chi-restraints excluded: chain S residue 177 VAL Chi-restraints excluded: chain S residue 179 ASN Chi-restraints excluded: chain S residue 185 VAL Chi-restraints excluded: chain S residue 200 TYR Chi-restraints excluded: chain S residue 203 LYS Chi-restraints excluded: chain S residue 205 ASN Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 33 THR Chi-restraints excluded: chain T residue 124 MET Chi-restraints excluded: chain T residue 149 LEU Chi-restraints excluded: chain U residue 133 SER Chi-restraints excluded: chain V residue 101 ILE Chi-restraints excluded: chain V residue 108 THR Chi-restraints excluded: chain V residue 109 LYS Chi-restraints excluded: chain V residue 125 ILE Chi-restraints excluded: chain V residue 129 ILE Chi-restraints excluded: chain V residue 137 ILE Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain V residue 159 ARG Chi-restraints excluded: chain V residue 162 ILE Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain X residue 86 VAL Chi-restraints excluded: chain X residue 142 ILE Chi-restraints excluded: chain Y residue 91 SER Chi-restraints excluded: chain Y residue 100 PHE Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Y residue 108 VAL Chi-restraints excluded: chain Z residue 90 LEU Chi-restraints excluded: chain Z residue 130 LYS Chi-restraints excluded: chain Z residue 133 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 582 optimal weight: 7.9990 chunk 68 optimal weight: 7.9990 chunk 343 optimal weight: 8.9990 chunk 440 optimal weight: 5.9990 chunk 341 optimal weight: 7.9990 chunk 508 optimal weight: 5.9990 chunk 337 optimal weight: 0.0570 chunk 601 optimal weight: 5.9990 chunk 376 optimal weight: 8.9990 chunk 366 optimal weight: 10.0000 chunk 277 optimal weight: 0.9980 overall best weight: 3.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 ASN ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 ASN F 108 ASN K 76 HIS ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 83 HIS ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 205 ASN ** S 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 99967 Z= 0.377 Angle : 0.736 16.462 149969 Z= 0.368 Chirality : 0.041 0.294 19134 Planarity : 0.006 0.066 7664 Dihedral : 23.860 178.454 50863 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.44 % Favored : 88.47 % Rotamer: Outliers : 7.41 % Allowed : 19.53 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: 3296 helix: -0.88 (0.16), residues: 904 sheet: -2.09 (0.21), residues: 500 loop : -2.37 (0.13), residues: 1892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP 0 73 HIS 0.031 0.002 HIS Q 178 PHE 0.025 0.002 PHE F 175 TYR 0.040 0.002 TYR O 122 ARG 0.007 0.001 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 829 residues out of total 2847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 618 time to evaluate : 3.956 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: 1 17 LYS cc_start: 0.7797 (mmtt) cc_final: 0.7585 (mtpp) REVERT: 4 118 GLN cc_start: 0.8357 (pp30) cc_final: 0.7892 (pp30) REVERT: 5 2 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8355 (mtpp) REVERT: 6 99 LYS cc_start: 0.6736 (mtpm) cc_final: 0.6244 (tmtt) REVERT: 7 49 SER cc_start: 0.8756 (t) cc_final: 0.8317 (p) REVERT: C 129 THR cc_start: 0.8117 (p) cc_final: 0.7913 (m) REVERT: C 164 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6656 (tt0) REVERT: D 170 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7555 (pt0) REVERT: D 190 LEU cc_start: 0.6811 (OUTLIER) cc_final: 0.6200 (pt) REVERT: D 250 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8037 (mmt) REVERT: D 261 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7825 (pt) REVERT: E 89 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8396 (tp) REVERT: E 218 LYS cc_start: 0.7391 (tttm) cc_final: 0.6502 (mmtp) REVERT: E 228 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8220 (mt) REVERT: E 254 TYR cc_start: 0.7745 (t80) cc_final: 0.7312 (t80) REVERT: G 189 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.7387 (tpt90) REVERT: K 184 LYS cc_start: 0.7325 (tttm) cc_final: 0.6931 (tttp) REVERT: L 1 MET cc_start: 0.7895 (OUTLIER) cc_final: 0.7126 (mmm) REVERT: M 93 LYS cc_start: 0.8220 (ttmm) cc_final: 0.7669 (ttpt) REVERT: M 166 GLU cc_start: 0.7469 (mm-30) cc_final: 0.6901 (mm-30) REVERT: M 198 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7990 (tp) REVERT: N 32 TYR cc_start: 0.7915 (m-80) cc_final: 0.7320 (m-80) REVERT: P 127 ILE cc_start: 0.8290 (tp) cc_final: 0.7862 (tt) REVERT: Q 182 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.8087 (ttm170) REVERT: R 75 TYR cc_start: 0.5679 (m-10) cc_final: 0.5384 (m-10) REVERT: R 86 TYR cc_start: 0.8771 (m-10) cc_final: 0.8349 (m-80) REVERT: R 94 ARG cc_start: 0.7092 (mmt180) cc_final: 0.6734 (mmt180) REVERT: S 124 PHE cc_start: 0.7787 (OUTLIER) cc_final: 0.7044 (t80) REVERT: S 230 TYR cc_start: 0.6553 (p90) cc_final: 0.5802 (p90) REVERT: T 32 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.8031 (tp) REVERT: T 92 GLN cc_start: 0.7113 (tt0) cc_final: 0.6785 (pm20) REVERT: T 102 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7416 (mtmt) REVERT: U 146 MET cc_start: 0.7053 (mtm) cc_final: 0.6769 (mtp) REVERT: V 82 GLU cc_start: 0.7475 (pm20) cc_final: 0.7106 (pm20) REVERT: V 159 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8032 (mpp80) REVERT: Y 84 LYS cc_start: 0.8069 (ttpp) cc_final: 0.7722 (ptmt) REVERT: Y 97 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7467 (tpm-80) REVERT: Z 136 LEU cc_start: 0.8045 (tt) cc_final: 0.7510 (mt) outliers start: 211 outliers final: 161 residues processed: 739 average time/residue: 0.9277 time to fit residues: 1152.0942 Evaluate side-chains 783 residues out of total 2847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 605 time to evaluate : 3.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 8 THR Chi-restraints excluded: chain 1 residue 26 TRP Chi-restraints excluded: chain 1 residue 37 SER Chi-restraints excluded: chain 2 residue 11 VAL Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 34 ILE Chi-restraints excluded: chain 2 residue 35 THR Chi-restraints excluded: chain 3 residue 95 LEU Chi-restraints excluded: chain 3 residue 136 CYS Chi-restraints excluded: chain 3 residue 138 LYS Chi-restraints excluded: chain 4 residue 92 MET Chi-restraints excluded: chain 4 residue 142 ASP Chi-restraints excluded: chain 4 residue 153 LEU Chi-restraints excluded: chain 5 residue 2 LYS Chi-restraints excluded: chain 5 residue 3 ILE Chi-restraints excluded: chain 5 residue 10 ILE Chi-restraints excluded: chain 5 residue 25 VAL Chi-restraints excluded: chain 7 residue 91 ILE Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 250 MET Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 125 ARG Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 249 GLU Chi-restraints excluded: chain E residue 256 ASN Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 149 MET Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 171 ASN Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain G residue 43 ILE Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain G residue 189 ARG Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 133 ILE Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 187 THR Chi-restraints excluded: chain K residue 189 ASP Chi-restraints excluded: chain K residue 238 ASP Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 9 ASN Chi-restraints excluded: chain L residue 18 GLU Chi-restraints excluded: chain L residue 21 CYS Chi-restraints excluded: chain L residue 24 ILE Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 193 GLU Chi-restraints excluded: chain M residue 196 LEU Chi-restraints excluded: chain M residue 198 LEU Chi-restraints excluded: chain M residue 210 LEU Chi-restraints excluded: chain M residue 234 VAL Chi-restraints excluded: chain N residue 2 LEU Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain N residue 120 ILE Chi-restraints excluded: chain N residue 123 SER Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain N residue 131 PHE Chi-restraints excluded: chain N residue 133 ILE Chi-restraints excluded: chain N residue 134 SER Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 54 MET Chi-restraints excluded: chain O residue 77 LEU Chi-restraints excluded: chain P residue 54 THR Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 90 THR Chi-restraints excluded: chain Q residue 163 SER Chi-restraints excluded: chain Q residue 171 SER Chi-restraints excluded: chain Q residue 178 HIS Chi-restraints excluded: chain Q residue 181 ILE Chi-restraints excluded: chain Q residue 182 ARG Chi-restraints excluded: chain Q residue 208 VAL Chi-restraints excluded: chain Q residue 222 LEU Chi-restraints excluded: chain Q residue 226 LEU Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain R residue 62 ILE Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 83 HIS Chi-restraints excluded: chain R residue 100 ILE Chi-restraints excluded: chain S residue 124 PHE Chi-restraints excluded: chain S residue 128 VAL Chi-restraints excluded: chain S residue 136 VAL Chi-restraints excluded: chain S residue 141 TRP Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 164 VAL Chi-restraints excluded: chain S residue 166 THR Chi-restraints excluded: chain S residue 177 VAL Chi-restraints excluded: chain S residue 179 ASN Chi-restraints excluded: chain S residue 185 VAL Chi-restraints excluded: chain S residue 200 TYR Chi-restraints excluded: chain S residue 203 LYS Chi-restraints excluded: chain S residue 205 ASN Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 33 THR Chi-restraints excluded: chain T residue 102 LYS Chi-restraints excluded: chain T residue 124 MET Chi-restraints excluded: chain T residue 149 LEU Chi-restraints excluded: chain U residue 133 SER Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain V residue 101 ILE Chi-restraints excluded: chain V residue 108 THR Chi-restraints excluded: chain V residue 125 ILE Chi-restraints excluded: chain V residue 129 ILE Chi-restraints excluded: chain V residue 137 ILE Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain V residue 159 ARG Chi-restraints excluded: chain V residue 162 ILE Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain X residue 86 VAL Chi-restraints excluded: chain X residue 142 ILE Chi-restraints excluded: chain Y residue 91 SER Chi-restraints excluded: chain Y residue 97 ARG Chi-restraints excluded: chain Y residue 100 PHE Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Y residue 108 VAL Chi-restraints excluded: chain Z residue 90 LEU Chi-restraints excluded: chain Z residue 115 MET Chi-restraints excluded: chain Z residue 130 LYS Chi-restraints excluded: chain Z residue 133 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 372 optimal weight: 7.9990 chunk 240 optimal weight: 5.9990 chunk 359 optimal weight: 7.9990 chunk 181 optimal weight: 0.4980 chunk 118 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 chunk 382 optimal weight: 8.9990 chunk 409 optimal weight: 8.9990 chunk 297 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 472 optimal weight: 6.9990 overall best weight: 4.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 119 HIS ** C 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 ASN D 138 GLN ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 ASN F 90 ASN G 114 ASN ** M 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 178 HIS ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 99 GLN ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.088 99967 Z= 0.472 Angle : 0.828 18.125 149969 Z= 0.413 Chirality : 0.046 0.322 19134 Planarity : 0.007 0.079 7664 Dihedral : 23.961 177.964 50863 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.12 % Allowed : 11.86 % Favored : 88.02 % Rotamer: Outliers : 7.69 % Allowed : 19.92 % Favored : 72.39 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: -3.05 (0.13), residues: 3296 helix: -1.21 (0.16), residues: 902 sheet: -2.09 (0.22), residues: 499 loop : -2.49 (0.13), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP 0 73 HIS 0.054 0.003 HIS R 83 PHE 0.035 0.003 PHE F 175 TYR 0.027 0.003 TYR T 58 ARG 0.007 0.001 ARG R 50 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 2847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 618 time to evaluate : 3.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 118 GLN cc_start: 0.8396 (pp30) cc_final: 0.7903 (pp30) REVERT: 5 2 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8359 (mtpp) REVERT: 6 99 LYS cc_start: 0.6701 (mtpm) cc_final: 0.6093 (tmtt) REVERT: 7 49 SER cc_start: 0.8881 (t) cc_final: 0.8400 (p) REVERT: C 164 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6700 (tt0) REVERT: D 170 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7550 (pt0) REVERT: D 250 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8108 (mmt) REVERT: D 261 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.8014 (pt) REVERT: E 218 LYS cc_start: 0.7425 (tttm) cc_final: 0.6640 (mmtp) REVERT: E 254 TYR cc_start: 0.7663 (t80) cc_final: 0.7211 (t80) REVERT: F 59 THR cc_start: 0.4871 (p) cc_final: 0.4618 (p) REVERT: G 189 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7468 (tpt90) REVERT: K 184 LYS cc_start: 0.7446 (tttm) cc_final: 0.7033 (tttp) REVERT: K 243 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7993 (m-30) REVERT: L 1 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.7496 (mmm) REVERT: M 93 LYS cc_start: 0.8288 (ttmm) cc_final: 0.7733 (ttpt) REVERT: M 166 GLU cc_start: 0.7474 (mm-30) cc_final: 0.6925 (mm-30) REVERT: M 196 LEU cc_start: 0.6673 (OUTLIER) cc_final: 0.6368 (mt) REVERT: M 198 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8051 (tp) REVERT: N 32 TYR cc_start: 0.8043 (m-80) cc_final: 0.7368 (m-80) REVERT: O 43 ARG cc_start: 0.8151 (tpt-90) cc_final: 0.7916 (tpt-90) REVERT: O 122 TYR cc_start: 0.7756 (t80) cc_final: 0.6868 (t80) REVERT: P 127 ILE cc_start: 0.8349 (tp) cc_final: 0.8092 (tt) REVERT: Q 182 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.8069 (ttm170) REVERT: R 75 TYR cc_start: 0.5658 (m-10) cc_final: 0.5348 (m-10) REVERT: R 86 TYR cc_start: 0.8686 (m-10) cc_final: 0.8310 (m-80) REVERT: R 94 ARG cc_start: 0.7121 (mmt180) cc_final: 0.6749 (mmt180) REVERT: S 124 PHE cc_start: 0.8121 (OUTLIER) cc_final: 0.7273 (t80) REVERT: S 230 TYR cc_start: 0.6644 (p90) cc_final: 0.5852 (p90) REVERT: T 32 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8045 (tp) REVERT: T 92 GLN cc_start: 0.7127 (tt0) cc_final: 0.6702 (pm20) REVERT: T 102 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7509 (mtmt) REVERT: T 109 ILE cc_start: 0.8111 (mm) cc_final: 0.7905 (mm) REVERT: U 146 MET cc_start: 0.7077 (mtm) cc_final: 0.6817 (mtp) REVERT: V 82 GLU cc_start: 0.7547 (pm20) cc_final: 0.7137 (pm20) REVERT: V 159 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.8069 (mpp80) REVERT: Y 84 LYS cc_start: 0.8117 (ttpp) cc_final: 0.7751 (ptmt) REVERT: Y 97 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7496 (tpm-80) REVERT: Z 94 ARG cc_start: 0.7989 (ptm-80) cc_final: 0.7773 (tmm-80) outliers start: 219 outliers final: 169 residues processed: 740 average time/residue: 0.9513 time to fit residues: 1190.1129 Evaluate side-chains 785 residues out of total 2847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 600 time to evaluate : 3.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 8 THR Chi-restraints excluded: chain 1 residue 26 TRP Chi-restraints excluded: chain 1 residue 37 SER Chi-restraints excluded: chain 2 residue 11 VAL Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 34 ILE Chi-restraints excluded: chain 2 residue 35 THR Chi-restraints excluded: chain 3 residue 136 CYS Chi-restraints excluded: chain 3 residue 138 LYS Chi-restraints excluded: chain 4 residue 142 ASP Chi-restraints excluded: chain 4 residue 153 LEU Chi-restraints excluded: chain 5 residue 2 LYS Chi-restraints excluded: chain 5 residue 3 ILE Chi-restraints excluded: chain 5 residue 10 ILE Chi-restraints excluded: chain 5 residue 25 VAL Chi-restraints excluded: chain 6 residue 137 LYS Chi-restraints excluded: chain 7 residue 91 ILE Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 161 ILE Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 229 HIS Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 250 MET Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 125 ARG Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 256 ASN Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 149 MET Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 171 ASN Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain G residue 43 ILE Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain G residue 189 ARG Chi-restraints excluded: chain G residue 207 GLU Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 133 ILE Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 187 THR Chi-restraints excluded: chain K residue 189 ASP Chi-restraints excluded: chain K residue 238 ASP Chi-restraints excluded: chain K residue 243 ASP Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 9 ASN Chi-restraints excluded: chain L residue 18 GLU Chi-restraints excluded: chain L residue 21 CYS Chi-restraints excluded: chain L residue 24 ILE Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 154 LEU Chi-restraints excluded: chain M residue 196 LEU Chi-restraints excluded: chain M residue 198 LEU Chi-restraints excluded: chain M residue 234 VAL Chi-restraints excluded: chain N residue 2 LEU Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain N residue 120 ILE Chi-restraints excluded: chain N residue 123 SER Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain N residue 131 PHE Chi-restraints excluded: chain N residue 133 ILE Chi-restraints excluded: chain N residue 134 SER Chi-restraints excluded: chain O residue 44 ILE Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 54 MET Chi-restraints excluded: chain O residue 77 LEU Chi-restraints excluded: chain P residue 54 THR Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 90 THR Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain Q residue 163 SER Chi-restraints excluded: chain Q residue 171 SER Chi-restraints excluded: chain Q residue 178 HIS Chi-restraints excluded: chain Q residue 181 ILE Chi-restraints excluded: chain Q residue 182 ARG Chi-restraints excluded: chain Q residue 208 VAL Chi-restraints excluded: chain Q residue 222 LEU Chi-restraints excluded: chain Q residue 226 LEU Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain R residue 62 ILE Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 100 ILE Chi-restraints excluded: chain S residue 124 PHE Chi-restraints excluded: chain S residue 128 VAL Chi-restraints excluded: chain S residue 136 VAL Chi-restraints excluded: chain S residue 141 TRP Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 164 VAL Chi-restraints excluded: chain S residue 166 THR Chi-restraints excluded: chain S residue 177 VAL Chi-restraints excluded: chain S residue 185 VAL Chi-restraints excluded: chain S residue 200 TYR Chi-restraints excluded: chain S residue 203 LYS Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 33 THR Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 102 LYS Chi-restraints excluded: chain T residue 124 MET Chi-restraints excluded: chain T residue 149 LEU Chi-restraints excluded: chain U residue 133 SER Chi-restraints excluded: chain U residue 138 VAL Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain V residue 99 VAL Chi-restraints excluded: chain V residue 101 ILE Chi-restraints excluded: chain V residue 108 THR Chi-restraints excluded: chain V residue 125 ILE Chi-restraints excluded: chain V residue 129 ILE Chi-restraints excluded: chain V residue 137 ILE Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain V residue 159 ARG Chi-restraints excluded: chain V residue 162 ILE Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain X residue 86 VAL Chi-restraints excluded: chain X residue 123 VAL Chi-restraints excluded: chain X residue 142 ILE Chi-restraints excluded: chain Y residue 91 SER Chi-restraints excluded: chain Y residue 97 ARG Chi-restraints excluded: chain Y residue 100 PHE Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Y residue 108 VAL Chi-restraints excluded: chain Z residue 90 LEU Chi-restraints excluded: chain Z residue 115 MET Chi-restraints excluded: chain Z residue 130 LYS Chi-restraints excluded: chain Z residue 133 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 547 optimal weight: 5.9990 chunk 576 optimal weight: 5.9990 chunk 525 optimal weight: 10.0000 chunk 560 optimal weight: 10.0000 chunk 337 optimal weight: 0.3980 chunk 244 optimal weight: 1.9990 chunk 440 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 chunk 506 optimal weight: 4.9990 chunk 530 optimal weight: 10.0000 chunk 558 optimal weight: 9.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 119 HIS C 102 HIS C 197 ASN ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 ASN ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 ASN F 90 ASN G 103 GLN G 114 ASN M 102 HIS N 35 GLN Q 178 HIS R 53 GLN ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 205 ASN ** S 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 99967 Z= 0.336 Angle : 0.717 16.389 149969 Z= 0.360 Chirality : 0.040 0.294 19134 Planarity : 0.006 0.062 7664 Dihedral : 23.905 175.674 50863 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.04 % Favored : 88.87 % Rotamer: Outliers : 7.13 % Allowed : 20.83 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: -2.87 (0.13), residues: 3296 helix: -0.91 (0.16), residues: 897 sheet: -2.04 (0.22), residues: 483 loop : -2.45 (0.13), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP 0 73 HIS 0.018 0.002 HIS R 83 PHE 0.030 0.002 PHE F 175 TYR 0.033 0.002 TYR T 58 ARG 0.008 0.001 ARG L 107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 2847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 613 time to evaluate : 3.679 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: 4 118 GLN cc_start: 0.8474 (pp30) cc_final: 0.8020 (pp30) REVERT: 5 2 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8340 (mtpp) REVERT: 6 99 LYS cc_start: 0.6739 (mtpm) cc_final: 0.6164 (tmtt) REVERT: 7 49 SER cc_start: 0.8832 (t) cc_final: 0.8364 (p) REVERT: C 129 THR cc_start: 0.8095 (p) cc_final: 0.7881 (m) REVERT: C 164 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6625 (tt0) REVERT: D 170 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7545 (pt0) REVERT: D 190 LEU cc_start: 0.6720 (OUTLIER) cc_final: 0.6115 (pt) REVERT: D 250 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8048 (mmt) REVERT: D 261 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7847 (pt) REVERT: E 89 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8395 (tp) REVERT: E 194 MET cc_start: 0.7443 (ttm) cc_final: 0.7105 (mtt) REVERT: E 205 SER cc_start: 0.8597 (m) cc_final: 0.8385 (m) REVERT: E 218 LYS cc_start: 0.7485 (tttm) cc_final: 0.6675 (mmtp) REVERT: E 254 TYR cc_start: 0.7765 (t80) cc_final: 0.7327 (t80) REVERT: G 189 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7433 (tpt90) REVERT: K 184 LYS cc_start: 0.7407 (tttm) cc_final: 0.7000 (tttp) REVERT: L 1 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7382 (mmm) REVERT: M 93 LYS cc_start: 0.8163 (ttmm) cc_final: 0.7621 (ttpt) REVERT: M 196 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.6942 (mt) REVERT: M 198 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7914 (tp) REVERT: N 32 TYR cc_start: 0.7971 (m-80) cc_final: 0.7387 (m-80) REVERT: O 43 ARG cc_start: 0.8092 (tpt-90) cc_final: 0.7838 (tpt-90) REVERT: O 122 TYR cc_start: 0.7662 (t80) cc_final: 0.6800 (t80) REVERT: P 127 ILE cc_start: 0.8305 (tp) cc_final: 0.8020 (tt) REVERT: Q 182 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.8023 (ttm170) REVERT: R 75 TYR cc_start: 0.5566 (m-10) cc_final: 0.5309 (m-10) REVERT: R 86 TYR cc_start: 0.8704 (m-10) cc_final: 0.8339 (m-80) REVERT: R 94 ARG cc_start: 0.7117 (mmt180) cc_final: 0.6503 (mmt180) REVERT: S 124 PHE cc_start: 0.7863 (OUTLIER) cc_final: 0.7034 (t80) REVERT: S 133 GLN cc_start: 0.8479 (mt0) cc_final: 0.8270 (mt0) REVERT: S 188 GLU cc_start: 0.5200 (OUTLIER) cc_final: 0.4845 (pm20) REVERT: S 230 TYR cc_start: 0.6629 (p90) cc_final: 0.5792 (p90) REVERT: T 32 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8003 (tp) REVERT: T 102 LYS cc_start: 0.7686 (OUTLIER) cc_final: 0.7356 (mtmt) REVERT: U 146 MET cc_start: 0.7028 (mtm) cc_final: 0.6786 (mtp) REVERT: V 82 GLU cc_start: 0.7446 (pm20) cc_final: 0.7066 (pm20) REVERT: V 159 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8025 (mpp80) REVERT: Y 84 LYS cc_start: 0.8057 (ttpp) cc_final: 0.7704 (ptmt) REVERT: Y 97 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7415 (tpm-80) REVERT: Z 136 LEU cc_start: 0.8081 (tt) cc_final: 0.7511 (mt) outliers start: 203 outliers final: 159 residues processed: 724 average time/residue: 0.9179 time to fit residues: 1120.7339 Evaluate side-chains 783 residues out of total 2847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 606 time to evaluate : 3.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 8 THR Chi-restraints excluded: chain 1 residue 26 TRP Chi-restraints excluded: chain 1 residue 37 SER Chi-restraints excluded: chain 2 residue 11 VAL Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 34 ILE Chi-restraints excluded: chain 2 residue 35 THR Chi-restraints excluded: chain 3 residue 95 LEU Chi-restraints excluded: chain 3 residue 136 CYS Chi-restraints excluded: chain 3 residue 138 LYS Chi-restraints excluded: chain 4 residue 142 ASP Chi-restraints excluded: chain 4 residue 153 LEU Chi-restraints excluded: chain 5 residue 2 LYS Chi-restraints excluded: chain 5 residue 3 ILE Chi-restraints excluded: chain 5 residue 10 ILE Chi-restraints excluded: chain 5 residue 25 VAL Chi-restraints excluded: chain 6 residue 137 LYS Chi-restraints excluded: chain 7 residue 91 ILE Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 250 MET Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 125 ARG Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 149 MET Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 171 ASN Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain G residue 43 ILE Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain G residue 189 ARG Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 133 ILE Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 187 THR Chi-restraints excluded: chain K residue 189 ASP Chi-restraints excluded: chain K residue 238 ASP Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 9 ASN Chi-restraints excluded: chain L residue 18 GLU Chi-restraints excluded: chain L residue 21 CYS Chi-restraints excluded: chain L residue 24 ILE Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 154 LEU Chi-restraints excluded: chain M residue 196 LEU Chi-restraints excluded: chain M residue 198 LEU Chi-restraints excluded: chain N residue 2 LEU Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain N residue 123 SER Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain N residue 131 PHE Chi-restraints excluded: chain N residue 133 ILE Chi-restraints excluded: chain N residue 134 SER Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 54 MET Chi-restraints excluded: chain O residue 77 LEU Chi-restraints excluded: chain P residue 54 THR Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 90 THR Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain Q residue 163 SER Chi-restraints excluded: chain Q residue 171 SER Chi-restraints excluded: chain Q residue 178 HIS Chi-restraints excluded: chain Q residue 181 ILE Chi-restraints excluded: chain Q residue 182 ARG Chi-restraints excluded: chain Q residue 208 VAL Chi-restraints excluded: chain Q residue 222 LEU Chi-restraints excluded: chain Q residue 226 LEU Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain R residue 62 ILE Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 100 ILE Chi-restraints excluded: chain R residue 106 ASN Chi-restraints excluded: chain S residue 124 PHE Chi-restraints excluded: chain S residue 128 VAL Chi-restraints excluded: chain S residue 136 VAL Chi-restraints excluded: chain S residue 141 TRP Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 164 VAL Chi-restraints excluded: chain S residue 166 THR Chi-restraints excluded: chain S residue 177 VAL Chi-restraints excluded: chain S residue 185 VAL Chi-restraints excluded: chain S residue 188 GLU Chi-restraints excluded: chain S residue 200 TYR Chi-restraints excluded: chain S residue 203 LYS Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 33 THR Chi-restraints excluded: chain T residue 102 LYS Chi-restraints excluded: chain T residue 124 MET Chi-restraints excluded: chain T residue 149 LEU Chi-restraints excluded: chain U residue 133 SER Chi-restraints excluded: chain U residue 138 VAL Chi-restraints excluded: chain U residue 165 LEU Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain V residue 101 ILE Chi-restraints excluded: chain V residue 108 THR Chi-restraints excluded: chain V residue 125 ILE Chi-restraints excluded: chain V residue 129 ILE Chi-restraints excluded: chain V residue 137 ILE Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain V residue 159 ARG Chi-restraints excluded: chain V residue 162 ILE Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain X residue 123 VAL Chi-restraints excluded: chain X residue 142 ILE Chi-restraints excluded: chain Y residue 91 SER Chi-restraints excluded: chain Y residue 97 ARG Chi-restraints excluded: chain Y residue 100 PHE Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Y residue 108 VAL Chi-restraints excluded: chain Z residue 90 LEU Chi-restraints excluded: chain Z residue 115 MET Chi-restraints excluded: chain Z residue 130 LYS Chi-restraints excluded: chain Z residue 133 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 368 optimal weight: 10.0000 chunk 592 optimal weight: 8.9990 chunk 361 optimal weight: 5.9990 chunk 281 optimal weight: 0.0060 chunk 411 optimal weight: 8.9990 chunk 621 optimal weight: 10.0000 chunk 572 optimal weight: 6.9990 chunk 495 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 382 optimal weight: 10.0000 chunk 303 optimal weight: 6.9990 overall best weight: 5.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 119 HIS ** C 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 ASN ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 ASN ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 ASN G 114 ASN L 49 ASN M 102 HIS Q 178 HIS ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 113 ASN S 205 ASN ** S 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 68 HIS 0 42 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.099 99967 Z= 0.555 Angle : 0.896 18.972 149969 Z= 0.443 Chirality : 0.049 0.336 19134 Planarity : 0.007 0.082 7664 Dihedral : 23.999 178.645 50863 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.12 % Allowed : 13.08 % Favored : 86.80 % Rotamer: Outliers : 6.99 % Allowed : 21.39 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: 3296 helix: -1.31 (0.15), residues: 907 sheet: -2.26 (0.22), residues: 500 loop : -2.56 (0.13), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.004 TRP 0 73 HIS 0.023 0.003 HIS N 13 PHE 0.028 0.003 PHE F 175 TYR 0.033 0.003 TYR T 58 ARG 0.008 0.001 ARG M 92 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6592 Ramachandran restraints generated. 3296 Oldfield, 0 Emsley, 3296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 2847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 627 time to evaluate : 3.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 4 118 GLN cc_start: 0.8514 (pp30) cc_final: 0.8003 (pp30) REVERT: 5 2 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8335 (mtpp) REVERT: 6 99 LYS cc_start: 0.6646 (mtpm) cc_final: 0.6149 (tmtt) REVERT: 7 49 SER cc_start: 0.8981 (t) cc_final: 0.8476 (p) REVERT: C 164 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6663 (tt0) REVERT: C 197 ASN cc_start: 0.7877 (OUTLIER) cc_final: 0.7599 (t0) REVERT: D 170 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7582 (pt0) REVERT: D 190 LEU cc_start: 0.7057 (OUTLIER) cc_final: 0.6401 (pt) REVERT: D 250 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8282 (mtt) REVERT: D 261 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.8027 (pt) REVERT: E 205 SER cc_start: 0.8599 (m) cc_final: 0.8395 (m) REVERT: E 218 LYS cc_start: 0.7523 (tttm) cc_final: 0.6681 (mmtp) REVERT: E 254 TYR cc_start: 0.7749 (t80) cc_final: 0.7307 (t80) REVERT: F 59 THR cc_start: 0.4999 (p) cc_final: 0.4686 (p) REVERT: G 189 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7622 (tpt90) REVERT: K 184 LYS cc_start: 0.7441 (tttm) cc_final: 0.7043 (tttp) REVERT: L 1 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7452 (mmm) REVERT: M 93 LYS cc_start: 0.8258 (ttmm) cc_final: 0.7705 (ttpt) REVERT: M 198 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.8013 (tp) REVERT: O 43 ARG cc_start: 0.8226 (tpt-90) cc_final: 0.7873 (mmm-85) REVERT: O 122 TYR cc_start: 0.7809 (t80) cc_final: 0.6706 (t80) REVERT: Q 182 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.8039 (ttm170) REVERT: R 75 TYR cc_start: 0.5645 (m-10) cc_final: 0.5354 (m-10) REVERT: R 94 ARG cc_start: 0.7095 (mmt180) cc_final: 0.6738 (mmt180) REVERT: S 124 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.7247 (t80) REVERT: S 188 GLU cc_start: 0.5551 (OUTLIER) cc_final: 0.5202 (pm20) REVERT: S 230 TYR cc_start: 0.6763 (p90) cc_final: 0.5986 (p90) REVERT: T 32 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.7998 (tp) REVERT: T 102 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7558 (mtmt) REVERT: U 146 MET cc_start: 0.7090 (mtm) cc_final: 0.6835 (mtp) REVERT: U 177 MET cc_start: 0.7103 (mtm) cc_final: 0.6888 (mtm) REVERT: V 82 GLU cc_start: 0.7629 (pm20) cc_final: 0.7178 (pm20) REVERT: V 101 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.8098 (pt) REVERT: V 159 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.7973 (mpp80) REVERT: Y 84 LYS cc_start: 0.8136 (ttpp) cc_final: 0.7773 (ptmt) REVERT: Y 97 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7505 (tpm-80) outliers start: 199 outliers final: 169 residues processed: 743 average time/residue: 0.9077 time to fit residues: 1136.6705 Evaluate side-chains 802 residues out of total 2847 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 615 time to evaluate : 3.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 8 THR Chi-restraints excluded: chain 1 residue 26 TRP Chi-restraints excluded: chain 1 residue 37 SER Chi-restraints excluded: chain 2 residue 11 VAL Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 34 ILE Chi-restraints excluded: chain 2 residue 35 THR Chi-restraints excluded: chain 3 residue 136 CYS Chi-restraints excluded: chain 3 residue 138 LYS Chi-restraints excluded: chain 4 residue 142 ASP Chi-restraints excluded: chain 4 residue 153 LEU Chi-restraints excluded: chain 5 residue 2 LYS Chi-restraints excluded: chain 5 residue 3 ILE Chi-restraints excluded: chain 5 residue 10 ILE Chi-restraints excluded: chain 5 residue 25 VAL Chi-restraints excluded: chain 6 residue 137 LYS Chi-restraints excluded: chain 7 residue 91 ILE Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 58 TYR Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 102 HIS Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain C residue 140 ILE Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 177 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 90 ILE Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 229 HIS Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 250 MET Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 125 ARG Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 214 GLU Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 90 ASN Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 149 MET Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 171 ASN Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 212 THR Chi-restraints excluded: chain G residue 43 ILE Chi-restraints excluded: chain G residue 74 ILE Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 169 THR Chi-restraints excluded: chain G residue 189 ARG Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 60 LEU Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain K residue 133 ILE Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 161 VAL Chi-restraints excluded: chain K residue 187 THR Chi-restraints excluded: chain K residue 189 ASP Chi-restraints excluded: chain K residue 238 ASP Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 9 ASN Chi-restraints excluded: chain L residue 18 GLU Chi-restraints excluded: chain L residue 21 CYS Chi-restraints excluded: chain L residue 24 ILE Chi-restraints excluded: chain L residue 42 VAL Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 87 ILE Chi-restraints excluded: chain M residue 109 SER Chi-restraints excluded: chain M residue 154 LEU Chi-restraints excluded: chain M residue 198 LEU Chi-restraints excluded: chain M residue 234 VAL Chi-restraints excluded: chain N residue 2 LEU Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 109 VAL Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain N residue 123 SER Chi-restraints excluded: chain N residue 127 ILE Chi-restraints excluded: chain N residue 131 PHE Chi-restraints excluded: chain N residue 133 ILE Chi-restraints excluded: chain N residue 134 SER Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 54 MET Chi-restraints excluded: chain O residue 77 LEU Chi-restraints excluded: chain P residue 54 THR Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 73 LEU Chi-restraints excluded: chain P residue 90 THR Chi-restraints excluded: chain P residue 99 SER Chi-restraints excluded: chain P residue 152 VAL Chi-restraints excluded: chain Q residue 163 SER Chi-restraints excluded: chain Q residue 171 SER Chi-restraints excluded: chain Q residue 178 HIS Chi-restraints excluded: chain Q residue 181 ILE Chi-restraints excluded: chain Q residue 182 ARG Chi-restraints excluded: chain Q residue 208 VAL Chi-restraints excluded: chain Q residue 222 LEU Chi-restraints excluded: chain Q residue 226 LEU Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain R residue 62 ILE Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 69 ILE Chi-restraints excluded: chain R residue 100 ILE Chi-restraints excluded: chain R residue 106 ASN Chi-restraints excluded: chain S residue 124 PHE Chi-restraints excluded: chain S residue 128 VAL Chi-restraints excluded: chain S residue 136 VAL Chi-restraints excluded: chain S residue 141 TRP Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 164 VAL Chi-restraints excluded: chain S residue 166 THR Chi-restraints excluded: chain S residue 177 VAL Chi-restraints excluded: chain S residue 179 ASN Chi-restraints excluded: chain S residue 185 VAL Chi-restraints excluded: chain S residue 188 GLU Chi-restraints excluded: chain S residue 200 TYR Chi-restraints excluded: chain S residue 203 LYS Chi-restraints excluded: chain S residue 205 ASN Chi-restraints excluded: chain T residue 32 ILE Chi-restraints excluded: chain T residue 33 THR Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 52 GLN Chi-restraints excluded: chain T residue 102 LYS Chi-restraints excluded: chain T residue 124 MET Chi-restraints excluded: chain T residue 149 LEU Chi-restraints excluded: chain U residue 133 SER Chi-restraints excluded: chain U residue 138 VAL Chi-restraints excluded: chain U residue 139 ASP Chi-restraints excluded: chain U residue 165 LEU Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain V residue 101 ILE Chi-restraints excluded: chain V residue 108 THR Chi-restraints excluded: chain V residue 125 ILE Chi-restraints excluded: chain V residue 129 ILE Chi-restraints excluded: chain V residue 137 ILE Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain V residue 159 ARG Chi-restraints excluded: chain V residue 162 ILE Chi-restraints excluded: chain V residue 164 THR Chi-restraints excluded: chain X residue 123 VAL Chi-restraints excluded: chain X residue 142 ILE Chi-restraints excluded: chain Y residue 91 SER Chi-restraints excluded: chain Y residue 97 ARG Chi-restraints excluded: chain Y residue 100 PHE Chi-restraints excluded: chain Y residue 101 VAL Chi-restraints excluded: chain Y residue 108 VAL Chi-restraints excluded: chain Z residue 90 LEU Chi-restraints excluded: chain Z residue 115 MET Chi-restraints excluded: chain Z residue 130 LYS Chi-restraints excluded: chain Z residue 133 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 624 random chunks: chunk 393 optimal weight: 9.9990 chunk 527 optimal weight: 10.0000 chunk 151 optimal weight: 0.9990 chunk 456 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 495 optimal weight: 10.0000 chunk 207 optimal weight: 0.9990 chunk 509 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 119 HIS ** C 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 ASN D 169 GLN ** E 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 ASN G 114 ASN ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 42 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.159455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.127940 restraints weight = 133563.973| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 0.94 r_work: 0.3175 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.177 99967 Z= 0.386 Angle : 0.923 59.157 149969 Z= 0.475 Chirality : 0.044 0.855 19134 Planarity : 0.007 0.099 7664 Dihedral : 23.999 178.581 50861 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 13.11 % Favored : 86.74 % Rotamer: Outliers : 6.71 % Allowed : 22.27 % Favored : 71.02 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: -3.19 (0.13), residues: 3296 helix: -1.29 (0.16), residues: 908 sheet: -2.29 (0.21), residues: 510 loop : -2.56 (0.13), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP 0 73 HIS 0.144 0.003 HIS Q 178 PHE 0.024 0.003 PHE F 175 TYR 0.026 0.003 TYR T 58 ARG 0.019 0.001 ARG F 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19934.05 seconds wall clock time: 352 minutes 46.88 seconds (21166.88 seconds total)