Starting phenix.real_space_refine on Sat Feb 7 00:21:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9unl_64355/02_2026/9unl_64355.cif Found real_map, /net/cci-nas-00/data/ceres_data/9unl_64355/02_2026/9unl_64355.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9unl_64355/02_2026/9unl_64355.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9unl_64355/02_2026/9unl_64355.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9unl_64355/02_2026/9unl_64355.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9unl_64355/02_2026/9unl_64355.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.017 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: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 17946 2.51 5 N 5158 2.21 5 O 5496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28626 Number of models: 1 Model: "" Number of chains: 22 Chain: "E" Number of atoms: 1948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1948 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 8, 'TRANS': 241} Chain: "C" Number of atoms: 1940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1940 Classifications: {'peptide': 249} Link IDs: {'CIS': 2, 'PTRANS': 8, 'TRANS': 238} Chain: "A" Number of atoms: 1940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1940 Classifications: {'peptide': 249} Link IDs: {'CIS': 2, 'PTRANS': 8, 'TRANS': 238} Chain: "U" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 643 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "S" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 691 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 1, 'TRANS': 89} Chain: "Q" Number of atoms: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 613 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "O" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 691 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 1, 'TRANS': 89} Chain: "M" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 567 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "K" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 575 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "I" Number of atoms: 1948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1948 Classifications: {'peptide': 250} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 240} Chain: "G" Number of atoms: 1948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1948 Classifications: {'peptide': 250} Link IDs: {'CIS': 2, 'PTRANS': 8, 'TRANS': 239} Chain: "F" Number of atoms: 2075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2075 Classifications: {'peptide': 262} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 2, 'PTRANS': 8, 'TRANS': 251} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 2084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2084 Classifications: {'peptide': 263} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 4, 'PTRANS': 8, 'TRANS': 250} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2075 Classifications: {'peptide': 262} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 252} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "V" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 823 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 1, 'TRANS': 103} Chain: "T" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 823 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 1, 'TRANS': 103} Chain: "R" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 758 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 1, 'TRANS': 95} Chain: "P" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 823 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 1, 'TRANS': 103} Chain: "N" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 758 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 1, 'TRANS': 95} Chain: "L" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 753 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 1, 'TRANS': 94} Chain: "J" Number of atoms: 2075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2075 Classifications: {'peptide': 262} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 3, 'PTRANS': 8, 'TRANS': 250} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 2075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2075 Classifications: {'peptide': 262} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 8, 'TRANS': 253} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 6.94, per 1000 atoms: 0.24 Number of scatterers: 28626 At special positions: 0 Unit cell: (129.56, 174.66, 182.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 5496 8.00 N 5158 7.00 C 17946 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.55 Conformation dependent library (CDL) restraints added in 1.2 seconds 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6970 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 27 sheets defined 61.1% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'E' and resid 21 through 26 Processing helix chain 'E' and resid 102 through 107 Processing helix chain 'E' and resid 118 through 132 Processing helix chain 'E' and resid 137 through 142 Processing helix chain 'E' and resid 142 through 162 Processing helix chain 'E' and resid 177 through 231 removed outlier: 4.039A pdb=" N GLU E 181 " --> pdb=" O LYS E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 251 Processing helix chain 'C' and resid 21 through 26 Processing helix chain 'C' and resid 118 through 132 Processing helix chain 'C' and resid 135 through 141 Processing helix chain 'C' and resid 144 through 161 removed outlier: 3.666A pdb=" N PHE C 161 " --> pdb=" O ARG C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 230 removed outlier: 4.417A pdb=" N VAL C 200 " --> pdb=" O ALA C 196 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLU C 201 " --> pdb=" O ARG C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 251 Processing helix chain 'A' and resid 22 through 26 Processing helix chain 'A' and resid 99 through 101 No H-bonds generated for 'chain 'A' and resid 99 through 101' Processing helix chain 'A' and resid 102 through 110 Processing helix chain 'A' and resid 118 through 133 Processing helix chain 'A' and resid 134 through 142 removed outlier: 3.858A pdb=" N GLU A 138 " --> pdb=" O PHE A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 159 Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 176 through 232 Processing helix chain 'A' and resid 233 through 251 Processing helix chain 'U' and resid 186 through 196 Processing helix chain 'U' and resid 197 through 232 removed outlier: 4.235A pdb=" N GLU U 222 " --> pdb=" O SER U 218 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU U 223 " --> pdb=" O LYS U 219 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ALA U 225 " --> pdb=" O ALA U 221 " (cutoff:3.500A) Processing helix chain 'U' and resid 233 through 251 Processing helix chain 'S' and resid 181 through 232 removed outlier: 4.070A pdb=" N THR S 230 " --> pdb=" O ASN S 226 " (cutoff:3.500A) Processing helix chain 'S' and resid 234 through 252 Processing helix chain 'Q' and resid 190 through 232 removed outlier: 3.514A pdb=" N SER Q 227 " --> pdb=" O LEU Q 223 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N THR Q 230 " --> pdb=" O ASN Q 226 " (cutoff:3.500A) Processing helix chain 'Q' and resid 233 through 251 Processing helix chain 'O' and resid 180 through 232 removed outlier: 4.119A pdb=" N THR O 230 " --> pdb=" O ASN O 226 " (cutoff:3.500A) Processing helix chain 'O' and resid 233 through 251 Processing helix chain 'M' and resid 196 through 231 removed outlier: 3.714A pdb=" N GLU M 222 " --> pdb=" O SER M 218 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU M 223 " --> pdb=" O LYS M 219 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ALA M 225 " --> pdb=" O ALA M 221 " (cutoff:3.500A) Processing helix chain 'M' and resid 233 through 251 Processing helix chain 'K' and resid 196 through 231 Processing helix chain 'K' and resid 233 through 251 Processing helix chain 'I' and resid 102 through 110 Processing helix chain 'I' and resid 119 through 122 Processing helix chain 'I' and resid 123 through 134 Processing helix chain 'I' and resid 137 through 143 Processing helix chain 'I' and resid 143 through 162 removed outlier: 4.047A pdb=" N GLU I 156 " --> pdb=" O ASP I 152 " (cutoff:3.500A) Processing helix chain 'I' and resid 178 through 232 Processing helix chain 'I' and resid 233 through 251 Processing helix chain 'G' and resid 42 through 44 No H-bonds generated for 'chain 'G' and resid 42 through 44' Processing helix chain 'G' and resid 101 through 106 Processing helix chain 'G' and resid 120 through 131 removed outlier: 4.098A pdb=" N LYS G 128 " --> pdb=" O THR G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 142 Processing helix chain 'G' and resid 142 through 162 removed outlier: 4.489A pdb=" N VAL G 146 " --> pdb=" O GLN G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 232 removed outlier: 4.166A pdb=" N THR G 230 " --> pdb=" O ASN G 226 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 251 Processing helix chain 'F' and resid 35 through 40 Processing helix chain 'F' and resid 56 through 60 Processing helix chain 'F' and resid 113 through 115 No H-bonds generated for 'chain 'F' and resid 113 through 115' Processing helix chain 'F' and resid 116 through 123 removed outlier: 3.508A pdb=" N GLN F 122 " --> pdb=" O PRO F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 145 removed outlier: 4.196A pdb=" N ASN F 138 " --> pdb=" O PRO F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 173 removed outlier: 3.569A pdb=" N LYS F 173 " --> pdb=" O THR F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 210 Processing helix chain 'F' and resid 212 through 245 removed outlier: 4.048A pdb=" N LYS F 244 " --> pdb=" O GLU F 240 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASN F 245 " --> pdb=" O ALA F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 265 removed outlier: 4.163A pdb=" N LYS F 250 " --> pdb=" O PRO F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 278 No H-bonds generated for 'chain 'F' and resid 276 through 278' Processing helix chain 'F' and resid 288 through 294 Processing helix chain 'D' and resid 35 through 39 Processing helix chain 'D' and resid 55 through 60 Processing helix chain 'D' and resid 116 through 124 Processing helix chain 'D' and resid 127 through 132 Processing helix chain 'D' and resid 132 through 147 removed outlier: 3.551A pdb=" N ILE D 136 " --> pdb=" O VAL D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 175 removed outlier: 3.706A pdb=" N PHE D 175 " --> pdb=" O ARG D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 243 removed outlier: 3.830A pdb=" N GLN D 201 " --> pdb=" O VAL D 197 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA D 241 " --> pdb=" O MET D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 265 removed outlier: 3.502A pdb=" N LYS D 250 " --> pdb=" O PRO D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 279 Processing helix chain 'D' and resid 285 through 296 removed outlier: 3.771A pdb=" N ARG D 289 " --> pdb=" O GLU D 285 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLY D 290 " --> pdb=" O SER D 286 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N SER D 291 " --> pdb=" O PHE D 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 39 Processing helix chain 'B' and resid 119 through 124 removed outlier: 3.602A pdb=" N ARG B 123 " --> pdb=" O SER B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 145 Proline residue: B 134 - end of helix removed outlier: 3.603A pdb=" N ASN B 138 " --> pdb=" O PRO B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 158 No H-bonds generated for 'chain 'B' and resid 156 through 158' Processing helix chain 'B' and resid 159 through 175 removed outlier: 5.071A pdb=" N ARG B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU B 167 " --> pdb=" O LEU B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 245 removed outlier: 3.859A pdb=" N GLU B 215 " --> pdb=" O GLN B 211 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA B 241 " --> pdb=" O MET B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 265 removed outlier: 3.655A pdb=" N LYS B 250 " --> pdb=" O PRO B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 279 Processing helix chain 'B' and resid 285 through 287 No H-bonds generated for 'chain 'B' and resid 285 through 287' Processing helix chain 'B' and resid 288 through 294 Processing helix chain 'V' and resid 192 through 243 Processing helix chain 'V' and resid 246 through 266 removed outlier: 3.604A pdb=" N LYS V 250 " --> pdb=" O PRO V 246 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N THR V 266 " --> pdb=" O LYS V 262 " (cutoff:3.500A) Processing helix chain 'V' and resid 276 through 278 No H-bonds generated for 'chain 'V' and resid 276 through 278' Processing helix chain 'V' and resid 284 through 287 Processing helix chain 'V' and resid 288 through 293 Processing helix chain 'T' and resid 192 through 243 Processing helix chain 'T' and resid 246 through 265 removed outlier: 3.514A pdb=" N LYS T 250 " --> pdb=" O PRO T 246 " (cutoff:3.500A) Processing helix chain 'T' and resid 276 through 278 No H-bonds generated for 'chain 'T' and resid 276 through 278' Processing helix chain 'T' and resid 284 through 287 Processing helix chain 'T' and resid 288 through 295 Processing helix chain 'R' and resid 200 through 245 removed outlier: 4.249A pdb=" N LYS R 244 " --> pdb=" O GLU R 240 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ASN R 245 " --> pdb=" O ALA R 241 " (cutoff:3.500A) Processing helix chain 'R' and resid 246 through 265 Processing helix chain 'R' and resid 276 through 279 Processing helix chain 'R' and resid 288 through 295 Processing helix chain 'P' and resid 192 through 245 removed outlier: 3.671A pdb=" N ALA P 241 " --> pdb=" O MET P 237 " (cutoff:3.500A) Processing helix chain 'P' and resid 247 through 265 Processing helix chain 'P' and resid 276 through 279 Processing helix chain 'P' and resid 288 through 295 Processing helix chain 'N' and resid 200 through 245 removed outlier: 3.579A pdb=" N ALA N 241 " --> pdb=" O MET N 237 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS N 244 " --> pdb=" O GLU N 240 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN N 245 " --> pdb=" O ALA N 241 " (cutoff:3.500A) Processing helix chain 'N' and resid 246 through 265 Processing helix chain 'N' and resid 276 through 279 Processing helix chain 'N' and resid 285 through 287 No H-bonds generated for 'chain 'N' and resid 285 through 287' Processing helix chain 'N' and resid 288 through 295 Processing helix chain 'L' and resid 201 through 245 removed outlier: 3.626A pdb=" N ALA L 241 " --> pdb=" O MET L 237 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS L 244 " --> pdb=" O GLU L 240 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN L 245 " --> pdb=" O ALA L 241 " (cutoff:3.500A) Processing helix chain 'L' and resid 246 through 267 removed outlier: 3.887A pdb=" N THR L 266 " --> pdb=" O LYS L 262 " (cutoff:3.500A) Processing helix chain 'L' and resid 285 through 295 removed outlier: 3.502A pdb=" N ARG L 289 " --> pdb=" O GLU L 285 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLY L 290 " --> pdb=" O SER L 286 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N SER L 291 " --> pdb=" O PHE L 287 " (cutoff:3.500A) Processing helix chain 'J' and resid 35 through 40 Processing helix chain 'J' and resid 55 through 57 No H-bonds generated for 'chain 'J' and resid 55 through 57' Processing helix chain 'J' and resid 58 through 62 removed outlier: 3.667A pdb=" N ASP J 61 " --> pdb=" O VAL J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 116 through 124 removed outlier: 4.663A pdb=" N GLN J 122 " --> pdb=" O PRO J 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 132 through 147 removed outlier: 4.315A pdb=" N VAL J 140 " --> pdb=" O ILE J 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 158 through 175 removed outlier: 3.556A pdb=" N LEU J 162 " --> pdb=" O ALA J 158 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU J 168 " --> pdb=" O ILE J 164 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR J 169 " --> pdb=" O ARG J 165 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ARG J 171 " --> pdb=" O GLU J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 190 through 245 removed outlier: 3.647A pdb=" N GLN J 208 " --> pdb=" O GLN J 204 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLN J 211 " --> pdb=" O ALA J 207 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE J 212 " --> pdb=" O GLN J 208 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N GLU J 215 " --> pdb=" O GLN J 211 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS J 218 " --> pdb=" O VAL J 214 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU J 238 " --> pdb=" O ALA J 234 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU J 240 " --> pdb=" O LYS J 236 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ALA J 241 " --> pdb=" O MET J 237 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS J 244 " --> pdb=" O GLU J 240 " (cutoff:3.500A) Processing helix chain 'J' and resid 246 through 266 removed outlier: 3.604A pdb=" N LYS J 250 " --> pdb=" O PRO J 246 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N THR J 266 " --> pdb=" O LYS J 262 " (cutoff:3.500A) Processing helix chain 'J' and resid 276 through 278 No H-bonds generated for 'chain 'J' and resid 276 through 278' Processing helix chain 'J' and resid 285 through 294 removed outlier: 3.655A pdb=" N ARG J 289 " --> pdb=" O GLU J 285 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLY J 290 " --> pdb=" O SER J 286 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N SER J 291 " --> pdb=" O PHE J 287 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 39 Processing helix chain 'H' and resid 116 through 124 Processing helix chain 'H' and resid 127 through 132 Processing helix chain 'H' and resid 132 through 148 removed outlier: 3.890A pdb=" N ASN H 138 " --> pdb=" O PRO H 134 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLU H 139 " --> pdb=" O SER H 135 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS H 142 " --> pdb=" O ASN H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 156 through 175 Processing helix chain 'H' and resid 190 through 245 removed outlier: 4.035A pdb=" N LYS H 244 " --> pdb=" O GLU H 240 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN H 245 " --> pdb=" O ALA H 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 246 through 266 removed outlier: 3.585A pdb=" N LYS H 250 " --> pdb=" O PRO H 246 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N THR H 266 " --> pdb=" O LYS H 262 " (cutoff:3.500A) Processing helix chain 'H' and resid 276 through 279 Processing helix chain 'H' and resid 284 through 287 Processing helix chain 'H' and resid 288 through 295 Processing sheet with id=AA1, first strand: chain 'E' and resid 27 through 30 Processing sheet with id=AA2, first strand: chain 'E' and resid 44 through 50 removed outlier: 6.117A pdb=" N GLN E 46 " --> pdb=" O ASP E 40 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ASP E 40 " --> pdb=" O GLN E 46 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ILE E 48 " --> pdb=" O ILE E 38 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG E 35 " --> pdb=" O PHE E 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 72 through 80 removed outlier: 6.718A pdb=" N ASN E 89 " --> pdb=" O LEU E 173 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU E 173 " --> pdb=" O ASN E 89 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N THR E 91 " --> pdb=" O THR E 171 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU E 95 " --> pdb=" O ASP E 167 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ASP E 167 " --> pdb=" O LEU E 95 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ARG E 97 " --> pdb=" O LEU E 165 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N LEU E 165 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 257 through 260 removed outlier: 6.239A pdb=" N THR G 258 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG H 270 " --> pdb=" O ILE G 257 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N THR M 258 " --> pdb=" O LEU L 273 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ILE M 257 " --> pdb=" O ARG N 270 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N TYR N 272 " --> pdb=" O ILE M 257 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N TYR M 259 " --> pdb=" O TYR N 272 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N THR N 274 " --> pdb=" O TYR M 259 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N THR O 258 " --> pdb=" O LEU N 273 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG P 270 " --> pdb=" O ILE O 257 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N THR Q 258 " --> pdb=" O LEU P 273 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE S 257 " --> pdb=" O ARG T 270 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N TYR T 272 " --> pdb=" O ILE S 257 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N TYR S 259 " --> pdb=" O TYR T 272 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N THR T 274 " --> pdb=" O TYR S 259 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE U 257 " --> pdb=" O ARG V 270 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N TYR V 272 " --> pdb=" O ILE U 257 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N TYR U 259 " --> pdb=" O TYR V 272 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N THR V 274 " --> pdb=" O TYR U 259 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N TYR B 272 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TYR A 259 " --> pdb=" O TYR B 272 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N THR B 274 " --> pdb=" O TYR A 259 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N THR E 258 " --> pdb=" O LEU D 273 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 35 through 37 Processing sheet with id=AA6, first strand: chain 'C' and resid 72 through 80 removed outlier: 5.913A pdb=" N ASN C 89 " --> pdb=" O HIS C 172 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N HIS C 172 " --> pdb=" O ASN C 89 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N THR C 91 " --> pdb=" O LEU C 170 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LEU C 170 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ARG C 93 " --> pdb=" O VAL C 168 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL C 168 " --> pdb=" O ARG C 93 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU C 95 " --> pdb=" O ASP C 166 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE C 164 " --> pdb=" O ARG C 97 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 44 through 45 Processing sheet with id=AA8, first strand: chain 'A' and resid 75 through 76 removed outlier: 6.548A pdb=" N ARG A 93 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N LEU A 170 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU A 95 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N VAL A 168 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 45 through 50 removed outlier: 5.645A pdb=" N ILE I 38 " --> pdb=" O GLN I 46 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ILE I 48 " --> pdb=" O ALA I 36 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ALA I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL I 50 " --> pdb=" O HIS I 34 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N HIS I 34 " --> pdb=" O VAL I 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 74 through 80 removed outlier: 6.329A pdb=" N ASN I 89 " --> pdb=" O LEU I 173 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU I 173 " --> pdb=" O ASN I 89 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N THR I 91 " --> pdb=" O THR I 171 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG I 97 " --> pdb=" O LEU I 165 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N LEU I 165 " --> pdb=" O ARG I 97 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 36 through 40 removed outlier: 3.507A pdb=" N LYS G 63 " --> pdb=" O PHE G 39 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 72 through 76 removed outlier: 3.520A pdb=" N ARG G 72 " --> pdb=" O PHE G 96 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 72 through 76 removed outlier: 3.520A pdb=" N ARG G 72 " --> pdb=" O PHE G 96 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N THR G 91 " --> pdb=" O HIS G 172 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N HIS G 172 " --> pdb=" O THR G 91 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ARG G 93 " --> pdb=" O LEU G 170 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LEU G 170 " --> pdb=" O ARG G 93 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 63 through 65 Processing sheet with id=AB6, first strand: chain 'F' and resid 86 through 90 removed outlier: 6.265A pdb=" N ARG F 107 " --> pdb=" O VAL F 182 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N VAL F 182 " --> pdb=" O ARG F 107 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU F 109 " --> pdb=" O ASP F 180 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASP F 180 " --> pdb=" O LEU F 109 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 103 through 104 Processing sheet with id=AB8, first strand: chain 'D' and resid 40 through 41 Processing sheet with id=AB9, first strand: chain 'D' and resid 47 through 52 Processing sheet with id=AC1, first strand: chain 'D' and resid 86 through 87 Processing sheet with id=AC2, first strand: chain 'B' and resid 49 through 50 Processing sheet with id=AC3, first strand: chain 'B' and resid 86 through 92 removed outlier: 6.538A pdb=" N SER B 105 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ILE B 184 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ARG B 107 " --> pdb=" O VAL B 182 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N VAL B 182 " --> pdb=" O ARG B 107 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU B 109 " --> pdb=" O ASP B 180 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 64 through 65 Processing sheet with id=AC5, first strand: chain 'J' and resid 88 through 96 removed outlier: 6.227A pdb=" N ARG J 88 " --> pdb=" O ARG J 107 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG J 107 " --> pdb=" O ARG J 88 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE J 90 " --> pdb=" O SER J 105 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N SER J 105 " --> pdb=" O ILE J 90 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N SER J 92 " --> pdb=" O ASN J 103 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASN J 103 " --> pdb=" O SER J 92 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N THR J 94 " --> pdb=" O MET J 101 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N MET J 101 " --> pdb=" O THR J 94 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 40 through 42 Processing sheet with id=AC7, first strand: chain 'H' and resid 48 through 53 Processing sheet with id=AC8, first strand: chain 'H' and resid 89 through 94 Processing sheet with id=AC9, first strand: chain 'H' and resid 111 through 112 1868 hydrogen bonds defined for protein. 5442 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.03 Time building geometry restraints manager: 3.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5051 1.32 - 1.44: 6796 1.44 - 1.57: 17052 1.57 - 1.69: 2 1.69 - 1.81: 47 Bond restraints: 28948 Sorted by residual: bond pdb=" CA THR D 94 " pdb=" C THR D 94 " ideal model delta sigma weight residual 1.523 1.476 0.047 1.34e-02 5.57e+03 1.21e+01 bond pdb=" CA LEU J 68 " pdb=" C LEU J 68 " ideal model delta sigma weight residual 1.523 1.477 0.046 1.34e-02 5.57e+03 1.18e+01 bond pdb=" CG GLN F 60 " pdb=" CD GLN F 60 " ideal model delta sigma weight residual 1.516 1.598 -0.082 2.50e-02 1.60e+03 1.08e+01 bond pdb=" C LEU J 68 " pdb=" N HIS J 69 " ideal model delta sigma weight residual 1.332 1.373 -0.040 1.40e-02 5.10e+03 8.21e+00 bond pdb=" C SER B 110 " pdb=" N ARG B 111 " ideal model delta sigma weight residual 1.325 1.360 -0.035 1.24e-02 6.50e+03 8.14e+00 ... (remaining 28943 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 38394 2.89 - 5.77: 570 5.77 - 8.66: 59 8.66 - 11.54: 18 11.54 - 14.43: 5 Bond angle restraints: 39046 Sorted by residual: angle pdb=" C VAL A 78 " pdb=" N ILE A 79 " pdb=" CA ILE A 79 " ideal model delta sigma weight residual 121.70 136.13 -14.43 1.80e+00 3.09e-01 6.42e+01 angle pdb=" C TRP B 74 " pdb=" N PHE B 75 " pdb=" CA PHE B 75 " ideal model delta sigma weight residual 121.70 135.69 -13.99 1.80e+00 3.09e-01 6.04e+01 angle pdb=" C ALA F 146 " pdb=" N LYS F 147 " pdb=" CA LYS F 147 " ideal model delta sigma weight residual 121.70 134.09 -12.39 1.80e+00 3.09e-01 4.74e+01 angle pdb=" C LYS D 89 " pdb=" N ILE D 90 " pdb=" CA ILE D 90 " ideal model delta sigma weight residual 121.70 134.01 -12.31 1.80e+00 3.09e-01 4.67e+01 angle pdb=" C GLN F 60 " pdb=" N ASP F 61 " pdb=" CA ASP F 61 " ideal model delta sigma weight residual 121.94 135.22 -13.28 2.00e+00 2.50e-01 4.41e+01 ... (remaining 39041 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 17267 17.89 - 35.79: 484 35.79 - 53.68: 174 53.68 - 71.58: 66 71.58 - 89.47: 19 Dihedral angle restraints: 18010 sinusoidal: 7312 harmonic: 10698 Sorted by residual: dihedral pdb=" CA ASP L 276 " pdb=" C ASP L 276 " pdb=" N ASN L 277 " pdb=" CA ASN L 277 " ideal model delta harmonic sigma weight residual 180.00 153.60 26.40 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA LEU A 170 " pdb=" C LEU A 170 " pdb=" N THR A 171 " pdb=" CA THR A 171 " ideal model delta harmonic sigma weight residual 0.00 -24.18 24.18 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA PHE C 107 " pdb=" C PHE C 107 " pdb=" N THR C 108 " pdb=" CA THR C 108 " ideal model delta harmonic sigma weight residual 180.00 156.30 23.70 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 18007 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3749 0.060 - 0.120: 695 0.120 - 0.180: 95 0.180 - 0.239: 9 0.239 - 0.299: 3 Chirality restraints: 4551 Sorted by residual: chirality pdb=" CA LYS F 147 " pdb=" N LYS F 147 " pdb=" C LYS F 147 " pdb=" CB LYS F 147 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA PHE B 75 " pdb=" N PHE B 75 " pdb=" C PHE B 75 " pdb=" CB PHE B 75 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA PRO B 73 " pdb=" N PRO B 73 " pdb=" C PRO B 73 " pdb=" CB PRO B 73 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 4548 not shown) Planarity restraints: 5118 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 182 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C VAL B 182 " 0.056 2.00e-02 2.50e+03 pdb=" O VAL B 182 " -0.021 2.00e-02 2.50e+03 pdb=" N ALA B 183 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 217 " 0.014 2.00e-02 2.50e+03 2.72e-02 7.41e+00 pdb=" C ASP C 217 " -0.047 2.00e-02 2.50e+03 pdb=" O ASP C 217 " 0.018 2.00e-02 2.50e+03 pdb=" N SER C 218 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 265 " -0.013 2.00e-02 2.50e+03 2.57e-02 6.58e+00 pdb=" C SER C 265 " 0.044 2.00e-02 2.50e+03 pdb=" O SER C 265 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL C 266 " -0.015 2.00e-02 2.50e+03 ... (remaining 5115 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 819 2.70 - 3.25: 31365 3.25 - 3.80: 47787 3.80 - 4.35: 64825 4.35 - 4.90: 100660 Nonbonded interactions: 245456 Sorted by model distance: nonbonded pdb=" OH TYR B 81 " pdb=" O PRO B 118 " model vdw 2.149 3.040 nonbonded pdb=" OG1 THR I 91 " pdb=" OG1 THR I 171 " model vdw 2.236 3.040 nonbonded pdb=" O ARG G 157 " pdb=" OG1 THR G 160 " model vdw 2.262 3.040 nonbonded pdb=" OG SER M 254 " pdb=" OD1 ASN M 256 " model vdw 2.275 3.040 nonbonded pdb=" OG SER J 91 " pdb=" OD1 ASN J 103 " model vdw 2.304 3.040 ... (remaining 245451 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = (chain 'E' and resid 21 through 269) selection = (chain 'G' and resid 21 through 269) selection = (chain 'I' and resid 21 through 269) } ncs_group { reference = chain 'B' selection = (chain 'D' and resid 34 through 295) selection = chain 'F' selection = chain 'H' selection = chain 'J' } ncs_group { reference = (chain 'K' and resid 195 through 269) selection = chain 'M' selection = (chain 'Q' and resid 195 through 269) selection = (chain 'U' and resid 195 through 269) } ncs_group { reference = chain 'L' selection = (chain 'N' and resid 200 through 295) selection = (chain 'P' and resid 200 through 295) selection = (chain 'R' and resid 200 through 295) selection = (chain 'T' and resid 200 through 295) selection = (chain 'V' and resid 200 through 295) } ncs_group { reference = chain 'O' selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.900 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: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 26.620 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.070 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:7.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 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 : 0.005 0.082 28948 Z= 0.267 Angle : 0.906 14.425 39046 Z= 0.525 Chirality : 0.047 0.299 4551 Planarity : 0.007 0.054 5118 Dihedral : 11.461 89.470 11040 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.69 % Allowed : 8.18 % Favored : 91.13 % Rotamer: Outliers : 0.17 % Allowed : 1.12 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.13), residues: 3619 helix: 0.36 (0.11), residues: 1966 sheet: -1.92 (0.30), residues: 242 loop : -2.02 (0.16), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 88 TYR 0.031 0.003 TYR J 121 PHE 0.026 0.003 PHE G 39 TRP 0.015 0.002 TRP I 60 HIS 0.009 0.001 HIS J 69 Details of bonding type rmsd covalent geometry : bond 0.00510 (28948) covalent geometry : angle 0.90613 (39046) hydrogen bonds : bond 0.13689 ( 1863) hydrogen bonds : angle 7.10156 ( 5442) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 855 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 850 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 122 ILE cc_start: 0.6868 (mm) cc_final: 0.6581 (tt) REVERT: E 125 GLU cc_start: 0.7043 (tp30) cc_final: 0.6555 (tp30) REVERT: E 149 GLN cc_start: 0.8346 (mm-40) cc_final: 0.8145 (mm110) REVERT: E 205 GLN cc_start: 0.8409 (mm-40) cc_final: 0.8113 (mm110) REVERT: E 208 LYS cc_start: 0.8181 (mttt) cc_final: 0.7897 (mtmm) REVERT: E 237 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7588 (mm-30) REVERT: E 250 GLN cc_start: 0.8309 (mm-40) cc_final: 0.8075 (mm-40) REVERT: C 145 LEU cc_start: 0.8078 (mt) cc_final: 0.7837 (mt) REVERT: A 213 SER cc_start: 0.8708 (p) cc_final: 0.8368 (m) REVERT: U 255 ARG cc_start: 0.7943 (mtt180) cc_final: 0.7683 (mtt180) REVERT: S 204 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7152 (mm-30) REVERT: O 215 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7539 (mt-10) REVERT: I 149 GLN cc_start: 0.8276 (tp40) cc_final: 0.7634 (tp40) REVERT: I 195 ARG cc_start: 0.7164 (tmm160) cc_final: 0.6473 (tmm160) REVERT: I 198 PHE cc_start: 0.8159 (m-80) cc_final: 0.7934 (m-10) REVERT: I 218 SER cc_start: 0.8210 (p) cc_final: 0.8001 (p) REVERT: I 239 ARG cc_start: 0.8519 (mmt-90) cc_final: 0.8160 (mtp85) REVERT: G 34 HIS cc_start: 0.6473 (m-70) cc_final: 0.6203 (m-70) REVERT: G 58 ILE cc_start: 0.7545 (mt) cc_final: 0.7183 (pp) REVERT: G 76 VAL cc_start: 0.8926 (t) cc_final: 0.8696 (m) REVERT: G 222 GLU cc_start: 0.8051 (tp30) cc_final: 0.7782 (tp30) REVERT: F 127 ASP cc_start: 0.7808 (t0) cc_final: 0.7295 (t0) REVERT: F 231 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7707 (mm-30) REVERT: D 119 SER cc_start: 0.7520 (p) cc_final: 0.6999 (p) REVERT: D 120 MET cc_start: 0.7411 (mmm) cc_final: 0.6957 (mmm) REVERT: D 170 GLU cc_start: 0.6971 (mt-10) cc_final: 0.6767 (mt-10) REVERT: D 236 LYS cc_start: 0.7907 (ttpt) cc_final: 0.7693 (ttpt) REVERT: D 274 THR cc_start: 0.8342 (p) cc_final: 0.7991 (t) REVERT: B 231 GLU cc_start: 0.8016 (tp30) cc_final: 0.7765 (tp30) REVERT: B 252 ARG cc_start: 0.8345 (tpt90) cc_final: 0.8089 (tpt90) REVERT: T 219 GLN cc_start: 0.7904 (tp40) cc_final: 0.7621 (tp40) REVERT: R 236 LYS cc_start: 0.7920 (tttp) cc_final: 0.7687 (tttp) REVERT: R 240 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7353 (mt-10) REVERT: L 252 ARG cc_start: 0.8274 (tpt90) cc_final: 0.8064 (tmt170) REVERT: L 289 ARG cc_start: 0.7721 (tpt170) cc_final: 0.7507 (tpt170) REVERT: J 167 GLU cc_start: 0.9232 (mt-10) cc_final: 0.8903 (mt-10) REVERT: J 204 GLN cc_start: 0.7495 (tt0) cc_final: 0.7212 (tt0) REVERT: J 222 ARG cc_start: 0.8262 (tpt170) cc_final: 0.7759 (mmm160) REVERT: J 225 ILE cc_start: 0.8447 (mt) cc_final: 0.8207 (mm) REVERT: J 231 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7508 (mm-30) REVERT: J 236 LYS cc_start: 0.7406 (mttt) cc_final: 0.7164 (mttt) REVERT: J 274 THR cc_start: 0.8613 (t) cc_final: 0.8348 (p) REVERT: J 293 SER cc_start: 0.8021 (m) cc_final: 0.7796 (m) REVERT: H 109 LEU cc_start: 0.6671 (mt) cc_final: 0.6209 (tm) REVERT: H 163 LEU cc_start: 0.8249 (mt) cc_final: 0.7762 (mt) REVERT: H 216 LYS cc_start: 0.8353 (ttpp) cc_final: 0.8137 (ttpp) REVERT: H 231 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7357 (mm-30) REVERT: H 252 ARG cc_start: 0.8260 (tpt90) cc_final: 0.8059 (mmm160) outliers start: 5 outliers final: 4 residues processed: 855 average time/residue: 0.7939 time to fit residues: 769.4821 Evaluate side-chains 746 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 742 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain B residue 142 LYS Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain H residue 71 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 187 GLN E 256 ASN C 142 GLN ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN C 250 GLN Q 256 ASN M 226 ASN ** G 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 191 GLN F 245 ASN F 283 GLN ** D 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 GLN D 204 GLN D 205 GLN D 208 GLN D 245 ASN D 277 ASN V 269 ASN V 277 ASN ** V 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 277 ASN N 269 ASN L 221 GLN L 227 GLN L 281 ASN J 211 GLN J 269 ASN H 100 GLN H 219 GLN H 269 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.206550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.163772 restraints weight = 50554.604| |-----------------------------------------------------------------------------| r_work (start): 0.4068 rms_B_bonded: 2.61 r_work: 0.3917 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 28948 Z= 0.214 Angle : 0.754 13.856 39046 Z= 0.401 Chirality : 0.046 0.324 4551 Planarity : 0.005 0.062 5118 Dihedral : 5.431 42.345 4014 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.55 % Allowed : 6.19 % Favored : 93.26 % Rotamer: Outliers : 2.35 % Allowed : 9.23 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.45 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.13), residues: 3619 helix: 0.98 (0.11), residues: 1956 sheet: -1.71 (0.31), residues: 249 loop : -1.82 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 171 TYR 0.016 0.002 TYR J 77 PHE 0.037 0.002 PHE G 96 TRP 0.009 0.001 TRP B 74 HIS 0.007 0.001 HIS E 55 Details of bonding type rmsd covalent geometry : bond 0.00444 (28948) covalent geometry : angle 0.75397 (39046) hydrogen bonds : bond 0.07590 ( 1863) hydrogen bonds : angle 5.67494 ( 5442) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 839 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 768 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 70 ARG cc_start: 0.7374 (ptt180) cc_final: 0.7150 (mtm-85) REVERT: E 84 ASP cc_start: 0.7152 (p0) cc_final: 0.6887 (p0) REVERT: E 170 LEU cc_start: 0.8104 (mp) cc_final: 0.7882 (mt) REVERT: E 205 GLN cc_start: 0.8692 (mm-40) cc_final: 0.8417 (mm110) REVERT: E 250 GLN cc_start: 0.8503 (mm-40) cc_final: 0.8277 (mm-40) REVERT: C 93 ARG cc_start: 0.7773 (mmm160) cc_final: 0.7468 (mmm-85) REVERT: C 148 ARG cc_start: 0.7637 (tmm-80) cc_final: 0.6987 (tpm-80) REVERT: A 213 SER cc_start: 0.8423 (p) cc_final: 0.8129 (m) REVERT: U 255 ARG cc_start: 0.7810 (mtt180) cc_final: 0.7354 (mtt180) REVERT: S 204 GLU cc_start: 0.7355 (mm-30) cc_final: 0.6937 (mm-30) REVERT: O 250 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8361 (mm110) REVERT: K 222 GLU cc_start: 0.7593 (tp30) cc_final: 0.7387 (tp30) REVERT: I 72 ARG cc_start: 0.8355 (mmm160) cc_final: 0.7974 (mmp80) REVERT: I 106 ILE cc_start: 0.8370 (mt) cc_final: 0.7890 (mt) REVERT: I 115 ASP cc_start: 0.7521 (p0) cc_final: 0.6710 (p0) REVERT: I 127 LEU cc_start: 0.7802 (mt) cc_final: 0.7560 (mt) REVERT: I 149 GLN cc_start: 0.8275 (tp40) cc_final: 0.7704 (tp40) REVERT: I 195 ARG cc_start: 0.6974 (tmm160) cc_final: 0.6390 (tmm160) REVERT: I 217 ASP cc_start: 0.7609 (m-30) cc_final: 0.7374 (m-30) REVERT: I 239 ARG cc_start: 0.8504 (mmt-90) cc_final: 0.7926 (mtp85) REVERT: I 258 THR cc_start: 0.8641 (m) cc_final: 0.8435 (m) REVERT: G 58 ILE cc_start: 0.7991 (mt) cc_final: 0.7783 (pp) REVERT: G 222 GLU cc_start: 0.7994 (tp30) cc_final: 0.7661 (tp30) REVERT: G 239 ARG cc_start: 0.8547 (mmt180) cc_final: 0.7795 (tpp-160) REVERT: F 139 GLU cc_start: 0.6992 (mm-30) cc_final: 0.6614 (mm-30) REVERT: F 157 ARG cc_start: 0.7263 (mtp-110) cc_final: 0.6776 (ttp-170) REVERT: F 192 GLU cc_start: 0.7154 (tp30) cc_final: 0.6773 (tp30) REVERT: F 231 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7521 (mm-30) REVERT: F 268 GLN cc_start: 0.8260 (mp10) cc_final: 0.8023 (mt0) REVERT: D 101 MET cc_start: 0.7027 (pmm) cc_final: 0.6064 (tmm) REVERT: D 111 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.7512 (ptm160) REVERT: D 120 MET cc_start: 0.7620 (mmm) cc_final: 0.7157 (mmm) REVERT: D 189 PHE cc_start: 0.8707 (m-80) cc_final: 0.8438 (m-80) REVERT: D 236 LYS cc_start: 0.8305 (ttpt) cc_final: 0.8027 (ttpt) REVERT: B 222 ARG cc_start: 0.7189 (ttp80) cc_final: 0.6946 (ttp80) REVERT: B 231 GLU cc_start: 0.7896 (tp30) cc_final: 0.7641 (tp30) REVERT: B 252 ARG cc_start: 0.8633 (tpt90) cc_final: 0.8225 (mmm160) REVERT: V 268 GLN cc_start: 0.7900 (mm-40) cc_final: 0.7283 (mm110) REVERT: T 219 GLN cc_start: 0.8024 (tp40) cc_final: 0.7762 (tp40) REVERT: L 223 GLN cc_start: 0.7521 (tp40) cc_final: 0.7297 (tp40) REVERT: L 252 ARG cc_start: 0.8418 (tpt90) cc_final: 0.8155 (tmt170) REVERT: J 101 MET cc_start: 0.6888 (mtp) cc_final: 0.6512 (mtp) REVERT: J 120 MET cc_start: 0.6092 (mtp) cc_final: 0.5228 (mtp) REVERT: J 166 ARG cc_start: 0.8815 (ttp80) cc_final: 0.8614 (ttp80) REVERT: J 176 SER cc_start: 0.8180 (OUTLIER) cc_final: 0.7300 (p) REVERT: J 220 GLU cc_start: 0.7110 (tt0) cc_final: 0.6810 (tt0) REVERT: J 222 ARG cc_start: 0.8115 (tpt170) cc_final: 0.7673 (mmm160) REVERT: J 231 GLU cc_start: 0.7105 (mm-30) cc_final: 0.6752 (mm-30) REVERT: J 236 LYS cc_start: 0.7648 (mttt) cc_final: 0.7320 (mttt) REVERT: J 240 GLU cc_start: 0.7205 (pm20) cc_final: 0.6984 (pm20) REVERT: J 274 THR cc_start: 0.8617 (t) cc_final: 0.8397 (p) REVERT: J 285 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7738 (mm-30) REVERT: H 88 ARG cc_start: 0.7365 (ttt180) cc_final: 0.7119 (ttt180) REVERT: H 100 GLN cc_start: 0.5509 (tp-100) cc_final: 0.5100 (tp-100) REVERT: H 109 LEU cc_start: 0.6897 (mt) cc_final: 0.6378 (tm) REVERT: H 167 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7249 (mt-10) REVERT: H 216 LYS cc_start: 0.8111 (ttpp) cc_final: 0.7773 (ttpp) REVERT: H 231 GLU cc_start: 0.7378 (mm-30) cc_final: 0.7096 (mm-30) REVERT: H 249 ILE cc_start: 0.8441 (mt) cc_final: 0.8235 (mm) REVERT: H 268 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.7412 (mm-40) REVERT: H 270 ARG cc_start: 0.7501 (mmm160) cc_final: 0.7180 (mmm160) outliers start: 71 outliers final: 31 residues processed: 796 average time/residue: 0.8816 time to fit residues: 792.6865 Evaluate side-chains 762 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 727 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 194 GLU Chi-restraints excluded: chain E residue 242 GLU Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 206 GLN Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain S residue 258 THR Chi-restraints excluded: chain Q residue 242 GLU Chi-restraints excluded: chain O residue 250 GLN Chi-restraints excluded: chain I residue 66 ILE Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 254 SER Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 236 ILE Chi-restraints excluded: chain F residue 190 SER Chi-restraints excluded: chain D residue 111 ARG Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain V residue 226 VAL Chi-restraints excluded: chain T residue 252 ARG Chi-restraints excluded: chain P residue 262 LYS Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 110 SER Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 143 SER Chi-restraints excluded: chain J residue 176 SER Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 75 PHE Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 268 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 290 optimal weight: 0.5980 chunk 168 optimal weight: 0.4980 chunk 138 optimal weight: 1.9990 chunk 225 optimal weight: 5.9990 chunk 301 optimal weight: 1.9990 chunk 198 optimal weight: 0.6980 chunk 350 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 327 optimal weight: 0.7980 chunk 245 optimal weight: 0.9980 chunk 163 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 55 HIS E 205 GLN C 62 GLN ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN A 206 GLN M 226 ASN ** I 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN F 205 GLN F 219 GLN F 227 GLN F 245 ASN F 269 ASN D 100 GLN ** D 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 GLN D 208 GLN ** D 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 ASN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 277 ASN ** V 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 277 ASN N 269 ASN L 227 GLN L 259 ASN L 283 GLN ** J 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 ASN H 219 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.205648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.162669 restraints weight = 50280.643| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 2.60 r_work: 0.3889 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 28948 Z= 0.202 Angle : 0.697 13.140 39046 Z= 0.372 Chirality : 0.045 0.248 4551 Planarity : 0.005 0.064 5118 Dihedral : 5.262 42.883 4006 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.71 % Favored : 92.84 % Rotamer: Outliers : 2.94 % Allowed : 11.64 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.45 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.14), residues: 3619 helix: 1.15 (0.11), residues: 1930 sheet: -1.77 (0.31), residues: 272 loop : -1.77 (0.16), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 111 TYR 0.031 0.002 TYR J 128 PHE 0.040 0.002 PHE A 107 TRP 0.009 0.001 TRP F 74 HIS 0.005 0.001 HIS J 69 Details of bonding type rmsd covalent geometry : bond 0.00416 (28948) covalent geometry : angle 0.69664 (39046) hydrogen bonds : bond 0.07176 ( 1863) hydrogen bonds : angle 5.40049 ( 5442) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 822 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 733 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 70 ARG cc_start: 0.7445 (ptt180) cc_final: 0.7169 (mtm-85) REVERT: E 149 GLN cc_start: 0.8279 (mm110) cc_final: 0.8055 (mm110) REVERT: E 237 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7728 (mm-30) REVERT: C 72 ARG cc_start: 0.6301 (tpp80) cc_final: 0.5969 (mpp80) REVERT: C 105 ARG cc_start: 0.7888 (tpt170) cc_final: 0.7302 (tpt170) REVERT: C 148 ARG cc_start: 0.7632 (tmm-80) cc_final: 0.7091 (tpm-80) REVERT: U 255 ARG cc_start: 0.7819 (mtt180) cc_final: 0.7453 (mtt180) REVERT: S 204 GLU cc_start: 0.7326 (mm-30) cc_final: 0.6927 (mm-30) REVERT: S 250 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.7952 (mp10) REVERT: O 246 ASP cc_start: 0.7896 (t0) cc_final: 0.7658 (t0) REVERT: I 72 ARG cc_start: 0.8271 (mmm160) cc_final: 0.7975 (mmp-170) REVERT: I 115 ASP cc_start: 0.7050 (p0) cc_final: 0.6735 (p0) REVERT: I 126 ILE cc_start: 0.7508 (mp) cc_final: 0.7280 (mt) REVERT: I 127 LEU cc_start: 0.7867 (mt) cc_final: 0.7609 (mt) REVERT: I 157 ARG cc_start: 0.8053 (mtp-110) cc_final: 0.7669 (mtp-110) REVERT: I 215 GLU cc_start: 0.7307 (tt0) cc_final: 0.7045 (tt0) REVERT: I 222 GLU cc_start: 0.7858 (tp30) cc_final: 0.7614 (tp30) REVERT: I 255 ARG cc_start: 0.7623 (mtt180) cc_final: 0.7375 (mtt180) REVERT: G 58 ILE cc_start: 0.8061 (mt) cc_final: 0.7752 (pp) REVERT: G 222 GLU cc_start: 0.8065 (tp30) cc_final: 0.7725 (tp30) REVERT: F 124 LEU cc_start: 0.8445 (tp) cc_final: 0.8238 (tm) REVERT: F 157 ARG cc_start: 0.7270 (mtp-110) cc_final: 0.6735 (ttm-80) REVERT: F 168 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8085 (mt) REVERT: F 192 GLU cc_start: 0.7220 (tp30) cc_final: 0.6725 (tp30) REVERT: F 198 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7439 (mt-10) REVERT: F 202 VAL cc_start: 0.8632 (t) cc_final: 0.8355 (m) REVERT: D 120 MET cc_start: 0.7489 (mmm) cc_final: 0.7115 (mmm) REVERT: D 189 PHE cc_start: 0.8745 (m-80) cc_final: 0.8489 (m-80) REVERT: D 236 LYS cc_start: 0.8504 (ttpt) cc_final: 0.8175 (ttpt) REVERT: B 101 MET cc_start: 0.5805 (mmm) cc_final: 0.5599 (mmm) REVERT: B 177 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7437 (mp) REVERT: B 222 ARG cc_start: 0.7307 (ttp80) cc_final: 0.7070 (ttp80) REVERT: B 223 GLN cc_start: 0.7708 (tp40) cc_final: 0.7349 (tp40) REVERT: B 231 GLU cc_start: 0.7909 (tp30) cc_final: 0.7617 (tp30) REVERT: B 243 SER cc_start: 0.8258 (m) cc_final: 0.8033 (m) REVERT: B 252 ARG cc_start: 0.8576 (tpt90) cc_final: 0.8126 (tpt90) REVERT: V 227 GLN cc_start: 0.8359 (mt0) cc_final: 0.8156 (tp40) REVERT: V 268 GLN cc_start: 0.7910 (mm-40) cc_final: 0.7561 (mm110) REVERT: T 219 GLN cc_start: 0.7998 (tp40) cc_final: 0.7751 (tp40) REVERT: T 227 GLN cc_start: 0.8043 (mt0) cc_final: 0.7741 (mt0) REVERT: R 225 ILE cc_start: 0.8227 (mm) cc_final: 0.8012 (mm) REVERT: R 255 ARG cc_start: 0.8138 (mtt180) cc_final: 0.7922 (ttt180) REVERT: R 284 ASP cc_start: 0.7644 (t70) cc_final: 0.7398 (t70) REVERT: L 223 GLN cc_start: 0.7508 (tp40) cc_final: 0.7276 (tp40) REVERT: L 236 LYS cc_start: 0.8237 (mttt) cc_final: 0.7979 (tttt) REVERT: J 101 MET cc_start: 0.6771 (mtp) cc_final: 0.6405 (mtp) REVERT: J 120 MET cc_start: 0.5938 (mtp) cc_final: 0.5099 (mtp) REVERT: J 167 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8572 (mt-10) REVERT: J 176 SER cc_start: 0.8291 (OUTLIER) cc_final: 0.7292 (p) REVERT: J 201 GLN cc_start: 0.7459 (OUTLIER) cc_final: 0.7121 (mp10) REVERT: J 220 GLU cc_start: 0.7170 (tt0) cc_final: 0.6794 (tt0) REVERT: J 221 GLN cc_start: 0.7829 (tt0) cc_final: 0.7572 (tt0) REVERT: J 222 ARG cc_start: 0.8143 (tpt170) cc_final: 0.7661 (mmm160) REVERT: J 236 LYS cc_start: 0.7663 (mttt) cc_final: 0.7458 (mttt) REVERT: J 285 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7716 (mm-30) REVERT: H 109 LEU cc_start: 0.7020 (mt) cc_final: 0.6549 (tm) REVERT: H 175 PHE cc_start: 0.8850 (m-80) cc_final: 0.8644 (m-80) REVERT: H 201 GLN cc_start: 0.7134 (mm-40) cc_final: 0.6912 (mm-40) REVERT: H 216 LYS cc_start: 0.8135 (ttpp) cc_final: 0.7882 (ttpp) REVERT: H 231 GLU cc_start: 0.7462 (mm-30) cc_final: 0.7129 (mm-30) REVERT: H 240 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7594 (tt0) REVERT: H 268 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.7407 (mm-40) outliers start: 89 outliers final: 42 residues processed: 768 average time/residue: 0.7902 time to fit residues: 687.3480 Evaluate side-chains 757 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 708 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 242 GLU Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 219 LYS Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain U residue 267 LEU Chi-restraints excluded: chain S residue 250 GLN Chi-restraints excluded: chain S residue 258 THR Chi-restraints excluded: chain Q residue 267 LEU Chi-restraints excluded: chain M residue 258 THR Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 142 GLN Chi-restraints excluded: chain I residue 254 SER Chi-restraints excluded: chain G residue 68 ASP Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 190 SER Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain V residue 238 LEU Chi-restraints excluded: chain T residue 252 ARG Chi-restraints excluded: chain N residue 249 ILE Chi-restraints excluded: chain J residue 51 PHE Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 110 SER Chi-restraints excluded: chain J residue 117 LEU Chi-restraints excluded: chain J residue 176 SER Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 201 GLN Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain J residue 293 SER Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 75 PHE Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 240 GLU Chi-restraints excluded: chain H residue 268 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 73 optimal weight: 8.9990 chunk 161 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 71 optimal weight: 0.5980 chunk 298 optimal weight: 9.9990 chunk 310 optimal weight: 6.9990 chunk 272 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 chunk 286 optimal weight: 0.9980 chunk 344 optimal weight: 0.9990 chunk 52 optimal weight: 20.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN A 190 GLN M 226 ASN ** I 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 34 HIS G 264 GLN F 219 GLN F 227 GLN F 245 ASN D 76 GLN ** D 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 GLN D 208 GLN ** D 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 ASN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 277 ASN ** V 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 277 ASN L 269 ASN L 283 GLN ** J 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.204524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.161890 restraints weight = 49846.712| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 2.66 r_work: 0.3851 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 28948 Z= 0.223 Angle : 0.697 14.986 39046 Z= 0.371 Chirality : 0.045 0.328 4551 Planarity : 0.005 0.069 5118 Dihedral : 5.259 43.611 4006 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.55 % Favored : 93.06 % Rotamer: Outliers : 3.31 % Allowed : 13.53 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.42 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.14), residues: 3619 helix: 1.16 (0.11), residues: 1930 sheet: -1.96 (0.29), residues: 306 loop : -1.76 (0.16), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 253 TYR 0.023 0.002 TYR D 128 PHE 0.018 0.001 PHE I 107 TRP 0.008 0.001 TRP F 74 HIS 0.003 0.001 HIS E 172 Details of bonding type rmsd covalent geometry : bond 0.00474 (28948) covalent geometry : angle 0.69692 (39046) hydrogen bonds : bond 0.07157 ( 1863) hydrogen bonds : angle 5.36390 ( 5442) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 839 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 739 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 149 GLN cc_start: 0.8349 (mm110) cc_final: 0.8128 (mm110) REVERT: E 167 ASP cc_start: 0.7139 (t0) cc_final: 0.6937 (t0) REVERT: E 237 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7618 (mm-30) REVERT: E 250 GLN cc_start: 0.8611 (mm-40) cc_final: 0.8389 (mm-40) REVERT: C 72 ARG cc_start: 0.6291 (OUTLIER) cc_final: 0.5817 (mpp80) REVERT: C 148 ARG cc_start: 0.7621 (tmm-80) cc_final: 0.7152 (tpm-80) REVERT: C 149 GLN cc_start: 0.8252 (tt0) cc_final: 0.8026 (pt0) REVERT: A 78 VAL cc_start: 0.4091 (OUTLIER) cc_final: 0.3693 (t) REVERT: A 150 VAL cc_start: 0.5486 (t) cc_final: 0.5160 (t) REVERT: U 246 ASP cc_start: 0.7730 (m-30) cc_final: 0.7470 (m-30) REVERT: S 204 GLU cc_start: 0.7350 (mm-30) cc_final: 0.6911 (mm-30) REVERT: S 246 ASP cc_start: 0.8005 (t0) cc_final: 0.7727 (t0) REVERT: O 246 ASP cc_start: 0.7967 (t0) cc_final: 0.7751 (t0) REVERT: O 255 ARG cc_start: 0.7961 (mtt180) cc_final: 0.7738 (mtt90) REVERT: I 127 LEU cc_start: 0.7948 (mt) cc_final: 0.7587 (mt) REVERT: I 142 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7680 (tt0) REVERT: I 149 GLN cc_start: 0.8148 (tp40) cc_final: 0.7723 (tp40) REVERT: I 157 ARG cc_start: 0.8220 (mtp-110) cc_final: 0.7971 (mtp-110) REVERT: I 215 GLU cc_start: 0.7227 (tt0) cc_final: 0.6995 (tt0) REVERT: I 222 GLU cc_start: 0.7852 (tp30) cc_final: 0.7637 (tp30) REVERT: I 255 ARG cc_start: 0.7751 (mtt180) cc_final: 0.7510 (mtt180) REVERT: G 126 ILE cc_start: 0.6961 (mt) cc_final: 0.6488 (tt) REVERT: G 222 GLU cc_start: 0.8008 (tp30) cc_final: 0.7681 (tp30) REVERT: F 157 ARG cc_start: 0.7284 (mtp-110) cc_final: 0.7070 (ttm110) REVERT: F 168 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8206 (mt) REVERT: F 192 GLU cc_start: 0.7209 (tp30) cc_final: 0.6735 (tp30) REVERT: F 198 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7514 (mt-10) REVERT: F 202 VAL cc_start: 0.8653 (t) cc_final: 0.8369 (m) REVERT: F 218 LYS cc_start: 0.7591 (OUTLIER) cc_final: 0.7284 (mtmm) REVERT: F 268 GLN cc_start: 0.8321 (mp10) cc_final: 0.7939 (mt0) REVERT: D 101 MET cc_start: 0.7537 (pmm) cc_final: 0.6881 (mmm) REVERT: D 104 ILE cc_start: 0.8703 (mp) cc_final: 0.8303 (tt) REVERT: D 111 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7590 (ptm160) REVERT: D 120 MET cc_start: 0.7643 (mmm) cc_final: 0.7220 (mmm) REVERT: D 189 PHE cc_start: 0.8719 (m-80) cc_final: 0.8505 (m-80) REVERT: D 218 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8347 (mtmm) REVERT: D 231 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7614 (mm-30) REVERT: D 236 LYS cc_start: 0.8639 (ttpt) cc_final: 0.8299 (ttpt) REVERT: B 101 MET cc_start: 0.5838 (mmm) cc_final: 0.5573 (mmm) REVERT: B 231 GLU cc_start: 0.7978 (tp30) cc_final: 0.7666 (tp30) REVERT: B 243 SER cc_start: 0.8289 (m) cc_final: 0.8066 (m) REVERT: B 252 ARG cc_start: 0.8594 (tpt90) cc_final: 0.8173 (tpt90) REVERT: V 227 GLN cc_start: 0.8374 (mt0) cc_final: 0.8160 (tp40) REVERT: T 219 GLN cc_start: 0.8027 (tp40) cc_final: 0.7754 (tp40) REVERT: R 284 ASP cc_start: 0.7809 (t70) cc_final: 0.7522 (t70) REVERT: N 252 ARG cc_start: 0.8737 (tpt90) cc_final: 0.8272 (tmt170) REVERT: L 223 GLN cc_start: 0.7557 (tp40) cc_final: 0.7281 (tp40) REVERT: L 236 LYS cc_start: 0.8289 (mttt) cc_final: 0.8052 (tttt) REVERT: J 101 MET cc_start: 0.6634 (mtp) cc_final: 0.6264 (mtp) REVERT: J 167 GLU cc_start: 0.8914 (mt-10) cc_final: 0.8557 (mt-10) REVERT: J 176 SER cc_start: 0.8292 (m) cc_final: 0.7972 (p) REVERT: J 201 GLN cc_start: 0.7560 (OUTLIER) cc_final: 0.7356 (pm20) REVERT: J 220 GLU cc_start: 0.7237 (tt0) cc_final: 0.6921 (tt0) REVERT: J 222 ARG cc_start: 0.8094 (tpt170) cc_final: 0.7618 (mmm160) REVERT: J 285 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7659 (mm-30) REVERT: H 88 ARG cc_start: 0.7542 (ttt180) cc_final: 0.7326 (ttt180) REVERT: H 109 LEU cc_start: 0.7141 (mt) cc_final: 0.6613 (tm) REVERT: H 165 ARG cc_start: 0.7845 (ptp-170) cc_final: 0.7619 (ptp-170) REVERT: H 167 GLU cc_start: 0.8393 (mm-30) cc_final: 0.7929 (mm-30) REVERT: H 171 ARG cc_start: 0.7793 (mtt90) cc_final: 0.7206 (mtt90) REVERT: H 182 VAL cc_start: 0.5426 (t) cc_final: 0.5128 (m) REVERT: H 185 THR cc_start: 0.6062 (OUTLIER) cc_final: 0.5807 (p) REVERT: H 231 GLU cc_start: 0.7489 (mm-30) cc_final: 0.7171 (mm-30) REVERT: H 268 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.7345 (mm-40) REVERT: H 270 ARG cc_start: 0.7662 (mmm160) cc_final: 0.7218 (mmm160) outliers start: 100 outliers final: 54 residues processed: 776 average time/residue: 0.7746 time to fit residues: 681.4956 Evaluate side-chains 785 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 721 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 227 SER Chi-restraints excluded: chain E residue 242 GLU Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 219 LYS Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain U residue 254 SER Chi-restraints excluded: chain U residue 267 LEU Chi-restraints excluded: chain S residue 258 THR Chi-restraints excluded: chain Q residue 242 GLU Chi-restraints excluded: chain O residue 242 GLU Chi-restraints excluded: chain M residue 258 THR Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 142 GLN Chi-restraints excluded: chain I residue 183 VAL Chi-restraints excluded: chain I residue 217 ASP Chi-restraints excluded: chain I residue 254 SER Chi-restraints excluded: chain G residue 68 ASP Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 190 SER Chi-restraints excluded: chain F residue 218 LYS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 ARG Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 218 LYS Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain V residue 238 LEU Chi-restraints excluded: chain V residue 295 ILE Chi-restraints excluded: chain T residue 252 ARG Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain P residue 262 LYS Chi-restraints excluded: chain J residue 51 PHE Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 121 TYR Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 201 GLN Chi-restraints excluded: chain J residue 293 SER Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 75 PHE Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 190 SER Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 236 LYS Chi-restraints excluded: chain H residue 255 ARG Chi-restraints excluded: chain H residue 268 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 121 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 163 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 334 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 331 optimal weight: 0.9990 chunk 170 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 264 GLN ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 GLN ** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 226 ASN G 34 HIS F 219 GLN F 227 GLN ** D 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 GLN D 208 GLN D 259 ASN ** D 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 ASN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 268 GLN V 277 ASN ** V 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 221 GLN T 227 GLN T 277 ASN R 277 ASN L 283 GLN ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.204885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.161216 restraints weight = 49890.738| |-----------------------------------------------------------------------------| r_work (start): 0.4025 rms_B_bonded: 2.68 r_work: 0.3862 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 28948 Z= 0.211 Angle : 0.690 12.742 39046 Z= 0.366 Chirality : 0.045 0.339 4551 Planarity : 0.005 0.069 5118 Dihedral : 5.178 44.153 4006 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.66 % Favored : 92.93 % Rotamer: Outliers : 3.31 % Allowed : 14.88 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.42 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.14), residues: 3619 helix: 1.18 (0.11), residues: 1925 sheet: -1.88 (0.29), residues: 310 loop : -1.73 (0.16), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 111 TYR 0.043 0.002 TYR J 128 PHE 0.027 0.001 PHE E 134 TRP 0.008 0.001 TRP F 74 HIS 0.003 0.001 HIS A 172 Details of bonding type rmsd covalent geometry : bond 0.00446 (28948) covalent geometry : angle 0.69047 (39046) hydrogen bonds : bond 0.06996 ( 1863) hydrogen bonds : angle 5.26959 ( 5442) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 828 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 728 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 149 GLN cc_start: 0.8286 (mm110) cc_final: 0.8035 (mm110) REVERT: E 237 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7662 (mm-30) REVERT: E 250 GLN cc_start: 0.8602 (mm-40) cc_final: 0.8362 (mm-40) REVERT: C 148 ARG cc_start: 0.7624 (tmm-80) cc_final: 0.7270 (tpm-80) REVERT: A 78 VAL cc_start: 0.4422 (OUTLIER) cc_final: 0.4118 (t) REVERT: A 88 VAL cc_start: 0.6572 (m) cc_final: 0.5999 (p) REVERT: A 93 ARG cc_start: 0.5548 (mpp-170) cc_final: 0.5168 (mpp-170) REVERT: A 150 VAL cc_start: 0.5449 (t) cc_final: 0.5237 (t) REVERT: U 246 ASP cc_start: 0.7739 (m-30) cc_final: 0.7490 (m-30) REVERT: S 246 ASP cc_start: 0.8023 (t0) cc_final: 0.7736 (t0) REVERT: O 246 ASP cc_start: 0.7961 (t0) cc_final: 0.7756 (t0) REVERT: O 255 ARG cc_start: 0.7959 (mtt180) cc_final: 0.7712 (mtt90) REVERT: I 102 GLN cc_start: 0.8905 (tp40) cc_final: 0.8571 (tm-30) REVERT: I 127 LEU cc_start: 0.7963 (mt) cc_final: 0.7603 (mt) REVERT: I 142 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7477 (tt0) REVERT: I 157 ARG cc_start: 0.8252 (mtp-110) cc_final: 0.7961 (mtp-110) REVERT: I 175 PHE cc_start: 0.8751 (m-10) cc_final: 0.8550 (m-10) REVERT: I 222 GLU cc_start: 0.7854 (tp30) cc_final: 0.7631 (tp30) REVERT: I 246 ASP cc_start: 0.8043 (t0) cc_final: 0.7759 (t0) REVERT: I 255 ARG cc_start: 0.7732 (mtt180) cc_final: 0.7486 (mtt180) REVERT: G 222 GLU cc_start: 0.8006 (tp30) cc_final: 0.7667 (tp30) REVERT: F 157 ARG cc_start: 0.7184 (mtp-110) cc_final: 0.6968 (ttm110) REVERT: F 192 GLU cc_start: 0.7249 (tp30) cc_final: 0.6776 (tp30) REVERT: F 198 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7411 (mt-10) REVERT: F 202 VAL cc_start: 0.8661 (t) cc_final: 0.8383 (m) REVERT: F 218 LYS cc_start: 0.7525 (OUTLIER) cc_final: 0.7218 (mtmm) REVERT: F 252 ARG cc_start: 0.8773 (tpt90) cc_final: 0.7651 (mtp180) REVERT: F 268 GLN cc_start: 0.8301 (mp10) cc_final: 0.7916 (mt0) REVERT: D 101 MET cc_start: 0.7555 (pmm) cc_final: 0.7043 (mmm) REVERT: D 111 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7584 (ptm160) REVERT: D 120 MET cc_start: 0.7611 (mmm) cc_final: 0.7235 (mmm) REVERT: D 189 PHE cc_start: 0.8699 (m-80) cc_final: 0.8492 (m-80) REVERT: D 218 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8352 (mtmm) REVERT: D 236 LYS cc_start: 0.8622 (ttpt) cc_final: 0.8283 (ttpt) REVERT: B 101 MET cc_start: 0.5839 (mmm) cc_final: 0.5548 (mmm) REVERT: B 231 GLU cc_start: 0.7997 (tp30) cc_final: 0.7687 (tp30) REVERT: B 243 SER cc_start: 0.8275 (m) cc_final: 0.8039 (m) REVERT: B 252 ARG cc_start: 0.8579 (tpt90) cc_final: 0.8159 (tpt90) REVERT: V 227 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.8133 (tt0) REVERT: V 294 LEU cc_start: 0.8870 (mt) cc_final: 0.8659 (mp) REVERT: T 219 GLN cc_start: 0.7973 (tp40) cc_final: 0.7709 (tp40) REVERT: T 227 GLN cc_start: 0.8108 (mt0) cc_final: 0.7432 (mt0) REVERT: R 255 ARG cc_start: 0.8213 (ttt180) cc_final: 0.7913 (ttt180) REVERT: R 268 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.7672 (mm-40) REVERT: R 284 ASP cc_start: 0.7785 (t70) cc_final: 0.7497 (t70) REVERT: N 252 ARG cc_start: 0.8722 (tpt90) cc_final: 0.8247 (tmt170) REVERT: L 223 GLN cc_start: 0.7510 (tp40) cc_final: 0.7233 (tp40) REVERT: L 236 LYS cc_start: 0.8270 (mttt) cc_final: 0.7935 (tttt) REVERT: J 101 MET cc_start: 0.6696 (mtp) cc_final: 0.6163 (mtp) REVERT: J 166 ARG cc_start: 0.8874 (ttp80) cc_final: 0.8373 (ttp80) REVERT: J 167 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8489 (mt-10) REVERT: J 176 SER cc_start: 0.8357 (m) cc_final: 0.7676 (p) REVERT: J 204 GLN cc_start: 0.7315 (tm-30) cc_final: 0.7059 (tm-30) REVERT: J 220 GLU cc_start: 0.7280 (tt0) cc_final: 0.6970 (tt0) REVERT: J 221 GLN cc_start: 0.7802 (tt0) cc_final: 0.7572 (tt0) REVERT: J 222 ARG cc_start: 0.8132 (tpt170) cc_final: 0.7695 (mmm160) REVERT: J 285 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7462 (mm-30) REVERT: H 109 LEU cc_start: 0.7126 (mt) cc_final: 0.6622 (tm) REVERT: H 165 ARG cc_start: 0.7810 (ptp-170) cc_final: 0.7602 (ptp-170) REVERT: H 171 ARG cc_start: 0.7637 (mtt90) cc_final: 0.7153 (ttt90) REVERT: H 182 VAL cc_start: 0.5361 (t) cc_final: 0.5089 (m) REVERT: H 185 THR cc_start: 0.6070 (OUTLIER) cc_final: 0.5589 (p) REVERT: H 231 GLU cc_start: 0.7497 (mm-30) cc_final: 0.7195 (mm-30) REVERT: H 268 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7323 (mm-40) REVERT: H 270 ARG cc_start: 0.7702 (mmm160) cc_final: 0.7274 (mmm160) outliers start: 100 outliers final: 57 residues processed: 766 average time/residue: 0.8792 time to fit residues: 760.7893 Evaluate side-chains 764 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 698 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 128 LYS Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 242 GLU Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 219 LYS Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain U residue 254 SER Chi-restraints excluded: chain U residue 267 LEU Chi-restraints excluded: chain S residue 250 GLN Chi-restraints excluded: chain S residue 258 THR Chi-restraints excluded: chain Q residue 242 GLU Chi-restraints excluded: chain Q residue 267 LEU Chi-restraints excluded: chain M residue 258 THR Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 142 GLN Chi-restraints excluded: chain I residue 183 VAL Chi-restraints excluded: chain I residue 254 SER Chi-restraints excluded: chain G residue 68 ASP Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 190 SER Chi-restraints excluded: chain F residue 218 LYS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 ARG Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 218 LYS Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain V residue 227 GLN Chi-restraints excluded: chain V residue 295 ILE Chi-restraints excluded: chain T residue 252 ARG Chi-restraints excluded: chain T residue 294 LEU Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain R residue 268 GLN Chi-restraints excluded: chain R residue 295 ILE Chi-restraints excluded: chain P residue 262 LYS Chi-restraints excluded: chain J residue 51 PHE Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 293 SER Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 75 PHE Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 236 LYS Chi-restraints excluded: chain H residue 255 ARG Chi-restraints excluded: chain H residue 268 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 3 optimal weight: 3.9990 chunk 224 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 241 optimal weight: 0.6980 chunk 317 optimal weight: 2.9990 chunk 222 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 295 optimal weight: 0.5980 chunk 192 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 226 ASN ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 34 HIS F 219 GLN F 223 GLN F 227 GLN ** D 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 GLN D 208 GLN ** D 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 ASN B 100 GLN B 227 GLN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 268 GLN V 277 ASN ** V 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 277 ASN R 277 ASN L 283 GLN ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 100 GLN J 259 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.203918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.159734 restraints weight = 49955.048| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 2.82 r_work: 0.3834 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 28948 Z= 0.215 Angle : 0.697 12.705 39046 Z= 0.368 Chirality : 0.045 0.339 4551 Planarity : 0.005 0.082 5118 Dihedral : 5.155 44.615 4006 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.39 % Allowed : 6.69 % Favored : 92.93 % Rotamer: Outliers : 3.77 % Allowed : 15.41 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.42 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.14), residues: 3619 helix: 1.21 (0.11), residues: 1903 sheet: -2.00 (0.28), residues: 329 loop : -1.66 (0.16), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG I 35 TYR 0.026 0.002 TYR J 128 PHE 0.027 0.001 PHE I 134 TRP 0.008 0.001 TRP F 74 HIS 0.006 0.001 HIS A 172 Details of bonding type rmsd covalent geometry : bond 0.00461 (28948) covalent geometry : angle 0.69702 (39046) hydrogen bonds : bond 0.06970 ( 1863) hydrogen bonds : angle 5.25301 ( 5442) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 829 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 715 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 61 VAL cc_start: 0.5703 (OUTLIER) cc_final: 0.5311 (p) REVERT: E 72 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8274 (ptp90) REVERT: E 133 ARG cc_start: 0.7784 (mtm-85) cc_final: 0.7576 (ttp-110) REVERT: E 167 ASP cc_start: 0.7265 (t0) cc_final: 0.7050 (t0) REVERT: E 237 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7741 (mm-30) REVERT: E 250 GLN cc_start: 0.8620 (mm-40) cc_final: 0.8372 (mm-40) REVERT: C 148 ARG cc_start: 0.7674 (tmm-80) cc_final: 0.7336 (tpm-80) REVERT: A 78 VAL cc_start: 0.4139 (OUTLIER) cc_final: 0.3890 (t) REVERT: A 93 ARG cc_start: 0.5320 (mpp-170) cc_final: 0.4997 (mpp-170) REVERT: U 246 ASP cc_start: 0.7801 (m-30) cc_final: 0.7562 (m-30) REVERT: S 246 ASP cc_start: 0.8073 (t0) cc_final: 0.7787 (t0) REVERT: O 255 ARG cc_start: 0.8098 (mtt180) cc_final: 0.7843 (mtt90) REVERT: I 126 ILE cc_start: 0.7610 (mp) cc_final: 0.7330 (mt) REVERT: I 127 LEU cc_start: 0.7967 (mt) cc_final: 0.7541 (mt) REVERT: I 157 ARG cc_start: 0.8264 (mtp-110) cc_final: 0.7994 (mtp-110) REVERT: I 175 PHE cc_start: 0.8778 (m-10) cc_final: 0.8568 (m-10) REVERT: I 222 GLU cc_start: 0.7929 (tp30) cc_final: 0.7707 (tp30) REVERT: I 246 ASP cc_start: 0.8102 (t0) cc_final: 0.7820 (t0) REVERT: G 222 GLU cc_start: 0.8054 (tp30) cc_final: 0.7718 (tp30) REVERT: G 239 ARG cc_start: 0.8612 (mmt180) cc_final: 0.7784 (tpp-160) REVERT: F 192 GLU cc_start: 0.7347 (tp30) cc_final: 0.6861 (tp30) REVERT: F 198 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7468 (mt-10) REVERT: F 202 VAL cc_start: 0.8678 (t) cc_final: 0.8392 (m) REVERT: F 218 LYS cc_start: 0.7569 (OUTLIER) cc_final: 0.7267 (mtmm) REVERT: F 252 ARG cc_start: 0.8777 (tpt90) cc_final: 0.7867 (ttt90) REVERT: F 268 GLN cc_start: 0.8358 (mp10) cc_final: 0.7972 (mt0) REVERT: D 101 MET cc_start: 0.7548 (pmm) cc_final: 0.7240 (mmm) REVERT: D 104 ILE cc_start: 0.8765 (mp) cc_final: 0.8516 (tt) REVERT: D 111 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7680 (ptm160) REVERT: D 120 MET cc_start: 0.7685 (mmm) cc_final: 0.7295 (mmm) REVERT: D 189 PHE cc_start: 0.8733 (m-80) cc_final: 0.8485 (m-80) REVERT: D 236 LYS cc_start: 0.8655 (ttpt) cc_final: 0.8302 (ttpt) REVERT: B 101 MET cc_start: 0.5836 (mmm) cc_final: 0.5539 (mmm) REVERT: B 177 LEU cc_start: 0.7405 (mm) cc_final: 0.7200 (mt) REVERT: B 231 GLU cc_start: 0.8047 (tp30) cc_final: 0.7754 (tp30) REVERT: B 243 SER cc_start: 0.8286 (m) cc_final: 0.8060 (m) REVERT: B 252 ARG cc_start: 0.8609 (tpt90) cc_final: 0.8195 (tpt90) REVERT: V 227 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.8167 (tt0) REVERT: T 219 GLN cc_start: 0.7966 (tp40) cc_final: 0.7689 (tp40) REVERT: T 227 GLN cc_start: 0.8201 (mt0) cc_final: 0.7351 (mt0) REVERT: R 255 ARG cc_start: 0.8344 (ttt180) cc_final: 0.8019 (ttt180) REVERT: R 284 ASP cc_start: 0.7849 (t70) cc_final: 0.7564 (t70) REVERT: N 252 ARG cc_start: 0.8743 (tpt90) cc_final: 0.8258 (tmt170) REVERT: L 223 GLN cc_start: 0.7535 (tp40) cc_final: 0.7256 (tp40) REVERT: L 236 LYS cc_start: 0.8305 (mttt) cc_final: 0.8095 (tttt) REVERT: J 101 MET cc_start: 0.6702 (mtp) cc_final: 0.6192 (mtp) REVERT: J 167 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8488 (mt-10) REVERT: J 176 SER cc_start: 0.8313 (m) cc_final: 0.7757 (p) REVERT: J 220 GLU cc_start: 0.7277 (tt0) cc_final: 0.6966 (tt0) REVERT: J 221 GLN cc_start: 0.7840 (tt0) cc_final: 0.7552 (tt0) REVERT: J 222 ARG cc_start: 0.8173 (tpt170) cc_final: 0.7784 (mmm-85) REVERT: J 237 MET cc_start: 0.6652 (OUTLIER) cc_final: 0.6198 (ptm) REVERT: J 285 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7467 (mm-30) REVERT: H 109 LEU cc_start: 0.7198 (mt) cc_final: 0.6696 (tm) REVERT: H 165 ARG cc_start: 0.7867 (ptp-170) cc_final: 0.7656 (ptp-170) REVERT: H 182 VAL cc_start: 0.5597 (t) cc_final: 0.5327 (m) REVERT: H 231 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7304 (mm-30) REVERT: H 268 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7342 (mm-40) REVERT: H 270 ARG cc_start: 0.7762 (mmm160) cc_final: 0.7316 (mmm160) outliers start: 114 outliers final: 68 residues processed: 764 average time/residue: 0.8832 time to fit residues: 761.0796 Evaluate side-chains 768 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 692 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 242 GLU Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 219 LYS Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain U residue 254 SER Chi-restraints excluded: chain U residue 267 LEU Chi-restraints excluded: chain S residue 238 LEU Chi-restraints excluded: chain S residue 250 GLN Chi-restraints excluded: chain S residue 258 THR Chi-restraints excluded: chain Q residue 242 GLU Chi-restraints excluded: chain Q residue 267 LEU Chi-restraints excluded: chain O residue 238 LEU Chi-restraints excluded: chain O residue 242 GLU Chi-restraints excluded: chain M residue 258 THR Chi-restraints excluded: chain I residue 34 HIS Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 149 GLN Chi-restraints excluded: chain I residue 183 VAL Chi-restraints excluded: chain I residue 208 LYS Chi-restraints excluded: chain I residue 215 GLU Chi-restraints excluded: chain I residue 254 SER Chi-restraints excluded: chain G residue 68 ASP Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 236 ILE Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 218 LYS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 ARG Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain V residue 227 GLN Chi-restraints excluded: chain V residue 295 ILE Chi-restraints excluded: chain T residue 252 ARG Chi-restraints excluded: chain T residue 255 ARG Chi-restraints excluded: chain T residue 294 LEU Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain R residue 295 ILE Chi-restraints excluded: chain P residue 262 LYS Chi-restraints excluded: chain N residue 249 ILE Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 293 SER Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 236 LYS Chi-restraints excluded: chain H residue 249 ILE Chi-restraints excluded: chain H residue 255 ARG Chi-restraints excluded: chain H residue 262 LYS Chi-restraints excluded: chain H residue 268 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 218 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 287 optimal weight: 0.5980 chunk 157 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 124 optimal weight: 20.0000 chunk 273 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 259 optimal weight: 9.9990 chunk 279 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 264 GLN ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 226 ASN ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 34 HIS F 219 GLN F 227 GLN D 208 GLN D 259 ASN ** D 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 ASN B 227 GLN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 277 ASN ** V 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 221 GLN R 277 ASN P 269 ASN L 283 GLN ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.203775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.159904 restraints weight = 49608.697| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 2.75 r_work: 0.3848 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.4802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 28948 Z= 0.229 Angle : 0.712 13.718 39046 Z= 0.377 Chirality : 0.046 0.337 4551 Planarity : 0.006 0.119 5118 Dihedral : 5.182 44.788 4006 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.96 % Favored : 92.68 % Rotamer: Outliers : 3.77 % Allowed : 16.37 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.42 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.14), residues: 3619 helix: 1.16 (0.11), residues: 1906 sheet: -1.95 (0.28), residues: 323 loop : -1.69 (0.16), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 253 TYR 0.022 0.002 TYR J 128 PHE 0.027 0.001 PHE I 107 TRP 0.008 0.001 TRP F 74 HIS 0.005 0.001 HIS A 172 Details of bonding type rmsd covalent geometry : bond 0.00496 (28948) covalent geometry : angle 0.71167 (39046) hydrogen bonds : bond 0.07080 ( 1863) hydrogen bonds : angle 5.27226 ( 5442) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 713 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 167 ASP cc_start: 0.7154 (t0) cc_final: 0.6932 (t0) REVERT: E 237 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7667 (mm-30) REVERT: E 250 GLN cc_start: 0.8589 (mm-40) cc_final: 0.8345 (mm-40) REVERT: C 148 ARG cc_start: 0.7608 (tmm-80) cc_final: 0.7279 (tpm-80) REVERT: C 149 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7678 (pp30) REVERT: C 253 ARG cc_start: 0.4612 (ptp-170) cc_final: 0.3966 (ptp-170) REVERT: A 78 VAL cc_start: 0.4265 (OUTLIER) cc_final: 0.4030 (t) REVERT: A 93 ARG cc_start: 0.5350 (mpp-170) cc_final: 0.5078 (mpp-170) REVERT: U 246 ASP cc_start: 0.7748 (m-30) cc_final: 0.7505 (m-30) REVERT: S 246 ASP cc_start: 0.8006 (t0) cc_final: 0.7720 (t0) REVERT: O 255 ARG cc_start: 0.7974 (mtt180) cc_final: 0.7722 (mtt90) REVERT: I 105 ARG cc_start: 0.8190 (tmm-80) cc_final: 0.7912 (tmm-80) REVERT: I 126 ILE cc_start: 0.7726 (mp) cc_final: 0.7523 (mt) REVERT: I 127 LEU cc_start: 0.8009 (mt) cc_final: 0.7572 (mt) REVERT: I 157 ARG cc_start: 0.8245 (mtp-110) cc_final: 0.7923 (mtp85) REVERT: I 175 PHE cc_start: 0.8783 (m-10) cc_final: 0.8582 (m-10) REVERT: I 239 ARG cc_start: 0.8483 (mtp85) cc_final: 0.8231 (mtp85) REVERT: I 246 ASP cc_start: 0.8028 (t0) cc_final: 0.7749 (t0) REVERT: G 222 GLU cc_start: 0.8014 (tp30) cc_final: 0.7657 (tp30) REVERT: G 239 ARG cc_start: 0.8596 (mmt180) cc_final: 0.7768 (tpp-160) REVERT: F 192 GLU cc_start: 0.7295 (tp30) cc_final: 0.6852 (tp30) REVERT: F 198 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7426 (mt-10) REVERT: F 202 VAL cc_start: 0.8671 (t) cc_final: 0.8387 (m) REVERT: F 218 LYS cc_start: 0.7577 (OUTLIER) cc_final: 0.7270 (mtmm) REVERT: F 252 ARG cc_start: 0.8768 (tpt90) cc_final: 0.7697 (mtp180) REVERT: F 268 GLN cc_start: 0.8299 (mp10) cc_final: 0.7706 (mt0) REVERT: D 104 ILE cc_start: 0.8760 (mp) cc_final: 0.8531 (tt) REVERT: D 111 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7644 (ptm160) REVERT: D 120 MET cc_start: 0.7605 (mmm) cc_final: 0.7282 (mmm) REVERT: D 189 PHE cc_start: 0.8726 (m-80) cc_final: 0.8493 (m-80) REVERT: D 206 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7634 (mm-30) REVERT: D 236 LYS cc_start: 0.8658 (ttpt) cc_final: 0.8313 (ttpt) REVERT: D 268 GLN cc_start: 0.8309 (mp-120) cc_final: 0.8035 (mp10) REVERT: B 101 MET cc_start: 0.5878 (mmm) cc_final: 0.5587 (mmm) REVERT: B 137 VAL cc_start: 0.1832 (m) cc_final: 0.1526 (m) REVERT: B 231 GLU cc_start: 0.7987 (tp30) cc_final: 0.7687 (tp30) REVERT: B 243 SER cc_start: 0.8284 (m) cc_final: 0.8039 (m) REVERT: V 227 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.8109 (tt0) REVERT: T 219 GLN cc_start: 0.7935 (tp40) cc_final: 0.7664 (tp40) REVERT: R 268 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7624 (mm-40) REVERT: N 252 ARG cc_start: 0.8731 (tpt90) cc_final: 0.8297 (tmt170) REVERT: L 223 GLN cc_start: 0.7490 (tp40) cc_final: 0.7196 (tp40) REVERT: L 236 LYS cc_start: 0.8266 (mttt) cc_final: 0.7960 (tttt) REVERT: L 268 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7448 (mt0) REVERT: J 101 MET cc_start: 0.6723 (mtp) cc_final: 0.6298 (mtp) REVERT: J 128 TYR cc_start: 0.7298 (OUTLIER) cc_final: 0.7042 (m-80) REVERT: J 166 ARG cc_start: 0.8810 (tmm-80) cc_final: 0.8339 (tmm-80) REVERT: J 167 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8519 (mt-10) REVERT: J 176 SER cc_start: 0.8199 (m) cc_final: 0.7652 (p) REVERT: J 220 GLU cc_start: 0.7280 (tt0) cc_final: 0.6971 (tt0) REVERT: J 222 ARG cc_start: 0.8163 (tpt170) cc_final: 0.7772 (mmm-85) REVERT: J 237 MET cc_start: 0.6665 (OUTLIER) cc_final: 0.6330 (ptm) REVERT: J 285 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7423 (mm-30) REVERT: H 109 LEU cc_start: 0.7123 (mt) cc_final: 0.6594 (tm) REVERT: H 165 ARG cc_start: 0.7854 (ptp-170) cc_final: 0.7641 (ptp-170) REVERT: H 171 ARG cc_start: 0.7872 (tpp-160) cc_final: 0.7201 (tpp-160) REVERT: H 221 GLN cc_start: 0.8398 (tt0) cc_final: 0.8166 (tt0) REVERT: H 231 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7258 (mm-30) REVERT: H 268 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7352 (mm-40) REVERT: H 270 ARG cc_start: 0.7701 (mmm160) cc_final: 0.7236 (mmm160) outliers start: 114 outliers final: 75 residues processed: 767 average time/residue: 0.8893 time to fit residues: 770.1823 Evaluate side-chains 785 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 700 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 215 GLU Chi-restraints excluded: chain E residue 242 GLU Chi-restraints excluded: chain E residue 264 GLN Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 149 GLN Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 219 LYS Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 96 PHE Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain U residue 254 SER Chi-restraints excluded: chain U residue 267 LEU Chi-restraints excluded: chain S residue 238 LEU Chi-restraints excluded: chain S residue 250 GLN Chi-restraints excluded: chain S residue 258 THR Chi-restraints excluded: chain Q residue 242 GLU Chi-restraints excluded: chain Q residue 267 LEU Chi-restraints excluded: chain O residue 238 LEU Chi-restraints excluded: chain O residue 242 GLU Chi-restraints excluded: chain M residue 258 THR Chi-restraints excluded: chain K residue 242 GLU Chi-restraints excluded: chain I residue 34 HIS Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 183 VAL Chi-restraints excluded: chain I residue 208 LYS Chi-restraints excluded: chain I residue 215 GLU Chi-restraints excluded: chain I residue 254 SER Chi-restraints excluded: chain G residue 68 ASP Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 190 SER Chi-restraints excluded: chain F residue 218 LYS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 ARG Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain V residue 227 GLN Chi-restraints excluded: chain V residue 295 ILE Chi-restraints excluded: chain T residue 252 ARG Chi-restraints excluded: chain T residue 255 ARG Chi-restraints excluded: chain T residue 294 LEU Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain R residue 268 GLN Chi-restraints excluded: chain R residue 295 ILE Chi-restraints excluded: chain P residue 255 ARG Chi-restraints excluded: chain P residue 262 LYS Chi-restraints excluded: chain N residue 249 ILE Chi-restraints excluded: chain L residue 268 GLN Chi-restraints excluded: chain J residue 128 TYR Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 293 SER Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 120 MET Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 236 LYS Chi-restraints excluded: chain H residue 255 ARG Chi-restraints excluded: chain H residue 262 LYS Chi-restraints excluded: chain H residue 268 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 57 optimal weight: 0.9990 chunk 49 optimal weight: 90.0000 chunk 14 optimal weight: 1.9990 chunk 177 optimal weight: 0.9980 chunk 91 optimal weight: 9.9990 chunk 12 optimal weight: 0.7980 chunk 295 optimal weight: 0.7980 chunk 243 optimal weight: 0.9980 chunk 319 optimal weight: 1.9990 chunk 250 optimal weight: 10.0000 chunk 201 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 219 GLN F 227 GLN D 208 GLN ** D 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 ASN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 277 ASN ** V 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 221 GLN R 277 ASN P 259 ASN L 283 GLN ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.203661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.159593 restraints weight = 49852.437| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 2.76 r_work: 0.3830 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 28948 Z= 0.221 Angle : 0.720 13.821 39046 Z= 0.379 Chirality : 0.045 0.325 4551 Planarity : 0.005 0.071 5118 Dihedral : 5.161 45.150 4006 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.88 % Favored : 92.79 % Rotamer: Outliers : 3.17 % Allowed : 17.69 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.42 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.14), residues: 3619 helix: 1.19 (0.11), residues: 1899 sheet: -1.90 (0.29), residues: 318 loop : -1.67 (0.16), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 111 TYR 0.043 0.002 TYR J 121 PHE 0.025 0.001 PHE E 134 TRP 0.008 0.001 TRP F 74 HIS 0.005 0.001 HIS A 172 Details of bonding type rmsd covalent geometry : bond 0.00480 (28948) covalent geometry : angle 0.72010 (39046) hydrogen bonds : bond 0.07001 ( 1863) hydrogen bonds : angle 5.25341 ( 5442) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 710 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 167 ASP cc_start: 0.7100 (t0) cc_final: 0.6872 (t0) REVERT: E 237 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7714 (mm-30) REVERT: E 250 GLN cc_start: 0.8595 (mm-40) cc_final: 0.8349 (mm-40) REVERT: E 255 ARG cc_start: 0.7796 (mpt180) cc_final: 0.7438 (mpt180) REVERT: C 148 ARG cc_start: 0.7673 (tmm-80) cc_final: 0.7270 (tpm-80) REVERT: C 149 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.7674 (pp30) REVERT: A 72 ARG cc_start: 0.7071 (mtm-85) cc_final: 0.6763 (mtm-85) REVERT: A 93 ARG cc_start: 0.5378 (mpp-170) cc_final: 0.5144 (mpp-170) REVERT: A 249 TYR cc_start: 0.8651 (t80) cc_final: 0.8349 (t80) REVERT: U 246 ASP cc_start: 0.7791 (m-30) cc_final: 0.7555 (m-30) REVERT: S 246 ASP cc_start: 0.8051 (t0) cc_final: 0.7762 (t0) REVERT: O 255 ARG cc_start: 0.7993 (mtt180) cc_final: 0.7738 (mtt90) REVERT: I 97 ARG cc_start: 0.6677 (ttm110) cc_final: 0.6218 (ttm-80) REVERT: I 127 LEU cc_start: 0.8026 (mt) cc_final: 0.7599 (mt) REVERT: I 157 ARG cc_start: 0.8254 (mtp-110) cc_final: 0.7897 (mtp85) REVERT: I 175 PHE cc_start: 0.8813 (m-10) cc_final: 0.8584 (m-10) REVERT: I 237 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7482 (mt-10) REVERT: I 239 ARG cc_start: 0.8511 (mtp85) cc_final: 0.8017 (mtp85) REVERT: I 246 ASP cc_start: 0.8060 (t0) cc_final: 0.7781 (t0) REVERT: I 255 ARG cc_start: 0.7771 (mtt180) cc_final: 0.7509 (mtt180) REVERT: G 97 ARG cc_start: 0.7156 (ptm160) cc_final: 0.6831 (ptm-80) REVERT: G 222 GLU cc_start: 0.8043 (tp30) cc_final: 0.7684 (tp30) REVERT: G 239 ARG cc_start: 0.8608 (mmt180) cc_final: 0.7790 (tpp-160) REVERT: F 111 ARG cc_start: 0.7062 (ttm110) cc_final: 0.6688 (ttp80) REVERT: F 192 GLU cc_start: 0.7310 (tp30) cc_final: 0.6862 (tp30) REVERT: F 198 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7327 (mt-10) REVERT: F 202 VAL cc_start: 0.8639 (t) cc_final: 0.8341 (m) REVERT: F 218 LYS cc_start: 0.7586 (OUTLIER) cc_final: 0.7273 (mtmm) REVERT: F 233 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7631 (mm-30) REVERT: F 252 ARG cc_start: 0.8813 (tpt90) cc_final: 0.7683 (mtp180) REVERT: F 268 GLN cc_start: 0.8280 (mp10) cc_final: 0.7337 (mt0) REVERT: D 104 ILE cc_start: 0.8825 (mp) cc_final: 0.8621 (tt) REVERT: D 111 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7651 (ptm160) REVERT: D 120 MET cc_start: 0.7643 (mmm) cc_final: 0.7329 (mmm) REVERT: D 189 PHE cc_start: 0.8744 (m-80) cc_final: 0.8499 (m-80) REVERT: D 206 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7668 (mm-30) REVERT: D 236 LYS cc_start: 0.8672 (ttpt) cc_final: 0.8314 (ttpt) REVERT: D 268 GLN cc_start: 0.8154 (mp-120) cc_final: 0.7951 (mp-120) REVERT: B 101 MET cc_start: 0.5921 (mmm) cc_final: 0.5648 (mmm) REVERT: B 137 VAL cc_start: 0.1838 (m) cc_final: 0.1543 (m) REVERT: B 231 GLU cc_start: 0.8024 (tp30) cc_final: 0.7716 (tp30) REVERT: B 243 SER cc_start: 0.8285 (m) cc_final: 0.8047 (m) REVERT: V 227 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.8126 (tt0) REVERT: T 219 GLN cc_start: 0.7960 (tp40) cc_final: 0.7683 (tp40) REVERT: R 255 ARG cc_start: 0.8271 (ttt180) cc_final: 0.8062 (ttt180) REVERT: R 268 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.7620 (mm-40) REVERT: N 252 ARG cc_start: 0.8733 (tpt90) cc_final: 0.8251 (tmt170) REVERT: L 223 GLN cc_start: 0.7477 (tp40) cc_final: 0.7181 (tp40) REVERT: L 268 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7441 (mt0) REVERT: J 51 PHE cc_start: 0.5871 (OUTLIER) cc_final: 0.5622 (t80) REVERT: J 101 MET cc_start: 0.6747 (mtp) cc_final: 0.6284 (mtp) REVERT: J 166 ARG cc_start: 0.8895 (tmm-80) cc_final: 0.8680 (tmm-80) REVERT: J 167 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8718 (mt-10) REVERT: J 220 GLU cc_start: 0.7333 (tt0) cc_final: 0.7023 (tt0) REVERT: J 222 ARG cc_start: 0.8167 (tpt170) cc_final: 0.7723 (mmm160) REVERT: J 237 MET cc_start: 0.6764 (OUTLIER) cc_final: 0.6443 (ptm) REVERT: J 285 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7417 (mm-30) REVERT: H 165 ARG cc_start: 0.7859 (ptp-170) cc_final: 0.7578 (ptp-170) REVERT: H 171 ARG cc_start: 0.7887 (tpp-160) cc_final: 0.7566 (mmp80) REVERT: H 231 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7279 (mm-30) REVERT: H 268 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7363 (mm-40) REVERT: H 270 ARG cc_start: 0.7735 (mmm160) cc_final: 0.7252 (mmm160) outliers start: 96 outliers final: 75 residues processed: 752 average time/residue: 0.8689 time to fit residues: 737.5548 Evaluate side-chains 790 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 705 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 215 GLU Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 149 GLN Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 219 LYS Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain U residue 254 SER Chi-restraints excluded: chain U residue 267 LEU Chi-restraints excluded: chain S residue 238 LEU Chi-restraints excluded: chain S residue 250 GLN Chi-restraints excluded: chain S residue 258 THR Chi-restraints excluded: chain Q residue 242 GLU Chi-restraints excluded: chain Q residue 267 LEU Chi-restraints excluded: chain O residue 238 LEU Chi-restraints excluded: chain O residue 242 GLU Chi-restraints excluded: chain M residue 258 THR Chi-restraints excluded: chain K residue 242 GLU Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 183 VAL Chi-restraints excluded: chain I residue 208 LYS Chi-restraints excluded: chain I residue 215 GLU Chi-restraints excluded: chain I residue 237 GLU Chi-restraints excluded: chain I residue 254 SER Chi-restraints excluded: chain G residue 68 ASP Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 190 SER Chi-restraints excluded: chain F residue 218 LYS Chi-restraints excluded: chain F residue 237 MET Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 111 ARG Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain V residue 227 GLN Chi-restraints excluded: chain V residue 295 ILE Chi-restraints excluded: chain T residue 252 ARG Chi-restraints excluded: chain T residue 255 ARG Chi-restraints excluded: chain T residue 294 LEU Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain R residue 268 GLN Chi-restraints excluded: chain R residue 295 ILE Chi-restraints excluded: chain P residue 255 ARG Chi-restraints excluded: chain P residue 262 LYS Chi-restraints excluded: chain N residue 249 ILE Chi-restraints excluded: chain L residue 268 GLN Chi-restraints excluded: chain J residue 51 PHE Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 293 SER Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 75 PHE Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 236 LYS Chi-restraints excluded: chain H residue 249 ILE Chi-restraints excluded: chain H residue 255 ARG Chi-restraints excluded: chain H residue 262 LYS Chi-restraints excluded: chain H residue 268 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 220 optimal weight: 0.4980 chunk 17 optimal weight: 0.5980 chunk 159 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 41 optimal weight: 6.9990 chunk 149 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 49 optimal weight: 90.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 219 GLN F 227 GLN D 208 GLN ** D 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 ASN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 277 ASN ** V 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 277 ASN P 259 ASN L 283 GLN ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 221 GLN J 259 ASN H 201 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.204804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.161009 restraints weight = 49895.785| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 2.72 r_work: 0.3849 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.5141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 28948 Z= 0.189 Angle : 0.723 13.811 39046 Z= 0.381 Chirality : 0.045 0.327 4551 Planarity : 0.006 0.077 5118 Dihedral : 5.136 45.628 4006 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.77 % Favored : 92.93 % Rotamer: Outliers : 3.04 % Allowed : 18.42 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.45 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.14), residues: 3619 helix: 1.26 (0.11), residues: 1897 sheet: -1.71 (0.30), residues: 306 loop : -1.70 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 72 TYR 0.035 0.002 TYR J 121 PHE 0.064 0.001 PHE A 107 TRP 0.010 0.001 TRP E 60 HIS 0.005 0.001 HIS A 172 Details of bonding type rmsd covalent geometry : bond 0.00403 (28948) covalent geometry : angle 0.72304 (39046) hydrogen bonds : bond 0.06719 ( 1863) hydrogen bonds : angle 5.19580 ( 5442) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 720 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 72 ARG cc_start: 0.8576 (ptp-170) cc_final: 0.8246 (ptp90) REVERT: E 116 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7365 (mm-30) REVERT: E 149 GLN cc_start: 0.8179 (mm-40) cc_final: 0.7759 (mt0) REVERT: E 153 ASP cc_start: 0.7612 (m-30) cc_final: 0.7367 (m-30) REVERT: E 237 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7700 (mm-30) REVERT: E 250 GLN cc_start: 0.8586 (mm-40) cc_final: 0.8340 (mm-40) REVERT: E 255 ARG cc_start: 0.7829 (mpt180) cc_final: 0.7590 (mpt180) REVERT: C 105 ARG cc_start: 0.7795 (tpt170) cc_final: 0.7246 (tpt170) REVERT: C 148 ARG cc_start: 0.7645 (tmm-80) cc_final: 0.7260 (tpm-80) REVERT: C 149 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7891 (pp30) REVERT: A 249 TYR cc_start: 0.8641 (t80) cc_final: 0.8354 (t80) REVERT: U 246 ASP cc_start: 0.7773 (m-30) cc_final: 0.7533 (m-30) REVERT: S 246 ASP cc_start: 0.8041 (t0) cc_final: 0.7751 (t0) REVERT: O 255 ARG cc_start: 0.7999 (mtt180) cc_final: 0.7736 (mtt90) REVERT: M 253 ARG cc_start: 0.7816 (mmp80) cc_final: 0.7500 (mmp80) REVERT: I 113 ASP cc_start: 0.8082 (t0) cc_final: 0.7772 (t0) REVERT: I 127 LEU cc_start: 0.7997 (mt) cc_final: 0.7605 (mt) REVERT: I 146 VAL cc_start: 0.7042 (t) cc_final: 0.6746 (m) REVERT: I 157 ARG cc_start: 0.8194 (mtp-110) cc_final: 0.7792 (mtp85) REVERT: I 175 PHE cc_start: 0.8726 (m-10) cc_final: 0.8497 (m-10) REVERT: I 222 GLU cc_start: 0.7858 (tp30) cc_final: 0.7646 (tp30) REVERT: I 237 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7466 (mt-10) REVERT: I 239 ARG cc_start: 0.8478 (mtp85) cc_final: 0.8007 (mtp85) REVERT: I 246 ASP cc_start: 0.8048 (t0) cc_final: 0.7765 (t0) REVERT: G 97 ARG cc_start: 0.7118 (ptm160) cc_final: 0.6787 (ptm160) REVERT: G 148 ARG cc_start: 0.8273 (ttt-90) cc_final: 0.7988 (ttt-90) REVERT: G 222 GLU cc_start: 0.7994 (tp30) cc_final: 0.7654 (tp30) REVERT: G 239 ARG cc_start: 0.8580 (mmt180) cc_final: 0.7742 (tpp-160) REVERT: F 127 ASP cc_start: 0.7491 (t0) cc_final: 0.7276 (t0) REVERT: F 165 ARG cc_start: 0.7928 (tpp-160) cc_final: 0.7656 (mmm-85) REVERT: F 187 LEU cc_start: 0.7980 (mt) cc_final: 0.7762 (mm) REVERT: F 192 GLU cc_start: 0.7303 (tp30) cc_final: 0.6841 (tp30) REVERT: F 198 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7290 (mt-10) REVERT: F 202 VAL cc_start: 0.8647 (t) cc_final: 0.8350 (m) REVERT: F 218 LYS cc_start: 0.7515 (OUTLIER) cc_final: 0.7214 (mtmm) REVERT: F 233 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7584 (mm-30) REVERT: F 252 ARG cc_start: 0.8693 (tpt90) cc_final: 0.7647 (mtp180) REVERT: F 293 SER cc_start: 0.8631 (t) cc_final: 0.8280 (p) REVERT: D 120 MET cc_start: 0.7582 (mmm) cc_final: 0.7273 (mmm) REVERT: D 189 PHE cc_start: 0.8760 (m-80) cc_final: 0.8499 (m-80) REVERT: D 206 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7641 (mm-30) REVERT: D 236 LYS cc_start: 0.8652 (ttpt) cc_final: 0.8295 (ttpt) REVERT: D 268 GLN cc_start: 0.8192 (mp-120) cc_final: 0.7931 (mp10) REVERT: B 101 MET cc_start: 0.5889 (mmm) cc_final: 0.5626 (mmm) REVERT: B 137 VAL cc_start: 0.1869 (m) cc_final: 0.1577 (m) REVERT: B 231 GLU cc_start: 0.8011 (tp30) cc_final: 0.7719 (tp30) REVERT: B 243 SER cc_start: 0.8256 (m) cc_final: 0.8011 (m) REVERT: T 219 GLN cc_start: 0.7940 (tp40) cc_final: 0.7664 (tp40) REVERT: R 255 ARG cc_start: 0.8281 (ttt180) cc_final: 0.8027 (ttt180) REVERT: R 268 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7619 (mm-40) REVERT: N 252 ARG cc_start: 0.8687 (tpt90) cc_final: 0.8217 (tmt170) REVERT: L 223 GLN cc_start: 0.7438 (tp40) cc_final: 0.7155 (tp40) REVERT: L 224 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7906 (ttmm) REVERT: L 268 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7419 (mt0) REVERT: J 51 PHE cc_start: 0.5817 (OUTLIER) cc_final: 0.5522 (t80) REVERT: J 101 MET cc_start: 0.6655 (mtp) cc_final: 0.6234 (mtp) REVERT: J 121 TYR cc_start: 0.4573 (OUTLIER) cc_final: 0.4176 (m-10) REVERT: J 166 ARG cc_start: 0.8942 (tmm-80) cc_final: 0.8609 (tmm-80) REVERT: J 167 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8695 (mt-10) REVERT: J 222 ARG cc_start: 0.8161 (tpt170) cc_final: 0.7747 (mmm160) REVERT: J 237 MET cc_start: 0.6751 (OUTLIER) cc_final: 0.6494 (ptm) REVERT: J 285 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7408 (mm-30) REVERT: H 71 ARG cc_start: 0.4693 (OUTLIER) cc_final: 0.3938 (ttm-80) REVERT: H 109 LEU cc_start: 0.6663 (mm) cc_final: 0.5787 (tm) REVERT: H 165 ARG cc_start: 0.7870 (ptp-170) cc_final: 0.7580 (ptp-170) REVERT: H 225 ILE cc_start: 0.8535 (mm) cc_final: 0.8316 (mp) REVERT: H 231 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7267 (mm-30) REVERT: H 268 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7335 (mm-40) REVERT: H 270 ARG cc_start: 0.7755 (mmm160) cc_final: 0.7269 (mmm160) outliers start: 92 outliers final: 64 residues processed: 754 average time/residue: 0.7755 time to fit residues: 661.5910 Evaluate side-chains 793 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 718 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 215 GLU Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 149 GLN Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 219 LYS Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain U residue 254 SER Chi-restraints excluded: chain U residue 267 LEU Chi-restraints excluded: chain S residue 250 GLN Chi-restraints excluded: chain S residue 258 THR Chi-restraints excluded: chain Q residue 242 GLU Chi-restraints excluded: chain Q residue 267 LEU Chi-restraints excluded: chain O residue 238 LEU Chi-restraints excluded: chain O residue 242 GLU Chi-restraints excluded: chain M residue 258 THR Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 183 VAL Chi-restraints excluded: chain I residue 237 GLU Chi-restraints excluded: chain I residue 254 SER Chi-restraints excluded: chain G residue 68 ASP Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 190 SER Chi-restraints excluded: chain F residue 218 LYS Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain V residue 295 ILE Chi-restraints excluded: chain T residue 252 ARG Chi-restraints excluded: chain T residue 255 ARG Chi-restraints excluded: chain T residue 294 LEU Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain R residue 268 GLN Chi-restraints excluded: chain P residue 255 ARG Chi-restraints excluded: chain P residue 262 LYS Chi-restraints excluded: chain N residue 249 ILE Chi-restraints excluded: chain L residue 224 LYS Chi-restraints excluded: chain L residue 268 GLN Chi-restraints excluded: chain J residue 51 PHE Chi-restraints excluded: chain J residue 121 TYR Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 237 MET Chi-restraints excluded: chain J residue 293 SER Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 75 PHE Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 236 LYS Chi-restraints excluded: chain H residue 249 ILE Chi-restraints excluded: chain H residue 255 ARG Chi-restraints excluded: chain H residue 268 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 329 optimal weight: 0.9990 chunk 142 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 175 optimal weight: 0.8980 chunk 262 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 183 optimal weight: 0.2980 chunk 163 optimal weight: 8.9990 chunk 45 optimal weight: 0.6980 chunk 357 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 219 GLN F 227 GLN D 201 GLN ** D 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 ASN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 277 ASN ** V 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 221 GLN R 277 ASN P 259 ASN N 283 GLN L 283 GLN ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 ASN H 201 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.205270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.161954 restraints weight = 49503.491| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 2.71 r_work: 0.3859 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.5301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 28948 Z= 0.187 Angle : 0.735 13.657 39046 Z= 0.385 Chirality : 0.045 0.313 4551 Planarity : 0.006 0.077 5118 Dihedral : 5.110 46.074 4006 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.60 % Favored : 93.12 % Rotamer: Outliers : 2.65 % Allowed : 18.88 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.45 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.14), residues: 3619 helix: 1.30 (0.11), residues: 1902 sheet: -1.60 (0.30), residues: 315 loop : -1.71 (0.16), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 70 TYR 0.034 0.002 TYR J 121 PHE 0.028 0.001 PHE E 134 TRP 0.008 0.001 TRP F 74 HIS 0.005 0.001 HIS A 172 Details of bonding type rmsd covalent geometry : bond 0.00398 (28948) covalent geometry : angle 0.73465 (39046) hydrogen bonds : bond 0.06634 ( 1863) hydrogen bonds : angle 5.16269 ( 5442) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7238 Ramachandran restraints generated. 3619 Oldfield, 0 Emsley, 3619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 795 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 715 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 72 ARG cc_start: 0.8588 (ptp-170) cc_final: 0.8112 (ptt180) REVERT: E 117 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7329 (mtm180) REVERT: E 250 GLN cc_start: 0.8588 (mm-40) cc_final: 0.8347 (mm-40) REVERT: C 105 ARG cc_start: 0.7765 (tpt170) cc_final: 0.7233 (tpt170) REVERT: C 148 ARG cc_start: 0.7617 (tmm-80) cc_final: 0.7208 (tpm-80) REVERT: C 149 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.7959 (pp30) REVERT: A 249 TYR cc_start: 0.8631 (t80) cc_final: 0.8339 (t80) REVERT: U 246 ASP cc_start: 0.7764 (m-30) cc_final: 0.7527 (m-30) REVERT: S 246 ASP cc_start: 0.8042 (t0) cc_final: 0.7746 (t0) REVERT: M 253 ARG cc_start: 0.7802 (mmp80) cc_final: 0.7489 (mmp80) REVERT: I 126 ILE cc_start: 0.7603 (mp) cc_final: 0.7340 (mt) REVERT: I 127 LEU cc_start: 0.8031 (mt) cc_final: 0.7617 (mt) REVERT: I 175 PHE cc_start: 0.8704 (m-10) cc_final: 0.8441 (m-80) REVERT: I 237 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7467 (mt-10) REVERT: I 239 ARG cc_start: 0.8473 (mtp85) cc_final: 0.7879 (mtp85) REVERT: I 246 ASP cc_start: 0.8026 (t0) cc_final: 0.7730 (t0) REVERT: G 68 ASP cc_start: 0.6079 (OUTLIER) cc_final: 0.5626 (p0) REVERT: G 88 VAL cc_start: 0.7198 (t) cc_final: 0.6845 (m) REVERT: G 97 ARG cc_start: 0.7071 (ptm160) cc_final: 0.6762 (ptm160) REVERT: G 148 ARG cc_start: 0.8288 (ttt-90) cc_final: 0.8003 (ttt-90) REVERT: G 179 PHE cc_start: 0.7053 (m-80) cc_final: 0.6812 (m-10) REVERT: G 222 GLU cc_start: 0.7993 (tp30) cc_final: 0.7633 (tp30) REVERT: G 239 ARG cc_start: 0.8578 (mmt180) cc_final: 0.7809 (tpp-160) REVERT: F 165 ARG cc_start: 0.7867 (tpp-160) cc_final: 0.7624 (mmm-85) REVERT: F 188 SER cc_start: 0.8151 (m) cc_final: 0.7857 (t) REVERT: F 192 GLU cc_start: 0.7301 (tp30) cc_final: 0.6839 (tp30) REVERT: F 198 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7308 (mt-10) REVERT: F 202 VAL cc_start: 0.8644 (t) cc_final: 0.8354 (m) REVERT: F 218 LYS cc_start: 0.7495 (OUTLIER) cc_final: 0.7179 (mtmm) REVERT: F 222 ARG cc_start: 0.7692 (tpt170) cc_final: 0.7270 (tpt170) REVERT: F 231 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7509 (mm-30) REVERT: F 233 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7500 (mm-30) REVERT: F 252 ARG cc_start: 0.8669 (tpt90) cc_final: 0.7486 (mmm160) REVERT: F 268 GLN cc_start: 0.8277 (mp10) cc_final: 0.7790 (mt0) REVERT: F 293 SER cc_start: 0.8647 (t) cc_final: 0.8286 (p) REVERT: D 120 MET cc_start: 0.7553 (mmm) cc_final: 0.7265 (mmm) REVERT: D 189 PHE cc_start: 0.8780 (m-80) cc_final: 0.8513 (m-80) REVERT: D 206 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7603 (mm-30) REVERT: D 236 LYS cc_start: 0.8638 (ttpt) cc_final: 0.8271 (ttpt) REVERT: B 101 MET cc_start: 0.5932 (mmm) cc_final: 0.5644 (mmm) REVERT: B 137 VAL cc_start: 0.1905 (m) cc_final: 0.1612 (m) REVERT: B 231 GLU cc_start: 0.8016 (tp30) cc_final: 0.7724 (tp30) REVERT: B 243 SER cc_start: 0.8218 (m) cc_final: 0.7976 (m) REVERT: T 219 GLN cc_start: 0.7954 (tp40) cc_final: 0.7677 (tp40) REVERT: R 255 ARG cc_start: 0.8244 (ttt180) cc_final: 0.7993 (ttt180) REVERT: R 268 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.7589 (mm-40) REVERT: N 252 ARG cc_start: 0.8691 (tpt90) cc_final: 0.8239 (tmt170) REVERT: L 223 GLN cc_start: 0.7395 (tp40) cc_final: 0.7118 (tp40) REVERT: L 224 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7889 (ttmm) REVERT: L 268 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.7432 (mt0) REVERT: J 51 PHE cc_start: 0.5818 (OUTLIER) cc_final: 0.5522 (t80) REVERT: J 101 MET cc_start: 0.6579 (mtp) cc_final: 0.6184 (mtp) REVERT: J 121 TYR cc_start: 0.4849 (OUTLIER) cc_final: 0.4450 (m-10) REVERT: J 166 ARG cc_start: 0.8982 (tmm-80) cc_final: 0.8591 (tmm-80) REVERT: J 167 GLU cc_start: 0.9062 (mt-10) cc_final: 0.8619 (mt-10) REVERT: J 201 GLN cc_start: 0.7592 (mp10) cc_final: 0.7341 (pm20) REVERT: J 216 LYS cc_start: 0.7790 (mttt) cc_final: 0.7507 (mttt) REVERT: J 222 ARG cc_start: 0.8098 (tpt170) cc_final: 0.7700 (mmm160) REVERT: J 231 GLU cc_start: 0.7086 (mm-30) cc_final: 0.6828 (mm-30) REVERT: J 237 MET cc_start: 0.6659 (mtp) cc_final: 0.6447 (ptm) REVERT: J 285 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7390 (mm-30) REVERT: H 71 ARG cc_start: 0.4779 (OUTLIER) cc_final: 0.3996 (ttm-80) REVERT: H 165 ARG cc_start: 0.7918 (ptp-170) cc_final: 0.7612 (ptp-170) REVERT: H 225 ILE cc_start: 0.8519 (mm) cc_final: 0.8303 (mp) REVERT: H 231 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7274 (mm-30) REVERT: H 270 ARG cc_start: 0.7729 (mmm160) cc_final: 0.7237 (mmm160) outliers start: 80 outliers final: 67 residues processed: 746 average time/residue: 0.8298 time to fit residues: 699.2925 Evaluate side-chains 777 residues out of total 3044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 699 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 117 ARG Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 215 GLU Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 149 GLN Chi-restraints excluded: chain C residue 201 GLU Chi-restraints excluded: chain C residue 219 LYS Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain U residue 254 SER Chi-restraints excluded: chain U residue 267 LEU Chi-restraints excluded: chain S residue 238 LEU Chi-restraints excluded: chain S residue 250 GLN Chi-restraints excluded: chain S residue 258 THR Chi-restraints excluded: chain Q residue 242 GLU Chi-restraints excluded: chain Q residue 267 LEU Chi-restraints excluded: chain O residue 238 LEU Chi-restraints excluded: chain O residue 242 GLU Chi-restraints excluded: chain M residue 258 THR Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 183 VAL Chi-restraints excluded: chain I residue 237 GLU Chi-restraints excluded: chain I residue 254 SER Chi-restraints excluded: chain G residue 68 ASP Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 241 LEU Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 162 LEU Chi-restraints excluded: chain F residue 190 SER Chi-restraints excluded: chain F residue 218 LYS Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 224 LYS Chi-restraints excluded: chain V residue 295 ILE Chi-restraints excluded: chain T residue 252 ARG Chi-restraints excluded: chain T residue 255 ARG Chi-restraints excluded: chain T residue 294 LEU Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain R residue 268 GLN Chi-restraints excluded: chain R residue 295 ILE Chi-restraints excluded: chain P residue 255 ARG Chi-restraints excluded: chain P residue 262 LYS Chi-restraints excluded: chain N residue 249 ILE Chi-restraints excluded: chain L residue 224 LYS Chi-restraints excluded: chain L residue 268 GLN Chi-restraints excluded: chain J residue 51 PHE Chi-restraints excluded: chain J residue 121 TYR Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 293 SER Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 201 GLN Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 236 LYS Chi-restraints excluded: chain H residue 249 ILE Chi-restraints excluded: chain H residue 255 ARG Chi-restraints excluded: chain H residue 268 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 39 optimal weight: 7.9990 chunk 187 optimal weight: 0.4980 chunk 177 optimal weight: 0.9990 chunk 355 optimal weight: 0.9990 chunk 223 optimal weight: 6.9990 chunk 310 optimal weight: 10.0000 chunk 357 optimal weight: 1.9990 chunk 314 optimal weight: 0.4980 chunk 320 optimal weight: 0.9980 chunk 65 optimal weight: 8.9990 chunk 298 optimal weight: 4.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 GLN ** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 187 GLN F 219 GLN F 227 GLN D 201 GLN ** D 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 ASN ** B 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 277 ASN ** V 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 277 ASN R 277 ASN P 259 ASN N 283 GLN L 281 ASN L 283 GLN ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 259 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.204578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.162365 restraints weight = 49555.628| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 2.61 r_work: 0.3861 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.5414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 28948 Z= 0.212 Angle : 0.740 13.843 39046 Z= 0.391 Chirality : 0.045 0.297 4551 Planarity : 0.006 0.092 5118 Dihedral : 5.133 46.183 4006 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.74 % Favored : 92.95 % Rotamer: Outliers : 2.94 % Allowed : 18.75 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.45 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.14), residues: 3619 helix: 1.28 (0.11), residues: 1901 sheet: -1.59 (0.30), residues: 307 loop : -1.74 (0.16), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG E 157 TYR 0.033 0.002 TYR J 121 PHE 0.052 0.001 PHE A 107 TRP 0.008 0.001 TRP F 74 HIS 0.006 0.001 HIS C 34 Details of bonding type rmsd covalent geometry : bond 0.00460 (28948) covalent geometry : angle 0.74017 (39046) hydrogen bonds : bond 0.06821 ( 1863) hydrogen bonds : angle 5.18669 ( 5442) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15040.33 seconds wall clock time: 255 minutes 51.57 seconds (15351.57 seconds total)