Starting phenix.real_space_refine on Wed Sep 17 17:13:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k3k_62017/09_2025/9k3k_62017.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k3k_62017/09_2025/9k3k_62017.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k3k_62017/09_2025/9k3k_62017.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k3k_62017/09_2025/9k3k_62017.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k3k_62017/09_2025/9k3k_62017.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k3k_62017/09_2025/9k3k_62017.map" } resolution = 3.12 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= 0.019 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 71 5.16 5 C 6187 2.51 5 N 1675 2.21 5 O 1822 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9755 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2057 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 7, 'TRANS': 262} Chain breaks: 2 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Planarities with less than four sites: {'TYR:plan': 3, 'ASP:plan': 1, 'GLU:plan': 3, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 44 Chain: "A" Number of atoms: 1942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1942 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 1 Chain: "B" Number of atoms: 2595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2595 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "G" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 427 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 963 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1771 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 Time building chain proxies: 2.21, per 1000 atoms: 0.23 Number of scatterers: 9755 At special positions: 0 Unit cell: (87.822, 130.662, 125.307, 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 71 16.00 O 1822 8.00 N 1675 7.00 C 6187 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 40 " - pdb=" SG CYS R 279 " distance=2.01 Simple disulfide: pdb=" SG CYS R 271 " - pdb=" SG CYS R 277 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 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: 0.87 Conformation dependent library (CDL) restraints added in 299.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2346 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 15 sheets defined 34.6% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'R' and resid 47 through 72 removed outlier: 3.778A pdb=" N PHE R 51 " --> pdb=" O SER R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 107 Processing helix chain 'R' and resid 130 through 153 removed outlier: 3.524A pdb=" N LEU R 134 " --> pdb=" O CYS R 130 " (cutoff:3.500A) Processing helix chain 'R' and resid 153 through 161 removed outlier: 3.864A pdb=" N HIS R 158 " --> pdb=" O ALA R 154 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ASN R 159 " --> pdb=" O LEU R 155 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N MET R 161 " --> pdb=" O TYR R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 163 through 184 Processing helix chain 'R' and resid 194 through 228 removed outlier: 3.612A pdb=" N ILE R 198 " --> pdb=" O ILE R 194 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR R 199 " --> pdb=" O ILE R 195 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N MET R 200 " --> pdb=" O CYS R 196 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET R 218 " --> pdb=" O HIS R 214 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL R 228 " --> pdb=" O LYS R 224 " (cutoff:3.500A) Processing helix chain 'R' and resid 238 through 257 Processing helix chain 'R' and resid 258 through 271 removed outlier: 3.799A pdb=" N ILE R 269 " --> pdb=" O LEU R 265 " (cutoff:3.500A) Processing helix chain 'R' and resid 274 through 282 Processing helix chain 'R' and resid 283 through 295 removed outlier: 3.793A pdb=" N SER R 295 " --> pdb=" O ILE R 291 " (cutoff:3.500A) Processing helix chain 'R' and resid 297 through 303 Processing helix chain 'R' and resid 306 through 316 removed outlier: 3.588A pdb=" N THR R 312 " --> pdb=" O GLU R 308 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS R 314 " --> pdb=" O ARG R 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 39 removed outlier: 4.059A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 63 removed outlier: 3.806A pdb=" N TYR A 63 " --> pdb=" O GLN A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 239 Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.635A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.687A pdb=" N ARG A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 10 through 24 removed outlier: 3.758A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'S' and resid 62 through 65 removed outlier: 3.572A pdb=" N LYS S 65 " --> pdb=" O ASP S 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 62 through 65' Processing helix chain 'S' and resid 74 through 76 No H-bonds generated for 'chain 'S' and resid 74 through 76' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.883A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.566A pdb=" N ASP S 223 " --> pdb=" O GLU S 220 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 220 through 224' Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.044A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.233A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 52 removed outlier: 4.286A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.798A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.853A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.666A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 6.527A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.628A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.451A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.573A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER N 25 " --> pdb=" O GLN N 3 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR N 80 " --> pdb=" O SER N 71 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.645A pdb=" N THR N 125 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.519A pdb=" N THR S 78 " --> pdb=" O ASP S 73 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.135A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.135A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.755A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 155 through 160 removed outlier: 3.543A pdb=" N VAL S 155 " --> pdb=" O ILE S 216 " (cutoff:3.500A) 457 hydrogen bonds defined for protein. 1269 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: 1.47 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3168 1.34 - 1.46: 1973 1.46 - 1.58: 4708 1.58 - 1.69: 0 1.69 - 1.81: 103 Bond restraints: 9952 Sorted by residual: bond pdb=" CA TYR R 268 " pdb=" C TYR R 268 " ideal model delta sigma weight residual 1.523 1.493 0.030 1.34e-02 5.57e+03 5.11e+00 bond pdb=" CA PHE R 45 " pdb=" C PHE R 45 " ideal model delta sigma weight residual 1.531 1.507 0.025 1.12e-02 7.97e+03 4.82e+00 bond pdb=" CA ALA B 299 " pdb=" C ALA B 299 " ideal model delta sigma weight residual 1.522 1.484 0.037 1.72e-02 3.38e+03 4.75e+00 bond pdb=" CA HIS R 264 " pdb=" C HIS R 264 " ideal model delta sigma weight residual 1.525 1.496 0.029 1.37e-02 5.33e+03 4.46e+00 bond pdb=" CA LEU R 263 " pdb=" C LEU R 263 " ideal model delta sigma weight residual 1.524 1.500 0.024 1.27e-02 6.20e+03 3.57e+00 ... (remaining 9947 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 13049 1.61 - 3.23: 365 3.23 - 4.84: 52 4.84 - 6.46: 16 6.46 - 8.07: 2 Bond angle restraints: 13484 Sorted by residual: angle pdb=" N VAL R 124 " pdb=" CA VAL R 124 " pdb=" C VAL R 124 " ideal model delta sigma weight residual 112.96 108.30 4.66 1.00e+00 1.00e+00 2.17e+01 angle pdb=" N ALA B 140 " pdb=" CA ALA B 140 " pdb=" C ALA B 140 " ideal model delta sigma weight residual 110.44 115.35 -4.91 1.20e+00 6.94e-01 1.67e+01 angle pdb=" N LEU R 263 " pdb=" CA LEU R 263 " pdb=" C LEU R 263 " ideal model delta sigma weight residual 111.07 106.80 4.27 1.07e+00 8.73e-01 1.60e+01 angle pdb=" N ASN R 123 " pdb=" CA ASN R 123 " pdb=" C ASN R 123 " ideal model delta sigma weight residual 114.75 110.09 4.66 1.26e+00 6.30e-01 1.37e+01 angle pdb=" N PHE R 45 " pdb=" CA PHE R 45 " pdb=" C PHE R 45 " ideal model delta sigma weight residual 110.70 105.22 5.48 1.55e+00 4.16e-01 1.25e+01 ... (remaining 13479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.77: 5341 16.77 - 33.53: 490 33.53 - 50.30: 69 50.30 - 67.07: 13 67.07 - 83.84: 13 Dihedral angle restraints: 5926 sinusoidal: 2286 harmonic: 3640 Sorted by residual: dihedral pdb=" CA GLY B 202 " pdb=" C GLY B 202 " pdb=" N ALA B 203 " pdb=" CA ALA B 203 " ideal model delta harmonic sigma weight residual -180.00 -157.26 -22.74 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -123.35 37.35 1 1.00e+01 1.00e-02 1.97e+01 dihedral pdb=" CA GLY B 162 " pdb=" C GLY B 162 " pdb=" N ASP B 163 " pdb=" CA ASP B 163 " ideal model delta harmonic sigma weight residual 180.00 160.13 19.87 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 5923 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 935 0.035 - 0.069: 414 0.069 - 0.104: 136 0.104 - 0.138: 47 0.138 - 0.173: 6 Chirality restraints: 1538 Sorted by residual: chirality pdb=" CG LEU S 174 " pdb=" CB LEU S 174 " pdb=" CD1 LEU S 174 " pdb=" CD2 LEU S 174 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.48e-01 chirality pdb=" CG LEU R 141 " pdb=" CB LEU R 141 " pdb=" CD1 LEU R 141 " pdb=" CD2 LEU R 141 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.64e-01 chirality pdb=" CB THR N 28 " pdb=" CA THR N 28 " pdb=" OG1 THR N 28 " pdb=" CG2 THR N 28 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.64e-01 ... (remaining 1535 not shown) Planarity restraints: 1711 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN G 59 " -0.082 5.00e-02 4.00e+02 1.23e-01 2.41e+01 pdb=" N PRO G 60 " 0.212 5.00e-02 4.00e+02 pdb=" CA PRO G 60 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO G 60 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " -0.039 5.00e-02 4.00e+02 6.00e-02 5.77e+00 pdb=" N PRO G 49 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN R 294 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.18e+00 pdb=" CG ASN R 294 " 0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN R 294 " -0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN R 294 " -0.013 2.00e-02 2.50e+03 ... (remaining 1708 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 484 2.72 - 3.27: 9630 3.27 - 3.81: 15748 3.81 - 4.36: 19211 4.36 - 4.90: 33754 Nonbonded interactions: 78827 Sorted by model distance: nonbonded pdb=" NH1 ARG B 22 " pdb=" O ASP B 258 " model vdw 2.179 3.120 nonbonded pdb=" O ARG B 22 " pdb=" NE2 GLN B 259 " model vdw 2.212 3.120 nonbonded pdb=" CA PHE R 267 " pdb=" OG SER R 270 " model vdw 2.234 3.470 nonbonded pdb=" OE1 GLU A 330 " pdb=" OG1 THR A 335 " model vdw 2.240 3.040 nonbonded pdb=" OD1 ASP S 62 " pdb=" NZ LYS S 65 " model vdw 2.282 3.120 ... (remaining 78822 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.460 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: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.310 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.910 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 9958 Z= 0.204 Angle : 0.744 41.898 13496 Z= 0.416 Chirality : 0.045 0.173 1538 Planarity : 0.006 0.123 1711 Dihedral : 13.291 83.835 3562 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: -0.23 (0.24), residues: 1236 helix: 1.15 (0.27), residues: 397 sheet: -0.19 (0.30), residues: 323 loop : -1.12 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 219 TYR 0.033 0.002 TYR B 59 PHE 0.034 0.002 PHE S 68 TRP 0.016 0.002 TRP R 174 HIS 0.010 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00442 ( 9952) covalent geometry : angle 0.64979 (13484) SS BOND : bond 0.00791 ( 6) SS BOND : angle 12.19777 ( 12) hydrogen bonds : bond 0.18918 ( 453) hydrogen bonds : angle 6.96523 ( 1269) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 0.296 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: R 97 ASN cc_start: 0.8439 (m-40) cc_final: 0.8171 (m-40) REVERT: R 289 ILE cc_start: 0.8698 (tp) cc_final: 0.8237 (tp) REVERT: B 329 THR cc_start: 0.9104 (m) cc_final: 0.8879 (p) REVERT: N 126 VAL cc_start: 0.8752 (t) cc_final: 0.8526 (m) REVERT: S 223 ASP cc_start: 0.7675 (m-30) cc_final: 0.7302 (m-30) outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 0.1194 time to fit residues: 44.3680 Evaluate side-chains 195 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.4980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 8.9990 chunk 53 optimal weight: 0.0870 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 264 HIS R 294 ASN A 29 GLN A 294 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN N 82 GLN ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 77 ASN S 194 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.093292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.062176 restraints weight = 20420.304| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 3.17 r_work: 0.2586 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9958 Z= 0.138 Angle : 0.630 10.104 13496 Z= 0.329 Chirality : 0.044 0.217 1538 Planarity : 0.005 0.075 1711 Dihedral : 4.708 20.934 1364 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.41 % Allowed : 9.03 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: 0.24 (0.24), residues: 1236 helix: 1.74 (0.27), residues: 384 sheet: 0.20 (0.30), residues: 312 loop : -1.02 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 22 TYR 0.027 0.001 TYR R 187 PHE 0.018 0.002 PHE R 261 TRP 0.012 0.001 TRP B 339 HIS 0.008 0.001 HIS R 264 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 9952) covalent geometry : angle 0.62958 (13484) SS BOND : bond 0.00239 ( 6) SS BOND : angle 1.04874 ( 12) hydrogen bonds : bond 0.04101 ( 453) hydrogen bonds : angle 4.85820 ( 1269) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 211 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 156 GLN cc_start: 0.8787 (mp10) cc_final: 0.8480 (mp10) REVERT: R 161 MET cc_start: 0.8552 (ppp) cc_final: 0.8224 (ppp) REVERT: R 302 TYR cc_start: 0.8646 (m-80) cc_final: 0.8392 (m-80) REVERT: A 38 ARG cc_start: 0.8488 (mtp-110) cc_final: 0.7992 (ttp80) REVERT: A 60 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.8636 (mtm) REVERT: A 239 ASN cc_start: 0.8626 (t0) cc_final: 0.8302 (t0) REVERT: B 273 ILE cc_start: 0.9301 (mp) cc_final: 0.9074 (mp) REVERT: B 323 ASP cc_start: 0.8807 (t0) cc_final: 0.8347 (t0) REVERT: B 329 THR cc_start: 0.9398 (m) cc_final: 0.8969 (p) REVERT: B 337 LYS cc_start: 0.8792 (mttm) cc_final: 0.8493 (mttp) REVERT: G 29 LYS cc_start: 0.9003 (mmmm) cc_final: 0.8760 (mmmm) REVERT: N 73 ASP cc_start: 0.7877 (t0) cc_final: 0.6696 (t0) REVERT: N 79 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7971 (tt) REVERT: N 89 GLU cc_start: 0.9025 (mp0) cc_final: 0.8625 (pm20) REVERT: S 218 ARG cc_start: 0.8962 (mtm110) cc_final: 0.8577 (mpp80) REVERT: S 222 GLU cc_start: 0.8361 (pm20) cc_final: 0.8120 (pm20) REVERT: S 223 ASP cc_start: 0.8388 (m-30) cc_final: 0.7380 (m-30) outliers start: 15 outliers final: 6 residues processed: 217 average time/residue: 0.1089 time to fit residues: 31.6263 Evaluate side-chains 195 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 187 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 79 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 78 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 264 HIS R 294 ASN A 29 GLN A 31 GLN ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.091493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.060090 restraints weight = 20443.851| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 3.10 r_work: 0.2534 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9958 Z= 0.172 Angle : 0.606 9.939 13496 Z= 0.315 Chirality : 0.043 0.174 1538 Planarity : 0.004 0.049 1711 Dihedral : 4.601 21.175 1364 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.60 % Allowed : 11.48 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: 0.40 (0.24), residues: 1236 helix: 1.90 (0.27), residues: 384 sheet: 0.24 (0.28), residues: 328 loop : -0.94 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 72 TYR 0.027 0.001 TYR R 187 PHE 0.016 0.001 PHE R 261 TRP 0.010 0.001 TRP B 82 HIS 0.011 0.001 HIS R 264 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 9952) covalent geometry : angle 0.60604 (13484) SS BOND : bond 0.00192 ( 6) SS BOND : angle 0.86360 ( 12) hydrogen bonds : bond 0.03842 ( 453) hydrogen bonds : angle 4.60686 ( 1269) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 199 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 156 GLN cc_start: 0.8737 (mp10) cc_final: 0.8436 (mp10) REVERT: R 161 MET cc_start: 0.8565 (ppp) cc_final: 0.8165 (ppp) REVERT: R 241 MET cc_start: 0.8465 (mmp) cc_final: 0.7835 (ttp) REVERT: R 257 CYS cc_start: 0.9018 (m) cc_final: 0.8794 (m) REVERT: R 302 TYR cc_start: 0.8721 (m-80) cc_final: 0.8365 (m-80) REVERT: B 10 GLU cc_start: 0.8896 (mp0) cc_final: 0.8681 (pm20) REVERT: B 262 MET cc_start: 0.8868 (tpp) cc_final: 0.7811 (tpp) REVERT: B 273 ILE cc_start: 0.9359 (mp) cc_final: 0.9120 (mp) REVERT: B 323 ASP cc_start: 0.9008 (t0) cc_final: 0.8746 (t0) REVERT: G 29 LYS cc_start: 0.8966 (mmmm) cc_final: 0.8671 (mmmm) REVERT: G 32 LYS cc_start: 0.9274 (mtpp) cc_final: 0.8770 (tptm) REVERT: G 36 ASP cc_start: 0.9175 (m-30) cc_final: 0.8847 (m-30) REVERT: N 73 ASP cc_start: 0.7918 (t0) cc_final: 0.6607 (t0) REVERT: N 76 LYS cc_start: 0.9658 (mtmm) cc_final: 0.9412 (mtmm) REVERT: N 87 LYS cc_start: 0.9046 (ptpt) cc_final: 0.8403 (ptpp) REVERT: S 83 MET cc_start: 0.9330 (mtm) cc_final: 0.9095 (mtm) REVERT: S 218 ARG cc_start: 0.8928 (mtm110) cc_final: 0.8560 (mpp80) REVERT: S 220 GLU cc_start: 0.8589 (mp0) cc_final: 0.8250 (mp0) REVERT: S 222 GLU cc_start: 0.8474 (pm20) cc_final: 0.8128 (tm-30) REVERT: S 223 ASP cc_start: 0.8516 (m-30) cc_final: 0.8140 (m-30) outliers start: 17 outliers final: 12 residues processed: 204 average time/residue: 0.1181 time to fit residues: 32.0650 Evaluate side-chains 198 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 186 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 164 LYS Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 186 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 46 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 11 optimal weight: 0.0670 chunk 8 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 93 optimal weight: 0.7980 chunk 113 optimal weight: 6.9990 overall best weight: 0.6722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 222 HIS R 285 ASN A 31 GLN ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 ASN ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.092828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.061033 restraints weight = 20760.980| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 3.17 r_work: 0.2564 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 9958 Z= 0.124 Angle : 0.568 6.974 13496 Z= 0.297 Chirality : 0.042 0.239 1538 Planarity : 0.004 0.039 1711 Dihedral : 4.522 41.356 1364 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.69 % Allowed : 13.26 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: 0.56 (0.24), residues: 1236 helix: 2.06 (0.27), residues: 384 sheet: 0.45 (0.28), residues: 319 loop : -0.94 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 356 TYR 0.027 0.001 TYR R 187 PHE 0.016 0.001 PHE R 280 TRP 0.010 0.001 TRP B 82 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 9952) covalent geometry : angle 0.56369 (13484) SS BOND : bond 0.00748 ( 6) SS BOND : angle 2.42177 ( 12) hydrogen bonds : bond 0.03422 ( 453) hydrogen bonds : angle 4.43528 ( 1269) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 192 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 156 GLN cc_start: 0.8791 (mp10) cc_final: 0.8497 (mp10) REVERT: R 161 MET cc_start: 0.8530 (ppp) cc_final: 0.8063 (ppp) REVERT: R 241 MET cc_start: 0.8484 (mmp) cc_final: 0.7866 (ttp) REVERT: R 302 TYR cc_start: 0.8795 (m-80) cc_final: 0.8435 (m-80) REVERT: A 38 ARG cc_start: 0.8565 (mtp-110) cc_final: 0.8126 (ttp80) REVERT: B 262 MET cc_start: 0.8834 (tpp) cc_final: 0.7807 (tpp) REVERT: B 273 ILE cc_start: 0.9373 (mp) cc_final: 0.9130 (mp) REVERT: B 323 ASP cc_start: 0.9100 (t0) cc_final: 0.8840 (t0) REVERT: G 29 LYS cc_start: 0.8930 (mmmm) cc_final: 0.8607 (mmmm) REVERT: G 32 LYS cc_start: 0.9262 (mtpp) cc_final: 0.8766 (tptm) REVERT: G 36 ASP cc_start: 0.9168 (m-30) cc_final: 0.8890 (m-30) REVERT: G 46 LYS cc_start: 0.9367 (tppp) cc_final: 0.8982 (tppt) REVERT: N 65 LYS cc_start: 0.8981 (ttmt) cc_final: 0.8697 (ttmm) REVERT: N 73 ASP cc_start: 0.8055 (t0) cc_final: 0.6679 (t0) REVERT: N 76 LYS cc_start: 0.9619 (mtmm) cc_final: 0.9337 (mtmm) REVERT: N 87 LYS cc_start: 0.8959 (ptpt) cc_final: 0.8411 (ptpp) REVERT: S 73 ASP cc_start: 0.8699 (t70) cc_final: 0.8493 (p0) REVERT: S 76 LYS cc_start: 0.9475 (ptpp) cc_final: 0.9255 (ptpp) REVERT: S 83 MET cc_start: 0.9272 (mtm) cc_final: 0.9004 (mtm) REVERT: S 183 GLN cc_start: 0.9046 (mt0) cc_final: 0.8811 (mt0) REVERT: S 218 ARG cc_start: 0.8912 (mtm110) cc_final: 0.8512 (mpp80) REVERT: S 220 GLU cc_start: 0.8426 (mp0) cc_final: 0.8180 (mp0) REVERT: S 222 GLU cc_start: 0.8547 (pm20) cc_final: 0.7858 (pm20) REVERT: S 223 ASP cc_start: 0.8589 (m-30) cc_final: 0.6988 (m-30) outliers start: 18 outliers final: 11 residues processed: 198 average time/residue: 0.1184 time to fit residues: 31.2325 Evaluate side-chains 195 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 184 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 171 SER Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 281 MET Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 247 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 67 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 110 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 23 optimal weight: 7.9990 chunk 103 optimal weight: 0.7980 chunk 90 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.091228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.059580 restraints weight = 20631.673| |-----------------------------------------------------------------------------| r_work (start): 0.2696 rms_B_bonded: 3.12 r_work: 0.2526 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9958 Z= 0.161 Angle : 0.600 10.572 13496 Z= 0.309 Chirality : 0.043 0.253 1538 Planarity : 0.004 0.037 1711 Dihedral : 4.516 31.414 1364 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.54 % Allowed : 14.11 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: 0.64 (0.24), residues: 1236 helix: 2.08 (0.27), residues: 384 sheet: 0.42 (0.28), residues: 328 loop : -0.82 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 27 TYR 0.028 0.001 TYR R 187 PHE 0.012 0.001 PHE R 313 TRP 0.009 0.001 TRP B 82 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 9952) covalent geometry : angle 0.59781 (13484) SS BOND : bond 0.00362 ( 6) SS BOND : angle 1.78476 ( 12) hydrogen bonds : bond 0.03498 ( 453) hydrogen bonds : angle 4.34450 ( 1269) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 190 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 156 GLN cc_start: 0.8771 (mp10) cc_final: 0.8470 (mp10) REVERT: R 161 MET cc_start: 0.8619 (ppp) cc_final: 0.8116 (ppp) REVERT: R 241 MET cc_start: 0.8481 (mmp) cc_final: 0.7863 (ttp) REVERT: R 302 TYR cc_start: 0.8802 (m-80) cc_final: 0.8396 (m-80) REVERT: R 305 ARG cc_start: 0.8704 (mmm-85) cc_final: 0.8472 (mmm-85) REVERT: A 38 ARG cc_start: 0.8617 (mtp-110) cc_final: 0.8238 (ttp80) REVERT: B 14 LEU cc_start: 0.9442 (mm) cc_final: 0.8806 (mm) REVERT: B 262 MET cc_start: 0.8865 (tpp) cc_final: 0.8204 (tpp) REVERT: B 273 ILE cc_start: 0.9397 (mp) cc_final: 0.9140 (mp) REVERT: B 323 ASP cc_start: 0.9151 (t0) cc_final: 0.8865 (t0) REVERT: G 29 LYS cc_start: 0.8959 (mmmm) cc_final: 0.8609 (mmmm) REVERT: G 32 LYS cc_start: 0.9251 (mtpp) cc_final: 0.8760 (tptm) REVERT: G 36 ASP cc_start: 0.9205 (m-30) cc_final: 0.8921 (m-30) REVERT: G 46 LYS cc_start: 0.9430 (tppp) cc_final: 0.8997 (tppt) REVERT: N 65 LYS cc_start: 0.9053 (ttmt) cc_final: 0.8752 (ttmm) REVERT: N 73 ASP cc_start: 0.8189 (t0) cc_final: 0.7018 (t0) REVERT: N 76 LYS cc_start: 0.9639 (mtmm) cc_final: 0.9374 (mtmm) REVERT: N 87 LYS cc_start: 0.9082 (ptpt) cc_final: 0.8586 (ptpp) REVERT: S 34 MET cc_start: 0.9566 (mmm) cc_final: 0.9264 (mmm) REVERT: S 73 ASP cc_start: 0.8683 (t70) cc_final: 0.8270 (p0) REVERT: S 76 LYS cc_start: 0.9493 (ptpp) cc_final: 0.9151 (ptpp) REVERT: S 83 MET cc_start: 0.9303 (mtm) cc_final: 0.8991 (mtm) REVERT: S 183 GLN cc_start: 0.9048 (mt0) cc_final: 0.8792 (mt0) REVERT: S 218 ARG cc_start: 0.8898 (mtm110) cc_final: 0.8574 (mpp80) REVERT: S 222 GLU cc_start: 0.8603 (pm20) cc_final: 0.8337 (pm20) REVERT: S 223 ASP cc_start: 0.8575 (m-30) cc_final: 0.7439 (m-30) outliers start: 27 outliers final: 16 residues processed: 205 average time/residue: 0.1165 time to fit residues: 31.7064 Evaluate side-chains 199 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 183 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 164 LYS Chi-restraints excluded: chain R residue 171 SER Chi-restraints excluded: chain R residue 172 CYS Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 281 MET Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 247 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 57 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 105 optimal weight: 0.8980 chunk 7 optimal weight: 20.0000 chunk 64 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 62 ASN A 31 GLN ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.091758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.060535 restraints weight = 20579.554| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 3.10 r_work: 0.2552 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9958 Z= 0.127 Angle : 0.590 9.496 13496 Z= 0.302 Chirality : 0.042 0.164 1538 Planarity : 0.004 0.038 1711 Dihedral : 4.411 26.810 1364 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.98 % Allowed : 14.86 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: 0.72 (0.24), residues: 1236 helix: 2.15 (0.27), residues: 384 sheet: 0.48 (0.28), residues: 328 loop : -0.78 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 356 TYR 0.029 0.001 TYR R 187 PHE 0.036 0.001 PHE R 313 TRP 0.010 0.001 TRP B 82 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 9952) covalent geometry : angle 0.58847 (13484) SS BOND : bond 0.00261 ( 6) SS BOND : angle 1.45444 ( 12) hydrogen bonds : bond 0.03276 ( 453) hydrogen bonds : angle 4.24748 ( 1269) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 192 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 156 GLN cc_start: 0.8785 (mp10) cc_final: 0.8486 (mp10) REVERT: R 161 MET cc_start: 0.8636 (ppp) cc_final: 0.8107 (ppp) REVERT: R 187 TYR cc_start: 0.8433 (t80) cc_final: 0.8117 (t80) REVERT: R 241 MET cc_start: 0.8465 (mmp) cc_final: 0.7840 (ttp) REVERT: R 304 LEU cc_start: 0.8612 (mm) cc_final: 0.8085 (mt) REVERT: R 305 ARG cc_start: 0.8712 (mmm-85) cc_final: 0.8502 (mmm-85) REVERT: A 38 ARG cc_start: 0.8590 (mtp-110) cc_final: 0.8229 (ttp80) REVERT: B 226 GLU cc_start: 0.9167 (mt-10) cc_final: 0.8958 (mt-10) REVERT: B 262 MET cc_start: 0.8866 (tpp) cc_final: 0.7816 (tpp) REVERT: B 273 ILE cc_start: 0.9393 (mp) cc_final: 0.9133 (mp) REVERT: B 323 ASP cc_start: 0.9137 (t0) cc_final: 0.8887 (t0) REVERT: G 32 LYS cc_start: 0.9256 (mtpp) cc_final: 0.8746 (tptm) REVERT: G 36 ASP cc_start: 0.9261 (m-30) cc_final: 0.8993 (m-30) REVERT: G 46 LYS cc_start: 0.9446 (tppp) cc_final: 0.9041 (tppt) REVERT: N 65 LYS cc_start: 0.8942 (ttmt) cc_final: 0.8622 (ttmm) REVERT: N 73 ASP cc_start: 0.8205 (t0) cc_final: 0.6959 (t0) REVERT: N 76 LYS cc_start: 0.9648 (mtmm) cc_final: 0.9360 (mtmm) REVERT: S 83 MET cc_start: 0.9288 (mtm) cc_final: 0.8937 (mtm) REVERT: S 153 GLU cc_start: 0.8909 (pt0) cc_final: 0.8705 (pt0) REVERT: S 183 GLN cc_start: 0.9020 (mt0) cc_final: 0.8766 (mt0) REVERT: S 201 ASP cc_start: 0.9182 (p0) cc_final: 0.8950 (p0) REVERT: S 218 ARG cc_start: 0.8714 (mtm110) cc_final: 0.8381 (mpp80) REVERT: S 220 GLU cc_start: 0.8629 (mp0) cc_final: 0.8276 (pm20) REVERT: S 222 GLU cc_start: 0.8481 (pm20) cc_final: 0.7997 (pp20) REVERT: S 223 ASP cc_start: 0.8692 (m-30) cc_final: 0.7799 (m-30) outliers start: 21 outliers final: 13 residues processed: 202 average time/residue: 0.1198 time to fit residues: 31.9107 Evaluate side-chains 196 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 183 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 137 ILE Chi-restraints excluded: chain R residue 164 LYS Chi-restraints excluded: chain R residue 171 SER Chi-restraints excluded: chain R residue 172 CYS Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 281 MET Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain S residue 186 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 2.9990 chunk 7 optimal weight: 30.0000 chunk 23 optimal weight: 0.0270 chunk 83 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 15 optimal weight: 0.0980 chunk 12 optimal weight: 8.9990 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.091621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.060279 restraints weight = 20619.099| |-----------------------------------------------------------------------------| r_work (start): 0.2718 rms_B_bonded: 3.15 r_work: 0.2549 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9958 Z= 0.137 Angle : 0.608 9.330 13496 Z= 0.310 Chirality : 0.043 0.177 1538 Planarity : 0.004 0.049 1711 Dihedral : 4.363 22.193 1364 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.79 % Allowed : 15.71 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: 0.84 (0.24), residues: 1236 helix: 2.34 (0.27), residues: 379 sheet: 0.46 (0.28), residues: 330 loop : -0.70 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 72 TYR 0.027 0.001 TYR R 187 PHE 0.014 0.001 PHE R 261 TRP 0.010 0.001 TRP B 82 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 9952) covalent geometry : angle 0.60700 (13484) SS BOND : bond 0.00220 ( 6) SS BOND : angle 1.32396 ( 12) hydrogen bonds : bond 0.03292 ( 453) hydrogen bonds : angle 4.21326 ( 1269) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 186 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 156 GLN cc_start: 0.8756 (mp10) cc_final: 0.8457 (mp10) REVERT: R 161 MET cc_start: 0.8691 (ppp) cc_final: 0.8158 (ppp) REVERT: R 187 TYR cc_start: 0.8407 (t80) cc_final: 0.8127 (t80) REVERT: R 241 MET cc_start: 0.8428 (mmp) cc_final: 0.7766 (ttp) REVERT: R 292 MET cc_start: 0.8649 (mtp) cc_final: 0.8392 (mmm) REVERT: R 304 LEU cc_start: 0.8678 (mm) cc_final: 0.8178 (mt) REVERT: R 305 ARG cc_start: 0.8734 (mmm-85) cc_final: 0.8513 (mmm-85) REVERT: A 38 ARG cc_start: 0.8605 (mtp-110) cc_final: 0.8234 (ttp80) REVERT: B 226 GLU cc_start: 0.9192 (mt-10) cc_final: 0.8942 (mt-10) REVERT: B 262 MET cc_start: 0.8862 (tpp) cc_final: 0.7756 (tpp) REVERT: B 273 ILE cc_start: 0.9381 (mp) cc_final: 0.9114 (mp) REVERT: B 323 ASP cc_start: 0.9177 (t0) cc_final: 0.8862 (t0) REVERT: B 325 MET cc_start: 0.8944 (tpp) cc_final: 0.8694 (tpp) REVERT: G 29 LYS cc_start: 0.8766 (mmmm) cc_final: 0.8216 (mmmm) REVERT: G 32 LYS cc_start: 0.9265 (mtpp) cc_final: 0.8748 (tptm) REVERT: G 36 ASP cc_start: 0.9279 (m-30) cc_final: 0.8995 (m-30) REVERT: G 46 LYS cc_start: 0.9459 (tppp) cc_final: 0.9090 (tppt) REVERT: G 47 GLU cc_start: 0.8826 (mp0) cc_final: 0.8582 (mp0) REVERT: G 54 VAL cc_start: 0.9201 (m) cc_final: 0.8959 (p) REVERT: N 65 LYS cc_start: 0.8991 (ttmt) cc_final: 0.8685 (ttmm) REVERT: N 73 ASP cc_start: 0.8256 (t0) cc_final: 0.7088 (t0) REVERT: N 76 LYS cc_start: 0.9659 (mtmm) cc_final: 0.9354 (mtmm) REVERT: N 88 PRO cc_start: 0.9205 (Cg_exo) cc_final: 0.8934 (Cg_endo) REVERT: S 34 MET cc_start: 0.9533 (mmm) cc_final: 0.9292 (mmm) REVERT: S 83 MET cc_start: 0.9314 (mtm) cc_final: 0.8958 (mtm) REVERT: S 201 ASP cc_start: 0.9189 (p0) cc_final: 0.8963 (p0) REVERT: S 223 ASP cc_start: 0.8502 (m-30) cc_final: 0.7917 (m-30) outliers start: 19 outliers final: 15 residues processed: 193 average time/residue: 0.1166 time to fit residues: 30.0207 Evaluate side-chains 194 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 179 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 137 ILE Chi-restraints excluded: chain R residue 164 LYS Chi-restraints excluded: chain R residue 171 SER Chi-restraints excluded: chain R residue 182 ILE Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 281 MET Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 186 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 16 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 7 optimal weight: 30.0000 chunk 57 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.091899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.060746 restraints weight = 20634.547| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 3.14 r_work: 0.2551 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9958 Z= 0.130 Angle : 0.628 13.296 13496 Z= 0.316 Chirality : 0.043 0.227 1538 Planarity : 0.004 0.036 1711 Dihedral : 4.312 19.566 1364 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.69 % Allowed : 16.46 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: 0.93 (0.25), residues: 1236 helix: 2.40 (0.27), residues: 377 sheet: 0.52 (0.28), residues: 328 loop : -0.62 (0.28), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 356 TYR 0.026 0.001 TYR R 187 PHE 0.055 0.001 PHE R 184 TRP 0.009 0.001 TRP B 82 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 9952) covalent geometry : angle 0.62706 (13484) SS BOND : bond 0.00204 ( 6) SS BOND : angle 1.19276 ( 12) hydrogen bonds : bond 0.03200 ( 453) hydrogen bonds : angle 4.18195 ( 1269) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 188 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 156 GLN cc_start: 0.8760 (mp10) cc_final: 0.8462 (mp10) REVERT: R 157 TYR cc_start: 0.8791 (t80) cc_final: 0.8550 (t80) REVERT: R 161 MET cc_start: 0.8716 (ppp) cc_final: 0.8198 (ppp) REVERT: R 187 TYR cc_start: 0.8372 (t80) cc_final: 0.8155 (t80) REVERT: R 241 MET cc_start: 0.8409 (mmp) cc_final: 0.7743 (ttp) REVERT: R 292 MET cc_start: 0.8651 (mtp) cc_final: 0.8432 (mmm) REVERT: R 304 LEU cc_start: 0.8698 (mm) cc_final: 0.8385 (mm) REVERT: A 38 ARG cc_start: 0.8582 (mtp-110) cc_final: 0.8209 (ttp80) REVERT: B 262 MET cc_start: 0.8845 (tpp) cc_final: 0.7740 (tpp) REVERT: B 273 ILE cc_start: 0.9383 (mp) cc_final: 0.9118 (mp) REVERT: B 323 ASP cc_start: 0.9157 (t0) cc_final: 0.8841 (t0) REVERT: B 325 MET cc_start: 0.8932 (tpp) cc_final: 0.8703 (tpp) REVERT: G 29 LYS cc_start: 0.8796 (mmmm) cc_final: 0.8264 (mmmm) REVERT: G 32 LYS cc_start: 0.9253 (mtpp) cc_final: 0.8751 (tptm) REVERT: G 36 ASP cc_start: 0.9279 (m-30) cc_final: 0.9006 (m-30) REVERT: G 46 LYS cc_start: 0.9460 (tppp) cc_final: 0.9095 (tppt) REVERT: G 47 GLU cc_start: 0.8828 (mp0) cc_final: 0.8589 (mp0) REVERT: G 54 VAL cc_start: 0.9211 (m) cc_final: 0.9006 (p) REVERT: N 65 LYS cc_start: 0.8990 (ttmt) cc_final: 0.8723 (ttmm) REVERT: N 73 ASP cc_start: 0.8303 (t0) cc_final: 0.6977 (t0) REVERT: N 76 LYS cc_start: 0.9645 (mtmm) cc_final: 0.9332 (mtmm) REVERT: N 88 PRO cc_start: 0.9220 (Cg_exo) cc_final: 0.8954 (Cg_endo) REVERT: S 34 MET cc_start: 0.9562 (mmm) cc_final: 0.9279 (mmm) REVERT: S 83 MET cc_start: 0.9308 (mtm) cc_final: 0.8938 (mtm) REVERT: S 201 ASP cc_start: 0.9217 (p0) cc_final: 0.8967 (p0) REVERT: S 218 ARG cc_start: 0.8232 (mpp80) cc_final: 0.7988 (mpp80) REVERT: S 220 GLU cc_start: 0.8918 (mp0) cc_final: 0.8686 (mp0) REVERT: S 223 ASP cc_start: 0.8550 (m-30) cc_final: 0.7981 (m-30) outliers start: 18 outliers final: 15 residues processed: 195 average time/residue: 0.1109 time to fit residues: 28.9489 Evaluate side-chains 197 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 182 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 164 LYS Chi-restraints excluded: chain R residue 171 SER Chi-restraints excluded: chain R residue 172 CYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 247 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 22 optimal weight: 2.9990 chunk 114 optimal weight: 30.0000 chunk 28 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 105 optimal weight: 0.2980 chunk 27 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 100 optimal weight: 0.2980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 159 ASN A 31 GLN ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.091165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.059789 restraints weight = 20569.208| |-----------------------------------------------------------------------------| r_work (start): 0.2705 rms_B_bonded: 3.14 r_work: 0.2531 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9958 Z= 0.155 Angle : 0.658 13.490 13496 Z= 0.329 Chirality : 0.044 0.252 1538 Planarity : 0.004 0.036 1711 Dihedral : 4.367 18.968 1364 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.79 % Allowed : 16.93 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: 0.88 (0.25), residues: 1236 helix: 2.23 (0.27), residues: 384 sheet: 0.52 (0.28), residues: 330 loop : -0.60 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 72 TYR 0.025 0.001 TYR R 187 PHE 0.051 0.002 PHE R 184 TRP 0.009 0.001 TRP B 82 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 9952) covalent geometry : angle 0.65734 (13484) SS BOND : bond 0.00195 ( 6) SS BOND : angle 1.16124 ( 12) hydrogen bonds : bond 0.03343 ( 453) hydrogen bonds : angle 4.22976 ( 1269) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 182 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 120 ASN cc_start: 0.7567 (m-40) cc_final: 0.7314 (m110) REVERT: R 156 GLN cc_start: 0.8748 (mp10) cc_final: 0.8470 (mp10) REVERT: R 161 MET cc_start: 0.8720 (ppp) cc_final: 0.8184 (ppp) REVERT: R 204 MET cc_start: 0.7863 (mmp) cc_final: 0.7644 (mmt) REVERT: R 241 MET cc_start: 0.8416 (mmp) cc_final: 0.7762 (ttp) REVERT: R 292 MET cc_start: 0.8668 (mtp) cc_final: 0.8444 (mmm) REVERT: R 304 LEU cc_start: 0.8738 (mm) cc_final: 0.8398 (mm) REVERT: A 38 ARG cc_start: 0.8617 (mtp-110) cc_final: 0.8164 (ttp80) REVERT: B 10 GLU cc_start: 0.9237 (mp0) cc_final: 0.9018 (mp0) REVERT: B 262 MET cc_start: 0.8864 (tpp) cc_final: 0.7755 (tpp) REVERT: B 273 ILE cc_start: 0.9389 (mp) cc_final: 0.9114 (mp) REVERT: B 323 ASP cc_start: 0.9168 (t0) cc_final: 0.8838 (t0) REVERT: B 325 MET cc_start: 0.9005 (tpp) cc_final: 0.8786 (tpp) REVERT: G 29 LYS cc_start: 0.8820 (mmmm) cc_final: 0.8277 (mmmm) REVERT: G 32 LYS cc_start: 0.9260 (mtpp) cc_final: 0.8760 (tptm) REVERT: G 36 ASP cc_start: 0.9283 (m-30) cc_final: 0.9003 (m-30) REVERT: G 46 LYS cc_start: 0.9485 (tppp) cc_final: 0.9114 (tppt) REVERT: G 47 GLU cc_start: 0.8851 (mp0) cc_final: 0.8599 (mp0) REVERT: G 54 VAL cc_start: 0.9261 (m) cc_final: 0.9042 (p) REVERT: G 58 GLU cc_start: 0.9040 (pm20) cc_final: 0.8837 (pm20) REVERT: N 39 GLN cc_start: 0.9345 (OUTLIER) cc_final: 0.8665 (tt0) REVERT: N 65 LYS cc_start: 0.9030 (ttmt) cc_final: 0.8761 (ttmm) REVERT: N 73 ASP cc_start: 0.8291 (t0) cc_final: 0.6925 (t0) REVERT: N 76 LYS cc_start: 0.9655 (mtmm) cc_final: 0.9331 (mtmm) REVERT: N 88 PRO cc_start: 0.9206 (Cg_exo) cc_final: 0.8976 (Cg_endo) REVERT: S 34 MET cc_start: 0.9566 (mmm) cc_final: 0.9300 (mmm) REVERT: S 83 MET cc_start: 0.9316 (mtm) cc_final: 0.8951 (mtm) REVERT: S 201 ASP cc_start: 0.9199 (p0) cc_final: 0.8951 (p0) REVERT: S 218 ARG cc_start: 0.8039 (mpp80) cc_final: 0.7760 (mpp80) REVERT: S 220 GLU cc_start: 0.8824 (mp0) cc_final: 0.8453 (mp0) REVERT: S 223 ASP cc_start: 0.8088 (m-30) cc_final: 0.7346 (m-30) outliers start: 19 outliers final: 16 residues processed: 191 average time/residue: 0.1068 time to fit residues: 27.5487 Evaluate side-chains 198 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 181 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 137 ILE Chi-restraints excluded: chain R residue 164 LYS Chi-restraints excluded: chain R residue 171 SER Chi-restraints excluded: chain R residue 172 CYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 247 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 23 optimal weight: 9.9990 chunk 117 optimal weight: 6.9990 chunk 25 optimal weight: 0.0030 chunk 120 optimal weight: 0.3980 chunk 46 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.8392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.091765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.060538 restraints weight = 20493.353| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 3.14 r_work: 0.2550 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9958 Z= 0.135 Angle : 0.655 14.201 13496 Z= 0.325 Chirality : 0.043 0.253 1538 Planarity : 0.004 0.037 1711 Dihedral : 4.312 21.761 1364 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.79 % Allowed : 17.03 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: 0.89 (0.25), residues: 1236 helix: 2.18 (0.27), residues: 384 sheet: 0.50 (0.28), residues: 329 loop : -0.53 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 356 TYR 0.033 0.001 TYR R 187 PHE 0.047 0.001 PHE R 184 TRP 0.009 0.001 TRP A 234 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 9952) covalent geometry : angle 0.65456 (13484) SS BOND : bond 0.00197 ( 6) SS BOND : angle 1.07225 ( 12) hydrogen bonds : bond 0.03242 ( 453) hydrogen bonds : angle 4.16672 ( 1269) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 183 time to evaluate : 0.375 Fit side-chains REVERT: R 120 ASN cc_start: 0.7613 (m-40) cc_final: 0.7350 (m110) REVERT: R 156 GLN cc_start: 0.8763 (mp10) cc_final: 0.8471 (mp10) REVERT: R 157 TYR cc_start: 0.8815 (t80) cc_final: 0.8589 (t80) REVERT: R 161 MET cc_start: 0.8729 (ppp) cc_final: 0.8216 (ppp) REVERT: R 241 MET cc_start: 0.8373 (mmp) cc_final: 0.7706 (ttp) REVERT: R 304 LEU cc_start: 0.8748 (mm) cc_final: 0.8419 (mm) REVERT: A 38 ARG cc_start: 0.8598 (mtp-110) cc_final: 0.8140 (ttp80) REVERT: B 10 GLU cc_start: 0.9193 (mp0) cc_final: 0.8959 (mp0) REVERT: B 262 MET cc_start: 0.8865 (tpp) cc_final: 0.7750 (tpp) REVERT: B 273 ILE cc_start: 0.9377 (mp) cc_final: 0.9107 (mp) REVERT: B 323 ASP cc_start: 0.9163 (t0) cc_final: 0.8883 (t0) REVERT: G 29 LYS cc_start: 0.8802 (mmmm) cc_final: 0.8260 (mmmm) REVERT: G 32 LYS cc_start: 0.9249 (mtpp) cc_final: 0.8749 (tptm) REVERT: G 36 ASP cc_start: 0.9287 (m-30) cc_final: 0.9003 (m-30) REVERT: G 46 LYS cc_start: 0.9485 (tppp) cc_final: 0.9116 (tppt) REVERT: G 47 GLU cc_start: 0.8853 (mp0) cc_final: 0.8594 (mp0) REVERT: G 54 VAL cc_start: 0.9275 (m) cc_final: 0.9061 (p) REVERT: N 39 GLN cc_start: 0.9330 (OUTLIER) cc_final: 0.8677 (tt0) REVERT: N 73 ASP cc_start: 0.8289 (t0) cc_final: 0.6908 (t0) REVERT: N 76 LYS cc_start: 0.9651 (mtmm) cc_final: 0.9314 (mtmm) REVERT: N 88 PRO cc_start: 0.9213 (Cg_exo) cc_final: 0.8972 (Cg_endo) REVERT: S 34 MET cc_start: 0.9527 (mmm) cc_final: 0.9281 (mmm) REVERT: S 83 MET cc_start: 0.9291 (mtm) cc_final: 0.8911 (mtm) REVERT: S 183 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.8533 (pm20) REVERT: S 201 ASP cc_start: 0.9183 (p0) cc_final: 0.8950 (p0) REVERT: S 218 ARG cc_start: 0.7986 (mpp80) cc_final: 0.7722 (mpp80) REVERT: S 220 GLU cc_start: 0.8849 (mp0) cc_final: 0.8475 (mp0) REVERT: S 223 ASP cc_start: 0.8002 (m-30) cc_final: 0.7232 (m-30) outliers start: 19 outliers final: 15 residues processed: 191 average time/residue: 0.1074 time to fit residues: 27.8904 Evaluate side-chains 199 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 182 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 137 ILE Chi-restraints excluded: chain R residue 164 LYS Chi-restraints excluded: chain R residue 171 SER Chi-restraints excluded: chain R residue 172 CYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 39 GLN Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 186 GLN Chi-restraints excluded: chain S residue 247 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 5 optimal weight: 0.8980 chunk 47 optimal weight: 0.4980 chunk 83 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 111 optimal weight: 0.2980 chunk 65 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 159 ASN A 31 GLN ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 183 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.090729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.059453 restraints weight = 20690.600| |-----------------------------------------------------------------------------| r_work (start): 0.2698 rms_B_bonded: 3.16 r_work: 0.2526 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9958 Z= 0.187 Angle : 0.673 14.323 13496 Z= 0.335 Chirality : 0.044 0.245 1538 Planarity : 0.004 0.039 1711 Dihedral : 4.365 21.721 1364 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.98 % Allowed : 17.12 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: 0.89 (0.25), residues: 1236 helix: 2.19 (0.27), residues: 382 sheet: 0.52 (0.28), residues: 329 loop : -0.53 (0.28), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 72 TYR 0.033 0.001 TYR R 187 PHE 0.045 0.002 PHE R 184 TRP 0.009 0.001 TRP B 82 HIS 0.006 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 9952) covalent geometry : angle 0.67254 (13484) SS BOND : bond 0.00211 ( 6) SS BOND : angle 1.10154 ( 12) hydrogen bonds : bond 0.03348 ( 453) hydrogen bonds : angle 4.19211 ( 1269) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2373.18 seconds wall clock time: 41 minutes 29.77 seconds (2489.77 seconds total)