Starting phenix.real_space_refine on Sat Aug 8 15:08:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x30_38024/08_2026/8x30_38024.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x30_38024/08_2026/8x30_38024.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x30_38024/08_2026/8x30_38024.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x30_38024/08_2026/8x30_38024.map" model { file = "/net/cci-nas-00/data/ceres_data/8x30_38024/08_2026/8x30_38024.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x30_38024/08_2026/8x30_38024.cif" } resolution = 4.3 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= -0.012 sd= 0.431 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9562 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 290 5.49 5 S 41 5.16 5 C 12780 2.51 5 N 3827 2.21 5 O 4641 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21579 Number of models: 1 Model: "" Number of chains: 17 Chain: "K" Number of atoms: 2304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2304 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 10, 'TRANS': 261} Chain: "M" Number of atoms: 1485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1485 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Chain breaks: 1 Chain: "N" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 576 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain breaks: 1 Chain: "O" Number of atoms: 2380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2380 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 12, 'TRANS': 269} Chain: "P" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 283 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "Q" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1777 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 6, 'TRANS': 206} Chain breaks: 1 Chain: "R" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 813 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain breaks: 1 Chain: "I" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2990 Classifications: {'DNA': 146} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2990 Classifications: {'DNA': 146} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 145} Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "B" Number of atoms: 679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 679 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "C" Number of atoms: 750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 750 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "D" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "F" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 649 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain: "H" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 746 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Time building chain proxies: 4.37, per 1000 atoms: 0.20 Number of scatterers: 21579 At special positions: 0 Unit cell: (139.36, 184.08, 151.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 41 16.00 P 290 15.00 O 4641 8.00 N 3827 7.00 C 12780 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 575.8 milliseconds 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3652 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 4 sheets defined 55.2% alpha, 2.0% beta 144 base pairs and 240 stacking pairs defined. Time for finding SS restraints: 2.24 Creating SS restraints... Processing helix chain 'K' and resid 187 through 192 Processing helix chain 'K' and resid 244 through 259 removed outlier: 3.981A pdb=" N ASN K 250 " --> pdb=" O THR K 246 " (cutoff:3.500A) Processing helix chain 'K' and resid 315 through 330 Processing helix chain 'K' and resid 344 through 362 Processing helix chain 'K' and resid 369 through 374 removed outlier: 3.553A pdb=" N ILE K 373 " --> pdb=" O THR K 369 " (cutoff:3.500A) Processing helix chain 'K' and resid 383 through 391 removed outlier: 4.148A pdb=" N LEU K 391 " --> pdb=" O THR K 387 " (cutoff:3.500A) Processing helix chain 'K' and resid 412 through 416 removed outlier: 3.662A pdb=" N LEU K 416 " --> pdb=" O TYR K 413 " (cutoff:3.500A) Processing helix chain 'M' and resid 153 through 157 Processing helix chain 'M' and resid 165 through 177 removed outlier: 4.283A pdb=" N GLU M 169 " --> pdb=" O ASP M 165 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE M 171 " --> pdb=" O ARG M 167 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLN M 175 " --> pdb=" O PHE M 171 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL M 176 " --> pdb=" O LEU M 172 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN M 177 " --> pdb=" O ASN M 173 " (cutoff:3.500A) Processing helix chain 'M' and resid 188 through 193 removed outlier: 3.833A pdb=" N CYS M 193 " --> pdb=" O PHE M 189 " (cutoff:3.500A) Processing helix chain 'M' and resid 199 through 204 Processing helix chain 'M' and resid 216 through 220 removed outlier: 3.521A pdb=" N LEU M 220 " --> pdb=" O PHE M 217 " (cutoff:3.500A) Processing helix chain 'M' and resid 231 through 239 removed outlier: 3.679A pdb=" N LEU M 238 " --> pdb=" O LEU M 234 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASN M 239 " --> pdb=" O ARG M 235 " (cutoff:3.500A) Processing helix chain 'M' and resid 264 through 269 Processing helix chain 'M' and resid 271 through 287 removed outlier: 5.043A pdb=" N GLU M 281 " --> pdb=" O ASP M 277 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG M 282 " --> pdb=" O TYR M 278 " (cutoff:3.500A) Processing helix chain 'M' and resid 337 through 356 Processing helix chain 'N' and resid 11 through 16 Processing helix chain 'N' and resid 16 through 40 removed outlier: 3.722A pdb=" N GLU N 20 " --> pdb=" O ASN N 16 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLU N 26 " --> pdb=" O ARG N 22 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N GLU N 27 " --> pdb=" O TYR N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 112 removed outlier: 4.061A pdb=" N GLU N 85 " --> pdb=" O SER N 81 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LYS N 86 " --> pdb=" O LEU N 82 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N CYS N 87 " --> pdb=" O GLN N 83 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL N 88 " --> pdb=" O ARG N 84 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ILE N 97 " --> pdb=" O ALA N 93 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N HIS N 100 " --> pdb=" O LEU N 96 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU N 112 " --> pdb=" O ILE N 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 186 through 192 Processing helix chain 'O' and resid 210 through 218 Processing helix chain 'O' and resid 245 through 258 Processing helix chain 'O' and resid 308 through 312 removed outlier: 3.647A pdb=" N TYR O 311 " --> pdb=" O LEU O 308 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN O 312 " --> pdb=" O PRO O 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 308 through 312' Processing helix chain 'O' and resid 316 through 329 Processing helix chain 'O' and resid 345 through 361 Processing helix chain 'O' and resid 370 through 375 removed outlier: 4.068A pdb=" N SER O 375 " --> pdb=" O ASP O 371 " (cutoff:3.500A) Processing helix chain 'O' and resid 382 through 389 removed outlier: 4.556A pdb=" N HIS O 386 " --> pdb=" O THR O 382 " (cutoff:3.500A) Processing helix chain 'P' and resid 15 through 25 removed outlier: 5.164A pdb=" N ARG P 22 " --> pdb=" O SER P 18 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ARG P 23 " --> pdb=" O LEU P 19 " (cutoff:3.500A) Processing helix chain 'P' and resid 25 through 34 Processing helix chain 'P' and resid 34 through 40 Processing helix chain 'Q' and resid 132 through 137 removed outlier: 3.675A pdb=" N TYR Q 137 " --> pdb=" O TYR Q 133 " (cutoff:3.500A) Processing helix chain 'Q' and resid 153 through 157 removed outlier: 3.561A pdb=" N CYS Q 157 " --> pdb=" O VAL Q 154 " (cutoff:3.500A) Processing helix chain 'Q' and resid 165 through 175 removed outlier: 4.226A pdb=" N GLU Q 169 " --> pdb=" O ASP Q 165 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU Q 172 " --> pdb=" O ASP Q 168 " (cutoff:3.500A) Processing helix chain 'Q' and resid 185 through 203 removed outlier: 3.550A pdb=" N ILE Q 191 " --> pdb=" O ASP Q 187 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N SER Q 194 " --> pdb=" O GLU Q 190 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE Q 196 " --> pdb=" O LEU Q 192 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N HIS Q 201 " --> pdb=" O GLU Q 197 " (cutoff:3.500A) Processing helix chain 'Q' and resid 221 through 226 removed outlier: 4.075A pdb=" N LYS Q 226 " --> pdb=" O PRO Q 222 " (cutoff:3.500A) Processing helix chain 'Q' and resid 232 through 242 removed outlier: 3.671A pdb=" N ASN Q 239 " --> pdb=" O ARG Q 235 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU Q 241 " --> pdb=" O GLN Q 237 " (cutoff:3.500A) Processing helix chain 'Q' and resid 263 through 286 removed outlier: 3.700A pdb=" N LEU Q 267 " --> pdb=" O PRO Q 263 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N SER Q 273 " --> pdb=" O GLU Q 269 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LYS Q 274 " --> pdb=" O LYS Q 270 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLU Q 281 " --> pdb=" O ASP Q 277 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG Q 282 " --> pdb=" O TYR Q 278 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS Q 283 " --> pdb=" O TRP Q 279 " (cutoff:3.500A) Processing helix chain 'Q' and resid 331 through 367 removed outlier: 5.123A pdb=" N GLU Q 340 " --> pdb=" O ALA Q 336 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU Q 341 " --> pdb=" O LEU Q 337 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 15 removed outlier: 5.470A pdb=" N GLN R 12 " --> pdb=" O GLU R 8 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ASP R 13 " --> pdb=" O GLN R 9 " (cutoff:3.500A) Processing helix chain 'R' and resid 15 through 24 removed outlier: 4.256A pdb=" N SER R 19 " --> pdb=" O SER R 15 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 51 removed outlier: 4.989A pdb=" N GLN R 44 " --> pdb=" O LYS R 40 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LYS R 45 " --> pdb=" O LYS R 41 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLU R 46 " --> pdb=" O TYR R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 71 through 113 removed outlier: 4.367A pdb=" N GLU R 85 " --> pdb=" O SER R 81 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS R 86 " --> pdb=" O LEU R 82 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N HIS R 100 " --> pdb=" O LEU R 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 56 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.507A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 113 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.588A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL B 54 " --> pdb=" O ILE B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 94 Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 28 through 39 removed outlier: 3.908A pdb=" N ARG C 33 " --> pdb=" O GLY C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 65 Processing helix chain 'C' and resid 66 through 69 Processing helix chain 'C' and resid 70 through 75 Processing helix chain 'C' and resid 80 through 87 removed outlier: 4.230A pdb=" N LEU C 85 " --> pdb=" O THR C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 96 removed outlier: 3.867A pdb=" N ASP C 96 " --> pdb=" O ASP C 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 50 Processing helix chain 'D' and resid 60 through 87 removed outlier: 3.727A pdb=" N ILE D 64 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASN D 87 " --> pdb=" O LEU D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 104 Processing helix chain 'D' and resid 106 through 125 removed outlier: 3.617A pdb=" N SER D 125 " --> pdb=" O VAL D 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.639A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 4.040A pdb=" N ALA E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.519A pdb=" N ILE E 124 " --> pdb=" O GLN E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 38 Processing helix chain 'F' and resid 50 through 77 removed outlier: 4.019A pdb=" N ASP F 68 " --> pdb=" O SER F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 27 through 39 Processing helix chain 'G' and resid 49 through 75 removed outlier: 3.967A pdb=" N LEU G 53 " --> pdb=" O ALA G 49 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA G 55 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N GLU G 63 " --> pdb=" O TYR G 59 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLU G 66 " --> pdb=" O ALA G 62 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA G 72 " --> pdb=" O ALA G 68 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LYS G 73 " --> pdb=" O GLY G 69 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP G 74 " --> pdb=" O ASN G 70 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU G 75 " --> pdb=" O ALA G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 89 Processing helix chain 'G' and resid 91 through 96 removed outlier: 4.134A pdb=" N ASP G 96 " --> pdb=" O ASP G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 99 No H-bonds generated for 'chain 'G' and resid 97 through 99' Processing helix chain 'H' and resid 40 through 52 removed outlier: 3.654A pdb=" N ILE H 44 " --> pdb=" O TYR H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 87 Processing helix chain 'H' and resid 93 through 105 Processing helix chain 'H' and resid 106 through 126 Processing sheet with id=AA1, first strand: chain 'K' and resid 170 through 172 Processing sheet with id=AA2, first strand: chain 'K' and resid 226 through 230 removed outlier: 5.050A pdb=" N GLU K 227 " --> pdb=" O GLU K 238 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLU K 238 " --> pdb=" O GLU K 227 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'O' and resid 170 through 172 Processing sheet with id=AA4, first strand: chain 'O' and resid 229 through 230 removed outlier: 5.999A pdb=" N ARG O 278 " --> pdb=" O LEU O 286 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LEU O 286 " --> pdb=" O ARG O 278 " (cutoff:3.500A) 700 hydrogen bonds defined for protein. 2052 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 348 hydrogen bonds 696 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 240 stacking parallelities Total time for adding SS restraints: 4.11 Time building geometry restraints manager: 1.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3330 1.32 - 1.44: 7502 1.44 - 1.57: 11106 1.57 - 1.69: 580 1.69 - 1.81: 62 Bond restraints: 22580 Sorted by residual: bond pdb=" C3' DA I 61 " pdb=" O3' DA I 61 " ideal model delta sigma weight residual 1.435 1.346 0.089 1.30e-02 5.92e+03 4.68e+01 bond pdb=" C3' DG J 277 " pdb=" O3' DG J 277 " ideal model delta sigma weight residual 1.435 1.350 0.085 1.30e-02 5.92e+03 4.27e+01 bond pdb=" C3' DT I 48 " pdb=" O3' DT I 48 " ideal model delta sigma weight residual 1.435 1.352 0.083 1.30e-02 5.92e+03 4.04e+01 bond pdb=" C3' DT J 276 " pdb=" O3' DT J 276 " ideal model delta sigma weight residual 1.435 1.353 0.082 1.30e-02 5.92e+03 4.00e+01 bond pdb=" C3' DC I 129 " pdb=" O3' DC I 129 " ideal model delta sigma weight residual 1.435 1.355 0.080 1.30e-02 5.92e+03 3.74e+01 ... (remaining 22575 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.42: 30517 3.42 - 6.85: 1042 6.85 - 10.27: 124 10.27 - 13.70: 21 13.70 - 17.12: 3 Bond angle restraints: 31707 Sorted by residual: angle pdb=" O4' DT I 80 " pdb=" C4' DT I 80 " pdb=" C3' DT I 80 " ideal model delta sigma weight residual 106.00 101.27 4.73 6.00e-01 2.78e+00 6.21e+01 angle pdb=" O4' DA I 19 " pdb=" C4' DA I 19 " pdb=" C3' DA I 19 " ideal model delta sigma weight residual 106.00 101.47 4.53 6.00e-01 2.78e+00 5.70e+01 angle pdb=" O4' DG I 58 " pdb=" C4' DG I 58 " pdb=" C3' DG I 58 " ideal model delta sigma weight residual 106.00 101.89 4.11 6.00e-01 2.78e+00 4.69e+01 angle pdb=" O4' DT J 184 " pdb=" C4' DT J 184 " pdb=" C3' DT J 184 " ideal model delta sigma weight residual 106.00 101.91 4.09 6.00e-01 2.78e+00 4.65e+01 angle pdb=" CA TYR G 34 " pdb=" CB TYR G 34 " pdb=" CG TYR G 34 " ideal model delta sigma weight residual 113.90 125.99 -12.09 1.80e+00 3.09e-01 4.51e+01 ... (remaining 31702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.01: 10004 23.01 - 46.02: 2017 46.02 - 69.04: 924 69.04 - 92.05: 54 92.05 - 115.06: 3 Dihedral angle restraints: 13002 sinusoidal: 7376 harmonic: 5626 Sorted by residual: dihedral pdb=" CA LEU K 391 " pdb=" C LEU K 391 " pdb=" N ASN K 392 " pdb=" CA ASN K 392 " ideal model delta harmonic sigma weight residual -180.00 -119.53 -60.47 0 5.00e+00 4.00e-02 1.46e+02 dihedral pdb=" CA TYR G 59 " pdb=" C TYR G 59 " pdb=" N LEU G 60 " pdb=" CA LEU G 60 " ideal model delta harmonic sigma weight residual 180.00 123.32 56.68 0 5.00e+00 4.00e-02 1.29e+02 dihedral pdb=" CA ASP K 269 " pdb=" C ASP K 269 " pdb=" N PRO K 270 " pdb=" CA PRO K 270 " ideal model delta harmonic sigma weight residual -180.00 -133.72 -46.28 0 5.00e+00 4.00e-02 8.57e+01 ... (remaining 12999 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 2957 0.111 - 0.222: 554 0.222 - 0.333: 41 0.333 - 0.443: 2 0.443 - 0.554: 2 Chirality restraints: 3556 Sorted by residual: chirality pdb=" CG LEU G 60 " pdb=" CB LEU G 60 " pdb=" CD1 LEU G 60 " pdb=" CD2 LEU G 60 " both_signs ideal model delta sigma weight residual False -2.59 -2.04 -0.55 2.00e-01 2.50e+01 7.68e+00 chirality pdb=" CB ILE E 62 " pdb=" CA ILE E 62 " pdb=" CG1 ILE E 62 " pdb=" CG2 ILE E 62 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.47 2.00e-01 2.50e+01 5.51e+00 chirality pdb=" CB ILE K 171 " pdb=" CA ILE K 171 " pdb=" CG1 ILE K 171 " pdb=" CG2 ILE K 171 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.59e+00 ... (remaining 3553 not shown) Planarity restraints: 3001 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE H 73 " -0.046 2.00e-02 2.50e+03 2.92e-02 1.50e+01 pdb=" CG PHE H 73 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE H 73 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 PHE H 73 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE H 73 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 PHE H 73 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE H 73 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP O 353 " 0.037 2.00e-02 2.50e+03 2.43e-02 1.48e+01 pdb=" CG TRP O 353 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP O 353 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP O 353 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP O 353 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP O 353 " 0.019 2.00e-02 2.50e+03 pdb=" CE3 TRP O 353 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP O 353 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP O 353 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP O 353 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 19 " 0.053 2.00e-02 2.50e+03 2.28e-02 1.42e+01 pdb=" N9 DA I 19 " -0.034 2.00e-02 2.50e+03 pdb=" C8 DA I 19 " -0.012 2.00e-02 2.50e+03 pdb=" N7 DA I 19 " -0.011 2.00e-02 2.50e+03 pdb=" C5 DA I 19 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DA I 19 " -0.008 2.00e-02 2.50e+03 pdb=" N6 DA I 19 " 0.036 2.00e-02 2.50e+03 pdb=" N1 DA I 19 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 19 " -0.010 2.00e-02 2.50e+03 pdb=" N3 DA I 19 " -0.006 2.00e-02 2.50e+03 pdb=" C4 DA I 19 " -0.007 2.00e-02 2.50e+03 ... (remaining 2998 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 2084 2.71 - 3.26: 21315 3.26 - 3.80: 44995 3.80 - 4.35: 51482 4.35 - 4.90: 71280 Nonbonded interactions: 191156 Sorted by model distance: nonbonded pdb=" OH TYR B 72 " pdb=" O ASP B 85 " model vdw 2.160 3.040 nonbonded pdb=" O ILE D 64 " pdb=" OH TYR F 98 " model vdw 2.180 3.040 nonbonded pdb=" OG SER O 235 " pdb=" OG1 THR O 277 " model vdw 2.188 3.040 nonbonded pdb=" O LEU M 215 " pdb=" OH TYR M 276 " model vdw 2.196 3.040 nonbonded pdb=" O HIS K 386 " pdb=" OG1 THR K 390 " model vdw 2.205 3.040 ... (remaining 191151 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 101) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 113) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 36 through 128) } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = (chain 'O' and resid 160 through 431) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.900 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 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 : 0.012 0.096 22580 Z= 0.952 Angle : 1.494 17.120 31707 Z= 0.992 Chirality : 0.083 0.554 3556 Planarity : 0.009 0.067 3001 Dihedral : 25.514 115.061 9350 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.11 % Allowed : 13.34 % Favored : 86.55 % Rotamer: Outliers : 3.38 % Allowed : 13.99 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.77 % Twisted General : 1.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.37 (0.15), residues: 1866 helix: -3.41 (0.11), residues: 972 sheet: -3.98 (0.59), residues: 40 loop : -3.70 (0.18), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.050 0.003 ARG A 63 TYR 0.059 0.006 TYR G 59 PHE 0.046 0.005 PHE H 73 TRP 0.064 0.006 TRP O 353 HIS 0.028 0.004 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.01194 / 0.95 (22580) covalent geometry : angle 1.49390 / 0.99 (31707) hydrogen bonds : bond 0.15100 / 9.86 ( 1048) hydrogen bonds : angle 7.13046 / 4.80 ( 2748) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 544 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 209 LYS cc_start: 0.8860 (mmpt) cc_final: 0.8598 (mmmt) REVERT: K 243 LYS cc_start: 0.8902 (mptt) cc_final: 0.8440 (mptt) REVERT: K 284 HIS cc_start: 0.7625 (m-70) cc_final: 0.7011 (m-70) REVERT: K 302 VAL cc_start: 0.8850 (t) cc_final: 0.8148 (t) REVERT: K 311 TYR cc_start: 0.7022 (t80) cc_final: 0.6619 (t80) REVERT: K 319 LEU cc_start: 0.7952 (tp) cc_final: 0.7692 (pt) REVERT: K 327 LEU cc_start: 0.9202 (mt) cc_final: 0.8923 (pp) REVERT: K 356 THR cc_start: 0.8006 (p) cc_final: 0.7742 (p) REVERT: K 357 LEU cc_start: 0.8979 (tm) cc_final: 0.8743 (mt) REVERT: K 408 ASP cc_start: 0.7498 (t70) cc_final: 0.6602 (m-30) REVERT: M 156 ASP cc_start: 0.6693 (t70) cc_final: 0.6344 (p0) REVERT: M 214 ILE cc_start: 0.4805 (tt) cc_final: 0.4182 (tt) REVERT: M 215 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7705 (pt) REVERT: M 232 PHE cc_start: 0.8753 (p90) cc_final: 0.8084 (p90) REVERT: M 234 LEU cc_start: 0.9041 (mp) cc_final: 0.8780 (mp) REVERT: M 259 MET cc_start: 0.8207 (mpm) cc_final: 0.7980 (mpm) REVERT: M 278 TYR cc_start: 0.8616 (t80) cc_final: 0.8242 (t80) REVERT: O 200 PHE cc_start: 0.6820 (m-80) cc_final: 0.6552 (m-80) REVERT: O 230 ARG cc_start: 0.8128 (tmt170) cc_final: 0.7827 (ttp-170) REVERT: O 271 PHE cc_start: 0.8098 (p90) cc_final: 0.7360 (p90) REVERT: O 275 CYS cc_start: 0.8051 (t) cc_final: 0.7474 (t) REVERT: O 325 TYR cc_start: 0.8131 (m-10) cc_final: 0.7823 (m-80) REVERT: O 326 GLU cc_start: 0.8663 (tm-30) cc_final: 0.7633 (tm-30) REVERT: P 43 TYR cc_start: 0.8559 (m-80) cc_final: 0.8056 (m-10) REVERT: Q 133 TYR cc_start: 0.7360 (t80) cc_final: 0.7114 (t80) REVERT: Q 201 HIS cc_start: 0.9296 (m90) cc_final: 0.9044 (m-70) REVERT: Q 229 MET cc_start: 0.6912 (mmp) cc_final: 0.6183 (mmt) REVERT: R 102 ASN cc_start: 0.9057 (m-40) cc_final: 0.8735 (m-40) REVERT: A 50 GLU cc_start: 0.7770 (pt0) cc_final: 0.6983 (tp30) REVERT: A 54 PHE cc_start: 0.6801 (p90) cc_final: 0.6398 (p90) REVERT: A 58 THR cc_start: 0.7882 (p) cc_final: 0.7429 (t) REVERT: A 70 LEU cc_start: 0.8484 (pp) cc_final: 0.8212 (pp) REVERT: A 113 HIS cc_start: 0.6513 (t70) cc_final: 0.6215 (t70) REVERT: A 119 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8336 (mm) REVERT: B 25 ASN cc_start: 0.7381 (t0) cc_final: 0.7010 (t0) REVERT: B 27 GLN cc_start: 0.8170 (pm20) cc_final: 0.7596 (pm20) REVERT: B 34 ILE cc_start: 0.8727 (pp) cc_final: 0.8444 (tp) REVERT: B 59 LYS cc_start: 0.8306 (mptt) cc_final: 0.8096 (mmtt) REVERT: B 74 GLU cc_start: 0.8414 (tp30) cc_final: 0.7716 (tp30) REVERT: C 21 ARG cc_start: 0.7434 (tmt-80) cc_final: 0.6856 (tpt90) REVERT: C 32 LYS cc_start: 0.8717 (mmtt) cc_final: 0.8467 (tppt) REVERT: C 51 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.7634 (tp) REVERT: C 59 TYR cc_start: 0.7309 (p90) cc_final: 0.7059 (p90) REVERT: C 70 ASN cc_start: 0.8100 (p0) cc_final: 0.7884 (p0) REVERT: C 74 ASP cc_start: 0.6895 (p0) cc_final: 0.6381 (p0) REVERT: C 86 GLN cc_start: 0.7333 (mt0) cc_final: 0.6921 (mt0) REVERT: C 103 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8797 (pp) REVERT: D 65 LEU cc_start: 0.9036 (mt) cc_final: 0.8787 (mt) REVERT: D 68 PHE cc_start: 0.8183 (p90) cc_final: 0.7964 (p90) REVERT: D 72 ILE cc_start: 0.8925 (pt) cc_final: 0.8618 (pt) REVERT: D 79 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7139 (pp20) REVERT: D 83 LEU cc_start: 0.8871 (pp) cc_final: 0.8671 (pp) REVERT: D 87 ASN cc_start: 0.9046 (p0) cc_final: 0.8637 (p0) REVERT: D 111 LYS cc_start: 0.7848 (OUTLIER) cc_final: 0.7457 (pmmt) REVERT: D 124 TYR cc_start: 0.8315 (t80) cc_final: 0.8112 (t80) REVERT: E 41 TYR cc_start: 0.5758 (p90) cc_final: 0.5419 (p90) REVERT: E 64 LYS cc_start: 0.8072 (mppt) cc_final: 0.7700 (mmtm) REVERT: E 72 ARG cc_start: 0.6851 (mmt180) cc_final: 0.6428 (mmt180) REVERT: E 73 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7543 (mm-30) REVERT: E 94 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7387 (tt0) REVERT: E 120 GLN cc_start: 0.6643 (pp30) cc_final: 0.6181 (pp30) REVERT: E 130 LEU cc_start: 0.8636 (pp) cc_final: 0.8378 (pp) REVERT: F 46 ILE cc_start: 0.9177 (mp) cc_final: 0.8915 (mp) REVERT: F 50 ILE cc_start: 0.8280 (pp) cc_final: 0.7778 (mm) REVERT: F 61 PHE cc_start: 0.8303 (t80) cc_final: 0.8084 (t80) REVERT: F 71 THR cc_start: 0.8486 (m) cc_final: 0.7812 (m) REVERT: F 98 TYR cc_start: 0.6931 (t80) cc_final: 0.6404 (t80) REVERT: G 38 HIS cc_start: 0.8157 (p-80) cc_final: 0.7891 (p90) REVERT: G 52 TYR cc_start: 0.7512 (t80) cc_final: 0.7049 (t80) REVERT: G 53 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8586 (mp) REVERT: G 89 ILE cc_start: 0.8703 (mp) cc_final: 0.8324 (pt) REVERT: G 103 ILE cc_start: 0.6662 (pp) cc_final: 0.6245 (mp) REVERT: H 62 MET cc_start: 0.7821 (mmm) cc_final: 0.7593 (mmm) REVERT: H 66 ASN cc_start: 0.7744 (p0) cc_final: 0.7434 (p0) REVERT: H 68 PHE cc_start: 0.8178 (t80) cc_final: 0.7849 (t80) REVERT: H 74 GLU cc_start: 0.7776 (tp30) cc_final: 0.7354 (tp30) REVERT: H 86 TYR cc_start: 0.7113 (p90) cc_final: 0.6704 (p90) REVERT: H 96 GLU cc_start: 0.7038 (tm-30) cc_final: 0.6723 (tm-30) outliers start: 58 outliers final: 7 residues processed: 567 average time/residue: 0.1946 time to fit residues: 157.4080 Evaluate side-chains 463 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 449 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 10.0000 chunk 212 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 203 GLN M 173 ASN M 175 GLN ** M 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 285 HIS O 364 HIS Q 163 ASN Q 198 HIS Q 204 GLN ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 339 GLN R 9 GLN R 31 ASN A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 GLN D 59 GLN E 55 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 GLN H 112 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.116989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.091606 restraints weight = 87492.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.094777 restraints weight = 49399.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.096766 restraints weight = 32004.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.098112 restraints weight = 23069.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.098995 restraints weight = 18071.735| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 22580 Z= 0.239 Angle : 1.056 14.042 31707 Z= 0.576 Chirality : 0.060 0.289 3556 Planarity : 0.009 0.132 3001 Dihedral : 29.941 129.811 5372 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 26.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.36 % Favored : 88.64 % Rotamer: Outliers : 1.11 % Allowed : 8.74 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.77 % Twisted General : 0.49 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.39 (0.16), residues: 1866 helix: -2.46 (0.14), residues: 983 sheet: -3.11 (0.72), residues: 33 loop : -3.45 (0.19), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 40 TYR 0.057 0.003 TYR D 43 PHE 0.066 0.003 PHE H 73 TRP 0.036 0.003 TRP O 353 HIS 0.017 0.003 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.24 (22580) covalent geometry : angle 1.05613 / 0.58 (31707) hydrogen bonds : bond 0.07130 / 4.53 ( 1048) hydrogen bonds : angle 5.94849 / 3.98 ( 2748) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 516 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 284 HIS cc_start: 0.7559 (m-70) cc_final: 0.7127 (m-70) REVERT: K 302 VAL cc_start: 0.8883 (t) cc_final: 0.8025 (t) REVERT: K 311 TYR cc_start: 0.7157 (t80) cc_final: 0.6692 (t80) REVERT: K 327 LEU cc_start: 0.9266 (mt) cc_final: 0.9018 (pp) REVERT: K 343 ASP cc_start: 0.9033 (p0) cc_final: 0.8786 (p0) REVERT: M 175 GLN cc_start: 0.5278 (OUTLIER) cc_final: 0.4782 (pp30) REVERT: M 234 LEU cc_start: 0.9095 (mp) cc_final: 0.8781 (mp) REVERT: M 238 LEU cc_start: 0.8767 (tp) cc_final: 0.8420 (tt) REVERT: M 278 TYR cc_start: 0.8602 (t80) cc_final: 0.8183 (t80) REVERT: O 271 PHE cc_start: 0.7929 (p90) cc_final: 0.7221 (p90) REVERT: O 272 LEU cc_start: 0.7591 (mt) cc_final: 0.7335 (tt) REVERT: O 275 CYS cc_start: 0.8518 (t) cc_final: 0.8160 (t) REVERT: O 325 TYR cc_start: 0.8372 (m-10) cc_final: 0.8039 (m-80) REVERT: Q 229 MET cc_start: 0.6656 (mmp) cc_final: 0.4388 (mmp) REVERT: R 102 ASN cc_start: 0.8839 (m-40) cc_final: 0.8617 (m-40) REVERT: A 51 ILE cc_start: 0.8709 (mm) cc_final: 0.8129 (mm) REVERT: A 58 THR cc_start: 0.7869 (p) cc_final: 0.7431 (t) REVERT: A 73 GLU cc_start: 0.8075 (tt0) cc_final: 0.7756 (tt0) REVERT: A 85 GLN cc_start: 0.8300 (tm-30) cc_final: 0.7987 (tm-30) REVERT: A 100 LEU cc_start: 0.8685 (pp) cc_final: 0.8419 (mm) REVERT: A 121 LYS cc_start: 0.8865 (tttm) cc_final: 0.8664 (tmtt) REVERT: A 123 ASP cc_start: 0.7882 (m-30) cc_final: 0.7654 (m-30) REVERT: B 25 ASN cc_start: 0.7485 (t0) cc_final: 0.7060 (t0) REVERT: B 34 ILE cc_start: 0.8894 (pt) cc_final: 0.8672 (tp) REVERT: B 62 LEU cc_start: 0.8144 (mm) cc_final: 0.7874 (mm) REVERT: B 74 GLU cc_start: 0.8487 (tp30) cc_final: 0.7910 (tp30) REVERT: C 31 ILE cc_start: 0.9228 (mm) cc_final: 0.9021 (mm) REVERT: C 32 LYS cc_start: 0.8907 (mmtt) cc_final: 0.8556 (tptt) REVERT: C 70 ASN cc_start: 0.8069 (p0) cc_final: 0.7698 (p0) REVERT: C 74 ASP cc_start: 0.7533 (p0) cc_final: 0.6890 (p0) REVERT: C 84 HIS cc_start: 0.8154 (p90) cc_final: 0.7834 (p-80) REVERT: C 86 GLN cc_start: 0.7701 (mt0) cc_final: 0.7377 (mt0) REVERT: D 50 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8323 (pp30) REVERT: D 65 LEU cc_start: 0.8978 (mt) cc_final: 0.8674 (mt) REVERT: D 76 ILE cc_start: 0.8836 (pt) cc_final: 0.8569 (pt) REVERT: D 89 LYS cc_start: 0.8943 (tttm) cc_final: 0.8523 (tptm) REVERT: E 41 TYR cc_start: 0.6264 (p90) cc_final: 0.5744 (p90) REVERT: E 54 PHE cc_start: 0.6908 (p90) cc_final: 0.6655 (p90) REVERT: E 64 LYS cc_start: 0.8123 (mppt) cc_final: 0.7779 (mmtm) REVERT: E 69 ARG cc_start: 0.8014 (ptp90) cc_final: 0.7741 (ptp90) REVERT: E 115 LYS cc_start: 0.9119 (ptpp) cc_final: 0.8726 (ptpp) REVERT: E 120 GLN cc_start: 0.6345 (pp30) cc_final: 0.5688 (pp30) REVERT: F 46 ILE cc_start: 0.9110 (mp) cc_final: 0.8776 (mp) REVERT: F 50 ILE cc_start: 0.8350 (pt) cc_final: 0.7983 (mm) REVERT: F 87 VAL cc_start: 0.8189 (p) cc_final: 0.7851 (t) REVERT: F 88 TYR cc_start: 0.7224 (m-80) cc_final: 0.6985 (m-80) REVERT: G 59 TYR cc_start: 0.7126 (OUTLIER) cc_final: 0.6830 (p90) REVERT: G 60 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8115 (pp) REVERT: G 67 LEU cc_start: 0.8516 (mt) cc_final: 0.8220 (mt) REVERT: G 86 GLN cc_start: 0.7232 (mp10) cc_final: 0.6899 (mp10) REVERT: G 96 ASP cc_start: 0.8658 (p0) cc_final: 0.8371 (p0) REVERT: H 54 ASP cc_start: 0.8103 (p0) cc_final: 0.7644 (p0) REVERT: H 66 ASN cc_start: 0.7768 (p0) cc_final: 0.7465 (p0) REVERT: H 68 PHE cc_start: 0.8193 (t80) cc_final: 0.7849 (t80) REVERT: H 74 GLU cc_start: 0.8004 (tp30) cc_final: 0.7573 (tp30) REVERT: H 82 LYS cc_start: 0.8961 (tmmt) cc_final: 0.8649 (ttpp) REVERT: H 86 TYR cc_start: 0.7307 (p90) cc_final: 0.6923 (p90) REVERT: H 88 LYS cc_start: 0.9289 (ptpp) cc_final: 0.9077 (ptmm) REVERT: H 102 ARG cc_start: 0.8354 (ttm110) cc_final: 0.7957 (ptp-170) REVERT: H 105 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8640 (pp) REVERT: H 108 GLU cc_start: 0.8184 (pm20) cc_final: 0.7866 (pm20) REVERT: H 112 HIS cc_start: 0.7242 (m90) cc_final: 0.6318 (m90) REVERT: H 118 THR cc_start: 0.8624 (p) cc_final: 0.8125 (p) outliers start: 19 outliers final: 3 residues processed: 524 average time/residue: 0.1799 time to fit residues: 136.1894 Evaluate side-chains 479 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 471 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 122 optimal weight: 10.0000 chunk 163 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 7 optimal weight: 7.9990 chunk 180 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 205 optimal weight: 6.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 166 ASN K 203 GLN K 301 ASN M 173 ASN ** M 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 100 HIS ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.118356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.093201 restraints weight = 87822.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.096370 restraints weight = 48953.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.098405 restraints weight = 31436.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.099738 restraints weight = 22529.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.100612 restraints weight = 17611.212| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 22580 Z= 0.220 Angle : 0.993 13.476 31707 Z= 0.543 Chirality : 0.058 0.297 3556 Planarity : 0.008 0.116 3001 Dihedral : 29.622 127.824 5372 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 25.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.31 % Favored : 88.69 % Rotamer: Outliers : 0.23 % Allowed : 6.29 % Favored : 93.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.77 % Twisted General : 0.38 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.95 (0.17), residues: 1866 helix: -2.03 (0.15), residues: 971 sheet: -2.72 (0.74), residues: 33 loop : -3.35 (0.19), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 129 TYR 0.063 0.003 TYR G 59 PHE 0.073 0.003 PHE H 73 TRP 0.051 0.003 TRP O 353 HIS 0.018 0.003 HIS C 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.22 (22580) covalent geometry : angle 0.99314 / 0.54 (31707) hydrogen bonds : bond 0.06816 / 4.34 ( 1048) hydrogen bonds : angle 5.65608 / 3.79 ( 2748) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 520 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 209 LYS cc_start: 0.8771 (mmpt) cc_final: 0.8535 (mmpt) REVERT: K 284 HIS cc_start: 0.7623 (m-70) cc_final: 0.7169 (m-70) REVERT: K 302 VAL cc_start: 0.8733 (t) cc_final: 0.7857 (t) REVERT: K 311 TYR cc_start: 0.7220 (t80) cc_final: 0.6697 (t80) REVERT: K 319 LEU cc_start: 0.7900 (tp) cc_final: 0.7575 (pt) REVERT: K 327 LEU cc_start: 0.9318 (mt) cc_final: 0.9097 (pp) REVERT: K 343 ASP cc_start: 0.9029 (p0) cc_final: 0.8474 (p0) REVERT: M 203 ARG cc_start: 0.8269 (mpt-90) cc_final: 0.8005 (mpt-90) REVERT: M 234 LEU cc_start: 0.9141 (mp) cc_final: 0.8930 (mp) REVERT: M 278 TYR cc_start: 0.8712 (t80) cc_final: 0.8363 (t80) REVERT: O 271 PHE cc_start: 0.7937 (p90) cc_final: 0.7258 (p90) REVERT: O 272 LEU cc_start: 0.7545 (mt) cc_final: 0.7292 (tt) REVERT: O 275 CYS cc_start: 0.8646 (t) cc_final: 0.8141 (t) REVERT: Q 195 SER cc_start: 0.7340 (p) cc_final: 0.6803 (p) REVERT: A 50 GLU cc_start: 0.7184 (tm-30) cc_final: 0.6545 (tp30) REVERT: A 51 ILE cc_start: 0.8571 (mm) cc_final: 0.8093 (mm) REVERT: A 58 THR cc_start: 0.7512 (p) cc_final: 0.7068 (t) REVERT: A 68 GLN cc_start: 0.7750 (tm-30) cc_final: 0.7327 (tm-30) REVERT: A 73 GLU cc_start: 0.8061 (tt0) cc_final: 0.7844 (tt0) REVERT: A 85 GLN cc_start: 0.8297 (tm-30) cc_final: 0.8082 (tm-30) REVERT: B 25 ASN cc_start: 0.7506 (t0) cc_final: 0.7066 (t0) REVERT: B 74 GLU cc_start: 0.8260 (tp30) cc_final: 0.7918 (tp30) REVERT: C 30 ARG cc_start: 0.7899 (pmt-80) cc_final: 0.7537 (ptt-90) REVERT: C 31 ILE cc_start: 0.9168 (mm) cc_final: 0.8808 (pt) REVERT: C 32 LYS cc_start: 0.9015 (mmtt) cc_final: 0.8804 (tptt) REVERT: C 33 ARG cc_start: 0.8557 (pmt170) cc_final: 0.8238 (pmt170) REVERT: C 53 LEU cc_start: 0.7655 (mp) cc_final: 0.7284 (tt) REVERT: C 57 LEU cc_start: 0.8061 (mt) cc_final: 0.7660 (mt) REVERT: C 74 ASP cc_start: 0.7250 (p0) cc_final: 0.7049 (p0) REVERT: D 49 LYS cc_start: 0.8574 (mtmm) cc_final: 0.8266 (mttt) REVERT: D 64 ILE cc_start: 0.8736 (mm) cc_final: 0.8473 (mm) REVERT: D 76 ILE cc_start: 0.8969 (pt) cc_final: 0.8746 (pt) REVERT: D 79 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.7114 (pm20) REVERT: D 89 LYS cc_start: 0.9029 (tttm) cc_final: 0.8581 (tptm) REVERT: E 41 TYR cc_start: 0.6366 (p90) cc_final: 0.5803 (p90) REVERT: E 64 LYS cc_start: 0.8246 (mppt) cc_final: 0.7947 (mmtm) REVERT: E 72 ARG cc_start: 0.7608 (mmt180) cc_final: 0.4982 (mmt180) REVERT: E 74 ILE cc_start: 0.8632 (pt) cc_final: 0.8234 (pt) REVERT: E 81 ASP cc_start: 0.8365 (p0) cc_final: 0.8107 (p0) REVERT: E 83 ARG cc_start: 0.7953 (mmp80) cc_final: 0.7583 (mmp80) REVERT: E 94 GLU cc_start: 0.7279 (mt-10) cc_final: 0.6874 (tt0) REVERT: E 108 ASN cc_start: 0.8061 (m110) cc_final: 0.7692 (m110) REVERT: E 115 LYS cc_start: 0.9131 (ptpp) cc_final: 0.8727 (ptpp) REVERT: E 125 LYS cc_start: 0.8608 (mtmm) cc_final: 0.8317 (mtmm) REVERT: F 50 ILE cc_start: 0.8289 (pt) cc_final: 0.8071 (mm) REVERT: F 58 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7793 (pt) REVERT: F 87 VAL cc_start: 0.8107 (p) cc_final: 0.7762 (t) REVERT: G 32 LYS cc_start: 0.8677 (mmmt) cc_final: 0.8298 (mmmt) REVERT: G 52 TYR cc_start: 0.7558 (t80) cc_final: 0.7356 (t80) REVERT: G 67 LEU cc_start: 0.8596 (mt) cc_final: 0.8298 (mt) REVERT: G 89 ILE cc_start: 0.8804 (tp) cc_final: 0.8457 (pt) REVERT: H 62 MET cc_start: 0.7547 (mmp) cc_final: 0.7285 (mmm) REVERT: H 66 ASN cc_start: 0.7599 (p0) cc_final: 0.7314 (p0) REVERT: H 68 PHE cc_start: 0.8123 (t80) cc_final: 0.7745 (t80) REVERT: H 82 LYS cc_start: 0.8941 (tmmt) cc_final: 0.8591 (ttpp) REVERT: H 86 TYR cc_start: 0.7309 (p90) cc_final: 0.6869 (p90) REVERT: H 88 LYS cc_start: 0.9293 (ptpp) cc_final: 0.9058 (ptmm) REVERT: H 96 GLU cc_start: 0.7256 (tm-30) cc_final: 0.7014 (tm-30) REVERT: H 102 ARG cc_start: 0.8407 (ttm110) cc_final: 0.8194 (ttp-110) REVERT: H 105 LEU cc_start: 0.9107 (pp) cc_final: 0.8802 (pp) REVERT: H 108 GLU cc_start: 0.8200 (pm20) cc_final: 0.7917 (pm20) REVERT: H 112 HIS cc_start: 0.7491 (m90) cc_final: 0.6269 (m90) outliers start: 4 outliers final: 0 residues processed: 522 average time/residue: 0.1808 time to fit residues: 136.1913 Evaluate side-chains 463 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 461 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 71 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 212 optimal weight: 0.9990 chunk 191 optimal weight: 0.8980 chunk 133 optimal weight: 10.0000 chunk 207 optimal weight: 1.9990 chunk 121 optimal weight: 8.9990 chunk 171 optimal weight: 0.9980 chunk 28 optimal weight: 0.0020 chunk 184 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 166 ASN K 261 HIS M 260 ASN ** M 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 201 HIS ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 16 GLN ** G 84 HIS ** 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 = 0.4063 r_free = 0.4063 target = 0.119459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.093957 restraints weight = 88273.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.097133 restraints weight = 49600.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.099214 restraints weight = 32039.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 65)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.100577 restraints weight = 22986.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.101467 restraints weight = 17979.273| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.144 22580 Z= 0.207 Angle : 0.970 14.877 31707 Z= 0.529 Chirality : 0.056 0.296 3556 Planarity : 0.008 0.128 3001 Dihedral : 29.440 127.819 5372 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 25.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.83 % Favored : 89.17 % Rotamer: Outliers : 0.17 % Allowed : 5.83 % Favored : 94.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.77 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.71 (0.17), residues: 1866 helix: -1.83 (0.15), residues: 982 sheet: -2.59 (0.76), residues: 33 loop : -3.24 (0.19), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 83 TYR 0.053 0.003 TYR G 59 PHE 0.037 0.003 PHE Q 196 TRP 0.038 0.002 TRP O 353 HIS 0.031 0.002 HIS G 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.21 (22580) covalent geometry : angle 0.96997 / 0.53 (31707) hydrogen bonds : bond 0.06464 / 4.12 ( 1048) hydrogen bonds : angle 5.57743 / 3.73 ( 2748) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 504 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 284 HIS cc_start: 0.7583 (m-70) cc_final: 0.7104 (m-70) REVERT: K 302 VAL cc_start: 0.8757 (t) cc_final: 0.7861 (t) REVERT: K 310 GLN cc_start: 0.8135 (pm20) cc_final: 0.7833 (pm20) REVERT: K 311 TYR cc_start: 0.7217 (t80) cc_final: 0.6650 (t80) REVERT: K 327 LEU cc_start: 0.9317 (mt) cc_final: 0.9044 (pp) REVERT: K 372 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7608 (mt-10) REVERT: M 164 MET cc_start: -0.1383 (tpt) cc_final: -0.1679 (tpt) REVERT: M 234 LEU cc_start: 0.9163 (mp) cc_final: 0.8860 (mp) REVERT: M 260 ASN cc_start: 0.6795 (OUTLIER) cc_final: 0.6546 (t160) REVERT: M 278 TYR cc_start: 0.8672 (t80) cc_final: 0.8333 (t80) REVERT: O 178 GLU cc_start: 0.7861 (tp30) cc_final: 0.7287 (pm20) REVERT: O 271 PHE cc_start: 0.7964 (p90) cc_final: 0.7281 (p90) REVERT: O 272 LEU cc_start: 0.7535 (mt) cc_final: 0.7307 (tt) REVERT: O 275 CYS cc_start: 0.8610 (t) cc_final: 0.8292 (t) REVERT: O 329 LYS cc_start: 0.8854 (pptt) cc_final: 0.8583 (pttm) REVERT: O 353 TRP cc_start: 0.7251 (p90) cc_final: 0.6645 (p90) REVERT: Q 198 HIS cc_start: 0.9056 (m90) cc_final: 0.8775 (m170) REVERT: A 51 ILE cc_start: 0.8447 (mm) cc_final: 0.8033 (mm) REVERT: A 58 THR cc_start: 0.7540 (p) cc_final: 0.7026 (t) REVERT: A 85 GLN cc_start: 0.8420 (tm-30) cc_final: 0.8191 (tm-30) REVERT: A 100 LEU cc_start: 0.8796 (pp) cc_final: 0.8296 (mm) REVERT: B 25 ASN cc_start: 0.7419 (t0) cc_final: 0.6969 (t0) REVERT: B 34 ILE cc_start: 0.9140 (tp) cc_final: 0.8679 (tp) REVERT: B 61 PHE cc_start: 0.8119 (t80) cc_final: 0.7914 (t80) REVERT: B 63 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7839 (pm20) REVERT: B 74 GLU cc_start: 0.8296 (tp30) cc_final: 0.7917 (tp30) REVERT: B 77 LYS cc_start: 0.8921 (mttp) cc_final: 0.8693 (mttp) REVERT: C 31 ILE cc_start: 0.9164 (mm) cc_final: 0.8789 (pt) REVERT: C 32 LYS cc_start: 0.9020 (mmtt) cc_final: 0.8752 (tptt) REVERT: C 53 LEU cc_start: 0.8114 (mp) cc_final: 0.7754 (tt) REVERT: C 57 LEU cc_start: 0.8175 (mt) cc_final: 0.7885 (mt) REVERT: C 78 LYS cc_start: 0.8621 (ptpt) cc_final: 0.8244 (pttm) REVERT: D 51 THR cc_start: 0.8770 (p) cc_final: 0.8396 (p) REVERT: D 76 ILE cc_start: 0.9058 (pt) cc_final: 0.8687 (pt) REVERT: D 87 ASN cc_start: 0.9175 (p0) cc_final: 0.8938 (p0) REVERT: D 103 LEU cc_start: 0.8435 (pp) cc_final: 0.8198 (pp) REVERT: E 41 TYR cc_start: 0.6347 (p90) cc_final: 0.5793 (p90) REVERT: E 64 LYS cc_start: 0.8180 (mppt) cc_final: 0.7844 (mmtm) REVERT: E 72 ARG cc_start: 0.7578 (mmt180) cc_final: 0.5233 (mmt180) REVERT: E 81 ASP cc_start: 0.8337 (p0) cc_final: 0.8135 (p0) REVERT: E 83 ARG cc_start: 0.7945 (mmp80) cc_final: 0.7598 (mmp80) REVERT: E 115 LYS cc_start: 0.9134 (ptpp) cc_final: 0.8750 (ptpp) REVERT: E 125 LYS cc_start: 0.8651 (mtmm) cc_final: 0.8373 (mtmm) REVERT: F 25 ASN cc_start: 0.7733 (t0) cc_final: 0.7420 (m-40) REVERT: F 58 LEU cc_start: 0.8116 (pt) cc_final: 0.7771 (pt) REVERT: F 87 VAL cc_start: 0.8134 (p) cc_final: 0.7751 (t) REVERT: G 34 TYR cc_start: 0.8052 (p90) cc_final: 0.7208 (p90) REVERT: G 38 HIS cc_start: 0.7919 (p90) cc_final: 0.7675 (p90) REVERT: G 52 TYR cc_start: 0.7382 (t80) cc_final: 0.6380 (t80) REVERT: G 86 GLN cc_start: 0.7306 (mp10) cc_final: 0.6995 (mp10) REVERT: G 89 ILE cc_start: 0.8769 (tp) cc_final: 0.8419 (pt) REVERT: G 95 LEU cc_start: 0.8934 (mt) cc_final: 0.8620 (mt) REVERT: G 96 ASP cc_start: 0.8280 (p0) cc_final: 0.8074 (p0) REVERT: H 62 MET cc_start: 0.7544 (mmp) cc_final: 0.7344 (mmm) REVERT: H 66 ASN cc_start: 0.7617 (p0) cc_final: 0.7275 (p0) REVERT: H 68 PHE cc_start: 0.8072 (t80) cc_final: 0.7732 (t80) REVERT: H 73 PHE cc_start: 0.7092 (t80) cc_final: 0.6252 (t80) REVERT: H 86 TYR cc_start: 0.7215 (p90) cc_final: 0.6725 (p90) REVERT: H 88 LYS cc_start: 0.9303 (ptpp) cc_final: 0.9049 (ptmm) REVERT: H 108 GLU cc_start: 0.8130 (pm20) cc_final: 0.7903 (pm20) REVERT: H 112 HIS cc_start: 0.7548 (m90) cc_final: 0.6210 (m90) outliers start: 3 outliers final: 0 residues processed: 506 average time/residue: 0.1652 time to fit residues: 121.5377 Evaluate side-chains 456 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 454 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 187 optimal weight: 0.0470 chunk 148 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 208 optimal weight: 0.8980 chunk 141 optimal weight: 10.0000 chunk 159 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 146 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 34 GLN ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 GLN A 68 GLN A 93 GLN A 113 HIS ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.120819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.095122 restraints weight = 88194.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.098336 restraints weight = 49637.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.100449 restraints weight = 31977.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.101823 restraints weight = 22959.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.102720 restraints weight = 17992.404| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 22580 Z= 0.189 Angle : 0.950 13.554 31707 Z= 0.514 Chirality : 0.055 0.265 3556 Planarity : 0.007 0.142 3001 Dihedral : 29.259 129.099 5372 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 24.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.83 % Favored : 89.17 % Rotamer: Outliers : 0.06 % Allowed : 5.65 % Favored : 94.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.77 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.57 (0.18), residues: 1866 helix: -1.70 (0.15), residues: 985 sheet: -2.45 (0.82), residues: 33 loop : -3.20 (0.19), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 92 TYR 0.059 0.003 TYR G 59 PHE 0.030 0.003 PHE Q 196 TRP 0.033 0.002 TRP O 353 HIS 0.017 0.002 HIS C 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.19 (22580) covalent geometry : angle 0.95040 / 0.51 (31707) hydrogen bonds : bond 0.06147 / 3.94 ( 1048) hydrogen bonds : angle 5.41265 / 3.61 ( 2748) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 497 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 284 HIS cc_start: 0.7419 (m-70) cc_final: 0.6976 (m-70) REVERT: K 310 GLN cc_start: 0.8133 (pm20) cc_final: 0.7817 (pm20) REVERT: K 311 TYR cc_start: 0.7265 (t80) cc_final: 0.6678 (t80) REVERT: K 327 LEU cc_start: 0.9306 (mt) cc_final: 0.8991 (pp) REVERT: K 343 ASP cc_start: 0.9042 (p0) cc_final: 0.8750 (p0) REVERT: M 234 LEU cc_start: 0.9194 (mp) cc_final: 0.8857 (pp) REVERT: M 238 LEU cc_start: 0.8801 (tt) cc_final: 0.8564 (tp) REVERT: M 278 TYR cc_start: 0.8929 (t80) cc_final: 0.8679 (t80) REVERT: O 178 GLU cc_start: 0.7826 (tp30) cc_final: 0.7228 (pm20) REVERT: O 211 TYR cc_start: 0.6544 (m-80) cc_final: 0.4808 (m-80) REVERT: O 271 PHE cc_start: 0.7898 (p90) cc_final: 0.7217 (p90) REVERT: O 272 LEU cc_start: 0.7504 (mt) cc_final: 0.7286 (tt) REVERT: O 275 CYS cc_start: 0.8579 (t) cc_final: 0.8283 (t) REVERT: O 329 LYS cc_start: 0.8666 (pptt) cc_final: 0.8304 (ptpp) REVERT: O 353 TRP cc_start: 0.7202 (p90) cc_final: 0.6618 (p90) REVERT: O 360 LEU cc_start: 0.7716 (mt) cc_final: 0.7484 (pp) REVERT: Q 198 HIS cc_start: 0.9047 (m90) cc_final: 0.8761 (m90) REVERT: Q 326 ILE cc_start: 0.8262 (pt) cc_final: 0.8058 (pt) REVERT: A 48 LEU cc_start: 0.8075 (mm) cc_final: 0.7742 (pt) REVERT: A 51 ILE cc_start: 0.8592 (mm) cc_final: 0.8202 (mm) REVERT: A 73 GLU cc_start: 0.8030 (tt0) cc_final: 0.7805 (tt0) REVERT: A 85 GLN cc_start: 0.8383 (tm-30) cc_final: 0.7673 (tm-30) REVERT: A 87 SER cc_start: 0.9210 (t) cc_final: 0.8848 (p) REVERT: B 25 ASN cc_start: 0.7372 (t0) cc_final: 0.7073 (t0) REVERT: B 62 LEU cc_start: 0.8159 (mm) cc_final: 0.7897 (mm) REVERT: B 63 GLU cc_start: 0.7982 (pm20) cc_final: 0.7518 (mp0) REVERT: B 74 GLU cc_start: 0.8257 (tp30) cc_final: 0.7817 (tp30) REVERT: B 77 LYS cc_start: 0.8890 (mttp) cc_final: 0.8649 (mttp) REVERT: B 88 TYR cc_start: 0.8225 (m-10) cc_final: 0.7808 (m-10) REVERT: B 91 LYS cc_start: 0.8509 (pttm) cc_final: 0.8214 (pttm) REVERT: B 95 ARG cc_start: 0.7467 (ttm110) cc_final: 0.6863 (ttm-80) REVERT: C 31 ILE cc_start: 0.9233 (mm) cc_final: 0.8885 (pt) REVERT: C 32 LYS cc_start: 0.9013 (mmtt) cc_final: 0.8767 (tptt) REVERT: C 33 ARG cc_start: 0.8507 (pmt170) cc_final: 0.7914 (ptt-90) REVERT: C 34 TYR cc_start: 0.8196 (m-80) cc_final: 0.7960 (m-10) REVERT: C 53 LEU cc_start: 0.8381 (mp) cc_final: 0.8036 (tt) REVERT: C 57 LEU cc_start: 0.8223 (mt) cc_final: 0.7924 (mt) REVERT: C 60 LEU cc_start: 0.8897 (tp) cc_final: 0.8649 (tp) REVERT: C 109 LEU cc_start: 0.8170 (tt) cc_final: 0.7952 (tt) REVERT: D 47 VAL cc_start: 0.8890 (t) cc_final: 0.8630 (t) REVERT: D 51 THR cc_start: 0.8700 (p) cc_final: 0.8418 (p) REVERT: D 71 ASP cc_start: 0.8464 (p0) cc_final: 0.8202 (p0) REVERT: D 79 GLU cc_start: 0.7623 (pm20) cc_final: 0.7394 (pp20) REVERT: D 87 ASN cc_start: 0.9172 (p0) cc_final: 0.8929 (p0) REVERT: D 121 VAL cc_start: 0.8495 (m) cc_final: 0.8282 (p) REVERT: E 41 TYR cc_start: 0.6324 (p90) cc_final: 0.5726 (p90) REVERT: E 50 GLU cc_start: 0.8660 (pt0) cc_final: 0.8456 (pt0) REVERT: E 64 LYS cc_start: 0.8304 (mppt) cc_final: 0.8097 (mmtm) REVERT: E 72 ARG cc_start: 0.7500 (mmt180) cc_final: 0.7188 (mmt180) REVERT: E 83 ARG cc_start: 0.7875 (mmp80) cc_final: 0.7566 (mmp80) REVERT: E 94 GLU cc_start: 0.7218 (mt-10) cc_final: 0.6787 (tt0) REVERT: E 115 LYS cc_start: 0.9139 (ptpp) cc_final: 0.8794 (ptpp) REVERT: E 125 LYS cc_start: 0.8637 (mtmm) cc_final: 0.8344 (mtmm) REVERT: F 25 ASN cc_start: 0.7556 (t0) cc_final: 0.7232 (m-40) REVERT: F 87 VAL cc_start: 0.8063 (p) cc_final: 0.7748 (t) REVERT: F 91 LYS cc_start: 0.8357 (pttm) cc_final: 0.7924 (pttm) REVERT: G 32 LYS cc_start: 0.8815 (mmmt) cc_final: 0.8613 (mmmt) REVERT: G 38 HIS cc_start: 0.7913 (p90) cc_final: 0.7688 (p90) REVERT: G 48 LYS cc_start: 0.8517 (mmmt) cc_final: 0.8313 (mmmt) REVERT: G 89 ILE cc_start: 0.8795 (tp) cc_final: 0.8424 (pt) REVERT: G 95 LEU cc_start: 0.8949 (mt) cc_final: 0.8598 (mt) REVERT: H 66 ASN cc_start: 0.7633 (p0) cc_final: 0.7345 (p0) REVERT: H 82 LYS cc_start: 0.8902 (tmmt) cc_final: 0.8583 (tmtt) REVERT: H 86 TYR cc_start: 0.7234 (p90) cc_final: 0.6618 (p90) REVERT: H 88 LYS cc_start: 0.9300 (ptpp) cc_final: 0.9025 (ptmm) REVERT: H 102 ARG cc_start: 0.8371 (ttp-110) cc_final: 0.8072 (ttp80) REVERT: H 111 LYS cc_start: 0.8269 (pptt) cc_final: 0.8048 (pptt) REVERT: H 112 HIS cc_start: 0.7506 (m90) cc_final: 0.6174 (m90) outliers start: 1 outliers final: 1 residues processed: 498 average time/residue: 0.1735 time to fit residues: 125.7592 Evaluate side-chains 443 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 442 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 175 optimal weight: 0.9990 chunk 91 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 206 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 156 optimal weight: 0.6980 chunk 137 optimal weight: 9.9990 chunk 152 optimal weight: 0.5980 chunk 107 optimal weight: 7.9990 chunk 121 optimal weight: 9.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 166 ASN M 237 GLN ** M 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.121492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.095776 restraints weight = 88361.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.099081 restraints weight = 49304.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.101212 restraints weight = 31463.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.102578 restraints weight = 22339.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.103473 restraints weight = 17403.690| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 22580 Z= 0.189 Angle : 0.951 17.706 31707 Z= 0.511 Chirality : 0.055 0.307 3556 Planarity : 0.007 0.136 3001 Dihedral : 29.108 128.380 5372 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 25.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.04 % Favored : 88.96 % Rotamer: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.77 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.42 (0.18), residues: 1866 helix: -1.58 (0.15), residues: 973 sheet: -2.45 (0.82), residues: 33 loop : -3.11 (0.19), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG F 95 TYR 0.046 0.003 TYR G 34 PHE 0.086 0.003 PHE H 73 TRP 0.070 0.002 TRP O 353 HIS 0.027 0.002 HIS G 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.19 (22580) covalent geometry : angle 0.95080 / 0.51 (31707) hydrogen bonds : bond 0.06075 / 3.88 ( 1048) hydrogen bonds : angle 5.43149 / 3.63 ( 2748) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 490 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 212 GLU cc_start: 0.8169 (mp0) cc_final: 0.7894 (mp0) REVERT: K 284 HIS cc_start: 0.7443 (m-70) cc_final: 0.6992 (m-70) REVERT: K 302 VAL cc_start: 0.8639 (t) cc_final: 0.7749 (t) REVERT: K 310 GLN cc_start: 0.8109 (pm20) cc_final: 0.7806 (pm20) REVERT: K 325 TYR cc_start: 0.8357 (m-80) cc_final: 0.8143 (m-10) REVERT: K 327 LEU cc_start: 0.9287 (mt) cc_final: 0.8999 (pp) REVERT: K 343 ASP cc_start: 0.9055 (p0) cc_final: 0.8779 (p0) REVERT: K 376 MET cc_start: 0.8628 (pmm) cc_final: 0.8419 (pmm) REVERT: K 428 ARG cc_start: 0.6479 (mmp-170) cc_final: 0.5591 (mmm160) REVERT: M 238 LEU cc_start: 0.8817 (tt) cc_final: 0.8541 (tt) REVERT: M 278 TYR cc_start: 0.8952 (t80) cc_final: 0.8725 (t80) REVERT: O 211 TYR cc_start: 0.6737 (m-80) cc_final: 0.4971 (m-80) REVERT: O 271 PHE cc_start: 0.7987 (p90) cc_final: 0.7299 (p90) REVERT: O 272 LEU cc_start: 0.7497 (mt) cc_final: 0.7287 (tt) REVERT: O 275 CYS cc_start: 0.8549 (t) cc_final: 0.8290 (t) REVERT: O 326 GLU cc_start: 0.8744 (tm-30) cc_final: 0.8408 (tm-30) REVERT: O 329 LYS cc_start: 0.8656 (pptt) cc_final: 0.8336 (ptpp) REVERT: O 353 TRP cc_start: 0.7369 (p90) cc_final: 0.6782 (p90) REVERT: Q 198 HIS cc_start: 0.9088 (m90) cc_final: 0.8797 (m90) REVERT: A 51 ILE cc_start: 0.8790 (mm) cc_final: 0.8202 (mm) REVERT: A 59 GLU cc_start: 0.8692 (pm20) cc_final: 0.8127 (pm20) REVERT: A 71 VAL cc_start: 0.8917 (m) cc_final: 0.8709 (m) REVERT: A 84 PHE cc_start: 0.7045 (m-80) cc_final: 0.6843 (m-80) REVERT: A 125 LYS cc_start: 0.8275 (mtmm) cc_final: 0.8069 (ptpp) REVERT: B 25 ASN cc_start: 0.7342 (t0) cc_final: 0.7134 (t0) REVERT: B 34 ILE cc_start: 0.9138 (tp) cc_final: 0.8883 (tp) REVERT: B 63 GLU cc_start: 0.7926 (pm20) cc_final: 0.7631 (mp0) REVERT: B 74 GLU cc_start: 0.8339 (tp30) cc_final: 0.7836 (tp30) REVERT: B 83 SER cc_start: 0.8763 (m) cc_final: 0.8252 (m) REVERT: B 91 LYS cc_start: 0.8548 (pttp) cc_final: 0.8310 (ptpp) REVERT: C 31 ILE cc_start: 0.9136 (mm) cc_final: 0.8800 (mp) REVERT: C 53 LEU cc_start: 0.8411 (mp) cc_final: 0.7946 (tt) REVERT: C 57 LEU cc_start: 0.8202 (mt) cc_final: 0.7866 (mt) REVERT: C 78 LYS cc_start: 0.8561 (ptpt) cc_final: 0.8341 (pttm) REVERT: D 51 THR cc_start: 0.8717 (p) cc_final: 0.8291 (p) REVERT: D 71 ASP cc_start: 0.8466 (p0) cc_final: 0.8203 (p0) REVERT: D 87 ASN cc_start: 0.9195 (p0) cc_final: 0.8956 (p0) REVERT: E 41 TYR cc_start: 0.6395 (p90) cc_final: 0.5834 (p90) REVERT: E 54 PHE cc_start: 0.6620 (p90) cc_final: 0.6375 (p90) REVERT: E 60 LEU cc_start: 0.8700 (pp) cc_final: 0.8459 (pt) REVERT: E 72 ARG cc_start: 0.7668 (mmt180) cc_final: 0.7407 (mmt180) REVERT: E 83 ARG cc_start: 0.7743 (mmp80) cc_final: 0.7477 (mmp80) REVERT: E 104 PHE cc_start: 0.6874 (p90) cc_final: 0.6641 (p90) REVERT: E 108 ASN cc_start: 0.8168 (m-40) cc_final: 0.7966 (m-40) REVERT: E 115 LYS cc_start: 0.9164 (ptpp) cc_final: 0.8820 (ptpp) REVERT: E 123 ASP cc_start: 0.7234 (t70) cc_final: 0.6801 (t0) REVERT: E 125 LYS cc_start: 0.8605 (mtmm) cc_final: 0.8182 (mtmm) REVERT: F 60 SER cc_start: 0.8452 (p) cc_final: 0.7880 (p) REVERT: F 87 VAL cc_start: 0.8203 (p) cc_final: 0.7790 (t) REVERT: F 91 LYS cc_start: 0.8248 (pttm) cc_final: 0.7848 (pttm) REVERT: G 32 LYS cc_start: 0.8933 (mmmt) cc_final: 0.8634 (mmmt) REVERT: G 34 TYR cc_start: 0.8054 (p90) cc_final: 0.7575 (p90) REVERT: G 38 HIS cc_start: 0.8004 (p90) cc_final: 0.7685 (p90) REVERT: G 48 LYS cc_start: 0.8577 (mmmt) cc_final: 0.8324 (mmmt) REVERT: G 52 TYR cc_start: 0.7347 (t80) cc_final: 0.6747 (t80) REVERT: G 59 TYR cc_start: 0.7451 (p90) cc_final: 0.7094 (p90) REVERT: G 86 GLN cc_start: 0.7184 (mp10) cc_final: 0.6799 (mp10) REVERT: G 89 ILE cc_start: 0.8765 (tp) cc_final: 0.8390 (pt) REVERT: G 95 LEU cc_start: 0.8996 (mt) cc_final: 0.8721 (mt) REVERT: H 62 MET cc_start: 0.7576 (mmp) cc_final: 0.7321 (mmp) REVERT: H 66 ASN cc_start: 0.7641 (p0) cc_final: 0.7392 (p0) REVERT: H 86 TYR cc_start: 0.7010 (p90) cc_final: 0.6733 (p90) REVERT: H 88 LYS cc_start: 0.9275 (ptpp) cc_final: 0.9040 (ptmm) REVERT: H 102 ARG cc_start: 0.8396 (ttp-110) cc_final: 0.8090 (ttp80) outliers start: 0 outliers final: 0 residues processed: 490 average time/residue: 0.1939 time to fit residues: 136.9947 Evaluate side-chains 440 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 440 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 59 optimal weight: 1.9990 chunk 211 optimal weight: 3.9990 chunk 134 optimal weight: 8.9990 chunk 171 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 212 optimal weight: 0.8980 chunk 49 optimal weight: 9.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 260 ASN ** M 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 285 HIS ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** G 70 ASN ** 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 = 0.4053 r_free = 0.4053 target = 0.118574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.093106 restraints weight = 88516.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.096302 restraints weight = 49435.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.098332 restraints weight = 31758.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.099680 restraints weight = 22732.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.100532 restraints weight = 17705.588| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.4636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 22580 Z= 0.242 Angle : 0.974 13.075 31707 Z= 0.527 Chirality : 0.056 0.446 3556 Planarity : 0.008 0.145 3001 Dihedral : 28.980 121.573 5372 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 28.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.36 % Favored : 88.64 % Rotamer: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.37 (0.18), residues: 1866 helix: -1.50 (0.15), residues: 974 sheet: -2.41 (0.77), residues: 33 loop : -3.14 (0.19), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG K 249 TYR 0.028 0.003 TYR E 99 PHE 0.060 0.003 PHE H 73 TRP 0.050 0.003 TRP O 353 HIS 0.017 0.002 HIS C 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.24 (22580) covalent geometry : angle 0.97385 / 0.53 (31707) hydrogen bonds : bond 0.06891 / 4.45 ( 1048) hydrogen bonds : angle 5.42865 / 3.63 ( 2748) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 494 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 284 HIS cc_start: 0.7408 (m-70) cc_final: 0.7041 (m-70) REVERT: K 302 VAL cc_start: 0.8763 (t) cc_final: 0.7999 (t) REVERT: K 310 GLN cc_start: 0.8060 (pm20) cc_final: 0.7593 (pm20) REVERT: K 311 TYR cc_start: 0.7550 (t80) cc_final: 0.7257 (t80) REVERT: K 327 LEU cc_start: 0.9320 (mt) cc_final: 0.9047 (pp) REVERT: K 343 ASP cc_start: 0.9126 (p0) cc_final: 0.8842 (p0) REVERT: K 353 TRP cc_start: 0.5300 (p-90) cc_final: 0.5042 (p-90) REVERT: M 234 LEU cc_start: 0.9317 (mp) cc_final: 0.8901 (pp) REVERT: M 238 LEU cc_start: 0.8917 (tt) cc_final: 0.8613 (tt) REVERT: M 278 TYR cc_start: 0.8947 (t80) cc_final: 0.8693 (t80) REVERT: O 237 PHE cc_start: 0.7478 (m-10) cc_final: 0.7073 (m-10) REVERT: O 271 PHE cc_start: 0.7993 (p90) cc_final: 0.7338 (p90) REVERT: O 272 LEU cc_start: 0.7522 (mt) cc_final: 0.7304 (tt) REVERT: O 275 CYS cc_start: 0.8702 (t) cc_final: 0.8374 (t) REVERT: O 325 TYR cc_start: 0.8793 (m-80) cc_final: 0.8458 (m-80) REVERT: O 326 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8352 (tm-30) REVERT: O 353 TRP cc_start: 0.7300 (p90) cc_final: 0.6711 (p90) REVERT: Q 150 PHE cc_start: 0.8274 (m-80) cc_final: 0.7973 (m-80) REVERT: Q 198 HIS cc_start: 0.9097 (m90) cc_final: 0.8827 (m90) REVERT: Q 326 ILE cc_start: 0.8220 (pt) cc_final: 0.7997 (pt) REVERT: Q 342 LYS cc_start: 0.6966 (mptt) cc_final: 0.6578 (mmtp) REVERT: A 59 GLU cc_start: 0.8916 (pm20) cc_final: 0.8376 (pm20) REVERT: A 87 SER cc_start: 0.9231 (t) cc_final: 0.8761 (p) REVERT: A 113 HIS cc_start: 0.7023 (t-90) cc_final: 0.6630 (t-90) REVERT: A 124 ILE cc_start: 0.8350 (mp) cc_final: 0.7778 (tp) REVERT: B 27 GLN cc_start: 0.8079 (pm20) cc_final: 0.7731 (pm20) REVERT: B 34 ILE cc_start: 0.9035 (tp) cc_final: 0.8803 (tp) REVERT: B 62 LEU cc_start: 0.8294 (mm) cc_final: 0.8077 (mm) REVERT: B 74 GLU cc_start: 0.8393 (tp30) cc_final: 0.7912 (tp30) REVERT: B 83 SER cc_start: 0.8588 (m) cc_final: 0.8327 (m) REVERT: C 31 ILE cc_start: 0.9127 (mm) cc_final: 0.8882 (mp) REVERT: C 33 ARG cc_start: 0.8388 (pmt170) cc_final: 0.8107 (ptt-90) REVERT: C 53 LEU cc_start: 0.8618 (mp) cc_final: 0.8139 (tt) REVERT: C 57 LEU cc_start: 0.8297 (mt) cc_final: 0.8044 (mt) REVERT: C 60 LEU cc_start: 0.8887 (tp) cc_final: 0.8658 (tp) REVERT: D 47 VAL cc_start: 0.8837 (t) cc_final: 0.8545 (t) REVERT: D 49 LYS cc_start: 0.8779 (mmmt) cc_final: 0.8468 (mmmt) REVERT: D 71 ASP cc_start: 0.8535 (p0) cc_final: 0.8201 (p0) REVERT: D 75 ARG cc_start: 0.8675 (ptm-80) cc_final: 0.8428 (ptm-80) REVERT: D 76 ILE cc_start: 0.9266 (pt) cc_final: 0.8615 (pt) REVERT: D 89 LYS cc_start: 0.9082 (tttm) cc_final: 0.8692 (tptt) REVERT: D 98 GLN cc_start: 0.7966 (mp10) cc_final: 0.7534 (mp10) REVERT: D 103 LEU cc_start: 0.8591 (pp) cc_final: 0.8293 (pp) REVERT: E 41 TYR cc_start: 0.6759 (p90) cc_final: 0.6231 (p90) REVERT: E 56 LYS cc_start: 0.8841 (tmtt) cc_final: 0.8617 (tmtt) REVERT: E 64 LYS cc_start: 0.8589 (mppt) cc_final: 0.8123 (mmmm) REVERT: E 74 ILE cc_start: 0.8666 (pt) cc_final: 0.8172 (pt) REVERT: E 115 LYS cc_start: 0.9153 (ptpp) cc_final: 0.8814 (ptpp) REVERT: F 46 ILE cc_start: 0.9148 (mp) cc_final: 0.8743 (tp) REVERT: F 57 VAL cc_start: 0.8621 (m) cc_final: 0.8335 (p) REVERT: F 63 GLU cc_start: 0.8445 (pm20) cc_final: 0.8104 (pm20) REVERT: F 75 HIS cc_start: 0.7660 (t-90) cc_final: 0.7342 (t70) REVERT: F 91 LYS cc_start: 0.8254 (pttm) cc_final: 0.7849 (pttm) REVERT: G 32 LYS cc_start: 0.8899 (mmmt) cc_final: 0.8408 (mmmm) REVERT: G 38 HIS cc_start: 0.7946 (p90) cc_final: 0.7635 (p90) REVERT: G 48 LYS cc_start: 0.8756 (mmmt) cc_final: 0.8448 (mmmt) REVERT: G 52 TYR cc_start: 0.7501 (t80) cc_final: 0.7275 (t80) REVERT: G 59 TYR cc_start: 0.7489 (p90) cc_final: 0.7052 (p90) REVERT: G 86 GLN cc_start: 0.7301 (mp10) cc_final: 0.6835 (mp10) REVERT: G 89 ILE cc_start: 0.8838 (tp) cc_final: 0.8520 (pt) REVERT: G 95 LEU cc_start: 0.9066 (mt) cc_final: 0.8709 (mt) REVERT: H 62 MET cc_start: 0.7839 (mmp) cc_final: 0.7638 (mmm) REVERT: H 66 ASN cc_start: 0.7751 (p0) cc_final: 0.7477 (p0) REVERT: H 72 ILE cc_start: 0.7554 (tt) cc_final: 0.7331 (tt) REVERT: H 82 LYS cc_start: 0.8975 (tmmt) cc_final: 0.8618 (tmtt) REVERT: H 86 TYR cc_start: 0.7260 (p90) cc_final: 0.6900 (p90) REVERT: H 88 LYS cc_start: 0.9293 (ptpp) cc_final: 0.9087 (ptmm) REVERT: H 102 ARG cc_start: 0.8407 (ttp-110) cc_final: 0.8098 (ttp80) REVERT: H 111 LYS cc_start: 0.8337 (pptt) cc_final: 0.8043 (pptt) REVERT: H 112 HIS cc_start: 0.7693 (m90) cc_final: 0.6366 (m90) outliers start: 0 outliers final: 0 residues processed: 494 average time/residue: 0.1794 time to fit residues: 128.0294 Evaluate side-chains 446 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 446 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 174 optimal weight: 0.5980 chunk 37 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 16 optimal weight: 0.6980 chunk 85 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 124 optimal weight: 8.9990 chunk 86 optimal weight: 6.9990 chunk 95 optimal weight: 0.0770 chunk 145 optimal weight: 0.9980 overall best weight: 1.2740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 260 ASN ** M 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN ** O 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 100 HIS ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.120265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.094669 restraints weight = 87907.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.097901 restraints weight = 49041.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.100005 restraints weight = 31429.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.101346 restraints weight = 22424.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.102246 restraints weight = 17528.200| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.4886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22580 Z= 0.202 Angle : 0.966 14.975 31707 Z= 0.519 Chirality : 0.055 0.345 3556 Planarity : 0.008 0.125 3001 Dihedral : 28.961 128.019 5372 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 25.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.25 % Favored : 88.75 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.32 (0.18), residues: 1866 helix: -1.53 (0.15), residues: 978 sheet: -2.23 (0.83), residues: 33 loop : -3.05 (0.19), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG K 169 TYR 0.044 0.003 TYR F 72 PHE 0.085 0.003 PHE H 73 TRP 0.046 0.002 TRP O 353 HIS 0.013 0.002 HIS G 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.20 (22580) covalent geometry : angle 0.96563 / 0.52 (31707) hydrogen bonds : bond 0.06280 / 4.06 ( 1048) hydrogen bonds : angle 5.43065 / 3.62 ( 2748) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 503 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 212 GLU cc_start: 0.8185 (mp0) cc_final: 0.7965 (mp0) REVERT: K 284 HIS cc_start: 0.7432 (m-70) cc_final: 0.7050 (m-70) REVERT: K 302 VAL cc_start: 0.8674 (t) cc_final: 0.7660 (t) REVERT: K 310 GLN cc_start: 0.7881 (pm20) cc_final: 0.7383 (pm20) REVERT: K 327 LEU cc_start: 0.9283 (mt) cc_final: 0.9076 (pp) REVERT: K 343 ASP cc_start: 0.9106 (p0) cc_final: 0.8824 (p0) REVERT: M 234 LEU cc_start: 0.9274 (mp) cc_final: 0.8930 (pp) REVERT: M 238 LEU cc_start: 0.8932 (tt) cc_final: 0.8605 (tp) REVERT: M 278 TYR cc_start: 0.8932 (t80) cc_final: 0.8697 (t80) REVERT: O 237 PHE cc_start: 0.7207 (m-10) cc_final: 0.6860 (m-10) REVERT: O 271 PHE cc_start: 0.7996 (p90) cc_final: 0.7331 (p90) REVERT: O 272 LEU cc_start: 0.7499 (mt) cc_final: 0.7283 (tt) REVERT: O 325 TYR cc_start: 0.8783 (m-80) cc_final: 0.8575 (m-80) REVERT: O 329 LYS cc_start: 0.8766 (pptt) cc_final: 0.8552 (pttm) REVERT: O 353 TRP cc_start: 0.7292 (p90) cc_final: 0.6746 (p90) REVERT: O 395 ARG cc_start: 0.7563 (mmp-170) cc_final: 0.7231 (tpp-160) REVERT: Q 147 TYR cc_start: 0.6145 (m-80) cc_final: 0.5775 (m-10) REVERT: Q 150 PHE cc_start: 0.8227 (m-80) cc_final: 0.7789 (m-80) REVERT: Q 198 HIS cc_start: 0.9110 (m90) cc_final: 0.8816 (m90) REVERT: Q 326 ILE cc_start: 0.8218 (pt) cc_final: 0.8016 (pt) REVERT: A 48 LEU cc_start: 0.8165 (mm) cc_final: 0.7731 (mm) REVERT: A 51 ILE cc_start: 0.8765 (mm) cc_final: 0.8339 (mm) REVERT: A 59 GLU cc_start: 0.8873 (pm20) cc_final: 0.8353 (pm20) REVERT: A 63 ARG cc_start: 0.6916 (tmt-80) cc_final: 0.6537 (tmt-80) REVERT: A 73 GLU cc_start: 0.7994 (tt0) cc_final: 0.7255 (tp30) REVERT: A 84 PHE cc_start: 0.7494 (m-80) cc_final: 0.7068 (m-80) REVERT: A 87 SER cc_start: 0.9230 (t) cc_final: 0.8728 (p) REVERT: B 24 ASP cc_start: 0.7566 (p0) cc_final: 0.7306 (p0) REVERT: B 34 ILE cc_start: 0.9016 (tp) cc_final: 0.8766 (tp) REVERT: B 55 ARG cc_start: 0.7690 (mmp80) cc_final: 0.7354 (tpp-160) REVERT: B 62 LEU cc_start: 0.8342 (mm) cc_final: 0.8051 (mm) REVERT: B 63 GLU cc_start: 0.8298 (mp0) cc_final: 0.7867 (mp0) REVERT: B 74 GLU cc_start: 0.8403 (tp30) cc_final: 0.7979 (tp30) REVERT: B 83 SER cc_start: 0.8571 (m) cc_final: 0.8210 (m) REVERT: C 31 ILE cc_start: 0.9076 (mm) cc_final: 0.8863 (mp) REVERT: C 53 LEU cc_start: 0.8662 (mp) cc_final: 0.8175 (tt) REVERT: C 57 LEU cc_start: 0.8355 (mt) cc_final: 0.8079 (mt) REVERT: C 60 LEU cc_start: 0.8851 (tp) cc_final: 0.8620 (tp) REVERT: C 103 ILE cc_start: 0.9086 (tt) cc_final: 0.8643 (tt) REVERT: D 47 VAL cc_start: 0.8828 (t) cc_final: 0.8568 (t) REVERT: D 49 LYS cc_start: 0.8666 (mmmt) cc_final: 0.8284 (mmmt) REVERT: D 51 THR cc_start: 0.8886 (p) cc_final: 0.8369 (p) REVERT: D 89 LYS cc_start: 0.9052 (tttm) cc_final: 0.8822 (tptt) REVERT: E 41 TYR cc_start: 0.6637 (p90) cc_final: 0.6153 (p90) REVERT: E 64 LYS cc_start: 0.8569 (mppt) cc_final: 0.8191 (mmmm) REVERT: E 72 ARG cc_start: 0.7939 (mmt180) cc_final: 0.6004 (mmt180) REVERT: E 94 GLU cc_start: 0.7101 (mt-10) cc_final: 0.6836 (tt0) REVERT: E 104 PHE cc_start: 0.7081 (p90) cc_final: 0.6879 (p90) REVERT: E 108 ASN cc_start: 0.8394 (m-40) cc_final: 0.8095 (m-40) REVERT: E 115 LYS cc_start: 0.9169 (ptpp) cc_final: 0.8805 (ptpp) REVERT: E 122 LYS cc_start: 0.8594 (pttp) cc_final: 0.8369 (tmmt) REVERT: F 49 LEU cc_start: 0.8321 (mm) cc_final: 0.7810 (tp) REVERT: F 57 VAL cc_start: 0.8629 (m) cc_final: 0.8350 (p) REVERT: F 91 LYS cc_start: 0.8235 (pttm) cc_final: 0.7951 (pttm) REVERT: F 93 GLN cc_start: 0.7821 (pp30) cc_final: 0.7535 (pp30) REVERT: G 32 LYS cc_start: 0.8904 (mmmt) cc_final: 0.8665 (mmmt) REVERT: G 38 HIS cc_start: 0.7966 (p90) cc_final: 0.7678 (p90) REVERT: G 48 LYS cc_start: 0.8649 (mmmt) cc_final: 0.8344 (mmmt) REVERT: G 59 TYR cc_start: 0.7449 (p90) cc_final: 0.7087 (p90) REVERT: G 86 GLN cc_start: 0.7190 (mp10) cc_final: 0.6794 (mp10) REVERT: G 89 ILE cc_start: 0.8809 (tp) cc_final: 0.8496 (pt) REVERT: G 95 LEU cc_start: 0.9048 (mt) cc_final: 0.8645 (mt) REVERT: H 66 ASN cc_start: 0.7722 (p0) cc_final: 0.7319 (p0) REVERT: H 73 PHE cc_start: 0.7571 (t80) cc_final: 0.7272 (t80) REVERT: H 74 GLU cc_start: 0.8090 (tp30) cc_final: 0.7875 (tp30) REVERT: H 82 LYS cc_start: 0.8963 (tmmt) cc_final: 0.8542 (tmtt) REVERT: H 88 LYS cc_start: 0.9315 (ptpp) cc_final: 0.9095 (ptmm) REVERT: H 96 GLU cc_start: 0.7603 (tm-30) cc_final: 0.7387 (tm-30) REVERT: H 102 ARG cc_start: 0.8352 (ttp-110) cc_final: 0.8056 (ttp80) outliers start: 0 outliers final: 0 residues processed: 503 average time/residue: 0.1810 time to fit residues: 131.4709 Evaluate side-chains 450 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 450 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 2 optimal weight: 0.9980 chunk 145 optimal weight: 0.9980 chunk 188 optimal weight: 0.4980 chunk 87 optimal weight: 10.0000 chunk 156 optimal weight: 0.8980 chunk 205 optimal weight: 1.9990 chunk 194 optimal weight: 0.2980 chunk 1 optimal weight: 0.4980 chunk 178 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 4 optimal weight: 9.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 260 ASN ** M 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 100 HIS ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 HIS ** 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 = 0.4109 r_free = 0.4109 target = 0.122052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.096230 restraints weight = 88158.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.099512 restraints weight = 49410.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.101646 restraints weight = 31774.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.103014 restraints weight = 22789.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.103908 restraints weight = 17828.677| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.5175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22580 Z= 0.193 Angle : 0.973 14.653 31707 Z= 0.521 Chirality : 0.055 0.285 3556 Planarity : 0.007 0.146 3001 Dihedral : 28.901 130.787 5372 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 24.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.20 % Favored : 88.80 % Rotamer: Outliers : 0.06 % Allowed : 1.11 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.29 (0.18), residues: 1866 helix: -1.51 (0.15), residues: 971 sheet: -2.08 (0.87), residues: 33 loop : -3.01 (0.20), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 116 TYR 0.058 0.003 TYR G 34 PHE 0.085 0.003 PHE H 73 TRP 0.043 0.002 TRP O 353 HIS 0.016 0.002 HIS C 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.19 (22580) covalent geometry : angle 0.97346 / 0.52 (31707) hydrogen bonds : bond 0.05974 / 3.88 ( 1048) hydrogen bonds : angle 5.39839 / 3.59 ( 2748) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 507 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 212 GLU cc_start: 0.8185 (mp0) cc_final: 0.7983 (mp0) REVERT: K 273 PHE cc_start: 0.8384 (m-10) cc_final: 0.8157 (m-10) REVERT: K 274 TYR cc_start: 0.7785 (p90) cc_final: 0.7355 (p90) REVERT: K 284 HIS cc_start: 0.7463 (m-70) cc_final: 0.7044 (m-70) REVERT: K 310 GLN cc_start: 0.7705 (pm20) cc_final: 0.7230 (pm20) REVERT: K 311 TYR cc_start: 0.7632 (t80) cc_final: 0.7431 (t80) REVERT: K 319 LEU cc_start: 0.8015 (tp) cc_final: 0.7717 (pt) REVERT: K 343 ASP cc_start: 0.9081 (p0) cc_final: 0.8801 (p0) REVERT: K 353 TRP cc_start: 0.5235 (p-90) cc_final: 0.4989 (p-90) REVERT: M 238 LEU cc_start: 0.8908 (tt) cc_final: 0.8630 (tt) REVERT: M 278 TYR cc_start: 0.8919 (t80) cc_final: 0.8708 (t80) REVERT: O 237 PHE cc_start: 0.7044 (m-10) cc_final: 0.6733 (m-10) REVERT: O 271 PHE cc_start: 0.8015 (p90) cc_final: 0.7328 (p90) REVERT: O 275 CYS cc_start: 0.8407 (t) cc_final: 0.7881 (t) REVERT: O 325 TYR cc_start: 0.8776 (m-80) cc_final: 0.8448 (m-80) REVERT: O 353 TRP cc_start: 0.7262 (p90) cc_final: 0.6721 (p90) REVERT: Q 150 PHE cc_start: 0.8241 (m-80) cc_final: 0.7754 (m-80) REVERT: Q 198 HIS cc_start: 0.9117 (m90) cc_final: 0.8811 (m-70) REVERT: A 51 ILE cc_start: 0.8788 (mm) cc_final: 0.8167 (mm) REVERT: A 59 GLU cc_start: 0.8879 (pm20) cc_final: 0.8370 (pm20) REVERT: A 84 PHE cc_start: 0.7535 (m-80) cc_final: 0.7059 (m-80) REVERT: A 85 GLN cc_start: 0.8323 (tm-30) cc_final: 0.7582 (tm-30) REVERT: A 87 SER cc_start: 0.9189 (t) cc_final: 0.8771 (p) REVERT: B 34 ILE cc_start: 0.9009 (tp) cc_final: 0.8731 (tp) REVERT: B 55 ARG cc_start: 0.7717 (mmp80) cc_final: 0.7452 (tpp-160) REVERT: B 61 PHE cc_start: 0.8280 (t80) cc_final: 0.8015 (t80) REVERT: B 63 GLU cc_start: 0.8330 (mp0) cc_final: 0.7895 (mp0) REVERT: B 74 GLU cc_start: 0.8330 (tp30) cc_final: 0.7975 (tp30) REVERT: B 83 SER cc_start: 0.8622 (m) cc_final: 0.7781 (m) REVERT: C 53 LEU cc_start: 0.8599 (mp) cc_final: 0.8176 (tt) REVERT: C 78 LYS cc_start: 0.8874 (ptpt) cc_final: 0.8564 (pttm) REVERT: C 103 ILE cc_start: 0.9107 (tt) cc_final: 0.8639 (tt) REVERT: D 45 TYR cc_start: 0.7064 (t80) cc_final: 0.6848 (t80) REVERT: D 47 VAL cc_start: 0.8823 (t) cc_final: 0.8468 (t) REVERT: D 48 LEU cc_start: 0.7668 (pp) cc_final: 0.6463 (pp) REVERT: D 51 THR cc_start: 0.8904 (p) cc_final: 0.8307 (p) REVERT: D 57 ILE cc_start: 0.7812 (pt) cc_final: 0.7496 (tp) REVERT: D 116 GLU cc_start: 0.7751 (pm20) cc_final: 0.7384 (pm20) REVERT: D 124 TYR cc_start: 0.6516 (t80) cc_final: 0.6197 (t80) REVERT: E 41 TYR cc_start: 0.6620 (p90) cc_final: 0.6140 (p90) REVERT: E 54 PHE cc_start: 0.7069 (p90) cc_final: 0.6777 (p90) REVERT: E 60 LEU cc_start: 0.9099 (tp) cc_final: 0.8692 (tp) REVERT: E 64 LYS cc_start: 0.8585 (mppt) cc_final: 0.8283 (mmmm) REVERT: E 72 ARG cc_start: 0.7947 (mmt180) cc_final: 0.5987 (mmt180) REVERT: E 104 PHE cc_start: 0.6805 (p90) cc_final: 0.6498 (p90) REVERT: E 115 LYS cc_start: 0.9123 (ptpp) cc_final: 0.8790 (ptpp) REVERT: E 122 LYS cc_start: 0.8558 (pttp) cc_final: 0.8338 (tmmt) REVERT: F 25 ASN cc_start: 0.7083 (t0) cc_final: 0.6834 (t0) REVERT: F 30 THR cc_start: 0.8336 (p) cc_final: 0.8080 (p) REVERT: F 49 LEU cc_start: 0.8332 (mm) cc_final: 0.7794 (tp) REVERT: F 57 VAL cc_start: 0.8646 (m) cc_final: 0.8344 (p) REVERT: F 63 GLU cc_start: 0.8502 (pm20) cc_final: 0.8196 (pm20) REVERT: F 85 ASP cc_start: 0.7975 (p0) cc_final: 0.7627 (p0) REVERT: F 93 GLN cc_start: 0.8247 (pp30) cc_final: 0.7307 (pp30) REVERT: G 32 LYS cc_start: 0.8922 (mmmt) cc_final: 0.8657 (mmmt) REVERT: G 34 TYR cc_start: 0.8072 (p90) cc_final: 0.7351 (p90) REVERT: G 38 HIS cc_start: 0.7902 (p90) cc_final: 0.7655 (p90) REVERT: G 48 LYS cc_start: 0.8577 (mmmt) cc_final: 0.8263 (mmmt) REVERT: G 52 TYR cc_start: 0.7195 (t80) cc_final: 0.6118 (t80) REVERT: G 83 ARG cc_start: 0.7301 (ptm-80) cc_final: 0.6933 (ptm-80) REVERT: G 86 GLN cc_start: 0.7205 (mp10) cc_final: 0.6869 (mp10) REVERT: G 89 ILE cc_start: 0.8772 (tp) cc_final: 0.8503 (pt) REVERT: G 95 LEU cc_start: 0.9001 (mt) cc_final: 0.8619 (mt) REVERT: G 98 LEU cc_start: 0.8630 (pt) cc_final: 0.8000 (mp) REVERT: H 41 SER cc_start: 0.8465 (m) cc_final: 0.8149 (m) REVERT: H 62 MET cc_start: 0.7871 (mmp) cc_final: 0.7508 (mmp) REVERT: H 66 ASN cc_start: 0.7866 (p0) cc_final: 0.7619 (p0) REVERT: H 72 ILE cc_start: 0.7593 (tt) cc_final: 0.7265 (tt) REVERT: H 82 LYS cc_start: 0.8996 (tmmt) cc_final: 0.8497 (tmtt) REVERT: H 88 LYS cc_start: 0.9307 (ptpp) cc_final: 0.9085 (ptmm) REVERT: H 99 THR cc_start: 0.8726 (m) cc_final: 0.8343 (p) REVERT: H 105 LEU cc_start: 0.9143 (pp) cc_final: 0.8851 (pp) REVERT: H 112 HIS cc_start: 0.7723 (m90) cc_final: 0.7159 (m90) outliers start: 1 outliers final: 1 residues processed: 507 average time/residue: 0.1744 time to fit residues: 127.5688 Evaluate side-chains 453 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 452 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 32 optimal weight: 3.9990 chunk 198 optimal weight: 0.7980 chunk 197 optimal weight: 0.9990 chunk 174 optimal weight: 0.6980 chunk 145 optimal weight: 0.6980 chunk 115 optimal weight: 9.9990 chunk 204 optimal weight: 0.8980 chunk 163 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 260 ASN ** M 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 100 HIS ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN E 55 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 HIS ** 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 = 0.4108 r_free = 0.4108 target = 0.121969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.096080 restraints weight = 89295.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.099371 restraints weight = 50438.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.101460 restraints weight = 32475.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.102829 restraints weight = 23372.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.103720 restraints weight = 18297.073| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.5398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 22580 Z= 0.199 Angle : 0.977 15.066 31707 Z= 0.525 Chirality : 0.056 0.460 3556 Planarity : 0.008 0.168 3001 Dihedral : 28.835 130.070 5372 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 24.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.83 % Favored : 89.17 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.19 (0.18), residues: 1866 helix: -1.45 (0.15), residues: 974 sheet: -1.89 (0.87), residues: 33 loop : -2.94 (0.20), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.001 ARG H 102 TYR 0.046 0.003 TYR K 311 PHE 0.085 0.003 PHE H 73 TRP 0.042 0.002 TRP O 353 HIS 0.014 0.002 HIS G 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.20 (22580) covalent geometry : angle 0.97747 / 0.52 (31707) hydrogen bonds : bond 0.05947 / 3.86 ( 1048) hydrogen bonds : angle 5.43821 / 3.62 ( 2748) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 504 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 212 GLU cc_start: 0.8275 (mp0) cc_final: 0.8072 (mp0) REVERT: K 273 PHE cc_start: 0.8409 (m-10) cc_final: 0.8183 (m-10) REVERT: K 274 TYR cc_start: 0.7821 (p90) cc_final: 0.7333 (p90) REVERT: K 284 HIS cc_start: 0.7560 (m-70) cc_final: 0.7046 (m-70) REVERT: K 327 LEU cc_start: 0.9315 (mt) cc_final: 0.9060 (pp) REVERT: K 343 ASP cc_start: 0.9120 (p0) cc_final: 0.8838 (p0) REVERT: M 202 GLU cc_start: 0.8340 (pp20) cc_final: 0.8014 (pp20) REVERT: M 228 ASP cc_start: 0.8710 (m-30) cc_final: 0.8451 (m-30) REVERT: M 234 LEU cc_start: 0.9188 (mt) cc_final: 0.8915 (mp) REVERT: M 238 LEU cc_start: 0.8966 (tt) cc_final: 0.8684 (tt) REVERT: N 95 PHE cc_start: 0.7063 (t80) cc_final: 0.6812 (t80) REVERT: O 237 PHE cc_start: 0.7185 (m-10) cc_final: 0.6704 (m-10) REVERT: O 271 PHE cc_start: 0.8055 (p90) cc_final: 0.7282 (p90) REVERT: O 275 CYS cc_start: 0.8497 (t) cc_final: 0.8272 (t) REVERT: O 325 TYR cc_start: 0.8771 (m-80) cc_final: 0.8532 (m-80) REVERT: O 353 TRP cc_start: 0.7283 (p90) cc_final: 0.6738 (p90) REVERT: Q 147 TYR cc_start: 0.6251 (m-10) cc_final: 0.5969 (m-80) REVERT: Q 150 PHE cc_start: 0.8318 (m-80) cc_final: 0.7733 (m-80) REVERT: Q 198 HIS cc_start: 0.9127 (m90) cc_final: 0.8826 (m-70) REVERT: Q 326 ILE cc_start: 0.8249 (pt) cc_final: 0.8019 (pt) REVERT: A 51 ILE cc_start: 0.8812 (mm) cc_final: 0.8439 (mm) REVERT: A 59 GLU cc_start: 0.8939 (pm20) cc_final: 0.8434 (pm20) REVERT: A 84 PHE cc_start: 0.7441 (m-80) cc_final: 0.7001 (m-80) REVERT: A 85 GLN cc_start: 0.8308 (tm-30) cc_final: 0.7460 (tm-30) REVERT: A 87 SER cc_start: 0.9188 (t) cc_final: 0.8778 (p) REVERT: A 115 LYS cc_start: 0.9404 (ptpp) cc_final: 0.9131 (ptpp) REVERT: A 124 ILE cc_start: 0.8376 (mp) cc_final: 0.8174 (mp) REVERT: B 62 LEU cc_start: 0.8279 (mm) cc_final: 0.8029 (mm) REVERT: B 63 GLU cc_start: 0.8319 (mp0) cc_final: 0.7936 (mp0) REVERT: B 74 GLU cc_start: 0.8365 (tp30) cc_final: 0.8009 (tp30) REVERT: B 83 SER cc_start: 0.8652 (m) cc_final: 0.7817 (m) REVERT: B 88 TYR cc_start: 0.8036 (m-10) cc_final: 0.7664 (m-80) REVERT: C 53 LEU cc_start: 0.8500 (mp) cc_final: 0.8114 (tt) REVERT: C 57 LEU cc_start: 0.8321 (mt) cc_final: 0.8083 (mt) REVERT: C 60 LEU cc_start: 0.8787 (tp) cc_final: 0.8543 (mm) REVERT: C 78 LYS cc_start: 0.8648 (ptpt) cc_final: 0.8276 (pttm) REVERT: D 47 VAL cc_start: 0.8778 (t) cc_final: 0.8332 (t) REVERT: D 51 THR cc_start: 0.8795 (p) cc_final: 0.8373 (p) REVERT: D 86 TYR cc_start: 0.8385 (m-10) cc_final: 0.8124 (m-80) REVERT: D 103 LEU cc_start: 0.8431 (pp) cc_final: 0.8230 (pp) REVERT: D 116 GLU cc_start: 0.7765 (pm20) cc_final: 0.7383 (pm20) REVERT: E 41 TYR cc_start: 0.6684 (p90) cc_final: 0.6189 (p90) REVERT: E 54 PHE cc_start: 0.7114 (p90) cc_final: 0.6806 (p90) REVERT: E 60 LEU cc_start: 0.9077 (tp) cc_final: 0.8537 (tp) REVERT: E 64 LYS cc_start: 0.8666 (mppt) cc_final: 0.8372 (mmmm) REVERT: E 72 ARG cc_start: 0.8040 (mmt180) cc_final: 0.6459 (mmt180) REVERT: E 81 ASP cc_start: 0.8350 (p0) cc_final: 0.8084 (p0) REVERT: E 89 ILE cc_start: 0.8731 (pt) cc_final: 0.8369 (pt) REVERT: E 96 VAL cc_start: 0.8703 (t) cc_final: 0.8499 (t) REVERT: E 104 PHE cc_start: 0.6859 (p90) cc_final: 0.6352 (p90) REVERT: E 108 ASN cc_start: 0.8354 (m-40) cc_final: 0.8149 (m-40) REVERT: E 115 LYS cc_start: 0.9112 (ptpp) cc_final: 0.8769 (ptpp) REVERT: E 121 LYS cc_start: 0.9123 (tmmt) cc_final: 0.8168 (tttp) REVERT: E 123 ASP cc_start: 0.6688 (t0) cc_final: 0.6427 (t70) REVERT: F 49 LEU cc_start: 0.8405 (mm) cc_final: 0.7914 (tp) REVERT: F 79 LYS cc_start: 0.6602 (pttm) cc_final: 0.5935 (ptmt) REVERT: F 85 ASP cc_start: 0.8060 (p0) cc_final: 0.7681 (p0) REVERT: F 91 LYS cc_start: 0.8228 (pttm) cc_final: 0.7843 (pttm) REVERT: G 32 LYS cc_start: 0.8902 (mmmt) cc_final: 0.8678 (mmmt) REVERT: G 34 TYR cc_start: 0.8074 (p90) cc_final: 0.7473 (p90) REVERT: G 38 HIS cc_start: 0.7866 (p90) cc_final: 0.7583 (p90) REVERT: G 48 LYS cc_start: 0.8599 (mmmt) cc_final: 0.8310 (mmmt) REVERT: G 52 TYR cc_start: 0.7095 (t80) cc_final: 0.6041 (t80) REVERT: G 83 ARG cc_start: 0.7208 (ptm-80) cc_final: 0.6878 (ptm-80) REVERT: G 86 GLN cc_start: 0.7233 (mp10) cc_final: 0.6885 (mp10) REVERT: G 89 ILE cc_start: 0.8818 (tp) cc_final: 0.8494 (pt) REVERT: G 95 LEU cc_start: 0.9020 (mt) cc_final: 0.8586 (mt) REVERT: G 98 LEU cc_start: 0.8649 (pt) cc_final: 0.8087 (mp) REVERT: H 62 MET cc_start: 0.7804 (mmp) cc_final: 0.7589 (mmm) REVERT: H 66 ASN cc_start: 0.7718 (p0) cc_final: 0.7389 (p0) REVERT: H 72 ILE cc_start: 0.7497 (tt) cc_final: 0.7261 (tt) REVERT: H 82 LYS cc_start: 0.8866 (tmmt) cc_final: 0.8413 (tmtt) REVERT: H 88 LYS cc_start: 0.9342 (ptpp) cc_final: 0.9094 (ptmm) outliers start: 0 outliers final: 0 residues processed: 504 average time/residue: 0.1745 time to fit residues: 127.0695 Evaluate side-chains 451 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 451 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 45 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 10 optimal weight: 0.0060 chunk 106 optimal weight: 0.4980 chunk 61 optimal weight: 8.9990 chunk 82 optimal weight: 10.0000 chunk 127 optimal weight: 9.9990 chunk 48 optimal weight: 0.9980 chunk 181 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 overall best weight: 1.0798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 260 ASN M 287 ASN ** M 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN E 55 GLN E 108 ASN F 25 ASN ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.121948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.096010 restraints weight = 88395.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.099262 restraints weight = 50278.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.101381 restraints weight = 32619.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.102737 restraints weight = 23402.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.103674 restraints weight = 18310.158| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.5603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 22580 Z= 0.198 Angle : 0.981 14.975 31707 Z= 0.524 Chirality : 0.055 0.501 3556 Planarity : 0.008 0.137 3001 Dihedral : 28.796 129.482 5372 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 25.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % Rotamer: Outliers : 0.06 % Allowed : 0.93 % Favored : 99.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.25 (0.18), residues: 1866 helix: -1.47 (0.15), residues: 983 sheet: -1.76 (0.87), residues: 33 loop : -3.04 (0.19), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 33 TYR 0.036 0.003 TYR G 34 PHE 0.080 0.003 PHE H 73 TRP 0.041 0.002 TRP O 353 HIS 0.015 0.002 HIS C 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.20 (22580) covalent geometry : angle 0.98076 / 0.52 (31707) hydrogen bonds : bond 0.06009 / 3.91 ( 1048) hydrogen bonds : angle 5.37224 / 3.56 ( 2748) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4783.91 seconds wall clock time: 83 minutes 14.31 seconds (4994.31 seconds total)