Starting phenix.real_space_refine on Sun Jul 5 15:41:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x30_38024/07_2026/8x30_38024.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x30_38024/07_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_38024/07_2026/8x30_38024.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x30_38024/07_2026/8x30_38024.map" model { file = "/net/cci-nas-00/data/ceres_data/8x30_38024/07_2026/8x30_38024.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x30_38024/07_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-dev-6108/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: 4.15, per 1000 atoms: 0.19 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: 1.70 Conformation dependent library (CDL) restraints added in 488.3 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: 2.80 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: 4.24 Time building geometry restraints manager: 2.29 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: 2.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.300 Find NCS groups from input model: 0.280 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.790 ------------------------------------------------------------------------------- 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= 0.951 Angle : 1.492 17.120 31707 Z= 0.990 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 1.49232 / 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 : 0.636 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: 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: 0.7012 (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: 0.7744 (p) REVERT: K 357 LEU cc_start: 0.8979 (tm) cc_final: 0.8744 (mt) REVERT: K 408 ASP cc_start: 0.7498 (t70) cc_final: 0.6603 (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: 0.7982 (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: 0.7826 (ttp-170) REVERT: O 271 PHE cc_start: 0.8098 (p90) cc_final: 0.7356 (p90) REVERT: O 275 CYS cc_start: 0.8051 (t) cc_final: 0.7473 (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: 0.7634 (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: 0.7113 (t80) REVERT: Q 201 HIS cc_start: 0.9296 (m90) cc_final: 0.9043 (m-70) REVERT: Q 229 MET cc_start: 0.6912 (mmp) cc_final: 0.6185 (mmt) REVERT: R 102 ASN cc_start: 0.9057 (m-40) cc_final: 0.8736 (m-40) REVERT: A 50 GLU cc_start: 0.7770 (pt0) cc_final: 0.6978 (tp30) REVERT: A 54 PHE cc_start: 0.6801 (p90) cc_final: 0.6389 (p90) REVERT: A 58 THR cc_start: 0.7882 (p) cc_final: 0.7426 (t) REVERT: A 70 LEU cc_start: 0.8484 (pp) cc_final: 0.8199 (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: 0.8323 (mm) REVERT: B 25 ASN cc_start: 0.7381 (t0) cc_final: 0.7015 (t0) REVERT: B 27 GLN cc_start: 0.8170 (pm20) cc_final: 0.7595 (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: 0.8098 (mmtt) REVERT: B 74 GLU cc_start: 0.8414 (tp30) cc_final: 0.7723 (tp30) REVERT: C 21 ARG cc_start: 0.7434 (tmt-80) cc_final: 0.6852 (tpt90) REVERT: C 32 LYS cc_start: 0.8717 (mmtt) cc_final: 0.8451 (tppt) REVERT: C 51 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.7635 (tp) REVERT: C 59 TYR cc_start: 0.7309 (p90) cc_final: 0.7063 (p90) REVERT: C 70 ASN cc_start: 0.8100 (p0) cc_final: 0.7886 (p0) REVERT: C 74 ASP cc_start: 0.6895 (p0) cc_final: 0.6384 (p0) REVERT: C 86 GLN cc_start: 0.7333 (mt0) cc_final: 0.6925 (mt0) REVERT: C 103 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8799 (pp) REVERT: D 65 LEU cc_start: 0.9036 (mt) cc_final: 0.8788 (mt) REVERT: D 68 PHE cc_start: 0.8183 (p90) cc_final: 0.7955 (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 87 ASN cc_start: 0.9046 (p0) cc_final: 0.8630 (p0) REVERT: D 89 LYS cc_start: 0.8595 (tmtp) cc_final: 0.8254 (tmtt) REVERT: D 111 LYS cc_start: 0.7848 (OUTLIER) cc_final: 0.7459 (pmmt) REVERT: D 124 TYR cc_start: 0.8315 (t80) cc_final: 0.8110 (t80) REVERT: E 41 TYR cc_start: 0.5758 (p90) cc_final: 0.5418 (p90) REVERT: E 64 LYS cc_start: 0.8072 (mppt) cc_final: 0.7706 (mmtm) REVERT: E 72 ARG cc_start: 0.6851 (mmt180) cc_final: 0.6378 (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: 0.7392 (tt0) REVERT: E 120 GLN cc_start: 0.6643 (pp30) cc_final: 0.6180 (pp30) REVERT: E 130 LEU cc_start: 0.8636 (pp) cc_final: 0.8381 (pp) REVERT: F 50 ILE cc_start: 0.8280 (pp) cc_final: 0.7775 (mm) REVERT: F 61 PHE cc_start: 0.8303 (t80) cc_final: 0.8085 (t80) REVERT: F 71 THR cc_start: 0.8486 (m) cc_final: 0.7808 (m) REVERT: F 98 TYR cc_start: 0.6931 (t80) cc_final: 0.6403 (t80) REVERT: G 38 HIS cc_start: 0.8157 (p-80) cc_final: 0.7888 (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: 0.8585 (mp) REVERT: G 89 ILE cc_start: 0.8703 (mp) cc_final: 0.8326 (pt) REVERT: G 103 ILE cc_start: 0.6662 (pp) cc_final: 0.6242 (mp) REVERT: H 62 MET cc_start: 0.7821 (mmm) cc_final: 0.7595 (mmm) REVERT: H 66 ASN cc_start: 0.7744 (p0) cc_final: 0.7431 (p0) REVERT: H 68 PHE cc_start: 0.8178 (t80) cc_final: 0.7852 (t80) REVERT: H 74 GLU cc_start: 0.7776 (tp30) cc_final: 0.7360 (tp30) REVERT: H 86 TYR cc_start: 0.7113 (p90) cc_final: 0.6699 (p90) REVERT: H 96 GLU cc_start: 0.7038 (tm-30) cc_final: 0.6724 (tm-30) outliers start: 58 outliers final: 7 residues processed: 567 average time/residue: 0.1996 time to fit residues: 161.7299 Evaluate side-chains 461 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 447 time to evaluate : 0.650 ------------------------------------------------------------------------------- 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: 4.9990 chunk 124 optimal weight: 2.9990 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** ** 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.116922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.091547 restraints weight = 87479.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.094722 restraints weight = 49333.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.096711 restraints weight = 31902.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.098068 restraints weight = 23002.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.098967 restraints weight = 18033.553| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 22580 Z= 0.239 Angle : 1.051 13.816 31707 Z= 0.575 Chirality : 0.060 0.291 3556 Planarity : 0.009 0.132 3001 Dihedral : 29.980 130.310 5372 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 26.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.58 % Favored : 88.42 % Rotamer: Outliers : 1.11 % Allowed : 8.45 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.77 % Twisted General : 0.44 % 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: -4.42 (0.16), residues: 1866 helix: -2.49 (0.14), residues: 981 sheet: -3.12 (0.72), residues: 33 loop : -3.46 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.049 0.002 ARG C 83 TYR 0.054 0.004 TYR D 43 PHE 0.063 0.003 PHE H 73 TRP 0.037 0.003 TRP O 353 HIS 0.016 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.24 (22580) covalent geometry : angle 1.05126 / 0.57 (31707) hydrogen bonds : bond 0.07190 / 4.56 ( 1048) hydrogen bonds : angle 5.97139 / 4.00 ( 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 532 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 513 time to evaluate : 0.675 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: 0.7553 (m-70) cc_final: 0.7113 (m-70) REVERT: K 302 VAL cc_start: 0.8884 (t) cc_final: 0.8041 (t) REVERT: K 311 TYR cc_start: 0.7156 (t80) cc_final: 0.6696 (t80) REVERT: K 327 LEU cc_start: 0.9264 (mt) cc_final: 0.9012 (pp) REVERT: K 343 ASP cc_start: 0.9031 (p0) cc_final: 0.8785 (p0) REVERT: K 357 LEU cc_start: 0.9098 (tp) cc_final: 0.8794 (mt) REVERT: M 175 GLN cc_start: 0.5274 (OUTLIER) cc_final: 0.4768 (pp30) REVERT: M 234 LEU cc_start: 0.9091 (mp) cc_final: 0.8784 (mp) REVERT: M 238 LEU cc_start: 0.8758 (tp) cc_final: 0.8415 (tt) REVERT: M 278 TYR cc_start: 0.8598 (t80) cc_final: 0.8185 (t80) REVERT: O 271 PHE cc_start: 0.7924 (p90) cc_final: 0.7207 (p90) REVERT: O 272 LEU cc_start: 0.7586 (mt) cc_final: 0.7339 (tt) REVERT: O 275 CYS cc_start: 0.8497 (t) cc_final: 0.8145 (t) REVERT: O 325 TYR cc_start: 0.8380 (m-10) cc_final: 0.8061 (m-80) REVERT: Q 229 MET cc_start: 0.6661 (mmp) cc_final: 0.4426 (mmp) REVERT: R 102 ASN cc_start: 0.8853 (m-40) cc_final: 0.8629 (m-40) REVERT: A 51 ILE cc_start: 0.8708 (mm) cc_final: 0.8224 (mm) REVERT: A 58 THR cc_start: 0.7872 (p) cc_final: 0.7417 (t) REVERT: A 73 GLU cc_start: 0.8071 (tt0) cc_final: 0.7744 (tt0) REVERT: A 82 LEU cc_start: 0.8276 (pt) cc_final: 0.7912 (tp) REVERT: A 85 GLN cc_start: 0.8280 (tm-30) cc_final: 0.7978 (tm-30) REVERT: A 100 LEU cc_start: 0.8693 (pp) cc_final: 0.8420 (mm) REVERT: A 121 LYS cc_start: 0.8870 (tttm) cc_final: 0.8643 (tmtt) REVERT: B 25 ASN cc_start: 0.7494 (t0) cc_final: 0.7013 (t0) REVERT: B 62 LEU cc_start: 0.8139 (mm) cc_final: 0.7890 (mm) REVERT: B 74 GLU cc_start: 0.8490 (tp30) cc_final: 0.7898 (tp30) REVERT: C 21 ARG cc_start: 0.6993 (tmt-80) cc_final: 0.6731 (tpt90) REVERT: C 30 ARG cc_start: 0.7888 (pmt-80) cc_final: 0.7370 (ptt-90) REVERT: C 32 LYS cc_start: 0.8955 (mmtt) cc_final: 0.8626 (tptt) REVERT: C 79 ARG cc_start: 0.7216 (pmt-80) cc_final: 0.6866 (pmt-80) REVERT: D 50 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8340 (pp30) REVERT: D 65 LEU cc_start: 0.8977 (mt) cc_final: 0.8658 (mt) REVERT: D 71 ASP cc_start: 0.8119 (p0) cc_final: 0.7895 (p0) REVERT: D 76 ILE cc_start: 0.8815 (pt) cc_final: 0.8553 (pt) REVERT: E 41 TYR cc_start: 0.6236 (p90) cc_final: 0.5737 (p90) REVERT: E 54 PHE cc_start: 0.6940 (p90) cc_final: 0.6677 (p90) REVERT: E 64 LYS cc_start: 0.8123 (mppt) cc_final: 0.7808 (mmtm) REVERT: E 115 LYS cc_start: 0.9119 (ptpp) cc_final: 0.8727 (ptpp) REVERT: E 120 GLN cc_start: 0.6353 (pp30) cc_final: 0.5731 (pp30) REVERT: F 50 ILE cc_start: 0.8374 (pt) cc_final: 0.8031 (mm) REVERT: F 87 VAL cc_start: 0.8185 (p) cc_final: 0.7796 (t) REVERT: F 88 TYR cc_start: 0.7224 (m-80) cc_final: 0.6967 (m-80) REVERT: F 98 TYR cc_start: 0.6924 (OUTLIER) cc_final: 0.6675 (t80) REVERT: G 59 TYR cc_start: 0.7118 (OUTLIER) cc_final: 0.6813 (p90) REVERT: G 60 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8111 (pp) REVERT: G 67 LEU cc_start: 0.8527 (mt) cc_final: 0.8266 (mt) REVERT: G 86 GLN cc_start: 0.7233 (mp10) cc_final: 0.6898 (mp10) REVERT: G 96 ASP cc_start: 0.8650 (p0) cc_final: 0.8358 (p0) REVERT: H 54 ASP cc_start: 0.8117 (p0) cc_final: 0.7645 (p0) REVERT: H 66 ASN cc_start: 0.7758 (p0) cc_final: 0.7462 (p0) REVERT: H 68 PHE cc_start: 0.8191 (t80) cc_final: 0.7840 (t80) REVERT: H 74 GLU cc_start: 0.8004 (tp30) cc_final: 0.7552 (tp30) REVERT: H 82 LYS cc_start: 0.8938 (tmmt) cc_final: 0.8621 (ttpp) REVERT: H 86 TYR cc_start: 0.7292 (p90) cc_final: 0.6885 (p90) REVERT: H 88 LYS cc_start: 0.9293 (ptpp) cc_final: 0.9066 (ptmm) REVERT: H 105 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8609 (pp) REVERT: H 108 GLU cc_start: 0.8177 (pm20) cc_final: 0.7854 (pm20) REVERT: H 112 HIS cc_start: 0.7237 (m90) cc_final: 0.6342 (m90) REVERT: H 118 THR cc_start: 0.8630 (p) cc_final: 0.8147 (p) outliers start: 19 outliers final: 3 residues processed: 521 average time/residue: 0.1818 time to fit residues: 136.7908 Evaluate side-chains 472 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 463 time to evaluate : 0.662 ------------------------------------------------------------------------------- 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: 0.1980 chunk 130 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 chunk 7 optimal weight: 0.4980 chunk 180 optimal weight: 2.9990 chunk 109 optimal weight: 0.2980 chunk 38 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 205 optimal weight: 0.2980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 261 HIS K 301 ASN M 173 ASN M 240 HIS ** M 266 GLN ** 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** ** 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 75 HIS ** C 70 ASN ** 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 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 16 GLN ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.119902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.094627 restraints weight = 87620.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.097798 restraints weight = 48858.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.099850 restraints weight = 31382.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.101173 restraints weight = 22551.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.102062 restraints weight = 17600.897| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 22580 Z= 0.205 Angle : 0.986 14.120 31707 Z= 0.536 Chirality : 0.057 0.271 3556 Planarity : 0.008 0.122 3001 Dihedral : 29.653 132.419 5372 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 23.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.04 % Favored : 88.96 % Rotamer: Outliers : 0.29 % Allowed : 6.18 % Favored : 93.53 % 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: -3.98 (0.17), residues: 1866 helix: -2.14 (0.14), residues: 981 sheet: -2.71 (0.75), residues: 33 loop : -3.25 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG A 129 TYR 0.064 0.003 TYR G 59 PHE 0.073 0.003 PHE H 73 TRP 0.051 0.002 TRP O 353 HIS 0.015 0.002 HIS O 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.20 (22580) covalent geometry : angle 0.98552 / 0.54 (31707) hydrogen bonds : bond 0.06504 / 4.13 ( 1048) hydrogen bonds : angle 5.64297 / 3.77 ( 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 525 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 520 time to evaluate : 0.497 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 209 LYS cc_start: 0.8741 (mmpt) cc_final: 0.8504 (mmpt) REVERT: K 284 HIS cc_start: 0.7521 (m-70) cc_final: 0.7048 (m-70) REVERT: K 302 VAL cc_start: 0.8662 (t) cc_final: 0.7794 (t) REVERT: K 311 TYR cc_start: 0.7094 (t80) cc_final: 0.6641 (t80) REVERT: K 319 LEU cc_start: 0.7877 (tp) cc_final: 0.7552 (pt) REVERT: K 327 LEU cc_start: 0.9294 (mt) cc_final: 0.9063 (pp) REVERT: K 343 ASP cc_start: 0.8972 (p0) cc_final: 0.8433 (p0) REVERT: K 357 LEU cc_start: 0.9018 (tp) cc_final: 0.8664 (mt) REVERT: M 203 ARG cc_start: 0.8200 (mpt-90) cc_final: 0.7930 (mpt-90) REVERT: M 234 LEU cc_start: 0.9121 (mp) cc_final: 0.8881 (mp) REVERT: M 278 TYR cc_start: 0.8695 (t80) cc_final: 0.8350 (t80) REVERT: O 271 PHE cc_start: 0.7892 (p90) cc_final: 0.7169 (p90) REVERT: O 272 LEU cc_start: 0.7509 (mt) cc_final: 0.7256 (tt) REVERT: O 275 CYS cc_start: 0.8598 (t) cc_final: 0.8078 (t) REVERT: Q 195 SER cc_start: 0.7285 (p) cc_final: 0.6800 (p) REVERT: A 58 THR cc_start: 0.7360 (p) cc_final: 0.6915 (t) REVERT: A 61 LEU cc_start: 0.9039 (mm) cc_final: 0.8829 (mt) REVERT: A 121 LYS cc_start: 0.8661 (tttm) cc_final: 0.8130 (tppt) REVERT: B 25 ASN cc_start: 0.7449 (t0) cc_final: 0.6981 (t0) REVERT: B 34 ILE cc_start: 0.9134 (tp) cc_final: 0.8702 (tp) REVERT: B 37 LEU cc_start: 0.8852 (mm) cc_final: 0.8588 (pp) REVERT: B 44 LYS cc_start: 0.8640 (pptt) cc_final: 0.8104 (pptt) REVERT: B 74 GLU cc_start: 0.8442 (tp30) cc_final: 0.7845 (tp30) REVERT: C 30 ARG cc_start: 0.7735 (pmt-80) cc_final: 0.7328 (ptt-90) REVERT: C 32 LYS cc_start: 0.9006 (mmtt) cc_final: 0.8792 (tptt) REVERT: C 33 ARG cc_start: 0.8489 (pmt170) cc_final: 0.8156 (pmt170) REVERT: C 53 LEU cc_start: 0.7543 (mp) cc_final: 0.7160 (tt) REVERT: C 57 LEU cc_start: 0.8017 (mt) cc_final: 0.7655 (mt) REVERT: D 64 ILE cc_start: 0.8707 (mm) cc_final: 0.8414 (mm) REVERT: D 72 ILE cc_start: 0.9047 (pt) cc_final: 0.8798 (pt) REVERT: D 76 ILE cc_start: 0.8976 (pt) cc_final: 0.8725 (pt) REVERT: D 79 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.7022 (pm20) REVERT: D 97 ILE cc_start: 0.8590 (tp) cc_final: 0.8363 (tp) REVERT: E 41 TYR cc_start: 0.6231 (p90) cc_final: 0.5676 (p90) REVERT: E 64 LYS cc_start: 0.8193 (mppt) cc_final: 0.7908 (mmtm) REVERT: E 72 ARG cc_start: 0.7738 (mmt180) cc_final: 0.4966 (mmt180) REVERT: E 74 ILE cc_start: 0.8575 (pt) cc_final: 0.8331 (pt) REVERT: E 81 ASP cc_start: 0.8327 (p0) cc_final: 0.8058 (p0) REVERT: E 83 ARG cc_start: 0.7940 (mmp80) cc_final: 0.7596 (mmp80) REVERT: E 94 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6767 (tt0) REVERT: E 108 ASN cc_start: 0.8211 (m110) cc_final: 0.7768 (m-40) REVERT: E 115 LYS cc_start: 0.9131 (ptpp) cc_final: 0.8721 (ptpp) REVERT: E 123 ASP cc_start: 0.7343 (m-30) cc_final: 0.7040 (t0) REVERT: E 125 LYS cc_start: 0.8577 (mtmm) cc_final: 0.8313 (mtmm) REVERT: F 87 VAL cc_start: 0.8031 (p) cc_final: 0.7639 (t) REVERT: G 32 LYS cc_start: 0.8654 (mmmt) cc_final: 0.8271 (mmmt) REVERT: G 52 TYR cc_start: 0.7479 (t80) cc_final: 0.7236 (t80) REVERT: G 67 LEU cc_start: 0.8553 (mt) cc_final: 0.8223 (mt) REVERT: G 89 ILE cc_start: 0.8728 (tp) cc_final: 0.8390 (pt) REVERT: H 62 MET cc_start: 0.7457 (mmp) cc_final: 0.7250 (mmm) REVERT: H 66 ASN cc_start: 0.7538 (p0) cc_final: 0.7307 (p0) REVERT: H 68 PHE cc_start: 0.8082 (t80) cc_final: 0.7879 (t80) REVERT: H 82 LYS cc_start: 0.8878 (tmmt) cc_final: 0.8555 (ttpp) REVERT: H 86 TYR cc_start: 0.7236 (p90) cc_final: 0.6765 (p90) REVERT: H 88 LYS cc_start: 0.9270 (ptpp) cc_final: 0.9056 (ptmm) REVERT: H 105 LEU cc_start: 0.9105 (pp) cc_final: 0.8790 (pp) REVERT: H 108 GLU cc_start: 0.8199 (pm20) cc_final: 0.7916 (pm20) REVERT: H 112 HIS cc_start: 0.7402 (m90) cc_final: 0.6101 (m90) outliers start: 5 outliers final: 1 residues processed: 521 average time/residue: 0.1694 time to fit residues: 127.3314 Evaluate side-chains 465 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 463 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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: 0.8980 chunk 14 optimal weight: 0.0770 chunk 212 optimal weight: 6.9990 chunk 191 optimal weight: 3.9990 chunk 133 optimal weight: 8.9990 chunk 207 optimal weight: 0.6980 chunk 121 optimal weight: 8.9990 chunk 171 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 184 optimal weight: 0.5980 chunk 181 optimal weight: 2.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 166 ASN M 260 ASN ** M 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 386 HIS ** O 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 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** ** 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 = 0.4076 r_free = 0.4076 target = 0.120312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.095118 restraints weight = 87734.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.098291 restraints weight = 49226.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.100382 restraints weight = 31665.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.101743 restraints weight = 22597.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 69)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.102642 restraints weight = 17610.108| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 22580 Z= 0.194 Angle : 0.948 13.702 31707 Z= 0.516 Chirality : 0.056 0.312 3556 Planarity : 0.007 0.138 3001 Dihedral : 29.436 130.025 5372 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 23.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.83 % Favored : 89.17 % Rotamer: Outliers : 0.12 % Allowed : 5.36 % Favored : 94.52 % 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: -3.73 (0.17), residues: 1866 helix: -1.87 (0.15), residues: 1002 sheet: -2.43 (0.78), residues: 33 loop : -3.24 (0.19), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 83 TYR 0.057 0.003 TYR C 59 PHE 0.036 0.003 PHE Q 196 TRP 0.038 0.002 TRP O 353 HIS 0.028 0.002 HIS G 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.19 (22580) covalent geometry : angle 0.94813 / 0.52 (31707) hydrogen bonds : bond 0.06179 / 3.92 ( 1048) hydrogen bonds : angle 5.51851 / 3.69 ( 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 502 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 500 time to evaluate : 0.555 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 273 PHE cc_start: 0.8053 (m-80) cc_final: 0.7669 (m-10) REVERT: K 284 HIS cc_start: 0.7563 (m-70) cc_final: 0.7072 (m-70) REVERT: K 310 GLN cc_start: 0.8186 (pm20) cc_final: 0.7894 (pm20) REVERT: K 311 TYR cc_start: 0.7246 (t80) cc_final: 0.6708 (t80) REVERT: K 319 LEU cc_start: 0.7982 (tp) cc_final: 0.7734 (pp) REVERT: K 325 TYR cc_start: 0.8375 (m-80) cc_final: 0.8124 (m-10) REVERT: K 327 LEU cc_start: 0.9305 (mt) cc_final: 0.9003 (pp) REVERT: M 164 MET cc_start: -0.1583 (tpt) cc_final: -0.1911 (tpt) REVERT: M 260 ASN cc_start: 0.6763 (OUTLIER) cc_final: 0.6500 (t160) REVERT: M 278 TYR cc_start: 0.8695 (t80) cc_final: 0.8367 (t80) REVERT: O 245 ARG cc_start: 0.8166 (tpm170) cc_final: 0.7850 (tpp-160) REVERT: O 271 PHE cc_start: 0.7988 (p90) cc_final: 0.7299 (p90) REVERT: O 272 LEU cc_start: 0.7502 (mt) cc_final: 0.7280 (tt) REVERT: O 275 CYS cc_start: 0.8489 (t) cc_final: 0.7934 (t) REVERT: O 329 LYS cc_start: 0.8830 (pptt) cc_final: 0.8613 (pttm) REVERT: O 331 GLU cc_start: 0.8235 (pt0) cc_final: 0.7560 (pp20) REVERT: O 353 TRP cc_start: 0.7218 (p90) cc_final: 0.6587 (p90) REVERT: Q 326 ILE cc_start: 0.8206 (pt) cc_final: 0.7986 (pt) REVERT: A 51 ILE cc_start: 0.8698 (mm) cc_final: 0.8471 (mm) REVERT: A 58 THR cc_start: 0.7365 (p) cc_final: 0.6857 (t) REVERT: A 73 GLU cc_start: 0.8098 (tt0) cc_final: 0.7765 (tt0) REVERT: A 82 LEU cc_start: 0.8072 (mp) cc_final: 0.7370 (tp) REVERT: A 100 LEU cc_start: 0.8821 (pp) cc_final: 0.8313 (mm) REVERT: B 25 ASN cc_start: 0.7379 (t0) cc_final: 0.7140 (t0) REVERT: B 44 LYS cc_start: 0.8628 (pptt) cc_final: 0.8079 (pptt) REVERT: B 58 LEU cc_start: 0.8578 (mm) cc_final: 0.8351 (mm) REVERT: B 63 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7806 (pm20) REVERT: B 74 GLU cc_start: 0.8288 (tp30) cc_final: 0.7853 (tp30) REVERT: C 31 ILE cc_start: 0.9165 (mm) cc_final: 0.8756 (pt) REVERT: C 33 ARG cc_start: 0.8561 (pmt170) cc_final: 0.7898 (ptt-90) REVERT: C 53 LEU cc_start: 0.7944 (mp) cc_final: 0.7570 (tt) REVERT: C 57 LEU cc_start: 0.8103 (mt) cc_final: 0.7819 (mt) REVERT: C 103 ILE cc_start: 0.9133 (pt) cc_final: 0.8833 (tt) REVERT: D 69 VAL cc_start: 0.8651 (m) cc_final: 0.8275 (p) REVERT: D 87 ASN cc_start: 0.9116 (p0) cc_final: 0.8869 (p0) REVERT: D 103 LEU cc_start: 0.8419 (pp) cc_final: 0.8115 (pp) REVERT: E 41 TYR cc_start: 0.6253 (p90) cc_final: 0.5673 (p90) REVERT: E 54 PHE cc_start: 0.6624 (p90) cc_final: 0.6315 (p90) REVERT: E 64 LYS cc_start: 0.8076 (mppt) cc_final: 0.7763 (mmtm) REVERT: E 69 ARG cc_start: 0.7661 (ptp90) cc_final: 0.7455 (ptp90) REVERT: E 72 ARG cc_start: 0.7694 (mmt180) cc_final: 0.7393 (mmt180) REVERT: E 81 ASP cc_start: 0.8346 (p0) cc_final: 0.8105 (p0) REVERT: E 83 ARG cc_start: 0.7946 (mmp80) cc_final: 0.7564 (mmp80) REVERT: E 94 GLU cc_start: 0.7128 (mt-10) cc_final: 0.6695 (tt0) REVERT: E 108 ASN cc_start: 0.8223 (m110) cc_final: 0.7865 (m-40) REVERT: E 109 LEU cc_start: 0.9116 (tp) cc_final: 0.8883 (tp) REVERT: E 115 LYS cc_start: 0.9071 (ptpp) cc_final: 0.8698 (ptpp) REVERT: E 124 ILE cc_start: 0.8778 (pt) cc_final: 0.8478 (pt) REVERT: E 125 LYS cc_start: 0.8585 (mtmm) cc_final: 0.8342 (mtmm) REVERT: F 27 GLN cc_start: 0.8320 (mp10) cc_final: 0.7987 (mp10) REVERT: F 58 LEU cc_start: 0.7844 (pt) cc_final: 0.7583 (pt) REVERT: F 87 VAL cc_start: 0.8076 (p) cc_final: 0.7669 (t) REVERT: G 34 TYR cc_start: 0.8006 (p90) cc_final: 0.7205 (p90) REVERT: G 38 HIS cc_start: 0.7956 (p90) cc_final: 0.7693 (p90) REVERT: G 52 TYR cc_start: 0.7294 (t80) cc_final: 0.6594 (t80) REVERT: G 59 TYR cc_start: 0.7351 (p90) cc_final: 0.6933 (p90) REVERT: G 86 GLN cc_start: 0.7063 (mp10) cc_final: 0.6710 (mp10) REVERT: G 89 ILE cc_start: 0.8800 (tp) cc_final: 0.8432 (pt) REVERT: G 95 LEU cc_start: 0.8922 (mt) cc_final: 0.8660 (mt) REVERT: G 96 ASP cc_start: 0.8292 (p0) cc_final: 0.8033 (p0) REVERT: H 62 MET cc_start: 0.7636 (mmp) cc_final: 0.7401 (mmp) REVERT: H 66 ASN cc_start: 0.7563 (p0) cc_final: 0.7305 (p0) REVERT: H 73 PHE cc_start: 0.6951 (t80) cc_final: 0.6229 (t80) REVERT: H 86 TYR cc_start: 0.7162 (p90) cc_final: 0.6675 (p90) REVERT: H 88 LYS cc_start: 0.9285 (ptpp) cc_final: 0.9041 (ptmm) REVERT: H 105 LEU cc_start: 0.9096 (pp) cc_final: 0.8888 (pp) REVERT: H 108 GLU cc_start: 0.8127 (pm20) cc_final: 0.7903 (pm20) REVERT: H 111 LYS cc_start: 0.8016 (pptt) cc_final: 0.7813 (pptt) REVERT: H 112 HIS cc_start: 0.7513 (m90) cc_final: 0.6278 (m90) outliers start: 2 outliers final: 0 residues processed: 501 average time/residue: 0.1726 time to fit residues: 124.9910 Evaluate side-chains 446 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 444 time to evaluate : 0.573 ------------------------------------------------------------------------------- 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: 0.5980 chunk 148 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 chunk 208 optimal weight: 0.8980 chunk 141 optimal weight: 9.9990 chunk 159 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 166 ASN K 301 ASN ** M 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 386 HIS P 34 GLN ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 HIS ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 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 55 GLN ** 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 = 0.4095 r_free = 0.4095 target = 0.121220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.096098 restraints weight = 87412.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.099315 restraints weight = 48480.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.101422 restraints weight = 30954.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.102780 restraints weight = 22013.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.103618 restraints weight = 17041.666| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 22580 Z= 0.191 Angle : 0.933 13.125 31707 Z= 0.505 Chirality : 0.054 0.300 3556 Planarity : 0.007 0.155 3001 Dihedral : 29.252 129.229 5372 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 24.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.83 % Favored : 89.17 % Rotamer: Outliers : 0.06 % Allowed : 5.48 % Favored : 94.46 % 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: -3.54 (0.18), residues: 1866 helix: -1.73 (0.15), residues: 982 sheet: -2.35 (0.80), residues: 33 loop : -3.11 (0.19), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 30 TYR 0.035 0.003 TYR A 41 PHE 0.031 0.003 PHE A 67 TRP 0.032 0.002 TRP O 353 HIS 0.022 0.002 HIS C 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.19 (22580) covalent geometry : angle 0.93334 / 0.50 (31707) hydrogen bonds : bond 0.06079 / 3.89 ( 1048) hydrogen bonds : angle 5.39142 / 3.60 ( 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 496 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 495 time to evaluate : 0.816 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: K 243 LYS cc_start: 0.8767 (mptt) cc_final: 0.8242 (mptt) REVERT: K 273 PHE cc_start: 0.8089 (m-10) cc_final: 0.7778 (m-10) REVERT: K 284 HIS cc_start: 0.7290 (m-70) cc_final: 0.6857 (m-70) REVERT: K 310 GLN cc_start: 0.8082 (pm20) cc_final: 0.7841 (pm20) REVERT: K 327 LEU cc_start: 0.9284 (mt) cc_final: 0.8964 (pp) REVERT: M 202 GLU cc_start: 0.8537 (pp20) cc_final: 0.8316 (pp20) REVERT: M 234 LEU cc_start: 0.9165 (mp) cc_final: 0.8819 (pp) REVERT: M 238 LEU cc_start: 0.8757 (tt) cc_final: 0.8550 (tt) REVERT: M 278 TYR cc_start: 0.8908 (t80) cc_final: 0.8673 (t80) REVERT: M 279 TRP cc_start: 0.8363 (t60) cc_final: 0.8148 (t60) REVERT: N 9 GLN cc_start: 0.8609 (tp-100) cc_final: 0.8406 (tp-100) REVERT: O 178 GLU cc_start: 0.7806 (tp30) cc_final: 0.7216 (pm20) REVERT: O 271 PHE cc_start: 0.7947 (p90) cc_final: 0.7278 (p90) REVERT: O 272 LEU cc_start: 0.7482 (mt) cc_final: 0.7257 (tt) REVERT: O 275 CYS cc_start: 0.8578 (t) cc_final: 0.8211 (t) REVERT: O 329 LYS cc_start: 0.8700 (pptt) cc_final: 0.8383 (ptpp) REVERT: O 331 GLU cc_start: 0.8215 (pt0) cc_final: 0.7521 (pp20) REVERT: O 353 TRP cc_start: 0.7192 (p90) cc_final: 0.6604 (p90) REVERT: Q 198 HIS cc_start: 0.9203 (m90) cc_final: 0.8933 (m170) REVERT: A 48 LEU cc_start: 0.8077 (mm) cc_final: 0.7789 (pt) REVERT: A 51 ILE cc_start: 0.8675 (mm) cc_final: 0.8184 (mm) REVERT: A 73 GLU cc_start: 0.8132 (tt0) cc_final: 0.7808 (tt0) REVERT: A 82 LEU cc_start: 0.8001 (mp) cc_final: 0.7485 (tt) REVERT: A 85 GLN cc_start: 0.7939 (tm-30) cc_final: 0.7663 (tm-30) REVERT: A 119 ILE cc_start: 0.8362 (mm) cc_final: 0.8155 (tp) REVERT: B 36 ARG cc_start: 0.7965 (ptp90) cc_final: 0.7669 (ptp90) REVERT: B 44 LYS cc_start: 0.8569 (pptt) cc_final: 0.7944 (pptt) REVERT: B 62 LEU cc_start: 0.8178 (mm) cc_final: 0.7869 (mm) REVERT: B 63 GLU cc_start: 0.7884 (pm20) cc_final: 0.7406 (mp0) REVERT: B 74 GLU cc_start: 0.8374 (tp30) cc_final: 0.7790 (tp30) REVERT: B 77 LYS cc_start: 0.8893 (mttp) cc_final: 0.8662 (mttp) REVERT: C 31 ILE cc_start: 0.9181 (mm) cc_final: 0.8967 (mp) REVERT: C 32 LYS cc_start: 0.8846 (tptt) cc_final: 0.8295 (tptt) REVERT: C 33 ARG cc_start: 0.8371 (pmt170) cc_final: 0.7970 (ptt-90) REVERT: C 44 ARG cc_start: 0.6678 (tmm-80) cc_final: 0.6249 (ptt-90) REVERT: C 53 LEU cc_start: 0.8268 (mp) cc_final: 0.7834 (tt) REVERT: C 57 LEU cc_start: 0.8205 (mt) cc_final: 0.7884 (mt) REVERT: C 103 ILE cc_start: 0.9223 (pt) cc_final: 0.8975 (tt) REVERT: D 76 ILE cc_start: 0.9065 (pt) cc_final: 0.8352 (pt) REVERT: D 79 GLU cc_start: 0.6990 (pp20) cc_final: 0.6760 (pp20) REVERT: D 87 ASN cc_start: 0.9158 (p0) cc_final: 0.8850 (p0) REVERT: E 41 TYR cc_start: 0.6286 (p90) cc_final: 0.5708 (p90) REVERT: E 54 PHE cc_start: 0.6624 (p90) cc_final: 0.6351 (p90) REVERT: E 64 LYS cc_start: 0.8278 (mppt) cc_final: 0.8024 (mmtm) REVERT: E 72 ARG cc_start: 0.7533 (mmt180) cc_final: 0.7118 (mmt180) REVERT: E 81 ASP cc_start: 0.8370 (p0) cc_final: 0.8096 (p0) REVERT: E 83 ARG cc_start: 0.7788 (mmp80) cc_final: 0.7535 (mmp80) REVERT: E 94 GLU cc_start: 0.7084 (mt-10) cc_final: 0.6720 (tt0) REVERT: E 108 ASN cc_start: 0.8221 (m110) cc_final: 0.7983 (m-40) REVERT: E 109 LEU cc_start: 0.9135 (tp) cc_final: 0.8905 (tp) REVERT: E 115 LYS cc_start: 0.9104 (ptpp) cc_final: 0.8711 (ptpp) REVERT: E 125 LYS cc_start: 0.8685 (mtmm) cc_final: 0.8364 (mtmm) REVERT: F 27 GLN cc_start: 0.8293 (mp10) cc_final: 0.7818 (mp10) REVERT: F 58 LEU cc_start: 0.7941 (pt) cc_final: 0.7703 (pt) REVERT: F 87 VAL cc_start: 0.8017 (p) cc_final: 0.7641 (t) REVERT: G 38 HIS cc_start: 0.7933 (p90) cc_final: 0.7676 (p90) REVERT: G 48 LYS cc_start: 0.8446 (mmmt) cc_final: 0.8245 (mmmt) REVERT: G 54 THR cc_start: 0.8420 (t) cc_final: 0.8155 (t) REVERT: G 59 TYR cc_start: 0.7024 (p90) cc_final: 0.6793 (p90) REVERT: G 89 ILE cc_start: 0.8764 (tp) cc_final: 0.8411 (pt) REVERT: G 95 LEU cc_start: 0.8892 (mt) cc_final: 0.8568 (mt) REVERT: G 96 ASP cc_start: 0.8224 (p0) cc_final: 0.7961 (p0) REVERT: H 62 MET cc_start: 0.7452 (mmp) cc_final: 0.7065 (mmp) REVERT: H 63 SER cc_start: 0.7866 (t) cc_final: 0.7609 (t) REVERT: H 66 ASN cc_start: 0.7619 (p0) cc_final: 0.7366 (p0) REVERT: H 82 LYS cc_start: 0.8819 (tmmt) cc_final: 0.8474 (tmtt) REVERT: H 86 TYR cc_start: 0.7200 (p90) cc_final: 0.6613 (p90) REVERT: H 88 LYS cc_start: 0.9245 (ptpp) cc_final: 0.9037 (ptmm) REVERT: H 111 LYS cc_start: 0.8192 (pptt) cc_final: 0.7978 (pptt) REVERT: H 112 HIS cc_start: 0.7494 (m90) cc_final: 0.6304 (m90) REVERT: H 116 GLU cc_start: 0.8408 (mm-30) cc_final: 0.7335 (mm-30) outliers start: 1 outliers final: 0 residues processed: 496 average time/residue: 0.1728 time to fit residues: 122.6621 Evaluate side-chains 435 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 435 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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: 4.9990 chunk 91 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 206 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 156 optimal weight: 0.7980 chunk 137 optimal weight: 9.9990 chunk 152 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 121 optimal weight: 8.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 301 ASN ** 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** ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 339 GLN ** R 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 GLN ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 HIS ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 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** ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 87 ASN ** 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 = 0.4040 r_free = 0.4040 target = 0.117688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.092136 restraints weight = 88080.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.095365 restraints weight = 49382.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.097438 restraints weight = 31800.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.098772 restraints weight = 22797.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 65)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.099660 restraints weight = 17826.615| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.141 22580 Z= 0.256 Angle : 0.983 12.324 31707 Z= 0.537 Chirality : 0.056 0.319 3556 Planarity : 0.008 0.179 3001 Dihedral : 29.087 120.887 5372 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 28.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.68 % Favored : 88.32 % Rotamer: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % 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: -3.39 (0.18), residues: 1866 helix: -1.54 (0.15), residues: 977 sheet: -2.38 (0.76), residues: 33 loop : -3.13 (0.19), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 79 TYR 0.048 0.003 TYR O 325 PHE 0.077 0.004 PHE H 73 TRP 0.073 0.003 TRP O 353 HIS 0.022 0.003 HIS C 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.26 (22580) covalent geometry : angle 0.98251 / 0.54 (31707) hydrogen bonds : bond 0.07290 / 4.69 ( 1048) hydrogen bonds : angle 5.51275 / 3.69 ( 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 509 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 509 time to evaluate : 0.662 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 243 LYS cc_start: 0.8829 (mptt) cc_final: 0.8359 (mptt) REVERT: K 273 PHE cc_start: 0.8339 (m-10) cc_final: 0.7859 (m-80) REVERT: K 274 TYR cc_start: 0.7633 (p90) cc_final: 0.7221 (p90) REVERT: K 284 HIS cc_start: 0.7465 (m-70) cc_final: 0.7037 (m-70) REVERT: K 327 LEU cc_start: 0.9323 (mt) cc_final: 0.9053 (pp) REVERT: K 343 ASP cc_start: 0.9117 (p0) cc_final: 0.8821 (p0) REVERT: K 376 MET cc_start: 0.8656 (pmm) cc_final: 0.8403 (pmm) REVERT: M 234 LEU cc_start: 0.9114 (mp) cc_final: 0.8828 (mt) REVERT: M 238 LEU cc_start: 0.8866 (tt) cc_final: 0.8603 (tt) REVERT: M 278 TYR cc_start: 0.8972 (t80) cc_final: 0.8695 (t80) REVERT: O 237 PHE cc_start: 0.7677 (m-10) cc_final: 0.7246 (m-80) REVERT: O 271 PHE cc_start: 0.7990 (p90) cc_final: 0.7309 (p90) REVERT: O 272 LEU cc_start: 0.7556 (mt) cc_final: 0.7304 (tt) REVERT: O 275 CYS cc_start: 0.8669 (t) cc_final: 0.8286 (t) REVERT: O 331 GLU cc_start: 0.8395 (pt0) cc_final: 0.7806 (pp20) REVERT: O 353 TRP cc_start: 0.7430 (p90) cc_final: 0.6837 (p90) REVERT: Q 198 HIS cc_start: 0.9222 (m90) cc_final: 0.8988 (m170) REVERT: Q 326 ILE cc_start: 0.8148 (pt) cc_final: 0.7943 (pt) REVERT: A 51 ILE cc_start: 0.8716 (mm) cc_final: 0.8311 (mm) REVERT: A 59 GLU cc_start: 0.8976 (pm20) cc_final: 0.8337 (pm20) REVERT: A 71 VAL cc_start: 0.8921 (m) cc_final: 0.8683 (p) REVERT: A 80 THR cc_start: 0.7705 (t) cc_final: 0.7071 (t) REVERT: A 82 LEU cc_start: 0.8427 (mp) cc_final: 0.8121 (tp) REVERT: A 85 GLN cc_start: 0.8246 (tm-30) cc_final: 0.8037 (tm-30) REVERT: A 119 ILE cc_start: 0.8642 (mm) cc_final: 0.8240 (tp) REVERT: B 27 GLN cc_start: 0.8141 (pm20) cc_final: 0.7768 (pm20) REVERT: B 34 ILE cc_start: 0.9119 (tp) cc_final: 0.8602 (tp) REVERT: B 36 ARG cc_start: 0.8036 (ptp90) cc_final: 0.7801 (ptp90) REVERT: B 44 LYS cc_start: 0.8935 (pptt) cc_final: 0.8583 (pptt) REVERT: B 63 GLU cc_start: 0.7932 (pm20) cc_final: 0.7683 (mp0) REVERT: B 74 GLU cc_start: 0.8425 (tp30) cc_final: 0.7927 (tp30) REVERT: B 77 LYS cc_start: 0.8968 (mttp) cc_final: 0.8590 (mttp) REVERT: B 83 SER cc_start: 0.8659 (m) cc_final: 0.8407 (m) REVERT: B 88 TYR cc_start: 0.8267 (m-10) cc_final: 0.7598 (m-10) REVERT: C 31 ILE cc_start: 0.9140 (mm) cc_final: 0.8513 (tp) REVERT: C 33 ARG cc_start: 0.8576 (pmt170) cc_final: 0.8187 (ptt-90) REVERT: C 34 TYR cc_start: 0.8456 (m-10) cc_final: 0.8234 (m-80) REVERT: C 53 LEU cc_start: 0.8576 (mp) cc_final: 0.8156 (tt) REVERT: C 57 LEU cc_start: 0.8318 (mt) cc_final: 0.8062 (mt) REVERT: C 60 LEU cc_start: 0.8937 (tp) cc_final: 0.8703 (tp) REVERT: C 103 ILE cc_start: 0.9043 (pt) cc_final: 0.8812 (tt) REVERT: C 109 LEU cc_start: 0.8588 (tt) cc_final: 0.8374 (tt) REVERT: D 47 VAL cc_start: 0.8833 (t) cc_final: 0.8591 (t) REVERT: D 51 THR cc_start: 0.8933 (p) cc_final: 0.8569 (p) REVERT: D 62 MET cc_start: 0.8382 (pmm) cc_final: 0.8073 (pmm) REVERT: D 71 ASP cc_start: 0.8545 (p0) cc_final: 0.8153 (p0) REVERT: D 76 ILE cc_start: 0.9015 (pt) cc_final: 0.8582 (pt) REVERT: D 86 TYR cc_start: 0.8376 (m-10) cc_final: 0.7955 (m-10) REVERT: E 41 TYR cc_start: 0.6780 (p90) cc_final: 0.6153 (p90) REVERT: E 54 PHE cc_start: 0.6690 (p90) cc_final: 0.6416 (p90) REVERT: E 60 LEU cc_start: 0.8720 (pp) cc_final: 0.8329 (pt) REVERT: E 64 LYS cc_start: 0.8575 (mppt) cc_final: 0.8245 (mmmm) REVERT: E 65 LEU cc_start: 0.8926 (mm) cc_final: 0.8716 (mm) REVERT: E 72 ARG cc_start: 0.7824 (mmt180) cc_final: 0.7567 (mmt180) REVERT: E 83 ARG cc_start: 0.7938 (mmp80) cc_final: 0.7426 (mmp80) REVERT: E 94 GLU cc_start: 0.7151 (mt-10) cc_final: 0.6839 (tt0) REVERT: E 109 LEU cc_start: 0.9116 (tp) cc_final: 0.8850 (tp) REVERT: E 115 LYS cc_start: 0.9126 (ptpp) cc_final: 0.8808 (ptpp) REVERT: E 125 LYS cc_start: 0.8752 (mtmm) cc_final: 0.8284 (mtmm) REVERT: F 27 GLN cc_start: 0.8486 (mp10) cc_final: 0.7449 (mp10) REVERT: F 52 GLU cc_start: 0.7446 (pm20) cc_final: 0.6988 (pm20) REVERT: F 58 LEU cc_start: 0.8327 (pt) cc_final: 0.7992 (pt) REVERT: F 87 VAL cc_start: 0.8261 (p) cc_final: 0.7916 (t) REVERT: G 32 LYS cc_start: 0.8970 (mmmt) cc_final: 0.8630 (mmmm) REVERT: G 34 TYR cc_start: 0.8127 (p90) cc_final: 0.7570 (p90) REVERT: G 38 HIS cc_start: 0.8043 (p90) cc_final: 0.7726 (p90) REVERT: G 48 LYS cc_start: 0.8717 (mmmt) cc_final: 0.8429 (mmmt) REVERT: G 52 TYR cc_start: 0.7487 (t80) cc_final: 0.6722 (t80) REVERT: G 54 THR cc_start: 0.8544 (t) cc_final: 0.5844 (t) REVERT: G 59 TYR cc_start: 0.7340 (p90) cc_final: 0.6944 (p90) REVERT: G 60 LEU cc_start: 0.8791 (pp) cc_final: 0.8504 (pp) REVERT: G 86 GLN cc_start: 0.7439 (mp10) cc_final: 0.7048 (mp10) REVERT: G 89 ILE cc_start: 0.8821 (tp) cc_final: 0.8588 (pt) REVERT: G 95 LEU cc_start: 0.9038 (mt) cc_final: 0.8654 (mt) REVERT: G 96 ASP cc_start: 0.8110 (p0) cc_final: 0.7893 (p0) REVERT: H 66 ASN cc_start: 0.7758 (p0) cc_final: 0.7465 (p0) REVERT: H 72 ILE cc_start: 0.7517 (tt) cc_final: 0.7199 (tt) REVERT: H 86 TYR cc_start: 0.7375 (p90) cc_final: 0.6854 (p90) REVERT: H 88 LYS cc_start: 0.9314 (ptpp) cc_final: 0.9071 (ptmm) REVERT: H 111 LYS cc_start: 0.8293 (pptt) cc_final: 0.7981 (pptt) REVERT: H 112 HIS cc_start: 0.7516 (m90) cc_final: 0.6476 (m90) outliers start: 0 outliers final: 0 residues processed: 509 average time/residue: 0.1663 time to fit residues: 122.8139 Evaluate side-chains 447 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 447 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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: 0.9980 chunk 211 optimal weight: 0.9990 chunk 134 optimal weight: 8.9990 chunk 171 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 201 optimal weight: 0.9980 chunk 3 optimal weight: 8.9990 chunk 212 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** 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 = 0.4087 r_free = 0.4087 target = 0.120669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.095020 restraints weight = 88572.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.098241 restraints weight = 49437.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.100307 restraints weight = 31782.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.101636 restraints weight = 22796.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.102522 restraints weight = 17870.469| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.4667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 22580 Z= 0.192 Angle : 0.955 13.900 31707 Z= 0.512 Chirality : 0.055 0.293 3556 Planarity : 0.007 0.159 3001 Dihedral : 29.079 130.888 5372 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 24.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.04 % Favored : 88.96 % Rotamer: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % 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: -3.30 (0.18), residues: 1866 helix: -1.44 (0.15), residues: 987 sheet: -2.27 (0.80), residues: 33 loop : -3.14 (0.19), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG K 249 TYR 0.032 0.002 TYR K 311 PHE 0.062 0.003 PHE H 73 TRP 0.050 0.002 TRP O 353 HIS 0.020 0.002 HIS C 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.19 (22580) covalent geometry : angle 0.95544 / 0.51 (31707) hydrogen bonds : bond 0.06133 / 3.96 ( 1048) hydrogen bonds : angle 5.41443 / 3.62 ( 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 502 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 502 time to evaluate : 0.395 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: K 212 GLU cc_start: 0.8162 (mp0) cc_final: 0.7943 (mp0) REVERT: K 273 PHE cc_start: 0.8341 (m-10) cc_final: 0.8029 (m-80) REVERT: K 274 TYR cc_start: 0.7775 (p90) cc_final: 0.7297 (p90) REVERT: K 284 HIS cc_start: 0.7413 (m-70) cc_final: 0.6939 (m-70) REVERT: K 310 GLN cc_start: 0.7996 (pm20) cc_final: 0.7541 (pm20) REVERT: K 311 TYR cc_start: 0.7528 (t80) cc_final: 0.7150 (t80) REVERT: K 327 LEU cc_start: 0.9299 (mt) cc_final: 0.9042 (pp) REVERT: K 343 ASP cc_start: 0.9093 (p0) cc_final: 0.8803 (p0) REVERT: M 234 LEU cc_start: 0.9158 (mp) cc_final: 0.8858 (mt) REVERT: M 238 LEU cc_start: 0.8876 (tt) cc_final: 0.8562 (tt) REVERT: M 278 TYR cc_start: 0.8930 (t80) cc_final: 0.8710 (t80) REVERT: M 279 TRP cc_start: 0.8591 (t60) cc_final: 0.8304 (t60) REVERT: O 237 PHE cc_start: 0.7470 (m-10) cc_final: 0.7080 (m-10) REVERT: O 271 PHE cc_start: 0.7985 (p90) cc_final: 0.7303 (p90) REVERT: O 275 CYS cc_start: 0.8642 (t) cc_final: 0.8331 (t) REVERT: O 325 TYR cc_start: 0.8929 (m-80) cc_final: 0.8663 (m-80) REVERT: O 326 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8384 (tm-30) REVERT: O 353 TRP cc_start: 0.7253 (p90) cc_final: 0.6677 (p90) REVERT: Q 198 HIS cc_start: 0.9224 (m90) cc_final: 0.8970 (m170) REVERT: A 59 GLU cc_start: 0.9019 (pm20) cc_final: 0.8435 (pm20) REVERT: A 80 THR cc_start: 0.7562 (t) cc_final: 0.7166 (t) REVERT: A 82 LEU cc_start: 0.8332 (mp) cc_final: 0.7691 (tt) REVERT: A 85 GLN cc_start: 0.8175 (tm-30) cc_final: 0.7878 (tm-30) REVERT: A 99 TYR cc_start: 0.8528 (t80) cc_final: 0.8140 (t80) REVERT: A 113 HIS cc_start: 0.7056 (t-90) cc_final: 0.6398 (t-90) REVERT: A 119 ILE cc_start: 0.8658 (mm) cc_final: 0.8331 (tp) REVERT: B 27 GLN cc_start: 0.8021 (pm20) cc_final: 0.7611 (pm20) REVERT: B 62 LEU cc_start: 0.8296 (mm) cc_final: 0.8033 (mm) REVERT: B 63 GLU cc_start: 0.7950 (pm20) cc_final: 0.7711 (mp0) REVERT: B 74 GLU cc_start: 0.8343 (tp30) cc_final: 0.7989 (tp30) REVERT: B 77 LYS cc_start: 0.8894 (mttp) cc_final: 0.8526 (mttp) REVERT: B 83 SER cc_start: 0.8614 (m) cc_final: 0.8361 (m) REVERT: B 88 TYR cc_start: 0.8123 (m-10) cc_final: 0.7844 (m-10) REVERT: B 95 ARG cc_start: 0.7737 (ttm110) cc_final: 0.7391 (mtt90) REVERT: C 31 ILE cc_start: 0.9093 (mm) cc_final: 0.8887 (mp) REVERT: C 33 ARG cc_start: 0.8524 (pmt170) cc_final: 0.8158 (ptt-90) REVERT: C 44 ARG cc_start: 0.7181 (tmm-80) cc_final: 0.6777 (ptt-90) REVERT: C 53 LEU cc_start: 0.8545 (mp) cc_final: 0.8150 (tt) REVERT: C 57 LEU cc_start: 0.8388 (mt) cc_final: 0.7953 (mt) REVERT: C 103 ILE cc_start: 0.9016 (pt) cc_final: 0.8622 (tt) REVERT: D 51 THR cc_start: 0.8731 (p) cc_final: 0.8247 (p) REVERT: D 71 ASP cc_start: 0.8480 (p0) cc_final: 0.8016 (p0) REVERT: D 76 ILE cc_start: 0.9102 (pt) cc_final: 0.8505 (pt) REVERT: D 86 TYR cc_start: 0.8365 (m-10) cc_final: 0.8045 (m-10) REVERT: D 124 TYR cc_start: 0.6945 (t80) cc_final: 0.6735 (t80) REVERT: E 41 TYR cc_start: 0.6570 (p90) cc_final: 0.6076 (p90) REVERT: E 54 PHE cc_start: 0.6531 (p90) cc_final: 0.6142 (p90) REVERT: E 56 LYS cc_start: 0.8787 (tmtt) cc_final: 0.8583 (tmtt) REVERT: E 60 LEU cc_start: 0.8697 (pp) cc_final: 0.8448 (pt) REVERT: E 64 LYS cc_start: 0.8647 (mppt) cc_final: 0.8373 (mmmm) REVERT: E 72 ARG cc_start: 0.7828 (mmt180) cc_final: 0.7466 (mmt180) REVERT: E 73 GLU cc_start: 0.7511 (pm20) cc_final: 0.7054 (pm20) REVERT: E 83 ARG cc_start: 0.7628 (mmp80) cc_final: 0.7390 (mmp80) REVERT: E 94 GLU cc_start: 0.7182 (mt-10) cc_final: 0.6843 (tt0) REVERT: E 108 ASN cc_start: 0.8555 (m110) cc_final: 0.8260 (m-40) REVERT: E 115 LYS cc_start: 0.9140 (ptpp) cc_final: 0.8761 (ptpp) REVERT: E 123 ASP cc_start: 0.6998 (t70) cc_final: 0.6760 (t70) REVERT: E 125 LYS cc_start: 0.8730 (mtmm) cc_final: 0.8388 (mtmm) REVERT: F 27 GLN cc_start: 0.8304 (mp10) cc_final: 0.7643 (mp10) REVERT: F 52 GLU cc_start: 0.7552 (pm20) cc_final: 0.7148 (pm20) REVERT: F 57 VAL cc_start: 0.8598 (m) cc_final: 0.8321 (p) REVERT: F 60 SER cc_start: 0.8407 (p) cc_final: 0.7871 (p) REVERT: F 63 GLU cc_start: 0.8395 (pt0) cc_final: 0.8192 (pp20) REVERT: F 87 VAL cc_start: 0.8272 (p) cc_final: 0.7971 (t) REVERT: G 32 LYS cc_start: 0.8917 (mmmt) cc_final: 0.8451 (mmmm) REVERT: G 34 TYR cc_start: 0.8105 (p90) cc_final: 0.7743 (p90) REVERT: G 38 HIS cc_start: 0.7914 (p90) cc_final: 0.7642 (p90) REVERT: G 48 LYS cc_start: 0.8626 (mmmt) cc_final: 0.8328 (mmmt) REVERT: G 52 TYR cc_start: 0.7328 (t80) cc_final: 0.6827 (t80) REVERT: G 86 GLN cc_start: 0.7116 (mp10) cc_final: 0.6664 (mp10) REVERT: G 89 ILE cc_start: 0.8721 (tp) cc_final: 0.8360 (pt) REVERT: G 95 LEU cc_start: 0.9025 (mt) cc_final: 0.8717 (mt) REVERT: H 63 SER cc_start: 0.7841 (t) cc_final: 0.7595 (t) REVERT: H 66 ASN cc_start: 0.7806 (p0) cc_final: 0.7513 (p0) REVERT: H 82 LYS cc_start: 0.8920 (tmmt) cc_final: 0.8536 (tmtt) REVERT: H 88 LYS cc_start: 0.9324 (ptpp) cc_final: 0.9091 (ptmm) REVERT: H 111 LYS cc_start: 0.8301 (pptt) cc_final: 0.7986 (pptt) REVERT: H 112 HIS cc_start: 0.7548 (m90) cc_final: 0.6394 (m90) outliers start: 0 outliers final: 0 residues processed: 502 average time/residue: 0.1668 time to fit residues: 121.6531 Evaluate side-chains 454 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 454 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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: 2.9990 chunk 37 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 chunk 16 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 chunk 26 optimal weight: 0.5980 chunk 124 optimal weight: 8.9990 chunk 86 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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** O 285 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** ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** 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 = 0.4081 r_free = 0.4081 target = 0.120085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.094352 restraints weight = 88755.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.097577 restraints weight = 49808.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.099680 restraints weight = 32050.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.101030 restraints weight = 22948.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.101913 restraints weight = 17948.264| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.4975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 22580 Z= 0.206 Angle : 0.961 13.239 31707 Z= 0.518 Chirality : 0.054 0.283 3556 Planarity : 0.007 0.141 3001 Dihedral : 29.002 128.291 5372 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 26.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.15 % Favored : 88.85 % Rotamer: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.89 % 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: -3.19 (0.18), residues: 1866 helix: -1.41 (0.15), residues: 969 sheet: -2.35 (0.79), residues: 33 loop : -2.97 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG K 249 TYR 0.046 0.003 TYR F 72 PHE 0.055 0.003 PHE H 73 TRP 0.044 0.002 TRP O 353 HIS 0.019 0.002 HIS G 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.21 (22580) covalent geometry : angle 0.96062 / 0.52 (31707) hydrogen bonds : bond 0.06299 / 4.07 ( 1048) hydrogen bonds : angle 5.42550 / 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 504 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 504 time to evaluate : 0.546 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: K 212 GLU cc_start: 0.8177 (mp0) cc_final: 0.7956 (mp0) REVERT: K 233 TYR cc_start: 0.6938 (t80) cc_final: 0.6485 (t80) REVERT: K 273 PHE cc_start: 0.8345 (m-10) cc_final: 0.7923 (m-80) REVERT: K 274 TYR cc_start: 0.7710 (p90) cc_final: 0.7244 (p90) REVERT: K 284 HIS cc_start: 0.7497 (m-70) cc_final: 0.7014 (m-70) REVERT: K 310 GLN cc_start: 0.7898 (pm20) cc_final: 0.7369 (pm20) REVERT: K 319 LEU cc_start: 0.8131 (tp) cc_final: 0.7851 (pt) REVERT: K 325 TYR cc_start: 0.8325 (m-80) cc_final: 0.7921 (m-80) REVERT: K 343 ASP cc_start: 0.9113 (p0) cc_final: 0.8833 (p0) REVERT: K 353 TRP cc_start: 0.5139 (p-90) cc_final: 0.4535 (p-90) REVERT: K 376 MET cc_start: 0.8722 (pmm) cc_final: 0.8508 (pmm) REVERT: M 238 LEU cc_start: 0.8880 (tt) cc_final: 0.8568 (tt) REVERT: M 278 TYR cc_start: 0.8924 (t80) cc_final: 0.8702 (t80) REVERT: M 279 TRP cc_start: 0.8596 (t60) cc_final: 0.8325 (t60) REVERT: O 237 PHE cc_start: 0.7645 (m-10) cc_final: 0.7174 (m-80) REVERT: O 271 PHE cc_start: 0.8056 (p90) cc_final: 0.7354 (p90) REVERT: O 275 CYS cc_start: 0.8631 (t) cc_final: 0.8267 (t) REVERT: O 325 TYR cc_start: 0.8932 (m-80) cc_final: 0.8656 (m-80) REVERT: O 326 GLU cc_start: 0.8924 (tm-30) cc_final: 0.8457 (tm-30) REVERT: O 329 LYS cc_start: 0.8536 (ptpp) cc_final: 0.8308 (pttm) REVERT: O 353 TRP cc_start: 0.7282 (p90) cc_final: 0.6731 (p90) REVERT: O 385 LEU cc_start: 0.7673 (mm) cc_final: 0.7433 (mp) REVERT: Q 198 HIS cc_start: 0.9222 (m90) cc_final: 0.8970 (m170) REVERT: A 48 LEU cc_start: 0.8293 (mm) cc_final: 0.7953 (tp) REVERT: A 59 GLU cc_start: 0.9081 (pm20) cc_final: 0.8494 (pm20) REVERT: A 85 GLN cc_start: 0.8339 (tm-30) cc_final: 0.8027 (tm-30) REVERT: A 99 TYR cc_start: 0.8562 (t80) cc_final: 0.8147 (t80) REVERT: A 119 ILE cc_start: 0.8759 (mm) cc_final: 0.8396 (tp) REVERT: A 124 ILE cc_start: 0.8349 (mp) cc_final: 0.8074 (tp) REVERT: B 27 GLN cc_start: 0.8094 (pm20) cc_final: 0.7761 (pm20) REVERT: B 36 ARG cc_start: 0.7244 (ptp-170) cc_final: 0.7013 (ptp-170) REVERT: B 63 GLU cc_start: 0.8076 (pm20) cc_final: 0.7545 (pm20) REVERT: B 74 GLU cc_start: 0.8311 (tp30) cc_final: 0.7901 (tp30) REVERT: B 83 SER cc_start: 0.8593 (m) cc_final: 0.8229 (m) REVERT: B 95 ARG cc_start: 0.7694 (ttm110) cc_final: 0.7457 (mtt90) REVERT: C 31 ILE cc_start: 0.9135 (mm) cc_final: 0.8860 (mp) REVERT: C 33 ARG cc_start: 0.8620 (pmt170) cc_final: 0.7917 (ptt-90) REVERT: C 44 ARG cc_start: 0.7293 (tmm-80) cc_final: 0.7036 (ptt-90) REVERT: C 53 LEU cc_start: 0.8569 (mp) cc_final: 0.8175 (tt) REVERT: C 57 LEU cc_start: 0.8373 (mt) cc_final: 0.8090 (mt) REVERT: C 103 ILE cc_start: 0.9121 (pt) cc_final: 0.8655 (tp) REVERT: D 47 VAL cc_start: 0.8779 (t) cc_final: 0.8477 (t) REVERT: D 51 THR cc_start: 0.8860 (p) cc_final: 0.8607 (p) REVERT: E 41 TYR cc_start: 0.6730 (p90) cc_final: 0.6207 (p90) REVERT: E 60 LEU cc_start: 0.9101 (pp) cc_final: 0.8740 (tp) REVERT: E 64 LYS cc_start: 0.8655 (mppt) cc_final: 0.8220 (mmmm) REVERT: E 72 ARG cc_start: 0.7917 (mmt180) cc_final: 0.7601 (mmt180) REVERT: E 94 GLU cc_start: 0.7239 (mt-10) cc_final: 0.7028 (tt0) REVERT: E 108 ASN cc_start: 0.8551 (m110) cc_final: 0.8220 (m-40) REVERT: E 115 LYS cc_start: 0.9173 (ptpp) cc_final: 0.8800 (ptpp) REVERT: E 123 ASP cc_start: 0.7244 (t70) cc_final: 0.7039 (t70) REVERT: F 52 GLU cc_start: 0.7649 (pm20) cc_final: 0.7141 (pm20) REVERT: F 57 VAL cc_start: 0.8707 (m) cc_final: 0.8404 (p) REVERT: F 58 LEU cc_start: 0.8487 (pt) cc_final: 0.8278 (pt) REVERT: F 60 SER cc_start: 0.8436 (p) cc_final: 0.7888 (p) REVERT: F 63 GLU cc_start: 0.8452 (pt0) cc_final: 0.8248 (pp20) REVERT: F 87 VAL cc_start: 0.8389 (p) cc_final: 0.8124 (t) REVERT: F 91 LYS cc_start: 0.8455 (pttm) cc_final: 0.8172 (pttm) REVERT: G 32 LYS cc_start: 0.8908 (mmmt) cc_final: 0.8501 (mmmm) REVERT: G 38 HIS cc_start: 0.7947 (p90) cc_final: 0.7677 (p90) REVERT: G 48 LYS cc_start: 0.8634 (mmmt) cc_final: 0.8340 (mmmt) REVERT: G 54 THR cc_start: 0.6760 (t) cc_final: 0.5590 (t) REVERT: G 86 GLN cc_start: 0.7324 (mp10) cc_final: 0.6843 (mp10) REVERT: G 89 ILE cc_start: 0.8743 (tp) cc_final: 0.8392 (pt) REVERT: G 95 LEU cc_start: 0.9032 (mt) cc_final: 0.8679 (mt) REVERT: H 44 ILE cc_start: 0.8794 (mt) cc_final: 0.8588 (mm) REVERT: H 63 SER cc_start: 0.7841 (t) cc_final: 0.7601 (t) REVERT: H 66 ASN cc_start: 0.7787 (p0) cc_final: 0.7503 (p0) REVERT: H 82 LYS cc_start: 0.8929 (tmmt) cc_final: 0.8575 (tmtt) REVERT: H 86 TYR cc_start: 0.7242 (p90) cc_final: 0.6801 (p90) REVERT: H 88 LYS cc_start: 0.9314 (ptpp) cc_final: 0.9090 (ptmm) REVERT: H 111 LYS cc_start: 0.8576 (pptt) cc_final: 0.8194 (pptt) REVERT: H 112 HIS cc_start: 0.7617 (m90) cc_final: 0.6408 (m90) outliers start: 0 outliers final: 0 residues processed: 504 average time/residue: 0.1648 time to fit residues: 120.5055 Evaluate side-chains 445 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 445 time to evaluate : 0.609 ------------------------------------------------------------------------------- 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: 6.9990 chunk 145 optimal weight: 0.6980 chunk 188 optimal weight: 1.9990 chunk 87 optimal weight: 20.0000 chunk 156 optimal weight: 0.8980 chunk 205 optimal weight: 0.5980 chunk 194 optimal weight: 9.9990 chunk 1 optimal weight: 0.0980 chunk 178 optimal weight: 0.3980 chunk 101 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 364 HIS ** 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 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 100 HIS ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 GLN ** 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 = 0.4118 r_free = 0.4118 target = 0.122409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.096880 restraints weight = 89300.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.100135 restraints weight = 49843.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.102214 restraints weight = 31910.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.103531 restraints weight = 22787.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.104401 restraints weight = 17824.865| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.5247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22580 Z= 0.187 Angle : 0.970 14.636 31707 Z= 0.519 Chirality : 0.054 0.432 3556 Planarity : 0.007 0.124 3001 Dihedral : 28.950 134.110 5372 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 23.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -3.17 (0.18), residues: 1866 helix: -1.39 (0.15), residues: 973 sheet: -1.90 (0.89), residues: 33 loop : -2.99 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 33 TYR 0.049 0.003 TYR G 34 PHE 0.097 0.003 PHE H 73 TRP 0.043 0.002 TRP O 353 HIS 0.016 0.002 HIS G 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.19 (22580) covalent geometry : angle 0.97020 / 0.52 (31707) hydrogen bonds : bond 0.05885 / 3.79 ( 1048) hydrogen bonds : angle 5.38851 / 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 504 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 504 time to evaluate : 0.469 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: K 212 GLU cc_start: 0.8225 (mp0) cc_final: 0.8019 (mp0) REVERT: K 273 PHE cc_start: 0.8353 (m-10) cc_final: 0.7883 (m-10) REVERT: K 274 TYR cc_start: 0.7771 (p90) cc_final: 0.7280 (p90) REVERT: K 284 HIS cc_start: 0.7393 (m-70) cc_final: 0.6983 (m-70) REVERT: K 319 LEU cc_start: 0.8156 (tp) cc_final: 0.7910 (pt) REVERT: K 325 TYR cc_start: 0.8339 (m-80) cc_final: 0.7978 (m-80) REVERT: K 327 LEU cc_start: 0.9304 (mt) cc_final: 0.9057 (pp) REVERT: K 343 ASP cc_start: 0.9087 (p0) cc_final: 0.8802 (p0) REVERT: K 353 TRP cc_start: 0.5092 (p-90) cc_final: 0.4590 (p-90) REVERT: M 228 ASP cc_start: 0.8622 (m-30) cc_final: 0.8401 (m-30) REVERT: M 234 LEU cc_start: 0.9130 (mt) cc_final: 0.8838 (mp) REVERT: M 238 LEU cc_start: 0.8906 (tt) cc_final: 0.8612 (tt) REVERT: M 278 TYR cc_start: 0.8882 (t80) cc_final: 0.8679 (t80) REVERT: M 279 TRP cc_start: 0.8681 (t60) cc_final: 0.8398 (t60) REVERT: O 237 PHE cc_start: 0.7153 (m-10) cc_final: 0.6805 (m-10) REVERT: O 271 PHE cc_start: 0.7959 (p90) cc_final: 0.7250 (p90) REVERT: O 275 CYS cc_start: 0.8608 (t) cc_final: 0.8098 (t) REVERT: O 325 TYR cc_start: 0.8900 (m-80) cc_final: 0.8626 (m-80) REVERT: O 353 TRP cc_start: 0.7236 (p90) cc_final: 0.6696 (p90) REVERT: O 385 LEU cc_start: 0.7642 (mm) cc_final: 0.7384 (mp) REVERT: O 395 ARG cc_start: 0.7472 (mmp-170) cc_final: 0.7160 (tpp-160) REVERT: Q 198 HIS cc_start: 0.9213 (m90) cc_final: 0.8938 (m170) REVERT: A 59 GLU cc_start: 0.9073 (pm20) cc_final: 0.8459 (pm20) REVERT: A 85 GLN cc_start: 0.8274 (tm-30) cc_final: 0.7886 (tm-30) REVERT: A 113 HIS cc_start: 0.6791 (t-90) cc_final: 0.6511 (t-90) REVERT: A 119 ILE cc_start: 0.8619 (mm) cc_final: 0.8321 (tp) REVERT: B 34 ILE cc_start: 0.9040 (tp) cc_final: 0.8358 (tp) REVERT: B 55 ARG cc_start: 0.7811 (mmp80) cc_final: 0.7420 (tpp-160) REVERT: B 59 LYS cc_start: 0.8403 (tptt) cc_final: 0.8183 (tppt) REVERT: B 63 GLU cc_start: 0.8056 (pm20) cc_final: 0.7365 (pm20) REVERT: B 74 GLU cc_start: 0.8415 (tp30) cc_final: 0.7880 (tp30) REVERT: B 95 ARG cc_start: 0.7720 (ttm110) cc_final: 0.7366 (mtm-85) REVERT: C 31 ILE cc_start: 0.9099 (mm) cc_final: 0.8810 (mp) REVERT: C 33 ARG cc_start: 0.8532 (pmt170) cc_final: 0.7836 (ptt-90) REVERT: C 44 ARG cc_start: 0.7329 (tmm-80) cc_final: 0.7046 (ptt-90) REVERT: C 53 LEU cc_start: 0.8525 (mp) cc_final: 0.8120 (tt) REVERT: C 57 LEU cc_start: 0.8298 (mt) cc_final: 0.8079 (mt) REVERT: C 78 LYS cc_start: 0.8641 (ptpt) cc_final: 0.8335 (pttm) REVERT: D 47 VAL cc_start: 0.8790 (t) cc_final: 0.8497 (p) REVERT: D 51 THR cc_start: 0.8842 (p) cc_final: 0.8040 (p) REVERT: D 62 MET cc_start: 0.8366 (pmm) cc_final: 0.8057 (pmm) REVERT: D 71 ASP cc_start: 0.8431 (p0) cc_final: 0.8023 (p0) REVERT: D 76 ILE cc_start: 0.9110 (pt) cc_final: 0.8257 (pt) REVERT: D 79 GLU cc_start: 0.7340 (pp20) cc_final: 0.6992 (pp20) REVERT: E 41 TYR cc_start: 0.6613 (p90) cc_final: 0.6133 (p90) REVERT: E 60 LEU cc_start: 0.9003 (pp) cc_final: 0.8593 (tp) REVERT: E 96 VAL cc_start: 0.8605 (t) cc_final: 0.8185 (t) REVERT: E 97 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7262 (mm-30) REVERT: E 108 ASN cc_start: 0.8561 (m110) cc_final: 0.8316 (m-40) REVERT: E 115 LYS cc_start: 0.9145 (ptpp) cc_final: 0.8748 (ptpp) REVERT: F 52 GLU cc_start: 0.7733 (pm20) cc_final: 0.7193 (pm20) REVERT: F 57 VAL cc_start: 0.8677 (m) cc_final: 0.8375 (p) REVERT: F 58 LEU cc_start: 0.8412 (pt) cc_final: 0.8206 (pt) REVERT: F 60 SER cc_start: 0.8417 (p) cc_final: 0.7954 (p) REVERT: F 63 GLU cc_start: 0.8460 (pt0) cc_final: 0.8227 (pp20) REVERT: F 87 VAL cc_start: 0.8432 (p) cc_final: 0.8121 (t) REVERT: G 32 LYS cc_start: 0.8894 (mmmt) cc_final: 0.8596 (mmmt) REVERT: G 34 TYR cc_start: 0.8072 (p90) cc_final: 0.7457 (p90) REVERT: G 38 HIS cc_start: 0.7896 (p90) cc_final: 0.7629 (p90) REVERT: G 52 TYR cc_start: 0.7323 (t80) cc_final: 0.6433 (t80) REVERT: G 86 GLN cc_start: 0.7229 (mp10) cc_final: 0.6849 (mp10) REVERT: G 89 ILE cc_start: 0.8752 (tp) cc_final: 0.8447 (pt) REVERT: G 95 LEU cc_start: 0.9008 (mt) cc_final: 0.8765 (mt) REVERT: H 63 SER cc_start: 0.7830 (t) cc_final: 0.7617 (t) REVERT: H 82 LYS cc_start: 0.8901 (tmmt) cc_final: 0.8449 (tmtt) REVERT: H 88 LYS cc_start: 0.9302 (ptpp) cc_final: 0.9078 (ptmm) REVERT: H 105 LEU cc_start: 0.9101 (pp) cc_final: 0.8896 (pp) REVERT: H 123 LYS cc_start: 0.8856 (mmtm) cc_final: 0.8469 (ptpp) outliers start: 0 outliers final: 0 residues processed: 504 average time/residue: 0.1777 time to fit residues: 127.5071 Evaluate side-chains 447 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 447 time to evaluate : 0.515 ------------------------------------------------------------------------------- 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: 0.6980 chunk 197 optimal weight: 0.9980 chunk 174 optimal weight: 9.9990 chunk 145 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 204 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 244 GLN ** 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** ** O 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 163 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 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 100 HIS ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN E 68 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.121528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.095735 restraints weight = 88899.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.099032 restraints weight = 49946.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.101143 restraints weight = 32128.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.102457 restraints weight = 22953.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.103404 restraints weight = 17971.931| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.5421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 22580 Z= 0.202 Angle : 0.964 13.357 31707 Z= 0.518 Chirality : 0.054 0.480 3556 Planarity : 0.007 0.101 3001 Dihedral : 28.907 130.747 5372 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 24.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.72 % Favored : 89.28 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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: -3.13 (0.18), residues: 1866 helix: -1.34 (0.16), residues: 975 sheet: -1.90 (0.88), residues: 33 loop : -2.99 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG G 44 TYR 0.048 0.003 TYR E 99 PHE 0.097 0.003 PHE H 73 TRP 0.041 0.002 TRP O 353 HIS 0.012 0.002 HIS G 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.20 (22580) covalent geometry : angle 0.96397 / 0.52 (31707) hydrogen bonds : bond 0.06107 / 3.93 ( 1048) hydrogen bonds : angle 5.36746 / 3.59 ( 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 499 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 499 time to evaluate : 0.496 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: K 212 GLU cc_start: 0.8253 (mp0) cc_final: 0.8042 (mp0) REVERT: K 233 TYR cc_start: 0.6692 (t80) cc_final: 0.6315 (t80) REVERT: K 273 PHE cc_start: 0.8341 (m-10) cc_final: 0.7852 (m-10) REVERT: K 284 HIS cc_start: 0.7548 (m-70) cc_final: 0.7085 (m-70) REVERT: K 319 LEU cc_start: 0.8100 (tp) cc_final: 0.7831 (pt) REVERT: K 325 TYR cc_start: 0.8301 (m-80) cc_final: 0.7907 (m-80) REVERT: K 343 ASP cc_start: 0.9120 (p0) cc_final: 0.8824 (p0) REVERT: K 353 TRP cc_start: 0.5179 (p-90) cc_final: 0.4645 (p-90) REVERT: M 234 LEU cc_start: 0.9184 (mt) cc_final: 0.8918 (mt) REVERT: M 278 TYR cc_start: 0.8907 (t80) cc_final: 0.8704 (t80) REVERT: M 279 TRP cc_start: 0.8640 (t60) cc_final: 0.8362 (t60) REVERT: O 237 PHE cc_start: 0.7332 (m-10) cc_final: 0.6918 (m-80) REVERT: O 271 PHE cc_start: 0.8065 (p90) cc_final: 0.7295 (p90) REVERT: O 275 CYS cc_start: 0.8724 (t) cc_final: 0.8244 (t) REVERT: O 325 TYR cc_start: 0.8854 (m-80) cc_final: 0.8576 (m-80) REVERT: O 329 LYS cc_start: 0.8586 (ptpp) cc_final: 0.8335 (pttm) REVERT: O 353 TRP cc_start: 0.7251 (p90) cc_final: 0.6720 (p90) REVERT: O 385 LEU cc_start: 0.7681 (mm) cc_final: 0.7391 (mp) REVERT: O 395 ARG cc_start: 0.7475 (mmp-170) cc_final: 0.7210 (tpp-160) REVERT: Q 198 HIS cc_start: 0.9235 (m90) cc_final: 0.9000 (m170) REVERT: A 59 GLU cc_start: 0.9127 (pm20) cc_final: 0.8503 (pm20) REVERT: A 69 ARG cc_start: 0.8616 (mtm-85) cc_final: 0.7544 (ptp-170) REVERT: A 85 GLN cc_start: 0.8230 (tm-30) cc_final: 0.7886 (tm-30) REVERT: A 119 ILE cc_start: 0.8668 (mm) cc_final: 0.8357 (tp) REVERT: A 123 ASP cc_start: 0.7820 (m-30) cc_final: 0.7619 (m-30) REVERT: B 25 ASN cc_start: 0.7679 (t0) cc_final: 0.6904 (t0) REVERT: B 55 ARG cc_start: 0.7669 (mmp80) cc_final: 0.7420 (tpp-160) REVERT: B 63 GLU cc_start: 0.8048 (pm20) cc_final: 0.7395 (pm20) REVERT: B 74 GLU cc_start: 0.8445 (tp30) cc_final: 0.7882 (tp30) REVERT: B 78 ARG cc_start: 0.7150 (tpp-160) cc_final: 0.6668 (tpp80) REVERT: B 92 ARG cc_start: 0.9016 (tpt90) cc_final: 0.8801 (tpt90) REVERT: C 31 ILE cc_start: 0.9080 (mm) cc_final: 0.8793 (mp) REVERT: C 33 ARG cc_start: 0.8519 (pmt170) cc_final: 0.7966 (ptt-90) REVERT: C 44 ARG cc_start: 0.7368 (tmm-80) cc_final: 0.7040 (ptt-90) REVERT: C 53 LEU cc_start: 0.8562 (mp) cc_final: 0.8132 (tt) REVERT: C 78 LYS cc_start: 0.8556 (ptpt) cc_final: 0.8306 (pttm) REVERT: C 81 THR cc_start: 0.8488 (p) cc_final: 0.8092 (p) REVERT: C 84 HIS cc_start: 0.7910 (p90) cc_final: 0.7693 (p90) REVERT: D 51 THR cc_start: 0.8772 (p) cc_final: 0.8361 (p) REVERT: D 62 MET cc_start: 0.8391 (pmm) cc_final: 0.8072 (pmm) REVERT: D 71 ASP cc_start: 0.8405 (p0) cc_final: 0.8176 (p0) REVERT: E 41 TYR cc_start: 0.6706 (p90) cc_final: 0.6206 (p90) REVERT: E 54 PHE cc_start: 0.7038 (p90) cc_final: 0.6417 (p90) REVERT: E 56 LYS cc_start: 0.8913 (tmtt) cc_final: 0.8700 (tmtt) REVERT: E 67 PHE cc_start: 0.7229 (p90) cc_final: 0.6933 (p90) REVERT: E 108 ASN cc_start: 0.8596 (m110) cc_final: 0.8250 (m-40) REVERT: E 115 LYS cc_start: 0.9145 (ptpp) cc_final: 0.8760 (ptpp) REVERT: E 121 LYS cc_start: 0.8587 (tmmt) cc_final: 0.8105 (ptmt) REVERT: E 123 ASP cc_start: 0.7639 (m-30) cc_final: 0.7312 (t70) REVERT: E 124 ILE cc_start: 0.8935 (pt) cc_final: 0.8700 (pt) REVERT: F 52 GLU cc_start: 0.7764 (pm20) cc_final: 0.7255 (pm20) REVERT: F 55 ARG cc_start: 0.8158 (ttm-80) cc_final: 0.7681 (mmt90) REVERT: F 57 VAL cc_start: 0.8720 (m) cc_final: 0.8465 (p) REVERT: F 60 SER cc_start: 0.8478 (p) cc_final: 0.7970 (p) REVERT: F 63 GLU cc_start: 0.8517 (pt0) cc_final: 0.8282 (pp20) REVERT: G 32 LYS cc_start: 0.8845 (mmmt) cc_final: 0.8616 (mmmt) REVERT: G 34 TYR cc_start: 0.8209 (p90) cc_final: 0.7345 (p90) REVERT: G 52 TYR cc_start: 0.7304 (t80) cc_final: 0.6626 (t80) REVERT: G 54 THR cc_start: 0.6712 (t) cc_final: 0.5071 (t) REVERT: G 86 GLN cc_start: 0.7128 (mp10) cc_final: 0.6705 (mp10) REVERT: G 89 ILE cc_start: 0.8755 (tp) cc_final: 0.8448 (pt) REVERT: G 95 LEU cc_start: 0.8989 (mt) cc_final: 0.8682 (mt) REVERT: H 72 ILE cc_start: 0.7588 (tt) cc_final: 0.7250 (tt) REVERT: H 82 LYS cc_start: 0.8895 (tmmt) cc_final: 0.8475 (tmtt) REVERT: H 88 LYS cc_start: 0.9310 (ptpp) cc_final: 0.9105 (ptmm) REVERT: H 116 GLU cc_start: 0.6456 (pp20) cc_final: 0.5485 (pp20) outliers start: 0 outliers final: 0 residues processed: 499 average time/residue: 0.1808 time to fit residues: 128.3328 Evaluate side-chains 454 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 454 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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: 4.9990 chunk 24 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 10 optimal weight: 0.0060 chunk 106 optimal weight: 0.0980 chunk 61 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 127 optimal weight: 9.9990 chunk 48 optimal weight: 0.8980 chunk 181 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 364 HIS ** 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 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** ** Q 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 100 HIS E 55 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** 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 = 0.4115 r_free = 0.4115 target = 0.122403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.096685 restraints weight = 88141.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.099959 restraints weight = 49707.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.102079 restraints weight = 31890.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.103435 restraints weight = 22852.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.104326 restraints weight = 17820.849| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.5614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 22580 Z= 0.198 Angle : 0.986 15.656 31707 Z= 0.527 Chirality : 0.055 0.454 3556 Planarity : 0.008 0.173 3001 Dihedral : 28.894 132.453 5372 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 24.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.93 % Favored : 89.07 % Rotamer: Outliers : 0.06 % Allowed : 0.82 % Favored : 99.13 % 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: -3.20 (0.18), residues: 1866 helix: -1.42 (0.15), residues: 988 sheet: -1.84 (0.89), residues: 33 loop : -3.03 (0.19), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG R 84 TYR 0.044 0.003 TYR B 88 PHE 0.087 0.003 PHE H 73 TRP 0.039 0.002 TRP O 353 HIS 0.014 0.002 HIS G 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.20 (22580) covalent geometry : angle 0.98647 / 0.53 (31707) hydrogen bonds : bond 0.06063 / 3.92 ( 1048) hydrogen bonds : angle 5.38658 / 3.59 ( 2748) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4646.79 seconds wall clock time: 80 minutes 50.51 seconds (4850.51 seconds total)