Starting phenix.real_space_refine on Mon Aug 25 15:03:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x30_38024/08_2025/8x30_38024.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x30_38024/08_2025/8x30_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 { model { file = "/net/cci-nas-00/data/ceres_data/8x30_38024/08_2025/8x30_38024.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x30_38024/08_2025/8x30_38024.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8x30_38024/08_2025/8x30_38024.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x30_38024/08_2025/8x30_38024.map" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.012 sd= 0.431 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9562 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 290 5.49 5 S 41 5.16 5 C 12780 2.51 5 N 3827 2.21 5 O 4641 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 3.69, per 1000 atoms: 0.17 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: 1.20 Conformation dependent library (CDL) restraints added in 601.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 3.69 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: 3.59 Time building geometry restraints manager: 1.62 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=" C LEU G 109 " pdb=" N PRO G 110 " ideal model delta sigma weight residual 1.333 1.301 0.032 1.01e-02 9.80e+03 1.03e+01 bond pdb=" CG GLN E 93 " pdb=" CD GLN E 93 " ideal model delta sigma weight residual 1.516 1.441 0.075 2.50e-02 1.60e+03 9.12e+00 bond pdb=" C ILE K 177 " pdb=" N GLU K 178 " ideal model delta sigma weight residual 1.331 1.252 0.079 2.83e-02 1.25e+03 7.74e+00 bond pdb=" CZ ARG E 63 " pdb=" NH2 ARG E 63 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.21e+00 bond pdb=" CA ASP H 54 " pdb=" CB ASP H 54 " ideal model delta sigma weight residual 1.527 1.461 0.066 2.48e-02 1.63e+03 7.18e+00 ... (remaining 22575 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.42: 30601 3.42 - 6.85: 958 6.85 - 10.27: 124 10.27 - 13.70: 21 13.70 - 17.12: 3 Bond angle restraints: 31707 Sorted by residual: 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 angle pdb=" C THR B 71 " pdb=" N TYR B 72 " pdb=" CA TYR B 72 " ideal model delta sigma weight residual 122.06 110.69 11.37 1.86e+00 2.89e-01 3.74e+01 angle pdb=" C LEU A 103 " pdb=" N PHE A 104 " pdb=" CA PHE A 104 " ideal model delta sigma weight residual 122.38 111.57 10.81 1.81e+00 3.05e-01 3.56e+01 angle pdb=" C LYS D 111 " pdb=" N HIS D 112 " pdb=" CA HIS D 112 " ideal model delta sigma weight residual 121.14 111.52 9.62 1.75e+00 3.27e-01 3.02e+01 angle pdb=" N VAL Q 286 " pdb=" CA VAL Q 286 " pdb=" C VAL Q 286 " ideal model delta sigma weight residual 112.83 107.45 5.38 9.90e-01 1.02e+00 2.96e+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: 3046 0.111 - 0.222: 468 0.222 - 0.333: 38 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: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 19.700 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 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= 0.544 Angle : 1.443 17.120 31707 Z= 0.795 Chirality : 0.080 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 aren 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 covalent geometry : bond 0.01183 (22580) covalent geometry : angle 1.44279 (31707) hydrogen bonds : bond 0.15100 ( 1048) hydrogen bonds : angle 7.13046 ( 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 : 0.476 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: 0.4806 (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: 0.7355 (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: 0.7769 (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: 0.6896 (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: 0.8382 (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: 0.6402 (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: 0.1722 time to fit residues: 138.0317 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 : 0.469 ------------------------------------------------------------------------------- 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: 0.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 0.8980 chunk 212 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 261 HIS M 175 GLN M 204 GLN ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 240 HIS ** M 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 260 ASN ** M 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN ** O 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 285 HIS O 364 HIS 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 75 HIS ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN E 55 GLN E 68 GLN ** 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 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 GLN H 112 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.119971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.094511 restraints weight = 86954.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.097699 restraints weight = 48883.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.099729 restraints weight = 31567.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.101134 restraints weight = 22762.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.101961 restraints weight = 17793.676| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 22580 Z= 0.201 Angle : 0.908 13.739 31707 Z= 0.498 Chirality : 0.049 0.245 3556 Planarity : 0.009 0.255 3001 Dihedral : 29.219 126.128 5372 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 22.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 0.76 % Allowed : 7.63 % Favored : 91.61 % 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 aren not related in a simple way. whole: -4.21 (0.16), residues: 1866 helix: -2.30 (0.14), residues: 1001 sheet: -2.94 (0.72), residues: 33 loop : -3.41 (0.19), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 428 TYR 0.043 0.003 TYR G 59 PHE 0.069 0.003 PHE H 73 TRP 0.032 0.002 TRP O 353 HIS 0.030 0.002 HIS C 84 Details of bonding type rmsd covalent geometry : bond 0.00431 (22580) covalent geometry : angle 0.90770 (31707) hydrogen bonds : bond 0.05910 ( 1048) hydrogen bonds : angle 5.48730 ( 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 540 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 527 time to evaluate : 0.535 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 209 LYS cc_start: 0.8761 (mmpt) cc_final: 0.8486 (mmpt) REVERT: K 243 LYS cc_start: 0.8792 (mptt) cc_final: 0.8297 (mptt) REVERT: K 284 HIS cc_start: 0.7637 (m-70) cc_final: 0.7174 (m-70) REVERT: K 310 GLN cc_start: 0.8176 (pm20) cc_final: 0.7898 (pm20) REVERT: K 311 TYR cc_start: 0.6996 (t80) cc_final: 0.6458 (t80) REVERT: K 325 TYR cc_start: 0.8398 (m-10) cc_final: 0.8182 (m-10) REVERT: K 327 LEU cc_start: 0.9320 (mt) cc_final: 0.9017 (pp) REVERT: M 175 GLN cc_start: 0.5480 (OUTLIER) cc_final: 0.5002 (pp30) REVERT: M 234 LEU cc_start: 0.9129 (mp) cc_final: 0.8808 (pp) REVERT: M 238 LEU cc_start: 0.8832 (tp) cc_final: 0.8553 (tt) REVERT: M 260 ASN cc_start: 0.6842 (OUTLIER) cc_final: 0.6590 (t0) REVERT: M 278 TYR cc_start: 0.8728 (t80) cc_final: 0.8382 (t80) REVERT: N 16 ASN cc_start: 0.7535 (p0) cc_final: 0.7317 (p0) REVERT: O 271 PHE cc_start: 0.8061 (p90) cc_final: 0.7360 (p90) REVERT: O 272 LEU cc_start: 0.7626 (mt) cc_final: 0.7399 (tt) REVERT: O 275 CYS cc_start: 0.8595 (t) cc_final: 0.8142 (t) REVERT: O 325 TYR cc_start: 0.8393 (m-10) cc_final: 0.8119 (m-80) REVERT: P 43 TYR cc_start: 0.8771 (m-80) cc_final: 0.8137 (m-10) REVERT: Q 201 HIS cc_start: 0.9237 (m90) cc_final: 0.8907 (m-70) REVERT: Q 229 MET cc_start: 0.6508 (mmp) cc_final: 0.3614 (mmp) REVERT: A 51 ILE cc_start: 0.8745 (mm) cc_final: 0.8120 (mm) REVERT: A 59 GLU cc_start: 0.8832 (pm20) cc_final: 0.8221 (pm20) REVERT: A 82 LEU cc_start: 0.8285 (pt) cc_final: 0.8060 (mt) REVERT: A 85 GLN cc_start: 0.8160 (tm-30) cc_final: 0.7955 (tm-30) REVERT: A 100 LEU cc_start: 0.8591 (pp) cc_final: 0.8278 (mm) REVERT: A 119 ILE cc_start: 0.8456 (pt) cc_final: 0.8174 (mm) REVERT: A 121 LYS cc_start: 0.8869 (tttm) cc_final: 0.8654 (tppt) REVERT: B 25 ASN cc_start: 0.7682 (t0) cc_final: 0.7351 (t0) REVERT: B 58 LEU cc_start: 0.8598 (mm) cc_final: 0.8353 (mm) REVERT: B 74 GLU cc_start: 0.8461 (tp30) cc_final: 0.7835 (tp30) REVERT: B 88 TYR cc_start: 0.8203 (m-10) cc_final: 0.8000 (m-80) REVERT: C 21 ARG cc_start: 0.7300 (tmt-80) cc_final: 0.6909 (tpt90) REVERT: C 31 ILE cc_start: 0.9264 (mm) cc_final: 0.8844 (pt) REVERT: C 33 ARG cc_start: 0.8434 (pmt170) cc_final: 0.8098 (ptt-90) REVERT: C 75 LEU cc_start: 0.8908 (mp) cc_final: 0.8694 (mt) REVERT: C 84 HIS cc_start: 0.7655 (p90) cc_final: 0.7220 (p-80) REVERT: C 89 ILE cc_start: 0.8461 (mm) cc_final: 0.8090 (mm) REVERT: D 65 LEU cc_start: 0.9029 (mt) cc_final: 0.8650 (mt) REVERT: D 71 ASP cc_start: 0.8223 (p0) cc_final: 0.7902 (p0) REVERT: D 103 LEU cc_start: 0.8206 (pp) cc_final: 0.7998 (pp) REVERT: D 124 TYR cc_start: 0.7980 (t80) cc_final: 0.7729 (t80) REVERT: E 41 TYR cc_start: 0.6323 (p90) cc_final: 0.5739 (p90) REVERT: E 64 LYS cc_start: 0.8204 (mppt) cc_final: 0.7942 (mmtm) REVERT: E 70 LEU cc_start: 0.8793 (tp) cc_final: 0.8587 (mt) REVERT: E 72 ARG cc_start: 0.7572 (mmt180) cc_final: 0.7229 (mmt180) REVERT: E 74 ILE cc_start: 0.8676 (pt) cc_final: 0.8422 (pt) REVERT: E 81 ASP cc_start: 0.8352 (p0) cc_final: 0.8051 (p0) REVERT: E 115 LYS cc_start: 0.9131 (ptpp) cc_final: 0.8715 (ptpp) REVERT: E 120 GLN cc_start: 0.6212 (pp30) cc_final: 0.5728 (pm20) REVERT: E 123 ASP cc_start: 0.7801 (m-30) cc_final: 0.6412 (m-30) REVERT: E 125 LYS cc_start: 0.8628 (mtmm) cc_final: 0.8189 (mtmm) REVERT: F 44 LYS cc_start: 0.9248 (tppt) cc_final: 0.8919 (mmmm) REVERT: F 50 ILE cc_start: 0.8329 (pt) cc_final: 0.8040 (mm) REVERT: F 67 ARG cc_start: 0.8294 (mtm110) cc_final: 0.7881 (mtm-85) REVERT: F 77 LYS cc_start: 0.8364 (mptt) cc_final: 0.7985 (mmtp) REVERT: G 31 ILE cc_start: 0.8256 (pt) cc_final: 0.7739 (tt) REVERT: G 52 TYR cc_start: 0.7542 (t80) cc_final: 0.7110 (t80) REVERT: G 86 GLN cc_start: 0.7394 (mp10) cc_final: 0.6998 (mp10) REVERT: G 96 ASP cc_start: 0.8649 (p0) cc_final: 0.8393 (p0) REVERT: H 52 HIS cc_start: 0.7317 (t70) cc_final: 0.7060 (t70) REVERT: H 62 MET cc_start: 0.7935 (mmm) cc_final: 0.7688 (mmm) REVERT: H 66 ASN cc_start: 0.7652 (p0) cc_final: 0.7308 (p0) REVERT: H 68 PHE cc_start: 0.8115 (t80) cc_final: 0.7901 (t80) REVERT: H 82 LYS cc_start: 0.9017 (tmmt) cc_final: 0.8718 (ptmm) REVERT: H 86 TYR cc_start: 0.7335 (p90) cc_final: 0.6851 (p90) REVERT: H 88 LYS cc_start: 0.9305 (ptpp) cc_final: 0.9057 (ptmm) REVERT: H 101 VAL cc_start: 0.8722 (p) cc_final: 0.8476 (m) REVERT: H 102 ARG cc_start: 0.8392 (ttm110) cc_final: 0.8106 (ptp-170) REVERT: H 105 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8588 (pp) REVERT: H 108 GLU cc_start: 0.8194 (pm20) cc_final: 0.7872 (pm20) REVERT: H 112 HIS cc_start: 0.7450 (m90) cc_final: 0.6625 (m90) outliers start: 13 outliers final: 1 residues processed: 533 average time/residue: 0.1756 time to fit residues: 133.7731 Evaluate side-chains 470 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 466 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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: 2.9990 chunk 163 optimal weight: 0.8980 chunk 161 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 180 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 46 optimal weight: 0.7980 chunk 205 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 301 ASN ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 245 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** A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 16 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.121490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.096403 restraints weight = 87488.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.099610 restraints weight = 49175.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.101696 restraints weight = 31585.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.103040 restraints weight = 22511.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.103963 restraints weight = 17561.307| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 22580 Z= 0.194 Angle : 0.854 12.013 31707 Z= 0.468 Chirality : 0.047 0.231 3556 Planarity : 0.007 0.087 3001 Dihedral : 28.820 120.252 5372 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 22.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 0.23 % Allowed : 7.52 % Favored : 92.25 % 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 aren not related in a simple way. whole: -3.45 (0.18), residues: 1866 helix: -1.64 (0.15), residues: 971 sheet: -2.91 (0.74), residues: 35 loop : -3.05 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 428 TYR 0.031 0.003 TYR C 52 PHE 0.032 0.002 PHE H 73 TRP 0.057 0.002 TRP O 353 HIS 0.011 0.002 HIS C 84 Details of bonding type rmsd covalent geometry : bond 0.00421 (22580) covalent geometry : angle 0.85416 (31707) hydrogen bonds : bond 0.05576 ( 1048) hydrogen bonds : angle 5.19713 ( 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 537 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 533 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 212 GLU cc_start: 0.8030 (mp0) cc_final: 0.7771 (mp0) REVERT: K 273 PHE cc_start: 0.8270 (m-80) cc_final: 0.7897 (m-10) REVERT: K 284 HIS cc_start: 0.7555 (m-70) cc_final: 0.7213 (m-70) REVERT: K 302 VAL cc_start: 0.8516 (t) cc_final: 0.7060 (t) REVERT: K 319 LEU cc_start: 0.8006 (tp) cc_final: 0.7750 (pt) REVERT: K 325 TYR cc_start: 0.8393 (m-10) cc_final: 0.8191 (m-10) REVERT: K 327 LEU cc_start: 0.9269 (mt) cc_final: 0.9004 (pp) REVERT: K 343 ASP cc_start: 0.8962 (p0) cc_final: 0.8474 (p0) REVERT: K 376 MET cc_start: 0.8622 (pmm) cc_final: 0.8394 (pmm) REVERT: M 234 LEU cc_start: 0.9142 (mp) cc_final: 0.8785 (pp) REVERT: M 237 GLN cc_start: 0.8922 (tp-100) cc_final: 0.8669 (tp-100) REVERT: M 238 LEU cc_start: 0.8783 (tp) cc_final: 0.8516 (tt) REVERT: M 278 TYR cc_start: 0.8822 (t80) cc_final: 0.8529 (t80) REVERT: M 279 TRP cc_start: 0.8348 (t60) cc_final: 0.8123 (t60) REVERT: N 16 ASN cc_start: 0.7521 (p0) cc_final: 0.7212 (p0) REVERT: O 271 PHE cc_start: 0.8025 (p90) cc_final: 0.7393 (p90) REVERT: O 275 CYS cc_start: 0.8595 (t) cc_final: 0.8236 (t) REVERT: O 353 TRP cc_start: 0.7130 (p90) cc_final: 0.6602 (p90) REVERT: Q 198 HIS cc_start: 0.8967 (m90) cc_final: 0.8752 (m90) REVERT: Q 326 ILE cc_start: 0.8211 (pt) cc_final: 0.7975 (pt) REVERT: A 51 ILE cc_start: 0.8724 (mm) cc_final: 0.8515 (mm) REVERT: A 59 GLU cc_start: 0.8822 (pm20) cc_final: 0.8218 (pm20) REVERT: A 61 LEU cc_start: 0.9132 (mm) cc_final: 0.8904 (mt) REVERT: A 64 LYS cc_start: 0.9221 (mppt) cc_final: 0.9008 (mmtm) REVERT: A 73 GLU cc_start: 0.8119 (tt0) cc_final: 0.7858 (tt0) REVERT: A 82 LEU cc_start: 0.8421 (pt) cc_final: 0.8186 (mt) REVERT: A 85 GLN cc_start: 0.8465 (tm-30) cc_final: 0.7819 (tm-30) REVERT: A 87 SER cc_start: 0.9215 (t) cc_final: 0.8753 (p) REVERT: A 100 LEU cc_start: 0.8693 (pp) cc_final: 0.8354 (mm) REVERT: A 122 LYS cc_start: 0.8557 (ptpp) cc_final: 0.8352 (ptmm) REVERT: B 27 GLN cc_start: 0.7701 (pm20) cc_final: 0.7415 (pm20) REVERT: B 36 ARG cc_start: 0.8371 (ttp-110) cc_final: 0.8162 (ptp90) REVERT: B 74 GLU cc_start: 0.8429 (tp30) cc_final: 0.7923 (tp30) REVERT: B 88 TYR cc_start: 0.8196 (m-10) cc_final: 0.7698 (m-10) REVERT: B 95 ARG cc_start: 0.6883 (mtm180) cc_final: 0.6411 (mtm-85) REVERT: C 31 ILE cc_start: 0.9252 (mm) cc_final: 0.8739 (pt) REVERT: C 32 LYS cc_start: 0.8966 (tptt) cc_final: 0.8697 (tptt) REVERT: C 33 ARG cc_start: 0.8601 (pmt170) cc_final: 0.8017 (ptt-90) REVERT: C 34 TYR cc_start: 0.8450 (m-80) cc_final: 0.8212 (m-80) REVERT: C 35 LEU cc_start: 0.8269 (mm) cc_final: 0.8013 (mt) REVERT: C 53 LEU cc_start: 0.8354 (mp) cc_final: 0.8008 (tt) REVERT: C 78 LYS cc_start: 0.8215 (ptpt) cc_final: 0.7932 (pttm) REVERT: C 98 LEU cc_start: 0.8604 (pt) cc_final: 0.7924 (mp) REVERT: D 86 TYR cc_start: 0.8266 (m-80) cc_final: 0.7932 (m-10) REVERT: D 114 VAL cc_start: 0.8318 (m) cc_final: 0.8091 (p) REVERT: E 41 TYR cc_start: 0.6585 (p90) cc_final: 0.5998 (p90) REVERT: E 54 PHE cc_start: 0.6536 (p90) cc_final: 0.6265 (p90) REVERT: E 56 LYS cc_start: 0.8754 (tmtt) cc_final: 0.8518 (tmtt) REVERT: E 64 LYS cc_start: 0.8610 (mppt) cc_final: 0.8177 (mmmm) REVERT: E 70 LEU cc_start: 0.8807 (tp) cc_final: 0.8601 (mt) REVERT: E 97 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7179 (mm-30) REVERT: E 115 LYS cc_start: 0.9150 (ptpp) cc_final: 0.8792 (ptpp) REVERT: E 120 GLN cc_start: 0.6467 (pp30) cc_final: 0.6109 (pm20) REVERT: E 123 ASP cc_start: 0.7702 (m-30) cc_final: 0.6262 (m-30) REVERT: E 125 LYS cc_start: 0.8674 (mtmm) cc_final: 0.8440 (mtmm) REVERT: F 50 ILE cc_start: 0.8440 (pt) cc_final: 0.8118 (mm) REVERT: F 58 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.8005 (pt) REVERT: F 82 THR cc_start: 0.7646 (p) cc_final: 0.7301 (p) REVERT: F 91 LYS cc_start: 0.8521 (pttp) cc_final: 0.8167 (pttm) REVERT: G 34 TYR cc_start: 0.7914 (p90) cc_final: 0.7565 (p90) REVERT: G 52 TYR cc_start: 0.7341 (t80) cc_final: 0.6732 (t80) REVERT: G 59 TYR cc_start: 0.7246 (p90) cc_final: 0.6678 (p90) REVERT: G 60 LEU cc_start: 0.8715 (pp) cc_final: 0.8333 (pp) REVERT: G 96 ASP cc_start: 0.8331 (p0) cc_final: 0.8009 (p0) REVERT: H 62 MET cc_start: 0.8061 (mmm) cc_final: 0.7790 (mmp) REVERT: H 66 ASN cc_start: 0.7827 (p0) cc_final: 0.7545 (p0) REVERT: H 72 ILE cc_start: 0.7826 (tp) cc_final: 0.7461 (tt) REVERT: H 82 LYS cc_start: 0.8954 (tmmt) cc_final: 0.8594 (tmtt) REVERT: H 86 TYR cc_start: 0.7127 (p90) cc_final: 0.6746 (p90) REVERT: H 88 LYS cc_start: 0.9360 (ptpp) cc_final: 0.9108 (ptmm) REVERT: H 96 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7349 (tm-30) REVERT: H 102 ARG cc_start: 0.8405 (ttm110) cc_final: 0.8179 (ttp-110) REVERT: H 105 LEU cc_start: 0.9113 (pp) cc_final: 0.8888 (pp) REVERT: H 111 LYS cc_start: 0.8413 (pptt) cc_final: 0.8150 (pptt) REVERT: H 112 HIS cc_start: 0.7665 (m90) cc_final: 0.6710 (m90) REVERT: H 116 GLU cc_start: 0.8010 (mp0) cc_final: 0.7479 (mp0) REVERT: H 119 ARG cc_start: 0.8088 (ttp-110) cc_final: 0.7570 (mtm110) outliers start: 4 outliers final: 2 residues processed: 534 average time/residue: 0.1726 time to fit residues: 132.3321 Evaluate side-chains 464 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 461 time to evaluate : 0.653 ------------------------------------------------------------------------------- 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: 4.9990 chunk 14 optimal weight: 4.9990 chunk 212 optimal weight: 2.9990 chunk 191 optimal weight: 5.9990 chunk 133 optimal weight: 2.9990 chunk 207 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 171 optimal weight: 0.6980 chunk 28 optimal weight: 9.9990 chunk 184 optimal weight: 3.9990 chunk 181 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 414 ASN M 204 GLN ** M 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 260 ASN ** M 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 204 GLN ** 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 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 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 = 0.4034 r_free = 0.4034 target = 0.117685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.091956 restraints weight = 87969.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.095220 restraints weight = 50198.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.097295 restraints weight = 32494.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.098648 restraints weight = 23417.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.099544 restraints weight = 18306.229| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.5285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 22580 Z= 0.271 Angle : 0.892 11.492 31707 Z= 0.494 Chirality : 0.050 0.328 3556 Planarity : 0.007 0.113 3001 Dihedral : 28.674 125.239 5372 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 27.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.47 % Favored : 88.53 % Rotamer: Outliers : 0.17 % Allowed : 7.34 % Favored : 92.48 % 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 aren not related in a simple way. whole: -3.43 (0.17), residues: 1866 helix: -1.45 (0.15), residues: 997 sheet: -2.83 (0.75), residues: 33 loop : -3.32 (0.19), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 428 TYR 0.034 0.003 TYR C 52 PHE 0.029 0.003 PHE H 73 TRP 0.038 0.002 TRP O 353 HIS 0.015 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00593 (22580) covalent geometry : angle 0.89250 (31707) hydrogen bonds : bond 0.06743 ( 1048) hydrogen bonds : angle 5.27492 ( 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 543 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 540 time to evaluate : 0.529 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 233 TYR cc_start: 0.7519 (t80) cc_final: 0.6807 (t80) REVERT: K 284 HIS cc_start: 0.7734 (m-70) cc_final: 0.7369 (m-70) REVERT: K 302 VAL cc_start: 0.8760 (t) cc_final: 0.7852 (t) REVERT: K 310 GLN cc_start: 0.7942 (pm20) cc_final: 0.7462 (pm20) REVERT: K 311 TYR cc_start: 0.7730 (t80) cc_final: 0.7433 (t80) REVERT: K 325 TYR cc_start: 0.8448 (m-10) cc_final: 0.8117 (m-10) REVERT: K 343 ASP cc_start: 0.9216 (p0) cc_final: 0.9015 (p0) REVERT: K 391 LEU cc_start: -0.1377 (OUTLIER) cc_final: -0.1793 (tt) REVERT: M 214 ILE cc_start: 0.5509 (tt) cc_final: 0.5181 (tt) REVERT: M 215 LEU cc_start: 0.8024 (pp) cc_final: 0.7813 (pt) REVERT: M 233 ASN cc_start: 0.8149 (p0) cc_final: 0.7844 (p0) REVERT: M 234 LEU cc_start: 0.9317 (mp) cc_final: 0.8892 (mp) REVERT: M 237 GLN cc_start: 0.8898 (tp-100) cc_final: 0.8677 (tp-100) REVERT: M 238 LEU cc_start: 0.8914 (tp) cc_final: 0.8594 (tt) REVERT: M 278 TYR cc_start: 0.8711 (t80) cc_final: 0.8426 (t80) REVERT: M 280 ARG cc_start: 0.5593 (mmp-170) cc_final: 0.4809 (mmm160) REVERT: N 16 ASN cc_start: 0.8117 (p0) cc_final: 0.7823 (p0) REVERT: O 178 GLU cc_start: 0.7978 (tp30) cc_final: 0.7395 (pm20) REVERT: O 237 PHE cc_start: 0.7239 (m-80) cc_final: 0.6727 (m-80) REVERT: O 271 PHE cc_start: 0.8079 (p90) cc_final: 0.7389 (p90) REVERT: O 275 CYS cc_start: 0.8832 (t) cc_final: 0.8597 (t) REVERT: O 323 PHE cc_start: 0.8847 (t80) cc_final: 0.8637 (t80) REVERT: O 331 GLU cc_start: 0.8653 (pt0) cc_final: 0.8217 (pp20) REVERT: O 353 TRP cc_start: 0.7231 (p90) cc_final: 0.6691 (p90) REVERT: Q 147 TYR cc_start: 0.6943 (m-10) cc_final: 0.6658 (m-10) REVERT: Q 198 HIS cc_start: 0.9048 (m90) cc_final: 0.8784 (m90) REVERT: Q 326 ILE cc_start: 0.8048 (pt) cc_final: 0.7736 (pt) REVERT: A 50 GLU cc_start: 0.6774 (tm-30) cc_final: 0.6572 (tp30) REVERT: A 59 GLU cc_start: 0.9099 (pm20) cc_final: 0.8565 (pm20) REVERT: A 62 ILE cc_start: 0.9087 (pt) cc_final: 0.8686 (pt) REVERT: A 64 LYS cc_start: 0.9108 (mppt) cc_final: 0.8900 (mmtm) REVERT: A 70 LEU cc_start: 0.8684 (pp) cc_final: 0.8238 (pp) REVERT: A 71 VAL cc_start: 0.9131 (m) cc_final: 0.8887 (p) REVERT: A 72 ARG cc_start: 0.7754 (tpp-160) cc_final: 0.7007 (tpp-160) REVERT: A 73 GLU cc_start: 0.7863 (tt0) cc_final: 0.7588 (tt0) REVERT: A 78 PHE cc_start: 0.7411 (m-80) cc_final: 0.6544 (m-80) REVERT: A 87 SER cc_start: 0.9139 (t) cc_final: 0.8740 (p) REVERT: A 123 ASP cc_start: 0.7954 (m-30) cc_final: 0.7696 (m-30) REVERT: A 124 ILE cc_start: 0.8580 (mp) cc_final: 0.8059 (tp) REVERT: B 27 GLN cc_start: 0.8496 (pm20) cc_final: 0.7819 (pm20) REVERT: B 34 ILE cc_start: 0.9064 (tp) cc_final: 0.8511 (tp) REVERT: B 74 GLU cc_start: 0.8373 (tp30) cc_final: 0.8132 (tp30) REVERT: B 83 SER cc_start: 0.8655 (m) cc_final: 0.8402 (m) REVERT: C 25 GLN cc_start: 0.7809 (tp40) cc_final: 0.7502 (tp40) REVERT: C 32 LYS cc_start: 0.8759 (mmmt) cc_final: 0.8184 (tppt) REVERT: C 33 ARG cc_start: 0.8460 (pmt170) cc_final: 0.8081 (ptt-90) REVERT: C 44 ARG cc_start: 0.7547 (ptm-80) cc_final: 0.6865 (ptt90) REVERT: C 53 LEU cc_start: 0.8663 (mp) cc_final: 0.8271 (tt) REVERT: C 60 LEU cc_start: 0.8951 (tp) cc_final: 0.8590 (mm) REVERT: C 79 ARG cc_start: 0.7114 (pmt-80) cc_final: 0.6865 (pmt-80) REVERT: C 84 HIS cc_start: 0.7684 (p90) cc_final: 0.7328 (p-80) REVERT: D 47 VAL cc_start: 0.8775 (t) cc_final: 0.7879 (t) REVERT: D 49 LYS cc_start: 0.8685 (mtmm) cc_final: 0.8433 (mttt) REVERT: D 51 THR cc_start: 0.9091 (p) cc_final: 0.8548 (p) REVERT: D 64 ILE cc_start: 0.8848 (mm) cc_final: 0.8130 (tp) REVERT: D 65 LEU cc_start: 0.9019 (mt) cc_final: 0.8655 (mt) REVERT: D 99 THR cc_start: 0.8327 (p) cc_final: 0.7127 (p) REVERT: D 101 VAL cc_start: 0.8543 (m) cc_final: 0.8286 (p) REVERT: D 102 ARG cc_start: 0.7614 (ptt90) cc_final: 0.7233 (ptt90) REVERT: D 112 HIS cc_start: 0.7195 (p90) cc_final: 0.6929 (p-80) REVERT: E 41 TYR cc_start: 0.6873 (p90) cc_final: 0.6387 (p90) REVERT: E 56 LYS cc_start: 0.8925 (tmtt) cc_final: 0.8723 (tmtt) REVERT: E 60 LEU cc_start: 0.8507 (tp) cc_final: 0.8195 (tp) REVERT: E 64 LYS cc_start: 0.8822 (mppt) cc_final: 0.8260 (mmmm) REVERT: E 67 PHE cc_start: 0.7699 (p90) cc_final: 0.7339 (p90) REVERT: E 72 ARG cc_start: 0.8366 (mmt180) cc_final: 0.8051 (mmt180) REVERT: E 99 TYR cc_start: 0.8437 (t80) cc_final: 0.8225 (t80) REVERT: E 107 THR cc_start: 0.8643 (m) cc_final: 0.8171 (m) REVERT: E 108 ASN cc_start: 0.8238 (m-40) cc_final: 0.7876 (m110) REVERT: E 115 LYS cc_start: 0.9115 (ptpp) cc_final: 0.8867 (ptpp) REVERT: E 125 LYS cc_start: 0.8812 (mtmm) cc_final: 0.8446 (mtmm) REVERT: F 49 LEU cc_start: 0.8366 (mm) cc_final: 0.7722 (tp) REVERT: F 50 ILE cc_start: 0.8645 (pt) cc_final: 0.8236 (mm) REVERT: F 57 VAL cc_start: 0.8781 (m) cc_final: 0.8557 (p) REVERT: F 60 SER cc_start: 0.8530 (p) cc_final: 0.7954 (p) REVERT: F 63 GLU cc_start: 0.8520 (pt0) cc_final: 0.8232 (pp20) REVERT: F 64 SER cc_start: 0.8980 (p) cc_final: 0.8679 (p) REVERT: F 82 THR cc_start: 0.7985 (p) cc_final: 0.7307 (p) REVERT: G 32 LYS cc_start: 0.8763 (mmmt) cc_final: 0.7830 (mmmm) REVERT: G 36 LYS cc_start: 0.8799 (mptt) cc_final: 0.8349 (pttt) REVERT: G 48 LYS cc_start: 0.9223 (mmmt) cc_final: 0.8924 (mmmt) REVERT: G 54 THR cc_start: 0.8710 (t) cc_final: 0.5274 (t) REVERT: G 60 LEU cc_start: 0.8907 (pp) cc_final: 0.8591 (pp) REVERT: G 78 LYS cc_start: 0.8683 (mtmt) cc_final: 0.8383 (mtmt) REVERT: G 83 ARG cc_start: 0.8171 (ptm-80) cc_final: 0.7445 (ptm-80) REVERT: G 86 GLN cc_start: 0.7264 (mp10) cc_final: 0.6790 (mp10) REVERT: G 89 ILE cc_start: 0.9009 (mt) cc_final: 0.8779 (mp) REVERT: H 46 LYS cc_start: 0.8779 (pttm) cc_final: 0.8514 (ttpp) REVERT: H 49 LYS cc_start: 0.8597 (pttm) cc_final: 0.8221 (pttp) REVERT: H 52 HIS cc_start: 0.7885 (t70) cc_final: 0.7664 (t70) REVERT: H 66 ASN cc_start: 0.8156 (p0) cc_final: 0.7729 (p0) REVERT: H 73 PHE cc_start: 0.7651 (t80) cc_final: 0.7325 (t80) REVERT: H 74 GLU cc_start: 0.8206 (tp30) cc_final: 0.7938 (tp30) REVERT: H 82 LYS cc_start: 0.8944 (tmmt) cc_final: 0.8730 (tmtt) REVERT: H 86 TYR cc_start: 0.7268 (p90) cc_final: 0.6969 (p90) REVERT: H 88 LYS cc_start: 0.9362 (ptpp) cc_final: 0.9095 (ptmm) REVERT: H 99 THR cc_start: 0.8875 (m) cc_final: 0.8673 (p) outliers start: 3 outliers final: 1 residues processed: 542 average time/residue: 0.1754 time to fit residues: 134.9890 Evaluate side-chains 486 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 484 time to evaluate : 0.664 ------------------------------------------------------------------------------- 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: 0.9980 chunk 148 optimal weight: 0.8980 chunk 109 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 208 optimal weight: 0.5980 chunk 141 optimal weight: 2.9990 chunk 159 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 146 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 166 ASN ** K 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 245 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** ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 34 GLN ** Q 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 GLN ** E 108 ASN ** 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 = 0.4097 r_free = 0.4097 target = 0.121717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.095949 restraints weight = 88306.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.099184 restraints weight = 50546.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.101292 restraints weight = 32898.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.102690 restraints weight = 23717.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.103619 restraints weight = 18556.719| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.5744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22580 Z= 0.188 Angle : 0.856 11.729 31707 Z= 0.464 Chirality : 0.047 0.236 3556 Planarity : 0.006 0.090 3001 Dihedral : 28.548 126.371 5372 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 21.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer: Outliers : 0.12 % Allowed : 4.84 % Favored : 95.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.02 (0.18), residues: 1866 helix: -1.17 (0.16), residues: 974 sheet: -2.54 (0.79), residues: 35 loop : -3.02 (0.20), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 67 TYR 0.024 0.002 TYR K 397 PHE 0.036 0.003 PHE E 54 TRP 0.061 0.002 TRP O 353 HIS 0.019 0.002 HIS Q 240 Details of bonding type rmsd covalent geometry : bond 0.00406 (22580) covalent geometry : angle 0.85603 (31707) hydrogen bonds : bond 0.05390 ( 1048) hydrogen bonds : angle 5.07480 ( 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 530 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 528 time to evaluate : 0.506 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 209 LYS cc_start: 0.8646 (mmpt) cc_final: 0.8252 (mmpt) REVERT: K 212 GLU cc_start: 0.8240 (mp0) cc_final: 0.8040 (mp0) REVERT: K 233 TYR cc_start: 0.7198 (t80) cc_final: 0.6508 (t80) REVERT: K 273 PHE cc_start: 0.7997 (m-10) cc_final: 0.7741 (m-10) REVERT: K 274 TYR cc_start: 0.7650 (p90) cc_final: 0.7209 (p90) REVERT: K 281 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8650 (tp30) REVERT: K 284 HIS cc_start: 0.7929 (m-70) cc_final: 0.7352 (m-70) REVERT: K 311 TYR cc_start: 0.7773 (t80) cc_final: 0.7534 (t80) REVERT: K 325 TYR cc_start: 0.8471 (m-10) cc_final: 0.8181 (m-80) REVERT: K 343 ASP cc_start: 0.9153 (p0) cc_final: 0.8853 (p0) REVERT: K 404 PHE cc_start: 0.7187 (p90) cc_final: 0.6880 (p90) REVERT: M 233 ASN cc_start: 0.8151 (p0) cc_final: 0.7856 (p0) REVERT: M 234 LEU cc_start: 0.9289 (mp) cc_final: 0.8846 (mp) REVERT: M 237 GLN cc_start: 0.8919 (tp-100) cc_final: 0.8668 (tm-30) REVERT: M 278 TYR cc_start: 0.8605 (t80) cc_final: 0.8360 (t80) REVERT: M 280 ARG cc_start: 0.5292 (mmp-170) cc_final: 0.5064 (mmp-170) REVERT: O 237 PHE cc_start: 0.7078 (m-80) cc_final: 0.6717 (m-10) REVERT: O 271 PHE cc_start: 0.8065 (p90) cc_final: 0.7369 (p90) REVERT: O 275 CYS cc_start: 0.8699 (t) cc_final: 0.8298 (t) REVERT: O 325 TYR cc_start: 0.8880 (m-80) cc_final: 0.8596 (m-80) REVERT: O 431 TRP cc_start: 0.7552 (m-90) cc_final: 0.7346 (m-90) REVERT: P 43 TYR cc_start: 0.8811 (m-80) cc_final: 0.8406 (m-10) REVERT: Q 198 HIS cc_start: 0.9055 (m90) cc_final: 0.8782 (m90) REVERT: R 14 VAL cc_start: 0.7551 (p) cc_final: 0.7032 (p) REVERT: A 48 LEU cc_start: 0.7742 (pt) cc_final: 0.7513 (pt) REVERT: A 51 ILE cc_start: 0.8400 (mm) cc_final: 0.7506 (mm) REVERT: A 64 LYS cc_start: 0.9150 (mppt) cc_final: 0.8813 (mmtm) REVERT: A 65 LEU cc_start: 0.8620 (pp) cc_final: 0.8103 (pt) REVERT: A 69 ARG cc_start: 0.8736 (mtm-85) cc_final: 0.7681 (ptp-170) REVERT: A 73 GLU cc_start: 0.8077 (tt0) cc_final: 0.7715 (tt0) REVERT: A 84 PHE cc_start: 0.6800 (m-10) cc_final: 0.6321 (m-10) REVERT: A 87 SER cc_start: 0.9121 (t) cc_final: 0.8707 (p) REVERT: A 99 TYR cc_start: 0.8747 (t80) cc_final: 0.8525 (t80) REVERT: A 119 ILE cc_start: 0.8636 (mt) cc_final: 0.8381 (tp) REVERT: B 25 ASN cc_start: 0.7692 (t0) cc_final: 0.7123 (t0) REVERT: B 74 GLU cc_start: 0.8314 (tp30) cc_final: 0.8099 (tp30) REVERT: C 25 GLN cc_start: 0.7597 (tp40) cc_final: 0.7175 (tp40) REVERT: C 35 LEU cc_start: 0.8527 (mm) cc_final: 0.8297 (mt) REVERT: C 53 LEU cc_start: 0.8657 (mp) cc_final: 0.8095 (tt) REVERT: C 60 LEU cc_start: 0.8947 (tp) cc_final: 0.8591 (mm) REVERT: C 84 HIS cc_start: 0.7452 (p90) cc_final: 0.7146 (p90) REVERT: C 98 LEU cc_start: 0.8623 (pt) cc_final: 0.8272 (pp) REVERT: D 47 VAL cc_start: 0.8483 (t) cc_final: 0.7715 (t) REVERT: D 68 PHE cc_start: 0.8376 (p90) cc_final: 0.8152 (p90) REVERT: D 73 PHE cc_start: 0.8388 (t80) cc_final: 0.8098 (t80) REVERT: D 76 ILE cc_start: 0.9202 (pt) cc_final: 0.8455 (pt) REVERT: D 79 GLU cc_start: 0.8081 (pt0) cc_final: 0.7879 (pp20) REVERT: D 99 THR cc_start: 0.8312 (p) cc_final: 0.6638 (p) REVERT: D 101 VAL cc_start: 0.8476 (m) cc_final: 0.8148 (p) REVERT: D 102 ARG cc_start: 0.7371 (ptt90) cc_final: 0.7007 (ptt90) REVERT: E 41 TYR cc_start: 0.6677 (p90) cc_final: 0.6250 (p90) REVERT: E 56 LYS cc_start: 0.8842 (tmtt) cc_final: 0.8594 (tmtt) REVERT: E 60 LEU cc_start: 0.8303 (tp) cc_final: 0.7977 (tp) REVERT: E 64 LYS cc_start: 0.8772 (mppt) cc_final: 0.8237 (mtmm) REVERT: E 72 ARG cc_start: 0.8415 (mmt180) cc_final: 0.6705 (mmt180) REVERT: E 99 TYR cc_start: 0.8370 (t80) cc_final: 0.8126 (t80) REVERT: E 115 LYS cc_start: 0.9146 (ptpp) cc_final: 0.8836 (ptpp) REVERT: E 116 ARG cc_start: 0.7798 (tmm-80) cc_final: 0.5284 (tmm-80) REVERT: E 122 LYS cc_start: 0.8944 (mppt) cc_final: 0.8664 (mmmt) REVERT: E 125 LYS cc_start: 0.8881 (mtmm) cc_final: 0.7989 (mtmm) REVERT: F 45 ARG cc_start: 0.7814 (ptm-80) cc_final: 0.6564 (ttp80) REVERT: F 50 ILE cc_start: 0.8653 (pt) cc_final: 0.8153 (mm) REVERT: F 57 VAL cc_start: 0.8782 (m) cc_final: 0.8542 (p) REVERT: F 60 SER cc_start: 0.8527 (p) cc_final: 0.8084 (p) REVERT: F 82 THR cc_start: 0.7716 (p) cc_final: 0.7015 (p) REVERT: F 91 LYS cc_start: 0.8370 (pttp) cc_final: 0.8167 (pttm) REVERT: G 34 TYR cc_start: 0.8217 (p90) cc_final: 0.6995 (p90) REVERT: G 51 ILE cc_start: 0.8993 (pt) cc_final: 0.8714 (pt) REVERT: G 54 THR cc_start: 0.7471 (t) cc_final: 0.4866 (t) REVERT: G 59 TYR cc_start: 0.7331 (p90) cc_final: 0.7010 (p90) REVERT: G 60 LEU cc_start: 0.8755 (pp) cc_final: 0.8445 (pp) REVERT: G 74 ASP cc_start: 0.8110 (p0) cc_final: 0.7851 (p0) REVERT: G 78 LYS cc_start: 0.8606 (mtmt) cc_final: 0.8355 (mtmt) REVERT: G 86 GLN cc_start: 0.7232 (mp10) cc_final: 0.6793 (mp10) REVERT: G 89 ILE cc_start: 0.8987 (mt) cc_final: 0.8742 (mp) REVERT: H 44 ILE cc_start: 0.8889 (mt) cc_final: 0.8682 (mm) REVERT: H 46 LYS cc_start: 0.8740 (pttm) cc_final: 0.8500 (ttpp) REVERT: H 49 LYS cc_start: 0.8525 (pttm) cc_final: 0.8083 (pttp) REVERT: H 52 HIS cc_start: 0.7940 (t70) cc_final: 0.7611 (t70) REVERT: H 66 ASN cc_start: 0.8183 (p0) cc_final: 0.7730 (p0) REVERT: H 74 GLU cc_start: 0.8275 (tp30) cc_final: 0.7567 (tp30) REVERT: H 88 LYS cc_start: 0.9326 (ptpp) cc_final: 0.9004 (ptmm) REVERT: H 105 LEU cc_start: 0.9082 (pp) cc_final: 0.8730 (pp) REVERT: H 112 HIS cc_start: 0.7713 (m90) cc_final: 0.7195 (m90) REVERT: H 116 GLU cc_start: 0.7576 (tm-30) cc_final: 0.6182 (pp20) REVERT: H 124 TYR cc_start: 0.7539 (p90) cc_final: 0.6736 (p90) outliers start: 2 outliers final: 0 residues processed: 530 average time/residue: 0.1778 time to fit residues: 133.6867 Evaluate side-chains 468 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 468 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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: 9.9990 chunk 91 optimal weight: 10.0000 chunk 44 optimal weight: 0.8980 chunk 206 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 27 optimal weight: 0.0870 chunk 156 optimal weight: 0.1980 chunk 137 optimal weight: 2.9990 chunk 152 optimal weight: 0.0020 chunk 107 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 overall best weight: 0.8368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 166 ASN ** K 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 400 GLN ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 245 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** ** O 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN F 25 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.122636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.096721 restraints weight = 88013.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.100011 restraints weight = 50160.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.102127 restraints weight = 32584.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.103503 restraints weight = 23447.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.104433 restraints weight = 18394.210| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.6217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 22580 Z= 0.188 Angle : 0.863 11.281 31707 Z= 0.466 Chirality : 0.047 0.359 3556 Planarity : 0.006 0.103 3001 Dihedral : 28.356 127.220 5372 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 21.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % Rotamer: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.95 (0.18), residues: 1866 helix: -1.14 (0.16), residues: 978 sheet: -1.84 (0.86), residues: 33 loop : -3.00 (0.20), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 249 TYR 0.034 0.002 TYR D 86 PHE 0.041 0.003 PHE H 73 TRP 0.048 0.002 TRP O 353 HIS 0.019 0.002 HIS G 84 Details of bonding type rmsd covalent geometry : bond 0.00409 (22580) covalent geometry : angle 0.86347 (31707) hydrogen bonds : bond 0.05318 ( 1048) hydrogen bonds : angle 5.01661 ( 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 517 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 517 time to evaluate : 0.676 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 209 LYS cc_start: 0.8626 (mmpt) cc_final: 0.8198 (mmpt) REVERT: K 217 LYS cc_start: 0.5320 (tptp) cc_final: 0.5009 (tptp) REVERT: K 273 PHE cc_start: 0.8022 (m-80) cc_final: 0.7789 (m-10) REVERT: K 274 TYR cc_start: 0.7657 (p90) cc_final: 0.6715 (p90) REVERT: K 284 HIS cc_start: 0.7882 (m-70) cc_final: 0.7415 (m-70) REVERT: K 311 TYR cc_start: 0.7428 (t80) cc_final: 0.6881 (t80) REVERT: K 343 ASP cc_start: 0.9123 (p0) cc_final: 0.8869 (p0) REVERT: K 404 PHE cc_start: 0.7247 (p90) cc_final: 0.6947 (p90) REVERT: M 234 LEU cc_start: 0.9362 (mp) cc_final: 0.9116 (pp) REVERT: M 278 TYR cc_start: 0.8578 (t80) cc_final: 0.8356 (t80) REVERT: M 280 ARG cc_start: 0.5101 (mmp-170) cc_final: 0.4632 (mmp-170) REVERT: O 237 PHE cc_start: 0.6895 (m-80) cc_final: 0.6264 (m-10) REVERT: O 271 PHE cc_start: 0.8026 (p90) cc_final: 0.7354 (p90) REVERT: O 275 CYS cc_start: 0.8607 (t) cc_final: 0.8286 (t) REVERT: O 325 TYR cc_start: 0.8843 (m-80) cc_final: 0.8487 (m-80) REVERT: O 353 TRP cc_start: 0.7073 (p90) cc_final: 0.6531 (p90) REVERT: O 431 TRP cc_start: 0.7587 (m-90) cc_final: 0.7368 (m-90) REVERT: P 43 TYR cc_start: 0.8804 (m-80) cc_final: 0.8395 (m-10) REVERT: Q 198 HIS cc_start: 0.9104 (m90) cc_final: 0.8821 (m90) REVERT: R 14 VAL cc_start: 0.7604 (p) cc_final: 0.7300 (p) REVERT: A 69 ARG cc_start: 0.8695 (mtm-85) cc_final: 0.7914 (ptp-170) REVERT: A 70 LEU cc_start: 0.8483 (pp) cc_final: 0.7955 (pp) REVERT: A 73 GLU cc_start: 0.7954 (tt0) cc_final: 0.7621 (tt0) REVERT: A 84 PHE cc_start: 0.6887 (m-10) cc_final: 0.6202 (m-80) REVERT: A 87 SER cc_start: 0.9065 (t) cc_final: 0.8626 (p) REVERT: A 94 GLU cc_start: 0.8201 (pp20) cc_final: 0.7954 (tm-30) REVERT: A 99 TYR cc_start: 0.8739 (t80) cc_final: 0.8490 (t80) REVERT: A 119 ILE cc_start: 0.8622 (mt) cc_final: 0.8363 (tp) REVERT: A 123 ASP cc_start: 0.7947 (m-30) cc_final: 0.7551 (m-30) REVERT: B 25 ASN cc_start: 0.8093 (t0) cc_final: 0.7195 (t0) REVERT: B 58 LEU cc_start: 0.8965 (pp) cc_final: 0.8634 (pp) REVERT: B 61 PHE cc_start: 0.8439 (t80) cc_final: 0.8155 (t80) REVERT: B 70 VAL cc_start: 0.8920 (m) cc_final: 0.8637 (p) REVERT: B 74 GLU cc_start: 0.8244 (tp30) cc_final: 0.7959 (tp30) REVERT: B 88 TYR cc_start: 0.7925 (m-10) cc_final: 0.7425 (m-80) REVERT: C 25 GLN cc_start: 0.7627 (tp40) cc_final: 0.7207 (tp40) REVERT: C 33 ARG cc_start: 0.8390 (pmt170) cc_final: 0.7825 (ptt-90) REVERT: C 53 LEU cc_start: 0.8627 (mp) cc_final: 0.8222 (tt) REVERT: D 65 LEU cc_start: 0.8944 (mt) cc_final: 0.8391 (pp) REVERT: D 73 PHE cc_start: 0.8187 (t80) cc_final: 0.7902 (t80) REVERT: D 76 ILE cc_start: 0.9300 (pt) cc_final: 0.8801 (pt) REVERT: E 41 TYR cc_start: 0.6714 (p90) cc_final: 0.6337 (p90) REVERT: E 56 LYS cc_start: 0.8858 (tmtt) cc_final: 0.8598 (tmtt) REVERT: E 60 LEU cc_start: 0.8228 (tp) cc_final: 0.7940 (tp) REVERT: E 64 LYS cc_start: 0.8872 (mppt) cc_final: 0.8533 (mmtm) REVERT: E 72 ARG cc_start: 0.8363 (mmt180) cc_final: 0.6573 (mmt180) REVERT: E 76 GLN cc_start: 0.8865 (pm20) cc_final: 0.8546 (pm20) REVERT: E 84 PHE cc_start: 0.6911 (m-10) cc_final: 0.6396 (m-10) REVERT: E 97 GLU cc_start: 0.7286 (mm-30) cc_final: 0.7011 (mm-30) REVERT: E 115 LYS cc_start: 0.8947 (ptpp) cc_final: 0.8659 (ptpp) REVERT: E 123 ASP cc_start: 0.7847 (m-30) cc_final: 0.7095 (m-30) REVERT: F 50 ILE cc_start: 0.8613 (pt) cc_final: 0.8149 (mm) REVERT: F 57 VAL cc_start: 0.8736 (m) cc_final: 0.8532 (p) REVERT: F 62 LEU cc_start: 0.8138 (pp) cc_final: 0.7877 (pp) REVERT: F 63 GLU cc_start: 0.8419 (pm20) cc_final: 0.8215 (pm20) REVERT: F 82 THR cc_start: 0.7640 (p) cc_final: 0.6966 (p) REVERT: G 32 LYS cc_start: 0.8831 (mmmt) cc_final: 0.8552 (mmmm) REVERT: G 34 TYR cc_start: 0.8142 (p90) cc_final: 0.7604 (p90) REVERT: G 48 LYS cc_start: 0.8987 (mmpt) cc_final: 0.8720 (mmmt) REVERT: G 52 TYR cc_start: 0.7216 (t80) cc_final: 0.6404 (t80) REVERT: G 74 ASP cc_start: 0.8025 (p0) cc_final: 0.6787 (p0) REVERT: G 83 ARG cc_start: 0.6847 (ptm-80) cc_final: 0.6639 (ptm160) REVERT: G 86 GLN cc_start: 0.6904 (mp10) cc_final: 0.6403 (mp10) REVERT: G 89 ILE cc_start: 0.8913 (mt) cc_final: 0.8677 (mp) REVERT: H 46 LYS cc_start: 0.8747 (pttm) cc_final: 0.8545 (ttpp) REVERT: H 49 LYS cc_start: 0.8540 (pttm) cc_final: 0.8172 (pttp) REVERT: H 66 ASN cc_start: 0.8124 (p0) cc_final: 0.7780 (p0) REVERT: H 74 GLU cc_start: 0.8171 (tp30) cc_final: 0.7971 (tp30) REVERT: H 82 LYS cc_start: 0.8958 (tmmt) cc_final: 0.8535 (tmtt) REVERT: H 88 LYS cc_start: 0.9291 (ptpp) cc_final: 0.9042 (ptmm) REVERT: H 105 LEU cc_start: 0.9054 (pp) cc_final: 0.8797 (pp) REVERT: H 112 HIS cc_start: 0.7659 (m90) cc_final: 0.7186 (m90) outliers start: 0 outliers final: 0 residues processed: 517 average time/residue: 0.1675 time to fit residues: 124.8551 Evaluate side-chains 459 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 459 time to evaluate : 0.517 ------------------------------------------------------------------------------- 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: 5.9990 chunk 211 optimal weight: 0.5980 chunk 134 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 28 optimal weight: 0.4980 chunk 41 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 201 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 212 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 166 ASN K 222 HIS ** K 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 245 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** ** O 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 243 ASN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.122865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.096843 restraints weight = 88673.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.100188 restraints weight = 50479.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.102350 restraints weight = 32716.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.103755 restraints weight = 23498.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.104685 restraints weight = 18382.322| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.6569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 22580 Z= 0.191 Angle : 0.878 13.467 31707 Z= 0.471 Chirality : 0.048 0.363 3556 Planarity : 0.006 0.111 3001 Dihedral : 28.298 128.170 5372 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 21.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Rotamer: Outliers : 0.06 % Allowed : 3.26 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.80 (0.18), residues: 1866 helix: -1.03 (0.16), residues: 974 sheet: -1.90 (0.84), residues: 33 loop : -2.88 (0.20), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 428 TYR 0.028 0.002 TYR K 325 PHE 0.051 0.003 PHE H 73 TRP 0.039 0.002 TRP O 353 HIS 0.019 0.001 HIS Q 240 Details of bonding type rmsd covalent geometry : bond 0.00416 (22580) covalent geometry : angle 0.87832 (31707) hydrogen bonds : bond 0.05308 ( 1048) hydrogen bonds : angle 5.05657 ( 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 524 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 523 time to evaluate : 0.460 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 209 LYS cc_start: 0.8628 (mmpt) cc_final: 0.8189 (mmpt) REVERT: K 273 PHE cc_start: 0.8087 (m-10) cc_final: 0.7649 (m-10) REVERT: K 276 MET cc_start: 0.8197 (tmm) cc_final: 0.7995 (tmm) REVERT: K 284 HIS cc_start: 0.7740 (m-70) cc_final: 0.7275 (m-70) REVERT: K 311 TYR cc_start: 0.6918 (t80) cc_final: 0.6595 (t80) REVERT: K 319 LEU cc_start: 0.8320 (pp) cc_final: 0.8094 (pt) REVERT: K 325 TYR cc_start: 0.8232 (m-80) cc_final: 0.7917 (m-80) REVERT: K 343 ASP cc_start: 0.9098 (p0) cc_final: 0.8855 (p0) REVERT: K 404 PHE cc_start: 0.7165 (p90) cc_final: 0.6859 (p90) REVERT: K 415 ARG cc_start: 0.8003 (mtm-85) cc_final: 0.7696 (mtt180) REVERT: M 215 LEU cc_start: 0.7890 (pt) cc_final: 0.7675 (pt) REVERT: M 234 LEU cc_start: 0.9419 (mp) cc_final: 0.9206 (pp) REVERT: M 280 ARG cc_start: 0.4892 (mmp-170) cc_final: 0.4367 (mmp-170) REVERT: O 237 PHE cc_start: 0.6997 (m-80) cc_final: 0.6361 (m-80) REVERT: O 265 TYR cc_start: 0.7264 (p90) cc_final: 0.7037 (p90) REVERT: O 271 PHE cc_start: 0.8107 (p90) cc_final: 0.7478 (p90) REVERT: O 275 CYS cc_start: 0.8697 (t) cc_final: 0.8301 (t) REVERT: O 325 TYR cc_start: 0.8785 (m-80) cc_final: 0.8519 (m-80) REVERT: O 353 TRP cc_start: 0.7123 (p90) cc_final: 0.6653 (p90) REVERT: P 43 TYR cc_start: 0.8798 (m-80) cc_final: 0.8389 (m-10) REVERT: Q 164 MET cc_start: 0.6077 (mtt) cc_final: 0.5394 (mtt) REVERT: Q 198 HIS cc_start: 0.9137 (m90) cc_final: 0.8825 (m90) REVERT: Q 235 ARG cc_start: 0.6476 (tmm-80) cc_final: 0.6067 (tmm-80) REVERT: Q 326 ILE cc_start: 0.8247 (pt) cc_final: 0.8023 (pt) REVERT: R 14 VAL cc_start: 0.7431 (p) cc_final: 0.7145 (p) REVERT: A 73 GLU cc_start: 0.7969 (tt0) cc_final: 0.7673 (tt0) REVERT: A 83 ARG cc_start: 0.7399 (mmt180) cc_final: 0.7179 (mmt180) REVERT: A 87 SER cc_start: 0.9074 (t) cc_final: 0.8700 (p) REVERT: A 99 TYR cc_start: 0.8707 (t80) cc_final: 0.8476 (t80) REVERT: A 123 ASP cc_start: 0.7817 (m-30) cc_final: 0.7336 (m-30) REVERT: B 36 ARG cc_start: 0.8683 (ttp80) cc_final: 0.8372 (ptp90) REVERT: B 50 ILE cc_start: 0.8498 (tp) cc_final: 0.8244 (tp) REVERT: B 61 PHE cc_start: 0.8402 (t80) cc_final: 0.8114 (t80) REVERT: B 63 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7707 (pm20) REVERT: B 74 GLU cc_start: 0.8302 (tp30) cc_final: 0.7976 (tp30) REVERT: B 88 TYR cc_start: 0.7732 (m-10) cc_final: 0.7477 (m-80) REVERT: C 32 LYS cc_start: 0.8604 (tptt) cc_final: 0.8276 (tppt) REVERT: C 33 ARG cc_start: 0.8421 (pmt170) cc_final: 0.7920 (ptt-90) REVERT: C 34 TYR cc_start: 0.8436 (m-80) cc_final: 0.8178 (m-80) REVERT: C 35 LEU cc_start: 0.8522 (mm) cc_final: 0.8282 (mt) REVERT: C 57 LEU cc_start: 0.8529 (mt) cc_final: 0.8162 (mt) REVERT: C 60 LEU cc_start: 0.8923 (tp) cc_final: 0.8550 (tp) REVERT: C 67 LEU cc_start: 0.9163 (mm) cc_final: 0.8711 (mm) REVERT: C 79 ARG cc_start: 0.7464 (ppt170) cc_final: 0.7096 (pmt-80) REVERT: C 84 HIS cc_start: 0.7355 (p90) cc_final: 0.6954 (p-80) REVERT: C 85 LEU cc_start: 0.8738 (tp) cc_final: 0.8505 (tp) REVERT: D 47 VAL cc_start: 0.8597 (t) cc_final: 0.7898 (t) REVERT: D 49 LYS cc_start: 0.8443 (mtmm) cc_final: 0.8104 (ptpt) REVERT: D 51 THR cc_start: 0.9016 (p) cc_final: 0.8587 (p) REVERT: D 73 PHE cc_start: 0.8182 (t80) cc_final: 0.7911 (t80) REVERT: D 76 ILE cc_start: 0.9120 (pt) cc_final: 0.8680 (pt) REVERT: D 98 GLN cc_start: 0.8112 (mp10) cc_final: 0.7762 (mp10) REVERT: E 41 TYR cc_start: 0.6688 (p90) cc_final: 0.6298 (p90) REVERT: E 49 ARG cc_start: 0.8352 (pmt-80) cc_final: 0.7865 (pmt-80) REVERT: E 51 ILE cc_start: 0.8423 (mm) cc_final: 0.8114 (mm) REVERT: E 54 PHE cc_start: 0.7118 (p90) cc_final: 0.6741 (p90) REVERT: E 56 LYS cc_start: 0.8939 (tmtt) cc_final: 0.8691 (tmtt) REVERT: E 60 LEU cc_start: 0.8213 (tp) cc_final: 0.7965 (tp) REVERT: E 64 LYS cc_start: 0.8839 (mppt) cc_final: 0.8527 (mmtm) REVERT: E 100 LEU cc_start: 0.8848 (pt) cc_final: 0.8619 (pt) REVERT: E 103 LEU cc_start: 0.8696 (pp) cc_final: 0.8482 (pp) REVERT: E 108 ASN cc_start: 0.8928 (t0) cc_final: 0.8482 (t0) REVERT: E 115 LYS cc_start: 0.8761 (ptpp) cc_final: 0.8559 (ptpp) REVERT: E 120 GLN cc_start: 0.8386 (pm20) cc_final: 0.8135 (pm20) REVERT: E 122 LYS cc_start: 0.8917 (mppt) cc_final: 0.8664 (mmmt) REVERT: E 125 LYS cc_start: 0.9088 (mtmt) cc_final: 0.8362 (mtmm) REVERT: F 30 THR cc_start: 0.8725 (p) cc_final: 0.8086 (p) REVERT: F 50 ILE cc_start: 0.8601 (pt) cc_final: 0.8157 (mm) REVERT: F 57 VAL cc_start: 0.8831 (m) cc_final: 0.8616 (p) REVERT: F 59 LYS cc_start: 0.8459 (ptpp) cc_final: 0.8173 (pttm) REVERT: F 62 LEU cc_start: 0.8197 (pp) cc_final: 0.7976 (pp) REVERT: F 63 GLU cc_start: 0.8537 (pm20) cc_final: 0.8163 (pm20) REVERT: F 82 THR cc_start: 0.7768 (p) cc_final: 0.7040 (p) REVERT: F 87 VAL cc_start: 0.8579 (t) cc_final: 0.8317 (t) REVERT: G 34 TYR cc_start: 0.8069 (p90) cc_final: 0.7809 (p90) REVERT: G 37 ARG cc_start: 0.7785 (ptt180) cc_final: 0.7477 (ptt180) REVERT: G 52 TYR cc_start: 0.7233 (t80) cc_final: 0.6828 (t80) REVERT: G 59 TYR cc_start: 0.7492 (p90) cc_final: 0.7157 (p90) REVERT: G 74 ASP cc_start: 0.8174 (p0) cc_final: 0.6346 (p0) REVERT: G 86 GLN cc_start: 0.6936 (mp10) cc_final: 0.6580 (mp10) REVERT: G 89 ILE cc_start: 0.8987 (mt) cc_final: 0.8721 (mp) REVERT: H 49 LYS cc_start: 0.8523 (pttm) cc_final: 0.8189 (pttp) REVERT: H 52 HIS cc_start: 0.7968 (t70) cc_final: 0.7730 (t70) REVERT: H 62 MET cc_start: 0.8100 (mmp) cc_final: 0.7845 (mmm) REVERT: H 66 ASN cc_start: 0.8116 (p0) cc_final: 0.7723 (p0) REVERT: H 72 ILE cc_start: 0.7768 (tt) cc_final: 0.7128 (tt) REVERT: H 74 GLU cc_start: 0.8105 (tp30) cc_final: 0.7788 (tp30) REVERT: H 79 GLU cc_start: 0.7727 (pm20) cc_final: 0.7503 (pm20) REVERT: H 82 LYS cc_start: 0.8867 (tmmt) cc_final: 0.8555 (tmtt) REVERT: H 88 LYS cc_start: 0.9252 (ptpp) cc_final: 0.9045 (ptmm) REVERT: H 112 HIS cc_start: 0.7767 (m90) cc_final: 0.7250 (m90) REVERT: H 116 GLU cc_start: 0.6912 (pp20) cc_final: 0.5970 (pp20) REVERT: H 124 TYR cc_start: 0.7416 (p90) cc_final: 0.6950 (p90) outliers start: 1 outliers final: 0 residues processed: 523 average time/residue: 0.1684 time to fit residues: 126.0523 Evaluate side-chains 477 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 476 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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: 3.9990 chunk 37 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 85 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 95 optimal weight: 7.9990 chunk 145 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 166 ASN ** K 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 260 ASN ** O 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN E 68 GLN E 85 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.123927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.098247 restraints weight = 88818.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.101543 restraints weight = 50920.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.103661 restraints weight = 33072.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.105043 restraints weight = 23817.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.105989 restraints weight = 18683.369| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.6936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 22580 Z= 0.186 Angle : 0.889 12.861 31707 Z= 0.476 Chirality : 0.048 0.296 3556 Planarity : 0.007 0.149 3001 Dihedral : 28.236 129.819 5372 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 21.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Rotamer: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.80 (0.18), residues: 1866 helix: -0.98 (0.16), residues: 980 sheet: -1.63 (0.85), residues: 33 loop : -2.98 (0.20), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 22 TYR 0.030 0.002 TYR K 325 PHE 0.044 0.003 PHE H 73 TRP 0.038 0.002 TRP O 353 HIS 0.016 0.001 HIS D 112 Details of bonding type rmsd covalent geometry : bond 0.00405 (22580) covalent geometry : angle 0.88883 (31707) hydrogen bonds : bond 0.05191 ( 1048) hydrogen bonds : angle 5.04309 ( 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 527 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 527 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 209 LYS cc_start: 0.8592 (mmpt) cc_final: 0.8167 (mmpt) REVERT: K 273 PHE cc_start: 0.7996 (m-10) cc_final: 0.7567 (m-10) REVERT: K 284 HIS cc_start: 0.7940 (m-70) cc_final: 0.7368 (m-70) REVERT: K 319 LEU cc_start: 0.8240 (pp) cc_final: 0.7989 (pt) REVERT: K 325 TYR cc_start: 0.8106 (m-80) cc_final: 0.7880 (m-80) REVERT: K 343 ASP cc_start: 0.9043 (p0) cc_final: 0.8802 (p0) REVERT: K 404 PHE cc_start: 0.7098 (p90) cc_final: 0.6796 (p90) REVERT: M 215 LEU cc_start: 0.7815 (pt) cc_final: 0.7397 (pt) REVERT: M 234 LEU cc_start: 0.9437 (mp) cc_final: 0.9209 (pp) REVERT: M 235 ARG cc_start: 0.8702 (ptt90) cc_final: 0.8112 (ptt90) REVERT: O 236 PHE cc_start: 0.5965 (m-80) cc_final: 0.5191 (m-80) REVERT: O 237 PHE cc_start: 0.6940 (m-80) cc_final: 0.6600 (m-80) REVERT: O 271 PHE cc_start: 0.8178 (p90) cc_final: 0.7561 (p90) REVERT: O 323 PHE cc_start: 0.8610 (t80) cc_final: 0.8378 (t80) REVERT: O 325 TYR cc_start: 0.9002 (m-80) cc_final: 0.8533 (m-80) REVERT: O 353 TRP cc_start: 0.6899 (p90) cc_final: 0.6389 (p90) REVERT: P 43 TYR cc_start: 0.8778 (m-80) cc_final: 0.8408 (m-10) REVERT: Q 147 TYR cc_start: 0.6915 (m-80) cc_final: 0.6687 (m-10) REVERT: Q 198 HIS cc_start: 0.9120 (m90) cc_final: 0.8827 (m-70) REVERT: Q 235 ARG cc_start: 0.6312 (tmm-80) cc_final: 0.5862 (tmm-80) REVERT: R 14 VAL cc_start: 0.7380 (p) cc_final: 0.7085 (p) REVERT: A 69 ARG cc_start: 0.8580 (mtm-85) cc_final: 0.7776 (ptp-170) REVERT: A 73 GLU cc_start: 0.7938 (tt0) cc_final: 0.7637 (tt0) REVERT: A 84 PHE cc_start: 0.6768 (m-80) cc_final: 0.6312 (m-80) REVERT: A 87 SER cc_start: 0.9013 (t) cc_final: 0.8661 (p) REVERT: A 99 TYR cc_start: 0.8632 (t80) cc_final: 0.8416 (t80) REVERT: A 107 THR cc_start: 0.8290 (p) cc_final: 0.7618 (p) REVERT: A 119 ILE cc_start: 0.8891 (tp) cc_final: 0.8260 (tp) REVERT: A 121 LYS cc_start: 0.8765 (tptm) cc_final: 0.8430 (tppt) REVERT: A 124 ILE cc_start: 0.8294 (mp) cc_final: 0.8038 (mp) REVERT: B 25 ASN cc_start: 0.7950 (t0) cc_final: 0.7531 (t0) REVERT: B 50 ILE cc_start: 0.8415 (tp) cc_final: 0.8139 (tp) REVERT: B 53 GLU cc_start: 0.8518 (pm20) cc_final: 0.8242 (pm20) REVERT: B 59 LYS cc_start: 0.8418 (tptp) cc_final: 0.8065 (tppt) REVERT: B 62 LEU cc_start: 0.8390 (mm) cc_final: 0.8161 (mm) REVERT: B 63 GLU cc_start: 0.8131 (pm20) cc_final: 0.7261 (pm20) REVERT: B 70 VAL cc_start: 0.8967 (m) cc_final: 0.8657 (p) REVERT: C 32 LYS cc_start: 0.8553 (tptt) cc_final: 0.8248 (tppt) REVERT: C 67 LEU cc_start: 0.9110 (mm) cc_final: 0.8505 (mm) REVERT: C 79 ARG cc_start: 0.7379 (ppt170) cc_final: 0.7151 (ptt-90) REVERT: C 85 LEU cc_start: 0.8680 (tp) cc_final: 0.8463 (tp) REVERT: D 49 LYS cc_start: 0.8468 (mtmm) cc_final: 0.8142 (mttt) REVERT: D 73 PHE cc_start: 0.8126 (t80) cc_final: 0.7831 (t80) REVERT: D 76 ILE cc_start: 0.9115 (pt) cc_final: 0.8656 (pt) REVERT: D 116 GLU cc_start: 0.8122 (pm20) cc_final: 0.7512 (pm20) REVERT: E 41 TYR cc_start: 0.6733 (p90) cc_final: 0.6337 (p90) REVERT: E 49 ARG cc_start: 0.8365 (pmt-80) cc_final: 0.7910 (pmt-80) REVERT: E 56 LYS cc_start: 0.8939 (tmtt) cc_final: 0.8646 (tmtt) REVERT: E 60 LEU cc_start: 0.8180 (tp) cc_final: 0.7909 (tp) REVERT: E 97 GLU cc_start: 0.7087 (mm-30) cc_final: 0.6857 (mm-30) REVERT: E 108 ASN cc_start: 0.8893 (t0) cc_final: 0.8514 (t0) REVERT: E 123 ASP cc_start: 0.8216 (m-30) cc_final: 0.7972 (m-30) REVERT: F 50 ILE cc_start: 0.8594 (pt) cc_final: 0.8198 (tp) REVERT: F 63 GLU cc_start: 0.8521 (pm20) cc_final: 0.8286 (pm20) REVERT: F 79 LYS cc_start: 0.6921 (pttm) cc_final: 0.6330 (ptmt) REVERT: F 82 THR cc_start: 0.7620 (p) cc_final: 0.6870 (p) REVERT: F 87 VAL cc_start: 0.8672 (t) cc_final: 0.8328 (t) REVERT: F 95 ARG cc_start: 0.8273 (ttp80) cc_final: 0.7800 (ttp-110) REVERT: G 32 LYS cc_start: 0.8602 (tptm) cc_final: 0.8351 (mmmt) REVERT: G 38 HIS cc_start: 0.7625 (m-70) cc_final: 0.7341 (m90) REVERT: G 52 TYR cc_start: 0.7080 (t80) cc_final: 0.6787 (t80) REVERT: G 74 ASP cc_start: 0.7966 (p0) cc_final: 0.7669 (p0) REVERT: G 86 GLN cc_start: 0.7172 (mp10) cc_final: 0.6745 (mp10) REVERT: G 89 ILE cc_start: 0.9019 (mt) cc_final: 0.8720 (mp) REVERT: H 49 LYS cc_start: 0.8541 (pttm) cc_final: 0.8193 (pttp) REVERT: H 52 HIS cc_start: 0.7955 (t70) cc_final: 0.7669 (t70) REVERT: H 62 MET cc_start: 0.8104 (mmp) cc_final: 0.7812 (mmm) REVERT: H 64 ILE cc_start: 0.8834 (pt) cc_final: 0.8442 (pt) REVERT: H 66 ASN cc_start: 0.8210 (p0) cc_final: 0.7785 (p0) REVERT: H 72 ILE cc_start: 0.7499 (tt) cc_final: 0.7164 (tt) REVERT: H 74 GLU cc_start: 0.7921 (tp30) cc_final: 0.7666 (tp30) REVERT: H 82 LYS cc_start: 0.8897 (tmmt) cc_final: 0.8552 (tmtt) REVERT: H 105 LEU cc_start: 0.9033 (pp) cc_final: 0.8733 (pp) REVERT: H 112 HIS cc_start: 0.7671 (m90) cc_final: 0.7264 (m90) REVERT: H 124 TYR cc_start: 0.7397 (p90) cc_final: 0.6927 (p90) outliers start: 0 outliers final: 0 residues processed: 527 average time/residue: 0.1708 time to fit residues: 129.4723 Evaluate side-chains 480 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 480 time to evaluate : 0.753 ------------------------------------------------------------------------------- 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: 10.0000 chunk 145 optimal weight: 0.6980 chunk 188 optimal weight: 2.9990 chunk 87 optimal weight: 9.9990 chunk 156 optimal weight: 0.7980 chunk 205 optimal weight: 5.9990 chunk 194 optimal weight: 9.9990 chunk 1 optimal weight: 0.3980 chunk 178 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 chunk 4 optimal weight: 9.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 166 ASN ** K 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 260 ASN ** O 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN E 68 GLN E 85 GLN ** E 108 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 = 0.4084 r_free = 0.4084 target = 0.120972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.095293 restraints weight = 88153.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.098513 restraints weight = 50882.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.100621 restraints weight = 33269.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.101995 restraints weight = 24016.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.102918 restraints weight = 18837.149| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.7243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 22580 Z= 0.228 Angle : 0.921 12.633 31707 Z= 0.494 Chirality : 0.049 0.305 3556 Planarity : 0.007 0.079 3001 Dihedral : 28.263 127.427 5372 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 25.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.83 % Favored : 89.17 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.76 (0.19), residues: 1866 helix: -1.01 (0.16), residues: 979 sheet: -1.64 (0.81), residues: 33 loop : -2.87 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 119 TYR 0.063 0.003 TYR B 88 PHE 0.044 0.003 PHE E 54 TRP 0.075 0.003 TRP O 353 HIS 0.021 0.002 HIS Q 240 Details of bonding type rmsd covalent geometry : bond 0.00505 (22580) covalent geometry : angle 0.92077 (31707) hydrogen bonds : bond 0.05854 ( 1048) hydrogen bonds : angle 5.14320 ( 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 521 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 521 time to evaluate : 0.515 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 209 LYS cc_start: 0.8629 (mmpt) cc_final: 0.8192 (mmpt) REVERT: K 273 PHE cc_start: 0.7882 (m-10) cc_final: 0.7335 (m-10) REVERT: K 284 HIS cc_start: 0.7921 (m-70) cc_final: 0.7480 (m-70) REVERT: K 325 TYR cc_start: 0.8087 (m-80) cc_final: 0.7862 (m-80) REVERT: K 327 LEU cc_start: 0.9290 (mt) cc_final: 0.9089 (mt) REVERT: K 404 PHE cc_start: 0.7256 (p90) cc_final: 0.6973 (p90) REVERT: M 232 PHE cc_start: 0.9133 (p90) cc_final: 0.8629 (p90) REVERT: M 233 ASN cc_start: 0.8604 (p0) cc_final: 0.8366 (p0) REVERT: M 234 LEU cc_start: 0.9457 (mp) cc_final: 0.9245 (mt) REVERT: M 237 GLN cc_start: 0.8725 (tm-30) cc_final: 0.8473 (tm-30) REVERT: O 237 PHE cc_start: 0.7139 (m-80) cc_final: 0.6515 (m-80) REVERT: O 265 TYR cc_start: 0.7301 (p90) cc_final: 0.6950 (p90) REVERT: O 271 PHE cc_start: 0.8133 (p90) cc_final: 0.7545 (p90) REVERT: O 275 CYS cc_start: 0.8670 (t) cc_final: 0.8335 (t) REVERT: O 325 TYR cc_start: 0.8933 (m-80) cc_final: 0.8215 (m-80) REVERT: P 43 TYR cc_start: 0.8767 (m-80) cc_final: 0.8437 (m-10) REVERT: Q 147 TYR cc_start: 0.6814 (m-80) cc_final: 0.6514 (m-10) REVERT: Q 198 HIS cc_start: 0.9096 (m90) cc_final: 0.8788 (m90) REVERT: Q 326 ILE cc_start: 0.8182 (pt) cc_final: 0.7965 (pt) REVERT: R 14 VAL cc_start: 0.7287 (p) cc_final: 0.7036 (p) REVERT: R 100 HIS cc_start: 0.8468 (t70) cc_final: 0.8264 (t-90) REVERT: A 69 ARG cc_start: 0.8626 (mtm-85) cc_final: 0.7765 (ptp-170) REVERT: A 78 PHE cc_start: 0.7376 (m-80) cc_final: 0.7111 (m-80) REVERT: A 87 SER cc_start: 0.9066 (t) cc_final: 0.8806 (p) REVERT: A 119 ILE cc_start: 0.9079 (tp) cc_final: 0.8668 (tp) REVERT: A 120 GLN cc_start: 0.7814 (pm20) cc_final: 0.7556 (pt0) REVERT: A 121 LYS cc_start: 0.8749 (tptm) cc_final: 0.8305 (tppp) REVERT: A 122 LYS cc_start: 0.8773 (ptpt) cc_final: 0.8522 (mtmm) REVERT: B 25 ASN cc_start: 0.8049 (t0) cc_final: 0.7656 (t0) REVERT: B 53 GLU cc_start: 0.8579 (pm20) cc_final: 0.8217 (pm20) REVERT: B 61 PHE cc_start: 0.8437 (t80) cc_final: 0.8021 (t80) REVERT: B 62 LEU cc_start: 0.8424 (mm) cc_final: 0.8167 (mm) REVERT: B 63 GLU cc_start: 0.8093 (pm20) cc_final: 0.7452 (pm20) REVERT: B 84 LEU cc_start: 0.8513 (mm) cc_final: 0.8247 (mm) REVERT: B 88 TYR cc_start: 0.7377 (m-80) cc_final: 0.7101 (m-80) REVERT: B 96 THR cc_start: 0.7417 (p) cc_final: 0.7052 (p) REVERT: C 25 GLN cc_start: 0.7813 (tp40) cc_final: 0.7613 (tp40) REVERT: C 33 ARG cc_start: 0.8433 (pmt170) cc_final: 0.8044 (ptt-90) REVERT: C 34 TYR cc_start: 0.8446 (m-80) cc_final: 0.8188 (m-10) REVERT: C 36 LYS cc_start: 0.8881 (mptt) cc_final: 0.8313 (mmmm) REVERT: C 51 ILE cc_start: 0.8554 (pt) cc_final: 0.8344 (pt) REVERT: C 60 LEU cc_start: 0.8734 (mm) cc_final: 0.8415 (tp) REVERT: C 79 ARG cc_start: 0.7614 (ppt170) cc_final: 0.7117 (pmt-80) REVERT: C 84 HIS cc_start: 0.6959 (p90) cc_final: 0.6255 (p90) REVERT: D 47 VAL cc_start: 0.8702 (t) cc_final: 0.8118 (t) REVERT: D 51 THR cc_start: 0.8899 (p) cc_final: 0.8569 (p) REVERT: D 60 LYS cc_start: 0.8564 (ptpp) cc_final: 0.8204 (ptpp) REVERT: D 73 PHE cc_start: 0.8139 (t80) cc_final: 0.7831 (t80) REVERT: D 76 ILE cc_start: 0.9102 (pt) cc_final: 0.8625 (pt) REVERT: D 99 THR cc_start: 0.8217 (p) cc_final: 0.7150 (p) REVERT: D 102 ARG cc_start: 0.7658 (ptt90) cc_final: 0.7129 (ppt90) REVERT: D 103 LEU cc_start: 0.8691 (pp) cc_final: 0.8376 (pp) REVERT: D 109 LEU cc_start: 0.8160 (pt) cc_final: 0.7885 (pt) REVERT: E 41 TYR cc_start: 0.6842 (p90) cc_final: 0.6420 (p90) REVERT: E 49 ARG cc_start: 0.8615 (pmt-80) cc_final: 0.8259 (pmt-80) REVERT: E 54 PHE cc_start: 0.7215 (p90) cc_final: 0.6726 (p90) REVERT: E 56 LYS cc_start: 0.8992 (tmtt) cc_final: 0.8760 (tmtt) REVERT: E 60 LEU cc_start: 0.8561 (tp) cc_final: 0.7452 (tp) REVERT: E 64 LYS cc_start: 0.8831 (mppt) cc_final: 0.8444 (mmmm) REVERT: E 67 PHE cc_start: 0.7842 (p90) cc_final: 0.7438 (p90) REVERT: E 70 LEU cc_start: 0.8321 (mm) cc_final: 0.7650 (mm) REVERT: E 72 ARG cc_start: 0.8384 (mmt180) cc_final: 0.8063 (mmp80) REVERT: E 79 LYS cc_start: 0.8444 (tmtt) cc_final: 0.8207 (tmtt) REVERT: E 84 PHE cc_start: 0.6975 (m-10) cc_final: 0.6253 (m-80) REVERT: E 103 LEU cc_start: 0.8689 (pp) cc_final: 0.8478 (pp) REVERT: E 115 LYS cc_start: 0.9004 (ptpt) cc_final: 0.8787 (ptpt) REVERT: F 63 GLU cc_start: 0.8513 (pm20) cc_final: 0.8111 (pm20) REVERT: F 79 LYS cc_start: 0.7374 (pttm) cc_final: 0.6845 (ptmt) REVERT: F 82 THR cc_start: 0.7486 (p) cc_final: 0.6765 (p) REVERT: F 87 VAL cc_start: 0.8667 (t) cc_final: 0.8289 (p) REVERT: F 95 ARG cc_start: 0.8136 (ttp80) cc_final: 0.7880 (ttp-110) REVERT: G 38 HIS cc_start: 0.7783 (m-70) cc_final: 0.7494 (m90) REVERT: G 59 TYR cc_start: 0.7403 (p90) cc_final: 0.6970 (p90) REVERT: G 70 ASN cc_start: 0.7737 (p0) cc_final: 0.7370 (p0) REVERT: G 74 ASP cc_start: 0.7945 (p0) cc_final: 0.7698 (p0) REVERT: G 86 GLN cc_start: 0.7141 (mp10) cc_final: 0.6713 (mp10) REVERT: G 96 ASP cc_start: 0.8022 (p0) cc_final: 0.7802 (p0) REVERT: H 46 LYS cc_start: 0.9018 (tmmt) cc_final: 0.8693 (pttp) REVERT: H 49 LYS cc_start: 0.8783 (pttm) cc_final: 0.8580 (pttp) REVERT: H 52 HIS cc_start: 0.8118 (t70) cc_final: 0.7829 (t70) REVERT: H 62 MET cc_start: 0.8268 (mmp) cc_final: 0.8010 (mmm) REVERT: H 66 ASN cc_start: 0.8214 (p0) cc_final: 0.7827 (p0) REVERT: H 72 ILE cc_start: 0.7602 (tt) cc_final: 0.6970 (tt) REVERT: H 76 ILE cc_start: 0.8219 (tp) cc_final: 0.7960 (tp) REVERT: H 82 LYS cc_start: 0.8838 (tmmt) cc_final: 0.8478 (tmtt) REVERT: H 112 HIS cc_start: 0.7815 (m90) cc_final: 0.7321 (m90) REVERT: H 116 GLU cc_start: 0.6801 (pp20) cc_final: 0.6371 (pp20) REVERT: H 123 LYS cc_start: 0.8582 (mtmm) cc_final: 0.8375 (ptpp) REVERT: H 124 TYR cc_start: 0.7532 (p90) cc_final: 0.7070 (p90) outliers start: 0 outliers final: 0 residues processed: 521 average time/residue: 0.1638 time to fit residues: 122.7016 Evaluate side-chains 476 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 476 time to evaluate : 0.674 ------------------------------------------------------------------------------- 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: 10.0000 chunk 198 optimal weight: 0.6980 chunk 197 optimal weight: 0.0570 chunk 174 optimal weight: 0.9990 chunk 145 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 204 optimal weight: 0.9980 chunk 163 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 chunk 71 optimal weight: 0.6980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 166 ASN ** K 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 260 ASN ** O 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN E 55 GLN E 68 GLN E 85 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.124344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.098171 restraints weight = 88540.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.101477 restraints weight = 50989.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.103647 restraints weight = 33315.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.105059 restraints weight = 23981.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.105995 restraints weight = 18815.778| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.7532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 22580 Z= 0.188 Angle : 0.912 14.388 31707 Z= 0.485 Chirality : 0.049 0.292 3556 Planarity : 0.006 0.060 3001 Dihedral : 28.223 130.288 5372 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 22.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.66 (0.19), residues: 1866 helix: -0.91 (0.16), residues: 964 sheet: -1.52 (0.83), residues: 33 loop : -2.82 (0.20), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 119 TYR 0.046 0.003 TYR B 88 PHE 0.038 0.002 PHE E 54 TRP 0.080 0.003 TRP O 353 HIS 0.020 0.002 HIS Q 240 Details of bonding type rmsd covalent geometry : bond 0.00412 (22580) covalent geometry : angle 0.91153 (31707) hydrogen bonds : bond 0.05164 ( 1048) hydrogen bonds : angle 5.07810 ( 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 519 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 519 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 209 LYS cc_start: 0.8557 (mmpt) cc_final: 0.8096 (mmpt) REVERT: K 273 PHE cc_start: 0.7755 (m-10) cc_final: 0.7327 (m-10) REVERT: K 281 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8387 (mm-30) REVERT: K 284 HIS cc_start: 0.7919 (m-70) cc_final: 0.7404 (m-70) REVERT: K 319 LEU cc_start: 0.8280 (pp) cc_final: 0.8020 (pt) REVERT: K 325 TYR cc_start: 0.8082 (m-80) cc_final: 0.7819 (m-80) REVERT: K 376 MET cc_start: 0.8868 (pmm) cc_final: 0.8489 (pmm) REVERT: K 404 PHE cc_start: 0.7160 (p90) cc_final: 0.6875 (p90) REVERT: M 232 PHE cc_start: 0.9090 (p90) cc_final: 0.8520 (p90) REVERT: M 233 ASN cc_start: 0.8661 (p0) cc_final: 0.8460 (p0) REVERT: M 237 GLN cc_start: 0.8747 (tm-30) cc_final: 0.8525 (tm-30) REVERT: M 279 TRP cc_start: 0.8523 (t60) cc_final: 0.8111 (t60) REVERT: O 237 PHE cc_start: 0.6972 (m-80) cc_final: 0.6710 (m-80) REVERT: O 265 TYR cc_start: 0.7262 (p90) cc_final: 0.6920 (p90) REVERT: O 271 PHE cc_start: 0.8147 (p90) cc_final: 0.7570 (p90) REVERT: O 353 TRP cc_start: 0.6690 (p90) cc_final: 0.6246 (p90) REVERT: P 43 TYR cc_start: 0.8748 (m-80) cc_final: 0.8406 (m-10) REVERT: Q 147 TYR cc_start: 0.6781 (m-80) cc_final: 0.6559 (m-10) REVERT: Q 198 HIS cc_start: 0.9092 (m90) cc_final: 0.8767 (m-70) REVERT: R 14 VAL cc_start: 0.7559 (p) cc_final: 0.7325 (p) REVERT: R 100 HIS cc_start: 0.8372 (t70) cc_final: 0.8162 (t-90) REVERT: A 69 ARG cc_start: 0.8637 (mtm-85) cc_final: 0.7760 (ptp-170) REVERT: A 82 LEU cc_start: 0.8929 (mt) cc_final: 0.8475 (tp) REVERT: A 83 ARG cc_start: 0.7020 (mmt180) cc_final: 0.6794 (mmt-90) REVERT: A 87 SER cc_start: 0.9017 (t) cc_final: 0.8775 (p) REVERT: A 115 LYS cc_start: 0.9432 (ptpp) cc_final: 0.9224 (ptpp) REVERT: A 119 ILE cc_start: 0.9067 (tp) cc_final: 0.8786 (tp) REVERT: A 123 ASP cc_start: 0.7110 (t70) cc_final: 0.6516 (t0) REVERT: B 25 ASN cc_start: 0.8212 (t160) cc_final: 0.7807 (t0) REVERT: B 45 ARG cc_start: 0.7984 (tpt170) cc_final: 0.7727 (tpt170) REVERT: B 50 ILE cc_start: 0.8314 (tp) cc_final: 0.7968 (tp) REVERT: B 59 LYS cc_start: 0.8408 (tptp) cc_final: 0.8173 (tppt) REVERT: B 61 PHE cc_start: 0.8411 (t80) cc_final: 0.8137 (t80) REVERT: B 62 LEU cc_start: 0.8394 (mm) cc_final: 0.8120 (mm) REVERT: B 63 GLU cc_start: 0.8088 (pm20) cc_final: 0.7376 (pm20) REVERT: B 70 VAL cc_start: 0.9001 (m) cc_final: 0.8680 (p) REVERT: B 84 LEU cc_start: 0.8489 (mm) cc_final: 0.8194 (mm) REVERT: B 96 THR cc_start: 0.7232 (p) cc_final: 0.6842 (p) REVERT: C 34 TYR cc_start: 0.8337 (m-80) cc_final: 0.8017 (m-80) REVERT: C 57 LEU cc_start: 0.8556 (mt) cc_final: 0.8304 (mt) REVERT: C 79 ARG cc_start: 0.7453 (ppt170) cc_final: 0.7246 (pmt-80) REVERT: D 47 VAL cc_start: 0.8657 (t) cc_final: 0.7947 (t) REVERT: D 49 LYS cc_start: 0.8497 (mtmm) cc_final: 0.8224 (mttt) REVERT: D 51 THR cc_start: 0.8921 (p) cc_final: 0.8631 (p) REVERT: D 60 LYS cc_start: 0.8538 (ptpp) cc_final: 0.8307 (ptpp) REVERT: D 64 ILE cc_start: 0.8431 (mm) cc_final: 0.8184 (mp) REVERT: D 76 ILE cc_start: 0.9127 (pt) cc_final: 0.8650 (pt) REVERT: E 41 TYR cc_start: 0.6872 (p90) cc_final: 0.6414 (p90) REVERT: E 46 VAL cc_start: 0.5444 (m) cc_final: 0.4362 (p) REVERT: E 49 ARG cc_start: 0.8607 (pmt-80) cc_final: 0.8022 (pmt-80) REVERT: E 51 ILE cc_start: 0.8619 (mm) cc_final: 0.7235 (mm) REVERT: E 52 ARG cc_start: 0.8552 (mmt180) cc_final: 0.8285 (mmt180) REVERT: E 54 PHE cc_start: 0.7153 (p90) cc_final: 0.6638 (p90) REVERT: E 56 LYS cc_start: 0.8923 (tmtt) cc_final: 0.8716 (tmtt) REVERT: E 64 LYS cc_start: 0.8868 (mppt) cc_final: 0.8437 (mmmm) REVERT: E 67 PHE cc_start: 0.7768 (p90) cc_final: 0.7508 (p90) REVERT: E 70 LEU cc_start: 0.8663 (mm) cc_final: 0.8306 (mm) REVERT: E 84 PHE cc_start: 0.6960 (m-10) cc_final: 0.6022 (m-80) REVERT: E 108 ASN cc_start: 0.8778 (t0) cc_final: 0.8452 (t0) REVERT: F 50 ILE cc_start: 0.8731 (tp) cc_final: 0.8503 (mm) REVERT: F 59 LYS cc_start: 0.8730 (ptpp) cc_final: 0.8442 (ptpt) REVERT: F 75 HIS cc_start: 0.7652 (t-90) cc_final: 0.7255 (t70) REVERT: F 79 LYS cc_start: 0.7183 (pttm) cc_final: 0.6540 (ptmt) REVERT: F 82 THR cc_start: 0.7407 (p) cc_final: 0.6935 (p) REVERT: F 87 VAL cc_start: 0.8670 (t) cc_final: 0.8286 (p) REVERT: F 95 ARG cc_start: 0.8147 (ttp80) cc_final: 0.7818 (ttp-110) REVERT: G 34 TYR cc_start: 0.7605 (p90) cc_final: 0.7373 (p90) REVERT: G 36 LYS cc_start: 0.8360 (ptpp) cc_final: 0.8063 (pttm) REVERT: G 59 TYR cc_start: 0.7597 (p90) cc_final: 0.6959 (p90) REVERT: G 70 ASN cc_start: 0.7738 (p0) cc_final: 0.7467 (p0) REVERT: G 74 ASP cc_start: 0.7855 (p0) cc_final: 0.7591 (p0) REVERT: G 86 GLN cc_start: 0.7061 (mp10) cc_final: 0.6593 (mp10) REVERT: H 44 ILE cc_start: 0.8918 (mt) cc_final: 0.8687 (mm) REVERT: H 46 LYS cc_start: 0.9009 (tmmt) cc_final: 0.8681 (pttp) REVERT: H 49 LYS cc_start: 0.8764 (pttm) cc_final: 0.8494 (pttp) REVERT: H 52 HIS cc_start: 0.8112 (t70) cc_final: 0.7801 (t70) REVERT: H 54 ASP cc_start: 0.8178 (p0) cc_final: 0.7867 (t0) REVERT: H 66 ASN cc_start: 0.8232 (p0) cc_final: 0.7909 (p0) REVERT: H 72 ILE cc_start: 0.7494 (tt) cc_final: 0.6875 (tt) REVERT: H 76 ILE cc_start: 0.8239 (tp) cc_final: 0.7767 (tp) REVERT: H 82 LYS cc_start: 0.8791 (tmmt) cc_final: 0.8417 (tmtt) REVERT: H 112 HIS cc_start: 0.7928 (m90) cc_final: 0.7365 (m90) REVERT: H 116 GLU cc_start: 0.6808 (pp20) cc_final: 0.6401 (pp20) REVERT: H 124 TYR cc_start: 0.7425 (p90) cc_final: 0.7073 (p90) outliers start: 0 outliers final: 0 residues processed: 519 average time/residue: 0.1666 time to fit residues: 123.9573 Evaluate side-chains 477 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 477 time to evaluate : 0.674 ------------------------------------------------------------------------------- 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: 6.9990 chunk 24 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 82 optimal weight: 9.9990 chunk 127 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 181 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 245 HIS ** M 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 260 ASN ** O 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN D 50 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 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 = 0.4049 r_free = 0.4049 target = 0.118649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.092385 restraints weight = 88375.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.095606 restraints weight = 50988.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.097688 restraints weight = 33399.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.099072 restraints weight = 24259.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.099978 restraints weight = 19156.688| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.7718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 22580 Z= 0.283 Angle : 0.961 13.677 31707 Z= 0.519 Chirality : 0.052 0.278 3556 Planarity : 0.007 0.073 3001 Dihedral : 28.341 127.122 5372 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 29.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % 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 : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.76 (0.18), residues: 1866 helix: -1.00 (0.16), residues: 975 sheet: -1.72 (0.79), residues: 33 loop : -2.86 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 55 TYR 0.040 0.003 TYR G 34 PHE 0.047 0.004 PHE H 73 TRP 0.084 0.004 TRP O 353 HIS 0.025 0.002 HIS Q 240 Details of bonding type rmsd covalent geometry : bond 0.00630 (22580) covalent geometry : angle 0.96094 (31707) hydrogen bonds : bond 0.06388 ( 1048) hydrogen bonds : angle 5.28477 ( 2748) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4577.77 seconds wall clock time: 79 minutes 34.59 seconds (4774.59 seconds total)