Starting phenix.real_space_refine on Wed Sep 17 07:44:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mk9_48323/09_2025/9mk9_48323.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mk9_48323/09_2025/9mk9_48323.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mk9_48323/09_2025/9mk9_48323.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mk9_48323/09_2025/9mk9_48323.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mk9_48323/09_2025/9mk9_48323.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mk9_48323/09_2025/9mk9_48323.map" } resolution = 3.22 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= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 4253 2.51 5 N 1188 2.21 5 O 1258 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6751 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3629 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 13, 'TRANS': 426} Chain: "B" Number of atoms: 3122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3122 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 13, 'TRANS': 368} Time building chain proxies: 2.29, per 1000 atoms: 0.34 Number of scatterers: 6751 At special positions: 0 Unit cell: (70.882, 99.064, 108.458, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1258 8.00 N 1188 7.00 C 4253 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: 0.43 Conformation dependent library (CDL) restraints added in 382.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1586 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 0 sheets defined 81.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 7 through 14 removed outlier: 3.599A pdb=" N CYS A 11 " --> pdb=" O GLU A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 40 removed outlier: 3.523A pdb=" N PHE A 34 " --> pdb=" O SER A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 65 removed outlier: 4.004A pdb=" N CYS A 54 " --> pdb=" O LYS A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 85 Processing helix chain 'A' and resid 88 through 93 Processing helix chain 'A' and resid 93 through 108 removed outlier: 3.555A pdb=" N TRP A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 128 removed outlier: 3.646A pdb=" N ALA A 113 " --> pdb=" O GLN A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 150 removed outlier: 4.835A pdb=" N GLY A 143 " --> pdb=" O ASP A 139 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ARG A 146 " --> pdb=" O GLU A 142 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS A 148 " --> pdb=" O TRP A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 168 removed outlier: 3.566A pdb=" N LYS A 158 " --> pdb=" O ASN A 154 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA A 164 " --> pdb=" O CYS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 188 Processing helix chain 'A' and resid 193 through 205 removed outlier: 4.678A pdb=" N SER A 197 " --> pdb=" O TYR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 219 Processing helix chain 'A' and resid 224 through 238 removed outlier: 3.565A pdb=" N LEU A 230 " --> pdb=" O GLN A 226 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 256 removed outlier: 3.539A pdb=" N CYS A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS A 254 " --> pdb=" O ARG A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 270 removed outlier: 3.721A pdb=" N GLN A 263 " --> pdb=" O ASP A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 297 removed outlier: 3.500A pdb=" N ASN A 295 " --> pdb=" O HIS A 291 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ARG A 296 " --> pdb=" O HIS A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 320 removed outlier: 4.233A pdb=" N LYS A 306 " --> pdb=" O SER A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 344 removed outlier: 4.561A pdb=" N PHE A 335 " --> pdb=" O TYR A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 359 removed outlier: 4.033A pdb=" N LYS A 359 " --> pdb=" O LYS A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 381 removed outlier: 3.611A pdb=" N MET A 381 " --> pdb=" O GLN A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 397 removed outlier: 3.811A pdb=" N ILE A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 421 removed outlier: 3.569A pdb=" N LEU A 419 " --> pdb=" O ALA A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 446 removed outlier: 3.670A pdb=" N ALA A 428 " --> pdb=" O SER A 424 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU A 429 " --> pdb=" O ASP A 425 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS A 446 " --> pdb=" O GLN A 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 13 removed outlier: 3.531A pdb=" N LEU B 13 " --> pdb=" O LEU B 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 9 through 13' Processing helix chain 'B' and resid 14 through 16 No H-bonds generated for 'chain 'B' and resid 14 through 16' Processing helix chain 'B' and resid 33 through 39 removed outlier: 4.426A pdb=" N ARG B 37 " --> pdb=" O HIS B 33 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N CYS B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 65 removed outlier: 3.512A pdb=" N THR B 52 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR B 59 " --> pdb=" O ASP B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 84 removed outlier: 3.653A pdb=" N GLU B 72 " --> pdb=" O LYS B 68 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA B 77 " --> pdb=" O CYS B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 108 removed outlier: 3.574A pdb=" N GLU B 90 " --> pdb=" O ASN B 86 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE B 91 " --> pdb=" O ASP B 87 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU B 94 " --> pdb=" O GLU B 90 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL B 95 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N THR B 96 " --> pdb=" O ARG B 92 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN B 99 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA B 101 " --> pdb=" O TRP B 97 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP B 102 " --> pdb=" O GLY B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 127 removed outlier: 4.064A pdb=" N ALA B 115 " --> pdb=" O SER B 111 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TYR B 116 " --> pdb=" O GLU B 112 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG B 121 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL B 123 " --> pdb=" O LYS B 119 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE B 127 " --> pdb=" O VAL B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 149 removed outlier: 3.690A pdb=" N GLU B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR B 145 " --> pdb=" O GLU B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 166 removed outlier: 3.653A pdb=" N MET B 157 " --> pdb=" O GLU B 153 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N CYS B 158 " --> pdb=" O ARG B 154 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU B 164 " --> pdb=" O GLU B 160 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 186 removed outlier: 3.653A pdb=" N SER B 174 " --> pdb=" O PRO B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 203 Processing helix chain 'B' and resid 207 through 221 removed outlier: 3.676A pdb=" N ARG B 219 " --> pdb=" O LEU B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 237 Processing helix chain 'B' and resid 240 through 255 Processing helix chain 'B' and resid 256 through 269 removed outlier: 3.776A pdb=" N ALA B 260 " --> pdb=" O ASN B 256 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG B 269 " --> pdb=" O GLY B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 295 removed outlier: 4.212A pdb=" N LEU B 280 " --> pdb=" O PRO B 276 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN B 293 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASN B 294 " --> pdb=" O GLU B 290 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B 295 " --> pdb=" O GLN B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 323 removed outlier: 4.642A pdb=" N GLU B 309 " --> pdb=" O GLN B 305 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET B 315 " --> pdb=" O ARG B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 349 removed outlier: 3.877A pdb=" N ILE B 336 " --> pdb=" O TYR B 332 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP B 337 " --> pdb=" O SER B 333 " (cutoff:3.500A) Proline residue: B 339 - end of helix removed outlier: 3.665A pdb=" N GLN B 346 " --> pdb=" O GLU B 342 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET B 347 " --> pdb=" O ARG B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 375 removed outlier: 3.642A pdb=" N ARG B 373 " --> pdb=" O GLN B 369 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS B 374 " --> pdb=" O GLU B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 386 removed outlier: 3.870A pdb=" N ALA B 379 " --> pdb=" O SER B 375 " (cutoff:3.500A) 420 hydrogen bonds defined for protein. 1260 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.06 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2245 1.34 - 1.46: 864 1.46 - 1.58: 3696 1.58 - 1.69: 0 1.69 - 1.81: 77 Bond restraints: 6882 Sorted by residual: bond pdb=" N VAL A 300 " pdb=" CA VAL A 300 " ideal model delta sigma weight residual 1.461 1.497 -0.037 1.19e-02 7.06e+03 9.44e+00 bond pdb=" N VAL A 222 " pdb=" CA VAL A 222 " ideal model delta sigma weight residual 1.461 1.497 -0.037 1.19e-02 7.06e+03 9.42e+00 bond pdb=" N ARG B 26 " pdb=" CA ARG B 26 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.21e-02 6.83e+03 9.42e+00 bond pdb=" N LYS A 218 " pdb=" CA LYS A 218 " ideal model delta sigma weight residual 1.459 1.496 -0.036 1.23e-02 6.61e+03 8.77e+00 bond pdb=" N ARG A 297 " pdb=" CA ARG A 297 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.21e-02 6.83e+03 8.62e+00 ... (remaining 6877 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 8923 1.95 - 3.89: 296 3.89 - 5.84: 25 5.84 - 7.79: 3 7.79 - 9.73: 1 Bond angle restraints: 9248 Sorted by residual: angle pdb=" C MET A 299 " pdb=" CA MET A 299 " pdb=" CB MET A 299 " ideal model delta sigma weight residual 116.63 110.09 6.54 1.16e+00 7.43e-01 3.18e+01 angle pdb=" C LEU A 329 " pdb=" N GLU A 330 " pdb=" CA GLU A 330 " ideal model delta sigma weight residual 121.54 131.27 -9.73 1.91e+00 2.74e-01 2.60e+01 angle pdb=" N SER B 301 " pdb=" CA SER B 301 " pdb=" C SER B 301 " ideal model delta sigma weight residual 111.71 106.09 5.62 1.15e+00 7.56e-01 2.39e+01 angle pdb=" CA HIS A 223 " pdb=" C HIS A 223 " pdb=" O HIS A 223 " ideal model delta sigma weight residual 120.63 115.70 4.93 1.08e+00 8.57e-01 2.09e+01 angle pdb=" N SER B 32 " pdb=" CA SER B 32 " pdb=" C SER B 32 " ideal model delta sigma weight residual 110.35 105.24 5.11 1.36e+00 5.41e-01 1.41e+01 ... (remaining 9243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.99: 3682 16.99 - 33.97: 422 33.97 - 50.96: 112 50.96 - 67.94: 32 67.94 - 84.93: 16 Dihedral angle restraints: 4264 sinusoidal: 1819 harmonic: 2445 Sorted by residual: dihedral pdb=" CA PHE A 44 " pdb=" C PHE A 44 " pdb=" N GLN A 45 " pdb=" CA GLN A 45 " ideal model delta harmonic sigma weight residual -180.00 -160.20 -19.80 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA GLY A 143 " pdb=" C GLY A 143 " pdb=" N TRP A 144 " pdb=" CA TRP A 144 " ideal model delta harmonic sigma weight residual 180.00 162.24 17.76 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA ASP B 360 " pdb=" C ASP B 360 " pdb=" N LEU B 361 " pdb=" CA LEU B 361 " ideal model delta harmonic sigma weight residual 180.00 -162.81 -17.19 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 4261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 628 0.035 - 0.070: 248 0.070 - 0.105: 68 0.105 - 0.140: 16 0.140 - 0.175: 8 Chirality restraints: 968 Sorted by residual: chirality pdb=" CB ILE A 195 " pdb=" CA ILE A 195 " pdb=" CG1 ILE A 195 " pdb=" CG2 ILE A 195 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.65e-01 chirality pdb=" CA LEU A 219 " pdb=" N LEU A 219 " pdb=" C LEU A 219 " pdb=" CB LEU A 219 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.62e-01 chirality pdb=" CA ARG A 260 " pdb=" N ARG A 260 " pdb=" C ARG A 260 " pdb=" CB ARG A 260 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.33e-01 ... (remaining 965 not shown) Planarity restraints: 1208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 219 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.13e+00 pdb=" C LEU A 219 " 0.039 2.00e-02 2.50e+03 pdb=" O LEU A 219 " -0.015 2.00e-02 2.50e+03 pdb=" N ASP A 220 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 353 " 0.021 2.00e-02 2.50e+03 1.68e-02 4.93e+00 pdb=" CG PHE A 353 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE A 353 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 353 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 353 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 353 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 353 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 215 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.25e+00 pdb=" C LEU A 215 " -0.036 2.00e-02 2.50e+03 pdb=" O LEU A 215 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA A 216 " 0.012 2.00e-02 2.50e+03 ... (remaining 1205 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 502 2.74 - 3.28: 6956 3.28 - 3.82: 10414 3.82 - 4.36: 12316 4.36 - 4.90: 20790 Nonbonded interactions: 50978 Sorted by model distance: nonbonded pdb=" OE2 GLU B 78 " pdb=" NH2 ARG B 93 " model vdw 2.201 3.120 nonbonded pdb=" O GLY A 439 " pdb=" NE2 GLN A 443 " model vdw 2.212 3.120 nonbonded pdb=" OE2 GLU A 141 " pdb=" NH1 ARG B 92 " model vdw 2.274 3.120 nonbonded pdb=" O SER A 426 " pdb=" ND1 HIS A 430 " model vdw 2.365 3.120 nonbonded pdb=" O LYS A 306 " pdb=" OE1 GLU A 310 " model vdw 2.427 3.040 ... (remaining 50973 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 8.510 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 6882 Z= 0.307 Angle : 0.726 9.734 9248 Z= 0.478 Chirality : 0.043 0.175 968 Planarity : 0.004 0.046 1208 Dihedral : 16.383 84.926 2678 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.34 % Allowed : 0.82 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.28), residues: 818 helix: 0.82 (0.21), residues: 592 sheet: None (None), residues: 0 loop : -1.21 (0.37), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 417 TYR 0.019 0.002 TYR A 331 PHE 0.037 0.002 PHE A 353 TRP 0.029 0.001 TRP A 144 HIS 0.008 0.001 HIS A 370 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 6882) covalent geometry : angle 0.72644 ( 9248) hydrogen bonds : bond 0.24059 ( 420) hydrogen bonds : angle 5.82975 ( 1260) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 VAL cc_start: 0.2192 (OUTLIER) cc_final: 0.1924 (t) REVERT: A 344 LYS cc_start: 0.9091 (ttmt) cc_final: 0.8842 (tmmt) REVERT: A 373 TYR cc_start: 0.7536 (t80) cc_final: 0.7292 (t80) REVERT: A 418 ARG cc_start: 0.5883 (tpt90) cc_final: 0.5603 (tpt90) REVERT: B 49 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7716 (mt-10) REVERT: B 118 ASP cc_start: 0.7914 (m-30) cc_final: 0.7670 (m-30) outliers start: 17 outliers final: 5 residues processed: 127 average time/residue: 0.1402 time to fit residues: 21.5246 Evaluate side-chains 68 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 297 ARG Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 34 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.0670 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN A 317 ASN ** A 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 GLN A 377 GLN B 41 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.150367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.117043 restraints weight = 11400.862| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 3.02 r_work: 0.3252 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6882 Z= 0.142 Angle : 0.555 9.303 9248 Z= 0.296 Chirality : 0.038 0.153 968 Planarity : 0.004 0.046 1208 Dihedral : 5.588 51.268 927 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.24 % Allowed : 6.59 % Favored : 92.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.29), residues: 818 helix: 1.39 (0.21), residues: 611 sheet: None (None), residues: 0 loop : -1.31 (0.39), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 417 TYR 0.018 0.001 TYR A 286 PHE 0.024 0.002 PHE A 353 TRP 0.015 0.001 TRP A 144 HIS 0.009 0.002 HIS A 370 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 6882) covalent geometry : angle 0.55520 ( 9248) hydrogen bonds : bond 0.05379 ( 420) hydrogen bonds : angle 4.13145 ( 1260) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 LYS cc_start: 0.8239 (tppt) cc_final: 0.7861 (mmtp) REVERT: A 297 ARG cc_start: 0.2152 (OUTLIER) cc_final: 0.1383 (ttm170) REVERT: A 357 LEU cc_start: 0.7823 (pp) cc_final: 0.7502 (tt) REVERT: A 373 TYR cc_start: 0.7815 (t80) cc_final: 0.7585 (t80) REVERT: A 418 ARG cc_start: 0.6110 (tpt170) cc_final: 0.5747 (tpt90) REVERT: B 118 ASP cc_start: 0.7946 (m-30) cc_final: 0.7690 (m-30) REVERT: B 309 GLU cc_start: 0.8324 (mm-30) cc_final: 0.8111 (mp0) outliers start: 9 outliers final: 6 residues processed: 80 average time/residue: 0.1247 time to fit residues: 12.6345 Evaluate side-chains 69 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LYS Chi-restraints excluded: chain A residue 287 ARG Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 297 ARG Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain B residue 48 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 12 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS ** A 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 GLN A 412 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.146289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.111365 restraints weight = 11268.988| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 3.03 r_work: 0.3157 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6882 Z= 0.152 Angle : 0.546 9.068 9248 Z= 0.286 Chirality : 0.039 0.210 968 Planarity : 0.004 0.041 1208 Dihedral : 4.947 52.438 920 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.10 % Allowed : 9.34 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.29), residues: 818 helix: 1.56 (0.21), residues: 617 sheet: None (None), residues: 0 loop : -1.47 (0.39), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 259 TYR 0.012 0.001 TYR A 286 PHE 0.021 0.001 PHE A 251 TRP 0.010 0.001 TRP A 144 HIS 0.007 0.002 HIS B 19 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 6882) covalent geometry : angle 0.54570 ( 9248) hydrogen bonds : bond 0.05589 ( 420) hydrogen bonds : angle 3.97832 ( 1260) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.301 Fit side-chains REVERT: A 287 ARG cc_start: 0.7223 (OUTLIER) cc_final: 0.6685 (mmm-85) REVERT: A 357 LEU cc_start: 0.7979 (pp) cc_final: 0.7652 (tt) REVERT: A 413 ARG cc_start: 0.8211 (mtp85) cc_final: 0.8007 (mtm110) REVERT: A 418 ARG cc_start: 0.6097 (tpt170) cc_final: 0.5769 (tpt90) REVERT: B 309 GLU cc_start: 0.8421 (mm-30) cc_final: 0.8211 (mp0) outliers start: 8 outliers final: 4 residues processed: 70 average time/residue: 0.1057 time to fit residues: 9.5093 Evaluate side-chains 64 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 ARG Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 375 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 37 optimal weight: 0.0970 chunk 18 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 47 optimal weight: 0.0370 chunk 56 optimal weight: 0.6980 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.149206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.113084 restraints weight = 11358.215| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.93 r_work: 0.3193 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6882 Z= 0.112 Angle : 0.481 6.859 9248 Z= 0.252 Chirality : 0.036 0.147 968 Planarity : 0.003 0.039 1208 Dihedral : 4.030 17.632 912 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.51 % Allowed : 11.40 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.30), residues: 818 helix: 1.84 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -1.34 (0.41), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 417 TYR 0.013 0.001 TYR A 331 PHE 0.028 0.001 PHE A 353 TRP 0.005 0.001 TRP B 144 HIS 0.005 0.001 HIS A 318 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 6882) covalent geometry : angle 0.48076 ( 9248) hydrogen bonds : bond 0.04179 ( 420) hydrogen bonds : angle 3.71803 ( 1260) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 287 ARG cc_start: 0.7122 (OUTLIER) cc_final: 0.6684 (mmm-85) REVERT: A 381 MET cc_start: 0.7090 (OUTLIER) cc_final: 0.6886 (tmm) REVERT: A 418 ARG cc_start: 0.6226 (tpt170) cc_final: 0.5883 (tpt90) outliers start: 11 outliers final: 5 residues processed: 76 average time/residue: 0.1025 time to fit residues: 10.3197 Evaluate side-chains 65 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 ARG Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 304 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 68 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 45 optimal weight: 0.0370 chunk 56 optimal weight: 0.5980 chunk 67 optimal weight: 0.0270 chunk 9 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.149133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.112081 restraints weight = 11465.340| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.82 r_work: 0.3227 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6882 Z= 0.107 Angle : 0.481 7.440 9248 Z= 0.248 Chirality : 0.035 0.146 968 Planarity : 0.003 0.040 1208 Dihedral : 3.895 17.803 912 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.79 % Allowed : 11.95 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.30), residues: 818 helix: 1.99 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -1.39 (0.41), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 417 TYR 0.010 0.001 TYR A 373 PHE 0.016 0.001 PHE A 301 TRP 0.005 0.001 TRP B 144 HIS 0.014 0.001 HIS A 370 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 6882) covalent geometry : angle 0.48075 ( 9248) hydrogen bonds : bond 0.03971 ( 420) hydrogen bonds : angle 3.60701 ( 1260) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 287 ARG cc_start: 0.7206 (OUTLIER) cc_final: 0.6726 (mmm-85) REVERT: A 328 MET cc_start: 0.5801 (tpp) cc_final: 0.5437 (tpp) REVERT: A 372 ARG cc_start: 0.7976 (ttp-170) cc_final: 0.7681 (mtm-85) REVERT: A 418 ARG cc_start: 0.6434 (tpt170) cc_final: 0.6108 (tpt90) REVERT: B 309 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7564 (pt0) outliers start: 13 outliers final: 9 residues processed: 73 average time/residue: 0.0977 time to fit residues: 9.3346 Evaluate side-chains 68 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 287 ARG Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 375 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 12 optimal weight: 0.0070 chunk 29 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 16 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 45 optimal weight: 0.1980 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.149080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.114193 restraints weight = 11460.651| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 3.02 r_work: 0.3201 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6882 Z= 0.104 Angle : 0.481 9.365 9248 Z= 0.244 Chirality : 0.035 0.142 968 Planarity : 0.003 0.040 1208 Dihedral : 3.901 21.264 912 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.51 % Allowed : 12.91 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.30), residues: 818 helix: 2.07 (0.21), residues: 617 sheet: None (None), residues: 0 loop : -1.49 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 383 TYR 0.013 0.001 TYR A 389 PHE 0.016 0.001 PHE A 251 TRP 0.005 0.001 TRP B 144 HIS 0.012 0.001 HIS A 370 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 6882) covalent geometry : angle 0.48117 ( 9248) hydrogen bonds : bond 0.03795 ( 420) hydrogen bonds : angle 3.55634 ( 1260) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 167 LYS cc_start: 0.8236 (tppt) cc_final: 0.7885 (mmtp) REVERT: A 287 ARG cc_start: 0.7071 (OUTLIER) cc_final: 0.6555 (mmm-85) REVERT: A 328 MET cc_start: 0.5859 (tpp) cc_final: 0.5521 (tpp) REVERT: A 372 ARG cc_start: 0.8010 (ttp-170) cc_final: 0.7743 (mtm-85) REVERT: A 418 ARG cc_start: 0.6393 (tpt170) cc_final: 0.6129 (tpt90) REVERT: B 304 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7924 (mtm-85) outliers start: 11 outliers final: 7 residues processed: 75 average time/residue: 0.1008 time to fit residues: 9.9675 Evaluate side-chains 67 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 287 ARG Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 375 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 40 optimal weight: 8.9990 chunk 21 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 78 optimal weight: 0.0570 chunk 5 optimal weight: 2.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.148518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.113568 restraints weight = 11305.375| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.55 r_work: 0.3254 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6882 Z= 0.109 Angle : 0.488 9.142 9248 Z= 0.248 Chirality : 0.035 0.164 968 Planarity : 0.003 0.040 1208 Dihedral : 3.871 20.743 912 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.06 % Allowed : 12.50 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.92 (0.30), residues: 818 helix: 2.12 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -1.51 (0.40), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 417 TYR 0.007 0.001 TYR A 331 PHE 0.016 0.001 PHE A 251 TRP 0.005 0.001 TRP B 144 HIS 0.014 0.001 HIS A 370 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 6882) covalent geometry : angle 0.48811 ( 9248) hydrogen bonds : bond 0.03903 ( 420) hydrogen bonds : angle 3.54667 ( 1260) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 287 ARG cc_start: 0.7216 (OUTLIER) cc_final: 0.6665 (mmm-85) REVERT: A 328 MET cc_start: 0.5931 (tpp) cc_final: 0.5624 (tpp) REVERT: A 372 ARG cc_start: 0.8043 (ttp-170) cc_final: 0.7766 (mtm-85) REVERT: A 418 ARG cc_start: 0.6423 (tpt170) cc_final: 0.6185 (tpt90) REVERT: B 304 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7842 (mtm-85) outliers start: 15 outliers final: 8 residues processed: 70 average time/residue: 0.1061 time to fit residues: 9.8551 Evaluate side-chains 69 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 287 ARG Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 375 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 10 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 0.2980 chunk 38 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 26 optimal weight: 0.0370 chunk 24 optimal weight: 0.9990 overall best weight: 0.5460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.148249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.112190 restraints weight = 11614.423| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.72 r_work: 0.3241 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6882 Z= 0.109 Angle : 0.480 9.918 9248 Z= 0.246 Chirality : 0.035 0.161 968 Planarity : 0.003 0.039 1208 Dihedral : 3.844 20.259 912 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.65 % Allowed : 13.87 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.97 (0.30), residues: 818 helix: 2.16 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -1.50 (0.40), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 417 TYR 0.006 0.001 TYR A 280 PHE 0.016 0.001 PHE A 251 TRP 0.005 0.001 TRP B 144 HIS 0.019 0.002 HIS A 370 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 6882) covalent geometry : angle 0.48033 ( 9248) hydrogen bonds : bond 0.03891 ( 420) hydrogen bonds : angle 3.53552 ( 1260) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 ARG cc_start: 0.8026 (ttp-170) cc_final: 0.7726 (mtm-85) REVERT: B 304 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7855 (mtm-85) outliers start: 12 outliers final: 8 residues processed: 73 average time/residue: 0.0893 time to fit residues: 8.7013 Evaluate side-chains 68 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 291 HIS Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 375 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 78 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 33 optimal weight: 0.4980 chunk 47 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 37 optimal weight: 0.0570 chunk 68 optimal weight: 0.5980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.147925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.112840 restraints weight = 11494.495| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.58 r_work: 0.3250 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6882 Z= 0.111 Angle : 0.505 11.070 9248 Z= 0.256 Chirality : 0.035 0.162 968 Planarity : 0.003 0.039 1208 Dihedral : 3.860 19.987 912 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.79 % Allowed : 14.15 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.98 (0.30), residues: 818 helix: 2.14 (0.21), residues: 620 sheet: None (None), residues: 0 loop : -1.47 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 64 TYR 0.016 0.001 TYR A 389 PHE 0.016 0.001 PHE A 251 TRP 0.005 0.001 TRP B 144 HIS 0.020 0.002 HIS A 370 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 6882) covalent geometry : angle 0.50505 ( 9248) hydrogen bonds : bond 0.03912 ( 420) hydrogen bonds : angle 3.55085 ( 1260) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 ARG cc_start: 0.8060 (ttp-170) cc_final: 0.7758 (mtm-85) REVERT: A 418 ARG cc_start: 0.5918 (tpt90) cc_final: 0.5636 (tpt90) REVERT: B 304 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7833 (mtm-85) outliers start: 13 outliers final: 9 residues processed: 73 average time/residue: 0.0835 time to fit residues: 8.3420 Evaluate side-chains 72 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 375 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 68 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 0.0170 chunk 38 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 67 optimal weight: 0.0980 chunk 3 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.148139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.112747 restraints weight = 11413.364| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.56 r_work: 0.3255 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6882 Z= 0.111 Angle : 0.517 11.387 9248 Z= 0.264 Chirality : 0.035 0.162 968 Planarity : 0.004 0.037 1208 Dihedral : 3.860 19.819 912 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.51 % Allowed : 14.15 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.98 (0.30), residues: 818 helix: 2.15 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -1.44 (0.41), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 320 TYR 0.038 0.001 TYR A 391 PHE 0.015 0.001 PHE A 251 TRP 0.005 0.001 TRP B 144 HIS 0.020 0.002 HIS A 370 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 6882) covalent geometry : angle 0.51651 ( 9248) hydrogen bonds : bond 0.03807 ( 420) hydrogen bonds : angle 3.58241 ( 1260) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 372 ARG cc_start: 0.8093 (ttp-170) cc_final: 0.7870 (mtm-85) REVERT: A 418 ARG cc_start: 0.5937 (tpt90) cc_final: 0.5660 (tpt90) REVERT: B 304 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7859 (mtm-85) outliers start: 11 outliers final: 9 residues processed: 72 average time/residue: 0.0881 time to fit residues: 8.6840 Evaluate side-chains 71 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 375 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 38 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.144284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.109149 restraints weight = 11362.845| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 3.07 r_work: 0.3144 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6882 Z= 0.145 Angle : 0.554 11.346 9248 Z= 0.285 Chirality : 0.037 0.161 968 Planarity : 0.004 0.039 1208 Dihedral : 4.028 20.011 912 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.65 % Allowed : 14.29 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.80 (0.30), residues: 818 helix: 2.03 (0.21), residues: 618 sheet: None (None), residues: 0 loop : -1.55 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 320 TYR 0.025 0.001 TYR A 389 PHE 0.018 0.001 PHE A 251 TRP 0.006 0.001 TRP A 144 HIS 0.022 0.002 HIS A 370 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 6882) covalent geometry : angle 0.55416 ( 9248) hydrogen bonds : bond 0.04897 ( 420) hydrogen bonds : angle 3.77111 ( 1260) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1838.32 seconds wall clock time: 32 minutes 15.94 seconds (1935.94 seconds total)