Starting phenix.real_space_refine on Mon Apr 28 01:24:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mk9_48323/04_2025/9mk9_48323.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mk9_48323/04_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9mk9_48323/04_2025/9mk9_48323.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mk9_48323/04_2025/9mk9_48323.map" model { file = "/net/cci-nas-00/data/ceres_data/9mk9_48323/04_2025/9mk9_48323.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mk9_48323/04_2025/9mk9_48323.cif" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 4.71, per 1000 atoms: 0.70 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: 1.65 Conformation dependent library (CDL) restraints added in 895.7 milliseconds 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: 0.63 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: 1.65 Time building geometry restraints manager: 1.95 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: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.220 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.750 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.029 0.001 TRP A 144 HIS 0.008 0.001 HIS A 370 PHE 0.037 0.002 PHE A 353 TYR 0.019 0.002 TYR A 331 ARG 0.008 0.001 ARG A 417 Details of bonding type rmsd hydrogen bonds : bond 0.24059 ( 420) hydrogen bonds : angle 5.82975 ( 1260) covalent geometry : bond 0.00467 ( 6882) covalent geometry : angle 0.72644 ( 9248) *********************** 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 : 0.838 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: 0.7290 (t80) REVERT: A 418 ARG cc_start: 0.5883 (tpt90) cc_final: 0.5604 (tpt90) REVERT: B 49 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7723 (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: 0.2927 time to fit residues: 45.2119 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 : 0.770 ------------------------------------------------------------------------------- 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 69 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN ** A 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 GLN A 377 GLN A 412 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.146660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.112834 restraints weight = 11427.947| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 3.08 r_work: 0.3190 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6882 Z= 0.181 Angle : 0.595 9.030 9248 Z= 0.319 Chirality : 0.040 0.161 968 Planarity : 0.004 0.046 1208 Dihedral : 5.754 51.010 927 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.65 % Allowed : 7.01 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.29), residues: 818 helix: 1.23 (0.21), residues: 613 sheet: None (None), residues: 0 loop : -1.43 (0.39), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 144 HIS 0.009 0.002 HIS A 370 PHE 0.025 0.002 PHE A 251 TYR 0.019 0.001 TYR A 286 ARG 0.007 0.000 ARG B 303 Details of bonding type rmsd hydrogen bonds : bond 0.06233 ( 420) hydrogen bonds : angle 4.27959 ( 1260) covalent geometry : bond 0.00414 ( 6882) covalent geometry : angle 0.59500 ( 9248) *********************** 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 82 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 297 ARG cc_start: 0.2076 (OUTLIER) cc_final: 0.1262 (ttm170) REVERT: A 331 TYR cc_start: 0.7749 (m-80) cc_final: 0.7393 (m-80) REVERT: A 357 LEU cc_start: 0.7811 (pp) cc_final: 0.7472 (tt) REVERT: A 373 TYR cc_start: 0.7743 (t80) cc_final: 0.7537 (t80) REVERT: A 418 ARG cc_start: 0.6003 (tpt170) cc_final: 0.5661 (tpt90) REVERT: B 118 ASP cc_start: 0.7996 (m-30) cc_final: 0.7722 (m-30) REVERT: B 309 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8060 (mp0) outliers start: 12 outliers final: 8 residues processed: 80 average time/residue: 0.2499 time to fit residues: 25.6045 Evaluate side-chains 71 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 ASN Chi-restraints excluded: chain A residue 290 VAL 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 A residue 371 LEU Chi-restraints excluded: chain B residue 36 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 33 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 4 optimal weight: 0.0000 chunk 49 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN A 377 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.148552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.114290 restraints weight = 11394.584| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.91 r_work: 0.3219 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6882 Z= 0.128 Angle : 0.521 8.194 9248 Z= 0.273 Chirality : 0.038 0.197 968 Planarity : 0.004 0.042 1208 Dihedral : 4.589 52.448 916 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.37 % Allowed : 9.89 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.29), residues: 818 helix: 1.58 (0.21), residues: 617 sheet: None (None), residues: 0 loop : -1.42 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 144 HIS 0.010 0.002 HIS A 318 PHE 0.019 0.001 PHE A 251 TYR 0.012 0.001 TYR A 281 ARG 0.003 0.000 ARG B 304 Details of bonding type rmsd hydrogen bonds : bond 0.04879 ( 420) hydrogen bonds : angle 3.89955 ( 1260) covalent geometry : bond 0.00276 ( 6882) covalent geometry : angle 0.52122 ( 9248) *********************** 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 74 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.818 Fit side-chains REVERT: A 357 LEU cc_start: 0.7975 (pp) cc_final: 0.7667 (tt) REVERT: A 371 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8384 (tp) REVERT: A 418 ARG cc_start: 0.6199 (tpt170) cc_final: 0.5859 (tpt90) outliers start: 10 outliers final: 6 residues processed: 71 average time/residue: 0.2408 time to fit residues: 22.3817 Evaluate side-chains 63 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 ASN 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 371 LEU Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 48 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 48 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 35 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 78 optimal weight: 0.4980 chunk 53 optimal weight: 0.9980 chunk 12 optimal weight: 0.0870 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS A 377 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.147728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.111637 restraints weight = 11392.224| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.85 r_work: 0.3180 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6882 Z= 0.123 Angle : 0.497 6.886 9248 Z= 0.262 Chirality : 0.036 0.152 968 Planarity : 0.004 0.039 1208 Dihedral : 4.113 17.919 912 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.51 % Allowed : 11.26 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.29), residues: 818 helix: 1.77 (0.21), residues: 615 sheet: None (None), residues: 0 loop : -1.44 (0.39), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 144 HIS 0.009 0.001 HIS A 318 PHE 0.017 0.001 PHE A 251 TYR 0.013 0.001 TYR A 373 ARG 0.006 0.000 ARG A 417 Details of bonding type rmsd hydrogen bonds : bond 0.04558 ( 420) hydrogen bonds : angle 3.77909 ( 1260) covalent geometry : bond 0.00264 ( 6882) covalent geometry : angle 0.49698 ( 9248) *********************** 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 76 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.849 Fit side-chains revert: symmetry clash REVERT: A 357 LEU cc_start: 0.7997 (pp) cc_final: 0.7752 (tt) REVERT: A 418 ARG cc_start: 0.6275 (tpt170) cc_final: 0.5931 (tpt90) outliers start: 11 outliers final: 7 residues processed: 74 average time/residue: 0.1919 time to fit residues: 19.4859 Evaluate side-chains 66 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 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 371 LEU Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 375 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 21 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 0.2980 chunk 3 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 67 optimal weight: 0.0870 chunk 52 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 377 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.148742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.112518 restraints weight = 11297.339| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.74 r_work: 0.3220 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3181 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= 0.108 Angle : 0.486 7.155 9248 Z= 0.249 Chirality : 0.035 0.137 968 Planarity : 0.003 0.038 1208 Dihedral : 3.968 17.729 912 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.37 % Allowed : 12.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.30), residues: 818 helix: 1.95 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -1.48 (0.40), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 144 HIS 0.008 0.001 HIS A 318 PHE 0.016 0.001 PHE A 251 TYR 0.019 0.001 TYR A 373 ARG 0.002 0.000 ARG A 417 Details of bonding type rmsd hydrogen bonds : bond 0.03949 ( 420) hydrogen bonds : angle 3.64054 ( 1260) covalent geometry : bond 0.00231 ( 6882) covalent geometry : angle 0.48555 ( 9248) *********************** 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 78 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.827 Fit side-chains REVERT: A 328 MET cc_start: 0.5845 (tpp) cc_final: 0.5533 (tpp) REVERT: A 372 ARG cc_start: 0.8048 (ttp-170) cc_final: 0.7765 (mtm-85) REVERT: A 418 ARG cc_start: 0.6393 (tpt170) cc_final: 0.6116 (tpt90) outliers start: 10 outliers final: 6 residues processed: 77 average time/residue: 0.1841 time to fit residues: 19.6595 Evaluate side-chains 65 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 ASN Chi-restraints excluded: chain A residue 225 ASN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 55 optimal weight: 0.5980 chunk 32 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 40 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.146387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.111871 restraints weight = 11317.381| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.73 r_work: 0.3217 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6882 Z= 0.131 Angle : 0.518 8.730 9248 Z= 0.265 Chirality : 0.036 0.150 968 Planarity : 0.004 0.040 1208 Dihedral : 4.109 22.118 912 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.06 % Allowed : 13.05 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.30), residues: 818 helix: 1.92 (0.21), residues: 620 sheet: None (None), residues: 0 loop : -1.65 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 144 HIS 0.006 0.001 HIS A 318 PHE 0.018 0.001 PHE A 251 TYR 0.012 0.001 TYR A 389 ARG 0.002 0.000 ARG A 417 Details of bonding type rmsd hydrogen bonds : bond 0.04667 ( 420) hydrogen bonds : angle 3.76500 ( 1260) covalent geometry : bond 0.00294 ( 6882) covalent geometry : angle 0.51788 ( 9248) *********************** 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 82 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.839 Fit side-chains revert: symmetry clash REVERT: A 150 THR cc_start: 0.8542 (t) cc_final: 0.8325 (t) REVERT: A 328 MET cc_start: 0.5948 (tpp) cc_final: 0.5575 (tpp) REVERT: A 372 ARG cc_start: 0.8070 (ttp-170) cc_final: 0.7781 (mtm-85) REVERT: A 418 ARG cc_start: 0.6409 (tpt170) cc_final: 0.6128 (tpt90) REVERT: B 309 GLU cc_start: 0.8025 (mp0) cc_final: 0.7750 (mp0) outliers start: 15 outliers final: 10 residues processed: 77 average time/residue: 0.2155 time to fit residues: 22.1194 Evaluate side-chains 74 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.842 ------------------------------------------------------------------------------- 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 341 ILE Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 357 LEU 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 375 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 0.1980 chunk 36 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 14 optimal weight: 0.2980 chunk 4 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 47 optimal weight: 0.0370 chunk 25 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 overall best weight: 0.4058 ------------------------------------------------------------------------------- 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 = 0.3937 r_free = 0.3937 target = 0.149011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.113225 restraints weight = 11248.138| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.54 r_work: 0.3259 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3499 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= 0.102 Angle : 0.483 8.692 9248 Z= 0.244 Chirality : 0.034 0.167 968 Planarity : 0.003 0.040 1208 Dihedral : 3.946 21.930 912 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.30), residues: 818 helix: 2.10 (0.21), residues: 616 sheet: None (None), residues: 0 loop : -1.58 (0.40), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 144 HIS 0.009 0.001 HIS A 318 PHE 0.015 0.001 PHE A 376 TYR 0.006 0.001 TYR A 100 ARG 0.002 0.000 ARG A 417 Details of bonding type rmsd hydrogen bonds : bond 0.03604 ( 420) hydrogen bonds : angle 3.57549 ( 1260) covalent geometry : bond 0.00214 ( 6882) covalent geometry : angle 0.48318 ( 9248) *********************** 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 74 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.874 Fit side-chains REVERT: A 328 MET cc_start: 0.6004 (tpp) cc_final: 0.5445 (tpp) REVERT: A 372 ARG cc_start: 0.8128 (ttp-170) cc_final: 0.7863 (mtm-85) outliers start: 11 outliers final: 9 residues processed: 70 average time/residue: 0.2085 time to fit residues: 19.9610 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 : 0.862 ------------------------------------------------------------------------------- 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 347 ASP 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 375 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 78 optimal weight: 0.0980 chunk 33 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 49 optimal weight: 0.9990 chunk 62 optimal weight: 0.2980 overall best weight: 0.5982 ------------------------------------------------------------------------------- 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 = 0.3924 r_free = 0.3924 target = 0.147693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.112229 restraints weight = 11315.717| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.52 r_work: 0.3243 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6882 Z= 0.116 Angle : 0.514 11.908 9248 Z= 0.260 Chirality : 0.036 0.164 968 Planarity : 0.004 0.040 1208 Dihedral : 4.029 21.568 912 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.79 % Allowed : 14.42 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.30), residues: 818 helix: 2.05 (0.21), residues: 619 sheet: None (None), residues: 0 loop : -1.62 (0.40), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 144 HIS 0.019 0.002 HIS A 370 PHE 0.015 0.001 PHE A 251 TYR 0.015 0.001 TYR A 389 ARG 0.002 0.000 ARG A 320 Details of bonding type rmsd hydrogen bonds : bond 0.04082 ( 420) hydrogen bonds : angle 3.68289 ( 1260) covalent geometry : bond 0.00253 ( 6882) covalent geometry : angle 0.51449 ( 9248) *********************** 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: 13 poor density : 63 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 328 MET cc_start: 0.5925 (tpp) cc_final: 0.5342 (tpp) REVERT: A 372 ARG cc_start: 0.8174 (ttp-170) cc_final: 0.7854 (mtm-85) outliers start: 13 outliers final: 9 residues processed: 71 average time/residue: 0.2071 time to fit residues: 20.0637 Evaluate side-chains 69 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.773 ------------------------------------------------------------------------------- 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 314 LEU 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 375 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 70 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 36 optimal weight: 10.0000 chunk 68 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 HIS ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.146179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.110777 restraints weight = 11235.894| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.54 r_work: 0.3226 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6882 Z= 0.132 Angle : 0.528 10.637 9248 Z= 0.272 Chirality : 0.036 0.161 968 Planarity : 0.004 0.039 1208 Dihedral : 4.041 21.418 912 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.37 % Allowed : 15.38 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.29), residues: 818 helix: 1.98 (0.21), residues: 619 sheet: None (None), residues: 0 loop : -1.63 (0.39), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 144 HIS 0.021 0.002 HIS A 370 PHE 0.016 0.001 PHE A 251 TYR 0.007 0.001 TYR B 371 ARG 0.002 0.000 ARG A 287 Details of bonding type rmsd hydrogen bonds : bond 0.04434 ( 420) hydrogen bonds : angle 3.71824 ( 1260) covalent geometry : bond 0.00301 ( 6882) covalent geometry : angle 0.52806 ( 9248) *********************** 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 73 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.866 Fit side-chains revert: symmetry clash REVERT: A 150 THR cc_start: 0.8466 (t) cc_final: 0.8229 (t) REVERT: A 328 MET cc_start: 0.5821 (tpp) cc_final: 0.5428 (tpp) REVERT: A 372 ARG cc_start: 0.8190 (ttp-170) cc_final: 0.7882 (mtm-85) outliers start: 10 outliers final: 8 residues processed: 70 average time/residue: 0.1999 time to fit residues: 19.3211 Evaluate side-chains 69 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.861 ------------------------------------------------------------------------------- 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 314 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 25 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 33 optimal weight: 0.0670 overall best weight: 0.6118 ------------------------------------------------------------------------------- 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** A 377 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.146901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.109753 restraints weight = 11442.741| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.82 r_work: 0.3181 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6882 Z= 0.122 Angle : 0.543 10.749 9248 Z= 0.274 Chirality : 0.036 0.160 968 Planarity : 0.004 0.039 1208 Dihedral : 4.095 21.246 912 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.10 % Allowed : 15.93 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.29), residues: 818 helix: 2.02 (0.21), residues: 619 sheet: None (None), residues: 0 loop : -1.60 (0.40), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 144 HIS 0.022 0.002 HIS A 370 PHE 0.015 0.001 PHE A 376 TYR 0.027 0.001 TYR A 389 ARG 0.003 0.000 ARG A 297 Details of bonding type rmsd hydrogen bonds : bond 0.04136 ( 420) hydrogen bonds : angle 3.72021 ( 1260) covalent geometry : bond 0.00268 ( 6882) covalent geometry : angle 0.54271 ( 9248) ********************** 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 71 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.869 Fit side-chains revert: symmetry clash REVERT: A 328 MET cc_start: 0.5810 (tpp) cc_final: 0.5368 (tpp) REVERT: A 372 ARG cc_start: 0.8198 (ttp-170) cc_final: 0.7910 (mtm-85) outliers start: 8 outliers final: 8 residues processed: 68 average time/residue: 0.2127 time to fit residues: 19.9568 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 : 0.833 ------------------------------------------------------------------------------- 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 314 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 32 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3895 r_free = 0.3895 target = 0.145593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.110511 restraints weight = 11324.785| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 3.07 r_work: 0.3159 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3769 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= 0.132 Angle : 0.540 10.311 9248 Z= 0.276 Chirality : 0.036 0.161 968 Planarity : 0.004 0.039 1208 Dihedral : 4.075 21.237 912 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.10 % Allowed : 16.07 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.29), residues: 818 helix: 1.98 (0.21), residues: 619 sheet: None (None), residues: 0 loop : -1.65 (0.40), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 144 HIS 0.022 0.002 HIS A 370 PHE 0.016 0.001 PHE A 376 TYR 0.008 0.001 TYR B 371 ARG 0.002 0.000 ARG A 418 Details of bonding type rmsd hydrogen bonds : bond 0.04476 ( 420) hydrogen bonds : angle 3.74923 ( 1260) covalent geometry : bond 0.00296 ( 6882) covalent geometry : angle 0.53979 ( 9248) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3613.85 seconds wall clock time: 62 minutes 41.22 seconds (3761.22 seconds total)