Starting phenix.real_space_refine on Tue Mar 11 20:20:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wuj_21914/03_2025/6wuj_21914.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wuj_21914/03_2025/6wuj_21914.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wuj_21914/03_2025/6wuj_21914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wuj_21914/03_2025/6wuj_21914.map" model { file = "/net/cci-nas-00/data/ceres_data/6wuj_21914/03_2025/6wuj_21914.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wuj_21914/03_2025/6wuj_21914.cif" } resolution = 3.7 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= 0.015 sd= 0.109 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 13 5.16 5 C 4260 2.51 5 N 1198 2.21 5 O 1228 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6699 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2191 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 22, 'TRANS': 259} Chain breaks: 2 Chain: "B" Number of atoms: 2352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2352 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 19, 'TRANS': 298} Chain breaks: 4 Chain: "C" Number of atoms: 2156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2156 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 19, 'TRANS': 264} Chain breaks: 4 Time building chain proxies: 4.22, per 1000 atoms: 0.63 Number of scatterers: 6699 At special positions: 0 Unit cell: (83.74, 81.62, 125.08, 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 13 16.00 O 1228 8.00 N 1198 7.00 C 4260 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: 1.76 Conformation dependent library (CDL) restraints added in 1.0 seconds 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1620 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 10 sheets defined 38.3% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 39 through 44 removed outlier: 4.019A pdb=" N LEU A 44 " --> pdb=" O ARG A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 63 removed outlier: 4.152A pdb=" N ARG A 62 " --> pdb=" O ASP A 58 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU A 63 " --> pdb=" O SER A 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 58 through 63' Processing helix chain 'A' and resid 69 through 82 removed outlier: 4.666A pdb=" N TRP A 75 " --> pdb=" O GLY A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 121 No H-bonds generated for 'chain 'A' and resid 119 through 121' Processing helix chain 'A' and resid 122 through 127 Processing helix chain 'A' and resid 152 through 162 removed outlier: 3.622A pdb=" N TYR A 156 " --> pdb=" O ARG A 152 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ALA A 158 " --> pdb=" O GLN A 154 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 173 removed outlier: 3.734A pdb=" N ASN A 166 " --> pdb=" O HIS A 162 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' Processing helix chain 'A' and resid 178 through 187 removed outlier: 3.995A pdb=" N VAL A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 215 removed outlier: 3.667A pdb=" N ALA A 198 " --> pdb=" O ARG A 194 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA A 199 " --> pdb=" O ALA A 195 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA A 207 " --> pdb=" O GLN A 203 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU A 210 " --> pdb=" O ARG A 206 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA A 215 " --> pdb=" O GLN A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 255 removed outlier: 3.519A pdb=" N ASP A 248 " --> pdb=" O ARG A 244 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 280 removed outlier: 3.956A pdb=" N TYR A 278 " --> pdb=" O ALA A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 285 Processing helix chain 'A' and resid 302 through 306 removed outlier: 3.519A pdb=" N LYS A 306 " --> pdb=" O GLY A 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 302 through 306' Processing helix chain 'A' and resid 311 through 321 Processing helix chain 'B' and resid 369 through 374 removed outlier: 3.852A pdb=" N ASP B 373 " --> pdb=" O GLY B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 461 removed outlier: 3.532A pdb=" N VAL B 454 " --> pdb=" O VAL B 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 32 Processing helix chain 'C' and resid 43 through 47 removed outlier: 3.753A pdb=" N VAL C 47 " --> pdb=" O PRO C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 73 Processing helix chain 'C' and resid 106 through 120 removed outlier: 3.861A pdb=" N SER C 120 " --> pdb=" O THR C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 130 removed outlier: 4.001A pdb=" N SER C 130 " --> pdb=" O LEU C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 148 Processing helix chain 'C' and resid 153 through 156 removed outlier: 3.550A pdb=" N TRP C 156 " --> pdb=" O PRO C 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 153 through 156' Processing helix chain 'C' and resid 157 through 169 removed outlier: 3.570A pdb=" N ALA C 161 " --> pdb=" O THR C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 255 removed outlier: 4.389A pdb=" N VAL C 249 " --> pdb=" O ALA C 245 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL C 252 " --> pdb=" O GLU C 248 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU C 255 " --> pdb=" O ASP C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 282 removed outlier: 3.742A pdb=" N GLY C 277 " --> pdb=" O CYS C 273 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA C 280 " --> pdb=" O PHE C 276 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU C 281 " --> pdb=" O GLY C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 300 removed outlier: 3.756A pdb=" N MET C 296 " --> pdb=" O LEU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 315 removed outlier: 3.586A pdb=" N PHE C 306 " --> pdb=" O ALA C 302 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG C 311 " --> pdb=" O VAL C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 320 removed outlier: 3.825A pdb=" N LYS C 320 " --> pdb=" O GLN C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 333 removed outlier: 3.950A pdb=" N ALA C 333 " --> pdb=" O GLN C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 352 removed outlier: 3.711A pdb=" N LEU C 344 " --> pdb=" O SER C 340 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA C 352 " --> pdb=" O ARG C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 376 removed outlier: 4.551A pdb=" N TRP C 360 " --> pdb=" O LEU C 356 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG C 371 " --> pdb=" O ALA C 367 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU C 372 " --> pdb=" O ARG C 368 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL C 373 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU C 374 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA C 375 " --> pdb=" O ARG C 371 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 32 Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 54 removed outlier: 6.246A pdb=" N LEU A 52 " --> pdb=" O LEU A 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 158 through 159 removed outlier: 3.540A pdb=" N VAL B 159 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR B 168 " --> pdb=" O VAL B 159 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 171 through 172 removed outlier: 3.524A pdb=" N VAL B 171 " --> pdb=" O ASN B 184 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 199 through 202 removed outlier: 3.870A pdb=" N THR B 235 " --> pdb=" O THR B 275 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA B 239 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER B 400 " --> pdb=" O GLY B 338 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY B 342 " --> pdb=" O PHE B 396 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA B 397 " --> pdb=" O ARG B 426 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 199 through 202 removed outlier: 3.870A pdb=" N THR B 235 " --> pdb=" O THR B 275 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA B 239 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL B 314 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU B 339 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER B 400 " --> pdb=" O GLY B 338 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY B 342 " --> pdb=" O PHE B 396 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA B 397 " --> pdb=" O ARG B 426 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 206 through 210 Processing sheet with id=AA8, first strand: chain 'B' and resid 417 through 421 Processing sheet with id=AA9, first strand: chain 'B' and resid 417 through 421 removed outlier: 3.607A pdb=" N GLY B 508 " --> pdb=" O ARG B 482 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 6 removed outlier: 3.643A pdb=" N THR C 54 " --> pdb=" O HIS C 6 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR C 62 " --> pdb=" O ASP C 57 " (cutoff:3.500A) 271 hydrogen bonds defined for protein. 756 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: 2.07 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1084 1.30 - 1.43: 1844 1.43 - 1.56: 3910 1.56 - 1.68: 0 1.68 - 1.81: 21 Bond restraints: 6859 Sorted by residual: bond pdb=" CA ASP C 286 " pdb=" C ASP C 286 " ideal model delta sigma weight residual 1.524 1.454 0.070 1.27e-02 6.20e+03 3.00e+01 bond pdb=" C VAL A 223 " pdb=" O VAL A 223 " ideal model delta sigma weight residual 1.245 1.177 0.068 1.41e-02 5.03e+03 2.34e+01 bond pdb=" N VAL C 287 " pdb=" CA VAL C 287 " ideal model delta sigma weight residual 1.461 1.406 0.055 1.23e-02 6.61e+03 2.04e+01 bond pdb=" C SER A 224 " pdb=" O SER A 224 " ideal model delta sigma weight residual 1.234 1.187 0.047 1.09e-02 8.42e+03 1.83e+01 bond pdb=" N VAL A 223 " pdb=" CA VAL A 223 " ideal model delta sigma weight residual 1.460 1.424 0.036 8.60e-03 1.35e+04 1.78e+01 ... (remaining 6854 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 8849 1.82 - 3.64: 410 3.64 - 5.45: 66 5.45 - 7.27: 14 7.27 - 9.09: 7 Bond angle restraints: 9346 Sorted by residual: angle pdb=" N PHE C 12 " pdb=" CA PHE C 12 " pdb=" C PHE C 12 " ideal model delta sigma weight residual 112.97 119.52 -6.55 1.06e+00 8.90e-01 3.82e+01 angle pdb=" N VAL C 287 " pdb=" CA VAL C 287 " pdb=" CB VAL C 287 " ideal model delta sigma weight residual 111.21 103.78 7.43 1.40e+00 5.10e-01 2.82e+01 angle pdb=" N ASP C 286 " pdb=" CA ASP C 286 " pdb=" C ASP C 286 " ideal model delta sigma weight residual 107.99 98.90 9.09 1.77e+00 3.19e-01 2.64e+01 angle pdb=" C PRO C 288 " pdb=" N ARG C 289 " pdb=" CA ARG C 289 " ideal model delta sigma weight residual 123.16 116.92 6.24 1.23e+00 6.61e-01 2.58e+01 angle pdb=" N VAL A 223 " pdb=" CA VAL A 223 " pdb=" C VAL A 223 " ideal model delta sigma weight residual 113.71 117.69 -3.98 9.50e-01 1.11e+00 1.76e+01 ... (remaining 9341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 3654 17.36 - 34.72: 358 34.72 - 52.09: 44 52.09 - 69.45: 3 69.45 - 86.81: 3 Dihedral angle restraints: 4062 sinusoidal: 1545 harmonic: 2517 Sorted by residual: dihedral pdb=" CA HIS C 51 " pdb=" C HIS C 51 " pdb=" N LEU C 52 " pdb=" CA LEU C 52 " ideal model delta harmonic sigma weight residual -180.00 -150.25 -29.75 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA LEU A 101 " pdb=" C LEU A 101 " pdb=" N PRO A 102 " pdb=" CA PRO A 102 " ideal model delta harmonic sigma weight residual 180.00 -156.30 -23.70 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA ALA B 213 " pdb=" C ALA B 213 " pdb=" N SER B 214 " pdb=" CA SER B 214 " ideal model delta harmonic sigma weight residual -180.00 -157.10 -22.90 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 4059 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 958 0.082 - 0.163: 86 0.163 - 0.245: 5 0.245 - 0.326: 2 0.326 - 0.408: 1 Chirality restraints: 1052 Sorted by residual: chirality pdb=" CB VAL A 223 " pdb=" CA VAL A 223 " pdb=" CG1 VAL A 223 " pdb=" CG2 VAL A 223 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.16e+00 chirality pdb=" CA VAL A 223 " pdb=" N VAL A 223 " pdb=" C VAL A 223 " pdb=" CB VAL A 223 " both_signs ideal model delta sigma weight residual False 2.44 2.14 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA PHE C 12 " pdb=" N PHE C 12 " pdb=" C PHE C 12 " pdb=" CB PHE C 12 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 1049 not shown) Planarity restraints: 1211 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 287 " 0.057 5.00e-02 4.00e+02 8.68e-02 1.21e+01 pdb=" N PRO C 288 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO C 288 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 288 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO C 285 " -0.015 2.00e-02 2.50e+03 2.93e-02 8.57e+00 pdb=" C PRO C 285 " 0.051 2.00e-02 2.50e+03 pdb=" O PRO C 285 " -0.019 2.00e-02 2.50e+03 pdb=" N ASP C 286 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 222 " -0.015 2.00e-02 2.50e+03 2.86e-02 8.20e+00 pdb=" C ILE A 222 " 0.050 2.00e-02 2.50e+03 pdb=" O ILE A 222 " -0.018 2.00e-02 2.50e+03 pdb=" N VAL A 223 " -0.017 2.00e-02 2.50e+03 ... (remaining 1208 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 102 2.63 - 3.20: 6170 3.20 - 3.76: 9408 3.76 - 4.33: 13024 4.33 - 4.90: 21934 Nonbonded interactions: 50638 Sorted by model distance: nonbonded pdb=" OG SER B 308 " pdb=" O LEU B 347 " model vdw 2.059 3.040 nonbonded pdb=" OG1 THR B 257 " pdb=" OD2 ASP B 386 " model vdw 2.078 3.040 nonbonded pdb=" O GLY C 13 " pdb=" NH1 ARG C 311 " model vdw 2.128 3.120 nonbonded pdb=" OG1 THR B 230 " pdb=" OD1 ASP B 234 " model vdw 2.155 3.040 nonbonded pdb=" O LEU C 14 " pdb=" N SER C 16 " model vdw 2.165 3.120 ... (remaining 50633 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.600 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.850 Find NCS groups from input model: 0.130 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 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 : 0.007 0.107 6859 Z= 0.484 Angle : 0.926 9.088 9346 Z= 0.527 Chirality : 0.051 0.408 1052 Planarity : 0.006 0.087 1211 Dihedral : 13.198 86.810 2442 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 16.08 % Favored : 83.80 % Rotamer: Outliers : 0.15 % Allowed : 5.98 % Favored : 93.88 % 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: -5.66 (0.22), residues: 858 helix: -3.53 (0.20), residues: 310 sheet: -3.16 (0.41), residues: 148 loop : -4.19 (0.25), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 8 HIS 0.005 0.001 HIS B 215 PHE 0.015 0.002 PHE B 309 TYR 0.019 0.002 TYR B 421 ARG 0.006 0.000 ARG B 494 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 192 ASN cc_start: 0.8026 (t0) cc_final: 0.7624 (t0) REVERT: B 248 THR cc_start: 0.8891 (p) cc_final: 0.8586 (t) REVERT: C 250 LEU cc_start: 0.8856 (mm) cc_final: 0.8574 (mm) outliers start: 1 outliers final: 1 residues processed: 126 average time/residue: 0.2772 time to fit residues: 43.2727 Evaluate side-chains 90 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 44 optimal weight: 20.0000 chunk 35 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS B 192 ASN B 419 GLN C 50 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.136645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.110001 restraints weight = 10018.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.112380 restraints weight = 6968.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.113931 restraints weight = 5442.622| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6859 Z= 0.234 Angle : 0.698 9.077 9346 Z= 0.349 Chirality : 0.045 0.160 1052 Planarity : 0.006 0.060 1211 Dihedral : 5.580 43.383 964 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.07 % Favored : 88.93 % Rotamer: Outliers : 1.90 % Allowed : 11.66 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.21 (0.26), residues: 858 helix: -1.88 (0.26), residues: 314 sheet: -2.40 (0.46), residues: 137 loop : -3.75 (0.26), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 8 HIS 0.003 0.001 HIS B 478 PHE 0.027 0.002 PHE C 346 TYR 0.019 0.002 TYR B 289 ARG 0.004 0.000 ARG C 311 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 192 ASN cc_start: 0.7900 (OUTLIER) cc_final: 0.7503 (t0) REVERT: B 248 THR cc_start: 0.8682 (p) cc_final: 0.8395 (t) REVERT: B 378 LYS cc_start: 0.8420 (ttpt) cc_final: 0.8129 (tttm) REVERT: C 250 LEU cc_start: 0.8713 (mm) cc_final: 0.8382 (mm) outliers start: 13 outliers final: 9 residues processed: 114 average time/residue: 0.1646 time to fit residues: 25.9609 Evaluate side-chains 97 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 192 ASN Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 21 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 17 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 0 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN B 192 ASN C 51 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.137590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.112096 restraints weight = 10135.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.114390 restraints weight = 6960.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.115261 restraints weight = 5028.684| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6859 Z= 0.208 Angle : 0.662 8.879 9346 Z= 0.327 Chirality : 0.044 0.144 1052 Planarity : 0.005 0.048 1211 Dihedral : 5.245 32.896 964 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.72 % Favored : 89.28 % Rotamer: Outliers : 2.19 % Allowed : 13.41 % Favored : 84.40 % 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: -3.39 (0.28), residues: 858 helix: -0.96 (0.29), residues: 306 sheet: -2.02 (0.50), residues: 127 loop : -3.42 (0.27), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 8 HIS 0.003 0.001 HIS B 478 PHE 0.014 0.001 PHE A 27 TYR 0.012 0.001 TYR C 278 ARG 0.002 0.000 ARG A 244 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 192 ASN cc_start: 0.7840 (OUTLIER) cc_final: 0.7473 (t0) REVERT: B 209 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.7898 (tt0) REVERT: B 248 THR cc_start: 0.8680 (p) cc_final: 0.8380 (t) REVERT: C 40 ILE cc_start: 0.8751 (mm) cc_final: 0.8502 (mt) REVERT: C 250 LEU cc_start: 0.8713 (mm) cc_final: 0.8387 (mm) outliers start: 15 outliers final: 6 residues processed: 103 average time/residue: 0.1729 time to fit residues: 24.9283 Evaluate side-chains 101 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 192 ASN Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 21 CYS Chi-restraints excluded: chain C residue 255 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 63 optimal weight: 0.0770 chunk 60 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 overall best weight: 1.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 192 ASN C 51 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.135783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.109167 restraints weight = 10193.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.111586 restraints weight = 7060.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.113204 restraints weight = 5504.586| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 6859 Z= 0.300 Angle : 0.684 8.711 9346 Z= 0.338 Chirality : 0.045 0.150 1052 Planarity : 0.005 0.050 1211 Dihedral : 5.208 26.854 963 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.70 % Favored : 87.30 % Rotamer: Outliers : 2.33 % Allowed : 14.14 % Favored : 83.53 % 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: -3.09 (0.29), residues: 858 helix: -0.61 (0.30), residues: 307 sheet: -1.96 (0.51), residues: 129 loop : -3.29 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 8 HIS 0.003 0.001 HIS B 215 PHE 0.023 0.002 PHE C 346 TYR 0.017 0.001 TYR B 421 ARG 0.002 0.000 ARG A 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.632 Fit side-chains revert: symmetry clash REVERT: B 192 ASN cc_start: 0.7812 (OUTLIER) cc_final: 0.7458 (t0) REVERT: B 209 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7889 (tt0) REVERT: B 248 THR cc_start: 0.8738 (p) cc_final: 0.8423 (t) REVERT: C 40 ILE cc_start: 0.8842 (mm) cc_final: 0.8614 (mt) REVERT: C 250 LEU cc_start: 0.8756 (mm) cc_final: 0.8403 (mm) outliers start: 16 outliers final: 9 residues processed: 105 average time/residue: 0.1649 time to fit residues: 24.1162 Evaluate side-chains 98 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 192 ASN Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 21 CYS Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 314 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 26 optimal weight: 3.9990 chunk 14 optimal weight: 0.0010 chunk 39 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 49 optimal weight: 0.0040 chunk 25 optimal weight: 0.4980 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 51 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.139049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.112634 restraints weight = 10099.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.115141 restraints weight = 6976.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.116868 restraints weight = 5406.711| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6859 Z= 0.170 Angle : 0.640 10.097 9346 Z= 0.313 Chirality : 0.043 0.160 1052 Planarity : 0.005 0.050 1211 Dihedral : 4.873 23.591 963 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 2.19 % Allowed : 15.74 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.66 (0.29), residues: 858 helix: -0.32 (0.30), residues: 316 sheet: -1.48 (0.52), residues: 125 loop : -3.11 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 63 HIS 0.002 0.001 HIS C 51 PHE 0.020 0.001 PHE C 276 TYR 0.017 0.001 TYR B 421 ARG 0.003 0.000 ARG A 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.709 Fit side-chains revert: symmetry clash REVERT: B 192 ASN cc_start: 0.7766 (t0) cc_final: 0.7486 (t0) REVERT: B 209 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7764 (tt0) REVERT: B 248 THR cc_start: 0.8615 (p) cc_final: 0.8293 (t) REVERT: C 40 ILE cc_start: 0.8762 (mm) cc_final: 0.8473 (mt) REVERT: C 42 SER cc_start: 0.8409 (t) cc_final: 0.8191 (m) REVERT: C 250 LEU cc_start: 0.8683 (mm) cc_final: 0.8364 (mm) REVERT: C 251 ASP cc_start: 0.7599 (t0) cc_final: 0.7387 (t0) REVERT: C 351 MET cc_start: 0.8458 (ttm) cc_final: 0.8154 (ttm) REVERT: C 359 GLU cc_start: 0.8079 (mp0) cc_final: 0.7353 (mp0) outliers start: 15 outliers final: 9 residues processed: 109 average time/residue: 0.1558 time to fit residues: 23.9852 Evaluate side-chains 100 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 21 CYS Chi-restraints excluded: chain C residue 314 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 8 optimal weight: 0.1980 chunk 59 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 65 optimal weight: 0.0970 chunk 58 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 215 HIS C 51 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.137248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.110644 restraints weight = 10051.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.113096 restraints weight = 6976.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.114808 restraints weight = 5433.865| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6859 Z= 0.216 Angle : 0.638 8.771 9346 Z= 0.314 Chirality : 0.043 0.142 1052 Planarity : 0.005 0.045 1211 Dihedral : 4.801 24.359 963 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer: Outliers : 2.04 % Allowed : 17.06 % Favored : 80.90 % 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: -2.46 (0.29), residues: 858 helix: -0.13 (0.31), residues: 316 sheet: -1.36 (0.52), residues: 127 loop : -3.03 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 291 HIS 0.006 0.001 HIS C 51 PHE 0.015 0.001 PHE C 276 TYR 0.013 0.001 TYR B 421 ARG 0.002 0.000 ARG A 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.689 Fit side-chains REVERT: B 192 ASN cc_start: 0.7755 (t0) cc_final: 0.7505 (t0) REVERT: B 209 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7808 (tt0) REVERT: B 248 THR cc_start: 0.8646 (p) cc_final: 0.8331 (t) REVERT: C 40 ILE cc_start: 0.8803 (mm) cc_final: 0.8516 (mt) REVERT: C 42 SER cc_start: 0.8389 (t) cc_final: 0.8163 (m) REVERT: C 250 LEU cc_start: 0.8688 (mm) cc_final: 0.8370 (mm) REVERT: C 251 ASP cc_start: 0.7618 (t0) cc_final: 0.7418 (t0) REVERT: C 359 GLU cc_start: 0.8159 (mp0) cc_final: 0.7485 (mp0) outliers start: 14 outliers final: 10 residues processed: 98 average time/residue: 0.1496 time to fit residues: 20.8789 Evaluate side-chains 95 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 418 LEU Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 21 CYS Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 314 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 12 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 9 optimal weight: 0.0060 chunk 71 optimal weight: 8.9990 chunk 58 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN C 51 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.139602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.114725 restraints weight = 9868.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.116491 restraints weight = 7305.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.118083 restraints weight = 5974.691| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6859 Z= 0.188 Angle : 0.630 8.727 9346 Z= 0.308 Chirality : 0.042 0.143 1052 Planarity : 0.005 0.043 1211 Dihedral : 4.718 24.077 963 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 1.46 % Allowed : 17.78 % Favored : 80.76 % 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: -2.25 (0.30), residues: 858 helix: 0.12 (0.31), residues: 311 sheet: -1.26 (0.52), residues: 128 loop : -2.94 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 63 HIS 0.004 0.001 HIS C 51 PHE 0.022 0.001 PHE C 276 TYR 0.015 0.001 TYR B 421 ARG 0.008 0.000 ARG C 247 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.721 Fit side-chains REVERT: B 209 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7773 (tt0) REVERT: B 248 THR cc_start: 0.8632 (p) cc_final: 0.8291 (t) REVERT: C 40 ILE cc_start: 0.8799 (mm) cc_final: 0.8542 (mt) REVERT: C 250 LEU cc_start: 0.8607 (mm) cc_final: 0.8211 (mm) REVERT: C 251 ASP cc_start: 0.7640 (t0) cc_final: 0.7381 (t0) REVERT: C 359 GLU cc_start: 0.8153 (mp0) cc_final: 0.7472 (mp0) outliers start: 10 outliers final: 7 residues processed: 100 average time/residue: 0.1658 time to fit residues: 23.4016 Evaluate side-chains 94 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 21 CYS Chi-restraints excluded: chain C residue 314 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 31 optimal weight: 0.1980 chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 18 optimal weight: 0.0870 chunk 21 optimal weight: 1.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN C 51 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.139627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.113622 restraints weight = 10076.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.116068 restraints weight = 7046.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.117733 restraints weight = 5468.628| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6859 Z= 0.181 Angle : 0.631 12.766 9346 Z= 0.305 Chirality : 0.042 0.144 1052 Planarity : 0.005 0.042 1211 Dihedral : 4.573 24.389 963 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 1.75 % Allowed : 17.93 % Favored : 80.32 % 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: -2.01 (0.30), residues: 858 helix: 0.36 (0.31), residues: 310 sheet: -1.16 (0.52), residues: 128 loop : -2.81 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 63 HIS 0.006 0.001 HIS C 51 PHE 0.018 0.001 PHE C 276 TYR 0.017 0.001 TYR B 240 ARG 0.005 0.000 ARG A 30 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.706 Fit side-chains REVERT: B 209 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7788 (tt0) REVERT: B 248 THR cc_start: 0.8619 (p) cc_final: 0.8267 (t) REVERT: C 40 ILE cc_start: 0.8776 (mm) cc_final: 0.8551 (mt) REVERT: C 250 LEU cc_start: 0.8623 (mm) cc_final: 0.8253 (mm) REVERT: C 359 GLU cc_start: 0.8148 (mp0) cc_final: 0.7451 (mp0) outliers start: 12 outliers final: 8 residues processed: 103 average time/residue: 0.1519 time to fit residues: 22.2409 Evaluate side-chains 94 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 21 CYS Chi-restraints excluded: chain C residue 255 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 36 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 38 optimal weight: 0.3980 chunk 80 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 69 optimal weight: 0.4980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN C 51 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.139696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.115109 restraints weight = 9955.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.117136 restraints weight = 7366.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.118471 restraints weight = 5946.527| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6859 Z= 0.205 Angle : 0.653 12.734 9346 Z= 0.314 Chirality : 0.042 0.147 1052 Planarity : 0.005 0.042 1211 Dihedral : 4.607 24.318 963 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 1.60 % Allowed : 18.51 % Favored : 79.88 % 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: -1.91 (0.30), residues: 858 helix: 0.47 (0.31), residues: 310 sheet: -1.09 (0.52), residues: 126 loop : -2.79 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 168 HIS 0.003 0.001 HIS C 122 PHE 0.019 0.001 PHE C 276 TYR 0.014 0.001 TYR B 240 ARG 0.005 0.000 ARG C 299 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.721 Fit side-chains REVERT: B 209 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7795 (tt0) REVERT: B 248 THR cc_start: 0.8645 (p) cc_final: 0.8287 (t) REVERT: C 40 ILE cc_start: 0.8812 (mm) cc_final: 0.8598 (mt) REVERT: C 250 LEU cc_start: 0.8696 (mm) cc_final: 0.8401 (mm) REVERT: C 359 GLU cc_start: 0.8147 (mp0) cc_final: 0.7472 (mp0) outliers start: 11 outliers final: 9 residues processed: 93 average time/residue: 0.1526 time to fit residues: 20.7230 Evaluate side-chains 91 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 21 CYS Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 314 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 50 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 6 optimal weight: 0.3980 chunk 8 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN C 51 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.139903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.116225 restraints weight = 10074.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.117071 restraints weight = 8246.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.118466 restraints weight = 6829.982| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6859 Z= 0.197 Angle : 0.645 12.186 9346 Z= 0.312 Chirality : 0.042 0.147 1052 Planarity : 0.005 0.042 1211 Dihedral : 4.555 25.488 963 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 1.46 % Allowed : 18.95 % Favored : 79.59 % 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: -1.83 (0.30), residues: 858 helix: 0.54 (0.31), residues: 310 sheet: -1.16 (0.51), residues: 128 loop : -2.70 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 63 HIS 0.004 0.001 HIS C 51 PHE 0.020 0.001 PHE C 276 TYR 0.014 0.001 TYR B 240 ARG 0.005 0.000 ARG C 299 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.697 Fit side-chains REVERT: B 209 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7758 (tt0) REVERT: B 248 THR cc_start: 0.8604 (p) cc_final: 0.8246 (t) REVERT: C 40 ILE cc_start: 0.8845 (mm) cc_final: 0.8633 (mt) REVERT: C 250 LEU cc_start: 0.8680 (mm) cc_final: 0.8331 (mm) REVERT: C 359 GLU cc_start: 0.8102 (mp0) cc_final: 0.7475 (mp0) outliers start: 10 outliers final: 7 residues processed: 92 average time/residue: 0.1455 time to fit residues: 19.4222 Evaluate side-chains 93 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 21 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 5 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 55 optimal weight: 0.3980 chunk 21 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN C 51 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.140473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.116433 restraints weight = 9940.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.117894 restraints weight = 7462.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.118314 restraints weight = 6277.724| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6859 Z= 0.190 Angle : 0.640 12.119 9346 Z= 0.308 Chirality : 0.042 0.148 1052 Planarity : 0.005 0.042 1211 Dihedral : 4.503 24.312 963 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 1.31 % Allowed : 19.24 % Favored : 79.45 % 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: -1.69 (0.30), residues: 858 helix: 0.68 (0.32), residues: 310 sheet: -1.11 (0.51), residues: 128 loop : -2.64 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 63 HIS 0.003 0.001 HIS C 122 PHE 0.018 0.001 PHE C 276 TYR 0.011 0.001 TYR B 421 ARG 0.005 0.000 ARG C 299 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2145.80 seconds wall clock time: 37 minutes 55.96 seconds (2275.96 seconds total)