Starting phenix.real_space_refine on Tue Feb 11 20:50:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wuj_21914/02_2025/6wuj_21914.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wuj_21914/02_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_21914/02_2025/6wuj_21914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wuj_21914/02_2025/6wuj_21914.map" model { file = "/net/cci-nas-00/data/ceres_data/6wuj_21914/02_2025/6wuj_21914.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wuj_21914/02_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-5592/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: 4.28, per 1000 atoms: 0.64 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: 1.73 Conformation dependent library (CDL) restraints added in 1.1 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: 0.73 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: 2.40 Time building geometry restraints manager: 2.03 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: 0.420 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.350 Find NCS groups from input model: 0.120 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: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.150 ------------------------------------------------------------------------------- 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 : 0.757 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: 0.2685 time to fit residues: 41.7109 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 : 0.784 ------------------------------------------------------------------------------- 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 = 0.110002 restraints weight = 10018.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.112380 restraints weight = 6967.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.113932 restraints weight = 5442.518| |-----------------------------------------------------------------------------| 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 43.382 964 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 : 0.831 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: 0.1983 time to fit residues: 31.4493 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 : 0.834 ------------------------------------------------------------------------------- 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: 0.4980 chunk 82 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 chunk 0 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 = 0.3595 r_free = 0.3595 target = 0.136496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.110798 restraints weight = 10177.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.113299 restraints weight = 6991.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.114281 restraints weight = 4998.522| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6859 Z= 0.256 Angle : 0.680 8.798 9346 Z= 0.336 Chirality : 0.045 0.146 1052 Planarity : 0.006 0.049 1211 Dihedral : 5.327 32.521 964 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.89 % Favored : 88.11 % Rotamer: Outliers : 2.48 % Allowed : 12.97 % Favored : 84.55 % 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: -3.44 (0.28), residues: 858 helix: -1.01 (0.29), residues: 306 sheet: -2.08 (0.50), residues: 129 loop : -3.43 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 8 HIS 0.003 0.001 HIS B 215 PHE 0.015 0.002 PHE A 27 TYR 0.011 0.001 TYR B 240 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: 17 poor density : 94 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 192 ASN cc_start: 0.7846 (OUTLIER) cc_final: 0.7431 (t0) REVERT: B 248 THR cc_start: 0.8727 (p) cc_final: 0.8422 (t) REVERT: C 40 ILE cc_start: 0.8785 (mm) cc_final: 0.8544 (mt) REVERT: C 250 LEU cc_start: 0.8745 (mm) cc_final: 0.8411 (mm) outliers start: 17 outliers final: 8 residues processed: 103 average time/residue: 0.1647 time to fit residues: 23.6674 Evaluate side-chains 100 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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 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: 7.9990 chunk 60 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 82 optimal weight: 0.0270 chunk 25 optimal weight: 0.4980 chunk 39 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 overall best weight: 1.2242 ------------------------------------------------------------------------------- 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 = 0.3601 r_free = 0.3601 target = 0.136856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.111531 restraints weight = 10151.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.113946 restraints weight = 7016.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.114904 restraints weight = 5044.968| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2240 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= 0.239 Angle : 0.668 9.701 9346 Z= 0.327 Chirality : 0.044 0.146 1052 Planarity : 0.005 0.049 1211 Dihedral : 5.107 25.949 963 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.19 % Favored : 88.81 % Rotamer: Outliers : 2.04 % Allowed : 13.85 % Favored : 84.11 % 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: -3.03 (0.29), residues: 858 helix: -0.56 (0.30), residues: 307 sheet: -1.91 (0.50), residues: 129 loop : -3.26 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 8 HIS 0.002 0.001 HIS B 215 PHE 0.016 0.001 PHE C 276 TYR 0.010 0.001 TYR B 240 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 114 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.851 Fit side-chains revert: symmetry clash REVERT: B 192 ASN cc_start: 0.7772 (OUTLIER) cc_final: 0.7434 (t0) REVERT: B 209 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7882 (tt0) REVERT: B 248 THR cc_start: 0.8698 (p) cc_final: 0.8387 (t) REVERT: B 478 HIS cc_start: 0.7340 (t-90) cc_final: 0.7093 (t-90) REVERT: C 40 ILE cc_start: 0.8835 (mm) cc_final: 0.8611 (mt) REVERT: C 250 LEU cc_start: 0.8751 (mm) cc_final: 0.8413 (mm) outliers start: 14 outliers final: 9 residues processed: 107 average time/residue: 0.1650 time to fit residues: 24.6447 Evaluate side-chains 97 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 26 optimal weight: 0.9980 chunk 14 optimal weight: 0.0570 chunk 39 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 49 optimal weight: 0.0980 chunk 25 optimal weight: 4.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 51 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.139256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.115521 restraints weight = 10059.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.115476 restraints weight = 8557.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.116454 restraints weight = 7434.474| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6859 Z= 0.170 Angle : 0.634 10.551 9346 Z= 0.310 Chirality : 0.042 0.157 1052 Planarity : 0.005 0.052 1211 Dihedral : 4.830 23.342 963 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 2.04 % Allowed : 15.74 % Favored : 82.22 % 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: -2.59 (0.29), residues: 858 helix: -0.26 (0.30), residues: 316 sheet: -1.47 (0.52), residues: 127 loop : -3.08 (0.29), residues: 415 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 0.021 0.001 PHE C 276 TYR 0.012 0.001 TYR C 278 ARG 0.002 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 115 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: B 192 ASN cc_start: 0.7849 (t0) cc_final: 0.7565 (t0) REVERT: B 209 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.7789 (tt0) REVERT: B 248 THR cc_start: 0.8620 (p) cc_final: 0.8301 (t) REVERT: C 250 LEU cc_start: 0.8685 (mm) cc_final: 0.8343 (mm) REVERT: C 251 ASP cc_start: 0.7556 (t0) cc_final: 0.7345 (t0) REVERT: C 351 MET cc_start: 0.8362 (ttm) cc_final: 0.8093 (ttm) REVERT: C 359 GLU cc_start: 0.8062 (mp0) cc_final: 0.7385 (mp0) outliers start: 14 outliers final: 8 residues processed: 109 average time/residue: 0.1472 time to fit residues: 22.9544 Evaluate side-chains 100 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.799 ------------------------------------------------------------------------------- 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 314 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 8 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 10 optimal weight: 0.0970 chunk 54 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 37 optimal weight: 0.0870 overall best weight: 0.5756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 51 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 = 0.3635 r_free = 0.3635 target = 0.139711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.115301 restraints weight = 10008.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.116578 restraints weight = 7859.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.117251 restraints weight = 6563.288| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6859 Z= 0.168 Angle : 0.619 8.735 9346 Z= 0.302 Chirality : 0.042 0.140 1052 Planarity : 0.005 0.046 1211 Dihedral : 4.653 23.697 963 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 1.60 % Allowed : 17.06 % Favored : 81.34 % 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: -2.32 (0.29), residues: 858 helix: 0.01 (0.31), residues: 317 sheet: -1.30 (0.51), residues: 128 loop : -2.97 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 63 HIS 0.006 0.001 HIS C 51 PHE 0.020 0.001 PHE C 276 TYR 0.009 0.001 TYR C 278 ARG 0.002 0.000 ARG A 40 *********************** 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 107 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: A 30 ARG cc_start: 0.6550 (mtt180) cc_final: 0.6129 (mtt-85) REVERT: B 209 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7719 (tt0) REVERT: B 248 THR cc_start: 0.8587 (p) cc_final: 0.8233 (t) REVERT: C 250 LEU cc_start: 0.8648 (mm) cc_final: 0.8319 (mm) REVERT: C 251 ASP cc_start: 0.7562 (t0) cc_final: 0.7342 (t0) REVERT: C 359 GLU cc_start: 0.8140 (mp0) cc_final: 0.7486 (mp0) outliers start: 11 outliers final: 8 residues processed: 103 average time/residue: 0.1596 time to fit residues: 22.9225 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 : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 SER 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: 2.9990 chunk 76 optimal weight: 5.9990 chunk 9 optimal weight: 0.0980 chunk 71 optimal weight: 8.9990 chunk 58 optimal weight: 0.0010 chunk 50 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 49 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- 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 = 0.3628 r_free = 0.3628 target = 0.138887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.112919 restraints weight = 10090.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.115354 restraints weight = 6987.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.117010 restraints weight = 5436.351| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6859 Z= 0.202 Angle : 0.624 8.621 9346 Z= 0.305 Chirality : 0.042 0.142 1052 Planarity : 0.005 0.045 1211 Dihedral : 4.657 23.771 963 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 1.60 % Allowed : 18.22 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.20 (0.30), residues: 858 helix: 0.15 (0.31), residues: 317 sheet: -1.48 (0.50), residues: 134 loop : -2.86 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 168 HIS 0.003 0.001 HIS C 51 PHE 0.020 0.001 PHE C 276 TYR 0.012 0.001 TYR C 278 ARG 0.002 0.000 ARG B 494 *********************** 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 97 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.717 Fit side-chains revert: symmetry clash REVERT: A 30 ARG cc_start: 0.6578 (mtt180) cc_final: 0.6159 (mtt-85) REVERT: B 209 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7747 (tt0) REVERT: B 248 THR cc_start: 0.8629 (p) cc_final: 0.8293 (t) REVERT: C 251 ASP cc_start: 0.7566 (t0) cc_final: 0.7312 (t0) REVERT: C 359 GLU cc_start: 0.8176 (mp0) cc_final: 0.7494 (mp0) outliers start: 11 outliers final: 9 residues processed: 93 average time/residue: 0.1639 time to fit residues: 21.2115 Evaluate side-chains 95 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.696 ------------------------------------------------------------------------------- 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 314 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 31 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 28 optimal weight: 6.9990 chunk 50 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 18 optimal weight: 0.0570 chunk 21 optimal weight: 0.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 GLN B 419 GLN C 51 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.140426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.114150 restraints weight = 10078.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.116618 restraints weight = 7031.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.118309 restraints weight = 5473.978| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6859 Z= 0.171 Angle : 0.608 8.421 9346 Z= 0.297 Chirality : 0.042 0.146 1052 Planarity : 0.005 0.043 1211 Dihedral : 4.544 24.780 963 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 1.46 % Allowed : 18.37 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.02 (0.30), residues: 858 helix: 0.34 (0.31), residues: 316 sheet: -1.35 (0.50), residues: 134 loop : -2.80 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 63 HIS 0.005 0.001 HIS C 51 PHE 0.018 0.001 PHE C 276 TYR 0.009 0.001 TYR C 278 ARG 0.002 0.000 ARG B 494 *********************** 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 101 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.776 Fit side-chains REVERT: A 30 ARG cc_start: 0.6560 (mtt180) cc_final: 0.6156 (mtt-85) REVERT: B 209 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7695 (tt0) REVERT: B 248 THR cc_start: 0.8598 (p) cc_final: 0.8242 (t) REVERT: C 251 ASP cc_start: 0.7553 (t0) cc_final: 0.7317 (t0) REVERT: C 359 GLU cc_start: 0.8156 (mp0) cc_final: 0.7452 (mp0) outliers start: 10 outliers final: 8 residues processed: 96 average time/residue: 0.1667 time to fit residues: 22.4924 Evaluate side-chains 95 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.694 ------------------------------------------------------------------------------- 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 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 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: 4.9990 chunk 38 optimal weight: 0.4980 chunk 80 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN A 211 GLN B 419 GLN C 51 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.137856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.113112 restraints weight = 10023.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.115073 restraints weight = 7470.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.116298 restraints weight = 6084.585| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 6859 Z= 0.259 Angle : 0.664 8.195 9346 Z= 0.323 Chirality : 0.044 0.148 1052 Planarity : 0.005 0.042 1211 Dihedral : 4.747 25.753 963 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.72 % Favored : 89.28 % Rotamer: Outliers : 2.04 % Allowed : 19.10 % Favored : 78.86 % 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: 0.45 (0.32), residues: 303 sheet: -1.44 (0.50), residues: 134 loop : -2.76 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 168 HIS 0.003 0.001 HIS C 122 PHE 0.019 0.001 PHE C 276 TYR 0.012 0.001 TYR B 240 ARG 0.002 0.000 ARG B 426 *********************** 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 95 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.761 Fit side-chains REVERT: B 209 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7747 (tt0) REVERT: B 248 THR cc_start: 0.8667 (p) cc_final: 0.8350 (t) REVERT: C 250 LEU cc_start: 0.8714 (mm) cc_final: 0.8373 (mm) REVERT: C 251 ASP cc_start: 0.7610 (t0) cc_final: 0.7320 (t0) REVERT: C 359 GLU cc_start: 0.8131 (mp0) cc_final: 0.7454 (mp0) outliers start: 14 outliers final: 11 residues processed: 88 average time/residue: 0.1617 time to fit residues: 20.1858 Evaluate side-chains 91 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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 B residue 503 LEU 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: 0.4980 chunk 42 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 75 optimal weight: 0.0170 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- 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 = 0.140435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.116564 restraints weight = 10062.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.117862 restraints weight = 7589.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.118180 restraints weight = 6155.538| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6859 Z= 0.172 Angle : 0.641 12.681 9346 Z= 0.307 Chirality : 0.042 0.147 1052 Planarity : 0.005 0.043 1211 Dihedral : 4.552 23.825 963 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 1.60 % Allowed : 19.39 % Favored : 79.01 % 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: -1.76 (0.30), residues: 858 helix: 0.61 (0.32), residues: 309 sheet: -1.12 (0.51), residues: 128 loop : -2.66 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 63 HIS 0.002 0.001 HIS C 122 PHE 0.021 0.001 PHE C 276 TYR 0.015 0.001 TYR B 240 ARG 0.004 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 95 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.701 Fit side-chains REVERT: B 209 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7639 (tt0) REVERT: B 248 THR cc_start: 0.8601 (p) cc_final: 0.8283 (t) REVERT: C 250 LEU cc_start: 0.8680 (mm) cc_final: 0.8339 (mm) REVERT: C 251 ASP cc_start: 0.7546 (t0) cc_final: 0.7288 (t0) REVERT: C 359 GLU cc_start: 0.8132 (mp0) cc_final: 0.7463 (mp0) outliers start: 11 outliers final: 8 residues processed: 91 average time/residue: 0.1572 time to fit residues: 20.3153 Evaluate side-chains 93 residues out of total 686 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 5 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 75 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 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 = 0.3628 r_free = 0.3628 target = 0.139834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.116341 restraints weight = 9952.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.117212 restraints weight = 7669.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.117485 restraints weight = 6480.584| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6859 Z= 0.195 Angle : 0.645 13.228 9346 Z= 0.309 Chirality : 0.042 0.143 1052 Planarity : 0.005 0.042 1211 Dihedral : 4.525 26.462 963 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 1.75 % Allowed : 19.24 % Favored : 79.01 % 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: -1.71 (0.30), residues: 858 helix: 0.69 (0.32), residues: 309 sheet: -1.35 (0.50), residues: 134 loop : -2.57 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 63 HIS 0.006 0.001 HIS C 51 PHE 0.018 0.001 PHE C 276 TYR 0.011 0.001 TYR C 278 ARG 0.003 0.000 ARG C 299 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2094.11 seconds wall clock time: 38 minutes 27.62 seconds (2307.62 seconds total)