Starting phenix.real_space_refine on Thu Sep 18 12:58:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o11_49994/09_2025/9o11_49994.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o11_49994/09_2025/9o11_49994.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9o11_49994/09_2025/9o11_49994.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o11_49994/09_2025/9o11_49994.map" model { file = "/net/cci-nas-00/data/ceres_data/9o11_49994/09_2025/9o11_49994.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o11_49994/09_2025/9o11_49994.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.013 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: 5 Type Number sf(0) Gaussians S 44 5.16 5 C 5520 2.51 5 N 1356 2.21 5 O 1444 1.98 5 H 8772 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17136 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 4284 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain: "B" Number of atoms: 4284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 4284 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain: "C" Number of atoms: 4284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 4284 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain: "D" Number of atoms: 4284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 4284 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Time building chain proxies: 3.05, per 1000 atoms: 0.18 Number of scatterers: 17136 At special positions: 0 Unit cell: (119.623, 119.623, 78.015, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 O 1444 8.00 N 1356 7.00 C 5520 6.00 H 8772 1.00 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: 1.28 Conformation dependent library (CDL) restraints added in 469.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1992 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 4 sheets defined 83.2% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 168 through 181 Processing helix chain 'A' and resid 185 through 209 Processing helix chain 'A' and resid 226 through 251 Processing helix chain 'A' and resid 253 through 259 Processing helix chain 'A' and resid 260 through 269 Processing helix chain 'A' and resid 270 through 282 removed outlier: 3.895A pdb=" N TYR A 274 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 302 removed outlier: 4.164A pdb=" N ARG A 294 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLN A 297 " --> pdb=" O ARG A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 313 removed outlier: 3.627A pdb=" N LEU A 310 " --> pdb=" O ILE A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 327 removed outlier: 3.594A pdb=" N GLN A 318 " --> pdb=" O SER A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 354 removed outlier: 3.611A pdb=" N ILE A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE A 351 " --> pdb=" O SER A 347 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA A 352 " --> pdb=" O LEU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 366 No H-bonds generated for 'chain 'A' and resid 364 through 366' Processing helix chain 'A' and resid 367 through 376 Processing helix chain 'A' and resid 387 through 406 removed outlier: 3.553A pdb=" N CYS A 398 " --> pdb=" O GLY A 394 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE A 399 " --> pdb=" O GLY A 395 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL A 402 " --> pdb=" O CYS A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 426 removed outlier: 3.853A pdb=" N GLN A 423 " --> pdb=" O PHE A 419 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS A 424 " --> pdb=" O TYR A 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 181 Processing helix chain 'B' and resid 182 through 184 No H-bonds generated for 'chain 'B' and resid 182 through 184' Processing helix chain 'B' and resid 185 through 209 Processing helix chain 'B' and resid 226 through 251 Processing helix chain 'B' and resid 253 through 260 removed outlier: 3.912A pdb=" N GLY B 260 " --> pdb=" O LYS B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 269 removed outlier: 3.774A pdb=" N ASP B 266 " --> pdb=" O LEU B 262 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU B 267 " --> pdb=" O ASN B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 281 removed outlier: 3.897A pdb=" N TYR B 274 " --> pdb=" O ILE B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 302 removed outlier: 4.753A pdb=" N ARG B 294 " --> pdb=" O GLN B 290 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLN B 297 " --> pdb=" O ARG B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 313 removed outlier: 3.630A pdb=" N LEU B 310 " --> pdb=" O ILE B 307 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG B 312 " --> pdb=" O LYS B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 327 removed outlier: 3.660A pdb=" N GLN B 318 " --> pdb=" O SER B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 354 removed outlier: 3.697A pdb=" N ILE B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE B 351 " --> pdb=" O SER B 347 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA B 352 " --> pdb=" O LEU B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 366 No H-bonds generated for 'chain 'B' and resid 364 through 366' Processing helix chain 'B' and resid 367 through 376 removed outlier: 3.516A pdb=" N THR B 376 " --> pdb=" O THR B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 406 removed outlier: 3.728A pdb=" N CYS B 398 " --> pdb=" O GLY B 394 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE B 399 " --> pdb=" O GLY B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 426 removed outlier: 3.730A pdb=" N GLN B 423 " --> pdb=" O PHE B 419 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS B 424 " --> pdb=" O TYR B 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 181 Processing helix chain 'C' and resid 182 through 184 No H-bonds generated for 'chain 'C' and resid 182 through 184' Processing helix chain 'C' and resid 185 through 209 Processing helix chain 'C' and resid 226 through 251 Processing helix chain 'C' and resid 253 through 260 removed outlier: 3.891A pdb=" N GLY C 260 " --> pdb=" O LYS C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 269 removed outlier: 3.788A pdb=" N LEU C 267 " --> pdb=" O ASN C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 removed outlier: 3.792A pdb=" N TYR C 274 " --> pdb=" O ILE C 270 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE C 277 " --> pdb=" O TYR C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 302 Processing helix chain 'C' and resid 303 through 313 removed outlier: 3.627A pdb=" N LEU C 310 " --> pdb=" O ILE C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 327 removed outlier: 3.590A pdb=" N GLN C 318 " --> pdb=" O SER C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 354 removed outlier: 3.680A pdb=" N ILE C 335 " --> pdb=" O LEU C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 366 No H-bonds generated for 'chain 'C' and resid 364 through 366' Processing helix chain 'C' and resid 367 through 376 removed outlier: 3.509A pdb=" N THR C 376 " --> pdb=" O THR C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 406 removed outlier: 3.781A pdb=" N ILE C 399 " --> pdb=" O GLY C 395 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL C 402 " --> pdb=" O CYS C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 426 removed outlier: 3.699A pdb=" N GLN C 423 " --> pdb=" O PHE C 419 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LYS C 424 " --> pdb=" O TYR C 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 181 Processing helix chain 'D' and resid 182 through 184 No H-bonds generated for 'chain 'D' and resid 182 through 184' Processing helix chain 'D' and resid 185 through 209 Processing helix chain 'D' and resid 226 through 251 Processing helix chain 'D' and resid 253 through 260 removed outlier: 3.930A pdb=" N GLY D 260 " --> pdb=" O LYS D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 269 removed outlier: 3.785A pdb=" N LEU D 267 " --> pdb=" O ASN D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 282 removed outlier: 3.726A pdb=" N TYR D 274 " --> pdb=" O ILE D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 302 Processing helix chain 'D' and resid 303 through 313 removed outlier: 3.669A pdb=" N LEU D 310 " --> pdb=" O ILE D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 327 removed outlier: 3.579A pdb=" N GLN D 318 " --> pdb=" O SER D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 354 removed outlier: 3.785A pdb=" N ILE D 335 " --> pdb=" O LEU D 331 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE D 351 " --> pdb=" O SER D 347 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA D 352 " --> pdb=" O LEU D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 366 No H-bonds generated for 'chain 'D' and resid 364 through 366' Processing helix chain 'D' and resid 367 through 376 removed outlier: 3.513A pdb=" N THR D 376 " --> pdb=" O THR D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 406 removed outlier: 3.561A pdb=" N CYS D 398 " --> pdb=" O GLY D 394 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE D 399 " --> pdb=" O GLY D 395 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL D 402 " --> pdb=" O CYS D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 426 removed outlier: 3.966A pdb=" N GLN D 423 " --> pdb=" O PHE D 419 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LYS D 424 " --> pdb=" O TYR D 420 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 216 through 217 Processing sheet with id=AA2, first strand: chain 'B' and resid 216 through 217 Processing sheet with id=AA3, first strand: chain 'C' and resid 216 through 217 Processing sheet with id=AA4, first strand: chain 'D' and resid 216 through 217 596 hydrogen bonds defined for protein. 1695 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: 3.48 Time building geometry restraints manager: 1.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8752 1.03 - 1.23: 29 1.23 - 1.42: 3443 1.42 - 1.62: 5028 1.62 - 1.81: 68 Bond restraints: 17320 Sorted by residual: bond pdb=" N CYS D 167 " pdb=" CA CYS D 167 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.10e+00 bond pdb=" N CYS B 167 " pdb=" CA CYS B 167 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 bond pdb=" N CYS A 167 " pdb=" CA CYS A 167 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 bond pdb=" N CYS C 167 " pdb=" CA CYS C 167 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N CYS A 167 " pdb=" H CYS A 167 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.33e+00 ... (remaining 17315 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.92: 28231 0.92 - 1.84: 3045 1.84 - 2.76: 157 2.76 - 3.68: 36 3.68 - 4.60: 23 Bond angle restraints: 31492 Sorted by residual: angle pdb=" N LYS C 424 " pdb=" CA LYS C 424 " pdb=" C LYS C 424 " ideal model delta sigma weight residual 114.56 110.22 4.34 1.27e+00 6.20e-01 1.17e+01 angle pdb=" CA LYS C 424 " pdb=" C LYS C 424 " pdb=" N ARG C 425 " ideal model delta sigma weight residual 119.26 117.15 2.11 1.14e+00 7.69e-01 3.44e+00 angle pdb=" CA TYR A 380 " pdb=" CB TYR A 380 " pdb=" CG TYR A 380 " ideal model delta sigma weight residual 113.90 117.19 -3.29 1.80e+00 3.09e-01 3.35e+00 angle pdb=" CA TYR B 380 " pdb=" CB TYR B 380 " pdb=" CG TYR B 380 " ideal model delta sigma weight residual 113.90 117.12 -3.22 1.80e+00 3.09e-01 3.20e+00 angle pdb=" CA TYR C 380 " pdb=" CB TYR C 380 " pdb=" CG TYR C 380 " ideal model delta sigma weight residual 113.90 117.10 -3.20 1.80e+00 3.09e-01 3.16e+00 ... (remaining 31487 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 7404 17.98 - 35.96: 451 35.96 - 53.94: 165 53.94 - 71.92: 24 71.92 - 89.90: 16 Dihedral angle restraints: 8060 sinusoidal: 4384 harmonic: 3676 Sorted by residual: dihedral pdb=" CA ARG B 425 " pdb=" C ARG B 425 " pdb=" N GLN B 426 " pdb=" CA GLN B 426 " ideal model delta harmonic sigma weight residual -180.00 -160.26 -19.74 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA ARG A 425 " pdb=" C ARG A 425 " pdb=" N GLN A 426 " pdb=" CA GLN A 426 " ideal model delta harmonic sigma weight residual -180.00 -160.81 -19.19 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA TYR D 380 " pdb=" C TYR D 380 " pdb=" N GLY D 381 " pdb=" CA GLY D 381 " ideal model delta harmonic sigma weight residual 180.00 -163.09 -16.91 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 8057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 729 0.023 - 0.047: 387 0.047 - 0.070: 151 0.070 - 0.094: 68 0.094 - 0.117: 29 Chirality restraints: 1364 Sorted by residual: chirality pdb=" CA PRO D 410 " pdb=" N PRO D 410 " pdb=" C PRO D 410 " pdb=" CB PRO D 410 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.43e-01 chirality pdb=" CA PRO B 410 " pdb=" N PRO B 410 " pdb=" C PRO B 410 " pdb=" CB PRO B 410 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.40e-01 chirality pdb=" CA PRO C 410 " pdb=" N PRO C 410 " pdb=" C PRO C 410 " pdb=" CB PRO C 410 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.33e-01 ... (remaining 1361 not shown) Planarity restraints: 2408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 418 " -0.008 2.00e-02 2.50e+03 1.69e-02 2.87e+00 pdb=" C GLU D 418 " 0.029 2.00e-02 2.50e+03 pdb=" O GLU D 418 " -0.011 2.00e-02 2.50e+03 pdb=" N PHE D 419 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 407 " 0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO A 408 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 408 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 408 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 407 " 0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO D 408 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO D 408 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 408 " 0.022 5.00e-02 4.00e+02 ... (remaining 2405 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 1149 2.22 - 2.81: 36058 2.81 - 3.41: 44318 3.41 - 4.00: 55644 4.00 - 4.60: 86570 Nonbonded interactions: 223739 Sorted by model distance: nonbonded pdb=" OD2 ASP A 266 " pdb="HH21 ARG A 312 " model vdw 1.622 2.450 nonbonded pdb=" OE2 GLU B 353 " pdb=" HG1 THR B 387 " model vdw 1.627 2.450 nonbonded pdb=" OG SER D 327 " pdb="HD21 ASN D 415 " model vdw 1.649 2.450 nonbonded pdb=" OG SER B 327 " pdb="HD21 ASN B 415 " model vdw 1.655 2.450 nonbonded pdb=" OG SER C 327 " pdb="HD21 ASN C 415 " model vdw 1.663 2.450 ... (remaining 223734 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 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: 0.080 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 15.150 Find NCS groups from input model: 0.200 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 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 : 0.004 0.033 8548 Z= 0.153 Angle : 0.489 4.448 11572 Z= 0.268 Chirality : 0.037 0.117 1364 Planarity : 0.004 0.039 1408 Dihedral : 13.208 89.904 3140 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.11 % Allowed : 7.76 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.27), residues: 1036 helix: 1.80 (0.19), residues: 808 sheet: None (None), residues: 0 loop : -1.28 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 303 TYR 0.015 0.002 TYR A 273 PHE 0.007 0.001 PHE C 416 TRP 0.006 0.001 TRP A 370 HIS 0.002 0.001 HIS D 231 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 8548) covalent geometry : angle 0.48877 (11572) hydrogen bonds : bond 0.11243 ( 596) hydrogen bonds : angle 4.14936 ( 1695) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 247 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 ASP cc_start: 0.8755 (m-30) cc_final: 0.8479 (m-30) REVERT: A 226 ASN cc_start: 0.8665 (t0) cc_final: 0.8427 (t0) REVERT: B 177 ASP cc_start: 0.8742 (m-30) cc_final: 0.8538 (m-30) REVERT: B 180 GLU cc_start: 0.8603 (tt0) cc_final: 0.8216 (tt0) REVERT: B 226 ASN cc_start: 0.8676 (t0) cc_final: 0.8332 (t0) REVERT: B 297 GLN cc_start: 0.9113 (mm110) cc_final: 0.8876 (mm-40) REVERT: C 177 ASP cc_start: 0.8576 (m-30) cc_final: 0.8369 (m-30) REVERT: C 180 GLU cc_start: 0.8528 (tt0) cc_final: 0.8205 (tt0) REVERT: C 226 ASN cc_start: 0.8683 (t0) cc_final: 0.8398 (t0) REVERT: C 297 GLN cc_start: 0.9020 (mm110) cc_final: 0.8776 (mm110) REVERT: D 177 ASP cc_start: 0.8693 (m-30) cc_final: 0.8410 (m-30) REVERT: D 180 GLU cc_start: 0.8541 (tt0) cc_final: 0.8193 (tt0) REVERT: D 226 ASN cc_start: 0.8673 (t0) cc_final: 0.8395 (t0) outliers start: 1 outliers final: 1 residues processed: 248 average time/residue: 0.2482 time to fit residues: 79.1833 Evaluate side-chains 198 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 197 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 331 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 0.2980 chunk 61 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 GLN B 423 GLN C 263 ASN C 291 ASN C 423 GLN D 209 ASN D 291 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.125135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.087006 restraints weight = 45861.723| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 3.29 r_work: 0.3155 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8548 Z= 0.141 Angle : 0.556 7.317 11572 Z= 0.297 Chirality : 0.036 0.111 1364 Planarity : 0.005 0.050 1408 Dihedral : 3.982 44.215 1114 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.65 % Allowed : 11.64 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.97 (0.28), residues: 1036 helix: 2.00 (0.19), residues: 808 sheet: None (None), residues: 0 loop : -1.26 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 247 TYR 0.012 0.001 TYR D 380 PHE 0.011 0.001 PHE C 416 TRP 0.006 0.001 TRP A 370 HIS 0.002 0.001 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 8548) covalent geometry : angle 0.55618 (11572) hydrogen bonds : bond 0.04392 ( 596) hydrogen bonds : angle 3.70527 ( 1695) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 209 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 ASP cc_start: 0.9115 (m-30) cc_final: 0.8761 (m-30) REVERT: A 180 GLU cc_start: 0.9151 (tt0) cc_final: 0.8790 (mt-10) REVERT: A 226 ASN cc_start: 0.8250 (t0) cc_final: 0.7785 (t0) REVERT: A 243 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8315 (mt-10) REVERT: A 426 GLN cc_start: 0.8694 (tm-30) cc_final: 0.8267 (tm-30) REVERT: B 177 ASP cc_start: 0.8976 (m-30) cc_final: 0.8720 (m-30) REVERT: B 180 GLU cc_start: 0.9013 (tt0) cc_final: 0.8738 (tt0) REVERT: B 226 ASN cc_start: 0.8213 (t0) cc_final: 0.7542 (t0) REVERT: B 228 GLN cc_start: 0.8715 (mp10) cc_final: 0.8313 (mp10) REVERT: C 177 ASP cc_start: 0.8908 (m-30) cc_final: 0.8696 (m-30) REVERT: C 226 ASN cc_start: 0.8223 (t0) cc_final: 0.7798 (t0) REVERT: C 243 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8342 (mt-10) REVERT: C 297 GLN cc_start: 0.9117 (mm110) cc_final: 0.8817 (mm110) REVERT: D 177 ASP cc_start: 0.9000 (m-30) cc_final: 0.8691 (m-30) REVERT: D 180 GLU cc_start: 0.9009 (tt0) cc_final: 0.8767 (tt0) outliers start: 6 outliers final: 4 residues processed: 211 average time/residue: 0.2108 time to fit residues: 59.1629 Evaluate side-chains 206 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 202 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain D residue 266 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 72 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 31 optimal weight: 20.0000 chunk 96 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 102 optimal weight: 0.7980 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.122963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.084693 restraints weight = 46878.914| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 3.30 r_work: 0.3101 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8548 Z= 0.213 Angle : 0.581 7.741 11572 Z= 0.309 Chirality : 0.037 0.112 1364 Planarity : 0.004 0.040 1408 Dihedral : 3.690 23.672 1112 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.08 % Allowed : 11.75 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.94 (0.27), residues: 1036 helix: 2.02 (0.19), residues: 808 sheet: None (None), residues: 0 loop : -1.46 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 293 TYR 0.012 0.001 TYR C 380 PHE 0.016 0.001 PHE A 289 TRP 0.004 0.001 TRP B 239 HIS 0.002 0.001 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00484 ( 8548) covalent geometry : angle 0.58091 (11572) hydrogen bonds : bond 0.04589 ( 596) hydrogen bonds : angle 3.89165 ( 1695) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 201 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.9590 (mmtp) cc_final: 0.9381 (mtpt) REVERT: A 177 ASP cc_start: 0.9132 (m-30) cc_final: 0.8775 (m-30) REVERT: A 226 ASN cc_start: 0.8351 (t0) cc_final: 0.7909 (t0) REVERT: A 294 ARG cc_start: 0.8675 (ttm110) cc_final: 0.8214 (ptp-170) REVERT: A 426 GLN cc_start: 0.8767 (tm-30) cc_final: 0.8344 (tm-30) REVERT: B 177 ASP cc_start: 0.9005 (m-30) cc_final: 0.8759 (m-30) REVERT: B 180 GLU cc_start: 0.9059 (tt0) cc_final: 0.8807 (tt0) REVERT: B 226 ASN cc_start: 0.8326 (t0) cc_final: 0.7651 (t0) REVERT: B 228 GLN cc_start: 0.8799 (mp10) cc_final: 0.8367 (mp10) REVERT: B 243 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8442 (mt-10) REVERT: B 353 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8424 (mm-30) REVERT: C 177 ASP cc_start: 0.8914 (m-30) cc_final: 0.8680 (m-30) REVERT: C 180 GLU cc_start: 0.9138 (tt0) cc_final: 0.8928 (tt0) REVERT: C 226 ASN cc_start: 0.8257 (t0) cc_final: 0.7588 (t0) REVERT: C 228 GLN cc_start: 0.8796 (mp10) cc_final: 0.8379 (mp10) REVERT: C 243 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8371 (mt-10) REVERT: C 297 GLN cc_start: 0.9137 (mm110) cc_final: 0.8813 (mm110) REVERT: D 177 ASP cc_start: 0.9026 (m-30) cc_final: 0.8715 (m-30) REVERT: D 180 GLU cc_start: 0.9013 (tt0) cc_final: 0.8762 (tt0) REVERT: D 226 ASN cc_start: 0.8263 (t0) cc_final: 0.7795 (t0) outliers start: 10 outliers final: 8 residues processed: 205 average time/residue: 0.2136 time to fit residues: 58.8268 Evaluate side-chains 199 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 191 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 ARG Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 380 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 33 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.121702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.082780 restraints weight = 45631.923| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 3.26 r_work: 0.2904 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8548 Z= 0.119 Angle : 0.517 7.199 11572 Z= 0.270 Chirality : 0.035 0.111 1364 Planarity : 0.004 0.037 1408 Dihedral : 3.502 21.527 1112 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.40 % Allowed : 12.39 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.36 (0.28), residues: 1036 helix: 2.29 (0.20), residues: 808 sheet: None (None), residues: 0 loop : -1.18 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 300 TYR 0.011 0.001 TYR B 380 PHE 0.008 0.001 PHE C 257 TRP 0.008 0.001 TRP A 370 HIS 0.002 0.001 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 8548) covalent geometry : angle 0.51748 (11572) hydrogen bonds : bond 0.04034 ( 596) hydrogen bonds : angle 3.58864 ( 1695) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 202 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.9581 (mmtp) cc_final: 0.9379 (mtpt) REVERT: A 177 ASP cc_start: 0.9101 (m-30) cc_final: 0.8749 (m-30) REVERT: A 180 GLU cc_start: 0.9125 (tt0) cc_final: 0.8756 (mt-10) REVERT: A 226 ASN cc_start: 0.8367 (t0) cc_final: 0.7945 (t0) REVERT: A 243 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8372 (mt-10) REVERT: A 294 ARG cc_start: 0.8707 (ttm110) cc_final: 0.8259 (ptp-170) REVERT: A 426 GLN cc_start: 0.8762 (tm-30) cc_final: 0.8323 (tm-30) REVERT: B 177 ASP cc_start: 0.8991 (m-30) cc_final: 0.8753 (m-30) REVERT: B 180 GLU cc_start: 0.9020 (tt0) cc_final: 0.8748 (tt0) REVERT: B 226 ASN cc_start: 0.8358 (t0) cc_final: 0.7661 (t0) REVERT: B 228 GLN cc_start: 0.8774 (mp10) cc_final: 0.8305 (mp10) REVERT: B 243 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8446 (mt-10) REVERT: C 177 ASP cc_start: 0.8849 (m-30) cc_final: 0.8632 (m-30) REVERT: C 226 ASN cc_start: 0.8262 (t0) cc_final: 0.7567 (t0) REVERT: C 228 GLN cc_start: 0.8792 (mp10) cc_final: 0.8430 (mp10) REVERT: C 243 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8412 (mt-10) REVERT: C 297 GLN cc_start: 0.9147 (mm110) cc_final: 0.8823 (mm110) REVERT: D 177 ASP cc_start: 0.8997 (m-30) cc_final: 0.8692 (m-30) REVERT: D 180 GLU cc_start: 0.9001 (tt0) cc_final: 0.8742 (tt0) REVERT: D 226 ASN cc_start: 0.8246 (t0) cc_final: 0.7692 (t0) outliers start: 13 outliers final: 11 residues processed: 205 average time/residue: 0.2039 time to fit residues: 56.4849 Evaluate side-chains 208 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 197 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 380 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 71 optimal weight: 1.9990 chunk 89 optimal weight: 8.9990 chunk 19 optimal weight: 0.2980 chunk 73 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 57 optimal weight: 30.0000 chunk 65 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 31 optimal weight: 6.9990 chunk 96 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.122004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.082981 restraints weight = 45110.542| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 3.21 r_work: 0.2922 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8548 Z= 0.106 Angle : 0.507 6.761 11572 Z= 0.263 Chirality : 0.035 0.116 1364 Planarity : 0.004 0.040 1408 Dihedral : 3.376 19.607 1112 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.62 % Allowed : 13.69 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.60 (0.28), residues: 1036 helix: 2.44 (0.20), residues: 808 sheet: None (None), residues: 0 loop : -1.03 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 300 TYR 0.011 0.001 TYR D 380 PHE 0.030 0.001 PHE A 289 TRP 0.006 0.001 TRP C 370 HIS 0.002 0.001 HIS D 231 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 8548) covalent geometry : angle 0.50740 (11572) hydrogen bonds : bond 0.03730 ( 596) hydrogen bonds : angle 3.48572 ( 1695) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 205 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.9590 (mmtp) cc_final: 0.9377 (mtpt) REVERT: A 177 ASP cc_start: 0.9066 (m-30) cc_final: 0.8716 (m-30) REVERT: A 226 ASN cc_start: 0.8295 (t0) cc_final: 0.7899 (t0) REVERT: A 243 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8324 (mt-10) REVERT: A 294 ARG cc_start: 0.8711 (ttm110) cc_final: 0.8381 (mtm180) REVERT: A 426 GLN cc_start: 0.8759 (tm-30) cc_final: 0.8385 (tm-30) REVERT: B 177 ASP cc_start: 0.8982 (m-30) cc_final: 0.8739 (m-30) REVERT: B 180 GLU cc_start: 0.8997 (tt0) cc_final: 0.8707 (tt0) REVERT: B 226 ASN cc_start: 0.8271 (t0) cc_final: 0.7486 (t0) REVERT: B 228 GLN cc_start: 0.8767 (mp10) cc_final: 0.8342 (mp10) REVERT: B 243 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8440 (mt-10) REVERT: C 177 ASP cc_start: 0.8875 (m-30) cc_final: 0.8670 (m-30) REVERT: C 226 ASN cc_start: 0.8237 (t0) cc_final: 0.7527 (t0) REVERT: C 228 GLN cc_start: 0.8762 (mp10) cc_final: 0.8405 (mp10) REVERT: C 243 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8402 (mt-10) REVERT: C 297 GLN cc_start: 0.9123 (mm110) cc_final: 0.8827 (mm110) REVERT: D 177 ASP cc_start: 0.8981 (m-30) cc_final: 0.8667 (m-30) REVERT: D 180 GLU cc_start: 0.9009 (tt0) cc_final: 0.8755 (tt0) REVERT: D 228 GLN cc_start: 0.8806 (mp10) cc_final: 0.8466 (mp10) REVERT: D 274 TYR cc_start: 0.9368 (m-10) cc_final: 0.8960 (m-10) outliers start: 15 outliers final: 8 residues processed: 207 average time/residue: 0.2162 time to fit residues: 60.3761 Evaluate side-chains 206 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 198 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 380 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 71 optimal weight: 0.9980 chunk 1 optimal weight: 8.9990 chunk 102 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.122733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.083720 restraints weight = 44890.898| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 3.22 r_work: 0.2934 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8548 Z= 0.102 Angle : 0.510 8.354 11572 Z= 0.261 Chirality : 0.034 0.111 1364 Planarity : 0.003 0.028 1408 Dihedral : 3.274 17.975 1112 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.94 % Allowed : 14.12 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.76 (0.28), residues: 1036 helix: 2.54 (0.20), residues: 808 sheet: None (None), residues: 0 loop : -0.92 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 293 TYR 0.011 0.001 TYR C 380 PHE 0.034 0.001 PHE A 289 TRP 0.006 0.001 TRP A 370 HIS 0.001 0.000 HIS C 231 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 8548) covalent geometry : angle 0.50998 (11572) hydrogen bonds : bond 0.03511 ( 596) hydrogen bonds : angle 3.41302 ( 1695) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 204 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.9579 (mmtp) cc_final: 0.9375 (mtpt) REVERT: A 177 ASP cc_start: 0.9064 (m-30) cc_final: 0.8732 (m-30) REVERT: A 226 ASN cc_start: 0.8297 (t0) cc_final: 0.7926 (t0) REVERT: A 243 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8324 (mt-10) REVERT: A 294 ARG cc_start: 0.8728 (ttm110) cc_final: 0.8365 (ptp-170) REVERT: A 426 GLN cc_start: 0.8772 (tm-30) cc_final: 0.8447 (tm-30) REVERT: B 177 ASP cc_start: 0.8969 (m-30) cc_final: 0.8724 (m-30) REVERT: B 180 GLU cc_start: 0.8986 (tt0) cc_final: 0.8679 (tt0) REVERT: B 226 ASN cc_start: 0.8306 (t0) cc_final: 0.7546 (t0) REVERT: B 228 GLN cc_start: 0.8796 (mp10) cc_final: 0.8405 (mp10) REVERT: B 243 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8245 (mt-10) REVERT: C 177 ASP cc_start: 0.8862 (m-30) cc_final: 0.8659 (m-30) REVERT: C 228 GLN cc_start: 0.8764 (mp10) cc_final: 0.8382 (mp10) REVERT: C 243 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8413 (mt-10) REVERT: D 177 ASP cc_start: 0.8914 (m-30) cc_final: 0.8594 (m-30) REVERT: D 180 GLU cc_start: 0.8979 (tt0) cc_final: 0.8716 (tt0) REVERT: D 228 GLN cc_start: 0.8804 (mp10) cc_final: 0.8435 (mp10) outliers start: 18 outliers final: 12 residues processed: 207 average time/residue: 0.1932 time to fit residues: 54.4856 Evaluate side-chains 210 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 198 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 380 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 56 optimal weight: 5.9990 chunk 79 optimal weight: 0.6980 chunk 59 optimal weight: 8.9990 chunk 17 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 76 optimal weight: 0.2980 chunk 73 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.120515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.080858 restraints weight = 45845.388| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 3.31 r_work: 0.2913 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8548 Z= 0.124 Angle : 0.516 7.567 11572 Z= 0.268 Chirality : 0.035 0.112 1364 Planarity : 0.004 0.050 1408 Dihedral : 3.267 17.289 1112 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.08 % Allowed : 15.19 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.77 (0.28), residues: 1036 helix: 2.55 (0.20), residues: 808 sheet: None (None), residues: 0 loop : -0.91 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 293 TYR 0.011 0.001 TYR D 380 PHE 0.008 0.001 PHE C 257 TRP 0.004 0.001 TRP A 370 HIS 0.001 0.000 HIS D 231 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 8548) covalent geometry : angle 0.51569 (11572) hydrogen bonds : bond 0.03580 ( 596) hydrogen bonds : angle 3.47313 ( 1695) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 201 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.9586 (mmtp) cc_final: 0.9383 (mtpt) REVERT: A 177 ASP cc_start: 0.9071 (m-30) cc_final: 0.8735 (m-30) REVERT: A 226 ASN cc_start: 0.8292 (t0) cc_final: 0.7922 (t0) REVERT: A 243 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8474 (mt-10) REVERT: A 426 GLN cc_start: 0.8776 (tm-30) cc_final: 0.8452 (tm-30) REVERT: B 177 ASP cc_start: 0.8983 (m-30) cc_final: 0.8740 (m-30) REVERT: B 180 GLU cc_start: 0.8980 (tt0) cc_final: 0.8665 (tt0) REVERT: B 226 ASN cc_start: 0.8321 (t0) cc_final: 0.7547 (t0) REVERT: B 228 GLN cc_start: 0.8797 (mp10) cc_final: 0.8397 (mp10) REVERT: B 243 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8271 (mt-10) REVERT: C 177 ASP cc_start: 0.8882 (m-30) cc_final: 0.8679 (m-30) REVERT: C 226 ASN cc_start: 0.8278 (t0) cc_final: 0.7869 (t0) REVERT: C 228 GLN cc_start: 0.8777 (mp10) cc_final: 0.8283 (mp10) REVERT: C 243 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8398 (mt-10) REVERT: C 297 GLN cc_start: 0.9148 (mm110) cc_final: 0.8771 (mm-40) REVERT: D 177 ASP cc_start: 0.8950 (m-30) cc_final: 0.8625 (m-30) REVERT: D 180 GLU cc_start: 0.8963 (tt0) cc_final: 0.8707 (tt0) REVERT: D 228 GLN cc_start: 0.8797 (mp10) cc_final: 0.8410 (mp10) REVERT: D 243 GLU cc_start: 0.8929 (tt0) cc_final: 0.8697 (mt-10) outliers start: 10 outliers final: 9 residues processed: 203 average time/residue: 0.2351 time to fit residues: 64.8479 Evaluate side-chains 206 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 197 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 380 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 45 optimal weight: 0.3980 chunk 83 optimal weight: 9.9990 chunk 50 optimal weight: 0.3980 chunk 3 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 100 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.123530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.084624 restraints weight = 45011.701| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 3.20 r_work: 0.2944 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 8548 Z= 0.099 Angle : 0.506 7.186 11572 Z= 0.259 Chirality : 0.034 0.111 1364 Planarity : 0.004 0.050 1408 Dihedral : 3.213 18.464 1112 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.86 % Allowed : 15.73 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.01 (0.28), residues: 1036 helix: 2.69 (0.20), residues: 808 sheet: None (None), residues: 0 loop : -0.69 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 293 TYR 0.012 0.001 TYR C 380 PHE 0.008 0.001 PHE C 257 TRP 0.007 0.001 TRP C 370 HIS 0.001 0.000 HIS C 231 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 8548) covalent geometry : angle 0.50550 (11572) hydrogen bonds : bond 0.03303 ( 596) hydrogen bonds : angle 3.33096 ( 1695) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 204 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 ASP cc_start: 0.9044 (m-30) cc_final: 0.8704 (m-30) REVERT: A 226 ASN cc_start: 0.8252 (t0) cc_final: 0.7897 (t0) REVERT: A 243 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8288 (mt-10) REVERT: A 293 ARG cc_start: 0.8536 (ttm110) cc_final: 0.8312 (ttm110) REVERT: A 426 GLN cc_start: 0.8774 (tm-30) cc_final: 0.8493 (tm-30) REVERT: B 177 ASP cc_start: 0.8951 (m-30) cc_final: 0.8715 (m-30) REVERT: B 180 GLU cc_start: 0.8985 (tt0) cc_final: 0.8676 (tt0) REVERT: B 226 ASN cc_start: 0.8254 (t0) cc_final: 0.7468 (t0) REVERT: B 228 GLN cc_start: 0.8795 (mp10) cc_final: 0.8419 (mp10) REVERT: B 243 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8262 (mt-10) REVERT: C 177 ASP cc_start: 0.8858 (m-30) cc_final: 0.8658 (m-30) REVERT: C 228 GLN cc_start: 0.8767 (mp10) cc_final: 0.8368 (mp10) REVERT: C 243 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8436 (mt-10) REVERT: C 297 GLN cc_start: 0.9133 (mm110) cc_final: 0.8755 (mm-40) REVERT: D 177 ASP cc_start: 0.8925 (m-30) cc_final: 0.8606 (m-30) REVERT: D 180 GLU cc_start: 0.8981 (tt0) cc_final: 0.8742 (tt0) REVERT: D 228 GLN cc_start: 0.8779 (mp10) cc_final: 0.8403 (mp10) REVERT: D 243 GLU cc_start: 0.8929 (tt0) cc_final: 0.8684 (mt-10) outliers start: 8 outliers final: 8 residues processed: 206 average time/residue: 0.2337 time to fit residues: 65.5649 Evaluate side-chains 208 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 200 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 380 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 97 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.121323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.082185 restraints weight = 45325.985| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 3.21 r_work: 0.2907 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8548 Z= 0.150 Angle : 0.528 7.788 11572 Z= 0.277 Chirality : 0.035 0.114 1364 Planarity : 0.004 0.047 1408 Dihedral : 3.219 17.622 1112 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.97 % Allowed : 15.62 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.89 (0.28), residues: 1036 helix: 2.62 (0.20), residues: 808 sheet: None (None), residues: 0 loop : -0.80 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 293 TYR 0.012 0.001 TYR C 380 PHE 0.009 0.001 PHE C 257 TRP 0.002 0.001 TRP B 239 HIS 0.001 0.001 HIS D 231 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 8548) covalent geometry : angle 0.52775 (11572) hydrogen bonds : bond 0.03641 ( 596) hydrogen bonds : angle 3.51462 ( 1695) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 204 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 ASP cc_start: 0.9067 (m-30) cc_final: 0.8723 (m-30) REVERT: A 226 ASN cc_start: 0.8276 (t0) cc_final: 0.7909 (t0) REVERT: A 243 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8469 (mt-10) REVERT: A 294 ARG cc_start: 0.8754 (ttm110) cc_final: 0.8431 (ptp-170) REVERT: A 426 GLN cc_start: 0.8785 (tm-30) cc_final: 0.8502 (tm-30) REVERT: B 177 ASP cc_start: 0.8976 (m-30) cc_final: 0.8736 (m-30) REVERT: B 180 GLU cc_start: 0.8954 (tt0) cc_final: 0.8650 (tt0) REVERT: B 226 ASN cc_start: 0.8277 (t0) cc_final: 0.7510 (t0) REVERT: B 228 GLN cc_start: 0.8842 (mp10) cc_final: 0.8469 (mp10) REVERT: B 243 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8229 (mt-10) REVERT: B 353 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8268 (mm-30) REVERT: C 177 ASP cc_start: 0.8886 (m-30) cc_final: 0.8684 (m-30) REVERT: C 226 ASN cc_start: 0.8277 (t0) cc_final: 0.7849 (t0) REVERT: C 228 GLN cc_start: 0.8807 (mp10) cc_final: 0.8305 (mp10) REVERT: C 243 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8369 (mt-10) REVERT: C 423 GLN cc_start: 0.7721 (pt0) cc_final: 0.7482 (pp30) REVERT: D 177 ASP cc_start: 0.8952 (m-30) cc_final: 0.8634 (m-30) REVERT: D 180 GLU cc_start: 0.8975 (tt0) cc_final: 0.8704 (tt0) REVERT: D 228 GLN cc_start: 0.8822 (mp10) cc_final: 0.8434 (mp10) REVERT: D 243 GLU cc_start: 0.8937 (tt0) cc_final: 0.8698 (mt-10) outliers start: 9 outliers final: 8 residues processed: 206 average time/residue: 0.2395 time to fit residues: 66.0030 Evaluate side-chains 208 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 200 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 380 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 91 optimal weight: 0.0270 chunk 48 optimal weight: 1.9990 chunk 87 optimal weight: 0.2980 chunk 15 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 11 optimal weight: 20.0000 chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 chunk 72 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 5 optimal weight: 7.9990 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 215 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.123892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.084632 restraints weight = 44720.222| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.26 r_work: 0.2941 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 8548 Z= 0.102 Angle : 0.521 7.750 11572 Z= 0.267 Chirality : 0.034 0.112 1364 Planarity : 0.004 0.050 1408 Dihedral : 3.197 17.031 1112 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.86 % Allowed : 15.95 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.13 (0.28), residues: 1036 helix: 2.76 (0.20), residues: 808 sheet: None (None), residues: 0 loop : -0.59 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 293 TYR 0.012 0.001 TYR C 380 PHE 0.021 0.001 PHE A 289 TRP 0.008 0.001 TRP C 370 HIS 0.001 0.000 HIS B 231 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 8548) covalent geometry : angle 0.52083 (11572) hydrogen bonds : bond 0.03337 ( 596) hydrogen bonds : angle 3.32643 ( 1695) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 204 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 ASP cc_start: 0.9042 (m-30) cc_final: 0.8692 (m-30) REVERT: A 226 ASN cc_start: 0.8222 (t0) cc_final: 0.7865 (t0) REVERT: A 243 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8449 (mt-10) REVERT: A 426 GLN cc_start: 0.8786 (tm-30) cc_final: 0.8536 (tm-30) REVERT: B 177 ASP cc_start: 0.8958 (m-30) cc_final: 0.8726 (m-30) REVERT: B 180 GLU cc_start: 0.8964 (tt0) cc_final: 0.8596 (tt0) REVERT: B 226 ASN cc_start: 0.8233 (t0) cc_final: 0.7442 (t0) REVERT: B 228 GLN cc_start: 0.8800 (mp10) cc_final: 0.8425 (mp10) REVERT: B 243 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8234 (mt-10) REVERT: C 177 ASP cc_start: 0.8854 (m-30) cc_final: 0.8653 (m-30) REVERT: C 226 ASN cc_start: 0.8231 (t0) cc_final: 0.7814 (t0) REVERT: C 228 GLN cc_start: 0.8769 (mp10) cc_final: 0.8288 (mp10) REVERT: C 243 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8389 (mt-10) REVERT: C 423 GLN cc_start: 0.7789 (pt0) cc_final: 0.7502 (pp30) REVERT: D 177 ASP cc_start: 0.8921 (m-30) cc_final: 0.8609 (m-30) REVERT: D 180 GLU cc_start: 0.8960 (tt0) cc_final: 0.8706 (tt0) REVERT: D 228 GLN cc_start: 0.8797 (mp10) cc_final: 0.8413 (mp10) REVERT: D 243 GLU cc_start: 0.8944 (tt0) cc_final: 0.8661 (mt-10) outliers start: 8 outliers final: 7 residues processed: 206 average time/residue: 0.2128 time to fit residues: 59.6972 Evaluate side-chains 211 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 204 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 380 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 33 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 71 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 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 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.123222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.083867 restraints weight = 45132.380| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 3.24 r_work: 0.2947 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 8548 Z= 0.105 Angle : 0.516 7.628 11572 Z= 0.266 Chirality : 0.034 0.113 1364 Planarity : 0.004 0.052 1408 Dihedral : 3.145 16.643 1112 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.65 % Allowed : 16.16 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.19 (0.28), residues: 1036 helix: 2.80 (0.20), residues: 808 sheet: None (None), residues: 0 loop : -0.57 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 293 TYR 0.012 0.001 TYR C 380 PHE 0.008 0.001 PHE C 257 TRP 0.005 0.001 TRP C 370 HIS 0.001 0.000 HIS D 231 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 8548) covalent geometry : angle 0.51614 (11572) hydrogen bonds : bond 0.03272 ( 596) hydrogen bonds : angle 3.33363 ( 1695) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3827.34 seconds wall clock time: 65 minutes 34.93 seconds (3934.93 seconds total)