Starting phenix.real_space_refine on Wed Sep 17 14:00:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zi9_60122/09_2025/8zi9_60122.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zi9_60122/09_2025/8zi9_60122.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zi9_60122/09_2025/8zi9_60122.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zi9_60122/09_2025/8zi9_60122.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zi9_60122/09_2025/8zi9_60122.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zi9_60122/09_2025/8zi9_60122.map" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 P 2 5.49 5 S 52 5.16 5 C 5670 2.51 5 N 1510 2.21 5 O 1665 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 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: 8899 Number of models: 1 Model: "" Number of chains: 3 Chain: "M" Number of atoms: 5974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 742, 5974 Classifications: {'peptide': 742} Link IDs: {'PTRANS': 28, 'TRANS': 713} Chain breaks: 3 Chain: "F" Number of atoms: 2898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2898 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.20, per 1000 atoms: 0.25 Number of scatterers: 8899 At special positions: 0 Unit cell: (123.67, 97.94, 116.2, 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 52 16.00 P 2 15.00 O 1665 8.00 N 1510 7.00 C 5670 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 339.1 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2078 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 14 sheets defined 52.0% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'M' and resid 12 through 17 Processing helix chain 'M' and resid 19 through 28 removed outlier: 3.615A pdb=" N THR M 28 " --> pdb=" O LEU M 24 " (cutoff:3.500A) Processing helix chain 'M' and resid 81 through 85 Processing helix chain 'M' and resid 89 through 93 Processing helix chain 'M' and resid 97 through 111 removed outlier: 3.808A pdb=" N VAL M 101 " --> pdb=" O HIS M 97 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU M 102 " --> pdb=" O GLU M 98 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 134 removed outlier: 3.709A pdb=" N TYR M 134 " --> pdb=" O LEU M 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 131 through 134' Processing helix chain 'M' and resid 135 through 143 removed outlier: 3.783A pdb=" N VAL M 139 " --> pdb=" O THR M 135 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG M 143 " --> pdb=" O VAL M 139 " (cutoff:3.500A) Processing helix chain 'M' and resid 153 through 169 removed outlier: 3.676A pdb=" N ILE M 157 " --> pdb=" O HIS M 153 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 199 Processing helix chain 'M' and resid 217 through 231 Proline residue: M 225 - end of helix Processing helix chain 'M' and resid 270 through 274 Processing helix chain 'M' and resid 283 through 291 removed outlier: 4.331A pdb=" N TYR M 287 " --> pdb=" O TYR M 283 " (cutoff:3.500A) Processing helix chain 'M' and resid 294 through 302 removed outlier: 3.602A pdb=" N LEU M 298 " --> pdb=" O LYS M 294 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 309 Processing helix chain 'M' and resid 310 through 315 removed outlier: 4.079A pdb=" N GLN M 315 " --> pdb=" O ALA M 311 " (cutoff:3.500A) Processing helix chain 'M' and resid 324 through 338 Processing helix chain 'M' and resid 342 through 360 removed outlier: 3.505A pdb=" N LYS M 346 " --> pdb=" O THR M 342 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY M 360 " --> pdb=" O ILE M 356 " (cutoff:3.500A) Processing helix chain 'M' and resid 378 through 389 Processing helix chain 'M' and resid 391 through 401 Processing helix chain 'M' and resid 416 through 448 Processing helix chain 'M' and resid 472 through 505 Processing helix chain 'M' and resid 514 through 522 removed outlier: 4.949A pdb=" N CYS M 520 " --> pdb=" O ASP M 516 " (cutoff:3.500A) Processing helix chain 'M' and resid 529 through 540 Processing helix chain 'M' and resid 544 through 557 Processing helix chain 'M' and resid 592 through 598 removed outlier: 3.713A pdb=" N LYS M 598 " --> pdb=" O LEU M 594 " (cutoff:3.500A) Processing helix chain 'M' and resid 602 through 611 Processing helix chain 'M' and resid 615 through 620 removed outlier: 3.551A pdb=" N THR M 619 " --> pdb=" O LYS M 615 " (cutoff:3.500A) Processing helix chain 'M' and resid 646 through 663 Processing helix chain 'M' and resid 685 through 697 Processing helix chain 'M' and resid 697 through 706 Processing helix chain 'M' and resid 715 through 723 Processing helix chain 'M' and resid 724 through 726 No H-bonds generated for 'chain 'M' and resid 724 through 726' Processing helix chain 'M' and resid 739 through 748 Processing helix chain 'M' and resid 766 through 781 Processing helix chain 'F' and resid 56 through 61 removed outlier: 3.597A pdb=" N SER F 60 " --> pdb=" O ASP F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 93 removed outlier: 3.757A pdb=" N GLU F 93 " --> pdb=" O THR F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 101 removed outlier: 3.814A pdb=" N HIS F 101 " --> pdb=" O PRO F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 126 removed outlier: 4.256A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 145 Processing helix chain 'F' and resid 172 through 175 Processing helix chain 'F' and resid 181 through 194 Processing helix chain 'F' and resid 202 through 217 removed outlier: 3.884A pdb=" N GLU F 207 " --> pdb=" O THR F 203 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 233 Processing helix chain 'F' and resid 252 through 257 Processing helix chain 'F' and resid 258 through 262 Processing helix chain 'F' and resid 273 through 285 removed outlier: 3.536A pdb=" N TYR F 279 " --> pdb=" O HIS F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 296 Processing helix chain 'F' and resid 301 through 306 removed outlier: 4.274A pdb=" N TYR F 306 " --> pdb=" O THR F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 321 Processing helix chain 'F' and resid 337 through 349 Processing helix chain 'F' and resid 350 through 355 removed outlier: 3.866A pdb=" N GLN F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 366 Processing helix chain 'F' and resid 367 through 372 removed outlier: 3.536A pdb=" N ARG F 372 " --> pdb=" O ILE F 369 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'M' and resid 39 through 40 removed outlier: 4.225A pdb=" N VAL M 39 " --> pdb=" O VAL M 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 49 through 51 removed outlier: 3.555A pdb=" N VAL M 69 " --> pdb=" O ALA M 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 115 through 117 removed outlier: 5.843A pdb=" N SER M 173 " --> pdb=" O HIS M 668 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL M 670 " --> pdb=" O SER M 173 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N LEU M 175 " --> pdb=" O VAL M 670 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N CYS M 672 " --> pdb=" O LEU M 175 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N THR M 177 " --> pdb=" O CYS M 672 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE M 252 " --> pdb=" O GLN M 454 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE M 456 " --> pdb=" O ILE M 250 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE M 250 " --> pdb=" O PHE M 456 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLY M 458 " --> pdb=" O ILE M 248 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE M 248 " --> pdb=" O GLY M 458 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER M 260 " --> pdb=" O HIS M 251 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 232 through 233 Processing sheet with id=AA5, first strand: chain 'M' and resid 364 through 366 Processing sheet with id=AA6, first strand: chain 'M' and resid 403 through 405 Processing sheet with id=AA7, first strand: chain 'M' and resid 577 through 581 removed outlier: 3.504A pdb=" N PHE M 577 " --> pdb=" O TYR M 588 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 711 through 714 removed outlier: 3.502A pdb=" N ASN M 711 " --> pdb=" O PHE M 765 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE M 713 " --> pdb=" O VAL M 763 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 8 through 10 removed outlier: 6.446A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 17 through 19 Processing sheet with id=AB2, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AB3, first strand: chain 'F' and resid 169 through 170 Processing sheet with id=AB4, first strand: chain 'F' and resid 169 through 170 removed outlier: 6.521A pdb=" N ASN F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 238 through 242 removed outlier: 4.560A pdb=" N LEU F 242 " --> pdb=" O GLN F 246 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N GLN F 246 " --> pdb=" O LEU F 242 " (cutoff:3.500A) 424 hydrogen bonds defined for protein. 1164 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.49 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2841 1.34 - 1.45: 1386 1.45 - 1.57: 4770 1.57 - 1.69: 3 1.69 - 1.81: 91 Bond restraints: 9091 Sorted by residual: bond pdb=" N GLU M 409 " pdb=" CA GLU M 409 " ideal model delta sigma weight residual 1.456 1.487 -0.032 1.23e-02 6.61e+03 6.62e+00 bond pdb=" N ASN M 408 " pdb=" CA ASN M 408 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.47e+00 bond pdb=" CB VAL F 152 " pdb=" CG1 VAL F 152 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.78e+00 bond pdb=" CB ARG F 335 " pdb=" CG ARG F 335 " ideal model delta sigma weight residual 1.520 1.462 0.058 3.00e-02 1.11e+03 3.72e+00 bond pdb=" CG1 ILE F 329 " pdb=" CD1 ILE F 329 " ideal model delta sigma weight residual 1.513 1.440 0.073 3.90e-02 6.57e+02 3.48e+00 ... (remaining 9086 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 11870 1.69 - 3.39: 346 3.39 - 5.08: 49 5.08 - 6.78: 8 6.78 - 8.47: 2 Bond angle restraints: 12275 Sorted by residual: angle pdb=" N PRO M 541 " pdb=" CA PRO M 541 " pdb=" C PRO M 541 " ideal model delta sigma weight residual 112.47 118.08 -5.61 2.06e+00 2.36e-01 7.42e+00 angle pdb=" CA GLU M 409 " pdb=" C GLU M 409 " pdb=" O GLU M 409 " ideal model delta sigma weight residual 121.23 118.39 2.84 1.07e+00 8.73e-01 7.05e+00 angle pdb=" CA ASN M 408 " pdb=" C ASN M 408 " pdb=" O ASN M 408 " ideal model delta sigma weight residual 121.34 118.29 3.05 1.18e+00 7.18e-01 6.69e+00 angle pdb=" CB MET M 690 " pdb=" CG MET M 690 " pdb=" SD MET M 690 " ideal model delta sigma weight residual 112.70 105.39 7.31 3.00e+00 1.11e-01 5.93e+00 angle pdb=" CA LEU F 171 " pdb=" CB LEU F 171 " pdb=" CG LEU F 171 " ideal model delta sigma weight residual 116.30 124.77 -8.47 3.50e+00 8.16e-02 5.86e+00 ... (remaining 12270 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 4898 17.84 - 35.69: 476 35.69 - 53.53: 83 53.53 - 71.38: 20 71.38 - 89.22: 12 Dihedral angle restraints: 5489 sinusoidal: 2256 harmonic: 3233 Sorted by residual: dihedral pdb=" CA LYS F 373 " pdb=" C LYS F 373 " pdb=" N CYS F 374 " pdb=" CA CYS F 374 " ideal model delta harmonic sigma weight residual 180.00 160.00 20.00 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" C5' ADP F 401 " pdb=" O5' ADP F 401 " pdb=" PA ADP F 401 " pdb=" O2A ADP F 401 " ideal model delta sinusoidal sigma weight residual -60.00 7.09 -67.08 1 2.00e+01 2.50e-03 1.47e+01 dihedral pdb=" CA TYR M 266 " pdb=" C TYR M 266 " pdb=" N LEU M 267 " pdb=" CA LEU M 267 " ideal model delta harmonic sigma weight residual 180.00 162.69 17.31 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 5486 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 875 0.044 - 0.087: 354 0.087 - 0.131: 103 0.131 - 0.174: 2 0.174 - 0.218: 4 Chirality restraints: 1338 Sorted by residual: chirality pdb=" CB ILE F 71 " pdb=" CA ILE F 71 " pdb=" CG1 ILE F 71 " pdb=" CG2 ILE F 71 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CB ILE M 506 " pdb=" CA ILE M 506 " pdb=" CG1 ILE M 506 " pdb=" CG2 ILE M 506 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.74e-01 chirality pdb=" CA PRO M 541 " pdb=" N PRO M 541 " pdb=" C PRO M 541 " pdb=" CB PRO M 541 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.40e-01 ... (remaining 1335 not shown) Planarity restraints: 1580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE M 540 " 0.045 5.00e-02 4.00e+02 6.84e-02 7.48e+00 pdb=" N PRO M 541 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO M 541 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO M 541 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO F 332 " 0.030 5.00e-02 4.00e+02 4.60e-02 3.38e+00 pdb=" N PRO F 333 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO F 333 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 333 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 242 " -0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO F 243 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO F 243 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO F 243 " -0.022 5.00e-02 4.00e+02 ... (remaining 1577 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 387 2.71 - 3.25: 9317 3.25 - 3.80: 14513 3.80 - 4.35: 18483 4.35 - 4.90: 30740 Nonbonded interactions: 73440 Sorted by model distance: nonbonded pdb=" OH TYR M 162 " pdb=" O GLY M 256 " model vdw 2.157 3.040 nonbonded pdb=" O ALA M 233 " pdb=" OG SER M 241 " model vdw 2.198 3.040 nonbonded pdb=" NH2 ARG M 281 " pdb=" O THR M 318 " model vdw 2.219 3.120 nonbonded pdb=" O ILE M 478 " pdb=" OG1 THR M 481 " model vdw 2.220 3.040 nonbonded pdb=" OE2 GLU M 536 " pdb=" NZ LYS M 551 " model vdw 2.223 3.120 ... (remaining 73435 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.520 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.210 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 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 : 0.008 0.073 9091 Z= 0.341 Angle : 0.713 8.470 12275 Z= 0.392 Chirality : 0.049 0.218 1338 Planarity : 0.004 0.068 1580 Dihedral : 14.971 89.220 3411 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % 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: -2.50 (0.22), residues: 1103 helix: -1.21 (0.20), residues: 516 sheet: -1.46 (0.42), residues: 136 loop : -2.13 (0.26), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 147 TYR 0.016 0.002 TYR M 310 PHE 0.017 0.002 PHE M 38 TRP 0.017 0.003 TRP F 79 HIS 0.007 0.001 HIS F 73 Details of bonding type rmsd covalent geometry : bond 0.00805 ( 9091) covalent geometry : angle 0.71322 (12275) hydrogen bonds : bond 0.14049 ( 422) hydrogen bonds : angle 5.66656 ( 1164) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 92 MET cc_start: 0.6451 (mmm) cc_final: 0.6031 (mmp) REVERT: M 277 LEU cc_start: 0.7243 (mm) cc_final: 0.6909 (mt) REVERT: M 317 GLU cc_start: 0.6928 (mm-30) cc_final: 0.6565 (mm-30) REVERT: M 443 ILE cc_start: 0.7399 (mm) cc_final: 0.6928 (mt) REVERT: M 447 LEU cc_start: 0.7016 (tt) cc_final: 0.6613 (mt) REVERT: M 461 ASP cc_start: 0.5749 (t0) cc_final: 0.5404 (m-30) REVERT: M 503 LYS cc_start: 0.7312 (tmmt) cc_final: 0.7069 (ptmm) REVERT: M 719 ARG cc_start: 0.6974 (mtp85) cc_final: 0.6749 (mtt-85) REVERT: M 758 PHE cc_start: 0.4061 (t80) cc_final: 0.3601 (t80) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.1224 time to fit residues: 31.1092 Evaluate side-chains 102 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 0.0370 chunk 97 optimal weight: 0.1980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 75 GLN M 79 GLN M 163 GLN M 219 GLN M 358 HIS M 418 GLN M 444 ASN M 482 ASN M 562 ASN M 623 ASN M 676 ASN M 691 HIS M 696 ASN M 711 ASN M 726 ASN F 73 HIS F 162 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.100918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.082130 restraints weight = 19985.823| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.53 r_work: 0.3254 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9091 Z= 0.151 Angle : 0.606 6.761 12275 Z= 0.318 Chirality : 0.045 0.155 1338 Planarity : 0.005 0.052 1580 Dihedral : 5.200 50.641 1218 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.67 % Allowed : 13.99 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.25), residues: 1103 helix: 0.48 (0.23), residues: 508 sheet: -0.31 (0.49), residues: 124 loop : -1.13 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG M 453 TYR 0.017 0.002 TYR M 162 PHE 0.025 0.002 PHE M 247 TRP 0.026 0.002 TRP M 130 HIS 0.008 0.001 HIS M 97 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 9091) covalent geometry : angle 0.60602 (12275) hydrogen bonds : bond 0.03722 ( 422) hydrogen bonds : angle 4.38542 ( 1164) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 16 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.7224 (tt) REVERT: M 92 MET cc_start: 0.7369 (mmm) cc_final: 0.7004 (mmt) REVERT: M 365 LYS cc_start: 0.8697 (ptmm) cc_final: 0.8423 (pttp) REVERT: M 690 MET cc_start: 0.6810 (tmm) cc_final: 0.6523 (tmm) REVERT: F 47 MET cc_start: 0.6107 (ptm) cc_final: 0.4157 (mmp) outliers start: 16 outliers final: 5 residues processed: 120 average time/residue: 0.1170 time to fit residues: 19.0902 Evaluate side-chains 78 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 359 PHE Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 375 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 17 optimal weight: 0.0770 chunk 35 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 84 optimal weight: 0.0670 chunk 80 optimal weight: 0.6980 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 97 HIS M 104 ASN M 755 GLN F 297 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.096652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.077099 restraints weight = 20157.023| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.66 r_work: 0.3155 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.5237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9091 Z= 0.144 Angle : 0.554 5.466 12275 Z= 0.288 Chirality : 0.043 0.167 1338 Planarity : 0.004 0.051 1580 Dihedral : 4.893 48.618 1218 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.09 % Allowed : 15.97 % Favored : 81.94 % 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: 0.30 (0.26), residues: 1103 helix: 1.10 (0.24), residues: 498 sheet: 0.23 (0.51), residues: 124 loop : -0.71 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 777 TYR 0.014 0.001 TYR M 162 PHE 0.019 0.002 PHE M 247 TRP 0.028 0.002 TRP M 130 HIS 0.004 0.001 HIS F 73 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 9091) covalent geometry : angle 0.55362 (12275) hydrogen bonds : bond 0.03815 ( 422) hydrogen bonds : angle 4.15124 ( 1164) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.340 Fit side-chains REVERT: M 92 MET cc_start: 0.7951 (mmm) cc_final: 0.7578 (mmt) REVERT: M 193 GLN cc_start: 0.7777 (mt0) cc_final: 0.7520 (pt0) REVERT: M 365 LYS cc_start: 0.8641 (ptmm) cc_final: 0.8370 (pttp) REVERT: M 621 PHE cc_start: 0.5832 (p90) cc_final: 0.5520 (p90) REVERT: F 154 ASP cc_start: 0.7483 (t70) cc_final: 0.7191 (t70) REVERT: F 227 MET cc_start: 0.8733 (tpp) cc_final: 0.8384 (mmm) outliers start: 20 outliers final: 8 residues processed: 100 average time/residue: 0.1037 time to fit residues: 14.6251 Evaluate side-chains 74 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 341 PHE Chi-restraints excluded: chain M residue 359 PHE Chi-restraints excluded: chain M residue 461 ASP Chi-restraints excluded: chain M residue 506 ILE Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 375 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 89 optimal weight: 3.9990 chunk 54 optimal weight: 0.3980 chunk 64 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 9 optimal weight: 0.0570 chunk 70 optimal weight: 3.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 80 ASN M 292 ASN F 92 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.093075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.074374 restraints weight = 20609.415| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.59 r_work: 0.3113 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.6338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9091 Z= 0.159 Angle : 0.583 14.414 12275 Z= 0.297 Chirality : 0.044 0.163 1338 Planarity : 0.004 0.050 1580 Dihedral : 4.967 47.198 1218 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.82 % Allowed : 16.39 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.26), residues: 1103 helix: 1.20 (0.24), residues: 502 sheet: 0.08 (0.49), residues: 136 loop : -0.65 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 739 TYR 0.018 0.002 TYR M 287 PHE 0.020 0.001 PHE M 247 TRP 0.017 0.002 TRP M 130 HIS 0.005 0.001 HIS M 358 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 9091) covalent geometry : angle 0.58342 (12275) hydrogen bonds : bond 0.03943 ( 422) hydrogen bonds : angle 4.08973 ( 1164) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 77 time to evaluate : 0.399 Fit side-chains REVERT: M 92 MET cc_start: 0.8228 (mmm) cc_final: 0.7993 (mmt) REVERT: M 365 LYS cc_start: 0.8683 (ptmm) cc_final: 0.8415 (pttp) REVERT: M 579 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8946 (mp) REVERT: M 765 PHE cc_start: 0.6860 (m-80) cc_final: 0.6643 (m-80) REVERT: F 47 MET cc_start: 0.6443 (ptm) cc_final: 0.4471 (mmp) REVERT: F 154 ASP cc_start: 0.7483 (t70) cc_final: 0.7239 (t70) REVERT: F 171 LEU cc_start: 0.8619 (mm) cc_final: 0.8402 (mp) REVERT: F 227 MET cc_start: 0.8739 (tpp) cc_final: 0.8348 (mmm) outliers start: 27 outliers final: 11 residues processed: 98 average time/residue: 0.0990 time to fit residues: 13.9945 Evaluate side-chains 74 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 341 PHE Chi-restraints excluded: chain M residue 446 THR Chi-restraints excluded: chain M residue 455 TYR Chi-restraints excluded: chain M residue 461 ASP Chi-restraints excluded: chain M residue 506 ILE Chi-restraints excluded: chain M residue 579 LEU Chi-restraints excluded: chain M residue 752 ASP Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 375 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 109 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 chunk 61 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 64 optimal weight: 0.1980 chunk 42 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 371 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.092057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.073653 restraints weight = 20345.924| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.54 r_work: 0.3095 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.6716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9091 Z= 0.150 Angle : 0.553 10.427 12275 Z= 0.284 Chirality : 0.043 0.147 1338 Planarity : 0.004 0.050 1580 Dihedral : 4.829 46.790 1218 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.71 % Allowed : 17.75 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.26), residues: 1103 helix: 1.37 (0.24), residues: 503 sheet: 0.17 (0.49), residues: 134 loop : -0.59 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 694 TYR 0.013 0.001 TYR M 103 PHE 0.026 0.001 PHE M 46 TRP 0.020 0.002 TRP M 130 HIS 0.004 0.001 HIS M 358 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 9091) covalent geometry : angle 0.55283 (12275) hydrogen bonds : bond 0.03710 ( 422) hydrogen bonds : angle 4.06162 ( 1164) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 64 time to evaluate : 0.380 Fit side-chains REVERT: M 50 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8616 (ptmt) REVERT: M 365 LYS cc_start: 0.8683 (ptmm) cc_final: 0.8475 (pttm) REVERT: M 621 PHE cc_start: 0.5959 (p90) cc_final: 0.5699 (p90) REVERT: F 47 MET cc_start: 0.6663 (ptm) cc_final: 0.4923 (mmp) REVERT: F 154 ASP cc_start: 0.7466 (t70) cc_final: 0.7230 (t70) REVERT: F 227 MET cc_start: 0.8755 (tpp) cc_final: 0.8526 (tpp) outliers start: 26 outliers final: 12 residues processed: 84 average time/residue: 0.0768 time to fit residues: 10.0808 Evaluate side-chains 72 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 50 LYS Chi-restraints excluded: chain M residue 52 VAL Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 341 PHE Chi-restraints excluded: chain M residue 359 PHE Chi-restraints excluded: chain M residue 446 THR Chi-restraints excluded: chain M residue 455 TYR Chi-restraints excluded: chain M residue 506 ILE Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 375 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 101 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 chunk 45 optimal weight: 0.7980 chunk 13 optimal weight: 0.4980 chunk 52 optimal weight: 0.7980 chunk 24 optimal weight: 0.3980 chunk 38 optimal weight: 0.0770 chunk 20 optimal weight: 0.9980 chunk 91 optimal weight: 0.3980 chunk 27 optimal weight: 0.0170 overall best weight: 0.2576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 760 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.093023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.075107 restraints weight = 20085.877| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.49 r_work: 0.3152 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.6870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9091 Z= 0.096 Angle : 0.496 10.214 12275 Z= 0.252 Chirality : 0.041 0.140 1338 Planarity : 0.004 0.046 1580 Dihedral : 4.469 42.267 1218 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.40 % Allowed : 18.37 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.26), residues: 1103 helix: 1.61 (0.24), residues: 501 sheet: 0.35 (0.49), residues: 134 loop : -0.50 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 434 TYR 0.013 0.001 TYR M 310 PHE 0.011 0.001 PHE M 247 TRP 0.014 0.001 TRP M 130 HIS 0.004 0.001 HIS M 358 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 9091) covalent geometry : angle 0.49589 (12275) hydrogen bonds : bond 0.03058 ( 422) hydrogen bonds : angle 3.89171 ( 1164) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.362 Fit side-chains REVERT: F 47 MET cc_start: 0.6500 (ptm) cc_final: 0.4823 (mmp) REVERT: F 154 ASP cc_start: 0.7353 (t70) cc_final: 0.7108 (t70) REVERT: F 171 LEU cc_start: 0.8566 (mm) cc_final: 0.8352 (mp) REVERT: F 227 MET cc_start: 0.8776 (tpp) cc_final: 0.8467 (mmm) outliers start: 23 outliers final: 13 residues processed: 87 average time/residue: 0.0850 time to fit residues: 11.1306 Evaluate side-chains 75 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 52 VAL Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 296 GLU Chi-restraints excluded: chain M residue 305 ASN Chi-restraints excluded: chain M residue 341 PHE Chi-restraints excluded: chain M residue 359 PHE Chi-restraints excluded: chain M residue 455 TYR Chi-restraints excluded: chain M residue 506 ILE Chi-restraints excluded: chain M residue 617 LEU Chi-restraints excluded: chain M residue 674 ILE Chi-restraints excluded: chain M residue 770 LEU Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 375 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 93 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3529 r_free = 0.3529 target = 0.090213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.072498 restraints weight = 20347.176| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.49 r_work: 0.3077 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.7089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9091 Z= 0.153 Angle : 0.550 9.552 12275 Z= 0.280 Chirality : 0.043 0.166 1338 Planarity : 0.004 0.046 1580 Dihedral : 4.686 44.299 1218 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.98 % Allowed : 18.89 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.26), residues: 1103 helix: 1.61 (0.24), residues: 501 sheet: -0.04 (0.47), residues: 145 loop : -0.45 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 694 TYR 0.014 0.001 TYR M 287 PHE 0.014 0.001 PHE M 247 TRP 0.011 0.001 TRP F 340 HIS 0.004 0.001 HIS M 358 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 9091) covalent geometry : angle 0.55014 (12275) hydrogen bonds : bond 0.03756 ( 422) hydrogen bonds : angle 3.99411 ( 1164) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.382 Fit side-chains REVERT: M 50 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8604 (ptmt) REVERT: M 744 LYS cc_start: 0.4118 (ttpt) cc_final: 0.3912 (mptt) REVERT: F 47 MET cc_start: 0.6593 (ptm) cc_final: 0.5081 (mmp) REVERT: F 154 ASP cc_start: 0.7419 (t70) cc_final: 0.7200 (t70) REVERT: F 171 LEU cc_start: 0.8663 (mm) cc_final: 0.8458 (mp) REVERT: F 369 ILE cc_start: 0.8626 (tp) cc_final: 0.8376 (tp) outliers start: 19 outliers final: 15 residues processed: 80 average time/residue: 0.0788 time to fit residues: 9.7988 Evaluate side-chains 79 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 50 LYS Chi-restraints excluded: chain M residue 52 VAL Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 305 ASN Chi-restraints excluded: chain M residue 315 GLN Chi-restraints excluded: chain M residue 341 PHE Chi-restraints excluded: chain M residue 357 MET Chi-restraints excluded: chain M residue 359 PHE Chi-restraints excluded: chain M residue 446 THR Chi-restraints excluded: chain M residue 506 ILE Chi-restraints excluded: chain M residue 617 LEU Chi-restraints excluded: chain M residue 674 ILE Chi-restraints excluded: chain M residue 770 LEU Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 375 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 31 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 20 optimal weight: 0.3980 chunk 52 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 0.0050 chunk 48 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 overall best weight: 0.4794 ------------------------------------------------------------------------------- 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 = 0.3533 r_free = 0.3533 target = 0.090567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.072972 restraints weight = 20149.641| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.48 r_work: 0.3092 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.7260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9091 Z= 0.123 Angle : 0.524 9.173 12275 Z= 0.265 Chirality : 0.042 0.157 1338 Planarity : 0.004 0.048 1580 Dihedral : 4.584 41.151 1218 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.09 % Allowed : 18.16 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.26), residues: 1103 helix: 1.67 (0.24), residues: 501 sheet: 0.32 (0.48), residues: 135 loop : -0.46 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 237 TYR 0.013 0.001 TYR M 624 PHE 0.012 0.001 PHE M 247 TRP 0.023 0.002 TRP M 508 HIS 0.004 0.001 HIS M 358 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 9091) covalent geometry : angle 0.52390 (12275) hydrogen bonds : bond 0.03407 ( 422) hydrogen bonds : angle 3.92214 ( 1164) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 60 time to evaluate : 0.371 Fit side-chains REVERT: M 765 PHE cc_start: 0.7573 (m-80) cc_final: 0.7344 (m-10) REVERT: F 47 MET cc_start: 0.6622 (ptm) cc_final: 0.5175 (mmp) REVERT: F 154 ASP cc_start: 0.7385 (t70) cc_final: 0.7157 (t70) REVERT: F 171 LEU cc_start: 0.8647 (mm) cc_final: 0.8441 (mp) REVERT: F 369 ILE cc_start: 0.8618 (tp) cc_final: 0.8360 (tp) outliers start: 20 outliers final: 17 residues processed: 75 average time/residue: 0.0863 time to fit residues: 9.9076 Evaluate side-chains 76 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 52 VAL Chi-restraints excluded: chain M residue 116 THR Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 305 ASN Chi-restraints excluded: chain M residue 315 GLN Chi-restraints excluded: chain M residue 341 PHE Chi-restraints excluded: chain M residue 357 MET Chi-restraints excluded: chain M residue 359 PHE Chi-restraints excluded: chain M residue 446 THR Chi-restraints excluded: chain M residue 455 TYR Chi-restraints excluded: chain M residue 506 ILE Chi-restraints excluded: chain M residue 617 LEU Chi-restraints excluded: chain M residue 674 ILE Chi-restraints excluded: chain M residue 770 LEU Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 375 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 101 optimal weight: 0.7980 chunk 14 optimal weight: 0.0470 chunk 59 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 38 optimal weight: 0.0970 chunk 70 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 19 optimal weight: 0.2980 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 711 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.090821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.073396 restraints weight = 20180.119| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.43 r_work: 0.3105 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.7333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9091 Z= 0.115 Angle : 0.519 8.726 12275 Z= 0.263 Chirality : 0.041 0.141 1338 Planarity : 0.003 0.046 1580 Dihedral : 4.512 40.670 1218 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.88 % Allowed : 18.58 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.26), residues: 1103 helix: 1.69 (0.24), residues: 501 sheet: 0.11 (0.46), residues: 145 loop : -0.31 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 739 TYR 0.011 0.001 TYR M 624 PHE 0.011 0.001 PHE M 247 TRP 0.029 0.002 TRP M 508 HIS 0.004 0.001 HIS M 358 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 9091) covalent geometry : angle 0.51935 (12275) hydrogen bonds : bond 0.03307 ( 422) hydrogen bonds : angle 3.91304 ( 1164) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.371 Fit side-chains REVERT: M 765 PHE cc_start: 0.7590 (m-80) cc_final: 0.7370 (m-10) REVERT: F 47 MET cc_start: 0.6733 (ptm) cc_final: 0.5234 (mmp) REVERT: F 154 ASP cc_start: 0.7766 (t70) cc_final: 0.7539 (t70) REVERT: F 171 LEU cc_start: 0.8711 (mm) cc_final: 0.8497 (mp) REVERT: F 369 ILE cc_start: 0.8593 (tp) cc_final: 0.8318 (tp) outliers start: 18 outliers final: 17 residues processed: 74 average time/residue: 0.0795 time to fit residues: 9.1686 Evaluate side-chains 75 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 52 VAL Chi-restraints excluded: chain M residue 116 THR Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 296 GLU Chi-restraints excluded: chain M residue 315 GLN Chi-restraints excluded: chain M residue 341 PHE Chi-restraints excluded: chain M residue 357 MET Chi-restraints excluded: chain M residue 359 PHE Chi-restraints excluded: chain M residue 446 THR Chi-restraints excluded: chain M residue 455 TYR Chi-restraints excluded: chain M residue 506 ILE Chi-restraints excluded: chain M residue 617 LEU Chi-restraints excluded: chain M residue 674 ILE Chi-restraints excluded: chain M residue 770 LEU Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 375 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 55 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 92 optimal weight: 0.4980 chunk 46 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 48 optimal weight: 0.0670 chunk 3 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 97 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.090472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.072720 restraints weight = 20408.245| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.44 r_work: 0.3081 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.7515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9091 Z= 0.134 Angle : 0.543 8.886 12275 Z= 0.275 Chirality : 0.042 0.150 1338 Planarity : 0.004 0.047 1580 Dihedral : 4.633 42.560 1218 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.88 % Allowed : 18.58 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.26), residues: 1103 helix: 1.66 (0.23), residues: 501 sheet: 0.09 (0.46), residues: 143 loop : -0.32 (0.31), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 237 TYR 0.013 0.001 TYR M 287 PHE 0.012 0.001 PHE M 247 TRP 0.032 0.002 TRP M 508 HIS 0.004 0.001 HIS M 358 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 9091) covalent geometry : angle 0.54315 (12275) hydrogen bonds : bond 0.03613 ( 422) hydrogen bonds : angle 3.97601 ( 1164) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.343 Fit side-chains REVERT: M 765 PHE cc_start: 0.7817 (m-80) cc_final: 0.7550 (m-10) REVERT: F 47 MET cc_start: 0.6851 (ptm) cc_final: 0.5375 (mmp) REVERT: F 154 ASP cc_start: 0.7752 (t70) cc_final: 0.7535 (t70) REVERT: F 171 LEU cc_start: 0.8723 (mm) cc_final: 0.8510 (mp) REVERT: F 369 ILE cc_start: 0.8619 (tp) cc_final: 0.8353 (tp) outliers start: 18 outliers final: 16 residues processed: 75 average time/residue: 0.0870 time to fit residues: 10.0270 Evaluate side-chains 75 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 52 VAL Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 305 ASN Chi-restraints excluded: chain M residue 315 GLN Chi-restraints excluded: chain M residue 341 PHE Chi-restraints excluded: chain M residue 357 MET Chi-restraints excluded: chain M residue 359 PHE Chi-restraints excluded: chain M residue 446 THR Chi-restraints excluded: chain M residue 455 TYR Chi-restraints excluded: chain M residue 506 ILE Chi-restraints excluded: chain M residue 617 LEU Chi-restraints excluded: chain M residue 674 ILE Chi-restraints excluded: chain M residue 770 LEU Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 375 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 38 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 chunk 10 optimal weight: 0.2980 chunk 50 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 98 optimal weight: 0.5980 chunk 87 optimal weight: 0.0470 chunk 72 optimal weight: 0.4980 chunk 57 optimal weight: 0.2980 chunk 17 optimal weight: 0.9980 overall best weight: 0.3478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 97 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.090788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.073586 restraints weight = 19752.710| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.42 r_work: 0.3117 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.7568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9091 Z= 0.108 Angle : 0.518 8.487 12275 Z= 0.262 Chirality : 0.041 0.137 1338 Planarity : 0.003 0.046 1580 Dihedral : 4.458 39.135 1218 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.67 % Allowed : 19.31 % Favored : 79.02 % 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: 1.05 (0.26), residues: 1103 helix: 1.77 (0.23), residues: 501 sheet: 0.16 (0.44), residues: 155 loop : -0.28 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 237 TYR 0.010 0.001 TYR M 103 PHE 0.014 0.001 PHE M 230 TRP 0.026 0.002 TRP M 508 HIS 0.004 0.001 HIS M 358 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 9091) covalent geometry : angle 0.51754 (12275) hydrogen bonds : bond 0.03171 ( 422) hydrogen bonds : angle 3.88911 ( 1164) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2466.40 seconds wall clock time: 43 minutes 10.41 seconds (2590.41 seconds total)