Starting phenix.real_space_refine on Thu Feb 13 13:08:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zi9_60122/02_2025/8zi9_60122.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zi9_60122/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8zi9_60122/02_2025/8zi9_60122.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zi9_60122/02_2025/8zi9_60122.map" model { file = "/net/cci-nas-00/data/ceres_data/8zi9_60122/02_2025/8zi9_60122.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zi9_60122/02_2025/8zi9_60122.cif" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 6.52, per 1000 atoms: 0.73 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: 2.46 Conformation dependent library (CDL) restraints added in 997.7 milliseconds 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: 1.13 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: 2.84 Time building geometry restraints manager: 2.80 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: 10.500 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.430 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.260 ------------------------------------------------------------------------------- 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= 0.534 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (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 TRP 0.017 0.003 TRP F 79 HIS 0.007 0.001 HIS F 73 PHE 0.017 0.002 PHE M 38 TYR 0.016 0.002 TYR M 310 ARG 0.006 0.001 ARG M 147 *********************** 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 : 1.048 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: 0.6930 (mt) REVERT: M 447 LEU cc_start: 0.7016 (tt) cc_final: 0.6612 (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: 0.2535 time to fit residues: 64.1013 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 : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 0.0770 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 418 GLN M 482 ASN M 562 ASN M 623 ASN M 676 ASN M 691 HIS M 696 ASN M 726 ASN F 73 HIS F 162 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.099549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.080134 restraints weight = 20309.346| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.59 r_work: 0.3223 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9091 Z= 0.259 Angle : 0.631 6.061 12275 Z= 0.334 Chirality : 0.046 0.159 1338 Planarity : 0.005 0.054 1580 Dihedral : 5.357 51.495 1218 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.77 % Allowed : 14.09 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.25), residues: 1103 helix: 0.52 (0.23), residues: 501 sheet: -0.46 (0.48), residues: 127 loop : -1.08 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP M 130 HIS 0.009 0.002 HIS M 97 PHE 0.029 0.002 PHE M 247 TYR 0.018 0.002 TYR M 162 ARG 0.007 0.001 ARG M 721 *********************** 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 132 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: M 92 MET cc_start: 0.7664 (mmm) cc_final: 0.7418 (mmt) REVERT: M 277 LEU cc_start: 0.7866 (mm) cc_final: 0.7624 (mt) REVERT: M 365 LYS cc_start: 0.8697 (ptmm) cc_final: 0.8417 (pttp) REVERT: M 690 MET cc_start: 0.6826 (tmm) cc_final: 0.6543 (tmm) REVERT: F 47 MET cc_start: 0.6212 (ptm) cc_final: 0.4190 (mmp) REVERT: F 154 ASP cc_start: 0.7250 (t70) cc_final: 0.6932 (t70) REVERT: F 227 MET cc_start: 0.8765 (tpp) cc_final: 0.8462 (mmm) outliers start: 17 outliers final: 6 residues processed: 123 average time/residue: 0.2332 time to fit residues: 39.3502 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 : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 M residue 394 ASP 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 30 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 57 optimal weight: 0.2980 chunk 107 optimal weight: 0.1980 chunk 81 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 108 optimal weight: 0.5980 chunk 6 optimal weight: 0.0050 chunk 91 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 755 GLN F 297 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.098411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.078649 restraints weight = 20249.906| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.67 r_work: 0.3188 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.5071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9091 Z= 0.171 Angle : 0.520 6.255 12275 Z= 0.270 Chirality : 0.042 0.161 1338 Planarity : 0.004 0.046 1580 Dihedral : 4.813 45.560 1218 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.77 % Allowed : 16.08 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.26), residues: 1103 helix: 1.17 (0.24), residues: 499 sheet: 0.24 (0.52), residues: 122 loop : -0.75 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP M 130 HIS 0.002 0.001 HIS F 73 PHE 0.017 0.001 PHE M 621 TYR 0.015 0.001 TYR M 162 ARG 0.002 0.000 ARG M 23 *********************** 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 101 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 1.097 Fit side-chains REVERT: M 92 MET cc_start: 0.7892 (mmm) cc_final: 0.7488 (mmt) REVERT: M 277 LEU cc_start: 0.7778 (mm) cc_final: 0.7552 (mt) REVERT: M 365 LYS cc_start: 0.8644 (ptmm) cc_final: 0.8394 (pttp) REVERT: M 621 PHE cc_start: 0.5810 (p90) cc_final: 0.5515 (p90) REVERT: F 154 ASP cc_start: 0.7410 (t70) cc_final: 0.7132 (t70) REVERT: F 171 LEU cc_start: 0.8602 (mm) cc_final: 0.8393 (mp) REVERT: F 227 MET cc_start: 0.8737 (tpp) cc_final: 0.8450 (mmm) REVERT: F 369 ILE cc_start: 0.8639 (tp) cc_final: 0.8353 (tp) outliers start: 17 outliers final: 8 residues processed: 96 average time/residue: 0.1969 time to fit residues: 27.8087 Evaluate side-chains 79 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 1.379 ------------------------------------------------------------------------------- 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 236 VAL Chi-restraints excluded: chain M residue 302 LEU Chi-restraints excluded: chain M residue 359 PHE 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 34 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 106 optimal weight: 0.0030 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 104 ASN F 92 ASN F 297 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.093383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.074489 restraints weight = 20417.928| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 2.58 r_work: 0.3114 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.6146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9091 Z= 0.242 Angle : 0.590 11.183 12275 Z= 0.302 Chirality : 0.044 0.175 1338 Planarity : 0.004 0.050 1580 Dihedral : 4.969 45.662 1218 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.61 % Allowed : 17.01 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.26), residues: 1103 helix: 1.25 (0.24), residues: 501 sheet: -0.07 (0.47), residues: 142 loop : -0.62 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP M 130 HIS 0.003 0.001 HIS M 666 PHE 0.020 0.002 PHE M 247 TYR 0.019 0.002 TYR M 287 ARG 0.006 0.000 ARG M 694 *********************** 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 100 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 1.202 Fit side-chains REVERT: M 92 MET cc_start: 0.8186 (mmm) cc_final: 0.7939 (mmt) REVERT: M 277 LEU cc_start: 0.7917 (mm) cc_final: 0.7663 (mt) REVERT: M 365 LYS cc_start: 0.8672 (ptmm) cc_final: 0.8397 (pttp) REVERT: M 579 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8906 (mp) REVERT: F 47 MET cc_start: 0.6558 (ptm) cc_final: 0.4318 (mmp) REVERT: F 154 ASP cc_start: 0.7458 (t70) cc_final: 0.7224 (t70) REVERT: F 227 MET cc_start: 0.8734 (tpp) cc_final: 0.8309 (mmm) outliers start: 25 outliers final: 11 residues processed: 95 average time/residue: 0.1901 time to fit residues: 26.8948 Evaluate side-chains 75 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 1.090 ------------------------------------------------------------------------------- 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 236 VAL Chi-restraints excluded: chain M residue 357 MET Chi-restraints excluded: chain M residue 455 TYR Chi-restraints excluded: chain M residue 496 LEU 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 67 optimal weight: 0.0870 chunk 63 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 29 optimal weight: 0.0040 chunk 32 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 69 optimal weight: 0.4980 chunk 54 optimal weight: 0.0980 chunk 16 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 overall best weight: 0.2770 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.094732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.076601 restraints weight = 20054.288| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.52 r_work: 0.3151 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.6346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9091 Z= 0.153 Angle : 0.506 9.905 12275 Z= 0.257 Chirality : 0.041 0.154 1338 Planarity : 0.003 0.046 1580 Dihedral : 4.537 41.847 1218 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.26), residues: 1103 helix: 1.53 (0.24), residues: 502 sheet: 0.31 (0.49), residues: 134 loop : -0.56 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP M 130 HIS 0.003 0.001 HIS M 358 PHE 0.037 0.001 PHE M 621 TYR 0.011 0.001 TYR M 103 ARG 0.002 0.000 ARG M 434 *********************** 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 93 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.975 Fit side-chains REVERT: M 365 LYS cc_start: 0.8707 (ptmm) cc_final: 0.8486 (pttp) REVERT: M 579 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8848 (mp) REVERT: F 47 MET cc_start: 0.6468 (ptm) cc_final: 0.4361 (mmp) REVERT: F 154 ASP cc_start: 0.7359 (t70) cc_final: 0.7126 (t70) REVERT: F 171 LEU cc_start: 0.8595 (mm) cc_final: 0.8378 (mp) REVERT: F 227 MET cc_start: 0.8752 (tpp) cc_final: 0.8439 (mmm) REVERT: F 369 ILE cc_start: 0.8617 (tp) cc_final: 0.8336 (tp) outliers start: 19 outliers final: 8 residues processed: 89 average time/residue: 0.1816 time to fit residues: 24.3177 Evaluate side-chains 74 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 52 VAL Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 357 MET Chi-restraints excluded: chain M residue 359 PHE Chi-restraints excluded: chain M residue 506 ILE Chi-restraints excluded: chain M residue 579 LEU 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 25 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 71 optimal weight: 0.0040 chunk 19 optimal weight: 0.1980 chunk 33 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- 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 = 0.3551 r_free = 0.3551 target = 0.092191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.073576 restraints weight = 20244.619| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.56 r_work: 0.3094 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.6728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9091 Z= 0.230 Angle : 0.553 9.018 12275 Z= 0.282 Chirality : 0.043 0.165 1338 Planarity : 0.004 0.047 1580 Dihedral : 4.711 44.148 1218 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.51 % Allowed : 18.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.26), residues: 1103 helix: 1.59 (0.24), residues: 495 sheet: -0.08 (0.46), residues: 145 loop : -0.50 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP M 130 HIS 0.003 0.001 HIS F 73 PHE 0.014 0.001 PHE M 247 TYR 0.017 0.001 TYR M 103 ARG 0.004 0.000 ARG M 694 *********************** 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 91 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 67 time to evaluate : 0.948 Fit side-chains REVERT: M 50 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8626 (ptmt) REVERT: M 277 LEU cc_start: 0.7859 (mm) cc_final: 0.7604 (mt) REVERT: M 365 LYS cc_start: 0.8698 (ptmm) cc_final: 0.8437 (pttp) REVERT: F 47 MET cc_start: 0.6676 (ptm) cc_final: 0.4642 (mmp) REVERT: F 154 ASP cc_start: 0.7498 (t70) cc_final: 0.7275 (t70) REVERT: F 171 LEU cc_start: 0.8651 (mm) cc_final: 0.8430 (mp) REVERT: F 369 ILE cc_start: 0.8591 (tp) cc_final: 0.8341 (tp) outliers start: 24 outliers final: 15 residues processed: 85 average time/residue: 0.1878 time to fit residues: 24.0847 Evaluate side-chains 80 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 1.073 ------------------------------------------------------------------------------- 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 76 VAL Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 357 MET Chi-restraints excluded: chain M residue 455 TYR Chi-restraints excluded: chain M residue 496 LEU Chi-restraints excluded: chain M residue 506 ILE Chi-restraints excluded: chain M residue 617 LEU 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 93 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 23 optimal weight: 0.3980 chunk 33 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 7 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3545 r_free = 0.3545 target = 0.091737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.073350 restraints weight = 20479.390| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.55 r_work: 0.3088 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.6965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9091 Z= 0.221 Angle : 0.534 8.185 12275 Z= 0.272 Chirality : 0.043 0.160 1338 Planarity : 0.004 0.048 1580 Dihedral : 4.664 42.603 1218 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.88 % Allowed : 19.31 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.26), residues: 1103 helix: 1.60 (0.24), residues: 495 sheet: -0.05 (0.46), residues: 147 loop : -0.47 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP M 130 HIS 0.006 0.001 HIS M 97 PHE 0.013 0.001 PHE M 247 TYR 0.013 0.001 TYR M 103 ARG 0.003 0.000 ARG M 694 *********************** 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 83 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 65 time to evaluate : 1.122 Fit side-chains REVERT: M 39 VAL cc_start: 0.8054 (OUTLIER) cc_final: 0.7764 (m) REVERT: M 50 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8668 (ptmt) REVERT: M 624 TYR cc_start: 0.4855 (OUTLIER) cc_final: 0.4634 (m-80) REVERT: M 702 ILE cc_start: 0.8717 (pt) cc_final: 0.8396 (mt) REVERT: M 765 PHE cc_start: 0.7642 (m-80) cc_final: 0.7439 (m-10) REVERT: F 47 MET cc_start: 0.6803 (ptm) cc_final: 0.4928 (mmp) REVERT: F 154 ASP cc_start: 0.7487 (t70) cc_final: 0.7271 (t70) REVERT: F 171 LEU cc_start: 0.8612 (mm) cc_final: 0.8385 (mp) REVERT: F 369 ILE cc_start: 0.8616 (tp) cc_final: 0.8344 (tp) outliers start: 18 outliers final: 14 residues processed: 78 average time/residue: 0.1866 time to fit residues: 22.2513 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 : 0.995 ------------------------------------------------------------------------------- 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 236 VAL 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 624 TYR 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 33 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 91 optimal weight: 0.4980 chunk 61 optimal weight: 2.9990 chunk 19 optimal weight: 0.2980 chunk 67 optimal weight: 1.9990 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 = 0.3526 r_free = 0.3526 target = 0.090242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.072948 restraints weight = 20606.919| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.44 r_work: 0.3076 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.7208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9091 Z= 0.244 Angle : 0.553 7.785 12275 Z= 0.282 Chirality : 0.043 0.164 1338 Planarity : 0.004 0.049 1580 Dihedral : 4.757 44.043 1218 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.19 % Allowed : 19.21 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.26), residues: 1103 helix: 1.56 (0.24), residues: 496 sheet: -0.05 (0.46), residues: 145 loop : -0.48 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP M 130 HIS 0.004 0.001 HIS M 97 PHE 0.013 0.001 PHE M 247 TYR 0.013 0.001 TYR M 103 ARG 0.003 0.000 ARG M 694 *********************** 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 84 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 1.000 Fit side-chains REVERT: M 39 VAL cc_start: 0.8192 (OUTLIER) cc_final: 0.7930 (m) REVERT: M 277 LEU cc_start: 0.7954 (mm) cc_final: 0.7705 (mt) REVERT: M 702 ILE cc_start: 0.8834 (pt) cc_final: 0.8524 (mt) REVERT: M 744 LYS cc_start: 0.4165 (ttpt) cc_final: 0.3910 (mptt) REVERT: M 765 PHE cc_start: 0.7937 (m-80) cc_final: 0.7669 (m-10) REVERT: F 47 MET cc_start: 0.6755 (ptm) cc_final: 0.5001 (mmp) REVERT: F 154 ASP cc_start: 0.7787 (t70) cc_final: 0.7570 (t70) REVERT: F 369 ILE cc_start: 0.8671 (tp) cc_final: 0.8416 (tp) outliers start: 21 outliers final: 17 residues processed: 80 average time/residue: 0.1878 time to fit residues: 22.8785 Evaluate side-chains 80 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 52 VAL Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 315 GLN 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 496 LEU Chi-restraints excluded: chain M residue 506 ILE Chi-restraints excluded: chain M residue 617 LEU 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 3 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3505 r_free = 0.3505 target = 0.089714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.071722 restraints weight = 20472.721| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.52 r_work: 0.3059 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.7378 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= 0.264 Angle : 0.562 7.407 12275 Z= 0.288 Chirality : 0.044 0.171 1338 Planarity : 0.004 0.049 1580 Dihedral : 4.846 44.635 1218 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.88 % Allowed : 19.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.26), residues: 1103 helix: 1.53 (0.24), residues: 496 sheet: 0.08 (0.45), residues: 153 loop : -0.50 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP M 508 HIS 0.005 0.001 HIS M 97 PHE 0.014 0.001 PHE M 247 TYR 0.014 0.001 TYR M 103 ARG 0.003 0.000 ARG M 694 *********************** 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 82 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 1.030 Fit side-chains REVERT: M 39 VAL cc_start: 0.8132 (OUTLIER) cc_final: 0.7889 (m) REVERT: M 277 LEU cc_start: 0.7866 (mm) cc_final: 0.7650 (mt) REVERT: M 702 ILE cc_start: 0.8722 (pt) cc_final: 0.8443 (mt) REVERT: M 765 PHE cc_start: 0.7982 (m-80) cc_final: 0.7655 (m-10) REVERT: F 47 MET cc_start: 0.6789 (ptm) cc_final: 0.5119 (mmp) REVERT: F 154 ASP cc_start: 0.7522 (t70) cc_final: 0.7294 (t70) outliers start: 18 outliers final: 17 residues processed: 78 average time/residue: 0.1944 time to fit residues: 22.8016 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 : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 52 VAL Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 315 GLN 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 496 LEU Chi-restraints excluded: chain M residue 506 ILE Chi-restraints excluded: chain M residue 617 LEU 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 44 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 17 optimal weight: 0.2980 chunk 90 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3508 r_free = 0.3508 target = 0.089922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.072040 restraints weight = 20508.456| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.51 r_work: 0.3061 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.7496 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= 0.239 Angle : 0.558 7.336 12275 Z= 0.284 Chirality : 0.043 0.164 1338 Planarity : 0.004 0.048 1580 Dihedral : 4.802 43.277 1218 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.98 % Allowed : 19.10 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.26), residues: 1103 helix: 1.50 (0.24), residues: 496 sheet: 0.05 (0.45), residues: 153 loop : -0.47 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP M 508 HIS 0.004 0.001 HIS M 97 PHE 0.013 0.001 PHE M 247 TYR 0.014 0.001 TYR M 103 ARG 0.002 0.000 ARG M 434 ********************** 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 79 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 1.001 Fit side-chains REVERT: M 39 VAL cc_start: 0.8159 (OUTLIER) cc_final: 0.7942 (m) REVERT: M 507 GLU cc_start: 0.4716 (mp0) cc_final: 0.4350 (tp30) REVERT: M 702 ILE cc_start: 0.8730 (pt) cc_final: 0.8451 (mt) REVERT: M 765 PHE cc_start: 0.7979 (m-80) cc_final: 0.7659 (m-10) REVERT: F 47 MET cc_start: 0.6805 (ptm) cc_final: 0.5146 (mmp) REVERT: F 154 ASP cc_start: 0.7512 (t70) cc_final: 0.7288 (t70) outliers start: 19 outliers final: 17 residues processed: 75 average time/residue: 0.1715 time to fit residues: 19.9362 Evaluate side-chains 77 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 39 VAL Chi-restraints excluded: chain M residue 52 VAL Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 76 VAL Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 315 GLN 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 496 LEU Chi-restraints excluded: chain M residue 506 ILE Chi-restraints excluded: chain M residue 617 LEU 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 99 optimal weight: 0.9990 chunk 9 optimal weight: 0.0980 chunk 47 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 86 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3503 r_free = 0.3503 target = 0.089643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.071902 restraints weight = 20446.936| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.51 r_work: 0.3070 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.7580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9091 Z= 0.229 Angle : 0.549 7.145 12275 Z= 0.280 Chirality : 0.043 0.164 1338 Planarity : 0.004 0.048 1580 Dihedral : 4.759 42.577 1218 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.98 % Allowed : 18.79 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.26), residues: 1103 helix: 1.54 (0.24), residues: 496 sheet: -0.06 (0.44), residues: 163 loop : -0.42 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP M 508 HIS 0.004 0.001 HIS M 97 PHE 0.012 0.001 PHE M 247 TYR 0.014 0.001 TYR M 103 ARG 0.002 0.000 ARG M 434 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4477.59 seconds wall clock time: 80 minutes 49.39 seconds (4849.39 seconds total)