Starting phenix.real_space_refine on Thu Mar 13 15:45:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zi9_60122/03_2025/8zi9_60122.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zi9_60122/03_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_60122/03_2025/8zi9_60122.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zi9_60122/03_2025/8zi9_60122.map" model { file = "/net/cci-nas-00/data/ceres_data/8zi9_60122/03_2025/8zi9_60122.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zi9_60122/03_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 7.20, per 1000 atoms: 0.81 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: 2.23 Conformation dependent library (CDL) restraints added in 896.4 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: 1.55 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: 3.57 Time building geometry restraints manager: 2.60 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: 9.150 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: 0.350 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 26.290 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: 0.000 Load rotamer database and sin/cos tables:3.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.620 ------------------------------------------------------------------------------- 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 : 0.938 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: 0.2399 time to fit residues: 60.8592 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 : 1.055 ------------------------------------------------------------------------------- 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 = 0.3685 r_free = 0.3685 target = 0.099967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.080164 restraints weight = 20353.556| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.65 r_work: 0.3221 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 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 : 1.127 Fit side-chains revert: symmetry clash REVERT: M 92 MET cc_start: 0.7663 (mmm) cc_final: 0.7420 (mmt) REVERT: M 277 LEU cc_start: 0.7888 (mm) cc_final: 0.7648 (mt) REVERT: M 365 LYS cc_start: 0.8718 (ptmm) cc_final: 0.8447 (pttp) REVERT: M 690 MET cc_start: 0.6842 (tmm) cc_final: 0.6563 (tmm) REVERT: F 47 MET cc_start: 0.6168 (ptm) cc_final: 0.4175 (mmp) REVERT: F 154 ASP cc_start: 0.7270 (t70) cc_final: 0.6953 (t70) REVERT: F 227 MET cc_start: 0.8783 (tpp) cc_final: 0.8479 (mmm) outliers start: 17 outliers final: 6 residues processed: 123 average time/residue: 0.2495 time to fit residues: 42.7009 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 : 0.918 ------------------------------------------------------------------------------- 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: 0.9980 chunk 14 optimal weight: 0.9990 chunk 57 optimal weight: 0.2980 chunk 107 optimal weight: 0.4980 chunk 81 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 108 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 52 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 224 ASN M 755 GLN F 92 ASN F 297 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.095753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.076477 restraints weight = 20384.655| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.61 r_work: 0.3151 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.5450 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= 0.224 Angle : 0.554 5.821 12275 Z= 0.289 Chirality : 0.043 0.170 1338 Planarity : 0.004 0.050 1580 Dihedral : 4.913 48.417 1218 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.98 % Allowed : 15.97 % Favored : 82.05 % 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: 0.23 (0.26), residues: 1103 helix: 1.04 (0.24), residues: 504 sheet: 0.04 (0.51), residues: 127 loop : -0.73 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP M 130 HIS 0.003 0.001 HIS F 73 PHE 0.018 0.001 PHE M 247 TYR 0.015 0.001 TYR M 162 ARG 0.004 0.001 ARG M 190 *********************** 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 98 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 1.162 Fit side-chains REVERT: M 92 MET cc_start: 0.8041 (mmm) cc_final: 0.7740 (mmt) REVERT: M 365 LYS cc_start: 0.8643 (ptmm) cc_final: 0.8380 (pttp) REVERT: M 579 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8874 (mp) REVERT: M 621 PHE cc_start: 0.5812 (p90) cc_final: 0.5519 (p90) REVERT: F 47 MET cc_start: 0.6416 (ptm) cc_final: 0.4672 (mmp) REVERT: F 154 ASP cc_start: 0.7409 (t70) cc_final: 0.7151 (t70) REVERT: F 227 MET cc_start: 0.8780 (tpp) cc_final: 0.8439 (mmm) outliers start: 19 outliers final: 7 residues processed: 93 average time/residue: 0.2550 time to fit residues: 35.4148 Evaluate side-chains 72 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 1.250 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 34 optimal weight: 0.7980 chunk 21 optimal weight: 0.3980 chunk 108 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 11 optimal weight: 0.0980 chunk 98 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 104 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.093506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.074742 restraints weight = 20393.952| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.56 r_work: 0.3117 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.6277 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= 0.231 Angle : 0.564 12.059 12275 Z= 0.287 Chirality : 0.044 0.162 1338 Planarity : 0.004 0.049 1580 Dihedral : 4.862 46.199 1218 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.09 % Allowed : 17.95 % Favored : 79.96 % 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: 1.23 (0.24), residues: 502 sheet: -0.07 (0.46), residues: 144 loop : -0.60 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP M 130 HIS 0.003 0.001 HIS M 691 PHE 0.021 0.001 PHE M 46 TYR 0.015 0.001 TYR M 287 ARG 0.003 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 91 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 1.105 Fit side-chains REVERT: M 92 MET cc_start: 0.8197 (mmm) cc_final: 0.7984 (mmt) REVERT: M 365 LYS cc_start: 0.8708 (ptmm) cc_final: 0.8440 (pttp) REVERT: M 765 PHE cc_start: 0.6985 (m-80) cc_final: 0.6715 (m-80) REVERT: F 47 MET cc_start: 0.6443 (ptm) cc_final: 0.4953 (mmp) REVERT: F 154 ASP cc_start: 0.7445 (t70) cc_final: 0.7217 (t70) REVERT: F 171 LEU cc_start: 0.8646 (mm) cc_final: 0.8438 (mp) REVERT: F 227 MET cc_start: 0.8758 (tpp) cc_final: 0.8380 (mmm) outliers start: 20 outliers final: 10 residues processed: 87 average time/residue: 0.1888 time to fit residues: 24.6225 Evaluate side-chains 71 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.969 ------------------------------------------------------------------------------- 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 506 ILE 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: 0.7980 chunk 63 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 69 optimal weight: 0.0370 chunk 54 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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 M 760 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.092514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.073948 restraints weight = 20363.452| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.57 r_work: 0.3101 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.6629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9091 Z= 0.218 Angle : 0.541 9.515 12275 Z= 0.276 Chirality : 0.043 0.166 1338 Planarity : 0.004 0.049 1580 Dihedral : 4.736 45.032 1218 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.30 % Allowed : 18.16 % 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 (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: 0.56 (0.26), residues: 1103 helix: 1.41 (0.24), residues: 501 sheet: -0.07 (0.46), residues: 147 loop : -0.58 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP M 130 HIS 0.005 0.001 HIS M 97 PHE 0.038 0.001 PHE M 621 TYR 0.012 0.001 TYR M 103 ARG 0.003 0.000 ARG M 694 *********************** 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 88 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.958 Fit side-chains REVERT: M 50 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8612 (ptmt) REVERT: M 579 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8887 (mp) REVERT: M 765 PHE cc_start: 0.7349 (m-80) cc_final: 0.7120 (m-80) REVERT: F 47 MET cc_start: 0.6552 (ptm) cc_final: 0.5205 (mmp) REVERT: F 154 ASP cc_start: 0.7480 (t70) cc_final: 0.7260 (t70) REVERT: F 171 LEU cc_start: 0.8653 (mm) cc_final: 0.8418 (mp) outliers start: 22 outliers final: 12 residues processed: 83 average time/residue: 0.2053 time to fit residues: 25.5963 Evaluate side-chains 71 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.864 ------------------------------------------------------------------------------- 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 236 VAL Chi-restraints excluded: chain M residue 357 MET Chi-restraints excluded: chain M residue 359 PHE 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 770 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: 0.7980 chunk 12 optimal weight: 0.1980 chunk 110 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3542 r_free = 0.3542 target = 0.091561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.073160 restraints weight = 20167.165| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.54 r_work: 0.3085 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.6926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9091 Z= 0.232 Angle : 0.548 9.101 12275 Z= 0.281 Chirality : 0.043 0.167 1338 Planarity : 0.004 0.049 1580 Dihedral : 4.750 43.472 1218 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.30 % Allowed : 18.06 % Favored : 79.65 % 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: 0.62 (0.26), residues: 1103 helix: 1.49 (0.24), residues: 495 sheet: -0.03 (0.46), residues: 147 loop : -0.57 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 130 HIS 0.004 0.001 HIS M 97 PHE 0.014 0.001 PHE M 247 TYR 0.014 0.001 TYR M 103 ARG 0.002 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 83 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 61 time to evaluate : 1.052 Fit side-chains REVERT: M 39 VAL cc_start: 0.8054 (OUTLIER) cc_final: 0.7761 (m) REVERT: M 50 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8650 (ptmt) REVERT: M 579 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8902 (mp) REVERT: M 765 PHE cc_start: 0.7561 (m-80) cc_final: 0.7349 (m-80) REVERT: F 47 MET cc_start: 0.6596 (ptm) cc_final: 0.5425 (mmp) REVERT: F 154 ASP cc_start: 0.7477 (t70) cc_final: 0.7252 (t70) REVERT: F 171 LEU cc_start: 0.8626 (mm) cc_final: 0.8397 (mp) outliers start: 22 outliers final: 14 residues processed: 78 average time/residue: 0.1780 time to fit residues: 21.3519 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 : 1.632 ------------------------------------------------------------------------------- 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 496 LEU Chi-restraints excluded: chain M residue 506 ILE Chi-restraints excluded: chain M residue 579 LEU Chi-restraints excluded: chain M residue 617 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: 0.6980 chunk 109 optimal weight: 0.0020 chunk 4 optimal weight: 0.0770 chunk 27 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 overall best weight: 0.3946 ------------------------------------------------------------------------------- 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 = 0.3564 r_free = 0.3564 target = 0.092350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.075108 restraints weight = 20170.946| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.42 r_work: 0.3121 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.7057 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= 0.176 Angle : 0.510 8.215 12275 Z= 0.259 Chirality : 0.041 0.157 1338 Planarity : 0.004 0.047 1580 Dihedral : 4.542 41.046 1218 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.09 % Allowed : 18.58 % Favored : 79.33 % 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: 0.77 (0.26), residues: 1103 helix: 1.60 (0.24), residues: 495 sheet: 0.03 (0.46), residues: 147 loop : -0.47 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 130 HIS 0.004 0.001 HIS M 97 PHE 0.011 0.001 PHE M 247 TYR 0.012 0.001 TYR M 103 ARG 0.002 0.000 ARG M 434 *********************** 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: 20 poor density : 65 time to evaluate : 0.954 Fit side-chains REVERT: M 39 VAL cc_start: 0.8151 (OUTLIER) cc_final: 0.7870 (m) REVERT: M 507 GLU cc_start: 0.5049 (mp0) cc_final: 0.4774 (tp30) REVERT: M 690 MET cc_start: 0.6853 (tmm) cc_final: 0.6490 (tmm) REVERT: M 744 LYS cc_start: 0.4062 (ttpt) cc_final: 0.3843 (mptt) REVERT: F 47 MET cc_start: 0.6631 (ptm) cc_final: 0.5485 (mmp) REVERT: F 154 ASP cc_start: 0.7671 (t70) cc_final: 0.7462 (t70) REVERT: F 171 LEU cc_start: 0.8733 (mm) cc_final: 0.8505 (mp) REVERT: F 369 ILE cc_start: 0.8652 (tp) cc_final: 0.8393 (tp) outliers start: 20 outliers final: 16 residues processed: 80 average time/residue: 0.1865 time to fit residues: 22.3046 Evaluate side-chains 77 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 36 ASP 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 33 optimal weight: 0.5980 chunk 101 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 28 optimal weight: 0.2980 chunk 22 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3528 r_free = 0.3528 target = 0.090185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.072643 restraints weight = 20463.091| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.48 r_work: 0.3091 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.7193 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= 0.215 Angle : 0.536 7.892 12275 Z= 0.272 Chirality : 0.043 0.180 1338 Planarity : 0.004 0.048 1580 Dihedral : 4.628 42.094 1218 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.88 % Allowed : 18.48 % Favored : 79.65 % 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: 0.77 (0.26), residues: 1103 helix: 1.59 (0.24), residues: 495 sheet: 0.02 (0.46), residues: 147 loop : -0.46 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 340 HIS 0.006 0.001 HIS M 97 PHE 0.013 0.001 PHE M 247 TYR 0.014 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 80 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 1.015 Fit side-chains REVERT: M 39 VAL cc_start: 0.8175 (OUTLIER) cc_final: 0.7912 (m) REVERT: M 744 LYS cc_start: 0.4244 (ttpt) cc_final: 0.3976 (mptt) REVERT: F 154 ASP cc_start: 0.7724 (t70) cc_final: 0.7513 (t70) REVERT: F 171 LEU cc_start: 0.8746 (mm) cc_final: 0.8527 (mp) REVERT: F 369 ILE cc_start: 0.8704 (tp) cc_final: 0.8436 (tp) outliers start: 18 outliers final: 15 residues processed: 76 average time/residue: 0.1860 time to fit residues: 21.2908 Evaluate side-chains 77 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 61 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 108 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 98 optimal weight: 0.4980 chunk 95 optimal weight: 0.8980 chunk 15 optimal weight: 0.4980 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 = 0.3520 r_free = 0.3520 target = 0.089881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.072524 restraints weight = 20179.310| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.45 r_work: 0.3077 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.7336 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= 0.225 Angle : 0.543 7.901 12275 Z= 0.277 Chirality : 0.043 0.181 1338 Planarity : 0.004 0.048 1580 Dihedral : 4.671 42.187 1218 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.67 % Allowed : 18.37 % Favored : 79.96 % 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: 0.81 (0.26), residues: 1103 helix: 1.60 (0.24), residues: 496 sheet: 0.13 (0.46), residues: 145 loop : -0.45 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP M 508 HIS 0.005 0.001 HIS M 97 PHE 0.013 0.001 PHE M 247 TYR 0.015 0.001 TYR M 103 ARG 0.002 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 79 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.971 Fit side-chains REVERT: M 39 VAL cc_start: 0.8121 (OUTLIER) cc_final: 0.7877 (m) REVERT: F 47 MET cc_start: 0.6742 (ptm) cc_final: 0.5167 (mmp) REVERT: F 154 ASP cc_start: 0.7399 (t70) cc_final: 0.7186 (t70) REVERT: F 171 LEU cc_start: 0.8632 (mm) cc_final: 0.8414 (mp) REVERT: F 369 ILE cc_start: 0.8648 (tp) cc_final: 0.8406 (tp) outliers start: 16 outliers final: 15 residues processed: 75 average time/residue: 0.1922 time to fit residues: 21.6020 Evaluate side-chains 77 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 1.137 ------------------------------------------------------------------------------- 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 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 F residue 122 ILE 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: 1.9990 chunk 59 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 17 optimal weight: 0.1980 chunk 90 optimal weight: 0.0010 chunk 98 optimal weight: 0.6980 chunk 84 optimal weight: 0.4980 overall best weight: 0.4186 ------------------------------------------------------------------------------- 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 = 0.3530 r_free = 0.3530 target = 0.090567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.073245 restraints weight = 20163.933| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.45 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: 0.8330 moved from start: 0.7432 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= 0.181 Angle : 0.522 7.425 12275 Z= 0.266 Chirality : 0.042 0.156 1338 Planarity : 0.004 0.047 1580 Dihedral : 4.560 40.632 1218 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.67 % Allowed : 18.48 % Favored : 79.85 % 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: 0.85 (0.26), residues: 1103 helix: 1.62 (0.24), residues: 496 sheet: 0.13 (0.46), residues: 145 loop : -0.40 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP M 508 HIS 0.006 0.001 HIS M 97 PHE 0.011 0.001 PHE M 247 TYR 0.014 0.001 TYR M 103 ARG 0.002 0.000 ARG M 739 ********************** 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: 16 poor density : 63 time to evaluate : 1.178 Fit side-chains REVERT: M 39 VAL cc_start: 0.8105 (OUTLIER) cc_final: 0.7881 (m) REVERT: M 765 PHE cc_start: 0.7722 (m-80) cc_final: 0.7496 (m-10) REVERT: F 47 MET cc_start: 0.6635 (ptm) cc_final: 0.5050 (mmp) REVERT: F 154 ASP cc_start: 0.7382 (t70) cc_final: 0.7169 (t70) REVERT: F 171 LEU cc_start: 0.8613 (mm) cc_final: 0.8401 (mp) REVERT: F 369 ILE cc_start: 0.8642 (tp) cc_final: 0.8375 (tp) outliers start: 16 outliers final: 14 residues processed: 76 average time/residue: 0.2151 time to fit residues: 25.2799 Evaluate side-chains 74 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 36 ASP 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 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 617 LEU Chi-restraints excluded: chain F residue 122 ILE 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: 0.0870 chunk 9 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 34 optimal weight: 0.0870 overall best weight: 0.5136 ------------------------------------------------------------------------------- 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 = 0.3525 r_free = 0.3525 target = 0.090358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.073511 restraints weight = 20253.827| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.39 r_work: 0.3084 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.7514 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= 0.205 Angle : 0.537 7.389 12275 Z= 0.274 Chirality : 0.042 0.159 1338 Planarity : 0.004 0.047 1580 Dihedral : 4.600 41.691 1218 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.77 % Allowed : 18.48 % 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 (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: 0.88 (0.26), residues: 1103 helix: 1.64 (0.24), residues: 496 sheet: 0.21 (0.45), residues: 155 loop : -0.41 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP M 508 HIS 0.004 0.001 HIS M 760 PHE 0.011 0.001 PHE M 247 TYR 0.016 0.001 TYR M 103 ARG 0.002 0.000 ARG F 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4629.70 seconds wall clock time: 82 minutes 27.24 seconds (4947.24 seconds total)