Starting phenix.real_space_refine on Wed Jun 3 10:04:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k90_62183/06_2026/9k90_62183.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k90_62183/06_2026/9k90_62183.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k90_62183/06_2026/9k90_62183.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k90_62183/06_2026/9k90_62183.map" model { file = "/net/cci-nas-00/data/ceres_data/9k90_62183/06_2026/9k90_62183.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k90_62183/06_2026/9k90_62183.cif" } resolution = 3.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 1987 2.51 5 N 454 2.21 5 O 495 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2960 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2960 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 11, 'TRANS': 359} Chain breaks: 1 Time building chain proxies: 1.17, per 1000 atoms: 0.40 Number of scatterers: 2960 At special positions: 0 Unit cell: (73.7, 68.2, 75.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 24 16.00 O 495 8.00 N 454 7.00 C 1987 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 143 " - pdb=" SG CYS A 382 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.26 Conformation dependent library (CDL) restraints added in 133.1 milliseconds 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 700 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 0 sheets defined 79.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 35 through 59 removed outlier: 4.104A pdb=" N SER A 39 " --> pdb=" O HIS A 35 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU A 50 " --> pdb=" O GLY A 46 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N VAL A 52 " --> pdb=" O SER A 48 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N TRP A 53 " --> pdb=" O SER A 49 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA A 56 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 57 " --> pdb=" O TRP A 53 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 83 removed outlier: 3.829A pdb=" N THR A 67 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN A 69 " --> pdb=" O TYR A 65 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU A 73 " --> pdb=" O GLN A 69 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL A 74 " --> pdb=" O ILE A 70 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS A 75 " --> pdb=" O THR A 71 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE A 82 " --> pdb=" O ILE A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 88 No H-bonds generated for 'chain 'A' and resid 86 through 88' Processing helix chain 'A' and resid 89 through 111 removed outlier: 3.722A pdb=" N CYS A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA A 102 " --> pdb=" O SER A 98 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN A 105 " --> pdb=" O CYS A 101 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER A 109 " --> pdb=" O GLN A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 145 removed outlier: 3.515A pdb=" N THR A 118 " --> pdb=" O THR A 114 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU A 121 " --> pdb=" O ASP A 117 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A 122 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 133 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 134 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR A 144 " --> pdb=" O ASN A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 173 removed outlier: 3.518A pdb=" N GLY A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER A 160 " --> pdb=" O GLY A 156 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLY A 161 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL A 162 " --> pdb=" O GLY A 158 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 210 removed outlier: 3.530A pdb=" N CYS A 208 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 238 removed outlier: 3.770A pdb=" N LYS A 237 " --> pdb=" O MET A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 252 removed outlier: 4.142A pdb=" N ASN A 250 " --> pdb=" O MET A 246 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 268 removed outlier: 3.751A pdb=" N SER A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 292 removed outlier: 3.659A pdb=" N VAL A 276 " --> pdb=" O SER A 272 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N SER A 290 " --> pdb=" O PHE A 286 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG A 291 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N TYR A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 296 Processing helix chain 'A' and resid 299 through 306 removed outlier: 4.284A pdb=" N ASN A 304 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N THR A 306 " --> pdb=" O LYS A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 319 Processing helix chain 'A' and resid 322 through 328 removed outlier: 3.699A pdb=" N ILE A 327 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 331 No H-bonds generated for 'chain 'A' and resid 329 through 331' Processing helix chain 'A' and resid 339 through 357 removed outlier: 3.608A pdb=" N GLN A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 374 through 404 removed outlier: 3.589A pdb=" N ILE A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL A 386 " --> pdb=" O CYS A 382 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE A 390 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL A 391 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE A 397 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TRP A 398 " --> pdb=" O PHE A 394 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TYR A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE A 402 " --> pdb=" O TRP A 398 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N TYR A 403 " --> pdb=" O THR A 399 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASN A 404 " --> pdb=" O THR A 400 " (cutoff:3.500A) 165 hydrogen bonds defined for protein. 477 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: 0.41 Time building geometry restraints manager: 0.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 866 1.35 - 1.47: 804 1.47 - 1.59: 1332 1.59 - 1.72: 0 1.72 - 1.84: 35 Bond restraints: 3037 Sorted by residual: bond pdb=" CB CYS A 382 " pdb=" SG CYS A 382 " ideal model delta sigma weight residual 1.808 1.838 -0.030 3.30e-02 9.18e+02 8.34e-01 bond pdb=" C LEU A 47 " pdb=" O LEU A 47 " ideal model delta sigma weight residual 1.236 1.245 -0.008 1.15e-02 7.56e+03 5.10e-01 bond pdb=" N PRO A 293 " pdb=" CA PRO A 293 " ideal model delta sigma weight residual 1.465 1.479 -0.014 2.03e-02 2.43e+03 5.03e-01 bond pdb=" CG LEU A 133 " pdb=" CD2 LEU A 133 " ideal model delta sigma weight residual 1.521 1.500 0.021 3.30e-02 9.18e+02 4.10e-01 bond pdb=" CG LEU A 369 " pdb=" CD1 LEU A 369 " ideal model delta sigma weight residual 1.521 1.501 0.020 3.30e-02 9.18e+02 3.64e-01 ... (remaining 3032 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 3996 1.29 - 2.59: 106 2.59 - 3.88: 12 3.88 - 5.18: 6 5.18 - 6.47: 3 Bond angle restraints: 4123 Sorted by residual: angle pdb=" N ILE A 408 " pdb=" CA ILE A 408 " pdb=" C ILE A 408 " ideal model delta sigma weight residual 112.96 109.94 3.02 1.00e+00 1.00e+00 9.11e+00 angle pdb=" C VAL A 360 " pdb=" CA VAL A 360 " pdb=" CB VAL A 360 " ideal model delta sigma weight residual 113.70 111.40 2.30 9.50e-01 1.11e+00 5.84e+00 angle pdb=" N PRO A 293 " pdb=" CA PRO A 293 " pdb=" C PRO A 293 " ideal model delta sigma weight residual 110.70 113.54 -2.84 1.22e+00 6.72e-01 5.42e+00 angle pdb=" C THR A 359 " pdb=" N VAL A 360 " pdb=" CA VAL A 360 " ideal model delta sigma weight residual 120.43 122.53 -2.10 9.60e-01 1.09e+00 4.79e+00 angle pdb=" N TYR A 292 " pdb=" CA TYR A 292 " pdb=" C TYR A 292 " ideal model delta sigma weight residual 109.81 114.02 -4.21 2.21e+00 2.05e-01 3.64e+00 ... (remaining 4118 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.37: 1609 16.37 - 32.74: 120 32.74 - 49.11: 24 49.11 - 65.48: 3 65.48 - 81.85: 1 Dihedral angle restraints: 1757 sinusoidal: 676 harmonic: 1081 Sorted by residual: dihedral pdb=" CA ILE A 61 " pdb=" CB ILE A 61 " pdb=" CG1 ILE A 61 " pdb=" CD1 ILE A 61 " ideal model delta sinusoidal sigma weight residual 180.00 122.36 57.64 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" CB MET A 37 " pdb=" CG MET A 37 " pdb=" SD MET A 37 " pdb=" CE MET A 37 " ideal model delta sinusoidal sigma weight residual 60.00 109.40 -49.40 3 1.50e+01 4.44e-03 8.77e+00 dihedral pdb=" CA LYS A 33 " pdb=" CB LYS A 33 " pdb=" CG LYS A 33 " pdb=" CD LYS A 33 " ideal model delta sinusoidal sigma weight residual 180.00 131.80 48.20 3 1.50e+01 4.44e-03 8.60e+00 ... (remaining 1754 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 249 0.026 - 0.051: 137 0.051 - 0.077: 70 0.077 - 0.102: 25 0.102 - 0.128: 7 Chirality restraints: 488 Sorted by residual: chirality pdb=" CA PHE A 257 " pdb=" N PHE A 257 " pdb=" C PHE A 257 " pdb=" CB PHE A 257 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.07e-01 chirality pdb=" CA VAL A 183 " pdb=" N VAL A 183 " pdb=" C VAL A 183 " pdb=" CB VAL A 183 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 chirality pdb=" CA ILE A 85 " pdb=" N ILE A 85 " pdb=" C ILE A 85 " pdb=" CB ILE A 85 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.48e-01 ... (remaining 485 not shown) Planarity restraints: 497 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 176 " 0.022 5.00e-02 4.00e+02 3.34e-02 1.78e+00 pdb=" N PRO A 177 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 177 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 177 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 360 " -0.020 5.00e-02 4.00e+02 3.02e-02 1.46e+00 pdb=" N PRO A 361 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 361 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 361 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 293 " -0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO A 294 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 294 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 294 " -0.017 5.00e-02 4.00e+02 ... (remaining 494 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 658 2.78 - 3.31: 3003 3.31 - 3.84: 4568 3.84 - 4.37: 5297 4.37 - 4.90: 8531 Nonbonded interactions: 22057 Sorted by model distance: nonbonded pdb=" NE2 GLN A 105 " pdb=" OE2 GLU A 196 " model vdw 2.247 3.120 nonbonded pdb=" O GLN A 255 " pdb=" OG1 THR A 400 " model vdw 2.301 3.040 nonbonded pdb=" O ASP A 287 " pdb=" OG SER A 290 " model vdw 2.308 3.040 nonbonded pdb=" N LYS A 374 " pdb=" OE1 GLU A 377 " model vdw 2.496 3.120 nonbonded pdb=" O GLN A 105 " pdb=" OG SER A 109 " model vdw 2.497 3.040 ... (remaining 22052 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 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: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 5.110 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5576 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 : 0.003 0.030 3038 Z= 0.137 Angle : 0.554 6.472 4125 Z= 0.303 Chirality : 0.041 0.128 488 Planarity : 0.004 0.033 497 Dihedral : 12.064 81.851 1054 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.51 % Allowed : 6.02 % Favored : 92.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.45), residues: 367 helix: 0.69 (0.33), residues: 256 sheet: None (None), residues: 0 loop : -0.46 (0.62), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 319 TYR 0.005 0.001 TYR A 152 PHE 0.009 0.001 PHE A 365 TRP 0.009 0.001 TRP A 325 HIS 0.005 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 ( 3037) covalent geometry : angle 0.55321 / 0.30 ( 4123) SS BOND : bond 0.00556 / 0.29 ( 1) SS BOND : angle 1.70203 / 0.95 ( 2) hydrogen bonds : bond 0.20384 / 13.18 ( 165) hydrogen bonds : angle 6.06258 / 4.43 ( 477) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASN cc_start: 0.7668 (t0) cc_final: 0.7341 (t0) REVERT: A 139 PHE cc_start: 0.5581 (m-10) cc_final: 0.5055 (m-10) REVERT: A 165 PHE cc_start: 0.7050 (t80) cc_final: 0.6774 (t80) REVERT: A 347 MET cc_start: 0.4608 (mmp) cc_final: 0.3881 (tpp) REVERT: A 387 ILE cc_start: 0.6703 (mm) cc_final: 0.6084 (mt) REVERT: A 394 PHE cc_start: 0.7129 (t80) cc_final: 0.6827 (t80) outliers start: 5 outliers final: 2 residues processed: 66 average time/residue: 0.0592 time to fit residues: 4.7356 Evaluate side-chains 58 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 382 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.1980 chunk 13 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN A 69 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.197005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.177088 restraints weight = 5123.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.180917 restraints weight = 3206.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.183918 restraints weight = 2237.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.185929 restraints weight = 1655.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.187277 restraints weight = 1301.531| |-----------------------------------------------------------------------------| r_work (final): 0.4450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5797 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3038 Z= 0.202 Angle : 0.662 6.344 4125 Z= 0.351 Chirality : 0.044 0.116 488 Planarity : 0.005 0.032 497 Dihedral : 5.721 44.844 385 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 5.72 % Allowed : 11.14 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.44), residues: 367 helix: 0.65 (0.33), residues: 249 sheet: None (None), residues: 0 loop : -0.70 (0.60), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.003 ARG A 319 TYR 0.018 0.001 TYR A 274 PHE 0.022 0.002 PHE A 390 TRP 0.015 0.002 TRP A 251 HIS 0.003 0.001 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.20 ( 3037) covalent geometry : angle 0.65951 / 0.35 ( 4123) SS BOND : bond 0.02066 / 1.09 ( 1) SS BOND : angle 2.75395 / 1.52 ( 2) hydrogen bonds : bond 0.05925 / 3.90 ( 165) hydrogen bonds : angle 4.48384 / 3.33 ( 477) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.098 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.5946 (tttt) cc_final: 0.5535 (tptt) REVERT: A 54 ASN cc_start: 0.7788 (t0) cc_final: 0.7570 (t0) REVERT: A 87 LYS cc_start: 0.4485 (ttmt) cc_final: 0.4252 (ttmt) REVERT: A 124 PHE cc_start: 0.4412 (OUTLIER) cc_final: 0.3732 (m-10) REVERT: A 165 PHE cc_start: 0.7315 (t80) cc_final: 0.7058 (t80) REVERT: A 347 MET cc_start: 0.4746 (mmp) cc_final: 0.3904 (tpp) REVERT: A 358 ASN cc_start: 0.7654 (t0) cc_final: 0.7329 (t0) outliers start: 19 outliers final: 10 residues processed: 74 average time/residue: 0.0487 time to fit residues: 4.5682 Evaluate side-chains 72 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 205 PHE Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 382 CYS Chi-restraints excluded: chain A residue 384 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 25 optimal weight: 0.9980 chunk 31 optimal weight: 0.4980 chunk 23 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 5 optimal weight: 0.0770 chunk 27 optimal weight: 0.0870 chunk 7 optimal weight: 0.2980 chunk 1 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 34 optimal weight: 0.2980 overall best weight: 0.2516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.198312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.180391 restraints weight = 5304.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.184132 restraints weight = 3307.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.186959 restraints weight = 2268.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.188726 restraints weight = 1652.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.190238 restraints weight = 1287.654| |-----------------------------------------------------------------------------| r_work (final): 0.4434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5730 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3038 Z= 0.128 Angle : 0.546 6.256 4125 Z= 0.283 Chirality : 0.039 0.117 488 Planarity : 0.004 0.031 497 Dihedral : 5.054 34.683 385 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.81 % Allowed : 15.96 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.46), residues: 367 helix: 0.81 (0.33), residues: 256 sheet: None (None), residues: 0 loop : -0.42 (0.65), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 291 TYR 0.008 0.001 TYR A 274 PHE 0.011 0.001 PHE A 42 TRP 0.008 0.001 TRP A 251 HIS 0.002 0.001 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 ( 3037) covalent geometry : angle 0.54422 / 0.28 ( 4123) SS BOND : bond 0.01516 / 0.80 ( 1) SS BOND : angle 2.11127 / 1.13 ( 2) hydrogen bonds : bond 0.04656 / 3.09 ( 165) hydrogen bonds : angle 3.92703 / 2.94 ( 477) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.109 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 MET cc_start: 0.4471 (mmp) cc_final: 0.3670 (tpp) REVERT: A 358 ASN cc_start: 0.7677 (t0) cc_final: 0.7427 (t0) outliers start: 6 outliers final: 5 residues processed: 62 average time/residue: 0.0467 time to fit residues: 3.7053 Evaluate side-chains 61 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 384 PHE Chi-restraints excluded: chain A residue 389 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 0.0980 chunk 31 optimal weight: 0.0020 chunk 27 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 11 optimal weight: 0.0020 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 0.3980 overall best weight: 0.2196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 54 ASN ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 GLN ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.196489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.177924 restraints weight = 5147.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.181747 restraints weight = 3208.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.184536 restraints weight = 2205.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.186574 restraints weight = 1615.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.187882 restraints weight = 1247.340| |-----------------------------------------------------------------------------| r_work (final): 0.4415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5728 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3038 Z= 0.120 Angle : 0.548 7.788 4125 Z= 0.273 Chirality : 0.039 0.124 488 Planarity : 0.004 0.042 497 Dihedral : 4.428 13.133 383 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.18 % Favored : 97.55 % Rotamer: Outliers : 5.12 % Allowed : 15.36 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.46), residues: 367 helix: 1.00 (0.33), residues: 256 sheet: None (None), residues: 0 loop : -0.31 (0.65), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 291 TYR 0.009 0.001 TYR A 274 PHE 0.018 0.001 PHE A 257 TRP 0.004 0.001 TRP A 325 HIS 0.001 0.000 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 ( 3037) covalent geometry : angle 0.54625 / 0.27 ( 4123) SS BOND : bond 0.00948 / 0.50 ( 1) SS BOND : angle 1.85508 / 0.98 ( 2) hydrogen bonds : bond 0.04197 / 2.81 ( 165) hydrogen bonds : angle 3.80967 / 2.86 ( 477) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.090 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 PHE cc_start: 0.4745 (OUTLIER) cc_final: 0.4373 (m-10) REVERT: A 347 MET cc_start: 0.3932 (mmp) cc_final: 0.3207 (tpp) outliers start: 17 outliers final: 11 residues processed: 64 average time/residue: 0.0530 time to fit residues: 4.2842 Evaluate side-chains 64 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 384 PHE Chi-restraints excluded: chain A residue 389 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 14 optimal weight: 0.0870 chunk 21 optimal weight: 0.8980 chunk 5 optimal weight: 0.0570 chunk 6 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 31 optimal weight: 0.0770 chunk 29 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 34 optimal weight: 0.0970 overall best weight: 0.1832 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.199304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.179069 restraints weight = 5129.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.183132 restraints weight = 3224.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.185993 restraints weight = 2235.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.188096 restraints weight = 1664.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.189447 restraints weight = 1315.479| |-----------------------------------------------------------------------------| r_work (final): 0.4439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5735 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3038 Z= 0.115 Angle : 0.554 6.702 4125 Z= 0.279 Chirality : 0.038 0.119 488 Planarity : 0.004 0.044 497 Dihedral : 4.321 14.434 383 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.45 % Favored : 97.28 % Rotamer: Outliers : 4.52 % Allowed : 15.96 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.46), residues: 367 helix: 1.07 (0.34), residues: 256 sheet: None (None), residues: 0 loop : -0.25 (0.66), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.001 ARG A 291 TYR 0.006 0.001 TYR A 274 PHE 0.012 0.001 PHE A 257 TRP 0.005 0.001 TRP A 325 HIS 0.001 0.000 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 ( 3037) covalent geometry : angle 0.55259 / 0.28 ( 4123) SS BOND : bond 0.00773 / 0.41 ( 1) SS BOND : angle 1.67674 / 0.88 ( 2) hydrogen bonds : bond 0.03920 / 2.64 ( 165) hydrogen bonds : angle 3.83364 / 2.86 ( 477) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.101 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 PHE cc_start: 0.4564 (OUTLIER) cc_final: 0.3966 (m-10) REVERT: A 347 MET cc_start: 0.3941 (mmp) cc_final: 0.3500 (tpp) outliers start: 15 outliers final: 11 residues processed: 62 average time/residue: 0.0469 time to fit residues: 3.7713 Evaluate side-chains 64 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 382 CYS Chi-restraints excluded: chain A residue 384 PHE Chi-restraints excluded: chain A residue 389 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 18 optimal weight: 0.2980 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 19 optimal weight: 0.1980 chunk 14 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 284 GLN A 343 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.194956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.174709 restraints weight = 4995.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.178859 restraints weight = 3056.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.181816 restraints weight = 2061.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.183931 restraints weight = 1503.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.185312 restraints weight = 1166.018| |-----------------------------------------------------------------------------| r_work (final): 0.4378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5834 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3038 Z= 0.179 Angle : 0.621 7.035 4125 Z= 0.325 Chirality : 0.043 0.124 488 Planarity : 0.004 0.046 497 Dihedral : 4.897 16.363 383 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 5.12 % Allowed : 17.47 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.46), residues: 367 helix: 0.76 (0.33), residues: 257 sheet: None (None), residues: 0 loop : -0.17 (0.70), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 319 TYR 0.012 0.001 TYR A 192 PHE 0.025 0.002 PHE A 205 TRP 0.004 0.001 TRP A 53 HIS 0.003 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.18 ( 3037) covalent geometry : angle 0.61806 / 0.32 ( 4123) SS BOND : bond 0.01496 / 0.79 ( 1) SS BOND : angle 2.83847 / 1.52 ( 2) hydrogen bonds : bond 0.04934 / 3.30 ( 165) hydrogen bonds : angle 4.16915 / 3.09 ( 477) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 PHE cc_start: 0.4498 (OUTLIER) cc_final: 0.3954 (m-10) REVERT: A 165 PHE cc_start: 0.7416 (t80) cc_final: 0.7031 (t80) outliers start: 17 outliers final: 12 residues processed: 70 average time/residue: 0.0484 time to fit residues: 4.3941 Evaluate side-chains 66 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 382 CYS Chi-restraints excluded: chain A residue 384 PHE Chi-restraints excluded: chain A residue 389 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 25 optimal weight: 0.4980 chunk 5 optimal weight: 0.0000 chunk 36 optimal weight: 0.3980 chunk 31 optimal weight: 0.0870 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 0.0470 chunk 29 optimal weight: 0.0370 chunk 23 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.1138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 GLN A 316 ASN A 343 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.198934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.178255 restraints weight = 5169.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.182252 restraints weight = 3279.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.185077 restraints weight = 2284.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.187120 restraints weight = 1708.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.188481 restraints weight = 1352.524| |-----------------------------------------------------------------------------| r_work (final): 0.4417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5768 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 3038 Z= 0.118 Angle : 0.573 8.931 4125 Z= 0.290 Chirality : 0.039 0.118 488 Planarity : 0.004 0.046 497 Dihedral : 4.402 14.768 383 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 5.72 % Allowed : 17.77 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.47), residues: 367 helix: 1.08 (0.34), residues: 255 sheet: None (None), residues: 0 loop : -0.06 (0.68), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 319 TYR 0.008 0.001 TYR A 274 PHE 0.008 0.001 PHE A 257 TRP 0.005 0.001 TRP A 325 HIS 0.001 0.000 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 ( 3037) covalent geometry : angle 0.57194 / 0.29 ( 4123) SS BOND : bond 0.00687 / 0.36 ( 1) SS BOND : angle 1.34668 / 0.71 ( 2) hydrogen bonds : bond 0.03893 / 2.62 ( 165) hydrogen bonds : angle 3.96992 / 2.92 ( 477) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 0.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.6267 (mmm) cc_final: 0.5824 (mmp) REVERT: A 124 PHE cc_start: 0.4559 (OUTLIER) cc_final: 0.3996 (m-10) REVERT: A 145 MET cc_start: 0.4583 (tpp) cc_final: 0.4309 (tpt) REVERT: A 165 PHE cc_start: 0.7439 (t80) cc_final: 0.7094 (t80) outliers start: 19 outliers final: 14 residues processed: 69 average time/residue: 0.0523 time to fit residues: 4.5835 Evaluate side-chains 70 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 367 LYS Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 382 CYS Chi-restraints excluded: chain A residue 384 PHE Chi-restraints excluded: chain A residue 389 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 17 optimal weight: 0.0980 chunk 27 optimal weight: 0.0470 chunk 33 optimal weight: 0.8980 chunk 31 optimal weight: 0.0970 chunk 25 optimal weight: 0.0170 chunk 26 optimal weight: 0.9990 chunk 32 optimal weight: 0.0000 chunk 34 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 overall best weight: 0.0518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 105 GLN A 284 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.199838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.178959 restraints weight = 5176.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.183133 restraints weight = 3226.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.186148 restraints weight = 2207.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.188119 restraints weight = 1629.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.189747 restraints weight = 1288.444| |-----------------------------------------------------------------------------| r_work (final): 0.4434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5712 moved from start: 0.4533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 3038 Z= 0.110 Angle : 0.569 8.448 4125 Z= 0.281 Chirality : 0.038 0.120 488 Planarity : 0.004 0.055 497 Dihedral : 4.151 14.793 383 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 5.72 % Allowed : 18.67 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.46), residues: 367 helix: 1.46 (0.34), residues: 243 sheet: None (None), residues: 0 loop : -0.22 (0.61), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 319 TYR 0.005 0.001 TYR A 240 PHE 0.015 0.001 PHE A 257 TRP 0.007 0.001 TRP A 325 HIS 0.001 0.000 HIS A 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 ( 3037) covalent geometry : angle 0.56890 / 0.28 ( 4123) SS BOND : bond 0.00412 / 0.22 ( 1) SS BOND : angle 1.07429 / 0.57 ( 2) hydrogen bonds : bond 0.03283 / 2.19 ( 165) hydrogen bonds : angle 3.80269 / 2.79 ( 477) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 PHE cc_start: 0.4584 (OUTLIER) cc_final: 0.4042 (m-10) REVERT: A 149 MET cc_start: 0.5589 (mtp) cc_final: 0.4837 (tpp) REVERT: A 157 ILE cc_start: 0.6150 (OUTLIER) cc_final: 0.5947 (mt) REVERT: A 165 PHE cc_start: 0.7344 (t80) cc_final: 0.7006 (t80) REVERT: A 251 TRP cc_start: 0.7631 (t60) cc_final: 0.5754 (t60) outliers start: 19 outliers final: 10 residues processed: 69 average time/residue: 0.0472 time to fit residues: 4.1566 Evaluate side-chains 68 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 382 CYS Chi-restraints excluded: chain A residue 384 PHE Chi-restraints excluded: chain A residue 389 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 20 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 32 optimal weight: 0.2980 chunk 0 optimal weight: 3.9990 chunk 23 optimal weight: 0.0980 chunk 17 optimal weight: 0.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.195240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.174734 restraints weight = 5166.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.178593 restraints weight = 3248.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.181418 restraints weight = 2261.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.183170 restraints weight = 1689.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.184815 restraints weight = 1360.934| |-----------------------------------------------------------------------------| r_work (final): 0.4375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5836 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3038 Z= 0.171 Angle : 0.654 7.356 4125 Z= 0.335 Chirality : 0.043 0.126 488 Planarity : 0.005 0.050 497 Dihedral : 4.627 16.421 383 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 5.12 % Allowed : 20.48 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.47), residues: 367 helix: 0.98 (0.33), residues: 257 sheet: None (None), residues: 0 loop : -0.02 (0.70), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 319 TYR 0.012 0.002 TYR A 274 PHE 0.028 0.002 PHE A 205 TRP 0.005 0.001 TRP A 53 HIS 0.004 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 ( 3037) covalent geometry : angle 0.65176 / 0.33 ( 4123) SS BOND : bond 0.01471 / 0.77 ( 1) SS BOND : angle 2.74164 / 1.47 ( 2) hydrogen bonds : bond 0.04394 / 2.93 ( 165) hydrogen bonds : angle 4.14277 / 3.04 ( 477) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 PHE cc_start: 0.4600 (OUTLIER) cc_final: 0.4110 (m-10) REVERT: A 165 PHE cc_start: 0.7403 (t80) cc_final: 0.7025 (t80) outliers start: 17 outliers final: 15 residues processed: 66 average time/residue: 0.0448 time to fit residues: 3.8610 Evaluate side-chains 69 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 139 PHE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 382 CYS Chi-restraints excluded: chain A residue 384 PHE Chi-restraints excluded: chain A residue 389 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 7 optimal weight: 0.5980 chunk 25 optimal weight: 0.4980 chunk 30 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 2 optimal weight: 0.0980 chunk 3 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 284 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.193438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.173693 restraints weight = 5201.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.177410 restraints weight = 3354.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.180134 restraints weight = 2348.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.181917 restraints weight = 1762.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.183457 restraints weight = 1415.792| |-----------------------------------------------------------------------------| r_work (final): 0.4385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5835 moved from start: 0.4964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 3038 Z= 0.161 Angle : 0.677 9.851 4125 Z= 0.338 Chirality : 0.043 0.164 488 Planarity : 0.004 0.046 497 Dihedral : 4.647 18.960 383 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 5.12 % Allowed : 21.69 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.46), residues: 367 helix: 0.89 (0.33), residues: 257 sheet: None (None), residues: 0 loop : -0.04 (0.70), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 291 TYR 0.009 0.001 TYR A 274 PHE 0.014 0.001 PHE A 257 TRP 0.004 0.001 TRP A 325 HIS 0.003 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 ( 3037) covalent geometry : angle 0.67554 / 0.34 ( 4123) SS BOND : bond 0.01311 / 0.69 ( 1) SS BOND : angle 2.41087 / 1.29 ( 2) hydrogen bonds : bond 0.04417 / 2.95 ( 165) hydrogen bonds : angle 4.22983 / 3.10 ( 477) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 51 time to evaluate : 0.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 PHE cc_start: 0.4583 (OUTLIER) cc_final: 0.4127 (m-10) REVERT: A 149 MET cc_start: 0.5876 (mtp) cc_final: 0.5065 (tpp) REVERT: A 165 PHE cc_start: 0.7336 (t80) cc_final: 0.6986 (t80) outliers start: 17 outliers final: 14 residues processed: 62 average time/residue: 0.0427 time to fit residues: 3.4752 Evaluate side-chains 66 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LYS Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 284 GLN Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 382 CYS Chi-restraints excluded: chain A residue 384 PHE Chi-restraints excluded: chain A residue 389 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 23 optimal weight: 0.0470 chunk 12 optimal weight: 0.5980 chunk 11 optimal weight: 0.4980 chunk 36 optimal weight: 0.9980 chunk 31 optimal weight: 0.0870 chunk 3 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 24 optimal weight: 0.1980 chunk 29 optimal weight: 0.0470 chunk 19 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 overall best weight: 0.1754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.194146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.173047 restraints weight = 5224.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.177198 restraints weight = 3248.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.180085 restraints weight = 2219.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.182183 restraints weight = 1651.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.183796 restraints weight = 1298.684| |-----------------------------------------------------------------------------| r_work (final): 0.4382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5835 moved from start: 0.4996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.409 3038 Z= 0.522 Angle : 1.400 65.866 4125 Z= 0.861 Chirality : 0.049 0.521 488 Planarity : 0.013 0.262 497 Dihedral : 4.695 19.018 383 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 5.12 % Allowed : 21.99 % Favored : 72.89 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.46), residues: 367 helix: 0.86 (0.33), residues: 257 sheet: None (None), residues: 0 loop : -0.04 (0.70), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 291 TYR 0.009 0.001 TYR A 274 PHE 0.014 0.002 PHE A 257 TRP 0.004 0.001 TRP A 325 HIS 0.003 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.01055 / 0.52 ( 3037) covalent geometry : angle 1.39983 / 0.86 ( 4123) SS BOND : bond 0.01281 / 0.67 ( 1) SS BOND : angle 2.37522 / 1.27 ( 2) hydrogen bonds : bond 0.04389 / 2.93 ( 165) hydrogen bonds : angle 4.25193 / 3.13 ( 477) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 744.54 seconds wall clock time: 13 minutes 28.85 seconds (808.85 seconds total)