Starting phenix.real_space_refine on Tue Mar 3 13:47:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uh6_26505/03_2026/7uh6_26505.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uh6_26505/03_2026/7uh6_26505.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7uh6_26505/03_2026/7uh6_26505.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uh6_26505/03_2026/7uh6_26505.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uh6_26505/03_2026/7uh6_26505.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uh6_26505/03_2026/7uh6_26505.map" } resolution = 3.44 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= 0.003 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2933 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians S 17 5.16 5 Na 3 4.78 5 C 2032 2.51 5 N 504 2.21 5 O 538 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3095 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3092 Classifications: {'peptide': 416} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 397} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'EFC:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' NA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 0.83, per 1000 atoms: 0.27 Number of scatterers: 3095 At special positions: 0 Unit cell: (74.124, 76.68, 70.716, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 17 16.00 Na 3 11.00 F 1 9.00 O 538 8.00 N 504 7.00 C 2032 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.28 Conformation dependent library (CDL) restraints added in 140.8 milliseconds 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 748 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 86.8% 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 1 through 9 removed outlier: 3.592A pdb=" N LYS A 6 " --> pdb=" O GLY A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 33 removed outlier: 3.543A pdb=" N LEU A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR A 33 " --> pdb=" O ILE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 43 removed outlier: 3.500A pdb=" N VAL A 39 " --> pdb=" O TYR A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 57 removed outlier: 4.042A pdb=" N GLY A 47 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 73 Processing helix chain 'A' and resid 81 through 108 removed outlier: 3.543A pdb=" N TYR A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A 90 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE A 102 " --> pdb=" O THR A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 136 Processing helix chain 'A' and resid 141 through 149 removed outlier: 4.086A pdb=" N LEU A 146 " --> pdb=" O PRO A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 170 removed outlier: 3.919A pdb=" N TYR A 167 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET A 169 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN A 170 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 221 removed outlier: 3.524A pdb=" N LYS A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN A 199 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N TYR A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Proline residue: A 206 - end of helix removed outlier: 3.547A pdb=" N HIS A 219 " --> pdb=" O HIS A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 246 removed outlier: 4.014A pdb=" N GLY A 226 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU A 227 " --> pdb=" O HIS A 223 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TYR A 236 " --> pdb=" O THR A 232 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 254 removed outlier: 3.734A pdb=" N LEU A 251 " --> pdb=" O TYR A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 276 removed outlier: 3.613A pdb=" N LYS A 263 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS A 264 " --> pdb=" O SER A 260 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ASP A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ALA A 268 " --> pdb=" O HIS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 292 removed outlier: 3.695A pdb=" N THR A 285 " --> pdb=" O THR A 281 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU A 291 " --> pdb=" O ARG A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 310 removed outlier: 4.113A pdb=" N LEU A 303 " --> pdb=" O TYR A 299 " (cutoff:3.500A) Proline residue: A 304 - end of helix removed outlier: 4.579A pdb=" N THR A 308 " --> pdb=" O PRO A 304 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN A 310 " --> pdb=" O GLY A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 330 removed outlier: 3.511A pdb=" N ALA A 326 " --> pdb=" O THR A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 352 removed outlier: 3.620A pdb=" N THR A 340 " --> pdb=" O GLY A 336 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL A 342 " --> pdb=" O GLN A 338 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY A 351 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 371 removed outlier: 3.626A pdb=" N ILE A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ALA A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N MET A 365 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL A 366 " --> pdb=" O MET A 362 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER A 369 " --> pdb=" O MET A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 389 removed outlier: 3.672A pdb=" N ILE A 386 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ILE A 389 " --> pdb=" O EFC A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 415 removed outlier: 3.564A pdb=" N LEU A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLY A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR A 398 " --> pdb=" O ASP A 394 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N MET A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL A 400 " --> pdb=" O GLY A 396 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A 412 " --> pdb=" O GLY A 408 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR A 415 " --> pdb=" O ILE A 411 " (cutoff:3.500A) 218 hydrogen bonds defined for protein. 654 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: 0.49 Time building geometry restraints manager: 0.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.37: 980 1.37 - 1.55: 2140 1.55 - 1.73: 0 1.73 - 1.92: 32 1.92 - 2.10: 1 Bond restraints: 3153 Sorted by residual: bond pdb=" N ILE A 309 " pdb=" CA ILE A 309 " ideal model delta sigma weight residual 1.461 1.495 -0.033 1.17e-02 7.31e+03 8.12e+00 bond pdb=" N VAL A 320 " pdb=" CA VAL A 320 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.44e+00 bond pdb=" N THR A 281 " pdb=" CA THR A 281 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.25e-02 6.40e+03 6.80e+00 bond pdb=" N ASN A 310 " pdb=" CA ASN A 310 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.23e-02 6.61e+03 6.08e+00 bond pdb=" N ASP A 312 " pdb=" CA ASP A 312 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 5.95e+00 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 4160 1.55 - 3.10: 108 3.10 - 4.66: 18 4.66 - 6.21: 7 6.21 - 7.76: 5 Bond angle restraints: 4298 Sorted by residual: angle pdb=" CA MET A 311 " pdb=" C MET A 311 " pdb=" O MET A 311 " ideal model delta sigma weight residual 121.67 118.00 3.67 9.30e-01 1.16e+00 1.55e+01 angle pdb=" CA ILE A 309 " pdb=" C ILE A 309 " pdb=" O ILE A 309 " ideal model delta sigma weight residual 121.17 117.88 3.29 1.06e+00 8.90e-01 9.66e+00 angle pdb=" N THR A 281 " pdb=" CA THR A 281 " pdb=" C THR A 281 " ideal model delta sigma weight residual 112.93 109.65 3.28 1.12e+00 7.97e-01 8.57e+00 angle pdb=" CA GLY A 319 " pdb=" C GLY A 319 " pdb=" O GLY A 319 " ideal model delta sigma weight residual 121.00 118.14 2.86 1.08e+00 8.57e-01 7.03e+00 angle pdb=" O VAL A 320 " pdb=" C VAL A 320 " pdb=" N ALA A 321 " ideal model delta sigma weight residual 121.87 124.42 -2.55 9.70e-01 1.06e+00 6.93e+00 ... (remaining 4293 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.54: 1657 11.54 - 23.07: 121 23.07 - 34.61: 55 34.61 - 46.14: 12 46.14 - 57.68: 3 Dihedral angle restraints: 1848 sinusoidal: 669 harmonic: 1179 Sorted by residual: dihedral pdb=" CB MET A 59 " pdb=" CG MET A 59 " pdb=" SD MET A 59 " pdb=" CE MET A 59 " ideal model delta sinusoidal sigma weight residual -180.00 -122.32 -57.68 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" CG ARG A 395 " pdb=" CD ARG A 395 " pdb=" NE ARG A 395 " pdb=" CZ ARG A 395 " ideal model delta sinusoidal sigma weight residual 180.00 138.77 41.23 2 1.50e+01 4.44e-03 9.27e+00 dihedral pdb=" CA GLU A 291 " pdb=" C GLU A 291 " pdb=" N MET A 292 " pdb=" CA MET A 292 " ideal model delta harmonic sigma weight residual 180.00 164.87 15.13 0 5.00e+00 4.00e-02 9.15e+00 ... (remaining 1845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 390 0.040 - 0.080: 114 0.080 - 0.120: 28 0.120 - 0.159: 5 0.159 - 0.199: 1 Chirality restraints: 538 Sorted by residual: chirality pdb=" CA MET A 311 " pdb=" N MET A 311 " pdb=" C MET A 311 " pdb=" CB MET A 311 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.93e-01 chirality pdb=" CA LEU A 316 " pdb=" N LEU A 316 " pdb=" C LEU A 316 " pdb=" CB LEU A 316 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.66e-01 chirality pdb=" CA ILE A 309 " pdb=" N ILE A 309 " pdb=" C ILE A 309 " pdb=" CB ILE A 309 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.24e-01 ... (remaining 535 not shown) Planarity restraints: 529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 108 " 0.007 2.00e-02 2.50e+03 1.46e-02 2.14e+00 pdb=" C ASN A 108 " -0.025 2.00e-02 2.50e+03 pdb=" O ASN A 108 " 0.009 2.00e-02 2.50e+03 pdb=" N PRO A 109 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 301 " -0.009 2.00e-02 2.50e+03 1.09e-02 2.06e+00 pdb=" CG PHE A 301 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 301 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE A 301 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 301 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 301 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 301 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 89 " 0.011 2.00e-02 2.50e+03 8.85e-03 1.57e+00 pdb=" CG TYR A 89 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR A 89 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR A 89 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 89 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 89 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 89 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 89 " 0.001 2.00e-02 2.50e+03 ... (remaining 526 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 18 2.59 - 3.17: 2822 3.17 - 3.74: 4845 3.74 - 4.32: 6175 4.32 - 4.90: 9892 Nonbonded interactions: 23752 Sorted by model distance: nonbonded pdb=" OD1 ASP A 312 " pdb="NA NA A 504 " model vdw 2.012 2.470 nonbonded pdb=" O SER A 349 " pdb="NA NA A 503 " model vdw 2.145 2.470 nonbonded pdb=" OH TYR A 236 " pdb=" O ILE A 392 " model vdw 2.263 3.040 nonbonded pdb=" O LEU A 282 " pdb=" OG1 THR A 285 " model vdw 2.291 3.040 nonbonded pdb=" O VAL A 412 " pdb=" OG1 THR A 415 " model vdw 2.338 3.040 ... (remaining 23747 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 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: 3.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.990 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 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 0.047 3153 Z= 0.222 Angle : 0.633 7.760 4298 Z= 0.363 Chirality : 0.041 0.199 538 Planarity : 0.003 0.026 529 Dihedral : 10.580 57.677 1100 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.31 % Allowed : 0.31 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.39), residues: 410 helix: 0.86 (0.28), residues: 314 sheet: None (None), residues: 0 loop : -0.13 (0.64), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 52 TYR 0.021 0.001 TYR A 89 PHE 0.025 0.001 PHE A 301 HIS 0.002 0.000 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 3153) covalent geometry : angle 0.63286 ( 4298) hydrogen bonds : bond 0.30386 ( 218) hydrogen bonds : angle 7.02588 ( 654) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.128 Fit side-chains REVERT: A 1 MET cc_start: 0.5669 (ptt) cc_final: 0.5321 (ptp) REVERT: A 343 LEU cc_start: 0.9136 (tt) cc_final: 0.8815 (mt) outliers start: 1 outliers final: 0 residues processed: 42 average time/residue: 0.0378 time to fit residues: 2.2296 Evaluate side-chains 32 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 22 optimal weight: 0.3980 chunk 37 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3727 r_free = 0.3727 target = 0.084757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.071014 restraints weight = 13656.202| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 3.92 r_work: 0.3257 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3153 Z= 0.144 Angle : 0.650 10.245 4298 Z= 0.320 Chirality : 0.039 0.131 538 Planarity : 0.004 0.036 529 Dihedral : 3.805 24.102 443 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.93 % Allowed : 8.36 % Favored : 90.71 % 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: 1.88 (0.41), residues: 410 helix: 1.62 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -0.03 (0.75), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 397 TYR 0.013 0.001 TYR A 88 PHE 0.016 0.002 PHE A 323 HIS 0.005 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 3153) covalent geometry : angle 0.65017 ( 4298) hydrogen bonds : bond 0.06199 ( 218) hydrogen bonds : angle 4.51849 ( 654) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.122 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4712 (ptt) cc_final: 0.4398 (ptp) REVERT: A 227 GLU cc_start: 0.8528 (mp0) cc_final: 0.8291 (mp0) REVERT: A 343 LEU cc_start: 0.9079 (tt) cc_final: 0.8787 (mt) REVERT: A 362 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7665 (ttt) outliers start: 3 outliers final: 1 residues processed: 43 average time/residue: 0.0367 time to fit residues: 2.2284 Evaluate side-chains 38 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 406 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 19 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 = 0.3649 r_free = 0.3649 target = 0.080779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.066783 restraints weight = 13963.522| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 3.90 r_work: 0.3162 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3153 Z= 0.205 Angle : 0.674 9.272 4298 Z= 0.340 Chirality : 0.041 0.149 538 Planarity : 0.004 0.033 529 Dihedral : 3.874 18.262 443 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.86 % Allowed : 13.31 % Favored : 84.83 % 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: 1.97 (0.42), residues: 410 helix: 1.60 (0.28), residues: 327 sheet: None (None), residues: 0 loop : 0.35 (0.77), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 395 TYR 0.013 0.002 TYR A 317 PHE 0.016 0.002 PHE A 143 HIS 0.004 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 3153) covalent geometry : angle 0.67377 ( 4298) hydrogen bonds : bond 0.06426 ( 218) hydrogen bonds : angle 4.56503 ( 654) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.121 Fit side-chains REVERT: A 1 MET cc_start: 0.4852 (ptt) cc_final: 0.4533 (ptp) REVERT: A 108 ASN cc_start: 0.8967 (t0) cc_final: 0.8689 (t0) REVERT: A 227 GLU cc_start: 0.8463 (mp0) cc_final: 0.8186 (mp0) REVERT: A 236 TYR cc_start: 0.8760 (OUTLIER) cc_final: 0.7901 (m-10) REVERT: A 343 LEU cc_start: 0.9089 (tt) cc_final: 0.8758 (mt) REVERT: A 362 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8211 (ttt) outliers start: 6 outliers final: 4 residues processed: 39 average time/residue: 0.0416 time to fit residues: 2.2849 Evaluate side-chains 40 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 406 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 15 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 39 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 11 optimal weight: 0.0060 chunk 18 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 overall best weight: 0.5796 ------------------------------------------------------------------------------- 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 = 0.3721 r_free = 0.3721 target = 0.084646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.070927 restraints weight = 13715.752| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 3.93 r_work: 0.3262 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3153 Z= 0.120 Angle : 0.613 10.305 4298 Z= 0.295 Chirality : 0.040 0.151 538 Planarity : 0.004 0.035 529 Dihedral : 3.649 17.879 443 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.48 % Allowed : 12.69 % Favored : 84.83 % 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: 2.24 (0.42), residues: 410 helix: 1.78 (0.28), residues: 329 sheet: None (None), residues: 0 loop : 0.49 (0.80), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 287 TYR 0.010 0.001 TYR A 299 PHE 0.012 0.001 PHE A 261 HIS 0.003 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 3153) covalent geometry : angle 0.61291 ( 4298) hydrogen bonds : bond 0.04504 ( 218) hydrogen bonds : angle 4.08858 ( 654) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.123 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4706 (ptt) cc_final: 0.4344 (ptp) REVERT: A 227 GLU cc_start: 0.8318 (mp0) cc_final: 0.8051 (mp0) REVERT: A 269 MET cc_start: 0.9008 (mtm) cc_final: 0.8496 (mtm) REVERT: A 270 LEU cc_start: 0.9527 (mm) cc_final: 0.9285 (pp) REVERT: A 343 LEU cc_start: 0.8963 (tt) cc_final: 0.8674 (mt) REVERT: A 362 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.7862 (ttt) outliers start: 8 outliers final: 4 residues processed: 43 average time/residue: 0.0301 time to fit residues: 1.8392 Evaluate side-chains 43 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 406 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 34 optimal weight: 0.2980 chunk 37 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3721 r_free = 0.3721 target = 0.084631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.070752 restraints weight = 13491.889| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 3.94 r_work: 0.3261 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3153 Z= 0.119 Angle : 0.626 9.385 4298 Z= 0.296 Chirality : 0.040 0.153 538 Planarity : 0.004 0.034 529 Dihedral : 3.557 17.170 443 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.17 % Allowed : 15.17 % Favored : 82.66 % 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: 2.22 (0.43), residues: 410 helix: 1.78 (0.28), residues: 332 sheet: None (None), residues: 0 loop : 0.34 (0.82), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 287 TYR 0.009 0.001 TYR A 383 PHE 0.010 0.001 PHE A 261 HIS 0.004 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 3153) covalent geometry : angle 0.62568 ( 4298) hydrogen bonds : bond 0.04390 ( 218) hydrogen bonds : angle 4.05741 ( 654) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.094 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4757 (ptt) cc_final: 0.4389 (ptp) REVERT: A 227 GLU cc_start: 0.8310 (mp0) cc_final: 0.8006 (mp0) REVERT: A 236 TYR cc_start: 0.8521 (OUTLIER) cc_final: 0.7902 (m-10) REVERT: A 270 LEU cc_start: 0.9541 (mm) cc_final: 0.9294 (pp) REVERT: A 362 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.7727 (ttt) outliers start: 7 outliers final: 5 residues processed: 41 average time/residue: 0.0312 time to fit residues: 1.7968 Evaluate side-chains 43 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 406 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 12 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 7 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3698 r_free = 0.3698 target = 0.083158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.069188 restraints weight = 13867.743| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 4.00 r_work: 0.3219 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3153 Z= 0.139 Angle : 0.633 8.957 4298 Z= 0.304 Chirality : 0.041 0.152 538 Planarity : 0.004 0.033 529 Dihedral : 3.598 17.582 443 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.17 % Allowed : 16.41 % Favored : 81.42 % 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: 2.14 (0.43), residues: 410 helix: 1.72 (0.28), residues: 332 sheet: None (None), residues: 0 loop : 0.31 (0.82), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 395 TYR 0.009 0.001 TYR A 383 PHE 0.010 0.001 PHE A 261 HIS 0.005 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 3153) covalent geometry : angle 0.63271 ( 4298) hydrogen bonds : bond 0.04790 ( 218) hydrogen bonds : angle 4.17226 ( 654) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.111 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4708 (ptt) cc_final: 0.4342 (ptp) REVERT: A 227 GLU cc_start: 0.8325 (mp0) cc_final: 0.8071 (mp0) REVERT: A 236 TYR cc_start: 0.8629 (OUTLIER) cc_final: 0.8022 (m-10) REVERT: A 270 LEU cc_start: 0.9551 (mm) cc_final: 0.9312 (pp) REVERT: A 311 MET cc_start: 0.8458 (mmt) cc_final: 0.8237 (mmt) REVERT: A 362 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7773 (ttt) REVERT: A 365 MET cc_start: 0.8433 (tmm) cc_final: 0.8232 (tmm) outliers start: 7 outliers final: 4 residues processed: 39 average time/residue: 0.0345 time to fit residues: 1.8918 Evaluate side-chains 42 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 406 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 15 optimal weight: 0.3980 chunk 9 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3719 r_free = 0.3719 target = 0.084323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.070379 restraints weight = 13807.394| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 4.01 r_work: 0.3254 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3153 Z= 0.121 Angle : 0.649 9.891 4298 Z= 0.304 Chirality : 0.040 0.164 538 Planarity : 0.004 0.034 529 Dihedral : 3.569 18.961 443 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.17 % Allowed : 16.10 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.43), residues: 410 helix: 1.73 (0.28), residues: 332 sheet: None (None), residues: 0 loop : -0.05 (0.80), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 397 TYR 0.019 0.001 TYR A 299 PHE 0.010 0.001 PHE A 261 HIS 0.005 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 3153) covalent geometry : angle 0.64911 ( 4298) hydrogen bonds : bond 0.04285 ( 218) hydrogen bonds : angle 4.04315 ( 654) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.079 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4691 (ptt) cc_final: 0.4336 (ptp) REVERT: A 227 GLU cc_start: 0.8159 (mp0) cc_final: 0.7858 (mp0) REVERT: A 236 TYR cc_start: 0.8540 (OUTLIER) cc_final: 0.7799 (m-10) REVERT: A 270 LEU cc_start: 0.9537 (mm) cc_final: 0.9298 (pp) REVERT: A 362 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7618 (ttt) REVERT: A 365 MET cc_start: 0.8421 (tmm) cc_final: 0.8215 (tmm) outliers start: 7 outliers final: 4 residues processed: 43 average time/residue: 0.0304 time to fit residues: 1.8384 Evaluate side-chains 44 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 406 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 21 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 17 optimal weight: 0.1980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3732 r_free = 0.3732 target = 0.084957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.071132 restraints weight = 13909.953| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 4.02 r_work: 0.3269 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3153 Z= 0.117 Angle : 0.646 10.082 4298 Z= 0.302 Chirality : 0.040 0.171 538 Planarity : 0.004 0.034 529 Dihedral : 3.540 20.651 443 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.17 % Allowed : 16.72 % Favored : 81.11 % 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: 2.04 (0.43), residues: 410 helix: 1.73 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -0.11 (0.79), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 397 TYR 0.021 0.001 TYR A 299 PHE 0.010 0.001 PHE A 261 HIS 0.006 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 3153) covalent geometry : angle 0.64580 ( 4298) hydrogen bonds : bond 0.04101 ( 218) hydrogen bonds : angle 3.99168 ( 654) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.153 Fit side-chains REVERT: A 1 MET cc_start: 0.4604 (ptt) cc_final: 0.4270 (ptp) REVERT: A 227 GLU cc_start: 0.8054 (mp0) cc_final: 0.7816 (mp0) REVERT: A 236 TYR cc_start: 0.8509 (OUTLIER) cc_final: 0.7775 (m-10) REVERT: A 270 LEU cc_start: 0.9503 (mm) cc_final: 0.9289 (pp) REVERT: A 311 MET cc_start: 0.8425 (mmt) cc_final: 0.8137 (mmt) REVERT: A 362 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.7563 (ttt) outliers start: 7 outliers final: 4 residues processed: 44 average time/residue: 0.0363 time to fit residues: 2.2545 Evaluate side-chains 45 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 406 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 = 0.3721 r_free = 0.3721 target = 0.084320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.070429 restraints weight = 13901.689| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 4.01 r_work: 0.3255 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3153 Z= 0.128 Angle : 0.692 11.112 4298 Z= 0.324 Chirality : 0.041 0.167 538 Planarity : 0.004 0.034 529 Dihedral : 3.610 21.392 443 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.86 % Allowed : 17.96 % Favored : 80.19 % 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: 2.07 (0.43), residues: 410 helix: 1.74 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -0.06 (0.78), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 397 TYR 0.021 0.001 TYR A 299 PHE 0.010 0.001 PHE A 261 HIS 0.006 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 3153) covalent geometry : angle 0.69206 ( 4298) hydrogen bonds : bond 0.04322 ( 218) hydrogen bonds : angle 4.07939 ( 654) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.096 Fit side-chains REVERT: A 1 MET cc_start: 0.4630 (ptt) cc_final: 0.4296 (ptp) REVERT: A 236 TYR cc_start: 0.8556 (OUTLIER) cc_final: 0.7828 (m-10) REVERT: A 270 LEU cc_start: 0.9495 (mm) cc_final: 0.9278 (pp) REVERT: A 311 MET cc_start: 0.8506 (mmt) cc_final: 0.8290 (mmt) REVERT: A 362 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7802 (ttt) outliers start: 6 outliers final: 3 residues processed: 42 average time/residue: 0.0366 time to fit residues: 2.1581 Evaluate side-chains 42 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 406 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 25 optimal weight: 0.0170 chunk 28 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 4 optimal weight: 0.1980 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 27 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 11 optimal weight: 0.0770 chunk 31 optimal weight: 0.7980 overall best weight: 0.3376 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.085892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.071936 restraints weight = 13669.442| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 3.97 r_work: 0.3272 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3153 Z= 0.123 Angle : 0.703 10.602 4298 Z= 0.328 Chirality : 0.041 0.173 538 Planarity : 0.004 0.035 529 Dihedral : 3.519 21.899 443 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.24 % Allowed : 18.89 % Favored : 79.88 % 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: 2.05 (0.43), residues: 410 helix: 1.72 (0.29), residues: 333 sheet: None (None), residues: 0 loop : -0.11 (0.80), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 287 TYR 0.024 0.001 TYR A 299 PHE 0.011 0.001 PHE A 261 HIS 0.006 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 3153) covalent geometry : angle 0.70281 ( 4298) hydrogen bonds : bond 0.03774 ( 218) hydrogen bonds : angle 3.98391 ( 654) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.166 Fit side-chains REVERT: A 1 MET cc_start: 0.4353 (ptt) cc_final: 0.4077 (ptp) REVERT: A 236 TYR cc_start: 0.8501 (OUTLIER) cc_final: 0.7723 (m-10) REVERT: A 270 LEU cc_start: 0.9481 (mm) cc_final: 0.9275 (pp) REVERT: A 311 MET cc_start: 0.8338 (mmt) cc_final: 0.8012 (mmt) REVERT: A 362 MET cc_start: 0.7994 (ttp) cc_final: 0.7466 (ttt) outliers start: 4 outliers final: 3 residues processed: 43 average time/residue: 0.0391 time to fit residues: 2.3817 Evaluate side-chains 41 residues out of total 323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 406 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 3 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 36 optimal weight: 5.9990 chunk 11 optimal weight: 0.0010 chunk 37 optimal weight: 0.6980 overall best weight: 0.5786 ------------------------------------------------------------------------------- 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 = 0.3726 r_free = 0.3726 target = 0.085413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.071336 restraints weight = 14084.138| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 4.01 r_work: 0.3258 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3153 Z= 0.124 Angle : 0.712 10.246 4298 Z= 0.333 Chirality : 0.041 0.173 538 Planarity : 0.004 0.034 529 Dihedral : 3.503 21.845 443 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.55 % Allowed : 18.89 % Favored : 79.57 % 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: 2.00 (0.43), residues: 410 helix: 1.71 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -0.20 (0.79), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 397 TYR 0.024 0.001 TYR A 299 PHE 0.011 0.001 PHE A 261 HIS 0.006 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 3153) covalent geometry : angle 0.71247 ( 4298) hydrogen bonds : bond 0.03947 ( 218) hydrogen bonds : angle 4.03103 ( 654) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 866.58 seconds wall clock time: 15 minutes 29.74 seconds (929.74 seconds total)