Starting phenix.real_space_refine on Wed Mar 4 00:40:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7adm_11731/03_2026/7adm_11731.cif Found real_map, /net/cci-nas-00/data/ceres_data/7adm_11731/03_2026/7adm_11731.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7adm_11731/03_2026/7adm_11731.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7adm_11731/03_2026/7adm_11731.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7adm_11731/03_2026/7adm_11731.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7adm_11731/03_2026/7adm_11731.map" } resolution = 3.5 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 3 5.16 5 C 3083 2.51 5 N 851 2.21 5 O 990 1.98 5 H 4799 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 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: 9726 Number of models: 1 Model: "" Number of chains: 1 Chain: "C" Number of atoms: 9726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 9726 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 22, 'TRANS': 591} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 1.54, per 1000 atoms: 0.16 Number of scatterers: 9726 At special positions: 0 Unit cell: (100.57, 90.4, 110.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 3 16.00 O 990 8.00 N 851 7.00 C 3083 6.00 H 4799 1.00 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: 0.75 Conformation dependent library (CDL) restraints added in 199.4 milliseconds 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1144 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 6 sheets defined 33.1% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'C' and resid 152 through 158 Processing helix chain 'C' and resid 181 through 195 removed outlier: 3.842A pdb=" N GLN C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA C 189 " --> pdb=" O LYS C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 218 Processing helix chain 'C' and resid 223 through 225 No H-bonds generated for 'chain 'C' and resid 223 through 225' Processing helix chain 'C' and resid 226 through 232 removed outlier: 3.669A pdb=" N SER C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 234 No H-bonds generated for 'chain 'C' and resid 233 through 234' Processing helix chain 'C' and resid 235 through 237 No H-bonds generated for 'chain 'C' and resid 235 through 237' Processing helix chain 'C' and resid 238 through 254 removed outlier: 3.561A pdb=" N GLN C 243 " --> pdb=" O SER C 239 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN C 244 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU C 247 " --> pdb=" O GLN C 243 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ARG C 248 " --> pdb=" O ASN C 244 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N TYR C 249 " --> pdb=" O THR C 245 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS C 251 " --> pdb=" O GLU C 247 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N MET C 252 " --> pdb=" O ARG C 248 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP C 254 " --> pdb=" O LYS C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 263 removed outlier: 4.162A pdb=" N LYS C 263 " --> pdb=" O ASN C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 269 removed outlier: 4.051A pdb=" N LYS C 268 " --> pdb=" O GLU C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 289 removed outlier: 4.193A pdb=" N ILE C 285 " --> pdb=" O ASN C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 291 No H-bonds generated for 'chain 'C' and resid 290 through 291' Processing helix chain 'C' and resid 292 through 296 Processing helix chain 'C' and resid 300 through 309 removed outlier: 3.580A pdb=" N LEU C 307 " --> pdb=" O SER C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 337 Processing helix chain 'C' and resid 338 through 351 removed outlier: 3.907A pdb=" N SER C 349 " --> pdb=" O ARG C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 369 Processing helix chain 'C' and resid 380 through 389 removed outlier: 4.057A pdb=" N TYR C 384 " --> pdb=" O VAL C 380 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS C 387 " --> pdb=" O PRO C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 431 Processing helix chain 'C' and resid 432 through 442 removed outlier: 3.582A pdb=" N GLN C 440 " --> pdb=" O ILE C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 469 Processing helix chain 'C' and resid 519 through 523 Processing helix chain 'C' and resid 566 through 576 Processing helix chain 'C' and resid 599 through 603 Processing helix chain 'C' and resid 654 through 658 removed outlier: 3.963A pdb=" N LEU C 657 " --> pdb=" O SER C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 710 removed outlier: 3.693A pdb=" N TYR C 707 " --> pdb=" O ASN C 703 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N PHE C 708 " --> pdb=" O LEU C 704 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR C 710 " --> pdb=" O LYS C 706 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 131 through 133 removed outlier: 7.292A pdb=" N GLU C 140 " --> pdb=" O VAL C 178 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N VAL C 178 " --> pdb=" O GLU C 140 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLU C 142 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU C 144 " --> pdb=" O LYS C 174 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS C 174 " --> pdb=" O GLU C 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 312 through 313 Processing sheet with id=AA3, first strand: chain 'C' and resid 318 through 321 removed outlier: 3.735A pdb=" N GLU C 325 " --> pdb=" O ASN C 321 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 375 through 379 removed outlier: 3.831A pdb=" N ARG C 397 " --> pdb=" O ASP C 420 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TYR C 449 " --> pdb=" O GLU C 478 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N PHE C 480 " --> pdb=" O TYR C 449 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ILE C 451 " --> pdb=" O PHE C 480 " (cutoff:3.500A) removed outlier: 11.170A pdb=" N ASP C 473 " --> pdb=" O ILE C 499 " (cutoff:3.500A) removed outlier: 10.302A pdb=" N GLU C 501 " --> pdb=" O ASP C 473 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLN C 475 " --> pdb=" O GLU C 501 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N SER C 503 " --> pdb=" O GLN C 475 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LEU C 477 " --> pdb=" O SER C 503 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TYR C 505 " --> pdb=" O LEU C 477 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LEU C 479 " --> pdb=" O TYR C 505 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 554 through 555 removed outlier: 6.097A pdb=" N LEU C 554 " --> pdb=" O ASP C 610 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 650 through 651 removed outlier: 6.695A pdb=" N PHE C 650 " --> pdb=" O ARG C 689 " (cutoff:3.500A) 120 hydrogen bonds defined for protein. 318 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.95 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.89 - 1.08: 1364 1.08 - 1.26: 4304 1.26 - 1.45: 1327 1.45 - 1.63: 2819 1.63 - 1.81: 6 Bond restraints: 9820 Sorted by residual: bond pdb=" CD2 TYR C 539 " pdb=" HD2 TYR C 539 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N ARG C 450 " pdb=" H ARG C 450 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N GLY C 593 " pdb=" H GLY C 593 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" NE2 GLN C 153 " pdb="HE22 GLN C 153 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N LYS C 272 " pdb=" H LYS C 272 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 ... (remaining 9815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 12480 1.97 - 3.95: 3936 3.95 - 5.92: 805 5.92 - 7.90: 423 7.90 - 9.87: 59 Bond angle restraints: 17703 Sorted by residual: angle pdb=" N LYS C 500 " pdb=" CA LYS C 500 " pdb=" C LYS C 500 " ideal model delta sigma weight residual 111.28 121.15 -9.87 1.35e+00 5.49e-01 5.35e+01 angle pdb=" CA ASP C 420 " pdb=" CB ASP C 420 " pdb=" CG ASP C 420 " ideal model delta sigma weight residual 112.60 119.90 -7.30 1.00e+00 1.00e+00 5.33e+01 angle pdb=" CA HIS C 590 " pdb=" CB HIS C 590 " pdb=" CG HIS C 590 " ideal model delta sigma weight residual 113.80 121.09 -7.29 1.00e+00 1.00e+00 5.32e+01 angle pdb=" CA ASP C 483 " pdb=" CB ASP C 483 " pdb=" CG ASP C 483 " ideal model delta sigma weight residual 112.60 119.84 -7.24 1.00e+00 1.00e+00 5.24e+01 angle pdb=" CA ASP C 557 " pdb=" CB ASP C 557 " pdb=" CG ASP C 557 " ideal model delta sigma weight residual 112.60 118.53 -5.93 1.00e+00 1.00e+00 3.51e+01 ... (remaining 17698 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 4132 17.31 - 34.62: 331 34.62 - 51.92: 95 51.92 - 69.23: 55 69.23 - 86.54: 12 Dihedral angle restraints: 4625 sinusoidal: 2539 harmonic: 2086 Sorted by residual: dihedral pdb=" CA ILE C 499 " pdb=" C ILE C 499 " pdb=" N LYS C 500 " pdb=" CA LYS C 500 " ideal model delta harmonic sigma weight residual 180.00 150.87 29.13 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA LYS C 500 " pdb=" C LYS C 500 " pdb=" N GLU C 501 " pdb=" CA GLU C 501 " ideal model delta harmonic sigma weight residual 180.00 150.99 29.01 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA LYS C 497 " pdb=" C LYS C 497 " pdb=" N ASN C 498 " pdb=" CA ASN C 498 " ideal model delta harmonic sigma weight residual 180.00 151.90 28.10 0 5.00e+00 4.00e-02 3.16e+01 ... (remaining 4622 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 437 0.093 - 0.185: 229 0.185 - 0.277: 40 0.277 - 0.369: 8 0.369 - 0.461: 3 Chirality restraints: 717 Sorted by residual: chirality pdb=" CA LYS C 500 " pdb=" N LYS C 500 " pdb=" C LYS C 500 " pdb=" CB LYS C 500 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.32e+00 chirality pdb=" CA SER C 717 " pdb=" N SER C 717 " pdb=" C SER C 717 " pdb=" CB SER C 717 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" CA ASP C 557 " pdb=" N ASP C 557 " pdb=" C ASP C 557 " pdb=" CB ASP C 557 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.09e+00 ... (remaining 714 not shown) Planarity restraints: 1488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 337 " 0.247 2.00e-02 2.50e+03 1.00e-01 3.02e+02 pdb=" CG TYR C 337 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR C 337 " -0.099 2.00e-02 2.50e+03 pdb=" CD2 TYR C 337 " -0.067 2.00e-02 2.50e+03 pdb=" CE1 TYR C 337 " -0.045 2.00e-02 2.50e+03 pdb=" CE2 TYR C 337 " -0.058 2.00e-02 2.50e+03 pdb=" CZ TYR C 337 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR C 337 " 0.176 2.00e-02 2.50e+03 pdb=" HD1 TYR C 337 " -0.074 2.00e-02 2.50e+03 pdb=" HD2 TYR C 337 " -0.039 2.00e-02 2.50e+03 pdb=" HE1 TYR C 337 " 0.015 2.00e-02 2.50e+03 pdb=" HE2 TYR C 337 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 580 " -0.162 9.50e-02 1.11e+02 1.04e-01 1.79e+02 pdb=" NE ARG C 580 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG C 580 " -0.029 2.00e-02 2.50e+03 pdb=" NH1 ARG C 580 " -0.024 2.00e-02 2.50e+03 pdb=" NH2 ARG C 580 " -0.052 2.00e-02 2.50e+03 pdb="HH11 ARG C 580 " 0.142 2.00e-02 2.50e+03 pdb="HH12 ARG C 580 " -0.152 2.00e-02 2.50e+03 pdb="HH21 ARG C 580 " -0.015 2.00e-02 2.50e+03 pdb="HH22 ARG C 580 " 0.150 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 527 " 0.173 2.00e-02 2.50e+03 6.64e-02 1.77e+02 pdb=" CG TRP C 527 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP C 527 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP C 527 " -0.064 2.00e-02 2.50e+03 pdb=" NE1 TRP C 527 " -0.083 2.00e-02 2.50e+03 pdb=" CE2 TRP C 527 " -0.051 2.00e-02 2.50e+03 pdb=" CE3 TRP C 527 " -0.059 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 527 " 0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 527 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP C 527 " 0.048 2.00e-02 2.50e+03 pdb=" HD1 TRP C 527 " 0.054 2.00e-02 2.50e+03 pdb=" HE1 TRP C 527 " -0.015 2.00e-02 2.50e+03 pdb=" HE3 TRP C 527 " -0.083 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 527 " 0.027 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 527 " -0.000 2.00e-02 2.50e+03 pdb=" HH2 TRP C 527 " 0.095 2.00e-02 2.50e+03 ... (remaining 1485 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 890 2.22 - 2.82: 18202 2.82 - 3.41: 26010 3.41 - 4.01: 33717 4.01 - 4.60: 49631 Nonbonded interactions: 128450 Sorted by model distance: nonbonded pdb=" OE2 GLU C 456 " pdb=" HG SER C 482 " model vdw 1.629 2.450 nonbonded pdb=" HH TYR C 388 " pdb=" OD2 ASP C 442 " model vdw 1.635 2.450 nonbonded pdb=" HH TYR C 167 " pdb=" OD2 ASP C 347 " model vdw 1.645 2.450 nonbonded pdb=" O GLU C 382 " pdb=" HG SER C 385 " model vdw 1.645 2.450 nonbonded pdb=" O GLN C 587 " pdb=" HG SER C 604 " model vdw 1.657 2.450 ... (remaining 128445 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: 0.250 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: 0.050 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.890 Find NCS groups from input model: 0.030 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 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 : 0.013 0.105 5021 Z= 0.803 Angle : 1.978 9.870 6770 Z= 1.320 Chirality : 0.108 0.461 717 Planarity : 0.015 0.121 897 Dihedral : 15.369 86.540 1914 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.93 % Favored : 88.07 % Rotamer: Outliers : 0.73 % Allowed : 6.79 % Favored : 92.48 % Cbeta Deviations : 0.52 % 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: -2.91 (0.30), residues: 612 helix: -3.29 (0.30), residues: 152 sheet: 1.91 (1.10), residues: 22 loop : -1.73 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 362 TYR 0.215 0.021 TYR C 337 PHE 0.067 0.014 PHE C 625 TRP 0.121 0.035 TRP C 527 HIS 0.011 0.004 HIS C 170 Details of bonding type rmsd covalent geometry : bond 0.01319 ( 5021) covalent geometry : angle 1.97760 ( 6770) hydrogen bonds : bond 0.20832 ( 120) hydrogen bonds : angle 8.93276 ( 318) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Evaluate side-chains 132 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 128 time to evaluate : 0.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 190 LYS cc_start: 0.7613 (mmtm) cc_final: 0.7354 (mttt) REVERT: C 298 LYS cc_start: 0.6752 (ttmt) cc_final: 0.6406 (tttp) REVERT: C 345 ARG cc_start: 0.7148 (ttm170) cc_final: 0.6738 (ttm-80) REVERT: C 365 ASP cc_start: 0.7718 (t70) cc_final: 0.7372 (t0) REVERT: C 425 ASN cc_start: 0.6655 (t0) cc_final: 0.6017 (t0) REVERT: C 437 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7560 (mt-10) REVERT: C 538 GLU cc_start: 0.4530 (OUTLIER) cc_final: 0.2604 (tt0) REVERT: C 607 THR cc_start: 0.8431 (p) cc_final: 0.8212 (t) REVERT: C 639 THR cc_start: 0.9016 (p) cc_final: 0.8532 (p) REVERT: C 701 ARG cc_start: 0.5563 (mtt180) cc_final: 0.5317 (tpp80) REVERT: C 712 GLU cc_start: 0.6971 (mm-30) cc_final: 0.6347 (mm-30) outliers start: 4 outliers final: 0 residues processed: 129 average time/residue: 0.2303 time to fit residues: 35.3252 Evaluate side-chains 82 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 538 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 290 ASN C 293 GLN ** C 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 590 HIS C 663 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.178550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.149397 restraints weight = 21164.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.155845 restraints weight = 9507.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.160021 restraints weight = 5742.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.162845 restraints weight = 4096.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.164637 restraints weight = 3196.169| |-----------------------------------------------------------------------------| r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5021 Z= 0.152 Angle : 0.643 5.078 6770 Z= 0.355 Chirality : 0.042 0.144 717 Planarity : 0.004 0.034 897 Dihedral : 7.586 49.957 674 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 1.10 % Allowed : 10.64 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -2.26 (0.32), residues: 612 helix: -2.25 (0.35), residues: 154 sheet: 1.87 (1.01), residues: 32 loop : -1.56 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 154 TYR 0.014 0.002 TYR C 644 PHE 0.016 0.002 PHE C 206 TRP 0.013 0.001 TRP C 527 HIS 0.008 0.002 HIS C 590 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 5021) covalent geometry : angle 0.64335 ( 6770) hydrogen bonds : bond 0.04488 ( 120) hydrogen bonds : angle 5.85414 ( 318) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Evaluate side-chains 94 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 190 LYS cc_start: 0.7014 (mmtm) cc_final: 0.6558 (mttt) REVERT: C 338 ASN cc_start: 0.8434 (t0) cc_final: 0.7955 (t0) REVERT: C 345 ARG cc_start: 0.7450 (ttm170) cc_final: 0.6912 (ttm-80) REVERT: C 356 TYR cc_start: 0.8629 (p90) cc_final: 0.8161 (p90) REVERT: C 365 ASP cc_start: 0.7726 (t70) cc_final: 0.7463 (t70) REVERT: C 567 GLU cc_start: 0.7467 (tp30) cc_final: 0.6926 (mt-10) outliers start: 6 outliers final: 5 residues processed: 92 average time/residue: 0.1961 time to fit residues: 22.1898 Evaluate side-chains 69 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 168 GLN Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 446 ILE Chi-restraints excluded: chain C residue 704 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 17 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.167154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.141138 restraints weight = 21120.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.146975 restraints weight = 9029.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.150831 restraints weight = 5257.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.153290 restraints weight = 3641.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.155073 restraints weight = 2819.625| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 5021 Z= 0.222 Angle : 0.644 4.926 6770 Z= 0.354 Chirality : 0.043 0.149 717 Planarity : 0.005 0.065 897 Dihedral : 6.572 34.999 671 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.62 % Favored : 89.38 % Rotamer: Outliers : 2.02 % Allowed : 12.66 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -2.34 (0.31), residues: 612 helix: -2.08 (0.36), residues: 160 sheet: 1.85 (1.02), residues: 32 loop : -1.71 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 346 TYR 0.011 0.002 TYR C 167 PHE 0.013 0.002 PHE C 206 TRP 0.009 0.002 TRP C 527 HIS 0.019 0.003 HIS C 590 Details of bonding type rmsd covalent geometry : bond 0.00516 ( 5021) covalent geometry : angle 0.64438 ( 6770) hydrogen bonds : bond 0.04368 ( 120) hydrogen bonds : angle 5.68163 ( 318) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Evaluate side-chains 79 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 162 ASN cc_start: 0.8478 (t0) cc_final: 0.8081 (t0) REVERT: C 190 LYS cc_start: 0.7240 (mmtm) cc_final: 0.6876 (mttt) REVERT: C 345 ARG cc_start: 0.7297 (ttm170) cc_final: 0.6741 (ttm-80) REVERT: C 356 TYR cc_start: 0.8678 (p90) cc_final: 0.8100 (p90) REVERT: C 365 ASP cc_start: 0.7759 (t70) cc_final: 0.7219 (t0) REVERT: C 474 ILE cc_start: 0.7800 (OUTLIER) cc_final: 0.7591 (mt) REVERT: C 634 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7697 (mt-10) outliers start: 11 outliers final: 6 residues processed: 76 average time/residue: 0.1339 time to fit residues: 13.4515 Evaluate side-chains 71 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 446 ILE Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 704 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 5 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 453 ASN C 529 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.167316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.142311 restraints weight = 21219.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.147921 restraints weight = 9297.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.151667 restraints weight = 5492.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.154002 restraints weight = 3826.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.155749 restraints weight = 2983.330| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 5021 Z= 0.206 Angle : 0.591 4.882 6770 Z= 0.323 Chirality : 0.041 0.144 717 Planarity : 0.004 0.052 897 Dihedral : 6.250 33.801 671 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Rotamer: Outliers : 2.94 % Allowed : 11.74 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.32 (0.32), residues: 612 helix: -1.98 (0.37), residues: 162 sheet: 0.49 (1.10), residues: 32 loop : -1.59 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 346 TYR 0.009 0.001 TYR C 167 PHE 0.009 0.001 PHE C 319 TRP 0.009 0.002 TRP C 527 HIS 0.013 0.002 HIS C 590 Details of bonding type rmsd covalent geometry : bond 0.00481 ( 5021) covalent geometry : angle 0.59063 ( 6770) hydrogen bonds : bond 0.03998 ( 120) hydrogen bonds : angle 5.47659 ( 318) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Evaluate side-chains 82 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 162 ASN cc_start: 0.8504 (t0) cc_final: 0.8066 (t0) REVERT: C 190 LYS cc_start: 0.7185 (mmtm) cc_final: 0.6855 (mttt) REVERT: C 308 GLU cc_start: 0.6498 (tp30) cc_final: 0.6098 (tp30) REVERT: C 345 ARG cc_start: 0.7276 (ttm170) cc_final: 0.6700 (ttm170) REVERT: C 356 TYR cc_start: 0.8668 (p90) cc_final: 0.8101 (p90) REVERT: C 365 ASP cc_start: 0.7795 (t70) cc_final: 0.7298 (t0) REVERT: C 425 ASN cc_start: 0.7951 (t0) cc_final: 0.7651 (t0) REVERT: C 453 ASN cc_start: 0.8195 (m-40) cc_final: 0.7982 (m-40) REVERT: C 538 GLU cc_start: 0.4475 (OUTLIER) cc_final: 0.2938 (tt0) REVERT: C 567 GLU cc_start: 0.7475 (mm-30) cc_final: 0.6678 (mt-10) REVERT: C 634 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7880 (mt-10) outliers start: 16 outliers final: 11 residues processed: 78 average time/residue: 0.1356 time to fit residues: 14.1505 Evaluate side-chains 72 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 446 ILE Chi-restraints excluded: chain C residue 538 GLU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 714 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 40 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 ASN C 663 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.168736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.140708 restraints weight = 21508.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.146803 restraints weight = 9773.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.150828 restraints weight = 5947.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.153521 restraints weight = 4247.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.155246 restraints weight = 3330.070| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.4829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 5021 Z= 0.194 Angle : 0.575 4.928 6770 Z= 0.314 Chirality : 0.041 0.142 717 Planarity : 0.004 0.051 897 Dihedral : 6.015 32.885 671 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.62 % Favored : 89.38 % Rotamer: Outliers : 3.49 % Allowed : 12.66 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.23 (0.32), residues: 612 helix: -1.61 (0.39), residues: 156 sheet: 0.32 (1.08), residues: 32 loop : -1.66 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 346 TYR 0.009 0.001 TYR C 167 PHE 0.007 0.001 PHE C 390 TRP 0.007 0.002 TRP C 527 HIS 0.013 0.002 HIS C 590 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 5021) covalent geometry : angle 0.57520 ( 6770) hydrogen bonds : bond 0.03781 ( 120) hydrogen bonds : angle 5.40152 ( 318) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Evaluate side-chains 81 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 162 ASN cc_start: 0.8469 (t0) cc_final: 0.8009 (t0) REVERT: C 164 THR cc_start: 0.8460 (p) cc_final: 0.8252 (p) REVERT: C 190 LYS cc_start: 0.7372 (mmtm) cc_final: 0.6910 (mttt) REVERT: C 308 GLU cc_start: 0.6635 (tp30) cc_final: 0.6224 (tp30) REVERT: C 345 ARG cc_start: 0.7310 (ttm170) cc_final: 0.6730 (ttm170) REVERT: C 356 TYR cc_start: 0.8660 (p90) cc_final: 0.8090 (p90) REVERT: C 365 ASP cc_start: 0.7757 (t70) cc_final: 0.7303 (t0) REVERT: C 425 ASN cc_start: 0.7969 (t0) cc_final: 0.7740 (t0) REVERT: C 474 ILE cc_start: 0.7728 (OUTLIER) cc_final: 0.7486 (mt) REVERT: C 509 ASN cc_start: 0.8508 (t0) cc_final: 0.8297 (t0) REVERT: C 538 GLU cc_start: 0.4602 (OUTLIER) cc_final: 0.3007 (tt0) REVERT: C 565 SER cc_start: 0.8822 (t) cc_final: 0.8359 (p) REVERT: C 567 GLU cc_start: 0.7404 (mm-30) cc_final: 0.6658 (mt-10) REVERT: C 634 GLU cc_start: 0.8233 (mt-10) cc_final: 0.8021 (mt-10) outliers start: 19 outliers final: 14 residues processed: 77 average time/residue: 0.1422 time to fit residues: 14.5393 Evaluate side-chains 77 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 168 GLN Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 446 ILE Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 538 GLU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 645 ASN Chi-restraints excluded: chain C residue 681 ASN Chi-restraints excluded: chain C residue 704 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 2 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 29 optimal weight: 7.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.169844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.141997 restraints weight = 21464.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.148195 restraints weight = 9613.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.152240 restraints weight = 5791.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.154927 restraints weight = 4111.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.156771 restraints weight = 3210.377| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.5053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 5021 Z= 0.150 Angle : 0.531 4.768 6770 Z= 0.289 Chirality : 0.040 0.138 717 Planarity : 0.004 0.046 897 Dihedral : 5.621 30.365 671 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 2.94 % Allowed : 13.58 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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 (0.32), residues: 612 helix: -1.23 (0.41), residues: 154 sheet: 0.85 (1.11), residues: 27 loop : -1.65 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 346 TYR 0.008 0.001 TYR C 167 PHE 0.009 0.001 PHE C 390 TRP 0.008 0.001 TRP C 527 HIS 0.009 0.002 HIS C 590 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 5021) covalent geometry : angle 0.53131 ( 6770) hydrogen bonds : bond 0.03405 ( 120) hydrogen bonds : angle 5.08832 ( 318) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Evaluate side-chains 80 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 190 LYS cc_start: 0.7337 (mmtm) cc_final: 0.6885 (mttt) REVERT: C 308 GLU cc_start: 0.6821 (tp30) cc_final: 0.6367 (tp30) REVERT: C 365 ASP cc_start: 0.7691 (t70) cc_final: 0.7297 (t0) REVERT: C 425 ASN cc_start: 0.7985 (t0) cc_final: 0.7776 (t0) REVERT: C 474 ILE cc_start: 0.7652 (OUTLIER) cc_final: 0.7445 (mt) REVERT: C 538 GLU cc_start: 0.4621 (OUTLIER) cc_final: 0.3052 (tt0) REVERT: C 567 GLU cc_start: 0.7415 (mm-30) cc_final: 0.6693 (mt-10) REVERT: C 634 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7954 (mt-10) outliers start: 16 outliers final: 12 residues processed: 76 average time/residue: 0.1110 time to fit residues: 11.7267 Evaluate side-chains 75 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 168 GLN Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 446 ILE Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 538 GLU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 681 ASN Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 714 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 58 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 212 ASN ** C 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.166216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.140789 restraints weight = 21062.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.146538 restraints weight = 9085.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.150369 restraints weight = 5332.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.152839 restraints weight = 3702.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.154656 restraints weight = 2853.847| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.5227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 5021 Z= 0.202 Angle : 0.571 4.887 6770 Z= 0.312 Chirality : 0.041 0.143 717 Planarity : 0.004 0.050 897 Dihedral : 5.723 31.865 671 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 3.67 % Allowed : 13.76 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.18 (0.32), residues: 612 helix: -1.26 (0.41), residues: 157 sheet: 0.75 (1.12), residues: 27 loop : -1.78 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 430 TYR 0.013 0.001 TYR C 578 PHE 0.008 0.001 PHE C 390 TRP 0.008 0.002 TRP C 286 HIS 0.014 0.002 HIS C 590 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 5021) covalent geometry : angle 0.57139 ( 6770) hydrogen bonds : bond 0.03713 ( 120) hydrogen bonds : angle 5.20416 ( 318) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Evaluate side-chains 77 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 190 LYS cc_start: 0.7386 (mmtm) cc_final: 0.6945 (mttt) REVERT: C 365 ASP cc_start: 0.7707 (t70) cc_final: 0.7298 (t0) REVERT: C 474 ILE cc_start: 0.7743 (OUTLIER) cc_final: 0.7494 (mt) REVERT: C 538 GLU cc_start: 0.4581 (OUTLIER) cc_final: 0.2935 (tt0) REVERT: C 567 GLU cc_start: 0.7506 (mm-30) cc_final: 0.6821 (mt-10) outliers start: 20 outliers final: 15 residues processed: 73 average time/residue: 0.1151 time to fit residues: 11.8083 Evaluate side-chains 72 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 168 GLN Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 446 ILE Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 538 GLU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 645 ASN Chi-restraints excluded: chain C residue 681 ASN Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 714 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 24 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 ASN C 529 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.167008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.141811 restraints weight = 20989.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.147492 restraints weight = 9245.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.151289 restraints weight = 5484.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.153770 restraints weight = 3824.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.155522 restraints weight = 2937.937| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.5329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 5021 Z= 0.155 Angle : 0.536 4.752 6770 Z= 0.292 Chirality : 0.040 0.137 717 Planarity : 0.004 0.048 897 Dihedral : 5.482 30.370 671 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 3.49 % Allowed : 15.05 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.02 (0.32), residues: 612 helix: -1.01 (0.42), residues: 154 sheet: 0.73 (1.10), residues: 27 loop : -1.71 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 430 TYR 0.009 0.001 TYR C 578 PHE 0.007 0.001 PHE C 390 TRP 0.008 0.001 TRP C 527 HIS 0.009 0.002 HIS C 590 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 5021) covalent geometry : angle 0.53620 ( 6770) hydrogen bonds : bond 0.03388 ( 120) hydrogen bonds : angle 5.04073 ( 318) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Evaluate side-chains 76 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 190 LYS cc_start: 0.7222 (mmtm) cc_final: 0.6788 (mttt) REVERT: C 365 ASP cc_start: 0.7649 (t70) cc_final: 0.7225 (t0) REVERT: C 453 ASN cc_start: 0.8094 (m-40) cc_final: 0.7885 (m-40) REVERT: C 474 ILE cc_start: 0.7574 (OUTLIER) cc_final: 0.7338 (mt) REVERT: C 538 GLU cc_start: 0.4388 (OUTLIER) cc_final: 0.2853 (tt0) REVERT: C 567 GLU cc_start: 0.7417 (mm-30) cc_final: 0.6699 (mt-10) REVERT: C 634 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7730 (pt0) outliers start: 19 outliers final: 13 residues processed: 71 average time/residue: 0.1087 time to fit residues: 10.6538 Evaluate side-chains 71 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 168 GLN Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 446 ILE Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 538 GLU Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 645 ASN Chi-restraints excluded: chain C residue 681 ASN Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 714 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 12 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.166320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.140751 restraints weight = 20982.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.146606 restraints weight = 9007.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.150530 restraints weight = 5274.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.152914 restraints weight = 3639.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.154784 restraints weight = 2818.060| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.5429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 5021 Z= 0.169 Angle : 0.546 4.854 6770 Z= 0.299 Chirality : 0.040 0.139 717 Planarity : 0.004 0.048 897 Dihedral : 5.438 30.452 671 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer: Outliers : 3.30 % Allowed : 14.68 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.01 (0.32), residues: 612 helix: -0.92 (0.42), residues: 157 sheet: 0.64 (1.10), residues: 27 loop : -1.74 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 430 TYR 0.008 0.001 TYR C 578 PHE 0.007 0.001 PHE C 390 TRP 0.007 0.001 TRP C 527 HIS 0.011 0.002 HIS C 590 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 5021) covalent geometry : angle 0.54605 ( 6770) hydrogen bonds : bond 0.03441 ( 120) hydrogen bonds : angle 5.00516 ( 318) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Evaluate side-chains 74 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 190 LYS cc_start: 0.7411 (mmtm) cc_final: 0.6976 (mttt) REVERT: C 252 MET cc_start: 0.8506 (tmm) cc_final: 0.8063 (tmm) REVERT: C 365 ASP cc_start: 0.7672 (t70) cc_final: 0.7249 (t0) REVERT: C 474 ILE cc_start: 0.7724 (OUTLIER) cc_final: 0.7477 (mt) REVERT: C 538 GLU cc_start: 0.4651 (OUTLIER) cc_final: 0.3172 (tt0) REVERT: C 567 GLU cc_start: 0.7470 (mm-30) cc_final: 0.6839 (mt-10) REVERT: C 634 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7754 (pt0) outliers start: 18 outliers final: 13 residues processed: 69 average time/residue: 0.1111 time to fit residues: 10.8064 Evaluate side-chains 69 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 168 GLN Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 446 ILE Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 538 GLU Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 645 ASN Chi-restraints excluded: chain C residue 681 ASN Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 714 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 3 optimal weight: 0.0470 chunk 44 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 ASN C 529 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.169963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.144615 restraints weight = 20654.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.150463 restraints weight = 8902.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.154302 restraints weight = 5214.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.156865 restraints weight = 3617.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.158549 restraints weight = 2764.293| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.5495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5021 Z= 0.125 Angle : 0.524 5.371 6770 Z= 0.284 Chirality : 0.039 0.135 717 Planarity : 0.004 0.043 897 Dihedral : 5.232 28.448 671 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Rotamer: Outliers : 2.75 % Allowed : 15.05 % Favored : 82.20 % 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: -1.85 (0.33), residues: 612 helix: -0.81 (0.42), residues: 158 sheet: 0.70 (1.09), residues: 27 loop : -1.63 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 430 TYR 0.007 0.001 TYR C 578 PHE 0.007 0.001 PHE C 390 TRP 0.008 0.001 TRP C 527 HIS 0.007 0.001 HIS C 590 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 5021) covalent geometry : angle 0.52450 ( 6770) hydrogen bonds : bond 0.03171 ( 120) hydrogen bonds : angle 4.88432 ( 318) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Evaluate side-chains 73 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 162 ASN cc_start: 0.8460 (t0) cc_final: 0.8141 (t0) REVERT: C 190 LYS cc_start: 0.7411 (mmtm) cc_final: 0.6985 (mttt) REVERT: C 474 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7448 (mt) REVERT: C 538 GLU cc_start: 0.4641 (OUTLIER) cc_final: 0.3051 (tt0) REVERT: C 567 GLU cc_start: 0.7404 (mm-30) cc_final: 0.6820 (mt-10) REVERT: C 634 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7562 (pt0) outliers start: 15 outliers final: 10 residues processed: 69 average time/residue: 0.1104 time to fit residues: 10.7182 Evaluate side-chains 68 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 168 GLN Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 446 ILE Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 538 GLU Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 645 ASN Chi-restraints excluded: chain C residue 681 ASN Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 714 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 17 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 46 optimal weight: 0.4980 chunk 14 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.172667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.147703 restraints weight = 20644.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.153536 restraints weight = 8879.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.157467 restraints weight = 5172.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.159992 restraints weight = 3538.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.161751 restraints weight = 2703.292| |-----------------------------------------------------------------------------| r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.5604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5021 Z= 0.113 Angle : 0.514 5.112 6770 Z= 0.279 Chirality : 0.039 0.129 717 Planarity : 0.004 0.037 897 Dihedral : 4.987 27.720 671 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Rotamer: Outliers : 2.02 % Allowed : 15.78 % Favored : 82.20 % 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: -1.68 (0.33), residues: 612 helix: -0.59 (0.43), residues: 157 sheet: 0.67 (1.09), residues: 28 loop : -1.54 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 430 TYR 0.006 0.001 TYR C 578 PHE 0.006 0.001 PHE C 319 TRP 0.009 0.001 TRP C 527 HIS 0.006 0.001 HIS C 590 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 5021) covalent geometry : angle 0.51366 ( 6770) hydrogen bonds : bond 0.02968 ( 120) hydrogen bonds : angle 4.71695 ( 318) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1846.90 seconds wall clock time: 32 minutes 4.67 seconds (1924.67 seconds total)