Starting phenix.real_space_refine on Fri Mar 14 05:34:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7adm_11731/03_2025/7adm_11731.cif Found real_map, /net/cci-nas-00/data/ceres_data/7adm_11731/03_2025/7adm_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7adm_11731/03_2025/7adm_11731.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7adm_11731/03_2025/7adm_11731.map" model { file = "/net/cci-nas-00/data/ceres_data/7adm_11731/03_2025/7adm_11731.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7adm_11731/03_2025/7adm_11731.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 4.53, per 1000 atoms: 0.47 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: 2.77 Conformation dependent library (CDL) restraints added in 701.0 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: 0.94 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: 3.56 Time building geometry restraints manager: 3.11 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: 0.150 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.070 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.990 ------------------------------------------------------------------------------- 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= 0.858 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (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 TRP 0.121 0.035 TRP C 527 HIS 0.011 0.004 HIS C 170 PHE 0.067 0.014 PHE C 625 TYR 0.215 0.021 TYR C 337 ARG 0.007 0.001 ARG C 362 *********************** 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 : 0.850 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: 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: 0.6397 (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: 0.7381 (t0) REVERT: C 425 ASN cc_start: 0.6655 (t0) cc_final: 0.6023 (t0) REVERT: C 437 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7559 (mt-10) REVERT: C 538 GLU cc_start: 0.4530 (OUTLIER) cc_final: 0.2603 (tt0) REVERT: C 607 THR cc_start: 0.8431 (p) cc_final: 0.8214 (t) REVERT: C 639 THR cc_start: 0.9016 (p) cc_final: 0.8533 (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: 0.6346 (mm-30) outliers start: 4 outliers final: 1 residues processed: 129 average time/residue: 0.5974 time to fit residues: 93.5232 Evaluate side-chains 84 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 82 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 377 LYS 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 51 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 212 ASN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.177113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.151067 restraints weight = 20191.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.157007 restraints weight = 8922.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.160932 restraints weight = 5256.521| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6627 moved from start: 0.3053 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= 0.198 Angle : 0.644 5.050 6770 Z= 0.357 Chirality : 0.042 0.143 717 Planarity : 0.004 0.036 897 Dihedral : 7.598 50.451 678 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 1.28 % Allowed : 10.64 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.32), residues: 612 helix: -2.12 (0.36), residues: 148 sheet: 1.86 (1.00), residues: 32 loop : -1.50 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 527 HIS 0.009 0.002 HIS C 590 PHE 0.016 0.002 PHE C 206 TYR 0.014 0.002 TYR C 644 ARG 0.006 0.001 ARG C 154 *********************** 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 96 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.910 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: C 190 LYS cc_start: 0.6760 (mmtm) cc_final: 0.6325 (mttt) REVERT: C 338 ASN cc_start: 0.8352 (t0) cc_final: 0.7843 (t0) REVERT: C 345 ARG cc_start: 0.7389 (ttm170) cc_final: 0.6847 (ttm-80) REVERT: C 356 TYR cc_start: 0.8639 (p90) cc_final: 0.8126 (p90) REVERT: C 365 ASP cc_start: 0.7756 (t70) cc_final: 0.7490 (t70) REVERT: C 567 GLU cc_start: 0.7414 (tp30) cc_final: 0.6810 (mt-10) REVERT: C 634 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7795 (mt-10) outliers start: 7 outliers final: 6 residues processed: 93 average time/residue: 0.4578 time to fit residues: 53.7904 Evaluate side-chains 68 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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 377 LYS 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 49 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 46 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.173291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.144431 restraints weight = 21428.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.150643 restraints weight = 9707.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.154723 restraints weight = 5894.941| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 5021 Z= 0.263 Angle : 0.602 4.866 6770 Z= 0.330 Chirality : 0.041 0.149 717 Planarity : 0.004 0.059 897 Dihedral : 6.504 33.720 675 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.32), residues: 612 helix: -1.94 (0.37), residues: 162 sheet: 1.91 (1.01), residues: 32 loop : -1.55 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 527 HIS 0.013 0.003 HIS C 590 PHE 0.014 0.002 PHE C 206 TYR 0.011 0.001 TYR C 578 ARG 0.010 0.001 ARG C 346 *********************** 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 : 0.704 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: C 190 LYS cc_start: 0.6948 (mmtm) cc_final: 0.6432 (mttt) REVERT: C 345 ARG cc_start: 0.7368 (ttm170) cc_final: 0.6892 (ttm-80) REVERT: C 356 TYR cc_start: 0.8640 (p90) cc_final: 0.8153 (p90) REVERT: C 365 ASP cc_start: 0.7580 (t70) cc_final: 0.7057 (t0) REVERT: C 377 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7496 (tttt) REVERT: C 474 ILE cc_start: 0.7541 (OUTLIER) cc_final: 0.7288 (mt) REVERT: C 494 LEU cc_start: 0.6194 (mt) cc_final: 0.5931 (mt) REVERT: C 567 GLU cc_start: 0.7400 (tp30) cc_final: 0.6737 (mt-10) REVERT: C 634 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7792 (mt-10) REVERT: C 701 ARG cc_start: 0.5779 (mtt180) cc_final: 0.5516 (tpp80) outliers start: 11 outliers final: 6 residues processed: 76 average time/residue: 0.3625 time to fit residues: 35.6496 Evaluate side-chains 72 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.705 ------------------------------------------------------------------------------- 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 377 LYS 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 43 optimal weight: 8.9990 chunk 44 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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 = 0.3987 r_free = 0.3987 target = 0.171332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.142676 restraints weight = 21276.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.148799 restraints weight = 9733.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.152859 restraints weight = 5960.341| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 5021 Z= 0.290 Angle : 0.583 4.854 6770 Z= 0.317 Chirality : 0.041 0.143 717 Planarity : 0.004 0.047 897 Dihedral : 6.235 34.518 675 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 2.75 % Allowed : 13.03 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.32), residues: 612 helix: -1.83 (0.38), residues: 160 sheet: 0.73 (1.10), residues: 32 loop : -1.48 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 527 HIS 0.013 0.002 HIS C 590 PHE 0.009 0.001 PHE C 390 TYR 0.009 0.001 TYR C 388 ARG 0.004 0.001 ARG C 346 *********************** 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 84 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 158 ARG cc_start: 0.7977 (tpp-160) cc_final: 0.7549 (tpp-160) REVERT: C 190 LYS cc_start: 0.7251 (mmtm) cc_final: 0.6926 (mttt) REVERT: C 308 GLU cc_start: 0.6493 (tp30) cc_final: 0.6039 (tp30) REVERT: C 337 TYR cc_start: 0.8353 (m-80) cc_final: 0.7904 (m-80) REVERT: C 345 ARG cc_start: 0.7319 (ttm170) cc_final: 0.6764 (ttm170) REVERT: C 365 ASP cc_start: 0.7682 (t70) cc_final: 0.7196 (t0) REVERT: C 425 ASN cc_start: 0.7805 (t0) cc_final: 0.7553 (t0) REVERT: C 538 GLU cc_start: 0.4604 (OUTLIER) cc_final: 0.3009 (tt0) REVERT: C 567 GLU cc_start: 0.7576 (tp30) cc_final: 0.6917 (mt-10) REVERT: C 634 GLU cc_start: 0.8370 (mt-10) cc_final: 0.7997 (mt-10) REVERT: C 701 ARG cc_start: 0.5886 (mtt180) cc_final: 0.5388 (tpp80) outliers start: 15 outliers final: 9 residues processed: 81 average time/residue: 0.3738 time to fit residues: 39.4764 Evaluate side-chains 73 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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 350 GLU Chi-restraints excluded: chain C residue 399 SER 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 713 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 47 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 33 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 = 0.3948 r_free = 0.3948 target = 0.167916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.142662 restraints weight = 21041.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.148368 restraints weight = 9277.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.152182 restraints weight = 5505.037| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.4744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 5021 Z= 0.283 Angle : 0.567 4.880 6770 Z= 0.309 Chirality : 0.041 0.144 717 Planarity : 0.004 0.048 897 Dihedral : 5.907 32.401 671 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.62 % Favored : 89.38 % Rotamer: Outliers : 3.30 % Allowed : 13.39 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.32), residues: 612 helix: -1.64 (0.39), residues: 155 sheet: 0.32 (1.08), residues: 32 loop : -1.58 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 527 HIS 0.013 0.002 HIS C 590 PHE 0.008 0.001 PHE C 390 TYR 0.009 0.001 TYR C 167 ARG 0.004 0.001 ARG C 346 *********************** 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 82 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 190 LYS cc_start: 0.7169 (mmtm) cc_final: 0.6685 (mttt) REVERT: C 308 GLU cc_start: 0.6441 (tp30) cc_final: 0.6027 (tp30) REVERT: C 345 ARG cc_start: 0.7255 (ttm170) cc_final: 0.6713 (ttm170) REVERT: C 365 ASP cc_start: 0.7716 (t70) cc_final: 0.7290 (t0) REVERT: C 425 ASN cc_start: 0.8003 (t0) cc_final: 0.7711 (t0) REVERT: C 474 ILE cc_start: 0.7520 (OUTLIER) cc_final: 0.7286 (mt) REVERT: C 509 ASN cc_start: 0.8495 (t0) cc_final: 0.8250 (t0) REVERT: C 538 GLU cc_start: 0.4365 (OUTLIER) cc_final: 0.2812 (tt0) REVERT: C 565 SER cc_start: 0.8856 (t) cc_final: 0.8283 (p) REVERT: C 567 GLU cc_start: 0.7426 (tp30) cc_final: 0.6712 (mt-10) REVERT: C 634 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8028 (mt-10) REVERT: C 701 ARG cc_start: 0.5831 (mtt180) cc_final: 0.5245 (tpp80) outliers start: 18 outliers final: 13 residues processed: 78 average time/residue: 0.3624 time to fit residues: 37.9159 Evaluate side-chains 76 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.774 ------------------------------------------------------------------------------- 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 287 LEU Chi-restraints excluded: chain C residue 325 GLU Chi-restraints excluded: chain C residue 350 GLU 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 681 ASN Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 714 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 26 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 46 optimal weight: 0.2980 chunk 1 optimal weight: 2.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- 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 = 0.3941 r_free = 0.3941 target = 0.166991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.141870 restraints weight = 21008.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.147577 restraints weight = 9285.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.151362 restraints weight = 5503.767| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.5004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 5021 Z= 0.296 Angle : 0.565 4.786 6770 Z= 0.308 Chirality : 0.041 0.145 717 Planarity : 0.004 0.054 897 Dihedral : 5.829 32.437 671 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.62 % Favored : 89.38 % Rotamer: Outliers : 3.12 % Allowed : 15.05 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.32), residues: 612 helix: -1.46 (0.40), residues: 155 sheet: 0.56 (1.09), residues: 27 loop : -1.70 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP C 527 HIS 0.013 0.002 HIS C 590 PHE 0.009 0.001 PHE C 650 TYR 0.010 0.001 TYR C 167 ARG 0.003 0.001 ARG C 346 *********************** 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 78 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 190 LYS cc_start: 0.7170 (mmtm) cc_final: 0.6751 (mttt) REVERT: C 308 GLU cc_start: 0.6631 (tp30) cc_final: 0.6177 (tp30) REVERT: C 365 ASP cc_start: 0.7834 (t70) cc_final: 0.7471 (t0) REVERT: C 425 ASN cc_start: 0.8120 (t0) cc_final: 0.7846 (t0) REVERT: C 474 ILE cc_start: 0.7587 (OUTLIER) cc_final: 0.7358 (mt) REVERT: C 509 ASN cc_start: 0.8531 (t0) cc_final: 0.8282 (t0) REVERT: C 538 GLU cc_start: 0.4222 (OUTLIER) cc_final: 0.2679 (tt0) REVERT: C 567 GLU cc_start: 0.7448 (tp30) cc_final: 0.6873 (mt-10) REVERT: C 634 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8094 (mt-10) REVERT: C 701 ARG cc_start: 0.5595 (mtt180) cc_final: 0.4928 (tpp80) outliers start: 17 outliers final: 13 residues processed: 75 average time/residue: 0.3571 time to fit residues: 34.9981 Evaluate side-chains 74 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.683 ------------------------------------------------------------------------------- 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 287 LEU Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 350 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 43 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3988 r_free = 0.3988 target = 0.171352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.145635 restraints weight = 20815.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.151634 restraints weight = 8992.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.155623 restraints weight = 5265.053| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.5126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5021 Z= 0.186 Angle : 0.512 4.718 6770 Z= 0.278 Chirality : 0.039 0.138 717 Planarity : 0.004 0.044 897 Dihedral : 5.401 29.253 671 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 2.94 % Allowed : 14.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.32), residues: 612 helix: -1.16 (0.41), residues: 155 sheet: 0.58 (1.07), residues: 27 loop : -1.59 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 527 HIS 0.007 0.001 HIS C 590 PHE 0.007 0.001 PHE C 390 TYR 0.007 0.001 TYR C 167 ARG 0.002 0.000 ARG C 346 *********************** 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: 16 poor density : 61 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 190 LYS cc_start: 0.7278 (mmtm) cc_final: 0.6836 (mttt) REVERT: C 308 GLU cc_start: 0.6697 (tp30) cc_final: 0.6279 (tp30) REVERT: C 365 ASP cc_start: 0.7686 (t70) cc_final: 0.7286 (t0) REVERT: C 453 ASN cc_start: 0.7970 (m-40) cc_final: 0.7026 (t0) REVERT: C 474 ILE cc_start: 0.7372 (OUTLIER) cc_final: 0.7133 (mt) REVERT: C 538 GLU cc_start: 0.4458 (OUTLIER) cc_final: 0.2961 (tt0) REVERT: C 567 GLU cc_start: 0.7359 (tp30) cc_final: 0.6870 (mt-10) REVERT: C 634 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8038 (mt-10) REVERT: C 701 ARG cc_start: 0.5657 (mtt180) cc_final: 0.4985 (tpp80) outliers start: 16 outliers final: 13 residues processed: 73 average time/residue: 0.3356 time to fit residues: 32.8180 Evaluate side-chains 74 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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 350 GLU Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 427 GLU 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 704 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 19 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.3924 r_free = 0.3924 target = 0.165553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.140242 restraints weight = 21419.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.145886 restraints weight = 9528.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.149564 restraints weight = 5677.607| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 moved from start: 0.5285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 5021 Z= 0.363 Angle : 0.594 4.904 6770 Z= 0.324 Chirality : 0.042 0.149 717 Planarity : 0.004 0.052 897 Dihedral : 5.766 32.615 671 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.44 % Favored : 88.56 % Rotamer: Outliers : 3.49 % Allowed : 14.86 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.32), residues: 612 helix: -1.32 (0.40), residues: 155 sheet: -0.92 (0.83), residues: 42 loop : -1.83 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 286 HIS 0.016 0.003 HIS C 590 PHE 0.009 0.002 PHE C 650 TYR 0.015 0.001 TYR C 578 ARG 0.003 0.001 ARG C 430 *********************** 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 81 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 190 LYS cc_start: 0.7221 (mmtm) cc_final: 0.6796 (mttt) REVERT: C 252 MET cc_start: 0.8579 (tmm) cc_final: 0.8176 (tmm) REVERT: C 365 ASP cc_start: 0.7730 (t70) cc_final: 0.7311 (t0) REVERT: C 474 ILE cc_start: 0.7649 (OUTLIER) cc_final: 0.7418 (mt) REVERT: C 538 GLU cc_start: 0.4432 (OUTLIER) cc_final: 0.3060 (tt0) REVERT: C 567 GLU cc_start: 0.7501 (tp30) cc_final: 0.6940 (mt-10) REVERT: C 613 ARG cc_start: 0.7882 (ptp-170) cc_final: 0.7624 (mtm110) REVERT: C 634 GLU cc_start: 0.8337 (mt-10) cc_final: 0.8077 (mt-10) REVERT: C 701 ARG cc_start: 0.5692 (mtt180) cc_final: 0.4974 (tpp80) outliers start: 19 outliers final: 13 residues processed: 77 average time/residue: 0.3807 time to fit residues: 38.0194 Evaluate side-chains 75 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 168 GLN 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 350 GLU 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 2 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3987 r_free = 0.3987 target = 0.171168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.145974 restraints weight = 20801.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.151809 restraints weight = 9216.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.155687 restraints weight = 5449.774| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.5350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5021 Z= 0.187 Angle : 0.519 5.282 6770 Z= 0.283 Chirality : 0.039 0.134 717 Planarity : 0.004 0.046 897 Dihedral : 5.270 28.892 671 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 2.02 % Allowed : 16.33 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.32), residues: 612 helix: -1.01 (0.41), residues: 155 sheet: 0.52 (1.07), residues: 27 loop : -1.64 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 527 HIS 0.006 0.001 HIS C 590 PHE 0.008 0.001 PHE C 319 TYR 0.010 0.001 TYR C 578 ARG 0.002 0.000 ARG C 346 *********************** 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 71 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 190 LYS cc_start: 0.7192 (mmtm) cc_final: 0.6760 (mttt) REVERT: C 252 MET cc_start: 0.8459 (tmm) cc_final: 0.8046 (tmm) REVERT: C 365 ASP cc_start: 0.7661 (t70) cc_final: 0.7250 (t0) REVERT: C 453 ASN cc_start: 0.7938 (m-40) cc_final: 0.7000 (t0) REVERT: C 474 ILE cc_start: 0.7398 (OUTLIER) cc_final: 0.7173 (mt) REVERT: C 538 GLU cc_start: 0.4389 (OUTLIER) cc_final: 0.2918 (tt0) REVERT: C 567 GLU cc_start: 0.7365 (tp30) cc_final: 0.6842 (mt-10) REVERT: C 634 GLU cc_start: 0.8270 (mt-10) cc_final: 0.8014 (mt-10) REVERT: C 701 ARG cc_start: 0.5660 (mtt180) cc_final: 0.4946 (tpp80) outliers start: 11 outliers final: 8 residues processed: 68 average time/residue: 0.3476 time to fit residues: 30.8312 Evaluate side-chains 64 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 168 GLN Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 350 GLU 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 704 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 56 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- 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 703 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.169930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.144453 restraints weight = 20692.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.150370 restraints weight = 8893.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.154233 restraints weight = 5196.932| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.5487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 5021 Z= 0.204 Angle : 0.526 5.165 6770 Z= 0.287 Chirality : 0.039 0.136 717 Planarity : 0.004 0.041 897 Dihedral : 5.121 27.762 671 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 2.20 % Allowed : 17.06 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.33), residues: 612 helix: -0.88 (0.42), residues: 157 sheet: -0.29 (0.88), residues: 37 loop : -1.62 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 527 HIS 0.008 0.001 HIS C 590 PHE 0.007 0.001 PHE C 390 TYR 0.008 0.001 TYR C 578 ARG 0.002 0.000 ARG C 430 ********************** 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 70 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 190 LYS cc_start: 0.7406 (mmtm) cc_final: 0.6971 (mttt) REVERT: C 252 MET cc_start: 0.8498 (tmm) cc_final: 0.8104 (tmm) REVERT: C 308 GLU cc_start: 0.6796 (tp30) cc_final: 0.6246 (tp30) REVERT: C 453 ASN cc_start: 0.7968 (m-40) cc_final: 0.7165 (t0) REVERT: C 474 ILE cc_start: 0.7516 (OUTLIER) cc_final: 0.7271 (mt) REVERT: C 538 GLU cc_start: 0.4695 (OUTLIER) cc_final: 0.3092 (tt0) REVERT: C 567 GLU cc_start: 0.7509 (tp30) cc_final: 0.7111 (mt-10) REVERT: C 634 GLU cc_start: 0.8259 (mt-10) cc_final: 0.8059 (mt-10) REVERT: C 701 ARG cc_start: 0.5671 (mtt180) cc_final: 0.4984 (tpp80) outliers start: 12 outliers final: 9 residues processed: 66 average time/residue: 0.3765 time to fit residues: 31.9374 Evaluate side-chains 69 residues out of total 546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 168 GLN Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 350 GLU 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 704 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 43 optimal weight: 7.9990 chunk 14 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 1 optimal weight: 0.0980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.4006 r_free = 0.4006 target = 0.173141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.148064 restraints weight = 20535.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.153987 restraints weight = 8777.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.157884 restraints weight = 5102.777| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.5616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5021 Z= 0.169 Angle : 0.499 4.894 6770 Z= 0.271 Chirality : 0.039 0.132 717 Planarity : 0.004 0.037 897 Dihedral : 4.879 28.269 671 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 2.02 % Allowed : 16.88 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.33), residues: 612 helix: -0.67 (0.43), residues: 156 sheet: -0.35 (0.82), residues: 43 loop : -1.48 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 527 HIS 0.006 0.001 HIS C 590 PHE 0.007 0.001 PHE C 390 TYR 0.007 0.001 TYR C 578 ARG 0.002 0.000 ARG C 574 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3839.48 seconds wall clock time: 67 minutes 55.50 seconds (4075.50 seconds total)