Starting phenix.real_space_refine on Wed Sep 25 05:38:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adm_11731/09_2024/7adm_11731.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adm_11731/09_2024/7adm_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adm_11731/09_2024/7adm_11731.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adm_11731/09_2024/7adm_11731.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adm_11731/09_2024/7adm_11731.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adm_11731/09_2024/7adm_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-5461/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: 5.08, per 1000 atoms: 0.52 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: 2.74 Conformation dependent library (CDL) restraints added in 676.0 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: 0.86 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: 3.30 Time building geometry restraints manager: 3.26 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: 0.010 Normalize map: mean=0, sd=1: 0.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.160 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.020 Find NCS groups from input model: 0.060 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.010 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 4 poor density : 128 time to evaluate : 0.835 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: 0.5191 time to fit residues: 81.6362 Evaluate side-chains 84 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 82 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 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 fitting. rotamer outliers: 7 poor density : 89 time to evaluate : 0.736 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: 0.7154 (mmtm) cc_final: 0.6689 (mttt) REVERT: C 338 ASN cc_start: 0.8472 (t0) cc_final: 0.8071 (t0) REVERT: C 345 ARG cc_start: 0.7511 (ttm170) cc_final: 0.7011 (ttm-80) REVERT: C 356 TYR cc_start: 0.8538 (p90) cc_final: 0.8081 (p90) REVERT: C 365 ASP cc_start: 0.7774 (t70) cc_final: 0.7523 (t70) REVERT: C 567 GLU cc_start: 0.7527 (tp30) cc_final: 0.7045 (mt-10) REVERT: C 634 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7938 (mt-10) outliers start: 7 outliers final: 6 residues processed: 93 average time/residue: 0.4342 time to fit residues: 50.0123 Evaluate side-chains 68 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 62 time to evaluate : 0.844 ------------------------------------------------------------------------------- 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 30 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.3934 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= 0.210 Angle : 0.576 4.850 6770 Z= 0.315 Chirality : 0.041 0.144 717 Planarity : 0.004 0.058 897 Dihedral : 6.347 32.277 675 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 1.83 % Allowed : 12.66 % Favored : 85.50 % 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: -1.98 (0.32), residues: 612 helix: -1.82 (0.37), residues: 162 sheet: 1.96 (1.01), residues: 32 loop : -1.44 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 527 HIS 0.011 0.002 HIS C 590 PHE 0.010 0.001 PHE C 206 TYR 0.011 0.001 TYR C 566 ARG 0.008 0.000 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 84 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 74 time to evaluate : 0.788 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: 0.7150 (mmtm) cc_final: 0.6698 (mttt) REVERT: C 345 ARG cc_start: 0.7446 (ttm170) cc_final: 0.6985 (ttm-80) REVERT: C 356 TYR cc_start: 0.8610 (p90) cc_final: 0.8145 (p90) REVERT: C 365 ASP cc_start: 0.7498 (t70) cc_final: 0.7004 (t0) REVERT: C 377 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.7443 (tttt) REVERT: C 567 GLU cc_start: 0.7382 (tp30) cc_final: 0.6825 (mt-10) REVERT: C 634 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7874 (mt-10) outliers start: 10 outliers final: 6 residues processed: 81 average time/residue: 0.4072 time to fit residues: 42.9971 Evaluate side-chains 71 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 64 time to evaluate : 0.861 ------------------------------------------------------------------------------- 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 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 41 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 49 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 453 ASN C 529 ASN C 663 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 5021 Z= 0.378 Angle : 0.637 5.001 6770 Z= 0.348 Chirality : 0.043 0.152 717 Planarity : 0.005 0.080 897 Dihedral : 6.474 34.892 675 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer: Outliers : 2.75 % Allowed : 12.84 % Favored : 84.40 % 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: -2.25 (0.32), residues: 612 helix: -1.92 (0.37), residues: 161 sheet: 0.61 (1.09), residues: 32 loop : -1.56 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 527 HIS 0.018 0.003 HIS C 590 PHE 0.013 0.002 PHE C 206 TYR 0.012 0.002 TYR C 167 ARG 0.008 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 81 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 66 time to evaluate : 0.863 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: 0.7448 (mmtm) cc_final: 0.7021 (mttt) REVERT: C 345 ARG cc_start: 0.7404 (ttm170) cc_final: 0.6869 (ttm170) REVERT: C 365 ASP cc_start: 0.7681 (t70) cc_final: 0.7197 (t0) REVERT: C 425 ASN cc_start: 0.7790 (t0) cc_final: 0.7498 (t0) REVERT: C 474 ILE cc_start: 0.7902 (OUTLIER) cc_final: 0.7647 (mt) REVERT: C 538 GLU cc_start: 0.4433 (OUTLIER) cc_final: 0.2811 (tt0) REVERT: C 567 GLU cc_start: 0.7657 (tp30) cc_final: 0.7078 (mt-10) REVERT: C 634 GLU cc_start: 0.8310 (mt-10) cc_final: 0.8013 (mt-10) outliers start: 15 outliers final: 9 residues processed: 78 average time/residue: 0.3355 time to fit residues: 35.1149 Evaluate side-chains 74 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 63 time to evaluate : 0.791 ------------------------------------------------------------------------------- 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 413 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.4723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 5021 Z= 0.316 Angle : 0.585 4.909 6770 Z= 0.320 Chirality : 0.042 0.146 717 Planarity : 0.005 0.064 897 Dihedral : 6.098 33.602 671 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.46 % Favored : 89.54 % Rotamer: Outliers : 3.49 % Allowed : 12.84 % Favored : 83.67 % 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: -2.26 (0.32), residues: 612 helix: -1.75 (0.38), residues: 156 sheet: 0.21 (1.05), residues: 32 loop : -1.63 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 527 HIS 0.014 0.002 HIS C 590 PHE 0.009 0.001 PHE C 390 TYR 0.009 0.001 TYR C 167 ARG 0.005 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 83 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 64 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 190 LYS cc_start: 0.7344 (mmtm) cc_final: 0.6883 (mttt) REVERT: C 308 GLU cc_start: 0.6685 (tp30) cc_final: 0.6270 (tp30) REVERT: C 345 ARG cc_start: 0.7368 (ttm170) cc_final: 0.6850 (ttm170) REVERT: C 365 ASP cc_start: 0.7842 (t70) cc_final: 0.7403 (t0) REVERT: C 425 ASN cc_start: 0.7890 (t0) cc_final: 0.7651 (t0) REVERT: C 474 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7670 (mt) REVERT: C 538 GLU cc_start: 0.4322 (OUTLIER) cc_final: 0.2727 (tt0) REVERT: C 565 SER cc_start: 0.8881 (t) cc_final: 0.8332 (p) REVERT: C 567 GLU cc_start: 0.7542 (tp30) cc_final: 0.6979 (mt-10) REVERT: C 634 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8130 (mt-10) outliers start: 19 outliers final: 13 residues processed: 79 average time/residue: 0.3176 time to fit residues: 33.5561 Evaluate side-chains 76 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 61 time to evaluate : 0.706 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.4997 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= 0.291 Angle : 0.570 4.815 6770 Z= 0.310 Chirality : 0.041 0.147 717 Planarity : 0.005 0.059 897 Dihedral : 5.891 32.621 671 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer: Outliers : 2.94 % Allowed : 15.23 % 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: -2.23 (0.32), residues: 612 helix: -1.52 (0.40), residues: 155 sheet: 0.60 (1.06), 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 0.008 0.001 PHE C 650 TYR 0.015 0.001 TYR C 578 ARG 0.004 0.000 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 76 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 60 time to evaluate : 0.819 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: 0.7480 (mmtm) cc_final: 0.7025 (mttt) REVERT: C 308 GLU cc_start: 0.6715 (tp30) cc_final: 0.6262 (tp30) REVERT: C 365 ASP cc_start: 0.7922 (t70) cc_final: 0.7580 (t0) REVERT: C 425 ASN cc_start: 0.8038 (t0) cc_final: 0.7786 (t0) REVERT: C 474 ILE cc_start: 0.7900 (OUTLIER) cc_final: 0.7689 (mt) REVERT: C 538 GLU cc_start: 0.4499 (OUTLIER) cc_final: 0.2896 (tt0) REVERT: C 567 GLU cc_start: 0.7536 (tp30) cc_final: 0.7136 (mt-10) REVERT: C 634 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8156 (mt-10) outliers start: 16 outliers final: 12 residues processed: 73 average time/residue: 0.2868 time to fit residues: 28.7648 Evaluate side-chains 74 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 60 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 33 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 49 optimal weight: 0.0370 chunk 32 optimal weight: 3.9990 chunk 58 optimal weight: 0.2980 chunk 36 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 348 ASN C 529 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.5123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5021 Z= 0.138 Angle : 0.492 4.621 6770 Z= 0.266 Chirality : 0.039 0.132 717 Planarity : 0.004 0.058 897 Dihedral : 5.152 29.930 671 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 1.83 % Allowed : 15.41 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.33), residues: 612 helix: -1.03 (0.42), residues: 154 sheet: 0.70 (1.04), residues: 27 loop : -1.48 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 527 HIS 0.003 0.001 HIS C 590 PHE 0.008 0.001 PHE C 319 TYR 0.007 0.001 TYR C 578 ARG 0.003 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 76 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 66 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 190 LYS cc_start: 0.7368 (mmtm) cc_final: 0.6932 (mttt) REVERT: C 308 GLU cc_start: 0.6643 (tp30) cc_final: 0.6328 (tp30) REVERT: C 538 GLU cc_start: 0.4168 (OUTLIER) cc_final: 0.2568 (tt0) REVERT: C 565 SER cc_start: 0.8753 (t) cc_final: 0.8253 (p) REVERT: C 567 GLU cc_start: 0.7442 (tp30) cc_final: 0.7062 (mt-10) outliers start: 10 outliers final: 8 residues processed: 73 average time/residue: 0.2860 time to fit residues: 28.6803 Evaluate side-chains 67 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 58 time to evaluate : 0.839 ------------------------------------------------------------------------------- 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 325 GLU Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain C residue 427 GLU Chi-restraints excluded: chain C residue 446 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 56 optimal weight: 0.3980 chunk 51 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 425 ASN C 529 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.5218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5021 Z= 0.191 Angle : 0.516 5.108 6770 Z= 0.279 Chirality : 0.039 0.136 717 Planarity : 0.004 0.050 897 Dihedral : 5.078 28.164 671 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 2.20 % Allowed : 15.96 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.72 (0.33), residues: 612 helix: -0.82 (0.42), residues: 157 sheet: 0.67 (1.07), residues: 27 loop : -1.47 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 527 HIS 0.008 0.001 HIS C 590 PHE 0.007 0.001 PHE C 390 TYR 0.007 0.001 TYR C 578 ARG 0.003 0.000 ARG C 346 *********************** 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 72 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 60 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 190 LYS cc_start: 0.7404 (mmtm) cc_final: 0.6960 (mttt) REVERT: C 308 GLU cc_start: 0.6625 (tp30) cc_final: 0.6315 (tp30) REVERT: C 538 GLU cc_start: 0.4456 (OUTLIER) cc_final: 0.2846 (tt0) REVERT: C 565 SER cc_start: 0.8801 (t) cc_final: 0.8096 (p) REVERT: C 567 GLU cc_start: 0.7540 (tp30) cc_final: 0.7152 (mt-10) REVERT: C 634 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7758 (pt0) outliers start: 12 outliers final: 8 residues processed: 69 average time/residue: 0.2902 time to fit residues: 28.3644 Evaluate side-chains 66 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 57 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 328 SER 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 573 LEU Chi-restraints excluded: chain C residue 704 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 chunk 16 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 529 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.5307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5021 Z= 0.216 Angle : 0.525 4.643 6770 Z= 0.286 Chirality : 0.039 0.139 717 Planarity : 0.004 0.049 897 Dihedral : 5.092 27.960 671 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % 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: -1.79 (0.33), residues: 612 helix: -0.79 (0.42), residues: 157 sheet: -0.20 (0.90), residues: 37 loop : -1.51 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 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 0.003 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 70 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 59 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 190 LYS cc_start: 0.7432 (mmtm) cc_final: 0.6994 (mttt) REVERT: C 308 GLU cc_start: 0.6660 (tp30) cc_final: 0.6345 (tp30) REVERT: C 538 GLU cc_start: 0.4527 (OUTLIER) cc_final: 0.2975 (tt0) REVERT: C 567 GLU cc_start: 0.7581 (tp30) cc_final: 0.7198 (mt-10) REVERT: C 634 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7802 (pt0) outliers start: 11 outliers final: 8 residues processed: 67 average time/residue: 0.2729 time to fit residues: 25.4220 Evaluate side-chains 66 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 57 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 328 SER 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 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 55 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 529 ASN C 703 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.5436 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= 0.200 Angle : 0.514 4.569 6770 Z= 0.279 Chirality : 0.039 0.135 717 Planarity : 0.004 0.049 897 Dihedral : 4.976 27.362 671 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 1.83 % Allowed : 16.51 % 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: -1.63 (0.33), residues: 612 helix: -0.63 (0.43), residues: 156 sheet: 1.48 (1.14), residues: 22 loop : -1.48 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 527 HIS 0.008 0.001 HIS C 590 PHE 0.007 0.001 PHE C 390 TYR 0.006 0.001 TYR C 167 ARG 0.002 0.000 ARG C 346 ********************** 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 67 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 57 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 190 LYS cc_start: 0.7440 (mmtm) cc_final: 0.7013 (mttt) REVERT: C 308 GLU cc_start: 0.6657 (tp30) cc_final: 0.6346 (tp30) REVERT: C 538 GLU cc_start: 0.4503 (OUTLIER) cc_final: 0.2925 (tt0) REVERT: C 567 GLU cc_start: 0.7553 (tp30) cc_final: 0.7163 (mt-10) outliers start: 10 outliers final: 8 residues processed: 64 average time/residue: 0.3012 time to fit residues: 27.0859 Evaluate side-chains 66 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 57 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 328 SER 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 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 48 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 529 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.173430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.148228 restraints weight = 20425.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.154158 restraints weight = 8851.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.158146 restraints weight = 5182.723| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.5504 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= 0.179 Angle : 0.501 4.605 6770 Z= 0.272 Chirality : 0.039 0.134 717 Planarity : 0.004 0.048 897 Dihedral : 4.867 27.432 671 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 1.83 % Allowed : 16.70 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.53 (0.34), residues: 612 helix: -0.57 (0.43), residues: 157 sheet: 0.07 (0.87), residues: 42 loop : -1.38 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 527 HIS 0.006 0.001 HIS C 590 PHE 0.007 0.001 PHE C 390 TYR 0.006 0.001 TYR C 578 ARG 0.003 0.000 ARG C 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2740.84 seconds wall clock time: 48 minutes 23.77 seconds (2903.77 seconds total)