Starting phenix.real_space_refine (version: dev) on Fri May 13 02:57:39 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adm_11731/05_2022/7adm_11731.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adm_11731/05_2022/7adm_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_11731/05_2022/7adm_11731.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adm_11731/05_2022/7adm_11731.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adm_11731/05_2022/7adm_11731.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adm_11731/05_2022/7adm_11731.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "C TYR 539": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/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: 5.04, 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 - 3.50 Amino acid : False - 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: 7.88 Conformation dependent library (CDL) restraints added in 951.7 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: 0.35 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: 3.42 Time building geometry restraints manager: 8.19 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=" CD1 TYR C 539 " pdb=" HD1 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: 98.67 - 105.87: 330 105.87 - 113.07: 10496 113.07 - 120.27: 4522 120.27 - 127.47: 2320 127.47 - 134.67: 35 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: 3556 17.31 - 34.62: 288 34.62 - 51.92: 57 51.92 - 69.23: 41 69.23 - 86.54: 12 Dihedral angle restraints: 3954 sinusoidal: 1868 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 3951 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 1.850 nonbonded pdb=" HH TYR C 388 " pdb=" OD2 ASP C 442 " model vdw 1.635 1.850 nonbonded pdb=" HH TYR C 167 " pdb=" OD2 ASP C 347 " model vdw 1.645 1.850 nonbonded pdb=" O GLU C 382 " pdb=" HG SER C 385 " model vdw 1.645 1.850 nonbonded pdb=" O GLN C 587 " pdb=" HG SER C 604 " model vdw 1.657 1.850 ... (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 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. 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: 0.160 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: 1.860 Check model and map are aligned: 0.150 Convert atoms to be neutral: 0.090 Process input model: 33.720 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 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 : 0.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.93 % Favored : 88.07 % Rotamer Outliers : 0.73 % 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 *********************** 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 outliers start: 4 outliers final: 1 residues processed: 129 average time/residue: 0.4387 time to fit residues: 69.0153 Evaluate side-chains 76 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 0.783 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5564 time to fit residues: 1.6699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 290 ASN C 293 GLN ** C 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 590 HIS C 663 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.132 5021 Z= 0.232 Angle : 0.713 21.471 6770 Z= 0.375 Chirality : 0.042 0.144 717 Planarity : 0.004 0.034 897 Dihedral : 7.185 32.504 671 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer Outliers : 1.28 % 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: -2.06 (0.32), residues: 612 helix: -2.09 (0.36), residues: 142 sheet: 2.13 (1.01), residues: 32 loop : -1.48 (0.29), residues: 438 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Evaluate side-chains 94 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 87 time to evaluate : 0.713 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 outliers start: 7 outliers final: 4 residues processed: 90 average time/residue: 0.3465 time to fit residues: 40.1494 Evaluate side-chains 65 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 61 time to evaluate : 0.788 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.1120 time to fit residues: 1.8299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 37 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.109 5021 Z= 0.174 Angle : 0.590 9.299 6770 Z= 0.320 Chirality : 0.039 0.134 717 Planarity : 0.004 0.053 897 Dihedral : 6.203 31.126 671 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer Outliers : 1.10 % 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: -1.95 (0.32), residues: 612 helix: -1.76 (0.38), residues: 154 sheet: 2.33 (1.02), residues: 32 loop : -1.48 (0.28), residues: 426 *********************** 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 73 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 67 time to evaluate : 0.722 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 outliers start: 6 outliers final: 3 residues processed: 72 average time/residue: 0.2777 time to fit residues: 27.7043 Evaluate side-chains 63 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 0.799 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1276 time to fit residues: 1.7057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 453 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.128 5021 Z= 0.370 Angle : 0.661 9.581 6770 Z= 0.362 Chirality : 0.042 0.147 717 Planarity : 0.005 0.051 897 Dihedral : 6.311 34.855 671 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.97 % Favored : 90.03 % Rotamer Outliers : 1.10 % 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: -2.29 (0.32), residues: 612 helix: -2.02 (0.36), residues: 163 sheet: 2.23 (1.05), residues: 32 loop : -1.71 (0.29), residues: 417 *********************** 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 68 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 62 time to evaluate : 0.836 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 outliers start: 6 outliers final: 5 residues processed: 67 average time/residue: 0.2392 time to fit residues: 22.9927 Evaluate side-chains 62 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.676 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.0983 time to fit residues: 1.7766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 40 optimal weight: 0.4980 chunk 30 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 212 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.4761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.064 5021 Z= 0.348 Angle : 0.613 6.998 6770 Z= 0.332 Chirality : 0.042 0.144 717 Planarity : 0.005 0.056 897 Dihedral : 6.199 34.121 671 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.60 % Favored : 88.40 % Rotamer Outliers : 2.39 % 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: -2.27 (0.32), residues: 612 helix: -1.84 (0.38), residues: 155 sheet: 2.90 (1.23), residues: 22 loop : -1.73 (0.29), residues: 435 *********************** 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 73 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 60 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 72 average time/residue: 0.2506 time to fit residues: 25.7400 Evaluate side-chains 67 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 57 time to evaluate : 0.774 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1171 time to fit residues: 3.1178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.5001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.154 5021 Z= 0.336 Angle : 0.680 16.532 6770 Z= 0.370 Chirality : 0.041 0.156 717 Planarity : 0.004 0.056 897 Dihedral : 6.088 33.453 671 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.93 % Favored : 88.07 % Rotamer Outliers : 1.10 % 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: -2.46 (0.32), residues: 612 helix: -1.85 (0.38), residues: 156 sheet: 0.68 (1.04), residues: 32 loop : -1.84 (0.29), residues: 424 *********************** 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 66 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 60 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 63 average time/residue: 0.2653 time to fit residues: 23.7344 Evaluate side-chains 60 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 0.689 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1066 time to fit residues: 1.7455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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: 0.7204 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 5021 Z= 0.253 Angle : 0.608 13.104 6770 Z= 0.323 Chirality : 0.040 0.145 717 Planarity : 0.004 0.051 897 Dihedral : 5.865 32.278 671 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.60 % Favored : 88.40 % Rotamer Outliers : 0.92 % 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: -2.32 (0.32), residues: 612 helix: -1.77 (0.38), residues: 158 sheet: 2.37 (1.18), residues: 22 loop : -1.78 (0.29), residues: 432 *********************** 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 61 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 60 average time/residue: 0.2667 time to fit residues: 22.6673 Evaluate side-chains 56 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 0.726 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1279 time to fit residues: 1.4987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 56 optimal weight: 5.9990 chunk 51 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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: 0.7176 moved from start: 0.5169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.018 1.095 5021 Z= 0.915 Angle : 1.380 98.387 6770 Z= 0.545 Chirality : 0.040 0.248 717 Planarity : 0.006 0.140 897 Dihedral : 5.701 30.570 671 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.17 % 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 (0.33), residues: 612 helix: -1.64 (0.39), residues: 158 sheet: 2.52 (1.17), residues: 22 loop : -1.68 (0.29), residues: 432 *********************** 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 59 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 57 average time/residue: 0.2827 time to fit residues: 23.0107 Evaluate side-chains 55 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 53 time to evaluate : 0.849 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1312 time to fit residues: 1.4171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.5227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.018 1.089 5021 Z= 0.923 Angle : 1.376 98.824 6770 Z= 0.533 Chirality : 0.041 0.278 717 Planarity : 0.005 0.088 897 Dihedral : 5.598 30.997 671 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.17 % 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: -2.11 (0.33), residues: 612 helix: -1.48 (0.39), residues: 158 sheet: 2.45 (1.16), residues: 22 loop : -1.69 (0.29), residues: 432 *********************** 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 53 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 52 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 53 average time/residue: 0.2581 time to fit residues: 19.9919 Evaluate side-chains 51 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.739 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 5 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.5276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.018 1.070 5021 Z= 0.931 Angle : 1.374 96.912 6770 Z= 0.550 Chirality : 0.042 0.325 717 Planarity : 0.005 0.087 897 Dihedral : 5.630 31.704 671 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.60 % Favored : 88.40 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.17 % 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 (0.33), residues: 612 helix: -1.51 (0.40), residues: 158 sheet: 0.62 (1.03), residues: 32 loop : -1.78 (0.30), residues: 422 ********************** 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 54 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 53 average time/residue: 0.2580 time to fit residues: 19.7880 Evaluate side-chains 52 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 51 time to evaluate : 0.821 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1703 time to fit residues: 1.3732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 chunk 2 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 55 optimal weight: 0.2980 chunk 32 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 645 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.170260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.144513 restraints weight = 20678.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.150444 restraints weight = 8907.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.154367 restraints weight = 5177.305| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.5347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.018 1.075 5021 Z= 0.911 Angle : 1.218 83.222 6770 Z= 0.501 Chirality : 0.041 0.363 717 Planarity : 0.004 0.061 897 Dihedral : 5.376 29.147 671 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.17 % 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: -2.11 (0.33), residues: 612 helix: -1.37 (0.40), residues: 157 sheet: 0.87 (1.04), residues: 32 loop : -1.69 (0.30), residues: 423 =============================================================================== Job complete usr+sys time: 2567.57 seconds wall clock time: 45 minutes 57.82 seconds (2757.82 seconds total)