Starting phenix.real_space_refine (version: 1.21rc1) on Fri Aug 11 12:02:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adm_11731/08_2023/7adm_11731.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adm_11731/08_2023/7adm_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_11731/08_2023/7adm_11731.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adm_11731/08_2023/7adm_11731.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adm_11731/08_2023/7adm_11731.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adm_11731/08_2023/7adm_11731.pdb" } 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 Residue "C ARG 128": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 140": "OE1" <-> "OE2" Residue "C GLU 142": "OE1" <-> "OE2" Residue "C ASP 157": "OD1" <-> "OD2" Residue "C GLU 186": "OE1" <-> "OE2" Residue "C ASP 191": "OD1" <-> "OD2" Residue "C TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 200": "OD1" <-> "OD2" Residue "C ASP 226": "OD1" <-> "OD2" Residue "C PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 247": "OE1" <-> "OE2" Residue "C ASP 254": "OD1" <-> "OD2" Residue "C GLU 265": "OE1" <-> "OE2" Residue "C GLU 269": "OE1" <-> "OE2" Residue "C GLU 283": "OE1" <-> "OE2" Residue "C ASP 292": "OD1" <-> "OD2" Residue "C GLU 304": "OE1" <-> "OE2" Residue "C PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 322": "OE1" <-> "OE2" Residue "C GLU 336": "OE1" <-> "OE2" Residue "C GLU 350": "OE1" <-> "OE2" Residue "C ASP 355": "OD1" <-> "OD2" Residue "C GLU 358": "OE1" <-> "OE2" Residue "C ARG 362": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 366": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 378": "OE1" <-> "OE2" Residue "C ARG 397": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 403": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 420": "OD1" <-> "OD2" Residue "C GLU 437": "OE1" <-> "OE2" Residue "C ASP 442": "OD1" <-> "OD2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 450": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 456": "OE1" <-> "OE2" Residue "C ASP 483": "OD1" <-> "OD2" Residue "C GLU 495": "OE1" <-> "OE2" Residue "C GLU 501": "OE1" <-> "OE2" Residue "C TYR 539": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 557": "OD1" <-> "OD2" Residue "C GLU 559": "OE1" <-> "OE2" Residue "C ARG 580": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 585": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 624": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 636": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 647": "OE1" <-> "OE2" Residue "C TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 650": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 651": "OE1" <-> "OE2" Residue "C ASP 655": "OD1" <-> "OD2" Residue "C GLU 659": "OE1" <-> "OE2" Residue "C GLU 699": "OE1" <-> "OE2" Residue "C ARG 701": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 702": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 712": "OE1" <-> "OE2" Residue "C ARG 715": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 739": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 9726 Number of models: 1 Model: "" Number of chains: 1 Chain: "C" Number of atoms: 9726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 9726 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 22, 'TRANS': 591} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 4.44, per 1000 atoms: 0.46 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: 7.79 Conformation dependent library (CDL) restraints added in 804.9 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: 0.72 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: 3.15 Time building geometry restraints manager: 8.14 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: 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 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: 0.150 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: 0.130 Extract box with map and model: 1.830 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 33.090 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.340 ------------------------------------------------------------------------------- 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 % 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 : 0.829 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: 0.4944 time to fit residues: 76.8601 Evaluate side-chains 77 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 76 time to evaluate : 0.701 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.6009 time to fit residues: 1.6970 ------------------------------------------------------------------------------- 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: 0.9980 chunk 31 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 overall best weight: 0.9780 ------------------------------------------------------------------------------- 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: 0.6950 moved from start: 0.3283 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= 0.206 Angle : 0.619 5.043 6770 Z= 0.340 Chirality : 0.041 0.136 717 Planarity : 0.004 0.031 897 Dihedral : 7.049 31.934 671 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -2.08 (0.32), residues: 612 helix: -2.12 (0.36), residues: 150 sheet: 2.18 (1.01), residues: 32 loop : -1.46 (0.29), residues: 430 *********************** 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 93 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 87 time to evaluate : 0.797 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 outliers start: 6 outliers final: 4 residues processed: 90 average time/residue: 0.3785 time to fit residues: 43.7713 Evaluate side-chains 65 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 61 time to evaluate : 0.824 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1254 time to fit residues: 1.9206 ------------------------------------------------------------------------------- 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: 10.0000 chunk 17 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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: 0.7002 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 5021 Z= 0.192 Angle : 0.557 5.017 6770 Z= 0.304 Chirality : 0.040 0.136 717 Planarity : 0.004 0.057 897 Dihedral : 6.106 31.623 671 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer Outliers : 0.73 % 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: -1.91 (0.32), residues: 612 helix: -1.65 (0.38), residues: 156 sheet: 2.33 (1.03), residues: 32 loop : -1.48 (0.29), residues: 424 *********************** 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 72 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 68 time to evaluate : 0.839 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 outliers start: 4 outliers final: 2 residues processed: 72 average time/residue: 0.2649 time to fit residues: 26.7509 Evaluate side-chains 62 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 0.719 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1096 time to fit residues: 1.3219 ------------------------------------------------------------------------------- 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: 1.9990 chunk 28 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 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: 2.9988 ------------------------------------------------------------------------------- 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: 0.7118 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.068 5021 Z= 0.352 Angle : 0.611 4.974 6770 Z= 0.333 Chirality : 0.042 0.146 717 Planarity : 0.004 0.051 897 Dihedral : 6.214 34.226 671 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer Outliers : 2.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (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: -2.18 (0.32), residues: 612 helix: -1.84 (0.37), residues: 157 sheet: 2.48 (1.03), residues: 32 loop : -1.71 (0.29), residues: 423 *********************** 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 73 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 59 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 69 average time/residue: 0.2735 time to fit residues: 26.3145 Evaluate side-chains 68 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 58 time to evaluate : 0.714 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1213 time to fit residues: 3.0610 ------------------------------------------------------------------------------- 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: 8.9990 chunk 43 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 212 ASN ** C 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.4996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.090 5021 Z= 0.464 Angle : 0.686 5.200 6770 Z= 0.376 Chirality : 0.045 0.178 717 Planarity : 0.005 0.064 897 Dihedral : 6.610 36.212 671 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.40 % Favored : 86.60 % Rotamer Outliers : 1.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.70 (0.32), residues: 612 helix: -2.09 (0.36), residues: 158 sheet: -0.12 (0.95), residues: 42 loop : -1.96 (0.29), residues: 412 *********************** 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 70 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 63 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 69 average time/residue: 0.2949 time to fit residues: 28.0901 Evaluate side-chains 63 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 0.750 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1286 time to fit residues: 1.8257 ------------------------------------------------------------------------------- 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: 0.6980 chunk 34 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 59 optimal weight: 0.0370 chunk 48 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 168 GLN ** C 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.5138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 5021 Z= 0.157 Angle : 0.521 4.756 6770 Z= 0.283 Chirality : 0.039 0.133 717 Planarity : 0.003 0.044 897 Dihedral : 5.629 29.334 671 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer Outliers : 0.55 % 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: -2.03 (0.33), residues: 612 helix: -1.55 (0.39), residues: 160 sheet: 1.90 (1.12), residues: 27 loop : -1.57 (0.30), residues: 425 *********************** 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 64 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 61 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 63 average time/residue: 0.2894 time to fit residues: 25.5497 Evaluate side-chains 57 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 0.787 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1366 time to fit residues: 1.7333 ------------------------------------------------------------------------------- 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: 2.9990 chunk 32 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 11 optimal weight: 0.2980 overall best weight: 2.2386 ------------------------------------------------------------------------------- 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: 0.7127 moved from start: 0.5321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 5021 Z= 0.278 Angle : 0.565 4.888 6770 Z= 0.306 Chirality : 0.041 0.147 717 Planarity : 0.004 0.047 897 Dihedral : 5.674 31.691 671 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.09 % Favored : 87.91 % Rotamer Outliers : 0.55 % 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: -2.18 (0.33), residues: 612 helix: -1.54 (0.39), residues: 160 sheet: 2.47 (1.13), residues: 22 loop : -1.73 (0.29), residues: 430 *********************** 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: 3 poor density : 58 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 59 average time/residue: 0.3652 time to fit residues: 28.4050 Evaluate side-chains 59 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 0.778 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1409 time to fit residues: 1.4845 ------------------------------------------------------------------------------- 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: 0.9980 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 chunk 56 optimal weight: 7.9990 chunk 51 optimal weight: 0.2980 chunk 54 optimal weight: 0.4980 chunk 32 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.5411 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= 0.147 Angle : 0.495 4.669 6770 Z= 0.265 Chirality : 0.038 0.131 717 Planarity : 0.003 0.038 897 Dihedral : 5.172 27.708 671 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer Outliers : 0.37 % 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: -1.12 (0.41), residues: 154 sheet: 1.88 (1.12), residues: 27 loop : -1.55 (0.30), residues: 431 *********************** 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 60 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 58 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 outliers start: 2 outliers final: 1 residues processed: 59 average time/residue: 0.3574 time to fit residues: 28.0492 Evaluate side-chains 58 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 57 time to evaluate : 0.795 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1247 time to fit residues: 1.3310 ------------------------------------------------------------------------------- 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: 7.9990 chunk 43 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 54 optimal weight: 0.1980 chunk 35 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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: 0.7108 moved from start: 0.5484 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= 0.246 Angle : 0.537 4.804 6770 Z= 0.290 Chirality : 0.040 0.142 717 Planarity : 0.003 0.042 897 Dihedral : 5.285 29.590 671 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.09 % Favored : 87.91 % Rotamer Outliers : 0.37 % 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: -1.90 (0.33), residues: 612 helix: -1.01 (0.42), residues: 154 sheet: 2.48 (1.13), residues: 22 loop : -1.67 (0.29), residues: 436 *********************** 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 58 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 57 average time/residue: 0.3459 time to fit residues: 26.3819 Evaluate side-chains 57 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.821 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1719 time to fit residues: 1.3806 ------------------------------------------------------------------------------- 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: 0.7980 chunk 48 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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: 0.7074 moved from start: 0.5565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 5021 Z= 0.181 Angle : 0.503 4.622 6770 Z= 0.271 Chirality : 0.039 0.136 717 Planarity : 0.003 0.040 897 Dihedral : 5.097 27.961 671 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer Outliers : 0.00 % 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: -1.73 (0.33), residues: 612 helix: -0.81 (0.43), residues: 153 sheet: 2.52 (1.14), residues: 22 loop : -1.57 (0.29), residues: 437 ********************** 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 55 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.3519 time to fit residues: 25.8819 Evaluate side-chains 55 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.800 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0657 ------------------------------------------------------------------------------- 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: 3.9990 chunk 20 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.171189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.143545 restraints weight = 21070.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.149664 restraints weight = 9495.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.153701 restraints weight = 5743.676| |-----------------------------------------------------------------------------| r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.5612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 5021 Z= 0.228 Angle : 0.521 4.745 6770 Z= 0.281 Chirality : 0.040 0.141 717 Planarity : 0.003 0.041 897 Dihedral : 5.145 28.677 671 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.44 % Favored : 88.56 % Rotamer Outliers : 0.37 % 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: -0.81 (0.43), residues: 153 sheet: 2.37 (1.13), residues: 22 loop : -1.63 (0.29), residues: 437 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2635.77 seconds wall clock time: 47 minutes 24.05 seconds (2844.05 seconds total)