Starting phenix.real_space_refine on Sat Dec 9 01:45:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adm_11731/12_2023/7adm_11731.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adm_11731/12_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_11731/12_2023/7adm_11731.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adm_11731/12_2023/7adm_11731.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adm_11731/12_2023/7adm_11731.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7adm_11731/12_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-1.21rc1-5172/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: 4.68, per 1000 atoms: 0.48 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: 7.32 Conformation dependent library (CDL) restraints added in 979.7 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: 0.82 Creating SS restraints... Processing helix chain 'C' and resid 152 through 158 Processing helix chain 'C' and resid 181 through 195 removed outlier: 3.842A pdb=" N GLN C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA C 189 " --> pdb=" O LYS C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 218 Processing helix chain 'C' and resid 223 through 225 No H-bonds generated for 'chain 'C' and resid 223 through 225' Processing helix chain 'C' and resid 226 through 232 removed outlier: 3.669A pdb=" N SER C 230 " --> pdb=" O ASP C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 234 No H-bonds generated for 'chain 'C' and resid 233 through 234' Processing helix chain 'C' and resid 235 through 237 No H-bonds generated for 'chain 'C' and resid 235 through 237' Processing helix chain 'C' and resid 238 through 254 removed outlier: 3.561A pdb=" N GLN C 243 " --> pdb=" O SER C 239 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN C 244 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU C 247 " --> pdb=" O GLN C 243 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ARG C 248 " --> pdb=" O ASN C 244 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N TYR C 249 " --> pdb=" O THR C 245 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS C 251 " --> pdb=" O GLU C 247 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N MET C 252 " --> pdb=" O ARG C 248 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP C 254 " --> pdb=" O LYS C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 263 removed outlier: 4.162A pdb=" N LYS C 263 " --> pdb=" O ASN C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 269 removed outlier: 4.051A pdb=" N LYS C 268 " --> pdb=" O GLU C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 289 removed outlier: 4.193A pdb=" N ILE C 285 " --> pdb=" O ASN C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 291 No H-bonds generated for 'chain 'C' and resid 290 through 291' Processing helix chain 'C' and resid 292 through 296 Processing helix chain 'C' and resid 300 through 309 removed outlier: 3.580A pdb=" N LEU C 307 " --> pdb=" O SER C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 337 Processing helix chain 'C' and resid 338 through 351 removed outlier: 3.907A pdb=" N SER C 349 " --> pdb=" O ARG C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 369 Processing helix chain 'C' and resid 380 through 389 removed outlier: 4.057A pdb=" N TYR C 384 " --> pdb=" O VAL C 380 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS C 387 " --> pdb=" O PRO C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 431 Processing helix chain 'C' and resid 432 through 442 removed outlier: 3.582A pdb=" N GLN C 440 " --> pdb=" O ILE C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 469 Processing helix chain 'C' and resid 519 through 523 Processing helix chain 'C' and resid 566 through 576 Processing helix chain 'C' and resid 599 through 603 Processing helix chain 'C' and resid 654 through 658 removed outlier: 3.963A pdb=" N LEU C 657 " --> pdb=" O SER C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 710 removed outlier: 3.693A pdb=" N TYR C 707 " --> pdb=" O ASN C 703 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N PHE C 708 " --> pdb=" O LEU C 704 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR C 710 " --> pdb=" O LYS C 706 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 131 through 133 removed outlier: 7.292A pdb=" N GLU C 140 " --> pdb=" O VAL C 178 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N VAL C 178 " --> pdb=" O GLU C 140 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLU C 142 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU C 144 " --> pdb=" O LYS C 174 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS C 174 " --> pdb=" O GLU C 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 312 through 313 Processing sheet with id=AA3, first strand: chain 'C' and resid 318 through 321 removed outlier: 3.735A pdb=" N GLU C 325 " --> pdb=" O ASN C 321 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 375 through 379 removed outlier: 3.831A pdb=" N ARG C 397 " --> pdb=" O ASP C 420 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TYR C 449 " --> pdb=" O GLU C 478 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N PHE C 480 " --> pdb=" O TYR C 449 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ILE C 451 " --> pdb=" O PHE C 480 " (cutoff:3.500A) removed outlier: 11.170A pdb=" N ASP C 473 " --> pdb=" O ILE C 499 " (cutoff:3.500A) removed outlier: 10.302A pdb=" N GLU C 501 " --> pdb=" O ASP C 473 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLN C 475 " --> pdb=" O GLU C 501 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N SER C 503 " --> pdb=" O GLN C 475 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LEU C 477 " --> pdb=" O SER C 503 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TYR C 505 " --> pdb=" O LEU C 477 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LEU C 479 " --> pdb=" O TYR C 505 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 554 through 555 removed outlier: 6.097A pdb=" N LEU C 554 " --> pdb=" O ASP C 610 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 650 through 651 removed outlier: 6.695A pdb=" N PHE C 650 " --> pdb=" O ARG C 689 " (cutoff:3.500A) 120 hydrogen bonds defined for protein. 318 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.30 Time building geometry restraints manager: 7.62 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: 4063 17.31 - 34.62: 306 34.62 - 51.92: 69 51.92 - 69.23: 41 69.23 - 86.54: 12 Dihedral angle restraints: 4491 sinusoidal: 2405 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 4488 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: 0.340 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: 1.500 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 32.640 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.105 5021 Z= 0.858 Angle : 1.978 9.870 6770 Z= 1.320 Chirality : 0.108 0.461 717 Planarity : 0.015 0.121 897 Dihedral : 15.369 86.540 1914 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.93 % Favored : 88.07 % Rotamer: Outliers : 0.73 % Allowed : 6.79 % Favored : 92.48 % Cbeta Deviations : 0.52 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.30), residues: 612 helix: -3.29 (0.30), residues: 152 sheet: 1.91 (1.10), residues: 22 loop : -1.73 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.121 0.035 TRP C 527 HIS 0.011 0.004 HIS C 170 PHE 0.067 0.014 PHE C 625 TYR 0.215 0.021 TYR C 337 ARG 0.007 0.001 ARG C 362 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Evaluate side-chains 132 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 128 time to evaluate : 0.750 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: 0.4865 time to fit residues: 75.7799 Evaluate side-chains 77 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 76 time to evaluate : 0.749 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5965 time to fit residues: 1.6936 ------------------------------------------------------------------------------- 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: 0.9990 chunk 25 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 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: 0.9990 chunk 55 optimal weight: 0.9980 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: 0.6956 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5021 Z= 0.206 Angle : 0.634 5.047 6770 Z= 0.351 Chirality : 0.042 0.142 717 Planarity : 0.004 0.033 897 Dihedral : 7.129 32.356 671 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 1.10 % Allowed : 11.01 % Favored : 87.89 % 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: -2.11 (0.32), residues: 612 helix: -2.20 (0.35), residues: 150 sheet: 2.19 (1.00), residues: 32 loop : -1.46 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 527 HIS 0.008 0.002 HIS C 590 PHE 0.015 0.002 PHE C 206 TYR 0.011 0.001 TYR C 644 ARG 0.005 0.001 ARG C 154 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Evaluate side-chains 93 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 87 time to evaluate : 0.793 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 outliers start: 6 outliers final: 4 residues processed: 90 average time/residue: 0.3895 time to fit residues: 44.4476 Evaluate side-chains 64 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 60 time to evaluate : 0.728 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.1136 time to fit residues: 1.8433 ------------------------------------------------------------------------------- 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: 3.9990 chunk 37 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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: 0.7073 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 5021 Z= 0.286 Angle : 0.613 4.954 6770 Z= 0.336 Chirality : 0.042 0.140 717 Planarity : 0.004 0.051 897 Dihedral : 6.473 34.304 671 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.97 % Favored : 90.03 % Rotamer: Outliers : 1.28 % Allowed : 12.66 % Favored : 86.06 % 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: -2.22 (0.32), residues: 612 helix: -1.91 (0.37), residues: 156 sheet: 2.26 (1.04), residues: 32 loop : -1.71 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 527 HIS 0.015 0.003 HIS C 590 PHE 0.013 0.002 PHE C 206 TYR 0.011 0.001 TYR C 566 ARG 0.008 0.001 ARG C 346 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Evaluate side-chains 73 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 66 time to evaluate : 0.778 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: 7 outliers final: 5 residues processed: 73 average time/residue: 0.2827 time to fit residues: 28.3656 Evaluate side-chains 61 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 0.769 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1183 time to fit residues: 2.0141 ------------------------------------------------------------------------------- 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: 2.9990 chunk 28 optimal weight: 0.0030 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: 4.9990 chunk 29 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 overall best weight: 2.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 168 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.4648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5021 Z= 0.264 Angle : 0.566 4.893 6770 Z= 0.308 Chirality : 0.041 0.135 717 Planarity : 0.004 0.048 897 Dihedral : 6.071 32.797 671 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 1.83 % Allowed : 13.39 % Favored : 84.77 % 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: -2.17 (0.32), residues: 612 helix: -1.75 (0.38), residues: 157 sheet: 2.31 (1.04), residues: 32 loop : -1.72 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 527 HIS 0.012 0.002 HIS C 590 PHE 0.009 0.001 PHE C 242 TYR 0.009 0.001 TYR C 167 ARG 0.006 0.001 ARG C 346 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Evaluate side-chains 73 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 0.689 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: 10 outliers final: 6 residues processed: 72 average time/residue: 0.2678 time to fit residues: 26.9591 Evaluate side-chains 64 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.726 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1141 time to fit residues: 2.1557 ------------------------------------------------------------------------------- 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: 6.9990 chunk 0 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 212 ASN C 225 ASN C 663 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.5136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.099 5021 Z= 0.535 Angle : 0.721 5.343 6770 Z= 0.396 Chirality : 0.047 0.172 717 Planarity : 0.006 0.071 897 Dihedral : 6.769 36.893 671 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.38 % Favored : 85.62 % Rotamer: Outliers : 1.83 % Allowed : 15.23 % Favored : 82.94 % 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: -2.86 (0.32), residues: 612 helix: -2.18 (0.36), residues: 156 sheet: -0.17 (0.96), residues: 42 loop : -2.09 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.003 TRP C 286 HIS 0.014 0.003 HIS C 590 PHE 0.015 0.002 PHE C 650 TYR 0.013 0.002 TYR C 167 ARG 0.005 0.001 ARG C 346 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Evaluate side-chains 68 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 58 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: 10 outliers final: 9 residues processed: 66 average time/residue: 0.2790 time to fit residues: 25.7889 Evaluate side-chains 67 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 58 time to evaluate : 0.821 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1250 time to fit residues: 2.9874 ------------------------------------------------------------------------------- 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: 0.8980 chunk 14 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 529 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.5263 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= 0.307 Angle : 0.597 4.963 6770 Z= 0.326 Chirality : 0.041 0.145 717 Planarity : 0.004 0.059 897 Dihedral : 6.262 33.509 671 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.25 % Favored : 87.75 % Rotamer: Outliers : 0.55 % Allowed : 17.25 % Favored : 82.20 % 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: -2.60 (0.32), residues: 612 helix: -1.90 (0.38), residues: 157 sheet: 1.49 (1.15), residues: 27 loop : -2.01 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 286 HIS 0.010 0.002 HIS C 590 PHE 0.009 0.001 PHE C 390 TYR 0.009 0.001 TYR C 167 ARG 0.004 0.001 ARG C 346 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Evaluate side-chains 61 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 59 average time/residue: 0.2846 time to fit residues: 23.3503 Evaluate side-chains 56 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 53 time to evaluate : 0.750 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1177 time to fit residues: 1.6240 ------------------------------------------------------------------------------- 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: 3.9990 chunk 58 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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: 0.7183 moved from start: 0.5481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 5021 Z= 0.375 Angle : 0.625 5.007 6770 Z= 0.341 Chirality : 0.043 0.145 717 Planarity : 0.005 0.066 897 Dihedral : 6.222 34.088 671 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.56 % Favored : 86.44 % Rotamer: Outliers : 0.55 % Allowed : 18.17 % Favored : 81.28 % 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: -2.84 (0.32), residues: 612 helix: -1.98 (0.37), residues: 157 sheet: -0.22 (0.97), residues: 37 loop : -2.13 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 286 HIS 0.008 0.002 HIS C 590 PHE 0.010 0.002 PHE C 650 TYR 0.010 0.001 TYR C 167 ARG 0.003 0.001 ARG C 346 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Evaluate side-chains 61 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 61 average time/residue: 0.3805 time to fit residues: 30.3668 Evaluate side-chains 55 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 0.697 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1208 time to fit residues: 1.2352 ------------------------------------------------------------------------------- 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: 4.9990 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 ASN ** C 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.5599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5021 Z= 0.160 Angle : 0.515 4.661 6770 Z= 0.278 Chirality : 0.039 0.132 717 Planarity : 0.004 0.044 897 Dihedral : 5.450 28.815 671 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 0.92 % Allowed : 17.98 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.33), residues: 612 helix: -1.25 (0.42), residues: 153 sheet: 1.46 (1.14), residues: 27 loop : -1.83 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 527 HIS 0.005 0.001 HIS C 590 PHE 0.008 0.001 PHE C 319 TYR 0.006 0.001 TYR C 505 ARG 0.004 0.000 ARG C 346 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Evaluate side-chains 60 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 57 average time/residue: 0.3456 time to fit residues: 26.2858 Evaluate side-chains 55 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 53 time to evaluate : 0.712 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1501 time to fit residues: 1.4278 ------------------------------------------------------------------------------- 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: 7.9990 chunk 16 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 60 optimal weight: 0.0980 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 425 ASN ** C 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.5665 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= 0.201 Angle : 0.517 4.730 6770 Z= 0.279 Chirality : 0.039 0.132 717 Planarity : 0.004 0.042 897 Dihedral : 5.317 28.975 671 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.95 % Favored : 89.05 % Rotamer: Outliers : 0.37 % Allowed : 18.72 % Favored : 80.92 % 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: -0.98 (0.42), residues: 152 sheet: 1.51 (1.15), residues: 27 loop : -1.80 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 527 HIS 0.007 0.001 HIS C 590 PHE 0.007 0.001 PHE C 319 TYR 0.007 0.001 TYR C 167 ARG 0.002 0.000 ARG C 346 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Evaluate side-chains 57 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 55 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 56 average time/residue: 0.3532 time to fit residues: 26.4004 Evaluate side-chains 54 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 53 time to evaluate : 0.725 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1121 time to fit residues: 1.1104 ------------------------------------------------------------------------------- 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: 0.6980 chunk 5 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 602 GLN ** C 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.5723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5021 Z= 0.150 Angle : 0.492 4.574 6770 Z= 0.264 Chirality : 0.039 0.131 717 Planarity : 0.003 0.036 897 Dihedral : 5.052 27.048 671 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 0.55 % Allowed : 18.72 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.33), residues: 612 helix: -0.75 (0.43), residues: 152 sheet: 0.48 (0.99), residues: 37 loop : -1.73 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 527 HIS 0.004 0.001 HIS C 590 PHE 0.008 0.001 PHE C 319 TYR 0.006 0.001 TYR C 505 ARG 0.002 0.000 ARG C 346 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 500 is missing expected H atoms. Skipping. Evaluate side-chains 62 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 60 average time/residue: 0.3842 time to fit residues: 30.9470 Evaluate side-chains 59 residues out of total 546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 0.809 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1662 time to fit residues: 1.6129 ------------------------------------------------------------------------------- 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: 4.9990 chunk 20 optimal weight: 0.0980 chunk 49 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 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 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.172068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.144499 restraints weight = 21038.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.150624 restraints weight = 9544.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.154639 restraints weight = 5774.291| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.5791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5021 Z= 0.191 Angle : 0.509 4.903 6770 Z= 0.274 Chirality : 0.039 0.132 717 Planarity : 0.004 0.035 897 Dihedral : 5.040 27.055 671 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer: Outliers : 0.18 % Allowed : 19.08 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.33), residues: 612 helix: -0.67 (0.43), residues: 152 sheet: 0.42 (0.98), residues: 37 loop : -1.73 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 527 HIS 0.006 0.001 HIS C 590 PHE 0.007 0.001 PHE C 319 TYR 0.006 0.001 TYR C 249 ARG 0.002 0.000 ARG C 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2617.89 seconds wall clock time: 47 minutes 4.42 seconds (2824.42 seconds total)