Starting phenix.real_space_refine on Mon Nov 13 21:55:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtw_24691/11_2023/7rtw_24691.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtw_24691/11_2023/7rtw_24691.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtw_24691/11_2023/7rtw_24691.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtw_24691/11_2023/7rtw_24691.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtw_24691/11_2023/7rtw_24691.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rtw_24691/11_2023/7rtw_24691.pdb" } resolution = 3.23 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 Ca 2 9.91 5 S 24 5.16 5 C 3625 2.51 5 N 931 2.21 5 O 1062 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 148": "OE1" <-> "OE2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 5644 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3027 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 14, 'TRANS': 373} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2418 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Unusual residues: {' CA': 2, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.57, per 1000 atoms: 0.63 Number of scatterers: 5644 At special positions: 0 Unit cell: (68.22, 92.097, 131.892, 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) Ca 2 19.99 S 24 16.00 O 1062 8.00 N 931 7.00 C 3625 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 271 " - pdb=" SG CYS A 381 " distance=2.03 Simple disulfide: pdb=" SG CYS A 299 " - pdb=" SG CYS A 366 " distance=2.04 Simple disulfide: pdb=" SG CYS B 271 " - pdb=" SG CYS B 381 " distance=2.03 Simple disulfide: pdb=" SG CYS B 299 " - pdb=" SG CYS B 366 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " NAG-ASN " NAG A 601 " - " ASN A 144 " " NAG C 1 " - " ASN A 126 " " NAG D 1 " - " ASN A 351 " " NAG E 1 " - " ASN B 126 " " NAG F 1 " - " ASN B 144 " " NAG G 1 " - " ASN B 351 " Time building additional restraints: 2.54 Conformation dependent library (CDL) restraints added in 828.9 milliseconds 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1304 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 0 sheets defined 85.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 9 through 17 removed outlier: 4.122A pdb=" N LEU A 15 " --> pdb=" O TRP A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 41 Processing helix chain 'A' and resid 41 through 48 removed outlier: 3.674A pdb=" N LEU A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 63 removed outlier: 3.687A pdb=" N ALA A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 147 removed outlier: 3.621A pdb=" N ALA A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 152 Processing helix chain 'A' and resid 161 through 183 removed outlier: 3.722A pdb=" N LEU A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA A 167 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 233 removed outlier: 4.295A pdb=" N ILE A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG A 233 " --> pdb=" O VAL A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 273 removed outlier: 4.467A pdb=" N ASP A 273 " --> pdb=" O ASP A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 286 removed outlier: 4.001A pdb=" N PHE A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 297 Processing helix chain 'A' and resid 306 through 329 removed outlier: 4.157A pdb=" N LYS A 310 " --> pdb=" O PRO A 306 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLY A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N SER A 314 " --> pdb=" O LYS A 310 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLU A 327 " --> pdb=" O ASP A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 336 removed outlier: 4.300A pdb=" N GLU A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 364 removed outlier: 4.146A pdb=" N LEU A 343 " --> pdb=" O THR A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 409 removed outlier: 4.471A pdb=" N LEU A 369 " --> pdb=" O ASP A 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 147 Processing helix chain 'B' and resid 147 through 157 removed outlier: 3.721A pdb=" N GLN B 152 " --> pdb=" O GLU B 148 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER B 153 " --> pdb=" O PRO B 149 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 183 removed outlier: 4.147A pdb=" N ARG B 166 " --> pdb=" O GLN B 162 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU B 171 " --> pdb=" O ALA B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 234 Processing helix chain 'B' and resid 243 through 270 removed outlier: 4.492A pdb=" N VAL B 247 " --> pdb=" O CYS B 243 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU B 248 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU B 250 " --> pdb=" O GLY B 246 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER B 253 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLY B 255 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ALA B 256 " --> pdb=" O ILE B 252 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU B 261 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA B 262 " --> pdb=" O GLY B 258 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE B 270 " --> pdb=" O GLY B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 286 removed outlier: 4.051A pdb=" N PHE B 277 " --> pdb=" O ASP B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 298 Processing helix chain 'B' and resid 307 through 323 removed outlier: 3.631A pdb=" N SER B 312 " --> pdb=" O GLN B 308 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY B 313 " --> pdb=" O GLN B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 332 removed outlier: 3.698A pdb=" N ARG B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 364 removed outlier: 4.121A pdb=" N GLU B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 381 removed outlier: 4.324A pdb=" N LEU B 369 " --> pdb=" O ASP B 365 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU B 371 " --> pdb=" O ARG B 367 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ASP B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY B 379 " --> pdb=" O GLN B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 393 removed outlier: 4.011A pdb=" N TYR B 390 " --> pdb=" O GLU B 386 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 405 removed outlier: 3.649A pdb=" N ALA B 399 " --> pdb=" O SER B 395 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHE B 402 " --> pdb=" O THR B 398 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER B 403 " --> pdb=" O ALA B 399 " (cutoff:3.500A) 441 hydrogen bonds defined for protein. 1317 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: 1.42 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1790 1.34 - 1.46: 1317 1.46 - 1.58: 2622 1.58 - 1.70: 0 1.70 - 1.82: 30 Bond restraints: 5759 Sorted by residual: bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.482 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.81e+00 bond pdb=" C1 BMA C 3 " pdb=" C2 BMA C 3 " ideal model delta sigma weight residual 1.519 1.551 -0.032 2.00e-02 2.50e+03 2.57e+00 bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.549 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.19e+00 ... (remaining 5754 not shown) Histogram of bond angle deviations from ideal: 98.06 - 105.24: 76 105.24 - 112.43: 3142 112.43 - 119.61: 1895 119.61 - 126.79: 2653 126.79 - 133.98: 97 Bond angle restraints: 7863 Sorted by residual: angle pdb=" N ARG A 156 " pdb=" CA ARG A 156 " pdb=" C ARG A 156 " ideal model delta sigma weight residual 111.30 106.71 4.59 1.43e+00 4.89e-01 1.03e+01 angle pdb=" C ARG A 145 " pdb=" N THR A 146 " pdb=" CA THR A 146 " ideal model delta sigma weight residual 122.79 117.90 4.89 1.78e+00 3.16e-01 7.55e+00 angle pdb=" CA ARG A 156 " pdb=" CB ARG A 156 " pdb=" CG ARG A 156 " ideal model delta sigma weight residual 114.10 119.13 -5.03 2.00e+00 2.50e-01 6.33e+00 angle pdb=" N VAL A 332 " pdb=" CA VAL A 332 " pdb=" C VAL A 332 " ideal model delta sigma weight residual 108.88 113.95 -5.07 2.16e+00 2.14e-01 5.51e+00 angle pdb=" N ILE A 238 " pdb=" CA ILE A 238 " pdb=" C ILE A 238 " ideal model delta sigma weight residual 111.91 109.96 1.95 8.90e-01 1.26e+00 4.80e+00 ... (remaining 7858 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.17: 2865 16.17 - 32.35: 311 32.35 - 48.52: 69 48.52 - 64.70: 12 64.70 - 80.87: 9 Dihedral angle restraints: 3266 sinusoidal: 1240 harmonic: 2026 Sorted by residual: dihedral pdb=" CB CYS B 271 " pdb=" SG CYS B 271 " pdb=" SG CYS B 381 " pdb=" CB CYS B 381 " ideal model delta sinusoidal sigma weight residual 93.00 146.25 -53.25 1 1.00e+01 1.00e-02 3.86e+01 dihedral pdb=" CB CYS A 271 " pdb=" SG CYS A 271 " pdb=" SG CYS A 381 " pdb=" CB CYS A 381 " ideal model delta sinusoidal sigma weight residual 93.00 143.40 -50.40 1 1.00e+01 1.00e-02 3.48e+01 dihedral pdb=" CA GLU A 155 " pdb=" C GLU A 155 " pdb=" N ARG A 156 " pdb=" CA ARG A 156 " ideal model delta harmonic sigma weight residual 180.00 155.73 24.27 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 3263 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 923 0.083 - 0.165: 51 0.165 - 0.248: 1 0.248 - 0.331: 6 0.331 - 0.413: 1 Chirality restraints: 982 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN B 351 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.27e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN B 126 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.89e+00 ... (remaining 979 not shown) Planarity restraints: 969 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 341 " -0.050 5.00e-02 4.00e+02 7.54e-02 9.09e+00 pdb=" N PRO B 342 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO B 342 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 342 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 346 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.35e+00 pdb=" C VAL B 346 " -0.036 2.00e-02 2.50e+03 pdb=" O VAL B 346 " 0.014 2.00e-02 2.50e+03 pdb=" N GLN B 347 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 347 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.81e+00 pdb=" C GLN B 347 " 0.029 2.00e-02 2.50e+03 pdb=" O GLN B 347 " -0.011 2.00e-02 2.50e+03 pdb=" N GLU B 348 " -0.010 2.00e-02 2.50e+03 ... (remaining 966 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 776 2.75 - 3.29: 5852 3.29 - 3.83: 9409 3.83 - 4.36: 9783 4.36 - 4.90: 17338 Nonbonded interactions: 43158 Sorted by model distance: nonbonded pdb=" OH TYR A 39 " pdb=" OD2 ASP A 269 " model vdw 2.213 2.440 nonbonded pdb=" OD1 ASN B 126 " pdb=" N2 NAG E 1 " model vdw 2.316 2.520 nonbonded pdb=" OD2 ASP A 113 " pdb="CA CA A 603 " model vdw 2.346 2.510 nonbonded pdb=" O3 NAG C 1 " pdb=" O5 NAG C 2 " model vdw 2.353 2.440 nonbonded pdb=" OE2 GLU A 110 " pdb="CA CA A 602 " model vdw 2.355 2.510 ... (remaining 43153 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'C' and (resid 1 through 2 or (resid 3 and (name C1 or name C2 or name C3 \ or name C4 or name C5 or name C6 or name O2 or name O3 or name O4 or name O5 )) \ )) selection = (chain 'D' and (resid 1 through 2 or (resid 3 and (name C1 or name C2 or name C3 \ or name C4 or name C5 or name C6 or name O2 or name O3 or name O4 or name O5 )) \ )) selection = (chain 'E' and (resid 1 through 2 or (resid 3 and (name C1 or name C2 or name C3 \ or name C4 or name C5 or name C6 or name O2 or name O3 or name O4 or name O5 )) \ )) selection = chain 'G' } 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 individual isotropic 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: 2.330 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: 0.010 Extract box with map and model: 12.040 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 19.220 Find NCS groups from input model: 0.170 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 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 : 0.004 0.076 5759 Z= 0.249 Angle : 0.676 7.329 7863 Z= 0.319 Chirality : 0.046 0.413 982 Planarity : 0.004 0.075 963 Dihedral : 14.675 80.870 1950 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % 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: 2.01 (0.34), residues: 693 helix: 1.98 (0.23), residues: 546 sheet: None (None), residues: 0 loop : -1.19 (0.53), residues: 147 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.572 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.2035 time to fit residues: 21.0695 Evaluate side-chains 60 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.619 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 0.0170 chunk 52 optimal weight: 6.9990 chunk 29 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5759 Z= 0.191 Angle : 0.610 6.851 7863 Z= 0.300 Chirality : 0.040 0.272 982 Planarity : 0.004 0.060 963 Dihedral : 4.122 23.086 759 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.70 % Allowed : 10.54 % Favored : 87.76 % 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: 2.21 (0.33), residues: 693 helix: 2.17 (0.23), residues: 553 sheet: None (None), residues: 0 loop : -1.51 (0.52), residues: 140 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 66 time to evaluate : 0.635 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 72 average time/residue: 0.1705 time to fit residues: 16.5232 Evaluate side-chains 69 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 0.571 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0596 time to fit residues: 1.4940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 34 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 62 optimal weight: 0.3980 chunk 67 optimal weight: 10.0000 chunk 55 optimal weight: 20.0000 chunk 21 optimal weight: 0.5980 chunk 50 optimal weight: 0.0980 chunk 47 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5759 Z= 0.207 Angle : 0.599 7.100 7863 Z= 0.293 Chirality : 0.040 0.275 982 Planarity : 0.004 0.040 963 Dihedral : 4.111 24.501 759 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.85 % Allowed : 15.48 % Favored : 83.67 % 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: 2.20 (0.33), residues: 693 helix: 2.18 (0.23), residues: 556 sheet: None (None), residues: 0 loop : -1.69 (0.52), residues: 137 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 66 time to evaluate : 0.654 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 68 average time/residue: 0.1972 time to fit residues: 17.5687 Evaluate side-chains 70 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 66 time to evaluate : 0.606 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0556 time to fit residues: 1.1847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 32 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 62 optimal weight: 0.1980 chunk 66 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 55 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5759 Z= 0.170 Angle : 0.563 6.497 7863 Z= 0.273 Chirality : 0.039 0.240 982 Planarity : 0.003 0.036 963 Dihedral : 4.006 24.025 759 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.85 % Allowed : 17.86 % Favored : 81.29 % 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: 2.39 (0.33), residues: 693 helix: 2.32 (0.23), residues: 557 sheet: None (None), residues: 0 loop : -1.72 (0.51), residues: 136 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 0.551 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 70 average time/residue: 0.1863 time to fit residues: 17.2281 Evaluate side-chains 65 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 0.658 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0526 time to fit residues: 1.1331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 34 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 16 optimal weight: 0.0470 chunk 22 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.9480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5759 Z= 0.199 Angle : 0.577 7.096 7863 Z= 0.280 Chirality : 0.039 0.257 982 Planarity : 0.003 0.033 963 Dihedral : 4.072 25.735 759 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.53 % Allowed : 18.88 % Favored : 79.59 % 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: 2.35 (0.33), residues: 693 helix: 2.30 (0.23), residues: 557 sheet: None (None), residues: 0 loop : -1.76 (0.51), residues: 136 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 61 time to evaluate : 0.643 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 67 average time/residue: 0.2018 time to fit residues: 17.8024 Evaluate side-chains 68 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 61 time to evaluate : 0.769 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0765 time to fit residues: 1.8787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 39 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 55 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5759 Z= 0.195 Angle : 0.578 7.302 7863 Z= 0.280 Chirality : 0.039 0.249 982 Planarity : 0.003 0.031 963 Dihedral : 4.063 26.294 759 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.87 % Allowed : 18.71 % Favored : 79.42 % 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: 2.41 (0.33), residues: 693 helix: 2.35 (0.23), residues: 556 sheet: None (None), residues: 0 loop : -1.74 (0.51), residues: 137 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 62 time to evaluate : 0.665 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 71 average time/residue: 0.2161 time to fit residues: 19.8839 Evaluate side-chains 63 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 0.551 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0544 time to fit residues: 1.2292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 48 optimal weight: 0.4980 chunk 37 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 0.0170 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5759 Z= 0.171 Angle : 0.570 7.051 7863 Z= 0.274 Chirality : 0.039 0.231 982 Planarity : 0.003 0.036 963 Dihedral : 3.989 25.477 759 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.19 % Allowed : 21.60 % Favored : 77.21 % 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: 2.59 (0.34), residues: 693 helix: 2.48 (0.23), residues: 558 sheet: None (None), residues: 0 loop : -1.76 (0.51), residues: 135 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 61 time to evaluate : 0.640 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 66 average time/residue: 0.1899 time to fit residues: 16.5217 Evaluate side-chains 61 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 0.575 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0645 time to fit residues: 1.1907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 12 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 58 optimal weight: 0.1980 chunk 61 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5759 Z= 0.175 Angle : 0.577 7.293 7863 Z= 0.279 Chirality : 0.038 0.230 982 Planarity : 0.003 0.029 963 Dihedral : 3.950 25.374 759 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.85 % Allowed : 22.11 % Favored : 77.04 % 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: 2.59 (0.33), residues: 693 helix: 2.48 (0.23), residues: 558 sheet: None (None), residues: 0 loop : -1.77 (0.51), residues: 135 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 62 time to evaluate : 0.631 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 65 average time/residue: 0.1887 time to fit residues: 16.1531 Evaluate side-chains 61 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 0.611 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0535 time to fit residues: 1.0293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 26 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 61 optimal weight: 0.2980 chunk 40 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5759 Z= 0.194 Angle : 0.600 7.545 7863 Z= 0.289 Chirality : 0.039 0.242 982 Planarity : 0.004 0.035 963 Dihedral : 3.985 25.868 759 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.19 % Allowed : 22.45 % Favored : 76.36 % 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: 2.58 (0.33), residues: 693 helix: 2.47 (0.23), residues: 558 sheet: None (None), residues: 0 loop : -1.78 (0.51), residues: 135 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 0.568 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 64 average time/residue: 0.1933 time to fit residues: 16.3006 Evaluate side-chains 63 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 0.619 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0607 time to fit residues: 1.2593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 68 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5759 Z= 0.205 Angle : 0.612 7.554 7863 Z= 0.297 Chirality : 0.039 0.232 982 Planarity : 0.003 0.030 963 Dihedral : 3.996 26.400 759 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.17 % Allowed : 22.79 % Favored : 77.04 % 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: 2.54 (0.33), residues: 693 helix: 2.45 (0.22), residues: 558 sheet: None (None), residues: 0 loop : -1.80 (0.51), residues: 135 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1386 Ramachandran restraints generated. 693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 0.606 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 61 average time/residue: 0.2074 time to fit residues: 16.5529 Evaluate side-chains 59 residues out of total 589 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 0.606 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0686 time to fit residues: 1.0122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 15 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 3 optimal weight: 0.0030 chunk 39 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 GLN ** 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 = 0.4300 r_free = 0.4300 target = 0.158577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.140817 restraints weight = 11119.840| |-----------------------------------------------------------------------------| r_work (start): 0.4108 rms_B_bonded: 2.47 r_work: 0.4012 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5759 Z= 0.182 Angle : 0.608 9.434 7863 Z= 0.290 Chirality : 0.039 0.232 982 Planarity : 0.003 0.028 963 Dihedral : 3.941 25.218 759 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.34 % Allowed : 23.13 % Favored : 76.53 % 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: 2.62 (0.34), residues: 693 helix: 2.51 (0.23), residues: 558 sheet: None (None), residues: 0 loop : -1.80 (0.50), residues: 135 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1370.83 seconds wall clock time: 25 minutes 31.03 seconds (1531.03 seconds total)